Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021373.1 Corchorus olitorius cultivar O-4 contig21406, 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: 125138
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:311 original size:49 final size:47
Alignment explanation
Indices: 234--374 Score: 160
Period size: 49 Copynumber: 2.9 Consensus size: 47
224 CAAGCAATCC
* *
234 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT
* * *
282 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT
* *
331 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA
375 TTGGCACGCT
Statistics
Matches: 79, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
47 15 0.19
48 22 0.28
49 35 0.44
50 7 0.09
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (47 bp):
TTTAATTTTCATTGCACTTTTTCTCAATTTTTATACAAAATTGAACT
Found at i:3700 original size:20 final size:21
Alignment explanation
Indices: 3672--3717 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
3662 TTTTTTGGGT
3672 TTGAATGTTCATCAT-TGTTC
1 TTGAATGTTCATCATGTGTTC
* * *
3692 TTGATTGTTCTTGATGTGTTC
1 TTGAATGTTCATCATGTGTTC
3713 TTGAA
1 TTGAA
3718 AAAGTTGGGC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.17, C:0.11, G:0.20, T:0.52
Consensus pattern (21 bp):
TTGAATGTTCATCATGTGTTC
Found at i:3713 original size:11 final size:10
Alignment explanation
Indices: 3685--3716 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
3675 AATGTTCATC
3685 ATTGTTCTTG
1 ATTGTTCTTG
3695 ATTGTTCTTG
1 ATTGTTCTTG
3705 ATGTGTTCTTG
1 AT-TGTTCTTG
3716 A
1 A
3717 AAAAGTTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.12, C:0.09, G:0.22, T:0.56
Consensus pattern (10 bp):
ATTGTTCTTG
Found at i:19971 original size:52 final size:51
Alignment explanation
Indices: 19881--19986 Score: 151
Period size: 52 Copynumber: 2.1 Consensus size: 51
19871 ATTGCATCCA
* * *
19881 TGATTCTTGCTTCAAGCTTGTAGAATACCAGGGTAGAGGAGCTAAATTCTTC
1 TGATTCTTGCTTCAAGCTTGTAGAACACCAGGGAAGAGGAACT-AATTCTTC
*
19933 TGATTCTTGCTTCAAG-TGTGTAGAACACCGGGGAAGAGGAACTAATTCTTC
1 TGATTCTTGCTTCAAGCT-TGTAGAACACCAGGGAAGAGGAACTAATTCTTC
19984 TGA
1 TGA
19987 CACGCCGATT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
51 12 0.24
52 37 0.76
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (51 bp):
TGATTCTTGCTTCAAGCTTGTAGAACACCAGGGAAGAGGAACTAATTCTTC
Found at i:33068 original size:79 final size:79
Alignment explanation
Indices: 32969--33191 Score: 374
Period size: 79 Copynumber: 2.8 Consensus size: 79
32959 TTATGCTGGG
* * *
32969 ACCAATCTTGGTGTTTGGCCGCTTGTGATGAAACGGTCTCAATGGAGACGATCGTTTCATTTATT
1 ACCAATGTTGGTGTTCGGCCGTTTGTGATGAAACGGTCTCAATGGAGACGATCGTTTCATTTATT
33034 TATGATACGGGGAC
66 TATGATACGGGGAC
* **
33048 ACCAATGTTGGTGTTCGGCCGTTTGTGATGAAACAGTCTCAATGGAGACGATTATTTCATTTATT
1 ACCAATGTTGGTGTTCGGCCGTTTGTGATGAAACGGTCTCAATGGAGACGATCGTTTCATTTATT
*
33113 TCTGATACGGGGAC
66 TATGATACGGGGAC
*
33127 ACCAATGTTGGTGTTCGGCCGTTTGTGATGGAACGGTCTCAATGGAGACGATCGTTTCATTTATT
1 ACCAATGTTGGTGTTCGGCCGTTTGTGATGAAACGGTCTCAATGGAGACGATCGTTTCATTTATT
33192 CAAAATGTTT
Statistics
Matches: 133, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 133 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (79 bp):
ACCAATGTTGGTGTTCGGCCGTTTGTGATGAAACGGTCTCAATGGAGACGATCGTTTCATTTATT
TATGATACGGGGAC
Found at i:43428 original size:33 final size:33
Alignment explanation
Indices: 43391--43458 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
43381 CAATTATTGC
**
43391 ATTTGTATTGTTATTTTAATTGATAAGTGCATG
1 ATTTGTATTGTTAGCTTAATTGATAAGTGCATG
43424 ATTTGTATTGTTAGCTTAATTGATAAGTGCATG
1 ATTTGTATTGTTAGCTTAATTGATAAGTGCATG
43457 AT
1 AT
43459 GTCGAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.49
Consensus pattern (33 bp):
ATTTGTATTGTTAGCTTAATTGATAAGTGCATG
Found at i:45289 original size:12 final size:12
Alignment explanation
Indices: 45262--45296 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
45252 GTTTTACTAC
*
45262 TTGACCCTTTCAT
1 TTGACCC-TCCAT
45275 TTGACCCTCCAT
1 TTGACCCTCCAT
45287 TTGACCCTCC
1 TTGACCCTCC
45297 TAACGTGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.14, C:0.40, G:0.09, T:0.37
Consensus pattern (12 bp):
TTGACCCTCCAT
Found at i:48479 original size:22 final size:23
Alignment explanation
Indices: 48437--48479 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
48427 TTTTTATGAT
*
48437 TTCCTTATGAAATTCTGATAAAC
1 TTCCTTATGAAATTCTAATAAAC
*
48460 TTCC-TATGAAATTTTAATAA
1 TTCCTTATGAAATTCTAATAA
48480 CAACACTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (23 bp):
TTCCTTATGAAATTCTAATAAAC
Found at i:48525 original size:22 final size:22
Alignment explanation
Indices: 48486--48613 Score: 66
Period size: 22 Copynumber: 5.8 Consensus size: 22
48476 ATAACAACAC
* ** *
48486 TATGGAATTTTGAGAACCTTTT
1 TATGAAATTTTGTTAACCTTCT
*
48508 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGTTAACCTTCT
* *
48530 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGTTAACCTTCT
* * *
48552 TAAGGAATTTTG-AAGACCTTAC-
1 TATGAAATTTTGTTA-ACCTT-CT
* *
48574 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGTTAACCTT-CT
* *
48596 AATGAAATTTTGATAACC
1 TATGAAATTTTGTTAACC
48614 AACACTATGA
Statistics
Matches: 82, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
21 7 0.09
22 69 0.84
23 6 0.07
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGTTAACCTTCT
Found at i:48571 original size:44 final size:44
Alignment explanation
Indices: 48530--48639 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 44
48520 TTAACCTTCT
* *
48530 TATGAAATTTTGTTAACCTCCCTAA-GGAATTTTGAAGACCTTAC
1 TATGAAATTTTGATAACCTCCC-AATGAAATTTTGAAGACCTTAC
* **
48574 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATA-ACCAACAC
1 TATGAAATTTTGATAACCTCCCAATGAAATTTTGA-AGACC-TTAC
* *
48619 TATGAGATGTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
48640 ATATGATATA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
43 2 0.04
44 32 0.58
45 21 0.38
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCAATGAAATTTTGAAGACCTTAC
Found at i:48657 original size:45 final size:45
Alignment explanation
Indices: 48530--48839 Score: 110
Period size: 44 Copynumber: 7.0 Consensus size: 45
48520 TTAACCTTCT
* * * **
48530 TATGAAATTTTGTTAACCTCCCTAA-GGAATTTTGA-AGACC-TTAC
1 TATGAAATGTTGATAACCTCCC-AATGAAATTTTGATA-ACCAACAC
* *
48574 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCTCCCAATGAAATTTTGATAACCAACAC
* * **
48619 TATGAGATGTTGATAACCT-CCATATGATATATTT-ATAACC-ACGT
1 TATGAAATGTTGATAACCTCCCA-ATGAAAT-TTTGATAACCAACAC
* * *
48663 TATGAAA-GTTTAAAAACCT-CCATATG-AATTGTT-AGTAATC-ACAC
1 TATGAAATG-TTGATAACCTCCCA-ATGAAATT-TTGA-TAACCAACAC
* * * * * * * * *
48707 TTTGAAATTTTGATAATCACACTATGAAATTGTGATAACC-TCGC
1 TATGAAATGTTGATAACCTCCCAATGAAATTTTGATAACCAACAC
* * ** * *
48751 TATGAAATTTTGATAAACCTTCTTATAAAATTTTGATAAACC-TC-C
1 TATGAAATGTTGAT-AACCTCCCAATGAAATTTTGAT-AACCAACAC
* * ** *
48796 TTATAAAATTTTGATAACCTCCTTATGAAATCTTGATAA-CAACA
1 -TATGAAATGTTGATAACCTCCCAATGAAATTTTGATAACCAACA
48840 AATTTTGATA
Statistics
Matches: 206, Mismatches: 43, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
42 1 0.00
43 9 0.04
44 102 0.50
45 72 0.35
46 22 0.11
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCCAATGAAATTTTGATAACCAACAC
Found at i:48723 original size:22 final size:22
Alignment explanation
Indices: 48698--48938 Score: 101
Period size: 22 Copynumber: 11.1 Consensus size: 22
48688 GAATTGTTAG
*
48698 TAATCACACTTTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
48720 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
48742 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * *
48764 TAAAC-CTTCTTATAAAATTTTGA
1 TAATCAC-AC-TATGAAATTTTGA
* * *
48787 TAAAC-CTCCTTATAAAATTTTGA
1 TAATCAC-AC-TATGAAATTTTGA
* * *
48810 TAACCTC-CTTATGAAATCTTGA
1 TAATCACAC-TATGAAATTTTGA
48832 TAA-CA-AC----AAATTTTGA
1 TAATCACACTATGAAATTTTGA
* **
48848 TAACTAAC-CTATGATTTTTTGA
1 TAA-TCACACTATGAAATTTTGA
* * * **
48870 TAACCTCATTATGAAATTTTTT
1 TAATCACACTATGAAATTTTGA
*
48892 TAATCTGC-CTATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
* *
48914 -AAACTAAACTATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
48936 TAA
1 TAA
48939 CCTTCATATA
Statistics
Matches: 170, Mismatches: 34, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
16 11 0.06
18 2 0.01
21 8 0.05
22 107 0.63
23 41 0.24
24 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:48781 original size:23 final size:23
Alignment explanation
Indices: 48733--48834 Score: 129
Period size: 23 Copynumber: 4.5 Consensus size: 23
48723 TCACACTATG
* *
48733 AAATTGTGAT-AACCTCGC-TATG
1 AAATTTTGATAAACCTC-CTTATA
*
48755 AAATTTTGATAAACCTTCTTATA
1 AAATTTTGATAAACCTCCTTATA
48778 AAATTTTGATAAACCTCCTTATA
1 AAATTTTGATAAACCTCCTTATA
*
48801 AAATTTTGAT-AACCTCCTTATG
1 AAATTTTGATAAACCTCCTTATA
*
48823 AAATCTTGATAA
1 AAATTTTGATAA
48835 CAACAAATTT
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
22 30 0.42
23 41 0.58
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCTTATA
Found at i:49152 original size:44 final size:44
Alignment explanation
Indices: 49104--49275 Score: 145
Period size: 44 Copynumber: 3.9 Consensus size: 44
49094 ATAACCTTTT
* * * *
49104 TATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCTCTCTATAAAATTTTGATAACCCCGC
* * *
49148 TATGAAATTTTGATAATCACAT-TATATAATTTTGATAATCCCGC
1 TATGAAATTTTGATAATCTC-TCTATAAAATTTTGATAACCCCGC
* * *
49192 TTTGAAATTTTGATAATCT-TCCTAT-AAATTTTGATAATCCGATCTC
1 TATGAAATTTTGATAATCTCT-CTATAAAATTTTGATAA-CC--CCGC
* * * *
49238 TATGAAATTTCGATAATCACTCTATGAGA-TTTGATAAC
1 TATGAAATTTTGATAATCTCTCTATAAAATTTTGATAAC
49276 ATTCTATCAA
Statistics
Matches: 103, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
42 1 0.01
43 11 0.11
44 56 0.54
45 2 0.02
46 30 0.29
47 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (44 bp):
TATGAAATTTTGATAATCTCTCTATAAAATTTTGATAACCCCGC
Found at i:49222 original size:21 final size:22
Alignment explanation
Indices: 49057--49291 Score: 111
Period size: 22 Copynumber: 10.7 Consensus size: 22
49047 CCAGAAATAC
* *
49057 CACTATGAAATTTCGGTAATCA
1 CACTATGAAATTTTGATAATCA
* * * * *
49079 CATTTTGAAAATTTGATAACCT
1 CACTATGAAATTTTGATAATCA
*** * *
49101 TTTTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAATCA
* * * * * *
49123 CTCTATAAAATTTTGTTGACCC
1 CACTATGAAATTTTGATAATCA
*
49145 CTCTATGAAATTTTGATAATCA
1 CACTATGAAATTTTGATAATCA
* *
49167 CATTAT-ATAATTTTGATAATCC
1 CACTATGA-AATTTTGATAATCA
* * *
49189 CGCTTTGAAATTTTGATAATCTT
1 CACTATGAAATTTTGATAATC-A
49212 C-CTAT-AAATTTTGATAATCCGA
1 CACTATGAAATTTTGATAAT-C-A
* *
49234 TCTCTATGAAATTTCGATAATCA
1 -CACTATGAAATTTTGATAATCA
* *
49257 CTCTATGAGA-TTTGATAA-CA
1 CACTATGAAATTTTGATAATCA
** *
49277 TTCTATCAAATTTTG
1 CACTATGAAATTTTG
49292 GTACTCCTTA
Statistics
Matches: 167, Mismatches: 38, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
20 9 0.05
21 25 0.15
22 112 0.67
23 4 0.02
24 5 0.03
25 12 0.07
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
CACTATGAAATTTTGATAATCA
Found at i:49343 original size:22 final size:21
Alignment explanation
Indices: 49314--49387 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 21
49304 AAATTGAGAC
49314 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTTC-TATGAAA
**
49335 TTTTGATAACCACACTATGAAA
1 TTTTGATAACC-TTCTATGAAA
* *
49357 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCT-TCTATGAAA
49379 TTTTGATAA
1 TTTTGATAA
49388 TCTCTTTGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 6 0.14
22 34 0.79
23 3 0.07
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (21 bp):
TTTTGATAACCTTCTATGAAA
Found at i:49460 original size:78 final size:78
Alignment explanation
Indices: 49313--49465 Score: 186
Period size: 78 Copynumber: 2.0 Consensus size: 78
49303 GAAATTGAGA
* * * * * *
49313 CTTTTATAACCTTCATATGAAATTTTGATAACCACACTATGAAATTCTTATAACCTCGCTATGAC
1 CTTTGATAACCTTCATATAAAATTGTGATAACCACACTATGAAATTCTAATAACCTCGCTAAGAA
*
49378 ATTTTGATAATCT
66 ATTTTAATAATCT
*
49391 CTTTGATAACCTTTC-TATAAAATTGTGATAACCACACTATGAAATT-TCAATAACTTTC-CTAA
1 CTTTGATAACC-TTCATATAAAATTGTGATAACCACACTATGAAATTCT-AATAAC-CTCGCTAA
49453 GAAATTTTAATAA
63 GAAATTTTAATAA
49466 CCTGATCTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
77 1 0.02
78 58 0.91
79 5 0.08
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.39
Consensus pattern (78 bp):
CTTTGATAACCTTCATATAAAATTGTGATAACCACACTATGAAATTCTAATAACCTCGCTAAGAA
ATTTTAATAATCT
Found at i:49546 original size:22 final size:21
Alignment explanation
Indices: 49501--49591 Score: 74
Period size: 22 Copynumber: 4.2 Consensus size: 21
49491 CACACTATAC
*
49501 AATTTTGATAACCTCCCATGA
1 AATTTTGACAACCTCCCATGA
* *
49522 AATTTTGACAACTTCCATATGA
1 AATTTTGACAACCTCC-CATGA
** * * *
49544 AATTTTGGTAACCACACTATGG
1 AATTTTGACAACCTC-CCATGA
*
49566 AATTTTGATAACCTCCTCATGA
1 AATTTTGACAACCTCC-CATGA
49588 AATT
1 AATT
49592 ATAATAACCA
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
21 15 0.27
22 39 0.71
23 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (21 bp):
AATTTTGACAACCTCCCATGA
Found at i:49598 original size:22 final size:22
Alignment explanation
Indices: 49573--49623 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
49563 TGGAATTTTG
49573 ATAACC-TCCTCATGAAATTATA
1 ATAACCAT-CTCATGAAATTATA
* *
49595 ATAACCATCTTATGAAATTTTA
1 ATAACCATCTCATGAAATTATA
49617 ATAACCA
1 ATAACCA
49624 CATAGAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (22 bp):
ATAACCATCTCATGAAATTATA
Found at i:49614 original size:44 final size:43
Alignment explanation
Indices: 49392--49622 Score: 146
Period size: 44 Copynumber: 5.2 Consensus size: 43
49382 TGATAATCTC
* * * *
49392 TTTGATAACCTTTCTATAAAATTGTGATAACCA-CACTATGAAAT
1 TTTGATAACC-TCCTATGAAATTTTAATAACCATC-CTATGAAAT
** * * * *
49436 TTCAATAACTTTCCTAAGAAATTTTAATAACCTGATCTTATGGAAT
1 TTTGATAAC-CTCCTATGAAATTTTAATAACC--ATCCTATGAAAT
* * * *
49482 TTTGGTAACCACACTAT-ACAATTTTGATAACC-TCCCATGAAAT
1 TTTGATAACCTC-CTATGA-AATTTTAATAACCATCCTATGAAAT
* * ** *
49525 TTTGACAACTTCCATATGAAATTTTGGTAACCA-CACTATGGAAT
1 TTTGATAACCTCC-TATGAAATTTTAATAACCATC-CTATGAAAT
* *
49569 TTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAAT
1 TTTGATAACCTCCT-ATGAAATTTTAATAACCATCCTATGAAAT
*
49613 TTTAATAACC
1 TTTGATAACC
49623 ACATAGAGAC
Statistics
Matches: 140, Mismatches: 35, Indels: 24
0.70 0.18 0.12
Matches are distributed among these distances:
42 1 0.01
43 33 0.24
44 73 0.52
45 3 0.02
46 29 0.21
47 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (43 bp):
TTTGATAACCTCCTATGAAATTTTAATAACCATCCTATGAAAT
Found at i:50854 original size:2 final size:2
Alignment explanation
Indices: 50847--50878 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
50837 ATTCGTACTT
50847 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
50879 CTAGTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51019 original size:22 final size:22
Alignment explanation
Indices: 50988--51513 Score: 216
Period size: 22 Copynumber: 24.2 Consensus size: 22
50978 TACGCTATTA
*
50988 TTGATGACCTCCTTATGAAATT
1 TTGATAACCTCCTTATGAAATT
51010 TTGATAACCTTCC-TATGAAATT
1 TTGATAACC-TCCTTATGAAATT
* * * *
51032 TTAATAACGATAC-TATGGAATT
1 TTGATAAC-CTCCTTATGAAATT
* * ** *
51054 TTGA-GATCTTTTTAT-AATTTT
1 TTGATAACCTCCTTATGAA-ATT
** *
51075 TTTTTAACCTTCTTATGAAATT
1 TTGATAACCTCCTTATGAAATT
* * * *
51097 TTGTTAACCTCCCTAAGGAATT
1 TTGATAACCTCCTTATGAAATT
* *
51119 TT-AAAGATCTCAC-TATGAAATT
1 TTGATA-ACCTC-CTTATGAAATT
* **
51141 TTGATAACTTCCCAATGAAATT
1 TTGATAACCTCCTTATGAAATT
** * *
51163 TTGATAA-CTAATCTATGAGATG
1 TTGATAACCTCCT-TATGAAATT
* * * *
51185 TTGATAACTTACATATG-ATTT
1 TTGATAACCTCCTTATGAAATT
* * *
51206 ATTGATAACCACATTATGAAAAT
1 -TTGATAACCTCCTTATGAAATT
* * * * *
51229 CTAAAAACTTCCATATG-AATT
1 TTGATAACCTCCTTATGAAATT
* * * *
51250 GTT-AGTAATCACCCTCTGAAATT
1 -TTGA-TAACCTCCTTATGAAATT
* *
51273 TTGATAATCATAC-TATGAAATT
1 TTGATAA-CCTCCTTATGAAATT
* * *
51295 GTAATAACCTCGTTATGAAATT
1 TTGATAACCTCCTTATGAAATT
* *
51317 TTGATAAACCTCCCTATAAAATT
1 TTGAT-AACCTCCTTATGAAATT
*
51340 TTGATAACCTCCTTATG-AATC
1 TTGATAACCTCCTTATGAAATT
*
51361 TTGATAA----C-TA-CAAATT
1 TTGATAACCTCCTTATGAAATT
*
51377 TTGATAACCTCTCCCTATGAAATT
1 TTGATAA-C-CTCCTTATGAAATT
* * *
51401 TTGATCTACATAC-TATGAAATT
1 TTGAT-AACCTCCTTATGAAATT
51423 TTGATAACC-CTCTTATGAAATT
1 TTGATAACCTC-CTTATGAAATT
51445 TTGATAACC-CTCTTATGAAATT
1 TTGATAACCTC-CTTATGAAATT
* *
51467 TTGATAACCTTCATATGAAATT
1 TTGATAACCTCCTTATGAAATT
* *
51489 TTGATATCCTCC--CTGAAATT
1 TTGATAACCTCCTTATGAAATT
51509 TTGAT
1 TTGAT
51514 TACTCCATAA
Statistics
Matches: 370, Mismatches: 100, Indels: 70
0.69 0.19 0.13
Matches are distributed among these distances:
16 12 0.03
17 1 0.00
20 14 0.04
21 31 0.08
22 259 0.70
23 41 0.11
24 11 0.03
25 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
TTGATAACCTCCTTATGAAATT
Found at i:51418 original size:61 final size:61
Alignment explanation
Indices: 51312--51430 Score: 152
Period size: 61 Copynumber: 2.0 Consensus size: 61
51302 CCTCGTTATG
* *
51312 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCCTTATG-AATCTTGATAACTAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACATACTTATGAAATCTTGATAACTAC
* * * *
51372 AAATTTTGATAACCTCTCCCTATGAAATTTTGATCTACATAC-TATGAAATTTTGATAAC
1 AAATTTTGATAAAC-CTCCCTATAAAATTTTGAT-AACATACTTATGAAATCTTGATAAC
51431 CCTCTTATGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
60 13 0.26
61 22 0.44
62 15 0.30
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (61 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAACATACTTATGAAATCTTGATAACTAC
Found at i:51421 original size:128 final size:128
Alignment explanation
Indices: 51261--51494 Score: 330
Period size: 128 Copynumber: 1.8 Consensus size: 128
51251 TTAGTAATCA
*
51261 CCCTCTGAAATTTTGATAATCATACTATGAAATTGTAATAA-CCTCGTTATGAAATTTTGATAAA
1 CCCTATGAAATTTTGATAATCATACTATGAAATTGTAATAACCCTC-TTATGAAATTTTGATAAA
*
51325 CCTCCCTATAAAATTTTGATAACCTCCTTATG-AATCTTGATAACTACAAATTTTGATAACCTCT
65 CCT-CCTATAAAATTTTGATAACCTCCATATGAAATCTTGATAACTACAAATTTTGATAACCTCT
* * * *
51389 CCCTATGAAATTTTGAT-CTACATACTATGAAATTTTGATAACCCTCTTATGAAATTTTGATAAC
1 CCCTATGAAATTTTGATAAT-CATACTATGAAATTGTAATAACCCTCTTATGAAATTTTGATAAA
* * * *
51453 CCTCTTATGAAATTTTGATAACCTTCATATGAAATTTTGATA
65 CCTCCTATAAAATTTTGATAACCTCCATATGAAATCTTGATA
51495 TCCTCCCTGA
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
127 25 0.27
128 64 0.69
129 4 0.04
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.39
Consensus pattern (128 bp):
CCCTATGAAATTTTGATAATCATACTATGAAATTGTAATAACCCTCTTATGAAATTTTGATAAAC
CTCCTATAAAATTTTGATAACCTCCATATGAAATCTTGATAACTACAAATTTTGATAACCTCT
Found at i:51714 original size:44 final size:44
Alignment explanation
Indices: 51594--51831 Score: 173
Period size: 44 Copynumber: 5.4 Consensus size: 44
51584 AGAAATACCA
* * * *
51594 CTATGAAATTTTGGTAATCACATTTTGAAAATTCGATAACCTCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
* * * * * * *
51638 TTATGAAATTTTGATAACCTC-TCTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCTCT
* *
51682 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
* * *
51726 CTTTGAAATTTTGATAA-CA-ACTCTATGAAATTTCGATAATCT-T
1 CTATGAAATTTTGATAATCACA-T-TATGAAATTTTGATAACCTCT
* * ** *
51769 CCTAT-AAATTTTGATAATCCGATCTTTGTGAAATTTCAATAACCACT
1 -CTATGAAATTTTGATAAT-C-A-CATTATGAAATTTTGATAACCTCT
*
51816 CTATGAGA-TTTGATAA
1 CTATGAAATTTTGATAA
51832 CCTTCTATCA
Statistics
Matches: 150, Mismatches: 32, Indels: 22
0.74 0.16 0.11
Matches are distributed among these distances:
42 1 0.01
43 16 0.11
44 99 0.66
45 2 0.01
46 28 0.19
47 4 0.03
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.40
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
Found at i:51743 original size:88 final size:88
Alignment explanation
Indices: 51594--51758 Score: 233
Period size: 88 Copynumber: 1.9 Consensus size: 88
51584 AGAAATACCA
* * * **
51594 CTATGAAATTTTGGTAATCACATTTTGAAAATTCGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAATCACATTATGAAAATTCGATAACCTCCTTATGAAATTTTGATAACAAC
51659 TCTATAAAATTTTGTTGACCCCT
66 TCTATAAAATTTTGTTGACCCCT
* * *
51682 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAA
1 CTATGAAATTTTGATAATCACATTATGAAAATTCGATAACCTC-CTTATGAAATTTTGATAACAA
*
51746 CTCTATGAAATTT
65 CTCTATAAAATTT
51759 CGATAATCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
88 65 0.97
89 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (88 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTCGATAACCTCCTTATGAAATTTTGATAACAAC
TCTATAAAATTTTGTTGACCCCT
Found at i:51985 original size:22 final size:21
Alignment explanation
Indices: 51619--52204 Score: 189
Period size: 22 Copynumber: 26.8 Consensus size: 21
51609 AATCACATTT
* * *
51619 TGAAAATTCGATAACCTCTTTA
1 TGAAATTTTGATAACCTC-CTA
51641 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTC-CTA
* * * *
51663 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTC-CTA
* * *
51685 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTC-CTA
* *
51707 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTC-CTA
51729 TGAAATTTTGATAACAACT-CTA
1 TGAAATTTTGATAAC--CTCCTA
* *
51751 TGAAATTTCGATAATCTTCCTA
1 TGAAATTTTGATAA-CCTCCTA
* *
51773 T-AAATTTTGATAATCCGATCTTTG
1 TGAAATTTTGATAA-CC--TC-CTA
** *
51797 TGAAATTTCAATAACCACTCTA
1 TGAAATTTTGATAACCTC-CTA
* *
51819 TGAGA-TTTGATAACCTTCTA
1 TGAAATTTTGATAACCTCCTA
* *
51839 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCC-TA
* *
51859 TGAAATTGAGACTTTTATAACCGTCATA
1 TGAAA-T-----TTTGATAACC-TCCTA
*
51887 TGAAATTTTGATAACCTCCCGA
1 TGAAATTTTGATAACCT-CCTA
* *
51909 TGAGATATT-AGTAACCTCCTTA
1 TGAAATTTTGA-TAACCTCC-TA
* *
51931 TGAAATTTTGTTAA-C-CATA
1 TGAAATTTTGATAACCTCCTA
51950 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTC-CTA
* * **
51972 TGACATTTTGATAATCTTTTTGA
1 TGAAATTTTGATAA-CCTCCT-A
* * * * * *
51995 TAACCACACTATGA-AA-TTTCAA
1 TGA--A-ATTTTGATAACCTCCTA
**
52017 T-AAGA---CAATAACCTTCCTA
1 TGAA-ATTTTGATAACC-TCCTA
* * *
52036 AGAAATTTTAATAACCTGATTCTA
1 TGAAATTTTGATAACC---TCCTA
* *
52060 TGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
52082 TGAAATTTTGATAACCTTCCTA
1 TGAAATTTTGATAACC-TCCTA
*
52104 TGAAATTTTGATAACTTCCATA
1 TGAAATTTTGATAACCTCC-TA
* *
52126 TGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
*
52148 TGAAAATTTGATAACCT-C-A
1 TGAAATTTTGATAACCTCCTA
* * * *
52167 TAAAATTATAATAACCATCTTA
1 TGAAATTTTGATAACC-TCCTA
52189 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
52205 ACACAGAGAC
Statistics
Matches: 415, Mismatches: 100, Indels: 98
0.68 0.16 0.16
Matches are distributed among these distances:
16 1 0.00
17 2 0.00
19 34 0.08
20 21 0.05
21 40 0.10
22 248 0.60
23 13 0.03
24 23 0.06
25 12 0.03
26 9 0.02
27 2 0.00
28 8 0.02
29 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:52148 original size:66 final size:67
Alignment explanation
Indices: 52024--52208 Score: 238
Period size: 66 Copynumber: 2.8 Consensus size: 67
52014 CAATAAGACA
* *
52024 ATAACCTTCCTAAGAAATTTTAATAACCTGATTCTATGAAATTTTGGTAACCACACTATGAAATT
1 ATAACCTTCCTAAGAAATTTTAATAACCT-ATCCTATGAAATTTTGGTAACCACACTATGAAAAT
52089 TTG
65 TTG
* *
52092 ATAACCTTCCTATGAAATTTTGATAA-CT-TCCATATGAAATTTTGGTAACCACACTATGAAAAT
1 ATAACCTTCCTAAGAAATTTTAATAACCTATCC-TATGAAATTTTGGTAACCACACTATGAAAAT
52155 TTG
65 TTG
* * * *
52158 ATAACC-TCAT-A-AAATTATAATAACC-ATCTTATGAAATTTTGATAACCACAC
1 ATAACCTTCCTAAGAAATTTTAATAACCTATCCTATGAAATTTTGGTAACCACAC
52209 AGAGACAAGA
Statistics
Matches: 104, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
63 31 0.30
64 3 0.03
65 5 0.05
66 39 0.38
67 2 0.02
68 24 0.23
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (67 bp):
ATAACCTTCCTAAGAAATTTTAATAACCTATCCTATGAAATTTTGGTAACCACACTATGAAAATT
TG
Found at i:52692 original size:20 final size:20
Alignment explanation
Indices: 52654--52692 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
52644 TATTGACATT
52654 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
52674 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
52693 AATAATAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:56410 original size:19 final size:20
Alignment explanation
Indices: 56359--56410 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
56349 CAGTGGTGTT
56359 TTTAATAA-TAATTATTCAA
1 TTTAATAATTAATTATTCAA
** *
56378 TAAAATAATT-ATTATT-TA
1 TTTAATAATTAATTATTCAA
56396 TTTAATAATTAATTA
1 TTTAATAATTAATTA
56411 ATTTCAACCC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 9 0.35
19 16 0.62
20 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAATAATTAATTATTCAA
Found at i:63643 original size:93 final size:93
Alignment explanation
Indices: 63529--63709 Score: 317
Period size: 93 Copynumber: 1.9 Consensus size: 93
63519 TCCCACTCCG
* *
63529 TTGCTCATTTGACCCACTTTCAGGACCTGATAAAGGTATATTGACCACATCACTATGAGCAGTAC
1 TTGCTCATTTGACCCAATTTCAGGACCTGATAAAGGTATATTGACCACATCACTACGAGCAGTAC
*
63594 TGCTTACCTCTGACTTAGTTGTATTCCA
66 TGCTTACCTCTGACTTAATTGTATTCCA
* *
63622 TTGCTCATTTGACCCAATTTCAGGACCTGATAAAGGTATATTGATCACATCACTACGAGCAGTGC
1 TTGCTCATTTGACCCAATTTCAGGACCTGATAAAGGTATATTGACCACATCACTACGAGCAGTAC
63687 TGCTTACCTCTGACTTAATTGTA
66 TGCTTACCTCTGACTTAATTGTA
63710 GATTGAACAT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (93 bp):
TTGCTCATTTGACCCAATTTCAGGACCTGATAAAGGTATATTGACCACATCACTACGAGCAGTAC
TGCTTACCTCTGACTTAATTGTATTCCA
Found at i:70633 original size:13 final size:14
Alignment explanation
Indices: 70615--70643 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
70605 CTCATTTTGC
70615 TTCAAATGATA-TA
1 TTCAAATGATAGTA
70628 TTCAAATGATAGTA
1 TTCAAATGATAGTA
70642 TT
1 TT
70644 AATTTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (14 bp):
TTCAAATGATAGTA
Found at i:71741 original size:6 final size:6
Alignment explanation
Indices: 71730--71754 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
71720 CGCGCCCCCA
71730 AATCCC AATCCC AATCCC AATCCC A
1 AATCCC AATCCC AATCCC AATCCC A
71755 CCCCACCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (6 bp):
AATCCC
Found at i:78297 original size:32 final size:32
Alignment explanation
Indices: 78261--78322 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
78251 ATAAAAAATG
* * * *
78261 TATGTTTATTATTAAGTTTGTTATTATTAATA
1 TATGTGTATGATTAACTTTATTATTATTAATA
*
78293 TATGTGTATGGTTAACTTTATTATTATTAA
1 TATGTGTATGATTAACTTTATTATTATTAA
78323 AAGTGTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (32 bp):
TATGTGTATGATTAACTTTATTATTATTAATA
Found at i:78777 original size:13 final size:12
Alignment explanation
Indices: 78753--78783 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
78743 TATCCACTAG
78753 TAATATATATAA
1 TAATATATATAA
78765 TAATATAATATAA
1 TAATAT-ATATAA
78778 TAATAT
1 TAATAT
78784 GATGATATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATATATAA
Found at i:85340 original size:45 final size:44
Alignment explanation
Indices: 85210--85344 Score: 162
Period size: 45 Copynumber: 3.0 Consensus size: 44
85200 TAATTCATTC
* * * *
85210 ACATCAGCAGCCACAGGAGTTTGAGGGTCATTGGCCCCATCATTA
1 ACATCAGCAGCCACAGGAATTTG-GGGTCATTGACCCCATTAGTA
* * * *
85255 ACATCAGCAGCCACTGGATTTTGGGGGTTATTAACCCCATTAGTA
1 ACATCAGCAGCCACAGGAATTT-GGGGTCATTGACCCCATTAGTA
*
85300 ACATCAGCAGCCACCGGAATTTGGGAGTCATTGACCCCATTAGTA
1 ACATCAGCAGCCACAGGAATTTGGG-GTCATTGACCCCATTAGTA
85345 GCATTACACA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
44 3 0.04
45 73 0.95
46 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.24
Consensus pattern (44 bp):
ACATCAGCAGCCACAGGAATTTGGGGTCATTGACCCCATTAGTA
Found at i:90146 original size:484 final size:484
Alignment explanation
Indices: 89238--90206 Score: 1902
Period size: 484 Copynumber: 2.0 Consensus size: 484
89228 GGAGAGCTTT
89238 ACCCCCATAGTGGTCCCCAACTCGAACAAGATTAACTTGTAAATATACCAAAATAAGAAAATAAT
1 ACCCCCATAGTGGTCCCCAACTCGAACAAGATTAACTTGTAAATATACCAAAATAAGAAAATAAT
89303 TTAAACTGGGCCAAACGGAAAATCCATAAATGTTTTCCAGAAACACTTTTTAGTTGCTTTTGAAC
66 TTAAACTGGGCCAAACGGAAAATCCATAAATGTTTTCCAGAAACACTTTTTAGTTGCTTTTGAAC
*
89368 TAAGAGGCAGAACCTCTAAATTGAAACTTTTTCCAGGAGCCATTTTTCAGAAGAGGTTTAAGCTA
131 TAAGAGGCAGAACCTCTAAATTGAAACTTTTTCCAGGAGCCATTTTTCAGAAGAGGTTCAAGCTA
* *
89433 AGCCAAACGGGTCCATATAGCTTGCCCAAGCTTGTTCAATTAAAAAAAGTTTTGCCCAAGTTCAC
196 AGCCAAACGGGTCCATATAGCTTGCCCAAACTTGTTCAATTAAAAAAAGTTTTGCCCAAATTCAC
89498 CCGTTTAGTAATTAAATATATAATATTTATTTATTTTTTAACTCATTTAAAATATATTTATTATT
261 CCGTTTAGTAATTAAATATATAATATTTATTTATTTTTTAACTCATTTAAAATATATTTATTATT
89563 TTTTTATGGGTGAATTATTAACAAGTGTAGCTGTAACGAATCTCATACACCTTACCTATATTGCC
326 TTTTTATGGGTGAATTATTAACAAGTGTAGCTGTAACGAATCTCATACACCTTACCTATATTGCC
89628 CTTTACAAAAATTTTGAAAACATAGAAATCAGTTATTCTTAATTCAGAAAATGAAAGCTCTCTTG
391 CTTTACAAAAATTTTGAAAACATAGAAATCAGTTATTCTTAATTCAGAAAATGAAAGCTCTCTTG
89693 GTTCCCAATTTCCAAATCAATTCCAATAG
456 GTTCCCAATTTCCAAATCAATTCCAATAG
89722 ACCCCCATAGTGGTCCCCAACTCGAACAAGATTAACTTGTAAATATACCAAAATAAGAAAATAAT
1 ACCCCCATAGTGGTCCCCAACTCGAACAAGATTAACTTGTAAATATACCAAAATAAGAAAATAAT
89787 TTAAACTGGGCCAAACGGAAAATCCATAAATGTTTTCCAGAAACACTTTTTAGTTGCTTTTGAAC
66 TTAAACTGGGCCAAACGGAAAATCCATAAATGTTTTCCAGAAACACTTTTTAGTTGCTTTTGAAC
89852 TAAGAGGCAGAACCTCTAAATTGAAACTTTTTCCAGGAGCCATTTTTCAGAAGAGGTTCAAGCTA
131 TAAGAGGCAGAACCTCTAAATTGAAACTTTTTCCAGGAGCCATTTTTCAGAAGAGGTTCAAGCTA
89917 AGCCAAACGGGTCCATATAGCTTGCCCAAACTTGTTCAATTAAAAAAAGTTTTGCCCAAATTCAC
196 AGCCAAACGGGTCCATATAGCTTGCCCAAACTTGTTCAATTAAAAAAAGTTTTGCCCAAATTCAC
89982 CCGTTTAGTAATTAAATATATAATATTTATTTATTTTTTAACTCATTTAAAATATATTTATTATT
261 CCGTTTAGTAATTAAATATATAATATTTATTTATTTTTTAACTCATTTAAAATATATTTATTATT
*
90047 TTTTTATGGGTGAATTATTCACAAGTGTAGCTGTAACGAATCTCATACACCTTACCTATATTGCC
326 TTTTTATGGGTGAATTATTAACAAGTGTAGCTGTAACGAATCTCATACACCTTACCTATATTGCC
90112 CTTTACAAAAATTTTGAAAACATAGAAATCAGTTATTCTTAATTCAGAAAATGAAAGCTCTCTTG
391 CTTTACAAAAATTTTGAAAACATAGAAATCAGTTATTCTTAATTCAGAAAATGAAAGCTCTCTTG
90177 GTTCCCAATTTCCAAATCAATTCCAATAG
456 GTTCCCAATTTCCAAATCAATTCCAATAG
90206 A
1 A
90207 GAGATATGAA
Statistics
Matches: 481, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
484 481 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (484 bp):
ACCCCCATAGTGGTCCCCAACTCGAACAAGATTAACTTGTAAATATACCAAAATAAGAAAATAAT
TTAAACTGGGCCAAACGGAAAATCCATAAATGTTTTCCAGAAACACTTTTTAGTTGCTTTTGAAC
TAAGAGGCAGAACCTCTAAATTGAAACTTTTTCCAGGAGCCATTTTTCAGAAGAGGTTCAAGCTA
AGCCAAACGGGTCCATATAGCTTGCCCAAACTTGTTCAATTAAAAAAAGTTTTGCCCAAATTCAC
CCGTTTAGTAATTAAATATATAATATTTATTTATTTTTTAACTCATTTAAAATATATTTATTATT
TTTTTATGGGTGAATTATTAACAAGTGTAGCTGTAACGAATCTCATACACCTTACCTATATTGCC
CTTTACAAAAATTTTGAAAACATAGAAATCAGTTATTCTTAATTCAGAAAATGAAAGCTCTCTTG
GTTCCCAATTTCCAAATCAATTCCAATAG
Found at i:93110 original size:4 final size:4
Alignment explanation
Indices: 93096--93132 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
93086 TTTTGTAATT
*
93096 TAAA TTAAA TAAA TAAA TTAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
93133 GCGTAACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (4 bp):
TAAA
Found at i:97158 original size:15 final size:15
Alignment explanation
Indices: 97135--97169 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
97125 GATCTTGGAT
* *
97135 GTTTTAGTCAGTTTA
1 GTTTGAGTCAGTTGA
97150 GTTTGAGTCAGTTGA
1 GTTTGAGTCAGTTGA
97165 GTTTG
1 GTTTG
97170 TTTTGAGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.29, T:0.49
Consensus pattern (15 bp):
GTTTGAGTCAGTTGA
Found at i:101296 original size:34 final size:33
Alignment explanation
Indices: 101233--101298 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
101223 TTATTAATGT
* **
101233 ATTTATAATATATTATTATTTTTCTTAATTTAG
1 ATTTATAATATATTATTATATTTAATAATTTAG
101266 ATTTATATATATATTATT-TAATTTAATAATTTA
1 ATTTATA-ATATATTATTAT-ATTTAATAATTTA
101299 TAATAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 8 0.29
34 20 0.71
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (33 bp):
ATTTATAATATATTATTATATTTAATAATTTAG
Found at i:108286 original size:7 final size:7
Alignment explanation
Indices: 108274--108300 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
108264 TAATTGAGAT
108274 TCCAGAG
1 TCCAGAG
108281 TCCAGAG
1 TCCAGAG
108288 TCCAGAG
1 TCCAGAG
108295 TCCAGA
1 TCCAGA
108301 CCCAACCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.15
Consensus pattern (7 bp):
TCCAGAG
Found at i:110967 original size:19 final size:20
Alignment explanation
Indices: 110943--110982 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
110933 GATAAAGAGC
110943 AAAAATT-AACAACTCAAAA
1 AAAAATTAAACAACTCAAAA
110962 AAAAATTCAAACAACTCAAAA
1 AAAAATT-AAACAACTCAAAA
110983 TTAAAGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.68, C:0.17, G:0.00, T:0.15
Consensus pattern (20 bp):
AAAAATTAAACAACTCAAAA
Found at i:112279 original size:75 final size:75
Alignment explanation
Indices: 112189--112418 Score: 388
Period size: 75 Copynumber: 3.1 Consensus size: 75
112179 CTGAGTTTTC
** *
112189 ATGCATTCTCTTATAATTTTCAGATATTGTCTCAAAATAATCTTCCCACAGTTTTCTCACATTTG
1 ATGCATTCTCTTATAATTTTCAGGCATTGCCTCAAAATAATCTTCCCACAGTTTTCTCACATTTG
112254 CGGGTTCACA
66 CGGGTTCACA
* *
112264 ATGCATTCTCTTATAATTTTTAGGCATTGCCTCAAAATAATATTCCCACAGTTTTCTCACATTTG
1 ATGCATTCTCTTATAATTTTCAGGCATTGCCTCAAAATAATCTTCCCACAGTTTTCTCACATTTG
*
112329 CGTGTTCACA
66 CGGGTTCACA
*
112339 ATGCATTCTCTTATAATTTTCAGGCATTGCCTCAAAATAATCTTCCCACAGTTTCCTCACATTTG
1 ATGCATTCTCTTATAATTTTCAGGCATTGCCTCAAAATAATCTTCCCACAGTTTTCTCACATTTG
*
112404 CTGGTTCACA
66 CGGGTTCACA
112414 ATGCA
1 ATGCA
112419 CTAATAAAGT
Statistics
Matches: 144, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 144 1.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.39
Consensus pattern (75 bp):
ATGCATTCTCTTATAATTTTCAGGCATTGCCTCAAAATAATCTTCCCACAGTTTTCTCACATTTG
CGGGTTCACA
Found at i:113379 original size:83 final size:83
Alignment explanation
Indices: 113240--113406 Score: 318
Period size: 83 Copynumber: 2.0 Consensus size: 83
113230 TCTTGAGTCA
113240 TACCCACCTAGCATTCTGAAGGTGGTATTGTGATATTAAATACAAAAGCTTAACAAAGAAAATAT
1 TACCCACCTAGCATTCTGAAGGTGGTATTGTGATATTAAATACAAAAGCTTAACAAAGAAAATAT
113305 ATAATTTTGTTGTAAAAC
66 ATAATTTTGTTGTAAAAC
113323 TACCCACCTAGCA-TCTTGAAGGTGGTATTGTGATATTAAATACAAAAGCTTAACAAAGAAAATA
1 TACCCACCTAGCATTC-TGAAGGTGGTATTGTGATATTAAATACAAAAGCTTAACAAAGAAAATA
113387 TATAATTTTGTTGTAAAAC
65 TATAATTTTGTTGTAAAAC
113406 T
1 T
113407 TTTGAATCGG
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
82 2 0.02
83 81 0.98
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (83 bp):
TACCCACCTAGCATTCTGAAGGTGGTATTGTGATATTAAATACAAAAGCTTAACAAAGAAAATAT
ATAATTTTGTTGTAAAAC
Found at i:113478 original size:16 final size:15
Alignment explanation
Indices: 113448--113491 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
113438 TTTAATTTTT
*
113448 TTATAATATTCATTAA
1 TTAT-ATATTAATTAA
113464 TTAATATATTAATTAA
1 TT-ATATATTAATTAA
113480 TTATATAATTAA
1 TTATAT-ATTAA
113492 ACTTTACTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 4 0.16
16 19 0.76
17 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATATATTAATTAA
Found at i:113805 original size:17 final size:17
Alignment explanation
Indices: 113747--113798 Score: 86
Period size: 19 Copynumber: 2.9 Consensus size: 17
113737 AGAGTTTTGT
113747 AAATTGACATGCTAAGC
1 AAATTGACATGCTAAGC
113764 AAATTGACACATGCTAAGC
1 AAATTG--ACATGCTAAGC
113783 AAATTGACATGCTAAG
1 AAATTGACATGCTAAG
113799 TATATTGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.48
19 17 0.52
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (17 bp):
AAATTGACATGCTAAGC
Found at i:115240 original size:12 final size:12
Alignment explanation
Indices: 115223--115248 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
115213 AGAGCTAGCT
115223 AGTAATTTAAAA
1 AGTAATTTAAAA
115235 AGTAATTTAAAA
1 AGTAATTTAAAA
115247 AG
1 AG
115249 CAGTAATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.31
Consensus pattern (12 bp):
AGTAATTTAAAA
Found at i:115678 original size:20 final size:20
Alignment explanation
Indices: 115653--115694 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
115643 TGTCCATGGG
115653 ATTCGAACTCCCAACACTTA
1 ATTCGAACTCCCAACACTTA
115673 ATTCGAACTCCCAACACTTA
1 ATTCGAACTCCCAACACTTA
115693 AT
1 AT
115695 GAGCAAAAAA
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:0.33, G:0.05, T:0.26
Consensus pattern (20 bp):
ATTCGAACTCCCAACACTTA
Found at i:115981 original size:25 final size:25
Alignment explanation
Indices: 115953--116016 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
115943 CTTCCTCCTC
115953 TGTATTATTTCTTGTCCTTGTTCTT
1 TGTATTATTTCTTGTCCTTGTTCTT
115978 TGTATTATTTCTTGTCCTTGTTCTT
1 TGTATTATTTCTTGTCCTTGTTCTT
116003 TGTATTATTTCTTG
1 TGTATTATTTCTTG
116017 ATTCCGTCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.09, C:0.14, G:0.12, T:0.64
Consensus pattern (25 bp):
TGTATTATTTCTTGTCCTTGTTCTT
Found at i:117752 original size:28 final size:28
Alignment explanation
Indices: 117692--117744 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
117682 TGTAAGTACT
117692 GAATA-TTAGGAGCTTGATGCCAAAAAA
1 GAATATTTAGGAGCTTGATGCCAAAAAA
117719 GAATATTTAGGAGCTTG-TGCCAAAAA
1 GAATATTTAGGAGCTTGATGCCAAAAA
117745 GATAATATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.25
Consensus pattern (28 bp):
GAATATTTAGGAGCTTGATGCCAAAAAA
Done.