Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018442.1 Corchorus olitorius cultivar O-4 contig18475, 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: 178618
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:13 original size:2 final size:2
Alignment explanation
Indices: 7--38 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1 TAACTA
7 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
39 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:43 original size:2 final size:2
Alignment explanation
Indices: 38--62 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28 TCTCTCTCTC
38 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
63 TTGTTTATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4196 original size:2 final size:2
Alignment explanation
Indices: 4189--4220 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4179 TTAGGATTTC
4189 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
4221 TTATTAGCCG
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):
AT
Found at i:6409 original size:72 final size:72
Alignment explanation
Indices: 6292--6435 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
6282 CTACCTTTTT
*
6292 TGAGCATATTTCTTTTACACATGTCAAAAGAGAAGCTAACTATTGTGCCCATAGTTTGGCAAGAT
1 TGAGCATATTTCTCTTACACATGTCAAAAGAGAAGCTAACTATTGTGCCCATAGTTTGGCAAGAT
*
6357 TAGCTAG
66 CAGCTAG
6364 TGAGCATATTTCTCTTACACATGTCAAAAGAGAAGCTAACTATTGTGCCCATAGTTTGGCAAGAT
1 TGAGCATATTTCTCTTACACATGTCAAAAGAGAAGCTAACTATTGTGCCCATAGTTTGGCAAGAT
6429 CAGCTAG
66 CAGCTAG
6436 CTCTAATAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (72 bp):
TGAGCATATTTCTCTTACACATGTCAAAAGAGAAGCTAACTATTGTGCCCATAGTTTGGCAAGAT
CAGCTAG
Found at i:11591 original size:21 final size:20
Alignment explanation
Indices: 11565--11628 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 20
11555 GCTGCTCTAA
11565 TAATCTCATCTGTACAGTATC
1 TAATCTCATCTGTACAGT-TC
* *
11586 TAATCTAATCTGTACAG-TG
1 TAATCTCATCTGTACAGTTC
11605 TAATCTCATCTGTACAGTTGC
1 TAATCTCATCTGTACAGTT-C
11626 TAA
1 TAA
11629 ACAGTGTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
20 1 0.03
21 19 0.51
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTTC
Found at i:15194 original size:2 final size:2
Alignment explanation
Indices: 15187--15223 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
15177 GCATATCTGT
15187 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
15224 GATATACTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:19055 original size:24 final size:24
Alignment explanation
Indices: 19027--19073 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
19017 AGAAAAGAAA
* *
19027 AAAAAAGCAAGCAAACTAACAAACT
1 AAAAAA-CAAACAAACAAACAAACT
19052 AAAAAACAAACAAACAAACAAA
1 AAAAAACAAACAAACAAACAAA
19074 AAAATTCCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.72, C:0.19, G:0.04, T:0.04
Consensus pattern (24 bp):
AAAAAACAAACAAACAAACAAACT
Found at i:19077 original size:20 final size:20
Alignment explanation
Indices: 19038--19077 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19028 AAAAAGCAAG
* *
19038 CAAACTAACAAACTAAAAAA
1 CAAACAAACAAACAAAAAAA
19058 CAAACAAACAAACAAAAAAA
1 CAAACAAACAAACAAAAAAA
19078 TTCCCTGTAC
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:0.75, C:0.20, G:0.00, T:0.05
Consensus pattern (20 bp):
CAAACAAACAAACAAAAAAA
Found at i:20451 original size:25 final size:25
Alignment explanation
Indices: 20423--20475 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
20413 TCTCACAACC
20423 GAATGACAACACA-TCAGGTTAATAG
1 GAATGACAACACATTC-GGTTAATAG
* *
20448 GAATGACAACATATTCGGTTATTAG
1 GAATGACAACACATTCGGTTAATAG
20473 GAA
1 GAA
20476 AACGTTACGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.25
Consensus pattern (25 bp):
GAATGACAACACATTCGGTTAATAG
Found at i:21985 original size:13 final size:13
Alignment explanation
Indices: 21967--22010 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
21957 CTCGAAACTT
* *
21967 ATAAATATAAATC
1 ATAAATAAAAATA
21980 ATAAATAAAAATA
1 ATAAATAAAAATA
21993 ATAAATAAAAATA
1 ATAAATAAAAATA
22006 A-AAAT
1 ATAAAT
22011 CTTATTAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 4 0.14
13 25 0.86
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (13 bp):
ATAAATAAAAATA
Found at i:22004 original size:19 final size:19
Alignment explanation
Indices: 21969--22010 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
21959 CGAAACTTAT
*
21969 AAATATAAATCATAAATAA
1 AAATATAAATCAAAAATAA
21988 AAATAATAAAT-AAAAATAA
1 AAAT-ATAAATCAAAAATAA
22007 AAAT
1 AAAT
22011 CTTATTAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATATAAATCAAAAATAA
Found at i:23304 original size:70 final size:70
Alignment explanation
Indices: 23221--23357 Score: 215
Period size: 70 Copynumber: 2.0 Consensus size: 70
23211 ATAAGAAAAC
* *
23221 ATCAACCTAACATACATAGATAG-AGTTAAGTTATACATAAG-GATAGATTCATACTTCATTGAT
1 ATCAACCTAACATACATAGATAGCA-TCAAGTTATACAT-AGCCATAGATTCATACTTCATTGAT
23284 TCATCAT
64 TCATCAT
*
23291 ATCAACCTAACATACATAGATAGCATCAAGTTATACATAGCCATAGATTCATACTTCCTTGATTC
1 ATCAACCTAACATACATAGATAGCATCAAGTTATACATAGCCATAGATTCATACTTCATTGATTC
23356 AT
66 AT
23358 TACCATTTCT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
69 2 0.03
70 59 0.95
71 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (70 bp):
ATCAACCTAACATACATAGATAGCATCAAGTTATACATAGCCATAGATTCATACTTCATTGATTC
ATCAT
Found at i:23862 original size:27 final size:28
Alignment explanation
Indices: 23829--23892 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
23819 ATGGGCTGAG
* *
23829 TCTTGAAGAGA-AGGCTGCTCTGGCTGT
1 TCTTGAAGAGATAGGCTGCTCTGCCTGC
* *
23856 TTTTGAAGA-ATAGGCTGCTTTGCCTGC
1 TCTTGAAGAGATAGGCTGCTCTGCCTGC
23883 TCTTGAAGAG
1 TCTTGAAGAG
23893 GAGAATGCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (28 bp):
TCTTGAAGAGATAGGCTGCTCTGCCTGC
Found at i:24510 original size:18 final size:19
Alignment explanation
Indices: 24487--24524 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
24477 AGTGAGTTAG
*
24487 AAATGAAA-ACTAAATTGC
1 AAATGAAAGAATAAATTGC
24505 AAATGAAAGAATAAATTGC
1 AAATGAAAGAATAAATTGC
24524 A
1 A
24525 GTAGGTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.58, C:0.08, G:0.13, T:0.21
Consensus pattern (19 bp):
AAATGAAAGAATAAATTGC
Found at i:24680 original size:98 final size:98
Alignment explanation
Indices: 24569--24768 Score: 260
Period size: 98 Copynumber: 2.0 Consensus size: 98
24559 AAATGACAAT
* *** * * *
24569 AGAAGTGTAAGAAGTTACATGAATGGGTTTTTTATATGAAAGTAAATAGAAATAGGTTGG-AGAA
1 AGAAGTGTAAGAAGATACATGAATGAAATGTTTATATGAAAGTAAACAGAAATAAGTTGGAAG-A
24633 TGTATTGCAAAA-TCTGGAAACCATGGCAGTGGAA
65 TGTATTGCAAAACT-TGGAAACCATGGCAGTGGAA
* * *
24667 AGAAGTGTGAGAAGATACATGAATGAAATGTTTCTATGAAAGTAAACATAAATAAGTTGGAAGAT
1 AGAAGTGTAAGAAGATACATGAATGAAATGTTTATATGAAAGTAAACAGAAATAAGTTGGAAGAT
* *
24732 GTATTGTAAAACTTGGAAATCATGGCAGTGGAA
66 GTATTGCAAAACTTGGAAACCATGGCAGTGGAA
24765 AGAA
1 AGAA
24769 TGAATGAGAC
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
98 85 0.97
99 3 0.03
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.27
Consensus pattern (98 bp):
AGAAGTGTAAGAAGATACATGAATGAAATGTTTATATGAAAGTAAACAGAAATAAGTTGGAAGAT
GTATTGCAAAACTTGGAAACCATGGCAGTGGAA
Found at i:24803 original size:83 final size:83
Alignment explanation
Indices: 24685--24848 Score: 233
Period size: 83 Copynumber: 2.0 Consensus size: 83
24675 GAGAAGATAC
* * *
24685 ATGAATGAAATGTTTCTATGAAAGTAAACATAAATAAGTTGGAAGA-TGTATTGT-AAAACTTGG
1 ATGAATGAAACGTTTATATGAAAGTAAACAGAAATAAGTTGGAA-ATTGTATTGTCAAAAC-TGG
24748 AAATCATGGCAGTGGAAAGA
64 AAATCATGGCAGTGGAAAGA
* * *
24768 ATGAATGAGACGTTTATATGAAAGTAATCAGAAATAATTTGGAAATTGTATTGTCAAAACTGGAA
1 ATGAATGAAACGTTTATATGAAAGTAAACAGAAATAAGTTGGAAATTGTATTGTCAAAACTGGAA
*
24833 ATCATGGTAGTGGAAA
66 ATCATGGCAGTGGAAA
24849 TAAGTATAAG
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
82 1 0.01
83 66 0.92
84 5 0.07
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.29
Consensus pattern (83 bp):
ATGAATGAAACGTTTATATGAAAGTAAACAGAAATAAGTTGGAAATTGTATTGTCAAAACTGGAA
ATCATGGCAGTGGAAAGA
Found at i:24903 original size:181 final size:181
Alignment explanation
Indices: 24599--24946 Score: 459
Period size: 181 Copynumber: 1.9 Consensus size: 181
24589 GAATGGGTTT
*
24599 TTTATATGAAAGTAAATAGAAATAGGTTGGAGAATGTATTGCAAAATCTGGAAACCATGGCAGTG
1 TTTATATGAAAGTAAATAGAAATAAGTTGGAGAATGTATTGCAAAATCTGGAAACCATGGCAGTG
* * * * * *
24664 GAAAGAAGTGTGAGAAGATACATGAATGAAATGTTTCTATGAAAGTAAACATAAATAAGTTGGAA
66 GAAAGAAGTATAAGAAGATACATGAATGAAATGTTTATATGAAAGAAAACAAAAATAAGTTAGAA
****
24729 GATGTATTGTAAAACTTGGAAATCATGGCAGTGGAAAGAATGAATGAGACG
131 GATGTATTGTAAAAAACAGAAATCATGGCAGTGGAAAGAATGAATGAGACG
* * *
24780 TTTATATGAAAGT-AATCAGAAATAATTTGGA-AATTGTATTGTCAAAA-CTGGAAATCATGGTA
1 TTTATATGAAAGTAAAT-AGAAATAAGTTGGAGAA-TGTATTG-CAAAATCTGGAAACCATGGCA
* * * * *
24842 GTGGAAATAAGTATAAGAGGTTGCATGAATGAGATGTTTATATGAAAGAAAACAAAAATAAGTTA
63 GTGGAAAGAAGTATAAGAAGATACATGAATGAAATGTTTATATGAAAGAAAACAAAAATAAGTTA
* *
24907 GATGATGTATTGTAAAAAACAGAAATCATGGCGGTGGAAA
128 GAAGATGTATTGTAAAAAACAGAAATCATGGCAGTGGAAA
24947 CCTCAGTGTA
Statistics
Matches: 143, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
180 5 0.03
181 133 0.93
182 5 0.03
ACGTcount: A:0.43, C:0.06, G:0.24, T:0.27
Consensus pattern (181 bp):
TTTATATGAAAGTAAATAGAAATAAGTTGGAGAATGTATTGCAAAATCTGGAAACCATGGCAGTG
GAAAGAAGTATAAGAAGATACATGAATGAAATGTTTATATGAAAGAAAACAAAAATAAGTTAGAA
GATGTATTGTAAAAAACAGAAATCATGGCAGTGGAAAGAATGAATGAGACG
Found at i:24916 original size:98 final size:98
Alignment explanation
Indices: 24768--24946 Score: 227
Period size: 98 Copynumber: 1.8 Consensus size: 98
24758 AGTGGAAAGA
* * * * * * *
24768 ATGAATGAGACGTTTATATGAAAGTAATCAGAAATAATTTGGAAATTGTATTGT-CAAAACTGGA
1 ATGAATGAGACGTTTATATGAAAGAAAACAAAAATAAGTTAGAAATTGTATTGTAAAAAAC-AGA
*
24832 AATCATGGTAGTGGAAATAAGTATAAGAGGTTGC
65 AATCATGGCAGTGGAAATAAGTATAAGAGGTTGC
* *
24866 ATGAATGAGATGTTTATATGAAAGAAAACAAAAATAAGTTAGATGA-TGTATTGTAAAAAACAGA
1 ATGAATGAGACGTTTATATGAAAGAAAACAAAAATAAGTTAGA-AATTGTATTGTAAAAAACAGA
*
24930 AATCATGGCGGTGGAAA
65 AATCATGGCAGTGGAAA
24947 CCTCAGTGTA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
98 62 0.91
99 6 0.09
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (98 bp):
ATGAATGAGACGTTTATATGAAAGAAAACAAAAATAAGTTAGAAATTGTATTGTAAAAAACAGAA
ATCATGGCAGTGGAAATAAGTATAAGAGGTTGC
Found at i:42524 original size:9 final size:9
Alignment explanation
Indices: 42507--42538 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
42497 TATGGCCCGA
*
42507 CCGGTTGAC
1 CCGGGTGAC
42516 CCGGGTGAC
1 CCGGGTGAC
42525 CCGGGTGAC
1 CCGGGTGAC
42534 CCGGG
1 CCGGG
42539 ACCCGGAGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.09, C:0.34, G:0.44, T:0.12
Consensus pattern (9 bp):
CCGGGTGAC
Found at i:47028 original size:13 final size:13
Alignment explanation
Indices: 46997--47034 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
46987 AGCAACAATG
*
46997 AGGAGAGAATAGT
1 AGGAGAGAAAAGT
47010 AGGAGAGAAAAG-
1 AGGAGAGAAAAGT
47022 A-GAGAGAAAAGT
1 AGGAGAGAAAAGT
47034 A
1 A
47035 AAATAAGGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.43
12 2 0.09
13 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.37, T:0.08
Consensus pattern (13 bp):
AGGAGAGAAAAGT
Found at i:48571 original size:19 final size:19
Alignment explanation
Indices: 48547--48584 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
48537 CTTTTACCTT
48547 AAAGTCACAAAAAGCTAAC
1 AAAGTCACAAAAAGCTAAC
* *
48566 AAAGTCATAATAAGCTAAC
1 AAAGTCACAAAAAGCTAAC
48585 CATTTAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.18, G:0.11, T:0.16
Consensus pattern (19 bp):
AAAGTCACAAAAAGCTAAC
Found at i:53170 original size:24 final size:24
Alignment explanation
Indices: 53138--53185 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
53128 TTCATTTACA
53138 ATTGCAATGGTCCCACGGGATCGC
1 ATTGCAATGGTCCCACGGGATCGC
53162 ATTGCAATGGTCCCACGGGATCGC
1 ATTGCAATGGTCCCACGGGATCGC
53186 CTGTTAGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (24 bp):
ATTGCAATGGTCCCACGGGATCGC
Found at i:57051 original size:2 final size:2
Alignment explanation
Indices: 57044--57095 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
57034 TGAATAATGA
* * * * *
57044 AT AT AT AT AT AT AT AT AA AT CT AT AT CT AT AT CT AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57086 AT AT -T AT AT A
1 AT AT AT AT AT A
57096 AGTCTAAACT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57367 original size:39 final size:40
Alignment explanation
Indices: 57311--57391 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
57301 TTTAATTCCT
57311 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
57351 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
57390 AT
1 AT
57392 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:63321 original size:16 final size:16
Alignment explanation
Indices: 63300--63332 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
63290 CATGCATCAT
63300 AATCTTAATATATGCC
1 AATCTTAATATATGCC
63316 AATCTTAATATATGCC
1 AATCTTAATATATGCC
63332 A
1 A
63333 TAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (16 bp):
AATCTTAATATATGCC
Found at i:66438 original size:36 final size:36
Alignment explanation
Indices: 66391--66460 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
66381 GAGATTTTGG
* *
66391 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
66427 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
66461 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:69335 original size:2 final size:2
Alignment explanation
Indices: 69323--69360 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
69313 TTAACTAGTG
*
69323 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69361 GATTGGAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:91572 original size:17 final size:17
Alignment explanation
Indices: 91552--91584 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
91542 TTGATCACCA
91552 GTGATCTTACATCACTG
1 GTGATCTTACATCACTG
*
91569 GTGATCTTAGATCACT
1 GTGATCTTACATCACT
91585 AGTGGTGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.36
Consensus pattern (17 bp):
GTGATCTTACATCACTG
Found at i:105420 original size:20 final size:21
Alignment explanation
Indices: 105397--105439 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
105387 CAAATCAAGG
*
105397 AATAGGCAATC-AAGCAAAGC
1 AATAAGCAATCAAAGCAAAGC
* *
105417 AATAATCAATCAAATCAAAGC
1 AATAAGCAATCAAAGCAAAGC
105438 AA
1 AA
105440 ATGAGTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.14
Consensus pattern (21 bp):
AATAAGCAATCAAAGCAAAGC
Found at i:115396 original size:13 final size:13
Alignment explanation
Indices: 115378--115409 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
115368 TGCTACATGA
115378 CCCTCCAACTTGT
1 CCCTCCAACTTGT
*
115391 CCCTCCAATTTGT
1 CCCTCCAACTTGT
115404 CCCTCC
1 CCCTCC
115410 TGACGTGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.50, G:0.06, T:0.31
Consensus pattern (13 bp):
CCCTCCAACTTGT
Found at i:115569 original size:40 final size:40
Alignment explanation
Indices: 115509--115589 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
115499 TTTATAACTA
* * * *
115509 GGGGCTAAATCTGGATTTAATTTCTTACCTTAATTATTAG
1 GGGGCTAAACCTGAAATTAATTTATTACCTTAATTATTAG
**
115549 GGGGCTAAACCTGAAATTAATTTATTTTCTTAATTATTAG
1 GGGGCTAAACCTGAAATTAATTTATTACCTTAATTATTAG
115589 G
1 G
115590 AGGGTCAAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (40 bp):
GGGGCTAAACCTGAAATTAATTTATTACCTTAATTATTAG
Found at i:115606 original size:13 final size:13
Alignment explanation
Indices: 115588--115624 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
115578 TTAATTATTA
*
115588 GGAGGGTCAAGTT
1 GGAGGGTCAAATT
*
115601 GGAGGGACAAATT
1 GGAGGGTCAAATT
115614 GGAGGGTCAAA
1 GGAGGGTCAAA
115625 AAGAATTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.08, G:0.43, T:0.16
Consensus pattern (13 bp):
GGAGGGTCAAATT
Found at i:123421 original size:31 final size:31
Alignment explanation
Indices: 123324--123420 Score: 140
Period size: 31 Copynumber: 3.1 Consensus size: 31
123314 TTTGTGCACG
**
123324 TGGCATGCCACGTGTCACTTTTTGAAACACA
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
*
123355 TGGCATGCCATGTGTCACTTTTTGGTACACA
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
* * *
123386 TGGCGTGCCACATGTCACTTTTTGGTACACG
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
123417 TGGC
1 TGGC
123421 GGAGAGATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.32
Consensus pattern (31 bp):
TGGCATGCCACGTGTCACTTTTTGGTACACA
Found at i:126062 original size:22 final size:23
Alignment explanation
Indices: 126023--126068 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
126013 AATTTACTAT
126023 TTTTATATTTATGATTAAGTGTG
1 TTTTATATTTATGATTAAGTGTG
*
126046 TTTTA-ATTATAT-ATTAATTGTG
1 TTTTATATT-TATGATTAAGTGTG
126068 T
1 T
126069 GTGGATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (23 bp):
TTTTATATTTATGATTAAGTGTG
Found at i:140485 original size:17 final size:17
Alignment explanation
Indices: 140465--140499 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
140455 AAGGAGTGAA
*
140465 AAATTCAAAGAATTTGT
1 AAATTCAAAAAATTTGT
140482 AAATTCAAAAAATTTGT
1 AAATTCAAAAAATTTGT
140499 A
1 A
140500 TGAGTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (17 bp):
AAATTCAAAAAATTTGT
Found at i:142356 original size:21 final size:21
Alignment explanation
Indices: 142332--142373 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
142322 AGTGAAACAC
142332 TAGGAATATCACACAGACCAA
1 TAGGAATATCACACAGACCAA
* **
142353 TAGGAATTTTTCACAGACCAA
1 TAGGAATATCACACAGACCAA
142374 GGCAATGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (21 bp):
TAGGAATATCACACAGACCAA
Found at i:166424 original size:15 final size:15
Alignment explanation
Indices: 166401--166430 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
166391 ACCTCCATAA
*
166401 ATACTCTTATCTCCC
1 ATACCCTTATCTCCC
166416 ATACCCTTATCTCCC
1 ATACCCTTATCTCCC
166431 TCTCTCTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.43, G:0.00, T:0.37
Consensus pattern (15 bp):
ATACCCTTATCTCCC
Found at i:167914 original size:21 final size:21
Alignment explanation
Indices: 167888--167927 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
167878 GAATTCAAAA
167888 TGCTCT-TTAAGCTCTCTTTCT
1 TGCTCTCTT-AGCTCTCTTTCT
*
167909 TGCTCTCTTATCTCTCTTT
1 TGCTCTCTTAGCTCTCTTT
167928 TTTGGTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.07, C:0.30, G:0.07, T:0.55
Consensus pattern (21 bp):
TGCTCTCTTAGCTCTCTTTCT
Found at i:170542 original size:2 final size:2
Alignment explanation
Indices: 170535--170574 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
170525 TATTAGTCCG
170535 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
170575 TTGATACACC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:174220 original size:31 final size:29
Alignment explanation
Indices: 174152--174239 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 29
174142 TGGGCCACTA
* *
174152 ACACATCACACACACTAAAAGAGGCCCAAC
1 ACACTTCACACACA-TAAAAGAGGCCCAAT
174182 ACACTTCACACACATTAAAAGAGGGCCCAAT
1 ACACTTCACACACA-TAAAAGA-GGCCCAAT
**
174213 ATGCTTCACACAC-TAAAA-AGGCCCAAT
1 ACACTTCACACACATAAAAGAGGCCCAAT
174240 GAATTTCTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
27 8 0.15
28 1 0.02
29 5 0.10
30 20 0.38
31 18 0.35
ACGTcount: A:0.43, C:0.32, G:0.11, T:0.14
Consensus pattern (29 bp):
ACACTTCACACACATAAAAGAGGCCCAAT
Found at i:175741 original size:43 final size:43
Alignment explanation
Indices: 175692--175774 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
175682 ATCAAAATAA
** *
175692 TATTTTAATTATTCCATTATTAAAATATATAAAATTGCCAATC
1 TATTTTAATTAAGCCATCATTAAAATATATAAAATTGCCAATC
*
175735 TATTTTAATTAAGCCATCATTAGAATATATAAAATTGCCA
1 TATTTTAATTAAGCCATCATTAAAATATATAAAATTGCCA
175775 TTGTTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (43 bp):
TATTTTAATTAAGCCATCATTAAAATATATAAAATTGCCAATC
Found at i:177108 original size:22 final size:22
Alignment explanation
Indices: 177060--177406 Score: 101
Period size: 22 Copynumber: 15.9 Consensus size: 22
177050 GTTGTCTCTG
* * **
177060 TGTTGTCAAAATTTAATAATGA
1 TGTTATCAAAATTTCATAGCGA
* * * *
177082 GGTTATCGAAATTTCATAGTGT
1 TGTTATCAAAATTTCATAGCGA
* *
177104 TGTTATCAAAATTACGTAGCGA
1 TGTTATCAAAATTTCATAGCGA
*
177126 TGTTATCAAAATTTCATAAG-AA
1 TGTTATCAAAATTTCAT-AGCGA
* * * * *
177148 AGTTCTCACAATTTCACAGTG-
1 TGTTATCAAAATTTCATAGCGA
*
177169 TGGTTATCAAAATTTCATAG-TA
1 T-GTTATCAAAATTTCATAGCGA
*
177191 TGATTA-CGAAAATTTCATAAG-AA
1 TG-TTATC-AAAATTTCAT-AGCGA
* * *
177214 GGTTATCAAAGTTTCATAAG-AA
1 TGTTATCAAAATTTCAT-AGCGA
* * **
177236 GGTTATTAAAATTTCATA-ATA
1 TGTTATCAAAATTTCATAGCGA
* *
177257 TGGTTATCAACATTTCAT-GTGA
1 T-GTTATCAAAATTTCATAGCGA
* * * *
177279 AGATTACCAAAATTTCATTGGGA
1 TG-TTATCAAAATTTCATAGCGA
* * * **
177302 GGTTACCAAAATTTTTATATTG-
1 TGTTATCAAAA-TTTCATAGCGA
* * *
177324 TGATATTAAAATTTCATAGAGA
1 TGTTATCAAAATTTCATAGCGA
*
177346 --TTAACAAAATTTCATAAG-GA
1 TGTTATCAAAATTTCAT-AGCGA
* * *
177366 TGTTA-CTAAAATCTAATAGTG-
1 TGTTATC-AAAATTTCATAGCGA
177387 TGGTTATCAAAATTTCATAG
1 T-GTTATCAAAATTTCATAG
177407 AGAGACAATC
Statistics
Matches: 244, Mismatches: 59, Indels: 44
0.70 0.17 0.13
Matches are distributed among these distances:
20 14 0.06
21 20 0.08
22 192 0.79
23 18 0.07
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TGTTATCAAAATTTCATAGCGA
Found at i:177205 original size:44 final size:44
Alignment explanation
Indices: 177067--177406 Score: 182
Period size: 44 Copynumber: 7.8 Consensus size: 44
177057 CTGTGTTGTC
* * * *
177067 AAAATTTAATAATGAGGTTATCGAAATTTCATAGTGTTG-TTA-T
1 AAAATTTCATAGTGAGGTTATCAAAATTTCATAGT-ATGATTACT
* * * * * *
177110 CAAAATTACGTAGCGATGTTATCAAAATTTCATAAGAAAG-TT-CT
1 -AAAATTTCATAGTGAGGTTATCAAAATTTCAT-AGTATGATTACT
* * * *
177154 CACAATTTCACAGTGTGGTTATCAAAATTTCATAGTATGATTACG
1 -AAAATTTCATAGTGAGGTTATCAAAATTTCATAGTATGATTACT
* * * * *
177199 AAAATTTCATAAG-AAGGTTATCAAAGTTTCATAAG-AAGGTTATT
1 AAAATTTCAT-AGTGAGGTTATCAAAATTTCAT-AGTATGATTACT
* * * *
177243 AAAATTTCATAAT-ATGGTTATCAACATTTCAT-GTGAAGATTACC
1 AAAATTTCATAGTGA-GGTTATCAAAATTTCATAGT-ATGATTACT
* * * * * * *
177287 AAAATTTCATTGGGAGGTTACCAAAATTTTTATATTGTGA-TATT
1 AAAATTTCATAGTGAGGTTATCAAAA-TTTCATAGTATGATTACT
* * *
177331 AAAATTTCATA--GAGATTAACAAAATTTCATAAGGATG-TTACT
1 AAAATTTCATAGTGAGGTTATCAAAATTTCAT-AGTATGATTACT
* * *
177373 AAAATCTAATAGTGTGGTTATCAAAATTTCATAG
1 AAAATTTCATAGTGAGGTTATCAAAATTTCATAG
177407 AGAGACAATC
Statistics
Matches: 220, Mismatches: 59, Indels: 35
0.70 0.19 0.11
Matches are distributed among these distances:
41 5 0.02
42 27 0.12
43 8 0.04
44 164 0.75
45 15 0.07
46 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (44 bp):
AAAATTTCATAGTGAGGTTATCAAAATTTCATAGTATGATTACT
Found at i:177229 original size:66 final size:65
Alignment explanation
Indices: 177060--177229 Score: 184
Period size: 66 Copynumber: 2.6 Consensus size: 65
177050 GTTGTCTCTG
* * * * *
177060 TGTTGTCAAAATTTAATAATG-AGGTTATCGAAATTTCATAGTGTTGTTATCAAAATTACGTAGC
1 TGTTATCAAAATTTCATAA-GAAGGTTATC-AAATTTCACAGTGTGGTTATCAAAATTACATAGC
177124 GA
64 GA
* * * *
177126 TGTTATCAAAATTTCATAAGAAAGTTCTCACAATTTCACAGTGTGGTTATCAAAATTTCATAG-T
1 TGTTATCAAAATTTCATAAGAAGGTTATCA-AATTTCACAGTGTGGTTATCAAAATTACATAGCG
177190 A
65 A
177191 TGATTA-CGAAAATTTCATAAGAAGGTTATCAAAGTTTCA
1 TG-TTATC-AAAATTTCATAAGAAGGTTATCAAA-TTTCA
177230 TAAGAAGGTT
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
65 8 0.09
66 80 0.91
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (65 bp):
TGTTATCAAAATTTCATAAGAAGGTTATCAAATTTCACAGTGTGGTTATCAAAATTACATAGCGA
Found at i:177272 original size:66 final size:66
Alignment explanation
Indices: 177127--177274 Score: 167
Period size: 66 Copynumber: 2.2 Consensus size: 66
177117 ACGTAGCGAT
* * ** *
177127 GTTATCAAAATTTCATAAGAAAGTTCTCACAATTTCACAGTGTGGTTATCAAAATTTCATAGTAT
1 GTTATCAAAATTTCATAAGAAAGTTATCACAATTTCAAAGTAAGGTTATCAAAATTTCATAATAT
177192 G
66 G
* * *
177193 ATTA-CGAAAATTTCATAAGAAGGTTATCA-AAGTTTCATAAG-AAGGTTATTAAAATTTCATAA
1 GTTATC-AAAATTTCATAAGAAAGTTATCACAA-TTTCA-AAGTAAGGTTATCAAAATTTCATAA
177255 TATG
63 TATG
*
177259 GTTATCAACATTTCAT
1 GTTATCAAAATTTCAT
177275 GTGAAGATTA
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
65 3 0.04
66 62 0.91
67 3 0.04
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (66 bp):
GTTATCAAAATTTCATAAGAAAGTTATCACAATTTCAAAGTAAGGTTATCAAAATTTCATAATAT
G
Found at i:177295 original size:66 final size:66
Alignment explanation
Indices: 177170--177363 Score: 171
Period size: 66 Copynumber: 3.0 Consensus size: 66
177160 TTCACAGTGT
* * * *
177170 GGTTATCAAAATTTCATAGTATGATTACGAAAATTTCATAAGAAGGTTATCAAAGTTTCATAAGA
1 GGTTATCAAAATTTCATAATATGATTACGAAAATTTCATAAGAAGATTACCAAAATTTCATAAGA
177235 A
66 A
* * * ** **
177236 GGTTATTAAAATTTCATAATATGGTTATC-AACATTTCATGTGAAGATTACCAAAATTTCATTGG
1 GGTTATCAAAATTTCATAATATGATTA-CGAAAATTTCATAAGAAGATTACCAAAATTTCATAAG
*
177300 GA
65 AA
* * * * ** *
177302 GGTTACCAAAATTTTTATATTGTGA-TATTAAAATTTCAT-AG-AGATTAACAAAATTTCATAAG
1 GGTTATCAAAA-TTTCATAATATGATTACGAAAATTTCATAAGAAGATTACCAAAATTTCATAAG
177364 GATGTTACTA
Statistics
Matches: 101, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
64 18 0.18
65 1 0.01
66 72 0.71
67 10 0.10
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (66 bp):
GGTTATCAAAATTTCATAATATGATTACGAAAATTTCATAAGAAGATTACCAAAATTTCATAAGA
A
Found at i:177371 original size:64 final size:64
Alignment explanation
Indices: 177199--177433 Score: 168
Period size: 66 Copynumber: 3.6 Consensus size: 64
177189 TATGATTACG
* * * * ** * * * * *
177199 AAAATTTCATAAGAAGGTTATCAAAGTTTCATAAGAAGGTTATTAAAATTTCATAATATGGTTAT
1 AAAATTTCAT-AG-AGATTAACAAAATTTCATAAGGAGGTTACCAAAATCTAATAGTGTGGATAT
177264 C
64 C
* * * ** * * *
177265 AACATTTCATGTGAAGATTACCAAAATTTCATTGGGAGGTTACCAAAATTTTTATATTGT-GATA
1 AAAATTTCAT-AG-AGATTAACAAAATTTCATAAGGAGGTTACCAAAA-TCTAATAGTGTGGATA
*
177329 TT
63 TC
* * *
177331 AAAATTTCATAGAGATTAACAAAATTTCATAAGGATGTTACTAAAATCTAATAGTGTGGTTATC
1 AAAATTTCATAGAGATTAACAAAATTTCATAAGGAGGTTACCAAAATCTAATAGTGTGGATATC
**
177395 AAAATTTCATAGAGAGACAATC-AAATTTCATAAGGAGGT
1 AAAATTTCATAGAGA-TTAA-CAAAATTTCATAAGGAGGT
177434 AAGCGAAGTC
Statistics
Matches: 134, Mismatches: 31, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
63 8 0.06
64 48 0.36
65 19 0.14
66 51 0.38
67 8 0.06
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (64 bp):
AAAATTTCATAGAGATTAACAAAATTTCATAAGGAGGTTACCAAAATCTAATAGTGTGGATATC
Found at i:177484 original size:13 final size:13
Alignment explanation
Indices: 177447--177497 Score: 75
Period size: 13 Copynumber: 3.8 Consensus size: 13
177437 CGAAGTCTCG
177447 TAACCCTAAACCC
1 TAACCCTAAACCC
177460 TTAAACCCTAAACCC
1 -T-AACCCTAAACCC
*
177475 TAACCATAAACCC
1 TAACCCTAAACCC
177488 TAACCCTAAA
1 TAACCCTAAA
177498 GAGGTTATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
13 20 0.59
14 2 0.06
15 12 0.35
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.18
Consensus pattern (13 bp):
TAACCCTAAACCC
Found at i:177492 original size:6 final size:7
Alignment explanation
Indices: 177448--177497 Score: 68
Period size: 7 Copynumber: 7.3 Consensus size: 7
177438 GAAGTCTCGT
177448 AACCCTA
1 AACCCTA
177455 AACCCTTA
1 AACCC-TA
177463 AACCCTA
1 AACCCTA
177470 AACCCT-
1 AACCCTA
*
177476 AACCATA
1 AACCCTA
177483 AACCCT-
1 AACCCTA
177489 AACCCTA
1 AACCCTA
177496 AA
1 AA
177498 GAGGTTATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 11 0.29
7 20 0.53
8 7 0.18
ACGTcount: A:0.44, C:0.40, G:0.00, T:0.16
Consensus pattern (7 bp):
AACCCTA
Found at i:177526 original size:22 final size:21
Alignment explanation
Indices: 177498--177703 Score: 135
Period size: 22 Copynumber: 9.4 Consensus size: 21
177488 TAACCCTAAA
*
177498 GAGGTTATCAAAATTCCATATG
1 GAGGTTATCAAAATTTCATA-G
*
177520 GAGGTTATCAAGATTTCATAG
1 GAGGTTATCAAAATTTCATAG
* * *
177541 TGTGGTT-TCCGAAATTTCATAAA
1 -GAGGTTAT-CAAAATTTCAT-AG
*
177564 GAGGTTATCAAAATTTTATAG
1 GAGGTTATCAAAATTTCATAG
* * * *
177585 TGTGCTTACCAAAATTTCATACA
1 -GAGGTTATCAAAATTTCATA-G
* *
177608 GACGTTATCAAAATTCCATAG
1 GAGGTTATCAAAATTTCATAG
* * *
177629 TGTGGTTATCGAAATTTCATGG
1 -GAGGTTATCAAAATTTCATAG
* *
177651 GATGGTTATCGAAATTTCATGGG
1 GA-GGTTATCAAAATTTCAT-AG
* *
177674 GAGGATATCAAAATTTTATATG
1 GAGGTTATCAAAATTTCATA-G
*
177696 CAGGTTAT
1 GAGGTTAT
177704 GGAAATTTTA
Statistics
Matches: 141, Mismatches: 33, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
21 4 0.03
22 131 0.93
23 6 0.04
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (21 bp):
GAGGTTATCAAAATTTCATAG
Found at i:177571 original size:44 final size:44
Alignment explanation
Indices: 177520--177670 Score: 171
Period size: 44 Copynumber: 3.4 Consensus size: 44
177510 ATTCCATATG
*
177520 GAGGTTATCAAGATTTCATAGTGTGGTTTCCGAAATTTCATAAA
1 GAGGTTATCAAAATTTCATAGTGTGGTTTCCGAAATTTCATAAA
* * * * *
177564 GAGGTTATCAAAATTTTATAGTGTGCTTACCAAAATTTCATACA
1 GAGGTTATCAAAATTTCATAGTGTGGTTTCCGAAATTTCATAAA
* * **
177608 GACGTTATCAAAATTCCATAGTGTGGTTAT-CGAAATTTCAT-GG
1 GAGGTTATCAAAATTTCATAGTGTGGTT-TCCGAAATTTCATAAA
*
177651 GATGGTTATCGAAATTTCAT
1 GA-GGTTATCAAAATTTCAT
177671 GGGGAGGATA
Statistics
Matches: 88, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
43 2 0.02
44 86 0.98
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (44 bp):
GAGGTTATCAAAATTTCATAGTGTGGTTTCCGAAATTTCATAAA
Done.