Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012064.1 Corchorus capsularis cultivar CVL-1 contig12085, 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: 64739
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2999 original size:16 final size:15
Alignment explanation
Indices: 2979--3024 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
2969 AACCTGCCCG
2979 AACCCGAACCCGAAA
1 AACCCGAACCCGAAA
* *
2994 ATACCCGACCCCGAGAC
1 A-ACCCGAACCCGA-AA
3011 AACCCGAACCCGAA
1 AACCCGAACCCGAA
3025 CCCCACCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.39, C:0.43, G:0.15, T:0.02
Consensus pattern (15 bp):
AACCCGAACCCGAAA
Found at i:3780 original size:6 final size:6
Alignment explanation
Indices: 3771--3820 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
3761 ATATCGAAAG
* * * *
3771 CGAACC CGAACC CG-ACT CGGACC CGAACC CG-ATC CGAGCC CGAACC
1 CGAACC CGAACC CGAACC CGAACC CGAACC CGAACC CGAACC CGAACC
3817 CGAA
1 CGAA
3821 AATACCCAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
5 8 0.23
6 27 0.77
ACGTcount: A:0.28, C:0.46, G:0.22, T:0.04
Consensus pattern (6 bp):
CGAACC
Found at i:3796 original size:17 final size:16
Alignment explanation
Indices: 3774--3819 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
3764 TCGAAAGCGA
*
3774 ACCCGAACCCGACTCGG
1 ACCCGAACCCGA-TCCG
3791 ACCCGAACCCGATCCG
1 ACCCGAACCCGATCCG
3807 AGCCCGAACCCGA
1 A-CCCGAACCCGA
3820 AAATACCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.26, C:0.48, G:0.22, T:0.04
Consensus pattern (16 bp):
ACCCGAACCCGATCCG
Found at i:3873 original size:15 final size:16
Alignment explanation
Indices: 3809--3881 Score: 94
Period size: 16 Copynumber: 4.6 Consensus size: 16
3799 CCGATCCGAG
3809 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
* *
3825 CCCAAACCCGAAAAAA
1 CCCGAACCCGAAAATA
*
3841 CCCGAACCTGAAAATA
1 CCCGAACCCGAAAATA
*
3857 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
*
3872 CCTGAACCCG
1 CCCGAACCCG
3882 CCCAATTGCC
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
15 13 0.27
16 36 0.73
ACGTcount: A:0.41, C:0.38, G:0.14, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:4682 original size:128 final size:127
Alignment explanation
Indices: 4436--4688 Score: 305
Period size: 128 Copynumber: 2.0 Consensus size: 127
4426 GGTTAATTAA
* * *
4436 TAAGAAGACCCTCAATTAGTTTCTTATCATTCCCTTCTCCTCCAGTCCTTTTTCGTAATTGCAAA
1 TAAGAAGACCCTCAATTAGTTTCTCACCATTCCCTTCTCCTCCAGTCCTTTTTCGTAATTACAAA
* * *
4501 GGTTTTTAACCAATTGAATGTGAAAGCATTTATTGACCATAAAATCATGTATTATTTATTTAC
66 GGTTTTTAACCAATTCAA-GTGAAAACATTTATTGACCATAAAATCATCTATTATTTATTTAC
* ** * * * *
4564 TAAGAAGGCCCTCAATTAGTTTCTCACCATTCTTTTTTCCTTC-G-CCTTTTTTGTAATTACAAG
1 TAAGAAGACCCTCAATTAGTTTCTCACCATTCCCTTCTCCTCCAGTCCTTTTTCGTAATTACAAA
* *
4627 GGTTTTTAGCCACTTCAA-TGAAACACATTTATTGACCATAAAATCAAGTACTATTATTTATT
66 GGTTTTTAACCAATTCAAGTGAAA-ACATTTATTGACCATAAAATC-A-T-CTATTATTTATT
4689 CACTTCATCA
Statistics
Matches: 106, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
124 5 0.05
125 20 0.19
126 32 0.30
127 2 0.02
128 47 0.44
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (127 bp):
TAAGAAGACCCTCAATTAGTTTCTCACCATTCCCTTCTCCTCCAGTCCTTTTTCGTAATTACAAA
GGTTTTTAACCAATTCAAGTGAAAACATTTATTGACCATAAAATCATCTATTATTTATTTAC
Found at i:5855 original size:31 final size:31
Alignment explanation
Indices: 5817--5877 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
5807 CATGAACTAA
*
5817 CTCAAACATTCAAGATCTAAAGATCTGGAGG
1 CTCAAACATCCAAGATCTAAAGATCTGGAGG
5848 CTCAAACATCCAAGATCTAAAGATCTGGAG
1 CTCAAACATCCAAGATCTAAAGATCTGGAG
5878 ACTGATAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (31 bp):
CTCAAACATCCAAGATCTAAAGATCTGGAGG
Found at i:6395 original size:1 final size:1
Alignment explanation
Indices: 6389--6421 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
6379 GCCATTCACC
6389 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6422 GCTTTACTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6511 original size:60 final size:61
Alignment explanation
Indices: 6441--6556 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 61
6431 ATCGAAGGAG
* *
6441 ATTTCTTCTTTCTTCTTTTTTTCCCCTGG-TTTTGCTTTACTTATCGAAGGAGATTTCTTTT
1 ATTTCTTCTTT-TTCTTTTTTTCCCCTGGTTTTTGCTTTACTCATCGAAAGAGATTTCTTTT
*** *
6502 ATTT-TTCTTTTTCTTTTTTTTTTCTGGTTTTTGCTTTACTCATGGAAAGAGATTT
1 ATTTCTTCTTTTTCTTTTTTTCCCCTGGTTTTTGCTTTACTCATCGAAAGAGATTT
6557 GCATACCAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 14 0.29
60 30 0.62
61 4 0.08
ACGTcount: A:0.13, C:0.16, G:0.12, T:0.59
Consensus pattern (61 bp):
ATTTCTTCTTTTTCTTTTTTTCCCCTGGTTTTTGCTTTACTCATCGAAAGAGATTTCTTTT
Found at i:6516 original size:17 final size:17
Alignment explanation
Indices: 6494--6526 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6484 TCGAAGGAGA
6494 TTTCTTTTATTTTTCTT
1 TTTCTTTTATTTTTCTT
*
6511 TTTCTTTTTTTTTTCT
1 TTTCTTTTATTTTTCT
6527 GGTTTTTGCT
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:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTCTTTTATTTTTCTT
Found at i:6943 original size:106 final size:106
Alignment explanation
Indices: 6747--6947 Score: 285
Period size: 106 Copynumber: 1.9 Consensus size: 106
6737 ACCACCATTT
* ** *
6747 TTTGAAATTTTCCCTTAAAATAAAATTAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTT
1 TTTGAAATTTACCCTTAAAATAAAATTAAAATTTTAATTTAAGACTAAACTTAGTGAAATTAGTT
* * **
6812 TTGTATTTTATTTCCATTACGCTATAATAATAAATTATTAA
66 TTATATTCTATTTCCAAAACGCTATAATAATAAATTATTAA
* * *
6853 TTTGGAATTTACCCTTGAAATAAAATTAAAATTTTAATTTAAGACTAAACTTAGTGAAATTATTT
1 TTTGAAATTTACCCTTAAAATAAAATTAAAATTTTAATTTAAGACTAAACTTAGTGAAATTAGTT
* *
6918 TTATATTCTATTTCTAAAACTCTATAATAA
66 TTATATTCTATTTCCAAAACGCTATAATAA
6948 AATTTTTTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
106 82 1.00
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (106 bp):
TTTGAAATTTACCCTTAAAATAAAATTAAAATTTTAATTTAAGACTAAACTTAGTGAAATTAGTT
TTATATTCTATTTCCAAAACGCTATAATAATAAATTATTAA
Found at i:12220 original size:2 final size:2
Alignment explanation
Indices: 12215--12246 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12205 TTTGAGTGAC
12215 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
12247 CTACACTAGC
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:12944 original size:18 final size:18
Alignment explanation
Indices: 12917--12953 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
12907 TGAACGTAAC
12917 ATTTTGTTTTTGGTATAT
1 ATTTTGTTTTTGGTATAT
*
12935 ATTTTTTTTTTGGTATAT
1 ATTTTGTTTTTGGTATAT
12953 A
1 A
12954 ACGTAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.68
Consensus pattern (18 bp):
ATTTTGTTTTTGGTATAT
Found at i:18292 original size:88 final size:88
Alignment explanation
Indices: 18143--18322 Score: 360
Period size: 88 Copynumber: 2.0 Consensus size: 88
18133 ACTCCTATAC
18143 AATTTGGTATATATGTAGTAGATTTATATATATTTATTGTCATTGTTTTATACATCAATTCATTT
1 AATTTGGTATATATGTAGTAGATTTATATATATTTATTGTCATTGTTTTATACATCAATTCATTT
18208 AAAATCCTTCCACTTTTATTCTA
66 AAAATCCTTCCACTTTTATTCTA
18231 AATTTGGTATATATGTAGTAGATTTATATATATTTATTGTCATTGTTTTATACATCAATTCATTT
1 AATTTGGTATATATGTAGTAGATTTATATATATTTATTGTCATTGTTTTATACATCAATTCATTT
18296 AAAATCCTTCCACTTTTATTCTA
66 AAAATCCTTCCACTTTTATTCTA
18319 AATT
1 AATT
18323 ATAATTATGC
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 92 1.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (88 bp):
AATTTGGTATATATGTAGTAGATTTATATATATTTATTGTCATTGTTTTATACATCAATTCATTT
AAAATCCTTCCACTTTTATTCTA
Found at i:18344 original size:88 final size:87
Alignment explanation
Indices: 18151--18346 Score: 297
Period size: 88 Copynumber: 2.2 Consensus size: 87
18141 ACAATTTGGT
* *
18151 ATATATGTAGTAGATTTATATATATTTATTGTCATTGTTTTATACATCAATTCATTTAAAATCCT
1 ATATATGAAGTAAATTTATATATATTTATTGTCATTGTTTTATACATCAATTCATTTAAAATCCT
*
18216 TCCACTTTTATTCTAAATTTGGT
66 TCCACTTTTATTCTAAATTT-GA
* *
18239 ATATATGTAGTAGATTTATATATATTTATTGTCATTGTTTTATACATCAATTCATTTAAAATCCT
1 ATATATGAAGTAAATTTATATATATTTATTGTCATTGTTTTATACATCAATTCATTTAAAATCCT
18304 TCCACTTTTATTCTAAATTAT-A
66 TCCACTTTTATTCTAAATT-TGA
18326 AT-TATGCAAGTTAAATTTATA
1 ATATATG-AAG-TAAATTTATA
18347 AGTAAATTGA
Statistics
Matches: 102, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
86 4 0.04
87 4 0.04
88 93 0.91
89 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (87 bp):
ATATATGAAGTAAATTTATATATATTTATTGTCATTGTTTTATACATCAATTCATTTAAAATCCT
TCCACTTTTATTCTAAATTTGA
Found at i:19455 original size:178 final size:178
Alignment explanation
Indices: 19085--19462 Score: 467
Period size: 178 Copynumber: 2.1 Consensus size: 178
19075 TTCCACCATA
* * * *
19085 AGCACAAATTATGTAATATTAAGTAGATCATCTATTTCCGTTAACCGAAACAACTAATTTTTTGA
1 AGCAAAAATTATATAATATTAAGTAGATCATCTATTCCCGTTAACCGAAACAACTAATTTTTCGA
* *
19150 AAGAATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCATTTATGAAAGTTGTAAATCAT
66 AAGAATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCATTCATGAAAGTTGTAAATCAT
* *
19215 GGAACAATCTTTCAAGAAACACTTGAATCATCTCAATCAGATATCTGG
131 GGAACAATCTTTCAAGAAACACTTAAATCACCTCAATCAGATATCTGG
* * * * *
19263 AGCAAAAGTTATATAATATTAAGTGGATCGTTTATTCCCGTTAACCGGAACAA-TAAATTTTTCG
1 AGCAAAAATTATATAATATTAAGTAGATCATCTATTCCCGTTAACCGAAACAACT-AATTTTTCG
* * * **
19327 GAAGCATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGGTC
65 AAAGAATTTTTGATACCTTG-AACATTAAATTTAGTTTTCGAGTCATTCATGAAAGTTGTAAATC
* * * * * *
19391 ATGGAACAATCTTTTAATAGACATTTAAATCACCTTAATCGGATAATC-GG
129 ATGGAACAATCTTTCAAGAAACACTTAAATCACCTCAATCAGAT-ATCTGG
*
19441 AG-AGAAAATTATATAATGTTAA
1 AGCA-AAAATTATATAATATTAA
19463 ACAGACCGTT
Statistics
Matches: 170, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
177 6 0.04
178 161 0.95
179 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (178 bp):
AGCAAAAATTATATAATATTAAGTAGATCATCTATTCCCGTTAACCGAAACAACTAATTTTTCGA
AAGAATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCATTCATGAAAGTTGTAAATCAT
GGAACAATCTTTCAAGAAACACTTAAATCACCTCAATCAGATATCTGG
Found at i:21752 original size:35 final size:35
Alignment explanation
Indices: 21701--21769 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
21691 ATTATCTTTT
* *
21701 TTTAAATCCTTGAAAATAATAAGAGGTGAAAAATG
1 TTTAAATACTTGAAAATAATAAGAGATGAAAAATG
* *
21736 TTTAAATACTTTAAAATAATAAGAGATGACAAAT
1 TTTAAATACTTGAAAATAATAAGAGATGAAAAAT
21770 ATTCAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (35 bp):
TTTAAATACTTGAAAATAATAAGAGATGAAAAATG
Found at i:21785 original size:35 final size:35
Alignment explanation
Indices: 21713--21786 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
21703 TAAATCCTTG
* * * **
21713 AAAATAATAAGAGGTGAAAAATGTTTAAATACTTT
1 AAAATAATAAGAGATGAAAAATATTCAAATAAATT
* *
21748 AAAATAATAAGAGATGACAAATATTCAATTAAATT
1 AAAATAATAAGAGATGAAAAATATTCAAATAAATT
21783 AAAA
1 AAAA
21787 GTGAGAGCTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (35 bp):
AAAATAATAAGAGATGAAAAATATTCAAATAAATT
Found at i:26502 original size:15 final size:15
Alignment explanation
Indices: 26463--26502 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
26453 CCGAAACTGA
26463 AAAAT-ACCCAAACC
1 AAAATAACCCAAACC
26477 AAAATTAACCCAAACC
1 AAAA-TAACCCAAACC
*
26493 CAAATAACCC
1 AAAATAACCC
26503 GACAATTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 7 0.30
16 12 0.52
ACGTcount: A:0.55, C:0.35, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAATAACCCAAACC
Found at i:26858 original size:98 final size:98
Alignment explanation
Indices: 26740--26939 Score: 323
Period size: 98 Copynumber: 2.0 Consensus size: 98
26730 TTATTTTCAT
* *
26740 TTAATTAAATTCGTATTTTTATAATTATTTTATTTTTACCATTGTAATTTAAAAGTTTGTTTTTA
1 TTAATTAAATTCATATTTTTATAATTATTTTATTTTTACCATTGTAATTTAAAAGTTTATTTTTA
26805 CCATTTTACTA-TTTTCATTAAAAACTTGGATATA
66 CCA--TTACTATTTTTCATTAAAAACTTGGATATA
* *
26839 TTAATTAAATTCAT-TTTTTATAATTATTTTATTTTTATCATTTTAATTTAAAAGTTTATTTTTA
1 TTAATTAAATTCATATTTTTATAATTATTTTATTTTTACCATTGTAATTTAAAAGTTTATTTTTA
*
26903 CCATTACTATTTTTCATTAAAAATTTGGATATA
66 CCATTACTATTTTTCATTAAAAACTTGGATATA
26936 TTAA
1 TTAA
26940 AAATTTTTAA
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
96 6 0.06
97 26 0.27
98 50 0.53
99 13 0.14
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.55
Consensus pattern (98 bp):
TTAATTAAATTCATATTTTTATAATTATTTTATTTTTACCATTGTAATTTAAAAGTTTATTTTTA
CCATTACTATTTTTCATTAAAAACTTGGATATA
Found at i:27019 original size:149 final size:150
Alignment explanation
Indices: 26839--27198 Score: 636
Period size: 151 Copynumber: 2.4 Consensus size: 150
26829 CTTGGATATA
*
26839 TTAATTAAATTC-AT-TTTTTATAATTATTTTATTTTTATCATTTTAATTTAAAAGTTTATTTTT
1 TTAATTAAATTCAATATTTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAGTTTATTTTT
*
26902 ACCA-TTACTATTTTTCATTAAAAATTTGGATATATTAAAAATTTTTAATATATAGTTTGATTCT
66 ACCATTTACTATTTTTCATTAAAAACTTGGATATATTAAAAATTTTTAATATATAGTTTGATTCT
26966 ACTAAAAACTCTATTTTCAT
131 ACTAAAAACTCTATTTTCAT
*
26986 TTAATTAAATTCAATATTTCTATAATTATTTTATTTTTACCATTTTAATTTAAAAGTTTATTTTT
1 TTAATTAAATTCAATATTTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAGTTTATTTTT
*
27051 ACCATTTTACTATTTTTCATTAAAAACTTGGATATATTAAAATTTTTTAATATATAGTTTGATTC
66 ACCA-TTTACTATTTTTCATTAAAAACTTGGATATATTAAAAATTTTTAATATATAGTTTGATTC
*
27116 TACTAAAAGCTCTATTTTCAT
130 TACTAAAAACTCTATTTTCAT
*
27137 TTAATTAAATTCAATATTTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAGGTTATT
1 TTAATTAAATTCAATATTTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAGTTTATT
27199 GTAATTTACA
Statistics
Matches: 202, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
147 12 0.06
148 2 0.01
149 51 0.25
151 137 0.68
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.54
Consensus pattern (150 bp):
TTAATTAAATTCAATATTTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAGTTTATTTTT
ACCATTTACTATTTTTCATTAAAAACTTGGATATATTAAAAATTTTTAATATATAGTTTGATTCT
ACTAAAAACTCTATTTTCAT
Found at i:27032 original size:14 final size:14
Alignment explanation
Indices: 27013--27059 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
27003 TTCTATAATT
27013 ATTTTATTTTTACC
1 ATTTTATTTTTACC
* **
27027 ATTTTA-ATTTAAA
1 ATTTTATTTTTACC
*
27040 AGTTTATTTTTACC
1 ATTTTATTTTTACC
27054 ATTTTA
1 ATTTTA
27060 CTATTTTTCA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:31909 original size:14 final size:14
Alignment explanation
Indices: 31890--31932 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
31880 TCAAATTATC
31890 TATCTATATCTATA
1 TATCTATATCTATA
*
31904 TATCTATATCTACAA
1 TATCTATATCTA-TA
*
31919 CATCTATATCTATA
1 TATCTATATCTATA
31933 AAAGTAGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (14 bp):
TATCTATATCTATA
Found at i:31925 original size:15 final size:14
Alignment explanation
Indices: 31891--31930 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
31881 CAAATTATCT
* *
31891 ATCTATATCTATAT
1 ATCTATATCTAAAC
31905 ATCTATATCTACAAC
1 ATCTATATCTA-AAC
31920 ATCTATATCTA
1 ATCTATATCTA
31931 TAAAAGTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (14 bp):
ATCTATATCTAAAC
Found at i:33167 original size:21 final size:22
Alignment explanation
Indices: 33141--33182 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
33131 CAACACCATG
*
33141 CATAAAT-TAAAAGATTTTCTC
1 CATAAATATAAAAGAATTTCTC
*
33162 CATAAATATATAAGAATTTCT
1 CATAAATATAAAAGAATTTCT
33183 TGATCATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (22 bp):
CATAAATATAAAAGAATTTCTC
Found at i:34699 original size:166 final size:166
Alignment explanation
Indices: 34393--34708 Score: 449
Period size: 166 Copynumber: 1.9 Consensus size: 166
34383 TGAGTCATTT
*
34393 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATATAAAGTTAGGACAA
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCACCTCAAGAATATAAAGTTAGGACAA
* * * **
34458 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCCAGCTCATCATTAATATGGG
66 TTAAGTAATCGGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCCAGCTCATCATTAATACCGG
*
34523 GTATGGATCTTTTAGTAATTCCACTACTCTATTAAA
131 GTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * *
34559 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTATTCATCTCAAGAATCA-AAAGTTAGGGCA
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCACCTCAAGAAT-ATAAAGTTAGGACA
* ** * *
34623 TTTAAGTAATCGGTTAAGTGGGAAAAGACGAAAAAAAATTAGTTCTCTC-GCTCCTCATTAAT-C
65 ATTAAGTAATCGGCCAAGTAGGAAAAGACG-AAAAAAATTAGTTCTC-CAGCTCATCATTAATAC
34686 CGGGTAGGGATCTTTTAGTAATT
128 CGGGTAGGGATCTTTTAGTAATT
34709 TCCATATGTT
Statistics
Matches: 132, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
166 103 0.78
167 28 0.21
168 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (166 bp):
GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCACCTCAAGAATATAAAGTTAGGACAA
TTAAGTAATCGGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCCAGCTCATCATTAATACCGG
GTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:45568 original size:6 final size:6
Alignment explanation
Indices: 45557--45594 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
45547 TATATTCGGT
45557 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
45595 GCTTTGCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (6 bp):
TTTAGA
Found at i:46903 original size:3 final size:3
Alignment explanation
Indices: 46895--46928 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
46885 AAATAAAACT
*
46895 ATA ATA ATA ATA ATA AT- ATA ATA GTA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
46929 TACAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:46914 original size:17 final size:17
Alignment explanation
Indices: 46894--46928 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
46884 GAAATAAAAC
46894 TATAATAATAATAATAA
1 TATAATAATAATAATAA
*
46911 TATAATAGTAATAATAA
1 TATAATAATAATAATAA
46928 T
1 T
46929 TACAAAATTA
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:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
TATAATAATAATAATAA
Found at i:47821 original size:115 final size:115
Alignment explanation
Indices: 47614--48015 Score: 619
Period size: 115 Copynumber: 3.5 Consensus size: 115
47604 CACTTTGTGG
* * * *
47614 CAAGCTGTTAGGGGCCCACTAGCGGCAGTTACCCTGCTGGATAGCATGAAATTGCTTTAACCACC
1 CAAGGTGTTATGGGCCCACTGGCGGCAGTTACCCTGCTGGATAGCATGAGATTGCTTTAACCACC
*
47679 AGTAGGAAAAAGTAACGTAAGCTCTTAAGGTGGACAATCCCCATGAGTAC
66 AGTAGGAAAAAGTAACGTAAGCCCTTAAGGTGGACAATCCCCATGAGTAC
* * *
47729 CAAGGTGTTATGGGCCCACTGGCGGCAGTTACCCTGCTGGATAGCATGGGATTGTTTTAACCACT
1 CAAGGTGTTATGGGCCCACTGGCGGCAGTTACCCTGCTGGATAGCATGAGATTGCTTTAACCACC
* *
47794 AGCAGGAAAAAGTAACATAAGCCCTTAAGGTGGACAATCCCCATGAGTAC
66 AGTAGGAAAAAGTAACGTAAGCCCTTAAGGTGGACAATCCCCATGAGTAC
* *
47844 CAAGGTGTTAAGGGCCCACTGGCGGCAGTTACCCTGCTGGATAGCATGAGATTGTTTTAACCACC
1 CAAGGTGTTATGGGCCCACTGGCGGCAGTTACCCTGCTGGATAGCATGAGATTGCTTTAACCACC
*
47909 GGTAGGAAAAAGTAACGTAAGCCCTTAAGGTGGACAATCCCCATGAGTAC
66 AGTAGGAAAAAGTAACGTAAGCCCTTAAGGTGGACAATCCCCATGAGTAC
* * * * * *
47959 CAATGTG-TGT-GGTCCACTGGCGGCAGATACCCTCCTGGATAGTATGAGATTGCTTTA
1 CAAGGTGTTATGGGCCCACTGGCGGCAGTTACCCTGCTGGATAGCATGAGATTGCTTTA
48016 GCCGCCAGGA
Statistics
Matches: 263, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
113 42 0.16
114 1 0.00
115 220 0.84
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (115 bp):
CAAGGTGTTATGGGCCCACTGGCGGCAGTTACCCTGCTGGATAGCATGAGATTGCTTTAACCACC
AGTAGGAAAAAGTAACGTAAGCCCTTAAGGTGGACAATCCCCATGAGTAC
Found at i:48215 original size:42 final size:42
Alignment explanation
Indices: 48133--48216 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
48123 CCAGCATGCT
* * *
48133 CTCTATCAGCAAGCTCGTTATCAGAATATTTACAACAACGGG
1 CTCTAGCAGCAAGCTCGTTATCAGAAGAATTACAACAACGGG
* *
48175 CTCTAGCAGCAAGCTCGTT-TCCAGAAGAATTCCAATAACGGG
1 CTCTAGCAGCAAGCTCGTTAT-CAGAAGAATTACAACAACGGG
48217 TTATTCATAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 35 0.97
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (42 bp):
CTCTAGCAGCAAGCTCGTTATCAGAAGAATTACAACAACGGG
Found at i:48835 original size:14 final size:14
Alignment explanation
Indices: 48816--48844 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
48806 TTCCTCCCCA
48816 AAACCAAAAGAGAC
1 AAACCAAAAGAGAC
48830 AAACCAAAAGAGAC
1 AAACCAAAAGAGAC
48844 A
1 A
48845 TTTCTTCAAG
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:0.66, C:0.21, G:0.14, T:0.00
Consensus pattern (14 bp):
AAACCAAAAGAGAC
Found at i:51241 original size:110 final size:111
Alignment explanation
Indices: 51047--51349 Score: 356
Period size: 110 Copynumber: 2.6 Consensus size: 111
51037 GCTGGAAAGT
* *
51047 GCTGCTGGGCACTTTCACCTAAGTCTTATCCTTCATCAACAAAGGAGGTCAGCAGCATTACTAAC
1 GCTGCTGGGCACTTTCACCAAAGTCCTATCCTTCATCAACAAAGGAGGTCAGCAGCATTACTAAC
** *
51112 CTGGTGCAACCTTGCTGACGTGTCACTCTGCTG-GGAGAAGGTTCC
66 CTGGAACAACCTTGCTGACGTGTCACTCTGCCGAGGAGAAGGTTCC
* *
51157 GCTGCTGGGCACTTTCACCAAAGTCCTATCCTTCATCAACAAAGGAGGTTAGCAGCATTGCTAAC
1 GCTGCTGGGCACTTTCACCAAAGTCCTATCCTTCATCAACAAAGGAGGTCAGCAGCATTACTAAC
* * * *
51222 TTGGAACAACCTTGTTGACGTGTCAGTCTGCCGAGGAGGAGGTTTCGC
66 CTGGAACAACCTTGCTGACGTGTCACTCTGCCGAGGAGAAGG-TTC-C
* *
51270 TGTTGGAAAGTGCTGCTGGGCACTTTCACCAAAGTCTTATCCTCCATCAACAAAGGAGGTCAGCA
1 -----------GCTGCTGGGCACTTTCACCAAAGTCCTATCCTTCATCAACAAAGGAGGTCAGCA
*
51335 ACATTACTAACCTGG
55 GCATTACTAACCTGG
51350 TGGAACCTTA
Statistics
Matches: 162, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
110 88 0.54
111 7 0.04
112 3 0.02
113 1 0.01
124 63 0.39
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.26
Consensus pattern (111 bp):
GCTGCTGGGCACTTTCACCAAAGTCCTATCCTTCATCAACAAAGGAGGTCAGCAGCATTACTAAC
CTGGAACAACCTTGCTGACGTGTCACTCTGCCGAGGAGAAGGTTCC
Found at i:51387 original size:124 final size:124
Alignment explanation
Indices: 51157--51380 Score: 295
Period size: 124 Copynumber: 1.8 Consensus size: 124
51147 AGAAGGTTCC
* * * *
51157 GCTGCTGGGCACTTTCACCAAAGTCCTATCCTTCATCAACAAAGGAGGTTAGCAGCATTGCTAAC
1 GCTGCTGGGCACTTTCACCAAAGTCCTATCCTCCATCAACAAAGGAGGTCAGCAACATTACTAAC
* ** * ** *
51222 TTGGAACAACCTTGTTGACGTGTCAGTCTGCCGAGGAGGAGGTTTCGCTGTTGGAAAGT
66 CTGGAACAACCTTACTGACGCGTCAGTCCACCAAGGAGGAGGTTTCGCTGTTGGAAAGT
*
51281 GCTGCTGGGCACTTTCACCAAAGTCTTATCCTCCATCAACAAAGGAGGTCAGCAACATTACTAAC
1 GCTGCTGGGCACTTTCACCAAAGTCCTATCCTCCATCAACAAAGGAGGTCAGCAACATTACTAAC
*** * *
51346 CTGGTGGAACCTTACTGACGCGTCATTCCATCAAG
66 CTGGAACAACCTTACTGACGCGTCAGTCCACCAAG
51381 AGGGAGGCAC
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
124 83 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.25
Consensus pattern (124 bp):
GCTGCTGGGCACTTTCACCAAAGTCCTATCCTCCATCAACAAAGGAGGTCAGCAACATTACTAAC
CTGGAACAACCTTACTGACGCGTCAGTCCACCAAGGAGGAGGTTTCGCTGTTGGAAAGT
Found at i:52689 original size:22 final size:23
Alignment explanation
Indices: 52646--52693 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
52636 ATTTATATAA
* *
52646 TTTAATGGAAATACATATAAAAT
1 TTTAATGAAAATACATAGAAAAT
*
52669 TTTAATGAAAATATA-AGAAAAT
1 TTTAATGAAAATACATAGAAAAT
52691 TTT
1 TTT
52694 CTACGTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (23 bp):
TTTAATGAAAATACATAGAAAAT
Found at i:53882 original size:11 final size:11
Alignment explanation
Indices: 53865--53895 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
53855 AATATACTGC
53865 AAAAAAAAGAAG
1 AAAAAAAA-AAG
53877 AAAAAAAAAAG
1 AAAAAAAAAAG
53888 AAAAAAAA
1 AAAAAAAA
53896 CGAACTGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:53884 original size:14 final size:13
Alignment explanation
Indices: 53865--53895 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
53855 AATATACTGC
53865 AAAAAAAAGAAGAA
1 AAAAAAAAGAA-AA
53879 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
53892 AAAA
1 AAAA
53896 CGAACTGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:55797 original size:11 final size:11
Alignment explanation
Indices: 55773--55809 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
55763 GAAGGAGGAG
*
55773 GAAGAAGAAGAA
1 GAAG-AGAAAAA
55785 GAAGAGAAAAA
1 GAAGAGAAAAA
55796 GAAGAGAAAAA
1 GAAGAGAAAAA
55807 GAA
1 GAA
55810 AAAAGAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (11 bp):
GAAGAGAAAAA
Found at i:56647 original size:35 final size:35
Alignment explanation
Indices: 56605--57848 Score: 1560
Period size: 35 Copynumber: 35.7 Consensus size: 35
56595 CAGTAATAAG
*
56605 TAACTTAATTCAGGGTAATTAAGTGATTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* *
56640 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTTAC
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
*
56675 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* * * *
56710 CAACTTAATTCAGGGTAATTAAATCAGTCGGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* * * *
56745 AAACTTAATTCAGGGTAATTAAGTAATTCAATAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
*
56780 CAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* *
56815 TAACTTAATTCAGGGTAATTAAGTGATTCAGTAAG
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
*
56850 TAACTTAATTCAGGGCAATTAAGTGAGTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* *
56885 TAACTTAATTCAAGGTAATTAAGTAAGTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* * *
56920 CAACTTAATTCAGGGTAATTAAGTCAGTCGGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* * * *
56955 AAACTTAATTCAGGGTAATTAAGTAATTCAATAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
*
56990 CAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
*
57025 TAACTTAATTCAGGGTAATTAAGTGATTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
*
57060 TAACTTAATTCAGGGCAATTAAGTGAGTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* * *
57095 CAACTTAATTCAGGGTAATTAAGTCAGTCGGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* * * * * *
57130 AAACTTAATTTAGGGTAATTAAGTAATTTAATAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
*
57165 CAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* * *
57200 AAGCAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
1 ---TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
*
57238 TAACTTAATTCAGGGCAATTAAGTGAGTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
57273 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* * *
57308 AAGCAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
1 ---TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
*
57346 TAACTTAATTCAGGGCAATTAAGTGAGTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
57381 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* * *
57416 TAACTTAATTCAGGGTAATTAAGTAATTAAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* * *
57451 CAACTTAATTCAGGATAATTAAGTGAGTCAGTAAG
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* *
57486 TAGCTTAATTCAGGGTAATT-A---AGTCAGTAAG
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* * * *
57517 TAGCTTAATTCAGGGTAATTAAGTAAAGTCAGTTAG
1 TAACTTAATTCAGGGTAATTAAGT-GAGTCAGTAAT
* * * * *
57553 TAACTTAGTTCAGGGAAATTAAATAAGGCAG----
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* *
57584 TAACTTAATTCAGGGTAATTAAGTAATTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* *
57619 CAACTTAGTTCAGGGTAATTAAGTGAGTCAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* *
57654 CAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAG
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* *
57689 TAGCTTAATTCAGGGTAATT-A---AGTCAGTAAG
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* * * * *
57720 TAACTTAATTCAAGGTAATTAAGTAACTCATTAAA
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* * * *
57755 AAACTTAATTCAGGGTAATTAAGTAATTCAGTTAT
1 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
* * *
57790 TAATTTAATTTAGGGTAATTAAGT-AGTTTAGTAAT
1 TAACTTAATTCAGGGTAATTAAGTGAG-TCAGTAAT
* *
57825 CAACTTAATTCAAGGTAATTAAGT
1 TAACTTAATTCAGGGTAATTAAGT
57849 TTAGTAAGAA
Statistics
Matches: 1059, Mismatches: 130, Indels: 40
0.86 0.11 0.03
Matches are distributed among these distances:
31 84 0.08
32 2 0.00
34 3 0.00
35 876 0.83
36 29 0.03
38 65 0.06
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (35 bp):
TAACTTAATTCAGGGTAATTAAGTGAGTCAGTAAT
Found at i:63070 original size:14 final size:14
Alignment explanation
Indices: 63051--63087 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
63041 TGCATAAAAA
63051 AAAAGAGAAAGAAG
1 AAAAGAGAAAGAAG
*
63065 AAAAGAAAAAGAAG
1 AAAAGAGAAAGAAG
*
63079 AAAAAAGAA
1 AAAAGAGAA
63088 GCTCTACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAAGAGAAAGAAG
Found at i:63080 original size:21 final size:19
Alignment explanation
Indices: 63046--63087 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
63036 TCAAGTGCAT
*
63046 AAAAAAAAAGAGAAAGAAG
1 AAAAAAAAAGAGAAAAAAG
63065 AAAAGAAAAAGAAGAAAAAAG
1 AAAA-AAAAAG-AGAAAAAAG
63086 AA
1 AA
63088 GCTCTACGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 6 0.30
21 10 0.50
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGAGAAAAAAG
Found at i:64469 original size:2 final size:2
Alignment explanation
Indices: 64462--64506 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
64452 TAAAATTATC
* *
64462 AT AT AT AT AT AT AT AT GT AT AT GT 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
64504 AT A
1 AT A
64507 ACAATCTCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:64679 original size:4 final size:4
Alignment explanation
Indices: 64670--64722 Score: 61
Period size: 4 Copynumber: 12.2 Consensus size: 4
64660 TATAAATGGG
*
64670 GGGA GGGA GGGA GGGA GAGAGA GCGA GGGA GGGA GGGA GGGA GAGAGA
1 GGGA GGGA GGGA GGGA G-G-GA GGGA GGGA GGGA GGGA GGGA G-G-GA
64718 GGGA G
1 GGGA G
64723 AGAGAGAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
4 34 0.79
5 3 0.07
6 6 0.14
ACGTcount: A:0.30, C:0.02, G:0.68, T:0.00
Consensus pattern (4 bp):
GGGA
Found at i:64699 original size:14 final size:14
Alignment explanation
Indices: 64676--64732 Score: 82
Period size: 14 Copynumber: 4.2 Consensus size: 14
64666 TGGGGGGAGG
64676 GAGGGAGGGAGAGA
1 GAGGGAGGGAGAGA
*
64690 GAGCGAGGGAG-G-
1 GAGGGAGGGAGAGA
64702 GAGGGAGGGAGAGA
1 GAGGGAGGGAGAGA
*
64716 GAGGGAGAGAGAGA
1 GAGGGAGGGAGAGA
64730 GAG
1 GAG
64733 AGAGAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
12 10 0.26
13 2 0.05
14 26 0.68
ACGTcount: A:0.35, C:0.02, G:0.63, T:0.00
Consensus pattern (14 bp):
GAGGGAGGGAGAGA
Found at i:64700 original size:22 final size:22
Alignment explanation
Indices: 64672--64739 Score: 100
Period size: 22 Copynumber: 3.1 Consensus size: 22
64662 TAAATGGGGG
*
64672 GAGGGAGGGAGGGAGAGAGAGC
1 GAGGGAGGGAGGGAGAGAGAGA
*
64694 GAGGGAGGGAGGGAGGGAGAGA
1 GAGGGAGGGAGGGAGAGAGAGA
* *
64716 GAGGGAGAGAGAGAGAGAGAGA
1 GAGGGAGGGAGGGAGAGAGAGA
64738 GA
1 GA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.37, C:0.01, G:0.62, T:0.00
Consensus pattern (22 bp):
GAGGGAGGGAGGGAGAGAGAGA
Found at i:64723 original size:8 final size:8
Alignment explanation
Indices: 64672--64739 Score: 57
Period size: 8 Copynumber: 8.2 Consensus size: 8
64662 TAAATGGGGG
*
64672 GAGGGAGG
1 GAGGGAGA
64680 GAGGGAGA
1 GAGGGAGA
*
64688 GAGAGCGAGG
1 GAG-G-GAGA
*
64698 GAGGGAGG
1 GAGGGAGA
64706 GAGGGAGA
1 GAGGGAGA
64714 GAGAGG-GA
1 GAG-GGAGA
*
64722 GAGAGAGA
1 GAGGGAGA
*
64730 GAGAGAGA
1 GAGGGAGA
64738 GA
1 GA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
7 1 0.02
8 41 0.79
9 4 0.08
10 6 0.12
ACGTcount: A:0.37, C:0.01, G:0.62, T:0.00
Consensus pattern (8 bp):
GAGGGAGA
Found at i:64727 original size:4 final size:4
Alignment explanation
Indices: 64684--64739 Score: 58
Period size: 4 Copynumber: 14.0 Consensus size: 4
64674 GGGAGGGAGG
* * * * * *
64684 GAGA GAGA GCGA GGGA GGGA GGGA GGGA GAGA GAGG GAGA GAGA GAGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
64732 GAGA GAGA
1 GAGA GAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.39, C:0.02, G:0.59, T:0.00
Consensus pattern (4 bp):
GAGA
Found at i:64731 original size:18 final size:18
Alignment explanation
Indices: 64680--64736 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
64670 GGGAGGGAGG
* *
64680 GAGGGAGAGAGAGCGAGG
1 GAGGGAGAGAGAGAGAGA
* *
64698 GAGGGAGGGAGGGAGAGA
1 GAGGGAGAGAGAGAGAGA
64716 GAGGGAGAGAGAGAGAGA
1 GAGGGAGAGAGAGAGAGA
64734 GAG
1 GAG
64737 AGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.37, C:0.02, G:0.61, T:0.00
Consensus pattern (18 bp):
GAGGGAGAGAGAGAGAGA
Done.