Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009997.1 Corchorus capsularis cultivar CVL-1 contig10018, 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: 97927
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:515 original size:6 final size:6
Alignment explanation
Indices: 504--534 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
494 TTATACTTCA
504 TTGTAT TTGTAT TTGTAT TTGTAT TTGTAT T
1 TTGTAT TTGTAT TTGTAT TTGTAT TTGTAT T
535 CCTTGACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TTGTAT
Found at i:754 original size:22 final size:22
Alignment explanation
Indices: 729--785 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
719 CCATACAATC
729 AAATTTTGATAACATCCATATG
1 AAATTTTGATAACATCCATATG
* * *
751 AAATTTTAATGACATCCTTATG
1 AAATTTTGATAACATCCATATG
773 AAATTTTGATAAC
1 AAATTTTGATAAC
786 CACACAATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACATCCATATG
Found at i:11152 original size:27 final size:28
Alignment explanation
Indices: 11096--11152 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
11086 TAACTATCCA
*
11096 TTTTGGGACAAATTGGCCCCTTAACTTT
1 TTTTGGGACAAATTGACCCCTTAACTTT
11124 TTTTGGGACAAATTGACCCCTTAACTTT
1 TTTTGGGACAAATTGACCCCTTAACTTT
11152 T
1 T
11153 AAAAACGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (28 bp):
TTTTGGGACAAATTGACCCCTTAACTTT
Found at i:13543 original size:45 final size:45
Alignment explanation
Indices: 13492--13577 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
13482 AAAGTAGTGA
*
13492 AATTACTAAAAGATCCCTATACCGAATTAATGATGAGCTGGGTGG
1 AATTACTAAAAGATCCCTACACCGAATTAATGATGAGCTGGGTGG
* * * *
13537 AATTACTGAAAGATCTCTACCCCGGATTAATGATGAGCTGG
1 AATTACTAAAAGATCCCTACACCGAATTAATGATGAGCTGG
13578 AGAAGTAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (45 bp):
AATTACTAAAAGATCCCTACACCGAATTAATGATGAGCTGGGTGG
Found at i:13690 original size:211 final size:211
Alignment explanation
Indices: 13326--13897 Score: 975
Period size: 211 Copynumber: 2.7 Consensus size: 211
13316 AACATATGGA
* * * * * * *
13326 AATTACTAAAAGATCCCTACCCCGGATTAATGAGGCGC-GAGAGAACTAATTTTTTTCGTCTTTT
1 AATTACTGAAAGATCTCTACCCCGGATTAATGATGAGCTG-GAGAAGTAATCTTTTTCGTCTTTA
* * * * **
13390 CCCACTTGTCCGATTACTTAAATGACCTAACTTTTGATTCTTGAGATGATTAAATAACTAGACTT
65 CCCACTTGGCAGATTACTTAAATGTCCTAACTTTTTATTCTTGAGGGGATTAAATAACTAGACTT
13455 TTTGGTCATTTCTCAATTGACTTTAATAAAGTAGTGAAATTACTAAAAGATCCCTATACCGAATT
130 TTTGGTCATTTCTCAATTGACTTTAATAAAGTAGTGAAATTACTAAAAGATCCCTATACCGAATT
13520 AATGATGAGCTGGGTGG
195 AATGATGAGCTGGGTGG
13537 AATTACTGAAAGATCTCTACCCCGGATTAATGATGAGCTGGAGAAGTAATCTTTTTCGTCTTTAC
1 AATTACTGAAAGATCTCTACCCCGGATTAATGATGAGCTGGAGAAGTAATCTTTTTCGTCTTTAC
13602 CCACTTGGCAGATTACTTAAATGTCCTAACTTTTTATTCTTGAGGGGATTAAATAACTAGACTTT
66 CCACTTGGCAGATTACTTAAATGTCCTAACTTTTTATTCTTGAGGGGATTAAATAACTAGACTTT
13667 TTGGTCATTTCTCAATTGACTTTAATAAAGTAGTGAAATTACTAAAAGATCCCTATACCGAATTA
131 TTGGTCATTTCTCAATTGACTTTAATAAAGTAGTGAAATTACTAAAAGATCCCTATACCGAATTA
13732 ATGATGAGCTGGGTGG
196 ATGATGAGCTGGGTGG
13748 AATTACTGAAAGATCTCTACCCCGGATTAATGATGAGCTGGAGAAGTAATCTTTTTCGTCTTTAC
1 AATTACTGAAAGATCTCTACCCCGGATTAATGATGAGCTGGAGAAGTAATCTTTTTCGTCTTTAC
* * * *
13813 CTACTTGGCAGATTACTTAAATGTCCTAACTTTTTATTCTTGAGGGGATTAAATATCTAAAATTT
66 CCACTTGGCAGATTACTTAAATGTCCTAACTTTTTATTCTTGAGGGGATTAAATAACTAGACTTT
13878 TTGGTCATTTCTCAATTGAC
131 TTGGTCATTTCTCAATTGAC
13898 AAATGACTCA
Statistics
Matches: 343, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
211 342 1.00
212 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (211 bp):
AATTACTGAAAGATCTCTACCCCGGATTAATGATGAGCTGGAGAAGTAATCTTTTTCGTCTTTAC
CCACTTGGCAGATTACTTAAATGTCCTAACTTTTTATTCTTGAGGGGATTAAATAACTAGACTTT
TTGGTCATTTCTCAATTGACTTTAATAAAGTAGTGAAATTACTAAAAGATCCCTATACCGAATTA
ATGATGAGCTGGGTGG
Found at i:13754 original size:45 final size:45
Alignment explanation
Indices: 13703--13788 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
13693 AAAGTAGTGA
*
13703 AATTACTAAAAGATCCCTATACCGAATTAATGATGAGCTGGGTGG
1 AATTACTAAAAGATCCCTACACCGAATTAATGATGAGCTGGGTGG
* * * *
13748 AATTACTGAAAGATCTCTACCCCGGATTAATGATGAGCTGG
1 AATTACTAAAAGATCCCTACACCGAATTAATGATGAGCTGG
13789 AGAAGTAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (45 bp):
AATTACTAAAAGATCCCTACACCGAATTAATGATGAGCTGGGTGG
Found at i:14537 original size:165 final size:166
Alignment explanation
Indices: 14262--14580 Score: 518
Period size: 165 Copynumber: 1.9 Consensus size: 166
14252 AAATAAACAT
*
14262 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGAGGAGCGAGAGAACTAATTTTTTTCGTCT
1 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGAGGAGCGAGAGAACTAATCTTTTTCGTCT
* *
14327 TTTCCCACTTGACAGATTACCTAAATGTCCTAACTTTTGATTCTTGA-GGGATTAAATAACTAGA
66 TTACCCACTTGACAGATTACCTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAA
14391 CTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTA
131 CTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTA
* *
14427 GTGGAATTACTAAAAGATCCCTACCTCGGATTAATGATGAGCTG-GAGAACTAATCTTTTTCGTC
1 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGAGGAGC-GAGAGAACTAATCTTTTTCGTC
* * **
14491 TTTACCTACTTGGCAGATTATTTAAATGTCCTAAC-TTTGTATTCTTGAGGGGATTAAATAACTA
65 TTTACCCACTTGACAGATTACCTAAATGTCCTAACTTTTG-ATTCTTGAGGGGATTAAATAACTA
14555 AACTTTTTGGTCATTTCTCAATTGAC
129 AACTTTTTGGTCATTTCTCAATTGAC
14581 AAATGACTCA
Statistics
Matches: 142, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
164 4 0.03
165 97 0.68
166 41 0.29
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (166 bp):
GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGAGGAGCGAGAGAACTAATCTTTTTCGTCT
TTACCCACTTGACAGATTACCTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAA
CTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTA
Found at i:15091 original size:45 final size:45
Alignment explanation
Indices: 15040--15174 Score: 243
Period size: 45 Copynumber: 3.0 Consensus size: 45
15030 TAATATAGTA
15040 GTGGAATTACTAAAAGATCCCTACCCTGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCTGGATTAATGATGAGCTGG
15085 GTGGAATTACTAAAAGATCCCTACCCTGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCTGGATTAATGATGAGCTGG
* **
15130 GTTGAATTACTAAAAGATCCCTACCCCCGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCTGGATTAATGATGAGCTGG
15175 AGAAGTAATA
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 87 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCTGGATTAATGATGAGCTGG
Found at i:20732 original size:156 final size:156
Alignment explanation
Indices: 20352--20738 Score: 362
Period size: 156 Copynumber: 2.5 Consensus size: 156
20342 CGGACTTAGC
* * * *
20352 ATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGAGGAGACAAACCAACTTCT-CTATG
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGAGAAACCAAGTT-TACTATG
* * * *
20416 CTA-GAGAGTTCGGTTTTACTTAGATTTTTTTCCATAGCCTTATGGTGATAATCTAAGTATACTG
65 -AAGGAAAGCTCGGTTTTACTTAGAATTTTTTCCATAGCCTTATGGTGATAATCTAAGTATACT-
* * *
20480 GTGGAAAATCAACTTCGTTGGACTTAGAG
128 GTGGAAAATCAACTTCATTAGACCTAGAG
* * ** * * * * *
20509 AAG-AAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAGGGGTG-GAAACCTAGTTCACCATC
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGAC-AGTTTGAGGTGAGAAACCAAGTTTACTATG
* * * *
20572 AAGGAAAGCTCGGTTTTACTTAGAATTTTTTCCATGGTCTTAT-GTGGATATTCTAAG-ATCCT-
65 AAGGAAAGCTCGGTTTTACTTAGAATTTTTTCCATAGCCTTATGGT-GATAATCTAAGTATACTG
*
20634 TGGAAAAATTTCAGC-TCATTCAGACCTAGA-
129 TGG-AAAA--TCAACTTCATT-AGACCTAGAG
* *
20664 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGAGAAGCTC-GGTTTACTATG
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGAGAAAC-CAAGTTTACTATG
*
20728 AAGGAAGGCTC
65 AAGGAAAGCTC
20739 AGAACAAGCC
Statistics
Matches: 183, Mismatches: 36, Indels: 23
0.76 0.15 0.10
Matches are distributed among these distances:
153 3 0.02
154 4 0.02
155 20 0.11
156 147 0.80
157 9 0.05
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (156 bp):
ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGAGAAACCAAGTTTACTATGA
AGGAAAGCTCGGTTTTACTTAGAATTTTTTCCATAGCCTTATGGTGATAATCTAAGTATACTGTG
GAAAATCAACTTCATTAGACCTAGAG
Found at i:21080 original size:17 final size:18
Alignment explanation
Indices: 21060--21095 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
21050 AGCCTATCAC
21060 CTCATACTACCTA-GTAT
1 CTCATACTACCTAGGTAT
21077 CTCATACTACCTAGGTAT
1 CTCATACTACCTAGGTAT
21095 C
1 C
21096 ATGAGGAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (18 bp):
CTCATACTACCTAGGTAT
Found at i:22848 original size:27 final size:27
Alignment explanation
Indices: 22817--22895 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
22807 GACATTAATG
22817 AATAATGTGATTATTCATGAATCAATT
1 AATAATGTGATTATTCATGAATCAATT
*
22844 AATAATGTGATTATTCATGAATTAATT
1 AATAATGTGATTATTCATGAATCAATT
*
22871 AATATTGTGATTATTCATGAATCAA
1 AATAATGTGATTATTCATGAATCAA
22896 GAAGTTGTCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (27 bp):
AATAATGTGATTATTCATGAATCAATT
Found at i:23004 original size:41 final size:41
Alignment explanation
Indices: 22915--22993 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
22905 TCGTGAAAAT
22915 ACATGTATCTATTTAAAGTTGTCTTTATCCAAAAGACAAAG
1 ACATGTATCTATTTAAAGTTGTCTTTATCCAAAAGACAAAG
*
22956 ACATGTATCTATTTAATGTTGTCTTTATCCAAAAGACA
1 ACATGTATCTATTTAAAGTTGTCTTTATCCAAAAGACA
22994 TGTTTATGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (41 bp):
ACATGTATCTATTTAAAGTTGTCTTTATCCAAAAGACAAAG
Found at i:27832 original size:31 final size:30
Alignment explanation
Indices: 27764--27833 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
27754 GGATTGCCAC
*
27764 TTTGCACCC-AACTTTTTTATTTTGATAAT
1 TTTGCACCCTAACTGTTTTATTTTGATAAT
* *
27793 ATTGCACCCTAA-TGTTTTATTTTGGGTACAT
1 TTTGCACCCTAACTGTTTTATTTT-GATA-AT
27824 TTTGCACCCT
1 TTTGCACCCT
27834 TTGTGACGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 18 0.53
30 5 0.15
31 11 0.32
ACGTcount: A:0.21, C:0.20, G:0.11, T:0.47
Consensus pattern (30 bp):
TTTGCACCCTAACTGTTTTATTTTGATAAT
Found at i:30636 original size:22 final size:22
Alignment explanation
Indices: 30611--30782 Score: 102
Period size: 22 Copynumber: 7.8 Consensus size: 22
30601 ATGATCCCAT
30611 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
30633 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
30655 TATGGAATTTCGAGAACCTTTTT
1 TATGAAATTTTGATAACC-TTCC
* ** *
30678 TAT-AATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
*
30699 TATGAAATTTTGTTAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
30720 TTAAGAAATTTTGA-AGACC-TCAA
1 -TATGAAATTTTGATA-ACCTTC-C
30743 TATGAAATTTTGATAA-CTTCGC
1 TATGAAATTTTGATAACCTTC-C
*
30765 AATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
30783 AACACTATAT
Statistics
Matches: 111, Mismatches: 31, Indels: 15
0.71 0.20 0.10
Matches are distributed among these distances:
21 10 0.09
22 95 0.86
23 6 0.05
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:30824 original size:22 final size:23
Alignment explanation
Indices: 30699--30829 Score: 110
Period size: 22 Copynumber: 5.8 Consensus size: 23
30689 TTAACCTTCT
* *
30699 TATGAAATTTTGTTAACCTC-CT
1 TATGAAATTTTGATAACCTCACA
*
30721 TAAGAAATTTTGA-AGACCTCA-A
1 TATGAAATTTTGATA-ACCTCACA
* *
30743 TATGAAATTTTGATAACTTCGCA
1 TATGAAATTTTGATAACCTCACA
*
30766 -ATGAAATTTTGATAACCAACACTA
1 TATGAAATTTTGATAACC-TCAC-A
* *
30790 TATGAGATGTTGATAACCTC-CA
1 TATGAAATTTTGATAACCTCACA
* *
30812 TATGATATATTGATAACC
1 TATGAAATTTTGATAACC
30830 ACATTATGAA
Statistics
Matches: 88, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.01
22 65 0.74
23 5 0.06
24 2 0.02
25 15 0.17
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (23 bp):
TATGAAATTTTGATAACCTCACA
Found at i:30837 original size:22 final size:23
Alignment explanation
Indices: 30774--30838 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 23
30764 CAATGAAATT
*
30774 TTGATAACCAACACTATATGAGATG
1 TTGATAACCAACA-T-TATGAGATA
** *
30799 TTGATAACCTCCA-TATGATATA
1 TTGATAACCAACATTATGAGATA
30821 TTGATAACC-ACATTATGA
1 TTGATAACCAACATTATGA
30839 AAATTTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 2 0.06
22 21 0.62
25 11 0.32
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (23 bp):
TTGATAACCAACATTATGAGATA
Found at i:30906 original size:18 final size:16
Alignment explanation
Indices: 30890--30935 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
30880 CCAAACCTGA
30890 GAACCCGCCCGAACCT
1 GAACCCGCCCGAACCT
30906 GAACCCGCCCGAACAC-
1 GAACCCGCCCGAAC-CT
30922 GAACCCGCCC-AACC
1 GAACCCGCCCGAACC
30936 CGATTTGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.03
15 3 0.10
16 24 0.83
17 1 0.03
ACGTcount: A:0.28, C:0.52, G:0.17, T:0.02
Consensus pattern (16 bp):
GAACCCGCCCGAACCT
Found at i:31010 original size:32 final size:32
Alignment explanation
Indices: 30974--31034 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
30964 GAACCCGCCC
* *
30974 GACCCAAGACCTGGATGACCCGCAACCCAAAG
1 GACCCAAGACCCGAATGACCCGCAACCCAAAG
* *
31006 GACCCGAGACCCGAATGACCCGTAACCCA
1 GACCCAAGACCCGAATGACCCGCAACCCA
31035 GATGACCTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.33, C:0.39, G:0.21, T:0.07
Consensus pattern (32 bp):
GACCCAAGACCCGAATGACCCGCAACCCAAAG
Found at i:31050 original size:32 final size:32
Alignment explanation
Indices: 30988--31052 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
30978 CAAGACCTGG
*
30988 ATGACCCGCAACCCAAAGGACCCGAGACCCGA
1 ATGACCCGCAACCCAAAGGACCCGAAACCCGA
* * * *
31020 ATGACCCGTAACCCAGATGACCTGAAACCCGA
1 ATGACCCGCAACCCAAAGGACCCGAAACCCGA
31052 A
1 A
31053 ACCCGAATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.37, G:0.20, T:0.08
Consensus pattern (32 bp):
ATGACCCGCAACCCAAAGGACCCGAAACCCGA
Found at i:31080 original size:39 final size:39
Alignment explanation
Indices: 31007--31089 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
30997 AACCCAAAGG
* *
31007 ACCCGAGACCCGAATGACCCGTAACCCAGATGACCTGAA
1 ACCCGAAACCCGAATGACCCGTAACCCAGATGACCCGAA
** *
31046 ACCCGAAACCCGAATGAGTCGTAACCCA-AGTGACCCGAG
1 ACCCGAAACCCGAATGACCCGTAACCCAGA-TGACCCGAA
31085 ACCCG
1 ACCCG
31090 TATGACCCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 1 0.03
39 37 0.97
ACGTcount: A:0.33, C:0.36, G:0.22, T:0.10
Consensus pattern (39 bp):
ACCCGAAACCCGAATGACCCGTAACCCAGATGACCCGAA
Found at i:31966 original size:16 final size:16
Alignment explanation
Indices: 31940--32054 Score: 128
Period size: 16 Copynumber: 7.2 Consensus size: 16
31930 GACCCGAGAA
*
31940 CCGAGACCCGAATGAC
1 CCGAAACCCGAATGAC
*
31956 CCGGAACCCGAATGAC
1 CCGAAACCCGAATGAC
*
31972 CC-ATGACCCGAATGAC
1 CCGA-AACCCGAATGAC
*
31988 CCGAAACCCGTATGAC
1 CCGAAACCCGAATGAC
*
32004 CCGAAACCCGAATAAC
1 CCGAAACCCGAATGAC
* *
32020 ACG-AACCC-AGATGAT
1 CCGAAACCCGA-ATGAC
32035 CCGAAACCCGAATGAC
1 CCGAAACCCGAATGAC
32051 CCGA
1 CCGA
32055 GAAAACTGTC
Statistics
Matches: 81, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
14 1 0.01
15 10 0.12
16 68 0.84
17 2 0.02
ACGTcount: A:0.35, C:0.37, G:0.20, T:0.09
Consensus pattern (16 bp):
CCGAAACCCGAATGAC
Found at i:31989 original size:25 final size:23
Alignment explanation
Indices: 31945--32017 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 23
31935 GAGAACCGAG
*
31945 ACCCGAATGACCCGGAACCCGAAT
1 ACCCG-ATGACCCGAAACCCGAAT
31969 GACCC-ATGACCCGAATGACCCGAA-
1 -ACCCGATGACCCGAA--ACCCGAAT
31993 ACCCGTATGACCCGAAACCCGAAT
1 ACCCG-ATGACCCGAAACCCGAAT
32017 A
1 A
32018 ACACGAACCC
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
23 20 0.48
24 1 0.02
25 21 0.50
ACGTcount: A:0.34, C:0.37, G:0.19, T:0.10
Consensus pattern (23 bp):
ACCCGATGACCCGAAACCCGAAT
Found at i:32012 original size:23 final size:23
Alignment explanation
Indices: 31914--32015 Score: 86
Period size: 23 Copynumber: 4.3 Consensus size: 23
31904 GAACCCGCCT
*
31914 AACCCGAGACCCGGTA-GACCCGA
1 AACCCGAAACCC-GTATGACCCGA
* * *
31937 GAA-CCGAGACCCGAATGACCCGG
1 -AACCCGAAACCCGTATGACCCGA
31960 AACCCGAATGACCC--ATGACCCGA
1 AACCCGAA--ACCCGTATGACCCGA
31983 ATGACCCGAAACCCGTATGACCCGA
1 A--ACCCGAAACCCGTATGACCCGA
32008 AACCCGAA
1 AACCCGAA
32016 TAACACGAAC
Statistics
Matches: 66, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
22 4 0.06
23 39 0.59
24 2 0.03
25 21 0.32
ACGTcount: A:0.33, C:0.37, G:0.23, T:0.07
Consensus pattern (23 bp):
AACCCGAAACCCGTATGACCCGA
Found at i:32342 original size:22 final size:22
Alignment explanation
Indices: 32317--32362 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
32307 GAATTTCGAG
* *
32317 AATCTTTTTATAAAATTTTTTT
1 AATCTTCTTATAAAATTTTGTT
*
32339 AATCTTCTTATGAAATTTTGTT
1 AATCTTCTTATAAAATTTTGTT
32361 AA
1 AA
32363 CCTCCCTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.57
Consensus pattern (22 bp):
AATCTTCTTATAAAATTTTGTT
Found at i:32470 original size:22 final size:22
Alignment explanation
Indices: 32391--32600 Score: 107
Period size: 22 Copynumber: 9.8 Consensus size: 22
32381 AAGATCTCAA
*
32391 TATGAAATTTTGATAACTTCCT
1 TATGAAATTTTGATAACTTACT
* * ** *
32413 AATAAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACTTAC-T
* * *
32436 TATGAGATGTTGATAACTTTCT
1 TATGAAATTTTGATAACTTACT
*
32458 TATGAAATCTTGATAAC-TA--
1 TATGAAATTTTGATAACTTACT
* * *
32477 -A--AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACTTACT
** * *
32496 TATGATTTTTTGATACCTCA-T
1 TATGAAATTTTGATAACTTACT
* *
32517 TATGAAATTTTGTTAATCTT-CC
1 TATGAAATTTTGATAA-CTTACT
* *
32539 TATGAAATTTTGATCTACATAC-
1 TATGAAATTTTGAT-AACTTACT
*
32561 TATGAAATTTTGATAACCCT-CT
1 TATGAAATTTTGATAA-CTTACT
*
32583 TATGAAATTTTGAAAACT
1 TATGAAATTTTGATAACT
32601 AAACTAAACT
Statistics
Matches: 136, Mismatches: 39, Indels: 27
0.67 0.19 0.13
Matches are distributed among these distances:
16 12 0.09
17 1 0.01
18 1 0.01
20 1 0.01
21 16 0.12
22 89 0.65
23 16 0.12
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACTTACT
Found at i:32520 original size:21 final size:22
Alignment explanation
Indices: 32481--32521 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
32471 TAACTAAAAA
*
32481 TTTTGATAACCTCCCTATGATT
1 TTTTGATAACCTCACTATGATT
*
32503 TTTTGAT-ACCTCATTATGA
1 TTTTGATAACCTCACTATGA
32522 AATTTTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (22 bp):
TTTTGATAACCTCACTATGATT
Found at i:32869 original size:30 final size:31
Alignment explanation
Indices: 32828--32888 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
32818 TAATGGTAAT
32828 TTAGAAATATGTTTTAAAAA-AAAGGTACAA
1 TTAGAAATATGTTTTAAAAATAAAGGTACAA
* *
32858 TTAGAATTATGTTTTAAAAATAAGGGTACAA
1 TTAGAAATATGTTTTAAAAATAAAGGTACAA
32889 ATGGAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.33
Consensus pattern (31 bp):
TTAGAAATATGTTTTAAAAATAAAGGTACAA
Found at i:32929 original size:2 final size:2
Alignment explanation
Indices: 32922--32960 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
32912 TATTCGTACT
*
32922 TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
32961 GATAATTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:59178 original size:31 final size:31
Alignment explanation
Indices: 59128--59287 Score: 122
Period size: 31 Copynumber: 5.5 Consensus size: 31
59118 ACGGTGTCCG
* *
59128 ACGTGGCACGCCACGTGTACCAAAAAATGAC
1 ACGTGGCATGCCACATGTACCAAAAAATGAC
* *
59159 ATGTGGCATGTCACATGTACCAAAAAAT---
1 ACGTGGCATGCCACATGTACCAAAAAATGAC
* *
59187 -CGT-G--T--CACATGTATCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAATGAC
* * * * *
59212 ACATGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAATGAC
* ** *
59243 ATGTGGCATGCCACATGTTTCAAAAAATGGC
1 ACGTGGCATGCCACATGTACCAAAAAATGAC
59274 ACGTGGCATGCCAC
1 ACGTGGCATGCCAC
59288 GTGCACAAAA
Statistics
Matches: 98, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
22 15 0.15
24 1 0.01
26 3 0.03
27 2 0.02
31 77 0.79
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.20
Consensus pattern (31 bp):
ACGTGGCATGCCACATGTACCAAAAAATGAC
Found at i:59413 original size:23 final size:22
Alignment explanation
Indices: 59368--59411 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
59358 AGAAGGTGCA
59368 AAGTGGCACAAAAATAAAATTT
1 AAGTGGCACAAAAATAAAATTT
59390 AAGTGGCACAAAAATAAAATTT
1 AAGTGGCACAAAAATAAAATTT
59412 TAGGGTACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.09, G:0.14, T:0.23
Consensus pattern (22 bp):
AAGTGGCACAAAAATAAAATTT
Found at i:60192 original size:16 final size:16
Alignment explanation
Indices: 60171--60205 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
60161 CTGAAATTTC
60171 AGAATCAAAATTAGAG
1 AGAATCAAAATTAGAG
60187 AGAATCAAAATTAGAG
1 AGAATCAAAATTAGAG
60203 AGA
1 AGA
60206 TATTCTCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.17
Consensus pattern (16 bp):
AGAATCAAAATTAGAG
Found at i:63460 original size:15 final size:16
Alignment explanation
Indices: 63440--63477 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
63430 TCAAGTTTTT
*
63440 AAAGGAAATG-AAGGG
1 AAAGGAAAGGAAAGGG
63455 AAAGGAAAGGAAAGGG
1 AAAGGAAAGGAAAGGG
*
63471 AAGGGAA
1 AAAGGAA
63478 GTTTTTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (16 bp):
AAAGGAAAGGAAAGGG
Found at i:73716 original size:2 final size:2
Alignment explanation
Indices: 73709--73734 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
73699 ATTGTTATGG
73709 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
73735 CTAATAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76139 original size:2 final size:2
Alignment explanation
Indices: 76132--76157 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
76122 TTTTCTATGA
76132 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
76158 TAGAAATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79944 original size:29 final size:28
Alignment explanation
Indices: 79912--79976 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
79902 CTCTGAAAAT
*
79912 CACAAACAA-ACCTTTTGCGAGTAGATTGG
1 CACAAA-AATACCTTTT-CAAGTAGATTGG
*
79941 CACAAAAATTTCCTTTTCAAGTAGATTGG
1 CACAAAAA-TACCTTTTCAAGTAGATTGG
*
79970 CATAAAA
1 CACAAAA
79977 GTTTCATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 2 0.06
29 23 0.74
30 6 0.19
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (28 bp):
CACAAAAATACCTTTTCAAGTAGATTGG
Found at i:79981 original size:29 final size:30
Alignment explanation
Indices: 79922--79987 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
79912 CACAAACAAA
*
79922 CCTTTTGCGAGTAGATTGGCACAAAAATTT
1 CCTTTTGCAAGTAGATTGGCACAAAAATTT
* *
79952 CCTTTT-CAAGTAGATTGGCATAAAAGTTT
1 CCTTTTGCAAGTAGATTGGCACAAAAATTT
*
79981 CATTTTG
1 CCTTTTG
79988 ACATGCTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (30 bp):
CCTTTTGCAAGTAGATTGGCACAAAAATTT
Found at i:80792 original size:11 final size:11
Alignment explanation
Indices: 80749--80786 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
80739 TTCCTATATA
*
80749 AAATAAATTAT
1 AAATTAATTAT
80760 CAAA-TAATTAT
1 -AAATTAATTAT
80771 AAATTAATTAT
1 AAATTAATTAT
80782 AAATT
1 AAATT
80787 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:81130 original size:14 final size:14
Alignment explanation
Indices: 81111--81181 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
81101 CAAAATTTCA
*
81111 TTTCTTAACTGAAT
1 TTTCTTAAATGAAT
*
81125 TTTCTTAAAAGAA-
1 TTTCTTAAATGAAT
* * * *
81138 TTTATAAAATAAAA
1 TTTCTTAAATGAAT
*
81152 TTTCTTAACTGAAT
1 TTTCTTAAATGAAT
*
81166 TTTCTTAAAAGAAT
1 TTTCTTAAATGAAT
81180 TT
1 TT
81182 ATAAAATAAA
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
13 9 0.21
14 34 0.79
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (14 bp):
TTTCTTAAATGAAT
Found at i:81159 original size:41 final size:41
Alignment explanation
Indices: 81110--81192 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
81100 ACAAAATTTC
81110 ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
81151 ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
81192 A
1 A
81193 CAGCCGCACG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (41 bp):
ATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATAAA
Found at i:81301 original size:32 final size:33
Alignment explanation
Indices: 81225--81318 Score: 163
Period size: 33 Copynumber: 2.9 Consensus size: 33
81215 GGAAAATTCT
*
81225 AGTATGTATTAAATTGGTAGAAAACTCAATTAC
1 AGTATGTATTAAATTGGAAGAAAACTCAATTAC
81258 AGTATGTATTAAATTGGAAGAAAACTCAATTA-
1 AGTATGTATTAAATTGGAAGAAAACTCAATTAC
*
81290 ATTATGTATTAAATTGGAAGAAAACTCAA
1 AGTATGTATTAAATTGGAAGAAAACTCAA
81319 AGGAAAAAGG
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 28 0.47
33 31 0.53
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (33 bp):
AGTATGTATTAAATTGGAAGAAAACTCAATTAC
Found at i:82865 original size:16 final size:17
Alignment explanation
Indices: 82846--82883 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
82836 TTATTTGCTC
*
82846 TAAGT-TATATTGTAAT
1 TAAGTATATATTGTAAA
82862 TAAGTAGTATATTGTAAA
1 TAAGTA-TATATTGTAAA
82880 TAAG
1 TAAG
82884 AAAAAATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
18 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (17 bp):
TAAGTATATATTGTAAA
Found at i:83298 original size:4 final size:4
Alignment explanation
Indices: 83289--83322 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
83279 AAGAAATGAA
*
83289 AAAT AAAT AAAT AAAT GAA- AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
83323 AACTACATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 2 0.07
4 25 0.93
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:83306 original size:19 final size:19
Alignment explanation
Indices: 83282--83322 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
83272 AATAATGAAG
83282 AAATGAAAAATAAATAAAT
1 AAATGAAAAATAAATAAAT
83301 AAATGAAAAATAAATAAAT
1 AAATGAAAAATAAATAAAT
83320 AAA
1 AAA
83323 AACTACATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (19 bp):
AAATGAAAAATAAATAAAT
Found at i:83311 original size:15 final size:14
Alignment explanation
Indices: 83293--83324 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
83283 AATGAAAAAT
83293 AAATAAATAAATGAA
1 AAATAAATAAAT-AA
83308 AAATAAATAAATAA
1 AAATAAATAAATAA
83322 AAA
1 AAA
83325 CTACATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (14 bp):
AAATAAATAAATAA
Found at i:83858 original size:3 final size:3
Alignment explanation
Indices: 83850--83885 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
83840 ACCTTAGGAT
*
83850 TTA TTA TTA ATA TTA TTA TTA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
83886 GAAATTGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:85111 original size:22 final size:22
Alignment explanation
Indices: 85086--85134 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
85076 TTTTATATAT
*
85086 TTTTTTTAACCT-TCTTATGAAA
1 TTTTGTTAACCTGTCTTA-GAAA
*
85108 TTTTGTTAACCTGTCTTAGGAA
1 TTTTGTTAACCTGTCTTAGAAA
85130 TTTTG
1 TTTTG
85135 AAGACCTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.53
Consensus pattern (22 bp):
TTTTGTTAACCTGTCTTAGAAA
Found at i:85214 original size:22 final size:22
Alignment explanation
Indices: 85176--85226 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
85166 CAATTAAATT
*
85176 TTGATAACCACATTATGAGATG
1 TTGATAACCACATTATGAGATA
* *
85198 TTGATAACCTTCA-TATGATATA
1 TTGATAACC-ACATTATGAGATA
85220 TTGATAA
1 TTGATAA
85227 ACATGTTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (22 bp):
TTGATAACCACATTATGAGATA
Found at i:85346 original size:23 final size:23
Alignment explanation
Indices: 85279--85404 Score: 102
Period size: 23 Copynumber: 5.6 Consensus size: 23
85269 AATCGCACTC
*
85279 TGAAATTTTGAT-AATC-ACGCTA
1 TGAAATTTTGATAAATCTTC-CTA
*
85301 TG-AATTTGTGAT-AA-CCTCGCTA
1 TGAAATTT-TGATAAATCTTC-CTA
85323 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGATAAATCTTCCTA
* * *
85346 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGATAAATCTTCCTA
* * *
85369 TAAAATTTTGATAACT-TTCTTA
1 TGAAATTTTGATAAATCTTCCTA
*
85391 TGAAATCTTGATAA
1 TGAAATTTTGATAA
85405 CTACAAATTT
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
21 6 0.07
22 35 0.40
23 44 0.50
24 3 0.03
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (23 bp):
TGAAATTTTGATAAATCTTCCTA
Found at i:85375 original size:46 final size:45
Alignment explanation
Indices: 85303--85404 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 45
85293 TCACGCTATG
* *
85303 AATTTGTGAT-AACCTCGCTATGAAATTTTGATAAATCTTCCTATAA
1 AATTT-TGATAAACCTCCCTATAAAATTTTGATAAAT-TTCCTATAA
* * *
85349 AATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTATGA
1 AATTTTGATAAACCTCCCTATAAAATTTTGATAAATTTCCTATAA
*
85394 AATCTTGATAA
1 AATTTTGATAA
85405 CTACAAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
45 21 0.43
46 28 0.57
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (45 bp):
AATTTTGATAAACCTCCCTATAAAATTTTGATAAATTTCCTATAA
Found at i:85441 original size:128 final size:127
Alignment explanation
Indices: 85281--85534 Score: 314
Period size: 128 Copynumber: 2.0 Consensus size: 127
85271 TCGCACTCTG
* *
85281 AAATTTTGATAATCACGCTATGAATTTGTGATAACCTCGCTAT-GAAATTTTGATAAATCTTCCT
1 AAATTTTGATAATCACGCTATGAATTTGTGATAACCTCACTATGGAAATTTTG-TAAATCTCCCT
* ** *
85345 ATAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTATGAAATCTTGATAACTAC
65 ATAAAATTTTGATAAACCT-ACTATAAAATTTTGATAACCCTCTTATGAAATCTTGAAAACTAC
* * * * *
85409 AAATTTTGATAATCTC-CATATGATTTTTTGATAACCTCATTATGGAAATTTTGTTAATCTCCCT
1 AAATTTTGATAATCACGC-TATGAATTTGTGATAACCTCACTATGGAAATTTTGTAAATCTCCCT
* ** * * *
85473 ATGAAATTTTGATCTACGTACTATGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTA
65 ATAAAATTTTGATAAACCTACTATAAAATTTTGATAACCCTCTTATGAAATCTTGAAAACTA
85535 AACTATGAAA
Statistics
Matches: 107, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
127 38 0.36
128 60 0.56
129 9 0.08
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (127 bp):
AAATTTTGATAATCACGCTATGAATTTGTGATAACCTCACTATGGAAATTTTGTAAATCTCCCTA
TAAAATTTTGATAAACCTACTATAAAATTTTGATAACCCTCTTATGAAATCTTGAAAACTAC
Found at i:85481 original size:22 final size:22
Alignment explanation
Indices: 85409--85528 Score: 86
Period size: 22 Copynumber: 5.4 Consensus size: 22
85399 TGATAACTAC
85409 AAATTTTGATAATCTCCATATG
1 AAATTTTGATAATCTCCATATG
** *
85431 ATTTTTTGATAACCT-CATTATGG
1 AAATTTTGATAATCTCCA-TAT-G
* *
85454 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAATCTCCATATG
* *
85476 AAATTTTGAT-CTACGTAC-TATG
1 AAATTTTGATAAT-C-TCCATATG
* *
85498 AAATTTTGATAA-CCCTCTTATG
1 AAATTTTGATAATCTC-CATATG
85520 AAATTTTGA
1 AAATTTTGA
85529 AAACTAAACT
Statistics
Matches: 76, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
21 5 0.07
22 53 0.70
23 17 0.22
24 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (22 bp):
AAATTTTGATAATCTCCATATG
Found at i:97904 original size:15 final size:15
Alignment explanation
Indices: 97884--97916 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
97874 TCAGAAATCT
97884 CTGCAACTTCCCTCA
1 CTGCAACTTCCCTCA
97899 CTGCAACTTCCCTCA
1 CTGCAACTTCCCTCA
97914 CTG
1 CTG
97917 AGATGGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.45, G:0.09, T:0.27
Consensus pattern (15 bp):
CTGCAACTTCCCTCA
Done.