Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009393.1 Corchorus capsularis cultivar CVL-1 contig09414, 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: 111062
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5532 original size:14 final size:13
Alignment explanation
Indices: 5506--5544 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
5496 AATCGAAAAT
5506 GATGAAAAAAGAA
1 GATGAAAAAAGAA
5519 GATGAAACAAAGAA
1 GATGAAA-AAAGAA
*
5533 GA-GAAAAGAGAA
1 GATGAAAAAAGAA
5545 AAAAAAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 5 0.21
13 11 0.46
14 8 0.33
ACGTcount: A:0.67, C:0.03, G:0.26, T:0.05
Consensus pattern (13 bp):
GATGAAAAAAGAA
Found at i:6232 original size:8 final size:8
Alignment explanation
Indices: 6219--6250 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
6209 CTCCGCATTC
6219 GAAGAAAA
1 GAAGAAAA
6227 GAAGAAAA
1 GAAGAAAA
*
6235 GAATAAAA
1 GAAGAAAA
6243 GAAGAAAA
1 GAAGAAAA
6251 AACTAGGCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (8 bp):
GAAGAAAA
Found at i:6841 original size:5 final size:5
Alignment explanation
Indices: 6833--6925 Score: 75
Period size: 5 Copynumber: 17.6 Consensus size: 5
6823 TAAAAAGTTG
6833 AAAGA AAAGA AAAGCA AAAGA AAA-A TAAATTG- AAAGA AAAGA AAAGCA
1 AAAGA AAAGA AAAG-A AAAGA AAAGA -AAA--GA AAAGA AAAGA AAAG-A
* *
6881 AAAGA AAATA AATTG- AAAGA AAAGA AAAGCA AAAGAA AAAGA AAA
1 AAAGA AAAGA AA-AGA AAAGA AAAGA AAAG-A AAAG-A AAAGA AAA
6926 AGAGGCTCTA
Statistics
Matches: 73, Mismatches: 5, Indels: 20
0.74 0.05 0.20
Matches are distributed among these distances:
4 3 0.04
5 47 0.64
6 23 0.32
ACGTcount: A:0.74, C:0.03, G:0.16, T:0.06
Consensus pattern (5 bp):
AAAGA
Found at i:6854 original size:16 final size:16
Alignment explanation
Indices: 6833--6925 Score: 93
Period size: 16 Copynumber: 5.8 Consensus size: 16
6823 TAAAAAGTTG
6833 AAAGAAAAGAAAAGCA
1 AAAGAAAAGAAAAGCA
***
6849 AAAGAAAA-ATAAATTG
1 AAAGAAAAGA-AAAGCA
6865 AAAGAAAAGAAAAGCA
1 AAAGAAAAGAAAAGCA
* *
6881 AAAGAAAATAAATTG--
1 AAAGAAAAGAAA-AGCA
6896 AAAGAAAAGAAAAGCA
1 AAAGAAAAGAAAAGCA
6912 AAAGAAAAAGAAAA
1 AAAG-AAAAGAAAA
6926 AGAGGCTCTA
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
14 1 0.02
15 12 0.20
16 37 0.61
17 11 0.18
ACGTcount: A:0.74, C:0.03, G:0.16, T:0.06
Consensus pattern (16 bp):
AAAGAAAAGAAAAGCA
Found at i:6866 original size:32 final size:32
Alignment explanation
Indices: 6830--6920 Score: 175
Period size: 31 Copynumber: 2.9 Consensus size: 32
6820 GTGTAAAAAG
6830 TTGAAAGAAAAGAAAAGCAAAAGAAAAATAAA
1 TTGAAAGAAAAGAAAAGCAAAAGAAAAATAAA
6862 TTGAAAGAAAAGAAAAGCAAAAG-AAAATAAA
1 TTGAAAGAAAAGAAAAGCAAAAGAAAAATAAA
6893 TTGAAAGAAAAGAAAAGCAAAAGAAAAA
1 TTGAAAGAAAAGAAAAGCAAAAGAAAAA
6921 GAAAAAGAGG
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
31 31 0.53
32 27 0.47
ACGTcount: A:0.71, C:0.03, G:0.16, T:0.09
Consensus pattern (32 bp):
TTGAAAGAAAAGAAAAGCAAAAGAAAAATAAA
Found at i:7941 original size:69 final size:68
Alignment explanation
Indices: 7795--8214 Score: 584
Period size: 69 Copynumber: 6.2 Consensus size: 68
7785 TTCAAGAATT
* *
7795 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAAATTAAGCCTTGGTTCCGTCCAAGCC
1 AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAAGTTAAGCCTTGGTTCCATCCAAGCC
7860 ACGA
66 AC-A
*
7864 AGGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAA-TTAAGCCTTGGTTCCATCCAAGC
1 A-GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAAGTTAAGCCTTGGTTCCATCCAAGC
7928 CACGA
65 CAC-A
* * **
7933 AGGGCTTTTCCATAAGCCAAACTCGTTTCCATGCGAGTCAAGTTAAGCCTTGGTTCTGTCCAAGC
1 A-GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAAGTTAAGCCTTGGTTCCATCCAAGC
7998 CACA
65 CACA
*
8002 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAA-TTAAGCTTTGGTTCCATCCAAGC
1 -AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAAGTTAAGCCTTGGTTCCATCCAAGC
8066 CACGA
65 CAC-A
* * *
8071 AGGGCTTTTCCATAAGCCAAACT-GTTTTCATACGAGTCAAGTTAAGCCTTGGTTCCGTCCAAGC
1 A-GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAAGTTAAGCCTTGGTTCCATCCAAGC
*
8135 CGCA
65 CACA
* * *
8139 TAGGC-TTTCCACAAGCCAAACTCGTTT-C-TATGAGTCAATTTAAGCCTTGGTTCTATCCAAGC
1 -AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAAGTTAAGCCTTGGTTCCATCCAAGC
8201 CACA
65 CACA
8205 AGG-TTTTCCA
1 AGGCTTTTCCA
8215 AAATCGGACT
Statistics
Matches: 321, Mismatches: 21, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
65 9 0.03
66 33 0.10
67 17 0.05
68 48 0.15
69 151 0.47
70 63 0.20
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (68 bp):
AGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAAGTTAAGCCTTGGTTCCATCCAAGCC
ACA
Found at i:8067 original size:138 final size:138
Alignment explanation
Indices: 7796--8214 Score: 665
Period size: 138 Copynumber: 3.1 Consensus size: 138
7786 TCAAGAATTA
* *
7796 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAAATTAAGCCTTGGTTCCGTCCAAGCCA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAAGTTAAGCCTTGGTTCCGTCCAAGCCA
*
7861 CGA-AGGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTAAGCCTTGGTTCCATCCA
66 C-ATA-GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTAAGCCTTGGTTCCATCCA
7925 AGCCACGAAG
129 AGCCACGAAG
* *
7935 GGCTTTTCCATAAGCCAAACTCGTTTCCATGCGAGTCAAGTTAAGCCTTGGTTCTGTCCAAGCCA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAAGTTAAGCCTTGGTTCCGTCCAAGCCA
*
8000 CATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTAAGCTTTGGTTCCATCCAAG
66 CATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTAAGCCTTGGTTCCATCCAAG
8065 CCACGAAG
131 CCACGAAG
* *
8073 GGCTTTTCCATAAGCCAAACT-GTTTTCATACGAGTCAAGTTAAGCCTTGGTTCCGTCCAAGCCG
1 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAAGTTAAGCCTTGGTTCCGTCCAAGCCA
* *
8137 CATAGGC-TTTCCACAAGCCAAACTCGTTT-C-TATGAGTCAATTTAAGCCTTGGTTCTATCCAA
66 CATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAA-TTAAGCCTTGGTTCCATCCAA
8199 GCCAC-AA-
130 GCCACGAAG
8206 GG-TTTTCCA
1 GGCTTTTCCA
8215 AAATCGGACT
Statistics
Matches: 265, Mismatches: 13, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
132 7 0.03
133 2 0.01
134 11 0.04
135 25 0.09
136 22 0.08
137 46 0.17
138 89 0.34
139 63 0.24
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (138 bp):
GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAAGTTAAGCCTTGGTTCCGTCCAAGCCA
CATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTAAGCCTTGGTTCCATCCAAG
CCACGAAG
Found at i:8355 original size:20 final size:20
Alignment explanation
Indices: 8330--8369 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
8320 CAGAGTTTGC
*
8330 ATTGGTAAGTCCTCCGGGCA
1 ATTGGTAAGACCTCCGGGCA
*
8350 ATTGGTAAGACTTCCGGGCA
1 ATTGGTAAGACCTCCGGGCA
8370 CAATTTCAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.25
Consensus pattern (20 bp):
ATTGGTAAGACCTCCGGGCA
Found at i:8847 original size:27 final size:27
Alignment explanation
Indices: 8816--8882 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
8806 AATAGGGTCG
8816 TTTTGGTCATTTTC-GGTATCAGGGGCA
1 TTTTGGTCATTTTCAGGT-TCAGGGGCA
* *
8843 TTTTGGTCATTTGCATGTTCAGGGGCA
1 TTTTGGTCATTTTCAGGTTCAGGGGCA
* *
8870 TTCTAGTCATTTT
1 TTTTGGTCATTTT
8883 GAGTCTACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 32 0.94
28 2 0.06
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.45
Consensus pattern (27 bp):
TTTTGGTCATTTTCAGGTTCAGGGGCA
Found at i:9440 original size:20 final size:20
Alignment explanation
Indices: 9415--9453 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
9405 AAATACAAGG
9415 CATTTGATTTACAAATTGGA
1 CATTTGATTTACAAATTGGA
*
9435 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
9454 TGCTCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Found at i:13827 original size:12 final size:12
Alignment explanation
Indices: 13807--13841 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
13797 TGTTTGGTGT
13807 CAAGGAAAATAC
1 CAAGGAAAATAC
* *
13819 TATGGAAAATAC
1 CAAGGAAAATAC
13831 CAAGGAAAATA
1 CAAGGAAAATA
13842 TTTTCTTAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.14
Consensus pattern (12 bp):
CAAGGAAAATAC
Found at i:25624 original size:59 final size:59
Alignment explanation
Indices: 25531--25658 Score: 213
Period size: 59 Copynumber: 2.2 Consensus size: 59
25521 TTCTCTCATT
* *
25531 CTTCATATTTTCTTCTTCTCCATATTCTATTGTCTCTCTATTCTCTTGTCTTTTACATA
1 CTTCATATTTTCTTCTTCTCCATATTATATTGTCTCTCTATTCTCTTGTCTTTAACATA
* *
25590 TTTCATATTTTCTTCTTTTCCATATTATATTGTCTCTCTATTCTCTTGTCTTTAACATA
1 CTTCATATTTTCTTCTTCTCCATATTATATTGTCTCTCTATTCTCTTGTCTTTAACATA
25649 CTTCA-ATTTT
1 CTTCATATTTT
25659 ACTCCATTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
58 5 0.08
59 59 0.92
ACGTcount: A:0.17, C:0.23, G:0.03, T:0.57
Consensus pattern (59 bp):
CTTCATATTTTCTTCTTCTCCATATTATATTGTCTCTCTATTCTCTTGTCTTTAACATA
Found at i:28169 original size:29 final size:29
Alignment explanation
Indices: 28125--28181 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
28115 TTTCAGTATG
28125 GCTTCAAGCATCTTGTACCTGCTAATTTA
1 GCTTCAAGCATCTTGTACCTGCTAATTTA
* *
28154 GCTTCAAGCATTTTGTACCTGCTGATTT
1 GCTTCAAGCATCTTGTACCTGCTAATTT
28182 TGCTACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (29 bp):
GCTTCAAGCATCTTGTACCTGCTAATTTA
Found at i:32220 original size:18 final size:17
Alignment explanation
Indices: 32184--32225 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
32174 CGGAGTAAAA
*
32184 TATTATTTTAGAGAGAT
1 TATTAATTTAGAGAGAT
*
32201 TATTAATTTATAGAG--
1 TATTAATTTAGAGAGAT
32216 TATTAATTTA
1 TATTAATTTA
32226 TGGAAGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
17 13 0.57
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (17 bp):
TATTAATTTAGAGAGAT
Found at i:32782 original size:66 final size:66
Alignment explanation
Indices: 32611--32816 Score: 324
Period size: 66 Copynumber: 3.1 Consensus size: 66
32601 CATCCATTTA
* *
32611 TAAGAAACCATAATAATTGAAAGTGAAATTACCTAAAATCCAATCCAATCTTAACTTCTCATTAT
1 TAAGAAACCATAATAATTGAAAGTGAAATTACCTAAAAACCAATCCAATCTTAACTTTTC-TTA-
*
32676 A-A
64 AGT
32678 TAAGAAACCATAATAATTGAAAGTGAAATTACCTAAAAACCAATCCAATCTTAACTTTTCTTAAG
1 TAAGAAACCATAATAATTGAAAGTGAAATTACCTAAAAACCAATCCAATCTTAACTTTTCTTAAG
32743 T
66 T
* * *
32744 TAAGAAACCATAATAATTGAGAGTGAAATTACCTAAAAACCAATCCAACCTTAACTTTTCATAAG
1 TAAGAAACCATAATAATTGAAAGTGAAATTACCTAAAAACCAATCCAATCTTAACTTTTCTTAAG
32809 T
66 T
32810 TGAAGAA
1 T-AAGAA
32817 CAAATGAGGA
Statistics
Matches: 131, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
65 1 0.01
66 67 0.51
67 63 0.48
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (66 bp):
TAAGAAACCATAATAATTGAAAGTGAAATTACCTAAAAACCAATCCAATCTTAACTTTTCTTAAG
T
Found at i:33830 original size:440 final size:433
Alignment explanation
Indices: 33040--34041 Score: 1079
Period size: 440 Copynumber: 2.3 Consensus size: 433
33030 CGCGTTGACT
* *
33040 TTTATTTTTGTATTGTTT-TTCCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTA
1 TTTATTTTTTTATTCTTTGTT-CTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGT-
* * * * * * *
33104 AG-TTCATGATCTGCAATTTTCATGAAGAATTCAAAAGCCAATTTTAATGTTTTGATTCTAAAAA
64 AGTTTCATGATCTACAACTTTCATGAAG-ACTCAAAAGCAAATTTTAATATTTTAATTCAAAAAA
* * ** * * * * *
33168 ATGATTCCGGAATTTTGTGGTTTTGATTGCCGGTCAATTTCATATCGTATAATTTTTTGTCCACA
128 ATGATTCCGAAATTTGGTCCTTTCGATTGCCGGTCAATTTAATACCATATAATTTTTCGTCCACA
* * * * *
33233 TGTCCGATTGAAGTTATTGAAGTGTCATTAAAAAATTATTGCATGATTTACGACTTTCATGAAGG
193 TGTCCGATTAAAGTTAATCAAGTGTCATTAAAAAATTACTGCATGATTTACGACTTTCATGAAGA
*
33298 ACCTGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGCTTCAA
258 ACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGCTTCAA
* * * * * * **
33363 GATCTCCATTAACAAAAATTTCTTATTTGGATTATTTGTCAAATGACCCTTATATTTTTTTCTAC
323 GATATCCATTAACAAAAATTTCTTATTTGAATTAGTTATCAAATAACCC-T-CATGCTTTTCTAC
** * * *
33428 TTTATACTACTTTTTCCTTTACAAATTCTAGATTTTAATCTAACGTTTAA-AA
386 TTTATACTACTTAGTCATATACAAATTCT--ATCTTAATC-AAC--TTAACAA
* * *
33480 TTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGTTGATTTATGTGTCTATTAAAAGGTAG
1 TTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAG
* * *
33545 TTTGATGATCTACAACTTTCATGAATGACTAAAAAGCAAATTTTTATATTTTAATT-AAAAAAAT
66 TTTCATGATCTACAACTTTCATGAA-GACTCAAAAGCAAATTTTAATATTTTAATTCAAAAAAAT
* * ** * *
33609 GCTTCCTAAATTTGGTCCTTTCGATTGTTGGTCTATTTAATACCATATAA-TTTTCGATTCACAT
130 GATTCCGAAATTTGGTCCTTTCGATTGCCGGTCAATTTAATACCATATAATTTTTCG-TCCACAT
* * ** *
33673 GTTCGATTAAAGTTAATCAAGTGTCGGTTAAAAGGTTACTGTATGATTTACGACTTTCATGAAGA
194 GTCCGATTAAAGTTAATCAAGTGTC-ATTAAAAAATTACTGCATGATTTACGACTTTCATGAAGA
* *
33738 ACCCGAAAG-TTAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGAGG-ATTTTTATGTTTCA
258 ACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAG-GGAATTTTTATGCTTCA
* * ** * *
33801 AGATATCTATTAAGAAATTTTTGCTTATTTGAATTAGTTATCAAATAACTCTCATGCTTTTCTAT
322 AGATATCCATTAACAAAAATTT-CTTATTTGAATTAGTTATCAAATAACCCTCATGCTTTTCTAC
* * * *
33866 TTTATGCTACTTAGTCATATACAAATTCTATCTTATTCGACTTAACAC
386 TTTATACTACTTAGTCATATACAAATTCTATCTTAATCAACTTAACAA
* * * *
33914 TTCA-TTTTTT-TTCTTTGTTCTATTTGTCC-AGTTAAGGTAATTCAGGTGTCTATTAAAATGTA
1 TTTATTTTTTTATTCTTTGTTCTATTTGTCCGA-TTAAGGTGATTCAAGTGTCTATTAAAAGGTA
* * ** * * * *
33976 ATTTTATGATCTACAACTTTCATGAAAGACTCAAAAGTTAATTTTCATGTTTCAATTCTAAAAAA
65 GTTTCATGATCTACAACTTTCATG-AAGACTCAAAAGCAAATTTTAATATTTTAATTCAAAAAAA
34041 T
129 T
34042 ACTTTTGAAA
Statistics
Matches: 470, Mismatches: 81, Indels: 29
0.81 0.14 0.05
Matches are distributed among these distances:
431 1 0.00
432 91 0.19
433 19 0.04
434 4 0.01
435 2 0.00
436 7 0.01
438 38 0.08
439 140 0.30
440 165 0.35
441 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.43
Consensus pattern (433 bp):
TTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAG
TTTCATGATCTACAACTTTCATGAAGACTCAAAAGCAAATTTTAATATTTTAATTCAAAAAAATG
ATTCCGAAATTTGGTCCTTTCGATTGCCGGTCAATTTAATACCATATAATTTTTCGTCCACATGT
CCGATTAAAGTTAATCAAGTGTCATTAAAAAATTACTGCATGATTTACGACTTTCATGAAGAACC
CGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGAT
ATCCATTAACAAAAATTTCTTATTTGAATTAGTTATCAAATAACCCTCATGCTTTTCTACTTTAT
ACTACTTAGTCATATACAAATTCTATCTTAATCAACTTAACAA
Found at i:34834 original size:25 final size:24
Alignment explanation
Indices: 34776--34847 Score: 110
Period size: 23 Copynumber: 3.0 Consensus size: 24
34766 CCAAACAATC
34776 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
*
34800 -TGAGTACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
*
34823 TTTGAGCACTCTCGCTCAGTCTCTA
1 -TTGAGCACTCTCGCTCGGTCTCTA
34848 ACAAATAAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 22 0.51
25 21 0.49
ACGTcount: A:0.14, C:0.32, G:0.19, T:0.35
Consensus pattern (24 bp):
TTGAGCACTCTCGCTCGGTCTCTA
Found at i:35753 original size:25 final size:25
Alignment explanation
Indices: 35719--35767 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
35709 CCAAACAATC
*
35719 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAACACTCTCGCTCGGTCTCTAT
35744 TTGAACACTCTCGCTCGGTCTCTA
1 TTGAACACTCTCGCTCGGTCTCTA
35768 ACAAACAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.33, G:0.18, T:0.35
Consensus pattern (25 bp):
TTGAACACTCTCGCTCGGTCTCTAT
Found at i:40381 original size:195 final size:195
Alignment explanation
Indices: 39928--40359 Score: 593
Period size: 195 Copynumber: 2.2 Consensus size: 195
39918 GCTTAATCAG
* * * *
39928 TTTGGCGCCAATACGTATTTGGCGGGAATGATACTTTTTGTGGCAAAACCTATATTGGTCACTAC
1 TTTGGCGCCAACATGCATATGGCGGGAATGATACTTTTTGTGGCAAAACCTATATTGGTCACTAC
* * *
39993 AAGTTTCATTTTTCTGTGACGAAAAAGTAGCTCGTCACATTTGTGTGTAACATTTTGTGACGACA
66 AAGTTTCAATTTTCTGTGACGAAAAAGTAGCTCGTCACATTTGTGTGTAACAGTTTGTGACAACA
** ** * *
40058 CGTTGTGTCACTAACAATTCAATTAATTAGTGGCTACACAATTCTATCACAAAAACGTTAGCCAT
131 AATCATGTCACTAACAATTCAACTAATTAGTGCCTACACAATTCTATCACAAAAACGTTAGCCAT
* *
40123 TTTGGCGCCAACATGGATATGGCGCGAATGATACTTTTTGTGGCAAAACCTATATTGGTCACTAC
1 TTTGGCGCCAACATGCATATGGCGGGAATGATACTTTTTGTGGCAAAACCTATATTGGTCACTAC
* * * *
40188 AAGTTTCAATTTTCTGTGACGAAAAATTA-CATGGTCGCTTTTGTGTGTAAC-GTTTGTGACAAC
66 AAGTTTCAATTTTCTGTGACGAAAAAGTAGC-TCGTCACATTTGTGTGTAACAGTTTGTGACAAC
* *
40251 AAATCATGTCACTAACAATTCAACTAATTAGTGCCTACGA-AATATC-GTCACAAAAAATGTTAG
130 AAATCATGTCACTAACAATTCAACTAATTAGTGCCTAC-ACAAT-TCTATCAC-AAAAACGTTAG
40314 CCAT
192 CCAT
* *
40318 TTTGGCGCCAACATGCATATGGCGGGAATGCTTCTTTTTGTG
1 TTTGGCGCCAACATGCATATGGCGGGAATGATACTTTTTGTG
40360 ACTAAACATA
Statistics
Matches: 209, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
194 50 0.24
195 159 0.76
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (195 bp):
TTTGGCGCCAACATGCATATGGCGGGAATGATACTTTTTGTGGCAAAACCTATATTGGTCACTAC
AAGTTTCAATTTTCTGTGACGAAAAAGTAGCTCGTCACATTTGTGTGTAACAGTTTGTGACAACA
AATCATGTCACTAACAATTCAACTAATTAGTGCCTACACAATTCTATCACAAAAACGTTAGCCAT
Found at i:40441 original size:195 final size:194
Alignment explanation
Indices: 39928--40441 Score: 481
Period size: 195 Copynumber: 2.6 Consensus size: 194
39918 GCTTAATCAG
* * * * * * * *
39928 TTTGGCGCCAATACGTATTTGGCGGGAATGATACTTTTTGTGGCAAAACCTATATTGGTCACTAC
1 TTTGGCGCCAACATGCATATGGCGCGAATGATACTTTTTGTGACAAAACATATACTGGTCACTAC
* * * * * *
39993 AAGTTTCATTTTTCTGTGACGAAAAAGTAGC-TCG-TCAC-ATTTGTGTGTAACATTTTGTGACG
66 AAATTTCAATTTTCTATGACGAAAAATTA-CAT-GATCACTA-TTGTGTATAACA-TTTGTGACA
** ** * *
40055 ACACGTTGTGTCACTAACAATTCAATTAATTAGTGGCTACACAATTCTATCACAAAAACGTTAGC
127 ACAAATCATGTCACTAACAATTCAACTAATTAGTGCCTACACAATTCTATCACAAAAACGTTAGC
40120 CAT
192 CAT
* * * *
40123 TTTGGCGCCAACATGGATATGGCGCGAATGATACTTTTTGTGGCAAAACCTATATTGGTCACTAC
1 TTTGGCGCCAACATGCATATGGCGCGAATGATACTTTTTGTGACAAAACATATACTGGTCACTAC
* * * * * * *
40188 AAGTTTCAATTTTCTGTGACGAAAAATTACATGGTCGCTTTTGTGTGTAACGTTTGTGACAACAA
66 AAATTTCAATTTTCTATGACGAAAAATTACATGATCACTATTGTGTATAACATTTGTGACAACAA
* *
40253 ATCATGTCACTAACAATTCAACTAATTAGTGCCTACGA-AATATC-GTCACAAAAAATGTTAGCC
131 ATCATGTCACTAACAATTCAACTAATTAGTGCCTAC-ACAAT-TCTATCAC-AAAAACGTTAGCC
40316 AT
193 AT
* * * * *
40318 TTTGGCGCCAACATGCATATGGCGGGAATGCTTCTTTTTGTGACTAAACATATGCTGGTCACTA-
1 TTTGGCGCCAACATGCATATGGCGCGAATGATACTTTTTGTGACAAAACATATACTGGTCACTAC
* * *
40382 ATAATTTC-ATTCTT-TAATGACGAAAAATTGTTCCTTATCACTATT-T-TATAACATTTGTGA
66 A-AATTTCAATT-TTCT-ATGACGAAAAA-T-TACATGATCACTATTGTGTATAACATTTGTGA
40442 TGATTATTTT
Statistics
Matches: 270, Mismatches: 38, Indels: 22
0.82 0.12 0.07
Matches are distributed among these distances:
194 56 0.21
195 203 0.75
196 2 0.01
197 9 0.03
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (194 bp):
TTTGGCGCCAACATGCATATGGCGCGAATGATACTTTTTGTGACAAAACATATACTGGTCACTAC
AAATTTCAATTTTCTATGACGAAAAATTACATGATCACTATTGTGTATAACATTTGTGACAACAA
ATCATGTCACTAACAATTCAACTAATTAGTGCCTACACAATTCTATCACAAAAACGTTAGCCAT
Found at i:45235 original size:2 final size:2
Alignment explanation
Indices: 45228--45254 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45218 ACACAAATGA
45228 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
45255 AATGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45309 original size:31 final size:29
Alignment explanation
Indices: 45274--45375 Score: 78
Period size: 31 Copynumber: 3.4 Consensus size: 29
45264 AAAATTGGCT
45274 AAATAAGGGCCTAATGTTTACCAAAATACTC
1 AAATAAGGGCCTAATGTTT--CAAAATACTC
* * * * ** *
45305 AAATAAGGGTCTGATCTTTTAATTTAGTC
1 AAATAAGGGCCTAATGTTTCAAAATACTC
* * *
45334 AAATAAGGGTCTAACGTTTGTCAAAATGCTC
1 AAATAAGGGCCTAATG-TT-TCAAAATACTC
45365 AAATAAGGGCC
1 AAATAAGGGCC
45376 CGATCTTTGA
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
29 19 0.36
30 2 0.04
31 32 0.60
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (29 bp):
AAATAAGGGCCTAATGTTTCAAAATACTC
Found at i:45367 original size:60 final size:60
Alignment explanation
Indices: 45274--45435 Score: 225
Period size: 60 Copynumber: 2.7 Consensus size: 60
45264 AAAATTGGCT
* * * * * * * *
45274 AAATAAGGGCCTAATGTTTACCAAAATACTCAAATAAGGGTCTGATCTTTTAATTTAGTC
1 AAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTAGCC
* *
45334 AAATAAGGGTCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGCC
1 AAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTAGCC
*
45394 AAATAAGGGTCTAACATTTGCCAAAATGCTCAAATAAGGGCC
1 AAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
45436 TATCTCATAC
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 90 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (60 bp):
AAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTAGCC
Found at i:45431 original size:31 final size:29
Alignment explanation
Indices: 45332--45433 Score: 91
Period size: 31 Copynumber: 3.4 Consensus size: 29
45322 TTTAATTTAG
45332 TCAAATAAGGGTCTAACGTTTGTCAAAATGC
1 TCAAATAAGGGTCTAAC-TTTG-CAAAATGC
* * * **
45363 TCAAATAAGGGCCCGATCTTTG-AATTTGGC
1 TCAAATAAGGG-TCTAACTTTGCAAAAT-GC
45393 -CAAATAAGGGTCTAACATTTGCCAAAATGC
1 TCAAATAAGGGTCTAAC-TTTG-CAAAATGC
45423 TCAAATAAGGG
1 TCAAATAAGGG
45434 CCTATCTCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
28 3 0.05
29 17 0.31
30 4 0.07
31 28 0.51
32 3 0.05
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (29 bp):
TCAAATAAGGGTCTAACTTTGCAAAATGC
Found at i:45568 original size:31 final size:29
Alignment explanation
Indices: 45468--45632 Score: 124
Period size: 31 Copynumber: 5.6 Consensus size: 29
45458 AACTGAAACC
*
45468 AGGCCCTTATTTGAGCATTTTC-AACGTT
1 AGGCCCTTATTTGAGCATTTTCAAAAGTT
** *
45496 AGGCCCTTATTTG-GCAAAATT-AAAAGATC
1 AGGCCCTTATTTGAGC-ATTTTCAAAAG-TT
* *
45525 AGACTCTTATTTGAGCATTTTCAATAATGTT
1 AGGCCCTTATTTGAGCATTTTCAA-AA-GTT
** *
45556 AGGCCCTTATTTG-GCCAAATT-AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTCAAAAG-TT
* *
45585 AGACCCTTATTTGAGCATTTTGGCAAATGTT
1 AGGCCCTTATTTGAGCATTTT--CAAAAGTT
45616 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
45633 ATTAGCCAAA
Statistics
Matches: 104, Mismatches: 20, Indels: 23
0.71 0.14 0.16
Matches are distributed among these distances:
27 2 0.02
28 20 0.19
29 34 0.33
30 8 0.08
31 35 0.34
32 5 0.05
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (29 bp):
AGGCCCTTATTTGAGCATTTTCAAAAGTT
Found at i:45576 original size:60 final size:58
Alignment explanation
Indices: 45471--45633 Score: 247
Period size: 60 Copynumber: 2.7 Consensus size: 58
45461 TGAAACCAGG
*
45471 CCCTTATTTGAGCATTTTC-AACGTTAGGCCCTTATTTGGCAAAATTAAAAGATCAGA
1 CCCTTATTTGAGCATTTTCAAATGTTAGGCCCTTATTTGGCAAAATTAAAAGATCAGA
* *
45528 CTCTTATTTGAGCATTTTCAATAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGAGCATTTTC-A-AATGTTAGGCCCTTATTTGGCAAAATTAAAAGATCAGA
45588 CCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGAGCAA
1 CCCTTATTTGAGCATTTT--CAAATGTTAGGCCCTTATTTG-GCAA
45634 TTAGCCAAAA
Statistics
Matches: 95, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
57 18 0.19
60 72 0.76
61 4 0.04
62 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (58 bp):
CCCTTATTTGAGCATTTTCAAATGTTAGGCCCTTATTTGGCAAAATTAAAAGATCAGA
Found at i:45595 original size:29 final size:29
Alignment explanation
Indices: 45499--45597 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 29
45489 CAACGTTAGG
*
45499 CCCTTATTTGGCAAAATTAAAAGATCAGA
1 CCCTTATTTGGCCAAATTAAAAGATCAGA
* ** * *
45528 CTCTTATTTGAG-CATTTTCAATAATG-TTAGG
1 CCCTTATTTG-GCCAAATT-AA-AA-GATCAGA
45559 CCCTTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGGCCAAATTAAAAGATCAGA
45588 CCCTTATTTG
1 CCCTTATTTG
45598 AGCATTTTGG
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 1 0.02
29 27 0.51
30 6 0.11
31 18 0.34
32 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:49427 original size:30 final size:31
Alignment explanation
Indices: 49393--49529 Score: 179
Period size: 31 Copynumber: 4.5 Consensus size: 31
49383 TCTTTTTGTG
* * *
49393 CACGTGGCATGCCACGTGGCA-CTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACCTTTTGATA
*
49423 CACGTGGCGTGACACGTGTCA-CTTTTGATA
1 CACGTGGCGTGCCACGTGTCACCTTTTGATA
* *
49453 CACGTGGCGTGACACGTGTCACCTTTTGAAA
1 CACGTGGCGTGCCACGTGTCACCTTTTGATA
* *
49484 CACATGGCGTGCCACATGTCACCTTTTGATA
1 CACGTGGCGTGCCACGTGTCACCTTTTGATA
*
49515 CACGTGACGTGCCAC
1 CACGTGGCGTGCCAC
49530 CTTTTGATAC
Statistics
Matches: 95, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 47 0.49
31 48 0.51
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (31 bp):
CACGTGGCGTGCCACGTGTCACCTTTTGATA
Found at i:49529 original size:31 final size:31
Alignment explanation
Indices: 49393--49525 Score: 171
Period size: 30 Copynumber: 4.4 Consensus size: 31
49383 TCTTTTTGTG
* * * *
49393 CACGTGGCATGCCACGTGGCA-CTTTTGGTA
1 CACGTGGCGTGACACGTGTCACCTTTTGATA
49423 CACGTGGCGTGACACGTGTCA-CTTTTGATA
1 CACGTGGCGTGACACGTGTCACCTTTTGATA
*
49453 CACGTGGCGTGACACGTGTCACCTTTTGAAA
1 CACGTGGCGTGACACGTGTCACCTTTTGATA
* * *
49484 CACATGGCGTGCCACATGTCACCTTTTGATA
1 CACGTGGCGTGACACGTGTCACCTTTTGATA
*
49515 CACGTGACGTG
1 CACGTGGCGTG
49526 CCACCTTTTG
Statistics
Matches: 91, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
30 47 0.52
31 44 0.48
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.27
Consensus pattern (31 bp):
CACGTGGCGTGACACGTGTCACCTTTTGATA
Found at i:49530 original size:24 final size:24
Alignment explanation
Indices: 49503--49573 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
49493 TGCCACATGT
49503 CACCTTTTGATACACGTGACGTGC
1 CACCTTTTGATACACGTGACGTGC
49527 CACCTTTTGATACACGTGACGTGC
1 CACCTTTTGATACACGTGACGTGC
* *
49551 CACCTTTTGGTACACGTGGCGTG
1 CACCTTTTGATACACGTGACGTG
49574 TCACATGTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.18, C:0.28, G:0.24, T:0.30
Consensus pattern (24 bp):
CACCTTTTGATACACGTGACGTGC
Found at i:51705 original size:2 final size:2
Alignment explanation
Indices: 51698--51725 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
51688 TTAAAGAATA
51698 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
51726 TTAAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56021 original size:15 final size:16
Alignment explanation
Indices: 56003--56043 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
55993 GTTCGGGTAC
56003 TTCGGGTTCGTG-ATT
1 TTCGGGTTCGTGTATT
56018 TTCGGGTTCGTGTATT
1 TTCGGGTTCGTGTATT
*
56034 TTCTGGTTCG
1 TTCGGGTTCG
56044 GGTCCGAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.05, C:0.15, G:0.32, T:0.49
Consensus pattern (16 bp):
TTCGGGTTCGTGTATT
Found at i:56602 original size:31 final size:31
Alignment explanation
Indices: 56567--56638 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
56557 TAAATTGTAG
* *
56567 CAAATTAAAACAAAT-TAAGTATTAAATTAAA
1 CAAATTAAAA-AAATGCAAGCATTAAATTAAA
* ** *
56598 CAAATCATCAAAATGCAAGCCTTAAATTAAA
1 CAAATTAAAAAAATGCAAGCATTAAATTAAA
56629 CAAATTAAAA
1 CAAATTAAAA
56639 GCTAATGGAC
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.25
Consensus pattern (31 bp):
CAAATTAAAAAAATGCAAGCATTAAATTAAA
Found at i:56872 original size:16 final size:16
Alignment explanation
Indices: 56847--56881 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
56837 TCTCGAGTTT
*
56847 GGGTATTTTCGGGTTC
1 GGGTAATTTCGGGTTC
56863 GGGTAATTTCGGGTTC
1 GGGTAATTTCGGGTTC
56879 GGG
1 GGG
56882 ACGTTGACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.09, C:0.11, G:0.43, T:0.37
Consensus pattern (16 bp):
GGGTAATTTCGGGTTC
Found at i:58692 original size:27 final size:27
Alignment explanation
Indices: 58662--58714 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
58652 TCTGAAAAAC
58662 AAGGAAAATGGACAATTAAAAAGGAAT
1 AAGGAAAATGGACAATTAAAAAGGAAT
58689 AAGGAAAATGGACAATTAAAAAGGAA
1 AAGGAAAATGGACAATTAAAAAGGAA
58715 CAAAGGGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.60, C:0.04, G:0.23, T:0.13
Consensus pattern (27 bp):
AAGGAAAATGGACAATTAAAAAGGAAT
Found at i:58954 original size:43 final size:44
Alignment explanation
Indices: 58845--58977 Score: 232
Period size: 44 Copynumber: 3.0 Consensus size: 44
58835 AATGACAGGT
58845 GACCTTACATATCAACCTTTTTTTTTTGGTAAATACAAAAGACCA
1 GACCTTACATATCAA-CTTTTTTTTTTGGTAAATACAAAAGACCA
*
58890 GACCTTACATATCAACTTTTTTTTTTGCTAAATACAAAAGACCA
1 GACCTTACATATCAACTTTTTTTTTTGGTAAATACAAAAGACCA
*
58934 GACCTTACATATCAAC-TTTTTTTTTGGTAAATACGAAAGACCA
1 GACCTTACATATCAACTTTTTTTTTTGGTAAATACAAAAGACCA
58977 G
1 G
58978 CTGCATCATA
Statistics
Matches: 85, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
43 26 0.31
44 44 0.52
45 15 0.18
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (44 bp):
GACCTTACATATCAACTTTTTTTTTTGGTAAATACAAAAGACCA
Found at i:61566 original size:20 final size:20
Alignment explanation
Indices: 61537--61576 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61527 GTCTATTGGC
*
61537 TTAATTAAATCCTTCCATAT
1 TTAATCAAATCCTTCCATAT
*
61557 TTAATCAAATCCTTGCATAT
1 TTAATCAAATCCTTCCATAT
61577 CTAAATCACA
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:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (20 bp):
TTAATCAAATCCTTCCATAT
Found at i:64834 original size:56 final size:56
Alignment explanation
Indices: 64724--64835 Score: 154
Period size: 56 Copynumber: 2.0 Consensus size: 56
64714 AAAAAGGAGC
* * *
64724 AGAGTCAAGATAATGGTAATCAGTCAATCAGTAAATCAGTAAAAAAAGATTAATCA
1 AGAGTCAAGATAATAGTAATCAGTAAATCAGTAAATCAGTAAAAAAAGAGTAATCA
* * *
64780 AGAGTCAAGGTAATAGTAATCAGTAAATCAGT-AATCAAGTAAAAAGATAGTAATCA
1 AGAGTCAAGATAATAGTAATCAGTAAATCAGTAAATC-AGTAAAAAAAGAGTAATCA
64836 GTAATTTGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
55 4 0.08
56 45 0.92
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (56 bp):
AGAGTCAAGATAATAGTAATCAGTAAATCAGTAAATCAGTAAAAAAAGAGTAATCA
Found at i:64855 original size:71 final size:70
Alignment explanation
Indices: 64774--64910 Score: 170
Period size: 71 Copynumber: 1.9 Consensus size: 70
64764 AAAAAAAGAT
* *
64774 TAATCAAGAGTCAAGGTAATAG-TAATCAGTAAATCAGTAATCAA-GTAAAAAGATAGTAATCAG
1 TAATCAAGAGTCAAGGTAAGAGATAATCAGTAAATAAG-AATCAAGGT-AAAA-ATAGTAATCAG
64837 TAATTTGA
63 TAATTTGA
* * * *
64845 TAATTAAGAGTTAAGGTAAGAGATTAATCAGTAATTAAGAGTCAAGGTAAAAATAGTAATCAGTA
1 TAATCAAGAGTCAAGGTAAGAGA-TAATCAGTAAATAAGAATCAAGGTAAAAATAGTAATCAGTA
64910 A
65 A
64911 ATCAGTAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
71 33 0.58
72 9 0.16
73 15 0.26
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (70 bp):
TAATCAAGAGTCAAGGTAAGAGATAATCAGTAAATAAGAATCAAGGTAAAAATAGTAATCAGTAA
TTTGA
Found at i:64910 original size:32 final size:31
Alignment explanation
Indices: 64845--64910 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
64835 AGTAATTTGA
* *
64845 TAATTAAGAGTTAAGGTAAGAGATTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAATTAATCAG
64876 TAATTAAGAGTCAAGGTAA-AAATAGTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAAT--TAATCAG
64908 TAA
1 TAA
64911 ATCAGTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 3 0.10
31 18 0.58
32 10 0.32
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAGAAATTAATCAG
Found at i:64920 original size:71 final size:71
Alignment explanation
Indices: 64774--64929 Score: 160
Period size: 71 Copynumber: 2.2 Consensus size: 71
64764 AAAAAAAGAT
* * *
64774 TAATCAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGATAGTAATCAGTA
1 TAATTAAGAGTCAAGGTAAGAGTAATCAGTAAATAAGTAATCAAGTAAAAAGATAGTAATCAGTA
**
64839 ATTTGA
66 ATCAGA
* * *
64845 TAATTAAGAGTTAAGGTAAGAGATTAATCAGTAATTAAG-AGTCAAGGT-AAAA-ATAGTAATCA
1 TAATTAAGAGTCAAGGTAAGAG--TAATCAGTAAATAAGTAATCAA-GTAAAAAGATAGTAATCA
64907 GTAAATCAG-
63 GT-AATCAGA
64916 TAATT-AGAAGTCAA
1 TAATTAAG-AGTCAA
64930 TGGATTAGTT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
70 2 0.03
71 41 0.58
72 13 0.18
73 15 0.21
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (71 bp):
TAATTAAGAGTCAAGGTAAGAGTAATCAGTAAATAAGTAATCAAGTAAAAAGATAGTAATCAGTA
ATCAGA
Found at i:65141 original size:35 final size:35
Alignment explanation
Indices: 65096--65190 Score: 145
Period size: 35 Copynumber: 2.7 Consensus size: 35
65086 TAAAATGATA
65096 AAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGGT
1 AAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGGT
* *
65131 AAAAAGTAAAGAATAATCAGTAAAGGAAGAATGGT
1 AAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGGT
* * *
65166 AAAGAGTAAAGGGTAATCAGCAAAA
1 AAAAAGTAAAGAGTAATCAGTAAAA
65191 AGTAAAAAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.57, C:0.04, G:0.23, T:0.16
Consensus pattern (35 bp):
AAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGGT
Found at i:65271 original size:49 final size:50
Alignment explanation
Indices: 65170--65274 Score: 133
Period size: 49 Copynumber: 2.1 Consensus size: 50
65160 AATGGTAAAG
* *
65170 AGTAAAGGGTAATCAGCAAAAAGTAAAAAGATAATCAGTAAAGAATAAAAT
1 AGTAAAAGGTAATCAACAAAAAGT-AAAAGATAATCAGTAAAGAATAAAAT
* * *
65221 AGTAAAAGGTAATCAATAAAAAGT-AATGATAATCAGTAAA-AGGTAAAAT
1 AGTAAAAGGTAATCAACAAAAAGTAAAAGATAATCAGTAAAGA-ATAAAAT
65270 AGTAA
1 AGTAA
65275 TCAGTAAGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
48 1 0.02
49 26 0.54
51 21 0.44
ACGTcount: A:0.58, C:0.05, G:0.17, T:0.20
Consensus pattern (50 bp):
AGTAAAAGGTAATCAACAAAAAGTAAAAGATAATCAGTAAAGAATAAAAT
Found at i:65295 original size:21 final size:21
Alignment explanation
Indices: 65245--65341 Score: 104
Period size: 21 Copynumber: 4.5 Consensus size: 21
65235 AATAAAAAGT
* * *
65245 AATGATAATCAGTAAAAGGTAA
1 AATGGTAATCAGTAAGA-GCAA
*
65267 AATAGTAATCAGTAAGAGCAA
1 AATGGTAATCAGTAAGAGCAA
* *
65288 AATGGTAATCAATGAGAGCAA
1 AATGGTAATCAGTAAGAGCAA
* *
65309 AACGGTAATCAGTAATCAGCAA
1 AATGGTAATCAGTAA-GAGCAA
65331 AATGGTAATCA
1 AATGGTAATCA
65342 TTAAAAAGTA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
21 33 0.53
22 29 0.47
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (21 bp):
AATGGTAATCAGTAAGAGCAA
Found at i:65359 original size:22 final size:22
Alignment explanation
Indices: 65334--65376 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
65324 TCAGCAAAAT
* *
65334 GGTAATCATTAAAAAGTAAGAA
1 GGTAACCAGTAAAAAGTAAGAA
*
65356 GGTAACCAGTAAAGAGTAAGA
1 GGTAACCAGTAAAAAGTAAGA
65377 TGATAAAGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.07, G:0.23, T:0.19
Consensus pattern (22 bp):
GGTAACCAGTAAAAAGTAAGAA
Found at i:65403 original size:15 final size:15
Alignment explanation
Indices: 65385--65462 Score: 59
Period size: 15 Copynumber: 5.9 Consensus size: 15
65375 GATGATAAAG
65385 AGTAAAATAGTAATC
1 AGTAAAATAGTAATC
*
65400 AGTAAAAGA-TAATC
1 AGTAAAATAGTAATC
65414 AGT--AA-AG--A--
1 AGTAAAATAGTAATC
65422 -GTAAAATAGTAATC
1 AGTAAAATAGTAATC
*
65436 AGTAAAATGGTAATC
1 AGTAAAATAGTAATC
*
65451 ATTAAAA-AGTAA
1 AGTAAAATAGTAA
65463 GAAGGTAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 19
0.68 0.05 0.26
Matches are distributed among these distances:
7 2 0.04
9 2 0.04
10 3 0.06
11 1 0.02
12 3 0.06
14 12 0.24
15 27 0.54
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.24
Consensus pattern (15 bp):
AGTAAAATAGTAATC
Found at i:65414 original size:14 final size:15
Alignment explanation
Indices: 65385--65425 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
65375 GATGATAAAG
*
65385 AGTAAAATAGTAATC
1 AGTAAAAGAGTAATC
65400 AGTAAAAGA-TAATC
1 AGTAAAAGAGTAATC
65414 AGT-AAAGAGTAA
1 AGTAAAAGAGTAA
65426 AATAGTAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 5 0.21
14 11 0.46
15 8 0.33
ACGTcount: A:0.56, C:0.05, G:0.17, T:0.22
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:65417 original size:51 final size:52
Alignment explanation
Indices: 65348--65543 Score: 184
Period size: 51 Copynumber: 3.7 Consensus size: 52
65338 ATCATTAAAA
* * *
65348 AGTAAGAAGGTAACCAGTAAAGAGTAAGAT-GATAAAGAGTAAAATAGTAATC
1 AGTAAGAAGATAATCAGTAAAGAGTAAAATAG-TAAAGAGTAAAATAGTAATC
** *
65400 AGTAA-AAGATAATCAGTAAAGAGTAAAATAGTAATCAGTAAAATGGTAATC
1 AGTAAGAAGATAATCAGTAAAGAGTAAAATAGTAAAGAGTAAAATAGTAATC
* *
65451 ATTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATCAGCAAAGAGTAAAATAGTAATC
1 -------AGTAAGAAGATAATCAGTAAAGAGTAAAAT-AGTAAAGAGTAAAATAGTAATC
* * *
65511 AATAA-AAGATAATCAG-CAAGAGTAAAACAGTAA
1 AGTAAGAAGATAATCAGTAAAGAGTAAAATAGTAA
65544 CCAGTAAGAG
Statistics
Matches: 118, Mismatches: 16, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
50 4 0.03
51 48 0.41
52 16 0.14
53 4 0.03
58 5 0.04
59 23 0.19
60 18 0.15
ACGTcount: A:0.55, C:0.07, G:0.19, T:0.20
Consensus pattern (52 bp):
AGTAAGAAGATAATCAGTAAAGAGTAAAATAGTAAAGAGTAAAATAGTAATC
Found at i:65426 original size:36 final size:36
Alignment explanation
Indices: 65380--65550 Score: 202
Period size: 36 Copynumber: 4.7 Consensus size: 36
65370 AGTAAGATGA
65380 TAAAGAGTAAAATAGTAATCAGTAAAAGATAATCAG
1 TAAAGAGTAAAATAGTAATCAGTAAAAGATAATCAG
* *
65416 TAAAGAGTAAAATAGTAATCAGTAAAATGGTAATCAT
1 TAAAGAGTAAAATAGTAATCAGTAAAA-GATAATCAG
* * *
65453 TAAAAAGTAAGAA-GGTAATCAGTAAAGAGTAAAATCAG
1 TAAAGAGTAA-AATAGTAATCAGTAAA-AG-ATAATCAG
* *
65491 CAAAGAGTAAAATAGTAATCAATAAAAGATAATCAG
1 TAAAGAGTAAAATAGTAATCAGTAAAAGATAATCAG
* * *
65527 -CAAGAGTAAAACAGTAACCAGTAA
1 TAAAGAGTAAAATAGTAATCAGTAA
65551 GAGCAAAGTG
Statistics
Matches: 114, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
35 20 0.18
36 34 0.30
37 33 0.29
38 27 0.24
ACGTcount: A:0.55, C:0.08, G:0.17, T:0.20
Consensus pattern (36 bp):
TAAAGAGTAAAATAGTAATCAGTAAAAGATAATCAG
Found at i:65437 original size:22 final size:21
Alignment explanation
Indices: 65400--65486 Score: 69
Period size: 22 Copynumber: 4.3 Consensus size: 21
65390 AATAGTAATC
65400 AGTAAAAGATAATCAGTAAAG
1 AGTAAAAGATAATCAGTAAAG
*
65421 AGTAAAATAGTAATCAGTAAA-
1 AGTAAAAGA-TAATCAGTAAAG
* * *
65442 A-T----GGTAATCATTAAAA
1 AGTAAAAGATAATCAGTAAAG
*
65458 AGTAAGAAGGTAATCAGTAAAG
1 AGTAA-AAGATAATCAGTAAAG
65480 AGTAAAA
1 AGTAAAA
65487 TCAGCAAAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
15 10 0.19
16 1 0.02
17 1 0.02
20 1 0.02
21 11 0.21
22 28 0.54
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.22
Consensus pattern (21 bp):
AGTAAAAGATAATCAGTAAAG
Found at i:65451 original size:110 final size:110
Alignment explanation
Indices: 65318--65550 Score: 369
Period size: 110 Copynumber: 2.1 Consensus size: 110
65308 AAACGGTAAT
* * * *
65318 CAGTAATCAGCAAAATGGTAATCATTAAAAAGTAAGAAGGTAACCAGTAAAGAGTAAGATGA-TA
1 CAGTAATCAGTAAAATGGTAATCATTAAAAAGTAAGAAGGTAACCAGTAAAGAGTAAAATCAGCA
*
65382 AAGAGTAAAATAGTAATCAGTAAAAGATAATCAGTAAAGAGTAAAA
66 AAGAGTAAAATAGTAATCAATAAAAGATAATCAG-AAAGAGTAAAA
* *
65428 TAGTAATCAGTAAAATGGTAATCATTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATCAGCA
1 CAGTAATCAGTAAAATGGTAATCATTAAAAAGTAAGAAGGTAACCAGTAAAGAGTAAAATCAGCA
*
65493 AAGAGTAAAATAGTAATCAATAAAAGATAATCAGCAAGAGTAAAA
66 AAGAGTAAAATAGTAATCAATAAAAGATAATCAGAAAGAGTAAAA
*
65538 CAGTAACCAGTAA
1 CAGTAATCAGTAA
65551 GAGCAAAGTG
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
110 78 0.70
111 34 0.30
ACGTcount: A:0.54, C:0.08, G:0.18, T:0.20
Consensus pattern (110 bp):
CAGTAATCAGTAAAATGGTAATCATTAAAAAGTAAGAAGGTAACCAGTAAAGAGTAAAATCAGCA
AAGAGTAAAATAGTAATCAATAAAAGATAATCAGAAAGAGTAAAA
Found at i:65488 original size:16 final size:16
Alignment explanation
Indices: 65469--65508 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
65459 GTAAGAAGGT
65469 AATCAGTAAAGAGTAA
1 AATCAGTAAAGAGTAA
*
65485 AATCAGCAAAGAGTAA
1 AATCAGTAAAGAGTAA
65501 AAT-AGTAA
1 AATCAGTAA
65509 TCAATAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.17
Consensus pattern (16 bp):
AATCAGTAAAGAGTAA
Found at i:65518 original size:59 final size:59
Alignment explanation
Indices: 65400--65517 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 59
65390 AATAGTAATC
* ** *
65400 AGTAA-AAGATAATCAGTAAAGAGTAAAATAGTAATCAGTAAAATGGTAATCATTAAAA
1 AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAAAGAGTAAAATAGTAATCATTAAAA
* *
65458 AGTAAGAAGGTAATCAGTAAAGAGTAAAATCAGCAAAGAGTAAAATAGTAATCAATAAAA
1 AGTAAGAAGGTAATCAGTAAAGAGTAAAAT-AGTAAAGAGTAAAATAGTAATCATTAAAA
65518 GATAATCAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 5 0.10
59 23 0.44
60 24 0.46
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.21
Consensus pattern (59 bp):
AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAAAGAGTAAAATAGTAATCATTAAAA
Found at i:65690 original size:13 final size:13
Alignment explanation
Indices: 65674--65720 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
65664 GGTAATAAAT
65674 AAAAGAGAGTAAG
1 AAAAGAGAGTAAG
* *
65687 AAAAGAGTAATTAG
1 AAAAGAG-AGTAAG
65701 TAAAA-AGAGTAAG
1 -AAAAGAGAGTAAG
65714 AAAAGAG
1 AAAAGAG
65721 TAAAAATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.13
Consensus pattern (13 bp):
AAAAGAGAGTAAG
Found at i:66342 original size:21 final size:21
Alignment explanation
Indices: 66318--66359 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
66308 ATGTGCGGTC
66318 ATGTGACCGGATGTTTGTTAG
1 ATGTGACCGGATGTTTGTTAG
66339 ATGTGACCGGATGTTTGTTAG
1 ATGTGACCGGATGTTTGTTAG
66360 TGGAGGGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.10, G:0.33, T:0.38
Consensus pattern (21 bp):
ATGTGACCGGATGTTTGTTAG
Found at i:69159 original size:26 final size:26
Alignment explanation
Indices: 69123--69198 Score: 107
Period size: 28 Copynumber: 2.8 Consensus size: 26
69113 ACCAGATCAT
*
69123 ATTAAACTTCCATATTATTAATATAA
1 ATTAAACTTCCATATTATTAATAAAA
* *
69149 ATTAAACTTCCATATTCAGTCAAAAAAA
1 ATTAAACTTCCATATT-A-TTAATAAAA
69177 ATTAAACTTCCATATTATTAAT
1 ATTAAACTTCCATATTATTAAT
69199 TTGAGATGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
26 19 0.44
27 2 0.05
28 22 0.51
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.38
Consensus pattern (26 bp):
ATTAAACTTCCATATTATTAATAAAA
Found at i:71198 original size:60 final size:60
Alignment explanation
Indices: 71117--71230 Score: 194
Period size: 60 Copynumber: 1.9 Consensus size: 60
71107 GGGTTGAGTG
* *
71117 GAAGGAATTCAATACCTTTTATACAAGATCTCAGGTTCGAATTTTATTAATAAAGAAGTA
1 GAAGAAATTCAATACCTTTTATACAAGATCTCAGGTTCAAATTTTATTAATAAAGAAGTA
71177 GAAGAAATTCAA-AGCCTTTTATACAAGATCTCAGGTTCAAATTTTATTAATAAA
1 GAAGAAATTCAATA-CCTTTTATACAAGATCTCAGGTTCAAATTTTATTAATAAA
71231 AAAATAAACC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
59 1 0.02
60 50 0.98
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (60 bp):
GAAGAAATTCAATACCTTTTATACAAGATCTCAGGTTCAAATTTTATTAATAAAGAAGTA
Found at i:74481 original size:18 final size:18
Alignment explanation
Indices: 74460--74502 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 18
74450 TACAAGCAAG
74460 AACATTATTACAGGGAGA
1 AACATTATTACAGGGAGA
*
74478 AAC---ATTACAGGTAGA
1 AACATTATTACAGGGAGA
74493 AACATTATTA
1 AACATTATTA
74503 GGCTTTGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
15 14 0.67
18 7 0.33
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.26
Consensus pattern (18 bp):
AACATTATTACAGGGAGA
Found at i:74484 original size:15 final size:15
Alignment explanation
Indices: 74466--74499 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
74456 CAAGAACATT
74466 ATTACAGGGAGAAAC
1 ATTACAGGGAGAAAC
*
74481 ATTACAGGTAGAAAC
1 ATTACAGGGAGAAAC
74496 ATTA
1 ATTA
74500 TTAGGCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.21
Consensus pattern (15 bp):
ATTACAGGGAGAAAC
Found at i:77570 original size:18 final size:18
Alignment explanation
Indices: 77532--77571 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
77522 AAGAAGATTC
*
77532 TTTTTTTTTTCTAACTTT
1 TTTTTTTTTTCTAACTCT
77550 TTTTTTTGTTTCT-ACTCT
1 TTTTTTT-TTTCTAACTCT
77568 TTTT
1 TTTT
77572 CATTGTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTTTTTTTCTAACTCT
Found at i:86184 original size:26 final size:26
Alignment explanation
Indices: 86130--86184 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
86120 ACCCACATTT
* *
86130 AAAATTTAACATATTAATAATACATA
1 AAAAATTAACATATTAATAACACATA
86156 AAAAATTAA-ATATTGAATGAACACA-A
1 AAAAATTAACATATT-AAT-AACACATA
86182 AAA
1 AAA
86185 CATAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 5 0.20
26 15 0.60
27 5 0.20
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (26 bp):
AAAAATTAACATATTAATAACACATA
Found at i:86735 original size:2 final size:2
Alignment explanation
Indices: 86730--86759 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
86720 TTGAAAAAAA
86730 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
86760 GCTCTAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89162 original size:142 final size:142
Alignment explanation
Indices: 88906--89175 Score: 488
Period size: 142 Copynumber: 1.9 Consensus size: 142
88896 CAAATATTTG
* *
88906 TTCACATTTTTTAAACATAAAATCCGATCTAACCTGATTCAAATTCGATACACAGTTTAACCAAT
1 TTCACATTTTTTAAACATAAAATCCGATCTAACCCGATTCAAATCCGATACACAGTTTAACCAAT
*
88971 CAGACCGACCAGTATGGTTTCAAAAACATTTGGGGCATGAAATAAATAAATAAACTTGTATATTC
66 CAGACCAACCAGTATGGTTTCAAAAACATTTGGGGCATGAAATAAATAAATAAACTTGTATATTC
89036 GAAAGAAGAGCT
131 GAAAGAAGAGCT
89048 TTCACATTTTTTAAACATAAAATCCGATCTAACCCGATTCAAATCCGATACACAGTTTAACCAAT
1 TTCACATTTTTTAAACATAAAATCCGATCTAACCCGATTCAAATCCGATACACAGTTTAACCAAT
*
89113 CAGACCAACCAGT-TCGGTTTCAAAAATATTTGGGGCATGAAATAAATAAATAAACTTGTATAT
66 CAGACCAACCAGTAT-GGTTTCAAAAACATTTGGGGCATGAAATAAATAAATAAACTTGTATAT
89176 CTATATCTGT
Statistics
Matches: 123, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
141 1 0.01
142 122 0.99
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (142 bp):
TTCACATTTTTTAAACATAAAATCCGATCTAACCCGATTCAAATCCGATACACAGTTTAACCAAT
CAGACCAACCAGTATGGTTTCAAAAACATTTGGGGCATGAAATAAATAAATAAACTTGTATATTC
GAAAGAAGAGCT
Found at i:89396 original size:23 final size:23
Alignment explanation
Indices: 89368--89413 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
89358 TTTTTACCAT
89368 TTTACTATTTTCAATAAAATTGG
1 TTTACTATTTTCAATAAAATTGG
89391 TTTACTATTTTCAATAAAATTGG
1 TTTACTATTTTCAATAAAATTGG
89414 AGATATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (23 bp):
TTTACTATTTTCAATAAAATTGG
Found at i:91740 original size:7 final size:7
Alignment explanation
Indices: 91728--91755 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
91718 GGTCTAGGAC
91728 AAACATG
1 AAACATG
91735 AAACATG
1 AAACATG
91742 AAACATG
1 AAACATG
91749 AAACATG
1 AAACATG
91756 TTAAGATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (7 bp):
AAACATG
Found at i:110139 original size:42 final size:41
Alignment explanation
Indices: 110092--110396 Score: 253
Period size: 42 Copynumber: 7.2 Consensus size: 41
110082 CGACAGATTA
110092 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGAC-TTTTGTT
*
110134 AGTCGTTGCGAAATCTTAAACTTTTCGCGACGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
* * * * * * **
110175 AGTCGTTGCTTATTATATTTTACAAATTGATTTTCGTAGCGAC-CTTGAA
1 AGTCGTTGC-GA--A-ATCTT--AAA---CTTTTCGCAACGACTTTTGTT
* * * * * * *** *
110224 AGTCGCTACAGAAAAACATGATTACTTTT-GAAACGACAGAT-TA
1 AGTCGTTGC-G-AAATC-TTA-AACTTTTCGCAACGACTTTTGTT
*
110267 AGTCGTTGTGAAATCTTAAAC-TTTCGCAACGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
110307 AGTCGTTGCGAAATCTT--ACTTTTCGCAACGACTTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGAC-TTTTGTT
110347 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
110388 AGTCGTTGC
1 AGTCGTTGC
110397 TTAATATATT
Statistics
Matches: 208, Mismatches: 36, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
38 5 0.02
39 22 0.11
40 43 0.21
41 36 0.17
42 50 0.24
43 13 0.06
44 6 0.03
45 4 0.02
46 1 0.00
47 5 0.02
48 2 0.01
49 10 0.05
50 11 0.05
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (41 bp):
AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
Found at i:110294 original size:174 final size:171
Alignment explanation
Indices: 109946--110355 Score: 608
Period size: 174 Copynumber: 2.4 Consensus size: 171
109936 ACCCTTTTTA
* * * * * * * *
109946 CAACGACTTCTATTAGTCGCTGCGAATTCATAGTCTTTTCGCAACGACTTCTGCTAGTCGTTGTT
1 CAACGACTTTTGTTAGTCGTTGCGAAATCTTA--CTTTTCGCAACGACTTTTGTTAGTCGTTGCT
* * *
110011 TAATATATTTTACAAATTTATTTTTGTAGCATCCTTGAAAGTCGCTACAAAAAACATGATTTCTT
64 TAATATATTTTACAAATTGATTTTCGTAGCATCCTTGAAAGTCGCTACAAAAAACATGATTACTT
110076 TTGAAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTTCG
129 TTGAAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTTCG
*
110119 CAACGACTTTTTGTTAGTCGTTGCGAAATCTTAAACTTTTCGCGACGACTTTTGTTAGTCGTTGC
1 CAACGAC-TTTTGTTAGTCGTTGCGAAATCTT--ACTTTTCGCAACGACTTTTGTTAGTCGTTGC
*
110184 TTATTATATTTTACAAATTGATTTTCGTAGCGA-CCTTGAAAGTCGCTACAGAAAAACATGATTA
63 TTAATATATTTTACAAATTGATTTTCGTAGC-ATCCTTGAAAGTCGCTACA-AAAAACATGATTA
*
110248 CTTTTGAAACGACAGATTAAGTCGTTGTGAAATCTTAAAC-TTTCG
126 CTTTTGAAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTTCG
110293 CAACGACTTTTGTTAGTCGTTGCGAAATCTTACTTTTCGCAACGACTTTTTGTTAGTCGTTGC
1 CAACGACTTTTGTTAGTCGTTGCGAAATCTTACTTTTCGCAACGAC-TTTTGTTAGTCGTTGC
110356 GAAATCTTAA
Statistics
Matches: 216, Mismatches: 15, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
171 14 0.06
172 16 0.07
173 31 0.14
174 102 0.47
175 52 0.24
176 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (171 bp):
CAACGACTTTTGTTAGTCGTTGCGAAATCTTACTTTTCGCAACGACTTTTGTTAGTCGTTGCTTA
ATATATTTTACAAATTGATTTTCGTAGCATCCTTGAAAGTCGCTACAAAAAACATGATTACTTTT
GAAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTTCG
Found at i:110320 original size:40 final size:41
Alignment explanation
Indices: 110267--110396 Score: 221
Period size: 40 Copynumber: 3.2 Consensus size: 41
110257 CGACAGATTA
*
110267 AGTCGTTGTGAAATCTTAAAC-TTTCGCAACGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
110307 AGTCGTTGCGAAATCTT--ACTTTTCGCAACGACTTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGAC-TTTTGTT
110347 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
110388 AGTCGTTGC
1 AGTCGTTGC
110397 TTAATATATT
Statistics
Matches: 85, Mismatches: 1, Indels: 7
0.91 0.01 0.08
Matches are distributed among these distances:
38 2 0.02
39 12 0.14
40 40 0.47
41 16 0.19
42 15 0.18
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (41 bp):
AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
Found at i:110355 original size:213 final size:211
Alignment explanation
Indices: 110092--110525 Score: 656
Period size: 213 Copynumber: 2.0 Consensus size: 211
110082 CGACAGATTA
110092 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTTGTTAGTCGTTGCGAAATCTTAAACTT
1 AGTCGTTGCGAAATCTT-AACTTTTCGCAACGACTTTTTGTTAGTCGTTGCGAAATCTTAAACTT
* * * ** * * *
110157 TTCGCGACGACTTTTGTTAGTCGTTGCTTATTATATTTTACAAATTGATTTTCGTAGCGACCTTG
65 TTCGCAACGACTTTTGTTAGTCGTTGCTTAATATATTTTACAAATTGAATTTCACAACGACATTA
*
110222 AAAGTCGCTACAGAAAAACATGATTACTTTTGAAACGACAGATTAAGTCGTTGTGAAATCTTAAA
130 AAAGTCGCTACA-AAAAACATGATTACTTTTGAAACGACAAATTAA---GTTGTGAAATCTTAAA
* * *
110287 CT-TTCGCAACGACTTTTGTT
191 CTATTCACAACAACTTCTGTT
110307 AGTCGTTGCGAAATCTT-ACTTTTCGCAACGACTTTTTGTTAGTCGTTGCGAAATCTTAAACTTT
1 AGTCGTTGCGAAATCTTAACTTTTCGCAACGACTTTTTGTTAGTCGTTGCGAAATCTTAAACTTT
110371 TCGCAACGACTTTTGTTAGTCGTTGCTTAATATATTTTACAAATTGAATTTCACAACGACATTAA
66 TCGCAACGACTTTTGTTAGTCGTTGCTTAATATATTTTACAAATTGAATTTCACAACGACATTAA
* * **
110436 AAGTTGCTACAAAAGACATGATTACTTTTGAAACGACAAATTAAGTTGTGAAATCTTATTCTATT
131 AAGTCGCTACAAAAAACATGATTACTTTTGAAACGACAAATTAAGTTGTGAAATCTTAAACTATT
*
110501 TACAACAACTTCTGTT
196 CACAACAACTTCTGTT
110517 AGTCGTTGC
1 AGTCGTTGC
110526 TTAATATATT
Statistics
Matches: 201, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
209 16 0.08
210 23 0.11
212 31 0.15
213 114 0.57
215 17 0.08
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (211 bp):
AGTCGTTGCGAAATCTTAACTTTTCGCAACGACTTTTTGTTAGTCGTTGCGAAATCTTAAACTTT
TCGCAACGACTTTTGTTAGTCGTTGCTTAATATATTTTACAAATTGAATTTCACAACGACATTAA
AAGTCGCTACAAAAAACATGATTACTTTTGAAACGACAAATTAAGTTGTGAAATCTTAAACTATT
CACAACAACTTCTGTT
Done.