Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024619.1 Corchorus olitorius cultivar O-4 contig24652, 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: 28910
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:504 original size:23 final size:23
Alignment explanation
Indices: 466--509 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
456 TCATCCTCCC
* *
466 TTTCATCTTTCTTTTTCTTTTCA
1 TTTCATCATTCATTTTCTTTTCA
*
489 TTTCATCATTCATTTTTTTTT
1 TTTCATCATTCATTTTCTTTT
510 TGGGCCTAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTCATCATTCATTTTCTTTTCA
Found at i:2267 original size:344 final size:337
Alignment explanation
Indices: 1583--2238 Score: 822
Period size: 344 Copynumber: 1.9 Consensus size: 337
1573 AATCCTATCA
* * *
1583 GTTATAAAGGTTATGGAAAACATTATATTACTATCTAGATACAAGTAATCTTACATCCTTATTAA
1 GTTATAAAGGTTATGGAAAACATTATAGTACTATCTAGATACAAATAACCTTACATCCTTATTAA
1648 TTTAAGTAACTTTTTATCAATAATATTGAAAGTTACCAATTTTATTACTTAAGTAATCTACTAAA
66 TTTAAGTAACTTTTTATCAATAATA-T-AAAGTTACCAATTTTATTACTTAAGT-ATCTACTAAA
* *
1713 AAAGCTATAAAAGTTATTAAAATTGTATTTACCATTTGTTACATTCTTAATAACATTAGTAAACT
128 AAAGCTATAAAAGTTATTAAAATTGTATTTACCAATTCTTACATTCTTAATAACATTAGTAAACT
* *
1778 TTCATCAATGGTGAGGATTTACCGTTTTTTCTCAAAAGTTATCGAAAAACCTATGATAATCATAA
193 TTCATCAATGGTGAAGATTTACCGTTTTTTCTCAAAAGTTATCAAAAAACCTATGATAATCATAA
* * *
1843 AAAAGGTACGGTACTATCAACTTATTCAATGACCTTACATTATAAAGGTATAATACTGATTTTCT
258 AAAAGGTACAGTACTATCAACTAATTCAATAACCTTACATTAT--A--TATAATAC-GATTTTCT
1908 TATCTAAGATTTCTTAAAAG
318 TATCTAAGATTTCTTAAAAG
1928 GTTATAAAGGTTATGG-AAACATTATAGTACTATCTAGATTA-AAATAACCTTACATCCTTATTA
1 GTTATAAAGGTTATGGAAAACATTATAGTACTATCTAGA-TACAAATAACCTTACATCCTTATTA
* * *
1991 ATTTTAGTAATTTTTTATCATTAATA-AAAGTTACCAATTTTATTACTTAAGT-T-TACTAAAAA
65 ATTTAAGTAACTTTTTATCAATAATATAAAGTTACCAATTTTATTACTTAAGTATCTACTAAAAA
* *
2053 AGCTATAAAAGTTATTATAATTGTATTTACCAATTCTTATATTCTTAATAACATTAGTGTAACAT
130 AGCTATAAAAGTTATTAAAATTGTATTTACCAATTCTTACATTC-T--T---A--A---TAACA-
* * *
2118 TAGTAGTAAACTTTCGTCAATGGTGAATATTTACCATTTTTTTCTCAAAAGTTA-CTAAAAAACC
183 T--TAGTAAACTTTCATCAATGGTGAAGATTTACC-GTTTTTTCTCAAAAGTTATC-AAAAAACC
* * *
2182 TAT-ATAATGATCATAAAAGAGTTATAGTACTATCAACTAATTCAATAACCTTACATT
244 TATGAT-A--ATCATAAAAAAGGTACAGTACTATCAACTAATTCAATAACCTTACATT
2239 TTTTGTAGTT
Statistics
Matches: 270, Mismatches: 21, Indels: 30
0.84 0.07 0.09
Matches are distributed among these distances:
338 49 0.18
339 2 0.01
341 27 0.10
344 65 0.24
345 18 0.07
346 1 0.00
349 5 0.02
350 1 0.00
352 32 0.12
353 28 0.10
355 42 0.16
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (337 bp):
GTTATAAAGGTTATGGAAAACATTATAGTACTATCTAGATACAAATAACCTTACATCCTTATTAA
TTTAAGTAACTTTTTATCAATAATATAAAGTTACCAATTTTATTACTTAAGTATCTACTAAAAAA
GCTATAAAAGTTATTAAAATTGTATTTACCAATTCTTACATTCTTAATAACATTAGTAAACTTTC
ATCAATGGTGAAGATTTACCGTTTTTTCTCAAAAGTTATCAAAAAACCTATGATAATCATAAAAA
AGGTACAGTACTATCAACTAATTCAATAACCTTACATTATATATAATACGATTTTCTTATCTAAG
ATTTCTTAAAAG
Found at i:9301 original size:20 final size:20
Alignment explanation
Indices: 9262--9303 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
9252 CTCGGCTCGA
*
9262 GAAAAATTCGAGTTCGGCTC
1 GAAAAATTCGAGTCCGGCTC
9282 GAAAAATTCGAG-CCGAGCTC
1 GAAAAATTCGAGTCCG-GCTC
9302 GA
1 GA
9304 GCTCGAGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (20 bp):
GAAAAATTCGAGTCCGGCTC
Found at i:15753 original size:14 final size:12
Alignment explanation
Indices: 15714--15753 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
15704 GACCAACAGC
*
15714 AAAATAAAAGTA
1 AAAATGAAAGTA
15726 AAAATGAAAGTA
1 AAAATGAAAGTA
15738 AAAATGGAAGAGTA
1 AAAAT-GAA-AGTA
15752 AA
1 AA
15754 GTTTTAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 16 0.64
13 3 0.12
14 6 0.24
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (12 bp):
AAAATGAAAGTA
Found at i:16693 original size:4 final size:4
Alignment explanation
Indices: 16686--16711 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
16676 AAGATCTCTT
16686 TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
16712 CAGTTAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:18813 original size:22 final size:24
Alignment explanation
Indices: 18787--18832 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
18777 ATTGAAATGG
*
18787 AAAAACTGTTT-TGTTC-AAAATT
1 AAAAACAGTTTGTGTTCGAAAATT
*
18809 AAAAAGAGTTTGTGTTCGAAAATT
1 AAAAACAGTTTGTGTTCGAAAATT
18833 GTTCTCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (24 bp):
AAAAACAGTTTGTGTTCGAAAATT
Found at i:19031 original size:108 final size:109
Alignment explanation
Indices: 18919--19114 Score: 234
Period size: 108 Copynumber: 1.8 Consensus size: 109
18909 CCGAAAATCA
* * *
18919 AAATTCAAAAAGATCAAGAATCA-ATCTTCGAAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTT
1 AAATTCAAAAAGATC-ACAATCAGATCTTCAAAATTTTCAAATTGGGAAAGTTCCCACCAGGTTT
*
18983 TAGTTTTTAAATT-GGGAAAGTTCCCAACAAGTTTTTAAGTTTTC
65 TAGTTTTCAAATTAGGGAAAGTTCCCAACAAGTTTTTAAGTTTTC
*** * * * * * * *
19027 AAATTGGGAAAGTTCCCATTCAGTTTTTCAAAATTTTTAAATTGGGAAAGTTCCCATCAGGTTTT
1 AAATTCAAAAAGATCACAATCAGATCTTCAAAATTTTCAAATTGGGAAAGTTCCCACCAGGTTTT
*
19092 AGTTTTCAATTTAGGGAAAGTTC
66 AGTTTTCAAATTAGGGAAAGTTC
19115 TCATCATTTT
Statistics
Matches: 71, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
107 4 0.06
108 57 0.80
109 10 0.14
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (109 bp):
AAATTCAAAAAGATCACAATCAGATCTTCAAAATTTTCAAATTGGGAAAGTTCCCACCAGGTTTT
AGTTTTCAAATTAGGGAAAGTTCCCAACAAGTTTTTAAGTTTTC
Found at i:19120 original size:35 final size:35
Alignment explanation
Indices: 18949--19120 Score: 204
Period size: 34 Copynumber: 4.8 Consensus size: 35
18939 TCAATCTTCG
*
18949 AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT
1 AAGTTTTCAAATTGGGAAAGTTCCCATCAGGTTTT
* * *
18984 -AGTTTTTAAATTGGGAAAGTTCCCAACAAGTTTTT
1 AAGTTTTCAAATTGGGAAAGTTCCCATC-AGGTTTT
*
19019 AAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTT
1 AAGTTTTCAAATTGGGAAAGTTCCCA-TCAGGTTTT
* *
19055 CAAAATTTTTAAATTGGGAAAGTTCCCATCAGGTTTT
1 --AAGTTTTCAAATTGGGAAAGTTCCCATCAGGTTTT
* *
19092 -AGTTTTCAATTTAGGGAAAGTTCTCATCA
1 AAGTTTTCAAATT-GGGAAAGTTCCCATCA
19121 TTTTCAGTTT
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
34 34 0.29
35 21 0.18
36 31 0.26
37 9 0.08
38 24 0.20
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (35 bp):
AAGTTTTCAAATTGGGAAAGTTCCCATCAGGTTTT
Found at i:19147 original size:74 final size:75
Alignment explanation
Indices: 18979--19158 Score: 192
Period size: 74 Copynumber: 2.4 Consensus size: 75
18969 TTCCCACCAG
* *
18979 GTTTTAGTTTTTAAATTGGGAAAGTTCCCAACAAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCC
1 GTTTTAG--TTTAAATTGGGAAAGTTCCCATCAAGGTTTTAAGTTTTCAAATTGGGAAAGTTCCC
19044 ATTCAGTTTTTCA
64 ATTCAG-TTTTCA
*** * *
19057 AAATT--TTTAAATTGGGAAAGTTCCCATC-AGGTTTT-AGTTTTCAATTTAGGGAAAGTTCTCA
1 GTTTTAGTTTAAATTGGGAAAGTTCCCATCAAGGTTTTAAGTTTTCAAATT-GGGAAAGTTCCCA
19118 -TCA-TTTTCA
65 TTCAGTTTTCA
*
19127 GTTTTAGTTTCCAAAGTGGGAAAGTTCCCATC
1 GTTTTAGTTT--AAATTGGGAAAGTTCCCATC
19159 GAAAATCAGT
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
70 8 0.09
72 17 0.20
73 18 0.21
74 41 0.48
78 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (75 bp):
GTTTTAGTTTAAATTGGGAAAGTTCCCATCAAGGTTTTAAGTTTTCAAATTGGGAAAGTTCCCAT
TCAGTTTTCA
Found at i:19177 original size:108 final size:107
Alignment explanation
Indices: 18949--19178 Score: 241
Period size: 108 Copynumber: 2.1 Consensus size: 107
18939 TCAATCTTCG
* *
18949 AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTTAGTTTTTAAATTGGGAAAGTTCCCAACAAG
1 AAGTTTTAAAATTGGGAAAGTTCCCACCAGGTTTTAGTTTTCAAATTGGGAAAGTTCCCAACAAG
* * ****
19014 TTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTTC
66 TTTTTAAGTTTCCAAAGTGGGAAAGTTCCCATTCAGAAAATC
* * * * * *
19056 AAAATTTTTAAATTGGGAAAGTTCCCATCAGGTTTTAGTTTTCAATTTAGGGAAAGTTCTCATCA
1 -AAGTTTTAAAATTGGGAAAGTTCCCACCAGGTTTTAGTTTTCAAATT-GGGAAAGTTCCCAACA
** *
19121 TTTTCAGTTTTAGTTTCCAAAGTGGGAAAGTTCCCA-TC-GAAAATC
64 AGTT---TTTAAGTTTCCAAAGTGGGAAAGTTCCCATTCAGAAAATC
19166 -AGTTTTAAAATTG
1 AAGTTTTAAAATTG
19179 AGTCGTTTTA
Statistics
Matches: 100, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
108 53 0.53
109 16 0.16
110 3 0.03
111 2 0.02
112 26 0.26
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (107 bp):
AAGTTTTAAAATTGGGAAAGTTCCCACCAGGTTTTAGTTTTCAAATTGGGAAAGTTCCCAACAAG
TTTTTAAGTTTCCAAAGTGGGAAAGTTCCCATTCAGAAAATC
Found at i:23855 original size:14 final size:14
Alignment explanation
Indices: 23836--23866 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
23826 AGGATTTTTC
*
23836 AAAAATGGTTTCTA
1 AAAAATGGTTTCCA
23850 AAAAATGGTTTCCA
1 AAAAATGGTTTCCA
23864 AAA
1 AAA
23867 TTTGTTCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (14 bp):
AAAAATGGTTTCCA
Found at i:24182 original size:6 final size:7
Alignment explanation
Indices: 24172--24215 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
24162 AAGTCAAAAA
*
24172 AAAAATG
1 AAAATTG
24179 AAAATTG
1 AAAATTG
*
24186 -AAAGTG
1 AAAATTG
24192 AAAA-TG
1 AAAATTG
24198 AAAATTG
1 AAAATTG
24205 AAAATTG
1 AAAATTG
24212 AAAA
1 AAAA
24216 AGGTATAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 11 0.33
7 22 0.67
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (7 bp):
AAAATTG
Found at i:24193 original size:13 final size:13
Alignment explanation
Indices: 24177--24214 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
24167 AAAAAAAAAA
24177 TGAAAATTGAAAG
1 TGAAAATTGAAAG
*
24190 TGAAAA-TGAAAAT
1 TGAAAATTG-AAAG
24203 TGAAAATTGAAA
1 TGAAAATTGAAA
24215 AAGGTATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 2 0.09
13 18 0.82
14 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (13 bp):
TGAAAATTGAAAG
Found at i:25789 original size:143 final size:142
Alignment explanation
Indices: 25605--25951 Score: 482
Period size: 143 Copynumber: 2.4 Consensus size: 142
25595 GCTTTCAAGT
* *
25605 TGATCTAGGGCGATCATTCTTCAGTCTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATT
1 TGATCCAGGGCGATCATTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATT
* * *
25670 CCAATTGACCC-GGGTGGTCTTTTCTTCAGTTTATGCCGGAATGACCCAGGGTGGTCTTTTCTTC
66 CCAATTGACCCAGGGCGGTC-TCTCTTCAGTTTATGCCAG-ATGACCCAGGGTGGTCTTTTCTTC
*
25734 AGTTTATGTCGGAA
129 AGTTTATGCCGGAA
* *
25748 TGATCGAGGGCGATCATTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTCTATT
1 TGATCCAGGGCGATCATTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATT
* * * *
25813 CCAGTTGACCCAGGGCGGTCTCTCTTTAGTTTATTCCAGTTGACCCAGGGTGGTCTTTTCTTCAG
66 CCAATTGACCCAGGGCGGTCTCTCTTCAGTTTATGCCAGATGACCCAGGGTGGTCTTTTCTTCAG
25878 TTTATGCCGGAA
131 TTTATGCCGGAA
* * * * * * *
25890 TGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAG-CGACCCAGAGTGGTCTTTCTTCAGTTT
1 TGATCCAGGGCGATC-ATTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTT
25952 GTGTCGGAAT
Statistics
Matches: 182, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
142 70 0.38
143 105 0.58
144 7 0.04
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (142 bp):
TGATCCAGGGCGATCATTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATT
CCAATTGACCCAGGGCGGTCTCTCTTCAGTTTATGCCAGATGACCCAGGGTGGTCTTTTCTTCAG
TTTATGCCGGAA
Found at i:25899 original size:179 final size:179
Alignment explanation
Indices: 25585--25919 Score: 564
Period size: 179 Copynumber: 1.9 Consensus size: 179
25575 AGGGCAGTCT
* * * *
25585 TTCTTCAGTTGCTTTCAAGTTGATCTAGGGCGATCATTCTTCAGTCTATTTCAGTTGACCCAGGG
1 TTCTTCAGTTGATTTCAAGTTGACCCAGGGCGATCATTCTTCAGTCTATTCCAGTTGACCCAGGG
*
25650 CGGTCTTTCTTCAGTTTATTCCAATTGACCCGGGTGGTCTTTTCTTCAGTTTATGCCGGAATGAC
66 CGGTCTCTCTTCAGTTTATTCCAATTGACCCGGGTGGTCTTTTCTTCAGTTTATGCCGGAATGAC
25715 CCAGGGTGGTCTTTTCTTCAGTTTATGTCGGAATGATCGAGGGCGATCA
131 CCAGGGTGGTCTTTTCTTCAGTTTATGTCGGAATGATCGAGGGCGATCA
* * *
25764 TTCTTCAGTTTATTTC-AGTTGACCCAGGGCGGTCTTTCTTCAGTCTATTCCAGTTGACCCAGGG
1 TTCTTCAGTTGATTTCAAGTTGACCCAGGGCGATCATTCTTCAGTCTATTCCAGTTGACCCAGGG
* *
25828 CGGTCTCTCTTTAGTTTATTCCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGCCGGAATGA
66 CGGTCTCTCTTCAGTTTATTCCAATTGACCC-GGGTGGTCTTTTCTTCAGTTTATGCCGGAATGA
25893 CCCAGGGTGGTCTTTTCTTCAGTTTAT
130 CCCAGGGTGGTCTTTTCTTCAGTTTAT
25920 TTCAGCGACC
Statistics
Matches: 145, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
178 71 0.49
179 74 0.51
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (179 bp):
TTCTTCAGTTGATTTCAAGTTGACCCAGGGCGATCATTCTTCAGTCTATTCCAGTTGACCCAGGG
CGGTCTCTCTTCAGTTTATTCCAATTGACCCGGGTGGTCTTTTCTTCAGTTTATGCCGGAATGAC
CCAGGGTGGTCTTTTCTTCAGTTTATGTCGGAATGATCGAGGGCGATCA
Found at i:25985 original size:107 final size:108
Alignment explanation
Indices: 25656--26165 Score: 407
Period size: 107 Copynumber: 4.7 Consensus size: 108
25646 AGGGCGGTCT
* * * *
25656 TTCTTCAGTTTAT-TC-CAATTGACCC-GGGTGGTCTTTTCTTCAGTTTATGCCGGAATGACCCA
1 TTCTTCAGTTTATGTCGGAA-TGACCCAGGGTGGTCTTTTCTTCAGTTTATTCCAG-TTGACCCA
* * *
25718 GGGTGGTCTTTTCTTCAGTTTATGTCGGAATGATCGAGGGCGATCA
64 GGGTGGTC-TTTCTTCAGTTTATGTCGGAATGATCGAGGGTGGTTA
* * * * *
25764 TTCTTCAGTTTATTTCAG-TTGACCCAGGGCGGTC-TTTCTTCAGTCTATTCCAGTTGACCCAGG
1 TTCTTCAGTTTATGTCGGAATGACCCAGGGTGGTCTTTTCTTCAGTTTATTCCAGTTGACCCAGG
* * * * * * * *
25827 GCGGTCTCTCTTTAGTTTAT-TC-CAGTTGACCCAGGGTGGTCTT
66 GTGGTCTTTCTTCAGTTTATGTCGGA-ATGATCGAGGGTGGT-TA
* * * *
25870 TTCTTCAGTTTATGCCGGAATGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAG-CGACCCAGA
1 TTCTTCAGTTTATGTCGGAATGACCCAGGGTGGTCTTTTCTTCAGTTTATTCCAGTTGACCCAGG
* * *
25934 GTGGTCTTTCTTCAGTTTGTGTCGGAATGATTGAGGGTGGTTG
66 GTGGTCTTTCTTCAGTTTATGTCGGAATGATCGAGGGTGGTTA
* * * * * *
25977 TTCCTCAGTTCA-GTTCGGAATGATCGAGGGTGGT-TGTTCTTCAGTTTATTTCAGTTGACCCAG
1 TTCTTCAGTTTATG-TCGGAATGACCCAGGGTGGTCTTTTCTTCAGTTTATTCCAGTTGACCCAG
* * ** *
26040 GGTGGTCCTTCTTGAGTTGGTGTCGGAATGATCGAGGGTGGCCATTTT
65 GGTGGTCTTTCTTCAGTTTATGTCGGAATGATCGAGGGTGG----TTA
* * * * ** * *
26088 TTTTTCAGTTTATTTC--AAGTGACCTAGGGTGGTC-TTGCTTCAACTTATTTCAGAATGACCCA
1 TTCTTCAGTTTATGTCGGAA-TGACCCAGGGTGGTCTTTTCTTCAGTTTATTCCAG-TTGACCCA
26150 GGGTGGTCTTTCTTCA
64 GGGTGGTCTTTCTTCA
26166 ATTCTTCAAG
Statistics
Matches: 320, Mismatches: 63, Indels: 35
0.77 0.15 0.08
Matches are distributed among these distances:
104 1 0.00
105 12 0.04
106 47 0.15
107 122 0.38
108 65 0.20
109 12 0.04
110 27 0.08
111 34 0.11
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (108 bp):
TTCTTCAGTTTATGTCGGAATGACCCAGGGTGGTCTTTTCTTCAGTTTATTCCAGTTGACCCAGG
GTGGTCTTTCTTCAGTTTATGTCGGAATGATCGAGGGTGGTTA
Found at i:26025 original size:179 final size:178
Alignment explanation
Indices: 25570--26161 Score: 523
Period size: 179 Copynumber: 3.3 Consensus size: 178
25560 ATTTTCAATC
** ** * * * * * * *
25570 GACCCAGGGCAGTCTTTCTTCAGTTGCTTTCAAGTTGATCTAGGGCGATCATTCTTCAGTCTATT
1 GACCCAGGGTGGTCTTTCTTCAGTTTATGTC-AGATGACCCAGGGCGGTCTTTCCTCAGTCTATT
* * *
25635 TCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTCCAATTGACCC-GGGTGGTCTTTTCTTCAG
65 CCAGATGACCCAGGGCGGTCTTTCTTCAGTTTATTCCAGTTGACCCAGGGTGGTCTTTTCTTCAG
* *
25699 TTTATGCCGGAATGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCGGAAT
130 TTTATGCCGGAATGACCCAGGGTGGTCTTTTCTTCAGTTTATTTC-GAGT
* * * * * * * *
25749 GATCGAGGGCGATCATTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTCTATTC
1 GACCCAGGGTGGTCTTTCTTCAGTTTATGTCAGATGACCCAGGGCGGTCTTTCCTCAGTCTATTC
* * *
25814 CAGTTGACCCAGGGCGGTCTCTCTTTAGTTTATTCCAGTTGACCCAGGGTGGTCTTTTCTTCAGT
66 CAGATGACCCAGGGCGGTCTTTCTTCAGTTTATTCCAGTTGACCCAGGGTGGTCTTTTCTTCAGT
*
25879 TTATGCCGGAATGACCCAGGGTGGTCTTTTCTTCAGTTTATTTC-AGC
131 TTATGCCGGAATGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCGAGT
* * * *** *
25926 GACCCAGAGTGGTCTTTCTTCAGTTTGTGTCGGAATGATTGAGGGTGGT-TGTTCCTCAGT-TCA
1 GACCCAGGGTGGTCTTTCTTCAGTTTATGTCAG-ATGACCCAGGGCGGTCT-TTCCTCAGTCT-A
* * * * * *
25989 GTT-CGGAATGATCGAGGGTGGT-TGTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTC-CTTC
63 -TTCCAG-ATGACCCAGGGCGGTCT-TTCTTCAGTTTATTCCAGTTGACCCAGGGTGGTCTTTTC
* ** * * * * * *
26051 TTGAGTTGGTGTCGGAATGATCGAGGGTGGCCATTTTTTTTTCAGTTTATTTCAAGT
125 TTCAGTTTATGCCGGAATGACCCAGGGTGG---TCTTTTCTTCAGTTTATTTCGAGT
* * ** * *
26108 GACCTAGGGTGGTCTTGCTTCAACTTATTTCAGAATGACCCAGGGTGGTCTTTC
1 GACCCAGGGTGGTCTTTCTTCAGTTTATGTCAG-ATGACCCAGGGCGGTCTTTC
26162 TTCAATTCTT
Statistics
Matches: 339, Mismatches: 62, Indels: 21
0.80 0.15 0.05
Matches are distributed among these distances:
177 27 0.08
178 120 0.35
179 130 0.38
181 18 0.05
182 43 0.13
183 1 0.00
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (178 bp):
GACCCAGGGTGGTCTTTCTTCAGTTTATGTCAGATGACCCAGGGCGGTCTTTCCTCAGTCTATTC
CAGATGACCCAGGGCGGTCTTTCTTCAGTTTATTCCAGTTGACCCAGGGTGGTCTTTTCTTCAGT
TTATGCCGGAATGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCGAGT
Found at i:26052 original size:35 final size:35
Alignment explanation
Indices: 25526--26165 Score: 374
Period size: 35 Copynumber: 17.9 Consensus size: 35
25516 ATGTTCAAAG
* * * * *
25526 TTTCAGTTGACCTAGGGCGGTC-TCCATTCAGATCA
1 TTTCAGTTGACCCAGGGTGGTCTTTC-TTCAGTTTA
* * ** **
25561 TTTTCAATCGACCCAGGGCAGTCTTTCTTCAGTTGC
1 -TTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTA
* * * * * *
25597 TTTCAAGTTGATCTAGGGCGATCATTCTTCAGTCTA
1 TTTC-AGTTGACCCAGGGTGGTCTTTCTTCAGTTTA
*
25633 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA
1 TTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTA
* *
25668 TTCCAATTGACCC-GGGTGGTCTTTTCTTCAGTTTA
1 TTTCAGTTGACCCAGGGTGGTC-TTTCTTCAGTTTA
** * *
25703 TGCCGGAATGACCCAGGGTGGTCTTTTCTTCAGTTTA
1 TTTCAG-TTGACCCAGGGTGGTC-TTTCTTCAGTTTA
* * * * * * * *
25740 TGTCGGAATGATCGAGGGCGATCATTCTTCAGTTTA
1 TTTCAG-TTGACCCAGGGTGGTCTTTCTTCAGTTTA
* *
25776 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTCTA
1 TTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTA
* * * *
25811 TTCCAGTTGACCCAGGGCGGTCTCTCTTTAGTTTA
1 TTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTA
*
25846 TTCCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTA
1 TTTCAGTTGACCCAGGGTGGTC-TTTCTTCAGTTTA
** * *
25882 TGCCGGAATGACCCAGGGTGGTCTTTTCTTCAGTTTA
1 TTTCAG-TTGACCCAGGGTGGTC-TTTCTTCAGTTTA
* * *
25919 TTTCAG-CGACCCAGAGTGGTCTTTCTTCAGTTTG
1 TTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTA
* * * *** * *
25953 TGTCGGAATGATTGAGGGTGGT-TGTTCCTCAGTTCA
1 TTTCAG-TTGACCCAGGGTGGTCT-TTCTTCAGTTTA
* * * * *
25989 GTTCGGAATGATCGAGGGTGGT-TGTTCTTCAGTTTA
1 TTTCAG-TTGACCCAGGGTGGTCT-TTCTTCAGTTTA
* * **
26025 TTTCAGTTGACCCAGGGTGGTCCTTCTTGAGTTGG
1 TTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTA
* * * * * * *
26060 TGTCGGAATGATCGAGGGTGGCCATTTTTTTTTCAGTTTA
1 TTTCAG-TTGACCCAGGGTGG----TCTTTCTTCAGTTTA
* * **
26100 TTTCAAG-TGACCTAGGGTGGTCTTGCTTCAACTTA
1 TTTC-AGTTGACCCAGGGTGGTCTTTCTTCAGTTTA
*
26135 TTTCAGAATGACCCAGGGTGGTCTTTCTTCA
1 TTTCAG-TTGACCCAGGGTGGTCTTTCTTCA
26166 ATTCTTCAAG
Statistics
Matches: 479, Mismatches: 106, Indels: 38
0.77 0.17 0.06
Matches are distributed among these distances:
34 25 0.05
35 185 0.39
36 171 0.36
37 74 0.15
39 11 0.02
40 12 0.03
41 1 0.00
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.38
Consensus pattern (35 bp):
TTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTA
Found at i:26080 original size:36 final size:36
Alignment explanation
Indices: 25859--26080 Score: 137
Period size: 36 Copynumber: 6.2 Consensus size: 36
25849 CAGTTGACCC
* * * * *
25859 AGGGTGGTCTTTTCTTCAGTTTATGCCGGAATGACCC
1 AGGGTGGTC-GTTCTTCAGTTTGTGTCGGAATGATCG
* * * ** * *
25896 AGGGTGGTCTTTTCTTCAGTTTATTTC--AGCGACCC
1 AGGGTGGTC-GTTCTTCAGTTTGTGTCGGAATGATCG
* * *
25931 AGAGTGGTCTTTCTTCAGTTTGTGTCGGAATGATTG
1 AGGGTGGTCGTTCTTCAGTTTGTGTCGGAATGATCG
* * *
25967 AGGGTGGTTGTTCCTCAGTTCAGT-TCGGAATGATCG
1 AGGGTGGTCGTTCTTCAGTT-TGTGTCGGAATGATCG
* * * * * * *
26003 AGGGTGGTTGTTCTTCAGTTTATTTCAG-TTGACCC
1 AGGGTGGTCGTTCTTCAGTTTGTGTCGGAATGATCG
* * *
26038 AGGGTGGTCCTTCTTGAGTTGGTGTCGGAATGATCG
1 AGGGTGGTCGTTCTTCAGTTTGTGTCGGAATGATCG
26074 AGGGTGG
1 AGGGTGG
26081 CCATTTTTTT
Statistics
Matches: 145, Mismatches: 35, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
34 15 0.10
35 40 0.28
36 63 0.43
37 27 0.19
ACGTcount: A:0.15, C:0.17, G:0.31, T:0.37
Consensus pattern (36 bp):
AGGGTGGTCGTTCTTCAGTTTGTGTCGGAATGATCG
Found at i:26124 original size:71 final size:68
Alignment explanation
Indices: 25991--26124 Score: 155
Period size: 75 Copynumber: 1.9 Consensus size: 68
25981 TCAGTTCAGT
25991 TCGGAATGATCGAGGGTGGTTGTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCCTTCTTGAG
1 TCGGAATGATCGAGGGTGGTTGTTCTTCAGTTTATTTCAGTTGACCCAGGGTGG--C-TCTTGAG
26056 TTGGTG
63 TTGGTG
* * *
26062 TCGGAATGATCGAGGGTGGCCATTTTTTTTTCAGTTTATTTCAAG-TGACCTAGGGTGG-TCTTG
1 TCGGAATGATCGAGGGTGG----TTGTTCTTCAGTTTATTTC-AGTTGACCCAGGGTGGCTCTTG
26125 CTTCAACTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
71 24 0.44
75 29 0.53
76 2 0.04
ACGTcount: A:0.16, C:0.15, G:0.31, T:0.39
Consensus pattern (68 bp):
TCGGAATGATCGAGGGTGGTTGTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGCTCTTGAGTTG
GTG
Found at i:26153 original size:36 final size:35
Alignment explanation
Indices: 26097--26166 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 35
26087 TTTTTTCAGT
* *
26097 TTATTTCAAGTGACCTAGGGTGGTCTTGCTTCAAC
1 TTATTTCAAATGACCCAGGGTGGTCTTGCTTCAAC
*
26132 TTATTTCAGAATGACCCAGGGTGGTCTTTCTTCAA
1 TTATTTCA-AATGACCCAGGGTGGTCTTGCTTCAA
26167 TTCTTCAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 8 0.26
36 23 0.74
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (35 bp):
TTATTTCAAATGACCCAGGGTGGTCTTGCTTCAAC
Found at i:27287 original size:14 final size:12
Alignment explanation
Indices: 27248--27287 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
27238 GACCAGCAGC
*
27248 AAAATAAAAGTA
1 AAAATGAAAGTA
27260 AAAATGAAAGTA
1 AAAATGAAAGTA
27272 AAAATGGAAGAGTA
1 AAAAT-GAA-AGTA
27286 AA
1 AA
27288 GTTTTAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 16 0.64
13 3 0.12
14 6 0.24
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (12 bp):
AAAATGAAAGTA
Done.