Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014575.1 Corchorus olitorius cultivar O-4 contig14608, 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: 60225
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:5775 original size:19 final size:20
Alignment explanation
Indices: 5738--5783 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
5728 CTATAACTAA
5738 CGGAAAATTGACGTGGAAGT
1 CGGAAAATTGACGTGGAAGT
*
5758 CGGAACATTGAC-TGGAAGT
1 CGGAAAATTGACGTGGAAGT
5777 CTGGAAA
1 C-GGAAA
5784 GTGGAGAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.20
Consensus pattern (20 bp):
CGGAAAATTGACGTGGAAGT
Found at i:8557 original size:61 final size:60
Alignment explanation
Indices: 8450--8569 Score: 177
Period size: 61 Copynumber: 2.0 Consensus size: 60
8440 TTCAAGGTTG
*
8450 AAATTTAGTCATCGGGTATTTAATCCGGTGGTAGAGTACTGGACTCTTAATTCCAGCATT
1 AAATTTAGTCATCGGGTATTTAAGCCGGTGGTAGAGTACTGGACTCTTAATTCCAGCATT
* ** * *
8510 AAATTTAGTCATTGGGTATTTTGGCCTGGTGGTAGAGTATTGGACTCTTAGTTCCAGCAT
1 AAATTTAGTCATCGGGTATTTAAGCC-GGTGGTAGAGTACTGGACTCTTAATTCCAGCAT
8570 ACCTGAACTA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
60 22 0.42
61 31 0.58
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (60 bp):
AAATTTAGTCATCGGGTATTTAAGCCGGTGGTAGAGTACTGGACTCTTAATTCCAGCATT
Found at i:9236 original size:17 final size:18
Alignment explanation
Indices: 9210--9244 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
9200 ACAAGTGATC
*
9210 GAAAAGGAAAAA-AAAAA
1 GAAAAAGAAAAATAAAAA
9227 GAAAAAGAAAAATAAAAA
1 GAAAAAGAAAAATAAAAA
9245 ACCAAATCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (18 bp):
GAAAAAGAAAAATAAAAA
Found at i:16356 original size:3 final size:3
Alignment explanation
Indices: 16350--16394 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
16340 CAAAAAAAGA
16350 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
16395 CAAAATCTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40399 original size:14 final size:14
Alignment explanation
Indices: 40382--40411 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40372 TTTAATTTTA
40382 TAATAAATTATAAC
1 TAATAAATTATAAC
*
40396 TAATAGATTATAAC
1 TAATAAATTATAAC
40410 TA
1 TA
40412 CAAAGAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (14 bp):
TAATAAATTATAAC
Found at i:52964 original size:26 final size:25
Alignment explanation
Indices: 52920--54236 Score: 1904
Period size: 26 Copynumber: 52.0 Consensus size: 25
52910 TCATATAAAT
*
52920 CATATTCTAGTAGGGGACATTTAGTTG
1 CATATTC-AGTA-GGGACATGTAGTTG
52947 CATATTCAGTAGGAGACATGTAGTTG
1 CATATTCAGTAGG-GACATGTAGTTG
*
52973 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
*
52998 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
*
53023 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
53048 CATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
*
53074 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
*
53099 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
*
53124 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
53149 CATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
*
53175 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
53200 CATATTCAGTAGGTGACATGTAGTTG
1 CATATTCAGTAGG-GACATGTAGTTG
53226 CATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
53252 CATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
*
53278 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
53303 CATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
53329 CATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
53355 CATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
53381 CATATTCAGTAGGGACATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
53406 CATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
53432 CATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
53458 CATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
*
53484 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
53509 CATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
53535 CATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
53561 CATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
53587 CATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
*
53613 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
*
53638 CATATTCAGTAGGTACATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
*
53663 CATATTCAGTAGGGGACATGTAGCTG
1 CATATTCAGTA-GGGACATGTAGTTG
*
53689 CATATTCAGTAGGGGACATGTAGTTA
1 CATATTCAGTA-GGGACATGTAGTTG
*
53715 CATATTCAGTAGGGGTCATGTAGTTG
1 CATATTCAGTA-GGGACATGTAGTTG
53741 C--A-T-AG--GGGACATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
*
53760 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
*
53785 CATATTCAGTAGGAGACATGTAGTTT
1 CATATTCAGTAGG-GACATGTAGTTG
*
53811 CATATTCAGTATGGGTCATGTAGTTG
1 CATATTCAGTA-GGGACATGTAGTTG
53837 C--A-T-AG--GGGACATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
*
53856 CATATTCAGTAGGGTCCATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
*
53882 CATATTCAGTAGGGTCCATGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
* *
53908 CATATTCAGTAGGTACACGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
* *
53933 CATATACAGTAGGGTACACGTAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
*
53959 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
* ** *
53984 CATAATCAGTTTGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
*
54009 CATATTCAGTAGAGGTCATGTAGTTG
1 CATATTCAGTAG-GGACATGTAGTTG
*
54035 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
* *
54060 CATAATCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
*
54085 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
54110 CATATTCAGTAGGGGACATGTAGTTG
1 CATATTCAGTA-GGGACATGTAGTTG
*
54136 CATATTCAGTAGGGTACATATAGTTG
1 CATATTCAGTAGGG-ACATGTAGTTG
* * *
54162 CCTATTCAATA-GGATCATATAGTTG
1 CATATTCAGTAGGGA-CATGTAGTTG
* *
54187 CATATTCAATAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
*
54212 CATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGACATGTAGTTG
54237 TCATGTAGTT
Statistics
Matches: 1208, Mismatches: 52, Indels: 62
0.91 0.04 0.05
Matches are distributed among these distances:
19 28 0.02
21 2 0.00
22 6 0.00
23 6 0.00
24 3 0.00
25 512 0.42
26 642 0.53
27 9 0.01
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (25 bp):
CATATTCAGTAGGGACATGTAGTTG
Found at i:52998 original size:51 final size:50
Alignment explanation
Indices: 52920--54334 Score: 1942
Period size: 51 Copynumber: 27.7 Consensus size: 50
52910 TCATATAAAT
* *
52920 CATATTCTAGTAGGGGACATTTAGTTGCATATTCAGTAGGAGACATGTAGTTG
1 CATATTC-AGTA-GGGTCATGTAGTTGCATATTCAGTAGG-GACATGTAGTTG
*
52973 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGACATGTAGTTG
53023 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGG-ACATGTAGTTG
*
53074 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGACATGTAGTTG
53124 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGG-ACATGTAGTTG
53175 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGTGACATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGG-GACATGTAGTTG
*
53226 CATATTCAGTAGGGAACATGTAGTTGCATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-TCATGTAGTTGCATATTCAGTAGGG-ACATGTAGTTG
53278 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGG-ACATGTAGTTG
*
53329 CATATTCAGTAGGGAACATGTAGTTGCATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-TCATGTAGTTGCATATTCAGTAGGG-ACATGTAGTTG
*
53381 CATATTCAGTAGGGACATGTAGTTGCATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGG-ACATGTAGTTG
*
53432 CATATTCAGTAGGGAACATGTAGTTGCATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-TCATGTAGTTGCATATTCAGTAGGG-ACATGTAGTTG
53484 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGG-ACATGTAGTTG
*
53535 CATATTCAGTAGGGAACATGTAGTTGCATATTCAGTAGGGAACATGTAGTTG
1 CATATTCAGTAGGG-TCATGTAGTTGCATATTCAGTAGGG-ACATGTAGTTG
* *
53587 CATATTCAGTAGGGAACATGTAGTTGCATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGG-TCATGTAGTTGCATATTCAGTAGGGACATGTAGTTG
*
53638 CATATTCAGTA-GGTACATGTAGTTGCATATTCAGTAGGGGACATGTAGCTG
1 CATATTCAGTAGGGT-CATGTAGTTGCATATTCAGTA-GGGACATGTAGTTG
* * *
53689 CATATTCAGTAGGGGACATGTAGTTACATATTCAGTAGGGGTCATGTAGTTG
1 CATATTCAGTA-GGGTCATGTAGTTGCATATTCAGTA-GGGACATGTAGTTG
* *
53741 C--A-T-AG--GGGACATGTAGTTGCATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGACATGTAGTTG
* * *
53785 CATATTCAGTAGGAGACATGTAGTTTCATATTCAGTATGGGTCATGTAGTTG
1 CATATTCAGTAGG-GTCATGTAGTTGCATATTCAGTA-GGGACATGTAGTTG
* *
53837 C--A-T-AG--GGGACATGTAGTTGCATATTCAGTAGGGTCCATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGG-ACATGTAGTTG
* *
53882 CATATTCAGTAGGGTCCATGTAGTTGCATATTCAGTAGGTACACGTAGTTG
1 CATATTCAGTAGGGT-CATGTAGTTGCATATTCAGTAGGGACATGTAGTTG
* * *
53933 CATATACAGTAGGGTACACGTAGTTGCATATTCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGT-CATGTAGTTGCATATTCAGTAGGGACATGTAGTTG
* ** *
53984 CATAATCAGTTTGGTCATGTAGTTGCATATTCAGTAGAGGTCATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAG-GGACATGTAGTTG
* *
54035 CATATTCAGTAGGGTCATGTAGTTGCATAATCAGTAGGGTCATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGACATGTAGTTG
54085 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGGACATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTA-GGGACATGTAGTTG
* * * *
54136 CATATTCAGTAGGGTACATATAGTTGCCTATTCAATA-GGATCATATAGTTG
1 CATATTCAGTAGGGT-CATGTAGTTGCATATTCAGTAGGGA-CATGTAGTTG
*
54187 CATATTCAATAGGGTCATGTAGTTGCATATTCAGTAGGGTCATGTAGTTGTCATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTA-GG----G-A-----CATGTAGTTG
* * * *
54248 CATATTCAGTAGGGACATGTAGTTGCATAATCTG-AGGGGTCATGTAGTTG
1 CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTA-GGGACATGTAGTTG
*
54298 CATATTCAGTAGGGGTCATGCAGTTGCATATTCAGTA
1 CATATTCAGTA-GGGTCATGTAGTTGCATATTCAGTA
54335 TGGGTGATGT
Statistics
Matches: 1255, Mismatches: 62, Indels: 91
0.89 0.04 0.06
Matches are distributed among these distances:
44 18 0.01
45 57 0.05
46 3 0.00
47 2 0.00
48 7 0.01
49 4 0.00
50 237 0.19
51 549 0.44
52 322 0.26
53 9 0.01
56 2 0.00
57 1 0.00
60 4 0.00
61 40 0.03
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (50 bp):
CATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGACATGTAGTTG
Found at i:53748 original size:19 final size:19
Alignment explanation
Indices: 53724--53763 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
53714 ACATATTCAG
*
53724 TAGGGGTCATGTAGTTGCA
1 TAGGGGACATGTAGTTGCA
53743 TAGGGGACATGTAGTTGCA
1 TAGGGGACATGTAGTTGCA
53762 TA
1 TA
53764 TTCAGTAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.35, T:0.30
Consensus pattern (19 bp):
TAGGGGACATGTAGTTGCA
Found at i:54240 original size:36 final size:36
Alignment explanation
Indices: 54200--54272 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
54190 ATTCAATAGG
*
54200 GTCATGTAGTTGCATATTCAGTAGGGTCATGTAGTT
1 GTCATGTAGTTGCATATTCAGTAGGGACATGTAGTT
54236 GTCATGTAGTTGCATATTCAGTAGGGACATGTAGTT
1 GTCATGTAGTTGCATATTCAGTAGGGACATGTAGTT
54272 G
1 G
54273 CATAATCTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (36 bp):
GTCATGTAGTTGCATATTCAGTAGGGACATGTAGTT
Found at i:54276 original size:61 final size:61
Alignment explanation
Indices: 54176--54302 Score: 186
Period size: 61 Copynumber: 2.1 Consensus size: 61
54166 TTCAATAGGA
* *
54176 TCATATAGTTGCATATTCAATAGGGTCATGTAGTTGCATATTCAGTA-GGGTCATGTAGTTG
1 TCATATAGTTGCATATTCAATAGGGACATGTAGTTGCATAATCAG-AGGGGTCATGTAGTTG
* * *
54237 TCATGTAGTTGCATATTCAGTAGGGACATGTAGTTGCATAATCTGAGGGGTCATGTAGTTG
1 TCATATAGTTGCATATTCAATAGGGACATGTAGTTGCATAATCAGAGGGGTCATGTAGTTG
54298 -CATAT
1 TCATAT
54303 TCAGTAGGGG
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
60 5 0.08
61 54 0.92
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (61 bp):
TCATATAGTTGCATATTCAATAGGGACATGTAGTTGCATAATCAGAGGGGTCATGTAGTTG
Found at i:54301 original size:86 final size:86
Alignment explanation
Indices: 54156--54323 Score: 234
Period size: 86 Copynumber: 1.9 Consensus size: 86
54146 AGGGTACATA
* *
54156 TAGTTGCCTATTCAATAGGATCATATAGTTGCATATTCAATAGGGTCATGTAGTTGCATATTCAG
1 TAGTTGCATATTCAATAGGATCATATAGTTGCATAATC-ATAGGGTCATGTAGTTGCATATTCAG
*
54221 TA-GGGTCATGTAGTTGTCATG
65 TAGGGGTCATGCAGTTGTCATG
* *
54242 TAGTTGCATATTCAGTAGGGA-CATGTAGTTGCATAATC-TGAGGGGTCATGTAGTTGCATATTC
1 TAGTTGCATATTCAATA-GGATCATATAGTTGCATAATCAT-A-GGGTCATGTAGTTGCATATTC
54305 AGTAGGGGTCATGCAGTTG
63 AGTAGGGGTCATGCAGTTG
54324 CATATTCAGT
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
84 1 0.01
85 1 0.01
86 55 0.75
87 16 0.22
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.35
Consensus pattern (86 bp):
TAGTTGCATATTCAATAGGATCATATAGTTGCATAATCATAGGGTCATGTAGTTGCATATTCAGT
AGGGGTCATGCAGTTGTCATG
Found at i:54333 original size:26 final size:26
Alignment explanation
Indices: 54236--54346 Score: 154
Period size: 25 Copynumber: 4.3 Consensus size: 26
54226 TCATGTAGTT
54236 GTCATGTAGTTGCATATTCAGTA-GG
1 GTCATGTAGTTGCATATTCAGTAGGG
* * *
54261 GACATGTAGTTGCATAATCTG-AGGG
1 GTCATGTAGTTGCATATTCAGTAGGG
54286 GTCATGTAGTTGCATATTCAGTAGGG
1 GTCATGTAGTTGCATATTCAGTAGGG
* *
54312 GTCATGCAGTTGCATATTCAGTATGG
1 GTCATGTAGTTGCATATTCAGTAGGG
*
54338 GTGATGTAG
1 GTCATGTAG
54347 AAATTAATTT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
24 1 0.01
25 38 0.51
26 35 0.47
ACGTcount: A:0.24, C:0.12, G:0.31, T:0.33
Consensus pattern (26 bp):
GTCATGTAGTTGCATATTCAGTAGGG
Found at i:54994 original size:332 final size:329
Alignment explanation
Indices: 54344--58066 Score: 3412
Period size: 332 Copynumber: 11.4 Consensus size: 329
54334 ATGGGTGATG
* ** * * *
54344 TAGAAATTAATTTGGAAAATAGGAAAAATGATAGCATAAGCATGAAAAGCCCTTAAATTTTTTTA
1 TAGAAATTAATTCGGAAAATAGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTTTTG
* * *
54409 GCGATGAGTTATATATTTTTATGAGTATTGTGGCCAAAAAGTGAGGAAAAATTTTTCGGGATAGT
66 GCGTTGAATTATATATTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGATAGT
* * * * * ** * * *
54474 TTTTGCATAATTTTTGCCGAAATCCTATACTAACAATCATTGTTTGTAGCTAAAAACACGTGTTC
131 TTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAC-CGCGTTC
* * *
54539 -TGGGTCCTGA-TTAGTTTTGCATGATTTTTGGTAGCAAGACTCCTTAAAATATTTATATTCATC
195 TTGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATATTCATC
* ** * * *
54602 TAACCAAATATTGGCCACAATGGATTTAAGGAT-ATTTTTTTACGAGCAGCAGAATTATGTTTCG
260 TAACCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTT-CGAGCATC-TAATTATGTTTCG
54666 ATTTAAT
323 ATTTAAT
* * *
54673 TAAAAATTAATTCGGAAAAATATGAAAAATTATATTAGAAGCCTGAAAAGCCCTTAAATTTTTTT
1 TAGAAATTAATTCGG-AAAATAGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTTTT
* * *
54738 GGCGTTGAATTATATATTTGTTATGTGTATTGTGGCCAAATATTGA-GAAAAAATTTTCGGGATA
65 GGCGTTGAATTATATATTT-TTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGATA
* * * * *
54802 GTATTTGCAAAATTTTGGCTGAAATCGTGTACTAATCATTACTGTTTTTGGCTAAAAACGCGCGT
129 GTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAC-CGCGT
* * * * *
54867 TTTTGGGCCCTGACTTAGTTTTGCTTGATTTTTGACAGCAAGACTCCTTAAAATATTTATATTAA
193 TCTTGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATATTCA
* * *
54932 TCTAATCAAATCTCAGCCATAATGGATTTAAGAATAATTTTTTTCGAGTATCTAATTTATGTTTC
258 TCTAACCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTTCGAGCATCTAA-TTATGTTTC
*
54997 AATTTAAT
322 GATTTAAT
* * ** * *
55005 TTGAAATTAATTCGGAAAATAGGAAAAATGATATTA-ATAGCCTAAAAAGTACTAAAATTTTATT
1 TAGAAATTAATTCGGAAAATAGGAAAAATGATATTAGA-AGCCTGAAAAGCCCTTAAATTTTTTT
* * *
55069 GGCGTTGAATTATATA-TTTT-T---TA---T-G------ATTGAGGAACAATTTTTCCGGATCG
65 GGCGTTGAATTATATATTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGATAG
* * * * ** *
55119 TTTTTGCAAAATTTTAGCCGAAATCATATACTAACCATCACAGTTTTTGAC-AAAAAATGTGTTC
130 TTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACCGCGTTC
* ** ** * ** *
55183 TTCGGCCCCGACACAGTTTTGCATGATTTTTGGC-GTCAAGTGTCATTGTAATATCTATATTCAT
195 TTGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAG-CAAGACTCCTTAAAATATTTATATTCAT
* * * * * * * * *
55247 CTAAACAATTCTCGGCCACATTGGATTT-A-AATATTTGTTTTTATGAGAATTTGAATTATATTT
259 CTAACCAAATCTCAGCCACAATGGATTTAAGAATAATT-TTTTT-CGAGCATCT-AATTATGTTT
* *
55310 CAATATAAT
321 CGATTTAAT
* * * * ** * * *
55319 TAGAAATTAATTCGAAAAAATTTA-GAAAAACGAAAATT-GAAGCATCTAAAGCCCTTCAGTCTT
1 TAGAAATTAATTCG-GAAAA--TAGGAAAAATG-ATATTAGAAGCCTGAAAAGCCCTTAAATTTT
** * * *
55382 TTTGGATTTGAATAATATAATTTTTATGAGTGTTGTGGCCAAAATTTGAGGAAAAATTTTTC-GG
62 TTTGGCGTTGAATTATAT-ATTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGG
* ** * *
55446 ---G----TG----A---T-------ATTGTGTACTAACCATTGCTGTTTTTGGGTAAAAACGCG
126 ATAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAC-CG
* * * * * *
55490 CGTTCTGGGGCCTCGGCTTACTTTTGCTTGATTTTTGACAGCAAGACTCCTTAAAATATTTATAT
190 CGTTCTTGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATAT
* * *
55555 TCATATAACCAAATCTCAGCCACAATGGATTTAAGAATAATATTTTACGAG-ATTCTAAATTATG
255 TCATCTAACCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTTCGAGCA-TCT-AATTATG
*
55619 TTTCGATTTAAA
318 TTTCGATTTAAT
* *
55631 TGGAAATTAATTCGGAAAATAGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTG
1 TAGAAATTAATTCGGAAAATAGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTTTTG
* * * * * * *
55696 GCGTTCATTTATATATTTTCTATGAGTGTTGTGGTCAAAAATTGGGGAAAAA-TTTTCCGGAGAG
66 GCGTTGAATTATATATTTT-TATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGATAG
* * * *
55760 ATTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACAGTTTTTGGCTAAAAA-TGCGTTC
130 TTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACCGCGTTC
* * * ** * * *
55824 TTAGGCTCCGGCACAGTTTTGGATGATTTTTGGCAGCAAGACTCCTTAAAATATCTATTTTCATC
195 TTGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATATTCATC
* *** ** ** *
55889 TAACAAAATCTCATATACAATGGATTTAACG-ATAAGGTTTTAGGAGCATCTTAATTATGTTTCA
260 TAACCAAATCTCAGCCACAATGGATTTAA-GAATAATTTTTTTCGAGCATC-TAATTATGTTTCG
55953 ATTTAAT
323 ATTTAAT
* * * * * *
55960 TAGAAATTAATTTGAAAAATAGGAAAAACGATATTATAAGCATGAAAAGCCCTTAAATTTTTTTA
1 TAGAAATTAATTCGGAAAATAGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTTTTG
* * * * * *
56025 GCGATGAGTTATATATTTTTTATGAGTATTGTGACCAAAAAGTGAGGAAAAATTTTT-GAGAGAG
66 GCGTTGAATTATATA-TTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGATAG
* * *
56089 TTTTTGCAAAATTTTGACCAAAATCGTGTACTTACCATCACAGTTTTTGGCTAAAAACACGCGTT
130 TTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAC-CGCGTT
* *
56154 C-TGGAG-CCCGACTTAGTTTTGCATGATTTTTGGCATCAAGACTCCTTAAAACATTTATATTCA
194 CTTGG-GCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATATTCA
* * * * *
56217 TCTAATCAAATATCAGCCACAATGGATTTAAGGATAATTTTTTACGAGTATCTGAATTATGTTTC
258 TCTAACCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTTCGAGCATCT-AATTATGTTTC
56282 GATTTAAT
322 GATTTAAT
* *
56290 TAGAAATTAATTC--------GGAAAAATTATATTAGAAGCCTGAAAAGCCCTT-AATTTTAATT
1 TAGAAATTAATTCGGAAAATAGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTT-TTT
* * * *
56346 GGCCTTGAATTATATTTTTGTTATGAGTATTGTGGCCACAATTTGAGGAAAAATTTTTCGGGATA
65 GGCGTTGAATTATATATTT-TTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGATA
* * *
56411 GTTTTTGCAAAATTCTGGCCGATATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCGCGT
129 GTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAC-CGCGT
* * * * *
56476 TCTAGGGCCCCGACTTAGATTTGCTTGATTTTTGACAACAAGACTCCTTAAAATATTTATATTCA
193 TCTTGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATATTCA
* * * *
56541 TATAACAAAATCTCAGCCACAATGGATTTAAGAATAATATTTTAT-GAGCATCTAAATTATGTTC
258 TCTAACCAAATCTCAGCCACAATGGATTTAAGAATAAT-TTTTTTCGAGCATCT-AATTATGTTT
56605 CGATTTAAAT
321 CGATTT-AAT
* *
56615 T-GAAATTAATTCGGAAAATAGGAAAAATGATATTAGATA-CCTGAAAAGCCCATAAATTTTATT
1 TAGAAATTAATTCGGAAAATAGGAAAAATGATATTAGA-AGCCTGAAAAGCCCTTAAATTTTTTT
* * * *
56678 GGCGTTGATTTATATATTTTCTATGAGTATTGTGGTCAAAAATTGAGGAAAAATTTTTCCGGACA
65 GGCGTTGAATTATATATTTT-TATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGATA
* ** * *
56743 GTTTTTGCAAAATTTTAGCCGAAATC----A-T---CATCACAAATTTTGACTAAAAA-TGCGTT
129 GTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACCGCGTT
* ** ** * ** *
56799 CTTCGGCCCCGACACAGTTTTGCATGATTTTTGGC-GCCAAGTGTCATTGTAATATCTATATTCA
194 CTTGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAG-CAAGACTCCTTAAAATATTTATATTCA
* * * * * * * *
56863 TCTAAACAATTCTCGGCCACATTGGATTT-A-AATATTTGTTTTTATGAGAATCAGAATTATGTT
258 TCTAACCAAATCTCAGCCACAATGGATTTAAGAATAATT-TTTTT-CGAGCATC-TAATTATGTT
56926 TCGATTTAAT
320 TCGATTTAAT
* * * ** * * *
56936 TAGAAATTAATTCGGAACAAATTA-GAAAAACGAAAATT-GAAGCGTCTAAAGCCCTTCAGTCTT
1 TAGAAATTAATTCGG-A-AAA-TAGGAAAAATG-ATATTAGAAGCCTGAAAAGCCCTTAAATTTT
** * *
56999 TTTGGATTTGAATAATATAATTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGG
62 TTTGGCGTTGAATTATAT-ATTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGG
* ** * ** * *
57064 ACAGTTTTTGCAAAATTCAGGCCGATATCGTGTACTAACCATTGCTGTTTTTGGGTAAAAACGCG
126 ATAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAC-CG
* * * * *
57129 CGTTCTGGGGCCTCGGCTTAGTTTTGCTTGATTTTTGACAGCAAGACTCCTTAAAATATTTATAT
190 CGTTCTTGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATAT
* * *
57194 TCATATAACCAAATCTCAGCCACAATGGATTTAAGAATAATATTTTACGAGCATCTAAATTATGT
255 TCATCTAACCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTTCGAGCATCT-AATTATGT
*
57259 TTCGATTTAAA
319 TTCGATTTAAT
* *
57270 TGGAAATTAATTCGGAAAATAGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTG
1 TAGAAATTAATTCGGAAAATAGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTTTTG
* * * * *
57335 GCGTTCATTTATATATTTTCTATGAGTATTGTGGTCAAAAATTGAGGAAAAATTTTTCCGGACAG
66 GCGTTGAATTATATATTTT-TATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGATAG
* * * * *
57400 ATTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCACAGTTTTTGACTAAAAA-TGCGTTC
130 TTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACCGCGTTC
** ** * ** *
57464 TTGGGCCCCGACACAGTTTTGCATGATTTTTGGC-GCCAAGTGTCATTGTAATATCTATATTCAT
195 TTGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAG-CAAGACTCCTTAAAATATTTATATTCAT
* * * * * *
57528 CTAAACAATTCTCGGCCACATTGGATTT-A-AATATTTGTTTTTATGAGCATCTGAATTATGTTT
259 CTAACCAAATCTCAGCCACAATGGATTTAAGAATAATT-TTTTT-CGAGCATCT-AATTATGTTT
57591 CGATTTAAT
321 CGATTTAAT
* * * * ** * * ** * * * *
57600 TTGAAATTTATTTGGAAAAAATTAGAAAATCGAAAATT-GAAGCGTCTAAAGCCATTCAGTCTTT
1 TAGAAATTAATTCGGAAAATAGGA-AAAAT-G-ATATTAGAAGCCTGAAAAGCCCTTAAATTTTT
* *
57664 TT-GCATTTGAATAATATAATTTTTATGAG-AGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGG
63 TTGGC-GTTGAATTATAT-ATTTTTATGAGTA-TTGTGGCCAAAAATTGAGGAAAAATTTTTCGG
* * **
57727 GACAGTTTTTGCAAAATTTTGACCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAA-TA
125 GATAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACCG
** * ** * * *
57791 CGTTCTTAAGCCCCGGCACAGTTTTGGATGATTTTTGGCAGCAAGACTCCTTAAAATATCTATTT
190 CGTTCTTGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATAT
* * ** * ** * *
57856 TGATCTAACCAAATCTCAGACACGGTGGATTTAAGGATAAGGTTTTACGAGTATCTGAATTATGT
255 TCATCTAACCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTTCGAGCATCT-AATTATGT
*
57921 TTCTATTTAAT
319 TTCGATTTAAT
* * * * * * *
57932 TAGAAATTAATTCAGAAAATAGGACAAACGATATTATAAGCATGAAAAGCCCTTAAATTTTGTTA
1 TAGAAATTAATTCGGAAAATAGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTTTTG
** * * * * * * *
57997 GCGACGAGTTCTATATTTTTTATGAGTGTTGTAGTCAAAAATTGAGGAAAAATTTTTTGGGATAC
66 GCGTTGAATTATATA-TTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGATAG
58062 TTTTT
130 TTTTT
58067 ACTTAAAAGA
Statistics
Matches: 2732, Mismatches: 525, Indels: 273
0.77 0.15 0.08
Matches are distributed among these distances:
309 16 0.01
310 90 0.03
311 10 0.00
312 114 0.04
313 14 0.01
314 115 0.04
315 16 0.01
316 92 0.03
317 11 0.00
318 4 0.00
319 2 0.00
320 10 0.00
321 16 0.01
322 189 0.07
323 67 0.02
324 243 0.09
325 22 0.01
326 1 0.00
327 1 0.00
328 9 0.00
329 295 0.11
330 457 0.17
331 153 0.06
332 625 0.23
333 31 0.01
334 118 0.04
335 6 0.00
336 5 0.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (329 bp):
TAGAAATTAATTCGGAAAATAGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTTTTG
GCGTTGAATTATATATTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGATAGT
TTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACCGCGTTCT
TGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATATTCATCT
AACCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTTCGAGCATCTAATTATGTTTCGATT
TAAT
Found at i:57764 original size:664 final size:660
Alignment explanation
Indices: 55705--58053 Score: 2869
Period size: 656 Copynumber: 3.6 Consensus size: 660
55695 GGCGTTCATT
* * * * * *
55705 TATATATTTTCTATGAGTGTTGTGGTCAAAAATTGGGGAAAAA-TTTTCCGGAGAGATTTTGCAA
1 TATA-ATTTT-TATGAGAGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAA
* * * *
55769 AATT-TTAGCCGAAATCATGTACTAACCATCACAGTTTTTGGCTAAAAATGCGTTCTTAGGCTCC
64 AATTCTGA-CCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCTTAGGCCCC
* * * *
55833 GGCACAGTTTTGGATGATTTTTGGCAGCAAGACTCCTTAAAATATCTATTTTCATCTAACAAAAT
128 GGCACAGTTTTGCATGATTTTTGACAGCAAGACTCCTTAAAATATCTATATTCATATAACAAAAT
* * * * * * *
55898 CTCATATACAATGGATTTAACG-ATAAGGTTTTAGGAGCATCTTAATTATGTTTCAATTTAATTA
193 CTCAGACACAATGGATTTAA-GAATAAGATTTTACGAGCATCTAAATTATGTTTCGATTTAAATA
* * * *
55962 GAAATTAATTTGAAAAATAGGAAAAACGATATTATAAGCATGAAAAGCCCTTAAATTTTTTTAGC
257 GAAATTAATTCGGAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCCCTTAAATTTTATTAGC
* * * ** * *
56027 GATGAGTTATATATTTTTTATGAGTATTGTGACCAAAAAGTGAGGAAAAATTTTT--GAGAGAGT
322 GTTCAGTTATATATTTTCTATGAGTATTGTGGTCAAAAATTGAGGAAAAATTTTTCCG-GACAGT
* * *
56090 TTTTGCAAAATTTT-GACCAAAATCGTGTACTTACCATCACAGTTTTTGGCTAAAAACACGCGTT
386 TTTTGCAAAATTTTAG-CCGAAATC-TGTAC-TACCATCACAGTTTTTGACT-AAAA-ATGCGTT
** ** ** * ** * *
56154 C-TGGAG-CCCGACTTAGTTTTGCATGATTTTTGGCATCAAGACTCCTTAAAACATTTATATTCA
446 CTTGG-GCCCCGACACAGTTTTGCATGATTTTTGGCGCCAAGTGTCATTGTAATATCTATATTCA
* * * * * * * *
56217 TCTAATCAAATATCAGCCACAATGGATTTAAGGATA-AT-TTTTTACGAGTATCTGAATTATGTT
510 TCTAAACAATTCTCGGCCACATTGGATTTAA--ATATTTGTTTTTATGAGAATCTGAATTATGTT
* **
56280 TCGATTTAATTAGAAATTAATTCGG-AAAAATT-----AT-----ATTAGAAGCCTGAAAAGCCC
573 TCGATTTAATTAGAAATTAATTCGGAAAAAATTAGAAAATCGAAAATT-GAAGCGTCTAAAGCCC
* * *
56334 TT-AAT-TTTAATTGGC-CTTGAATTA
637 TTCAGTCTTT--TT-GCATTTGAATAA
* * * *
56358 TAT-TTTTGTTATGAGTA-TTGTGGCCACAATTTGAGGAAAAATTTTTCGGGATAGTTTTTGCAA
1 TATAATTT-TTATGAG-AGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAA
* * *
56421 AATTCTGGCCGATATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCGCGTTC-TAGGGCC
64 AATTCTGACCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAA--CGCGTTCTTA-GGCC
* ** * * * *
56485 CCGACTTAGATTTGCTTGATTTTTGACAACAAGACTCCTTAAAATATTTATATTCATATAACAAA
126 CCGGCACAGTTTTGCATGATTTTTGACAGCAAGACTCCTTAAAATATCTATATTCATATAACAAA
* * * *
56550 ATCTCAGCCACAATGGATTTAAGAATAATATTTTATGAGCATCTAAATTATGTTCCGATTTAAAT
191 ATCTCAGACACAATGGATTTAAGAATAAGATTTTACGAGCATCTAAATTATGTTTCGATTTAAAT
* * * * *
56615 TGAAATTAATTCGGAAAATAGGAAAAATGATATTAGATA-CCTGAAAAGCCCATAAATTTTATTG
256 AGAAATTAATTCGGAAAATAGGAAAAACGATATTAGA-AGCATGAAAAGCCCTTAAATTTTATTA
* *
56679 GCGTTGATTTATATATTTTCTATGAGTATTGTGGTCAAAAATTGAGGAAAAATTTTTCCGGACAG
320 GCGTTCAGTTATATATTTTCTATGAGTATTGTGGTCAAAAATTGAGGAAAAATTTTTCCGGACAG
** *
56744 TTTTTGCAAAATTTTAGCCGAAATC---A-T--CATCACAAATTTTGACTAAAAATGCGTTCTTC
385 TTTTTGCAAAATTTTAGCCGAAATCTGTACTACCATCACAGTTTTTGACTAAAAATGCGTTCTTG
56803 GGCCCCGACACAGTTTTGCATGATTTTTGGCGCCAAGTGTCATTGTAATATCTATATTCATCTAA
450 GGCCCCGACACAGTTTTGCATGATTTTTGGCGCCAAGTGTCATTGTAATATCTATATTCATCTAA
*
56868 ACAATTCTCGGCCACATTGGATTTAAATATTTGTTTTTATGAGAATCAGAATTATGTTTCGATTT
515 ACAATTCTCGGCCACATTGGATTTAAATATTTGTTTTTATGAGAATCTGAATTATGTTTCGATTT
* *
56933 AATTAGAAATTAATTCGGAACAAATTAGAAAAACGAAAATTGAAGCGTCTAAAGCCCTTCAGTCT
580 AATTAGAAATTAATTCGGAAAAAATTAGAAAATCGAAAATTGAAGCGTCTAAAGCCCTTCAGTCT
*
56998 TTTTGGATTTGAATAA
645 TTTTGCATTTGAATAA
*
57014 TATAATTTTTATGAGTGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAA
1 TATAATTTTTATGAGAGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAA
* * * ** * * ** *
57079 TTCAGGCCGATATCGTGTACTAACCATTGCTGTTTTTGGGTAAAAACGCGCGTTCTGGGGCCTCG
66 TTCTGACCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAA--CGCGTTCTTAGGCCCCG
** * * *
57144 GCTTAGTTTTGCTTGATTTTTGACAGCAAGACTCCTTAAAATATTTATATTCATATAACCAAATC
129 GCACAGTTTTGCATGATTTTTGACAGCAAGACTCCTTAAAATATCTATATTCATATAACAAAATC
* * *
57209 TCAGCCACAATGGATTTAAGAATAATATTTTACGAGCATCTAAATTATGTTTCGATTTAAATGGA
194 TCAGACACAATGGATTTAAGAATAAGATTTTACGAGCATCTAAATTATGTTTCGATTTAAATAGA
* * *
57274 AATTAATTCGGAAAATAGGAAAAATGATATTAGAAGCCTGAAAAGCCCTTAAATTTTATTGGCGT
259 AATTAATTCGGAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCCCTTAAATTTTATTAGCGT
* *
57339 TCATTTATATATTTTCTATGAGTATTGTGGTCAAAAATTGAGGAAAAATTTTTCCGGACAGATTT
324 TCAGTTATATATTTTCTATGAGTATTGTGGTCAAAAATTGAGGAAAAATTTTTCCGGACAGTTTT
57404 TGCAAAATTTTAGCCGAAATCATGTACTAACCATCACAGTTTTTGACTAAAAATGCGTTCTTGGG
389 TGCAAAATTTTAGCCGAAATC-TGTACT-ACCATCACAGTTTTTGACTAAAAATGCGTTCTTGGG
57469 CCCCGACACAGTTTTGCATGATTTTTGGCGCCAAGTGTCATTGTAATATCTATATTCATCTAAAC
452 CCCCGACACAGTTTTGCATGATTTTTGGCGCCAAGTGTCATTGTAATATCTATATTCATCTAAAC
*
57534 AATTCTCGGCCACATTGGATTTAAATATTTGTTTTTATGAGCATCTGAATTATGTTTCGATTTAA
517 AATTCTCGGCCACATTGGATTTAAATATTTGTTTTTATGAGAATCTGAATTATGTTTCGATTTAA
* * * *
57599 TTTGAAATTTATTTGGAAAAAATTAGAAAATCGAAAATTGAAGCGTCTAAAGCCATTCAGTCTTT
582 TTAGAAATTAATTCGGAAAAAATTAGAAAATCGAAAATTGAAGCGTCTAAAGCCCTTCAGTCTTT
57664 TTGCATTTGAATAA
647 TTGCATTTGAATAA
57678 TATAATTTTTATGAGAGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAA
1 TATAATTTTTATGAGAGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAA
* ** *
57743 TTTTGACCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAATACGTTCTTAAGCCCCGGC
66 TTCTGACCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCTTAGGCCCCGGC
* * * * * *
57808 ACAGTTTTGGATGATTTTTGGCAGCAAGACTCCTTAAAATATCTATTTTGATCTAACCAAATCTC
131 ACAGTTTTGCATGATTTTTGACAGCAAGACTCCTTAAAATATCTATATTCATATAACAAAATCTC
** * * * * * *
57873 AGACACGGTGGATTTAAGGATAAGGTTTTACGAGTATCTGAATTATGTTTCTATTTAATTAGAAA
196 AGACACAATGGATTTAAGAATAAGATTTTACGAGCATCTAAATTATGTTTCGATTTAAATAGAAA
* * * * *
57938 TTAATTCAGAAAATAGGACAAACGATATTATAAGCATGAAAAGCCCTTAAATTTTGTTAGCG-AC
261 TTAATTCGGAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCCCTTAAATTTTATTAGCGTTC
* * * *
58002 GAGTTCTATATTTTTTATGAGTGTTGTAGTCAAAAATTGAGGAAAAATTTTT
326 -AGTTATATATTTTCTATGAGTATTGTGGTCAAAAATTGAGGAAAAATTTTT
58054 TGGGATACTT
Statistics
Matches: 1483, Mismatches: 170, Indels: 77
0.86 0.10 0.04
Matches are distributed among these distances:
644 3 0.00
645 9 0.01
646 125 0.08
647 20 0.01
649 1 0.00
651 30 0.02
652 61 0.04
653 7 0.00
654 220 0.15
655 29 0.02
656 407 0.27
657 8 0.01
658 3 0.00
660 1 0.00
661 2 0.00
662 224 0.15
664 333 0.22
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (660 bp):
TATAATTTTTATGAGAGTTGTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAA
TTCTGACCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCTTAGGCCCCGGC
ACAGTTTTGCATGATTTTTGACAGCAAGACTCCTTAAAATATCTATATTCATATAACAAAATCTC
AGACACAATGGATTTAAGAATAAGATTTTACGAGCATCTAAATTATGTTTCGATTTAAATAGAAA
TTAATTCGGAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCCCTTAAATTTTATTAGCGTTC
AGTTATATATTTTCTATGAGTATTGTGGTCAAAAATTGAGGAAAAATTTTTCCGGACAGTTTTTG
CAAAATTTTAGCCGAAATCTGTACTACCATCACAGTTTTTGACTAAAAATGCGTTCTTGGGCCCC
GACACAGTTTTGCATGATTTTTGGCGCCAAGTGTCATTGTAATATCTATATTCATCTAAACAATT
CTCGGCCACATTGGATTTAAATATTTGTTTTTATGAGAATCTGAATTATGTTTCGATTTAATTAG
AAATTAATTCGGAAAAAATTAGAAAATCGAAAATTGAAGCGTCTAAAGCCCTTCAGTCTTTTTGC
ATTTGAATAA
Found at i:58925 original size:20 final size:20
Alignment explanation
Indices: 58900--58939 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
58890 ATTGAGCTAT
58900 ATCATATGTAATGCAGAAAA
1 ATCATATGTAATGCAGAAAA
*
58920 ATCATATGTAATGTAGAAAA
1 ATCATATGTAATGCAGAAAA
58940 GGAGTCTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (20 bp):
ATCATATGTAATGCAGAAAA
Found at i:59676 original size:10 final size:10
Alignment explanation
Indices: 59663--59726 Score: 60
Period size: 10 Copynumber: 6.4 Consensus size: 10
59653 AGGTACACGA
*
59663 GAAGACAAAG
1 GAAGACAGAG
59673 GAAGACAGAG
1 GAAGACAGAG
59683 GAAGACAGAG
1 GAAGACAGAG
*
59693 GAAGGCACGAAG
1 GAAGACA-G-AG
* *
59705 GTACAC-GA-
1 GAAGACAGAG
59713 GAAGACAGAG
1 GAAGACAGAG
59723 GAAG
1 GAAG
59727 GAAGAGGCCT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
8 4 0.09
9 3 0.07
10 30 0.70
11 1 0.02
12 5 0.12
ACGTcount: A:0.48, C:0.12, G:0.38, T:0.02
Consensus pattern (10 bp):
GAAGACAGAG
Found at i:59677 original size:39 final size:39
Alignment explanation
Indices: 59605--59679 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
59595 CTTAACAAGG
* * *
59605 CAGACACGATGGTACACGAGATAACACATGAAGACACGA
1 CAGACACGAAGGTACACGAGATAACAAAGGAAGACACGA
59644 CAGACACGAAGGTACACGAGA-AGACAAAGGAAGACA
1 CAGACACGAAGGTACACGAGATA-ACAAAGGAAGACA
59680 GAGGAAGACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.47, C:0.21, G:0.25, T:0.07
Consensus pattern (39 bp):
CAGACACGAAGGTACACGAGATAACAAAGGAAGACACGA
Found at i:59765 original size:62 final size:62
Alignment explanation
Indices: 59695--59936 Score: 204
Period size: 62 Copynumber: 3.6 Consensus size: 62
59685 AGACAGAGGA
*
59695 AGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGC
1 AGGCACGAAGGTACACGAGAAGACAAAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGC
* *
59757 AGGCACGAAGGTACACGAGAAGACAAAGGAAGGAAGAGG---CAG-AGGAAGGAAGAGGCCTCCG
1 AGGCACGAAGGTACACGAGAAGACAAAGGAAGGAAGAGGCCTCCGCAGG-AGG-CGAGG----C-
*
59818 CAGG
59 CAGC
* * * *
59822 AGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAGAGGAAAGAAGAGGCCTCCGCAGGAGG
1 AGGC-A---C-GAAGGTAC--------ACGAGAAGACAAAGGAAGGAAGAGGCCTCCGCAGGAGG
59887 CGAGGCCAGC
53 CGAGGCCAGC
59897 AGGCACGAAGGTACACGAGAAGACAAAGGAAGGAAGAGGC
1 AGGCACGAAGGTACACGAGAAGACAAAGGAAGGAAGAGGC
59937 AGAGGAAGGA
Statistics
Matches: 141, Mismatches: 15, Indels: 48
0.69 0.07 0.24
Matches are distributed among these distances:
58 3 0.02
59 5 0.04
60 4 0.03
62 62 0.44
64 1 0.01
65 7 0.05
66 1 0.01
69 1 0.01
70 12 0.09
71 1 0.01
74 1 0.01
75 7 0.05
76 1 0.01
78 23 0.16
80 4 0.03
81 5 0.04
82 3 0.02
ACGTcount: A:0.37, C:0.20, G:0.40, T:0.03
Consensus pattern (62 bp):
AGGCACGAAGGTACACGAGAAGACAAAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGC
Found at i:59821 original size:78 final size:78
Alignment explanation
Indices: 59718--59874 Score: 296
Period size: 78 Copynumber: 2.0 Consensus size: 78
59708 CACGAGAAGA
59718 CAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAA
1 CAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAA
*
59783 AGGAAGGAAGAGG
66 AGGAAAGAAGAGG
*
59796 CAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAG
1 CAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAA
59861 AGGAAAGAAGAGG
66 AGGAAAGAAGAGG
59874 C
1 C
59875 CTCCGCAGGA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.37, C:0.20, G:0.41, T:0.03
Consensus pattern (78 bp):
CAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAA
AGGAAAGAAGAGG
Found at i:59872 original size:140 final size:140
Alignment explanation
Indices: 59695--60005 Score: 613
Period size: 140 Copynumber: 2.2 Consensus size: 140
59685 AGACAGAGGA
*
59695 AGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 AGGCACGAAGGTACACGAGAAGACAGAGGAAAGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
59760 CACGAAGGTACACGAGAAGACAAAGGAAGGAAGAGGCAGAGGAAGGAAGAGGCCTCCGCAGGAGG
66 CACGAAGGTACACGAGAAGACAAAGGAAGGAAGAGGCAGAGGAAGGAAGAGGCCTCCGCAGGAGG
59825 CGAGGCCAGC
131 CGAGGCCAGC
59835 AGGCACGAAGGTACACGAGAAGACAGAGGAAAGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 AGGCACGAAGGTACACGAGAAGACAGAGGAAAGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
59900 CACGAAGGTACACGAGAAGACAAAGGAAGGAAGAGGCAGAGGAAGGAAGAGGCCTCCGCAGGAGG
66 CACGAAGGTACACGAGAAGACAAAGGAAGGAAGAGGCAGAGGAAGGAAGAGGCCTCCGCAGGAGG
59965 CGAGGCCAGC
131 CGAGGCCAGC
59975 AGGCACGAAGGTACACGAGAAGACAGAGGAA
1 AGGCACGAAGGTACACGAGAAGACAGAGGAA
60006 GACAGACACG
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 170 1.00
ACGTcount: A:0.37, C:0.20, G:0.40, T:0.03
Consensus pattern (140 bp):
AGGCACGAAGGTACACGAGAAGACAGAGGAAAGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
CACGAAGGTACACGAGAAGACAAAGGAAGGAAGAGGCAGAGGAAGGAAGAGGCCTCCGCAGGAGG
CGAGGCCAGC
Found at i:59899 original size:78 final size:78
Alignment explanation
Indices: 59739--59977 Score: 223
Period size: 78 Copynumber: 3.1 Consensus size: 78
59729 AGAGGCCTCC
* *
59739 GCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAAAGGAAGGAAGAGG---CAG-A
1 GCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCA
* *
59800 GGAAGGAAGAGGCCTCC
66 GG-AGG-CGAGG-C-CA
*
59817 GCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAGAGGAAAGAAGAGGCCTCCGCA
1 GCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCA
59882 GGAGGCGAGGCCA
66 GGAGGCGAGGCCA
* *
59895 GCAGGCA--CGAAGGTACACGAG-AAG-ACAAAGG-A-A-G-GAAGAGGCAGAGGAAGGAAGAGG
1 GCAGG-AGGCG-AGG--C-C-AGCAGGCACGAAGGTACACGAGAAGA--CAGAGGAAGGAAGAGG
59952 CCTCCGCAGGAGGCGAGGCCA
58 CCTCCGCAGGAGGCGAGGCCA
59973 GCAGG
1 GCAGG
59978 CACGAAGGTA
Statistics
Matches: 141, Mismatches: 8, Indels: 24
0.82 0.05 0.14
Matches are distributed among these distances:
76 5 0.04
77 3 0.02
78 106 0.75
79 3 0.02
80 11 0.08
81 8 0.06
82 5 0.04
ACGTcount: A:0.36, C:0.21, G:0.41, T:0.03
Consensus pattern (78 bp):
GCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCA
GGAGGCGAGGCCA
Found at i:59961 original size:62 final size:60
Alignment explanation
Indices: 59799--59953 Score: 179
Period size: 62 Copynumber: 2.5 Consensus size: 60
59789 GAAGAGGCAG
* * * *
59799 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAG
1 AGGAAAGAAGAGG-C-CAGCAGGAGGAGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAA
* *
59861 AGGAAAGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAA
1 AGGAAAGAAGAGG-C-CAGCAGGAGGAGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAA
*
59923 AGGAAGGAAGAGG-CAG-AGGAAGGAAGAGGCC
1 AGGAAAGAAGAGGCCAGCAGG-AGG-AGAGGCC
59954 TCCGCAGGAG
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
58 3 0.03
59 5 0.06
60 6 0.07
62 72 0.84
ACGTcount: A:0.37, C:0.20, G:0.41, T:0.03
Consensus pattern (60 bp):
AGGAAAGAAGAGGCCAGCAGGAGGAGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAA
Found at i:59978 original size:78 final size:78
Alignment explanation
Indices: 59858--60006 Score: 280
Period size: 78 Copynumber: 1.9 Consensus size: 78
59848 CACGAGAAGA
59858 CAGAGGAAAGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAA
1 CAGAGGAAAGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAA
59923 AGGAAGGAAGAGG
66 AGGAAGGAAGAGG
* *
59936 CAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAG
1 CAGAGGAAAGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAA
60001 AGGAAG
66 AGGAAG
60007 ACAGACACGA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.37, C:0.20, G:0.40, T:0.03
Consensus pattern (78 bp):
CAGAGGAAAGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAA
AGGAAGGAAGAGG
Found at i:60021 original size:34 final size:34
Alignment explanation
Indices: 59978--60067 Score: 180
Period size: 34 Copynumber: 2.6 Consensus size: 34
59968 GGCCAGCAGG
59978 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
60012 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
60046 CACGAAGGTACACGAGAAGACA
1 CACGAAGGTACACGAGAAGACA
60068 CAGTGGTGCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.47, C:0.19, G:0.31, T:0.03
Consensus pattern (34 bp):
CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
Found at i:60176 original size:2 final size:2
Alignment explanation
Indices: 60171--60225 Score: 101
Period size: 2 Copynumber: 27.0 Consensus size: 2
60161 AGAAACACAC
60171 AG AG AG AG AG AG AG AG AG AG TAG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG
60214 AG AG AG AG AG AG
1 AG AG AG AG AG AG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 50 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
AG
Done.