Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009290.1 Corchorus capsularis cultivar CVL-1 contig09311, 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: 30518
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Found at i:158 original size:26 final size:23
Alignment explanation
Indices: 58--187 Score: 74
Period size: 26 Copynumber: 5.5 Consensus size: 23
48 TTTTTATATA
58 ATATATATT-TAAAATATATTA-T
1 ATATATATTAT-AAATATATTATT
* * * *
80 ATATATGTTTCTATTATATATAAATAT
1 ATATAT-ATTATA-AATATAT-TAT-T
* *
107 ATATAAATT-TAAA-ATA-TACT
1 ATATATATTATAAATATATTATT
*
127 ATATATATTATAAATATATTTTCT
1 ATATATATTATAAATATATTAT-T
151 ATAAATATATT-TAAAATATATTATT
1 AT--ATATATTAT-AAATATATTATT
176 ATATATATTATA
1 ATATATATTATA
188 TTTGTTTTTA
Statistics
Matches: 82, Mismatches: 12, Indels: 27
0.68 0.10 0.22
Matches are distributed among these distances:
20 9 0.11
21 5 0.06
22 9 0.11
23 15 0.18
24 12 0.15
25 7 0.09
26 19 0.23
27 6 0.07
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (23 bp):
ATATATATTATAAATATATTATT
Found at i:206 original size:2 final size:2
Alignment explanation
Indices: 52--188 Score: 53
Period size: 2 Copynumber: 73.5 Consensus size: 2
42 TAGAAATTTT
* * * * *
52 TA TA TA -A TA TA TA TT TA -A AA TA TA T- TA TA TA TA TG TT TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
91 TA T- TA TA TA TA AA TA TA TA TA AA TT TA -A AA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * * *
132 TA T- TA TA AA TA TA T- TT TC TA TA AA TA TA TT TA -A AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
171 T- TA T- TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
189 TTGTTTTTAT
Statistics
Matches: 100, Mismatches: 23, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
1 11 0.11
2 87 0.87
3 2 0.02
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9430 original size:2 final size:2
Alignment explanation
Indices: 9423--9453 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9413 TTTGTTGCAT
9423 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9454 ACACACACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:9459 original size:2 final size:2
Alignment explanation
Indices: 9454--9490 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9444 CTCTCTCTCT
9454 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
9491 GAGACAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:13081 original size:48 final size:48
Alignment explanation
Indices: 13029--13331 Score: 175
Period size: 48 Copynumber: 6.3 Consensus size: 48
13019 TGTGGGAGGA
* * *
13029 GGAGGTGATTTATAGTAGTATGGAGGTGGAGGGGAGGGTGATGGTGGT
1 GGAGGGGATTTATAGTAGTATGGAGGGGGAGGGGATGGTGATGGTGGT
* * * * * * *
13077 GGAGGAGACTTGTAATAGTATGGAGGGGGAGGTGATGGTGAAGGAGGT
1 GGAGGGGATTTATAGTAGTATGGAGGGGGAGGGGATGGTGATGGTGGT
* * * * * * * **
13125 GGCGGTGACTTGTAG-AGGTAAGGAGGTGGTGGGCTTGGTGATGGTGGT
1 GGAGGGGATTTATAGTA-GTATGGAGGGGGAGGGGATGGTGATGGTGGT
* * * * * * *
13173 GGTGGGGATTTATAG-ACATAAGGAGGGGGAGGTGAGGGAGATGGTGGA
1 GGAGGGGATTTATAGTA-GTATGGAGGGGGAGGGGATGGTGATGGTGGT
* * * *
13221 GGAGGGGACTTGTA-AAT-GTATGGAGGAGGTGGCGATGGTGATGGTGGT
1 GGAGGGGA-TT-TATAGTAGTATGGAGGGGGAGGGGATGGTGATGGTGGT
* * * * * * * *
13269 GGTGGAGACTTATAG-ATGTAAGGAGGGGGTGGTGATGGAGAAGGTGGT
1 GGAGGGGATTTATAGTA-GTATGGAGGGGGAGGGGATGGTGATGGTGGT
*
13317 GGTGGGGATTTATAG
1 GGAGGGGATTTATAG
13332 ACATAGGGTG
Statistics
Matches: 193, Mismatches: 55, Indels: 14
0.74 0.21 0.05
Matches are distributed among these distances:
46 2 0.01
47 3 0.02
48 183 0.95
49 3 0.02
50 2 0.01
ACGTcount: A:0.22, C:0.03, G:0.51, T:0.24
Consensus pattern (48 bp):
GGAGGGGATTTATAGTAGTATGGAGGGGGAGGGGATGGTGATGGTGGT
Found at i:13332 original size:48 final size:48
Alignment explanation
Indices: 13065--13693 Score: 553
Period size: 48 Copynumber: 13.1 Consensus size: 48
13055 TGGAGGGGAG
* * * * *
13065 GGTGATGGTGGTGGAGGAGACTTGTA-ATAGTATGGAGGGGGAGGTGAT
1 GGTGATGGTGGTGGTGGAGACTTGTAGACA-TAAGGAGGAGGTGGTGAT
* * * * ** * *
13113 GGTGAAGGAGGTGGCGGTGACTTGTAGAGGTAAGGAGGTGGTGG-GCTT
1 GGTGATGGTGGTGGTGGAGACTTGTAGACATAAGGAGGAGGTGGTG-AT
* * * * * *
13161 GGTGATGGTGGTGGTGGGGATTTATAGACATAAGGAGGGGGAGGTGAG
1 GGTGATGGTGGTGGTGGAGACTTGTAGACATAAGGAGGAGGTGGTGAT
* * * * * ** * *
13209 GGAGATGGTGGAGGAGGGGACTTGTAAATGTATGGAGGAGGTGGCGAT
1 GGTGATGGTGGTGGTGGAGACTTGTAGACATAAGGAGGAGGTGGTGAT
* ** *
13257 GGTGATGGTGGTGGTGGAGACTTATAGATGTAAGGAGGGGGTGGTGAT
1 GGTGATGGTGGTGGTGGAGACTTGTAGACATAAGGAGGAGGTGGTGAT
* * * * * * * * * *
13305 GGAGAAGGTGGTGGTGGGGATTTATAGACATAGGGTGGGGGTGGAGAA
1 GGTGATGGTGGTGGTGGAGACTTGTAGACATAAGGAGGAGGTGGTGAT
* * * *
13353 GGAGACGGAGGTGGTGGGGACTTGTAGACATAAGGAGGAGGTGGTGAT
1 GGTGATGGTGGTGGTGGAGACTTGTAGACATAAGGAGGAGGTGGTGAT
* * * *
13401 GGTGATGGCGGAGGTGGAGACTTGTAGATATATGGAGGAGGTGGTGAT
1 GGTGATGGTGGTGGTGGAGACTTGTAGACATAAGGAGGAGGTGGTGAT
* * *
13449 GGCGATGGTGGAGGTGGAGACTTGTAGACATAAGGAGGAGGTGGAGAT
1 GGTGATGGTGGTGGTGGAGACTTGTAGACATAAGGAGGAGGTGGTGAT
* * * *
13497 GGCGATGGTGGAGGTGGAGACTTGTACACATAAGGAGGAGGTGGAGAT
1 GGTGATGGTGGTGGTGGAGACTTGTAGACATAAGGAGGAGGTGGTGAT
* * * * * *
13545 GGTGATGGTGGAGGTGGAGACTTATAAACATATGGAGGAGGTGGGGAG
1 GGTGATGGTGGTGGTGGAGACTTGTAGACATAAGGAGGAGGTGGTGAT
* *
13593 GGTGATGGTGGTGGAGGAGACTTATAGACATAAGGAGGAGGTGGTGAT
1 GGTGATGGTGGTGGTGGAGACTTGTAGACATAAGGAGGAGGTGGTGAT
* * * * * * * *
13641 GGAGATGGAGGTGGCGGAGATTTGTAGGA-ATATGAAGGAGGTGGAGGT
1 GGTGATGGTGGTGGTGGAGACTTGTA-GACATAAGGAGGAGGTGGTGAT
13689 GGTGA
1 GGTGA
13694 CTTGTAGAAG
Statistics
Matches: 479, Mismatches: 98, Indels: 8
0.82 0.17 0.01
Matches are distributed among these distances:
47 1 0.00
48 474 0.99
49 4 0.01
ACGTcount: A:0.24, C:0.04, G:0.49, T:0.22
Consensus pattern (48 bp):
GGTGATGGTGGTGGTGGAGACTTGTAGACATAAGGAGGAGGTGGTGAT
Found at i:13511 original size:21 final size:21
Alignment explanation
Indices: 13432--13564 Score: 79
Period size: 21 Copynumber: 5.8 Consensus size: 21
13422 TTGTAGATAT
*
13432 ATGGAGGAGGTGGTGATGGCG
1 ATGGAGGAGGTGGAGATGGCG
*
13453 ATGGTGGAGGTGGAGACTTGTAGAC-
1 ATGGAGGAGGTGGAGA--TG--G-CG
13478 ATAAGGAGGAGGTGGAGATGGCG
1 AT--GGAGGAGGTGGAGATGGCG
* * *
13501 ATGGTGGAGGTGGAGACTTGTACAC
1 ATGGAGGAGGTGGAGA--TG-GC-G
*
13526 ATAAGGAGGAGGTGGAGATGGTG
1 AT--GGAGGAGGTGGAGATGGCG
*
13549 ATGGTGGAGGTGGAGA
1 ATGGAGGAGGTGGAGA
13565 CTTATAAACA
Statistics
Matches: 87, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
21 40 0.46
22 1 0.01
23 9 0.10
24 1 0.01
25 9 0.10
26 1 0.01
27 26 0.30
ACGTcount: A:0.26, C:0.05, G:0.50, T:0.20
Consensus pattern (21 bp):
ATGGAGGAGGTGGAGATGGCG
Found at i:16552 original size:15 final size:15
Alignment explanation
Indices: 16534--16564 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16524 AGTAAGGTGG
16534 TGGTGGAGAAGGAGA
1 TGGTGGAGAAGGAGA
*
16549 TGGTGGAGGAGGAGA
1 TGGTGGAGAAGGAGA
16564 T
1 T
16565 TTGTAGTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.55, T:0.16
Consensus pattern (15 bp):
TGGTGGAGAAGGAGA
Found at i:16611 original size:144 final size:144
Alignment explanation
Indices: 16409--16917 Score: 564
Period size: 144 Copynumber: 3.5 Consensus size: 144
16399 CTTCATTGGA
* *
16409 GGAGGAGGTGATTTGTAGTAGTA-GGGAGGTGGTGGTGAGGGAGATGGTGGAGGGGGTGACTTAT
1 GGAGGAGGAGATTTGTAGTAGTATGGG-GGTGGTGGTGAAGGAGATGGTGGAGGGGGTGACTTAT
* * * * *
16473 AATAGTAAGGTGGTGGTGGTGA-TGGAGAAGGAGGTGGTGGGGATTTGTAGTAGTAAGGTGGTGG
65 AATAGTATGGTGGTGGTGG-GACTGGAGAAGGTGGTGGTGGAGACTTGTAGTAGTAAGGTGGAGG
*
16537 TGGAGAAGGAGATGGT
129 TGGAGATGGAGATGGT
*
16553 GGAGGAGGAGATTTGTAGTAGTATGGGGGTGGTGGTGAAGGAGATGGTGG-GGGTGGTGACTTGT
1 GGAGGAGGAGATTTGTAGTAGTATGGGGGTGGTGGTGAAGGAGATGGTGGAGGG-GGTGACTTAT
* * * * *
16617 AGTAGTATGGTGGTGGT-GGACTAGGAGATGGTGGAGGTGGTGACTTGTAGTAGTAAGGAGGAGG
65 AATAGTATGGTGGTGGTGGGACT-GGAGAAGGTGGTGGTGGAGACTTGTAGTAGTAAGGTGGAGG
*
16681 TGGTGATGGAGATGGT
129 TGGAGATGGAGATGGT
* * * * * * * *
16697 GGGGGTGGTGATTTGTAGTGGTATGGTGGTGGTGG-GCTAGGAGATGGTGGAGGTGGTGACTTGT
1 GGAGGAGGAGATTTGTAGTAGTATGGGGGTGGTGGTG-AAGGAGATGGTGGAGGGGGTGACTTAT
* *
16761 AGTAGTATGGTGGTGG-GGGACTTGGTGAAGGTGGTGGTGGAGACTTGTAGTAGTAAGGTGGAGG
65 AATAGTATGGTGGTGGTGGGAC-TGGAGAAGGTGGTGGTGGAGACTTGTAGTAGTAAGGTGGAGG
* * *
16825 GGGAGATGGCGATGGA
129 TGGAGATGGAGATGGT
* * * * * * * * * *
16841 GGTGGAGGAGATTTGTA-CACATAAGGAGGAGGAGGTGAAGGAGACGGTGGTGGGGGAGACTTAT
1 GGAGGAGGAGATTTGTAGTA-GTATGGGGGTGGTGGTGAAGGAGATGGTGGAGGGGGTGACTTAT
16905 AATAGTATGGTGG
65 AATAGTATGGTGG
16918 AGGAGGAGAT
Statistics
Matches: 308, Mismatches: 47, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
142 2 0.01
143 6 0.02
144 293 0.95
145 7 0.02
ACGTcount: A:0.22, C:0.03, G:0.50, T:0.25
Consensus pattern (144 bp):
GGAGGAGGAGATTTGTAGTAGTATGGGGGTGGTGGTGAAGGAGATGGTGGAGGGGGTGACTTATA
ATAGTATGGTGGTGGTGGGACTGGAGAAGGTGGTGGTGGAGACTTGTAGTAGTAAGGTGGAGGTG
GAGATGGAGATGGT
Found at i:16829 original size:27 final size:27
Alignment explanation
Indices: 16742--16830 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 27
16732 GCTAGGAGAT
* * *
16742 GGTGGAGGTGGTGACTTGTAGTAGTAT
1 GGTGGAGGGGGAGACTTGTAGTAGTAA
*
16769 GGTGG-TGGGG-GACTTG--GT-G-AA
1 GGTGGAGGGGGAGACTTGTAGTAGTAA
* *
16790 GGTGGTGGTGGAGACTTGTAGTAGTAA
1 GGTGGAGGGGGAGACTTGTAGTAGTAA
16817 GGTGGAGGGGGAGA
1 GGTGGAGGGGGAGA
16831 TGGCGATGGA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
21 6 0.12
22 4 0.08
23 8 0.16
25 8 0.16
26 4 0.08
27 19 0.39
ACGTcount: A:0.19, C:0.03, G:0.52, T:0.26
Consensus pattern (27 bp):
GGTGGAGGGGGAGACTTGTAGTAGTAA
Found at i:16839 original size:96 final size:97
Alignment explanation
Indices: 16415--16839 Score: 468
Period size: 96 Copynumber: 4.4 Consensus size: 97
16405 TGGAGGAGGA
* * * * * * * *
16415 GGTGATTTGTAGTAGTAGGGAGGTGGTGGTGA-GGGAGATGGTGGAGGGGGTGACTTATAATAGT
1 GGTGACTTGTAGTAGTAAGGTGGTGGTGGAGATAGGAGATGGTGGAGGTGGTGACTTGTAGTAGT
* *
16479 AAGGTGGTGGTGGTGATGGAGAAGGAGGTGGT
66 AAGGTGGTGGTGGTGATGGAGAAGGTGGGGGT
* * * * *
16511 GGGGATTTGTAGTAGTAAGGTGGTGGTGGAGA-AGGAGATGGTGGAGGAGGAGATTTGTAGTAGT
1 GGTGACTTGTAGTAGTAAGGTGGTGGTGGAGATAGGAGATGGTGGAGGTGGTGACTTGTAGTAGT
* * * *
16575 ATGGGGGTGGTGGTGAAGGAGATGGTGGGGGT
66 AAGGTGGTGGTGGTGATGGAGAAGGTGGGGGT
* *
16607 GGTGACTTGTAGTAGTATGGTGGTGGTGGA-CTAGGAGATGGTGGAGGTGGTGACTTGTAGTAGT
1 GGTGACTTGTAGTAGTAAGGTGGTGGTGGAGATAGGAGATGGTGGAGGTGGTGACTTGTAGTAGT
* * *
16671 AAGGAGGAGGTGGTGATGGAGATGGTGGGGGT
66 AAGGTGGTGGTGGTGATGGAGAAGGTGGGGGT
* * * *
16703 GGTGATTTGTAGTGGTATGGTGGTGGTGG-GCTAGGAGATGGTGGAGGTGGTGACTTGTAGTAGT
1 GGTGACTTGTAGTAGTAAGGTGGTGGTGGAGATAGGAGATGGTGGAGGTGGTGACTTGTAGTAGT
* * *
16767 ATGGTGGTGG-GG-GACTTGGTGAAGGTGGTGGT
66 AAGGTGGTGGTGGTGA--TGGAGAAGGTGGGGGT
* * * *
16799 GGAGACTTGTAGTAGTAAGGTGGAGGGGGAGAT-GGCGATGG
1 GGTGACTTGTAGTAGTAAGGTGGTGGTGGAGATAGGAGATGG
16840 AGGTGGAGGA
Statistics
Matches: 281, Mismatches: 43, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
94 2 0.01
95 2 0.01
96 275 0.98
97 2 0.01
ACGTcount: A:0.20, C:0.02, G:0.51, T:0.27
Consensus pattern (97 bp):
GGTGACTTGTAGTAGTAAGGTGGTGGTGGAGATAGGAGATGGTGGAGGTGGTGACTTGTAGTAGT
AAGGTGGTGGTGGTGATGGAGAAGGTGGGGGT
Found at i:16845 original size:48 final size:48
Alignment explanation
Indices: 16421--17012 Score: 411
Period size: 48 Copynumber: 12.4 Consensus size: 48
16411 AGGAGGTGAT
* * * * * * *
16421 TTGTAGTAGTAGGGAGGTGGTGGTGAGGGAGATGGTGGAGGGGGTGAC
1 TTGTAGTAGTAAGGTGGTGGTGGAGATGGAGATGGTGGTGGTGGAGAC
* * * * * * *
16469 TTATAATAGTAAGGTGGTGGTGGTGATGGAGAAGGAGGTGGTGGGGAT
1 TTGTAGTAGTAAGGTGGTGGTGGAGATGGAGATGGTGGTGGTGGAGAC
* * * *
16517 TTGTAGTAGTAAGGTGGTGGTGGAGAAGGAGATGGTGGAGGAGGAGAT
1 TTGTAGTAGTAAGGTGGTGGTGGAGATGGAGATGGTGGTGGTGGAGAC
* * * * * *
16565 TTGTAGTAGTATGGGGGTGGTGGTGAAGGAGATGGTGGGGGTGGTGAC
1 TTGTAGTAGTAAGGTGGTGGTGGAGATGGAGATGGTGGTGGTGGAGAC
* * * *
16613 TTGTAGTAGTATGGTGGTGGTGGA-CTAGGAGATGGTGGAGGTGGTGAC
1 TTGTAGTAGTAAGGTGGTGGTGGAGAT-GGAGATGGTGGTGGTGGAGAC
* * * * * *
16661 TTGTAGTAGTAAGGAGGAGGTGGTGATGGAGATGGTGGGGGTGGTGAT
1 TTGTAGTAGTAAGGTGGTGGTGGAGATGGAGATGGTGGTGGTGGAGAC
* * * * *
16709 TTGTAGTGGTATGGTGGTGGTGG-GCTAGGAGATGGTGGAGGTGGTGAC
1 TTGTAGTAGTAAGGTGGTGGTGGAGAT-GGAGATGGTGGTGGTGGAGAC
* * ** * *
16757 TTGTAGTAGTATGGTGGTGGGGGACTTGGTGAAGGTGGTGGTGGAGAC
1 TTGTAGTAGTAAGGTGGTGGTGGAGATGGAGATGGTGGTGGTGGAGAC
* * * * * *
16805 TTGTAGTAGTAAGGTGGAGGGGGAGATGGCGATGGAGGTGGAGGAGAT
1 TTGTAGTAGTAAGGTGGTGGTGGAGATGGAGATGGTGGTGGTGGAGAC
* * * * * * * * *
16853 TTGTA-CACATAAGGAGGAGGAGGTGAAGGAGACGGTGGTGGGGGAGAC
1 TTGTAGTA-GTAAGGTGGTGGTGGAGATGGAGATGGTGGTGGTGGAGAC
* * * * * * * * *
16901 TTATAATAGTATGGTGGAGGAGGAGATGGGGATGGCGGTGGAGGGGAC
1 TTGTAGTAGTAAGGTGGTGGTGGAGATGGAGATGGTGGTGGTGGAGAC
* * * * * * * *
16949 TTATAG-ACGTAGGGAGGAGGAGGTGATGGAGAAGGTGGTGGCGGAGAC
1 TTGTAGTA-GTAAGGTGGTGGTGGAGATGGAGATGGTGGTGGTGGAGAC
*
16997 TTATAGTAGT-AGGTGG
1 TTGTAGTAGTAAGGTGG
17013 GAGGTGGTGG
Statistics
Matches: 439, Mismatches: 97, Indels: 17
0.79 0.18 0.03
Matches are distributed among these distances:
47 8 0.02
48 427 0.97
49 4 0.01
ACGTcount: A:0.22, C:0.03, G:0.51, T:0.24
Consensus pattern (48 bp):
TTGTAGTAGTAAGGTGGTGGTGGAGATGGAGATGGTGGTGGTGGAGAC
Found at i:16857 original size:96 final size:97
Alignment explanation
Indices: 16415--17012 Score: 464
Period size: 96 Copynumber: 6.2 Consensus size: 97
16405 TGGAGGAGGA
* * * * * * * * *
16415 GGTGATTTGTAGTAGTAGGGAGGTGGTGGTGA-GGGAGATGGTGGAGGGGGTGACTTATAATAGT
1 GGTGACTTGTAGTAGTAAGGTGGTGGTGGAGATAGGAGATGGTGGAGGAGGAGACTTGTAGTAGT
* * * *
16479 AAGGTGGTGGTGGTGATGGAGAAGGAGGTGGT
66 ATGGAGGTGGTGGTGATGGAGAAGGTGGGGGT
* * *
16511 GGGGATTTGTAGTAGTAAGGTGGTGGTGGAGA-AGGAGATGGTGGAGGAGGAGATTTGTAGTAGT
1 GGTGACTTGTAGTAGTAAGGTGGTGGTGGAGATAGGAGATGGTGGAGGAGGAGACTTGTAGTAGT
* * *
16575 ATGGGGGTGGTGGTGAAGGAGATGGTGGGGGT
66 ATGGAGGTGGTGGTGATGGAGAAGGTGGGGGT
* * * *
16607 GGTGACTTGTAGTAGTATGGTGGTGGTGGA-CTAGGAGATGGTGGAGGTGGTGACTTGTAGTAGT
1 GGTGACTTGTAGTAGTAAGGTGGTGGTGGAGATAGGAGATGGTGGAGGAGGAGACTTGTAGTAGT
* * *
16671 AAGGAGGAGGTGGTGATGGAGATGGTGGGGGT
66 ATGGAGGTGGTGGTGATGGAGAAGGTGGGGGT
* * * * * *
16703 GGTGATTTGTAGTGGTATGGTGGTGGTGG-GCTAGGAGATGGTGGAGGTGGTGACTTGTAGTAGT
1 GGTGACTTGTAGTAGTAAGGTGGTGGTGGAGATAGGAGATGGTGGAGGAGGAGACTTGTAGTAGT
* * *
16767 ATGGTGGTGG-GG-GACTTGGTGAAGGTGGTGGT
66 ATGGAGGTGGTGGTGA--TGGAGAAGGTGGGGGT
* * * * * * * * *
16799 GGAGACTTGTAGTAGTAAGGTGGAGGGGGAGAT-GGCGATGGAGGTGGAGGAGATTTGTA-CACA
1 GGTGACTTGTAGTAGTAAGGTGGTGGTGGAGATAGGAGATGGTGGAGGAGGAGACTTGTAGTA-G
* * * * *
16862 TAAGGAGGAGGAGGTGAAGGAGACGGTGGTGGG-
65 TATGGAGGTGGTGGTGATGGAGAAGGTGG-GGGT
* * * * * * * * * * *
16895 GGAGACTTATAATAGTATGGTGGAGGAGGAGAT-GGGGATGGCGGTGGAGGGGACTTATAG-ACG
1 GGTGACTTGTAGTAGTAAGGTGGTGGTGGAGATAGGAGATGGTGGAGGAGGAGACTTGTAGTA-G
* * * * *
16958 TAGGGAGGAGGAGGTGATGGAGAAGGTGGTGGC
65 TATGGAGGTGGTGGTGATGGAGAAGGTGGGGGT
* *
16991 GGAGACTTATAGTAGT-AGGTGG
1 GGTGACTTGTAGTAGTAAGGTGG
17013 GAGGTGGTGG
Statistics
Matches: 418, Mismatches: 73, Indels: 23
0.81 0.14 0.04
Matches are distributed among these distances:
94 2 0.00
95 10 0.02
96 398 0.95
97 6 0.01
98 2 0.00
ACGTcount: A:0.22, C:0.03, G:0.51, T:0.24
Consensus pattern (97 bp):
GGTGACTTGTAGTAGTAAGGTGGTGGTGGAGATAGGAGATGGTGGAGGAGGAGACTTGTAGTAGT
ATGGAGGTGGTGGTGATGGAGAAGGTGGGGGT
Found at i:16941 original size:144 final size:143
Alignment explanation
Indices: 16409--16995 Score: 534
Period size: 144 Copynumber: 4.1 Consensus size: 143
16399 CTTCATTGGA
* * * *
16409 GGAGGAGGTGATTTGTAGTAGTAGGGAGGTGGTGGTGAGGGAGATGGTGGAGGGGGTGACTTATA
1 GGAGGAGGAGATTTGTA-CAGTATGGAGGTGGTGGTGAAGGAGATGGTGGAGGGGGTGACTTATA
* * * * *
16474 ATAGTAAGGTGGTGGTGGTGATGGAGAAGGAGGTGGTGGGGATTTGTAGTAGTAAGGTGGTGGTG
65 ATAGTATGGTGGTGGTGGAGATGGAGAAGGTGGTGGTGGGGACTTGTAGTAGTAAGGTGGAGGTG
*
16539 GAGAAGGAGATGGT
130 GAGATGGAGATGGT
* * *
16553 GGAGGAGGAGATTTGTAGTAGTATGGGGGTGGTGGTGAAGGAGATGGTGG-GGGTGGTGACTTGT
1 GGAGGAGGAGATTTGTA-CAGTATGGAGGTGGTGGTGAAGGAGATGGTGGAGGG-GGTGACTTAT
* * * * * *
16617 AGTAGTATGGTGGTGGTGGA-CTAGGAGATGGTGGAGGTGGTGACTTGTAGTAGTAAGGAGGAGG
64 AATAGTATGGTGGTGGTGGAGAT-GGAGAAGGTGGTGGTGGGGACTTGTAGTAGTAAGGTGGAGG
*
16681 TGGTGATGGAGATGGT
128 TGGAGATGGAGATGGT
* * * ** * * * *
16697 GGGGGTGGTGATTTGTAGTGGTATGGTGGTGGTGG-GCTAGGAGATGGTGGAGGTGGTGACTTGT
1 GGAGGAGGAGATTTGTA-CAGTATGGAGGTGGTGGTG-AAGGAGATGGTGGAGGGGGTGACTTAT
* * ** * * *
16761 AGTAGTATGGTGGTGGGGGACTTGGTGAAGGTGGTGGTGGAGACTTGTAGTAGTAAGGTGGAGGG
64 AATAGTATGGTGGTGGTGGAGATGGAGAAGGTGGTGGTGGGGACTTGTAGTAGTAAGGTGGAGGT
* *
16826 GGAGATGGCGATGGA
129 GGAGATGGAGATGGT
* * * * * * * *
16841 GGTGGAGGAGATTTGTACACATAAGGAGGAGGAGGTGAAGGAGACGGTGGTGGGGGAGACTTATA
1 GGAGGAGGAGATTTGTACA-GTATGGAGGTGGTGGTGAAGGAGATGGTGGAGGGGGTGACTTATA
* * * * * * * * * *
16906 ATAGTATGGTGGAGGAGGAGATGGGGATGGCGGTGGAGGGGACTTATAG-ACGTAGGGAGGAGGA
65 ATAGTATGGTGGTGGTGGAGATGGAGAAGGTGGTGGTGGGGACTTGTAGTA-GTAAGGTGGAGGT
* *
16970 GGTGATGGAGAAGGT
129 GGAGATGGAGATGGT
* *
16985 GGTGGCGGAGA
1 GGAGGAGGAGA
16996 CTTATAGTAG
Statistics
Matches: 364, Mismatches: 71, Indels: 16
0.81 0.16 0.04
Matches are distributed among these distances:
143 6 0.02
144 354 0.97
145 4 0.01
ACGTcount: A:0.22, C:0.03, G:0.51, T:0.24
Consensus pattern (143 bp):
GGAGGAGGAGATTTGTACAGTATGGAGGTGGTGGTGAAGGAGATGGTGGAGGGGGTGACTTATAA
TAGTATGGTGGTGGTGGAGATGGAGAAGGTGGTGGTGGGGACTTGTAGTAGTAAGGTGGAGGTGG
AGATGGAGATGGT
Found at i:22892 original size:53 final size:53
Alignment explanation
Indices: 22813--22918 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
22803 CTCCATTAGA
22813 TAGATTTCCCATGATAGCCTTCCATGAACAGCGATCTTCTTTTCTTCTTTTCT
1 TAGATTTCCCATGATAGCCTTCCATGAACAGCGATCTTCTTTTCTTCTTTTCT
22866 TAGATTTCCCATGATAGCCTTCCATGAACAGCGATCTTCTTTTCTTCTTTTCT
1 TAGATTTCCCATGATAGCCTTCCATGAACAGCGATCTTCTTTTCTTCTTTTCT
22919 AAATTGTTCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.19, C:0.26, G:0.11, T:0.43
Consensus pattern (53 bp):
TAGATTTCCCATGATAGCCTTCCATGAACAGCGATCTTCTTTTCTTCTTTTCT
Found at i:30492 original size:13 final size:13
Alignment explanation
Indices: 30474--30498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30464 TTTGTTTCCG
30474 GGACAAATTGGAA
1 GGACAAATTGGAA
30487 GGACAAATTGGA
1 GGACAAATTGGA
30499 GATTCTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.32, T:0.16
Consensus pattern (13 bp):
GGACAAATTGGAA
Done.