Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015443.1 Corchorus olitorius cultivar O-4 contig15476, 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: 79952
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:644 original size:330 final size:332
Alignment explanation
Indices: 17--960 Score: 1687
Period size: 330 Copynumber: 2.8 Consensus size: 332
7 CGTGTACTAA
* * * * * *
17 TACTATCCATCACGGTTTTTGGCTGAATACGCATTCC-GGCCCCCGGCTCAGTTTTGAATGAGTT
1 TACTATCCATCACGGTTTTTGCCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTT
81 TTGGCACCAAGACTCATTGAAATATCTATATTCATCTAACGAAACCTCAGCCACAATGGATTTAA
66 TTGGCACCAAGACTCATTGAAATATCTATATTCATCTAACGAAACCTCAGCCACAATGGATTTAA
146 GGATTTGTTTTTACGAGTATCAGAATCCAGTTTCGATTTAATTAGAAATTAATTTGAAAAAAAAT
131 GGATTTGTTTTTACGAGTATCAGAATCCAGTTTCGATTTAATTAGAAATTAATTTG-AAAAAAA-
211 GTAGGAAAAATGATATTAGAAGCGTGAAAAGTCTTTCAATCTTTTTGGCATTGAATTATATATTT
194 -TAGGAAAAATGATATTAGAAGCGTGAAAAGTCTTTCAATCTTTTTGGCATTGAATTATATATTT
276 TTTATGAGTATCGTAGCCAAAACTTGAGAAAAAATCTTTCAGGTCAATTTTTACAAAATTTTAGC
258 TTTATGAGTATCGTAGCCAAAACTTGAGAAAAAATCTTTCAGGTCAATTTTTACAAAATTTTAGC
341 CGAAATCGTG
323 CGAAATCGTG
*
351 TACTATCCATCACGGTTTTTGCCTGAAAACGCGTTCCGGGGCCTCGGCTCAGTTTTGCATGATTT
1 TACTATCCATCACGGTTTTTGCCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTT
416 TTGGCACCAAGACTCATTGAAATATCTATATTCATCTAACGAAACCTCAGCCACAATGGATTTAA
66 TTGGCACCAAGACTCATTGAAATATCTATATTCATCTAACGAAACCTCAGCCACAATGGATTTAA
481 GGATTTGTTTTTACGAG-ATCAGAATCCAGTTTCGATTTAATTAGAAATTAATTTGAAAAAAATA
131 GGATTTGTTTTTACGAGTATCAGAATCCAGTTTCGATTTAATTAGAAATTAATTTGAAAAAAATA
*
545 GG-AAAATGATATTAGAAGCGTGAAAAGTCCTTCAATCTTTTTGGCATTGAATTATATATTTTTT
196 GGAAAAATGATATTAGAAGCGTGAAAAGTCTTTCAATCTTTTTGGCATTGAATTATATATTTTTT
*
609 ATGAGTATCGTAGCCAAAACTTGAGAAAAAATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGA
261 ATGAGTATCGTAGCCAAAACTTGAGAAAAAATCTTTCAGGTCAATTTTTACAAAATTTTAGCCGA
* *
674 ACTCGTT
326 AATCGTG
*
681 TACTATCCATCACGGTTTTTGCCTGAAAACGCGTTCCGGGGCCCCAGCTCAGTTTTGCATGATTT
1 TACTATCCATCACGGTTTTTGCCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTT
746 TTGGCACCAAGACTCATTGAAATATCTATATTCATCTAACGAAACCTCAGCCACAATGGATTTAA
66 TTGGCACCAAGACTCATTGAAATATCTATATTCATCTAACGAAACCTCAGCCACAATGGATTTAA
*
811 GGATTTGCTTTTACGAGTATCAGAATCCAGTTTCGATTTAATTAGAAATTAATTTGAAAAAAATA
131 GGATTTGTTTTTACGAGTATCAGAATCCAGTTTCGATTTAATTAGAAATTAATTTGAAAAAAATA
*
876 GGAAAAATGATATTAGAAGCGTGAAAAGTCTTTCAATCTTTTTGGCATTGATTTATATATTTTTT
196 GGAAAAATGATATTAGAAGCGTGAAAAGTCTTTCAATCTTTTTGGCATTGAATTATATATTTTTT
* * *
941 ACGAGTATTGTAGCTAAAAC
261 ATGAGTATCGTAGCCAAAAC
961 CCCTATCTTC
Statistics
Matches: 588, Mismatches: 19, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
330 274 0.47
331 53 0.09
332 77 0.13
333 7 0.01
334 72 0.12
335 105 0.18
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (332 bp):
TACTATCCATCACGGTTTTTGCCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTT
TTGGCACCAAGACTCATTGAAATATCTATATTCATCTAACGAAACCTCAGCCACAATGGATTTAA
GGATTTGTTTTTACGAGTATCAGAATCCAGTTTCGATTTAATTAGAAATTAATTTGAAAAAAATA
GGAAAAATGATATTAGAAGCGTGAAAAGTCTTTCAATCTTTTTGGCATTGAATTATATATTTTTT
ATGAGTATCGTAGCCAAAACTTGAGAAAAAATCTTTCAGGTCAATTTTTACAAAATTTTAGCCGA
AATCGTG
Found at i:4084 original size:3 final size:3
Alignment explanation
Indices: 4078--4102 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4068 AAAAAAAAAA
4078 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
4103 TAAGAAGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5811 original size:17 final size:17
Alignment explanation
Indices: 5791--5824 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5781 TGAAAATTTG
5791 AATTAAA-AGAAAAAAAA
1 AATTAAATA-AAAAAAAA
5808 AATTAAATAAAAAAAAA
1 AATTAAATAAAAAAAAA
5825 GGTAATCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (17 bp):
AATTAAATAAAAAAAAA
Found at i:8434 original size:148 final size:148
Alignment explanation
Indices: 8166--8442 Score: 473
Period size: 148 Copynumber: 1.9 Consensus size: 148
8156 GATAAATAAG
**
8166 TATTTGGGAGGCAAGCACAGAAGCACTAATTAACATCAGTTGTTAGAACTAAACTTAAGTAAAAT
1 TATTTGGGAGGCAAGCACAGAAGCACTAATTAACATCAGTCCTTAGAACTAAACTTAAGTAAAAT
*
8231 CTTAAATGCTGTAATCATGCCCTACAACTGACTTTGTATAAGGTTATTATATGCATTTTCCAAAT
66 CTTAAATGCTGTAATCATGCCCTACAACTGACTTTGTATAAGGTCATTATATGCATTTTCCAAAT
8296 ATAGAGAAACACTGTAAT
131 ATAGAGAAACACTGTAAT
* * * * *
8314 TATTTGGGTGGTAAGCACAGAAGCACTAATTCACATCAGTCCTTAGAATTGAACTTAAGTAAAAT
1 TATTTGGGAGGCAAGCACAGAAGCACTAATTAACATCAGTCCTTAGAACTAAACTTAAGTAAAAT
*
8379 CTTAAATGCTGTAATTATGCCCTACAACTGACTTTGTATAAGGTCATTATATGCATTTTCCAAA
66 CTTAAATGCTGTAATCATGCCCTACAACTGACTTTGTATAAGGTCATTATATGCATTTTCCAAA
8443 CCTATCGAAA
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
148 120 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (148 bp):
TATTTGGGAGGCAAGCACAGAAGCACTAATTAACATCAGTCCTTAGAACTAAACTTAAGTAAAAT
CTTAAATGCTGTAATCATGCCCTACAACTGACTTTGTATAAGGTCATTATATGCATTTTCCAAAT
ATAGAGAAACACTGTAAT
Found at i:12288 original size:105 final size:104
Alignment explanation
Indices: 12171--12364 Score: 370
Period size: 105 Copynumber: 1.9 Consensus size: 104
12161 TTTTTTTACC
*
12171 AAAAAAAAATTACCAATAGGTAGCCTATCTTATTACCTGCAAGAATCATGCCAAAAGTTAATTAA
1 AAAAAAAAATTACCAATAGGTAGCCTATCTTATTACCTGCAAGAATCATGCC-AAAGGTAATTAA
12236 TTTTAGTGCTATAAAAGATGCCTAAGCCTAACATATGGAG
65 TTTTAGTGCTATAAAAGATGCCTAAGCCTAACATATGGAG
12276 AAAAAAAAATTACCAATAGGTAGCCTATCTTATTACCTGCAAGAATCATGCCAAAGGTAATTAAT
1 AAAAAAAAATTACCAATAGGTAGCCTATCTTATTACCTGCAAGAATCATGCCAAAGGTAATTAAT
12341 TTTAGTGCTATAAAAGATGCCTAA
66 TTTAGTGCTATAAAAGATGCCTAA
12365 CAAATGATGG
Statistics
Matches: 88, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
104 36 0.41
105 52 0.59
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (104 bp):
AAAAAAAAATTACCAATAGGTAGCCTATCTTATTACCTGCAAGAATCATGCCAAAGGTAATTAAT
TTTAGTGCTATAAAAGATGCCTAAGCCTAACATATGGAG
Found at i:21922 original size:70 final size:70
Alignment explanation
Indices: 21809--21951 Score: 277
Period size: 70 Copynumber: 2.0 Consensus size: 70
21799 CGTTTGATGC
21809 ATCGGTTAAATGGAATTTTAGATGTAATCTCCGTTTCAATCGCTGCTCTAATAATCTCAATTGTA
1 ATCGGTTAAATGGAATTTTAGATGTAATCTCCGTTTCAATCGCTGCTCTAATAATCTCAATTGTA
21874 CATCA
66 CATCA
21879 ATCGGTTAAATGGAATTTTAGATGTAATCTCCGTTTCAATCGCTGCTCTAATAATCTCAATTGTA
1 ATCGGTTAAATGGAATTTTAGATGTAATCTCCGTTTCAATCGCTGCTCTAATAATCTCAATTGTA
*
21944 TATCA
66 CATCA
21949 ATC
1 ATC
21952 ACACCGTTCT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (70 bp):
ATCGGTTAAATGGAATTTTAGATGTAATCTCCGTTTCAATCGCTGCTCTAATAATCTCAATTGTA
CATCA
Found at i:24369 original size:114 final size:114
Alignment explanation
Indices: 24215--24445 Score: 435
Period size: 114 Copynumber: 2.0 Consensus size: 114
24205 ATTAACTTCC
*
24215 TTTCTCAATTTTTCTATCATGTCATCTAGAGTCAACTCAGGAGGCTTGGTGGATGATTCCTTGGC
1 TTTCTCAATTTTTCTATCATGTCATCTAGAGCCAACTCAGGAGGCTTGGTGGATGATTCCTTGGC
24280 TTTCAAGTTTTGCTGCTTCAGTTTTTTAGCCCCACCCTCCAACTCTGCA
66 TTTCAAGTTTTGCTGCTTCAGTTTTTTAGCCCCACCCTCCAACTCTGCA
* *
24329 TTTCTCAATTTTTCTATCATGTTATTTAGAGCCAACTCAGGAGGCTTGGTGGATGATTCCTTGGC
1 TTTCTCAATTTTTCTATCATGTCATCTAGAGCCAACTCAGGAGGCTTGGTGGATGATTCCTTGGC
24394 TTTCAAGTTTTGCTGCTTCAGTTTTTTAGCCCCACCCTCCAACTCTGCA
66 TTTCAAGTTTTGCTGCTTCAGTTTTTTAGCCCCACCCTCCAACTCTGCA
24443 TTT
1 TTT
24446 GAGGTTCTAC
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (114 bp):
TTTCTCAATTTTTCTATCATGTCATCTAGAGCCAACTCAGGAGGCTTGGTGGATGATTCCTTGGC
TTTCAAGTTTTGCTGCTTCAGTTTTTTAGCCCCACCCTCCAACTCTGCA
Found at i:29127 original size:119 final size:118
Alignment explanation
Indices: 28885--29103 Score: 296
Period size: 119 Copynumber: 1.8 Consensus size: 118
28875 ATCCTTTATT
*
28885 CCAACATAATAAGAGACCATGGTAAATGCCCCAAAGATCAGCCACCATGATGGAAGAGTAGCCGA
1 CCAACATAACAAGAGACCATGGTAAATGCCCCAAAGATCAGCCACCATGATGGAAGAGTAGCCGA
** ** * * * * **
28950 CGTGACAAGTGAAACCTTCCAGTCACAGTCCATCCTTGTTTGTATCCTTTATC
66 CACGACAAGTGAAACCTTCCAACCACAGGCCATCCTCGTATCTATCCTGAATC
*
29003 CCAACATAACAAGAGACCATGGTAAATGCCCCAAAGCTGCAGCCACCATGATGGAAGAGTAGCCG
1 CCAACATAACAAGAGACCATGGTAAATGCCCCAAAGAT-CAGCCACCATGATGGAAGAGTAGCCG
*
29068 ATACGACAAGTGAAACCTTCCAACCAC-GGCCTATCC
65 ACACGACAAGTGAAACCTTCCAACCACAGGCC-ATCC
29104 CGATCTCTCA
Statistics
Matches: 91, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
118 39 0.43
119 52 0.57
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (118 bp):
CCAACATAACAAGAGACCATGGTAAATGCCCCAAAGATCAGCCACCATGATGGAAGAGTAGCCGA
CACGACAAGTGAAACCTTCCAACCACAGGCCATCCTCGTATCTATCCTGAATC
Found at i:31592 original size:98 final size:99
Alignment explanation
Indices: 31418--31602 Score: 250
Period size: 98 Copynumber: 1.9 Consensus size: 99
31408 TTGCTCAAGT
* * *
31418 TGTAGCTTAGTAGGAAACAAAGCCCTTTAATTTTAGCTACCAATACCTCAAATGCAACATTCCTT
1 TGTAGCTTAGTAGGAAACAAAGACCTTTAATTTTAGCCACCAATACCCCAAATGCAACATTCCTT
* *
31483 GTTTTAGTTTTCAATAATGAGCGAGTGCCGCAGG
66 GTTTCAATTTTCAATAATGAGCGAGTGCCGCAGG
* * *
31517 TGTAGGTTAGTAGGAAAC-AAGACCTTTACA-TTTAGCCAGCAATACCCCAGATGCAACA-TCCT
1 TGTAGCTTAGTAGGAAACAAAGACCTTTA-ATTTTAGCCACCAATACCCCAAATGCAACATTCC-
*
31579 TTGTTTCAATTTTCATTAATGAGC
64 TTGTTTCAATTTTCAATAATGAGC
31603 AAGATGGATC
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
97 3 0.04
98 54 0.72
99 18 0.24
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (99 bp):
TGTAGCTTAGTAGGAAACAAAGACCTTTAATTTTAGCCACCAATACCCCAAATGCAACATTCCTT
GTTTCAATTTTCAATAATGAGCGAGTGCCGCAGG
Found at i:50051 original size:318 final size:317
Alignment explanation
Indices: 49296--50803 Score: 1220
Period size: 318 Copynumber: 4.7 Consensus size: 317
49286 ATATACTCAT
* * *
49296 ACTTTTCTA-GCTTTTAGTATCGTTTTTCATATTTTTTCTGAATGAATTTCTAATTAAATCGAAA
1 ACTTTTC-ACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTTATTAAATCGAAA
* *
49360 CAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGCCTGATATTTGATTAGATGAA
64 CAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGATTAGATGAA
* * ** * **
49425 TAAAGATATTTCAAGCAGTCTCAATGCCAAAAATCATGCAAAACAGAGCTATGGCCCTGGAACGC
129 TAAAGATATTTCAAGGAGTCTCGACACCAAAAATCATGCAAAACTGAG-TCGGGCCCTGGAACGC
*
49490 GTTTTTAGCCAAAAACTGTGATTGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCC
193 GTTTTTAGCCGAAAACTGTGA-TGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCC
* *
49555 GAAAGA-TATTTCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTTGACATAAAAAAG
257 GAAAGATTTTTTCTCAATTTTTGGCTAAAATACT-AT-----A-AT-TAA----ACGTAAAAAAG
*
49619 ATTGAAGG
310 ATTGGAGG
* * * * *
49627 GCTTTTAACGCTTCTAATATTGTTTTTCATATTTTT-TCAAATTAATTT-TTAATTAAATCGAAA
1 ACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCT-GAATTAATTTCTT-ATTAAATCGAAA
* * * ** *
49690 CAAGATTGAGATGCTCGTAAAAACAAATCCTTAAATTTAATGTGACTGAGATTTGGTTAGATGAA
64 CAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGATTAGATGAA
* * * * *
49755 TATAGATATTTCGAGGAGTCTTGACACAAAAAATCAAGCAAAACTGAGTCGGGCCCTGGAACGCA
129 TAAAGATATTTCAAGGAGTCTCGACACCAAAAATCATGCAAAACTGAGTCGGGCCCTGGAACGC-
* * *
49820 G-TTTTAGCCGAAAACTGTGATGGTTAGTATATGATTTCGGCTAAAATTATGCAAACATTGACCC
193 GTTTTTAGCCGAAAACTGTGAT-GTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCC
* * * * * * *
49884 GAAAGATTTTTTCTCGATTTCTAGCGAAAATACTATAATTCAACGTTAAAAGGATTGGAGG
257 GAAAGATTTTTTCTCAATTTTTGGCTAAAATACTATAATTAAACGTAAAAAAGATTGGAGG
* *
49945 ACTTTTCACGCTTGTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTTATTAAATAGAAACA
1 ACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTTATTAAATCGAAACA
* * * *
50010 AGATTCAGATTCACATAAAAACAAATCCTTAAATCTAATGTGCCTGAGATTTGATTAGATAAATA
66 AGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGATTAGATGAATA
* * * *
50075 AAGATATTTCAAGGAGTCTCGGCACCAAAAAGCATGCAAAACTGAGTCGGGCCTTGGAATGCGTT
131 AAGATATTTCAAGGAGTCTCGACACCAAAAATCATGCAAAACTGAGTCGGGCCCTGGAACGCGTT
* * * * *
50140 TTTGGCCGAAAACCGTGA-G--A-TACACGATTTTGGCTAAAATTTTGCAAAAATTGGCCCGAAA
196 TTTAGCCGAAAACTGTGATGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA
*
50201 GATTTTTTCATCAATTTTTGGCTAAAATACTCATGAATATATATAATTTAACGTCAAAAAGATTG
261 GATTTTTTC-TCAATTTTTGGCTAAAATA--C-T--ATA-AT-T-A---AACGTAAAAAAGATTG
50266 GAGG
314 GAGG
** *
50270 ACTTATT-ACATTTTTAATATCATTTTTCATATTTTTCTGAATTAATTTC-TAGTTAAATCGAAA
1 ACTT-TTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTTA-TTAAATCGAAA
* * * * * * * * *
50333 CAAGATTAAAATGCTCGTAAAAACAAATTCTTCAATCCAATGT-AGCTGAAATTAGATTAAATGA
64 CAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGA-CTGAGATTTGATTAGATGA
* * * * * * * *
50397 CTATAGATATCTCAAAGAGTC-CTGGCACC--AAA-C-T-------T-AGCCGGGAACCGGGAAC
128 ATAAAGATATTTCAAGGAGTCTC-GACACCAAAAATCATGCAAAACTGAGTCGGG-CCCTGGAAC
* * * *
50449 GCGTTTTTAGCCAAAAACTGTGATGATTATTACACGATTTCGGCTAGAATTTTGCAAAAATTGAC
191 GCGTTTTTAGCCGAAAACTGTGATG-TTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * ** * * **
50514 TCAAAAG-TTTTTTC-CTATATTTTTATCCACAATACTCATAAAAATTATATAATTCAACGCCAA
255 CCGAAAGATTTTTTCTC-A-ATTTTTGGCTAAAATACT-AT----A--AT-T-A---AACGTAAA
* *
50577 AAAGACTGAAGG
306 AAAGATTGGAGG
** * * * * *
50589 GTTTTTCATGCTTTTAATATAGTTTTTCCTATTATTTTCCGAATTAATTTCTAATTAAATCGAAA
1 ACTTTTCACGCTTTTAATATCGTTTTTCATA-T-TTTTCTGAATTAATTTCTTATTAAATCGAAA
* * *** *** * * * *
50654 CATGATTTAGATGCTTGT-TTTACAAATCCTTAAATTCAATGTGGCTGAGATTTGGTTAAATGAA
64 CAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGATTAGATGAA
** * * * **
50718 TGTAGATATTTCAAGGAGTCTCGACGCAAAAAATCATGCAACACTGAACCGAGG-CCTGGGAACG
129 TAAAGATATTTCAAGGAGTCTCGACACCAAAAATCATGCAAAACTGAGTCG-GGCCCT-GGAACG
* * *
50782 CATTTTTAGCCAAAAACCGTGA
192 CGTTTTTAGCCGAAAACTGTGA
50804 ATTTTACAAA
Statistics
Matches: 960, Mismatches: 159, Indels: 115
0.78 0.13 0.09
Matches are distributed among these distances:
313 50 0.05
314 44 0.05
315 2 0.00
316 4 0.00
317 3 0.00
318 219 0.23
319 89 0.09
320 57 0.06
321 44 0.05
322 7 0.01
323 6 0.01
324 5 0.01
325 143 0.15
326 2 0.00
328 1 0.00
329 81 0.08
330 144 0.15
331 27 0.03
332 30 0.03
333 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (317 bp):
ACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTTATTAAATCGAAACA
AGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGATTAGATGAATA
AAGATATTTCAAGGAGTCTCGACACCAAAAATCATGCAAAACTGAGTCGGGCCCTGGAACGCGTT
TTTAGCCGAAAACTGTGATGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA
GATTTTTTCTCAATTTTTGGCTAAAATACTATAATTAAACGTAAAAAAGATTGGAGG
Found at i:51159 original size:15 final size:15
Alignment explanation
Indices: 51131--51180 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
51121 GTTTCATGAC
* *
51131 TATAAATAATAATAT
1 TATAATTAAAAATAT
51146 TATAATTAAAAATAT
1 TATAATTAAAAATAT
*
51161 TATACTCTAAAAATAAT
1 TATAAT-TAAAAAT-AT
51178 TAT
1 TAT
51181 TAGAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 18 0.60
16 7 0.23
17 5 0.17
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (15 bp):
TATAATTAAAAATAT
Found at i:51453 original size:8 final size:8
Alignment explanation
Indices: 51427--51462 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
51417 TTTTATATAG
51427 TAGTAAGA
1 TAGTAAGA
51435 TAAGATAAGA
1 T-AG-TAAGA
51445 TAGTAAGA
1 TAGTAAGA
51453 TAGTAAGA
1 TAGTAAGA
51461 TA
1 TA
51463 TATAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 16 0.62
9 4 0.15
10 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (8 bp):
TAGTAAGA
Found at i:62974 original size:19 final size:19
Alignment explanation
Indices: 62950--62986 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
62940 CAGCCATACA
62950 TATTGGATTGGATTTTGAC
1 TATTGGATTGGATTTTGAC
62969 TATTGGATTGGATTTTGA
1 TATTGGATTGGATTTTGA
62987 TCGAGTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.49
Consensus pattern (19 bp):
TATTGGATTGGATTTTGAC
Found at i:79789 original size:31 final size:29
Alignment explanation
Indices: 79751--79918 Score: 115
Period size: 31 Copynumber: 5.6 Consensus size: 29
79741 TTGGGCTAAT
79751 TGCTCAAATAAGGGCCTAATGTTTACCAAAA
1 TGCTCAAATAAGGGCCTAATGTTT--CAAAA
* * * * **
79782 TGCTCAAATAAGGGTCTGATCTTTTAATT
1 TGCTCAAATAAGGGCCTAATGTTTCAAAA
* *
79811 TGGC-CAAATAAGGGCCTAACGTTAATGAAAA
1 T-GCTCAAATAAGGGCCTAATGTT--TCAAAA
** * * **
79842 TGCTCAAATAAGGGCCCGATCTTTTAATT
1 TGCTCAAATAAGGGCCTAATGTTTCAAAA
*
79871 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTT--CAAAA
79902 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
79919 GGCATCGATG
Statistics
Matches: 102, Mismatches: 27, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
29 38 0.37
30 8 0.08
31 56 0.55
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (29 bp):
TGCTCAAATAAGGGCCTAATGTTTCAAAA
Found at i:79848 original size:60 final size:59
Alignment explanation
Indices: 79755--79917 Score: 238
Period size: 60 Copynumber: 2.7 Consensus size: 59
79745 GCTAATTGCT
* ** * *
79755 CAAATAAGGGCCTAATGTTTACCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-TTATGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
79815 CAAATAAGGGCCTAACGTTAATGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTT-ATGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
79875 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATG--AAAATGCTCAAATAAGGGCC
79918 TGGCATCGAT
Statistics
Matches: 95, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
58 2 0.02
59 2 0.02
60 91 0.96
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (59 bp):
CAAATAAGGGCCTAACGTTATGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:79886 original size:29 final size:29
Alignment explanation
Indices: 79786--79886 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
79776 CCAAAATGCT
* *
79786 CAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCCGATCTTTTAATTTGGC
* * * **
79815 CAAATAAGGG-CCTAACGTTAATGAAAAT-GC
1 CAAATAAGGGCCCGATC-TT--TTAATTTGGC
79845 TCAAATAAGGGCCCGATCTTTTAATTTGGC
1 -CAAATAAGGGCCCGATCTTTTAATTTGGC
79875 CAAATAAGGGCC
1 CAAATAAGGGCC
79887 TAACGTTTGC
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 3 0.05
29 28 0.51
30 4 0.07
31 16 0.29
32 4 0.07
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (29 bp):
CAAATAAGGGCCCGATCTTTTAATTTGGC
Done.