Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014447.1 Corchorus capsularis cultivar CVL-1 contig14468, 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: 75409
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6468 original size:42 final size:42
Alignment explanation
Indices: 6421--6544 Score: 248
Period size: 42 Copynumber: 3.0 Consensus size: 42
6411 CCCTAGGCCT
6421 ACACAGTTTTGAAATACCTTAATCTAAAGAAGCTAAATTAGA
1 ACACAGTTTTGAAATACCTTAATCTAAAGAAGCTAAATTAGA
6463 ACACAGTTTTGAAATACCTTAATCTAAAGAAGCTAAATTAGA
1 ACACAGTTTTGAAATACCTTAATCTAAAGAAGCTAAATTAGA
6505 ACACAGTTTTGAAATACCTTAATCTAAAGAAGCTAAATTA
1 ACACAGTTTTGAAATACCTTAATCTAAAGAAGCTAAATTA
6545 AAAATAAAAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (42 bp):
ACACAGTTTTGAAATACCTTAATCTAAAGAAGCTAAATTAGA
Found at i:9290 original size:442 final size:434
Alignment explanation
Indices: 8407--9677 Score: 1196
Period size: 405 Copynumber: 3.0 Consensus size: 434
8397 GCATGTTCGG
* * *
8407 AATCAATAATTTTGCGTTGGACCACCGGCTAGAGGCCCAAACACATTGGGCCTACAGTGTGTTTG
1 AATCAATAATTTTGCGTTGGACCACCAGTTAGAGGCCCAAACACATTGGGCCTACAGTGCGTTTG
* * *
8472 GACTCAATAATCTCCACCACAACTTTTAACTTCACCATCACCGCTATGCTGGACAGGGCCGTATT
66 GACTCAATAATCTCCACCACAACTTTTAACTTCACCATCACCGCTATGCTGAACAGGGCCATAAT
* * * *
8537 CCAGTACAATGTGAAATACATGAAATTTAACCCATGACAAGTACTTTCATCAATGAATTTCCATG
131 CCACTACAATGTGAAATACATGAAATTTAACCCATGACAAGTA-TGTCACCAATGAATTTCAATG
* * *
8602 GCATATTTCATGCTCATTTCATGGATAATTACTTTTGAATTTGAATTTGAATATGAATTTGCTTA
195 GCA-ATCTCATGCTCATTTCATGGATAATTACTTTTAAATTTGAATTTGAATATGAATTTGATTA
* * *
8667 GTAATTAAGGTAACCTTCTGAAGGATTCGCTGGCAAATTTTACGGTATATGGATAGAAGTGTACC
259 GTAATTAACGTAACCTTCTGAAGGACTCGCTGGCAAATTTTACGGTACATGGATAGAAGTGTACC
* * *
8732 ACGTCAGAACTTCGTTAATATCGCCATATATGTGAAAAAGTTGTTGGCATACATTTTCTCTATAT
324 ACGTCAGAACTTCATTAATATCGCCATATATGTGAAAAAGTGGTTGGCATAAATTTTCTCTATAT
* * *
8797 ATGTTAAGGGTTCGCTGGCAAATTTACGTTACATATTTACGTTCAA
389 ATGTGAAGAGTCCGCTGGCAAATTTACGTTACATATTTACGTTCAA
** * * *
8843 AATCAATAATCATGCGTTGGGCCAACAGTTAGAGGCCCAAACGCATTGGGCCTACAGTGCGTTTG
1 AATCAATAATTTTGCGTTGGACCACCAGTTAGAGGCCCAAACACATTGGGCCTACAGTGCGTTTG
* * *
8908 GACTCGATAATCTCCACCACAACTTTTAACTTCACCAATGTCGCTCTCGCCGCTATGCTGAATAG
66 GACTCAATAATCTCCACCACAACTTTTAACTTCACC-A--------TCACCGCTATGCTGAACAG
* * * * * ** **
8973 GGCCATAATCCACTATAATGTGAGATACATGATATTTTA-GC-T-A-GGGT-TGTCACCGTTGAA
122 GGCCATAATCCACTACAATGTGAAATACATGAAATTTAACCCATGACAAGTATGTCACCAATGAA
* *
9033 TTTCAATGGC-A-CTCATGCTCATTTCATGGATTATTACTTTTAAATTTGAA-TTGAATTTGAAT
187 TTTCAATGGCAATCTCATGCTCATTTCATGGATAATTACTTTTAAATTTGAATTTGAATATGAAT
* *
9095 TT-ATTAGTACTTAACGTAACCTCTCCATCAATGTGAAGGACTCGCTGGCAAA-TTTACGTTACA
252 TTGATTAGTAATTAACGTAA-C-CT---TC----TGAAGGACTCGCTGGCAAATTTTACGGTACA
* *
9158 TGGATAGAAGTGTACCATGTCAGAACTTCATTAATATCGCCATATATGTGAAAAGGTGGTTGGCA
308 TGGATAGAAGTGTACCACGTCAGAACTTCATTAATATCGCCATATATGTGAAAAAGTGGTTGGCA
* **
9223 TAAATTTTCTCTGTATATGTGAAGAGTCCGCTGGCAAATTTACGTTACATATTTACGTTTGA
373 TAAATTTTCTCTATATATGTGAAGAGTCCGCTGGCAAATTTACGTTACATATTTACGTTCAA
* * * *
9285 AATCAATAATTTTGTGTTGGACCACCAGTTAGAGGCCC--A-AC--T-CG-ATATA--GC--TT-
1 AATCAATAATTTTGCGTTGGACCACCAGTTAGAGGCCCAAACACATTGGGCCTACAGTGCGTTTG
* * ***
9338 ---T---TAA-CTTCA-C-C-A---TT-A--TCACTC-TCACTGCTATGCTGAACAGGGTTGTAA
66 GACTCAATAATCTCCACCACAACTTTTAACTTCAC-CATCACCGCTATGCTGAACAGGGCCATAA
* * * ** * *
9386 TCCACTACAATGTGAGATACATGAAATTTCA-GC-T-A-GGGT-TTTCACCAATGAATTTCCATG
130 TCCACTACAATGTGAAATACATGAAATTTAACCCATGACAAGTATGTCACCAATGAATTTCAATG
* * * * * *
9446 GCATATTTCATGCTCATTTCAGGGATAATTACTTTTGAATTTGAATTTGAATTTG-CTTAGTATT
195 GCA-ATCTCATGCTCATTTCATGGATAATTACTTTTAAATTTGAATTTGAATATGAATTTG-ATT
* * * * * * * *
9510 --TAAGGTAACCTCTGCATCCATGTGAAGGATTCGCTGTCAAATTTTACGTTACATGGATAGAAG
258 AGTAA-TTAA---C-GTAACCTTCTGAAGGACTCGCTGGCAAATTTTACGGTACATGGATAGAAG
* * * * *
9573 TGTACCATGTCAGAACTTCGTTAATATCACCATATATGTGAAAAGGTGGTTGACATAAATTTTCT
318 TGTACCACGTCAGAACTTCATTAATATCGCCATATATGTGAAAAAGTGGTTGGCATAAATTTTCT
* *
9638 CTATATATGTGAAGGGTCCACTGGCAAATTTACGTTACAT
383 CTATATATGTGAAGAGTCCGCTGGCAAATTTACGTTACAT
9678 TTTTTTTTTG
Statistics
Matches: 713, Mismatches: 91, Indels: 93
0.79 0.10 0.10
Matches are distributed among these distances:
404 17 0.02
405 196 0.27
407 1 0.00
408 40 0.06
409 12 0.02
410 3 0.00
411 1 0.00
412 2 0.00
413 2 0.00
414 4 0.01
415 1 0.00
416 1 0.00
417 2 0.00
420 1 0.00
421 1 0.00
422 1 0.00
423 4 0.01
424 3 0.00
427 1 0.00
431 2 0.00
433 2 0.00
434 14 0.02
435 17 0.02
436 131 0.18
437 3 0.00
439 21 0.03
440 1 0.00
441 2 0.00
442 159 0.22
443 19 0.03
444 1 0.00
445 48 0.07
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (434 bp):
AATCAATAATTTTGCGTTGGACCACCAGTTAGAGGCCCAAACACATTGGGCCTACAGTGCGTTTG
GACTCAATAATCTCCACCACAACTTTTAACTTCACCATCACCGCTATGCTGAACAGGGCCATAAT
CCACTACAATGTGAAATACATGAAATTTAACCCATGACAAGTATGTCACCAATGAATTTCAATGG
CAATCTCATGCTCATTTCATGGATAATTACTTTTAAATTTGAATTTGAATATGAATTTGATTAGT
AATTAACGTAACCTTCTGAAGGACTCGCTGGCAAATTTTACGGTACATGGATAGAAGTGTACCAC
GTCAGAACTTCATTAATATCGCCATATATGTGAAAAAGTGGTTGGCATAAATTTTCTCTATATAT
GTGAAGAGTCCGCTGGCAAATTTACGTTACATATTTACGTTCAA
Found at i:15300 original size:32 final size:31
Alignment explanation
Indices: 15243--15303 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
15233 ATTCCTCTAA
15243 TTATTCAAAATCAGAAATCATTACCCAAAGT
1 TTATTCAAAATCAGAAATCATTACCCAAAGT
*
15274 TTATTCAAAATGA-AATCATCATTACCCAAA
1 TTATTCAAAATCAGAA--ATCATTACCCAAA
15304 ATGGAGCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 2 0.07
31 12 0.44
32 13 0.48
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.30
Consensus pattern (31 bp):
TTATTCAAAATCAGAAATCATTACCCAAAGT
Found at i:18659 original size:13 final size:13
Alignment explanation
Indices: 18641--18665 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18631 ACTTTCTTTT
18641 CTTGTTTTTCTTA
1 CTTGTTTTTCTTA
18654 CTTGTTTTTCTT
1 CTTGTTTTTCTT
18666 TTCTCTCTCT
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:0.04, C:0.16, G:0.08, T:0.72
Consensus pattern (13 bp):
CTTGTTTTTCTTA
Found at i:20896 original size:15 final size:15
Alignment explanation
Indices: 20876--20907 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
20866 CGGAGTGGAG
20876 TATGTGTAACATATA
1 TATGTGTAACATATA
20891 TATGTGTAACATATA
1 TATGTGTAACATATA
20906 TA
1 TA
20908 GCTGTCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (15 bp):
TATGTGTAACATATA
Found at i:23212 original size:31 final size:31
Alignment explanation
Indices: 23143--23307 Score: 197
Period size: 31 Copynumber: 5.3 Consensus size: 31
23133 TCCTTTTGTG
* * **
23143 CACGTGGCATGCCACGTGCCA-TTTTCTGAAA
1 CACGTGGCGTGCCACGTGTCACTTTT-TGGTA
* *
23174 CAGGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
23205 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* * *
23236 CACATGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
23267 CATGTGGCGTGCCACATGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
23298 CACGTGGCGT
1 CACGTGGCGT
23308 TCACGTCGGA
Statistics
Matches: 118, Mismatches: 15, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
31 114 0.97
32 4 0.03
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (31 bp):
CACGTGGCGTGCCACGTGTCACTTTTTGGTA
Found at i:34466 original size:2 final size:2
Alignment explanation
Indices: 34459--34488 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34449 TATGATGTGT
34459 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34489 CTGAATCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36902 original size:519 final size:519
Alignment explanation
Indices: 35923--36962 Score: 2080
Period size: 519 Copynumber: 2.0 Consensus size: 519
35913 AACTTTCTTT
35923 TGTCAAACTATTTTAAAGTTTTAATTCTGGTTTGATTTTTTCCCCAAAATCTTATTCGTTGTGGG
1 TGTCAAACTATTTTAAAGTTTTAATTCTGGTTTGATTTTTTCCCCAAAATCTTATTCGTTGTGGG
35988 TAATATAGTTGGATATCTATCTTTAATCATCTTATTTGTTTTACCATTAATGTGATACATGGATT
66 TAATATAGTTGGATATCTATCTTTAATCATCTTATTTGTTTTACCATTAATGTGATACATGGATT
36053 ATTGGGAGGTGTGATAGGAATCATAGACTGATTTGGCTGTCTTATCTATAATTGATTGTAAGTAA
131 ATTGGGAGGTGTGATAGGAATCATAGACTGATTTGGCTGTCTTATCTATAATTGATTGTAAGTAA
36118 TCTGCCATAAGTTAATAGTATCTTTTAAGTTTTAAGAATTTAGCAACATATTTTTTGTGGCAATA
196 TCTGCCATAAGTTAATAGTATCTTTTAAGTTTTAAGAATTTAGCAACATATTTTTTGTGGCAATA
36183 AGCTTATTGAATCATCTCCTGTGATTGTGTTATACATGCTAACCCAACTTGCATCCACTTCAAGG
261 AGCTTATTGAATCATCTCCTGTGATTGTGTTATACATGCTAACCCAACTTGCATCCACTTCAAGG
36248 ATGTTAAAGTGTTTTCAAAATATACAAAGTCAAAATGTAAAGACTCCTTAGACTAGGTATATGTT
326 ATGTTAAAGTGTTTTCAAAATATACAAAGTCAAAATGTAAAGACTCCTTAGACTAGGTATATGTT
36313 TATATGTTTTTGTTTTAAAGTCAGGTTAAGGCGCCTGGGTCCCACTTCTCTTCTTCCCTTAAAGT
391 TATATGTTTTTGTTTTAAAGTCAGGTTAAGGCGCCTGGGTCCCACTTCTCTTCTTCCCTTAAAGT
36378 TAAACTCACATGGTTTTCATTTCTTATTCTGCTTGAGCTGTCTTTAAGAAATTGGTTGATACCC
456 TAAACTCACATGGTTTTCATTTCTTATTCTGCTTGAGCTGTCTTTAAGAAATTGGTTGATACCC
36442 TGTCAAACTATTTTAAAGTTTTAATTCTGGTTTGATTTTTTCCCCAAAATCTTATTCGTTGTGGG
1 TGTCAAACTATTTTAAAGTTTTAATTCTGGTTTGATTTTTTCCCCAAAATCTTATTCGTTGTGGG
36507 TAATATAGTTGGATATCTATCTTTAATCATCTTATTTGTTTTACCATTAATGTGATACATGGATT
66 TAATATAGTTGGATATCTATCTTTAATCATCTTATTTGTTTTACCATTAATGTGATACATGGATT
36572 ATTGGGAGGTGTGATAGGAATCATAGACTGATTTGGCTGTCTTATCTATAATTGATTGTAAGTAA
131 ATTGGGAGGTGTGATAGGAATCATAGACTGATTTGGCTGTCTTATCTATAATTGATTGTAAGTAA
36637 TCTGCCATAAGTTAATAGTATCTTTTAAGTTTTAAGAATTTAGCAACATATTTTTTGTGGCAATA
196 TCTGCCATAAGTTAATAGTATCTTTTAAGTTTTAAGAATTTAGCAACATATTTTTTGTGGCAATA
36702 AGCTTATTGAATCATCTCCTGTGATTGTGTTATACATGCTAACCCAACTTGCATCCACTTCAAGG
261 AGCTTATTGAATCATCTCCTGTGATTGTGTTATACATGCTAACCCAACTTGCATCCACTTCAAGG
36767 ATGTTAAAGTGTTTTCAAAATATACAAAGTCAAAATGTAAAGACTCCTTAGACTAGGTATATGTT
326 ATGTTAAAGTGTTTTCAAAATATACAAAGTCAAAATGTAAAGACTCCTTAGACTAGGTATATGTT
36832 TATATGTTTTTGTTTTAAAGTCAGGTTAAGGCGCCTGGGTCCCACTTCTCTTCTTCCCTTAAAGT
391 TATATGTTTTTGTTTTAAAGTCAGGTTAAGGCGCCTGGGTCCCACTTCTCTTCTTCCCTTAAAGT
36897 TAAACTCACATGGTTTTCATTTCTTATTCTGCTTGAGCTGTCTTTAAGAAATTGGTTGATACCC
456 TAAACTCACATGGTTTTCATTTCTTATTCTGCTTGAGCTGTCTTTAAGAAATTGGTTGATACCC
36961 TG
1 TG
36963 CAGGTTCTGA
Statistics
Matches: 521, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
519 521 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (519 bp):
TGTCAAACTATTTTAAAGTTTTAATTCTGGTTTGATTTTTTCCCCAAAATCTTATTCGTTGTGGG
TAATATAGTTGGATATCTATCTTTAATCATCTTATTTGTTTTACCATTAATGTGATACATGGATT
ATTGGGAGGTGTGATAGGAATCATAGACTGATTTGGCTGTCTTATCTATAATTGATTGTAAGTAA
TCTGCCATAAGTTAATAGTATCTTTTAAGTTTTAAGAATTTAGCAACATATTTTTTGTGGCAATA
AGCTTATTGAATCATCTCCTGTGATTGTGTTATACATGCTAACCCAACTTGCATCCACTTCAAGG
ATGTTAAAGTGTTTTCAAAATATACAAAGTCAAAATGTAAAGACTCCTTAGACTAGGTATATGTT
TATATGTTTTTGTTTTAAAGTCAGGTTAAGGCGCCTGGGTCCCACTTCTCTTCTTCCCTTAAAGT
TAAACTCACATGGTTTTCATTTCTTATTCTGCTTGAGCTGTCTTTAAGAAATTGGTTGATACCC
Found at i:41854 original size:33 final size:34
Alignment explanation
Indices: 41788--41873 Score: 156
Period size: 33 Copynumber: 2.5 Consensus size: 34
41778 ATTAAGTATT
41788 AACATGTGAATTTCGCAATTCTAAAAAAAAAAAAA
1 AACATGTGAATTTCGCAATTCT-AAAAAAAAAAAA
41823 AACATGTGAATTTCGCAATTCT-AAAAAAAAAAA
1 AACATGTGAATTTCGCAATTCTAAAAAAAAAAAA
41856 AACATGTGAATTTCGCAA
1 AACATGTGAATTTCGCAA
41874 CAACCAAAGG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
33 29 0.57
35 22 0.43
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.24
Consensus pattern (34 bp):
AACATGTGAATTTCGCAATTCTAAAAAAAAAAAA
Found at i:42289 original size:14 final size:14
Alignment explanation
Indices: 42270--42306 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
42260 TAATTAAGTC
42270 ACAAAGACACAAAG
1 ACAAAGACACAAAG
42284 ACAAAGACACAAAG
1 ACAAAGACACAAAG
*
42298 ACGAAGACA
1 ACAAAGACA
42307 TAATAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.62, C:0.22, G:0.16, T:0.00
Consensus pattern (14 bp):
ACAAAGACACAAAG
Found at i:43030 original size:16 final size:16
Alignment explanation
Indices: 42980--43030 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
42970 TCCTAATTCT
* *
42980 AATTAACTTGACCTGA
1 AATTAATTTGACCCGA
* *
42996 AATAAATTCGAACCC-A
1 AATTAATTTG-ACCCGA
43012 AATTAATTTGACCCGA
1 AATTAATTTGACCCGA
43028 AAT
1 AAT
43031 GAACTCGGCC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 4 0.15
16 20 0.74
17 3 0.11
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (16 bp):
AATTAATTTGACCCGA
Found at i:46848 original size:2 final size:2
Alignment explanation
Indices: 46841--46869 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
46831 TGATGATTTG
46841 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46870 TATTATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:46873 original size:8 final size:9
Alignment explanation
Indices: 46841--46879 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
46831 TGATGATTTG
46841 ATATATA-T
1 ATATATATT
46849 ATATATA-T
1 ATATATATT
46857 ATATATATT
1 ATATATATT
46866 ATAT-TATT
1 ATATATATT
46874 AT-TATA
1 ATATATA
46880 ATACCACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.03
8 23 0.79
9 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:46876 original size:11 final size:13
Alignment explanation
Indices: 46841--46879 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
46831 TGATGATTTG
46841 ATATATATATA-T
1 ATATATATATATT
46853 ATATATATATATT
1 ATATATATATATT
46866 ATAT-TAT-TATT
1 ATATATATATATT
46877 ATA
1 ATA
46880 ATACCACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.27
12 14 0.54
13 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATATATATATT
Found at i:49789 original size:27 final size:27
Alignment explanation
Indices: 49748--49811 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 27
49738 TAGTATATAC
49748 TCCCTCTGTTCCTTTTTAATTGTCCATT
1 TCCCT-TGTTCCTTTTTAATTGTCCATT
*
49776 TCCCTTGTTGCTTTTTAATTGTCCATT
1 TCCCTTGTTCCTTTTTAATTGTCCATT
49803 TCCCTTGTT
1 TCCCTTGTT
49812 TTCCAGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 30 0.86
28 5 0.14
ACGTcount: A:0.09, C:0.27, G:0.09, T:0.55
Consensus pattern (27 bp):
TCCCTTGTTCCTTTTTAATTGTCCATT
Found at i:51263 original size:16 final size:17
Alignment explanation
Indices: 51232--51266 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
51222 AGCCTAGTCA
51232 TTAATTTGGATAAATCT
1 TTAATTTGGATAAATCT
*
51249 TTAATTT-GTTAAATCT
1 TTAATTTGGATAAATCT
51265 TT
1 TT
51267 TTTAAATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.54
Consensus pattern (17 bp):
TTAATTTGGATAAATCT
Found at i:63632 original size:331 final size:331
Alignment explanation
Indices: 62759--65064 Score: 2316
Period size: 329 Copynumber: 7.0 Consensus size: 331
62749 CCAATGTTAA
* * * * * * *
62759 CTCAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATCAAAAATC-GGTTTCGATTTAATTA
1 CTCAGCCACACTGCATTTAAGAATTTGTTTTTACGAGCATC-AGAATCTTGTTTCGA-TTAACTA
* * * * * *
62823 GAAAATAAGTC-TAAAAAAAAGAAAACAA--A-ATTAGAAGCAG-GAAAATCCTTTCAATCATTT
64 GAAATTAATTCGGAAAAAATAGAAAA-AACGATATTAGAAGC-GTGAAAATCCATTCAATCTTTT
* * * * ** * *
62883 TGACACTAT-TATATATATATTTTTTATGAGTATAGCGGC-CAAAATTG--AGGAAAATTTATTC
127 TG-GAGT-TGAAT-TATATATTTTTTATGAGTATTGTAGCGAAAAATTGAAAGAAAAATTT-TT-
* * * *
62944 GGTCCAATTTTTGCAAAATTTTA-CCTGAGATCGTG---T-ACCATCACAATTTTTGGACTAAAA
187 GGTTCAATTTTTGCAAAATATTAGCC-GAAATCGTGTACTAACCATCACGATTTTTGG-CTAAAA
* * * * *
63004 ACGCGTTTCGGGGTTTCA--GCTCAGTTTTGCATGATTTTTTGTGCGAAAACTCCATT--AATGA
250 ACGCGTTCCGGGG--TCATGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC-TTGAAAT-A
*
63065 TCTATATTCATCTAACCAAAT
311 TTTATATTCATCTAACCAAAT
* * * * *
63086 CTCAGCCACATTGGATTTAATG-ATTTGTTTTTTCGAGCATCAAAAT-TTGATTTCGATTTAAAT
1 CTCAGCCACACTGCATTTAA-GAATTTGTTTTTACGAGCATCAGAATCTTG-TTTCGA-TTAACT
* *** ** * * *
63149 AGAAAATAATTCGGAAAAAATAGATTTAACGATATTAGAAAAGTGAAAAGCCCTTCAAT-TAATT
63 AGAAATTAATTCGGAAAAAATAGAAAAAACGATATTAGAAGCGTGAAAATCCATTCAATCT-TTT
* ** * * * * *
63213 TGGCGTTGAA-TATATACACTTTTATGAGTATTGAAGCCAAAAATTG-AGGAAAAATCATTCGGT
127 TGGAGTTGAATTATATA-TTTTTTATGAGTATTGTAGCGAAAAATTGAAAGAAAAAT-TTTTGGT
* * * *
63276 T-GATCTTTTGCTAAATTTTAGCCGAAATCGAT-TATTAACCATCACGATTTTTGGCTAAAAACG
190 TCAAT-TTTTGCAAAATATTAGCCGAAATCG-TGTACTAACCATCACGATTTTTGGCTAAAAACG
* ** * * *
63339 TGTTTTGGGGTCATGACTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATTTTTATAT
253 CGTTCCGGGGTCATGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATTTATAT
**
63404 TCATCTAAGAAAAT
318 TCATCTAACCAAAT
* *
63418 CTCAGCCACACTGCATTTAAGAATTTATTTTTACGAGAATCAGAATCTTGTTTCGATTAACTAGA
1 CTCAGCCACACTGCATTTAAGAATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTAACTAGA
*
63483 AATTAATTCGGAAAAAATAGAAAAAATGATATTAGAAGCGTGAAAATCCATTCAATCTTTTTGGA
66 AATTAATTCGGAAAAAATAGAAAAAACGATATTAGAAGCGTGAAAATCCATTCAATCTTTTTGGA
* *
63548 GTTAAATTATATATTTTTTATGAGTATTTTAGCGAAAAATTGAAAGAAAAATTTTTGGTTCAATT
131 GTTGAATTATATATTTTTTATGAGTATTGTAGCGAAAAATTGAAAGAAAAATTTTTGGTTCAATT
* **
63613 TTTGCAAAATATTAGCCGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACATGTTCCGG
196 TTTGCAAAATATTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCGG
* * * * * *
63678 GGTCCA-GGTTCAGTTTTGCATGTTTTTTGGCGTCAAGACTCCTTGATATATCTATATTCATCTC
261 GGT-CATGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATTTATATTCATCTA
63742 ACCAAAT
325 ACCAAAT
* * * * * *
63749 CTTAGCCACAATGCATTTAAGAATTTGTTTTTACGAGCATACAAAATGTTGTTTTGATTAATTAG
1 CTCAGCCACACTGCATTTAAGAATTTGTTTTTACGAGCAT-CAGAATCTTGTTTCGATTAACTAG
* * * *
63814 AAATTAATTC-GAAAAAA-GGGAAAAATGATATTAGAAGCGTGAAAATCTATTCAATCTTTTTGG
65 AAATTAATTCGGAAAAAATAGAAAAAACGATATTAGAAGCGTGAAAATCCATTCAATCTTTTTGG
* *
63877 TGTTGAATTATATATATTTTTATGAGTATTGTGGC-ATAAAATTG-AAGAAAAATTTTTGGTTCA
130 AGTTGAATTATATAT-TTTTTATGAGTATTGTAGCGA-AAAATTGAAAGAAAAATTTTTGGTTCA
* * * * * *
63940 ATTTTTGTAAAATTTTAGCTGAAATCGTGTACTAACTATCAC-AGTTTTTGGCTAAAAATGCATT
193 ATTTTTGCAAAATATTAGCCGAAATCGTGTACTAACCATCACGA-TTTTTGGCTAAAAACGCGTT
* * * * * *
64004 -CGGGGTCCTGACTTAGTTTTGCATGATTTTTGTCGCCAAGACTCCTTGAAATTTTTATACTCAT
257 CCGGGGTCATGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATTTATATTCAT
64068 CTAACCAAAT
322 CTAACCAAAT
* * * * *
64078 CGCAACCACAATTCATTTAAGAATTTGTTTTTACGAGCATTAGAATCTT-TTTCCGATTAACTAG
1 CTCAGCCACACTGCATTTAAGAATTTGTTTTTACGAGCATCAGAATCTTGTTT-CGATTAACTAG
** * * * * * *
64142 AAATTAATTCATAAAAAATAGGAAAAATGAAATTAGAAGCGTGAAAATTCATTCAATTTTTTTAG
65 AAATTAATTCGGAAAAAATAGAAAAAACGATATTAGAAGCGTGAAAATCCATTCAATCTTTTTGG
* * * * *
64207 AGTTGAATTATATA-GTTTTATGAGTATTGT-GGGAAAAAATGAAATAAAAATTTTTTGGTTTAA
130 AGTTGAATTATATATTTTTTATGAGTATTGTAGCGAAAAATTGAAAGAAAAA-TTTTTGGTTCAA
* * * * *
64270 TTTTTGTAAAATATTAACCGAAATCATGTACTAACCATCACGGTTTTTGGCTAACAACGCGTTCC
194 TTTTTGCAAAATATTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCC
** * * * *
64335 GGAAATC-TGGCTCAGTTTTACATGATTTTTGGCGCCAAGACTCCTTGAGATATCTATATTCATG
259 GG-GGTCATGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATTTATATTCATC
64399 TAACCAAAT
323 TAACCAAAT
* * *
64408 CACAGCCACACTGCATTTACGAA-TT-TTTTT-CGAGCATCAGAATCTTGTTTCAATTAACTAGA
1 CTCAGCCACACTGCATTTAAGAATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTAACTAGA
*
64470 AATTAATTCGGCAAAAATA-AGAAAAACGATATTAGAAGCGTGAAAATCCATTCAATCTTTTTGG
66 AATTAATTCGGAAAAAATAGA-AAAAACGATATTAGAAGCGTGAAAATCCATTCAATCTTTTTGG
* * * *
64534 AGTTAAATTATATATTTTTTATGTGTATTTTAGCGAAAAATTGAAAGAAAAATTATTGGTTCAAT
130 AGTTGAATTATATATTTTTTATGAGTATTGTAGCGAAAAATTGAAAGAAAAATTTTTGGTTCAA-
* * * * *
64599 TTTTTGCAAAATAGTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAACAACACGTTCC
194 TTTTTGCAAAATATTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCC
*** * * *
64664 GGAAACCTGGCTTAG-TTTGACATGATTTTTGGCGCCAAGACTCCTTGAAATATTTATATTCATG
259 GGGGTCATGGCTCAGTTTTG-CATGATTTTTGGCGCCAAGACTCCTTGAAATATTTATATTCATC
*
64728 TAAACAAAT
323 TAACCAAAT
* * * *
64737 CACAGCCACACTGCATTTAAGAATCTGTTTTTTACGAGCATCATAATCTTGTTTTGATTAACTAG
1 CTCAGCCACACTGCATTTAAGAATTTG-TTTTTACGAGCATCAGAATCTTGTTTCGATTAACTAG
** * * * *
64802 AAATTAATAAGGAAAAAGTAGGAAAAACGATATTAGAAGTGTGAAAATCCATTAAATCTTTTTGG
65 AAATTAATTCGGAAAAAATAGAAAAAACGATATTAGAAGCGTGAAAATCCATTCAATCTTTTTGG
* * * *
64867 AGTTGAATTATATATTTTTTATGAGTATTTTGGCGAAAAATTGAAAG----ATTTTT-TTTAAAA
130 AGTTGAATTATATATTTTTTATGAGTATTGTAGCGAAAAATTGAAAGAAAAATTTTTGGTT-CAA
* * **
64927 GTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CATCAC-ATTTTTTGGCTAAAAGTGCGTTC
194 TTTTTGCAAAATATTAGCCGAAATCGTGTACTAACCATCACGA-TTTTTGGCTAAAAACGCGTTC
* * * * * * * *
64990 CAGGGTCCTGGCTCAGTTTTGCAAGATTTTTGTCGCCAAGAATCATTGAAATTTTTATACTCATC
258 CGGGGTCATGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATTTATATTCATC
*
65055 TTACCTAAAT
323 TAACC-AAAT
65065 ACATGAAACC
Statistics
Matches: 1668, Mismatches: 248, Indels: 125
0.82 0.12 0.06
Matches are distributed among these distances:
326 6 0.00
327 244 0.15
328 155 0.09
329 367 0.22
330 300 0.18
331 282 0.17
332 163 0.10
333 151 0.09
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (331 bp):
CTCAGCCACACTGCATTTAAGAATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTAACTAGA
AATTAATTCGGAAAAAATAGAAAAAACGATATTAGAAGCGTGAAAATCCATTCAATCTTTTTGGA
GTTGAATTATATATTTTTTATGAGTATTGTAGCGAAAAATTGAAAGAAAAATTTTTGGTTCAATT
TTTGCAAAATATTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCGG
GGTCATGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATTTATATTCATCTAA
CCAAAT
Found at i:64097 original size:660 final size:651
Alignment explanation
Indices: 62896--65039 Score: 2360
Period size: 660 Copynumber: 3.3 Consensus size: 651
62886 CACTATTATA
* * *
62896 TATATATTTTTTATGAGTA---TAGCGGCCAAAATTG--AGGAAAATTTATTCGGTCCAATTTTT
1 TATATATTTTTTATGAGTATTTTAGC-G-AAAAATTGAAAGAAAAATTT-TT-GGTTCAATTTTT
* * *
62956 GCAAAATTTTA-CCTGAGATCGTG---T-ACCATCACAATTTTTGGACTAAAAACGCGTTTCGGG
62 GCAAAATATTAGCC-GAAATCGTGTACTAACCATCACAATTTTTGG-CTAAAAACGCGTTCCGGG
*
63016 GTTTCA-GCTCAGTTTTGCATGATTTTTTGTGCG-AAAACTCCATT-AATGATCTATATTCATCT
125 G--TCAGGCTCAGTTTTGCATG-TTTTTTG-GCGCAAGACTCC-TTGAAT-ATCTATATTCATCT
* *
63078 AACCAAATCTCAGCCACATTGGATTTAATG-ATTTGTTTTTTCGAGCATCAAAATTTGATTTCGA
184 AACCAAATCTCAGCCACAATGCATTTAA-GAATTTG-TTTTTCGAGCATCAAAATTTG-TTTCGA
* ** ** * *
63142 TTTAAATAGAAAATAATTCGGAAAAAATAGATTTAACGATATTAGAAAAGTGAAAAGCCCTTCAA
246 -TTAAATAGAAATTAATTCGGAAAAAA-AGA-AAAACGATATTAGAAGCGTGAAAATCCATTCAA
* * * * * * * *
63207 T-TAATTTGGCGTTGAA-TATATACACTTTTATGAGTATTGAAGCCAAAAATTGAGGAAAAATCA
308 TCT-TTTTGGAGTTGAATTATATATATTTTTATGAGTATTG-TGGCAAAAATTGAAGAAAAAT-T
* * *
63270 TTCGGTT-GATCTTTTGCT-AAATTTTAGCCGAAATCGAT-TATTAACCATCACGATTTTTGGCT
370 TTTGGTTCAAT-TTTTG-TAAAATTTTAGCCGAAATCG-TGTACTAACCATCACG-TTTTTGGCT
* * * * *
63332 AAAAACGTG-TTTTGGGGTCATGACTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
431 AAAAA--TGCATTCGGGGTCCTGACTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
* *
63396 TTTTATATTCATCTAAGA-AAATCTCAGCCACACTGCATTTAAGAATTTATTTTTACGAGAATCA
494 TTTTATATTCATCTAA-ACAAATCACAGCCACACTGCATTTAAGAATTT-TTTTTACGAGCATCA
*
63460 GAATCTTGTTTCGATTAACTAGAAATTAATTCGGAAAAAATAGAAAAAATGATATTAGAAGCGTG
557 GAATCTTGTTTCGATTAACTAGAAATTAATTCGGAAAAAATAGGAAAAATGATATTAGAAGCGTG
*
63525 AAAATCCATTCAATCTTTTTGGAGTTAAAT
622 AAAATCCATTCAATCTTTTTGGAGTTGAAT
63555 TATATATTTTTTATGAGTATTTTAGCGAAAAATTGAAAGAAAAATTTTTGGTTCAATTTTTGCAA
1 TATATATTTTTTATGAGTATTTTAGCGAAAAATTGAAAGAAAAATTTTTGGTTCAATTTTTGCAA
**
63620 AATATTAGCCGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACATGTTCCGGGGTCCAG
66 AATATTAGCCGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGTTCCGGGGT-CAG
* *
63685 GTTCAGTTTTGCATGTTTTTTGGCGTCAAGACTCCTTGATATATCTATATTCATCTCACCAAATC
130 GCTCAGTTTTGCATGTTTTTTGGCG-CAAGACTCCTTGA-ATATCTATATTCATCTAACCAAATC
* * *
63750 TTAGCCACAATGCATTTAAGAATTTGTTTTTACGAGCATACAAAATGTTGTTTTGATTAATTAGA
193 TCAGCCACAATGCATTTAAGAATTTGTTTTT-CGAGCAT-CAAAAT-TTGTTTCGATTAAATAGA
* * * *
63815 AATTAATTC-GAAAAAAGGGAAAAATGATATTAGAAGCGTGAAAATCTATTCAATCTTTTTGGTG
255 AATTAATTCGGAAAAAA-AGAAAAACGATATTAGAAGCGTGAAAATCCATTCAATCTTTTTGGAG
63879 TTGAATTATATATATTTTTATGAGTATTGTGGCATAAAATTGAAGAAAAATTTTTGGTTCAATTT
319 TTGAATTATATATATTTTTATGAGTATTGTGGCA-AAAATTGAAGAAAAATTTTTGGTTCAATTT
* *
63944 TTGTAAAATTTTAGCTGAAATCGTGTACTAACTATCACAGTTTTTGGCTAAAAATGCATTCGGGG
383 TTGTAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-GTTTTTGGCTAAAAATGCATTCGGGG
* * *
64009 TCCTGACTTAGTTTTGCATGATTTTTGTCGCCAAGACTCCTTGAAATTTTTATACTCATCTAACC
447 TCCTGACTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATTTTTATATTCATCTAAAC
* * * * *
64074 AAATCGCAACCACAATTCATTTAAGAATTTGTTTTTACGAGCATTAGAATCTT-TTTCCGATTAA
512 AAATCACAGCCACACTGCATTTAAGAATTT-TTTTTACGAGCATCAGAATCTTGTTT-CGATTAA
** * * *
64138 CTAGAAATTAATTCATAAAAAATAGGAAAAATGAAATTAGAAGCGTGAAAATTCATTCAATTTTT
575 CTAGAAATTAATTCGGAAAAAATAGGAAAAATGATATTAGAAGCGTGAAAATCCATTCAATCTTT
*
64203 TTAGAGTTGAAT
640 TTGGAGTTGAAT
* * * * * * *
64215 TATATA-GTTTTATGAGTATTGT-GGGAAAAAATGAAATAAAAATTTTTTGGTTTAATTTTTGTA
1 TATATATTTTTTATGAGTATTTTAGCGAAAAATTGAAAGAAAAA-TTTTTGGTTCAATTTTTGCA
* * ** * ** *
64278 AAATATTAACCGAAATCATGTACTAACCATCACGGTTTTTGGCTAACAACGCGTTCCGGAAATCT
65 AAATATTAGCCGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGTTCCGG-GGTCA
* * *
64343 GGCTCAGTTTTACATGATTTTTGGCGCCAAGACTCCTTGAGATATCTATATTCATGTAACCAAAT
129 GGCTCAGTTTTGCATGTTTTTTGGCG-CAAGACTCCTTGA-ATATCTATATTCATCTAACCAAAT
* * * * * *
64408 CACAGCCACACTGCATTTACGAA-TT-TTTTTCGAGCATCAGAATCTTGTTTCAATTAACTAGAA
192 CTCAGCCACAATGCATTTAAGAATTTGTTTTTCGAGCATCAAAAT-TTGTTTCGATTAAATAGAA
64471 ATTAATTCGGCAAAAATAAGAAAAACGATATTAGAAGCGTGAAAATCCATTCAATCTTTTTGGAG
256 ATTAATTCGG-AAAAA-AAGAAAAACGATATTAGAAGCGTGAAAATCCATTCAATCTTTTTGGAG
* * * * *
64536 TTAAATTATATAT-TTTTTATGTGTATTTTAGCGAAAAATTGAAAGAAAAATTATTGGTTCAATT
319 TTGAATTATATATATTTTTATGAGTATTGTGGC-AAAAATTG-AAGAAAAATTTTTGGTTCAA-T
* ** * * ** *
64600 TTTTGCAAAATAGTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAACAACACGTTCCG
381 TTTTGTAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-GTTTTTGGCTAAAAATGCATT-CG
*** * * *
64665 GAAACCTGGCTTAG-TTTGACATGATTTTTGGCGCCAAGACTCCTTGAAATATTTATATTCATGT
444 GGGTCCTGACTTAGTTTTG-CATGATTTTTGGCGCCAAGACTCCTTGAAATTTTTATATTCATCT
* *
64729 AAACAAATCACAGCCACACTGCATTTAAGAATCTGTTTTTTACGAGCATCATAATCTTGTTTTGA
508 AAACAAATCACAGCCACACTGCATTTAAGAAT-T-TTTTTTACGAGCATCAGAATCTTGTTTCGA
** * * * *
64794 TTAACTAGAAATTAATAAGGAAAAAGTAGGAAAAACGATATTAGAAGTGTGAAAATCCATTAAAT
571 TTAACTAGAAATTAATTCGGAAAAAATAGGAAAAATGATATTAGAAGCGTGAAAATCCATTCAAT
64859 CTTTTTGGAGTTGAAT
636 CTTTTTGGAGTTGAAT
* * * *
64875 TATATATTTTTTATGAGTATTTTGGCGAAAAATTGAAAG----ATTTTT-TTTAAAAGTTTTGCA
1 TATATATTTTTTATGAGTATTTTAGCGAAAAATTGAAAGAAAAATTTTTGGTT-CAATTTTTGCA
* * ** * *
64935 AAATTTTAGCCGAAATCGTGTACTAA-CATCACATTTTTTGGCTAAAAGTGCGTTCCAGGGTCCT
65 AAATATTAGCCGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGTTCCGGGGT-CA
* * * * *
64999 GGCTCAGTTTTGCAAGATTTTTGTCGCCAAGAATCATTGAA
129 GGCTCAGTTTTGCATGTTTTTTGGCG-CAAGACTCCTTGAA
65040 ATTTTTATAC
Statistics
Matches: 1269, Mismatches: 169, Indels: 98
0.83 0.11 0.06
Matches are distributed among these distances:
655 31 0.02
656 96 0.08
657 121 0.10
658 77 0.06
659 266 0.21
660 329 0.26
661 120 0.09
662 91 0.07
663 105 0.08
664 30 0.02
665 3 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (651 bp):
TATATATTTTTTATGAGTATTTTAGCGAAAAATTGAAAGAAAAATTTTTGGTTCAATTTTTGCAA
AATATTAGCCGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGTTCCGGGGTCAGG
CTCAGTTTTGCATGTTTTTTGGCGCAAGACTCCTTGAATATCTATATTCATCTAACCAAATCTCA
GCCACAATGCATTTAAGAATTTGTTTTTCGAGCATCAAAATTTGTTTCGATTAAATAGAAATTAA
TTCGGAAAAAAAGAAAAACGATATTAGAAGCGTGAAAATCCATTCAATCTTTTTGGAGTTGAATT
ATATATATTTTTATGAGTATTGTGGCAAAAATTGAAGAAAAATTTTTGGTTCAATTTTTGTAAAA
TTTTAGCCGAAATCGTGTACTAACCATCACGTTTTTGGCTAAAAATGCATTCGGGGTCCTGACTT
AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATTTTTATATTCATCTAAACAAATCACAG
CCACACTGCATTTAAGAATTTTTTTTACGAGCATCAGAATCTTGTTTCGATTAACTAGAAATTAA
TTCGGAAAAAATAGGAAAAATGATATTAGAAGCGTGAAAATCCATTCAATCTTTTTGGAGTTGAA
T
Found at i:65511 original size:231 final size:230
Alignment explanation
Indices: 65139--65593 Score: 623
Period size: 230 Copynumber: 2.0 Consensus size: 230
65129 TCAACTACAT
* * * * * * *
65139 TGCATTTAGGAATTTGTTTTTATGAACATTAGAGTCTTGTTTCGATTAATTAGAAATTGATTCGG
1 TGCATTTAAGAATTTGTTTTTACGAACATCAGAATCTTGTTTCGATTAACTAGAAATTAATTAGG
* * *
65204 CAAAAATAGGAAAAAACGACATTAGAAGCGTGAAAATCCATTCAATCTTTTTGGAGTTGAATTAT
66 CAAAAATAGGAAAAAACGACATTACAAGCGTGAAAATCCACTAAATCTTTTTGGAGTTGAATTAT
* * *
65269 ATATTTTTTATGAGTATCTTAGCGA-AAAATTTAAAGAAAAATTTTTGGTTCAATTTTTGC-AAC
131 ATATTTTTTATGAGTAT-TTAG-GAGAAAATTGAAAGAAAAATTTTTGGTTCAATTTTTACAAAA
*
65332 TTATTAGCTGAAATCGTATACTAACCATCACAGCCACAC
194 TT-TTAGCCGAAATCGTATACTAA-CATCACAGCCACAC
* * *
65371 TGCATTTAAGAATTTGTTTTTTACGAGCATCAGAATCTTGTTTTGATTTACTAGAAATTAATTAG
1 TGCATTTAAGAATTTG-TTTTTACGAACATCAGAATCTTGTTTCGATTAACTAGAAATTAATTAG
*
65436 G-AAAAAGTAGG-AAAAACGATATTACAAGCGTG-AAATCCACTAAATCTTTTTGGAGTTGAATT
65 GCAAAAA-TAGGAAAAAACGACATTACAAGCGTGAAAATCCACTAAATCTTTTTGGAGTTGAATT
* * *
65498 GTATATTTTTTATGAGTATTTTGGAGAAAATTGAAAGAAAAATTTTTTGTTCAATTTTTACAAAA
129 ATATATTTTTTATGAGTATTTAGGAGAAAATTGAAAGAAAAATTTTTGGTTCAATTTTTACAAAA
*
65563 TTTTAGCCGAAATCGTGTACTAACATCACAG
194 TTTTAGCCGAAATCGTATACTAACATCACAG
65594 TTTTTTTGGC
Statistics
Matches: 197, Mismatches: 22, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
229 10 0.05
230 54 0.27
231 50 0.25
232 39 0.20
233 44 0.22
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (230 bp):
TGCATTTAAGAATTTGTTTTTACGAACATCAGAATCTTGTTTCGATTAACTAGAAATTAATTAGG
CAAAAATAGGAAAAAACGACATTACAAGCGTGAAAATCCACTAAATCTTTTTGGAGTTGAATTAT
ATATTTTTTATGAGTATTTAGGAGAAAATTGAAAGAAAAATTTTTGGTTCAATTTTTACAAAATT
TTAGCCGAAATCGTATACTAACATCACAGCCACAC
Done.