Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2790
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: 42443
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:538 original size:47 final size:47
Alignment explanation
Indices: 468--1042 Score: 926
Period size: 47 Copynumber: 12.2 Consensus size: 47
458 ATCTATCTCT
*
468 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCGCATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
* * * * * * *
515 CTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
*
562 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCGCATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
609 CTTTCACATTCATCACATCGGCCATTA-GCCTTATCACATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
655 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACA
*
704 CATTCACATTCATCACATC-GCCATTAGGCCTTATCACATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
*
750 CTTTCACATTCATCACATCGGCCATTAGACCTTATCACATATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACA
799 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
* *
846 CTTTCACATTCATCACATCAGCCATTAGACC-TATCACATATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACA
*
894 C-TTCACATCCATCACATCGGCCATTAGGCC-TATCACATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
939 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
*
986 CTTTCACATTCATCACATCGGCCATTAGACCTTATCACATATATACA
1 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1033 CTTTCACATT
1 CTTTCACATT
1043 ACCAACCCTT
Statistics
Matches: 490, Mismatches: 28, Indels: 20
0.91 0.05 0.04
Matches are distributed among these distances:
45 10 0.02
46 106 0.22
47 273 0.56
48 28 0.06
49 73 0.15
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.31
Consensus pattern (47 bp):
CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
Found at i:976 original size:284 final size:281
Alignment explanation
Indices: 468--1042 Score: 924
Period size: 284 Copynumber: 2.0 Consensus size: 281
458 ATCTATCTCT
* * *
468 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCGCATATATACACTTTCACATCCATCACGT
1 CTTTCACATTCATCACATCGGCCATTAGACCTTATCACATATATACACTTTCACATCCATCACAT
* * * * *
533 TGGCCACTCGGCCCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
66 CGGCCACTAGGCCCTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGACCTTATC
* *
598 GCATATATACACTTTCACATTCATCACATCGGCCATTAGCCTTATCACATATATACACTTTCACA
131 ACATATATACACTTTCACATCCATCACATCGGCCATTAGCCTTATCACATATATACACTTTCACA
663 TTCATCACATCGGCCATTAGGCCTTATCACATATATATACACATTCACATTCATCACATC-GCCA
196 TTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACATTCACATTCATCACATCGGCCA
*
727 TTAGGCCTTATCACATATATACA
259 TTAGACCTTATCACATATATACA
*
750 CTTTCACATTCATCACATCGGCCATTAGACCTTATCACATATATATACACTTTCACATTCATCAC
1 CTTTCACATTCATCACATCGGCCATTAGACCTTATCAC--ATATATACACTTTCACATCCATCAC
* *
815 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGACC-TA
64 ATCGGCCACTAGGCCCTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGACCTTA
879 TCACATATATATACAC-TTCACATCCATCACATCGGCCATTAGGCC-TATCACATATATACACTT
129 TCAC--ATATATACACTTTCACATCCATCACATCGGCCATTA-GCCTTATCACATATATACACTT
*
942 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
191 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACATTCACATTCATCACATCGG
1007 CCATTAGACCTTATCACATATATACA
256 CCATTAGACCTTATCACATATATACA
1033 CTTTCACATT
1 CTTTCACATT
1043 ACCAACCCTT
Statistics
Matches: 272, Mismatches: 15, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
282 63 0.23
283 41 0.15
284 155 0.57
285 13 0.05
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.31
Consensus pattern (281 bp):
CTTTCACATTCATCACATCGGCCATTAGACCTTATCACATATATACACTTTCACATCCATCACAT
CGGCCACTAGGCCCTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGACCTTATC
ACATATATACACTTTCACATCCATCACATCGGCCATTAGCCTTATCACATATATACACTTTCACA
TTCATCACATCGGCCATTAGGCCTTATCACATATATACACATTCACATTCATCACATCGGCCATT
AGACCTTATCACATATATACA
Found at i:1295 original size:40 final size:40
Alignment explanation
Indices: 1246--1357 Score: 145
Period size: 40 Copynumber: 2.8 Consensus size: 40
1236 CAGAATTTAA
** *
1246 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACATAAC
* *
1286 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACATAAC
* *
1326 CCGGATTTAGTAACTCACACAAATGCCTTCGG
1 CCGGATATAGTAACTCGCACAAATGCCTTCGG
1358 ATCTTAGTCT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.02
40 62 0.98
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACATAAC
Found at i:19601 original size:46 final size:44
Alignment explanation
Indices: 19544--19713 Score: 128
Period size: 46 Copynumber: 3.7 Consensus size: 44
19534 TGTGTGAGCT
* *
19544 AGTGTAAGACATGTTTGGGACATGCATCAGTCT-CGGGACGTAAGCC
1 AGTGTAAGACATGTTTGGGACATGCATC-GGCTACGAGACGT--GCC
* *** * *
19590 AGTGTAGGACATGTCCAGGATATGCATCGGCTACGAGATGTGCC
1 AGTGTAAGACATGTTTGGGACATGCATCGGCTACGAGACGTGCC
* *
19634 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCT-CGATGATGATCGTC
1 AGTGTAAGA-CATGTTTGGGACAT-GCATCGG-CTACGA-GACG-T-GCC
*
19683 AGTGTAAGAACATGTTTGGGATATGGCATCG
1 AGTGTAAG-ACATGTTTGGGACAT-GCATCG
19714 ACACCTCATC
Statistics
Matches: 101, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
44 11 0.11
45 13 0.13
46 39 0.39
47 6 0.06
48 1 0.01
49 30 0.30
50 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (44 bp):
AGTGTAAGACATGTTTGGGACATGCATCGGCTACGAGACGTGCC
Found at i:33061 original size:15 final size:15
Alignment explanation
Indices: 33041--33069 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33031 GCTGAGGTAT
33041 TTTCAATTTCTGTTC
1 TTTCAATTTCTGTTC
33056 TTTCAATTTCTGTT
1 TTTCAATTTCTGTT
33070 TTAATTCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.17, G:0.07, T:0.62
Consensus pattern (15 bp):
TTTCAATTTCTGTTC
Found at i:33174 original size:78 final size:79
Alignment explanation
Indices: 33080--33231 Score: 270
Period size: 78 Copynumber: 1.9 Consensus size: 79
33070 TTAATTCATG
33080 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTCAAGACACGCTGAGGTAATTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCA
*
33144 GTTTCTGTTTCTGC
66 ATTTCTGTTTCTGC
* *
33158 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCA
33223 ATTTCTGTT
66 ATTTCTGTT
33232 CTTCCAATTT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 39 0.56
79 31 0.44
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (79 bp):
TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCA
ATTTCTGTTTCTGC
Found at i:33373 original size:79 final size:79
Alignment explanation
Indices: 33257--33406 Score: 257
Period size: 79 Copynumber: 1.9 Consensus size: 79
33247 TTAATTCATG
*
33257 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGCTAATTTT-
1 TTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGCT-ATTTTC
33321 AATTTCTGTTTTTGC
65 AATTTCTGTTTTTGC
* *
33336 TTTTCAAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
1 TTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGCTATTTTCA
33401 ATTTCT
66 ATTTCT
33407 ATTCTTCCAA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
78 5 0.07
79 62 0.93
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (79 bp):
TTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGCTATTTTCA
ATTTCTGTTTTTGC
Found at i:33414 original size:178 final size:177
Alignment explanation
Indices: 32980--33596 Score: 909
Period size: 178 Copynumber: 3.4 Consensus size: 177
32970 TTAATTTATA
*
32980 CTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
1 CTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
*
33045 AATTTCTGTTCTTTCAATTTCTGTTTTAATTCATGTTTTCAAAAATCAACTCATATTGCGAGAGG
66 AATTTCTGTTCTTCCAATTTCTGTTTTAATTCATGTTTTCAAAAATCAACTCATATTGCGAGAGG
* * *
33110 TGAGTTGAG-CTCAAGACACGCTGAGGTAATTTCAGTTTCTGTTTCTG
131 TGAGTTGAGCCTCAGGACACGCTGA-GTAATTTCAATTTCTGTTTTTG
33157 CTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
1 CTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
*
33222 AATTTCTGTTCTTCCAATTTATGTTTTAATTCATGTTTTCAAAAATCAACTCATATTGCGAGAGG
66 AATTTCTGTTCTTCCAATTTCTGTTTTAATTCATGTTTTCAAAAATCAACTCATATTGCGAGAGG
*
33287 TGAGTTGAGCCTCAGGACACGCTGAGCTAATTTTAATTTCTGTTTTTG
131 TGAGTTGAGCCTCAGGACACGCTGAG-TAATTTCAATTTCTGTTTTTG
**
33335 CTTTTCAAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
1 CTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
* * *
33400 AATTTCTATTCTTCCAATTTCTATTTTAATTCATGATTTT-AAAAATCAACTCATATTGCGAGAA
66 AATTTCTGTTCTTCCAATTTCTGTTTTAATTCATG-TTTTCAAAAATCAACTCATATTGCGAGAG
*
33464 GTGAGTTGAGCTTCAGGACACGCTGAG-ACATCTTCAATTTCTGTTTTTAATTTATG
130 GTGAGTTGAGCCTCAGGACACGCTGAGTA-AT-TTCAATTTCTG----T--TTT-TG
* * * **
33520 TTTTTCAAAAATGAACTCATACTGCGAGAGGTGAGTTGAG-CTTTGGCTCACACGCTGAGGTATT
1 CTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATT
33584 TTCAATTTCTGTT
63 TTCAATTTCTGTT
33597 TTCAGTTTCT
Statistics
Matches: 402, Mismatches: 23, Indels: 20
0.90 0.05 0.04
Matches are distributed among these distances:
176 1 0.00
177 139 0.35
178 186 0.46
179 4 0.01
182 1 0.00
184 7 0.02
185 37 0.09
187 27 0.07
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (177 bp):
CTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
AATTTCTGTTCTTCCAATTTCTGTTTTAATTCATGTTTTCAAAAATCAACTCATATTGCGAGAGG
TGAGTTGAGCCTCAGGACACGCTGAGTAATTTCAATTTCTGTTTTTG
Found at i:33554 original size:86 final size:86
Alignment explanation
Indices: 33409--33648 Score: 288
Period size: 88 Copynumber: 2.8 Consensus size: 86
33399 CAATTTCTAT
* * * *
33409 TCTTCCAATTTCT-ATTTTAATTCATGATTTT-AAAAATCAACTCATATTGCGAGAAGTGAGTTG
1 TCTT-CAATTTCTGTTTTTAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG
33472 AGCTTCAGG-ACACGCTGAGACA
65 AGCTT-AGGCACACGCTGAGACA
* *
33494 TCTTCAATTTCTGTTTTTAATTTATGTTTTTCAAAAATGAACTCATACTGCGAGAGGTGAGTTGA
1 TCTTCAATTTCTGTTTTTAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* **
33559 GCTTTGGCTCACACGCTGAGGTA
66 GCTTAGG--CACACGCTGAGACA
* * * * * *
33582 TTTTCAATTTCTGTTTTCAGTTTCTATTTTTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGA
1 TCTTCAATTTCTGTTTTTAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
33647 GC
66 GC
33649 CTTTTAATTT
Statistics
Matches: 134, Mismatches: 16, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
84 8 0.06
85 21 0.16
86 34 0.25
88 71 0.53
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.39
Consensus pattern (86 bp):
TCTTCAATTTCTGTTTTTAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
GCTTAGGCACACGCTGAGACA
Found at i:33841 original size:59 final size:58
Alignment explanation
Indices: 33769--33940 Score: 253
Period size: 59 Copynumber: 3.0 Consensus size: 58
33759 TCTACCTTTT
*
33769 AAAAATCAACTCATATTGCGAGAGGTTAGTTGAGCCCTTTCAATTTATGTTTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTT-AATTTATGTTTTTCAAAA
* * *
33828 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTTTAAATTCATGTTTTTC----
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTT-AATTTATGTTTTTCAAAA
*
33883 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTTAATTTCTGTTTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTTAATTTATGTTTTTCAAAA
33941 TGTGACAGCC
Statistics
Matches: 100, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
54 12 0.12
55 38 0.38
59 50 0.50
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (58 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCTTTAATTTATGTTTTTCAAAA
Found at i:36292 original size:47 final size:47
Alignment explanation
Indices: 36223--36742 Score: 819
Period size: 47 Copynumber: 11.1 Consensus size: 47
36213 GAAATGATAG
36223 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * *
36270 TAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
36317 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
36364 TAAGGCCAAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
36411 TAAGGCCAAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
36458 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
36505 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAGGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
36552 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
36599 TAAGGCCTAATGGCC-ACTGTGATGAATGTGAAAGTGTATATATGTTA
1 TAAGGCCTAATGGCCGA-TGTGATGAATGTGAAAGTGTATATATGTGA
36646 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * *
36692 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
36739 TAAG
1 TAAG
36743 TCCCGAAGGG
Statistics
Matches: 445, Mismatches: 25, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
46 40 0.09
47 404 0.91
48 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:38798 original size:43 final size:43
Alignment explanation
Indices: 38750--38895 Score: 292
Period size: 43 Copynumber: 3.4 Consensus size: 43
38740 TTGGTTTTCA
38750 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
38793 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
38836 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
38879 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
38896 TTGAAATGCA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 103 1.00
ACGTcount: A:0.23, C:0.15, G:0.36, T:0.27
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:38912 original size:29 final size:29
Alignment explanation
Indices: 38877--38950 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
38867 GTTGTGAGAT
* *
38877 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
38906 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
38935 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
38951 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:39379 original size:40 final size:41
Alignment explanation
Indices: 39256--39412 Score: 133
Period size: 40 Copynumber: 3.9 Consensus size: 41
39246 TTAAATGATG
* * *
39256 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCT-AGTGACTATA
* * * * * *
39296 TCCGGACTAAGATCCGAA-AGCATTGGTGCAAGTTACTAAA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGACTATA
*
39336 TCCGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTGA-TATA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGACTATA
* * * * * *
39376 TCCGTGCTAAATCCCGAAGAGCAATCATGCTGGTGAC
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGAC
39413 GTGTATTCGG
Statistics
Matches: 91, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
40 71 0.78
41 20 0.22
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (41 bp):
TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGACTATA
Done.