Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3438
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: 47984
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:11663 original size:44 final size:43
Alignment explanation
Indices: 11424--11843 Score: 173
Period size: 46 Copynumber: 9.6 Consensus size: 43
11414 AGCGGATTAA
* * * * *
11424 AGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACAT-C
1 AGGATCTTATCTCCCTGAAGTTACAGTGGAGTAGATAAAATAC
** * *
11466 AGG-TCTTATCTCCCTG-AGATTACAGTGGAACAGACCGAAGAAATGC
1 AGGATCTTATCTCCCTGAAG-TTACAGTGGAGTAGA---TA-AAATAC
* ** * *
11512 A-GATCTTGTCTCCCTG-AGATTACAGTGGAACAGACCGAAGAAATGC
1 AGGATCTTATCTCCCTGAAG-TTACAGTGGAGTAGA---TA-AAATAC
* * * * * *
11558 A-GATCTTGTCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATAT
1 AGGATCTTATCTCCCTGAAGTTACAGTGGAGTAGAT--AAAATAC
* ** *
11602 A--ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAA
1 AGGATCTTATCTCCCTGAAGTTACAGTGGAGTAGA-TAAAATAC
* * ***
11644 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT-C
1 AGGATCTTATCTCCCTGAAGTTACAGTGGAGTAGATAAAATAC
* *
11686 AGG-TCTTATCTCCCTG-AGATTACAGTGGAGTAGACCGAAGAATTGC
1 AGGATCTTATCTCCCTGAAG-TTACAGTGGAGTAGA--TAA-AA-TAC
* * ** *
11732 A-GATCTTATAC-CCCTGAAGTTACAGCGGAGCAGATCGAAGAC
1 AGGATCTTAT-CTCCCTGAAGTTACAGTGGAGTAGATAAAATAC
** * * * *
11774 ACTATCCTATCTCCCTGAAGTTACAGTGGAGTGGGTTAAAATAA
1 AGGATCTTATCTCCCTGAAGTTACAGTGGAGT-AGATAAAATAC
* *
11818 AGGATCTTATCTCTCTGAGGTTACAG
1 AGGATCTTATCTCCCTGAAGTTACAG
11844 CAGAGTAGGT
Statistics
Matches: 294, Mismatches: 59, Indels: 48
0.73 0.15 0.12
Matches are distributed among these distances:
40 4 0.01
41 50 0.17
42 15 0.05
43 56 0.19
44 59 0.20
45 7 0.02
46 99 0.34
47 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (43 bp):
AGGATCTTATCTCCCTGAAGTTACAGTGGAGTAGATAAAATAC
Found at i:11681 original size:87 final size:86
Alignment explanation
Indices: 11559--11848 Score: 284
Period size: 87 Copynumber: 3.3 Consensus size: 86
11549 AAGAAATGCA
* * *
11559 GATCTTGTCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGAAGTTAC
1 GATCTTATCTCCCTGAAGTTACAGCAGAGCAGATCGAAGATAT-ATCCTATCTCCCTGAAGTTAC
*
11624 AGTGGAGCGGATTAAAATAAAG
65 AGTGGAGTGGATTAAAATAAAG
* * * * ** *
11646 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG--CATCAGGTCTTATCTCCCTG-AGATTA
1 GATCTTATCTCCCTGAAGTTACAGCAGAGCAGATCGAAGAT-ATATCCTATCTCCCTGAAG-TTA
* ** **
11708 CAGTGGAGTAGACCGAAGAATTGCA-
64 CAGTGGAGTGGA-TTAA-AA-TAAAG
* *
11733 GATCTTATAC-CCCTGAAGTTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 GATCTTAT-CTCCCTGAAGTTACAGCAGAGCAGATCGAAGATA-TATCCTATCTCCCTGAAGTTA
*
11797 CAGTGGAGTGGGTTAAAATAAAG
64 CAGTGGAGTGGATTAAAATAAAG
* *
11820 GATCTTATCTCTCTGAGGTTACAGCAGAG
1 GATCTTATCTCCCTGAAGTTACAGCAGAG
11849 TAGGTCGCAT
Statistics
Matches: 157, Mismatches: 34, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
84 2 0.01
85 27 0.17
86 6 0.04
87 88 0.56
88 6 0.04
89 26 0.17
90 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (86 bp):
GATCTTATCTCCCTGAAGTTACAGCAGAGCAGATCGAAGATATATCCTATCTCCCTGAAGTTACA
GTGGAGTGGATTAAAATAAAG
Found at i:11735 original size:174 final size:174
Alignment explanation
Indices: 11515--11893 Score: 575
Period size: 174 Copynumber: 2.2 Consensus size: 174
11505 GAAATGCAGA
* * * *
11515 TCTTGTCTCCCTGAGATTACAGTGGAACAGACCGAAGAAATGCAGATCTTGT-CTCCCTGAGGTT
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATGCAGATCTTATAC-CCCTGAAGTT
*
11579 ACAGCGGAGCAGATCGAAGATA-TAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATA
65 ACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATA
* *
11643 AAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
129 AAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAAG
* *
11689 TCTTATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTGCAGATCTTATACCCCTGAAGTTA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATGCAGATCTTATACCCCTGAAGTTA
* *
11754 CAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGTGGGTTAAAATAAA
66 CAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAA
* *
11819 GGATCTTATCTCTCTGAGGTTACAGCAGAGTAGGTCGCATCAAG
131 GGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAAG
* *
11863 TCTTATTTCCCTGAAGA-TGCAGTGGAATAGA
1 TCTTATCTCCCTG-AGATTACAGTGGAATAGA
11894 TTGAAAACCA
Statistics
Matches: 186, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
174 181 0.97
175 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (174 bp):
TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATGCAGATCTTATACCCCTGAAGTTA
CAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAA
GGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAAG
Found at i:11747 original size:46 final size:45
Alignment explanation
Indices: 11469--11804 Score: 238
Period size: 46 Copynumber: 7.6 Consensus size: 45
11459 TCACATCAGG
*
11469 TCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAAATGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAG-AATGCAGA
* *
11515 TCTTGTCTCCCTGAGATTACAGTGGAACAGACCGAAGAAATGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAG-AATGCAGA
* * * *
11561 TCTTGTCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATAT--A-A
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGA-ATGCAGA
* * ** **
11604 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGA-TTAA-AATAAAGGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGACCGAAGAATGCA-GA
* * * * * *
11648 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATC---GCAT-CAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGACCGAAGAATGCAGA
*
11689 TCTTATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAA-TGCAGA
* * *
11735 TCTTATAC-CCCTGA-AGTTACAGCGGAGCAGATCGAAG-A--CACTA
1 TCTTAT-CTCCCTGAGA-TTACAGTGGAGCAGACCGAAGAATGCA-GA
*
11778 TCCTATCTCCCTGA-AGTTACAGTGGAG
1 TCTTATCTCCCTGAGA-TTACAGTGGAG
11805 TGGGTTAAAA
Statistics
Matches: 240, Mismatches: 32, Indels: 39
0.77 0.10 0.13
Matches are distributed among these distances:
40 2 0.01
41 30 0.12
42 8 0.03
43 52 0.22
44 30 0.12
45 4 0.02
46 113 0.47
47 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (45 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATGCAGA
Found at i:13111 original size:3 final size:3
Alignment explanation
Indices: 13103--13197 Score: 93
Period size: 3 Copynumber: 31.3 Consensus size: 3
13093 TTTGTTAATT
*
13103 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA CTA TTA TTA TCT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA
* * * * * * *
13149 TTA CTA TTA TTG TTA GTA TTA TTA CTA CTA TTA TTA TTA CTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13197 T
1 T
13198 ATTTATACCT
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
2 1 0.01
3 70 0.93
4 4 0.05
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:13373 original size:36 final size:34
Alignment explanation
Indices: 13333--13401 Score: 86
Period size: 36 Copynumber: 2.0 Consensus size: 34
13323 CATATTTTCG
13333 TATATTTTATAA-TTTGTATATACATATACTTATATC
1 TATATTTTATAACTTT-TATA-A-ATATACTTATATC
* *
13369 TATATTTTCTAACTTTTATAAATATATTTATAT
1 TATATTTTATAACTTTTATAAATATACTTATAT
13402 GTACATACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 11 0.37
35 1 0.03
36 15 0.50
37 3 0.10
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.55
Consensus pattern (34 bp):
TATATTTTATAACTTTTATAAATATACTTATATC
Found at i:13521 original size:14 final size:14
Alignment explanation
Indices: 13504--13534 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13494 CTATTTACTC
*
13504 TTTTTTATTTTTAT
1 TTTTTTATTATTAT
13518 TTTTTTATTATTAT
1 TTTTTTATTATTAT
13532 TTT
1 TTT
13535 CAAATTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTATTATTAT
Found at i:18081 original size:16 final size:15
Alignment explanation
Indices: 18062--18094 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
18052 GACTTGTGCC
18062 TTCAGCCATCAGACAA
1 TTCAGCCATCAGA-AA
18078 TTCAGCCATCAGAAA
1 TTCAGCCATCAGAAA
18093 TT
1 TT
18095 GAAAAAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.24
Consensus pattern (15 bp):
TTCAGCCATCAGAAA
Found at i:24627 original size:23 final size:22
Alignment explanation
Indices: 24590--24643 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
24580 CAGTTAAGAA
*
24590 ATTTCCATTTGGCACAATAATT
1 ATTTCCACTTGGCACAATAATT
*
24612 ATTTGCCACTTGGCACGATAATT
1 ATTT-CCACTTGGCACAATAATT
24635 ATTTTCCAC
1 A-TTTCCAC
24644 ATGTCTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 4 0.14
23 21 0.75
24 3 0.11
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (22 bp):
ATTTCCACTTGGCACAATAATT
Found at i:25974 original size:16 final size:16
Alignment explanation
Indices: 25931--25974 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
25921 TTTCCTTTTA
*
25931 TTTTT-TTTCTTTTTC
1 TTTTTCTTTCTTTATC
**
25946 TTTTTCTAGCTTTATC
1 TTTTTCTTTCTTTATC
25962 TTTTTCTTTCTTT
1 TTTTTCTTTCTTT
25975 CTTTTGTTAG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTTCTTTCTTTATC
Found at i:29836 original size:39 final size:39
Alignment explanation
Indices: 29782--29895 Score: 174
Period size: 39 Copynumber: 2.9 Consensus size: 39
29772 AGAAATATGG
*
29782 TGATTATTCGGGCTATGTGCCTAGTAGGCTTTGTGCCGA
1 TGATTATTCGGGCTATGTGCCTAGAAGGCTTTGTGCCGA
* *
29821 TGATTATTCGGGCTATGTGCCTAGAAGGCTTTGTGTCGG
1 TGATTATTCGGGCTATGTGCCTAGAAGGCTTTGTGCCGA
* * *
29860 TGATTATTCAGGCTATGTGCCTAGCAGGCTATGTGC
1 TGATTATTCGGGCTATGTGCCTAGAAGGCTTTGTGC
29896 TGGTGTATTG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.17, C:0.18, G:0.31, T:0.35
Consensus pattern (39 bp):
TGATTATTCGGGCTATGTGCCTAGAAGGCTTTGTGCCGA
Found at i:33799 original size:11 final size:11
Alignment explanation
Indices: 33783--33848 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
33773 CATAAATTAT
33783 AAAATATATAA
1 AAAATATATAA
*
33794 AAAATATATAT
1 AAAATATATAA
*
33805 AAAGTATATTAA
1 AAAATATA-TAA
* * *
33817 AAAAAAGAAAA
1 AAAATATATAA
33828 AAATTATATATATA
1 AAA--ATATATA-A
33842 AAAATAT
1 AAAATAT
33849 GTACATATAT
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
11 22 0.54
12 11 0.27
13 4 0.10
14 4 0.10
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
AAAATATATAA
Found at i:34014 original size:21 final size:22
Alignment explanation
Indices: 33962--34016 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
33952 TATATACAAC
* *
33962 TTATAAA-ATATAGAAAAATGA
1 TTATAAATATATACAAAAAAGA
*
33983 TTTTAAGATATATACAAAAAAGA
1 TTATAA-ATATATACAAAAAAGA
34006 -TATAAATATAT
1 TTATAAATATAT
34017 GTATGTTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.39
22 5 0.18
23 12 0.43
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (22 bp):
TTATAAATATATACAAAAAAGA
Found at i:36213 original size:41 final size:41
Alignment explanation
Indices: 36156--36853 Score: 259
Period size: 44 Copynumber: 16.3 Consensus size: 41
36146 TACTATCTTT
* *
36156 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATAC
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATTC
* * * * * *
36197 GATCTTCTCTACTGTAA-CTTTAGAGAGATAAGATCCTTTATTTT
1 GATCTGCTCCACTGTAATC-TCAGGGAGATAAGA-CC-TGA-TTC
* * * * *
36241 AATC-CCTCCATTGTAATCTCAGGGAGATAGGATTACTG-TCTC
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGA--CCTGAT-TC
* *
36283 TGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTC
1 -GATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTG--A---TTC
* *
36330 GGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATAC
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATTC
** * *
36371 GATCCACTCTACTGTAA-CTTCAGAGAGATAAGATCCT--TT-
1 GATCTGCTCCACTGTAATC-TCAGGGAGATAAGA-CCTGATTC
* * * * * * *
36410 AATCCGTTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTC
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGA--CCT-GATTC
* * * * *
36454 AATCTGCTGCGCTGTAATCTTAGGGAGATAAGATCTGAAATTC
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTG--ATTC
* * * * * *
36497 TTCAGTCTGTTCCACTGTAATCTTAGGGAAATAAGACCTGGTGC
1 --GA-TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATTC
** * *
36541 GATCCACTCTACTGTAA-CTTCAGAGAGATAAGATCCT--TT-
1 GATCTGCTCCACTGTAATC-TCAGGGAGATAAGA-CCTGATTC
* * * * * *
36580 AATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTC
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGA--CCT-GATTC
* * * *
36624 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTAAAATTC
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGACCT--GATTC
* * * * *
36667 TTCAGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGC
1 --GA-TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATTC
* * * * *
36711 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTCATTTT
1 GATCTGCTCCACTGTAATC-TCAGGGAGATAAGA-CC-TGA-TTC
* *** * * *
36755 AATCCATTCCACCGTAATCTCAGGGAGATAAGATTACTAGCTTC
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGA--CCT-GATTC
* * * * **
36799 AATCTGCTCCGCTGTAATCACAGGGAGATAAGATCTGACAC
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATTC
*
36840 AATCTGCTCCACTG
1 GATCTGCTCCACTG
36854 CAACCAATGG
Statistics
Matches: 489, Mismatches: 121, Indels: 94
0.69 0.17 0.13
Matches are distributed among these distances:
39 49 0.10
40 14 0.03
41 117 0.24
42 22 0.04
43 38 0.08
44 147 0.30
45 5 0.01
46 94 0.19
47 2 0.00
48 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (41 bp):
GATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATTC
Found at i:36300 original size:128 final size:124
Alignment explanation
Indices: 36064--36316 Score: 366
Period size: 128 Copynumber: 2.0 Consensus size: 124
36054 GGAAGGTAAA
36064 ACCTGATACGATTCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCACTCCACTGTAA
1 ACCTGATACGATTCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCACTCCACTGTAA
*
36129 TCTCAAGGAGACAAGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
66 TCTCAAGGAGACAAGATTACTATCTCTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
* *
36188 ACCTGATACGA-TCTTCTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTAATCC-CTCCA
1 ACCTGATACGATTC-ACTCTACTGTAACTTCAGAGAGATAAGATCC-----TTTAATCCACTCCA
* * * * *
36251 TTGTAATCTCAGGGAGATAGGATTACTGTCTCTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
60 CTGTAATCTCAAGGAGACAAGATTACTATCTCTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
36316 A
1 A
36317 TCTGTAATTC
Statistics
Matches: 115, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
123 2 0.02
124 40 0.35
128 65 0.57
129 8 0.07
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (124 bp):
ACCTGATACGATTCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCACTCCACTGTAA
TCTCAAGGAGACAAGATTACTATCTCTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
Found at i:36438 original size:39 final size:40
Alignment explanation
Indices: 36336--36439 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 40
36326 CTTCGGTCTG
*
36336 CTCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCCA
1 CTCCACTGTAATCTCAAGGAGATAAGACCTGATAC-ATCCA
* * *
36377 CTCTACTGTAA-CTTC-AGAGAGATAAGATCCT-TTA-ATCCG
1 CTCCACTGTAATC-TCAAG-GAGATAAGA-CCTGATACATCCA
*
36416 TTCCACTGTAATCTCAAGGAGATA
1 CTCCACTGTAATCTCAAGGAGATA
36440 GGATTACTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
39 21 0.40
40 5 0.10
41 23 0.44
42 3 0.06
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (40 bp):
CTCCACTGTAATCTCAAGGAGATAAGACCTGATACATCCA
Found at i:36513 original size:170 final size:171
Alignment explanation
Indices: 36158--36836 Score: 972
Period size: 170 Copynumber: 3.9 Consensus size: 171
36148 CTATCTTTGA
* * ** *
36158 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGATCTTCTCTACTGTAACTTTAGAGA
1 TCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGA
* * *
36223 GATAAGATCCTTTATTTTAATCC-CTCCATTGTAATCTCAGGGAGATAGGATTACT-G-TCTCTG
66 GATAAGATCC----TTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGCT-TC-A
* *
36285 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGG
125 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCAG
*
36332 TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGA
1 TCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGA
*
36397 GATAAGATCC-TTTAATCCGTTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGC
66 GATAAGATCCTTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGC
* *
36461 TGCGCTGTAATCTTAGGGAGATAAGATCTGAAATTCTTCAG
131 TCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCAG
* * * *
36502 TCTGTTCCACTGTAATCTTAGGGAAATAAGACCTGGTGCGATCCACTCTACTGTAACTTCAGAGA
1 TCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGA
36567 GATAAGATCC-TTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGC
66 GATAAGATCCTTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGC
*
36631 TCCGCTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCAG
131 TCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCAG
* * * *
36672 TCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGA
1 TCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGA
** * * *
36737 GATAAGATCCTTCATTTTAATCCATTCCACCGTAATCTCAGGGAGATAAGATTACTAGCTTCAAT
66 GATAAGAT-C--C-TTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTCAAT
*
36802 CTGCTCCGCTGTAATCACAGGGAGATAAGATCTGA
127 CTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
36837 CACAATCTGC
Statistics
Matches: 467, Mismatches: 30, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
169 8 0.02
170 304 0.65
171 4 0.01
172 1 0.00
173 1 0.00
174 71 0.15
175 78 0.17
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (171 bp):
TCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGA
GATAAGATCCTTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGC
TCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCAG
Found at i:36944 original size:87 final size:88
Alignment explanation
Indices: 36839--37003 Score: 226
Period size: 88 Copynumber: 1.9 Consensus size: 88
36829 AGATCTGACA
* * * * ** *
36839 CAATCTGCTCCACTGCAACCAATGGAGGCAAGGCTTTGT-T-TTCGATCTGCTTCGTTGTTAACG
1 CAATCAGCTCCACCGCAACCAATGGAGACAAAGC-TTGTATCTTCGATCTGCTTCACTGTCAACG
36902 CAGGAAGGCAAGATATGCTATCTT
65 CAGGAAGGCAAGATATGCTATCTT
* *
36926 CAATCAGCTCCACCGCAACCGATGGAGACAAAGCTTGTATCTTCGATCTGCTTCACTGTCAAGGC
1 CAATCAGCTCCACCGCAACCAATGGAGACAAAGCTTGTATCTTCGATCTGCTTCACTGTCAACGC
36991 AGGAAGGCAAGAT
66 AGGAAGGCAAGAT
37004 CTGTTGTCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
86 4 0.06
87 30 0.45
88 33 0.49
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (88 bp):
CAATCAGCTCCACCGCAACCAATGGAGACAAAGCTTGTATCTTCGATCTGCTTCACTGTCAACGC
AGGAAGGCAAGATATGCTATCTT
Done.