Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3629
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: 43019
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:8181 original size:44 final size:42
Alignment explanation
Indices: 8041--8882 Score: 330
Period size: 44 Copynumber: 19.8 Consensus size: 42
8031 ATTATACAGG
* * * *
8041 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAA---GA-A
** *
8087 TCTTATCTCCCTGAG-TTACAGCGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-AAGA-A
8130 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-AG-AA
* * ** * *
8174 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG--G-A
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGAA
* ** * * ** *
8213 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCACATCAG-G
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCAAAGAAGAA
* * * * * ***
8254 TCTTATTTCCCTGAGGTTACAGTGGTAGACCGA-GAATTTCAG-A
1 TCTTATCTCCCTGAGATTACAGCGG-AG-CAGATCAA-AGAAGAA
* ** *
8297 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-AAGA-A
8341 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-AG-AA
* * *
8385 TCCTATCT-CCTGAGATTACA--GGAGCGGATTAAAG--G-A
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGAA
* ** * ** *
8421 TCTTATCTCTCTGA-AGTTACAGTAGAG-AGATCACATCAG-G
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCAAAGAAGAA
* * * * * ** *
8461 TCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAA---GA-A
* ** *
8507 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-AAGA-A
8551 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-AG-AA
* * ** * *
8595 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG--G-A
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGAA
* ** * * ** *
8634 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCACATCAG-G
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCAAAGAAGAA
* * * * * ** *
8675 TCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAA---GA-A
* ** *
8721 TCTTATCTCCCT--GATTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-AAGA-A
* * **
8763 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGACACTA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-AGAA
* * * * * *
8806 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATAAAGGA
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGA-TCAAA-GAAGAA
* * * *
8850 TCTTATCTCTCTGAGGTTACAGCAGAGTAGATC
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATC
8883 GCATCAAGTC
Statistics
Matches: 608, Mismatches: 138, Indels: 103
0.72 0.16 0.12
Matches are distributed among these distances:
36 9 0.01
37 9 0.01
38 8 0.01
39 55 0.09
40 23 0.04
41 73 0.12
42 25 0.04
43 88 0.14
44 238 0.39
45 21 0.03
46 58 0.10
47 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (42 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGAA
Found at i:8519 original size:210 final size:213
Alignment explanation
Indices: 8037--8922 Score: 1432
Period size: 210 Copynumber: 4.2 Consensus size: 213
8027 GTTTATTATA
* * ** **
8037 CAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTCAGATCTTATCTCCCTGAG
8102 TTACAGCGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG
66 TTACAGCGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG
8167 ATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTA
131 ATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTA
8232 CAGTAGAGAAGATCACAT
196 CAGTAGAGAAGATCACAT
8250 CAGGTCTTATTTCCCTGAGGTTACAGT-G-GTAGACC-GAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTCAGATCTTATCTCCCTGA-
8312 GTTACAGCGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAA
65 GTTACAGCGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAA
8377 GATAGTAATCCTATCTCC-TGAGATTAC-A-GGAGCGGATTAAAGGATCTTATCTCTCTGAAGTT
130 GATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTT
8439 ACAGTAGAG-AGATCACAT
195 ACAGTAGAGAAGATCACAT
8457 CAGGTCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTCAGATCTTATCTCCCTGA-
8522 GTTACAGCGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAA
65 GTTACAGCGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAA
8587 GATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTT
130 GATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTT
8652 ACAGTAGAGAAGATCACAT
195 ACAGTAGAGAAGATCACAT
8671 CAGGTCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTCAGATCTTATCTCCCTGA-
1 CAGGTCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTCAGATCTTATCTCCCTGAG
* * *
8735 TTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG
66 TTACAGCGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG
* * * *
8800 ACACT-ATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTG
131 ATAGTAATCCTATCTCCTTGAGA-TTACAATGGAGCGGA-T----TAAAGGATCTTATCTCTCTG
* * * *
8863 AGGTTACAGCAGAGTAGATCGCAT
190 AAGTTACAGTAGAGAAGATCACAT
* * * * *
8887 CAAGTCTTATTTCCCTGAAGATGCAGTGGAATAGAC
1 CAGGTCTTATTTCCCTGAGGTTACAGTGGAGTAGAC
8923 TGAAAACAAC
Statistics
Matches: 638, Mismatches: 21, Indels: 25
0.93 0.03 0.04
Matches are distributed among these distances:
207 36 0.06
208 44 0.07
209 8 0.01
210 145 0.23
211 125 0.20
212 68 0.11
213 68 0.11
214 73 0.11
216 71 0.11
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (213 bp):
CAGGTCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTCAGATCTTATCTCCCTGAG
TTACAGCGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG
ATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTA
CAGTAGAGAAGATCACAT
Found at i:10569 original size:3 final size:3
Alignment explanation
Indices: 10561--10609 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
10551 GAATTAGTCC
* * *
10561 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAC TAC TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
10608 TA
1 TA
10610 CCTATTTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:11100 original size:22 final size:23
Alignment explanation
Indices: 11047--11100 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
11037 AAATATACTT
*
11047 TATATATTTTGTTAATTCATGTA
1 TATATATATTGTTAATTCATGTA
* * * *
11070 TACACATATT-TTAGTTCATGTC
1 TATATATATTGTTAATTCATGTA
11092 TATATATAT
1 TATATATAT
11101 CTTTTATACT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.52
Consensus pattern (23 bp):
TATATATATTGTTAATTCATGTA
Found at i:19157 original size:16 final size:18
Alignment explanation
Indices: 19114--19148 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19104 TTTAATGGCG
19114 AAATAGAAATAATAGTTT
1 AAATAGAAATAATAGTTT
19132 AAATAAGAAA-AATAGTT
1 AAAT-AGAAATAATAGTT
19149 AATAGGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
AAATAGAAATAATAGTTT
Found at i:20670 original size:20 final size:21
Alignment explanation
Indices: 20637--20676 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
20627 TTTTGTAATT
20637 TTATTCTTGGGTTT-TGTTTA
1 TTATTCTTGGGTTTCTGTTTA
20657 TTATT-TTGGTGTTTCTGTTT
1 TTATTCTTGG-GTTTCTGTTT
20677 GGGCTGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 9 0.50
21 5 0.28
ACGTcount: A:0.07, C:0.05, G:0.20, T:0.68
Consensus pattern (21 bp):
TTATTCTTGGGTTTCTGTTTA
Found at i:21210 original size:45 final size:44
Alignment explanation
Indices: 21114--21226 Score: 138
Period size: 45 Copynumber: 2.5 Consensus size: 44
21104 CAGTCTGCTC
* * *
21114 CACTGCAACTTCAGGGAGATAA-GACTTATAACTTCAACTTGCCC
1 CACTGCAACTTCAGGG-GATAAGGACTCATAACTTCAACCTGCCA
* *
21158 CACTGCAACTTCAGAGGGATAAGGACTCGTAACTTCAACCTGTCA
1 CACTGCAACTTCAG-GGGATAAGGACTCATAACTTCAACCTGCCA
*
21203 CATTGCAACTTCAGGGGGATAAGG
1 CACTGCAACTTCA-GGGGATAAGG
21227 TTTATAGCTT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
44 19 0.32
45 40 0.67
46 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (44 bp):
CACTGCAACTTCAGGGGATAAGGACTCATAACTTCAACCTGCCA
Found at i:21442 original size:88 final size:88
Alignment explanation
Indices: 21307--21847 Score: 685
Period size: 88 Copynumber: 6.2 Consensus size: 88
21297 ACAACTTTAG
* ** * * * *
21307 GGAGATAAGAATTGTGGCTTC-AATCGCTACAATGCCATTTTAAGGAGAAGAGATTTGTAGCTTT
1 GGAGATACGAATTGTGGCTTCGAGCCGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTC
* *
21371 AATCTACTACGCTAGAACTTCAA
66 GATCTACTCCGCTAGAACTTCAA
** * *
21394 GGAGATAAAAATTATGGCTTCGAGCCGCTCCAATGTCATTTCAGGGAGAAGAGATTTGTAGCTTC
1 GGAGATACGAATTGTGGCTTCGAGCCGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTC
*
21459 GATCTACTCCACTAGAACTTCAA
66 GATCTACTCCGCTAGAACTTCAA
* * * ** * *
21482 AGAGATACGAATTATGACTTCGAGCCATTCCAATGTCATTTCAGGGAGAAGAGA-TTGTAGCCTC
1 GGAGATACGAATTGTGGCTTCGAGCCGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTC
*
21546 GACCTACTCCGCTAGAACTTCAA
66 GATCTACTCCGCTAGAACTTCAA
* * *
21569 GGAGATACGAATTGTGGCTTCGAGCCGCTCCAATGCCATTTTAGGGAGAAAAAATTTGTAGCCTT
1 GGAGATACGAATTGTGGCTTCGAGCCGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAG-CTT
* ** * *
21634 -GGTCTACTCAACTGGAATTTCAA
65 CGATCTACTCCGCTAGAACTTCAA
* * * *
21657 GGAGATACGAACTGTGGCTTCGAGCCGCTCTAATGCCATTTCAGGGAGAAGAGATTTGCAGCTTT
1 GGAGATACGAATTGTGGCTTCGAGCCGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTC
* *
21722 GATCTACTCCGCTGGAGCTTCAA
66 GATCTACTCCGCTAGAACTTCAA
* *
21745 GGAGATACGAATTGTGGCTTCGAGCCGCTCCAATGTCATTTCAGGGAGAAGAGATTTGTAACTTC
1 GGAGATACGAATTGTGGCTTCGAGCCGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTC
*
21810 GATCTACTCTGCT-GAAACTTCAA
66 GATCTACTCCGCTAG-AACTTCAA
21833 GGAGATACGAATTGT
1 GGAGATACGAATTGT
21848 TGATTTCAAC
Statistics
Matches: 393, Mismatches: 56, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
87 98 0.25
88 293 0.75
89 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (88 bp):
GGAGATACGAATTGTGGCTTCGAGCCGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTC
GATCTACTCCGCTAGAACTTCAA
Found at i:21460 original size:44 final size:42
Alignment explanation
Indices: 21410--21811 Score: 149
Period size: 44 Copynumber: 9.2 Consensus size: 42
21400 AAAAATTATG
*
21410 GCTTCGAGCCGCTCCAATGTCATTTCAGGGAGAAGAGATTTGTA
1 GCTTCGAGCCACTCCAATG-CATTTCAGGGAGAAGA-ATTTGTA
* * * * * **
21454 GCTTCGATCTACTCCACTAGAACTTCAAAGAGATACGAATTATG-A
1 GCTTCGAGCCACTCCAAT-GCATTTCAGGGAGA-A-GAATT-TGTA
*
21499 -CTTCGAGCCATTCCAATGTCATTTCAGGGAGAAGAGA-TTGTA
1 GCTTCGAGCCACTCCAATG-CATTTCAGGGAGAAGA-ATTTGTA
* ** * * * *
21541 GCCTCGA-CCTACTCCGCTAGAACTTCAAGGAGATACGAA-TTGTG
1 GCTTCGAGCC-ACTCCAAT-GCATTTCAGGGAGA-A-GAATTTGTA
* * *
21585 GCTTCGAGCCGCTCCAATGCCATTTTAGGGAGAAAAAATTTGTA
1 GCTTCGAGCCACTCCAATG-CATTTCAGGGAG-AAGAATTTGTA
* * * * *
21629 GCCTT-G-GTCTACT-CAACTGGAATTTCAAGGAGATACGAA-CTGTG
1 G-CTTCGAG-CCACTCCAA-T-GCATTTCAGGGAGA-A-GAATTTGTA
* * *
21673 GCTTCGAGCCGCTCTAATGCCATTTCAGGGAGAAGAGATTTGCA
1 GCTTCGAGCCACTCCAATG-CATTTCAGGGAGAAGA-ATTTGTA
* * * ** * * * *
21717 GCTTTGATCTACTCCGCTGGAGCTTCAAGGAGATACGAA-TTGTG
1 GCTTCGAGCCACTCCAATGCA-TTTCAGGGAGA-A-GAATTTGTA
*
21761 GCTTCGAGCCGCTCCAATGTCATTTCAGGGAGAAGAGATTTGTA
1 GCTTCGAGCCACTCCAATG-CATTTCAGGGAGAAGA-ATTTGTA
*
21805 ACTTCGA
1 GCTTCGA
21812 TCTACTCTGC
Statistics
Matches: 251, Mismatches: 73, Indels: 68
0.64 0.19 0.17
Matches are distributed among these distances:
41 2 0.01
42 10 0.04
43 40 0.16
44 170 0.68
45 23 0.09
46 6 0.02
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (42 bp):
GCTTCGAGCCACTCCAATGCATTTCAGGGAGAAGAATTTGTA
Found at i:28540 original size:18 final size:17
Alignment explanation
Indices: 28517--28591 Score: 71
Period size: 18 Copynumber: 4.2 Consensus size: 17
28507 TTGAATCATC
28517 TTTTTTTTTTTATTCTAA
1 TTTTTTTTTTTATT-TAA
* *
28535 TTTTTTTATTTATTTTA
1 TTTTTTTTTTTATTTAA
28552 TTTTTATTTTTCT-TTTAA
1 TTTTT-TTTTT-TATTTAA
* *
28570 TTTTTATTTTCATTTCAA
1 TTTTTTTTTTTATTT-AA
28588 TTTT
1 TTTT
28592 ATTATTTTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
17 14 0.30
18 32 0.68
19 1 0.02
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTTTTTTATTTAA
Found at i:28551 original size:23 final size:21
Alignment explanation
Indices: 28517--28577 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 21
28507 TTGAATCATC
28517 TTTTTTTTTTTATTCTAATTT
1 TTTTTTTTTTTATTCTAATTT
* *
28538 TTTTATTTATTTTATTTTTATTT
1 TTTT-TTT-TTTTATTCTAATTT
28561 TTCTTTTAATTTTTATT
1 TT-TTTT--TTTTTATT
28578 TTCATTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 4 0.12
22 3 0.09
23 16 0.48
24 9 0.27
25 1 0.03
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTTTTTTATTCTAATTT
Found at i:28574 original size:7 final size:6
Alignment explanation
Indices: 28517--28584 Score: 59
Period size: 6 Copynumber: 11.5 Consensus size: 6
28507 TTGAATCATC
* * * *
28517 TTTTTT TTTTTA TTCTAA TTTTT- TTATTTA -TTTTA TTTTTA TTTTTC
1 TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA
* *
28564 TTTTAA TTTTTA TTTTCA TTT
1 TTTTTA TTTTTA TTTTTA TTT
28585 CAATTTTATT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
5 6 0.12
6 43 0.88
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:28592 original size:35 final size:35
Alignment explanation
Indices: 28518--28594 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
28508 TGAATCATCT
* * * *
28518 TTTTTTTTTTATTCTAATTTTTTTATTTATTTTAT
1 TTTTATTTTTATTCTAATTTTTTTATTCATTTCAA
* *
28553 TTTTATTTTTCTTTTAATTTTTATT-TTCATTTCAA
1 TTTTATTTTTATTCTAATTTTT-TTATTCATTTCAA
28588 TTTTATT
1 TTTTATT
28595 ATTTTGTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 33 0.94
36 2 0.06
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (35 bp):
TTTTATTTTTATTCTAATTTTTTTATTCATTTCAA
Found at i:31915 original size:44 final size:44
Alignment explanation
Indices: 31867--32271 Score: 210
Period size: 44 Copynumber: 9.2 Consensus size: 44
31857 GCTCCACCAT
*
31867 TGCTTAGGGAGATAAGATCTTTAATTTTCAGCCTGTTACCCTAC
1 TGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
* * ** * * *
31911 TGCTTAAGGG-GTTAAGGCTCACT-GTTTTC-GATCTGCT-CCGCTAC
1 TGCTT-AGGGAGATAA-GATCTGTAATTTTCAG-CCTGTTACC-CTAC
*
31955 TGCTTAGGGAGATAAGATCTGTAATTTTTAGCCTGTTACCCTAC
1 TGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
* * * * * * * *
31999 TACTTAGGGGGTTAAGGCTCAT-T-GTCTTC-GATCTGCT-CCACTAC
1 TGCTTAGGGAGATAA-GATC-TGTAATTTTCAG-CCTGTTACC-CTAC
* * * *
32043 TACTTTGGGAGATAAGATCTGTAATTTCCAGCCTGTTACACTAC
1 TGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
* * * ** * * *
32087 TGCTTAGGGGGTTAAGAT-TCATCGTCTTC-GATCTGCT-CCGCTAC
1 TGCTTAGGGAGATAAGATCT-GTAATTTTCAG-CCTGTTACC-CTAC
* *
32131 TGCTTAGGGAGATAAGATCTGTAATTTCCAACCTGTTACCCTAC
1 TGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
* * * * * * * *
32175 TGCTTAGGGGGTTAAGGCTCACCGT--CTTTGA-TCTGCT-CCGCTAC
1 TGCTTAGGGAGATAA-GAT--CTGTAATTTTCAGCCTGTTACC-CTAC
*
32219 TGCTTAGGGAGATAAGATCTGTAATTTTTAGCCTGTTACCCTAC
1 TGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
32263 TGCTTAGGG
1 TGCTTAGGG
32272 GGTTAAGGCT
Statistics
Matches: 258, Mismatches: 73, Indels: 60
0.66 0.19 0.15
Matches are distributed among these distances:
41 3 0.01
42 1 0.00
43 29 0.11
44 194 0.75
45 27 0.10
46 1 0.00
47 3 0.01
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (44 bp):
TGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
Found at i:31941 original size:88 final size:88
Alignment explanation
Indices: 31846--32343 Score: 746
Period size: 88 Copynumber: 5.7 Consensus size: 88
31836 AAGATTCGCC
* * * *
31846 GTCTTCGATCTGCTCCACCATTGCTTAGGGAGATAAGATCTTTAATTTTCAGCCTGTTACCCTAC
1 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
*
31911 TGCTTAAGGGGTTAAGGCTCACT
66 TGCTTAGGGGGTTAAGGCTCACT
* *
31934 GTTTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCCTGTTACCCTAC
1 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
* *
31999 TACTTAGGGGGTTAAGGCTCATT
66 TGCTTAGGGGGTTAAGGCTCACT
* * * * *
32022 GTCTTCGATCTGCTCCACTACTACTTTGGGAGATAAGATCTGTAATTTCCAGCCTGTTACACTAC
1 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
**
32087 TGCTTAGGGGGTTAAGATTCA-T
66 TGCTTAGGGGGTTAAGGCTCACT
* *
32109 CGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTGTTACCCTA
1 -GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTA
*
32174 CTGCTTAGGGGGTTAAGGCTCACC
65 CTGCTTAGGGGGTTAAGGCTCACT
* *
32198 GTCTTTGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCCTGTTACCCTAC
1 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
*
32263 TGCTTAGGGGGTTAAGGCTCACC
66 TGCTTAGGGGGTTAAGGCTCACT
* * * *
32286 GTCTTCGATCTGCTCCGCTATTGCTTAGAGAGATAAGATCTGTAATCTTCAGTCTGTT
1 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTT
32344 TCCTTGGTAC
Statistics
Matches: 371, Mismatches: 37, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
87 1 0.00
88 370 1.00
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (88 bp):
GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
TGCTTAGGGGGTTAAGGCTCACT
Found at i:32311 original size:44 final size:44
Alignment explanation
Indices: 32083--32313 Score: 132
Period size: 44 Copynumber: 5.2 Consensus size: 44
32073 GCCTGTTACA
** * *
32083 CTACTGCTTAGGGGGTTAAGATTCATCGTCTTCGATCTGCTCCG
1 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTAGATCTGCTCCG
* * * * *** * * *
32127 CTACTGCTTAGGGAGATAAGATCTGTAATTTC-CA-ACCTGTTACC-
1 CTACTGCTTAGGGGGTTAAG-GCT-CACCGTCTTAGATCTGCT-CCG
*
32171 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCG
1 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTAGATCTGCTCCG
* * * * ** * * *
32215 CTACTGCTTAGGGAGATAAGATCTGTA-ATTTTTAG-CCTGTTACC-
1 CTACTGCTTAGGGGGTTAAG-GCT-CACCGTCTTAGATCTGCT-CCG
*
32259 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCG
1 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTAGATCTGCTCCG
*
32303 CTATTGCTTAG
1 CTACTGCTTAG
32314 AGAGATAAGA
Statistics
Matches: 131, Mismatches: 44, Indels: 24
0.66 0.22 0.12
Matches are distributed among these distances:
42 4 0.03
43 12 0.09
44 100 0.76
45 11 0.08
46 4 0.03
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.33
Consensus pattern (44 bp):
CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTAGATCTGCTCCG
Found at i:33478 original size:11 final size:11
Alignment explanation
Indices: 33464--33490 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
33454 AATATTAAAA
33464 ATATATAGAAC
1 ATATATAGAAC
33475 ATATATAGAAC
1 ATATATAGAAC
33486 ATATA
1 ATATA
33491 CAATACGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (11 bp):
ATATATAGAAC
Found at i:34389 original size:16 final size:14
Alignment explanation
Indices: 34359--34399 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 14
34349 GTAAAAAAAA
34359 TTTATTTTTTATTT
1 TTTATTTTTTATTT
34373 TTTATTTCTTGTATTT
1 TTTATTT-TT-TATTT
34389 TTTATATTTTT
1 TTTAT-TTTTT
34400 TAATATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.29
15 3 0.12
16 12 0.50
17 2 0.08
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (14 bp):
TTTATTTTTTATTT
Found at i:34412 original size:7 final size:7
Alignment explanation
Indices: 34359--34399 Score: 55
Period size: 7 Copynumber: 5.4 Consensus size: 7
34349 GTAAAAAAAA
34359 TTTATTT
1 TTTATTT
34366 TTTATTT
1 TTTATTT
34373 TTTATTT
1 TTTATTT
34380 CTTGTATTT
1 -TT-TATTT
34389 TTTATATT
1 TTTAT-TT
34397 TTT
1 TTT
34400 TAATATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 17 0.55
8 9 0.29
9 5 0.16
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (7 bp):
TTTATTT
Found at i:35789 original size:72 final size:72
Alignment explanation
Indices: 35557--35809 Score: 391
Period size: 73 Copynumber: 3.5 Consensus size: 72
35547 ACATGTGAAC
* * *
35557 TGAGGCTCAACGCACTTT-TCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCT
1 TGAGGCTCAACTCA-TTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCT
* *
35621 CAGCGTGTCC
63 CAACGTGTCT
*
35631 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAACAGAAATTGAAAATACCTCA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAAATTACCTCA
35696 ACGTGTCT
65 ACGTGTCT
35704 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
* *
35769 TGCGTCT
66 CGTGTCT
35776 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
35810 TTCTTTCAAA
Statistics
Matches: 168, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
72 68 0.40
73 71 0.42
74 29 0.17
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (72 bp):
TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
CGTGTCT
Found at i:35891 original size:88 final size:87
Alignment explanation
Indices: 35742--35986 Score: 296
Period size: 88 Copynumber: 2.8 Consensus size: 87
35732 AGTTGAATTT
* ** * * **
35742 TGAAAACAGAAATTGAAATTACCTCAATGCGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
1 TGAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
35807 TGA-TTCTTTCAAAAACATAATAA
66 TGATTTCTTTCAAAAACA-AA-AA
* *
35830 TGAAAACAGAAATGGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 TGAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * *
35895 TGATTTTTTTGAAAAACAGAAA
66 TGATTTCTTTCAAAAACAAAAA
* **
35917 TCAAAAGGC-TTAATTGAAAATACCTCGGCTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TGAAAA--CAGAAATTGAAAATACCTCGG-TGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
35981 AGTTGA
63 AGTTGA
35987 AATTAAACAC
Statistics
Matches: 136, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
87 7 0.05
88 76 0.56
89 53 0.39
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (87 bp):
TGAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTCTTTCAAAAACAAAAA
Found at i:36171 original size:73 final size:73
Alignment explanation
Indices: 36084--36258 Score: 212
Period size: 72 Copynumber: 2.4 Consensus size: 73
36074 ATTAAAAGGT
* * * * * *
36084 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAA-ACAGAAATTGAAATTACCTCATCGT-
1 TCAACTCACCTCTCGCAATATGAGTTGATTATT-AAAACACAAAAATTGAAAATACCTCAGCGTG
*
36147 CTCCTGAGGC
65 C-CCCGAGGC
* *
36157 TCAACTCACCTCTCGCAATATGAATTGA-AATTAAAACACAAAAATTGAAAATACCTCAGCGTGC
1 TCAACTCACCTCTCGCAATATGAGTTGATTATTAAAACACAAAAATTGAAAATACCTCAGCGTGC
36221 CCCGAGGC
66 CCCGAGGC
* *
36229 TCAACTCACCTCTTGCAATATGAGCTGATT
1 TCAACTCACCTCTCGCAATATGAGTTGATT
36259 TTGGAAAAGT
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
71 3 0.03
72 56 0.65
73 27 0.31
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (73 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTATTAAAACACAAAAATTGAAAATACCTCAGCGTGC
CCCGAGGC
Found at i:36269 original size:199 final size:198
Alignment explanation
Indices: 35950--36385 Score: 818
Period size: 199 Copynumber: 2.2 Consensus size: 198
35940 CTCGGCTGTG
*
35950 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAACACAAAAATTGAAAATACCTC
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGAAATTAAACACAAAAATTGAAAATACCTC
*
36015 AGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGGTTTTGAAAAAGTAGAAATTAAA
66 AGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAA
*
36080 AGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATC
131 AGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAAAAATTGAAATTACCTCATC
36145 GTC
196 GTC
36148 TCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGAAATTAAAACACAAAAATTGAAAATACCT
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGAAATT-AAACACAAAAATTGAAAATACCT
*
36213 CAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTGGAAAAGTAGAAATTAA
65 CAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAA
36278 AAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAAAAATTGAAATTACCTCAT
130 AAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAAAAATTGAAATTACCTCAT
*
36343 CGTG
195 CGTC
36347 TCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGAAA
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGAAA
36386 AAAATACCAC
Statistics
Matches: 232, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
198 40 0.17
199 192 0.83
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.26
Consensus pattern (198 bp):
TCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGAAATTAAACACAAAAATTGAAAATACCTC
AGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAA
AGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAAAAATTGAAATTACCTCATC
GTC
Found at i:36708 original size:75 final size:74
Alignment explanation
Indices: 36406--36741 Score: 446
Period size: 72 Copynumber: 4.5 Consensus size: 74
36396 AGTGTGTAAT
* * *
36406 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTTTAAAAACAGAAATTGAAAATACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCT
* *
36471 CAGCATGTGAAC
66 CA--ACGTG-TC
*
36483 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCT
36547 CAACGTGTC
66 CAACGTGTC
* ** * * *
36556 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCT
*
36619 CAGCGTGTC
66 CAACGTGTC
** *
36628 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATT-AAAATTAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA-AACAGAAATTGAAAA-TAC
36692 CTCAACGTGTC
64 CTCAACGTGTC
*
36703 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
36742 GAAAAACAAA
Statistics
Matches: 233, Mismatches: 21, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
72 67 0.29
73 1 0.00
74 44 0.19
75 59 0.25
76 61 0.26
77 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (74 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCT
CAACGTGTC
Found at i:36714 original size:147 final size:147
Alignment explanation
Indices: 36406--36759 Score: 475
Period size: 147 Copynumber: 2.4 Consensus size: 147
36396 AGTGTGTAAT
* * *
36406 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTTTAAAAACAGAAATTGAAAATACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAAATACCT
36471 CAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAAT
64 CAGCA-GTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAAT
36536 TGAAAATACCTCAACGTGTC
128 TGAAAATACCTCAACGTGTC
* ** * *
36556 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCA
* ** * *
36621 GC-GTG-TCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATT
66 GCAGTGAACC-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAA-AACAGAAATT
36684 -AAAATTACCTCAACGTGTC
129 GAAAA-TACCTCAACGTGTC
* *
36703 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTG-ATTTTGAAAAACAAAAATT-AAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAAAA
36760 GGCTTAACTC
Statistics
Matches: 180, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
145 2 0.01
146 55 0.31
147 64 0.36
148 29 0.16
150 30 0.17
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (147 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCA
GCAGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAATTGA
AAATACCTCAACGTGTC
Done.