Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3687_ERROPOS42312
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: 42312
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Found at i:1922 original size:27 final size:27
Alignment explanation
Indices: 1884--1940 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
1874 ACTTACCTCG
1884 TACATGAAATTGACAAATCGGATCGAT
1 TACATGAAATTGACAAATCGGATCGAT
*
1911 TACATGAAATTGACGAATCGGATCGAT
1 TACATGAAATTGACAAATCGGATCGAT
1938 TAC
1 TAC
1941 TCGATAACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (27 bp):
TACATGAAATTGACAAATCGGATCGAT
Found at i:15075 original size:29 final size:29
Alignment explanation
Indices: 15038--15135 Score: 160
Period size: 29 Copynumber: 3.4 Consensus size: 29
15028 CACTAGGCTC
*
15038 AATCTCATTCATATGGCCCATTAGGCCCA
1 AATCACATTCATATGGCCCATTAGGCCCA
**
15067 AATCACATTTGTATGGCCCATTAGGCCCA
1 AATCACATTCATATGGCCCATTAGGCCCA
*
15096 AACCACATTCATATGGCCCATTAGGCCCA
1 AATCACATTCATATGGCCCATTAGGCCCA
15125 AATCACATTCA
1 AATCACATTCA
15136 CATTCACATT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.26
Consensus pattern (29 bp):
AATCACATTCATATGGCCCATTAGGCCCA
Found at i:17664 original size:49 final size:47
Alignment explanation
Indices: 17316--17663 Score: 529
Period size: 47 Copynumber: 7.3 Consensus size: 47
17306 CCCTTCGGGA
* * * *
17316 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTT-GG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
*
17362 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
17410 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
17457 CTTATCACATATATACACTTTGACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
17504 CTTATCACATATATATACACTTTCTCATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
17553 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17602 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17649 CTTATCACATATATA
1 CTTATCACATATATA
17664 TACATTCAAA
Statistics
Matches: 279, Mismatches: 18, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
46 4 0.01
47 182 0.65
48 2 0.01
49 91 0.33
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:17710 original size:96 final size:95
Alignment explanation
Indices: 17316--17671 Score: 488
Period size: 96 Copynumber: 3.7 Consensus size: 95
17306 CCCTTCGGGA
* * * * * *
17316 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTT-GG-CTCTGTCACATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGCCT-TATCACATATATAT
* *
17379 ACTTTCACATTCATCACATCGGCCATTA-GGC
64 ACATTCACATTCATCACATTGGCCATTACGGC
* * *
17410 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* * *
17475 TTTGACATTCATCACATCGGCCATTA-GGC
66 ATTCACATTCATCACATTGGCCATTACGGC
*
17504 CTTATCACATATATATACACTTTCTCATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
17569 ACACTTTCACATTCATCACATTGGCCATT-CGGC
64 ACA--TTCACATTCATCACATTGGCCATTACGGC
17602 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
17667 ATTCA
66 ATTCA
17672 AATCACAATT
Statistics
Matches: 239, Mismatches: 16, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
93 2 0.01
94 91 0.38
95 2 0.01
96 111 0.46
98 33 0.14
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (95 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ATTCACATTCATCACATTGGCCATTACGGC
Found at i:21295 original size:40 final size:40
Alignment explanation
Indices: 21263--21444 Score: 249
Period size: 40 Copynumber: 4.5 Consensus size: 40
21253 CCAGCATGAT
* * *
21263 TGCTCTTCAGG-ACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTC-GGAACTTAGCCCGGATATATCACTAGCACGAA
*
21303 TGCTCTTCGGAACTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
* *
21343 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
* * *
21383 TGCTCTTTGGGATTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
* *
21423 TGCTCTTCGAAACTTAGTCCGG
1 TGCTCTTCGGAACTTAGCCCGG
21445 TCGGAACTTA
Statistics
Matches: 124, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
39 2 0.02
40 122 0.98
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
Found at i:21471 original size:96 final size:96
Alignment explanation
Indices: 21349--21540 Score: 366
Period size: 96 Copynumber: 2.0 Consensus size: 96
21339 CGAATGCTCT
*
21349 TCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCTTTGGGATTTAGCCCGGATATATCAC
1 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTTGGGATTTAGCCCGGATATATCAC
21414 TAGCACGAATGCTCTTCGAAACTTAGTCCGG
66 TAGCACGAATGCTCTTCGAAACTTAGTCCGG
21445 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTTGGGATTTAGCCCGGATATATCAC
1 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTTGGGATTTAGCCCGGATATATCAC
*
21510 TAGCACGAATGCTCTTCGGAACTTAGTCCGG
66 TAGCACGAATGCTCTTCGAAACTTAGTCCGG
21541 ATACATCACT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (96 bp):
TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTTGGGATTTAGCCCGGATATATCAC
TAGCACGAATGCTCTTCGAAACTTAGTCCGG
Found at i:21512 original size:40 final size:40
Alignment explanation
Indices: 21445--21906 Score: 674
Period size: 40 Copynumber: 11.6 Consensus size: 40
21435 CTTAGTCCGG
* * *
21445 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* * *
21485 TTGGGATTTAGCCCGGATATATCACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* * ** *
21525 TCGGAACTTAGTCCGGATACATCACTAGCATTAATGATCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* *
21565 TCGGGATTTAGCCCGGATATATCACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* * *
21605 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
*
21645 TCGGGACTTAGCCCGGATACATCACTAGCACAAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
*
21685 TCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* *
21725 TCGGGATTTAGCCCGGATATATCACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* ** *
21765 TCGGAACTTAGTTCGGATACATCACTAGCATGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* *
21805 TTGGGACTTAGCCCGGATACATCACTAGCACAAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
*
21845 TCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
21885 TCGGGACTTAGCCCGGAT-CATC
1 TCGGGACTTAGCCCGGATACATC
21907 GTCGAGACCT
Statistics
Matches: 372, Mismatches: 50, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
39 4 0.01
40 368 0.99
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (40 bp):
TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
Found at i:21578 original size:80 final size:80
Alignment explanation
Indices: 21445--21902 Score: 754
Period size: 80 Copynumber: 5.7 Consensus size: 80
21435 CTTAGTCCGG
* * * *
21445 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTTGGGATTTAGCCCGGATATATCAC
1 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCAC
21510 TAGCACGAATGCTCT
66 TAGCACGAATGCTCT
* * *
21525 TCGGAACTTAGTCCGGATACATCACTAGCATTAATGATCTTCGGGATTTAGCCCGGATATATCAC
1 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCAC
21590 TAGCACGAATGCTCT
66 TAGCACGAATGCTCT
*
21605 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCAC
1 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCAC
*
21670 TAGCACAAATGCTCT
66 TAGCACGAATGCTCT
* * *
21685 TCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGATTTAGCCCGGATATATCAC
1 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCAC
21750 TAGCACGAATGCTCT
66 TAGCACGAATGCTCT
* * *
21765 TCGGAACTTAGTTCGGATACATCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACATCAC
1 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCAC
*
21830 TAGCACAAATGCTCT
66 TAGCACGAATGCTCT
* *
21845 TCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
1 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
21903 CATCGTCGAG
Statistics
Matches: 352, Mismatches: 26, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 352 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (80 bp):
TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCAC
TAGCACGAATGCTCT
Found at i:22029 original size:38 final size:38
Alignment explanation
Indices: 21960--22034 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
21950 GAATTTTAAT
*
21960 CCGGACATAATCTCTGTACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCTGTACATAGCCAACGGGTCTTTAC
* *
21998 CCGGACATAATCTCT-TCATATAGTCAACGGGTCTTTA
1 CCGGACATAATCTCTGT-ACATAGCCAACGGGTCTTTA
22035 AACTCGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTGTACATAGCCAACGGGTCTTTAC
Found at i:25813 original size:39 final size:39
Alignment explanation
Indices: 25761--25931 Score: 202
Period size: 39 Copynumber: 4.3 Consensus size: 39
25751 GGACTAAGAT
*
25761 CCGAAGGCATTTGTGCGAGATACAAGTTCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGATACAA-ATCCGGGTTAAGTC
*
25800 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
* * *
25840 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
25880 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
25919 CCGAAGGCATTTG
1 CCGAAGGCATTTG
25932 AACGAGGAGC
Statistics
Matches: 115, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
39 65 0.57
40 50 0.43
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:25844 original size:79 final size:79
Alignment explanation
Indices: 25708--25931 Score: 222
Period size: 79 Copynumber: 2.8 Consensus size: 79
25698 TTGAATGCTG
* * * * * * *
25708 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAAACCGGGCTAAG-TCCCGAAGGCAT
*
25771 TTGTGCGAGATA-CAAGT
63 TTGTGCGAGATATCAA-A
* * * *
25788 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTT
* *
25852 GTGCGAGTTATTAAA
65 GTGCGAGATATCAAA
* * *
25867 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
25932 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 90 0.74
80 30 0.25
81 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAAA
Found at i:25949 original size:79 final size:80
Alignment explanation
Indices: 25788--25964 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
25778 AGATACAAGT
* * *
25788 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
25852 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
25867 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
25931 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
25946 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
25965 TATGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 16 0.19
79 59 0.71
80 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:33752 original size:39 final size:39
Alignment explanation
Indices: 33700--33870 Score: 202
Period size: 39 Copynumber: 4.3 Consensus size: 39
33690 GGACTAAGAT
*
33700 CCGAAGGCATTTGTGCGAGATACAAGTTCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGATACAA-ATCCGGGTTAAGTC
*
33739 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
* * *
33779 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
33819 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
33858 CCGAAGGCATTTG
1 CCGAAGGCATTTG
33871 AACGAGGAGC
Statistics
Matches: 115, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
39 65 0.57
40 50 0.43
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:33783 original size:79 final size:79
Alignment explanation
Indices: 33647--33870 Score: 222
Period size: 79 Copynumber: 2.8 Consensus size: 79
33637 TTGAATGCTG
* * * * * * *
33647 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAAACCGGGCTAAG-TCCCGAAGGCAT
*
33710 TTGTGCGAGATA-CAAGT
63 TTGTGCGAGATATCAA-A
* * * *
33727 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTT
* *
33791 GTGCGAGTTATTAAA
65 GTGCGAGATATCAAA
* * *
33806 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
33871 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 90 0.74
80 30 0.25
81 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAAA
Found at i:33888 original size:79 final size:80
Alignment explanation
Indices: 33727--33903 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
33717 AGATACAAGT
* * *
33727 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
33791 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
33806 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
33870 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
33885 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
33904 TATGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 16 0.19
79 59 0.71
80 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:35470 original size:49 final size:47
Alignment explanation
Indices: 35251--35607 Score: 527
Period size: 47 Copynumber: 7.5 Consensus size: 47
35241 GGGTGTTACA
* * * * * *
35251 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-CT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
*
35297 CTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 -TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
* *
35345 CATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
*
35392 TATCACATATATACACTTTGACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
*
35439 TATCACATATATATACACTTTCTCATTCATCACATCGGCCATTAGGCCT
1 TATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
* *
35488 TATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCT
1 TATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
35537 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
* *
35584 TATCACATATATATACATTCACAT
1 TATCACATATATACACTTTCACAT
35608 CACAATTATC
Statistics
Matches: 285, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
47 192 0.67
48 2 0.01
49 91 0.32
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
Found at i:35643 original size:96 final size:95
Alignment explanation
Indices: 35251--35607 Score: 488
Period size: 96 Copynumber: 3.7 Consensus size: 95
35241 GGGTGTTACA
* * * * * * * * *
35251 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-CTCTGTCACATATATACACT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT-TATCACATATATATACA
*
35315 TTCACATTCATCACATCGGCCATTA-GGCCT
65 TTCACATTCATCACATTGGCCATTACGGCCT
* * * *
35345 CATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAT
* *
35410 TGACATTCATCACATCGGCCATTA-GGCCT
66 TCACATTCATCACATTGGCCATTACGGCCT
*
35439 TATCACATATATATACACTTTCTCATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 TATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
35504 ACTTTCACATTCATCACATTGGCCATT-CGGCCT
64 A--TTCACATTCATCACATTGGCCATTACGGCCT
35537 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAT
35602 TCACAT
66 TCACAT
35608 CACAATTATC
Statistics
Matches: 239, Mismatches: 18, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
94 93 0.39
95 2 0.01
96 111 0.46
98 33 0.14
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (95 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAT
TCACATTCATCACATTGGCCATTACGGCCT
Found at i:39230 original size:40 final size:40
Alignment explanation
Indices: 39198--39379 Score: 249
Period size: 40 Copynumber: 4.5 Consensus size: 40
39188 CCAGCATGAT
* * *
39198 TGCTCTTCAGG-ACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTC-GGAACTTAGCCCGGATATATCACTAGCACGAA
*
39238 TGCTCTTCGGAACTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
* *
39278 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
* * *
39318 TGCTCTTTGGGATTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
* *
39358 TGCTCTTCGAAACTTAGTCCGG
1 TGCTCTTCGGAACTTAGCCCGG
39380 TCGGAACTTA
Statistics
Matches: 124, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
39 2 0.02
40 122 0.98
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
Found at i:39406 original size:96 final size:96
Alignment explanation
Indices: 39284--39475 Score: 366
Period size: 96 Copynumber: 2.0 Consensus size: 96
39274 CGAATGCTCT
*
39284 TCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCTTTGGGATTTAGCCCGGATATATCAC
1 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTTGGGATTTAGCCCGGATATATCAC
39349 TAGCACGAATGCTCTTCGAAACTTAGTCCGG
66 TAGCACGAATGCTCTTCGAAACTTAGTCCGG
39380 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTTGGGATTTAGCCCGGATATATCAC
1 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTTGGGATTTAGCCCGGATATATCAC
*
39445 TAGCACGAATGCTCTTCGGAACTTAGTCCGG
66 TAGCACGAATGCTCTTCGAAACTTAGTCCGG
39476 ATACATCACT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (96 bp):
TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTTGGGATTTAGCCCGGATATATCAC
TAGCACGAATGCTCTTCGAAACTTAGTCCGG
Found at i:39447 original size:40 final size:40
Alignment explanation
Indices: 39380--39840 Score: 674
Period size: 40 Copynumber: 11.6 Consensus size: 40
39370 CTTAGTCCGG
* * *
39380 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* * *
39420 TTGGGATTTAGCCCGGATATATCACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* * **
39460 TCGGAACTTAGTCCGGATACATCACTAGCATTAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* * *
39500 TCGAGATTTAGCCCGGATATATCACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* * *
39540 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
*
39580 TCGGGACTTAGCCCGGATACATCACTAGCACAAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
*
39620 TCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* * *
39660 TCGGGATTTAGCCTGGATATATCACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* ** *
39700 TCGGAACTTAGTTCGGATACATCACTAGCATGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
*
39740 TCGGGACTTAGCCCGGATACATCACTAGCACAAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
39780 TC-GGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
39819 TCGGGACTTAGCCCGGAT-CATC
1 TCGGGACTTAGCCCGGATACATC
39841 GTCGAGACCT
Statistics
Matches: 371, Mismatches: 49, Indels: 3
0.88 0.12 0.01
Matches are distributed among these distances:
39 42 0.11
40 329 0.89
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (40 bp):
TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
Found at i:39513 original size:80 final size:80
Alignment explanation
Indices: 39380--39836 Score: 745
Period size: 80 Copynumber: 5.7 Consensus size: 80
39370 CTTAGTCCGG
* * * *
39380 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTTGGGATTTAGCCCGGATATATCAC
1 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCAC
39445 TAGCACGAATGCTCT
66 TAGCACGAATGCTCT
* * *
39460 TCGGAACTTAGTCCGGATACATCACTAGCATTAATGCTCTTCGAGATTTAGCCCGGATATATCAC
1 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCAC
39525 TAGCACGAATGCTCT
66 TAGCACGAATGCTCT
*
39540 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCAC
1 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCAC
*
39605 TAGCACAAATGCTCT
66 TAGCACGAATGCTCT
* * * *
39620 TCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGATTTAGCCTGGATATATCAC
1 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCAC
39685 TAGCACGAATGCTCT
66 TAGCACGAATGCTCT
* *
39700 TCGGAACTTAGTTCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCAC
1 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCAC
*
39765 TAGCACAAATGCTCT
66 TAGCACGAATGCTCT
* *
39780 TCGG-ACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
39837 CATCGTCGAG
Statistics
Matches: 351, Mismatches: 26, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
79 50 0.14
80 301 0.86
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (80 bp):
TCGGAACTTAGTCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATATCAC
TAGCACGAATGCTCT
Found at i:39963 original size:38 final size:38
Alignment explanation
Indices: 39894--39968 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
39884 GAATTTTAAT
*
39894 CCGGACATAATCTCTGTACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCTGTACATAGCCAACGGGTCTTTAC
* *
39932 CCGGACATAATCTCT-TCATATAGTCAACGGGTCTTTA
1 CCGGACATAATCTCTGT-ACATAGCCAACGGGTCTTTA
39969 AACTCGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTGTACATAGCCAACGGGTCTTTAC
Found at i:42177 original size:47 final size:47
Alignment explanation
Indices: 42099--42312 Score: 304
Period size: 47 Copynumber: 4.5 Consensus size: 47
42089 GCCCTTCGGA
* * * * * *
42099 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42145 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42193 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42240 CTTATCACATATATACACTTTGACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42287 CTTATCACATATATATACACTTTCAC
1 CTTATCAC--ATATATACACTTTCAC
Statistics
Matches: 150, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
46 2 0.01
47 131 0.87
48 2 0.01
49 15 0.10
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Done.