Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008244.1 Hibiscus syriacus cultivar Beakdansim tig00110894_pilon, 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: 84438
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:25390 original size:9 final size:8
Alignment explanation
Indices: 25373--25419 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
25363 TCTACAAAAA
25373 TATTTTAT
1 TATTTTAT
25381 TATATTTAT
1 TAT-TTTAT
*
25390 T-TATTAT
1 TATTTTAT
25397 TATTATTAT
1 TATT-TTAT
25406 TATTTTAT
1 TATTTTAT
25414 TATTTT
1 TATTTT
25420 TTTTAGGCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 5 0.15
8 15 0.44
9 14 0.41
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TATTTTAT
Found at i:25396 original size:3 final size:3
Alignment explanation
Indices: 25373--25417 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
25363 TCTACAAAAA
25373 TAT T-T TAT TA- TATT TATT TAT TAT TAT TAT TAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
25417 T
1 T
25418 TTTTTTAGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.16
3 26 0.68
4 6 0.16
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:25510 original size:33 final size:33
Alignment explanation
Indices: 25472--25553 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
25462 AAAAATAAAT
25472 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
*
25505 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
*
25538 CGAA-GCATTTGAGTCC
1 C-AACGTATTTGAGTCC
25554 AAGAAGGACT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 44 0.96
34 2 0.04
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (33 bp):
CAACGTATTTGAGTCCTATTAAAACACTAAAAC
Found at i:26094 original size:7 final size:7
Alignment explanation
Indices: 26082--26133 Score: 67
Period size: 7 Copynumber: 7.9 Consensus size: 7
26072 ATGATAATAC
26082 ATTATTT
1 ATTATTT
26089 ATTA-TT
1 ATTATTT
26095 ATTTATTT
1 A-TTATTT
26103 A-T-TTT
1 ATTATTT
26108 ATTA-TT
1 ATTATTT
26114 ATTATTT
1 ATTATTT
26121 ATTATTT
1 ATTATTT
26128 ATTATT
1 ATTATT
26134 CATTTTTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
5 4 0.10
6 11 0.28
7 22 0.55
8 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTATTT
Found at i:26095 original size:3 final size:3
Alignment explanation
Indices: 26082--26133 Score: 52
Period size: 3 Copynumber: 16.0 Consensus size: 3
26072 ATGATAATAC
26082 ATT ATTT ATT ATT ATTT ATTT ATT -TT ATT ATT ATT ATTT ATT ATTT
1 ATT A-TT ATT ATT A-TT A-TT ATT ATT ATT ATT ATT A-TT ATT A-TT
26128 ATT ATT
1 ATT ATT
26134 CATTTTTTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 2 0.05
3 26 0.59
4 16 0.36
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Found at i:28924 original size:96 final size:94
Alignment explanation
Indices: 28789--28973 Score: 289
Period size: 96 Copynumber: 1.9 Consensus size: 94
28779 TATAATATTA
* *
28789 TATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTAGTTAAACGCCCCGGCTTTATTGG
1 TATATATACAAAAAAGCTTGAGTTGTCCCTATAAAGCAATTAGTTAAACGCCCCGGCTTTA-TGG
* * *
28854 ATAATATTCGGCTAGCCTGATAAAGGTGAG
65 ATAAGATTCAGCTAACCTGATAAAGGTGAG
* *
28884 TATACTATACAAAAAAGCTTGAGTTGTCCCTATAAGGCAATTGGTTAAACGCCCCGGCTTTATGG
1 TATA-TATACAAAAAAGCTTGAGTTGTCCCTATAAAGCAATTAGTTAAACGCCCCGGCTTTATGG
28949 ATAAGATTCAGCTAACCTGATAAAG
65 ATAAGATTCAGCTAACCTGATAAAG
28974 ATGTTTACAT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
95 29 0.35
96 53 0.65
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (94 bp):
TATATATACAAAAAAGCTTGAGTTGTCCCTATAAAGCAATTAGTTAAACGCCCCGGCTTTATGGA
TAAGATTCAGCTAACCTGATAAAGGTGAG
Found at i:30573 original size:110 final size:110
Alignment explanation
Indices: 30375--30575 Score: 348
Period size: 110 Copynumber: 1.8 Consensus size: 110
30365 TCCCAGTTTT
*
30375 AGAGCCAATTTCAACTTCACAACGAAGAATATTGGACTCAAGACAGCACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAACGAAGAATATTGGACTCAAGACAACACAAGCTCAACTTCACAG
*
30440 CGAAGGGGCGACTGACTGTCAACAAACACCTTTTTAGTTTCATTC
66 CGAAGGGGCGACTGACTATCAACAAACACCTTTTTAGTTTCATTC
* *
30485 AGAGTCAATTTCAACTTCACAACGAAGAATATTGGACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAACGAAGAATATTGGACTCAAGACAACACAAGCTCAACTTCACAG
* *
30550 CGAAGGGGCGGCTGGCTATCAACAAA
66 CGAAGGGGCGACTGACTATCAACAAA
30576 TAATTTCCCA
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 85 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (110 bp):
AGAGCCAATTTCAACTTCACAACGAAGAATATTGGACTCAAGACAACACAAGCTCAACTTCACAG
CGAAGGGGCGACTGACTATCAACAAACACCTTTTTAGTTTCATTC
Found at i:31164 original size:21 final size:21
Alignment explanation
Indices: 31138--31205 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
31128 CAAGGGGTCA
31138 TCTCTCTTGAAACAAATTTTG
1 TCTCTCTTGAAACAAATTTTG
*
31159 TCTCTCTTGAGAC-AA--TT-
1 TCTCTCTTGAAACAAATTTTG
31176 TC-C-CTTGAAACAAAGTTTTG
1 TCTCTCTTGAAACAAA-TTTTG
31196 TCTCTCTTGA
1 TCTCTCTTGA
31206 GATAGTTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
15 7 0.18
16 3 0.08
17 2 0.05
18 2 0.05
19 2 0.05
20 4 0.11
21 13 0.34
22 5 0.13
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (21 bp):
TCTCTCTTGAAACAAATTTTG
Found at i:31201 original size:37 final size:36
Alignment explanation
Indices: 31143--31224 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 36
31133 GGTCATCTCT
31143 CTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCC
* * *
31179 CTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCT
1 CTTGAAACAAA-TTTTGTCTCTCTTGAGACAATTTCC
31216 CTTGAAACA
1 CTTGAAACA
31225 CCAATCTTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 11 0.26
37 31 0.74
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCC
Found at i:31319 original size:33 final size:33
Alignment explanation
Indices: 31277--31392 Score: 141
Period size: 33 Copynumber: 3.6 Consensus size: 33
31267 TCTGGAGACA
31277 GTTTCTCTTGAAACACAAAAAACCTTTGAAGTC
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAGTC
* * *
31310 GTTTCTCTTGAAACACAAAAAACCTTTAAAATAT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAGT-C
*
31344 TTTTCTCTTG-AA-A-AAAAAACCTTTGAAAG-C
1 GTTTCTCTTGAAACACAAAAAACCTTTG-AAGTC
*
31374 ATTTCTCTTGAAACACAAA
1 GTTTCTCTTGAAACACAAA
31393 GACCTTCGAG
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
30 9 0.13
31 13 0.19
32 4 0.06
33 35 0.50
34 9 0.13
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.32
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAGTC
Found at i:31541 original size:83 final size:83
Alignment explanation
Indices: 31388--31734 Score: 448
Period size: 83 Copynumber: 4.2 Consensus size: 83
31378 CTCTTGAAAC
* *
31388 ACAAAGACCTTCGAGTTTGACCACGCTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGGC
1 ACAAAGACCTTCGAGTTTGACCACGCTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGC
*
31453 TAGAAGGGTTATCTGCCA
66 TAGAAGGGTTATCTGTCA
* * * ** * *
31471 ACAAAGACCTTCGAGTTCGACCACGCTCAGCTTAAAGGCACATCATTTGCAGCATGGCTTAAGTC
1 ACAAAGACCTTCGAGTTTGACCACGCTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGC
* *
31536 GAGAAGGGTTATTTGTCA
66 TAGAAGGGTTATCTGTCA
* * * *
31554 ACAAAGACCTTCGAGTTTGACTACGCTTAGCTCCAAGGCACATCATTTACATCATAACTCAAGGC
1 ACAAAGACCTTCGAGTTTGACCACGCTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGC
*
31619 TAGAAGGGTTATCTGTTA
66 TAGAAGGGTTATCTGTCA
** * *
31637 ACAAAGACCTTCGAGTTTGATTACGTTCAGCTCAAAGGCACCATCATTTACAGCATAGCTCAAGG
1 ACAAAGACCTTCGAGTTTGACCACGCTCAGCTCAAAGGCA-CATCATTTACAGCATAACTCAAGG
** *
31702 AAATAAGGGTTATCTG-C-
65 CTAGAAGGGTTATCTGTCA
31719 -CAAAGACCTTCGAGTT
1 ACAAAGACCTTCGAGTT
31735 CGATTTCATT
Statistics
Matches: 227, Mismatches: 36, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
81 16 0.07
83 176 0.78
84 35 0.15
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (83 bp):
ACAAAGACCTTCGAGTTTGACCACGCTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGC
TAGAAGGGTTATCTGTCA
Found at i:31676 original size:166 final size:165
Alignment explanation
Indices: 31387--31734 Score: 502
Period size: 166 Copynumber: 2.1 Consensus size: 165
31377 TCTCTTGAAA
31387 CACAAAGACCTTCGAGTTTGACCACGCTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGG
1 CACAAAGACCTTCGAGTTTGACCACGCTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGG
*
31452 CTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACCACGCTCAGCTTAAAGGCA-CATCA
66 CTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACCACGCTCAGCTCAAAGGCACCATCA
* * * *** *
31516 TTTGCAGCATGGCTTAAGTCGAGAAGGGTTATTTG
131 TTTACAGCATAGCTCAAGGAAAGAAGGGTTATCTG
* * *
31551 TCAACAAAGACCTTCGAGTTTGACTACGCTTAGCTCCAAGGCACATCATTTACATCATAACTCAA
1 -C-ACAAAGACCTTCGAGTTTGACCACGCTCAGCTCCAAGGCACATCATTTACAACATAACTCAA
** * ** *
31616 GGCTAGAAGGGTTATCTGTTAACAAAGACCTTCGAGTTTGATTACGTTCAGCTCAAAGGCACCAT
64 GGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACCACGCTCAGCTCAAAGGCACCAT
*
31681 CATTTACAGCATAGCTCAAGGAAATAAGGGTTATCTG
129 CATTTACAGCATAGCTCAAGGAAAGAAGGGTTATCTG
31718 C-CAAAGACCTTCGAGTT
1 CACAAAGACCTTCGAGTT
31735 CGATTTCATT
Statistics
Matches: 163, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
164 16 0.10
165 1 0.01
166 114 0.70
167 32 0.20
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (165 bp):
CACAAAGACCTTCGAGTTTGACCACGCTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGG
CTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACCACGCTCAGCTCAAAGGCACCATCA
TTTACAGCATAGCTCAAGGAAAGAAGGGTTATCTG
Found at i:32683 original size:23 final size:23
Alignment explanation
Indices: 32657--32717 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
32647 CTCGTATAAA
*
32657 TGCACCGAAGTGCTACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
32680 TGCACTGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
32703 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
32718 TATAAAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:35387 original size:3 final size:3
Alignment explanation
Indices: 35374--35433 Score: 65
Period size: 3 Copynumber: 20.3 Consensus size: 3
35364 TCTACAAAAA
35374 TAT TA- TAT TAT TA- TAT T-T TATT TATT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT
35419 TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT T
35434 TTTGCAGGAC
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 8 0.15
3 33 0.63
4 11 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:35524 original size:33 final size:33
Alignment explanation
Indices: 35487--35553 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
35477 GAAAATAAAT
35487 CAACGTACTTGAGTCC-TATTGAAACACTAAAAC
1 CAACGTACTTGAGTCCAT-TTGAAACACTAAAAC
*
35520 CAACGTATTTGAGTCCATTTGAAACACTAAAAC
1 CAACGTACTTGAGTCCATTTGAAACACTAAAAC
35553 C
1 C
35554 GAAGCATTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (33 bp):
CAACGTACTTGAGTCCATTTGAAACACTAAAAC
Found at i:35563 original size:33 final size:34
Alignment explanation
Indices: 35495--35569 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 34
35485 ATCAACGTAC
*
35495 TTGAGTCC-TATTGAAACACTAAAACCAACGTAT
1 TTGAGTCCATATTGAAACACTAAAACCAACGCAT
35528 TTGAGTCCAT-TTGAAACACTAAAACCGAA-GCAT
1 TTGAGTCCATATTGAAACACTAAAACC-AACGCAT
35561 TTGAGTCCA
1 TTGAGTCCA
35570 AGAATGACTC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
33 36 0.92
34 3 0.08
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (34 bp):
TTGAGTCCATATTGAAACACTAAAACCAACGCAT
Found at i:36112 original size:7 final size:7
Alignment explanation
Indices: 36100--36155 Score: 71
Period size: 7 Copynumber: 7.9 Consensus size: 7
36090 ATGATAATAC
36100 ATTATTT
1 ATTATTT
36107 ATTA-TT
1 ATTATTT
36113 ATTTATTT
1 A-TTATTT
36121 ATTATTT
1 ATTATTT
36128 ATTTATTTT
1 A-TTA-TTT
36137 ATTA-TT
1 ATTATTT
36143 ATTATTT
1 ATTATTT
36150 ATTATT
1 ATTATT
36156 CATTTTTTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
6 9 0.20
7 22 0.50
8 9 0.20
9 4 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTATTT
Found at i:36113 original size:3 final size:3
Alignment explanation
Indices: 36100--36155 Score: 51
Period size: 3 Copynumber: 17.0 Consensus size: 3
36090 ATGATAATAC
36100 ATT ATTT ATT ATT ATTT ATTT ATT ATTT ATTT ATT -TT ATT ATT ATT
1 ATT A-TT ATT ATT A-TT A-TT ATT A-TT A-TT ATT ATT ATT ATT ATT
36146 ATTT ATT ATT
1 A-TT ATT ATT
36156 CATTTTTTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
2 2 0.04
3 26 0.54
4 20 0.42
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Found at i:36118 original size:4 final size:4
Alignment explanation
Indices: 36101--36152 Score: 53
Period size: 4 Copynumber: 14.2 Consensus size: 4
36091 TGATAATACA
36101 TTAT TTA- TTA- TTAT TTAT TTA- TTAT TTAT TTAT TT-T ATTA- TTA-
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT
36144 TTAT TTAT T
1 TTAT TTAT T
36153 ATTCATTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
3 16 0.37
4 27 0.63
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:36147 original size:33 final size:33
Alignment explanation
Indices: 36105--36169 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
36095 AATACATTAT
36105 TTATTATTATTTATTTATT-ATTTATTTATTTTA
1 TTATTATTATTTA-TTATTCATTTATTTATTTTA
* *
36138 TTATTATTATTTATTATTCATTTTTTTCTTTT
1 TTATTATTATTTATTATTCATTTATTTATTTT
36170 TGTTTAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 5 0.17
33 24 0.83
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (33 bp):
TTATTATTATTTATTATTCATTTATTTATTTTA
Found at i:37848 original size:16 final size:16
Alignment explanation
Indices: 37784--37844 Score: 79
Period size: 16 Copynumber: 3.9 Consensus size: 16
37774 ATAAATTAAA
37784 TTCAGGTTACTTTCAG
1 TTCAGGTTACTTTCAG
* * *
37800 TTCAAGTTATTTTTAG
1 TTCAGGTTACTTTCAG
*
37816 TTC-GGTTACTTTCGG
1 TTCAGGTTACTTTCAG
37831 TTCAGGTTACTTTC
1 TTCAGGTTACTTTC
37845 GGTTTAACTA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
15 11 0.30
16 26 0.70
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.49
Consensus pattern (16 bp):
TTCAGGTTACTTTCAG
Found at i:48530 original size:37 final size:36
Alignment explanation
Indices: 48471--48590 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
48461 ATCCCATTAT
* *
48471 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
48507 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
*
48543 CA-TTTTCAAAGAAACATTTACCATACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
48578 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
48591 TTGGTTATCA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 34 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:48546 original size:21 final size:21
Alignment explanation
Indices: 48522--48582 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
48512 TTCAAAGAAA
48522 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
48543 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
*
48557 CATTTACCATACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
48578 CATTT
1 CATTT
48583 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 6 0.20
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.33
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:52680 original size:16 final size:16
Alignment explanation
Indices: 52656--52694 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
52646 TATCGCCGAC
*
52656 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
52672 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
52688 CGTAAAT
1 CG-AAAT
52695 AGTAACCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:53156 original size:37 final size:36
Alignment explanation
Indices: 53097--53216 Score: 147
Period size: 35 Copynumber: 3.3 Consensus size: 36
53087 ATCCCATTAT
*
53097 CATTTTTC-AACAAAC-ATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACAAT-TACCAAACTTTGAAAAA
*
53132 CTATTTTTCAAAGAAACAATTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACAATTACCAAACTTTGAAAAA
* * *
53169 CA-TTTTCAAAGAAACATTTACCAAACTTTGAGAAT
1 CATTTTTCAAAGAAACAATTACCAAACTTTGAAAAA
53204 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
53217 TTGGTTACTA
Statistics
Matches: 75, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
35 33 0.44
36 8 0.11
37 32 0.43
38 2 0.03
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACAATTACCAAACTTTGAAAAA
Found at i:56585 original size:3 final size:3
Alignment explanation
Indices: 56577--56635 Score: 82
Period size: 3 Copynumber: 18.7 Consensus size: 3
56567 AATAACACAT
56577 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TCTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA
*
56624 TATA ATA TTA TT
1 T-TA TTA TTA TT
56636 TTAATTTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
3 43 0.84
4 8 0.16
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:64858 original size:37 final size:38
Alignment explanation
Indices: 64791--64864 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
64781 GCGGATTAAA
* *
64791 TTTTTTAAATAGTTATAAAATATTATATATTCATATTT
1 TTTTTTAAATAGTTAAAAAATATTATATATTAATATTT
*
64829 TTTTTTAATTA-TTAAATAAATATTA-ATATTAATATT
1 TTTTTTAAATAGTTAAA-AAATATTATATATTAATATT
64865 AGATAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (38 bp):
TTTTTTAAATAGTTAAAAAATATTATATATTAATATTT
Found at i:74629 original size:16 final size:17
Alignment explanation
Indices: 74608--74649 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
74598 CACGGAATGT
74608 AAGATTACCG-GGGAAA
1 AAGATTACCGTGGGAAA
* *
74624 AAGATTATCGGTGGGAAT
1 AAGATTA-CCGTGGGAAA
74642 AAGATTAC
1 AAGATTAC
74650 TGAGAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 3 0.14
18 12 0.55
ACGTcount: A:0.40, C:0.10, G:0.29, T:0.21
Consensus pattern (17 bp):
AAGATTACCGTGGGAAA
Found at i:76664 original size:20 final size:20
Alignment explanation
Indices: 76641--76692 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
76631 AACGCGATCC
76641 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
76661 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
76681 CCAAAATCGCAA
1 CCAGAATCGCAA
76693 CGCGATTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:76709 original size:21 final size:21
Alignment explanation
Indices: 76683--76805 Score: 63
Period size: 21 Copynumber: 5.7 Consensus size: 21
76673 ATCAGTTTCC
76683 AAAATCGCAACGCGATTATGG
1 AAAATCGCAACGCGATTATGG
* *
76704 AAAATCGCAATGCGAGCGATTCTTG
1 AAAATCGCAA--C--GCGATTATGG
* * *
76729 AAAATCGCGATGCGA-TA-GT
1 AAAATCGCAACGCGATTATGG
** * **
76748 ACAAATTCGCATTGCGATTTTCC
1 A-AAA-TCGCAACGCGATTATGG
* *
76771 ATAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTATGG
76791 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
76806 ACACATAAAT
Statistics
Matches: 75, Mismatches: 19, Indels: 17
0.68 0.17 0.15
Matches are distributed among these distances:
19 1 0.01
20 18 0.24
21 34 0.45
22 3 0.04
23 2 0.03
25 17 0.23
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (21 bp):
AAAATCGCAACGCGATTATGG
Found at i:76731 original size:25 final size:25
Alignment explanation
Indices: 76694--76743 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
76684 AAATCGCAAC
76694 GCGATTATGGAAAATCGCAATGCGA
1 GCGATTATGGAAAATCGCAATGCGA
* * *
76719 GCGATTCTTGAAAATCGCGATGCGA
1 GCGATTATGGAAAATCGCAATGCGA
76744 TAGTACAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (25 bp):
GCGATTATGGAAAATCGCAATGCGA
Found at i:76798 original size:20 final size:20
Alignment explanation
Indices: 76773--76966 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
76763 GATTTTCCAT
* *
76773 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
76793 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
76813 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
76833 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
76853 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
76873 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
76893 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
76913 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
76934 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
76954 AATCGCAACGCGA
1 AATCGCAACGCGA
76967 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:76818 original size:40 final size:39
Alignment explanation
Indices: 76769--76966 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
76759 TTGCGATTTT
* ** *
76769 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
76807 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
76848 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
76888 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
76927 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
76967 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:76842 original size:60 final size:60
Alignment explanation
Indices: 76773--76966 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
76763 GATTTTCCAT
** * *
76773 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * * *** *
76833 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * **
76893 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
76954 AATCGCAACGCGA
1 AATCGCAACGCGA
76967 TATTTAAAGC
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:77385 original size:33 final size:33
Alignment explanation
Indices: 77346--77416 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
77336 TTCACTTAGA
*
77346 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
77379 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
77412 TTTCA
1 TTTCA
77417 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:77556 original size:14 final size:14
Alignment explanation
Indices: 77537--77591 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
77527 AGAATGACTG
77537 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
77551 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
77570 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
77584 TCGCAACG
1 TCGCAACG
77592 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:77574 original size:33 final size:33
Alignment explanation
Indices: 77537--77607 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
77527 AGAATGACTG
**
77537 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
77570 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
77603 TCGCA
1 TCGCA
77608 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:77625 original size:19 final size:19
Alignment explanation
Indices: 77603--77700 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
77593 GAAACCAAAA
*
77603 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
77622 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
77636 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
77655 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
77669 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
77688 TCGCGTTGCGATT
1 TCGCGTTGCGATT
77701 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:77644 original size:14 final size:14
Alignment explanation
Indices: 77625--77714 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
77615 TTTCATTTCG
77625 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
77639 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
77658 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
77672 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
77689 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
77705 CGTTGCGATT
1 CGTTGCGATT
77715 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:77650 original size:33 final size:33
Alignment explanation
Indices: 77608--77722 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
77598 CAAAATCGCA
77608 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
77641 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
77674 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
77707 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
77723 AACCAAAGAC
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:78810 original size:185 final size:186
Alignment explanation
Indices: 78498--78964 Score: 918
Period size: 185 Copynumber: 2.5 Consensus size: 186
78488 TAGATTGCTT
*
78498 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
78563 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
78628 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
78683 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
78748 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
78813 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
78869 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
78934 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
78965 TTCAATTTGC
Statistics
Matches: 280, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
185 154 0.55
186 126 0.45
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:78812 original size:93 final size:93
Alignment explanation
Indices: 78498--78964 Score: 918
Period size: 93 Copynumber: 5.0 Consensus size: 93
78488 TAGATTGCTT
*
78498 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
78563 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
78591 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
78655 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
78683 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
78748 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
78776 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
78841 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
78869 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
78934 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
78962 AGT
1 AGT
78965 TTCAATTTGC
Statistics
Matches: 372, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.25
93 280 0.75
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:79036 original size:19 final size:19
Alignment explanation
Indices: 78996--79124 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
78986 TAGTTTACTT
* *
78996 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
79016 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
79035 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
79054 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
79068 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
79087 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
79101 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
79120 TCGCA
1 TCGCA
79125 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:79075 original size:33 final size:32
Alignment explanation
Indices: 79032--79124 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
79022 CGCGAAACCA
**
79032 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
79064 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
79097 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
79125 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:79122 original size:52 final size:52
Alignment explanation
Indices: 78996--79124 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
78986 TAGTTTACTT
**
78996 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
79048 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
79101 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
79125 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:79142 original size:19 final size:19
Alignment explanation
Indices: 79120--79254 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
79110 GAAACCAAAA
*
79120 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
79139 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
79155 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
79172 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
79188 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
79205 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
79224 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
79244 TCGTGTTGCGA
1 TCGCGTTGCGA
79255 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:79161 original size:14 final size:14
Alignment explanation
Indices: 79142--79198 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
79132 TTTCATTTCG
79142 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
79156 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
79173 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
79189 CGTTGCGATT
1 CGTTGCGATT
79199 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:79167 original size:33 final size:33
Alignment explanation
Indices: 79125--79217 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
79115 CAAAATCGCA
*
79125 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
79158 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
79191 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
79218 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:81189 original size:14 final size:14
Alignment explanation
Indices: 81170--81205 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
81160 ATTGTTTAAT
81170 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
81184 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
81198 TGATTTGT
1 TGATTTGT
81206 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:81328 original size:19 final size:19
Alignment explanation
Indices: 81312--81413 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
81302 AAAAATGACT
81312 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
81331 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
81350 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
81364 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
81383 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
81403 ATCGCAATGCG
1 ATCGCAATGCG
81414 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:81462 original size:33 final size:33
Alignment explanation
Indices: 81420--81741 Score: 262
Period size: 33 Copynumber: 9.5 Consensus size: 33
81410 TGCGTTTATA
81420 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
81453 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
81486 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
81519 ATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
81559 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
* *
81590 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* * * * *
81628 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
81659 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
81692 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
81726 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
81742 GTATTTTCCG
Statistics
Matches: 236, Mismatches: 31, Indels: 44
0.76 0.10 0.14
Matches are distributed among these distances:
31 26 0.11
32 7 0.03
33 117 0.50
34 31 0.13
35 7 0.03
36 7 0.03
37 4 0.02
38 25 0.11
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:81466 original size:19 final size:19
Alignment explanation
Indices: 81442--81741 Score: 322
Period size: 19 Copynumber: 17.4 Consensus size: 19
81432 GATTATCTCG
81442 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
81461 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
81475 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
81494 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
81508 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
81527 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
81546 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
81560 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
81579 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
81598 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
81617 TTGCGA--TTC---TCG--
1 TTGCGATTTTCATTTCGCA
81629 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
81648 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
81667 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
81681 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
81701 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
81715 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
81734 TTGCGATT
1 TTGCGATT
81742 GTATTTTCCG
Statistics
Matches: 240, Mismatches: 8, Indels: 66
0.76 0.03 0.21
Matches are distributed among these distances:
12 6 0.03
14 41 0.17
16 32 0.13
17 34 0.14
18 3 0.01
19 112 0.47
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:81480 original size:14 final size:14
Alignment explanation
Indices: 81428--81515 Score: 68
Period size: 14 Copynumber: 5.6 Consensus size: 14
81418 TAATTTCGCA
* *
81428 TTGCGATTATCTCG
1 TTGCGATTCTTTCG
81442 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
81459 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
81475 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
81492 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
81508 TTGCGATT
1 TTGCGATT
81516 TTCATTTCGC
Statistics
Matches: 62, Mismatches: 2, Indels: 20
0.74 0.02 0.24
Matches are distributed among these distances:
14 20 0.32
16 15 0.24
17 15 0.24
19 12 0.19
ACGTcount: A:0.12, C:0.20, G:0.19, T:0.48
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:81498 original size:52 final size:52
Alignment explanation
Indices: 81442--81713 Score: 334
Period size: 52 Copynumber: 5.2 Consensus size: 52
81432 GATTATCTCG
81442 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
*
81494 TTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCA
*
81546 TTGCGA--TTC-TGTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCA
81598 TTGCGATTTTCATTTCGCATTGCGATTC--TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
*
81648 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTT-CGCA
81701 TTGCGATTTTCAT
1 TTGCGATTTTCAT
81714 GTTGGGATTT
Statistics
Matches: 203, Mismatches: 4, Indels: 25
0.88 0.02 0.11
Matches are distributed among these distances:
47 6 0.03
49 8 0.04
50 55 0.27
52 101 0.50
53 17 0.08
54 3 0.01
55 7 0.03
57 6 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
Found at i:84033 original size:12 final size:12
Alignment explanation
Indices: 84016--84040 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
84006 TTCTTCGGGA
84016 CTTTTTCTTCTT
1 CTTTTTCTTCTT
84028 CTTTTTCTTCTT
1 CTTTTTCTTCTT
84040 C
1 C
84041 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:84249 original size:24 final size:24
Alignment explanation
Indices: 84215--84261 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
84205 CTGAAACATC
84215 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
84239 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
84262 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Done.