Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005916.1 Hibiscus syriacus cultivar Beakdansim tig00013892_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: 79569
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:864 original size:31 final size:31
Alignment explanation
Indices: 826--889 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
816 GGTCAGAAGT
826 AAACTACCATGATGAAGGGATAGCTATATGG
1 AAACTACCATGATGAAGGGATAGCTATATGG
857 AAACTACCATGATGAAGGGATAGCTATATGG
1 AAACTACCATGATGAAGGGATAGCTATATGG
888 AA
1 AA
890 CGCTTCGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (31 bp):
AAACTACCATGATGAAGGGATAGCTATATGG
Found at i:3421 original size:13 final size:13
Alignment explanation
Indices: 3395--3428 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
3385 TAATAAAGTG
3395 ATTAAAAATCTAA
1 ATTAAAAATCTAA
3408 ATCTAAAAAT-TAA
1 AT-TAAAAATCTAA
3421 ATTAAAAA
1 ATTAAAAA
3429 GTTATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 7 0.35
14 7 0.35
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (13 bp):
ATTAAAAATCTAA
Found at i:6850 original size:54 final size:54
Alignment explanation
Indices: 6788--6983 Score: 221
Period size: 54 Copynumber: 3.4 Consensus size: 54
6778 AACTGTGGCA
6788 CTGAATTTGGATGATGATAATGAAAATGGTAATGGTGAGTTGAAGGAAGTGAAG
1 CTGAATTTGGATGATGATAATGAAAATGGTAATGGTGAGTTGAAGGAAGTGAAG
*
6842 CTGAATTTGAATGATGATAATGATGATGGTGATGGTAATGGTAATGGTGAGTTGAAGGAAGTGAA
1 CTGAATTTGGATGATGAT-A--ATGA-----A----AATGGTAATGGTGAGTTGAAGGAAGTGAA
6907 G
54 G
* * * * * *
6908 CTGAAGTTAGATGATGGTAATGAGAATGGTAATGGTGGGTTGAAAGAAGTGAAG
1 CTGAATTTGGATGATGATAATGAAAATGGTAATGGTGAGTTGAAGGAAGTGAAG
6962 CTGAATTTGGATGATGATAATG
1 CTGAATTTGGATGATGATAATG
6984 GTACCGGTAC
Statistics
Matches: 119, Mismatches: 11, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
54 64 0.54
55 1 0.01
57 4 0.03
62 1 0.01
63 4 0.03
65 1 0.01
66 44 0.37
ACGTcount: A:0.35, C:0.02, G:0.34, T:0.29
Consensus pattern (54 bp):
CTGAATTTGGATGATGATAATGAAAATGGTAATGGTGAGTTGAAGGAAGTGAAG
Found at i:6880 original size:18 final size:18
Alignment explanation
Indices: 6853--6891 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6843 TGAATTTGAA
*
6853 TGATGATAATGATGATGG
1 TGATGATAATGATAATGG
* *
6871 TGATGGTAATGGTAATGG
1 TGATGATAATGATAATGG
6889 TGA
1 TGA
6892 GTTGAAGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (18 bp):
TGATGATAATGATAATGG
Found at i:6901 original size:66 final size:66
Alignment explanation
Indices: 6812--6943 Score: 205
Period size: 66 Copynumber: 2.0 Consensus size: 66
6802 TGATAATGAA
* *
6812 AATGGTAATGGTGAGTTGAAGGAAGTGAAGCTGAA-TTTGAATGATGATAATGATG-ATGGTGAT
1 AATGGTAATGGTGAGTTGAAGGAAGTGAAGCTGAAGTTAG-ATGATGATAATGA-GAATGGTAAT
6875 GGT
64 GGT
*
6878 AATGGTAATGGTGAGTTGAAGGAAGTGAAGCTGAAGTTAGATGATGGTAATGAGAATGGTAATGG
1 AATGGTAATGGTGAGTTGAAGGAAGTGAAGCTGAAGTTAGATGATGATAATGAGAATGGTAATGG
6943 T
66 T
6944 GGGTTGAAAG
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
65 1 0.02
66 57 0.93
67 3 0.05
ACGTcount: A:0.34, C:0.02, G:0.36, T:0.29
Consensus pattern (66 bp):
AATGGTAATGGTGAGTTGAAGGAAGTGAAGCTGAAGTTAGATGATGATAATGAGAATGGTAATGG
T
Found at i:20736 original size:43 final size:43
Alignment explanation
Indices: 20675--20767 Score: 150
Period size: 43 Copynumber: 2.1 Consensus size: 43
20665 AAAAGAGAGA
*
20675 CGTTTTGTTTAGTCCTTTTCGTGTTTATTGACCGGAGCCTTAC
1 CGTTTTGTTTAGTCCTTTTAGTGTTTATTGACCGGAGCCTTAC
* *
20718 CGTTTTGTTTAGTCCTTTTAGTGTTTATTGACTGGAGCCTTGC
1 CGTTTTGTTTAGTCCTTTTAGTGTTTATTGACCGGAGCCTTAC
20761 CGATTTT
1 CG-TTTT
20768 CACCGGTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
43 42 0.91
44 4 0.09
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (43 bp):
CGTTTTGTTTAGTCCTTTTAGTGTTTATTGACCGGAGCCTTAC
Found at i:32185 original size:15 final size:16
Alignment explanation
Indices: 32160--32192 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
32150 TATCGCCGAC
32160 CGAATTTCACTATTCA
1 CGAATTTCACTATTCA
32176 CGAA-TTCACTATTCA
1 CGAATTTCACTATTCA
32191 CG
1 CG
32193 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.33
Consensus pattern (16 bp):
CGAATTTCACTATTCA
Found at i:34441 original size:3 final size:3
Alignment explanation
Indices: 34435--34460 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
34425 GTTTTAGAGT
34435 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
34461 TATTTTGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:37171 original size:22 final size:22
Alignment explanation
Indices: 37120--37175 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
37110 GATTCAACAT
37120 AATTTTTTTAAATTTGTTATTA
1 AATTTTTTTAAATTTGTTATTA
*
37142 AATGTTTTTAGAATTT-TTATT-
1 AATTTTTTTA-AATTTGTTATTA
*
37163 TATTTTTTTAAAT
1 AATTTTTTTAAAT
37176 AATTATGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 3 0.10
21 8 0.27
22 14 0.47
23 5 0.17
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (22 bp):
AATTTTTTTAAATTTGTTATTA
Found at i:37901 original size:35 final size:35
Alignment explanation
Indices: 37862--37930 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
37852 TACCGTTAAA
37862 TAGTTAATGGCGTTAAAACAATACCATTTTAAAAT
1 TAGTTAATGGCGTTAAAACAATACCATTTTAAAAT
37897 TAGTTAATGGCGTTAAAACAATACCATTTTAAAA
1 TAGTTAATGGCGTTAAAACAATACCATTTTAAAA
37931 AGAAAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (35 bp):
TAGTTAATGGCGTTAAAACAATACCATTTTAAAAT
Found at i:38363 original size:20 final size:20
Alignment explanation
Indices: 38340--38391 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
38330 AACGCGATCC
38340 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
38360 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
38380 CCAAAATCGCAA
1 CCAGAATCGCAA
38392 CGCGATTCTT
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:38408 original size:21 final size:20
Alignment explanation
Indices: 38382--38499 Score: 85
Period size: 20 Copynumber: 5.8 Consensus size: 20
38372 ATCAGTTTCC
38382 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * **
38403 AAAATCGCGATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
38422 ACAAATTCGCATTGCGATTTTCC
1 A-AAA-TCGCAACGCGATTTT-G
* * *
38445 ATAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
* *
38465 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
38485 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
38500 ACACATAAAT
Statistics
Matches: 78, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.01
20 38 0.49
21 36 0.46
22 2 0.03
23 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:38528 original size:20 final size:20
Alignment explanation
Indices: 38447--38659 Score: 223
Period size: 20 Copynumber: 10.6 Consensus size: 20
38437 GATTTTCCAT
* ** *
38447 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* ** *
38467 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
38487 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
38507 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
38527 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
38547 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
38567 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
38587 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
38607 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
38628 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
38648 AATCGCAACGCG
1 AATCGCAACGCG
38660 ATATTTAAAG
Statistics
Matches: 165, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 145 0.88
21 17 0.10
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:38530 original size:60 final size:60
Alignment explanation
Indices: 38447--38660 Score: 248
Period size: 60 Copynumber: 3.5 Consensus size: 60
38437 GATTTTCCAT
* ** * ** * *
38447 AATCGCAACGCGAATATGAAAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATA
* * * ***
38507 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATA
* * * **
38567 AATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACAT-A
38628 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
38661 TATTTAAAGC
Statistics
Matches: 127, Mismatches: 26, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 96 0.76
61 31 0.24
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATA
Found at i:39079 original size:33 final size:33
Alignment explanation
Indices: 39040--39110 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
39030 TTCACTTAGA
*
39040 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
39073 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
39106 TTTCA
1 TTTCA
39111 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:39250 original size:14 final size:14
Alignment explanation
Indices: 39231--39285 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
39221 AGAATGACTG
39231 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
39245 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
39264 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
39278 TCGCAACG
1 TCGCAACG
39286 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:39268 original size:33 final size:33
Alignment explanation
Indices: 39231--39301 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
39221 AGAATGACTG
**
39231 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
39264 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
39297 TCGCA
1 TCGCA
39302 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:39319 original size:19 final size:19
Alignment explanation
Indices: 39297--39394 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
39287 GAAACCAAAA
*
39297 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
39316 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
39330 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
39349 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
39363 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
39382 TCGCGTTGCGATT
1 TCGCGTTGCGATT
39395 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:39338 original size:14 final size:14
Alignment explanation
Indices: 39319--39408 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
39309 TTTCATTTCG
39319 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
39333 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
39352 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
39366 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
39383 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
39399 CGTTGCGATT
1 CGTTGCGATT
39409 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:39344 original size:33 final size:33
Alignment explanation
Indices: 39302--39416 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
39292 CAAAATCGCA
39302 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
39335 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
39368 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
39401 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
39417 AACCAAAAGA
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:41345 original size:185 final size:185
Alignment explanation
Indices: 41115--41586 Score: 917
Period size: 185 Copynumber: 2.6 Consensus size: 185
41105 TAGATTGCTT
*
41115 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
41180 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGTCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
41245 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
41300 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41365 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
41430 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
41485 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41550 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
41587 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 284 1.00
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:41412 original size:93 final size:93
Alignment explanation
Indices: 41115--41586 Score: 903
Period size: 93 Copynumber: 5.1 Consensus size: 93
41105 TAGATTGCTT
*
41115 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41180 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
41208 AGTAAATTTGTTCGGTTGCTGTCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41272 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
41300 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41365 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
41393 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41457 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
41485 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41550 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
41578 AGTAAATTT
1 AGTAAATTT
41587 ATCCATTCAA
Statistics
Matches: 372, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 182 0.49
93 190 0.51
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:41670 original size:19 final size:19
Alignment explanation
Indices: 41630--41758 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
41620 TTGTTTACTT
* *
41630 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
41650 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
41669 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
41688 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
41702 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
41721 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
41735 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
41754 TCGCA
1 TCGCA
41759 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:41709 original size:33 final size:32
Alignment explanation
Indices: 41666--41758 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
41656 CGCGAAACCA
**
41666 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
41698 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
41731 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
41759 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:41756 original size:52 final size:52
Alignment explanation
Indices: 41630--41758 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
41620 TTGTTTACTT
**
41630 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
41682 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
41735 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
41759 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:41776 original size:19 final size:19
Alignment explanation
Indices: 41754--41888 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
41744 GAAACCAAAA
*
41754 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
41773 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
41789 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
41806 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
41822 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
41839 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
41858 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
41878 TCGTGTTGCGA
1 TCGCGTTGCGA
41889 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:41795 original size:14 final size:14
Alignment explanation
Indices: 41776--41832 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
41766 TTTCATTTCG
41776 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
41790 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
41807 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
41823 CGTTGCGATT
1 CGTTGCGATT
41833 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:41801 original size:33 final size:33
Alignment explanation
Indices: 41759--41851 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
41749 CAAAATCGCA
*
41759 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
41792 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
41825 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
41852 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:43812 original size:14 final size:14
Alignment explanation
Indices: 43793--43828 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
43783 ATTGTTTAAT
43793 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
43807 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
43821 TGATTTGT
1 TGATTTGT
43829 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:43951 original size:19 final size:19
Alignment explanation
Indices: 43935--44036 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
43925 AAAAATGACT
43935 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
43954 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
43973 ATCACAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
43987 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
44006 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
44026 ATCGCAATGCG
1 ATCGCAATGCG
44037 TTTATAATTT
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 19 0.26
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:44089 original size:19 final size:19
Alignment explanation
Indices: 44065--44338 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
44055 GATTATCTCG
44065 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44084 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44103 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
44117 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44136 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44155 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44174 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
44193 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
44212 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
44226 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44245 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
44264 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
44278 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
44298 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
44312 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
44331 TTGCGATT
1 TTGCGATT
44339 GTATTTTCCG
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 20 0.09
18 3 0.01
19 138 0.61
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:44105 original size:52 final size:52
Alignment explanation
Indices: 44043--44310 Score: 437
Period size: 52 Copynumber: 5.0 Consensus size: 52
44033 TGCGTTTATA
*
44043 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
44095 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
44147 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
44204 ATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
44256 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
44309 AT
1 AT
44311 GTTGGGATTT
Statistics
Matches: 204, Mismatches: 6, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
52 129 0.63
53 17 0.08
54 7 0.03
55 8 0.04
57 43 0.21
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:44194 original size:109 final size:102
Alignment explanation
Indices: 44065--44305 Score: 176
Period size: 109 Copynumber: 2.3 Consensus size: 102
44055 GATTATCTCG
44065 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
44127 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
44174 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * * * *
44236 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
44278 TTGCGATTTTCATTTCCGCATTGCGATT
1 TTGCGATTTTCATTT-CGCATTGCGATT
44306 TTCATGTTGG
Statistics
Matches: 120, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
102 7 0.06
103 6 0.05
104 20 0.17
105 11 0.09
107 2 0.02
109 74 0.62
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (102 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:46635 original size:12 final size:12
Alignment explanation
Indices: 46618--46642 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46608 TCTTCGGGGA
46618 CTTTTTCTTCTT
1 CTTTTTCTTCTT
46630 CTTTTTCTTCTT
1 CTTTTTCTTCTT
46642 C
1 C
46643 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:46851 original size:24 final size:24
Alignment explanation
Indices: 46817--46863 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
46807 CTGAAACATC
46817 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
46841 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
46864 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
Found at i:47574 original size:20 final size:20
Alignment explanation
Indices: 47546--47914 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
47536 AAATTTAAGT
* * * *
47546 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
47566 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
47586 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
47606 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
47626 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
47646 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
47666 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
47686 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
47706 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
47726 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
47746 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
47766 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
47786 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
47806 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
47826 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
47846 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
47866 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
47886 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
47906 GTTGCGATT
1 GTTGCGATT
47915 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:59156 original size:530 final size:530
Alignment explanation
Indices: 58155--59651 Score: 2661
Period size: 530 Copynumber: 2.8 Consensus size: 530
58145 AGACGAATCC
*
58155 AAACTGCTTATATCCGGGCGATTTGCGATATGTACTGTAGATCTACTACATACGTCAGGACTACA
1 AAACTGCTTATATCCGGGCGATTCGCGATATGTACTGTAGATCTACTACATACGTCAGGACTACA
* *
58220 GTTGGCGACACCGAGGCATTCCTGGTGGAAATCGGACTCCACCAGGGGTCGGCTCTTAGCCCTTA
66 GTTGGCGACACCGAGGCATTCCCGGTGGAAATCGGACTCCACCAGGGGTCAGCTCTTAGCCCTTA
*
58285 CATCTTCGCCTTGATTATGGACGACATCTATTGTGCGACACCAGACAATGTTTCATGGTGTATGC
131 CATCTTCGCCTTGATTATGGACGACATCTATTGTGCGACACCAGACAATGTTCCATGGTGTATGC
* **
58350 TTTTCGCTGATGACATTGACCTAGTTAATGAAACAAAAAATGAGTTGAATAGTAGACTGGCTACC
196 TTTTCGCTGACGACATTGACCTAGTTGCTGAAACAAAAAATGAGTTGAATAGTAGACTGGCTACC
*
58415 TGGAAGACTACTTTGGAAGAAAAAGGTCTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTC
261 TGGAAGACTGCTTTGGAAGAAAAAGGTCTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTC
*
58480 AAACTTCAGTGGGAACCAAAACGTTGAAGATGTAGAAGTTTGCATCGAAGGACACGTTATCCCCT
326 AAACTTCAGTGGGAACCAAAACGTTGAAGATGTAGAAGTTTGCATCGAAGGACACGTTCTCCCCT
58545 CAAAGAATTGTTTCAAGTACCTAGGGTCTATGATACATAAAGATGGGGGTATAGGTGATGACGTT
391 CAAAGAATTGTTTCAAGTACCTAGGGTCTATGATACATAAAGATGGGGGTATAGGTGATGACGTT
58610 ACACACCGTATAAAGGCGGGATGGCTAAAGTGGAGGGCTGCTACTGGAGTTTTGTGTGACAAGAA
456 ACACACCGTATAAAGGCGGGATGGCTAAAGTGGAGGGCTGCTACTGGAGTTTTGTGTGACAAGAA
58675 GGTGCCTCTA
521 GGTGCCTCTA
*
58685 AAACTGCTTATATCCGGGCGATTCGCGATATGTACTGTAGATATACTACATACGTCAGGACTACA
1 AAACTGCTTATATCCGGGCGATTCGCGATATGTACTGTAGATCTACTACATACGTCAGGACTACA
*
58750 GTTGGCGACACCGAGGCATTCCCGGTGGAAATCGGACTCCACCAAGGGTCAGCTCTTAGCCCTTA
66 GTTGGCGACACCGAGGCATTCCCGGTGGAAATCGGACTCCACCAGGGGTCAGCTCTTAGCCCTTA
*
58815 CATCTTCGCCTTGATTATGGACGACATCTATTGTGCGAGACCAGACAATGTTCCATGGTGTATGC
131 CATCTTCGCCTTGATTATGGACGACATCTATTGTGCGACACCAGACAATGTTCCATGGTGTATGC
*
58880 TTTTCGCTGACGACATTGACCTAGTTGCTGAAACAAAAAATGAGTTGAATAGTAGACTGACTACC
196 TTTTCGCTGACGACATTGACCTAGTTGCTGAAACAAAAAATGAGTTGAATAGTAGACTGGCTACC
* *
58945 TGAAAGACTGCTTTAGAAGAAAAAGGTCTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTC
261 TGGAAGACTGCTTTGGAAGAAAAAGGTCTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTC
* * *
59010 AAACTTCAGTGGGAACAAAAACGTTGAAGATTTAGAAGTTTGCATCGAAGGACACATTCTCCCCT
326 AAACTTCAGTGGGAACCAAAACGTTGAAGATGTAGAAGTTTGCATCGAAGGACACGTTCTCCCCT
*
59075 CAAAGAATTGTTTCAAGTACCTAGGGTCTATGATACATAAAGATGGGGGTGTAGGTGATGACGTT
391 CAAAGAATTGTTTCAAGTACCTAGGGTCTATGATACATAAAGATGGGGGTATAGGTGATGACGTT
59140 ACACACCGTATAAAGGCGGGATGGCTAAAGTGGAGGGCTGCTACTGGAGTTTTGTGTGACAAGAA
456 ACACACCGTATAAAGGCGGGATGGCTAAAGTGGAGGGCTGCTACTGGAGTTTTGTGTGACAAGAA
59205 GGTGCCTCTA
521 GGTGCCTCTA
* * * *
59215 AAACTGCTTATATCCGGGTGATTCGTGATATGTATTGTATATCTACTACATACGTCAGGACTACA
1 AAACTGCTTATATCCGGGCGATTCGCGATATGTACTGTAGATCTACTACATACGTCAGGACTACA
* * * * *
59280 GTTGGTGACACTGAGGCATTCCCGGGGGAAATCGGACTCCATCAGGGGTCATCTCTTAGCCCTTA
66 GTTGGCGACACCGAGGCATTCCCGGTGGAAATCGGACTCCACCAGGGGTCAGCTCTTAGCCCTTA
* * *
59345 CATCTTCGCCTTGATTATGGATGACTTCCATTGTGCGACACCAGACAATGTTCCATGGTGTATGC
131 CATCTTCGCCTTGATTATGGACGACATCTATTGTGCGACACCAGACAATGTTCCATGGTGTATGC
* * *
59410 TTTTCGCTGACGACATTAACCTAGTTGCTGAAATAAAAAATAAGTTGAATAGTAGACTGGCTACC
196 TTTTCGCTGACGACATTGACCTAGTTGCTGAAACAAAAAATGAGTTGAATAGTAGACTGGCTACC
* *
59475 TGGAAGACTGTTTTGGAAGAAAAAGGTCTAAGGATCAATATTGAAAAGACAAAGTATTTATGTTC
261 TGGAAGACTGCTTTGGAAGAAAAAGGTCTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTC
*
59540 AAACTTCAGTGGGAACCAAAACGTTGAAGATGTAGAAGTTTGCATCGAAGGACACGTTCTCCCTT
326 AAACTTCAGTGGGAACCAAAACGTTGAAGATGTAGAAGTTTGCATCGAAGGACACGTTCTCCCCT
59605 CAAAGAATTGTTTCAAGTACCTAGGGTCTATGATACATAAAGATGGG
391 CAAAGAATTGTTTCAAGTACCTAGGGTCTATGATACATAAAGATGGG
59652 TGTAACATCC
Statistics
Matches: 921, Mismatches: 46, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
530 921 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (530 bp):
AAACTGCTTATATCCGGGCGATTCGCGATATGTACTGTAGATCTACTACATACGTCAGGACTACA
GTTGGCGACACCGAGGCATTCCCGGTGGAAATCGGACTCCACCAGGGGTCAGCTCTTAGCCCTTA
CATCTTCGCCTTGATTATGGACGACATCTATTGTGCGACACCAGACAATGTTCCATGGTGTATGC
TTTTCGCTGACGACATTGACCTAGTTGCTGAAACAAAAAATGAGTTGAATAGTAGACTGGCTACC
TGGAAGACTGCTTTGGAAGAAAAAGGTCTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTC
AAACTTCAGTGGGAACCAAAACGTTGAAGATGTAGAAGTTTGCATCGAAGGACACGTTCTCCCCT
CAAAGAATTGTTTCAAGTACCTAGGGTCTATGATACATAAAGATGGGGGTATAGGTGATGACGTT
ACACACCGTATAAAGGCGGGATGGCTAAAGTGGAGGGCTGCTACTGGAGTTTTGTGTGACAAGAA
GGTGCCTCTA
Found at i:60378 original size:21 final size:21
Alignment explanation
Indices: 60352--60396 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
60342 GATTTCTGGG
* *
60352 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
60373 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
60394 CAA
1 CAA
60397 ACAAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:62247 original size:23 final size:23
Alignment explanation
Indices: 62214--62281 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
62204 ATTATTATAT
62214 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
62237 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
62260 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
62282 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:64895 original size:2 final size:2
Alignment explanation
Indices: 64883--64934 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
64873 ACAGTTGAGC
*
64883 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64925 AT AT AT AT AT
1 AT AT AT AT AT
64935 TCTTTCACGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69938 original size:30 final size:31
Alignment explanation
Indices: 69886--69959 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 31
69876 ATTGCACGTC
69886 TAGTACCTAAACTATCAGTTTTGGTTCATTT
1 TAGTACCTAAACTATCAGTTTTGGTTCATTT
* *
69917 TAGTACCT-AATTATTAGTTTTGGTTCATTT
1 TAGTACCTAAACTATCAGTTTTGGTTCATTT
*
69947 TAGTACATAAACT
1 TAGTACCTAAACT
69960 TTCAATATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 27 0.71
31 11 0.29
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (31 bp):
TAGTACCTAAACTATCAGTTTTGGTTCATTT
Found at i:70417 original size:45 final size:45
Alignment explanation
Indices: 70306--70402 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 45
70296 AATGTAACTG
* * ** *
70306 AAAATGTT-ATAT-AAAATATAATATTTTGGATTGGACGTAATCT
1 AAAATGTTAATTTAAAAAAATAATATTTTAAATTGCACGTAATCT
*
70349 AAAATGTTAATTTAAAAAAATAATATTTTAAATTGCACTTAA-CT
1 AAAATGTTAATTTAAAAAAATAATATTTTAAATTGCACGTAATCT
70393 AAAAGTGTTA
1 AAAA-TGTTA
70403 TTTTTTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 8 0.18
44 9 0.20
45 28 0.62
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.38
Consensus pattern (45 bp):
AAAATGTTAATTTAAAAAAATAATATTTTAAATTGCACGTAATCT
Found at i:75391 original size:52 final size:51
Alignment explanation
Indices: 75303--75420 Score: 125
Period size: 52 Copynumber: 2.3 Consensus size: 51
75293 ACGATGAGTT
* ** *
75303 AATAAAATAA-TT-TTTTATTAAAACTTGTCAACTTGACATAACAAATTTT
1 AATAAAAAAATTTATTTTATTAAAACTTCACAACTTGACATAACAAATTTG
* * * *
75352 AATAAAAGAATTATATTTTATTAAAAC-TCACAACGTTGACGTAACGAGTTTG
1 AATAAAAAAATT-TATTTTATTAAAACTTCACAAC-TTGACATAACAAATTTG
75404 AATAAAAAAATTTATTT
1 AATAAAAAAATTTATTT
75421 GAGCAAATTA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
49 9 0.16
50 1 0.02
51 11 0.19
52 36 0.63
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.37
Consensus pattern (51 bp):
AATAAAAAAATTTATTTTATTAAAACTTCACAACTTGACATAACAAATTTG
Done.