Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000769.1 Hibiscus syriacus cultivar Beakdansim tig00001494_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: 63929
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2810 original size:29 final size:29
Alignment explanation
Indices: 2750--2885 Score: 181
Period size: 28 Copynumber: 4.8 Consensus size: 29
2740 ACACAATTAT
* * * *
2750 CACCCTTTTAAGAA-ATTTATGAAACTAT
1 CACCCTTTTAAAAATATTTACGAAAATAA
2778 CACCCTTTTAAAAATATTTACGAAAATAA
1 CACCCTTTTAAAAATATTTACGAAAATAA
*
2807 CA-CCTTTTAAAAATATTTACGAAAATAG
1 CACCCTTTTAAAAATATTTACGAAAATAA
2835 CACCCTTTTAAAAATATTTACG-AAATAA
1 CACCCTTTTAAAAATATTTACGAAAATAA
* *
2863 CATCCTTTTAAAAA-AATTACGAA
1 CACCCTTTTAAAAATATTTACGAA
2886 CTAACATCCA
Statistics
Matches: 97, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
27 6 0.06
28 59 0.61
29 32 0.33
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (29 bp):
CACCCTTTTAAAAATATTTACGAAAATAA
Found at i:2825 original size:57 final size:56
Alignment explanation
Indices: 2753--2885 Score: 196
Period size: 57 Copynumber: 2.4 Consensus size: 56
2743 CAATTATCAC
* * * *
2753 CCTTTTAAGAAATTTATGAAACTATCACCCTTTTAAAAATATTTACGAAAATAACA-
1 CCTTTTAAAAAATTTACGAAAATAGCACCCTTTTAAAAATATTTACG-AAATAACAT
2809 CCTTTTAAAAATATTTACGAAAATAGCACCCTTTTAAAAATATTTACGAAATAACAT
1 CCTTTTAAAAA-ATTTACGAAAATAGCACCCTTTTAAAAATATTTACGAAATAACAT
*
2866 CCTTTTAAAAAAATTACGAA
1 CCTTTTAAAAAATTTACGAA
2886 CTAACATCCA
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
56 26 0.37
57 44 0.63
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.33
Consensus pattern (56 bp):
CCTTTTAAAAAATTTACGAAAATAGCACCCTTTTAAAAATATTTACGAAATAACAT
Found at i:5669 original size:20 final size:20
Alignment explanation
Indices: 5632--5670 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5622 TTATGTTCTG
*
5632 AACAGAAAGTTTAGAAAATC
1 AACAGAAAGTTTAAAAAATC
5652 AACAGAAA-TTATAAAAAAT
1 AACAGAAAGTT-TAAAAAAT
5671 AATTGAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.21
Consensus pattern (20 bp):
AACAGAAAGTTTAAAAAATC
Found at i:6480 original size:21 final size:22
Alignment explanation
Indices: 6454--6653 Score: 154
Period size: 21 Copynumber: 9.3 Consensus size: 22
6444 CATATTCGTA
*
6454 TTGCGA-TAGTCCAAGTTTGCG
1 TTGCGATTATTCCAAGTTTGCG
6475 TTGCGATTTATTCCAAG-TT-CG
1 TTGCGA-TTATTCCAAGTTTGCG
*
6496 TTGCGATTTATTCCAA-ATT-CG
1 TTGCGA-TTATTCCAAGTTTGCG
*
6517 TTGCGATTTATTCCAAGTTCGCG
1 TTGCGA-TTATTCCAAGTTTGCG
* *
6540 TTGCGATTTATTCCAA--ATCCG
1 TTGCGA-TTATTCCAAGTTTGCG
* *
6561 TTGCGA-TAGTCGAAGTTTGCG
1 TTGCGATTATTCCAAGTTTGCG
*
6582 TTGCGATTTATTCCAA-ATT-CG
1 TTGCGA-TTATTCCAAGTTTGCG
* * *
6603 TTGCGATTTATTCCAAATTCGCA
1 TTGCGA-TTATTCCAAGTTTGCG
6626 TTGCGATTTATTCCAAG-TT-CG
1 TTGCGA-TTATTCCAAGTTTGCG
6647 TTGCGAT
1 TTGCGAT
6654 AGTCCAAAAT
Statistics
Matches: 149, Mismatches: 19, Indels: 23
0.78 0.10 0.12
Matches are distributed among these distances:
19 6 0.04
20 1 0.01
21 86 0.58
22 7 0.05
23 49 0.33
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (22 bp):
TTGCGATTATTCCAAGTTTGCG
Found at i:6535 original size:65 final size:65
Alignment explanation
Indices: 6463--6653 Score: 246
Period size: 65 Copynumber: 2.9 Consensus size: 65
6453 ATTGCGATAG
*
6463 TCCAAGTTTGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATTCGTTGCGATTTAT
1 TCCAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATTTAT
* * * * *
6528 TCCAAGTTCGCGTTGCGATTTATTCCAAATCCGTTGCGA--TAGTCGAAGTTTGCGTTGCGATTT
1 TCCAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAA-ATT-CGTTGCGATTT
6591 AT
64 AT
* *
6593 TCCAA-ATT-CGTTGCGATTTATTCCAAATTCGCATTGCGATTTATTCCAAGTTCGTTGCGAT
1 TCCAAGTTTGCGTTGCGATTTATTCCAAATTCG--TTGCGATTTATTCCAAATTCGTTGCGAT
6654 AGTCCAAAAT
Statistics
Matches: 108, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
63 28 0.26
64 3 0.03
65 69 0.64
66 2 0.02
67 6 0.06
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (65 bp):
TCCAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATTTAT
Found at i:6563 original size:86 final size:87
Alignment explanation
Indices: 6473--6660 Score: 285
Period size: 86 Copynumber: 2.2 Consensus size: 87
6463 TCCAAGTTTG
* *
6473 CGTTGCGATTTATTCCAAG-TT-CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTT
1 CGTTGCGA-TTAGTCCAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
*
6536 CGCGTTGCGATTTATTCCAAATC
65 CGCATTGCGATTTATTCCAAATC
*
6559 CGTTGCGA-TAGTCGAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTC
1 CGTTGCGATTAGTCCAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTC
* *
6623 GCATTGCGATTTATTCCAAGTT
66 GCATTGCGATTTATTCCAAATC
6645 CGTTGCGA-TAGTCCAA
1 CGTTGCGATTAGTCCAA
6661 AATCGCAACG
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
84 7 0.08
85 2 0.02
86 84 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (87 bp):
CGTTGCGATTAGTCCAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTC
GCATTGCGATTTATTCCAAATC
Found at i:6581 original size:107 final size:106
Alignment explanation
Indices: 6454--6653 Score: 348
Period size: 107 Copynumber: 1.9 Consensus size: 106
6444 CATATTCGTA
*
6454 TTGCGATAGTCCAAGTTTGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATTCG-T
1 TTGCGATAGTCCAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGAT
6518 TGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATCCG
66 TGCGATTTATTCCAAGTT--CGTTGCGATTTATTCCAAATCCG
*
6561 TTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGCA
1 TTGCGATAGTCCAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCG-A
6626 TTGCGATTTATTCCAAGTTCGTTGCGAT
65 TTGCGATTTATTCCAAGTTCGTTGCGAT
6654 AGTCCAAAAT
Statistics
Matches: 89, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
107 70 0.79
109 19 0.21
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (106 bp):
TTGCGATAGTCCAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGAT
TGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATCCG
Found at i:6757 original size:6 final size:6
Alignment explanation
Indices: 6746--6799 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
6736 GACACGTATT
6746 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
6792 ACC-CG ACC
1 ACCACG ACC
6800 CGAGACGGCG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.31
6 33 0.69
ACGTcount: A:0.30, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:7417 original size:21 final size:21
Alignment explanation
Indices: 7390--7485 Score: 124
Period size: 21 Copynumber: 4.6 Consensus size: 21
7380 CGTTGCGATT
*
7390 TTGGACTATCGCAATGCGAGC
1 TTGGACTATCGCAATGCGAAC
*
7411 TTTGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
*
7432 TTGGACTATCGCAATGTGAA-
1 TTGGACTATCGCAATGCGAAC
* *
7452 TATGTA-AATCGCAATGCGAAC
1 T-TGGACTATCGCAATGCGAAC
7473 TTGGACTATCGCA
1 TTGGACTATCGCA
7486 TTACGATTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
20 16 0.25
21 47 0.75
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:7524 original size:21 final size:21
Alignment explanation
Indices: 7500--7553 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
7490 GATTTACATA
*
7500 TTCGTATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
7521 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
7542 TTCGCGTTGCGA
1 TTCGCATTGCGA
7554 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:11502 original size:19 final size:19
Alignment explanation
Indices: 11478--11517 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
11468 AACTTACATA
11478 GAAAAAATATACTCAAATT
1 GAAAAAATATACTCAAATT
11497 GAAAAAATATACTCAAATT
1 GAAAAAATATACTCAAATT
11516 GA
1 GA
11518 GTTTGATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.25
Consensus pattern (19 bp):
GAAAAAATATACTCAAATT
Found at i:13465 original size:15 final size:16
Alignment explanation
Indices: 13445--13476 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13435 CATTTTTAAA
13445 TCAAATT-TTTCTTTT
1 TCAAATTCTTTCTTTT
13460 TCAAATTCTTTCTTTT
1 TCAAATTCTTTCTTTT
13476 T
1 T
13477 TCTTTTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.66
Consensus pattern (16 bp):
TCAAATTCTTTCTTTT
Found at i:17180 original size:13 final size:13
Alignment explanation
Indices: 17162--17186 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17152 ACCACCTAGG
17162 TGAGCTGGCATAC
1 TGAGCTGGCATAC
17175 TGAGCTGGCATA
1 TGAGCTGGCATA
17187 ACAATATATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (13 bp):
TGAGCTGGCATAC
Found at i:19438 original size:21 final size:21
Alignment explanation
Indices: 19409--19462 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
19399 ATATAGGGAG
*
19409 GTACTGATACACTCCTCGGAT
1 GTACCGATACACTCCTCGGAT
19430 GTACCGATACACTCCTCGGAT
1 GTACCGATACACTCCTCGGAT
*
19451 GTACCAATACAC
1 GTACCGATACAC
19463 CCCAATTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (21 bp):
GTACCGATACACTCCTCGGAT
Found at i:26205 original size:21 final size:21
Alignment explanation
Indices: 26181--26220 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
26171 TTTATTTTAT
26181 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
26202 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
26221 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:26268 original size:33 final size:33
Alignment explanation
Indices: 26215--26313 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
26205 TTTGTTTCAA
26215 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
26247 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
26280 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
26313 T
1 T
26314 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:26342 original size:13 final size:13
Alignment explanation
Indices: 26299--26353 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
26289 TTGGAAGTAT
26299 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
26312 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
26326 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
26339 TTAAGTATTTGAA
1 TTAAGTATTTCAA
26352 TT
1 TT
26354 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:26575 original size:21 final size:21
Alignment explanation
Indices: 26549--26605 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
26539 TGGAGCATGG
*
26549 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
26570 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
26591 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
26606 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:26810 original size:17 final size:18
Alignment explanation
Indices: 26790--26823 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26780 GTTTTTTTAT
26790 AACC-GATTTTTTAAAAA
1 AACCGGATTTTTTAAAAA
*
26807 AACCGGTTTTTTTAAAA
1 AACCGGATTTTTTAAAA
26824 CCGAAACCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (18 bp):
AACCGGATTTTTTAAAAA
Found at i:26823 original size:15 final size:15
Alignment explanation
Indices: 26771--26826 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
26761 ATCTGGAATA
*
26771 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
* *
26786 TTATAACCGATTTTT
1 TTAAAACCGGTTTTT
*
26801 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
26818 TTAAAACCG
1 TTAAAACCG
26827 AAACCGGTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 20 0.62
17 12 0.38
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:26943 original size:15 final size:17
Alignment explanation
Indices: 26917--26948 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
26907 TTCTATGGGA
26917 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
26933 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
26949 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:29452 original size:24 final size:24
Alignment explanation
Indices: 29425--29481 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
29415 CTTCATCTCC
29425 TTCCACACATAATAAATAAAAAAA
1 TTCCACACATAATAAATAAAAAAA
*
29449 TTCCACACATAATAAATAAACAAA
1 TTCCACACATAATAAATAAAAAAA
*
29473 TTCCTCACA
1 TTCCACACA
29482 ATTTTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (24 bp):
TTCCACACATAATAAATAAAAAAA
Found at i:34660 original size:1 final size:1
Alignment explanation
Indices: 34622--34646 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
34612 AACTTCTATC
34622 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
34647 TTAAACAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:37707 original size:20 final size:21
Alignment explanation
Indices: 37656--37698 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
37646 ATACGTTACA
*
37656 ATCA-GAAATTTGGATATCCG
1 ATCAGGAAATTTGGATACCCG
37676 ATCAGGAAATTTGGATACCCG
1 ATCAGGAAATTTGGATACCCG
37697 AT
1 AT
37699 TTGAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (21 bp):
ATCAGGAAATTTGGATACCCG
Found at i:39574 original size:21 final size:21
Alignment explanation
Indices: 39550--39622 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
39540 CACCAAAGTG
39550 CCACATAATTGTCCCGAAGGA
1 CCACATAATTGTCCCGAAGGA
*
39571 CCACATAGGTT-TGCACCGAAGTG-
1 CCACATA-ATTGT-C-CCGAAG-GA
*
39594 CCACAT-ATTAGTCTCGAAGGA
1 CCACATAATT-GTCCCGAAGGA
39615 CCACATAA
1 CCACATAA
39623 AACCCTCAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 15
0.69 0.05 0.25
Matches are distributed among these distances:
20 1 0.02
21 21 0.51
22 5 0.12
23 13 0.32
24 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (21 bp):
CCACATAATTGTCCCGAAGGA
Found at i:39597 original size:23 final size:21
Alignment explanation
Indices: 39535--39600 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
39525 ACAACTCGTA
*
39535 AATTGCACCAAAGTGCCACAT
1 AATTGCACCGAAGTGCCACAT
39556 AATTGTC-CCGAAG-GACCACAT
1 AATTG-CACCGAAGTG-CCACAT
*
39577 AGGTTTGCACCGAAGTGCCACAT
1 A--ATTGCACCGAAGTGCCACAT
39600 A
1 A
39601 TTAGTCTCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 1 0.03
21 17 0.46
22 2 0.05
23 16 0.43
24 1 0.03
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (21 bp):
AATTGCACCGAAGTGCCACAT
Found at i:39600 original size:44 final size:44
Alignment explanation
Indices: 39537--39621 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 44
39527 AACTCGTAAA
39537 TTGCACCAAAGTGCCACATAATT-GTCCCGAAGGACCACATAGGT
1 TTGCACCAAAGTGCCACAT-ATTAGTCCCGAAGGACCACATAGGT
* *
39581 TTGCACCGAAGTGCCACATATTAGTCTCGAAGGACCACATA
1 TTGCACCAAAGTGCCACATATTAGTCCCGAAGGACCACATA
39622 AAACCCTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 3 0.08
44 35 0.92
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (44 bp):
TTGCACCAAAGTGCCACATATTAGTCCCGAAGGACCACATAGGT
Found at i:46260 original size:21 final size:22
Alignment explanation
Indices: 46194--46293 Score: 88
Period size: 21 Copynumber: 4.7 Consensus size: 22
46184 AATTTGCACT
46194 GAAGTG-CCACATAATTGTCCC
1 GAAGTGACCACATAATTGTCCC
*
46215 GAAG-GACTACA-AAGGTT-TGCACC
1 GAAGTGACCACATAA--TTGT-C-CC
*
46238 GAAGTG-CCACATATTTGTCCC
1 GAAGTGACCACATAATTGTCCC
*
46259 GAA-TGACCACATAATAGTCCC
1 GAAGTGACCACATAATTGTCCC
46280 GAA-TGACCACATAA
1 GAAGTGACCACATAA
46294 AACCCTCGAC
Statistics
Matches: 65, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
20 5 0.08
21 41 0.63
22 6 0.09
23 11 0.17
24 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (22 bp):
GAAGTGACCACATAATTGTCCC
Found at i:46968 original size:20 final size:23
Alignment explanation
Indices: 46936--46995 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 23
46926 TACCATCCCC
**
46936 CTGGTATTAATACTACCC-TC-A
1 CTGGTATCGATACTACCCTTCAA
46957 CT-GTATCGATAC--CCTCTTCAA
1 CTGGTATCGATACTACC-CTTCAA
46978 CTGGTATCGATACTACCC
1 CTGGTATCGATACTACCC
46996 ATAAGAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 10 0.32
21 5 0.16
22 10 0.32
23 1 0.03
24 2 0.06
ACGTcount: A:0.25, C:0.32, G:0.12, T:0.32
Consensus pattern (23 bp):
CTGGTATCGATACTACCCTTCAA
Found at i:49049 original size:20 final size:20
Alignment explanation
Indices: 49021--49071 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
49011 CTGTTGGGGA
* *
49021 GTATTGATATTATACCCTTG
1 GTATCGATACTATACCCTTG
49041 GTATCGATACTATACCCTTG
1 GTATCGATACTATACCCTTG
49061 GTATCGATACT
1 GTATCGATACT
49072 CACATGAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (20 bp):
GTATCGATACTATACCCTTG
Found at i:49929 original size:15 final size:16
Alignment explanation
Indices: 49901--49930 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49891 AAGAGAAGAA
49901 GAGAAAAAGAAGAGTT
1 GAGAAAAAGAAGAGTT
49917 GAGAAAAAG-AGAGT
1 GAGAAAAAGAAGAGT
49931 GCCAGCCGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.00, G:0.33, T:0.10
Consensus pattern (16 bp):
GAGAAAAAGAAGAGTT
Found at i:52845 original size:11 final size:11
Alignment explanation
Indices: 52829--52872 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
52819 TGGGACAATG
52829 TCGAGCTTGAA
1 TCGAGCTTGAA
*
52840 TCGAGCTCAGAA
1 TCGAGCT-TGAA
* *
52852 TCTAGCTTCAA
1 TCGAGCTTGAA
52863 TCGAGCTTGA
1 TCGAGCTTGA
52873 GTCTCGAGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:53151 original size:16 final size:16
Alignment explanation
Indices: 53130--53160 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
53120 AAAAAAATTA
53130 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
53146 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
53161 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:54837 original size:23 final size:22
Alignment explanation
Indices: 54801--54861 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
54791 TAACTATGTA
* * *
54801 TTTATAACACATTTTCTTTCGTC
1 TTTATGACATATTTTCGTT-GTC
54824 TTTATGACATATTTTTCGTTGTC
1 TTTATGACATA-TTTTCGTTGTC
*
54847 TTTATGACATGTTTT
1 TTTATGACATATTTT
54862 TCTCTATCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 4 0.12
23 22 0.67
24 7 0.21
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (22 bp):
TTTATGACATATTTTCGTTGTC
Found at i:54862 original size:24 final size:24
Alignment explanation
Indices: 54812--54863 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
54802 TTATAACACA
*
54812 TTTTCTTTCGTCTTTATGACATAT
1 TTTTCGTTCGTCTTTATGACATAT
*
54836 TTTTCGTT-GTCTTTATGACATGT
1 TTTTCGTTCGTCTTTATGACATAT
54859 TTTTC
1 TTTTC
54864 TCTATCCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.13, C:0.15, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTTCGTTCGTCTTTATGACATAT
Found at i:62032 original size:2 final size:2
Alignment explanation
Indices: 62021--62056 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
62011 TTGAAACAAT
62021 TA TA -A TA TA TA TA TA T- TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62057 GTATGATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:62043 original size:13 final size:13
Alignment explanation
Indices: 62025--62049 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62015 AACAATTATA
62025 ATATATATATATT
1 ATATATATATATT
62038 ATATATATATAT
1 ATATATATATAT
62050 ATAATATGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATATATATATT
Found at i:62056 original size:13 final size:13
Alignment explanation
Indices: 62021--62056 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
62011 TTGAAACAAT
62021 TATAATATATATA
1 TATAATATATATA
62034 TATTATATATATATA
1 TA-TA-ATATATATA
62049 TATAATAT
1 TATAATAT
62057 GTATGATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 4 0.19
15 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATAATATATATA
Found at i:63613 original size:4 final size:4
Alignment explanation
Indices: 63604--63652 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
63594 TCACGGTCAA
* * *
63604 CGGT CGGT CGGT CAGT CGGGT CGGT CAGT CGGGT CGGT CGGT CAGT CGG
1 CGGT CGGT CGGT CGGT C-GGT CGGT CGGT C-GGT CGGT CGGT CGGT CGG
63653 GGTCAAACCG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
4 31 0.84
5 6 0.16
ACGTcount: A:0.06, C:0.24, G:0.47, T:0.22
Consensus pattern (4 bp):
CGGT
Found at i:63625 original size:13 final size:13
Alignment explanation
Indices: 63609--63642 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
63599 GTCAACGGTC
63609 GGTCGGTCAGTCG
1 GGTCGGTCAGTCG
63622 GGTCGGTCAGTCG
1 GGTCGGTCAGTCG
63635 GGTCGGTC
1 GGTCGGTC
63643 GGTCAGTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.06, C:0.24, G:0.47, T:0.24
Consensus pattern (13 bp):
GGTCGGTCAGTCG
Found at i:63625 original size:17 final size:17
Alignment explanation
Indices: 63605--63653 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
63595 CACGGTCAAC
63605 GGTCGGTCGGTCAGTC-
1 GGTCGGTCGGTCAGTCG
63621 -G--GGTCGGTCAGTCG
1 GGTCGGTCGGTCAGTCG
63635 GGTCGGTCGGTCAGTCG
1 GGTCGGTCGGTCAGTCG
63652 GG
1 GG
63654 GTCAAACCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 12 0.41
15 2 0.07
17 15 0.52
ACGTcount: A:0.06, C:0.22, G:0.49, T:0.22
Consensus pattern (17 bp):
GGTCGGTCGGTCAGTCG
Done.