Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006808.1 Hibiscus syriacus cultivar Beakdansim tig00017281_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: 94156
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1845 original size:14 final size:14
Alignment explanation
Indices: 1826--1861 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1816 CCTAATTAAT
1826 TTTATGTTAGTTCG
1 TTTATGTTAGTTCG
*
1840 TTTATGTTCGTTCG
1 TTTATGTTAGTTCG
*
1854 TTTGTGTT
1 TTTATGTT
1862 TGTTTATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.08, C:0.08, G:0.22, T:0.61
Consensus pattern (14 bp):
TTTATGTTAGTTCG
Found at i:9475 original size:69 final size:70
Alignment explanation
Indices: 9379--9532 Score: 168
Period size: 69 Copynumber: 2.2 Consensus size: 70
9369 AAACACTATG
* * * * * *
9379 TTCGGTTCAAACAGACAATAGTCGGACAAGGAAGCCGAAGA-CACCACAAACTGA-AAACAAAAC
1 TTCGGTCCAAACAAACAACAGTCGGACAAGGAAACCAAAGACCACCACAAAATGATAAACAAAAC
9442 CGGTA
66 CGGTA
*
9447 TTCGGTCCAGAACAAACAACAGTTGGACAAGGAAACCAAAGACGCACCACAAAATGATAAACGAA
1 TTCGGTCCA-AACAAACAACAGTCGGACAAGGAAACCAAAGAC-CACCACAAAATGATAAAC-AA
* * *
9512 ACCCGATT
63 AACCGGTA
*
9520 TTCGGTTCAAACA
1 TTCGGTCCAAACA
9533 GACGACGGTC
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
68 8 0.11
69 27 0.39
71 12 0.17
72 8 0.11
73 15 0.21
ACGTcount: A:0.44, C:0.24, G:0.19, T:0.14
Consensus pattern (70 bp):
TTCGGTCCAAACAAACAACAGTCGGACAAGGAAACCAAAGACCACCACAAAATGATAAACAAAAC
CGGTA
Found at i:19310 original size:22 final size:22
Alignment explanation
Indices: 19241--19348 Score: 117
Period size: 22 Copynumber: 4.9 Consensus size: 22
19231 TATTTTCTCT
19241 TATCAGTGCTAAGGCACTTTAG
1 TATCAGTGCTAAGGCACTTTAG
* * ** *
19263 TATCATTGCAAATCACACTTTCG
1 TATCAGTGCTAA-GGCACTTTAG
*
19286 TATCAGTGCTGAGGCACTTTAG
1 TATCAGTGCTAAGGCACTTTAG
* *
19308 TATTAGTGCTAAGGCATTTTAG
1 TATCAGTGCTAAGGCACTTTAG
* *
19330 TATTAGTACTAAGGCACTT
1 TATCAGTGCTAAGGCACTT
19349 CTGATATACA
Statistics
Matches: 69, Mismatches: 16, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
22 53 0.77
23 16 0.23
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (22 bp):
TATCAGTGCTAAGGCACTTTAG
Found at i:19897 original size:3 final size:3
Alignment explanation
Indices: 19884--19941 Score: 66
Period size: 3 Copynumber: 19.3 Consensus size: 3
19874 TCTACAAAAA
*
19884 ATT ATTT ATT ATT ATT ACT -TT ATT ATT ATT ATT A-T ATTT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
*
19929 ATT ATT TTT ATT A
1 ATT ATT ATT ATT A
19942 AAATATTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 3 0.06
3 39 0.83
4 5 0.11
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:21470 original size:30 final size:29
Alignment explanation
Indices: 21386--21637 Score: 176
Period size: 30 Copynumber: 8.6 Consensus size: 29
21376 TATTTTGTAA
* * * *
21386 TTACTGTTTAGCCCTTTTAGTTTCTGTTA
1 TTACTATTTAGCCCTTTAAGTTTCTATTT
* *
21415 ATA-TCATTTTAGACCC-TTAATTTTCTATTT
1 TTACT-A-TTTAG-CCCTTTAAGTTTCTATTT
*
21445 TTACTATTATAGCCCTTTAAGTTTCTTTTT
1 TTACTATT-TAGCCCTTTAAGTTTCTATTT
* * * *
21475 TTGCCATTTTAGTCCTTTAAATTT-TAGTTT
1 TTACTA-TTTAGCCCTTTAAGTTTCTA-TTT
21505 TTACTATTTAGCCCTTTAAGTTTCTATTT
1 TTACTATTTAGCCCTTTAAGTTTCTATTT
* * * *
21534 TT-GTAATTTTAGTCCTTTTACTTTCT-TCTT
1 TTACT-A-TTTAGCCCTTTAAGTTTCTAT-TT
* *
21564 TTATTATTTAGTCCTTTAAGTTTCTATTT
1 TTACTATTTAGCCCTTTAAGTTTCTATTT
* * *
21593 TT-CTGTTTAGCCTTTTAAATTTCTA-TT
1 TTACTATTTAGCCCTTTAAGTTTCTATTT
21620 TTAGCTATTTTAGCCCTT
1 TTA-CTA-TTTAGCCCTT
21638 CAAGCTTATT
Statistics
Matches: 174, Mismatches: 32, Indels: 33
0.73 0.13 0.14
Matches are distributed among these distances:
27 4 0.02
28 20 0.11
29 53 0.30
30 90 0.52
31 7 0.04
ACGTcount: A:0.19, C:0.16, G:0.08, T:0.57
Consensus pattern (29 bp):
TTACTATTTAGCCCTTTAAGTTTCTATTT
Found at i:21535 original size:59 final size:59
Alignment explanation
Indices: 21386--21637 Score: 248
Period size: 59 Copynumber: 4.3 Consensus size: 59
21376 TATTTTGTAA
* * * ** * * * *
21386 TTACTGTTTAGCCCTTTTAGTTTCTGTTAATATCATTTTAGACCCTTAATTTTCTATTT
1 TTACTATTTAGCCCTTTAAGTTTCTATTTTTGTCATTTTAGTCCTTTAAATTTCTATTT
* *
21445 TTACTATTATAGCCCTTTAAGTTTCTTTTTTTGCCATTTTAGTCCTTTAAATTT-TAGTTT
1 TTACTATT-TAGCCCTTTAAGTTTCTATTTTTGTCATTTTAGTCCTTTAAATTTCTA-TTT
* * *
21505 TTACTATTTAGCCCTTTAAGTTTCTATTTTTGTAATTTTAGTCCTTTTACTTTCT-TCTT
1 TTACTATTTAGCCCTTTAAGTTTCTATTTTTGTCATTTTAGTCCTTTAAATTTCTAT-TT
* *
21564 TTATTATTTAGTCCTTTAAGTTTCTA-TTTT-TC-TGTTTAG-CCTTTTAAATTTCTA-TT
1 TTACTATTTAGCCCTTTAAGTTTCTATTTTTGTCAT-TTTAGTCC-TTTAAATTTCTATTT
21620 TTAGCTATTTTAGCCCTT
1 TTA-CTA-TTTAGCCCTT
21638 CAAGCTTATT
Statistics
Matches: 162, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
56 8 0.05
57 17 0.10
58 14 0.09
59 75 0.46
60 48 0.30
ACGTcount: A:0.19, C:0.16, G:0.08, T:0.57
Consensus pattern (59 bp):
TTACTATTTAGCCCTTTAAGTTTCTATTTTTGTCATTTTAGTCCTTTAAATTTCTATTT
Found at i:23562 original size:51 final size:51
Alignment explanation
Indices: 23465--23562 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
23455 TAATATTGCA
* * * *
23465 TTTAAACTCTAACGAACCTGATTTATTAGAGATTGATGAGCTAATAAAACG
1 TTTAAACTCTAACAAACCTAATTTATCAGAGATTGATGAGCAAATAAAACG
* * *
23516 TTTAAACTCTAATAAACCTAATTTATCATAGATTGATGAGGAAATAA
1 TTTAAACTCTAACAAACCTAATTTATCAGAGATTGATGAGCAAATAA
23563 TGGATGGGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (51 bp):
TTTAAACTCTAACAAACCTAATTTATCAGAGATTGATGAGCAAATAAAACG
Found at i:32410 original size:21 final size:21
Alignment explanation
Indices: 32384--32425 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
32374 AGTTTATTTT
32384 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
32405 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
32426 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:32473 original size:33 final size:33
Alignment explanation
Indices: 32420--32517 Score: 148
Period size: 32 Copynumber: 3.0 Consensus size: 33
32410 TTTGTTTCAA
32420 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
32452 TTATCGAACTTGGAAGTTTTTAA-TATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
32484 TTATCAAACTTGGAA-TTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTT-TTTAAGTATTTGAAT
32517 T
1 T
32518 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
31 2 0.03
32 39 0.64
33 20 0.33
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:33789 original size:15 final size:17
Alignment explanation
Indices: 33763--33794 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
33753 TTCTATGGGA
33763 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
33779 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
33795 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:35921 original size:21 final size:21
Alignment explanation
Indices: 35897--35938 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
35887 AGTTTATTTT
35897 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
35918 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
35939 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:35986 original size:33 final size:33
Alignment explanation
Indices: 35933--36031 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
35923 TTTGTTTCAA
35933 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
35965 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
35998 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
36031 T
1 T
36032 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:37296 original size:15 final size:17
Alignment explanation
Indices: 37270--37301 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
37260 TTCTATGGGA
37270 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
37286 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
37302 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:38169 original size:29 final size:31
Alignment explanation
Indices: 38111--38169 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 31
38101 AACCCATAAA
* *
38111 TTTTCCAAAAATTTATGAATTGATCCCCAAC
1 TTTTCCAAAAATTTATGAATCGATCACCAAC
38142 TTTT-CAAAAA-TTATGAAATCG-TCACCAA
1 TTTTCCAAAAATTTATG-AATCGATCACCAA
38170 TTCTTCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 11 0.44
30 10 0.40
31 4 0.16
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (31 bp):
TTTTCCAAAAATTTATGAATCGATCACCAAC
Found at i:43802 original size:30 final size:30
Alignment explanation
Indices: 43768--43854 Score: 129
Period size: 30 Copynumber: 2.9 Consensus size: 30
43758 ATAGTGATGA
* *
43768 ACAGTATCATGAACAGTGCATCGATGCGCT
1 ACAGTAACGTGAACAGTGCATCGATGCGCT
* *
43798 ACAGTAACGTGAACAGTGTATAGATGCGCT
1 ACAGTAACGTGAACAGTGCATCGATGCGCT
*
43828 ACAGTAACGTGAACAATGCATCGATGC
1 ACAGTAACGTGAACAGTGCATCGATGC
43855 ATCAAAACAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (30 bp):
ACAGTAACGTGAACAGTGCATCGATGCGCT
Found at i:43919 original size:30 final size:30
Alignment explanation
Indices: 43878--43938 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
43868 ATTAATATTA
*
43878 TGCATCGATACGCTACAGTAACTGCTACAG
1 TGCATCAATACGCTACAGTAACTGCTACAG
*
43908 TGCATCAATACGCTACAGTAACTTCTACAG
1 TGCATCAATACGCTACAGTAACTGCTACAG
43938 T
1 T
43939 AACTTCCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (30 bp):
TGCATCAATACGCTACAGTAACTGCTACAG
Found at i:43937 original size:12 final size:12
Alignment explanation
Indices: 43920--43944 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43910 CATCAATACG
43920 CTACAGTAACTT
1 CTACAGTAACTT
43932 CTACAGTAACTT
1 CTACAGTAACTT
43944 C
1 C
43945 CTAAAATACA
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:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (12 bp):
CTACAGTAACTT
Found at i:44392 original size:46 final size:46
Alignment explanation
Indices: 44319--44490 Score: 210
Period size: 46 Copynumber: 3.8 Consensus size: 46
44309 TATAAAATCT
*
44319 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
44364 CTTACCATTTAAATTCCATAAGC-CGTAAGCTTATTTTACCAAAATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
44410 CATACCATTTAGATTCCATAAGCTCGTAAGCTTAATTTT-CCAATATA
1 CTTACCATTTA-ATTCCATAAGCTCGTAAGCTT-ATTTTACCAAAATA
** * * *
44457 CTTGTCA-TT-ATTTCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
44491 GCATGGTTAC
Statistics
Matches: 113, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
43 4 0.04
44 18 0.16
45 11 0.10
46 45 0.40
47 30 0.27
48 5 0.04
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.38
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:44748 original size:47 final size:47
Alignment explanation
Indices: 44679--44785 Score: 205
Period size: 47 Copynumber: 2.3 Consensus size: 47
44669 TAAGCTTATG
*
44679 CTATAGTGCTAATCCGGACATAAACCTGCACTTAGTGTCCTTACACA
1 CTATAGTGCTAATCCGGACATAAACATGCACTTAGTGTCCTTACACA
44726 CTATAGTGCTAATCCGGACATAAACATGCACTTAGTGTCCTTACACA
1 CTATAGTGCTAATCCGGACATAAACATGCACTTAGTGTCCTTACACA
44773 CTATAGTGCTAAT
1 CTATAGTGCTAAT
44786 ATAAACCTAC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (47 bp):
CTATAGTGCTAATCCGGACATAAACATGCACTTAGTGTCCTTACACA
Found at i:49250 original size:26 final size:26
Alignment explanation
Indices: 49214--49266 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
49204 TTTGTTTGTC
*
49214 TCTTAATAGAATCATTTAACGTTGAA
1 TCTTAATAGAATCATTCAACGTTGAA
49240 TCTTAATAGAATCATTCAACGTTGAA
1 TCTTAATAGAATCATTCAACGTTGAA
49266 T
1 T
49267 GTTGAACCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (26 bp):
TCTTAATAGAATCATTCAACGTTGAA
Found at i:54603 original size:14 final size:16
Alignment explanation
Indices: 54572--54603 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54562 TATAACATAG
54572 TAATAAACAATGATAT
1 TAATAAACAATGATAT
54588 TAATAAA-AAT-ATAT
1 TAATAAACAATGATAT
54602 TA
1 TA
54604 TTTTGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (16 bp):
TAATAAACAATGATAT
Found at i:58915 original size:36 final size:36
Alignment explanation
Indices: 58846--58918 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
58836 TCATGTTACA
* * * *
58846 AACCAAACAGAAGTAGCAAATAGTTGCAATGGCCTT
1 AACCAAACAAAAATAGCAAAGAGTTACAATGGCCTT
* *
58882 AACCAAACAAAAATAGCAAAGAGTTATAGTGGCCTT
1 AACCAAACAAAAATAGCAAAGAGTTACAATGGCCTT
58918 A
1 A
58919 CATTAGGGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.19
Consensus pattern (36 bp):
AACCAAACAAAAATAGCAAAGAGTTACAATGGCCTT
Found at i:60407 original size:30 final size:30
Alignment explanation
Indices: 60358--60418 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
60348 CTAAATTCAG
*
60358 AAAACAAATAAACGTGACAAT-ACCCTAGCT
1 AAAACAAATAAACGAGACAATAACCC-AGCT
60388 AAAACAAAT-AACTGAGACAATAACCCAGCT
1 AAAACAAATAAAC-GAGACAATAACCCAGCT
60418 A
1 A
60419 TAACTCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 3 0.11
30 21 0.75
31 4 0.14
ACGTcount: A:0.52, C:0.23, G:0.10, T:0.15
Consensus pattern (30 bp):
AAAACAAATAAACGAGACAATAACCCAGCT
Found at i:64642 original size:21 final size:21
Alignment explanation
Indices: 64614--64711 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 21
64604 TCTTGTCTCC
64614 CATGCTTTTCATGCCGCTTCT
1 CATGCTTTTCATGCCGCTTCT
* *
64635 CATCCTTTTCATGTCGCTTCT
1 CATGCTTTTCATGCCGCTTCT
* * *
64656 CGTGCTTTTCGTGCTGCTTCT
1 CATGCTTTTCATGCCGCTTCT
* *
64677 CGTGCTTTTCGTGCCGCTTCT
1 CATGCTTTTCATGCCGCTTCT
64698 CATG-TTTATCATGC
1 CATGCTTT-TCATGC
64712 TTTTCCCGTT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
20 3 0.05
21 63 0.95
ACGTcount: A:0.07, C:0.31, G:0.17, T:0.45
Consensus pattern (21 bp):
CATGCTTTTCATGCCGCTTCT
Found at i:68486 original size:23 final size:20
Alignment explanation
Indices: 68432--68486 Score: 56
Period size: 24 Copynumber: 2.5 Consensus size: 20
68422 AAAATTTTAT
*
68432 AAAATTTTAATAAAGTAAAA
1 AAAATTTTAATAAAATAAAA
68452 ATAAATTATTAATTAAAAATAAAA
1 A-AAATT-TTAA-T-AAAATAAAA
68476 AAAATATTTAA
1 AAAAT-TTTAA
68487 AATACATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 1 0.03
21 5 0.17
22 4 0.14
23 9 0.31
24 10 0.34
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAATTTTAATAAAATAAAA
Found at i:70722 original size:24 final size:24
Alignment explanation
Indices: 70693--70744 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
70683 CTTTGGTAAG
*
70693 TTCTCCCTTAGATCCTTCAGTCAC
1 TTCTCCCTTAGATCCTTAAGTCAC
70717 TTCTCCCTTAGATCCTTAAGTCAC
1 TTCTCCCTTAGATCCTTAAGTCAC
70741 TTCT
1 TTCT
70745 TCAATTCCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.17, C:0.35, G:0.08, T:0.40
Consensus pattern (24 bp):
TTCTCCCTTAGATCCTTAAGTCAC
Found at i:71376 original size:22 final size:22
Alignment explanation
Indices: 71350--71392 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
71340 CCTAGTTTTT
71350 CCGGGCTAAACTAGAACCTTTA
1 CCGGGCTAAACTAGAACCTTTA
71372 CCGGGCTAAACTAGAACCTTT
1 CCGGGCTAAACTAGAACCTTT
71393 CCCTAGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (22 bp):
CCGGGCTAAACTAGAACCTTTA
Found at i:72541 original size:21 final size:20
Alignment explanation
Indices: 72512--72627 Score: 88
Period size: 21 Copynumber: 5.7 Consensus size: 20
72502 ATTCTGACTA
*
72512 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTT-CCGAAT
* *
72533 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGA-TTTCCGAAT
* * *
72554 TCGCATTGTGATTTACGTAT
1 TCGCATTGCGATTTCCGAAT
* * *
72574 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTCCGAAT
* * *
72594 TCACGTTGCGATTTTCCTAAT
1 TCGCATTGCGA-TTTCCGAAT
*
72615 TCGCAATGCGATT
1 TCGCATTGCGATT
72628 ACGTAAATCG
Statistics
Matches: 77, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
20 36 0.47
21 38 0.49
22 3 0.04
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTCCGAAT
Found at i:72577 original size:20 final size:20
Alignment explanation
Indices: 72512--72632 Score: 91
Period size: 20 Copynumber: 6.0 Consensus size: 20
72502 ATTCTGACTA
* **
72512 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTT-ACGTAT
* * *
72533 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
*
72554 TCGCATTGTGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
*
72574 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * * *
72594 TCACGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
*
72615 TCGCAATGCGA-TTACGTA
1 TCGCATTGCGATTTACGTA
72633 AATCGCAATG
Statistics
Matches: 80, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
19 1 0.01
20 40 0.50
21 39 0.49
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:72645 original size:61 final size:61
Alignment explanation
Indices: 72531--72645 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 61
72521 GATTTCCCAA
* * * * **
72531 ATTCGCGTTGCGATTTTCCTAATTCGCATTGTGATTTACGTATTCGCGTTGCGATTTACGT
1 ATTCACGTTGCGATTTTCCTAATTCGCAATGCGATTTACGTAATCGCAATGCGATTTACGT
72592 ATTCACGTTGCGATTTTCCTAATTCGCAATGCGA-TTACGTAAATCGCAATGCGA
1 ATTCACGTTGCGATTTTCCTAATTCGCAATGCGATTTACGT-AATCGCAATGCGA
72646 ATTAGGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 6 0.13
61 41 0.87
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (61 bp):
ATTCACGTTGCGATTTTCCTAATTCGCAATGCGATTTACGTAATCGCAATGCGATTTACGT
Found at i:72656 original size:21 final size:21
Alignment explanation
Indices: 72615--72688 Score: 116
Period size: 20 Copynumber: 3.6 Consensus size: 21
72605 TTTTCCTAAT
72615 TCGCAATGCG-ATTACGTAAA
1 TCGCAATGCGAATTACGTAAA
* *
72635 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGTAAA
72656 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGTAAA
72676 TCGCAATGCGAAT
1 TCGCAATGCGAAT
72689 CTGACTATTG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
20 28 0.58
21 20 0.42
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTACGTAAA
Found at i:73278 original size:21 final size:20
Alignment explanation
Indices: 73217--73292 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
73207 TTCTAAACTT
73217 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGA-GAAAATG
73237 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGA-GAAAATG
**
73257 ACTATCGCAACGAGATAAATG
1 AAAATCGCAACGAGA-AAATG
73278 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
73293 GAATCGCAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
20 30 0.61
21 19 0.39
ACGTcount: A:0.51, C:0.18, G:0.17, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACGAGAAAATG
Found at i:73385 original size:20 final size:20
Alignment explanation
Indices: 73320--73408 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
73310 CAAAATCGCA
73320 TTGCGATTTTCATTT-CACG
1 TTGCGATTTTCATTTCCACG
*
73339 TTGCGA--TTC---T-CTCG
1 TTGCGATTTTCATTTCCACG
**
73353 TTGCGATAGTCATTTCCACG
1 TTGCGATTTTCATTTCCACG
*
73373 TTGCGATTTTCA-TTCTCTCG
1 TTGCGATTTTCATTTC-CACG
73393 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
73409 AACCAAAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 10 0.18
20 28 0.50
21 3 0.05
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTCATTTCCACG
Found at i:73971 original size:14 final size:14
Alignment explanation
Indices: 73949--73987 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
73939 TTTATTGTTT
73949 AATTGATTTGTAAA
1 AATTGATTTGTAAA
73963 AGA-TGATTTGTAAA
1 A-ATTGATTTGTAAA
73977 AATTGATTTGT
1 AATTGATTTGT
73988 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:74139 original size:33 final size:33
Alignment explanation
Indices: 74094--74173 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
74084 AAAAATGACT
* ** * *
74094 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCACAACGACAAA
74127 ATCGCAACGCGAAATGAAAATCACAACGACAAA
1 ATCGCAACGCGAAATGAAAATCACAACGACAAA
74160 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
74174 CTAAATTCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCACAACGACAAA
Found at i:74201 original size:19 final size:19
Alignment explanation
Indices: 74179--74263 Score: 72
Period size: 19 Copynumber: 4.7 Consensus size: 19
74169 CGAAACTAAA
74179 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
74198 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
74213 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
74231 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
74250 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
74264 AGACATTAAG
Statistics
Matches: 50, Mismatches: 10, Indels: 11
0.70 0.14 0.15
Matches are distributed among these distances:
14 8 0.16
16 3 0.06
17 3 0.06
19 26 0.52
20 10 0.20
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:74262 original size:20 final size:20
Alignment explanation
Indices: 74216--74309 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
74206 GCGATTCCCT
**
74216 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
74235 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
74255 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
74274 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
74296 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
74310 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:76740 original size:24 final size:24
Alignment explanation
Indices: 76713--76771 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
76703 CTGTTTCATC
76713 ATCAAAATTCGGGTATTGACCAAG
1 ATCAAAATTCGGGTATTGACCAAG
* * *
76737 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATTCGGGTATTGACCAAG
*
76761 ATCAAATTTCG
1 ATCAAAATTCG
76772 AATACTGACT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (24 bp):
ATCAAAATTCGGGTATTGACCAAG
Found at i:77735 original size:21 final size:21
Alignment explanation
Indices: 77629--77735 Score: 121
Period size: 20 Copynumber: 5.2 Consensus size: 21
77619 AGAATCTCGT
*
77629 TGCGATTTAC-TAAATCGCAA
1 TGCGAATTACGTAAATCGCAA
77649 TGCG-ATTACGTAAATCGCAA
1 TGCGAATTACGTAAATCGCAA
77669 TGCG-ATTACGTAAATCGCAA
1 TGCGAATTACGTAAATCGCAA
* * *
77689 TGCAAATTAGGAAAATCGCAA
1 TGCGAATTACGTAAATCGCAA
* ** *
77710 AGCGAATTTGGGAAATCGCAA
1 TGCGAATTACGTAAATCGCAA
77731 TGCGA
1 TGCGA
77736 TAGTCAGAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
19 4 0.05
20 37 0.49
21 35 0.46
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.23
Consensus pattern (21 bp):
TGCGAATTACGTAAATCGCAA
Found at i:77764 original size:62 final size:60
Alignment explanation
Indices: 77609--77764 Score: 145
Period size: 62 Copynumber: 2.5 Consensus size: 60
77599 AATTCAGTAT
* * *** * *
77609 TGCGATAGTCAGAATCTCGTTGCGATTTACTAAATCGCAATGCGATTACGTAAATCGCAA
1 TGCGATAGTCAGAATCGCGTTGCGAATTGGAAAATCGCAAAGCGATTACGGAAATCGCAA
** * **
77669 TGCGATTACGT-A-AATCGCAATGCAAATTAGGAAAATCGCAAAGCGAATTTGGGAAATCGCAA
1 TGCGA-TA-GTCAGAATCGCGTTGCGAATT-GGAAAATCGCAAAGCG-ATTACGGAAATCGCAA
77731 TGCGATAGTCAGAATCGCGTTGCGAATCTGGAAA
1 TGCGATAGTCAGAATCGCGTTGCGAAT-TGGAAA
77765 CTGATTTGCG
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
60 18 0.24
61 18 0.24
62 37 0.50
63 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (60 bp):
TGCGATAGTCAGAATCGCGTTGCGAATTGGAAAATCGCAAAGCGATTACGGAAATCGCAA
Found at i:78788 original size:22 final size:22
Alignment explanation
Indices: 78740--78788 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
78730 TTTTAAATCA
*
78740 AAATTTTGTTTTTCAAAACTAT
1 AAATTTTATTTTTCAAAACTAT
* * *
78762 CAATTTTATTTTTGAAAACTCT
1 AAATTTTATTTTTCAAAACTAT
78784 AAATT
1 AAATT
78789 CTTTTTCAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (22 bp):
AAATTTTATTTTTCAAAACTAT
Found at i:81245 original size:14 final size:16
Alignment explanation
Indices: 81212--81248 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
81202 GAAACTCCTC
81212 TTTTCTTTCTCTCAAT
1 TTTTCTTTCTCTCAAT
81228 TTTTCTTTCTC-CAAT
1 TTTTCTTTCTCTCAAT
81243 TTTTCT
1 TTTTCT
81249 CAATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.11, C:0.24, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTCTTTCTCTCAAT
Found at i:85133 original size:24 final size:24
Alignment explanation
Indices: 85043--85133 Score: 132
Period size: 23 Copynumber: 3.9 Consensus size: 24
85033 TATTATATGA
*
85043 CACTACGGTGC-ATTTCTACGCGG
1 CACTTCGGTGCAATTTCTACGCGG
85066 CACTTCGGTGC-ATTTCTACGCGG
1 CACTTCGGTGCAATTTCTACGCGG
*
85089 CACTTCGGTGCAAATTCTACGCGG
1 CACTTCGGTGCAATTTCTACGCGG
* *
85113 CACTTCGGTACAATTTATACG
1 CACTTCGGTGCAATTTCTACG
85134 AGCTGTGGTG
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
23 33 0.53
24 29 0.47
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.29
Consensus pattern (24 bp):
CACTTCGGTGCAATTTCTACGCGG
Found at i:85782 original size:21 final size:21
Alignment explanation
Indices: 85752--85791 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
85742 AGCAGTACTG
*
85752 TAGCATTGCATCGATGCACTA
1 TAGCAATGCATCGATGCACTA
85773 TAGCAATGCATCGATGCAC
1 TAGCAATGCATCGATGCAC
85792 AATTTTGCTT
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:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGCAATGCATCGATGCACTA
Found at i:90489 original size:90 final size:90
Alignment explanation
Indices: 90333--90510 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
90323 CCTAACACAC
* *
90333 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGCTTTCATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTCATTATTTCAAATTAATTAAATATAT
* *
90398 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* * *
90423 CCTTTTATATCCAAGTTACCCTAATCATATTATGGATTTTATTATTTCAAATTAATTAAATATAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTCATTATTTCAAATTAATTAAATATAT
90488 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
90511 TTCAGGATTA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTCATTATTTCAAATTAATTAAATATAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:90490 original size:22 final size:23
Alignment explanation
Indices: 90465--90535 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 23
90455 TGGATTTTAT
90465 TATTTCAAATTAATT-AAATATA
1 TATTTCAAATTAATTAAAATATA
*
90487 TATTT--AATTAATTGAAAT-TA
1 TATTTCAAATTAATTAAAATATA
* *
90507 AATATTCAGGATT-ATTAAAATATA
1 TAT-TTCA-AATTAATTAAAATATA
90531 TATTT
1 TATTT
90536 AATTAGCTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
20 12 0.31
21 6 0.15
22 5 0.13
23 9 0.23
24 7 0.18
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (23 bp):
TATTTCAAATTAATTAAAATATA
Found at i:90497 original size:20 final size:21
Alignment explanation
Indices: 90472--90540 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
90462 TATTATTTCA
90472 AATTAATT-AAATATATATTT
1 AATTAATTAAAATATATATTT
* * *
90492 AATTAATTGAAATTAAATATTC
1 AATTAATT-AAAATATATATTT
90514 AGGATT-ATTAAAATATATATTT
1 A--ATTAATTAAAATATATATTT
90536 AATTA
1 AATTA
90541 GCTCCAGATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
20 11 0.29
22 21 0.55
23 3 0.08
24 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (21 bp):
AATTAATTAAAATATATATTT
Done.