Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006675.1 Hibiscus syriacus cultivar Beakdansim tig00016544_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: 123304
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1745 original size:12 final size:12
Alignment explanation
Indices: 1728--1757 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1718 CTACTCCATT
1728 TGCGGTAATGCG
1 TGCGGTAATGCG
*
1740 TGCGGTAATTCG
1 TGCGGTAATGCG
1752 TGCGGT
1 TGCGGT
1758 TCACGTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.17, G:0.40, T:0.30
Consensus pattern (12 bp):
TGCGGTAATGCG
Found at i:11988 original size:2 final size:2
Alignment explanation
Indices: 11981--12025 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
11971 GCCAATTGAT
11981 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12023 TA T
1 TA T
12026 CTTAAGCTGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12565 original size:18 final size:18
Alignment explanation
Indices: 12542--12587 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
12532 AGGAATTTGA
12542 TCCTCTGGCT-GTGCTTGT
1 TCCTCT-GCTCGTGCTTGT
12560 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
12578 TCCTCGTGCT
1 TCCTC-TGCT
12588 GTTCTGGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.00, C:0.33, G:0.24, T:0.43
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:12597 original size:18 final size:19
Alignment explanation
Indices: 12552--12602 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
12542 TCCTCTGGCT
*
12552 GTGCTTGTTCCTC-TGCTC
1 GTGCTGGTTCCTCGTGCTC
*
12570 GTGCTTGTTCCTCGTGCT-
1 GTGCTGGTTCCTCGTGCTC
* *
12588 GTTCTGGTTCATCGT
1 GTGCTGGTTCCTCGT
12603 CGGAGTCGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.02, C:0.27, G:0.25, T:0.45
Consensus pattern (19 bp):
GTGCTGGTTCCTCGTGCTC
Found at i:14133 original size:22 final size:21
Alignment explanation
Indices: 14108--14167 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 21
14098 GGGGTATTGA
*
14108 TTCCCCTACAGAGGGGAATCGG
1 TTCCCCTTCA-AGGGGAATCGG
14130 TTCCCCTTCAAAGGGGGAATCGG
1 TTCCCCTTC-AA-GGGGAATCGG
14153 TTCCCCTTCAAGGGG
1 TTCCCCTTCAAGGGG
14168 GTATCGATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
21 4 0.11
22 11 0.31
23 20 0.57
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.22
Consensus pattern (21 bp):
TTCCCCTTCAAGGGGAATCGG
Found at i:14168 original size:22 final size:23
Alignment explanation
Indices: 14120--14179 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
14110 CCCCTACAGA
14120 GGGGAATCGGTTCCCCTTCAAAG
1 GGGGAATCGGTTCCCCTTCAAAG
14143 GGGGAATCGGTTCCCCTTC-AAG
1 GGGGAATCGGTTCCCCTTCAAAG
* *
14165 GGGGTATCGATTCCC
1 GGGGAATCGGTTCCC
14180 TTTGCACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (23 bp):
GGGGAATCGGTTCCCCTTCAAAG
Found at i:22039 original size:19 final size:18
Alignment explanation
Indices: 21986--22041 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
21976 CCAAGTTATT
*
21986 TCTCTTAAATTCACATTAA
1 TCTCTTAAATTCTCA-TAA
* *
22005 CCTCTGTAAGTT-TCATAGA
1 TCTCT-TAAATTCTCATA-A
22024 TCTCTTAAATTCTCATAA
1 TCTCTTAAATTCTCATAA
22042 ATTCCCTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
18 8 0.28
19 16 0.55
20 5 0.17
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.41
Consensus pattern (18 bp):
TCTCTTAAATTCTCATAA
Found at i:29008 original size:229 final size:228
Alignment explanation
Indices: 28566--29106 Score: 644
Period size: 229 Copynumber: 2.3 Consensus size: 228
28556 TTCATGGATA
*
28566 CAACCCATTTTATTAATAAAAATATTAACATTCCATATCGCAACCTATTTATTATTGAACCATGA
1 CAACCCATTTTATTAATAAAAATATTAACATTCCATATCGCAA-CTATTTATTAGTGAACCATGA
* * * * *
28631 CATTGTTGGACAG-AACTCATTTTATTAATAAAAATATTAACACTCTAGATCGCAACTTATTTAT
65 CATTCTTGGGC-GCAACCCATTTTATTAATAAAAATATTAACACTCTAGACCGAAACTTATTTAT
* * * * **
28695 TAGTGAACCATGACATTCTTGGATCTAACCCATTTTATTAATAAAAATATTAATATTCTAGATTG
129 GAGTGAACCATGACATTCTTGGAGCCAACCCATTTTATTAATAAAAATATTAAAATTCTAGACCG
* * * *
28760 TAATCTATTTATTAGTGAACCATGACATTATTGGG
194 CAAACTATTTATGAGTGAACCAGGACATTATTGGG
** * * * *
28795 -TGCTCATTTTAATTAATAAAAATATTAACATTCCAGATAGCAACTTATTTCTTAGTGAACCATG
1 CAACCCATTTT-ATTAATAAAAATATTAACATTCCATATCGCAAC-TATTTATTAGTGAACCATG
* *
28859 ACATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACA-TTTCATACCGTAAAC-TATTT
64 ACATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACACTCT-AGACCG-AAACTTATTT
* * *
28922 CTGAGTGAACCATGATATTCTTGG-GCGCAACCCATTTTATTAATAAAAATATTAAAATT-TCAT
127 ATGAGTGAACCATGACATTCTTGGAGC-CAACCCATTTTATTAATAAAAATATTAAAATTCT-AG
* *
28985 ACCGCAAACTATTTCTGAGTGAACCAGGACATTCTTGGG
190 ACCGCAAACTATTTATGAGTGAACCAGGACATTATTGGG
*
29024 CCCAACCCATTTTATTAATAAAAAATATTAACATTCCATATCGCAAACTATTTTTTAGTGAACCA
1 --CAACCCATTTTATTAAT-AAAAATATTAACATTCCATATCGC-AACTATTTATTAGTGAACCA
* *
29089 TGACATTTTTAGGCGCAA
62 TGACATTCTTGGGCGCAA
29107 TCGTATTTCT
Statistics
Matches: 263, Mismatches: 37, Indels: 21
0.82 0.12 0.07
Matches are distributed among these distances:
228 13 0.05
229 177 0.67
230 3 0.01
231 6 0.02
232 61 0.23
233 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (228 bp):
CAACCCATTTTATTAATAAAAATATTAACATTCCATATCGCAACTATTTATTAGTGAACCATGAC
ATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACACTCTAGACCGAAACTTATTTATGA
GTGAACCATGACATTCTTGGAGCCAACCCATTTTATTAATAAAAATATTAAAATTCTAGACCGCA
AACTATTTATGAGTGAACCAGGACATTATTGGG
Found at i:29122 original size:77 final size:77
Alignment explanation
Indices: 28536--29106 Score: 661
Period size: 77 Copynumber: 7.4 Consensus size: 77
28526 CGCAACCCAT
* ***
28536 TTTATTAGTGAACCATGACATTCATGGATACAACCCATTTTATTAATAAAAATATTAACATTCCA
1 TTTATTAGTGAACCATGACATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCA
*
28601 TATCGCAACCTA
66 TATCGCAAACTA
* * * * * *
28613 TTTATTATTGAACCATGACATTGTTGGACAG-AACTCATTTTATTAATAAAAATATTAACACTCT
1 TTTATTAGTGAACCATGACATTCTTGGGC-GCAACCCATTTTATTAATAAAAATATTAACATTCC
*
28677 AGATCGC-AACTTA
65 ATATCGCAAAC-TA
* * * *
28690 TTTATTAGTGAACCATGACATTCTTGGATC-TAACCCATTTTATTAATAAAAATATTAATATTCT
1 TTTATTAGTGAACCATGACATTCTTGG-GCGCAACCCATTTTATTAATAAAAATATTAACATTCC
* * * *
28754 AGATTGTAATCTA
65 ATATCGCAAACTA
* * *
28767 TTTATTAGTGAACCATGACATTATTGGGTG---CTCATTTTAATTAATAAAAATATTAACATTCC
1 TTTATTAGTGAACCATGACATTCTTGGGCGCAACCCATTTT-ATTAATAAAAATATTAACATTCC
* *
28829 AGATAGC-AACTTA
65 ATATCGCAAAC-TA
* *
28842 TTTCTTAGTGAACCATGACATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACATTTCA
1 TTTATTAGTGAACCATGACATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCA
* *
28907 TACCGTAAACTA
66 TATCGCAAACTA
* * * * *
28919 TTTCTGAGTGAACCATGATATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAAAATTTCA
1 TTTATTAGTGAACCATGACATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCA
*
28984 TACCGCAAACTA
66 TATCGCAAACTA
* * * *
28996 TTTCTGAGTGAACCAGGACATTCTTGGGCCCAACCCATTTTATTAATAAAAAATATTAACATTCC
1 TTTATTAGTGAACCATGACATTCTTGGGCGCAACCCATTTTATTAAT-AAAAATATTAACATTCC
29061 ATATCGCAAACTA
65 ATATCGCAAACTA
* * *
29074 TTTTTTAGTGAACCATGACATTTTTAGGCGCAA
1 TTTATTAGTGAACCATGACATTCTTGGGCGCAA
29107 TCGTATTTCT
Statistics
Matches: 428, Mismatches: 53, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
74 9 0.02
75 55 0.13
76 2 0.00
77 295 0.69
78 67 0.16
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (77 bp):
TTTATTAGTGAACCATGACATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCA
TATCGCAAACTA
Found at i:29276 original size:15 final size:15
Alignment explanation
Indices: 29234--29276 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
29224 GTTAATAATA
29234 TTTATAACATTTATTT
1 TTTATAAC-TTTATTT
29250 TTTATAAC-TTATTT
1 TTTATAACTTTATTT
* *
29264 TTTTTACCTTTAT
1 TTTATAACTTTAT
29277 AACATTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.50
15 4 0.17
16 8 0.33
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTATAACTTTATTT
Found at i:30790 original size:34 final size:34
Alignment explanation
Indices: 30751--30924 Score: 109
Period size: 34 Copynumber: 5.3 Consensus size: 34
30741 ATCCAACCAG
*
30751 ATATCTTTTAATATTCAAATTTAAATAGATAATA
1 ATATCTTTTAATATTCAAATTTAAAAAGATAATA
* *
30785 ATATCTTTTAAT-TTGAAATATTCAAAAGATAA-A
1 ATATCTTTTAATATTCAAAT-TTAAAAAGATAATA
** * * *
30818 ACT-TCTTTTACCATTTAAACTTAAATAGAT-AT-
1 A-TATCTTTTAATATTCAAATTTAAAAAGATAATA
* *
30850 -TA--TTTTAAT-TTGAAATATACAAAAG-TATATA
1 ATATCTTTTAATATTCAAATTTA-AAAAGATA-ATA
* *
30881 ATTATC-TTTAATATTCAAAGTTAAAAAGATAACAA
1 A-TATCTTTTAATATTCAAATTTAAAAAGATAA-TA
30916 ATATCTTTT
1 ATATCTTTT
30925 TAAATTGACT
Statistics
Matches: 104, Mismatches: 19, Indels: 33
0.67 0.12 0.21
Matches are distributed among these distances:
28 8 0.08
29 9 0.09
30 3 0.03
32 1 0.01
33 25 0.24
34 44 0.42
35 14 0.13
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (34 bp):
ATATCTTTTAATATTCAAATTTAAAAAGATAATA
Found at i:34467 original size:34 final size:34
Alignment explanation
Indices: 34413--34477 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
34403 ATCCAACCAG
*
34413 ATATCTTTTAATATTCAATATT-AAACAGATAATA
1 ATATCTTTTAATATTAAATATTCAAA-AGATAATA
34447 ATATCTTTTAAT-TTGAAATATTCAAAAGATA
1 ATATCTTTTAATATT-AAATATTCAAAAGATA
34478 GAACTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 2 0.07
34 23 0.82
35 3 0.11
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.42
Consensus pattern (34 bp):
ATATCTTTTAATATTAAATATTCAAAAGATAATA
Found at i:35798 original size:9 final size:9
Alignment explanation
Indices: 35784--35896 Score: 82
Period size: 10 Copynumber: 11.8 Consensus size: 9
35774 GGCTGCTGGA
35784 AACCGGTTT
1 AACCGGTTT
35793 AACCGGTTTT
1 AACCGG-TTT
35803 CAACCGGTTCT
1 -AACCGGTT-T
*
35814 GACCGGTTT
1 AACCGGTTT
*
35823 GACCGGTTT
1 AACCGGTTT
*
35832 CAACCGGTTCG
1 -AACCGGTT-T
35843 AACCGGTTT
1 AACCGGTTT
* *
35852 GACCGGTCTG
1 AACCGGT-TT
*
35862 AACCAGTTT
1 AACCGGTTT
* *
35871 GACCGGTCTG
1 AACCGGT-TT
35881 AACCGGTTT
1 AACCGGTTT
*
35890 GACCGGT
1 AACCGGT
35897 CTGACCCGAC
Statistics
Matches: 82, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
9 35 0.43
10 40 0.49
11 7 0.09
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (9 bp):
AACCGGTTT
Found at i:35829 original size:19 final size:19
Alignment explanation
Indices: 35804--35900 Score: 126
Period size: 19 Copynumber: 5.1 Consensus size: 19
35794 ACCGGTTTTC
*
35804 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
*
35824 -ACCGGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
35843 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
35862 AACCAGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
35881 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
35900 A
1 A
35901 CCCGACCCGA
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
18 2 0.03
19 58 0.84
20 9 0.13
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:35847 original size:29 final size:28
Alignment explanation
Indices: 35785--35889 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 28
35775 GCTGCTGGAA
*
35785 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
35815 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * * *
35843 AACCGGTTTGACCGGTCTGAACCAGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
*
35872 ACCGGTCTGAACCGGTTT
1 ACCGGTTTG-ACCGGTTT
35890 GACCGGTCTG
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
28 9 0.14
29 44 0.67
30 13 0.20
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:35909 original size:5 final size:5
Alignment explanation
Indices: 35899--35956 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
35889 TGACCGGTCT
* *
35899 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
35948 GACCC GACC
1 GACCC GACC
35957 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:35913 original size:38 final size:38
Alignment explanation
Indices: 35834--35913 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 38
35824 ACCGGTTTCA
***
35834 ACCGGTTCGAACCGGTTTGACCGGTCTGAACCAGTTTG
1 ACCGGTTCGAACCGGTTTGACCGGTCTGAACCAGCCCG
*
35872 ACCGG-TCTGAACCGGTTTGACCGGTCTG-ACCCGACCCG
1 ACCGGTTC-GAACCGGTTTGACCGGTCTGAACCAG-CCCG
35910 ACCG
1 ACCG
35914 TTGACCCGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 6 0.17
38 30 0.83
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (38 bp):
ACCGGTTCGAACCGGTTTGACCGGTCTGAACCAGCCCG
Found at i:35925 original size:22 final size:22
Alignment explanation
Indices: 35899--35963 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
35889 TGACCGGTCT
35899 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
35921 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
35943 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
35964 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:43141 original size:9 final size:9
Alignment explanation
Indices: 43127--43239 Score: 91
Period size: 10 Copynumber: 11.8 Consensus size: 9
43117 GGCTGCTGGA
43127 AACCGGTTT
1 AACCGGTTT
43136 AACCGGTTTT
1 AACCGG-TTT
43146 CAACCGGTTCT
1 -AACCGGTT-T
*
43157 GACCGGTTT
1 AACCGGTTT
*
43166 GACCGGTTT
1 AACCGGTTT
*
43175 CAACCGGTTCG
1 -AACCGGTT-T
43186 AACCGGTTT
1 AACCGGTTT
* *
43195 GACCGGTCTG
1 AACCGGT-TT
43205 AACCGGTTT
1 AACCGGTTT
* *
43214 GACCGGTCTG
1 AACCGGT-TT
43224 AACCGGTTT
1 AACCGGTTT
*
43233 GACCGGT
1 AACCGGT
43240 CTGACCCGAC
Statistics
Matches: 84, Mismatches: 13, Indels: 14
0.76 0.12 0.13
Matches are distributed among these distances:
9 36 0.43
10 41 0.49
11 7 0.08
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (9 bp):
AACCGGTTT
Found at i:43172 original size:19 final size:19
Alignment explanation
Indices: 43147--43243 Score: 135
Period size: 19 Copynumber: 5.1 Consensus size: 19
43137 ACCGGTTTTC
*
43147 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
*
43167 -ACCGGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
43186 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
43205 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
43224 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
43243 A
1 A
43244 CCCGACCCGA
Statistics
Matches: 71, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
18 2 0.03
19 60 0.85
20 9 0.13
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:43190 original size:29 final size:28
Alignment explanation
Indices: 43128--43232 Score: 129
Period size: 29 Copynumber: 3.6 Consensus size: 28
43118 GCTGCTGGAA
*
43128 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
43158 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * *
43186 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
*
43215 ACCGGTCTGAACCGGTTT
1 ACCGGTTTG-ACCGGTTT
43233 GACCGGTCTG
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
28 9 0.13
29 45 0.67
30 13 0.19
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:43252 original size:5 final size:5
Alignment explanation
Indices: 43242--43299 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
43232 TGACCGGTCT
* *
43242 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
43291 GACCC GACC
1 GACCC GACC
43300 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:43256 original size:38 final size:38
Alignment explanation
Indices: 43177--43256 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
43167 ACCGGTTTCA
****
43177 ACCGGTTCGAACCGGTTTGACCGGTCTGAACCGGTTTG
1 ACCGGTTCGAACCGGTTTGACCGGTCTGAACCGACCCG
*
43215 ACCGG-TCTGAACCGGTTTGACCGGTCTGACCCGACCCG
1 ACCGGTTC-GAACCGGTTTGACCGGTCTGAACCGACCCG
43253 ACCG
1 ACCG
43257 TTGACCCGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 2 0.06
38 34 0.94
ACGTcount: A:0.16, C:0.33, G:0.30, T:0.21
Consensus pattern (38 bp):
ACCGGTTCGAACCGGTTTGACCGGTCTGAACCGACCCG
Found at i:43268 original size:22 final size:22
Alignment explanation
Indices: 43242--43306 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
43232 TGACCGGTCT
43242 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
43264 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
43286 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
43307 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:47836 original size:26 final size:26
Alignment explanation
Indices: 47776--47841 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 26
47766 AAAATTAAAA
* *
47776 TAAATGACCGAAATAACATCGAGTAC
1 TAAATGACCAAAATAACACCGAGTAC
* *
47802 CAAAGTGACTAAAATAAC-CCGAGTAC
1 TAAA-TGACCAAAATAACACCGAGTAC
47828 TTAAATGACGCAAA
1 -TAAATGAC-CAAA
47842 TACCCTCTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
26 14 0.45
27 17 0.55
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (26 bp):
TAAATGACCAAAATAACACCGAGTAC
Found at i:48903 original size:60 final size:59
Alignment explanation
Indices: 48733--48912 Score: 175
Period size: 60 Copynumber: 3.0 Consensus size: 59
48723 ACCTGTTATG
* * * * *
48733 ATCTTTCATATTAGCCTCCTAGATCTTAGTGGTCTAGGGTAAGTCTTTATGGATACATGT
1 ATCTTCCATATTAGGCTCTTAGATC-TAGAGGTCTAGGGTAAGTCTTTATGGATACTTGT
* * * * * *
48793 ATCTTCCATATT-GGACT-TATATATCCTAGGGGTTTAGGTTAGGTCTTTATGGATGCTTGT
1 ATCTTCCATATTAGG-CTCT-TAGAT-CTAGAGGTCTAGGGTAAGTCTTTATGGATACTTGT
* * *
48853 ATCTTCCATATTAGGCTCTTAGATGCTAGAAGTCTAGGGTAAGTCCTTATGGATTCTTGT
1 ATCTTCCATATTAGGCTCTTAGAT-CTAGAGGTCTAGGGTAAGTCTTTATGGATACTTGT
48913 TCTGGTATTT
Statistics
Matches: 96, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
59 1 0.01
60 91 0.95
61 4 0.04
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (59 bp):
ATCTTCCATATTAGGCTCTTAGATCTAGAGGTCTAGGGTAAGTCTTTATGGATACTTGT
Found at i:50387 original size:19 final size:19
Alignment explanation
Indices: 50363--50401 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
50353 GAATGTATGT
50363 TTAACTAGTTAAGGTCTGG
1 TTAACTAGTTAAGGTCTGG
50382 TTAACTAGTTAAGGTCTGG
1 TTAACTAGTTAAGGTCTGG
50401 T
1 T
50402 AGAGGAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (19 bp):
TTAACTAGTTAAGGTCTGG
Found at i:50721 original size:18 final size:19
Alignment explanation
Indices: 50695--50731 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
50685 TTTAGGAAAC
50695 CCATGGTTTTTCTCTCTCT
1 CCATGGTTTTTCTCTCTCT
*
50714 CCAT-GTTTTTCTTTCTCT
1 CCATGGTTTTTCTCTCTCT
50732 TCTTTTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.05, C:0.30, G:0.08, T:0.57
Consensus pattern (19 bp):
CCATGGTTTTTCTCTCTCT
Found at i:54751 original size:15 final size:15
Alignment explanation
Indices: 54733--54763 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
54723 TTTTTATTGT
54733 TATTTTTATTATTAA
1 TATTTTTATTATTAA
54748 TATTTTTATTATTAA
1 TATTTTTATTATTAA
54763 T
1 T
54764 GGATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTATTATTAA
Found at i:60322 original size:17 final size:16
Alignment explanation
Indices: 60295--60344 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
60285 CCAGACAAAT
*
60295 TTATTATTTTAAAGAG
1 TTATTAATTTAAAGAG
**
60311 TCTATTAATTTACCGAG
1 T-TATTAATTTAAAGAG
60328 -TATTAATTTAAAGAG
1 TTATTAATTTAAAGAG
60343 TT
1 TT
60345 TCTACTGTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 13 0.48
16 2 0.07
17 12 0.44
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (16 bp):
TTATTAATTTAAAGAG
Found at i:69028 original size:85 final size:84
Alignment explanation
Indices: 68902--69067 Score: 305
Period size: 85 Copynumber: 2.0 Consensus size: 84
68892 ACATGAATAT
68902 ATAATGTATATAGTTAATTTTGTTGTACGGTAGGAAGATTTCAAGGTGAGTGAATTTTGTAACTT
1 ATAATGTATATAGTTAATTTTGTTGTACGGTAGGAAGATTTCAAGGTGAGTGAA-TTTGTAACTT
68967 GCTTGTGAAGGATAAAGGAA
65 GCTTGTGAAGGATAAAGGAA
**
68987 ATAATGTATATAGTTAATTTTGTTGTATTGTAGGAAGATTTCAAGGTGAGTGAATTTGTAACTTG
1 ATAATGTATATAGTTAATTTTGTTGTACGGTAGGAAGATTTCAAGGTGAGTGAATTTGTAACTTG
69052 CTTGTGAAGGATAAAG
66 CTTGTGAAGGATAAAG
69068 TAACCCATGT
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
84 27 0.34
85 52 0.66
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (84 bp):
ATAATGTATATAGTTAATTTTGTTGTACGGTAGGAAGATTTCAAGGTGAGTGAATTTGTAACTTG
CTTGTGAAGGATAAAGGAA
Found at i:69653 original size:2 final size:2
Alignment explanation
Indices: 69646--69705 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
69636 CCAATCTAAG
69646 AT AT AT AT 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
69688 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
69706 TCTCATCTCC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70399 original size:20 final size:21
Alignment explanation
Indices: 70361--70399 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
70351 GAAATTTTTT
* *
70361 AAAATTCGAATTTTCATTTAA
1 AAAATTCAAAGTTTCATTTAA
70382 AAAATTCAAAGTTT-ATTT
1 AAAATTCAAAGTTTCATTT
70400 CATTAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (21 bp):
AAAATTCAAAGTTTCATTTAA
Found at i:74250 original size:19 final size:18
Alignment explanation
Indices: 74199--74250 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
74189 AATTATGACT
*
74199 AAATTAAA-TAAAAACTA
1 AAATTAAATTATAAACTA
* *
74216 AAATTTACATTCTAAACTA
1 AAA-TTAAATTATAAACTA
74235 AAGATTAAATTATAAA
1 AA-ATTAAATTATAAA
74251 TTTTAAAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 3 0.11
18 4 0.15
19 19 0.70
20 1 0.04
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATTAAATTATAAACTA
Found at i:75484 original size:12 final size:12
Alignment explanation
Indices: 75467--75513 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
75457 TCGATTCAAG
75467 CTCAAACTCGAA
1 CTCAAACTCGAA
75479 CTCAAACTCG-A
1 CTCAAACTCGAA
* *
75490 TTCAAGCTCGAA
1 CTCAAACTCGAA
75502 CTCAAACTCGAA
1 CTCAAACTCGAA
75514 GTTGAACCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.38, C:0.32, G:0.11, T:0.19
Consensus pattern (12 bp):
CTCAAACTCGAA
Found at i:75499 original size:23 final size:23
Alignment explanation
Indices: 75468--75512 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
75458 CGATTCAAGC
75468 TCAAACTCGAACTCAAACTCGAT
1 TCAAACTCGAACTCAAACTCGAT
*
75491 TCAAGCTCGAACTCAAACTCGA
1 TCAAACTCGAACTCAAACTCGA
75513 AGTTGAACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.31, G:0.11, T:0.20
Consensus pattern (23 bp):
TCAAACTCGAACTCAAACTCGAT
Found at i:79978 original size:19 final size:18
Alignment explanation
Indices: 79927--79978 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
79917 AATTATGACT
*
79927 AAATTAAA-TAAAAACTA
1 AAATTAAATTATAAACTA
* *
79944 AAATTTACATTCTAAACTA
1 AAA-TTAAATTATAAACTA
79963 AAGATTAAATTATAAA
1 AA-ATTAAATTATAAA
79979 TTTTAAAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 3 0.11
18 4 0.15
19 19 0.70
20 1 0.04
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATTAAATTATAAACTA
Found at i:81164 original size:17 final size:18
Alignment explanation
Indices: 81138--81184 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
81128 TATGAAATTG
* *
81138 GATTTCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
*
81155 GATTCTAATTCCTTCACA
1 GATTCCAATTCCTTCACA
81173 GATTCCAATTCC
1 GATTCCAATTCC
81185 CTCAGAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:88725 original size:23 final size:23
Alignment explanation
Indices: 88690--88735 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
88680 CCACAAAAAA
88690 AAATATGATAATAATAAAGAAAGG
1 AAATATGATAATAATAAA-AAAGG
88714 AAATAT-ATAATAATAAAAAAGG
1 AAATATGATAATAATAAAAAAGG
88736 TATCATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.23
23 11 0.50
24 6 0.27
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.22
Consensus pattern (23 bp):
AAATATGATAATAATAAAAAAGG
Found at i:90406 original size:16 final size:16
Alignment explanation
Indices: 90382--90414 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
90372 GATGTTGGTT
*
90382 TCAATGTCAACATAGA
1 TCAACGTCAACATAGA
90398 TCAACGTCAACATAGA
1 TCAACGTCAACATAGA
90414 T
1 T
90415 GAGGACTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.24
Consensus pattern (16 bp):
TCAACGTCAACATAGA
Found at i:103357 original size:21 final size:22
Alignment explanation
Indices: 103316--103361 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
103306 TTCTTATTTG
103316 TATTAATTGATTATAATAATTA
1 TATTAATTGATTATAATAATTA
103338 TATTAACTTG-TTAT-ATAATTA
1 TATTAA-TTGATTATAATAATTA
103359 TAT
1 TAT
103362 ATAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.43
22 10 0.43
23 3 0.13
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (22 bp):
TATTAATTGATTATAATAATTA
Found at i:103543 original size:21 final size:21
Alignment explanation
Indices: 103514--103553 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
103504 AATATATTAA
*
103514 ATAATTATTTAACATATAAAT
1 ATAACTATTTAACATATAAAT
* *
103535 ATAACTATTTTATATATAA
1 ATAACTATTTAACATATAA
103554 TGTTATATGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAACTATTTAACATATAAAT
Found at i:112774 original size:16 final size:17
Alignment explanation
Indices: 112741--112777 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
112731 AAATTAAACG
*
112741 AACATATATTAAATATA
1 AACATATATTAAAAATA
112758 AACATAT-TTAAAAATA
1 AACATATATTAAAAATA
112774 AACA
1 AACA
112778 AAAATGACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (17 bp):
AACATATATTAAAAATA
Found at i:123041 original size:72 final size:73
Alignment explanation
Indices: 122920--123058 Score: 158
Period size: 72 Copynumber: 1.9 Consensus size: 73
122910 AAAGCCAAGT
* *
122920 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTGAGCGTTCATCAAAGAGAAG-TGAAGCAAACC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCATCAAAGAG-AGTTGAAGCAAACC
122984 ATCTTAAGC
65 ATCTTAAGC
* ** * * * *
122993 CTTCACCGAA-AGTAGTGAAGCCTATCCTTTTTAAGCCTTC-TCGGAAGAGTGTTGGAGCAAACC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCATC-AAAGAGAGTTGAAGCAAACC
123056 ATC
65 ATC
123059 ACTATCAGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
71 3 0.05
72 43 0.78
73 9 0.16
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (73 bp):
CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCATCAAAGAGAGTTGAAGCAAACCA
TCTTAAGC
Done.