Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007056.1 Hibiscus syriacus cultivar Beakdansim tig00018308_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: 68514
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4967 original size:102 final size:102
Alignment explanation
Indices: 4786--4974 Score: 315
Period size: 102 Copynumber: 1.9 Consensus size: 102
4776 ATGGAATGAC
* *
4786 TCTACCTGACTAGCTTGGGGGTGGAAGGTATGCTCCCTTTCACCTAGAGTATGGGATGGTAGGTG
1 TCTACCTGACTAGATTGGGGATGGAAGGTATGCTCCCTTTCACCTAGAGTATGGGATGGTAGGTG
4851 TGATGGGCTGACTCCCTTCGTAGCAGAATAAAAAAAA
66 TGATGGGCTGACTCCCTTCGTAGCAGAATAAAAAAAA
* * * *
4888 TCTATCTGACTAGATTGTGGATGGAAGGTATGCTCCCTTTCATCTAGAGTGTGGGATGGTAGGTG
1 TCTACCTGACTAGATTGGGGATGGAAGGTATGCTCCCTTTCACCTAGAGTATGGGATGGTAGGTG
*
4953 TGATGGTCTGACTCCCTTCGTA
66 TGATGGGCTGACTCCCTTCGTA
4975 AAAAAAATAA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 80 1.00
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (102 bp):
TCTACCTGACTAGATTGGGGATGGAAGGTATGCTCCCTTTCACCTAGAGTATGGGATGGTAGGTG
TGATGGGCTGACTCCCTTCGTAGCAGAATAAAAAAAA
Found at i:17063 original size:21 final size:20
Alignment explanation
Indices: 17039--17100 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
17029 CTCAAATCAG
17039 TTTCCAGATTCGCAATGCGAT
1 TTTCCA-ATTCGCAATGCGAT
**
17060 TTTCCAATTTCGCGTTGCGAT
1 TTTCCAA-TTCGCAATGCGAT
17081 TTTCCCAATTCGCAATGCGA
1 TTT-CCAATTCGCAATGCGA
17101 ATAAGTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 30 0.86
22 4 0.11
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (20 bp):
TTTCCAATTCGCAATGCGAT
Found at i:17133 original size:21 final size:21
Alignment explanation
Indices: 17090--17162 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
17080 TTTTCCCAAT
** *
17090 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
17110 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
17131 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
17152 TCGCAATGCGA
1 TCGCAATGCGA
17163 TACTGACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 12 0.24
21 37 0.76
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:17176 original size:20 final size:20
Alignment explanation
Indices: 17160--17239 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
17150 AATCGCAATG
*
17160 CGATACTGACTATCGCAACG
1 CGATACTGACTATCGCAACA
* *
17180 CGATAAT-ACAAAATCGCAACA
1 CGATACTGAC--TATCGCAACA
*
17201 CGATACTGACTTTCGCAACA
1 CGATACTGACTATCGCAACA
* *
17221 AGATTCTGACTATCGCAAC
1 CGATACTGACTATCGCAAC
17240 GGGATAATAC
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (20 bp):
CGATACTGACTATCGCAACA
Found at i:18002 original size:24 final size:24
Alignment explanation
Indices: 17975--18028 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
17965 CTATTCGAAA
17975 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
17999 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
18023 TTTGAT
1 TTTGAT
18029 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:20573 original size:20 final size:20
Alignment explanation
Indices: 20495--20607 Score: 111
Period size: 20 Copynumber: 5.7 Consensus size: 20
20485 CGCAACGGGG
* *
20495 AAATCGCAACGCGAAAATGG
1 AAATCGCAATGCGAAAATGA
** * * *
20515 CTATCGCAACGCGGAAATGG
1 AAATCGCAATGCGAAAATGA
**
20535 CTATCGCAATGCG-AAATGA
1 AAATCGCAATGCGAAAATGA
20554 AAATCGCAATGCGAAAATGA
1 AAATCGCAATGCGAAAATGA
* *
20574 AAATCACATTGCGAAAATGA
1 AAATCGCAATGCGAAAATGA
*
20594 AAATCGCATTGCGA
1 AAATCGCAATGCGA
20608 TTTTCTCGTT
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
19 16 0.20
20 66 0.80
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (20 bp):
AAATCGCAATGCGAAAATGA
Found at i:20638 original size:19 final size:16
Alignment explanation
Indices: 20597--20642 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 16
20587 AAAATGAAAA
20597 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
20613 TCG--TTGCGATTTTC
1 TCGCATTGCGATTTTC
20627 ATTTCGCATTGCGATT
1 ---TCGCATTGCGATT
20643 CTCTTGTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.44
16 3 0.12
17 3 0.12
19 8 0.32
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.46
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:20672 original size:20 final size:20
Alignment explanation
Indices: 20647--20684 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20637 GCGATTCTCT
20647 TGTTGCGATAGTCAGTTTCG
1 TGTTGCGATAGTCAGTTTCG
*
20667 TGTTGCGATAGTCTGTTT
1 TGTTGCGATAGTCAGTTT
20685 TGCCTTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.29, T:0.45
Consensus pattern (20 bp):
TGTTGCGATAGTCAGTTTCG
Found at i:22282 original size:41 final size:42
Alignment explanation
Indices: 22228--22319 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
22218 CCTCTTCAAC
* * *
22228 GATGACAGTGGCCTCTTAAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTAAACGAGTGGAGGGGACTATTGAGG
* * *
22269 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTATTGAGG
1 GATGACAGGGGCCTCTTAAACGAGTGGAGGGGACTATTGAGG
22311 GATGACAGG
1 GATGACAGG
22320 TGAGTCAGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 19 0.44
42 24 0.56
ACGTcount: A:0.23, C:0.14, G:0.41, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTAAACGAGTGGAGGGGACTATTGAGG
Found at i:22703 original size:20 final size:19
Alignment explanation
Indices: 22661--22785 Score: 107
Period size: 20 Copynumber: 6.7 Consensus size: 19
22651 TAGTTTACTT
* *
22661 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
22681 TCGCAACGCGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
22701 TCGCAACGCGGAAATGGTTA
1 TCGCAACGC-GAAATGAAAA
*
22721 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
22740 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
22759 TCGCAA--CG-AA--AAAA
1 TCGCAACGCGAAATGAAAA
22773 TCGCAACGCGAAA
1 TCGCAACGCGAAA
22786 CACAAATCGC
Statistics
Matches: 90, Mismatches: 10, Indels: 13
0.80 0.09 0.12
Matches are distributed among these distances:
14 10 0.11
16 4 0.04
17 4 0.04
19 32 0.36
20 36 0.40
21 4 0.04
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:22855 original size:19 final size:19
Alignment explanation
Indices: 22792--22914 Score: 112
Period size: 20 Copynumber: 6.6 Consensus size: 19
22782 GAAACACAAA
*
22792 TCGCATTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
22812 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
22828 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
22845 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
22864 CCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
22884 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
22904 TCGTGTTGCGA
1 TCGCGTTGCGA
22915 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
19 31 0.37
20 37 0.45
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:24688 original size:16 final size:16
Alignment explanation
Indices: 24667--24721 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 16
24657 AGTTTACATA
24667 TTAATTTCATTTTATT
1 TTAATTTCATTTTATT
*
24683 TTAATTTCGGTCTTTATAT
1 TTAATTTC-AT-TTTAT-T
*
24702 TTAATGTGCATTTTATT
1 TTAAT-TTCATTTTATT
24719 TTA
1 TTA
24722 GTCCCAAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 8 0.25
17 5 0.16
18 10 0.31
19 7 0.22
20 2 0.06
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (16 bp):
TTAATTTCATTTTATT
Found at i:27857 original size:20 final size:20
Alignment explanation
Indices: 27799--27866 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
27789 GAAACTTAAA
**
27799 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
27819 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
27839 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
27859 ATCGCAAC
1 ATCGCAAC
27867 CGATTTTCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.43, C:0.25, G:0.16, T:0.16
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:28126 original size:22 final size:22
Alignment explanation
Indices: 28099--28153 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
28089 GGAGATAGAC
28099 GGATTTCGCCGGAGATGGGGAA
1 GGATTTCGCCGGAGATGGGGAA
* *
28121 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGGAA
*
28143 GGATGTCGCCG
1 GGATTTCGCCG
28154 TAGAGAGTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GGATTTCGCCGGAGATGGGGAA
Found at i:30520 original size:28 final size:28
Alignment explanation
Indices: 30486--30579 Score: 114
Period size: 28 Copynumber: 3.6 Consensus size: 28
30476 AATTTTAATG
30486 AGCTTAACGAGCAACGAGCTGATTAACA
1 AGCTTAACGAGCAACGAGCTGATTAACA
*
30514 AGCTT-------AACGAGCTAATTAACA
1 AGCTTAACGAGCAACGAGCTGATTAACA
30535 AGCTTAACGAGCAACGAGCTGATTAACA
1 AGCTTAACGAGCAACGAGCTGATTAACA
*
30563 GGCTTAACGAGC-ACGAG
1 AGCTTAACGAGCAACGAG
30580 TCGAGTAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
21 20 0.36
27 5 0.09
28 31 0.55
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.18
Consensus pattern (28 bp):
AGCTTAACGAGCAACGAGCTGATTAACA
Found at i:30523 original size:21 final size:21
Alignment explanation
Indices: 30498--30546 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
30488 CTTAACGAGC
*
30498 AACGAGCTGATTAACAAGCTT
1 AACGAGCTAATTAACAAGCTT
30519 AACGAGCTAATTAACAAGCTT
1 AACGAGCTAATTAACAAGCTT
30540 AACGAGC
1 AACGAGC
30547 AACGAGCTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (21 bp):
AACGAGCTAATTAACAAGCTT
Found at i:30588 original size:27 final size:28
Alignment explanation
Indices: 30519--30591 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
30509 TAACAAGCTT
* *
30519 AACGAGCTAATTAACAAGCTTAACGAGC
1 AACGAGCTGAGTAACAAGCTTAACGAGC
* *
30547 AACGAGCTGATTAACAGGCTTAACGAGC
1 AACGAGCTGAGTAACAAGCTTAACGAGC
30575 -ACGAG-TCGAGTAACAAG
1 AACGAGCT-GAGTAACAAG
30592 TTTTTTTAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.03
27 13 0.32
28 26 0.65
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16
Consensus pattern (28 bp):
AACGAGCTGAGTAACAAGCTTAACGAGC
Found at i:37073 original size:29 final size:29
Alignment explanation
Indices: 37041--37177 Score: 132
Period size: 29 Copynumber: 4.6 Consensus size: 29
37031 ATCATTTTTT
* *
37041 TAATATTTTCGATTATTTTTAACGCCTAA
1 TAATATTTTCGATTATTTTTAATGTCTAA
* * * *
37070 TAATATTTTCGGTCATTTTTTAGTGTTTAA
1 TAATATTTTCGATTA-TTTTTAATGTCTAA
* * *
37100 TAATATTTTTGGTTATTTTTAAGGTCTAA
1 TAATATTTTCGATTATTTTTAATGTCTAA
* *
37129 TAATGA-TTTCGATCATTTTTTTAGTGTCTAA
1 TAAT-ATTTTCGAT--TATTTTTAATGTCTAA
37160 TAATATTTTCGATTATTT
1 TAATATTTTCGATTATTT
37178 GTTATCGGTT
Statistics
Matches: 86, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
29 37 0.43
30 25 0.29
31 24 0.28
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (29 bp):
TAATATTTTCGATTATTTTTAATGTCTAA
Found at i:37116 original size:59 final size:60
Alignment explanation
Indices: 37041--37177 Score: 197
Period size: 59 Copynumber: 2.3 Consensus size: 60
37031 ATCATTTTTT
* *
37041 TAATATTTTCGATTATTTTTAACGCCTAATAAT-ATTTTCGGTCA-TTTTTTAGTGTTTAA
1 TAATATTTTCGATTATTTTTAACGCCTAATAATGA-TTTCGATCATTTTTTTAGTGTCTAA
* * * *
37100 TAATATTTTTGGTTATTTTTAAGGTCTAATAATGATTTCGATCATTTTTTTAGTGTCTAA
1 TAATATTTTCGATTATTTTTAACGCCTAATAATGATTTCGATCATTTTTTTAGTGTCTAA
37160 TAATATTTTCGATTATTT
1 TAATATTTTCGATTATTT
37178 GTTATCGGTT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 37 0.54
60 31 0.46
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (60 bp):
TAATATTTTCGATTATTTTTAACGCCTAATAATGATTTCGATCATTTTTTTAGTGTCTAA
Found at i:37158 original size:31 final size:30
Alignment explanation
Indices: 37041--37177 Score: 136
Period size: 30 Copynumber: 4.6 Consensus size: 30
37031 ATCATTTTTT
* ** *
37041 TAATATTTTCGATTA-TTTTTAACGCCTAA
1 TAATATTTTCGATCATTTTTTAGTGTCTAA
* *
37070 TAATATTTTCGGTCATTTTTTAGTGTTTAA
1 TAATATTTTCGATCATTTTTTAGTGTCTAA
* * * *
37100 TAATATTTTTGGTTATTTTTAAG-GTCTAA
1 TAATATTTTCGATCATTTTTTAGTGTCTAA
37129 TAATGA-TTTCGATCATTTTTTTAGTGTCTAA
1 TAAT-ATTTTCGATCA-TTTTTTAGTGTCTAA
*
37160 TAATATTTTCGATTATTT
1 TAATATTTTCGATCATTT
37178 GTTATCGGTT
Statistics
Matches: 88, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
29 28 0.32
30 42 0.48
31 18 0.20
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (30 bp):
TAATATTTTCGATCATTTTTTAGTGTCTAA
Found at i:38199 original size:2 final size:2
Alignment explanation
Indices: 38192--38224 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
38182 TGAAGGGTTA
38192 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
38225 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:38229 original size:2 final size:2
Alignment explanation
Indices: 38224--38253 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38214 TCTCTCTCTC
38224 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
38254 CTTGATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50371 original size:23 final size:23
Alignment explanation
Indices: 50342--50387 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
50332 CAAAAAATTA
*
50342 GTCATTTTAGTTATACAAATACT
1 GTCATTTTAGTAATACAAATACT
50365 GTCATTTTAGTAATACAAATACT
1 GTCATTTTAGTAATACAAATACT
50388 ATACAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (23 bp):
GTCATTTTAGTAATACAAATACT
Found at i:50871 original size:197 final size:198
Alignment explanation
Indices: 50530--50925 Score: 670
Period size: 197 Copynumber: 2.0 Consensus size: 198
50520 AAAATCGAGC
*
50530 GTCATGAGAAAACTATCTCTGAATACAAACCGCGTATACAAATATAATTTGATGGTTCAAAGCAA
1 GTCATGAGAAAACTATCTCTGAATACAAACCGCGTATACAAATATAATTTGATGGTCCAAAGCAA
*
50595 AGAAGATCAACATGAATGTATAATTTTAATTCTTATGATTAGGTCCTAAATGCATAATTGGTTGT
66 AGAAGATCAACATGAATGTATAATTTTAATTCTTATGATTAGGTCATAAATGCATAATTGGTTGT
*
50660 AATTAGGTTATATAGTTCTGATTCTACTCAATTAGGTCATGAATTTATAA-TTTTAGTTAGTAAT
131 AATTAGGCTATATAGTTCTGATTCTACTCAATTAGGTCATGAATTTATAATTTTTAGTTAGTAAT
50724 TAG
196 TAG
* * *
50727 GTCATGAGAAGACTATCTCTGAATACAAA-CGTTGTATTCAAATATAATTTGATGGTCCAAAGCA
1 GTCATGAGAAAACTATCTCTGAATACAAACCG-CGTATACAAATATAATTTGATGGTCCAAAGCA
* *
50791 GAGAATATCAACATGAATGTATAATTTTAATTCTTATGATTAGGTCATAAATGCATAATTGGTTG
65 AAGAAGATCAACATGAATGTATAATTTTAATTCTTATGATTAGGTCATAAATGCATAATTGGTTG
* * *
50856 TAATTAGGCTATATAGTTCTTATTCTACTTAATTAGGTCATGAATTTATAATTTTTATTTAGTAA
130 TAATTAGGCTATATAGTTCTGATTCTACTCAATTAGGTCATGAATTTATAATTTTTAGTTAGTAA
50921 TTAG
195 TTAG
50925 G
1 G
50926 CTAATTTTTT
Statistics
Matches: 186, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
196 2 0.01
197 167 0.90
198 17 0.09
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (198 bp):
GTCATGAGAAAACTATCTCTGAATACAAACCGCGTATACAAATATAATTTGATGGTCCAAAGCAA
AGAAGATCAACATGAATGTATAATTTTAATTCTTATGATTAGGTCATAAATGCATAATTGGTTGT
AATTAGGCTATATAGTTCTGATTCTACTCAATTAGGTCATGAATTTATAATTTTTAGTTAGTAAT
TAG
Found at i:51817 original size:61 final size:60
Alignment explanation
Indices: 51732--51910 Score: 200
Period size: 61 Copynumber: 3.0 Consensus size: 60
51722 TTCGTGCTTA
* * * *
51732 ATTCTTCTTAAATAAGTCCTAAATGCATAATTTTGATTAGTAATTAGGCCTTATAATTTCG
1 ATTCTTCTTAATTAGGTCCCAAATGCATAATTTTG-TTAGTAATTAAGCCTTATAATTTCG
* * * * * *
51793 TTTCTTCTTAATTAGGTCCCAAATGAATAA-TTAGTAAGTAATTAAACCTTATAATTTTG
1 ATTCTTCTTAATTAGGTCCCAAATGCATAATTTTGTTAGTAATTAAGCCTTATAATTTCG
* * *
51852 ATTCCTCTCAATTAGGTCCTC-AATGCATAATTTTGGTTAGTAATTATGCCTTATAATTT
1 ATTCTTCTTAATTAGGTCC-CAAATGCATAATTTT-GTTAGTAATTAAGCCTTATAATTT
51911 TTATTCTTTT
Statistics
Matches: 97, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
59 45 0.46
60 6 0.06
61 46 0.47
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (60 bp):
ATTCTTCTTAATTAGGTCCCAAATGCATAATTTTGTTAGTAATTAAGCCTTATAATTTCG
Found at i:51911 original size:61 final size:61
Alignment explanation
Indices: 51747--51916 Score: 193
Period size: 59 Copynumber: 2.8 Consensus size: 61
51737 TCTTAAATAA
* * * * * * *
51747 GTCCTAAATGCATAATTTTGATTAGTAATTAGGCCTTATAATTTCGTTTCTTCTTAATTAG
1 GTCCTCAATGCATAATTTTGGTTAGTAATTAAGCCTTATAATTTTGATTCCTCTCAATTAG
* * * *
51808 GTCC-CAAATGAATAA--TTAGTAAGTAATTAAACCTTATAATTTTGATTCCTCTCAATTAG
1 GTCCTC-AATGCATAATTTTGGTTAGTAATTAAGCCTTATAATTTTGATTCCTCTCAATTAG
* *
51867 GTCCTCAATGCATAATTTTGGTTAGTAATTATGCCTTATAATTTTTATTC
1 GTCCTCAATGCATAATTTTGGTTAGTAATTAAGCCTTATAATTTTGATTC
51917 TTTTTTATTT
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
59 47 0.53
60 1 0.01
61 40 0.45
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.44
Consensus pattern (61 bp):
GTCCTCAATGCATAATTTTGGTTAGTAATTAAGCCTTATAATTTTGATTCCTCTCAATTAG
Found at i:52021 original size:41 final size:41
Alignment explanation
Indices: 51976--52058 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
51966 AACTTTTAAT
51976 TAAATATGTTTTGGGCAATAAATCAAGATTATTAATTTAGC
1 TAAATATGTTTTGGGCAATAAATCAAGATTATTAATTTAGC
52017 TAAATATGTTTTGGGCAATAAATCAAGATTATTAATTTAGC
1 TAAATATGTTTTGGGCAATAAATCAAGATTATTAATTTAGC
52058 T
1 T
52059 TAATTCAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (41 bp):
TAAATATGTTTTGGGCAATAAATCAAGATTATTAATTTAGC
Found at i:53206 original size:39 final size:39
Alignment explanation
Indices: 53130--53254 Score: 144
Period size: 39 Copynumber: 3.2 Consensus size: 39
53120 ACAAACAGAC
* * * *
53130 ATCAAAAGGAATTAAACATTTAATTTTAGCAACTCAATA
1 ATCAAAAGCAACTAATCCTTTAATTTTAGCAACTCAATA
* * * *
53169 ATCGAAAGGAACTAATCCTTTACTTTTTA-CAATTCAATA
1 ATCAAAAGCAACTAATCCTTTA-ATTTTAGCAACTCAATA
* *
53208 ATCAAAAGCAATTTATCCTTTAATTTTAGCAACTCAATA
1 ATCAAAAGCAACTAATCCTTTAATTTTAGCAACTCAATA
53247 ATCAAAAG
1 ATCAAAAG
53255 TCTTTGACTA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
38 5 0.07
39 62 0.86
40 5 0.07
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (39 bp):
ATCAAAAGCAACTAATCCTTTAATTTTAGCAACTCAATA
Found at i:54531 original size:12 final size:12
Alignment explanation
Indices: 54514--54541 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
54504 AAATATAATA
54514 AATTATAAATTT
1 AATTATAAATTT
54526 AATTATAAATTT
1 AATTATAAATTT
54538 AATT
1 AATT
54542 TATTAACGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTATAAATTT
Done.