Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006202.1 Hibiscus syriacus cultivar Beakdansim tig00014768_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: 60629
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:1044 original size:17 final size:18
Alignment explanation
Indices: 1022--1059 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1012 TACTGTCAAC
1022 ATTTAAAATTGTAAT-CA
1 ATTTAAAATTGTAATCCA
*
1039 ATTTAAAATTTTAATCCA
1 ATTTAAAATTGTAATCCA
1057 ATT
1 ATT
1060 ACCATTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (18 bp):
ATTTAAAATTGTAATCCA
Found at i:1152 original size:21 final size:21
Alignment explanation
Indices: 1127--1172 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1117 ATTTGGTTGC
1127 TTTCCTCCCATTGACTTCATT
1 TTTCCTCCCATTGACTTCATT
*
1148 TTTCCTTCCATTGACTTCATT
1 TTTCCTCCCATTGACTTCATT
1169 TTTC
1 TTTC
1173 TTTCATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.30, G:0.04, T:0.52
Consensus pattern (21 bp):
TTTCCTCCCATTGACTTCATT
Found at i:1366 original size:18 final size:19
Alignment explanation
Indices: 1325--1369 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1315 GCCATTTATA
*
1325 ACCTAAAATATCATTTTCT
1 ACCTATAATATCATTTTCT
1344 ACCTATAATATCATTTT-T
1 ACCTATAATATCATTTTCT
1362 ACCTATAA
1 ACCTATAA
1370 ATATTAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (19 bp):
ACCTATAATATCATTTTCT
Found at i:2063 original size:182 final size:181
Alignment explanation
Indices: 1756--2402 Score: 850
Period size: 182 Copynumber: 3.6 Consensus size: 181
1746 TACGCGTACT
** * * *
1756 TATTAAAGAATCGACACTTTCAACATATTCGATATCTATTTACCGGTTTTGTCA-TTTTGAGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACT-TTTACCGGTTTTGTCATTTTTGAGACC
* * *
1820 GGTTTTATCATATTTTTACCTGTTATATTGTTTTGGATCGATACATTTTCATAAAGTGTCGACAC
65 -GTTTTATCATATTTTTACATGTTATATTGTTATGGATCAATACATTTTCATAAAGTGTCGACAC
* *
1885 TTTTTAAGCGCTATAACTTCTTCTCTTTTAAATTAAGAAAGTGTCGATACTTA
129 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* **
1938 TATTAAATTATCGACACTTTTAACATATCCGGTAACTTTTTTCGGTTTTGTCATTTTTGAGACCT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACTTTTACCGGTTTTGTCATTTTTGAGACC-
* *
2003 GTTTTATCATATTTTTACATGTTATATTGGTAAGGATCAATACATTTTCATAAAGTGTCGACACT
65 GTTTTATCATATTTTTACATGTTATATTGTTATGGATCAATACATTTTCATAAAGTGTCGACACT
* *
2068 TTTTAGGCGTTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTAA
130 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * *
2120 TATTAAATTATTGACACTTTCAATATATCCGGTAACGTTTT-CCGGTTTTGTCATTTATGAGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAAC-TTTTACCGGTTTTGTCATTTTTGAGACC
* * ** *
2184 GATTTTATCATATTTTTACATGTTATATTGTTGTGGATCAATATATTTTTTTAAAGTATCGACAC
65 G-TTTTATCATATTTTTACATGTTATATTGTTATGGATCAATACATTTTCATAAAGTGTCGACAC
* * * * *
2249 TTTATAGGCACTATAGCTTCTTCTCTTTTAAATTCAGAAAGTTTTGATACTTA
129 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * * * *
2302 TATTAAATTATCGACACTTTCAATATATCCGGTAGCATTTTACCCGTTTTGTCA-TTTTGGGATC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAAC-TTTTACCGGTTTTGTCATTTTTGAGACC
* * * * *
2366 GATTTTGTCATATTTGTACCTGTAATATTGCTATGGA
65 G-TTTTATCATATTTTTACATGTTATATTGTTATGGA
2403 GCGATCCATT
Statistics
Matches: 411, Mismatches: 50, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
181 15 0.04
182 381 0.93
183 15 0.04
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (181 bp):
TATTAAATTATCGACACTTTCAACATATCCGGTAACTTTTACCGGTTTTGTCATTTTTGAGACCG
TTTTATCATATTTTTACATGTTATATTGTTATGGATCAATACATTTTCATAAAGTGTCGACACTT
TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
Found at i:5288 original size:14 final size:14
Alignment explanation
Indices: 5269--5303 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5259 CCTCTAATCG
5269 AACATAAATGAACA
1 AACATAAATGAACA
*
5283 AACATAAATGAACG
1 AACATAAATGAACA
5297 AACATAA
1 AACATAA
5304 GCAAACATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.63, C:0.14, G:0.09, T:0.14
Consensus pattern (14 bp):
AACATAAATGAACA
Found at i:5625 original size:30 final size:31
Alignment explanation
Indices: 5589--5653 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
5579 TCGGGGACCA
** *
5589 TATTGCAAATGGACTAAATGTT-GGGGGCTG
1 TATTGCAAACAGACTAAATGTTAGGGGACTG
5619 TATTGCAAACAGACTAAATGTTAGGGGACTG
1 TATTGCAAACAGACTAAATGTTAGGGGACTG
5650 TATT
1 TATT
5654 ACAAGTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.31
Consensus pattern (31 bp):
TATTGCAAACAGACTAAATGTTAGGGGACTG
Found at i:17791 original size:19 final size:20
Alignment explanation
Indices: 17750--17798 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
17740 AATAAAGGAC
* *
17750 TATTGAATTTTAAGATTTTA
1 TATTCAATTTTAAGATATTA
17770 TATTCAATTTTAA-ATATTA
1 TATTCAATTTTAAGATATTA
17789 TATTCAATTT
1 TATTCAATTT
17799 AATTATTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (20 bp):
TATTCAATTTTAAGATATTA
Found at i:20816 original size:22 final size:22
Alignment explanation
Indices: 20791--20832 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
20781 ACCAACAGTG
20791 GCAGAACAGGTACCAAACAGCC
1 GCAGAACAGGTACCAAACAGCC
*
20813 GCAGAATAGGTACCAAACAG
1 GCAGAACAGGTACCAAACAG
20833 TGGAACAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.26, G:0.24, T:0.07
Consensus pattern (22 bp):
GCAGAACAGGTACCAAACAGCC
Found at i:21151 original size:23 final size:23
Alignment explanation
Indices: 21121--21167 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
21111 ATGTAGAAAT
* *
21121 AGAGTTTTCCGGCTCTGGTAAAC
1 AGAGTTTTCCGACTCTAGTAAAC
*
21144 AGAGTTTTTCGACTCTAGTAAAC
1 AGAGTTTTCCGACTCTAGTAAAC
21167 A
1 A
21168 TGATTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (23 bp):
AGAGTTTTCCGACTCTAGTAAAC
Found at i:23416 original size:22 final size:23
Alignment explanation
Indices: 23366--23418 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
23356 AAACCTGATA
23366 TTTCCTAAAATAATAATATTCTT
1 TTTCCTAAAATAATAATATTCTT
*
23389 TTTCCTAAAA-AGATAATTTTC-T
1 TTTCCTAAAATA-ATAATATTCTT
23411 TTTCCTAA
1 TTTCCTAA
23419 TAATTAACGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.36, C:0.15, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTCCTAAAATAATAATATTCTT
Found at i:31772 original size:12 final size:12
Alignment explanation
Indices: 31755--31785 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31745 GATTATCCGG
*
31755 CCCGATACTCGT
1 CCCGATACCCGT
31767 CCCGATACCCGT
1 CCCGATACCCGT
31779 CCCGATA
1 CCCGATA
31786 AATATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.45, G:0.16, T:0.19
Consensus pattern (12 bp):
CCCGATACCCGT
Found at i:31813 original size:4 final size:4
Alignment explanation
Indices: 31804--31893 Score: 52
Period size: 4 Copynumber: 24.5 Consensus size: 4
31794 AAATTATTAT
* * * *
31804 TATA TATA TATA TATA TA-A TAT- TA-A TAAA TTTA -ATT TAAA T-TA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
31847 -ATA TATA TATA TATA -ATA TTTA TATA TTTA -ATT TAAA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
31892 TA
1 TA
31894 CTCGGCCCGA
Statistics
Matches: 63, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
3 15 0.24
4 48 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:31813 original size:6 final size:6
Alignment explanation
Indices: 31804--31893 Score: 52
Period size: 6 Copynumber: 16.3 Consensus size: 6
31794 AAATTATTAT
* * * *
31804 TATATA TATATA TATATA -ATAT- TA-ATA AATTTA -ATTTA AAT-TA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
31847 -ATATA TATATA TATA-A TATTTA TATATT TA-ATT TAAATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
31892 TA
1 TA
31894 CTCGGCCCGA
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
4 4 0.06
5 24 0.35
6 41 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATA
Found at i:31862 original size:40 final size:40
Alignment explanation
Indices: 31802--31893 Score: 143
Period size: 40 Copynumber: 2.3 Consensus size: 40
31792 AAAAATTATT
31802 ATTATATATATATATATATAATATTAATAAATTTAATTTAA
1 ATTA-ATATATATATATATAATATTAATAAATTTAATTTAA
* *
31843 ATTAATATATATATATATAATATTTATATATTTAATTTAA
1 ATTAATATATATATATATAATATTAATAAATTTAATTTAA
31883 A-T-ATATATATA
1 ATTAATATATATA
31894 CTCGGCCCGA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
38 9 0.18
39 1 0.02
40 35 0.71
41 4 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (40 bp):
ATTAATATATATATATATAATATTAATAAATTTAATTTAA
Found at i:31872 original size:17 final size:17
Alignment explanation
Indices: 31848--31893 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
31838 TTTAAATTAA
31848 TATATATATATATAATAT
1 TATATATATATATAAT-T
31866 T-TATATAT-T-TAATT
1 TATATATATATATAATT
*
31880 TAAATATATATATA
1 TATATATATATATA
31894 CTCGGCCCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
14 2 0.08
15 10 0.42
16 2 0.08
17 9 0.38
18 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATATATATAATT
Found at i:33530 original size:20 final size:20
Alignment explanation
Indices: 33486--33853 Score: 339
Period size: 20 Copynumber: 18.2 Consensus size: 20
33476 AATGACCAAC
*
33486 AAAATCGCAACGCGAAAT-A-
1 AAAATCGCAACGCG-ATTCAG
*
33505 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
33525 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
33545 AAAATCGCAACG-G--TCAAAAG
1 AAAATCGCAACGCGATTC---AG
33565 AAAATCGCAACGCGATATTCCA-
1 AAAATCGCAACGCG--ATT-CAG
* * *
33587 AGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
33607 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
33629 AGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTCAG
33649 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
33669 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
33689 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
33709 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
33729 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
33749 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
33769 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
33789 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
33809 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
33829 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
33849 AAAAT
1 AAAAT
33854 GAGTAAATTC
Statistics
Matches: 294, Mismatches: 28, Indels: 53
0.78 0.07 0.14
Matches are distributed among these distances:
18 3 0.01
19 26 0.09
20 222 0.76
21 11 0.04
22 28 0.10
23 2 0.01
25 1 0.00
26 1 0.00
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:33556 original size:40 final size:40
Alignment explanation
Indices: 33486--33853 Score: 485
Period size: 40 Copynumber: 9.1 Consensus size: 40
33476 AATGACCAAC
* * *
33486 AAAATCGCAACGCGAAAT--AAAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCG-ATTCCAAGAATCGCAACGCGATTAAG
* **** *
33525 AAAATCGCAACGTTGAAAAGAA-AATCGCAACG-G-TCAAAAG
1 AAAATCGCAACG-CGATTCCAAGAATCGCAACGCGAT-TA-AG
*
33565 AAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTAAG
* * *
33607 AGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTAAG
33649 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
33689 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
*
33729 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
*
33769 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
*
33809 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
33849 AAAAT
1 AAAAT
33854 GAGTAAATTC
Statistics
Matches: 300, Mismatches: 17, Indels: 23
0.88 0.05 0.07
Matches are distributed among these distances:
38 1 0.00
39 16 0.05
40 213 0.71
41 5 0.02
42 62 0.21
43 2 0.01
44 1 0.00
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.16
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
Found at i:33960 original size:6 final size:6
Alignment explanation
Indices: 33949--34016 Score: 129
Period size: 6 Copynumber: 11.5 Consensus size: 6
33939 GACACGTATT
33949 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
33997 ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
34017 CGAGACGAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.08
6 57 0.92
ACGTcount: A:0.32, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:34529 original size:6 final size:6
Alignment explanation
Indices: 34518--34550 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
34508 TCTCGTCTCG
34518 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
34551 AATACGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:34679 original size:20 final size:20
Alignment explanation
Indices: 34654--34852 Score: 262
Period size: 20 Copynumber: 9.8 Consensus size: 20
34644 TCATTTTCTT
34654 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
34674 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
34694 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
34714 AATCGCGTTGCGATTTTCTT--
1 AATCGCGTTGCGA--TTCTTGG
34734 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
*
34754 AATCGCGTTGCGATT-TTCTG
1 AATCGCGTTGCGATTCTT-GG
*
34774 AATCGCATTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
*
34794 AAGATCGCGTTGCGATTCTCT-T
1 -A-ATCGCGTTGCGATTCT-TGG
*
34816 AATCGCATTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
34836 AATATCGCGTTGCGATT
1 -A-ATCGCGTTGCGATT
34853 TTCTTTTGAC
Statistics
Matches: 159, Mismatches: 8, Indels: 22
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.03
19 3 0.02
20 112 0.70
21 5 0.03
22 33 0.21
23 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTTGG
Found at i:34869 original size:42 final size:40
Alignment explanation
Indices: 34646--34933 Score: 286
Period size: 40 Copynumber: 7.1 Consensus size: 40
34636 GAATTTACTC
*
34646 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
34686 A--TTCTTGGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTT-G-ATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*
34726 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*
34766 ATTTTC-TGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTG-ATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* * *
34808 ATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
1 ATTTTCTTGATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
**** *
34850 ATTTTCTTTTGA-C-CGTTGCGATT-TTCTTTTCAACGTTGCG
1 ATTTTC--TTGATCGCGTTGCGATTCTTGGAATC-GCGTTGCG
** * *
34890 ATTTTCTAAATCGCGTTGCGATT-TT-TATTTCGCGTTGCG
1 ATTTTCTTGATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
34929 ATTTT
1 ATTTT
34934 GTTGGTCATT
Statistics
Matches: 215, Mismatches: 19, Indels: 29
0.82 0.07 0.11
Matches are distributed among these distances:
38 7 0.03
39 17 0.08
40 116 0.54
41 3 0.01
42 67 0.31
43 2 0.01
44 3 0.01
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.41
Consensus pattern (40 bp):
ATTTTCTTGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:34906 original size:20 final size:20
Alignment explanation
Indices: 34646--34933 Score: 204
Period size: 20 Copynumber: 14.2 Consensus size: 20
34636 GAATTTACTC
*
34646 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
34666 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
34686 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
34706 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
34726 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
34746 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
34766 ATTTTCTGAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
34786 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* * *
34808 ATTCTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
34828 ATTCTT-GGAATATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
34850 ATTTTCTTTTG-A-C-CGTTGCG
1 ATTTTC---TGAATCGCGTTGCG
** *
34870 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
*
34890 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
34910 ATTTT-T-ATTTCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
34929 ATTTT
1 ATTTT
34934 GTTGGTCATT
Statistics
Matches: 223, Mismatches: 24, Indels: 43
0.77 0.08 0.15
Matches are distributed among these distances:
17 1 0.00
18 2 0.01
19 20 0.09
20 156 0.70
21 16 0.07
22 27 0.12
25 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:35251 original size:35 final size:35
Alignment explanation
Indices: 35200--35275 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
35190 AACACAGTAA
*
35200 TCAATTTCATTATAAACCCCAAATTCCAAAATAAT
1 TCAATTACATTATAAACCCCAAATTCCAAAATAAT
* * * *
35235 TCAATTACATTTTAAACCCTAAATTCTAAAATACT
1 TCAATTACATTATAAACCCCAAATTCCAAAATAAT
35270 TCAATT
1 TCAATT
35276 TAAGATTTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (35 bp):
TCAATTACATTATAAACCCCAAATTCCAAAATAAT
Found at i:41978 original size:24 final size:24
Alignment explanation
Indices: 41923--41978 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
41913 CACCGAAGTG
41923 CCACGTAGAATTTGTCCTGAAGGA
1 CCACGTAGAATTTGTCCTGAAGGA
* **
41947 TCGTGTAGAATTTGTCCCT-AAGGA
1 CCACGTAGAATTTGT-CCTGAAGGA
41971 CCACGTAG
1 CCACGTAG
41979 GAATATCCCG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCTGAAGGA
Found at i:42825 original size:64 final size:64
Alignment explanation
Indices: 42754--42940 Score: 173
Period size: 64 Copynumber: 2.9 Consensus size: 64
42744 GCATCAATCC
* *
42754 ATGCATCGATGCACCATT-GAATAAATT-GAACATCGAATGCATTTCTTGCATCGATGCACTCTC
1 ATGCATCGATGCA-C-TTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTC
42817 T
64 T
** ** *** *
42818 ATGCATCGATGCACTTGGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGCA
1 ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCT
* * * ** * *
42882 ATGCACCGATGCACTCAGG-CTATTTTCAAACATCGAATGCATTTTATGCATCGATGCAC
1 ATGCATCGATGCACT-TGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCAC
42941 ACTTGGTGCA
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
62 2 0.02
63 6 0.06
64 93 0.90
65 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (64 bp):
ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCT
Found at i:42951 original size:64 final size:63
Alignment explanation
Indices: 42782--42961 Score: 204
Period size: 64 Copynumber: 2.8 Consensus size: 63
42772 GAATAAATTG
* * * * *
42782 AACATCGAATGCATTTCT-TGCATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTT-TATGCATCGATGCACACT-TATGCACCGATGCACTAGGCTATTATTAA
* * *
42846 AACATCGAATGCATTTCATGCATCGATGCACAAGC-AATGCACCGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTTATGCATCGATGCAC-A-CTTATGCACCGATGCACT-AGGCTATTATTA
42909 A
63 A
*
42910 AACATCGAATGCATTTTATGCATCGATGCACACTTGGTGCACCGATGCACTA
1 AACATCGAATGCATTTTATGCATCGATGCACACTT-ATGCACCGATGCACTA
42962 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 90 0.91
65 5 0.05
66 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTTATGCATCGATGCACACTTATGCACCGATGCACTAGGCTATTATTAA
Found at i:50337 original size:21 final size:21
Alignment explanation
Indices: 50295--50338 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
50285 ACTCCGAGAG
* *
50295 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
50316 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
50337 CT
1 CT
50339 CCTCCTCCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:51451 original size:64 final size:64
Alignment explanation
Indices: 51375--51561 Score: 173
Period size: 64 Copynumber: 2.9 Consensus size: 64
51365 GCATCAATCC
*
51375 ATGCATCGATGCACCATT-GAATAAATT-GAACATCGAATGCATTTCATGCATCGATGCACTCTC
1 ATGCATCGATGCA-C-TTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTC
51438 T
64 T
* ** ** *** *
51439 ATGCATTGATGCACTTGGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGCA
1 ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCT
* * * ** * *
51503 ATGCACCGATGCACTCAGG-CTATTTTCAAACATCGAATGCATTTTATGCATCGATGCAC
1 ATGCATCGATGCACT-TGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCAC
51562 ACTTGGTGCA
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
62 2 0.02
63 6 0.06
64 92 0.90
65 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (64 bp):
ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCT
Found at i:51572 original size:64 final size:63
Alignment explanation
Indices: 51403--51582 Score: 211
Period size: 64 Copynumber: 2.8 Consensus size: 63
51393 GAATAAATTG
* ** * * *
51403 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATTGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTAGGCTATTATTAA
* *
51467 AACATCGAATGCATTTCATGCATCGATGCACAAGC-AATGCACCGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACT-AGGCTATTATTA
51530 A
63 A
* *
51531 AACATCGAATGCATTTTATGCATCGATGCACACTTGGTGCACCGATGCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCACCGATGCACTA
51583 AGTGTTCCAA
Statistics
Matches: 100, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 91 0.91
65 5 0.05
66 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTAGGCTATTATTAA
Found at i:52464 original size:53 final size:54
Alignment explanation
Indices: 52378--52519 Score: 182
Period size: 53 Copynumber: 2.6 Consensus size: 54
52368 GATACTTCCC
* *
52378 TTCAAGGGTATCG-TACCTCCTCATGGTACCGATACCAAAATAGCATTCGATG-
1 TTCAAGGGTATCGATACCTCCTCAAGGTATCGATACCAAAATAGCATTCGATGT
** * *
52430 TTCAAGGGTATCGATACCTCCTCAAGGTATCGATACCAATCTGGTATTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTATCGATACCAAAATAGCATTCGATGT
*
52484 TTCAAGGGTATCGATATCATCCTTC-AGGTATCGATA
1 TTCAAGGGTATCGATA-CCTCC-TCAAGGTATCGATA
52520 ATACCCCTTA
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
52 13 0.16
53 33 0.42
54 16 0.20
55 15 0.19
56 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTCCTCAAGGTATCGATACCAAAATAGCATTCGATGT
Done.