Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009282.1 Hibiscus syriacus cultivar Beakdansim tig00112969_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: 71792
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:3645 original size:18 final size:17
Alignment explanation
Indices: 3624--3686 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
3614 TATGATCAAA
3624 ATTAAATAAAATAATATT
1 ATTAAATAAAAT-ATATT
* *
3642 ATTAATTAATATCATATT
1 ATTAAATAAAAT-ATATT
* *
3660 TTTAAGTATAAATATATT
1 ATTAAATA-AAATATATT
3678 ATTTAAATA
1 A-TTAAATA
3687 GAATTTAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 26 0.74
19 9 0.26
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
ATTAAATAAAATATATT
Found at i:4259 original size:13 final size:14
Alignment explanation
Indices: 4235--4276 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
4225 AAATAAAATT
4235 ATTTTCTAAAAAAC
1 ATTTTCTAAAAAAC
*
4249 ATTTTCTAAAAAAA
1 ATTTTCTAAAAAAC
*
4263 ATTATTCTGAAAAA
1 ATT-TTCTAAAAAA
4277 TAAAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (14 bp):
ATTTTCTAAAAAAC
Found at i:5188 original size:19 final size:19
Alignment explanation
Indices: 5164--5201 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5154 ATAAGTCATG
5164 TACTTTTTGGATTTGTTTT
1 TACTTTTTGGATTTGTTTT
5183 TACTTTTTGGATTTGTTTT
1 TACTTTTTGGATTTGTTTT
5202 CTCTCTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.05, G:0.16, T:0.68
Consensus pattern (19 bp):
TACTTTTTGGATTTGTTTT
Found at i:9463 original size:21 final size:21
Alignment explanation
Indices: 9430--9482 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
9420 ATTCTGACTA
9430 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
9451 TCGCGTTGTGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
9472 TCGCAATGCGA
1 TCGCATTGCGA
9483 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:9514 original size:20 final size:20
Alignment explanation
Indices: 9491--9604 Score: 156
Period size: 20 Copynumber: 5.7 Consensus size: 20
9481 GAATATGTAA
* *
9491 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
* * *
9511 ATCGAAACGCGATTCTAATT
1 ATCGCAACGCGATTCTGACT
*
9531 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
9551 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
9571 ATCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTCTGACT
*
9591 ATCGCAATGCGATT
1 ATCGCAACGCGATT
9605 TTCAAAGCGC
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:9804 original size:22 final size:22
Alignment explanation
Indices: 9779--9843 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
9769 GGCGACATCC
9779 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
9801 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
9823 GTCCCAATCTCCGACGAAATC
1 GTCCCCATCTCCGACGAAATC
9844 CGCCTATCTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.28, C:0.40, G:0.14, T:0.18
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:10208 original size:19 final size:20
Alignment explanation
Indices: 10178--10215 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
10168 TTTAGTATTT
10178 GAAATCGAAAATCGCAACGC
1 GAAATCGAAAATCGCAACGC
10198 GAAAT-GAAAATCGCAACG
1 GAAATCGAAAATCGCAACG
10216 ACAGAATCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (20 bp):
GAAATCGAAAATCGCAACGC
Found at i:11014 original size:300 final size:300
Alignment explanation
Indices: 10423--11024 Score: 1125
Period size: 300 Copynumber: 2.0 Consensus size: 300
10413 TATTGTTCTT
*
10423 GGTATATCTTCACAGTGTAGTTTTTGGTATATCTAACTTGGTATGTTTATTGTTTTTGTAGAACT
1 GGTATATCTTCACAGTGTAGTTTTTGGTATATCTAACTTGGTATGTTTATTGTTTTTATAGAACT
* *
10488 TTTATTCGGCTCAATTGACCTTAAGAAATAAAGTAAGCTTGGCCAAAACAATTGCGTCGAAGCTT
66 TTTATTCGACTCAATTGACCTTAAGAAATAAAGTAAGCCTGGCCAAAACAATTGCGTCGAAGCTT
10553 TCACATGCACAAAGAAAAATATTTGAGGATACTTGCTTCGGGCCATGGCTGAAAGTACAACATCC
131 TCACATGCACAAAGAAAAATATTTGAGGATACTTGCTTCGGGCCATGGCTGAAAGTACAACATCC
10618 GGGTGGAGATGCTATGTTGACCCCATCTGTTTCTTCAAACCATGACTAGAGATCTACCAGAGACT
196 GGGTGGAGATGCTATGTTGACCCCATCTGTTTCTTCAAACCATGACTAGAGATCTACCAGAGACT
10683 ATACAACGTCGTAATGAAGAGATATGTTTGATTTTCCATC
261 ATACAACGTCGTAATGAAGAGATATGTTTGATTTTCCATC
*
10723 GGTATATCTTCACAGTGTAGTTTTTGGTATGTCTAACTTGGTATGTTTATTGTTTTTATAGAACT
1 GGTATATCTTCACAGTGTAGTTTTTGGTATATCTAACTTGGTATGTTTATTGTTTTTATAGAACT
10788 TTTATTCGACTCAATTGACCTTAAGAAATAAAGTAAGCCTGGCCAAAACAATTGCGTCGAAGCTT
66 TTTATTCGACTCAATTGACCTTAAGAAATAAAGTAAGCCTGGCCAAAACAATTGCGTCGAAGCTT
*
10853 TCACCTGCACAAAGAAAAATATTTGAGGATACTTGCTTCGGGCCATGGCTGAAAGTACAACATCC
131 TCACATGCACAAAGAAAAATATTTGAGGATACTTGCTTCGGGCCATGGCTGAAAGTACAACATCC
*
10918 GGGTGGAGATGCTATGTTGA-CCCATCTGTTTCTTCAAACCATGACTAGCGATCTACCAGAGACT
196 GGGTGGAGATGCTATGTTGACCCCATCTGTTTCTTCAAACCATGACTAGAGATCTACCAGAGACT
*
10982 ATACAACGTCGTGATGAAGAGATATGGTTTGATTTTCCATC
261 ATACAACGTCGTAATGAAGAGATAT-GTTTGATTTTCCATC
11023 GG
1 GG
11025 CGTATACGTG
Statistics
Matches: 294, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
299 67 0.23
300 227 0.77
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (300 bp):
GGTATATCTTCACAGTGTAGTTTTTGGTATATCTAACTTGGTATGTTTATTGTTTTTATAGAACT
TTTATTCGACTCAATTGACCTTAAGAAATAAAGTAAGCCTGGCCAAAACAATTGCGTCGAAGCTT
TCACATGCACAAAGAAAAATATTTGAGGATACTTGCTTCGGGCCATGGCTGAAAGTACAACATCC
GGGTGGAGATGCTATGTTGACCCCATCTGTTTCTTCAAACCATGACTAGAGATCTACCAGAGACT
ATACAACGTCGTAATGAAGAGATATGTTTGATTTTCCATC
Found at i:12324 original size:18 final size:18
Alignment explanation
Indices: 12301--12350 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
12291 TTTACTCGTA
12301 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
12319 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
12337 ATTTCACTTAGATT
1 ATTTCACTTAGATT
12351 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:12597 original size:20 final size:21
Alignment explanation
Indices: 12568--12621 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
12558 GCGATTCTCT
*
12568 TGTTGGGATAGTCAAATTCG-
1 TGTTGCGATAGTCAAATTCGC
**
12588 TGTTGCGATAGTCATTTTCGC
1 TGTTGCGATAGTCAAATTCGC
12609 T-TTGCGATAGTCA
1 TGTTGCGATAGTCA
12622 CTCGTGTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.39
Consensus pattern (21 bp):
TGTTGCGATAGTCAAATTCGC
Found at i:13197 original size:21 final size:22
Alignment explanation
Indices: 13124--13199 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 22
13114 GACTCACTAG
**
13124 TCAT-CGTTCAAGAGGCCTCCCC
1 TCATCCGTTCAAGAGGCC-CCTA
13146 T-AT-CGTTCAAGAGGCCCCTA
1 TCATCCGTTCAAGAGGCCCCTA
* * *
13166 TCATCC-CTCAAGAGTCCCCTC
1 TCATCCGTTCAAGAGGCCCCTA
13187 TCA-CCGTTCAAGA
1 TCATCCGTTCAAGA
13200 CGCCACTGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 5 0.11
21 38 0.84
22 2 0.04
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (22 bp):
TCATCCGTTCAAGAGGCCCCTA
Found at i:13215 original size:21 final size:20
Alignment explanation
Indices: 13124--13220 Score: 61
Period size: 21 Copynumber: 4.7 Consensus size: 20
13114 GACTCACTAG
**
13124 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGA-GCC-CCTA
13146 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGA-GCCCCTA
** *
13166 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAG-CCCCTA
* * *
13187 TCACCGTTCAAGACGCCACTG
1 TCATCGTTCAAGA-GCCCCTA
*
13208 TCATCGTTGAAGA
1 TCATCGTTCAAGA
13221 TGTCCCTCCC
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
20 4 0.07
21 54 0.90
22 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (20 bp):
TCATCGTTCAAGAGCCCCTA
Found at i:14794 original size:20 final size:20
Alignment explanation
Indices: 14769--14822 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
14759 AGGTACAATT
*
14769 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
**
14789 TCGCAATACGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
14809 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
14823 TCAATTCGCG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.44, C:0.28, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:14942 original size:20 final size:20
Alignment explanation
Indices: 14865--14995 Score: 150
Period size: 20 Copynumber: 6.8 Consensus size: 20
14855 GCGATTTTCT
*
14865 CGTTGCGATAGTCAAATAC-
1 CGTTGCGATAGTCAAATTCG
* *
14884 CTGTTGCGATAATCAAATTCA
1 C-GTTGCGATAGTCAAATTCG
*
14905 CGTTGCGATAGTCAAATTCT
1 CGTTGCGATAGTCAAATTCG
14925 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
14945 CGTTGC-A-A-T---TTTCG
1 CGTTGCGATAGTCAAATTCG
14959 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
14979 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
14996 GAATGTGTAA
Statistics
Matches: 96, Mismatches: 8, Indels: 15
0.81 0.07 0.13
Matches are distributed among these distances:
14 10 0.10
15 1 0.01
16 1 0.01
17 2 0.02
18 1 0.01
19 2 0.02
20 78 0.81
21 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:14963 original size:94 final size:93
Alignment explanation
Indices: 14816--14995 Score: 245
Period size: 94 Copynumber: 1.9 Consensus size: 93
14806 AAATCGCAAC
* * * *
14816 GCGAAAGTCAATTCGCGTTGCGATAGCCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAA
1 GCGAAAGTCAATTCGCGTTGCGATAGCCAAATACGCGTTGCAATTTTCGCGTTGCGATAGTCAAA
14881 TAC-CTGTTGCGATAATCAAATTCACGTT
66 TACGC-GTTGCGATAATCAAATTCACGTT
* * * *
14909 GCGATAGTCAAATTCTCGTTGCGATAGTCAAATTCGCGTTGCAATTTTCGCGTTGCGATAGTCAA
1 GCGAAAGTC-AATTCGCGTTGCGATAGCCAAATACGCGTTGCAATTTTCGCGTTGCGATAGTCAA
* *
14974 ATTCGCGTTGCGATATTCAAAT
65 ATACGCGTTGCGATAATCAAAT
14996 GAATGTGTAA
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
93 8 0.11
94 66 0.88
95 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (93 bp):
GCGAAAGTCAATTCGCGTTGCGATAGCCAAATACGCGTTGCAATTTTCGCGTTGCGATAGTCAAA
TACGCGTTGCGATAATCAAATTCACGTT
Found at i:15189 original size:18 final size:18
Alignment explanation
Indices: 15166--15200 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
15156 AAGCAGGTTG
*
15166 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
15184 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
15201 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:17474 original size:24 final size:24
Alignment explanation
Indices: 17447--17500 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
17437 CTGAGACATC
*
17447 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
17471 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
17495 ATCAAA
1 ATCAAA
17501 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:17514 original size:24 final size:24
Alignment explanation
Indices: 17463--17514 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
17453 ATCTGAGTAT
** *
17463 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
17487 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
17511 TGAC
1 TGAC
17515 TAGTACTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:18390 original size:20 final size:20
Alignment explanation
Indices: 18367--18425 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
18357 ATCTCGCTGC
* * *
18367 GATAATCATAATCGCGTTGT
1 GATAGTCATAATCGCATTGA
*
18387 GATAGTCAGAATCGCATTGA
1 GATAGTCATAATCGCATTGA
18407 GATAGTCATAATCGCATTG
1 GATAGTCATAATCGCATTG
18426 CGATTTACAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (20 bp):
GATAGTCATAATCGCATTGA
Found at i:18416 original size:40 final size:40
Alignment explanation
Indices: 18330--18429 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 40
18320 GTGTTGCAAC
* * * * * *
18330 AGTCAAAATAGCGTTGCGATAGTTAGAATCTCGCTGCGAT
1 AGTCATAATCGCGTTGCGATAGTCAGAATCGCACTGAGAT
* * *
18370 AATCATAATCGCGTTGTGATAGTCAGAATCGCATTGAGAT
1 AGTCATAATCGCGTTGCGATAGTCAGAATCGCACTGAGAT
*
18410 AGTCATAATCGCATTGCGAT
1 AGTCATAATCGCGTTGCGAT
18430 TTACATATTC
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (40 bp):
AGTCATAATCGCGTTGCGATAGTCAGAATCGCACTGAGAT
Found at i:18469 original size:21 final size:21
Alignment explanation
Indices: 18445--18490 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
18435 TATTCGCATT
18445 GCGAATTCGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
* *
18466 GCGAATTTGGAAAATCGCAAT
1 GCGAATTCGGAAAATCGCAAC
18487 GCGA
1 GCGA
18491 TAATCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:19159 original size:14 final size:15
Alignment explanation
Indices: 19128--19161 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
19118 TTAAAGGATG
19128 AAATTTTAAAAATAA
1 AAATTTTAAAAATAA
*
19143 AAATTTT-AAATTAA
1 AAATTTTAAAAATAA
19157 AAATT
1 AAATT
19162 CGTTACGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTTTAAAAATAA
Found at i:33358 original size:16 final size:16
Alignment explanation
Indices: 33322--33367 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
33312 ATAAATATTA
33322 ATAATTA-A-TATTTT
1 ATAATTATATTATTTT
33336 -TAA-TATATTATTTT
1 ATAATTATATTATTTT
*
33350 ATAATTATATTATATT
1 ATAATTATATTATTTT
33366 AT
1 AT
33368 TAAAAAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 2 0.07
13 4 0.15
14 6 0.22
15 3 0.11
16 12 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATAATTATATTATTTT
Found at i:36472 original size:36 final size:37
Alignment explanation
Indices: 36424--36498 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
36414 ATAGCAAAAG
*
36424 AAATCGTCTTTATTCGAA-TTTTGCCAAAAATAGCAA
1 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
36460 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
1 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
36497 AA
1 AA
36499 TCCCGAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 17 0.46
37 20 0.54
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (37 bp):
AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
Found at i:40979 original size:15 final size:15
Alignment explanation
Indices: 40961--40990 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40951 CCACGGTGCT
40961 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
40976 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
40991 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:41461 original size:36 final size:37
Alignment explanation
Indices: 41413--41487 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
41403 ATAGCAAAAG
*
41413 AAATCGTCTTTATTCGAA-TTTTGCCAAAAATAGCAA
1 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
41449 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
1 AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
41486 AA
1 AA
41488 TCCCGAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 17 0.46
37 20 0.54
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (37 bp):
AAATCGTATTTATTCGAATTTTTGCCAAAAATAGCAA
Found at i:46478 original size:21 final size:21
Alignment explanation
Indices: 46441--46521 Score: 81
Period size: 21 Copynumber: 3.9 Consensus size: 21
46431 CGATCGTTAT
* * *
46441 TATTGATATTATAATTTATAG
1 TATTGATGTGATAATTTATAA
* * *
46462 TGTTGATGTGATGATTTAAAA
1 TATTGATGTGATAATTTATAA
**
46483 TATTGATACGATAATTTATAA
1 TATTGATGTGATAATTTATAA
*
46504 TATTGATGTGATAGTTTA
1 TATTGATGTGATAATTTA
46522 GGAAGATAAT
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.47
Consensus pattern (21 bp):
TATTGATGTGATAATTTATAA
Found at i:60218 original size:38 final size:38
Alignment explanation
Indices: 60146--60225 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
60136 GCGTTTATTT
* *
60146 ATTAAATGAACGAACATGAACAAGATTTGTGTTCGTTA
1 ATTAAATGAACGAACATGAACAAGATCTGCGTTCGTTA
* *
60184 ATTAAATGAACGAACATGAACATAGGTCT-CGTTCGTTC
1 ATTAAATGAACGAACATGAACA-AGATCTGCGTTCGTTA
60222 ATTA
1 ATTA
60226 CGTTCGTGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 33 0.89
39 4 0.11
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (38 bp):
ATTAAATGAACGAACATGAACAAGATCTGCGTTCGTTA
Found at i:60258 original size:14 final size:14
Alignment explanation
Indices: 60236--60309 Score: 130
Period size: 14 Copynumber: 5.3 Consensus size: 14
60226 CGTTCGTGAA
60236 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
60250 CGTTTGGTTATGTT
1 CGTTCGGTTATGTT
60264 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
60278 CGTTTGGTTATGTT
1 CGTTCGGTTATGTT
60292 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
60306 CGTT
1 CGTT
60310 TATGTTCATT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 56 1.00
ACGTcount: A:0.07, C:0.12, G:0.28, T:0.53
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:60268 original size:28 final size:28
Alignment explanation
Indices: 60236--60310 Score: 150
Period size: 28 Copynumber: 2.7 Consensus size: 28
60226 CGTTCGTGAA
60236 CGTTCGGTTATGTTCGTTTGGTTATGTT
1 CGTTCGGTTATGTTCGTTTGGTTATGTT
60264 CGTTCGGTTATGTTCGTTTGGTTATGTT
1 CGTTCGGTTATGTTCGTTTGGTTATGTT
60292 CGTTCGGTTATGTTCGTTT
1 CGTTCGGTTATGTTCGTTT
60311 ATGTTCATTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.07, C:0.12, G:0.28, T:0.53
Consensus pattern (28 bp):
CGTTCGGTTATGTTCGTTTGGTTATGTT
Found at i:61199 original size:23 final size:23
Alignment explanation
Indices: 61169--61233 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
61159 TGGGGCAATG
61169 TCGAGCTTGAATCAAGCTCAAAA
1 TCGAGCTTGAATCAAGCTCAAAA
61192 TCGAGCTTGAATCAAGCTCAAAA
1 TCGAGCTTGAATCAAGCTCAAAA
* * *
61215 TAGAGCTTCAATCGAGCTC
1 TCGAGCTTGAATCAAGCTC
61234 GAGTCTCGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (23 bp):
TCGAGCTTGAATCAAGCTCAAAA
Found at i:61478 original size:16 final size:16
Alignment explanation
Indices: 61457--61495 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
61447 GGGTCTCCAA
61457 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
61473 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
61489 CGTTTAT
1 CGTTTAT
61496 TTATTAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:70835 original size:43 final size:43
Alignment explanation
Indices: 70774--70859 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
70764 CGGACTTTTA
*
70774 AAATTCTAGTTGACGAAAAAATATTATCAATAAATAAGATTAT
1 AAATTCTAGTTGACGAAAAAAGATTATCAATAAATAAGATTAT
* *
70817 AAATTCTAGTTGACGAAAATAGATTATCAATAGATAAGATTAT
1 AAATTCTAGTTGACGAAAAAAGATTATCAATAAATAAGATTAT
70860 TAACAGATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.33
Consensus pattern (43 bp):
AAATTCTAGTTGACGAAAAAAGATTATCAATAAATAAGATTAT
Done.