Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004162.1 Hibiscus syriacus cultivar Beakdansim tig00009103_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: 63100
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1390 original size:14 final size:14
Alignment explanation
Indices: 1371--1406 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1361 ATTGTTTAAT
1371 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1385 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1399 TGATTTGT
1 TGATTTGT
1407 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1587 original size:19 final size:19
Alignment explanation
Indices: 1565--1715 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
1555 CGAAACTAAA
1565 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1584 TTCGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1599 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1617 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1631 TTCGCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1650 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1665 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1683 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1702 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1716 AGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1611 original size:33 final size:32
Alignment explanation
Indices: 1569--1695 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
1559 ACTAAATTCG
*
1569 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
1602 CGTTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
1635 CGTTGCAATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1668 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1696 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1646 original size:66 final size:66
Alignment explanation
Indices: 1562--1694 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1552 ACGCGAAACT
* *
1562 AAATTCGCGTTGCGATTTTCATTTCGCATTGTGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1627 G
66 G
*
1628 AAATTCGCGTTGCAATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1693 G
66 G
1694 A
1 A
1695 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTCGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:3990 original size:12 final size:12
Alignment explanation
Indices: 3973--3997 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3963 TCTTCGGGGA
3973 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3985 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3997 C
1 C
3998 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:5058 original size:20 final size:20
Alignment explanation
Indices: 5025--5098 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
5015 AATTTGGAAA
* *
5025 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
5045 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
5066 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
*
5086 TTCGCAACGAGAT
1 ATCGCAACGAGAT
5099 TCTAAAAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 25 0.58
21 14 0.33
22 2 0.05
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:5067 original size:41 final size:40
Alignment explanation
Indices: 5022--5113 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 40
5012 GCGAATTTGG
*
5022 AAAATCGCAATGCGATACTGACTATCGCAACGAGATAATA
1 AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
* * * **
5062 CAAAATCGCAACGAGATTCTGACTTTCGCAACGAGATTCTA
1 -AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
5103 AAAATCGCAAT
1 AAAATCGCAAT
5114 CATCTTCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 10 0.23
41 34 0.77
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (40 bp):
AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
Found at i:5110 original size:20 final size:20
Alignment explanation
Indices: 5045--5112 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
5035 GATACTGACT
**
5045 ATCGCAACGAGATAATACAAA
1 ATCGCAACGAGATTCTA-AAA
* **
5066 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTAAAA
*
5086 TTCGCAACGAGATTCTAAAA
1 ATCGCAACGAGATTCTAAAA
5106 ATCGCAA
1 ATCGCAA
5113 TCATCTTCAA
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 23 0.62
21 14 0.38
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGATTCTAAAA
Found at i:5382 original size:20 final size:20
Alignment explanation
Indices: 5309--5384 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
5299 CATTCATTGA
**
5309 CTATCGCAACGCGAAAATGG
1 CTATCGCAACTAGAAAATGG
* *
5329 CTATCGCAA-TTG-AAATGA
1 CTATCGCAACTAGAAAATGG
**
5347 AAATCGCAAC-ACGAAAATGG
1 CTATCGCAACTA-GAAAATGG
5367 CTATCGCAACTAGAAAAT
1 CTATCGCAACTAGAAAAT
5385 CGCAATGCGA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
18 12 0.28
19 2 0.05
20 28 0.65
21 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
CTATCGCAACTAGAAAATGG
Found at i:5427 original size:14 final size:14
Alignment explanation
Indices: 5408--5461 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
5398 GAAAATCGCA
5408 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
5422 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
5439 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
5455 TTGCGAT
1 TTGCGAT
5462 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:5427 original size:33 final size:33
Alignment explanation
Indices: 5390--5460 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
5380 AAAATCGCAA
5390 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
5423 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
5456 TGCGA
1 TGCGA
5461 TAGTCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:7079 original size:41 final size:42
Alignment explanation
Indices: 7034--7125 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
7024 CCTCTTCAAC
*
7034 GATGACAGTGGCCTCTTGAACG-GTGGAGGGGACTCTGGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTGGAGG
* * *
7075 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTGGAGG
*
7117 AATGACAGG
1 GATGACAGG
7126 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 20 0.45
42 24 0.55
ACGTcount: A:0.23, C:0.15, G:0.41, T:0.21
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTGGAGG
Found at i:7509 original size:20 final size:20
Alignment explanation
Indices: 7486--7552 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
7476 AAACTTACTT
*
7486 TCGCAACGCGGAAATGACTC
1 TCGCAACGCGGAAATGACTA
*
7506 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
7526 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
7545 TCGCAACG
1 TCGCAACG
7553 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:7600 original size:19 final size:19
Alignment explanation
Indices: 7578--7644 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
7568 GAAACACAAA
7578 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTTATT
* *
7597 TCGCGTTGCGA--TTT-TG
1 TCGCATTGCGATTTTTATT
*
7613 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTTATT
*
7630 TCGCATTGCGGTTTT
1 TCGCATTGCGATTTT
7645 GTCTTTGCGA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
14 6 0.16
16 6 0.16
17 7 0.18
19 19 0.50
ACGTcount: A:0.10, C:0.18, G:0.22, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTTATT
Found at i:7625 original size:33 final size:33
Alignment explanation
Indices: 7583--7674 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
7573 ACAAATCGCA
* *
7583 TTGCGATTTTTATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
* *
7616 TTGCGATTTTCATTTCGCATTGCGGTTTTGTCT
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
7649 TTGCGATTTTCATTTCGTATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
7675 AGCCATTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.11, C:0.16, G:0.22, T:0.51
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:7673 original size:19 final size:19
Alignment explanation
Indices: 7616--7674 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
7606 GATTTTGTCG
*
7616 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGTA
* *
7635 TTGCG-GTTT--TGTC-T-
1 TTGCGATTTTCATTTCGTA
7649 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGTA
7668 TTGCGAT
1 TTGCGAT
7675 AGCCATTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
14 5 0.17
15 3 0.10
16 3 0.10
17 3 0.10
18 4 0.13
19 12 0.40
ACGTcount: A:0.12, C:0.17, G:0.20, T:0.51
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGTA
Found at i:7691 original size:20 final size:20
Alignment explanation
Indices: 7668--7713 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
7658 TCATTTCGTA
7668 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
* *
7688 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTTCGCG
7708 TTGCGA
1 TTGCGA
7714 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCG
Found at i:8271 original size:18 final size:18
Alignment explanation
Indices: 8248--8295 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
8238 CGGGTCAATC
8248 AGGTGATGGCTCTGGGCG
1 AGGTGATGGCTCTGGGCG
* *
8266 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGCG
8284 AGGTGATGGCTC
1 AGGTGATGGCTC
8296 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.46, T:0.25
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGCG
Found at i:9639 original size:20 final size:20
Alignment explanation
Indices: 9614--9656 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
9604 AATAGTTTCT
9614 GAAAATGAA-AATCGCAACAC
1 GAAAAT-AACAATCGCAACAC
*
9634 GAAAATAACAATCGCAACGC
1 GAAAATAACAATCGCAACAC
9654 GAA
1 GAA
9657 TTTGACTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.53, C:0.21, G:0.16, T:0.09
Consensus pattern (20 bp):
GAAAATAACAATCGCAACAC
Found at i:9961 original size:22 final size:22
Alignment explanation
Indices: 9934--9977 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
9924 GATGGAGATA
9934 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
9956 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
9978 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:10195 original size:20 final size:20
Alignment explanation
Indices: 10170--10236 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
10160 GTATTATCTC
*
10170 GTTGCGAAAGTCAGTATTGA
1 GTTGCGAAAGTCAGTATCGA
* *
10190 GTTGCGAAATTAAGTATCGA
1 GTTGCGAAAGTCAGTATCGA
*
10210 GTTGCGAAAGTCAGTATCGT
1 GTTGCGAAAGTCAGTATCGA
10230 GTTGCGA
1 GTTGCGA
10237 TTTTGTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30
Consensus pattern (20 bp):
GTTGCGAAAGTCAGTATCGA
Found at i:10280 original size:20 final size:20
Alignment explanation
Indices: 10255--10297 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
10245 TATTGCGTTA
*
10255 CGATTTTCAAATTCGCATTG
1 CGATTTACAAATTCGCATTG
**
10275 CGATTTACTTATTCGCATTG
1 CGATTTACAAATTCGCATTG
10295 CGA
1 CGA
10298 ATTGGGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (20 bp):
CGATTTACAAATTCGCATTG
Found at i:13857 original size:30 final size:32
Alignment explanation
Indices: 13811--13886 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
13801 ATTGAAAACA
*
13811 AATGTATATCTAATGTTAAGAA-GATCAATA-AT
1 AATGTATA--TAATGTTAAAAATGATCAATATAT
* **
13843 AATGTATATAATGTTAAAAATTATGTATATAT
1 AATGTATATAATGTTAAAAATGATCAATATAT
13875 AATGTATATAAT
1 AATGTATATAAT
13887 ATATTACGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 11 0.29
31 5 0.13
32 22 0.58
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (32 bp):
AATGTATATAATGTTAAAAATGATCAATATAT
Found at i:34356 original size:14 final size:14
Alignment explanation
Indices: 34337--34364 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34327 TCGATTATAT
34337 GTTCATTTATGTTC
1 GTTCATTTATGTTC
34351 GTTCATTTATGTTC
1 GTTCATTTATGTTC
34365 ATTTATATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:34668 original size:10 final size:10
Alignment explanation
Indices: 34653--34692 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
34643 TATTATGTTC
*
34653 GTTCGTTTGT
1 GTTCGTTTAT
*
34663 GTTCGTTTAC
1 GTTCGTTTAT
34673 GTTCGTTTAT
1 GTTCGTTTAT
34683 GTTCGTTTAT
1 GTTCGTTTAT
34693 CATTTAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.07, C:0.12, G:0.23, T:0.57
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:34677 original size:20 final size:20
Alignment explanation
Indices: 34652--34691 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
34642 TTATTATGTT
*
34652 CGTTCGTTTGTGTTCGTTTA
1 CGTTCGTTTATGTTCGTTTA
34672 CGTTCGTTTATGTTCGTTTA
1 CGTTCGTTTATGTTCGTTTA
34692 TCATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.15, G:0.23, T:0.55
Consensus pattern (20 bp):
CGTTCGTTTATGTTCGTTTA
Found at i:34787 original size:16 final size:16
Alignment explanation
Indices: 34766--34796 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34756 CAAAAAAAAT
34766 GTGTTCATTTATGTTC
1 GTGTTCATTTATGTTC
*
34782 GTGTTCGTTTATGTT
1 GTGTTCATTTATGTT
34797 TGTTTATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.23, T:0.58
Consensus pattern (16 bp):
GTGTTCATTTATGTTC
Found at i:36877 original size:19 final size:19
Alignment explanation
Indices: 36822--36878 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
36812 ATTTTTTTTG
36822 TATTAAAATA-ATATTATT
1 TATTAAAATATATATTATT
* *
36840 AATTAACAAATATTTTATTATT
1 TATT-A-AAATA-TATATTATT
36862 TATTAAAATATATATTA
1 TATTAAAATATATATTA
36879 GTTAACATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
18 3 0.10
19 7 0.23
20 10 0.32
21 1 0.03
22 10 0.32
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTAAAATATATATTATT
Found at i:36884 original size:38 final size:40
Alignment explanation
Indices: 36812--36899 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 40
36802 TTAGGGTTGG
36812 ATTTTTT-TTGTATTAAAATAATATTATTAATTAACA-AAT
1 ATTTTTTATT-TATTAAAATAATATTATTAATTAACATAAT
* *
36851 ATTTTATTATTTATTAAAAT-ATA-TATTAGTTAACATATT
1 ATTTT-TTATTTATTAAAATAATATTATTAATTAACATAAT
36890 ATTTTTTATT
1 ATTTTTTATT
36900 ATTTAGTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
38 16 0.36
39 15 0.34
40 11 0.25
41 2 0.05
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (40 bp):
ATTTTTTATTTATTAAAATAATATTATTAATTAACATAAT
Found at i:36898 original size:34 final size:38
Alignment explanation
Indices: 36812--36900 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 38
36802 TTAGGGTTGG
36812 ATTT-TTTTTGTATTAAAATAATATTATTAATTAACAAAT
1 ATTTATTTTT-TATTAAAATAATATTATTAATTAAC-AAT
* *
36851 ATTTTATTATTTATTAAAAT-ATA-TATTAGTTAAC-AT
1 A-TTTATTTTTTATTAAAATAATATTATTAATTAACAAT
36887 A-TTATTTTTTATTA
1 ATTTATTTTTTATTA
36901 TTTAGTAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
34 12 0.27
36 3 0.07
38 10 0.22
39 4 0.09
40 12 0.27
41 4 0.09
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (38 bp):
ATTTATTTTTTATTAAAATAATATTATTAATTAACAAT
Found at i:39577 original size:21 final size:21
Alignment explanation
Indices: 39543--39595 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
39533 CCCTATATCC
39543 TAAA-TCTCAAACCTCAAATCA
1 TAAACTCT-AAACCTCAAATCA
* * *
39564 TATACTCTAAACCTTAAATCC
1 TAAACTCTAAACCTCAAATCA
39585 TAAACTCTAAA
1 TAAACTCTAAA
39596 ACATAAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAACTCTAAACCTCAAATCA
Found at i:39602 original size:21 final size:21
Alignment explanation
Indices: 39539--39602 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
39529 TCCACCCTAT
* *
39539 ATCCTAAA-TCTCAAACCTCAA
1 ATCCTAAACTCTAAAACAT-AA
* * * *
39560 ATCATATACTCTAAACCTTAA
1 ATCCTAAACTCTAAAACATAA
39581 ATCCTAAACTCTAAAACATAA
1 ATCCTAAACTCTAAAACATAA
39602 A
1 A
39603 GTTTAAATAT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 26 0.79
22 7 0.21
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (21 bp):
ATCCTAAACTCTAAAACATAA
Found at i:39752 original size:3 final size:3
Alignment explanation
Indices: 39744--39785 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
39734 TAACCCATAT
39744 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39786 TTATTATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:49433 original size:16 final size:17
Alignment explanation
Indices: 49403--49434 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49393 ATATTTATTT
49403 ATATAAAATATAATATA
1 ATATAAAATATAATATA
49420 ATATAAAA-ATAATAT
1 ATATAAAATATAATAT
49435 TATGATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:50905 original size:14 final size:14
Alignment explanation
Indices: 50886--50921 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
50876 GACAAACATC
50886 GAAAGAACGAAAGA
1 GAAAGAACGAAAGA
50900 GAAAGAACGAAAGA
1 GAAAGAACGAAAGA
50914 GAAAGAAC
1 GAAAGAAC
50922 TTCCGATACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (14 bp):
GAAAGAACGAAAGA
Found at i:51182 original size:2 final size:2
Alignment explanation
Indices: 51175--51205 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
51165 TTTTGCTTCT
51175 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
51206 TCTTTGTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:60464 original size:3 final size:3
Alignment explanation
Indices: 60456--60481 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
60446 GACTAAAACG
60456 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
60482 CACACACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.