Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001475.1 Hibiscus syriacus cultivar Beakdansim tig00002860_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: 96055
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8233 original size:23 final size:23
Alignment explanation
Indices: 8188--8234 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
8178 ATTTTATGAA
*
8188 AATATATTAATTTAAATATAAAT
1 AATATATTAATTTAAATAGAAAT
* **
8211 AATATATTTATTTATTTAGAAAT
1 AATATATTAATTTAAATAGAAAT
8234 A
1 A
8235 TCATAAAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AATATATTAATTTAAATAGAAAT
Found at i:9863 original size:3 final size:3
Alignment explanation
Indices: 9857--9896 Score: 62
Period size: 3 Copynumber: 12.7 Consensus size: 3
9847 ATTTATTATT
9857 TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A T-AA TAA TA
9897 TTCAAATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 30 0.86
4 4 0.11
5 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17406 original size:20 final size:20
Alignment explanation
Indices: 17381--17430 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
17371 TCTGGGCAGA
17381 GGGAATCGATACCTATGAAG
1 GGGAATCGATACCTATGAAG
17401 GGGAATCGATACCTATGAAG
1 GGGAATCGATACCTATGAAG
17421 GGGAATCGAT
1 GGGAATCGAT
17431 TCCCCTTCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (20 bp):
GGGAATCGATACCTATGAAG
Found at i:17505 original size:21 final size:20
Alignment explanation
Indices: 17466--17503 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17456 AGTATGTTCA
*
17466 GGGGGTATTAATTCCCCCTG
1 GGGGGTATCAATTCCCCCTG
*
17486 GGGGGTATCGATTCCCCC
1 GGGGGTATCAATTCCCCC
17504 CTAAATGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.29, G:0.32, T:0.26
Consensus pattern (20 bp):
GGGGGTATCAATTCCCCCTG
Found at i:18564 original size:23 final size:23
Alignment explanation
Indices: 18530--18641 Score: 104
Period size: 24 Copynumber: 4.8 Consensus size: 23
18520 CAATCTTATA
*
18530 TGGCACTACGGTGAAATTCTACG
1 TGGCACTTCGGTGAAATTCTACG
* * *
18553 TGGCACTTCGGTGCATTTCTACA
1 TGGCACTTCGGTGAAATTCTACG
*
18576 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG--AAATTCTACG
18600 TGGCACTTCGG-GATAAATTCTACG
1 TGGCACTTCGGTG--AAATTCTACG
*
18624 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTGAAATT
18642 TATATGAGCT
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
22 1 0.01
23 32 0.44
24 39 0.53
25 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGAAATTCTACG
Found at i:21278 original size:6 final size:6
Alignment explanation
Indices: 21267--21301 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
21257 CTGACAAAGG
* *
21267 AATTAC AATTAC AATTAC AATTGC AATTGC AATTA
1 AATTAC AATTAC AATTAC AATTAC AATTAC AATTA
21302 TTTTCTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (6 bp):
AATTAC
Found at i:21599 original size:17 final size:17
Alignment explanation
Indices: 21577--21623 Score: 85
Period size: 17 Copynumber: 2.7 Consensus size: 17
21567 TTAAATTAAT
21577 GCGAAAATATAATATAA
1 GCGAAAATATAATATAA
21594 GCGAAAATATAATATAA
1 GCGAAAATATAATATAA
21611 GCGAAAATGATAA
1 GCGAAAAT-ATAA
21624 ATTGAGTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 25 0.86
18 4 0.14
ACGTcount: A:0.57, C:0.06, G:0.15, T:0.21
Consensus pattern (17 bp):
GCGAAAATATAATATAA
Found at i:22262 original size:13 final size:13
Alignment explanation
Indices: 22244--22291 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
22234 AACAAACAAA
22244 AATAAACGAACAT
1 AATAAACGAACAT
*
22257 AATAAAAGAACAT
1 AATAAACGAACAT
*
22270 -A-AAA-GAACAC
1 AATAAACGAACAT
22280 AATAAACGAACA
1 AATAAACGAACA
22292 ACACAAACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 5 0.17
11 4 0.13
12 4 0.13
13 17 0.57
ACGTcount: A:0.67, C:0.15, G:0.08, T:0.10
Consensus pattern (13 bp):
AATAAACGAACAT
Found at i:22277 original size:23 final size:23
Alignment explanation
Indices: 22210--22291 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 23
22200 TCATTTAAAT
* * *
22210 AATAAACGAACGTAAACGAACAC
1 AATAAAAGAACATAAAAGAACAC
* * * *
22233 AA-ACAAACAAAAATAAACGAACAT
1 AATA-AAA-GAACATAAAAGAACAC
22257 AATAAAAGAACATAAAAGAACAC
1 AATAAAAGAACATAAAAGAACAC
*
22280 AATAAACGAACA
1 AATAAAAGAACA
22292 ACACAAACAC
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
22 1 0.02
23 27 0.59
24 17 0.37
25 1 0.02
ACGTcount: A:0.66, C:0.17, G:0.09, T:0.09
Consensus pattern (23 bp):
AATAAAAGAACATAAAAGAACAC
Found at i:25517 original size:25 final size:26
Alignment explanation
Indices: 25487--25572 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 26
25477 ACTAAATTAT
*
25487 TATATTA-ATGTTAAATATATATATA
1 TATATTACATATTAAATATATATATA
*
25512 TATATTACATATTATTAATA-ATTTA-A
1 TATATTACATATTA--AATATATATATA
*
25538 TAATATTATATTATTAAA-ATAATATATA
1 T-ATATTACA-TATTAAATAT-ATATATA
25566 TATATTA
1 TATATTA
25573 ATAATTTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
25 8 0.16
26 9 0.18
27 21 0.43
28 11 0.22
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (26 bp):
TATATTACATATTAAATATATATATA
Found at i:25554 original size:17 final size:18
Alignment explanation
Indices: 25503--25581 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 18
25493 AATGTTAAAT
25503 ATATATATATATATTACATA
1 ATAT-TATATATATTA-ATA
*
25523 TTATTA-ATA-ATTTAATA
1 ATATTATATATA-TTAATA
25540 ATATTATAT-TATTAA-A
1 ATATTATATATATTAATA
25556 ATAATATATATATATTAATA
1 AT-AT-TATATATATTAATA
25576 AT-TTAT
1 ATATTAT
25582 TTAAAAATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
16 3 0.06
17 18 0.36
18 15 0.30
19 8 0.16
20 6 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTATATATATTAATA
Found at i:25560 original size:22 final size:24
Alignment explanation
Indices: 25511--25577 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 24
25501 ATATATATAT
*
25511 ATATATTACATATTATTAATAATTTA
1 ATATA-TATATATTATTAATAA-TTA
25537 ATA-ATATTATATTATTAA-AA-TA
1 ATATATA-TATATTATTAATAATTA
*
25559 ATATATATATATTAATAAT
1 ATATATATATATTATTAAT
25578 TTATTTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
22 15 0.42
23 3 0.08
24 4 0.11
25 11 0.31
26 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATATATATATTATTAATAATTA
Found at i:25602 original size:58 final size:56
Alignment explanation
Indices: 25484--25658 Score: 148
Period size: 55 Copynumber: 3.1 Consensus size: 56
25474 AATACTAAAT
* *
25484 TATTATATTAATGTTAAATATATATATATATATTACATATTATTAATAATTTAATAA
1 TATTATATT-ATGTAAAATATATATATATATATTACATATTATTAAAAATTTAATAA
*
25541 TATTATATTAT-TAAAATA-ATATATATATATTA-ATAATTTATTTAAAAATTTCAT-A
1 TATTATATTATGTAAAATATATATATATATATTACAT-A-TTA-TTAAAAATTTAATAA
* * * * *
25596 TCA-TATTTTAT-TATAATATATCTGAGTATATATTA-ATATAATATTAAAAATATAATAT
1 T-ATTATATTATGTAAAATATATAT-A-TATATATTACATAT--TATTAAAAATTTAATAA
25654 TATTA
1 TATTA
25659 AAATTATATT
Statistics
Matches: 98, Mismatches: 9, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
53 2 0.02
54 15 0.15
55 24 0.24
56 18 0.18
57 23 0.23
58 16 0.16
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (56 bp):
TATTATATTATGTAAAATATATATATATATATTACATATTATTAAAAATTTAATAA
Found at i:25653 original size:19 final size:18
Alignment explanation
Indices: 25629--25672 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
25619 GAGTATATAT
25629 TAATATAATATTAAAAATA
1 TAATAT-ATATTAAAAATA
*
25648 TAATAT-TATTAAAATTA
1 TAATATATATTAAAAATA
*
25665 TATTATAT
1 TAATATAT
25673 GTATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 15 0.68
18 1 0.05
19 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATATATATTAAAAATA
Found at i:25727 original size:19 final size:19
Alignment explanation
Indices: 25703--25739 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25693 ATTCATATCT
25703 TATTAAAATAATATTAAAA
1 TATTAAAATAATATTAAAA
**
25722 TATTAATTTAATATTAAA
1 TATTAAAATAATATTAAA
25740 CGTAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TATTAAAATAATATTAAAA
Found at i:28437 original size:6 final size:6
Alignment explanation
Indices: 28428--28465 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
28418 TCGTGAGCTG
28428 GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT GA
1 GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT GA
28466 TCTCTCTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.18, C:0.32, G:0.34, T:0.16
Consensus pattern (6 bp):
GAGCCT
Found at i:32071 original size:20 final size:20
Alignment explanation
Indices: 32042--32114 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
32032 GCAACTGAAA
*
32042 ATCGCGTTGCGATTTTCCAT
1 ATCGCATTGCGATTTTCCAT
*
32062 ATCGCATTGCGATTTTTCAT
1 ATCGCATTGCGATTTTCCAT
*
32082 TTCGCATTGCGATTTTCCAT
1 ATCGCATTGCGATTTTCCAT
* *
32102 TTCGCGTTGCGAT
1 ATCGCATTGCGAT
32115 AGTTGAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.42
Consensus pattern (20 bp):
ATCGCATTGCGATTTTCCAT
Found at i:32129 original size:21 final size:21
Alignment explanation
Indices: 32103--32152 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
32093 ATTTTCCATT
32103 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
32124 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
32145 TCGCGTTG
1 TCGCGTTG
32153 TGATTTTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:32182 original size:20 final size:20
Alignment explanation
Indices: 32080--32182 Score: 57
Period size: 21 Copynumber: 5.0 Consensus size: 20
32070 GCGATTTTTC
* ** *
32080 ATTTCGCATTGCGATTTTCC
1 ATTTCGCGTTGCGATAGTCT
32100 ATTTCGCGTTGCGATAGT-T
1 ATTTCGCGTTGCGATAGTCT
**
32119 GAAAATCGCGTTGCGATAGT-T
1 --ATTTCGCGTTGCGATAGTCT
** * **
32140 GAAAATCGCGTTGTGATTTTCT
1 --ATTTCGCGTTGCGATAGTCT
32162 ATTTCGCGTTGCGATAGTCT
1 ATTTCGCGTTGCGATAGTCT
32182 A
1 A
32183 CAGTTGTCGT
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
20 31 0.47
21 34 0.52
22 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.39
Consensus pattern (20 bp):
ATTTCGCGTTGCGATAGTCT
Found at i:32193 original size:22 final size:22
Alignment explanation
Indices: 32168--32239 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
32158 TTCTATTTCG
32168 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
** * *
32190 CGTTGCGATTTTCCA-AATT-T
1 CGTTGCGATAGTCTACAGTTGT
32210 -GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
32231 CGTTGCGAT
1 CGTTGCGAT
32240 TTTTCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 11 0.28
20 4 0.10
21 4 0.10
22 20 0.51
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:32214 original size:41 final size:41
Alignment explanation
Indices: 32168--32261 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
32158 TTCTATTTCG
32168 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
* *
32209 TGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
*
32250 CGTTGCAATAGT
1 CGTTGCGATAGT
32262 TAAAAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:32230 original size:19 final size:19
Alignment explanation
Indices: 32169--32230 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
32159 TCTATTTCGC
32169 GTTGCGATAGTCTACAGTTGT
1 GTTGCGATAGTCTACAG-T-T
** * * *
32190 CGTTGCGATTTTCCAAATTT
1 -GTTGCGATAGTCTACAGTT
32210 GTTGCGATAGTCTACAGTT
1 GTTGCGATAGTCTACAGTT
32229 GT
1 GT
32231 CGTTGCGATT
Statistics
Matches: 30, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
19 16 0.53
20 1 0.03
21 1 0.03
22 12 0.40
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.40
Consensus pattern (19 bp):
GTTGCGATAGTCTACAGTT
Found at i:32254 original size:19 final size:19
Alignment explanation
Indices: 32189--32255 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
32179 TCTACAGTTG
*
32189 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTACAAAT
* * **
32208 TTGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTACAAAT
*
32229 GTCGTTGCGATTTTTCAAAT
1 -TCGTTGCGATTTTACAAAT
32249 TCGTTGC
1 TCGTTGC
32256 AATAGTTAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
19 16 0.46
20 5 0.14
21 5 0.14
22 9 0.26
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGTTGCGATTTTACAAAT
Found at i:32916 original size:6 final size:6
Alignment explanation
Indices: 32900--32930 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
32890 TCTCGTCTCG
32900 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GG
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GG
32931 GGTAGATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.16, G:0.55, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:36126 original size:16 final size:16
Alignment explanation
Indices: 36105--36137 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
36095 GATTAAGCGT
36105 TGAATGATTCAAATGC
1 TGAATGATTCAAATGC
*
36121 TGAATGATTCAGATGC
1 TGAATGATTCAAATGC
36137 T
1 T
36138 CTGTATGAAT
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:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (16 bp):
TGAATGATTCAAATGC
Found at i:36214 original size:27 final size:27
Alignment explanation
Indices: 36184--36247 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
36174 ATAATGATTC
36184 TGAATCATTCTGAATGTACTTTGATGT
1 TGAATCATTCTGAATGTACTTTGATGT
36211 TGAATCATTCTGAATGTACTTTGATGT
1 TGAATCATTCTGAATGTACTTTGATGT
36238 TGAATCATTC
1 TGAATCATTC
36248 AACACTGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (27 bp):
TGAATCATTCTGAATGTACTTTGATGT
Found at i:38481 original size:17 final size:19
Alignment explanation
Indices: 38439--38479 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
38429 ATAAAATTTA
*
38439 AAAAATATTTAGAAGTAAT
1 AAAAATATTTAGAAATAAT
*
38458 AAAAATATTTA-AAATGAT
1 AAAAATATTTAGAAATAAT
38476 AAAA
1 AAAA
38480 TAAATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (19 bp):
AAAAATATTTAGAAATAAT
Found at i:38877 original size:44 final size:44
Alignment explanation
Indices: 38814--38912 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 44
38804 ACTGATACAT
*
38814 GTATCGATACCAATATGTAAAAATACACTACAA-TACCAATACTG
1 GTATCGATACTAATATGTAAAAATACACTA-AAGTACCAATACTG
* * * *
38858 GTATCGATACTAGTGTGTAAAAATACACTAAAGTACCGATATTG
1 GTATCGATACTAATATGTAAAAATACACTAAAGTACCAATACTG
38902 GTA-CTGATACT
1 GTATC-GATACT
38913 CCTGTTAAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 3 0.06
44 45 0.94
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.28
Consensus pattern (44 bp):
GTATCGATACTAATATGTAAAAATACACTAAAGTACCAATACTG
Found at i:39766 original size:26 final size:26
Alignment explanation
Indices: 39733--39794 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
39723 GACTGCCGTG
39733 GTAGTTTCTAGAAGATCCAGTCAGT-A
1 GTAGTTTCTAGAAGATCCAGTCA-TCA
*
39759 GTAGTTTCTAGAAGGTCCAGTCATCA
1 GTAGTTTCTAGAAGATCCAGTCATCA
*
39785 GTATTTTCTA
1 GTAGTTTCTA
39795 TAATGTACCG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 1 0.03
26 32 0.97
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.35
Consensus pattern (26 bp):
GTAGTTTCTAGAAGATCCAGTCATCA
Found at i:40708 original size:26 final size:26
Alignment explanation
Indices: 40652--40701 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
40642 CTATTTTGCA
40652 TCATTATTGTTCTCAATTATTTACTT
1 TCATTATTGTTCTCAATTATTTACTT
*
40678 TCATTATT-TT-TCAATTTTTTACTT
1 TCATTATTGTTCTCAATTATTTACTT
40702 AGTCATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.57
25 2 0.09
26 8 0.35
ACGTcount: A:0.22, C:0.14, G:0.02, T:0.62
Consensus pattern (26 bp):
TCATTATTGTTCTCAATTATTTACTT
Found at i:49833 original size:22 final size:21
Alignment explanation
Indices: 49785--49856 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
49775 CATCGAAGTG
*
49785 CCACATAATTAT-CCCAAATGA
1 CCACATAATT-TGCCCGAATGA
*
49806 CCACATAGTTTGCACCGAA-GTA
1 CCACATAATTTGC-CCGAATG-A
*
49828 CCACATAATTTTCCCGAATGA
1 CCACATAATTTGCCCGAATGA
49849 CCACATAA
1 CCACATAA
49857 AACCCTCGAC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
20 1 0.02
21 25 0.58
22 17 0.40
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.24
Consensus pattern (21 bp):
CCACATAATTTGCCCGAATGA
Found at i:50444 original size:19 final size:20
Alignment explanation
Indices: 50410--50447 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
50400 AGGTTCAATG
*
50410 TTTCAAGGGTATCGATACCT
1 TTTCAAGGGTACCGATACCT
50430 TTTCAA-GGTACCGATACC
1 TTTCAAGGGTACCGATACC
50448 AATCTGGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
TTTCAAGGGTACCGATACCT
Found at i:50496 original size:20 final size:22
Alignment explanation
Indices: 50471--50522 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
50461 ATATTTTAAG
*
50471 GGTATCGATACCT-TCC-TACA
1 GGTATCGATACCTACCCTTACA
50491 GGTATCGATA-CTACCCTTACA
1 GGTATCGATACCTACCCTTACA
50512 -GTATCGATACC
1 GGTATCGATACC
50523 ACTATCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 21 0.75
21 5 0.18
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (22 bp):
GGTATCGATACCTACCCTTACA
Found at i:59801 original size:3 final size:3
Alignment explanation
Indices: 59793--59841 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
59783 CAATTTGCTT
*
59793 TTA TTA TTA TTA TTA TTA TACA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
59839 TTA
1 TTA
59842 AATAAATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 41 0.95
4 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:61762 original size:148 final size:148
Alignment explanation
Indices: 61470--61748 Score: 397
Period size: 148 Copynumber: 1.9 Consensus size: 148
61460 TAGTCATATT
*
61470 TTAATATTTATTTATTTTTTAATATTAAGAAATGAGTTGTATTAAAGCACCTAGAAGTCATTTTC
1 TTAATATTTATTTATTTTTTAATATTAAGAAATGAGCTGTATTAAAGCACCTAGAAGTCATTTTC
* * * * * *
61535 TGATATTCTTAAATAAATAAATATCCTATTTTTATCAATTATATATATTGATTTATTTTAATTAT
66 TGATATTCTTAAATAAATAAATATCCTATATTTATAAATTAAAAATATTGATATATATTAATTAT
61600 TTTTAGAGAAATATTTTA
131 TTTTAGAGAAATATTTTA
* * *
61618 TTAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCCTTTTC
1 TTAATATTTATTTATTTTTTAATATTAAGAAATGAGCTGTATTAAAGCACCTAGAAGTCATTTTC
*
61683 TGATATT-TCTAAGTAAATAAATAT-CT-TATTTATAAATATAAAAATA-T-ATATATATTAATA
66 TGATATTCT-TAAATAAATAAATATCCTATATTTATAAAT-TAAAAATATTGATATATATTAAT-
61743 TATTTT
128 TATTTT
61749 CTTAAAATTA
Statistics
Matches: 117, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
145 10 0.09
146 16 0.14
147 9 0.08
148 82 0.70
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.48
Consensus pattern (148 bp):
TTAATATTTATTTATTTTTTAATATTAAGAAATGAGCTGTATTAAAGCACCTAGAAGTCATTTTC
TGATATTCTTAAATAAATAAATATCCTATATTTATAAATTAAAAATATTGATATATATTAATTAT
TTTTAGAGAAATATTTTA
Found at i:64058 original size:14 final size:14
Alignment explanation
Indices: 64039--64069 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
64029 TCGGTAATAT
*
64039 GTTCGTTTATGTTC
1 GTTCGTTTATGTGC
64053 GTTCGTTTATGTGC
1 GTTCGTTTATGTGC
64067 GTT
1 GTT
64070 AATTATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.13, G:0.26, T:0.55
Consensus pattern (14 bp):
GTTCGTTTATGTGC
Found at i:64261 original size:10 final size:10
Alignment explanation
Indices: 64238--64353 Score: 51
Period size: 10 Copynumber: 11.2 Consensus size: 10
64228 AGAAAAAAAT
* *
64238 TTTATTTTCA
1 TTTATGTTCG
64248 TTTATGTTCG
1 TTTATGTTCG
*
64258 TTTATGTTCA
1 TTTATGTTCG
64268 TTTA--TT-G
1 TTTATGTTCG
*
64275 TGTTA-ATTCG
1 T-TTATGTTCG
*
64285 TTTGTGTTCG
1 TTTATGTTCG
* *
64295 TTAACGTTCG
1 TTTATGTTCG
*
64305 TTTATTGTATTCA
1 TTTA-TG--TTCG
*
64318 TTTATGTTTG
1 TTTATGTTCG
64328 TTTACATCTGTTCG
1 TTT--A--TGTTCG
64342 TTTATGTTCG
1 TTTATGTTCG
64352 TT
1 TT
64354 CATTTGTGTT
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
7 1 0.01
8 5 0.06
9 4 0.05
10 50 0.62
11 1 0.01
12 4 0.05
13 7 0.09
14 8 0.10
ACGTcount: A:0.15, C:0.10, G:0.16, T:0.59
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:64363 original size:24 final size:24
Alignment explanation
Indices: 64285--64370 Score: 84
Period size: 24 Copynumber: 3.6 Consensus size: 24
64275 TGTTAATTCG
* *
64285 TTTGTGTTCGTTAACGTTCGTTTA
1 TTTGTGTTCGTTTATGTTCGTTTA
* * *
64309 -TTGTATTCATTTATGTTTGTTTA
1 TTTGTGTTCGTTTATGTTCGTTTA
** * *
64332 CATCTGTTCGTTTATGTTCGTTCA
1 TTTGTGTTCGTTTATGTTCGTTTA
64356 TTTGTGTTCGTTTAT
1 TTTGTGTTCGTTTAT
64371 CAATTAAATG
Statistics
Matches: 47, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
23 18 0.38
24 29 0.62
ACGTcount: A:0.13, C:0.12, G:0.17, T:0.58
Consensus pattern (24 bp):
TTTGTGTTCGTTTATGTTCGTTTA
Found at i:69661 original size:29 final size:29
Alignment explanation
Indices: 69590--69691 Score: 138
Period size: 29 Copynumber: 3.6 Consensus size: 29
69580 TAACATACAT
* *
69590 AACACACTCCTTTAATCTCTTGCACACAC
1 AACACACTCCTTTCATCTCTTACACACAC
* *
69619 -A-A-ACTCATTTCATCTCTCACACACAC
1 AACACACTCCTTTCATCTCTTACACACAC
69645 AACACACTCCTTTCATCTCTTACACACAC
1 AACACACTCCTTTCATCTCTTACACACAC
*
69674 AACACACCCCTTTCATCT
1 AACACACTCCTTTCATCT
69692 TCAATCTCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
26 20 0.32
27 2 0.03
28 2 0.03
29 39 0.62
ACGTcount: A:0.31, C:0.40, G:0.01, T:0.27
Consensus pattern (29 bp):
AACACACTCCTTTCATCTCTTACACACAC
Found at i:72978 original size:17 final size:16
Alignment explanation
Indices: 72948--73000 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
72938 ATGAATGAAA
72948 TTTTTTT-ATT-AAAT
1 TTTTTTTAATTAAAAT
72962 TTTATTTTAATTAAAAT
1 TTT-TTTTAATTAAAAT
72979 TATTTTTTAATTAAAGAT
1 T-TTTTTTAATTAAA-AT
72997 TTTT
1 TTTT
73001 CATTTTGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.09
15 4 0.12
16 3 0.09
17 19 0.56
18 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTTTTTAATTAAAAT
Found at i:75824 original size:24 final size:24
Alignment explanation
Indices: 75797--75846 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
75787 ATTTAACAAA
75797 AATGAAAAATT-AAAACAATTCTTT
1 AATG-AAAATTGAAAACAATTCTTT
* * *
75821 AATGGAATTTGAGAACAATTCTTT
1 AATGAAAATTGAAAACAATTCTTT
75845 AA
1 AA
75847 GGGAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (24 bp):
AATGAAAATTGAAAACAATTCTTT
Found at i:75851 original size:24 final size:24
Alignment explanation
Indices: 75810--75862 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
75800 GAAAAATTAA
*
75810 AACAATTCTTTAATGGAATTTGAG
1 AACAATTCTTTAAGGGAATTTGAG
75834 AACAATTCTTTAAGGGAATTTGAG
1 AACAATTCTTTAAGGGAATTTGAG
75858 AACAA
1 AACAA
75863 AAAGATGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (24 bp):
AACAATTCTTTAAGGGAATTTGAG
Found at i:76778 original size:29 final size:30
Alignment explanation
Indices: 76739--76807 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
76729 TTCGCTAGAC
*
76739 TTTATTATAAAA-AAATTTAATTAAATATT
1 TTTATTTTAAAATAAATTTAATTAAATATT
* **
76768 TTTATTTTAAAATCAATTTTGTTAAATATT
1 TTTATTTTAAAATAAATTTAATTAAATATT
*
76798 TAATATTTTA
1 T-TTATTTTA
76808 TTTTATAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 11 0.33
30 15 0.45
31 7 0.21
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (30 bp):
TTTATTTTAAAATAAATTTAATTAAATATT
Found at i:85774 original size:70 final size:71
Alignment explanation
Indices: 85694--85835 Score: 241
Period size: 72 Copynumber: 2.0 Consensus size: 71
85684 CACAAATGTC
*
85694 TGTTTATGTTTCCTATTTATAA-TTATTTTGTACAAATCAATGTAGAGACTATAGCAGCAATGTA
1 TGTTTATGTTTCCTATTTATAAGTTATTTTGTACAAATCAATGTAGAGACTAGAGCAGCAATGTA
85758 CTAAGA
66 CTAAGA
* *
85764 TGTTTATGTTTCCTATTTATAAGTTTTTTTTGTACAAATGAATGTAGAGACTAGAGCAGCAATGT
1 TGTTTATGTTTCCTATTTATAAG-TTATTTTGTACAAATCAATGTAGAGACTAGAGCAGCAATGT
85829 ACTAAGA
65 ACTAAGA
85836 GGTGTTTCTA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 22 0.33
72 45 0.67
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (71 bp):
TGTTTATGTTTCCTATTTATAAGTTATTTTGTACAAATCAATGTAGAGACTAGAGCAGCAATGTA
CTAAGA
Found at i:86033 original size:39 final size:39
Alignment explanation
Indices: 85988--86068 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 39
85978 TACTAATAAA
* *
85988 ATAAAATACTAA-TAATTAATCTTAATCGTAATATAACTC
1 ATAAAATAATAATTAA-TAATCCTAATCGTAATATAACTC
86027 ATAAAATAATAATTAATAATCCTAATCGTAATATAACTC
1 ATAAAATAATAATTAATAATCCTAATCGTAATATAACTC
86066 ATA
1 ATA
86069 GTCCCACTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
39 36 0.92
40 3 0.08
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (39 bp):
ATAAAATAATAATTAATAATCCTAATCGTAATATAACTC
Found at i:88979 original size:80 final size:80
Alignment explanation
Indices: 88831--88982 Score: 227
Period size: 80 Copynumber: 1.9 Consensus size: 80
88821 ACACAGATGA
* *
88831 ATTTGGTGTTTTAGGAGAGTCCAATGGGCTAATGGTTTGGTGTAGTTTTCAATGTTAGGTGTGGT
1 ATTTGGTGTTTTAGGAGAGTCCAATGGGCTAATGGTTTGGTGTAGTTTTCAATGTCAGGTGTGAT
88896 AGTGGTGTTAAGTGG
66 AGTGGTGTTAAGTGG
* * *
88911 ATTTGGTGTTTTTGGTGAGTCCAATGGGTTAATGGTTTGGTGTA-TGTTTCAATGTCAGGTGCT-
1 ATTTGGTGTTTTAGGAGAGTCCAATGGGCTAATGGTTTGGTGTAGT-TTTCAATGTCAGGTG-TG
88974 ATAGTGGTG
64 ATAGTGGTG
88983 CTAGGTGGTC
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
79 1 0.02
80 63 0.97
81 1 0.02
ACGTcount: A:0.18, C:0.06, G:0.35, T:0.41
Consensus pattern (80 bp):
ATTTGGTGTTTTAGGAGAGTCCAATGGGCTAATGGTTTGGTGTAGTTTTCAATGTCAGGTGTGAT
AGTGGTGTTAAGTGG
Found at i:90963 original size:35 final size:37
Alignment explanation
Indices: 90897--90971 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 37
90887 TACTAATAAA
* *
90897 ATAAAATACTAATAATTAATCCTAATCATAATATATCTC
1 ATAAAATACTAATAATTAA--CTAATAATAATATAACTC
90936 ATAAAATACTAATAATT-A-TAATAATAATATAACTC
1 ATAAAATACTAATAATTAACTAATAATAATATAACTC
90971 A
1 A
90972 GTTTCATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 16 0.47
38 1 0.03
39 17 0.50
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (37 bp):
ATAAAATACTAATAATTAACTAATAATAATATAACTC
Done.