Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004147.1 Hibiscus syriacus cultivar Beakdansim tig00009070_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: 76441
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:129 original size:3 final size:3
Alignment explanation
Indices: 123--178 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
113 CCCATTTTTA
* * * *
123 TAT TAT TAT TAC TAT AAT TAT TAT TAT TAT AAT TAT TA- TACA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
168 TAT TAT TAT TA
1 TAT TAT TAT TA
179 AAAATAATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:144 original size:15 final size:15
Alignment explanation
Indices: 124--178 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
114 CCATTTTTAT
124 ATTATTATTACTATA
1 ATTATTATTACTATA
*
139 ATTATTATTATTATA
1 ATTATTATTACTATA
*
154 ATTATTA-TACATATT
1 ATTATTATTAC-TATA
169 ATTATTATTA
1 ATTATTATTA
179 AAAATAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
14 2 0.06
15 31 0.89
16 2 0.06
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTATTATTACTATA
Found at i:1752 original size:23 final size:26
Alignment explanation
Indices: 1720--1769 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
1710 CCTTTTCTGA
*
1720 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
1743 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
1769 T
1 T
1770 TTTCTCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:4090 original size:22 final size:22
Alignment explanation
Indices: 4062--4105 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
4052 AAATCCAACA
4062 CCGGTGCTTCGGGTATTTCCTC
1 CCGGTGCTTCGGGTATTTCCTC
4084 CCGGTGCTTCGGGTATTTCCTC
1 CCGGTGCTTCGGGTATTTCCTC
4106 TGGTGTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.05, C:0.32, G:0.27, T:0.36
Consensus pattern (22 bp):
CCGGTGCTTCGGGTATTTCCTC
Found at i:7695 original size:18 final size:19
Alignment explanation
Indices: 7672--7728 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
7662 TCAGTAATCA
7672 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTT
7690 TATTCCCACTGGTAATCTTT
1 TATT-CCACTGGTAATCTTT
* *
7710 GATTTCCACTAGTAATCTT
1 TA-TTCCACTGGTAATCTT
7729 ACATTTCGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.12
19 2 0.06
20 26 0.76
21 2 0.06
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.46
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTT
Found at i:7703 original size:20 final size:20
Alignment explanation
Indices: 7678--7728 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
7668 ATCATATTCC
*
7678 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTGATTCCCA
*
7698 CTGGTAATCTTTGATTTCCA
1 CTGGTAATCTTTGATTCCCA
*
7718 CTAGTAATCTT
1 CTGGTAATCTT
7729 ACATTTCGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTTGATTCCCA
Found at i:7734 original size:20 final size:20
Alignment explanation
Indices: 7681--7735 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
7671 ATATTCCCTG
* * *
7681 GTAATCTTTTATTCCCACTG
1 GTAATCTTTCATTTCCACTA
*
7701 GTAATCTTTGATTTCCACTA
1 GTAATCTTTCATTTCCACTA
*
7721 GTAATCTTACATTTC
1 GTAATCTTTCATTTC
7736 GTGAATTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (20 bp):
GTAATCTTTCATTTCCACTA
Found at i:9543 original size:12 final size:13
Alignment explanation
Indices: 9516--9545 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
9506 ATATAAATTC
9516 ATTTTCTATAATA
1 ATTTTCTATAATA
9529 ATTTTCTAT-ATA
1 ATTTTCTATAATA
9541 ATTTT
1 ATTTT
9546 AACTTACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTTCTATAATA
Found at i:17257 original size:30 final size:29
Alignment explanation
Indices: 17223--17289 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
17213 GTTTATTATT
*
17223 AAAATATTATTTTTATAATTTTA-TAAATAA
1 AAAATATTATTATTAT-ATTTTATTAAAT-A
**
17253 AAAATAAGATTATTATATTTTATTAAATA
1 AAAATATTATTATTATATTTTATTAAATA
17282 AAAATATT
1 AAAATATT
17290 GTAAATTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (29 bp):
AAAATATTATTATTATATTTTATTAAATA
Found at i:17320 original size:21 final size:21
Alignment explanation
Indices: 17291--17360 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
17281 AAAAATATTG
* *
17291 TAAATTATATTAATTATTTAT
1 TAAAATATATCAATTATTTAT
17312 TAAAATATA-CATATTATATTAT
1 TAAAATATATCA-ATTAT-TTAT
* *
17334 T-AATTATATCAATTACTTAT
1 TAAAATATATCAATTATTTAT
17354 TAAAATA
1 TAAAATA
17361 ATAATATTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
20 6 0.15
21 27 0.68
22 7 0.17
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAAATATATCAATTATTTAT
Found at i:17331 original size:42 final size:42
Alignment explanation
Indices: 17285--17378 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
17275 TTAAATAAAA
* * *
17285 ATATTGTAAATTATATTAATTATTTATTAAAAT-ATACATATT
1 ATATTATAAATTATATCAATTACTTATTAAAATAATA-ATATT
*
17327 ATATTATTAATTATATCAATTACTTATTAAAATAATAATATT
1 ATATTATAAATTATATCAATTACTTATTAAAATAATAATATT
*
17369 ACTATAATAA
1 A-TATTATAA
17379 TAAAAGAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 35 0.80
43 9 0.20
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (42 bp):
ATATTATAAATTATATCAATTACTTATTAAAATAATAATATT
Found at i:17371 original size:21 final size:21
Alignment explanation
Indices: 17303--17371 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
17293 AATTATATTA
*
17303 ATTATTTATTAAAAT-ATACAT
1 ATTACTTATTAAAATAATA-AT
* * *
17324 ATTATATTATT-AATTATATCA-
1 ATTA-CTTATTAAAATA-ATAAT
17345 ATTACTTATTAAAATAATAAT
1 ATTACTTATTAAAATAATAAT
17366 ATTACT
1 ATTACT
17372 ATAATAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
20 8 0.22
21 21 0.57
22 6 0.16
23 2 0.05
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTACTTATTAAAATAATAAT
Found at i:17522 original size:20 final size:20
Alignment explanation
Indices: 17499--17571 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
17489 GTTTCCAGAT
*
17499 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
*
17519 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
*
17540 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
17560 TCGCAACGCGAT
1 TCGCAACGCGAT
17572 AATACAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.04
20 27 0.59
21 15 0.33
22 2 0.04
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:17544 original size:21 final size:21
Alignment explanation
Indices: 17518--17592 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
17508 GATTTTGACT
17518 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
**
17539 ATCGCAACGCGATTCTGAC-T-
1 ATCGCAACGCGATAAT-ACATA
*
17559 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACATA
*
17580 ATCGCAATGCGAT
1 ATCGCAACGCGAT
17593 TTTCAAAGCG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.04
20 14 0.31
21 27 0.60
22 2 0.04
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATAATACATA
Found at i:17558 original size:41 final size:41
Alignment explanation
Indices: 17499--17593 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
17489 GTTTCCAGAT
* *
17499 TCGCAACGCGATTTTGACTATCGCAACGCGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAA
17540 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAA
*
17581 TCGCAATGCGATT
1 TCGCAACGCGATT
17594 TTCAAAGCGC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAA
Found at i:17761 original size:22 final size:22
Alignment explanation
Indices: 17733--17826 Score: 161
Period size: 22 Copynumber: 4.3 Consensus size: 22
17723 ACTCTACGGC
17733 TCCGTCCCCATCTCCGACGAAA
1 TCCGTCCCCATCTCCGACGAAA
17755 TCCGTCCCCATCTCCGACGAAA
1 TCCGTCCCCATCTCCGACGAAA
*
17777 TCCGTCCCCATCTCTGACGAAA
1 TCCGTCCCCATCTCCGACGAAA
* *
17799 TCCATCCCCATCTCCGGCGAAA
1 TCCGTCCCCATCTCCGACGAAA
17821 TCCGTC
1 TCCGTC
17827 TATCTCCATC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 67 1.00
ACGTcount: A:0.21, C:0.45, G:0.14, T:0.20
Consensus pattern (22 bp):
TCCGTCCCCATCTCCGACGAAA
Found at i:18226 original size:20 final size:20
Alignment explanation
Indices: 18201--18298 Score: 82
Period size: 20 Copynumber: 5.2 Consensus size: 20
18191 AAAATCGCAA
18201 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** *
18221 CGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
*
18241 CGAT--T---A-TCTCGTTG
1 CGATAGTCAAATTCGCGTTG
18255 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
* ** *
18275 TGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
18295 CGAT
1 CGAT
18299 TTTAAGTTTC
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
14 10 0.17
16 1 0.02
18 1 0.02
19 1 0.02
20 47 0.78
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.39
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:20227 original size:20 final size:20
Alignment explanation
Indices: 20204--20250 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
20194 CGAAACTTAA
*
20204 ATCGCAACGCGGAA-ATGACT
1 ATCGCAACAC-GAAGATGACT
*
20224 ATCGCAACACGAAGTTGACT
1 ATCGCAACACGAAGATGACT
20244 ATCGCAA
1 ATCGCAA
20251 TAGGATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACACGAAGATGACT
Found at i:20397 original size:38 final size:38
Alignment explanation
Indices: 20319--20400 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 38
20309 CTATCGCAAC
* * * *
20319 GCGAATTTAGTTTCGCGTTGCGATTTTGGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTTGCGATTTTGATTTAGCATT
* *
20357 GCGATTTTGGTTTCGCGTTGCGATTTTTATTTAGCATT
1 GCGATTTTAGTTTCGCGTTGCGATTTTGATTTAGCATT
20395 GCGATT
1 GCGATT
20401 ATCCCGTTGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.12, C:0.15, G:0.27, T:0.46
Consensus pattern (38 bp):
GCGATTTTAGTTTCGCGTTGCGATTTTGATTTAGCATT
Found at i:20400 original size:19 final size:19
Alignment explanation
Indices: 20328--20383 Score: 112
Period size: 19 Copynumber: 2.9 Consensus size: 19
20318 CGCGAATTTA
20328 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
20347 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
20366 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
20384 TATTTAGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.05, C:0.16, G:0.30, T:0.48
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:20470 original size:20 final size:20
Alignment explanation
Indices: 20423--20473 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
20413 TAGTCAAATT
*
20423 CGCATTGCGATAGTCATTTC
1 CGCATTGTGATAGTCATTTC
* *
20443 CGCGTTGTGATAGTCATTTT
1 CGCATTGTGATAGTCATTTC
*
20463 TGCATTGTGAT
1 CGCATTGTGAT
20474 TTAAGTTTCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.41
Consensus pattern (20 bp):
CGCATTGTGATAGTCATTTC
Found at i:21034 original size:21 final size:21
Alignment explanation
Indices: 21010--21079 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
21000 TTATCATCCC
21010 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* ** *
21031 TCAAGAGGCCCCTGTCATCGT
1 TCAAGAGTCCCCTCCCACCGT
* *
21052 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTCCCACCGT
21073 TCAAGAG
1 TCAAGAG
21080 CCCGATTCAT
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
20 1 0.03
21 35 0.95
22 1 0.03
ACGTcount: A:0.23, C:0.37, G:0.20, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:21049 original size:42 final size:42
Alignment explanation
Indices: 20986--21079 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
20976 CACCTGTCAT
*
20986 CGTTCAAGAGGCCCTTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
21028 CGTTCAAGAGGCCCCTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCAC
*
21070 CATTCAAGAG
1 CGTTCAAGAG
21080 CCCGATTCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 43 0.96
43 2 0.04
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:22651 original size:20 final size:20
Alignment explanation
Indices: 22628--22665 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22618 CGCTAAACTT
* *
22628 AAAATTGCAATGCGAAAGCC
1 AAAATCGCAACGCGAAAGCC
22648 AAAATCGCAACGCGAAAG
1 AAAATCGCAACGCGAAAG
22666 TCAATTCGCG
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:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAGCC
Found at i:22733 original size:20 final size:20
Alignment explanation
Indices: 22708--22796 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
22698 ACGATTTTCT
* *
22708 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCA
*
22728 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
22748 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
22768 CGTTGCGATAGTCAAATT-A
1 CGTTGCGATAGTCAAATTCA
22787 GCGTTGCGAT
1 -CGTTGCGAT
22797 TTTTGCATTG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.29
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:22809 original size:14 final size:14
Alignment explanation
Indices: 22790--22838 Score: 98
Period size: 14 Copynumber: 3.5 Consensus size: 14
22780 CAAATTAGCG
22790 TTGCGATTTTTGCA
1 TTGCGATTTTTGCA
22804 TTGCGATTTTTGCA
1 TTGCGATTTTTGCA
22818 TTGCGATTTTTGCA
1 TTGCGATTTTTGCA
22832 TTGCGAT
1 TTGCGAT
22839 AGTCAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGCGATTTTTGCA
Found at i:22856 original size:34 final size:34
Alignment explanation
Indices: 22770--22892 Score: 143
Period size: 34 Copynumber: 3.8 Consensus size: 34
22760 CAAATTCGCG
*
22770 TTGCGATAGTCAAATTAGCGTTGCGATTTTTGCA
1 TTGCGATAGTCAAATTTGCGTTGCGATTTTTGCA
*
22804 TTGCGAT--T----TTTGCATTGCGATTTTTGCA
1 TTGCGATAGTCAAATTTGCGTTGCGATTTTTGCA
22832 TTGCGATAGTCAAATTTGCGTTGCGATTTTTG-A
1 TTGCGATAGTCAAATTTGCGTTGCGATTTTTGCA
* * *
22865 GTTGCAATAATCAAATTCGCGTTGCGAT
1 -TTGCGATAGTCAAATTTGCGTTGCGAT
22893 ATTCAAATGA
Statistics
Matches: 76, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
28 25 0.33
30 1 0.01
32 1 0.01
33 1 0.01
34 48 0.63
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.41
Consensus pattern (34 bp):
TTGCGATAGTCAAATTTGCGTTGCGATTTTTGCA
Found at i:23127 original size:140 final size:140
Alignment explanation
Indices: 22870--23153 Score: 523
Period size: 140 Copynumber: 2.0 Consensus size: 140
22860 TTTGAGTTGC
*
22870 AATAATCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATC
1 AATAATCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATC
22935 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
66 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
23000 AAATACACAT
131 AAATACACAT
* *
23010 AATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATC
1 AATAATCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATC
* *
23075 ATAGCAATGTTTAAACTCAAGTTACTAATACATGTCTAACTGAAAATGTTAAAAGTTTACACATA
66 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
23140 AAATACACAT
131 AAATACACAT
23150 AATA
1 AATA
23154 CAACATTTGC
Statistics
Matches: 139, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (140 bp):
AATAATCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATC
ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
AAATACACAT
Found at i:23234 original size:18 final size:18
Alignment explanation
Indices: 23211--23245 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
23201 AAGCCGGTTG
*
23211 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
23229 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
23246 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:25536 original size:24 final size:24
Alignment explanation
Indices: 25502--25555 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
25492 CTGAAACATC
25502 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
25526 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
25550 ATCAAA
1 ATCAAA
25556 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:26401 original size:20 final size:20
Alignment explanation
Indices: 26376--26482 Score: 117
Period size: 20 Copynumber: 5.3 Consensus size: 20
26366 GAAATTCAGT
*
26376 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
26396 GTTGCGATAGTCAGAATCAC
1 GTTGCGATAGTCAGAATCGC
* *
26416 GTTCCGATAGTCAGAATCAC
1 GTTGCGATAGTCAGAATCGC
* * *
26436 GTTGCGAT-TTACATATTCGC
1 GTTGCGATAGT-CAGAATCGC
* *
26456 ATTGCGATAGTCAAAATCGC
1 GTTGCGATAGTCAGAATCGC
26476 GTTGCGA
1 GTTGCGA
26483 ATCTGGAAAC
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.01
20 70 0.97
21 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:26520 original size:20 final size:19
Alignment explanation
Indices: 26497--26542 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
26487 GGAAACTGAT
* *
26497 TTGCGATAATGGAGATCGCG
1 TTGCGAT-ATAGAGATCGCA
*
26517 TTGCGATTTAGAGATCGCA
1 TTGCGATATAGAGATCGCA
26536 TTGCGAT
1 TTGCGAT
26543 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATATAGAGATCGCA
Found at i:26532 original size:19 final size:19
Alignment explanation
Indices: 26508--26544 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
26498 TGCGATAATG
*
26508 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
26527 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
26545 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:26873 original size:17 final size:17
Alignment explanation
Indices: 26853--26885 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
26843 TTAAAAGTAT
26853 TAATAAATATATTTTAA
1 TAATAAATATATTTTAA
*
26870 TAATAAATATTTTTTA
1 TAATAAATATATTTTA
26886 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATAAATATATTTTAA
Found at i:26913 original size:43 final size:43
Alignment explanation
Indices: 26840--26922 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
26830 TTATATTATA
* * *
26840 TTATTAAAAGTATTAATAAATATATTTTAATAATAAATATTTT
1 TTATTAAAAGTAATAATAAATACATATTAATAATAAATATTTT
* *
26883 TTATTAAAA-TAATATTAAATAGCATATTAATATTAAATAT
1 TTATTAAAAGTAATAATAAATA-CATATTAATAATAAATAT
26923 ATAAAATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 10 0.29
43 24 0.71
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (43 bp):
TTATTAAAAGTAATAATAAATACATATTAATAATAAATATTTT
Found at i:30198 original size:5 final size:5
Alignment explanation
Indices: 30180--30216 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
30170 TTCAGTATGC
30180 TATAA TATATA TATAA TATAA TATAA TATAA TATAA T
1 TATAA TATA-A TATAA TATAA TATAA TATAA TATAA T
30217 GTTTTGATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:31080 original size:29 final size:31
Alignment explanation
Indices: 31047--31109 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
31037 GATTAGGGAT
31047 TTATATATAT-A-TA-TAATAATATTATATTA
1 TTATATATATAATTATTAATAATATTAT-TTA
*
31076 TTATATATTTAATTATTAATAATATTATTTA
1 TTATATATATAATTATTAATAATATTATTTA
31107 TTA
1 TTA
31110 AACTTATGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 9 0.30
30 1 0.03
31 8 0.27
32 12 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TTATATATATAATTATTAATAATATTATTTA
Found at i:31109 original size:16 final size:16
Alignment explanation
Indices: 31060--31110 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
31050 TATATATATA
31060 TAATAATATTATATTAT
1 TAATAATATTAT-TTAT
*
31077 T-AT-ATATTTAATTAT
1 TAATAATA-TTATTTAT
31092 TAATAATATTATTTAT
1 TAATAATATTATTTAT
31108 TAA
1 TAA
31111 ACTTATGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 8 0.28
16 17 0.59
17 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATAATATTATTTAT
Found at i:33379 original size:184 final size:184
Alignment explanation
Indices: 33070--33408 Score: 443
Period size: 184 Copynumber: 1.8 Consensus size: 184
33060 ATTTTTATTT
* *
33070 AATATATGAATTATAAACTCGACACGACTCAAAATAATAAAAAAATTATTTTTATTCAATAAAAA
1 AATATATGAATTAGAAACTCGACACGACCCAAAATAATAAAAAAATTATTTTTATTCAATAAAAA
* * * ** * *
33135 CATTGACTAAATATATAAGGTAAAATTATATATTTTTTTTGGGTCGATCCAGTTTTTTTCACCCT
66 CAATGACTAAATACACAAGCCAAAATTATATATTATTTTCGGGTCGATCCAGTTTTTTTCACCCT
33200 AAACCCGAAC-CTGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCG
131 AAACCCGAACTC-GACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCG
* * * *
33254 AATATATGAATTAGAAATTCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTTAATAAAAA
1 AATATATGAATTAGAAACTCGACACGACCCAAAATAATAAAAAAATTATTTTTATTCAATAAAAA
* * * ** *
33319 CAATGAGTTAATCCGACCCAA-CCCGAATTATATA-TATTTTCGGGTCGGTCCAG-TTTTTTCAC
66 CAATGACTAAAT---ACACAAGCCAAAATTATATATTATTTTCGGGTCGATCCAGTTTTTTTCAC
33381 CCTAAACCCGAACTCGACCCGACCCGAA
128 CCTAAACCCGAACTCGACCCGACCCGAA
33409 TATCACACTT
Statistics
Matches: 132, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
184 103 0.78
185 17 0.13
186 9 0.07
187 3 0.02
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (184 bp):
AATATATGAATTAGAAACTCGACACGACCCAAAATAATAAAAAAATTATTTTTATTCAATAAAAA
CAATGACTAAATACACAAGCCAAAATTATATATTATTTTCGGGTCGATCCAGTTTTTTTCACCCT
AAACCCGAACTCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCG
Found at i:33461 original size:32 final size:33
Alignment explanation
Indices: 33395--33473 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
33385 AACCCGAACT
33395 CGACCCGACCCGAATATCACACTTAAAAAAACC
1 CGACCCGACCCGAATATCACACTTAAAAAAACC
*
33428 CGACCCGACTCGAATATCACACTT-AAAAAACC
1 CGACCCGACCCGAATATCACACTTAAAAAAACC
33460 CGACCCGACCCGAA
1 CGACCCGACCCGAA
33474 CAAAATAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 21 0.48
33 23 0.52
ACGTcount: A:0.39, C:0.38, G:0.11, T:0.11
Consensus pattern (33 bp):
CGACCCGACCCGAATATCACACTTAAAAAAACC
Found at i:33496 original size:249 final size:249
Alignment explanation
Indices: 33207--33922 Score: 1109
Period size: 248 Copynumber: 2.9 Consensus size: 249
33197 CCTAAACCCG
33207 AACCTGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAAT
1 AACC-GACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAAT
* *
33272 TCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTTAATAAAAACAATGAGTTAATCCGACC
65 CCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTTAATAAAAACAATGACTTAATCCGACC
*
33337 CAACCCGAATTATATATATTTTCGGGTCGGTCCAG-TTTTTTCACCCTAAACCCGAA-CTCGACC
130 CGACCCGAATTATATATATTTTCGGGTCGGTCCAGTTTTTTTCACCCTAAACCCGAACCT-GACC
33400 CGACCCGAATATCACACTTAAAAAAACCCGACCCGA-CT-CGAATATCACACTTAAAA
194 CGACCCGAATATCACACTTAAAAAAA-CCGACCCGACCTCCGAATATCACACTT-AAA
33456 AACCCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAAT
1 AA-CCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAAT
33521 CCGACCCGACCCGAAATAAT-AAAAAATTATTTTTATTTAATAAAAACAATGACTTAATCCGACC
65 CCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTTAATAAAAACAATGACTTAATCCGACC
33585 CGACCCGAATTATATATATTTTCGGGTCGGTCCAGTTTTTTTCACCCTAAACCCGAACCCGACCT
130 CGACCCGAATTATATATATTTTCGGGTCGGTCCAGTTTTTTTCACCCTAAACCCG-A----ACCT
* *
33650 GACCCGATCCGAATATCACACTTAAAAAAACCGATCCGACTCTACCCGAATATCACACTTAAA
190 GACCCGACCCGAATATCACACTTAAAAAAACCGACCCGAC-CT--CCGAATATCACACTTAAA
33713 AA---ACCCGACCCGAACAAAATAAAGTTTCAT-----CCGACCCGAATATATGAATTAGAAATC
1 AACCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATC
* *
33770 CAACCCGACCCGAAATAATAAAAAAA-TATTTTTATTTAATAAAAACAGTGACTTAATCCGACCC
66 CGACCCGACCCGAAATAATAAAAAAATTATTTTTATTTAATAAAAACAATGACTTAATCCGACCC
* * * *
33834 GACCTGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCAAACCTGACCCA
131 GACCCGAATTATATATATTTTCGGGTCGGTCCAGTTTTTTTCACCCTAAACCCGAACCTGACCCG
*
33899 ACCCGAATAACACACTTAAAAAAA
196 ACCCGAATATCACACTTAAAAAAA
33923 TCAGATCCGA
Statistics
Matches: 440, Mismatches: 13, Indels: 34
0.90 0.03 0.07
Matches are distributed among these distances:
243 31 0.07
247 1 0.00
248 210 0.48
249 106 0.24
250 3 0.01
253 36 0.08
254 30 0.07
255 4 0.01
257 5 0.01
258 14 0.03
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (249 bp):
AACCGACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATC
CGACCCGACCCGAAATAATAAAAAAATTATTTTTATTTAATAAAAACAATGACTTAATCCGACCC
GACCCGAATTATATATATTTTCGGGTCGGTCCAGTTTTTTTCACCCTAAACCCGAACCTGACCCG
ACCCGAATATCACACTTAAAAAAACCGACCCGACCTCCGAATATCACACTTAAA
Found at i:43444 original size:23 final size:23
Alignment explanation
Indices: 43418--43495 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
43408 CACCACAACT
43418 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
43441 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
43464 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
43487 TATAATAAT
1 CAT-ATAAT
43496 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:43673 original size:103 final size:103
Alignment explanation
Indices: 43502--43822 Score: 599
Period size: 103 Copynumber: 3.1 Consensus size: 103
43492 TAATGTCCAT
*
43502 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
43567 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
43605 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
43670 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
43708 AAGGACCACATATCATTCCTTAAGAATCATATACATATGAC-AAGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-ACTAGGGATCAAGTATGTGTCTCACC
*
43772 AGACTTCACACATGTTCCAAAGAATACATATATGTCCTG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
43811 AAGGACCACATA
1 AAGGACCACATA
43823 GACCCTCGAC
Statistics
Matches: 214, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
103 212 0.99
104 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:44692 original size:64 final size:64
Alignment explanation
Indices: 44559--44701 Score: 166
Period size: 64 Copynumber: 2.2 Consensus size: 64
44549 TAATGAAGGT
* * ** *
44559 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATATATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACTGATGCATCAGTGCATAAAATACATTCGATGTTTGTTTATTAAAGAG
* * *
44623 ATGCATCGATGCACTACTTATGCATCAGTGCATAAATTGCATTCGATGTATT-TATT-TTAAA-A
1 ATGCATCGATGCACTACTGATGCATCAGTGCATAAAATACATTCGATGT-TTGT-TTATTAAAGA
44685 G
64 G
44686 AGTGCATCGATGCACT
1 A-TGCATCGATGCACT
44702 TCCTGTGCAT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 2 0.03
64 62 0.91
65 4 0.06
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTGATGCATCAGTGCATAAAATACATTCGATGTTTGTTTATTAAAGAG
Found at i:49496 original size:23 final size:23
Alignment explanation
Indices: 49470--49547 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
49460 CACCACAACT
49470 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
49493 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
49516 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
49539 TATAATAAT
1 CAT-ATAAT
49548 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:49725 original size:103 final size:102
Alignment explanation
Indices: 49554--49874 Score: 570
Period size: 103 Copynumber: 3.1 Consensus size: 102
49544 TAATGTCCAT
*
49554 AAGGACCAAATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCAC-A
49619 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
49657 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCATCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCA-CA
*
49722 GACTTCACACATGTTCCAAAGAATACATATATGTCCCA
65 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
49760 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCA-CA
49825 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
49863 AAGGACCACATA
1 AAGGACCACATA
49875 GACCCTCGAC
Statistics
Matches: 210, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
103 209 1.00
104 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACAG
ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:50744 original size:64 final size:64
Alignment explanation
Indices: 50611--50765 Score: 179
Period size: 64 Copynumber: 2.4 Consensus size: 64
50601 TAATGAAGGT
* * * ** *
50611 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATACATTCGATGTTTATTTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGGTGCACAAAATACATTCGATGTTTATTTATAAAAGAG
* * *
50675 ATGCATCGATGCACTACTTATGCATCGGTGCACGAATTGCATTCGATGTATTTATTT-TAAAAGA
1 ATGCATCGATGCACTACTTATGCATCGGTGCACAAAATACATTCGATG--TTTATTTATAAAAGA
50739 G
64 G
* *
50740 -TGCATCGATGCACTTCTTGTGCATCG
1 ATGCATCGATGCACTACTTATGCATCG
50766 ATACACCTTC
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 67 0.86
65 4 0.05
66 7 0.09
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGGTGCACAAAATACATTCGATGTTTATTTATAAAAGAG
Found at i:53924 original size:21 final size:21
Alignment explanation
Indices: 53898--53937 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53888 TCCCCTTTGA
*
53898 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
53919 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
53938 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:58752 original size:12 final size:12
Alignment explanation
Indices: 58731--58775 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
58721 AAAAATTTTC
58731 ACTGTTCATGGT
1 ACTGTTCATGGT
*
58743 ACTATTCATGGT
1 ACTGTTCATGGT
*
58755 ATTGTTCATGGT
1 ACTGTTCATGGT
58767 ACTGTTCAT
1 ACTGTTCAT
58776 ACTGTATAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.44
Consensus pattern (12 bp):
ACTGTTCATGGT
Found at i:61364 original size:14 final size:14
Alignment explanation
Indices: 61345--61378 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
61335 TAAGGTTGGG
61345 TCATGGAAGTGCAT
1 TCATGGAAGTGCAT
61359 TCATGGAAGTGCAT
1 TCATGGAAGTGCAT
61373 TCATGG
1 TCATGG
61379 TAGATTGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (14 bp):
TCATGGAAGTGCAT
Found at i:61918 original size:21 final size:20
Alignment explanation
Indices: 61866--61923 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
61856 TACTGGTATC
*
61866 AAGGGTGGGTATCGATACTA
1 AAGGGTAGGTATCGATACTA
*
61886 TAGGGTAGGTATCGATACTA
1 AAGGGTAGGTATCGATACTA
61906 AAGGGGTTA-GTATCGATA
1 AA-GGG-TAGGTATCGATA
61924 TCATCATACT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.58
21 12 0.36
22 2 0.06
ACGTcount: A:0.31, C:0.09, G:0.33, T:0.28
Consensus pattern (20 bp):
AAGGGTAGGTATCGATACTA
Found at i:63169 original size:24 final size:25
Alignment explanation
Indices: 63131--63177 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
63121 TAATGAAATT
63131 AATATAATAATAAAATTATATTTTA
1 AATATAATAATAAAATTATATTTTA
*
63156 AATATTATAA-AAAATTATATTT
1 AATATAATAATAAAATTATATTT
63178 AGAATTTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AATATAATAATAAAATTATATTTTA
Found at i:63178 original size:23 final size:26
Alignment explanation
Indices: 63131--63186 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
63121 TAATGAAATT
*
63131 AATATAATAATAAAATTATATTTTA-
1 AATATTATAATAAAATTATATTTTAG
63156 AATATTATAA-AAAATTATA-TTTAG
1 AATATTATAATAAAATTATATTTTAG
63180 AAT-TTAT
1 AATATTAT
63187 CCTCGTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 8 0.28
24 12 0.41
25 9 0.31
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
AATATTATAATAAAATTATATTTTAG
Found at i:68324 original size:60 final size:60
Alignment explanation
Indices: 68222--68367 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 60
68212 TATATGTCTT
* * * * * *
68222 CAAATTATAACTCTCATTTTAAATTGATCTTTAAACTTTTAAATATTTTAATTTCATCCC
1 CAAACTATGACTCTCATTTTAAATTGATCCTTAAACTTTTAAATATTCTAATTCCATACC
* *
68282 CAAACTATGACTCTCATTTTGAATT-AGTCCTTACACTTTTAAATATTCTAATTCCATACC
1 CAAACTATGACTCTCATTTTAAATTGA-TCCTTAAACTTTTAAATATTCTAATTCCATACC
** *
68342 TGAACTATGACTTTC-TTTCTAAATTG
1 CAAACTATGACTCTCATTT-TAAATTG
68368 GTCACCAAAC
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
59 4 0.06
60 67 0.94
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (60 bp):
CAAACTATGACTCTCATTTTAAATTGATCCTTAAACTTTTAAATATTCTAATTCCATACC
Found at i:68619 original size:29 final size:27
Alignment explanation
Indices: 68530--68620 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 27
68520 ATATACGTAT
*
68530 AGTTTGGGATAAAATTGGAATGTTCAAAA
1 AGTTTGGGAT-AAATTGAAATGTTC-AAA
* * * * *
68559 AGTTTGGGATCAATTTAGAATG-GCCAT
1 AGTTTGGGATAAATTGA-AATGTTCAAA
68586 AGTTTGGGGATGAAATTGAAATGTTCAAA
1 AGTTT-GGGAT-AAATTGAAATGTTCAAA
68615 AGTTTG
1 AGTTTG
68621 AGAATTAATT
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
27 6 0.13
28 15 0.32
29 26 0.55
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.33
Consensus pattern (27 bp):
AGTTTGGGATAAATTGAAATGTTCAAA
Found at i:68631 original size:57 final size:56
Alignment explanation
Indices: 68528--68637 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 56
68518 GTATATACGT
* *
68528 ATAGTTTGGGATAAAATTGGAATGTTCAAAAAGTTTGGGATCAATTTAGAATGGCC
1 ATAGTTTGGGATAAAATTGAAATGTTCAAAAAGTTTGGAATCAATTTAGAATGGCC
* * *
68584 ATAGTTTGGGGATGAAATTGAAATGTTC-AAAAGTTTGAGAATTAATTTATAATG
1 ATAGTTT-GGGATAAAATTGAAATGTTCAAAAAGTTTG-GAATCAATTTAGAATG
68638 ATAGTAATAG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
56 16 0.34
57 31 0.66
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.35
Consensus pattern (56 bp):
ATAGTTTGGGATAAAATTGAAATGTTCAAAAAGTTTGGAATCAATTTAGAATGGCC
Found at i:70532 original size:18 final size:20
Alignment explanation
Indices: 70497--70534 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
70487 AGAAAAATGT
70497 GTTACATTAATCAATATTTA
1 GTTACATTAATCAATATTTA
70517 GTTA-ATTAAT-AATATTTA
1 GTTACATTAATCAATATTTA
70535 ATCTTATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 6 0.33
20 4 0.22
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (20 bp):
GTTACATTAATCAATATTTA
Found at i:70656 original size:15 final size:15
Alignment explanation
Indices: 70636--70666 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
70626 ACAATATTTC
70636 ACTCACTGTATTTTA
1 ACTCACTGTATTTTA
70651 ACTCACTGTATTTTA
1 ACTCACTGTATTTTA
70666 A
1 A
70667 ATCTTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.45
Consensus pattern (15 bp):
ACTCACTGTATTTTA
Found at i:72348 original size:2 final size:2
Alignment explanation
Indices: 72341--72376 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
72331 ATAGATGGGG
72341 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
72377 TAAATTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.