Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008605.1 Hibiscus syriacus cultivar Beakdansim tig00111561_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: 71030
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:10485 original size:38 final size:38
Alignment explanation
Indices: 10432--10510 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
10422 GTTCATAAAC
* *
10432 TTCTTCCTGGTATTATCCTATGTTGCCTAATTATTCTT
1 TTCTTCCTGGGATTATCCTATCTTGCCTAATTATTCTT
*
10470 TTCTTCCTGGGATTATCCTATCTTGCCTAATTATTTTT
1 TTCTTCCTGGGATTATCCTATCTTGCCTAATTATTCTT
10508 TTC
1 TTC
10511 ATTGTATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.15, C:0.22, G:0.10, T:0.53
Consensus pattern (38 bp):
TTCTTCCTGGGATTATCCTATCTTGCCTAATTATTCTT
Found at i:14756 original size:21 final size:21
Alignment explanation
Indices: 14732--14771 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14722 GGTTATGGAG
*
14732 TTATGATTTAGGGTTTAAGAT
1 TTATAATTTAGGGTTTAAGAT
*
14753 TTATAATTTAGTGTTTAAG
1 TTATAATTTAGGGTTTAAG
14772 TTAGGGATAA
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:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (21 bp):
TTATAATTTAGGGTTTAAGAT
Found at i:16029 original size:3 final size:3
Alignment explanation
Indices: 16004--16059 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
15994 TGTTTTTTAT
* * * *
16004 TTA TTA CTA TAA TTA TT- TTA TTA TTA ATA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16051 TTA TTA TTA
1 TTA TTA TTA
16060 AATAATAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:16714 original size:16 final size:16
Alignment explanation
Indices: 16693--16729 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
16683 CACACGTTGT
16693 TGAAGAACCAAAACGG
1 TGAAGAACCAAAACGG
16709 TGAAGAACCAAAACGG
1 TGAAGAACCAAAACGG
16725 TGAAG
1 TGAAG
16730 GTAAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.27, T:0.08
Consensus pattern (16 bp):
TGAAGAACCAAAACGG
Found at i:17507 original size:20 final size:18
Alignment explanation
Indices: 17439--17533 Score: 56
Period size: 18 Copynumber: 5.2 Consensus size: 18
17429 TTAGTCACTA
*
17439 ATTTTAATACT-TTCATTT
1 ATTTTAATA-TGTTTATTT
*
17457 ATTTTACAAAT-TTTA-TT
1 ATTTTA-ATATGTTTATTT
*
17474 ACTTTTTA-AT-TTTATTT
1 A-TTTTAATATGTTTATTT
17491 ATTTTAATCATTGTTTATTT
1 ATTTTAAT-A-TGTTTATTT
* *
17511 ATATTTTATATGTTTATAT
1 AT-TTTAATATGTTTATTT
17530 ATTT
1 ATTT
17534 AATTATTATT
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
16 11 0.17
17 7 0.11
18 17 0.27
19 13 0.21
20 10 0.16
21 5 0.08
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.64
Consensus pattern (18 bp):
ATTTTAATATGTTTATTT
Found at i:17835 original size:140 final size:140
Alignment explanation
Indices: 17679--18059 Score: 644
Period size: 140 Copynumber: 2.7 Consensus size: 140
17669 TAATCATATT
* *
17679 TTAATATTTATTTATTTTTTAATATTAAGAAATGAGTTGTCTTAAAGCATCTAGAAGTTC-TTTT
1 TTAATATTTATTTATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAG-TCATTTT
17743 CTGATATTCTTAAATAAATAAATATACTATTTTTATAAATTATATATTAATTTTTTATTTTTAGA
65 CTGATATTCTTAAATAAATAAATATACTATTTTTATAAATTATATATTAATTTTTTATTTTTAGA
17808 AAAATGTTTTA
130 AAAATGTTTTA
* * *
17819 TTAATATTTATTTATTTTTTAATATTAAGAAATGTGCTGTCTTAAAGTACCTAGAAGTCATGTTC
1 TTAATATTTATTTATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCATTTTC
17884 TGATATTCTTAAATAAATAAATATACTATTTTTATAAATTATATATTAATTTTTTATTTTTAGAA
66 TGATATTCTTAAATAAATAAATATACTATTTTTATAAATTATATATTAATTTTTTATTTTTAGAA
17949 AAATGTTTTA
131 AAATGTTTTA
*
17959 TTAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCATTTTC
1 TTAATATTTATTTATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCATTTTC
* *
18024 TGATATT-TCTAAGTAAATAAATAT-C-ATATTTATAAA
66 TGATATTCT-TAAATAAATAAATATACTATTTTTATAAA
18060 AATAAAAATA
Statistics
Matches: 229, Mismatches: 10, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
138 10 0.04
139 4 0.02
140 215 0.94
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.48
Consensus pattern (140 bp):
TTAATATTTATTTATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCATTTTC
TGATATTCTTAAATAAATAAATATACTATTTTTATAAATTATATATTAATTTTTTATTTTTAGAA
AAATGTTTTA
Found at i:17850 original size:41 final size:41
Alignment explanation
Indices: 17773--17850 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
17763 AATATACTAT
* *
17773 TTTTATAAATTATATATTAATTTTTTATTTTTAGAAAAATG
1 TTTTATAAATTATATATTAATTTTTTATATTAAGAAAAATG
* * *
17814 TTTTATTAA-TATTTATTTATTTTTTAATATTAAGAAA
1 TTTTATAAATTATATATTAATTTTTT-ATATTAAGAAA
17851 TGTGCTGTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 14 0.45
41 17 0.55
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (41 bp):
TTTTATAAATTATATATTAATTTTTTATATTAAGAAAAATG
Found at i:17990 original size:41 final size:41
Alignment explanation
Indices: 17913--17990 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
17903 AATATACTAT
* *
17913 TTTTATAAATTATATATTAATTTTTTATTTTTAGAAAAATG
1 TTTTATAAATTATATATTAATTTTTTATATTAAGAAAAATG
* * *
17954 TTTTATTAA-TATTTATTTATTTTTTAATATTAAGAAA
1 TTTTATAAATTATATATTAATTTTTT-ATATTAAGAAA
17991 TGGGCTGTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 14 0.45
41 17 0.55
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (41 bp):
TTTTATAAATTATATATTAATTTTTTATATTAAGAAAAATG
Found at i:24843 original size:18 final size:18
Alignment explanation
Indices: 24803--24844 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
24793 GCACCACTAA
24803 CGCCGCCGCGGCACACAC
1 CGCCGCCGCGGCACACAC
*
24821 GGCCGCCGC-GCACACCAC
1 CGCCGCCGCGGCACA-CAC
24839 CGCCGC
1 CGCCGC
24845 ACCGACCGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.14, C:0.57, G:0.29, T:0.00
Consensus pattern (18 bp):
CGCCGCCGCGGCACACAC
Found at i:25959 original size:79 final size:79
Alignment explanation
Indices: 25828--25981 Score: 290
Period size: 79 Copynumber: 1.9 Consensus size: 79
25818 ACAAATGATG
* *
25828 CCCGACTTATTAAGTTTCTAAGTTATCAAAAGTTATGAAATAATTTTTCGACTATAAAATATTAC
1 CCCGACTTATTAAGTTTCTAAGTTATCAAAAATTATGAAATAATCTTTCGACTATAAAATATTAC
25893 TTTGTTGAATACTT
66 TTTGTTGAATACTT
25907 CCCGACTTATTAAGTTTCTAAGTTATCAAAAATTATGAAATAATCTTTCGACTATAAAATATTAC
1 CCCGACTTATTAAGTTTCTAAGTTATCAAAAATTATGAAATAATCTTTCGACTATAAAATATTAC
25972 TTTGTTGAAT
66 TTTGTTGAAT
25982 CATTTGATTA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (79 bp):
CCCGACTTATTAAGTTTCTAAGTTATCAAAAATTATGAAATAATCTTTCGACTATAAAATATTAC
TTTGTTGAATACTT
Found at i:31553 original size:135 final size:135
Alignment explanation
Indices: 31312--31561 Score: 396
Period size: 135 Copynumber: 1.9 Consensus size: 135
31302 ATAAAAGTTA
* *
31312 AACAGATTCAAGTTCAACAGCTTGTAATCCATGCTAATTTCCAGCTAAAAACAAAGTTAGATGAG
1 AACAGATTAAAGTTCAACAGCTTGTAATCCATGCTAATTTCCAGCTAAAAACAAAGTTAAATGAG
** *
31377 ATCTCCTTGCGAATTTTATAATCTACCGTCATACAAAGATT-AATCTAAATGATTATAATTTAGC
66 ATCTCCAAGCGAATTGTATAATCTACCGTCATACAAAGATTAAATCTAAATGATTATAATTTAGC
31441 ATCCT
131 ATCCT
* * *
31446 AACAGATTAAAGTTCAACAGCTTGTAATCCATGCTGATTTCCATCTAAAAAACAAGGTTAAATGA
1 AACAGATTAAAGTTCAACAGCTTGTAATCCATGCTAATTTCCAGCT-AAAAACAAAGTTAAATGA
31511 GATCTCCAAGCGAATTGTATAATCTACCGTCATA-AAAGGATTAAATCTAAA
65 GATCTCCAAGCGAATTGTATAATCTACCGTCATACAAA-GATTAAATCTAAA
31562 CAAAAAACTG
Statistics
Matches: 105, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
134 46 0.44
135 51 0.49
136 8 0.08
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (135 bp):
AACAGATTAAAGTTCAACAGCTTGTAATCCATGCTAATTTCCAGCTAAAAACAAAGTTAAATGAG
ATCTCCAAGCGAATTGTATAATCTACCGTCATACAAAGATTAAATCTAAATGATTATAATTTAGC
ATCCT
Found at i:32517 original size:35 final size:35
Alignment explanation
Indices: 32471--32537 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
32461 GTGTCTAACG
32471 TTACAAAGGTTGTCACTTTAAATGCCTCGACCTTC
1 TTACAAAGGTTGTCACTTTAAATGCCTCGACCTTC
*
32506 TTACAAAGGTTGTCACTTTAATTGCCTCGACC
1 TTACAAAGGTTGTCACTTTAAATGCCTCGACC
32538 GTAACAGTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (35 bp):
TTACAAAGGTTGTCACTTTAAATGCCTCGACCTTC
Found at i:32913 original size:47 final size:47
Alignment explanation
Indices: 32859--32949 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
32849 TTAATTGGTT
32859 AAATTATTTATCTTTATTCGTTCATATTTATTTTTATAGAGTTCTTC
1 AAATTATTTATCTTTATTCGTTCATATTTATTTTTATAGAGTTCTTC
* *
32906 AAATTATTTATCTTTGTTCGTTTATATTTATTTTTATAGAGTTC
1 AAATTATTTATCTTTATTCGTTCATATTTATTTTTATAGAGTTC
32950 CTTATCTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.25, C:0.09, G:0.08, T:0.58
Consensus pattern (47 bp):
AAATTATTTATCTTTATTCGTTCATATTTATTTTTATAGAGTTCTTC
Found at i:33417 original size:20 final size:21
Alignment explanation
Indices: 33392--33443 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
33382 TTTTCCCAAT
*
33392 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
33412 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
33433 TCGCAATGCGA
1 TCGCAATGCGA
33444 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:33457 original size:20 final size:20
Alignment explanation
Indices: 33432--33545 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
33422 AATTGGGAAA
*
33432 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
33452 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
33472 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
33493 ATCGCAACGAGATAATGACT
1 ATCGCAACGCGATACTGACT
* *
33513 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
33533 TTCGCAACGCGAT
1 ATCGCAACGCGAT
33546 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 63 0.78
21 14 0.17
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:33476 original size:61 final size:61
Alignment explanation
Indices: 33429--33545 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
33419 GCGAATTGGG
* * * * * *
33429 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATAATGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
33490 AAAATCGCAACGAGATAATGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATAATGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
33546 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATAATGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:34139 original size:19 final size:19
Alignment explanation
Indices: 34103--34144 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
34093 ACGAGAGAAT
*
34103 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
* *
34122 CGCAACGCGAAACCAAAAT
1 CGCAACGCGAAACAAAAAA
34141 CGCA
1 CGCA
34145 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.29, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:34162 original size:19 final size:19
Alignment explanation
Indices: 34140--34265 Score: 92
Period size: 19 Copynumber: 7.1 Consensus size: 19
34130 GAAACCAAAA
34140 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
34159 TCGCGTTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
*
34173 TCTCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
34192 TCGCGTTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
**
34208 TCG--TTGCGATAGTCATT
1 TCGCATTGCGATTTTCATT
* *
34225 TCGCGTTGCGATTCTCATT
1 TCGCATTGCGATTTTCATT
*
34244 ATCTCATTGCGATTTTCATT
1 -TCGCATTGCGATTTTCATT
34264 TC
1 TC
34266 AACCAAAAGA
Statistics
Matches: 83, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
14 15 0.18
16 9 0.11
17 10 0.12
19 33 0.40
20 16 0.19
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:34185 original size:33 final size:33
Alignment explanation
Indices: 34143--34240 Score: 169
Period size: 33 Copynumber: 3.0 Consensus size: 33
34133 ACCAAAATCG
34143 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
34176 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
* **
34209 CGTTGCGATAGTCATTTCGCGTTGCGATTCTC
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTC
34241 ATTATCTCAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.43
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:35816 original size:63 final size:63
Alignment explanation
Indices: 35717--35847 Score: 262
Period size: 63 Copynumber: 2.1 Consensus size: 63
35707 GTTACGTGAT
35717 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
35780 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
35843 GAGGT
1 GAGGT
35848 GTCTACTTTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.24
Consensus pattern (63 bp):
GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
Found at i:36517 original size:42 final size:42
Alignment explanation
Indices: 36421--36621 Score: 170
Period size: 42 Copynumber: 4.8 Consensus size: 42
36411 CTCGCCTGTT
* * * * * *
36421 ATCCCTCAAGAGTCCACTCCTATCGTTGAAGATGCCCCTATC
1 ATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATC
* * * *
36463 ATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCATTGTC
1 ATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATC
* * * * * *
36505 ATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATC
1 ATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATC
* ** *
36547 ATTCCTTGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTC
1 ATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATC
** * *
36589 ATCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 ATCCCTCAAGA-GTCCCCTCCCACCGTTCAAGAG
36622 CCCGATGCAC
Statistics
Matches: 122, Mismatches: 36, Indels: 2
0.76 0.22 0.01
Matches are distributed among these distances:
42 120 0.98
43 2 0.02
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.24
Consensus pattern (42 bp):
ATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATC
Found at i:36579 original size:21 final size:21
Alignment explanation
Indices: 36555--36621 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
36545 TCATTCCTTG
36555 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
36576 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
36597 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
36618 AGAG
1 AGAG
36622 CCCGATGCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:36600 original size:84 final size:84
Alignment explanation
Indices: 36416--36591 Score: 307
Period size: 84 Copynumber: 2.1 Consensus size: 84
36406 CCCGACTCGC
* * *
36416 CTGTTATCCCTCAAGAGTCCACTCCTATCGTTGAAGATGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
36481 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* *
36500 TTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTTGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
36565 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
36584 CTGTCATC
1 CTGTCATC
36592 GTTGAAGAGG
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.22, C:0.36, G:0.16, T:0.26
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:36621 original size:84 final size:84
Alignment explanation
Indices: 36416--36621 Score: 270
Period size: 84 Copynumber: 2.5 Consensus size: 84
36406 CCCGACTCGC
* * * * * *
36416 CTGTTATCCCTCAAGAGTCCACTCCTATCGTTGAAGATGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
36481 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * * *
36500 TTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTTGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
36565 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
36584 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
36622 CCCGATGCAC
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
84 105 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.25
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:37997 original size:14 final size:14
Alignment explanation
Indices: 37978--38013 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
37968 ATTGTTTAAT
37978 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
37992 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
38006 TGATTTGT
1 TGATTTGT
38014 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:38157 original size:14 final size:14
Alignment explanation
Indices: 38138--38194 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
38128 GCGAAATGAA
38138 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
38152 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
38171 AATCGCAACGAGAG
1 AATCGCAACGAGAG
38185 AATCGCAACG
1 AATCGCAACG
38195 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:38165 original size:33 final size:33
Alignment explanation
Indices: 38120--38209 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
38110 AAAAAGTAAT
*
38120 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
38153 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
38186 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
38210 GTTGCGATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:38179 original size:19 final size:19
Alignment explanation
Indices: 38120--38180 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
38110 AAAAAGTAAT
*
38120 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
38139 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
38153 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
38172 ATCGCAACG
1 ATCGCAACG
38181 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:38227 original size:19 final size:19
Alignment explanation
Indices: 38205--38355 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
38195 CGAAATTAAA
38205 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
38224 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
38239 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
** *
38257 TTCGTATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
38271 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
38290 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
38305 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
38323 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
38342 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
38356 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:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:38251 original size:33 final size:32
Alignment explanation
Indices: 38209--38335 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
38199 ATTAAATTCG
38209 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
38242 CGTTGCGATTTTCATTTCGTATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
38275 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
38308 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
38336 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:38282 original size:66 final size:66
Alignment explanation
Indices: 38202--38334 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
38192 ACGCGAAATT
* *
38202 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGTATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
38267 G
66 G
*
38268 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
38333 G
66 G
38334 A
1 A
38335 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:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:40644 original size:12 final size:12
Alignment explanation
Indices: 40627--40651 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40617 TCTTCGGGGA
40627 CTTTTTCTTCTT
1 CTTTTTCTTCTT
40639 CTTTTTCTTCTT
1 CTTTTTCTTCTT
40651 C
1 C
40652 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:40860 original size:24 final size:24
Alignment explanation
Indices: 40826--40879 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
40816 CTGAAACATC
*
40826 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
40850 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
40874 ATCAAA
1 ATCAAA
40880 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:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:41643 original size:20 final size:20
Alignment explanation
Indices: 41618--41668 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
41608 TGTATTATCT
*
41618 CGTTGCGAAAGTCATAATCG
1 CGTTGCGAAAGTCAGAATCG
41638 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
41658 CGTTGCGAAAG
1 CGTTGCGAAAG
41669 GCAATCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:41959 original size:19 final size:20
Alignment explanation
Indices: 41881--41970 Score: 164
Period size: 20 Copynumber: 4.5 Consensus size: 20
41871 ATTCATTTGA
41881 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
41901 CTATCGTAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
41921 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
41941 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
41960 CTATCGCAACG
1 CTATCGCAACG
41971 ACAAAATCGC
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
19 17 0.25
20 51 0.75
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:42037 original size:19 final size:19
Alignment explanation
Indices: 41996--42060 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
41986 GAAATGAAAA
41996 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
42012 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
42029 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
42048 TTGCATTGCGATT
1 TCGCATTGCGATT
42061 CTCTCGTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
14 11 0.26
16 3 0.07
17 3 0.07
19 26 0.60
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:42091 original size:20 final size:20
Alignment explanation
Indices: 42066--42104 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42056 CGATTCTCTC
42066 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
42086 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
42105 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:42206 original size:14 final size:15
Alignment explanation
Indices: 42187--42224 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
42177 CATCAATTAA
42187 ACAAATCAAC-ATTT
1 ACAAATCAACTATTT
* *
42201 ACAAATCATCTTTTT
1 ACAAATCAACTATTT
42216 ACAAATCAA
1 ACAAATCAA
42225 TTAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (15 bp):
ACAAATCAACTATTT
Found at i:44116 original size:20 final size:20
Alignment explanation
Indices: 44074--44139 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
44064 TAGTTTACTT
* * **
44074 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAATGACTA
44094 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * * *
44114 TCGTAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
44134 TCGCAA
1 TCGCAA
44140 TGCGAAATGA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:44148 original size:19 final size:20
Alignment explanation
Indices: 44093--44149 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
44083 GAAACTTAAA
* *
44093 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
44113 ATCGTAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
*
44133 ATCGCAATGC-GAAATGA
1 ATCGCAACGCGGAAATGA
44150 AAATCGCAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:44155 original size:19 final size:19
Alignment explanation
Indices: 44133--44190 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 19
44123 GGAAATGGCT
44133 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
44152 ATCGCAAT--G--A-CAAA
1 ATCGCAATGCGAAATGAAA
44166 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
44184 ATCGCAA
1 ATCGCAA
44191 CGACAAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
14 11 0.34
15 1 0.03
16 1 0.03
17 1 0.03
18 10 0.31
19 8 0.25
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:44196 original size:32 final size:33
Alignment explanation
Indices: 44133--44211 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
44123 GGAAATGGCT
*
44133 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
44166 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
44198 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
44212 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 28 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:44205 original size:14 final size:14
Alignment explanation
Indices: 44149--44206 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
44139 ATGCGAAATG
*
44149 AAAATCGCAATGAC
1 AAAATCGCAACGAC
*
44163 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
44179 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
44195 AAAATCGCAACG
1 AAAATCGCAACG
44207 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:44259 original size:14 final size:14
Alignment explanation
Indices: 44240--44297 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
44230 TTTCATTTCG
44240 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
44254 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
44270 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
44286 CGTTGCGATTTT
1 CGTTGCGATTTT
44298 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:44304 original size:33 final size:33
Alignment explanation
Indices: 44223--44313 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
44213 ACAAATCGCA
*
44223 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
44256 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
44288 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
44314 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:44332 original size:20 final size:19
Alignment explanation
Indices: 44298--44352 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
44288 TTGCGATTTT
*
44298 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
44317 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
44337 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
44353 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:44854 original size:18 final size:18
Alignment explanation
Indices: 44828--44872 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
44818 GTCGATCAGA
*
44828 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
44846 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
44864 TGATGGCTC
1 TGATGGCTC
44873 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:46217 original size:20 final size:20
Alignment explanation
Indices: 46192--46265 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
46182 AATAGTTTCT
*
46192 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
46212 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
46232 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
46252 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
46266 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:46524 original size:22 final size:22
Alignment explanation
Indices: 46497--46540 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
46487 GATGGAGATA
46497 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
46519 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
46541 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:46814 original size:20 final size:19
Alignment explanation
Indices: 46708--46842 Score: 108
Period size: 20 Copynumber: 6.7 Consensus size: 19
46698 CGCTTTGAAA
*
46708 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* * *
46729 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGT-AGT
* *
46749 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* * * *
46769 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
46790 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGT-AGT
46810 ATCGCATTGCGATAGTGAGT
1 ATCGCATTGCGATAGT-AGT
46830 ATCGCATTGCGAT
1 ATCGCATTGCGAT
46843 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:46814 original size:61 final size:61
Alignment explanation
Indices: 46708--46845 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
46698 CGCTTTGAAA
* * * *
46708 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
46769 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTGAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
46830 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
46846 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:46861 original size:61 final size:61
Alignment explanation
Indices: 46708--46863 Score: 152
Period size: 61 Copynumber: 2.6 Consensus size: 61
46698 CGCTTTGAAA
* ** * * * *
46708 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * * *
46769 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTGAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
46830 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
46864 TTACTTATTC
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
61 76 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:47776 original size:7 final size:7
Alignment explanation
Indices: 47766--47791 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
47756 ATATAAAATA
47766 TATAGTT
1 TATAGTT
47773 TATAGTT
1 TATAGTT
47780 TATAGTT
1 TATAGTT
47787 TATAG
1 TATAG
47792 ATTTGGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (7 bp):
TATAGTT
Found at i:58256 original size:14 final size:14
Alignment explanation
Indices: 58237--58264 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58227 AAAGACGAGT
58237 TTACCCTAAAACAA
1 TTACCCTAAAACAA
58251 TTACCCTAAAACAA
1 TTACCCTAAAACAA
58265 ATAATTTTTT
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:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (14 bp):
TTACCCTAAAACAA
Found at i:58857 original size:14 final size:14
Alignment explanation
Indices: 58838--58864 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58828 CACGGATCGA
58838 TCATAACTATATTC
1 TCATAACTATATTC
58852 TCATAACTATATT
1 TCATAACTATATT
58865 TAACTACGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (14 bp):
TCATAACTATATTC
Found at i:60183 original size:2 final size:2
Alignment explanation
Indices: 60176--60215 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
60166 ATTTATTTCA
60176 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60216 TAAACAACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68919 original size:33 final size:33
Alignment explanation
Indices: 68877--68944 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
68867 ATAGAGATCC
68877 CAGGTTCCATGGTGCTTCTTCGCTTGGTCCTCA
1 CAGGTTCCATGGTGCTTCTTCGCTTGGTCCTCA
68910 CAGGTTCCATGGTGCTTCTTCGCTTGGTCCTCA
1 CAGGTTCCATGGTGCTTCTTCGCTTGGTCCTCA
68943 CA
1 CA
68945 TCTATGATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.10, C:0.31, G:0.24, T:0.35
Consensus pattern (33 bp):
CAGGTTCCATGGTGCTTCTTCGCTTGGTCCTCA
Found at i:69179 original size:2 final size:2
Alignment explanation
Indices: 69172--69211 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
69162 ACACATTAAA
69172 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69212 ACTAAAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.