Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007875.1 Hibiscus syriacus cultivar Beakdansim tig00110251_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: 67816
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3158 original size:20 final size:20
Alignment explanation
Indices: 3055--3187 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
3045 ACCCAGTTTC
*
3055 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACACGAATTT
* **
3075 GTAAA-TCGCAACAC-ATAAGT
1 -CAAATTCGCAACACGA-ATTT
* *
3095 CAAATTCGTAACACAGAA-GT
1 CAAATTCGCAACAC-GAATTT
3115 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACAC-GAATTT
* *
3136 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT
*
3156 CAAATTCACAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
3176 -AATTTCGCAACA
1 CAAATTCGCAACA
3188 GGTTTTAGTT
Statistics
Matches: 91, Mismatches: 16, Indels: 12
0.76 0.13 0.10
Matches are distributed among these distances:
19 14 0.15
20 58 0.64
21 18 0.20
22 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:4153 original size:24 final size:24
Alignment explanation
Indices: 4102--4155 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
4092 GTATTCGAAA
*
4102 TTTGATCTTGGTCAATACCCGTAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
4126 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
4150 TTTGAT
1 TTTGAT
4156 GATGTTTCAG
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:0.20, C:0.19, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:6434 original size:18 final size:18
Alignment explanation
Indices: 6411--6446 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6401 AAGCAAAAGG
*
6411 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
6429 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
6447 CAACCAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:6737 original size:20 final size:20
Alignment explanation
Indices: 6691--6738 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
6681 ATTTTTTGTT
* *
6691 GCGAAAGTCAAATTCGCAAC
1 GCGAAAATCAAAATCGCAAC
*
6711 GCAAAAATCAAAATCGCAAAC
1 GCGAAAATCAAAATCGC-AAC
6732 -CGAAAAT
1 GCGAAAAT
6739 TGCAACGCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.50, C:0.23, G:0.15, T:0.12
Consensus pattern (20 bp):
GCGAAAATCAAAATCGCAAC
Found at i:6773 original size:20 final size:20
Alignment explanation
Indices: 6748--6826 Score: 95
Period size: 20 Copynumber: 4.0 Consensus size: 20
6738 TTGCAACGCG
6748 AATTTGACTTTCACGTTGCA
1 AATTTGACTTTCACGTTGCA
* * *** *
6768 AATTTGACTATCGCAACGCG
1 AATTTGACTTTCACGTTGCA
*
6788 AATTTGACTTTCGCGTTGCA
1 AATTTGACTTTCACGTTGCA
6808 AATTTGACTTTCACGTTGC
1 AATTTGACTTTCACGTTGC
6827 GAAAGTGCAC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (20 bp):
AATTTGACTTTCACGTTGCA
Found at i:6784 original size:40 final size:40
Alignment explanation
Indices: 6740--6816 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
6730 ACCGAAAATT
6740 GCAACGCGAATTTGACTTTCACGTTGCAAATTTGACTATC
1 GCAACGCGAATTTGACTTTCACGTTGCAAATTTGACTATC
*
6780 GCAACGCGAATTTGACTTTCGCGTTGCAAATTTGACT
1 GCAACGCGAATTTGACTTTCACGTTGCAAATTTGACT
6817 TTCACGTTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (40 bp):
GCAACGCGAATTTGACTTTCACGTTGCAAATTTGACTATC
Found at i:8455 original size:42 final size:42
Alignment explanation
Indices: 8409--8507 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
8399 GCGGACGTGA
*
8409 CCTCTTGAACGATGACAGGGGCCTCTTGAATGATGGGAGGTG
1 CCTCTTGAACGATGACAGGGGCCTCTTGAATGATAGGAGGTG
* * *
8451 CCTCTTCG-ATGATGAGAGGGGCTTCTTGAATGATAGGAGGTG
1 CCTCTT-GAACGATGACAGGGGCCTCTTGAATGATAGGAGGTG
8493 CCTCTTGAACGATGA
1 CCTCTTGAACGATGA
8508 TAGGTGCATA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
41 1 0.02
42 48 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.26
Consensus pattern (42 bp):
CCTCTTGAACGATGACAGGGGCCTCTTGAATGATAGGAGGTG
Found at i:8512 original size:21 final size:21
Alignment explanation
Indices: 8409--8514 Score: 108
Period size: 21 Copynumber: 5.0 Consensus size: 21
8399 GCGGACGTGA
* * *
8409 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAATGATGAGAGGTG
*
8430 CCTCTTGAATGATGGGAGGTG
1 CCTCTTGAATGATGAGAGGTG
*
8451 CCTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAATGATGAGAGGTG
*
8472 CTTCTTGAATGAT-AGGAGGTG
1 CCTCTTGAATGATGA-GAGGTG
* *
8493 CCTCTTGAACGATGATAGGTG
1 CCTCTTGAATGATGAGAGGTG
8514 C
1 C
8515 ATAAGACTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.03
21 66 0.94
22 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.26
Consensus pattern (21 bp):
CCTCTTGAATGATGAGAGGTG
Found at i:10634 original size:20 final size:20
Alignment explanation
Indices: 10611--10738 Score: 142
Period size: 20 Copynumber: 6.7 Consensus size: 20
10601 AAACTTAAAT
10611 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
10631 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
10651 TCGCAACGTGAACATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
10671 TCGCAACGCGAAACTAGAAAA
1 TCGCAACGCGAAAAT-GAAAA
10692 TCGCAACGC--AAAT----A
1 TCGCAACGCGAAAATGAAAA
* *
10706 TCGCAACGTGAAAATAAAAA
1 TCGCAACGCGAAAATGAAAA
*
10726 TTGCAACGCGAAA
1 TCGCAACGCGAAA
10739 CTAAAATCTT
Statistics
Matches: 90, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
14 9 0.10
16 4 0.04
19 3 0.03
20 60 0.67
21 14 0.16
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:11688 original size:19 final size:19
Alignment explanation
Indices: 11661--11697 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11651 ATGACCAATA
*
11661 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
11680 AAATTGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
11698 CAGTATCGCA
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:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:11814 original size:21 final size:20
Alignment explanation
Indices: 11783--11836 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 20
11773 GAATATGTAA
11783 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
11803 ATCGCAAACGCGATTCTGACT
1 ATCGC-AACGCGATTCTGACT
*
11824 ATCGTAACGCGAT
1 ATCGCAACGCGAT
11837 AAATACATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:13012 original size:19 final size:19
Alignment explanation
Indices: 12941--13006 Score: 116
Period size: 19 Copynumber: 3.5 Consensus size: 19
12931 TCTGAAACTT
12941 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
12960 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
12979 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAA-TG
12998 AAAATCGCA
1 AAAATCGCA
13007 TTGCGATCCT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 45 0.98
20 1 0.02
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:13392 original size:22 final size:22
Alignment explanation
Indices: 13362--13412 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
13352 GATGGAGATA
13362 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTTGCCGGAGATGGG
* *
13384 GATGGATTTTGTCGGAGATGGG
1 GACGGATTTTGCCGGAGATGGG
13406 GACGGAT
1 GACGGAT
13413 GTCGCCGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.10, G:0.45, T:0.25
Consensus pattern (22 bp):
GACGGATTTTGCCGGAGATGGG
Found at i:13623 original size:21 final size:21
Alignment explanation
Indices: 13598--13673 Score: 152
Period size: 21 Copynumber: 3.6 Consensus size: 21
13588 GATAGTCAGA
13598 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
13619 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
13640 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
13661 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
13674 AGTCAGAATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:16953 original size:21 final size:21
Alignment explanation
Indices: 16927--17001 Score: 141
Period size: 21 Copynumber: 3.6 Consensus size: 21
16917 GATTTACATA
16927 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
16948 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
16969 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
16990 TTCGCGTTGCGA
1 TTCGCATTGCGA
17002 ATCTGGAAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:19417 original size:16 final size:17
Alignment explanation
Indices: 19396--19430 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
19386 GTTTTTTAAT
*
19396 ATTTTTTATTTAAT-AA
1 ATTTTTTATCTAATCAA
19412 ATTTTTTATCTAATCAA
1 ATTTTTTATCTAATCAA
19429 AT
1 AT
19431 GGTGACATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTTTATCTAATCAA
Found at i:19589 original size:11 final size:12
Alignment explanation
Indices: 19572--19603 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
19562 TGGTATCTAG
19572 AATATAATTTAT
1 AATATAATTTAT
19584 -ATATAATTTAT
1 AATATAATTTAT
19595 AATATAATT
1 AATATAATT
19604 AATGATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATATAATTTAT
Found at i:20057 original size:34 final size:34
Alignment explanation
Indices: 20014--20098 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
20004 CCCGAACCCG
*
20014 AAAATATTATATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
20048 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
20082 AAAATATTATATATATA
1 AAAATATTATATATATA
20099 TATATAATCG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:20581 original size:2 final size:2
Alignment explanation
Indices: 20574--20602 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20564 TTATTTTTAT
20574 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20603 CAAATTATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25189 original size:20 final size:19
Alignment explanation
Indices: 25166--25212 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
25156 CGATATACCA
25166 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
25186 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
25206 GGTAAAA
1 GGTAAAA
25213 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:25351 original size:181 final size:182
Alignment explanation
Indices: 24954--25426 Score: 633
Period size: 181 Copynumber: 2.6 Consensus size: 182
24944 GATCCAAATT
* * * * ** **
24954 AAAAATGTGTCGATCCAAAACGATATAATAGGTAAAACTATGACAAAACTAGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * * * * *
25019 AAACCGGTAAAGTGCTACCGGATACATTTAAAATGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAAGATAGACAATTC
* ** *
25084 GTGAATTTAAAAGAGAAGCAGTTTTAAATTCTATAAAGTATCGATACTTTTA
131 GTGAATTTAAAAGAGAAGCAGCTTTAAAGCCTATAAAGTATCGATACTTTAA
* * *
25136 AAAATTGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
25201 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAAGATAGACAATTT
66 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAAGATAGACAATTC
** * *
25265 GTGAATTTAAAAGAGAAGCAGCTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGCTTTAAAGCCTATAAAGTATCGATACTTTAA
* * *
25317 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAATCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
25382 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
25427 CGTAAGTACG
Statistics
Matches: 253, Mismatches: 38, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
181 161 0.64
182 92 0.36
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAAGATAGACAATTC
GTGAATTTAAAAGAGAAGCAGCTTTAAAGCCTATAAAGTATCGATACTTTAA
Found at i:25370 original size:20 final size:19
Alignment explanation
Indices: 25347--25393 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
25337 CGATATAACA
*
25347 GGTAAAAATATGATAAAATC
1 GGTAAAAA-ATGATAAAACC
*
25367 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
25387 GGTAAAA
1 GGTAAAA
25394 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:27650 original size:21 final size:21
Alignment explanation
Indices: 27624--27688 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
27614 AAGACAATCA
*
27624 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
27645 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
27666 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
27687 AG
1 AG
27689 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:27764 original size:33 final size:33
Alignment explanation
Indices: 27722--27787 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
27712 AAATAGATGG
*
27722 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
27755 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
27788 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:29608 original size:19 final size:19
Alignment explanation
Indices: 29584--29632 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
29574 AATGTAGGGT
29584 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
29603 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
29622 TAATTTTGTAT
1 TAATTTTGTAT
29633 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:31185 original size:183 final size:183
Alignment explanation
Indices: 30824--32134 Score: 2261
Period size: 183 Copynumber: 7.1 Consensus size: 183
30814 CAAAGTTTTC
* * * * *
30824 ACACTTTTTAATATTGTGTCTGTACTTTATATCCAGAATGGAAGAAAAATGTGTCGATACTATTT
1 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* * *
30889 AAAAAAGTGTCG--ATTGAAAAAACATCAGAACCCAGAATTATAATGTAATAGATAATAGATAAT
66 AAAAAAGTGTCGACATT---TACACATCGGAACCCAGAA-T-T-A--TAAT-G-TAATAGATAAT
*
30952 TTTGTAATATAACCGGTATAAATATATCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
121 TTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
31015 ACACTTTTTAATATTGTGTCAGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTG
1 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATT-
*
31079 TCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
65 TAAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
31144 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
130 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
31198 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAAATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* *
31263 CACAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
31328 AACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
31381 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
31446 AAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* *
31511 AACCGGTATAAATATACCGGTTTTATGAACGAATAGGTCTACAACCTATATCT
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
31564 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
31629 AAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* *
31694 AACTGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
31747 ACACTTTTTAATATTGTGTCGAAACTTTATGTCTAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
31812 AAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
31877 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
31930 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTG
1 ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATT-
*
31994 TCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
65 TAAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
32059 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
130 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
32113 ACACTTTTTAATATTGTTTCGG
1 ACACTTTTTAATATTGTGTCGG
32135 TAATTTTAAG
Statistics
Matches: 1080, Mismatches: 35, Indels: 18
0.95 0.03 0.02
Matches are distributed among these distances:
182 4 0.00
183 975 0.90
184 5 0.00
185 4 0.00
187 1 0.00
188 1 0.00
189 1 0.00
190 19 0.02
191 67 0.06
193 3 0.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGAACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:35014 original size:23 final size:23
Alignment explanation
Indices: 34983--35055 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
34973 ATAGGTAAAA
* *
34983 ATATGATGTAATAGATAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
35006 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
35029 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
35052 ATAT
1 ATAT
35056 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:35502 original size:23 final size:23
Alignment explanation
Indices: 35471--35543 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
35461 ATAGGTAAAA
*
35471 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
35494 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
35517 ATATAATGTAATATGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
35540 ATAT
1 ATAT
35544 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:35561 original size:488 final size:490
Alignment explanation
Indices: 34637--35944 Score: 2423
Period size: 488 Copynumber: 2.7 Consensus size: 490
34627 AGGTATGTAC
*
34637 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAACTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
*
34702 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
* *
34767 TTTGGTTAA-ATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
34831 ATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
196 ATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
*
34896 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATAGAC
261 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATAGAC
34961 ACTTTCAATATAATAGGTAAAAATATGATGTAATAGATAGCGCTTATATAATGTAATAGGTAGCG
326 ACTTTCAATATAATAGGTAAAAATATGATGTAATAGATAGCGCTTATATAATGTAATAGGTAGCG
35026 TTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATATATCCTTTTTATAAAAGTGTCCAT
391 TTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATATATCCTTTTTATAAAAGTGTCCAT
35091 ACTTTTTTCACTGTGAAAAACATTAATTTAAGGTT
456 ACTTTTTTCACTGTGAAAAACATTAATTTAAGGTT
35126 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
*
35191 GTTACGATATATATTATTATTAAATTATAAAC-A-AAACATATATA-TACATATTTATTATTATC
66 GTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
35253 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
35318 ATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
196 ATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
35383 AAACATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATAGA
261 AAA-ATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATAGA
*
35448 CACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGC
325 CACTTTCAATATAATAGGTAAAAATATGATGTAATAGATAGCGCTTATATAATGTAATAGGTAGC
* *
35513 GTTTATATAATGTAATATGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCA
390 GTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATATATCCTTTTTATAAAAGTGTCCA
* *
35578 TTCTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
455 TACTTTTTTCACTGTGAAAAACATTAATTTAAGGTT
35614 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
*
35679 GTTACTATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
*
35744 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATAACAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
35809 ATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT--AA
196 ATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
*
35872 AAAATTGAAACATAAATTACATAACTTT-AAAAAAGTATCGATCTTTTTTATAAAAAAGTATAGA
261 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTAT-AAAAAGTATAGA
35936 CACTTTCAA
325 CACTTTCAA
35945 CATATTATAA
Statistics
Matches: 798, Mismatches: 15, Indels: 13
0.97 0.02 0.02
Matches are distributed among these distances:
486 27 0.03
487 154 0.19
488 363 0.45
489 100 0.13
490 11 0.01
491 143 0.18
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (490 bp):
ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
GTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
ATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATAGAC
ACTTTCAATATAATAGGTAAAAATATGATGTAATAGATAGCGCTTATATAATGTAATAGGTAGCG
TTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATATATCCTTTTTATAAAAGTGTCCAT
ACTTTTTTCACTGTGAAAAACATTAATTTAAGGTT
Found at i:36409 original size:60 final size:60
Alignment explanation
Indices: 36327--36441 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
36317 ATGATTCTTA
*
36327 TTTTAAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATTCCT-AAACTATGACTATCT
1 TTTTAAATTAGTCCCTAAACTTTTAAATATTTCAATTTCA-TCCTCAAACTATGACTATCT
* *
36387 TTTTAAATTAGT-CCTCAAACTTTTGAATATTTTAATTTCATCCTCAAACTATGAC
1 TTTTAAATTAGTCCCT-AAACTTTTAAATATTTCAATTTCATCCTCAAACTATGAC
36442 CTTCATTCTA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
59 7 0.14
60 43 0.86
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.44
Consensus pattern (60 bp):
TTTTAAATTAGTCCCTAAACTTTTAAATATTTCAATTTCATCCTCAAACTATGACTATCT
Found at i:36454 original size:60 final size:60
Alignment explanation
Indices: 36330--36470 Score: 162
Period size: 60 Copynumber: 2.4 Consensus size: 60
36320 ATTCTTATTT
* * *
36330 TAAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATTCCTAAACTATGACTATCTTTT
1 TAAATTAGTCCCTAAACTTTTAAATATTTCAATTTCATTCCTAAACTATGACTATCATTC
* *
36390 TAAATTAGT-CCTCAAACTTTTGAATATTTTAATTTCA-TCCTCAAACTATGACCT-TCATTC
1 TAAATTAGTCCCT-AAACTTTTAAATATTTCAATTTCATTCCT-AAACTATGA-CTATCATTC
* * *
36450 TAAATTGGACCCTAAATTTTT
1 TAAATTAGTCCCTAAACTTTT
36471 TTAACATTCT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
59 7 0.10
60 57 0.83
61 5 0.07
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (60 bp):
TAAATTAGTCCCTAAACTTTTAAATATTTCAATTTCATTCCTAAACTATGACTATCATTC
Found at i:36704 original size:60 final size:60
Alignment explanation
Indices: 36623--36771 Score: 203
Period size: 60 Copynumber: 2.5 Consensus size: 60
36613 GGATATTTTG
* * *
36623 AGGATGAAATTGAAATATTCAAAAGTTTGAAGACCAATTTAGAAAT-AGGGTCATAGTTTA
1 AGGATGAAATTAAAATATTCAAAAGTTTAAAGACCAATTTA-AAATGAGAGTCATAGTTTA
* * *
36683 ATGATGAAATTATAAAT-TTCAAAAGTTTAAAGACTAATTTATAATGAGAGTCATAGTTTA
1 AGGATGAAATTA-AAATATTCAAAAGTTTAAAGACCAATTTAAAATGAGAGTCATAGTTTA
*
36743 AGGATGAAATTAAAATATTAAAAAGTTTA
1 AGGATGAAATTAAAATATTCAAAAGTTTA
36772 TTAGGGACAT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
59 7 0.09
60 67 0.86
61 4 0.05
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.33
Consensus pattern (60 bp):
AGGATGAAATTAAAATATTCAAAAGTTTAAAGACCAATTTAAAATGAGAGTCATAGTTTA
Found at i:37631 original size:15 final size:15
Alignment explanation
Indices: 37608--37637 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
37598 TATCATTAAA
*
37608 TTAATTTATAAAATG
1 TTAACTTATAAAATG
37623 TTAACTTATAAAATG
1 TTAACTTATAAAATG
37638 CTAAACATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (15 bp):
TTAACTTATAAAATG
Found at i:38506 original size:31 final size:31
Alignment explanation
Indices: 38468--38530 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
38458 CGAATGACCA
*
38468 CTATCCATATGTCCCGAAGGACATAGGTAAC
1 CTATCCATATGTCCCGAAGAACATAGGTAAC
*
38499 CTATCCATATGTTCCGAAGAACATAGGTAAC
1 CTATCCATATGTCCCGAAGAACATAGGTAAC
38530 C
1 C
38531 CTCGATTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (31 bp):
CTATCCATATGTCCCGAAGAACATAGGTAAC
Found at i:41716 original size:31 final size:31
Alignment explanation
Indices: 41678--41771 Score: 120
Period size: 31 Copynumber: 3.0 Consensus size: 31
41668 CGAAGGACTA
41678 CTGTCCATATGTCCTGAAAGACATAGGTAAC
1 CTGTCCATATGTCCTGAAAGACATAGGTAAC
*
41709 CTGTCCATATGTTCC-G-AAGAACATAGGTAAA
1 CTGTCCATATG-TCCTGAAAG-ACATAGGTAAC
* * *
41740 CTATCTATATGTCTTGAAAGACATAGGTAAC
1 CTGTCCATATGTCCTGAAAGACATAGGTAAC
41771 C
1 C
41772 CTCGACTCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
30 5 0.09
31 43 0.80
32 6 0.11
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (31 bp):
CTGTCCATATGTCCTGAAAGACATAGGTAAC
Found at i:47736 original size:20 final size:21
Alignment explanation
Indices: 47653--47734 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
47643 AGCAGAACCC
*
47653 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGGAATCGATTCCCCT
** *
47674 GTGGGGGGAATCGGTTCCCCTT
1 CAGGGGGGAATCGATTCCCC-T
* *
47696 CAAAGGGGG-ATCG-TTTCCCT
1 C-AGGGGGGAATCGATTCCCCT
47716 CAGGGGGGAATCGATTCCC
1 CAGGGGGGAATCGATTCCC
47735 TCTGCACCAA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
19 6 0.13
20 6 0.13
21 25 0.53
22 5 0.11
23 5 0.11
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.23
Consensus pattern (21 bp):
CAGGGGGGAATCGATTCCCCT
Found at i:50432 original size:34 final size:34
Alignment explanation
Indices: 50389--50458 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
50379 TTGTTTTTCC
50389 TCCCAAGCTAGTAGTTCTAGTTGGCCCAAAAAGA
1 TCCCAAGCTAGTAGTTCTAGTTGGCCCAAAAAGA
50423 TCCCAAGCTAGTAGTTCTAGTTGGCCCAAAAAGA
1 TCCCAAGCTAGTAGTTCTAGTTGGCCCAAAAAGA
50457 TC
1 TC
50459 TAAATGGATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (34 bp):
TCCCAAGCTAGTAGTTCTAGTTGGCCCAAAAAGA
Found at i:51570 original size:22 final size:21
Alignment explanation
Indices: 51528--51567 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
51518 GAGTTTGTTT
*
51528 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
51549 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
51568 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:60170 original size:29 final size:29
Alignment explanation
Indices: 60128--60202 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
60118 TTTTATATTT
60128 TCATGTA-CTCATGTCATTTATCTTGTGA
1 TCATGTAGCTCATGTCATTTATCTTGTGA
*
60156 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTATCTTGTGA
60185 TCATGTAGCTCATGTCAT
1 TCATGTAGCTCATGTCAT
60203 GTTCTCATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTATCTTGTGA
Found at i:65494 original size:95 final size:94
Alignment explanation
Indices: 65324--65515 Score: 240
Period size: 95 Copynumber: 2.0 Consensus size: 94
65314 ATGCGCAACC
* * ** * * *
65324 TATGTGCAAAATAGAACCATACGAGTCAATGCTTGAATTTACACTCATACCAGAACAATGCAACT
1 TATGTGCAAAATAGAACCATACAAGTCAAAGCCAGAAATTACACCCACACCAGAACAATGCAACT
* * * *
65389 TGTGCTCAAAACCGGAACCATACAAGTCCA
66 TATGCACAAAA-CAGAACCATACAAGCCCA
* * * *
65419 TATGTGCAAAATAGAACCATATAAGTTAAAGCCAGAAATTACACCCACACTAGAACAATGTAACT
1 TATGTGCAAAATAGAACCATACAAGTCAAAGCCAGAAATTACACCCACACCAGAACAATGCAACT
65484 TATGCACAAAACAGAACCATACAAGCCCA
66 TATGCACAAAACAGAACCATACAAGCCCA
65513 TAT
1 TAT
65516 CAGTAGCCTA
Statistics
Matches: 82, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
94 19 0.23
95 63 0.77
ACGTcount: A:0.43, C:0.23, G:0.13, T:0.21
Consensus pattern (94 bp):
TATGTGCAAAATAGAACCATACAAGTCAAAGCCAGAAATTACACCCACACCAGAACAATGCAACT
TATGCACAAAACAGAACCATACAAGCCCA
Done.