Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005890.1 Hibiscus syriacus cultivar Beakdansim tig00013830_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: 53036
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5742 original size:20 final size:21
Alignment explanation
Indices: 5706--5747 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5696 AGTTTGGCGC
*
5706 ATTAACCAATACAAACC-GAT
1 ATTAACCAACACAAACCAGAT
5726 ATTAAGCCAACAC-AACCAGAT
1 ATTAA-CCAACACAAACCAGAT
5747 A
1 A
5748 CCTATTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.50, C:0.26, G:0.07, T:0.17
Consensus pattern (21 bp):
ATTAACCAACACAAACCAGAT
Found at i:5867 original size:24 final size:24
Alignment explanation
Indices: 5817--5869 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5807 TATAGTAGTT
**
5817 TACAACACAATAAAATTACAGACG
1 TACAACACAATAAAAGCACAGACG
* *
5841 TACAACACAATAAAAGCAGAGAGG
1 TACAACACAATAAAAGCACAGACG
5865 TACAA
1 TACAA
5870 AGTTAATAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (24 bp):
TACAACACAATAAAAGCACAGACG
Found at i:15089 original size:20 final size:19
Alignment explanation
Indices: 15064--15117 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
15054 GCGAAATAAA
15064 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
15084 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
15104 AATCGCAACGCGAT
1 AATCGCAACGCGAT
15118 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:15128 original size:21 final size:21
Alignment explanation
Indices: 15102--15199 Score: 69
Period size: 21 Copynumber: 4.7 Consensus size: 21
15092 ATCAGTTCCC
15102 AGAATCGCAACGCGATTATGA
1 AGAATCGCAACGCGATTATGA
*
15123 AGAATCGCAATGCGA-TA-GTA
1 AGAATCGCAACGCGATTATG-A
* ** * **
15143 CA-AATTAGCATTGCGATTTTCC
1 -AGAA-TCGCAACGCGATTATGA
*
15165 AGAATCGCAACGCGAATATGA
1 AGAATCGCAACGCGATTATGA
15186 A-AATCGCAACGCGA
1 AGAATCGCAACGCGA
15200 ACATATAAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
19 1 0.02
20 18 0.31
21 36 0.62
22 3 0.05
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (21 bp):
AGAATCGCAACGCGATTATGA
Found at i:15192 original size:20 final size:20
Alignment explanation
Indices: 15167--15378 Score: 117
Period size: 20 Copynumber: 10.5 Consensus size: 20
15157 GATTTTCCAG
*
15167 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
15187 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* * *
15207 AATCGCAATGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
15227 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
15248 AATCACAACGCGTATTC-ATA
1 AATCGCAACGCGAATACGA-A
15268 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
15289 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * * *
15309 AATTGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
15329 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGAA
* * *
15349 AATCGCAATGCGATTACGTA
1 AATCGCAACGCGAATACGAA
15369 AATCGCAACG
1 AATCGCAACG
15379 AGATTCTGAC
Statistics
Matches: 153, Mismatches: 29, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.02
20 115 0.75
21 34 0.22
22 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:15262 original size:21 final size:21
Alignment explanation
Indices: 15228--15378 Score: 127
Period size: 20 Copynumber: 7.4 Consensus size: 21
15218 GATTCTGACT
*
15228 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGTAAA
* * *
15249 ATCACAACGCGTATTCAT-AA
1 ATCGCAACGCGTATCCGTAAA
* *
15269 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGTAAA
15290 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
*
15310 ATTGCAACGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
* * *
15330 ATCGCAATGCGAATACGT-AA
1 ATCGCAACGCGTATCCGTAAA
* *
15350 ATCGCAATGCG-ATTACGT-AA
1 ATCGCAACGCGTA-TCCGTAAA
15370 ATCGCAACG
1 ATCGCAACG
15379 AGATTCTGAC
Statistics
Matches: 110, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.01
20 78 0.71
21 31 0.28
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGTATCCGTAAA
Found at i:15269 original size:61 final size:60
Alignment explanation
Indices: 15204--15356 Score: 166
Period size: 61 Copynumber: 2.5 Consensus size: 60
15194 ACGCGAACAT
* ** *
15204 ATAAATCGCAATGCGATTC-TGACTATCGCAACGAGTATCCGTAAAATCACAACGCGTATTC
1 ATAAATCGCAATGCGATACGT-AAAATCGCAACGAGTATCCGT-AAATCACAACGCGTATCC
* * * **
15265 ATAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATTGCAACGCGTATCC
1 ATAAATCGCAATG-CGATACGTAAAATCGCAACGAGTATCCGTAAATCACAACGCGTATCC
*
15326 GTAAATCGCAATGCGAATACGT-AAATCGCAA
1 ATAAATCGCAATGCG-ATACGTAAAATCGCAA
15357 TGCGATTACG
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
60 10 0.13
61 44 0.57
62 22 0.29
63 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (60 bp):
ATAAATCGCAATGCGATACGTAAAATCGCAACGAGTATCCGTAAATCACAACGCGTATCC
Found at i:15273 original size:41 final size:41
Alignment explanation
Indices: 15228--15356 Score: 152
Period size: 41 Copynumber: 3.2 Consensus size: 41
15218 GATTCTGACT
* * *
15228 ATCGCAACGAGTATCCGTAAAATCACAACGCGTATTCATAA
1 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATACGTAA
** * *
15269 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATACGTAA
* * * *
15310 ATTGCAACGCGTATCCGT-AAATCGCAATGCGAATACGTAA
1 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATACGTAA
15350 ATCGCAA
1 ATCGCAA
15357 TGCGATTACG
Statistics
Matches: 73, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
40 25 0.34
41 48 0.66
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATACGTAA
Found at i:16260 original size:24 final size:24
Alignment explanation
Indices: 16233--16286 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
16223 GTATTCGAAA
16233 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
16257 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
16281 TTTGAT
1 TTTGAT
16287 GATTTTTCAG
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:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:18844 original size:33 final size:33
Alignment explanation
Indices: 18802--18966 Score: 177
Period size: 33 Copynumber: 4.7 Consensus size: 33
18792 ATGTCTAACA
18802 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
* * *
18835 CAATGCGAAATGAAAATCACACAACGTGAAAATCG
1 CAATGCGAAATGAAAAT--CGCAACGAGAGAATCG
* * * *
18870 CAACGCGAATATGAATATCGCAACGCGGAAATTACTATCG
1 CAATGCGAA-ATGAAAATCGCAA--C-GAGA-GA--ATCG
18910 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
*
18943 CAAAGCGAAATGAAAATCGCAACG
1 CAATGCGAAATGAAAATCGCAACG
18967 CGAATTTAGT
Statistics
Matches: 109, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
33 44 0.40
34 4 0.04
35 22 0.20
36 11 0.10
37 3 0.03
38 1 0.01
39 12 0.11
40 12 0.11
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCG
Found at i:18889 original size:20 final size:19
Alignment explanation
Indices: 18806--18970 Score: 106
Period size: 19 Copynumber: 9.3 Consensus size: 19
18796 CTAACACAAT
18806 GCGAAATGAAAATCGCAA-
1 GCGAAATGAAAATCGCAAC
* *
18824 -CG--A-GAGAATCGCAAT
1 GCGAAATGAAAATCGCAAC
18839 GCGAAATGAAAAT--C-AC
1 GCGAAATGAAAATCGCAAC
* *
18855 AC-AACGTGAAAATCGCAAC
1 GCGAA-ATGAAAATCGCAAC
*
18874 GCGAATATGAATATCGCAAC
1 GCGAA-ATGAAAATCGCAAC
* ** *
18894 GCGGAAATTACTATCGCAAT
1 GC-GAAATGAAAATCGCAAC
18914 GCGAAATGAAAATCGCAA-
1 GCGAAATGAAAATCGCAAC
* *
18932 -CG--A-GAGAATCGCAAA
1 GCGAAATGAAAATCGCAAC
18947 GCGAAATGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAC
18966 GCGAA
1 GCGAA
18971 TTTAGTTTCG
Statistics
Matches: 113, Mismatches: 18, Indels: 31
0.70 0.11 0.19
Matches are distributed among these distances:
14 20 0.18
15 4 0.04
16 13 0.12
17 5 0.04
18 3 0.03
19 36 0.32
20 29 0.26
21 3 0.03
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
GCGAAATGAAAATCGCAAC
Found at i:18919 original size:75 final size:72
Alignment explanation
Indices: 18831--18968 Score: 204
Period size: 73 Copynumber: 1.9 Consensus size: 72
18821 CAACGAGAGA
* * *
18831 ATCGCAATGCGAAATGAAAATCACACAACGTGAAAATCGCAACGCGAATATGAATATCGCAACGC
1 ATCGCAATGCGAAATGAAAAT--CACAACGAGAAAATCGCAAAGCGAA-ATGAAAATCGCAACGC
18896 GGAAATTACT
63 GGAAATTACT
* *
18906 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGCG
1 ATCGCAATGCGAAATGAAAATCACAACGAGAAAATCGCAAAGCGAAATGAAAATCGCAACGCG
18969 AATTTAGTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
72 16 0.28
73 21 0.36
75 21 0.36
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (72 bp):
ATCGCAATGCGAAATGAAAATCACAACGAGAAAATCGCAAAGCGAAATGAAAATCGCAACGCGGA
AATTACT
Found at i:19001 original size:19 final size:19
Alignment explanation
Indices: 18966--19028 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
18956 AAATCGCAAC
*
18966 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
18985 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
19004 GCGATTTTCA-TTTCGCATT
1 GCGATTTT-AGTTTCGCGTT
19023 GCGATT
1 GCGATT
19029 CTCTCGTTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
19 40 0.98
20 1 0.02
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.44
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:19068 original size:19 final size:19
Alignment explanation
Indices: 18976--19060 Score: 92
Period size: 19 Copynumber: 4.7 Consensus size: 19
18966 GCGAATTTAG
*
18976 TTTCGCGTTGCGATTTT-A
1 TTTCGCATTGCGATTTTCA
*
18994 GTTTCGCGTTGCGATTTTCA
1 -TTTCGCATTGCGATTTTCA
19014 TTTCGCATTGCGA--TTC-
1 TTTCGCATTGCGATTTTCA
*
19030 TCTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
19047 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
19061 AGTCATTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 36 0.63
20 1 0.02
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:19177 original size:14 final size:14
Alignment explanation
Indices: 19158--19194 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
19148 CATCAATTAA
19158 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
19172 ACAAATCATCTTTT
1 ACAAATCAACTTTT
19186 ACAAATCAA
1 ACAAATCAA
19195 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:20612 original size:21 final size:21
Alignment explanation
Indices: 20546--20654 Score: 57
Period size: 21 Copynumber: 5.2 Consensus size: 21
20536 GTGAATCGGG
*
20546 CTCTTGAATGGTGGG-AGGGA
1 CTCTTGAACGGTGGGAAGGGA
* * *
20566 CCTCTTCAACGAT--GACAGTGGC
1 -CTCTTGAACGGTGGGA-AG-GGA
20588 CTCTTGAACGGTGGGAAGGGA
1 CTCTTGAACGGTGGGAAGGGA
* ** * *
20609 CTCTCG-A-GGAATGATAGGGGC
1 CTCTTGAACGG--TGGGAAGGGA
20630 CTCTTGAACGGTGGGAAGGGA
1 CTCTTGAACGGTGGGAAGGGA
20651 CTCT
1 CTCT
20655 CGAGGAATGA
Statistics
Matches: 62, Mismatches: 17, Indels: 18
0.64 0.18 0.19
Matches are distributed among these distances:
19 3 0.05
20 1 0.02
21 49 0.79
22 5 0.08
23 4 0.06
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAAGGGA
Found at i:20631 original size:42 final size:42
Alignment explanation
Indices: 20546--20681 Score: 186
Period size: 42 Copynumber: 3.2 Consensus size: 42
20536 GTGAATCGGG
* * * * *
20546 CTCTTGAATGGTGGG-AGGGACCTCTTCAACG-ATGACAGTGGC
1 CTCTTGAACGGTGGGAAGGGA-CTC-TCGAGGAATGATAGGGGC
20588 CTCTTGAACGGTGGGAAGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAAGGGACTCTCGAGGAATGATAGGGGC
20630 CTCTTGAACGGTGGGAAGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAAGGGACTCTCGAGGAATGATAGGGGC
*
20672 CTCTTCAACG
1 CTCTTGAACG
20682 ATAGGAGTGG
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
41 4 0.05
42 77 0.90
43 5 0.06
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAAGGGACTCTCGAGGAATGATAGGGGC
Found at i:20675 original size:21 final size:21
Alignment explanation
Indices: 20609--20675 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
20599 TGGGAAGGGA
20609 CTCTCGAGGAATGATAGGGGC
1 CTCTCGAGGAATGATAGGGGC
* ** * *
20630 CTCTTGAACGG--TGGGAAGGGA
1 CTCTCG-A-GGAATGATAGGGGC
20651 CTCTCGAGGAATGATAGGGGC
1 CTCTCGAGGAATGATAGGGGC
20672 CTCT
1 CTCT
20676 TCAACGATAG
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 2 0.06
20 1 0.03
21 26 0.81
22 1 0.03
23 2 0.06
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.21
Consensus pattern (21 bp):
CTCTCGAGGAATGATAGGGGC
Found at i:20694 original size:42 final size:42
Alignment explanation
Indices: 20585--20706 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 42
20575 CGATGACAGT
* * *
20585 GGCCTCTTGAACGGTGGGAAGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAAGGGACTCTCGAGGAATGATAGG
* * *
20627 GGCCTCTTGAACGGTGGGAAGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAAGGGACTCTCGAGGAATGATAGG
* *
20669 GGCCTCTTCAACGATAGG-AGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAAG-GGACTCTCGAGGAATGA
20707 CAGGCGAGTC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
41 2 0.03
42 72 0.97
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.20
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAAGGGACTCTCGAGGAATGATAGG
Found at i:20694 original size:84 final size:84
Alignment explanation
Indices: 20546--20706 Score: 184
Period size: 84 Copynumber: 1.9 Consensus size: 84
20536 GTGAATCGGG
* * * * *
20546 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGGTGGGAAGGGACT
1 CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGGGGCCTCTTCAACGATAGGAAGGGACT
20611 CTCGAGGAATGATAGGGGC
66 CTCGAGGAATGATAGGGGC
* * *
20630 CTCTTGAACGGTGGGAAGGGA-CTC-TCGAGGAATGATAGGGGCCTCTTCAACGATAGG-AGTGG
1 CTCTTGAACGGTGGG-AGGGACCTCTTCAACG-ATGACAGGGGCCTCTTCAACGATAGGAAG-GG
* *
20692 ACTCTTGAGGGATGA
63 ACTCTCGAGGAATGA
20707 CAGGCGAGTC
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
83 6 0.09
84 53 0.83
85 5 0.08
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (84 bp):
CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGGGGCCTCTTCAACGATAGGAAGGGACT
CTCGAGGAATGATAGGGGC
Found at i:21147 original size:19 final size:19
Alignment explanation
Indices: 21131--21194 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
21121 AAAAATGACT
21131 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
21150 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
21164 ATCACAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
21183 ATCGCAACGCGA
1 ATCGCAACGCGA
21195 TTATAGTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 9 0.25
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.09
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:21213 original size:19 final size:19
Alignment explanation
Indices: 21191--21253 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
21181 AAATCGCAAC
*
21191 GCGATTATAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
21210 GCGATTTTGGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
21229 GCAATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
21248 GCGATT
1 GCGATT
21254 CTTTCGTTGC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.44
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:21271 original size:31 final size:33
Alignment explanation
Indices: 21235--21300 Score: 100
Period size: 31 Copynumber: 2.0 Consensus size: 33
21225 CGTTGCAATT
*
21235 TTCATTTCGCGTTGCGATTC-TTT-CGTTGCGA
1 TTCATTTCACGTTGCGATTCATTTCCGTTGCGA
21266 TTCATTTCACGTTGCGATTCATTTCGCGTTGCGA
1 TTCATTTCACGTTGCGATTCATTTC-CGTTGCGA
21300 T
1 T
21301 AGTCATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
31 19 0.61
32 3 0.10
34 9 0.29
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
TTCATTTCACGTTGCGATTCATTTCCGTTGCGA
Found at i:21308 original size:19 final size:17
Alignment explanation
Indices: 21201--21300 Score: 107
Period size: 17 Copynumber: 5.8 Consensus size: 17
21191 GCGATTATAG
**
21201 TTTCGCGTTGCGATTTTGG
1 TTTCGCGTTGCGA--TTCA
*
21220 TTTCGCGTTGCAATTTTCA
1 TTTCGCGTTGCGA--TTCA
21239 TTTCGCGTTGCGATTC-
1 TTTCGCGTTGCGATTCA
21255 TTT--CGTTGCGATTCA
1 TTTCGCGTTGCGATTCA
*
21270 TTTCACGTTGCGATTCA
1 TTTCGCGTTGCGATTCA
21287 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
21301 AGTCATTTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
14 11 0.15
15 3 0.04
16 3 0.04
17 28 0.38
19 28 0.38
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (17 bp):
TTTCGCGTTGCGATTCA
Found at i:21618 original size:93 final size:94
Alignment explanation
Indices: 21388--21765 Score: 620
Period size: 93 Copynumber: 4.1 Consensus size: 94
21378 ATGGATTGCA
* * *
21388 TTAC-TTCAACCAAAAGACAAAACAAAGATAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
21452 TTAGCAGAATTGGCTGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
21481 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
21546 TTAGCAGAATTGGCAGCAACCG-ACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
21574 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
21639 TTAGCAGAATTGGCAACAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
21668 TTAC-TTCAGCCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * *
21732 TTT-GTAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
21761 TTACT
1 TTACT
21766 AAGCAATCTA
Statistics
Matches: 270, Mismatches: 11, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
93 141 0.52
94 129 0.48
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:21707 original size:187 final size:187
Alignment explanation
Indices: 21388--21765 Score: 618
Period size: 187 Copynumber: 2.0 Consensus size: 187
21378 ATGGATTGCA
* *
21388 TTAC-TTCAACCAAAAGACAAAACAAAGATAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
**
21452 TTAGCAGAATTGGCTGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
66 TTAGCAGAATTGGCAACAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
*
21517 TAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCG-ACAAAT
131 TAACTTCACAGTGTTAAAGAATAAACAGTTT-GCAGAATTGGCAGCAACCGAACAAAT
*
21574 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
* *
21639 TTAGCAGAATTGGCAACAACCGAATAAATTTAC-TTCAGCCAAAAGACAAAACAAAAGACAAATA
66 TTAGCAGAATTGGCAACAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAAGACAAATA
* * *
21703 CTAACTTCACAGTGTTAAAGAATAAACAGTTTGTAGTATTGGCAGCAACCGAATAAAT
130 CTAACTTCACAGTGTTAAAGAATAAACAGTTTGCAGAATTGGCAGCAACCGAACAAAT
21761 TTACT
1 TTACT
21766 AAGCAATCTA
Statistics
Matches: 178, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
186 39 0.22
187 139 0.78
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (187 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
TTAGCAGAATTGGCAACAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
TAACTTCACAGTGTTAAAGAATAAACAGTTTGCAGAATTGGCAGCAACCGAACAAAT
Found at i:23492 original size:20 final size:20
Alignment explanation
Indices: 23469--23524 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
23459 TGAAATGAAA
23469 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
23489 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
23509 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
23525 CGCAACGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:23528 original size:14 final size:14
Alignment explanation
Indices: 23509--23564 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
23499 GGAAATGACT
23509 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
23523 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
23542 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
23556 ATCGCAACG
1 ATCGCAACG
23565 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:23546 original size:19 final size:19
Alignment explanation
Indices: 23460--23619 Score: 98
Period size: 19 Copynumber: 9.1 Consensus size: 19
23450 TCTTTTGGTT
*
23460 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
23479 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
23499 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
23517 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
23533 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
23550 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
23566 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
23583 G--A-GAGAATCGTAACGC
1 GAAATGAAAATCGCAACGC
*
23599 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
23618 GA
1 GA
23620 TTCTCTCGTT
Statistics
Matches: 109, Mismatches: 15, Indels: 34
0.69 0.09 0.22
Matches are distributed among these distances:
14 27 0.25
15 3 0.03
16 6 0.06
17 5 0.05
18 4 0.04
19 34 0.31
20 28 0.26
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:23546 original size:33 final size:33
Alignment explanation
Indices: 23460--23614 Score: 211
Period size: 33 Copynumber: 4.5 Consensus size: 33
23450 TCTTTTGGTT
23460 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-GA--ATCGCAACGC
**
23499 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
23533 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
23566 GAAATTAAAATCGCAACGAGAGAATCGTAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
23599 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
23615 TGCGATTCTC
Statistics
Matches: 108, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
33 77 0.71
34 10 0.09
36 2 0.02
37 1 0.01
38 3 0.03
40 15 0.14
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:23646 original size:21 final size:20
Alignment explanation
Indices: 23627--23698 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
23617 CGATTCTCTC
23627 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
23647 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
23668 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
23688 GTTGCGATTTT
1 GTTGCGATTTT
23699 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:24308 original size:20 final size:20
Alignment explanation
Indices: 24280--24531 Score: 203
Period size: 20 Copynumber: 12.5 Consensus size: 20
24270 TACGTATTGT
24280 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTACAGATACG
* * * *
24300 CATTACGATTTAC-GTATTCT
1 CGTTGCGATTTACAG-ATACG
*
24320 CGTTGCGATTTACAGATACA
1 CGTTGCGATTTACAGATACG
24340 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTACAGATACG
* *
24360 CGTTGCGATTTAC-GTATTCT
1 CGTTGCGATTTACAG-ATACG
*
24380 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACAGATACG
*
24400 CGTTGCGATTTTAC-G-TATTG
1 CGTTGCGA-TTTACAGATA-CG
*
24420 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACAGATACG
* *
24441 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACAGATACG
*
24462 CGTTGCGATAGT-CAGA-ATCG
1 CGTTGCGAT-TTACAGATA-CG
* *
24482 CGTTGCGATTTATATG-TTCG
1 CGTTGCGATTTACA-GATACG
* * **
24502 CGTTGCGATTTTCATATTTG
1 CGTTGCGATTTACAGATACG
24522 CGTTGCGATT
1 CGTTGCGATT
24532 CTGGAAAATC
Statistics
Matches: 190, Mismatches: 26, Indels: 32
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.03
20 144 0.76
21 38 0.20
22 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTTACAGATACG
Found at i:24323 original size:40 final size:40
Alignment explanation
Indices: 24268--24372 Score: 140
Period size: 40 Copynumber: 2.6 Consensus size: 40
24258 GCGTTGCGAT
* *
24268 TTTACGTATTGTCGTTGCGATTTACAGATACGCATTACGA
1 TTTACGTATTCTCGTTGCGATTTACAGATACACATTACGA
* *
24308 TTTACGTATTCTCGTTGCGATTTACAGATACACGTTGCGA
1 TTTACGTATTCTCGTTGCGATTTACAGATACACATTACGA
* *
24348 TTTACAG-ATACGCGTTGCGATTTAC
1 TTTAC-GTATTCTCGTTGCGATTTAC
24373 GTATTCTCGT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 57 0.98
41 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (40 bp):
TTTACGTATTCTCGTTGCGATTTACAGATACACATTACGA
Found at i:24353 original size:60 final size:60
Alignment explanation
Indices: 24280--24410 Score: 226
Period size: 60 Copynumber: 2.2 Consensus size: 60
24270 TACGTATTGT
24280 CGTTGCGATTTACAGATACGCATTACGATTTACGTATTCTCGTTGCGATTTACAGATACA
1 CGTTGCGATTTACAGATACGCATTACGATTTACGTATTCTCGTTGCGATTTACAGATACA
* * * *
24340 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACAGATACGCATTACGATTTACGTATTCTCGTTGCGATTTACAGATACA
24400 CGTTGCGATTT
1 CGTTGCGATTT
24411 TACGTATTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (60 bp):
CGTTGCGATTTACAGATACGCATTACGATTTACGTATTCTCGTTGCGATTTACAGATACA
Found at i:24425 original size:41 final size:41
Alignment explanation
Indices: 24305--24470 Score: 221
Period size: 41 Copynumber: 4.1 Consensus size: 41
24295 ATACGCATTA
* * * * *
24305 CGATTTACGTATTCTCGTTGCGA-TTTACAG-ATACACGTTG
1 CGATTTACGGATACGCGTTGCGATTTTAC-GTATTCTCGTTG
*
24345 CGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTG
1 CGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTG
*
24385 CGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTG
1 CGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTG
* *
24426 CGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTG
1 CGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTG
24467 CGAT
1 CGAT
24471 AGTCAGAATC
Statistics
Matches: 113, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 54 0.48
41 58 0.51
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTG
Found at i:24525 original size:81 final size:82
Alignment explanation
Indices: 24340--24531 Score: 223
Period size: 81 Copynumber: 2.4 Consensus size: 82
24330 TACAGATACA
* * * *
24340 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGAATACGCGTT
*
24404 GCGATTTTACGTATTGT
66 GCGATTTTACGTATCGT
*
24421 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAAT-CGCG
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGGATACTCGTTGCGAT--TCACGAATACGCG
*
24484 TTGCGATTTATATGT-TCG-
64 TTGCGATTT-TACGTATCGT
* * **
24502 CGTTGCGATTTTCATATTTGCGTTGCGATT
1 CGTTGCGATTTACAGATACGCGTTGCGATT
24532 CTGGAAAATC
Statistics
Matches: 95, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
81 52 0.55
82 34 0.36
83 7 0.07
84 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (82 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGAATACGCGTT
GCGATTTTACGTATCGT
Found at i:27835 original size:31 final size:31
Alignment explanation
Indices: 27797--27857 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
27787 TGACCACATC
*
27797 TTAATTAAATAAAAACGAAAGTAACCATATT
1 TTAATTAAATAAAAACAAAAGTAACCATATT
*
27828 TTAATTAAATAAAAACAAAAGTGACCATAT
1 TTAATTAAATAAAAACAAAAGTAACCATAT
27858 CTTTTGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.28
Consensus pattern (31 bp):
TTAATTAAATAAAAACAAAAGTAACCATATT
Found at i:30485 original size:7 final size:7
Alignment explanation
Indices: 30464--30523 Score: 106
Period size: 7 Copynumber: 8.9 Consensus size: 7
30454 TATACTTGAT
30464 TATATGA
1 TATATGA
30471 -AT-TGA
1 TATATGA
30476 TATATGA
1 TATATGA
30483 TATATGA
1 TATATGA
30490 TATATGA
1 TATATGA
30497 TATATGA
1 TATATGA
30504 TATATGA
1 TATATGA
30511 TATATGA
1 TATATGA
30518 TATATG
1 TATATG
30524 TGATGCATGT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
5 3 0.06
6 4 0.08
7 44 0.86
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (7 bp):
TATATGA
Found at i:34981 original size:36 final size:36
Alignment explanation
Indices: 34926--35005 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
34916 CCCATTCTTA
* *
34926 TTTTC-AACAAACATCTACCAAACTTTGAAAAATAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
*
34961 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
34997 TTTTCAAAG
1 TTTTCAAAG
35006 TTGGTTGCCG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 5 0.12
36 36 0.88
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (36 bp):
TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
Found at i:35004 original size:21 final size:21
Alignment explanation
Indices: 34944--35004 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
34934 AAACATCTAC
*
34944 CAAACTTTGAAAAATATTTTT
1 CAAACTTTGAAAAACATTTTT
**
34965 CAAA----G--AAACATTTAC
1 CAAACTTTGAAAAACATTTTT
34980 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
35001 CAAA
1 CAAA
35005 GTTGGTTGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 12
0.63 0.11 0.26
Matches are distributed among these distances:
15 11 0.38
17 1 0.03
19 1 0.03
21 16 0.55
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.33
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:39526 original size:21 final size:20
Alignment explanation
Indices: 39502--39562 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
39492 CAAACTTTAC
39502 CAAACTTTGAAAAACATTTTT
1 CAAA-TTTGAAAAACATTTTT
**
39523 CAAA---G--AAACATTTAC
1 CAAATTTGAAAAACATTTTT
39538 CAAAATTTGAAAAACATTTTT
1 C-AAATTTGAAAAACATTTTT
39559 CAAA
1 CAAA
39563 GTTGGTTGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 13
0.64 0.09 0.28
Matches are distributed among these distances:
15 9 0.30
16 3 0.10
17 1 0.03
19 1 0.03
20 3 0.10
21 13 0.43
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (20 bp):
CAAATTTGAAAAACATTTTT
Found at i:39538 original size:36 final size:35
Alignment explanation
Indices: 39493--39563 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
39483 AACATCTACC
*
39493 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACTTTACCAAAATTTGAAAAACATTTTTCAAAG
39528 AAACATTTACCAAAATTTGAAAAACATTTTTCAAAG
1 AAAC-TTTACCAAAATTTGAAAAACATTTTTCAAAG
39564 TTGGTTGTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (35 bp):
AAACTTTACCAAAATTTGAAAAACATTTTTCAAAG
Found at i:41050 original size:22 final size:22
Alignment explanation
Indices: 41019--41073 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
41009 CGAGTCAAGT
*
41019 TTTTTTGAGTCGAAAAATTCAG
1 TTTTTCGAGTCGAAAAATTCAG
41041 TTTTTCGAGTCGAAAAATTCAG
1 TTTTTCGAGTCGAAAAATTCAG
41063 TTTTTCGAGTC
1 TTTTTCGAGTC
41074 AAGTCGAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (22 bp):
TTTTTCGAGTCGAAAAATTCAG
Found at i:51914 original size:10 final size:10
Alignment explanation
Indices: 51899--51924 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
51889 TTCTATAAAA
51899 TATATATAGT
1 TATATATAGT
51909 TATATATAGT
1 TATATATAGT
51919 TATATA
1 TATATA
51925 ATTTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (10 bp):
TATATATAGT
Done.