Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005226.1 Hibiscus syriacus cultivar Beakdansim tig00011834_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: 67138
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1780 original size:248 final size:249
Alignment explanation
Indices: 1315--1808 Score: 774
Period size: 248 Copynumber: 2.0 Consensus size: 249
1305 GGTGTAAAAT
*
1315 AATTAGGGTAGCCCTTTTTGTCTTTTACCTAATATTATTTTATTTTTTTAATTTATTGAGGACGT
1 AATTAGGGTAGCCCTATTTGTCTTTTACCTAATATTATTTTATTTTTTTAATTTATTGAGGACGT
*
1380 AGATATACCTTTTGTAATATAATTAGTAAATAAATTGAGTTTGAACGAATAAATTATGTTTCGTT
66 AGATATACCCTTTGTAATATAATTAGTAAATAAATTGAGTTTGAACGAATAAATTATGTTTCGTT
* *
1445 TTTATTTATTTTTTGTTTTTAAAAGTGTTTATATTTGATCGATATTATTTAATTTTTAATATCAT
131 TTTATTTATTTTTTGTTTTTAAAAGTGTTTATATTCGATCGATATTATTTAATATTTAATATCAT
1510 TTAAATTCGTGTTCATATATTTATTTTTGAAGGTCAT-ATTCGTTCGTTTAAGCA
196 TTAAATTCGTGTTCA-ATATTTATTTTTGAAGGTCATGATTCGTTCGTTTAAGCA
1564 AATTA-GGTAGCCCTATTTGTCTTTTACCTAATATTATTTTA-TTTTTTAATTTATTGAGGACGT
1 AATTAGGGTAGCCCTATTTGTCTTTTACCTAATATTATTTTATTTTTTTAATTTATTGAGGACGT
1627 AGATATACCCTTTGTAATATAATTAGGGGTGTAAATAAATTGAGTTTGAACGAATAAAATTA-G-
66 AGATATACCCTTTGTAATATAATTA-----GTAAATAAATTGAGTTTGAACGAAT-AAATTATGT
*
1690 TTCG-TTTTGTTTATTTGTTTGTTTTTAAAAGTGTTTATATTCGATCG-TA-TATTTAA-ATTTA
125 TTCGTTTTTATTTATTT-TTTGTTTTTAAAAGTGTTTATATTCGATCGATATTATTTAATATTTA
*
1751 ATATCATGTTCAAATTCGTGTTC-ATATTTATTTTTGAAGGTCATGTTTCGTTCGTTTA
189 ATATCAT-TT-AAATTCGTGTTCAATATTTATTTTTGAAGGTCATGATTCGTTCGTTTA
1809 GCATTCGAGA
Statistics
Matches: 229, Mismatches: 6, Indels: 20
0.90 0.02 0.08
Matches are distributed among these distances:
247 46 0.20
248 67 0.29
249 26 0.11
250 25 0.11
251 33 0.14
252 26 0.11
253 6 0.03
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.50
Consensus pattern (249 bp):
AATTAGGGTAGCCCTATTTGTCTTTTACCTAATATTATTTTATTTTTTTAATTTATTGAGGACGT
AGATATACCCTTTGTAATATAATTAGTAAATAAATTGAGTTTGAACGAATAAATTATGTTTCGTT
TTTATTTATTTTTTGTTTTTAAAAGTGTTTATATTCGATCGATATTATTTAATATTTAATATCAT
TTAAATTCGTGTTCAATATTTATTTTTGAAGGTCATGATTCGTTCGTTTAAGCA
Found at i:1933 original size:21 final size:23
Alignment explanation
Indices: 1898--1954 Score: 84
Period size: 21 Copynumber: 2.6 Consensus size: 23
1888 TAACGTTAGT
1898 GAAC-TTTTCATTTAGCTTTTGC
1 GAACATTTTCATTTAGCTTTTGC
*
1920 G-ACATTTT-ATTTAGTTTTTGC
1 GAACATTTTCATTTAGCTTTTGC
1941 GAACATTTTCATTT
1 GAACATTTTCATTT
1955 GTTGTTGAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 15 0.48
22 12 0.39
23 4 0.13
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.53
Consensus pattern (23 bp):
GAACATTTTCATTTAGCTTTTGC
Found at i:6897 original size:59 final size:59
Alignment explanation
Indices: 6834--6945 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 59
6824 GTCGGTTGAC
* * *
6834 CATTTTGTAACTTTTAATAGTCG-GGAGACTCAACAAATCAACACCCTATAGTCGGGGAT
1 CATTTTGTAACTTTTAATAATCGAGG-GACTCAACAAAACAACACCCAATAGTCGGGGAT
* *
6893 CATTTTGTAACTTTTAATAATCGAGGGACTCAATAAAACATCACCCAATAGTC
1 CATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAACAACACCCAATAGTC
6946 AAGGTACTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 45 0.96
60 2 0.04
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (59 bp):
CATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAACAACACCCAATAGTCGGGGAT
Found at i:7462 original size:20 final size:20
Alignment explanation
Indices: 7439--7480 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
7429 CAACGCGAAC
*
7439 TCCAATTTCACAACACAGTT
1 TCCAAATTCACAACACAGTT
* *
7459 TCCAAATTCGCAACTCAGTT
1 TCCAAATTCACAACACAGTT
7479 TC
1 TC
7481 TGAAATCGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (20 bp):
TCCAAATTCACAACACAGTT
Found at i:8051 original size:20 final size:20
Alignment explanation
Indices: 8028--8066 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
8018 TTTGAAACTT
8028 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
8048 AAATTCGCAACACGAAAAT
1 AAATTCGCAACACGAAAAT
8067 CGCAAGGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:8132 original size:20 final size:20
Alignment explanation
Indices: 8097--8160 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
8087 CGCAACGCGG
8097 TTTTAGTTTTCACGTTGCGAA
1 TTTTA-TTTTCACGTTGCGAA
*
8118 TTTTATTTTCGCGTTGCGAA
1 TTTTATTTTCACGTTGCGAA
* ***
8138 TTTCATTTTTTTGTTGCGAA
1 TTTTATTTTCACGTTGCGAA
8158 TTT
1 TTT
8161 AAGTTTCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
20 33 0.87
21 5 0.13
ACGTcount: A:0.16, C:0.12, G:0.17, T:0.55
Consensus pattern (20 bp):
TTTTATTTTCACGTTGCGAA
Found at i:9715 original size:42 final size:42
Alignment explanation
Indices: 9655--9753 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
9645 CCCCCCACTT
* * * *
9655 CGAGAGCCATCACTTGATCGAGCCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTAGACAC
*
9697 CGAGAGCCATCACCTGATCGAGCTGATTATACACCTAGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTAGACAC
9739 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
9754 ATTCCATCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.18
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACACCTAGACAC
Found at i:9937 original size:21 final size:21
Alignment explanation
Indices: 9913--9962 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
9903 TGGTGCATGG
9913 CGTGATGAGGTA-CGGTCTTTA
1 CGTGATGAGGTAGCGGT-TTTA
* *
9934 CGTGGTGAGGTAGCTGTTTTA
1 CGTGATGAGGTAGCGGTTTTA
*
9955 CGCGATGA
1 CGTGATGA
9963 CAATGGTGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (21 bp):
CGTGATGAGGTAGCGGTTTTA
Found at i:10335 original size:21 final size:21
Alignment explanation
Indices: 10309--10438 Score: 122
Period size: 21 Copynumber: 6.2 Consensus size: 21
10299 GAAACCTAAC
* *
10309 CCACCTACCATTGTTCAGGAT
1 CCACCTCCCATCGTTCAGGAT
*
10330 CCACCTCCCATTGTTCAGGAT
1 CCACCTCCCATCGTTCAGGAT
* ** * *
10351 TCACCTGTCATCGTTCAAGAGG
1 CCACCTCCCATCGTTCAGGA-T
10373 CC-CCTCCCATCGTTCAAGAGA-
1 CCACCTCCCATCGTTC-AG-GAT
*
10394 CC-CCTTCCATCGTTCAGGAT
1 CCACCTCCCATCGTTCAGGAT
*
10414 CCACCTCCCACCGTTCAGGAT
1 CCACCTCCCATCGTTCAGGAT
10435 CCAC
1 CCAC
10439 ATGGCATACT
Statistics
Matches: 90, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.02
20 4 0.04
21 80 0.89
22 2 0.02
23 2 0.02
ACGTcount: A:0.21, C:0.39, G:0.15, T:0.25
Consensus pattern (21 bp):
CCACCTCCCATCGTTCAGGAT
Found at i:11605 original size:22 final size:22
Alignment explanation
Indices: 11588--11654 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
11578 CTCGTATAAA
11588 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
11610 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
11632 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
11654 T
1 T
11655 TTGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:11915 original size:30 final size:31
Alignment explanation
Indices: 11874--11932 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
11864 TAGACATAGT
*
11874 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
11904 ATTTACATACCTTTATCACATAGTGCATA
1 ATTTACATACCTTTAACACATAGTGCATA
11933 GAACTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.36
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:12007 original size:29 final size:29
Alignment explanation
Indices: 11947--12014 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
11937 TTTTCTGCAT
* **
11947 ATTCATGTCATGTCATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* * *
11976 ATTCATGTCATGTAATACCTTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
12005 ATTCATGTCA
1 ATTCATGTCA
12015 AAATATGGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:12437 original size:68 final size:69
Alignment explanation
Indices: 12290--12442 Score: 209
Period size: 69 Copynumber: 2.2 Consensus size: 69
12280 TTTTCTCATG
* * * *
12290 GGGGAATCGGTTCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAGTCTGGAATTTCATATACGA
1 GGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGA
*
12355 TGAG
66 TGAA
* * * * *
12359 GGGGTATCGGTTCCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGT
1 GGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGA
12423 TGAA
66 TGAA
12427 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
12443 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
68 27 0.36
69 47 0.64
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (69 bp):
GGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGA
TGAA
Found at i:12452 original size:21 final size:21
Alignment explanation
Indices: 12422--12464 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12412 ATCATATTCG
* *
12422 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
12443 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
12464 T
1 T
12465 AACCCAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:18512 original size:22 final size:22
Alignment explanation
Indices: 18495--18561 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
18485 CTCGTATAAA
18495 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
18517 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
18539 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
18561 T
1 T
18562 TTGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:18822 original size:30 final size:31
Alignment explanation
Indices: 18781--18839 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
18771 TAGACATAGT
*
18781 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
18811 ATTTACATACCTTTATCACATAGTGCATA
1 ATTTACATACCTTTAACACATAGTGCATA
18840 GAACTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.36
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:18914 original size:29 final size:29
Alignment explanation
Indices: 18854--18921 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
18844 TTTTCTGCAT
* **
18854 ATTCATGTCATGTCATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* * *
18883 ATTCATGTCATGTAATACCTTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
18912 ATTCATGTCA
1 ATTCATGTCA
18922 AAATATGGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:19323 original size:68 final size:69
Alignment explanation
Indices: 19196--19348 Score: 202
Period size: 68 Copynumber: 2.2 Consensus size: 69
19186 TTTTTCTCAT
* * * *
19196 GGGGGAATCGGTT-CCCCCCTTAGGGGTATCGATTCCCCTCAAGCAGTCTGGAATTTCATATACG
1 GGGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACG
19260 ATGA
66 ATGA
* * * *
19264 GGGGGTATCGGTTCCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCG
1 GGGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACG
*
19328 TTGA
66 ATGA
*
19332 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
19349 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
68 39 0.53
69 35 0.47
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (69 bp):
GGGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACG
ATGA
Found at i:19358 original size:21 final size:21
Alignment explanation
Indices: 19328--19370 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
19318 ATCATATTCG
* *
19328 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
19349 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
19370 T
1 T
19371 AACCCAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:20916 original size:30 final size:30
Alignment explanation
Indices: 20880--20949 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
20870 GAGCATTTGG
20880 ATGTACTGTCTGGGGCAAATTGATGTATCA
1 ATGTACTGTCTGGGGCAAATTGATGTATCA
20910 ATGTACTGTCTGGGGCAAATTGATGTATCA
1 ATGTACTGTCTGGGGCAAATTGATGTATCA
* *
20940 TTGTGCTGTC
1 ATGTACTGTC
20950 AAGTGTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (30 bp):
ATGTACTGTCTGGGGCAAATTGATGTATCA
Found at i:20995 original size:16 final size:15
Alignment explanation
Indices: 20970--20999 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20960 AAGAATTATT
20970 ATTTTTGTTTAATTG
1 ATTTTTGTTTAATTG
20985 ATTTGTTGTTTAATT
1 ATTT-TTGTTTAATT
21000 TCAATCTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (15 bp):
ATTTTTGTTTAATTG
Found at i:27323 original size:20 final size:20
Alignment explanation
Indices: 27294--27331 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27284 CCCCTTCAAA
*
27294 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
27314 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
27332 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:33562 original size:20 final size:20
Alignment explanation
Indices: 33537--33606 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
33527 CAAAACATTT
33537 GTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
33557 GTGTTGCG-AATTCGAAAA-TC
1 GTGTTGCGAAATT--AAAATTC
* * **
33577 GAGTTACGAAAACAAAATTC
1 GTGTTGCGAAATTAAAATTC
*
33597 GTGTAGCGAA
1 GTGTTGCGAA
33607 TTAGAAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 8 0.21
20 25 0.64
21 6 0.15
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:33627 original size:40 final size:40
Alignment explanation
Indices: 33537--33628 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 40
33527 CAAAACATTT
** * * *
33537 GTGTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATC
1 GTGTTGCGAAAACAAAATTCGTGTAGCGAATTAGAAAATA
* *
33577 GAGTTACGAAAACAAAATTCGTGTAGCGAATTAGAAAATA
1 GTGTTGCGAAAACAAAATTCGTGTAGCGAATTAGAAAATA
*
33617 TTGTTGCGAAAA
1 GTGTTGCGAAAA
33629 GGAAACTTGT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (40 bp):
GTGTTGCGAAAACAAAATTCGTGTAGCGAATTAGAAAATA
Found at i:33728 original size:20 final size:20
Alignment explanation
Indices: 33649--33741 Score: 62
Period size: 20 Copynumber: 4.6 Consensus size: 20
33639 GTTGCGACAA
* * *
33649 GAAATTCGCGTTGCGAATTC
1 GAAAATCGCGTTACGAATTT
* * *
33669 AAAAATCGAGTTGCGAATTT
1 GAAAATCGCGTTACGAATTT
* * *
33689 GAAATTC-CATTTTGCGAATTT
1 GAAAATCGC--GTTACGAATTT
*
33710 GGAAATCGCGTTACGAATTT
1 GAAAATCGCGTTACGAATTT
*
33730 TAAAATCGCGTT
1 GAAAATCGCGTT
33742 GCGATTTCAG
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
20 40 0.71
21 15 0.27
22 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (20 bp):
GAAAATCGCGTTACGAATTT
Found at i:33774 original size:20 final size:21
Alignment explanation
Indices: 33751--33789 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
33741 TGCGATTTCA
33751 GAAACTGAGTTGC-AAATTTG
1 GAAACTGAGTTGCGAAATTTG
*
33771 GAAACTGTGTTGCGAAATT
1 GAAACTGAGTTGCGAAATT
33790 GGAGTTCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (21 bp):
GAAACTGAGTTGCGAAATTTG
Found at i:36155 original size:21 final size:22
Alignment explanation
Indices: 36126--36176 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
36116 TTAGTTTTCT
* *
36126 AATTCAAAAGAATAAAATT-AA
1 AATTAAAAAAAATAAAATTGAA
*
36147 AATTAAAAAAAATAAACTTGAA
1 AATTAAAAAAAATAAAATTGAA
36169 AA-TAAAAA
1 AATTAAAAA
36177 TTTACAGTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (22 bp):
AATTAAAAAAAATAAAATTGAA
Found at i:42261 original size:22 final size:23
Alignment explanation
Indices: 42231--42282 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
42221 ATACTGTATG
*
42231 AACAATACCATGAACAGTA-ATA
1 AACAGTACCATGAACAGTACATA
*
42253 AACAGTACCGTGAACAGTACCATA
1 AACAGTACCATGAACAGTA-CATA
42277 AACAGT
1 AACAGT
42283 GAAAACTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 17 0.65
24 9 0.35
ACGTcount: A:0.48, C:0.21, G:0.13, T:0.17
Consensus pattern (23 bp):
AACAGTACCATGAACAGTACATA
Found at i:42280 original size:12 final size:12
Alignment explanation
Indices: 42231--42282 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
42221 ATACTGTATG
* *
42231 AACAATACCATG
1 AACAGTACCATA
42243 AACAGTA--ATA
1 AACAGTACCATA
* *
42253 AACAGTACCGTG
1 AACAGTACCATA
42265 AACAGTACCATA
1 AACAGTACCATA
42277 AACAGT
1 AACAGT
42283 GAAAACTTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
10 9 0.28
12 23 0.72
ACGTcount: A:0.48, C:0.21, G:0.13, T:0.17
Consensus pattern (12 bp):
AACAGTACCATA
Found at i:42968 original size:24 final size:23
Alignment explanation
Indices: 42925--42969 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
42915 TATGTCATTT
42925 CATATAACATGTAATACATATTG
1 CATATAACATGTAATACATATTG
42948 CATATAATCATGT-ATATCATAT
1 CATATAA-CATGTAATA-CATAT
42970 ACTATATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (23 bp):
CATATAACATGTAATACATATTG
Found at i:44067 original size:8 final size:8
Alignment explanation
Indices: 44054--44083 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
44044 TAAATCATTG
44054 AACTTTTC
1 AACTTTTC
44062 AACTTTTC
1 AACTTTTC
44070 AACTTTTC
1 AACTTTTC
*
44078 CACTTT
1 AACTTT
44084 AATAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (8 bp):
AACTTTTC
Found at i:44583 original size:23 final size:23
Alignment explanation
Indices: 44557--44601 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
44547 GAAATTGTCC
* *
44557 TAAAAAGATAAAAAAAATAAAAT
1 TAAAAAAATAAAAAAAACAAAAT
*
44580 TAAAAAAATAAAACAAACAAAA
1 TAAAAAAATAAAAAAAACAAAA
44602 ACAAAGAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.13
Consensus pattern (23 bp):
TAAAAAAATAAAAAAAACAAAAT
Found at i:44647 original size:9 final size:9
Alignment explanation
Indices: 44635--44660 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
44625 AAATAAAGTA
44635 AATAAAAGG
1 AATAAAAGG
44644 AATAAAAGG
1 AATAAAAGG
44653 AATAAAAG
1 AATAAAAG
44661 AAAATTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (9 bp):
AATAAAAGG
Found at i:46041 original size:37 final size:37
Alignment explanation
Indices: 45950--46109 Score: 196
Period size: 37 Copynumber: 4.2 Consensus size: 37
45940 AATCATTTTT
* *** *
45950 AAAACTATATATGATATACGCTTTCAAAAATTATTTTC-
1 AAAACTATATATTATATATATTTTC-AAAA-TGTTTTCA
* *
45988 AAAACTATATAATATATATATTTTCGAAATGTTTTCA
1 AAAACTATATATTATATATATTTTCAAAATGTTTTCA
*
46025 AAAACTATATATTATATATATTTTCAAAACGTTTTCA
1 AAAACTATATATTATATATATTTTCAAAATGTTTTCA
*
46062 AAAACTATATATTATATATATGTTTTCAAAATATTTTCA
1 AAAACTATATATTATATATA--TTTTCAAAATGTTTTCA
46101 AAAACTATA
1 AAAACTATA
46110 CTATATTAAT
Statistics
Matches: 107, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
36 6 0.06
37 57 0.53
38 20 0.19
39 24 0.22
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (37 bp):
AAAACTATATATTATATATATTTTCAAAATGTTTTCA
Found at i:46073 original size:39 final size:39
Alignment explanation
Indices: 45983--46125 Score: 181
Period size: 39 Copynumber: 3.7 Consensus size: 39
45973 TCAAAAATTA
*
45983 TTTTC-AAAACTATATA-A-TATATATATTTTCGAAATG
1 TTTTCAAAAACTATATATATTATATATATTTTCAAAATG
*
46019 TTTTCAAAAAC--TATATATTATATATATTTTCAAAACG
1 TTTTCAAAAACTATATATATTATATATATTTTCAAAATG
* *
46056 TTTTCAAAAACTATATAT-TATATATATGTTTTCAAAATA
1 TTTTCAAAAACTATATATAT-TATATATATTTTCAAAATG
46095 TTTTCAAAAACTATACTATATTAATATATAT
1 TTTTCAAAAACTATA-TATATT-ATATATAT
46126 ATTAAATAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
35 4 0.04
36 6 0.07
37 33 0.36
38 1 0.01
39 36 0.39
40 4 0.04
41 8 0.09
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (39 bp):
TTTTCAAAAACTATATATATTATATATATTTTCAAAATG
Found at i:46742 original size:200 final size:200
Alignment explanation
Indices: 46398--46880 Score: 626
Period size: 200 Copynumber: 2.4 Consensus size: 200
46388 CAACCAGAAA
* * * * **
46398 ATATGCCCTCGAGCTGAATGAAATTGAACTCGAAGGTTTTTGTTGACAGATAACCGTTATCGTCT
1 ATATGCCTTCGAGCTGAATGGAATTGAACTCGAAGG-TTTTGTTGACAGATAACCCTTCTCACCT
* * * * * * *
46463 TGAACTATGCTATAAATTCGGCTGGGAGATAGTTCCTTGTTTCTAAATCATAGCTAACCTAGGAC
65 TGAGCTATGCTGTAAATTCGGATGGGAGATAATTCCTTGTTGCTAAATCACAGCCAACCTAGGAC
* * * *
46528 TTCTTCTTGACTTAAATACCTCAGTTTAAACTTCAATCGGAAAGTAGTTCCTCGTTGCTACCATG
130 TTCTTCTTGACTTAAAGACCTCAGTTTAAACTTCAACCAGAAAGTAGTTCCTCGTTGCTACCATA
46593 CAGTTG
195 CAGTTG
* * *
46599 ATATGCCTTCGAGCTGAATGGAATCGAACTCGAAAGTTTTGTTGAAAGATAACCCTTCTCACCTT
1 ATATGCCTTCGAGCTGAATGGAATTGAACTCGAAGGTTTTGTTGACAGATAACCCTTCTCACCTT
* * * * * ** *
46664 GAGCTATACTGTAATTTTGGATGGGATATAATTCTTTGTTGCTAAATTGCAGCCAACCTAGGTCT
66 GAGCTATGCTGTAAATTCGGATGGGAGATAATTCCTTGTTGCTAAATCACAGCCAACCTAGGACT
* *
46729 TCTTCTTGACTTAAAGACCTCAGTTTAAGCTTTAACCAGAAAGTAGTTCCTCGTTGCTACCATAC
131 TCTTCTTGACTTAAAGACCTCAGTTTAAACTTCAACCAGAAAGTAGTTCCTCGTTGCTACCATAC
*
46794 GGTTG
196 AGTTG
* * *
46799 ATATGCCTTCAAACTGAATGGAATTGAACTCGAAGGTTTTGTTGACAGATAACACTTCT-AGCCT
1 ATATGCCTTCGAGCTGAATGGAATTGAACTCGAAGGTTTTGTTGACAGATAACCCTTCTCA-CCT
*
46863 TGAGTTATGCTGTAAATT
65 TGAGCTATGCTGTAAATT
46881 GTTCCTCTAA
Statistics
Matches: 241, Mismatches: 40, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
199 1 0.00
200 208 0.86
201 32 0.13
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (200 bp):
ATATGCCTTCGAGCTGAATGGAATTGAACTCGAAGGTTTTGTTGACAGATAACCCTTCTCACCTT
GAGCTATGCTGTAAATTCGGATGGGAGATAATTCCTTGTTGCTAAATCACAGCCAACCTAGGACT
TCTTCTTGACTTAAAGACCTCAGTTTAAACTTCAACCAGAAAGTAGTTCCTCGTTGCTACCATAC
AGTTG
Found at i:47174 original size:86 final size:86
Alignment explanation
Indices: 46933--47399 Score: 630
Period size: 86 Copynumber: 5.4 Consensus size: 86
46923 TGGTCATAAT
* * * * * * *** *
46933 TCTTTAGATGAATCCTCTTTACGGGAAAGCCAAGTGGTATATTCCTCAGGCAATTCCCCTTCGCA
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGATATATTCCTCAGGTGGTTCCCCTTCGCG
*
46998 AGTCTGAACCAAGTGAGATGA
66 GGTCTGAACCAAGTGAGATGA
* * * * * * *
47019 TCTTTGAATGGCTCCCTTTTCATGGGAAAGCCATGTGATATATTCCTCAGGTGATTCCTCTTCAC
1 TCTTTGGATGACTCCC-CTTCACGGGAAAGCCATGTGATATATTCCTCAGGTGGTTCCCCTTCGC
47084 GGGTCTGAACCAAGTGAGATGA
65 GGGTCTGAACCAAGTGAGATGA
* *
47106 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTAATATATTCCTCAAGTGGTTCCCCTTCGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGATATATTCCTCAGGTGGTTCCCCTTCGCG
*
47171 GGTCTAAACCAAGTGAGATGA
66 GGTCTGAACCAAGTGAGATGA
* *
47192 TCTTTGGATGACTCCCCTTTACGGGAAAGCCATGTGATATATTCCTCAGGTGGTTCCCCTTCGTG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGATATATTCCTCAGGTGGTTCCCCTTCGCG
*
47257 GGTCTGAACCAAATGAGATGA
66 GGTCTGAACCAAGTGAGATGA
* * * *
47278 TCTTTGAATGACTCCCCTTCACGGGAAAGCTATGTGATATATTCCTCAGGTGGTTCTCCTTCGTG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGATATATTCCTCAGGTGGTTCCCCTTCGCG
* *
47343 GGTCTGAAGCAAGTAAGATGA
66 GGTCTGAACCAAGTGAGATGA
* *
47364 TCTTTGGATGACTCCCCTTAATGGGAAAG-CATGTGA
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGA
47400 AATGTTCTTC
Statistics
Matches: 337, Mismatches: 43, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
85 6 0.02
86 258 0.77
87 73 0.22
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (86 bp):
TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGATATATTCCTCAGGTGGTTCCCCTTCGCG
GGTCTGAACCAAGTGAGATGA
Found at i:47252 original size:42 final size:42
Alignment explanation
Indices: 47037--47253 Score: 122
Period size: 42 Copynumber: 5.1 Consensus size: 42
47027 TGGCTCCCTT
* * *
47037 TTCATGGGAAAGCCATGTGATATATTCCTCAGGTGATTCCTC
1 TTCACGGGAAAGCCATGTGATATATTCCTCAGGTGGTTCCCC
* * * ** **
47079 TTCACGGGTCTGAA-CCAAGTGAGATGA-T-CTTTGGATGACTCCCC
1 TTCACGGG---AAAGCCATGTGATAT-ATTCCTCAGG-TGGTTCCCC
* *
47123 TTCACGGGAAAGCCATGTAATATATTCCTCAAGTGGTTCCCC
1 TTCACGGGAAAGCCATGTGATATATTCCTCAGGTGGTTCCCC
* * * ** **
47165 TTCGCGGGTCTAAA-CCAAGTGAGATGA-T-CTTTGGATGACTCCCC
1 TTCACGGG---AAAGCCATGTGATAT-ATTCCTCAGG-TGGTTCCCC
*
47209 TTTACGGGAAAGCCATGTGATATATTCCTCAGGTGGTTCCCC
1 TTCACGGGAAAGCCATGTGATATATTCCTCAGGTGGTTCCCC
47251 TTC
1 TTC
47254 GTGGGTCTGA
Statistics
Matches: 124, Mismatches: 35, Indels: 32
0.65 0.18 0.17
Matches are distributed among these distances:
41 7 0.06
42 49 0.40
43 14 0.11
44 47 0.38
45 7 0.06
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (42 bp):
TTCACGGGAAAGCCATGTGATATATTCCTCAGGTGGTTCCCC
Found at i:48758 original size:99 final size:99
Alignment explanation
Indices: 48630--48916 Score: 403
Period size: 99 Copynumber: 2.9 Consensus size: 99
48620 GTAATTCGCG
* * * * * *
48630 TTTATCAGGCTAACTGAATGTTATCCATAAAGCTGGGGCATTTAACTAAATACTCTAGAGGGACA
1 TTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACA
* * *
48695 GCTCAAGATTTATTTTATATATATTATAATCACC
66 ACTCAAGCTTTATTGTATATATATTATAATCACC
*
48729 TTTATCAGGCTAGCTGAATCTTATCCATAAATCCGGGGCATTTAACCAATTGCTCTAGAGGGACA
1 TTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACA
48794 ACTCAAGCTTTATTGTATATATATTATAATCACC
66 ACTCAAGCTTTATTGTATATATATTATAATCACC
* * ** * * *
48828 TTTATCATGCTAGCTAAATCTTATTTATAAAGCCAGAGCGTTTAACCAATTGCTCTAGAGGGACA
1 TTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACA
* *
48893 ACTCAAGCTTTACTGTATACATAT
66 ACTCAAGCTTTATTGTATATATAT
48917 AATATTATAA
Statistics
Matches: 168, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 168 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (99 bp):
TTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACA
ACTCAAGCTTTATTGTATATATATTATAATCACC
Found at i:52850 original size:13 final size:13
Alignment explanation
Indices: 52817--52842 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52807 AGATCGAAAT
52817 AAAGTAAATAAAA
1 AAAGTAAATAAAA
52830 AAAGTAAATAAAA
1 AAAGTAAATAAAA
52843 GGAATAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAGTAAATAAAA
Found at i:54091 original size:14 final size:13
Alignment explanation
Indices: 54064--54107 Score: 63
Period size: 14 Copynumber: 3.3 Consensus size: 13
54054 GGGAAAATAT
54064 TAATTAAT-AAAA
1 TAATTAATGAAAA
54076 TAATTAATGGAAAA
1 TAATTAAT-GAAAA
54090 TAATTAATGAAAAA
1 TAATTAATG-AAAA
54104 TAAT
1 TAAT
54108 ATGTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.28
13 1 0.03
14 20 0.69
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (13 bp):
TAATTAATGAAAA
Found at i:54223 original size:28 final size:30
Alignment explanation
Indices: 54159--54227 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 30
54149 TTTCAAAAAT
*
54159 TATTTTC-GAAACTATATAATATATTATATA
1 TATTTTCAAAAACTATAT-ATATATTATATA
54189 TATTTTCAAAAACTATAT-TATA-TATATA
1 TATTTTCAAAAACTATATATATATTATATA
*
54217 TGTTTTCAAAA
1 TATTTTCAAAA
54228 TATTTTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 16 0.44
29 4 0.11
30 7 0.19
31 9 0.25
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.46
Consensus pattern (30 bp):
TATTTTCAAAAACTATATATATATTATATA
Found at i:55204 original size:3 final size:3
Alignment explanation
Indices: 55196--55220 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
55186 GCACATGTCA
55196 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
55221 CCTCATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:56925 original size:120 final size:120
Alignment explanation
Indices: 56712--56969 Score: 338
Period size: 120 Copynumber: 2.2 Consensus size: 120
56702 AGAACTGTAT
* * * * *
56712 CCATAAGGACTTACCCTAAGCCCAAAGGGCGTAAGAGCCAACCTAAAGGAACACCTTGGGTCTAC
1 CCATAAGGACTTACCTTAGGCCCAAAGAGCGTAAGAGCCAACCTAAAGGAACACCTTGGGACCAC
* * * *
56777 AAGGTCTTACCCTAGCCGAAACATAGGTGCCTACATGAGGGGTGTGCCCACTGGC
66 AAGGTCTTACCCTAACCGAAACATAGGTGCCCACACGAGGGGTGTGCCCACTGGA
* * * * *
56832 CCATAAAGACTTACCTTAGGCCCAAAGAGCGTAAGAGCCTACCTAAGGGAACATCTTGGGACCAT
1 CCATAAGGACTTACCTTAGGCCCAAAGAGCGTAAGAGCCAACCTAAAGGAACACCTTGGGACCAC
* * * * *
56897 AAGGTCTTACCCTAACCTAAGCGTAGGTGCCCACCCGAGGGGTGTGCCCATTGGA
66 AAGGTCTTACCCTAACCGAAACATAGGTGCCCACACGAGGGGTGTGCCCACTGGA
56952 CCATAAGGACTTA-CTTAG
1 CCATAAGGACTTACCTTAG
56970 AGCATAAGGC
Statistics
Matches: 118, Mismatches: 20, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
119 5 0.04
120 113 0.96
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.19
Consensus pattern (120 bp):
CCATAAGGACTTACCTTAGGCCCAAAGAGCGTAAGAGCCAACCTAAAGGAACACCTTGGGACCAC
AAGGTCTTACCCTAACCGAAACATAGGTGCCCACACGAGGGGTGTGCCCACTGGA
Found at i:59017 original size:3 final size:3
Alignment explanation
Indices: 58999--59041 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
58989 TAATGGGAAA
*
58999 AAG AAT AAG AAG -AG AAG AAG AAG AAG AAG AA- AA- AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
59042 CACGTGAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 6 0.17
3 30 0.83
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:61340 original size:16 final size:16
Alignment explanation
Indices: 61319--61350 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
61309 GTTATTTAGA
*
61319 CACTTATGTTGGTTTC
1 CACTTACGTTGGTTTC
61335 CACTTACGTTGGTTTC
1 CACTTACGTTGGTTTC
61351 GGACCTTGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (16 bp):
CACTTACGTTGGTTTC
Done.