Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006612.1 Hibiscus syriacus cultivar Beakdansim tig00016227_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: 111335
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2648 original size:36 final size:36
Alignment explanation
Indices: 2600--2676 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 36
2590 AACAAGTTGA
2600 AAAATATTATAT-ATTTTCTTTAAAAAATT-AAATTCAT
1 AAAATATTATATAATTTT-TTTAAAAAATTGAAA-T-AT
*
2637 AAAAT-TTATATAATTTTTTTACAAAATTGAAATAT
1 AAAATATTATATAATTTTTTTAAAAAATTGAAATAT
2672 AAAAT
1 AAAAT
2677 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
35 7 0.19
36 17 0.46
37 13 0.35
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (36 bp):
AAAATATTATATAATTTTTTTAAAAAATTGAAATAT
Found at i:4627 original size:21 final size:21
Alignment explanation
Indices: 4603--4663 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
4593 TTCAAAGAAA
4603 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
4624 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
*
4638 CATTTACCAAACTTTAAAAAC
1 CATTTACCAAACTTTGAAAAC
4659 CATTT
1 CATTT
4664 TTTTAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
20 7 0.23
21 10 0.33
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:4637 original size:35 final size:35
Alignment explanation
Indices: 4555--4664 Score: 150
Period size: 35 Copynumber: 3.1 Consensus size: 35
4545 CCATTATCAT
* * **
4555 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTTT
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAAC-CA
4591 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
*
4626 TTTTCAAAGAAACATTTACCAAACTTTAAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
4661 TTTT
1 TTTT
4665 TTTAAAGTTG
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
35 38 0.56
36 10 0.15
37 20 0.29
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.33
Consensus pattern (35 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:7901 original size:15 final size:16
Alignment explanation
Indices: 7873--7904 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
7863 AAAATCTTTC
7873 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
7889 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
7904 T
1 T
7905 CGATATGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:9156 original size:37 final size:36
Alignment explanation
Indices: 9094--9206 Score: 108
Period size: 37 Copynumber: 3.2 Consensus size: 36
9084 ATCCCATTAT
*
9094 CATTTTTC-AACAAACATCTATCAAACTTTGAAAAAC
1 CATTTTTCAAACAAACATCTACCAAACTTTG-AAAAC
* * *
9130 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAACAAACATCTACCAAACTTTGAAAAC
****
9166 CATTTTTTCAAA-ATTGGT-TACCAAAC-TTGAAAAC
1 CA-TTTTTCAAACAAACATCTACCAAACTTTGAAAAC
9200 CATTTTT
1 CATTTTT
9207 ATACTTTCAA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
33 5 0.08
34 10 0.15
35 8 0.12
36 15 0.23
37 28 0.42
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (36 bp):
CATTTTTCAAACAAACATCTACCAAACTTTGAAAAC
Found at i:9165 original size:36 final size:37
Alignment explanation
Indices: 9094--9177 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
9084 ATCCCATTAT
*
9094 CATTTTTC-AACAAACATCTATCAAACTTTGAAAAAC
1 CATTTTTCAAACAAACATCTACCAAACTTTGAAAAAC
* * *
9130 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAACAAACATCTACCAAACTTTGAAAAAC
9166 CATTTTTTCAAA
1 CA-TTTTTCAAA
9178 ATTGGTTACC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 13 0.32
37 28 0.68
ACGTcount: A:0.43, C:0.19, G:0.04, T:0.35
Consensus pattern (37 bp):
CATTTTTCAAACAAACATCTACCAAACTTTGAAAAAC
Found at i:14508 original size:24 final size:24
Alignment explanation
Indices: 14478--14585 Score: 76
Period size: 24 Copynumber: 4.3 Consensus size: 24
14468 TTTTATCTTT
14478 GTATTTTAGTTTAAATAGGTTTTA
1 GTATTTTAGTTTAAATAGGTTTTA
* * *
14502 GTATTTTA-ATTAAGTTTTAGGATATTA
1 GTATTTTAGTTTAA---ATAGG-TTTTA
* * * **
14529 -TTTTTATATTTTATATTTGTTTTA
1 GTATTT-TAGTTTAAATAGGTTTTA
14553 GGTATTTTAGTTTAAATAGGTTTTA
1 -GTATTTTAGTTTAAATAGGTTTTA
14578 GTATTTTA
1 GTATTTTA
14586 ATTAGGATTT
Statistics
Matches: 61, Mismatches: 15, Indels: 16
0.66 0.16 0.17
Matches are distributed among these distances:
23 4 0.07
24 20 0.33
25 16 0.26
26 12 0.20
27 6 0.10
28 3 0.05
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (24 bp):
GTATTTTAGTTTAAATAGGTTTTA
Found at i:14540 original size:32 final size:32
Alignment explanation
Indices: 14497--14558 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
14487 TTTAAATAGG
14497 TTTTAGTATTTTA-ATTAAGTTTTAGGATATTAT
1 TTTTAGTATTTTATATT-AGTTTTAGG-TATTAT
*
14530 TTTTA-TATTTTATATTTGTTTTAGGTATT
1 TTTTAGTATTTTATATTAGTTTTAGGTATT
14559 TTAGTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (32 bp):
TTTTAGTATTTTATATTAGTTTTAGGTATTAT
Found at i:14591 original size:19 final size:19
Alignment explanation
Indices: 14487--14597 Score: 61
Period size: 19 Copynumber: 5.8 Consensus size: 19
14477 TGTATTTTAG
*
14487 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
*
14506 TTTAATTAAGTTTTAGGATAT
1 TTTAATTAGGTTTTA-G-TAT
* **
14527 TATT-TTTATATTTTA-TAT
1 T-TTAATTAGGTTTTAGTAT
* *
14545 TTGT-TTTAGGTATTT--TAG
1 TT-TAATTAGGT-TTTAGTAT
*
14563 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
*
14582 TTTAATTAGGATTTAG
1 TTTAATTAGGTTTTAG
14598 AATATTATTT
Statistics
Matches: 71, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
17 5 0.07
18 19 0.27
19 32 0.45
20 1 0.01
21 12 0.17
22 2 0.03
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:14772 original size:13 final size:12
Alignment explanation
Indices: 14744--14768 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14734 TATCTCTCTC
14744 ATCTGAAAATAA
1 ATCTGAAAATAA
14756 ATCTGAAAATAA
1 ATCTGAAAATAA
14768 A
1 A
14769 ATCTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
ATCTGAAAATAA
Found at i:15158 original size:20 final size:20
Alignment explanation
Indices: 15133--15175 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
15123 CCGAGTTGGC
15133 AGCAAAGAATTGTCCTTGTA
1 AGCAAAGAATTGTCCTTGTA
15153 AGCAAAGAATTGTCCTTGTA
1 AGCAAAGAATTGTCCTTGTA
15173 AGC
1 AGC
15176 CGACGTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (20 bp):
AGCAAAGAATTGTCCTTGTA
Found at i:15301 original size:17 final size:17
Alignment explanation
Indices: 15276--15309 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15266 CTTTATCTCA
*
15276 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
15293 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
15310 TTATCTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:16855 original size:21 final size:21
Alignment explanation
Indices: 16831--16878 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
16821 AACTCATAGG
*
16831 AAAGTTA-TTGATTTCACAAGA
1 AAAGTTAGTTGA-ATCACAAGA
* *
16852 AAAGCTAGTTGAATCCCAAGA
1 AAAGTTAGTTGAATCACAAGA
16873 AAAGTT
1 AAAGTT
16879 CCAAAGTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (21 bp):
AAAGTTAGTTGAATCACAAGA
Found at i:18343 original size:16 final size:16
Alignment explanation
Indices: 18322--18353 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18312 GGAGGCAACC
*
18322 CATTTTGTTTTATTTT
1 CATTTTGCTTTATTTT
18338 CATTTTGCTTTATTTT
1 CATTTTGCTTTATTTT
18354 TAGCCAAATT
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:0.09, G:0.06, T:0.72
Consensus pattern (16 bp):
CATTTTGCTTTATTTT
Found at i:21035 original size:2 final size:2
Alignment explanation
Indices: 21024--21062 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
21014 TAAAAAATAC
* *
21024 AT AT AA AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21063 GATTAAAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21873 original size:35 final size:34
Alignment explanation
Indices: 21824--21935 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 34
21814 AAAACAGTCC
*
21824 TCAATTTCATTCTAAACCTCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
*
21859 TCAATTTCACTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
** * *
21894 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAA-CCCAAATTCCAAAATAAT
21929 TCAATTT
1 TCAATTT
21936 AAGGTTTAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
34 1 0.01
35 63 0.94
36 3 0.04
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:23596 original size:35 final size:35
Alignment explanation
Indices: 23550--23658 Score: 146
Period size: 35 Copynumber: 3.1 Consensus size: 35
23540 AATAAAGTAT
* * **
23550 TTGAAGTATTTTAGAATTTGGGGTTTAGAATTTAA
1 TTGAATTATTTTGGAATTTGGGGTTTAGAATGAAA
*
23585 TTGAATTATTTTGGAATTTAGGGTTTAGAATGAAA
1 TTGAATTATTTTGGAATTTGGGGTTTAGAATGAAA
* * *
23620 TTGACTTACTTTGGAATTTGAGGTTTAGAATGAAA
1 TTGAATTATTTTGGAATTTGGGGTTTAGAATGAAA
23655 TTGA
1 TTGA
23659 GGACTGTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.43
Consensus pattern (35 bp):
TTGAATTATTTTGGAATTTGGGGTTTAGAATGAAA
Found at i:29625 original size:3 final size:3
Alignment explanation
Indices: 29619--29667 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
29609 TTATTATTTT
* *
29619 TAA TAA TAA TAA TATA TAA TAA TTA TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29665 TAA
1 TAA
29668 AATGGGTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:30113 original size:116 final size:113
Alignment explanation
Indices: 29910--30615 Score: 885
Period size: 113 Copynumber: 6.2 Consensus size: 113
29900 TTGAATAAGC
* * * **
29910 TCTTCTCATTATGAACTTCTTCTTTCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGG
** * * *
29975 AAAAACTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
66 AAATGCTGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAAT
* * * *
30023 TCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGATGAGTTCTTCTTATTATGAACTCTACC
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAACTCTAAC
* * * * *
30088 TGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAAT
63 TGGAAATGCTGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAAT
*
30139 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCT--CTT
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCTAACTG
** * * * *
30202 GAAAAACTGATCCATCAAATGATGAATTCAATCAAGAAGTTGAACAAGT
65 GAAATGCTGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAAT
* * *
30251 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCAATATGAACTCGAACTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGG
* * ** * * ** *
30316 TAACGCTGATCCATTGAATCATGAATTCAAGCAAAAAGTTGAGTAAGT
66 AAATGCTGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAAT
*
30364 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGG
* * * * *
30429 AAATGTTGATCCACCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGT
66 AAATGCTGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAAT
* *
30477 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCAAAT
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAACTCTAAC
* * * *
30542 TGGAAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAAT
63 TGGAAATGCTGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAAT
30593 TCTTCTCATTATGAACTTCTTCT
1 TCTTCTCATTATGAACTTCTTCT
30616 GGAAAAGCTG
Statistics
Matches: 517, Mismatches: 67, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
111 2 0.00
112 95 0.18
113 224 0.43
114 4 0.01
115 2 0.00
116 190 0.37
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGG
AAATGCTGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAAT
Found at i:31598 original size:94 final size:94
Alignment explanation
Indices: 31439--31906 Score: 805
Period size: 94 Copynumber: 5.0 Consensus size: 94
31429 TTTCTACTAA
* * *
31439 GAGCACATTCATCTTTCAAATCCAATGATT-GGTTTTTGAGGTTCATACCAAACCAGATCAGATA
1 GAGCACATTCATCTTCCAAATTCAATGATTGGGTTTTTGGGGTTCATACCAAACCAGATCAGATA
* *
31503 ACTCAAAGAACACTTCTAGGAGATGCTAT
66 ACTCAAAGAACACTTCCAGAAGATGCTAT
31532 GAGCACATTCATCTTCCAAATTCAATGATTGGGTTTTTGGGGTTCATACCAAACCAGATCAGATA
1 GAGCACATTCATCTTCCAAATTCAATGATTGGGTTTTTGGGGTTCATACCAAACCAGATCAGATA
31597 ACTCAAAGAACACTTCCAGAAGATGCTAT
66 ACTCAAAGAACACTTCCAGAAGATGCTAT
* *
31626 GAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTAGGGTTCATACCAAACCAGATCAGATA
1 GAGCACATTCATCTTCCAAATTCAATGATTGGGTTTTTGGGGTTCATACCAAACCAGATCAGATA
31691 ACTCAAAGAACACTTCCAGAAGATGCTAT
66 ACTCAAAGAACACTTCCAGAAGATGCTAT
* *
31720 GAGCATATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGGTTCATACCAAACCAGATCAGATA
1 GAGCACATTCATCTTCCAAATTCAATGATTGGGTTTTTGGGGTTCATACCAAACCAGATCAGATA
31785 ACTCAAAGAACACTTCCAGAAGATGCTAT
66 ACTCAAAGAACACTTCCAGAAGATGCTAT
* *
31814 GAGCACATTCATCTTCCAAATTCAATGATT-GGTTTTTAGGGTTCATATCAAACCAGATCAGATA
1 GAGCACATTCATCTTCCAAATTCAATGATTGGGTTTTTGGGGTTCATACCAAACCAGATCAGATA
* *
31878 ACTCAAAAAACACTTCTAGAAGATGCTAT
66 ACTCAAAGAACACTTCCAGAAGATGCTAT
31907 TGGGTCTACG
Statistics
Matches: 359, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
93 86 0.24
94 273 0.76
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (94 bp):
GAGCACATTCATCTTCCAAATTCAATGATTGGGTTTTTGGGGTTCATACCAAACCAGATCAGATA
ACTCAAAGAACACTTCCAGAAGATGCTAT
Found at i:32916 original size:1 final size:1
Alignment explanation
Indices: 32912--32998 Score: 84
Period size: 1 Copynumber: 87.0 Consensus size: 1
32902 CTTGACCCCC
* * * * * * * *
32912 TTTTTTCTTTTTTCTCTTTTTTTTTTCTTTTTTTTCTTTTTTCTTTCTTTTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
32977 TTTCTTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTT
32999 CTCTTCAAGC
Statistics
Matches: 66, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:32923 original size:7 final size:7
Alignment explanation
Indices: 32911--32997 Score: 96
Period size: 7 Copynumber: 13.0 Consensus size: 7
32901 TCTTGACCCC
32911 CTTTTTT
1 CTTTTTT
32918 CTTTTTT
1 CTTTTTT
*
32925 CTCTTTT
1 CTTTTTT
32932 -TTTTTT
1 CTTTTTT
32938 CTTTTTT
1 CTTTTTT
32945 -TTCTTTT
1 CTT-TTTT
*
32952 -TTCTTT
1 CTTTTTT
32958 CTTTTTT
1 CTTTTTT
32965 CTTTTTT
1 CTTTTTT
32972 -TTTTTT
1 CTTTTTT
32978 -TTCTTTT
1 CTT-TTTT
32985 -TTTTTT
1 CTTTTTT
32991 CTTTTTT
1 CTTTTTT
32998 TCTCTTCAAG
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
6 22 0.31
7 49 0.69
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
CTTTTTT
Found at i:32937 original size:20 final size:20
Alignment explanation
Indices: 32912--33000 Score: 110
Period size: 20 Copynumber: 4.4 Consensus size: 20
32902 CTTGACCCCC
32912 TTTTTTCTTTTTTCTCTTTT
1 TTTTTTCTTTTTTCTCTTTT
*
32932 TTTTTTCTTTTTTTTCTTTT
1 TTTTTTCTTTTTTCTCTTTT
* *
32952 TTCTTTCTTTTTTCTTTTTTTT
1 TTTTTTCTTTTTTC--TCTTTT
32974 TTTTTTCTTTTTT-T-TTTCT
1 TTTTTTCTTTTTTCTCTTT-T
32993 TTTTTTCT
1 TTTTTTCT
33001 CTTCAAGCAT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
18 3 0.05
19 10 0.16
20 31 0.51
22 17 0.28
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (20 bp):
TTTTTTCTTTTTTCTCTTTT
Found at i:40320 original size:15 final size:15
Alignment explanation
Indices: 40300--40331 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40290 GAAATGAATA
*
40300 ATGTATGCAAAATGT
1 ATGTATGCAAAAGGT
40315 ATGTATGCAAAAGGT
1 ATGTATGCAAAAGGT
40330 AT
1 AT
40332 TGATCCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (15 bp):
ATGTATGCAAAAGGT
Found at i:45831 original size:3 final size:3
Alignment explanation
Indices: 45825--45885 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
45815 TATTATTTTT
* * *
45825 TAA TAA TAA TAA TATA TAA TAA TTA TAA TAA TTA TTA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
45871 TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
45886 AATGGGTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:45881 original size:12 final size:12
Alignment explanation
Indices: 45825--45883 Score: 91
Period size: 12 Copynumber: 4.8 Consensus size: 12
45815 TATTATTTTT
*
45825 TAATAATAATAA
1 TAATAATAATTA
45837 TATATAATAATTA
1 TA-ATAATAATTA
*
45850 TAATAATTATTA
1 TAATAATAATTA
45862 TAATAATAATTA
1 TAATAATAATTA
45874 TAATAATAAT
1 TAATAATAAT
45884 AAAATGGGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
12 32 0.74
13 11 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATAATAATTA
Found at i:47434 original size:60 final size:60
Alignment explanation
Indices: 47315--47474 Score: 160
Period size: 60 Copynumber: 2.7 Consensus size: 60
47305 CTTCATTTTT
* * ** * *
47315 AATTGGTCCTTAAACTTATAAATATTCTAATTTCATCCCCAAATTATGACTCTTATTCTA
1 AATTGGTCCTTAAACTTTTAAACATTCTAATTTCATCCCCAAACAATGACACCTATTCTA
* * * *
47375 AATTAGTCCTTAAACTTTTGAACATTCTAGTTTCATCCCTAAACAATGACACACT-TTCTA
1 AATTGGTCCTTAAACTTTTAAACATTCTAATTTCATCCCCAAACAATGACAC-CTATTCTA
** * * * *
47435 AATTGGTCCCCAAAATTTTTAACATTCCAATTTTATCCCC
1 AATTGGTCCTTAAACTTTTAAACATTCTAATTTCATCCCC
47475 CAATTCATCC
Statistics
Matches: 80, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
60 79 0.99
61 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.39
Consensus pattern (60 bp):
AATTGGTCCTTAAACTTTTAAACATTCTAATTTCATCCCCAAACAATGACACCTATTCTA
Found at i:47549 original size:3 final size:3
Alignment explanation
Indices: 47541--47614 Score: 141
Period size: 3 Copynumber: 25.0 Consensus size: 3
47531 CTTTTCAAAC
47541 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
47589 ATA ATA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
47615 TAACTTGGCC
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 68 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:47804 original size:61 final size:61
Alignment explanation
Indices: 47665--47801 Score: 158
Period size: 60 Copynumber: 2.3 Consensus size: 61
47655 GTATATATGT
* **
47665 ATAGCTTG-GGATGAAATTGGAATGTTCAAAATGTTTGGGGACCAACTTAGAATGTAGGTC
1 ATAGTTTGAGGATGAAATTGGAATGTTCAAAATGTTTAAGGACCAACTTAGAATGTAGGTC
* *
47725 ATAGTTTGAGGATGAAATTGTG-ATGTTCAAAA-GTTTAAGGACTAATTTAGAATGATA-GTC
1 ATAGTTTGAGGATGAAATTG-GAATGTTCAAAATGTTTAAGGACCAACTTAGAATG-TAGGTC
*
47785 CTAGTTT-AGGAATGAAA
1 ATAGTTTGAGG-ATGAAA
47802 ATTAGAACAT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
59 3 0.04
60 40 0.60
61 23 0.34
62 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (61 bp):
ATAGTTTGAGGATGAAATTGGAATGTTCAAAATGTTTAAGGACCAACTTAGAATGTAGGTC
Found at i:49141 original size:17 final size:17
Alignment explanation
Indices: 49096--49144 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 17
49086 TTTAGAGATT
*
49096 AATTTAAAATATATTAA
1 AATTTAAACTATATTAA
* *
49113 AATTTATCAACTATTTTAC
1 AATTTA--AACTATATTAA
49132 AATTTAAACTATA
1 AATTTAAACTATA
49145 GTTTAGGAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 12 0.46
19 14 0.54
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTAAACTATATTAA
Found at i:49838 original size:28 final size:27
Alignment explanation
Indices: 49789--49844 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
49779 TGAAAAAATG
*
49789 TTAAAAATTTAAACAGACACACACACAT
1 TTAAAAA-TTAAACAGACACACAAACAT
49817 TTAAAAA-TAAACAGACGGACACAAACAT
1 TTAAAAATTAAACAGAC--ACACAAACAT
49845 AACCTTGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 9 0.36
28 16 0.64
ACGTcount: A:0.55, C:0.20, G:0.07, T:0.18
Consensus pattern (27 bp):
TTAAAAATTAAACAGACACACAAACAT
Found at i:51177 original size:23 final size:23
Alignment explanation
Indices: 51146--51189 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
51136 ATATTATATT
51146 TTAAATATTT-TTTTATATTTTTA
1 TTAAATATTTATTTTA-ATTTTTA
*
51169 TTAATTATTTATTTTAATTTT
1 TTAAATATTTATTTTAATTTT
51190 CTAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTAAATATTTATTTTAATTTTTA
Found at i:51650 original size:24 final size:23
Alignment explanation
Indices: 51593--51652 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
51583 ATATTTTTAA
51593 AATTATTA-A-TAAATATATTTT
1 AATTATTATATTAAATATATTTT
*
51614 AATTATTTTTATTAAA-ATATTATT
1 AATTA-TTATATTAAATATATT-TT
51638 AGATTATTATATTAA
1 A-ATTATTATATTAA
51653 TATTAAATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 5 0.16
22 2 0.06
23 6 0.19
24 15 0.47
25 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
AATTATTATATTAAATATATTTT
Found at i:51775 original size:21 final size:21
Alignment explanation
Indices: 51719--51775 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
51709 TTAAATTAGT
*
51719 AAATAATATA-AATATTATTA
1 AAATAAAATATAATATTATTA
** *
51739 ATAATTTATTAT-ATATTATTA
1 A-AATAAAATATAATATTATTA
51760 AAATAAAATATAATAT
1 AAATAAAATATAATAT
51776 AACTGACCAT
Statistics
Matches: 27, Mismatches: 7, Indels: 5
0.69 0.18 0.13
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATAAAATATAATATTATTA
Found at i:51775 original size:23 final size:21
Alignment explanation
Indices: 51723--51776 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
51713 ATTAGTAAAT
51723 AATATAA-ATATTATTAATAA
1 AATATAATATATTATTAATAA
** *
51743 TTTATTATATATTATTAAAATAA
1 AATATAATATATTATT--AATAA
51766 AATATAATATA
1 AATATAATATA
51777 ACTGACCATA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
20 4 0.16
21 8 0.32
23 13 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATATAATATATTATTAATAA
Found at i:51816 original size:22 final size:23
Alignment explanation
Indices: 51788--51834 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
51778 CTGACCATAT
51788 TATTATAAT-ATTAAAAATA-TAA
1 TATTAT-ATCATTAAAAATATTAA
51810 TATTATATCATTAAAAATATTAA
1 TATTATATCATTAAAAATATTAA
51833 TA
1 TA
51835 AATATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 2 0.09
22 16 0.70
23 5 0.22
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TATTATATCATTAAAAATATTAA
Found at i:51839 original size:22 final size:22
Alignment explanation
Indices: 51797--51839 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
51787 TTATTATAAT
*
51797 ATTAAAAATATAATATTATATC
1 ATTAAAAATATAATATAATATC
51819 ATTAAAAATATTAATA-AATAT
1 ATTAAAAATA-TAATATAATAT
51840 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTAAAAATATAATATAATATC
Found at i:51846 original size:23 final size:23
Alignment explanation
Indices: 51789--51868 Score: 76
Period size: 23 Copynumber: 3.4 Consensus size: 23
51779 TGACCATATT
*
51789 ATTATAATATTAAAAATA-TAAT-
1 ATTAT-ATTTTAAAAATATTAATA
*
51811 ATTATATCATTAAAAATATTAATA
1 ATTATAT-TTTAAAAATATTAATA
*
51835 AATATATTTTAAATAAT-TTAATA
1 ATTATATTTTAAA-AATATTAATA
51858 ATTAATATTTT
1 ATT-ATATTTT
51869 TTATTAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
21 2 0.04
22 15 0.30
23 17 0.34
24 16 0.32
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTATATTTTAAAAATATTAATA
Found at i:52175 original size:17 final size:17
Alignment explanation
Indices: 52153--52187 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
52143 CTTCACCTCT
52153 CTAGCTTTCCAAGAGAA
1 CTAGCTTTCCAAGAGAA
*
52170 CTAGCTTTCCAGGAGAA
1 CTAGCTTTCCAAGAGAA
52187 C
1 C
52188 AGTCCCACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (17 bp):
CTAGCTTTCCAAGAGAA
Found at i:53301 original size:21 final size:22
Alignment explanation
Indices: 53277--53317 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53267 CTATTTACGT
*
53277 AAAATA-AATTATAAATTATGA
1 AAAATAGAATTAGAAATTATGA
*
53298 AAAATAGATTTAGAAATTAT
1 AAAATAGAATTAGAAATTAT
53318 TTTACGGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (22 bp):
AAAATAGAATTAGAAATTATGA
Found at i:54416 original size:138 final size:138
Alignment explanation
Indices: 54274--54540 Score: 304
Period size: 138 Copynumber: 1.9 Consensus size: 138
54264 TGCCCGAGGT
** * * *
54274 TCCATTTTAATTATTTGATTTC-ATAATTGGTTAAAATTGGTTAGG-ATTAATAATCAAAACCTT
1 TCCATTTTAATTATTTGA-ACCAATAATTGGATAAAATTGATTAGGTATTAAT-ATCAAAACCTC
* * *
54337 CATTTTAGGTTCAATTTCACTTTATTCCCATAATTTAGGAGAGTTTCTGATTTGGTCCTCACTTT
64 CATTTTAGGTTCAATTTCACTTTAGTCCCATAATTTAGGAGAATTTCTGATTTGGTCATCACTTT
54402 TTATAATTGA
129 TTATAATTGA
** * * * * * *
54412 TCCATTTTCGTTATTTGAACCAATAATTTGATAAAATTGATTAGGTTTTACTATTAGAGCCTCCA
1 TCCATTTTAATTATTTGAACCAATAATTGGATAAAATTGATTAGGTATTAATATCAAAACCTCCA
* ** * * *
54477 TTTTAGGTTTAATTTCACTTTAGTCCTTTAATTTAGGAGAATTTTTTATTTGGTCATCGCTTTT
66 TTTTAGGTTCAATTTCACTTTAGTCCCATAATTTAGGAGAATTTCTGATTTGGTCATCACTTTT
54541 GTCAGAGGGT
Statistics
Matches: 105, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
137 1 0.01
138 100 0.95
139 4 0.04
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (138 bp):
TCCATTTTAATTATTTGAACCAATAATTGGATAAAATTGATTAGGTATTAATATCAAAACCTCCA
TTTTAGGTTCAATTTCACTTTAGTCCCATAATTTAGGAGAATTTCTGATTTGGTCATCACTTTTT
ATAATTGA
Found at i:57669 original size:17 final size:18
Alignment explanation
Indices: 57638--57681 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
57628 GGAATATATG
*
57638 AAATTAAATTAAGTAAAT
1 AAATAAAATTAAGTAAAT
*
57656 AAATAAAATT-AGTATAT
1 AAATAAAATTAAGTAAAT
57673 AAATAAAAT
1 AAATAAAAT
57682 ACTGTTAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
AAATAAAATTAAGTAAAT
Found at i:64995 original size:20 final size:20
Alignment explanation
Indices: 64950--64995 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
64940 TACTATACTA
*
64950 TATGAATAATACGGATATTG
1 TATGAATAATACGGATAATG
64970 TATGAATAATATC-GATAATG
1 TATGAATAATA-CGGATAATG
*
64990 TGTGAA
1 TATGAA
64996 CAGTAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (20 bp):
TATGAATAATACGGATAATG
Found at i:66327 original size:19 final size:20
Alignment explanation
Indices: 66303--66349 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
66293 AACAATTTTC
* *
66303 TTTTGAAAGCAAAAATGGA-
1 TTTTGAAAACAAAAATGAAT
*
66322 TTTTGAAAACCAAAATGAAT
1 TTTTGAAAACAAAAATGAAT
66342 TTTTGAAA
1 TTTTGAAA
66350 TATGATTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAT
Found at i:68584 original size:11 final size:11
Alignment explanation
Indices: 68568--68608 Score: 82
Period size: 11 Copynumber: 3.7 Consensus size: 11
68558 TATTATTTTT
68568 GAATTCTTCTA
1 GAATTCTTCTA
68579 GAATTCTTCTA
1 GAATTCTTCTA
68590 GAATTCTTCTA
1 GAATTCTTCTA
68601 GAATTCTT
1 GAATTCTT
68609 TTTAACTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (11 bp):
GAATTCTTCTA
Found at i:82335 original size:32 final size:32
Alignment explanation
Indices: 82298--82380 Score: 148
Period size: 32 Copynumber: 2.6 Consensus size: 32
82288 GATCTTCGTC
82298 TAGTTTCTCTCGAACACTAAAGATCTTTAACT
1 TAGTTTCTCTCGAACACTAAAGATCTTTAACT
*
82330 TAGTTTCTCTCAAACACTAAAGATCTTTAACT
1 TAGTTTCTCTCGAACACTAAAGATCTTTAACT
*
82362 TAGTTTCTCTCGTACACTA
1 TAGTTTCTCTCGAACACTA
82381 TGTAATATAC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (32 bp):
TAGTTTCTCTCGAACACTAAAGATCTTTAACT
Found at i:83421 original size:11 final size:11
Alignment explanation
Indices: 83405--83431 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
83395 GTTTACATGA
83405 AATTTCTAGTT
1 AATTTCTAGTT
83416 AATTTCTAGTT
1 AATTTCTAGTT
83427 AATTT
1 AATTT
83432 GTCATTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (11 bp):
AATTTCTAGTT
Found at i:83970 original size:30 final size:31
Alignment explanation
Indices: 83913--83972 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
83903 GAAAATTACC
**
83913 ACTTTGGTATCTAAATTTTTCCCAATTTTAT
1 ACTTTGGTATCTAAATTTTTCAAAATTTTAT
83944 ACTTTGGTCATC-AAA-TTTTCAAAATTTTA
1 ACTTTGGT-ATCTAAATTTTTCAAAATTTTA
83973 CATTTTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 11 0.42
32 3 0.12
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (31 bp):
ACTTTGGTATCTAAATTTTTCAAAATTTTAT
Found at i:90908 original size:17 final size:17
Alignment explanation
Indices: 90886--90920 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
90876 ATGCATAAAT
90886 GTTTAGAATTTTGTGAG
1 GTTTAGAATTTTGTGAG
90903 GTTTAGAATTTTGTGAG
1 GTTTAGAATTTTGTGAG
90920 G
1 G
90921 AGGTCTGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (17 bp):
GTTTAGAATTTTGTGAG
Found at i:93504 original size:14 final size:14
Alignment explanation
Indices: 93470--93505 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
93460 ATATAATGAT
*
93470 TAATTTAAGTACAA
1 TAATTTAAATACAA
93484 TAA-TTAAATACAA
1 TAATTTAAATACAA
93497 TAATTTAAA
1 TAATTTAAA
93506 GTAACTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (14 bp):
TAATTTAAATACAA
Found at i:94841 original size:16 final size:15
Alignment explanation
Indices: 94817--94856 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
94807 TTTTTTAAAA
*
94817 TTTAAAATAAATATAT
1 TTTATAATAAATAT-T
94833 TTTATAAT-AATATT
1 TTTATAATAAATATT
94847 TTTATAATAA
1 TTTATAATAA
94857 TTTATTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 9 0.41
15 6 0.27
16 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTATAATAAATATT
Found at i:94851 original size:14 final size:15
Alignment explanation
Indices: 94826--94862 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
94816 ATTTAAAATA
94826 AATATATTTTATAAT
1 AATATATTTTATAAT
94841 AATAT-TTTTATAAT
1 AATATATTTTATAAT
*
94855 AATTTATT
1 AATATATT
94863 ATATTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATATATTTTATAAT
Found at i:94931 original size:40 final size:43
Alignment explanation
Indices: 94838--94937 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 43
94828 TATATTTTAT
94838 AATAATATT-TTTATAATAATTTATTATATTTTAAACAATTAA
1 AATAATATTATTTATAATAATTTATTATATTTTAAACAATTAA
* * *
94880 AATAATA-TATTTATATTAA-TT-TTATATTTTTAATAA-TAA
1 AATAATATTATTTATAATAATTTATTATATTTTAAACAATTAA
* *
94919 AATAAAATTATTTAGAATA
1 AATAATATTATTTATAATA
94938 TTAAATATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
39 9 0.18
40 22 0.44
41 3 0.06
42 16 0.32
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (43 bp):
AATAATATTATTTATAATAATTTATTATATTTTAAACAATTAA
Found at i:97518 original size:17 final size:17
Alignment explanation
Indices: 97489--97538 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
97479 TAATAGTTAA
*
97489 TTTAATAAATGAACTAG
1 TTTAATGAATGAACTAG
*
97506 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
*
97523 TTTAATTAATGAACTA
1 TTTAATGAATGAACTA
97539 CTTCCCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:100308 original size:36 final size:36
Alignment explanation
Indices: 100267--100342 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
100257 ATTTTCGGGA
*
100267 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
100303 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
100339 TTTT
1 TTTT
100343 TTTGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:100785 original size:15 final size:15
Alignment explanation
Indices: 100765--100794 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
100755 TATCACAATC
100765 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
100780 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
100795 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:105304 original size:36 final size:36
Alignment explanation
Indices: 105263--105338 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
105253 ATTTTCGGGA
*
105263 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
105299 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
105335 TTTT
1 TTTT
105339 TTTGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Done.