Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000916.1 Hibiscus syriacus cultivar Beakdansim tig00001829_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: 93407
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1534 original size:54 final size:54
Alignment explanation
Indices: 1476--1596 Score: 139
Period size: 49 Copynumber: 2.3 Consensus size: 54
1466 CATTATTTAG
*
1476 TTATTATTATTTTATTTTGGATTTA-GA-GTTTAGACATGTTTAGTTTGTTATTA-T
1 TTATTATTA-TTTATTTT--ATTTAGGACCTTTAGACATGTTTAGTTTGTTATTATT
*
1530 TTA-T-TTA-TTA-GTTATTTAGGACCTTTAGACATGTTTAGTTTGTTATTATT
1 TTATTATTATTTATTTTATTTAGGACCTTTAGACATGTTTAGTTTGTTATTATT
1580 TTATTCATTATTTATTT
1 TTATT-ATTATTTATTT
1597 AGGACATTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
47 5 0.09
48 2 0.04
49 27 0.48
50 7 0.12
51 1 0.02
52 3 0.05
53 4 0.07
54 6 0.11
55 1 0.02
ACGTcount: A:0.24, C:0.04, G:0.12, T:0.60
Consensus pattern (54 bp):
TTATTATTATTTATTTTATTTAGGACCTTTAGACATGTTTAGTTTGTTATTATT
Found at i:1573 original size:49 final size:50
Alignment explanation
Indices: 1504--1608 Score: 176
Period size: 50 Copynumber: 2.1 Consensus size: 50
1494 GGATTTAGAG
* *
1504 TTTAGACATGTTTAGTTTGTTATTA-TTTATTTATTAGTTATTTAGGACC
1 TTTAGACATGTTTAGTTTGTTATTATTTTATTCATTAGTTATTTAGGACA
*
1553 TTTAGACATGTTTAGTTTGTTATTATTTTATTCATTATTTATTTAGGACA
1 TTTAGACATGTTTAGTTTGTTATTATTTTATTCATTAGTTATTTAGGACA
1603 TTTAGA
1 TTTAGA
1609 ACTCACCCCT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
49 25 0.48
50 27 0.52
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (50 bp):
TTTAGACATGTTTAGTTTGTTATTATTTTATTCATTAGTTATTTAGGACA
Found at i:4642 original size:9 final size:8
Alignment explanation
Indices: 4621--4700 Score: 66
Period size: 7 Copynumber: 10.5 Consensus size: 8
4611 TACTTGCCTG
4621 AAAAATG-
1 AAAAATGA
4628 AAAAATGAA
1 AAAAATG-A
4637 AAAAATGA
1 AAAAATGA
4645 AAAAA-GA
1 AAAAATGA
4652 AAAAATGA
1 AAAAATGA
4660 GAAAAAT-A
1 -AAAAATGA
*
4668 AATAAA-GG
1 AA-AAATGA
*
4676 AAAGA-GA
1 AAAAATGA
4683 AAAAA-GA
1 AAAAATGA
4690 AAAAAT-A
1 AAAAATGA
4697 AAAA
1 AAAA
4701 GGGGTTCAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 14
0.77 0.05 0.17
Matches are distributed among these distances:
7 35 0.56
8 14 0.23
9 13 0.21
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (8 bp):
AAAAATGA
Found at i:4642 original size:16 final size:16
Alignment explanation
Indices: 4621--4700 Score: 69
Period size: 16 Copynumber: 5.2 Consensus size: 16
4611 TACTTGCCTG
*
4621 AAAAATGAAAAATGAA
1 AAAAATGAAAAAAGAA
4637 AAAAATGAAAAAAG-A
1 AAAAATGAAAAAAGAA
*
4652 AAAAATGAGAAAAATAA
1 AAAAATGA-AAAAAGAA
* * *
4669 ATAAA-GGAAAGAG-A
1 AAAAATGAAAAAAGAA
*
4683 AAAAA-GAAAAAATAA
1 AAAAATGAAAAAAGAA
4698 AAA
1 AAA
4701 GGGGTTCAAG
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
14 10 0.20
15 17 0.33
16 19 0.37
17 5 0.10
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (16 bp):
AAAAATGAAAAAAGAA
Found at i:6051 original size:44 final size:43
Alignment explanation
Indices: 5924--6202 Score: 355
Period size: 44 Copynumber: 6.4 Consensus size: 43
5914 AAGGTATTAT
* * * * *
5924 CCTTGCACATAACAAAAGAGCCTGGGGAAACTGTAATGCTTAC
1 CCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTAC
* *
5967 CCTTGCACACAGTAAAGGAACCT-GGGAAATTGTAAGGCTTAC
1 CCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTAC
* *
6009 CCTTGCACACAACAAATGG-GCCTCGGGGAAACTGTAAGGCTTAC
1 CCTTGCACACAGCAAA-GGAACCT-GGGGAAACTGTAAGGCTTAC
* *
6053 CCTTGCACATAGCAAAAGAACCTAGGGGAAACTGTAAGGCTTAC
1 CCTTGCACACAGCAAAGGAACCT-GGGGAAACTGTAAGGCTTAC
* *
6097 CCTTGCACACAGCAAAGGAACCTAAGGGAAACTGTAAGACTTAC
1 CCTTGCACACAGCAAAGGAACCT-GGGGAAACTGTAAGGCTTAC
* * *
6141 CCTTGCACAGAGCAAAGGAACCTGGGGAAACTGTAACGATTAC
1 CCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTAC
*
6184 CATTGCACACAGCAAAGGA
1 CCTTGCACACAGCAAAGGA
6203 GCCTACTGTA
Statistics
Matches: 205, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
42 34 0.17
43 54 0.26
44 117 0.57
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (43 bp):
CCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTAC
Found at i:10153 original size:25 final size:24
Alignment explanation
Indices: 10098--10164 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 24
10088 TATAAAGGGG
*
10098 TAATATTTTTC-AAATTTTTTATT
1 TAATATTTTTCAAAATTTTTTAAT
*
10121 TAACATTTTTCAAAATTCTTTTAAT
1 TAATATTTTTCAAAATT-TTTTAAT
*
10146 TGATATTTTTC-AAATTTTT
1 TAATATTTTTCAAAATTTTT
10165 GAAAATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.34
24 10 0.26
25 15 0.39
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.60
Consensus pattern (24 bp):
TAATATTTTTCAAAATTTTTTAAT
Found at i:11771 original size:35 final size:36
Alignment explanation
Indices: 11708--11825 Score: 112
Period size: 35 Copynumber: 3.3 Consensus size: 36
11698 CAAATTTTTG
* ** *
11708 TCTCACTAGAGACAGTTTTTCTTGAAACAAAATTGA
1 TCTCACTTGAGACAGTTTTTCTCAAAACAAAATTCA
** * **
11744 TCTCACTTGAGATTG-TTTTCTCAAAACAAATTTTT
1 TCTCACTTGAGACAGTTTTTCTCAAAACAAAATTCA
* * *
11779 TCTCGCTTGAGACAGTTTTTCTTAAAAAACAAATTCA
1 TCTCACTTGAGACAGTTTTTCTCAAAACA-AAATTCA
11816 TCTCACTTGA
1 TCTCACTTGA
11826 TATAATCTTC
Statistics
Matches: 63, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
35 27 0.43
36 23 0.37
37 13 0.21
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (36 bp):
TCTCACTTGAGACAGTTTTTCTCAAAACAAAATTCA
Found at i:11777 original size:72 final size:73
Alignment explanation
Indices: 11677--11825 Score: 212
Period size: 72 Copynumber: 2.1 Consensus size: 73
11667 TTTGTTTCCT
* * *
11677 TTGAGAATGTTTCTCTCGAAACAAATTTTTGTCTCACTAGAGACAGTTTTTCTTGAAACA-AAAT
1 TTGAGAATGTTTCTCTCAAAACAAATTTTT-TCTCACTAGAGACAGTTTTTCTTAAAAAACAAAT
*
11741 TGATCTCAC
65 TCATCTCAC
* * *
11750 TTGAGATTGTTT-TCTCAAAACAAATTTTTTCTCGCTTGAGACAGTTTTTCTTAAAAAACAAATT
1 TTGAGAATGTTTCTCTCAAAACAAATTTTTTCTCACTAGAGACAGTTTTTCTTAAAAAACAAATT
11814 CATCTCAC
66 CATCTCAC
11822 TTGA
1 TTGA
11826 TATAATCTTC
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
71 25 0.37
72 32 0.47
73 11 0.16
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (73 bp):
TTGAGAATGTTTCTCTCAAAACAAATTTTTTCTCACTAGAGACAGTTTTTCTTAAAAAACAAATT
CATCTCAC
Found at i:12134 original size:66 final size:66
Alignment explanation
Indices: 12057--12181 Score: 207
Period size: 66 Copynumber: 1.9 Consensus size: 66
12047 TGATAAAACT
*
12057 TTGAGATTGTTTCTC-TTGAAACAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGAGATTGTTTC-CATTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAC
12121 AA
65 AA
* *
12123 TTGAGATTGTTTCCATTGAAACAAATTTTGTCTTGCTTGAGATAGTTTCTCTTGAAACA
1 TTGAGATTGTTTCCATTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
12182 AATTATCCCT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 1 0.02
66 54 0.98
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (66 bp):
TTGAGATTGTTTCCATTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACA
A
Found at i:12575 original size:140 final size:140
Alignment explanation
Indices: 12180--12813 Score: 927
Period size: 139 Copynumber: 4.5 Consensus size: 140
12170 TCTCTTGAAA
* ** *
12180 CAAATTATCCCTAAAGATGGCTACATATCCTCATCACGTAGGAACAATGTCATCCAACGACCTGA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCTGA
* * * *
12245 TCTCCTCATCATGTAGGAGCA-TCGTCATCCTTATATAACCAGACTTCCTCATCACCTAGGAATC
66 TCTCCTCATCACGTAGGAGCAGT-GTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACC
*
12309 ATGTTGTCTCC
130 GTGTTGTCTCC
* *
12320 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAAGAA-AATGTCATCCACTGACCTGA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCTGA
** * *
12384 TCTCCTCATCACGTAGGAGCAACGTCATCCATAGATAACCAGACTTCCTCATCACGTAGAAACCG
66 TCTCCTCATCACGTAGGAGCAGTGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCG
*
12449 TGTTATCTCC
131 TGTTGTCTCC
* * * * * *
12459 CAAATTACCCCTAAAGATGGCTAGACATCCTCATTATGTACGAACAATTTCATCCACCGA-CTCG
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCT-G
* *
12523 ATCTCCTCATCACGTAGGAGCAGTATCATCCTTAGATAACCAGACTTCCTCATCAAGTAGGAACC
65 ATCTCCTCATCACGTAGGAGCAGTGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACC
12588 GTGTTGTCTCC
130 GTGTTGTCTCC
* * * *
12599 CAAATTATCCCTAAAAATGGCTATATGTCCTCATCACGTAGGAACAATGTCATCCACCGACCTAA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCTGA
*
12664 TCTCCTCATCACGTAGGA-CTAGTGTCATCCTTAGAT-ACCAGACTTCCTCATCACGTAGGAATC
66 TCTCCTCATCACGTAGGAGC-AGTGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACC
12727 GTGTTGTCTCC
130 GTGTTGTCTCC
* *
12738 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAATAATGTCATCCACCGACCAGA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCTGA
12803 TCTCCTCATCA
66 TCTCCTCATCA
12814 TGGAGGACTA
Statistics
Matches: 441, Mismatches: 48, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
139 231 0.52
140 208 0.47
141 2 0.00
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (140 bp):
CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCTGA
TCTCCTCATCACGTAGGAGCAGTGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCG
TGTTGTCTCC
Found at i:12874 original size:279 final size:278
Alignment explanation
Indices: 12180--12892 Score: 945
Period size: 279 Copynumber: 2.6 Consensus size: 278
12170 TCTCTTGAAA
* * *
12180 CAAATTATCCCTAAAGATGGCTACATATCCTCATCACGTAGGAACAATGTCATCCAACGACCTGA
1 CAAATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAACAATGTCATCCACCGACC-GA
** * * *
12245 TCTCCTCATCATGTAGGAGCATCGTCATCCTTATATAACCAGACTTCCTCATCACCTAGGAATCA
65 TCTCCTCATCATGTAGGAGCAGAGTCATCCTTAAATAACCAGACTTCCTCATCACATAGGAAACA
*
12310 TGTTGTCTCCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAAGAAAATGTCATCCA
130 TGTTGTCTCCCAAATTATCCCTAAAAATGGCTAGACGTCCTCATCACGTAAGAAAATGTCATCCA
* *
12375 CTGACCTGATCTCCTCATCACGTAGGAGCAACGTCATCCATAGATAACCAGACTTCCTCATCACG
195 CCGACCTAATCTCCTCATCACGTAGGAGCAACGTCATCCATAGATAACCAGACTTCCTCATCACG
12440 TAGAAACCGTGTTATCTCC
260 TAGAAACCGTGTTATCTCC
* * * * *
12459 CAAATTACCCCTAAAGATGGCTAGACATCCTCATTATGTACGAACAATTTCATCCACCGACTCGA
1 CAAATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAACAATGTCATCCACCGAC-CGA
* * *
12524 TCTCCTCATCACGTAGGAGCAGTA-TCATCCTTAGATAACCAGACTTCCTCATCA-AGTAGGAAC
65 TCTCCTCATCATGTAGGAGCAG-AGTCATCCTTAAATAACCAGACTTCCTCATCACA-TAGGAAA
* * * *
12587 CGTGTTGTCTCCCAAATTATCCCTAAAAATGGCTATATGTCCTCATCACGTAGGAACAATGTCAT
128 CATGTTGTCTCCCAAATTATCCCTAAAAATGGCTAGACGTCCTCATCACGTAAGAA-AATGTCAT
** *
12652 CCACCGACCTAATCTCCTCATCACGTAGGA-CTAGTGTCATCCTTAGAT-ACCAGACTTCCTCAT
192 CCACCGACCTAATCTCCTCATCACGTAGGAGC-AACGTCATCCATAGATAACCAGACTTCCTCAT
* * *
12715 CACGTAGGAATCGTGTTGTCTCC
256 CACGTAGAAACCGTGTTATCTCC
* *
12738 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAATAATGTCATCCACCGACCAGA
1 CAAATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAACAATGTCATCCACCGACC-GA
* * ** * * * *
12803 TCTCCTCATCATGGAGGA-CTAGAGCCATAATCAAATAACTAGGCTTCTTCATCACATAGGAAAC
65 TCTCCTCATCATGTAGGAGC-AGAGTCATCCTTAAATAACCAGACTTCCTCATCACATAGGAAAC
*
12867 ATGTTGTCT-CCAAATT-TACCTAAAAA
129 ATGTTGTCTCCCAAATTATCCCTAAAAA
12893 CGACCAGAAC
Statistics
Matches: 378, Mismatches: 47, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
277 9 0.02
278 10 0.03
279 308 0.81
280 51 0.13
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (278 bp):
CAAATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAGGAACAATGTCATCCACCGACCGAT
CTCCTCATCATGTAGGAGCAGAGTCATCCTTAAATAACCAGACTTCCTCATCACATAGGAAACAT
GTTGTCTCCCAAATTATCCCTAAAAATGGCTAGACGTCCTCATCACGTAAGAAAATGTCATCCAC
CGACCTAATCTCCTCATCACGTAGGAGCAACGTCATCCATAGATAACCAGACTTCCTCATCACGT
AGAAACCGTGTTATCTCC
Found at i:12880 original size:139 final size:140
Alignment explanation
Indices: 12180--12890 Score: 870
Period size: 139 Copynumber: 5.1 Consensus size: 140
12170 TCTCTTGAAA
* ** * *
12180 CAAATTATCCCTAAAGATGGCTACATATCCTCATCACGTAGGAACAATGTCATCCAACGACCTGA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* ** * * * *
12245 TCTCCTCATCATGTAGGAGCATCGTCATCCTTATATAACCAGACTTCCTCATCACCTAGGAATCA
66 TCTCCTCATCACGTAGGAGCAGAGTCATCCTTAGATAACCAGACTTCCTCATCACATAGGAAACG
12310 TGTTGTCTCC
131 TGTTGTCTCC
* * *
12320 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAAGAA-AATGTCATCCACTGACCTGA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* *
12384 TCTCCTCATCACGTAGGAGCA-ACGTCATCCATAGATAACCAGACTTCCTCATCACGTA-GAAAC
66 TCTCCTCATCACGTAGGAGCAGA-GTCATCCTTAGATAACCAGACTTCCTCATCACATAGGAAA-
*
12447 CGTGTTATCTCC
129 CGTGTTGTCTCC
* * * * * *
12459 CAAATTACCCCTAAAGATGGCTAGACATCCTCATTATGTACGAACAATTTCATCCACCGACTC-G
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGAC-CAG
12523 ATCTCCTCATCACGTAGGAGCAGTA-TCATCCTTAGATAACCAGACTTCCTCATCA-AGTAGGAA
65 ATCTCCTCATCACGTAGGAGCAG-AGTCATCCTTAGATAACCAGACTTCCTCATCACA-TAGGAA
*
12586 CCGTGTTGTCTCC
128 ACGTGTTGTCTCC
* * *
12599 CAAATTATCCCTAAAAATGGCTATATGTCCTCATCACGTAGGAACAATGTCATCCACCGACCTA-
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACC-AG
* * *
12663 ATCTCCTCATCACGTAGGA-CTAGTGTCATCCTTAGAT-ACCAGACTTCCTCATCACGTAGGAAT
65 ATCTCCTCATCACGTAGGAGC-AGAGTCATCCTTAGATAACCAGACTTCCTCATCACATAGGAAA
12726 CGTGTTGTCTCC
129 CGTGTTGTCTCC
*
12738 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAATAATGTCATCCACCGACCAGA
1 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
* * * ** * * * * *
12803 TCTCCTCATCATGGAGGA-CTAGAGCCATAATCAAATAACTAGGCTTCTTCATCACATAGGAAAC
66 TCTCCTCATCACGTAGGAGC-AGAGTCATCCTTAGATAACCAGACTTCCTCATCACATAGGAAAC
*
12867 ATGTTGTCT-C
130 GTGTTGTCTCC
*
12877 CAAATT-TACCTAAA
1 CAAATTATCCCTAAA
12891 AACGACCAGA
Statistics
Matches: 500, Mismatches: 56, Indels: 32
0.85 0.10 0.05
Matches are distributed among these distances:
138 11 0.02
139 250 0.50
140 234 0.47
141 4 0.01
142 1 0.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (140 bp):
CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGA
TCTCCTCATCACGTAGGAGCAGAGTCATCCTTAGATAACCAGACTTCCTCATCACATAGGAAACG
TGTTGTCTCC
Found at i:13149 original size:3 final size:3
Alignment explanation
Indices: 13141--13174 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
13131 TTTTATTAAC
13141 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
13175 GTATTAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:14288 original size:2 final size:2
Alignment explanation
Indices: 14281--14347 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
14271 TGTTGTACCT
14281 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14323 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
14348 CATCCCTTTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14520 original size:28 final size:28
Alignment explanation
Indices: 14483--14538 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
14473 TCCATCATTC
* *
14483 TTTTATTCAACAGTGTTTAACCTTTCAT
1 TTTTACTCAACAGTGTTTAACCGTTCAT
14511 TTTTACTCAACAGTGTTTAACCGTTCAT
1 TTTTACTCAACAGTGTTTAACCGTTCAT
14539 CTAACTGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.46
Consensus pattern (28 bp):
TTTTACTCAACAGTGTTTAACCGTTCAT
Found at i:14747 original size:81 final size:81
Alignment explanation
Indices: 14512--14903 Score: 545
Period size: 81 Copynumber: 4.9 Consensus size: 81
14502 ACCTTTCATT
* * *
14512 TTTACTCAACAGTGTTTAACCGTTCATCTAACTGACATAATTGGCACCTTTCTACCAATTGCACA
1 TTTACTCAACGGTATTTAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCACA
*
14577 TTTAGGCCATTATTCC
66 GTTAGGCCATTATTCC
* *
14593 TTTACTCAACGGTA-TTAAACGTTCATCTAACTGGA-ATAATTGGTACCTTTATACCAATTGCAC
1 TTTACTCAACGGTATTTAACCGTTCATCTAACT-GACATAATTGGTACCTTTCTACCAATTGCAC
*
14656 ATTTAGGCCATTATTCC
65 AGTTAGGCCATTATTCC
** * * *
14673 TTTACTCAACAATATTTAACCGTTCATCTGACTGACATAATTGGTACTTTTCTACCAATTGTACA
1 TTTACTCAACGGTATTTAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCACA
*
14738 GTTAGGCCATTATTCT
66 GTTAGGCCATTATTCC
* * * * * *
14754 TTTACTTAACGGTGTTTAATCGTTCATCTAACTGACATAATTGATACATTTCTACCAATTGCGCA
1 TTTACTCAACGGTATTTAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCACA
* *
14819 GTTAGGTCATTATTCT
66 GTTAGGCCATTATTCC
* **
14835 TTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTCCCTACCAATTGCACA
1 TTTACTCAACGGTATTTAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCACA
14900 GTTA
66 GTTA
14904 TGCCTTAAAG
Statistics
Matches: 274, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
80 74 0.27
81 200 0.73
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.37
Consensus pattern (81 bp):
TTTACTCAACGGTATTTAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCACA
GTTAGGCCATTATTCC
Found at i:15297 original size:53 final size:54
Alignment explanation
Indices: 15228--15374 Score: 201
Period size: 56 Copynumber: 2.7 Consensus size: 54
15218 ACATATATTT
*
15228 TCCCATAC-GAATATTCATACACTTGGTATGAATTTCTTA-GTTCGCACA-CATAG
1 TCCCATACAGAA-ATTCATACACTTAGTATGAATTTCTTATGTTCGCACACCA-AG
* *
15281 TCCCATACAGAAATTCATACACTTAGTATGAATTTCCTTATTTTTGCACACCAAG
1 TCCCATACAGAAATTCATACACTTAGTATGAATTT-CTTATGTTCGCACACCAAG
*
15336 TGCCCATACAGAAATTCATACACTTAGTATGAATATCTT
1 T-CCCATACAGAAATTCATACACTTAGTATGAATTTCTT
15375 GCAATTTTGG
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
53 30 0.35
54 7 0.08
55 13 0.15
56 35 0.41
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (54 bp):
TCCCATACAGAAATTCATACACTTAGTATGAATTTCTTATGTTCGCACACCAAG
Found at i:21106 original size:15 final size:15
Alignment explanation
Indices: 21088--21116 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21078 TTCATTTCAA
21088 AATTTTATAAAATAC
1 AATTTTATAAAATAC
21103 AATTTTATAAAATA
1 AATTTTATAAAATA
21117 ACTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTTATAAAATAC
Found at i:21149 original size:26 final size:25
Alignment explanation
Indices: 21112--21160 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
21102 CAATTTTATA
* *
21112 AAATAACTTAAAAAAATTAAAATGT
1 AAATAACATAAAAAAATAAAAATGT
*
21137 AAATAACAATAAAAATATAAAAAT
1 AAATAAC-ATAAAAAAATAAAAAT
21161 ATATACATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (25 bp):
AAATAACATAAAAAAATAAAAATGT
Found at i:27502 original size:17 final size:18
Alignment explanation
Indices: 27469--27508 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
27459 TAATAGTGAG
27469 TTATTATAAAATATATTT
1 TTATTATAAAATATATTT
*
27487 TTATTAT-AATTATATTT
1 TTATTATAAAATATATTT
27504 TTATT
1 TTATT
27509 TTTATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTATAAAATATATTT
Found at i:27516 original size:5 final size:6
Alignment explanation
Indices: 27499--27524 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27489 ATTATAATTA
27499 TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TA
27525 GTATAGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:27522 original size:17 final size:18
Alignment explanation
Indices: 27469--27534 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
27459 TAATAGTGAG
**
27469 TTATTATAAAATATATTT
1 TTATTATAATTTATATTT
27487 TTATTATAA-TTATATTT
1 TTATTATAATTTATATTT
* * *
27504 TTATTTTTATTTTTATTT
1 TTATTATAATTTATATTT
* *
27522 TTAGTATAGTTTA
1 TTATTATAATTTA
27535 AATTAATATA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
17 14 0.37
18 24 0.63
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTATTATAATTTATATTT
Found at i:27576 original size:27 final size:29
Alignment explanation
Indices: 27546--27602 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 29
27536 ATTAATATAT
27546 TTTATATAATAATA-ATATTTT-TT-TAAA
1 TTTAT-TAATAATATATATTTTATTCTAAA
*
27573 TTTATTTATAATATATATTTTATTCTAAA
1 TTTATTAATAATATATATTTTATTCTAAA
27602 T
1 T
27603 GGTTAAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 7 0.27
27 12 0.46
28 2 0.08
29 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTATTAATAATATATATTTTATTCTAAA
Found at i:28999 original size:23 final size:22
Alignment explanation
Indices: 28973--29036 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
28963 CAGCTTGTAT
*
28973 AATTGCACCTAAGTGCCACTTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
28996 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
29019 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
29037 TATAATAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:29183 original size:103 final size:103
Alignment explanation
Indices: 29052--29269 Score: 375
Period size: 103 Copynumber: 2.1 Consensus size: 103
29042 TAATGTCCAT
*
29052 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTAT-GTATATCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGT-TGGTATATCACC
* *
29116 AGACCTCACACATGTTTCAAAGAATACATATATGTTCCG
65 AGACCTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
29155 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTTGGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTTGGTATATCACCA
29220 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
29258 AAGGACCACATA
1 AAGGACCACATA
29270 GACCCTCTAC
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 1 0.01
103 108 0.99
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTTGGTATATCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:35918 original size:23 final size:22
Alignment explanation
Indices: 35887--35955 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
35877 CACCACAGCT
*
35887 CGTATAATTGCACCTAAGTGCCA
1 CGTAGAATTGCACCT-AGTGCCA
* * *
35910 CTTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACC-TAGTGCCA
35933 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACC-TAGTGCCA
35956 TATAATAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (22 bp):
CGTAGAATTGCACCTAGTGCCA
Found at i:36096 original size:103 final size:101
Alignment explanation
Indices: 35963--36186 Score: 369
Period size: 103 Copynumber: 2.2 Consensus size: 101
35953 CCATATAATA
* *
35963 ATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTAT-GT
1 ATGTCCCTAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAA-TATGGT
36027 GTCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
65 GTCTCACCAGACCTCACACATGTTCCAAAGAATAC--AT
* *
36066 ATGTCCCTAAGGATCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAATTTGGTG
1 ATGTCCCTAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAATATGGTG
36131 TCTCACCAGACCTCACACATGTTCCAAAGAATACAT
66 TCTCACCAGACCTCACACATGTTCCAAAGAATACAT
*
36167 ATGTCCCGAAGGACCACATA
1 ATGTCCCTAAGGACCACATA
36187 GACCCTCTAC
Statistics
Matches: 114, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
101 20 0.18
102 2 0.02
103 92 0.81
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (101 bp):
ATGTCCCTAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAATATGGTG
TCTCACCAGACCTCACACATGTTCCAAAGAATACAT
Found at i:36097 original size:21 final size:21
Alignment explanation
Indices: 36054--36102 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
36044 ACATGTTCCA
36054 AAGAAT-ACATATATGTCCCT
1 AAGAATCACATATATGTCCCT
* *
36074 AAGGATCACATATCAT-TCCTT
1 AAGAATCACATAT-ATGTCCCT
36095 AAGAATCA
1 AAGAATCA
36103 TATACATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.21
21 17 0.71
22 2 0.08
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (21 bp):
AAGAATCACATATATGTCCCT
Found at i:36759 original size:21 final size:21
Alignment explanation
Indices: 36735--36777 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
36725 TTCATATTCT
*
36735 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
36756 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
36777 T
1 T
36778 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:45874 original size:10 final size:10
Alignment explanation
Indices: 45859--45885 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
45849 GGAAAAAGAG
45859 AAAAGAAAAA
1 AAAAGAAAAA
45869 AAAAGAAAAA
1 AAAAGAAAAA
45879 AAAAGAA
1 AAAAGAA
45886 TATATAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:47767 original size:36 final size:36
Alignment explanation
Indices: 47727--47915 Score: 243
Period size: 36 Copynumber: 5.2 Consensus size: 36
47717 TCGAACTTCA
* **
47727 AAGCAAATCATTTTAAGCCTTCACAAAAGAGTAGTG
1 AAGCAAATCATCTTAAGCCTTCACGGAAGAGTAGTG
* *
47763 AAGCAAATCATCTTAAGCCTTTACGAAAGAGTAGTG
1 AAGCAAATCATCTTAAGCCTTCACGGAAGAGTAGTG
*
47799 AAGCAAATCAATCTTAAGCCTTCACGGATGAGTAGTG
1 AAGCAAATC-ATCTTAAGCCTTCACGGAAGAGTAGTG
* * * * *
47836 AGGCAGATCATCTTCAGCCTTCATGGAATAGTAGTG
1 AAGCAAATCATCTTAAGCCTTCACGGAAGAGTAGTG
* * *
47872 AAACAAATCATCTTAAGCCATCACAGAAGAGTAGTG
1 AAGCAAATCATCTTAAGCCTTCACGGAAGAGTAGTG
47908 AAGCAAAT
1 AAGCAAAT
47916 TAATATCGAG
Statistics
Matches: 131, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
36 100 0.76
37 31 0.24
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (36 bp):
AAGCAAATCATCTTAAGCCTTCACGGAAGAGTAGTG
Found at i:47821 original size:73 final size:72
Alignment explanation
Indices: 47727--47915 Score: 252
Period size: 73 Copynumber: 2.6 Consensus size: 72
47717 TCGAACTTCA
* * *
47727 AAGCAAATCATTTTAAGCCTTCACAAAAGAGTAGTGAAGCAAATCATCTTAAGCCTTTACGAAAG
1 AAGCAAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCATCTTAAGCCTTCACGAAAG
47792 AGTAGTG
66 AGTAGTG
* * * * * * *
47799 AAGCAAATCAATCTTAAGCCTTCACGGATGAGTAGTGAGGCAGATCATCTTCAGCCTTCATGGAA
1 AAGCAAATC-ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCATCTTAAGCCTTCACGAAA
*
47864 TAGTAGTG
65 GAGTAGTG
* *
47872 AAACAAATCATCTTAAGCCATCACAGAAGAGTAGTGAAGCAAAT
1 AAGCAAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAAT
47916 TAATATCGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
72 39 0.39
73 60 0.61
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (72 bp):
AAGCAAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCATCTTAAGCCTTCACGAAAG
AGTAGTG
Found at i:47996 original size:55 final size:54
Alignment explanation
Indices: 47934--48500 Score: 557
Period size: 55 Copynumber: 10.3 Consensus size: 54
47924 AGTCTGATCC
* * * * *
47934 CCCTGAAAGAATAGGGAGCATACATATTTGCTGAAGATTGTTCGAG-TCTTATACT
1 CCCTGAAAGAATAGGGAGCA-ACCTGTTTTCAGAAGATTGCTCGAGTTC-TATACT
* * * ** * ** *
47989 CCCTGAAAAAATAAGGAGAAGAAATGTTTGCTCAAGATTGTTCGAGTTCTATACT
1 CCCTGAAAGAATAGGGAGCA-ACCTGTTTTCAGAAGATTGCTCGAGTTCTATACT
* * * *
48044 CTCTGAAGGAATAGGGAGCAAACCCGTTTTCAGATGATTGCTCGAGTTCTATACT
1 CCCTGAAAGAATAGGGAGC-AACCTGTTTTCAGAAGATTGCTCGAGTTCTATACT
* **
48099 CCCT-AAAGCAATAGGGAGAGAACCAATTTTCAGAAGATTGCTCGAGTTCTATACT
1 CCCTGAAAG-AATAGGGAG-CAACCTGTTTTCAGAAGATTGCTCGAGTTCTATACT
* * **
48154 CCCTGAAGGAATAAGGAGCGAACCCATTTTCAGAAGATTGCTCGAGTTCTATACT
1 CCCTGAAAGAATAGGGAGC-AACCTGTTTTCAGAAGATTGCTCGAGTTCTATACT
* *
48209 CCCTGAAAGAATAGGGAGCGAACCTGTTTTCAGAATATTGCTCAAGTTCTATACT
1 CCCTGAAAGAATAGGGAGC-AACCTGTTTTCAGAAGATTGCTCGAGTTCTATACT
*
48264 CCCTG-AAGCAATAGGGAGCGAACCAGTTTTCAGAAGATTGCTCGAGTTCTATACT
1 CCCTGAAAG-AATAGGGAGC-AACCTGTTTTCAGAAGATTGCTCGAGTTCTATACT
* * * * **
48319 CCCTGAAAGAATATGGAGTGAACCGGTTTTCAAAAGATTATTCGAGTTCTATACT
1 CCCTGAAAGAATAGGGAG-CAACCTGTTTTCAGAAGATTGCTCGAGTTCTATACT
* * * * ** *
48374 TCCTGAAGGAATAGGGAGAAAACCCGTTTTCAGAAGATTTTTCGAGTTATATACT
1 CCCTGAAAGAATAGGGAG-CAACCTGTTTTCAGAAGATTGCTCGAGTTCTATACT
* * * * **
48429 CCCTGAAAGAATAGGGAGCGGACCCGTTTTCAGAAAACTATTCGAGTTCTATACT
1 CCCTGAAAGAATAGGGAGC-AACCTGTTTTCAGAAGATTGCTCGAGTTCTATACT
48484 CCCTG-AAGCAATAGGGA
1 CCCTGAAAG-AATAGGGA
48501 TCAGACCTAT
Statistics
Matches: 439, Mismatches: 62, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
54 9 0.02
55 421 0.96
56 9 0.02
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (54 bp):
CCCTGAAAGAATAGGGAGCAACCTGTTTTCAGAAGATTGCTCGAGTTCTATACT
Found at i:48097 original size:110 final size:110
Alignment explanation
Indices: 47934--48500 Score: 638
Period size: 110 Copynumber: 5.2 Consensus size: 110
47924 AGTCTGATCC
* * *** * * * *
47934 CCCTGAAAGAATAGGGAGCATACATATTTGCTGAAGATTGTTCGAG-TCTTATACTCCCTGAAAA
1 CCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGAAGATTGCTCGAGTTC-TATACTCCCTGAAAG
* * ** *
47998 AATAAGGAGAAGAA-ATGTTTGCTCAAGATTGTTCGAGTTCTATACT
65 AATAGGGAG-AGAACATGTTTTCAGAAGATTGCTCGAGTTCTATACT
* *
48044 CTCTGAAGGAATAGGGAGCAAACCCGTTTTCAGATGATTGCTCGAGTTCTATACTCCCT-AAAGC
1 CCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACTCCCTGAAAG-
*
48108 AATAGGGAGAGAACCA-ATTTTCAGAAGATTGCTCGAGTTCTATACT
65 AATAGGGAGAGAA-CATGTTTTCAGAAGATTGCTCGAGTTCTATACT
* * *
48154 CCCTGAAGGAATAAGGAGCGAACCCATTTTCAGAAGATTGCTCGAGTTCTATACTCCCTGAAAGA
1 CCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACTCCCTGAAAGA
* * * *
48219 ATAGGGAGCGAACCTGTTTTCAGAATATTGCTCAAGTTCTATACT
66 ATAGGGAGAGAACATGTTTTCAGAAGATTGCTCGAGTTCTATACT
* * *
48264 CCCTGAAGCAATAGGGAGCGAACCAGTTTTCAGAAGATTGCTCGAGTTCTATACTCCCTGAAAGA
1 CCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACTCCCTGAAAGA
* * ** * **
48329 ATATGGAGTGAACCGGTTTTCAAAAGATTATTCGAGTTCTATACT
66 ATAGGGAGAGAACATGTTTTCAGAAGATTGCTCGAGTTCTATACT
* * ** *
48374 TCCTGAAGGAATAGGGAGAAAACCCGTTTTCAGAAGATTTTTCGAGTTATATACTCCCTGAAAGA
1 CCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACTCCCTGAAAGA
* * ** * * **
48439 ATAGGGAGCGGACCCGTTTTCAGAAAACTATTCGAGTTCTATACT
66 ATAGGGAGAGAACATGTTTTCAGAAGATTGCTCGAGTTCTATACT
*
48484 CCCTGAAGCAATAGGGA
1 CCCTGAAGGAATAGGGA
48501 TCAGACCTAT
Statistics
Matches: 395, Mismatches: 56, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
109 8 0.02
110 380 0.96
111 7 0.02
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (110 bp):
CCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGAAGATTGCTCGAGTTCTATACTCCCTGAAAGA
ATAGGGAGAGAACATGTTTTCAGAAGATTGCTCGAGTTCTATACT
Found at i:48223 original size:165 final size:165
Alignment explanation
Indices: 48022--48496 Score: 657
Period size: 165 Copynumber: 2.9 Consensus size: 165
48012 ATGTTTGCTC
*
48022 AAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCAAACCCGTTTTCAGATGATTGCTC
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGATGATTGCTC
* *
48087 GAGTTCTATACTCCCTAAAGCAATAGGGAGAGAACCAATTTTCAGAAGATTGCTCGAGTTCTATA
66 GAGTTCTATACTCCCTAAAGCAATAGGGAGCGAACCAGTTTTCAGAAGATTGCTCGAGTTCTATA
*
48152 CTCCCTGAAGGAATAAGGAGCGAACCCATTTTCAG
131 CTCCCTGAAGGAATAAGGAGCGAACCCATTTTCAA
* * * *
48187 AAGATTGCTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCTGTTTTCAGAAT-ATTGCT
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCAAACCCGTTTTCAG-ATGATTGCT
* *
48251 CAAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCAGTTTTCAGAAGATTGCTCGAGTTCTAT
65 CGAGTTCTATACTCCCTAAAGCAATAGGGAGCGAACCAGTTTTCAGAAGATTGCTCGAGTTCTAT
* * * **
48316 ACTCCCTGAAAGAATATGGAGTGAACCGGTTTTCAA
130 ACTCCCTGAAGGAATAAGGAGCGAACCCATTTTCAA
* * * * **
48352 AAGATTATTCGAGTTCTATACTTCCTGAAGGAATAGGGAGAAAACCCGTTTTCAGAAGATTTTTC
1 AAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGATGATTGCTC
* * * * * **
48417 GAGTTATATACTCCCTGAAAG-AATAGGGAGCGGACCCGTTTTCAGAAAACTATTCGAGTTCTAT
66 GAGTTCTATACTCCCT-AAAGCAATAGGGAGCGAACCAGTTTTCAGAAGATTGCTCGAGTTCTAT
*
48481 ACTCCCTGAAGCAATA
130 ACTCCCTGAAGGAATA
48497 GGGATCAGAC
Statistics
Matches: 271, Mismatches: 36, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
164 1 0.00
165 265 0.98
166 5 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (165 bp):
AAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGGAGCAAACCCGTTTTCAGATGATTGCTC
GAGTTCTATACTCCCTAAAGCAATAGGGAGCGAACCAGTTTTCAGAAGATTGCTCGAGTTCTATA
CTCCCTGAAGGAATAAGGAGCGAACCCATTTTCAA
Found at i:48766 original size:2 final size:2
Alignment explanation
Indices: 48759--48794 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
48749 TACTCCAATT
48759 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48795 CTAATTAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48873 original size:17 final size:16
Alignment explanation
Indices: 48847--48881 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
48837 TTATATTATC
48847 ATGTGTGTGTTTAATT
1 ATGTGTGTGTTTAATT
48863 ATGTAGTGTGTTTAATT
1 ATGT-GTGTGTTTAATT
48880 AT
1 AT
48882 CTATGTAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (16 bp):
ATGTGTGTGTTTAATT
Found at i:48886 original size:21 final size:21
Alignment explanation
Indices: 48836--48890 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 21
48826 TGATTATCTA
48836 TTTATATTATC-ATGT-GTGTG
1 TTTA-ATTATCTATGTAGTGTG
48856 TTT-A--AT-TATGTAGTGTG
1 TTTAATTATCTATGTAGTGTG
48873 TTTAATTATCTATGTAGT
1 TTTAATTATCTATGTAGT
48891 TATGATTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
16 6 0.21
17 8 0.28
18 2 0.07
20 5 0.17
21 8 0.28
ACGTcount: A:0.24, C:0.04, G:0.18, T:0.55
Consensus pattern (21 bp):
TTTAATTATCTATGTAGTGTG
Found at i:48911 original size:2 final size:2
Alignment explanation
Indices: 48904--49013 Score: 202
Period size: 2 Copynumber: 55.0 Consensus size: 2
48894 GATTGTGATC
**
48904 AT AT AT AT GC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48946 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48988 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
49014 GTTATGATAA
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 104 1.00
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50920 original size:54 final size:54
Alignment explanation
Indices: 50857--50963 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 54
50847 TTGATGAAAA
*
50857 TCCCGAAACAAACATCGAGT-TGTGTGAGGTTCTCAAGGGCCTGAACCAAGACTC
1 TCCCGAAACAAACATCGAGTATG-GTGAGCTTCTCAAGGGCCTGAACCAAGACTC
*
50911 TCCCGAAACAAACATCGGGTATGGTGAGCTTCTCAAGGGCCTGAACCAAGACT
1 TCCCGAAACAAACATCGAGTATGGTGAGCTTCTCAAGGGCCTGAACCAAGACT
50964 ATCATAAAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
54 48 0.96
55 2 0.04
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (54 bp):
TCCCGAAACAAACATCGAGTATGGTGAGCTTCTCAAGGGCCTGAACCAAGACTC
Found at i:54057 original size:91 final size:91
Alignment explanation
Indices: 53917--54095 Score: 331
Period size: 91 Copynumber: 2.0 Consensus size: 91
53907 GAAACAAACT
*
53917 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
53982 GAACTCTCCACTGGAAATCTTGAACC
66 GAACTCTCCACTGGAAATCTTGAACC
54008 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
* *
54073 GAACTCTCCATTGGAAATGTTGA
66 GAACTCTCCACTGGAAATCTTGA
54096 TTCACCTCCT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (91 bp):
AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATCTTGAACC
Found at i:59210 original size:104 final size:103
Alignment explanation
Indices: 59031--59239 Score: 409
Period size: 104 Copynumber: 2.0 Consensus size: 103
59021 CCCAAAGCGG
59031 TCGTTCTTCATCATGACAAATTTCGGATGTAAAGTCCCTTGCAAGCATCTACCGAGACCCTTTCC
1 TCGTTCTTCATCATGACAAATTTCGGATGTAAAGTCCCTTGCAAGCATCTACCGAGACCCTTTCC
59096 AATTTTAGCTCCTTTTCCTAGAGTCTCTCGCACAATCA
66 AATTTTAGCTCCTTTTCCTAGAGTCTCTCGCACAATCA
59134 TCGTTCTTCATCATGACAAATTTCGGATTGTAAAGTCCCTTGCAAGCATCTACCGAGACCCTTTC
1 TCGTTCTTCATCATGACAAATTTCGGA-TGTAAAGTCCCTTGCAAGCATCTACCGAGACCCTTTC
59199 CAATTTTAGCTCCTTTTCCTAGAGTCTCTCGCACAATCA
65 CAATTTTAGCTCCTTTTCCTAGAGTCTCTCGCACAATCA
59238 TC
1 TC
59240 TTAGTGCAAT
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
103 27 0.26
104 78 0.74
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.33
Consensus pattern (103 bp):
TCGTTCTTCATCATGACAAATTTCGGATGTAAAGTCCCTTGCAAGCATCTACCGAGACCCTTTCC
AATTTTAGCTCCTTTTCCTAGAGTCTCTCGCACAATCA
Found at i:70686 original size:41 final size:41
Alignment explanation
Indices: 70637--70717 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
70627 CTTAATGTTA
* * *
70637 ATATAAAAATTTAATTTAAAATT-AATCACTTCAATTTTAG
1 ATATAAAAAATCAATTTAAAATTAAATCAATTCAATTTTAG
* *
70677 ATATGAAAAAATCAATTTAAATTTAAATCAATTTAATTTTA
1 ATAT-AAAAAATCAATTTAAAATTAAATCAATTCAATTTTA
70718 AAATAACGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 4 0.12
41 16 0.47
42 14 0.41
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (41 bp):
ATATAAAAAATCAATTTAAAATTAAATCAATTCAATTTTAG
Found at i:70706 original size:16 final size:16
Alignment explanation
Indices: 70685--70719 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
70675 AGATATGAAA
70685 AAATCAATTTAAATTT
1 AAATCAATTTAAATTT
*
70701 AAATCAATTTAATTTT
1 AAATCAATTTAAATTT
70717 AAA
1 AAA
70720 ATAACGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATCAATTTAAATTT
Found at i:81608 original size:16 final size:15
Alignment explanation
Indices: 81589--81618 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
81579 TATTTAATAA
81589 ATAAATATTATTTTTT
1 ATAAATATT-TTTTTT
81605 ATAAATATTTTTTT
1 ATAAATATTTTTTT
81619 AAAATACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATAAATATTTTTTTT
Found at i:83030 original size:21 final size:21
Alignment explanation
Indices: 82998--83045 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
82988 TTGGCCAAAA
82998 ATATCA-TTCAATGATATGAT
1 ATATCACTTCAATGATATGAT
83018 ATATCACTTCAATGATATGAT
1 ATATCACTTCAATGATATGAT
83039 ATATCAC
1 ATATCAC
83046 CGAATTGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (21 bp):
ATATCACTTCAATGATATGAT
Found at i:83175 original size:136 final size:135
Alignment explanation
Indices: 83003--83249 Score: 381
Period size: 136 Copynumber: 1.8 Consensus size: 135
82993 CAAAAATATC
*
83003 ATTCAATGATATGATATATCACTTCAATGATATGATATATCACCGAATTGAAGTGATATATCACT
1 ATTCAATGATATGATATATCACTTCAATGATATGATATATCACCGAATTGAAGTGATAGATCACT
* *
83068 AAAAAGTTTCATGTCATTGTGCATTAAATGGTCTCTTAGATAAAAGACATATTTCAATAAAAAAA
66 AAAAAGTTT-ATGTCATTGTGCATTAAATGGTCTCTGAGAAAAAAGACATATTTCAATAAAAAAA
83133 TAGGTT
130 TAGGTT
* * *
83139 ATTCAATGGTATGATATATCAC-TGAATTGA-AGTGATATATCACTGAATTGAAGTGATAGATCA
1 ATTCAATGATATGATATATCACTTCAA-TGATA-TGATATATCACCGAATTGAAGTGATAGATCA
* *
83202 CTGAAAAGTTTATGTCATTGTGCATTAAATTGTCTCTGAGAAAAAAGA
64 CTAAAAAGTTTATGTCATTGTGCATTAAATGGTCTCTGAGAAAAAAGA
83250 TGTTTTTCAT
Statistics
Matches: 101, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
135 38 0.38
136 63 0.62
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (135 bp):
ATTCAATGATATGATATATCACTTCAATGATATGATATATCACCGAATTGAAGTGATAGATCACT
AAAAAGTTTATGTCATTGTGCATTAAATGGTCTCTGAGAAAAAAGACATATTTCAATAAAAAAAT
AGGTT
Found at i:83176 original size:21 final size:21
Alignment explanation
Indices: 83150--83206 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
83140 TTCAATGGTA
83150 TGATATATCACTGAATTGAAG
1 TGATATATCACTGAATTGAAG
83171 TGATATATCACTGAATTGAAG
1 TGATATATCACTGAATTGAAG
*
83192 TGATAGATCACTGAA
1 TGATATATCACTGAA
83207 AAGTTTATGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (21 bp):
TGATATATCACTGAATTGAAG
Found at i:84187 original size:28 final size:28
Alignment explanation
Indices: 84149--84214 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
84139 TGAATTTAAG
84149 ATGACGCGCAACTGTGCGTCATAAATTT
1 ATGACGCGCAACTGTGCGTCATAAATTT
* *
84177 ATGACGTGCAACTGTGCGTCATAAGTTT
1 ATGACGCGCAACTGTGCGTCATAAATTT
84205 ATGACGCGCA
1 ATGACGCGCA
84215 TTTATGGCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (28 bp):
ATGACGCGCAACTGTGCGTCATAAATTT
Found at i:84259 original size:13 final size:13
Alignment explanation
Indices: 84202--84253 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
84192 GCGTCATAAG
84202 TTTATGACGCGCA
1 TTTATGACGCGCA
* *
84215 TTTATGGCACACACACA
1 TTTAT-G---ACGCGCA
84232 TTTATGACGCGCA
1 TTTATGACGCGCA
84245 TTTATGACG
1 TTTATGACG
84254 TTCATTGAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
13 19 0.61
14 1 0.03
16 1 0.03
17 10 0.32
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (13 bp):
TTTATGACGCGCA
Found at i:92743 original size:21 final size:22
Alignment explanation
Indices: 92705--92746 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
92695 AATTTTATGG
*
92705 TTTTTTAATCTAAATTATATTA
1 TTTTATAATCTAAATTATATTA
*
92727 TTTTATAATC-AACTTATATT
1 TTTTATAATCTAAATTATATT
92747 TTACGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTATAATCTAAATTATATTA
Done.