Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007879.1 Hibiscus syriacus cultivar Beakdansim tig00110257_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: 1117421
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:9043 original size:10 final size:10
Alignment explanation
Indices: 9017--9050 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
9007 AGTGAAAATG
9017 AAAAAATAAA
1 AAAAAATAAA
9027 AATAAAATAAA
1 AA-AAAATAAA
9038 AAAAAATAAA
1 AAAAAATAAA
9048 AAA
1 AAA
9051 TGAAAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:9044 original size:15 final size:14
Alignment explanation
Indices: 9011--9050 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
9001 AAAATGAGTG
* *
9011 AAAATGAAAAAATA
1 AAAATAAAAAAAAA
9025 AAAATAAAATAAAAA
1 AAAATAAAA-AAAAA
9040 AAAATAAAAAA
1 AAAATAAAAAA
9051 TGAAAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (14 bp):
AAAATAAAAAAAAA
Found at i:9060 original size:8 final size:7
Alignment explanation
Indices: 9011--9059 Score: 55
Period size: 8 Copynumber: 6.7 Consensus size: 7
9001 AAAATGAGTG
9011 AAAATGAA
1 AAAAT-AA
9019 AAAAT-A
1 AAAATAA
9025 AAAATAA
1 AAAATAA
*
9032 AATAAAAA
1 AA-AATAA
9040 AAAATAA
1 AAAATAA
9047 AAAATGAA
1 AAAAT-AA
9055 AAAAT
1 AAAAT
9060 GGAAAAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
6 6 0.17
7 12 0.33
8 18 0.50
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:9065 original size:8 final size:8
Alignment explanation
Indices: 9011--9067 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
9001 AAAATGAGTG
9011 AAAATGAA
1 AAAATGAA
9019 AAAAT--A
1 AAAATGAA
9025 AAAAT-AA
1 AAAATGAA
*
9032 AATAA-AAA
1 AA-AATGAA
9040 AAAAT-AA
1 AAAATGAA
9047 AAAATGAA
1 AAAATGAA
9055 AAAATGGAA
1 AAAAT-GAA
9064 AAAA
1 AAAA
9068 GAAGGGTTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
6 6 0.14
7 12 0.28
8 18 0.42
9 7 0.16
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (8 bp):
AAAATGAA
Found at i:10196 original size:55 final size:55
Alignment explanation
Indices: 9990--10492 Score: 688
Period size: 55 Copynumber: 9.1 Consensus size: 55
9980 CAATGGTTAT
* * * *
9990 TGAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* *
10045 TG-AGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGC-GACACGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * *
10098 T-AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAAT-AGGGAGCAGACACGATTGA
* *
10153 TGAAGATTGTTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGACACGAGTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* *
10208 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGCAGACACGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * * * *
10263 TGAAAATTGTTCGAGTCTTATACTCTCTGCATAAATAGGGAGCAGACACGACTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* *
10318 TGAAGATTGTTGGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGACACGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * * * * *
10373 TGAAGATTGTTCAAGTTTTTATATTCTCTGAAGGAATAGGGAGCAGACAAGATTTGT
1 TGAAGATTGTTCGAG-TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGA
* * * *
10430 TGAAGATTGTTTGGGTCTTATACTCTCTGAGGAAATAGGGAGCAGACACAATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
10485 TGAAGATT
1 TGAAGATT
10493 CTTCAAGTTC
Statistics
Matches: 396, Mismatches: 46, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
53 43 0.11
54 43 0.11
55 202 0.51
56 93 0.23
57 15 0.04
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
Found at i:15313 original size:27 final size:27
Alignment explanation
Indices: 15274--15325 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
15264 GTTTATCATA
*
15274 ATTTTTTAAAATTAA-TATATTGTTTT
1 ATTTTTTAAAATTAACAATATTGTTTT
*
15300 ATTTTTATATAATTAACAATATTGTT
1 ATTTTT-TAAAATTAACAATATTGTT
15326 GTTTATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 8 0.36
28 8 0.36
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (27 bp):
ATTTTTTAAAATTAACAATATTGTTTT
Found at i:15531 original size:2 final size:2
Alignment explanation
Indices: 15524--15563 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
15514 AACATAATTT
15524 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
15564 AATAAATCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16560 original size:23 final size:23
Alignment explanation
Indices: 16515--16561 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
16505 ACATTATAAA
* *
16515 TTTTATTGATTTTTATTTTTTAT
1 TTTTATTGATGTTAATTTTTTAT
16538 TTTTATTGA-GTTAATTTTATTAT
1 TTTTATTGATGTTAATTTT-TTAT
16561 T
1 T
16562 ATTCAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.72
Consensus pattern (23 bp):
TTTTATTGATGTTAATTTTTTAT
Found at i:18143 original size:3 final size:3
Alignment explanation
Indices: 18135--18160 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18125 GGAAGTTTGT
18135 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
18161 AAAGAGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:26331 original size:21 final size:20
Alignment explanation
Indices: 26293--26345 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
26283 AAATTCAAAC
26293 ATCTTA-GATTTTATTATTT
1 ATCTTAGGATTTTATTATTT
26312 -TGCTTAGGATTTTAATTATTT
1 AT-CTTAGGATTTT-ATTATTT
*
26333 ATTTTAGGATTTT
1 ATCTTAGGATTTT
26346 TAGTTTACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 1 0.03
19 4 0.14
20 6 0.21
21 17 0.59
22 1 0.03
ACGTcount: A:0.25, C:0.04, G:0.11, T:0.60
Consensus pattern (20 bp):
ATCTTAGGATTTTATTATTT
Found at i:28301 original size:32 final size:32
Alignment explanation
Indices: 28233--28304 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
28223 GTTTCGGCCA
* * *
28233 ACCCGACCCGACCCGAAAACTTTACATCCTTC
1 ACCCGACCCGACCCGAAAAATATACATCATTC
*
28265 ACCCGACCCGACCCGAAAAATATATATCA-TC
1 ACCCGACCCGACCCGAAAAATATACATCATTC
28296 TACCCGACC
1 -ACCCGACC
28305 TGAACCCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 2 0.06
32 33 0.94
ACGTcount: A:0.32, C:0.42, G:0.10, T:0.17
Consensus pattern (32 bp):
ACCCGACCCGACCCGAAAAATATACATCATTC
Found at i:31413 original size:62 final size:60
Alignment explanation
Indices: 31314--31429 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 60
31304 AAATGGTCAT
* *
31314 TCGACTACATGACATTACTTTATTGAGTCTCCTGACTATTTTAAATGTTACAAAATAGTTCA
1 TCGACTACAAGACATTACTTTATTGAGTCTCCTGACTA--TTAAAAGTTACAAAATAGTTCA
* * *
31376 TCGACTATAAGACGTTACTTTGTTGAGTC-CCTCGACTATTAAAAGTTACAAAAT
1 TCGACTACAAGACATTACTTTATTGAGTCTCCT-GACTATTAAAAGTTACAAAAT
31430 GATTACCTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 15 0.31
61 3 0.06
62 30 0.62
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (60 bp):
TCGACTACAAGACATTACTTTATTGAGTCTCCTGACTATTAAAAGTTACAAAATAGTTCA
Found at i:33209 original size:31 final size:31
Alignment explanation
Indices: 33174--33291 Score: 125
Period size: 31 Copynumber: 3.8 Consensus size: 31
33164 TTATTTAATT
*
33174 TAAGTACATAAATTATTTTTTTTTATCAAAA
1 TAAGTACTTAAATTATTTTTTTTTATCAAAA
* * * *
33205 TAAGTATTTATGATTA-TTGTTTTAATCAAAA
1 TAAGTACTTA-AATTATTTTTTTTTATCAAAA
33236 TAAGTACTTAAATTATTTTTTTTT-T-AAAA
1 TAAGTACTTAAATTATTTTTTTTTATCAAAA
* * *
33265 TAAATACTTAAAGTATTCATTTTTTAT
1 TAAGTACTTAAATTATT-TTTTTTTAT
33292 ATAAGTATCT
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
29 19 0.27
30 11 0.15
31 37 0.52
32 4 0.06
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (31 bp):
TAAGTACTTAAATTATTTTTTTTTATCAAAA
Found at i:33266 original size:29 final size:29
Alignment explanation
Indices: 33160--33298 Score: 109
Period size: 29 Copynumber: 4.7 Consensus size: 29
33150 GTATGCCCTC
* ** *
33160 TTTTTTATTTAATTTAAGTACATAAATTA
1 TTTTTTTTTTAAAATAAGTACTTAAATTA
* *
33189 TTTTTTTTTATCAAAATAAGTATTTATGATTA
1 TTTTTTTTT-T-AAAATAAGTACTTA-AATTA
** *
33221 TTGTTTTAATCAAAATAAGTACTTAAATTA
1 TT-TTTTTTTTAAAATAAGTACTTAAATTA
* *
33251 TTTTTTTTTTAAAATAAATACTTAAAGTA
1 TTTTTTTTTTAAAATAAGTACTTAAATTA
** *
33280 TTCATTTTTT-ATATAAGTA
1 TTTTTTTTTTAAAATAAGTA
33299 TCTAAAATAA
Statistics
Matches: 86, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
28 7 0.08
29 38 0.44
30 7 0.08
31 23 0.27
32 6 0.07
33 5 0.06
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (29 bp):
TTTTTTTTTTAAAATAAGTACTTAAATTA
Found at i:33290 original size:62 final size:62
Alignment explanation
Indices: 33174--33290 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 62
33164 TTATTTAATT
* * *
33174 TAAGTACATAAATTATTTTTTTTTATCAAAATAAGTATTTATGATTATTGTTTTAATCAAAA
1 TAAGTACATAAATTATTTTTTTTTATCAAAATAAATATTAAAGATTATTGTTTTAATCAAAA
*
33236 TAAGTACTTAAATTATTTTTTTTT-T-AAAATAAATACTTAAAGTATTCATT-TTTTA
1 TAAGTACATAAATTATTTTTTTTTATCAAAATAAATA-TTAAAG-ATT-ATTGTTTTA
33291 TATAAGTATC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
60 9 0.19
61 5 0.10
62 31 0.65
63 3 0.06
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (62 bp):
TAAGTACATAAATTATTTTTTTTTATCAAAATAAATATTAAAGATTATTGTTTTAATCAAAA
Found at i:33386 original size:28 final size:28
Alignment explanation
Indices: 33346--33403 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
33336 AAAATTTTTG
*
33346 AATAATTTAAGTA-CTTATTTTAACATAA
1 AATAATTTAAGTATC-TATTTTAACAAAA
* * *
33374 AATACTTTTAGTATCTATTTTGACAAAA
1 AATAATTTAAGTATCTATTTTAACAAAA
33402 AA
1 AA
33404 AAACTTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (28 bp):
AATAATTTAAGTATCTATTTTAACAAAA
Found at i:33857 original size:20 final size:19
Alignment explanation
Indices: 33827--33868 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
33817 CTAAAAATAT
33827 TAAAAAATAATATTTTAAA
1 TAAAAAATAATATTTTAAA
33846 TAAAATAATAATATTTTAAA
1 TAAAA-AATAATATTTTAAA
33866 TAA
1 TAA
33869 TTTTTTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAATAATATTTTAAA
Found at i:37541 original size:22 final size:22
Alignment explanation
Indices: 37516--37570 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
37506 CAGCTTTGTA
* *
37516 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
37538 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
37560 CAGGAGTTATA
1 CAGGAGTTATA
37571 ACAGCTGAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:43427 original size:22 final size:22
Alignment explanation
Indices: 43402--43456 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
43392 TCAGGAGTTA
* *
43402 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
43424 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
43446 CAGGAGTTATA
1 CAGGAGTTATA
43457 ACAGCTGAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:57507 original size:222 final size:222
Alignment explanation
Indices: 57112--57524 Score: 709
Period size: 222 Copynumber: 1.9 Consensus size: 222
57102 GTGTTACACA
57112 ACATGAAATTAAACATTTAGATGCTACCTGAGCCATTCCCTCTTAACAAGATACAATTTAACTAA
1 ACATGAAATTAAACATTTAGATGCTACCTGAGCCATTCCCTCTTAACAAGATACAATTTAACTAA
* * * **
57177 GAAATGAAGAGAATGTTTAAATATAATTTCCAAACTCATGCGAAATTCACAGAATATACAAAATG
66 GAAAAGAAGAGAACGTTTAAATATAATTCCCAAACTCATGCGAAATTCACAGAATATACAAAACA
57242 TGAAGAGTATAAATCTAGTTCACTAAACAATGATATCATTTCATAGTCCCAACTACACAAGCTAG
131 TGAAGAGTATAAATCTAGTTCACTAAACAATGATATCATTTCATAGTCCCAACTACACAAGCTAG
57307 AATACTATTTTAGCTATCCCACAGATG
196 AATACTATTTTAGCTATCCCACAGATG
* * *
57334 ACATGAAATTAAACCTTTAGATGCTACCTGAGCCATTCCCTCTTAACAAGATACAGTTTGACTAA
1 ACATGAAATTAAACATTTAGATGCTACCTGAGCCATTCCCTCTTAACAAGATACAATTTAACTAA
* *
57399 GAAAAGAAGAGAACGTTTAAATATAATTCCCAAACTCGTGCGAAATTCACAGAATATACAACACA
66 GAAAAGAAGAGAACGTTTAAATATAATTCCCAAACTCATGCGAAATTCACAGAATATACAAAACA
* * *
57464 TGAAGAGTATAAATTTAGTTCACTAAACAATGTTATGATTTCATAGTCCCAACTACACAAG
131 TGAAGAGTATAAATCTAGTTCACTAAACAATGATATCATTTCATAGTCCCAACTACACAAG
57525 TTGGACCTGG
Statistics
Matches: 178, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
222 178 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (222 bp):
ACATGAAATTAAACATTTAGATGCTACCTGAGCCATTCCCTCTTAACAAGATACAATTTAACTAA
GAAAAGAAGAGAACGTTTAAATATAATTCCCAAACTCATGCGAAATTCACAGAATATACAAAACA
TGAAGAGTATAAATCTAGTTCACTAAACAATGATATCATTTCATAGTCCCAACTACACAAGCTAG
AATACTATTTTAGCTATCCCACAGATG
Found at i:65719 original size:29 final size:30
Alignment explanation
Indices: 65686--65759 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
65676 AATTTTTAAA
65686 AAAAAAATCCGACTGATCCCAATTTTTTTT
1 AAAAAAATCCGACTGATCCCAATTTTTTTT
*
65716 --AAAAA-CCGGACCCGATCCCAATTTTTTTT
1 AAAAAAATCC-GA-CTGATCCCAATTTTTTTT
65745 AAAAAAAATCCGACT
1 -AAAAAAATCCGACT
65760 CAAATACCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
27 2 0.06
28 7 0.19
29 17 0.47
31 1 0.03
32 7 0.19
33 2 0.06
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (30 bp):
AAAAAAATCCGACTGATCCCAATTTTTTTT
Found at i:66075 original size:17 final size:17
Alignment explanation
Indices: 66050--66084 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
66040 TGAGTGAAGG
*
66050 AAAAGAAAAAGGAAATT
1 AAAAAAAAAAGGAAATT
*
66067 AAAAAAAAAAGTAAATT
1 AAAAAAAAAAGGAAATT
66084 A
1 A
66085 TATTCTAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.14
Consensus pattern (17 bp):
AAAAAAAAAAGGAAATT
Found at i:71490 original size:38 final size:38
Alignment explanation
Indices: 71442--71525 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
71432 TCGGATCGGG
**
71442 TATATATATATTTAAATTAAATATATAAATTTTATATA
1 TATATATATATTTAAATTAAATATATAAATAATATATA
* *
71480 TATATATATATTTAAATTAAATTTATTAATAATATATA
1 TATATATATATTTAAATTAAATATATAAATAATATATA
71518 TATATATA
1 TATATATA
71526 ATAATAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (38 bp):
TATATATATATTTAAATTAAATATATAAATAATATATA
Found at i:71543 original size:34 final size:35
Alignment explanation
Indices: 71475--71544 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
71465 TATAAATTTT
* *
71475 ATATATATATATATATTTAAATTAAATTTATTAATA
1 ATATATATATATATAATAAAATT-AATTTATTAATA
71511 ATATATATATATATAATAATAATT-ATTT-TTAATA
1 ATATATATATATATAATAA-AATTAATTTATTAATA
71545 TTTATCGGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 6 0.19
35 4 0.13
36 17 0.55
37 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (35 bp):
ATATATATATATATAATAAAATTAATTTATTAATA
Found at i:71628 original size:30 final size:30
Alignment explanation
Indices: 71592--71668 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 30
71582 CCCGCCCCCA
* *
71592 TCCCCGTCCCCGTTTAGCATAAACGGTTTT
1 TCCCCGTCCCCGTTTAACATAAACGATTTT
*
71622 TCCCCGTCCCAGTTTAACATAAACGATTTT
1 TCCCCGTCCCCGTTTAACATAAACGATTTT
*
71652 TCTCCGTCCCCGTTTAA
1 TCCCCGTCCCCGTTTAA
71669 TTCAGTTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.19, C:0.34, G:0.13, T:0.34
Consensus pattern (30 bp):
TCCCCGTCCCCGTTTAACATAAACGATTTT
Found at i:89370 original size:20 final size:20
Alignment explanation
Indices: 89331--89370 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
89321 TGAAATCTCG
*
89331 GAGAGCAAAATAGGGGGAGA
1 GAGAGCAAAATAGAGGGAGA
* *
89351 GAGAGCAAAGTAGAGTGAGA
1 GAGAGCAAAATAGAGGGAGA
89371 AACAGTGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.42, T:0.07
Consensus pattern (20 bp):
GAGAGCAAAATAGAGGGAGA
Found at i:94422 original size:28 final size:29
Alignment explanation
Indices: 94391--94448 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 29
94381 GAATTTAAAA
94391 TAAACATT-AATTT-ATGATTTTTATA-TTT
1 TAAA-ATTAAATTTGAT-ATTTTTATAGTTT
94419 TAAAATTAAATTTGATATTTTTATAGTTT
1 TAAAATTAAATTTGATATTTTTATAGTTT
94448 T
1 T
94449 TATAATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 3 0.11
28 18 0.67
29 6 0.22
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (29 bp):
TAAAATTAAATTTGATATTTTTATAGTTT
Found at i:94481 original size:43 final size:37
Alignment explanation
Indices: 94408--94484 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 37
94398 TAATTTATGA
94408 TTTTTATATTTTAAAATTAAATTTGATATTTTTATAG
1 TTTTTATATTTTAAAATTAAATTTGATATTTTTATAG
*
94445 TTTTTATAATTATATAAAATTATTATATTGATTATTTTTA
1 TTTTTAT-ATT-T-TAAAATTA-AAT-TTGA-TATTTTTA
94485 ATTTAATTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
37 7 0.21
38 3 0.09
39 1 0.03
40 8 0.24
41 2 0.06
42 4 0.12
43 8 0.24
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (37 bp):
TTTTTATATTTTAAAATTAAATTTGATATTTTTATAG
Found at i:94867 original size:30 final size:30
Alignment explanation
Indices: 94833--94891 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
94823 TTATTCTCTC
* *
94833 TTCTATTTTGCTCATTGAACTTTCCATTTT
1 TTCTAATTTGCTCATTGAACTTTACATTTT
94863 TTCTAATTTGCTCATTGAACTTTACATTT
1 TTCTAATTTGCTCATTGAACTTTACATTT
94892 GAATCATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.20, C:0.19, G:0.07, T:0.54
Consensus pattern (30 bp):
TTCTAATTTGCTCATTGAACTTTACATTTT
Found at i:94903 original size:30 final size:30
Alignment explanation
Indices: 94834--94906 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
94824 TATTCTCTCT
* **
94834 TCTATTTTGCTCATTGAACTTTCCATTTTT
1 TCTATTTTGCTCATTGAACTTTACATTTAA
*
94864 TCTAATTTGCTCATTGAACTTTACATTTGAA
1 TCTATTTTGCTCATTGAACTTTACATTT-AA
94895 TC-ATTTTGCTCA
1 TCTATTTTGCTCA
94907 CTCTGCCGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 35 0.95
31 2 0.05
ACGTcount: A:0.22, C:0.19, G:0.08, T:0.51
Consensus pattern (30 bp):
TCTATTTTGCTCATTGAACTTTACATTTAA
Found at i:95081 original size:32 final size:32
Alignment explanation
Indices: 95035--95097 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
95025 GAGTAAAGTT
*
95035 TAATGACTCATGGTGTAATTTATCATTTTTCC
1 TAATGACTCATGGTGTAATTTACCATTTTTCC
* *
95067 TAATTACTCATGGTGTAATTTACCCTTTTTC
1 TAATGACTCATGGTGTAATTTACCATTTTTC
95098 ATTCTCTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (32 bp):
TAATGACTCATGGTGTAATTTACCATTTTTCC
Found at i:96923 original size:12 final size:12
Alignment explanation
Indices: 96906--96938 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
96896 CATCACATTC
96906 TCTTTGTTTTAA
1 TCTTTGTTTTAA
96918 TCTTTGTTTTAA
1 TCTTTGTTTTAA
96930 TCTTTGTTT
1 TCTTTGTTT
96939 ATCGTTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.70
Consensus pattern (12 bp):
TCTTTGTTTTAA
Found at i:98078 original size:21 final size:21
Alignment explanation
Indices: 98054--98095 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
98044 TCATATAACT
98054 CATAATCAAATATATTCAAGG
1 CATAATCAAATATATTCAAGG
98075 CATAATCAAATATATTCAAGG
1 CATAATCAAATATATTCAAGG
98096 ACGACGTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (21 bp):
CATAATCAAATATATTCAAGG
Found at i:98760 original size:60 final size:59
Alignment explanation
Indices: 98647--98766 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 59
98637 TGAATAGTTT
* * ** **
98647 GATCATTTTGTAACTTTTAATAGATGAAGGACTTAACAAAACAATGTTGTATAGTTAGAG
1 GATCACTTTGTAACTTTTAATAGATGAAAGACTTAACAAAACAACATCCTATAGTT-GAG
* * *
98707 GATCACTTTGTAACTTTTAATAGTTGAAAGACTTAATAAAGCAACATCCTATAGTTGAG
1 GATCACTTTGTAACTTTTAATAGATGAAAGACTTAACAAAACAACATCCTATAGTTGAG
98766 G
1 G
98767 TACCATTTGA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
59 4 0.08
60 47 0.92
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (59 bp):
GATCACTTTGTAACTTTTAATAGATGAAAGACTTAACAAAACAACATCCTATAGTTGAG
Found at i:102264 original size:2 final size:2
Alignment explanation
Indices: 102257--102287 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
102247 AGCTACAACG
102257 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
102288 AGTGAGGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:103645 original size:2 final size:2
Alignment explanation
Indices: 103638--103664 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
103628 AACATGAATA
103638 AT 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 A
103665 GTCAAGAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:108398 original size:17 final size:18
Alignment explanation
Indices: 108364--108398 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
108354 ACCGAACACA
*
108364 GAATTTTATAAGAGGTAT
1 GAATTTTATAAGAAGTAT
108382 GAATTTT-TAAGAAGTAT
1 GAATTTTATAAGAAGTAT
108399 ATTAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (18 bp):
GAATTTTATAAGAAGTAT
Found at i:110344 original size:15 final size:15
Alignment explanation
Indices: 110320--110350 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
110310 GCCTAGTAAG
*
110320 ATAACTATGTCGAAC
1 ATAACCATGTCGAAC
110335 ATAACCATGTCGAAC
1 ATAACCATGTCGAAC
110350 A
1 A
110351 CTTAATTACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (15 bp):
ATAACCATGTCGAAC
Found at i:110509 original size:187 final size:187
Alignment explanation
Indices: 110194--110566 Score: 746
Period size: 187 Copynumber: 2.0 Consensus size: 187
110184 TTTTCTCGTA
110194 TATGTTCCTCAAGACGTCGCCTTCGAACACGGTGTAAGCGTATGATAAATTGTCTCGGTCTATTT
1 TATGTTCCTCAAGACGTCGCCTTCGAACACGGTGTAAGCGTATGATAAATTGTCTCGGTCTATTT
110259 CATCAACCTTGTGCTTCGAGTAATCCGATCCCCACCCTTCATTTTTTATCAGCCTAGTAAGATAA
66 CATCAACCTTGTGCTTCGAGTAATCCGATCCCCACCCTTCATTTTTTATCAGCCTAGTAAGATAA
110324 CTATGTCGAACATAACCATGTCGAACACTTAATTACCTTGAGCAAACGTGACCTTCG
131 CTATGTCGAACATAACCATGTCGAACACTTAATTACCTTGAGCAAACGTGACCTTCG
110381 TATGTTCCTCAAGACGTCGCCTTCGAACACGGTGTAAGCGTATGATAAATTGTCTCGGTCTATTT
1 TATGTTCCTCAAGACGTCGCCTTCGAACACGGTGTAAGCGTATGATAAATTGTCTCGGTCTATTT
110446 CATCAACCTTGTGCTTCGAGTAATCCGATCCCCACCCTTCATTTTTTATCAGCCTAGTAAGATAA
66 CATCAACCTTGTGCTTCGAGTAATCCGATCCCCACCCTTCATTTTTTATCAGCCTAGTAAGATAA
110511 CTATGTCGAACATAACCATGTCGAACACTTAATTACCTTGAGCAAACGTGACCTTC
131 CTATGTCGAACATAACCATGTCGAACACTTAATTACCTTGAGCAAACGTGACCTTC
110567 TTGATACTTC
Statistics
Matches: 186, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
187 186 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (187 bp):
TATGTTCCTCAAGACGTCGCCTTCGAACACGGTGTAAGCGTATGATAAATTGTCTCGGTCTATTT
CATCAACCTTGTGCTTCGAGTAATCCGATCCCCACCCTTCATTTTTTATCAGCCTAGTAAGATAA
CTATGTCGAACATAACCATGTCGAACACTTAATTACCTTGAGCAAACGTGACCTTCG
Found at i:110531 original size:15 final size:15
Alignment explanation
Indices: 110507--110537 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
110497 GCCTAGTAAG
*
110507 ATAACTATGTCGAAC
1 ATAACCATGTCGAAC
110522 ATAACCATGTCGAAC
1 ATAACCATGTCGAAC
110537 A
1 A
110538 CTTAATTACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (15 bp):
ATAACCATGTCGAAC
Found at i:111394 original size:19 final size:20
Alignment explanation
Indices: 111370--111407 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
111360 ATATAAATAA
111370 AAATTC-AAACATCCAAAAC
1 AAATTCAAAACATCCAAAAC
*
111389 AAATTCAAAACATTCAAAA
1 AAATTCAAAACATCCAAAA
111408 TGTTAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.61, C:0.21, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATTCAAAACATCCAAAAC
Found at i:112855 original size:13 final size:13
Alignment explanation
Indices: 112837--112870 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
112827 ATGGGCATAT
*
112837 TTTGAAAACTATG
1 TTTGAAAACAATG
112850 TTTGAAAACAATG
1 TTTGAAAACAATG
112863 TTTGAAAA
1 TTTGAAAA
112871 ATTAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:115129 original size:21 final size:21
Alignment explanation
Indices: 115103--115147 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
115093 GATTTCTGGG
* *
115103 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
115124 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
115145 CAA
1 CAA
115148 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:116377 original size:32 final size:32
Alignment explanation
Indices: 116336--116432 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
116326 GAGTCGAGGG
116336 TTTACCTATGTTTTACGGAACATATGGACAGT
1 TTTACCTATGTTTTACGGAACATATGGACAGT
116368 TTTACCTATGTCTTT-C-GAGACATATGGACAG-
1 TTTACCTATGT-TTTACGGA-ACATATGGACAGT
* * *
116399 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTTTACGGAACATATGGACAGT
116431 TT
1 TT
116433 ACCGAGGATC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
30 2 0.04
31 24 0.43
32 27 0.48
33 3 0.05
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (32 bp):
TTTACCTATGTTTTACGGAACATATGGACAGT
Found at i:116467 original size:30 final size:30
Alignment explanation
Indices: 116423--116516 Score: 145
Period size: 30 Copynumber: 3.1 Consensus size: 30
116413 AAGGAACATA
116423 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
116454 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
116484 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
116513 TGGA
1 TGGA
116517 TAGGTCCTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 18 0.30
30 35 0.58
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:119935 original size:21 final size:21
Alignment explanation
Indices: 119909--119953 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
119899 GATTTCTGGG
* *
119909 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
119930 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
119951 CAA
1 CAA
119954 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:121185 original size:32 final size:32
Alignment explanation
Indices: 121144--121240 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
121134 GAGTCGAGGG
121144 TTTACCTATGTTTTACGGAACATATGGACAGT
1 TTTACCTATGTTTTACGGAACATATGGACAGT
121176 TTTACCTATGTCTTT-C-GAGACATATGGACAG-
1 TTTACCTATGT-TTTACGGA-ACATATGGACAGT
* * *
121207 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTTTACGGAACATATGGACAGT
121239 TT
1 TT
121241 ACCGAGGATC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
30 2 0.04
31 24 0.43
32 27 0.48
33 3 0.05
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (32 bp):
TTTACCTATGTTTTACGGAACATATGGACAGT
Found at i:121275 original size:30 final size:30
Alignment explanation
Indices: 121231--121324 Score: 145
Period size: 30 Copynumber: 3.1 Consensus size: 30
121221 AAGGAACATA
121231 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
121262 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
121292 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
121321 TGGA
1 TGGA
121325 TAGGTCCTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 18 0.30
30 35 0.58
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:127928 original size:20 final size:20
Alignment explanation
Indices: 127903--127940 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
127893 AATTTACCAT
*
127903 GGGGGTATCGGTACCATCCA
1 GGGGGTACCGGTACCATCCA
127923 GGGGGTACCGGTACCATC
1 GGGGGTACCGGTACCATC
127941 TGAGCATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.26, G:0.37, T:0.18
Consensus pattern (20 bp):
GGGGGTACCGGTACCATCCA
Found at i:132404 original size:54 final size:53
Alignment explanation
Indices: 132311--132425 Score: 126
Period size: 54 Copynumber: 2.2 Consensus size: 53
132301 ATAAAATTTT
* * *
132311 TATAATTATTATAATTATAAATTTTGTTATATATATATATTTATTTAAAAGAGA
1 TATAATTATTATAACTATAAATTTTGTTATAAATATATATTTATCTAAAA-AGA
* * *
132365 TATAATTATTGTAACTATAAAATTCTT-TTA-AAATGTATATTTATCTAATAAGA
1 TATAATTATTATAACTAT-AAATT-TTGTTATAAATATATATTTATCTAAAAAGA
*
132418 TTTAATTA
1 TATAATTA
132426 AAATAAATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
53 10 0.19
54 32 0.62
55 8 0.15
56 2 0.04
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (53 bp):
TATAATTATTATAACTATAAATTTTGTTATAAATATATATTTATCTAAAAAGA
Found at i:132518 original size:2 final size:2
Alignment explanation
Indices: 132511--132539 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
132501 AAAATAATAC
132511 AT AT 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 A
132540 ATAAAATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:136831 original size:40 final size:39
Alignment explanation
Indices: 136795--136944 Score: 201
Period size: 40 Copynumber: 3.8 Consensus size: 39
136785 ACACATTCGA
136795 CCAAGCAGCAAATTAAAATGCATAATAACTAGACATTCTT
1 CCAAGCAGCAAATTAAAATGCATAATAAC-AGACATTCTT
* * *
136835 CCAAGCAACAAATTAAAATGCATAACAACAAGATATTCTT
1 CCAAGCAGCAAATTAAAATGCATAATAAC-AGACATTCTT
* * * *
136875 CCGAGCATCAAATTAAAATTCATAATTACACGACATTCTT
1 CCAAGCAGCAAATTAAAATGCATAATAACA-GACATTCTT
*
136915 CCAAGCAGCAAATTAAAATGCATGATAACA
1 CCAAGCAGCAAATTAAAATGCATAATAACA
136945 CTTATTGGAA
Statistics
Matches: 94, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
39 1 0.01
40 93 0.99
ACGTcount: A:0.46, C:0.21, G:0.09, T:0.24
Consensus pattern (39 bp):
CCAAGCAGCAAATTAAAATGCATAATAACAGACATTCTT
Found at i:140892 original size:21 final size:21
Alignment explanation
Indices: 140831--140886 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
140821 TCTGGGCTAG
140831 GGGAATCGGTACCCATTCAAT
1 GGGAATCGGTACCCATTCAAT
140852 GGGAATCGGTACCCATTCAAT
1 GGGAATCGGTACCCATTCAAT
*
140873 GGGAATCGATACCC
1 GGGAATCGGTACCC
140887 CGTCAACCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (21 bp):
GGGAATCGGTACCCATTCAAT
Found at i:141372 original size:2 final size:2
Alignment explanation
Indices: 141365--141430 Score: 114
Period size: 2 Copynumber: 33.0 Consensus size: 2
141355 TAGAACAATA
* *
141365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
141407 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
141431 TAGGAGATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:142518 original size:25 final size:24
Alignment explanation
Indices: 142444--142519 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 24
142434 CCTTCAAGAC
*
142444 AAATTCTACGCGGTC-CTTCGGGACA
1 AAATTCTACGCGG-CACTTCGTG-CA
* *
142469 AAATTCTACGTGACACTTCGATGCA
1 AAATTCTACGCGGCACTTCG-TGCA
142494 AAATTCTACGCGGCACTTCAGTGCA
1 AAATTCTACGCGGCACTTC-GTGCA
142519 A
1 A
142520 TTTATATGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.02
25 40 0.93
26 2 0.05
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (24 bp):
AAATTCTACGCGGCACTTCGTGCA
Found at i:152220 original size:20 final size:20
Alignment explanation
Indices: 152195--152255 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
152185 TTTTGGTGCA
*
152195 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
152215 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
152236 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
152256 CCACATGGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:159640 original size:21 final size:21
Alignment explanation
Indices: 159614--159653 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
159604 CCCCCTTTGA
*
159614 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
159635 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
159654 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:163901 original size:33 final size:31
Alignment explanation
Indices: 163848--163912 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
163838 TTTTAACATT
*
163848 TTGATTATTTTGGAATGTTTGAATTTGTGGA
1 TTGATTATTTTGGAATGTTTGAATTTATGGA
*
163879 TTGATTGATTTT-GAATTTGTTTGGATTTATGGA
1 TTGATT-ATTTTGGAA--TGTTTGAATTTATGGA
163912 T
1 T
163913 AGTGAGAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 9 0.31
32 5 0.17
33 15 0.52
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.54
Consensus pattern (31 bp):
TTGATTATTTTGGAATGTTTGAATTTATGGA
Found at i:165810 original size:2 final size:2
Alignment explanation
Indices: 165803--165828 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
165793 ACAATAATAG
165803 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
165829 TAGGAGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:166849 original size:24 final size:25
Alignment explanation
Indices: 166829--166880 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 25
166819 ATTTCTATGT
166829 GGTCCTTCGGGAC-AAATTCTACGC
1 GGTCCTTCGGGACAAAATTCTACGC
*
166853 GGTCCTTCGGGACAAAATTCTAAGC
1 GGTCCTTCGGGACAAAATTCTACGC
166878 GGT
1 GGT
166881 GCAATTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (25 bp):
GGTCCTTCGGGACAAAATTCTACGC
Found at i:171191 original size:22 final size:22
Alignment explanation
Indices: 171165--171224 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 22
171155 TTGGTGCAAA
171165 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* * *
171187 GGGAACCGAT-TCCCCTTGTAG
1 GGGAATCGATACCCCCTTGAAG
171208 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
171225 GGGGTTCTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.23, C:0.30, G:0.27, T:0.20
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:171731 original size:15 final size:15
Alignment explanation
Indices: 171695--171733 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
171685 CGCATATTAA
*
171695 TTTCAAAAC-TTGTT
1 TTTCAAAACATAGTT
171709 TTTC-AAACATAGTT
1 TTTCAAAACATAGTT
171723 TTTCAAAACAT
1 TTTCAAAACAT
171734 TGCCCATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 12 0.55
15 6 0.27
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (15 bp):
TTTCAAAACATAGTT
Found at i:189632 original size:28 final size:28
Alignment explanation
Indices: 189586--189640 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
189576 CTTTATCCCT
*
189586 GATTTAATAGTTTGAATTTAACTTAATA
1 GATTTAATAGTTTGAATTTAAATTAATA
*
189614 GATTTAATAGTTAT-TATTTAAATTAAT
1 GATTTAATAGTT-TGAATTTAAATTAAT
189641 CTTGGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (28 bp):
GATTTAATAGTTTGAATTTAAATTAATA
Found at i:204450 original size:64 final size:64
Alignment explanation
Indices: 204349--204477 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
204339 CAGTAATCTT
204349 CATAAAACTCATTGTTTCTATCGTACGAGACGCTTTACGATGTAATAAAGAAGTGGTGAGCGAA
1 CATAAAACTCATTGTTTCTATCGTACGAGACGCTTTACGATGTAATAAAGAAGTGGTGAGCGAA
204413 CATAAAACTCATTGTTTCTATCGTACGAGACGCTTTACGATGTAATAAAGAAGTGGTGAGCGAA
1 CATAAAACTCATTGTTTCTATCGTACGAGACGCTTTACGATGTAATAAAGAAGTGGTGAGCGAA
204477 C
1 C
204478 CAAATAATTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (64 bp):
CATAAAACTCATTGTTTCTATCGTACGAGACGCTTTACGATGTAATAAAGAAGTGGTGAGCGAA
Found at i:206089 original size:29 final size:30
Alignment explanation
Indices: 206047--206120 Score: 114
Period size: 29 Copynumber: 2.5 Consensus size: 30
206037 AACTATATTT
* *
206047 TAGTGTGAAAGAAAATTTATCCAAGAAA-A
1 TAGTGTGAAAGAAAATTTATCAAAAAAAGA
206076 TAGTGTGAAAGAAAATTTATCAAAAAAAGA
1 TAGTGTGAAAGAAAATTTATCAAAAAAAGA
*
206106 TATTGTGAAAGAAAA
1 TAGTGTGAAAGAAAA
206121 AAAAAAGAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 26 0.63
30 15 0.37
ACGTcount: A:0.54, C:0.04, G:0.18, T:0.24
Consensus pattern (30 bp):
TAGTGTGAAAGAAAATTTATCAAAAAAAGA
Found at i:212584 original size:2 final size:2
Alignment explanation
Indices: 212577--212615 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
212567 TAGTCTACCC
212577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
212616 AAAACTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:220785 original size:92 final size:92
Alignment explanation
Indices: 220628--220813 Score: 372
Period size: 92 Copynumber: 2.0 Consensus size: 92
220618 AGCAAGATGG
220628 TGAGATTTCCAAGAGACTCGAGATATTGAGATTGCTTGTTCAACACGAAACGATGTGGTTGAACA
1 TGAGATTTCCAAGAGACTCGAGATATTGAGATTGCTTGTTCAACACGAAACGATGTGGTTGAACA
220693 CGTGGACCGAAAAGAGCGAGGCTACGA
66 CGTGGACCGAAAAGAGCGAGGCTACGA
220720 TGAGATTTCCAAGAGACTCGAGATATTGAGATTGCTTGTTCAACACGAAACGATGTGGTTGAACA
1 TGAGATTTCCAAGAGACTCGAGATATTGAGATTGCTTGTTCAACACGAAACGATGTGGTTGAACA
220785 CGTGGACCGAAAAGAGCGAGGCTACGA
66 CGTGGACCGAAAAGAGCGAGGCTACGA
220812 TG
1 TG
220814 GAGTAACCGT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 94 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.22
Consensus pattern (92 bp):
TGAGATTTCCAAGAGACTCGAGATATTGAGATTGCTTGTTCAACACGAAACGATGTGGTTGAACA
CGTGGACCGAAAAGAGCGAGGCTACGA
Found at i:224470 original size:29 final size:29
Alignment explanation
Indices: 224428--224498 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
224418 GCAATACCCT
224428 ATAGTCGAGGGATCATTTTGTAACTTTTA
1 ATAGTCGAGGGATCATTTTGTAACTTTTA
*
224457 ATAGTCGATGGATCATTTTGTAACTTTTA
1 ATAGTCGAGGGATCATTTTGTAACTTTTA
*
224486 ATAGTTGAGGGAT
1 ATAGTCGAGGGAT
224499 TAAACAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (29 bp):
ATAGTCGAGGGATCATTTTGTAACTTTTA
Found at i:225230 original size:30 final size:31
Alignment explanation
Indices: 225196--225255 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
225186 CGACTGTTAT
*
225196 AATATTTATATAAT-TATAAATTTAGTCATC
1 AATATTTACATAATCTATAAATTTAGTCATC
* *
225226 AATATTTACATATTCTATCAATTTAGTCAT
1 AATATTTACATAATCTATAAATTTAGTCAT
225256 AAATCAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (31 bp):
AATATTTACATAATCTATAAATTTAGTCATC
Found at i:226096 original size:29 final size:28
Alignment explanation
Indices: 226063--226165 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 28
226053 TCCCCAAGCA
* * *
226063 TAGGTCGCCACGCCCTCCGGATGACCTTG
1 TAGGTCGCCATGCACTCCGG-CGACCTTG
226092 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCC-GGCGACCTTG
226121 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCC-GGCGACCTTG
*
226150 TAGGTTGCCATGCACT
1 TAGGTCGCCATGCACT
226166 ACCTCCTGCT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
29 66 0.97
30 2 0.03
ACGTcount: A:0.15, C:0.34, G:0.28, T:0.23
Consensus pattern (28 bp):
TAGGTCGCCATGCACTCCGGCGACCTTG
Found at i:236166 original size:18 final size:18
Alignment explanation
Indices: 236143--236181 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
236133 GCTAAGTCTT
**
236143 GGGATTTGGGGGGAATTG
1 GGGATTTGGGGAAAATTG
*
236161 GGGATTTTGGGAAAATTG
1 GGGATTTGGGGAAAATTG
236179 GGG
1 GGG
236182 GGTTAACTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.51, T:0.28
Consensus pattern (18 bp):
GGGATTTGGGGAAAATTG
Found at i:247699 original size:22 final size:22
Alignment explanation
Indices: 247668--247713 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
247658 AAATGGCCCC
*
247668 TTAACCTTTCCATACTTCCAAA
1 TTAACATTTCCATACTTCCAAA
247690 TTAACATTTCCATACTTCCAAA
1 TTAACATTTCCATACTTCCAAA
247712 TT
1 TT
247714 GATCCAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAACATTTCCATACTTCCAAA
Found at i:254593 original size:60 final size:60
Alignment explanation
Indices: 254521--254641 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
254511 TTGTTTTGTG
*
254521 TTTTTGGTAGAGGAGATAGGGGCTTTTGCAGTGTGGAGTGTAGGTGCAGGCAAATTCTGA
1 TTTTTGGTAGAGGAGATAGGGGCTTTTGCAGTGTGGAGTGTAGGTGCAGGCAAATTATGA
254581 TTTTTGGTAGAGGAGATAGGGGCTTTTGCAGTGTGGAGTGTAGGTGCAGGCAAATTATGA
1 TTTTTGGTAGAGGAGATAGGGGCTTTTGCAGTGTGGAGTGTAGGTGCAGGCAAATTATGA
254641 T
1 T
254642 GGACGAAGAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.22, C:0.07, G:0.38, T:0.32
Consensus pattern (60 bp):
TTTTTGGTAGAGGAGATAGGGGCTTTTGCAGTGTGGAGTGTAGGTGCAGGCAAATTATGA
Found at i:258167 original size:24 final size:24
Alignment explanation
Indices: 258135--258187 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
258125 ATACTCGGTG
*
258135 CATATTTGTATAACAGAAA-CGAAA
1 CATAGTTGTATAACAGAAATC-AAA
* *
258159 CATAGTTGTCTAATAGAAATCAAA
1 CATAGTTGTATAACAGAAATCAAA
258183 CATAG
1 CATAG
258188 ACATGTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (24 bp):
CATAGTTGTATAACAGAAATCAAA
Found at i:259116 original size:27 final size:27
Alignment explanation
Indices: 259086--259142 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
259076 TATAATATAT
* *
259086 AATTCACACATAAAAT-TTAAAAATTCA
1 AATT-ACACAAAAAATATTAAAAATTAA
* *
259113 AATTACATAAAAAATATTGAAAATTAA
1 AATTACACAAAAAATATTAAAAATTAA
259140 AAT
1 AAT
259143 AAAATGCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (27 bp):
AATTACACAAAAAATATTAAAAATTAA
Found at i:259199 original size:16 final size:17
Alignment explanation
Indices: 259178--259210 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
259168 TTTCTAAGTT
259178 AAAATAAATAT-TTTAA
1 AAAATAAATATATTTAA
*
259194 AAAATAATTATATTTAA
1 AAAATAAATATATTTAA
259211 TATGGAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATAAATATATTTAA
Found at i:259345 original size:2 final size:2
Alignment explanation
Indices: 259340--259372 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
259330 AATAAAAATG
259340 AT AT AT AT 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 A
259373 ATAAACCGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:273173 original size:16 final size:16
Alignment explanation
Indices: 273154--273185 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
273144 TACAAAATCT
273154 AATAATTCATAATATA
1 AATAATTCATAATATA
*
273170 AATAATTCATTATATA
1 AATAATTCATAATATA
273186 TATATATATA
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:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
AATAATTCATAATATA
Found at i:273187 original size:2 final size:2
Alignment explanation
Indices: 273180--273216 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
273170 AATAATTCAT
*
273180 TA TA TA TA TA TA TA TA T- TA TA TA TT 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
273217 AACTAACGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:273200 original size:17 final size:17
Alignment explanation
Indices: 273178--273213 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
273168 TAAATAATTC
273178 ATTATATATATATATAT
1 ATTATATATATATATAT
*
273195 ATTATATATTTATATAT
1 ATTATATATATATATAT
273212 AT
1 AT
273214 ATAAACTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTATATATATATATAT
Found at i:273547 original size:29 final size:29
Alignment explanation
Indices: 273505--273598 Score: 179
Period size: 29 Copynumber: 3.2 Consensus size: 29
273495 GAATTCTACA
273505 GCGACCTTGGAGGTCGCCATGGCATCCGG
1 GCGACCTTGGAGGTCGCCATGGCATCCGG
273534 GCGACCTTGGAGGTCGCCATGGCATCCGG
1 GCGACCTTGGAGGTCGCCATGGCATCCGG
*
273563 GCGACCTTGGAGGTCGCCATGGCATCCGA
1 GCGACCTTGGAGGTCGCCATGGCATCCGG
273592 GCGACCT
1 GCGACCT
273599 GTGTGGTGTT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.15, C:0.32, G:0.36, T:0.17
Consensus pattern (29 bp):
GCGACCTTGGAGGTCGCCATGGCATCCGG
Found at i:274270 original size:27 final size:28
Alignment explanation
Indices: 274240--274301 Score: 87
Period size: 25 Copynumber: 2.4 Consensus size: 28
274230 AGTTTGTTAG
274240 TATA-ATTATTAGTTT-GTAG-TTAAGT
1 TATATATTATTAGTTTAGTAGTTTAAGT
*
274265 TATATA-TATTAGTTTATTAGTTTAAGT
1 TATATATTATTAGTTTAGTAGTTTAAGT
274292 TATATATTAT
1 TATATATTAT
274302 ATATATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 13 0.41
26 4 0.12
27 12 0.38
28 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (28 bp):
TATATATTATTAGTTTAGTAGTTTAAGT
Found at i:274274 original size:25 final size:27
Alignment explanation
Indices: 274246--274298 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
274236 TTAGTATAAT
274246 TATTAGTTT-GTAG-TTAAGTTATATA
1 TATTAGTTTAGTAGTTTAAGTTATATA
*
274271 TATTAGTTTATTAGTTTAAGTTATATA
1 TATTAGTTTAGTAGTTTAAGTTATATA
274298 T
1 T
274299 TATATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.36
26 3 0.12
27 13 0.52
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (27 bp):
TATTAGTTTAGTAGTTTAAGTTATATA
Found at i:274516 original size:83 final size:81
Alignment explanation
Indices: 274419--274572 Score: 290
Period size: 83 Copynumber: 1.9 Consensus size: 81
274409 AGTTATATTA
274419 TAAAAAAATTAATTAGTGCTTAATTAGTTTGTTATTTTAACTAAGTTATATTATAATAAAGAAAT
1 TAAAAAAATTAATTAGTGCTTAATTAGTTTGTTATTTTAACTAAGTTATATTAT-ATAAAG-AAT
274484 AGTTTATATATATTAGTT
64 AGTTTATATATATTAGTT
274502 TAAAAAAATTAATTAGTGCTTAATTAGTTTGTTATTTTAACTAAGTTATATTATATAAAGAATAG
1 TAAAAAAATTAATTAGTGCTTAATTAGTTTGTTATTTTAACTAAGTTATATTATATAAAGAATAG
274567 TTTATA
66 TTTATA
274573 GTTTAAGGTA
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
81 11 0.15
82 6 0.08
83 54 0.76
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (81 bp):
TAAAAAAATTAATTAGTGCTTAATTAGTTTGTTATTTTAACTAAGTTATATTATATAAAGAATAG
TTTATATATATTAGTT
Found at i:274888 original size:17 final size:17
Alignment explanation
Indices: 274863--274919 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
274853 GATAATTTCC
*
274863 GTTTTAAAAAATATTGT
1 GTTTAAAAAAATATTGT
*
274880 GTTTAAAAATAT-TTAGT
1 GTTTAAAAAAATATT-GT
** *
274897 GTTTTTAAAAATATTTT
1 GTTTAAAAAAATATTGT
274914 GTTTAA
1 GTTTAA
274920 TTTACATTGT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
16 2 0.07
17 26 0.87
18 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.51
Consensus pattern (17 bp):
GTTTAAAAAAATATTGT
Found at i:278092 original size:15 final size:14
Alignment explanation
Indices: 278069--278099 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
278059 TACAACACTA
278069 AACTTTAATATAAT
1 AACTTTAATATAAT
278083 AACTTATAATATAAT
1 AACTT-TAATATAAT
278098 AA
1 AA
278100 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:278107 original size:16 final size:16
Alignment explanation
Indices: 278074--278120 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
278064 CACTAAACTT
*
278074 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
278089 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
278105 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
278121 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:278241 original size:32 final size:34
Alignment explanation
Indices: 278161--278242 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
278151 TTAAACCCTT
*
278161 AAAC-AACTAATAAAATATTCTTTTATATAACTA
1 AAACTAACTAATAAACTATTCTTTTATATAACTA
278194 AAACTAACTAATAAACTATT-TTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTCTTTT-A-TATAACTA
*
278227 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
278243 TACTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.25
33 12 0.27
34 16 0.36
35 5 0.11
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTCTTTTATATAACTA
Found at i:278359 original size:45 final size:45
Alignment explanation
Indices: 278282--278414 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
278272 TCAACAAACA
*
278282 AATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAAATAATTTTTT
* *
278330 TATATAACTAACTATTAACAAAACAAACTAATT-AATTATTTTTT
1 AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
278374 AACTAT-A-TAACTA-T--C-AAACATATACTAATTAAATAATTTTT
1 AA-TATAACTAACTATTAACAAAACA-A-ACTAATTAAATAATTTTT
278415 AATTTATGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
39 5 0.07
40 2 0.03
41 7 0.09
42 10 0.13
43 6 0.08
44 12 0.16
45 16 0.21
46 5 0.07
47 6 0.08
48 7 0.09
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (45 bp):
AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
Found at i:278442 original size:41 final size:40
Alignment explanation
Indices: 278354--278442 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
278344 TTAACAAAAC
* *
278354 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
278395 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
278436 AAACTAA
1 AAACTAA
278443 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:278982 original size:29 final size:29
Alignment explanation
Indices: 278949--279052 Score: 172
Period size: 29 Copynumber: 3.6 Consensus size: 29
278939 TCGTGAGTTA
**
278949 GGACTACATGGCGACCTACTTGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
*
278978 GGACTACATGGCGACCTACAAAGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
279007 GGACTACATGGCGACCTACAAGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
*
279036 GGACTGCATGGCGACCT
1 GGACTACATGGCGACCT
279053 CTCCATTCGT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.16
Consensus pattern (29 bp):
GGACTACATGGCGACCTACAAGGTCGCCG
Found at i:284709 original size:105 final size:105
Alignment explanation
Indices: 284537--284736 Score: 294
Period size: 105 Copynumber: 1.9 Consensus size: 105
284527 TTCTTTCTAA
** * * * *
284537 AAGTCCTGAATTCAGGTAGAATATGTAGTAAGGGGGGGTGTGTGCGTTATTAATTTATTAAGAAA
1 AAGTCCTGAATTCAGGTAGAATATGTAGTAAGAAGGGGTGTGCGCATTATCAATTGATTAAGAAA
284602 ATTTTGAACGAATATTATTGCATACTCTAATTATTCCTAG
66 ATTTTGAACGAATATTATTGCATACTCTAATTATTCCTAG
* * *
284642 AAGTCTTGAATTCAGGTAGAA-ATGTATGTAATAAGGGGTGTGCGCATTATCAGTTGATTAAGAA
1 AAGTCCTGAATTCAGGTAGAATATGTA-GTAAGAAGGGGTGTGCGCATTATCAATTGATTAAGAA
*
284706 AATTTTGAACGGATATTATTGCATACTCTAA
65 AATTTTGAACGAATATTATTGCATACTCTAA
284737 AACCTTAAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
104 5 0.06
105 79 0.94
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.35
Consensus pattern (105 bp):
AAGTCCTGAATTCAGGTAGAATATGTAGTAAGAAGGGGTGTGCGCATTATCAATTGATTAAGAAA
ATTTTGAACGAATATTATTGCATACTCTAATTATTCCTAG
Found at i:289626 original size:23 final size:23
Alignment explanation
Indices: 289600--289647 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
289590 ACGTTAAAGG
* *
289600 AACACGTTTGCGAATATTAAACA
1 AACACATTTGCGAACATTAAACA
* *
289623 AACACATTTGTGAACGTTAAACA
1 AACACATTTGCGAACATTAAACA
289646 AA
1 AA
289648 TGAATGCGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (23 bp):
AACACATTTGCGAACATTAAACA
Found at i:289727 original size:29 final size:29
Alignment explanation
Indices: 289674--289732 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
289664 CAAAAATAAA
* *
289674 TAAAAGAATATGAATAAATATTAAAAATT
1 TAAAAGAACATGAATAAACATTAAAAATT
*
289703 TAAAAGAACATGAATCAAACA-TAAACATT
1 TAAAAGAACATGAAT-AAACATTAAAAATT
289732 T
1 T
289733 TTAAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (29 bp):
TAAAAGAACATGAATAAACATTAAAAATT
Found at i:294039 original size:23 final size:23
Alignment explanation
Indices: 294009--294061 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
293999 TATTGTGTTG
294009 CACGTTTATCTTTGTC-TTTAAGA
1 CACGTTTATCTTTG-CATTTAAGA
*
294032 CACGTTTATCTTTGCATTTATGA
1 CACGTTTATCTTTGCATTTAAGA
294055 CACGTTT
1 CACGTTT
294062 TTCAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (23 bp):
CACGTTTATCTTTGCATTTAAGA
Found at i:296078 original size:42 final size:42
Alignment explanation
Indices: 296029--296125 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
296019 GAGACAGAGC
* *
296029 TTGAGAAGT-TGAAAAGCGAGACTGAGGGTGCTCAGGGTGAGG
1 TTGAGAAGTCT-AAAACCGAGACTGAGGGTACTCAGGGTGAGG
** *
296071 TTGAGAAGTCTAAAACCGAGGGTGAGGGTACTGAGGGTGAGG
1 TTGAGAAGTCTAAAACCGAGACTGAGGGTACTCAGGGTGAGG
*
296113 CTGAGAAGTCTAA
1 TTGAGAAGTCTAA
296126 CAATGAGGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
42 47 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.40, T:0.20
Consensus pattern (42 bp):
TTGAGAAGTCTAAAACCGAGACTGAGGGTACTCAGGGTGAGG
Found at i:296156 original size:42 final size:42
Alignment explanation
Indices: 296072--296158 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
296062 AGGGTGAGGT
* * * *
296072 TGAGAAGTCTAAAACCGAGGGTGAGGGTACTGAGGGTGAGGC
1 TGAGAAGTCTAAAACCGAGGGTGAAGGTACTAAAGGTAAGGC
* *
296114 TGAGAAGTCTAACAA-TGAGGGTGAAGGTGCTAAAGGTAAGGC
1 TGAGAAGTCTAA-AACCGAGGGTGAAGGTACTAAAGGTAAGGC
296156 TGA
1 TGA
296159 CAGTAAGAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 36 0.95
43 2 0.05
ACGTcount: A:0.32, C:0.10, G:0.39, T:0.18
Consensus pattern (42 bp):
TGAGAAGTCTAAAACCGAGGGTGAAGGTACTAAAGGTAAGGC
Found at i:297318 original size:15 final size:15
Alignment explanation
Indices: 297298--297342 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
297288 CTCAACAGAT
297298 AACACCAACACAACA
1 AACACCAACACAACA
*
297313 AACACCAACACAAGA
1 AACACCAACACAACA
**
297328 GGCACCAACACAACA
1 AACACCAACACAACA
297343 GTCAGTAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.56, C:0.38, G:0.07, T:0.00
Consensus pattern (15 bp):
AACACCAACACAACA
Found at i:306824 original size:17 final size:16
Alignment explanation
Indices: 306803--306833 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
306793 GCTTCTAATT
*
306803 TTTTTTTAGTTCAAGC
1 TTTTTTGAGTTCAAGC
306819 TTTTTTGAGTTCAAG
1 TTTTTTGAGTTCAAG
306834 TTTCAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (16 bp):
TTTTTTGAGTTCAAGC
Found at i:311951 original size:2 final size:2
Alignment explanation
Indices: 311944--312011 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
311934 CTATAATTTA
311944 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
311986 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
312012 CCATATTAAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:313829 original size:53 final size:53
Alignment explanation
Indices: 313765--313887 Score: 156
Period size: 53 Copynumber: 2.3 Consensus size: 53
313755 GGGATTAAGG
**
313765 AACTCGAACAATCTTCTAAAAATGGGTTCGCTCCCTCTTGCTTCAGGGAGTAC
1 AACTCGAACAATCTTCTAAAAACAGGTTCGCTCCCTCTTGCTTCAGGGAGTAC
* **** * *
313818 AACTCGAACAATCGTCTGCCTACAGGTTCGCTTCCTCTTGCTTCAGGGAGTAG
1 AACTCGAACAATCTTCTAAAAACAGGTTCGCTCCCTCTTGCTTCAGGGAGTAC
*
313871 AACTCGAACAATTTTCT
1 AACTCGAACAATCTTCT
313888 GGTGTAATTC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (53 bp):
AACTCGAACAATCTTCTAAAAACAGGTTCGCTCCCTCTTGCTTCAGGGAGTAC
Found at i:314415 original size:42 final size:42
Alignment explanation
Indices: 314310--314715 Score: 193
Period size: 42 Copynumber: 9.6 Consensus size: 42
314300 ACATCCTACC
* * * * *
314310 CGAAGGACTTACGGATGACCCGAATGATTT-ATTATCTTGAT
1 CGAAAGACTTACTGATGACCCGAATGATTTAATCATCATGCT
* * ***
314351 CAAAAGACTCAAAAATGACCCGAATGATTTAATCATCATGCT
1 CGAAAGACTTACTGATGACCCGAATGATTTAATCATCATGCT
*
314393 CGAAAGACTTACTGATGGCCCGAATGATTTAATCATCATGCT
1 CGAAAGACTTACTGATGACCCGAATGATTTAATCATCATGCT
* **
314435 CAAAAGACTTACTGATGACACTTACTG-ATGAATTTGCTTCA-CTACT-CTT
1 CGAAAGACTTACTGATGAC-C---C-GAATG-ATTT-AATCATC-A-TGC-T
* * ** * *
314484 CGGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCT
1 C-G-AAAGACTTACTGATGACCCGAATGATTTAATCATCATGCT
* * * *
314528 CGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCT
1 CGAAAGACTTACTGATGACCCGAATGATTTAATCATCATGCT
* * ** * * * *
314570 CGAAATACTTACTGATG---GGTTTGCTTCACTGC-TC-TTCT
1 CGAAAGACTTACTGATGACCCGAATGATTTAAT-CATCATGCT
* * ** * * * *
314608 -GTGAAGGCTTACAAATTACCCTAAGGATTTAATCATCATGCC
1 CG-AAAGACTTACTGATGACCCGAATGATTTAATCATCATGCT
* * * *
314650 CGAAAGACTTACTGATGGCCCTAAGGATTTAAGCATCATGCT
1 CGAAAGACTTACTGATGACCCGAATGATTTAATCATCATGCT
* * *
314692 CGCAAGACTTATTGATGGCCCGAA
1 CGAAAGACTTACTGATGACCCGAA
314716 GGACTTACTA
Statistics
Matches: 267, Mismatches: 74, Indels: 47
0.69 0.19 0.12
Matches are distributed among these distances:
37 1 0.00
38 12 0.04
39 6 0.02
40 2 0.01
41 31 0.12
42 164 0.61
43 3 0.01
44 3 0.01
45 5 0.02
46 10 0.04
47 9 0.03
48 5 0.02
49 3 0.01
50 1 0.00
51 12 0.04
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (42 bp):
CGAAAGACTTACTGATGACCCGAATGATTTAATCATCATGCT
Found at i:314459 original size:13 final size:13
Alignment explanation
Indices: 314441--314465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
314431 TGCTCAAAAG
314441 ACTTACTGATGAC
1 ACTTACTGATGAC
314454 ACTTACTGATGA
1 ACTTACTGATGA
314466 ATTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGAC
Found at i:314528 original size:135 final size:130
Alignment explanation
Indices: 314363--314708 Score: 447
Period size: 122 Copynumber: 2.7 Consensus size: 130
314353 AAAGACTCAA
* * *
314363 AAATGACCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAATGATTTAATCA
1 AAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAATCA
314428 TCATGCTCAAAAGACTTACTGATGACACTTACTGATGAATTTGCTTCACTACTCTTCGGTGAAGG
66 TCATGCTC--AAGACTTA-TGATG--ACTTACTGATGAATTTGCTTCACTACTCTTCGGTGAAGG
314493 CTTAC
126 CTTAC
* *
314498 AAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCA
1 AAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAATCA
** * *
314563 TCATGCTC--GA---A--AT-ACTTACTGATGGGTTTGCTTCACTGCTCTTCTGTGAAGGCTTAC
66 TCATGCTCAAGACTTATGATGACTTACTGATGAATTTGCTTCACTACTCTTCGGTGAAGGCTTAC
* * * *
314620 AAATTACCCTAAGGATTTAATCATCATGCCCGAAAGACTTACTGATGGCCCTAAGGATTTAAGCA
1 AAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAATCA
314685 TCATGCTCGCAAGACTTATTGATG
66 TCATGCT--CAAGACTTA-TGATG
314709 GCCCGAAGGA
Statistics
Matches: 185, Mismatches: 15, Indels: 24
0.83 0.07 0.11
Matches are distributed among these distances:
122 106 0.57
124 1 0.01
125 2 0.01
126 2 0.01
128 1 0.01
129 1 0.01
131 2 0.01
132 2 0.01
135 68 0.37
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (130 bp):
AAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTAATCA
TCATGCTCAAGACTTATGATGACTTACTGATGAATTTGCTTCACTACTCTTCGGTGAAGGCTTAC
Found at i:314895 original size:41 final size:43
Alignment explanation
Indices: 314830--314910 Score: 103
Period size: 41 Copynumber: 1.9 Consensus size: 43
314820 ATCCTACCCG
* * * *
314830 AAGGTCTTATGGATGGCCCGAAGGACTT-ATCATCTTGCTTTA
1 AAGGTCTTATAGATGACCCAAAGGACTTCATCATCATGCTTTA
*
314872 AAGG-CTTATAGATGACCCAAAGGATTTCATCATCATGCT
1 AAGGTCTTATAGATGACCCAAAGGACTTCATCATCATGCT
314911 CGAAAGACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 19 0.58
42 14 0.42
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (43 bp):
AAGGTCTTATAGATGACCCAAAGGACTTCATCATCATGCTTTA
Found at i:323465 original size:2 final size:2
Alignment explanation
Indices: 323458--323525 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
323448 TATAAATTTA
323458 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
323500 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
323526 CCATATTAAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:325539 original size:51 final size:50
Alignment explanation
Indices: 325480--325629 Score: 153
Period size: 50 Copynumber: 3.0 Consensus size: 50
325470 TAAAGCGTGC
*
325480 CCCCTGCACTGCGCTATACGATGATTTAGCGCCACGTGGGGTATAGCGCG
1 CCCCTGCACTGCGCTATACGATGATATAGCGCCACGTGGGGTATAGCGCG
* * ** *
325530 CCCCTTGCACCGCGCTATACGGTGAGCTGGCGCCACGT-GGGTATAGCGCGG
1 CCCC-TGCACTGCGCTATACGATGATATAGCGCCACGTGGGGTATAGCGC-G
* * * * *
325581 CCCCTGCAGTGTGCTATAC-CTG-TATATCTGACACGTGGGGTATAGCGCG
1 CCCCTGCACTGCGCTATACGATGATATAGC-GCCACGTGGGGTATAGCGCG
325630 GTGCAGGGGG
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
48 2 0.02
49 9 0.11
50 38 0.46
51 33 0.40
ACGTcount: A:0.17, C:0.30, G:0.31, T:0.22
Consensus pattern (50 bp):
CCCCTGCACTGCGCTATACGATGATATAGCGCCACGTGGGGTATAGCGCG
Found at i:325743 original size:20 final size:19
Alignment explanation
Indices: 325712--325750 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
325702 TTATCACACC
*
325712 AAATTTTCTCAAATTCTCT
1 AAATTTTCTCAAATACTCT
325731 AAATTTCTCTCAAATACTCT
1 AAATTT-TCTCAAATACTCT
325751 CTTTTTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTTTCTCAAATACTCT
Found at i:328061 original size:26 final size:24
Alignment explanation
Indices: 327988--328061 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
327978 TTATATTTGT
327988 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
** *
328013 ATTTTTTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
328037 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
328062 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
24 4 0.11
25 17 0.46
26 16 0.43
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.64
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:331748 original size:51 final size:50
Alignment explanation
Indices: 331632--331751 Score: 161
Period size: 51 Copynumber: 2.4 Consensus size: 50
331622 CAAAACGCGA
*
331632 TACCTGATCCGCGCTATATAAAATTATGTCAGAGTAAAGGTATGTCGCGG
1 TACCTGATCCGCGCTATATAAAATTATGTCAGAGTAAAGGTATGTCACGG
**
331682 TACCATGCCCCGCGCTATATAAAATTATGTCGAGAGTAAAGGTATAG-CACGG
1 TACC-TGATCCGCGCTATATAAAATTATGTC-AGAGTAAAGGTAT-GTCACGG
* *
331734 TTCCTGATCTGCGCTATA
1 TACCTGATCCGCGCTATA
331752 CCCCTACGTG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
50 4 0.07
51 35 0.58
52 20 0.33
53 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (50 bp):
TACCTGATCCGCGCTATATAAAATTATGTCAGAGTAAAGGTATGTCACGG
Found at i:331869 original size:51 final size:50
Alignment explanation
Indices: 331763--331890 Score: 148
Period size: 51 Copynumber: 2.5 Consensus size: 50
331753 CCCTACGTGG
* * * * *
331763 CGTATAGCGCGCTACAGGGGCCGCGCTATACCCACGTGGCGCCAACTCAC
1 CGTATAGCACGGTGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAC
* * * * *
331813 CGTATAGCACTGTTCAGGGGGTGCGCTATACCCCACGTGGTGCCAAATCAT
1 CGTATAGCACGGTGCAGGGGGCGCGCTATA-CCCACGTGGCGCCAAATCAC
*
331864 CGTATAGCGCGGTGCAGGGGGCGCGCT
1 CGTATAGCACGGTGCAGGGGGCGCGCT
331891 TTACTGCTAA
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
50 24 0.38
51 40 0.62
ACGTcount: A:0.19, C:0.31, G:0.32, T:0.18
Consensus pattern (50 bp):
CGTATAGCACGGTGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAC
Found at i:340018 original size:13 final size:13
Alignment explanation
Indices: 340000--340046 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
339990 ACTTCTATAT
340000 AATCAGTTAATCA
1 AATCAGTTAATCA
*
340013 AATCAGTTTATCA
1 AATCAGTTAATCA
**
340026 AATCAACTAATCA
1 AATCAGTTAATCA
*
340039 AATTAGTT
1 AATCAGTT
340047 GGTCAAACCA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (13 bp):
AATCAGTTAATCA
Found at i:343311 original size:208 final size:209
Alignment explanation
Indices: 342946--343363 Score: 829
Period size: 208 Copynumber: 2.0 Consensus size: 209
342936 TATATTCTTT
342946 AAGTTGTTTTTTAACATTCCCGCTGATGAAAAATTAACCTCGACAACCACAAAGTATGCAAAAGA
1 AAGTTGTTTTTTAACATTCCCGCTGATGAAAAATTAACCTCGACAACCACAAAGTATGCAAAAGA
343011 AGTGAAAATTATCATTTCATTCGTCAACATTCACAATCATCTGTCTTCATCATTTCTCAACCAAC
66 AGTGAAAATTATCATTTCATTCGTCAACATTCACAATCATCTGTCTTCATCATTTCTCAACCAAC
343076 AAATTGTATCAGTGAATCAATGGTTATATACCACAAATAAATTCAAACTTGAAGCCTCAGAACCC
131 AAATTGTATCAGTGAATCAATGGTTATATACCACAAATAAATTCAAACTTGAAGCCTCAGAACCC
343141 TAATGCACATTGAG
196 TAATGCACATTGAG
343155 AAGTTG-TTTTTAACATTCCCGCTGATGAAAAATTAACCTCGACAACCACAAAGTATGCAAAAGA
1 AAGTTGTTTTTTAACATTCCCGCTGATGAAAAATTAACCTCGACAACCACAAAGTATGCAAAAGA
343219 AGTGAAAATTATCATTTCATTCGTCAACATTCACAATCATCTGTCTTCATCATTTCTCAACCAAC
66 AGTGAAAATTATCATTTCATTCGTCAACATTCACAATCATCTGTCTTCATCATTTCTCAACCAAC
343284 AAATTGTATCAGTGAATCAATGGTTATATACCACAAATAAATTCAAACTTGAAGCCTCAGAACCC
131 AAATTGTATCAGTGAATCAATGGTTATATACCACAAATAAATTCAAACTTGAAGCCTCAGAACCC
343349 TAATGCACATTGAG
196 TAATGCACATTGAG
343363 A
1 A
343364 GACACAACTT
Statistics
Matches: 209, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
208 203 0.97
209 6 0.03
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (209 bp):
AAGTTGTTTTTTAACATTCCCGCTGATGAAAAATTAACCTCGACAACCACAAAGTATGCAAAAGA
AGTGAAAATTATCATTTCATTCGTCAACATTCACAATCATCTGTCTTCATCATTTCTCAACCAAC
AAATTGTATCAGTGAATCAATGGTTATATACCACAAATAAATTCAAACTTGAAGCCTCAGAACCC
TAATGCACATTGAG
Found at i:350517 original size:15 final size:15
Alignment explanation
Indices: 350496--350533 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
350486 GATATTTAGT
350496 TGGGCGGGCAGATG-
1 TGGGCGGGCAGATGC
*
350510 TGGGGCGGGCGGATGC
1 T-GGGCGGGCAGATGC
350526 TGGGCGGG
1 TGGGCGGG
350534 TAAGGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.08, C:0.16, G:0.63, T:0.13
Consensus pattern (15 bp):
TGGGCGGGCAGATGC
Found at i:352001 original size:24 final size:24
Alignment explanation
Indices: 351973--352022 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
351963 TTTTATTTTG
351973 TATGTTATCATTTTATTAGTGAAA
1 TATGTTATCATTTTATTAGTGAAA
351997 TATGTTATCATTTTATTAGTGAAA
1 TATGTTATCATTTTATTAGTGAAA
352021 TA
1 TA
352023 AATAACACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.50
Consensus pattern (24 bp):
TATGTTATCATTTTATTAGTGAAA
Found at i:353919 original size:45 final size:45
Alignment explanation
Indices: 353868--353956 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
353858 TTAACCAAAC
353868 ATTGTAATAC-TATATTTCTGCTAAATAAACCAAACACAACAATAA
1 ATTGTAAT-CTTATATTTCTGCTAAATAAACCAAACACAACAATAA
*
353913 ATTGTAATCTTATATTTCTGTTAAATAAACCAAACACAACAATA
1 ATTGTAATCTTATATTTCTGCTAAATAAACCAAACACAACAATA
353957 CAATATTCCC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 1 0.02
45 41 0.98
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.31
Consensus pattern (45 bp):
ATTGTAATCTTATATTTCTGCTAAATAAACCAAACACAACAATAA
Found at i:360227 original size:19 final size:19
Alignment explanation
Indices: 360203--360239 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
360193 ATGACCAACA
*
360203 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
360222 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
360240 CAGTATAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:360288 original size:20 final size:20
Alignment explanation
Indices: 360265--360336 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
360255 GTTTCCAGAT
*
360265 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
** * *
360285 TCGCAATACGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
*
360305 TCGCAACGCGATTGTGACTA
1 TCGCAACGCGATTATGACTA
360325 TCGCAACGCGAT
1 TCGCAACGCGAT
360337 AATACAAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.03
20 38 0.95
21 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:360994 original size:20 final size:20
Alignment explanation
Indices: 360969--361017 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
360959 GCGATTATCT
360969 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
360989 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
361009 TGTTGCGAT
1 CGTTGCGAT
361018 TTTCATTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:361023 original size:20 final size:20
Alignment explanation
Indices: 360985--361040 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
360975 GATAGTCAAA
* **
360985 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
361005 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
361025 TTGGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
361041 AAGTTTCAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.14, G:0.25, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Done.