Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004348.1 Hibiscus syriacus cultivar Beakdansim tig00009528_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: 86549
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:310 original size:13 final size:14
Alignment explanation
Indices: 281--316 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
271 CTCAAATCAA
*
281 TTTGTATCAATTTT
1 TTTGAATCAATTTT
295 TTTGAATCAA-TTT
1 TTTGAATCAATTTT
308 TTTGAATCA
1 TTTGAATCA
317 TTCAAGTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (14 bp):
TTTGAATCAATTTT
Found at i:622 original size:35 final size:35
Alignment explanation
Indices: 573--651 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
563 TGGGTTGGGC
*
573 ATGT-ATTAAAGTATTTTGGAATTT-GAGATTTAGA
1 ATGTAATTGAAGTATTTTGGAATTTAG-GATTTAGA
*
607 ATGTAATTGAAGTATTTTGGAATTTAGGGTTTAGA
1 ATGTAATTGAAGTATTTTGGAATTTAGGATTTAGA
642 ATGTAATTGA
1 ATGTAATTGA
652 TGTCTTTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
34 4 0.10
35 36 0.88
36 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGGAATTTAGGATTTAGA
Found at i:5124 original size:28 final size:28
Alignment explanation
Indices: 5093--5162 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
5083 TTTAGGGCTA
*
5093 AGTTTAAGATTTAAGTTTTAA-GGTTTAG
1 AGTTTAAGATTTAAG-GTTAAGGGTTTAG
* *
5121 AGTTTATGATTTGAGGTTAAGGGTTTAG
1 AGTTTAAGATTTAAGGTTAAGGGTTTAG
*
5149 -GATTTGAGATTTAA
1 AG-TTTAAGATTTAA
5163 ATGTTTCGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (28 bp):
AGTTTAAGATTTAAGGTTAAGGGTTTAG
Found at i:5137 original size:21 final size:21
Alignment explanation
Indices: 5113--5161 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5103 TTAAGTTTTA
*
5113 AGGTTTAGAGTTTATGATTTG
1 AGGTTTAGAGTTTAGGATTTG
* *
5134 AGGTTAAGGGTTTAGGATTTG
1 AGGTTTAGAGTTTAGGATTTG
*
5155 AGATTTA
1 AGGTTTA
5162 AATGTTTCGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.43
Consensus pattern (21 bp):
AGGTTTAGAGTTTAGGATTTG
Found at i:6461 original size:3 final size:3
Alignment explanation
Indices: 6453--6531 Score: 67
Period size: 3 Copynumber: 27.3 Consensus size: 3
6443 TTTTACTTAA
** * *
6453 ATT ATT ATT AAA ATT ATT ATT ATT ATT A-T ATA AAT A-T ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
6498 ATT ATAT AAT ATT ATT ATT ATT AAT A-T ATT ATT A
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT A
6532 CAAGGCCCAA
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
2 8 0.13
3 51 0.84
4 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:6479 original size:21 final size:21
Alignment explanation
Indices: 6453--6520 Score: 86
Period size: 21 Copynumber: 3.2 Consensus size: 21
6443 TTTTACTTAA
6453 ATTATTATTAAAATTATTATT
1 ATTATTATTAAAATTATTATT
6474 ATTATTA-TATAAATATATTATT
1 ATTATTATTA-AAAT-TATTATT
*
6496 A-TATTATATAATATTATTATT
1 ATTATTAT-TAAAATTATTATT
6517 ATTA
1 ATTA
6521 ATATATTATT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
20 2 0.05
21 24 0.59
22 13 0.32
23 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTATTATTAAAATTATTATT
Found at i:12726 original size:7 final size:7
Alignment explanation
Indices: 12713--12748 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
12703 CTCATCCAGC
12713 AAAGAAA
1 AAAGAAA
*
12720 GAAGAAA
1 AAAGAAA
12727 AAAGAAA
1 AAAGAAA
12734 AAAGAAA
1 AAAGAAA
*
12741 AAGGAAA
1 AAAGAAA
12748 A
1 A
12749 TTGAATCAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:15200 original size:114 final size:114
Alignment explanation
Indices: 15007--15219 Score: 372
Period size: 114 Copynumber: 1.9 Consensus size: 114
14997 TCGTAGTAGG
*
15007 AATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAA
1 AATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATAA
* *
15072 ACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTGCTCATAGTATA
66 ACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCATAGTATA
*
15121 AATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGA
1 AATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATAA
* *
15186 ACCCTAAAACCAATCATTGGAATTAAAAGATGAA
66 ACCCCAAAACCAATCATTAGAATTAAAAGATGAA
15220 CTGCATGATC
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 93 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (114 bp):
AATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATAA
ACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCATAGTATA
Found at i:16143 original size:35 final size:34
Alignment explanation
Indices: 16071--16136 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
16061 TTCAACCAGA
16071 AATAGAATATTGGGGCATTTTGAAGGCTCATAAC
1 AATAGAATATTGGGGCATTTTGAAGGCTCATAAC
* *
16105 AATATGAATATTTGGGCATTTTGAAGGTTCAT
1 AATA-GAATATTGGGGCATTTTGAAGGCTCAT
16137 CTCAATAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 4 0.14
35 25 0.86
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (34 bp):
AATAGAATATTGGGGCATTTTGAAGGCTCATAAC
Found at i:18554 original size:75 final size:76
Alignment explanation
Indices: 18374--19340 Score: 1708
Period size: 75 Copynumber: 12.9 Consensus size: 76
18364 CTATTTCCCA
18374 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATC-TTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
18437 AGCCTTAGGGT
66 AGCCTTAGGGT
18448 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
18512 AGCCTTAGGGT
66 AGCCTTAGGGT
18523 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
18587 AGCCTTAGGGT
66 AGCCTTAGGGT
*
18598 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
18663 AGCCTTAGGGT
66 AGCCTTAGGGT
18674 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGATC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
18737 ATCCTTAGGGT
66 AGCCTTAGGGT
*
18748 CATCTGTAAGTCCTTCAGTGCATGATGTTTCTAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
18813 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
18824 CATCTGTTAGTCCTTCAGTGCATGATG-TTCCAAAAAGCCTTTGGGATCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
18887 AGCCTTAGGGT
66 AGCCTTAGGGT
18898 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
18962 AACCTTAGGGT
66 AGCCTTAGGGT
18973 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTT-AA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
19037 AGCCTTAGGGT
66 AGCCTTAGGGT
*
19048 CATCTGTAAGTCCTTCAGTGCATGCTGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTT-AA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
19112 AGCCTTAGGGT
66 AGCCTTAGGGT
19123 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTT-AA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
19187 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
19198 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGATCTTTTTGATGTTTTCA
* *
19262 AAGTCTTCGGGT
65 AAGCCTTAGGGT
* *
19274 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGATCTTTTTGATGTTTTCA
19339 AA
65 AA
19341 ACCCTTCAAT
Statistics
Matches: 864, Mismatches: 18, Indels: 19
0.96 0.02 0.02
Matches are distributed among these distances:
74 164 0.19
75 475 0.55
76 223 0.26
77 2 0.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:19532 original size:15 final size:15
Alignment explanation
Indices: 19512--19598 Score: 65
Period size: 15 Copynumber: 5.8 Consensus size: 15
19502 TCATTTACTT
19512 AAATTATTATTATTA
1 AAATTATTATTATTA
19527 AAATTATTATTATT-
1 AAATTATTATTATTA
* *
19541 --ATTATTATAAATA
1 AAATTATTATTATTA
**
19554 TTATTATTATATATATA
1 AAATTATTAT-TAT-TA
*
19571 TATATTATTATTATT-
1 -AAATTATTATTATTA
19586 AAATATATTATTA
1 AAAT-TATTATTA
19599 CAAGGCCCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
12 10 0.17
14 3 0.05
15 30 0.51
16 2 0.03
17 5 0.08
18 9 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATTATTATTATTA
Found at i:19537 original size:18 final size:20
Alignment explanation
Indices: 19514--19598 Score: 99
Period size: 18 Copynumber: 4.3 Consensus size: 20
19504 ATTTACTTAA
19514 ATTATTATTATTA-AAAT-T
1 ATTATTATTATTATAAATAT
19532 ATTATTATTATTATTATAA-AT
1 ATTATTATTATTA-TA-AATAT
*
19553 ATTATTATTA-TATATATAT
1 ATTATTATTATTATAAATAT
19572 A-TATTATTATTATTAAATAT
1 ATTATTATTATTA-TAAATAT
19592 ATTATTA
1 ATTATTA
19599 CAAGGCCCAA
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
18 22 0.39
19 7 0.12
20 10 0.18
21 18 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTATTATTATTATAAATAT
Found at i:19540 original size:21 final size:22
Alignment explanation
Indices: 19514--19586 Score: 105
Period size: 21 Copynumber: 3.3 Consensus size: 22
19504 ATTTACTTAA
19514 ATTATTATTATTA-AAATTATT
1 ATTATTATTATTATAAATTATT
19535 ATTATTATTATTATAAA-TATT
1 ATTATTATTATTATAAATTATT
*
19556 ATTATTATATATATATATATTATT
1 ATTATTAT-TAT-TATAAATTATT
19580 ATTATTA
1 ATTATTA
19587 AATATATTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
21 25 0.53
22 6 0.13
23 5 0.11
24 11 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTATTATTATTATAAATTATT
Found at i:19597 original size:21 final size:20
Alignment explanation
Indices: 19514--19598 Score: 104
Period size: 21 Copynumber: 4.2 Consensus size: 20
19504 ATTTACTTAA
19514 ATTATTATTATTAAAATTATT
1 ATTATTATTATTAAAA-TATT
19535 ATTATTATTATTATAAATATT
1 ATTATTATTATTA-AAATATT
*
19556 ATTATTA-TA-T-ATATATAT
1 ATTATTATTATTAAAATAT-T
19574 ATTATTATTATTAAATATATT
1 ATTATTATTATTAAA-ATATT
19595 ATTA
1 ATTA
19599 CAAGGCCCAA
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
17 5 0.09
18 8 0.14
19 3 0.05
20 3 0.05
21 30 0.54
22 7 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTATTATTATTAAAATATT
Found at i:19598 original size:3 final size:3
Alignment explanation
Indices: 19514--19586 Score: 83
Period size: 3 Copynumber: 23.3 Consensus size: 3
19504 ATTTACTTAA
** * *
19514 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19562 ATAT ATAT ATAT ATT ATT ATT ATT A
1 AT-T AT-T AT-T ATT ATT ATT ATT A
19587 AATATATTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 50 0.82
4 11 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:26087 original size:12 final size:13
Alignment explanation
Indices: 26042--26087 Score: 60
Period size: 12 Copynumber: 3.6 Consensus size: 13
26032 AATTTCGTCC
26042 TTATATATATATAT
1 TTATAT-TATATAT
*
26056 TTATATTATA-AA
1 TTATATTATATAT
26068 TTATATTATATAT
1 TTATATTATATAT
26081 TTA-ATTA
1 TTATATTA
26088 CATTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 15 0.52
13 8 0.28
14 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATATTATATAT
Found at i:27297 original size:2 final size:2
Alignment explanation
Indices: 27290--27319 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27280 TTTTATTTTC
27290 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
27320 GTATTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31487 original size:21 final size:21
Alignment explanation
Indices: 31441--31497 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
31431 ACTTTGACGA
*
31441 AGAAGATAAAGCTAAAAAAAT
1 AGAAGATAAAGATAAAAAAAT
* *
31462 GGAAGA-AAAGATAAAAATATT
1 AGAAGATAAAGATAAAAA-AAT
*
31483 AGAAGATCAA-ATAAA
1 AGAAGATAAAGATAAA
31498 GATGGTCCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 10 0.34
21 17 0.59
22 2 0.07
ACGTcount: A:0.65, C:0.04, G:0.16, T:0.16
Consensus pattern (21 bp):
AGAAGATAAAGATAAAAAAAT
Found at i:38992 original size:105 final size:105
Alignment explanation
Indices: 38810--39643 Score: 1587
Period size: 105 Copynumber: 7.9 Consensus size: 105
38800 AGGTTTTACC
*
38810 CAGAGCCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
38875 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
38915 CAGAGCCAATTTCAACTTCGCAACGAGGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
38980 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
39020 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
39085 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
39125 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
39190 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
39230 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
39295 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
39335 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
39400 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
39440 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
39505 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* * *
39545 CAGAGCCAATTTCAACTTCGCAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
39610 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTC
39644 CCATTTTCAG
Statistics
Matches: 718, Mismatches: 10, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
105 713 0.99
106 5 0.01
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:41216 original size:2 final size:2
Alignment explanation
Indices: 41209--41248 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
41199 TTTTATTTTC
41209 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
41249 GTATTATTAT
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):
AT
Found at i:45680 original size:30 final size:30
Alignment explanation
Indices: 45635--45701 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
45625 CGAATATAGA
45635 TCGCCAAGTGATCTGGGCGACCAATAAAGG
1 TCGCCAAGTGATCTGGGCGACCAATAAAGG
* * *
45665 TCGCCAGGTGGTCTGGGCGACCAATGAAGG
1 TCGCCAAGTGATCTGGGCGACCAATAAAGG
45695 TCGCCAA
1 TCGCCAA
45702 TGAAGGTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.25, G:0.33, T:0.16
Consensus pattern (30 bp):
TCGCCAAGTGATCTGGGCGACCAATAAAGG
Found at i:45703 original size:13 final size:13
Alignment explanation
Indices: 45685--45713 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
45675 GTCTGGGCGA
45685 CCAATGAAGGTCG
1 CCAATGAAGGTCG
45698 CCAATGAAGGTCG
1 CCAATGAAGGTCG
45711 CCA
1 CCA
45714 GGTGGTCTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.14
Consensus pattern (13 bp):
CCAATGAAGGTCG
Found at i:45974 original size:49 final size:50
Alignment explanation
Indices: 45901--46006 Score: 178
Period size: 49 Copynumber: 2.1 Consensus size: 50
45891 TTTATCCTAT
* *
45901 TTTAGTATGTATTTATTTTTAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAATATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
45951 TTTAATATGTA-TTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAATATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
*
46000 TTCAATA
1 TTTAATA
46007 ATTTTTATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
49 43 0.81
50 10 0.19
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (50 bp):
TTTAATATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
Found at i:46393 original size:177 final size:177
Alignment explanation
Indices: 46097--46448 Score: 686
Period size: 177 Copynumber: 2.0 Consensus size: 177
46087 AAAATTTGTG
*
46097 AAATAATATTGTTGGTAGGGAGAAATAAATACATACTAAAATAGGATAAACAAGAAACATGTATG
1 AAATAATATCGTTGGTAGGGAGAAATAAATACATACTAAAATAGGATAAACAAGAAACATGTATG
46162 ACTAAATTATAATTAAACATAAATACTAAATAGTGGCTAAAATAACATGTTTACAAATTTCATGG
66 ACTAAATTATAATTAAACATAAATACTAAATAGTGGCTAAAATAACATGTTTACAAATTTCATGG
46227 CCAATTTCAAAAATTAAGGAAAATATATAAAACACATGAAATCAGGA
131 CCAATTTCAAAAATTAAGGAAAATATATAAAACACATGAAATCAGGA
46274 AAATAATATCGTTGGTAGGGAGAAATAAATACATACTAAAATAGGATAAACAAGAAACATGTATG
1 AAATAATATCGTTGGTAGGGAGAAATAAATACATACTAAAATAGGATAAACAAGAAACATGTATG
46339 ACTAAATTATAATTAAACATAAATACTAAATAGTGGCTAAAATAACATGTTTACAAATTTCATGG
66 ACTAAATTATAATTAAACATAAATACTAAATAGTGGCTAAAATAACATGTTTACAAATTTCATGG
*
46404 CCAATTTCGAAAATTAAGGAAAATATATAAAACACATGAAATCAG
131 CCAATTTCAAAAATTAAGGAAAATATATAAAACACATGAAATCAG
46449 TGATTAAAAT
Statistics
Matches: 173, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
177 173 1.00
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.26
Consensus pattern (177 bp):
AAATAATATCGTTGGTAGGGAGAAATAAATACATACTAAAATAGGATAAACAAGAAACATGTATG
ACTAAATTATAATTAAACATAAATACTAAATAGTGGCTAAAATAACATGTTTACAAATTTCATGG
CCAATTTCAAAAATTAAGGAAAATATATAAAACACATGAAATCAGGA
Found at i:46823 original size:30 final size:30
Alignment explanation
Indices: 46784--46845 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
46774 CCAGCATACA
*
46784 TGGCGACCTTCATTGGTCGCCCAGACCACC
1 TGGCAACCTTCATTGGTCGCCCAGACCACC
*
46814 TGGCAACCTTCATTGGTCGCCCAGATCACC
1 TGGCAACCTTCATTGGTCGCCCAGACCACC
46844 TG
1 TG
46846 ACGATCTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.18, C:0.37, G:0.23, T:0.23
Consensus pattern (30 bp):
TGGCAACCTTCATTGGTCGCCCAGACCACC
Found at i:47200 original size:10 final size:10
Alignment explanation
Indices: 47185--47218 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
47175 ACCATTTTTT
47185 AATATATATA
1 AATATATATA
47195 AATATATATA
1 AATATATATA
* *
47205 TATATATATT
1 AATATATATA
47215 AATA
1 AATA
47219 GTGATCGTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AATATATATA
Found at i:49975 original size:30 final size:31
Alignment explanation
Indices: 49898--49977 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
49888 ACTTGAATGT
* * * * *
49898 TTGGTATTACAAGAGAAACATTTTTAAAGGT
1 TTGGTGTTTCAAGAGAAACAATTTCAAAGGA
*
49929 TTTGTGTTTCAAGAGAAACAATTTCAAA-GA
1 TTGGTGTTTCAAGAGAAACAATTTCAAAGGA
49959 TTGGTGCTTT-AAGAGAAAC
1 TTGGTG-TTTCAAGAGAAAC
49978 TGTCTCAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 15 0.37
31 26 0.63
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.34
Consensus pattern (31 bp):
TTGGTGTTTCAAGAGAAACAATTTCAAAGGA
Found at i:50019 original size:37 final size:37
Alignment explanation
Indices: 49966--50050 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
49956 AGATTGGTGC
*
49966 TTTAAGAGAAACTGTCTCAAAAGAGACAAAACTTTGT
1 TTTAAGAGAAACTGTCTCAAAAGAGACAAAACTTAGT
* * * *
50003 TTTAAGGGAAATTGTCTCAAGAGAGACGAAACTTAGT
1 TTTAAGAGAAACTGTCTCAAAAGAGACAAAACTTAGT
* *
50040 TTCAAAAGAAA
1 TTTAAGAGAAA
50051 ATACCTCAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.26
Consensus pattern (37 bp):
TTTAAGAGAAACTGTCTCAAAAGAGACAAAACTTAGT
Found at i:50147 original size:29 final size:30
Alignment explanation
Indices: 50110--50177 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
50100 CGATTTTTTT
*
50110 AAGGAAAATAGATTAAAAGA-TTTTGCTTC
1 AAGGGAAATAGATTAAAAGATTTTTGCTTC
* * *
50139 AAGGGAAATTGATTCAAAGATTTTTGTTTC
1 AAGGGAAATAGATTAAAAGATTTTTGCTTC
50169 AAGGGAAAT
1 AAGGGAAAT
50178 TGTCTCCAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.50
30 17 0.50
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (30 bp):
AAGGGAAATAGATTAAAAGATTTTTGCTTC
Found at i:50164 original size:30 final size:29
Alignment explanation
Indices: 50110--50179 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 29
50100 CGATTTTTTT
* *
50110 AAGGAAAATAGATTAAAAGATTTTGCTTC
1 AAGGGAAATTGATTAAAAGATTTTGCTTC
* *
50139 AAGGGAAATTGATTCAAAGATTTTTGTTTC
1 AAGGGAAATTGATTAAAAGA-TTTTGCTTC
50169 AAGGGAAATTG
1 AAGGGAAATTG
50180 TCTCCAGAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (29 bp):
AAGGGAAATTGATTAAAAGATTTTGCTTC
Found at i:50191 original size:163 final size:162
Alignment explanation
Indices: 49998--50309 Score: 371
Period size: 163 Copynumber: 1.9 Consensus size: 162
49988 GAGACAAAAC
* *
49998 TTTGTTTTAAGGGAAATTGTCTCAAGAGAGACGAAACTTAGTTTCAAAAGAAAATACCTCAAGGG
1 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGAC-AAA---A-TTTCAAAAGAAAATACCTCAAGAG
* * * * *
50063 AGACAAAA-TT-TTCCAAGAGAAACTGTCTCGAGAGAGACG-ATTT-TTTTAAGGAAAATAGATT
61 AGACAAAATTTGTTCCAAAAGAAACTGTCTCAAGAGAGACGAATTTATTTCAAGGAAAACAAATT
*
50124 AAAAGATTTTGCTTCAAGGGAAATTGATTCAAAGATT
126 AAAAGATTTCGCTTCAAGGGAAATTGATTCAAAGATT
* * ** **
50161 TTTGTTTCAAGGGAAATTGTCTCCAGAGAGACAAAATTTTAAGGGAAAATGTCTCAAGAGAGACA
1 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTCAAAAGAAAATACCTCAAGAGAGACA
** * *
50226 AAATTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAAATTTATTTCAAGGAAAACAAATTTAAA
66 AAATTTGTTCCAAAAGAAACTGTCTCAAGAGAGACG-AATTTATTTCAAGGAAAACAAATTAAAA
*
50291 GATTTCGTTTCAAGGGAAA
130 GATTTCGCTTCAAGGGAAA
50310 CATTCTCAAG
Statistics
Matches: 125, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
158 26 0.21
159 3 0.02
160 24 0.19
162 7 0.06
163 65 0.52
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (162 bp):
TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTCAAAAGAAAATACCTCAAGAGAGACA
AAATTTGTTCCAAAAGAAACTGTCTCAAGAGAGACGAATTTATTTCAAGGAAAACAAATTAAAAG
ATTTCGCTTCAAGGGAAATTGATTCAAAGATT
Found at i:50214 original size:32 final size:32
Alignment explanation
Indices: 50169--50231 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
50159 TTTTTGTTTC
* *
50169 AAGGGAAATTGTCTCCAGAGAGACAAAATTTT
1 AAGGGAAAATGTCTCAAGAGAGACAAAATTTT
50201 AAGGGAAAATGTCTCAAGAGAGACAAAATTT
1 AAGGGAAAATGTCTCAAGAGAGACAAAATTT
50232 GTTTTAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (32 bp):
AAGGGAAAATGTCTCAAGAGAGACAAAATTTT
Found at i:50250 original size:36 final size:35
Alignment explanation
Indices: 50173--50267 Score: 97
Period size: 36 Copynumber: 2.8 Consensus size: 35
50163 TGTTTCAAGG
* * **
50173 GAAATTGTCTCCAGAGAGACAAAA---TTTTAAGG
1 GAAAATGTCTCAAGAGAGACAAAATTTTTTTAAAA
50205 GAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAA
1 GAAAATGTCTCAAGAGAGACAAAATTT-TTTTAAAA
* * *
50241 GAAACTGTCTCAAGGGAGACGAAATTT
1 GAAAATGTCTCAAGAGAGACAAAATTT
50268 ATTTCAAGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 22 0.42
36 30 0.58
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (35 bp):
GAAAATGTCTCAAGAGAGACAAAATTTTTTTAAAA
Found at i:50378 original size:101 final size:102
Alignment explanation
Indices: 50201--50883 Score: 463
Period size: 101 Copynumber: 6.7 Consensus size: 102
50191 ACAAAATTTT
50201 AAGGGAAA-ATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAAA
1 AAGGGAAACATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAAA
* * *
50265 TTTATTTCAAGGAAAACAAATTTAAAGATTTCGTTTC
66 TTTGTTTTAAGGAAAACAAATTCAAAGATTTCGTTTC
** * *
50302 AAGGGAAACAT-TCTCAAGAGAGACAAAATTTGTTTTAAAATTAACTGTCTCAAGGGACATGAAA
1 AAGGGAAACATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAAA
* **
50366 TTTGTTTTAAGGAAAACAGATTCAAAGATTTTTTTTC
66 TTTGTTTTAAGGAAAACAAATTCAAAGATTTCGTTTC
* * *
50403 ACGGGAAAC-TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAATGGAGACGAAA
1 AAGGGAAACATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAAA
* *
50467 TTTGTTTTAAGAGAAACTGTCTCAAGATAGACAAA-ACTTT-GTTTC
66 TTTGTTTTAAG-GAAA-----ACAA-AT--TCAAAGA-TTTCGTTTC
* * *** * ** * *
50512 AA-GGAAA-ATAATTTC-A-A-AG---TTTTTTTTTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 AAGGGAAACAT-GTCTCAAGAGAGACAAAATTTGTTTT-AAAAGAAACTGTCTCAAGGGAGACGA
* *
50569 AATTTGTTTTAAGAGAAAATGTCTTAAGAGATAT-AAA-ATAT-GTTTT
64 AATTTGTTTTAAG-GAAAA---C---A-A-AT-TCAAAGATTTCGTTTC
* * * *
50615 AAGAGAAAC-TGTCTCAAGAGAGACAAAACTTTG-TTTCAAGGAAATTGTCTCAAGGGAGACGAA
1 AAGGGAAACATGTCTCAAGAGAGACAAAA-TTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAA
* * **
50678 ATTTGTTTAAAGGAAAACAGATTCAAAGATTTTTTTTC
65 ATTTGTTTTAAGGAAAACAAATTCAAAGATTTCGTTTC
* ** * * * *
50716 AAGGGAAAC-TGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATTGTCTCAAGAGATACAAAA
1 AAGGGAAACATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAAA
* * * **** * *
50780 TTTATTTCAAGGGAAATGGTTTCAATG-TTTATGTTTC
66 TTTGTTTTAAGGAAAACAAATTCAAAGATTT-CGTTTC
* * * ** * * *
50817 AAGAGAAAC-TGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAA
1 AAGGGAAACATGTCTCAAGAGAGACAAAA-TTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAA
50881 ATT
65 ATT
50884 CATTTCAAGG
Statistics
Matches: 471, Mismatches: 74, Indels: 73
0.76 0.12 0.12
Matches are distributed among these distances:
98 1 0.00
99 5 0.01
100 11 0.02
101 261 0.55
102 42 0.09
103 18 0.04
104 51 0.11
105 2 0.00
106 8 0.02
107 8 0.02
108 42 0.09
109 12 0.03
110 10 0.02
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (102 bp):
AAGGGAAACATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAAA
TTTGTTTTAAGGAAAACAAATTCAAAGATTTCGTTTC
Found at i:50454 original size:36 final size:36
Alignment explanation
Indices: 50407--50897 Score: 341
Period size: 36 Copynumber: 14.1 Consensus size: 36
50397 TTTTTCACGG
*
50407 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
* *
50443 GAAACTGTCTCAATG-GAGACGAAATTTGTTTTAAGA
1 GAAACTGTCTCAA-GAGAGACAAAATTTGTTTCAAGA
*
50479 GAAACTGTCTCAAGATAGACAAAACTTTGTTTCAAG-
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGA
* * * **** * *
50515 GAAAATAATTTC-A-A-AG--TTTTTTTTTTTCAAGG
1 GAAACT-GTCTCAAGAGAGACAAAATTTGTTTCAAGA
*
50547 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
* * * * * *
50583 GAAAATGTCTTAAGAGATATAAAATATGTTTTAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
50619 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAG-
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGA
* * * *
50655 GAAATTGTCTCAAGGGAGACGAAATTTGTTTAAAG-
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
* * * *
50690 GAAAACAGAT-TC-A-A-AG----ATTTTTTTTCAAGG
1 G-AAACTG-TCTCAAGAGAGACAAAATTTGTTTCAAGA
*
50720 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
* * * *
50756 GAAATTGTCTCAAGAGATACAAAATTTATTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
* * *
50792 GAAA-TGGTTTC-A-A-TG-----TTTATGTTTCAAGA
1 GAAACT-GTCTCAAGAGAGACAAAATT-TGTTTCAAGA
* *
50821 GAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGA
* ** *
50858 GAAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
50894 GAAA
1 GAAA
50898 TGTTTTCAAT
Statistics
Matches: 357, Mismatches: 64, Indels: 68
0.73 0.13 0.14
Matches are distributed among these distances:
28 3 0.01
29 33 0.09
30 4 0.01
31 14 0.04
32 9 0.03
33 3 0.01
34 5 0.01
35 16 0.04
36 213 0.60
37 55 0.15
38 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
Found at i:50583 original size:140 final size:137
Alignment explanation
Indices: 50313--50658 Score: 466
Period size: 140 Copynumber: 2.5 Consensus size: 137
50303 AGGGAAACAT
* ** * *
50313 TCTCAAGAGAGACAAAATTTGTTTTAAAATTAACTGTCTCAAG-GGACATGAAA-TTTGTTTTAA
1 TCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAAGACA--AAACTTTGTTTCAA
*
50376 GGAAAACAGATTCAAAGATTTTTTTTCACGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAA
64 GGAAAACAGATTCAAAGATTTTTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAA
*
50441 GAGAAACTG
129 GAGAAAATG
*
50450 TCTCAATG-GAGACGAAATTTGTTTTAAGAGAAACTGTCTCAAGATAGACAAAACTTTGTTTCAA
1 TCTCAA-GAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGA-AGACAAAACTTTGTTTCAA
* *
50514 GGAAAATA-ATTTCAAAGTTTTTTTTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTT
64 GGAAAACAGA-TTCAAAG--ATTTTTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTT
50578 TAAGAGAAAATG
126 TAAGAGAAAATG
* * * *
50590 TCTTAAGAGATATAAAATATGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAG
1 TCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGA-AGACAAAACTTTGTTTCAAG
50655 GAAA
65 GAAA
50659 TTGTCTCAAG
Statistics
Matches: 185, Mismatches: 16, Indels: 13
0.86 0.07 0.06
Matches are distributed among these distances:
137 41 0.22
138 24 0.13
139 5 0.03
140 115 0.62
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (137 bp):
TCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAAGACAAAACTTTGTTTCAAGG
AAAACAGATTCAAAGATTTTTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGA
GAAAATG
Found at i:50862 original size:37 final size:37
Alignment explanation
Indices: 50811--50973 Score: 148
Period size: 37 Copynumber: 4.6 Consensus size: 37
50801 TCAATGTTTA
* *
50811 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
*
50848 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
** * ** *
50884 CATTTCAAGGGAAA-TGT-T-------TTCAATATTT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
*
50912 ATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
*
50950 TGTTTCAAGGGAAATTATCTCAAG
1 TGTTTCAAGGGAAACTATCTCAAG
50974 CGAGGTAAAA
Statistics
Matches: 97, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
27 4 0.04
28 2 0.02
29 11 0.11
30 2 0.02
31 1 0.01
34 1 0.01
35 2 0.02
36 14 0.14
37 53 0.55
38 7 0.07
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
Found at i:50880 original size:102 final size:102
Alignment explanation
Indices: 50607--50973 Score: 497
Period size: 102 Copynumber: 3.6 Consensus size: 102
50597 AGATATAAAA
* * * *
50607 TATGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAA-GGAAATTGTCTCAAGGG
1 TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAATTATCTCAAGAG
* * * * ** * *
50671 AGACGAAATTTGTTTAAAGGAAAACAGATTCAAAGATT
66 AGACAAAATTTATTTCAAGGGAAATGGTTTCAATG-TT
* * *
50709 T-TTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAATTGTCTCAAGAG
1 TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAATTATCTCAAGAG
*
50772 ATACAAAATTTATTTCAAGGGAAATGGTTTCAATGTT
66 AGACAAAATTTATTTCAAGGGAAATGGTTTCAATGTT
* *
50809 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAG
1 TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAATTATCTCAAGAG
* * *
50874 AGACAAAATTCATTTCAAGGGAAATGTTTTCAATATT
66 AGACAAAATTTATTTCAAGGGAAATGGTTTCAATGTT
* *
50911 TATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAATTATCTCAAG
1 TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAATTATCTCAAG
50974 CGAGGTAAAA
Statistics
Matches: 238, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
100 13 0.05
101 104 0.44
102 121 0.51
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (102 bp):
TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAATTATCTCAAGAG
AGACAAAATTTATTTCAAGGGAAATGGTTTCAATGTT
Found at i:50984 original size:102 final size:101
Alignment explanation
Indices: 50534--50973 Score: 490
Period size: 102 Copynumber: 4.3 Consensus size: 101
50524 TTCAAAGTTT
* * * * * * *
50534 TTTTTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTTAAGAG
1 TTTTGTTTCAAGGGAAATTATCTCAAGAGAGACAAAATTTATTTCAAG-GGAAATGT-TT--CA-
* *
50599 ATATAAAATATGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
61 ATAT---TTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * * * * * * *
50643 CTTTGTTTCAA-GGAAATTGTCTCAAGGGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAGA
1 TTTTGTTTCAAGGGAAATTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAA-TGTTTC-AATA
* *
50707 TTT-TTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
64 TTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
50744 -TTTGTTTCAAGGGAAATTGTCTCAAGAGATACAAAATTTATTTCAAGGGAAATGGTTTCAATGT
1 TTTTGTTTCAAGGGAAATTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAAT-GTTTCAATAT
*
50808 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
65 TTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
50845 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATAT
1 TTTTGTTTCAAGGGAAATTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAATG-TTTCAATAT
* *
50910 TTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA
65 TTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
50947 TTTTGTTTCAAGGGAAATTATCTCAAG
1 TTTTGTTTCAAGGGAAATTATCTCAAG
50974 CGAGGTAAAA
Statistics
Matches: 290, Mismatches: 34, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
100 15 0.05
101 102 0.35
102 120 0.41
105 3 0.01
106 1 0.00
107 7 0.02
108 33 0.11
109 9 0.03
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (101 bp):
TTTTGTTTCAAGGGAAATTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAATGTTTCAATATT
TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:58173 original size:42 final size:42
Alignment explanation
Indices: 58065--58201 Score: 150
Period size: 42 Copynumber: 3.2 Consensus size: 42
58055 TAAACAGCCT
* *
58065 GATTGAAAAAATTATGGAGCTTAATTCTAAAAGTAAAAAGTGA
1 GATTGAAAAAATTA-GGAGCTTAATTATAAAGGTAAAAAGTGA
* * *
58108 GATTAAAAAAAATTAGG-GCCTTAATTATAATGGTAAAAAGTTA
1 GATT-GAAAAAATTAGGAG-CTTAATTATAAAGGTAAAAAGTGA
* * * * *
58151 TATTGAAAAAATGAGGAGCTTAACTATAAAGGTACAAAGTGG
1 GATTGAAAAAATTAGGAGCTTAATTATAAAGGTAAAAAGTGA
58193 GATTGAAAA
1 GATTGAAAA
58202 TTTAGGATTA
Statistics
Matches: 77, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
42 38 0.49
43 30 0.39
44 9 0.12
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (42 bp):
GATTGAAAAAATTAGGAGCTTAATTATAAAGGTAAAAAGTGA
Found at i:59088 original size:179 final size:179
Alignment explanation
Indices: 58781--59141 Score: 695
Period size: 179 Copynumber: 2.0 Consensus size: 179
58771 TCAGAATAAT
* *
58781 AAAGGGCAAACTACTTTTTGGTCATTAGCTTATTATTTAATTTTTATTTTGGTCATTCAATTATT
1 AAAGGGAAAACTACTTTTTGGTCATTAGCTTATTATTTAATTTCTATTTTGGTCATTCAATTATT
58846 ATTATTATTTAAAAAATATATAATATTACGTTTTGATTATGTTTTGATCATATGCATTAAAAATT
66 ATTATTATTTAAAAAATATATAATATTACGTTTTGATTATGTTTTGATCATATGCATTAAAAATT
58911 AATACCGATGTTGACATGACACTATAAGATAATACCAAATCAACATTGA
131 AATACCGATGTTGACATGACACTATAAGATAATACCAAATCAACATTGA
58960 AAAGGGAAAACTACTTTTTGGTCATTAGCTTATTATTTAATTTCTATTTTGGTCATTCAATTATT
1 AAAGGGAAAACTACTTTTTGGTCATTAGCTTATTATTTAATTTCTATTTTGGTCATTCAATTATT
*
59025 ATTATTATTTAAAATATATATAATATTACGTTTTGATTATGTTTTGATCATATGCATTAAAAATT
66 ATTATTATTTAAAAAATATATAATATTACGTTTTGATTATGTTTTGATCATATGCATTAAAAATT
59090 AATACCGATGTTGACATGACACTATAAGATAATACCAAATCAACATTGA
131 AATACCGATGTTGACATGACACTATAAGATAATACCAAATCAACATTGA
59139 AAA
1 AAA
59142 ATAAAAACTG
Statistics
Matches: 179, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
179 179 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (179 bp):
AAAGGGAAAACTACTTTTTGGTCATTAGCTTATTATTTAATTTCTATTTTGGTCATTCAATTATT
ATTATTATTTAAAAAATATATAATATTACGTTTTGATTATGTTTTGATCATATGCATTAAAAATT
AATACCGATGTTGACATGACACTATAAGATAATACCAAATCAACATTGA
Found at i:62879 original size:13 final size:13
Alignment explanation
Indices: 62861--62889 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
62851 GATTTAAGAC
62861 GGCACCGTATTTT
1 GGCACCGTATTTT
62874 GGCACCGTATTTT
1 GGCACCGTATTTT
62887 GGC
1 GGC
62890 TAGGGTTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.24, G:0.28, T:0.34
Consensus pattern (13 bp):
GGCACCGTATTTT
Found at i:63064 original size:2 final size:2
Alignment explanation
Indices: 63057--63109 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
63047 TTTTCACTCA
*
63057 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
63099 TC TC TC TC TC T
1 TC TC TC TC TC T
63110 GATAGTATGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:65597 original size:6 final size:7
Alignment explanation
Indices: 65580--65605 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
65570 TTACCAACCA
65580 AAAAAAT
1 AAAAAAT
65587 AAAAAAT
1 AAAAAAT
65594 AAAAAAT
1 AAAAAAT
65601 AAAAA
1 AAAAA
65606 CCCGATCTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:77726 original size:7 final size:7
Alignment explanation
Indices: 77714--77753 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
77704 ATTTGTACGG
77714 ATTCCGT
1 ATTCCGT
77721 ATTCCGT
1 ATTCCGT
77728 ATTCCGT
1 ATTCCGT
77735 ATTCCGT
1 ATTCCGT
77742 ATTCCGT
1 ATTCCGT
77749 ATTCC
1 ATTCC
77754 CTTCAGTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.15, C:0.30, G:0.12, T:0.42
Consensus pattern (7 bp):
ATTCCGT
Found at i:78273 original size:17 final size:18
Alignment explanation
Indices: 78236--78276 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
78226 ATATTATGTA
78236 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
*
78254 TTTACTTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
78271 TTTAAT
1 TTTAAT
78277 AATATAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:80105 original size:30 final size:29
Alignment explanation
Indices: 80044--80105 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
80034 ACTGCTACGA
* *
80044 GTGTTAGATCGAGAAATATAATCTGACCG
1 GTGTTAGATCAAGAAATATAATCTCACCG
*
80073 GTGTTAGATCAATAAATAT-ATCGATCACCG
1 GTGTTAGATCAAGAAATATAATC--TCACCG
80103 GTG
1 GTG
80106 ATTTTTCAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.11
29 17 0.61
30 8 0.29
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.29
Consensus pattern (29 bp):
GTGTTAGATCAAGAAATATAATCTCACCG
Found at i:81776 original size:36 final size:36
Alignment explanation
Indices: 81729--81868 Score: 203
Period size: 36 Copynumber: 3.9 Consensus size: 36
81719 TGAATAAGAA
*
81729 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAAAT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
*
81765 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGAA-
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAA-AAT
*
81801 GAACGAAAGGAAGCATCGGCACTTTCGATTC-AAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
* * *
81836 GAACGGAATGAAGCATCCGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAA
81869 TTGTTCATCT
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
34 1 0.01
35 29 0.31
36 62 0.66
37 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (36 bp):
GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
Found at i:83256 original size:39 final size:40
Alignment explanation
Indices: 83188--83271 Score: 136
Period size: 39 Copynumber: 2.1 Consensus size: 40
83178 TACATATCCG
*
83188 ACACTGTCCATACCTTTGATCATCTAACCCTAACCCAACA
1 ACACAGTCCATACCTTTGATCATCTAACCCTAACCCAACA
83228 ACACAGTCCATGA-CTTTG-TCATCTAACCCTAACCCAACA
1 ACACAGTCCAT-ACCTTTGATCATCTAACCCTAACCCAACA
83267 ACACA
1 ACACA
83272 TTTGACTACT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
39 26 0.62
40 15 0.36
41 1 0.02
ACGTcount: A:0.35, C:0.37, G:0.06, T:0.23
Consensus pattern (40 bp):
ACACAGTCCATACCTTTGATCATCTAACCCTAACCCAACA
Found at i:86117 original size:20 final size:19
Alignment explanation
Indices: 86079--86117 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
86069 TATTTAGGAA
**
86079 AATATGTTAAATTTAATTT
1 AATATGTTAAAAATAATTT
86098 AATATGTTAAAAAATAATTT
1 AATATGTT-AAAAATAATTT
86118 TTTTGCATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
AATATGTTAAAAATAATTT
Done.