Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000560.1 Hibiscus syriacus cultivar Beakdansim tig00001093_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: 95159
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:912 original size:2 final size:2
Alignment explanation
Indices: 905--985 Score: 155
Period size: 2 Copynumber: 41.0 Consensus size: 2
895 TATAAAATTA
905 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
947 AT AT AT AT AT AT AT AT AT -T 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
986 GAAATAAAAC
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 77 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1274 original size:26 final size:26
Alignment explanation
Indices: 1244--1295 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1234 CGAATAATGA
*
1244 GATGCACTAATTTTTTTTGGATAATT
1 GATGCACTAATTTTTATTGGATAATT
*
1270 GATGCACTAATTTTTATTGGCTAATT
1 GATGCACTAATTTTTATTGGATAATT
1296 TGATAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.48
Consensus pattern (26 bp):
GATGCACTAATTTTTATTGGATAATT
Found at i:4225 original size:21 final size:21
Alignment explanation
Indices: 4187--4226 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4177 ATATATATAA
* *
4187 TATTAAATGAATTTATTGAGT
1 TATTAAATGAAATAATTGAGT
*
4208 TATTAAATTAAATAATTGA
1 TATTAAATGAAATAATTGA
4227 TTTAAGTGAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (21 bp):
TATTAAATGAAATAATTGAGT
Found at i:10827 original size:2 final size:2
Alignment explanation
Indices: 10820--10845 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10810 CACGAGAAAG
10820 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
10846 TCCTCCCCCT
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:11632 original size:14 final size:14
Alignment explanation
Indices: 11613--11640 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11603 CTTCAGGCTT
11613 TGTATATACAAATA
1 TGTATATACAAATA
11627 TGTATATACAAATA
1 TGTATATACAAATA
11641 AATACAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
TGTATATACAAATA
Found at i:17539 original size:39 final size:39
Alignment explanation
Indices: 17496--17632 Score: 168
Period size: 39 Copynumber: 3.5 Consensus size: 39
17486 ACATGTTGGA
* *
17496 GCATCAAGAGCTGCAAGCCCGGGTGATGAGCATCCTGTT
1 GCATCAAGAGCTGCAAGTCCGGATGATGAGCATCCTGTT
* *
17535 GCATCGAGAGCTGCAAGTCCGGATGATGAGCATCATGTT
1 GCATCAAGAGCTGCAAGTCCGGATGATGAGCATCCTGTT
* * * * *
17574 ACATCGAGAGTTGCAAGTCCGGATGATGAGCATTCTGCT
1 GCATCAAGAGCTGCAAGTCCGGATGATGAGCATCCTGTT
*
17613 GCGTCAAGAG-TGGCAAGTCC
1 GCATCAAGAGCT-GCAAGTCC
17633 TGCTTTGGTT
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
38 1 0.01
39 84 0.99
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.22
Consensus pattern (39 bp):
GCATCAAGAGCTGCAAGTCCGGATGATGAGCATCCTGTT
Found at i:23752 original size:7 final size:7
Alignment explanation
Indices: 23740--23775 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
23730 CAACAGTTGT
23740 GGGAGGA
1 GGGAGGA
23747 GGGAGGA
1 GGGAGGA
23754 GGGAGGA
1 GGGAGGA
23761 GGGAGGA
1 GGGAGGA
23768 -GGAGGA
1 GGGAGGA
23774 GG
1 GG
23776 ACCTTTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.28, C:0.00, G:0.72, T:0.00
Consensus pattern (7 bp):
GGGAGGA
Found at i:28204 original size:13 final size:13
Alignment explanation
Indices: 28186--28214 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
28176 AGAAAATTGT
28186 TTCTTATGAAATA
1 TTCTTATGAAATA
28199 TTCTTATGAAATA
1 TTCTTATGAAATA
28212 TTC
1 TTC
28215 AGGATCCTAG
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:0.34, C:0.10, G:0.07, T:0.48
Consensus pattern (13 bp):
TTCTTATGAAATA
Found at i:31874 original size:44 final size:44
Alignment explanation
Indices: 31826--31909 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
31816 GGAATATGTA
* *
31826 GGAA-TTGAAATCCAATTCCATATTCTGTTTGGTTGGCAGAAAAT
1 GGAATTTG-AATCCAATTCCATATTCTATTTGGTTCGCAGAAAAT
*
31870 GGAATTTGAATCCAATTTCATATTCTATTTGGTTCGCAGA
1 GGAATTTGAATCCAATTCCATATTCTATTTGGTTCGCAGA
31910 CATGTCAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 33 0.92
45 3 0.08
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (44 bp):
GGAATTTGAATCCAATTCCATATTCTATTTGGTTCGCAGAAAAT
Found at i:32981 original size:38 final size:38
Alignment explanation
Indices: 32926--33009 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 38
32916 CCCGAACCCG
*
32926 ACCCGACCCAATCCGACCTGAATATCACACATAAAAAA
1 ACCCGACCCAATCCGACCCGAATATCACACATAAAAAA
* *
32964 ACCCGACCTAA-CTCGACCCGAATATCACAC-TTAAAAA
1 ACCCGACCCAATC-CGACCCGAATATCACACATAAAAAA
*
33001 ATCCGACCC
1 ACCCGACCC
33010 GAACAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
37 14 0.35
38 26 0.65
ACGTcount: A:0.40, C:0.37, G:0.08, T:0.14
Consensus pattern (38 bp):
ACCCGACCCAATCCGACCCGAATATCACACATAAAAAA
Found at i:33249 original size:264 final size:251
Alignment explanation
Indices: 32367--33229 Score: 949
Period size: 264 Copynumber: 3.4 Consensus size: 251
32357 TATAAGGTAA
*
32367 AATTATATATTTTTTTCGGGTCGGTCCGGTTTTTTT-ACCCTAAACCCGAACCCGACCCGACCCG
1 AATTATATA-TATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCG-A----ACCCGA-CCG
* * *
32431 AATATCACACTTAAAAAAA--C--CCGACTCG---T-CTCGACCCGAATATTACACTTAAAAAAA
59 AATATCACACTTAAAAAAACTCAACCGACCCGACCTAATC-ACCCGAATATCACACTTAAAAAAA
* *
32488 TGACCCGACCCGAACAAAATAAAATTTCATCCGACCCTACCCGAATATATGAATTAGAAATCCGA
123 T---CCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCGA
* *
32553 CCCGACCCGAAATAATAAAAAAAATATTTTTATTTAATAAAAACAGTGATTTAATCCGACTCGAC
185 CCCGACCCGAAATAAT-AAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGAC
32618 CTG
249 CTG
* * *
32621 AATTATATATATATTTTTGGGTCGGTCCGGTTTTTTTCACCGTAAACCCGAACCCGAGCCAAATA
1 AA-T-TATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGA-CCGAATA
* * *
32686 TCACACTT--AAAAA--CACCCGACCCGA-C---TCGATCTGAATATCACACTTAAAAAACCCGA
63 TCACACTTAAAAAAACTCAACCGACCCGACCTAATC-ACCCGAATATCACACTTAAAAAA----A
* * *
32743 CCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATAAGAATTAGAAATCTGACCC
123 TCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCGACCC
* * * *
32808 GATCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGGGACTTAATCCGACCCGACCCG
188 GACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCTG
* *
32872 AATTATATATATTTTCGGATCAGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGACCCA-
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGA-CCGA---AT
* * * * ***
32936 ATC-CGACCTGAATATCACACATAAAAAAACCCGACCTAACTCGACCCGAATATCACACTT-AAA
62 ATCAC-A-CTTAA-A-AAAAC-TCAACCGACCCGACCTAA-TC-ACCCGAATATCACACTTAAAA
32999 AAATCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCGA
120 AAATCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCG-
33064 CCCAACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACC
184 ----ACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACC
33129 CGACCTG
245 CGACCTG
*
33136 AATTATATATATTTTCGGGTCGGCCCGGTTTTTTTCACCCTAAACCCG-ACCCGACTCGAATATC
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGAC-CGAATATC
*
33200 ACACTTAAAAAAACTCGATCCGACCCGACC
65 ACACTTAAAAAAACTC-AACCGACCCGACC
33230 AAAATAAAAT
Statistics
Matches: 518, Mismatches: 54, Indels: 70
0.81 0.08 0.11
Matches are distributed among these distances:
249 57 0.11
250 2 0.00
251 102 0.20
252 75 0.14
254 2 0.00
255 28 0.05
256 19 0.04
257 1 0.00
258 12 0.02
259 67 0.13
260 6 0.01
261 4 0.01
262 2 0.00
263 14 0.03
264 127 0.25
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (251 bp):
AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCGAATATCA
CACTTAAAAAAACTCAACCGACCCGACCTAATCACCCGAATATCACACTTAAAAAAATCCGACCC
GAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCGACCCGACCCGAA
ATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCTG
Found at i:36244 original size:41 final size:41
Alignment explanation
Indices: 36199--36283 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 41
36189 AAAGACTCAC
*
36199 TCACTAAAATCATGTATATAATACC-AGTTAATCTAAATTAA
1 TCACTAAAATCAAGTATATAATACCGA-TTAATCTAAATTAA
* * *
36240 TCACTAAAATCAAGTATGTAATGCCGATTAATCTGAATTAA
1 TCACTAAAATCAAGTATATAATACCGATTAATCTAAATTAA
36281 TCA
1 TCA
36284 GGACAAAGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 38 0.97
42 1 0.03
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (41 bp):
TCACTAAAATCAAGTATATAATACCGATTAATCTAAATTAA
Found at i:36630 original size:41 final size:40
Alignment explanation
Indices: 36568--36698 Score: 145
Period size: 40 Copynumber: 3.2 Consensus size: 40
36558 GAACTCCAAT
* * * * ***
36568 TTCGCAACGCGAATATATAAATCACATTGCATTTTTTCAAA
1 TTCGCAACGCGAATTTGTAAATCACAATACATAAGTT-AAA
* *
36609 TTCGCAACGCGAATTTGTAAATCGCAATACATAAGTTAGA
1 TTCGCAACGCGAATTTGTAAATCACAATACATAAGTTAAA
* * *
36649 TTCGCAACGCGAATTTGTAAATCACAACACATAAGTCAAT
1 TTCGCAACGCGAATTTGTAAATCACAATACATAAGTTAAA
36689 TTCGCAACGC
1 TTCGCAACGC
36699 AAAAGTCAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 47 0.62
41 29 0.38
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (40 bp):
TTCGCAACGCGAATTTGTAAATCACAATACATAAGTTAAA
Found at i:36663 original size:40 final size:39
Alignment explanation
Indices: 36607--36741 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 39
36597 CATTTTTTCA
* * *
36607 AATTCGCAACGCGAATTTGTAAATCGCAATACATAAGTT
1 AATTCGCAACGCGAATTTGTAAATCACAACACATAAGTC
36646 AGATTCGCAACGCGAATTTGTAAATCACAACACATAAGTC
1 A-ATTCGCAACGCGAATTTGTAAATCACAACACATAAGTC
** * * *
36686 AATTTCGCAACGC-AA-AAGTCAAATTCGCAACGCAAAAGTC
1 AA-TTCGCAACGCGAATTTGT-AAA-TCACAACACATAAGTC
36726 AAATTCGCAACGCGAA
1 -AATTCGCAACGCGAA
36742 ACACAATATT
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
38 2 0.02
39 7 0.09
40 69 0.84
41 4 0.05
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (39 bp):
AATTCGCAACGCGAATTTGTAAATCACAACACATAAGTC
Found at i:36704 original size:20 final size:20
Alignment explanation
Indices: 36681--36738 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
36671 CACAACACAT
*
36681 AAGTCAATTTCGCAACGCAA
1 AAGTCAAATTCGCAACGCAA
36701 AAGTCAAATTCGCAACGCAA
1 AAGTCAAATTCGCAACGCAA
36721 AAGTCAAATTCGCAACGC
1 AAGTCAAATTCGCAACGC
36739 GAAACACAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.41, C:0.26, G:0.16, T:0.17
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCAA
Found at i:36877 original size:22 final size:22
Alignment explanation
Indices: 36852--36897 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
36842 CTACGGCGAC
*
36852 ATCCGTCCCCATCTCCGACGAA
1 ATCCATCCCCATCTCCGACGAA
36874 ATCCATCCCCATCTCCGACGAA
1 ATCCATCCCCATCTCCGACGAA
36896 AT
1 AT
36898 ATGTCTATCT
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:0.26, C:0.43, G:0.11, T:0.20
Consensus pattern (22 bp):
ATCCATCCCCATCTCCGACGAA
Found at i:39462 original size:42 final size:42
Alignment explanation
Indices: 39415--39554 Score: 122
Period size: 42 Copynumber: 3.3 Consensus size: 42
39405 GATGCACCTA
*
39415 TCATCATTCAAGAGGCATCTCCTATCGTTCAAGAGGTCACTC
1 TCATCATTCAAGAGGCCTCTCCTATCGTTCAAGAGGTCACTC
* * * * * * *
39457 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGCCTCTCCTATCGTTCAAGAGGTCACTC
* * * *
39499 TCATCGTTCAAGAGGCCTCT-GTCATCGTTCAAGAGGTCTCGC
1 TCATCATTCAAGAGGCCTCTCCT-ATCGTTCAAGAGGTCACTC
* *
39541 TCGTCGTTCAAGAG
1 TCATCATTCAAGAG
39555 CCCGATTCAT
Statistics
Matches: 76, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
41 2 0.03
42 72 0.95
43 2 0.03
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCTCTCCTATCGTTCAAGAGGTCACTC
Found at i:39495 original size:21 final size:21
Alignment explanation
Indices: 39438--39534 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
39428 GGCATCTCCT
* * *
39438 ATCGTTCAAGAGGTCACTCTC
1 ATCGTTCAAGAGGCCCCTGTC
* * **
39459 ATC-ATCGAAGAAGCCCCTCCC
1 ATCGTTC-AAGAGGCCCCTGTC
*
39480 ACCGTTCAAGAGGCCCCTGTC
1 ATCGTTCAAGAGGCCCCTGTC
*
39501 ATCGTTCAAGAGGCCTCTGTC
1 ATCGTTCAAGAGGCCCCTGTC
39522 ATCGTTCAAGAGG
1 ATCGTTCAAGAGG
39535 TCTCGCTCGT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
20 2 0.03
21 58 0.94
22 2 0.03
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.23
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTGTC
Found at i:39547 original size:21 final size:21
Alignment explanation
Indices: 39482--39554 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
39472 CCCCTCCCAC
*
39482 CGTTCAAGAGGCCCCTGTCAT
1 CGTTCAAGAGGCCTCTGTCAT
39503 CGTTCAAGAGGCCTCTGTCAT
1 CGTTCAAGAGGCCTCTGTCAT
* *
39524 CGTTCAAGAGGTCTC-GCTCGT
1 CGTTCAAGAGGCCTCTG-TCAT
39545 CGTTCAAGAG
1 CGTTCAAGAG
39555 CCCGATTCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 1 0.02
21 47 0.98
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (21 bp):
CGTTCAAGAGGCCTCTGTCAT
Found at i:41014 original size:14 final size:14
Alignment explanation
Indices: 40972--41005 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
40962 TGTTTAATTT
*
40972 ATTTATAAAAGTTG
1 ATTTGTAAAAGTTG
40986 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
41000 ATTTGT
1 ATTTGT
41006 TTAATTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:41062 original size:81 final size:78
Alignment explanation
Indices: 40915--41072 Score: 244
Period size: 81 Copynumber: 2.0 Consensus size: 78
40905 TTTTACATTG
* *
40915 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTTATTTATAA
1 AAAGTTGATTTGTTTAATTGACGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTATAA
40980 AAGTTGATTTGTA
66 AAGTTGATTTGTA
* * *
40993 AAAGTTGATTTGTTTAATTTGACGTGTAAATAAGAAATTATTTTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTAA-TTGACGAGGAAATAAG-AATTA-TTTTTTGCTTGTTTAATTGATTTA
41058 TAAAAGTTGATTTGT
63 TAAAAGTTGATTTGT
41073 TGTTTTAAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
78 17 0.24
79 13 0.18
80 5 0.07
81 37 0.51
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (78 bp):
AAAGTTGATTTGTTTAATTGACGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTATAA
AAGTTGATTTGTA
Found at i:41221 original size:13 final size:14
Alignment explanation
Indices: 41185--41223 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
41175 GATAGTCAAA
41185 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
41199 TTCG-GTTTGCGA-T
1 TTCGCG-TTGCGATT
41212 TTCGCGTTGCGA
1 TTCGCGTTGCGA
41224 ATTTGACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.08, C:0.21, G:0.31, T:0.41
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:41227 original size:14 final size:14
Alignment explanation
Indices: 41185--41227 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
41175 GATAGTCAAA
*
41185 TTCGCGTTGCGATT
1 TTCGCGTTGCGAAT
41199 TTCG-GTTTGCG-AT
1 TTCGCG-TTGCGAAT
41212 TTCGCGTTGCGAAT
1 TTCGCGTTGCGAAT
41226 TT
1 TT
41228 GACTTTCGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (14 bp):
TTCGCGTTGCGAAT
Found at i:41542 original size:12 final size:12
Alignment explanation
Indices: 41524--41573 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
41514 GTGAAGCCGG
**
41524 TTGTGATTGGGA
1 TTGTGATTTTGA
*
41536 TTTTGATTTTGA
1 TTGTGATTTTGA
*
41548 TTTTGATTTTGA
1 TTGTGATTTTGA
41560 TTGTGATTTTGA
1 TTGTGATTTTGA
41572 TT
1 TT
41574 TCCTTTTGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (12 bp):
TTGTGATTTTGA
Found at i:41543 original size:6 final size:6
Alignment explanation
Indices: 41534--41574 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
41524 TTGTGATTGG
*
41534 GATTTT GATTTT GATTTT GATTTT GATTGT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
41575 CCTTTTGCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.17, C:0.00, G:0.20, T:0.63
Consensus pattern (6 bp):
GATTTT
Found at i:41555 original size:18 final size:18
Alignment explanation
Indices: 41524--41574 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
41514 GTGAAGCCGG
**
41524 TTGTGATTGGGATTTTGA
1 TTGTGATTTTGATTTTGA
*
41542 TTTTGATTTTGATTTTGA
1 TTGTGATTTTGATTTTGA
41560 TTGTGATTTTGATTT
1 TTGTGATTTTGATTT
41575 CCTTTTGCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.61
Consensus pattern (18 bp):
TTGTGATTTTGATTTTGA
Found at i:44025 original size:12 final size:12
Alignment explanation
Indices: 44004--44037 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
43994 GGTTGTGGGT
*
44004 TTTGAGATTGTG
1 TTTGATATTGTG
44016 TTTGATATTGTG
1 TTTGATATTGTG
*
44028 TTTGGTATTG
1 TTTGATATTG
44038 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:44853 original size:20 final size:19
Alignment explanation
Indices: 44828--44896 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
44818 AAACATGTTA
*
44828 CGAATTCGAAAATCTAATTG
1 CGAATTTGAAAATC-AATTG
* *
44848 CGAATTTGAAATTCAGTTG
1 CGAATTTGAAAATCAATTG
* *
44867 CGAATTTGAAATTCCACGTTG
1 CGAATTTGAAAAT-CA-ATTG
44888 CGAATTTGA
1 CGAATTTGA
44897 CTTTTGTGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.39
20 14 0.32
21 13 0.30
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (19 bp):
CGAATTTGAAAATCAATTG
Found at i:44867 original size:19 final size:21
Alignment explanation
Indices: 44845--44896 Score: 90
Period size: 19 Copynumber: 2.6 Consensus size: 21
44835 GAAAATCTAA
44845 TTGCGAATTTGAAATT-CA-G
1 TTGCGAATTTGAAATTCCACG
44864 TTGCGAATTTGAAATTCCACG
1 TTGCGAATTTGAAATTCCACG
44885 TTGCGAATTTGA
1 TTGCGAATTTGA
44897 CTTTTGTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 16 0.52
20 2 0.06
21 13 0.42
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (21 bp):
TTGCGAATTTGAAATTCCACG
Found at i:44909 original size:20 final size:20
Alignment explanation
Indices: 44884--44927 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
44874 GAAATTCCAC
44884 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
44904 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
44924 GTTG
1 GTTG
44928 TCATTTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.14, C:0.09, G:0.27, T:0.50
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:44953 original size:20 final size:20
Alignment explanation
Indices: 44924--44967 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
44914 TGACTTTTGT
44924 GTTGTCATTTACAAATTCGC
1 GTTGTCATTTACAAATTCGC
* *
44944 GTTGTGATTTACATATTCGC
1 GTTGTCATTTACAAATTCGC
44964 GTTG
1 GTTG
44968 CGAAATTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (20 bp):
GTTGTCATTTACAAATTCGC
Found at i:45007 original size:20 final size:19
Alignment explanation
Indices: 44958--45011 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
44948 TGATTTACAT
44958 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** *
44977 AAACTGGGTTGCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
44997 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
45012 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:45403 original size:21 final size:21
Alignment explanation
Indices: 45363--45412 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
45353 GATTCTTGAA
45363 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATAGTACAG
* **
45383 AATTCGCATTGCGATTTTACAG
1 AA-TCGCAATGCGATAGTACAG
45405 AATCGCAA
1 AATCGCAA
45413 CGAGAATATG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (21 bp):
AATCGCAATGCGATAGTACAG
Found at i:45466 original size:20 final size:20
Alignment explanation
Indices: 45443--45633 Score: 233
Period size: 20 Copynumber: 9.6 Consensus size: 20
45433 CTCGAACACA
45443 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
45463 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
45483 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
45503 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
45523 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
45543 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
45563 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
45583 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * * *
45603 TAAATTGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
45623 TAAATCACAAC
1 TAAATCGCAAC
45634 ACTGAAATTT
Statistics
Matches: 148, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
19 1 0.01
20 147 0.99
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:46360 original size:24 final size:23
Alignment explanation
Indices: 46321--46366 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
46311 AAATTTGGTC
46321 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGA-TTTGATA
46345 TTGGTCAATA-CACGGATTTGAT
1 TTGGTCAATATC-CGGATTTGAT
46367 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (23 bp):
TTGGTCAATATCCGGATTTGATA
Found at i:48719 original size:33 final size:33
Alignment explanation
Indices: 48639--48851 Score: 191
Period size: 33 Copynumber: 6.2 Consensus size: 33
48629 CGGAAATTAC
*
48639 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
*
48672 AATCCCAAC-ATGAAAAT-GCAATGCGGAAATGAA
1 AATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
* * * *
48705 AATCGCAATGTGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--CG--A-GAAAATCGCAATGCGA-AAT-GAA
* *
48744 AATGCGGAA-AATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACGA-GAAAATCGCAATGCGAAATGAA
*
48778 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
* *
48811 AATCGCAACGAGAGAATCGCAATGCGAAATTTAA
1 AATCGCAACGAGAAAATCGCAATGCGAAA-TGAA
48845 AATCGCA
1 AATCGCA
48852 TTGCGATTCT
Statistics
Matches: 150, Mismatches: 16, Indels: 27
0.78 0.08 0.14
Matches are distributed among these distances:
32 8 0.05
33 83 0.55
34 17 0.11
35 16 0.11
38 10 0.07
39 11 0.07
40 5 0.03
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (33 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:48764 original size:21 final size:19
Alignment explanation
Indices: 48653--48857 Score: 164
Period size: 19 Copynumber: 11.7 Consensus size: 19
48643 GCAACGAGAG
48653 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
48672 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
48686 AAT-GCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
48705 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
*
48724 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
48738 AATCGCAATGCGGAAAATGAA
1 AATCGCAATGC-G-AAATGAA
48759 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
48778 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
48792 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
48811 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
48825 AATCGCAATGCGAAATTTAA
1 AATCGCAATGCGAAA-TGAA
*
48845 AATCGCATTGCGA
1 AATCGCAATGCGA
48858 TTCTCTCGTT
Statistics
Matches: 149, Mismatches: 12, Indels: 49
0.71 0.06 0.23
Matches are distributed among these distances:
13 3 0.02
14 38 0.26
15 4 0.03
16 5 0.03
17 7 0.05
18 2 0.01
19 56 0.38
20 21 0.14
21 13 0.09
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:48766 original size:54 final size:53
Alignment explanation
Indices: 48653--48818 Score: 266
Period size: 54 Copynumber: 3.2 Consensus size: 53
48643 GCAACGAGAG
* *
48653 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAAT-GCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
*
48705 AATCGCAATGTGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGG-AAATGAA
48759 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
48811 AATCGCAA
1 AATCGCAA
48819 CGAGAGAATC
Statistics
Matches: 107, Mismatches: 4, Indels: 6
0.91 0.03 0.05
Matches are distributed among these distances:
52 46 0.43
53 11 0.10
54 50 0.47
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:48797 original size:14 final size:14
Alignment explanation
Indices: 48778--48832 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
48768 GCGAAATGAA
48778 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
48792 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
48811 AATCGCAACGAGAG
1 AATCGCAACGAGAG
48825 AATCGCAA
1 AATCGCAA
48833 TGCGAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:48807 original size:87 final size:85
Alignment explanation
Indices: 48639--48857 Score: 275
Period size: 87 Copynumber: 2.6 Consensus size: 85
48629 CGGAAATTAC
* * * *
48639 AATCGCAACGAGAGAATCGCAATGCG-AAATGAAAATCCCAACATG-AAAATGCAATGCGGAAAT
1 AATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCGC-A-ATGCGAAATGAAATGCGCAAAT
*
48702 GAAAATCGCAATGTGAAATGAA
64 GAAAATCGCAATGCGAAATGAA
48724 AATCGCAACGAGAGAATCGCAATGCGGAAAATGAAAATCGCAATGCGAAATGAAAAT-CGCAACG
1 AATCGCAACGAGAGAATCGCAATGC-GAAAATGAAAATCGCAATGCGAAATG-AAATGCGCAA--
*
48788 A-GAGAATCGCAATGCGAAATGAA
62 ATGAAAATCGCAATGCGAAATGAA
* * *
48811 AATCGCAACGAGAGAATCGCAATGCGAAATTTAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAATGCGA
48858 TTCTCTCGTT
Statistics
Matches: 119, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
85 28 0.24
86 30 0.25
87 60 0.50
88 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (85 bp):
AATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAATGCGAAATGAAATGCGCAAATGA
AAATCGCAATGCGAAATGAA
Found at i:48960 original size:52 final size:53
Alignment explanation
Indices: 48847--48963 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
48837 AAATTTAAAA
48847 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
48900 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
48952 TCGCATTGCGAT
1 TCGCATTGCGAT
48964 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:48971 original size:19 final size:19
Alignment explanation
Indices: 48866--48963 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
48856 GATTCTCTCG
48866 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
48886 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
48905 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
48919 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48938 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48957 TTGCGAT
1 TTGCGAT
48964 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:49179 original size:11 final size:11
Alignment explanation
Indices: 49163--49198 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
49153 AATCAACTTT
49163 ACAATCAATAA
1 ACAATCAATAA
*
49174 ACAATCAAAAA
1 ACAATCAATAA
49185 ACAATCAATTAA
1 ACAATCAA-TAA
49197 AC
1 AC
49199 TATTGAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.64, C:0.19, G:0.00, T:0.17
Consensus pattern (11 bp):
ACAATCAATAA
Found at i:49794 original size:27 final size:27
Alignment explanation
Indices: 49756--49812 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
49746 ACTATTGTCT
49756 TAAGGGATGGGAGCTGAAGCTCGACGA
1 TAAGGGATGGGAGCTGAAGCTCGACGA
49783 TAAGGGATGGGAGCTGAAGCTCGACGA
1 TAAGGGATGGGAGCTGAAGCTCGACGA
49810 TAA
1 TAA
49813 TCCCAATGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.39, T:0.16
Consensus pattern (27 bp):
TAAGGGATGGGAGCTGAAGCTCGACGA
Found at i:51063 original size:19 final size:19
Alignment explanation
Indices: 51021--51184 Score: 141
Period size: 19 Copynumber: 9.1 Consensus size: 19
51011 TAGTTTACTT
* *
51021 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
51041 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
51060 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
51079 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
51098 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
51117 TTGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
51131 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
51150 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
51164 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
51183 TC
1 TC
51185 ACAATGCGAT
Statistics
Matches: 118, Mismatches: 16, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
14 17 0.14
15 1 0.01
16 7 0.06
17 7 0.06
18 1 0.01
19 73 0.62
20 12 0.10
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:51142 original size:33 final size:33
Alignment explanation
Indices: 51096--51184 Score: 151
Period size: 33 Copynumber: 2.7 Consensus size: 33
51086 GCGAAACCAA
*
51096 AATCGCAACGCGAAATGAAAATTGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
51129 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
51162 AATCGCAACGCGAAATGAAAATC
1 AATCGCAACGCGAAATGAAAATC
51185 ACAATGCGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:51211 original size:19 final size:19
Alignment explanation
Indices: 51189--51247 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
51179 AAAATCACAA
51189 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
51208 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
51222 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
51241 TGCGATT
1 TGCGATT
51248 CTTTTGTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.34
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 19 0.54
ACGTcount: A:0.07, C:0.15, G:0.31, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:51224 original size:14 final size:14
Alignment explanation
Indices: 51205--51231 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51195 TTTGGTTTCG
51205 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
51219 CGTTGCGATTTTG
1 CGTTGCGATTTTG
51232 GTTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:51231 original size:33 final size:32
Alignment explanation
Indices: 51189--51311 Score: 149
Period size: 33 Copynumber: 3.8 Consensus size: 32
51179 AAAATCACAA
51189 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTT-TCGT
*
51222 TGCGATTTTGGTTTCGCGTTGCGATTCTTTTGT
1 TGCGATTTTGGTTTCGCGTTGCGATT-TTTCGT
** *
51255 TGCGA-TTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATT-TTTCGT
* *
51287 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
51312 AAGTAAACTA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
32 28 0.35
33 37 0.47
34 14 0.18
ACGTcount: A:0.09, C:0.17, G:0.27, T:0.47
Consensus pattern (32 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTTCGT
Found at i:51258 original size:14 final size:14
Alignment explanation
Indices: 51238--51293 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
51228 TTTGGTTTCG
51238 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
51252 TGTTGCGATTTCATTT
1 CGTTGCGA-TTC-TTT
*
51268 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTTT
51284 CGTTGCGATT
1 CGTTGCGATT
51294 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 17 0.49
15 3 0.09
16 5 0.14
17 3 0.09
18 7 0.20
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:51274 original size:32 final size:32
Alignment explanation
Indices: 51200--51294 Score: 129
Period size: 32 Copynumber: 2.9 Consensus size: 32
51190 GCGATTTTGG
**
51200 TTTCGCGTTGCGATT-TTGTCGTTGCGATTTTGG
1 TTTCGCGTTGCGATTCTT-TCGTTGCGA-TTTCA
*
51233 TTTCGCGTTGCGATTCTTTTGTTGCGATTTCA
1 TTTCGCGTTGCGATTCTTTCGTTGCGATTTCA
*
51265 TTTCGCGTTGCGATTCTCTCGTTGCGATTT
1 TTTCGCGTTGCGATTCTTTCGTTGCGATTT
51295 TAAGTTTCGT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
32 31 0.55
33 23 0.41
34 2 0.04
ACGTcount: A:0.07, C:0.19, G:0.25, T:0.48
Consensus pattern (32 bp):
TTTCGCGTTGCGATTCTTTCGTTGCGATTTCA
Found at i:51492 original size:92 final size:92
Alignment explanation
Indices: 51358--51636 Score: 519
Period size: 91 Copynumber: 3.1 Consensus size: 92
51348 ATGGATTGCA
51358 TTACTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTT
51422 AGCAGAATTGGCAGCAACCGAACAAAT
66 AGCAGAATTGGCAGCAACCGAACAAAT
51449 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTT
51514 AGCAGAATTGGCAGCAACCGAACAAAT
66 AGCAGAATTGGCAGCAACCGAACAAAT
51541 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACA--GTTAAAGAATACACAGTT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
51604 TAGCAGAATTGGCAGCAACCGAATAAAT
65 TAGCAGAATTGGCAGCAACCGAACAAAT
51632 TTACT
1 TTACT
51637 AAGCAATCTA
Statistics
Matches: 185, Mismatches: 1, Indels: 5
0.97 0.01 0.03
Matches are distributed among these distances:
90 1 0.01
91 72 0.39
92 72 0.39
93 40 0.22
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (92 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTT
AGCAGAATTGGCAGCAACCGAACAAAT
Found at i:53344 original size:20 final size:20
Alignment explanation
Indices: 53313--53409 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
53303 TTTTGGTTGA
53313 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
53333 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
53353 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
53372 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
53387 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
53407 AAT
1 AAT
53410 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:53365 original size:21 final size:21
Alignment explanation
Indices: 53311--53375 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
53301 TCTTTTGGTT
53311 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
53332 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
53352 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
53373 GAA
1 GAA
53376 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:53379 original size:14 final size:14
Alignment explanation
Indices: 53360--53416 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
53350 GAGAAATGAA
53360 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
53374 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
53393 AATCGCAACGAGAG
1 AATCGCAACGAGAG
53407 AATCGCAACG
1 AATCGCAACG
53417 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:53392 original size:33 final size:33
Alignment explanation
Indices: 53311--53433 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
53301 TCTTTTGGTT
*
53311 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
53352 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
53385 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
53418 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
53434 TGCGATTTGG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:53468 original size:14 final size:14
Alignment explanation
Indices: 53449--53505 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
53439 TTTGGTTTCG
53449 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
53463 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
53482 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
53496 CGTTGCGATT
1 CGTTGCGATT
53506 TTCATTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:53484 original size:33 final size:34
Alignment explanation
Indices: 53444--53521 Score: 140
Period size: 33 Copynumber: 2.3 Consensus size: 34
53434 TGCGATTTGG
53444 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
53477 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
*
53511 TTTCTCGTTGC
1 TTTCGCGTTGC
53522 AGATAGTCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 33 0.77
34 10 0.23
ACGTcount: A:0.08, C:0.24, G:0.21, T:0.47
Consensus pattern (34 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
Found at i:53533 original size:21 final size:20
Alignment explanation
Indices: 53460--53565 Score: 109
Period size: 21 Copynumber: 5.5 Consensus size: 20
53450 GTTGCGATTC
53460 TCTCGTTGCGATTTTCA-TT
1 TCTCGTTGCGATTTTCATTT
*
53479 TCGCGTTGCGA--TTC----
1 TCTCGTTGCGATTTTCATTT
53493 TCTCGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
**
53513 TCTCGTTGCAGATAGTCATTT
1 TCTCGTTGC-GATTTTCATTT
*
53534 TCACGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
53554 ATCTCGTTGCGA
1 -TCTCGTTGCGA
53566 CTCTTCTGCA
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 10 0.14
20 18 0.25
21 27 0.38
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (20 bp):
TCTCGTTGCGATTTTCATTT
Found at i:53686 original size:33 final size:33
Alignment explanation
Indices: 53644--53714 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
53634 AATACTAACT
*
53644 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
* *
53677 TGAAAATCGCAACAAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
53710 TGAAA
1 TGAAA
53715 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
Found at i:54119 original size:20 final size:20
Alignment explanation
Indices: 54094--54266 Score: 206
Period size: 20 Copynumber: 8.6 Consensus size: 20
54084 CTTTAAAAAT
54094 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
54114 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
54134 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
54155 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
54175 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
54195 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
54215 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
54235 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
54255 CGCGTTGCGATT
1 CGCGTTGCGATT
54267 CTGTAAAATC
Statistics
Matches: 132, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 114 0.86
21 18 0.14
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:54284 original size:21 final size:20
Alignment explanation
Indices: 54260--54309 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
54250 ATATTCGCGT
54260 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
54281 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
54302 TGCGATTT
1 TGCGATTT
54310 TCAAGAATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
22 3 0.12
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:60163 original size:23 final size:24
Alignment explanation
Indices: 60112--60163 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
60102 ATCCACGAAT
60112 GCTAAACGAACATATTGACAAACA
1 GCTAAACGAACATATTGACAAACA
* *
60136 -TTAAACGAACATGTTTG-CAAA-A
1 GCTAAACGAACAT-ATTGACAAACA
60158 GCTAAA
1 GCTAAA
60164 TGAGCCAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
22 1 0.04
23 19 0.83
24 3 0.13
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.21
Consensus pattern (24 bp):
GCTAAACGAACATATTGACAAACA
Found at i:72014 original size:130 final size:131
Alignment explanation
Indices: 71873--72121 Score: 419
Period size: 131 Copynumber: 1.9 Consensus size: 131
71863 TATTTATATA
*
71873 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCA-TTTAATTAGGATCTGACATGT
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTTAATCAGGATCTGACATGT
* *
71937 GTTAGCACATGATCATGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTTATATATGC
66 GTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGC
72002 T
131 T
72003 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTTAATCAGGATCTGACATGT
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTTAATCAGGATCTGACATGT
* * * * *
72068 GTTAACACATGATCGTGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 GTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
72122 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
130 43 0.39
131 67 0.61
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.37
Consensus pattern (131 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTTAATCAGGATCTGACATGT
GTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGC
T
Found at i:72152 original size:131 final size:129
Alignment explanation
Indices: 71887--72152 Score: 302
Period size: 131 Copynumber: 2.0 Consensus size: 129
71877 ATTTGGTCCT
* *
71887 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
71952 TGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
72017 AAATTAAATAAAATTTAATAAATTAATCATTTTAATCAGGATCTGACATGTGTTAACACATGATC
1 AAATTAAATAAAATTTAATAAATTAATCA-TTTAATCAGGATCTGACATGTGTTAACACATGATC
* * * * * *
72082 GTGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAG
65 ATGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAG
72146 T-A
127 TCA
72148 AAATT
1 AAATT
72153 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
130 29 0.26
131 71 0.63
133 8 0.07
134 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:72477 original size:28 final size:27
Alignment explanation
Indices: 72446--72508 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
72436 AGTTGATACA
*
72446 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
72474 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
72502 ATATTTT
1 ATATTTT
72509 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:72606 original size:16 final size:18
Alignment explanation
Indices: 72585--72618 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
72575 ATTTCTTATT
72585 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
72601 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
72619 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:72763 original size:21 final size:21
Alignment explanation
Indices: 72739--72781 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
72729 TATTACCTTA
72739 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
72760 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
72781 A
1 A
72782 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:72799 original size:35 final size:35
Alignment explanation
Indices: 72750--72835 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
72740 ATTGAAGTAT
** * *
72750 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
72785 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
72820 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
72836 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:81563 original size:15 final size:15
Alignment explanation
Indices: 81543--81574 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
81533 TAGGTGTAAC
81543 AATCTTATCTGACTT
1 AATCTTATCTGACTT
81558 AATCTTATCTGACTT
1 AATCTTATCTGACTT
81573 AA
1 AA
81575 GGATCGGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (15 bp):
AATCTTATCTGACTT
Found at i:84617 original size:21 final size:20
Alignment explanation
Indices: 84587--84626 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
84577 TAATTAATGT
*
84587 TTTATTTTAAATGATTTATC
1 TTTATTTTAAATAATTTATC
*
84607 TTTATATTTAATTAATTTAT
1 TTTAT-TTTAAATAATTTAT
84627 AATTATACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTATTTTAAATAATTTATC
Found at i:85011 original size:29 final size:29
Alignment explanation
Indices: 84976--85061 Score: 136
Period size: 29 Copynumber: 3.0 Consensus size: 29
84966 AAACTATGTA
84976 AGCATGTAATTTAATTGGAATTACTATAG
1 AGCATGTAATTTAATTGGAATTACTATAG
85005 AGCATGTAATTTAATTGGAATTACTATAG
1 AGCATGTAATTTAATTGGAATTACTATAG
* ** *
85034 AGCATGAAATTTGTTTGGAATTAATATA
1 AGCATGTAATTTAATTGGAATTACTATA
85062 CACCAAACAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (29 bp):
AGCATGTAATTTAATTGGAATTACTATAG
Found at i:93866 original size:22 final size:19
Alignment explanation
Indices: 93841--93886 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
93831 TAAGGAAATA
93841 AATTAATTGAAATAAAATATCT
1 AATTAATT-AAA-AAAA-ATCT
93863 AATTAATTAAAAAAAATCT
1 AATTAATTAAAAAAAATCT
93882 AATTA
1 AATTA
93887 GAGAAGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.38
20 4 0.17
21 3 0.12
22 8 0.33
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
AATTAATTAAAAAAAATCT
Done.