Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004402.1 Hibiscus syriacus cultivar Beakdansim tig00009650_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: 60000
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2659 original size:27 final size:27
Alignment explanation
Indices: 2621--2683 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
2611 AAGATCAACT
2621 AGCAGATATTTTTACAAAGCCATTGAG
1 AGCAGATATTTTTACAAAGCCATTGAG
2648 AGCAGATATTTTTACAAAGCCATTGAG
1 AGCAGATATTTTTACAAAGCCATTGAG
2675 AGCAGATAT
1 AGCAGATAT
2684 ATTCAACCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (27 bp):
AGCAGATATTTTTACAAAGCCATTGAG
Found at i:4415 original size:17 final size:18
Alignment explanation
Indices: 4393--4431 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
4383 ATATTAATTT
4393 GGGCTTCTTAG-TTGTTA
1 GGGCTTCTTAGTTTGTTA
4410 GGGCTTCTTAGTTTGTTA
1 GGGCTTCTTAGTTTGTTA
4428 GGGC
1 GGGC
4432 CCACATAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.10, C:0.13, G:0.33, T:0.44
Consensus pattern (18 bp):
GGGCTTCTTAGTTTGTTA
Found at i:5307 original size:21 final size:21
Alignment explanation
Indices: 5261--5308 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
5251 AATTACATCA
*
5261 AAATTTAATTGATTTAATTATT
1 AAATTTAATT-ATTTAAATATT
5283 -AATTTAATT-TTTACAATATT
1 AAATTTAATTATTTA-AATATT
5303 AAATTT
1 AAATTT
5309 TGGTGCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 5 0.22
21 14 0.61
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
AAATTTAATTATTTAAATATT
Found at i:8469 original size:3 final size:3
Alignment explanation
Indices: 8461--8492 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
8451 TGTAATTATA
8461 AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
8493 GAAAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:8992 original size:45 final size:45
Alignment explanation
Indices: 8936--9033 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
8926 CCCGAAAGCT
* * * ** *
8936 TTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGA
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGA
*
8981 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGA
9026 TTTTGAAA
1 TTTTGAAA
9034 TCAAAAAAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGA
Found at i:9078 original size:210 final size:205
Alignment explanation
Indices: 8692--9082 Score: 570
Period size: 210 Copynumber: 1.9 Consensus size: 205
8682 TTATAGATGG
* * *
8692 CCCGGAGGCTTTAAATATCAAAAAGCTCCCGAAAGCTTTTTGAAAACATTCTGCACTGTAGGTCT
1 CCCGAAGGCTTTAAACATCAAAAAGCTCCCGAAAGCTTTTTGAAAACATCCTGCACTGTAGGTCT
* * * * * * * *
8757 TATGGATGGCCCTGAGGTCTTATCATCTTGCACTGCAGGTCTTACAGATGACCCGGAGGATTTAA
66 TATGGATGACCCTGAGATCTTAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGGATTTAA
* *
8822 GATCAAGAAACCTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATCATGTACTGAAGGGC
131 GATCAAAAAAACTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATCATGTACTGAAGGGC
8887 TTACAAATGA
196 TTACAAATGA
8897 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAAGCTTTTTGAAAACATCCTGCACTGTAGGT
1 CCCGAAGGCTTT--AAACATCAAAAAGCTCCCGAAAGCTTTTTGAAAACATCCTGCACTGTAGGT
*
8962 CTTATGGATGACCC-GAAGATTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGG
64 CTTATGGATGACCCTG-AGATCTT---AACATCATGCACTGAAGGGCTTACAGATGACCAGAAGG
*
9026 TTTTGAA-ATCAAAAAAACTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATC
125 ATTT-AAGATCAAAAAAACTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATC
9083 CTGCACTGTA
Statistics
Matches: 164, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
205 11 0.07
206 1 0.01
207 67 0.41
210 83 0.51
211 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (205 bp):
CCCGAAGGCTTTAAACATCAAAAAGCTCCCGAAAGCTTTTTGAAAACATCCTGCACTGTAGGTCT
TATGGATGACCCTGAGATCTTAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGGATTTAA
GATCAAAAAAACTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATCATGTACTGAAGGGC
TTACAAATGA
Found at i:9140 original size:22 final size:23
Alignment explanation
Indices: 9079--9141 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 23
9069 CATTTGAAAA
*
9079 CATCCTGCACTGTAGGTCTTATG
1 CATCTTGCACTGTAGGTCTTATG
* * *
9102 GA--TGGCTCTG-AGGTCTTAT-
1 CATCTTGCACTGTAGGTCTTATG
9121 CATCTTGCACTGTAGGTCTTA
1 CATCTTGCACTGTAGGTCTTA
9142 CATATGACCC
Statistics
Matches: 30, Mismatches: 7, Indels: 7
0.68 0.16 0.16
Matches are distributed among these distances:
19 1 0.03
20 9 0.30
21 11 0.37
22 8 0.27
23 1 0.03
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (23 bp):
CATCTTGCACTGTAGGTCTTATG
Found at i:9301 original size:45 final size:45
Alignment explanation
Indices: 9190--9475 Score: 500
Period size: 45 Copynumber: 6.3 Consensus size: 45
9180 AAGGCTTTTT
9190 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
9235 CATTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 --TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
9282 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
9327 TTTTGAAAACATCATGTACTGAAGGTCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
9372 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
9417 TTTTGAAAACATCATGCACTGAAGGGCTTAAAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
9462 CTTTGAAAATATCA
1 TTTTGAAAACATCA
9476 AAAAGCTTCC
Statistics
Matches: 230, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
45 185 0.80
47 45 0.20
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:9510 original size:76 final size:76
Alignment explanation
Indices: 9410--9855 Score: 657
Period size: 76 Copynumber: 5.9 Consensus size: 76
9400 TACAGATGAC
*
9410 CCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTAAAGATGACCCGAAGGCTTTGAAAATA
1 CCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATA
9473 TCAAAAAGCTT
66 TCAAAAAGCTT
* * * *
9484 CCGAAGGCTTTATGAAAACATCATGCATTGAAGGGCTTATAGATGACCCGAAGGCTTTAAAAATA
1 CCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATA
9549 TCAAAAAGC-T
66 TCAAAAAGCTT
* * *
9559 CCAAAAGGATTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGCTTTGAAAAT
1 CC-GAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAT
9624 ATCAAAAAGC-T
65 ATCAAAAAGCTT
*
9635 CCAGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAT
1 CC-GAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAT
*
9700 ATCAAAAAGCTC
65 ATCAAAAAGCTT
* *
9712 CCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATA
1 CCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATA
*
9777 TCAAAAAGCTC
66 TCAAAAAGCTT
* * * * ** * *
9788 CCGAAGGCTTTTTGAAAATATCCTGCACTGTAGGCCTTATGGATGACCCGAAGGTTTTGAAAACA
1 CCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATA
9853 TCA
66 TCA
9856 TGCACTGTAT
Statistics
Matches: 345, Mismatches: 23, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
74 7 0.02
75 3 0.01
76 333 0.97
77 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (76 bp):
CCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATA
TCAAAAAGCTT
Found at i:10586 original size:22 final size:22
Alignment explanation
Indices: 10531--10587 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
10521 AATAAAACTT
*
10531 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
10553 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
10575 TCATCTTTGAAGA
1 TCATCTTTGAAGA
10588 ATGTAGATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:11108 original size:2 final size:2
Alignment explanation
Indices: 11101--11164 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
11091 TTATTATTAA
11101 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
11143 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
11165 TACAAATTAC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12494 original size:27 final size:27
Alignment explanation
Indices: 12432--12511 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
12422 TATTTGGCAA
12432 TTTAATATTATTGCTTTTA-AAT-TTAT
1 TTTAATATTATT-CTTTTATAATATTAT
*
12458 TTTAAATATTATTCATTTATAATATTAT
1 TTT-AATATTATTCTTTTATAATATTAT
* *
12486 TTTATTATTA--CTTTTATATTATTAT
1 TTTAATATTATTCTTTTATAATATTAT
12511 T
1 T
12512 ATTTTCATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
25 14 0.30
26 8 0.17
27 18 0.38
28 7 0.15
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (27 bp):
TTTAATATTATTCTTTTATAATATTAT
Found at i:12507 original size:17 final size:16
Alignment explanation
Indices: 12482--12523 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
12472 ATTTATAATA
*
12482 TTATTTTATTATTACTT
1 TTATATTATTATTA-TT
12499 TTATATTATTATTATT
1 TTATATTATTATTATT
12515 TTCATATTA
1 TT-ATATTA
12524 GTCACATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATATTATTATTATT
Found at i:12513 original size:11 final size:12
Alignment explanation
Indices: 12463--12511 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
12453 TTTATTTTAA
12463 ATATTATTCATTT
1 ATATTATT-ATTT
*
12476 ATAATATTATTT
1 ATATTATTATTT
12488 -TATTATTACTTTT
1 ATATTATTA--TTT
12501 ATATTATTATT
1 ATATTATTATT
12512 ATTTTCATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 7 0.23
12 6 0.19
13 10 0.32
14 8 0.26
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (12 bp):
ATATTATTATTT
Found at i:12540 original size:2 final size:2
Alignment explanation
Indices: 12533--12568 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
12523 AGTCACATAA
* *
12533 AT AT AT AT AT AT AT AT AG AT AG 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
12569 TTTAAATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:20165 original size:114 final size:114
Alignment explanation
Indices: 19965--20184 Score: 377
Period size: 114 Copynumber: 1.9 Consensus size: 114
19955 CATGTTCTCG
*
19965 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* *
20030 GGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
*
20079 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * *
20144 GGTAGGAACCTCAGAACCAATCATTGGAATTGAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
20185 CTGCATGATC
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
Found at i:21436 original size:76 final size:74
Alignment explanation
Indices: 21288--21458 Score: 189
Period size: 76 Copynumber: 2.3 Consensus size: 74
21278 AATAAGAAGC
* *
21288 AAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATGTTGATGTATCCTGAATAT
1 AAATG-TGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAACAT
*
21353 TTATATCAGCA
65 TCATATCAG-A
* ** * ** *
21364 AAATGATGGGGCATGCTGAAAGCTTTTTTCAATCAGAATGAAGAATGTTGATGTATTTTGAACGT
1 AAATG-TGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAACAT
* *
21429 TCGTATCAGT
65 TCATATCAGA
*
21439 AATTGTCGGGGCATGCTGAA
1 AAATGT-GGGGCATGCTGAA
21459 GGCCCACATC
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
74 1 0.01
75 17 0.21
76 62 0.77
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.32
Consensus pattern (74 bp):
AAATGTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAACATT
CATATCAGA
Found at i:22819 original size:22 final size:22
Alignment explanation
Indices: 22793--22872 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
22783 TACATCTACA
22793 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
22815 CTCTTCAAAGATGTTAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* * *
22837 CTTTTTAAAGATGATAGATTGT
1 CTCTTCAAAGATGATAGATTCT
*
22859 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
22873 AAGCTTTATT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:23871 original size:73 final size:73
Alignment explanation
Indices: 23749--24321 Score: 1058
Period size: 73 Copynumber: 7.8 Consensus size: 73
23739 GTTTTCAAAT
*
23749 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTATCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
23814 CTCGAAAC
66 CTCGAAAC
23822 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
23887 CTCGAAAC
66 CTCGAAAC
23895 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
23960 CTCGAAAC
66 CTCGAAAC
* *
23968 AGAACTTTATCTCACTTGAGATTTTTTTTCTTAAAACAAAATTTTTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
24033 CTCGAAAC
66 CTCGAAAC
*
24041 AGAACTTTATCTCACTTGATATTGTTTTTCTTAAAACAAAA-TTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
24105 CTCGAAAC
66 CTCGAAAC
24113 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
24178 CTCGAAAC
66 CTCGAAAC
*
24186 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
*
24251 CTTGAAAC
66 CTCGAAAC
* *
24259 AAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAGATTTGTCTCGCTTGAGACAGTT
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTTGTCTCGCTTGAGACAGTT
24322 ATTTCGAGCT
Statistics
Matches: 486, Mismatches: 12, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
72 70 0.14
73 395 0.81
74 21 0.04
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (73 bp):
AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
CTCGAAAC
Found at i:24194 original size:218 final size:219
Alignment explanation
Indices: 23749--24321 Score: 1058
Period size: 218 Copynumber: 2.6 Consensus size: 219
23739 GTTTTCAAAT
23749 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTATCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTATCTCGCTTGAGACAGTTTCA
23814 CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGA
66 CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGA
23879 CAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTC
131 CAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTC
23944 GCTTGAGACAGTTTCACTCGAAAC
196 GCTTGAGACAGTTTCACTCGAAAC
* *
23968 AGAACTTTATCTCACTTGAGATTTTTTTTCTTAAAACAAAATTTTTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTATCTCGCTTGAGACAGTTTCA
*
24033 CTCGAAACAGAACTTTATCTCACTTGATATTGTTTTTCTTAAAACAAAA-TTGTCTCGCTTGAGA
66 CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGA
24097 CAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTC
131 CAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTC
24162 GCTTGAGACAGTTTCACTCGAAAC
196 GCTTGAGACAGTTTCACTCGAAAC
* *
24186 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTATCTCGCTTGAGACAGTTTCA
* * *
24251 CTTGAAACAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAGATTTGTCTCGCTTGAG
66 CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTTGTCTCGCTTGAG
24316 ACAGTT
130 ACAGTT
24322 ATTTCGAGCT
Statistics
Matches: 342, Mismatches: 10, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
218 210 0.61
219 112 0.33
220 20 0.06
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (219 bp):
AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTATCTCGCTTGAGACAGTTTCA
CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGA
CAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTC
GCTTGAGACAGTTTCACTCGAAAC
Found at i:24679 original size:16 final size:17
Alignment explanation
Indices: 24660--24728 Score: 76
Period size: 16 Copynumber: 4.2 Consensus size: 17
24650 TAATTATAAT
24660 TATTATTAATATA-ATA
1 TATTATTAATATATATA
24676 TATTATTAA-ATATATA
1 TATTATTAATATATATA
24692 TA-TA-T-ATATATATA
1 TATTATTAATATATATA
24706 TATATATATATATATATATA
1 TAT-TAT-TA-ATATATATA
24726 TAT
1 TAT
24729 ACAAATTACA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.02
14 10 0.22
15 5 0.11
16 16 0.36
18 1 0.02
20 12 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTATTAATATATATA
Found at i:24690 original size:2 final size:2
Alignment explanation
Indices: 24668--24729 Score: 94
Period size: 2 Copynumber: 32.5 Consensus size: 2
24658 ATTATTATTA
*
24668 AT AT A- AT AT AT -T AT -T AA 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
24707 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
24730 CAAATTACAT
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
1 3 0.05
2 52 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26051 original size:16 final size:16
Alignment explanation
Indices: 26010--26045 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
26000 TTGCTTTTAA
26010 ATTTATTT-TAAATATT
1 ATTTATTTAT-AATATT
26026 ATTTATTTATAATATT
1 ATTTATTTATAATATT
26042 ATTT
1 ATTT
26046 TGTTATTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTATTTATAATATT
Found at i:26068 original size:17 final size:17
Alignment explanation
Indices: 26048--26081 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
26038 TATTATTTTG
26048 TTATTACTTTT-ATATTA
1 TTATTA-TTTTCATATTA
26065 TTATTATTTTCATATTA
1 TTATTATTTTCATATTA
26082 GTAACATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTCATATTA
Found at i:26098 original size:2 final size:2
Alignment explanation
Indices: 26091--26122 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
26081 AGTAACATAA
26091 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
26123 TTTAAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26232 original size:22 final size:22
Alignment explanation
Indices: 26207--26252 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
26197 GATATTTTAA
26207 ATAATTAAATATTATAAAAATT
1 ATAATTAAATATTATAAAAATT
* * **
26229 ATAATTTAATTTTATTTAAATT
1 ATAATTAAATATTATAAAAATT
26251 AT
1 AT
26253 TATATTTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAATTAAATATTATAAAAATT
Found at i:29883 original size:122 final size:122
Alignment explanation
Indices: 29666--29911 Score: 429
Period size: 122 Copynumber: 2.0 Consensus size: 122
29656 GACATTAGCC
* *
29666 TTCATTGGACTAATTAAAGGGTTCAACTCATCACAATGTCTTTGATTTGACAATCACAATAGAGC
1 TTCATTAGACTAATTAAAGGGTTCAACTCATCACAATGTCTTTGAATTGACAATCACAATAGAGC
29731 AAACACCAAACTGACAAATACCCGATCAAGGTCATGCTTTGAATATATGACTTTTTT
66 AAACACCAAACTGACAAATACCCGATCAAGGTCATGCTTTGAATATATGACTTTTTT
* *
29788 TTCATTAGACTAATTAAAGGGTTCAACTCATCACAATGTCTTTGAATTGACAATCACAGTGGAGC
1 TTCATTAGACTAATTAAAGGGTTCAACTCATCACAATGTCTTTGAATTGACAATCACAATAGAGC
* * *
29853 AAATACCGAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATATGACTTTTTT
66 AAACACCAAACTGACAAATACCCGATCAAGGTCATGCTTTGAATATATGACTTTTTT
29910 TT
1 TT
29912 TTTCTTTTTC
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
122 117 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (122 bp):
TTCATTAGACTAATTAAAGGGTTCAACTCATCACAATGTCTTTGAATTGACAATCACAATAGAGC
AAACACCAAACTGACAAATACCCGATCAAGGTCATGCTTTGAATATATGACTTTTTT
Found at i:31993 original size:13 final size:13
Alignment explanation
Indices: 31975--32013 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
31965 CAATGCAAAG
31975 ATGAAAATATAAA
1 ATGAAAATATAAA
*
31988 ATGAAAATGT-AA
1 ATGAAAATATAAA
32000 ATGAAAATATAAA
1 ATGAAAATATAAA
32013 A
1 A
32014 ATGCAAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (13 bp):
ATGAAAATATAAA
Found at i:32003 original size:12 final size:12
Alignment explanation
Indices: 31975--32012 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
31965 CAATGCAAAG
31975 ATGAAAATATAAA
1 ATGAAAATAT-AA
*
31988 ATGAAAATGTAA
1 ATGAAAATATAA
32000 ATGAAAATATAA
1 ATGAAAATATAA
32012 A
1 A
32013 AATGCAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (12 bp):
ATGAAAATATAA
Found at i:32003 original size:25 final size:26
Alignment explanation
Indices: 31966--32027 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
31956 CAAACTGTGC
31966 AATGCAAAGATGAAAATAT-AAAATGAA
1 AATGC-AA-ATGAAAATATAAAAATGAA
* *
31993 AATGTAAATGAAAATATAAAAATGCA
1 AATGCAAATGAAAATATAAAAATGAA
32019 AATGCAAAT
1 AATGCAAAT
32028 ATAAAAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.32
26 17 0.55
27 4 0.13
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (26 bp):
AATGCAAATGAAAATATAAAAATGAA
Found at i:32036 original size:21 final size:20
Alignment explanation
Indices: 31991--32042 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
31981 ATATAAAATG
*
31991 AAAATGTAAATGAAAATATA
1 AAAATGCAAATGAAAATATA
*
32011 AAAATGCAAATGCAAATATAA
1 AAAATGCAAATGAAAATAT-A
32032 AAAATGCAAAT
1 AAAATGCAAAT
32043 ATAATGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.21
Consensus pattern (20 bp):
AAAATGCAAATGAAAATATA
Found at i:32036 original size:47 final size:47
Alignment explanation
Indices: 31966--32074 Score: 125
Period size: 47 Copynumber: 2.3 Consensus size: 47
31956 CAAACTGTGC
* * *
31966 AATGCAAAGATG-AAA-ATATAAAATGAAAATGTAAATGAAAATATAAA
1 AATGCAAA-ATGCAAATATAAAAAATGAAAATAT-AATGAAAAAATAAA
* **
32013 AATGC-AAATGCAAATATAAAAAATGCAAATATAATGAAAAAATACG
1 AATGCAAAATGCAAATATAAAAAATGAAAATATAATGAAAAAATAAA
32059 AATGCAAAATGCAAAT
1 AATGCAAAATGCAAAT
32075 GCAACAAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
45 3 0.06
46 21 0.40
47 29 0.55
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.20
Consensus pattern (47 bp):
AATGCAAAATGCAAATATAAAAAATGAAAATATAATGAAAAAATAAA
Found at i:32038 original size:15 final size:15
Alignment explanation
Indices: 32018--32046 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
32008 ATAAAAATGC
32018 AAATGCAAATATAAA
1 AAATGCAAATATAAA
32033 AAATGCAAATATAA
1 AAATGCAAATATAA
32047 TGAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (15 bp):
AAATGCAAATATAAA
Found at i:34963 original size:3 final size:3
Alignment explanation
Indices: 34955--35000 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
34945 TGTAATTATA
*
34955 AAT AAT AAT AAT AAT AAT -AT ATT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
35001 AATGAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:34985 original size:23 final size:23
Alignment explanation
Indices: 34947--35001 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
34937 CTTGGGCTTG
34947 TAAT-TATAAATAATAATAATAA
1 TAATATATAAATAATAATAATAA
*
34969 TAATATATTAATAATAATAATAA
1 TAATATATAAATAATAATAATAA
34992 TAATA-ATAAA
1 TAATATATAAA
35002 ATGAAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 8 0.27
23 22 0.73
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TAATATATAAATAATAATAATAA
Found at i:38289 original size:18 final size:18
Alignment explanation
Indices: 38263--38303 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
38253 ATGAAATCTG
* *
38263 ATTAAATTAAAGATAATT
1 ATTATATTAAAAATAATT
*
38281 ATTATATTAAAAATTATT
1 ATTATATTAAAAATAATT
38299 ATTAT
1 ATTAT
38304 TTTGAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
ATTATATTAAAAATAATT
Found at i:39404 original size:2 final size:2
Alignment explanation
Indices: 39397--39430 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39387 TAGAAAAATC
39397 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
39431 TTGTTTTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45809 original size:3 final size:3
Alignment explanation
Indices: 45801--45830 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
45791 TATAGACAAG
45801 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
45831 AATATTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:56506 original size:2 final size:2
Alignment explanation
Indices: 56499--56566 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
56489 TTTTATTAAA
56499 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A- AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
56540 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
56567 TATATATATA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.