Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003156.1 Hibiscus syriacus cultivar Beakdansim tig00006637_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: 119623
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:10161 original size:26 final size:25
Alignment explanation
Indices: 10124--10172 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
10114 TAAAGTGATC
*
10124 ATTTTAGTCAAAATAGGTACCTATT
1 ATTTTAGTCAAAATAGATACCTATT
10149 ATTTTATGTCAAAATAGATACCTA
1 ATTTTA-GTCAAAATAGATACCTA
10173 AACTATTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (25 bp):
ATTTTAGTCAAAATAGATACCTATT
Found at i:13221 original size:2 final size:2
Alignment explanation
Indices: 13154--13248 Score: 51
Period size: 2 Copynumber: 49.0 Consensus size: 2
13144 ATACACCCAT
*
13154 TA TA TCA TA TA GTA TA T- TA TA GTA TA TA -A TA TA -A TA TG TA
1 TA TA T-A TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * *
13194 TA T- TT TA TA TA -A TA TA AA CA TA -A TA TA TA TA CTA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* *
13233 TA TA AA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA
13249 GTCATATAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
1 7 0.10
2 57 0.79
3 8 0.11
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (2 bp):
TA
Found at i:25467 original size:26 final size:26
Alignment explanation
Indices: 25431--25482 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
25421 TTTTGCCTAC
25431 CTCCTCGAACACTACTAAAATAATAT
1 CTCCTCGAACACTACTAAAATAATAT
25457 CTCCTCGAACACTACTAAAATAATAT
1 CTCCTCGAACACTACTAAAATAATAT
25483 TTCACTAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.27, G:0.04, T:0.27
Consensus pattern (26 bp):
CTCCTCGAACACTACTAAAATAATAT
Found at i:27712 original size:3 final size:3
Alignment explanation
Indices: 27671--29649 Score: 3598
Period size: 3 Copynumber: 669.3 Consensus size: 3
27661 TTTTACCCAA
* * * * *
27671 TAT TAT TAC TAT TAC TAT TAC TAT TAC TAT TAC TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27719 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27767 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27815 TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27861 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27907 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27955 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28003 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28050 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28098 TAT TAT TA- TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28144 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28191 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28238 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28286 TAT TA- TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28332 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28379 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28426 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28472 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28520 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28567 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28615 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28662 TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28707 TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
28753 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28800 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28848 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28896 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
28942 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28990 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29037 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29085 TA- TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29131 TAT TAT TAT TAT TA- TAT TAT T-T TAT TAT TA- TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29175 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29222 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29269 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
29314 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29360 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29408 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29454 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29502 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TATT TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA-T
29548 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29596 TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
29643 TAT TAT T
1 TAT TAT T
29650 GCTCTTACTC
Statistics
Matches: 1923, Mismatches: 10, Indels: 86
0.95 0.00 0.04
Matches are distributed among these distances:
2 72 0.04
3 1830 0.95
4 21 0.01
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:39719 original size:16 final size:16
Alignment explanation
Indices: 39694--39727 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
39684 TCATATATAC
39694 AACGTCAATCGATCCA
1 AACGTCAATCGATCCA
*
39710 AACGTGAATCGATCCA
1 AACGTCAATCGATCCA
39726 AA
1 AA
39728 TTAGTCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.18
Consensus pattern (16 bp):
AACGTCAATCGATCCA
Found at i:41217 original size:13 final size:14
Alignment explanation
Indices: 41201--41235 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
41191 TAAACCATAT
*
41201 CCCTAACTTA-AAA
1 CCCTAAATTATAAA
41214 CCCTAAATTATAAA
1 CCCTAAATTATAAA
41228 CCCTAAAT
1 CCCTAAAT
41236 CATAGTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.26
Consensus pattern (14 bp):
CCCTAAATTATAAA
Found at i:41273 original size:7 final size:7
Alignment explanation
Indices: 41240--41273 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
41230 CTAAATCATA
*
41240 GTTTAAG
1 GTTTAGG
*
41247 GTTTAGA
1 GTTTAGG
41254 GTTTAGG
1 GTTTAGG
41261 GTTTAGG
1 GTTTAGG
41268 GTTTAG
1 GTTTAG
41274 AAGTTATGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:42689 original size:2 final size:2
Alignment explanation
Indices: 42684--42715 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42674 AATTTTTTAA
42684 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
42716 TCCAACTTGT
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:43586 original size:19 final size:17
Alignment explanation
Indices: 43548--43590 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
43538 GATTTATTCG
43548 ATTTAATATGTGATATA
1 ATTTAATATGTGATATA
43565 ATTTGAATATGATGAT-TAA
1 ATTT-AATATG-TGATAT-A
43584 ATTTAAT
1 ATTTAAT
43591 CTGAAACCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.17
18 10 0.43
19 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
ATTTAATATGTGATATA
Found at i:44536 original size:16 final size:17
Alignment explanation
Indices: 44491--44536 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
44481 TGTTTATGAG
44491 AGAATTGGAATCTGTGAA
1 AGAATTGGAATCTGT-AA
* *
44509 ATAATTGCAATCTGT-A
1 AGAATTGGAATCTGTAA
44525 AGAATTGGAATC
1 AGAATTGGAATC
44537 CAATTCCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 11 0.46
18 13 0.54
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (17 bp):
AGAATTGGAATCTGTAA
Found at i:45187 original size:27 final size:28
Alignment explanation
Indices: 45129--45191 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
45119 CGACCCGACC
*
45129 CGACCCGAATATCACACTTAAAAAACCT
1 CGACCCGAATATCACACTTAAAAAACCA
45157 CGACCCGAATATCACACTTAAAAAA-CA
1 CGACCCGAATATCACACTTAAAAAACCA
45184 CGACCCGA
1 CGACCCGA
45192 CCCGAACAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 9 0.26
28 25 0.74
ACGTcount: A:0.43, C:0.33, G:0.10, T:0.14
Consensus pattern (28 bp):
CGACCCGAATATCACACTTAAAAAACCA
Found at i:55541 original size:120 final size:120
Alignment explanation
Indices: 55328--55671 Score: 607
Period size: 120 Copynumber: 2.9 Consensus size: 120
55318 TAAAACAAAC
* ***
55328 TGAAAGTTTAGATATTAAAACGGATCAAAATTGATAGTTTAGGTACTAAACGCGTTAAATTTTTA
1 TGAAAGTTTAGATACTAAAATATATCAAAATTGATAGTTTAGGTACTAAACGCGTTAAATTTTTA
55393 ACAATGAGGTACTAAAGTGAAACAAAAACTAAATATTATGTATGATTTTAAAAAA
66 ACAATGAGGTACTAAAGTGAAACAAAAACTAAATATTATGTATGATTTTAAAAAA
*
55448 TGAAAGTTTAGATACTAAAATATATCAAAATTGATAGTTTATGTACTAAACGCGTTAAATTTTTA
1 TGAAAGTTTAGATACTAAAATATATCAAAATTGATAGTTTAGGTACTAAACGCGTTAAATTTTTA
* *
55513 AGAATAAGGTACTAAAGTGAAACAAAAACTAAATATTATGTATGATTTTAAAAAA
66 ACAATGAGGTACTAAAGTGAAACAAAAACTAAATATTATGTATGATTTTAAAAAA
* *
55568 TGAAAGTTTAAATACTAAAATATATCAAAATTGATAGTTTAGGTATTAAACGCGTTAAATTTTTA
1 TGAAAGTTTAGATACTAAAATATATCAAAATTGATAGTTTAGGTACTAAACGCGTTAAATTTTTA
55633 ACAATGAGGTACTAAAGTGAAACAAAAACTAAATATTAT
66 ACAATGAGGTACTAAAGTGAAACAAAAACTAAATATTAT
55672 CTATTTAATT
Statistics
Matches: 212, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 212 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (120 bp):
TGAAAGTTTAGATACTAAAATATATCAAAATTGATAGTTTAGGTACTAAACGCGTTAAATTTTTA
ACAATGAGGTACTAAAGTGAAACAAAAACTAAATATTATGTATGATTTTAAAAAA
Found at i:57671 original size:26 final size:26
Alignment explanation
Indices: 57634--57688 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
57624 TCGTATTCAT
* *
57634 AAAACCTCTGC-AACAAACAAAAAAC
1 AAAAACTCTGCAAAAAAACAAAAAAC
*
57659 AAAAACTCGTGCAAAAAAACGAAAAAC
1 AAAAACTC-TGCAAAAAAACAAAAAAC
57686 AAA
1 AAA
57689 GAAAGAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 3 0.12
27 15 0.60
ACGTcount: A:0.64, C:0.22, G:0.07, T:0.07
Consensus pattern (26 bp):
AAAAACTCTGCAAAAAAACAAAAAAC
Found at i:63265 original size:19 final size:19
Alignment explanation
Indices: 63238--63274 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
63228 ATGATCAACA
*
63238 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
63257 AAATTGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
63275 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:63401 original size:19 final size:19
Alignment explanation
Indices: 63379--63441 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
63369 AAATTTACAT
*
63379 TAGTCCAAATTCGTTACGA
1 TAGTCCAAATTCGTTGCGA
* *
63398 TAGTCGAAGATCGCGTTGCGA
1 TAGTCCAA-AT-TCGTTGCGA
**
63419 TTTTCCAAATTCGTTGCGA
1 TAGTCCAAATTCGTTGCGA
63438 TAGT
1 TAGT
63442 TCAAGTTTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
19 17 0.52
20 4 0.12
21 12 0.36
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (19 bp):
TAGTCCAAATTCGTTGCGA
Found at i:63874 original size:19 final size:19
Alignment explanation
Indices: 63850--63939 Score: 90
Period size: 19 Copynumber: 4.4 Consensus size: 19
63840 TTATTTTGGA
*
63850 TTTTTCACTATCGCAACAT
1 TTTTTCACTATCGCAACAC
63869 TTTTTCACTATCGTAACAACAC
1 TTTTTCACTATCG---CAACAC
63891 GTTTTTCAAACTATCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* *
63913 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
63932 ATTTTTCA
1 -TTTTTCA
63940 AAATCGCATT
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
19 26 0.44
20 5 0.08
21 4 0.07
22 11 0.19
23 6 0.10
25 7 0.12
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.38
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:63911 original size:44 final size:41
Alignment explanation
Indices: 63849--63941 Score: 109
Period size: 44 Copynumber: 2.2 Consensus size: 41
63839 CTTATTTTGG
** *
63849 ATTTTTC--ACTATCGCAACATTTTTTCACTATCGTAACAACAC
1 ATTTTTCAAACTATCGCAACACATTTTAACTATCG---CAACAC
*
63891 GTTTTTCAAACTATCGCAACACATTTTAACTATCGCAACAC
1 ATTTTTCAAACTATCGCAACACATTTTAACTATCGCAACAC
63932 ATTTTTCAAA
1 ATTTTTCAAA
63942 ATCGCATTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
41 15 0.34
42 6 0.14
44 23 0.52
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (41 bp):
ATTTTTCAAACTATCGCAACACATTTTAACTATCGCAACAC
Found at i:63945 original size:20 final size:20
Alignment explanation
Indices: 63885--63947 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
63875 ACTATCGTAA
*
63885 CAACACGTTTTTCAAACTATCG
1 CAACACATTTTTCAAA--ATCG
*
63907 CAACACA-TTTT-AACTATCG
1 CAACACATTTTTCAA-AATCG
63926 CAACACATTTTTCAAAATCG
1 CAACACATTTTTCAAAATCG
63946 CA
1 CA
63948 TTGTGAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 11 0.31
20 12 0.34
21 6 0.17
22 6 0.17
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (20 bp):
CAACACATTTTTCAAAATCG
Found at i:69488 original size:2 final size:2
Alignment explanation
Indices: 69481--69517 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
69471 TGTGCCGTAC
*
69481 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69518 AGCATAAGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:71868 original size:29 final size:29
Alignment explanation
Indices: 71721--71861 Score: 212
Period size: 29 Copynumber: 4.9 Consensus size: 29
71711 ATTAAGTACA
* * *
71721 TCGACTATTAAAAATTACAAAAT-GATCTT
1 TCGATTATTAAAAGTTACAAAATGGTTC-T
* * *
71750 TCGACTATTAAAAATTATAAAATGGTTCT
1 TCGATTATTAAAAGTTACAAAATGGTTCT
71779 TCGATTATTAAAAGTTACAAAATGGTTCT
1 TCGATTATTAAAAGTTACAAAATGGTTCT
71808 TCGATTATTAAAAGTTACAAAATGGTTCT
1 TCGATTATTAAAAGTTACAAAATGGTTCT
71837 TCGATTATTAAAAGTTACAAAATGG
1 TCGATTATTAAAAGTTACAAAATGG
71862 CCCTTCGGCT
Statistics
Matches: 106, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
29 103 0.97
30 3 0.03
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (29 bp):
TCGATTATTAAAAGTTACAAAATGGTTCT
Found at i:73128 original size:273 final size:273
Alignment explanation
Indices: 72620--73152 Score: 834
Period size: 273 Copynumber: 2.0 Consensus size: 273
72610 CCTATAGTTG
* *
72620 TTAAACTCGAACAAAAAATAGATACGAACAAAGCTAATTACATCGAAAAGTGAACCACAAAAATA
1 TTAAACTCGAACAAAAAATAGATACGAACAAAGCTAACTACATCGAAAAGTGAACCACAAAAAGA
*
72685 AATGAAGCTATTGAAGACCTCAAGAAAATTGCAAATCAAAATCGAGCAATGTGAAAATACTATCC
66 AATGAAGCTATTGAAAACCTCAAGAAAATTGCAAATCAAAATCGAGCAATGTGAAAATACTATCC
* * * * * *
72750 ACGAACGTAAATCGCGTATCCAAATCCGATTCGAGGGTCCAAATCATAGAAGATCAATAAGATAA
131 ACGAAAGCAAAACGCGTATCCAAATCCGATTCGAAGGTCCAAAGCATAGAAGATCAACAAGATAA
* * *
72815 CAGATAAACATCATCTTTATCAGTCGTGACGATATCAAATTCAACCCCG-AAAAAATATATTGTG
196 CAGATAAACATCATCATTATCAGTCGCGACGATATCAAATTCAA-CCCGAAAAAAAAATATTGTG
72879 ACCTAAAACTCCAA
260 ACCTAAAACTCCAA
* * * *
72893 TTAAACTCGAACAAAAGATAGATACGAACAAATCTAACTGCATCGAAAAGTGAACTACAAAAAGA
1 TTAAACTCGAACAAAAAATAGATACGAACAAAGCTAACTACATCGAAAAGTGAACCACAAAAAGA
* *
72958 AATGAAGCTATTGAAAACCTGAGGAAAATTGCAAATCAAAATCGAGCAATGTGAAAATACTATCC
66 AATGAAGCTATTGAAAACCTCAAGAAAATTGCAAATCAAAATCGAGCAATGTGAAAATACTATCC
* *
73023 ACGAAAGCAAAACGCGTATCTAAATCCGATTCGAATGTCCAAAGCATAGAAGATCAACAAGATAA
131 ACGAAAGCAAAACGCGTATCCAAATCCGATTCGAAGGTCCAAAGCATAGAAGATCAACAAGATAA
* * * *
73088 CAGATAAACGTCATCATTATTAGTCGCGACGATGTCAAATTCAATCCGAAAAAAAAATATTGTGA
196 CAGATAAACATCATCATTATCAGTCGCGACGATATCAAATTCAACCCGAAAAAAAAATATTGTGA
73153 GACTTAAAGC
Statistics
Matches: 235, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
272 3 0.01
273 232 0.99
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (273 bp):
TTAAACTCGAACAAAAAATAGATACGAACAAAGCTAACTACATCGAAAAGTGAACCACAAAAAGA
AATGAAGCTATTGAAAACCTCAAGAAAATTGCAAATCAAAATCGAGCAATGTGAAAATACTATCC
ACGAAAGCAAAACGCGTATCCAAATCCGATTCGAAGGTCCAAAGCATAGAAGATCAACAAGATAA
CAGATAAACATCATCATTATCAGTCGCGACGATATCAAATTCAACCCGAAAAAAAAATATTGTGA
CCTAAAACTCCAA
Found at i:73656 original size:21 final size:21
Alignment explanation
Indices: 73541--73656 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
73531 GCGAAATAAA
**
73541 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
73561 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
73581 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
73602 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
73622 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
73644 AATCGCAACGCGA
1 AATCGCAACGCGA
73657 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:73669 original size:20 final size:20
Alignment explanation
Indices: 73644--73836 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
73634 GATTTTCCAG
* ** *
73644 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
73664 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
73684 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
73704 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
73724 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
73744 AATCGCAATGCGTATTCGTA
1 AATCGCAACGCGTATCCGTA
*
73764 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
73784 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
73805 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
73825 AATCGCAACGCG
1 AATCGCAACGCG
73837 ATTTTTAAAG
Statistics
Matches: 149, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
19 1 0.01
20 129 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:74255 original size:33 final size:33
Alignment explanation
Indices: 74216--74286 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
74206 TTCACTTAGA
74216 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
74249 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
74282 TTTCA
1 TTTCA
74287 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:74392 original size:21 final size:20
Alignment explanation
Indices: 74366--74472 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
74356 TGCAGAAGAG
74366 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
74387 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
74407 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
74429 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
74443 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
74462 TCGCAACGAGA
1 TCGCAACGAGA
74473 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:74446 original size:14 final size:14
Alignment explanation
Indices: 74427--74483 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
74417 GAAAAATGAA
74427 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
74441 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
74460 AATCGCAACGAGAG
1 AATCGCAACGAGAG
74474 AATCGCAACG
1 AATCGCAACG
74484 CGAAACCAAA
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:74458 original size:33 final size:33
Alignment explanation
Indices: 74420--74499 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
74410 GCAACGAGAA
74420 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
74453 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
74486 AAACCAAAATCGCA
1 AAATGAAAATCGCA
74500 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:74517 original size:19 final size:19
Alignment explanation
Indices: 74495--74622 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
74485 GAAACCAAAA
*
74495 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
74514 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
74528 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
74547 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
74561 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
74581 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
74601 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
74621 TC
1 TC
74623 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:74536 original size:14 final size:14
Alignment explanation
Indices: 74517--74573 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
74507 TTTCATTTCG
74517 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
74531 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
74550 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
74564 CGTTGCGATT
1 CGTTGCGATT
74574 TTCATTTCTC
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:74542 original size:33 final size:33
Alignment explanation
Indices: 74500--74622 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
74490 CAAAATCGCA
74500 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
74533 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
74566 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
74607 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
74623 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:74584 original size:21 final size:21
Alignment explanation
Indices: 74558--74622 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
74548 CGCGTTGCGA
74558 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
74579 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
74599 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
74620 TTC
1 TTC
74623 AACCAAAAGA
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:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:76592 original size:14 final size:14
Alignment explanation
Indices: 76573--76608 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
76563 ATTGTTTAAT
76573 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
76587 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
76601 TGATTTGT
1 TGATTTGT
76609 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:76731 original size:19 final size:19
Alignment explanation
Indices: 76715--76793 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
76705 AAAAATGACT
76715 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
76734 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
76753 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
76767 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
76787 ATCGCAA
1 ATCGCAA
76794 CGAGAGAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 1 0.02
17 3 0.06
19 27 0.52
20 10 0.19
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:76787 original size:34 final size:34
Alignment explanation
Indices: 76733--76811 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
76723 GCGAAATGAA
76733 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
76766 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
76800 AATCGCAATGCG
1 AATCGCAATGCG
76812 ATTTTCATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 11 0.24
34 34 0.76
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (34 bp):
AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
Found at i:76830 original size:19 final size:19
Alignment explanation
Indices: 76802--77010 Score: 259
Period size: 19 Copynumber: 11.7 Consensus size: 19
76792 AACGAGAGAA
*
76802 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
76821 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
76840 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
76857 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
76874 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
76893 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
76909 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
76926 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
76945 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
76964 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
76982 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
76998 TCGCATTGCGATT
1 TCGCATTGCGATT
77011 CTCTCGTTGC
Statistics
Matches: 166, Mismatches: 7, Indels: 34
0.80 0.03 0.16
Matches are distributed among these distances:
14 23 0.14
16 14 0.08
17 14 0.08
18 4 0.02
19 85 0.51
20 26 0.16
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:77032 original size:33 final size:33
Alignment explanation
Indices: 76879--77024 Score: 195
Period size: 33 Copynumber: 4.2 Consensus size: 33
76869 TCATTTCGCA
76879 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
76912 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
76948 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
76984 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
77017 TTGCGATT
1 TTGCGATT
77025 GTAATTTCCG
Statistics
Matches: 99, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
32 1 0.01
33 47 0.47
34 14 0.14
35 3 0.03
36 6 0.06
37 3 0.03
38 15 0.15
39 10 0.10
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:77032 original size:105 final size:103
Alignment explanation
Indices: 76808--77024 Score: 316
Period size: 105 Copynumber: 2.1 Consensus size: 103
76798 AGAATCGCAA
76808 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCA-
76873 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
65 TTCG-ATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
76913 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC-TCT-CG--TTGCGAT
*
76977 TTTCA-T-G-TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
60 TTTCATTCGATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
77018 TGCGATT
1 TGCGATT
77025 GTAATTTCCG
Statistics
Matches: 104, Mismatches: 2, Indels: 12
0.88 0.02 0.10
Matches are distributed among these distances:
104 10 0.10
105 73 0.70
106 3 0.03
107 3 0.03
108 3 0.03
110 12 0.12
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (103 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TCGATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:79324 original size:12 final size:12
Alignment explanation
Indices: 79307--79331 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
79297 TCTTCGGGGA
79307 CTTTTTCTTCTT
1 CTTTTTCTTCTT
79319 CTTTTTCTTCTT
1 CTTTTTCTTCTT
79331 C
1 C
79332 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:80273 original size:20 final size:20
Alignment explanation
Indices: 80245--80413 Score: 187
Period size: 20 Copynumber: 8.4 Consensus size: 20
80235 AAATTTCAGT
* * * *
80245 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
80265 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
80285 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
80305 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
80325 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
80345 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
80365 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
80385 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
80405 GTTGCGATT
1 GTTGCGATT
80414 CTTGAAAATC
Statistics
Matches: 127, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
20 126 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:80466 original size:21 final size:20
Alignment explanation
Indices: 80381--80478 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
80371 ATTTATGTGT
* *
80381 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
80401 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
80422 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
80443 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
80464 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
80479 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:80474 original size:42 final size:43
Alignment explanation
Indices: 80381--80479 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
80371 ATTTATGTGT
* *
80381 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
80422 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
80464 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
80480 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:83674 original size:60 final size:60
Alignment explanation
Indices: 83571--83683 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
83561 AGTGGTCATC
* * *
83571 TTGTAACTCTTAATAGTCGAAAGACTCAACAAAGCATCTTCTTATAGTCGAAGAATCTTT
1 TTGTAACTCTTAATAGTCAAAAGACTCAACAAAGAATCATCTTATAGTCGAAGAATCTTT
* * * *
83631 TTGTAACTTTTAATGGTCAAAAGACTCAATAAAGTAAT-ATCTTATAGTTGAAG
1 TTGTAACTCTTAATAGTCAAAAGACTCAACAAAG-AATCATCTTATAGTCGAAG
83684 GACCATTTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
60 43 0.96
61 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (60 bp):
TTGTAACTCTTAATAGTCAAAAGACTCAACAAAGAATCATCTTATAGTCGAAGAATCTTT
Found at i:90963 original size:14 final size:14
Alignment explanation
Indices: 90944--90979 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
90934 ATCCTCTATT
90944 CGAACATAAATGAA
1 CGAACATAAATGAA
90958 CGAACATAAATGAA
1 CGAACATAAATGAA
90972 CGAACATA
1 CGAACATA
90980 TAATTTAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.17, G:0.14, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:97018 original size:2 final size:2
Alignment explanation
Indices: 97011--97048 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
97001 CCACTCTCCA
*
97011 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
97049 AAAGCTATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:101941 original size:20 final size:20
Alignment explanation
Indices: 101916--101955 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
101906 GTAATCCTAT
* *
101916 TCACTGGTAATCTTTTATTC
1 TCACTGATAATCTTATATTC
101936 TCACTGATAATCTTATATTC
1 TCACTGATAATCTTATATTC
101956 CGTGAACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TCACTGATAATCTTATATTC
Found at i:102820 original size:122 final size:122
Alignment explanation
Indices: 102659--102963 Score: 484
Period size: 123 Copynumber: 2.5 Consensus size: 122
102649 TAAACTACGA
*
102659 GTTTAGTACCTAAACTATCAATTTTGATCCATTATAGTACCTAAACTTTCAATTTTTTTTAAATC
1 GTTTAGTACCTAAACTATCAATTTTGGTCCATTATAGTACCTAAACTTTCAATTTTTTTTAAATC
102724 ATACTTAGCATTTAGTTTTTATTTCATTTTAGTACCTCGCCGTTAAAGACTTAACGC
66 ATACTTAGCATTTAGTTTTTATTTCATTTTAGTACCTCGCCGTTAAAGACTTAACGC
* *
102781 GTTTAGTACCTAAACTATCAATTTTGGTCCATTATAGTACCTAAACTTACAATTTTTTTCAAAAT
1 GTTTAGTACCTAAACTATCAATTTTGGTCCATTATAGTACCTAAACTTTCAATTTTTTT-TAAAT
* * * * *
102846 CATACTTAGTATTTAGTTTTTGTTTCATTTTAGTACCTTGCCGTTAAATACTTAACGT
65 CATACTTAGCATTTAGTTTTTATTTCATTTTAGTACCTCGCCGTTAAAGACTTAACGC
* * * * *
102904 GTTTAGTACCTAAACTATCAATTTTGGTCCGTTTTAATACCCACACTTTCAATTTTTTTT
1 GTTTAGTACCTAAACTATCAATTTTGGTCCATTATAGTACCTAAACTTTCAATTTTTTTT
102964 CTTCAAAACT
Statistics
Matches: 167, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
122 57 0.34
123 110 0.66
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.45
Consensus pattern (122 bp):
GTTTAGTACCTAAACTATCAATTTTGGTCCATTATAGTACCTAAACTTTCAATTTTTTTTAAATC
ATACTTAGCATTTAGTTTTTATTTCATTTTAGTACCTCGCCGTTAAAGACTTAACGC
Found at i:104286 original size:31 final size:31
Alignment explanation
Indices: 104251--104312 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
104241 GTATTAAAAT
* *
104251 TTACATTCGAAGCATTAACTCATACATTACA
1 TTACATTAGAAACATTAACTCATACATTACA
* *
104282 TTACATTAGAAACATTAACTCCTATATTACA
1 TTACATTAGAAACATTAACTCATACATTACA
104313 ATATAATAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (31 bp):
TTACATTAGAAACATTAACTCATACATTACA
Found at i:104323 original size:31 final size:31
Alignment explanation
Indices: 104263--104323 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
104253 ACATTCGAAG
* *
104263 CATTAACTCATACATTACATTACATTAGAAA
1 CATTAACTCATACATTACAATACAATAGAAA
* * *
104294 CATTAACTCCTATATTACAATATAATAGAA
1 CATTAACTCATACATTACAATACAATAGAA
104324 GCGTTAAGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.33
Consensus pattern (31 bp):
CATTAACTCATACATTACAATACAATAGAAA
Found at i:106101 original size:50 final size:50
Alignment explanation
Indices: 105972--106251 Score: 359
Period size: 50 Copynumber: 5.6 Consensus size: 50
105962 TACATCGATA
* * *
105972 TAAGTATGTGTTAAGTGCTATATATTTTTTATTTTATTTACTTACACCGTTG
1 TAAGTATGTGTTAAGTGC--TACATTTTTTATTTTATTCACTTACACCGGTG
* *
106024 TAAGTATGTGTTAAGTGTTACACTTTTTTA-TTTATTCACTTACACCTGTG
1 TAAGTATGTGTTAAGTGCTACA-TTTTTTATTTTATTCACTTACACCGGTG
*
106074 T-AGTATGTGTTAAGTGCTACACTTTTTTATTTTTTTCACTTACACCGGTG
1 TAAGTATGTGTTAAGTGCTACA-TTTTTTATTTTATTCACTTACACCGGTG
* * * *
106124 T-TGTATGTGTTAAGTACTACATTTTTTGTTTTATTAACTTACACCGGTG
1 TAAGTATGTGTTAAGTGCTACATTTTTTATTTTATTCACTTACACCGGTG
* * **
106173 TAAGTATGTGTTAAGTGCTATACTTTTTTATTTTACTCACTTACATTGGTG
1 TAAGTATGTGTTAAGTGCTACA-TTTTTTATTTTATTCACTTACACCGGTG
*
106224 TAAGCATGTGTTAAGTGCTACATTTTTT
1 TAAGTATGTGTTAAGTGCTACATTTTTT
106252 CTAGTATGAA
Statistics
Matches: 201, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
49 53 0.26
50 81 0.40
51 50 0.25
52 17 0.08
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.49
Consensus pattern (50 bp):
TAAGTATGTGTTAAGTGCTACATTTTTTATTTTATTCACTTACACCGGTG
Found at i:106250 original size:149 final size:149
Alignment explanation
Indices: 105975--106251 Score: 396
Period size: 149 Copynumber: 1.8 Consensus size: 149
105965 ATCGATATAA
* * * *
105975 GTATGTGTTAAGTGCTATATATTTTTTATTTTATTTACTTACACCGTTGTAAGTATGTGTTAAGT
1 GTATGTGTTAAGTAC-ATACATTTTTTATTTTATTAACTTACACCGGTGTAAGTATGTGTTAAGT
* * *
106040 GTTACACTTTTTTATTTATTCACTTACACCTGTGTAGTATGTGTTAAGTGCTACACTTTTTTATT
65 GCTACACTTTTTTATTTACTCACTTACACCTGTGTAGCATGTGTTAAGTGCTACAC-TTTTTATT
106105 TTTTTCACTTACACCGGTGTT
129 TTTTTCACTTACACCGGTGTT
*
106126 GTATGTGTTAAGTAC-TACATTTTTTGTTTTATTAACTTACACCGGTGTAAGTATGTGTTAAGTG
1 GTATGTGTTAAGTACATACATTTTTTATTTTATTAACTTACACCGGTGTAAGTATGTGTTAAGTG
* * *
106190 CTATACTTTTTTATTTTACTCACTTACA-TTGGTGTAAGCATGTGTTAAGTGCTACATTTTTT
66 CTACACTTTTTTA-TTTACTCACTTACACCT-GTGT-AGCATGTGTTAAGTGCTACACTTTTT
106252 CTAGTATGAA
Statistics
Matches: 112, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
149 57 0.51
150 22 0.20
151 33 0.29
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.49
Consensus pattern (149 bp):
GTATGTGTTAAGTACATACATTTTTTATTTTATTAACTTACACCGGTGTAAGTATGTGTTAAGTG
CTACACTTTTTTATTTACTCACTTACACCTGTGTAGCATGTGTTAAGTGCTACACTTTTTATTTT
TTTCACTTACACCGGTGTT
Found at i:106997 original size:16 final size:16
Alignment explanation
Indices: 106973--107009 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
106963 TCCTTATTTT
*
106973 TATTGAATAAAAATAA
1 TATTTAATAAAAATAA
*
106989 TATTTAATAAATATAA
1 TATTTAATAAAAATAA
107005 TATTT
1 TATTT
107010 CAGGTCGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TATTTAATAAAAATAA
Found at i:107588 original size:21 final size:21
Alignment explanation
Indices: 107558--107629 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
107548 TATATCAGAC
* * *
107558 TATCAACACTATGGACTGCCA
1 TATCAGCACTGTGAACTGCCA
**
107579 CGTCAGCACTGTGAACTGCCA
1 TATCAGCACTGTGAACTGCCA
107600 TATCAGCACTGTGAACTGCCA
1 TATCAGCACTGTGAACTGCCA
107621 TATCAGCAC
1 TATCAGCAC
107630 CGTAACGGTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (21 bp):
TATCAGCACTGTGAACTGCCA
Found at i:117743 original size:36 final size:38
Alignment explanation
Indices: 117696--117775 Score: 137
Period size: 36 Copynumber: 2.2 Consensus size: 38
117686 GAATGAACTT
*
117696 TTAGTTGTAGTACATGAACTT-AAA-ACACTTTAACCC
1 TTAGTTATAGTACATGAACTTAAAATACACTTTAACCC
117732 TTAGTTATAGTACATGAACTTAAAATACACTTTAACCC
1 TTAGTTATAGTACATGAACTTAAAATACACTTTAACCC
117770 TTAGTT
1 TTAGTT
117776 GAAGCACCCG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 20 0.49
37 3 0.07
38 18 0.44
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (38 bp):
TTAGTTATAGTACATGAACTTAAAATACACTTTAACCC
Done.