Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003324.1 Hibiscus syriacus cultivar Beakdansim tig00007002_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: 60362
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:8222 original size:2 final size:2
Alignment explanation
Indices: 8215--8239 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8205 CAAAAACTAC
8215 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 A
8240 CTCCTTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8405 original size:24 final size:23
Alignment explanation
Indices: 8370--8443 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 23
8360 CTTTTCATAA
8370 AATTTG-CACCGAAGTGCCACGTA-
1 AATTTGTC-CCGAAG-GCCACGTAG
**
8393 AATTTTGTCCCGAAAGGCCGTGTAG
1 AA-TTTGTCCCG-AAGGCCACGTAG
*
8418 AATTTGTCCCGAAGGACCGCGTAG
1 AATTTGTCCCGAAGG-CCACGTAG
8442 AA
1 AA
8444 CCCTCAACTC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
23 6 0.14
24 31 0.72
25 6 0.14
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
AATTTGTCCCGAAGGCCACGTAG
Found at i:8580 original size:30 final size:30
Alignment explanation
Indices: 8544--8604 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
8534 AAGTGTCTTT
*
8544 TATTCACGTAGAACACATTTACATATATCA
1 TATTCACATAGAACACATTTACATATATCA
* * *
8574 TATTCACATAGAACATATTTACTTATTTCA
1 TATTCACATAGAACACATTTACATATATCA
8604 T
1 T
8605 GTACTCATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (30 bp):
TATTCACATAGAACACATTTACATATATCA
Found at i:8590 original size:15 final size:15
Alignment explanation
Indices: 8544--8592 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
8534 AAGTGTCTTT
*
8544 TATTCACGTAGAACA
1 TATTCACATAGAACA
* * * *
8559 CATTTACATATATCA
1 TATTCACATAGAACA
8574 TATTCACATAGAACA
1 TATTCACATAGAACA
8589 TATT
1 TATT
8593 TACTTATTTC
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (15 bp):
TATTCACATAGAACA
Found at i:13411 original size:36 final size:34
Alignment explanation
Indices: 13348--13448 Score: 118
Period size: 31 Copynumber: 3.0 Consensus size: 34
13338 ATATTAACAT
*
13348 ATATAGTTTTTGAAAACA-TTAT--ATATATATA
1 ATATAGTTTTTGAAAACATTTTTGAATATATATA
**
13379 ATATAGTTTTTGAAAACATTTTTGAACGTATATA
1 ATATAGTTTTTGAAAACATTTTTGAATATATATA
* *
13413 ATATATGGTTTTGAAAGCATTTTTCGAATATATATA
1 ATATA-GTTTTTGAAAACATTTTT-GAATATATATA
13449 TAATATTATT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
31 18 0.31
32 3 0.05
34 12 0.21
35 16 0.28
36 9 0.16
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.45
Consensus pattern (34 bp):
ATATAGTTTTTGAAAACATTTTTGAATATATATA
Found at i:13504 original size:22 final size:22
Alignment explanation
Indices: 13477--13518 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
13467 ATAATGTCAT
*
13477 TTTATTGATTTATTTATTTTCA
1 TTTATTGATTTATTCATTTTCA
*
13499 TTTATTTATTTATTCATTTT
1 TTTATTGATTTATTCATTTT
13519 GTTATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTATTGATTTATTCATTTTCA
Found at i:13507 original size:18 final size:17
Alignment explanation
Indices: 13475--13512 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
13465 ATATAATGTC
13475 ATTTTATTGATTTATTT
1 ATTTTATTGATTTATTT
*
13492 ATTTTCATTTATTTATTT
1 ATTTT-ATTGATTTATTT
13510 ATT
1 ATT
13513 CATTTTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTTATTGATTTATTT
Found at i:13525 original size:16 final size:16
Alignment explanation
Indices: 13477--13517 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 16
13467 ATAATGTCAT
*
13477 TTTATTGATTTATTTA
1 TTTATTCATTTATTTA
13493 -TT-TTCATTTATTTA
1 TTTATTCATTTATTTA
13507 TTTATTCATTT
1 TTTATTCATTT
13518 TGTTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.50
15 4 0.18
16 7 0.32
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTATTCATTTATTTA
Found at i:14645 original size:18 final size:18
Alignment explanation
Indices: 14619--14657 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
14609 CTTTAGATTT
*
14619 TTTATTTATTTTCTTTTA
1 TTTAATTATTTTCTTTTA
14637 TTTAATTATTTTCTTTTA
1 TTTAATTATTTTCTTTTA
14655 TTT
1 TTT
14658 TAAAAACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTAATTATTTTCTTTTA
Found at i:14746 original size:20 final size:20
Alignment explanation
Indices: 14693--14749 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
14683 TTATCTTTAC
14693 TATTATTA-TTTA--TTATT
1 TATTATTATTTTATTTTATT
**
14710 TATTA-TATTTCCCTTTTATT
1 TATTATTATTT-TATTTTATT
14730 TATTATTATTTTATTTTATT
1 TATTATTATTTTATTTTATT
14750 ATATATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
16 2 0.06
17 7 0.23
20 17 0.55
21 5 0.16
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTATTATTTTATTTTATT
Found at i:14747 original size:16 final size:16
Alignment explanation
Indices: 14723--14759 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
14713 TATATTTCCC
14723 TTTTATTTATTAT-TA
1 TTTTATTTATTATATA
14738 TTTTATTTTATTATATA
1 TTTTA-TTTATTATATA
14755 TTTTA
1 TTTTA
14760 ACTTTACCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 8 0.40
17 7 0.35
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATTTATTATATA
Found at i:15148 original size:5 final size:5
Alignment explanation
Indices: 15138--15229 Score: 55
Period size: 5 Copynumber: 17.4 Consensus size: 5
15128 TTCTTTTTTA
* *
15138 TATTT TATTT TGTTT TATTTT TATTT TCCCACTT T--TT TATTT TATTT
1 TATTT TATTT TATTT TA-TTT TATTT T---ATTT TATTT TATTT TATTT
* *
15185 TATTT TATTTT TATTT TCTCACT T-TTT TATTT TATTTT TATTT TA
1 TATTT TA-TTT TATTT TAT--TT TATTT TATTT TA-TTT TATTT TA
15230 ACACTTTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 22
0.71 0.06 0.22
Matches are distributed among these distances:
3 3 0.04
4 2 0.03
5 43 0.61
6 16 0.23
7 2 0.03
8 4 0.06
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:15161 original size:16 final size:17
Alignment explanation
Indices: 15133--15229 Score: 72
Period size: 21 Copynumber: 5.3 Consensus size: 17
15123 AACACTTCTT
*
15133 TTTTATATTTTATTTTG
1 TTTTATATTTTATTTTA
15150 TTTTAT-TTTTATTTTCCCA
1 TTTTATATTTTATTTT---A
*
15169 CTTTTTTATTTTATTTTA
1 -TTTTATATTTTATTTTA
15187 TTTTAT-TTTTATTTTCTCA
1 TTTTATATTTTA-TTT-T-A
*
15206 CTTTTTTATTTTATTTTTA
1 -TTTTATATTTTA-TTTTA
15225 TTTTA
1 TTTTA
15230 ACACTTTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
16 14 0.22
17 14 0.22
18 6 0.09
19 2 0.03
20 11 0.17
21 18 0.28
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.75
Consensus pattern (17 bp):
TTTTATATTTTATTTTA
Found at i:15179 original size:37 final size:37
Alignment explanation
Indices: 15132--15229 Score: 160
Period size: 37 Copynumber: 2.6 Consensus size: 37
15122 TAACACTTCT
*
15132 TTTTTATATTTTATTTTGTTTTATTTTTATTTTCCCAC
1 TTTTT-TATTTTATTTTATTTTATTTTTATTTTCCCAC
*
15170 TTTTTTATTTTATTTTATTTTATTTTTATTTTCTCAC
1 TTTTTTATTTTATTTTATTTTATTTTTATTTTCCCAC
15207 TTTTTTATTTTATTTTTATTTTA
1 TTTTTTATTTTA-TTTTATTTTA
15230 ACACTTTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
37 42 0.74
38 15 0.26
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.76
Consensus pattern (37 bp):
TTTTTTATTTTATTTTATTTTATTTTTATTTTCCCAC
Found at i:15234 original size:27 final size:27
Alignment explanation
Indices: 15182--15244 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
15172 TTTTATTTTA
**
15182 TTTTATTTTATTTTTATTTTCTCACTT
1 TTTTATTTTATTTTTATTTTAACACTT
15209 TTTTATTTTATTTTTATTTTAACACTT
1 TTTTATTTTATTTTTATTTTAACACTT
15236 TTTTATTTT
1 TTTTATTTT
15245 TCTTCTCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTTATTTTATTTTTATTTTAACACTT
Found at i:15238 original size:16 final size:14
Alignment explanation
Indices: 15155--15244 Score: 56
Period size: 16 Copynumber: 6.7 Consensus size: 14
15145 TTTTGTTTTA
15155 TTTTTATTTTCCCACT
1 TTTTTATTTT--CACT
15171 TTTTTATTTT-A--
1 TTTTTATTTTCACT
15182 -TTTTATTTT-A--
1 TTTTTATTTTCACT
15192 TTTTTATTTTCTCACT
1 TTTTTA-TTT-TCACT
15208 TTTTTATTTT-A--
1 TTTTTATTTTCACT
15219 TTTTTATTTTAACACT
1 TTTTTATTTT--CACT
15235 TTTTTATTTT
1 TTTTTATTTT
15245 TCTTCTCTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 22
0.74 0.00 0.26
Matches are distributed among these distances:
10 10 0.16
11 15 0.24
12 3 0.05
13 3 0.05
14 3 0.05
15 3 0.05
16 26 0.41
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTATTTTCACT
Found at i:15261 original size:64 final size:63
Alignment explanation
Indices: 15145--15304 Score: 166
Period size: 64 Copynumber: 2.5 Consensus size: 63
15135 TTATATTTTA
* ** * *
15145 TTTTGTTTTATTTTTATTTTCCCACTTTTTTATTTTATTTTATTT-TATTTT-TATTTTCTCACT
1 TTTTATTTTATTTTTATTTTAACACTTTTTTATTTTATCTTATTTAAATTTTATATTTTCT---T
*
15208 T
63 C
*
15209 TTTTATTTTATTTTTATTTTAACACTTTTTTATTTT-TCTTCTCTTAAATTTTATATTTTCTTC
1 TTTTATTTTATTTTTATTTTAACACTTTTTTATTTTATCTTAT-TTAAATTTTATATTTTCTTC
* *
15272 ATTTATTTTATTTTTTCTTTTAACA-TTTTTTAT
1 TTTTATTTTA-TTTTTATTTTAACACTTTTTTAT
15305 ATAACATTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
63 22 0.27
64 48 0.58
65 5 0.06
66 8 0.10
ACGTcount: A:0.17, C:0.10, G:0.01, T:0.72
Consensus pattern (63 bp):
TTTTATTTTATTTTTATTTTAACACTTTTTTATTTTATCTTATTTAAATTTTATATTTTCTTC
Found at i:15320 original size:64 final size:64
Alignment explanation
Indices: 15210--15351 Score: 150
Period size: 64 Copynumber: 2.2 Consensus size: 64
15200 TTCTCACTTT
* ** *
15210 TTTATTTTA-TTTTTATTTTAACACTTTTTTATTTTTCTTCTCTT-AAATTTTATATTTTC-TTC
1 TTTATTTTATTTTTTATTTTAACACTTTTTTATATAACTTCTCTTAAAATTTAATA-TTTCATTC
* * *
15272 ATTTATTTTATTTTTTCTTTTAACA-TTTTTTATATAACATTTTTTTAAAATTTAATATTTCATT
1 -TTTATTTTATTTTTTATTTTAACACTTTTTTATATAAC-TTCTCTTAAAATTTAATATTTCATT
15336 C
64 C
15337 TTTGA-TTTATTTTTT
1 TTT-ATTTTATTTTTT
15352 TAAATTTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
63 19 0.28
64 35 0.52
65 13 0.19
ACGTcount: A:0.23, C:0.08, G:0.01, T:0.68
Consensus pattern (64 bp):
TTTATTTTATTTTTTATTTTAACACTTTTTTATATAACTTCTCTTAAAATTTAATATTTCATTC
Found at i:23432 original size:18 final size:18
Alignment explanation
Indices: 23409--23451 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
23399 CTTTAGATTA
*
23409 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
23427 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
23445 TTTATTT
1 TTTATTT
23452 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:23879 original size:16 final size:16
Alignment explanation
Indices: 23858--23888 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
23848 TTCCTATAGT
23858 TTTGATGCGCAATTCG
1 TTTGATGCGCAATTCG
23874 TTTGATGCGCAATTC
1 TTTGATGCGCAATTC
23889 TTTCCTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (16 bp):
TTTGATGCGCAATTCG
Found at i:23937 original size:25 final size:26
Alignment explanation
Indices: 23909--23965 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
23899 TTTTCTTTAA
23909 ATTTTAACACTTC-TTTTTTTATTTT
1 ATTTTAACACTTCTTTTTTTTATTTT
**
23934 ATTTTCCCACTTCTTTTTTTTATTTT
1 ATTTTAACACTTCTTTTTTTTATTTT
23960 ATTTTA
1 ATTTTA
23966 TTTTATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.68
Consensus pattern (26 bp):
ATTTTAACACTTCTTTTTTTTATTTT
Found at i:23961 original size:5 final size:5
Alignment explanation
Indices: 23947--23980 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
23937 TTCCCACTTC
23947 TTTT- TTTTA TTTTA TTTTA TTTTA TTTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTT
23981 CTCTTTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTA
Found at i:25661 original size:24 final size:23
Alignment explanation
Indices: 25642--25699 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
25632 CACCGAAGTG
*
25642 CCACGTAGATTTTGTCCCGAAAGA
1 CCACGTAGAATTTGTCCCG-AAGA
*
25666 CCATGTAGAATTTGTCCCGAAGGA
1 CCACGTAGAATTTGTCCCGAA-GA
*
25690 CCGCGTAGAA
1 CCACGTAGAA
25700 CCCTCGACTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (23 bp):
CCACGTAGAATTTGTCCCGAAGA
Found at i:25834 original size:30 final size:30
Alignment explanation
Indices: 25800--25862 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
25790 AAGTGTCTTT
*
25800 TATTCACGTAGAACACATTTACATATATCA
1 TATTCACATAGAACACATTTACATATATCA
* * *
25830 TATTCACATAGAACATATTTACTTATTTCA
1 TATTCACATAGAACACATTTACATATATCA
25860 TAT
1 TAT
25863 ACTCATACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (30 bp):
TATTCACATAGAACACATTTACATATATCA
Found at i:25846 original size:15 final size:15
Alignment explanation
Indices: 25800--25848 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
25790 AAGTGTCTTT
*
25800 TATTCACGTAGAACA
1 TATTCACATAGAACA
* * * *
25815 CATTTACATATATCA
1 TATTCACATAGAACA
25830 TATTCACATAGAACA
1 TATTCACATAGAACA
25845 TATT
1 TATT
25849 TACTTATTTC
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (15 bp):
TATTCACATAGAACA
Found at i:35431 original size:21 final size:21
Alignment explanation
Indices: 35405--35450 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
35395 CAATTAAGTA
*
35405 ATATCTCGAAATCGAATCTTT
1 ATATCTCGAAATCGAATATTT
*
35426 ATATCTCGAATTCGAATATTT
1 ATATCTCGAAATCGAATATTT
35447 ATAT
1 ATAT
35451 ATATGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (21 bp):
ATATCTCGAAATCGAATATTT
Found at i:40425 original size:2 final size:2
Alignment explanation
Indices: 40418--40471 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
40408 TTTAAGGTGC
40418 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
40460 AT AT AT AT AT AT
1 AT AT AT AT AT AT
40472 TAACAACACA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40850 original size:20 final size:20
Alignment explanation
Indices: 40825--40875 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
40815 AAGCATGGAA
*
40825 TATCGATACCATGTTA-AGGG
1 TATCGATACCA-ATTATAGGG
*
40845 TATCGATACTCAATTATATGG
1 TATCGATAC-CAATTATAGGG
40866 TATCGATACC
1 TATCGATACC
40876 CTTGGTCAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (20 bp):
TATCGATACCAATTATAGGG
Found at i:45110 original size:19 final size:19
Alignment explanation
Indices: 45053--45110 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
45043 TAATAATGTG
* *
45053 CTTTTGTCTGTTAGGTTAA
1 CTTTTGTATGTTAGGTTTA
*
45072 CTTTTTGTA--TT--GTATA
1 C-TTTTGTATGTTAGGTTTA
45088 CTTTTGTATGTTAGGTTTA
1 CTTTTGTATGTTAGGTTTA
45107 CTTT
1 CTTT
45111 ACTGATTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
15 7 0.23
16 4 0.13
17 2 0.07
18 2 0.07
19 9 0.30
20 6 0.20
ACGTcount: A:0.16, C:0.09, G:0.17, T:0.59
Consensus pattern (19 bp):
CTTTTGTATGTTAGGTTTA
Found at i:45328 original size:13 final size:13
Alignment explanation
Indices: 45310--45343 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
45300 GGTATTTGTA
45310 TTATAATATGCGT
1 TTATAATATGCGT
45323 TTATAAAATATGCGT
1 TTAT--AATATGCGT
45338 TTATAA
1 TTATAA
45344 AAATATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.32
15 13 0.68
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (13 bp):
TTATAATATGCGT
Found at i:45334 original size:15 final size:16
Alignment explanation
Indices: 45314--45350 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
45304 TTTGTATTAT
45314 AATATGCGTTTAT-AA
1 AATATGCGTTTATAAA
45329 AATATGCGTTTATAAA
1 AATATGCGTTTATAAA
45345 AATATG
1 AATATG
45351 TATTAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (16 bp):
AATATGCGTTTATAAA
Found at i:45423 original size:15 final size:16
Alignment explanation
Indices: 45405--45443 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
45395 TAGATTGATA
45405 TGATTTAGGGTTTA-T
1 TGATTTAGGGTTTACT
45420 TGATTTAGGGTTTACT
1 TGATTTAGGGTTTACT
45436 TGTATTTA
1 TG-ATTTA
45444 AATATTATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 14 0.64
16 3 0.14
17 5 0.23
ACGTcount: A:0.21, C:0.03, G:0.23, T:0.54
Consensus pattern (16 bp):
TGATTTAGGGTTTACT
Found at i:46447 original size:93 final size:96
Alignment explanation
Indices: 46300--46510 Score: 286
Period size: 93 Copynumber: 2.2 Consensus size: 96
46290 ATACCGAGGA
* * * * *
46300 GGTAGTATCGATACCATGATAAGGGGTATCGATACCAAGCAATATCGAATCTAATTTTGGTATCG
1 GGTAGTATCAATACCATGGTAAGGGGTATCAATACCAAGCAACATCGAACCTAATTTTGGTATCG
46365 ATACCGG-AAGGGGTATCG-TACCATAGTAT
66 ATACCGGAAAGGGGTATCGTTACCATAGTAT
* *
46394 GGTAGCATCAATACCATGGTAA-GGGTATCAATACC-AGATAACATCGAACCTAATTTTGGTATC
1 GGTAGTATCAATACCATGGTAAGGGGTATCAATACCAAG-CAACATCGAACCTAATTTTGGTATC
46457 GATACCGGATAAGGGGTATCGTTACCATAGTAT
65 GATACCGGA-AAGGGGTATCGTTACCATAGTAT
* * *
46490 AGAAGTATCAATACCAGGGTA
1 GGTAGTATCAATACCATGGTA
46511 GTAGTATCGT
Statistics
Matches: 102, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
92 2 0.02
93 42 0.41
94 19 0.19
95 11 0.11
96 28 0.27
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (96 bp):
GGTAGTATCAATACCATGGTAAGGGGTATCAATACCAAGCAACATCGAACCTAATTTTGGTATCG
ATACCGGAAAGGGGTATCGTTACCATAGTAT
Found at i:46918 original size:55 final size:55
Alignment explanation
Indices: 46834--47210 Score: 594
Period size: 55 Copynumber: 6.9 Consensus size: 55
46824 TGTGTACTAT
46834 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
** *
46889 AGGCACTTCGTGTGCATATTCATAGAATTCATCATGAGTTAATGAATCACCGTAC
1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
46944 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
* * *
46999 AGGCACTTCGTGTGCATATTCATGGAATTCGTCATCAGTTGATGAATCACCGTAC
1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
* * *
47054 AAGCACTTCGTGTGCATATTCACGGAATTTATCATGATTTGATGAATCACCGTAC
1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
* *
47109 AGGCACTTCGTGTGCATATTCACAGAATTCATCATGAGTTGATGAATCACCGTAT
1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
** * * *
47164 AAACACCTT-GTGTGCAAATCCACGGATTTCATCATGAGTTGATGAAT
1 AGGCA-CTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAAT
47211 TTTTGTATGG
Statistics
Matches: 295, Mismatches: 26, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
55 292 0.99
56 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (55 bp):
AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
Found at i:53537 original size:95 final size:95
Alignment explanation
Indices: 53357--53540 Score: 273
Period size: 94 Copynumber: 1.9 Consensus size: 95
53347 CTGATTCAAT
* *
53357 TAGTATCGATACCATGATAAGGGTTATCGATACCAAGCAATATCGAATCTAATTTTGGTATCGAT
1 TAGTATCGATACCATGATAAGGGTTATCGATACCAAGCAACATCGAACCTAATTTTGGTATCGAT
* *
53422 ACCTGAAGGGGTATCGGTACCATATTATGG
66 ACCGGAAGGGGTATCAGTACCATATTATGG
* *
53452 TAGTATCGATACCATGGTAAGGG-TATCGATACC-AGACAACATCGAACCTAATTTTGGTATTGA
1 TAGTATCGATACCATGATAAGGGTTATCGATACCAAG-CAACATCGAACCTAATTTTGGTATCGA
*
53515 TACCGGATGGGGGTATCAGTACCATA
65 TACCGGA-AGGGGTATCAGTACCATA
53541 GATAGAAGTA
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
93 2 0.03
94 40 0.50
95 38 0.47
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.29
Consensus pattern (95 bp):
TAGTATCGATACCATGATAAGGGTTATCGATACCAAGCAACATCGAACCTAATTTTGGTATCGAT
ACCGGAAGGGGTATCAGTACCATATTATGG
Found at i:53639 original size:29 final size:29
Alignment explanation
Indices: 53592--53657 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
53582 ATGGAGCCAA
53592 AATGTTAAAATAGACTGATATTGGTATAG
1 AATGTTAAAATAGACTGATATTGGTATAG
**
53621 AATGTTAAAATAGGTTGATATTGGTATAG
1 AATGTTAAAATAGACTGATATTGGTATAG
*
53650 AAAGTTAA
1 AATGTTAA
53658 TGATGCGTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.42, C:0.02, G:0.21, T:0.35
Consensus pattern (29 bp):
AATGTTAAAATAGACTGATATTGGTATAG
Found at i:54025 original size:55 final size:55
Alignment explanation
Indices: 53941--54269 Score: 496
Period size: 55 Copynumber: 6.0 Consensus size: 55
53931 TGTTCTATAG
* *
53941 GCACTTCGTGTGCATATTCATGGAATTCATCATGAGTTGATGAATTACCGTACAA
1 GCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTACAA
* ** ***
53996 GCACTTCGTGTGTATATTCATAGAATTCATCATGAGTTGATGAATCACCGTATTG
1 GCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTACAA
* *
54051 GCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCAACGTACAG
1 GCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTACAA
* * *
54106 GCACTTCGTGTGCATATTCACGGAATTTTATCATGAGTTGATGGATCATCGTACAA
1 GCACTTCGTGTGCATATTCACGGAA-TTCATCATGAGTTGATGAATCACCGTACAA
* *
54162 GCACTTCGTGTACATATTCACGGAATTCATCATGAGTTGATGAATCACCGTACAT
1 GCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTACAA
* *
54217 GCACTTCATGTGCATATTCACGGAATTCAACATGAGTTGATGAATCACCGTAC
1 GCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
54270 GGGCACCTTG
Statistics
Matches: 249, Mismatches: 24, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
55 199 0.80
56 50 0.20
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (55 bp):
GCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTACAA
Found at i:54212 original size:166 final size:166
Alignment explanation
Indices: 53939--54316 Score: 539
Period size: 166 Copynumber: 2.3 Consensus size: 166
53929 TGTGTTCTAT
* *
53939 AGGCACTTCGTGTGCATATTCATGGAA-TTCATCATGAGTTGATGAATTACCGTACAAGCACTTC
1 AGGCACTTCGTGTGCATATTCATGGAATTTTATCATGAGTTGATGAATCACCGTACAAGCACTTC
** * * *
54003 GTGTGTATATTCATAGAATTCATCATGAGTTGATGAATCACCGTA-TTGGCACTTCGTGTGCATA
66 GTGTACATATTCACAGAATTCATCATGAGTTGATGAATCACCGTACAT-GCACTTCATGTGCATA
*
54067 TTCACGGAATTCATCATGAGTTGATGAATCAACGTAC
130 TTCACGGAATTCAACATGAGTTGATGAATCAACGTAC
* * *
54104 AGGCACTTCGTGTGCATATTCACGGAATTTTATCATGAGTTGATGGATCATCGTACAAGCACTTC
1 AGGCACTTCGTGTGCATATTCATGGAATTTTATCATGAGTTGATGAATCACCGTACAAGCACTTC
*
54169 GTGTACATATTCACGGAATTCATCATGAGTTGATGAATCACCGTACATGCACTTCATGTGCATAT
66 GTGTACATATTCACAGAATTCATCATGAGTTGATGAATCACCGTACATGCACTTCATGTGCATAT
*
54234 TCACGGAATTCAACATGAGTTGATGAATCACCGTAC
131 TCACGGAATTCAACATGAGTTGATGAATCAACGTAC
* * * * * *
54270 GGGCACCTT-GTGTGTAAATCCATGG-ATTTTATCATAAGTTAATGAAT
1 AGGCA-CTTCGTGTGCATATTCATGGAATTTTATCATGAGTTGATGAAT
54317 TTCTATACAG
Statistics
Matches: 189, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
165 45 0.24
166 140 0.74
167 4 0.02
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (166 bp):
AGGCACTTCGTGTGCATATTCATGGAATTTTATCATGAGTTGATGAATCACCGTACAAGCACTTC
GTGTACATATTCACAGAATTCATCATGAGTTGATGAATCACCGTACATGCACTTCATGTGCATAT
TCACGGAATTCAACATGAGTTGATGAATCAACGTAC
Found at i:55522 original size:21 final size:21
Alignment explanation
Indices: 55496--55545 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
55486 CAAGATGAAC
*
55496 AAGTAGAGGAT-AAGCAAGTTG
1 AAGTAGAAGATGAA-CAAGTTG
55517 AAGTAGAAGATGAACAAGTTG
1 AAGTAGAAGATGAACAAGTTG
*
55538 AAGAAGAA
1 AAGTAGAA
55546 TAAGATGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.50, C:0.04, G:0.30, T:0.16
Consensus pattern (21 bp):
AAGTAGAAGATGAACAAGTTG
Found at i:55836 original size:3 final size:3
Alignment explanation
Indices: 55828--55871 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
55818 AGTTTATTTT
** *
55828 TTA TTA TTA AAA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
55872 TAAATAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:55851 original size:18 final size:18
Alignment explanation
Indices: 55828--55876 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
55818 AGTTTATTTT
55828 TTATTATTAAAATTATTA
1 TTATTATTAAAATTATTA
*
55846 TTATTATTATAATTATTA
1 TTATTATTAAAATTATTA
*
55864 TTATTATTTAAAT
1 TTATTATTAAAAT
55877 AAATATTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTATTAAAATTATTA
Found at i:57430 original size:3 final size:3
Alignment explanation
Indices: 57422--57457 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
57412 ATATATTTAT
*
57422 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
57458 CAAATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:57794 original size:28 final size:28
Alignment explanation
Indices: 57758--57821 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
57748 ATTTATAAGT
*
57758 AAATAAATATATATTTATAAAAAT-ATAA
1 AAATAAATAGAT-TTTATAAAAATCATAA
* *
57786 AAATTAATAGATTTTATTAAAATCATAA
1 AAATAAATAGATTTTATAAAAATCATAA
*
57814 TAATAAAT
1 AAATAAAT
57822 TTGAAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 10 0.33
28 20 0.67
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (28 bp):
AAATAAATAGATTTTATAAAAATCATAA
Found at i:58123 original size:12 final size:12
Alignment explanation
Indices: 58102--58136 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
58092 GGCGACTCCC
58102 AAAA-CATTTTA
1 AAAATCATTTTA
58113 AAAATCATTTTA
1 AAAATCATTTTA
58125 AAAATCATTTTA
1 AAAATCATTTTA
58137 TCCACATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATCATTTTA
Done.