Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001143.1 Hibiscus syriacus cultivar Beakdansim tig00002284_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: 53781
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:166 original size:3 final size:3
Alignment explanation
Indices: 158--241 Score: 89
Period size: 3 Copynumber: 27.7 Consensus size: 3
148 CGAGTTGGTT
* * * *
158 TTA TTA TTA TTTA TTA TTA TCA TTTA TTA TTA TAA TAA TAA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
* *
205 TTA TAA TTA TTA TTA TTA TTA TTA TT- TTA TTA ATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
242 TTTTTTTTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.03
3 63 0.90
4 5 0.07
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:9650 original size:2 final size:2
Alignment explanation
Indices: 9643--9698 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
9633 AATAAAATTG
9643 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
9685 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
9699 TACTAATTCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11513 original size:2 final size:2
Alignment explanation
Indices: 11506--11566 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
11496 CCACTATCCT
11506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11548 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
11567 CGCTTGATAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12296 original size:43 final size:43
Alignment explanation
Indices: 12239--12445 Score: 206
Period size: 43 Copynumber: 4.8 Consensus size: 43
12229 GACGTTTATA
* * *
12239 TCCAAAAACGCCGCTATAAATATGACCTTTTGCAGCGTTTGTG
1 TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTG
* * *
12282 TCCAAAAACACCGCTATAGATCTGACCTCTTGCGGCGTTT-TT
1 TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTG
** * *
12324 TTTAAAAA-TCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTA
1 TCCAAAAACGCCGCTATAGATC-TGACCTTTTGCGGCGTTTGTG
* * *
12367 TCCAACAACGCCGCTATATATCT-ACCATTTTGCGGCGTTTTTG
1 TCCAAAAACGCCGCTATAGATCTGACC-TTTTGCGGCGTTTGTG
* * * *
12410 -CCAAAAACTCCGCTAGAGAACTTGACATTTTGCGGC
1 TCCAAAAACGCCGCTATAGATC-TGACCTTTTGCGGC
12446 ATTTTTATAT
Statistics
Matches: 134, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
41 12 0.09
42 43 0.32
43 66 0.49
44 13 0.10
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (43 bp):
TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTG
Found at i:12400 original size:85 final size:86
Alignment explanation
Indices: 12240--12445 Score: 240
Period size: 85 Copynumber: 2.4 Consensus size: 86
12230 ACGTTTATAT
* * * *
12240 CCAAAAACGCCGCTATA-AA-TATGACCTTTTGCAGCGTTTGTGTCCAAAAACACCGCTATAGAT
1 CCAAAAACTCCGCTAGAGAACT-TGACCTTTTGCGGCGTTTGTATCCAAAAACACCGCTATAGAT
*
12303 CTGACCTCTTGCGGCGTTTTTT
65 CTGACCTCTTGCGGCGTTTTTG
** * * * * *
12325 TTAAAAA-TCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTATCCAACAACGCCGCTATATATC
1 CCAAAAACTCCGCTAGAGAACTTGACCTTTTGCGGCGTTTGTATCCAAAAACACCGCTATAGATC
*
12389 T-ACCATTTTGCGGCGTTTTTG
66 TGACC-TCTTGCGGCGTTTTTG
*
12410 CCAAAAACTCCGCTAGAGAACTTGACATTTTGCGGC
1 CCAAAAACTCCGCTAGAGAACTTGACCTTTTGCGGC
12446 ATTTTTATAT
Statistics
Matches: 101, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
84 11 0.11
85 64 0.63
86 26 0.26
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (86 bp):
CCAAAAACTCCGCTAGAGAACTTGACCTTTTGCGGCGTTTGTATCCAAAAACACCGCTATAGATC
TGACCTCTTGCGGCGTTTTTG
Found at i:15689 original size:31 final size:31
Alignment explanation
Indices: 15648--15723 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
15638 CAATTACGTC
*
15648 GGAGACCATATTACAAACGGACTAAATGTTG-
1 GGAGATCATATTA-AAACGGACTAAATGTTGA
*
15679 GGAGATCATATTGAAAATGGACTAAATGTTGA
1 GGAGATCATATT-AAAACGGACTAAATGTTGA
* *
15711 GGGGATTATATTA
1 GGAGATCATATTA
15724 TAAGTTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 28 0.72
32 11 0.28
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (31 bp):
GGAGATCATATTAAAACGGACTAAATGTTGA
Found at i:18612 original size:7 final size:7
Alignment explanation
Indices: 18590--18628 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
18580 CCGACCCGAC
18590 CCGTTGA
1 CCGTTGA
18597 CCAGTTGA
1 CC-GTTGA
18605 CCGTTGA
1 CCGTTGA
18612 CCGTTGA
1 CCGTTGA
*
18619 CCTTTGA
1 CCGTTGA
18626 CCG
1 CCG
18629 GCGTTGACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.15, C:0.31, G:0.26, T:0.28
Consensus pattern (7 bp):
CCGTTGA
Found at i:21229 original size:24 final size:24
Alignment explanation
Indices: 21107--21222 Score: 164
Period size: 24 Copynumber: 4.8 Consensus size: 24
21097 TTCGATTTGA
21107 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
21131 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
21155 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
21179 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
*
21202 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
21223 CTGATTTATG
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 80 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:21245 original size:24 final size:24
Alignment explanation
Indices: 21159--21232 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
21149 ACATGGATTC
* * *
21159 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
21183 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
21207 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
21231 TG
1 TG
21233 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:22399 original size:15 final size:16
Alignment explanation
Indices: 22379--22408 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
22369 TATTATGGTT
22379 TCATTGT-TTTATTTG
1 TCATTGTATTTATTTG
22394 TCATTGTATTTATTT
1 TCATTGTATTTATTT
22409 ATTTTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (16 bp):
TCATTGTATTTATTTG
Found at i:33183 original size:25 final size:24
Alignment explanation
Indices: 33150--33220 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 24
33140 TATCATTTAT
*
33150 AATATTTTTATATGTTAACTTTAAGA
1 AATA-TTTTATATATTAACTTTAA-A
* *
33176 AATGTTTTTTATATTAACTTATTAAA
1 AATATTTTATATATTAAC-T-TTAAA
33202 AATATTTTAT-TATTAACTT
1 AATATTTTATATATTAACTT
33221 AATTTAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 1 0.03
24 1 0.03
25 19 0.50
26 13 0.34
27 4 0.11
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (24 bp):
AATATTTTATATATTAACTTTAAA
Found at i:33204 original size:26 final size:26
Alignment explanation
Indices: 33150--33239 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 26
33140 TATCATTTAT
*
33150 AATATTTTTATATGTTAAC-T-TTAAGA
1 AATATTTTT-TATATTAACTTATTAA-A
*
33176 AATGTTTTTTATATTAACTTATTAAA
1 AATATTTTTTATATTAACTTATTAAA
*
33202 AATATTTTAT-TATTAACTTAATTTAAAA
1 AATATTTTTTATATTAACTT-A-TT-AAA
33230 AATTATTTTT
1 AA-TATTTTT
33240 AATGTCAAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
25 17 0.32
26 19 0.36
27 6 0.11
28 5 0.09
29 6 0.11
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (26 bp):
AATATTTTTTATATTAACTTATTAAA
Found at i:33221 original size:25 final size:26
Alignment explanation
Indices: 33182--33230 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
33172 AAGAAATGTT
33182 TTTTATATTAACTT-A-TTAAAAATA
1 TTTTATATTAACTTAATTTAAAAATA
33206 TTTTATTATTAACTTAATTTAAAAA
1 TTTTA-TATTAACTTAATTTAAAAA
33231 ATTATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.23
25 9 0.41
26 1 0.05
27 7 0.32
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTTATATTAACTTAATTTAAAAATA
Found at i:33517 original size:31 final size:31
Alignment explanation
Indices: 33474--33542 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
33464 ACCCGTGGTG
* *
33474 ATCACATCTTAATTAAATAAAAACTAAAATA
1 ATCATATCTTAATTAAATAAAAACGAAAATA
*
33505 ATTATATCTTAATTAAATAAAAACGAAAATA
1 ATCATATCTTAATTAAATAAAAACGAAAATA
33536 ATCATAT
1 ATCATAT
33543 AGTATGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.57, C:0.10, G:0.01, T:0.32
Consensus pattern (31 bp):
ATCATATCTTAATTAAATAAAAACGAAAATA
Found at i:34559 original size:16 final size:16
Alignment explanation
Indices: 34540--34627 Score: 94
Period size: 16 Copynumber: 5.5 Consensus size: 16
34530 TTAGAGGGAA
*
34540 AAATGAATAAATGAAA-
1 AAATGAAAAAAT-AAAT
34556 AAATGAAGAATAA-AAAT
1 AAATGAA-AA-AATAAAT
34573 AAAT-AAAAAATAAAT
1 AAATGAAAAAATAAAT
*
34588 AAAAGAAAAAATAAAT
1 AAATGAAAAAATAAAT
34604 AAAT-AAATAAATAAAT
1 AAATGAAA-AAATAAAT
34620 AAATGAAA
1 AAATGAAA
34628 TATTAATATA
Statistics
Matches: 62, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
14 2 0.03
15 12 0.19
16 38 0.61
17 8 0.13
18 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (16 bp):
AAATGAAAAAATAAAT
Found at i:34578 original size:4 final size:4
Alignment explanation
Indices: 34569--34629 Score: 81
Period size: 4 Copynumber: 15.2 Consensus size: 4
34559 TGAAGAATAA
*
34569 AAAT AAAT AAA- AAAT AAAT AAA- AGAAA AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT
34616 AAAT AAAT GAAAT A
1 AAAT AAAT -AAAT A
34630 TTAATATATA
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
3 4 0.08
4 43 0.83
5 5 0.10
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:34716 original size:18 final size:18
Alignment explanation
Indices: 34667--34720 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 18
34657 AAAATAGAAA
*
34667 AATAATAATCATAACAATAAT
1 AATAGTAAT-ATAA-AAT-AT
34688 AATAGTAATATGAAAATAT
1 AATAGTAATAT-AAAATAT
34707 AATA-TAATATAAAA
1 AATAGTAATATAAAA
34721 AAACCAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 4 0.13
18 6 0.19
19 6 0.19
20 5 0.16
21 10 0.32
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
AATAGTAATATAAAATAT
Found at i:34721 original size:18 final size:19
Alignment explanation
Indices: 34671--34721 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
34661 TAGAAAAATA
*
34671 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
*
34691 AGTAATATGAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
34710 ATAATATAAAAA
1 ATAATATAAAAA
34722 AACCAAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 6 0.22
20 7 0.26
21 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:34738 original size:33 final size:33
Alignment explanation
Indices: 34700--34782 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 33
34690 TAGTAATATG
34700 AAAATATAATATAATATAAAAAAACCAAAAACA
1 AAAATATAATATAATATAAAAAAACCAAAAACA
* * *
34733 AAAATA-AATA-AATAT--ATAAACCAAATATA
1 AAAATATAATATAATATAAAAAAACCAAAAACA
*
34762 AAAGTATACATATAATGATAA
1 AAAATATA-ATATAAT-ATAA
34783 TTGGATTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
29 16 0.40
30 1 0.03
31 8 0.20
32 7 0.17
33 8 0.20
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.23
Consensus pattern (33 bp):
AAAATATAATATAATATAAAAAAACCAAAAACA
Found at i:34917 original size:2 final size:2
Alignment explanation
Indices: 34912--34952 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
34902 TAAAAAAAAG
*
34912 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34953 GTATTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:35544 original size:37 final size:37
Alignment explanation
Indices: 35494--35598 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
35484 GTGCTTGTGG
* * * *
35494 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTT
* * *
35531 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTT
35568 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
35599 GACGAAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTT
Found at i:36445 original size:105 final size:105
Alignment explanation
Indices: 36141--36771 Score: 898
Period size: 105 Copynumber: 6.0 Consensus size: 105
36131 GCATTGTTCC
* * ** *
36141 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * * *
36205 ACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
36247 AATTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTATTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
36307 CAGCGGTCCCTTCGTCGT-AGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGA-AGTTGAACTTGCGTTGTCTG
36347 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
36412 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
36452 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* * *
36517 CAGTGGTCCATTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
36557 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTATTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
36622 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
36662 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
36727 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
36768 GAGT
1 GAGT
36772 GTCACGATAT
Statistics
Matches: 479, Mismatches: 37, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
99 1 0.00
100 79 0.16
101 1 0.00
102 7 0.01
104 5 0.01
105 302 0.63
106 84 0.18
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:37018 original size:36 final size:36
Alignment explanation
Indices: 36971--37046 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
36961 TGTTTGGAGA
* *
36971 GAAACTGTCTCAAGGGAGACAAAATTCGA-TTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTC-ATTTCAAGG
*
37007 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
37043 GAAA
1 GAAA
37047 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 1 0.03
36 35 0.97
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:37163 original size:103 final size:104
Alignment explanation
Indices: 36946--37262 Score: 498
Period size: 103 Copynumber: 3.1 Consensus size: 104
36936 TTCGTTAAAT
* ** * *
36946 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GATTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
37008 AAACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
* *
37047 TGTTTTCAATGTTTATATTTCAAGAGAAACTGTCTCAAGGGAGATAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
37112 AAACTATCTCAAGAGA-AAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
37150 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
37215 AAACTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
37254 TGTTTTCAA
1 TGTTTTCAA
37263 GAGAAACTAT
Statistics
Matches: 197, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
101 44 0.22
103 101 0.51
104 52 0.26
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:37219 original size:39 final size:39
Alignment explanation
Indices: 37165--37239 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
37155 TCAATGTTTA
* *
37165 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTC-AGGAGAGAAAAAATTTTC
* *
37204 TGTTTCGAGGGAAACTATCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATT
37240 AATTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATTTTC
Found at i:37417 original size:36 final size:36
Alignment explanation
Indices: 37377--37490 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 36
37367 CTTTCGAGTG
* *
37377 AAAACGGTCTCAAGCGAGACAAATCTTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
* ** * * * **
37413 AAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
* *
37449 AAAACAGTCTCAAGTGAGACAAAGT-ATGCTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAA-TCTTGTTTTAAGA
37485 AAAACA
1 AAAACA
37491 AATTTGAGTG
Statistics
Matches: 57, Mismatches: 20, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
36 56 0.98
37 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.25
Consensus pattern (36 bp):
AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
Found at i:37432 original size:76 final size:72
Alignment explanation
Indices: 37336--37506 Score: 202
Period size: 72 Copynumber: 2.3 Consensus size: 72
37326 AATCTTCTTA
** * *
37336 AAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAA-
1 AAAAACAATCTTGAGTGAAAT-AAAT--CTTCTTTCGAG-AAAAACAGTCTCAAGCGAGACAAAG
* *
37400 TCTTGTTTTAAG
62 T-ATGCTTTAAG
*
37412 AAAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGAAAAACAGTCTCAAGTGAGACAAAGTATG
1 AAAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGAAAAACAGTCTCAAGCGAGACAAAGTATG
37477 CTTTAAG
66 CTTTAAG
*
37484 AAAAACAAAT-TTGAGTGAGATAA
1 AAAAAC-AATCTTGAGTGAAATAA
37507 TCATCTGCAT
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
72 47 0.55
73 15 0.18
75 4 0.05
76 19 0.22
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (72 bp):
AAAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGAAAAACAGTCTCAAGCGAGACAAAGTATG
CTTTAAG
Found at i:38920 original size:183 final size:183
Alignment explanation
Indices: 38610--39146 Score: 914
Period size: 183 Copynumber: 2.9 Consensus size: 183
38600 ATCAGGTTTA
* *
38610 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAATGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* ** * *
38675 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATATATTCATAAAGCCAGGGGTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
* **
38739 TTCCTCTATAACTAATTATCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
38793 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
38858 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
38923 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGTGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
38976 ATTGAAGGGTTCATCTTATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
39041 GCCAAGTGTCCGAGTAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
39106 TACTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
39147 CGGATTTAAT
Statistics
Matches: 336, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
183 335 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:43064 original size:15 final size:16
Alignment explanation
Indices: 43031--43112 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 16
43021 TGTCAGAGGG
*
43031 AAAAATGAATAAATGA
1 AAAAATGAATAAATAA
*
43047 AAAAATGAA-GAATAA
1 AAAAATGAATAAATAA
*
43062 AAATAA-GTAAAAAATAA
1 AAA-AATG-AATAAATAA
*
43079 ATAAAAGGAA-AAATAA
1 A-AAAATGAATAAATAA
* *
43095 ATAAATAAATGAAATAA
1 AAAAATGAAT-AAATAA
43112 A
1 A
43113 TGAAATATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
15 13 0.25
16 20 0.38
17 17 0.32
18 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (16 bp):
AAAAATGAATAAATAA
Found at i:43082 original size:4 final size:4
Alignment explanation
Indices: 43062--43119 Score: 50
Period size: 4 Copynumber: 14.2 Consensus size: 4
43052 TGAAGAATAA
*
43062 AAAT AAGT AAA- AAAT AAAT AAA- AGGAA- AAAT AAAT AAAT AAAT GAAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT A--AAT AAAT AAAT AAAT AAAT -AAAT
43110 AAAT GAAAT A
1 AAAT -AAAT A
43120 TATATATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
3 6 0.13
4 29 0.63
5 11 0.24
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:43124 original size:2 final size:2
Alignment explanation
Indices: 43117--43153 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
43107 AATAAATGAA
43117 AT AT AT AT AT 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
43154 AATGAGTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43329 original size:2 final size:2
Alignment explanation
Indices: 43322--43381 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
43312 ACATACATAC
43322 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
43364 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
43382 GTAAAGTAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43465 original size:2 final size:2
Alignment explanation
Indices: 43460--43490 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43450 AAAAAAAAAG
43460 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43491 TAAAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44359 original size:13 final size:14
Alignment explanation
Indices: 44341--44369 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
44331 TAATTGTCAT
44341 AACAATT-TTTTAA
1 AACAATTATTTTAA
44354 AACAATTATTTTAA
1 AACAATTATTTTAA
44368 AA
1 AA
44370 AAATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AACAATTATTTTAA
Found at i:44710 original size:19 final size:19
Alignment explanation
Indices: 44688--44724 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44678 ATTATAATCT
*
44688 ATTTATTGAATATTAATTG
1 ATTTATTCAATATTAATTG
*
44707 ATTTATTCTATATTAATT
1 ATTTATTCAATATTAATT
44725 ATTAAAAGAA
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:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTTATTCAATATTAATTG
Found at i:44945 original size:6 final size:6
Alignment explanation
Indices: 44930--44992 Score: 65
Period size: 6 Copynumber: 9.8 Consensus size: 6
44920 TAAATAAAAC
*
44930 AAAATG AAAATA AAAATTA AAAATA AAAATA AAAAT- AAAATGA AATATTATA
1 AAAATA AAAATA AAAA-TA AAAATA AAAATA AAAATA AAAAT-A AA-A--ATA
44982 AAAATA AAAAT
1 AAAATA AAAAT
44993 TACCATTATT
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
5 5 0.10
6 30 0.60
7 8 0.16
8 2 0.04
9 3 0.06
10 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:44958 original size:19 final size:18
Alignment explanation
Indices: 44930--44992 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
44920 TAAATAAAAC
*
44930 AAAATGAAAATAAAAATTA
1 AAAATAAAAATAAAAA-TA
44949 AAAATAAAAATAAAAAT-
1 AAAATAAAAATAAAAATA
44966 AAAATGAAATATTATAAAAATA
1 AAAAT-AAA-A--ATAAAAATA
44988 AAAAT
1 AAAAT
44993 TACCATTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 5 0.13
18 4 0.11
19 16 0.42
21 8 0.21
22 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (18 bp):
AAAATAAAAATAAAAATA
Found at i:46762 original size:11 final size:11
Alignment explanation
Indices: 46748--46781 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
46738 AGTATAATAA
46748 TAATAATAAAT
1 TAATAATAAAT
*
46759 TAATAATAAGT
1 TAATAATAAAT
46770 TAATAA-AAAT
1 TAATAATAAAT
46780 TA
1 TA
46782 GAACCTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (11 bp):
TAATAATAAAT
Found at i:49230 original size:94 final size:95
Alignment explanation
Indices: 49038--49272 Score: 298
Period size: 94 Copynumber: 2.5 Consensus size: 95
49028 ATAGTATTTC
* * *
49038 TTGAAACAAAATTGATCCCAATTGAGATTGTTCT-CTCAAAACAAATTTCGTCTTGCTTAAGACA
1 TTGAAACAAAATTGATCTCAATTGAGATTGTTTTCCTAAAAACAAATTTCGTCTTGCTTAAGACA
*
49102 ATTTTCAAAAAATTTTGAATTTTTTTACAC
66 ATTTTCAAAAAATTTTGAATTTTTTTACAA
* *
49132 TTGAAACAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATTTCGTCTTGCTTGAGACA
1 TTGAAACAAAATTGATCTCAATTGAGATTGTTTTCCTAAAAACAAATTTCGTCTTGCTTAAGACA
* * ** * *
49197 GTTTTCGAAATTTTTTTAA-TTTTTTGCAA
66 ATTTTCAAAAAATTTTGAATTTTTTTACAA
* * *
49226 TTGAAACAAAATTGATCT-AATTTGAAATTATTTTCTTAAAAA-AAATT
1 TTGAAACAAAATTGATCTCAA-TTGAGATTGTTTTCCTAAAAACAAATT
49273 GTACACCAAT
Statistics
Matches: 123, Mismatches: 16, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
93 6 0.05
94 75 0.61
95 42 0.34
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (95 bp):
TTGAAACAAAATTGATCTCAATTGAGATTGTTTTCCTAAAAACAAATTTCGTCTTGCTTAAGACA
ATTTTCAAAAAATTTTGAATTTTTTTACAA
Found at i:53222 original size:30 final size:30
Alignment explanation
Indices: 53171--53229 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
53161 AGAAAATATT
** *
53171 TTTTATTTTTATTTTTTAAAAATA-TTTTA
1 TTTTATTTTTAAATTTAAAAAATACTTTTA
53200 TTTTATTTTTTAAATTTAAAAAATACTTTT
1 TTTTA-TTTTTAAATTTAAAAAATACTTTT
53230 GATTAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.20
30 16 0.64
31 4 0.16
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (30 bp):
TTTTATTTTTAAATTTAAAAAATACTTTTA
Found at i:53245 original size:26 final size:26
Alignment explanation
Indices: 53216--53279 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
53206 TTTTTAAATT
* *
53216 TAAAAAATACTTTTGATTAATAAAAA
1 TAAAAAATACTTTTCATAAATAAAAA
*
53242 TAAAAATTTA-TTTTCATAAATAAAAA
1 TAAAAA-ATACTTTTCATAAATAAAAA
53268 TAATGAAAATAC
1 TAA--AAAATAC
53280 GTTTAGTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
26 23 0.77
27 4 0.13
28 3 0.10
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (26 bp):
TAAAAAATACTTTTCATAAATAAAAA
Done.