Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000111.1 Hibiscus syriacus cultivar Beakdansim tig00000200_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: 62761
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:498 original size:70 final size:72
Alignment explanation
Indices: 384--553 Score: 256
Period size: 70 Copynumber: 2.4 Consensus size: 72
374 CTATTTCCCA
*
384 CATCTGTAAGACCTACAGTGTATGATGCTTTCAAAAAGCCTTCGGGAGCTTTTTGATC-TAAAG-
1 CATCTGTAAGA-CTACAGTGCATGATGCTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
*
447 CTCAGGTT
65 CTCAGGGT
455 CATCTGTAAGACTACAGTGCATGATG-TATTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACTACAGTGCATGATGCT-TTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
519 CTCAGGGT
65 CTCAGGGT
* *
527 CATCTGTAAGCCCTACAGTGCAAGATG
1 CATCTGTAAG-ACTACAGTGCATGATG
554 ATAAGACCTT
Statistics
Matches: 91, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
69 1 0.01
70 43 0.47
71 16 0.18
72 17 0.19
73 14 0.15
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (72 bp):
CATCTGTAAGACTACAGTGCATGATGCTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCC
TCAGGGT
Found at i:1004 original size:123 final size:123
Alignment explanation
Indices: 722--1038 Score: 405
Period size: 122 Copynumber: 2.6 Consensus size: 123
712 GCGTTGCCAT
* * *
722 AGAAAGTTCATAATGAGAAGAATTTATCTGAAGA-GAAGAAGAAGTTCATAATAAGAAGAGCTTG
1 AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * *
786 TTCAATCTTTTGCATGACTCTATCACATAAGGAGATAGATCAACACCAACTTTTCCAG
66 TTCAACCTTTTGCATGACTCTATCACAAAAAGAGATAGAACAACACCAACTTTTCCAG
*
844 AGAAAGTTCATAATGAGAAGAACTTAT-TGAAGAGGAAGAGGAAGTTCATAATGAGAAGAACTTG
1 AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * * *
908 TTCAACCTTTTGCTTGACTCCATTTC-CAAAAAGAGATAGAACAGCA-GAGCTATTTCCAG
66 TTCAACCTTTTGCATGACT-C-TATCACAAAAAGAGATAGAACAACACCAACT-TTTCCAG
* * *
967 -GTGAAGTTCATAATGAGAAGAA-TCATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTT
1 AG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
1030 G-TCAACCTT
65 GTTCAACCTT
1039 GCATTGATTC
Statistics
Matches: 172, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
121 6 0.03
122 85 0.49
123 78 0.45
124 3 0.02
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (123 bp):
AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAACCTTTTGCATGACTCTATCACAAAAAGAGATAGAACAACACCAACTTTTCCAG
Found at i:1264 original size:136 final size:138
Alignment explanation
Indices: 959--1310 Score: 410
Period size: 137 Copynumber: 2.6 Consensus size: 138
949 CAGCAGAGCT
959 ATTTCCAG-GTGAAGTTCATAATGAGAAGAA-TCATCTGAAGAGGAAGAAAAAGTTCATAATGAG
1 ATTTCCAGAG-GAAGTTCATAATGAGAAGAACTCATCTGAA-AGGAAGAAAAAGTTCATAATGAG
* * * * * * * *
1022 AAGAACTTG-TCAACCTTGCATTGATTCATCTCCTATGGAATTGAATGAAAGAATAACCTCATTT
64 AAGAATTTGTTCAACATTACATTAATTCATCACATATGGAATTGAATCAAAAAATAACCTCATTT
* *
1086 GAGGATCAAT
129 GAAGATCAAC
* * * * *
1096 ATTTTCAGAGGAAATTAATAATGAGAAGAACTCATCTGAAAGGAAGAAGAAG-TCATAATAAGAA
1 ATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAAGGAAGAAAAAGTTCATAATGAGAA
* * * * *
1160 AAATTTGTTCAACATTACCTTAATTCATCACATATGGAGTTGAATCAAAAAAT-CCCTCTTTTGA
66 GAATTTGTTCAACATTACATTAATTCATCACATATGGAATTGAATCAAAAAATAACCTCATTTGA
1224 AGATCAAC
131 AGATCAAC
* * * *
1232 ATTTCCAGAAGG-AGTTCATAATGAGAATAACTCATCTGAAAAAGAAGAATAAGTTCATAATGAT
1 ATTTCCAG-AGGAAGTTCATAATGAGAAGAACTCATCTG-AAAGGAAGAAAAAGTTCATAATGAG
1296 AAGAATTTGTTCAAC
64 AAGAATTTGTTCAAC
1311 TTTTTTCTAG
Statistics
Matches: 180, Mismatches: 29, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
136 61 0.34
137 87 0.48
138 32 0.18
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (138 bp):
ATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAAGGAAGAAAAAGTTCATAATGAGAA
GAATTTGTTCAACATTACATTAATTCATCACATATGGAATTGAATCAAAAAATAACCTCATTTGA
AGATCAAC
Found at i:2650 original size:2 final size:2
Alignment explanation
Indices: 2643--2710 Score: 94
Period size: 2 Copynumber: 37.0 Consensus size: 2
2633 TATTTATTAA
2643 AT AT AT AT AT AT A- AT AT AT AT AT AT AT A- AT AT A- 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
2682 AT AT -T AT -T AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2711 TGATTTTAGT
Statistics
Matches: 60, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
1 6 0.10
2 54 0.90
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2940 original size:18 final size:19
Alignment explanation
Indices: 2907--2947 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2897 TTTAAATAAT
2907 TAAA-TATATTACTTTT-A
1 TAAATTATATTACTTTTAA
2924 TAAATTATATCTA-TTTTAA
1 TAAATTATAT-TACTTTTAA
2943 TAAAT
1 TAAAT
2948 GCTTTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.19
18 9 0.43
19 8 0.38
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAATTATATTACTTTTAA
Found at i:12741 original size:129 final size:132
Alignment explanation
Indices: 12507--12874 Score: 485
Period size: 129 Copynumber: 2.8 Consensus size: 132
12497 ATAATTTTAA
* * * * * *
12507 GAGAGAAAATGATAATATCTAATTATTTTCGATTGAGAATAAATGACCTCTCATACCTTAAAACA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACATCTCATACCTTAAAGCA
* * *
12572 ATCATTTATTACTCCAATCCAAATGAAGAGATATCACTATTCCATCTTAAAATTC-A-A-TCGAT
66 ATCATTTATTACTCCAATCAAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATTCAAT
12634 TC
131 TC
* * *
12636 GGGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAATTGACATCTCATACCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACATCTCATACCTTAAAGCA
* * *
12701 CTCATTTATTACTCCAATCAAAATTAAGAGATATCACTATTCCATCTTAAAAATCAATATTTAAT
66 ATCATTTATTACTCCAATCAAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATTCAAT
12766 TC
131 TC
* * * *
12768 GAGAGAAAACAATAATAT-TGAATTATTTCTAATCGAGAATAAATGACATTTCATGCCTTAAAGC
1 GAGAGAAAACGATAATATCT-AATTATTTCCAATCGAGAATAAATGACATCTCATACCTTAAAGC
* * *
12832 AATCATTTATTACT-CAAACTAAAATGAAAAGATATTACTATTC
65 AATCATTTATTACTCCAATC-AAAATGAAGAGATATCACTATTC
12875 TCAATATCGA
Statistics
Matches: 207, Mismatches: 27, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
129 107 0.52
130 1 0.00
131 6 0.03
132 93 0.45
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.33
Consensus pattern (132 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACATCTCATACCTTAAAGCA
ATCATTTATTACTCCAATCAAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATTCAAT
TC
Found at i:13880 original size:20 final size:20
Alignment explanation
Indices: 13857--13924 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
13847 TAGTAAACGG
*
13857 TACTGTTCATACAGTATCGA
1 TACTATTCATACAGTATCGA
* *
13877 TACTATTCATACAGTGTTGA
1 TACTATTCATACAGTATCGA
*
13897 TACTATTCATATAGTA-C-A
1 TACTATTCATACAGTATCGA
13915 GTACTATTCA
1 -TACTATTCA
13925 CAAAAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 1 0.02
19 9 0.22
20 31 0.76
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (20 bp):
TACTATTCATACAGTATCGA
Found at i:16204 original size:18 final size:18
Alignment explanation
Indices: 16151--16212 Score: 106
Period size: 18 Copynumber: 3.4 Consensus size: 18
16141 AAAATCAAGA
*
16151 GTGCATCGATGCATGGTA
1 GTGCATCGATGCATGGTT
*
16169 GTACATCGATGCATGGTT
1 GTGCATCGATGCATGGTT
16187 GTGCATCGATGCATGGTT
1 GTGCATCGATGCATGGTT
16205 GTGCATCG
1 GTGCATCG
16213 GTACAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (18 bp):
GTGCATCGATGCATGGTT
Found at i:18546 original size:23 final size:23
Alignment explanation
Indices: 18520--18568 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
18510 ATAAGGAACC
*
18520 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
18543 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
18566 AAA
1 AAA
18569 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Found at i:21865 original size:20 final size:20
Alignment explanation
Indices: 21840--21900 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
21830 TGAAGAAATG
21840 AGAGAAAAAATAAAAGTTAA
1 AGAGAAAAAATAAAAGTTAA
* * *
21860 AGAGAAAAAATTAAGGATGAA
1 AGAGAAAAAATAAAAG-TTAA
*
21881 AGAGAAAAGA-AAAAGTTAA
1 AGAGAAAAAATAAAAGTTAA
21900 A
1 A
21901 TATTTAAGAG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
19 4 0.12
20 17 0.52
21 12 0.36
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (20 bp):
AGAGAAAAAATAAAAGTTAA
Found at i:26141 original size:21 final size:21
Alignment explanation
Indices: 26117--26159 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
26107 GAATTGCTTT
26117 TGCCTTGGCATTAGAATCTGG
1 TGCCTTGGCATTAGAATCTGG
26138 TGCCTTGGCATTAGAATCTGG
1 TGCCTTGGCATTAGAATCTGG
26159 T
1 T
26160 ACACTACTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (21 bp):
TGCCTTGGCATTAGAATCTGG
Found at i:27055 original size:11 final size:11
Alignment explanation
Indices: 27039--27069 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
27029 ATGAAAAATG
27039 GTAAATAAACA
1 GTAAATAAACA
27050 GTAAATAAACA
1 GTAAATAAACA
*
27061 GCAAATAAA
1 GTAAATAAA
27070 ATGAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.16
Consensus pattern (11 bp):
GTAAATAAACA
Found at i:27576 original size:23 final size:23
Alignment explanation
Indices: 27550--27598 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
27540 ATAAAGAACC
*
27550 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
27573 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
27596 AAA
1 AAA
27599 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Found at i:29025 original size:13 final size:13
Alignment explanation
Indices: 29003--29040 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
28993 TCCTAATGGG
29003 CAAT-TTTGAAAA
1 CAATGTTTGAAAA
*
29015 CTATGTTTGAAAA
1 CAATGTTTGAAAA
29028 CAATGTTTGAAAA
1 CAATGTTTGAAAA
29041 TAAATATGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 3 0.13
13 20 0.87
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:29585 original size:44 final size:44
Alignment explanation
Indices: 29536--29622 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
29526 ATCGACGTAC
* *
29536 ATTCAATGAATGCATCGGTGCA-TCTTTATAGTGCATCAATGCAT
1 ATTCAAGGAATGCATCGGTACACT-TTTATAGTGCATCAATGCAT
*
29580 ATTCAAGGAATGCATCGGTACACTTTTATAGTGTATCAATGCA
1 ATTCAAGGAATGCATCGGTACACTTTTATAGTGCATCAATGCA
29623 CATTGCACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 38 0.97
45 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (44 bp):
ATTCAAGGAATGCATCGGTACACTTTTATAGTGCATCAATGCAT
Found at i:31270 original size:26 final size:26
Alignment explanation
Indices: 31234--31289 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
31224 GTCCTCAAAA
31234 GAAAGAACAAATTAGTGAATTATTTG
1 GAAAGAACAAATTAGTGAATTATTTG
*
31260 GAAAGAACAAATTAGTGAATTTTTTG
1 GAAAGAACAAATTAGTGAATTATTTG
31286 GAAA
1 GAAA
31290 AATTCTTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (26 bp):
GAAAGAACAAATTAGTGAATTATTTG
Found at i:32601 original size:23 final size:23
Alignment explanation
Indices: 32575--32645 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
32565 GAAAGTGTAC
*
32575 CGATGCATCTCTTGAATATGCAT
1 CGATGCATCTCTTGAATGTGCAT
* * *
32598 CGATACA-CT-ATGAATGTGCAC
1 CGATGCATCTCTTGAATGTGCAT
*
32619 CAATGCAT-TCTTTGAATGTGCAT
1 CGATGCATCTC-TTGAATGTGCAT
32642 CGAT
1 CGAT
32646 ACACTCGATT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
21 15 0.42
22 2 0.06
23 19 0.53
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (23 bp):
CGATGCATCTCTTGAATGTGCAT
Found at i:32625 original size:44 final size:44
Alignment explanation
Indices: 32551--32650 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 44
32541 GTTGACACTA
* *
32551 CATCGATACACTATGAAAGTGTACCGATGCA-TCTCTTGAATATG
1 CATCGATACACTATGAAAGTGCACCAATGCATTCT-TTGAATATG
* *
32595 CATCGATACACTATGAATGTGCACCAATGCATTCTTTGAATGTG
1 CATCGATACACTATGAAAGTGCACCAATGCATTCTTTGAATATG
32639 CATCGATACACT
1 CATCGATACACT
32651 CGATTGTGCA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 48 0.94
45 3 0.06
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (44 bp):
CATCGATACACTATGAAAGTGCACCAATGCATTCTTTGAATATG
Found at i:32660 original size:20 final size:20
Alignment explanation
Indices: 32635--32672 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32625 ATTCTTTGAA
32635 TGTGCATCGATACACTCGAT
1 TGTGCATCGATACACTCGAT
* *
32655 TGTGCATTGCTACACTCG
1 TGTGCATCGATACACTCG
32673 TCAGGTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (20 bp):
TGTGCATCGATACACTCGAT
Found at i:33135 original size:19 final size:19
Alignment explanation
Indices: 33088--33136 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 19
33078 ATTGCTTTAA
*
33088 TTTTGAAATTTGATGTTTTT
1 TTTTGAAAATT-ATGTTTTT
33108 TATTT---AATTATGTTTTT
1 T-TTTGAAAATTATGTTTTT
33125 TTTTGAAAATTA
1 TTTTGAAAATTA
33137 CATATTGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 9
0.71 0.03 0.26
Matches are distributed among these distances:
16 3 0.12
17 9 0.38
18 3 0.12
19 5 0.21
20 1 0.04
21 3 0.12
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (19 bp):
TTTTGAAAATTATGTTTTT
Found at i:36307 original size:19 final size:19
Alignment explanation
Indices: 36279--36328 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
36269 CCTCTTCTTG
36279 AGTATAGCCTTGAGCAACA
1 AGTATAGCCTTGAGCAACA
*
36298 AGTCTAGCCTTGAGCAACA
1 AGTATAGCCTTGAGCAACA
36317 AGTATAGCCTTG
1 AGTATAGCCTTG
36329 TTTCTCACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (19 bp):
AGTATAGCCTTGAGCAACA
Found at i:46343 original size:5 final size:5
Alignment explanation
Indices: 46333--46387 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
46323 GAACTTCTCT
46333 TTTTC TTTTC TTTTC TTCTT- TTCTTC TTTTC TTCTT- TTTGTC TTTTC
1 TTTTC TTTTC TTTTC TT-TTC TT-TTC TTTTC TT-TTC TTT-TC TTTTC
46380 -TTTC TTTT
1 TTTTC TTTT
46388 TGCACTCCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 5 0.11
5 30 0.68
6 9 0.20
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:46351 original size:8 final size:8
Alignment explanation
Indices: 46340--46387 Score: 71
Period size: 8 Copynumber: 5.9 Consensus size: 8
46330 TCTTTTTCTT
46340 TTCTTTTC
1 TTCTTTTC
46348 TTCTTTTC
1 TTCTTTTC
46356 TTCTTTTC
1 TTCTTTTC
46364 TTCTTTT-
1 TTCTTTTC
46371 TGTCTTTTC
1 T-TCTTTTC
46380 TTTCTTTT
1 -TTCTTTT
46388 TGCACTCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.03
8 29 0.78
9 6 0.16
10 1 0.03
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:48970 original size:111 final size:109
Alignment explanation
Indices: 48730--49115 Score: 366
Period size: 111 Copynumber: 3.5 Consensus size: 109
48720 TAACAATAGC
* * * *
48730 CATATCCATGACAATAATAATTTCAAATGGCATAGAACTTTAACTATTCACATTCTTTTTTTCCA
1 CATAT-CATAACAATAATAATTTCAAATGACAGAGAATTTTAACTATT--CATTCTTTTTTT-CA
* ** * * * * **
48795 GTAAAATGTCACATCAGATTAAAACTTTAATTATAGTGAAAGGGAAAT
62 GTGAAACATCACCTCAAATCAGAACTTTAATTATAGTGAAAGAAAAAT
* ** * * *
48843 CATATTGAGGATAATAATAATTTTAAATGACAGAGAATTTTAACTATTCGTGT-TTTTTTTCTAG
1 CATA-TCATAACAATAATAATTTCAAATGACAGAGAATTTTAACTATTCAT-TCTTTTTTTC-AG
48907 TGAAACATCACCTCAAATCAGAACTTTAATTATAGT-AGAAGAAAAAT
63 TGAAACATCACCTCAAATCAGAACTTTAATTATAGTGA-AAGAAAAAT
* * * * **
48954 CATACTCATAACAATAATAATTTCAAATAAAAGAGAATTTTAACTATTCACATCCTTTTTTCAAC
1 CATA-TCATAACAATAATAATTTCAAATGACAGAGAATTTTAACTATTCA-TTCTTTTTTTCAGT
*
49019 GAAACATCACCTCAAATCAGAACTTTCATTATAGTGAAAGAAAAAT
64 GAAACATCACCTCAAATCAGAACTTTAATTATAGTGAAAGAAAAAT
* * *
49065 CAGATC-TAGGACAATAATAATTTCAAATGAC-GTAAAATCTTAACTATTCAT
1 CATATCATA--ACAATAATAATTTCAAATGACAG-AGAATTTTAACTATTCAT
49116 GTCCTTGTTT
Statistics
Matches: 226, Mismatches: 37, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
109 2 0.01
110 5 0.02
111 170 0.75
112 9 0.04
113 39 0.17
114 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (109 bp):
CATATCATAACAATAATAATTTCAAATGACAGAGAATTTTAACTATTCATTCTTTTTTTCAGTGA
AACATCACCTCAAATCAGAACTTTAATTATAGTGAAAGAAAAAT
Found at i:49411 original size:14 final size:13
Alignment explanation
Indices: 49364--49411 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
49354 TATGTCATGT
*
49364 TTTTTTAATTTTA
1 TTTTTTATTTTTA
*
49377 TTTATTTATTATTA
1 TTT-TTTATTTTTA
49391 TTATTTTATTTTTAA
1 TT-TTTTATTTTT-A
49406 TTTTTT
1 TTTTTT
49412 GAAAATGAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 3 0.10
14 22 0.76
15 4 0.14
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:53339 original size:20 final size:19
Alignment explanation
Indices: 53315--53367 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
53305 CACACAATAT
*
53315 CGGTACTATTTATACAGTA
1 CGGTACTATTCATACAGTA
53334 CTGGTACTATTCATACAGTA
1 C-GGTACTATTCATACAGTA
*
53354 CAGTACTATTCATA
1 CGGTACTATTCATA
53368 AAAACATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (19 bp):
CGGTACTATTCATACAGTA
Found at i:53624 original size:20 final size:19
Alignment explanation
Indices: 53580--53624 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
53570 ATATTTAATG
53580 AAAAAGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
*
53599 ACAAAAGGATATGAATTGTTA
1 A-AAAA-GATATCAATTGTTA
53620 AAAAA
1 AAAAA
53625 TACAAATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 8 0.35
21 14 0.61
ACGTcount: A:0.56, C:0.04, G:0.13, T:0.27
Consensus pattern (19 bp):
AAAAAGATATCAATTGTTA
Found at i:57053 original size:30 final size:30
Alignment explanation
Indices: 57019--57085 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
57009 GGTATTAAAT
* *
57019 GAACACGTTGAACAATAAATAAACGAAAAC
1 GAACACGTTCAAAAATAAATAAACGAAAAC
* * *
57049 GAACACCTTCAAAAATAAATAAACTAACAC
1 GAACACGTTCAAAAATAAATAAACGAAAAC
57079 GAACACG
1 GAACACG
57086 AAATAAACAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.55, C:0.21, G:0.10, T:0.13
Consensus pattern (30 bp):
GAACACGTTCAAAAATAAATAAACGAAAAC
Found at i:60847 original size:25 final size:25
Alignment explanation
Indices: 60830--60880 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
60820 TTATCTTGAT
*
60830 TCGAGTTTTAATTTTTTATTTCGAG
1 TCGAGCTTTAATTTTTTATTTCGAG
60855 TCGAGCTTTAATTTTTTATTTCGAG
1 TCGAGCTTTAATTTTTTATTTCGAG
60880 T
1 T
60881 TTGAATCGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.10, G:0.16, T:0.55
Consensus pattern (25 bp):
TCGAGCTTTAATTTTTTATTTCGAG
Done.