Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002860.1 Hibiscus syriacus cultivar Beakdansim tig00005898_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: 84440
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:169 original size:13 final size:13
Alignment explanation
Indices: 151--181 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
141 AAATACGTTT
151 ACTTATCTAAAAC
1 ACTTATCTAAAAC
164 ACTTATCTAAAAC
1 ACTTATCTAAAAC
*
177 TCTTA
1 ACTTA
182 CTTATCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (13 bp):
ACTTATCTAAAAC
Found at i:522 original size:13 final size:13
Alignment explanation
Indices: 504--534 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
494 AAATACGTTT
504 ACTTATCTAAAAC
1 ACTTATCTAAAAC
517 ACTTATCTAAAAC
1 ACTTATCTAAAAC
*
530 TCTTA
1 ACTTA
535 CTTATCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (13 bp):
ACTTATCTAAAAC
Found at i:2030 original size:60 final size:60
Alignment explanation
Indices: 1951--2069 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 60
1941 ATACTGCAGA
* * *
1951 ACATACATCCATAAAGACTTACCCTAGACCATTAGGATCTATGAGTCCAATATGGAAGAC
1 ACATACATCCATAAAGACTTACCCTAGACCACTAGGATCTAAGAGTCCAATATGAAAGAC
* * *
2011 ACATGCATCCATAAGGACTTACCCTATACCACTAGGATCTAAGAGTCCAATATGAAAGA
1 ACATACATCCATAAAGACTTACCCTAGACCACTAGGATCTAAGAGTCCAATATGAAAGA
2070 TCATAACAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.23
Consensus pattern (60 bp):
ACATACATCCATAAAGACTTACCCTAGACCACTAGGATCTAAGAGTCCAATATGAAAGAC
Found at i:3661 original size:16 final size:16
Alignment explanation
Indices: 3640--3676 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
3630 TTGACTTTTG
*
3640 GTCAAAGTCAATCCTA
1 GTCAAAGTCAATCATA
3656 GTCAAAGTCAATCATA
1 GTCAAAGTCAATCATA
3672 GTCAA
1 GTCAA
3677 CTCTGGTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (16 bp):
GTCAAAGTCAATCATA
Found at i:6378 original size:60 final size:60
Alignment explanation
Indices: 6275--6569 Score: 459
Period size: 60 Copynumber: 4.9 Consensus size: 60
6265 CCAGAACAAG
*
6275 CATCTATAAGGACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATGGAAGATACAGA
1 CATCCATAAGGACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATGGAAGATACAGA
* *
6335 CATCCATAAAGACTTACCTTAGACCACTAGGATCTAGGAGTCCAATATGGAAGATAC-GA
1 CATCCATAAGGACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATGGAAGATACAGA
* *
6394 GCATCCATAAGGACTTACCCTAGACCACTAAGATCTAGGAGTCCAATATGGAATATACAGA
1 -CATCCATAAGGACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATGGAAGATACAGA
* * * *
6455 CATCCATAAGGACTTACCCTAGACCTCTAGGATCTAGGAATCCAATAAGGAAGAAACATG-
1 CATCCATAAGGACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATGGAAGATACA-GA
* *
6515 CATCCATAAGGACTTAACCTAGACCACTAGGATCTATGAGTCCAATATGGAAGAT
1 CATCCATAAGGACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATGGAAGAT
6570 CAAAATAGGC
Statistics
Matches: 213, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
59 2 0.01
60 208 0.98
61 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (60 bp):
CATCCATAAGGACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATGGAAGATACAGA
Found at i:6705 original size:14 final size:13
Alignment explanation
Indices: 6673--6720 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
6663 TAATATCAGA
6673 AATCAGGAACTAG
1 AATCAGGAACTAG
6686 AGATCAGGAACTAG
1 A-ATCAGGAACTAG
**
6700 TAATCAAAAACTAG
1 -AATCAGGAACTAG
6714 ACATCAG
1 A-ATCAG
6721 AAATCATACT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 2 0.07
14 26 0.90
15 1 0.03
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.17
Consensus pattern (13 bp):
AATCAGGAACTAG
Found at i:7989 original size:65 final size:64
Alignment explanation
Indices: 7879--8032 Score: 195
Period size: 65 Copynumber: 2.4 Consensus size: 64
7869 TACAATTGGG
* * * * *
7879 GTGCATCGGTACACT-AATTACATTCGATGTTTCAAAAGAGCCAGGAGTGTATCGATGCATGGTC
1 GTGCATCGGTACA-TAAAATGCATTCGATGTTTCAAAAGAACCAGGAGTGCATCGATGCATGG-A
7943 T
64 T
* *
7944 GTGCATCGGTACATAAAATGCATTCGATGTTTTAATAA-AATCAGGAGTGCATCGATGCATGGAT
1 GTGCATCGGTACATAAAATGCATTCGATGTTTCAA-AAGAACCAGGAGTGCATCGATGCATGGAT
*
8008 GTGCATCGATACATAAAATGCATTC
1 GTGCATCGGTACATAAAATGCATTC
8033 TAATTAGGGT
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 26 0.33
65 51 0.65
66 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATGCATTCGATGTTTCAAAAGAACCAGGAGTGCATCGATGCATGGAT
Found at i:33431 original size:28 final size:27
Alignment explanation
Indices: 33399--33462 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 27
33389 ACTCCCTAAA
33399 TTTTTTGGGATTTT-TAGGAATTTAAGAG
1 TTTTTTGGGATTTTCT-GGAATTTAAG-G
*
33427 TTTTTTGAGATTTTCTGGAATTTAAGG
1 TTTTTTGGGATTTTCTGGAATTTAAGG
33454 TTTTTTGGG
1 TTTTTTGGG
33463 GAATTTCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 9 0.27
28 23 0.70
29 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.25, T:0.53
Consensus pattern (27 bp):
TTTTTTGGGATTTTCTGGAATTTAAGG
Found at i:35526 original size:21 final size:22
Alignment explanation
Indices: 35476--35526 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
35466 GTCGAGGGTT
*
35476 CTATGTGGTCATTCGGGACAAA
1 CTATGTGATCATTCGGGACAAA
* *
35498 CCTATGTGATCCTTCGGGATAAA
1 -CTATGTGATCATTCGGGACAAA
35521 -TATGTG
1 CTATGTG
35527 GCACTTCGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.24
23 19 0.76
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (22 bp):
CTATGTGATCATTCGGGACAAA
Found at i:36474 original size:24 final size:24
Alignment explanation
Indices: 36442--36497 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
36432 ATACTACACA
36442 ACTCAAACGGTCGTCTTGATGATC
1 ACTCAAACGGTCGTCTTGATGATC
36466 ACTCAAACGGTCGTCTTGATGATC
1 ACTCAAACGGTCGTCTTGATGATC
*
36490 GCTCAAAC
1 ACTCAAAC
36498 TACTGTGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (24 bp):
ACTCAAACGGTCGTCTTGATGATC
Found at i:37517 original size:27 final size:27
Alignment explanation
Indices: 37459--37640 Score: 109
Period size: 27 Copynumber: 6.4 Consensus size: 27
37449 ATATCTTTAG
*
37459 AAATATATTTTATTTTTATCTTAATTTATT
1 AAATATATTTTATTATTATCTTAA--T-TT
*
37489 AAATATATTTTATTATTAACTTAATTT
1 AAATATATTTTATTATTATCTTAATTT
* * *
37516 AAGAT-TGTTTTATTATTTTTTTAATTT
1 AA-ATATATTTTATTATTATCTTAATTT
* * * *
37543 AAAAATATGTATTTTATTGTTATCTCAGCTTA
1 --AAATA--TATTTTATTATTATCTTA-ATTT
* *
37575 AATATATATTTTATTCTTATTTTAATTT
1 AA-ATATATTTTATTATTATCTTAATTT
* * *
37603 AAAAATATGTTATT-TTATTTTTAATTT
1 AAATATATTTTATTATTA-TCTTAATTT
37630 ATAA-ATATTTT
1 A-AATATATTTT
37641 TAATTTTTTA
Statistics
Matches: 121, Mismatches: 21, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
26 3 0.02
27 48 0.40
28 11 0.09
29 17 0.14
30 24 0.20
31 16 0.13
32 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (27 bp):
AAATATATTTTATTATTATCTTAATTT
Found at i:37724 original size:28 final size:28
Alignment explanation
Indices: 37692--37854 Score: 96
Period size: 28 Copynumber: 5.5 Consensus size: 28
37682 TACTGATTTA
**
37692 AAAATATTTTTTAAATTATGATAAAAAT
1 AAAATATTTTTTAAATTAACATAAAAAT
** *
37720 AAAATATTTTTTATGTTAACATAAGAAT
1 AAAATATTTTTTAAATTAACATAAAAAT
* *
37748 AAAATATACATTTTTAAATTAAAAATAATAAT
1 AAAATAT---TTTTTAAATT-AACATAAAAAT
* * * * *
37780 AAAACA-ATCTTAAGTTAA-ATTAATAAT
1 AAAATATTTTTTAAATTAACA-TAAAAAT
* *
37807 AAAATATATATTTAATAAGTTAAGATAAAAAT
1 AAAATAT-T-TTT--TAAATTAACATAAAAAT
37839 AAAATATATTTTTAAA
1 AAAATAT-TTTTTAAA
37855 GATATATAAA
Statistics
Matches: 106, Mismatches: 18, Indels: 21
0.73 0.12 0.14
Matches are distributed among these distances:
26 1 0.01
27 14 0.13
28 37 0.35
29 3 0.03
30 2 0.02
31 11 0.10
32 37 0.35
33 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (28 bp):
AAAATATTTTTTAAATTAACATAAAAAT
Found at i:37840 original size:32 final size:32
Alignment explanation
Indices: 37790--37853 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
37780 AAAACAATCT
*
37790 TAAGTTAAATTAATAATAAAATATATATTTAA
1 TAAGTTAAATTAAAAATAAAATATATATTTAA
*
37822 TAAGTTAAGA-TAAAAATAAAATATATTTTTAA
1 TAAGTTAA-ATTAAAAATAAAATATATATTTAA
37854 AGATATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (32 bp):
TAAGTTAAATTAAAAATAAAATATATATTTAA
Found at i:41015 original size:42 final size:43
Alignment explanation
Indices: 40968--41055 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 43
40958 AACTCGTACT
* * **
40968 TTAGTGACGTTTTTGTAGAAAACA-CCGTAATTTCATGTTACA
1 TTAGTGACGTTTTTGTAAAAAAAAGCCACAATTTCATGTTACA
* *
41010 TTAGTGGCGTTTTTGTAAAAAAAAGTCACAATTTCATGTTACA
1 TTAGTGACGTTTTTGTAAAAAAAAGCCACAATTTCATGTTACA
41053 TTA
1 TTA
41056 ATAGTGTTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 21 0.54
43 18 0.46
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (43 bp):
TTAGTGACGTTTTTGTAAAAAAAAGCCACAATTTCATGTTACA
Found at i:49197 original size:22 final size:22
Alignment explanation
Indices: 49172--49215 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
49162 TACCAAATAG
*
49172 TTTGAAAGCATATGCCAAAGCT
1 TTTGAAAGCATATACCAAAGCT
49194 TTTGAAAGCATATACCAAAGCT
1 TTTGAAAGCATATACCAAAGCT
49216 GGAAAAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (22 bp):
TTTGAAAGCATATACCAAAGCT
Found at i:55565 original size:44 final size:44
Alignment explanation
Indices: 55468--55695 Score: 181
Period size: 44 Copynumber: 5.2 Consensus size: 44
55458 CATATATTTA
* * * * * * * *
55468 GCGGCGTTTGTATCAAAAAAATGCCGCTATGTACCA-ACTTTTA
1 GCGGCGTTTGTATCCAAAAAACGTCACTATATACCAGACCTATC
* *
55511 GCGGCGTTTGTATCCTAAAAACGTCACTATATACCAGAGCTATC
1 GCGGCGTTTGTATCCAAAAAACGTCACTATATACCAGACCTATC
* * * *
55555 GCGACGTTTGTGTCCAAAAAAC-TCCGCTATATACCATACCTATC
1 GCGGCGTTTGTATCCAAAAAACGT-CACTATATACCAGACCTATC
* ** * * *
55599 ACGGCGTTTGTATAGAAAAAACGCCACTATATACCAGTCCTATA
1 GCGGCGTTTGTATCCAAAAAACGTCACTATATACCAGACCTATC
* * * * * * *
55643 GTGGTGTTTGTACCCTAAAAACGTCGCTAAATACCAGACCTATT
1 GCGGCGTTTGTATCCAAAAAACGTCACTATATACCAGACCTATC
*
55687 GTGGCGTTT
1 GCGGCGTTT
55696 TCATAAAAAA
Statistics
Matches: 143, Mismatches: 39, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
43 31 0.22
44 112 0.78
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (44 bp):
GCGGCGTTTGTATCCAAAAAACGTCACTATATACCAGACCTATC
Found at i:55759 original size:40 final size:43
Alignment explanation
Indices: 55715--55805 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 43
55705 AAATGTTGCA
*
55715 AAATATCAACA-C-ATTGCGGCGTTTGTGAA-A-AAACGCCGCT
1 AAATATCAACACCTATTGCGGCATTT-TGAAGACAAACGCCGCT
* *
55755 AAATATTAACACCTATTGCGGCATTTTTAAGACAAACGCCGCT
1 AAATATCAACACCTATTGCGGCATTTTGAAGACAAACGCCGCT
55798 AAATATCA
1 AAATATCA
55806 GTACATATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
40 10 0.23
41 4 0.09
42 12 0.28
43 17 0.40
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.25
Consensus pattern (43 bp):
AAATATCAACACCTATTGCGGCATTTTGAAGACAAACGCCGCT
Found at i:55830 original size:27 final size:27
Alignment explanation
Indices: 55788--55841 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
55778 TTTTTAAGAC
55788 AAACGCCGCTAAATATCAG-TACATATT
1 AAACGCCGCTAAATATC-GTTACATATT
*
55815 AAACGCCGCTATATATCGTTACATATT
1 AAACGCCGCTAAATATCGTTACATATT
55842 GCTGCGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (27 bp):
AAACGCCGCTAAATATCGTTACATATT
Found at i:61223 original size:36 final size:36
Alignment explanation
Indices: 61182--61257 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
61172 ATTTTCGGGA
*
61182 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
61218 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
61254 TTTT
1 TTTT
61258 TTGCTATAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:61699 original size:15 final size:15
Alignment explanation
Indices: 61679--61708 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
61669 TATCACAATC
61679 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
61694 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
61709 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:66189 original size:35 final size:36
Alignment explanation
Indices: 66115--66188 Score: 125
Period size: 35 Copynumber: 2.1 Consensus size: 36
66105 ATTTTCGGGA
*
66115 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
66151 TTTTGCTA-TTTTGGCAAAATTCGAAT-AAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
66185 TTTT
1 TTTT
66189 TTTGCTATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
34 11 0.30
35 18 0.49
36 8 0.22
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:70398 original size:22 final size:23
Alignment explanation
Indices: 70355--70405 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
70345 ACCAATAATC
*
70355 AATATTAGTGTTTGACAGTAACAA
1 AATATTAG-GTTTGACAATAACAA
*
70379 AATATTA-GTTTGCCAATAACAA
1 AATATTAGGTTTGACAATAACAA
70401 AATAT
1 AATAT
70406 AAAGTTTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 18 0.72
24 7 0.28
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (23 bp):
AATATTAGGTTTGACAATAACAA
Found at i:75150 original size:156 final size:157
Alignment explanation
Indices: 74885--75410 Score: 644
Period size: 155 Copynumber: 3.4 Consensus size: 157
74875 AATTGAAATT
* * * * * * * *
74885 ACATGGTATTCTATTGTGGTATATGAGCATGTGGTTTAAATTTGGT-AAAAATGAACCTAAAATA
1 ACAT-GTATTCTACTATGGTTTAGGAGCATGTGGCTCAAATTTGGTAAAAAAAG-ACTTAAAATA
* *
74949 AATGACAAATTG-ATGGAATAAGGAGATTATGAAAAATTGAAGGACTATATTGAAAAATAAAAAA
64 AATGACAAATTGAAT-AAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAA
75013 TTTGTTATCAAAAAGAAGAATTGAAAGAAC
128 TTTGTTATCAAAAAGAAGAATTGAAAGAAC
* * * * *
75043 ACAAGTATTCTACTATGGTTTAGGAACATGCGGCTCAAATTTGGTAAAAACAGATTTAAAATAAA
1 ACATGTATTCTACTATGGTTTAGGAGCATGTGGCTCAAATTTGGTAAAAAAAGACTTAAAATAAA
*
75108 T-AAAAATTGAATAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAAT-AAAAATTT
66 TGACAAATTGAATAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTT
* *
75171 GTTATCAAAAAGATGAATTGAAAGTAC
131 GTTATCAAAAAGAAGAATTGAAAGAAC
* ** * * *
75198 ACGTGTATTCTACTATGGTTTAGGAGCATGTAACTCAAATATGCTAAAAAAAGACTGAAAATAAA
1 ACATGTATTCTACTATGGTTTAGGAGCATGTGGCTCAAATTTGGTAAAAAAAGACTTAAAATAAA
* * *
75263 TGACAAATTGAAGAAATAAGGAGATTATGAAAAATTAAAGGACTAAATT-AAAAAAATAAAAATT
66 TGACAAATTGAATAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATA-AAAAATT
*
75327 TGTTATC--AAA-AAG---TGGAAGTAA-
130 TGTTATCAAAAAGAAGAATTGAAAG-AAC
* * *
75349 ACATGTATTCTACTATGGTTTAAGAGCATGTGGTTCAAATTTGGTAAAAAAGGACTTAAAAT
1 ACATGTATTCTACTATGGTTTAGGAGCATGTGGCTCAAATTTGGTAAAAAAAGACTTAAAAT
75411 CGAAGAGGAA
Statistics
Matches: 317, Mismatches: 45, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
151 58 0.18
152 1 0.00
154 2 0.01
155 96 0.30
156 92 0.29
157 60 0.19
158 8 0.03
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.28
Consensus pattern (157 bp):
ACATGTATTCTACTATGGTTTAGGAGCATGTGGCTCAAATTTGGTAAAAAAAGACTTAAAATAAA
TGACAAATTGAATAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTT
GTTATCAAAAAGAAGAATTGAAAGAAC
Found at i:75235 original size:155 final size:156
Alignment explanation
Indices: 74885--75410 Score: 665
Period size: 156 Copynumber: 3.4 Consensus size: 156
74875 AATTGAAATT
* * * * * * * *
74885 ACATGGTATTCTATTGTGGTATATGAGCATGTGGTTTAAATTTGGT-AAAAATGAACCTAAAATA
1 ACAT-GTATTCTACTATGGTTTAGGAGCATGTGGCTCAAATTTGGTAAAAAAAG-ACTTAAAATA
* *
74949 AATGACAAATTG-ATGGAATAAGGAGATTATGAAAAATTGAAGGACTATATTGAAAAATAAAAAA
64 AATGACAAATTGAAT-AAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAAT-AAAAA
* *
75013 TTTGTTATCAAAAAGAAGAATTGAAAGAAC
127 TTTGTTATCAAAAAGATGAATTGAAAGTAC
* * * * *
75043 ACAAGTATTCTACTATGGTTTAGGAACATGCGGCTCAAATTTGGTAAAAACAGATTTAAAATAAA
1 ACATGTATTCTACTATGGTTTAGGAGCATGTGGCTCAAATTTGGTAAAAAAAGACTTAAAATAAA
*
75108 T-AAAAATTGAATAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAATTTG
66 TGACAAATTGAATAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAATTTG
75172 TTATCAAAAAGATGAATTGAAAGTAC
131 TTATCAAAAAGATGAATTGAAAGTAC
* ** * * *
75198 ACGTGTATTCTACTATGGTTTAGGAGCATGTAACTCAAATATGCTAAAAAAAGACTGAAAATAAA
1 ACATGTATTCTACTATGGTTTAGGAGCATGTGGCTCAAATTTGGTAAAAAAAGACTTAAAATAAA
* * *
75263 TGACAAATTGAAGAAATAAGGAGATTATGAAAAATTAAAGGACTAAATTAAAAAAATAAAAATTT
66 TGACAAATTGAATAAATAAGGAGATTATGAAAAATTGAAGGACTAAATT-GAAAAATAAAAATTT
*
75328 GTTATCAAAAAG-TG----G-AAGTAA
130 GTTATCAAAAAGATGAATTGAAAGTAC
* * *
75349 ACATGTATTCTACTATGGTTTAAGAGCATGTGGTTCAAATTTGGTAAAAAAGGACTTAAAAT
1 ACATGTATTCTACTATGGTTTAGGAGCATGTGGCTCAAATTTGGTAAAAAAAGACTTAAAAT
75411 CGAAGAGGAA
Statistics
Matches: 321, Mismatches: 43, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
151 58 0.18
152 1 0.00
155 88 0.27
156 94 0.29
157 72 0.22
158 8 0.02
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.28
Consensus pattern (156 bp):
ACATGTATTCTACTATGGTTTAGGAGCATGTGGCTCAAATTTGGTAAAAAAAGACTTAAAATAAA
TGACAAATTGAATAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAATTTG
TTATCAAAAAGATGAATTGAAAGTAC
Found at i:77430 original size:27 final size:27
Alignment explanation
Indices: 77392--77472 Score: 144
Period size: 27 Copynumber: 3.0 Consensus size: 27
77382 AGCCAATTCA
77392 AAAATTAACCAAACTATAAACCGAAAG
1 AAAATTAACCAAACTATAAACCGAAAG
*
77419 AAAATTAACCAAACTATAAACCTAAAG
1 AAAATTAACCAAACTATAAACCGAAAG
77446 AAAATTAACCAAACTATAAACCTGAAA
1 AAAATTAACCAAACTATAAACC-GAAA
77473 CTTACCCACT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 48 0.94
28 3 0.06
ACGTcount: A:0.59, C:0.19, G:0.05, T:0.17
Consensus pattern (27 bp):
AAAATTAACCAAACTATAAACCGAAAG
Found at i:81735 original size:39 final size:39
Alignment explanation
Indices: 81678--81783 Score: 121
Period size: 39 Copynumber: 2.7 Consensus size: 39
81668 TAAAATTATC
*
81678 AAATTATTTCAC-TCTAACATTCTAAATTC-CTAATTGCTT
1 AAATTATTCCACAT-TAACATTCTAAATTCTC-AATTGCTT
*
81717 AAATT-TTGCCACCA-TAACATTCTAAATTCTCAATTTCTT
1 AAATTATT-CCA-CATTAACATTCTAAATTCTCAATTGCTT
*
81756 AAATTATTTCACATTAACATTCTAAATT
1 AAATTATTCCACATTAACATTCTAAATT
81784 ATTTTTTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
38 4 0.07
39 50 0.86
40 4 0.07
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.42
Consensus pattern (39 bp):
AAATTATTCCACATTAACATTCTAAATTCTCAATTGCTT
Found at i:82072 original size:16 final size:17
Alignment explanation
Indices: 82051--82086 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
82041 GACACGGGCC
82051 AAAATTTT-GATACCCA
1 AAAATTTTGGATACCCA
*
82067 AAAATTTTGGGTACCCA
1 AAAATTTTGGATACCCA
82084 AAA
1 AAA
82087 GTATAACCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (17 bp):
AAAATTTTGGATACCCA
Found at i:84133 original size:47 final size:47
Alignment explanation
Indices: 84082--84178 Score: 140
Period size: 47 Copynumber: 2.1 Consensus size: 47
84072 AACACGGGAA
* *
84082 AAGATATATATTTAATAAAAACTTTTTAAGTATCAAAAATCAATTTT
1 AAGATATATATTTAATAAAAACTTTTTAAGCATCAAAAATCAATTAT
* * * *
84129 AAGATATATTTTTAATAAAACCTTTTTAAGCATTAAAAATCGATTAT
1 AAGATATATATTTAATAAAAACTTTTTAAGCATCAAAAATCAATTAT
84176 AAG
1 AAG
84179 TACAAAAAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.39
Consensus pattern (47 bp):
AAGATATATATTTAATAAAAACTTTTTAAGCATCAAAAATCAATTAT
Found at i:84256 original size:47 final size:47
Alignment explanation
Indices: 84187--84332 Score: 193
Period size: 52 Copynumber: 3.0 Consensus size: 47
84177 AGTACAAAAA
*
84187 ACATATTTTTAATAAAAACTTTTTAAGCATCAAAATTCAATTTTAAG
1 ACATATTTTTAATAAAAACTTTTTAAGCATCAAAAATCAATTTTAAG
* * * * *
84234 ACATATTTTTAATAAAACCTTTTTAAGTATTAAAAAACAATTTAAGTAAAAA
1 ACATATTTTTAATAAAAACTTTTTAAGCATCAAAAATCAATTT---T--AAG
84286 ACATATTTTTAATAAAAACTTTTTAAGCATCAAAAATCAATTTTAAG
1 ACATATTTTTAATAAAAACTTTTTAAGCATCAAAAATCAATTTTAAG
84333 TATAGTTTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
47 40 0.48
49 1 0.01
50 1 0.01
52 41 0.49
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (47 bp):
ACATATTTTTAATAAAAACTTTTTAAGCATCAAAAATCAATTTTAAG
Found at i:84326 original size:99 final size:101
Alignment explanation
Indices: 84087--84332 Score: 406
Period size: 102 Copynumber: 2.4 Consensus size: 101
84077 GGGAAAAGAT
* * *
84087 ATATATTTAATAAAAACTTTTTAAGTATCAAAAATCAATTTTAAGATATATTTTTAATAAAACCT
1 ATATTTTTAATAAAAACTTTTTAAGCATCAAAAATCAATTTTAAGACATATTTTTAATAAAACCT
* *
84152 TTTTAAGCATTAAAAATCGATTATAAGTACAAAAAAC
66 TTTTAAGCATTAAAAAACAATTATAAGTA-AAAAAAC
*
84189 ATATTTTTAATAAAAACTTTTTAAGCATCAAAATTCAATTTTAAGACATATTTTTAATAAAACCT
1 ATATTTTTAATAAAAACTTTTTAAGCATCAAAAATCAATTTTAAGACATATTTTTAATAAAACCT
*
84254 TTTTAAGTATTAAAAAACAATT-TAAGT-AAAAAAC
66 TTTTAAGCATTAAAAAACAATTATAAGTAAAAAAAC
84288 ATATTTTTAATAAAAACTTTTTAAGCATCAAAAATCAATTTTAAG
1 ATATTTTTAATAAAAACTTTTTAAGCATCAAAAATCAATTTTAAG
84333 TATAGTTTAA
Statistics
Matches: 136, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
99 51 0.38
101 5 0.04
102 80 0.59
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.38
Consensus pattern (101 bp):
ATATTTTTAATAAAAACTTTTTAAGCATCAAAAATCAATTTTAAGACATATTTTTAATAAAACCT
TTTTAAGCATTAAAAAACAATTATAAGTAAAAAAAC
Done.