Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005055.1 Hibiscus syriacus cultivar Beakdansim tig00011348_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: 84989
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:1629 original size:42 final size:42
Alignment explanation
Indices: 1529--1673 Score: 193
Period size: 43 Copynumber: 3.4 Consensus size: 42
1519 CCCCCAGACA
* *
1529 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAA-TTT
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT--TCCAAGGTT
*
1572 CCTTTGCTGTGTGCAAGGCTAAGCCTTACAGTTTCCAAGGTT
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCAAGGTT
* *
1614 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCATGGCT
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCAAGGTT
* *
1657 CTTTTGCTATGTGCAAG
1 CCTTTGCTGTGTGCAAG
1674 TATAAGACCT
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
41 4 0.04
42 35 0.38
43 53 0.58
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (42 bp):
CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCAAGGTT
Found at i:3493 original size:13 final size:13
Alignment explanation
Indices: 3475--3504 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3465 ACCGGTCATA
3475 ACCCGACCCGTTG
1 ACCCGACCCGTTG
3488 ACCCGACCCGTTG
1 ACCCGACCCGTTG
3501 -CCCG
1 ACCCG
3505 TTGACTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.13, C:0.50, G:0.23, T:0.13
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:6343 original size:43 final size:43
Alignment explanation
Indices: 6277--6593 Score: 392
Period size: 43 Copynumber: 7.4 Consensus size: 43
6267 TTAATTACAG
*
6277 TTACAGTTTCCCCCAGGTCCCTTTGTTGTGTTCAAGGGTAAGCC
1 TTACAGTTT-CCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
* *
6321 TTACAGTTTCCCCAGGCCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
*
6364 TTACAG-TTCGCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTC-CCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
*
6407 TTACAG-TTCCCTTAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCC-CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
* * * * * *
6450 TTATAATTCCCCCAGG-CACCTTTGCTGTGTGCAAGGATAAACC
1 TTACAGTTTCCCCAGGTC-CCTTTGTTGTGTGCAAGGGTAAGCC
* * *
6493 TTATAG-TTCTCCCAGTTTCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTC-CCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
* * * *
6536 TTACA-TTTTCCCATGTTCCTTTTTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
6578 TTACAGTTTCCCCAGG
1 TTACAGTTTCCCCAGG
6594 ATCTTTTGCT
Statistics
Matches: 238, Mismatches: 27, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
42 43 0.18
43 182 0.76
44 13 0.05
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (43 bp):
TTACAGTTTCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
Found at i:6515 original size:129 final size:127
Alignment explanation
Indices: 6288--6625 Score: 453
Period size: 129 Copynumber: 2.6 Consensus size: 127
6278 TACAGTTTCC
* *
6288 CCCAGGTCCCTTTGTTGTGTTCAAGGGTAAGCCTTACAGTTTCCCCAGGCCCCTTTGCTGTGTGC
1 CCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGCACCTTTGCTGTGTGC
* * *
6353 AAGGGTAAGCCTTACAGTTCGCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT
66 AAGGATAAACCTTATAGTTCGCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT
* * *
6415 CCCTTAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTATAATTCCCCCAGGCACCTTTGCTGTGT
1 CCC--AGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGCACCTTTGCTGTGT
* * * * *
6480 GCAAGGATAAACCTTATAGTTCTCCCAGTTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACATTTT
64 GCAAGGATAAACCTTATAGTTCGCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACA-GTT
* * * * *
6545 CCCATGTTCCTTTTTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGG-ATCTTTTGCTATGTG
1 CCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGCA-CCTTTGCTGTGTG
*
6609 CAAGTATAAGACCTTAT
65 CAAGGATAA-ACCTTAT
6626 CATTTTTGCA
Statistics
Matches: 184, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
127 4 0.02
128 59 0.32
129 116 0.63
130 5 0.03
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.34
Consensus pattern (127 bp):
CCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGCACCTTTGCTGTGTGC
AAGGATAAACCTTATAGTTCGCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT
Found at i:8031 original size:30 final size:30
Alignment explanation
Indices: 7990--8051 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
7980 GTTCTTTGTG
* * * *
7990 AGTTGTTTATGTCTTCTAACTGCTCTACCA
1 AGTTGTATATGTCTTCCAAATGCTCCACCA
8020 AGTTGTATATGTCTTCCAAATGCTCCACCA
1 AGTTGTATATGTCTTCCAAATGCTCCACCA
8050 AG
1 AG
8052 CTATCCCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (30 bp):
AGTTGTATATGTCTTCCAAATGCTCCACCA
Found at i:14306 original size:30 final size:30
Alignment explanation
Indices: 14272--14349 Score: 129
Period size: 30 Copynumber: 2.6 Consensus size: 30
14262 TTATGTATCT
* *
14272 CAAATGCTCCACCAAGTTGTATATGTCTTC
1 CAAATGCTCCACCAAGCTATATATGTCTTC
*
14302 CAAATGCTCCACTAAGCTATATATGTCTTC
1 CAAATGCTCCACCAAGCTATATATGTCTTC
14332 CAAATGCTCCACCAAGCT
1 CAAATGCTCCACCAAGCT
14350 GTCCCAATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (30 bp):
CAAATGCTCCACCAAGCTATATATGTCTTC
Found at i:22866 original size:24 final size:24
Alignment explanation
Indices: 22814--22863 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
22804 TTTCTAATTC
22814 GAATTCTATTATGATACCTGATCT
1 GAATTCTATTATGATACCTGATCT
* * *
22838 GAATTCTTTTTTGATATCTGAT-T
1 GAATTCTATTATGATACCTGATCT
22861 GAA
1 GAA
22864 ATTATGTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (24 bp):
GAATTCTATTATGATACCTGATCT
Found at i:24938 original size:658 final size:658
Alignment explanation
Indices: 23663--24973 Score: 1922
Period size: 658 Copynumber: 2.0 Consensus size: 658
23653 ATCAATAGTT
23663 CTTATACTATATATACAAGATTCTTCATAAAATATCATAATAAGAGTTGAATTATTCCTAAATGT
1 CTTATACTATATATACAAGATTCTTCATAAAATATCATAATAAGAGTTGAATTATTCCTAAATGT
* **
23728 AAACGTAACCTTGTTTAAAAAAGTTTTGAATTCGAACCATACTTCATGCACTATAAATCTATTAA
66 AAACATAACCAAGTTTAAAAAAGTTTTGAATTCGAACCATACTTCATGCACTATAAATCTATTAA
* * * * * * *
23793 TAAATGACCCTATTTGAATATTTTGCATCCTTAAAAAATATACATTTTTTTCTCTCCTCTTTCTT
131 TAAATGACCCTATTGGAATATTTTACATCCTAAAAAAAGATACATTTGTTCCGCTCCTCTTTCTT
* * *
23858 TAATATAAGAAATTTATAAATTCAATCTTTAGTGAACCCATGCTTGGTAGTGACATGCTCCCCAA
196 TAATATAAGAAAGTTATAAATTCAACCTTTAGTGAACCCATGCTTGGCAGTGACATGCTCCCCAA
* *
23923 CTTTACGAGGGGAACATAATTAGATTGTATCTTTTCATGCTCTATGTATTTCGAAAATTTGGAGA
261 CTTTACGAGGGGAACATAATTAGATTGTATCTTTTCATGCTCTATGTATGTCGAAAATGTGGAGA
* * * *
23988 ACTACATACTACAACTCTTCGAGATGATTTTAACAAATTACTCCCTTTAATATTCAGTATATGTG
326 ACTACATACAACAACTCTTCAAGATGATTTTAACAAATCACTCCCTTTAATATTCAATATATGTG
* *
24053 ATCCACTTGGTCCAATCATTGTTAAGGCCATGATGGATTATATATATCGTAATTAAACTACTATA
391 ATCCACTTGGTCCAATCATTGTTAAGGCCATGATAGATTATATATATCATAATTAAACTACTATA
* * *
24118 TTTAGTTTTCCAATGGCTTTTTCGAAACTTTCCAAGATATTGTCGGTCTTTCCCAATGTCGGACC
456 TTTAGTTTTCCAATGGCTTTTTCGAAACATTCCAAGATATTGTCGGCCTTTCCCAATGTCGAACC
* * *
24183 CCCAAACAATTTCTTCATTCTCTTCTACCTTAGTGAAAACAAACCTTACTCTTTCTAAAATTTTG
521 CCCAAACAATTTCATCACTCTCTTCTACCTCAGTGAAAACAAACCTTACTCTTTCTAAAATTTTG
* *
24248 TAAAATATTTATTAAATTTTACATTATTTTCCAAATGACCAAGAACACGTCAATTACGATCAATA
586 TAAAATATTTATTAAATTTTACACTATTTTCCAAATGACCAAGAACACGTCAATTACGATAAATA
24313 CTACAATA
651 CTACAATA
* * * * *
24321 CTTATGCTATATGTACAATATTCTTCGTAAAATATCATAATACA-AGTTGAATTATTCCTTAATG
1 CTTATACTATATATACAAGATTCTTCATAAAATATCATAATA-AGAGTTGAATTATTCCTAAATG
** *
24385 TAAACATAACCAAGTTTAGGAAAGTTTTGAATTTGAACCATACTTCATGCACTATAAATCTATTA
65 TAAACATAACCAAGTTTAAAAAAGTTTTGAATTCGAACCATACTTCATGCACTATAAATCTATTA
* *
24450 ATAAATGACCCTATTGGAATCTTTTACGTCCATGAAAAATAAGATACATTTGTTCCGCTCCTCTT
130 ATAAATGACCCTATTGGAATATTTTACATCC-T-AAAAA-AAGATACATTTGTTCCGCTCCTCTT
* *
24515 TCTTTAATATAAGAAAGTTATAAATTCAACCTTTAGTGAACCCATTCTTGGCAGTGACATGCTTC
192 TCTTTAATATAAGAAAGTTATAAATTCAACCTTTAGTGAACCCATGCTTGGCAGTGACATGCTCC
** * *
24580 CC-ACATTTACGAGGGGAATGTCATTAGATTGTGATCTTTTCATGCTCTATTTATGTCTG-AAAT
257 CCAAC-TTTACGAGGGGAACATAATTAGATTGT-ATCTTTTCATGCTCTATGTATGTC-GAAAAT
* *
24643 GTGGAGAACTACATACAACAATTCTTCAAGATGATTTTAATAAATCACTCCCTTTAATATTCAAT
319 GTGGAGAACTACATACAACAACTCTTCAAGATGATTTTAACAAATCACTCCCTTTAATATTCAAT
* * *
24708 ATATGTGATCCACTTGGTCCAATCATTGTTAAGGTCATGATAGATTCTATATCTCATAATTAAAC
384 ATATGTGATCCACTTGGTCCAATCATTGTTAAGGCCATGATAGATTATATATATCATAATTAAAC
* ** *
24773 TACTATATTTAGTTTT-TAAT-G-TTTTTTTAAACATTCCAAGATATCT-TCGGCCTTTCCCATT
449 TACTATATTTAGTTTTCCAATGGCTTTTTCGAAACATTCCAAGATAT-TGTCGGCCTTTCCCAAT
*
24834 GT-GAAACCCCCAATA-AATTTCATCACTCTCTTCTACCTCAGTGAAAACAAACC-TACTCTTTT
513 GTCG-AACCCCCAA-ACAATTTCATCACTCTCTTCTACCTCAGTGAAAACAAACCTTACTCTTTC
* * * **
24896 TAAAATTTTGTAAAATATTTCTTAAATTTTATACTATTTTCCAAATGACCAAGACCGTGTCAATT
576 TAAAATTTTGTAAAATATTTATTAAATTTTACACTATTTTCCAAATGACCAAGAACACGTCAATT
24961 ACGATAAATACTA
641 ACGATAAATACTA
24974 ATGATATCTC
Statistics
Matches: 583, Mismatches: 60, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
658 223 0.38
659 80 0.14
660 9 0.02
661 110 0.19
662 160 0.27
663 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (658 bp):
CTTATACTATATATACAAGATTCTTCATAAAATATCATAATAAGAGTTGAATTATTCCTAAATGT
AAACATAACCAAGTTTAAAAAAGTTTTGAATTCGAACCATACTTCATGCACTATAAATCTATTAA
TAAATGACCCTATTGGAATATTTTACATCCTAAAAAAAGATACATTTGTTCCGCTCCTCTTTCTT
TAATATAAGAAAGTTATAAATTCAACCTTTAGTGAACCCATGCTTGGCAGTGACATGCTCCCCAA
CTTTACGAGGGGAACATAATTAGATTGTATCTTTTCATGCTCTATGTATGTCGAAAATGTGGAGA
ACTACATACAACAACTCTTCAAGATGATTTTAACAAATCACTCCCTTTAATATTCAATATATGTG
ATCCACTTGGTCCAATCATTGTTAAGGCCATGATAGATTATATATATCATAATTAAACTACTATA
TTTAGTTTTCCAATGGCTTTTTCGAAACATTCCAAGATATTGTCGGCCTTTCCCAATGTCGAACC
CCCAAACAATTTCATCACTCTCTTCTACCTCAGTGAAAACAAACCTTACTCTTTCTAAAATTTTG
TAAAATATTTATTAAATTTTACACTATTTTCCAAATGACCAAGAACACGTCAATTACGATAAATA
CTACAATA
Found at i:25221 original size:23 final size:23
Alignment explanation
Indices: 25175--25240 Score: 105
Period size: 23 Copynumber: 2.8 Consensus size: 23
25165 CAAAATTTAA
*
25175 CCATGTATAAATATGATTGATACTT
1 CCAT-TATAAA-ATGTTTGATACTT
25200 CCATTATAAAATGTTTGATACTT
1 CCATTATAAAATGTTTGATACTT
25223 CCATTATAAAATGTTTGA
1 CCATTATAAAATGTTTGA
25241 AAAAAGTAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 30 0.75
24 6 0.15
25 4 0.10
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (23 bp):
CCATTATAAAATGTTTGATACTT
Found at i:32784 original size:24 final size:23
Alignment explanation
Indices: 32748--32795 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
32738 AGATATCAGG
*
32748 AATCAAAATAGAATTCAGAGTAAA
1 AATCAAAACAGAATTCAGA-TAAA
*
32772 AATCAGAACAGAATTCAGATAAA
1 AATCAAAACAGAATTCAGATAAA
32795 A
1 A
32796 CATTAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.19
Consensus pattern (23 bp):
AATCAAAACAGAATTCAGATAAA
Found at i:34334 original size:17 final size:17
Alignment explanation
Indices: 34294--34335 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
34284 TAATGGTCCA
* **
34294 GTCAATAGCGGTTTACG
1 GTCAATGGCGGTCAACG
34311 GTCAATGGCGGTCAACG
1 GTCAATGGCGGTCAACG
34328 GTCAATGG
1 GTCAATGG
34336 TGGCTCTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (17 bp):
GTCAATGGCGGTCAACG
Found at i:36486 original size:24 final size:24
Alignment explanation
Indices: 36418--36489 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
36408 AAACGGAGAT
* *
36418 ATCAGAAATCAAAATAGAATTCAG
1 ATCAGAAATCAAAATAAAATCCAG
* * *
36442 ATCAGATAGCAAAATATAATCCAG
1 ATCAGAAATCAAAATAAAATCCAG
* *
36466 ATCAGAAATCATAACAAAATCCAG
1 ATCAGAAATCAAAATAAAATCCAG
36490 GTTAGGTATC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.53, C:0.17, G:0.11, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAATAAAATCCAG
Found at i:37201 original size:13 final size:13
Alignment explanation
Indices: 37183--37210 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
37173 TAACGAATAT
37183 CCACTTCTTAGTA
1 CCACTTCTTAGTA
37196 CCACTTCTTAGTA
1 CCACTTCTTAGTA
37209 CC
1 CC
37211 GAATGCGCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.36, G:0.07, T:0.36
Consensus pattern (13 bp):
CCACTTCTTAGTA
Found at i:41807 original size:24 final size:24
Alignment explanation
Indices: 41797--41911 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
41787 CATAATTCAC
* * *
41797 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
* *
41821 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
41845 GTTAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
41869 GTC-AGATATCAGATCATAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
41893 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
41912 ATCAAATCGA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 2 0.03
24 75 0.95
25 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:41928 original size:48 final size:48
Alignment explanation
Indices: 41777--41928 Score: 141
Period size: 48 Copynumber: 3.2 Consensus size: 48
41767 GGATATATCA
* * * * *
41777 AAAATCAAATCATAATTCACGTCAAGTATCATATCA-AAATCCAGGTC
1 AAAATCAGATCATAATCCAAGTCAAGTATCAGATCAGAAATCCAAGTC
* * *
41824 AAGTAA-CAGATCAGAATCCAAGTTAAGTATCAGATCAG-AATCCATGTC
1 AA--AATCAGATCATAATCCAAGTCAAGTATCAGATCAGAAATCCAAGTC
* * *
41872 AGATATCAGATCATAATCCATGTCAAGTATCAGATCAGAAAT-CAAATC
1 A-AAATCAGATCATAATCCAAGTCAAGTATCAGATCAGAAATCCAAGTC
41920 GAAAATCAG
1 -AAAATCAG
41929 GTAAAATATT
Statistics
Matches: 84, Mismatches: 14, Indels: 13
0.76 0.13 0.12
Matches are distributed among these distances:
47 3 0.04
48 74 0.88
49 7 0.08
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (48 bp):
AAAATCAGATCATAATCCAAGTCAAGTATCAGATCAGAAATCCAAGTC
Found at i:41928 original size:72 final size:71
Alignment explanation
Indices: 41777--41928 Score: 155
Period size: 72 Copynumber: 2.1 Consensus size: 71
41767 GGATATATCA
* * * *
41777 AAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAGGTCAAGTAACAGATCAGAATC
1 AAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAGGTCAAGTAACAGATCAGAATC
* *
41842 CAAGTT
66 CAAATG
* * * * *
41848 AAGTATCAGATCAGAATCCATGTC-AGATATCAGATCATAATCCATGTCAAGTATCAGATCAGAA
1 AA-AATCAGATCAGAATCCACGTCAAG-TATCAGATCAAAATCCAGGTCAAGTAACAGATCAG-A
41912 AT-CAAATCG
63 ATCCAAAT-G
41921 AAAATCAG
1 AAAATCAG
41929 GTAAAATATT
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
71 4 0.06
72 56 0.86
73 5 0.08
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (71 bp):
AAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAGGTCAAGTAACAGATCAGAATC
CAAATG
Found at i:46488 original size:24 final size:24
Alignment explanation
Indices: 46461--46592 Score: 151
Period size: 24 Copynumber: 5.5 Consensus size: 24
46451 ATATCAAAAA
* * *
46461 ATCAAATCATAATTCATGTCAAGT
1 ATCAGATCAGAATCCATGTCAAGT
* * *
46485 ATCATATCAAAATCCAGGTCAAGT
1 ATCAGATCAGAATCCATGTCAAGT
*
46509 AAT-AGATCAGAATCCAAGTCAAGT
1 -ATCAGATCAGAATCCATGTCAAGT
*
46533 ATCAGATCAGAATCCATCTC-AGAT
1 ATCAGATCAGAATCCATGTCAAG-T
*
46557 ATCAGATCATAATCCATGTCAAGT
1 ATCAGATCAGAATCCATGTCAAGT
46581 ATCAGATCAGAA
1 ATCAGATCAGAA
46593 ATCAAATCGA
Statistics
Matches: 92, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
23 4 0.04
24 84 0.91
25 4 0.04
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.26
Consensus pattern (24 bp):
ATCAGATCAGAATCCATGTCAAGT
Found at i:46609 original size:48 final size:47
Alignment explanation
Indices: 46458--46609 Score: 139
Period size: 48 Copynumber: 3.2 Consensus size: 47
46448 GATATATCAA
* * * **
46458 AAAATCAAATCATAATTCATGTCAAGTATCATATCA-AAATCCAGGTC
1 AAAATCAGATCATAATCCATGTCAAGTATCAGATCAGAAAT-CAAATC
* * **
46505 AAGTAAT-AGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCATCTC
1 AA--AATCAGATCATAATCCATGTCAAGTATCAGATCAGAAAT-CAAATC
*
46553 AGATATCAGATCATAATCCATGTCAAGTATCAGATCAGAAATCAAATC
1 A-AAATCAGATCATAATCCATGTCAAGTATCAGATCAGAAATCAAATC
46601 GAAAATCAG
1 -AAAATCAG
46610 GTAAAATATT
Statistics
Matches: 85, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
47 4 0.05
48 73 0.86
49 8 0.09
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.24
Consensus pattern (47 bp):
AAAATCAGATCATAATCCATGTCAAGTATCAGATCAGAAATCAAATC
Found at i:46609 original size:72 final size:71
Alignment explanation
Indices: 46458--46609 Score: 157
Period size: 72 Copynumber: 2.1 Consensus size: 71
46448 GATATATCAA
* * * * *
46458 AAAATCAAATCATAATTCATGTCAAGTATCATATCAAAATCCAGGTCAAGTAATAGATCAGAATC
1 AAAATCAGATCAGAATCCATCTCAAGTATCAGATCAAAATCCAGGTCAAGTAATAGATCAGAATC
*
46523 CAAGTC
66 CAAATC
* * *
46529 AAGTATCAGATCAGAATCCATCTC-AGATATCAGATCATAATCCATGTCAAGT-ATCAGATCAGA
1 AA-AATCAGATCAGAATCCATCTCAAG-TATCAGATCAAAATCCAGGTCAAGTAAT-AGATCAG-
46592 AAT-CAAATC
62 AATCCAAATC
46601 GAAAATCAG
1 -AAAATCAG
46610 GTAAAATATT
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
71 6 0.09
72 55 0.83
73 5 0.08
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.24
Consensus pattern (71 bp):
AAAATCAGATCAGAATCCATCTCAAGTATCAGATCAAAATCCAGGTCAAGTAATAGATCAGAATC
CAAATC
Found at i:49040 original size:13 final size:13
Alignment explanation
Indices: 49022--49083 Score: 61
Period size: 13 Copynumber: 4.4 Consensus size: 13
49012 CACCGGTCAA
49022 CGGGTCAATGGGT
1 CGGGTCAATGGGT
49035 CGGGTCAACAGGTCGGGT
1 CGGGTC-A-A--T-GGGT
49053 CGGGTCAATGGGT
1 CGGGTCAATGGGT
* *
49066 CGGGTAAACGGGT
1 CGGGTCAATGGGT
49079 CGGGT
1 CGGGT
49084 TGGGTCGGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
13 26 0.62
14 2 0.05
15 1 0.02
16 1 0.02
17 2 0.05
18 10 0.24
ACGTcount: A:0.16, C:0.18, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCAATGGGT
Found at i:49042 original size:31 final size:30
Alignment explanation
Indices: 49006--49080 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
48996 TCAAAGTTTT
49006 GGTCAACACCGGTC-AACGGGTCAATGGGTCG
1 GGTCAACA--GGTCGAACGGGTCAATGGGTCG
**
49037 GGTCAACAGGTCGGGTCGGGTCAATGGGTCG
1 GGTCAACAGGTC-GAACGGGTCAATGGGTCG
* *
49068 GGTAAACGGGTCG
1 GGTCAACAGGTCG
49081 GGTTGGGTCG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 4 0.11
30 1 0.03
31 33 0.87
ACGTcount: A:0.20, C:0.21, G:0.41, T:0.17
Consensus pattern (30 bp):
GGTCAACAGGTCGAACGGGTCAATGGGTCG
Found at i:49054 original size:18 final size:18
Alignment explanation
Indices: 49031--49070 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
49021 ACGGGTCAAT
49031 GGGTCGGGTCAACAGGTC
1 GGGTCGGGTCAACAGGTC
**
49049 GGGTCGGGTCAATGGGTC
1 GGGTCGGGTCAACAGGTC
49067 GGGT
1 GGGT
49071 AAACGGGTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.17, G:0.50, T:0.20
Consensus pattern (18 bp):
GGGTCGGGTCAACAGGTC
Found at i:49081 original size:31 final size:31
Alignment explanation
Indices: 49022--49089 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
49012 CACCGGTCAA
*
49022 CGGGTCAATGGGTCGGGTCAACAGGTCGGGT
1 CGGGTCAATGGGTCGGGTAAACAGGTCGGGT
*
49053 CGGGTCAATGGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAATGGGTCGGGTAAACAGGTCGGGT
*
49084 TGGGTC
1 CGGGTC
49090 GGGTTATGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.15, C:0.18, G:0.47, T:0.21
Consensus pattern (31 bp):
CGGGTCAATGGGTCGGGTAAACAGGTCGGGT
Found at i:52241 original size:29 final size:29
Alignment explanation
Indices: 52209--52386 Score: 180
Period size: 29 Copynumber: 6.1 Consensus size: 29
52199 TTTGAAAATA
* * **
52209 TCACCTTTTTCAAAAAAATTCTTAGAATG
1 TCACATTTTTCAAAAAATTTCCCAGAATG
* * *
52238 TCACCTTTTTCAAAATATTTCCTAGAATG
1 TCACATTTTTCAAAAAATTTCCCAGAATG
* * *
52267 TCACCTTTTT-AAAATATTTCCCAAAATG
1 TCACATTTTTCAAAAAATTTCCCAGAATG
*
52295 TCACATTTTTTAAAAATATTTCCCAGAATG
1 TCACATTTTTCAAAAA-ATTTCCCAGAATG
** *
52325 TCACATTTTTCAAACTATTTCTCAGAATG
1 TCACATTTTTCAAAAAATTTCCCAGAATG
**
52354 TCACATTTTTCACAAAAA-TTCCTTGAATG
1 TCACATTTTTCA-AAAAATTTCCCAGAATG
52383 TCAC
1 TCAC
52387 TGGGTTGGGT
Statistics
Matches: 129, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
28 25 0.19
29 76 0.59
30 28 0.22
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.39
Consensus pattern (29 bp):
TCACATTTTTCAAAAAATTTCCCAGAATG
Found at i:52313 original size:30 final size:30
Alignment explanation
Indices: 52209--52365 Score: 182
Period size: 29 Copynumber: 5.4 Consensus size: 30
52199 TTTGAAAATA
* * **
52209 TCAC-CTTTTTCAAAAAAATTCTTAGAATG
1 TCACACTTTTTCAAAATATTTCCCAGAATG
*
52238 TCAC-CTTTTTCAAAATATTTCCTAGAATG
1 TCACACTTTTTCAAAATATTTCCCAGAATG
*
52267 TCAC-CTTTTT-AAAATATTTCCCAAAATG
1 TCACACTTTTTCAAAATATTTCCCAGAATG
* *
52295 TCACATTTTTTAAAAATATTTCCCAGAATG
1 TCACACTTTTTCAAAATATTTCCCAGAATG
* *
52325 TCACA-TTTTTCAAACTATTTCTCAGAATG
1 TCACACTTTTTCAAAATATTTCCCAGAATG
52354 TCACA-TTTTTCA
1 TCACACTTTTTCA
52366 CAAAAATTCC
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
28 20 0.17
29 74 0.64
30 22 0.19
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.41
Consensus pattern (30 bp):
TCACACTTTTTCAAAATATTTCCCAGAATG
Found at i:65565 original size:3 final size:3
Alignment explanation
Indices: 65559--65660 Score: 120
Period size: 3 Copynumber: 34.7 Consensus size: 3
65549 TTCATTTGAA
*
65559 TAT TAT T-T ATAT T-T TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
65603 TAT AAT TAT TAT AAT TAT TAT TAT AAT TAT TAT TAT AAT TA- TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
65650 TAT TAT TAT TA
1 TAT TAT TAT TA
65661 AATAATTACA
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
2 5 0.06
3 77 0.93
4 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:73812 original size:8 final size:9
Alignment explanation
Indices: 73785--73815 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
73775 AAATGGCAAT
73785 CATTCTTTA
1 CATTCTTTA
73794 CATTCTTTA
1 CATTCTTTA
73803 CATT-TTTA
1 CATTCTTTA
73811 CATTC
1 CATTC
73816 ATTATGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (9 bp):
CATTCTTTA
Found at i:73825 original size:17 final size:17
Alignment explanation
Indices: 73785--73819 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
73775 AAATGGCAAT
*
73785 CATTCTTTACATTCTTTA
1 CATT-TTTACATTCATTA
73803 CATTTTTACATTCATTA
1 CATTTTTACATTCATTA
73820 TGTTTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.26, C:0.20, G:0.00, T:0.54
Consensus pattern (17 bp):
CATTTTTACATTCATTA
Found at i:77808 original size:21 final size:21
Alignment explanation
Indices: 77767--77809 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
77757 TATCTATTTG
**
77767 AAATTCAATTTCTTTTGTTTT
1 AAATTCAATTTCAATTGTTTT
77788 AAATTCAATTTACAATT-TTTT
1 AAATTCAATTT-CAATTGTTTT
77809 A
1 A
77810 TAAACATCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (21 bp):
AAATTCAATTTCAATTGTTTT
Found at i:79310 original size:112 final size:113
Alignment explanation
Indices: 79119--79644 Score: 465
Period size: 112 Copynumber: 4.6 Consensus size: 113
79109 AATAGTTCAT
* *
79119 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA-TTTATAATGAGAATAATTTGTTCAACCTT
1 AATGAGAAGAACTCATCTGAAGAAGGAAGAA-AAAGTTCATAATGAGAAGAATTTGTTCAACCTT
** * *
79183 TTGCTTTAATTCATCACCCAATGGATTAACGTTACCAG-GTAGAGTTCGA
65 TTGCTCGAATTCATCACCCAATGGATCAACGTTACCAGAG-AAAGTTCGA
* * *
79232 AATGAGAATAACTCATCTGAAGAATG-AGAAAAAGTTCATAGTGAGAAGAATTTGTTCAACCTTT
1 AATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
* * * * *
79296 TGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCGT
66 TGCTCGAATTCATCACCCAATGGATCAACGTTACCAGAGAAAGTTCGA
* * * **
79344 AATGAGAAGAACTTATCTAAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
1 AATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
* ** * **
79408 TGCAT-G-ACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTTTCAGAGAAAGTTC-A
66 TGC-TCGAATTC-ATCAC----CCA-AT-G----G-ATCAAC-GTTACCAGAGAAAGTTCGA
* * * * * *
79467 TAATGAGAAGAGCTCATCTGAAGAAGGAAGTAGATGTTCATAATGAGAAGAACTTGTTTAACCTT
1 -AATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTT
* * * * * * *
79532 TTGTTTGAATTCATTACTCAATGGATCAACTTTTCCAGAGAAAGTTCGT
65 TTGCTCGAATTCATCACCCAATGGATCAACGTTACCAGAGAAAGTTCGA
* * * *
79581 AATGAGAAGAACTTATATGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
1 AATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
79645 GTTTGATTCT
Statistics
Matches: 343, Mismatches: 48, Indels: 45
0.79 0.11 0.10
Matches are distributed among these distances:
111 8 0.02
112 169 0.49
113 61 0.18
114 6 0.02
115 1 0.00
117 2 0.01
118 1 0.00
119 1 0.00
120 2 0.01
121 1 0.00
122 1 0.00
123 6 0.02
124 36 0.10
125 45 0.13
126 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
AATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
TGCTCGAATTCATCACCCAATGGATCAACGTTACCAGAGAAAGTTCGA
Found at i:79513 original size:125 final size:121
Alignment explanation
Indices: 79318--79735 Score: 466
Period size: 125 Copynumber: 3.5 Consensus size: 121
79308 TCACTCGATG
* *
79318 GATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTTATCTAAAGAGGAAGAAGAAGTTCAT
1 GATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
* ** *
79383 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCA
66 AATGAGAAGAACTTGTTCAACCTTTTGTTTGAATCTATCACA-AAGGAGATAGATCA
* * * * *
79440 GCATCAACTTTTTTCAGAGAAAGTTCATAATGAGAAGAGCTCATCTGAAGAAGGAAGTAGATGTT
1 G-ATCAAC-TTTTCCAGAGAAAGTTCGTAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTT
* * **
79505 CATAATGAGAAGAACTTGTTTAACCTTTTGTTTGAAT-TCATTAC---TCA-AT-G----
63 CATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATCT-ATCACAAAGGAGATAGATCA
* *
79555 GATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTTATATGAAGAGGAAGAAGAAGTTCAT
1 GATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
*
79620 AATGAGAAGAACTTGTTCAACC-TTTGTTTGATTCTATCACATAAGGAGATAGATCA
66 AATGAGAAGAACTTGTTCAACCTTTTGTTTGAATCTATCACA-AAGGAGATAGATCA
* * * *
79676 GTATCAGCATTTCCAGA-AGGAGTTCTTAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAA
1 G-ATCAACTTTTCCAGAGA-AAGTTCGTAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAA
79736 TTTGTTCAAC
Statistics
Matches: 245, Mismatches: 33, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
111 14 0.06
112 37 0.15
113 36 0.15
114 6 0.02
115 2 0.01
116 2 0.01
117 1 0.00
119 1 0.00
120 2 0.01
121 3 0.01
122 47 0.19
123 9 0.04
124 37 0.15
125 48 0.20
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (121 bp):
GATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTTGTTTGAATCTATCACAAAGGAGATAGATCA
Found at i:79544 original size:237 final size:235
Alignment explanation
Indices: 79232--79729 Score: 721
Period size: 237 Copynumber: 2.1 Consensus size: 235
79222 TAGAGTTCGA
* * * *
79232 AATGAGAATAACTCATCTGAAGAATG-AGAAAAAGTTCATAGTGAGAAGAATTTGTTCAACCTTT
1 AATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
* *
79296 TGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTTATC
66 TGCTCGAATTCATCACTCAATGGATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTTATA
*
79361 TAAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAG
131 TAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTTGCATGACTCTATCACAG
* *
79426 AAGGAGATAGATCAGCATCAACTTTTTTCAG-AGAAAGTTCAT
195 AAGGAGATAGATCAGCATCAAC-ATTTCCAGAAG-AAGTTCAT
* * * * *
79468 AATGAGAAGAGCTCATCTGAAGAAGGAAGTAGATGTTCATAATGAGAAGAACTTGTTTAACCTTT
1 AATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
* * *
79533 TGTTTGAATTCATTACTCAATGGATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTTATA
66 TGCTCGAATTCATCACTCAATGGATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTTATA
* ** * *
79598 TGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGTTTGATTCTATCACATA
131 TAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCATGACTCTATCACAGA
* * * *
79663 AGGAGATAGATCAGTATCAGCATTTCCAGAAGGAGTTCTT
196 AGGAGATAGATCAGCATCAACATTTCCAGAAGAAGTTCAT
79703 AATGAGAAGAACTCATCTGAAGAAGGA
1 AATGAGAAGAACTCATCTGAAGAAGGA
79730 GAAGAATTTG
Statistics
Matches: 233, Mismatches: 27, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
235 38 0.16
236 61 0.26
237 134 0.58
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (235 bp):
AATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
TGCTCGAATTCATCACTCAATGGATCAACTTTTCCAGAGAAAGTTCGTAATGAGAAGAACTTATA
TAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCATGACTCTATCACAGA
AGGAGATAGATCAGCATCAACATTTCCAGAAGAAGTTCAT
Found at i:79974 original size:3 final size:3
Alignment explanation
Indices: 79968--80034 Score: 86
Period size: 3 Copynumber: 22.7 Consensus size: 3
79958 TTCATTTGAA
79968 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TATT TAT TA- TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
*
80013 TAT TA- TAT TTT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
80035 AATAATTACA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
2 5 0.09
3 48 0.84
4 4 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:81401 original size:11 final size:11
Alignment explanation
Indices: 81343--81401 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
81333 TTATTTGCAA
81343 TATTA-TTTAT
1 TATTATTTTAT
81353 TATTATTTT-T
1 TATTATTTTAT
81363 TATATATGTTTAAAT
1 TAT-TAT-TTT--AT
* *
81378 TATTAGTTCAT
1 TATTATTTTAT
81389 TATTATTTTAT
1 TATTATTTTAT
81400 TA
1 TA
81402 GTCATATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
10 9 0.23
11 19 0.49
12 3 0.08
13 2 0.05
14 2 0.05
15 4 0.10
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:82436 original size:13 final size:13
Alignment explanation
Indices: 82418--82443 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
82408 GGAGTAGGGG
82418 AAGATCCATGGGA
1 AAGATCCATGGGA
82431 AAGATCCATGGGA
1 AAGATCCATGGGA
82444 TCACATCCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (13 bp):
AAGATCCATGGGA
Found at i:83770 original size:20 final size:21
Alignment explanation
Indices: 83734--83772 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
83724 ATACAAAAGG
83734 TAGGTAAGTATATATACTAAC
1 TAGGTAAGTATATATACTAAC
83755 TAGGT-AGTATCA-ATACTA
1 TAGGTAAGTAT-ATATACTA
83773 CCAGCATTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (21 bp):
TAGGTAAGTATATATACTAAC
Done.