Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001514.1 Hibiscus syriacus cultivar Beakdansim tig00002961_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: 92458
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:6854 original size:2 final size:2
Alignment explanation
Indices: 6847--6911 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
6837 TTATCTATCT
6847 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
6889 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
6912 TATTAACATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7435 original size:4 final size:4
Alignment explanation
Indices: 7426--7456 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
7416 CAATACATGT
7426 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
7457 CATAGTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:8358 original size:4 final size:4
Alignment explanation
Indices: 8349--8375 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
8339 CAATGCATGT
8349 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
8376 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:9066 original size:919 final size:921
Alignment explanation
Indices: 7282--9117 Score: 3534
Period size: 919 Copynumber: 2.0 Consensus size: 921
7272 ATTGAAAACA
*
7282 ACAACAACAAAACCCTATTCCCATATGCGATGGGGTAAGGGGAGGTAGGGTAGTATGTTGCCTCC
1 ACAACAACAAAACCCTATTCCCATATGCGATGGGGTAAGGGGAGGTAGGGTAGTAGGTTGCCTCC
* *
7347 AACGCCAGGTTTAGAGCAGCTTCCGTGGAAGATCTCCGACAGTCAGAAAAATAAAAATAAAGATA
66 AACGCCAGGTTGAGAGCAGCTTCCGTGGAAGACCTCCGACAGTCAGAAAAATAAAAATAAAGATA
*
7412 AATGCAATACATGTATAAATAAATAAATAAATAAATAAATAAATACATAGTTGAACAGTCTTTAT
131 AATACAATACATG-AT-AATAAATAAATAAATAAATAAATAAATACATAGTTGAACAGTCTTTAT
7477 ATGCGCGTCTTTAATGGGAAGTAATCCCTGCAAATAAATCTCTGCGTAAAAAAAACTCTGCATAT
194 ATGCGCGTCTTTAATGGGAAGTAATCCCTGCAAATAAATCTCTGCGTAAAAAAAACTCTGCATAT
7542 ATACAGAAGATATAAGACCCGGCTAAATTTAAAAAGAGGTAACCTGAAGAGAAAGATACACAATA
259 ATACAGAAGATATAAGACCCGGCTAAATTTAAAAAGAGGTAACCTGAAGAGAAAGATACACAATA
7607 ATCAACGATAGCAAGCTACGAGACGGAATAAAGTCAAATGGGTTAACACATAAACTAAGGCAACA
324 ATCAACGATAGCAAGCTACGAGACGGAATAAAGTCAAATGGGTTAACACATAAACTAAGGCAACA
7672 CTAATACCCTACCCTAGTTCTAAGCCTTCATAAATTACAATGCCAGGAACTTATATAAAGTAGAA
389 CTAATACCCTACCCTAGTTCTAAGCCTTCATAAATTACAATGCCAGGAACTTATATAAAGTAGAA
7737 GTCATGGAAATAACTATAAAGACATTTAAAATAAGACAGAGAATGTTACACCTTATGGTTGTGAC
454 GTCATGGAAATAACTATAAAGACATTTAAAATAAGACAGAGAATGTTACACCTTATGGTTGTGAC
7802 CTGCACTACTCGGCTACCATGGTCTTAAGTCTCCATACTTTCCTATCAGAGGTCATGTCCTCGGT
519 CTGCACTACTCGGCTACCATGGTCTTAAGTCTCCATACTTTCCTATCAGAGGTCATGTCCTCGGT
7867 AAGGGCTAAATCGTTCACATCATATCTCAAGCAGTCTTCCCACTTCCGCTTTGGTCGTCCTCTCC
584 AAGGGCTAAATCGTTCACATCATATCTCAAGCAGTCTTCCCACTTCCGCTTTGGTCGTCCTCTCC
7932 TTCTGGCACCGTCGACTGTAATCGACTCTACTCTCCTGACCGCATCCAACGGTTGTCGCCTAAGG
649 TTCTGGCACCGTCGACTGTAATCGACTCTACTCTCCTGACCGCATCCAACGGTTGTCGCCTAAGG
7997 ACATGTCCAAACCACCGTAGTCTTCCCTCCCTCAATTTTTCGGATACAGACACCGCCCCCAAGGA
714 ACATGTCCAAACCACCGTAGTCTTCCCTCCCTCAATTTTTCGGATACAGACACCGCCCCCAAGGA
8062 CATCCTAATAGCAGAGTTTGGTGTCATGTCCCACAGAGTCCTACCACATGCCCATCTAAGCATTC
779 CATCCTAATAGCAGAGTTTGGTGTCATGTCCCACAGAGTCCTACCACATGCCCATCTAAGCATTC
*
8127 TCATTTCTGCGGCATCCATCCTCCTTACGTGATCCTTCTTGATTGCCCAACATTCTGATCCATAC
844 TCATTTCTGCGGCATCCATCCTCCTTACGTGATCATTCTTGATTGCCCAACATTCTGATCCATAC
8192 AGCAGCGTTGGAT
909 AGCAGCGTTGGAT
*
8205 ACAACAACAAAACCCTATTCTCATATGCGATGGGGTAAGGGGAGGTAGGGTAGTAGGTTGCCTCC
1 ACAACAACAAAACCCTATTCCCATATGCGATGGGGTAAGGGGAGGTAGGGTAGTAGGTTGCCTCC
*
8270 AACGCCAGGTTGAGAGCAGCTTCCGTGGAAGACCTCTGACAGTCA-AAAAATAAAAATAAAGATA
66 AACGCCAGGTTGAGAGCAGCTTCCGTGGAAGACCTCCGACAGTCAGAAAAATAAAAATAAAGAT-
*
8334 AAATACAATGCATG-T-ATAAATAAATAAATAAATAAATAAATACATAGTTGAACAGTCTTTATA
130 AAATACAATACATGATAATAAATAAATAAATAAATAAATAAATACATAGTTGAACAGTCTTTATA
8397 TGCGCGTCTTTAATGGGAAGTAATCCCTGCAAATAAATCTCTGCGTAAAAAAAACTCTGCATATA
195 TGCGCGTCTTTAATGGGAAGTAATCCCTGCAAATAAATCTCTGCGTAAAAAAAACTCTGCATATA
8462 TACAGAAGATATAAGACCCGGCTAAATTTAAAAAGAGGTAACCTGAAGAGAAAGATACACAATAA
260 TACAGAAGATATAAGACCCGGCTAAATTTAAAAAGAGGTAACCTGAAGAGAAAGATACACAATAA
8527 TCAACGATAGCAAGCTACGAGACGGAATAAAGTCAAATGGGTTAACACATAAACTAAGGCAACAC
325 TCAACGATAGCAAGCTACGAGACGGAATAAAGTCAAATGGGTTAACACATAAACTAAGGCAACAC
8592 TAATACCCTACCCTAGTTCTAAGCCTTCATAAATTACAATGCCAGGAACTTATATAAAGTAGAAG
390 TAATACCCTACCCTAGTTCTAAGCCTTCATAAATTACAATGCCAGGAACTTATATAAAGTAGAAG
8657 TCATGGAAATAACTATAAAGACATTTAAAATAAGACAGAGAATGTTACACCTTATGGTTGTGACC
455 TCATGGAAATAACTATAAAGACATTTAAAATAAGACAGAGAATGTTACACCTTATGGTTGTGACC
8722 TGCACTACTCGGCTACCATGGTCTTAAGTCTCCATACTTTCCTATCAGAGGTCATGTCCTCGGTA
520 TGCACTACTCGGCTACCATGGTCTTAAGTCTCCATACTTTCCTATCAGAGGTCATGTCCTCGGTA
8787 AGGGCTAAATCGTTCACATCATATCTCAAGCAGTCTTCCCACTTCCGCTTTGGTCGTCCTCTCCT
585 AGGGCTAAATCGTTCACATCATATCTCAAGCAGTCTTCCCACTTCCGCTTTGGTCGTCCTCTCCT
8852 TCTGGCACCGTCGACTGTAATCGACTCTACTCTCCTGACCGCATCCAACGGTTGTCGCCTAAGGA
650 TCTGGCACCGTCGACTGTAATCGACTCTACTCTCCTGACCGCATCCAACGGTTGTCGCCTAAGGA
8917 CATGTCCAAACCACCGTAGTCTTCCCTCCCTCAATTTTTCGGATACAGACACCGCCCCCAAGGAC
715 CATGTCCAAACCACCGTAGTCTTCCCTCCCTCAATTTTTCGGATACAGACACCGCCCCCAAGGAC
8982 ATCCTAATAGCAGAGTTTGGTGTCATGTCCCACAGAGTCCTACCACATGCCCATCTAAGCATTCT
780 ATCCTAATAGCAGAGTTTGGTGTCATGTCCCACAGAGTCCTACCACATGCCCATCTAAGCATTCT
* *
9047 CATTTCTGCGGCCTCCATCCTCCTTACGTGATCATTCTTGATTGCCCAACATTCTGATTCATACA
845 CATTTCTGCGGCATCCATCCTCCTTACGTGATCATTCTTGATTGCCCAACATTCTGATCCATACA
9112 GCAGCG
910 GCAGCG
9118 CTGGTCTTAT
Statistics
Matches: 902, Mismatches: 10, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
919 766 0.85
921 1 0.00
922 18 0.02
923 117 0.13
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (921 bp):
ACAACAACAAAACCCTATTCCCATATGCGATGGGGTAAGGGGAGGTAGGGTAGTAGGTTGCCTCC
AACGCCAGGTTGAGAGCAGCTTCCGTGGAAGACCTCCGACAGTCAGAAAAATAAAAATAAAGATA
AATACAATACATGATAATAAATAAATAAATAAATAAATAAATACATAGTTGAACAGTCTTTATAT
GCGCGTCTTTAATGGGAAGTAATCCCTGCAAATAAATCTCTGCGTAAAAAAAACTCTGCATATAT
ACAGAAGATATAAGACCCGGCTAAATTTAAAAAGAGGTAACCTGAAGAGAAAGATACACAATAAT
CAACGATAGCAAGCTACGAGACGGAATAAAGTCAAATGGGTTAACACATAAACTAAGGCAACACT
AATACCCTACCCTAGTTCTAAGCCTTCATAAATTACAATGCCAGGAACTTATATAAAGTAGAAGT
CATGGAAATAACTATAAAGACATTTAAAATAAGACAGAGAATGTTACACCTTATGGTTGTGACCT
GCACTACTCGGCTACCATGGTCTTAAGTCTCCATACTTTCCTATCAGAGGTCATGTCCTCGGTAA
GGGCTAAATCGTTCACATCATATCTCAAGCAGTCTTCCCACTTCCGCTTTGGTCGTCCTCTCCTT
CTGGCACCGTCGACTGTAATCGACTCTACTCTCCTGACCGCATCCAACGGTTGTCGCCTAAGGAC
ATGTCCAAACCACCGTAGTCTTCCCTCCCTCAATTTTTCGGATACAGACACCGCCCCCAAGGACA
TCCTAATAGCAGAGTTTGGTGTCATGTCCCACAGAGTCCTACCACATGCCCATCTAAGCATTCTC
ATTTCTGCGGCATCCATCCTCCTTACGTGATCATTCTTGATTGCCCAACATTCTGATCCATACAG
CAGCGTTGGAT
Found at i:14401 original size:27 final size:27
Alignment explanation
Indices: 14371--14513 Score: 286
Period size: 27 Copynumber: 5.3 Consensus size: 27
14361 CGAATTCTAA
14371 AAATTTATATTATAATTATTAAATTTT
1 AAATTTATATTATAATTATTAAATTTT
14398 AAATTTATATTATAATTATTAAATTTT
1 AAATTTATATTATAATTATTAAATTTT
14425 AAATTTATATTATAATTATTAAATTTT
1 AAATTTATATTATAATTATTAAATTTT
14452 AAATTTATATTATAATTATTAAATTTT
1 AAATTTATATTATAATTATTAAATTTT
14479 AAATTTATATTATAATTATTAAATTTT
1 AAATTTATATTATAATTATTAAATTTT
14506 AAATTTAT
1 AAATTTAT
14514 TTTTATTATG
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 116 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
AAATTTATATTATAATTATTAAATTTT
Found at i:14543 original size:81 final size:81
Alignment explanation
Indices: 14371--14544 Score: 251
Period size: 81 Copynumber: 2.1 Consensus size: 81
14361 CGAATTCTAA
*
14371 AAATTTATATTATAATTATTAAATTTTAAATTTATATTATAATTATTAAATTTTAAATTTATATT
1 AAATTGATATTATAATTATTAAATTTTAAATTTATATTATAATTATTAAATTTTAAATTTATATT
* *
14436 ATAATTATTAAATTTT
66 ATAATGATTAAATGTT
* *
14452 AAATTTATATTATAATTATTAAATTTTAAATTTATATTATAATTATTAAATTTTAAATTTATTTT
1 AAATTGATATTATAATTATTAAATTTTAAATTTATATTATAATTATTAAATTTTAAATTTA-TAT
* **
14517 TATTATGATTTTATGTT
65 TATAATGATTAAATGTT
*
14534 -AGTTGATATTA
1 AAATTGATATTA
14545 AGAAAAAAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 70 0.83
82 14 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (81 bp):
AAATTGATATTATAATTATTAAATTTTAAATTTATATTATAATTATTAAATTTTAAATTTATATT
ATAATGATTAAATGTT
Found at i:16874 original size:3 final size:3
Alignment explanation
Indices: 16866--16937 Score: 72
Period size: 3 Copynumber: 23.3 Consensus size: 3
16856 CGTCCCGACT
* * * *
16866 TTA TTA TTA TTT TTA TAA TTA TTA TTG TTA TTA TTA TTA TTA TTA TGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
16914 GTAA TTAA TTA TTA CTA TTA TTA T
1 -TTA TT-A TTA TTA TTA TTA TTA T
16938 AAATAAAATA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
3 51 0.91
4 5 0.09
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:19210 original size:131 final size:127
Alignment explanation
Indices: 19065--19426 Score: 386
Period size: 131 Copynumber: 2.8 Consensus size: 127
19055 ATAGATATTG
* * *
19065 AGAATAGTAATATCTTTTCATTTCATTTGGAGTAATAAATGACTTCTATAAGGCATGAAATGTCA
1 AGAATAGTGATATCTTTTCATTTCA-TTGGAGTAATAAATGACTTCTTTAAGGCATGAAAGGTCA
* * * * *
19130 TTTATTCTCGATTAGAAATAATTCGATATTTTCATTCTCTCTCAAATTAATATTGATTTTTACGA
65 TTTATTCTCGATT-GAAATAATTAGATATTATCATTCTCACTCAAATCAATATTGAATTTTA--A
19195 T
127 T
* * * ** *
19196 AGAATAATGATATCTCTTT-ATTTCAATTGGAGCAATAAATGACTGCTTTAAGTTATGAGAGGTC
1 AGAATAGTGATATCT-TTTCATTTC-ATTGGAGTAATAAATGACTTCTTTAAGGCATGAAAGGTC
* * * * *
19260 ATTTATTCTCGATTGGAAATCATTAGATATTATCGTTTTCACTCGAATCGATATTGAATTTTAAT
64 ATTTATTCTCGATT-GAAATAATTAGATATTATCATTCTCACTCAAATCAATATTGAATTTTAAT
* ** *
19325 ACGGAATAGTGATATCTCTTCATTTCGATCAGAGTAATAAATGA-TTGTTTTAAGGCATGAAAGG
1 A--GAATAGTGATATCTTTTCATTTC-ATTGGAGTAATAAATGACTT-CTTTAAGGCATGAAAGG
*
19389 TCATTTATTCTCGATTGAAAATAATTATATATTATCAT
62 TCATTTATTCTCGATTG-AAATAATTAGATATTATCAT
19427 GTTTCATCCA
Statistics
Matches: 190, Mismatches: 34, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
129 3 0.02
130 4 0.02
131 179 0.94
132 4 0.02
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (127 bp):
AGAATAGTGATATCTTTTCATTTCATTGGAGTAATAAATGACTTCTTTAAGGCATGAAAGGTCAT
TTATTCTCGATTGAAATAATTAGATATTATCATTCTCACTCAAATCAATATTGAATTTTAAT
Found at i:22918 original size:72 final size:72
Alignment explanation
Indices: 22823--22971 Score: 235
Period size: 72 Copynumber: 2.1 Consensus size: 72
22813 GATGATGTAA
* * * * *
22823 GAGATGGATTAGAGCCTGAGACTGAGGAAGCTCAGAGGATTTTAGATTTACTAGGGTACATGGAG
1 GAGAAGGACTAGAGCCCGAGACTGAGGAAGCTCAGAGGATTTTAGATTTACTAGGGCACATGCAG
22888 CAATTAG
66 CAATTAG
* *
22895 GAGAAGGACTAGAGCCCGAGACTGAGGAAGCTTAGAGGATTTTAGATTTACTGGGGCACATGCAG
1 GAGAAGGACTAGAGCCCGAGACTGAGGAAGCTCAGAGGATTTTAGATTTACTAGGGCACATGCAG
22960 CAATTAG
66 CAATTAG
22967 GAGAA
1 GAGAA
22972 ATAGCTCAGA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.33, C:0.13, G:0.32, T:0.22
Consensus pattern (72 bp):
GAGAAGGACTAGAGCCCGAGACTGAGGAAGCTCAGAGGATTTTAGATTTACTAGGGCACATGCAG
CAATTAG
Found at i:32068 original size:21 final size:21
Alignment explanation
Indices: 32042--32083 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
32032 ATTTGAATAT
*
32042 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
32063 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
32084 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:34728 original size:21 final size:21
Alignment explanation
Indices: 34703--34744 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34693 AACCAGATTG
34703 CCCAGAGGGAATAGATTCCCC
1 CCCAGAGGGAATAGATTCCCC
* * *
34724 CCCAGGGGGTATCGATTCCCC
1 CCCAGAGGGAATAGATTCCCC
34745 GGGAACAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.17
Consensus pattern (21 bp):
CCCAGAGGGAATAGATTCCCC
Found at i:34899 original size:21 final size:21
Alignment explanation
Indices: 34873--34914 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
34863 ATTTGAATAT
*
34873 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
34894 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
34915 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:34976 original size:21 final size:21
Alignment explanation
Indices: 34943--34982 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
34933 TTTTTGCAAA
*
34943 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
34965 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
34983 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:35236 original size:34 final size:32
Alignment explanation
Indices: 35198--35267 Score: 77
Period size: 34 Copynumber: 2.1 Consensus size: 32
35188 TTTTGTAAAG
* * * *
35198 GGGAAATGTTTTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
35232 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
35264 GGGA
1 GGGA
35268 GTTGTAATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 11 0.35
33 1 0.03
34 19 0.61
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:37817 original size:22 final size:22
Alignment explanation
Indices: 37791--37874 Score: 89
Period size: 22 Copynumber: 3.8 Consensus size: 22
37781 ATAGGGCAGA
37791 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* * *
37813 GGGAACCGATTCCCCCTTTGAAT
1 GGGAATCGATACCCCC-TTGAAG
** *
37836 GGGAA-CTGATTTCCCCTTGTAG
1 GGGAATC-GATACCCCCTTGAAG
37858 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
37875 GGGGTTTCTA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
22 32 0.63
23 19 0.37
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.24
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:39474 original size:18 final size:18
Alignment explanation
Indices: 39453--39493 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
39443 AGAACAGCAC
39453 GAGGAACAAGCACGAA-CA
1 GAGGAACAAGCAC-AACCA
39471 GAGGAACAAGCACAACCA
1 GAGGAACAAGCACAACCA
39489 GAGGA
1 GAGGA
39494 TCAAATGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.49, C:0.22, G:0.29, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGCACAACCA
Found at i:42266 original size:22 final size:22
Alignment explanation
Indices: 42240--42288 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
42230 CAGAAGAATG
*
42240 AAAAATGAAAAACAA-AAAGAAC
1 AAAAATGAAAAA-AAGAAAGAAA
42262 AAAAATGAAAAAAAGAAAGAAA
1 AAAAATGAAAAAAAGAAAGAAA
42284 AAAAA
1 AAAAA
42289 AAGAATAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.82, C:0.04, G:0.10, T:0.04
Consensus pattern (22 bp):
AAAAATGAAAAAAAGAAAGAAA
Found at i:42286 original size:11 final size:11
Alignment explanation
Indices: 42240--42293 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
42230 CAGAAGAATG
*
42240 AAAAATGAAAA
1 AAAAAAGAAAA
*
42251 ACAAAAAG-AAC
1 A-AAAAAGAAAA
*
42262 AAAAATGAAAA
1 AAAAAAGAAAA
42273 AAAGAAAGAAAA
1 AAA-AAAGAAAA
42285 AAAAAAGAA
1 AAAAAAGAA
42294 TAAGCAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 5 0.14
11 15 0.43
12 15 0.43
ACGTcount: A:0.81, C:0.04, G:0.11, T:0.04
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:42287 original size:15 final size:16
Alignment explanation
Indices: 42246--42293 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
42236 AATGAAAAAT
42246 GAAAAACAAAAAGAACA
1 GAAAAA-AAAAAGAACA
*
42263 AAAATGAAAAAAAGAA-A
1 GAAA--AAAAAAAGAACA
42280 GAAAAAAAAAAGAA
1 GAAAAAAAAAAGAA
42294 TAAGCAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 10 0.37
17 7 0.26
18 8 0.30
19 2 0.07
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.02
Consensus pattern (16 bp):
GAAAAAAAAAAGAACA
Found at i:43952 original size:267 final size:265
Alignment explanation
Indices: 43477--44047 Score: 774
Period size: 267 Copynumber: 2.1 Consensus size: 265
43467 ATTCAACTCA
*
43477 ATTCAATCTTCCTTGAAGAACAGTGGAATGAATTAACGTCCCCAGATCTGATTTTCCCTCAAGAA
1 ATTCAATCTTCCTTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
* * * *
43542 GAAGCGAAACATATCTCTCTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCCCCCTC
66 GAAGCGAAAAATACCTCTCTTCAAGAATTAATATTCCCTAAGTAACAGTGGAACAAGTCCCCCTC
* * ** *
43607 GATTCAATTTTCCCTGAGTAACAGTGGAATGAATCAACGTCCCCAGATTTGATTTTCCCTCAAGA
131 GATTCAATCTTCCCTGAGTAACAATAAAATGAATCAAAGTCCCCAGATTTGATTTTCCCTCAAGA
*
43672 AGAAGCGAAACAGATCCCTCTCTTTCAAGATTTGGTATTCCCTAG-GTAACAGTAGAAAAAGTCT
196 AGAAGCGAAACAGATCCCTCTCTTTCAAGATTTGATATT-CCTAGAGTAACAGTAGAAAAAGTCT
*
43736 GCCTCG
260 ACCTCG
*
43742 ATTCAATCTTCCCTG-AGTAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGA
1 ATTCAATCTTCCTTGAAG-AACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGA
* * * * **
43806 A-AAGCGGAATAAATCCCTTTCTTTCAAGAATTAATATTCCCTGAGTAACAGTGGACCAAGTCTG
65 AGAAGC-GAA-AAATACCTCTC-TTCAAGAATTAATATTCCCTAAGTAACAGTGGAACAAGTCCC
*
43870 CCTTGATTCAATCTTCCCTGAAG-AACAATAAAATGAATCAAAGTCCCCAGATTTGAATTTT-CC
127 CCTCGATTCAATCTTCCCTG-AGTAACAATAAAATGAATCAAAGTCCCCAGATTTG-ATTTTCCC
* * * * *
43933 TCAAGAAGAAGCTAAACAGATCCCTCTCTTTCAAGATTTGATCTTCCTTGAGTAACATTAGAACA
190 TCAAGAAGAAGCGAAACAGATCCCTCTCTTTCAAGATTTGATATTCCTAGAGTAACAGTAGAAAA
*
43998 AGTTTACCTCG
255 AGTCTACCTCG
* * * *
44009 TTTCCATCTTCCTTGAAGAACATTGGAATGAGTCAACGT
1 ATTCAATCTTCCTTGAAGAACAGTGGAATGAATCAACGT
44048 TTCTTGATCT
Statistics
Matches: 267, Mismatches: 31, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
264 6 0.02
265 63 0.24
266 11 0.04
267 178 0.67
268 9 0.03
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (265 bp):
ATTCAATCTTCCTTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
GAAGCGAAAAATACCTCTCTTCAAGAATTAATATTCCCTAAGTAACAGTGGAACAAGTCCCCCTC
GATTCAATCTTCCCTGAGTAACAATAAAATGAATCAAAGTCCCCAGATTTGATTTTCCCTCAAGA
AGAAGCGAAACAGATCCCTCTCTTTCAAGATTTGATATTCCTAGAGTAACAGTAGAAAAAGTCTA
CCTCG
Found at i:44073 original size:134 final size:134
Alignment explanation
Indices: 43477--44047 Score: 726
Period size: 134 Copynumber: 4.3 Consensus size: 134
43467 ATTCAACTCA
* *
43477 ATTCAATCTTCCTTGAAGAACAGTGGAATGAATTAACGTCCCCAGATCTGATTTTCCCTCAAGAA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
* * * **
43542 GAAGCGAAACATAT--CTCTC-TTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTCCCC
66 GAAGCGAAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTAGAACAAGTCTGC
43604 CTCG
131 CTCG
* *
43608 ATTCAATTTTCCCTG-AGTAACAGTGGAATGAATCAACGTCCCCAGATTTGATTTTCCCTCAAGA
1 ATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGA
* *
43672 AGAAGCGAAACAGATCCCTCTCTTTCAAGATTTGGTATTCCCT-AGGTAACAGTAGAAAAAGTCT
65 AGAAGCGAAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGA-GTAACAGTAGAACAAGTCT
43736 GCCTCG
129 GCCTCG
43742 ATTCAATCTTCCCTG-AGTAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGA
1 ATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGA
* * * * * * * *
43806 A-AAGCGGAATAAATCCCTTTCTTTCAAGAATTAATATTCCCTGAGTAACAGTGGACCAAGTCTG
65 AGAAGCGAAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTAGAACAAGTCTG
*
43870 CCTTG
130 CCTCG
* ** * *
43875 ATTCAATCTTCCCTGAAGAACAATAAAATGAATCAAAGTCCCCAGATTTGAATTTT-CCTCAAGA
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTG-ATTTTCCCTCAAGA
* * * * * *
43939 AGAAGCTAAACAGATCCCTCTCTTTCAAGATTTGATCTTCCTTGAGTAACATTAGAACAAGTTTA
65 AGAAGCGAAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTAGAACAAGTCTG
44004 CCTCG
130 CCTCG
* * * * *
44009 TTTCCATCTTCCTTGAAGAACATTGGAATGAGTCAACGT
1 ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGT
44048 TTCTTGATCT
Statistics
Matches: 380, Mismatches: 51, Indels: 15
0.85 0.11 0.03
Matches are distributed among these distances:
130 2 0.01
131 71 0.19
133 112 0.29
134 195 0.51
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (134 bp):
ATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
GAAGCGAAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTAGAACAAGTCTGC
CTCG
Found at i:44275 original size:3 final size:3
Alignment explanation
Indices: 44217--44259 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
44207 TGTCCCGACT
* * * *
44217 TTA TTA TTA TTT TTA TAA TCA TTA TTG TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
44260 GAGTAATTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:44841 original size:5 final size:5
Alignment explanation
Indices: 44831--44855 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
44821 ATTATTATTC
44831 CGGGT CGGGT CGGGT CGGGT CGGGT
1 CGGGT CGGGT CGGGT CGGGT CGGGT
44856 TTCTAAGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (5 bp):
CGGGT
Found at i:46989 original size:131 final size:131
Alignment explanation
Indices: 46765--47109 Score: 444
Period size: 131 Copynumber: 2.6 Consensus size: 131
46755 GTAATATATT
* * * *
46765 TTCATTTCGGTTGGAGTAATAAACGACTGCTCTAAGGCATTAGAGGTCATTTATTCTCGATTGGA
1 TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
* * * * *
46830 AATAATTCGATATTATCATTCTCTCTCGAATTAATATTGATTTTTAAGATGGAATAATGACATCT
66 AATAATTAGATATTATCATTCTCACTCGAATCAATATTGAATTTTAAGACGGAATAATGACATCT
46895 C
131 C
* * *
46896 TTCATTTCGATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGATCATTTATTCTCGATTGGA
1 TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
* * * * * * *
46961 AATCATTAGATATTATCGTTTTCACTCGAATCGATATTGAATTTTAATACGGAATAGTGATATCT
66 AATAATTAGATATTATCATTCTCACTCGAATCAATATTGAATTTTAAGACGGAATAATGACATCT
47026 C
131 C
* * * *
47027 TTCATTTCGATCGGAGTAATAAATGATTGTTTTAAGGCATGAAAGGTCATTTATTCTCGATT-GA
1 TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
*
47091 AA-AATTTA-TTATTATCATT
66 AATAA-TTAGATATTATCATT
47110 TTCTCTCTTA
Statistics
Matches: 184, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
129 10 0.05
130 7 0.04
131 167 0.91
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (131 bp):
TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
AATAATTAGATATTATCATTCTCACTCGAATCAATATTGAATTTTAAGACGGAATAATGACATCT
C
Found at i:50676 original size:17 final size:17
Alignment explanation
Indices: 50650--50685 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
50640 AAGAAATTAG
*
50650 GAGTATTTAAAATGTAA
1 GAGTACTTAAAATGTAA
*
50667 GAGTACTTAAAATTTAA
1 GAGTACTTAAAATGTAA
50684 GA
1 GA
50686 AATTAAGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (17 bp):
GAGTACTTAAAATGTAA
Found at i:70411 original size:17 final size:16
Alignment explanation
Indices: 70375--70413 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
70365 ATAATCACAA
70375 TTTTATTTTATTTCAT
1 TTTTATTTTATTTCAT
70391 TTTTATTTTAATTAT-AT
1 TTTTATTTT-ATT-TCAT
70408 TTTTAT
1 TTTTAT
70414 ATTTTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 11 0.52
18 1 0.05
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTATTTTATTTCAT
Found at i:73356 original size:2 final size:2
Alignment explanation
Indices: 73349--73378 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
73339 GGATCGGGAC
73349 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
73379 AATTCTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:78464 original size:22 final size:22
Alignment explanation
Indices: 78434--78553 Score: 154
Period size: 22 Copynumber: 5.5 Consensus size: 22
78424 GGCATGTGAA
* *
78434 ATATATCCCGAAGGACCTCTGT
1 ATATGTCCCGAAAGACCTCTGT
78456 ATATGTCCCGAAAGACCTCTGT
1 ATATGTCCCGAAAGACCTCTGT
* *
78478 ATA--TCCCGAAGGACCTATGT
1 ATATGTCCCGAAAGACCTCTGT
*
78498 ATATGTCCCGAATGACCTCTGT
1 ATATGTCCCGAAAGACCTCTGT
* *
78520 ATATGTCCTGAAAGACCTATGT
1 ATATGTCCCGAAAGACCTCTGT
*
78542 ATATGTCTCGAA
1 ATATGTCCCGAA
78554 TGACTTATGT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
20 18 0.21
22 67 0.79
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (22 bp):
ATATGTCCCGAAAGACCTCTGT
Found at i:78499 original size:42 final size:42
Alignment explanation
Indices: 78435--78553 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
78425 GCATGTGAAA
*
78435 TATATCCCGAAGGACCTCTGTATATGTCCCGAAAGACCTCTG
1 TATATCCCGAAGGACCTATGTATATGTCCCGAAAGACCTCTG
*
78477 TATATCCCGAAGGACCTATGTATATGTCCCGAATGACCTCTG
1 TATATCCCGAAGGACCTATGTATATGTCCCGAAAGACCTCTG
* * *
78519 TATATGTCCTGAAAGACCTATGTATATGTCTCGAA
1 TATA--TCCCGAAGGACCTATGTATATGTCCCGAA
78554 TGACTTATGT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 44 0.63
44 26 0.37
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (42 bp):
TATATCCCGAAGGACCTATGTATATGTCCCGAAAGACCTCTG
Found at i:81569 original size:53 final size:54
Alignment explanation
Indices: 81446--81807 Score: 539
Period size: 54 Copynumber: 6.7 Consensus size: 54
81436 AGAGCACATG
* * * * *
81446 TAGTGCCTATACGGTCGTTCATCAACACATGATGAATTCCGTGGGTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
* * *
81500 TAGTGCCTATACGGTTGTTCATCAACTCATGATAAATTCCGTGG-TTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
* *
81553 TAGTGCTTGTATGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
* *
81607 TAGTACTTGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
* * **
81661 TAGTGCATGTACGATTGTTCATCAACTCATGATGTATTATGTGGGTTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGT-GGTTTGCACACA
81716 TAGTGCATGTACGGTTGTTCAT-AACTCATGATGAATTCCGTGGTTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
* *
81769 TAGTGCATGTACGGTTATTCATCAACTCATGAGGAATTC
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTC
81808 TGTTGCACAC
Statistics
Matches: 284, Mismatches: 21, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
53 82 0.29
54 169 0.60
55 33 0.12
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (54 bp):
TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
Found at i:83617 original size:20 final size:20
Alignment explanation
Indices: 83594--83653 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 20
83584 AACCTCATGC
* *
83594 ATCCCGAAAGACTCGTGTAT
1 ATCCCGAAGGACTCGTATAT
*
83614 ATCCTGAAGGACCTCGTATAT
1 ATCCCGAAGGA-CTCGTATAT
*
83635 ATCCCGAAGGACTCATATA
1 ATCCCGAAGGACTCGTATA
83654 ACCCTCGACT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCCCGAAGGACTCGTATAT
Done.