Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003464.1 Hibiscus syriacus cultivar Beakdansim tig00007319_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: 79195
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:1182 original size:18 final size:18
Alignment explanation
Indices: 1153--1199 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1143 TATGTCTCTT
*
1153 ATTTATTTATTTAATTT-TA
1 ATTTA-TTATTT-ATTTAAA
1172 ATTTATTATTTATTTAAA
1 ATTTATTATTTATTTAAA
1190 ATTTATTATT
1 ATTTATTATT
1200 GTTAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 17 0.65
19 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTATTATTTATTTAAA
Found at i:1507 original size:17 final size:17
Alignment explanation
Indices: 1482--1516 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1472 ATTTTGATTA
1482 ATAAAATTTTAAAATTT
1 ATAAAATTTTAAAATTT
*
1499 ATAATATTTTAAAATTT
1 ATAAAATTTTAAAATTT
1516 A
1 A
1517 AAGACCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAAAATTTTAAAATTT
Found at i:1678 original size:13 final size:13
Alignment explanation
Indices: 1656--1691 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1646 CATGATATTA
*
1656 AAATAGAAAATAT
1 AAATATAAAATAT
1669 AAATATAAAATAT
1 AAATATAAAATAT
1682 AAATATAAAA
1 AAATATAAAA
1692 ATTATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (13 bp):
AAATATAAAATAT
Found at i:1700 original size:19 final size:19
Alignment explanation
Indices: 1663--1707 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1653 TTAAAATAGA
*
1663 AAATATAAATATAAAATAT
1 AAATATAAAAATAAAATAT
* *
1682 AAATATAAAAATTATATAT
1 AAATATAAAAATAAAATAT
*
1701 ATATATA
1 AAATATA
1708 TATTTGGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATATAAAAATAAAATAT
Found at i:9372 original size:16 final size:17
Alignment explanation
Indices: 9341--9376 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
9331 ATCCCAATAA
*
9341 ACCCCTCCACAAGTGTC
1 ACCCCTCCAAAAGTGTC
9358 ACCCCT-CAAAAGTGTC
1 ACCCCTCCAAAAGTGTC
9374 ACC
1 ACC
9377 ACTAAGACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.28, C:0.44, G:0.11, T:0.17
Consensus pattern (17 bp):
ACCCCTCCAAAAGTGTC
Found at i:14028 original size:16 final size:16
Alignment explanation
Indices: 14007--14037 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
13997 AAAGTTTTTT
14007 TAAAAAATAATACTTA
1 TAAAAAATAATACTTA
14023 TAAAAAATAATACTT
1 TAAAAAATAATACTT
14038 GATGAAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAAAAATAATACTTA
Found at i:19872 original size:48 final size:48
Alignment explanation
Indices: 19749--19879 Score: 190
Period size: 51 Copynumber: 2.7 Consensus size: 48
19739 TTCATACTAC
* * *
19749 AAAAAAAATGTAGCACTTAACACATACTTACATCGGTGTAAGTGAATA
1 AAAAAAAATGTAGCACTTAACACATACTTACAACAGTGTAAGTAAATA
*
19797 AAATAAAAATGTATATCACTTAACACATACTTACAACAGTGTAAGTAAATA
1 AAA-AAAAATG--TAGCACTTAACACATACTTACAACAGTGTAAGTAAATA
*
19848 AAAAAAAATGTAGCACTTAACACATATTTACA
1 AAAAAAAATGTAGCACTTAACACATACTTACA
19880 CTGATGTAAG
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
48 23 0.31
49 7 0.09
50 7 0.09
51 37 0.50
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.26
Consensus pattern (48 bp):
AAAAAAAATGTAGCACTTAACACATACTTACAACAGTGTAAGTAAATA
Found at i:20736 original size:16 final size:17
Alignment explanation
Indices: 20701--20741 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
20691 TATGGGATGA
20701 AAAAATAGTATTATTGT
1 AAAAATAGTATTATTGT
20718 AAAAAT-GTAATTATT-T
1 AAAAATAGT-ATTATTGT
20734 AAATAATA
1 AAA-AATA
20742 TTTTACTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (17 bp):
AAAAATAGTATTATTGT
Found at i:20777 original size:17 final size:17
Alignment explanation
Indices: 20755--20787 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20745 TACTATCATA
*
20755 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
20772 ATATTATATTTTATAT
1 ATATTATATTTTATAT
20788 AAATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:24377 original size:21 final size:21
Alignment explanation
Indices: 24326--24378 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
24316 ATTCTGACTA
24326 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
24347 TTGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
24368 TCGCAATGCGA
1 TCGCATTGCGA
24379 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:24393 original size:20 final size:20
Alignment explanation
Indices: 24368--24481 Score: 174
Period size: 20 Copynumber: 5.7 Consensus size: 20
24358 TTTTCCTAAT
24368 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
24388 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
24409 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
24429 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
24449 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
24469 TCGCAATGTGAAT
1 TCGCAATGCGAAT
24482 CTGACTATCG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
20 68 0.81
21 16 0.19
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:24461 original size:40 final size:40
Alignment explanation
Indices: 24368--24499 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
24358 TTTTCCTAAT
* **
24368 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAA-TACGAAAA
*
24409 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGAAAA
* **
24449 TCGCAATGCGAATACGTAAATCGCAATGTGAAT-CTGACTA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATAC-GAAAA
24489 TCGCAATGCGA
1 TCGCAATGCGA
24500 TTTACATAGC
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 50 0.61
41 31 0.38
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATACGAAAA
Found at i:25083 original size:33 final size:34
Alignment explanation
Indices: 25035--25107 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
25025 ACTATCGCAA
* * *
25035 TGCGATTCTGTCGTTGCGAT-TTTCATTTCGCGT
1 TGCGATTCTGTCGTTGCGATAGTTAAATTCGCGT
25068 TGCGATTCT-TACGTTGCGATAGTTAAATTCGCGT
1 TGCGATTCTGT-CGTTGCGATAGTTAAATTCGCGT
25102 TGCGAT
1 TGCGAT
25108 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 18 0.51
34 16 0.46
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.41
Consensus pattern (34 bp):
TGCGATTCTGTCGTTGCGATAGTTAAATTCGCGT
Found at i:25118 original size:20 final size:20
Alignment explanation
Indices: 25079--25143 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
25069 GCGATTCTTA
* **
25079 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCATTTTCG
25099 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
25119 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
25139 TGTTG
1 CGTTG
25144 TGATTTAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.45
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:25148 original size:20 final size:20
Alignment explanation
Indices: 25095--25149 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
25085 GATAGTTAAA
* **
25095 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
25115 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
25135 TTCGTGTTGTGATTT
1 TTCGTGTTGCGATTT
25150 AAAGTTTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.15, G:0.24, T:0.51
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:27054 original size:20 final size:20
Alignment explanation
Indices: 27029--27263 Score: 210
Period size: 20 Copynumber: 12.4 Consensus size: 20
27019 AATAGTTTAT
27029 TATCGCAATGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
*
27049 TATCGCAAAGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
* *
27069 TATTGCAA--CG-AGA-GA-
1 TATCGCAATGCGAAAATGAC
* *
27084 -ATCGCAATGTG-AAATGAA
1 TATCGCAATGCGAAAATGAC
*
27102 AATCGCAA--C-AACAA--A-
1 TATCGCAATGCGAA-AATGAC
*
27117 -ATCGCAATGCGAAAATAAC
1 TATCGCAATGCGAAAATGAC
*
27136 TATCGCAACGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
* * *
27156 TATCGCAACGCAAAAATGAT
1 TATCGCAATGCGAAAATGAC
* *
27176 TATCACAACGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
*
27196 TATCGCAACGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
27216 TATCGCAATGCGAAAATGAC
1 TATCGCAATGCGAAAATGAC
** *
27236 TATCGCAATGCGAATTTGAT
1 TATCGCAATGCGAAAATGAC
27256 TATCGCAA
1 TATCGCAA
27264 CGAAAGAATC
Statistics
Matches: 182, Mismatches: 19, Indels: 28
0.79 0.08 0.12
Matches are distributed among these distances:
14 13 0.07
16 9 0.05
17 7 0.04
18 5 0.03
19 7 0.04
20 141 0.77
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (20 bp):
TATCGCAATGCGAAAATGAC
Found at i:27338 original size:20 final size:20
Alignment explanation
Indices: 27310--27376 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
27300 GATTCTCTCG
* *
27310 TTGCAATAGTTAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
27330 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
27350 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
27370 TTGCGAT
1 TTGCGAT
27377 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:27901 original size:18 final size:19
Alignment explanation
Indices: 27862--27905 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
27852 CTCACCTGTC
27862 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
27883 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
27901 ATCGT
1 ATCGT
27906 CCCTCAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.43
21 13 0.57
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.25
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:29521 original size:33 final size:34
Alignment explanation
Indices: 29484--29559 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
29474 GGAAATGACT
29484 ATCGCAACGAGAGAATCGCAATGCG-AAATAAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATAAAA
*
29517 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATAAAA
29551 ATCGCAACG
1 ATCGCAACG
29560 CGAAAATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 25 0.61
34 16 0.39
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATAAAA
Found at i:29636 original size:33 final size:34
Alignment explanation
Indices: 29574--29649 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
29564 AATAAATTCG
29574 CGTTGCGATTTTCATTTTCACATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCACATTGCGATTCACT
* *
29608 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCACATTGCGATTCACT
29641 CGTTGCGAT
1 CGTTGCGAT
29650 AGTCAATTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 26 0.65
34 14 0.35
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCACATTGCGATTCACT
Found at i:29666 original size:20 final size:20
Alignment explanation
Indices: 29641--29735 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
29631 GCGATTCTCT
29641 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
29661 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
*
29681 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
* *
29701 TGTTGTGATAGTCATATT-CG
1 CGTTGCGATAGTCA-ATTCCG
29721 CGTTGCGATAGTCAA
1 CGTTGCGATAGTCAA
29736 ATGAATGTCT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
19 1 0.01
20 65 0.96
21 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:32195 original size:24 final size:24
Alignment explanation
Indices: 32144--32198 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
32134 AAAATCCGAG
**
32144 TATTGACCAAGATCAAAGTCAGGG
1 TATTGACCAAGATCAAAGTCAGAA
*
32168 TATTGACCAAGATCAAATTTC-GAA
1 TATTGACCAAGATCAAA-GTCAGAA
32192 TATTGAC
1 TATTGAC
32199 TAGTACTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (24 bp):
TATTGACCAAGATCAAAGTCAGAA
Found at i:33052 original size:20 final size:20
Alignment explanation
Indices: 33027--33077 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
33017 TTCAGTATTA
33027 CGATAGTCAGAATCTCGTTG
1 CGATAGTCAGAATCTCGTTG
*
33047 CGATAGTCAAAATCTCGTTG
1 CGATAGTCAGAATCTCGTTG
*
33067 CGATTGTCAGA
1 CGATAGTCAGA
33078 TTCGCATTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (20 bp):
CGATAGTCAGAATCTCGTTG
Found at i:35901 original size:206 final size:204
Alignment explanation
Indices: 35523--35938 Score: 796
Period size: 206 Copynumber: 2.0 Consensus size: 204
35513 ATTCTTTTAG
35523 ATCGAACGTAGCTTAAAATTAAATAACTTGTGGTTATTACTTAGCCACGTCATTGGTTGGACTAG
1 ATCGAACGTAGCTTAAAATTAAATAACTTGTGGTTATTACTTAGCCACGTCATTGGTTGGACTAG
35588 GACTGTAAATGAGACGAGATAGATCGCGAGTTACTCGAGATCGACTCGATCTTGGCTCGATAAAT
66 GACTGTAAATGAGACGAGATAGATCGCGAGTTACTCGAGATCGACTCGATCTTGGCTCGATAAAT
35653 ACTCGGATCGAATGAACTCGACTCGTGCTCGAACTCGACTCGAGTTCTTAACGAGCCGAAACGAG
131 ACTCGGATCGAATGAACTCGACTCGTGCTCGAACTCGACTCGAGTTCTTAACGAGCCGAAACGAG
35718 CTACTCGAT
196 CTACTCGAT
35727 ATCGAACGTAGCTTAAAAATTAAATAAACTTGTGGTTATTACTTAGCCACGTCATTGGTTGGACT
1 ATCGAACGTAGCTT-AAAATTAAAT-AACTTGTGGTTATTACTTAGCCACGTCATTGGTTGGACT
35792 AGGACTGTAAATGAGACGAGATAGATCGCGAGTTACTCGAGATCGACTCGATCTTGGCTCGATAA
64 AGGACTGTAAATGAGACGAGATAGATCGCGAGTTACTCGAGATCGACTCGATCTTGGCTCGATAA
*
35857 ATACTCGGATCGAATGAACTCGATTCGTGCTCGAACTCGACTCGAGTTCTTAACGAGCCGAAACG
129 ATACTCGGATCGAATGAACTCGACTCGTGCTCGAACTCGACTCGAGTTCTTAACGAGCCGAAACG
35922 AGCTACTCGAT
194 AGCTACTCGAT
35933 ACTCGA
1 A-TCGA
35939 CTCGAAACGC
Statistics
Matches: 208, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
204 14 0.07
205 10 0.05
206 180 0.87
207 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (204 bp):
ATCGAACGTAGCTTAAAATTAAATAACTTGTGGTTATTACTTAGCCACGTCATTGGTTGGACTAG
GACTGTAAATGAGACGAGATAGATCGCGAGTTACTCGAGATCGACTCGATCTTGGCTCGATAAAT
ACTCGGATCGAATGAACTCGACTCGTGCTCGAACTCGACTCGAGTTCTTAACGAGCCGAAACGAG
CTACTCGAT
Found at i:36019 original size:11 final size:11
Alignment explanation
Indices: 36003--36065 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
35993 AAAATTACAT
36003 TATTAAAAATA
1 TATTAAAAATA
36014 TATTAAAAATA
1 TATTAAAAATA
* ***
36025 CATTATTGATA
1 TATTAAAAATA
*
36036 -CTTATAAAAT-
1 TATTA-AAAATA
36046 T-TTAAAAATA
1 TATTAAAAATA
36056 TATTAAAAAT
1 TATTAAAAAT
36066 TCTATAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
9 5 0.12
10 7 0.17
11 28 0.70
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:36236 original size:14 final size:14
Alignment explanation
Indices: 36197--36236 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
36187 ACCCTAAACC
*
36197 TAAACCCTAAAGTA
1 TAAACCCTAAATTA
36211 TAAACCCTAAATTA
1 TAAACCCTAAATTA
36225 TAAACCCTAAAT
1 TAAACCCTAAAT
36237 CTACGACCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.50, C:0.23, G:0.03, T:0.25
Consensus pattern (14 bp):
TAAACCCTAAATTA
Found at i:36273 original size:27 final size:27
Alignment explanation
Indices: 36188--36277 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
36178 TTAGATTACA
*
36188 CCCTAAACC-TAAACCCTAAAGTATAAA
1 CCCTAAACCATAAACCCT-AAGTATAAG
** * * *
36215 CCCTAAATTATAAACCCTAAATCTACG
1 CCCTAAACCATAAACCCTAAGTATAAG
*
36242 ACCTAAACCATAAACCCTAAGCT-TAAG
1 CCCTAAACCATAAACCCTAAG-TATAAG
36269 CCCTAAACC
1 CCCTAAACC
36278 CTTAATCCGA
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
27 40 0.82
28 9 0.18
ACGTcount: A:0.43, C:0.32, G:0.04, T:0.20
Consensus pattern (27 bp):
CCCTAAACCATAAACCCTAAGTATAAG
Found at i:36415 original size:21 final size:21
Alignment explanation
Indices: 36389--36437 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
36379 CCCTTATCCC
*
36389 AAACCCTAAGCCATAAGTCCT
1 AAACCCTAAGCCATAAGCCCT
*
36410 AAACCCTAAGCCCTAAGCCCT
1 AAACCCTAAGCCATAAGCCCT
36431 AAACCCT
1 AAACCCT
36438 TAATTCGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.39, G:0.08, T:0.16
Consensus pattern (21 bp):
AAACCCTAAGCCATAAGCCCT
Found at i:36419 original size:14 final size:14
Alignment explanation
Indices: 36389--36437 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
36379 CCCTTATCCC
*
36389 AAACCCTAAGCCAT
1 AAACCCTAAGCCCT
** *
36403 AAGTCCTAAACCCT
1 AAACCCTAAGCCCT
*
36417 AAGCCCTAAGCCCT
1 AAACCCTAAGCCCT
36431 AAACCCT
1 AAACCCT
36438 TAATTCGATT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.37, C:0.39, G:0.08, T:0.16
Consensus pattern (14 bp):
AAACCCTAAGCCCT
Found at i:37834 original size:11 final size:11
Alignment explanation
Indices: 37801--37844 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
37791 GTGAGCACTC
37801 GAGTTTGAATT
1 GAGTTTGAATT
*
37812 GAGTTAGAATT
1 GAGTTTGAATT
*
37823 GAGTTTGTATT
1 GAGTTTGAATT
37834 GAGCTTTGAAT
1 GAG-TTTGAAT
37845 CAAGCTCGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 22 0.79
12 6 0.21
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.43
Consensus pattern (11 bp):
GAGTTTGAATT
Found at i:39677 original size:29 final size:29
Alignment explanation
Indices: 39644--39713 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
39634 ATGATCTTAA
39644 GCAGAAACATGACATGAA-A-TAAATCACAT
1 GCAGAAACATGAC--GAAGATTAAATCACAT
* *
39673 GCAGAAACAGGACGAAGATTAAATCTCAT
1 GCAGAAACATGACGAAGATTAAATCACAT
*
39702 GCATAAACATGA
1 GCAGAAACATGA
39714 AGAGGAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 3 0.09
28 1 0.03
29 31 0.89
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (29 bp):
GCAGAAACATGACGAAGATTAAATCACAT
Found at i:42397 original size:2 final size:2
Alignment explanation
Indices: 42390--42465 Score: 85
Period size: 2 Copynumber: 41.5 Consensus size: 2
42380 CTGCCCCGAT
*
42390 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
42429 TT TA TA T- TA -A T- TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42466 TTACGGGTTA
Statistics
Matches: 65, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
1 7 0.11
2 58 0.89
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:44059 original size:9 final size:9
Alignment explanation
Indices: 44031--44071 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
44021 AACTCAAGAG
44031 AAAATA-GA
1 AAAATATGA
44039 AAAATATG-
1 AAAATATGA
44047 AAAATATGAA
1 AAAATATG-A
*
44057 AAAATAAGA
1 AAAATATGA
44066 AAAATA
1 AAAATA
44072 ATAGTCACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 14 0.48
9 8 0.28
10 7 0.24
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (9 bp):
AAAATATGA
Found at i:44061 original size:18 final size:16
Alignment explanation
Indices: 44029--44068 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
44019 AAAACTCAAG
44029 AGAAAATAGAAAAATA
1 AGAAAATAGAAAAATA
*
44045 TGAAAATATGAAAAAATA
1 AGAAAATA-G-AAAAATA
44063 AGAAAA
1 AGAAAA
44069 ATAATAGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.15
Consensus pattern (16 bp):
AGAAAATAGAAAAATA
Found at i:48119 original size:38 final size:38
Alignment explanation
Indices: 48075--48163 Score: 160
Period size: 38 Copynumber: 2.3 Consensus size: 38
48065 AAACCTTTAT
48075 ATCTCATTTTCATCTTTCACTTTCATATCCAATTTCAC
1 ATCTCATTTTCATCTTTCACTTTCATATCCAATTTCAC
*
48113 ATCTCATTTTCATCTTTCACTTTCATATCCAGTTTCAC
1 ATCTCATTTTCATCTTTCACTTTCATATCCAATTTCAC
*
48151 ATTTCATTTTCAT
1 ATCTCATTTTCAT
48164 AATTCGTACT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.22, C:0.27, G:0.01, T:0.49
Consensus pattern (38 bp):
ATCTCATTTTCATCTTTCACTTTCATATCCAATTTCAC
Found at i:48272 original size:19 final size:18
Alignment explanation
Indices: 48218--48269 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
48208 TTGTTTCTGG
48218 ACTCATAACTTATTTCAT
1 ACTCATAACTTATTTCAT
* *
48236 ATTCATAATTTAATTTCAT
1 ACTCATAACTT-ATTTCAT
*
48255 ACTCATAGCTTATTT
1 ACTCATAACTTATTT
48270 TCAATTTCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (18 bp):
ACTCATAACTTATTTCAT
Found at i:51040 original size:29 final size:30
Alignment explanation
Indices: 51008--51077 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 30
50998 GGTCAAAATA
* *
51008 CCTAAATTTTGAA-AATTACAC-TTTTGATC
1 CCTAAATTTTAAAGAATTACACTTTTTG-CC
* *
51037 CCTAAACGTTTAAAGAATTACCCTTTTTGCC
1 CCTAAA-TTTTAAAGAATTACACTTTTTGCC
51068 CCTAAATTTT
1 CCTAAATTTT
51078 TCCTAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
29 6 0.18
30 8 0.24
31 14 0.42
32 5 0.15
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.40
Consensus pattern (30 bp):
CCTAAATTTTAAAGAATTACACTTTTTGCC
Found at i:52660 original size:104 final size:103
Alignment explanation
Indices: 52528--52745 Score: 391
Period size: 104 Copynumber: 2.1 Consensus size: 103
52518 TAAAGGGTTC
* *
52528 ATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATACT
1 ATGTGGTCCTTCGGGACATATATATATTCTTTAGAACATATGTGAGGTCTGGTGAGACACATACT
*
52593 TGATCCTTGGTATATGTATATGATTCTTAAGGAATGAT
66 TGATCCTTGGCATATGTATATGATTCTTAAGGAATGAT
*
52631 ATGTGGTCCTTCGGGGACATATATATATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATAC
1 ATGTGGTCCTTC-GGGACATATATATATTCTTTAGAACATATGTGAGGTCTGGTGAGACACATAC
52696 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGAT
65 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGAT
52735 ATGTGGTCCTT
1 ATGTGGTCCTT
52746 ATGGACATTA
Statistics
Matches: 110, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
103 12 0.11
104 98 0.89
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
ATGTGGTCCTTCGGGACATATATATATTCTTTAGAACATATGTGAGGTCTGGTGAGACACATACT
TGATCCTTGGCATATGTATATGATTCTTAAGGAATGAT
Found at i:52794 original size:23 final size:23
Alignment explanation
Indices: 52761--52823 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
52751 CATTATTAAT
52761 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
52784 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
52807 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
52824 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:58949 original size:20 final size:20
Alignment explanation
Indices: 58924--58961 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
58914 GAATGCTAGA
*
58924 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
58944 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
58962 TAATAAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:59633 original size:104 final size:104
Alignment explanation
Indices: 59440--59658 Score: 386
Period size: 104 Copynumber: 2.1 Consensus size: 104
59430 ATAGAGGGTT
*
59440 TATGTGGTCC-TTCGGGACATATATGTATTCTTTTGAACATGTGTGAGGTCTGGTGAGACACATA
1 TATGTGGTCCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATA
* *
59504 CTTGATCATTGGTATATGTATATGATTCTTAATGAATGA
66 CTTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
*
59543 TATGTGGTCCTTTGGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATA
1 TATGTGGTCCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATA
*
59608 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 CTTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
59647 TATGTGGTCCTT
1 TATGTGGTCCTT
59659 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
103 10 0.09
104 100 0.91
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (104 bp):
TATGTGGTCCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATA
CTTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:59708 original size:23 final size:23
Alignment explanation
Indices: 59675--59737 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
59665 ATTATTATAT
59675 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
59698 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
59721 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
59738 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:66357 original size:29 final size:30
Alignment explanation
Indices: 66325--66387 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
66315 AGTTACAATT
* **
66325 AAGTCACTCAATTAATTGA-TGTAACGATC
1 AAGTAACTCAATTAATTGATTGTAAAAATC
*
66354 AAGTAACTTAATTAATTGATTGTAAAAATC
1 AAGTAACTCAATTAATTGATTGTAAAAATC
66384 AAGT
1 AAGT
66388 TACGTGTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (30 bp):
AAGTAACTCAATTAATTGATTGTAAAAATC
Found at i:72778 original size:21 final size:21
Alignment explanation
Indices: 72754--72803 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
72744 ACCATAAACA
72754 TTATTATTTCTACCGGTTTTG
1 TTATTATTTCTACCGGTTTTG
* *
72775 TTATTTTTTCTATCGGTTTTG
1 TTATTATTTCTACCGGTTTTG
72796 TTATTATT
1 TTATTATT
72804 AGATATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.14, C:0.10, G:0.12, T:0.64
Consensus pattern (21 bp):
TTATTATTTCTACCGGTTTTG
Found at i:75365 original size:31 final size:31
Alignment explanation
Indices: 75327--75412 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
75317 GTTTTGAAAA
*
75327 AAAATTGAAAGTTTAGGTACTAAAACGGACC
1 AAAATTGATAGTTTAGGTACTAAAACGGACC
*
75358 AAAATTGATAGTTTAGGTACTAAAATGGACC
1 AAAATTGATAGTTTAGGTACTAAAACGGACC
* *
75389 GAAACTGATAGTTTAGGTACTAAA
1 AAAATTGATAGTTTAGGTACTAAA
75413 TATGTTAAGG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (31 bp):
AAAATTGATAGTTTAGGTACTAAAACGGACC
Done.