Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002393.1 Hibiscus syriacus cultivar Beakdansim tig00004895_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: 84896
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2833 original size:14 final size:14
Alignment explanation
Indices: 2814--2848 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
2804 TCATTCAAAT
2814 CTAATTGGTATTTC
1 CTAATTGGTATTTC
2828 CTAATTGGTATTTC
1 CTAATTGGTATTTC
2842 CTAATTG
1 CTAATTG
2849 CTAAATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (14 bp):
CTAATTGGTATTTC
Found at i:27583 original size:19 final size:19
Alignment explanation
Indices: 27559--27603 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
27549 CAAGTTTGAG
*
27559 TACCATGAATGTCAGATCT
1 TACCATGAATGTAAGATCT
27578 TACCATGAATGTAAGATCT
1 TACCATGAATGTAAGATCT
27597 TACCATG
1 TACCATG
27604 CAAAGAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (19 bp):
TACCATGAATGTAAGATCT
Found at i:28750 original size:26 final size:26
Alignment explanation
Indices: 28711--28779 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
28701 AAGTGCTAAT
28711 ACACATAAGGTCATGCCCACCGTAAA
1 ACACATAAGGTCATGCCCACCGTAAA
* * * *
28737 ACACATTAGATCATGTCCACCGTAAT
1 ACACATAAGGTCATGCCCACCGTAAA
*
28763 ACACATGAGGTCATGCC
1 ACACATAAGGTCATGCC
28780 TACCATATAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.20
Consensus pattern (26 bp):
ACACATAAGGTCATGCCCACCGTAAA
Found at i:32095 original size:29 final size:29
Alignment explanation
Indices: 32044--32122 Score: 124
Period size: 29 Copynumber: 2.8 Consensus size: 29
32034 TTATATTTTA
*
32044 TATGTTCATGTA-CTCATGTCATTTCTCT
1 TATGATCATGTAGCTCATGTCATTTCTCT
32072 TATGATCATGTAGCTCATGTCATTTCTCT
1 TATGATCATGTAGCTCATGTCATTTCTCT
* *
32101 TGTGATCATATAGCTCATGTCA
1 TATGATCATGTAGCTCATGTCA
32123 CTTCATATCA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 11 0.23
29 36 0.77
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (29 bp):
TATGATCATGTAGCTCATGTCATTTCTCT
Found at i:32155 original size:12 final size:12
Alignment explanation
Indices: 32138--32173 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
32128 TATCATGTTC
32138 TCATATCACATG
1 TCATATCACATG
*
32150 TCATATCACATA
1 TCATATCACATG
*
32162 TAATATCACATG
1 TCATATCACATG
32174 AACATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:32239 original size:23 final size:25
Alignment explanation
Indices: 32190--32239 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
32180 TATATGTCTG
32190 ATGCATGTATCACAACAATTATCATAT
1 ATGCATGTATCACAAC-A-TATCATAT
*
32217 ATGCATGT-TCACAAC-TATTATAT
1 ATGCATGTATCACAACATATCATAT
32240 TATGAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 7 0.32
26 7 0.32
27 8 0.36
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (25 bp):
ATGCATGTATCACAACATATCATAT
Found at i:32646 original size:64 final size:63
Alignment explanation
Indices: 32480--32703 Score: 245
Period size: 64 Copynumber: 3.5 Consensus size: 63
32470 TAATGAAGGT
* * ** * *
32480 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCAATGTAGTATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGTATTCGATGT-TTATTATTAATGGG
* **
32544 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGTATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGTATTCGATGTTT-ATTATTAATGGG
* * * **
32608 ATGCATCGATGCACTACTTATGCATCAATGCATGAATTGCATTCGATGTTT-TTATTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGTATTCGATGTTTATTA--TTAATGGG
**
32671 AGTGCATCGATGCACTACCAATGCATCGATGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
32704 CATTCAAACA
Statistics
Matches: 137, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 131 0.96
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGTATTCGATGTTTATTATTAATGGG
Found at i:33772 original size:14 final size:14
Alignment explanation
Indices: 33755--33787 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
33745 ATTTCTATGT
33755 AGGGAATTATTTGC
1 AGGGAATTATTTGC
33769 AGGGAATTATTTGC
1 AGGGAATTATTTGC
33783 AGGGA
1 AGGGA
33788 TTACTCCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.06, G:0.33, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTGC
Found at i:34273 original size:40 final size:38
Alignment explanation
Indices: 34192--34294 Score: 104
Period size: 40 Copynumber: 2.7 Consensus size: 38
34182 GAAGCAACTT
* *
34192 AAAATATTACATTCTTCATAAT-TTTTTCGATTAACCT
1 AAAATATTACATTTTTCATAATATTTTTCGATTAACCA
* *
34229 AAAATATTATATTTTTCATAATATTTTTTG-TTGCCAACCA
1 AAAATATTACATTTTTCATAATATTTTTCGATT---AACCA
*
34269 AAAATCTTACATTCTTT-ATAATATTT
1 AAAATATTACATT-TTTCATAATATTT
34295 AAGTTCAGTC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
37 22 0.40
38 6 0.11
40 24 0.44
41 3 0.05
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.48
Consensus pattern (38 bp):
AAAATATTACATTTTTCATAATATTTTTCGATTAACCA
Found at i:35765 original size:7 final size:7
Alignment explanation
Indices: 35746--35806 Score: 61
Period size: 7 Copynumber: 8.6 Consensus size: 7
35736 CTTTGCCCCC
35746 AAATCCCT
1 AAAT-CCT
*
35754 AAATCAT
1 AAATCCT
35761 AAATCCT
1 AAATCCT
*
35768 AAATCTT
1 AAATCCT
35775 AAATCCT
1 AAATCCT
**
35782 AAATTTT
1 AAATCCT
35789 AAATCACT
1 AAATC-CT
35797 -AATCCT
1 AAATCCT
35803 AAAT
1 AAAT
35807 TTAATAGGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
6 2 0.05
7 36 0.84
8 5 0.12
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (7 bp):
AAATCCT
Found at i:35790 original size:14 final size:14
Alignment explanation
Indices: 35746--35798 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
35736 CTTTGCCCCC
*
35746 AAATCCCTAAATCAT
1 AAAT-CCTAAATCTT
35761 AAATCCTAAATCTT
1 AAATCCTAAATCTT
*
35775 AAATCCTAAATTTT
1 AAATCCTAAATCTT
35789 AAATCACTAA
1 AAATC-CTAA
35799 TCCTAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
14 27 0.77
15 8 0.23
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATCCTAAATCTT
Found at i:36414 original size:9 final size:10
Alignment explanation
Indices: 36392--36433 Score: 54
Period size: 9 Copynumber: 4.5 Consensus size: 10
36382 ATCATTTTAT
36392 TAATTATTAA
1 TAATTATTAA
36402 -AATT-TTAA
1 TAATTATTAA
*
36410 TAATTATTTA
1 TAATTATTAA
36420 TAATTATTAA
1 TAATTATTAA
36430 -AATT
1 TAATT
36434 TTAGTAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 4 0.14
9 12 0.43
10 12 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAATTATTAA
Found at i:36424 original size:28 final size:29
Alignment explanation
Indices: 36387--36441 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
36377 TGGTAATCAT
36387 TTTATTAATTATTAAAATTTTAATAATTA
1 TTTATTAATTATTAAAATTTTAATAATTA
*
36416 TTTA-TAATTATTAAAATTTTAGTAAT
1 TTTATTAATTATTAAAATTTTAATAAT
36442 AGTTAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
TTTATTAATTATTAAAATTTTAATAATTA
Found at i:44561 original size:12 final size:13
Alignment explanation
Indices: 44535--44580 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 13
44525 TCATTCGATA
*
44535 TTATATAATATAT
1 TTATATTATATAT
44548 TTATATTATA-AT
1 TTATATTATATAT
*
44560 TTATATTACATA-
1 TTATATTATATAT
*
44572 ATATATTAT
1 TTATATTAT
44581 TCATTTCTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATATTATATAT
Found at i:45754 original size:2 final size:2
Alignment explanation
Indices: 45747--45795 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
45737 TTCATATTAC
45747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45789 -T AT AT AT
1 AT AT AT AT
45796 TATTATTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:46193 original size:24 final size:24
Alignment explanation
Indices: 46148--46193 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
46138 TAGATTATCA
*
46148 CTATTCTATTTTATGTTTTTTTGT
1 CTATTCTATTTTATGTTCTTTTGT
*
46172 CTATTTTATTTT-TGTTCCTTTT
1 CTATTCTATTTTATGTT-CTTTT
46194 TATTTTCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.72
Consensus pattern (24 bp):
CTATTCTATTTTATGTTCTTTTGT
Found at i:46194 original size:16 final size:17
Alignment explanation
Indices: 46175--46213 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
46165 TTTTTGTCTA
* *
46175 TTTTATTTT-TGTTCCT
1 TTTTATTTTCTCTACCT
46191 TTTTATTTTCTCTACCT
1 TTTTATTTTCTCTACCT
46208 TTTTAT
1 TTTTAT
46214 CTTCATGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.10, C:0.15, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTATTTTCTCTACCT
Found at i:50506 original size:23 final size:23
Alignment explanation
Indices: 50468--50517 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
50458 AAAAAGAAGC
*
50468 AAAAGAGCAAAAAAC-AAA-GAA
1 AAAAGAGAAAAAAACAAAAGGAA
50489 AAAAGAGAAACAAGAACAAAAGGAA
1 AAAAGAGAAA-AA-AACAAAAGGAA
50514 AAAA
1 AAAA
50518 AGGAAAGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 9 0.38
22 2 0.08
23 3 0.12
24 3 0.12
25 7 0.29
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAGAGAAAAAAACAAAAGGAA
Found at i:50514 original size:16 final size:17
Alignment explanation
Indices: 50479--50519 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
50469 AAAGAGCAAA
50479 AAACAAAGAAAAAAGAG
1 AAACAAAGAAAAAAGAG
50496 AAAC-AAGAACAAAAG-G
1 AAACAAAGAA-AAAAGAG
*
50512 AAAAAAAG
1 AAACAAAG
50520 GAAAGAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (17 bp):
AAACAAAGAAAAAAGAG
Found at i:50551 original size:28 final size:28
Alignment explanation
Indices: 50445--50545 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 28
50435 AAGATCCAAT
* * *
50445 CAAGAACAAAAATAAAAAGAAGCAAAAGAG
1 CAAGAACAAAAAGAAAAA-AAG-GAAAGAA
*
50475 CAA-AA-AACAAAG-AAAAAA-GAGA-AA
1 CAAGAACAA-AAAGAAAAAAAGGAAAGAA
*
50499 CAAGAACAAAAGGAAAAAAAGGAAAGAA
1 CAAGAACAAAAAGAAAAAAAGGAAAGAA
50527 CAAGAATCAAAAAGAAAAA
1 CAAGAA-CAAAAAGAAAAA
50546 GGGAAAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
24 4 0.07
25 7 0.12
26 8 0.14
27 5 0.09
28 14 0.25
29 16 0.28
30 3 0.05
ACGTcount: A:0.73, C:0.09, G:0.16, T:0.02
Consensus pattern (28 bp):
CAAGAACAAAAAGAAAAAAAGGAAAGAA
Found at i:50557 original size:29 final size:28
Alignment explanation
Indices: 50445--50554 Score: 79
Period size: 28 Copynumber: 4.0 Consensus size: 28
50435 AAGATCCAAT
* * *
50445 CAAGAACAAAAATAAAAAGAAGCAAAAGAG
1 CAAGAACAAAAAGAAAAA-AAGGAAAA-AA
*
50475 CAA-AA-AACAAAG-AAAAAA-G-AGAAA
1 CAAGAACAA-AAAGAAAAAAAGGAAAAAA
* *
50499 CAAGAACAAAAGGAAAAAAAGGAAAGAA
1 CAAGAACAAAAAGAAAAAAAGGAAAAAA
*
50527 CAAGAATCAAAAAG-AAAAAGGGAAAAAA
1 CAAGAA-CAAAAAGAAAAAAAGGAAAAAA
50555 ACACATGTGA
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
24 4 0.06
25 7 0.11
26 8 0.13
27 3 0.05
28 27 0.43
29 11 0.17
30 3 0.05
ACGTcount: A:0.73, C:0.08, G:0.17, T:0.02
Consensus pattern (28 bp):
CAAGAACAAAAAGAAAAAAAGGAAAAAA
Found at i:52409 original size:180 final size:185
Alignment explanation
Indices: 52090--52459 Score: 655
Period size: 180 Copynumber: 2.0 Consensus size: 185
52080 CGTAATTTCC
52090 AATAAAACTAACATTTCTTATACACGTCAATTTTTATCAGATCAATATGTCTGTAAAATCCTCTT
1 AATAAAACTAACATTTCTTATA-ACGTCAATTTTTATCAGATCAATATGTCTGTAAAATCCTCTT
52155 ATCTAATTCCATATTCAAATCTTGTCTTTTATAACATAAGGGTATTTTCATAATTTTACCCTACC
65 ATCTAATTCCATATTCAAATCTTGTCTTTTATAACATAAGGGTATTTTCATAATTTTACCCTACC
52220 AGATATTCTCATAATTTCCC-A-AAATACCTTTAACATTTAACCTTTGATGAAATA
130 AGATATTCTCATAATTTCCCAACAAATACCTTTAACATTTAACCTTTGATGAAATA
52274 AATAAAACTAACATTTCTTAT-AC-TCAATTTTT-TCAGATCAATAT-TCTGTAAAATCCTCTTA
1 AATAAAACTAACATTTCTTATAACGTCAATTTTTATCAGATCAATATGTCTGTAAAATCCTCTTA
52335 TCTAACTTCCATATTCAAATCTTGTCTTTTATAACATAAGGGTA-TTTCATAATTTTACCCTACC
66 TCTAA-TTCCATATTCAAATCTTGTCTTTTATAACATAAGGGTATTTTCATAATTTTACCCTACC
52399 AGATTATTCTCATAATTTCCCAACCAAATACCTTTAACATTTAACCTTTGATGAAATA
130 AGA-TATTCTCATAATTTCCCAA-CAAATACCTTTAACATTTAACCTTTGATGAAATA
52457 AAT
1 AAT
52460 TATAAGTTGC
Statistics
Matches: 181, Mismatches: 0, Indels: 11
0.94 0.00 0.06
Matches are distributed among these distances:
179 45 0.25
180 67 0.37
181 10 0.06
182 2 0.01
183 36 0.20
184 21 0.12
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.40
Consensus pattern (185 bp):
AATAAAACTAACATTTCTTATAACGTCAATTTTTATCAGATCAATATGTCTGTAAAATCCTCTTA
TCTAATTCCATATTCAAATCTTGTCTTTTATAACATAAGGGTATTTTCATAATTTTACCCTACCA
GATATTCTCATAATTTCCCAACAAATACCTTTAACATTTAACCTTTGATGAAATA
Found at i:52852 original size:106 final size:106
Alignment explanation
Indices: 52733--53266 Score: 847
Period size: 106 Copynumber: 5.0 Consensus size: 106
52723 ATATCGTGCC
* * *
52733 ACTCAAGACAACACAAGTTCAACTTTACAATGAAGGGACGACTGGTTGTCAACAAATAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
52798 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
52839 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGA-TGATTGTCAACAAACAATTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGAC-GACTGGTTGTCAACAAACAATTTCC
*
52903 CAATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
52945 ACTCAAGACAATACAAGTTCAACTTCACAGCGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
*
53010 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
53051 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
* *
53116 AATTTCATAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
53157 ACTCAAGACAACACAAGTTCAACTTTACAACGAAGGGACGGCTGGTTGTCAACCAACAATTT-CC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
* * * * *
53221 TAGTTCAAGAACCAATTTCAACTTCACGGCAAAGGATATTGG
66 AATTTC-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
53263 ACTC
1 ACTC
53267 GGAACAATAC
Statistics
Matches: 397, Mismatches: 28, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
105 7 0.02
106 388 0.98
107 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.23
Consensus pattern (106 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:54282 original size:14 final size:14
Alignment explanation
Indices: 54263--54309 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
54253 ATTTTGTCTT
54263 TATATAAATTAAAC
1 TATATAAATTAAAC
54277 TATAT-AATT----
1 TATATAAATTAAAC
54286 TATATAAATTAAAC
1 TATATAAATTAAAC
*
54300 TATATTAATT
1 TATATAAATT
54310 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:54288 original size:23 final size:24
Alignment explanation
Indices: 54261--54310 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
54251 TTATTTTGTC
54261 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
54284 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
54308 TTT
1 TTT
54311 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:54599 original size:16 final size:16
Alignment explanation
Indices: 54578--54648 Score: 115
Period size: 16 Copynumber: 4.4 Consensus size: 16
54568 TGGATCATTT
54578 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
54594 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
54610 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* *
54626 ACAAGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
54642 ACAGGTC
1 ACAGGTC
54649 GGGTAATACC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.18
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:54614 original size:32 final size:32
Alignment explanation
Indices: 54578--54648 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
54568 TGGATCATTT
*
54578 ACAGGTCAGGTTAAAAACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAAACAAGTCAGGTTGAAA
54610 ACAGGTCAGGTTAAAAACAAGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAAACAAGTCAGGTTGAAA
54642 ACAGGTC
1 ACAGGTC
54649 GGGTAATACC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.18
Consensus pattern (32 bp):
ACAGGTCAGGTTAAAAACAAGTCAGGTTGAAA
Found at i:55054 original size:73 final size:73
Alignment explanation
Indices: 54935--55097 Score: 308
Period size: 73 Copynumber: 2.2 Consensus size: 73
54925 TACAGCCCTA
*
54935 GTAGGACATACCAAGAACGAAGTTTCATCATCATCTCTCTACACTAATTATGAAGTCAAGTCAAC
1 GTAGGACATACCAAGAACGAAGTTTCATCATCATCTCTCTACACTAATTAAGAAGTCAAGTCAAC
55000 CGTAGCCT
66 CGTAGCCT
*
55008 GTAGGACATACCAAGAAGGAAGTTTCATCATCATCTCTCTACACTAATTAAGAAGTCAAGTCAAC
1 GTAGGACATACCAAGAACGAAGTTTCATCATCATCTCTCTACACTAATTAAGAAGTCAAGTCAAC
55073 CGTAGCCT
66 CGTAGCCT
55081 GTAGGACATACCAAGAA
1 GTAGGACATACCAAGAA
55098 AAGTCTTCAA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 88 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (73 bp):
GTAGGACATACCAAGAACGAAGTTTCATCATCATCTCTCTACACTAATTAAGAAGTCAAGTCAAC
CGTAGCCT
Found at i:61963 original size:2 final size:2
Alignment explanation
Indices: 61956--62008 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
61946 TAAATATGAC
61956 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61998 AT AT AT A- AT AT
1 AT AT AT AT AT AT
62009 TATTGAACAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:72512 original size:117 final size:118
Alignment explanation
Indices: 72322--72650 Score: 518
Period size: 117 Copynumber: 2.8 Consensus size: 118
72312 GGTTAGTTTA
* * *
72322 ATTTTCAGGTGGATGTTTCTCT-AAGTGTGTTGTTATTGTTGCTATTATTATTATTATTATTATT
1 ATTTTCACGTGGAAGTTTCTCTAAAAT-TGTTGTTATTGTT-CTATTATTATTATTATTATTATT
72386 TTACTCCATGATGTTTTCTGTAAAACCAATTGTAAACAAGGATGGTTTCATTTTC
64 TTACTCCATGATGTTTTCTGTAAAACCAATTGTAAACAAGGATGGTTTCATTTTC
* *
72441 ATTTTCACGTGGAAGTTTCTCTAAAATTGTTTTTATTGTT-TCTTATTATTATTATTATTATTTT
1 ATTTTCACGTGGAAGTTTCTCTAAAATTGTTGTTATTGTTCTATTATTATTATTATTATTATTTT
72505 ACTCCATGATGTTTTCTGTAAAACCAATTGTAAACAAGGATGGTTTCATTTTC
66 ACTCCATGATGTTTTCTGTAAAACCAATTGTAAACAAGGATGGTTTCATTTTC
*
72558 ATTTTCACGTGGAAGTTTCTCTAAGATTGTTGTTATTGTTGCTATTATTAGTATTATTATTATTA
1 ATTTTCACGTGGAAGTTTCTCTAAAATTGTTGTTATTGTT-CTATTA-T--TATTATTATTATTA
* *
72623 TTTTACTACATGACGTTTTCTGTAAAAC
62 TTTTACTCCATGATGTTTTCTGTAAAAC
72651 TGCTTGTAAA
Statistics
Matches: 194, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
117 114 0.59
119 36 0.19
120 4 0.02
122 40 0.21
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (118 bp):
ATTTTCACGTGGAAGTTTCTCTAAAATTGTTGTTATTGTTCTATTATTATTATTATTATTATTTT
ACTCCATGATGTTTTCTGTAAAACCAATTGTAAACAAGGATGGTTTCATTTTC
Found at i:75456 original size:31 final size:31
Alignment explanation
Indices: 75421--75481 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
75411 AATGATCCCC
** *
75421 GATTATAGGGTATTATTTTAATGAGTCTCCA
1 GATTATAGGACATTACTTTAATGAGTCTCCA
*
75452 GATTATAGGACATTACTTTATTGAGTCTCC
1 GATTATAGGACATTACTTTAATGAGTCTCC
75482 GACTATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (31 bp):
GATTATAGGACATTACTTTAATGAGTCTCCA
Found at i:76789 original size:45 final size:44
Alignment explanation
Indices: 76725--76989 Score: 274
Period size: 45 Copynumber: 6.2 Consensus size: 44
76715 CTGACCCAGT
*
76725 TCCAAAGCCACATCCAGTATTGTTTCCTGTG-TGACCCCATGATTG
1 TCCAACGCCACATCCAGTATTGTTTCCTG-GCTGACCCC-TGATTG
76770 TCCAACGCCACATCCAGTATTGTTTCCTGTG-TGACCCCATGATTG
1 TCCAACGCCACATCCAGTATTGTTTCCTG-GCTGACCCC-TGATTG
* *
76815 TCCAACGCCACATCCAGCACTGTTTCCTGGCTGACTCCCTGATTG
1 TCCAACGCCACATCCAGTATTGTTTCCTGGCTGAC-CCCTGATTG
*
76860 TCCAACGCCACATGCAGTATTG--T--T---T----CCTGATTG
1 TCCAACGCCACATCCAGTATTGTTTCCTGGCTGACCCCTGATTG
* *
76893 TCCAACACCACATCCAGTATTGTTTCTTGGCTGACCCCCTGATTG
1 TCCAACGCCACATCCAGTATTGTTTCCTGGCTGA-CCCCTGATTG
* *
76938 TCCAACACTACATCC---ATTGTTTCCTGGCTGACCCCCTGATTG
1 TCCAACGCCACATCCAGTATTGTTTCCTGGCTGA-CCCCTGATTG
*
76980 TCCAATGCCA
1 TCCAACGCCA
76990 ATTCCAATAC
Statistics
Matches: 193, Mismatches: 13, Indels: 31
0.81 0.05 0.13
Matches are distributed among these distances:
33 28 0.15
35 1 0.01
37 1 0.01
38 1 0.01
40 1 0.01
41 1 0.01
42 33 0.17
43 1 0.01
44 1 0.01
45 122 0.63
46 3 0.02
ACGTcount: A:0.20, C:0.33, G:0.17, T:0.30
Consensus pattern (44 bp):
TCCAACGCCACATCCAGTATTGTTTCCTGGCTGACCCCTGATTG
Found at i:76894 original size:33 final size:33
Alignment explanation
Indices: 76852--76918 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
76842 TGGCTGACTC
* *
76852 CCTGATTGTCCAACGCCACATGCAGTATTGTTT
1 CCTGATTGTCCAACACCACATCCAGTATTGTTT
76885 CCTGATTGTCCAACACCACATCCAGTATTGTTT
1 CCTGATTGTCCAACACCACATCCAGTATTGTTT
76918 C
1 C
76919 TTGGCTGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (33 bp):
CCTGATTGTCCAACACCACATCCAGTATTGTTT
Found at i:76928 original size:123 final size:120
Alignment explanation
Indices: 76764--76989 Score: 337
Period size: 123 Copynumber: 1.9 Consensus size: 120
76754 TGTGACCCCA
* *
76764 TGATTGTCCAACGCCACATCCAGTATTGTTTCCTGTGTGACCCCATGATTGTCCAACGCCACATC
1 TGATTGTCCAACACCACATCCAGTATTGTTTCCTGTGTGACCCCATGATTGTCCAACACCACAT-
*
76829 CAGCACTGTTTCCTGGCTGACTCCCTGATTGTCCAACGCCACATGCAGTATTGTTTCC
65 C--CACTGTTTCCTGGCTGACCCCCTGATTGTCCAACGCCACATGCAGTATTGTTTCC
* * *
76887 TGATTGTCCAACACCACATCCAGTATTGTTTCTTG-GCTGACCCCCTGATTGTCCAACACTACAT
1 TGATTGTCCAACACCACATCCAGTATTGTTTCCTGTG-TGACCCCATGATTGTCCAACACCACAT
* *
76951 CCATTGTTTCCTGGCTGACCCCCTGATTGTCCAATGCCA
65 CCACTGTTTCCTGGCTGACCCCCTGATTGTCCAACGCCA
76990 ATTCCAATAC
Statistics
Matches: 94, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
120 35 0.37
122 2 0.02
123 57 0.61
ACGTcount: A:0.20, C:0.33, G:0.17, T:0.31
Consensus pattern (120 bp):
TGATTGTCCAACACCACATCCAGTATTGTTTCCTGTGTGACCCCATGATTGTCCAACACCACATC
CACTGTTTCCTGGCTGACCCCCTGATTGTCCAACGCCACATGCAGTATTGTTTCC
Found at i:76970 original size:42 final size:43
Alignment explanation
Indices: 76885--76984 Score: 157
Period size: 42 Copynumber: 2.3 Consensus size: 43
76875 AGTATTGTTT
*
76885 CCTGATTGTCCAACACCACATCCAGTATTGTTTCTTGGCTGACCC
1 CCTGATTGTCCAACACCACATCCA--ATTGTTTCCTGGCTGACCC
*
76930 CCTGATTGTCCAACACTACATCC-ATTGTTTCCTGGCTGACCC
1 CCTGATTGTCCAACACCACATCCAATTGTTTCCTGGCTGACCC
76972 CCTGATTGTCCAA
1 CCTGATTGTCCAA
76985 TGCCAATTCC
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
42 31 0.58
45 22 0.42
ACGTcount: A:0.20, C:0.34, G:0.15, T:0.31
Consensus pattern (43 bp):
CCTGATTGTCCAACACCACATCCAATTGTTTCCTGGCTGACCC
Found at i:79423 original size:34 final size:34
Alignment explanation
Indices: 79380--79448 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
79370 CGAAATCACG
79380 GTAAATGAAGCTTTTATATGAAGTTCATGATACA
1 GTAAATGAAGCTTTTATATGAAGTTCATGATACA
79414 GTAAATGAAGCTTTTATATGAAGTTCATGATACA
1 GTAAATGAAGCTTTTATATGAAGTTCATGATACA
79448 G
1 G
79449 AATCAACTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.35
Consensus pattern (34 bp):
GTAAATGAAGCTTTTATATGAAGTTCATGATACA
Found at i:79616 original size:34 final size:34
Alignment explanation
Indices: 79573--79641 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
79563 CGAAATCACG
79573 GTAAATGAAGCTTTTATATGAAGTTCATGATACA
1 GTAAATGAAGCTTTTATATGAAGTTCATGATACA
79607 GTAAATGAAGCTTTTATATGAAGTTCATGATACA
1 GTAAATGAAGCTTTTATATGAAGTTCATGATACA
79641 G
1 G
79642 AATCAACTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.35
Consensus pattern (34 bp):
GTAAATGAAGCTTTTATATGAAGTTCATGATACA
Found at i:79656 original size:193 final size:193
Alignment explanation
Indices: 79327--79712 Score: 772
Period size: 193 Copynumber: 2.0 Consensus size: 193
79317 AGACCTTTTG
79327 AGTCGCATAATTTAATGGCGGAAGCAAACAAACTTGTTGGCATCGAAATCACGGTAAATGAAGCT
1 AGTCGCATAATTTAATGGCGGAAGCAAACAAACTTGTTGGCATCGAAATCACGGTAAATGAAGCT
79392 TTTATATGAAGTTCATGATACAGTAAATGAAGCTTTTATATGAAGTTCATGATACAGAATCAACT
66 TTTATATGAAGTTCATGATACAGTAAATGAAGCTTTTATATGAAGTTCATGATACAGAATCAACT
79457 CAATCGTATGCTCAAAATGGAAGAAGCCATATGAATTGTGAATTTACAGCAAAGAAGCTATGA
131 CAATCGTATGCTCAAAATGGAAGAAGCCATATGAATTGTGAATTTACAGCAAAGAAGCTATGA
79520 AGTCGCATAATTTAATGGCGGAAGCAAACAAACTTGTTGGCATCGAAATCACGGTAAATGAAGCT
1 AGTCGCATAATTTAATGGCGGAAGCAAACAAACTTGTTGGCATCGAAATCACGGTAAATGAAGCT
79585 TTTATATGAAGTTCATGATACAGTAAATGAAGCTTTTATATGAAGTTCATGATACAGAATCAACT
66 TTTATATGAAGTTCATGATACAGTAAATGAAGCTTTTATATGAAGTTCATGATACAGAATCAACT
79650 CAATCGTATGCTCAAAATGGAAGAAGCCATATGAATTGTGAATTTACAGCAAAGAAGCTATGA
131 CAATCGTATGCTCAAAATGGAAGAAGCCATATGAATTGTGAATTTACAGCAAAGAAGCTATGA
79713 TTTCCTTGGC
Statistics
Matches: 193, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
193 193 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (193 bp):
AGTCGCATAATTTAATGGCGGAAGCAAACAAACTTGTTGGCATCGAAATCACGGTAAATGAAGCT
TTTATATGAAGTTCATGATACAGTAAATGAAGCTTTTATATGAAGTTCATGATACAGAATCAACT
CAATCGTATGCTCAAAATGGAAGAAGCCATATGAATTGTGAATTTACAGCAAAGAAGCTATGA
Done.