Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005549.1 Hibiscus syriacus cultivar Beakdansim tig00012862_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: 70951
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1463 original size:19 final size:19
Alignment explanation
Indices: 1439--1501 Score: 101
Period size: 19 Copynumber: 3.4 Consensus size: 19
1429 CGCGATTTTG
*
1439 AAAATGTGTTGTGATAGTT
1 AAAATGTGTTGCGATAGTT
1458 AAAATGTGTTGCGATAG-T
1 AAAATGTGTTGCGATAGTT
*
1476 GAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
1495 AAAATGT
1 AAAATGT
1502 TGCGATTCAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
18 17 0.43
19 23 0.57
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:19389 original size:17 final size:17
Alignment explanation
Indices: 19367--19399 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19357 GACCAACAAA
19367 ATCGCAATGCGATCTCT
1 ATCGCAATGCGATCTCT
*
19384 ATCGCATTGCGATCTC
1 ATCGCAATGCGATCTC
19400 CACTATCGCA
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:0.21, C:0.30, G:0.18, T:0.30
Consensus pattern (17 bp):
ATCGCAATGCGATCTCT
Found at i:19466 original size:41 final size:41
Alignment explanation
Indices: 19421--19683 Score: 419
Period size: 41 Copynumber: 6.5 Consensus size: 41
19411 ATTCGCGTTG
*
19421 CATTTCGCGTTGCGATAGTTGGAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
19462 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
19503 CATTTCGCGTTGCTATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
19544 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
19585 CATTTTGCGTTGCGATAGTTGAAAATCGCGTTGCGA-TTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
19625 CATTTCGCGTTGCGATAGTCT-ACAAT-GTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
*
19666 CAAATT--CGTTGCGATAGT
1 C-ATTTCGCGTTGCGATAGT
19684 CTACAGTTGT
Statistics
Matches: 211, Mismatches: 7, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
39 1 0.00
40 46 0.22
41 161 0.76
42 3 0.01
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:19695 original size:19 final size:20
Alignment explanation
Indices: 19633--19715 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 20
19623 TCCATTTCGC
*
19633 GTTGCGATAGTCTACAATGTC
1 GTTGCGATAGTCTAC-ATGTT
** * * *
19654 GTTGCGATTTTCCAAAT-TC
1 GTTGCGATAGTCTACATGTT
19673 GTTGCGATAGTCTACAGTTGTT
1 GTTGCGATAGTCTACA--TGTT
*
19695 GTTGCGAAAGTCTACA-GTT
1 GTTGCGATAGTCTACATGTT
19714 GT
1 GT
19716 CGTTGCGATT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
19 19 0.39
20 2 0.04
21 12 0.24
22 16 0.33
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCTACATGTT
Found at i:19700 original size:22 final size:22
Alignment explanation
Indices: 19632--19724 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
19622 TTCCATTTCG
*
19632 CGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
19653 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
19672 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
19694 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
19716 CGTTGCGAT
1 CGTTGCGAT
19725 TTTCCAAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
19 14 0.24
20 2 0.03
21 14 0.24
22 28 0.48
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:21956 original size:22 final size:21
Alignment explanation
Indices: 21904--21958 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
21894 GCAACGCGAT
*
21904 TTTGAAAAA-TGTTGCGATAG
1 TTTGAAAAAGTGTTGCGAGAG
*
21924 -TT-AAAATGTGTTGCGAGAG
1 TTTGAAAAAGTGTTGCGAGAG
21943 TTTGAAAAACGTGTTG
1 TTTGAAAAA-GTGTTG
21959 TTGCGATAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.14
19 12 0.43
20 2 0.07
21 4 0.14
22 6 0.21
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (21 bp):
TTTGAAAAAGTGTTGCGAGAG
Found at i:21973 original size:22 final size:19
Alignment explanation
Indices: 21913--21973 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 19
21903 TTTTGAAAAA
*
21913 TGTTGCGATAGTTAAAATG
1 TGTTGCGATAGTGAAAATG
*
21932 TGTTGCGAGAGTTTGAAAAACGTG
1 TGTTGCGATAG--TG-AAAA--TG
21956 TTGTTGCGATAGTGAAAA
1 -TGTTGCGATAGTGAAAA
21974 ATCCAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
19 10 0.30
21 1 0.03
22 8 0.24
23 2 0.06
24 2 0.06
25 10 0.30
ACGTcount: A:0.31, C:0.07, G:0.30, T:0.33
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAATG
Found at i:22415 original size:21 final size:21
Alignment explanation
Indices: 22389--22456 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
22379 GCGATTTTAG
22389 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
* * *
22410 TCGCAA--CAAATTTGGA-AA
1 TCGCAACGCGAACTTGGACTA
* *
22428 TCACAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTGGACTA
22449 TCGCAACG
1 TCGCAACG
22457 AATTGGAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
18 6 0.17
19 8 0.23
20 7 0.20
21 14 0.40
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTGGACTA
Found at i:22448 original size:39 final size:39
Alignment explanation
Indices: 22392--22474 Score: 123
Period size: 39 Copynumber: 2.1 Consensus size: 39
22382 ATTTTAGTCG
*
22392 CAACGCGAACTTGGACTATCGCAACAAATTTGG-AAATCA
1 CAACGCGAACTTCGACTATCGCAACAAA-TTGGAAAATCA
* *
22431 CAACGCGAACTTCGACTATCGCAACGAATTGGAAAATCG
1 CAACGCGAACTTCGACTATCGCAACAAATTGGAAAATCA
22470 CAACG
1 CAACG
22475 AATTTGGACT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 4 0.10
39 36 0.90
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.18
Consensus pattern (39 bp):
CAACGCGAACTTCGACTATCGCAACAAATTGGAAAATCA
Found at i:22550 original size:20 final size:20
Alignment explanation
Indices: 22521--22591 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
22511 ATTTTGTATT
22521 ATCGCATTGCGATAGTCAGA
1 ATCGCATTGCGATAGTCAGA
* *
22541 ATCGCGTTGCGAT--T-ATGT
1 ATCGCATTGCGATAGTCA-GA
22559 ATCGCATTGCGATAGTCAGA
1 ATCGCATTGCGATAGTCAGA
*
22579 ATCGCGTTGCGAT
1 ATCGCATTGCGAT
22592 TTTGTATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
17 1 0.02
18 14 0.33
20 26 0.62
21 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.30
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGA
Found at i:22560 original size:41 final size:41
Alignment explanation
Indices: 22499--22612 Score: 180
Period size: 38 Copynumber: 2.9 Consensus size: 41
22489 TAAATTGGAA
*
22499 AATCGCATTGCGATTTTGTATTATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAG
*
22540 AATCGCGTTGCGATTATG---TATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAG
*
22578 AATCGCGTTGCGATTTTGTATTATCGCGTTGCGAT
1 AATCGCGTTGCGATTTTGTATTATCGCATTGCGAT
22613 TTACATATTC
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
38 37 0.56
41 29 0.44
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.36
Consensus pattern (41 bp):
AATCGCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAG
Found at i:22731 original size:20 final size:19
Alignment explanation
Indices: 22708--22753 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
22698 GGAAACTGAT
* *
22708 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
22728 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
22747 TTGCGAT
1 TTGCGAT
22754 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:22743 original size:19 final size:19
Alignment explanation
Indices: 22719--22755 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22709 TGCGATACTG
*
22719 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
22738 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
22756 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:27071 original size:42 final size:41
Alignment explanation
Indices: 27010--27106 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
27000 ACAATTTAAG
* * * *
27010 TCCTTCGAGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGAGTCATCAGTAAGCCTTTAGAGCAAGATGAT-AAA
* *
27052 TCCTTCGAGTCATCTGTAAGCCTTTAGAGCAAGATGATAAG
1 TCCTTCGAGTCATCAGTAAGCCTTTAGAGCAAGATGATAAA
* *
27093 TCATTCGGGTCATC
1 TCCTTCGAGTCATC
27107 CATAAGACAT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 14 0.30
42 33 0.70
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (41 bp):
TCCTTCGAGTCATCAGTAAGCCTTTAGAGCAAGATGATAAA
Found at i:27286 original size:41 final size:41
Alignment explanation
Indices: 27225--27314 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
27215 ACTTAGTAAG
* *
27225 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTC-GACCATCAATAAGTCTTTCGAGCATGATGATTAAA
*
27267 TCCTTCGACCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGACCATCAATAAGTCTTTCGAGCATGATGATTAAA
*
27308 TCTTTCG
1 TCCTTCG
27315 GGTAATTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 38 0.86
42 6 0.14
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (41 bp):
TCCTTCGACCATCAATAAGTCTTTCGAGCATGATGATTAAA
Found at i:27312 original size:22 final size:21
Alignment explanation
Indices: 27245--27314 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
27235 CATCAATAAG
27245 TCTTTCGAGCATGATGCTTAAA
1 TCTTTCGAGCATGATG-TTAAA
* * * *
27267 TCCTTCGACCATCA-G-TAAG
1 TCTTTCGAGCATGATGTTAAA
27286 TCTTTCGAGCATGATGATTAAA
1 TCTTTCGAGCATGATG-TTAAA
27308 TCTTTCG
1 TCTTTCG
27315 GGTAATTTGT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
19 14 0.38
20 1 0.03
21 1 0.03
22 21 0.57
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (21 bp):
TCTTTCGAGCATGATGTTAAA
Found at i:27444 original size:42 final size:41
Alignment explanation
Indices: 27385--27467 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 41
27375 TAAGTCTTTC
27385 GAGCATGATGATAAAGTCCTTCGGGCCATCAGTAAGCCTTCA
1 GAGCATGATGATAAAGTCCTTCGGGCCATC-GTAAGCCTTCA
* *
27427 GAGCATGATGATTAAGTCCTTCGGGCCATCTTAAGCCTTCA
1 GAGCATGATGATAAAGTCCTTCGGGCCATCGTAAGCCTTCA
27468 CAGAAGAGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 10 0.26
42 29 0.74
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.27
Consensus pattern (41 bp):
GAGCATGATGATAAAGTCCTTCGGGCCATCGTAAGCCTTCA
Found at i:27447 original size:23 final size:22
Alignment explanation
Indices: 27375--27449 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
27365 GTGATATCAA
*
27375 TAAGTCTTTCGAGCATGATGAT
1 TAAGTCCTTCGAGCATGATGAT
* * *
27397 AAAGTCCTTCGGGCCATCA-G--
1 TAAGTCCTTCGAG-CATGATGAT
27417 TAAG-CCTTCAGAGCATGATGAT
1 TAAGTCCTTC-GAGCATGATGAT
27439 TAAGTCCTTCG
1 TAAGTCCTTCG
27450 GGCCATCTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
19 9 0.22
20 6 0.15
22 16 0.40
23 9 0.22
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (22 bp):
TAAGTCCTTCGAGCATGATGAT
Found at i:27481 original size:134 final size:134
Alignment explanation
Indices: 27236--27486 Score: 364
Period size: 134 Copynumber: 1.9 Consensus size: 134
27226 CCTTCGGGCC
* *
27236 ATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGACCATCAGTAAGTCTTTCGAGCATGAT
1 ATCAATAAGTCTTTCGAGCATGATGCATAAATCCTTCGACCATCAGTAAGTCCTTCGAGCATGAT
* * * * *
27301 GATTAAATCTTTCGGGTAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAATCCCATCAGTAAG
66 GATTAAATCCTTCGGGCAATCTGTAAGCCTTCACAGAAGAGCAGTGAAGCAATCCCATCAGTAAG
27366 TGAT
131 TGAT
*
27370 ATCAATAAGTCTTTCGAGCATGATG-ATAAAGTCCTTCGGGCCATCAGTAAG-CCTTCAGAGCAT
1 ATCAATAAGTCTTTCGAGCATGATGCATAAA-TCCTTC-GACCATCAGTAAGTCCTTC-GAGCAT
* *
27433 GATGATTAAGTCCTTCGGGCCATCT-TAAGCCTTCACAGAAGAGCAGTGAAGCAA
63 GATGATTAAATCCTTCGGGCAATCTGTAAGCCTTCACAGAAGAGCAGTGAAGCAA
27487 ACCATCTTAA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
133 4 0.04
134 62 0.60
135 38 0.37
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (134 bp):
ATCAATAAGTCTTTCGAGCATGATGCATAAATCCTTCGACCATCAGTAAGTCCTTCGAGCATGAT
GATTAAATCCTTCGGGCAATCTGTAAGCCTTCACAGAAGAGCAGTGAAGCAATCCCATCAGTAAG
TGAT
Found at i:27657 original size:36 final size:36
Alignment explanation
Indices: 27607--27676 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
27597 GTCCCCCGGG
** *
27607 CCATCTTATGCCTTCACGGAAGAGTAGTGAAGCAAA
1 CCATCTTAAACCTTCACAGAAGAGTAGTGAAGCAAA
27643 CCATCTTAAACCTTCACAGAAGAGTAGTGAAGCA
1 CCATCTTAAACCTTCACAGAAGAGTAGTGAAGCA
27677 GAATCACACC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (36 bp):
CCATCTTAAACCTTCACAGAAGAGTAGTGAAGCAAA
Found at i:27753 original size:53 final size:53
Alignment explanation
Indices: 27686--27857 Score: 249
Period size: 53 Copynumber: 3.2 Consensus size: 53
27676 AGAATCACAC
27686 CAGAAGATTGTTCGAGTTCTACTCCTTAAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCTTAAAGCAAGAGGGAGCGAACCCGTAGG
* *
27739 CAGAAGATTATTCGAGTTCTACTCCCTGAAA-CAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACT-CCTTAAAGCAAGAGGGAGCGAACCCGTAGG
* * * * *
27792 CAGAAGATTGTTTGAGTTCTACTCCCTAAAGCAAGAGGGAACGAATCCGCTAGT
1 CAGAAGATTGTTCGAGTTCTACTCCTTAAAGCAAGAGGGAGCGAACCCG-TAGG
27846 C-GAAGATTGTTC
1 CAGAAGATTGTTC
27858 AAAGAAGATG
Statistics
Matches: 106, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
52 5 0.05
53 91 0.86
54 10 0.09
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCTTAAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:28034 original size:20 final size:20
Alignment explanation
Indices: 28006--28050 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
27996 TTTGTCTGGG
*
28006 TTATAAATATTATATTATAA
1 TTATAAATAATATATTATAA
*
28026 TTATTAATAATATATTATAA
1 TTATAAATAATATATTATAA
*
28046 CTATA
1 TTATA
28051 TCATTATTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATAAATAATATATTATAA
Found at i:33169 original size:11 final size:11
Alignment explanation
Indices: 33153--33182 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
33143 TGTAACACCC
33153 CCAACCCGTAT
1 CCAACCCGTAT
33164 CCAACCCGTAT
1 CCAACCCGTAT
*
33175 CCGACCCG
1 CCAACCCG
33183 GATACGAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.23, C:0.50, G:0.13, T:0.13
Consensus pattern (11 bp):
CCAACCCGTAT
Found at i:33900 original size:32 final size:31
Alignment explanation
Indices: 33846--33963 Score: 148
Period size: 32 Copynumber: 3.7 Consensus size: 31
33836 GTTCCTTAGA
*
33846 ACATAGGTATACTATCCATATGTCTCGAAAG
1 ACATAGGTATACTGTCCATATGTCTCGAAAG
* * *
33877 ACATAGGTAATTCTGTCCATATGT-TCCATAG
1 ACATAGGT-ATACTGTCCATATGTCTCGAAAG
*
33908 AACATAGGTATAATGTCCATATGTCTCGAAAG
1 -ACATAGGTATACTGTCCATATGTCTCGAAAG
*
33940 ACATAGGTAATTCTGTCCATATGT
1 ACATAGGT-ATACTGTCCATATGT
33964 TCCGTAGAAC
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
31 34 0.47
32 39 0.53
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (31 bp):
ACATAGGTATACTGTCCATATGTCTCGAAAG
Found at i:33916 original size:63 final size:63
Alignment explanation
Indices: 33829--33983 Score: 274
Period size: 63 Copynumber: 2.5 Consensus size: 63
33819 AGGTAAACTA
*
33829 TCCATATGTTCCTTAGAACATAGGTATACTATCCATATGTCTCGAAAGACATAGGTAATTCTG
1 TCCATATGTTCCATAGAACATAGGTATACTATCCATATGTCTCGAAAGACATAGGTAATTCTG
* *
33892 TCCATATGTTCCATAGAACATAGGTATAATGTCCATATGTCTCGAAAGACATAGGTAATTCTG
1 TCCATATGTTCCATAGAACATAGGTATACTATCCATATGTCTCGAAAGACATAGGTAATTCTG
*
33955 TCCATATGTTCCGTAGAACATAGGTATAC
1 TCCATATGTTCCATAGAACATAGGTATAC
33984 CCTCGACTCT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 87 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (63 bp):
TCCATATGTTCCATAGAACATAGGTATACTATCCATATGTCTCGAAAGACATAGGTAATTCTG
Found at i:33976 original size:32 final size:32
Alignment explanation
Indices: 33794--33980 Score: 165
Period size: 31 Copynumber: 5.9 Consensus size: 32
33784 ATCTTCGGTA
* * *
33794 ACTGTCTATAGGTTCCGGT-GAACCTAGGTAA-
1 ACTGTCCATATGTTCC-GTAGAACATAGGTAAT
* *
33825 ACTATCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* *
33856 ACTATCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAGA-ACATAGGTAAT
* *
33888 TCTGTCCATATGTTCCATAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* *
33919 AATGTCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAGA-ACATAGGTAAT
*
33951 TCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTTCCGTAGAACATAGGTA
33981 TACCCTCGAC
Statistics
Matches: 126, Mismatches: 18, Indels: 23
0.75 0.11 0.14
Matches are distributed among these distances:
30 10 0.08
31 64 0.51
32 44 0.35
33 8 0.06
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:42579 original size:17 final size:16
Alignment explanation
Indices: 42557--42590 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
42547 TAAAAACAGT
42557 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
42574 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
42590 A
1 A
42591 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:45581 original size:15 final size:15
Alignment explanation
Indices: 45558--45592 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
45548 GTCCGTCCGT
*
45558 CTCGTCTCGTCTCGG
1 CTCGTCTCGGCTCGG
*
45573 CTCGGCTCGGCTCGG
1 CTCGTCTCGGCTCGG
45588 CTCGT
1 CTCGT
45593 GGTCGTGGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.40, G:0.31, T:0.29
Consensus pattern (15 bp):
CTCGTCTCGGCTCGG
Found at i:57382 original size:60 final size:61
Alignment explanation
Indices: 57314--57456 Score: 186
Period size: 60 Copynumber: 2.4 Consensus size: 61
57304 TTTTTAAATG
* * *
57314 TTTCAATTTTATCCCTAAACTATGAC-TATCATTCT-AATTTAATCCTCAAAC-TTTTGAGCA
1 TTTCAATTTCATCCCTAAACTATGACAT-TCATTCTAAATTGAATCC-CAAACTTTTTGAACA
* **
57374 TTTCAATTTCATCCCTAAACTCTGACATTCATTCTAAATTGGTTCCCAAACTTTTTGAACA
1 TTTCAATTTCATCCCTAAACTATGACATTCATTCTAAATTGAATCCCAAACTTTTTGAACA
57435 TTTCAATTTCATCCC-AAACTAT
1 TTTCAATTTCATCCCTAAACTAT
57457 ATGTATATAC
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
60 42 0.58
61 31 0.42
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.41
Consensus pattern (61 bp):
TTTCAATTTCATCCCTAAACTATGACATTCATTCTAAATTGAATCCCAAACTTTTTGAACA
Found at i:57393 original size:29 final size:29
Alignment explanation
Indices: 57314--57394 Score: 69
Period size: 29 Copynumber: 2.7 Consensus size: 29
57304 TTTTTAAATG
*
57314 TTTCAATTTTATCCCTAAAC-TATGACTA
1 TTTCAATTTAATCCCTAAACTTATGACTA
*
57342 TCATTCTAATTTAAT-CCTCAAACTTTTGAGC-A
1 T--TTC-AATTTAATCCCT-AAACTTATGA-CTA
*
57374 TTTCAATTTCATCCCTAAACT
1 TTTCAATTTAATCCCTAAACT
57395 CTGACATTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
28 1 0.02
29 12 0.28
30 12 0.28
31 11 0.26
32 6 0.14
33 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42
Consensus pattern (29 bp):
TTTCAATTTAATCCCTAAACTTATGACTA
Found at i:57632 original size:60 final size:59
Alignment explanation
Indices: 57562--57713 Score: 184
Period size: 60 Copynumber: 2.5 Consensus size: 59
57552 TTTGTATGAA
*
57562 TTTAGGGATGAAATTAGAATATTCAAAAGTTT-GGCCTCTAATTTAGAAAGAGG-ATCATAG
1 TTTAGGGATGAAATTAGAATATTCAAAAGTTTAGG--ACTAATTTAGAAAG-GGAATCATAG
* * *
57622 TTTAGAGATGAAATTA-AAGTGTTCAAAAGTTTAAGGACTAATTTAGAATGGGAATCATAG
1 TTTAGGGATGAAATTAGAA-TATTCAAAAGTTT-AGGACTAATTTAGAAAGGGAATCATAG
* *
57682 TTTGGGGATGAAATTAGAATATTTAAAAGTTT
1 TTTAGGGATGAAATTAGAATATTCAAAAGTTT
57714 CTAGGATCAA
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
59 4 0.05
60 71 0.90
61 2 0.03
62 2 0.03
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (59 bp):
TTTAGGGATGAAATTAGAATATTCAAAAGTTTAGGACTAATTTAGAAAGGGAATCATAG
Found at i:66510 original size:15 final size:17
Alignment explanation
Indices: 66477--66510 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
66467 CGTATCCAAT
66477 AGTTCCAGATTATTAGA
1 AGTTCCAGATTATTAGA
66494 AGTTCCA-ATTA-TAGA
1 AGTTCCAGATTATTAGA
66509 AG
1 AG
66511 CTTCTTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 4 0.24
17 7 0.41
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (17 bp):
AGTTCCAGATTATTAGA
Done.