Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000352.1 Hibiscus syriacus cultivar Beakdansim tig00000646_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: 150517
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:6769 original size:14 final size:14
Alignment explanation
Indices: 6750--6780 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
6740 TTAACAAATA
6750 AAAAATGTAAATGT
1 AAAAATGTAAATGT
6764 AAAAATGTAAATGT
1 AAAAATGTAAATGT
6778 AAA
1 AAA
6781 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (14 bp):
AAAAATGTAAATGT
Found at i:9940 original size:31 final size:31
Alignment explanation
Indices: 9883--9941 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
9873 CATTTCTTAA
9883 TAAAAAAAATAAATAAATGTTAATAAAACAT
1 TAAAAAAAATAAATAAATGTTAATAAAACAT
*
9914 TAAAAAATAATATATATAAT-TT-ATAAAA
1 TAAAAAA-AATAAATA-AATGTTAATAAAA
9942 ATAAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 13 0.52
32 9 0.36
33 3 0.12
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (31 bp):
TAAAAAAAATAAATAAATGTTAATAAAACAT
Found at i:9944 original size:22 final size:22
Alignment explanation
Indices: 9916--9967 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
9906 TAAAACATTA
*
9916 AAAAATAATATATATAATTTA-T
1 AAAAATAAAATAT-TAATTTATT
*
9938 AAAAATAAAATATTTATTTATTT
1 AAAAATAAAATATTAATTTA-TT
9961 AAAAATA
1 AAAAATA
9968 TCAGAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.23
22 12 0.46
23 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATAAAATATTAATTTATT
Found at i:10141 original size:3 final size:3
Alignment explanation
Indices: 10135--10164 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
10125 TATATATTTG
10135 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
10165 ATAAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:11654 original size:16 final size:15
Alignment explanation
Indices: 11633--11694 Score: 65
Period size: 16 Copynumber: 4.1 Consensus size: 15
11623 CTGATGTAAT
11633 TTTAATATATATATTA
1 TTTAATA-ATATATTA
* *
11649 TTTAATAATAAATAA
1 TTTAATAATATATTA
*
11664 TAATAATAATATA-TA
1 T-TTAATAATATATTA
11679 TTTAATAAT-TATTA
1 TTTAATAATATATTA
11693 TT
1 TT
11695 ATTATATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 2 0.05
14 11 0.29
15 9 0.24
16 16 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAATAATATATTA
Found at i:13892 original size:2 final size:2
Alignment explanation
Indices: 13885--13915 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13875 ATAGGTCATC
13885 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13916 CTACATGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15136 original size:41 final size:41
Alignment explanation
Indices: 15073--15186 Score: 196
Period size: 41 Copynumber: 2.8 Consensus size: 41
15063 ACCCCAAAGG
* *
15073 CCCAAAC-ACAAC-AAAACACACACAAACACCCATACATAC
1 CCCAAACTACAACAAAAACTCACACCAACACCCATACATAC
15112 CCCAAACTACAACAAAAACTCACACCAACACCCATACATAC
1 CCCAAACTACAACAAAAACTCACACCAACACCCATACATAC
15153 CCCAAACTACAACAAAAACTCACACCAACACCCA
1 CCCAAACTACAACAAAAACTCACACCAACACCCA
15187 ATGACAACGA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
39 7 0.10
40 5 0.07
41 59 0.83
ACGTcount: A:0.51, C:0.42, G:0.00, T:0.07
Consensus pattern (41 bp):
CCCAAACTACAACAAAAACTCACACCAACACCCATACATAC
Found at i:15612 original size:25 final size:22
Alignment explanation
Indices: 15582--15648 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
15572 AAGGAGTTGA
*
15582 AATATTATTAACTATATATTAT
1 AATATTATTAACTATAAATTAT
*
15604 CATTATATT-CTAAC-ATAAATTAT
1 -A--ATATTATTAACTATAAATTAT
*
15627 AATATTATTAACTATAATTTAT
1 AATATTATTAACTATAAATTAT
15649 TTTTTTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
20 5 0.14
21 4 0.11
22 9 0.25
23 9 0.25
24 4 0.11
25 5 0.14
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATTATTAACTATAAATTAT
Found at i:29473 original size:14 final size:14
Alignment explanation
Indices: 29454--29496 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
29444 TGGCATCGAC
*
29454 ATTAATCACTTAGA
1 ATTAATAACTTAGA
29468 ATTAATAACTTAGA
1 ATTAATAACTTAGA
29482 ATTAATAACTTAGA
1 ATTAATAACTTAGA
29496 A
1 A
29497 CTATACGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (14 bp):
ATTAATAACTTAGA
Found at i:33613 original size:60 final size:59
Alignment explanation
Indices: 33546--33706 Score: 178
Period size: 60 Copynumber: 2.7 Consensus size: 59
33536 AAATAATTTG
* ** *
33546 TAAATTAGTCTTTAAACTTTTAAATACTTTAATTTCTTCCTTAAACTATGACTCTCATTA
1 TAAATTAGTCTTTAAACTTTTAAATA-TTTAATTTCATCCCCAAACTATGAATCTCATTA
* * * * * *
33606 TAAATTAGTATTTAAACTTTTGAACATTCTAATTTCATCCCCAAATTATGAATTTCATTC
1 TAAATTAGTCTTTAAACTTTTAAATATT-TAATTTCATCCCCAAACTATGAATCTCATTA
** *
33666 TAAATTAGTCCCTAAACTTTTAGATATTTCAATTTCATCCC
1 TAAATTAGTCTTTAAACTTTTAAATATTT-AATTTCATCCC
33707 AAATTCATCC
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
59 3 0.04
60 80 0.96
ACGTcount: A:0.34, C:0.18, G:0.04, T:0.44
Consensus pattern (59 bp):
TAAATTAGTCTTTAAACTTTTAAATATTTAATTTCATCCCCAAACTATGAATCTCATTA
Found at i:33955 original size:41 final size:41
Alignment explanation
Indices: 33903--34260 Score: 337
Period size: 41 Copynumber: 8.8 Consensus size: 41
33893 CATTTATAGA
* *
33903 ACAAACGCCGCTAAATACTCGTATTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * * *
33944 ATAAACGCCGCTAAACAAT-GTACTTTAGTAGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * *
33984 ACAAACACCGCTAAAGA-TTGTACTTTAGTGGC-ATTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * * **
34023 ACAAACGTCGCTATAGTCAAGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * * * *
34064 ACAAACGCCGTTAAAGACTCATAATTTAGTGGTGCTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * * * * * *
34105 GA-AAGCGCTGATAAAGACTTGTACTTTAGAGTCGTTTTGAT
1 -ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * *
34146 ATAAACGTCGCTAAAGACTCGTACTTTAGTGGTGTTTTTAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* * * * * * *
34187 ACAAACGTCACTATAGACTAGTGCTTTAGTGGCATTTTGAT
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
* *
34228 ACAAACGCTGTTAAAGACTCGTACTTTAGTGGC
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGC
34261 ATTTGTTTTT
Statistics
Matches: 250, Mismatches: 62, Indels: 10
0.78 0.19 0.03
Matches are distributed among these distances:
39 20 0.08
40 59 0.24
41 170 0.68
42 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (41 bp):
ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
Found at i:34351 original size:25 final size:25
Alignment explanation
Indices: 34319--34377 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
34309 CCTTTAACAC
34319 TTTTTCATTTTCCCACTTCACCTAT
1 TTTTTCATTTTCCCACTTCACCTAT
34344 TTTTTCATTTTCCCACTTCACCTAT
1 TTTTTCATTTTCCCACTTCACCTAT
34369 TTTTTCATT
1 TTTTTCATT
34378 CTAGCCGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.15, C:0.29, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTTCATTTTCCCACTTCACCTAT
Found at i:36457 original size:12 final size:12
Alignment explanation
Indices: 36430--36468 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
36420 TTTTTTATAC
*
36430 TTTCTCTTATTAT
1 TTTCTCTTCTT-T
*
36443 TTTCTTTTCTTT
1 TTTCTCTTCTTT
36455 TTTCTCTTCTTT
1 TTTCTCTTCTTT
36467 TT
1 TT
36469 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTCTCTTCTTT
Found at i:38016 original size:12 final size:12
Alignment explanation
Indices: 37999--38026 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
37989 ACATTTAAAA
37999 AAAATAAAACAT
1 AAAATAAAACAT
38011 AAAATAAAACAT
1 AAAATAAAACAT
38023 AAAA
1 AAAA
38027 ACATTCTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAATAAAACAT
Found at i:39543 original size:51 final size:51
Alignment explanation
Indices: 39369--40035 Score: 920
Period size: 51 Copynumber: 12.9 Consensus size: 51
39359 TCATAAAATG
* * * ** *
39369 TGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAACG
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGAC-T---CAATCTTCAA-CGAACT
* * * * * ** *
39425 GGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCCATAAACA
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACT
* * * * * * *
39480 GGTCCGCTCCCTATTCTTTCAGAGAGTACATGACTCAATCTTTAACAAACG
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
* * * * * *
39531 TGTTCGCTCCCTATCCGTTCAGGGAGTATAGAACTCAATCTTCAACAAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
39582 TGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
39633 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
39684 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAGGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
* *
39735 TGTCCGCTCCCTATTCATTCAGAGAGTATAAGACTCAATCTTCAAGGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
39786 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAGGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
39837 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
39888 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
39939 TGTCCACTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
* * *
39990 TGTTCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAAC
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
40036 AAACAAATTT
Statistics
Matches: 563, Mismatches: 44, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
51 489 0.87
52 1 0.00
55 36 0.06
56 37 0.07
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (51 bp):
TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
Found at i:40329 original size:17 final size:17
Alignment explanation
Indices: 40297--40329 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40287 TATCTTCATC
40297 TCAATGCTTCAATATCT
1 TCAATGCTTCAATATCT
40314 TCAAT-CTTCAACTATC
1 TCAATGCTTCAA-TATC
40330 ATTGGGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.39
Consensus pattern (17 bp):
TCAATGCTTCAATATCT
Found at i:41379 original size:27 final size:26
Alignment explanation
Indices: 41349--41412 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 26
41339 TTGAACCCTC
41349 CTTTTATTTCTCTTTTTCCATTTTTCT
1 CTTTT-TTTCTCTTTTTCCATTTTTCT
*
41376 CTTTTTCTTC-CATTTTCCATTTTTTCT
1 CTTTTT-TTCTCTTTTTCCA-TTTTTCT
41403 CTTTTTTTCT
1 CTTTTTTTCT
41413 TTTCGTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 12 0.36
27 21 0.64
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.70
Consensus pattern (26 bp):
CTTTTTTTCTCTTTTTCCATTTTTCT
Found at i:41399 original size:19 final size:19
Alignment explanation
Indices: 41364--41402 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41354 ATTTCTCTTT
*
41364 TTCCATTTTTCTCTTTTTC
1 TTCCATTTTCCTCTTTTTC
41383 TTCCATTTTCCAT-TTTTTC
1 TTCCATTTTCC-TCTTTTTC
41402 T
1 T
41403 CTTTTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.67
Consensus pattern (19 bp):
TTCCATTTTCCTCTTTTTC
Found at i:41456 original size:18 final size:19
Alignment explanation
Indices: 41433--41471 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
41423 TCCATCATTT
41433 TTTTCTCATTT-TTTCTTC
1 TTTTCTCATTTATTTCTTC
*
41451 TTTTCTCTTTTATTTCTTC
1 TTTTCTCATTTATTTCTTC
41470 TT
1 TT
41472 CAAGCAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTCTCATTTATTTCTTC
Found at i:51175 original size:44 final size:46
Alignment explanation
Indices: 51111--51208 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 46
51101 TTGTTATCCA
51111 CAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC-TTATT
1 CAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATT
* *
51156 CAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATT
1 CAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATT
51202 CGAAAAA
1 C-AAAAA
51209 AACGAAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
44 28 0.58
45 9 0.19
46 6 0.12
47 5 0.10
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (46 bp):
CAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATT
Found at i:54453 original size:2 final size:2
Alignment explanation
Indices: 54448--54496 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
54438 ATCACACACA
*
54448 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54489 AT AT AT AT
1 AT AT AT AT
54497 CTGAGATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55384 original size:15 final size:15
Alignment explanation
Indices: 55364--55402 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
55354 TATCATAACC
55364 TTTAGCGGCGTTAAT
1 TTTAGCGGCGTTAAT
55379 TTTAGCGGCGTTAAT
1 TTTAGCGGCGTTAAT
*
55394 TTCAGCGGC
1 TTTAGCGGC
55403 ACTTTTAGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (15 bp):
TTTAGCGGCGTTAAT
Found at i:62333 original size:13 final size:14
Alignment explanation
Indices: 62315--62348 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
62305 ACACTAATTT
62315 TAAATATTCG-ATA
1 TAAATATTCGAATA
62328 TAAATA-TCGAATA
1 TAAATATTCGAATA
62341 TAAATATT
1 TAAATATT
62349 TTAAGATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 15 0.79
14 1 0.05
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (14 bp):
TAAATATTCGAATA
Found at i:69831 original size:19 final size:19
Alignment explanation
Indices: 69790--69843 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
69780 AAATAGAGAT
* ** *
69790 ATCAGAAATCATAGTAGAG
1 ATCAGAGATCATAACAGAA
69809 ATCAGAGATCATAACAGAA
1 ATCAGAGATCATAACAGAA
*
69828 ATCAGAGATCAGAACA
1 ATCAGAGATCATAACA
69844 TATATCAAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.17
Consensus pattern (19 bp):
ATCAGAGATCATAACAGAA
Found at i:69850 original size:19 final size:19
Alignment explanation
Indices: 69809--69878 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
69799 CATAGTAGAG
* *
69809 ATCAGAGATCATAACAGAA
1 ATCAGAGATCAGAACAAAA
* *
69828 ATCAGAGATCAGAACATAT
1 ATCAGAGATCAGAACAAAA
* * *
69847 ATCAAAGTTCAGAGCAAAA
1 ATCAGAGATCAGAACAAAA
*
69866 ATCAGAGGTCAGA
1 ATCAGAGATCAGA
69879 CTGTATTTCA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.17
Consensus pattern (19 bp):
ATCAGAGATCAGAACAAAA
Found at i:71326 original size:18 final size:18
Alignment explanation
Indices: 71303--71344 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
71293 AATTTACGTT
71303 AGAAACTAAACTTAATTG
1 AGAAACTAAACTTAATTG
*
71321 AGAAACTGAACTTAATTG
1 AGAAACTAAACTTAATTG
71339 AGAAAC
1 AGAAAC
71345 CAACTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (18 bp):
AGAAACTAAACTTAATTG
Found at i:72327 original size:14 final size:15
Alignment explanation
Indices: 72280--72327 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
72270 TCCTAATCCC
*
72280 TAAACCC-AAAATTC
1 TAAACCCTAAAATTA
*
72294 TAAAACTCTAAAATTA
1 T-AAACCCTAAAATTA
72310 TAAACCCTAAAA-TA
1 TAAACCCTAAAATTA
72324 TAAA
1 TAAA
72328 TATTAAACGC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 7 0.24
15 15 0.52
16 7 0.24
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAACCCTAAAATTA
Found at i:79581 original size:23 final size:23
Alignment explanation
Indices: 79555--79606 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
79545 CAAATGTTCT
* * *
79555 GACCAGGCCGGGACCAATGAGCG
1 GACCAGGCCAGAACCAATAAGCG
*
79578 GACCAGGTCAGAACCAATAAGCG
1 GACCAGGCCAGAACCAATAAGCG
79601 GACCAG
1 GACCAG
79607 TCCGCCCGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.29, G:0.33, T:0.06
Consensus pattern (23 bp):
GACCAGGCCAGAACCAATAAGCG
Found at i:79900 original size:14 final size:14
Alignment explanation
Indices: 79883--79917 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
79873 ATATGTTCGT
79883 TTATGTTTGTTCAG
1 TTATGTTTGTTCAG
*
79897 TTATGTTTGTTCAT
1 TTATGTTTGTTCAG
79911 TTATGTT
1 TTATGTT
79918 CGAACAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.06, G:0.17, T:0.63
Consensus pattern (14 bp):
TTATGTTTGTTCAG
Found at i:81410 original size:232 final size:232
Alignment explanation
Indices: 81004--81468 Score: 858
Period size: 232 Copynumber: 2.0 Consensus size: 232
80994 GTGTCTGAAC
81004 ACTTAATATGTAATCACATGGCATACTGTGCTCACAACAAATAAAAACATTACATAGCTTCAAAT
1 ACTTAATATGTAATCACATGGCATACTGTGCTCACAACAAATAAAAACATTACATAGCTTCAAAT
*
81069 ATTTGTTAAAGAATTTTAAATTTTATTAAAAATCTAATTAATTTCTTTCATTATCACAGTCGATA
66 ATTTGTTAAAGAATTCTAAATTTTATTAAAAATCTAATTAATTTCTTTCATTATCACAGTCGATA
* *
81134 CGTGAATAGTTTTCTGATGTGTGAATTTCTCTCGGCACACATTAGCGGGGATAATGGCTTCTGAG
131 CGTGAATAGTGTTCTGATGTGTGAATTTCTCTCGGCACACATTAGCAGGGATAATGGCTTCTGAG
81199 AAATCTACTGTGGCGATCCGATCATCTCCTCAAAGTT
196 AAATCTACTGTGGCGATCCGATCATCTCCTCAAAGTT
*
81236 ACTTAATATGTAATCACATGGCATATTGTGCTCACAACAAATAAAAACATTACATAGCTTCAAAT
1 ACTTAATATGTAATCACATGGCATACTGTGCTCACAACAAATAAAAACATTACATAGCTTCAAAT
81301 ATTTGTTAAAGAATTCTAAATTTTATTAAAAATCTAATTAATTTCTTTCATTATCACAGTCGATA
66 ATTTGTTAAAGAATTCTAAATTTTATTAAAAATCTAATTAATTTCTTTCATTATCACAGTCGATA
** *
81366 CGTGAATAGTGTTCTGATGTGTGGGTTTCTCTCGGCACACATTAGCAGGGCTAATGGCTTCTGAG
131 CGTGAATAGTGTTCTGATGTGTGAATTTCTCTCGGCACACATTAGCAGGGATAATGGCTTCTGAG
*
81431 AAATCTGCTGTGGCGATCCGATCATCTCCTCAAAGTT
196 AAATCTACTGTGGCGATCCGATCATCTCCTCAAAGTT
81468 A
1 A
81469 TTTCTTTTCT
Statistics
Matches: 225, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
232 225 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (232 bp):
ACTTAATATGTAATCACATGGCATACTGTGCTCACAACAAATAAAAACATTACATAGCTTCAAAT
ATTTGTTAAAGAATTCTAAATTTTATTAAAAATCTAATTAATTTCTTTCATTATCACAGTCGATA
CGTGAATAGTGTTCTGATGTGTGAATTTCTCTCGGCACACATTAGCAGGGATAATGGCTTCTGAG
AAATCTACTGTGGCGATCCGATCATCTCCTCAAAGTT
Found at i:92665 original size:15 final size:16
Alignment explanation
Indices: 92647--92684 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
92637 ATGAAAATTT
*
92647 ATTTTATTTTCTT-TA
1 ATTTTATTTTCTTAAA
*
92662 ATTTTCTTTTCTTAAA
1 ATTTTATTTTCTTAAA
92678 ATTTTAT
1 ATTTTAT
92685 AAATTTGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTATTTTCTTAAA
Found at i:108692 original size:21 final size:21
Alignment explanation
Indices: 108666--108752 Score: 88
Period size: 21 Copynumber: 4.2 Consensus size: 21
108656 GATTTACATA
108666 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
108687 TTCGCATTGTGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * ** *
108708 TTTGCGTTGCGATTTTCCAAA
1 TTCGCATTGCGATAGTCCAAG
* *
108729 TACG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
108748 TTCGC
1 TTCGC
108753 GCGAGACGAC
Statistics
Matches: 51, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
19 14 0.27
21 37 0.73
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:108773 original size:6 final size:6
Alignment explanation
Indices: 108758--108790 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
108748 TTCGCGCGAG
108758 ACGA-C ACGACC ACGACC ACGACC ACGACC ACGA
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGA
108791 GACGACACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.36, C:0.45, G:0.18, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:111644 original size:18 final size:18
Alignment explanation
Indices: 111621--111669 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
111611 AGATTGGTGC
111621 AATTGATTTCTTCTGAGA
1 AATTGATTTCTTCTGAGA
111639 AATTGATTTCTTCTGAGA
1 AATTGATTTCTTCTGAGA
111657 AATTGATTTCTTC
1 AATTGATTTCTTC
111670 GACTTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (18 bp):
AATTGATTTCTTCTGAGA
Found at i:115936 original size:51 final size:51
Alignment explanation
Indices: 115871--116121 Score: 301
Period size: 51 Copynumber: 5.0 Consensus size: 51
115861 GTGTGCTCCC
* *
115871 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCCAGTAAGT
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGA
* * * *
115922 CTCATCAGCGAAGTGATGAGAAAAACCAATCCGGGGCAACCTCGAGTAAGA
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGA
* * * *
115973 CTCATCAGCCAAGTGATAAGAAGAACCAATCCAGGGCAACCTTGAGTAAGA
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGA
* * * * * * *
116024 --C-TCAGCAAAATGATGAGGACAACCAATCCAGAGAGACCTTGAATAAGA
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGA
* * *
116072 GTCATCAGCAAAGGGATGAGAAGAACCAATCCGGGGAAACCTCGAGTAAG
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAG
116122 CTTAAAAGAA
Statistics
Matches: 168, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
48 38 0.23
49 1 0.01
50 1 0.01
51 128 0.76
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.14
Consensus pattern (51 bp):
CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGA
Found at i:116079 original size:99 final size:101
Alignment explanation
Indices: 115871--116122 Score: 312
Period size: 99 Copynumber: 2.5 Consensus size: 101
115861 GTGTGCTCCC
* * * *
115871 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCCAGTAAGTCTCATCAGCGAAGT
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAG-CACATCAGCAAAAT
* * *
115936 GATGAGAAAAACCAATCCGGGGCAACCTCGAGTAAGA
65 GATGAGAAAAACCAATCCAGAGCAACCTCGAATAAGA
* * * *
115973 CTCATCAGCCAAGTGATAAGAAGAACCAATCCAGGGCAACCTTGAGTAAG-AC-TCAGCAAAATG
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGCACATCAGCAAAATG
* * *
116036 ATGAGGACAACCAATCCAGAG-AGACCTTGAATAAGA
66 ATGAGAAAAACCAATCCAGAGCA-ACCTCGAATAAGA
* * *
116072 GTCATCAGCAAAGGGATGAGAAGAACCAATCCGGGGAAACCTCGAGTAAGC
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGC
116123 TTAAAAGAAA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
98 1 0.01
99 80 0.63
100 1 0.01
102 45 0.35
ACGTcount: A:0.39, C:0.23, G:0.24, T:0.14
Consensus pattern (101 bp):
CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGCACATCAGCAAAATG
ATGAGAAAAACCAATCCAGAGCAACCTCGAATAAGA
Found at i:123635 original size:16 final size:16
Alignment explanation
Indices: 123614--123647 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
123604 TGACTATTCA
*
123614 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
123630 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
123646 CG
1 CG
123648 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:145725 original size:36 final size:36
Alignment explanation
Indices: 145651--145737 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
145641 CACCCCTAGC
* ** *
145651 GAACATGTTCGTTTATATGTTCATGAATGTATTCAT
1 GAACATGTTCATTTATATGTTCACAAAAGTATTCAT
* * *
145687 GAACATGTTTATTTATATGTTCACAAAAGTGTTTAT
1 GAACATGTTCATTTATATGTTCACAAAAGTATTCAT
* *
145723 GAACAAGTTCGTTTA
1 GAACATGTTCATTTA
145738 ACGTTCATTA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (36 bp):
GAACATGTTCATTTATATGTTCACAAAAGTATTCAT
Found at i:146023 original size:12 final size:12
Alignment explanation
Indices: 146002--146047 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
145992 GAACGAGTTG
*
146002 ATAAATGAACTC
1 ATAAACGAACTC
146014 ATAAACGAACTC
1 ATAAACGAACTC
*
146026 ATAAACGAGCTC
1 ATAAACGAACTC
146038 ATAAACGAAC
1 ATAAACGAAC
146048 CGAACACACC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.50, C:0.22, G:0.11, T:0.17
Consensus pattern (12 bp):
ATAAACGAACTC
Done.