Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001140.1 Hibiscus syriacus cultivar Beakdansim tig00002274_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: 59355
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:495 original size:3 final size:3
Alignment explanation
Indices: 487--548 Score: 67
Period size: 3 Copynumber: 20.7 Consensus size: 3
477 AATAGTATAT
*
487 TTA TTA TTA TATA TT- TTA TTA TTA TTA TCTA TTA -TA TT- TTA CTTT
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA -TTA
532 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
549 CTTTTTTCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
2 6 0.12
3 37 0.73
4 8 0.16
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:604 original size:23 final size:25
Alignment explanation
Indices: 563--616 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
553 TTTCATTTTA
*
563 ATATA-TATATATTATCACTATTAT
1 ATATACTATATATTATCACTAGTAT
587 AT-TACTATAT-TTATCACTAGTAT
1 ATATACTATATATTATCACTAGTAT
610 ATATACT
1 ATATACT
617 TTGATATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (25 bp):
ATATACTATATATTATCACTAGTAT
Found at i:2596 original size:16 final size:18
Alignment explanation
Indices: 2564--2615 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
2554 TTATGTTTTA
2564 TATATTTTTAAAAAAAA-
1 TATATTTTTAAAAAAAAT
2581 TATTATTTTTAAAAAAAAT
1 TA-TATTTTTAAAAAAAAT
2600 TATATTTTTAAAAAAA
1 TATATTTTTAAAAAAA
2616 TTGAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.06
18 29 0.88
19 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATATTTTTAAAAAAAAT
Found at i:6363 original size:10 final size:10
Alignment explanation
Indices: 6348--6406 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
6338 CATTTAATAA
6348 ATAAACGAAC
1 ATAAACGAAC
6358 ATAAACGAAC
1 ATAAACGAAC
** *
6368 ACGAAC-ATAA
1 ATAAACGA-AC
6378 ATGAACACGAAC
1 AT-AA-ACGAAC
6390 ATAAACGAAC
1 ATAAACGAAC
6400 ATAAACG
1 ATAAACG
6407 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 1 0.03
10 29 0.74
11 3 0.08
12 5 0.13
13 1 0.03
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:6373 original size:16 final size:16
Alignment explanation
Indices: 6352--6400 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
6342 TAATAAATAA
6352 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
6368 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
6384 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
6400 A
1 A
6401 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:7506 original size:24 final size:24
Alignment explanation
Indices: 7478--7547 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
7468 AGATTGGGTT
** *
7478 AAACATAAATGAAAGAACATAAAC
1 AAACATAACCGAACGAACATAAAC
7502 AAACATAACCGAACGAACATAAAC
1 AAACATAACCGAACGAACATAAAC
*
7526 GAACATAACCGAACGAACATAA
1 AAACATAACCGAACGAACATAA
7548 CTGAACGTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.60, C:0.20, G:0.10, T:0.10
Consensus pattern (24 bp):
AAACATAACCGAACGAACATAAAC
Found at i:7522 original size:14 final size:14
Alignment explanation
Indices: 7503--7554 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
7493 AACATAAACA
7503 AACATAACCGAACG
1 AACATAACCGAACG
7517 AACAT-A---AACG
1 AACATAACCGAACG
7527 AACATAACCGAACG
1 AACATAACCGAACG
*
7541 AACATAACTGAACG
1 AACATAACCGAACG
7555 TTCACGAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 9 0.27
11 1 0.03
13 1 0.03
14 22 0.67
ACGTcount: A:0.52, C:0.25, G:0.13, T:0.10
Consensus pattern (14 bp):
AACATAACCGAACG
Found at i:10354 original size:21 final size:21
Alignment explanation
Indices: 10309--10364 Score: 89
Period size: 20 Copynumber: 2.7 Consensus size: 21
10299 AATTATTTTT
10309 AAAATATAAAAATGATATTTC
1 AAAATATAAAAATGATATTTC
10330 -AAATATAAAAATGATATTTC
1 AAAATATAAAAATGATATTTC
10350 AAAAT-TGAAAAATGA
1 AAAATAT-AAAAATGA
10365 AAATAATCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 21 0.64
21 12 0.36
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAATATAAAAATGATATTTC
Found at i:17010 original size:65 final size:65
Alignment explanation
Indices: 16879--17034 Score: 160
Period size: 65 Copynumber: 2.4 Consensus size: 65
16869 CACACCCATT
* *
16879 TCGAA-TGCATTTTATGCACCGATGCACAGTCATGCTTAGATGCACTCAAGATTTTATTAAAACA
1 TCGAATTGCATTTTATGCACCGATGCACAGTCATGCATAGATGCACTCAAGATATTATTAAAACA
* * * * *
16943 TCGAATTG-ATTTTGTGTACCGATGCACA-TACCATGCATCGATGCACTCCAGGATATT-TTGAA
1 TCGAATTGCATTTTATGCACCGATGCACAGT--CATGCATAGATGCACT-CAAGATATTATTAAA
17005 ACA
63 ACA
* * *
17008 TCGAA-TGCAATTAATGCATCGATGCAC
1 TCGAATTGCATTTTATGCACCGATGCAC
17035 CTTTAGTGTA
Statistics
Matches: 75, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
63 1 0.01
64 25 0.33
65 42 0.56
66 7 0.09
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (65 bp):
TCGAATTGCATTTTATGCACCGATGCACAGTCATGCATAGATGCACTCAAGATATTATTAAAACA
Found at i:20205 original size:131 final size:130
Alignment explanation
Indices: 20037--20372 Score: 429
Period size: 131 Copynumber: 2.6 Consensus size: 130
20027 CGTTCGGAGT
* * * * *
20037 AATAAATGAATGCTTTAAGGCATGATAGGTCATTTATTCTCGATTGGAAATAATTTGATATTGTT
1 AATAAATG-ATACTTTAAGGCATGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATC
* * * *
20102 GTTTTCTTTCGAATTAATATCGATTTTTAAGATGGAATAGTGATATCTCTTCATTTCGATTAGAG
65 GTTTTCTCTCGAATTAATATCGAATTTTAAGACGGAATAGTGATATCTATTCATTTCGATTAGAG
20167 C
130 C
* * * *
20168 AATAAATGACTACTTTAAGGCATGAAAGATCATTTATTCTCGATTGAAAATCATTAGTTATTATC
1 AATAAATGA-TACTTTAAGGCATGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATC
* *
20233 GTTTTCTCTCGAATTGATATCGAATTTTAAGACGGAATAGTGATATCTATTCATTTCGATTGGAG
65 GTTTTCTCTCGAATTAATATCGAATTTTAAGACGGAATAGTGATATCTATTCATTTCGATTAGAG
*
20298 T
130 C
** * * * * *
20299 AATAAATGATTGTTTCAAGGCATGAGAGGTAATTTATTATAGATTAGAAATAATTAGATATTATC
1 AATAAATGATACTTT-AAGGCATGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATC
*
20364 GTTCTCTCT
65 GTTTTCTCT
20373 TAAAATTATT
Statistics
Matches: 175, Mismatches: 28, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
130 5 0.03
131 170 0.97
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (130 bp):
AATAAATGATACTTTAAGGCATGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCG
TTTTCTCTCGAATTAATATCGAATTTTAAGACGGAATAGTGATATCTATTCATTTCGATTAGAGC
Found at i:25799 original size:22 final size:23
Alignment explanation
Indices: 25751--25808 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 23
25741 ACCGGAGGGG
25751 AGTATCGGTACCACAGCATACATAGA
1 AGTATCGGTACCACAG---ACATAGA
25777 AGTATCGGTACCACAG-CATAGA
1 AGTATCGGTACCACAGACATAGA
25799 AGTAT-GGTAC
1 AGTATCGGTAC
25809 TGTGATGGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.16
22 11 0.34
26 16 0.50
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (23 bp):
AGTATCGGTACCACAGACATAGA
Found at i:33794 original size:7 final size:7
Alignment explanation
Indices: 33784--33937 Score: 93
Period size: 7 Copynumber: 20.6 Consensus size: 7
33774 AAAAAAGAAG
33784 AGAAAAA
1 AGAAAAA
33791 AGAAAAA
1 AGAAAAA
33798 AG--AAA
1 AGAAAAA
33803 AGAAAGAA
1 AGAAA-AA
33811 AGAAAAA
1 AGAAAAA
33818 ATGATGAAAA
1 A-GA--AAAA
33828 ATGAAAAA
1 A-GAAAAA
*
33836 TGAAAAA
1 AGAAAAA
33843 A-AAGAAA
1 AGAA-AAA
*
33850 A-AAGAA
1 AGAAAAA
33856 AGAAATAA
1 AGAAA-AA
33864 AGAAAAA
1 AGAAAAA
33871 ATGATGAAAA
1 A-GA--AAAA
33881 ATGAAAAA
1 A-GAAAAA
*
33889 TGAAAAA
1 AGAAAAA
33896 A-AAAGAA
1 AGAAA-AA
*
33903 TGAAAAA
1 AGAAAAA
33910 AGAAAAA
1 AGAAAAA
*
33917 AAATGAAAA
1 AGA--AAAA
33926 AGAAAAA
1 AGAAAAA
33933 TAGAA
1 -AGAA
33938 TAAACAAAAG
Statistics
Matches: 120, Mismatches: 10, Indels: 33
0.74 0.06 0.20
Matches are distributed among these distances:
5 5 0.04
6 8 0.07
7 52 0.43
8 33 0.28
9 6 0.05
10 16 0.13
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.08
Consensus pattern (7 bp):
AGAAAAA
Found at i:33836 original size:17 final size:15
Alignment explanation
Indices: 33784--33937 Score: 81
Period size: 17 Copynumber: 9.9 Consensus size: 15
33774 AAAAAAGAAG
*
33784 AGAAAAAAGA-AAAA
1 AGAAAAATGAGAAAA
33798 AG-AAAA-GA-AAGAA
1 AGAAAAATGAGAA-AA
33811 AGAAAAAATGATGAAAA
1 AG-AAAAATGA-GAAAA
*
33828 ATGAAAAATGAAAAAAA
1 A-GAAAAATG-AGAAAA
*
33845 AGAAAAAAGAAAGAAATAA
1 AGAAAAATG--AG-AA-AA
33864 AGAAAAAATGATGAAAA
1 AG-AAAAATGA-GAAAA
33881 ATGAAAAATGA-AAAA
1 A-GAAAAATGAGAAAA
33896 A-AAAGAATGA-AAAA
1 AGAAA-AATGAGAAAA
**
33910 AGAAAAAAAATGAAAA
1 AGAAAAATGA-GAAAA
33926 AGAAAAAT-AGAA
1 AGAAAAATGAGAA
33938 TAAACAAAAG
Statistics
Matches: 115, Mismatches: 7, Indels: 36
0.73 0.04 0.23
Matches are distributed among these distances:
12 4 0.03
13 11 0.10
14 18 0.16
15 13 0.11
16 20 0.17
17 28 0.24
18 10 0.09
19 5 0.04
20 6 0.05
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.08
Consensus pattern (15 bp):
AGAAAAATGAGAAAA
Found at i:33899 original size:54 final size:55
Alignment explanation
Indices: 33765--33902 Score: 217
Period size: 53 Copynumber: 2.5 Consensus size: 55
33755 GTACTTCGCC
* *
33765 TGAAGAATGAAAAAAGAAGAGAAAAAAGAAAAAAGAAAAGAAAGAAAGAAAAAATGA
1 TGAAAAATGAAAAATGAA-A-AAAAAAGAAAAAAGAAAAGAAAGAAAGAAAAAATGA
*
33822 TGAAAAATGAAAAATG-AAAAAAAAGAAAAAAG-AAAGAAATAAAGAAAAAATGA
1 TGAAAAATGAAAAATGAAAAAAAAAGAAAAAAGAAAAGAAAGAAAGAAAAAATGA
33875 TGAAAAATGAAAAATGAAAAAAAAAGAA
1 TGAAAAATGAAAAATGAAAAAAAAAGAA
33903 TGAAAAAAGA
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
53 36 0.47
54 25 0.32
55 1 0.01
56 1 0.01
57 14 0.18
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (55 bp):
TGAAAAATGAAAAATGAAAAAAAAAGAAAAAAGAAAAGAAAGAAAGAAAAAATGA
Found at i:33912 original size:54 final size:56
Alignment explanation
Indices: 33765--33926 Score: 185
Period size: 53 Copynumber: 2.9 Consensus size: 56
33755 GTACTTCGCC
* * * *
33765 TGAAGAATGAAAAAAGAAGAGAAAA-AAGAAAAAAGAAAAGAAAGAAAGAAAAAATGA
1 TGAAAAATGAAAAATGAAAAAAAAAGAAGAAAAAAG-AAAGAAAG-AAGAAAAAATGA
*
33822 TGAAAAATGAAAAATG---AAAAAA-AAGAAAAAAGAAAGAAATAAAGAAAAAATGA
1 TGAAAAATGAAAAATGAAAAAAAAAGAAGAAAAAAGAAAGAAA-GAAGAAAAAATGA
33875 TGAAAAATGAAAAATGAAAAAAAAAGAATGAAAAAAGAAA-AAA-AATGAAAAA
1 TGAAAAATGAAAAATGAAAAAAAAAGAA-GAAAAAAGAAAGAAAGAA-GAAAAA
33927 GAAAAATAGA
Statistics
Matches: 94, Mismatches: 4, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
53 35 0.37
54 15 0.16
55 2 0.02
56 12 0.13
57 19 0.20
58 11 0.12
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (56 bp):
TGAAAAATGAAAAATGAAAAAAAAAGAAGAAAAAAGAAAGAAAGAAGAAAAAATGA
Found at i:33931 original size:21 final size:20
Alignment explanation
Indices: 33784--33932 Score: 75
Period size: 20 Copynumber: 7.3 Consensus size: 20
33774 AAAAAAGAAG
33784 AGAAAAAAGAAAAAA-G-AAA
1 AGAAAAAA-AAAAAATGAAAA
33803 AGAAAGAAAGAAAAAATG---A
1 AGAAA-AAA-AAAAAATGAAAA
* **
33822 TGAAAAATGAAAAATGAAAA
1 AGAAAAAAAAAAAATGAAAA
33842 A-AAAGAAAAAAGAAA-GAAATAA
1 AGAAA-AAAAAA-AAATG-AA-AA
33864 AGAAAAAATGATGAAAAATGAAAA
1 AGAAAAAA--A--AAAAATGAAAA
*
33888 ATGAAAAAAAAAGAATG--AA
1 A-GAAAAAAAAAAAATGAAAA
*
33907 A-AAAGAAAAAAAATGAAAA
1 AGAAAAAAAAAAAATGAAAA
33926 AGAAAAA
1 AGAAAAA
33933 TAGAATAAAC
Statistics
Matches: 101, Mismatches: 10, Indels: 37
0.68 0.07 0.25
Matches are distributed among these distances:
17 19 0.19
18 2 0.02
19 19 0.19
20 20 0.20
21 12 0.12
22 6 0.06
23 4 0.04
24 4 0.04
25 12 0.12
26 3 0.03
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.07
Consensus pattern (20 bp):
AGAAAAAAAAAAAATGAAAA
Found at i:34276 original size:2 final size:2
Alignment explanation
Indices: 34269--34295 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34259 AGTAATATTA
34269 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
34296 ACACTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36225 original size:134 final size:133
Alignment explanation
Indices: 36059--36456 Score: 471
Period size: 134 Copynumber: 3.0 Consensus size: 133
36049 GTGAATCGAA
36059 CTCGATTAAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTCCTCATATCTGATTTTCCCTCA
1 CTCGATTAAATCTT-CCTGAAGAACAGTGGAATGAATCAACGTCCTCATATCTGATTTTCCCTCA
* * * * *
36124 TGAAAAAGGGGAACAGACCCCTCTCTTTCAAGATTTGATATTCCTTGAGTAACAGTGGAACAAGT
65 AGAAGAAGAGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCTTGAGTAACAGTGGAACAAGT
36189 ATAC
130 ATAC
* *
36193 CTCGATTTAATCTTCCTTGAAGAACAGTGGAATGAATCAACGTCCTCAAATCTGATTTTCCCTCA
1 CTCGATTAAATCTTCC-TGAAGAACAGTGGAATGAATCAACGTCCTCATATCTGATTTTCCCTCA
* * * * *
36258 AGAAGAAGCA-TAACATATCCATCTCTTTCTAGATTTGATATTCCCT-AGGTAACAGTGGAACAA
65 AGAAGAAG-AGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCTTGA-GTAACAGTGGAACAA
*
36321 GTATGC
128 GTATAC
* * * * * * * * *
36327 TTCGATTCAATGTTTCC-CAAGTGACAGTGGAATGAATCAATGTCCCCATATTTAATTTTCCCTC
1 CTCGATTAAAT-CTTCCTGAAG-AACAGTGGAATGAATCAACGTCCTCATATCTGATTTTCCCTC
* * **
36391 AAGAAGAAGAGGAACAAATCACTCTCTTTCAAGATTTTATATT-CTCTGAGTAGTAGTGGAACAA
64 AAGAAGAAGAGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCT-TGAGTAACAGTGGAACAA
36455 GT
128 GT
36457 TTGCTTCGAC
Statistics
Matches: 225, Mismatches: 31, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
133 8 0.04
134 212 0.94
135 5 0.02
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (133 bp):
CTCGATTAAATCTTCCTGAAGAACAGTGGAATGAATCAACGTCCTCATATCTGATTTTCCCTCAA
GAAGAAGAGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCTTGAGTAACAGTGGAACAAGTA
TAC
Found at i:38816 original size:131 final size:131
Alignment explanation
Indices: 38673--39037 Score: 463
Period size: 131 Copynumber: 2.8 Consensus size: 131
38663 TAAATATTGA
* *
38673 GAATAGTAATATCTTCTTATTTCGGTCGGAGTAATAAATTACTGCTTTAAGGCATGAGAGGTCAT
1 GAATAGTGATATCTTCTTATTTCGGTCGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
** * * * * *
38738 TTATTCTTTATTGGAAATAATTTGATATTGTCGTTTTCTCTCAAATTAATATCTATTTTTAAGAT
66 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCAAATCAATATCGATTTTTAAGAC
38803 G
131 G
* * *
38804 GAATAGTGATATC-TCTTCATTTCGATTGGAGCAATAAATGACTGCTTTAAGGCATGAGAGGTCA
1 GAATAGTGATATCTTCTT-ATTTCGGTCGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
* * * *
38868 TTTATTCTCGATCGAAAATCATTAGATATTATCGTTTTCTCTCGAATCAATATCGATTTTTAAGA
65 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCAAATCAATATCGATTTTTAAGA
38933 CG
130 CG
* * * *
38935 GAATAGTG-TATATTC--ATTTC-GACTGGAGTAATAAATGATTG-TTTCAAGGCATAAGAGGTC
1 GAATAGTGATATCTTCTTATTTCGGTC-GGAGTAATAAATGACTGCTTT-AAGGCATGAGAGGTC
* *
38995 ATTTATTCTCGATTAGAAATAATTAGATATTATCGTTATCTCT
64 ATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCT
39038 TAAAATTATT
Statistics
Matches: 202, Mismatches: 28, Indels: 11
0.84 0.12 0.05
Matches are distributed among these distances:
127 3 0.01
128 72 0.36
130 7 0.03
131 120 0.59
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (131 bp):
GAATAGTGATATCTTCTTATTTCGGTCGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCAAATCAATATCGATTTTTAAGAC
G
Found at i:48771 original size:15 final size:16
Alignment explanation
Indices: 48734--48776 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
48724 TAGGACTTTA
48734 TTTATTTTGATTTTCC
1 TTTATTTTGATTTTCC
48750 TTTATTTT-AGTTTTCC
1 TTTATTTTGA-TTTTCC
48766 -TTA-TTTGATTT
1 TTTATTTTGATTT
48777 AGACTCGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 14 0.56
ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70
Consensus pattern (16 bp):
TTTATTTTGATTTTCC
Found at i:54314 original size:2 final size:2
Alignment explanation
Indices: 54307--54345 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
54297 TTTTTAAAAT
54307 TA TA TA TA 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 TA TA TA TA T
54346 CCTTTTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55877 original size:2 final size:2
Alignment explanation
Indices: 55870--55906 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
55860 ATTAAAATCC
55870 TA TA TA 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 TA TA TA T
55907 TGAACAATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56617 original size:20 final size:20
Alignment explanation
Indices: 56572--56617 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
56562 GACCAACAAA
*
56572 ATCGCAATGCGATCGCTAAT
1 ATCGCAACGCGATCGCTAAT
* *
56592 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCGCTAAT
56611 ATCGCAA
1 ATCGCAA
56618 ATTCGCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCGCTAAT
Found at i:56721 original size:20 final size:21
Alignment explanation
Indices: 56696--56747 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
56686 TTTTCCCAAT
*
56696 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
56716 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
56737 TCGCAATGCGA
1 TCGCAATGCGA
56748 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:56761 original size:20 final size:20
Alignment explanation
Indices: 56736--56849 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
56726 AATTGGGAAA
*
56736 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
56756 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
56776 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
56797 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
56817 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
56837 TTCGCAACGCGAT
1 ATCGCAACGCGAT
56850 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:56780 original size:61 final size:61
Alignment explanation
Indices: 56733--56849 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
56723 GCGAATTGGG
* * * * *
56733 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
56794 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
56850 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:57443 original size:20 final size:19
Alignment explanation
Indices: 57403--57448 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
57393 GCAACGAGAT
*
57403 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
57422 AATTCGCAACGCGAAACCAA
1 AA-TCGCAACGCGAAACAAA
57442 AATCGCA
1 AATCGCA
57449 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.48, C:0.26, G:0.15, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:57466 original size:19 final size:19
Alignment explanation
Indices: 57444--57628 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
57434 GAAACCAAAA
*
57444 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
57463 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
57482 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
57501 TCGCAGTTGCGCTTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
57521 TCACGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
57537 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
57554 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
57568 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
57587 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
57607 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
57627 TC
1 TC
57629 AACCAAAAGA
Statistics
Matches: 134, Mismatches: 19, Indels: 26
0.75 0.11 0.15
Matches are distributed among these distances:
14 20 0.15
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.44
20 47 0.35
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:57521 original size:39 final size:38
Alignment explanation
Indices: 57444--57628 Score: 156
Period size: 33 Copynumber: 5.1 Consensus size: 38
57434 GAAACCAAAA
*
57444 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
57482 TCGCGTTGCGATTTTTATTTCGCAGTTGCGCTTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * * **
57521 TCACGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
57554 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
57587 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
57627 TC
1 TC
57629 AACCAAAAGA
Statistics
Matches: 120, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
31 3 0.03
33 36 0.30
34 10 0.08
35 1 0.01
36 3 0.03
38 21 0.17
39 28 0.23
40 18 0.15
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:57605 original size:20 final size:20
Alignment explanation
Indices: 57571--57628 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
57561 GCGATTCTCT
**
57571 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
57591 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
57611 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
57629 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:58942 original size:20 final size:20
Alignment explanation
Indices: 58914--58971 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
58904 ATTCATTTGA
58914 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
58934 CTATGGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
58954 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
58972 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:59014 original size:14 final size:15
Alignment explanation
Indices: 58994--59066 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
58984 TGAAAATCGC
58994 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
59009 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
59026 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
59044 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
59060 -TTGCGAT
1 ATTGCGAT
59067 AGTCTGTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:59031 original size:19 final size:19
Alignment explanation
Indices: 58990--59056 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
58980 GAAATGAAAA
58990 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
59006 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
59023 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
59041 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
59057 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:59174 original size:14 final size:14
Alignment explanation
Indices: 59155--59191 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
59145 CATCAATTAA
59155 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
59169 ACAAATCATCTTTT
1 ACAAATCAACATTT
59183 ACAAATCAA
1 ACAAATCAA
59192 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Done.