Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002065.1 Hibiscus syriacus cultivar Beakdansim tig00004210_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: 70689
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:2442 original size:2 final size:2
Alignment explanation
Indices: 2435--2487 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2425 TACTTATGAG
2435 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2477 TA TA TA TA TA T
1 TA TA TA TA TA T
2488 TTACAATCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3033 original size:30 final size:30
Alignment explanation
Indices: 2999--3058 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2989 AATTAATAAA
*
2999 ACTTTGTTTCTTCGGGTAACCTTTTGCTTT
1 ACTTTGTTTCTTCCGGTAACCTTTTGCTTT
*
3029 ACTTTGTTTCTTCCTGTAACCTTTTGCTTT
1 ACTTTGTTTCTTCCGGTAACCTTTTGCTTT
3059 TGTTTCGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.10, C:0.22, G:0.13, T:0.55
Consensus pattern (30 bp):
ACTTTGTTTCTTCCGGTAACCTTTTGCTTT
Found at i:3913 original size:15 final size:17
Alignment explanation
Indices: 3882--3913 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
3872 ATGTATTTTT
3882 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
3899 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
3914 TTATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:4033 original size:23 final size:23
Alignment explanation
Indices: 4002--4050 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 23
3992 ATAATGTAAT
4002 AAAGAAAAGGAAAAGAAAATAA-CA
1 AAAGAAAAGGAAAA-AAAA-AACCA
*
4026 AAAG-AAAGTAAAAAAAAAACCA
1 AAAGAAAAGGAAAAAAAAAACCA
4048 AAA
1 AAA
4051 ATCATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 2 0.09
22 9 0.39
23 8 0.35
24 4 0.17
ACGTcount: A:0.78, C:0.06, G:0.12, T:0.04
Consensus pattern (23 bp):
AAAGAAAAGGAAAAAAAAAACCA
Found at i:4061 original size:18 final size:18
Alignment explanation
Indices: 4038--4075 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4028 AGAAAGTAAA
* *
4038 AAAAAAACCAAAAATCAT
1 AAAAAAACAAAAAATAAT
4056 AAAAAAACAAAAAATAAT
1 AAAAAAACAAAAAATAAT
4074 AA
1 AA
4076 TATGTAGCGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (18 bp):
AAAAAAACAAAAAATAAT
Found at i:9136 original size:30 final size:30
Alignment explanation
Indices: 9100--9157 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
9090 AAATTCACGA
* * * *
9100 GTTAAATTGATATTTTATTTAAAGTTTAGG
1 GTTAAATTAATATTCTATCTAAAATTTAGG
9130 GTTAAATTAATATTCTATCTAAAATTTA
1 GTTAAATTAATATTCTATCTAAAATTTA
9158 AGTATTATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.48
Consensus pattern (30 bp):
GTTAAATTAATATTCTATCTAAAATTTAGG
Found at i:12819 original size:36 final size:36
Alignment explanation
Indices: 12772--12842 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
12762 GTGTATTTTA
12772 TACGAAAATTGAAAAGAAAATTAATAAAGAATAAAT
1 TACGAAAATTGAAAAGAAAATTAATAAAGAATAAAT
12808 TACGAAAATTGAAAAGAAAATTAATAAAGAATAAA
1 TACGAAAATTGAAAAGAAAATTAATAAAGAATAAA
12843 CTAAATTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.65, C:0.03, G:0.11, T:0.21
Consensus pattern (36 bp):
TACGAAAATTGAAAAGAAAATTAATAAAGAATAAAT
Found at i:13304 original size:21 final size:23
Alignment explanation
Indices: 13269--13314 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
13259 TTTACTTTAC
*
13269 TTTAGTTTTTTTATTA-AAATTT
1 TTTAGTTTATTTATTATAAATTT
13291 TTTA-TTTATTTATTATTAAATTT
1 TTTAGTTTATTTATTA-TAAATTT
13314 T
1 T
13315 AAGTTTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 4 0.19
23 7 0.33
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTAGTTTATTTATTATAAATTT
Found at i:16618 original size:19 final size:19
Alignment explanation
Indices: 16594--16632 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
16584 ATAGTTATGG
*
16594 ACTATATGTTGACTCTTAT
1 ACTATATGTCGACTCTTAT
16613 ACTATATGTCGACTCTTAT
1 ACTATATGTCGACTCTTAT
16632 A
1 A
16633 GTGTCGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (19 bp):
ACTATATGTCGACTCTTAT
Found at i:17524 original size:21 final size:21
Alignment explanation
Indices: 17498--17575 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 21
17488 TTATTAAAAA
17498 TATTATTTTTATCAATTTTAT
1 TATTATTTTTATCAATTTTAT
17519 TATTATTTAAGGTTTTATCAATTTTAT
1 TATTA--T----TTTTATCAATTTTAT
* ** *
17546 TATTATTTTAATGTATTTTGT
1 TATTATTTTTATCAATTTTAT
17567 TATTATTTT
1 TATTATTTT
17576 ATACTTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
21 25 0.53
23 1 0.02
25 1 0.02
27 20 0.43
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (21 bp):
TATTATTTTTATCAATTTTAT
Found at i:17612 original size:18 final size:20
Alignment explanation
Indices: 17589--17634 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
17579 CTTTATTAAA
*
17589 AATATTT-AA-AAAAATATT
1 AATATTTAAATAAAAATAAT
17607 AATATTTTAAATAAAAATAAT
1 AATA-TTTAAATAAAAATAAT
17628 AATATTT
1 AATATTT
17635 TATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.17
19 3 0.12
20 5 0.21
21 12 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATTTAAATAAAAATAAT
Found at i:20478 original size:20 final size:21
Alignment explanation
Indices: 20453--20494 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20443 AGTATCTTAA
*
20453 TTATTAATT-CTATTTTATTT
1 TTATTAATTAATATTTTATTT
*
20473 TTATTATTTAATATTTTATTT
1 TTATTAATTAATATTTTATTT
20494 T
1 T
20495 AAAATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
TTATTAATTAATATTTTATTT
Found at i:21251 original size:37 final size:35
Alignment explanation
Indices: 21169--21404 Score: 149
Period size: 35 Copynumber: 6.6 Consensus size: 35
21159 ATAGTTTAAA
* * * * **
21169 AAAATAGTTTTGGAAATATATAATATA-GTTTTGG
1 AAAATATTTTTGAAAACATATAATATATATTTTTT
* *
21203 AAAACGATTTTTGAAAACATATAGTATATATTTTTT
1 AAAA-TATTTTTGAAAACATATAATATATATTTTTT
* * *
21239 AAAAATATTTTTTG-AAGCGTATAACATATAGTTTTTT
1 -AAAATA-TTTTTGAAAACATATAATATATA-TTTTTT
* *
21276 AAAA-ACGGTTTTGAAAACATATGATATATATTTTTT
1 AAAATA--TTTTTGAAAACATATAATATATATTTTTT
* *** * *
21312 AAAATAATTAAAAAAACGTATAATATATAGTTTTT
1 AAAATATTTTTGAAAACATATAATATATATTTTTT
*
21347 -AAATATTTTTGAAAACGTATACA-ATATAATTTTTT
1 AAAATATTTTTGAAAACATATA-ATATAT-ATTTTTT
*
21382 GAAAACGTGTTTTTGAAAACATA
1 -AAAA--TATTTTTGAAAACATA
21405 GCATATGATT
Statistics
Matches: 155, Mismatches: 33, Indels: 23
0.73 0.16 0.11
Matches are distributed among these distances:
34 25 0.16
35 48 0.31
36 36 0.23
37 32 0.21
39 14 0.09
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.42
Consensus pattern (35 bp):
AAAATATTTTTGAAAACATATAATATATATTTTTT
Found at i:21310 original size:36 final size:36
Alignment explanation
Indices: 21211--21315 Score: 106
Period size: 37 Copynumber: 2.9 Consensus size: 36
21201 GGAAAACGAT
**
21211 TTTTGAAAACATATAGTATATATTTTTTAAAAATATT
1 TTTTGAAAACATATA-TATATATTTTTTAAAAATAGG
* * * *
21248 TTTTG-AAGCGTATAACATATAGTTTTTTAAAAA-CGG
1 TTTTGAAAACATAT-ATATATA-TTTTTTAAAAATAGG
21284 TTTTGAAAACATATGATATATATTTTTTAAAA
1 TTTTGAAAACATAT-ATATATATTTTTTAAAA
21316 TAATTAAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
36 26 0.47
37 29 0.53
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.45
Consensus pattern (36 bp):
TTTTGAAAACATATATATATATTTTTTAAAAATAGG
Found at i:21381 original size:35 final size:35
Alignment explanation
Indices: 21125--21401 Score: 120
Period size: 35 Copynumber: 7.6 Consensus size: 35
21115 AAACATACAG
* *
21125 TTTTTAAAATAATTTTTTAAAAACGTATAAATACATAGT
1 TTTTTAAAAT-A-TTTTTGAAAACGTATAAAT--ATAAT
*** * * *
21164 TTAAAAAAATAGTTTTGGAAA--TATATAATATAGT
1 TTTTTAAAATATTTTTGAAAACGTATA-AATATAAT
** * * *
21198 TTTGGAAAACGATTTTTGAAAACATAT-AGTATATAT
1 TTTTTAAAA-TATTTTTGAAAACGTATAAATATA-AT
* *
21234 TTTTTAAAAATATTTTTTG-AAGCGTATAACATATAGT
1 TTTTT-AAAATA-TTTTTGAAAACGTATAA-ATATAAT
* * *
21271 TTTTTAAAA-ACGGTTTTGAAAACATAT-GATATATAT
1 TTTTTAAAATA--TTTTTGAAAACGTATAAATATA-AT
* *** *
21307 TTTTTAAAATAATTAAAAAAACGTAT-AATATATAG
1 TTTTTAAAATATTTTTGAAAACGTATAAATATA-AT
21342 TTTTT-AAATATTTTTGAAAACGTATACAATATAAT
1 TTTTTAAAATATTTTTGAAAACGTATA-AATATAAT
*
21377 TTTTTGAAAACGTGTTTTTGAAAAC
1 TTTTT-AAAA--TATTTTTGAAAAC
21402 ATAGCATATG
Statistics
Matches: 179, Mismatches: 40, Indels: 38
0.70 0.16 0.15
Matches are distributed among these distances:
34 27 0.15
35 52 0.29
36 39 0.22
37 37 0.21
38 5 0.03
39 19 0.11
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (35 bp):
TTTTTAAAATATTTTTGAAAACGTATAAATATAAT
Found at i:21422 original size:106 final size:107
Alignment explanation
Indices: 21216--21423 Score: 248
Period size: 106 Copynumber: 1.9 Consensus size: 107
21206 ACGATTTTTG
* * * *
21216 AAAACATATAGTATATATTTTTTAAAAATATTTTTTGAAGCGTATAACATATAGTTTTTTAAAAA
1 AAAACATATAATATATAGTTTTT-AAAATATTTTTTGAAACGTATAACATATAATTTTTTAAAAA
* *
21281 CGGTTTTGAAAACATATGATATATATTTTTTAAAATAATTAAA
65 CGGTTTTGAAAACATATGATATAGATTTTTGAAAATAATTAAA
* *
21324 AAAACGTATAATATATAGTTTTT-AAATA-TTTTTGAAAACGTAT-ACAATATAATTTTTTGAAA
1 AAAACATATAATATATAGTTTTTAAAATATTTTTTG-AAACGTATAAC-ATATAATTTTTTAAAA
21386 ACGTGTTTTTGAAAACATA-GCATAT-GA-TTTTGAAAATA
64 ACG-G-TTTTGAAAACATATG-ATATAGATTTTTGAAAATA
21424 TAATATATTA
Statistics
Matches: 87, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
105 8 0.09
106 39 0.45
107 3 0.03
108 37 0.43
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (107 bp):
AAAACATATAATATATAGTTTTTAAAATATTTTTTGAAACGTATAACATATAATTTTTTAAAAAC
GGTTTTGAAAACATATGATATAGATTTTTGAAAATAATTAAA
Found at i:21431 original size:21 final size:21
Alignment explanation
Indices: 21392--21431 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21382 GAAAACGTGT
*
21392 TTTTGAAAACATAGCATATGA
1 TTTTGAAAACATAACATATGA
* *
21413 TTTTGAAAATATAATATAT
1 TTTTGAAAACATAACATAT
21432 TATATAGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (21 bp):
TTTTGAAAACATAACATATGA
Found at i:22777 original size:31 final size:32
Alignment explanation
Indices: 22742--22819 Score: 88
Period size: 31 Copynumber: 2.4 Consensus size: 32
22732 TATTTAGACC
22742 TTAATTTTATTTTTTTTAAATTCA-TTT-TTAT
1 TTAATTTTATTTTTTTT-AATTCAGTTTATTAT
* *
22773 TTAATTTTATATATTTTTTATTTTAGTTTATTAT
1 TTAATTTTAT-T-TTTTTTAATTCAGTTTATTAT
22807 TTAATATTTATTT
1 TTAAT-TTTATTT
22820 GGATTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
31 10 0.25
32 5 0.12
33 10 0.25
34 10 0.25
35 5 0.12
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.71
Consensus pattern (32 bp):
TTAATTTTATTTTTTTTAATTCAGTTTATTAT
Found at i:22791 original size:22 final size:20
Alignment explanation
Indices: 22766--22808 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
22756 TTTAAATTCA
*
22766 TTTTTATTTAATTTTATATAT
1 TTTTTATTTAAGTTTAT-TAT
*
22787 TTTTTATTTTAGTTTATTAT
1 TTTTTATTTAAGTTTATTAT
22807 TT
1 TT
22809 AATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTATTTAAGTTTATTAT
Found at i:28503 original size:23 final size:23
Alignment explanation
Indices: 28419--28495 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
28409 AAGTGCCACG
* *
28419 TAGATTTGTTC-CGAAGGACTGCG
1 TAGATTTG-TCACGAAGGACTACA
* *
28442 TAGAATTTGTCACGAAGGACCATA
1 TAG-ATTTGTCACGAAGGACTACA
*
28466 TAGAATTGTCACGAAGGACTACA
1 TAGATTTGTCACGAAGGACTACA
28489 TAGATTT
1 TAGATTT
28496 ATCCCGAAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
23 28 0.64
24 16 0.36
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (23 bp):
TAGATTTGTCACGAAGGACTACA
Found at i:28690 original size:15 final size:15
Alignment explanation
Indices: 28670--28705 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
28660 CCTTTTCACT
*
28670 CATTTTCATATATAA
1 CATTTTCAGATATAA
28685 CATTTTCAGATATAA
1 CATTTTCAGATATAA
28700 CATTTT
1 CATTTT
28706 TCACGTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (15 bp):
CATTTTCAGATATAA
Found at i:32429 original size:23 final size:23
Alignment explanation
Indices: 32388--32439 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
32378 TTTGTTTAGA
*
32388 GTTTGTGAACATGCCCGTTTAAC
1 GTTTGTGAACATACCCGTTTAAC
**
32411 GTTTGTGAACATATTCGTTTAAC
1 GTTTGTGAACATACCCGTTTAAC
*
32434 GATTGT
1 GTTTGT
32440 CAAACAACAT
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:0.23, C:0.15, G:0.21, T:0.40
Consensus pattern (23 bp):
GTTTGTGAACATACCCGTTTAAC
Found at i:33581 original size:20 final size:21
Alignment explanation
Indices: 33546--33585 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
33536 TTTTTTTTAC
33546 TTTTTAATCAACATTAATTTT
1 TTTTTAATCAACATTAATTTT
33567 TTTTTAATCAA-ATTAATTT
1 TTTTTAATCAACATTAATTT
33586 CCATATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTAATCAACATTAATTTT
Found at i:42152 original size:7 final size:7
Alignment explanation
Indices: 42140--42177 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
42130 AAGACAAGTC
42140 CATCATG
1 CATCATG
42147 CATCATG
1 CATCATG
42154 CATCATG
1 CATCATG
42161 CATCATG
1 CATCATG
42168 CATCATG
1 CATCATG
42175 CAT
1 CAT
42178 GTGCTTTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (7 bp):
CATCATG
Found at i:42310 original size:21 final size:20
Alignment explanation
Indices: 42257--42304 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
42247 ACATTTCTAA
42257 ATAGAAAATAATTTTAATTT
1 ATAGAAAATAATTTTAATTT
42277 ATAGAAAATAATTTTAATTT
1 ATAGAAAATAATTTTAATTT
*
42297 TTAGAAAA
1 ATAGAAAA
42305 AAAATTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (20 bp):
ATAGAAAATAATTTTAATTT
Found at i:56051 original size:2 final size:2
Alignment explanation
Indices: 56044--56112 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
56034 TCTGTGTTAA
56044 AT AT AT AT AT AT -T 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
56085 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
56113 GGATATGATC
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:56769 original size:20 final size:19
Alignment explanation
Indices: 56720--56777 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
56710 TTTTTATTTT
*
56720 TTAAAATAATTATAATATC
1 TTAAAATATTTATAATATC
*
56739 -TAAAATTTATTTATATTAATC
1 TTAAAA--TATTTATAAT-ATC
56760 TTAAAATATTTATAATAT
1 TTAAAATATTTATAATAT
56778 TTTCTGTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 5 0.16
19 2 0.06
20 17 0.53
21 3 0.09
22 5 0.16
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAAAATATTTATAATATC
Found at i:59989 original size:55 final size:55
Alignment explanation
Indices: 59905--60012 Score: 216
Period size: 55 Copynumber: 2.0 Consensus size: 55
59895 CGAGGACTTC
59905 GTGCCACTTCTCTATTCTTGTCTGTATGCATTAGGAAATGGCTCGATCGGATCTT
1 GTGCCACTTCTCTATTCTTGTCTGTATGCATTAGGAAATGGCTCGATCGGATCTT
59960 GTGCCACTTCTCTATTCTTGTCTGTATGCATTAGGAAATGGCTCGATCGGATC
1 GTGCCACTTCTCTATTCTTGTCTGTATGCATTAGGAAATGGCTCGATCGGATC
60013 AATGATAACG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (55 bp):
GTGCCACTTCTCTATTCTTGTCTGTATGCATTAGGAAATGGCTCGATCGGATCTT
Found at i:65353 original size:35 final size:35
Alignment explanation
Indices: 65281--65353 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
65271 TTTTAATAAC
* * * *
65281 TATTTAACATAAATATAAATTATATTCATATTTAT
1 TATTTAAAATAAATATAAATTAAATTAATATTCAT
*
65316 TATTTAAAATTAATATAAA-TAAATTAACTATTCAT
1 TATTTAAAATAAATATAAATTAAATTAA-TATTCAT
65351 TAT
1 TAT
65354 AAAGATAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 6 0.19
35 26 0.81
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (35 bp):
TATTTAAAATAAATATAAATTAAATTAATATTCAT
Found at i:68156 original size:43 final size:43
Alignment explanation
Indices: 68108--68290 Score: 135
Period size: 43 Copynumber: 4.2 Consensus size: 43
68098 TTTATTTTTG
* *
68108 TAATTGATGCTCTTAATCTTTT-TAATTTAATTTTTT-CTCTTTA
1 TAATTGAGGCTCTTAAT-TTTTATAATCTAATTTTTTAC-CTTTA
* *
68151 TAATTGAGGTTTTTAATTTTTATAATCTAATTTTTTACCTTTA
1 TAATTGAGGCTCTTAATTTTTATAATCTAATTTTTTACCTTTA
* * * * *
68194 TAACTGA-GATCCCTAATTTTTTTCAATACT-ATTTTTTACATTTA
1 TAATTGAGGCT-CTTAATTTTTAT-AAT-CTAATTTTTTACCTTTA
* * * * *
68238 TAATTGAGAC-CTCTAATTTTTTTAA-CCACACTTTCTACCTTTA
1 TAATTGAGGCTCT-TAATTTTTATAATCTA-ATTTTTTACCTTTA
68281 TAATTGAGGC
1 TAATTGAGGC
68291 CCCTCATTTT
Statistics
Matches: 112, Mismatches: 19, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
41 1 0.01
42 6 0.05
43 70 0.62
44 33 0.29
45 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (43 bp):
TAATTGAGGCTCTTAATTTTTATAATCTAATTTTTTACCTTTA
Found at i:68228 original size:44 final size:42
Alignment explanation
Indices: 68164--68343 Score: 141
Period size: 44 Copynumber: 4.1 Consensus size: 42
68154 TTGAGGTTTT
* *
68164 TAATTTTTATAAT-CTAATTTTTTACCTTTATAACTGAGATCCC
1 TAATTTTTTTAATACT-ATTTTTTACCTTTATAATTGAGA-CCC
*
68207 TAATTTTTTTCAATACTATTTTTTACATTTATAATTGAGACCTC
1 TAATTTTTTT-AATACTATTTTTTACCTTTATAATTGAGACC-C
* * * *
68251 TAATTTTTTTAACCAC-ACTTTCTACCTTTATAATTGAGGCCCC
1 TAATTTTTTTAA-TACTATTTTTTACCTTTATAATTGA-GACCC
* * * * * *
68294 TCATTTTTTTCAAT-CTCACTGTTTACTTTTATAATTTAGGCCC
1 TAATTTTTTT-AATACT-ATTTTTTACCTTTATAATTGAGACCC
68337 ATAATTT
1 -TAATTT
68344 AATTTTTTTA
Statistics
Matches: 112, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
42 1 0.01
43 45 0.40
44 64 0.57
45 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (42 bp):
TAATTTTTTTAATACTATTTTTTACCTTTATAATTGAGACCC
Found at i:68242 original size:87 final size:87
Alignment explanation
Indices: 68164--68329 Score: 201
Period size: 87 Copynumber: 1.9 Consensus size: 87
68154 TTGAGGTTTT
* * * * *
68164 TAATTTTTATAATCTA-ATTTTTTACCTTTATAACTGAGATCCCTAATTTTTTTCAATACT-ATT
1 TAATTTTTATAA-CCACACTTTCTACCTTTATAACTGAGACCCCTAATTTTTTTCAAT-CTCACT
*
68227 TTTTACATTTATAATTGAGACCTC
64 GTTTACATTTATAATTGAGACCTC
* * * *
68251 TAATTTTTTTAACCACACTTTCTACCTTTATAATTGAGGCCCCTCATTTTTTTCAATCTCACTGT
1 TAATTTTTATAACCACACTTTCTACCTTTATAACTGAGACCCCTAATTTTTTTCAATCTCACTGT
*
68316 TTACTTTTATAATT
66 TTACATTTATAATT
68330 TAGGCCCATA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
86 4 0.06
87 62 0.94
ACGTcount: A:0.27, C:0.18, G:0.05, T:0.50
Consensus pattern (87 bp):
TAATTTTTATAACCACACTTTCTACCTTTATAACTGAGACCCCTAATTTTTTTCAATCTCACTGT
TTACATTTATAATTGAGACCTC
Found at i:68300 original size:43 final size:44
Alignment explanation
Indices: 68184--68343 Score: 146
Period size: 44 Copynumber: 3.7 Consensus size: 44
68174 AATCTAATTT
* ** * * *
68184 TTTACCTTTATAACTGAGATCCCTAATTTTTTTCAA-TACTATTT
1 TTTACCTTTATAATTGAGGCCCCTAATTTTTTTCAACCAC-ACTG
* * *
68228 TTTACATTTATAATTGAGACCTCTAATTTTTTT-AACCACACT-
1 TTTACCTTTATAATTGAGGCCCCTAATTTTTTTCAACCACACTG
* * *
68270 TTCTACCTTTATAATTGAGGCCCCTCATTTTTTTCAATCTCACTG
1 TT-TACCTTTATAATTGAGGCCCCTAATTTTTTTCAACCACACTG
* * *
68315 TTTACTTTTATAATTTAGGCCCATAATTT
1 TTTACCTTTATAATTGAGGCCCCTAATTT
68344 AATTTTTTTA
Statistics
Matches: 96, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
42 2 0.02
43 31 0.32
44 61 0.64
45 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.47
Consensus pattern (44 bp):
TTTACCTTTATAATTGAGGCCCCTAATTTTTTTCAACCACACTG
Found at i:68899 original size:22 final size:22
Alignment explanation
Indices: 68871--68931 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
68861 TTTATTATCA
68871 TAATCGAATAAAGATTTTTTAT
1 TAATCGAATAAAGATTTTTTAT
*
68893 TAATCGAATAATA-TTTTTTTAT
1 TAATCGAATAA-AGATTTTTTAT
68915 TAATCGAATAAAGATTT
1 TAATCGAATAAAGATTT
68932 CAAATGTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (22 bp):
TAATCGAATAAAGATTTTTTAT
Found at i:69239 original size:21 final size:21
Alignment explanation
Indices: 69213--69255 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
69203 AAGCATTCAC
*
69213 ATGTGGTCATCGATGATGATG
1 ATGTGGTCATCGATGATAATG
69234 ATGTGGTCATCGATGATAATG
1 ATGTGGTCATCGATGATAATG
69255 A
1 A
69256 GGCGTTTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.09, G:0.30, T:0.33
Consensus pattern (21 bp):
ATGTGGTCATCGATGATAATG
Done.