Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002195.1 Hibiscus syriacus cultivar Beakdansim tig00004473_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: 93778
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:9022 original size:18 final size:18
Alignment explanation
Indices: 8999--9033 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
8989 ACTATTGCGA
8999 TCATTATGAATATCACCC
1 TCATTATGAATATCACCC
*
9017 TCATTATGGATATCACC
1 TCATTATGAATATCACC
9034 TTTGTGCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (18 bp):
TCATTATGAATATCACCC
Found at i:16290 original size:3 final size:3
Alignment explanation
Indices: 16276--16354 Score: 61
Period size: 3 Copynumber: 24.3 Consensus size: 3
16266 TTTGTTTAGT
* *
16276 ATA ATA ATTA ATA ATA ATA ATG ATAA ACA ATA ATA ACTA ATA ATA ATA
1 ATA ATA A-TA ATA ATA ATA ATA AT-A ATA ATA ATA A-TA ATA ATA ATA
*
16324 AGTA A-A AGTT ATA ATTA ATA ATA ATTA ATA A
1 A-TA ATA A-TA ATA A-TA ATA ATA A-TA ATA A
16355 ACGACAAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
2 2 0.03
3 43 0.69
4 17 0.27
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16291 original size:10 final size:10
Alignment explanation
Indices: 16276--16354 Score: 62
Period size: 10 Copynumber: 8.4 Consensus size: 10
16266 TTTGTTTAGT
16276 ATAATAATTA
1 ATAATAATTA
16286 ATAATAA-TA
1 ATAATAATTA
* **
16295 ATGATAAACA
1 ATAATAATTA
*
16305 ATAATAACTA
1 ATAATAATTA
16315 ATAATAA-TA
1 ATAATAATTA
*
16324 AGTAA-AAGT-
1 A-TAATAATTA
16333 -T-ATAATTA
1 ATAATAATTA
16341 ATAATAATTA
1 ATAATAATTA
16351 ATAA
1 ATAA
16355 ACGACAAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
6 1 0.02
7 4 0.07
9 14 0.25
10 37 0.66
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.33
Consensus pattern (10 bp):
ATAATAATTA
Found at i:16316 original size:29 final size:26
Alignment explanation
Indices: 16276--16348 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 26
16266 TTTGTTTAGT
16276 ATAATAATTAATAATAATAATGATAAACA
1 ATAATAATTAATAATAATAA-G-TAAA-A
*
16305 ATAATAACTAATAATAATAAGTAAAA
1 ATAATAATTAATAATAATAAGTAAAA
* *
16331 GTTATAATTAATAATAAT
1 ATAATAATTAATAATAAT
16349 TAATAAACGA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 16 0.40
27 4 0.10
28 1 0.03
29 19 0.47
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (26 bp):
ATAATAATTAATAATAATAAGTAAAA
Found at i:17533 original size:2 final size:2
Alignment explanation
Indices: 17526--17554 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17516 AATACCATCA
17526 AT 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 AT A
17555 AGCCATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18746 original size:16 final size:17
Alignment explanation
Indices: 18721--18754 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
18711 TCGAGGTGCC
18721 ACATTAACTTTT-CAAA
1 ACATTAACTTTTACAAA
*
18737 ACATTTACTTTTACAAA
1 ACATTAACTTTTACAAA
18754 A
1 A
18755 TAATTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (17 bp):
ACATTAACTTTTACAAA
Found at i:19411 original size:23 final size:23
Alignment explanation
Indices: 19361--19428 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
19351 GTGCCATATA
* * *
19361 AATTGTCCCGAAAGACCCCGTAG
1 AATTGTCCCGAAGGACCACATAG
* *
19384 GATTGTCTCGAAGGACCACATAG
1 AATTGTCCCGAAGGACCACATAG
*
19407 AATTGTCCCTAAGGACCACATA
1 AATTGTCCCGAAGGACCACATA
19429 TATGTTCCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
AATTGTCCCGAAGGACCACATAG
Found at i:19443 original size:21 final size:21
Alignment explanation
Indices: 19394--19509 Score: 101
Period size: 21 Copynumber: 5.4 Consensus size: 21
19384 GATTGTCTCG
* * *
19394 AAGGACCACATAGAATTGTCCCT
1 AAGGACCACATA-TA-TGTTCCA
19417 AAGGACCACATATATGTTCCA
1 AAGGACCACATATATGTTCCA
* * *
19438 AAGGACCAAATATATATGT-CG
1 AAGGACCACATATATGT-TCCA
*
19459 AAGGACCTCATATATGTTCCA
1 AAGGACCACATATATGTTCCA
* *
19480 AAGGATCACATATATG-TCTCG
1 AAGGACCACATATATGTTC-CA
19501 AAGGACCAC
1 AAGGACCAC
19510 GTAGAACCCT
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
20 3 0.04
21 59 0.78
22 2 0.03
23 12 0.16
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.23
Consensus pattern (21 bp):
AAGGACCACATATATGTTCCA
Found at i:19471 original size:42 final size:42
Alignment explanation
Indices: 19417--19509 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
19407 AATTGTCCCT
*
19417 AAGGACCACATATATGTTCCAAAGGACCAAATATATATGTCG
1 AAGGACCACATATATGTTCCAAAGGACCAAATATATATCTCG
* * * *
19459 AAGGACCTCATATATGTTCCAAAGGATCACATATATGTCTCG
1 AAGGACCACATATATGTTCCAAAGGACCAAATATATATCTCG
19501 AAGGACCAC
1 AAGGACCAC
19510 GTAGAACCCT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.24
Consensus pattern (42 bp):
AAGGACCACATATATGTTCCAAAGGACCAAATATATATCTCG
Found at i:25405 original size:33 final size:33
Alignment explanation
Indices: 25363--25430 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
25353 CTAGCAAGCA
*
25363 TTTCATCTCGCGCCGTAACTCCCTCGGTCAGAG
1 TTTCATCTCGCGCCGCAACTCCCTCGGTCAGAG
* *
25396 TTTCATCTCGCGCCGCAACTTCCTTGGTCAGAG
1 TTTCATCTCGCGCCGCAACTCCCTCGGTCAGAG
25429 TT
1 TT
25431 CCCTTGCGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.15, C:0.34, G:0.21, T:0.31
Consensus pattern (33 bp):
TTTCATCTCGCGCCGCAACTCCCTCGGTCAGAG
Found at i:26495 original size:2 final size:2
Alignment explanation
Indices: 26488--26542 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
26478 TTTACTAATT
26488 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
26530 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
26543 TTACGTTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26657 original size:18 final size:18
Alignment explanation
Indices: 26619--26657 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
26609 TTATATTTTA
*
26619 ATATATATGTATATAGGT
1 ATATATATGTATATACGT
*
26637 ATATATATGTATATACTT
1 ATATATATGTATATACGT
26655 ATA
1 ATA
26658 ATAGTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (18 bp):
ATATATATGTATATACGT
Found at i:37259 original size:12 final size:12
Alignment explanation
Indices: 37242--37269 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
37232 TCCTAAGTTG
37242 AAAAAAAAAGAA
1 AAAAAAAAAGAA
37254 AAAAAAAAAGAA
1 AAAAAAAAAGAA
37266 AAAA
1 AAAA
37270 CGTTTAGGGT
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:37284 original size:65 final size:65
Alignment explanation
Indices: 37208--37330 Score: 185
Period size: 65 Copynumber: 1.9 Consensus size: 65
37198 AATACTTCGC
* * * *
37208 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAAGAAAAA-AAAAAAGAAAAAACG
1 TTAGGATGAAAACCCAAAAGGGCGCCCTAAATTG-AAAAAAAAGAAAAAGAAAAAAGAAAAAACG
37272 T
65 T
*
37273 TTAGGGTGAAAACCCAAAAGGGCGCCCTAAATTGAAAAAAAAGAAAAAGAAAAAAGAA
1 TTAGGATGAAAACCCAAAAGGGCGCCCTAAATTGAAAAAAAAGAAAAAGAAAAAAGAA
37331 GAGAAAATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
64 14 0.27
65 38 0.73
ACGTcount: A:0.56, C:0.11, G:0.21, T:0.11
Consensus pattern (65 bp):
TTAGGATGAAAACCCAAAAGGGCGCCCTAAATTGAAAAAAAAGAAAAAGAAAAAAGAAAAAACGT
Found at i:38276 original size:105 final size:105
Alignment explanation
Indices: 38089--38897 Score: 1376
Period size: 105 Copynumber: 7.7 Consensus size: 105
38079 AGGTTTTACC
* *
38089 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
38154 ACGAAGGGACCGTTGGTTGTCAACAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATT
*
38194 CAGAGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
38259 GCGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATT
* *
38299 CAGAGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGAAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
38364 ACGAAGGGACCGCGGGTTGTCACCAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATT
* *
38404 CATAGCCAATTTCAACTTCACAACGAAGGATATTGGACCCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
38469 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATT
* *
38509 CAGAGCCAATTTCAACTTCATAACGAAGGGTATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
38574 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAA-TT
38614 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
38679 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAA-TT
* *
38719 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGAAAGTTTAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
38784 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCT-CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCCAA-TT
38825 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA-TCTCAC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT-TCAC
38889 GACG-AGGGA
65 GACGAAGGGA
38898 GTCATTTCAG
Statistics
Matches: 675, Mismatches: 26, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
104 3 0.00
105 597 0.88
106 75 0.11
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATT
Found at i:39221 original size:33 final size:33
Alignment explanation
Indices: 39179--39246 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
39169 CTAGTAAGCA
* *
39179 TTTCATCTCGCGCCGTAACTCCCTCGGTTAGAG
1 TTTCATCTCGCGCCGCAACTCCCTCGGTCAGAG
* *
39212 TTTCATCTCGCGCCGCAACTTCCTTGGTCAGAG
1 TTTCATCTCGCGCCGCAACTCCCTCGGTCAGAG
39245 TT
1 TT
39247 CCCTTGCGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.15, C:0.32, G:0.21, T:0.32
Consensus pattern (33 bp):
TTTCATCTCGCGCCGCAACTCCCTCGGTCAGAG
Found at i:40304 original size:2 final size:2
Alignment explanation
Indices: 40297--40327 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40287 TTTACTAATT
40297 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
40328 TTACGTTATT
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:43368 original size:24 final size:25
Alignment explanation
Indices: 43318--43376 Score: 86
Period size: 24 Copynumber: 2.4 Consensus size: 25
43308 AGTTTTTGCA
43318 CCGAAGTG-CCGCGTAGAAATTTATC
1 CCGAAG-GACCGCGTAGAAATTTATC
*
43343 CCGAAGGACCGCGTAG-AATTTGTC
1 CCGAAGGACCGCGTAGAAATTTATC
43367 CCGAAGGACC
1 CCGAAGGACC
43377 ATATATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (25 bp):
CCGAAGGACCGCGTAGAAATTTATC
Found at i:44068 original size:21 final size:21
Alignment explanation
Indices: 44044--44086 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
44034 TCATATTCGT
* *
44044 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
44065 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
44086 T
1 T
44087 AGCCCAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:44550 original size:3 final size:3
Alignment explanation
Indices: 44542--44617 Score: 143
Period size: 3 Copynumber: 25.0 Consensus size: 3
44532 TCTTCACGGT
44542 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
44590 GAA GAA GAA GAA GAA GAA GAA GAGA GAA
1 GAA GAA GAA GAA GAA GAA GAA GA-A GAA
44618 ATATCTGGAA
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 69 0.96
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:47079 original size:63 final size:64
Alignment explanation
Indices: 46944--47099 Score: 165
Period size: 64 Copynumber: 2.4 Consensus size: 64
46934 TTCGAGGTGT
* * * * **
46944 ATCGATGCACATGAAGTGCATCGATGCACTCTTTTAAAATACAAACATCGAATGTCATCAATGC
1 ATCGATGCATAAGGAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATGTCATCAATGC
* * **
47008 ATCGATGCATAAGGAGTGCATCGATGCACCCCCTT-AAATATAAACATCGAATAG-GATTTATGC
1 ATCGATGCATAAGGAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAAT-GTCATCAATGC
*
47071 ATCGATGCAT-GGTGTAGTGCATCGATGCA
1 ATCGATGCATAAG-G-AGTGCATCGATGCA
47100 TACCTTCATT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
62 1 0.01
63 33 0.42
64 44 0.56
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (64 bp):
ATCGATGCATAAGGAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATGTCATCAATGC
Found at i:47777 original size:23 final size:23
Alignment explanation
Indices: 47724--47784 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
47714 CAATCTTATA
* *
47724 TGGCACTACAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
47747 CGGCACTTCGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
47770 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
47785 TTTATATGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:54407 original size:23 final size:23
Alignment explanation
Indices: 54363--54407 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
54353 AATCTTATAT
*
54363 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
54386 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
54408 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:58808 original size:22 final size:22
Alignment explanation
Indices: 58783--58824 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
58773 TCGGTCGAAG
58783 TCAACAGTATGACCGATCAAAT
1 TCAACAGTATGACCGATCAAAT
* * *
58805 TCAACGGTCTGACCGGTCAA
1 TCAACAGTATGACCGATCAA
58825 CGATCAATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (22 bp):
TCAACAGTATGACCGATCAAAT
Found at i:60970 original size:2 final size:2
Alignment explanation
Indices: 60963--61034 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
60953 CCTTCAGGAC
60963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61035 CATTTGGAAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64984 original size:66 final size:64
Alignment explanation
Indices: 64870--64999 Score: 242
Period size: 66 Copynumber: 2.0 Consensus size: 64
64860 AAAATTCGAA
64870 TATTAACCTCTTCCAAAACGCGATCGACGCGGGAGGACTTTCAGATAACAAACCCGGTTGGGTT
1 TATTAACCTCTTCCAAAACGCGATCGACGCGGGAGGACTTTCAGATAACAAACCCGGTTGGGTT
64934 TATTAACCTCTTCCAAAACGACGATCGACGACGGGAGGACTTTCAGATAACAAACCCGGTTGGGT
1 TATTAACCTCTTCCAAAACG-CGATCGACG-CGGGAGGACTTTCAGATAACAAACCCGGTTGGGT
64999 T
64 T
65000 CTGGTCAGAA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
64 20 0.31
65 9 0.14
66 35 0.55
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (64 bp):
TATTAACCTCTTCCAAAACGCGATCGACGCGGGAGGACTTTCAGATAACAAACCCGGTTGGGTT
Found at i:68589 original size:199 final size:195
Alignment explanation
Indices: 68211--68606 Score: 756
Period size: 199 Copynumber: 2.0 Consensus size: 195
68201 TATTATTTAT
68211 TTTTCAATTAATTATATCACATGATATTATAGAAACCTATTATAGAACTAACCCTTTCAATTTAA
1 TTTTCAATTAATTATATCACATGATATTATAGAAACCTATTATAGAACTAACCCTTTCAATTTAA
68276 TTTTCATCATTCAATTAATCCGATGGGATATATTGAAAGGAGATCTTTTTTCCTGATAGTTTTAG
66 TTTTCATCATTCAATTAATCCGATGGGATATATTGAAAGGAGATCTTTTTTCCTGATAGTTTTAG
68341 GTCGTCAGAGCGACGATTAGTTTAGGCGGCGATGAACAATAACAACGTGAGAGAGAGAGAGAGAG
131 GTCGTCAGAGCGACGATTAGTTTAGGCGGCGATGAACAATAACAACGTGAGAGAGAGAGAGAGAG
68406 TTTTCAATTAAATTATATCACATGATATTATAGAAACCTATTATAGAACTAACCCTTTCAATTTA
1 TTTTCAATT-AATTATATCACATGATATTATAGAAACCTATTATAGAACTAACCCTTTCAATTTA
68471 ATTTTCATCATTCAATTAATCCGATGGGAATATAGATTGAAAGGAGATCTTTTTTCCTGATAGTT
65 ATTTTCATCATTCAATTAATCCGATGGG-ATAT--ATTGAAAGGAGATCTTTTTTCCTGATAGTT
68536 TTAGGTCGTCAGAGCGACGATTAGTTTAGGCGGCGATGAACAATAACAACGTGAGAGAGAGAGAG
127 TTAGGTCGTCAGAGCGACGATTAGTTTAGGCGGCGATGAACAATAACAACGTGAGAGAGAGAGAG
68601 AGAG
192 AGAG
68605 TT
1 TT
68607 AATTTTTTTT
Statistics
Matches: 197, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
195 9 0.05
196 83 0.42
197 4 0.02
199 101 0.51
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (195 bp):
TTTTCAATTAATTATATCACATGATATTATAGAAACCTATTATAGAACTAACCCTTTCAATTTAA
TTTTCATCATTCAATTAATCCGATGGGATATATTGAAAGGAGATCTTTTTTCCTGATAGTTTTAG
GTCGTCAGAGCGACGATTAGTTTAGGCGGCGATGAACAATAACAACGTGAGAGAGAGAGAGAGAG
Found at i:73615 original size:2 final size:2
Alignment explanation
Indices: 73608--73654 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
73598 CAACATATTC
73608 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73650 AT AT A
1 AT AT A
73655 AATCACCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:82242 original size:22 final size:22
Alignment explanation
Indices: 82217--82258 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
82207 TTTTAGTATT
*
82217 GGATT-AAATGGTAATTATGGAA
1 GGATTGAAAGGGTAA-TATGGAA
82239 GGATTGAAAGGGTAATATGG
1 GGATTGAAAGGGTAATATGG
82259 TAATTTAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (22 bp):
GGATTGAAAGGGTAATATGGAA
Found at i:82969 original size:55 final size:55
Alignment explanation
Indices: 82878--83002 Score: 214
Period size: 55 Copynumber: 2.3 Consensus size: 55
82868 AAATGTTCAA
82878 AGTGTATCGATACCCTCAAAATATCGAATGCCATTTGTGTATCGGTACACTGAGG
1 AGTGTATCGATACCCTCAAAATATCGAATGCCATTTGTGTATCGGTACACTGAGG
* * *
82933 AGTGTATCGATACCCTCAAAATATCGAGTGCTATTTGTGTATCGGTACACTGGGG
1 AGTGTATCGATACCCTCAAAATATCGAATGCCATTTGTGTATCGGTACACTGAGG
*
82988 AGTGCATCGATACCC
1 AGTGTATCGATACCC
83003 CCAAGTATGA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (55 bp):
AGTGTATCGATACCCTCAAAATATCGAATGCCATTTGTGTATCGGTACACTGAGG
Found at i:83861 original size:18 final size:18
Alignment explanation
Indices: 83814--83862 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
83804 GTGTTCTATA
*
83814 TGGTCCTTCGAGACATAG
1 TGGTCCTTCGGGACATAG
83832 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
*
83850 TGGTCCTACGGGA
1 TGGTCCTTCGGGA
83863 AAAATTCTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.27
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAG
Found at i:86022 original size:22 final size:22
Alignment explanation
Indices: 85975--86069 Score: 129
Period size: 22 Copynumber: 4.3 Consensus size: 22
85965 TTAAGGGTTC
85975 TATGTGGTCCTTCGGGACAAAAT
1 TATGTGGTCCTTCGGGAC-AAAT
*
85998 TATGTGGTCCTTTGGGACAAAT
1 TATGTGGTCCTTCGGGACAAAT
*
86020 TATGTGGTCATTCGGGACAAAT
1 TATGTGGTCCTTCGGGACAAAT
* *
86042 TATGTGGTACTTTGGTG-CAAAT
1 TATGTGGTCCTTCGG-GACAAAT
86064 TATGTG
1 TATGTG
86070 AGTTGTGGTG
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
22 47 0.72
23 18 0.28
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TATGTGGTCCTTCGGGACAAAT
Found at i:86063 original size:44 final size:45
Alignment explanation
Indices: 85975--86069 Score: 149
Period size: 44 Copynumber: 2.1 Consensus size: 45
85965 TTAAGGGTTC
* *
85975 TATGTGGTCCTTCGGGACAAAATTATGTGGTCCTTTGGGACAAAT
1 TATGTGGTCATTCGGGACAAAATTATGTGGTACTTTGGGACAAAT
86020 TATGTGGTCATTCGGGAC-AAATTATGTGGTACTTTGGTG-CAAAT
1 TATGTGGTCATTCGGGACAAAATTATGTGGTACTTTGG-GACAAAT
86064 TATGTG
1 TATGTG
86070 AGTTGTGGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
44 29 0.62
45 18 0.38
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (45 bp):
TATGTGGTCATTCGGGACAAAATTATGTGGTACTTTGGGACAAAT
Found at i:89014 original size:2 final size:2
Alignment explanation
Indices: 89007--89100 Score: 170
Period size: 2 Copynumber: 47.0 Consensus size: 2
88997 TCTTGTAGTT
* *
89007 TA TA TA TA TA TA TG TA TG 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
89049 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
89091 TA TA TA TA TA
1 TA TA TA TA TA
89101 ATTAAGAGGC
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:93612 original size:6 final size:6
Alignment explanation
Indices: 93601--93627 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
93591 CAATGTTCAT
93601 ACATAC ACATAC ACATAC ACATAC ACA
1 ACATAC ACATAC ACATAC ACATAC ACA
93628 CATGCATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (6 bp):
ACATAC
Done.