Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005811.1 Hibiscus syriacus cultivar Beakdansim tig00013621_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: 53510
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:638 original size:15 final size:16
Alignment explanation
Indices: 614--646 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
604 TATTATGTCA
*
614 TTTATTTTATTT-TAT
1 TTTATATTATTTATAT
629 TTTATATTATTTATAT
1 TTTATATTATTTATAT
645 TT
1 TT
647 GAATTTCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATATTATTTATAT
Found at i:5105 original size:290 final size:289
Alignment explanation
Indices: 4581--5160 Score: 1083
Period size: 290 Copynumber: 2.0 Consensus size: 289
4571 TGTACATAAT
*
4581 CTCCAAACGTCATCAGAAACATTACCATCCACAGATGGCTATCAACAGTAAAATAGGAACAAAAA
1 CTCCAAACGTCATCAGAAACATTACCATCCACAGATGGCTATCAAAAGTAAAATAGGAACAAAAA
*
4646 ACATGTTCAGCACTTCATCCCTTTCCTTTTCTGCCTCTGCACATTGCATCTATTCAGAGAACAAG
66 ACATGTTCAGCACTTCATCCCTTTCCTTTTCTGCCTCTGCACATTGCATCTATTCAGAGAACAAA
4711 GAAATGATACCAAAGTGGAGCAGAGAAGTTTAACAAAATGACTACTAGCAAAACAAAGCACAAAC
131 GAAATGATACCAAAGTGGAGCAGAGAAGTTTAACAAAATGACTACTAGCAAAACAAAGCACAAAC
4776 GAGTTTCATGCATTTTTATAAATGATAGAATGCTTTTTTATCACCAAAAGAAGGCGAACATTGTA
196 GAGTTTCATGCATTTTTATAAATGATAGAATGCTTTTTTATCACCAAAAGAAGGCGAACATTGTA
4841 CCATATTCAATAAATGCAACCCGATAGTA
261 CCATATTCAATAAATGCAACCCGATAGTA
4870 CTCCAAACGTCATCAGAAACATTACCATCCACAGATGGCTATCAAAAGTAAAAATAGGAACAAAA
1 CTCCAAACGTCATCAGAAACATTACCATCCACAGATGGCTATCAAAAGT-AAAATAGGAACAAAA
*
4935 AACATGTTCAGCACTTCATCCTTTTCCTTTTCTGCACTCTGCACATTGCATCTATTCAGAGAACA
65 AACATGTTCAGCACTTCATCCCTTTCCTTTTCTGC-CTCTGCACATTGCATCTATTCAGAGAACA
5000 AAGAAATGATACCAAAAGTGGAGCAGAGAAGTTTAACAAAATGACTACTAGCAAAACAAAGCACA
129 AAGAAATGATACC-AAAGTGGAGCAGAGAAGTTTAACAAAATGACTACTAGCAAAACAAAGCACA
*
5065 AATGAGTTTCATGCA-TTTT-TAAATGATAGAATGCTTTTTTATCACCAAAAGAAGGCGAACATT
193 AACGAGTTTCATGCATTTTTATAAATGATAGAATGCTTTTTTATCACCAAAAGAAGGCGAACATT
5128 GTACCATATTCAATAAATGCAACCCGATAGTA
258 GTACCATATTCAATAAATGCAACCCGATAGTA
5160 C
1 C
5161 CAAGTGATTT
Statistics
Matches: 284, Mismatches: 4, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
289 48 0.17
290 126 0.44
291 45 0.16
292 65 0.23
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (289 bp):
CTCCAAACGTCATCAGAAACATTACCATCCACAGATGGCTATCAAAAGTAAAATAGGAACAAAAA
ACATGTTCAGCACTTCATCCCTTTCCTTTTCTGCCTCTGCACATTGCATCTATTCAGAGAACAAA
GAAATGATACCAAAGTGGAGCAGAGAAGTTTAACAAAATGACTACTAGCAAAACAAAGCACAAAC
GAGTTTCATGCATTTTTATAAATGATAGAATGCTTTTTTATCACCAAAAGAAGGCGAACATTGTA
CCATATTCAATAAATGCAACCCGATAGTA
Found at i:11715 original size:13 final size:13
Alignment explanation
Indices: 11693--11733 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
11683 GCACGACTAG
11693 TTTATTTA-TTTA
1 TTTATTTATTTTA
11705 TTTATTTTATTTTA
1 TTTA-TTTATTTTA
11719 TTT-TTTCATTTTA
1 TTTATTT-ATTTTA
11732 TT
1 TT
11734 AGTTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 7 0.27
13 12 0.46
14 7 0.27
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:11720 original size:18 final size:18
Alignment explanation
Indices: 11693--11733 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
11683 GCACGACTAG
11693 TTTA-TTTATTTATTT-AT
1 TTTATTTTATTT-TTTCAT
11710 TTTATTTTATTTTTTCAT
1 TTTATTTTATTTTTTCAT
11728 TTTATT
1 TTTATT
11734 AGTTTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTATTTTATTTTTTCAT
Found at i:17388 original size:56 final size:56
Alignment explanation
Indices: 17264--17380 Score: 152
Period size: 56 Copynumber: 2.1 Consensus size: 56
17254 AATGCATTTC
* * *
17264 ATGCATCGATGCA-CATACTATGCATCGATGCACTCAGGGTTTTATGAAAACATCGA
1 ATGCATCGATGCACCA-GCCATGCATCGATGCACTCAGGCTTTTATGAAAACATCGA
17320 ATGCATCGATGCACCAGCCATGCATCGATGCACTCAGGCTATTT-TG-AAACAAT-GA
1 ATGCATCGATGCACCAGCCATGCATCGATGCACTCAGGCT-TTTATGAAAAC-ATCGA
17375 ATGCAT
1 ATGCAT
17381 TTTATGCATC
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
55 12 0.22
56 38 0.69
57 5 0.09
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (56 bp):
ATGCATCGATGCACCAGCCATGCATCGATGCACTCAGGCTTTTATGAAAACATCGA
Found at i:23899 original size:18 final size:18
Alignment explanation
Indices: 23875--23932 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
23865 GACCGGTCAC
23875 AACCCGACCCGACCCGTT
1 AACCCGACCCGACCCGTT
*
23893 GACCCGACCCGACCCGTT
1 AACCCGACCCGACCCGTT
23911 AACCCGACCCGACCCGTT
1 AACCCGACCCGACCCGTT
23929 AACC
1 AACC
23933 GTTGACCGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.22, C:0.50, G:0.17, T:0.10
Consensus pattern (18 bp):
AACCCGACCCGACCCGTT
Found at i:26479 original size:24 final size:24
Alignment explanation
Indices: 26383--26491 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
26373 GAATATTTTA
* *
26383 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
26407 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
26431 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
26455 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
* *
26479 TTTGATTTCTGAT
1 TCTGATATCTGAT
26492 ATCTCCGTTT
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
23 1 0.02
24 64 0.97
25 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:26660 original size:2 final size:2
Alignment explanation
Indices: 26653--26683 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
26643 CGGATGGGGG
26653 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
26684 GTTTTAAAAG
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:27355 original size:44 final size:43
Alignment explanation
Indices: 27288--27389 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 43
27278 TTTGTGCTTA
*
27288 GTGCATCGATACACTTAACAGTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATACACATAACAGTGCATCGATGCATCCC-TTGAAT
* *
27332 GTGCATCGATACACCATGA-AGTGCATCGATGCATGCCTTGAAT
1 GTGCATCGATACA-CATAACAGTGCATCGATGCATCCCTTGAAT
*
27375 GTGCATCGATGCACA
1 GTGCATCGATACACA
27390 CAAGGCCATG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
42 2 0.04
43 18 0.34
44 30 0.57
45 3 0.06
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (43 bp):
GTGCATCGATACACATAACAGTGCATCGATGCATCCCTTGAAT
Found at i:27357 original size:20 final size:21
Alignment explanation
Indices: 27287--27384 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 21
27277 TTTTGTGCTT
*
27287 AGTGCATCGATACA--CTTAA
1 AGTGCATCGATACATCCTTGA
*
27306 CAGTGCATCGATGCATCCCTTTGA
1 -AGTGCATCGATACAT-CC-TTGA
*
27330 ATGTGCATCGATACA-CCATGA
1 A-GTGCATCGATACATCCTTGA
*
27351 AGTGCATCGATGCATGCCTTGA
1 AGTGCATCGATACAT-CCTTGA
27373 ATGTGCATCGAT
1 A-GTGCATCGAT
27385 GCACACAAGG
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
20 25 0.39
21 4 0.06
22 8 0.12
23 12 0.19
24 15 0.23
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
AGTGCATCGATACATCCTTGA
Found at i:30166 original size:65 final size:63
Alignment explanation
Indices: 30048--30255 Score: 224
Period size: 65 Copynumber: 3.2 Consensus size: 63
30038 TTTCAAAGTG
* * **
30048 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCA-CAA-CCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATT
30111 TC
62 TC
* * *
30113 ATGTATCGATGCACATACTATGCATCGATGCACTCAGGGT-TTTATGAAAACATCGAATGCATTT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGCTATTT-TG-AAACATCGAATGCATTT
*
30177 G
63 C
* *
30178 ATGCATCGATGCACCAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
*
30242 ATGCATTGATGCAC
1 ATGCATCGATGCAC
30256 TCTTAGTGCA
Statistics
Matches: 123, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 48 0.39
65 65 0.53
66 5 0.04
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
Found at i:30273 original size:64 final size:64
Alignment explanation
Indices: 30096--30275 Score: 199
Period size: 65 Copynumber: 2.8 Consensus size: 64
30086 GAATAAATTG
* *
30096 AACATCGAATGCATTTCATGTATCGATGCACATACTA-TGCATCGATGCACTCAGGGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCAC-T-CTAGTGCATCGATGCACTCAGGCTTTTATGA
30160 A
64 A
*
30161 AACATCGAATGCATTTGATGCATCGATGCAC-C-AGCCATGCATCGATGCACTCAGGCTATTT-T
1 AACATCGAATGCATTTCATGCATCGATGCACTCTAG---TGCATCGATGCACTCAGGCT-TTTAT
30223 G-A
62 GAA
* * * *
30225 AACATCGAATGCATTTTATGCATTGATGCACTCTTAGTGCACCTATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACTC-TAGTGCATCGATGCACT
30276 AAGGTTCCAA
Statistics
Matches: 100, Mismatches: 7, Indels: 17
0.81 0.06 0.14
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
64 42 0.42
65 51 0.51
66 3 0.03
67 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTAGTGCATCGATGCACTCAGGCTTTTATGAA
Found at i:34040 original size:20 final size:20
Alignment explanation
Indices: 34002--34061 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
33992 CAGAACCCCA
*
34002 GGGGGGTATCGATTCCC-CTGT
1 GGGGGG-ATCGATTCCCTC-AT
*
34023 GGGGGGAATCGGTTCCCTCAT
1 GGGGGG-ATCGATTCCCTCAT
34044 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
34062 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.32
21 22 0.65
22 1 0.03
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (20 bp):
GGGGGGATCGATTCCCTCAT
Found at i:37913 original size:22 final size:21
Alignment explanation
Indices: 37871--37910 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
37861 GAGTTTGTTT
*
37871 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
37892 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
37911 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:41021 original size:22 final size:22
Alignment explanation
Indices: 40996--41057 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
40986 CAGTGCTAAG
* *
40996 GCACTTCTGTATTAGTGCGATC
1 GCACTTCTATATCAGTGCGATC
*
41018 GCACTTCTATATCAGTGCGAAC
1 GCACTTCTATATCAGTGCGATC
** *
41040 ATAATTCTATATCAGTGC
1 GCACTTCTATATCAGTGC
41058 TGAGGCATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (22 bp):
GCACTTCTATATCAGTGCGATC
Found at i:43969 original size:2 final size:2
Alignment explanation
Indices: 43962--44030 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
43952 ACAATTTTCT
43962 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
44004 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 T
44031 GTTTATCGTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44443 original size:15 final size:15
Alignment explanation
Indices: 44423--44457 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
44413 AAAAAAAAAC
44423 TAATACTTATTTTAT
1 TAATACTTATTTTAT
44438 TAATACTTATTTTAT
1 TAATACTTATTTTAT
44453 TAATA
1 TAATA
44458 TGCAGGTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATACTTATTTTAT
Found at i:46156 original size:26 final size:26
Alignment explanation
Indices: 46123--46181 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
46113 TTATAAATAC
*
46123 TTAT-TTAAAAATAAT-GTTATAATTT
1 TTATATTAAAAATAATATTTAT-ATTT
*
46148 TTTTATT-AAAATAATATTTATATTT
1 TTATATTAAAAATAATATTTATATTT
46173 TTATATTAA
1 TTATATTAA
46182 TTAATTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TTATATTAAAAATAATATTTATATTT
Found at i:47974 original size:42 final size:42
Alignment explanation
Indices: 47910--47991 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
47900 AGGCCACAGC
*
47910 GGTACATGCCCAACCCACCAGTTCAGATTCCATATCCGCAAA
1 GGTACATGCCCAACCCACCAGTTCAGATGCCATATCCGCAAA
* * * *
47952 GGTATATGCCCAACCCATCAGTTCATATGCCATCTCCGCA
1 GGTACATGCCCAACCCACCAGTTCAGATGCCATATCCGCA
47992 GGGTTACATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.22
Consensus pattern (42 bp):
GGTACATGCCCAACCCACCAGTTCAGATGCCATATCCGCAAA
Found at i:48589 original size:18 final size:18
Alignment explanation
Indices: 48566--48602 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
48556 TTAAATTATG
*
48566 TAATGTTTTTTAAATGTT
1 TAATGTTTGTTAAATGTT
48584 TAATGTTTGTTAAATGTT
1 TAATGTTTGTTAAATGTT
48602 T
1 T
48603 TTAAAATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (18 bp):
TAATGTTTGTTAAATGTT
Found at i:48646 original size:84 final size:83
Alignment explanation
Indices: 48475--48626 Score: 229
Period size: 84 Copynumber: 1.9 Consensus size: 83
48465 AATTTTATGT
* ** *
48475 AATTTTGTAATGTTTTTTAAATGTTTAATGGTTGTTATAAAAATGTTTTTAAAATTTAAATTCAA
1 AATTATGTAATGTTTTTTAAATGTTTAATGGTTGTTAT-AAAATGTTTTTAAAATGCAAATCCAA
48540 ATTCAACATGAAATGTTTA
65 ATTCAACATGAAATGTTTA
*
48559 AATTATGTAATGTTTTTTAAATGTTTAATGTTTG-T-T-AAATGTTTTTAAAATGCAAATCCAAA
1 AATTATGTAATGTTTTTTAAATGTTTAATGGTTGTTATAAAATGTTTTTAAAATGCAAATCCAAA
48621 TTCAAC
66 TTCAAC
48627 TTAATATTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
80 29 0.46
82 1 0.02
83 1 0.02
84 32 0.51
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.47
Consensus pattern (83 bp):
AATTATGTAATGTTTTTTAAATGTTTAATGGTTGTTATAAAATGTTTTTAAAATGCAAATCCAAA
TTCAACATGAAATGTTTA
Found at i:49227 original size:137 final size:136
Alignment explanation
Indices: 48959--49494 Score: 636
Period size: 137 Copynumber: 3.9 Consensus size: 136
48949 CAGCTTCTAA
* * * * * *
48959 TCCCATAAAAAATAATAGTTGTTTACATGAATAGT-TCCCCGCCGGGGGACATCACACATAATAG
1 TCCCATCAAACATAATAGGTGTTGACGTGAATAGTAT-CCCGTCGGGGGACATCACACATAATAG
* * * * * * *
49023 GGAAATTAGAACCTGTTCTCTGACAAAAATGAAAGGCACGTCTCACAAGAAGCGCTTCCACCACA
65 GGCAATTATAACCTATTCTCTGACAAAAAGGAAAGGCACATCCCACAAGAAGCGCTTTCACCACA
49088 TTGTTACG
130 TTGTT-CG
* *
49096 TCCCATCAAACATAATAGGTGTTGACGTGAATAGTATCCC-T-AGGGGACATCACACATAGTAGG
1 TCCCATCAAACATAATAGGTGTTGACGTGAATAGTATCCCGTCGGGGGACATCACACATAATAGG
* *
49159 GCAATTATAACCTATTCTCTGACAAAAAGAAAAGACGCGCATCCCACAAGAAGCGCTTTCACCAC
66 GCAATTATAACCTATTCTCTGACAAAAAGGAAAG--GCACATCCCACAAGAAGCGCTTTCACCAC
*
49224 ATTGTTGTG
129 ATTGTT-CG
* *
49233 TCCCATCAAACATAATAGGTGTTGAAGTGAATAGT-TCCCCGTCGGGGGACATCATACATAATAG
1 TCCCATCAAACATAATAGGTGTTGACGTGAATAGTAT-CCCGTCGGGGGACATCACACATAATAG
* * * * ** *
49297 GACAATTATAACTTATTTTTTGACAAAAAGGAAAGGCATGTCCCATAAGAAGCGCTTTCACCACA
65 GGCAATTATAACCTATTCTCTGACAAAAAGGAAAGGCACATCCCACAAGAAGCGCTTTCACCACA
49362 TT-TTCG
130 TTGTTCG
* * * *
49368 CATCCCATCAAACATAATAGGTGTTGACATGAATAGTACCCCAGTCGGGGGGCATCACACATAGT
1 --TCCCATCAAACATAATAGGTGTTGACGTGAATAGTATCCC-GTCGGGGGACATCACACATAAT
* *
49433 A-GGCAATTATAACCTATAT-TCTAACAAAAAGGAAAGGCGCATCCCACAAGAAGCGCTTTCAC
63 AGGGCAATTATAACCTAT-TCTCTGACAAAAAGGAAAGGCACATCCCACAAGAAGCGCTTTCAC
49495 GTTATTAAAT
Statistics
Matches: 341, Mismatches: 47, Indels: 22
0.83 0.11 0.05
Matches are distributed among these distances:
135 50 0.15
136 3 0.01
137 217 0.64
138 23 0.07
139 48 0.14
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (136 bp):
TCCCATCAAACATAATAGGTGTTGACGTGAATAGTATCCCGTCGGGGGACATCACACATAATAGG
GCAATTATAACCTATTCTCTGACAAAAAGGAAAGGCACATCCCACAAGAAGCGCTTTCACCACAT
TGTTCG
Found at i:49475 original size:274 final size:273
Alignment explanation
Indices: 48959--49494 Score: 744
Period size: 274 Copynumber: 2.0 Consensus size: 273
48949 CAGCTTCTAA
* *
48959 TCCCATAAAAAATAATAGTTGTTTACATGAATAGTTCCCCGCCGGGGGACATCACACATAATAGG
1 TCCCATAAAAAATAATAGGTGTTGACATGAATAGTTCCCCGCCGGGGGACATCACACATAATAGG
* * *
49024 GAAATTAGAACCTGTTCTCTGACAAAAATGAAAGGCACGTCTCACAAGAAGCGCTTCCACCACAT
66 GAAATTAGAACCTATTCTCTGACAAAAAGGAAAGGCACGTCCCACAAGAAGCGCTTCCACCACAT
* *
49089 TGTTACGTCCCATCAAACATAATAGGTGTTGACGTGAATAGTATCCCTAGGGGACATCACACATA
131 TGTTACGTCCCATCAAACATAATAGGTGTTGACATGAATAGTACCCCTAGGGGACATCACACATA
*
49154 GTAGGGCAATTATAACCTATTCTCTGACAAAAAGAAAAGACGCGCATCCCACAAGAAGCGCTTTC
196 GTAGGGCAATTATAACCTATTCTCTAACAAAAAGAAAAGA-GCGCATCCCACAAGAAGCGCTTTC
49219 ACCACATTGTTGTG
260 ACCACATTGTTGTG
* * * *
49233 TCCCATCAAACATAATAGGTGTTGA-AGTGAATAGTTCCCCGTCGGGGGACATCATACATAATA-
1 TCCCATAAAAAATAATAGGTGTTGACA-TGAATAGTTCCCCGCCGGGGGACATCACACATAATAG
* * * * * * *
49296 GGACAATTATAACTTATTTTTTGACAAAAAGGAAAGGCATGTCCCATAAGAAGCGCTTTCACCAC
65 GGA-AATTAGAACCTATTCTCTGACAAAAAGGAAAGGCACGTCCCACAAGAAGCGCTTCCACCAC
* *
49361 ATT-TT-CGCATCCCATCAAACATAATAGGTGTTGACATGAATAGTACCCCAGTCGGGGGGCATC
129 ATTGTTACG--TCCCATCAAACATAATAGGTGTTGACATGAATAGTACCCC--T-AGGGGACATC
*
49424 ACACATAGTA-GGCAATTATAACCTATAT-TCTAACAAAAAGGAAAG-GCGCATCCCACAAGAAG
189 ACACATAGTAGGGCAATTATAACCTAT-TCTCTAACAAAAAGAAAAGAGCGCATCCCACAAGAAG
49486 CGCTTTCAC
253 CGCTTTCAC
49495 GTTATTAAAT
Statistics
Matches: 232, Mismatches: 22, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
272 2 0.01
273 6 0.03
274 173 0.75
276 32 0.14
277 19 0.08
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (273 bp):
TCCCATAAAAAATAATAGGTGTTGACATGAATAGTTCCCCGCCGGGGGACATCACACATAATAGG
GAAATTAGAACCTATTCTCTGACAAAAAGGAAAGGCACGTCCCACAAGAAGCGCTTCCACCACAT
TGTTACGTCCCATCAAACATAATAGGTGTTGACATGAATAGTACCCCTAGGGGACATCACACATA
GTAGGGCAATTATAACCTATTCTCTAACAAAAAGAAAAGAGCGCATCCCACAAGAAGCGCTTTCA
CCACATTGTTGTG
Found at i:51635 original size:21 final size:21
Alignment explanation
Indices: 51609--51649 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
51599 AATATTCATG
*
51609 CTCTCATGTCATAGCAGCTTA
1 CTCTCATGTCATAGAAGCTTA
51630 CTCTCATGTCATAGAAGCTT
1 CTCTCATGTCATAGAAGCTT
51650 GCTCACATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (21 bp):
CTCTCATGTCATAGAAGCTTA
Found at i:52537 original size:28 final size:29
Alignment explanation
Indices: 52482--52537 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
52472 AGCCCGAATG
* * *
52482 GGTGTTACTTTGGGAAATATTGGAAAAAC
1 GGTGTTACATCGGGAAATATTAGAAAAAC
52511 GGTGTTACATCGGG-AATATTAGAAAAA
1 GGTGTTACATCGGGAAATATTAGAAAAA
52538 TATGGTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.29
Consensus pattern (29 bp):
GGTGTTACATCGGGAAATATTAGAAAAAC
Found at i:53005 original size:2 final size:2
Alignment explanation
Indices: 52998--53033 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
52988 TCCATTTGTA
52998 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53034 ATAGTCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.