Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003247.1 Hibiscus syriacus cultivar Beakdansim tig00006827_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: 92792
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2128 original size:14 final size:14
Alignment explanation
Indices: 2109--2138 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2099 ATACTATATT
*
2109 TACTCTACACAGAG
1 TACTCTAAACAGAG
2123 TACTCTAAACAGAG
1 TACTCTAAACAGAG
2137 TA
1 TA
2139 GCATCCGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (14 bp):
TACTCTAAACAGAG
Found at i:3589 original size:15 final size:13
Alignment explanation
Indices: 3568--3607 Score: 55
Period size: 12 Copynumber: 3.0 Consensus size: 13
3558 TTCATCATTC
3568 ATTATATTATATA
1 ATTATATTATATA
3581 GATTTATATTATA-A
1 -A-TTATATTATATA
3595 ATTATATTATATA
1 ATTATATTATATA
3608 TCCATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 10 0.42
13 2 0.08
14 2 0.08
15 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
ATTATATTATATA
Found at i:4930 original size:2 final size:2
Alignment explanation
Indices: 4923--4949 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4913 TTTATGTATG
4923 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
4950 TCATTTTACC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5192 original size:2 final size:2
Alignment explanation
Indices: 5187--5238 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
5177 TATATTCTAC
5187 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
5229 AT AT AT AT AT
1 AT AT AT AT AT
5239 TATTTATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5392 original size:19 final size:19
Alignment explanation
Indices: 5347--5397 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
5337 TTTTCATTGT
*
5347 TTTATATTTTATTTTATTA
1 TTTATATTTTATTTTATCA
* *
5366 TGTGTATTTT-TTTTATCCA
1 TTTATATTTTATTTTAT-CA
5385 TTTATATTTTATT
1 TTTATATTTTATT
5398 ATATTTTCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 6 0.24
19 17 0.68
20 2 0.08
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTATATTTTATTTTATCA
Found at i:5418 original size:23 final size:25
Alignment explanation
Indices: 5392--5439 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
5382 CCATTTATAT
5392 TTTA-TTATATTTTC-TTCTTTTTC
1 TTTATTTATATTTTCGTTCTTTTTC
* *
5415 TTTATTTGTATTTTCGTTTTTTTTC
1 TTTATTTATATTTTCGTTCTTTTTC
5440 CTTTGCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 9 0.43
25 8 0.38
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.75
Consensus pattern (25 bp):
TTTATTTATATTTTCGTTCTTTTTC
Found at i:5419 original size:38 final size:38
Alignment explanation
Indices: 5347--5419 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
5337 TTTTCATTGT
* *
5347 TTTATATTTTATTTTATTATGTGTATTTTTTTTATCCA
1 TTTATATTTTATTATATTATCTGTATTTTTTTTATCCA
* *
5385 TTTATATTTTATTATATTTTCT-TCTTTTTCTTTAT
1 TTTATATTTTATTATATTATCTGTATTTTT-TTTAT
5420 TTGTATTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 6 0.20
38 24 0.80
ACGTcount: A:0.19, C:0.07, G:0.03, T:0.71
Consensus pattern (38 bp):
TTTATATTTTATTATATTATCTGTATTTTTTTTATCCA
Found at i:15938 original size:20 final size:19
Alignment explanation
Indices: 15910--15953 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 19
15900 TCCTAAGTCG
15910 AAAAAAAAACGAAAAAAACA
1 AAAAAAAAAC-AAAAAAACA
15930 AAAACAAAAACAAAAAAACA
1 AAAA-AAAAACAAAAAAACA
15950 AAAA
1 AAAA
15954 GAGAAAAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.00
Consensus pattern (19 bp):
AAAAAAAAACAAAAAAACA
Found at i:15962 original size:14 final size:14
Alignment explanation
Indices: 15910--15953 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
15900 TCCTAAGTCG
15910 AAAAAAAAACGAAAA
1 AAAAAAAAAC-AAAA
*
15925 AAACAAAAACAAAA
1 AAAAAAAAACAAAA
*
15939 ACAAAAAAACAAAA
1 AAAAAAAAACAAAA
15953 A
1 A
15954 GAGAAAAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACAAAA
Found at i:16930 original size:105 final size:105
Alignment explanation
Indices: 16748--17569 Score: 1322
Period size: 105 Copynumber: 8.0 Consensus size: 105
16738 TTTTACCCAT
16748 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
16813 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
16853 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
16918 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
*
16958 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTCCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
17023 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
*
17063 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
17128 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
17168 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
17233 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCGG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
*
17273 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * *
17338 AAGGGACCGCTAGTTGTCAA-TAA-A-----CAAGTTC--
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
* ***
17369 -G---ATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
**
17430 AAGGGACCGCTGACTGT---C-AAC--TTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
* *
17464 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACAACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
17529 AAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAG
17570 CTTCACAACG
Statistics
Matches: 667, Mismatches: 31, Indels: 37
0.91 0.04 0.05
Matches are distributed among these distances:
89 2 0.00
92 69 0.10
93 6 0.01
95 1 0.00
96 1 0.00
98 6 0.01
99 69 0.10
103 4 0.01
104 2 0.00
105 495 0.74
106 12 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
Found at i:17435 original size:92 final size:91
Alignment explanation
Indices: 17278--17582 Score: 369
Period size: 92 Copynumber: 3.2 Consensus size: 91
17268 TTCGGAGCCA
* *
17278 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
17343 ACCGCTAGTTGTCAATAAACAAGTTCG
66 ACCGCT-GTTGTCAATAAACAATTTCG
***
17370 ATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGG
* ***
17435 ACCGCTGACTGTCAACTTCTCAATTTCAGAG
66 ACCGCTG-TTGTCAA-TAAACAATTTC---G
*
17466 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA-ACAACGCAAGTTCAACTTCACAACGA
1 ---ATTTCAACTTCACAACGAAGGATATTGGACT-CAAGACAACGCAAGTTCAACTTCACGACGA
*
17530 AGGGACCGCTGGTTGTCAATAAACAATTTCCCA
62 AGGGACCGCT-GTTGTCAATAAACAATTT--CG
*
17563 ATTTCAGCTTCACAACGAAG
1 ATTTCAACTTCACAACGAAG
17583 TATCTTTGGC
Statistics
Matches: 181, Mismatches: 20, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
91 1 0.01
92 72 0.40
93 7 0.04
94 19 0.10
96 1 0.01
98 7 0.04
99 69 0.38
100 5 0.03
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (91 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGTTGTCAATAAACAATTTCG
Found at i:17532 original size:191 final size:195
Alignment explanation
Indices: 17170--17582 Score: 627
Period size: 191 Copynumber: 2.1 Consensus size: 195
17160 AAATTCAGAG
* *
17170 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAA
** *
17235 GGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCGGAGCCAATTTCAACTTCACAACGAAGGA
66 GGGACCGCTGACTGT--ACAAACA-TTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGA
* * *
17300 TATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTAGTTGTCAATAAACAA
128 TATTGGACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTAGTTGTCAATAAACAA
17365 GTT
193 GTT
* **
17368 -CGATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAA
*
17432 GGGACCGCTGACTGT-C-AAC-TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 GGGACCGCTGACTGTACAAACATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* *
17494 TGGACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTT
131 TGGACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTAGTTGTCAATAAACAAGTT
*
17559 CCCAATTTCAGCTTCACAACGAAG
1 -CCAATTTCAACTTCACAACGAAG
17583 TATCTTTGGC
Statistics
Matches: 197, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
191 101 0.51
193 23 0.12
194 1 0.01
197 72 0.37
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (195 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAA
GGGACCGCTGACTGTACAAACATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
TGGACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTAGTTGTCAATAAACAAGTT
Found at i:17652 original size:20 final size:20
Alignment explanation
Indices: 17627--17668 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
17617 CCAGAACTCT
17627 GAGTTCGATTTCAACTTCAC
1 GAGTTCGATTTCAACTTCAC
*
17647 GAGTTCGATTTCAATTTCAC
1 GAGTTCGATTTCAACTTCAC
17667 GA
1 GA
17669 CGAAGGATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:17904 original size:15 final size:13
Alignment explanation
Indices: 17883--17922 Score: 55
Period size: 12 Copynumber: 3.0 Consensus size: 13
17873 TTCATCATTC
17883 ATTATATTATATA
1 ATTATATTATATA
17896 GATTTATATTATA-A
1 -A-TTATATTATATA
17910 ATTATATTATATA
1 ATTATATTATATA
17923 TCCATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 10 0.42
13 2 0.08
14 2 0.08
15 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
ATTATATTATATA
Found at i:19259 original size:2 final size:2
Alignment explanation
Indices: 19247--19291 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
19237 TTTATGTATG
*
19247 TA TA TA CA 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
19289 TA T
1 TA T
19292 CATTTTACCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19456 original size:20 final size:20
Alignment explanation
Indices: 19407--19460 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 20
19397 TACTTTTTAC
19407 TATTATTATTATTTATTTATT
1 TATTATTA-TATTTATTTATT
19428 TATGCTATTATATTATATTT-TT
1 TAT--TATTATATT-TATTTATT
19450 TATTATTATAT
1 TATTATTATAT
19461 ACGTATATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 8 0.27
21 3 0.10
22 9 0.30
23 10 0.33
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTATTATATTTATTTATT
Found at i:19461 original size:17 final size:18
Alignment explanation
Indices: 19409--19461 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
19399 CTTTTTACTA
*
19409 TTATTATTATTTATTTAT
1 TTATTATTATATATTTAT
*
19427 TTATGCTATTATATTATATTTT
1 TTAT--TATTATA-TAT-TTAT
19449 TTATTATTATATA
1 TTATTATTATATA
19462 CGTATATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 13 0.45
21 3 0.10
22 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TTATTATTATATATTTAT
Found at i:27115 original size:22 final size:22
Alignment explanation
Indices: 27090--27133 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
27080 TGCACTTTCG
27090 GTGCAACCCCTTTCTATGACTT
1 GTGCAACCCCTTTCTATGACTT
* *
27112 GTGCAGCCCCTTTTTATGACTT
1 GTGCAACCCCTTTCTATGACTT
27134 TTAACGAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.30, G:0.16, T:0.39
Consensus pattern (22 bp):
GTGCAACCCCTTTCTATGACTT
Found at i:29079 original size:19 final size:18
Alignment explanation
Indices: 29043--29082 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
29033 AAAAATTATT
*
29043 AATATTTTAAAAAGTCAA
1 AATATTTTAAAAACTCAA
*
29061 AATATTTCTAAAATCTCAA
1 AATATTT-TAAAAACTCAA
29080 AAT
1 AAT
29083 CTTTAATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.35
Consensus pattern (18 bp):
AATATTTTAAAAACTCAA
Found at i:29092 original size:15 final size:15
Alignment explanation
Indices: 29072--29110 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
29062 ATATTTCTAA
29072 AATCTCAAAATCTTT
1 AATCTCAAAATCTTT
29087 AATCTCAAAATCTTT
1 AATCTCAAAATCTTT
29102 AATCTCAAA
1 AATCTCAAA
29111 GCATCCACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.36
Consensus pattern (15 bp):
AATCTCAAAATCTTT
Found at i:40510 original size:20 final size:21
Alignment explanation
Indices: 40475--40520 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
40465 ATAATATTAT
40475 ATATATTTTAACATT-ACTAA
1 ATATATTTTAACATTAACTAA
** *
40495 ATATATTTTATTATTAACTTA
1 ATATATTTTAACATTAACTAA
40516 ATATA
1 ATATA
40521 AAAATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATATTTTAACATTAACTAA
Found at i:40522 original size:27 final size:25
Alignment explanation
Indices: 40478--40562 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 25
40468 ATATTATATA
*
40478 TATTTTAACATT-ACTAAATATATTT
1 TATTTTAAC-TTAAATAAATATATTT
*
40503 TATTATTAACTTAATATAAAAATATTT
1 TATT-TTAACTTAA-ATAAATATATTT
**
40530 TATTTTATTTTAAA-AATATATATTT
1 TATTTTAACTTAAATAA-ATATATTT
*
40555 TATGTTAA
1 TATTTTAA
40563 AATGTTTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
24 2 0.04
25 20 0.41
26 13 0.27
27 14 0.29
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (25 bp):
TATTTTAACTTAAATAAATATATTT
Found at i:40553 original size:20 final size:21
Alignment explanation
Indices: 40519--40564 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
40509 TAACTTAATA
* *
40519 TAAAAATATTTTATTTTATTT
1 TAAAAATATTATATTTTATGT
40540 TAAAAATA-TATATTTTATGT
1 TAAAAATATTATATTTTATGT
40560 TAAAA
1 TAAAA
40565 TGTTTTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TAAAAATATTATATTTTATGT
Found at i:40627 original size:30 final size:29
Alignment explanation
Indices: 40591--40650 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 29
40581 TAAGAATAAA
40591 AATATATTTAAT-AATTTAAAATAATAATAT
1 AATATATTTAATAAATTT-AAATAA-AATAT
40621 AATATATTTAATAAATTTAAATAAAATAT
1 AATATATTTAATAAATTTAAATAAAATAT
40650 A
1 A
40651 TATTCTGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 6 0.21
30 18 0.62
31 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AATATATTTAATAAATTTAAATAAAATAT
Found at i:40800 original size:24 final size:25
Alignment explanation
Indices: 40731--40809 Score: 92
Period size: 24 Copynumber: 3.2 Consensus size: 25
40721 AAATAAAAAT
40731 AAAATATTTTTAAATTAAGTTAATA-A
1 AAAATATTTTT-AA-TAAGTTAATATA
* *
40757 AAAA-ATATTTAATAATTTAATATA
1 AAAATATTTTTAATAAGTTAATATA
40781 AAAATATTTTTAA-AAGTTAATATA
1 AAAATATTTTTAATAAGTTAATATA
40805 TAAAA
1 -AAAA
40810 AATATTATGA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
23 9 0.20
24 17 0.37
25 16 0.35
26 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (25 bp):
AAAATATTTTTAATAAGTTAATATA
Found at i:40815 original size:27 final size:26
Alignment explanation
Indices: 40731--40815 Score: 81
Period size: 25 Copynumber: 3.3 Consensus size: 26
40721 AAATAAAAAT
40731 AAAATATTTTT-AAATTAAGT-TAATAA
1 AAAATATTTTTAAAATTAA-TAT-ATAA
* *
40757 AAAA-ATATTTAATAATTTA-ATAT-A
1 AAAATATTTTTAA-AATTAATATATAA
40781 AAAATATTTTTAAAAGTTAATATATAA
1 AAAATATTTTTAAAA-TTAATATATAA
40808 AAAATATT
1 AAAATATT
40816 ATGAATTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
24 7 0.15
25 17 0.35
26 10 0.21
27 14 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
AAAATATTTTTAAAATTAATATATAA
Found at i:41271 original size:31 final size:31
Alignment explanation
Indices: 41235--41293 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
41225 ACCACATCTC
* * * *
41235 AATTAAATATAAATAAAATTGATCATATTTT
1 AATTAAATAAAAACAAAAGTGAACATATTTT
41266 AATTAAATAAAAACAAAAGTGAACATAT
1 AATTAAATAAAAACAAAAGTGAACATAT
41294 ATTATGTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (31 bp):
AATTAAATAAAAACAAAAGTGAACATATTTT
Found at i:41974 original size:16 final size:15
Alignment explanation
Indices: 41944--42005 Score: 99
Period size: 16 Copynumber: 4.1 Consensus size: 15
41934 ATAAAATATT
41944 AATTATTTA-TTTTA
1 AATTATTTATTTTTA
41958 AATTATTTAATTTTTA
1 AATTATTT-ATTTTTA
41974 AATTATTTATTTTTTA
1 AATTATTTA-TTTTTA
41990 AATTATTTATTTTTA
1 AATTATTTATTTTTA
42005 A
1 A
42006 GCCTATAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.18
15 9 0.20
16 28 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
AATTATTTATTTTTA
Found at i:41982 original size:9 final size:9
Alignment explanation
Indices: 41954--41998 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
41944 AATTATTTAT
41954 TTTAAATTA
1 TTTAAATTA
41963 TTT-AATT-
1 TTTAAATTA
41970 TTTAAATTA
1 TTTAAATTA
*
41979 TTT--ATTT
1 TTTAAATTA
41986 TTTAAATTA
1 TTTAAATTA
41995 TTTA
1 TTTA
41999 TTTTTAAGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
7 9 0.30
8 8 0.27
9 13 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTAAATTA
Found at i:64548 original size:35 final size:35
Alignment explanation
Indices: 64502--64577 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
64492 AAAACAGACC
* *
64502 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
64537 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
64572 TCAATT
1 TCAATT
64578 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:65119 original size:130 final size:130
Alignment explanation
Indices: 64973--65220 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
64963 TATTTATATA
* **
64973 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
65038 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
65103 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
65168 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
65221 GAATAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:65251 original size:130 final size:129
Alignment explanation
Indices: 64987--65251 Score: 318
Period size: 130 Copynumber: 2.0 Consensus size: 129
64977 ATTTGGTCCT
* ** *
64987 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * * * **** *
65052 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAATAAAATAAGCTATCAAAGAAGT-CA
65117 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
65182 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAATAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AATAAAA-TAAGCTATCAAAGAAGT
65246 -A
128 CA
65247 AAATT
1 AAATT
65252 TGGGTCTTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 100 0.88
132 9 0.08
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAATAAAATAAGCTATCAAAGAAGTCA
Found at i:65490 original size:25 final size:25
Alignment explanation
Indices: 65461--65525 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
65451 TAAATGATGG
65461 GAAAATATTATATTTTTTTACAATA
1 GAAAATATTATATTTTTTTACAATA
65486 GAAAATATTATATTTTTTTACAATA
1 GAAAATATTATATTTTTTTACAATA
*
65511 AAAAATATTATATTT
1 GAAAATATTATATTT
65526 GATAAATTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (25 bp):
GAAAATATTATATTTTTTTACAATA
Found at i:65735 original size:16 final size:18
Alignment explanation
Indices: 65714--65747 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
65704 ATTTCTTATT
65714 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
65730 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
65748 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:75837 original size:55 final size:55
Alignment explanation
Indices: 75776--76603 Score: 468
Period size: 51 Copynumber: 15.9 Consensus size: 55
75766 GACTTGAAAC
*
75776 ATCTTCAAATGACGAG-CCTGCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACA
1 ATCTTCAAATAACGAGTCC-GCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACA
* * * * *
75831 ATCTTCATAA-AACGTGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACA
1 ATCTTCA-AATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* * * * *
75886 ATCTTTAATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAA
1 ATCTTCAA-ATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACA
* * *
75942 ATCTTC-AATAAAC-AGGTCCGCTCCCTATTCTTTCAGGGAGTATAGGACT----CA
1 ATCTTCAAAT-AACGA-GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** * * *
75993 ATCTTCAACGAACTAGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT----CA
1 ATCTTCAAATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** ** * *
76044 ATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT----CA
1 ATCTTCAAATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** *** * *
76095 ATCTTCAACGAATTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT----CA
1 ATCTTCAAATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** ** * *
76146 ATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT----CA
1 ATCTTCAAATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** ** * * *
76197 ATCTTCAACGAACTTGTCTGCTCCCTATTCATTCAGAGAGTATAGGACT----CA
1 ATCTTCAAATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** ** *
76248 ATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CA
1 ATCTTCAAATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** ** *
76299 ATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CA
1 ATCTTCAAATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** ** *
76350 ATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CA
1 ATCTTCAAATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** ** *
76401 ATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CA
1 ATCTTCAAATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** ** * *
76452 ATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT----CA
1 ATCTTCAAATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** ** * *
76503 ATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT----CA
1 ATCTTCAAATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** ** * *
76554 ATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC
1 ATCTTCAAATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTC
76604 AATCTTCAAC
Statistics
Matches: 730, Mismatches: 31, Indels: 27
0.93 0.04 0.03
Matches are distributed among these distances:
51 596 0.82
52 2 0.00
54 2 0.00
55 83 0.11
56 47 0.06
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (55 bp):
ATCTTCAAATAACGAGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
Found at i:76017 original size:51 final size:51
Alignment explanation
Indices: 75902--76613 Score: 1244
Period size: 51 Copynumber: 13.9 Consensus size: 51
75892 AATAAAACGG
* * * ** **
75902 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAG
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACTT
* * *
75957 GTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTA
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
76008 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
76059 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAATTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
76110 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
76161 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
76212 GTCTGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
76263 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
76314 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
76365 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
76416 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
76467 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
76518 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
76569 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
76614 AAACGAATTT
Statistics
Matches: 640, Mismatches: 17, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
51 609 0.95
55 31 0.05
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (51 bp):
GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:77976 original size:18 final size:18
Alignment explanation
Indices: 77953--78053 Score: 54
Period size: 18 Copynumber: 5.7 Consensus size: 18
77943 TCTTTTTTCA
77953 TTTTTCTCTTTTC-CTTCC
1 TTTTTCTCTTTTCTCTT-C
*
77971 TTTTTCCATTTTTTCTCTTC
1 TTTTT-C-TCTTTTCTCTTC
*
77991 TTTTT-TCTTTTC-GTT-
1 TTTTTCTCTTTTCTCTTC
* *
78006 TTTTCCATCATTT-T-TTC
1 TTTTTC-TCTTTTCTCTTC
*
78023 TTTTTTCTCATTTTTTCTTC
1 -TTTTTCTC-TTTTCTCTTC
78043 -TTTTCTCTTTT
1 TTTTTCTCTTTT
78054 ATTTCTTCTT
Statistics
Matches: 65, Mismatches: 7, Indels: 23
0.68 0.07 0.24
Matches are distributed among these distances:
15 4 0.06
16 4 0.06
17 17 0.26
18 20 0.31
19 2 0.03
20 15 0.23
21 3 0.05
ACGTcount: A:0.04, C:0.23, G:0.01, T:0.72
Consensus pattern (18 bp):
TTTTTCTCTTTTCTCTTC
Found at i:77996 original size:12 final size:13
Alignment explanation
Indices: 77977--78023 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
77967 TTCCTTTTTC
77977 CATTTTTTCTCTT
1 CATTTTTTCTCTT
*
77990 C-TTTTTTCTTTT
1 CATTTTTTCTCTT
* *
78002 CGTTTTTTC-CAT
1 CATTTTTTCTCTT
78014 CATTTTTTCT
1 CATTTTTTCT
78024 TTTTTCTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 20 0.71
13 8 0.29
ACGTcount: A:0.06, C:0.21, G:0.02, T:0.70
Consensus pattern (13 bp):
CATTTTTTCTCTT
Found at i:78000 original size:27 final size:26
Alignment explanation
Indices: 77943--78053 Score: 86
Period size: 27 Copynumber: 4.2 Consensus size: 26
77933 CTTTTATTTA
* *
77943 TCTTTTTTCATTTTTCTCTT-TTCCTT
1 TCTTTTTCCATTTTTCTCTTCTT-TTT
*
77969 CCTTTTTCCATTTTTTCTCTTCTTTTT
1 TCTTTTTCCA-TTTTTCTCTTCTTTTT
** *
77996 TC-TTTTCGTTTTTTC-CATCATTTTT
1 TCTTTTTCCATTTTTCTCTTC-TTTTT
*
78021 TCTTTTTTCTCATTTTT-TCTTCTTTTC
1 TC-TTTTTC-CATTTTTCTCTTCTTTTT
78048 TCTTTT
1 TCTTTT
78054 ATTTCTTCTT
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
24 3 0.04
25 13 0.19
26 17 0.25
27 24 0.36
28 10 0.15
ACGTcount: A:0.05, C:0.23, G:0.01, T:0.72
Consensus pattern (26 bp):
TCTTTTTCCATTTTTCTCTTCTTTTT
Found at i:78011 original size:45 final size:44
Alignment explanation
Indices: 77943--78053 Score: 127
Period size: 45 Copynumber: 2.5 Consensus size: 44
77933 CTTTTATTTA
* *
77943 TCTTTTTTCATTTTTCTCTTTTCCTTCCTTTTTCCATTTTTTCTC-T
1 TCTTTTTTC--TTTTCTCTTTTCCATCATTTTTCC-TTTTTTCTCAT
* *
77989 TCTTTTTTCTTTTCGTTTTTTCCATCATTTTTTCTTTTTTCTCAT
1 TCTTTTTTCTTTTC-TCTTTTCCATCATTTTTCCTTTTTTCTCAT
78034 T-TTTTCTTCTTTTCTCTTTT
1 TCTTTT-TTCTTTTCTCTTTT
78054 ATTTCTTCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
44 23 0.40
45 25 0.44
46 9 0.16
ACGTcount: A:0.05, C:0.23, G:0.01, T:0.72
Consensus pattern (44 bp):
TCTTTTTTCTTTTCTCTTTTCCATCATTTTTCCTTTTTTCTCAT
Found at i:78027 original size:20 final size:18
Alignment explanation
Indices: 77998--78060 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 18
77988 TTCTTTTTTC
77998 TTTTCGTTTTTTCCATCATT
1 TTTTC-TTTTTTCC-TCATT
78018 TTTTCTTTTTT-CTCATT
1 TTTTCTTTTTTCCTCATT
*
78035 TTTTCTTCTTTT-CTCTTT
1 TTTTCTT-TTTTCCTCATT
78053 TATTTCTT
1 T-TTTCTT
78061 CTTCAAGCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
17 12 0.30
18 11 0.28
19 12 0.30
20 5 0.12
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTCTTTTTTCCTCATT
Found at i:78058 original size:19 final size:18
Alignment explanation
Indices: 78013--78063 Score: 77
Period size: 17 Copynumber: 2.8 Consensus size: 18
78003 GTTTTTTCCA
78013 TCATTTTTTCTT-TTTTC
1 TCATTTTTTCTTCTTTTC
78030 TCATTTTTTCTTCTTTTC
1 TCATTTTTTCTTCTTTTC
*
78048 TCTTTTATTTCTTCTT
1 TCATTT-TTTCTTCTT
78064 CAAGCAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 12 0.39
18 10 0.32
19 9 0.29
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.75
Consensus pattern (18 bp):
TCATTTTTTCTTCTTTTC
Found at i:80444 original size:4 final size:4
Alignment explanation
Indices: 80437--80466 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
80427 ATACAACAAA
80437 GAAT GAAT GAAT GAAT GAAT GAAAT GAAT G
1 GAAT GAAT GAAT GAAT GAAT G-AAT GAAT G
80467 GGAAAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (4 bp):
GAAT
Found at i:86579 original size:44 final size:46
Alignment explanation
Indices: 86515--86612 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 46
86505 TTGTTATCCA
*
86515 CAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC-TTATT
1 CAAAAAGAAATCCTAACCGCATGATACCTAATTCGCATGCATTATT
* *
86560 CAAAAATAAA-CCTAACCGCATGATACCTAGTTCGCATGCATTTATT
1 CAAAAAGAAATCCTAACCGCATGATACCTAATTCGCATGCA-TTATT
86606 CGAAAAA
1 C-AAAAA
86613 ACGAAAATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
44 27 0.57
45 9 0.19
46 6 0.13
47 5 0.11
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (46 bp):
CAAAAAGAAATCCTAACCGCATGATACCTAATTCGCATGCATTATT
Done.