Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000276.1 Hibiscus syriacus cultivar Beakdansim tig00000510_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: 65030
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Found at i:3927 original size:287 final size:287
Alignment explanation
Indices: 3411--3988 Score: 1129
Period size: 287 Copynumber: 2.0 Consensus size: 287
3401 TTCGAAGCAT
3411 ATGGAGTTTTCAAGTTGGTAATGGACAGCTCATTCGGTTTTGGCAAGACCTTTGGGCGATGAACT
1 ATGGAGTTTTCAAGTTGGTAATGGACAGCTCATTCGGTTTTGGCAAGACCTTTGGGCGATGAACT
3476 ATCCGTTAATGGTTTTATTCCCTACACTGTTTTACATTTTGTTAAATAAGAATGGCAAGTTAATA
66 ATCCGTTAATGGTTTTATTCCCTACACTGTTTTACATTTTGTTAAATAAGAATGGCAAGTTAATA
3541 GAGTTTGGCGAGTTTCGATCAATGGGCTGGTTTTGGAATGTTCAATTGAGGAGAAATTTAAATGA
131 GAGTTTGGCGAGTTTCGATCAATGGGCTGGTTTTGGAATGTTCAATTGAGGAGAAATTTAAATGA
*
3606 TTGGGAATTTGAACAATGGTCTAATTTGATATCAATCATCTCAATTTTCAGCCTGTCCAATGAGC
196 TTGGGAATTTGAACAATGGTCTAATTTGATATCAATCATCTCAATTTTCACCCTGTCCAATGAGC
3671 TCAATGATGGTCTGATTTGGAAAGGTA
261 TCAATGATGGTCTGATTTGGAAAGGTA
3698 ATGGAGTTTTCAAGTTGGTAATGGACAGCTCATTCGGTTTTGGCAAGACCTTTGGGCGATGAACT
1 ATGGAGTTTTCAAGTTGGTAATGGACAGCTCATTCGGTTTTGGCAAGACCTTTGGGCGATGAACT
*
3763 ATCCGTTAATGGTTTTATTCCCTAGACTGTTTTACATTTTGTTAAATAAGAATGGCAAGTTAATA
66 ATCCGTTAATGGTTTTATTCCCTACACTGTTTTACATTTTGTTAAATAAGAATGGCAAGTTAATA
*
3828 GAGTTTGGCGAGTTTCGATTAATGGGCTGGTTTTGGAATGTTCAATTGAGGAGAAATTTAAATGA
131 GAGTTTGGCGAGTTTCGATCAATGGGCTGGTTTTGGAATGTTCAATTGAGGAGAAATTTAAATGA
3893 TTGGGAATTTGAACAATGGTCTAATTTGATATCAATCATCTCAATTTTCACCCTGTCCAATGAGC
196 TTGGGAATTTGAACAATGGTCTAATTTGATATCAATCATCTCAATTTTCACCCTGTCCAATGAGC
3958 TCAATGATGGTCTGATTTGGAAAGGTA
261 TCAATGATGGTCTGATTTGGAAAGGTA
3985 ATGG
1 ATGG
3989 GGAAAGTGTA
Statistics
Matches: 288, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
287 288 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.36
Consensus pattern (287 bp):
ATGGAGTTTTCAAGTTGGTAATGGACAGCTCATTCGGTTTTGGCAAGACCTTTGGGCGATGAACT
ATCCGTTAATGGTTTTATTCCCTACACTGTTTTACATTTTGTTAAATAAGAATGGCAAGTTAATA
GAGTTTGGCGAGTTTCGATCAATGGGCTGGTTTTGGAATGTTCAATTGAGGAGAAATTTAAATGA
TTGGGAATTTGAACAATGGTCTAATTTGATATCAATCATCTCAATTTTCACCCTGTCCAATGAGC
TCAATGATGGTCTGATTTGGAAAGGTA
Found at i:18036 original size:16 final size:16
Alignment explanation
Indices: 17996--18048 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
17986 GAAGTCGTCA
*
17996 AAGAAGAAGAAGAAGAAG
1 AAGAA-AAGAA-AAGGAG
*
18014 AAG-AAAGATAAGGAG
1 AAGAAAAGAAAAGGAG
*
18029 AAGAAAAGAAAAGGGG
1 AAGAAAAGAAAAGGAG
18045 AAGA
1 AAGA
18049 GCTTAAAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 8 0.27
16 18 0.60
17 1 0.03
18 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (16 bp):
AAGAAAAGAAAAGGAG
Found at i:19301 original size:15 final size:17
Alignment explanation
Indices: 19266--19306 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
19256 GAACTTATCA
19266 TATTTTAATTACATGATT
1 TATTTT-ATTACATGATT
19284 TATTTTATTA-AT-ATT
1 TATTTTATTACATGATT
*
19299 TATGTTAT
1 TATTTTAT
19307 ATGTGGCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 10 0.45
16 2 0.09
17 4 0.18
18 6 0.27
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (17 bp):
TATTTTATTACATGATT
Found at i:19324 original size:3 final size:3
Alignment explanation
Indices: 19316--19345 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
19306 TATGTGGCAT
19316 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19346 AAATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20962 original size:142 final size:142
Alignment explanation
Indices: 20787--21075 Score: 560
Period size: 142 Copynumber: 2.0 Consensus size: 142
20777 CAACAATTCT
*
20787 TTTTCCATGAAAGTCACTTGATTTATGTTATTCTATACAAAACCCAAACATATATATCGTACCAC
1 TTTTCCATGAAAGTCACTTGATTTATGCTATTCTATACAAAACCCAAACATATATATCGTACCAC
20852 TTTTATTATATTATATAAAATTTTACATTTAGAAAAAAAAGCTATATAATATTTTTATATGTCGA
66 TTTTATTATATTATATAAAATTTTACATTTAGAAAAAAAAGCTATATAATATTTTTATATGTCGA
20917 GTTTAAATTAAA
131 GTTTAAATTAAA
*
20929 TTTTCCATGAAAGTCACTTGATTTATGCTATTCTATACAAAACCCATACATATATATCGTACCAC
1 TTTTCCATGAAAGTCACTTGATTTATGCTATTCTATACAAAACCCAAACATATATATCGTACCAC
20994 TTTTATTATATTATATAAAATTTTACATTTAGAAAAAAAAGCTATATAATATTTTTATATGTCGA
66 TTTTATTATATTATATAAAATTTTACATTTAGAAAAAAAAGCTATATAATATTTTTATATGTCGA
21059 GTTTAAATTAAA
131 GTTTAAATTAAA
21071 TTTTC
1 TTTTC
21076 ATTAGGAATA
Statistics
Matches: 145, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 145 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (142 bp):
TTTTCCATGAAAGTCACTTGATTTATGCTATTCTATACAAAACCCAAACATATATATCGTACCAC
TTTTATTATATTATATAAAATTTTACATTTAGAAAAAAAAGCTATATAATATTTTTATATGTCGA
GTTTAAATTAAA
Found at i:21524 original size:33 final size:33
Alignment explanation
Indices: 21487--21552 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
21477 ATTTATAGCT
*
21487 GATGATGTAT-ATGTGCAAGAAATTAGGAAAATG
1 GATGATGTATGA-GGGCAAGAAATTAGGAAAATG
21520 GATGATGTATGAGGGCAAGAAATTAGGAAAATG
1 GATGATGTATGAGGGCAAGAAATTAGGAAAATG
21553 TGAGTCTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.30, T:0.24
Consensus pattern (33 bp):
GATGATGTATGAGGGCAAGAAATTAGGAAAATG
Found at i:21578 original size:53 final size:54
Alignment explanation
Indices: 21521--21664 Score: 188
Period size: 53 Copynumber: 2.7 Consensus size: 54
21511 AGGAAAATGG
21521 ATGATGTATGAGGGCAAGAAATTAGGAAAATGTGAGTCTTT-CATTTATGAATA
1 ATGATGTATGAGGGCAAGAAATTAGGAAAATGTGAGTCTTTCCATTTATGAATA
* * * *
21574 ATGATGCATGCA-TGCAAGAAATTAGGAAAATGTGAGT-TTTCCATTTATGGATG
1 ATGATGTATG-AGGGCAAGAAATTAGGAAAATGTGAGTCTTTCCATTTATGAATA
* *
21627 ATGATGTAT-ACGGGTAAGAAATTAGGAAAAGGTGAGTC
1 ATGATGTATGA-GGGCAAGAAATTAGGAAAATGTGAGTC
21665 ACCCCTTCAT
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
51 1 0.01
52 3 0.04
53 73 0.94
54 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (54 bp):
ATGATGTATGAGGGCAAGAAATTAGGAAAATGTGAGTCTTTCCATTTATGAATA
Found at i:23331 original size:29 final size:29
Alignment explanation
Indices: 23289--23348 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
23279 TAGTTAGTCA
23289 CTTTGGTGGTTCCGTGTGACATCTGAATC
1 CTTTGGTGGTTCCGTGTGACATCTGAATC
23318 CTTTGGTGGTTCCGTGTGACATCTGAATC
1 CTTTGGTGGTTCCGTGTGACATCTGAATC
23347 CT
1 CT
23349 CCAGATTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.13, C:0.22, G:0.27, T:0.38
Consensus pattern (29 bp):
CTTTGGTGGTTCCGTGTGACATCTGAATC
Found at i:23531 original size:41 final size:39
Alignment explanation
Indices: 23471--23554 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 39
23461 ACTATATTCG
* *
23471 AACCATATTCCTTTCAAAACGGAAGCTATACACTTAAAACA
1 AACCATATTCCTTTCAAAACGAAAGCCAT--ACTTAAAACA
23512 AACCATATTCCTTAT-AAAACGAAAGCCATACTTAAAACA
1 AACCATATTCCTT-TCAAAACGAAAGCCATACTTAAAACA
23551 AACC
1 AACC
23555 CTTAACTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
39 14 0.35
41 25 0.62
42 1 0.03
ACGTcount: A:0.46, C:0.25, G:0.06, T:0.23
Consensus pattern (39 bp):
AACCATATTCCTTTCAAAACGAAAGCCATACTTAAAACA
Found at i:28315 original size:26 final size:27
Alignment explanation
Indices: 28300--28367 Score: 104
Period size: 26 Copynumber: 2.6 Consensus size: 27
28290 TATCAAGTTC
28300 AACTCGAACTCAAAA-TATAATATTGA
1 AACTCGAACTCAAAATTATAATATTGA
28326 AACTCGAACTCAAAA-TATAATATTGA
1 AACTCGAACTCAAAATTATAATATTGA
*
28352 AACTTGAACTCGAAAA
1 AACTCGAACTC-AAAA
28368 GGCTTGAACT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 36 0.90
27 4 0.10
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (27 bp):
AACTCGAACTCAAAATTATAATATTGA
Found at i:30403 original size:16 final size:16
Alignment explanation
Indices: 30370--30412 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
30360 GTTTACTTCA
30370 GAATGATT-AAACGCT
1 GAATGATTCAAACGCT
*
30385 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
30401 GAATGATTCAAA
1 GAATGATTCAAA
30413 GGCTATGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:35255 original size:24 final size:24
Alignment explanation
Indices: 35184--35255 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 24
35174 GCTTATGACA
35184 TGATAATAT-TTAAATATTGTTTC
1 TGATAATATATTAAATATTGTTTC
* **
35207 TGTTTGTGATATTAAAATATTGTTT-
1 TGATAAT-ATATT-AAATATTGTTTC
35232 TGATAATATATTAAATATTAGTTT
1 TGATAATATATTAAATATT-GTTT
35256 AAATTTAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
23 11 0.28
24 11 0.28
25 6 0.15
26 11 0.28
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.53
Consensus pattern (24 bp):
TGATAATATATTAAATATTGTTTC
Found at i:39347 original size:16 final size:16
Alignment explanation
Indices: 39326--39364 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
39316 AACATAAAAA
*
39326 AAACATTTCCATTAAG
1 AAACATATCCATTAAG
39342 AAACATATCCATTAAG
1 AAACATATCCATTAAG
39358 AAACATA
1 AAACATA
39365 ATAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (16 bp):
AAACATATCCATTAAG
Found at i:40109 original size:16 final size:17
Alignment explanation
Indices: 40088--40133 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
40078 TATTGATTAA
40088 TAGTAA-AAAATATTTT
1 TAGTAATAAAATATTTT
40104 TAGTAAATAAAATATTTT
1 TAGT-AATAAAATATTTT
*
40122 T-GTAATCAAATA
1 TAGTAATAAAATA
40134 ACTATCCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 12 0.44
17 4 0.15
18 11 0.41
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (17 bp):
TAGTAATAAAATATTTT
Found at i:41342 original size:13 final size:14
Alignment explanation
Indices: 41316--41344 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41306 GGAGGGGTAG
41316 AATCAAAAAGAAAA
1 AATCAAAAAGAAAA
41330 AATCAAAAA-AAAA
1 AATCAAAAAGAAAA
41343 AA
1 AA
41345 GAAGAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.83, C:0.07, G:0.03, T:0.07
Consensus pattern (14 bp):
AATCAAAAAGAAAA
Found at i:42340 original size:6 final size:6
Alignment explanation
Indices: 42329--42359 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
42319 AAAAAGAATA
42329 TATTTT TATTTT TATTATT TATTTT TATTTT
1 TATTTT TATTTT TATT-TT TATTTT TATTTT
42360 AAAATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:42351 original size:13 final size:12
Alignment explanation
Indices: 42329--42359 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
42319 AAAAAGAATA
42329 TATTTTTATTTT
1 TATTTTTATTTT
42341 TATTATTTATTTT
1 TATT-TTTATTTT
42354 TATTTT
1 TATTTT
42360 AAAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TATTTTTATTTT
Found at i:42359 original size:18 final size:19
Alignment explanation
Indices: 42329--42370 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
42319 AAAAAGAATA
**
42329 TATTTTTATTTTTATTATT
1 TATTTTTATTTTTAAAATT
42348 TATTTTTA-TTTTAAAATT
1 TATTTTTATTTTTAAAATT
42366 TATTT
1 TATTT
42371 ATGAACCCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTTATTTTTAAAATT
Found at i:43386 original size:17 final size:17
Alignment explanation
Indices: 43366--43415 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
43356 TGGTAATTCC
43366 AAAAAAATAAAAAATAT
1 AAAAAAATAAAAAATAT
*
43383 AAAAATATAAAAAA-AT
1 AAAAAAATAAAAAATAT
*
43399 AAAAGAAATAATAAATA
1 AAAA-AAATAAAAAATA
43416 AAATATAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 6 0.21
17 21 0.75
18 1 0.04
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (17 bp):
AAAAAAATAAAAAATAT
Found at i:43394 original size:16 final size:15
Alignment explanation
Indices: 43368--43424 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
43358 GTAATTCCAA
43368 AAAAATA-AAAAATAT
1 AAAAATATAAAAA-AT
43383 AAAAATATAAAAAAAT
1 AAAAATAT-AAAAAAT
* *
43399 AAAAGAAATAATAAAT
1 AAAA-ATATAAAAAAT
43415 -AAAATATAAA
1 AAAAATATAAA
43425 GGAAATGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
14 5 0.14
15 10 0.29
16 12 0.34
17 8 0.23
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAAATATAAAAAAT
Found at i:43394 original size:25 final size:26
Alignment explanation
Indices: 43366--43415 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
43356 TGGTAATTCC
43366 AAAAAAATAAAA-AATATAA-AAATAT
1 AAAAAAATAAAAGAA-ATAATAAATAT
43391 AAAAAAATAAAAGAAATAATAAATA
1 AAAAAAATAAAAGAAATAATAAATA
43416 AAATATAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (26 bp):
AAAAAAATAAAAGAAATAATAAATAT
Found at i:43420 original size:9 final size:8
Alignment explanation
Indices: 43366--43418 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
43356 TGGTAATTCC
43366 AAAAAAAT
1 AAAAAAAT
43374 AAAAAATAT
1 AAAAAA-AT
*
43383 AAAAATAT
1 AAAAAAAT
43391 AAAAAAAT
1 AAAAAAAT
43399 AAAAGAAAT
1 AAAA-AAAT
*
43408 -AATAAAT
1 AAAAAAAT
43415 AAAA
1 AAAA
43419 TATAAAGGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
7 4 0.11
8 23 0.61
9 11 0.29
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (8 bp):
AAAAAAAT
Found at i:43429 original size:23 final size:19
Alignment explanation
Indices: 43374--43430 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 19
43364 CCAAAAAAAT
*
43374 AAAAAATATAA-AAATATA
1 AAAAAATAAAAGAAATATA
43392 AAAAAATAAAAGAAATAATA
1 AAAAAATAAAAGAAAT-ATA
43412 AATAAAATATAAAGGAAAT
1 AA-AAAATA-AAA-GAAAT
43431 GAAAAAAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 10 0.30
19 4 0.12
20 5 0.15
21 6 0.18
22 3 0.09
23 5 0.15
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAAAATAAAAGAAATATA
Found at i:44417 original size:21 final size:21
Alignment explanation
Indices: 44391--44433 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
44381 TGCGTTGGGA
44391 TCGATCCCGGATATTCCGGGG
1 TCGATCCCGGATATTCCGGGG
*
44412 TCGATCCCGGATATTCTGGGG
1 TCGATCCCGGATATTCCGGGG
44433 T
1 T
44434 GGCCGGTTGT
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:0.14, C:0.26, G:0.33, T:0.28
Consensus pattern (21 bp):
TCGATCCCGGATATTCCGGGG
Found at i:44857 original size:24 final size:25
Alignment explanation
Indices: 44830--44876 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
44820 ATATTATTAT
*
44830 TATAAAAAATAT-TTTCCAAAAACC
1 TATAAAAAATATATTTCAAAAAACC
* *
44854 TATATAATATATATTTCAAAAAA
1 TATAAAAAATATATTTCAAAAAA
44877 AATATTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (25 bp):
TATAAAAAATATATTTCAAAAAACC
Found at i:44891 original size:40 final size:41
Alignment explanation
Indices: 44833--44915 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
44823 TTATTATTAT
* *
44833 AAAAAATATTTTCCAAAAACCTATATA-ATATATATTTCAA
1 AAAAAATATTTTCAAAAAACATATATATATATATATTTCAA
* * *
44873 AAAAAATATTTTTAAAAAATATATATATATATATATTTTAA
1 AAAAAATATTTTCAAAAAACATATATATATATATATTTCAA
44914 AA
1 AA
44916 TGTTTTCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 23 0.62
41 14 0.38
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (41 bp):
AAAAAATATTTTCAAAAAACATATATATATATATATTTCAA
Found at i:44966 original size:25 final size:25
Alignment explanation
Indices: 44908--44983 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
44898 TATATATATA
* *
44908 TTTT-AAAATGTTTTCAAAATTAGATAG
1 TTTTCAAAATGATTTCAAAACT--AT-G
*
44935 TTTTCAAAAATG-TTTTAAAACTATG
1 TTTTC-AAAATGATTTCAAAACTATG
44960 TTTTCAAAATGATTTCAAAACTAT
1 TTTTCAAAATGATTTCAAAACTAT
44984 ATATTATATG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
24 6 0.14
25 17 0.40
26 2 0.05
27 4 0.09
28 8 0.19
29 6 0.14
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (25 bp):
TTTTCAAAATGATTTCAAAACTATG
Found at i:45000 original size:36 final size:35
Alignment explanation
Indices: 44960--45179 Score: 174
Period size: 37 Copynumber: 6.0 Consensus size: 35
44950 TAAAACTATG
* *
44960 TTTTCAAAATGATTTCAAAACTATATATTATATGTA
1 TTTTCAAAATGATTTCAAAACCATATATTATAT-AA
* *
44996 TTTTCAAAATGTTTTTCAAAAACCATATAATATATACA
1 TTTTCAAAATG-ATTTC-AAAACCATATATTATATA-A
* * *
45034 TTTTCAAAATGTTTTTCAAAAACTATATATATTAAATATA
1 TTTTCAAAATG-ATTTC-AAAAC--CATATATTATATA-A
45074 TATTTCAAAAT-ATTTTCAAAACCATATATTATATAA
1 T-TTTCAAAATGA-TTTCAAAACCATATATTATATAA
** ** * *
45110 GTTTTCTAATTTTTTTTAAAAACCATATTTTATATAA
1 -TTTTC-AAAATGATTTCAAAACCATATATTATATAA
* *
45147 TTTTCAAAATGATTTC-AAACTATATATAATATA
1 TTTTCAAAATGATTTCAAAACCATATATTATATA
45180 TCCTAAAAAT
Statistics
Matches: 150, Mismatches: 24, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
34 14 0.09
35 6 0.04
36 21 0.14
37 40 0.27
38 39 0.26
39 5 0.03
40 16 0.11
41 9 0.06
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.45
Consensus pattern (35 bp):
TTTTCAAAATGATTTCAAAACCATATATTATATAA
Found at i:45030 original size:38 final size:37
Alignment explanation
Indices: 44960--45165 Score: 199
Period size: 38 Copynumber: 5.5 Consensus size: 37
44950 TAAAACTATG
* * *
44960 TTTTCAAAATG-ATTTC-AAAACTATATATTATATGTA
1 TTTTCAAAATGTTTTTCAAAAACCATATATTATAT-AA
*
44996 TTTTCAAAATGTTTTTCAAAAACCATATAATATATACA
1 TTTTCAAAATGTTTTTCAAAAACCATATATTATATA-A
* *
45034 TTTTCAAAATGTTTTTCAAAAACTATATATATTAAATATA
1 TTTTCAAAATGTTTTTCAAAAAC--CATATATTATATA-A
*
45074 TATTTCAAAAT-ATTTTC-AAAACCATATATTATATAA
1 T-TTTCAAAATGTTTTTCAAAAACCATATATTATATAA
* * * *
45110 GTTTTC-TAATTTTTTTTAAAAACCATATTTTATATAA
1 -TTTTCAAAATGTTTTTCAAAAACCATATATTATATAA
*
45147 TTTTCAAAATG-ATTTCAAA
1 TTTTCAAAATGTTTTTCAAA
45166 CTATATATAA
Statistics
Matches: 141, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
35 3 0.02
36 31 0.22
37 37 0.26
38 39 0.28
39 5 0.04
40 17 0.12
41 9 0.06
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTTCAAAATGTTTTTCAAAAACCATATATTATATAA
Found at i:46121 original size:165 final size:163
Alignment explanation
Indices: 45807--46420 Score: 798
Period size: 165 Copynumber: 3.7 Consensus size: 163
45797 AAGGTATTTG
* * ** *
45807 TTGGCAGATAACCTTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTAAAGCTAAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* *
45872 CAAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
66 CGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTAGAGTTATGCTGTAAATGATGT-C
*
45937 CCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
130 CCTCGAAGCAGAGTGTAATCGAACTCGAGGGTCT
*
45971 TTGGCAGATAACCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
*
46036 CGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTAGAGTTATACTGTAAATGATGTA
66 CGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTAGAGTTATGCTGTAAATGATGT-
*
46101 CCCTCGAAGCAGAGTGTAATCGAACTTGAGGGTCT
129 CCCTCGAAGCAGAGTGTAATCGAACTCGAGGGTCT
* * *
46136 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATAATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * * * ** *
46201 CGAACTCGAAGGTCTTTGGTTAGCAGATAACCCTTCTCGACTTA-AGTTATGTTACAAATGATAT
66 CGAACTCGAAGGTCTTTGGTGA-CAGATAACCCTTCTAG-CCTAGAGTTATGCTGTAAATGATGT
* * * * * * *
46265 GCCTTGGAGCAGAGCGTAGTCAAACTCGAAGGTCTTT
129 CCCTCGAAGCAGAGTGTAATCGAACTCGAGGGTC--T
* *
46302 GGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGTCTTGGAGCTGAGCGTA
1 --TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTA
* * * * * * * *
46367 GTCGAACTCAAAAGTCTTCGTTGGCAGATAACCATTCTAGCATTGAGTTATGCT
64 GTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTAGAGTTATGCT
46421 ACAAATGTTG
Statistics
Matches: 394, Mismatches: 48, Indels: 13
0.87 0.11 0.03
Matches are distributed among these distances:
164 105 0.27
165 185 0.47
166 6 0.02
167 22 0.06
168 76 0.19
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (163 bp):
TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTAGAGTTATGCTGTAAATGATGTCC
CTCGAAGCAGAGTGTAATCGAACTCGAGGGTCT
Found at i:46139 original size:84 final size:82
Alignment explanation
Indices: 45726--46407 Score: 496
Period size: 84 Copynumber: 8.2 Consensus size: 82
45716 ACAATTTTAT
* * * * * * * * *
45726 TGACAGATAGCCCTTCTTGCCTTGATCTATACTGT-AATGATGTGCCTTGAAGCTAAGCGTAGTC
1 TGACAGATAACCCTTCTAGCC-TAAGCTATGCTGTAAATGATGTCCCTCGAAGCTGAGCGTAATC
* * *
45790 GAACTCAAAGGTATTTGT
65 GAACTCGAAGGTCTTTGG
* * * * * * ** * *
45808 TGGCAGATAACCTTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTAAAGCTAAGCGTAGTC
1 TGACAGATAACCCTTCTAG-CCTAAGCTATGCTGTAAATGATGTCCCTCGAAGCTGAGCGTAATC
*
45873 AAACTCGAAGGTCTTTGG
65 GAACTCGAAGGTCTTTGG
* * *
45891 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCC-TAAGCTATGCTGTAAATGATGT-CCCTCGAAGCTGAGCGTAAT
*
45956 CGAACTCGAGGGTCTTT-G
64 CGAACTCGAAGGTCTTTGG
* * * * * * *
45974 -G-CAGATAACCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCT-AGCCTAAGCTATGCTGTAAATGATGTCCCTCGAAGCTGAGCGTAATC
46037 GAACTCGAAGGTCTTTTGG
65 GAACTCGAAGGTC-TTTGG
* * * *
46056 TGACAGATAACCCTTCTAGCCTAGAGTTATACTGTAAATGATGTACCCTCGAAGCAGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTA-AGCTATGCTGTAAATGATGT-CCCTCGAAGCTGAGCGTAAT
* *
46121 CGAACTTGAGGGTCTTT-G
64 CGAACTCGAAGGTCTTTGG
* * * * * * * *
46139 -G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATAATGTGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAG-CCTAAGCTATGCTGTAAATGATGTCCCTCGAAGCTGAGCGTAATC
46202 GAACTCGAAGGTCTTTGG
65 GAACTCGAAGGTCTTTGG
* * * * * ** * * * * * *
46220 TTAGCAGATAACCCTTCTCGACTTAAGTTATGTTACAAATGATATGCCTTGGAGCAGAGCGTAGT
1 TGA-CAGATAACCCTTCTAG-CCTAAGCTATGCTGTAAATGATGTCCCTCGAAGCTGAGCGTAAT
*
46285 CAAACTCGAAGGTCTTTGG
64 CGAACTCGAAGGTCTTTGG
* * * * * ** * * *
46304 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGTCTTGGAGCTGAGCGTAGT
1 -TGACAGATAACCCTTCTAG-CCTAAGCTATGCTGTAAATGATGTCCCTCGAAGCTGAGCGTAAT
* * * *
46369 CGAACTCAAAAGTCTTCGT
64 CGAACTCGAAGGTCTTTGG
* *
46388 TGGCAGATAACCATTCTAGC
1 TGACAGATAACCCTTCTAGC
46408 ATTGAGTTAT
Statistics
Matches: 493, Mismatches: 90, Indels: 34
0.80 0.15 0.06
Matches are distributed among these distances:
80 57 0.12
81 68 0.14
82 35 0.07
83 102 0.21
84 204 0.41
85 27 0.05
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (82 bp):
TGACAGATAACCCTTCTAGCCTAAGCTATGCTGTAAATGATGTCCCTCGAAGCTGAGCGTAATCG
AACTCGAAGGTCTTTGG
Found at i:46246 original size:249 final size:247
Alignment explanation
Indices: 45761--46348 Score: 702
Period size: 249 Copynumber: 2.4 Consensus size: 247
45751 TCTATACTGT
* * * * * * *
45761 AATGATGTGCCTTGAAGCTAAGCGTAGTCGAACTCAAAGGTATTTGTTGGCAGATAACCTTTCTT
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTA
* * * *
45826 GACTTAAGCTATGCTGCAAATGATGTGCCTTAAAGCTAAGCGTAGTCAAACTCGAAGGTCTTTGG
66 GACTTAAGTTATGCTGCAAATGATGTCCCTCAAAGCTAAGCGTAATCAAACTCGAAGGTCTTTGG
* * * * *
45891 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
131 TGACAGATAACCCTTCTAGACTTAAGCTATGCTGTAAATAATGTGCCCTCGAAGCTGAGCGTAAT
* *
45956 CGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCAACTTAAGCTATGCTGCA
196 CGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCAACTTAAGCTATGCTACA
*
46008 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCT
* * * * * * * *
46073 AG-CCTAGAGTTATACTGTAAATGATGTACCCTCGAAGC-AGAGTGTAATCGAACTTGAGGGTCT
65 AGACTTA-AGTTATGCTGCAAATGATGT-CCCTCAAAGCTA-AGCGTAATCAAACTCGAAGGTCT
* * * *
46136 TT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATAATGTG-CCTTGGAGCTGAGCG
127 TTGGTGACAGATAACCCTTCTAGACTTAAGCTATGCTGTAAATAATGTGCCCTCGAAGCTGAGCG
* * * *
46197 TAGTCGAACTCGAAGGTCTTTGGTTAGCAGATAACCCTTCTCGACTTAAGTTATGTTACA
192 TAATCGAACTCGAAGGTCTTT-G---GCAGATAACCCTTCTCAACTTAAGCTATGCTACA
* * *
46257 AATGATATGCCTTGGAGCAGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCT
*
46322 CGACTTAAGTTATGCTGCAAATGATGT
65 AGACTTAAGTTATGCTGCAAATGATGT
46349 GTCTTGGAGC
Statistics
Matches: 288, Mismatches: 43, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
245 31 0.11
246 37 0.13
247 42 0.15
248 44 0.15
249 131 0.45
250 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (247 bp):
AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTA
GACTTAAGTTATGCTGCAAATGATGTCCCTCAAAGCTAAGCGTAATCAAACTCGAAGGTCTTTGG
TGACAGATAACCCTTCTAGACTTAAGCTATGCTGTAAATAATGTGCCCTCGAAGCTGAGCGTAAT
CGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCAACTTAAGCTATGCTACA
Found at i:47719 original size:95 final size:93
Alignment explanation
Indices: 47503--47750 Score: 336
Period size: 95 Copynumber: 2.6 Consensus size: 93
47493 GGCTAGTTGA
* *
47503 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTAATATCATTGTATAGATA
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAAC-TCA-AGC-TT-TATAGATA
47568 TTATAATCACCTTACCAGGCTAGCTGAATATT
62 TTATAATCACCTTACCAGGCTAGCTGAATATT
* *
47600 ATCCATAAAG-TCGGGGAGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATCGTATATT
1 ATCCATAAAGCT-GGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATAG-ATATT
* * *
47664 ATAATCACCTTTATCAGGTTAGCTGAATCTT
64 ATAATCACC-TTACCAGGCTAGCTGAATATT
* * *
47695 ATCCATAAAGCTGGGGCGTTTAACCAATTACTTTATAGGGACAACTCAAGCTTTAT
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTAT
47751 TGTTTATATA
Statistics
Matches: 136, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
93 4 0.03
94 16 0.12
95 70 0.51
96 4 0.03
97 42 0.31
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (93 bp):
ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATAGATATTAT
AATCACCTTACCAGGCTAGCTGAATATT
Found at i:49407 original size:65 final size:65
Alignment explanation
Indices: 49273--49431 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 65
49263 GCACTAAGAG
* * *
49273 TGCATCGATACATGAAATGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTTG
1 TGCATCGATACATAAAATGCATTCGATGTTTTCAAAATAGCCAGAATGCATCGATGCATGGCTTA
* * * * *
49337 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTGAATGCATCGATGCTTGG-TA
1 TGCATCGATACATAAAATGCATTCGATGTTTTCA-AAATAGCCAGAATGCATCGATGCATGGCT-
49400 TA
64 TA
* *
49402 TGCATCGATACATAAAATGCAATCAATGTT
1 TGCATCGATACATAAAATGCATTCGATGTT
49432 CAATTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 27 0.33
65 51 0.63
66 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (65 bp):
TGCATCGATACATAAAATGCATTCGATGTTTTCAAAATAGCCAGAATGCATCGATGCATGGCTTA
Found at i:49841 original size:21 final size:22
Alignment explanation
Indices: 49815--49866 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
49805 TTTGAAATTA
49815 CTCCCCCTTAC-TTTAACACTT
1 CTCCCCCTTACATTTAACACTT
* * *
49836 CTCCCCATAACATTTAACATTT
1 CTCCCCCTTACATTTAACACTT
49858 CTCCCCCTT
1 CTCCCCCTT
49867 TTTGTTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (22 bp):
CTCCCCCTTACATTTAACACTT
Found at i:50006 original size:13 final size:13
Alignment explanation
Indices: 49988--50024 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
49978 AGCCATTAGT
49988 TTCATAATCAATA
1 TTCATAATCAATA
50001 TTCATAATCAATA
1 TTCATAATCAATA
50014 TTCATAATCAA
1 TTCATAATCAA
50025 ATGTGAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (13 bp):
TTCATAATCAATA
Found at i:50331 original size:16 final size:16
Alignment explanation
Indices: 50310--50349 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
50300 CAAGAGAGAG
50310 AGCATCTATAAGTGCA
1 AGCATCTATAAGTGCA
50326 AGCATCTATAAGTGCA
1 AGCATCTATAAGTGCA
50342 AGCATCTA
1 AGCATCTA
50350 CCATTGAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (16 bp):
AGCATCTATAAGTGCA
Found at i:52228 original size:24 final size:23
Alignment explanation
Indices: 52177--52237 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 23
52167 GCATGGCAGT
52177 GTGCATCGATGCACATTCAAGGC
1 GTGCATCGATGCACATTCAAGGC
*
52200 GTGCATCGATGTACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGC
52223 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
52238 TGTTAAGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 18 0.53
24 16 0.47
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGC
Found at i:56084 original size:21 final size:21
Alignment explanation
Indices: 56050--56090 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
56040 GAGCTTATTT
*
56050 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
56071 TCATTTTT-ATATTTTAAAAC
1 TCATTTTTCA-ATTTTAAAAC
56091 CAATTTCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.51
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:58093 original size:64 final size:62
Alignment explanation
Indices: 58013--58218 Score: 216
Period size: 65 Copynumber: 3.2 Consensus size: 62
58003 CTAAGAGTGA
** *
58013 ATCGATGCAAGAAATGCATTCGATATTTCAAAATAGCCAAAGTGTATCGATGCATGGCTTGTGC
1 ATCGATGCATCAAATGCATTCGAT-TTTCAAAATATCCAAAGTGTATCGATGCATGG-TTGTGC
* *
58077 ATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTAAGTGCATCGATGCATGGTATGTG
1 ATCGATGCATCAAATGCATTCGA--TTTTCA-AAATATCCAAAGTGTATCGATGCATGGT-TGTG
58141 C
62 C
* * ** **
58142 ATCGATGCATAAAATGCATTCGATGTTCAATTTATTCCATGGTGTATCGATGCATGGATTGGTGC
1 ATCGATGCATCAAATGCATTCGATTTTCAAAATA-TCCAAAGTGTATCGATGCATGG-TT-GTGC
*
58207 ATCGGTGCATCA
1 ATCGATGCATCA
58219 CTTTGAACAA
Statistics
Matches: 119, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 41 0.34
65 67 0.56
66 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (62 bp):
ATCGATGCATCAAATGCATTCGATTTTCAAAATATCCAAAGTGTATCGATGCATGGTTGTGC
Found at i:61633 original size:15 final size:15
Alignment explanation
Indices: 61613--61662 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
61603 GTAATTCCAA
*
61613 AAAATAAAAAATAGT
1 AAAATAAAAAATAAT
*
61628 AAAATAATAAATAAT
1 AAAATAAAAAATAAT
61643 -AAATAAATAAA-AAT
1 AAAATAAA-AAATAAT
61657 AAAATA
1 AAAATA
61663 TAAAGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 9 0.30
15 21 0.70
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAATAAAAAATAAT
Found at i:63002 original size:3 final size:3
Alignment explanation
Indices: 62994--63055 Score: 52
Period size: 3 Copynumber: 18.7 Consensus size: 3
62984 AAATTAAAAT
* *
62994 TAA TAA TAAA TAAA TAA TAAA TAAA TAAA TAAA TAA CAA TAA TAA CAA
1 TAA TAA T-AA T-AA TAA T-AA T-AA T-AA T-AA TAA TAA TAA TAA TAA
63042 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
63056 TTATAAAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
3 31 0.58
4 22 0.42
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:63007 original size:4 final size:4
Alignment explanation
Indices: 62998--63029 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
62988 TAAAATTAAT
62998 AATA AATA AAT- AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA AATA A
63030 CAATAATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:63009 original size:11 final size:11
Alignment explanation
Indices: 62990--63029 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
62980 ACAAAAATTA
*
62990 AAATTAATAAT
1 AAATAAATAAT
63001 AAATAAATAAT
1 AAATAAATAAT
63012 AAATAAATAAAT
1 AAATAAAT-AAT
63024 AAATAA
1 AAATAA
63030 CAATAATAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:63016 original size:15 final size:14
Alignment explanation
Indices: 62994--63055 Score: 60
Period size: 12 Copynumber: 4.6 Consensus size: 14
62984 AAATTAAAAT
62994 TAATAATAAATAAA
1 TAATAATAAATAAA
63008 TAATAAATAAATAAA
1 TAAT-AATAAATAAA
*
63023 TAAATAA-CAAT-AA
1 T-AATAATAAATAAA
*
63036 TAACAAT-AAT-AA
1 TAATAATAAATAAA
63048 TAATAATA
1 TAATAATA
63056 TTATAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 15 0.37
13 3 0.07
14 7 0.17
15 13 0.32
16 3 0.07
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
TAATAATAAATAAA
Found at i:63055 original size:12 final size:13
Alignment explanation
Indices: 62994--63053 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 13
62984 AAATTAAAAT
62994 TAATAATAAAT-A
1 TAATAATAAATAA
63006 -AATAATAAAT-A
1 TAATAATAAATAA
63017 -AATAAATAAATAA
1 TAAT-AATAAATAA
*
63030 CAATAATAACAATAA
1 TAATAAT-A-AATAA
63045 TAATAATAA
1 TAATAATAA
63054 TATTATAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
11 14 0.33
12 7 0.17
13 5 0.12
14 5 0.12
15 11 0.26
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:63101 original size:37 final size:35
Alignment explanation
Indices: 63047--63148 Score: 100
Period size: 37 Copynumber: 2.8 Consensus size: 35
63037 AACAATAATA
*
63047 ATAATA-ATATTATAAAAATATTTTCCAAAAACCTAT
1 ATAATATATATT-TAAAAATATTTT-CAAAAACATAT
**
63083 ATAATATATATTTCAAAAAAATATTTT-AAAATTATAT
1 ATAATATATATTT---AAAAATATTTTCAAAAACATAT
* *
63120 ATTATATATATTTAAAAATGTTTTCAAAA
1 ATAATATATATTTAAAAATATTTTCAAAA
63149 TTATATAGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
34 10 0.18
35 4 0.07
36 7 0.12
37 24 0.43
39 11 0.20
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (35 bp):
ATAATATATATTTAAAAATATTTTCAAAAACATAT
Found at i:63126 original size:35 final size:35
Alignment explanation
Indices: 63044--63155 Score: 104
Period size: 35 Copynumber: 3.1 Consensus size: 35
63034 AATAACAATA
*
63044 ATAATA-ATAATATTATAAAAATATTTTCCAAAAACCTAT
1 ATAATATAT-ATATTA-AAAAATATTTT-C-AAAA-TTAT
63083 ATAATATATAT-TTCAAAAAAATATTTT-AAAATTAT
1 ATAATATATATATT--AAAAAATATTTTCAAAATTAT
* * *
63118 ATATTATATATATTTAAAAATGTTTTCAAAATTAT
1 ATAATATATATATTAAAAAATATTTTCAAAATTAT
63153 ATA
1 ATA
63156 GGTTTCAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
34 10 0.16
35 24 0.38
36 6 0.09
38 2 0.03
39 19 0.30
40 3 0.05
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (35 bp):
ATAATATATATATTAAAAAATATTTTCAAAATTAT
Found at i:63176 original size:28 final size:28
Alignment explanation
Indices: 63120--63176 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
63110 AAAATTATAT
*
63120 ATTATATATATTTAAAAATGTTTTCAAA
1 ATTATATAGATTTAAAAATGTTTTCAAA
* *
63148 ATTATATAGGTTTCAAATATGTTTT-AAA
1 ATTATATAGATTT-AAAAATGTTTTCAAA
63176 A
1 A
63177 CTATGTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (28 bp):
ATTATATAGATTTAAAAATGTTTTCAAA
Found at i:63186 original size:25 final size:25
Alignment explanation
Indices: 63158--63205 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
63148 ATTATATAGG
*
63158 TTTCAAATATG-TTTTAAAACTATGT
1 TTTCAAA-ATGATTTCAAAACTATGT
63183 TTTCAAAATGATTTCAAAACTAT
1 TTTCAAAATGATTTCAAAACTAT
63206 ATATTATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (25 bp):
TTTCAAAATGATTTCAAAACTATGT
Found at i:63330 original size:29 final size:31
Alignment explanation
Indices: 63267--63335 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
63257 TTTTAAAATA
* *
63267 TTTTCAAAAACTATATAATATTTTCAAACGT
1 TTTTCAAAAACTATATAATATTATCAAACAT
* *
63298 TTTTCAAAAACTATAT-ATATTAT-ATATAT
1 TTTTCAAAAACTATATAATATTATCAAACAT
63327 TTTTCAAAA
1 TTTTCAAAA
63336 TATTTTCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 12 0.35
30 6 0.18
31 16 0.47
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.45
Consensus pattern (31 bp):
TTTTCAAAAACTATATAATATTATCAAACAT
Found at i:63342 original size:40 final size:36
Alignment explanation
Indices: 63182--63434 Score: 170
Period size: 40 Copynumber: 6.9 Consensus size: 36
63172 TAAAACTATG
* *
63182 TTTTCAAAATGA-TTTCAAAACTATATATTATAT-GT
1 TTTTCAAAAT-ATTTTCAAAACCATATATTATATAAT
* * * *
63217 ATTTTCAAATTGTTTTTCAAAAACAATATAATATATACAT
1 -TTTTCAAAAT-ATTTTC-AAAACCATATATTATATA-AT
*
63257 TTTT-AAAATATTTTCAAAAAC-TATA-TA-AT-A-
1 TTTTCAAAATATTTTCAAAACCATATATTATATAAT
* *
63287 TTTTCAAACGT-TTTTCAAAAACTATATATATTATATATAT
1 TTTTCAAA-ATATTTTC-AAAAC--CATATATTATATA-AT
63327 TTTTCAAAATATTTTCAAAACCATATATTATATAAGT
1 TTTTCAAAATATTTTCAAAACCATATATTATATAA-T
* *
63364 TTTCTAAAAATATTTTTTAAAAACCATATATTATATAA-
1 TTT-TCAAAATA--TTTTCAAAACCATATATTATATAAT
* *
63402 TTTTCAAAATGA-TTTC-AAACTATATATAATATA
1 TTTTCAAAAT-ATTTTCAAAACCATATATTATATA
63435 TACTAAAAAA
Statistics
Matches: 176, Mismatches: 20, Indels: 44
0.73 0.08 0.18
Matches are distributed among these distances:
30 4 0.02
31 9 0.05
32 5 0.03
33 2 0.01
34 17 0.10
35 11 0.06
36 17 0.10
37 33 0.19
38 30 0.17
39 11 0.06
40 37 0.21
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (36 bp):
TTTTCAAAATATTTTCAAAACCATATATTATATAAT
Found at i:63353 original size:70 final size:69
Alignment explanation
Indices: 63216--63353 Score: 199
Period size: 70 Copynumber: 2.0 Consensus size: 69
63206 ATATTATATG
* *
63216 TATTTTCAAATTGTTTTTCAAAAACAATATAATATATACATTTTTAAAATATTTTCAAAAACTAT
1 TATTTTCAAATCGTTTTTCAAAAACAATATAATATATACATTTTTAAAATATTTTCAAAAACCAT
63281 ATAA
66 ATAA
* *
63285 TATTTTCAAA-CGTTTTTCAAAAACTATATATATTATATATATTTTTCAAAATATTTTC-AAAAC
1 TATTTTCAAATCGTTTTTCAAAAAC-A-ATATAATATATACATTTTT-AAAATATTTTCAAAAAC
63348 CATATA
63 CATATA
63354 TTATATAAGT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
68 13 0.21
69 11 0.18
70 27 0.44
71 11 0.18
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.44
Consensus pattern (69 bp):
TATTTTCAAATCGTTTTTCAAAAACAATATAATATATACATTTTTAAAATATTTTCAAAAACCAT
ATAA
Done.