Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000501.1 Hibiscus syriacus cultivar Beakdansim tig00000957_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: 54396
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:712 original size:19 final size:19
Alignment explanation
Indices: 688--733 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
678 ATTGAAGTTC
688 TACTTTTCTTTCCATCT-TT
1 TACTTTTCTTT-CATCTATT
707 TACTTTTCTTTCATCTATT
1 TACTTTTCTTTCATCTATT
726 TACTTTTC
1 TACTTTTC
734 ACATGTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.63
Consensus pattern (19 bp):
TACTTTTCTTTCATCTATT
Found at i:1272 original size:18 final size:18
Alignment explanation
Indices: 1232--1268 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1222 CTTTCAATTA
*
1232 TTATTTTTTTTTTCTTTG
1 TTATTTTATTTTTCTTTG
1250 TTATTTTATTTTT-TTTG
1 TTATTTTATTTTTCTTTG
1267 TT
1 TT
1269 TATTCAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.08, C:0.03, G:0.05, T:0.84
Consensus pattern (18 bp):
TTATTTTATTTTTCTTTG
Found at i:6892 original size:2 final size:2
Alignment explanation
Indices: 6885--6940 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
6875 AATCATATGA
6885 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
6927 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
6941 CTAATTTATG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7926 original size:20 final size:20
Alignment explanation
Indices: 7903--7998 Score: 92
Period size: 20 Copynumber: 5.0 Consensus size: 20
7893 GAGGGATTAT
*
7903 CAGTGGTCGTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
7923 CAGTGGTCCTTCGGGAC--A
1 CAGTGGTCCTTCGGGACAAA
* * * *
7941 TAGTGGTTCTTCGGAACAAT
1 CAGTGGTCCTTCGGGACAAA
*
7961 CAGTGGTCCTTC-GGA-ACA
1 CAGTGGTCCTTCGGGACAAA
* *
7979 TAGTAGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
7999 TATTCAGTGC
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
18 26 0.44
19 5 0.08
20 28 0.47
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (20 bp):
CAGTGGTCCTTCGGGACAAA
Found at i:7947 original size:18 final size:18
Alignment explanation
Indices: 7904--7996 Score: 96
Period size: 18 Copynumber: 4.9 Consensus size: 18
7894 AGGGATTATC
* *
7904 AGTGGTCGTTCGGGACAAAC
1 AGTGGTCCTTCGGGAC--AT
7924 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
7942 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
*
7961 CAGTGGTCCTTCGGAACAT
1 -AGTGGTCCTTCGGGACAT
*
7980 AGTAGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
7997 AATATTCAGT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
18 30 0.47
19 4 0.06
20 30 0.47
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:7965 original size:38 final size:38
Alignment explanation
Indices: 7904--7998 Score: 129
Period size: 38 Copynumber: 2.5 Consensus size: 38
7894 AGGGATTATC
*
7904 AGTGG-TCGTTCGGGACAAACAGTGGTCCTTCGGGACAT
1 AGTGGTTC-TTCGGGACAAACAGTGGTCCTTCGGAACAT
* *
7942 AGTGGTTCTTCGGAACAATCAGTGGTCCTTCGGAACAT
1 AGTGGTTCTTCGGGACAAACAGTGGTCCTTCGGAACAT
* *
7980 AGTAGTCCTTCGGGACAAA
1 AGTGGTTCTTCGGGACAAA
7999 TATTCAGTGC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
38 47 0.96
39 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.25
Consensus pattern (38 bp):
AGTGGTTCTTCGGGACAAACAGTGGTCCTTCGGAACAT
Found at i:8270 original size:4 final size:4
Alignment explanation
Indices: 8261--8340 Score: 151
Period size: 4 Copynumber: 19.8 Consensus size: 4
8251 ATGATAATGA
8261 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
8309 TATG TATG TATG TATG TATG TATG TAGTG TAT
1 TATG TATG TATG TATG TATG TATG TA-TG TAT
8341 TTGTTACATG
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
4 71 0.95
5 4 0.05
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:9191 original size:23 final size:23
Alignment explanation
Indices: 9165--9232 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
9155 CACCACAGCT
* *
9165 CGTATAAATGAATCGAAGTGCCA
1 CGTAGAAATGAACCGAAGTGCCA
* *
9188 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGAACCGAAGTGCCA
*
9211 CGTAG-AATTACACCGAAGTGCC
1 CGTAGAAATGA-ACCGAAGTGCC
9233 GTATAGAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
22 2 0.05
23 35 0.95
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGAACCGAAGTGCCA
Found at i:9239 original size:23 final size:23
Alignment explanation
Indices: 9178--9288 Score: 116
Period size: 23 Copynumber: 4.8 Consensus size: 23
9168 ATAAATGAAT
**
9178 CGAAGTGCCACGTAGAATTGCAC
1 CGAAGTGCCATATAGAATTGCAC
** *
9201 CGAAGTGCCACGTAGAATTACAC
1 CGAAGTGCCATATAGAATTGCAC
*
9224 CGAAGTGCCGTATAGAATTGCAC
1 CGAAGTGCCATATAGAATTGCAC
* * *
9247 CGAAGTGTCGTGTAGAATTGCAC
1 CGAAGTGCCATATAGAATTGCAC
*
9270 C-ATAGTGCCATATAAAATT
1 CGA-AGTGCCATATAGAATT
9289 TGTCCATAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
22 1 0.01
23 75 0.99
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (23 bp):
CGAAGTGCCATATAGAATTGCAC
Found at i:9245 original size:46 final size:46
Alignment explanation
Indices: 9181--9288 Score: 128
Period size: 46 Copynumber: 2.3 Consensus size: 46
9171 AATGAATCGA
**
9181 AGTGCCACGTAGAATTGCACCGAAGTGCCACGTAGAATTACACCGA-
1 AGTGCCATATAGAATTGCACCGAAGTGCCACGTAGAATTACACC-AT
* * ** *
9227 AGTGCCGTATAGAATTGCACCGAAGTGTCGTGTAGAATTGCACCAT
1 AGTGCCATATAGAATTGCACCGAAGTGCCACGTAGAATTACACCAT
*
9273 AGTGCCATATAAAATT
1 AGTGCCATATAGAATT
9289 TGTCCATAAG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 1 0.02
46 51 0.98
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (46 bp):
AGTGCCATATAGAATTGCACCGAAGTGCCACGTAGAATTACACCAT
Found at i:13541 original size:16 final size:19
Alignment explanation
Indices: 13527--13564 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
13517 TGATTATTTG
13527 ATTA-TTATTTTATTTAGGA
1 ATTAGTTATTTTATTTA-GA
13546 ATTAGTTATTTTA-TTAGA
1 ATTAGTTATTTTATTTAGA
13564 A
1 A
13565 CTCTTGGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 7 0.39
20 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (19 bp):
ATTAGTTATTTTATTTAGA
Found at i:14442 original size:36 final size:36
Alignment explanation
Indices: 14402--14485 Score: 161
Period size: 36 Copynumber: 2.4 Consensus size: 36
14392 ACACTATTCT
14402 ATTTATTTTATTTTATTTATTTAATTTGAGATTTAA
1 ATTTATTTTATTTTATTTATTTAATTTGAGATTTAA
14438 ATTTATTTTATTTTATTTATTTAATTTGAGATTTAA
1 ATTTATTTTATTTTATTTATTTAATTTGAGATTTAA
14474 ATTTA-TTTATTT
1 ATTTATTTTATTT
14486 GACAATTATG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 7 0.15
36 41 0.85
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (36 bp):
ATTTATTTTATTTTATTTATTTAATTTGAGATTTAA
Found at i:14477 original size:18 final size:18
Alignment explanation
Indices: 14420--14478 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
14410 TATTTTATTT
14420 ATTTAATTTGAGATTTAA
1 ATTTAATTTGAGATTTAA
* * *
14438 ATTT-ATTTTA-TTTTATTT
1 ATTTAATTTGAGATTTA--A
14456 ATTTAATTTGAGATTTAA
1 ATTTAATTTGAGATTTAA
14474 ATTTA
1 ATTTA
14479 TTTATTTGAC
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
16 4 0.13
17 5 0.16
18 13 0.42
19 5 0.16
20 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (18 bp):
ATTTAATTTGAGATTTAA
Found at i:24262 original size:2 final size:2
Alignment explanation
Indices: 24215--24243 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24205 TAATTATTGG
24215 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24244 AGATAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26261 original size:30 final size:30
Alignment explanation
Indices: 26143--26253 Score: 98
Period size: 30 Copynumber: 3.5 Consensus size: 30
26133 GACGAAACTT
*
26143 TGTTTCAACAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
* ** **
26173 TGTTTCAAGAGAATCTGTCTCAAGCGAGACAAAATT-
1 TGTTTCAAGAGAAACAATCTCAA---AG----GTTTA
26209 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
26239 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
26254 TGTCTCAAGT
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
29 2 0.03
30 34 0.55
33 4 0.06
36 20 0.32
37 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTTA
Found at i:26311 original size:133 final size:133
Alignment explanation
Indices: 26106--26432 Score: 521
Period size: 133 Copynumber: 2.5 Consensus size: 133
26096 AAAATAAATT
* * *
26106 TGTTTCAAGAGAAATTATCTCAGGTGAGACGAAACTTTGTTTC-AACAGAAACAATCTCAAAGGT
1 TGTTTCAAGAGAAACTATCTCAAGTGAGACAAAACTTTGTTTCGAA-AGAAACAATCTCAAAGGT
* *
26170 TTATGTTTCAAGAGAATCTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGG
65 TTATGTTTCAAGAGAATCGGTCTCAAGCGAGACAAAATTTGTTTAAAGAGAAACAATCTCAAAGG
26235 TTTA
130 TTTA
*
26239 TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAACTTTGTTTCGAAAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTATCTCAAGTGAGACAAAACTTTGTTTCGAAAGAAACAATCTCAAAGGTT
*
26304 TATGTTTCAAGAGAATCGGTCTCAAGCGAGACAAAATTTGTTTAAAGAGAAATAATCTCAAAGGT
66 TATGTTTCAAGAGAATCGGTCTCAAGCGAGACAAAATTTGTTTAAAGAGAAACAATCTCAAAGGT
*
26369 TTC
131 TTA
* ** * *
26372 TGTTTCAAGAGAAACTCTCTCAACCGAGACAAAACTTTGTTTCGAGAGAAACAAACTCAAA
1 TGTTTCAAGAGAAACTATCTCAAGTGAGACAAAACTTTGTTTCGAAAGAAACAATCTCAAA
26433 TGAGACCAAT
Statistics
Matches: 180, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
133 178 0.99
134 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (133 bp):
TGTTTCAAGAGAAACTATCTCAAGTGAGACAAAACTTTGTTTCGAAAGAAACAATCTCAAAGGTT
TATGTTTCAAGAGAATCGGTCTCAAGCGAGACAAAATTTGTTTAAAGAGAAACAATCTCAAAGGT
TTA
Found at i:26315 original size:67 final size:67
Alignment explanation
Indices: 26106--26432 Score: 471
Period size: 66 Copynumber: 4.9 Consensus size: 67
26096 AAAATAAATT
* * * * * *
26106 TGTTTCAAGAGAAATTATCTCAGGTGAGACGAAACTTTGTTTCAACAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
26171 TA
66 TA
*
26173 TGTTTCAAGAGAATCTGTCTCAAGCGAGACAAAA-TTTGTTTCAAGAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
26237 TA
66 TA
*
26239 TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAACTTTGTTTCGAA-AGAAACAATCTCAAAGGT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTC-AAGAGAAACAATCTCAAAGGT
26303 TTA
65 TTA
* * * *
26306 TGTTTCAAGAGAATCGGTCTCAAGCGAGACAAAA-TTTGTTTAAAGAGAAATAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
*
26370 TC
66 TA
* * * *
26372 TGTTTCAAGAGAAACTCTCTCAACCGAGACAAAACTTTGTTTCGAGAGAAACAAACTCAAA
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAA
26433 TGAGACCAAT
Statistics
Matches: 233, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
65 2 0.01
66 119 0.51
67 110 0.47
68 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
TA
Found at i:26431 original size:37 final size:36
Alignment explanation
Indices: 26372--26461 Score: 99
Period size: 37 Copynumber: 2.5 Consensus size: 36
26362 CAAAGGTTTC
*** *
26372 TGTTTCAAGAGAAACTCTCTCAACCGAGACAAAACTT
1 TGTTTCAAGAGAAACAAACTCAAACGAGAC-AAACTT
* * * *
26409 TGTTTCGAGAGAAACAAACTCAAATGAGACCAATTT
1 TGTTTCAAGAGAAACAAACTCAAACGAGACAAACTT
26445 TGTTTCAAGAGAAACAA
1 TGTTTCAAGAGAAACAA
26462 TTTCAAAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
36 20 0.45
37 24 0.55
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (36 bp):
TGTTTCAAGAGAAACAAACTCAAACGAGACAAACTT
Found at i:26431 original size:103 final size:102
Alignment explanation
Indices: 26331--26637 Score: 316
Period size: 103 Copynumber: 3.0 Consensus size: 102
26321 GGTCTCAAGC
* * * * * * *
26331 GAGACAAAATTTGTTTAAAGAGAAATAATCTCAAAGGTTTCTGTTTCAAGAGAAACTCTCTCAAC
1 GAGACAAATTTTGTTTCAAGAGAAACAATCTCAAA-ATTTGTGTTTCAAGAGAAACTATCTCAAG
*
26396 CGAGACAAAACTTTGTTTCGAGAGAAACAAACTCAAAT
65 CGAGACAAAACTTTGTTTTGAGAGAAACAAACTCAAAT
* * * * *
26434 GAGACCAATTTTGTTTCAAGAGAAACAATTTCAAAATTTGTGTTTCGAGGAAAAACTGTCTCAAG
1 GAGACAAATTTTGTTTCAAGAGAAACAATCTCAAAATTTGTGTTTC-AAGAGAAACTATCTCAAG
* * *
26499 TGAGACGAAA-TTTGTTTTTA-AGAAA-ATAATCTCAAAT
65 CGAGACAAAACTTTGTTTTGAGAGAAACA-AA-CTCAAAT
* * * * * *
26536 GAGATCAATTTCTTGTTTCAAGTGAAACAA-CTTCAAAATTTGGGCTTCAAGGGAAACTATCTAA
1 GAGA-CAAATT-TTGTTTCAAGAGAAACAATC-TCAAAATTTGTGTTTCAAGAGAAACTATCTCA
*
26600 AGCGAGACAAAACTTTGTTTTGAGAGAAACAATCTCAA
63 AGCGAGACAAAACTTTGTTTTGAGAGAAACAAACTCAA
26638 GGGAGACAGA
Statistics
Matches: 165, Mismatches: 30, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
100 1 0.01
101 7 0.04
102 28 0.17
103 77 0.47
104 45 0.27
105 6 0.04
106 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (102 bp):
GAGACAAATTTTGTTTCAAGAGAAACAATCTCAAAATTTGTGTTTCAAGAGAAACTATCTCAAGC
GAGACAAAACTTTGTTTTGAGAGAAACAAACTCAAAT
Found at i:26617 original size:104 final size:101
Alignment explanation
Indices: 26375--26637 Score: 287
Period size: 104 Copynumber: 2.6 Consensus size: 101
26365 AGGTTTCTGT
* * * **
26375 TTCAAGAGAAACTCTCTCAACCGAGACAAAACTTTGTTTCGAGAGAAACAAA-CTCAAATGAGAC
1 TTCAAGGGAAACTATCTCAAGCGAGACAAAACTTTGTTTTTA-AGAAA-AAATCTCAAATGAGAC
* * *
26439 CAATTTTGTTTCAAGAGAAACAATTTCAAAATTTGTGT
64 CAATTTTGTTTCAAGAGAAACAACTTCAAAATTTGGGC
* * * * * *
26477 TTCGAGGAAAAACTGTCTCAAGTGAGACGAAA-TTTGTTTTTAAGAAAATAATCTCAAATGAGAT
1 TTCAAGG-GAAACTATCTCAAGCGAGACAAAACTTTGTTTTTAAGAAAA-AATCTCAAATGAGAC
*
26541 CAATTTCTTGTTTCAAGTGAAACAACTTCAAAATTTGGGC
64 CAA-TT-TTGTTTCAAGAGAAACAACTTCAAAATTTGGGC
* * *
26581 TTCAAGGGAAACTATCTAAAGCGAGACAAAACTTTGTTTTGAGAGAAACAATCTCAA
1 TTCAAGGGAAACTATCTCAAGCGAGACAAAACTTTGTTTTTA-AGAAAAAATCTCAA
26638 GGGAGACAGA
Statistics
Matches: 132, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
100 1 0.01
101 7 0.05
102 27 0.20
103 40 0.30
104 52 0.39
105 5 0.04
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (101 bp):
TTCAAGGGAAACTATCTCAAGCGAGACAAAACTTTGTTTTTAAGAAAAAATCTCAAATGAGACCA
ATTTTGTTTCAAGAGAAACAACTTCAAAATTTGGGC
Found at i:28396 original size:18 final size:18
Alignment explanation
Indices: 28373--28443 Score: 124
Period size: 18 Copynumber: 3.9 Consensus size: 18
28363 ATGTGTTCTA
28373 AGTGGTCCGTCGGGACAT
1 AGTGGTCCGTCGGGACAT
28391 AGTGGTCCGTCGGGACAT
1 AGTGGTCCGTCGGGACAT
*
28409 AGTGGTCCTTCGGGACAT
1 AGTGGTCCGTCGGGACAT
*
28427 AGTGGTCCTTCGGGACA
1 AGTGGTCCGTCGGGACA
28444 AATTCTACGC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.17, C:0.23, G:0.37, T:0.24
Consensus pattern (18 bp):
AGTGGTCCGTCGGGACAT
Found at i:30176 original size:23 final size:23
Alignment explanation
Indices: 30150--30219 Score: 140
Period size: 23 Copynumber: 3.0 Consensus size: 23
30140 CTCGTATAAA
30150 TGCACCGAAGTGCCCGTAGAATT
1 TGCACCGAAGTGCCCGTAGAATT
30173 TGCACCGAAGTGCCCGTAGAATT
1 TGCACCGAAGTGCCCGTAGAATT
30196 TGCACCGAAGTGCCCGTAGAATT
1 TGCACCGAAGTGCCCGTAGAATT
30219 T
1 T
30220 TGTCCATAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCACCGAAGTGCCCGTAGAATT
Found at i:30554 original size:29 final size:29
Alignment explanation
Indices: 30512--30583 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
30502 TTTTCTGCAT
*
30512 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACGA
* *
30541 ATTCATGTCATGTAATACCTTTAATACGA
1 ATTCATGTCATGTAATACATATAATACGA
30570 ATTCATGTCATGTA
1 ATTCATGTCATGTA
30584 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACGA
Found at i:31033 original size:68 final size:69
Alignment explanation
Indices: 30886--31038 Score: 227
Period size: 69 Copynumber: 2.2 Consensus size: 69
30876 TTTTCTCATG
* * *
30886 GGGGAATCGGTTCCCCCCCTTAGGGGTATCGATTCCCCTCGAGCAGTCTGGAATTTCATATACGA
1 GGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCGAGCAGTCTGGAATATCATATACGA
*
30951 TGAG
66 TGAA
* * * *
30955 GGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGT
1 GGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCGAGCAGTCTGGAATATCATATACGA
31019 TGAA
66 TGAA
31023 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
31039 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
68 27 0.36
69 49 0.64
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (69 bp):
GGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCGAGCAGTCTGGAATATCATATACGA
TGAA
Found at i:31048 original size:21 final size:21
Alignment explanation
Indices: 31018--31060 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31008 ATCATATTCG
* *
31018 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
31039 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
31060 T
1 T
31061 AACCCAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:37125 original size:23 final size:23
Alignment explanation
Indices: 37099--37168 Score: 140
Period size: 23 Copynumber: 3.0 Consensus size: 23
37089 CTCGTATAAA
37099 TGCACCGAAGTGCCCGTAGAATT
1 TGCACCGAAGTGCCCGTAGAATT
37122 TGCACCGAAGTGCCCGTAGAATT
1 TGCACCGAAGTGCCCGTAGAATT
37145 TGCACCGAAGTGCCCGTAGAATT
1 TGCACCGAAGTGCCCGTAGAATT
37168 T
1 T
37169 TGTCCATAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCACCGAAGTGCCCGTAGAATT
Found at i:37499 original size:27 final size:28
Alignment explanation
Indices: 37461--37530 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
37451 TTTTCTGCAT
37461 ATTCATGTCATGTAATACATATAAT-GA
1 ATTCATGTCATGTAATACATATAATAGA
* *
37488 ATTCATGTCATGTAATACCTTTAATACGA
1 ATTCATGTCATGTAATACATATAATA-GA
37517 ATTCATGTCATGTA
1 ATTCATGTCATGTA
37531 TCATAATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 23 0.59
29 16 0.41
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATATAATAGA
Found at i:37958 original size:68 final size:68
Alignment explanation
Indices: 37832--37983 Score: 216
Period size: 68 Copynumber: 2.2 Consensus size: 68
37822 CTTTTCTCAT
* * *
37832 GGGGAATCGGTTCCCCCCCTTAGGGTATCGATTCCCCTCGAGCAGTCTGGAATTTCATATACGAT
1 GGGGTATCGGTTCCCCCCCTTAGGGTACCGATTCCCCTCGAGCAGTCTGGAATATCATATACGAT
*
37897 GAG
66 GAA
* * * *
37900 GGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGT
1 GGGGTATCGGTTCCCCCCCTTA-GGGTACCGATTCCCCTCGAGCAGTCTGGAATATCATATACGA
37964 TGAA
65 TGAA
37968 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
37984 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
68 48 0.64
69 27 0.36
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (68 bp):
GGGGTATCGGTTCCCCCCCTTAGGGTACCGATTCCCCTCGAGCAGTCTGGAATATCATATACGAT
GAA
Found at i:37993 original size:21 final size:21
Alignment explanation
Indices: 37963--38005 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
37953 ATCATATTCG
* *
37963 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
37984 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
38005 T
1 T
38006 AACCCAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:38965 original size:21 final size:22
Alignment explanation
Indices: 38916--38967 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
38906 CAATCCAAGT
*
38916 GACCCAAAACCCAACGTTACAA
1 GACCCAAAACCCAACGATACAA
38938 GACCCAAAACCCAAC-ATAGCAA
1 GACCCAAAACCCAACGATA-CAA
38960 -ACCCAAAA
1 GACCCAAAA
38968 TAATAACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.50, C:0.37, G:0.08, T:0.06
Consensus pattern (22 bp):
GACCCAAAACCCAACGATACAA
Found at i:39378 original size:21 final size:21
Alignment explanation
Indices: 39352--39488 Score: 174
Period size: 21 Copynumber: 6.6 Consensus size: 21
39342 GTTTCCAGAT
39352 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
39373 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
39393 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
39414 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
39435 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
39456 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
39477 TCGCAATGCGAA
1 TCGCAATGCGAA
39489 TATGTAAATC
Statistics
Matches: 102, Mismatches: 8, Indels: 12
0.84 0.07 0.10
Matches are distributed among these distances:
20 17 0.17
21 85 0.83
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:39527 original size:21 final size:21
Alignment explanation
Indices: 39503--39550 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
39493 TAAATCGCAA
39503 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
39524 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
39545 TGCGAT
1 TGCGAT
39551 TTATTCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:40370 original size:21 final size:21
Alignment explanation
Indices: 40346--40565 Score: 242
Period size: 21 Copynumber: 10.6 Consensus size: 21
40336 TTTGGAATAA
**
40346 ATCGCAACACGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
40367 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
*
40387 ATCGCAATGCGATA-GTCGACT
1 ATCGCAATGCGA-ACTTCGACT
40408 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
40429 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
40450 ATCGCAATGCGAA-TAT-G-CAA
1 ATCGCAATGCGAACT-TCGAC-T
*
40470 ATCGCAATGCGATA-GTCGACT
1 ATCGCAATGCGA-ACTTCGACT
40491 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
40512 ATCGCAATGCGAACTTCGAGC-
1 ATCGCAATGCGAACTTCGA-CT
*
40533 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
40554 ATCGCATTGCGA
1 ATCGCAATGCGA
40566 TTTACATATT
Statistics
Matches: 172, Mismatches: 13, Indels: 28
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.01
20 34 0.20
21 135 0.78
22 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:40460 original size:83 final size:83
Alignment explanation
Indices: 40346--40545 Score: 348
Period size: 83 Copynumber: 2.4 Consensus size: 83
40336 TTTGGAATAA
** *
40346 ATCGCAACACGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATC
1 ATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGCAAATCGCAATGCGATAGTCGACTATC
40411 GCAATGCGAACTTCGACT
66 GCAATGCGAACTTCGACT
40429 ATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGCAAATCGCAATGCGATAGTCGACTATC
1 ATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGCAAATCGCAATGCGATAGTCGACTATC
40494 GCAATGCGAACTTCGACT
66 GCAATGCGAACTTCGACT
*
40512 ATCGCAATGCGAACTTCGAGC-ATCGCAACGCGAA
1 ATCGCAATGCGAACTTCGA-CTATCGCAATGCGAA
40546 CTTCGACTAT
Statistics
Matches: 112, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
83 111 0.99
84 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (83 bp):
ATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGCAAATCGCAATGCGATAGTCGACTATC
GCAATGCGAACTTCGACT
Found at i:40501 original size:104 final size:105
Alignment explanation
Indices: 40387--40607 Score: 324
Period size: 104 Copynumber: 2.1 Consensus size: 105
40377 GAATATGTAA
*
40387 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTCGA-CTATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGATACGTCGACTATCGCAATGCGAACTTCGAGC-ATCGCAACGCGAACTTCGACT
*
40450 ATCGCAATGCGAATATGCA-AATCGCAATGCGATAGTCGACT
65 ATCGCAATGCG-ATATACATAATCGCAATGCGATAGTCGACT
*
40491 ATCGCAATGCGA-ACTTCGACTATCGCAATGCGAACTTCGAGCATCGCAACGCGAACTTCGACTA
1 ATCGCAATGCGATACGTCGACTATCGCAATGCGAACTTCGAGCATCGCAACGCGAACTTCGACTA
* * * *
40555 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCGACT
66 TCGCAATGCGATATACATAATCGCAATGCGATAGTCGACT
*
40595 ATCGCATTGCGAT
1 ATCGCAATGCGAT
40608 TTACATATTC
Statistics
Matches: 105, Mismatches: 8, Indels: 7
0.88 0.07 0.06
Matches are distributed among these distances:
103 6 0.06
104 98 0.93
105 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.25
Consensus pattern (105 bp):
ATCGCAATGCGATACGTCGACTATCGCAATGCGAACTTCGAGCATCGCAACGCGAACTTCGACTA
TCGCAATGCGATATACATAATCGCAATGCGATAGTCGACT
Found at i:40580 original size:20 final size:20
Alignment explanation
Indices: 40555--40627 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
40545 ACTTCGACTA
40555 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
40575 TCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCGAT-TTAC-A-TAT
40596 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
40616 TCGCATTGCGAT
1 TCGCATTGCGAT
40628 AGTCGACTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.04
20 27 0.59
21 15 0.33
22 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:40593 original size:41 final size:41
Alignment explanation
Indices: 40548--40675 Score: 213
Period size: 41 Copynumber: 3.1 Consensus size: 41
40538 AACGCGAACT
40548 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
40589 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
* *
40630 TCGACTATCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAG
1 TCGACTATCGCATTGCGAT-TTACATA-TTCGCATTGCGATAG
40672 TCGA
1 TCGA
40676 AGTTCGCGTT
Statistics
Matches: 83, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
41 61 0.73
42 22 0.27
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (41 bp):
TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
Found at i:40601 original size:21 final size:21
Alignment explanation
Indices: 40361--40675 Score: 200
Period size: 21 Copynumber: 15.2 Consensus size: 21
40351 AACACGAACT
40361 TCGACTATCGCAATGCGAATA-
1 TCGACTATCGCAATGCG-ATAG
*
40382 T-GTA-AATCGCAATGCGATAG
1 TCG-ACTATCGCAATGCGATAG
*
40402 TCGACTATCGCAATGCGA-ACT
1 TCGACTATCGCAATGCGATA-G
*
40423 TCGACTATCGCAATGCGA-ACT
1 TCGACTATCGCAATGCGATA-G
40444 TCGACTATCGCAATGCGAATA-
1 TCGACTATCGCAATGCG-ATAG
*
40465 T-G-CAAATCGCAATGCGATAG
1 TCGAC-TATCGCAATGCGATAG
*
40485 TCGACTATCGCAATGCGA-ACT
1 TCGACTATCGCAATGCGATA-G
*
40506 TCGACTATCGCAATGCGA-ACT
1 TCGACTATCGCAATGCGATA-G
* *
40527 TCGAGC-ATCGCAACGCGA-ACT
1 TCGA-CTATCGCAATGCGATA-G
*
40548 TCGACTATCGCATTGCGAT--
1 TCGACTATCGCAATGCGATAG
* *
40567 T-TACATATTCGCATTGCGATAG
1 TCGAC-TA-TCGCAATGCGATAG
*
40589 TCGACTATCGCATTGCGAT--
1 TCGACTATCGCAATGCGATAG
* *
40608 T-TACATATTCGCATTGCGATAG
1 TCGAC-TA-TCGCAATGCGATAG
*
40630 TCGACTATCGCATTGCGATAG
1 TCGACTATCGCAATGCGATAG
* * *
40651 TCCAAGT-TCGCATTGCGATAG
1 T-CGACTATCGCAATGCGATAG
40672 TCGA
1 TCGA
40676 AGTTCGCGTT
Statistics
Matches: 252, Mismatches: 16, Indels: 53
0.79 0.05 0.17
Matches are distributed among these distances:
18 4 0.02
19 13 0.05
20 56 0.22
21 162 0.64
22 12 0.05
23 5 0.02
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Consensus pattern (21 bp):
TCGACTATCGCAATGCGATAG
Found at i:40678 original size:21 final size:21
Alignment explanation
Indices: 40574--40689 Score: 116
Period size: 21 Copynumber: 5.6 Consensus size: 21
40564 GATTTACATA
40574 TTCGCATTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAC
*
40594 TATCGCATTGCGAT-TTAC-ATA-
1 T-TCGCATTGCGATAGT-CGA-AC
40615 TTCGCATTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAC
* *
40635 TATCGCATTGCGATAGTCCAAG
1 T-TCGCATTGCGATAGTCGAAC
*
40657 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAC
*
40678 TTCGCGTTGCGA
1 TTCGCATTGCGA
40690 ATCTGGAAAC
Statistics
Matches: 81, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.01
20 16 0.20
21 61 0.75
22 3 0.04
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAC
Found at i:41379 original size:10 final size:10
Alignment explanation
Indices: 41364--41401 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
41354 CTCTCTCTAA
41364 AAAATAAAAC
1 AAAATAAAAC
41374 AAAATAAAAC
1 AAAATAAAAC
*
41384 AAAAATGAAA-
1 -AAAATAAAAC
41394 AAAATAAA
1 AAAATAAA
41402 GAATATGGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 7 0.28
10 10 0.40
11 8 0.32
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.11
Consensus pattern (10 bp):
AAAATAAAAC
Found at i:41764 original size:22 final size:22
Alignment explanation
Indices: 41739--41809 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
41729 TTAATGGTAA
41739 ATTTTTATATTATATCTCTAAT
1 ATTTTTATATTATATCTCTAAT
* **
41761 A-TTTTATTTTCATTAAT-GGTAA-
1 ATTTTTATATT-A-T-ATCTCTAAT
41783 ATTTTTATATTATATCTCTAAT
1 ATTTTTATATTATATCTCTAAT
41805 ATTTT
1 ATTTT
41810 ATTTTCATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
20 2 0.05
21 12 0.32
22 9 0.24
23 12 0.32
24 2 0.05
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.59
Consensus pattern (22 bp):
ATTTTTATATTATATCTCTAAT
Found at i:41789 original size:44 final size:44
Alignment explanation
Indices: 41726--41818 Score: 186
Period size: 44 Copynumber: 2.1 Consensus size: 44
41716 GCTGTTATGG
41726 TCATTAATGGTAAATTTTTATATTATATCTCTAATATTTTATTT
1 TCATTAATGGTAAATTTTTATATTATATCTCTAATATTTTATTT
41770 TCATTAATGGTAAATTTTTATATTATATCTCTAATATTTTATTT
1 TCATTAATGGTAAATTTTTATATTATATCTCTAATATTTTATTT
41814 TCATT
1 TCATT
41819 TCGAGTCTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (44 bp):
TCATTAATGGTAAATTTTTATATTATATCTCTAATATTTTATTT
Found at i:44940 original size:24 final size:25
Alignment explanation
Indices: 44895--44946 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
44885 TTCAGTATGC
*
44895 ATTAACATCATATTTTTATTATA-A
1 ATTAAAATCATATTTTTATTATAGA
*
44919 ATTAAAAT-ATATTTTGTGTTATAGA
1 ATTAAAATCATATTTT-TATTATAGA
44944 ATT
1 ATT
44947 TTTCTTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.29
24 13 0.54
25 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (25 bp):
ATTAAAATCATATTTTTATTATAGA
Found at i:45044 original size:27 final size:28
Alignment explanation
Indices: 45010--45063 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
45000 ATAATAATAT
45010 TTTAATAATTA-TAGTTTAATTTTATTA
1 TTTAATAATTATTAGTTTAATTTTATTA
*
45037 TTTAATAATTATTTGTTTAATTTTATT
1 TTTAATAATTATTAGTTTAATTTTATT
45064 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTAATAATTATTAGTTTAATTTTATTA
Found at i:45062 original size:14 final size:14
Alignment explanation
Indices: 45023--45064 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
45013 AATAATTATA
45023 GTTTAATTTTA-TT
1 GTTTAATTTTATTT
* *
45036 ATTTAATAATTATTT
1 GTTTAAT-TTTATTT
45051 GTTTAATTTTATTT
1 GTTTAATTTTATTT
45065 TAAAAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
GTTTAATTTTATTT
Found at i:45074 original size:27 final size:25
Alignment explanation
Indices: 45007--45067 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 25
44997 TATATAATAA
45007 TATTTTAATAATTATAGTTTAATTT
1 TATTTTAATAATTATAGTTTAATTT
*
45032 TATTATTTAATAATTATTTGTTTAATTT
1 TA-T-TTTAATAATTA-TAGTTTAATTT
45060 TATTTTAA
1 TATTTTAA
45068 AAAATTAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 2 0.06
26 6 0.19
27 12 0.38
28 12 0.38
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (25 bp):
TATTTTAATAATTATAGTTTAATTT
Found at i:49774 original size:23 final size:24
Alignment explanation
Indices: 49739--49798 Score: 113
Period size: 23 Copynumber: 2.5 Consensus size: 24
49729 ATTTTACTTT
49739 TGTATGCCCCTTCCAGACATCCAC
1 TGTATGCCCCTTCCAGACATCCAC
49763 TGTAT-CCCCTTCCAGACATCCAC
1 TGTATGCCCCTTCCAGACATCCAC
49786 TGTATGCCCCTTC
1 TGTATGCCCCTTC
49799 ATTATTCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 23 0.66
24 12 0.34
ACGTcount: A:0.18, C:0.42, G:0.12, T:0.28
Consensus pattern (24 bp):
TGTATGCCCCTTCCAGACATCCAC
Done.