Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000855.1 Hibiscus syriacus cultivar Beakdansim tig00001658_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: 96552
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:419 original size:17 final size:17
Alignment explanation
Indices: 397--440 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
387 ATGTAAAAAT
397 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
414 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
431 AAATATTTAA
1 AAATATTTAA
441 TCAAGTATGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:2093 original size:60 final size:61
Alignment explanation
Indices: 1995--2116 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 61
1985 CATATAACTT
* ** *
1995 GGGATGAAATCGGAATGTTCAAAAAAGTTTAGGGACTAATTTAGAATGA-AGGTCATAGTTTG
1 GGGATGAAATCGAAATGTT-AAAAAAGTTTAAAGACTAATTTAGAATCATA-GTCATAGTTTG
* *
2057 GGGATGAAATTGAAATGTT-AAAAAGTTTAAAGACTAATTTAGAGTCATAGTCATAGTTTG
1 GGGATGAAATCGAAATGTTAAAAAAGTTTAAAGACTAATTTAGAATCATAGTCATAGTTTG
2117 AGAATAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
60 35 0.66
61 1 0.02
62 17 0.32
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.31
Consensus pattern (61 bp):
GGGATGAAATCGAAATGTTAAAAAAGTTTAAAGACTAATTTAGAATCATAGTCATAGTTTG
Found at i:2131 original size:60 final size:60
Alignment explanation
Indices: 2016--2155 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 60
2006 GGAATGTTCA
* * * * * * **
2016 AAAAAGTTTAGGGACTAATTTAGAATGAAGGTCATAGTTTGGGGATGAAATTGAAATGTT
1 AAAAAGTTTAAGGACTAATTTAGAATCAAGGTCATAGTTTGAGAATAAAAATGAAACATT
* *
2076 AAAAAGTTTAAAGACTAATTTAGAGTCATA-GTCATAGTTTGAGAATAAAAATGAAACATT
1 AAAAAGTTTAAGGACTAATTTAGAATCA-AGGTCATAGTTTGAGAATAAAAATGAAACATT
* *
2136 TAAAAGTTTAAGGAATAATT
1 AAAAAGTTTAAGGACTAATT
2156 AAAATAAGGA
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
60 65 0.98
61 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.31
Consensus pattern (60 bp):
AAAAAGTTTAAGGACTAATTTAGAATCAAGGTCATAGTTTGAGAATAAAAATGAAACATT
Found at i:6499 original size:23 final size:22
Alignment explanation
Indices: 6484--6526 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6474 AATTATATAT
6484 AGTTTTCTTTCGAAATATAATA
1 AGTTTTCTTTCGAAATATAATA
* *
6506 ATTTTTCTTTCTATAATATAA
1 AGTTTTCTTTCGA-AATATAA
6527 GGTAAAGTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (22 bp):
AGTTTTCTTTCGAAATATAATA
Found at i:9598 original size:10 final size:10
Alignment explanation
Indices: 9583--9610 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
9573 CCAAATTCAA
9583 CTTAAATTAT
1 CTTAAATTAT
9593 CTTAAATTAT
1 CTTAAATTAT
9603 CTTAAATT
1 CTTAAATT
9611 TAAACGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (10 bp):
CTTAAATTAT
Found at i:10553 original size:26 final size:25
Alignment explanation
Indices: 10516--10566 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
10506 GTTCGTGCAT
* * *
10516 TTTTTATGTTAATTTTTTATAAAATA
1 TTTTTATATTAAATTTATA-AAAATA
10542 TTTTTATATTAAATTTATAAAAATA
1 TTTTTATATTAAATTTATAAAAATA
10567 CAAAATTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTTTATATTAAATTTATAAAAATA
Found at i:12335 original size:46 final size:46
Alignment explanation
Indices: 12279--12370 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
12269 ATCATGGATC
12279 AAATTATATCTTTGTATAAAAATTAATGATTAATTAAATTTTATTT
1 AAATTATATCTTTGTATAAAAATTAATGATTAATTAAATTTTATTT
*
12325 AAATTGTATCTTTGTATAAAAATTAATGATTAATTAAATTTTATTT
1 AAATTATATCTTTGTATAAAAATTAATGATTAATTAAATTTTATTT
12371 GAAAAAACGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.50
Consensus pattern (46 bp):
AAATTATATCTTTGTATAAAAATTAATGATTAATTAAATTTTATTT
Found at i:21916 original size:16 final size:16
Alignment explanation
Indices: 21869--21916 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
21859 ATTAATATTA
21869 TTTTTTATTAATTATAT
1 TTTTTTA-TAATTATAT
*
21886 TTATATTTAAAATTATAT
1 TT-T-TTTATAATTATAT
*
21904 TTTTTTATCATTA
1 TTTTTTATAATTA
21917 CTTAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 8 0.31
17 3 0.12
18 11 0.42
19 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTTATAATTATAT
Found at i:26338 original size:79 final size:79
Alignment explanation
Indices: 26253--26415 Score: 281
Period size: 79 Copynumber: 2.1 Consensus size: 79
26243 TCCATATATA
*
26253 TATATATATCTTCTTGTAATTTAGGGGTTTCAATTTTCAATATGAAAACTCTACGTTTTTGTGTT
1 TATATATATCTTCTTGTAATTTAGCGGTTTCAATTTTCAATATGAAAACTCTACGTTTTTGTGTT
26318 CCATTTATCTTGTG
66 CCATTTATCTTGTG
*
26332 TATATATGTCTTCTTGTAATTTAGCGGTTTCAATTTTCAATATGAAAACTCTACGTTTTTGTGTT
1 TATATATATCTTCTTGTAATTTAGCGGTTTCAATTTTCAATATGAAAACTCTACGTTTTTGTGTT
* * *
26397 TCATTTGTCTTGTT
66 CCATTTATCTTGTG
26411 TATAT
1 TATAT
26416 CATTCAATGT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.51
Consensus pattern (79 bp):
TATATATATCTTCTTGTAATTTAGCGGTTTCAATTTTCAATATGAAAACTCTACGTTTTTGTGTT
CCATTTATCTTGTG
Found at i:31090 original size:33 final size:32
Alignment explanation
Indices: 31053--31143 Score: 112
Period size: 31 Copynumber: 2.8 Consensus size: 32
31043 AAAAAAAACG
*
31053 TATTTGAGTCCTATTAAAACACTAAAATCAACA
1 TATTTGAGT-CTATTAAAACACTAAAACCAACA
* * *
31086 TATTTGAGTC-ATTAAAATATTAAAACCAACG
1 TATTTGAGTCTATTAAAACACTAAAACCAACA
* *
31117 TATTTGAGTATATTGAAACACTAAAAC
1 TATTTGAGTCTATTAAAACACTAAAAC
31144 TGAAGCATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 26 0.53
32 14 0.29
33 9 0.18
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (32 bp):
TATTTGAGTCTATTAAAACACTAAAACCAACA
Found at i:31546 original size:28 final size:28
Alignment explanation
Indices: 31457--31546 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
31447 ATTTATTTAC
* * *
31457 TTTATATATATTT-TTCATTTTCTCATAAT
1 TTTATATATATTTATTTATTTT-TAAT-TT
* *
31486 TTTA-ATAATTTTTATTTCTTTTTACA-TT
1 TTTATAT-ATATTTATTTATTTTTA-ATTT
*
31514 ATTATATATATTTATTTATTTTTAATTT
1 TTTATATATATTTATTTATTTTTAATTT
31542 TTTAT
1 TTTAT
31547 TGAATATTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 11
0.70 0.13 0.16
Matches are distributed among these distances:
27 1 0.02
28 27 0.57
29 12 0.26
30 7 0.15
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTATATATATTTATTTATTTTTAATTT
Found at i:36219 original size:241 final size:241
Alignment explanation
Indices: 35354--36211 Score: 1420
Period size: 241 Copynumber: 3.6 Consensus size: 241
35344 CCCATTTTTA
* * * * *
35354 TTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTTGAAACAATAC-A--TACTTGGAT
1 TTCAAAGCCAATTTCAACTTCACGACGGAGGATATTGGACTCGAAACAATACAACTTACTTGGAT
*
35416 TTCAACTTCACGACAAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
66 TTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
* * *
35481 TTTCAACTCCATAATGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACGATGGAGGAT
131 TTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACGACGGAGGAT
35546 ATCGTGCCATTTGAGGCTCAACTTCACGACGAAGGGGCTTCCCAGT
196 ATCGTGCCATTTGAGGCTCAACTTCACGACGAAGGGGCTTCCCAGT
35592 TTCAAAGCCAATTTCAACTTCACGACGGAGGATATTGGACTCGAAACAATACAACTTACTTGGAT
1 TTCAAAGCCAATTTCAACTTCACGACGGAGGATATTGGACTCGAAACAATACAACTTACTTGGAT
* *
35657 TTCAACTTCACGATGAAGGATATTCAAGTCAATGCTCAACTTCACGACGAAGGGGCCATCCACGA
66 TTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
*
35722 TTTCAACTCCACAACGGAGGATATCATACCCACACATCCACGATTTCAACTCCACGACGGAGGAT
131 TTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACGACGGAGGAT
35787 ATCGTGCCATTTGAGGCTCAACTTCACGACGAAGGGGCTTCCCAGT
196 ATCGTGCCATTTGAGGCTCAACTTCACGACGAAGGGGCTTCCCAGT
*
35833 TTCAAAGCCAATTTCAACTTCAC-AGCGGAGGATATTGGACTCGAAATAATACAACTTACTTGGA
1 TTCAAAGCCAATTTCAACTTCACGA-CGGAGGATATTGGACTCGAAACAATACAACTTACTTGGA
* * * * *
35897 TTTTAACTTCACGACGAAGGATATGCAAGTCAAGGCTCAACTTCACGACGAATGAGCCATCCATG
65 TTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACG
* *
35962 ATTTCAACTCCACGACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCATGACGGAGGA
130 ATTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACGACGGAGGA
*
36027 TATCGTGCCATTTGAGGCTCAACTTCACGACGAAGTGGCTTCCCAGT
195 TATCGTGCCATTTGAGGCTCAACTTCACGACGAAGGGGCTTCCCAGT
* *
36074 TTCAGAGCCAATTTTAACTTCACGACGGAGGATATTGGACTCGAAACAATACAACTTACTTGGAT
1 TTCAAAGCCAATTTCAACTTCACGACGGAGGATATTGGACTCGAAACAATACAACTTACTTGGAT
* * * *
36139 TTCAACTTCACGACGAAGGATATCCAATTCAAGGCTTAACTTCACGACGGAGGGGCCATCCAC-A
66 TTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
36203 GTTTCAACT
131 -TTTCAACT
36212 TCACGACGAA
Statistics
Matches: 579, Mismatches: 35, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
238 47 0.08
239 1 0.00
240 2 0.00
241 528 0.91
242 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (241 bp):
TTCAAAGCCAATTTCAACTTCACGACGGAGGATATTGGACTCGAAACAATACAACTTACTTGGAT
TTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
TTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACGACGGAGGAT
ATCGTGCCATTTGAGGCTCAACTTCACGACGAAGGGGCTTCCCAGT
Found at i:36606 original size:5 final size:5
Alignment explanation
Indices: 36596--36644 Score: 59
Period size: 5 Copynumber: 10.0 Consensus size: 5
36586 CTACAAAAAC
36596 ATTAT ATTAT ATTAT ATTAT ATT-T ATTATT ATTATT ATTAT -TT-T ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTA-T ATTA-T ATTAT ATTAT ATTAT
36645 TTTTATAGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 1 0.03
4 8 0.20
5 20 0.50
6 11 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
ATTAT
Found at i:36626 original size:3 final size:3
Alignment explanation
Indices: 36596--36650 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
36586 CTACAAAAAC
36596 ATT A-T ATT A-T ATT A-T ATT A-T ATTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
*
36638 -TT ATT ATT TTT AT
1 ATT ATT ATT ATT AT
36651 AGGCCCCATA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
2 10 0.23
3 32 0.73
4 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:36630 original size:20 final size:19
Alignment explanation
Indices: 36600--36651 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
36590 AAAAACATTA
36600 TATTA-TATTATATTATATT
1 TATTATTATTATATTAT-TT
36619 TATTATTATTATTATTATTT
1 TATTATTATTA-TATTATTT
*
36639 TATTATTTTTATA
1 TATTATTATTATA
36652 GGCCCCATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 7 0.23
20 17 0.57
21 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTATTATTATATTATTT
Found at i:36736 original size:33 final size:33
Alignment explanation
Indices: 36699--36764 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
36689 GAAAATAAAT
36699 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
*
36732 CAACGTATTTGAGTCCTATTTAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
36765 TGAAGCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (33 bp):
CAACGTATTTGAGTCCTATTAAAACACTAAAAC
Found at i:36775 original size:33 final size:33
Alignment explanation
Indices: 36699--36779 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
36689 GAAAATAAAT
*
36699 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1 CAACGCATTTGAGTCCTATTAAAACACTAAAAC
* *
36732 CAACGTATTTGAGTCCTATTTAAACACTAAAAC
1 CAACGCATTTGAGTCCTATTAAAACACTAAAAC
*
36765 TGAA-GCATTTGAGTC
1 -CAACGCATTTGAGTC
36780 TAAGTAGGAC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 42 0.95
34 2 0.05
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (33 bp):
CAACGCATTTGAGTCCTATTAAAACACTAAAAC
Found at i:37160 original size:40 final size:44
Alignment explanation
Indices: 37116--37199 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 44
37106 ATAATTTTAA
*
37116 TATTTTTTTATATCTT-TTT-ACATTATTATA-T-ATATTTATT
1 TATTTTTTAATATCTTATTTAACATTATTATATTAATATTTATT
* * *
37156 TATTTTTTAATTTTTTATTTAATATTATTATATTAATATTTATT
1 TATTTTTTAATATCTTATTTAACATTATTATATTAATATTTATT
37200 ATTATTCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 13 0.36
41 3 0.08
42 10 0.28
43 1 0.03
44 9 0.25
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (44 bp):
TATTTTTTAATATCTTATTTAACATTATTATATTAATATTTATT
Found at i:37189 original size:15 final size:15
Alignment explanation
Indices: 37139--37201 Score: 52
Period size: 14 Copynumber: 4.6 Consensus size: 15
37129 CTTTTTACAT
37139 TATTATATATATTT-A
1 TATTAT-TATATTTAA
37154 T-TTATT-T-TTTAA
1 TATTATTATATTTAA
37166 T-TT-TT-TATTTAA
1 TATTATTATATTTAA
37178 TATTATTATA-TTAA
1 TATTATTATATTTAA
37192 TATTTATTAT
1 TA-TTATTAT
37202 TATTCTTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
11 6 0.14
12 11 0.26
13 3 0.07
14 12 0.29
15 10 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTATTATATTTAA
Found at i:55299 original size:34 final size:34
Alignment explanation
Indices: 55256--55340 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
55246 TATGATTGAT
55256 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
55290 CTCTCGGCGTCTTCAGTTGGATTCTTCGTAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
55324 ATCTCGGCGTCTTCAGT
1 CTCTCGGCGTCTTCAGT
55341 GCTGTGCATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (34 bp):
CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
Found at i:55394 original size:22 final size:22
Alignment explanation
Indices: 55362--55415 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
55352 GACTGGACGT
*
55362 GAGAAATCACGGGTTCTGCAAG
1 GAGAAAGCACGGGTTCTGCAAG
*
55384 GAGAGAGCACGGGTTCTGCAAG
1 GAGAAAGCACGGGTTCTGCAAG
55406 GAGAAAGCAC
1 GAGAAAGCAC
55416 ATAAATCACG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.19, G:0.35, T:0.13
Consensus pattern (22 bp):
GAGAAAGCACGGGTTCTGCAAG
Found at i:55471 original size:23 final size:23
Alignment explanation
Indices: 55445--55488 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
55435 TCCTGCAGGG
55445 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
55468 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
55489 GCATGCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:55495 original size:23 final size:22
Alignment explanation
Indices: 55442--55495 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
55432 GGGTCCTGCA
55442 GGGCTGCACGTCTGCATGTGGG
1 GGGCTGCACGTCTGCATGTGGG
*
55464 GGTCCTGCACGTCTGCATGTGGG
1 GG-GCTGCACGTCTGCATGTGGG
55487 GGGCATGCA
1 GGGC-TGCA
55496 ACTGTTGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 25 0.89
ACGTcount: A:0.11, C:0.24, G:0.43, T:0.22
Consensus pattern (22 bp):
GGGCTGCACGTCTGCATGTGGG
Found at i:56231 original size:171 final size:173
Alignment explanation
Indices: 55945--56302 Score: 569
Period size: 172 Copynumber: 2.1 Consensus size: 173
55935 TTGTAAAGTT
* * *
55945 TTAGGGACCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGCTAT
1 TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATTAAAAGTTGCTAT
*
56010 ACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTAGAAAGAATTTA-AAATTTA-T
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
*
56073 GGATTAAATTGCTAACTTTGAAAATGTTGAGAACCAAATAGTAA
131 -GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
* * *
56117 TTAGGGATCGTTTTGCAAAATTTGAGGAATTTAAGAAATTAGAGTAAATTA-TAAAAGTTGGTAT
1 TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATTAAAAGTTGCTAT
* *
56181 ACTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
* *
56246 GATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTAA
131 GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
*
56289 TTAGGGATCATTTT
1 TTAGGGATCGTTTT
56303 ATATTTGATG
Statistics
Matches: 171, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
171 64 0.37
172 106 0.62
173 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (173 bp):
TTAGGGATCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATTAAAAGTTGCTAT
ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
Found at i:58563 original size:14 final size:14
Alignment explanation
Indices: 58546--59010 Score: 123
Period size: 14 Copynumber: 33.9 Consensus size: 14
58536 AAGTCAAGTA
58546 ATTATTATTAAATC
1 ATTATTATTAAATC
**
58560 ATTAAAATTAAATC
1 ATTATTATTAAATC
** * *
58574 ATTAAAATTAAGTA
1 ATTATTATTAAATC
*
58588 ATTATTATTAAATT
1 ATTATTATTAAATC
**
58602 ATTAAAATTAAATC
1 ATTATTATTAAATC
* *
58616 ---ATTA--AAGTA
1 ATTATTATTAAATC
58625 ATTATTATTAAATC
1 ATTATTATTAAATC
*
58639 ATTAAATCATTAAATC
1 ATT--ATTATTAAATC
* *
58655 ATTAAATCATTAAAGTA
1 ATT--ATTATTAAA-TC
*
58672 ATTATTATTAAAGC
1 ATTATTATTAAATC
*
58686 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
* *
58700 ---ATTA--AAGTA
1 ATTATTATTAAATC
58709 ATTATTATTAAATC
1 ATTATTATTAAATC
*
58723 ATTAAATCATTAAATC
1 ATT--ATTATTAAATC
* *
58739 ATTAAATCATTAAAATA
1 ATT--ATTATT-AAATC
58756 ATTATTATTAAATC
1 ATTATTATTAAATC
*
58770 ATTAAATCATTAAATC
1 ATT--ATTATTAAATC
* *
58786 ---ATTA--AAGTA
1 ATTATTATTAAATC
58795 ATTATTATTAAATC
1 ATTATTATTAAATC
*
58809 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
*
58823 ATTAAATCATTAAA--
1 ATT--ATTATTAAATC
* *
58837 ATTAAATCATTAAAGTA
1 ATT--ATTATTAAA-TC
58854 ATTATTATTAAATC
1 ATTATTATTAAATC
**
58868 ATTAAAATTAAATC
1 ATTATTATTAAATC
* *
58882 ---ATTA--AAGTA
1 ATTATTATTAAATC
58891 ATTATTATTAAATC
1 ATTATTATTAAATC
*
58905 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
* *
58919 ---ATTA--AAGTA
1 ATTATTATTAAATC
58928 ATTATTATTAAATC
1 ATTATTATTAAATC
* *
58942 ATTA-AAGTTAAATA
1 ATTATTA-TTAAATC
58956 ATTATTATTAAATC
1 ATTATTATTAAATC
* *
58970 ATTA-AAGTTAAATA
1 ATTATTA-TTAAATC
* *
58984 ATTA-AATTTAAATA
1 ATTATTA-TTAAATC
58998 ATTATTATTAAAT
1 ATTATTATTAAAT
59011 ATGTACTCGA
Statistics
Matches: 338, Mismatches: 65, Indels: 96
0.68 0.13 0.19
Matches are distributed among these distances:
9 15 0.04
11 9 0.03
12 22 0.07
13 5 0.01
14 188 0.56
15 23 0.07
16 61 0.18
17 15 0.04
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (14 bp):
ATTATTATTAAATC
Found at i:58623 original size:84 final size:81
Alignment explanation
Indices: 58541--59010 Score: 473
Period size: 84 Copynumber: 5.8 Consensus size: 81
58531 CATTAAAGTC
*
58541 AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAA-ATT-AAGTAATTATTATTAAATTAT
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAACATTAAAGTAATTATTATTAAATCAT
58604 TAAAATTAAATCATTA
66 TAAAATTAAATCATTA
*
58620 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAAG
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTAAA-CATTAAAGTAATTATTATTAAAT
*
58685 CATTAAAGTTAAATCATTA
63 CATTAAAATTAAATCATTA
*
58704 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTAAATCATTAAAATAATTATTATTAAAT
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTAAA-CATTAAAGTAATTATTATTAAAT
58769 CATTAAATCATTAAATCATTA
63 CATTAAA--ATTAAATCATTA
* * *
58790 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAA--ATCATTAAAGT
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAA-CATT-AAAGTAATTATTATTAAA-T
* **
58853 AATTATTATTAAATCATTAA
63 CATTAAAATTAAATCATT-A
* * * ** * * * *
58873 AATTAA--ATCATTAAAGTAATTATTATTAAATCATTAAA-GTTAAA-TCATTA-AAGTAATTAT
1 AAGTAATTATTATTAAA-TCATTAAAATTAAATCATTAAACATTAAAGTAATTATTATTAA--AT
* *
58933 TATTAAATCATTAAA--GTTA
63 CATTAAA--ATTAAATCATTA
* * *
58952 AA-TAATTATTATTAAATCATTAAAGTTAAATAATTAAA-TTTAAA-TAATTATTATTAAAT
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAACATTAAAGTAATTATTATTAAAT
59011 ATGTACTCGA
Statistics
Matches: 335, Mismatches: 36, Indels: 41
0.81 0.09 0.10
Matches are distributed among these distances:
78 7 0.02
79 62 0.19
80 22 0.07
81 23 0.07
82 35 0.10
83 17 0.05
84 127 0.38
85 6 0.02
86 36 0.11
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (81 bp):
AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAACATTAAAGTAATTATTATTAAATCAT
TAAAATTAAATCATTA
Found at i:58633 original size:37 final size:37
Alignment explanation
Indices: 58583--58959 Score: 403
Period size: 37 Copynumber: 10.0 Consensus size: 37
58573 CATTAAAATT
*
58583 AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
58620 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTAAATCATTA
1 AAGT-A--ATTA-T---T-ATTAAATCATTAAA--ATTAAATCATTA
* *
58667 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
58704 AAGTAATTATTATTAAATCATTAAATCATTAAATCATT-
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTA
* * **
58742 -A--AATCATTA--AAATAATTATTATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* * * **
58774 AA-TCATTAAATCATTAAAGTAATTATTATTAAATCATTA
1 AAGTAATT--ATTATTAAA-TCATTAAAATTAAATCATTA
*
58813 AAGTTAA--ATCATTAAATCATTAAAATTAAATCATTA
1 AAG-TAATTATTATTAAATCATTAAAATTAAATCATTA
58849 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
*
58886 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* *
58923 AAGTAATTATTATTAAATCATTAAAGTTAAATAATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
58960 TTATTAAATC
Statistics
Matches: 297, Mismatches: 19, Indels: 48
0.82 0.05 0.13
Matches are distributed among these distances:
31 11 0.04
33 9 0.03
34 2 0.01
35 10 0.03
36 23 0.08
37 149 0.50
38 4 0.01
39 45 0.15
40 5 0.02
41 3 0.01
43 1 0.00
44 5 0.02
45 13 0.04
46 1 0.00
47 16 0.05
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (37 bp):
AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
Found at i:58688 original size:23 final size:23
Alignment explanation
Indices: 58608--59010 Score: 171
Period size: 23 Copynumber: 17.3 Consensus size: 23
58598 AATTATTAAA
58608 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
* *
58631 ATTAAATCATTAAA-TCATTAAATC
1 ATTAAATCATTAAAGTAATT--ATT
58655 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
* *
58678 ATTAAAGCATTAAAGTTAA--ATC
1 ATTAAATCATTAAAG-TAATTATT
* * * *
58700 ATTAAAGTAATTATTATTAA--ATC
1 ATTAAA-TCATTA-AAGTAATTATT
* *
58723 ATTAAATCATTAAA-TCATTAAATC
1 ATTAAATCATTAAAGTAATT--ATT
* * * *
58747 ATTAAAATAATTATTATTAA--ATC
1 ATT-AAATCATTA-AAGTAATTATT
* *
58770 ATTAAATCATTAAA-TCATTA-A
1 ATTAAATCATTAAAGTAATTATT
* * * *
58791 AGTAATTATTATTAAA-TCATTA-A
1 ATTAA--ATCATTAAAGTAATTATT
* **
58814 AGTTAAATCATTAAA-TCATTAAA
1 A-TTAAATCATTAAAGTAATTATT
58837 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
* *
58860 ATTAAATCATTAAAATTAAATCATT
1 ATTAAATCATT-AAAGT-AATTATT
* * * *
58885 AAAGTAATTATTATTAAA-TCATTA-A
1 --ATTAA--ATCATTAAAGTAATTATT
58910 AGTTAAATCATTAAAGTAATTATT
1 A-TTAAATCATTAAAGTAATTATT
58934 ATTAAATCATTAAAGTTAAATAATTATT
1 ATTAAATCATTAAAG-----TAATTATT
*
58962 ATTAAATCATTAAAGTTAA--ATA
1 ATTAAATCATTAAAG-TAATTATT
58984 ATTAAAT--TTAAA-TAATTATT
1 ATTAAATCATTAAAGTAATTATT
59004 ATTAAAT
1 ATTAAAT
59011 ATGTACTCGA
Statistics
Matches: 303, Mismatches: 41, Indels: 75
0.72 0.10 0.18
Matches are distributed among these distances:
18 3 0.01
20 18 0.06
21 6 0.02
22 70 0.23
23 106 0.35
24 40 0.13
25 18 0.06
26 4 0.01
27 7 0.02
28 26 0.09
29 5 0.02
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (23 bp):
ATTAAATCATTAAAGTAATTATT
Found at i:58907 original size:74 final size:73
Alignment explanation
Indices: 58541--59010 Score: 401
Period size: 74 Copynumber: 6.2 Consensus size: 73
58531 CATTAAAGTC
* * *
58541 AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAATTAAGTAATTATTATTAAATTATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATT-AAAGT---TAA--ATCATTAAATCATTA
58606 AAATTAAATCATTA
60 AAATTAAATCATTA
* * *
58620 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTAAAG
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATT-AA--AGT----TAA--ATCATTAAAT
*
58685 CATTAAAGTTAAATCATTA
55 CATTAAAATTAAATCATTA
* **
58704 AAGTAATTATTATTAAATCATTAAATCATTAAATC-----A-TTAAATCATTAAAATAATTATTA
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTAAAGTTAAATCATT-AAATCATTAAAA
58763 TTAAATCATTA
63 TTAAATCATTA
* * * **
58774 AA-TCATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAATCATTAAAA
1 AAGTAATT--ATTATTAAA-TCATTAAAATTAAATCATTAAAGTTAAATCATTAAATCATTAAAA
58838 TTAAATCATTA
63 TTAAATCATTA
* *
58849 AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAG-TAATTATTATTAAATCATTAAAGT
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAGTTAA--ATCATTAAATCATTAAAAT
58913 TAAATCATTA
64 TAAATCATTA
* * * *
58923 AAGTAATTATTATTAAATCATTAAAGTTAAATAATTATTA-TTAAATCATTAAAGT--TAAATAA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA-AAGTTAAATCATTAAA-TCATTAA-AA
58985 TTAAAT--TTA
63 TTAAATCATTA
58994 AA-TAATTATTATTAAAT
1 AAGTAATTATTATTAAAT
59011 ATGTACTCGA
Statistics
Matches: 339, Mismatches: 30, Indels: 53
0.80 0.07 0.13
Matches are distributed among these distances:
69 9 0.03
70 43 0.13
71 16 0.05
72 11 0.03
73 35 0.10
74 71 0.21
75 28 0.08
76 15 0.04
79 25 0.07
81 14 0.04
83 3 0.01
84 69 0.20
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (73 bp):
AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTA
AATCATTA
Found at i:58990 original size:8 final size:8
Alignment explanation
Indices: 58552--58975 Score: 267
Period size: 8 Copynumber: 56.8 Consensus size: 8
58542 AGTAATTATT
58552 ATTAAATC
1 ATTAAATC
58560 ATTAAA--
1 ATTAAATC
58566 ATTAAATC
1 ATTAAATC
58574 ATTAAA--
1 ATTAAATC
* *
58580 ATTAAGTA
1 ATTAAATC
*
58588 ATT--ATT
1 ATTAAATC
*
58594 ATTAAATT
1 ATTAAATC
58602 ATTAAA--
1 ATTAAATC
58608 ATTAAATC
1 ATTAAATC
*
58616 ATTAAAGTA
1 ATTAAA-TC
*
58625 ATT--ATT
1 ATTAAATC
58631 ATTAAATC
1 ATTAAATC
58639 ATTAAATC
1 ATTAAATC
58647 ATTAAATC
1 ATTAAATC
58655 ATTAAATC
1 ATTAAATC
*
58663 ATTAAAGTA
1 ATTAAA-TC
*
58672 ATT--ATT
1 ATTAAATC
*
58678 ATTAAAGC
1 ATTAAATC
58686 ATTAAA--
1 ATTAAATC
*
58692 GTTAAATC
1 ATTAAATC
*
58700 ATTAAAGTA
1 ATTAAA-TC
*
58709 ATT--ATT
1 ATTAAATC
58715 ATTAAATC
1 ATTAAATC
58723 ATTAAATC
1 ATTAAATC
58731 ATTAAATC
1 ATTAAATC
58739 ATTAAATC
1 ATTAAATC
*
58747 ATTAAAATA
1 ATT-AAATC
*
58756 ATT--ATT
1 ATTAAATC
58762 ATTAAATC
1 ATTAAATC
58770 ATTAAATC
1 ATTAAATC
58778 ATTAAATC
1 ATTAAATC
*
58786 ATTAAAGTA
1 ATTAAA-TC
*
58795 ATT--ATT
1 ATTAAATC
58801 ATTAAATC
1 ATTAAATC
58809 ATTAAA--
1 ATTAAATC
*
58815 GTTAAATC
1 ATTAAATC
58823 ATTAAATC
1 ATTAAATC
58831 ATTAAA--
1 ATTAAATC
58837 ATTAAATC
1 ATTAAATC
*
58845 ATTAAAGTA
1 ATTAAA-TC
*
58854 ATT--ATT
1 ATTAAATC
58860 ATTAAATC
1 ATTAAATC
58868 ATTAAA--
1 ATTAAATC
58874 ATTAAATC
1 ATTAAATC
*
58882 ATTAAAGTA
1 ATTAAA-TC
*
58891 ATT--ATT
1 ATTAAATC
58897 ATTAAATC
1 ATTAAATC
58905 ATTAAA--
1 ATTAAATC
*
58911 GTTAAATC
1 ATTAAATC
*
58919 ATTAAAGTA
1 ATTAAA-TC
*
58928 ATT--ATT
1 ATTAAATC
58934 ATTAAATC
1 ATTAAATC
58942 ATTAAA--
1 ATTAAATC
* *
58948 GTTAAATA
1 ATTAAATC
*
58956 ATT--ATT
1 ATTAAATC
58962 ATTAAATC
1 ATTAAATC
58970 ATTAAA
1 ATTAAA
58976 GTTAAATAAT
Statistics
Matches: 332, Mismatches: 38, Indels: 92
0.72 0.08 0.20
Matches are distributed among these distances:
6 91 0.27
7 7 0.02
8 199 0.60
9 35 0.11
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (8 bp):
ATTAAATC
Found at i:62378 original size:18 final size:18
Alignment explanation
Indices: 62355--62401 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
62345 AAATTATTAG
62355 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
62373 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
62391 TCTCACGCTTC
1 TCTCACGCTTC
62402 GGCCACAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (18 bp):
TCTCACGCTTCAGACGAA
Found at i:64171 original size:17 final size:17
Alignment explanation
Indices: 64151--64183 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
64141 ATATTTATTT
*
64151 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
64168 ATATAAAAAATAATAT
1 ATATAAAAAATAATAT
64184 TATAATCTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:64288 original size:16 final size:16
Alignment explanation
Indices: 64254--64336 Score: 57
Period size: 16 Copynumber: 5.2 Consensus size: 16
64244 TCAAAATTAT
*
64254 TTAT-TATTTTAAGTAA
1 TTATATATTTTAAAT-A
64270 TTATATATTTTAAATA
1 TTATATATTTTAAATA
*
64286 TTAT-TATTTTTAACT-
1 TTATATA-TTTTAAATA
* *
64301 TTATAAAATTATAAATAA
1 TTAT-ATATTTTAAAT-A
*
64319 TTA-ATATCTTAAATA
1 TTATATATTTTAAATA
64334 TTA
1 TTA
64337 AAGATATAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
15 10 0.19
16 30 0.57
17 10 0.19
18 3 0.06
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (16 bp):
TTATATATTTTAAATA
Found at i:66340 original size:20 final size:20
Alignment explanation
Indices: 66306--66359 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
66296 TACTATTTAA
66306 ATATATA-TAAA-AATTATT
1 ATATATATTAAATAATTATT
* *
66324 ATATATTTTAAATAATTTTT
1 ATATATATTAAATAATTATT
*
66344 ATCTATATTAATATAA
1 ATATATATTAA-ATAA
66360 AATTTTATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 6 0.21
19 4 0.14
20 15 0.52
21 4 0.14
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATATTAAATAATTATT
Found at i:66365 original size:22 final size:22
Alignment explanation
Indices: 66310--66367 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 22
66300 ATTTAAATAT
*
66310 ATATAAAAATTATTATATATTTTA
1 ATAT-AAAATT-TTATATATATTA
* *
66334 A-AT-AATTTTTATCTATATTA
1 ATATAAAATTTTATATATATTA
66354 ATATAAAATTTTAT
1 ATATAAAATTTTAT
66368 TGCTGATCCG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 11 0.39
21 6 0.21
22 8 0.29
23 2 0.07
24 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATAAAATTTTATATATATTA
Found at i:66608 original size:15 final size:15
Alignment explanation
Indices: 66588--66618 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
66578 CATTCTCAAG
66588 TAATTTTAAATTTTT
1 TAATTTTAAATTTTT
*
66603 TAATTTTTAATTTTT
1 TAATTTTAAATTTTT
66618 T
1 T
66619 TAAAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TAATTTTAAATTTTT
Found at i:66612 original size:16 final size:16
Alignment explanation
Indices: 66591--66621 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
66581 TCTCAAGTAA
66591 TTTTAAATTTTTTAAT
1 TTTTAAATTTTTTAAT
*
66607 TTTTAATTTTTTTAA
1 TTTTAAATTTTTTAA
66622 AATTTTATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTAAATTTTTTAAT
Found at i:75853 original size:16 final size:16
Alignment explanation
Indices: 75810--75860 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
75800 AACTTGTTGC
*
75810 TTAA-CTCGTTACTTG
1 TTAAGCTCGTTGCTTG
**
75825 TTAAGCTAATTGCTTG
1 TTAAGCTCGTTGCTTG
*
75841 TTAAGCTCGTTGCTCG
1 TTAAGCTCGTTGCTTG
75857 TTAA
1 TTAA
75861 ACTCAACAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
15 4 0.14
16 25 0.86
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.43
Consensus pattern (16 bp):
TTAAGCTCGTTGCTTG
Found at i:88742 original size:60 final size:61
Alignment explanation
Indices: 88645--88789 Score: 188
Period size: 60 Copynumber: 2.4 Consensus size: 61
88635 ATATCTACTC
* * * *
88645 AAACTATGATCCC-TATTCTAAATT-GATCCTTATACTTTTAAATGTTCCAATTTCATCCCC
1 AAACTATGA-CCCTTATTCTAAATTAGATCCTCAAACTTTTAAATATTCCAATTTCATCCCA
* ** *
88705 AAATTATGACTTTTATTCTAAATTAG-TCCTCAAACTTTTAAATATTTCAATTTCATCCCA
1 AAACTATGACCCTTATTCTAAATTAGATCCTCAAACTTTTAAATATTCCAATTTCATCCCA
88765 AAACTATGACCCTTATTCTAAATTA
1 AAACTATGACCCTTATTCTAAATTA
88790 ATCTCCAGAC
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
59 1 0.01
60 70 0.97
61 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (61 bp):
AAACTATGACCCTTATTCTAAATTAGATCCTCAAACTTTTAAATATTCCAATTTCATCCCA
Found at i:88812 original size:60 final size:59
Alignment explanation
Indices: 88644--88830 Score: 171
Period size: 60 Copynumber: 3.1 Consensus size: 59
88634 CATATCTACT
* * * * ** *
88644 CAAACTATGATCCC-TATTCTAAATTGATCCTTATACTTTTAAATGTTCCAATTTCATCCC
1 CAAACTATGA-CCCTTATTCTAAATTAATCCTCAAACTTCTAAACATTTCAATTTCAT-CC
* ** * * *
88704 CAAATTATGACTTTTATTCTAAATTAGTCCTCAAACTTTTAAATATTTCAATTTCATCC
1 CAAACTATGACCCTTATTCTAAATTAATCCTCAAACTTCTAAACATTTCAATTTCATCC
* * * *
88763 CAAAACTATGACCCTTATTCTAAATTAAT-CTCCAGACTTCTGAACATTTCAATTTAATCT
1 C-AAACTATGACCCTTATTCTAAATTAATCCT-CAAACTTCTAAACATTTCAATTTCATCC
88823 CAAACTAT
1 CAAACTAT
88831 CAAAAGTTTG
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
59 13 0.12
60 92 0.88
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (59 bp):
CAAACTATGACCCTTATTCTAAATTAATCCTCAAACTTCTAAACATTTCAATTTCATCC
Found at i:88967 original size:60 final size:61
Alignment explanation
Indices: 88903--89023 Score: 147
Period size: 60 Copynumber: 2.0 Consensus size: 61
88893 AAAGTTTGAG
* ** * * *
88903 GATGAAATTAGAATGTTCTAAAAATT-AAAGACTAATTTTATAT-AAAAATCATAAATTAAA
1 GATGAAATTAAAACATTC-AAAAATTAAAAGACCAATTTAAAATAAAAAATCATAAATTAAA
* *
88963 GATGAAATTAAAACATTCAAAAATTAAAATACCAATTTAAAATAAAAAATCATAATTTAAA
1 GATGAAATTAAAACATTCAAAAATTAAAAGACCAATTTAAAATAAAAAATCATAAATTAAA
89024 TATATATAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 7 0.14
60 28 0.55
61 16 0.31
ACGTcount: A:0.57, C:0.07, G:0.06, T:0.31
Consensus pattern (61 bp):
GATGAAATTAAAACATTCAAAAATTAAAAGACCAATTTAAAATAAAAAATCATAAATTAAA
Found at i:95086 original size:2 final size:2
Alignment explanation
Indices: 95079--95104 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
95069 TTATCTATGA
95079 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
95105 TCAAATGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.