Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005170.1 Hibiscus syriacus cultivar Beakdansim tig00011668_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: 84127
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8149 original size:46 final size:46
Alignment explanation
Indices: 8029--8132 Score: 158
Period size: 46 Copynumber: 2.3 Consensus size: 46
8019 CATGTTTTGG
8029 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCTGGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCTGGA
* *
8075 GTGCATCGATACATAAAATGCATTCGATGTTTCCATAA-AATCCT-GA
1 GTGCATCGATGCATAAAATGCATTCGATGTTT-CA-AACAAGCCTGGA
8121 GTGCATCGATGC
1 GTGCATCGATGC
8133 GTGGAAGTGC
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
46 44 0.83
47 7 0.13
48 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCTGGA
Found at i:8798 original size:27 final size:26
Alignment explanation
Indices: 8751--8815 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 26
8741 GTCATATGCT
* * *
8751 AAATAA-TGCAAAAATCTAATAAACCA
1 AAATAAGTTCAAAAACCAAATAAA-CA
* * *
8777 ATATAAGTTCAAAAACCAAATATATA
1 AAATAAGTTCAAAAACCAAATAAACA
8803 AAATAAGTTCAAA
1 AAATAAGTTCAAA
8816 CATTCAAAGT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
26 18 0.58
27 13 0.42
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.23
Consensus pattern (26 bp):
AAATAAGTTCAAAAACCAAATAAACA
Found at i:10549 original size:17 final size:17
Alignment explanation
Indices: 10527--10560 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
10517 GTGCATCGAT
10527 GCACATTCAAGGAGTGC
1 GCACATTCAAGGAGTGC
10544 GCACATTCAAGGAGTGC
1 GCACATTCAAGGAGTGC
10561 ATCGGTGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.18
Consensus pattern (17 bp):
GCACATTCAAGGAGTGC
Found at i:10618 original size:45 final size:44
Alignment explanation
Indices: 10544--10635 Score: 114
Period size: 45 Copynumber: 2.1 Consensus size: 44
10534 CAAGGAGTGC
* * *
10544 GCACATTCAAGGAGTGCATCGGTGCATCTTCATGGTGTATCGAT
1 GCACATTCAAGGAGTGCATCGATGAATCTTCATAGTGTATCGAT
* *
10588 GCACATTCATAGG-GATGCATTGATGAATCTTCATAGTGTATTGAT
1 GCACATTCA-AGGAG-TGCATCGATGAATCTTCATAGTGTATCGAT
10633 GCA
1 GCA
10636 TTATGCACAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
44 10 0.24
45 31 0.76
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (44 bp):
GCACATTCAAGGAGTGCATCGATGAATCTTCATAGTGTATCGAT
Found at i:14485 original size:20 final size:20
Alignment explanation
Indices: 14443--14485 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
14433 TATTTTCATT
* *
14443 TTTTTAATTTTGAAATATCA
1 TTTTTAATTTTGAAAAATAA
14463 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
14483 TTT
1 TTT
14486 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:16523 original size:18 final size:18
Alignment explanation
Indices: 16508--16566 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
16498 TGAGTGCAAT
*
16508 GATGTGTGGAAGTGCATC
1 GATGCGTGGAAGTGCATC
16526 GATGCGTGGAAGTGCATC
1 GATGCGTGGAAGTGCATC
16544 GATGCGTGGAAGTGCATC
1 GATGCGTGGAAGTGCATC
*
16562 AATGC
1 GATGC
16567 ATAAAATGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.24, C:0.15, G:0.37, T:0.24
Consensus pattern (18 bp):
GATGCGTGGAAGTGCATC
Found at i:17472 original size:18 final size:18
Alignment explanation
Indices: 17434--17469 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
17424 TAAATTGTTG
17434 TTAAATTTATCAAATAAT
1 TTAAATTTATCAAATAAT
17452 TTAAATTT-T-AAATAAT
1 TTAAATTTATCAAATAAT
17468 TT
1 TT
17470 TTAGTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 1 0.06
18 8 0.44
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAAATTTATCAAATAAT
Found at i:17507 original size:24 final size:25
Alignment explanation
Indices: 17461--17509 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
17451 TTTAAATTTT
* * *
17461 AAATAATTTTTAGTTAATTTTTTAA
1 AAATAATTTTCAGTAAATATTTTAA
17486 AAATAATTTTCA-TAAATATTTTAA
1 AAATAATTTTCAGTAAATATTTTAA
17510 TTAAAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (25 bp):
AAATAATTTTCAGTAAATATTTTAA
Found at i:23923 original size:29 final size:29
Alignment explanation
Indices: 23891--24066 Score: 132
Period size: 29 Copynumber: 6.2 Consensus size: 29
23881 TTTACACATT
* *
23891 TATCACCCTTTT-AAAAAAATTTACAAAAA
1 TATCACCATTTTCAAAAAAA-TTACGAAAA
* * *
23920 TATCACCCTTTTCAAAATAATTACTAAAA
1 TATCACCATTTTCAAAAAAATTACGAAAA
* * *
23949 TATCA--TTTTTAAAAAAATATATATG-AAA
1 TATCACCATTTTCAAAAAA-AT-TACGAAAA
*
23977 T-T-ATCATTTT-AAAAAAATTACGAAAA
1 TATCACCATTTTCAAAAAAATTACGAAAA
* ** * *
24003 TAGCATAATTTTCAAAATAATTACCAAAA
1 TATCACCATTTTCAAAAAAATTACGAAAA
* *
24032 TATCACCATTTTCAAAATAATTACTAAAA
1 TATCACCATTTTCAAAAAAATTACGAAAA
24061 TATCAC
1 TATCAC
24067 TCGATCAACG
Statistics
Matches: 121, Mismatches: 17, Indels: 18
0.78 0.11 0.12
Matches are distributed among these distances:
25 3 0.02
26 7 0.06
27 16 0.13
28 17 0.14
29 72 0.60
30 6 0.05
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (29 bp):
TATCACCATTTTCAAAAAAATTACGAAAA
Found at i:31274 original size:29 final size:28
Alignment explanation
Indices: 31216--31393 Score: 150
Period size: 29 Copynumber: 6.2 Consensus size: 28
31206 TTTACACATT
* * *
31216 TATCACCCTTTTTAAAAGTATTTACAAAAA
1 TATCA-CCTTTTCAAAA-TAATTACTAAAA
31246 TATCACTCTTTTCAAAATAATTACTAAAA
1 TATCAC-CTTTTCAAAATAATTACTAAAA
** * *
31275 TATCATTTTTTTTTAAAAT--TTA-TGAAAT
1 TATCA--CCTTTTCAAAATAATTACT-AAAA
* *
31303 TATCA-CTTTT-AAAAAAATTACGAAAA
1 TATCACCTTTTCAAAATAATTACTAAAA
* *
31329 TAACACCATTTTCAAAATAATTACCAAAA
1 TATCACC-TTTTCAAAATAATTACTAAAA
31358 TATCACCATTTTCAAAATAATTACTAAAA
1 TATCACC-TTTTCAAAATAATTACTAAAA
31387 TATCACC
1 TATCACC
31394 CGGTCAACGG
Statistics
Matches: 122, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
24 4 0.03
25 4 0.03
26 10 0.08
27 2 0.02
28 15 0.12
29 64 0.52
30 23 0.19
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.37
Consensus pattern (28 bp):
TATCACCTTTTCAAAATAATTACTAAAA
Found at i:33291 original size:31 final size:31
Alignment explanation
Indices: 33250--33309 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
33240 ATAAAGATTC
* *
33250 AAAGATGTTATGTCATCCA-ACTATCTTCTTA
1 AAAGACGTTATATCAT-CATACTATCTTCTTA
*
33281 AAAGACGTTATATCATTATACTATCTTCT
1 AAAGACGTTATATCATCATACTATCTTCT
33310 CCGATCATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (31 bp):
AAAGACGTTATATCATCATACTATCTTCTTA
Found at i:35012 original size:26 final size:26
Alignment explanation
Indices: 34976--35028 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
34966 TTAGAGAAAT
34976 CAATGCTATGCAAACTTCCAATTCCA
1 CAATGCTATGCAAACTTCCAATTCCA
35002 CAATGCTATGCAAACTTCCAATTCCA
1 CAATGCTATGCAAACTTCCAATTCCA
35028 C
1 C
35029 TTGTGTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.32, G:0.08, T:0.26
Consensus pattern (26 bp):
CAATGCTATGCAAACTTCCAATTCCA
Found at i:45477 original size:31 final size:31
Alignment explanation
Indices: 45440--45514 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
45430 CAGGGCCACG
45440 GGGCCTACCCAAGAAAGATCTCGAGGCCGCA
1 GGGCCTACCCAAGAAAGATCTCGAGGCCGCA
* *
45471 GGGCCTACCCAAGAAAGATCTCGGGGCCTCA
1 GGGCCTACCCAAGAAAGATCTCGAGGCCGCA
* *
45502 GAGTCTACCCAAG
1 GGGCCTACCCAAG
45515 GGTTGTCTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.28, C:0.32, G:0.28, T:0.12
Consensus pattern (31 bp):
GGGCCTACCCAAGAAAGATCTCGAGGCCGCA
Found at i:46632 original size:17 final size:17
Alignment explanation
Indices: 46610--46644 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
46600 AATAAAAAAA
46610 ATTCTAGGTCATTTGGT
1 ATTCTAGGTCATTTGGT
46627 ATTCTAGGTCATTTGGT
1 ATTCTAGGTCATTTGGT
46644 A
1 A
46645 ATTGAGGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.11, G:0.23, T:0.46
Consensus pattern (17 bp):
ATTCTAGGTCATTTGGT
Found at i:49999 original size:21 final size:21
Alignment explanation
Indices: 49974--50029 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
49964 TTATAAAATT
*
49974 TATATTAAAATATTCT-AAAA
1 TATATTAAAATATTATGAAAA
*
49994 GTATATTATAATATTATGAAAA
1 -TATATTAAAATATTATGAAAA
*
50016 TATTTTAAAATATT
1 TATATTAAAATATT
50030 TATTTAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (21 bp):
TATATTAAAATATTATGAAAA
Found at i:50027 original size:10 final size:10
Alignment explanation
Indices: 49978--50030 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
49968 AAAATTTATA
49978 TTAAAATATT
1 TTAAAATATT
* *
49988 CTAAAAGTATA
1 TTAAAA-TATT
*
49999 TTATAATATT
1 TTAAAATATT
*
50009 ATGAAAATATT
1 -TTAAAATATT
50020 TTAAAATATT
1 TTAAAATATT
50030 T
1 T
50031 ATTTAATTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
10 18 0.55
11 15 0.45
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (10 bp):
TTAAAATATT
Found at i:50274 original size:24 final size:23
Alignment explanation
Indices: 50247--50299 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
50237 AAAATAAATG
50247 TTTTTATAATAAGATAAATATACT
1 TTTTTATAATAAG-TAAATATACT
* * * *
50271 TTTTCATAATTAGTTAATATATT
1 TTTTTATAATAAGTAAATATACT
50294 TTTTTA
1 TTTTTA
50300 CAAAATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTTTATAATAAGTAAATATACT
Found at i:51261 original size:20 final size:20
Alignment explanation
Indices: 51238--51289 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
51228 AACGCGATCC
51238 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
51258 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
51278 CCAAAATCGCAA
1 CCAGAATCGCAA
51290 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:51306 original size:21 final size:20
Alignment explanation
Indices: 51280--51377 Score: 70
Period size: 21 Copynumber: 4.8 Consensus size: 20
51270 ATCAGTTTCC
51280 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * * *
51301 AAAATCGCGATGCGATAGTAG
1 AAAATCGCAACGCGAT-TTTG
* ** *
51322 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-G
* * *
51343 ATAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
51363 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
51378 ACACATAAAT
Statistics
Matches: 57, Mismatches: 18, Indels: 5
0.71 0.22 0.06
Matches are distributed among these distances:
20 15 0.26
21 42 0.74
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:51370 original size:20 final size:20
Alignment explanation
Indices: 51345--51538 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
51335 GATTTTCCAT
* *
51345 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
51365 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
51385 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
51405 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
51425 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
51445 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
51465 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
51485 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
51506 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
51526 AATCGCAACGCGA
1 AATCGCAACGCGA
51539 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:51390 original size:40 final size:39
Alignment explanation
Indices: 51341--51538 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
51331 TTGCGATTTT
* ** *
51341 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
51379 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
51420 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
51460 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
51499 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
51539 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:51428 original size:60 final size:60
Alignment explanation
Indices: 51345--51537 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
51335 GATTTTCCAT
* ** * *
51345 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
51405 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
51465 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
51526 AATCGCAACGCG
1 AATCGCAACGCG
51538 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:51958 original size:33 final size:33
Alignment explanation
Indices: 51919--51989 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
51909 TTCACTTAGA
*
51919 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
51952 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
51985 TTTCA
1 TTTCA
51990 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:52129 original size:14 final size:14
Alignment explanation
Indices: 52110--52164 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
52100 AGAATGACTG
52110 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
52124 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
52143 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
52157 TCGCAACG
1 TCGCAACG
52165 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:52147 original size:33 final size:33
Alignment explanation
Indices: 52110--52180 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
52100 AGAATGACTG
**
52110 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
52143 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
52176 TCGCA
1 TCGCA
52181 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:52215 original size:14 final size:14
Alignment explanation
Indices: 52198--52287 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
52188 TTTCATTTTG
52198 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
52212 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
52231 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
52245 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
52262 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
52278 CGTTGCGATT
1 CGTTGCGATT
52288 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:52223 original size:33 final size:33
Alignment explanation
Indices: 52181--52295 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
52171 CAAAATCGCA
*
52181 TTGCGATTTTCATTTTGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
52214 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
52247 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
52280 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
52296 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:52267 original size:19 final size:18
Alignment explanation
Indices: 52176--52288 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 18
52166 GAAACCAAAA
* *
52176 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
*
52195 TTGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
*
52211 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
52228 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
52244 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATC
52261 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
52277 T--CGTTGCGATTT
1 TCGCGTTGCGATTT
52289 TCATTTCAAC
Statistics
Matches: 78, Mismatches: 5, Indels: 26
0.72 0.05 0.24
Matches are distributed among these distances:
14 24 0.31
15 3 0.04
16 12 0.15
17 13 0.17
18 1 0.01
19 25 0.32
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATC
Found at i:54222 original size:185 final size:186
Alignment explanation
Indices: 53992--54556 Score: 1107
Period size: 185 Copynumber: 3.0 Consensus size: 186
53982 TAGATTGCTT
*
53992 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54057 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
54122 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
54177 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54241 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
54306 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
54362 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54427 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
54492 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
54548 AGTAAATTT
1 AGTAAATTT
54557 ATCCATTCAA
Statistics
Matches: 377, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
184 92 0.24
185 153 0.41
186 132 0.35
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:54398 original size:93 final size:93
Alignment explanation
Indices: 53992--54556 Score: 1107
Period size: 93 Copynumber: 6.1 Consensus size: 93
53982 TAGATTGCTT
*
53992 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54057 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54085 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54149 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54177 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54241 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54269 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54334 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54362 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54427 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54455 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54520 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54548 AGTAAATTT
1 AGTAAATTT
54557 ATCCATTCAA
Statistics
Matches: 470, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
92 184 0.39
93 286 0.61
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:54640 original size:19 final size:19
Alignment explanation
Indices: 54600--54728 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
54590 TAGTTTACTT
* *
54600 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
*
54620 TCGTAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
54639 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
54658 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
54672 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
54691 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
54705 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
54724 TCGCA
1 TCGCA
54729 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 12 0.14
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:54679 original size:33 final size:32
Alignment explanation
Indices: 54636--54728 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
54626 CGCGAAACCA
**
54636 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
54668 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
54701 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
54729 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:54726 original size:52 final size:52
Alignment explanation
Indices: 54600--54728 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
54590 TAGTTTACTT
** *
54600 TCGCAACACGAAACTTAAAATCGTAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
54652 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
54705 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
54729 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 41 0.67
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:54746 original size:19 final size:19
Alignment explanation
Indices: 54724--54858 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
54714 GAAACCAAAA
*
54724 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
54743 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
54759 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
54776 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
54792 T--CGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
**
54809 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
54828 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
54848 TCGTGTTGCGA
1 TCGCGTTGCGA
54859 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
14 15 0.16
16 10 0.11
17 11 0.12
19 46 0.49
20 12 0.13
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:54765 original size:14 final size:14
Alignment explanation
Indices: 54746--54802 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
54736 TTTCATTTCG
54746 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
54760 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
54777 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
54793 CGTTGCGATT
1 CGTTGCGATT
54803 TTAATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:54771 original size:33 final size:33
Alignment explanation
Indices: 54729--54821 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
54719 CAAAATCGCA
*
54729 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
54762 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
54795 TTGCGATTTTAATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
54822 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:56799 original size:14 final size:14
Alignment explanation
Indices: 56780--56815 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
56770 ATTGTTTAAT
56780 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
56794 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
56808 TGATTTGT
1 TGATTTGT
56816 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:56938 original size:19 final size:19
Alignment explanation
Indices: 56922--57023 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
56912 AAAAATGACT
56922 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
56941 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
56960 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
56974 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
56993 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
57013 ATCGCAATGCG
1 ATCGCAATGCG
57024 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:57076 original size:19 final size:19
Alignment explanation
Indices: 57052--57358 Score: 376
Period size: 19 Copynumber: 17.4 Consensus size: 19
57042 GATTATCTCG
57052 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
57071 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
57090 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
57104 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
57123 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
57142 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
57161 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
57180 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
57194 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
57213 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
57232 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
57246 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
57265 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
57284 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
57298 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
57318 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
57332 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
57351 TTGCGATT
1 TTGCGATT
57359 GTATTTTCCG
Statistics
Matches: 252, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 35 0.14
16 31 0.12
17 27 0.11
18 3 0.01
19 144 0.57
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:57127 original size:71 final size:71
Alignment explanation
Indices: 57052--57291 Score: 373
Period size: 71 Copynumber: 3.4 Consensus size: 71
57042 GATTATCTCG
57052 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
57117 TTCGCA
66 TTCGCA
*
57123 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
*
57186 TTC-TGTCG--
61 TTCATTTCGCA
*
57194 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
57259 TTCGCA
66 TTCGCA
57265 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
57292 CTCTCGTTGC
Statistics
Matches: 154, Mismatches: 5, Indels: 20
0.86 0.03 0.11
Matches are distributed among these distances:
66 6 0.04
68 7 0.05
69 6 0.04
71 115 0.75
73 6 0.04
74 8 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:57202 original size:142 final size:137
Alignment explanation
Indices: 57014--57358 Score: 516
Period size: 142 Copynumber: 2.5 Consensus size: 137
57004 GAAATGAAAA
*
57014 TCGCAATGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTT-TAATTTCGCATTGCGATT-T-TCGTTGCGATTTTCATTTCGCATTGCGAT
*
57078 TTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
63 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
*
57143 TGCGATTTTCATT
128 TGCGA--TTC-TC
57156 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATT-T-TCGTTGCGATTTTCATTTCGCATTGCGATT
57221 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
64 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
57286 GCGATTCTC
129 GCGATTCTC
* * *
57295 TCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCGTTGCGAT
1 TCGCATTGCGATTTTAATTT-CGCATTGCGATTTTC--GTTGCGATTTTCATTTCGCATTGCGAT
57358 T
63 T
57359 GTATTTTCCG
Statistics
Matches: 191, Mismatches: 8, Indels: 12
0.91 0.04 0.06
Matches are distributed among these distances:
136 2 0.01
137 15 0.08
138 38 0.20
139 4 0.02
140 3 0.02
142 126 0.66
143 3 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (137 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTTTCGTTGCGATTTTCATTTCGCATTGCGATTTT
CATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
GATTCTC
Found at i:57297 original size:52 final size:52
Alignment explanation
Indices: 57052--57330 Score: 388
Period size: 52 Copynumber: 5.2 Consensus size: 52
57042 GATTATCTCG
*
57052 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
*
57104 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
57161 TTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
57213 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
57265 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
57318 TTGCGATTTTCAT
1 TTGCGATTTTCAT
57331 GTTGGGATTT
Statistics
Matches: 217, Mismatches: 4, Indels: 11
0.94 0.02 0.05
Matches are distributed among these distances:
52 161 0.74
53 17 0.08
54 7 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:59523 original size:24 final size:24
Alignment explanation
Indices: 59489--59535 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
59479 CTGAAACATC
59489 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
59513 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
59536 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:60246 original size:20 final size:20
Alignment explanation
Indices: 60218--60586 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
60208 AAATTTCAGT
* * * *
60218 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
60238 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
60258 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
60278 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
60298 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
60318 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
60338 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
60358 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
60378 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
60398 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
60418 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
60438 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
60458 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
60478 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
60498 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
60518 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
60538 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
60558 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
60578 GTTGCGATT
1 GTTGCGATT
60587 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:79158 original size:12 final size:12
Alignment explanation
Indices: 79141--79166 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
79131 TTTTTTTATA
79141 ATGCTTTGATTG
1 ATGCTTTGATTG
79153 ATGCTTTGATTG
1 ATGCTTTGATTG
79165 AT
1 AT
79167 ATTGGCTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.08, G:0.23, T:0.50
Consensus pattern (12 bp):
ATGCTTTGATTG
Done.