Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002263.1 Hibiscus syriacus cultivar Beakdansim tig00004603_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: 89885
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:7053 original size:27 final size:25
Alignment explanation
Indices: 7002--7053 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
6992 AATGATGCTA
* * *
7002 TAAAAGTAGAAGAACAACCATTTCG
1 TAAAAGTAGAAAAACAAACACTTCG
7027 TAAAAGTAGACAAAAACAAACACTTCG
1 TAAAAGTAG--AAAAACAAACACTTCG
7054 AGAATATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 9 0.41
27 13 0.59
ACGTcount: A:0.52, C:0.17, G:0.13, T:0.17
Consensus pattern (25 bp):
TAAAAGTAGAAAAACAAACACTTCG
Found at i:9462 original size:27 final size:26
Alignment explanation
Indices: 9432--9491 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
9422 ATATTATCAC
9432 TTTTAGTTAATTTATTCA-AAAATATAA
1 TTTTA-TT-ATTTATTCACAAAATATAA
*
9459 TTTTATTATTTATTGACAAAATAT-A
1 TTTTATTATTTATTCACAAAATATAA
*
9484 TATTATTA
1 TTTTATTA
9492 AAAATACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 16 0.53
26 9 0.30
27 5 0.17
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (26 bp):
TTTTATTATTTATTCACAAAATATAA
Found at i:20753 original size:25 final size:25
Alignment explanation
Indices: 20725--20777 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
20715 CATGAATGGT
*
20725 CCATCCTGGCAAAGGTGAGCATTAA
1 CCATCCTAGCAAAGGTGAGCATTAA
*
20750 CCATCCTAGCAAAGGTGAGCATTGA
1 CCATCCTAGCAAAGGTGAGCATTAA
20775 CCA
1 CCA
20778 ATCCCAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (25 bp):
CCATCCTAGCAAAGGTGAGCATTAA
Found at i:23425 original size:24 final size:23
Alignment explanation
Indices: 23398--23453 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
23388 GGCTTTATAT
*
23398 TGTATAAACAACATGTTTAAAATG
1 TGTATAAACAACAGGTTTAAAA-G
* * *
23422 TGTAAAAAACAATAGGTTTAATAG
1 TGT-ATAAACAACAGGTTTAAAAG
23446 TGTATAAA
1 TGTATAAA
23454 TATAGTCGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 4 0.15
24 7 0.27
25 15 0.58
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.32
Consensus pattern (23 bp):
TGTATAAACAACAGGTTTAAAAG
Found at i:23467 original size:26 final size:26
Alignment explanation
Indices: 23421--23510 Score: 78
Period size: 26 Copynumber: 3.5 Consensus size: 26
23411 TGTTTAAAAT
* *
23421 GTGTA-AAAAACAATAG-GTTTAATA
1 GTGTATAAAAACAGTAGAATTTAATA
* * *
23445 GTGTATAAATATAGTCGAATTTAA-A
1 GTGTATAAAAACAGTAGAATTTAATA
*
23470 TGTGTATAAAAACATTAGAATTTAATA
1 -GTGTATAAAAACAGTAGAATTTAATA
*
23497 GTGCATAAACAACA
1 GTGTATAAA-AACA
23511 CATTTTAAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
24 5 0.10
25 8 0.16
26 33 0.65
27 5 0.10
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (26 bp):
GTGTATAAAAACAGTAGAATTTAATA
Found at i:23519 original size:50 final size:49
Alignment explanation
Indices: 23401--23529 Score: 125
Period size: 50 Copynumber: 2.6 Consensus size: 49
23391 TTTATATTGT
** * * *
23401 ATAAACAACATGTTTAAAATGTGTA-AAAAACAATAGGTTTAATAGTGT
1 ATAAACAACACATTTTAAATGTGTATAAAAACAATAGATTTAATAGTGC
* ** * *
23449 ATAAATATAGTCGAATTTAAATGTGTATAAAAACATTAGAATTTAATAGTGC
1 ATAAACA-ACAC-ATTTTAAATGTGTATAAAAACAATAG-ATTTAATAGTGC
*
23501 ATAAACAACACATTTTAAATTTGTATAAA
1 ATAAACAACACATTTTAAATGTGTATAAA
23530 CATCATGATT
Statistics
Matches: 62, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
48 6 0.10
49 1 0.02
50 27 0.44
51 12 0.19
52 16 0.26
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (49 bp):
ATAAACAACACATTTTAAATGTGTATAAAAACAATAGATTTAATAGTGC
Found at i:26625 original size:83 final size:82
Alignment explanation
Indices: 26524--26715 Score: 242
Period size: 83 Copynumber: 2.3 Consensus size: 82
26514 TTATAGCTTT
* * *
26524 GTTTTCTAAAAAAAGCCACTAAAGTACAAGTTTGT-AGCAGCGTTTGTTTAAAAACGCCACTATA
1 GTTTTCTAAAAAAAGCCACTAAAGTACAAGTCTGTAAG-AGCGTTTGTTCAAAAACACCACTATA
*
26588 TATGAAACTTATTGCGGA
65 TATGAAACCTATTGCGGA
* * * *
26606 GTTTTCTAAAAAAACGCCACTAAGGTACAAGTCTGTAAGGGCGTTTGTTCAAAAATATCACTATA
1 GTTTTCTAAAAAAA-GCCACTAAAGTACAAGTCTGTAAGAGCGTTTGTTCAAAAACACCACTATA
* *
26671 TATGAAACCTATTGTGGC
65 TATGAAACCTATTGCGGA
* *
26689 GTTTATGTAAAAAATGCCACTAAAGTA
1 GTTT-TCTAAAAAAAGCCACTAAAGTA
26716 TCAATTTTTT
Statistics
Matches: 94, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
82 14 0.15
83 70 0.74
84 10 0.11
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (82 bp):
GTTTTCTAAAAAAAGCCACTAAAGTACAAGTCTGTAAGAGCGTTTGTTCAAAAACACCACTATAT
ATGAAACCTATTGCGGA
Found at i:26690 original size:41 final size:41
Alignment explanation
Indices: 26645--26825 Score: 127
Period size: 41 Copynumber: 4.4 Consensus size: 41
26635 AGTCTGTAAG
*
26645 GGCGTTTGT-TCAAAAATATCACTATATATGAAACCTATTGT
1 GGCGTTTGTCT-AAAAATGTCACTATATATGAAACCTATTGT
* * * * * ** *
26686 GGCGTTTATGTAAAAAATGCCACTAAAGTAT-CAATTTTTTGT
1 GGCGTTTGTCT-AAAAATGTCACTATA-TATGAAACCTATTGT
* * * *
26728 GGCGGTTGTCTAAAAATGTCACAATATATGTACCCTATTGT
1 GGCGTTTGTCTAAAAATGTCACTATATATGAAACCTATTGT
* ** *
26769 GGCGTTTGTCTAAAAATG-CGACGATATAT-ATTCCCTATTGC
1 GGCGTTTGTCTAAAAATGTC-ACTATATATGA-AACCTATTGT
*
26810 GGCGTTTGTTTAAAAA
1 GGCGTTTGTCTAAAAA
26826 CACCACTAAA
Statistics
Matches: 109, Mismatches: 26, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
40 4 0.04
41 74 0.68
42 28 0.26
43 3 0.03
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (41 bp):
GGCGTTTGTCTAAAAATGTCACTATATATGAAACCTATTGT
Found at i:27058 original size:28 final size:27
Alignment explanation
Indices: 27008--27076 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 27
26998 ATATATGTTT
27008 TGTATAAAACAATATATTATTTAATAG
1 TGTATAAAACAATATATTATTTAATAG
* *
27035 TGTATAAAGACTATATAGTT-TTTAGTAG
1 TGTATAAA-ACAATATA-TTATTTAATAG
27063 TGTAT-AAACAATAT
1 TGTATAAAACAATAT
27077 GTTTTAGGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.16
27 10 0.27
28 19 0.51
29 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (27 bp):
TGTATAAAACAATATATTATTTAATAG
Found at i:27116 original size:21 final size:21
Alignment explanation
Indices: 27092--27138 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
27082 AGGATTTAGT
*
27092 TGTATAAAACAT-GTTTAAATG
1 TGTATAAAA-ATAATTTAAATG
27113 TGTATAAAAATAAATTTAAATG
1 TGTATAAAAAT-AATTTAAATG
27135 TGTA
1 TGTA
27139 GAAATAGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 2 0.09
21 9 0.39
22 12 0.52
ACGTcount: A:0.47, C:0.02, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTATAAAAATAATTTAAATG
Found at i:27540 original size:38 final size:38
Alignment explanation
Indices: 27498--27581 Score: 168
Period size: 38 Copynumber: 2.2 Consensus size: 38
27488 TTTTATAAAG
27498 AATCTCATACTTAGGTTATCTTCTGTCCAAACAGTAAC
1 AATCTCATACTTAGGTTATCTTCTGTCCAAACAGTAAC
27536 AATCTCATACTTAGGTTATCTTCTGTCCAAACAGTAAC
1 AATCTCATACTTAGGTTATCTTCTGTCCAAACAGTAAC
27574 AATCTCAT
1 AATCTCAT
27582 CTAATTGTCG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.35
Consensus pattern (38 bp):
AATCTCATACTTAGGTTATCTTCTGTCCAAACAGTAAC
Found at i:35028 original size:17 final size:19
Alignment explanation
Indices: 35006--35040 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
34996 TTAGACACCT
35006 ATTTTT-TA-ATAAAAAAA
1 ATTTTTATACATAAAAAAA
35023 ATTTTTATACATAAAAAA
1 ATTTTTATACATAAAAAA
35041 GTTAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTTTTATACATAAAAAAA
Found at i:36644 original size:16 final size:16
Alignment explanation
Indices: 36614--36644 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36604 TAATATTGAA
*
36614 ACTTGAACTCAAAAAG
1 ACTTGAACTAAAAAAG
36630 ACTTGAACTAAAAAA
1 ACTTGAACTAAAAAA
36645 AAATTTAGAA
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:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTAAAAAAG
Found at i:50676 original size:32 final size:32
Alignment explanation
Indices: 50630--50692 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
50620 GAAAATTTAA
*
50630 TTCAAGTCGGGTCAAAATCAGATCGGTTGGTT
1 TTCAAGTCGAGTCAAAATCAGATCGGTTGGTT
* *
50662 TTCAAGTCGAGTCAAAATCGGATCTGTTGGT
1 TTCAAGTCGAGTCAAAATCAGATCGGTTGGT
50693 GTCGAAGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (32 bp):
TTCAAGTCGAGTCAAAATCAGATCGGTTGGTT
Found at i:51219 original size:38 final size:38
Alignment explanation
Indices: 51177--51250 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 38
51167 TAACGAAATT
*
51177 GAAA-TCAACCAGAACAAAAATTAACTCAAACCGAAACC
1 GAAATTCAACC-GAACAAAAATTAACCCAAACCGAAACC
* ** *
51215 GAAATTTAACCGAACTGAAATTAACCCGAACCGAAA
1 GAAATTCAACCGAACAAAAATTAACCCAAACCGAAA
51251 GCAACCCGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 25 0.83
39 5 0.17
ACGTcount: A:0.51, C:0.24, G:0.11, T:0.14
Consensus pattern (38 bp):
GAAATTCAACCGAACAAAAATTAACCCAAACCGAAACC
Found at i:51247 original size:32 final size:33
Alignment explanation
Indices: 51211--51341 Score: 128
Period size: 32 Copynumber: 4.1 Consensus size: 33
51201 CTCAAACCGA
51211 AACCGAAATTTAA-CCGAACTGAAATTAACCCG
1 AACCGAAATTTAACCCGAACTGAAATTAACCCG
**
51243 AACCGAAA-GCAACCCGAACTGAAATTAA-CCG
1 AACCGAAATTTAACCCGAACTGAAATTAACCCG
** **
51274 AACC-AAATTTTAACCCGATTTGAAAGCAACCCG
1 AACCGAAA-TTTAACCCGAACTGAAATTAACCCG
* * * *
51307 AACCG-AATTTAACCCGACCCGAAAGTAACCTG
1 AACCGAAATTTAACCCGAACTGAAATTAACCCG
51339 AAC
1 AAC
51342 AGATTGAAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
30 3 0.04
31 9 0.11
32 60 0.74
33 9 0.11
ACGTcount: A:0.42, C:0.28, G:0.14, T:0.16
Consensus pattern (33 bp):
AACCGAAATTTAACCCGAACTGAAATTAACCCG
Found at i:51320 original size:16 final size:16
Alignment explanation
Indices: 51211--51341 Score: 97
Period size: 16 Copynumber: 8.2 Consensus size: 16
51201 CTCAAACCGA
51211 AACCGAAATTTAA-CCG
1 AACCGAAA-TTAACCCG
*
51227 AACTGAAATTAACCCG
1 AACCGAAATTAACCCG
**
51243 AACCGAAAGCAACCCG
1 AACCGAAATTAACCCG
*
51259 AACTGAAATTAA-CCG
1 AACCGAAATTAACCCG
51274 AACC-AAATTTTAACCCG
1 AACCGAAA--TTAACCCG
*** **
51291 ATTTGAAAGCAACCCG
1 AACCGAAATTAACCCG
*
51307 AACCGAATTTAACCCG
1 AACCGAAATTAACCCG
* * *
51323 ACCCGAAAGTAACCTG
1 AACCGAAATTAACCCG
51339 AAC
1 AAC
51342 AGATTGAAAT
Statistics
Matches: 86, Mismatches: 24, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
14 3 0.03
15 10 0.12
16 66 0.77
17 4 0.05
18 3 0.03
ACGTcount: A:0.42, C:0.28, G:0.14, T:0.16
Consensus pattern (16 bp):
AACCGAAATTAACCCG
Found at i:51336 original size:48 final size:47
Alignment explanation
Indices: 51211--51341 Score: 138
Period size: 48 Copynumber: 2.7 Consensus size: 47
51201 CTCAAACCGA
*
51211 AACCGAAATTTAACCGAACTGAAATTAACCCGAACCGAAAGCAACCCG
1 AACCG-AATTTAACCGAACCGAAATTAACCCGAACCGAAAGCAACCCG
* * ***
51259 AACTGAAATTAACCGAACC-AAATTTTAACCCGATTTGAAAGCAACCCG
1 AACCGAATTTAACCGAACCGAAA--TTAACCCGAACCGAAAGCAACCCG
* * *
51307 AACCGAATTTAACCCGACCCGAAAGTAACCTGAAC
1 AACCGAATTTAA-CCGAACCGAAATTAACCCGAAC
51342 AGATTGAAAT
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
46 3 0.05
47 12 0.18
48 42 0.64
49 6 0.09
50 3 0.05
ACGTcount: A:0.42, C:0.28, G:0.14, T:0.16
Consensus pattern (47 bp):
AACCGAATTTAACCGAACCGAAATTAACCCGAACCGAAAGCAACCCG
Found at i:52106 original size:33 final size:31
Alignment explanation
Indices: 52018--52115 Score: 108
Period size: 32 Copynumber: 3.0 Consensus size: 31
52008 TTGGCCTAAA
52018 CCAAAAATCAACCGATCTGATATTAACCCGAC
1 CCAAAAATCAACCGATCTG-TATTAACCCGAC
* *
52050 CC-GAAATCTAACCGATCTGGTATTAACTCGAC
1 CCAAAAATC-AACCGATCT-GTATTAACCCGAC
* *
52082 CCAAAAAATCAATCGATCCTGTATTGACCCGAC
1 CC-AAAAATCAACCGAT-CTGTATTAACCCGAC
52115 C
1 C
52116 TGATATTGAC
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
31 5 0.09
32 24 0.44
33 19 0.35
34 7 0.13
ACGTcount: A:0.36, C:0.31, G:0.12, T:0.21
Consensus pattern (31 bp):
CCAAAAATCAACCGATCTGTATTAACCCGAC
Found at i:52124 original size:16 final size:15
Alignment explanation
Indices: 52099--52129 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
52089 ATCAATCGAT
52099 CCTGTATTGACCCGA
1 CCTGTATTGACCCGA
52114 CCTGATATTGACCCGA
1 CCTG-TATTGACCCGA
52130 TCCAATCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (15 bp):
CCTGTATTGACCCGA
Found at i:52289 original size:15 final size:15
Alignment explanation
Indices: 52269--52300 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
52259 TTAATCTAGA
52269 CCGAAATGACCCGAC
1 CCGAAATGACCCGAC
*
52284 CCGAAATGACTCGAC
1 CCGAAATGACCCGAC
52299 CC
1 CC
52301 AAACTCGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.41, G:0.19, T:0.09
Consensus pattern (15 bp):
CCGAAATGACCCGAC
Found at i:53145 original size:16 final size:16
Alignment explanation
Indices: 53078--53162 Score: 57
Period size: 16 Copynumber: 5.3 Consensus size: 16
53068 GGTAACTTTT
*
53078 GGTTCGGGTTG-CTTTC
1 GGTTCGTGTTGAC-TTC
* *
53094 GATTCGGGTTGACTTC
1 GGTTCGTGTTGACTTC
** *
53110 GACTC-TAGTTGACTTT
1 GGTTCGT-GTTGACTTC
53126 GGTTCGTGTTGACTTC
1 GGTTCGTGTTGACTTC
** *
53142 GGTTATTGTTGATTTC
1 GGTTCGTGTTGACTTC
53158 GGTTC
1 GGTTC
53163 AGGTTGATTA
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
16 53 0.96
17 2 0.04
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.45
Consensus pattern (16 bp):
GGTTCGTGTTGACTTC
Found at i:53169 original size:32 final size:31
Alignment explanation
Indices: 53085--53169 Score: 73
Period size: 32 Copynumber: 2.6 Consensus size: 31
53075 TTTGGTTCGG
* * *
53085 GTTGCTTTCGATTCGGGTTGACTTCGACTCTA
1 GTTGATTTCGGTTC-GGTTGACTTCGACTATA
** *
53117 GTTGACTTT-GGTTCGTGTTGACTTCGGTTATT
1 GTTGA-TTTCGGTTCG-GTTGACTTCGACTATA
53149 GTTGATTTCGGTTCAGGTTGA
1 GTTGATTTCGGTTC-GGTTGA
53170 TTATGGTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
31 4 0.09
32 35 0.81
33 4 0.09
ACGTcount: A:0.12, C:0.15, G:0.28, T:0.45
Consensus pattern (31 bp):
GTTGATTTCGGTTCGGTTGACTTCGACTATA
Found at i:55609 original size:29 final size:29
Alignment explanation
Indices: 55577--55632 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
55567 ATTCTTAACA
*
55577 TTATCATATATTATTATCATTAATTCTTT
1 TTATCATATAATATTATCATTAATTCTTT
* *
55606 TTATTATATAATATTATCCTTAATTCT
1 TTATCATATAATATTATCATTAATTCT
55633 CATACACATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (29 bp):
TTATCATATAATATTATCATTAATTCTTT
Found at i:60367 original size:138 final size:137
Alignment explanation
Indices: 60125--60530 Score: 494
Period size: 138 Copynumber: 2.9 Consensus size: 137
60115 CATTTCTGAG
* * ** * * * *
60125 GAAGAGTTCGTAATAAGAAGAACTTTTCCGACAAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
1 GAAGGGTTCGGAATAAGAAGAACTCGTCCAACAA-GGAGAAGAACTTCGTAATGAGAAGAGCTTG
* *
60190 TTCAACCTGGAATCGACCATCGCACAAGGAGATGGATAAATGAAGAGTTCATAATGAGAAGAACT
65 TTCAACCTGGAATCGTCCATCGCACAAGGAGGTGGATAAATGAAGAGTTCATAATGAGAAGAACT
* *
60255 CAT-CTGAC
130 C-TCCCGAA
* *
60263 GAAGGGTTGGGAATGAGAAGAACTCGTCCAACAAGGAAGAAGAACTTCGTAATGAGAAGAGCTTG
1 GAAGGGTTCGGAATAAGAAGAACTCGTCCAACAAGG-AGAAGAACTTCGTAATGAGAAGAGCTTG
* * *
60328 TTCAACCTGGAATCGTCTATCGCACAAGGAGGTGGATAAATGAGGATTTCATAATGAGAAGAACT
65 TTCAACCTGGAATCGTCCATCGCACAAGGAGGTGGATAAATGAAGAGTTCATAATGAGAAGAACT
60393 CTCCCGAA
130 CTCCCGAA
* * * * * *
60401 GAAGGGTTCGTAATAAGAAAAACTCGTCCAACGATGGAGAAGAAGC-TCGTAATTAGAGGAGTTT
1 GAAGGGTTCGGAATAAGAAGAACTCGTCCAAC-AAGGAGAAGAA-CTTCGTAATGAGAAGAGCTT
* * * * *
60465 GTTTAACCTGGGATTGTCCATCACACAAAGAGGTGGAT-AATGAAGAGTTCATAATGAGAAGAAC
64 GTTCAACCTGGAATCGTCCATCGCACAAGGAGGTGGATAAATGAAGAGTTCATAATGAGAAGAAC
60529 TC
129 TC
60531 CCATAGAATA
Statistics
Matches: 231, Mismatches: 33, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
137 29 0.13
138 198 0.86
139 4 0.02
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (137 bp):
GAAGGGTTCGGAATAAGAAGAACTCGTCCAACAAGGAGAAGAACTTCGTAATGAGAAGAGCTTGT
TCAACCTGGAATCGTCCATCGCACAAGGAGGTGGATAAATGAAGAGTTCATAATGAGAAGAACTC
TCCCGAA
Found at i:62535 original size:16 final size:16
Alignment explanation
Indices: 62514--62561 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
62504 TATTTCTTTT
62514 TATTTAATTATTTTCC
1 TATTTAATTATTTTCC
*
62530 TATTTAATT-TTTGCC
1 TATTTAATTATTTTCC
*
62545 CA-TTAGATTATTTTCC
1 TATTTA-ATTATTTTCC
62561 T
1 T
62562 TTTTTTTCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 3 0.12
15 9 0.35
16 14 0.54
ACGTcount: A:0.23, C:0.15, G:0.04, T:0.58
Consensus pattern (16 bp):
TATTTAATTATTTTCC
Found at i:63434 original size:2 final size:2
Alignment explanation
Indices: 63427--63518 Score: 184
Period size: 2 Copynumber: 46.0 Consensus size: 2
63417 TTCAGTCTTT
63427 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63469 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63511 TA TA TA TA
1 TA TA TA TA
63519 AGTTATTGGT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 90 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64423 original size:29 final size:28
Alignment explanation
Indices: 64331--64427 Score: 65
Period size: 29 Copynumber: 3.3 Consensus size: 28
64321 TTTTAAATTA
64331 ATCCTCAAACTTTTAAACATTTCAATTTC
1 ATCCTCAAA-TTTTAAACATTTCAATTTC
*** * *
64360 AT-CTCCAAATTATGATTCTCATTGT-AAATTA
1 ATCCT-CAAATT-T--TAAACATT-TCAATTTC
64391 ATCCTCAAAGTTTTAAACATTTCAATTTC
1 ATCCTCAAA-TTTTAAACATTTCAATTTC
64420 ATCC-CAAA
1 ATCCTCAAA
64428 CACGCCCTCA
Statistics
Matches: 50, Mismatches: 10, Indels: 17
0.65 0.13 0.22
Matches are distributed among these distances:
28 9 0.18
29 20 0.40
31 16 0.32
32 5 0.10
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (28 bp):
ATCCTCAAATTTTAAACATTTCAATTTC
Found at i:67614 original size:15 final size:15
Alignment explanation
Indices: 67596--67625 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
67586 AGTTTAGTCC
*
67596 TTTATAATTTAAATT
1 TTTATAAATTAAATT
67611 TTTATAAATTAAATT
1 TTTATAAATTAAATT
67626 AATAATGCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTATAAATTAAATT
Found at i:69337 original size:21 final size:21
Alignment explanation
Indices: 69311--69350 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
69301 TGAAAGATGA
*
69311 CTTTTAGTGTTGGATATTTTG
1 CTTTTAATGTTGGATATTTTG
69332 CTTTTAATGTTGGATATTT
1 CTTTTAATGTTGGATATTT
69351 ATTTTTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.20, T:0.57
Consensus pattern (21 bp):
CTTTTAATGTTGGATATTTTG
Found at i:75527 original size:19 final size:20
Alignment explanation
Indices: 75503--75574 Score: 83
Period size: 19 Copynumber: 3.5 Consensus size: 20
75493 ATGCAAAAAT
*
75503 GGTATCGATACCATAATA-G
1 GGTATCGATACCATAGTAGG
*
75522 GGTATCGCTACCATAGTATGG
1 GGTATCGATACCATAGTA-GG
* *
75543 TAGTATCGATACCATGGTAGG
1 -GGTATCGATACCATAGTAGG
75564 GGTATCGATAC
1 GGTATCGATAC
75575 TGAGGAGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.36
20 10 0.23
21 3 0.07
22 15 0.34
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (20 bp):
GGTATCGATACCATAGTAGG
Found at i:75555 original size:22 final size:19
Alignment explanation
Indices: 75503--75574 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 19
75493 ATGCAAAAAT
*
75503 GGTATCGATACCATAATAG
1 GGTATCGATACCATAGTAG
*
75522 GGTATCGCTACCATAGTATG
1 GGTATCGATACCATAGTA-G
*
75542 GTAGTATCGATACCATGGTAGG
1 G--GTATCGATACCATAGTA-G
75564 GGTATCGATAC
1 GGTATCGATAC
75575 TGAGGAGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.36
20 12 0.27
22 17 0.38
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:75983 original size:55 final size:53
Alignment explanation
Indices: 75922--76067 Score: 159
Period size: 55 Copynumber: 2.7 Consensus size: 53
75912 GCAAAAAATT
* * *
75922 AAGAAATCTATACTATGTGTATGAATTTATGTATGGGCACTTTGTATGCAAAACA
1 AAGAAATCTATACTAAGTGTATGAATTT-TGTATGGGCACTATATATGC-AAACA
* * *
75977 AAGAAAT-TCATACTAAGTGTATGAATTTTCGTATGGGCACTATATGTGCGAACT
1 AAGAAATCT-ATACTAAGTGTATGAATTTT-GTATGGGCACTATATATGCAAACA
* * *
76031 AACAAATCCATATTAAGTGTATGAATTTCTGTATGGG
1 AAGAAATCTATACTAAGTGTATGAATTT-TGTATGGG
76068 AAATATATGT
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
54 36 0.46
55 42 0.54
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (53 bp):
AAGAAATCTATACTAAGTGTATGAATTTTGTATGGGCACTATATATGCAAACA
Found at i:76065 original size:54 final size:54
Alignment explanation
Indices: 75925--76078 Score: 166
Period size: 54 Copynumber: 2.8 Consensus size: 54
75915 AAAAATTAAG
* * * * * *
75925 AAATCTATACTATGTGTATGAATTTATGTATGGGCACTTTGTATGCAAAACAAAG
1 AAATCCATACTAAGTGTATGAATTT-TGTATGGGCACTATATGTGCAAAACAAAC
* * *
75980 AAATTCATACTAAGTGTATGAATTTTCGTATGGGCACTATATGTGC-GAACTAAC
1 AAATCCATACTAAGTGTATGAATTTT-GTATGGGCACTATATGTGCAAAACAAAC
* * *
76034 AAATCCATATTAAGTGTATGAATTTCTGTATGGGAAATATATGTG
1 AAATCCATACTAAGTGTATGAATTT-TGTATGGGCACTATATGTG
76079 AAATTATCCG
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
54 45 0.54
55 39 0.46
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (54 bp):
AAATCCATACTAAGTGTATGAATTTTGTATGGGCACTATATGTGCAAAACAAAC
Found at i:76565 original size:81 final size:81
Alignment explanation
Indices: 76348--77052 Score: 923
Period size: 81 Copynumber: 8.7 Consensus size: 81
76338 GTGCCTTTGA
* * * *
76348 GGCCTAACTGTGCA-ATGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
76412 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * *
76428 GG-CTGAGCTGTGCA-TTGGCAGAAATGTGTCAATTATGACAGTTAGATGAATGGTTAAAGACTG
1 GGCCT-AGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCG
76491 TTGAGTAAAAGATAAAT
65 TTGAGTAAAAGATAAAT
* * * ** * *
76508 GTCCTAGTTGTGCATTTGGTAGAAATATGTCAATTATGCCAGTTACATGAACAGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
*
76573 TAAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
** * *
76589 GGCCTAGCTGTGCATTTGATAGAAAGATGTCAATTATGCCAGTTAGATGACCGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
*
76654 TGAGTAAAAGATAAAA
66 TGAGTAAAAGATAAAT
* * * * * * *
76670 GGCCTAGTTATGCAATTGGTAGAAAGGTGTCAATTATGCTAGTTAGATAAATGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
76735 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * *
76751 GGCCTAGTTGTTCA-TTGGCAGAAATGTGTCAATTATGCTAGTTAGATGAACGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
76815 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * * *
76831 GGCCTAGCTATGCATTTGGCAAAAAGGTATCAATTATACCAGTTAGATGAACAGTTAAAGATCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
76896 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * *
76912 GGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGACAGTTAGATGAATGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
* *
76977 TCAATAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * * *
76993 GGCCTAACTGTGCATTTTGGAAGAAAAGTGTCAATCATGCAAGTTAGATGAAAGGTTAAA
1 GGCCTAGCTGTGCA-TTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAA
77053 TACATTTGGG
Statistics
Matches: 548, Mismatches: 72, Indels: 8
0.87 0.11 0.01
Matches are distributed among these distances:
79 2 0.00
80 151 0.28
81 357 0.65
82 38 0.07
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (81 bp):
GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
TGAGTAAAAGATAAAT
Found at i:76809 original size:242 final size:243
Alignment explanation
Indices: 76348--77052 Score: 1015
Period size: 242 Copynumber: 2.9 Consensus size: 243
76338 GTGCCTTTGA
* * *
76348 GGCCTAACTGTGCA-ATGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1 GGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
*
76412 TGAGTAAAAGATAAATGG-CTGAGCTGTGC-ATTGGCAGAAATGTGTCAATTATGACAGTTAGAT
66 TGAGTAAAAGATAAATGGCCT-AGCTGTGCAATTGGCAGAAAGGTGTCAATTATGACAGTTAGAT
* * * *
76475 GAATGGTTAAAGACTGTTGAGTAAAAGATAAATGTCCTAGTTGTGCATTTGGTAGAAATATGTCA
130 GAATGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGTTGTGCATTTGGAAGAAATGTGTCA
* * *
76540 ATTATGCCAGTTACATGAACAGTTAAAGACCGTTAAGTAAAAGATAAAT
195 ATTATGCAAGTTAGATGAACGGTTAAAGACCGTTAAGTAAAAGATAAAT
* * *
76589 GGCCTAGCTGTGCATTTGATAGAAAGATGTCAATTATGCCAGTTAGATGACCGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
* * * *
76654 TGAGTAAAAGATAAAAGGCCTAGTTATGCAATTGGTAGAAAGGTGTCAATTATG-CTAGTTAGAT
66 TGAGTAAAAGATAAATGGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGAC-AGTTAGAT
* * *
76718 AAATGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGTTGTTCA-TTGGCAGAAATGTGTCA
130 GAATGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGTTGTGCATTTGGAAGAAATGTGTCA
* *
76782 ATTATGCTAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAAT
195 ATTATGCAAGTTAGATGAACGGTTAAAGACCGTTAAGTAAAAGATAAAT
* * * * * * *
76831 GGCCTAGCTATGCATTTGGCAAAAAGGTATCAATTATACCAGTTAGATGAACAGTTAAAGATCGT
1 GGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
76896 TGAGTAAAAGATAAATGGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGACAGTTAGATG
66 TGAGTAAAAGATAAATGGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGACAGTTAGATG
* * ** *
76961 AATGGTTAAAGACCGTTCAATAAAAGATAAATGGCCTAACTGTGCATTTTGGAAGAAAAGTGTCA
131 AATGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGTTGTGCA-TTTGGAAGAAATGTGTCA
* *
77026 ATCATGCAAGTTAGATGAAAGGTTAAA
195 ATTATGCAAGTTAGATGAACGGTTAAA
77053 TACATTTGGG
Statistics
Matches: 411, Mismatches: 46, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
241 13 0.03
242 283 0.69
243 76 0.18
244 39 0.09
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (243 bp):
GGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
TGAGTAAAAGATAAATGGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGACAGTTAGATG
AATGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGTTGTGCATTTGGAAGAAATGTGTCAA
TTATGCAAGTTAGATGAACGGTTAAAGACCGTTAAGTAAAAGATAAAT
Found at i:76957 original size:323 final size:322
Alignment explanation
Indices: 76347--77052 Score: 995
Period size: 323 Copynumber: 2.2 Consensus size: 322
76337 AGTGCCTTTG
* * * *
76347 AGGCCTAACTGTGCAA-TGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCG
1 AGGCCTAACTATGCAATTGGTAGAAAGGTGTCAATTATGCAAGTTAGAT-AAAGGTTAAAGACCG
76411 TTGAGTAAAAGATAAATGGCTGAGCTGTGCATTGGCAGAAATGTGTCAATTATGACAGTTAGATG
65 TTGAGTAAAAGATAAATGGCTGAGCTGTGCATTGGCAGAAATGTGTCAATTATGACAGTTAGATG
* * * * * * * * *
76476 AATGGTTAAAGACTGTTGAGTAAAAGATAAATGTCCTAGTTGTGCATTTGGTAGAAATATGTCAA
130 AACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTATGCATTTGGCAAAAAGATATCAA
* *
76541 TTATGCCAGTTACATGAACAGTTAAAGACCGTTAAGTAAAAGATAAATGGCCTAGCTGTGCATTT
195 TTATACCAGTTACATGAACAGTTAAAGACCGTTAAGTAAAAGATAAATGGCCTAGCTGTGCAATT
* * * * *
76606 GATAGAAAGATGTCAATTATGCCAGTTAGATGACCGGTTAAAGACCGTTGAGTAAAAGATAAA
260 GACAGAAAGATGTCAATTATGACAGTTAGATGAACGGTTAAAGACCGTTCAATAAAAGATAAA
** *
76669 AGGCCTAGTTATGCAATTGGTAGAAAGGTGTCAATTATGCTAGTTAGATAAATGGTTAAAGACCG
1 AGGCCTAACTATGCAATTGGTAGAAAGGTGTCAATTATGCAAGTTAGATAAA-GGTTAAAGACCG
* *
76734 TTGAGTAAAAGATAAATGGCCT-AGTTGTTCATTGGCAGAAATGTGTCAATTATG-CTAGTTAGA
65 TTGAGTAAAAGATAAATGG-CTGAGCTGTGCATTGGCAGAAATGTGTCAATTATGAC-AGTTAGA
*
76797 TGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTATGCATTTGGCAAAAAGGTATC
128 TGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTATGCATTTGGCAAAAAGATATC
* * *
76862 AATTATACCAGTTAGATGAACAGTTAAAGATCGTTGAGTAAAAGATAAATGGCCTAGCTGTGCAA
193 AATTATACCAGTTACATGAACAGTTAAAGACCGTTAAGTAAAAGATAAATGGCCTAGCTGTGCAA
* * *
76927 TTGGCAGAAAGGTGTCAATTATGACAGTTAGATGAATGGTTAAAGACCGTTCAATAAAAGATAAA
258 TTGACAGAAAGATGTCAATTATGACAGTTAGATGAACGGTTAAAGACCGTTCAATAAAAGATAAA
* * * * * *
76992 TGGCCTAACTGTGCATTTTGGAAGAAAAGTGTCAATCATGCAAGTTAGATGAAAGGTTAAA
1 AGGCCTAACTATGCA-ATTGGTAGAAAGGTGTCAATTATGCAAGTTAGAT-AAAGGTTAAA
77053 TACATTTGGG
Statistics
Matches: 338, Mismatches: 40, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
322 16 0.05
323 281 0.83
324 38 0.11
325 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (322 bp):
AGGCCTAACTATGCAATTGGTAGAAAGGTGTCAATTATGCAAGTTAGATAAAGGTTAAAGACCGT
TGAGTAAAAGATAAATGGCTGAGCTGTGCATTGGCAGAAATGTGTCAATTATGACAGTTAGATGA
ACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTATGCATTTGGCAAAAAGATATCAAT
TATACCAGTTACATGAACAGTTAAAGACCGTTAAGTAAAAGATAAATGGCCTAGCTGTGCAATTG
ACAGAAAGATGTCAATTATGACAGTTAGATGAACGGTTAAAGACCGTTCAATAAAAGATAAA
Found at i:77246 original size:45 final size:45
Alignment explanation
Indices: 77191--77280 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
77181 AAGGCAAAAC
77191 ATATAATAGTGTATAAAAGGCATGAAAGAATGCCATAAATGAAAT
1 ATATAATAGTGTATAAAAGGCATGAAAGAATGCCATAAATGAAAT
* *
77236 ATATAATAGTGTATAAAAGGCATTAAAGAATGCCATCAATGAAAT
1 ATATAATAGTGTATAAAAGGCATGAAAGAATGCCATAAATGAAAT
77281 GCATATGGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.26
Consensus pattern (45 bp):
ATATAATAGTGTATAAAAGGCATGAAAGAATGCCATAAATGAAAT
Found at i:82981 original size:21 final size:21
Alignment explanation
Indices: 82957--83012 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
82947 CAGGGACTCC
*
82957 GGTCTCGATACTGAGACTGGT
1 GGTCTCGATACTGAGACTAGT
*
82978 GGTCTCAATACTGAGACTAGT
1 GGTCTCGATACTGAGACTAGT
*
82999 GGTCTCGAGACTGA
1 GGTCTCGATACTGA
83013 CGGCCCGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (21 bp):
GGTCTCGATACTGAGACTAGT
Found at i:84923 original size:156 final size:156
Alignment explanation
Indices: 84711--85022 Score: 615
Period size: 156 Copynumber: 2.0 Consensus size: 156
84701 TTGGAATATA
*
84711 TCTTCTCAAAGTTCTTCAAGTCATTGATGATCGTGATAAATCGACGGACATTGTCTTGATGTCTT
1 TCTTCTCAAAGTTCTTCAAGTCATTGATGATCATGATAAATCGACGGACATTGTCTTGATGTCTT
84776 CATCGGGCTTCATCTTGAAGTTCTTATAGTTGAGAGTGAGAATGAAAATCTTTGACTTCTTCACT
66 CATCGGGCTTCATCTTGAAGTTCTTATAGTTGAGAGTGAGAATGAAAATCTTTGACTTCTTCACT
84841 TGGCTTGTTCCTTCGTGGGTCATCTC
131 TGGCTTGTTCCTTCGTGGGTCATCTC
84867 TCTTCTCAAAGTTCTTCAAGTCATTGATGATCATGATAAATCGACGGACATTGTCTTGATGTCTT
1 TCTTCTCAAAGTTCTTCAAGTCATTGATGATCATGATAAATCGACGGACATTGTCTTGATGTCTT
84932 CATCGGGCTTCATCTTGAAGTTCTTATAGTTGAGAGTGAGAATGAAAATCTTTGACTTCTTCACT
66 CATCGGGCTTCATCTTGAAGTTCTTATAGTTGAGAGTGAGAATGAAAATCTTTGACTTCTTCACT
84997 TGGCTTGTTCCTTCGTGGGTCATCTC
131 TGGCTTGTTCCTTCGTGGGTCATCTC
85023 CAATTTGTCC
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 155 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (156 bp):
TCTTCTCAAAGTTCTTCAAGTCATTGATGATCATGATAAATCGACGGACATTGTCTTGATGTCTT
CATCGGGCTTCATCTTGAAGTTCTTATAGTTGAGAGTGAGAATGAAAATCTTTGACTTCTTCACT
TGGCTTGTTCCTTCGTGGGTCATCTC
Done.