Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003611.1 Hibiscus syriacus cultivar Beakdansim tig00007640_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: 155722
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:695 original size:60 final size:60
Alignment explanation
Indices: 624--773 Score: 162
Period size: 60 Copynumber: 2.5 Consensus size: 60
614 TATATTATAT
* * * *
624 ATCCCTAAACTATGACTCTCATTTTAAATTAAT-TCTTAAAC-TTTTAA-ATATTCTAATTTC
1 ATCCCTAAACTATGAATCTCATTCTAAATTAGTCT-TTAAACATTTTAACA-ATT-GAATTTC
** * * * *
684 ATCTTTAAACTATGATTGTAATTCTAAATTAGTCTTTAAACATTTTAACAATTGAATTTT
1 ATCCCTAAACTATGAATCTCATTCTAAATTAGTCTTTAAACATTTTAACAATTGAATTTC
744 ATCCCTAAACTATGAATCTCATTCTAAATT
1 ATCCCTAAACTATGAATCTCATTCTAAATT
774 GGCCCTTTAA
Statistics
Matches: 73, Mismatches: 14, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
60 62 0.85
61 10 0.14
62 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (60 bp):
ATCCCTAAACTATGAATCTCATTCTAAATTAGTCTTTAAACATTTTAACAATTGAATTTC
Found at i:1423 original size:21 final size:21
Alignment explanation
Indices: 1398--1442 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
1388 TCAAAAATAT
1398 TAAAAA-AATTAATATTTTAAA
1 TAAAAATAA-TAATATTTTAAA
1419 TAAAAATAATAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
1440 TAA
1 TAA
1443 TTTTTTATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAA
Found at i:3522 original size:28 final size:29
Alignment explanation
Indices: 3490--3574 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 29
3480 ATAGTTTAAG
*
3490 TACCTATTTTGAC-ATAAAATACTTTA-A
1 TACCTATTTTGACAAAAAAATACTTTAGA
* *
3517 TCACCTATTTTGACAAAAAAAAACTTTAGG
1 T-ACCTATTTTGACAAAAAAATACTTTAGA
* *
3547 TACTTATTTTGACTAAAAAATACTTTAG
1 TACCTATTTTGACAAAAAAATACTTTAG
3575 TTAAATAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.02
28 12 0.24
29 35 0.71
30 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (29 bp):
TACCTATTTTGACAAAAAAATACTTTAGA
Found at i:9340 original size:25 final size:25
Alignment explanation
Indices: 9280--9352 Score: 101
Period size: 26 Copynumber: 2.9 Consensus size: 25
9270 GTTTTCTTCT
* *
9280 CCTCCATAACTGTTTTTGTTTGCAA
1 CCTCCATAACCGTTTTTGTTTGAAA
* *
9305 CCCCTCGTAACCGTTTTTGTTTGAAA
1 CCTC-CATAACCGTTTTTGTTTGAAA
9331 CCTCCATAACCGTTTTTGTTTG
1 CCTCCATAACCGTTTTTGTTTG
9353 TAGCTGATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 20 0.49
26 21 0.51
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.42
Consensus pattern (25 bp):
CCTCCATAACCGTTTTTGTTTGAAA
Found at i:10372 original size:28 final size:28
Alignment explanation
Indices: 10315--10371 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
10305 AAAAGGTTTG
* *
10315 AATAGTTTAAGTACCTATTTTGACATAA
1 AATACTTTAAGTACCTATTTTAACATAA
10343 AATACTTTAAGTACCTATTTTAAC-TAA
1 AATACTTTAAGTACCTATTTTAACATAA
10370 AA
1 AA
10372 AAAAATTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (28 bp):
AATACTTTAAGTACCTATTTTAACATAA
Found at i:10385 original size:29 final size:28
Alignment explanation
Indices: 10320--10385 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
10310 GTTTGAATAG
* * * *
10320 TTTAAGTACCTATTTTGACATAAAATAC
1 TTTAAGTACCTATTTTAACAAAAAAAAA
10348 TTTAAGTACCTATTTTAACTAAAAAAAAA
1 TTTAAGTACCTATTTTAAC-AAAAAAAAA
*
10377 TTTAGGTAC
1 TTTAAGTAC
10386 TTGACTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (28 bp):
TTTAAGTACCTATTTTAACAAAAAAAAA
Found at i:10393 original size:24 final size:24
Alignment explanation
Indices: 10362--10423 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
10352 AGTACCTATT
10362 TTAACTAAAAAAAAATTTAGGTAC
1 TTAACTAAAAAAAAATTTAGGTAC
* * * *
10386 TTGACTAAAAAATATTTTAGTTAC
1 TTAACTAAAAAAAAATTTAGGTAC
*
10410 TTAAATAAAAAAAA
1 TTAACTAAAAAAAA
10424 GTGAGTATAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (24 bp):
TTAACTAAAAAAAAATTTAGGTAC
Found at i:11581 original size:2 final size:2
Alignment explanation
Indices: 11574--11610 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11564 ATTGATATTA
11574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11611 ATTTTATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21770 original size:116 final size:116
Alignment explanation
Indices: 21591--21914 Score: 325
Period size: 117 Copynumber: 2.8 Consensus size: 116
21581 AGAATGGAGC
* * * ** * *
21591 ACTTAAGGAGAAGCTTGCCTCTTGTGAAGCTGAGCTGAGGAAGACGAGAAGTTCGATC-AAGGCA
1 ACTTAAAGAGAAGCTTGCCTCTTGTGAAGCTGACCTGAGGATGTTGAGGA-TTCGA-CGGAGGCA
* ** * * * *
21655 GGAAAAAATGCATTGGCTGAATCGAATGCAAGGC-T-AGAACTA-GAAAACAAA
64 AGCCAAAATGCATTGACTGAATCCAATGCAAGACTTGAGAAC-ACCAAAACAAA
* *
21706 AGCTTAGAAG-GCAGCTTGCTTCTTGTGAAGCTGACCTGAGGATGTTGATGGATTCGACGGAGGC
1 A-CTTA-AAGAGAAGCTTGCCTCTTGTGAAGCTGACCTGAGGATGTTGA-GGATTCGACGGAGGC
* * * * * * *
21770 AAGCCAAAATGCATTGACCGAATCCAATTCACGACTTGAGCACACCAATAGAGA
63 AAGCCAAAATGCATTGACTGAATCCAATGCAAGACTTGAGAACACCAAAACAAA
* *
21824 ACTTAATGAGAAGCTTGCCACTTGTGAAGCTGACCTGAGGATGTTGAGGGATTCGACGGAGGCAA
1 ACTTAAAGAGAAGCTTGCCTCTTGTGAAGCTGACCTGAGGATGTTGA-GGATTCGACGGAGGCAA
21889 GCCAAAATGCATTGACTGAATCCAAT
65 GCCAAAATGCATTGACTGAATCCAAT
21915 TTACGACTCG
Statistics
Matches: 172, Mismatches: 29, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
115 2 0.01
116 73 0.42
117 87 0.51
118 10 0.06
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (116 bp):
ACTTAAAGAGAAGCTTGCCTCTTGTGAAGCTGACCTGAGGATGTTGAGGATTCGACGGAGGCAAG
CCAAAATGCATTGACTGAATCCAATGCAAGACTTGAGAACACCAAAACAAA
Found at i:21863 original size:117 final size:117
Alignment explanation
Indices: 21718--21969 Score: 405
Period size: 117 Copynumber: 2.2 Consensus size: 117
21708 CTTAGAAGGC
* *
21718 AGCTTGCTTCTTGTGAAGCTGACCTGAGGATGTTGATGGATTCGACGGAGGCAAGCCAAAATGCA
1 AGCTTGCTACTTGTGAAGCTGACCTGAGGATGTTGAGGGATTCGACGGAGGCAAGCCAAAATGCA
* * *
21783 TTGACCGAATCCAATTCACGACTTGAGCACACCAATAGAGAACTTAATGAGA
66 TTGACCGAATCCAATTCACGACTCGAGCACACAAACAGAGAACTTAATGAGA
*
21835 AGCTTGCCACTTGTGAAGCTGACCTGAGGATGTTGAGGGATTCGACGGAGGCAAGCCAAAATGCA
1 AGCTTGCTACTTGTGAAGCTGACCTGAGGATGTTGAGGGATTCGACGGAGGCAAGCCAAAATGCA
* * **
21900 TTGACTGAATCCAATTTACGACTCGAGCATGCAAACAGAGAACTTAATGAGA
66 TTGACCGAATCCAATTCACGACTCGAGCACACAAACAGAGAACTTAATGAGA
*
21952 AACTTGCTACTTGTGAAG
1 AGCTTGCTACTTGTGAAG
21970 TTGAGATATG
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
117 123 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (117 bp):
AGCTTGCTACTTGTGAAGCTGACCTGAGGATGTTGAGGGATTCGACGGAGGCAAGCCAAAATGCA
TTGACCGAATCCAATTCACGACTCGAGCACACAAACAGAGAACTTAATGAGA
Found at i:22296 original size:156 final size:156
Alignment explanation
Indices: 22012--22731 Score: 1156
Period size: 156 Copynumber: 4.6 Consensus size: 156
22002 GCAGAAGCTT
* * * *
22012 TGAATGAATCAAATTCAAGGCTAGTGCAGGTAAATGAAGCACTTGCTGAAAAGCTTGCAAGTTCT
1 TGAATGAATCGAATTCAAGGCTAGAGCAGGCAAATGAAGCACTTGGTGAAAAGCTTGCAAGTTCT
* * *
22077 GAAGCTGACCTGAGGAAGGTGAGGGAATCAAATAGAGAGCTTAATGAGAAGCTTGCCACTTGTGA
66 GAAGCTGAGCTGAGGAAGGTGAGGGAATCAAATAGAGAACTTAACGAGAAGCTTGCCACTTGTGA
* *
22142 AGCTGAGCCATGCATGTTAAAGGATC
131 AGCTGAGCTATGCAAGTTAAAGGATC
22168 TGAATGAATCGAATTCAAGGCTAGAGCAGGCAAATGAAGCACTTGGTGAAAAGCTTGCAAGTTCT
1 TGAATGAATCGAATTCAAGGCTAGAGCAGGCAAATGAAGCACTTGGTGAAAAGCTTGCAAGTTCT
* *
22233 GAAGTTGAGCTGAGGAAGGTGAGGGAATCAAATAGAGAACTTAACGAGAAGCTTGCCTCTTGTGA
66 GAAGCTGAGCTGAGGAAGGTGAGGGAATCAAATAGAGAACTTAACGAGAAGCTTGCCACTTGTGA
22298 AGCTGAGCTATGCAAGTTAAAGGATC
131 AGCTGAGCTATGCAAGTTAAAGGATC
* * * * ** *
22324 TGAACGAGTCAAATTCAAGGCTAGAGCAGACATTTGAAGCACTTGGTGAAAAGCTTGCAAATTCT
1 TGAATGAATCGAATTCAAGGCTAGAGCAGGCAAATGAAGCACTTGGTGAAAAGCTTGCAAGTTCT
*
22389 GAAGCTGAGCTGAGGAAGGTGAGGGAATCAAATAGAGAACTTAACGAGAAGGTTGCC-CTTTGTG
66 GAAGCTGAGCTGAGGAAGGTGAGGGAATCAAATAGAGAACTTAACGAGAAGCTTGCCAC-TTGTG
* *
22453 AATCTGAGCTATGCATGTTAAAGGATC
130 AAGCTGAGCTATGCAAGTTAAAGGATC
* * *
22480 TGAATGAATCGAATTCAAGGCTAGAGCAGGTAAATGAAGCACTTGGCGAAAAGCTTGCAAATTCT
1 TGAATGAATCGAATTCAAGGCTAGAGCAGGCAAATGAAGCACTTGGTGAAAAGCTTGCAAGTTCT
*
22545 AAAGCTGAGCTGAGGAAGGTGAGGGAATCAAATAGAGAACTTAACGAGAAGCTTGCCACTTGTGA
66 GAAGCTGAGCTGAGGAAGGTGAGGGAATCAAATAGAGAACTTAACGAGAAGCTTGCCACTTGTGA
22610 AGCTGAGCTATGCAAGTTAAAGGAT-
131 AGCTGAGCTATGCAAGTTAAAGGATC
* **
22635 TCGAGTGAATCGAATTCAAGGCTAGTCCAGGCAAATGAAGCACTTGGTGAAAAGCTTGCAAGTTC
1 T-GAATGAATCGAATTCAAGGCTAGAGCAGGCAAATGAAGCACTTGGTGAAAAGCTTGCAAGTTC
22700 TGAAGCTGAGCTGAGGAAGGTGAGGGAATCAA
65 TGAAGCTGAGCTGAGGAAGGTGAGGGAATCAA
22732 CCGAGATATG
Statistics
Matches: 520, Mismatches: 41, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
155 2 0.00
156 517 0.99
157 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (156 bp):
TGAATGAATCGAATTCAAGGCTAGAGCAGGCAAATGAAGCACTTGGTGAAAAGCTTGCAAGTTCT
GAAGCTGAGCTGAGGAAGGTGAGGGAATCAAATAGAGAACTTAACGAGAAGCTTGCCACTTGTGA
AGCTGAGCTATGCAAGTTAAAGGATC
Found at i:23798 original size:16 final size:15
Alignment explanation
Indices: 23777--23807 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
23767 AGTAAAATGA
23777 ATAGAACAAATAGAAG
1 ATAGAACAAA-AGAAG
23793 ATAGAACAAAAGAAG
1 ATAGAACAAAAGAAG
23808 TTCAAGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.65, C:0.06, G:0.19, T:0.10
Consensus pattern (15 bp):
ATAGAACAAAAGAAG
Found at i:28028 original size:44 final size:42
Alignment explanation
Indices: 27978--28069 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 42
27968 GGAGAGCTAC
* *
27978 AGAAAAGCTGAAACTAAGTACTTGGAAGAACAAATACAACTCGA
1 AGAAAAG--GAAACGAAGTACTTGGAAGAACAAAGACAACTCGA
* * * *
28022 AGAAAA-GAAGCGAAGTACTTGGAATAACAAAGACAACTTGC
1 AGAAAAGGAAACGAAGTACTTGGAAGAACAAAGACAACTCGA
28063 AGAAAAG
1 AGAAAAG
28070 ATCTTGACAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
41 35 0.85
44 6 0.15
ACGTcount: A:0.51, C:0.14, G:0.21, T:0.14
Consensus pattern (42 bp):
AGAAAAGGAAACGAAGTACTTGGAAGAACAAAGACAACTCGA
Found at i:28040 original size:41 final size:41
Alignment explanation
Indices: 27993--28070 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
27983 AGCTGAAACT
*
27993 AAGTACTTGGAAGAACAAATACAACTCGAAGAAAAGAAGCG
1 AAGTACTTGGAAGAACAAAGACAACTCGAAGAAAAGAAGCG
* * *
28034 AAGTACTTGGAATAACAAAGACAACTTGCAGAAAAGA
1 AAGTACTTGGAAGAACAAAGACAACTCGAAGAAAAGA
28071 TCTTGACATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.51, C:0.14, G:0.21, T:0.14
Consensus pattern (41 bp):
AAGTACTTGGAAGAACAAAGACAACTCGAAGAAAAGAAGCG
Found at i:31395 original size:14 final size:14
Alignment explanation
Indices: 31376--31416 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
31366 TTAAATTATA
*
31376 AACGAACACAAATG
1 AACGAACACAAACG
31390 AACGAACACAAACG
1 AACGAACACAAACG
31404 AACGTAA-ACAAAC
1 AACG-AACACAAAC
31417 ACAATAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 23 0.92
15 2 0.08
ACGTcount: A:0.59, C:0.24, G:0.12, T:0.05
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:31439 original size:33 final size:34
Alignment explanation
Indices: 31374--31458 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 34
31364 ATTTAAATTA
* *
31374 TAAACGAACACAAATGAACGAACACAAACGAACG
1 TAAACAAACACAAATAAACGAACACAAACGAACG
* * *
31408 TAAACAAACAC-AATAAATGAACATAATCGAACG
1 TAAACAAACACAAATAAACGAACACAAACGAACG
*
31441 TAAACAAACA-AAACAAAC
1 TAAACAAACACAAATAAAC
31459 ATATAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 33 0.77
34 10 0.23
ACGTcount: A:0.60, C:0.21, G:0.09, T:0.09
Consensus pattern (34 bp):
TAAACAAACACAAATAAACGAACACAAACGAACG
Found at i:31630 original size:24 final size:24
Alignment explanation
Indices: 31565--31630 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
31555 ATAAACAACC
*
31565 GAACATAAACGAACGAAAGTAAAT
1 GAACATAAACGAACGAACGTAAAT
31589 GAACATAAACGAACGAACGTAAAT
1 GAACATAAACGAACGAACGTAAAT
* * *
31613 GAACCTAAATGAATGAAC
1 GAACATAAACGAACGAAC
31631 ACAAACTAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.55, C:0.15, G:0.17, T:0.14
Consensus pattern (24 bp):
GAACATAAACGAACGAACGTAAAT
Found at i:36298 original size:10 final size:10
Alignment explanation
Indices: 36270--36304 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
36260 AAAAAAAAAA
36270 TTTATATAATT
1 TTTATAT-ATT
36281 TTTA-ATATT
1 TTTATATATT
36290 TTTATATATT
1 TTTATATATT
36300 TTTAT
1 TTTAT
36305 TGGGTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.30
10 12 0.52
11 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATATATT
Found at i:37713 original size:31 final size:31
Alignment explanation
Indices: 37666--37758 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
37656 GTCAATATCA
37666 GGTCGGGTCAATACCATATCGATTGATTTTTG
1 GGTC-GGTCAATACCATATCGATTGATTTTTG
* * * *
37698 GGTCGGTTAATACCATATTGTTTAGA-TTTAG
1 GGTCGGTCAATACCATATCGATT-GATTTTTG
* **
37729 GGTCGGTCAATATCGGATCGATTGATTTTT
1 GGTCGGTCAATACCATATCGATTGATTTTT
37759 CGGTTTAGGT
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
30 2 0.04
31 40 0.83
32 6 0.12
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.40
Consensus pattern (31 bp):
GGTCGGTCAATACCATATCGATTGATTTTTG
Found at i:38250 original size:19 final size:20
Alignment explanation
Indices: 38214--38252 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38204 TTAGTTGTTT
*
38214 TCTATTATTTTTATTATAAA
1 TCTAATATTTTTATTATAAA
38234 TCTAATATTTTTA-TATAAA
1 TCTAATATTTTTATTATAAA
38253 GTAAGATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TCTAATATTTTTATTATAAA
Found at i:38526 original size:16 final size:16
Alignment explanation
Indices: 38451--38616 Score: 107
Period size: 16 Copynumber: 10.3 Consensus size: 16
38441 GTTCGGTTGC
* *
38451 TTTCGGGTCGAGTTAA
1 TTTCGGTTCGGGTTAA
* ** **
38467 ATTCGGTTCAAGTTTC
1 TTTCGGTTCGGGTTAA
* *
38483 TTTCGGATCGTGTTAA
1 TTTCGGTTCGGGTTAA
*
38499 CATTCGGTTCGGGTTAA
1 -TTTCGGTTCGGGTTAA
* **
38516 TTTCAGTTCGGGTTGC
1 TTTCGGTTCGGGTTAA
38532 TTTCGGTTCGGGTTAA
1 TTTCGGTTCGGGTTAA
*** **
38548 TTTCGGTTCAAATTGC
1 TTTCGGTTCGGGTTAA
38564 TTTCGGTTCGGGTTAA
1 TTTCGGTTCGGGTTAA
*** **
38580 TTTCGGTTCAAATTGC
1 TTTCGGTTCGGGTTAA
*
38596 TTTTGGTTCGGGTTAA
1 TTTCGGTTCGGGTTAA
38612 TTTCG
1 TTTCG
38617 ATTTCGCTAA
Statistics
Matches: 106, Mismatches: 43, Indels: 2
0.70 0.28 0.01
Matches are distributed among these distances:
16 93 0.88
17 13 0.12
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.43
Consensus pattern (16 bp):
TTTCGGTTCGGGTTAA
Found at i:38532 original size:81 final size:79
Alignment explanation
Indices: 38441--38588 Score: 206
Period size: 81 Copynumber: 1.8 Consensus size: 79
38431 ATTTCAATTT
* * *
38441 GTTCGGTTGCTTTCGGGTCGAGTTAAATTCGGTTCAAGTTTCTTTCGGATCGTGTTAACATTCGG
1 GTTCGGTTGCTTTCGGGTCGAGTTAAATTCGGTTCAAATTGCTTTCGGATCGGGTTAA-ATTCGG
38506 TTCGGGTTAATTTCA
65 TTCGGGTTAATTTCA
* * * * *
38521 GTTCGGGTTGCTTTCGGTTCGGGTTAATTTCGGTTCAAATTGCTTTCGGTTCGGGTTAATTTCGG
1 GTTC-GGTTGCTTTCGGGTCGAGTTAAATTCGGTTCAAATTGCTTTCGGATCGGGTTAAATTCGG
38586 TTC
65 TTC
38589 AAATTGCTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
80 12 0.20
81 47 0.80
ACGTcount: A:0.14, C:0.16, G:0.28, T:0.43
Consensus pattern (79 bp):
GTTCGGTTGCTTTCGGGTCGAGTTAAATTCGGTTCAAATTGCTTTCGGATCGGGTTAAATTCGGT
TCGGGTTAATTTCA
Found at i:38542 original size:32 final size:32
Alignment explanation
Indices: 38501--38616 Score: 187
Period size: 32 Copynumber: 3.6 Consensus size: 32
38491 CGTGTTAACA
* ***
38501 TTCGGTTCGGGTTAATTTCAGTTCGGGTTGCT
1 TTCGGTTCGGGTTAATTTCGGTTCAAATTGCT
38533 TTCGGTTCGGGTTAATTTCGGTTCAAATTGCT
1 TTCGGTTCGGGTTAATTTCGGTTCAAATTGCT
38565 TTCGGTTCGGGTTAATTTCGGTTCAAATTGCT
1 TTCGGTTCGGGTTAATTTCGGTTCAAATTGCT
*
38597 TTTGGTTCGGGTTAATTTCG
1 TTCGGTTCGGGTTAATTTCG
38617 ATTTCGCTAA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 79 1.00
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.45
Consensus pattern (32 bp):
TTCGGTTCGGGTTAATTTCGGTTCAAATTGCT
Found at i:39590 original size:159 final size:158
Alignment explanation
Indices: 39346--39709 Score: 459
Period size: 159 Copynumber: 2.3 Consensus size: 158
39336 TTGAAAGAGT
* * * * * * * *
39346 GGTGCTGATAATGATGC---AAGAGCAATGTGGACCAGAAACCCAGTTTGAATGAAGGGAAGAAT
1 GGTGCTGATAATGATGCAATAAGAGCGATTTGGAACAGCAATCCGGTTCGAATGAAGGCAAGAAT
** * *
39408 TTGGTAAAGGATGGGAAAGAATCGGGTGGAGAAGTGATAGGAAACA-TGAGTGGGAAAGATAATG
66 TTGGTAAAGGATGGGAAAGAATCGAATGGAGAAGTGAAAGGAAACACT-AGTGGGAAAGATAACG
*
39472 GAGGAGATCAAGTTGATGGATCAAAAAG-G
130 GAGGAGATCAAATTGATGGATC-AAAAGTG
*
39501 GGTGCTGATAATGATGCAAGTAAGAGCGATTTGGATCAGCAATCCGGTTCGAATGAAGGCAAGAA
1 GGTGCTGATAATGATGCAA-TAAGAGCGATTTGGAACAGCAATCCGGTTCGAATGAAGGCAAGAA
* **
39566 TTTGGTAAAGGATTGGAAAGAATCGAATGGTTAAGTGAAAGGAAACACTAGTGGGAAAGATAACG
65 TTTGGTAAAGGATGGGAAAGAATCGAATGGAGAAGTGAAAGGAAACACTAGTGGGAAAGATAACG
39631 GAGGAGATCAAATTGATGGATCAAAAGTG
130 GAGGAGATCAAATTGATGGATCAAAAGTG
* ** * *
39660 GATGCTGACGATGATGCAAATAAGAGCGATTTGAAACAGCAATCGGGTTC
1 GGTGCTGATAATGATGC-AATAAGAGCGATTTGGAACAGCAATCCGGTTC
39710 AATTATGAAG
Statistics
Matches: 180, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
155 17 0.09
158 5 0.03
159 155 0.86
160 3 0.02
ACGTcount: A:0.38, C:0.10, G:0.32, T:0.20
Consensus pattern (158 bp):
GGTGCTGATAATGATGCAATAAGAGCGATTTGGAACAGCAATCCGGTTCGAATGAAGGCAAGAAT
TTGGTAAAGGATGGGAAAGAATCGAATGGAGAAGTGAAAGGAAACACTAGTGGGAAAGATAACGG
AGGAGATCAAATTGATGGATCAAAAGTG
Found at i:42643 original size:3 final size:3
Alignment explanation
Indices: 42637--42663 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42627 GAAAAATAAC
42637 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
42664 TTGATCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:44757 original size:23 final size:23
Alignment explanation
Indices: 44713--44757 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
44703 CCGGAAACTG
*
44713 ATCGGAGCCACAGATCCACAGAA
1 ATCGGAGCCACAGAACCACAGAA
*
44736 ATCGGAGCC-CGGAACCATCAGA
1 ATCGGAGCCACAGAACCA-CAGA
44758 GGTGATCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.36, C:0.31, G:0.24, T:0.09
Consensus pattern (23 bp):
ATCGGAGCCACAGAACCACAGAA
Found at i:45656 original size:29 final size:30
Alignment explanation
Indices: 45613--45669 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
45603 CCCTTTTTCT
*
45613 AGTTTAGTACGTAACATTT-ATTTCGTTCC
1 AGTTTAGTACCTAACATTTCATTTCGTTCC
* *
45642 AGTTTGGTACCTAACGTTTCATTTCGTT
1 AGTTTAGTACCTAACATTTCATTTCGTT
45670 ACTCAAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.46
Consensus pattern (30 bp):
AGTTTAGTACCTAACATTTCATTTCGTTCC
Found at i:46076 original size:9 final size:11
Alignment explanation
Indices: 46054--46079 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
46044 AATTGAAATT
46054 TATAAATAATA
1 TATAAATAATA
46065 TATAAATAATA
1 TATAAATAATA
46076 TATA
1 TATA
46080 TTATATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TATAAATAATA
Found at i:47552 original size:8 final size:8
Alignment explanation
Indices: 47540--47574 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
47530 TATTATTTTT
*
47540 ATATAAAT
1 ATATAAAA
47548 ATATAAAA
1 ATATAAAA
47556 ATAATAAAA
1 AT-ATAAAA
47565 ATATAAAA
1 ATATAAAA
47573 AT
1 AT
47575 TATTATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
ATATAAAA
Found at i:47562 original size:17 final size:17
Alignment explanation
Indices: 47542--47574 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
47532 TTATTTTTAT
*
47542 ATAAATATATAAAAATA
1 ATAAAAATATAAAAATA
47559 ATAAAAATATAAAAAT
1 ATAAAAATATAAAAAT
47575 TATTATTTAA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAAAATATAAAAATA
Found at i:47611 original size:28 final size:28
Alignment explanation
Indices: 47555--47611 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
47545 AATATATAAA
*
47555 AATAATAAAAATATAAAAATTATTATTT
1 AATAATAAAAATATAAAAATAATTATTT
* *
47583 AATAATAATATTATAAATAATAATT-TTT
1 AATAATAAAAATATAAA-AATAATTATTT
47611 A
1 A
47612 TATTTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
AATAATAAAAATATAAAAATAATTATTT
Found at i:57635 original size:38 final size:37
Alignment explanation
Indices: 57592--57683 Score: 112
Period size: 40 Copynumber: 2.4 Consensus size: 37
57582 ATATTATTTT
57592 TAATATTTTTAGTTGAATTAAAAATATTATAAATAATA
1 TAATATTTTT-GTTGAATTAAAAATATTATAAATAATA
* * * *
57630 TAATATTTTCGGTTATAAATTTAAAATATTATGAATAATA
1 TAATATTTT-TG-T-TGAATTAAAAATATTATAAATAATA
57670 TAATATTTTTGTTG
1 TAATATTTTTGTTG
57684 TCAATCAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
37 1 0.02
38 11 0.24
39 2 0.04
40 31 0.69
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.48
Consensus pattern (37 bp):
TAATATTTTTGTTGAATTAAAAATATTATAAATAATA
Found at i:57840 original size:2 final size:2
Alignment explanation
Indices: 57833--57864 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
57823 GTTAACCTTA
57833 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57865 GAGTTATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58067 original size:2 final size:2
Alignment explanation
Indices: 58060--58097 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
58050 AACTATAAGT
58060 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
58098 AATTAGATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59410 original size:20 final size:20
Alignment explanation
Indices: 59385--59424 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
59375 TTTTGATGAA
*
59385 AATCAATATGTATCTCGTAT
1 AATCAATATGTATCTAGTAT
59405 AATCAATATGTATCTAGTAT
1 AATCAATATGTATCTAGTAT
59425 TATTTATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (20 bp):
AATCAATATGTATCTAGTAT
Found at i:59852 original size:157 final size:157
Alignment explanation
Indices: 59566--60034 Score: 776
Period size: 157 Copynumber: 3.0 Consensus size: 157
59556 GCAGTTCACG
59566 TTAGTAACATGACAATCTATGATGCTGACATATCAGTCTAAGGTGACAGATTAACGTGACAAATG
1 TTAGTAACATGACAATCTATGATGCTGACATATCAGTCTAAGGTGACAGATTAACGTGACAAATG
*
59631 ACATGACAGATTGACTAAATTGATGACTCAAACATAGCAGATGGGCTGTCACATCAGCACTGTGA
66 ACATGACAGATTGACTAAATTGATGACTCAAACATAGCAGATGGGCTGCCACATCAGCACTGTGA
59696 AGTTACATGCCAATAATATAACGGTTA
131 AGTTACATGCCAATAATATAACGGTTA
* *
59723 TTAGTAACATGACAATCTATGATGCTGACATATCAATCTAAGGTGACGGATTAACGTGACAAATG
1 TTAGTAACATGACAATCTATGATGCTGACATATCAGTCTAAGGTGACAGATTAACGTGACAAATG
*
59788 ACATGACATATTGACTAAATTGATGACTCAAACATAGCAGATGGGCTGCCACATCAGCACTGTGA
66 ACATGACAGATTGACTAAATTGATGACTCAAACATAGCAGATGGGCTGCCACATCAGCACTGTGA
59853 AGTTACATGCCAATAATATAACGGTTA
131 AGTTACATGCCAATAATATAACGGTTA
* * *
59880 TTAGTAACATGACAATCTATGATACTGACATATCAGTCCAAGGTGACAGATTAATGTGACAAATG
1 TTAGTAACATGACAATCTATGATGCTGACATATCAGTCTAAGGTGACAGATTAACGTGACAAATG
* * * * ** *
59945 ACATGACAGATTGGCTAATTTGATGACTCAAACATAACAGATGGACAACCACATCAGCACCGTGA
66 ACATGACAGATTGACTAAATTGATGACTCAAACATAGCAGATGGGCTGCCACATCAGCACTGTGA
** * *
60010 AGTGGCACGCCAATACTATAACGGT
131 AGTTACATGCCAATAATATAACGGT
60035 CGACGACGAA
Statistics
Matches: 291, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
157 291 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.25
Consensus pattern (157 bp):
TTAGTAACATGACAATCTATGATGCTGACATATCAGTCTAAGGTGACAGATTAACGTGACAAATG
ACATGACAGATTGACTAAATTGATGACTCAAACATAGCAGATGGGCTGCCACATCAGCACTGTGA
AGTTACATGCCAATAATATAACGGTTA
Found at i:68083 original size:2 final size:2
Alignment explanation
Indices: 68032--68072 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
68022 ATTTAGATCA
68032 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68073 TAAACATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:68736 original size:112 final size:112
Alignment explanation
Indices: 68531--69105 Score: 981
Period size: 112 Copynumber: 5.1 Consensus size: 112
68521 TTGTCGGTTT
* * * * *
68531 GTGTCGATACTTTATAAAAATATATTGATCCTTAACAATATAACAAGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAT
68596 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
68644 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
*
68709 GGTCTATAAATGACAAAACATGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
68756 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
*
68821 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
68868 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAATGATAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
* * *
68932 GGTCTATAAATGACAAAACAGGTAAAGCGCCACCAGCTATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
68979 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
* * *
69044 GGTCTATAAATGACAAAATAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
69091 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
69106 TATAAGTATC
Statistics
Matches: 436, Mismatches: 25, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
111 104 0.24
112 289 0.66
113 43 0.10
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:69041 original size:223 final size:224
Alignment explanation
Indices: 68531--69105 Score: 990
Period size: 223 Copynumber: 2.6 Consensus size: 224
68521 TTGTCGGTTT
* * * *
68531 GTGTCGATACTTTATAAAAATATATTGATCCTTAACAATATAACAAGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
68596 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
*
68661 AAATGTATCTATCCATAACAATATAACAGGTAAAAAAATGACAAAATCGGTCTATAAATGACAAA
130 AAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATCGGTCTATAAATGACAAA
* * *
68726 ACATGTAAAGCGCTACCGGATATATTGAAA
195 ACAGGTAAAGCGCCACCAGATATATTGAAA
68756 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
68821 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
*
68886 AATGTATCGATCCATAACAATATAACAGGT-AAAAAATGATAAAATCGGTCTATAAATGACAAAA
131 AATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATCGGTCTATAAATGACAAAA
*
68950 CAGGTAAAGCGCCACCAGCTATATTGAAA
196 CAGGTAAAGCGCCACCAGATATATTGAAA
* *
68979 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
69044 GGTCTATAAATGACAAAATAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAT
69106 TATAAGTATC
Statistics
Matches: 333, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
223 179 0.54
224 110 0.33
225 44 0.13
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.25
Consensus pattern (224 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
AATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATCGGTCTATAAATGACAAAA
CAGGTAAAGCGCCACCAGATATATTGAAA
Found at i:69323 original size:162 final size:162
Alignment explanation
Indices: 69053--69385 Score: 612
Period size: 162 Copynumber: 2.1 Consensus size: 162
69043 CGGTCTATAA
* * *
69053 ATGACAAAATAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGA
1 ATGACAAAACAGGTAAAGAGCTACCGGATATGTTGATAGTGTCGAAACTTTATTATAAGTATCGA
* *
69118 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
69183 TATCGATCCATAACAATATAACAGGTAAAAAT
131 TATCGATCCATAACAATATAACAGGTAAAAAT
*
69215 ATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGAAACTTTATTATAAGTATCGA
1 ATGACAAAACAGGTAAAGAGCTACCGGATATGTTGATAGTGTCGAAACTTTATTATAAGTATCGA
69280 CACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
69345 TATCGATCCATAACAATATAACAGGTAAAAAT
131 TATCGATCCATAACAATATAACAGGTAAAAAT
69377 ATGACAAAA
1 ATGACAAAA
69386 TCGATATCGA
Statistics
Matches: 165, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
162 165 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (162 bp):
ATGACAAAACAGGTAAAGAGCTACCGGATATGTTGATAGTGTCGAAACTTTATTATAAGTATCGA
CACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATG
TATCGATCCATAACAATATAACAGGTAAAAAT
Found at i:70059 original size:23 final size:23
Alignment explanation
Indices: 70030--70077 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
70020 AAATAGGTCA
*
70030 ATATAAGAGCTACCTATTACATT
1 ATATAAGAGCTACCTAATACATT
* *
70053 ATATAAGCGCTACCTAATATATT
1 ATATAAGAGCTACCTAATACATT
70076 AT
1 AT
70078 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGAGCTACCTAATACATT
Found at i:85202 original size:139 final size:140
Alignment explanation
Indices: 84952--85232 Score: 555
Period size: 139 Copynumber: 2.0 Consensus size: 140
84942 GATATTTTTT
84952 GAACTCACATTTACAATTTGATTCAATTGCGAACAATTCTTTACAACATTTTATCATTCTCTCTC
1 GAACTCACATTTACAATTTGATTCAATTGCGAACAATTCTTTACAACATTTTATCATTCTCTCTC
85017 CTGAAACAAGAAAAAGAGAAAAACGTTTTCAAACAGAACAATCTCAGATATGAAATGTC-GTAAA
66 CTGAAACAAGAAAAAGAGAAAAACGTTTTCAAACAGAACAATCTCAGATATGAAATGTCTGTAAA
85081 GCCCAAGCTC
131 GCCCAAGCTC
85091 GAACTCACATTTACAATTTGATTCAATTGCGAACAATTCTTTACAACATTTTATCATTCTCTCTC
1 GAACTCACATTTACAATTTGATTCAATTGCGAACAATTCTTTACAACATTTTATCATTCTCTCTC
85156 CTGAAACAAGAAAAAGAGAAAAACGTTTTCAAACAGAACAATCTCAGATATGAAATGTCTGTAAA
66 CTGAAACAAGAAAAAGAGAAAAACGTTTTCAAACAGAACAATCTCAGATATGAAATGTCTGTAAA
85221 GCCCAAGCTC
131 GCCCAAGCTC
85231 GA
1 GA
85233 GAAGCAAATG
Statistics
Matches: 141, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
139 124 0.88
140 17 0.12
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (140 bp):
GAACTCACATTTACAATTTGATTCAATTGCGAACAATTCTTTACAACATTTTATCATTCTCTCTC
CTGAAACAAGAAAAAGAGAAAAACGTTTTCAAACAGAACAATCTCAGATATGAAATGTCTGTAAA
GCCCAAGCTC
Found at i:85978 original size:84 final size:81
Alignment explanation
Indices: 85788--86541 Score: 747
Period size: 84 Copynumber: 9.2 Consensus size: 81
85778 ACCTGCCACC
* * * *
85788 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAG
*
85853 AAGGGCTATCTG-CCA
66 AAGGGTTATCTGACCA
* * * * * * * * *
85868 AAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGACT
1 AAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCT
*
85932 AGAAGGGTTATCTGTTAGCA
64 AGAAGGGTTATCTG--ACCA
* ** *
85952 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCATAATAGCTT-A----AG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAG
*
86012 AAGGGCTATCTG-CCA
66 AAGGGTTATCTGACCA
** * * * * * * *
86027 AAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCTA
86092 GAAGGGTTATCTGTGACCAA
65 GAAGGGTTATC--TGACC-A
* * *
86112 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAG
*
86177 AAGGGCTATCTG-CCA
66 AAGGGTTATCTGACCA
** * * * * * *
86192 AAGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCTA
86257 GAAGGGTTATCTGCCAACCA
65 GAAGGGTTATCTG---ACCA
* * *
86277 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAC
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAG
* * *
86342 AAGGGTTGTTTGCCAACAA
66 AAGGGTTATCTG---ACCA
* * * * *
86361 AAGACCTTTGAGTTCGACTACGCTCAGCT-TAACGGCACATCATTTACAGCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCTA
86425 GAAGGGTTATCTGAGACCAA
65 GAAGGGTTATCT--GACC-A
* * *
86445 AAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAG
*
86510 AAGGGTTATCTG-CTA
66 AAGGGTTATCTGACCA
*
86525 AAGACCTTTGAGTTCGA
1 AAGACCTTCGAGTTCGA
86542 TTATATTCAA
Statistics
Matches: 550, Mismatches: 98, Indels: 52
0.79 0.14 0.07
Matches are distributed among these distances:
75 25 0.05
76 22 0.04
77 1 0.00
78 13 0.02
80 65 0.12
81 97 0.18
82 4 0.01
83 27 0.05
84 242 0.44
85 53 0.10
86 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (81 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAG
AAGGGTTATCTGACCA
Found at i:86234 original size:165 final size:164
Alignment explanation
Indices: 85760--86604 Score: 1049
Period size: 165 Copynumber: 5.1 Consensus size: 164
85750 TGCAGTTTAG
* * * ** *
85760 CTCAAGGCCAGAAGGGCTACCTGCCACC-AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
*
85824 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTAC
66 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGATTAC
* * *
85889 ACTCAGCTTCAAGGGCATAACATTTACAGCATAA
131 ACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* * * *
85923 CTCAAGACTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* **
85988 ACATCATTTGCATAATAGCTT-A----AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
66 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGATTAC
86048 ACTCAGCTTCGAGGGCACATCATTTACAGCATAA
131 ACTCAGCTTCGAGGGCACATCATTTACAGCATAA
86082 CTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
***
86147 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTA
65 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGATTA
*
86212 CACTCAGCTTCGAGGGCACATCATTTGCAGCATAA
130 CACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* * * **
86247 CTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* * * * * * * * * *
86312 CATATCATTTGCAGCACAACTTAAGTCTACAAGGGTTGTTTGCCAACAAAAGACCTTTGAGTTCG
65 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCTTGAGTTCG
* * * *
86377 ACTACGCTCAGCTT-AACGGCACATCATTTACAGCATAA
126 ATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* *
86415 CTCAAGGCTAGAAGGGTTATCTGAGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* * * * *
86480 CACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGCTAAAGACCTTTGAGTTCGATTA
65 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGATTA
* * * * * * * *
86545 TATTCAACTTAGA-GGCAAATCAAACTTACAGAATAG
130 CACTCAGCTTCGAGGGCACATC--ATTTACAGCATAA
*
86581 CTCAAGGCAAGAAGGGTTATCTGT
1 CTCAAGGCTAGAAGGGTTATCTGT
86605 CAATAAAATT
Statistics
Matches: 596, Mismatches: 70, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
159 91 0.15
160 56 0.09
161 1 0.00
163 22 0.04
164 89 0.15
165 160 0.27
166 36 0.06
167 4 0.01
168 112 0.19
169 25 0.04
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
CTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGATTAC
ACTCAGCTTCGAGGGCACATCATTTACAGCATAA
Found at i:87166 original size:106 final size:106
Alignment explanation
Indices: 86981--87710 Score: 1124
Period size: 106 Copynumber: 6.9 Consensus size: 106
86971 TCAAAATGAA
*
86981 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* *
87046 TAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
87087 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
*
87152 CAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * * * *
87193 TTCTACTTCACAACGAAGGGACCGCTGGTTGGCAATAAACAA-TTTTCCAATTTCAGAACCAATT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCT-CAATTTCAGAGCCAATT
* *
87257 TCAACTTCACAACGAAAGATATTGGACTCCAGACAACGTAAG
65 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * *
87299 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* **
87364 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACATAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * *
87405 TTCAACTTCACAACGAAGGGACCACTGGTTGTCAACAGACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
*
87470 CAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
87511 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
*
87576 CAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * * *
87617 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAA-TTTTCACAGTTCCAGAACCAAT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCA-A-TTTCAGAGCCAAT
**
87681 TTCAACTTCACGGCGGAA-GATATTGGACTC
64 TTCAACTTCACAAC-GAAGGATATTGGACTC
87711 GGAACAATAC
Statistics
Matches: 575, Mismatches: 44, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
105 8 0.01
106 527 0.92
107 37 0.06
108 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:88061 original size:84 final size:82
Alignment explanation
Indices: 87890--88097 Score: 218
Period size: 84 Copynumber: 2.5 Consensus size: 82
87880 TCCAACTCAA
* * * * * *
87890 AGAAGGATTATTTGTCAACAAGGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGATTATCTGTCACCAAAGACC-TCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTT
* *
87955 ACAGCATAGCTCAAGGCT
65 ACAGCATAACTCAAGGCG
* * *
87973 AGAAGGGTTATCTGTCACCAAAAGACCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
1 AGAAGGATTATCTGTCACC-AAAGACCTCGAGTTCGATTACACTCAGC-TCCAAGGCACATCATT
* * *
88038 TGCAGCATAACTTAAGTCG
64 TACAGCATAACTCAAGGCG
* *
88057 AGAAGGACTATCTGCCAACCAAAGACCTGACGAGTTCGATT
1 AGAAGGATTATCTGTC-ACCAAAGACCT--CGAGTTCGATT
88098 TCATTAAGCT
Statistics
Matches: 103, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
83 34 0.33
84 55 0.53
85 3 0.03
86 11 0.11
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (82 bp):
AGAAGGATTATCTGTCACCAAAGACCTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTA
CAGCATAACTCAAGGCG
Found at i:91773 original size:59 final size:59
Alignment explanation
Indices: 91681--91799 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
91671 AATCAATGGA
91681 ATGTCAATCGACCAATTAGGGATCAAAATACAAACATTCAAAACTTGATGTACTTGCTT
1 ATGTCAATCGACCAATTAGGGATCAAAATACAAACATTCAAAACTTGATGTACTTGCTT
*
91740 ATGTCAATCGACCAATTAGGGATCACAATACAAACATTCAAAACTTGATGTACTTGCTT
1 ATGTCAATCGACCAATTAGGGATCAAAATACAAACATTCAAAACTTGATGTACTTGCTT
91799 A
1 A
91800 CATTCGATAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (59 bp):
ATGTCAATCGACCAATTAGGGATCAAAATACAAACATTCAAAACTTGATGTACTTGCTT
Found at i:92956 original size:2 final size:2
Alignment explanation
Indices: 92951--92977 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
92941 GCTCTCTCTT
92951 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
92978 TCTAAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:101683 original size:15 final size:15
Alignment explanation
Indices: 101663--101696 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
101653 TCTTTTTCAC
* *
101663 TATTTTTATTAATTT
1 TATTTTTAATAAGTT
101678 TATTTTTAATAAGTT
1 TATTTTTAATAAGTT
101693 TATT
1 TATT
101697 AAAAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TATTTTTAATAAGTT
Found at i:101926 original size:16 final size:16
Alignment explanation
Indices: 101905--101942 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
101895 TGGGAATATG
*
101905 ATTACCGGAATATAAC
1 ATTACCGAAATATAAC
101921 ATTACCGAAATATAAC
1 ATTACCGAAATATAAC
101937 ATTACC
1 ATTACC
101943 TAACACATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (16 bp):
ATTACCGAAATATAAC
Found at i:105693 original size:18 final size:18
Alignment explanation
Indices: 105670--105704 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
105660 TTCCATCCGG
*
105670 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
105688 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
105705 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:107003 original size:7 final size:7
Alignment explanation
Indices: 106993--107029 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
106983 CGGTCAACGC
106993 CGGTCAA
1 CGGTCAA
107000 CGGTCAA
1 CGGTCAA
107007 CGGGTCAA
1 C-GGTCAA
107015 CGGTCAA
1 CGGTCAA
107022 CGGGTCAA
1 C-GGTCAA
107030 TGGGTCGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 15 0.54
8 13 0.46
ACGTcount: A:0.27, C:0.27, G:0.32, T:0.14
Consensus pattern (7 bp):
CGGTCAA
Found at i:107014 original size:8 final size:8
Alignment explanation
Indices: 106980--107048 Score: 69
Period size: 8 Copynumber: 9.1 Consensus size: 8
106970 TTTTGGTCAA
106980 CAAC-GGT
1 CAACGGGT
106987 CAACGCCGGT
1 CAACG--GGT
106997 CAAC-GGT
1 CAACGGGT
107004 CAACGGGT
1 CAACGGGT
107012 CAAC-GGT
1 CAACGGGT
107019 CAACGGGT
1 CAACGGGT
*
107027 CAATGGGT
1 CAACGGGT
107035 ---CGGGT
1 CAACGGGT
107040 CAACGGGT
1 CAACGGGT
107048 C
1 C
107049 GGGTCGGGTC
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
5 4 0.08
7 18 0.35
8 23 0.44
10 7 0.13
ACGTcount: A:0.23, C:0.28, G:0.35, T:0.14
Consensus pattern (8 bp):
CAACGGGT
Found at i:107014 original size:15 final size:15
Alignment explanation
Indices: 106980--107029 Score: 82
Period size: 15 Copynumber: 3.2 Consensus size: 15
106970 TTTTGGTCAA
106980 CAACGGTCAACGCCGGT
1 CAACGGTCAACG--GGT
106997 CAACGGTCAACGGGT
1 CAACGGTCAACGGGT
107012 CAACGGTCAACGGGT
1 CAACGGTCAACGGGT
107027 CAA
1 CAA
107030 TGGGTCGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 21 0.64
17 12 0.36
ACGTcount: A:0.28, C:0.30, G:0.30, T:0.12
Consensus pattern (15 bp):
CAACGGTCAACGGGT
Found at i:107040 original size:13 final size:13
Alignment explanation
Indices: 107022--107097 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 13
107012 CAACGGTCAA
*
107022 CGGGTCAATGGGT
1 CGGGTCAACGGGT
107035 CGGGTCAACGGGTCGGGT
1 CGGGTCAAC--G---GGT
*
107053 CGGGTCAACTGGT
1 CGGGTCAACGGGT
* *
107066 CGGATAAACGGGT
1 CGGGTCAACGGGT
*
107079 CGGGTAAACGGGT
1 CGGGTCAACGGGT
107092 CGGGTC
1 CGGGTC
107098 GGGTCGGGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
13 38 0.75
15 1 0.02
18 12 0.24
ACGTcount: A:0.17, C:0.20, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:107054 original size:18 final size:18
Alignment explanation
Indices: 107016--107068 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
107006 ACGGGTCAAC
107016 GGTCAACGGGTCAATGGGTCG
1 GGTCAACGGGTC---GGGTCG
107037 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
107055 GGTCAACTGGTCGG
1 GGTCAACGGGTCGG
107069 ATAAACGGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 19 0.61
21 12 0.39
ACGTcount: A:0.15, C:0.21, G:0.45, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:107060 original size:31 final size:31
Alignment explanation
Indices: 107022--107083 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
107012 CAACGGTCAA
* *
107022 CGGGTCAA-TGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACT-GGTCGGATAAACGGGTCGGGT
107053 CGGGTCAACTGGTCGGATAAACGGGTCGGGT
1 CGGGTCAACTGGTCGGATAAACGGGTCGGGT
107084 AAACGGGTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.16, C:0.19, G:0.45, T:0.19
Consensus pattern (31 bp):
CGGGTCAACTGGTCGGATAAACGGGTCGGGT
Found at i:110724 original size:18 final size:18
Alignment explanation
Indices: 110701--110735 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
110691 TTCCATCCGG
*
110701 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
110719 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
110736 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:112031 original size:17 final size:15
Alignment explanation
Indices: 112009--112070 Score: 65
Period size: 17 Copynumber: 4.1 Consensus size: 15
111999 TTTTGGTCAA
112009 CAACGGTCAACGCCGGT
1 CAACGGTCAACG--GGT
112026 CAACGGTCAACGGGT
1 CAACGGTCAACGGGT
*
112041 CAACGGGTCAATGGGT
1 CAAC-GGTCAACGGGT
*
112057 C--GGGTCAACGGGT
1 CAACGGTCAACGGGT
112070 C
1 C
112071 GGGTCGGGTC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.27
15 7 0.17
16 11 0.27
17 12 0.29
ACGTcount: A:0.23, C:0.27, G:0.35, T:0.15
Consensus pattern (15 bp):
CAACGGTCAACGGGT
Found at i:112043 original size:8 final size:8
Alignment explanation
Indices: 112009--112070 Score: 62
Period size: 8 Copynumber: 8.1 Consensus size: 8
111999 TTTTGGTCAA
112009 CAAC-GGT
1 CAACGGGT
112016 CAACGCCGGT
1 CAACG--GGT
112026 CAAC-GGT
1 CAACGGGT
112033 CAACGGGT
1 CAACGGGT
112041 CAACGGGT
1 CAACGGGT
*
112049 CAATGGGT
1 CAACGGGT
112057 ---CGGGT
1 CAACGGGT
112062 CAACGGGT
1 CAACGGGT
112070 C
1 C
112071 GGGTCGGGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
5 4 0.09
7 11 0.24
8 24 0.52
10 7 0.15
ACGTcount: A:0.23, C:0.27, G:0.35, T:0.15
Consensus pattern (8 bp):
CAACGGGT
Found at i:112062 original size:13 final size:13
Alignment explanation
Indices: 112030--112119 Score: 63
Period size: 13 Copynumber: 6.3 Consensus size: 13
112020 GCCGGTCAAC
112030 GGTCAACGGGTCAACG
1 GGTCAACGGGT---CG
*
112046 GGTCAATGGGTCG
1 GGTCAACGGGTCG
112059 GGTCAACGGGTCGGGTCG
1 GGTCAAC-----GGGTCG
*
112077 GGTCAACTGGTCG
1 GGTCAACGGGTCG
* *
112090 GATAAACGGGTCG
1 GGTCAACGGGTCG
*
112103 GGTAAACGGGTCG
1 GGTCAACGGGTCG
112116 GGTC
1 GGTC
112120 GGGTCGGTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
13 38 0.62
16 10 0.16
18 13 0.21
ACGTcount: A:0.19, C:0.20, G:0.43, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:112076 original size:18 final size:18
Alignment explanation
Indices: 112036--112090 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
112026 CAACGGTCAA
112036 CGGGTCAACGGGTCAATGGGT
1 CGGGTCAACGGGTC---GGGT
112057 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
112075 CGGGTCAACTGGTCGG
1 CGGGTCAACGGGTCGG
112091 ATAAACGGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 19 0.58
21 14 0.42
ACGTcount: A:0.15, C:0.22, G:0.45, T:0.18
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:112082 original size:31 final size:31
Alignment explanation
Indices: 112044--112105 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
112034 AACGGGTCAA
* *
112044 CGGGTCAA-TGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACT-GGTCGGATAAACGGGTCGGGT
112075 CGGGTCAACTGGTCGGATAAACGGGTCGGGT
1 CGGGTCAACTGGTCGGATAAACGGGTCGGGT
112106 AAACGGGTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.16, C:0.19, G:0.45, T:0.19
Consensus pattern (31 bp):
CGGGTCAACTGGTCGGATAAACGGGTCGGGT
Found at i:113751 original size:24 final size:22
Alignment explanation
Indices: 113711--113786 Score: 74
Period size: 24 Copynumber: 3.6 Consensus size: 22
113701 ATGAAATTAA
113711 TGCATCGATG--CA-TAAGGAG
1 TGCATCGATGCACAGTAAGGAG
113730 TGCATCGATGCACACGTTAAGG-G
1 TGCATCGATGCACA-G-TAAGGAG
*
113753 ATGCATCGATACACAGT-AGGA-
1 -TGCATCGATGCACAGTAAGGAG
113774 TGCATCGATGCAC
1 TGCATCGATGCAC
113787 TTCAAGGGGA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
19 10 0.21
20 12 0.25
21 5 0.10
22 1 0.02
23 2 0.04
24 18 0.38
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (22 bp):
TGCATCGATGCACAGTAAGGAG
Found at i:118600 original size:39 final size:39
Alignment explanation
Indices: 118502--118613 Score: 95
Period size: 39 Copynumber: 2.9 Consensus size: 39
118492 AATATTAAAA
* *
118502 AATGTTGATA-TGAACTAATTTAAGAAATTAAAAATTGAT
1 AATGTT-ATAGTGAAATAATTTAAGAAATTAAAAATTGAG
* * * * * *
118541 AACGTTATGGTGTTAA-AATTTAAGAAATTAAGATTTTAG
1 AATGTTATAGTG-AAATAATTTAAGAAATTAAAAATTGAG
* *
118580 AATGTTATAGTGAAATAATTTGAG-AATTATAAAT
1 AATGTTATAGTGAAATAATTTAAGAAATTAAAAAT
118614 AAAAAAATTA
Statistics
Matches: 55, Mismatches: 15, Indels: 7
0.71 0.19 0.09
Matches are distributed among these distances:
38 11 0.20
39 43 0.78
40 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.38
Consensus pattern (39 bp):
AATGTTATAGTGAAATAATTTAAGAAATTAAAAATTGAG
Found at i:122201 original size:20 final size:20
Alignment explanation
Indices: 122176--122217 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
122166 ACGTCATTAT
122176 AACCACTTAAAATTAACGGA
1 AACCACTTAAAATTAACGGA
122196 AACCACTTAAAATTAACGGA
1 AACCACTTAAAATTAACGGA
122216 AA
1 AA
122218 ATGACTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (20 bp):
AACCACTTAAAATTAACGGA
Found at i:125953 original size:27 final size:23
Alignment explanation
Indices: 125919--125983 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 23
125909 ACATGCAAAG
*
125919 CTCGGCGTCTTCAGCTTTGATGGAGCT
1 CTCGGCGTCTTCAGCTTGGAT--A--T
*
125946 CTCGGCGTCTTCAACTTGGATAT
1 CTCGGCGTCTTCAGCTTGGATAT
125969 CTCGGCGTCTTCAGC
1 CTCGGCGTCTTCAGC
125984 AGATGTGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 15 0.43
25 1 0.03
27 19 0.54
ACGTcount: A:0.12, C:0.29, G:0.26, T:0.32
Consensus pattern (23 bp):
CTCGGCGTCTTCAGCTTGGATAT
Found at i:126149 original size:76 final size:76
Alignment explanation
Indices: 126023--126184 Score: 272
Period size: 76 Copynumber: 2.1 Consensus size: 76
126013 TGTGTCTTCA
126023 ACGTGGGGACCAACTTTGTTATGTTTGGTAGCAGGAAGTTTGCAGCAAAATAA-GAAATTCATGG
1 ACGTGGGGACCAACTTTGTTATGTTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAAA-TCATGG
126087 GAAGAATAATGC
65 GAAGAATAATGC
* * * *
126099 ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCATGATGTTTGCAGGAAAATAAGGAAATCATGGG
1 ACGTGGGGACCAACTTTGTTATGTTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAAATCATGGG
126164 AAGAATAATGC
66 AAGAATAATGC
126175 ACGTGGGGAC
1 ACGTGGGGAC
126185 GGGAATGAGA
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
76 77 0.95
77 4 0.05
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (76 bp):
ACGTGGGGACCAACTTTGTTATGTTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAAATCATGGG
AAGAATAATGC
Found at i:129460 original size:8 final size:7
Alignment explanation
Indices: 129425--129588 Score: 62
Period size: 8 Copynumber: 23.4 Consensus size: 7
129415 ACTCGAGTAT
129425 ATATTTA
1 ATATTTA
*
129432 ATA-ATA
1 ATATTTA
129438 ATTATTTA
1 A-TATTTA
129446 A-ATTTA
1 ATATTTA
129452 ATCATTTA
1 AT-ATTTA
129460 A-ATTTA
1 ATATTTA
129466 ATGATTTA
1 AT-ATTTA
*
129474 ATA-ATA
1 ATATTTA
129480 ATTATTTA
1 A-TATTTA
*
129488 A-CTTTA
1 ATATTTA
*
129494 ATGATTTC
1 AT-ATTTA
*
129502 ATA-ATA
1 ATATTTA
129508 ATTATTTA
1 A-TATTTA
*
129516 A-CTTTA
1 ATATTTA
129522 ATGATTTA
1 AT-ATTTA
*
129530 A-ATTAA
1 ATATTTA
129536 ATACTTTA
1 ATA-TTTA
*
129544 ATA-ATA
1 ATATTTA
129550 ATTATTTA
1 A-TATTTA
*
129558 A-CTTTA
1 ATATTTA
129564 ATGATTTA
1 AT-ATTTA
*
129572 A-ATTAA
1 ATATTTA
129578 ATACTTTA
1 ATA-TTTA
129586 ATA
1 ATA
129589 ATAATTACTT
Statistics
Matches: 115, Mismatches: 20, Indels: 43
0.65 0.11 0.24
Matches are distributed among these distances:
6 48 0.42
7 15 0.13
8 52 0.45
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (7 bp):
ATATTTA
Found at i:129515 original size:42 final size:42
Alignment explanation
Indices: 129436--129698 Score: 300
Period size: 42 Copynumber: 6.3 Consensus size: 42
129426 TATTTAATAA
* * * * *
129436 TAATTATTTAAATTTAATCATTTAA-ATTTAATGATTTAA-TAA
1 TAATGATTTAAATTTAATGATTTAATA-ATAATTATTTAACT-T
* * *
129478 TAATTATTTAACTTTAATGATTTCATAATAATTATTTAACTT
1 TAATGATTTAAATTTAATGATTTAATAATAATTATTTAACTT
*
129520 TAATGATTTAAATTAAAT-ACTTTAATAATAATTATTTAACTT
1 TAATGATTTAAATTTAATGA-TTTAATAATAATTATTTAACTT
* *
129562 TAATGATTTAAATTAAAT-ACTTTAATAATAATTACTTAACTT
1 TAATGATTTAAATTTAATGA-TTTAATAATAATTATTTAACTT
* * *
129604 TAATGATTTAACTTTAATGATTTAATAATAATTACTTCACTT
1 TAATGATTTAAATTTAATGATTTAATAATAATTATTTAACTT
* * * *
129646 GAATAATTTAACTTTAATGATTTATTAATAATTATTTAACTT
1 TAATGATTTAAATTTAATGATTTAATAATAATTATTTAACTT
129688 TAATGATTTAA
1 TAATGATTTAA
129699 TAATAATTAA
Statistics
Matches: 196, Mismatches: 21, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.01
42 192 0.98
43 3 0.02
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (42 bp):
TAATGATTTAAATTTAATGATTTAATAATAATTATTTAACTT
Found at i:129656 original size:70 final size:68
Alignment explanation
Indices: 129604--129765 Score: 225
Period size: 70 Copynumber: 2.3 Consensus size: 68
129594 TACTTAACTT
* *
129604 TAATGATTTAACTTTAATGATTTAATAATAATTACTTCACTTGAATAATTTAACTTTAATGATTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTAATTCACTTGAATAATTTAA--TTAATGAATT
129669 ATTAA
64 ATTAA
* * * *
129674 TAATTATTTAACTTTAATGATTTAATAATAATTAATTCACTTTAATAATTAAACTTTAATGATTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTAATTCACTTGAATAATTTAA--TTAATGAATT
129739 ATTAA
64 ATTAA
*
129744 TAATTATTTAACTTTAATGATT
1 TAATGATTTAACTTTAATGATT
129766 AAAGTTTAAT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 88 1.00
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (68 bp):
TAATGATTTAACTTTAATGATTTAATAATAATTAATTCACTTGAATAATTTAATTAATGAATTAT
TAA
Found at i:129702 original size:28 final size:28
Alignment explanation
Indices: 129450--129719 Score: 214
Period size: 28 Copynumber: 9.6 Consensus size: 28
129440 TATTTAAATT
* *
129450 TAATCATTTAAATTTAATGATTTAATAA
1 TAATTATTTAACTTTAATGATTTAATAA
*
129478 TAATTATTTAACTTTAATGATTTCATAA
1 TAATTATTTAACTTTAATGATTTAATAA
*
129506 TAATTATTTAACTTTAATGATTTAA-AT
1 TAATTATTTAACTTTAATGATTTAATAA
* * * *
129533 TAAATACTTTAA-TAATAATTATTTAACT-T
1 TAATTA-TTTAACT-TTAATGATTTAA-TAA
* * *
129562 TAATGATTTAAATTAAAT-ACTTTAATAA
1 TAATTATTTAACTTTAATGA-TTTAATAA
* *
129590 TAATTACTTAACTTTAATGATTTAACT-T
1 TAATTATTTAACTTTAATGATTTAA-TAA
* * * * *
129618 TAATGATTTAA-TAATAATTACTTCACT--
1 TAATTATTTAACT-TTAATGA-TTTAATAA
* *
129645 TGAATAATTTAACTTTAATGATTTATTAA
1 T-AATTATTTAACTTTAATGATTTAATAA
129674 TAATTATTTAACTTTAATGATTTAATAA
1 TAATTATTTAACTTTAATGATTTAATAA
* *
129702 TAATTAATTCACTTTAAT
1 TAATTATTTAACTTTAAT
129720 AATTAAACTT
Statistics
Matches: 194, Mismatches: 33, Indels: 30
0.75 0.13 0.12
Matches are distributed among these distances:
27 15 0.08
28 166 0.86
29 13 0.07
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (28 bp):
TAATTATTTAACTTTAATGATTTAATAA
Found at i:129729 original size:42 final size:42
Alignment explanation
Indices: 129674--129787 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
129664 GATTTATTAA
* * *
129674 TAATTATTTAACTTTAATGATTTAATAATAATTAATTCACTT
1 TAATAATTAAACTTTAATGATTTAATAATAATTAATTAACTT
* *
129716 TAATAATTAAACTTTAATGATTTATTAATAATTATTTAACTT
1 TAATAATTAAACTTTAATGATTTAATAATAATTAATTAACTT
* * *
129758 TAATGATTAAAGTTTAATAATTTAATAATA
1 TAATAATTAAACTTTAATGATTTAATAATA
129788 GTAATGATAT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (42 bp):
TAATAATTAAACTTTAATGATTTAATAATAATTAATTAACTT
Found at i:129753 original size:84 final size:82
Alignment explanation
Indices: 129503--129792 Score: 204
Period size: 84 Copynumber: 3.5 Consensus size: 82
129493 AATGATTTCA
* *
129503 TAATAATTATTTAACTTTAATGATTTAA-ATTAAATACTTTA-ATAATAATTATTTAACTTTAAT
1 TAATAATTATTTAACTTTAATGATTTAATAAT-AATAATTTATATAATAATTA---AACTTTAAT
* *
129566 GATTTA--AATTAAATACTTTAA
62 GATTTATTAA-TAATTA-TTTAT
* * * * *
129587 TAATAATTACTTAACTTTAATGATTTAACT-TTAATGATTTA-ATAATAATTACTTCACTTGAAT
1 TAATAATTATTTAACTTTAATGATTTAA-TAATAATAATTTATATAATAATTA---AACTTTAAT
* *
129650 AATTTAACTT--TAATGATTTAT
62 GATTT-A-TTAATAATTATTTAT
* *
129671 TAATAATTATTTAACTTTAATGATTTAATAATAATTAATTCACTTTAATAATTAAACTTTAATGA
1 TAATAATTATTTAACTTTAATGATTTAATAATAA-TAATTTA-TATAATAATTAAACTTTAATGA
129736 TTTATTAATAATTATTTAACT
64 TTTATTAATAATTATTT-A-T
* * * * *
129757 T--TAATGATTAAAGTTTAATAATTTAATAATAGTAAT
1 TAATAATTATTTAACTTTAATGATTTAATAATAATAAT
129793 GATATTCGAT
Statistics
Matches: 168, Mismatches: 24, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
82 2 0.01
83 6 0.04
84 136 0.81
85 13 0.08
86 2 0.01
87 9 0.05
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (82 bp):
TAATAATTATTTAACTTTAATGATTTAATAATAATAATTTATATAATAATTAAACTTTAATGATT
TATTAATAATTATTTAT
Found at i:130718 original size:16 final size:16
Alignment explanation
Indices: 130662--130719 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
130652 AAATAATTAT
* *
130662 AAAAATCAACAAAATA
1 AAAAATAAACATAATA
* *
130678 AATAAATAAAAATATTA
1 AA-AAATAAACATAATA
* *
130695 TAATATAAACATAATA
1 AAAAATAAACATAATA
130711 AAAAATAAA
1 AAAAATAAA
130720 TTCGCTTATT
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
16 20 0.65
17 11 0.35
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATAAACATAATA
Found at i:132694 original size:76 final size:76
Alignment explanation
Indices: 132562--132722 Score: 286
Period size: 76 Copynumber: 2.1 Consensus size: 76
132552 CTCATTCCCA
*
132562 TCCCCACGTGCATTATTCTTCCCATGATTTTCTTATTTTCCTGCAAACATCATGCTACCAAACAT
1 TCCCCACGTGCATTATTCTTCCCATGAATTTCTTATTTTCCTGCAAACATCATGCTACCAAACAT
132627 AACAAAGCTGG
66 AACAAAGCTGG
* * *
132638 TCCCCACGTGCATTATTCTTCCCATGAATTTCTTATTTTGCTGCAAACTTCCTGCTACCAAACAT
1 TCCCCACGTGCATTATTCTTCCCATGAATTTCTTATTTTCCTGCAAACATCATGCTACCAAACAT
132703 AACAAAGCTGG
66 AACAAAGCTGG
132714 TCCCCACGT
1 TCCCCACGT
132723 TGAAGACACA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 81 1.00
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.32
Consensus pattern (76 bp):
TCCCCACGTGCATTATTCTTCCCATGAATTTCTTATTTTCCTGCAAACATCATGCTACCAAACAT
AACAAAGCTGG
Found at i:132825 original size:27 final size:23
Alignment explanation
Indices: 132762--132826 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 23
132752 ATGCACATCT
*
132762 GCTGAAGACGCCGAGATATCCAA
1 GCTGAAGACGCCGAGATATCAAA
*
132785 GTTGAAGACGCCGAGAGCTCCATCAAA
1 GCTGAAGACGCCGAGA--T--ATCAAA
132812 GCTGAAGACGCCGAG
1 GCTGAAGACGCCGAG
132827 CTTTGCATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 15 0.43
25 1 0.03
27 19 0.54
ACGTcount: A:0.32, C:0.26, G:0.29, T:0.12
Consensus pattern (23 bp):
GCTGAAGACGCCGAGATATCAAA
Found at i:134552 original size:15 final size:15
Alignment explanation
Indices: 134532--134561 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
134522 TATCACAATC
134532 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
134547 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
134562 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:141018 original size:31 final size:32
Alignment explanation
Indices: 140952--141022 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 32
140942 AAATTCAGGG
* **
140952 ATCAAATT-GATATTTTATCTAAAATTTAAGG
1 ATCAAATTAGATATTTTATCTAAAATTCAAAA
* *
140983 ATCAAATTAG-TATTTTATTTAAAGTTCAAAA
1 ATCAAATTAGATATTTTATCTAAAATTCAAAA
141014 ATCAAATTA
1 ATCAAATTA
141023 AAAATTAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (32 bp):
ATCAAATTAGATATTTTATCTAAAATTCAAAA
Found at i:141146 original size:31 final size:31
Alignment explanation
Indices: 141088--141146 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
141078 GTTCAATAAT
* *
141088 TAAAATTTAACAAATTGATAGAGTAAATGAC
1 TAAAATTTAACAAATCGATAGAATAAATGAC
*
141119 TAAAATTTAATAAATCGATA-ACATAAAT
1 TAAAATTTAACAAATCGATAGA-ATAAAT
141147 AATCAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 23 0.96
ACGTcount: A:0.54, C:0.07, G:0.08, T:0.31
Consensus pattern (31 bp):
TAAAATTTAACAAATCGATAGAATAAATGAC
Found at i:142455 original size:21 final size:21
Alignment explanation
Indices: 142423--142463 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
142413 CGTGTCTTTG
142423 TTCAGTTTTTATTAATGGAATT
1 TTCAGTTTTTA-TAATGGAATT
*
142445 TTCAG-TTTTATCATGGAAT
1 TTCAGTTTTTATAATGGAAT
142464 GTGAGAGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (21 bp):
TTCAGTTTTTATAATGGAATT
Found at i:144229 original size:26 final size:26
Alignment explanation
Indices: 144193--144248 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
144183 GAGTGCCATC
144193 TAAGAGGTTCAAGTCCAAGAGAGGGT
1 TAAGAGGTTCAAGTCCAAGAGAGGGT
144219 TAAGAGGTTCAAGTCCAAGAGAGGGT
1 TAAGAGGTTCAAGTCCAAGAGAGGGT
144245 TAAG
1 TAAG
144249 GCAGGGATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.34, T:0.20
Consensus pattern (26 bp):
TAAGAGGTTCAAGTCCAAGAGAGGGT
Found at i:146475 original size:22 final size:22
Alignment explanation
Indices: 146450--146491 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
146440 GGAGCAAATG
*
146450 CTCTAGCTTGGATTTTTTTCCT
1 CTCTAGCTTGGACTTTTTTCCT
**
146472 CTCTATTTTGGACTTTTTTC
1 CTCTAGCTTGGACTTTTTTC
146492 AGAATCACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.10, C:0.21, G:0.12, T:0.57
Consensus pattern (22 bp):
CTCTAGCTTGGACTTTTTTCCT
Found at i:148543 original size:26 final size:25
Alignment explanation
Indices: 148487--148544 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
148477 TATTTTTATT
148487 TTTTAAAAAACCTAAAATCTTTAAA
1 TTTTAAAAAACCTAAAATCTTTAAA
*
148512 TCTTTAAAAAACCTCAAA-CTTTTAAAA
1 T-TTTAAAAAACCTAAAATC-TTT-AAA
148539 TTTTAA
1 TTTTAA
148545 TTTTAATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 2 0.07
26 23 0.79
27 4 0.14
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (25 bp):
TTTTAAAAAACCTAAAATCTTTAAA
Found at i:151930 original size:13 final size:13
Alignment explanation
Indices: 151912--151936 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
151902 TGTGCCGACG
151912 TTGGAAGGCACGC
1 TTGGAAGGCACGC
151925 TTGGAAGGCACG
1 TTGGAAGGCACG
151937 TTGTTTGAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.40, T:0.16
Consensus pattern (13 bp):
TTGGAAGGCACGC
Done.