Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005376.1 Hibiscus syriacus cultivar Beakdansim tig00012257_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: 106490
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4389 original size:54 final size:54
Alignment explanation
Indices: 4331--4458 Score: 202
Period size: 54 Copynumber: 2.4 Consensus size: 54
4321 GTTGATTTTG
* * *
4331 TTCTAGAAATTTGGTTTCCAGTAATGGTGCCACTAGATGCCGAGTTTGAATCCC
1 TTCTAGAAATTTGGTTTCCAGAAATGATGACACTAGATGCCGAGTTTGAATCCC
* * *
4385 TTCTAGAAATTTGATTTCCAGAAATGATGACACTAGTTGCCGAGTTTGATTCCC
1 TTCTAGAAATTTGGTTTCCAGAAATGATGACACTAGATGCCGAGTTTGAATCCC
4439 TTCTAGAAATTTGGTTTCCA
1 TTCTAGAAATTTGGTTTCCA
4459 ATTATGATCC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (54 bp):
TTCTAGAAATTTGGTTTCCAGAAATGATGACACTAGATGCCGAGTTTGAATCCC
Found at i:5127 original size:14 final size:14
Alignment explanation
Indices: 5108--5136 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5098 TCATCACCTG
5108 ACAATGTAAGAAGA
1 ACAATGTAAGAAGA
5122 ACAATGTAAGAAGA
1 ACAATGTAAGAAGA
5136 A
1 A
5137 ACTAATCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
ACAATGTAAGAAGA
Found at i:15519 original size:2 final size:2
Alignment explanation
Indices: 15514--15575 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
15504 AAATATATGC
15514 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15556 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
15576 TTGGGAATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20756 original size:19 final size:19
Alignment explanation
Indices: 20729--20766 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20719 TAATTAGTAG
20729 TTAACTTTAATGATTTAAT
1 TTAACTTTAATGATTTAAT
* *
20748 TTAATTTTAATTATTTAAT
1 TTAACTTTAATGATTTAAT
20767 AATAATGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (19 bp):
TTAACTTTAATGATTTAAT
Found at i:20760 original size:36 final size:31
Alignment explanation
Indices: 20672--20747 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
20662 AATGATAAAA
* * *
20672 TTTAATGATTTGATACTAATTATTAGTTAAC
1 TTTAATGATTTAATAATAATTAGTAGTTAAC
20703 TTTAATGATTTAATAATAATTAGTAGTTAAC
1 TTTAATGATTTAATAATAATTAGTAGTTAAC
20734 TTTAATGATTTAAT
1 TTTAATGATTTAAT
20748 TTAATTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (31 bp):
TTTAATGATTTAATAATAATTAGTAGTTAAC
Found at i:20763 original size:14 final size:14
Alignment explanation
Indices: 20755--20786 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
20745 AATTTAATTT
*
20755 TAATTATTTAATAA
1 TAATGATTTAATAA
20769 TAATGATTTAATAA
1 TAATGATTTAATAA
20783 TAAT
1 TAAT
20787 AATGATATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:21907 original size:24 final size:27
Alignment explanation
Indices: 21879--21932 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
21869 TTGCATGATA
21879 CAGACGTGCA-GACC-C-CCCCACATG
1 CAGACGTGCAGGACCTCTCCCCACATG
*
21903 CAGACGTGCAGGCCCTCTCCCCACATG
1 CAGACGTGCAGGACCTCTCCCCACATG
21930 CAG
1 CAG
21933 CGTTCCGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 10 0.38
25 3 0.12
26 1 0.04
27 12 0.46
ACGTcount: A:0.22, C:0.44, G:0.22, T:0.11
Consensus pattern (27 bp):
CAGACGTGCAGGACCTCTCCCCACATG
Found at i:21996 original size:59 final size:59
Alignment explanation
Indices: 21926--22044 Score: 193
Period size: 59 Copynumber: 2.0 Consensus size: 59
21916 CCTCTCCCCA
* *
21926 CATGCAGCGTTCCGTGCTCACCCTGGGACATGCAACATCATCTCCCTGTTCAACCCGTG
1 CATGCAGCGTTCCATGCTCACCCTGGGACATGCAACAACATCTCCCTGTTCAACCCGTG
* * *
21985 CATGCAGCGTTCTATGCTCACCCTGTGACATGCAACAACATCTCCCTGTTCAACTCGTG
1 CATGCAGCGTTCCATGCTCACCCTGGGACATGCAACAACATCTCCCTGTTCAACCCGTG
22044 C
1 C
22045 TCTCTGTGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.20, C:0.36, G:0.18, T:0.25
Consensus pattern (59 bp):
CATGCAGCGTTCCATGCTCACCCTGGGACATGCAACAACATCTCCCTGTTCAACCCGTG
Found at i:22800 original size:30 final size:30
Alignment explanation
Indices: 22766--22889 Score: 90
Period size: 30 Copynumber: 4.1 Consensus size: 30
22756 AGTAACTATT
*
22766 TTGTATTAATTTAATAAGATCTAATAATTA
1 TTGTATTAAATTAATAAGATCTAATAATTA
** ** *
22796 TTGTACCAAAAAAAAAAGATCTAATAATTA
1 TTGTATTAAATTAATAAGATCTAATAATTA
** **
22826 TTGTACCAAAAAAAAATAAGATCTAATAATTA
1 TTGTA--TTAAATTAATAAGATCTAATAATTA
* *
22858 TTTTATAATAACTTAAT-AGAT-TAATAATTA
1 TTGTAT--TAAATTAATAAGATCTAATAATTA
22888 TT
1 TT
22890 TTATAATTTT
Statistics
Matches: 75, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
30 40 0.53
31 4 0.05
32 31 0.41
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (30 bp):
TTGTATTAAATTAATAAGATCTAATAATTA
Found at i:22836 original size:27 final size:28
Alignment explanation
Indices: 22781--22859 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 28
22771 TTAATTTAAT
22781 AAGATCTAATAATTATTGTACCAAAAAAAA
1 AAGATCTAATAATTATTGTACC--AAAAAA
22811 AAGATCTAATAATTATTGTACCAAAAAAAAA
1 AAGATCTAATAATTATTGTACC---AAAAAA
22842 TAAGATCTAATAATTATT
1 -AAGATCTAATAATTATT
22860 TTATAATAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 22 0.47
31 8 0.17
32 17 0.36
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.30
Consensus pattern (28 bp):
AAGATCTAATAATTATTGTACCAAAAAA
Found at i:25383 original size:2 final size:2
Alignment explanation
Indices: 25376--25408 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
25366 CAAATACTCC
25376 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 A
25409 GATTCTATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27721 original size:20 final size:20
Alignment explanation
Indices: 27644--27855 Score: 108
Period size: 20 Copynumber: 10.6 Consensus size: 20
27634 AATAACTAAT
* *
27644 AAATTCGCAACACGA-TCTC
1 AAATTCGCAACGCGATTTTC
* *
27663 AAATTTCGCAACAC-AGTTTTT
1 AAA-TTCGCAACGCGA-TTTTC
* * * * *
27684 AAATTTGTAACTCAATTTTG
1 AAATTCGCAACGCGATTTTC
27704 AAATTCGCAACGCGATTTTC
1 AAATTCGCAACGCGATTTTC
* *
27724 TAAATTTGCAATGCGATTTTC
1 -AAATTCGCAACGCGATTTTC
* ** *
27745 AAATTCGCAACACGAACTCC
1 AAATTCGCAACGCGATTTTC
* * * *
27765 AATTTTGCAACAC-AGTTTCC
1 AAATTCGCAACGCGA-TTTTC
*
27785 AAATTCGCAACTCGA-TTTC
1 AAATTCGCAACGCGATTTTC
* *
27804 TGAATTCGCAACGCGAATTTC
1 -AAATTCGCAACGCGATTTTC
*** * *
27825 TTTTTAGCAACGCGATTTTT
1 AAATTCGCAACGCGATTTTC
27845 AAATTCGCAAC
1 AAATTCGCAAC
27856 ATAAGTTTCC
Statistics
Matches: 145, Mismatches: 39, Indels: 17
0.72 0.19 0.08
Matches are distributed among these distances:
19 8 0.06
20 108 0.74
21 29 0.20
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (20 bp):
AAATTCGCAACGCGATTTTC
Found at i:27819 original size:101 final size:100
Alignment explanation
Indices: 27644--27856 Score: 277
Period size: 101 Copynumber: 2.1 Consensus size: 100
27634 AATAACTAAT
* ** * *
27644 AAATTCGCAACACGATCTCAAATTTCGCAACACAGTTTTTAAATTTGTAACTCAATTTTGAAATT
1 AAATTCGCAACACGAACTCAAATTTCGCAACACAGTTTCCAAATTCGCAACTCAATTTTGAAATT
* *
27709 CGCAACGCGATTTTCTAAATTT-GCAATGCGATTTTC
66 CGCAACGCGAATTTCT--ATTTAGCAACGCGATTTTC
* * *
27745 AAATTCGCAACACGAACTCCAATTTTGCAACACAGTTTCCAAATTCGCAACTCGATTTCTG-AAT
1 AAATTCGCAACACGAACTCAAATTTCGCAACACAGTTTCCAAATTCGCAACTCAATTT-TGAAAT
* *
27809 TCGCAACGCGAATTTCTTTTTAGCAACGCGATTTTT
65 TCGCAACGCGAATTTCTATTTAGCAACGCGATTTTC
27845 AAATTCGCAACA
1 AAATTCGCAACA
27857 TAAGTTTCCT
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
99 3 0.03
100 24 0.24
101 69 0.70
102 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (100 bp):
AAATTCGCAACACGAACTCAAATTTCGCAACACAGTTTCCAAATTCGCAACTCAATTTTGAAATT
CGCAACGCGAATTTCTATTTAGCAACGCGATTTTC
Found at i:27835 original size:40 final size:40
Alignment explanation
Indices: 27788--27943 Score: 138
Period size: 40 Copynumber: 3.9 Consensus size: 40
27778 AGTTTCCAAA
*
27788 TTCGCAACTCGATTTCTGAATTCGCAACGCGAATTTCTTT
1 TTCGCAACTCGATTTCTGAATTCGCAACACGAATTTCTTT
* * * * * *
27828 TTAGCAACGCGATTTTTAAATTCGCAACA-TAAGTTTCCTT
1 TTCGCAACTCGATTTCTGAATTCGCAACACGAA-TTTCTTT
* ** *
27868 TTCGCGACAAGATTTTCT-AATTCGCAACACAAATTT-TATT
1 TTCGCAACTCGA-TTTCTGAATTCGCAACACGAATTTCT-TT
* * *
27908 TTCGCAACTCTATTTCCGAACTCGCAACACGAATTT
1 TTCGCAACTCGATTTCTGAATTCGCAACACGAATTT
27944 TAATTTCGCA
Statistics
Matches: 90, Mismatches: 21, Indels: 10
0.74 0.17 0.08
Matches are distributed among these distances:
39 6 0.07
40 78 0.87
41 6 0.07
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (40 bp):
TTCGCAACTCGATTTCTGAATTCGCAACACGAATTTCTTT
Found at i:27911 original size:20 final size:20
Alignment explanation
Indices: 27888--27979 Score: 57
Period size: 20 Copynumber: 4.7 Consensus size: 20
27878 GATTTTCTAA
27888 TTCGCAACACAAATTTTATT
1 TTCGCAACACAAATTTTATT
* * * *
27908 TTCGCAACTC-TATTTCCGA-A
1 TTCGCAACACAAATTT--TATT
* * *
27928 CTCGCAACACGAATTTTAAT
1 TTCGCAACACAAATTTTATT
*
27948 TTCGC-A-ACAACTTTTATT
1 TTCGCAACACAAATTTTATT
*
27966 TTTGCAACACAAAT
1 TTCGCAACACAAAT
27980 GTTTTGCGTA
Statistics
Matches: 51, Mismatches: 15, Indels: 12
0.65 0.19 0.15
Matches are distributed among these distances:
18 13 0.25
19 7 0.14
20 26 0.51
21 5 0.10
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.36
Consensus pattern (20 bp):
TTCGCAACACAAATTTTATT
Found at i:28902 original size:24 final size:24
Alignment explanation
Indices: 28884--28930 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
28874 AGTCAGTATT
28884 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
* *
28908 CGGACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
28931 TCGGATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:28935 original size:24 final size:24
Alignment explanation
Indices: 28889--28935 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
28879 GTATTCGAAA
28889 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
*
28913 TTTGATCTTGGTCAATACTCGGA
1 TTTGATCTTGGTCAATACCCGGA
28936 TTTTAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:31509 original size:20 final size:20
Alignment explanation
Indices: 31486--31540 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
31476 AAATCGCAAC
31486 GCGAATTTGATTTTCGCGTT
1 GCGAATTTGATTTTCGCGTT
* *
31506 GCGAATTTGATTCTCTCGTT
1 GCGAATTTGATTTTCGCGTT
*
31526 GTGAATTTGATTTTC
1 GCGAATTTGATTTTC
31541 TTAAAGGTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.16, C:0.15, G:0.22, T:0.47
Consensus pattern (20 bp):
GCGAATTTGATTTTCGCGTT
Found at i:33061 original size:21 final size:21
Alignment explanation
Indices: 33035--33188 Score: 91
Period size: 21 Copynumber: 7.3 Consensus size: 21
33025 AGTATGCCAT
*
33035 GTGGATCCTGAACGGTGGGAG
1 GTGGATCCTGAACGATGGGAG
33056 GTGGATCCTGAACGATGGGAG
1 GTGGATCCTGAACGATGGGAG
* * *
33077 G-GGCCTCTTGAACGATGAGAG
1 GTGG-ATCCTGAACGATGGGAG
*
33098 G-GG-TCTCTTGAACAATGGGAG
1 GTGGATC-C-TGAACGATGGGAG
* * * **
33119 G-GGCCTCTTTAACGATGACAG
1 GTGG-ATCCTGAACGATGGGAG
* * ** *
33140 GTGAATCTTGAATAATGAGAG
1 GTGGATCCTGAACGATGGGAG
* *
33161 GTGGATCCTGAACAATGGTAG
1 GTGGATCCTGAACGATGGGAG
33182 GTGGATC
1 GTGGATC
33189 AAGCTTCTTC
Statistics
Matches: 104, Mismatches: 23, Indels: 12
0.75 0.17 0.09
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 97 0.93
22 1 0.01
23 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.37, T:0.23
Consensus pattern (21 bp):
GTGGATCCTGAACGATGGGAG
Found at i:33149 original size:42 final size:42
Alignment explanation
Indices: 33054--33161 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 42
33044 GAACGGTGGG
* * * *
33054 AGGTGGATCCTGAACGATGGGAGGGGCCTCTTGAACGATGAG
1 AGGTGAATCTTGAACAATGGGAGGGGCCTCTTGAACGATGAC
* ** *
33096 AGGGGTCTCTTGAACAATGGGAGGGGCCTCTTTAACGATGAC
1 AGGTGAATCTTGAACAATGGGAGGGGCCTCTTGAACGATGAC
* *
33138 AGGTGAATCTTGAATAATGAGAGG
1 AGGTGAATCTTGAACAATGGGAGG
33162 TGGATCCTGA
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (42 bp):
AGGTGAATCTTGAACAATGGGAGGGGCCTCTTGAACGATGAC
Found at i:33343 original size:4 final size:4
Alignment explanation
Indices: 33322--33355 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
33312 GGACTGCTAA
* *
33322 AAAT AAAT TAAT ACAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
33356 TACCGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:33569 original size:42 final size:43
Alignment explanation
Indices: 33476--33573 Score: 105
Period size: 42 Copynumber: 2.3 Consensus size: 43
33466 CGCATAACAG
*
33476 CTACCTCATCACATAAAGCAGATACCTCACAACGTAAAGCACC
1 CTACCTCATCACGTAAAGCAGATACCTCACAACGTAAAGCACC
* ** *
33519 AT-TGTCATCACGTAACA-CA-ACTACCTCACCACGTAAAG-ACC
1 CTACCTCATCACGTAA-AGCAGA-TACCTCACAACGTAAAGCACC
33560 CTACCTCATCACGT
1 CTACCTCATCACGT
33574 CATACATCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
41 5 0.11
42 37 0.84
43 2 0.05
ACGTcount: A:0.36, C:0.36, G:0.09, T:0.19
Consensus pattern (43 bp):
CTACCTCATCACGTAAAGCAGATACCTCACAACGTAAAGCACC
Found at i:33585 original size:63 final size:63
Alignment explanation
Indices: 33518--33636 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 63
33508 CGTAAAGCAC
*
33518 CATTGTCATCACGTAACACAA-CTACCTCACCACGTAAAG-ACCCT-ACCTCATCACGTCATACA
1 CATTGTCATCACGTAA-ACAACCGACCTCACCACGTAAAGTA--CTAACCTCATCACGTCATACA
33580 T
63 T
* * * *
33581 CATTGTCGTCATGTAAAGAACCGACCTCATCACGTAAAGTACTAACCTCATCACGT
1 CATTGTCATCACGTAAACAACCGACCTCACCACGTAAAGTACTAACCTCATCACGT
33637 AACTCCCCTA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
62 5 0.10
63 42 0.88
64 1 0.02
ACGTcount: A:0.33, C:0.33, G:0.11, T:0.24
Consensus pattern (63 bp):
CATTGTCATCACGTAAACAACCGACCTCACCACGTAAAGTACTAACCTCATCACGTCATACAT
Found at i:33617 original size:21 final size:21
Alignment explanation
Indices: 33593--33638 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
33583 TTGTCGTCAT
*
33593 GTAAAGAACCGACCTCATCAC
1 GTAAAGAACCAACCTCATCAC
* *
33614 GTAAAGTACTAACCTCATCAC
1 GTAAAGAACCAACCTCATCAC
33635 GTAA
1 GTAA
33639 CTCCCCTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.28, G:0.13, T:0.20
Consensus pattern (21 bp):
GTAAAGAACCAACCTCATCAC
Found at i:33809 original size:18 final size:18
Alignment explanation
Indices: 33788--33827 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
33778 GTAGAATCGG
*
33788 CTCGATCAGGTGATGGCT
1 CTCGATCAGGTGATGGAT
*
33806 CTCGATTAGGTGATGGAT
1 CTCGATCAGGTGATGGAT
33824 CTCG
1 CTCG
33828 GTGTCGAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (18 bp):
CTCGATCAGGTGATGGAT
Found at i:35684 original size:24 final size:23
Alignment explanation
Indices: 35656--35726 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 23
35646 CATCGATGCA
35656 TAAGGAGTGCATCGATGCACATGT
1 TAAGGAGTGCATCGATGCAC-TGT
*
35680 TAAGG-GATGCATCGATACACTG-
1 TAAGGAG-TGCATCGATGCACTGT
*
35702 T-A-GAATGCATCGATGCACT-T
1 TAAGGAGTGCATCGATGCACTGT
35722 TAAGG
1 TAAGG
35727 GGAAATTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
20 15 0.38
21 2 0.05
22 2 0.05
23 3 0.08
24 17 0.44
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (23 bp):
TAAGGAGTGCATCGATGCACTGT
Found at i:37264 original size:12 final size:12
Alignment explanation
Indices: 37249--37286 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
37239 GTTATTTAAA
37249 CGGGTATTGGGC
1 CGGGTATTGGGC
*
37261 CGGGTATTGGGT
1 CGGGTATTGGGC
37273 CGGGTATTGGGC
1 CGGGTATTGGGC
37285 CG
1 CG
37287 AGAATCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.16, G:0.50, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:37276 original size:24 final size:24
Alignment explanation
Indices: 37249--37303 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
37239 GTTATTTAAA
* * *
37249 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
37273 CGGGTATTGGGCCGAGAATCGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
37297 CGGGTAT
1 CGGGTAT
37304 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (24 bp):
CGGGTATTGGGCCGAGAATCGGGT
Found at i:37431 original size:13 final size:13
Alignment explanation
Indices: 37401--37449 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
37391 TTTAATATTT
*
37401 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
37413 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
37426 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
37439 ATCGGGGCGGG
1 ATCGGGGCGGG
37450 GATTACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
12 11 0.31
13 24 0.69
ACGTcount: A:0.12, C:0.16, G:0.55, T:0.16
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:37449 original size:26 final size:25
Alignment explanation
Indices: 37401--37449 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
37391 TTTAATATTT
*
37401 ATCGGGTCGGGTATCGGGGCGGGTA
1 ATCGGGGCGGGTATCGGGGCGGGTA
37426 ATCGGGGCGGGTAATCGGGGCGGG
1 ATCGGGGCGGGT-ATCGGGGCGGG
37450 GATTACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.12, C:0.16, G:0.55, T:0.16
Consensus pattern (25 bp):
ATCGGGGCGGGTATCGGGGCGGGTA
Found at i:37511 original size:6 final size:6
Alignment explanation
Indices: 37500--37524 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
37490 AAATGGGTTT
37500 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
37525 TTATCATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:37867 original size:23 final size:23
Alignment explanation
Indices: 37803--37859 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
37793 TTTATATGGA
*
37803 ACTTCGGTGCAATTCTACGTGGC
1 ACTTAGGTGCAATTCTACGTGGC
*
37826 ACTTTGGTGCAATTCTACGTGGC
1 ACTTAGGTGCAATTCTACGTGGC
37849 ACTTAGGTGCA
1 ACTTAGGTGCA
37860 TTTATACGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (23 bp):
ACTTAGGTGCAATTCTACGTGGC
Found at i:39277 original size:20 final size:20
Alignment explanation
Indices: 39227--39277 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
39217 AATTCGCAAC
*
39227 ATGAAAATCGCAACTCGAAA
1 ATGAAAATCGCAACGCGAAA
*
39247 ATGAAATTCGCAACGCGCAAA
1 ATGAAAATCGCAACGCG-AAA
*
39268 CT-AAAATCGC
1 ATGAAAATCGC
39278 GTTGCGAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.16
Consensus pattern (20 bp):
ATGAAAATCGCAACGCGAAA
Found at i:39327 original size:20 final size:20
Alignment explanation
Indices: 39304--39342 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39294 TTGCGTTGCG
39304 ATTTTCGTGTTACGAATTTC
1 ATTTTCGTGTTACGAATTTC
*
39324 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTACGAATTT
39343 AAGTTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (20 bp):
ATTTTCGTGTTACGAATTTC
Found at i:39349 original size:20 final size:20
Alignment explanation
Indices: 39306--39349 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
39296 GCGTTGCGAT
* *
39306 TTTCGTGTTACGAATTTCAT
1 TTTCGTGTTACGAATTTAAG
*
39326 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTACGAATTTAAG
39346 TTTC
1 TTTC
39350 AAAAACTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (20 bp):
TTTCGTGTTACGAATTTAAG
Found at i:40073 original size:20 final size:20
Alignment explanation
Indices: 40048--40088 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40038 GGCTCTGAGA
*
40048 GATGGAGATGAAGGGGGGTC
1 GATGGAGATGAAGGGAGGTC
*
40068 GATGGAGATGGAGGGAGGTC
1 GATGGAGATGAAGGGAGGTC
40088 G
1 G
40089 CCGGGATGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.56, T:0.15
Consensus pattern (20 bp):
GATGGAGATGAAGGGAGGTC
Found at i:40292 original size:20 final size:20
Alignment explanation
Indices: 40242--40308 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
40232 TAAATGCGCT
* *
40242 TTGCGAATTTAACTTCTGTG
1 TTGCGAATTTGACATCTGTG
* *
40262 TTACGAATTTGACCTCTGTG
1 TTGCGAATTTGACATCTGTG
40282 TTGCGAATTTGGA-ATCTGTG
1 TTGCGAATTT-GACATCTGTG
40302 TTGCGAA
1 TTGCGAA
40309 ATTGGAGTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (20 bp):
TTGCGAATTTGACATCTGTG
Found at i:40313 original size:20 final size:20
Alignment explanation
Indices: 40276--40314 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40266 GAATTTGACC
*
40276 TCTGTGTTGCGAATTTGGAA
1 TCTGTGTTGCGAAATTGGAA
40296 TCTGTGTTGCGAAATTGGA
1 TCTGTGTTGCGAAATTGGA
40315 GTTCATGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.10, G:0.31, T:0.38
Consensus pattern (20 bp):
TCTGTGTTGCGAAATTGGAA
Found at i:40591 original size:18 final size:18
Alignment explanation
Indices: 40565--40602 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40555 ATAGATGTTA
40565 TATTATAATTATTTAA-AT
1 TATTATAA-TATTTAAGAT
*
40583 TATTTTAATATTTAAGAT
1 TATTATAATATTTAAGAT
40601 TA
1 TA
40603 GAAGTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TATTATAATATTTAAGAT
Found at i:42185 original size:25 final size:25
Alignment explanation
Indices: 42157--42206 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
42147 TTAAAAAAAT
** *
42157 CTGACCCGTGGAATTGGGATACAGA
1 CTGACCCGTCAAATTCGGATACAGA
42182 CTGACCCGTCAAATTCGGATACAGA
1 CTGACCCGTCAAATTCGGATACAGA
42207 AGTATTGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (25 bp):
CTGACCCGTCAAATTCGGATACAGA
Found at i:48476 original size:180 final size:179
Alignment explanation
Indices: 48174--48544 Score: 697
Period size: 180 Copynumber: 2.1 Consensus size: 179
48164 TAGAATTTTG
48174 AAATTTTGTGTGCAGAAAGTCTTCAATGGCTCCAAACCTTCCCAAACGGCTAAAAACGACTAGTA
1 AAATTTTGTGTGCAGAAAGTCTTCAATGGCTCCAAACCTTCCCAAACGGCTAAAAACGACTAGTA
* *
48239 ACTCATTCTAACATATAAAAACAAGTTGAGGACACTTGAAGAAACAGACCAACACCTATCCAAGC
66 ACTCATTCCAACATATAAAAACAAGTTGAGGACACTTGAAGAAACAAACCAACACCTATCCAAGC
48304 AATTAAATACAAGAAAAAAACTTTTATTCTTTATTTCTTTTTCTCTTGT
131 AATTAAATACAAGAAAAAAACTTTTATTCTTTATTTCTTTTTCTCTTGT
48353 AAAATTTTGTGTGCAGAAAGTCTTCAATGGCTCCAAACCTTCCCAAACGGCTAAAAACGACTAGT
1 -AAATTTTGTGTGCAGAAAGTCTTCAATGGCTCCAAACCTTCCCAAACGGCTAAAAACGACTAGT
*
48418 AACTCATTCCAATATATAAAAACAAGTTGAGGACACTTGAAGAAACAAACCAACACCTATCCAAG
65 AACTCATTCCAACATATAAAAACAAGTTGAGGACACTTGAAGAAACAAACCAACACCTATCCAAG
48483 CAATTAAATACAAGAAAAAAACTTTTATTCTTTATTTCTTTTTCTCTTGT
130 CAATTAAATACAAGAAAAAAACTTTTATTCTTTATTTCTTTTTCTCTTGT
48533 AAATATTTGTGT
1 AAAT-TTTGTGT
48545 TTTTGTGAGC
Statistics
Matches: 187, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
179 4 0.02
180 183 0.98
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.30
Consensus pattern (179 bp):
AAATTTTGTGTGCAGAAAGTCTTCAATGGCTCCAAACCTTCCCAAACGGCTAAAAACGACTAGTA
ACTCATTCCAACATATAAAAACAAGTTGAGGACACTTGAAGAAACAAACCAACACCTATCCAAGC
AATTAAATACAAGAAAAAAACTTTTATTCTTTATTTCTTTTTCTCTTGT
Found at i:50600 original size:40 final size:38
Alignment explanation
Indices: 50542--50617 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 38
50532 AAGTTCGTTT
* * *
50542 ATTTTCGTTTATTTATTAAATGAATGAACATGAACAGG
1 ATTTTCGTTCATTTATTAAATGAACGAACACGAACAGG
50580 ATTTTACGTTCATTTAATTAAATGAACGAACACGAACA
1 ATTTT-CGTTCATTT-ATTAAATGAACGAACACGAACA
50618 AATGGCTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 5 0.15
39 8 0.24
40 20 0.61
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (38 bp):
ATTTTCGTTCATTTATTAAATGAACGAACACGAACAGG
Found at i:50682 original size:14 final size:14
Alignment explanation
Indices: 50659--50691 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
50649 CGCTTGATTA
*
50659 TATGTTCGTTCATT
1 TATGTCCGTTCATT
50673 TATGTCCGTTCATT
1 TATGTCCGTTCATT
50687 TATGT
1 TATGT
50692 TCGAACAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (14 bp):
TATGTCCGTTCATT
Found at i:51206 original size:10 final size:10
Alignment explanation
Indices: 51191--51220 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
51181 TGTGTTGTTC
*
51191 GTTCGTTTGT
1 GTTCGTTTAT
51201 GTTCGTTTAT
1 GTTCGTTTAT
51211 GTTCGTTTAT
1 GTTCGTTTAT
51221 CATTTAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.10, G:0.23, T:0.60
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:51590 original size:33 final size:33
Alignment explanation
Indices: 51553--51615 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
51543 TTAAAAAAAT
51553 TTATCCGACTCATATAAATATATACAAAAATTC
1 TTATCCGACTCATATAAATATATACAAAAATTC
* *
51586 TTATCCGGCTCATATAAATGTATACAAAAA
1 TTATCCGACTCATATAAATATATACAAAAA
51616 ATTTTATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.32
Consensus pattern (33 bp):
TTATCCGACTCATATAAATATATACAAAAATTC
Found at i:59197 original size:29 final size:31
Alignment explanation
Indices: 59153--59216 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
59143 CTATTTTGAC
*
59153 TATTTATTATGTATGTGTTTGATTCAAGTTT
1 TATTTATTATGTATGTGTTAGATTCAAGTTT
*
59184 TATTT-TTA-GTATGTGTTAGATTCACGTTT
1 TATTTATTATGTATGTGTTAGATTCAAGTTT
59213 TATT
1 TATT
59217 AAGTTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 23 0.74
30 3 0.10
31 5 0.16
ACGTcount: A:0.22, C:0.05, G:0.16, T:0.58
Consensus pattern (31 bp):
TATTTATTATGTATGTGTTAGATTCAAGTTT
Found at i:61528 original size:21 final size:21
Alignment explanation
Indices: 61503--61654 Score: 68
Period size: 21 Copynumber: 7.3 Consensus size: 21
61493 TAGATTCGCA
61503 TTGCGATTTATTCCAAATTCG
1 TTGCGATTTATTCCAAATTCG
** * *
61524 TTGCGA--TAGGCGAAGTTCGCG
1 TTGCGATTTATTCCAAATT--CG
61545 TTGCGATTTATTCC-AATTCG
1 TTGCGATTTATTCCAAATTCG
** * *
61565 TTGCGA--TAGGCGAAGTTTGCG
1 TTGCGATTTATTCCAA-ATT-CG
*
61586 TTGCAATTTATTCC-AATTCG
1 TTGCGATTTATTCCAAATTCG
** * *
61606 TTGCGA--TAGGCGAAGTTCGCG
1 TTGCGATTTATTCCAAATT--CG
*
61627 TTGCGATTCATTCCAAATTCG
1 TTGCGATTTATTCCAAATTCG
61648 TTGCGAT
1 TTGCGAT
61655 AGGCGAAGTT
Statistics
Matches: 90, Mismatches: 27, Indels: 28
0.62 0.19 0.19
Matches are distributed among these distances:
18 6 0.07
19 11 0.12
20 17 0.19
21 40 0.44
22 4 0.04
23 12 0.13
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
TTGCGATTTATTCCAAATTCG
Found at i:61575 original size:41 final size:42
Alignment explanation
Indices: 61497--61675 Score: 308
Period size: 41 Copynumber: 4.3 Consensus size: 42
61487 AGTTTCTAGA
*
61497 TTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGGCGAAG
1 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGGCGAAG
61539 TTCGCGTTGCGATTTATTCC-AATTCGTTGCGATAGGCGAAG
1 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGGCGAAG
* *
61580 TTTGCGTTGCAATTTATTCC-AATTCGTTGCGATAGGCGAAG
1 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGGCGAAG
*
61621 TTCGCGTTGCGATTCATTCCAAATTCGTTGCGATAGGCGAAG
1 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGGCGAAG
61663 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
61676 AGTTCAAATA
Statistics
Matches: 130, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
41 77 0.59
42 53 0.41
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.34
Consensus pattern (42 bp):
TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGGCGAAG
Found at i:61670 original size:21 final size:20
Alignment explanation
Indices: 61522--61677 Score: 88
Period size: 21 Copynumber: 7.5 Consensus size: 20
61512 ATTCCAAATT
61522 CGTTGCGATAGGCGAAGTTCG
1 CGTTGCGATAGGCGAAGTT-G
** *
61543 CGTTGCGATTTATTCCAA-TT-
1 CGTTGCGA--TAGGCGAAGTTG
61563 CGTTGCGATAGGCGAAGTTTG
1 CGTTGCGATAGGCGAAG-TTG
* ** *
61584 CGTTGCAATTTATTCCAA-TT-
1 CGTTGCGA--TAGGCGAAGTTG
61604 CGTTGCGATAGGCGAAGTTCG
1 CGTTGCGATAGGCGAAGTT-G
** * *
61625 CGTTGCGATTCATTCCAAATT-
1 CGTTGCGA-T-AGGCGAAGTTG
61646 CGTTGCGATAGGCGAAGTTCG
1 CGTTGCGATAGGCGAAGTT-G
61667 CGTTGCGATAG
1 CGTTGCGATAG
61678 TTCAAATATT
Statistics
Matches: 99, Mismatches: 22, Indels: 28
0.66 0.15 0.19
Matches are distributed among these distances:
18 10 0.10
19 8 0.08
20 18 0.18
21 44 0.44
22 3 0.03
23 16 0.16
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGGCGAAGTTG
Found at i:61815 original size:5 final size:6
Alignment explanation
Indices: 61755--61813 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
61745 GACACTTATT
61755 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
61801 ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACC
61814 CGGGACGGGA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.38
6 33 0.62
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:62654 original size:41 final size:41
Alignment explanation
Indices: 62585--62760 Score: 307
Period size: 41 Copynumber: 4.3 Consensus size: 41
62575 AATATTTGGA
62585 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGC
* *
62627 CTATCGCAACGAATTGGAATGAATCGCAATGCGAACTTCGT
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
*
62668 CTATCGCAACGAATTGGAATGAATCGCAACGCAAACTTCGC
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
*
62709 CTATCGCAACGAATTGGAATGAATCGCAATGCGAACTTCGC
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
62750 CTATCGCAACG
1 CTATCGCAACG
62761 CGAACTTCGC
Statistics
Matches: 127, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
41 114 0.90
42 13 0.10
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (41 bp):
CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
Found at i:62759 original size:62 final size:62
Alignment explanation
Indices: 62585--62822 Score: 231
Period size: 62 Copynumber: 3.8 Consensus size: 62
62575 AATATTTGGA
* * *
62585 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACG--AA-TTGGA
1 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGCAAACTTCGC
* * ** * *
62645 ATGAATCGCAATGCGAACTTCG--TCTATCGCAA--CGAA-TTGGAATGAATCGCAACGCAAACT
1 CT--ATCGCAA--CGAA-TTGGAATGAATCGCAACGCGAACTTCGACT--ATCGCAACGCAAACT
62705 TCGC
59 TCGC
* * *
62709 CTATCGCAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGCAAACTTCGC
*
62771 CTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACG
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACG
62823 AATTTGGAAT
Statistics
Matches: 143, Mismatches: 21, Indels: 26
0.75 0.11 0.14
Matches are distributed among these distances:
59 7 0.05
60 9 0.06
61 17 0.12
62 89 0.62
63 6 0.04
64 15 0.10
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (62 bp):
CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGCAAACTTCGC
Found at i:62766 original size:103 final size:104
Alignment explanation
Indices: 62649--62860 Score: 354
Period size: 103 Copynumber: 2.0 Consensus size: 104
62639 ATTGGAATGA
* * *
62649 ATCGCAATGCGAACTTCGTCTATCGCAACGAATTGGAATGAATCGCAACGCAAACTTCGCCTATC
1 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCAAACTTCGACTATC
* *
62714 GCAACGAA-TTGGAATGAATCGCAATGCGAACTTCGCCT
66 GCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACT
* *
62752 ATCGCAACGCGAACTTCGCCTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGACTATC
1 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCAAACTTCGACTATC
62817 GCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACT
66 GCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACT
62856 ATCGC
1 ATCGC
62861 GTTACGAATC
Statistics
Matches: 101, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
103 68 0.67
104 33 0.33
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.22
Consensus pattern (104 bp):
ATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCAAACTTCGACTATC
GCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACT
Found at i:62797 original size:41 final size:42
Alignment explanation
Indices: 62752--62860 Score: 202
Period size: 42 Copynumber: 2.6 Consensus size: 42
62742 AACTTCGCCT
*
62752 ATCGCAACGCGAACTTCGCCTATCGCAACG-ATTTGGAATGA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATGA
62793 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATGA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATGA
62835 ATCGCAACGCGAACTTCGACTATCGC
1 ATCGCAACGCGAACTTCGACTATCGC
62861 GTTACGAATC
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
41 29 0.44
42 37 0.56
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (42 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATGA
Found at i:63344 original size:143 final size:144
Alignment explanation
Indices: 63162--63450 Score: 379
Period size: 143 Copynumber: 2.0 Consensus size: 144
63152 TTAAATACAT
*
63162 AATTAAATATGACGACTTAAATTTCACTATAGAAAACCTAGTTTTCTCTCATTGGTGTACT-GCT
1 AATTAAATACGACGACTTAAATTTCACTATAGAAAACCTAGTTTTCTCTCATTGGTGT-CTCGCT
* * * *
63226 TATCTATTTT-TTTTCCGTCTTTGTTGATCGACGGCCAGCAACCAACACTATAAAATAACCAATC
65 CATCTATTTTCTTTTCCGTCTTTATTGATCGACGGCCAACAAACAACACTATAAAATAACCAATC
*
63290 AATTTCAAAATAAAA
130 AATCTCAAAATAAAA
*
63305 AATTAAATACGAC-AGCTTAAATTTCACTA-ATGAAAACCTAGTTTTCTCTCATTGGTGTGTCGC
1 AATTAAATACGACGA-CTTAAATTTCACTATA-GAAAACCTAGTTTTCTCTCATTGGTGTCTCGC
* ** * * * *
63368 TCATCTCTTTTCTTTTTTGTCTTTATTGATCGGCGGCCAACAAATAACATTATAAAATAATCAAT
64 TCATCTATTTTCTTTTCCGTCTTTATTGATCGACGGCCAACAAACAACACTATAAAATAACCAAT
* *
63433 TAATCTCAAATTAAAA
129 CAATCTCAAAATAAAA
63449 AA
1 AA
63451 AAATTAAATA
Statistics
Matches: 126, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
142 3 0.02
143 64 0.51
144 59 0.47
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (144 bp):
AATTAAATACGACGACTTAAATTTCACTATAGAAAACCTAGTTTTCTCTCATTGGTGTCTCGCTC
ATCTATTTTCTTTTCCGTCTTTATTGATCGACGGCCAACAAACAACACTATAAAATAACCAATCA
ATCTCAAAATAAAA
Found at i:64851 original size:46 final size:46
Alignment explanation
Indices: 64786--64874 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 46
64776 AAAAATTATA
* ** *
64786 TTTTATTCGAACTCGTCACATCGGCGTGACGAGTTCGAATAATTTT
1 TTTTATTCGAACTCATCACATCAACGTGACGAGTTCCAATAATTTT
64832 TTTTATT-GAAACTCATCACATCAACGTGACGAGTTCCAATAAT
1 TTTTATTCG-AACTCATCACATCAACGTGACGAGTTCCAATAAT
64875 AGTGTAGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 1 0.03
46 37 0.97
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (46 bp):
TTTTATTCGAACTCATCACATCAACGTGACGAGTTCCAATAATTTT
Found at i:65489 original size:2 final size:2
Alignment explanation
Indices: 65482--65534 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
65472 CTGCTTCTAT
65482 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
65524 TA TA TA TA TA T
1 TA TA TA TA TA T
65535 TTGGTATGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:68225 original size:21 final size:22
Alignment explanation
Indices: 68201--68249 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
68191 TCGAGGGTTC
68201 TATGTGGTCA-TTCGG-GACAAA-
1 TATGTGG-CACTTCGGTG-CAAAT
68222 TATGTGGCACTTCGGTGCAAAT
1 TATGTGGCACTTCGGTGCAAAT
68244 TATGTG
1 TATGTG
68250 AGCAATGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.08
21 16 0.64
22 7 0.28
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGCAAAT
Found at i:90150 original size:2 final size:2
Alignment explanation
Indices: 90143--90173 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
90133 TGTCTATGCC
90143 TA TA 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 TA TA T
90174 TAAAATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:91044 original size:24 final size:22
Alignment explanation
Indices: 90976--91046 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 22
90966 TAAAAGAATG
*
90976 ATAAACGAACATGTTTGTGAAC
1 ATAAATGAACATGTTTGTGAAC
* **
90998 ACTAAATGAACATATTCATGAAC
1 A-TAAATGAACATGTTTGTGAAC
*
91021 ATAAAAATGAACATGTTTGCGAAC
1 AT--AAATGAACATGTTTGTGAAC
91045 AT
1 AT
91047 TAAACGAGCA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
22 2 0.05
23 18 0.47
24 18 0.47
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (22 bp):
ATAAATGAACATGTTTGTGAAC
Found at i:95624 original size:16 final size:15
Alignment explanation
Indices: 95587--95633 Score: 78
Period size: 14 Copynumber: 3.1 Consensus size: 15
95577 ATAACAAACT
95587 TGTCTGTTTTCTACA
1 TGTCTGTTTTCTACA
95602 T-TCTGTTTTCTACA
1 TGTCTGTTTTCTACA
95616 TCGTCTGTTTTCTACA
1 T-GTCTGTTTTCTACA
95632 TG
1 TG
95634 GTATCACGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.47
15 2 0.07
16 14 0.47
ACGTcount: A:0.13, C:0.21, G:0.13, T:0.53
Consensus pattern (15 bp):
TGTCTGTTTTCTACA
Found at i:97467 original size:51 final size:51
Alignment explanation
Indices: 97391--97491 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 51
97381 TCAGGGGGAG
**
97391 AGTTACAAAGAATTTCAGCCTGTTCAAACCGATATTTCTTTACAGCCTATT
1 AGTTACAAAGAATTTCAAACTGTTCAAACCGATATTTCTTTACAGCCTATT
97442 AGTTAC-AAGAAATTTCAAACTGTTCAAACCGATATTTCTTTACAGCCTAT
1 AGTTACAAAG-AATTTCAAACTGTTCAAACCGATATTTCTTTACAGCCTAT
97492 CCTTTCCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 3 0.06
51 44 0.94
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.35
Consensus pattern (51 bp):
AGTTACAAAGAATTTCAAACTGTTCAAACCGATATTTCTTTACAGCCTATT
Found at i:99750 original size:16 final size:16
Alignment explanation
Indices: 99721--99761 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
99711 CAGACTTGTT
99721 TGTTTTCT--ACAGTC
1 TGTTTTCTACACAGTC
99735 TGTTTTCTACACAGTC
1 TGTTTTCTACACAGTC
99751 TGTTTTCTACA
1 TGTTTTCTACA
99762 AATACAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.32
16 17 0.68
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.49
Consensus pattern (16 bp):
TGTTTTCTACACAGTC
Found at i:100570 original size:24 final size:24
Alignment explanation
Indices: 100513--100575 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
100503 CCTCCATCGG
* **
100513 CATCATCATTGCCTTCACTGCCAA
1 CATCTTCATTGCCTTCACCACCAA
* * *
100537 TATATCCATTGCCTTCACCACCAA
1 CATCTTCATTGCCTTCACCACCAA
*
100561 CATCTTCATTCCCTT
1 CATCTTCATTGCCTT
100576 TTGTTGAACC
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.24, C:0.38, G:0.05, T:0.33
Consensus pattern (24 bp):
CATCTTCATTGCCTTCACCACCAA
Found at i:102219 original size:2 final size:2
Alignment explanation
Indices: 102206--102258 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
102196 ATACATATGC
*
102206 AT AT AT AC 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
102248 AT AT AT AT AT A
1 AT AT AT AT AT A
102259 ATTACATGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.