Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003241.1 Hibiscus syriacus cultivar Beakdansim tig00006815_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: 82241
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:701 original size:54 final size:54
Alignment explanation
Indices: 638--774 Score: 238
Period size: 54 Copynumber: 2.5 Consensus size: 54
628 TGTATTGCGG
*
638 ATAAATGTTTTGTTCAAGGATAAGTGCATGTATGTCCCCTACTTGAAGACGTGT
1 ATAAATGTTTTGTTCAAGAATAAGTGCATGTATGTCCCCTACTTGAAGACGTGT
*
692 ATAAATGTTTTGTTCGAGAATAAGTGCATGTATGTCCCCTACTTGAAGACGTGT
1 ATAAATGTTTTGTTCAAGAATAAGTGCATGTATGTCCCCTACTTGAAGACGTGT
* *
746 ATAAATGTTTTGTTCAATAATAATTGCAT
1 ATAAATGTTTTGTTCAAGAATAAGTGCAT
775 AGATTCGTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 78 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (54 bp):
ATAAATGTTTTGTTCAAGAATAAGTGCATGTATGTCCCCTACTTGAAGACGTGT
Found at i:2995 original size:21 final size:21
Alignment explanation
Indices: 2962--3038 Score: 113
Period size: 21 Copynumber: 3.8 Consensus size: 21
2952 CATATTCGCA
2962 TTGCGATAG--TCCAAGTTCG
1 TTGCGATAGTCTCCAAGTTCG
* *
2981 CTGCGATAGTCTCCAAGTGCG
1 TTGCGATAGTCTCCAAGTTCG
3002 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAGTCTCCAAGTTCG
*
3023 TTGTGATAGTCTCCAA
1 TTGCGATAGTCTCCAA
3039 AATAAATGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
19 8 0.16
21 43 0.84
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (21 bp):
TTGCGATAGTCTCCAAGTTCG
Found at i:7660 original size:21 final size:22
Alignment explanation
Indices: 7634--7680 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
7624 TAATTTTGTG
* *
7634 TAATATTATAATTAATAT-TTT
1 TAATATAATAATAAATATATTT
*
7655 TAATATAATAATAAATTTATTT
1 TAATATAATAATAAATATATTT
7677 TAAT
1 TAAT
7681 TCCAATTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATATAATAATAAATATATTT
Found at i:14745 original size:26 final size:27
Alignment explanation
Indices: 14716--14767 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
14706 TGTATGTATA
* * *
14716 TATATATATTTAAA-TATCTACTATGG
1 TATACATATATAAATTATCTAATATGG
14742 TATACATATATAAATTATCTAATATG
1 TATACATATATAAATTATCTAATATG
14768 ATTTTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (27 bp):
TATACATATATAAATTATCTAATATGG
Found at i:14990 original size:29 final size:29
Alignment explanation
Indices: 14899--14996 Score: 117
Period size: 29 Copynumber: 3.3 Consensus size: 29
14889 AGTTTAAGTC
14899 ATTAAACATTTTA-ACAATATATAGATACCAT
1 ATTAAACATTTTAGA-AATATA-AG-TACCAT
* * * *
14930 ATGAAATATTTTAGAAATATACGAACCAT
1 ATTAAACATTTTAGAAATATAAGTACCAT
14959 ATTAAACATTTTAGAAATATAAGTACCAT
1 ATTAAACATTTTAGAAATATAAGTACCAT
*
14988 ATTGAACAT
1 ATTAAACAT
14997 CTTATTAAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 38 0.67
30 1 0.02
31 17 0.30
32 1 0.02
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (29 bp):
ATTAAACATTTTAGAAATATAAGTACCAT
Found at i:33957 original size:3 final size:3
Alignment explanation
Indices: 33949--33973 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
33939 CCAAAAGCTT
33949 ACC ACC ACC ACC ACC ACC ACC ACC A
1 ACC ACC ACC ACC ACC ACC ACC ACC A
33974 TCGTCATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:34937 original size:11 final size:12
Alignment explanation
Indices: 34915--34946 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
34905 AAGGGGTAGC
34915 AGCAAGAGAAAG
1 AGCAAGAGAAAG
34927 AGCAA-AGAAAG
1 AGCAAGAGAAAG
34938 AG-AAGAGAA
1 AGCAAGAGAA
34947 CCCAGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 12 0.63
12 5 0.26
ACGTcount: A:0.62, C:0.06, G:0.31, T:0.00
Consensus pattern (12 bp):
AGCAAGAGAAAG
Found at i:35531 original size:20 final size:21
Alignment explanation
Indices: 35508--35562 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
35498 CAACGCGAAC
35508 TCCAAATTCGCAACAC-AGGT
1 TCCAAATTCGCAACACGAGGT
* * *
35528 TCCAAAATCGCAACGCGAGTT
1 TCCAAATTCGCAACACGAGGT
*
35549 TTCAAATTCGCAAC
1 TCCAAATTCGCAAC
35563 GCGAATAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.22
Consensus pattern (21 bp):
TCCAAATTCGCAACACGAGGT
Found at i:35581 original size:20 final size:20
Alignment explanation
Indices: 35532--35622 Score: 112
Period size: 20 Copynumber: 4.5 Consensus size: 20
35522 ACAGGTTCCA
* *
35532 AAATCGCAACGCGAGT-TTT
1 AAATCGCAACGCGAATATGT
*
35551 CAAATTCGCAACGCGAATAGGT
1 -AAA-TCGCAACGCGAATATGT
**
35573 AAATCGCAACGATAATATGT
1 AAATCGCAACGCGAATATGT
35593 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATATGT
35613 AAATCGCAAC
1 AAATCGCAAC
35623 ACATAAGTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 45 0.74
21 15 0.25
22 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:35640 original size:40 final size:42
Alignment explanation
Indices: 35550--35641 Score: 129
Period size: 40 Copynumber: 2.3 Consensus size: 42
35540 ACGCGAGTTT
*
35550 TCAAATTCGCAACGCGAATAGGTAAATCGCAACGATAATATG
1 TCAAATTCGCAACGCGAATAGGTAAATCGCAACGATAATAAG
* *
35592 T-AAA-TCGCAACGCGAATATGTAAATCGCAAC-A-CATAAG
1 TCAAATTCGCAACGCGAATAGGTAAATCGCAACGATAATAAG
35630 TCAAATTCGCAA
1 TCAAATTCGCAA
35642 AGCGCGTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
38 5 0.11
39 4 0.09
40 32 0.71
41 3 0.07
42 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (42 bp):
TCAAATTCGCAACGCGAATAGGTAAATCGCAACGATAATAAG
Found at i:35755 original size:20 final size:20
Alignment explanation
Indices: 35730--35775 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
35720 ATATAATCGC
*
35730 AAATCATAACCTAAAACCCT
1 AAATCATAACCAAAAACCCT
35750 AAATCATAACCAAAAACCCT
1 AAATCATAACCAAAAACCCT
35770 AAATCA
1 AAATCA
35776 CAACTCAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.54, C:0.28, G:0.00, T:0.17
Consensus pattern (20 bp):
AAATCATAACCAAAAACCCT
Found at i:35834 original size:22 final size:22
Alignment explanation
Indices: 35809--35859 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
35799 TCACTCTCTA
* * *
35809 CGGCGACATTCGTCCCCATCTC
1 CGGCGACATCCGTCCACATATC
*
35831 CGGCGAAATCCGTCCACATATC
1 CGGCGACATCCGTCCACATATC
35853 CGGCGAC
1 CGGCGAC
35860 CCCCTCTATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.41, G:0.22, T:0.18
Consensus pattern (22 bp):
CGGCGACATCCGTCCACATATC
Found at i:36279 original size:20 final size:20
Alignment explanation
Indices: 36254--36300 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
36244 AAAATCGCGT
36254 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
**
36274 GTTGCGATTTACCTATTCGC
1 GTTGCGATTTACAAATTCGC
36294 GTTGCGA
1 GTTGCGA
36301 ATCGCGTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:36501 original size:25 final size:25
Alignment explanation
Indices: 36473--36523 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
36463 TAAAAATCAT
36473 AAAAAGGTATTTTGTAATAAATTTA
1 AAAAAGGTATTTTGTAATAAATTTA
36498 AAAAAGGTATTTTGTAATAAATTTA
1 AAAAAGGTATTTTGTAATAAATTTA
36523 A
1 A
36524 GTTTTGAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (25 bp):
AAAAAGGTATTTTGTAATAAATTTA
Found at i:38512 original size:2 final size:2
Alignment explanation
Indices: 38505--38530 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38495 CGTGCATGTA
38505 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
38531 GACTTTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38922 original size:16 final size:16
Alignment explanation
Indices: 38901--38932 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38891 GAGGGCTAAA
*
38901 TTGATGTGAAAATACG
1 TTGATGAGAAAATACG
38917 TTGATGAGAAAATACG
1 TTGATGAGAAAATACG
38933 AATGGGGCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.25, T:0.28
Consensus pattern (16 bp):
TTGATGAGAAAATACG
Found at i:41037 original size:40 final size:40
Alignment explanation
Indices: 40993--41108 Score: 214
Period size: 40 Copynumber: 2.9 Consensus size: 40
40983 TATGAGCCCT
* *
40993 ATGTGGATTAATCTTTTAATATATTCATTGTGACTCGTCA
1 ATGTGGACTAATATTTTAATATATTCATTGTGACTCGTCA
41033 ATGTGGACTAATATTTTAATATATTCATTGTGACTCGTCA
1 ATGTGGACTAATATTTTAATATATTCATTGTGACTCGTCA
41073 ATGTGGACTAATATTTTAATATATTCATTGTGACTC
1 ATGTGGACTAATATTTTAATATATTCATTGTGACTC
41109 ATCACTTTGA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (40 bp):
ATGTGGACTAATATTTTAATATATTCATTGTGACTCGTCA
Found at i:41592 original size:19 final size:20
Alignment explanation
Indices: 41555--41593 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
41545 GTTTGTAATA
41555 AAATTATTTTATATTTATTT
1 AAATTATTTTATATTTATTT
41575 AAATT-TTTTA-ATTATATTT
1 AAATTATTTTATATT-TATTT
41594 TTAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 10 0.56
20 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
AAATTATTTTATATTTATTT
Found at i:47607 original size:22 final size:20
Alignment explanation
Indices: 47539--47595 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
47529 ACCAAATGTG
*
47539 AGTATCGATACCCGAGGGTC
1 AGTATCGATACTCGAGGGTC
*
47559 AATATCGATACTCGAGGGTC
1 AGTATCGATACTCGAGGGTC
47579 AGTATCGATACT-GAGGG
1 AGTATCGATACTCGAGGG
47596 GGCTCAGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 5 0.15
20 29 0.85
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (20 bp):
AGTATCGATACTCGAGGGTC
Found at i:52843 original size:19 final size:20
Alignment explanation
Indices: 52813--52850 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
52803 AGGGAAGGAT
*
52813 ACAAAGTATCAATGCTTTTC
1 ACAAAGTATCAATACTTTTC
52833 ACAAA-TATCAATACTTTT
1 ACAAAGTATCAATACTTTT
52851 GAATTGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (20 bp):
ACAAAGTATCAATACTTTTC
Found at i:52921 original size:72 final size:65
Alignment explanation
Indices: 52762--52926 Score: 168
Period size: 66 Copynumber: 2.4 Consensus size: 65
52752 GTATTGATAT
* *
52762 TTTTCACAACTATCGATACTTTTGAATTAAAAAAATGAAAAAGGGAAGGATACAAAGTATCAATG
1 TTTTCACAAATATCGATACTTTTGAATTAAAAAAATGAAAAAGGGAAGGATACAAAGAATCAAT-
*
52827 C
65 A
* * * * *
52828 TTTTCACAAATATCAATACTTTTGAATTGAAAGAAAATATGAAAAATGTGAAGGCTGCAATGAAT
1 TTTTCACAAATATCGATACTTTTGAATT--AA-AAAA-ATGAAAAA-GGGAAGGATACAAAGAAT
52893 CAATA
61 CAATA
* *
52898 TTTTCCCACAAATATTGATACTTTCGAAT
1 TTTT--CACAAATATCGATACTTTTGAAT
52927 ATTTTATAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
66 26 0.32
68 2 0.02
69 4 0.05
70 12 0.15
71 17 0.21
72 20 0.25
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (65 bp):
TTTTCACAAATATCGATACTTTTGAATTAAAAAAATGAAAAAGGGAAGGATACAAAGAATCAATA
Found at i:53160 original size:102 final size:102
Alignment explanation
Indices: 52982--53198 Score: 271
Period size: 102 Copynumber: 2.1 Consensus size: 102
52972 TGTGTTCGTG
* * * * *
52982 ATAACGTAGTAGGTCA-CG--CCTTTTTTAATGTCTATTATTTAAGTTATAAGTATGAAACCGTT
1 ATAACGTAGTAGGT-AGCGTACTTTTTTTAATATCAATTATTTAAGTTAAAAGAATGAAACCGTT
*
53044 TATATGATACAAAAGTAAGCCAAAAAAT-GTTTCTCATA
65 TATATGATACAAAAGTAAGACAAAAAATGGTTT-TCATA
* *
53082 ATAACGTATTAGGTAGCGTACTTTTTTTAATATCAATTGTTTAAGTTAAAAGAATGAAACCGTTT
1 ATAACGTAGTAGGTAGCGTACTTTTTTTAATATCAATTATTTAAGTTAAAAGAATGAAACCGTTT
* ** * *
53147 ATATTATGTAAAAGTAAGACAAACAATGGTTTTCATG
66 ATATGATACAAAAGTAAGACAAAAAATGGTTTTCATA
53184 ATAACGTAGTAGGTA
1 ATAACGTAGTAGGTA
53199 ATATCTTTTA
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
99 1 0.01
100 15 0.15
102 79 0.80
103 4 0.04
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (102 bp):
ATAACGTAGTAGGTAGCGTACTTTTTTTAATATCAATTATTTAAGTTAAAAGAATGAAACCGTTT
ATATGATACAAAAGTAAGACAAAAAATGGTTTTCATA
Found at i:53836 original size:81 final size:80
Alignment explanation
Indices: 53724--53876 Score: 188
Period size: 81 Copynumber: 1.9 Consensus size: 80
53714 TTTTTTTTGC
* **
53724 GCAACTTATTTCTTAGTGAATAATGACATTCTT-GA-ATGTACCTTATTTTATTAA-AAAAAATT
1 GCAACTTATTTCTTAGT-AATAATAACATTCTTGGACA-CAACC-TATTTTATTAATAAAAAATT
53786 AACATTATATTACAAATT
63 AACATTATATTACAAATT
*
53804 GCAACTTATTTTCTTAGT-ATACCATAACATTCTTGGACACAACCTATTTTATTAATAAAATATT
1 GCAACTTA-TTTCTTAGTAATA--ATAACATTCTTGGACACAACCTATTTTATTAATAAAAAATT
53868 AACATTATA
63 AACATTATA
53877 GATCACAACC
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
79 3 0.05
80 8 0.13
81 30 0.48
82 21 0.33
83 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.41
Consensus pattern (80 bp):
GCAACTTATTTCTTAGTAATAATAACATTCTTGGACACAACCTATTTTATTAATAAAAAATTAAC
ATTATATTACAAATT
Found at i:54193 original size:78 final size:78
Alignment explanation
Indices: 54034--54197 Score: 188
Period size: 77 Copynumber: 2.1 Consensus size: 78
54024 GACGCAACCC
* * * * * * *
54034 ATTTTATTATTAAAAATATAAAGATTTCATATTGCAACATGCTTTCTTAATGAACCATGACATTC
1 ATTTTATTAATAAAAATATAAACATTACAAATTACAACATGATTTCTTAATGAACCATGACATTA
* * *
54099 TTGCACGTAACTT
66 TTGAACGAAACAT
* * *
54112 ATTTTATTAATAAAAATATTAACATTACAAATTACAAC-TTATTTCTTAGTGAACCATGACATTA
1 ATTTTATTAATAAAAATATAAACATTACAAATTACAACATGATTTCTTAATGAACCATGACATTA
54176 TTGAACGAAACCAT
66 TTGAACGAAA-CAT
54190 A-TTTATTA
1 ATTTTATTA
54198 TAATATATTC
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
77 37 0.51
78 35 0.49
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (78 bp):
ATTTTATTAATAAAAATATAAACATTACAAATTACAACATGATTTCTTAATGAACCATGACATTA
TTGAACGAAACAT
Found at i:55995 original size:28 final size:28
Alignment explanation
Indices: 55956--56025 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
55946 TTTATGTTTT
55956 TTATTATT-TTTATTATTATT-TTATTAT-
1 TTATT-TTATTTATTATT-TTATTATTATA
* *
55983 TTGTTTTGATTTATTATTTTATTATTCTA
1 TTATTTT-ATTTATTATTTTATTATTATA
56012 TTATTTTATTTATT
1 TTATTTTATTTATT
56026 TTCTTATGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
26 2 0.06
27 6 0.17
28 22 0.61
29 6 0.17
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.73
Consensus pattern (28 bp):
TTATTTTATTTATTATTTTATTATTATA
Found at i:56002 original size:25 final size:24
Alignment explanation
Indices: 55901--56008 Score: 91
Period size: 25 Copynumber: 4.4 Consensus size: 24
55891 TTATTCTTTT
*
55901 TTTTATATATTTTTTTCCAATTTATTTA
1 TTTTAT-TATTTTTTT--GATTTA-TTA
* *
55929 TTTAATT-TTTTCTTTGATTTA-TG
1 TTTTATTATTTT-TTTGATTTATTA
55952 TTTT-TTATTATTTTT-A-TTATTA
1 TTTTATTATT-TTTTTGATTTATTA
55974 TTTTATTATTTGTTTTGATTTATTA
1 TTTTATTATTT-TTTTGATTTATTA
55999 TTTTATTATT
1 TTTTATTATT
56009 CTATTATTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
21 3 0.04
22 9 0.13
23 18 0.27
24 3 0.04
25 21 0.31
26 4 0.06
27 4 0.06
28 5 0.07
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.72
Consensus pattern (24 bp):
TTTTATTATTTTTTTGATTTATTA
Found at i:56024 original size:25 final size:24
Alignment explanation
Indices: 55955--56048 Score: 75
Period size: 25 Copynumber: 3.8 Consensus size: 24
55945 ATTTATGTTT
55955 TTTATTATTTTTATTATTATTTTATTA
1 TTTATTA-TTTTA-T-TTATTTTATTA
* *
55982 TTTGTTTTGATTTA-TTATTTTATTA
1 TTTATTAT--TTTATTTATTTTATTA
*
56007 TTCTATTATTTTATTTATTTTCTTA
1 TT-TATTATTTTATTTATTTTATTA
* *
56032 TGTAATA-TTTATTTATT
1 TTTATTATTTTATTTATT
56049 ACTTTTCTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
23 10 0.18
24 8 0.14
25 24 0.43
26 5 0.09
27 5 0.09
28 4 0.07
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.71
Consensus pattern (24 bp):
TTTATTATTTTATTTATTTTATTA
Found at i:61570 original size:84 final size:84
Alignment explanation
Indices: 61275--62415 Score: 1067
Period size: 84 Copynumber: 13.8 Consensus size: 84
61265 TTAAAGACAA
* * * * * *
61275 CATTTGCAGCATAACTCAAAG-CTAGAAGAGTTATCTGCCAA-CGAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAACT-TAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGATTA
61338 CGCTCAGCTCCAAGGCACAT
65 CGCTCAGCTCCAAGGCACAT
* * * * * *
61358 CATTTACAACATAGCTTAAGTCGAGAAGGGCTATC-T---GCCAAAGACCCTCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGATTAC
* * *
61419 GCTTAGCTTCGAGGGCACAAT
66 GCTCAGC-TCCAAGGCAC-AT
* * * * * * *
61440 -ATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGT--GACTAAAAGACCTTCGAGTTCGATT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCCAAC-CAAAGACCTTCGAGTTCGATT
*
61502 ACGCTCAGCTCCAAGGCATAT
64 ACGCTCAGCTCCAAGGCACAT
* *
61523 CATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGATTAC
* *
61588 GTTCAGCTCCAAGGCATAT
66 GCTCAGCTCCAAGGCACAT
* ** * * * * **
61607 CATTTGCAGTATAGGTTAAGTCGAGAAGGGCTATC-T---GCCAAAGACCCTCAAGTTTAATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGATTAC
* * *
61668 ACTCAGCTTCGAGAGCACAT
66 GCTCAGCTCCAAG-GCACAT
* * * * * *
61688 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT-C-ACCAAAGACCTTCGAGTTAGACTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCCAACCAAAGACCTTCGAGTTCGATTA
61751 CGCTCAGCTCCAAGGCACAT
65 CGCTCAGCTCCAAGGCACAT
* * * * *
61771 CATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGT-----CAAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCCAACCAAAGACCTTCGAGTTCGATTA
* *
61831 CGTTCAGCTCCAAGGCGCAT
65 CGCTCAGCTCCAAGGCACAT
* * * *
61851 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAA-CAAAGACCTTCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGATTAC
* * * *
61915 ACTCAGCTCAAAGGAACAA
66 GCTCAGCTCCAAGGCACAT
* * * * *
61934 CATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCAATTTTGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGATTAC
* * * *
61999 ACTCAGCTTCGAGGGCATAT
66 GCTCAGC-TCCAAGGCACAT
* * * *
62019 CATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTAGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGATTAC
*
62084 GCTCAGCTCCAAGGTACAT
66 GCTCAGCTCCAAGGCACAT
* * * * * *
62103 CATTTGTAGTATAGCTTAAGTCAAGAAGGGCTATCTGT-----CAAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCCAACCAAAGACCTTCGAGTTCGATTA
* * *
62163 AGTTCAGCTCCAAGGCGCAT
65 CGCTCAGCTCCAAGGCACAT
* * * * *
62183 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAA-CAAAGACCTTCGAGTTTGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGATTAC
* * *
62247 ACTCAGCTCAAAGGCACAA
66 GCTCAGCTCCAAGGCACAT
* * * * *
62266 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCAATTTTGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGATTAC
* * * *
62331 ACTCAGCTTCGAGGGCATAT
66 GCTCAGC-TCCAAGGCACAT
* * *
62351 CATTTGCAGTATAACTTAAGTCGAGAAGGATTATCTGCCAACCAAAGACCTTCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGATTAC
62416 TGATAACTCC
Statistics
Matches: 868, Mismatches: 162, Indels: 54
0.80 0.15 0.05
Matches are distributed among these distances:
80 188 0.22
81 69 0.08
82 5 0.01
83 209 0.24
84 230 0.26
85 167 0.19
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (84 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGATTAC
GCTCAGCTCCAAGGCACAT
Found at i:62106 original size:332 final size:331
Alignment explanation
Indices: 61271--62408 Score: 1470
Period size: 332 Copynumber: 3.4 Consensus size: 331
61261 TTTTTTAAAG
* * * * * *
61271 ACAACATTTGCAGCATAACTCAAAG-CTAGAAGAGTTATCTGCCAA-CGAAGACCTTCGAGTTCG
1 ACAACATTTGCAGCATAACT-TAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTTG
* * * * * * *
61334 ACTACGCTCAGC-TCCAAGGCACATCATTTACAACATAGCTTAAGTCGAGAAGGGCTATCTG---
65 ATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCA
* * * * * * ** ** * *
61395 CCAAAGACCCTCGAGTTCGATTACGCTTAGCTTCGAGGGCACAAT-ATTTACAACATAACTCAAG
130 CCAAAGACCTTCGAGTTAGACTACGCTCAGC-TCCAAGGCAC-ATCATTTGTAGTATAGCTTAAG
* * * * * **
61459 GCTAGAAGGGTTATCTGTGACTAAAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCATATC
193 TCAAGAAGGGCTATCTGT--C--AAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCGCATC
* * * * * * *
61524 ATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACG
254 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAA-CAAAGACCTTCGAGTTCGATTACA
* *
61589 TTCAGCTCCAAGGC
318 CTCAGCTCAAAGGC
* * * ** * * *
61603 ATATCATTTGCAGTATAGGTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCAAGTTTAA
1 ACAACATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTTGA
* * * * *
61664 TTACACTCAGCTTCGAGAGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAC
66 TTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAC
*
61729 CAAAGACCTTCGAGTTAGACTACGCTCAGCTCCAAGGCACATCATTTGTAGTATAGCTTAAGTCG
131 CAAAGACCTTCGAGTTAGACTACGCTCAGCTCCAAGGCACATCATTTGTAGTATAGCTTAAGTCA
61794 AGAAGGGCTATCTGTCAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCGCATCATTTGCA
196 AGAAGGGCTATCTGTCAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCGCATCATTTGCA
61859 GCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAGACCTTCGAGTTCGATTACACTCAGCTC
261 GCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
61924 AAAGGA
326 AAAGGC
* *
61930 ACAACATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCAATTTTGA
1 ACAACATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTTGA
* * *
61995 TTACACTCAGCTTCGAGGGCATATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAA
66 TTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-A
*
62060 CCAAAGACCTTCGAGTTAGACTACGCTCAGCTCCAAGGTACATCATTTGTAGTATAGCTTAAGTC
130 CCAAAGACCTTCGAGTTAGACTACGCTCAGCTCCAAGGCACATCATTTGTAGTATAGCTTAAGTC
*
62125 AAGAAGGGCTATCTGTCAAAGACCTTCGAGTTCGACTAAGTTCAGCTCCAAGGCGCATCATTTGC
195 AAGAAGGGCTATCTGTCAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCGCATCATTTGC
*
62190 AGCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAGACCTTCGAGTTTGATTACACTCAGCT
260 AGCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAGACCTTCGAGTTCGATTACACTCAGCT
62255 CAAAGGC
325 CAAAGGC
* * *
62262 ACAACATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCAATTTTGA
1 ACAACATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTTGA
* * * *
62327 TTACACTCAGCTTCGAGGGCATATCATTTGCAGTATAACTTAAGTCGAGAAGGATTATCTGCCAA
66 TTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-A
62392 CCAAAGACCTTCGAGTT
130 CCAAAGACCTTCGAGTT
62409 CGATTACTGA
Statistics
Matches: 713, Mismatches: 81, Indels: 24
0.87 0.10 0.03
Matches are distributed among these distances:
327 67 0.09
328 73 0.10
329 23 0.03
330 41 0.06
331 77 0.11
332 405 0.57
333 27 0.04
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (331 bp):
ACAACATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTTGA
TTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAC
CAAAGACCTTCGAGTTAGACTACGCTCAGCTCCAAGGCACATCATTTGTAGTATAGCTTAAGTCA
AGAAGGGCTATCTGTCAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCGCATCATTTGCA
GCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAGACCTTCGAGTTCGATTACACTCAGCTC
AAAGGC
Found at i:62214 original size:249 final size:248
Alignment explanation
Indices: 61275--62415 Score: 1296
Period size: 248 Copynumber: 4.6 Consensus size: 248
61265 TTAAAGACAA
* * * *
61275 CATTTGCAGCATAACTCAAAG-CTAGAAGAGTTATCTGCCAA-CGAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAACT-TAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* **
61338 CGCTCAGCTCCAAGGCACATCATTTACAACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
65 CGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* * * * * *
61403 CCTCGAGTTCGATTACGCTTAGCTTCGAGGGCACAAT-ATTTACAACATAACTCAAGGCTAGAAG
130 CTTCGAGTTCGATTACACTCAGC-TCCAAGGCAC-ATCATTTACAGCATAACTCAAGGCTAGAAG
** * * * *
61467 GGTTATCTG-TGACTAAAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCATAT
193 GGTTATCTGCCAAC-CAAAGACCTTCGAGTTTGATTACACTCAGCTCCAAGGCACAT
* *
61523 CATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
61588 GTTCAGCTCCAAGGCATATCATTTGCAGTATAGGTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * ** * *
61653 CTCAAGTTTAATTACACTCAGCTTCGAGAGCACATCATTTACAGCATAACTCAAGGCTAGAAGGG
131 TTCGAGTTCGATTACACTCAGCTCCAAG-GCACATCATTTACAGCATAACTCAAGGCTAGAAGGG
* * * *
61718 TTATCTGTC-ACCAAAGACCTTCGAGTTAGACTACGCTCAGCTCCAAGGCACAT
195 TTATCTGCCAACCAAAGACCTTCGAGTTTGATTACACTCAGCTCCAAGGCACAT
* * * * *
61771 CATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTG----TCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * * * * * * *
61832 GTTCAGCTCCAAGGCGCATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAG
66 GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCT-GC--CAAAG
* * * * * * *
61897 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGAACAACATTTGCAGCATAACTTAAGTCAAGAAG
128 ACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
* * * * *
61962 GGTTATCTGCCAACCAAAGACCTTCAATTTTGATTACACTCAGCTTCGAGGGCATAT
193 GGTTATCTGCCAACCAAAGACCTTCGAGTTTGATTACACTCAGC-TCCAAGGCACAT
* *
62019 CATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTAGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * *
62084 GCTCAGCTCCAAGGTACATCATTTGTAGTATAGCTTAAGTCAAGAAGGGCTATCTGTCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * * *
62149 TTCGAGTTCGACTA-AGTTCAGCTCCAAGGCGCATCATTTGCAGCATAACTCAAGGCTAGAAGGG
131 TTCGAGTTCGATTACA-CTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGG
* * *
62213 TTATCTACCAA-CAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACAA
195 TTATCTGCCAACCAAAGACCTTCGAGTTTGATTACACTCAGCTCCAAGGCACAT
* * * * * *
62266 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCAATTTTGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * * * **
62331 ACTCAGCTTCGAGGGCATATCATTTGCAGTATAACTTAAGTCGAGAAGGATTATCTGCCAACCAA
66 GCTCAGC-TCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG----CCAA
62396 AGACCTTCGAGTTCGATTAC
126 AGACCTTCGAGTTCGATTAC
62416 TGATAACTCC
Statistics
Matches: 756, Mismatches: 116, Indels: 37
0.83 0.13 0.04
Matches are distributed among these distances:
244 69 0.09
245 1 0.00
246 38 0.05
247 131 0.17
248 219 0.29
249 210 0.28
252 88 0.12
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (248 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
TTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGT
TATCTGCCAACCAAAGACCTTCGAGTTTGATTACACTCAGCTCCAAGGCACAT
Found at i:64457 original size:13 final size:13
Alignment explanation
Indices: 64439--64464 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64429 CATTGGCCAT
64439 GAGGAGGATCAGA
1 GAGGAGGATCAGA
64452 GAGGAGGATCAGA
1 GAGGAGGATCAGA
64465 ATGCCGGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.46, T:0.08
Consensus pattern (13 bp):
GAGGAGGATCAGA
Found at i:72151 original size:2 final size:2
Alignment explanation
Indices: 72146--72193 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
72136 AAAAAAAATA
72146 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
72188 AT AT AT
1 AT AT AT
72194 GAAGTTATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76282 original size:3 final size:3
Alignment explanation
Indices: 76274--76353 Score: 55
Period size: 3 Copynumber: 27.7 Consensus size: 3
76264 TGATTTATGT
* *
76274 TTA TTA TTA TTA TTT TTA TTA TTA TT- TTA TTA TT- TGTT TTGA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT-A -TTA
* *
76320 TTA TT- TTA -TA TTT TTA TTA TT- CTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
76354 TATTTTCTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
2 10 0.16
3 47 0.77
4 2 0.03
5 2 0.03
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:76305 original size:8 final size:8
Alignment explanation
Indices: 76268--76366 Score: 85
Period size: 8 Copynumber: 11.8 Consensus size: 8
76258 TTTCTTTGAT
76268 TTATGTTTA
1 TTAT-TTTA
76277 TTATTATTA
1 TTATT-TTA
*
76286 TTTTTATTA
1 TTATT-TTA
76295 TTATTTTA
1 TTATTTTA
*
76303 TTATTTGTT
1 TTATTT-TA
76312 TTGA-TTTA
1 TT-ATTTTA
76320 TTATTTTA
1 TTATTTTA
76328 -TATTTTTA
1 TTA-TTTTA
*
76336 TTATTCTA
1 TTATTTTA
76344 TTATTTTA
1 TTATTTTA
*
76352 TTTATTTTC
1 -TTATTTTA
76361 TTATTT
1 TTATTT
76367 AATATTTATT
Statistics
Matches: 76, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
7 3 0.04
8 39 0.51
9 33 0.43
10 1 0.01
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.73
Consensus pattern (8 bp):
TTATTTTA
Found at i:76337 original size:16 final size:16
Alignment explanation
Indices: 76268--76366 Score: 85
Period size: 17 Copynumber: 5.9 Consensus size: 16
76258 TTTCTTTGAT
76268 TTATGTTTATTATTATTA
1 TTAT-TTTATTATT-TTA
*
76286 TTTTTATTATTATTTTA
1 TTATT-TTATTATTTTA
*
76303 TTATTTGTTTTGA-TTTA
1 TTATTT-TATT-ATTTTA
76320 TTATTTTA-TATTTTTA
1 TTATTTTATTA-TTTTA
*
76336 TTATTCTATTATTTTA
1 TTATTTTATTATTTTA
*
76352 TTTATTTTCTTATTT
1 -TTATTTTATTATTT
76367 AATATTTATT
Statistics
Matches: 67, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
14 1 0.01
15 1 0.01
16 18 0.27
17 35 0.52
18 12 0.18
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.73
Consensus pattern (16 bp):
TTATTTTATTATTTTA
Found at i:76365 original size:41 final size:43
Alignment explanation
Indices: 76262--76381 Score: 133
Period size: 41 Copynumber: 2.8 Consensus size: 43
76252 ATTTTTTTTC
* *
76262 TTTG-ATTTATGTTTATTATTATTATTTTTATTATTATTTTATTA
1 TTTGTATTTAT-TTTATTATT-TTATATTTATTATTATTCTATTA
76306 TTTGT-TTTGA-TTTATTATTTTATATTT-TTATTATTCTATTA
1 TTTGTATTT-ATTTTATTATTTTATATTTATTATTATTCTATTA
* *
76347 TTT-TATTTATTTTCTTATTTAATATTTATTTATTA
1 TTTGTATTTATTTTATTATTTTATATTTA-TTATTA
76382 CTTTTCTATC
Statistics
Matches: 66, Mismatches: 4, Indels: 13
0.80 0.05 0.16
Matches are distributed among these distances:
40 2 0.03
41 34 0.52
42 7 0.11
43 15 0.23
44 7 0.11
45 1 0.02
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (43 bp):
TTTGTATTTATTTTATTATTTTATATTTATTATTATTCTATTA
Found at i:79301 original size:13 final size:13
Alignment explanation
Indices: 79283--79313 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
79273 TGAGCCTATA
79283 GACACTCATAGGG
1 GACACTCATAGGG
79296 GACACTCATAGGG
1 GACACTCATAGGG
79309 GACAC
1 GACAC
79314 ATTATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.29, T:0.13
Consensus pattern (13 bp):
GACACTCATAGGG
Found at i:79425 original size:9 final size:9
Alignment explanation
Indices: 79411--79441 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
79401 AGTAATTCTT
79411 TTATTTTTC
1 TTATTTTTC
79420 TTATTTTTC
1 TTATTTTTC
*
79429 TTAATTTTC
1 TTATTTTTC
79438 TTAT
1 TTAT
79442 GATTTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTTTTC
Found at i:79461 original size:35 final size:34
Alignment explanation
Indices: 79422--79487 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
79412 TATTTTTCTT
79422 ATTTTT-CTTAATTTTCTTATGATTTTTTTCAATTG
1 ATTTTTACTTAATTTT-TTAT-ATTTTTTTCAATTG
** *
79457 ATTTTTACTTTGTTTTTTATTTTTTTTTCAA
1 ATTTTTACTTAATTTTTTATATTTTTTTCAA
79488 AAAATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.37
35 10 0.37
36 7 0.26
ACGTcount: A:0.18, C:0.08, G:0.05, T:0.70
Consensus pattern (34 bp):
ATTTTTACTTAATTTTTTATATTTTTTTCAATTG
Found at i:80066 original size:11 final size:9
Alignment explanation
Indices: 80050--80092 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
80040 ATTTTGTTTC
80050 TTATTTCTTAT
1 TTATTT-TT-T
80061 TTATTTTTT
1 TTATTTTTT
80070 TCTATTTTTT
1 T-TATTTTTT
*
80080 TTATTTTTA
1 TTATTTTTT
80089 TTAT
1 TTAT
80093 GATTGATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 13 0.43
10 11 0.37
11 6 0.20
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (9 bp):
TTATTTTTT
Found at i:80083 original size:23 final size:23
Alignment explanation
Indices: 80040--80086 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 23
80030 TTATTGCTTA
80040 ATTTTGTTTCTTATTTCTTATTT
1 ATTTTGTTTCTTATTTCTTATTT
80063 ATTTT-TTTC-TATTT-TT-TTT
1 ATTTTGTTTCTTATTTCTTATTT
80082 ATTTT
1 ATTTT
80087 TATTATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.33
20 2 0.08
21 5 0.21
22 4 0.17
23 5 0.21
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (23 bp):
ATTTTGTTTCTTATTTCTTATTT
Done.