Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000577.1 Hibiscus syriacus cultivar Beakdansim tig00001129_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: 77710
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:5640 original size:37 final size:37
Alignment explanation
Indices: 5592--5703 Score: 179
Period size: 37 Copynumber: 3.0 Consensus size: 37
5582 AGACTCGATC
*
5592 TTGATTTGCTTCACTACTCTTCTGTGAATGCTTAAGA
1 TTGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGA
* *
5629 TTTATTTGCTTCACTACTCTCCTGTGAAGGCTTAAGA
1 TTGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGA
* *
5666 TTGATTTACTTCACTACTCTTCCGTGAAGGCTTAAGA
1 TTGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGA
5703 T
1 T
5704 AGCCCAGAGA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (37 bp):
TTGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGA
Found at i:5774 original size:42 final size:42
Alignment explanation
Indices: 5718--5838 Score: 143
Period size: 42 Copynumber: 2.9 Consensus size: 42
5708 CAGAGAACCT
* * *
5718 ATCATCTTGCTCGAAAGGCTTACAGATAACCCGAAGGATTTA
1 ATCATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTA
* * * * *
5760 ATCATCATGTTCGAAAGACTGAAAGATGACCCGAAAGTTTTA
1 ATCATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTA
* * *
5802 ATCATCATGCTCAAAAGACTTACTGATGGCCCGAAGG
1 ATCATCATGCTCGAAAGACTTACAGATGACCCGAAGG
5839 TCTTAATAAG
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (42 bp):
ATCATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTA
Found at i:14191 original size:2 final size:2
Alignment explanation
Indices: 14184--14246 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
14174 GAAAAACAAA
14184 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
14226 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
14247 CACACACACA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16563 original size:15 final size:15
Alignment explanation
Indices: 16543--16574 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
16533 GTGCATTTAA
16543 TTGTGTAACTATATG
1 TTGTGTAACTATATG
16558 TTGTGTAACTATATG
1 TTGTGTAACTATATG
16573 TT
1 TT
16575 ATACTAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (15 bp):
TTGTGTAACTATATG
Found at i:16691 original size:54 final size:54
Alignment explanation
Indices: 16628--16911 Score: 304
Period size: 54 Copynumber: 5.3 Consensus size: 54
16618 TTACCAAATA
*
16628 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATAAATAATCGTTTC
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCGTTTC
* * *
16682 GGCACTAAGTGTGTAATTCACAGAATTCATCATATGTTGATGAATAAACTTTTC
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCGTTTC
* * * *
16736 GGTACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCATTTC
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCGTTTC
* * * * *
16790 AGCACTAAGTGTGCAAAGT-A-TGAAATTCATCATATGTTGATGAATAATTGTTTT
1 GGCACTAAGTGTGC-AATTCACAG-AATTCATCATATGTTGATGAATAATCGTTTC
* * ** * * * * * * *
16844 GGCATTATGTGTGCAACCCACATAATTCATAATA-GTTTATGAATTACCGTATA
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCGTTTC
*
16897 GGCACTACGTGTGCA
1 GGCACTAAGTGTGCA
16912 TCGTAACGAA
Statistics
Matches: 193, Mismatches: 33, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
53 29 0.15
54 161 0.83
55 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCGTTTC
Found at i:17247 original size:26 final size:26
Alignment explanation
Indices: 17211--17262 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
17201 CTTTTGTAAA
*
17211 ATGATGAAACATTTGAATGATACTTT
1 ATGATAAAACATTTGAATGATACTTT
17237 ATGATAAAACATTTGAATGATACTTT
1 ATGATAAAACATTTGAATGATACTTT
17263 TTGTTATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (26 bp):
ATGATAAAACATTTGAATGATACTTT
Found at i:20310 original size:60 final size:61
Alignment explanation
Indices: 20243--20378 Score: 170
Period size: 60 Copynumber: 2.2 Consensus size: 61
20233 AGTTGAGTGG
* * * *
20243 CCATTTTGTAATTTTTAATAGTTTGAGGACTCAATAAAGCAACGTCCTATA-ATCC-AGAGA
1 CCATTTTGTAATTTTTAATAGTTGGA-GACCCAACAAAGCAACGACCTATATATCCAAGAGA
* * *
20303 CCATTTTGTATTTTTTAATAGTTGGAGACCCAACAAAGCAATGACCTATATATCCAAGGGA
1 CCATTTTGTAATTTTTAATAGTTGGAGACCCAACAAAGCAACGACCTATATATCCAAGAGA
20364 CCATTTGTGT-ATTTT
1 CCATTT-TGTAATTTT
20379 ACCCAATTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
59 20 0.31
60 28 0.43
61 14 0.22
62 3 0.05
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (61 bp):
CCATTTTGTAATTTTTAATAGTTGGAGACCCAACAAAGCAACGACCTATATATCCAAGAGA
Found at i:23063 original size:21 final size:21
Alignment explanation
Indices: 23037--23080 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
23027 ACCGTGGTGG
23037 ACGAGTCAAATGACCAGAAAA
1 ACGAGTCAAATGACCAGAAAA
23058 ACGAGTCAAATGACCAGAAAA
1 ACGAGTCAAATGACCAGAAAA
23079 AC
1 AC
23081 CAAGTCGGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.20, G:0.18, T:0.09
Consensus pattern (21 bp):
ACGAGTCAAATGACCAGAAAA
Found at i:26896 original size:140 final size:139
Alignment explanation
Indices: 26592--27208 Score: 641
Period size: 139 Copynumber: 4.4 Consensus size: 139
26582 TTAAATAGTC
* * * * * ** *
26592 AAAATGGAATCTCGAGCAAAAGCGAGGACCAAATCGAAAATTCTCCTAGATAAAAGGACT--AGG
1 AAAATGAAACCTCGAGCAAAAGCGAGGACCAAATCAAAAATTCCCCTAAATTTAAGGACTAAATG
* * *
26655 TGAAATTAAACCTAAAAGTAGAGGCTCTAAAAAACATCCTAATTAATTTTAA-CAATTATTTTAT
66 TGAAATTAAGCCTAAAA-TAGAGGCTCTAAAAAATATCCTAATTAATTTTAACCAATTATTTGAT
26719 TCGAATAATT
130 TCGAATAATT
* * * *
26729 AAAATAAAACCTTGAGCATAAGCGAGGACCAAATCAAAAATTCCCCTAAATTTAAGGGCTAAATG
1 AAAATGAAACCTCGAGCAAAAGCGAGGACCAAATCAAAAATTCCCCTAAATTTAAGGACTAAATG
* *
26794 TGAAATTAAGCCTAAGAATAGAGGTTCTAAAAAATATCCTAATTAATTTTAACCAATTACTTGAT
66 TGAAATTAAGCCTAA-AATAGAGGCTCTAAAAAATATCCTAATTAATTTTAACCAATTATTTGAT
26859 TCGAATAATT
130 TCGAATAATT
* * * * *
26869 AAAATGGAACCTCGAGCATAAGCGAGGACCAAATAAAAAAATCCCCCTAAATTTAAGGACTAAGT
1 AAAATGAAACCTCGAGCAAAAGCGAGGACCAAAT-CAAAAATTCCCCTAAATTTAAGGACTAAAT
* * * ** * * *
26934 GTGAAATTAAGCCTAAAATGGAAGCTCTAATAGTTAACCTAGTCAATTTTAACCAATTATTTGAT
65 GTGAAATTAAGCCTAAAATAGAGGCTCTAAAAAATATCCTAATTAATTTTAACCAATTATTTGAT
*
26999 TTGAATAATT
130 TCGAATAATT
* ** * * *
27009 AAAATGAAACCTCAAGCAAAAGCGATTACCAAATTAAAAATTCTCCTAAATTTAAGGACTAAGTG
1 AAAATGAAACCTCGAGCAAAAGCGAGGACCAAATCAAAAATTCCCCTAAATTTAAGGACTAAATG
* * * **** ** * * *
27074 TAAAATTAGGCCTAAAGT-GAAGGCTCTAATTGTTAAACTAATCAATTTTAACGAATTATTTTAT
66 TGAAATTAAGCCTAAAATAG-AGGCTCTAAAAAATATCCTAATTAATTTTAACCAATTATTTGAT
*
27138 TCAAATAATT
130 TCGAATAATT
** ** ** * *
27148 AAAATGAAACCTTTAAAAAAAGAAAAGACCAAATTAAAAATT-CCCTAAATTTAAGGACTAA
1 AAAATGAAACCTCGAGCAAAAGCGAGGACCAAATCAAAAATTCCCCTAAATTTAAGGACTAA
27209 GTGTAACCCC
Statistics
Matches: 411, Mismatches: 63, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
137 49 0.12
138 19 0.05
139 171 0.42
140 130 0.32
141 42 0.10
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (139 bp):
AAAATGAAACCTCGAGCAAAAGCGAGGACCAAATCAAAAATTCCCCTAAATTTAAGGACTAAATG
TGAAATTAAGCCTAAAATAGAGGCTCTAAAAAATATCCTAATTAATTTTAACCAATTATTTGATT
CGAATAATT
Found at i:28034 original size:24 final size:24
Alignment explanation
Indices: 27975--28055 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 24
27965 GATATCAAAA
* * * *
27975 ATCAAAACATAATTCATGTCAGAT
1 ATCAAAACAGAATCCAGGTCAGGT
* * *
27999 GTCATAATAGAATCCAGGTCAGGT
1 ATCAAAACAGAATCCAGGTCAGGT
*
28023 ATCAAAACAGAATCCAGTTCAGGT
1 ATCAAAACAGAATCCAGGTCAGGT
*
28047 ATCATAACA
1 ATCAAAACA
28056 TAATTCAAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.25
Consensus pattern (24 bp):
ATCAAAACAGAATCCAGGTCAGGT
Found at i:29524 original size:240 final size:240
Alignment explanation
Indices: 29101--29588 Score: 922
Period size: 240 Copynumber: 2.0 Consensus size: 240
29091 ATTCATCTTT
*
29101 GACTTTGAAAAATGATAAGGATGAGTTGTCATGGTTTTGTGGTAAATAAGAAGATTCATTAAGGG
1 GACTTTGAAAAATGATAAGGATGACTTGTCATGGTTTTGTGGTAAATAAGAAGATTCATTAAGGG
*
29166 TGATTTGGTCTTATCCCAATTTTACATTATATTCATTTAAGTGGAATATAATGTAAAATACTATG
66 TGATTTGGTCTTATCCCAATTTTACATTATATTCATTTAAGTGGAAAATAATGTAAAATACTATG
*
29231 AAATGCACCCAACATATCATTTCACTTGGTCATCTTCTTCTCCAAGCTGTCGTGGGTGTTTTTCA
131 AAATGCACCCAACATATCATTTCACTTGGTCATCTTCTTCTCCAAGCTGTCGTGGGTGTTCTTCA
29296 AAGGTGAGAGAAAGCTTCAACTCAATTTTCAAGCAATTTACTTAG
196 AAGGTGAGAGAAAGCTTCAACTCAATTTTCAAGCAATTTACTTAG
*
29341 GACTTTGAAAGATGATAAGGATGACTTGTCATGGTTTTGTGGTAAATAAGAAGATTCATTAAGGG
1 GACTTTGAAAAATGATAAGGATGACTTGTCATGGTTTTGTGGTAAATAAGAAGATTCATTAAGGG
29406 TGATTTGGTCTTATCCCAATTTTACATTATATTCATTTAAGTGGAAAATAATGTAAAATACTATG
66 TGATTTGGTCTTATCCCAATTTTACATTATATTCATTTAAGTGGAAAATAATGTAAAATACTATG
29471 AAATGCACCCAACATATCATTTCACTTGGTCATCTTCTTCTCCAAGCTGTCGTGGGTGTTCTTCA
131 AAATGCACCCAACATATCATTTCACTTGGTCATCTTCTTCTCCAAGCTGTCGTGGGTGTTCTTCA
*
29536 AAGGTGAGAGAAAGCTTCAACTCAATTTTCAAGTAATTTACTTAG
196 AAGGTGAGAGAAAGCTTCAACTCAATTTTCAAGCAATTTACTTAG
*
29581 GATTTTGA
1 GACTTTGA
29589 GTAAGTTGTA
Statistics
Matches: 242, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
240 242 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (240 bp):
GACTTTGAAAAATGATAAGGATGACTTGTCATGGTTTTGTGGTAAATAAGAAGATTCATTAAGGG
TGATTTGGTCTTATCCCAATTTTACATTATATTCATTTAAGTGGAAAATAATGTAAAATACTATG
AAATGCACCCAACATATCATTTCACTTGGTCATCTTCTTCTCCAAGCTGTCGTGGGTGTTCTTCA
AAGGTGAGAGAAAGCTTCAACTCAATTTTCAAGCAATTTACTTAG
Found at i:31226 original size:46 final size:45
Alignment explanation
Indices: 31074--31243 Score: 261
Period size: 45 Copynumber: 3.8 Consensus size: 45
31064 ATAAACTGGC
*
31074 AAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTA
31118 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * * *
31163 AAATAAGCTTACGAGCTTATGGATTAAATAGTAAGTATAATTGGGA
1 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTAT-ATTGGTA
* *
31209 AAATAAGTTTACAAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAG
31244 AGATTTTATA
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 24 0.21
45 54 0.47
46 36 0.32
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:31227 original size:91 final size:89
Alignment explanation
Indices: 31074--31243 Score: 277
Period size: 91 Copynumber: 1.9 Consensus size: 89
31064 ATAAACTGGC
* *
31074 AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATG
1 AAATAAGCTTACGAGCTTATGGAATAATAGTAAGTATATTGGGAAAATAAGCTTACAAGCTTATG
31139 GAATAAATGGTAAGTATATTGGTA
66 GAATAAATGGTAAGTATATTGGTA
* *
31163 AAATAAGCTTACGAGCTTATGGATTAAATAGTAAGTATAATTGGGAAAATAAGTTTACAAGCTTA
1 AAATAAGCTTACGAGCTTATGGAAT-AATAGTAAGTAT-ATTGGGAAAATAAGCTTACAAGCTTA
*
31228 TGGGATAAATGGTAAG
64 TGGAATAAATGGTAAG
31244 AGATTTTATA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
89 24 0.32
90 11 0.15
91 39 0.53
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (89 bp):
AAATAAGCTTACGAGCTTATGGAATAATAGTAAGTATATTGGGAAAATAAGCTTACAAGCTTATG
GAATAAATGGTAAGTATATTGGTA
Found at i:32241 original size:22 final size:22
Alignment explanation
Indices: 32224--32290 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
32214 CTCGTATAAA
32224 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
32246 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
32268 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
32290 T
1 T
32291 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:32558 original size:30 final size:29
Alignment explanation
Indices: 32491--32568 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
32481 CCGTAGTTCA
* * *
32491 TATCACGTAGACATAGTATTTCCATAACTT
1 TATCACATAGGCATA-TATTTACATAACTT
* *
32521 TAACACATAGGCATATCATTTACATACCTT
1 TATCACATAGGCATAT-ATTTACATAACTT
32551 TATCACATAGTGCATATA
1 TATCACATAG-GCATATA
32569 ACTTTTTCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.35
Consensus pattern (29 bp):
TATCACATAGGCATATATTTACATAACTT
Found at i:32624 original size:29 final size:29
Alignment explanation
Indices: 32582--32653 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
32572 TTTTCTGCAT
* **
32582 ATTCATGTCATGTAATACGTATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
32611 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
32640 ATTCATGTCATGTA
1 ATTCATGTCATGTA
32654 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:33079 original size:64 final size:65
Alignment explanation
Indices: 32972--33126 Score: 188
Period size: 64 Copynumber: 2.4 Consensus size: 65
32962 ATCGGTTCCC
* * *
32972 CCCCCTAGGGGTATCGATT-CCCTCAAGCAATCTGGAATTTCATATACGATGAGGGGGTATCGGT
1 CCCCCT-GGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGATGAAGGGGTATCGGT
33036 T
65 T
* * * *
33037 CCCCCTGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTTGAAGGGGTATCGGTT
1 CCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGATGAAGGGGTATCGGTT
*
33101 CCCCTTGAATGGGTACCGATTCCCCT
1 CCCCCTG---GGGTACCGATTCCCCT
33127 AACCCAGAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
64 40 0.51
65 22 0.28
67 16 0.21
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (65 bp):
CCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGATGAAGGGGTATCGGTT
Found at i:33114 original size:21 final size:21
Alignment explanation
Indices: 33084--33126 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
33074 ATCATATTCG
* *
33084 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
33105 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
33126 T
1 T
33127 AACCCAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:39179 original size:22 final size:22
Alignment explanation
Indices: 39162--39228 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
39152 CTCGTATAAA
39162 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
39184 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
39206 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
39228 T
1 T
39229 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:39498 original size:30 final size:29
Alignment explanation
Indices: 39431--39508 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
39421 CCGTAGTTCA
* * *
39431 TATCACGTAGACATAGTATTTCCATAACTT
1 TATCACATAGGCATA-TATTTACATAACTT
* *
39461 TAACACATAGGCATATCATTTACATACCTT
1 TATCACATAGGCATAT-ATTTACATAACTT
39491 TATCACATAGTGCATATA
1 TATCACATAG-GCATATA
39509 ACTTTTTCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.35
Consensus pattern (29 bp):
TATCACATAGGCATATATTTACATAACTT
Found at i:39564 original size:29 final size:29
Alignment explanation
Indices: 39522--39593 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
39512 TTTTCTGCAT
* **
39522 ATTCATGTCATGTAATACGTATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
39551 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
39580 ATTCATGTCATGTA
1 ATTCATGTCATGTA
39594 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:40043 original size:67 final size:68
Alignment explanation
Indices: 39897--40048 Score: 207
Period size: 68 Copynumber: 2.2 Consensus size: 68
39887 TTTTCTCATG
* * *
39897 GGGGAATCGGTTCCCCCCCCTAGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGTATCGGTT-CCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGA
*
39962 TGAG
65 TGAA
* * * * *
39966 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTTCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
40030 GAA
66 GAA
40033 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
40049 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
67 27 0.36
68 36 0.49
69 11 0.15
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (68 bp):
GGGGTATCGGTTCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
GAA
Found at i:40058 original size:21 final size:21
Alignment explanation
Indices: 40028--40070 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40018 ATCATATTCG
* *
40028 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
40049 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
40070 T
1 T
40071 AACCCAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:40060 original size:67 final size:67
Alignment explanation
Indices: 39897--40070 Score: 190
Period size: 67 Copynumber: 2.6 Consensus size: 67
39887 TTTTCTCATG
* * * *
39897 GGGGAATCGGTTCCCCCCCCTAGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGTATCGGTT--CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGA
*
39962 TGAG
64 TGAA
* * * *
39966 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
40030 GAA
65 GAA
* *
40033 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
40071 AACCCAGAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
65 6 0.07
67 39 0.42
68 36 0.39
69 11 0.12
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGATG
AA
Found at i:42804 original size:21 final size:21
Alignment explanation
Indices: 42779--42842 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
42769 CGGGCATGAA
*
42779 GGTCAGGGTTGGACTGGGTCG
1 GGTCAGGGTTGGACCGGGTCG
*
42800 GGTCAGGGTTAGACCGGGTCG
1 GGTCAGGGTTGGACCGGGTCG
* * *
42821 AGTCGGGGTTGGACCAGGTCG
1 GGTCAGGGTTGGACCGGGTCG
42842 G
1 G
42843 ATAACCTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.12, C:0.17, G:0.50, T:0.20
Consensus pattern (21 bp):
GGTCAGGGTTGGACCGGGTCG
Found at i:44912 original size:36 final size:35
Alignment explanation
Indices: 44872--45069 Score: 239
Period size: 36 Copynumber: 5.7 Consensus size: 35
44862 TAAAAATACG
44872 TATATAATATATAGTTTTTAAAACACTTTTGAAAAC
1 TATATAATATATAGTTTTTAAAACA-TTTTGAAAAC
* *
44908 TATATAATATATAATTTTTAAAATATTTTAGAAAA-
1 TATATAATATATAGTTTTTAAAACATTTT-GAAAAC
*
44943 TATATAATATATGGTTTTTAAAATCATTTTGAAAAC
1 TATATAATATATAGTTTTTAAAA-CATTTTGAAAAC
44979 TA-ATAAATATATAGTTTTTGAAAACATTTTTTGAAAA-
1 TATAT-AATATATAGTTTTT-AAAACA--TTTTGAAAAC
*
45016 T-TAT-ATA-ATA-TTTTTATAACATTTTGAAAAC
1 TATATAATATATAGTTTTTAAAACATTTTGAAAAC
*
45047 TATATAATATATAGTTTTGAAAA
1 TATATAATATATAGTTTTTAAAA
45070 ACTTTTTTTA
Statistics
Matches: 140, Mismatches: 9, Indels: 27
0.80 0.05 0.15
Matches are distributed among these distances:
30 9 0.06
31 1 0.01
32 8 0.06
33 8 0.06
34 6 0.04
35 42 0.30
36 50 0.36
37 7 0.05
38 9 0.06
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (35 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAAC
Found at i:44960 original size:71 final size:70
Alignment explanation
Indices: 44872--45069 Score: 253
Period size: 71 Copynumber: 2.8 Consensus size: 70
44862 TAAAAATACG
* *
44872 TATATAATATATAGTTTTTAAAACACTTTTGAAAACTATATAATATATAATTTTTAAAATA-TTT
1 TATATAATATAT-GTTTTTAAAACA-TTTTGAAAACTATATAATATATAGTTTTTAAAACATTTT
44936 TAGAAAA
64 TAGAAAA
44943 TATATAATATATGGTTTTTAAAATCATTTTGAAAACTA-ATAAATATATAGTTTTTGAAAACATT
1 TATATAATATAT-GTTTTTAAAA-CATTTTGAAAACTATAT-AATATATAGTTTTT-AAAACATT
*
45007 TTTTGAAAA
62 TTTAGAAAA
* * *
45016 T-TAT-ATA-ATATTTTTATAACATTTTGAAAACTATATAATATATAGTTTTGAAAA
1 TATATAATATATGTTTTTAAAACATTTTGAAAACTATATAATATATAGTTTTTAAAA
45070 ACTTTTTTTA
Statistics
Matches: 115, Mismatches: 7, Indels: 14
0.85 0.05 0.10
Matches are distributed among these distances:
67 4 0.03
68 27 0.23
69 10 0.09
70 4 0.03
71 50 0.43
72 10 0.09
73 10 0.09
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (70 bp):
TATATAATATATGTTTTTAAAACATTTTGAAAACTATATAATATATAGTTTTTAAAACATTTTTA
GAAAA
Found at i:45117 original size:2 final size:2
Alignment explanation
Indices: 45112--45141 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45102 TTTTTTTGAA
45112 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
45142 TATTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45606 original size:18 final size:20
Alignment explanation
Indices: 45569--45608 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
45559 AATAGCACCA
45569 AAACACCATCAACAGAAAAC
1 AAACACCATCAACAGAAAAC
*
45589 AAACATCATC-AC-GAAAAC
1 AAACACCATCAACAGAAAAC
45607 AA
1 AA
45609 CAGTGCCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.60, C:0.28, G:0.05, T:0.07
Consensus pattern (20 bp):
AAACACCATCAACAGAAAAC
Found at i:45610 original size:17 final size:16
Alignment explanation
Indices: 45568--45610 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
45558 AAATAGCACC
*
45568 AAAACACCATCAACAG
1 AAAACAACATCAACAG
*
45584 AAAACAAACATCATCACG
1 AAAAC-AACATCAACA-G
45602 AAAACAACA
1 AAAACAACA
45611 GTGCCACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 12 0.52
18 6 0.26
ACGTcount: A:0.60, C:0.28, G:0.05, T:0.07
Consensus pattern (16 bp):
AAAACAACATCAACAG
Found at i:46453 original size:14 final size:14
Alignment explanation
Indices: 46372--46459 Score: 53
Period size: 13 Copynumber: 6.6 Consensus size: 14
46362 ACCCTCTAAA
*
46372 ATTTTCATTTTATT
1 ATTTTTATTTTATT
46386 -TCTTTTA-TTTATT
1 AT-TTTTATTTTATT
* *
46399 ATTTTTA-ATCATT
1 ATTTTTATTTTATT
**
46412 ATTTTTCCTTT-TT
1 ATTTTTATTTTATT
** *
46425 -TCCTT-TTTAATT
1 ATTTTTATTTTATT
46437 ATTTTTATTTTATT
1 ATTTTTATTTTATT
46451 ATTTTTATT
1 ATTTTTATT
46460 AACTTTTTAT
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
11 2 0.04
12 5 0.09
13 27 0.49
14 21 0.38
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTTTATTTTATT
Found at i:46456 original size:25 final size:23
Alignment explanation
Indices: 46379--46482 Score: 68
Period size: 25 Copynumber: 4.2 Consensus size: 23
46369 AAAATTTTCA
*
46379 TTTTATT-TCTTTTATTTATTATT
1 TTTTATTAT-TTTTATTTTTTATT
* *
46402 TTTAATCATTATTTTTCCTTTTTTCCTT
1 TTT--T-ATTATTTTT-ATTTTTT-ATT
*
46430 TTTAATTATTTTTATTTTATTA-T
1 TTTTATTATTTTTATTTT-TTATT
46453 TTTTATTAACTTTTTATTTTTTCATT
1 TTTTATT-A-TTTTTATTTTTT-ATT
46479 TTTT
1 TTTT
46483 TCTCTTCATT
Statistics
Matches: 63, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
23 10 0.16
24 7 0.11
25 23 0.37
26 12 0.19
27 6 0.10
28 5 0.08
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTATTATTTTTATTTTTTATT
Found at i:46473 original size:41 final size:42
Alignment explanation
Indices: 46428--46517 Score: 105
Period size: 42 Copynumber: 2.1 Consensus size: 42
46418 CCTTTTTTCC
*
46428 TTTTTAATTATTTTTAT-TTTATTATTTTTATTAAC-T-TTTTAT
1 TTTTTAATT-TTTTTATCTTCATT-TTTTTATT-ACTTCTTTTAT
* *
46470 TTTTTCATTTTTTTCTCTTCATTTTTTTATTACTTCTTTTAT
1 TTTTTAATTTTTTTATCTTCATTTTTTTATTACTTCTTTTAT
46512 TTTTTA
1 TTTTTA
46518 TTTAATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
40 2 0.05
41 15 0.37
42 24 0.59
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (42 bp):
TTTTTAATTTTTTTATCTTCATTTTTTTATTACTTCTTTTAT
Found at i:46538 original size:41 final size:41
Alignment explanation
Indices: 46452--46537 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 41
46442 TATTTTATTA
**
46452 TTTTTATTAACTTTTTATTTTTTCATTTTTTTCTCTTCATT
1 TTTTTATTAACTTTTTATTTTTTCATTTAATTCTCTTCATT
46493 TTTTTATT-ACTTCTTTTATTTTTT-ATTTAATT-T-TTCATT
1 TTTTTATTAAC-T-TTTTATTTTTTCATTTAATTCTCTTCATT
46532 TCTTTT
1 T-TTTT
46538 TCCCTTCCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
39 7 0.17
40 7 0.17
41 15 0.38
42 11 0.28
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.74
Consensus pattern (41 bp):
TTTTTATTAACTTTTTATTTTTTCATTTAATTCTCTTCATT
Found at i:46563 original size:2 final size:2
Alignment explanation
Indices: 46558--46595 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
46548 GATTTTTTTG
46558 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46596 TTTTTCATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:47134 original size:24 final size:24
Alignment explanation
Indices: 47107--47194 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
47097 GATATCAAAA
* *
47107 ATCAAAACATAATTCATGTCAGAT
1 ATCAAAACAGAATTCAGGTCAGAT
* * *
47131 ATCAGAACAGAATCCAGGTCAGGT
1 ATCAAAACAGAATTCAGGTCAGAT
*
47155 ATCAAAACAGAA-TCTAGGTCAGTT
1 ATCAAAACAGAATTC-AGGTCAGAT
*
47179 ATCATAACAGAATTCA
1 ATCAAAACAGAATTCA
47195 AATCGAAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 1 0.02
24 50 0.94
25 2 0.04
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGGTCAGAT
Found at i:49892 original size:13 final size:13
Alignment explanation
Indices: 49874--49900 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49864 GTTGATATTT
49874 ACGATTCACGACG
1 ACGATTCACGACG
49887 ACGATTCACGACG
1 ACGATTCACGACG
49900 A
1 A
49901 GAAGTTTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.22, T:0.15
Consensus pattern (13 bp):
ACGATTCACGACG
Found at i:50438 original size:139 final size:138
Alignment explanation
Indices: 50243--50586 Score: 412
Period size: 139 Copynumber: 2.5 Consensus size: 138
50233 GGGGTGTGAC
* * * * * * *
50243 ACTAAGTTTGAAATTAAGCCTAGAAAG-AAAGCTT-TAATTATTAATCTAGTCGATTTTAACCAA
1 ACTAAGTGTGAAATTAGGCCT--AAAGTGAAGGTTCTAATTATTAACCTAATCAATTTTAACCAA
* *
50306 TTATTTGATTCGAATAATTAAAATGGAACCT-TGAGCAAAAGTGATGACCAAATTAAAAATTCTC
64 TTATTTGATTCAAATAATTAAAATGGAACCTCT-AGCAAAAGTGAGGACCAAATTAAAAATTC-C
*
50370 CTTAATTTAAA-
127 CTAAATTTAAAG
*
50381 AGCTAAGTGTGAAATTAGGCCTAAAGTGAAGGTTCTAATTGTTAACCTAATCAATTTTAACCAAT
1 A-CTAAGTGTGAAATTAGGCCTAAAGTGAAGGTTCTAATTATTAACCTAATCAATTTTAACCAAT
50446 TATTTGATTCAAATAATTAAAATGGAACCTCTAGCAAAAGTGAGGACCAAATTAAAAATTCCCTA
65 TATTTGATTCAAATAATTAAAATGGAACCTCTAGCAAAAGTGAGGACCAAATTAAAAATTCCCTA
*
50511 AATTTAAGG
130 AATTTAAAG
** * * * * *
50520 ACTAAGTGTGAAATTAAACCT-AAGATGGAGGCTCTAA-TATTATTCCTAATTAATTTTAATCAA
1 ACTAAGTGTGAAATTAGGCCTAAAG-TGAAGGTTCTAATTATTA-ACCTAATCAATTTTAACCAA
50583 TTAT
64 TTAT
50587 GTAATTATTC
Statistics
Matches: 179, Mismatches: 20, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
137 11 0.06
138 65 0.36
139 102 0.57
140 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (138 bp):
ACTAAGTGTGAAATTAGGCCTAAAGTGAAGGTTCTAATTATTAACCTAATCAATTTTAACCAATT
ATTTGATTCAAATAATTAAAATGGAACCTCTAGCAAAAGTGAGGACCAAATTAAAAATTCCCTAA
ATTTAAAG
Found at i:52665 original size:17 final size:16
Alignment explanation
Indices: 52610--52665 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
52600 GAAAAAGACC
52610 AAAAAATAATAACAATA
1 AAAAAATAATAA-AATA
* * *
52627 AAAATATAAT-AAGTG
1 AAAAAATAATAAAATA
*
52642 AATAAATAAATAAAATA
1 AAAAAAT-AATAAAATA
52659 AAAAAAT
1 AAAAAAT
52666 GTTAAAGAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
15 7 0.24
16 4 0.14
17 18 0.62
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (16 bp):
AAAAAATAATAAAATA
Found at i:52757 original size:18 final size:18
Alignment explanation
Indices: 52721--52768 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
52711 AAAATACGGT
*
52721 AATAATAAATAAGGAATA
1 AATAATAAATAAAGAATA
52739 ACATAATAAA-AAAGAATA
1 A-ATAATAAATAAAGAATA
52757 AATACATAAATA
1 AATA-ATAAATA
52769 TATATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 3 0.12
18 14 0.54
19 9 0.35
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (18 bp):
AATAATAAATAAAGAATA
Found at i:52810 original size:2 final size:2
Alignment explanation
Indices: 52803--52848 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
52793 AAATAAATAG
52803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52842 A- AT AT AT
1 AT AT AT AT
52849 GTAATAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.10
2 36 0.90
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:54048 original size:23 final size:23
Alignment explanation
Indices: 54022--54070 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
54012 GCACCATATG
54022 TAAAA-AATGAATAATATATTATA
1 TAAAATAATGAAT-ATATATTATA
*
54045 TAAAATAATGTATATATATTATA
1 TAAAATAATGAATATATATTATA
54068 TAA
1 TAA
54071 TATTAAAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
TAAAATAATGAATATATATTATA
Found at i:56047 original size:17 final size:17
Alignment explanation
Indices: 56018--56050 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
56008 CTTGAACCCA
56018 CCTTATTTTTCTTTTTT
1 CCTTATTTTTCTTTTTT
56035 CCTT-TTTTCTCTTTTT
1 CCTTATTTT-TCTTTTT
56051 CATATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (17 bp):
CCTTATTTTTCTTTTTT
Found at i:56058 original size:17 final size:16
Alignment explanation
Indices: 56021--56059 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
56011 GAACCCACCT
*
56021 TATTTTTCTTTTTTCC
1 TATTTTTCTTTTTTCA
56037 T-TTTTTCTCTTTTTCA
1 TATTTTTCT-TTTTTCA
56053 TATTTTT
1 TATTTTT
56060 TTTCAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 7 0.35
16 8 0.40
17 5 0.25
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTTTTCTTTTTTCA
Found at i:56120 original size:6 final size:7
Alignment explanation
Indices: 56106--56157 Score: 90
Period size: 7 Copynumber: 7.7 Consensus size: 7
56096 AACATTTTCC
56106 TCTTTTT
1 TCTTTTT
56113 TC-TTTT
1 TCTTTTT
56119 TCTTTTT
1 TCTTTTT
56126 TC-TTTT
1 TCTTTTT
56132 TCTTTTT
1 TCTTTTT
56139 TCTTTTT
1 TCTTTTT
56146 TCTTTTT
1 TCTTTTT
56153 TCTTT
1 TCTTT
56158 CTTCGACTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.28
7 31 0.72
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TCTTTTT
Found at i:56124 original size:13 final size:13
Alignment explanation
Indices: 56106--56157 Score: 95
Period size: 13 Copynumber: 3.9 Consensus size: 13
56096 AACATTTTCC
56106 TCTTTTTTCTTTT
1 TCTTTTTTCTTTT
56119 TCTTTTTTCTTTT
1 TCTTTTTTCTTTT
56132 TCTTTTTTCTTTTT
1 TCTTTTTTC-TTTT
56146 TCTTTTTTCTTT
1 TCTTTTTTCTTT
56158 CTTCGACTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 25 0.66
14 13 0.34
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TCTTTTTTCTTTT
Found at i:56131 original size:20 final size:20
Alignment explanation
Indices: 56106--56157 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
56096 AACATTTTCC
56106 TCTTTTTTCTTTTTCTTTTT
1 TCTTTTTTCTTTTTCTTTTT
56126 TC-TTTTTCTTTTTTCTTTTT
1 TCTTTTTTC-TTTTTCTTTTT
56146 TCTTTTTTCTTT
1 TCTTTTTTCTTT
56158 CTTCGACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.20
20 18 0.60
21 6 0.20
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TCTTTTTTCTTTTTCTTTTT
Found at i:67790 original size:22 final size:22
Alignment explanation
Indices: 67762--67812 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
67752 CATCTATCAG
67762 GGTACTAAATCAGTAACGTGGC
1 GGTACTAAATCAGTAACGTGGC
67784 GGTACTAAATCAGTAACGTGGC
1 GGTACTAAATCAGTAACGTGGC
67806 GGTACTA
1 GGTACTA
67813 CCCCAAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (22 bp):
GGTACTAAATCAGTAACGTGGC
Found at i:72292 original size:49 final size:49
Alignment explanation
Indices: 72233--72330 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
72223 CCCATAGCAT
*
72233 TCACCCCTAGTATGAATGCGGGAGATCAACTATTGCGCCCAATAACTGG
1 TCACCCCTAGTATGAATGCGGGAGATCAACTATTGCACCCAATAACTGG
* *
72282 TCACCCCTAGTATGAATGCGGGAGATCAGCTATTGCACCTAATAACTGG
1 TCACCCCTAGTATGAATGCGGGAGATCAACTATTGCACCCAATAACTGG
72331 ATATTACCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (49 bp):
TCACCCCTAGTATGAATGCGGGAGATCAACTATTGCACCCAATAACTGG
Found at i:73306 original size:30 final size:33
Alignment explanation
Indices: 73237--73307 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 33
73227 ATAGGATTAA
* *
73237 AAAATAAATTAAACATGTTAGAAAGACCAAATT
1 AAAATAAATTAAACATATTAGAAAGACCAAATC
* *
73270 AAAATAAATTAAA-A-ATTA-AGAGACTAAATC
1 AAAATAAATTAAACATATTAGAAAGACCAAATC
73300 AAAATAAA
1 AAAATAAA
73308 ATACAAAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.50
31 3 0.09
32 1 0.03
33 13 0.38
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (33 bp):
AAAATAAATTAAACATATTAGAAAGACCAAATC
Found at i:73629 original size:105 final size:107
Alignment explanation
Indices: 73463--73783 Score: 342
Period size: 105 Copynumber: 3.0 Consensus size: 107
73453 GAGTCACTAC
* * * * * ** * **
73463 ATATGACCAAAATGTAAAAACACGCTGAACTTAGAGTGACTAAATAGAAAATATTCTAATAAACA
1 ATATGACCAGAATG-CAAAAGAC-CTAAACTTAGAGGGACTAAATAGAAAATAACCCAATAAATG
* ** * * *
73528 TTTAACATACAAGAAAAATGGGTAAATAACAATTTTAGTCCTCA-
64 TATAACACGCATGAAAAA-GGGTAAATACCAATTTTGGTCCTCAT
* * *
73572 A-ATGACCAGAATGCAAAA-ATCTAAACTTATAGGGTCTAAATAGAAAATAACCCAATAAATGTA
1 ATATGACCAGAATGCAAAAGACCTAAACTTAGAGGGACTAAATAGAAAATAACCCAATAAATGTA
* * *
73635 TAACACGCATGAAAAAAGGGTAAATACCAATTTCGGTTCTTAT
66 TAACACGCATG-AAAAAGGGTAAATACCAATTTTGGTCCTCAT
* * *
73678 ATGTGACCAGAATGCAAAAGCGCCCTAAACTTAGAGGGACTAAATAAAAAATAACCCAATAAATG
1 ATATGACCAGAATGCAAAA--GACCTAAACTTAGAGGGACTAAATAGAAAATAACCCAATAAATG
73743 TATAACACGCATGAAAAAGGGTAAATACCAATTTTGGTCCT
64 TATAACACGCATGAAAAAGGGTAAATACCAATTTTGGTCCT
73784 TATAGGTAAC
Statistics
Matches: 177, Mismatches: 29, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
105 61 0.34
106 7 0.04
107 20 0.11
108 11 0.06
109 27 0.15
110 51 0.29
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (107 bp):
ATATGACCAGAATGCAAAAGACCTAAACTTAGAGGGACTAAATAGAAAATAACCCAATAAATGTA
TAACACGCATGAAAAAGGGTAAATACCAATTTTGGTCCTCAT
Found at i:73735 original size:110 final size:109
Alignment explanation
Indices: 73592--73805 Score: 338
Period size: 110 Copynumber: 2.0 Consensus size: 109
73582 ATGCAAAAAT
* * *
73592 CTAAACTTATAGGGTCTAAATAGAAAATAACCCAATAAATGTATAACACGCATGAAAAAAGGGTA
1 CTAAACTTAGAGGGACTAAATAAAAAATAACCCAATAAATGTATAACACGCATG-AAAAAGGGTA
* * * * *
73657 AATACCAATTTCGGTTCTTATATGTGACCAGAATGCAAAAGCGCC
65 AATACCAATTTCGGTCCTTATAGGTAACCAAAATGAAAAAGCGCC
73702 CTAAACTTAGAGGGACTAAATAAAAAATAACCCAATAAATGTATAACACGCATGAAAAAGGGTAA
1 CTAAACTTAGAGGGACTAAATAAAAAATAACCCAATAAATGTATAACACGCATGAAAAAGGGTAA
*
73767 ATACCAATTTTGGTCCTTATAGGTAACCAAAATGAAAAA
66 ATACCAATTTCGGTCCTTATAGGTAACCAAAATGAAAAA
73806 AACGCTAAAC
Statistics
Matches: 95, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
109 44 0.46
110 51 0.54
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.23
Consensus pattern (109 bp):
CTAAACTTAGAGGGACTAAATAAAAAATAACCCAATAAATGTATAACACGCATGAAAAAGGGTAA
ATACCAATTTCGGTCCTTATAGGTAACCAAAATGAAAAAGCGCC
Found at i:75272 original size:2 final size:2
Alignment explanation
Indices: 75265--75294 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
75255 GGTAAAAATT
75265 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
75295 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:75675 original size:19 final size:20
Alignment explanation
Indices: 75651--75698 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
75641 AATGAATGAA
75651 AATAGATGATTG-GATTAAC
1 AATAGATGATTGAGATTAAC
75670 AATAGAAGATGATTGAGATTAAC
1 AAT---AGATGATTGAGATTAAC
*
75693 AGTAGA
1 AATAGA
75699 AGATGATAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
22 9 0.38
23 9 0.38
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.27
Consensus pattern (20 bp):
AATAGATGATTGAGATTAAC
Found at i:75681 original size:22 final size:23
Alignment explanation
Indices: 75654--75705 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
75644 GAATGAAAAT
75654 AGATGATTG-GATTAACAATAGA
1 AGATGATTGAGATTAACAATAGA
*
75676 AGATGATTGAGATTAACAGTAGA
1 AGATGATTGAGATTAACAATAGA
75699 AGATGAT
1 AGATGAT
75706 AAGATATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.44, C:0.04, G:0.25, T:0.27
Consensus pattern (23 bp):
AGATGATTGAGATTAACAATAGA
Found at i:77037 original size:29 final size:29
Alignment explanation
Indices: 77003--77059 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
76993 ATAAGTAACT
* *
77003 AAATAATTAAAATAAAATAAATATTAAAC
1 AAATAAATAAAATAAAAGAAATATTAAAC
* *
77032 AAATAAATGAAATAAAAGAAATTTTAAA
1 AAATAAATAAAATAAAAGAAATATTAAA
77060 TTAATTGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (29 bp):
AAATAAATAAAATAAAAGAAATATTAAAC
Done.