Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007436.1 Hibiscus syriacus cultivar Beakdansim tig00020266_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: 132912
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4269 original size:21 final size:21
Alignment explanation
Indices: 4234--4277 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
4224 TAAAGGATTG
*
4234 AAATTAAACTAAATTAAAAGGC
1 AAATCAAACTAAATT-AAAGGC
4256 AAATCAAA-TAAATTAAAGGC
1 AAATCAAACTAAATTAAAGGC
4276 AA
1 AA
4278 TTGGTTGTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 6 0.29
22 7 0.33
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.20
Consensus pattern (21 bp):
AAATCAAACTAAATTAAAGGC
Found at i:10292 original size:24 final size:24
Alignment explanation
Indices: 10260--10307 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
10250 TACATTGAAC
10260 AATTTTCCTGTTGAAATAAGTTTT
1 AATTTTCCTGTTGAAATAAGTTTT
10284 AATTTTCCTGTTGAAATAAGTTTT
1 AATTTTCCTGTTGAAATAAGTTTT
10308 CTTTAGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.50
Consensus pattern (24 bp):
AATTTTCCTGTTGAAATAAGTTTT
Found at i:18948 original size:21 final size:21
Alignment explanation
Indices: 18924--18982 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
18914 TTGACTCGGC
*
18924 TGTGGTGGCATCTGAAATGGA
1 TGTGGTGCCATCTGAAATGGA
* *
18945 TGTGGTGCCATCTGATATGGC
1 TGTGGTGCCATCTGAAATGGA
*
18966 TGCGGTGCCATCTGAAA
1 TGTGGTGCCATCTGAAA
18983 CGGTTGTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (21 bp):
TGTGGTGCCATCTGAAATGGA
Found at i:20708 original size:35 final size:35
Alignment explanation
Indices: 20638--20715 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
20628 TACAGCTGCA
*
20638 AAAAATAATAAAAAATTAATACAATAAAATTTAAT
1 AAAAATAATAAAAAATTAATACAATAAAATATAAT
** * *
20673 AAAAATAATAAATTATTAAATA-ATTATAATATAAT
1 AAAAATAATAAAAAATT-AATACAATAAAATATAAT
20708 AGAAAATA
1 A-AAAATA
20716 TGTTATTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
35 26 0.72
36 10 0.28
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (35 bp):
AAAAATAATAAAAAATTAATACAATAAAATATAAT
Found at i:24563 original size:31 final size:31
Alignment explanation
Indices: 24528--24595 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
24518 GATAGTAGAG
*
24528 TGACCATTTTGTAACAAATTAATAACATTAA
1 TGACCATTTTGTAACAAATCAATAACATTAA
* * * *
24559 TGACCATTTTGTTACAAATCGATAATATTAG
1 TGACCATTTTGTAACAAATCAATAACATTAA
24590 TGACCA
1 TGACCA
24596 ATTACTTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (31 bp):
TGACCATTTTGTAACAAATCAATAACATTAA
Found at i:25190 original size:41 final size:35
Alignment explanation
Indices: 25120--25195 Score: 152
Period size: 35 Copynumber: 2.2 Consensus size: 35
25110 ATATTTATTT
25120 TTATAAAATTAATATTAATATTCTAAAAGTTAAAG
1 TTATAAAATTAATATTAATATTCTAAAAGTTAAAG
25155 TTATAAAATTAATATTAATATTCTAAAAGTTAAAG
1 TTATAAAATTAATATTAATATTCTAAAAGTTAAAG
25190 TTATAA
1 TTATAA
25196 TATTTTTATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (35 bp):
TTATAAAATTAATATTAATATTCTAAAAGTTAAAG
Found at i:31733 original size:115 final size:115
Alignment explanation
Indices: 31531--31767 Score: 474
Period size: 115 Copynumber: 2.1 Consensus size: 115
31521 ACGGGTTTCG
31531 ACCCGACTCGATCGGGTCAAGTTTTTTAAAAACAATATGGGTTAGGGTCGAGTCGTTCGAGTTTT
1 ACCCGACTCGATCGGGTCAAGTTTTTTAAAAACAATATGGGTTAGGGTCGAGTCGTTCGAGTTTT
31596 TTAAAAGGTGATCTTTGGATCGGGTCGGATTCGGGTTTAGGGTGAAAAAT
66 TTAAAAGGTGATCTTTGGATCGGGTCGGATTCGGGTTTAGGGTGAAAAAT
31646 ACCCGACTCGATCGGGTCAAGTTTTTTAAAAACAATATGGGTTAGGGTCGAGTCGTTCGAGTTTT
1 ACCCGACTCGATCGGGTCAAGTTTTTTAAAAACAATATGGGTTAGGGTCGAGTCGTTCGAGTTTT
31711 TTAAAAGGTGATCTTTGGATCGGGTCGGATTCGGGTTTAGGGTGAAAAAT
66 TTAAAAGGTGATCTTTGGATCGGGTCGGATTCGGGTTTAGGGTGAAAAAT
31761 ACCCGAC
1 ACCCGAC
31768 CCGACCTGGA
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 122 1.00
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.31
Consensus pattern (115 bp):
ACCCGACTCGATCGGGTCAAGTTTTTTAAAAACAATATGGGTTAGGGTCGAGTCGTTCGAGTTTT
TTAAAAGGTGATCTTTGGATCGGGTCGGATTCGGGTTTAGGGTGAAAAAT
Found at i:31806 original size:115 final size:113
Alignment explanation
Indices: 31560--31791 Score: 338
Period size: 115 Copynumber: 2.0 Consensus size: 113
31550 AGTTTTTTAA
*
31560 AAACAATATGGGTTAGGGTCGAGTCGTTCGAGTTTTTTAAAAGGTGATCTTTGGATCGGGTCGGA
1 AAACAATATGAGTTAGGGTCGAGTCGTTCGAGTTTTTTAAAAGGTGATCTTTGGATCGGGTCGGA
* * *** * *
31625 TTCGGGTTTAGGGTGAAAAATACCCGACTCGATCGGGTCAAGTTTTTT
66 TTCGGGTTTAGGGTGAAAAATACCCGACCCGACCGGAAAAAATATTTT
*
31673 AAAAACAATATGGGTTAGGGTCGAGTCGTTCGAGTTTTTTAAAAGGTGATCTTTGGATCGGGTCG
1 --AAACAATATGAGTTAGGGTCGAGTCGTTCGAGTTTTTTAAAAGGTGATCTTTGGATCGGGTCG
31738 GATTCGGGTTTAGGGTGAAAAATACCCGACCCGACCTGGAAAAAAATAATTTT
64 GATTCGGGTTTAGGGTGAAAAATACCCGACCCGACC-GG-AAAAAAT-ATTTT
31791 A
1 A
31792 CCTTATATAT
Statistics
Matches: 107, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
115 97 0.91
116 3 0.03
117 3 0.03
118 4 0.04
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (113 bp):
AAACAATATGAGTTAGGGTCGAGTCGTTCGAGTTTTTTAAAAGGTGATCTTTGGATCGGGTCGGA
TTCGGGTTTAGGGTGAAAAATACCCGACCCGACCGGAAAAAATATTTT
Found at i:32006 original size:32 final size:32
Alignment explanation
Indices: 31935--32007 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 32
31925 GGTCGAGTTC
* *
31935 GGGTCGGGTGAAGGGTATATAATTTTCAGGTT
1 GGGTCGGGTGAAGGATATAAAATTTTCAGGTT
* * * **
31967 AGATCGGGTGAATGATATAAAATTTTTTGGTT
1 GGGTCGGGTGAAGGATATAAAATTTTCAGGTT
31999 GGGTCGGGT
1 GGGTCGGGT
32008 TGGTCGAAAC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.23, C:0.05, G:0.36, T:0.36
Consensus pattern (32 bp):
GGGTCGGGTGAAGGATATAAAATTTTCAGGTT
Found at i:35682 original size:20 final size:20
Alignment explanation
Indices: 35657--35747 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
35647 AAAATTAAAT
35657 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGGATCAGTTTTA
* *
35677 ATTAGATAGCATCAGTTTTT
1 ATTAGATAGGATCAGTTTTA
* *
35697 ATT--CT---ATTAG--TT-
1 ATTAGATAGGATCAGTTTTA
*
35709 ATTAGATAGGATCATTTTTA
1 ATTAGATAGGATCAGTTTTA
*
35729 ATTAGATAGAATCAGTTTT
1 ATTAGATAGGATCAGTTTT
35748 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGGATCAGTTTTA
Found at i:35717 original size:52 final size:53
Alignment explanation
Indices: 35656--35781 Score: 218
Period size: 53 Copynumber: 2.4 Consensus size: 53
35646 CAAAATTAAA
* *
35656 TATTAGATAGGATCAGTTTTAATTAGATAGCATCAG-TTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
35708 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
*
35761 TATTAGATAGAATCATTTTTA
1 TATTAGATAGGATCATTTTTA
35782 TTCTGTTGTT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 34 0.49
53 36 0.51
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (53 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
Found at i:40376 original size:20 final size:20
Alignment explanation
Indices: 40351--40493 Score: 75
Period size: 20 Copynumber: 8.0 Consensus size: 20
40341 TAAATTAAAT
*
40351 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
40371 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
40391 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
40403 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
*
40423 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
40443 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
40455 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
40475 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
40494 TTATTCTATT
Statistics
Matches: 90, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
12 6 0.07
13 4 0.04
14 2 0.02
15 8 0.09
17 6 0.07
18 2 0.02
19 4 0.04
20 58 0.64
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.46
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:40428 original size:52 final size:52
Alignment explanation
Indices: 40350--40527 Score: 329
Period size: 52 Copynumber: 3.4 Consensus size: 52
40340 CTAAATTAAA
*
40350 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
40402 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
40454 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
*
40507 TATTAGATAGAATCATTTTTA
1 TATTAGATAGGATCATTTTTA
40528 TTCTGTTGCT
Statistics
Matches: 123, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
52 87 0.71
53 36 0.29
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:43306 original size:59 final size:60
Alignment explanation
Indices: 43231--43348 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
43221 TTAAAAGTTC
* * * **
43231 TTTTACTTTAATTAAAAGTTAATT-TTGTCGTTCTACTATAAAAGGGAACATTTTAGTCT
1 TTTTACTATAACTAAAAGTTAATTGTGGTCCCTCTACTATAAAAGGGAACATTTTAGTCT
** *
43290 TTTTACTATAACTAAAAGTTTGTTGTGGTCCCTCTACTATAAAAGGGGACATTTTAGTC
1 TTTTACTATAACTAAAAGTTAATTGTGGTCCCTCTACTATAAAAGGGAACATTTTAGTC
43349 CTTGTACGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
59 20 0.40
60 30 0.60
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (60 bp):
TTTTACTATAACTAAAAGTTAATTGTGGTCCCTCTACTATAAAAGGGAACATTTTAGTCT
Found at i:45579 original size:117 final size:117
Alignment explanation
Indices: 45401--45632 Score: 464
Period size: 117 Copynumber: 2.0 Consensus size: 117
45391 GAATTTTATT
45401 TTATAATTCAACTCGAATTTAGAACTTGTTAAACAAGTTAAGTCGGATTATTTTAACATTAAGAT
1 TTATAATTCAACTCGAATTTAGAACTTGTTAAACAAGTTAAGTCGGATTATTTTAACATTAAGAT
45466 TGTCTTTTCAAATAAAATCTAATTGAATTTTTTAACGTTAAATTAAAAAAAA
66 TGTCTTTTCAAATAAAATCTAATTGAATTTTTTAACGTTAAATTAAAAAAAA
45518 TTATAATTCAACTCGAATTTAGAACTTGTTAAACAAGTTAAGTCGGATTATTTTAACATTAAGAT
1 TTATAATTCAACTCGAATTTAGAACTTGTTAAACAAGTTAAGTCGGATTATTTTAACATTAAGAT
45583 TGTCTTTTCAAATAAAATCTAATTGAATTTTTTAACGTTAAATTAAAAAA
66 TGTCTTTTCAAATAAAATCTAATTGAATTTTTTAACGTTAAATTAAAAAA
45633 TTTTTTTATA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 115 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (117 bp):
TTATAATTCAACTCGAATTTAGAACTTGTTAAACAAGTTAAGTCGGATTATTTTAACATTAAGAT
TGTCTTTTCAAATAAAATCTAATTGAATTTTTTAACGTTAAATTAAAAAAAA
Found at i:45863 original size:21 final size:22
Alignment explanation
Indices: 45837--45886 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
45827 AAAAGAATCA
45837 TAAAAAATA-TTAAAATTCCTT
1 TAAAAAATACTTAAAATTCCTT
* *
45858 TGAAAAA-ACTTAAAATTTCTT
1 TAAAAAATACTTAAAATTCCTT
45879 TAAAAAAT
1 TAAAAAAT
45887 TGAGAAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAAAAATACTTAAAATTCCTT
Found at i:48044 original size:42 final size:42
Alignment explanation
Indices: 47979--48368 Score: 317
Period size: 42 Copynumber: 9.4 Consensus size: 42
47969 AAAATTGTGA
* * *
47979 CGTTTATTACAAAAACACCGCTAAGGTGCATGAATATCGCGG
1 CGTTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGG
* * * * * *
48021 TGTTTATTACAAAAACACTGCTAAAGTACATGATTATCGCGA
1 CGTTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGG
* *
48063 CGTTTATTACAAAAACACCGCTAAAGTGCATGATTATTGCGA
1 CGTTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGG
* * *
48105 CGTTTA-T-CAAAAAGTA--GCTAAAGTGCATGATTATTACGG
1 CGTTTATTACAAAAA-CACCGCTAAAGTGCATGACTATTGCGG
* ** * * *
48144 CATTTATTGTAAAAACGCCACTAAAGTGCATGATTATTGCGG
1 CGTTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGG
* * *
48186 TGTTTA-TA-AAAAAAAGCCGCTAAAGTACATGACTATTGCGG
1 CGTTTATTACAAAAACA-CCGCTAAAGTGCATGACTATTGCGG
* *** * * * * *
48227 CATTTATTAC-AAAATGTCGCTAAGGTACATTACTGTTACGG
1 CGTTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGG
*** *
48268 CGTTTATTACAAAAATGTCGCTAAATTGCATGACTATTGCGG
1 CGTTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGG
* * ** *
48310 CTTTTATTACAAAAAAAACTACTAAGGTGCATGACTATTGCGG
1 CGTTTATTAC-AAAAACACCGCTAAAGTGCATGACTATTGCGG
* *
48353 TGTTTATAACAAAAAC
1 CGTTTATTACAAAAAC
48369 GTCGCCTTAT
Statistics
Matches: 283, Mismatches: 55, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
39 26 0.09
40 12 0.04
41 63 0.22
42 150 0.53
43 32 0.11
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (42 bp):
CGTTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGG
Found at i:48170 original size:81 final size:82
Alignment explanation
Indices: 47981--48240 Score: 272
Period size: 81 Copynumber: 3.1 Consensus size: 82
47971 AATTGTGACG
* * * * ** *
47981 TTTATTACAAAAACACCGCTAAGGTGCATGAATATCGCGGTGTTTATTACAAAAACA-CTGCTAA
1 TTTATTACAAAAACACCACTAAAGTGCATGATTATTGCGACGTTTA-TA-AAAAA-AGCAGCTAA
* * *
48045 AGTACATGATTATCGCGACG
63 AGTACATGATTATTGCGGCA
* * *
48065 TTTATTACAAAAACACCGCTAAAGTGCATGATTATTGCGACGTTTAT-CAAAAAGTAGCTAAAGT
1 TTTATTACAAAAACACCACTAAAGTGCATGATTATTGCGACGTTTATAAAAAAAGCAGCTAAAGT
* *
48129 GCATGATTATTACGGCA
66 ACATGATTATTGCGGCA
** * ** *
48146 TTTATTGTAAAAACGCCACTAAAGTGCATGATTATTGCGGTGTTTATAAAAAAAAGCCGCTAAAG
1 TTTATTACAAAAACACCACTAAAGTGCATGATTATTGCGACGTTTAT-AAAAAAAGCAGCTAAAG
*
48211 TACATGACTATTGCGGCA
65 TACATGATTATTGCGGCA
48229 TTTATTACAAAA
1 TTTATTACAAAA
48241 TGTCGCTAAG
Statistics
Matches: 146, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
80 1 0.01
81 65 0.45
83 39 0.27
84 41 0.28
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (82 bp):
TTTATTACAAAAACACCACTAAAGTGCATGATTATTGCGACGTTTATAAAAAAAGCAGCTAAAGT
ACATGATTATTGCGGCA
Found at i:50489 original size:20 final size:20
Alignment explanation
Indices: 50466--50506 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
50456 AACTCGTTCT
50466 TTATTTAGTTT-ATTTATTAA
1 TTATTTA-TTTAATTTATTAA
*
50486 TTATTTATTTAATTTGTTAA
1 TTATTTATTTAATTTATTAA
50506 T
1 T
50507 CTTAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
TTATTTATTTAATTTATTAA
Found at i:51614 original size:22 final size:22
Alignment explanation
Indices: 51573--51615 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
51563 TATGGTCATT
* * *
51573 TTAAAATTTATTTTTTAAAATA
1 TTAAAATATATTTATAAAAATA
51595 TTAAAATATATTTATAAAAAT
1 TTAAAATATATTTATAAAAAT
51616 CCCTAGTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAAAATATATTTATAAAAATA
Found at i:52868 original size:20 final size:21
Alignment explanation
Indices: 52843--52935 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
52833 TTTTCCCAAT
*
52843 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
52863 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
52884 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
52904 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
52925 TCGCAATGCGA
1 TCGCAATGCGA
52936 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:52888 original size:41 final size:41
Alignment explanation
Indices: 52843--52935 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
52833 TTTTCCCAAT
52843 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
52884 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
52925 TCGCAATGCGA
1 TCGCAATGCGA
52936 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:52948 original size:41 final size:41
Alignment explanation
Indices: 52862--52996 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
52852 GAATAAGTAA
* *
52862 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
52903 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
52944 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
52985 TTCGCAACGCGA
1 ATCGCAACGCGA
52997 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:52949 original size:20 final size:20
Alignment explanation
Indices: 52924--53038 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
52914 AATTGGGAAA
52924 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * **
52944 ATCGCAATGCGATAATAAAAA
1 ATCGCAATGCGATACT-GACT
* * *
52965 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
52985 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
53005 TTCACAATGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
53025 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
53039 TTTCAAAGCG
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 47 0.64
21 25 0.34
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:53234 original size:22 final size:22
Alignment explanation
Indices: 53206--53249 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53196 CACTCTCTCA
53206 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
53228 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
53250 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:53536 original size:20 final size:20
Alignment explanation
Indices: 53511--53548 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53501 CGATTCTCTC
53511 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
53531 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
53549 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:54736 original size:18 final size:18
Alignment explanation
Indices: 54715--54759 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
54705 TCCACTTCGG
*
54715 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
54733 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
54751 GAGCCATCA
1 GAGCCATCA
54760 TCTGATCGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:54989 original size:19 final size:20
Alignment explanation
Indices: 54946--55001 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
54936 CGTAACACGA
54946 AAATGACTATCGCAACGCAG
1 AAATGACTATCGCAACGCAG
* *
54966 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCAG
**
54985 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
55002 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCAG
Found at i:55009 original size:14 final size:14
Alignment explanation
Indices: 54990--55029 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
54980 ATGCGAAATG
54990 AAAATCGCAACGAC
1 AAAATCGCAACGAC
55004 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
55018 AAAATTGCAACG
1 AAAATCGCAACG
55030 CGAAATGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.50, C:0.25, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:55082 original size:14 final size:14
Alignment explanation
Indices: 55063--55120 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
55053 TTGTGTTTCG
55063 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
55077 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
55093 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
55109 CGTTGCGATTTT
1 CGTTGCGATTTT
55121 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:55097 original size:32 final size:33
Alignment explanation
Indices: 55058--55128 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 33
55048 GCGATTTGTG
55058 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
55090 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
55123 TTTCGC
1 TTTCGC
55129 ATTACGATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 27 0.71
33 11 0.29
ACGTcount: A:0.08, C:0.20, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:55158 original size:20 final size:19
Alignment explanation
Indices: 55121--55174 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
55111 TTGCGATTTT
* *
55121 CATTTCGCATTACGATAGC
1 CATTTCGCGTTGCGATAGC
*
55140 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
55160 CATTTCGCGTTGCGA
1 CATTTCGCGTTGCGA
55175 ATTTAAGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:55170 original size:19 final size:19
Alignment explanation
Indices: 55109--55174 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
55099 GCGATTTTGT
**
55109 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
55128 CATTACGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
55148 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
55167 CGTTGCGA
1 CGTTGCGA
55175 ATTTAAGTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 22 0.58
20 16 0.42
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:57039 original size:14 final size:14
Alignment explanation
Indices: 57007--57041 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
56997 GATTGTTTAA
57007 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
57021 ATGATTTGTAAATG
1 TTGATTTGTAAAAG
57035 TTGATTT
1 TTGATTT
57042 TTTAATTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:57208 original size:20 final size:20
Alignment explanation
Indices: 57183--57239 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
57173 TCGCATTGCG
*
57183 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
*
57203 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAACC
*
57223 ATTTTCGCATTGCGATA
1 ATTTTCGCGTTGCGATA
57240 GTCAAATGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:57765 original size:19 final size:19
Alignment explanation
Indices: 57743--57809 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
57733 TATCGCAACG
57743 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
57762 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
57780 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
57794 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
57810 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:57885 original size:20 final size:20
Alignment explanation
Indices: 57828--57885 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
57818 TCGCATTGCG
* *
57828 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
57848 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
57868 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
57886 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:59531 original size:42 final size:42
Alignment explanation
Indices: 59485--59568 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
59475 CGATGACAGT
* *
59485 GGCCTCTTGAACGGT-GTGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAG-GAGGGGACTCTCGAGGAATGATAGG
* * *
59527 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
59569 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:60050 original size:20 final size:21
Alignment explanation
Indices: 60006--60044 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
59996 ACTACCATCT
60006 CACGTAGAGTGACAACCTCAC
1 CACGTAGAGTGACAACCTCAC
60027 CACGTA-AGTAGAC-ACCTC
1 CACGTAGAGT-GACAACCTC
60045 CACACGCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.15
Consensus pattern (21 bp):
CACGTAGAGTGACAACCTCAC
Found at i:61642 original size:33 final size:33
Alignment explanation
Indices: 61585--61682 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 33
61575 ACGAGATAAT
*
61585 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
61619 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
61652 GACAATCGCAACGCGAAATGAAAATCGCAAC
1 GAGAATCGCAACGCGAAATGACTATCGCAAC
61683 TGCGAAATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.40, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:61677 original size:19 final size:19
Alignment explanation
Indices: 61560--61744 Score: 183
Period size: 19 Copynumber: 10.1 Consensus size: 19
61550 TCTTTTGGTT
*
61560 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
61579 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
61599 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
61617 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
61633 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
61651 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
61666 GAAATGAAAATCGCAACTGC
1 GAAATGAAAATCGCAAC-GC
61686 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
61705 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
61724 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
61743 GA
1 GA
61745 TTTTGGTTTC
Statistics
Matches: 140, Mismatches: 13, Indels: 26
0.78 0.07 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 63 0.45
20 46 0.33
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:62356 original size:20 final size:20
Alignment explanation
Indices: 62331--62380 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
62321 GCGCTATGTA
62331 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
62351 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
62371 TATCTCGTTG
1 AATCGCGTTG
62381 TGATTTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:62417 original size:20 final size:20
Alignment explanation
Indices: 62392--62445 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
62382 GATTTTGTAT
62392 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
62412 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
62432 TATCGCATTGCGAT
1 TATCGCATTGCGAT
62446 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:62447 original size:61 final size:61
Alignment explanation
Indices: 62332--62448 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
62322 CGCTATGTAA
* * * * * *
62332 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGTGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
62393 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
62449 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:62464 original size:61 final size:61
Alignment explanation
Indices: 62332--62466 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
62322 CGCTATGTAA
* * * * * * ** *
62332 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGTGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
62393 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
62455 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
62467 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:65092 original size:25 final size:26
Alignment explanation
Indices: 65064--65112 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
65054 ATATATATAT
65064 ATAAAA-TAATAAT-AACAAATAAAAA
1 ATAAAAGTAA-AATAAACAAATAAAAA
*
65089 ATAAAAGTAAAATAAATAAATAAA
1 ATAAAAGTAAAATAAACAAATAAA
65113 TTATTTCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (26 bp):
ATAAAAGTAAAATAAACAAATAAAAA
Found at i:71657 original size:35 final size:36
Alignment explanation
Indices: 71611--71680 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 36
71601 AAAACCCTGG
*
71611 GGGAATCGGTACCCTCTGGG-GGGAATCTGTTCCCA
1 GGGAATCGGTACCCCCTGGGAGGGAATCTGTTCCCA
71646 GGGAATCGGTACCCCCTGGGAGGGAATCTGTTCCC
1 GGGAATCGGTACCCCCTGGGAGGGAATCTGTTCCC
71681 TCTGGGCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 19 0.58
36 14 0.42
ACGTcount: A:0.17, C:0.27, G:0.34, T:0.21
Consensus pattern (36 bp):
GGGAATCGGTACCCCCTGGGAGGGAATCTGTTCCCA
Found at i:71898 original size:19 final size:20
Alignment explanation
Indices: 71874--71913 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
71864 AATTTAATCG
*
71874 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
71893 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
71913 A
1 A
71914 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:77415 original size:37 final size:37
Alignment explanation
Indices: 77342--77416 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
77332 GTAGGAAAAT
* *
77342 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
77379 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
77416 A
1 A
77417 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:78528 original size:13 final size:12
Alignment explanation
Indices: 78512--78571 Score: 66
Period size: 13 Copynumber: 4.8 Consensus size: 12
78502 AATTGATTAA
*
78512 CACAATTAATACT
1 CACAATTAATA-G
78525 CACAATTAATAG
1 CACAATTAATAG
* *
78537 CACAATTAACATT
1 CACAATTAATA-G
*
78550 CATAATTAATAG
1 CACAATTAATAG
78562 CACAATTAAT
1 CACAATTAAT
78572 GCCAACAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
12 19 0.49
13 20 0.51
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.30
Consensus pattern (12 bp):
CACAATTAATAG
Found at i:78556 original size:25 final size:25
Alignment explanation
Indices: 78486--78570 Score: 100
Period size: 25 Copynumber: 3.4 Consensus size: 25
78476 ATACAATTAA
* *
78486 CACAATTAACATT-ACCAATTGATTAA
1 CACAATTAACATTCA-CAATT-AATAG
* *
78512 CACAATTAATACTCACAATTAATAG
1 CACAATTAACATTCACAATTAATAG
*
78537 CACAATTAACATTCATAATTAATAG
1 CACAATTAACATTCACAATTAATAG
78562 CACAATTAA
1 CACAATTAA
78571 TGCCAACAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
25 34 0.67
26 16 0.31
27 1 0.02
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.29
Consensus pattern (25 bp):
CACAATTAACATTCACAATTAATAG
Found at i:78662 original size:13 final size:13
Alignment explanation
Indices: 78644--78675 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
78634 TGACATTACC
78644 TATTAACAATTAA
1 TATTAACAATTAA
78657 TATTAACAATTAA
1 TATTAACAATTAA
*
78670 CATTAA
1 TATTAA
78676 AAAAAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTAACAATTAA
Found at i:80711 original size:42 final size:42
Alignment explanation
Indices: 80653--80909 Score: 399
Period size: 42 Copynumber: 6.1 Consensus size: 42
80643 GCAAAAACGA
* *
80653 TAAGGTCTTATCC-TTGCACACAACAAAGGAACCTGGGAAATTG
1 TAAGG-CTTA-CCTTTGCACACAACAAAGGGACCTGGGAAACTG
* *
80696 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTG
1 TAAGGCTTACCTTTGCACACAACAAAGGGACCT-GGGAAACTG
*
80739 TAAGGCTTACCTTTGCACACAACAAAGGGACTTGGGAAACTG
1 TAAGGCTTACCTTTGCACACAACAAAGGGACCTGGGAAACTG
* *
80781 TAAGGCTTACCTTTACACACAGCAAAGGGACCTGGGAAACTG
1 TAAGGCTTACCTTTGCACACAACAAAGGGACCTGGGAAACTG
80823 TAAGGCTTACCTTTGCACACAACAAAGGGACCTGGGAAACTG
1 TAAGGCTTACCTTTGCACACAACAAAGGGACCTGGGAAACTG
* *
80865 TAAGGCTTACTTTTGCACACAGCAAAGGGACCTGGGAAACTG
1 TAAGGCTTACCTTTGCACACAACAAAGGGACCTGGGAAACTG
80907 TAA
1 TAA
80910 CGGTAATTAA
Statistics
Matches: 201, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
41 2 0.01
42 156 0.78
43 43 0.21
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (42 bp):
TAAGGCTTACCTTTGCACACAACAAAGGGACCTGGGAAACTG
Found at i:87274 original size:21 final size:21
Alignment explanation
Indices: 87248--87308 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
87238 GGAATTACAG
87248 TGGCTATAGGAATTTCAGCAA
1 TGGCTATAGGAATTTCAGCAA
*
87269 TGGCTATAGGAATTTCAGCAG
1 TGGCTATAGGAATTTCAGCAA
* * *
87290 TGGTTGTAGGATTTTCAGC
1 TGGCTATAGGAATTTCAGC
87309 GGGTTTTGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (21 bp):
TGGCTATAGGAATTTCAGCAA
Found at i:92121 original size:42 final size:42
Alignment explanation
Indices: 92062--92146 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
92052 GACTTCATAA
92062 TATCACGTAGGATATTGTGGTATCCTATCATCAATTAGGACG
1 TATCACGTAGGATATTGTGGTATCCTATCATCAATTAGGACG
* *
92104 TATCACGTAGGTTATTGTGGTATCCTATTATCAATTAGGACG
1 TATCACGTAGGATATTGTGGTATCCTATCATCAATTAGGACG
92146 T
1 T
92147 GCAAGTCAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (42 bp):
TATCACGTAGGATATTGTGGTATCCTATCATCAATTAGGACG
Found at i:96348 original size:3 final size:3
Alignment explanation
Indices: 96340--96391 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
96330 ACATGTAAAT
* * **
96340 TAA TAA TAA TAA TAA TAG TAT TAA TAA TAA T-A TAA CGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
96387 TAA TA
1 TAA TA
96392 TTAAAAAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:96624 original size:43 final size:43
Alignment explanation
Indices: 96550--96887 Score: 208
Period size: 43 Copynumber: 7.8 Consensus size: 43
96540 TGGTGGGGAC
* ** * *
96550 GACACTGCTCATACGCAATGAAGAGGTCTGGTCGTCTAAGGGT
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCATCTAAGGGT
* * *
96593 GACACGGCTCCTACGTGATGAGGAGATCTGG---TC-AGGGGAT
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCATCTAAGGG-T
* * * *
96633 GACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGGAT
1 GACACGGCTCATACGTGATGAAGAGATC-TGGTCATC-TAAGGG-T
* * * * * * *
96679 GATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTT
1 G---ACACGGCTCATACGTGATGAAGA-GATCTGGTCATCTAAGGGT
** *
96725 GACACGGCTCATACGTGATGAAGAGATCTGGTC-TGGGAA--AT
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCAT-CTAAGGGT
* *
96766 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCATCT-AAGG-G-T
* * * * * * * *
96812 AACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTT
1 GACACGGCTCATACGTGATGAAGA-GATCTGGTCATCTAAGGGT
96855 GACACGGCTCATACGTGATGAAGAGATCTGGTC
1 GACACGGCTCATACGTGATGAAGAGATCTGGTC
96888 TGGGGATGAC
Statistics
Matches: 222, Mismatches: 52, Indels: 42
0.70 0.16 0.13
Matches are distributed among these distances:
39 4 0.02
40 27 0.12
41 35 0.16
42 6 0.03
43 77 0.35
44 2 0.01
45 3 0.01
46 37 0.17
47 4 0.02
48 6 0.03
49 20 0.09
50 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (43 bp):
GACACGGCTCATACGTGATGAAGAGATCTGGTCATCTAAGGGT
Found at i:96848 original size:130 final size:132
Alignment explanation
Indices: 96592--96915 Score: 528
Period size: 130 Copynumber: 2.5 Consensus size: 132
96582 CGTCTAAGGG
* * * *
96592 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA
* *
96657 GTTCTTGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATG
66 GTTCTTGGCCATCTTAAAGGATGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATG
96722 GT
131 GT
*
96724 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGAAATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGG-GATGACACGGCTCATACGTGATGAAG
96789 AGTTC-TGGCCATC-TAAAGG-TGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAT
65 AGTTCTTGGCCATCTTAAAGGATGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAT
96851 GGT
130 GGT
* * *
96854 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGA
96916 GGACGGCTGG
Statistics
Matches: 180, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
129 20 0.11
130 84 0.47
131 4 0.02
132 43 0.24
133 29 0.16
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.26
Consensus pattern (132 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA
GTTCTTGGCCATCTTAAAGGATGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATG
GT
Found at i:96875 original size:89 final size:83
Alignment explanation
Indices: 96765--96925 Score: 232
Period size: 83 Copynumber: 1.9 Consensus size: 83
96755 GTCTGGGAAA
* * *
96765 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG---TCT---GGGGATAACACGGTTCCTACATGA
96830 TGAGGACGGCTGGTTATCTATGGT
60 TGAGGACGGCTGGTTATCTATGGT
*
96854 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATGATGAGGA
96919 CGGCTGG
66 CGGCTGG
96926 CCATCTTTAG
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
83 34 0.50
86 3 0.04
89 31 0.46
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (83 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATGATGAGGA
CGGCTGGTTATCTATGGT
Found at i:97542 original size:67 final size:67
Alignment explanation
Indices: 97449--97818 Score: 659
Period size: 67 Copynumber: 5.5 Consensus size: 67
97439 TCATTTTAAG
* * *
97449 AGAAACAGATTCAAAGCTTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
97514 AA
66 AA
* * * *
97516 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGGAATTATCTTAAAAGAGACAAAATTTTGTTCCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
97581 AA
66 AA
*
97583 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
97648 AA
66 AA
97650 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
97715 AA
66 AA
*
97717 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTGTCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
97782 AA
66 AA
97784 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
97819 CAATCTCAAA
Statistics
Matches: 293, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 293 1.00
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:97892 original size:29 final size:29
Alignment explanation
Indices: 97767--97901 Score: 141
Period size: 30 Copynumber: 4.7 Consensus size: 29
97757 TTAAGAGAGA
* * *
97767 CAAA-ATTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTTTTTTCAAAAGGAACAAACT
* *
97795 CAAAGATTTTTGTTTCAAAAGAAACAATCT
1 CAAAGATTTTT-TTTCAAAAGGAACAAACT
* * *
97825 CAAAGATTTTTATTCAAAATGAGCAAACT
1 CAAAGATTTTTTTTCAAAAGGAACAAACT
*
97854 CAAAGA--TTTTTTCAAGAGGAACAAACT
1 CAAAGATTTTTTTTCAAAAGGAACAAACT
*
97881 CAAAGATTTTTTCCTCAAAAG
1 CAAAGATTTTTT-TTCAAAAG
97902 AAATTGTCTT
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
27 23 0.26
28 4 0.05
29 28 0.32
30 33 0.38
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (29 bp):
CAAAGATTTTTTTTCAAAAGGAACAAACT
Found at i:98225 original size:36 final size:36
Alignment explanation
Indices: 98155--98242 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 36
98145 GTCTCAAGCG
* * *
98155 AAATTTGC-TTTA-AGATATAGTCTCAAATGGGACA
1 AAATTTGCTTTTAGAGAAATAGTCTCAAACGAGACA
* *
98189 AAATTTGCTTTTAGAGAAATTGTCTCAAGCGAGACA
1 AAATTTGCTTTTAGAGAAATAGTCTCAAACGAGACA
* *
98225 AAGTTTG-TTTTTGAGAAA
1 AAATTTGCTTTTAGAGAAA
98243 ACGATCTCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
34 8 0.18
35 14 0.31
36 23 0.51
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (36 bp):
AAATTTGCTTTTAGAGAAATAGTCTCAAACGAGACA
Found at i:98251 original size:36 final size:36
Alignment explanation
Indices: 98185--98258 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
98175 TCTCAAATGG
**
98185 GACAAAATTTGCTTTTAGAGAAATTGTCTCAAGCGA
1 GACAAAATTTGCTTTTAGAGAAAACGTCTCAAGCGA
* * *
98221 GACAAAGTTTG-TTTTTGAGAAAACGATCTCAAGTGA
1 GACAAAATTTGCTTTTAGAGAAAACG-TCTCAAGCGA
98257 GA
1 GA
98259 TCAACTTTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 11 0.34
36 21 0.66
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (36 bp):
GACAAAATTTGCTTTTAGAGAAAACGTCTCAAGCGA
Found at i:98389 original size:105 final size:101
Alignment explanation
Indices: 98210--98442 Score: 292
Period size: 105 Copynumber: 2.3 Consensus size: 101
98200 TAGAGAAATT
*
98210 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
* *
98274 GTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
64 GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
98312 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
98376 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 TAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
98417 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
98443 AAAATTCTCA
Statistics
Matches: 115, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 5 0.04
104 4 0.03
105 78 0.68
106 5 0.04
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:99110 original size:13 final size:14
Alignment explanation
Indices: 99081--99112 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
99071 CAATTGTTTT
99081 ATTTGCCCCATCAA
1 ATTTGCCCCATCAA
99095 ATTTGCCCCA-CAA
1 ATTTGCCCCATCAA
99108 ATTTG
1 ATTTG
99113 TCTTCTCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.31
Consensus pattern (14 bp):
ATTTGCCCCATCAA
Found at i:106378 original size:3 final size:3
Alignment explanation
Indices: 106370--106421 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
106360 ACATGTAAAT
* **
106370 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA CGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
106417 TAA TA
1 TAA TA
106422 TTAAAAAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:109777 original size:23 final size:23
Alignment explanation
Indices: 109724--109777 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
109714 TGTTATGTTA
109724 AAATAA-TATAATGAAATTTTTT
1 AAATAATTATAATGAAATTTTTT
* **
109746 -AATATTTATAATTTAATTTTTT
1 AAATAATTATAATGAAATTTTTT
109768 AAATAATTAT
1 AAATAATTAT
109778 TTATTCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 4 0.15
22 14 0.54
23 8 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
AAATAATTATAATGAAATTTTTT
Found at i:110734 original size:79 final size:77
Alignment explanation
Indices: 110616--110766 Score: 212
Period size: 79 Copynumber: 1.9 Consensus size: 77
110606 ATGTTCAGAA
* * *
110616 GTGAAGTGTGAACACGAGCCACACTAATGGCCGGAGTTAAGACATTAATCTAGGTTGTATAATGC
1 GTGAAGTGTGAACACGAGCCACAATAATGGCCGGAGTTAAGACATTAATCTAGGCTGTATAATGA
110681 ATGAATCCAACG
66 ATGAATCCAACG
* * * * *
110693 GTGAAGTGTGAATACATGAGCCACAATAGTGGCTGGCGTTAAGGCATTAATCTAGGCTGTATAAT
1 GTGAAGTGTG-A-ACACGAGCCACAATAATGGCCGGAGTTAAGACATTAATCTAGGCTGTATAAT
110758 GAATGAATC
64 GAATGAATC
110767 TAGGTGTATA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 10 0.16
78 1 0.02
79 53 0.83
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (77 bp):
GTGAAGTGTGAACACGAGCCACAATAATGGCCGGAGTTAAGACATTAATCTAGGCTGTATAATGA
ATGAATCCAACG
Found at i:114015 original size:16 final size:16
Alignment explanation
Indices: 113974--114027 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
113964 ATTAATTTCT
*
113974 TTTTTTATTTAAATATTA
1 TTTTTTA-TTATATA-TA
*
113992 TATTTTATTATATATA
1 TTTTTTATTATATATA
114008 TTTTTTATTAGTAT-TA
1 TTTTTTATTA-TATATA
114024 TTTT
1 TTTT
114028 CCCTATCATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 17 0.53
17 9 0.28
18 6 0.19
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTTTTATTATATATA
Found at i:114131 original size:2 final size:2
Alignment explanation
Indices: 114124--114148 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
114114 TTTTACTTAT
114124 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 T
114149 TTGTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:114233 original size:16 final size:15
Alignment explanation
Indices: 114200--114250 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
114190 ATATTTACTA
114200 TTATTTTCTTTTTT-T
1 TTATTTT-TTTTTTCT
114215 TTATTTTATTTTTTCT
1 TTATTTT-TTTTTTCT
114231 TTATTTTTTCTTTTCT
1 TTATTTTTT-TTTTCT
114247 TTAT
1 TTAT
114251 CTTCACTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
15 15 0.45
16 18 0.55
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (15 bp):
TTATTTTTTTTTTCT
Found at i:114237 original size:23 final size:23
Alignment explanation
Indices: 114198--114244 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
114188 ATATATTTAC
114198 TATTATTTTCTTTTTTTTTATTT
1 TATTATTTTCTTTTTTTTTATTT
*
114221 TATT-TTTTCTTTATTTTTTCTTT
1 TATTATTTTCTTT-TTTTTTATTT
114244 T
1 T
114245 CTTTATCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (23 bp):
TATTATTTTCTTTTTTTTTATTT
Found at i:114276 original size:15 final size:16
Alignment explanation
Indices: 114246--114283 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
114236 TTTTCTTTTC
*
114246 TTTATCTTCACTTTATT
1 TTTAT-TTCACTTTATA
114263 TTTATTTC-CTTTATA
1 TTTATTTCACTTTATA
114278 TTTATT
1 TTTATT
114284 CTATTTCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 3 0.15
17 5 0.25
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTTCACTTTATA
Found at i:114367 original size:11 final size:11
Alignment explanation
Indices: 114200--114400 Score: 60
Period size: 11 Copynumber: 17.6 Consensus size: 11
114190 ATATTTACTA
*
114200 TTATTTTCTTT
1 TTATTTTATTT
114211 TT-TTTTA-TT
1 TTATTTTATTT
114220 TTATTTT-TTCT
1 TTATTTTATT-T
114231 TTATTTT-TTCT
1 TTATTTTATT-T
*
114242 TT-TCTTTATCT
1 TTAT-TTTATTT
* *
114253 TCACTTTATTT
1 TTATTTTATTT
*
114264 TTATTTCCTTTATAT
1 TTA--T--TTTATTT
*
114279 TTATTCTATTT
1 TTATTTTATTT
*
114290 CGTTA-TTTATGT
1 --TTATTTTATTT
114302 TTATGTTTA-TT
1 TTAT-TTTATTT
114313 TTATTCTTATTT
1 TTATT-TTATTT
114325 TTA-TTTATTT
1 TTATTTTATTT
* * *
114335 ATCA-TATATAT
1 -TTATTTTATTT
* *
114346 ATATATTATTT
1 TTATTTTATTT
114357 TTATTTTATTTT
1 TTATTTTA-TTT
*
114369 CTGTATTTTATAT
1 -T-TATTTTATTT
* *
114382 ATATTTTTTCTT
1 TTATTTTAT-TT
114394 TTATTTT
1 TTATTTT
114401 CTGTATCTTT
Statistics
Matches: 140, Mismatches: 28, Indels: 43
0.66 0.13 0.20
Matches are distributed among these distances:
9 4 0.03
10 21 0.15
11 67 0.48
12 25 0.18
13 7 0.05
14 7 0.05
15 9 0.06
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.72
Consensus pattern (11 bp):
TTATTTTATTT
Found at i:114381 original size:32 final size:32
Alignment explanation
Indices: 114309--114406 Score: 105
Period size: 32 Copynumber: 3.1 Consensus size: 32
114299 TGTTTATGTT
* *
114309 TATTTTAT-TCTTATTTTTA-TTTATTTATC-A
1 TATTTTATATATTATTTTTATTTTATTT-TCTG
*
114339 TATATATATATATTATTTTTATTTTATTTTCTG
1 TAT-TTTATATATTATTTTTATTTTATTTTCTG
*
114372 TATTTTATATA-TATTTTTTCTTTTATTTTCTG
1 TATTTTATATATTA-TTTTTATTTTATTTTCTG
114404 TAT
1 TAT
114407 CTTTCTTTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
30 3 0.05
31 6 0.10
32 39 0.67
33 10 0.17
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.69
Consensus pattern (32 bp):
TATTTTATATATTATTTTTATTTTATTTTCTG
Found at i:118381 original size:99 final size:99
Alignment explanation
Indices: 118209--118405 Score: 279
Period size: 99 Copynumber: 2.0 Consensus size: 99
118199 ATATTTTATA
*** * *** *
118209 TATACAATAAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCCCGGCTTTATGGATACG
1 TATACAATAAAACTTGAACCGTCCCTCTAGAGCAATTGGTTAAATACCCCAAATTTATGGATAAG
* *
118274 ATTTAGCTAGCCTGATAAAGGT-AGTTATAATATC
66 ATTCAGCTAGCCTGATAAAGATGA-TTATAATATC
*
118308 TATACAATAAAGCTTGAACCGTCCCTCTAGAGCAATTGGTTAAATACCCCAAATTTATGGATAAG
1 TATACAATAAAACTTGAACCGTCCCTCTAGAGCAATTGGTTAAATACCCCAAATTTATGGATAAG
118373 ATTCAGCTAGCCTGATAAAGATGATTATAATAT
66 ATTCAGCTAGCCTGATAAAGATGATTATAATAT
118406 TGAGCTGTCC
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 85 0.99
100 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (99 bp):
TATACAATAAAACTTGAACCGTCCCTCTAGAGCAATTGGTTAAATACCCCAAATTTATGGATAAG
ATTCAGCTAGCCTGATAAAGATGATTATAATATC
Found at i:119743 original size:156 final size:156
Alignment explanation
Indices: 119459--119780 Score: 457
Period size: 156 Copynumber: 2.1 Consensus size: 156
119449 ACCAATGTGA
* * *
119459 CCAATTCAAAGCTCAACTTCACAGCGAAAGAGTGTCTGTCAAGAAATAACTTTCTAGTTTCATTT
1 CCAATTCAAAGCTCAACTTCACAGCGAAAGAGTGTCTGTCAACAAACAACTTTCTAGTTTCATTC
* * * * *
119524 AGAGTCAATTTCAACTTCATAGCGAAGGATATTGGACTTGAAACAACACAACTTACACAAGATTG
66 AGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCGAAACAACAAAACTTACACAAGATTG
*
119589 GATTTCAACTTCACAATAAAGGATAT
131 GATTTCAACTTCACAACAAAGGATAT
* *
119615 CCAATTCAAAGCTCAACTTCACAGCGAAGGGGTGTCTGTCAACAAACAACTTT-TCAGTTTCATT
1 CCAATTCAAAGCTCAACTTCACAGCGAAAGAGTGTCTGTCAACAAACAACTTTCT-AGTTTCATT
*** * *
119679 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCGAAGTGACAAAATTTACTCAAGATT
65 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCGAAACAACAAAACTTACACAAGATT
* *
119744 GGATTTTAACTTCACAACGAAGGATAT
130 GGATTTCAACTTCACAACAAAGGATAT
*
119771 CCAACTCAAA
1 CCAATTCAAA
119781 ACCAATTTGG
Statistics
Matches: 146, Mismatches: 19, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
155 1 0.01
156 145 0.99
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (156 bp):
CCAATTCAAAGCTCAACTTCACAGCGAAAGAGTGTCTGTCAACAAACAACTTTCTAGTTTCATTC
AGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCGAAACAACAAAACTTACACAAGATTG
GATTTCAACTTCACAACAAAGGATAT
Found at i:119845 original size:62 final size:63
Alignment explanation
Indices: 119732--119896 Score: 198
Period size: 62 Copynumber: 2.7 Consensus size: 63
119722 GTGACAAAAT
* *
119732 TTACTCAAGATTGGATTTTAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
1 TTACTCAAGATTGGATTTCAACTT--CAACGAAGGATATCCAACTAAAAACCAATTTGGTGAAAC
* *
119797 TTACTCAAGATTGGATTTCAACTT-GACGAAGGATATCCAACTAAAAACCATTTTGGTGAAAC
1 TTACTCAAGATTGGATTTCAACTTCAACGAAGGATATCCAACTAAAAACCAATTTGGTGAAAC
* *
119859 --AATC---CTTGGATTTCAACTTCACAACGAAGGATATCCAA
1 TTACTCAAGATTGGATTTCAACTT--CAACGAAGGATATCCAA
119897 TTCAAAGCTC
Statistics
Matches: 90, Mismatches: 7, Indels: 11
0.83 0.06 0.10
Matches are distributed among these distances:
57 14 0.16
60 18 0.20
62 35 0.39
65 23 0.26
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (63 bp):
TTACTCAAGATTGGATTTCAACTTCAACGAAGGATATCCAACTAAAAACCAATTTGGTGAAAC
Found at i:120159 original size:85 final size:85
Alignment explanation
Indices: 120016--120609 Score: 550
Period size: 85 Copynumber: 7.0 Consensus size: 85
120006 CCCAGCCAAG
* * ** * *
120016 TACAACATAACTCAAGGCGAGAAGGG-TCATCTATCAATAAAGACATTTGAGTTCGATTACATTC
1 TACAACATAGCTCAAGGCGAGAAGGGCT-ATCTGTCAACCAAGACCTTCGAGTTCGATTACATTC
*
120080 AGCTCAAAGGCTCATCAAATT
65 AGCTCAAAGGCACATCAAATT
* * * *
120101 TACAAAATAGCTCAAGGTGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTTGATTATACTT-
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACA-TTC
* *
120165 AGCTCAGATGCACATCAAATT
65 AGCTCAAAGGCACATCAAATT
* * * * * *
120186 TACAGCATAGCTCAAGGCGAGAAGGGTTATATGTTAACAAAGACCTTCGAGTTTGATTACATTCA
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCA
120251 GCTCAAAGGCACATCAAATT
66 GCTCAAAGGCACATCAAATT
* * *
120271 TACAGCATTGCTCAAGGCGAGAAGGGCTATCTGTCAACCAATACCTTCGAGTTCGATTACACTT-
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACA-TTC
*
120335 AGCTCAAAGGCATATCAAATT
65 AGCTCAAAGGCACATCAAATT
* * * * *
120356 TATAACATAGCTCAAGGTGAGAAGGGCTATCTGACAACCAAGACCGTCGAGTTCAATTACATTCA
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCA
* *
120421 GCTC-TAGGACATATCAAATT
66 GCTCAAAGG-CACATCAAATT
* * * * * * * ** * * * *
120441 TATAGCATAACCCAGGGCAAGAAGGGTTATCTGTCAATAAATATCTTCGAGTTTGATTCCATTCA
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCA
* * * ***
120506 CCTCAAGGGTATGCCAAATT
66 GCTCAAAGGCACATCAAATT
* * * *** * * *
120526 TAAAACATAGCTTAAGTCGAGAAAAACTATCTATCAA-CAAGAAACTATCGAGTTCGATTCCATT
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAG-ACCT-TCGAGTTCGATTACATT
* * *
120590 CAGCTCGATGACACATCAAA
64 CAGCTCAAAGGCACATCAAA
120610 CACATGGTAG
Statistics
Matches: 413, Mismatches: 87, Indels: 17
0.80 0.17 0.03
Matches are distributed among these distances:
84 9 0.02
85 369 0.89
86 35 0.08
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (85 bp):
TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCA
GCTCAAAGGCACATCAAATT
Found at i:120491 original size:255 final size:254
Alignment explanation
Indices: 120026--120511 Score: 640
Period size: 255 Copynumber: 1.9 Consensus size: 254
120016 TACAACATAA
* *
120026 CTCAAGGCGAGAAGGGTCATCTATCAATAAAGACATTTGAGTTCGATTACATTCAGCTCAAAGGC
1 CTCAAGGCGAGAAGGGTCATCTATCAACAAAGACATTCGAGTTCGATTACATTCAGCTCAAAGGC
* * **
120091 TCATCAAATTTACAAAATAGCTCAAGGTGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTTG
66 TCATCAAATTTACAAAATAGCTCAAGGTGAGAAGGGCTATCTGACAACCAAGACCGTCGAGTTCA
* * * * *
120156 ATTATACTTAGCTCAGATGCACATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATATGTT
131 ATTACACTTAGCTCAGA-GCACATCAAATTTACAGCATAACCCAAGGCAAGAAGGGTTATATGTC
*
120221 AACAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAGGCACATCAAATTTACAGCATTG
195 AACAAAGACCTTCGAGTTTGATTACATTCACCTCAAAGGCACATCAAATTTACAGCATTG
* * * *
120281 CTCAAGGCGAGAAGGG-CTATCTGTCAACCAATACCTTCGAGTTCGATTACACTT-AGCTCAAAG
1 CTCAAGGCGAGAAGGGTC-ATCTATCAACAAAGACATTCGAGTTCGATTACA-TTCAGCTCAAAG
* *
120344 GCAT-ATCAAATTTATAACATAGCTCAAGGTGAGAAGGGCTATCTGACAACCAAGACCGTCGAGT
64 GC-TCATCAAATTTACAAAATAGCTCAAGGTGAGAAGGGCTATCTGACAACCAAGACCGTCGAGT
* * *
120408 TCAATTACA-TTCAGCTCTAG-GACATATCAAATTTATAGCATAACCCAGGGCAAGAAGGGTTAT
128 TCAATTACACTT-AGCTC-AGAG-CACATCAAATTTACAGCATAACCCAAGGCAAGAAGGGTTAT
* * * * *
120471 CTGTCAATAAATATCTTCGAGTTTGATTCCATTCACCTCAA
190 ATGTCAACAAAGACCTTCGAGTTTGATTACATTCACCTCAA
120512 GGGTATGCCA
Statistics
Matches: 199, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
254 4 0.02
255 190 0.95
256 5 0.03
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (254 bp):
CTCAAGGCGAGAAGGGTCATCTATCAACAAAGACATTCGAGTTCGATTACATTCAGCTCAAAGGC
TCATCAAATTTACAAAATAGCTCAAGGTGAGAAGGGCTATCTGACAACCAAGACCGTCGAGTTCA
ATTACACTTAGCTCAGAGCACATCAAATTTACAGCATAACCCAAGGCAAGAAGGGTTATATGTCA
ACAAAGACCTTCGAGTTTGATTACATTCACCTCAAAGGCACATCAAATTTACAGCATTG
Found at i:120526 original size:255 final size:254
Alignment explanation
Indices: 120026--120595 Score: 632
Period size: 255 Copynumber: 2.2 Consensus size: 254
120016 TACAACATAA
* *
120026 CTCAAGGCGAGAAGGGTCATCTATCAATAAAGACATTTGAGTTCGATTACATTCAGCTCAAAGGC
1 CTCAAGGCGAGAAGGGTCATCTATCAACAAAGACATTCGAGTTCGATTACATTCAGCTCAAAGGC
* * **
120091 TCATCAAATTTACAAAATAGCTCAAGGTGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTTG
66 TCATCAAATTTACAAAATAGCTCAAGGTGAGAAGGGCTATCTGACAACCAAGACCGTCGAGTTCA
* * * * *
120156 ATTATACTTAGCTCAGATGCACATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATATGTT
131 ATTACACTTAGCTCAGA-GCACATCAAATTTACAGCATAACCCAAGGCAAGAAGGGTTATATGTC
* *
120221 AACAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAGGCACATCAAATTTACAGCATTG
195 AACAAAGACCTTCGAGTTTGATTACATTCACCTCAAAGGCACACCAAATTTACAGCATTG
* * * *
120281 CTCAAGGCGAGAAGGG-CTATCTGTCAACCAATACCTTCGAGTTCGATTACACTT-AGCTCAAAG
1 CTCAAGGCGAGAAGGGTC-ATCTATCAACAAAGACATTCGAGTTCGATTACA-TTCAGCTCAAAG
* *
120344 GCAT-ATCAAATTTATAACATAGCTCAAGGTGAGAAGGGCTATCTGACAACCAAGACCGTCGAGT
64 GC-TCATCAAATTTACAAAATAGCTCAAGGTGAGAAGGGCTATCTGACAACCAAGACCGTCGAGT
* * *
120408 TCAATTACA-TTCAGCTCTAG-GACATATCAAATTTATAGCATAACCCAGGGCAAGAAGGGTTAT
128 TCAATTACACTT-AGCTC-AGAG-CACATCAAATTTACAGCATAACCCAAGGCAAGAAGGGTTAT
* * * * * * * ** * * *
120471 CTGTCAATAAATATCTTCGAGTTTGATTCCATTCACCTCAAGGGTATGCCAAATTTAAAACATAG
190 ATGTCAACAAAGACCTTCGAGTTTGATTACATTCACCTCAAAGGCACACCAAATTTACAGCATTG
* * *** * *
120536 CTTAAGTCGAGAA-AAACTATCTATCAAC-AAGAAACTATCGAGTTCGATTCCATTCAGCTC
1 CTCAAGGCGAGAAGGGTC-ATCTATCAACAAAGACA-T-TCGAGTTCGATTACATTCAGCTC
120596 GATGACACAT
Statistics
Matches: 262, Mismatches: 43, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
254 7 0.03
255 231 0.88
256 24 0.09
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (254 bp):
CTCAAGGCGAGAAGGGTCATCTATCAACAAAGACATTCGAGTTCGATTACATTCAGCTCAAAGGC
TCATCAAATTTACAAAATAGCTCAAGGTGAGAAGGGCTATCTGACAACCAAGACCGTCGAGTTCA
ATTACACTTAGCTCAGAGCACATCAAATTTACAGCATAACCCAAGGCAAGAAGGGTTATATGTCA
ACAAAGACCTTCGAGTTTGATTACATTCACCTCAAAGGCACACCAAATTTACAGCATTG
Found at i:122660 original size:22 final size:22
Alignment explanation
Indices: 122626--122679 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
122616 TGCCATGATT
*
122626 AATTTCTT-TTTTATT-TATTTA
1 AATTT-TTATTTTATTATATATA
122647 AATTTTATATTTTATTATATATA
1 AATTTT-TATTTTATTATATATA
*
122670 TATTTTTATT
1 AATTTTTATT
122680 AGTATTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 1 0.04
21 6 0.21
22 11 0.39
23 10 0.36
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
AATTTTTATTTTATTATATATA
Found at i:122813 original size:30 final size:30
Alignment explanation
Indices: 122741--122814 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
122731 TTTTTTCCCC
*
122741 TTTATTATTATTACTATCACTATATATTTT
1 TTTATTATTTTTACTATCACTATATATTTT
* *
122771 TATTTTTA-TTTTACTTATTA-TATATATTTT
1 T-TTATTATTTTTAC-TATCACTATATATTTT
122801 TTTATTATTTTTAC
1 TTTATTATTTTTAC
122815 CTAACATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 5 0.14
30 23 0.62
31 9 0.24
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTATTATTTTTACTATCACTATATATTTT
Found at i:122877 original size:4 final size:4
Alignment explanation
Indices: 122870--122896 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
122860 TTACTATTAT
122870 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
122897 TTATTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:123072 original size:10 final size:10
Alignment explanation
Indices: 123054--123098 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
123044 TTATCTTTAT
123054 TTTTA-TTTC
1 TTTTATTTTC
123063 TTTTATTTTC
1 TTTTATTTTC
*
123073 -TGTATTTTC
1 TTTTATTTTC
123082 TTTTATTTAT-
1 TTTTATTT-TC
123092 TTTTATT
1 TTTTATT
123099 ACTTTTTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 13 0.42
10 17 0.55
11 1 0.03
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (10 bp):
TTTTATTTTC
Found at i:123091 original size:44 final size:44
Alignment explanation
Indices: 123010--123098 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
123000 ATTATTATTA
* * *
123010 TTTTCTTTGTTTTATTTTCTGTATTTTTATATGTTTATCTTTAT
1 TTTTATTTCTTTTATTTTCTGTATTTTTATATATTTATCTTTAT
* *
123054 TTTTATTTCTTTTATTTTCTGTATTTTCT-TTTATTTATTTTTAT
1 TTTTATTTCTTTTATTTTCTGTATTTT-TATATATTTATCTTTAT
123098 T
1 T
123099 ACTTTTTTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 38 0.97
45 1 0.03
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.75
Consensus pattern (44 bp):
TTTTATTTCTTTTATTTTCTGTATTTTTATATATTTATCTTTAT
Found at i:123092 original size:14 final size:14
Alignment explanation
Indices: 122950--123094 Score: 62
Period size: 14 Copynumber: 9.8 Consensus size: 14
122940 TTCTATTTCG
122950 TTATTTATGTTTATT
1 TTATTTAT-TTTATT
* *
122965 TTA-TTCTTGT-TT
1 TTATTTATTTTATT
122977 TTATTTATTTATCATAT
1 TTATTTATTT-T-AT-T
122994 ATTATTATTATTATTATT
1 -TTA-T-TTATT-TTATT
* *
123012 TTCTTTGTTTTATT
1 TTATTTATTTTATT
* *
123026 TTCTGTATTTT-TAT
1 TTATTTATTTTAT-T
* *
123040 ATGTTTATCTTTATTT
1 TTATTTAT-TTTA-TT
*
123056 TTATTTCTTTTATT
1 TTATTTATTTTATT
* * *
123070 TTCTGTATTTTCTT
1 TTATTTATTTTATT
123084 TTATTTATTTT
1 TTATTTATTTT
123095 TATTACTTTT
Statistics
Matches: 97, Mismatches: 20, Indels: 27
0.67 0.14 0.19
Matches are distributed among these distances:
12 5 0.05
13 7 0.07
14 45 0.46
15 14 0.14
16 8 0.08
17 4 0.04
18 4 0.04
19 3 0.03
20 6 0.06
21 1 0.01
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72
Consensus pattern (14 bp):
TTATTTATTTTATT
Found at i:126295 original size:17 final size:17
Alignment explanation
Indices: 126273--126308 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
126263 TAAAACAGCT
*
126273 CTAACAAACTTCATAAG
1 CTAACAAACTTCACAAG
126290 CTAACAAACTTCACAAG
1 CTAACAAACTTCACAAG
126307 CT
1 CT
126309 TCTAGCACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.06, T:0.22
Consensus pattern (17 bp):
CTAACAAACTTCACAAG
Done.