Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2301.1
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: 264179
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.28
Warning! 35531 characters in sequence are not A, C, G, or T
Found at i:4347 original size:46 final size:46
Alignment explanation
Indices: 4280--4454 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
4270 TGTAACCCGC
4280 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
4326 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCACAT
* * * * *
4376 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
*
4419 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
4455 ATGCCCAAAT
Statistics
Matches: 112, Mismatches: 6, Indels: 22
0.80 0.04 0.16
Matches are distributed among these distances:
42 3 0.03
43 5 0.04
44 1 0.01
46 64 0.57
47 27 0.24
48 1 0.01
49 1 0.01
50 6 0.05
51 4 0.04
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
Found at i:4400 original size:93 final size:93
Alignment explanation
Indices: 4288--4459 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
4278 GCCCATAAGT
* *
4288 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
4353 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
4381 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
4446 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
4460 CAAATATCCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:8336 original size:27 final size:27
Alignment explanation
Indices: 8305--9292 Score: 1753
Period size: 27 Copynumber: 36.6 Consensus size: 27
8295 TAAATTGTGC
* * *
8305 GGCACTAAGTGTGCGATTCGACTATGT
1 GGCACTAAGTGTGCGATTTGATTACGT
* ** * *
8332 TGCACTAAGTGTGCGAAATGAATATGAT
1 GGCACTAAGTGTGCGATTTGATTACG-T
* ** * *
8360 -GCACTAAGTGTGCGAATTGACCATGC
1 GGCACTAAGTGTGCGATTTGATTACGT
* * *
8386 GGCACTAAGTGTGCGAGTCTGACTATGT
1 GGCACTAAGTGTGCGA-TTTGATTACGT
*
8414 AGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8441 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8468 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8495 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8522 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8549 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8576 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8603 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8630 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8657 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8684 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8711 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8738 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8765 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8792 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8819 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8846 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8873 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8900 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8927 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8954 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
8981 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
9008 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
9035 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
9062 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
9089 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
9116 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
9143 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
9170 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
9197 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
9224 GGCACTAAGTGTGCGATTTGATTACGT
1 GGCACTAAGTGTGCGATTTGATTACGT
* **
9251 GGCACTAAGTGTGCGAGTTGATTATAT
1 GGCACTAAGTGTGCGATTTGATTACGT
* *
9278 AGCACTGAGTGTGCG
1 GGCACTAAGTGTGCG
9293 GGCTCAATAT
Statistics
Matches: 935, Mismatches: 23, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
27 912 0.98
28 23 0.02
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (27 bp):
GGCACTAAGTGTGCGATTTGATTACGT
Found at i:13630 original size:15 final size:17
Alignment explanation
Indices: 13592--13631 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
13582 TTATGTAAAT
13592 TTAATGTTGTATTGTATG
1 TTAATG-TGTATTGTATG
13610 -TAATGTG-ATT-TATG
1 TTAATGTGTATTGTATG
13624 TTAATGTG
1 TTAATGTG
13632 CCTTACTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.19
15 10 0.48
16 2 0.10
17 5 0.24
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.53
Consensus pattern (17 bp):
TTAATGTGTATTGTATG
Found at i:17342 original size:6 final size:6
Alignment explanation
Indices: 17331--17356 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
17321 AGTTATGGTG
17331 GAATAT GAATAT GAATAT GAATAT GA
1 GAATAT GAATAT GAATAT GAATAT GA
17357 TTGATACGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (6 bp):
GAATAT
Found at i:21143 original size:56 final size:56
Alignment explanation
Indices: 21057--21288 Score: 446
Period size: 56 Copynumber: 4.1 Consensus size: 56
21047 ACAAGGGATG
21057 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
21113 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
21169 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
* *
21225 ATGGGCAAAACATGTCATCAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
21281 ATGGGCAA
1 ATGGGCAA
21289 TAAACTAATA
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 174 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:33956 original size:26 final size:26
Alignment explanation
Indices: 33907--33992 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 26
33897 CAAATAAATA
33907 AAAGAAAAA-AAGAAAGAGAAAAAGAAAC
1 AAAGAAAAACAA-AAAGAG--AAAGAAAC
* *
33935 AAAGTAAAACAAAACAG-GAAAGAAAG
1 AAAGAAAAACAAAA-AGAGAAAGAAAC
* *
33961 AAAGAAAAATAAAAAGAGAAAG-AAG
1 AAAGAAAAACAAAAAGAGAAAGAAAC
33986 AAAGAAA
1 AAAGAAA
33993 GCCATGGCCT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
25 12 0.24
26 24 0.47
28 11 0.22
29 4 0.08
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.02
Consensus pattern (26 bp):
AAAGAAAAACAAAAAGAGAAAGAAAC
Found at i:42148 original size:22 final size:22
Alignment explanation
Indices: 42123--42182 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
42113 TTCAAATAAT
*
42123 AACAACAAAATAGAAACAATAC
1 AACAACAAAATAGAAACAAAAC
* * * * *
42145 AACAGCAAGATGGCAGCAAAAC
1 AACAACAAAATAGAAACAAAAC
*
42167 AACAACAAAAGAGAAA
1 AACAACAAAATAGAAA
42183 GTTTAGGTTG
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.63, C:0.18, G:0.13, T:0.05
Consensus pattern (22 bp):
AACAACAAAATAGAAACAAAAC
Found at i:45770 original size:79 final size:77
Alignment explanation
Indices: 45626--45782 Score: 235
Period size: 79 Copynumber: 2.0 Consensus size: 77
45616 TTACCATGCG
* *
45626 TAATTATATGCGTAGGTGTTTGAGTCCCATCTGTGCAGTTGTCGTGTGAGTTTTAGTCGAGTTTC
1 TAATTATATGCATAGGTGTCTGAGTCCCATCTGTGCAGTTGTCGTGTGAGTTTTAGTCGAGTTTC
*
45691 TTAGCTTTCGTA
66 TTAGCTTTAGTA
* *
45703 TAATTTTATGCAT-GGTGTCTGAGTCCCATCATGTGCAGTTGTCATGTGTGAGTTTTAGTCTAGT
1 TAATTATATGCATAGGTGTCTGAGTCCCATC-TGTGCAGTTGTC--GTGTGAGTTTTAGTCGAGT
45767 TTCTTAGCTTTAGTA
63 TTCTTAGCTTTAGTA
45782 T
1 T
45783 GGATTGTACT
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
76 16 0.22
77 23 0.32
79 33 0.46
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.44
Consensus pattern (77 bp):
TAATTATATGCATAGGTGTCTGAGTCCCATCTGTGCAGTTGTCGTGTGAGTTTTAGTCGAGTTTC
TTAGCTTTAGTA
Found at i:46171 original size:1 final size:1
Alignment explanation
Indices: 46165--46209 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
46155 AGCTAAAGGC
* * * *
46165 AAAAAAAAAAAAAAAAAAAAAAAGAAAAAAGAAAAGAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
46210 CCCAAATAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:46187 original size:17 final size:17
Alignment explanation
Indices: 46165--46209 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
46155 AGCTAAAGGC
46165 AAAAAAA-AAAAAAAAA
1 AAAAAAAGAAAAAAAAA
*
46181 AAAAAAAGAAAAAAGAA
1 AAAAAAAGAAAAAAAAA
*
46198 AAGAAAAGAAAA
1 AAAAAAAGAAAA
46210 CCCAAATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAAA
Found at i:47604 original size:13 final size:13
Alignment explanation
Indices: 47586--47619 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
47576 ATAATATTTT
47586 TCTTTGTTGCTT-C
1 TCTTTGTT-CTTCC
47599 TCTTTGTTCTTCC
1 TCTTTGTTCTTCC
47612 TCTTTGTT
1 TCTTTGTT
47620 ATCAGACTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 3 0.15
13 17 0.85
ACGTcount: A:0.00, C:0.24, G:0.12, T:0.65
Consensus pattern (13 bp):
TCTTTGTTCTTCC
Found at i:65124 original size:92 final size:92
Alignment explanation
Indices: 65004--65186 Score: 348
Period size: 92 Copynumber: 2.0 Consensus size: 92
64994 TTTCTATTAT
65004 AGATCAAGAAGAACGAAATTCGGGGTTAGACCGAGGAAAGAAAAAGGTTGAGGACTAAATCAAAA
1 AGATCAAGAAGAACGAAATTCGGGGTTAGACCGAGGAAAGAAAAAGGTTGAGGACTAAATCAAAA
65069 TATTTGATCGTATTTTGTATCGAGGTC
66 TATTTGATCGTATTTTGTATCGAGGTC
* *
65096 AGATCAAGAAGAATGAAATTCGGGGTTAGACCTAGGAAAGAAAAAGGTTGAGGACTAAATCAAAA
1 AGATCAAGAAGAACGAAATTCGGGGTTAGACCGAGGAAAGAAAAAGGTTGAGGACTAAATCAAAA
65161 TATTTGATCGTATTTTGTATCGAGGT
66 TATTTGATCGTATTTTGTATCGAGGT
65187 AAGTTTGCGG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.39, C:0.10, G:0.26, T:0.25
Consensus pattern (92 bp):
AGATCAAGAAGAACGAAATTCGGGGTTAGACCGAGGAAAGAAAAAGGTTGAGGACTAAATCAAAA
TATTTGATCGTATTTTGTATCGAGGTC
Found at i:65566 original size:53 final size:53
Alignment explanation
Indices: 65383--65578 Score: 158
Period size: 53 Copynumber: 3.6 Consensus size: 53
65373 AGGATACTAA
* * * * * * * * *
65383 GTAAGACCATGCCAAGGCATGGTATTGGTAAGTTCTACAAGGCAAGGAAATCAT
1 GTAAGACCATACCAAGACATGGCAATGGTAAGTTC-ATAAGGCAAAGATACCAC
** * * * * * *
65437 GTAAGACCATGTCAAGACATGGCATTGATAAACTACGATAAGGCAAAGATCCCAT
1 GTAAGACCATACCAAGACATGGCAATGGT-AAGTTC-ATAAGGCAAAGATACCAC
* * * *
65492 GTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGCAAGGATACCAC
1 GTAAGACCATACCAAGACATGGCAATGGTAAGTTCATAAGGCAAAGATACCAC
* *
65545 GTAAGACCGTATCAAGACATGGCAATGGTAAGTT
1 GTAAGACCATACCAAGACATGGCAATGGTAAGTT
65579 TAAAAATGGA
Statistics
Matches: 114, Mismatches: 27, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 44 0.39
54 28 0.25
55 42 0.37
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (53 bp):
GTAAGACCATACCAAGACATGGCAATGGTAAGTTCATAAGGCAAAGATACCAC
Found at i:69764 original size:28 final size:28
Alignment explanation
Indices: 69716--69778 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
69706 CGTTGCATCT
* * *
69716 TCAATGTCTCGTACGCTAAGTGCCATAC
1 TCAATATCTCGTACACCAAGTGCCATAC
* *
69744 TCAATATCTCGTACACCAAGTTCCATTC
1 TCAATATCTCGTACACCAAGTGCCATAC
*
69772 TTAATAT
1 TCAATAT
69779 TTTTCACACT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (28 bp):
TCAATATCTCGTACACCAAGTGCCATAC
Found at i:69879 original size:40 final size:40
Alignment explanation
Indices: 69807--69882 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
69797 TATACATATA
*
69807 TAGCCGAAGCTATCTCCAATCACACACCAAGTGCCACATT
1 TAGCCGAAGCTATCTCCAACCACACACCAAGTGCCACATT
* * * **
69847 TAGCCGAAGCTATTTCGAACCGCACAGTAAGTGCCA
1 TAGCCGAAGCTATCTCCAACCACACACCAAGTGCCA
69883 TTTTTTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.20
Consensus pattern (40 bp):
TAGCCGAAGCTATCTCCAACCACACACCAAGTGCCACATT
Found at i:80578 original size:43 final size:42
Alignment explanation
Indices: 80530--80683 Score: 168
Period size: 43 Copynumber: 3.6 Consensus size: 42
80520 ATCCTAGATG
* * *
80530 TGGTCTTACATGTAATCAAATATCAATGCCACTGTCCCAGACA
1 TGGTCTTACACGAAATCAAATATCGATGCCA-TGTCCCAGACA
* *
80573 AGGTCTTACACGAAATCAAATAT-GATGCTGATGTCCCAGACA
1 TGGTCTTACACGAAATCAAATATCGATGC-CATGTCCCAGACA
* * *
80615 TGGTCTTACACGTAAATCTCAA-ATCGATACCAATGTCCCAGACG
1 TGGTCTTACACG-AAATC-AAATATCGATGCC-ATGTCCCAGACA
*
80659 TGGTCTTACACGAAATCACATATCG
1 TGGTCTTACACGAAATCAAATATCG
80684 GAAGTCCTAT
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
42 27 0.29
43 37 0.40
44 29 0.31
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (42 bp):
TGGTCTTACACGAAATCAAATATCGATGCCATGTCCCAGACA
Found at i:80657 original size:44 final size:44
Alignment explanation
Indices: 80562--80675 Score: 144
Period size: 44 Copynumber: 2.6 Consensus size: 44
80552 TCAATGCCAC
* * * **
80562 TGTCCCAGACAAGGTCTTACACGAAA--TCAAATATGATGCTGA
1 TGTCCCAGACATGGTCTTACACGAAATCTCAAATACGATACCAA
80604 TGTCCCAGACATGGTCTTACACGTAAATCTCAAAT-CGATACCAA
1 TGTCCCAGACATGGTCTTACACG-AAATCTCAAATACGATACCAA
*
80648 TGTCCCAGACGTGGTCTTACACGAAATC
1 TGTCCCAGACATGGTCTTACACGAAATC
80676 ACATATCGGA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
42 22 0.35
43 8 0.13
44 27 0.43
45 6 0.10
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (44 bp):
TGTCCCAGACATGGTCTTACACGAAATCTCAAATACGATACCAA
Found at i:88435 original size:16 final size:16
Alignment explanation
Indices: 88414--88444 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
88404 ATAAATTTGA
88414 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
88430 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
88445 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:93754 original size:20 final size:20
Alignment explanation
Indices: 93716--93754 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
93706 TGATTGGTTG
* *
93716 TGATTGAATTATATTTGAAT
1 TGATTAAATTATATGTGAAT
*
93736 TGATTAAATTGTATGTGAA
1 TGATTAAATTATATGTGAA
93755 ATGTATGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (20 bp):
TGATTAAATTATATGTGAAT
Found at i:95930 original size:10 final size:11
Alignment explanation
Indices: 95914--95951 Score: 55
Period size: 10 Copynumber: 3.7 Consensus size: 11
95904 TGTTGAGCTC
95914 AATGAGCTAGG
1 AATGAGCTAGG
95925 -ATGAGCTAGG
1 AATGAGCTAGG
95935 AATGAGCTA--
1 AATGAGCTAGG
95944 AATGAGCT
1 AATGAGCT
95952 TGTAGCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.31
10 10 0.38
11 8 0.31
ACGTcount: A:0.37, C:0.11, G:0.32, T:0.21
Consensus pattern (11 bp):
AATGAGCTAGG
Found at i:95949 original size:9 final size:10
Alignment explanation
Indices: 95914--95951 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 10
95904 TGTTGAGCTC
95914 AATGAGCTAG
1 AATGAGCTAG
*
95924 GATGAGCTAGG
1 AATGAGCTA-G
95935 AATGAGCTA-
1 AATGAGCTAG
95944 AATGAGCT
1 AATGAGCT
95952 TGTAGCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.32
10 8 0.32
11 9 0.36
ACGTcount: A:0.37, C:0.11, G:0.32, T:0.21
Consensus pattern (10 bp):
AATGAGCTAG
Found at i:98973 original size:27 final size:27
Alignment explanation
Indices: 98943--99120 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
98933 ATATTGAGTC
* * * *
98943 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
98970 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
98997 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
99025 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
99052 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
99079 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
99106 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
99121 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:99082 original size:82 final size:81
Alignment explanation
Indices: 98964--99119 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
98954 TGCTATATAA
* *
98964 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
99029 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
99046 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
99110 CACTTAGTGC
65 CACTTAGTGC
99120 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:110755 original size:48 final size:48
Alignment explanation
Indices: 110687--110879 Score: 264
Period size: 48 Copynumber: 4.0 Consensus size: 48
110677 GGTTATGTGT
* *
110687 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTATGG
1 GATCCCATGTAAGACAATGTCTGGGACATGGCATTGGCATCATTATGA
110735 GATCCCATGTAAGACAATGTCTGGGACATGGCATTGGCATCATTATGA
1 GATCCCATGTAAGACAATGTCTGGGACATGGCATTGGCATCATTATGA
* *
110783 GATCCCATGTAAGACAATGTCTGGGACAT-GCATTGGCATCGA-CATGT
1 GATCCCATGTAAGACAATGTCTGGGACATGGCATTGGCATC-ATTATGA
* * * * * * *
110830 GATCCCATGTAAGACCATATATTGGATATGGTATTGGCATCAATATGA
1 GATCCCATGTAAGACAATGTCTGGGACATGGCATTGGCATCATTATGA
110878 GA
1 GA
110880 CATCGTGTAA
Statistics
Matches: 130, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
47 39 0.30
48 91 0.70
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (48 bp):
GATCCCATGTAAGACAATGTCTGGGACATGGCATTGGCATCATTATGA
Found at i:110902 original size:95 final size:96
Alignment explanation
Indices: 110687--110879 Score: 273
Period size: 95 Copynumber: 2.0 Consensus size: 96
110677 GGTTATGTGT
*
110687 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTATGGGATCCCATGTAAGACAA
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATCATGGGATCCCATGTAAGACAA
* * *
110752 TGTCTGGGACATGGCATTGGCATCATTATGA
66 TATATGGGACATGGCATTGGCATCAATATGA
* * *
110783 GATCCCATGTAAGACAATGTCTGGGACAT-GCATTGGCATCGA-CATGTGATCCCATGTAAGACC
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC-ATCATGGGATCCCATGTAAGACA
* * *
110846 ATATATTGGATATGGTATTGGCATCAATATGA
65 ATATATGGGACATGGCATTGGCATCAATATGA
110878 GA
1 GA
110880 CATCGTGTAA
Statistics
Matches: 86, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
95 57 0.66
96 29 0.34
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (96 bp):
GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATCATGGGATCCCATGTAAGACAA
TATATGGGACATGGCATTGGCATCAATATGA
Found at i:120252 original size:55 final size:55
Alignment explanation
Indices: 120175--120316 Score: 151
Period size: 55 Copynumber: 2.6 Consensus size: 55
120165 TATTAAGGGC
* * ** *
120175 CACGCCCGTGTTAATCTAACAGGTTCGCCCAC-GATTGCTTGGCATGGGCGTGTCA
1 CACGCCCGTGTTAATTTGACAGGTTCGCCCACAG-TTGCAAGGCACGGGCGTGTCA
* * * *
120230 CACTCCCGTGTTAATTTGACAGGTTCGGCCACAGTTTCAAGGCACGGGTGTGTCA
1 CACGCCCGTGTTAATTTGACAGGTTCGCCCACAGTTGCAAGGCACGGGCGTGTCA
* ** *
120285 CACGCTCGTGTTGTTTTGGCAGGTTCGCCCAC
1 CACGCCCGTGTTAATTTGACAGGTTCGCCCAC
120317 TGCCATGTCA
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
55 70 0.99
56 1 0.01
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.27
Consensus pattern (55 bp):
CACGCCCGTGTTAATTTGACAGGTTCGCCCACAGTTGCAAGGCACGGGCGTGTCA
Found at i:121019 original size:37 final size:37
Alignment explanation
Indices: 120969--121079 Score: 213
Period size: 37 Copynumber: 3.0 Consensus size: 37
120959 GCAAAGTAGG
120969 TTGCATCATATTGTCAGTTTTAGTAGAATGGTTTAGA
1 TTGCATCATATTGTCAGTTTTAGTAGAATGGTTTAGA
121006 TTGCATCATATTGTCAGTTTTAGTAGAATGGTTTAGA
1 TTGCATCATATTGTCAGTTTTAGTAGAATGGTTTAGA
*
121043 TTGCATCATATTGTCAGTTTTAGTATAATGGTTTAGA
1 TTGCATCATATTGTCAGTTTTAGTAGAATGGTTTAGA
121080 CAATCACTTC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (37 bp):
TTGCATCATATTGTCAGTTTTAGTAGAATGGTTTAGA
Found at i:132629 original size:10 final size:10
Alignment explanation
Indices: 132613--132670 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
132603 CAACTCCGAC
132613 CAGCTCAATT
1 CAGCTCAATT
* *
132623 GAGCTCATTT
1 CAGCTCAATT
132633 CAGCTCAA-T
1 CAGCTCAATT
132642 CGAGCTCAATT
1 C-AGCTCAATT
*
132653 TAGCTACAATT
1 CAGCT-CAATT
132664 CAGCTCA
1 CAGCTCA
132671 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:132636 original size:20 final size:20
Alignment explanation
Indices: 132613--132673 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
132603 CAACTCCGAC
132613 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
132633 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
132654 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
132674 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:140620 original size:21 final size:21
Alignment explanation
Indices: 140596--140639 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
140586 ATCCTAATCT
140596 ATTCTAGAGATGAGGTAAAGC
1 ATTCTAGAGATGAGGTAAAGC
140617 ATTCTAGAGATGAGGTAAAGC
1 ATTCTAGAGATGAGGTAAAGC
140638 AT
1 AT
140640 ACCGAACACT
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:0.39, C:0.09, G:0.27, T:0.25
Consensus pattern (21 bp):
ATTCTAGAGATGAGGTAAAGC
Found at i:146788 original size:277 final size:277
Alignment explanation
Indices: 146294--146847 Score: 1027
Period size: 277 Copynumber: 2.0 Consensus size: 277
146284 TACATACCTT
*
146294 GATTAAGCTTGAATATGGCCGAACCTAGGTTTTCTTTTTCTTTTATTTTGCTTCGGAAACAACAC
1 GATTAAGCTTGAATATGGCCGAACCTAGGTTTTCTTTTTCTTTTATTTTGCTTCGGAAAAAACAC
*
146359 ACATAATAACACATATAATGGCTTTTATTTTTATGTTATAATATAACATATATTAACTTAATACT
66 AAATAATAACACATATAATGGCTTTTATTTTTATGTTATAATATAACATATATTAACTTAATACT
* * *
146424 TAATTTACATTTTTAACCTTTATAATAAAATTATAAAATCATTATAATCATGGTCGTTACCGTCC
131 TAATTTACATTTTTAACCTTTATAATAAAATTATAAAACCATTATAATCATGGCCATTACCGTCC
*
146489 ACTCTAATTTTCAATGGTCTAATTGCTTCATAAGTGATTCATATTAATAAGACAAGTTCAAATAA
196 ACTCTAATTGTCAATGGTCTAATTGCTTCATAAGTGATTCATATTAATAAGACAAGTTCAAATAA
146554 GCACTTTCACATTTAAC
261 GCACTTTCACATTTAAC
*
146571 GATTAAGCTTGAATATGGCCGAACCTAGGTTTTCTTTTTCTTTTATTTTGTTTCGGAAAAAACAC
1 GATTAAGCTTGAATATGGCCGAACCTAGGTTTTCTTTTTCTTTTATTTTGCTTCGGAAAAAACAC
146636 AAATAATAACACATATAATGGCTTTTATTTTTATGTTATAATATAACATATATTAACTTAATACT
66 AAATAATAACACATATAATGGCTTTTATTTTTATGTTATAATATAACATATATTAACTTAATACT
146701 TAATTTACATTTTTAACCTTTATAATAAAATTATAAAACCATTATAATCATGGCCATTACCGTCC
131 TAATTTACATTTTTAACCTTTATAATAAAATTATAAAACCATTATAATCATGGCCATTACCGTCC
* *
146766 ACTCTAATTGTCAATGGTCTAATTGCTTCATAAGTGCTTCATATTAATAAGACAAGTTCAATTAA
196 ACTCTAATTGTCAATGGTCTAATTGCTTCATAAGTGATTCATATTAATAAGACAAGTTCAAATAA
146831 GCACTTTCACATTTAAC
261 GCACTTTCACATTTAAC
146848 CACCAAATTT
Statistics
Matches: 268, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
277 268 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (277 bp):
GATTAAGCTTGAATATGGCCGAACCTAGGTTTTCTTTTTCTTTTATTTTGCTTCGGAAAAAACAC
AAATAATAACACATATAATGGCTTTTATTTTTATGTTATAATATAACATATATTAACTTAATACT
TAATTTACATTTTTAACCTTTATAATAAAATTATAAAACCATTATAATCATGGCCATTACCGTCC
ACTCTAATTGTCAATGGTCTAATTGCTTCATAAGTGATTCATATTAATAAGACAAGTTCAAATAA
GCACTTTCACATTTAAC
Found at i:149240 original size:21 final size:20
Alignment explanation
Indices: 149216--149255 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
149206 ATGTTCAAGT
*
149216 TCCAGACGGGCGTGTTGCCCA
1 TCCACACGGGCGTG-TGCCCA
149237 TCCACACGGGCGTGTGCCC
1 TCCACACGGGCGTGTGCCC
149256 TGTTTCTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.12, C:0.38, G:0.33, T:0.17
Consensus pattern (20 bp):
TCCACACGGGCGTGTGCCCA
Found at i:161652 original size:14 final size:14
Alignment explanation
Indices: 161633--161659 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
161623 CAAATTACAT
161633 GTTAGAATAGTATC
1 GTTAGAATAGTATC
161647 GTTAGAATAGTAT
1 GTTAGAATAGTAT
161660 GATTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:164294 original size:16 final size:16
Alignment explanation
Indices: 164275--164305 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
164265 CTTCTTCACT
164275 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
164291 TACTTACTTACTTAA
1 TACTCACTTACTTAA
164306 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:164311 original size:20 final size:20
Alignment explanation
Indices: 164272--164311 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
164262 AAACTTCTTC
* *
164272 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
164292 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
164312 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:164689 original size:55 final size:53
Alignment explanation
Indices: 164497--164753 Score: 240
Period size: 55 Copynumber: 4.8 Consensus size: 53
164487 ATACGCAGGT
* * * * *
164497 AACTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* *
164545 AAACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
1 -AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* * *
164599 AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G
* *** *
164653 TAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTTCTTGCCTTA-G
1 -AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* * *
164706 AAACTTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -AAC-TTACCAA-TGCCATGTCTTGACATGGTCTTACATGGGATCCTT
164754 AAACCCTAAT
Statistics
Matches: 174, Mismatches: 23, Indels: 16
0.82 0.11 0.08
Matches are distributed among these distances:
49 40 0.23
50 1 0.01
52 2 0.01
53 50 0.29
54 9 0.05
55 71 0.41
56 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.37
Consensus pattern (53 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
Found at i:164690 original size:108 final size:110
Alignment explanation
Indices: 164546--164746 Score: 318
Period size: 108 Copynumber: 1.8 Consensus size: 110
164536 ATCCTTTTGA
* *
164546 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AAC-TCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACTTCACCAA
164609 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * * *
164654 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTTCTTGCCTTAGAAACTTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACTTCACCAAT
164719 TGCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
164747 TATCCTTAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.58
109 6 0.07
110 28 0.33
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACTTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:174006 original size:32 final size:32
Alignment explanation
Indices: 173964--174028 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
173954 AATGCTTATC
173964 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
*
173996 ATGCGCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
174028 A
1 A
174029 AATGCATACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:176221 original size:40 final size:40
Alignment explanation
Indices: 176162--176474 Score: 545
Period size: 40 Copynumber: 7.8 Consensus size: 40
176152 GAGCATTGGA
*
176162 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
176202 ATATATCCGGGCTAGGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
176242 ATATATCCGGGCTAGGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
176282 ATATATCCGGGCTAGGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
176322 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
176362 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
176402 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
176442 ATATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATG
176475 TTTGCGGCTG
Statistics
Matches: 265, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 265 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:184632 original size:49 final size:49
Alignment explanation
Indices: 184517--184830 Score: 207
Period size: 49 Copynumber: 6.5 Consensus size: 49
184507 TAATGTCGAT
* * * ** *
184517 GCCATGTCCCAGACATGGTCTTACACTGGCTCATC--CATC-AAGTTGAT
1 GCCATGTCCCAGACATGGTCTTACACTGACT-ATCAAAATCGAGGCCGAC
* * * * *
184564 GCCCTATCCCACACATGGTCTTACATTGACTATCGAAATCGAGGCCGAC
1 GCCATGTCCCAGACATGGTCTTACACTGACTATCAAAATCGAGGCCGAC
* *
184613 GCTATGTCCCAGACATGGTCTTACACTGACTATCAAAATCGAGGTCGAC
1 GCCATGTCCCAGACATGGTCTTACACTGACTATCAAAATCGAGGCCGAC
* * * * * *
184662 TCCATGTCCCAGACATGGTCTTACACT-AGCTCTTACATATCCG-TGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGA-CTATCA-AAAT-CGAGGCCGAC
* * *** * * *
184712 GCCATGTCCCAGAGATGGTCTTACACT-AGCTCTC-GTCTCAATGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGA-CTATCAAAATCGAGGCCGAC
* * * * * * *
184760 GCCATGTCCCAGACATGGTCTTACACTGGCTCTTATAAT-GTGGCCAAT
1 GCCATGTCCCAGACATGGTCTTACACTGACTATCAAAATCGAGGCCGAC
184808 G-CATGTCCCAGACAT-GTCTTACA
1 GCCATGTCCCAGACATGGTCTTACA
184831 TTGGCACACA
Statistics
Matches: 217, Mismatches: 41, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
46 11 0.05
47 41 0.19
48 49 0.23
49 76 0.35
50 38 0.18
51 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (49 bp):
GCCATGTCCCAGACATGGTCTTACACTGACTATCAAAATCGAGGCCGAC
Found at i:189301 original size:29 final size:29
Alignment explanation
Indices: 189259--189359 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
189249 CATGAAATTG
189259 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
189288 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* * *
189317 GCACTAAGTGTGCGAGTTC-GATTATATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
189345 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
189360 ACTTACTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 19 0.29
29 46 0.71
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTCAAATTGTATA
Found at i:193486 original size:51 final size:50
Alignment explanation
Indices: 193408--193658 Score: 351
Period size: 51 Copynumber: 4.9 Consensus size: 50
193398 ATAGATACAT
*
193408 AGTGGCCTTCACATAGTACCACCCTTGTAG-CCAAAGCTACTTTATTCACAA
1 AGTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTA-TTTATTCACAA
* * * *
193459 GGTGGCCTTTACATAGTACCACACTTGTGTCTAAAGCTATTTTTTTCACAA
1 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTA-TTTATTCACAA
*
193510 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCCCAA
1 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATT-TATTCACAA
* *
193561 AGTAGCCTTCATATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAA
1 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATT-TATTCACAA
* *
193612 ACTGGCCTTCACATAGTACCACACTTGTGTCCAAAGTTATTTTATTC
1 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTA-TTTATTC
193659 CTAAGGTTCA
Statistics
Matches: 179, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
50 3 0.02
51 174 0.97
52 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (50 bp):
AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTATTCACAA
Found at i:193794 original size:28 final size:24
Alignment explanation
Indices: 193694--193793 Score: 155
Period size: 24 Copynumber: 4.0 Consensus size: 24
193684 ACTTTGCACA
193694 ATGCCATGGACTTATTTCACTTAG
1 ATGCCATGGACTTATTTCACTTAG
193718 ATGCCATGGACTTATTTCACTTAG
1 ATGCCATGGACTTATTTCACTTAG
193742 ATGCCATGGACTTATTTCACTTAG
1 ATGCCATGGACTTATTTCACTTAG
*
193766 CATATTGACATGGACTTATTTCACTTAG
1 ---A-TGCCATGGACTTATTTCACTTAG
193794 CGCAATGTCA
Statistics
Matches: 71, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
24 48 0.68
27 1 0.01
28 22 0.31
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (24 bp):
ATGCCATGGACTTATTTCACTTAG
Found at i:200302 original size:51 final size:51
Alignment explanation
Indices: 200224--200471 Score: 369
Period size: 51 Copynumber: 4.9 Consensus size: 51
200214 ACGGATACAC
*
200224 AGTGGCCTTCACATAGTACCACCCTTGTAG-CCAAAGCTATTTTATTCACAA
1 AGTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTTTATTCACAA
* *
200275 AGTGGCCTTCACATAGTACCAAACTTGTGTGCAAAGCTATTTTATTCACAA
1 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAA
*
200326 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAA
1 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAA
* * * *
200377 AGTGG-C--CATATAGTACCACAATTGTGTCCAAACCTATTATATTCACAA
1 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAA
* *
200425 ACTGGCCTTCACATAGTAACACACTTGTGTCCAAAGCTATTTTATTC
1 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
200472 CTAAGCTTCA
Statistics
Matches: 178, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
48 43 0.24
49 1 0.01
50 2 0.01
51 132 0.74
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (51 bp):
AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAA
Found at i:200449 original size:99 final size:101
Alignment explanation
Indices: 200226--200471 Score: 365
Period size: 99 Copynumber: 2.4 Consensus size: 101
200216 GGATACACAG
*
200226 TGGCCTTCACATAGTACCACCCTTGTAG-CCAAAGCTATTTTATTCACAAAGTGGCCTTCACATA
1 TGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTTTATTCACAAAGTGGCC-TCACATA
* * * *
200290 GTACCAAACTTGTGTGCAAAGCTATTTTATTCACAAAG
64 GTACCAAACTTGTGTCCAAACCTATTATATTCACAAAC
* *
200328 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAGTGG-C-CATATAGT
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAGTGGCCTCACATAGT
200391 ACCACAA-TTGTGTCCAAACCTATTATATTCACAAAC
66 ACCA-AACTTGTGTCCAAACCTATTATATTCACAAAC
*
200427 TGGCCTTCACATAGTAACACACTTGTGTCCAAAGCTATTTTATTC
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
200472 CTAAGCTTCA
Statistics
Matches: 133, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
99 79 0.59
100 2 0.02
101 2 0.02
102 50 0.38
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (101 bp):
TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAGTGGCCTCACATAGT
ACCAAACTTGTGTCCAAACCTATTATATTCACAAAC
Found at i:200527 original size:28 final size:28
Alignment explanation
Indices: 200495--200588 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 28
200485 GGAAAATTTC
200495 TCACTTAGCACAATACCATGGACTTATT
1 TCACTTAGCACAATACCATGGACTTATT
* *
200523 TCACTTAGCATATTGA-CATGGACTTATT
1 TCACTTAGCACAAT-ACCATGGACTTATT
* * *
200551 TCGCTTAG----ATGCCATGGTCTTATT
1 TCACTTAGCACAATACCATGGACTTATT
200575 TCACTTAGCACAAT
1 TCACTTAGCACAAT
200589 GTCATATCCT
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
24 19 0.36
28 33 0.62
29 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (28 bp):
TCACTTAGCACAATACCATGGACTTATT
Found at i:201948 original size:18 final size:17
Alignment explanation
Indices: 201918--201959 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
201908 TTACATTTCT
201918 CACATGAAAATCCATTAA
1 CACAT-AAAATCCATTAA
201936 CACATAAACATCCATTAA
1 CACATAAA-ATCCATTAA
201954 -ACATAA
1 CACATAA
201960 TCACATTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.21
Consensus pattern (17 bp):
CACATAAAATCCATTAA
Found at i:203380 original size:47 final size:47
Alignment explanation
Indices: 203327--203455 Score: 197
Period size: 47 Copynumber: 2.7 Consensus size: 47
203317 CAATCAATAC
*
203327 GTACCTATACCATGGCCC-TAAGCCAAATCAAGGTAACTTATCCCGGA
1 GTACCTATACCATGGCCCGT-AGCCAAATCAAGGTAACTCATCCCGGA
* * *
203374 GTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCCTCTCTGA
1 GTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCGGA
*
203421 ATACCTATACCATGGCCCGTAGCCAAATCAAGGTA
1 GTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
203456 TCACTCGCAA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
47 75 0.99
48 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (47 bp):
GTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCGGA
Found at i:208822 original size:40 final size:40
Alignment explanation
Indices: 208778--209002 Score: 281
Period size: 40 Copynumber: 5.6 Consensus size: 40
208768 CTTGCGCAAG
* * * *
208778 GCCTTCGGGTGTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
208818 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
208858 GCCTTCGGGTTTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
208898 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
208938 GCCTTCGGATCTTAGTCCGGTTATAGTCACTTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCAC-TAGCACAAAT
*
208979 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
209003 CATTCGAATA
Statistics
Matches: 158, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 129 0.82
41 28 0.18
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:218372 original size:40 final size:40
Alignment explanation
Indices: 218326--218550 Score: 238
Period size: 40 Copynumber: 5.6 Consensus size: 40
218316 CTTGCGCAAG
* * * * * *
218326 GCCTTCGGGTTTTAGCCTGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
*
218366 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
* *
218406 GCCTTCGGGTTTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
218446 GCCTTCGGGTCTTAGCCCTGATATAG-CAACTCA-CACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-GCT-AGCACAAAT
* * * * *
218486 GCCTTCGGATCTTAGTCCGGTTATAGTCACTTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCGC-TAGCACAAAT
* *
218527 GCCTTCGTGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
218551 CATTCGAATA
Statistics
Matches: 154, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.01
40 126 0.82
41 27 0.18
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.28
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:220303 original size:14 final size:16
Alignment explanation
Indices: 220281--220314 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
220271 TTAAGTCACG
220281 TAAATTTCACACAT-A
1 TAAATTTCACACATAA
220296 TAAA-TTCACACATAA
1 TAAATTTCACACATAA
220311 TAAA
1 TAAA
220315 CACTGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAATTTCACACATAA
Found at i:221646 original size:109 final size:106
Alignment explanation
Indices: 221441--221641 Score: 267
Period size: 114 Copynumber: 1.8 Consensus size: 106
221431 AAAACAAAAA
* *
221441 TTTATATTAAAATACTAAAAATAATATGCCAATAAAAAAATAAAAATATAACATAAACCATACAT
1 TTTATATTAAAATACTAAAAATAACATGCCAATAAAAAAATAAAAACATAACATAAACCATACAT
* *
221506 AATAAATACTATTATTATTATTTTAAAATTATAATAAGTAAATT
66 AATAAATACGAATATTATTA-TTT--AATTATAATAAGTAAATT
* *
221550 TTTATATTAAAATACTAAAAATAACATGCCGATAAAAAAATATAACATAAACATAACATAAACGA
1 TTTATATTAAAATACTAAAAATAACATGCCAAT-AAAAAA-AT-A-A-AAACATAACATAAACCA
*
221615 TACATAATAAATGCGAATATTATTATT
61 TACATAATAAATACGAATATTATTATT
221642 ATTATTTTAA
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
109 31 0.39
110 6 0.08
111 2 0.03
112 1 0.01
113 3 0.04
114 37 0.46
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.32
Consensus pattern (106 bp):
TTTATATTAAAATACTAAAAATAACATGCCAATAAAAAAATAAAAACATAACATAAACCATACAT
AATAAATACGAATATTATTATTTAATTATAATAAGTAAATT
Found at i:221942 original size:11 final size:9
Alignment explanation
Indices: 221918--221956 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
221908 TACCTACATA
221918 AAAAATAAT
1 AAAAATAAT
221927 AAAAATAAT
1 AAAAATAAT
221936 ATTAAAATAAT
1 A--AAAATAAT
*
221947 CAAAATAAT
1 AAAAATAAT
221956 A
1 A
221957 GCATGCCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 18 0.69
11 8 0.31
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAAATAAT
Found at i:221944 original size:20 final size:20
Alignment explanation
Indices: 221919--221956 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
221909 ACCTACATAA
221919 AAAATAATAAAAATAATATT
1 AAAATAATAAAAATAATATT
*
221939 AAAATAATCAAAATAATA
1 AAAATAATAAAAATAATA
221957 GCATGCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATAATAAAAATAATATT
Found at i:222186 original size:13 final size:13
Alignment explanation
Indices: 222168--222195 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
222158 AATACCCTAC
222168 AAAATTAAATTTA
1 AAAATTAAATTTA
222181 AAAATTAAATTTA
1 AAAATTAAATTTA
222194 AA
1 AA
222196 TTAATCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATTAAATTTA
Found at i:222303 original size:12 final size:12
Alignment explanation
Indices: 222286--222310 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
222276 TTATATTATT
222286 TTTCTCCTTCTC
1 TTTCTCCTTCTC
222298 TTTCTCCTTCTC
1 TTTCTCCTTCTC
222310 T
1 T
222311 CCCTATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTCTCCTTCTC
Found at i:222372 original size:3 final size:3
Alignment explanation
Indices: 222352--222417 Score: 64
Period size: 3 Copynumber: 22.3 Consensus size: 3
222342 CCTTTCTCGC
* * * *
222352 CTT CTC CTT CTC CTT CTT CTT CTT CTT CTA CTT CTT CTT -TT CTT CTC
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
222399 CTT C-T CTTT CTT CTC CTT C
1 CTT CTT C-TT CTT CTT CTT C
222418 ACTTACCTTC
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 4 0.08
3 44 0.88
4 2 0.04
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.59
Consensus pattern (3 bp):
CTT
Found at i:224051 original size:54 final size:53
Alignment explanation
Indices: 223903--224060 Score: 137
Period size: 51 Copynumber: 3.0 Consensus size: 53
223893 TTTATGTTAC
* * *
223903 TTTTAATTTATTTTAAAATTATTTTGTTAGTTACTATTATAAATTATTTGTTTA
1 TTTTAATTTA-TTTAAAGTTATTTTGTTAGTTACTATTATAAATTATTTATTAA
* * ** * *
223957 GTTTAA--TGTTTATTGTTA-TTTGTTAGGTTA-TGAATGTAAATT-TTTATTAA
1 TTTTAATTTATTTAAAGTTATTTTGTTA-GTTACT-ATTATAAATTATTTATTAA
* *
224007 TTTTTAATTTATTTGAAAGTTATTTTGTTAGTAACTATTATAAATTAATTATTA
1 -TTTTAATTTATTT-AAAGTTATTTTGTTAGTTACTATTATAAATTATTTATTA
224061 GTTTGTGATG
Statistics
Matches: 78, Mismatches: 17, Indels: 17
0.70 0.15 0.15
Matches are distributed among these distances:
50 14 0.18
51 24 0.31
52 1 0.01
53 4 0.05
54 21 0.27
55 14 0.18
ACGTcount: A:0.32, C:0.01, G:0.09, T:0.58
Consensus pattern (53 bp):
TTTTAATTTATTTAAAGTTATTTTGTTAGTTACTATTATAAATTATTTATTAA
Found at i:227729 original size:48 final size:48
Alignment explanation
Indices: 227630--227738 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
227620 ACTCCAATGT
* ** **
227630 ATCTAATTTATATTACAAAGTTTGTTCCTTGTTTTAATATTGCAATTA
1 ATCTAATTTAAATTACAAAGTTTGTTCCAAGTTTTAATATTGCAACGA
* * *
227678 ATCTAATTTAAATTACGAAGTTTGTTCCAAGTTTTAATGTTGTAACGA
1 ATCTAATTTAAATTACAAAGTTTGTTCCAAGTTTTAATATTGCAACGA
227726 ATCTTAA-TTAAAT
1 ATC-TAATTTAAAT
227739 AAATACAATG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 49 0.94
49 3 0.06
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (48 bp):
ATCTAATTTAAATTACAAAGTTTGTTCCAAGTTTTAATATTGCAACGA
Found at i:231480 original size:30 final size:30
Alignment explanation
Indices: 231446--231506 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
231436 TCCTTAACTC
231446 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
231476 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
231506 A
1 A
231507 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:236560 original size:21 final size:22
Alignment explanation
Indices: 236535--236593 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
236525 CAAAACACAT
* *
236535 TAATATTATACATACAGTA-AA
1 TAATAATATAAATACAGTACAA
* *
236556 TAATACTATAAATATAGTACAA
1 TAATAATATAAATACAGTACAA
*
236578 TAATAATATAACTACA
1 TAATAATATAAATACA
236594 ATAAAAGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.32
Consensus pattern (22 bp):
TAATAATATAAATACAGTACAA
Found at i:237004 original size:112 final size:109
Alignment explanation
Indices: 236822--237433 Score: 846
Period size: 108 Copynumber: 5.6 Consensus size: 109
236812 CAAATAAATC
* * * * * *
236822 AAAAACAAAAAAACTACATT-ATAATAAATCAAAATACACATTAAACT-AA-ACAAATAATTTAT
1 AAAAACAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTAT
*
236884 AACCTAATCATAAATTACTAAAAAAATAACTTTAAAATAATTTA
66 AACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTA
* *
236928 AAAAACACAAAAGAATTTACATTGATAAAAAATCACAATAAATACTAAACTAAACACAAACAATT
1 AAAAACA-AAAA-AA-TTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATT
** *
236993 TATAAAGTAATCATAAATTACTAACAAACTAACTTTAAAAATAATTTTA
63 TATAACCTAATCATAAATTACTAACAAAATAACTTT-AAAATAA-TTTA
* *
237042 AAAACACAAAAAATTTACATTCATAAAAAATCACAATAAACACTAAACTAAACCCAAACAATTTA
1 AAAA-ACAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTA
*
237107 TAACCTAATCATAAATTACTAACGAAATAACTTTAAAATAA--TA
65 TAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTA
* * * *
237150 ATAAACAAGAAAAATTACGTTCATAAAAAATCACAATAAACACCAAACTAAACAAAAACAATTTA
1 AAAAACAA-AAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTA
*
237215 TAACCTAATCATAAATTACTAACAAAATAACTTTAAAACAA--TA
65 TAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTA
* * *
237258 ATAAACAAGAAAAATTACATTCATAAAAAATCACAATAAACACCAAACTAAACAAAAACAATTTA
1 AAAAACAA-AAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTA
237323 TAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTTA
65 TAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAA-TTTA
* * *
237369 AAAAATAAAAAAATTACATTCATAAAAAATCACAA-AAA-ACTAAACTAAACAGAAATAATTTAT
1 AAAAACAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTAT
237432 AA
66 AA
237434 TAATTACTAA
Statistics
Matches: 459, Mismatches: 34, Indels: 24
0.89 0.07 0.05
Matches are distributed among these distances:
106 7 0.02
107 8 0.02
108 227 0.49
109 9 0.02
110 49 0.11
111 17 0.04
112 119 0.26
113 8 0.02
114 12 0.03
115 3 0.01
ACGTcount: A:0.59, C:0.15, G:0.01, T:0.25
Consensus pattern (109 bp):
AAAAACAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTAT
AACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTA
Found at i:237488 original size:27 final size:27
Alignment explanation
Indices: 237458--237517 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
237448 AAAACAACAT
*
237458 AAAAAATAACTAATCCCTTCT-ATTTAA
1 AAAAAATAACTAATCCCTT-TAAATTAA
*
237485 AAAAAATTACTAATCCCTTTAAATTAA
1 AAAAAATAACTAATCCCTTTAAATTAA
237512 AAAAAA
1 AAAAAA
237518 CATTAATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAAAATAACTAATCCCTTTAAATTAA
Found at i:238533 original size:35 final size:35
Alignment explanation
Indices: 238487--238566 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
238477 GGATAAATAG
* *
238487 TCTACTGGCTTTACAG-GGTGGCATCATGGGAATGA
1 TCTACTGGCTTTA-AGAAGTGGCATCATAGGAATGA
* *
238522 TCTACTGGCTTTATGAAGTGGCATCATATGAATGA
1 TCTACTGGCTTTAAGAAGTGGCATCATAGGAATGA
238557 TCTACTGGCT
1 TCTACTGGCT
238567 CTATAGAGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 1 0.03
35 39 0.98
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (35 bp):
TCTACTGGCTTTAAGAAGTGGCATCATAGGAATGA
Found at i:239079 original size:28 final size:28
Alignment explanation
Indices: 239015--239090 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
239005 AGAAGAGGCG
* *
239015 AAGTCCGCCAATGACTATCTTATGTGAA
1 AAGTCCGCCAAGGACTATCTTACGTGAA
* *
239043 AAGTACGCCAAGGACTATCTTACGTGGA
1 AAGTCCGCCAAGGACTATCTTACGTGAA
* *
239071 ATGTCCGCCAAGGACAATCT
1 AAGTCCGCCAAGGACTATCT
239091 ATTCTATAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (28 bp):
AAGTCCGCCAAGGACTATCTTACGTGAA
Found at i:240845 original size:15 final size:15
Alignment explanation
Indices: 240825--240854 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
240815 AAACTCGGAA
240825 TAATTTATGCGTGGG
1 TAATTTATGCGTGGG
240840 TAATTTATGCGTGGG
1 TAATTTATGCGTGGG
240855 GTTTAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.33, T:0.40
Consensus pattern (15 bp):
TAATTTATGCGTGGG
Found at i:246509 original size:17 final size:15
Alignment explanation
Indices: 246478--246512 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
246468 TTAAAGGTAA
246478 AATAATATATCATAC
1 AATAATATATCATAC
246493 AATAACTATAGTCATAC
1 AATAA-TATA-TCATAC
246510 AAT
1 AAT
246513 TATTCAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 4 0.22
17 9 0.50
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.31
Consensus pattern (15 bp):
AATAATATATCATAC
Found at i:246912 original size:41 final size:40
Alignment explanation
Indices: 246775--246915 Score: 110
Period size: 40 Copynumber: 3.6 Consensus size: 40
246765 AACACACCAG
* * * * *
246775 TTTGGCACCCAGTGCCTCATCGGATAATTCGAAGCAATAA
1 TTTGACACCCAGTGCCTCATCGAATTATCCGAAGTAATAA
* * * **
246815 GTTGACATCCAGTGTCTCATCG-GCTATGCCGAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGAATTAT-CCGAAGTAATAA
** *
246853 -TTGGTACCCAGTACCTCATCGAATTTATCCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGAA-TTATCCGAAGTAATAA
*
246893 TTTGACACCCAGTGTCTCATCGA
1 TTTGACACCCAGTGCCTCATCGA
246916 CTCGAAGTCG
Statistics
Matches: 75, Mismatches: 20, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
37 16 0.21
38 9 0.12
39 7 0.09
40 25 0.33
41 18 0.24
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGAATTATCCGAAGTAATAA
Found at i:249270 original size:93 final size:93
Alignment explanation
Indices: 249158--249328 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
249148 GCCCATAAGT
* *
249158 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
249223 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
249251 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
249316 CGAGTTCGGATGC
66 CGAGTTCGGATGC
249329 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:249325 original size:46 final size:46
Alignment explanation
Indices: 249150--249325 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
249140 TGTAACCCGC
* * *
249150 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
249196 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
249246 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
249289 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
249326 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:254434 original size:40 final size:40
Alignment explanation
Indices: 254355--254531 Score: 216
Period size: 40 Copynumber: 4.5 Consensus size: 40
254345 CGGATGATAA
* * * *
254355 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * * *
254395 CCGGGCTATGTCCTGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
* *
254435 TCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
254475 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
254515 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
254532 ATACTTGGGT
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.01
39 15 0.13
40 98 0.84
41 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:254799 original size:22 final size:22
Alignment explanation
Indices: 254759--254800 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
254749 GAATGTGCAT
*
254759 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
254781 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
254801 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:256395 original size:6 final size:6
Alignment explanation
Indices: 256384--256433 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
256374 GTTATTGCTG
* * * * *
256384 GAATAT GAATAT GAAAAT GAATGT AAATGT GAATAT GAATAT GAACAT
1 GAATAT GAATAT GAATAT GAATAT GAATAT GAATAT GAATAT GAATAT
256432 GA
1 GA
256434 CCAATATGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.28
Consensus pattern (6 bp):
GAATAT
Done.