Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3370.1
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: 136951
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 835 characters in sequence are not A, C, G, or T
Found at i:6849 original size:40 final size:40
Alignment explanation
Indices: 6794--6906 Score: 158
Period size: 40 Copynumber: 2.9 Consensus size: 40
6784 NNNNNNNNCG
*
6794 AAGGCAATTGTGCGAGTTACTATAACCGGGTTAAGTCCCA
1 AAGGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCA
*
6834 AAGGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCG
1 AAGGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCA
* * *
6874 AAGGCATTTGAGCGAG-TAGCTATATCC-GGCTAA
1 AAGGCAATTGTGCGAGTTA-CTATAACCGGGCTAA
6907 ACCCCGAAGG
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
39 8 0.12
40 59 0.88
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (40 bp):
AAGGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCA
Found at i:9078 original size:71 final size:71
Alignment explanation
Indices: 8962--9097 Score: 254
Period size: 71 Copynumber: 1.9 Consensus size: 71
8952 TAAAATGCCA
*
8962 ACAATTCAATTAACCAACACCTAATCATAAGTATCCATCATATGTTAGTCATTTGACAAATACAT
1 ACAATTCAATTAACCAACACCTAATCAGAAGTATCCATCATATGTTAGTCATTTGACAAATACAT
9027 AAAACC
66 AAAACC
*
9033 ACAATTCAATTAACCAACACTTAATCAGAAGTATCCATCATATGTTAGTCATTTGACAAATACAT
1 ACAATTCAATTAACCAACACCTAATCAGAAGTATCCATCATATGTTAGTCATTTGACAAATACAT
9098 GAAGCCATCC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (71 bp):
ACAATTCAATTAACCAACACCTAATCAGAAGTATCCATCATATGTTAGTCATTTGACAAATACAT
AAAACC
Found at i:9271 original size:23 final size:23
Alignment explanation
Indices: 9245--9338 Score: 68
Period size: 23 Copynumber: 4.0 Consensus size: 23
9235 TTTCAAGCCA
**
9245 TGATCGGTAAGCTCCTCCTGAGC
1 TGATCGGTAAGCTCCTAATGAGC
*
9268 TGATAGCAGTAAGCT-CTAATGAGC
1 TGAT--CGGTAAGCTCCTAATGAGC
* * *
9292 TGAAACGGTAAGCTCAT-AGGAGC
1 TG-ATCGGTAAGCTCCTAATGAGC
*
9315 TGAAACGGTAAGCTCC-AATGAGC
1 TG-ATCGGTAAGCTCCTAATGAGC
9338 T
1 T
9339 AAAACTGAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
23 38 0.67
24 10 0.18
25 9 0.16
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (23 bp):
TGATCGGTAAGCTCCTAATGAGC
Found at i:9335 original size:46 final size:49
Alignment explanation
Indices: 9276--9388 Score: 135
Period size: 46 Copynumber: 2.4 Consensus size: 49
9266 GCTGATAGCA
* *
9276 GTAAGCTCTAATGAGCTGAAACGGTAAGCTCATAGGAGCTGA-A-A-CG
1 GTAAGCTCCAATGAGCTGAAACGGAAAGCTCATAGGAGCTGATATATCG
* * * *
9322 GTAAGCTCCAATGAGCTAAAACTGAAAGCTCTTATGAGCTGATATATCG
1 GTAAGCTCCAATGAGCTGAAACGGAAAGCTCATAGGAGCTGATATATCG
9371 GTAAGCT-CATATGAGCTG
1 GTAAGCTCCA-ATGAGCTG
9389 TGGTGAGTCC
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
46 36 0.64
47 1 0.02
48 3 0.05
49 16 0.29
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.24
Consensus pattern (49 bp):
GTAAGCTCCAATGAGCTGAAACGGAAAGCTCATAGGAGCTGATATATCG
Found at i:9343 original size:23 final size:23
Alignment explanation
Indices: 9276--9387 Score: 84
Period size: 23 Copynumber: 4.7 Consensus size: 23
9266 GCTGATAGCA
* *
9276 GTAAGCTCTAATGAGCTGAAACG
1 GTAAGCTCCAATGAGCTAAAACG
* *
9299 GTAAGCT-CATAGGAGCTGAAACG
1 GTAAGCTCCA-ATGAGCTAAAACG
*
9322 GTAAGCTCCAATGAGCTAAAACT
1 GTAAGCTCCAATGAGCTAAAACG
* ** *
9345 GAAAGCTCTTATGAGCTGATATATCG
1 GTAAGCTCCAATGAGCT-A-A-AACG
9371 GTAAGCT-CATATGAGCT
1 GTAAGCTCCA-ATGAGCT
9388 GTGGTGAGTC
Statistics
Matches: 70, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
22 1 0.01
23 50 0.71
24 3 0.04
25 1 0.01
26 15 0.21
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (23 bp):
GTAAGCTCCAATGAGCTAAAACG
Found at i:14600 original size:74 final size:73
Alignment explanation
Indices: 14463--14606 Score: 209
Period size: 74 Copynumber: 2.0 Consensus size: 73
14453 GGTACGTAGC
* * * *
14463 GTAGCTAATGTACATGCGGTATAGTGTAATACGAAATCTGCTATACCGATAGGTTGCAATAAAAC
1 GTAGCTAACGTACATGCGGTACAGTGCAATACGAAATCTGCTATACCGACAGGTTGCAATAAAAC
14528 TGCCAAAT
66 TGCCAAAT
* *
14536 GTAGCTAACGTACATGCGGTACAGTGCAATGCGATAAT-TCGCTATACCGACAGGTTGCAGTAAA
1 GTAGCTAACGTACATGCGGTACAGTGCAATACGA-AATCT-GCTATACCGACAGGTTGCAATAAA
14600 ACTGCCA
64 ACTGCCA
14607 GTTTAGTCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
73 31 0.49
74 32 0.51
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (73 bp):
GTAGCTAACGTACATGCGGTACAGTGCAATACGAAATCTGCTATACCGACAGGTTGCAATAAAAC
TGCCAAAT
Found at i:15348 original size:13 final size:13
Alignment explanation
Indices: 15316--15340 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15306 TTAAATGTGT
15316 CTATTAATTAAGA
1 CTATTAATTAAGA
15329 CTATTAATTAAG
1 CTATTAATTAAG
15341 CTTATTAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
CTATTAATTAAGA
Found at i:16292 original size:21 final size:21
Alignment explanation
Indices: 16268--16322 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
16258 TAGCACATGG
* * * *
16268 CCGTGTGACGTAGGTACACGC
1 CCGTGTGAAGCAGGGACACGA
16289 CCGTGTGAAGCAGGGACACGA
1 CCGTGTGAAGCAGGGACACGA
16310 CCGTGTGAA-CAGG
1 CCGTGTGAAGCAGG
16323 TAGTGTAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.24, C:0.25, G:0.36, T:0.15
Consensus pattern (21 bp):
CCGTGTGAAGCAGGGACACGA
Found at i:17930 original size:40 final size:40
Alignment explanation
Indices: 17876--18033 Score: 237
Period size: 40 Copynumber: 4.0 Consensus size: 40
17866 CCGGATATAG
17876 TACCAGCACT-AAGCCTGCGGGATTTAACCCGGATATACTT
1 TACCAGCA-TGAAGCCTGCGGGATTTAACCCGGATATACTT
* * *
17916 TACTAGCATGAAGCCTACGGGATTTAACTCGGATATACTT
1 TACCAGCATGAAGCCTGCGGGATTTAACCCGGATATACTT
* *
17956 TACCAGCATGAAGCCTGCGGGATTTAACCCAGATATACAT
1 TACCAGCATGAAGCCTGCGGGATTTAACCCGGATATACTT
* *
17996 TACCAGCACGATGCCTGCGGGATTTAACCCGGATATAC
1 TACCAGCATGAAGCCTGCGGGATTTAACCCGGATATAC
18034 AATATATCGA
Statistics
Matches: 106, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 105 0.99
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (40 bp):
TACCAGCATGAAGCCTGCGGGATTTAACCCGGATATACTT
Found at i:17960 original size:80 final size:80
Alignment explanation
Indices: 17835--18033 Score: 242
Period size: 80 Copynumber: 2.5 Consensus size: 80
17825 CCGAATCCAG
* * * * *
17835 TTACTAGCACAAAGCCTATGGGACTTTAGGCCCGGATATA--GTACCAGCACT-AAGCCTGCGGG
1 TTACCAGCACGAAGCCTACGGGA-TTTA-ACCCGGATATACTTTACCAGCA-TGAAGCCTGCGGG
* *
17897 ATTTAACCCGGATATACT
63 ATTTAACCCAGATATACA
* * *
17915 TTACTAGCATGAAGCCTACGGGATTTAACTCGGATATACTTTACCAGCATGAAGCCTGCGGGATT
1 TTACCAGCACGAAGCCTACGGGATTTAACCCGGATATACTTTACCAGCATGAAGCCTGCGGGATT
17980 TAACCCAGATATACA
66 TAACCCAGATATACA
* *
17995 TTACCAGCACGATGCCTGCGGGATTTAACCCGGATATAC
1 TTACCAGCACGAAGCCTACGGGATTTAACCCGGATATAC
18034 AATATATCGA
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
78 9 0.09
79 5 0.05
80 89 0.86
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (80 bp):
TTACCAGCACGAAGCCTACGGGATTTAACCCGGATATACTTTACCAGCATGAAGCCTGCGGGATT
TAACCCAGATATACA
Found at i:25880 original size:40 final size:40
Alignment explanation
Indices: 25826--25944 Score: 150
Period size: 40 Copynumber: 3.0 Consensus size: 40
25816 CCAGATATAG
* * *
25826 TACCAGCACTAAGCCTGTGGGATTTAACTCGGATATACTT
1 TACCAGCACGAAGCCTGCGGGATTTAACTCGGATATACAT
* * *
25866 TACTAGCATGAAGCCTGCGGGATTTAACCCGGATATACAT
1 TACCAGCACGAAGCCTGCGGGATTTAACTCGGATATACAT
* *
25906 TACCAGTACGATGCCTGCGGGATTTAA-TCCGGATATACA
1 TACCAGCACGAAGCCTGCGGGATTTAACT-CGGATATACA
25945 ATATATCTAG
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (40 bp):
TACCAGCACGAAGCCTGCGGGATTTAACTCGGATATACAT
Found at i:26612 original size:2 final size:2
Alignment explanation
Indices: 26605--26629 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26595 CATGCATAAG
26605 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
26630 TATATATATT
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27750 original size:191 final size:191
Alignment explanation
Indices: 27426--27806 Score: 726
Period size: 191 Copynumber: 2.0 Consensus size: 191
27416 ACTAACTCAA
27426 ACTTCATTAAAATATGAGAACAACAATCTATCCTCTTCAATTTCTCCCATGGTCGAATGCTCAAA
1 ACTTCATTAAAATATGAGAACAACAATCTATCCTCTTCAATTTCTCCCATGGTCGAATGCTCAAA
*
27491 TCCTTCTCAAAAATCAAAATTTTAATATGGGTTGAATAAAGAACTTGGTAACTAACTTAAAATTA
66 TCCTTCCCAAAAATCAAAATTTTAATATGGGTTGAATAAAGAACTTGGTAACTAACTTAAAATTA
27556 ACAAAAAATTTAAGAATTAATTAGAAGTCTTACCTTGATTCAACCCTAAAGTAACCGAATG
131 ACAAAAAATTTAAGAATTAATTAGAAGTCTTACCTTGATTCAACCCTAAAGTAACCGAATG
*
27617 ACTTCATTAAAATATGAGAACAACAATCTATCCTCTTCAATTTCTCCCATGGTTGAATGCTCAAA
1 ACTTCATTAAAATATGAGAACAACAATCTATCCTCTTCAATTTCTCCCATGGTCGAATGCTCAAA
27682 TCCTTCCCAAAAATCAAAATTTTAATATGGGTTGAATAAAGAACTTGGTAACTAACTTAAAATTA
66 TCCTTCCCAAAAATCAAAATTTTAATATGGGTTGAATAAAGAACTTGGTAACTAACTTAAAATTA
* *
27747 ACAAAAATTTTAAGAATTAATTAGAAGTCTTACCTTGATTCAAGCCTAAAGTAACCGAAT
131 ACAAAAAATTTAAGAATTAATTAGAAGTCTTACCTTGATTCAACCCTAAAGTAACCGAAT
27807 AGAGCTTTCT
Statistics
Matches: 186, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
191 186 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (191 bp):
ACTTCATTAAAATATGAGAACAACAATCTATCCTCTTCAATTTCTCCCATGGTCGAATGCTCAAA
TCCTTCCCAAAAATCAAAATTTTAATATGGGTTGAATAAAGAACTTGGTAACTAACTTAAAATTA
ACAAAAAATTTAAGAATTAATTAGAAGTCTTACCTTGATTCAACCCTAAAGTAACCGAATG
Found at i:28334 original size:26 final size:26
Alignment explanation
Indices: 28280--28334 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
28270 CAACAATCCC
* *
28280 AAAAGAAAAGCCAGAGAAAACTCCCA
1 AAAAGAAAAGCAAGAGAAAACTCCAA
28306 AAAAGAAAAG-AAG-GAAGAACGTCCAA
1 AAAAGAAAAGCAAGAGAA-AAC-TCCAA
28332 AAA
1 AAA
28335 GAGACCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 3 0.12
25 5 0.20
26 17 0.68
ACGTcount: A:0.62, C:0.16, G:0.18, T:0.04
Consensus pattern (26 bp):
AAAAGAAAAGCAAGAGAAAACTCCAA
Found at i:28442 original size:26 final size:26
Alignment explanation
Indices: 28399--28448 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
28389 TAAAATAAAA
* * * *
28399 TAAAAATAAGTAGCAAAATAAAAACT
1 TAAAAAGAAGAAGAAAAAGAAAAACT
28425 TAAAAAGAAGAAGAAAAAGAAAAA
1 TAAAAAGAAGAAGAAAAAGAAAAA
28449 AATTCATCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.72, C:0.04, G:0.12, T:0.12
Consensus pattern (26 bp):
TAAAAAGAAGAAGAAAAAGAAAAACT
Found at i:31861 original size:15 final size:15
Alignment explanation
Indices: 31837--31868 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31827 TAAATCCCGA
*
31837 AATGCTGAAAAGTCG
1 AATGCCGAAAAGTCG
31852 AATGCCGAAAAGTCG
1 AATGCCGAAAAGTCG
31867 AA
1 AA
31869 AGTCTGGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.16
Consensus pattern (15 bp):
AATGCCGAAAAGTCG
Found at i:36641 original size:27 final size:27
Alignment explanation
Indices: 36583--37189 Score: 419
Period size: 27 Copynumber: 22.6 Consensus size: 27
36573 TTTGTTTACC
** * *
36583 AAATTACTGAAATACCCTCAAATTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
36610 AAATTACCAAAGTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
* *** **
36637 GAATTACCATTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
* * **** *
36664 GAATTATCGTTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
* *** * *
36691 AAATTACTATTTTACCCTTGATTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
* ***** **
36718 GAATTACTGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
* **
36745 AAATTACTAAAATACCCTC-AGTTTACA
1 AAATTACCAAAATACCCTCGA-TTTGTA
* **
36772 AAATTACCAAAATACCATCGATCAGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
36799 AAATTACCAAAATACCCT-AATCTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* * * *
36825 AAATTGCTAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
36852 AAATTACCGAAATACCCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
36879 AAATTACCAAAATACCCT-GGTCTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* * *
36905 AAATTGCTAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
*
36932 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTGTA
* *
36959 AAGTTACCAAAATACCACT-GGTTTGTA
1 AAATTACCAAAATACC-CTCGATTTGTA
*
36986 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTGTA
* *
37013 AAGTTACCAAAATACCACT-GGTTTGTA
1 AAATTACCAAAATACC-CTCGATTTGTA
* * *
37040 AAATTATCGAAATACCCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
*
37067 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTGTA
* *
37094 AAGTTACC-AAATACCACT-GGTTTGTA
1 AAATTACCAAAATACC-CTCGATTTGTA
* *
37120 AAATTACCAAAATACCCTCAATTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
**
37147 AAATTACCAAAATACCC-CTGATTTACA
1 AAATTACCAAAATACCCTC-GATTTGTA
* *
37174 AAGTTACAAAAATACC
1 AAATTACCAAAATACC
37190 ATTAACTTTC
Statistics
Matches: 474, Mismatches: 87, Indels: 38
0.79 0.15 0.06
Matches are distributed among these distances:
26 71 0.15
27 400 0.84
28 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTGTA
Found at i:36855 original size:80 final size:80
Alignment explanation
Indices: 36744--37191 Score: 469
Period size: 80 Copynumber: 5.6 Consensus size: 80
36734 CTCGATTTAC
* ** **
36744 AAAATTACTAAAATA-CCCTCAGTTTACAAAATTACCAAAATACCATCGATCAGTAAAATTACCA
1 AAAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCATCGATTTGTAAAATTACCA
*
36808 AAATACCCTAATCTGT
65 AAATACCCTAATTTGT
* * * * * * *
36824 AAAATTGCTAAAATACCCTTGGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAA
1 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCATCGATTTGTAAAATTACCAA
** *
36889 AATACCCTGGTCTGT
66 AATACCCTAATTTGT
* * * * * *
36904 AAAATTGCTAAAATACCCCTGGTTTGTAAAATTACCAAAATACC-CCTAGTTTGTAAAGTTACCA
1 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCATCGA-TTTGTAAAATTACCA
**
36968 AAATACCACTGGTTTGT
65 AAATACC-CTAATTTGT
* * * *
36985 AAAATTACCAAAATACCCCTAGTTTGTAAAGTTACCAAAATACCA-CTGGTTTGTAAAATTATCG
1 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCATC-GATTTGTAAAATTACCA
37049 AAATACCCTCAATTTGT
65 AAATACCCT-AATTTGT
* *
37066 AAAATTACCAAAATACCCCTAGTTTGTAAAGTTACC-AAATACCA-CTGGTTTGTAAAATTACCA
1 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCATC-GATTTGTAAAATTACCA
*
37129 AAATACCCTCAATTTAT
65 AAATACCCT-AATTTGT
* *
37146 AAAATTACCAAAATACCCCT-GATT-TACAAAGTTACAAAAATACCAT
1 AAAATTACCAAAATACCCCTAGTTTGTA-AAA-TTACCAAAATACCAT
37192 TAACTTTCTA
Statistics
Matches: 323, Mismatches: 35, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
78 2 0.01
79 7 0.02
80 194 0.60
81 120 0.37
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (80 bp):
AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCATCGATTTGTAAAATTACCAA
AATACCCTAATTTGT
Found at i:37346 original size:28 final size:28
Alignment explanation
Indices: 37294--37372 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 28
37284 AAATGACTAC
* *
37294 AATACCCCTAATA-GGTAAAAAGACCCGT
1 AATACCCCT-GTAGGGTAAAATGACCCGT
*
37322 AA-AGCCCCTGTAGGGTAAAGTGA-CCGT
1 AATA-CCCCTGTAGGGTAAAATGACCCGT
* *
37349 AATACCCTTGTATGGTAAAATGAC
1 AATACCCCTGTAGGGTAAAATGAC
37373 GAATATGCCC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
27 25 0.61
28 16 0.39
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (28 bp):
AATACCCCTGTAGGGTAAAATGACCCGT
Found at i:37988 original size:25 final size:25
Alignment explanation
Indices: 37959--38006 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
37949 TTATAATGTG
* * *
37959 AAAATGACTATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
37984 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
38007 GTTTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:38067 original size:20 final size:20
Alignment explanation
Indices: 38033--38108 Score: 113
Period size: 20 Copynumber: 3.9 Consensus size: 20
38023 GATACGTGGG
38033 GTATGATAT--ACATGAT-T
1 GTATGATATGCACATGATAT
38050 GATATGATATGCACATGATAT
1 G-TATGATATGCACATGATAT
38071 GTATGATATGCACATGATAT
1 GTATGATATGCACATGATAT
*
38091 GTATGAAATGCACATGAT
1 GTATGATATGCACATGAT
38109 GAATTCATAA
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
17 1 0.02
18 8 0.15
20 43 0.80
21 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (20 bp):
GTATGATATGCACATGATAT
Found at i:38069 original size:11 final size:11
Alignment explanation
Indices: 38053--38108 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
38043 CATGATTGAT
38053 ATGATATGCAC
1 ATGATATGCAC
*
38064 ATGATATG--T
1 ATGATATGCAC
38073 ATGATATGCAC
1 ATGATATGCAC
*
38084 ATGATATG--T
1 ATGATATGCAC
*
38093 ATGAAATGCAC
1 ATGATATGCAC
38104 ATGAT
1 ATGAT
38109 GAATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:38187 original size:26 final size:26
Alignment explanation
Indices: 38158--38332 Score: 255
Period size: 26 Copynumber: 6.8 Consensus size: 26
38148 GAGGAAGTGC
*
38158 AAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* **
38184 AAAAGGGCTTATGCCCCAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
38210 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
38236 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
***
38262 AAAAGGGCTTATGCCCCAGTTTATTA
1 AAAAGGGCTTATGCCCCAGTTTACCG
38288 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
38313 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
38333 ATTAAAGAGG
Statistics
Matches: 136, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
25 32 0.24
26 104 0.76
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:38292 original size:78 final size:77
Alignment explanation
Indices: 38158--38332 Score: 289
Period size: 78 Copynumber: 2.3 Consensus size: 77
38148 GAGGAAGTGC
* *
38158 AAAAGGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAATTTATTGAAAAGGGCTTATG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAATTTATTAAAAAGGGCTT-TG
**
38223 CCCCAGTTTATTG
65 CCCCAGTTTACCG
*
38236 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTAAAAAGGGCTTTGC
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAATTTATTAAAAAGGGCTTTGC
38301 CCCAGTTTACCG
66 CCCAGTTTACCG
38313 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
38333 ATTAAAGAGG
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
76 10 0.11
77 23 0.25
78 59 0.64
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (77 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAATTTATTAAAAAGGGCTTTGC
CCCAGTTTACCG
Found at i:38536 original size:42 final size:42
Alignment explanation
Indices: 38477--38564 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
38467 TAGTCTCCCC
* *
38477 AAATGGGCTTGCCTACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
*
38519 AAATGGGCTTGCATACATTCATTGATATTTCATGTGTTATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
38561 AAAT
1 AAAT
38565 AGGCCTATGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.41
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
Found at i:38627 original size:31 final size:31
Alignment explanation
Indices: 38592--38670 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
38582 CGTTTACAAT
*
38592 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGACTTATGA
* *
38623 AAAGGCTTCGGCCCAGTTATTTGACTTATGA
1 AAAGGCTTCGGCCCAGTGATATGACTTATGA
38654 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
38671 AACCGTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGACTTATGA
Found at i:41975 original size:20 final size:21
Alignment explanation
Indices: 41936--41982 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
41926 CCAGATATGG
41936 CCATGTGCTCATCCCACATGC
1 CCATGTGCTCATCCCACATGC
* *
41957 CCATGTG-TGATCTCACATGC
1 CCATGTGCTCATCCCACATGC
41977 CCATGT
1 CCATGT
41983 ATATGGGCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.19, C:0.36, G:0.17, T:0.28
Consensus pattern (21 bp):
CCATGTGCTCATCCCACATGC
Found at i:43791 original size:33 final size:34
Alignment explanation
Indices: 43743--43814 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 34
43733 ATAGGCCCAC
* * * * *
43743 ACTGTTACTGCATAGGGCTTAGGCCCAGACTG-T
1 ACTGTTAATGAATAGGGCTCAAGCCCAGACCGTT
43776 ACTGTTAATGAATAGGGCTCAAGCCCAGACCGTT
1 ACTGTTAATGAATAGGGCTCAAGCCCAGACCGTT
43810 ACTGT
1 ACTGT
43815 ATGCACTGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (34 bp):
ACTGTTAATGAATAGGGCTCAAGCCCAGACCGTT
Found at i:44293 original size:77 final size:77
Alignment explanation
Indices: 44166--44476 Score: 613
Period size: 77 Copynumber: 4.0 Consensus size: 77
44156 CGCGATTTAA
44166 TTTGAATTAATATCCCAAAGGAAAATATTTTGAGCAAACGTACGTGACGAGATGATTTGCAAACC
1 TTTGAATTAATATCCCAAAGGAAAATATTTTGAGCAAACGTACGTGACGAGATGATTTGCAAACC
44231 CCGTATAAAAGG
66 CCGTATAAAAGG
44243 TTTGAATTAATATCCCAAAGGAAAATATTTTGAGCAAACGTACGTGACGAGATGATTTGCAAACC
1 TTTGAATTAATATCCCAAAGGAAAATATTTTGAGCAAACGTACGTGACGAGATGATTTGCAAACC
44308 CCGTATAAAAGG
66 CCGTATAAAAGG
44320 TTTGAATTAATATCCCAAAGGAAAATATTTTGAGCAAACGTACGTGACGAGATGATTTGCAAACC
1 TTTGAATTAATATCCCAAAGGAAAATATTTTGAGCAAACGTACGTGACGAGATGATTTGCAAACC
44385 CCGTATAAAAGG
66 CCGTATAAAAGG
44397 TTTGAATTAATATCCCAAAGGAAAATATTTTGAGCAAACGTACGTGACGAGATGATTTGCAAACC
1 TTTGAATTAATATCCCAAAGGAAAATATTTTGAGCAAACGTACGTGACGAGATGATTTGCAAACC
*
44462 CCGTACAAAAGG
66 CCGTATAAAAGG
44474 TTT
1 TTT
44477 TACTTTTAGA
Statistics
Matches: 233, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 233 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (77 bp):
TTTGAATTAATATCCCAAAGGAAAATATTTTGAGCAAACGTACGTGACGAGATGATTTGCAAACC
CCGTATAAAAGG
Found at i:48838 original size:42 final size:42
Alignment explanation
Indices: 48774--48912 Score: 137
Period size: 41 Copynumber: 3.3 Consensus size: 42
48764 ATATCCCATA
*
48774 TATGGTCTTACATGGGATCTCATATCGATGCCAATAG-CCC-AAC
1 TATGGTCTTACA-CGGATCTCATATCGATGCC-AT-GTCCCAAAC
*
48817 TATGGTCTTACACGGTTCTCATATCGATGCCATGTCCCAAAC
1 TATGGTCTTACACGGATCTCATATCGATGCCATGTCCCAAAC
* * *
48859 -ATGGTCTTACACGAAATCTAATAAT-GATGCCATAT-CCAAA-
1 TATGGTCTTACACG-GATCTCAT-ATCGATGCCATGTCCCAAAC
*
48899 TATGGTATTACACG
1 TATGGTCTTACACG
48913 TAAACTCATA
Statistics
Matches: 84, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
40 1 0.01
41 35 0.42
42 34 0.40
43 14 0.17
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (42 bp):
TATGGTCTTACACGGATCTCATATCGATGCCATGTCCCAAAC
Found at i:48868 original size:41 final size:42
Alignment explanation
Indices: 48774--48871 Score: 130
Period size: 42 Copynumber: 2.3 Consensus size: 42
48764 ATATCCCATA
*
48774 TATGGTCTTACATGGGATCTCATATCGATGCCAATAGCCCAAC
1 TATGGTCTTACA-CGGATCTCATATCGATGCCAATAGCCCAAC
*
48817 TATGGTCTTACACGGTTCTCATATCGATGCC-AT-GTCCCAAAC
1 TATGGTCTTACACGGATCTCATATCGATGCCAATAG-CCC-AAC
48859 -ATGGTCTTACACG
1 TATGGTCTTACACG
48872 AAATCTAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
40 1 0.02
41 18 0.35
42 20 0.39
43 12 0.24
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.30
Consensus pattern (42 bp):
TATGGTCTTACACGGATCTCATATCGATGCCAATAGCCCAAC
Found at i:53777 original size:32 final size:32
Alignment explanation
Indices: 53741--53823 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
53731 AGGACAGGGT
*
53741 AATTTGGGCAGTGTGGGCCACACGGGCATGGC
1 AATTTGGGCAGTGTGGGCCACACGAGCATGGC
* * *
53773 AATTTGGGCCA-TATAGGCCACATGAGCATGGC
1 AATTTGGG-CAGTGTGGGCCACACGAGCATGGC
* *
53805 AATTTGGACCGTGTGGGCC
1 AATTTGGGCAGTGTGGGCC
53824 CAAAATTTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
31 1 0.02
32 38 0.93
33 2 0.05
ACGTcount: A:0.22, C:0.22, G:0.35, T:0.22
Consensus pattern (32 bp):
AATTTGGGCAGTGTGGGCCACACGAGCATGGC
Found at i:57758 original size:31 final size:31
Alignment explanation
Indices: 57715--57779 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
57705 GAAGATGAGT
* * *
57715 TAAAGGGGATATGGCAATCATGGGACGAGGC
1 TAAAGGGAATATGGAAATCATGGGACAAGGC
57746 TAAAGGGAATATGGAAATCATGGGACAAGGC
1 TAAAGGGAATATGGAAATCATGGGACAAGGC
57777 TAA
1 TAA
57780 GAACATGCGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.34, T:0.17
Consensus pattern (31 bp):
TAAAGGGAATATGGAAATCATGGGACAAGGC
Found at i:60674 original size:27 final size:27
Alignment explanation
Indices: 60657--60861 Score: 259
Period size: 27 Copynumber: 7.6 Consensus size: 27
60647 ATATCGAGTC
* * *
60657 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
60684 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
60711 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
60738 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAA-T
** ** *
60766 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
60793 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
60820 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
60847 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
60862 GTACAATTTA
Statistics
Matches: 159, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
27 135 0.85
28 24 0.15
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:64006 original size:22 final size:22
Alignment explanation
Indices: 63978--64102 Score: 71
Period size: 22 Copynumber: 5.4 Consensus size: 22
63968 ACATGTACAT
63978 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* *
64000 ATGTGATGAATG-TGAACAT-G-CA
1 ATGTGAT-AAGGCCG-A-ATGGCCA
64022 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCCGAATGGCCA
* * *
64047 ATGTGATGAATG-TGAACAT-GCAGA
1 ATGTGAT-AAGGCCG-A-ATGGC-CA
64071 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
64094 ATGTGATAA
1 ATGTGATAA
64103 ATGTGAACAT
Statistics
Matches: 77, Mismatches: 10, Indels: 32
0.65 0.08 0.27
Matches are distributed among these distances:
22 26 0.34
23 17 0.22
24 17 0.22
25 17 0.22
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.24
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:64147 original size:22 final size:22
Alignment explanation
Indices: 64072--64147 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
64062 ACATGCAGAT
*
64072 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCAGAATGGCCA
*
64094 ATGTGATAAATGTG-A-ACAT-GCATA
1 ATGTGAT-AA-G-GCAGA-ATGGC-CA
64118 TATGTGATAAGGCAGAATGGCCA
1 -ATGTGATAAGGCAGAATGGCCA
64141 ATGTGAT
1 ATGTGAT
64148 GAACGTGGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
22 15 0.36
23 10 0.24
24 9 0.21
25 8 0.19
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCAGAATGGCCA
Found at i:64184 original size:47 final size:47
Alignment explanation
Indices: 63952--64150 Score: 344
Period size: 47 Copynumber: 4.2 Consensus size: 47
63942 TTTAGGATTT
* *
63952 AATGTGATGAATGTGAACATGTACATATGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
*
63999 AATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
*
64046 AATGTGATGAATGTGAACATGCAGATATGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* *
64093 AATGTGATAAATGTGAACATGCATATATGTGATAAGGCAGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
64140 AATGTGATGAA
1 AATGTGATGAA
64151 CGTGGAAGTG
Statistics
Matches: 143, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 143 1.00
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (47 bp):
AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
Found at i:64217 original size:46 final size:46
Alignment explanation
Indices: 64164--64254 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
64154 GGAAGTGTAT
* * *
64164 ATATGTGGGAAAGCCGAATGGTTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
* * *
64210 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATG
64255 TGTATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.07, G:0.32, T:0.27
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
Found at i:67861 original size:27 final size:27
Alignment explanation
Indices: 67820--67873 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
67810 CAACCAGAGT
67820 TTGGGAAAGACTTCACTGTTTATAGTG
1 TTGGGAAAGACTTCACTGTTTATAGTG
*
67847 TTGGGAAAGAGTTCACTGTTTATAGTG
1 TTGGGAAAGACTTCACTGTTTATAGTG
67874 ATGCATCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.09, G:0.28, T:0.37
Consensus pattern (27 bp):
TTGGGAAAGACTTCACTGTTTATAGTG
Found at i:74594 original size:80 final size:79
Alignment explanation
Indices: 74510--74681 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
74500 GGACTAAGAT
*
74510 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
74574 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
74590 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
74655 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
74669 CCGAAGGCATTTG
1 CCGAAGGCATTTG
74682 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:74661 original size:39 final size:39
Alignment explanation
Indices: 74457--74679 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
74447 TTGAATGCTG
* * * * *
74457 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
74497 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
74536 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
74577 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
74617 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
74656 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
74680 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:74699 original size:79 final size:80
Alignment explanation
Indices: 74537--74714 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
74527 AGATACAAAT
* * * *
74537 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
74602 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
74617 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
74681 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
74696 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
74715 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:81355 original size:40 final size:40
Alignment explanation
Indices: 81300--82639 Score: 2196
Period size: 40 Copynumber: 33.5 Consensus size: 40
81290 TCAATTGCCT
* * * * * * * *
81300 TCGGGTCTTAACCCGGGTATAGCAACTCGCACGAATGCCT
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
* ** *
81340 TCGGGTCTTAGCCCGGATATATCAACTT-GCACAATTGCCT
1 TCGGGTCTTAGCCCGGATATATCAA-TTCGTACAAACGCCG
81380 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81420 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81460 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81500 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81540 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81580 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81620 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81660 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81700 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81740 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81780 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81820 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81860 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81900 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81940 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
81980 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
82020 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
82060 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
82100 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
82140 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
* * * *
82180 TCGGGTCTTAGCCCGGATATATCAGTTCGCACAAATGCCT
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
* * * *
82220 TCGGGTCTTATCCCGGATATATCAATTCGCACAAATGCCT
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
* * * *
82260 TCGGGTCTTATCCCGGATATATCAATTCGCACAAATGCCT
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
* * * *
82300 TCGGGTCTTATCCCGGATATATCAATTCGCACAAATGCCT
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
* * * *
82340 TCGGGTCTTATCCCGGATATATCAATTCGCACAAATGCCT
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
82380 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
* * * *
82420 TCGGGTCTTAGCCCGGATATATCAGTTCGCACAAATGCCT
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
* * * *
82460 TCGGGTCTTATCCCGGATATATCAATTCGCACAAATGCCT
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
* * *
82500 TCGGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCT
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
* * * *
82540 TCGGGTCTTATCCTGGATATATCAATTCGTACAAATGCCT
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
* * * *
82580 TCAGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCT
1 TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
*
82620 TCAGGTCTTAGCCCGGATAT
1 TCGGGTCTTAGCCCGGATAT
82640 CATTCAAATG
Statistics
Matches: 1264, Mismatches: 34, Indels: 4
0.97 0.03 0.00
Matches are distributed among these distances:
39 2 0.00
40 1261 1.00
41 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
TCGGGTCTTAGCCCGGATATATCAATTCGTACAAACGCCG
Found at i:86998 original size:21 final size:21
Alignment explanation
Indices: 86974--87014 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
86964 GGGGCTATCA
* *
86974 TACACGGGTGTGTGGGATTTC
1 TACACGGGCGTGTGCGATTTC
86995 TACACGGGCGTGTGCGATTT
1 TACACGGGCGTGTGCGATTT
87015 GCCAAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.17, G:0.37, T:0.32
Consensus pattern (21 bp):
TACACGGGCGTGTGCGATTTC
Found at i:89071 original size:46 final size:46
Alignment explanation
Indices: 89015--89120 Score: 114
Period size: 45 Copynumber: 2.4 Consensus size: 46
89005 AAAATGAATA
*
89015 GAAATAGAGAAATGGAAAAT-ATTCAAAAATGATTATGGTTTTCTCT
1 GAAAT-GAGAAATGGAAAATCATTCAAAAATGAATATGGTTTTCTCT
*** *
89061 GAAATGGAGAAAT-G-AAATCATTTGTAAATGAATGTGGTTTTCTCT
1 GAAAT-GAGAAATGGAAAATCATTCAAAAATGAATATGGTTTTCTCT
89106 -AAAT-AGAAATGGAAA
1 GAAATGAGAAATGGAAA
89121 TGAGAAATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
42 6 0.12
43 1 0.02
44 10 0.20
45 22 0.43
46 12 0.24
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (46 bp):
GAAATGAGAAATGGAAAATCATTCAAAAATGAATATGGTTTTCTCT
Found at i:93889 original size:22 final size:22
Alignment explanation
Indices: 93847--93887 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
93837 TAATAGGTTA
* *
93847 ATAAGTTAATAGTAAATAAATG
1 ATAAATTAAAAGTAAATAAATG
93869 ATAAATTAAAAGT-AATAAA
1 ATAAATTAAAAGTAAATAAA
93888 ATAACACTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (22 bp):
ATAAATTAAAAGTAAATAAATG
Found at i:94742 original size:25 final size:25
Alignment explanation
Indices: 94702--94806 Score: 108
Period size: 25 Copynumber: 4.2 Consensus size: 25
94692 GTCATTAGGG
*
94702 TTACCGAT-TTCAGCTCTTATGAGC
1 TTACCGATATTCAGCTCATATGAGC
94726 TTACCGATATTCAGCTCATATGAGC
1 TTACCGATATTCAGCTCATATGAGC
* *
94751 TTACCGTTATTCAGCTCGA-AGGAGC
1 TTACCGATATTCAGCTC-ATATGAGC
* ** *
94776 TTACC-ATTATTCAACTCGGAGGAGC
1 TTACCGA-TATTCAGCTCATATGAGC
94801 TTACCG
1 TTACCG
94807 TTTACAACTC
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.11
25 61 0.87
26 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (25 bp):
TTACCGATATTCAGCTCATATGAGC
Found at i:99274 original size:27 final size:27
Alignment explanation
Indices: 99143--99290 Score: 134
Period size: 27 Copynumber: 5.5 Consensus size: 27
99133 ACATATCAAG
** *
99143 AAAGAATAGCCTTTGTGGTGAACCCTA
1 AAAGAATAGCCTTTGTGGCAAACTCTA
99170 AAAGAATAGCCTTTGTGGCAAACTCTA
1 AAAGAATAGCCTTTGTGGCAAACTCTA
* * * *
99197 AAAGAATAGTCTTTGTAGAAAACTCTG
1 AAAGAATAGCCTTTGTGGCAAACTCTA
* * * **
99224 GAAGAATATCCTTTGTAGTGAACTCTA
1 AAAGAATAGCCTTTGTGGCAAACTCTA
* * * **
99251 GAAGAATAACCTTTTTGGCAAACTCCG
1 AAAGAATAGCCTTTGTGGCAAACTCTA
*
99278 AGAGAATAGCCTT
1 AAAGAATAGCCTT
99291 AATGACAAAT
Statistics
Matches: 98, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 98 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (27 bp):
AAAGAATAGCCTTTGTGGCAAACTCTA
Found at i:101025 original size:29 final size:27
Alignment explanation
Indices: 100976--101052 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
100966 GAAACCACCA
*
100976 TATAACATA-AATGC-AGAAAATATGTC
1 TATAACATATAATGCGATAAAAT-TGTC
101002 GTATAACATATAATGCGATAAAATTGTC
1 -TATAACATATAATGCGATAAAATTGTC
* *
101030 AATATCATATAATGCGATAAAAT
1 TATAACATATAATGCGATAAAAT
101053 CAAAAATCCC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
27 30 0.67
28 9 0.20
29 6 0.13
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (27 bp):
TATAACATATAATGCGATAAAATTGTC
Found at i:102699 original size:205 final size:205
Alignment explanation
Indices: 102340--102755 Score: 762
Period size: 205 Copynumber: 2.0 Consensus size: 205
102330 TAAAAAGCTG
* * *
102340 AAAAATATCCATTAAATCTTTAAAAATCTCCAAAATTTCAGATCTTGAAATTTAGGTTTTTATTT
1 AAAAATATCCATTAAATCTTTAAAAATCTCCAAAATTTCAAATCTAGAAATTTAGGTTTTTATTG
*
102405 ATCAAGATTTAGCAAGAAAACAAGAGAGAGAAAGATCTTACACAAGCTAGATGCTATGGGCGACA
66 ATCAAGATTTAGCAAGAAAACAAGAGAGAAAAAGATCTTACACAAGCTAGATGCTATGGGCGACA
*
102470 ATGGCACTTCTTGGAAATAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTGGGGCTGAT
131 ATGGCACTTCTTGGAAACAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTGGGGCTGAT
102535 TTAATTAGAT
196 TTAATTAGAT
102545 AAAAATATCCATTAAATCTTTAAAAATC-CCAAAAATTTCAAATCTAGAAATTTAGGTTTTTATT
1 AAAAATATCCATTAAATCTTTAAAAATCTCC-AAAATTTCAAATCTAGAAATTTAGGTTTTTATT
102609 GATCAAGATTTAGCAAGAAAACAAGAGAGAAAAAGATCTTACACAAGCTAGATGCTATGGGCGAC
65 GATCAAGATTTAGCAAGAAAACAAGAGAGAAAAAGATCTTACACAAGCTAGATGCTATGGGCGAC
*
102674 AATGGCACTTCTTGGAAACAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTTGGGCTGA
130 AATGGCACTTCTTGGAAACAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTGGGGCTGA
102739 TTTAATTAGAT
195 TTTAATTAGAT
102750 AAAAAT
1 AAAAAT
102756 GGCAGCAATA
Statistics
Matches: 204, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
204 2 0.01
205 202 0.99
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (205 bp):
AAAAATATCCATTAAATCTTTAAAAATCTCCAAAATTTCAAATCTAGAAATTTAGGTTTTTATTG
ATCAAGATTTAGCAAGAAAACAAGAGAGAAAAAGATCTTACACAAGCTAGATGCTATGGGCGACA
ATGGCACTTCTTGGAAACAATAGGGATCAATCTTGGAGACTTAATATTTCATATTTGGGGCTGAT
TTAATTAGAT
Found at i:115771 original size:18 final size:18
Alignment explanation
Indices: 115729--115771 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
115719 TTCTCATTTT
*
115729 TAGCAACTTCTTCTTCAA
1 TAGCAACTTCCTCTTCAA
* * *
115747 CAACAACTTCCTCTTCTA
1 TAGCAACTTCCTCTTCAA
115765 TAGCAAC
1 TAGCAAC
115772 AATTTTCTTT
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.33, G:0.05, T:0.33
Consensus pattern (18 bp):
TAGCAACTTCCTCTTCAA
Found at i:119887 original size:44 final size:44
Alignment explanation
Indices: 119823--119906 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
119813 GGGACAAGTG
*
119823 AAAGTTTTTTTCTCCCGATCCTCTGGTGCAATAGCAATTTTATT
1 AAAGTTTTTTTCTCCCGATCCTCTAGTGCAATAGCAATTTTATT
*
119867 AAAGTTTTTTTCTCCTGATCCTCTAGTGCAATAGCAATTT
1 AAAGTTTTTTTCTCCCGATCCTCTAGTGCAATAGCAATTT
119907 GATTGTACCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (44 bp):
AAAGTTTTTTTCTCCCGATCCTCTAGTGCAATAGCAATTTTATT
Found at i:121962 original size:21 final size:21
Alignment explanation
Indices: 121921--121962 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
121911 CATCTGAGTG
***
121921 TGTTGATTGTAATTTTGTTGT
1 TGTTGATTGTAATTCCCTTGT
121942 TGTTGATTGTAATTCCCTTGT
1 TGTTGATTGTAATTCCCTTGT
121963 CTGGGATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.07, G:0.21, T:0.57
Consensus pattern (21 bp):
TGTTGATTGTAATTCCCTTGT
Found at i:123074 original size:23 final size:23
Alignment explanation
Indices: 123045--123091 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
123035 GGAGTATGGT
123045 TCCATTGTTCCCTGGTATACCCA
1 TCCATTGTTCCCTGGTATACCCA
123068 TCCATTGTTCCCTGGTATACCCA
1 TCCATTGTTCCCTGGTATACCCA
123091 T
1 T
123092 ATTTCTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.34, G:0.13, T:0.36
Consensus pattern (23 bp):
TCCATTGTTCCCTGGTATACCCA
Found at i:125601 original size:13 final size:13
Alignment explanation
Indices: 125575--125615 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
125565 AAATGTCTCC
*
125575 TTTCATATATCCA
1 TTTCATATAACCA
125588 TTTCCATA-AACCA
1 TTT-CATATAACCA
125601 TTTCATATAACCA
1 TTTCATATAACCA
125614 TT
1 TT
125616 CTAATTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 4 0.16
13 17 0.68
14 4 0.16
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTCATATAACCA
Found at i:125703 original size:25 final size:25
Alignment explanation
Indices: 125675--125744 Score: 77
Period size: 26 Copynumber: 2.8 Consensus size: 25
125665 TATGTGGAAC
* *
125675 AATGCTCACACAAGCTGTAACTGTA
1 AATGCTCACACAAGCTGTAAATGGA
* *
125700 AATGCTCACGCAAGCTGTGAAATGGG
1 AATGCTCACACAAGCTGT-AAATGGA
**
125726 CCTGCTCACACAAGCTGTA
1 AATGCTCACACAAGCTGTA
125745 GGTCGGGATA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
25 18 0.49
26 19 0.51
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (25 bp):
AATGCTCACACAAGCTGTAAATGGA
Found at i:130071 original size:6 final size:6
Alignment explanation
Indices: 130060--130110 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
130050 AATACATATG
130060 TGGGCA TGGGCA TGGGCA TGGGCA TGGGCA TGGGCA TGGGCA TGGGCA
1 TGGGCA TGGGCA TGGGCA TGGGCA TGGGCA TGGGCA TGGGCA TGGGCA
130108 TGG
1 TGG
130111 AGAGAGGATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.16, C:0.16, G:0.51, T:0.18
Consensus pattern (6 bp):
TGGGCA
Found at i:131274 original size:16 final size:16
Alignment explanation
Indices: 131253--131283 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
131243 GCTCCCTTCG
131253 GTGTTTTAAAGGATAT
1 GTGTTTTAAAGGATAT
131269 GTGTTTTAAAGGATA
1 GTGTTTTAAAGGATA
131284 CTATGGCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (16 bp):
GTGTTTTAAAGGATAT
Found at i:132707 original size:273 final size:272
Alignment explanation
Indices: 132212--132820 Score: 1103
Period size: 273 Copynumber: 2.2 Consensus size: 272
132202 TTCTGTAGGA
* *
132212 CTTCA-TTCATTTAATTTTTTTACACGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTC
1 CTTCACTT-ATTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTC
*
132276 CCATGAGAGAAAAAAAATGTTGTATTGATTGATGTTTCTTTTGGTTCAATAAGAAATTTCCTAAA
65 CCATGAGAGAAAAAAAATGTTGTATTGATAGATGTTTCTTTTGGTTCAATAAGAAATTTCCTAAA
* *
132341 AAGCTATCAATGACTTTCAATGGTTTCTCTTAGGCTTAAAGGAAATGCATTGTCTCTGTGGTCTC
130 AAGCTATCAATGACTTTCAATGGTTTCTCTTAGGCTTAAAGGAAATGCATTATCTATGTGGTCTC
*
132406 TATTATGATGACTGGAAAACAAACTCCTCTATCATTATATGCTTTTGCATACATGTTCACATTTT
195 TATTATGATGACTGGAAAACAAACTCCTCTATCATCATATGCTTTTGCATACATGTTCACATTTT
132471 ATTTTCCAAGTGG
260 ATTTTCCAAGTGG
*
132484 CTTCACTTTTTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTCC
1 CTTCACTTATTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTCC
*
132549 CATGAGAGAAAAAAAAATGTTGTATTGATAGATGTTTCTTTTGGTTCATTAAGAAATTTCCTAAA
66 CATGAGAG-AAAAAAAATGTTGTATTGATAGATGTTTCTTTTGGTTCAATAAGAAATTTCCTAAA
*
132614 AAGCTATCAATGACTTTCAATGGTTTCTCTTAGGCTTGAAGGAAATGCATTATCTATGTGGTCTC
130 AAGCTATCAATGACTTTCAATGGTTTCTCTTAGGCTTAAAGGAAATGCATTATCTATGTGGTCTC
*
132679 TATTATGATGACTGGAAAACGAACTCCTCTATCATCATATGCTTTTGCATACATGTTCACATTTT
195 TATTATGATGACTGGAAAACAAACTCCTCTATCATCATATGCTTTTGCATACATGTTCACATTTT
132744 ATTTTCCAAGTGG
260 ATTTTCCAAGTGG
132757 CTTCACTTATTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTC
1 CTTCACTTATTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTC
132821 ACTCCTAAAA
Statistics
Matches: 324, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
272 67 0.21
273 257 0.79
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (272 bp):
CTTCACTTATTTAATTGTTTTACATGGATTCTTTACTATTTAGTAGCAGGTATAAATCCCCCTCC
CATGAGAGAAAAAAAATGTTGTATTGATAGATGTTTCTTTTGGTTCAATAAGAAATTTCCTAAAA
AGCTATCAATGACTTTCAATGGTTTCTCTTAGGCTTAAAGGAAATGCATTATCTATGTGGTCTCT
ATTATGATGACTGGAAAACAAACTCCTCTATCATCATATGCTTTTGCATACATGTTCACATTTTA
TTTTCCAAGTGG
Found at i:136663 original size:22 final size:22
Alignment explanation
Indices: 136635--136680 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
136625 TTGACGTGGT
136635 ATTAAATTATTGGAAAAGAATA
1 ATTAAATTATTGGAAAAGAATA
**
136657 ATTAAATTATTGGAATGGAATA
1 ATTAAATTATTGGAAAAGAATA
136679 AT
1 AT
136681 ATTCATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (22 bp):
ATTAAATTATTGGAAAAGAATA
Done.