Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 192 of 345
Found at i:54699924 original size:108 final size:110
Alignment explanation
Indices: 54699780--54699980 Score: 300
Period size: 108 Copynumber: 1.8 Consensus size: 110
54699770 ATCCTTTTGA
* *
54699780 AACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATGA-A-CTCACCAA
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTA-GAGACCTCACCAA
54699843 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * * *
54699888 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAGACCTTACCAAT
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAGACCTCACCAAT
* *
54699953 TTCCATGCCTTGGTATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
54699981 TATCCTTAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 2 0.02
108 47 0.57
109 7 0.09
110 26 0.32
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAGACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:54709315 original size:18 final size:18
Alignment explanation
Indices: 54709292--54709327 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
54709282 TTCTTGCAAA
54709292 CCTTATCTACTAACACAT
1 CCTTATCTACTAACACAT
54709310 CCTTATCTACTAACACAT
1 CCTTATCTACTAACACAT
54709328 ATTTGCCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (18 bp):
CCTTATCTACTAACACAT
Found at i:54711704 original size:180 final size:180
Alignment explanation
Indices: 54711433--54711789 Score: 493
Period size: 180 Copynumber: 2.0 Consensus size: 180
54711423 GAGTTATGGA
* * * *
54711433 ATTCCAAATTAAGATCCGTTAATTTTCCCAGAACCTAGACTCACATATATTCTTACCATAAAATT
1 ATTCCAAATTAAGAACAGTTAATTTTCCCAGAAACTAGAATCACATATATTCTTACCATAAAATT
* * * * ** * *
54711498 TTCAGAATTTTTTGTTTAGCCAATTAGTATAGTTTATTCATTAAATTTACCCCTATTTCACTGTC
66 TTCAGAATTTTTGGTTTAGCCAATTAGTACAATTTATTAATTAAAAATACCCCGATTTCACTATC
*
54711563 CAACAGTTCTGACCTCTT-TTCACTAAAAATTATTTATCTCATGGTACTGG
131 CAACAGTTCCGACCT-TTCTTCACTAAAAATTATTTATCTCATGGTACTGG
*
54711613 ATTCCAAATTAAGAACATTTAA-TTTCCTCAGAAACTAGAATCACATATATTCTTACCATAAAAT
1 ATTCCAAATTAAGAACAGTTAATTTTCC-CAGAAACTAGAATCACATATATTCTTACCATAAAAT
* * *
54711677 TTTTAGAATTTTTGGTTTAGCCAATTAGTACAATTTTTTAATTAAAAATACCCCGGTTTCACTAT
65 TTTCAGAATTTTTGGTTTAGCCAATTAGTACAATTTATTAATTAAAAATACCCCGATTTCACTAT
* * * *
54711742 CCGATAGTTCCGATCTTTCTTCACTAAAAATTGTTTATCTCATGGTAC
130 CCAACAGTTCCGACCTTTCTTCACTAAAAATTATTTATCTCATGGTAC
54711790 AGATCTTGGA
Statistics
Matches: 154, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
179 7 0.05
180 147 0.95
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.39
Consensus pattern (180 bp):
ATTCCAAATTAAGAACAGTTAATTTTCCCAGAAACTAGAATCACATATATTCTTACCATAAAATT
TTCAGAATTTTTGGTTTAGCCAATTAGTACAATTTATTAATTAAAAATACCCCGATTTCACTATC
CAACAGTTCCGACCTTTCTTCACTAAAAATTATTTATCTCATGGTACTGG
Found at i:54715426 original size:51 final size:50
Alignment explanation
Indices: 54715251--54715644 Score: 310
Period size: 50 Copynumber: 7.8 Consensus size: 50
54715241 TCGAAGCTCA
* * * * * *
54715251 CTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAAT
1 CTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGATCGAACTAT
* * ** * * *
54715301 CTGGTACACGTAGTAGCCTGCACTTAGTACTACATACATGA-CTTATCCAT
1 CTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGATC-GAACTAT
* * *
54715351 CTGATACA-AGTAGTAGCCTACACTTAGTACTACACATGTGATCGAAGCTAA
1 CTGGTACACA-TAGTAGCCTGCACTTAGTACTACACATGTGATCGAA-CTAT
* ** * * *
54715402 CGGGTATGCATAGTAGCCTGCACTTAGTACTATGCACA--TGACCTAACCAT
1 CTGGTACACATAGTAGCCTGCACTTAGTACTA--CACATGTGATCGAACTAT
* ** * *
54715452 CTGATACATGTAGTAGCCTGCACTTAGTACTACACACGTGATTGAAACTAT
1 CTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGATCG-AACTAT
* * * ** * * *
54715503 CAGGTACGCATAGTAGCCTGCTCTTAGTACTACACATGCAACCTAACAAT
1 CTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGATCGAACTAT
* * *
54715553 CTGGTACACGTAGTAACCTGCACTTAGTACTACACACGTGATCGAAAACTAT
1 CTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGATCG--AACTAT
*** *
54715605 CTTAAACACATAGTAGCCTGCACATAGTACTACACATGTG
1 CTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTG
54715645 TTCTCACAAT
Statistics
Matches: 265, Mismatches: 67, Indels: 22
0.75 0.19 0.06
Matches are distributed among these distances:
48 4 0.02
49 1 0.00
50 146 0.55
51 71 0.27
52 39 0.15
53 4 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (50 bp):
CTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGATCGAACTAT
Found at i:54715441 original size:101 final size:99
Alignment explanation
Indices: 54715261--54715642 Score: 408
Period size: 101 Copynumber: 3.8 Consensus size: 99
54715251 CTGGTACGCA
* * ** * * * *
54715261 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCTATC-AATCTGGTACACGTAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAACTAA-CAGGTACGCATAGTAGCCTGCAC
* *
54715324 TTAGTACTACATACATGACTTATCCATCTGATACAAG
65 TTAGTACTAC--ACATGACCTAACCATCTGATACAAG
* * * * *
54715361 TAGTAGCCTACACTTAGTACTACACATGTGATCGAAGCTAACGGGTATGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAACTAACAGGTACGCATAGTAGCCTGCACT
*
54715426 TAGTACTATGCACATGACCTAACCATCTGATACATG
66 TAGTACTA--CACATGACCTAACCATCTGATACAAG
* * *
54715462 TAGTAGCCTGCACTTAGTACTACACACGTGATTGAAACTATCAGGTACGCATAGTAGCCTGCTCT
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAACTAACAGGTACGCATAGTAGCCTGCACT
* * *
54715527 TAGTACTACACATGCAACCTAACAATCTGGTACACG
66 TAGTACTACACATG--ACCTAACCATCTGATACAAG
* * **** *
54715563 TAGTAACCTGCACTTAGTACTACACACGTGATCGAAAACTATCTTAAACACATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCG-AAACTAACAGGTACGCATAGTAGCCTGCAC
*
54715628 ATAGTACTACACATG
65 TTAGTACTACACATG
54715643 TGTTCTCACA
Statistics
Matches: 243, Mismatches: 32, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
99 6 0.02
100 29 0.12
101 167 0.69
102 40 0.16
103 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAACTAACAGGTACGCATAGTAGCCTGCACT
TAGTACTACACATGACCTAACCATCTGATACAAG
Found at i:54715567 original size:151 final size:150
Alignment explanation
Indices: 54715242--54715588 Score: 389
Period size: 151 Copynumber: 2.3 Consensus size: 150
54715232 CCCTTGTAAT
* * *
54715242 CGAAGCTCACTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTA
1 CGAAGCTAACTGGTACGCATAGTAGCCTGCACTTAGTACTACACAT-CGACCTAACAATCTGATA
* * *
54715307 CACGTAGTAGCCTGCACTTAGTACTACATACATGACTTATCCATCTGATACAAGTAGTAGCCTAC
65 CACGTAGTAGCCTGCACTTAGTACTACACACATGACTTAACCATCAGATACAAGTAGTAGCCTAC
** *
54715372 ACTTAGTACTACACATGTGAT
130 ACTTAGTACTACACATGCAAC
* * *
54715393 CGAAGCTAACGGGTATGCATAGTAGCCTGCACTTAGTACTATGCACAT-GACCTAACCATCTGAT
1 CGAAGCTAACTGGTACGCATAGTAGCCTGCACTTAGTACTA--CACATCGACCTAACAATCTGAT
* * * * *
54715457 ACATGTAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAACTATCAGGTACGCA-TAGTAGC
64 ACACGTAGTAGCCTGCACTTAGTACTACACACATGACTT--AACCATCAGATAC-AAGTAGTAGC
* *
54715520 CTGCTCTTAGTACTACACATGCAAC
126 CTACACTTAGTACTACACATGCAAC
* * * *
54715545 CTAA-C-AATCTGGTACACGTAGTAACCTGCACTTAGTACTACACA
1 CGAAGCTAA-CTGGTACGCATAGTAGCCTGCACTTAGTACTACACA
54715589 CGTGATCGAA
Statistics
Matches: 165, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
149 4 0.02
150 4 0.02
151 112 0.68
152 39 0.24
153 6 0.04
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (150 bp):
CGAAGCTAACTGGTACGCATAGTAGCCTGCACTTAGTACTACACATCGACCTAACAATCTGATAC
ACGTAGTAGCCTGCACTTAGTACTACACACATGACTTAACCATCAGATACAAGTAGTAGCCTACA
CTTAGTACTACACATGCAAC
Found at i:54716931 original size:17 final size:17
Alignment explanation
Indices: 54716909--54716944 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
54716899 AGGATCGACT
54716909 GAAGGTAGCATCAAACA
1 GAAGGTAGCATCAAACA
*
54716926 GAAGGTAGCATCAGACA
1 GAAGGTAGCATCAAACA
54716943 GA
1 GA
54716945 CATAATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.28, T:0.11
Consensus pattern (17 bp):
GAAGGTAGCATCAAACA
Found at i:54727410 original size:20 final size:20
Alignment explanation
Indices: 54727382--54727428 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
54727372 CGACAATGTT
54727382 TAAGTTGTGAAAGACTATGG
1 TAAGTTGTGAAAGACTATGG
* *
54727402 TATGTTGTGAAAGATTATGG
1 TAAGTTGTGAAAGACTATGG
54727422 TAAGTTG
1 TAAGTTG
54727429 CAAGTTGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTATGG
Found at i:54731706 original size:47 final size:48
Alignment explanation
Indices: 54731637--54731813 Score: 174
Period size: 47 Copynumber: 3.8 Consensus size: 48
54731627 TAATGCCGAC
* *
54731637 GCCATGTTCCAGACATGGTCTTACACTGGCTCTCATGCTAAGTC-GAT
1 GCCATGTCCCAGACATGGTCTTACACTGACTCTCATGCTAAGTCTGAT
* *
54731684 GCCATGTCCCAGACATGGTCTTATACTGACTCTCACG-TATCCA-TGCTGAT
1 GCCATGTCCCAGACATGGTCTTACACTGACTCTCATGCTA---AGT-CTGAT
* * *
54731734 GCCATGTCCTAGACATGGTCTTATACTGACACATCAT-CT-AG-CTGAT
1 GCCATGTCCCAGACATGGTCTTACACTGACTC-TCATGCTAAGTCTGAT
54731780 G-CATGTCCCAGACAT-GTCTTACACT-AGCTCTCAT
1 GCCATGTCCCAGACATGGTCTTACACTGA-CTCTCAT
54731814 CTCAATGCCA
Statistics
Matches: 111, Mismatches: 10, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
43 5 0.05
44 11 0.10
45 13 0.12
46 8 0.07
47 34 0.31
48 1 0.01
49 2 0.02
50 33 0.30
51 4 0.04
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (48 bp):
GCCATGTCCCAGACATGGTCTTACACTGACTCTCATGCTAAGTCTGAT
Found at i:54732744 original size:16 final size:16
Alignment explanation
Indices: 54732725--54732755 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54732715 CTTCTTCACT
54732725 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
54732741 TACTTACTTACTTAA
1 TACTCACTTACTTAA
54732756 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:54732761 original size:20 final size:20
Alignment explanation
Indices: 54732722--54732761 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54732712 AAACTTCTTC
* *
54732722 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
54732742 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
54732762 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:54738738 original size:28 final size:28
Alignment explanation
Indices: 54738678--54738742 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
54738668 CGTGTCCCTG
* * *
54738678 GCCCATGTCCCTCACACGGTCTAGAGAT
1 GCCCGTGTCCCTCACACGGCCTAGACAT
54738706 GCCCGTGTCCCTCACACGGCCTAGACACT
1 GCCCGTGTCCCTCACACGGCCTAGACA-T
54738735 -CCCGTGTC
1 GCCCGTGTC
54738743 ATCGCCCGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.17, C:0.42, G:0.22, T:0.20
Consensus pattern (28 bp):
GCCCGTGTCCCTCACACGGCCTAGACAT
Found at i:54743451 original size:17 final size:18
Alignment explanation
Indices: 54743429--54743462 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54743419 CAATCCTCGG
54743429 TGATAGATA-CTTGTTCT
1 TGATAGATACCTTGTTCT
*
54743446 TGATAGTTACCTTGTTC
1 TGATAGATACCTTGTTC
54743463 AGTTGTCGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.47
Consensus pattern (18 bp):
TGATAGATACCTTGTTCT
Found at i:54746566 original size:46 final size:46
Alignment explanation
Indices: 54746510--54746685 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
54746500 TATTTGGGCA
54746510 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
54746556 TCAGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54746601 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54746649 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54746686 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 28 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54746665 original size:93 final size:93
Alignment explanation
Indices: 54746506--54746677 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
54746496 GGGATATTTG
* *
54746506 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCAGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCAGAACTCGTTGAG
54746571 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
54746599 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCAGAACTCGTTGAG
54746664 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
54746678 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCAGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:54755202 original size:9 final size:9
Alignment explanation
Indices: 54755197--54755238 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
54755187 AAAAAAACAT
54755197 TTAAAAATA
1 TTAAAAATA
54755206 TTAAAAAATA
1 TT-AAAAATA
54755216 TTAAAAATA
1 TTAAAAATA
54755225 -T-AAAATA
1 TTAAAAATA
54755232 TTAAAAA
1 TTAAAAA
54755239 ATATATAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 6 0.20
8 2 0.07
9 13 0.43
10 9 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
TTAAAAATA
Found at i:54755219 original size:19 final size:19
Alignment explanation
Indices: 54755197--54755310 Score: 64
Period size: 19 Copynumber: 6.1 Consensus size: 19
54755187 AAAAAAACAT
54755197 TTAAAAATATTAAAAAATA
1 TTAAAAATATTAAAAAATA
54755216 TTAAAAATA-T--AAAATA
1 TTAAAAATATTAAAAAATA
* * *
54755232 TTAAAAA-A-TATATAATC
1 TTAAAAATATTAAAAAATA
54755249 TTATAAAA-ATTCATAAAAA-A
1 TTA-AAAATATT-A-AAAAATA
* *
54755269 TTATAAATATTATAAAAAAA
1 TTAAAAATATTA-AAAAATA
*
54755289 TCAAATTAAT-TTAAAAAATA
1 TTAAA--AATATTAAAAAATA
54755309 TT
1 TT
54755311 TTTTTAAATA
Statistics
Matches: 75, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
15 2 0.03
16 13 0.17
17 7 0.09
18 6 0.08
19 20 0.27
20 18 0.24
21 6 0.08
22 3 0.04
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
TTAAAAATATTAAAAAATA
Found at i:54755238 original size:17 final size:17
Alignment explanation
Indices: 54755210--54755258 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
54755200 AAAATATTAA
54755210 AAAATATT-AAAAATAT
1 AAAATATTAAAAAATAT
54755226 AAAATATTAAAAAATAT
1 AAAATATTAAAAAATAT
* *
54755243 ATAATCTTATAAAAAT
1 AAAATATTA-AAAAAT
54755259 TCATAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.28
17 15 0.52
18 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATATTAAAAAATAT
Found at i:54755241 original size:10 final size:10
Alignment explanation
Indices: 54755188--54755242 Score: 64
Period size: 10 Copynumber: 5.9 Consensus size: 10
54755178 AAAAACATAA
*
54755188 AAAAAACATT
1 AAAAAATATT
*
54755198 TAAAAATATT
1 AAAAAATATT
54755208 AAAAAATATT
1 AAAAAATATT
54755218 -AAAAATA-T
1 AAAAAATATT
54755226 --AAAATATT
1 AAAAAATATT
54755234 AAAAAATAT
1 AAAAAATAT
54755243 ATAATCTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
7 6 0.15
8 2 0.05
9 7 0.18
10 24 0.62
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAAAATATT
Found at i:54755264 original size:10 final size:9
Alignment explanation
Indices: 54755198--54755286 Score: 60
Period size: 9 Copynumber: 9.7 Consensus size: 9
54755188 AAAAAACATT
54755198 TAAAAA-TA
1 TAAAAATTA
*
54755206 TTAAAAAATA
1 -TAAAAATTA
54755216 TTAAAAA-TA
1 -TAAAAATTA
54755225 TAAAATATTA
1 TAAAA-ATTA
54755235 -AAAAA-TA
1 TAAAAATTA
**
54755242 TATAATCTTA
1 TA-AAAATTA
54755252 TAAAAATTCA
1 TAAAAATT-A
54755262 TAAAAAATTA
1 T-AAAAATTA
*
54755272 TAAATATTA
1 TAAAAATTA
54755281 TAAAAA
1 TAAAAA
54755287 AATCAAATTA
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
7 2 0.03
8 7 0.11
9 31 0.47
10 19 0.29
11 7 0.11
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAAAATTA
Found at i:54755272 original size:20 final size:19
Alignment explanation
Indices: 54755189--54755287 Score: 75
Period size: 19 Copynumber: 5.3 Consensus size: 19
54755179 AAAACATAAA
54755189 AAAAACATT-TAAAAA-TATT
1 AAAAA-ATTATAAAAATTA-T
54755208 AAAAAA-TATTAAAAA-TAT
1 AAAAAATTA-TAAAAATTAT
*
54755226 AAAATATTA-AAAAA-TAT
1 AAAAAATTATAAAAATTAT
* **
54755243 ATAATCTTATAAAAATTCAT
1 AAAAAATTATAAAAATT-AT
*
54755263 AAAAAATTATAAATATTAT
1 AAAAAATTATAAAAATTAT
54755282 AAAAAA
1 AAAAAA
54755288 ATCAAATTAA
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
17 16 0.24
18 12 0.18
19 24 0.36
20 15 0.22
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAAATTATAAAAATTAT
Found at i:54755289 original size:20 final size:20
Alignment explanation
Indices: 54755249--54755287 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54755239 ATATATAATC
54755249 TTATAAAAATTCATAAAAAA
1 TTATAAAAATTCATAAAAAA
*
54755269 TTATAAATATT-ATAAAAAA
1 TTATAAAAATTCATAAAAAA
54755288 ATCAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
TTATAAAAATTCATAAAAAA
Found at i:54756061 original size:9 final size:9
Alignment explanation
Indices: 54756047--54756096 Score: 54
Period size: 8 Copynumber: 5.9 Consensus size: 9
54756037 AATAAATGAT
54756047 TTTTTATAA
1 TTTTTATAA
54756056 TTTTTATAA
1 TTTTTATAA
54756065 -TTTT-T-A
1 TTTTTATAA
*
54756071 TTTTTAT-C
1 TTTTTATAA
54756079 TTTTTATAA
1 TTTTTATAA
54756088 GTTTTTATA
1 -TTTTTATA
54756097 CGTTTACAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
6 1 0.03
7 5 0.14
8 12 0.34
9 9 0.26
10 8 0.23
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (9 bp):
TTTTTATAA
Found at i:54756083 original size:24 final size:24
Alignment explanation
Indices: 54756047--54756095 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
54756037 AATAAATGAT
54756047 TTTTTATAATTTTTATAA-TTTTTA
1 TTTTTAT-ATTTTTATAAGTTTTTA
*
54756071 TTTTTATCTTTTTATAAGTTTTTA
1 TTTTTATATTTTTATAAGTTTTTA
54756095 T
1 T
54756096 ACGTTTACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTTTATATTTTTATAAGTTTTTA
Found at i:54756129 original size:18 final size:18
Alignment explanation
Indices: 54756081--54756128 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
54756071 TTTTTATCTT
*
54756081 TTTATAAGTTTTTATACG
1 TTTATAAGTTTTTAAACG
*
54756099 TTTACAAGTTTTTAAACG
1 TTTATAAGTTTTTAAACG
54756117 TTTATAA-TTTTT
1 TTTATAAGTTTTT
54756129 TTCAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.56
Consensus pattern (18 bp):
TTTATAAGTTTTTAAACG
Found at i:54756142 original size:21 final size:20
Alignment explanation
Indices: 54756117--54756190 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
54756107 TTTTTAAACG
54756117 TTTATAATTTTTTTCAATATT
1 TTTATAATTTTTTT-AATATT
* *
54756138 TTTATAA-ATTATTAATATT
1 TTTATAATTTTTTTAATATT
* *
54756157 TTATAATAAATTTTTTAATTTT
1 TT-T-ATAATTTTTTTAATATT
*
54756179 TTTATGATTTTT
1 TTTATAATTTTT
54756191 AGTAAAAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
19 8 0.19
20 12 0.28
21 12 0.28
22 11 0.26
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (20 bp):
TTTATAATTTTTTTAATATT
Found at i:54756678 original size:2 final size:2
Alignment explanation
Indices: 54756671--54756722 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
54756661 AACTATTGTT
54756671 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
54756713 TC TC TC TC TC
1 TC TC TC TC TC
54756723 CTGTTTTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:54777145 original size:46 final size:46
Alignment explanation
Indices: 54776991--54777163 Score: 210
Period size: 46 Copynumber: 3.8 Consensus size: 46
54776981 TGTAACCCGC
*
54776991 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
* * *
54777036 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACG-CTCGCAT
* ** * *
54777082 ACAT-CTTCGAACTCGGACTCAACTCATCGAGTTCGGACGCTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
*
54777128 CCATAAGTGAACCCGGACTCAACTCAACGAG-TCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
54777164 TGCCCAAATA
Statistics
Matches: 106, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
45 45 0.42
46 58 0.55
47 3 0.03
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
Found at i:54777155 original size:92 final size:90
Alignment explanation
Indices: 54776999--54777167 Score: 284
Period size: 92 Copynumber: 1.9 Consensus size: 90
54776989 GCCCATAAGT
* *
54776999 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCGCTCGCATCCATAAGTGAACCCGGACTCAACTCAAC
54777064 GAGCTCGGATGCCTAGTTACATCTTC
66 GAG-TCGGATGCCTAGTTACATCTTC
* *
54777090 GAACTCGGACTCAACTCATCGAGTTCGGACGCTCGCATCCATAAGTGAACCCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CGCTCGCATCCATAAGTGAACCCGGACTCAACTCAA
54777155 CGAGTCGGATGCC
65 CGAGTCGGATGCC
54777168 CAAATATCCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
91 35 0.48
92 38 0.52
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (90 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCGCTCGCATCCATAAGTGAACCCGGACTCAACTCAAC
GAGTCGGATGCCTAGTTACATCTTC
Found at i:54779138 original size:15 final size:15
Alignment explanation
Indices: 54779080--54779154 Score: 75
Period size: 15 Copynumber: 5.1 Consensus size: 15
54779070 CAAAGATAAC
*
54779080 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
54779094 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
54779109 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
54779123 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
54779138 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
54779153 AA
1 AA
54779155 AAACCCAAGA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
14 19 0.38
15 31 0.62
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:54782189 original size:93 final size:93
Alignment explanation
Indices: 54782077--54782248 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
54782067 GCCCATAAGT
* *
54782077 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54782142 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
54782170 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
54782235 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
54782249 CAAATATCCA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:54782244 original size:46 final size:46
Alignment explanation
Indices: 54782069--54782244 Score: 228
Period size: 46 Copynumber: 3.8 Consensus size: 46
54782059 TGTAACCCGC
* *
54782069 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
* * *
54782115 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACG-CTCGCAT
* *** *
54782161 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
*
54782208 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
54782245 TGCCCAAATA
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
46 74 0.67
47 36 0.33
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
Found at i:54788451 original size:40 final size:40
Alignment explanation
Indices: 54788374--54788576 Score: 245
Period size: 40 Copynumber: 5.1 Consensus size: 40
54788364 ACCCAAGTAT
* *
54788374 CTTCGGGATTTAG-CCGGATATCA--CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATAT-AGTC-ACTAGCACAAATGC
* * *
54788413 CTTTGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
54788453 CTTTGGGACTTAGCCCGGATATAGCCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
54788493 CTTCGGGACTTAGCCCGGGTATAGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
54788533 CTTCGGGACTTAGCCCGGA-ATAG-CAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
54788572 CTTCG
1 CTTCG
54788577 AATCTTAGTC
Statistics
Matches: 143, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 32 0.22
40 109 0.76
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:54788520 original size:80 final size:79
Alignment explanation
Indices: 54788374--54788576 Score: 284
Period size: 80 Copynumber: 2.6 Consensus size: 79
54788364 ACCCAAGTAT
* * * *
54788374 CTTCGGGATTTAG-CCGGATATCA-CAACTCGCACAAATGCCTTTGGGTCTTAGCCCGGATATAG
1 CTTCGGGACTTAGCCCGGA-AT-AGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
54788437 TCACTAGCATAAATGC
64 TCACTAGCATAAATGC
* ** *
54788453 CTTTGGGACTTAGCCCGGATATAGCCGCTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAGT
1 CTTCGGGACTTAGCCCGGA-ATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
54788518 CACTAGCATAAATGC
65 CACTAGCATAAATGC
*
54788533 CTTCGGGACTTAGCCCGGAATAGCAACTTGCACAAATGCCTTCG
1 CTTCGGGACTTAGCCCGGAATAGCAACTAGCACAAATGCCTTCG
54788577 AATCTTAGTC
Statistics
Matches: 110, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
79 34 0.31
80 76 0.69
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (79 bp):
CTTCGGGACTTAGCCCGGAATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTC
ACTAGCATAAATGC
Found at i:54805180 original size:22 final size:22
Alignment explanation
Indices: 54805152--54805195 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
54805142 ACTTAAGGTA
54805152 CTTAACCACTATGTCATTCCAC
1 CTTAACCACTATGTCATTCCAC
54805174 CTTAACCACTATGTCATTCCAC
1 CTTAACCACTATGTCATTCCAC
54805196 TTACTTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.36, G:0.05, T:0.32
Consensus pattern (22 bp):
CTTAACCACTATGTCATTCCAC
Found at i:54809020 original size:48 final size:47
Alignment explanation
Indices: 54808965--54809235 Score: 238
Period size: 48 Copynumber: 5.7 Consensus size: 47
54808955 GGTGAATTAT
* * *
54808965 CGATGCCATGTTCCAAACATGGTCTTACACCGGCTCACATGTTGAGGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCAT-TTGAGGC
* * * *
54809013 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATAATGTGGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCAT-TTGAGGC
* * * * * ** ***
54809061 CGATACCATGTCCCAAACATTGTCTTACACTAGCGCACATATCAATAT
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCAT-TTGAGGC
* * **
54809109 CGATGCCATATCCCAAACATGGTCTTACATTGGCTCTCATTAT-ATTTC
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATT-TGA-GGC
* * * * *
54809157 CGATGCCATGTTCCAAACATGGTCTTACATTGGCTCTTATATCATGGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATTTGA-GGC
*
54809205 CGATGCCATGTCCCAGACATGGTCTTACACT
1 CGATGCCATGTCCCAAACATGGTCTTACACT
54809236 AGTGCACATA
Statistics
Matches: 179, Mismatches: 41, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
47 3 0.02
48 176 0.98
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.30
Consensus pattern (47 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATTTGAGGC
Found at i:54809134 original size:96 final size:96
Alignment explanation
Indices: 54808965--54809235 Score: 278
Period size: 96 Copynumber: 2.8 Consensus size: 96
54808955 GGTGAATTAT
* * ** * *
54808965 CGATGCCATGTTCCAAACATGGTCTTACACCGGCTCACATGT--TGAGGCCGATGCCATGTCCCA
1 CGATACCATGTCCCAAACATGGTCTTACACTAGCGCACATATCATGA--CCGATGCCATGTCCCA
* *
54809028 GACATGGTCTTACACTGGCTTTCATAATGTGGC
64 GACATGGTCTTACACTGGCTCTCATAATATGGC
* * * *
54809061 CGATACCATGTCCCAAACATTGTCTTACACTAGCGCACATATCAAT-ATCGATGCCATATCCCAA
1 CGATACCATGTCCCAAACATGGTCTTACACTAGCGCACATATC-ATGACCGATGCCATGTCCCAG
* * **
54809125 ACATGGTCTTACATTGGCTCTCATTATATTTC
65 ACATGGTCTTACACTGGCTCTCATAATATGGC
* * * * * ** *
54809157 CGATGCCATGTTCCAAACATGGTCTTACATTGGCTCTTATATCATGGCCGATGCCATGTCCCAGA
1 CGATACCATGTCCCAAACATGGTCTTACACTAGCGCACATATCATGACCGATGCCATGTCCCAGA
54809222 CATGGTCTTACACT
66 CATGGTCTTACACT
54809236 AGTGCACATA
Statistics
Matches: 142, Mismatches: 29, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
95 2 0.01
96 138 0.97
98 1 0.01
99 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.30
Consensus pattern (96 bp):
CGATACCATGTCCCAAACATGGTCTTACACTAGCGCACATATCATGACCGATGCCATGTCCCAGA
CATGGTCTTACACTGGCTCTCATAATATGGC
Found at i:54809230 original size:144 final size:144
Alignment explanation
Indices: 54808962--54809248 Score: 375
Period size: 144 Copynumber: 2.0 Consensus size: 144
54808952 TTGGGTGAAT
* *
54808962 TATCGATGCCATGTTCCAAACATGGTCTTACACCGGCTCACATGTTGAGGCCGATGCCATGTCCC
1 TATCGATGCCATATCCCAAACATGGTCTTACACCGGCTCACATGTTGAGGCCGATGCCATGTCCC
* * *
54809027 AGACATGGTCTTACACTGGCTTTCATAATGTGGCCGATACCATGTCCCAAACATTGTCTTACACT
66 AAACATGGTCTTACACTGGCTTTCATAATATGGCCGATACCATGTCCCAAACATGGTCTTACACT
54809092 AGCGCACATATCAA
131 AGCGCACATATCAA
** * ** *
54809106 TATCGATGCCATATCCCAAACATGGTCTTACATTGGCTCTCAT-TAT-ATTTCCGATGCCATGTT
1 TATCGATGCCATATCCCAAACATGGTCTTACACCGGCTCACATGT-TGA-GGCCGATGCCATGTC
* * *
54809169 CCAAACATGGTCTTACATTGGCTCTT-AT-ATCATGGCCGATGCCATGTCCCAGACATGGTCTTA
64 CCAAACATGGTCTTACACTGGCT-TTCATAAT-ATGGCCGATACCATGTCCCAAACATGGTCTTA
*
54809232 CACTAGTGCACATATCA
127 CACTAGCGCACATATCA
54809249 CCCAGATGTC
Statistics
Matches: 124, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
143 4 0.03
144 118 0.95
145 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (144 bp):
TATCGATGCCATATCCCAAACATGGTCTTACACCGGCTCACATGTTGAGGCCGATGCCATGTCCC
AAACATGGTCTTACACTGGCTTTCATAATATGGCCGATACCATGTCCCAAACATGGTCTTACACT
AGCGCACATATCAA
Found at i:54812023 original size:33 final size:33
Alignment explanation
Indices: 54811986--54812051 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
54811976 GACAAATCCA
54811986 AAATTGATAAACCTCCATTGGACGAATTGCGAT
1 AAATTGATAAACCTCCATTGGACGAATTGCGAT
54812019 AAATTGATAAACCTCCATTGGACGAATTGCGAT
1 AAATTGATAAACCTCCATTGGACGAATTGCGAT
54812052 GATAGACAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (33 bp):
AAATTGATAAACCTCCATTGGACGAATTGCGAT
Found at i:54815359 original size:19 final size:19
Alignment explanation
Indices: 54815313--54815359 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
54815303 TAGGTAGTTC
54815313 TGGGCTTCGTTGGACCTAAA
1 TGGGC-TCGTTGGACCTAAA
*
54815333 TGGG-TCGTGTGGACC-CAA
1 TGGGCTCGT-TGGACCTAAA
54815351 TGGGCTCGT
1 TGGGCTCGT
54815360 AGGCCCTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 10 0.42
19 10 0.42
20 4 0.17
ACGTcount: A:0.15, C:0.21, G:0.36, T:0.28
Consensus pattern (19 bp):
TGGGCTCGTTGGACCTAAA
Found at i:54815618 original size:27 final size:27
Alignment explanation
Indices: 54815583--54815763 Score: 174
Period size: 27 Copynumber: 6.7 Consensus size: 27
54815573 AGACCTTGGA
54815583 TTGTAAAATTATCGAAATACCCCCGAT
1 TTGTAAAATTATCGAAATACCCCCGAT
54815610 TTGTAAAATTA-CTGAAATACCCCCGAT
1 TTGTAAAATTATC-GAAATACCCCCGAT
*
54815637 TTGTAAAATTGAT-GAAATACCCTCGAT
1 TTGTAAAATT-ATCGAAATACCCCCGAT
** *
54815664 ATT-TAAAATTATCGAAATACCCCTAAA
1 -TTGTAAAATTATCGAAATACCCCCGAT
* * *
54815691 TTGTAAAATTACCGAAGTACCCTCAGA-
1 TTGTAAAATTATCGAAATACCC-CCGAT
* * * *
54815718 TTGTAAAATTAACTAAATACCCCTGGT
1 TTGTAAAATTATCGAAATACCCCCGAT
*
54815745 TTGTGAAATTA-CTGAAATA
1 TTGTAAAATTATC-GAAATA
54815764 TCCTTGTAGT
Statistics
Matches: 129, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
26 8 0.06
27 116 0.90
28 5 0.04
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (27 bp):
TTGTAAAATTATCGAAATACCCCCGAT
Found at i:54815754 original size:81 final size:82
Alignment explanation
Indices: 54815582--54815792 Score: 218
Period size: 81 Copynumber: 2.6 Consensus size: 82
54815572 AAGACCTTGG
* * * * *
54815582 ATTGTAAAATTATCGAAATACCCCCGATTTGTAAAATTACTGAAATACCCCCGATTTGTAAAATT
1 ATTGTAAAATTATCGAAATACCCCTGAATTGTAAAATTACCGAAGTACCCCAGATTTGTAAAATT
*
54815647 GATGAAATACCCTCGAT
66 AATGAAATACCCTCGAT
*
54815664 ATT-TAAAATTATCGAAATACCCCTAAATTGTAAAATTACCGAAGTACCCTCAGA-TTGTAAAAT
1 ATTGTAAAATTATCGAAATACCCCTGAATTGTAAAATTACCGAAGTACCC-CAGATTTGTAAAAT
*
54815727 TAACT-AAATACCC-CTGGT
65 TAA-TGAAATACCCTC-GAT
* * * * * *
54815745 -TTGTGAAATTA-CTGAAATATCCTTGTAGTGTACAATTACCGAAGTACC
1 ATTGTAAAATTATC-GAAATACCCCTGAATTGTAAAATTACCGAAGTACC
54815793 ATTGTAGTGT
Statistics
Matches: 109, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
80 4 0.04
81 98 0.90
82 7 0.06
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (82 bp):
ATTGTAAAATTATCGAAATACCCCTGAATTGTAAAATTACCGAAGTACCCCAGATTTGTAAAATT
AATGAAATACCCTCGAT
Found at i:54815782 original size:54 final size:55
Alignment explanation
Indices: 54815719--54815835 Score: 130
Period size: 54 Copynumber: 2.1 Consensus size: 55
54815709 ACCCTCAGAT
* * * *
54815719 TGTAAAATTAACTAAATACCCCTGGT-TTGTGAAATTACTGAAATAT-CCTTGTAG
1 TGTAAAATTAACGAAATA-CCATGGTAGTGTAAAATTACTGAAATATCCCTTGTAG
* * * *
54815773 TGTACAATTACCGAAGTACCATTGTAGTGTAAAATTACTGAAATATCCCTTGTAG
1 TGTAAAATTAACGAAATACCATGGTAGTGTAAAATTACTGAAATATCCCTTGTAG
*
54815828 GGTAAAAT
1 TGTAAAAT
54815836 GACTGTTTTG
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
53 5 0.10
54 32 0.63
55 14 0.27
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (55 bp):
TGTAAAATTAACGAAATACCATGGTAGTGTAAAATTACTGAAATATCCCTTGTAG
Found at i:54815832 original size:28 final size:28
Alignment explanation
Indices: 54815719--54815840 Score: 117
Period size: 27 Copynumber: 4.5 Consensus size: 28
54815709 ACCCTCAGAT
* * *
54815719 TGTAAAATTAACT-AAATACCCCTGGT-T
1 TGTAAAATT-ACTGAAATATCCCTTGTAG
*
54815746 TGTGAAATTACTGAAATAT-CCTTGTAG
1 TGTAAAATTACTGAAATATCCCTTGTAG
* * * *
54815773 TGTACAATTACCGAAGTA-CCATTGTAG
1 TGTAAAATTACTGAAATATCCCTTGTAG
54815800 TGTAAAATTACTGAAATATCCCTTGTAG
1 TGTAAAATTACTGAAATATCCCTTGTAG
* *
54815828 GGTAAAATGACTG
1 TGTAAAATTACTG
54815841 TTTTGCCCTT
Statistics
Matches: 76, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
26 8 0.11
27 49 0.64
28 19 0.25
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (28 bp):
TGTAAAATTACTGAAATATCCCTTGTAG
Found at i:54815928 original size:34 final size:34
Alignment explanation
Indices: 54815880--54815945 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
54815870 AGACTGTGAA
* *
54815880 TTTAACTAATTTGACTGT-GATCGTATGACTATAT
1 TTTAACTAACTTGACAGTAG-TCGTATGACTATAT
*
54815914 TTTAACTGACTTGACAGTAGTCGTATGACTAT
1 TTTAACTAACTTGACAGTAGTCGTATGACTAT
54815946 TATGCTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.41
Consensus pattern (34 bp):
TTTAACTAACTTGACAGTAGTCGTATGACTATAT
Found at i:54820151 original size:2 final size:2
Alignment explanation
Indices: 54820144--54820191 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
54820134 CGGCTCTTGC
54820144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54820186 AT AT AT
1 AT AT AT
54820192 GTTTGCACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54820959 original size:40 final size:40
Alignment explanation
Indices: 54820900--54821097 Score: 269
Period size: 40 Copynumber: 5.0 Consensus size: 40
54820890 TCGAATGATG
* * *
54820900 TCCGGGCTAAG-TCCTGAAGGC-TCTGTGCTAAGTTACTAAA
1 TCCGGACTAAGATCC-GAAGGCATTTGTGC-GAGTTACTAAA
*
54820940 TCCGGACTAAGATCCGAAGGCAATTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
* *
54820980 TTCGAACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
54821020 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
*
54821060 TCCGGGA-TAAG-TCCCGAAGGCATTTGTGCGAGCTACTA
1 TCC-GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA
54821098 TAACCGGGCT
Statistics
Matches: 144, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 1 0.01
40 132 0.92
41 11 0.08
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54821105 original size:40 final size:40
Alignment explanation
Indices: 54820900--54821125 Score: 225
Period size: 40 Copynumber: 5.7 Consensus size: 40
54820890 TCGAATGATG
* * * *
54820900 TCCGGGCTAAGTCCTGAAGGC-TCTGTGCTAAGTTACTAAA
1 TCCGGGATAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
54820940 TCC-GGACTAAGAT-CCGAAGGCAATTGTGCGAGTTACTAAA
1 TCCGGGA-TAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
54820980 TTC-GAACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGA-TAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
54821020 TCC-GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGA-TAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54821060 TCCGGGATAAGTCCCGAAGGCATTTGTGCGAGCTACTATAA
1 TCCGGGATAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* * *
54821101 -CCGGGCTATGTCCCGAAGGTATTTG
1 TCCGGGATAAGTCCCGAAGGCATTTG
54821126 AACGAGTAGC
Statistics
Matches: 166, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
39 3 0.02
40 152 0.92
41 11 0.07
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGATAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54821139 original size:40 final size:40
Alignment explanation
Indices: 54820993--54821144 Score: 116
Period size: 40 Copynumber: 3.8 Consensus size: 40
54820983 GAACTAAGAT
** *
54820993 CCGAAGGCATTTGTGCGAGTTACTA-AATCC-GGACTAAGAT-
1 CCGAAGGCATTTGAACGAGCTACTATAA-CCGGGA-TAAG-TC
** *
54821033 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGATAAGTC
1 CCGAAGGCATTTGAACGAGCTACTATAA-CCGGGATAAGTC
** * *
54821073 CCGAAGGCATTTGTGCGAGCTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGAACGAGCTACTATAACCGGGATAAGTC
* *
54821113 CCGAAGGTATTTGAACGAG-TAGCTATATCCGG
1 CCGAAGGCATTTGAACGAGCTA-CTATAACCGG
54821145 TTAAACTCCG
Statistics
Matches: 101, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
39 3 0.03
40 93 0.92
41 5 0.05
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGAACGAGCTACTATAACCGGGATAAGTC
Found at i:54821144 original size:120 final size:120
Alignment explanation
Indices: 54820900--54821132 Score: 262
Period size: 120 Copynumber: 1.9 Consensus size: 120
54820890 TCGAATGATG
*
54820900 TCCGGGCTAAGTCCTGAAGGCTCTGTGCTAAGTTACTAAATCCGGACTAAGATCCGAAGGCAATT
1 TCCGGACTAAGTCCTGAAGGCTCTGTGCTAAGTTACTAAATCCGGACTAAGATCCGAAGGCAATT
* * **
54820965 GTGCGAGTTACTAAATTCGAACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
66 GTGCGAGCTACTAAATCCGAACTAAGATCCGAAGGCATTTGAACGAGTTACTAAA
* *
54821020 TCCGGACTAAGATCC-GAAGGCATTTGTGC-GAGTTACTAAATCCGGGA-TAAG-TCCCGAAGGC
1 TCCGGACTAAG-TCCTGAAGGC-TCTGTGCTAAGTTACTAAATCC-GGACTAAGAT-CCGAAGGC
* ** * *
54821081 ATTTGTGCGAGCTACTATAA-CCGGGCTATG-TCCCGAAGGTATTTGAACGAGT
62 AATTGTGCGAGCTACTA-AATCCGAACTAAGAT-CCGAAGGCATTTGAACGAGT
54821133 AGCTATATCC
Statistics
Matches: 95, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
119 2 0.02
120 79 0.83
121 14 0.15
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (120 bp):
TCCGGACTAAGTCCTGAAGGCTCTGTGCTAAGTTACTAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGCTACTAAATCCGAACTAAGATCCGAAGGCATTTGAACGAGTTACTAAA
Found at i:54825203 original size:16 final size:16
Alignment explanation
Indices: 54825184--54825215 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54825174 AATTGTTTTA
54825184 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
54825200 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
54825216 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:54825472 original size:50 final size:50
Alignment explanation
Indices: 54825414--54825803 Score: 363
Period size: 50 Copynumber: 7.8 Consensus size: 50
54825404 AACCGAAGCT
* * *
54825414 ATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCA
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCA
* * * * * * *
54825464 ATCCGGTACATGTAGTAACCTGCACTTAGTACTACACACGTGACTTAACC
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCA
* * *
54825514 ATCTGATACACGTAGTAGCCTACACTTAGTACTACACATGTGA-TTGAAGTCA
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCT--A-TCA
* ** * * *
54825566 A-CAGGTATGCATAGTAGCCTACACTTAGTACTACACATGCGACCTATCA
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCA
* * * * *
54825615 ATTTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTTAACC
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCA
* * * ** *
54825665 ATCTGATACACGTAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTA
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCA
* * * * * *
54825717 A-CAGGTACGCATAGTAGCTTGCACTTAGTACTACACATGCGACCTATTA
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCA
* * *
54825766 ATCTAGTACATGTAATAGCCTGCACTTAGTACTACACA
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA
54825804 CATGACTCAC
Statistics
Matches: 271, Mismatches: 61, Indels: 16
0.78 0.18 0.05
Matches are distributed among these distances:
49 10 0.04
50 186 0.69
51 71 0.26
52 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (50 bp):
ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCA
Found at i:54825697 original size:151 final size:151
Alignment explanation
Indices: 54825418--54825810 Score: 660
Period size: 151 Copynumber: 2.6 Consensus size: 151
54825408 GAAGCTATCT
* *
54825418 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCCGGTACATGTAGTAAC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACATGTAGTAGC
54825483 CTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTAGTAGCCTACACTTAGTACTA
66 CTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTAGTAGCCTACACTTAGTACTA
* *
54825548 CACATGTGATTGAAGTCAACA
131 CACACGTGATCGAAGTCAACA
* * * *
54825569 GGTATGCATAGTAGCCTACACTTAGTACTACACATGCGACCTATCAATTTGGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACATGTAGTAGC
54825634 CTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTAGTAGCCTACACTTAGTACTA
66 CTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTAGTAGCCTACACTTAGTACTA
*
54825699 CACACGTGATCGAAGTTAACA
131 CACACGTGATCGAAGTCAACA
* * * *
54825720 GGTACGCATAGTAGCTTGCACTTAGTACTACACATGCGACCTATTAATCTAGTACATGTAATAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACATGTAGTAGC
*
54825785 CTGCACTTAGTACTACACACATGACT
66 CTGCACTTAGTACTACACACGTGACT
54825811 CACAATGGAT
Statistics
Matches: 224, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
151 224 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (151 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACATGTAGTAGC
CTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTAGTAGCCTACACTTAGTACTA
CACACGTGATCGAAGTCAACA
Found at i:54825724 original size:101 final size:99
Alignment explanation
Indices: 54825416--54825809 Score: 335
Period size: 101 Copynumber: 3.9 Consensus size: 99
54825406 CCGAAGCTAT
* * * * * *
54825416 CTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCCGGTACATGTAGTA
1 CTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGATACACGTAGTA
* * * * *
54825481 ACCTGCACTTAGTACTACACACGTGACTTAACCAT
66 GCCTACACTTAGTACTACACACGTGAC-CAATCAA
* * * * * * ** *
54825516 CTGATACACGTAGTAGCCTACACTTAGTACTACACATGTGA-TTGAAGTCAA-CAGGTATGCATA
1 CTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCT-AA--CAATCTGATACACGTA
* * *
54825579 GTAGCCTACACTTAGTACTACACATGCGACCTATCAA
63 GTAGCCTACACTTAGTACTACACACGTGACCAATCAA
* * * * *
54825616 TTTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTAGT
1 -CTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGATACACGTAGT
* *
54825681 AGCCTACACTTAGTACTACACACGTGATCGAAGTTAA
65 AGCCTACACTTAGTACTACACACGTGA-CCAA-TCAA
* * * * ** * *
54825718 CAGGTACGCATAGTAGCTTGCACTTAGTACTACACATGCGACCTATTAATCT-AGTACATGTAAT
1 CTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGA-TACACGTAGT
* *
54825782 AGCCTGCACTTAGTACTACACACATGAC
65 AGCCTACACTTAGTACTACACACGTGAC
54825810 TCACAATGGA
Statistics
Matches: 235, Mismatches: 50, Indels: 18
0.78 0.17 0.06
Matches are distributed among these distances:
99 3 0.01
100 76 0.32
101 148 0.63
102 8 0.03
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (99 bp):
CTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGATACACGTAGTA
GCCTACACTTAGTACTACACACGTGACCAATCAA
Found at i:54826186 original size:19 final size:20
Alignment explanation
Indices: 54826158--54826204 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
54826148 AAGAACATGT
54826158 TATATCATCAAAATAATCACA
1 TATAT-ATCAAAATAATCACA
* *
54826179 TA-ATATCAAATTATTCACA
1 TATATATCAAAATAATCACA
54826198 TATATAT
1 TATATAT
54826205 ACTTACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATATCAAAATAATCACA
Found at i:54830961 original size:119 final size:119
Alignment explanation
Indices: 54830741--54830980 Score: 381
Period size: 119 Copynumber: 2.0 Consensus size: 119
54830731 AAGAAGAACC
** *
54830741 GATCCGTATCTTAGCTCATGAAGTTAAAGAACTAAGAAATACCAGAATTCTGTTAGTGAAAGTGA
1 GATCCGTATCTTAGCTCACAAAGTTAAAGAACTAAGAAATAACAGAATTCTGTTAGTGAAAGTGA
* * * * *
54830806 TGTGGCATCGGCACTGTATGGAAGAGGGCACGTGGGAGCCTGAATATGCTATGA
66 CGTGGCATCGGCACTGTATGGAAGAGGCCACATGGGAGCCTAAAGATGCTATGA
* *
54830860 GATCCGTATCTTAGCTCGCAAAGTTAAAGAACTAAGAAATAAGAGAATTCTGTTAGTGAAAGTGA
1 GATCCGTATCTTAGCTCACAAAGTTAAAGAACTAAGAAATAACAGAATTCTGTTAGTGAAAGTGA
*
54830925 CGTGGCATCGGCACTGTATTGAAGAGGCCACATGGGAGCCTAAAGATGCTATGA
66 CGTGGCATCGGCACTGTATGGAAGAGGCCACATGGGAGCCTAAAGATGCTATGA
54830979 GA
1 GA
54830981 CAGCAATATC
Statistics
Matches: 110, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
119 110 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.24
Consensus pattern (119 bp):
GATCCGTATCTTAGCTCACAAAGTTAAAGAACTAAGAAATAACAGAATTCTGTTAGTGAAAGTGA
CGTGGCATCGGCACTGTATGGAAGAGGCCACATGGGAGCCTAAAGATGCTATGA
Found at i:54839091 original size:25 final size:26
Alignment explanation
Indices: 54839057--54839130 Score: 91
Period size: 26 Copynumber: 2.9 Consensus size: 26
54839047 ACGAATTTTC
*
54839057 TCAAACTTTTA-TCGGGG-TAAAATCA
1 TCAAAATTTTACT-GGGGCTAAAATCA
*
54839082 TCAAAATTTTACTGGGGCTGAAATCA
1 TCAAAATTTTACTGGGGCTAAAATCA
*
54839108 TCAAAATTTTACTAGGG-TAAAAT
1 TCAAAATTTTACTGGGGCTAAAAT
54839131 TAGGATGAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.44
26 24 0.56
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (26 bp):
TCAAAATTTTACTGGGGCTAAAATCA
Found at i:54843083 original size:27 final size:27
Alignment explanation
Indices: 54843052--54843119 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
54843042 TTCAGAATTT
* * *
54843052 ACCACAAAGGTATTCGTTTCAGAGTGC
1 ACCACAAAGGCATTCCTTTCAAAGTGC
*
54843079 GCCACAAAGGCATTCCTTTCAAAGTGC
1 ACCACAAAGGCATTCCTTTCAAAGTGC
*
54843106 ACCACAGAGGCATT
1 ACCACAAAGGCATT
54843120 TATTTTAGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (27 bp):
ACCACAAAGGCATTCCTTTCAAAGTGC
Found at i:54844010 original size:21 final size:20
Alignment explanation
Indices: 54843986--54844025 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
54843976 CATGTATTTT
54843986 AATGATTGATGATAGATTATG
1 AATGATTGATGATAG-TTATG
*
54844007 AATGTTTGATGATAGTTAT
1 AATGATTGATGATAGTTAT
54844026 ACAAGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (20 bp):
AATGATTGATGATAGTTATG
Found at i:54844033 original size:20 final size:21
Alignment explanation
Indices: 54843991--54844033 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
54843981 ATTTTAATGA
*
54843991 TTGATGATAGATTATGAATGT
1 TTGATGATAGATTATGAAAGT
54844012 TTGATGATAG-TTAT-ACAAGT
1 TTGATGATAGATTATGA-AAGT
54844032 TT
1 TT
54844034 TGTTAAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 9 0.45
21 10 0.50
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (21 bp):
TTGATGATAGATTATGAAAGT
Found at i:54845705 original size:45 final size:45
Alignment explanation
Indices: 54845396--54845702 Score: 487
Period size: 45 Copynumber: 6.9 Consensus size: 45
54845386 CTAAATTCAT
* * * *
54845396 TCACCAGCATT-TCGCCTGCTAGGCTCGAA-GCCCG-ATA-TCATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATC
*
54845438 TCACCGGCATTATAGCCTGCTAGGCTTAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* *
54845483 TCACCGGTATTATAGCCTGCTAGGCTCAAAGACCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
54845528 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
*
54845573 TCACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* *
54845618 TCACCGGCGTTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
54845663 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATA
54845703 ATACTGTGCG
Statistics
Matches: 246, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
42 10 0.04
43 15 0.06
44 5 0.02
45 215 0.87
46 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
Found at i:54846564 original size:47 final size:47
Alignment explanation
Indices: 54846508--54846649 Score: 223
Period size: 47 Copynumber: 3.0 Consensus size: 47
54846498 AAAATTTTCT
* *
54846508 TTAACTAAGTAACTTATTCGGAAATAATAAGGGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
*
54846555 TTAACTAAGTAACTTATCCGGAAATATTAAGGGAAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
** *
54846602 TTAACTAAGTAACTTATCCAAAAATATTAAGAGC-AATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
54846648 TT
1 TT
54846650 TAAATTCAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 14 0.16
47 74 0.84
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (47 bp):
TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
Found at i:54853805 original size:2 final size:2
Alignment explanation
Indices: 54853798--54853823 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54853788 TCATATTTTC
54853798 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
54853824 CTTTACCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54854153 original size:47 final size:47
Alignment explanation
Indices: 54854097--54854235 Score: 235
Period size: 47 Copynumber: 3.0 Consensus size: 47
54854087 AAAATTTTCT
*
54854097 TTAACTAAGTAACTTATCCGGAAATAATAAGGGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
* *
54854144 TTAACTAAGTAACTTATCCAGAAATATTAAGGGAAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
*
54854191 TTAACTAAGTAACTTATCCGGAAATATTAAGAGC-AATTTAACAAG
1 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAG
54854236 TTTTAAATTC
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
46 11 0.13
47 75 0.87
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (47 bp):
TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
Found at i:54863903 original size:29 final size:29
Alignment explanation
Indices: 54863861--54863921 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
54863851 TAACCGCAAA
54863861 TAAATACACCACTCATCCAAACTCACTCT
1 TAAATACACCACTCATCCAAACTCACTCT
54863890 TAAATACACCACTCATCCAAACTCACTCT
1 TAAATACACCACTCATCCAAACTCACTCT
54863919 TAA
1 TAA
54863922 TTTGTTATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (29 bp):
TAAATACACCACTCATCCAAACTCACTCT
Found at i:54869368 original size:46 final size:46
Alignment explanation
Indices: 54869301--54869422 Score: 183
Period size: 46 Copynumber: 2.7 Consensus size: 46
54869291 CGCCCCTAAG
*
54869301 TGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAA
* * *
54869347 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAA
*
54869393 TGAACTCGGACTCAACTCAACGAGTTCGGA
1 TGAACTCGGACTCAACTCAACGAGCTCGGA
54869423 TCCTCAACCA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 2 0.03
46 69 0.97
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAA
Found at i:54869441 original size:46 final size:46
Alignment explanation
Indices: 54869299--54869441 Score: 132
Period size: 46 Copynumber: 3.1 Consensus size: 46
54869289 CCCGCCCCTA
* * * * *
54869299 AGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTC-GG-ATCCTCATCCATCCT
* * * *
54869345 AATGAACTCGGACTCAACTCAACGAGTTCGGA-CAT-TTGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATCCTCATCCATCC-T
*
54869390 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATCCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATCCTCATCCATCCT
54869437 AGTGA
1 AGTGA
54869442 CATGTCACTT
Statistics
Matches: 77, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
42 4 0.05
45 2 0.03
46 63 0.82
47 3 0.04
48 5 0.06
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATCCTCATCCATCCT
Found at i:54871783 original size:15 final size:15
Alignment explanation
Indices: 54871727--54871805 Score: 81
Period size: 15 Copynumber: 5.4 Consensus size: 15
54871717 CAAAGATAAC
*
54871727 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
*
54871741 AAGAAATCAAG-ATA
1 AAGAAATCCAGAATA
* * *
54871755 GAGAAACCCGGAATA
1 AAGAAATCCAGAATA
54871770 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
54871785 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
54871800 AAGAAA
1 AAGAAA
54871806 CCCAAGATAC
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
14 17 0.33
15 34 0.67
ACGTcount: A:0.58, C:0.13, G:0.19, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:54871814 original size:15 final size:15
Alignment explanation
Indices: 54871738--54871814 Score: 52
Period size: 15 Copynumber: 5.2 Consensus size: 15
54871728 AGAAAACCGA
*
54871738 ATAAAGAAA-TCAAG
1 ATAAAGAAACCCAAG
* *
54871752 ATAGAGAAACCC-GG
1 ATAAAGAAACCCAAG
*
54871766 AATAAAGAAATCC-AG
1 -ATAAAGAAACCCAAG
* * *
54871781 AATAAAGAGATCCAGG
1 -ATAAAGAAACCCAAG
54871797 ATAAAGAAACCCAAG
1 ATAAAGAAACCCAAG
54871812 ATA
1 ATA
54871815 CGATACTATG
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
14 9 0.18
15 39 0.80
16 1 0.02
ACGTcount: A:0.56, C:0.14, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAACCCAAG
Found at i:54874484 original size:46 final size:46
Alignment explanation
Indices: 54874431--54874605 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 46
54874421 TATTTGGGCA
*
54874431 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAGCG
*** * * *
54874477 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATACGA-GCG
* * **
54874524 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCAATTATGGATACGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAGCG
* *
54874570 CCCGAGCTCGTTGAGTTGAGTCC-AGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54874606 GCGGTTACAT
Statistics
Matches: 108, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
45 12 0.11
46 58 0.54
47 38 0.35
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAGCG
Found at i:54874586 original size:93 final size:92
Alignment explanation
Indices: 54874427--54874597 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 92
54874417 GGGATATTTG
* * * *
54874427 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATACGAACGCCCGAACTCGTTGAG
54874492 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCC-AGTTCGAGAGATGTAACTA
* * *
54874520 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCAATTATGGATACGAATGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATACGAACGCCCGAACTCGTTGAG
54874585 TTGAGTCCAGTTC
66 TTGAGTCCAGTTC
54874598 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 5 0.07
93 66 0.93
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (92 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATACGAACGCCCGAACTCGTTGAG
TTGAGTCCAGTTCGAGAGATGTAACTA
Found at i:54877552 original size:14 final size:15
Alignment explanation
Indices: 54877516--54877593 Score: 65
Period size: 15 Copynumber: 5.4 Consensus size: 15
54877506 GTATCTTGGG
*
54877516 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
54877531 TCTCTTTATTCT-GA
1 TTTCTTTATTCTGGA
* *
54877545 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
54877560 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
54877575 TTT-TTTATTC-GGT
1 TTTCTTTATTCTGGA
54877588 TTTCTT
1 TTTCTT
54877594 GTTATCTTTG
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
13 5 0.10
14 19 0.39
15 25 0.51
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:54880926 original size:46 final size:47
Alignment explanation
Indices: 54880764--54880934 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 47
54880754 AACCCGCCCC
* * *
54880764 TAAGTGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
* * *
54880810 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-ATTTGCATCCA
* * * *
54880858 TCA-CGAACTCGGACTCAGCTCAACCAGTTCGGA-CATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
*
54880903 TAAGTGAACTCAGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
54880935 ATGCTCAACC
Statistics
Matches: 101, Mismatches: 17, Indels: 14
0.77 0.13 0.11
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 53 0.52
47 29 0.29
48 3 0.03
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (47 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
Found at i:54880928 original size:93 final size:92
Alignment explanation
Indices: 54880769--54880938 Score: 252
Period size: 93 Copynumber: 1.8 Consensus size: 92
54880759 GCCCCTAAGT
* * *
54880769 GAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACCAGCTCGAGCATTCGCATCCATAAATGAACTCAGACTCAACTCAA
54880834 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTC-GATGCCTAGTTACATCTCAC
* * * *
54880862 GAACTCGGACTCAGCTCAACCAGTTCG-GACATTTGCATCCATAAGTGAACTCAGACTCAACTCA
1 GAACTCGGACTCAACTCAACCAGCTCGAG-CATTCGCATCCATAAATGAACTCAGACTCAACTCA
54880926 ACGAGTTCGATGC
65 ACGAGTTCGATGC
54880939 TCAACCATCC
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
92 6 0.09
93 63 0.91
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACCAGCTCGAGCATTCGCATCCATAAATGAACTCAGACTCAACTCAA
CGAGTTCGATGCCTAGTTACATCTCAC
Found at i:54886434 original size:40 final size:40
Alignment explanation
Indices: 54886197--54886420 Score: 344
Period size: 40 Copynumber: 5.6 Consensus size: 40
54886187 CGGATGATAA
* *
54886197 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
54886237 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
54886276 CCGGGCTAAGTCCCGAAGGCAATTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
54886316 CCGGGCTAAGTCCTGAAGGCATTTATGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
54886356 CCGGGATAAGTCCCGAAGGCAATTGTGCGAGTTACTATAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
54886396 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54886421 AGCAAGTAGC
Statistics
Matches: 167, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 35 0.21
40 132 0.79
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:54886434 original size:80 final size:80
Alignment explanation
Indices: 54886197--54886453 Score: 335
Period size: 80 Copynumber: 3.2 Consensus size: 80
54886187 CGGATGATAA
* * * *
54886197 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAG-CCCGAAGGCATTT
1 CCGGGATAAGTCCCGAAGGCAATTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTT
*
54886260 GTGCGAGTTACTATAT
65 GAGCGAGTTACTATAT
* * *
54886276 CCGGGCTAAGTCCCGAAGGCAATTGTGTGAGTTACTATATCCGGGCTAAGTCCTGAAGGCATTT-
1 CCGGGATAAGTCCCGAAGGCAATTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
54886340 ATGCGAGTTACTATAT
66 A-GCGAGTTACTATAT
*
54886356 CCGGGATAAGTCCCGAAGGCAATTGTGCGAGTTACTATAGCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGATAAGTCCCGAAGGCAATTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
*
54886421 AGCAAG-TAGCTATAT
66 AGCGAGTTA-CTATAT
* * *
54886436 -CTGGATAAATTCCGAAGG
1 CCGGGATAAGTCCCGAAGG
54886454 TACTTGGTTT
Statistics
Matches: 159, Mismatches: 14, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
79 61 0.38
80 97 0.61
81 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGGGATAAGTCCCGAAGGCAATTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
AGCGAGTTACTATAT
Found at i:54889593 original size:40 final size:40
Alignment explanation
Indices: 54889548--54889734 Score: 261
Period size: 40 Copynumber: 4.7 Consensus size: 40
54889538 ATAACCACAA
* *
54889548 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
54889588 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
*
54889628 GCACAAATGCCTTCAGGTCTTAACCCGGATATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* * *
54889668 GCACAAATGCCTTCGGGTCTTAACTCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT-AGCAACTC
* *
54889708 GCATAAATGCCTTCGGG-CTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAACCCGG
54889735 GTATCATTCA
Statistics
Matches: 132, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 8 0.06
40 122 0.92
41 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:54889633 original size:80 final size:79
Alignment explanation
Indices: 54889528--54889738 Score: 300
Period size: 80 Copynumber: 2.7 Consensus size: 79
54889518 TCTTCGGAAT
* *
54889528 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
54889592 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* * *
54889607 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCAGGTCTTAACCCGGATATAGCAACTCGCAC
1 TTAGCCCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
54889672 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* * * *
54889687 TTAACTCGGATATAATCACTAGCATAAATGCCTTCGGG-CTTAGCCCGGGTAT
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTAT
54889739 CATTCAATTG
Statistics
Matches: 117, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
79 17 0.15
80 99 0.85
81 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (79 bp):
TTAGCCCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACA
AATGCCTTCGGGTC
Found at i:54897743 original size:40 final size:40
Alignment explanation
Indices: 54897634--54897833 Score: 266
Period size: 40 Copynumber: 5.1 Consensus size: 40
54897624 CGGAATTTAG
* * *
54897634 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAAC
* *
54897674 CCGG-TATAGCAACT--CACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAAC
*
54897711 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAAC
* *
54897751 CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAAC
* *
54897791 CCGGATATAATC-ACTAGCATAAATGCCTTCGGG-CTTAGC
1 CCGGATATAA-CAACTAGCACAAATGCCTTCGGGTCTTAAC
54897830 CCGG
1 CCGG
54897834 GTATCATTCA
Statistics
Matches: 144, Mismatches: 12, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
37 25 0.17
38 9 0.06
39 16 0.11
40 93 0.65
41 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (40 bp):
CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:54905839 original size:40 final size:40
Alignment explanation
Indices: 54905735--54905951 Score: 280
Period size: 40 Copynumber: 5.5 Consensus size: 40
54905725 CGGATGATAA
* *
54905735 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
54905775 CCGAGCTAAG-CCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
54905814 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
54905854 CCGGGATAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
54905894 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
54905934 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
54905952 TACTTGGTTT
Statistics
Matches: 156, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 49 0.31
40 107 0.69
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:54912038 original size:15 final size:15
Alignment explanation
Indices: 54912018--54912047 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54912008 TATTTTATTT
*
54912018 ATATTAGGATAATTA
1 ATATTAAGATAATTA
54912033 ATATTAAGATAATTA
1 ATATTAAGATAATTA
54912048 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:54912075 original size:27 final size:26
Alignment explanation
Indices: 54912014--54912076 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
54912004 ACTCTATTTT
54912014 ATTTATATTAGGATAATTAATATTAAG
1 ATTT-TATTAGGATAATTAATATTAAG
* * * *
54912041 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
54912069 ATTTTATT
1 ATTTTATT
54912077 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:54914266 original size:20 final size:20
Alignment explanation
Indices: 54914241--54914281 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
54914231 ACACCTACAA
54914241 CCCAGGATGGAGGGACCACC
1 CCCAGGATGGAGGGACCACC
54914261 CCCAGGATGGAGGGACCACC
1 CCCAGGATGGAGGGACCACC
54914281 C
1 C
54914282 TAACATAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.37, G:0.34, T:0.05
Consensus pattern (20 bp):
CCCAGGATGGAGGGACCACC
Found at i:54915782 original size:11 final size:10
Alignment explanation
Indices: 54915752--54915807 Score: 67
Period size: 11 Copynumber: 5.3 Consensus size: 10
54915742 ACAACCAAAT
54915752 TTTTTTTTTA
1 TTTTTTTTTA
**
54915762 TTTTAGTTTA
1 TTTTTTTTTA
54915772 TTTTATTTTTA
1 TTTT-TTTTTA
54915783 TTTTTTTCTTA
1 TTTTTTT-TTA
54915794 TTTTTTTCTTA
1 TTTTTTT-TTA
54915805 TTT
1 TTT
54915808 ATTATTTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
10 15 0.38
11 25 0.62
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.82
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:54915794 original size:22 final size:20
Alignment explanation
Indices: 54915752--54915807 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
54915742 ACAACCAAAT
54915752 TTTTTTTTTATTTTAGTTTA
1 TTTTTTTTTATTTTAGTTTA
**
54915772 TTTTATTTTTATTTTTTTCTTA
1 TTTT-TTTTTATTTTAGT-TTA
54915794 TTTTTTTCTTATTT
1 TTTTTTT-TTATTT
54915808 ATTATTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 4 0.13
21 14 0.45
22 13 0.42
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTTTTTTTATTTTAGTTTA
Found at i:54915812 original size:18 final size:17
Alignment explanation
Indices: 54915750--54915815 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 17
54915740 AGACAACCAA
*
54915750 ATTTTTTTTTTA-TTTT
1 ATTTTTTTATTATTTTT
* *
54915766 AGTTTATT-TTATTTTT
1 ATTTTTTTATTATTTTT
*
54915782 ATTTTTTTCTTATTTTT
1 ATTTTTTTATTATTTTT
54915799 -TTCTTATTTATTATTTT
1 ATT-TT-TTTATTATTTT
54915816 CAAATATTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
15 3 0.07
16 18 0.44
17 10 0.24
18 10 0.24
ACGTcount: A:0.15, C:0.03, G:0.02, T:0.80
Consensus pattern (17 bp):
ATTTTTTTATTATTTTT
Found at i:54917254 original size:15 final size:15
Alignment explanation
Indices: 54917234--54917263 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54917224 CATTTTATTT
*
54917234 ATATTAGGATAATTA
1 ATATTAAGATAATTA
54917249 ATATTAAGATAATTA
1 ATATTAAGATAATTA
54917264 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:54917291 original size:27 final size:26
Alignment explanation
Indices: 54917230--54917292 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
54917220 ATTCCATTTT
54917230 ATTTATATTAGGATAATTAATATTAAG
1 ATTT-TATTAGGATAATTAATATTAAG
* * * *
54917257 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
54917285 ATTTTATT
1 ATTTTATT
54917293 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:54917307 original size:10 final size:10
Alignment explanation
Indices: 54917288--54917319 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
54917278 TTTTAGGATT
54917288 TTAT-TTTAA
1 TTATCTTTAA
54917297 TTATCTTTAA
1 TTATCTTTAA
54917307 TTATCTTTAA
1 TTATCTTTAA
54917317 TTA
1 TTA
54917320 AATGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:54921327 original size:2 final size:2
Alignment explanation
Indices: 54921320--54921361 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
54921310 AACTTGTATT
* *
54921320 TA TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54921362 CCATGTTCAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:54926900 original size:48 final size:48
Alignment explanation
Indices: 54926845--54927140 Score: 529
Period size: 48 Copynumber: 6.2 Consensus size: 48
54926835 TGTTACAACA
*
54926845 TTCACATTAGCCATTCGGCTTTACCACACATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
*
54926893 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
*
54926941 TTCACATTAGCCCTTCGGCTTTACCACATATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
*
54926989 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
*
54927037 TTCACATTAGCCCTTCGGCTTTACCACATATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
* *
54927085 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATGT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
54927133 TTCACATT
1 TTCACATT
54927141 CATCACATCG
Statistics
Matches: 237, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 237 1.00
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.32
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
Found at i:54927179 original size:96 final size:96
Alignment explanation
Indices: 54926887--54927379 Score: 360
Period size: 96 Copynumber: 5.1 Consensus size: 96
54926877 CACATCACAC
*
54926887 ATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTTCACATT-AG
1 ATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTTCACATTCAT
* * * * * * *
54926951 CCCTTCGG-CTTTA-CCACATATACACATCACAC
66 CACATCGGCCATTAGGC-CTTAT-CACA-CATAT
*
54926983 ATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTTCACATT-AG
1 ATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTTCACATTCAT
* * * * * * *
54927047 CCCTTCGG-CTTTA-CCACATATACACATCACAC
66 CACATCGGCCATTAGGC-CTTAT-CACA-CATAT
*
54927079 ATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATGTTTCACATTCAT
1 ATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTTCACATTCAT
54927144 CACATCGGCCATTAGGCCTTATCACACATAT
66 CACATCGGCCATTAGGCCTTATCACACATAT
* * * * * * *
54927175 ATATACCTTCACATTCATCACA-TCGGCCATTAGGC-CTTATCACATAT-ATAC---TCTTTCAC
1 ATATA-TTTCACATT-AGC-CATTCGG-CTTTA-CCACATAT-ACATATCACACATATATTTCAC
* *
54927234 ATTCATCACATTGGCCATTAGGCCTTATCACATATAT
60 ATTCATCACATCGGCCATTAGGCCTTATCACACATAT
* * * * * * * *
54927271 ATACACCTTCACATTCATCACA-TCGGCCATTAGGC-CTTATCACATAT-ATAC---TCTTTCAC
1 ATATA-TTTCACATT-AGC-CATTCGG-CTTTA-CCACATAT-ACATATCACACATATATTTCAC
54927330 ATTCATCACATCGGCCATTAGGCCTTAT--CACATAT
60 ATTCATCACATCGGCCATTAGGCCTTATCACACATAT
*
54927365 ATACTCTTTCACATT
1 ATA-TATTTCACATT
54927380 CATCACATCG
Statistics
Matches: 363, Mismatches: 24, Indels: 22
0.89 0.06 0.05
Matches are distributed among these distances:
94 17 0.05
96 292 0.80
97 19 0.05
98 14 0.04
99 14 0.04
100 7 0.02
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.33
Consensus pattern (96 bp):
ATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTTCACATTCAT
CACATCGGCCATTAGGCCTTATCACACATAT
Found at i:54927234 original size:192 final size:192
Alignment explanation
Indices: 54926845--54927424 Score: 538
Period size: 192 Copynumber: 3.0 Consensus size: 192
54926835 TGTTACAACA
*
54926845 TTCACATTAGCCATTCGGCTTTACCACACATACACATCACACATATATTTCACATTAGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATATTTCACATTAGCCATTCG
* * * * * *
54926910 GCTTTACCACATATACATATCACACATATATTTCACATT-AGCCCTTCGG-CTTTA-CCACATAT
66 GCTTTACCACATATACATATCACACATATATTTCACATTCATCACATCGGCCATTAGGC-CTTAT
* * * * * * *
54926972 ACACATCACACATATA-TTTCACATT-AGC-CATTCGG-CTTTA-CCACATAT-ACATATCACAC
130 -CACA-CATATATATACTTTCACATTCATCACA-TCGGCCATTAGGC-CTTATCACATAT-ATAC
*
54927031 ATATAT
190 ---TCT
*
54927037 TTCACATTAGCCCTTCGGCTTTACCACATATACACATCACACATATATTTCACATTAGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATATTTCACATTAGCCATTCG
*
54927102 GCTTTACCACATATACATATCACACATATGTTTCACATTCATCACATCGGCCATTAGGCCTTATC
66 GCTTTACCACATATACATATCACACATATATTTCACATTCATCACATCGGCCATTAGGCCTTATC
*
54927167 ACACATATATATACCTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTCT
131 ACACATATATATACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTCT
* * * * * * * * *
54927229 TTCACATTCATCACATT-GGCCATTAGGC-CTTAT-CACAT-ATATATACACCTTCACATTCATC
1 TTCACATT-AGC-CATTCGG-CTTTA-CCACATATACACATCACACATATA-TTTCACATT-AGC
* * * * *
54927290 ACA-TCGGCCATTAGGC-CTTATCACATAT-ATAC---TCTTTCACATTCATCACATCGGCCATT
60 -CATTCGG-CTTTA-CCACATAT-ACATATCACACATATATTTCACATTCATCACATCGGCCATT
54927349 AGGCCTTAT--CACATATATACT-CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
121 AGGCCTTATCACACATATATA-TACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
54927411 TATACTCT
185 TATACTCT
54927419 TTCACA
1 TTCACA
54927425 AATTTTAATA
Statistics
Matches: 334, Mismatches: 34, Indels: 42
0.81 0.08 0.10
Matches are distributed among these distances:
190 64 0.19
191 1 0.00
192 160 0.48
193 36 0.11
194 31 0.09
195 28 0.08
196 14 0.04
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.33
Consensus pattern (192 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATATTTCACATTAGCCATTCG
GCTTTACCACATATACATATCACACATATATTTCACATTCATCACATCGGCCATTAGGCCTTATC
ACACATATATATACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTCT
Found at i:54927237 original size:47 final size:47
Alignment explanation
Indices: 54927132--54927424 Score: 498
Period size: 47 Copynumber: 6.1 Consensus size: 47
54927122 CACACATATG
54927132 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATATA-TAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTAT--CACATATATACT-C
*
54927181 CTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTC
* *
54927228 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACTC
*
54927277 CTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTC
54927324 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTC
54927371 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTC
54927418 TTTCACA
1 TTTCACA
54927425 AATTTTAATA
Statistics
Matches: 233, Mismatches: 8, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
47 155 0.67
48 1 0.00
49 77 0.33
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTC
Found at i:54927356 original size:143 final size:144
Alignment explanation
Indices: 54927133--54927414 Score: 514
Period size: 143 Copynumber: 2.0 Consensus size: 144
54927123 ACACATATGT
54927133 TTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATATATACCTTCACATTCATCACAT
1 TTCACATTCATCACATCGGCCATTAGGCCTTAT-ACACATATATATACCTTCACATTCATCACAT
*
54927198 CGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTATC
65 CGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATCGGCCATTAGGCCTTATC
54927263 ACATATATATACACC
130 ACATATATATACACC
*
54927278 TTCACATTCATCACATCGGCCATTAGGCCTTAT-CACATATATACT-CTTTCACATTCATCACAT
1 TTCACATTCATCACATCGGCCATTAGGCCTTATACACATATATA-TACCTTCACATTCATCACAT
54927341 CGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATCGGCCATTAGGCCTTATC
65 CGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATCGGCCATTAGGCCTTATC
54927406 ACATATATA
130 ACATATATA
54927415 CTCTTTCACA
Statistics
Matches: 134, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
143 100 0.75
144 1 0.01
145 33 0.25
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (144 bp):
TTCACATTCATCACATCGGCCATTAGGCCTTATACACATATATATACCTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
CATATATATACACC
Found at i:54927414 original size:96 final size:94
Alignment explanation
Indices: 54927132--54927424 Score: 507
Period size: 96 Copynumber: 3.1 Consensus size: 94
54927122 CACACATATG
54927132 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATATA-TACCTTCACATTCATCAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTAT--CACATATATACT-CCTTCACATTCATCAC
54927196 ATCGGCCATTAGGCCTTATCACATATATACTC
63 ATCGGCCATTAGGCCTTATCACATATATACTC
* *
54927228 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACTCCTTCACATTCATCACA
54927293 TCGGCCATTAGGCCTTATCACATATATACTC
64 TCGGCCATTAGGCCTTATCACATATATACTC
*
54927324 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTCCTTCACATTCATCACATC
54927389 GGCCATTAGGCCTTATCACATATATACTC
66 GGCCATTAGGCCTTATCACATATATACTC
54927418 TTTCACA
1 TTTCACA
54927425 AATTTTAATA
Statistics
Matches: 189, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
94 65 0.34
96 124 0.66
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (94 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTCCTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACTC
Found at i:54932608 original size:18 final size:18
Alignment explanation
Indices: 54932557--54932609 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
54932547 GGCTAAGGAC
54932557 TAAATTAGAAATCAAAATTAT
1 TAAA-TAGAAAT--AAATTAT
*
54932578 TAAA-AGATGATAAATTAT
1 TAAATAGA-AATAAATTAT
54932596 TAAATAGAAATAAA
1 TAAATAGAAATAAA
54932610 AATCATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 16 0.57
19 6 0.21
20 2 0.07
21 4 0.14
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (18 bp):
TAAATAGAAATAAATTAT
Found at i:54936133 original size:39 final size:39
Alignment explanation
Indices: 54936049--54936239 Score: 292
Period size: 39 Copynumber: 4.9 Consensus size: 39
54936039 TATGGTAACC
* * * *
54936049 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCT
*
54936089 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
* * *
54936128 TGCACAATTGCCTTCAGGCTTAGCCCGAATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
*
54936167 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
54936206 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
54936240 CTCGAACATT
Statistics
Matches: 137, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 120 0.88
40 17 0.12
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.25
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
Found at i:54946423 original size:27 final size:27
Alignment explanation
Indices: 54946393--54946470 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
54946383 CTCATATTTA
* * *
54946393 TAGGCTAGTATTACTGAAATACCCCTG
1 TAGGATAGAATTACTAAAATACCCCTG
* *
54946420 TAGGATAGAATTACTAAAATGCCTCTG
1 TAGGATAGAATTACTAAAATACCCCTG
*
54946447 TAGGGTAGAATTACTAAAATACCC
1 TAGGATAGAATTACTAAAATACCC
54946471 TTGGTTTACA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (27 bp):
TAGGATAGAATTACTAAAATACCCCTG
Found at i:54946523 original size:53 final size:51
Alignment explanation
Indices: 54946455--54946665 Score: 167
Period size: 53 Copynumber: 3.9 Consensus size: 51
54946445 TGTAGGGTAG
*
54946455 AATTACTA-AAATACCCTTGGTTTACAAAATTACTGAATACCCTTGGTTTACAA
1 AATTAC-AGAAATACCCTTGATTTACAAAATTAC-GAATACCCTTGGTTT-CAA
* * * * * *
54946508 AATTACCA-AAATACCC-TCAATTAGCAAAATTACCAAAATCCCTTGATTTGGAA
1 AATTA-CAGAAATACCCTTGATTTA-CAAAATTACGAATA-CCCTTGGTTT-CAA
* * *
54946561 AATTACAGAAATACCCCTAATTTACAAAATTACAGAAGTACCCTTGACTTTCAA
1 AATTACAGAAATACCCTTGATTTACAAAATTAC-GAA-TACCCTTG-GTTTCAA
* * *
54946615 AACTTACAGAAATACCATTGGTTTGCAAAATTACCGAAATACCCTTGGTTT
1 AA-TTACAGAAATACCCTTGATTTACAAAATTA-CG-AATACCCTTGGTTT
54946666 GTACATTTAC
Statistics
Matches: 127, Mismatches: 20, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
52 9 0.07
53 56 0.44
54 21 0.17
55 38 0.30
56 3 0.02
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (51 bp):
AATTACAGAAATACCCTTGATTTACAAAATTACGAATACCCTTGGTTTCAA
Found at i:54946666 original size:27 final size:27
Alignment explanation
Indices: 54946455--54946666 Score: 184
Period size: 27 Copynumber: 7.9 Consensus size: 27
54946445 TGTAGGGTAG
*
54946455 AATTACTA-AAATACCCTTGGTTTACAA
1 AATTAC-AGAAATACCCTTGGTTTGCAA
* *
54946482 AATTACTG-AATACCCTTGGTTTACAA
1 AATTACAGAAATACCCTTGGTTTGCAA
*** *
54946508 AATTACCA-AAATACCCTCAATTAGCAA
1 AATTA-CAGAAATACCCTTGGTTTGCAA
* *
54946535 AATTACCA-AAAT-CCCTTGATTTGGAA
1 AATTA-CAGAAATACCCTTGGTTTGCAA
* ** *
54946561 AATTACAGAAATACCCCTAATTTACAA
1 AATTACAGAAATACCCTTGGTTTGCAA
* *
54946588 AATTACAGAAGTACCCTTGACTTT-CAA
1 AATTACAGAAATACCCTTG-GTTTGCAA
*
54946615 AACTTACAGAAATACCATTGGTTTGCAA
1 AA-TTACAGAAATACCCTTGGTTTGCAA
*
54946643 AATTACCGAAATACCCTTGGTTTG
1 AATTACAGAAATACCCTTGGTTTG
54946667 TACATTTACG
Statistics
Matches: 153, Mismatches: 24, Indels: 16
0.79 0.12 0.08
Matches are distributed among these distances:
25 2 0.01
26 42 0.27
27 86 0.56
28 23 0.15
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.30
Consensus pattern (27 bp):
AATTACAGAAATACCCTTGGTTTGCAA
Found at i:54946973 original size:41 final size:41
Alignment explanation
Indices: 54946926--54947045 Score: 177
Period size: 41 Copynumber: 2.9 Consensus size: 41
54946916 GGAGGAAGAA
* *
54946926 ATTGAGGATCACATGGTTTCTTGATGACCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGATGACCGTGGATCCACCG
* * *
54946967 ATTGAGGATCGCATAGTTGCTTGACGATCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGATGACCGTGGATCCACCG
* *
54947008 ATTAAGGATCGCATGGTTGCTTGATAACCGTGGATCCA
1 ATTGAGGATCGCATGGTTGCTTGATGACCGTGGATCCA
54947046 TTGCTGGCTT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (41 bp):
ATTGAGGATCGCATGGTTGCTTGATGACCGTGGATCCACCG
Found at i:54947231 original size:22 final size:22
Alignment explanation
Indices: 54947203--54947254 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
54947193 ATTATAGCTT
54947203 TGTGCCAACCT-ACATATGGCTC
1 TGTGCCAACCTGA-ATATGGCTC
* *
54947225 TGTGCCAACCTGATTATGGCTG
1 TGTGCCAACCTGAATATGGCTC
54947247 TGTGCCAA
1 TGTGCCAA
54947255 ACGTTTTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (22 bp):
TGTGCCAACCTGAATATGGCTC
Found at i:54951474 original size:26 final size:26
Alignment explanation
Indices: 54951438--54951489 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
54951428 GGTCGAGTTT
* *
54951438 GCTATTGAGTTAGTATCGGGAACATC
1 GCTATCGAGTTACTATCGGGAACATC
54951464 GCTATCGAGTTACTATCGGGAACATC
1 GCTATCGAGTTACTATCGGGAACATC
54951490 TTCGATATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (26 bp):
GCTATCGAGTTACTATCGGGAACATC
Found at i:54954266 original size:20 final size:20
Alignment explanation
Indices: 54954241--54954285 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
54954231 GGGAAAAAAA
*
54954241 ATGAAAAGTT-GTAAATTTT
1 ATGAAAAATTCGTAAATTTT
*
54954260 GATGAAAAATTCTTAAATTTT
1 -ATGAAAAATTCGTAAATTTT
54954281 ATGAA
1 ATGAA
54954286 TCCATGTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.44, C:0.02, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGAAAAATTCGTAAATTTT
Found at i:54954919 original size:20 final size:20
Alignment explanation
Indices: 54954882--54954927 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
54954872 TAAGGACTAA
* *
54954882 AATGAAAAGTTGTAAAATTT
1 AATGAAAAATTCTAAAATTT
*
54954902 AATGAAAAATTCTTAAATTT
1 AATGAAAAATTCTAAAATTT
*
54954922 TATGAA
1 AATGAA
54954928 TACATATGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (20 bp):
AATGAAAAATTCTAAAATTT
Found at i:54960651 original size:39 final size:39
Alignment explanation
Indices: 54960568--54960730 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
54960558 TATGGTAACC
** * * *
54960568 CGCACAAACGCCTTCGGGACTTAACCCGAATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAATT
* *
54960608 CGCACAATTGCCTTCGGGCTTAGCCCAGATATCATAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
54960647 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
54960686 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
54960725 CGCACA
1 CGCACA
54960731 TTCATTCACA
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 98 0.86
40 16 0.14
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
Found at i:54968384 original size:40 final size:39
Alignment explanation
Indices: 54968340--54968532 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
54968330 GTTCAAAACA
* * ** * *
54968340 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
54968380 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
54968420 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
54968459 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
54968498 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
54968533 TTCATTCACA
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:54968451 original size:39 final size:39
Alignment explanation
Indices: 54968370--54968532 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
54968360 TATGGTAACC
* *
54968370 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
54968410 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
54968449 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
54968488 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
54968527 CGCACA
1 CGCACA
54968533 TTCATTCACA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:54970623 original size:20 final size:20
Alignment explanation
Indices: 54970584--54970623 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54970574 TGAATAACCA
* *
54970584 ATTTGGTATGTTTCAATGTG
1 ATTTGGCATGTGTCAATGTG
*
54970604 ATTTGGCATGTGTCATTGTG
1 ATTTGGCATGTGTCAATGTG
54970624 GTAAGTTTGG
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:0.17, C:0.07, G:0.28, T:0.47
Consensus pattern (20 bp):
ATTTGGCATGTGTCAATGTG
Found at i:54973714 original size:49 final size:51
Alignment explanation
Indices: 54973580--54973727 Score: 228
Period size: 52 Copynumber: 2.9 Consensus size: 51
54973570 CCCTTGTAGT
* * *
54973580 CAAAGCTACCTTCTTCACAAAGTGGCCTTAACATAGTGTCACACTTGTGAC
1 CAAAGCTATCTTCTTCACAAAGTGGCCTTCACATAGTGCCACACTTGTGAC
*
54973631 CAAAGCTATCTTTCTTCACAAAGTGGCCTTCACATAGTACCACACTTGTGAC
1 CAAAGCTATC-TTCTTCACAAAGTGGCCTTCACATAGTGCCACACTTGTGAC
*
54973683 C-AAGCTATC-TCTTCTCAAAGTGGCCTTCACATAGTGCCACACTTG
1 CAAAGCTATCTTCTTCACAAAGTGGCCTTCACATAGTGCCACACTTG
54973728 AGTCACTAGT
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
49 34 0.38
51 17 0.19
52 39 0.43
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (51 bp):
CAAAGCTATCTTCTTCACAAAGTGGCCTTCACATAGTGCCACACTTGTGAC
Found at i:54978032 original size:27 final size:27
Alignment explanation
Indices: 54978002--54978091 Score: 137
Period size: 27 Copynumber: 3.3 Consensus size: 27
54977992 TTTAGTTTAC
*
54978002 TAAAATTACTGAAATACGCTTAG-CTTG
1 TAAAATTACTGAAATAC-CTTCGACTTG
* *
54978029 TAAAATTACTGAAATACCCTCGATTTG
1 TAAAATTACTGAAATACCTTCGACTTG
54978056 TAAAATTACTGAAATACCTTCGACTTG
1 TAAAATTACTGAAATACCTTCGACTTG
54978083 TAAAATTAC
1 TAAAATTAC
54978092 CAAAGTACCC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
26 3 0.05
27 54 0.95
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (27 bp):
TAAAATTACTGAAATACCTTCGACTTG
Found at i:54978069 original size:54 final size:53
Alignment explanation
Indices: 54978002--54978107 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 53
54977992 TTTAGTTTAC
*
54978002 TAAAATTACTGAAATACGCTTAG-CTTGTAAAATTACTGAAA-TACCCTCGATTTG
1 TAAAATTACTGAAATAC-CTTAGACTTGTAAAATTAC-CAAAGTACCC-CGATTTG
*
54978056 TAAAATTACTGAAATACCTTCGACTTGTAAAATTACCAAAGTACCCCGATTT
1 TAAAATTACTGAAATACCTTAGACTTGTAAAATTACCAAAGTACCCCGATTT
54978108 ACAGAATTAC
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
53 13 0.27
54 35 0.73
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (53 bp):
TAAAATTACTGAAATACCTTAGACTTGTAAAATTACCAAAGTACCCCGATTTG
Found at i:54978118 original size:26 final size:26
Alignment explanation
Indices: 54978086--54978145 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
54978076 CGACTTGTAA
54978086 AATTACCAAAGTACCCCGATTTACAG
1 AATTACCAAAGTACCCCGATTTACAG
*** *
54978112 AATTACCATTTTACCCCGATTTACAT
1 AATTACCAAAGTACCCCGATTTACAG
54978138 AATTACCA
1 AATTACCA
54978146 TTTTACCCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
AATTACCAAAGTACCCCGATTTACAG
Found at i:54978146 original size:26 final size:26
Alignment explanation
Indices: 54978097--54978162 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
54978087 ATTACCAAAG
54978097 TACCCCGATTTACAGAATTACCATTT
1 TACCCCGATTTACAGAATTACCATTT
*
54978123 TACCCCGATTTACATAATTACCATTT
1 TACCCCGATTTACAGAATTACCATTT
*
54978149 TACCCTCGTTTTAC
1 TACCC-CGATTTAC
54978163 CCTCGACTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
26 30 0.81
27 7 0.19
ACGTcount: A:0.27, C:0.29, G:0.06, T:0.38
Consensus pattern (26 bp):
TACCCCGATTTACAGAATTACCATTT
Found at i:54978180 original size:38 final size:37
Alignment explanation
Indices: 54978120--54978200 Score: 126
Period size: 38 Copynumber: 2.2 Consensus size: 37
54978110 AGAATTACCA
* *
54978120 TTTTACCCCGATTTACATAATTACCATTTTACCCTCG
1 TTTTACCCCGACTTACAGAATTACCATTTTACCCTCG
54978157 TTTTACCCTCGACTTACAGAATTACCATTTTACCCTCG
1 TTTTACCC-CGACTTACAGAATTACCATTTTACCCTCG
*
54978195 ATTTAC
1 TTTTAC
54978201 AGAATTATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 8 0.20
38 32 0.80
ACGTcount: A:0.25, C:0.30, G:0.06, T:0.40
Consensus pattern (37 bp):
TTTTACCCCGACTTACAGAATTACCATTTTACCCTCG
Found at i:54978187 original size:27 final size:27
Alignment explanation
Indices: 54978156--54978290 Score: 180
Period size: 27 Copynumber: 5.0 Consensus size: 27
54978146 TTTTACCCTC
* *
54978156 GTTTTACCCTCGACTTACAGAATTACC
1 GTTTTACCCTCGATTTACAGAATTACT
* *
54978183 ATTTTACCCTCGATTTACAGAATTATT
1 GTTTTACCCTCGATTTACAGAATTACT
* *
54978210 GTTTTACCGTCGATTTATAGAATTACT
1 GTTTTACCCTCGATTTACAGAATTACT
** *
54978237 GTTTTACCCTTAATTTACAAAATTACT
1 GTTTTACCCTCGATTTACAGAATTACT
*
54978264 GTTTTACCCTCGATTTACAAAATTACT
1 GTTTTACCCTCGATTTACAGAATTACT
54978291 AAAATACCCT
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (27 bp):
GTTTTACCCTCGATTTACAGAATTACT
Found at i:54978214 original size:54 final size:54
Alignment explanation
Indices: 54978156--54978316 Score: 178
Period size: 54 Copynumber: 3.0 Consensus size: 54
54978146 TTTTACCCTC
* * * *
54978156 GTTTTACCCTCGACTTACAGAATTACCATTTTACCCTCGATTTACAGAATTATT
1 GTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTACT
* * ** *
54978210 GTTTTACCGTCGATTTATAGAATTACTGTTTTACCCTTAATTTACAAAATTACT
1 GTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTACT
* * *** **
54978264 GTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGATTTACAAAATTAC
1 GTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTAC
54978317 CAAAATACCC
Statistics
Matches: 90, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 90 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (54 bp):
GTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTACT
Found at i:54978298 original size:27 final size:27
Alignment explanation
Indices: 54978268--54978487 Score: 162
Period size: 27 Copynumber: 8.1 Consensus size: 27
54978258 ATTACTGTTT
*
54978268 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
*
54978295 TACCCTTGATTTACAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
* *
54978322 TACCCTCGA-TCAGTAAAATTACCAAAA
1 TACCCTCGATTTA-CAAAATTACCAAAA
* ***
54978349 TA-CCTCTAGTTGGTAAAATTACCAAAA
1 TACCCTCGA-TTTACAAAATTACCAAAA
* *** *
54978376 TACCACT-GGTTTGTGAAATTACCGAAA
1 TACC-CTCGATTTACAAAATTACCAAAA
* **
54978403 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
*
54978430 TACCC-CTGATTTACAAAGTTA-CAGAAA
1 TACCCTC-GATTTACAAAATTACCA-AAA
* * * **
54978457 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTCGATTTACAAAATTACCAAAA
54978484 TACC
1 TACC
54978488 TTTGGTTTGT
Statistics
Matches: 156, Mismatches: 27, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
26 12 0.08
27 140 0.90
28 2 0.01
29 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCAAAA
Found at i:54978306 original size:81 final size:81
Alignment explanation
Indices: 54978156--54978316 Score: 178
Period size: 81 Copynumber: 2.0 Consensus size: 81
54978146 TTTTACCCTC
* * * * **** *
54978156 GTTTTACCCTCGACTTACAGAATTACCATTTTACCCTCGATTTACAGAATTATTGTTTTACCGTC
1 GTTTTACCCTCAACTTACAAAATTACCATTTTACCCTCGATTTACAAAATTACTAAAATACCCTC
* *
54978221 GATTTATAGAATTACT
66 GATTTACAAAATTACT
* * ** *
54978237 GTTTTACCCTTAATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTT
1 GTTTTACCCTCAACTTACAAAATTACCATTTTACCCTCGATTTACAAAATTACTAAAATACCCTC
54978302 GATTTACAAAATTAC
66 GATTTACAAAATTAC
54978317 CAAAATACCC
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
81 64 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (81 bp):
GTTTTACCCTCAACTTACAAAATTACCATTTTACCCTCGATTTACAAAATTACTAAAATACCCTC
GATTTACAAAATTACT
Done.