Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 95 of 186
Found at i:31176116 original size:20 final size:20
Alignment explanation
Indices: 31176091--31176133 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
31176081 GAAAATTTGC
* *
31176091 ATTTTTTGTCCCTTTCATAT
1 ATTTTTGGTCCCTCTCATAT
31176111 ATTTTTGGTCCCTCTCATAT
1 ATTTTTGGTCCCTCTCATAT
31176131 ATT
1 ATT
31176134 AATAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.21, G:0.07, T:0.56
Consensus pattern (20 bp):
ATTTTTGGTCCCTCTCATAT
Found at i:31195232 original size:116 final size:116
Alignment explanation
Indices: 31195028--31195261 Score: 389
Period size: 116 Copynumber: 2.0 Consensus size: 116
31195018 TTGACCCGAG
* * *
31195028 CAAAATTTCAGCCATACTTAACTGGAAGCCTCCAAGAAATATTATCGAAGTTCGGAGCTTCTTGG
1 CAAAATCTCAGCCATACTTAACTAGAAACCTCCAAGAAATATTATCGAAGTTCGGAGCTTCTTGG
*
31195093 GGCTCGCCGGTTATTACCGACGATTTGTCAAAGGTTTCTCGATGATAGCCA
66 GACTCGCCGGTTATTACCGACGATTTGTCAAAGGTTTCTCGATGATAGCCA
* * *
31195144 CAAAATCTCAGCCATACTTAACTAGAAACCTCCGAGAAATATTA-CTGAGGTTCGGAGCTTTTTG
1 CAAAATCTCAGCCATACTTAACTAGAAACCTCCAAGAAATATTATC-GAAGTTCGGAGCTTCTTG
31195208 GGACTCGCCGGTTATTACCGACGATTTGTCAAAGGTTTCTCGATGATAGCCA
65 GGACTCGCCGGTTATTACCGACGATTTGTCAAAGGTTTCTCGATGATAGCCA
31195260 CA
1 CA
31195262 CCAATGACGA
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
115 1 0.01
116 109 0.99
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (116 bp):
CAAAATCTCAGCCATACTTAACTAGAAACCTCCAAGAAATATTATCGAAGTTCGGAGCTTCTTGG
GACTCGCCGGTTATTACCGACGATTTGTCAAAGGTTTCTCGATGATAGCCA
Found at i:31198991 original size:39 final size:40
Alignment explanation
Indices: 31198896--31199157 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
31198886 TTGAATGATG
*
31198896 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
31198934 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
31198975 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
31199014 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
31199053 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
31199092 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
31199131 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
31199158 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:31201262 original size:39 final size:39
Alignment explanation
Indices: 31201194--31201309 Score: 196
Period size: 39 Copynumber: 3.0 Consensus size: 39
31201184 AGTATCCGTA
*
31201194 ACACATGCTGGATAACTCAACCACCGGTAGGACGTACGG
1 ACACATGCTGAATAACTCAACCACCGGTAGGACGTACGG
* * *
31201233 CCACAAGCTGAATAACTCAACCACTGGTAGGACGTACGG
1 ACACATGCTGAATAACTCAACCACCGGTAGGACGTACGG
31201272 ACACATGCTGAATAACTCAACCACCGGTAGGACGTACG
1 ACACATGCTGAATAACTCAACCACCGGTAGGACGTACG
31201310 AACTAATACC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (39 bp):
ACACATGCTGAATAACTCAACCACCGGTAGGACGTACGG
Found at i:31214957 original size:50 final size:50
Alignment explanation
Indices: 31214785--31215066 Score: 325
Period size: 49 Copynumber: 5.7 Consensus size: 50
31214775 CTAGTACGCA
** * * *
31214785 TAGTAGCCTGCACTTAGTACTACACATACAACCTAACAATCTTTTATA-G
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGTTACACG
** * * *
31214834 TAGTAGCCTGCACTTAGTACTACACATACAACCTAACAATCTTTTATA-G
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGTTACACG
* * *
31214883 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGTTACACG
* * * * * * *
31214933 TAGTAGCTTGCACTTAGTACTACACACGTGATCGAAGCTATCTGTTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAA-CAATCTGTTACACG
* * *
31214984 TAGTAGCCTACACTTAGTACTACACATGCGACCTAACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGTTACACG
*
31215034 TAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC
31215067 AAAAACCATT
Statistics
Matches: 203, Mismatches: 28, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
49 89 0.44
50 74 0.36
51 40 0.20
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGTTACACG
Found at i:31215017 original size:101 final size:101
Alignment explanation
Indices: 31214764--31215066 Score: 364
Period size: 101 Copynumber: 3.0 Consensus size: 101
31214754 CACTCTTGTA
* * * *
31214764 ACCGAAGCTCTCTAG-TACGCATAGTAGCCTGCACTTAGTACTACACATACAACCTAACAATCTT
1 ACCGAAGCTATCT-GTTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTG
* * ****
31214828 TTATA-GTAGTAGCCTGCACTTAGTACTACACATACA
65 ATACACGTAGTAGCCTGCACTTAGTACTACACACGTG
* * * * * * *
31214864 ACCTAA-CAATCTTTTA--TAGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTG
1 ACCGAAGCTATCTGTTACGCA-TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTG
*
31214926 ATACACGTAGTAGCTTGCACTTAGTACTACACACGTG
65 ATACACGTAGTAGCCTGCACTTAGTACTACACACGTG
* * *
31214963 ATCGAAGCTATCTGTTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTAACAATCTGG
1 ACCGAAGCTATCTGTTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGA
31215028 TACACGTAGTAGCCTGCACTTAGTACTACACACGTG
66 TACACGTAGTAGCCTGCACTTAGTACTACACACGTG
31215064 ACC
1 ACC
31215067 AAAAACCATT
Statistics
Matches: 167, Mismatches: 30, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
97 1 0.01
98 40 0.24
99 36 0.22
100 13 0.08
101 76 0.46
102 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (101 bp):
ACCGAAGCTATCTGTTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGA
TACACGTAGTAGCCTGCACTTAGTACTACACACGTG
Found at i:31217427 original size:21 final size:21
Alignment explanation
Indices: 31217401--31217440 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31217391 ATATGGCCGT
* *
31217401 GTGGCCACTCCACACGCCTGA
1 GTGGCCACCCCAAACGCCTGA
31217422 GTGGCCACCCCAAACGCCT
1 GTGGCCACCCCAAACGCCT
31217441 ATGCCCTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.45, G:0.23, T:0.12
Consensus pattern (21 bp):
GTGGCCACCCCAAACGCCTGA
Found at i:31219322 original size:48 final size:48
Alignment explanation
Indices: 31219242--31219521 Score: 291
Period size: 48 Copynumber: 5.9 Consensus size: 48
31219232 TCTGGGTAAT
* * *
31219242 ATGAGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAT
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAC
* * * * *
31219290 GTGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TAGAAC
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCG-AC
* * *
31219338 ATGAGAGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCCA-CCAT
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATCGAC
* * * *
31219386 ATGAGAGCCAGTGTAAGGCCATGTTTGGGACATGCCATCAGCAATCAGAC
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ATC-GAC
* * *
31219436 --GAGAGCTAGTGTAAGACCATGTCAGGGACATGG-ATCGGCCTCGAC
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAC
** * *
31219481 ATTTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG
31219522 TAATTCACCC
Statistics
Matches: 190, Mismatches: 33, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
45 3 0.02
46 2 0.01
47 35 0.18
48 147 0.77
49 2 0.01
50 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (48 bp):
ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAC
Found at i:31219408 original size:96 final size:96
Alignment explanation
Indices: 31219242--31219521 Score: 330
Period size: 96 Copynumber: 2.9 Consensus size: 96
31219232 TCTGGGTAAT
* * * * *
31219242 ATGAGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGATGTGTGTGCTAGTGTAA
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-CGATATGTGAGCCAGTGTAA
* *
31219306 GACCATGTCTGGGACATGGCATCGGCTAGAAC
65 GACCATGTTTGGGACATGGCATCGGCAAGAAC
* * *
31219338 ATGAGAGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCCACCATATGAGAGCCAGTGTAAG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGTGAGCCAGTGTAAG
* * * ** *
31219403 GCCATGTTTGGGACATGCCATCAGCAATCAG
66 ACCATGTTTGGGACATGGCATCGGCAAGAAC
* * * * * *
31219434 ACGAGAGCTAGTGTAAGACCATGTCAGGGACATGG-ATCGGCCTCGACATTTGAGCCAGTGTAAG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGTGAGCCAGTGTAAG
*
31219498 ACCATGTTTGGAACATGGCATCGG
66 ACCATGTTTGGGACATGGCATCGG
31219522 TAATTCACCC
Statistics
Matches: 154, Mismatches: 29, Indels: 3
0.83 0.16 0.02
Matches are distributed among these distances:
95 44 0.29
96 108 0.70
97 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (96 bp):
ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGTGAGCCAGTGTAAG
ACCATGTTTGGGACATGGCATCGGCAAGAAC
Found at i:31225967 original size:28 final size:28
Alignment explanation
Indices: 31225933--31225989 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
31225923 GAAAAAAGAC
31225933 TAAATCGCATAAAGTGCGAAAGTTTTGT
1 TAAATCGCATAAAGTGCGAAAGTTTTGT
31225961 TAAATCGCATAAAGTGCGAAAGTTTTGT
1 TAAATCGCATAAAGTGCGAAAGTTTTGT
31225989 T
1 T
31225990 CTACTAGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (28 bp):
TAAATCGCATAAAGTGCGAAAGTTTTGT
Found at i:31227045 original size:48 final size:48
Alignment explanation
Indices: 31226980--31227310 Score: 292
Period size: 48 Copynumber: 6.9 Consensus size: 48
31226970 TTTGGGTGAC
* * **
31226980 ATGAGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCTACATTGAT
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAT
* * * * * ** *
31227028 ATGTGTGCTAGTGTAAGACCATGTCTGAGACATAGCATCAGCCA-CAAC
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-GGCATTGAT
* * *
31227076 ATGAGAGCCAGTGTAAGACCATGTCTAGGACATAGCATCGGCATTGAT
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAT
* ** *
31227124 AT-ATGCGCTAGTGTAAGATAATGTCTGGGACATGGCATCGGCCACCT--T
1 ATGA-GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CA-TTGAT
* * * * * *
31227172 ATGAGAGCCAGCGTAAGACCATGTCTGGGACATTGCACCGGCAATGAG
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAT
* * * * * *
31227220 ACGAGAGCTAGTGTAAGACCATATTTGGGACATGGCATCGGCCTCGAC
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAT
* * *
31227268 ATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCA
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
31227311 ATTCACCCTC
Statistics
Matches: 225, Mismatches: 50, Indels: 16
0.77 0.17 0.05
Matches are distributed among these distances:
46 1 0.00
47 6 0.03
48 212 0.94
49 5 0.02
50 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (48 bp):
ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAT
Found at i:31227148 original size:96 final size:96
Alignment explanation
Indices: 31226978--31227310 Score: 380
Period size: 96 Copynumber: 3.5 Consensus size: 96
31226968 CATTTGGGTG
* ** * *
31226978 ACATGAGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCTACATTGATATGTGTGCTAGTGTA
1 ACATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATATGAGCTAGTGTA
* * *
31227043 AGACCATGTCTGAGACATAGCATCAGCCACA
66 AGACCATGTCTGGGACATGGCATCGGCCACA
* * *
31227074 ACATGAGAGCCAGTGTAAGACCATGTCTAGGACATAGCATCGGCATTGATATATGCGCTAGTGTA
1 ACATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATATGAGCTAGTGTA
** *
31227139 AGATAATGTCTGGGACATGGCATCGGCCACC
66 AGACCATGTCTGGGACATGGCATCGGCCACA
** * * * * * *
31227170 TTATGAGAGCCAGCGTAAGACCATGTCTGGGACATTGCACCGGCAATGAGACGA-GAGCTAGTGT
1 ACATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATA-TATGAGCTAGTGT
* * * *
31227234 AAGACCATATTTGGGACATGGCATCGGCCTCG
65 AAGACCATGTCTGGGACATGGCATCGGCCACA
* * * *
31227266 ACATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCA
1 ACATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
31227311 ATTCACCCTC
Statistics
Matches: 198, Mismatches: 38, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
96 197 0.99
97 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.23
Consensus pattern (96 bp):
ACATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATATGAGCTAGTGTA
AGACCATGTCTGGGACATGGCATCGGCCACA
Found at i:31232045 original size:3 final size:3
Alignment explanation
Indices: 31232033--31232237 Score: 240
Period size: 3 Copynumber: 68.0 Consensus size: 3
31232023 ATATGAAAGC
31232033 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31232080 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
31232128 ATA ATA ATA ATGA A-A ATGA AGA ATA ATA ATA ATA CATAA ATA ATA ATA
1 ATA ATA ATA AT-A ATA AT-A ATA ATA ATA ATA ATA -AT-A ATA ATA ATA
** * * * * *
31232176 A-A ATCA GGA ATA ATA ATA ATG ACA ACA ACA AT- GTAA ATA ATA AT-
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
*
31232220 ATA AAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA
31232238 GAAAGTGGAA
Statistics
Matches: 177, Mismatches: 14, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
2 9 0.05
3 157 0.89
4 10 0.06
5 1 0.01
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:31235205 original size:36 final size:36
Alignment explanation
Indices: 31235153--31235224 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
31235143 AGCTCCAAGC
* *
31235153 CCACTATGGTTGGGGATTACCTGCGTGGATGAAAAT
1 CCACTACGGTTCGGGATTACCTGCGTGGATGAAAAT
31235189 CCACTACGGTTCGGGATTACCTGCGTGGATGAAAAT
1 CCACTACGGTTCGGGATTACCTGCGTGGATGAAAAT
31235225 AAAAAGGGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (36 bp):
CCACTACGGTTCGGGATTACCTGCGTGGATGAAAAT
Found at i:31237272 original size:26 final size:26
Alignment explanation
Indices: 31237236--31237344 Score: 182
Period size: 26 Copynumber: 4.2 Consensus size: 26
31237226 ATGAAATGCC
*
31237236 TATCATGGAACATTTACCTAAACCAT
1 TATCATGGAACATTTACCTAACCCAT
*
31237262 TATCATAGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
* *
31237288 TATCATGGAATATTTACCTAATCCAT
1 TATCATGGAACATTTACCTAACCCAT
31237314 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
31237340 TATCA
1 TATCA
31237345 ATTTGTACTA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (26 bp):
TATCATGGAACATTTACCTAACCCAT
Found at i:31239529 original size:15 final size:15
Alignment explanation
Indices: 31239509--31239539 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31239499 AAGCGACCAC
31239509 CTTACCCTCTTGCAT
1 CTTACCCTCTTGCAT
31239524 CTTACCCTCTTGCAT
1 CTTACCCTCTTGCAT
31239539 C
1 C
31239540 AATACACATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.42, G:0.06, T:0.39
Consensus pattern (15 bp):
CTTACCCTCTTGCAT
Found at i:31242248 original size:12 final size:12
Alignment explanation
Indices: 31242231--31242261 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31242221 AGTACTACCT
31242231 CGGCCTCAACCA
1 CGGCCTCAACCA
*
31242243 CGGCCTCGACCA
1 CGGCCTCAACCA
31242255 CGGCCTC
1 CGGCCTC
31242262 TTCCCCGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.52, G:0.23, T:0.10
Consensus pattern (12 bp):
CGGCCTCAACCA
Found at i:31256535 original size:25 final size:27
Alignment explanation
Indices: 31256498--31256550 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
31256488 TCAAACATGC
31256498 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
31256524 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
31256550 A
1 A
31256551 AAACTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:31257976 original size:42 final size:42
Alignment explanation
Indices: 31257917--31258000 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
31257907 TTCTCTTCTC
31257917 TAACTTTCGGCTATGATGAACAAAGATGGACAAAACTTTGTT
1 TAACTTTCGGCTATGATGAACAAAGATGGACAAAACTTTGTT
31257959 TAACTTTCGGCTATGATGAACAAAGATGGACAAAACTTTGTT
1 TAACTTTCGGCTATGATGAACAAAGATGGACAAAACTTTGTT
31258001 CTTTTCACCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (42 bp):
TAACTTTCGGCTATGATGAACAAAGATGGACAAAACTTTGTT
Found at i:31258114 original size:26 final size:26
Alignment explanation
Indices: 31258079--31258237 Score: 239
Period size: 26 Copynumber: 6.2 Consensus size: 26
31258069 TGAAATGCCC
*
31258079 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
31258105 ATCATAGAACATTTACTTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
31258131 ATCATGGAATATTTGCCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
31258157 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
31258183 ATC-TGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
31258208 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
31258234 ATCA
1 ATCA
31258238 ATTTGTACCA
Statistics
Matches: 117, Mismatches: 15, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
25 23 0.20
26 94 0.80
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:31258211 original size:51 final size:52
Alignment explanation
Indices: 31258079--31258237 Score: 266
Period size: 51 Copynumber: 3.1 Consensus size: 52
31258069 TGAAATGCCC
* * * *
31258079 ATCATGGAACATTTACCTAAACCATTATCATAGAACATTTACTTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
*
31258131 ATCATGGAATATTTGCCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
31258183 ATC-TGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
31258234 ATCA
1 ATCA
31258238 ATTTGTACCA
Statistics
Matches: 100, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
51 50 0.50
52 50 0.50
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (52 bp):
ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
Found at i:31260334 original size:27 final size:27
Alignment explanation
Indices: 31260284--31260394 Score: 170
Period size: 27 Copynumber: 4.1 Consensus size: 27
31260274 AGCGTGGCTG
* *
31260284 CCAGAAAAGATA-ATGTGACAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
31260310 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
31260337 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
* * *
31260364 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
31260391 CCAG
1 CCAG
31260395 GACGCTTCCT
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
26 11 0.14
27 68 0.86
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (27 bp):
CCAGAACAGATATATGTGGCAGAGCCA
Found at i:31284283 original size:57 final size:58
Alignment explanation
Indices: 31284166--31284287 Score: 194
Period size: 57 Copynumber: 2.1 Consensus size: 58
31284156 ACAAAAATGG
* *
31284166 TGAAAATGGAGAAATGAGAAATTTTGGAAATGAAATATGGTTTTCTCCAAAATGAAAA
1 TGAAAAAGGAGAAATGAGAAAATTTGGAAATGAAATATGGTTTTCTCCAAAATGAAAA
*
31284224 TGAAAAAGGAGAAATG-GAAACATTTGGAAAT-AAATGTGGTTTTCTCCAAAATGAAAA
1 TGAAAAAGGAGAAATGAGAAA-ATTTGGAAATGAAATATGGTTTTCTCCAAAATGAAAA
31284281 TGAAAAA
1 TGAAAAA
31284288 TGACCTGGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
57 36 0.60
58 24 0.40
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.25
Consensus pattern (58 bp):
TGAAAAAGGAGAAATGAGAAAATTTGGAAATGAAATATGGTTTTCTCCAAAATGAAAA
Found at i:31285230 original size:18 final size:19
Alignment explanation
Indices: 31285204--31285243 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
31285194 TGTCAAACAT
*
31285204 AAATTAAAAAT-ATTTTAA
1 AAATAAAAAATAATTTTAA
*
31285222 AAATAAAAATTAATTTTAA
1 AAATAAAAAATAATTTTAA
31285241 AAA
1 AAA
31285244 GTATAAAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATAAAAAATAATTTTAA
Found at i:31292729 original size:17 final size:17
Alignment explanation
Indices: 31292702--31292735 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
31292692 AATGTAAACT
31292702 TAAAATATTTATAAAAAA
1 TAAAATATTTA-AAAAAA
31292720 TAAAAT-TTTAAAAAAA
1 TAAAATATTTAAAAAAA
31292736 AAAGACTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATATTTAAAAAAA
Found at i:31292736 original size:17 final size:18
Alignment explanation
Indices: 31292702--31292736 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
31292692 AATGTAAACT
*
31292702 TAAAATATTTATAAAAAA
1 TAAAATATTTAAAAAAAA
31292720 TAAAAT-TTTAAAAAAAA
1 TAAAATATTTAAAAAAAA
31292737 AAGACTCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATTTAAAAAAAA
Found at i:31294137 original size:18 final size:18
Alignment explanation
Indices: 31294114--31294151 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
31294104 ACTTTGTTCC
31294114 TTCAAATTCTTTAGATTA
1 TTCAAATTCTTTAGATTA
31294132 TTCAAATTCTTTAGATTA
1 TTCAAATTCTTTAGATTA
31294150 TT
1 TT
31294152 TACACTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (18 bp):
TTCAAATTCTTTAGATTA
Found at i:31298445 original size:16 final size:16
Alignment explanation
Indices: 31298424--31298454 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31298414 ATTTGGTAGG
31298424 AAAGAAAAAAAAATTA
1 AAAGAAAAAAAAATTA
*
31298440 AAAGAAAAAGAAATT
1 AAAGAAAAAAAAATT
31298455 TCATTTCCAT
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:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (16 bp):
AAAGAAAAAAAAATTA
Found at i:31309928 original size:20 final size:21
Alignment explanation
Indices: 31309903--31309941 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31309893 AGAGCAATTG
*
31309903 TTCTTTT-TTGTTCTCCCTCT
1 TTCTTTTCTTGGTCTCCCTCT
31309923 TTCTTTTCTTGGTCTCCCT
1 TTCTTTTCTTGGTCTCCCT
31309942 TTGAACTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.00, C:0.31, G:0.08, T:0.62
Consensus pattern (21 bp):
TTCTTTTCTTGGTCTCCCTCT
Found at i:31311381 original size:23 final size:23
Alignment explanation
Indices: 31311355--31311400 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
31311345 ATGAATTACA
31311355 TAGAAAATACATCAAAGAATATC
1 TAGAAAATACATCAAAGAATATC
31311378 TAGAAAATACATCAAAGAATATC
1 TAGAAAATACATCAAAGAATATC
31311401 ATACAGTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.13, G:0.09, T:0.22
Consensus pattern (23 bp):
TAGAAAATACATCAAAGAATATC
Found at i:31323563 original size:10 final size:10
Alignment explanation
Indices: 31323548--31323583 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
31323538 GTGATCACAA
31323548 ATAAATAAAG
1 ATAAATAAAG
31323558 ATAAATAAAG
1 ATAAATAAAG
31323568 ATAAATGAAA-
1 ATAAAT-AAAG
31323578 ATAAAT
1 ATAAAT
31323584 CCTAGAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 22 0.88
11 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (10 bp):
ATAAATAAAG
Found at i:31324919 original size:19 final size:19
Alignment explanation
Indices: 31324877--31324918 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
31324867 TGAAAAGAAC
* *
31324877 TAAAATTTTTGAGGGGAAG
1 TAAAACTTTTGAGGGGAAA
31324896 TAAAACTTTT-AGGGGAAA
1 TAAAACTTTTGAGGGGAAA
31324914 TAAAA
1 TAAAA
31324919 AGAAAAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.45, C:0.02, G:0.24, T:0.29
Consensus pattern (19 bp):
TAAAACTTTTGAGGGGAAA
Found at i:31328401 original size:24 final size:22
Alignment explanation
Indices: 31328360--31328409 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
31328350 ATTTGCTCTC
* *
31328360 ATTTAGTATTTATCTTCGGGACT
1 ATTTAGTATTTAGCTTC-GAACT
*
31328383 ATTTATGTATTTAGGTTCGAACT
1 ATTTA-GTATTTAGCTTCGAACT
31328406 ATTT
1 ATTT
31328410 TGGGTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.50
Consensus pattern (22 bp):
ATTTAGTATTTAGCTTCGAACT
Found at i:31329184 original size:20 final size:21
Alignment explanation
Indices: 31329155--31329194 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
31329145 AATATAAACA
*
31329155 TATCATATC-ATTCTTTCTAC
1 TATCACATCAATTCTTTCTAC
31329175 TATCACATCAAATTCTTTCT
1 TATCACATC-AATTCTTTCT
31329195 CGTTTCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (21 bp):
TATCACATCAATTCTTTCTAC
Found at i:31329849 original size:7 final size:7
Alignment explanation
Indices: 31329839--31329864 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31329829 ATATTATATT
31329839 CATATCA
1 CATATCA
31329846 CATATCA
1 CATATCA
31329853 CATATCA
1 CATATCA
31329860 CATAT
1 CATAT
31329865 TAATTATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (7 bp):
CATATCA
Found at i:31334771 original size:17 final size:17
Alignment explanation
Indices: 31334749--31334787 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
31334739 CAAGAGAAGG
31334749 GATTTCAACTTGGGACT
1 GATTTCAACTTGGGACT
31334766 GATTTCAACTTGGGACT
1 GATTTCAACTTGGGACT
31334783 GATTT
1 GATTT
31334788 AAATATGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (17 bp):
GATTTCAACTTGGGACT
Found at i:31336841 original size:42 final size:42
Alignment explanation
Indices: 31336746--31336902 Score: 201
Period size: 43 Copynumber: 3.7 Consensus size: 42
31336736 AACGAGATGA
*
31336746 GATTATGTGTAAGACCATGTCTGGGACATTGGCATC-ATATT
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATATT
*
31336787 GTTATTACGTGTAAGACCATGTCTGGGACATT-GCATCGTTATAT
1 G--ATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATAT-T
* *
31336831 GATTTCGTGTAAGACCATGTTTGGGACATTGGCATCGATATGT
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATAT-T
* * *
31336874 GATAACATGTAAGACCATATCTGGGACAT
1 GATTACGTGTAAGACCATGTCTGGGACAT
31336903 GACATTATAC
Statistics
Matches: 100, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.01
42 32 0.32
43 65 0.65
44 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (42 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGATATT
Found at i:31339542 original size:555 final size:555
Alignment explanation
Indices: 31338365--31341477 Score: 4306
Period size: 555 Copynumber: 5.6 Consensus size: 555
31338355 GGGTGTTACA
* * *
31338365 TTCAGGATCGATCTTGGAATTCAAGATTTCAAATTTGGTGCTGATTTAGATGAGGACAAATGTAA
1 TTCAGGATCGATCTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTTAGATGAGGACAAATGGAA
* * * *
31338430 GCAATAGATTAACGGAGATGGTGCACAATCTTGATACAAAAAGAAGACGAAAGAGATGGCAAAAG
66 GCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAGATGGTAAAAT
* * * * * * *
31338495 GGGAGGTGCATGCAACAACAACAATGGAAG-AAAGGAAAAAAA-A-GAAAATCAAAGAGAATGAG
131 GGGAGGTGTAGGCGACAACAACAATAGAGGAAAAGAAAAAAAACATTAAAATCAAAGAGAATGAG
* *
31338557 AGGAGGAGAGGAATGGCTAAGGCAATGAGGAGGAGGATTAAAGGCTGATTATTTGTGAAAAAATA
196 AGGAGGAGAGGAATGACTAGGGCAATGAGGAGGAGGATTAAAGGCTGATTATTTGTGAAAAAATA
*
31338622 ATACTTATACCTAGGTTTACTAGGCTTGGACGACACACACATTAAAACAAAGGGTTTTTGTCAAA
261 ATACTTATACCTAGGTTTACTAGGCTTGGACGACACACACATTAAAACAAGGGGTTTTTGTCAAA
*
31338687 AAATTAAATTATTTGCAAGAGAAGGGATTTGAACTTGGGACTGATTTAAATATGATTTAAAGACC
326 AAATTAAATTATTTGCAAGAGAAGGGATTTGAACTTGGGACTGATTTAAATACGATTTAAAGACC
* *
31338752 CATTTAAAAAATTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATTCCAAATCTGGAAA
391 CA-TTAAAAAACTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATTCCAAATCTAGAAA
* * *
31338817 TTTAAGTTTTT-ACTGGGCAAGATTA-ATAAAAAAATTGAAGAAAGAAGAGCTCTTACCCAAGCT
455 TTTAGGTTTTTAAAT-GGCAAGATTATAAAAAAAAATTGAAGAAAGAAGAGCTCTTACCCAAGCT
* *
31338880 AGTTGAGAGAAACGATAATGGCACTTTCTTGGAAATG
519 AGTTGAGAGAAACGATAATGCCACTTTCTTGGCAATG
* * * *
31338917 TTTAGGATTGATCTTTGAGTTCAAGATTTCAGATTTGGTGTTGATTTAGATGAGGACAAATGGAA
1 TTCAGGATCGATCTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTTAGATGAGGACAAATGGAA
* * * * *
31338982 GCAATAGATTAAATGATATGGTGCACAATCTTGCTACAAAAA-AAGAAGAAAAAGATGGTAAAAG
66 GCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAGATGGTAAAAT
* * * * *
31339046 GGGAGGTGTACGCGACAACAACAATAGATGAAAAG-AAAAGAATATTAGAAATCAAAGAGAATGG
131 GGGAGGTGTAGGCGACAACAACAATAGAGGAAAAGAAAAAAAACATTA-AAATCAAAGAGAATGA
* * * *
31339110 GAGGAGGAGAGGAATGAATAGGGCAATGAGGAGGAGGATTAAATGTTGATTATTTGTGAAAAATT
195 GAGGAGGAGAGGAATGACTAGGGCAATGAGGAGGAGGATTAAAGGCTGATTATTTGTGAAAAAAT
** *
31339175 AATACTTATACCTAGGTTTACTAGGCTCAGACGACACACAAATTAAAACAAGGGGTTTTTGTCAA
260 AATACTTATACCTAGGTTTACTAGGCTTGGACGACACACACATTAAAACAAGGGGTTTTTGTC-A
* * * *
31339240 AAAAATTAAATTATTTGTAAGAGAAGGGATTTGAACTTGAGACTGATTAAAATATGATTTAAAGA
324 AAAAATTAAATTATTTGCAAGAGAAGGGATTTGAACTTGGGACTGATTTAAATACGATTTAAAGA
* * * *
31339305 CCCATT-AAAAACTGAAAAAATATATTTAAAATAATCAAAATTCTCTCAAATTCAAAATCTGGAA
389 CCCATTAAAAAACTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATTCCAAATCTAGAA
* * * *
31339369 ATTTAGGTTTTTAAATGGCAATATTAGTAAAAAAAAATTGAAGAAATAAGACCTCTTACCCAAAC
454 ATTTAGGTTTTTAAATGGCAAGATTA-TAAAAAAAAATTGAAGAAAGAAGAGCTCTTACCCAAGC
* *
31339434 TAGTTGAGAGAAAAGATAATGCCATTTTCTTAGG-AATG
518 TAGTTGAGAGAAACGATAATGCCACTTTCTT-GGCAATG
* * * *
31339472 TTCAGGATCGATATTCGAGTTCAAGATTTTAGATTTGGTG-TAGATTTAGATGAGGATAAATGGA
1 TTCAGGATCGATCTTGGAGTTCAAGATTTCAGATTTGGTGCT-GATTTAGATGAGGACAAATGGA
* *
31339536 AGCAATAGATTAAAGGAGATGGTGCACAATATTGATACAAACAGAAGAAGAAAGAGATGGTAAAA
65 AGCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAGATGGTAAAA
* * * * * *
31339601 -GGAATGGTGTAGGCCAGAACAAAAATAGAGGAAAAGAAAAAAAAACATTAAAATCAAATAGATT
130 TGGGA-GGTGTAGGCGACAACAACAATAGAGGAAAAG-AAAAAAAACATTAAAATCAAAGAGAAT
* * ** ** *
31339665 GAGAGGAGGAAAGGAATGAGTAGGATAACT-AGGAGGAGGATTAAAGATTGATTATTTGTAAAAA
193 GAGAGGAGGAGAGGAATGACTAGGGCAA-TGAGGAGGAGGATTAAAGGCTGATTATTTGTGAAAA
* * * * * * *
31339729 AATAAAATTTATACCTTGATTTACTAGGCTTGGATG--ACACACATTAAAATAAGGGGGTTTTGT
257 AATAATACTTATACCTAGGTTTACTAGGCTTGGACGACACACACATTAAAACAAGGGGTTTTTGT
* * * * *
31339792 CAAAAAATTAAACTATTTGCAAGAGAAGGGATTTGAACTGGGGATTGATTTACATACGATTTCAA
322 CAAAAAATTAAATTATTTGCAAGAGAAGGGATTTGAACTTGGGACTGATTTAAATACGATTTAAA
* *
31339857 GACCCATTAAAAAACTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATTCCAAATTTTG
387 GACCCATTAAAAAACTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATTCCAAATCTAG
* * * *
31339922 AAATTTAGGTTTTT-AATTGCAAAGATTAGTAAAAAAAAGAATTGAAGACAGAAGATCCTCATAC
452 AAATTTAGGTTTTTAAATGGC-AAGATTA-T-AAAAAAA-AATTGAAGAAAGAAGA-GCTCTTAC
* *
31339986 CAAAGCTAGTTCAGAGAAACGATAATGCCACTTTCTTGGCAATG
512 CCAAGCTAGTTGAGAGAAACGATAATGCCACTTTCTTGGCAATG
* * *
31340030 TTTAGGATCGATCTTGGAGTTTAAGATTTTAGATTTGGTGCTGATTTAGATGAGGACAAATGGAA
1 TTCAGGATCGATCTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTTAGATGAGGACAAATGGAA
* *
31340095 GCAATAGATTAAAGGGGATGGTGCACAATCTTGATTCAAAAAGAAGAAGAAAGAGATGGTAAAAT
66 GCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAGATGGTAAAAT
* * *
31340160 GGGAGGTGTAGGTGACAACAACAATGGAGG-AAAGAAAAAAAAACATTAAAATCAAAGAAAATGA
131 GGGAGGTGTAGGCGACAACAACAATAGAGGAAAAG-AAAAAAAACATTAAAATCAAAGAGAATGA
* * * * * *
31340224 GAGGAGGAGTGGAATTACTCGAGCAATGAGGAGAAGAATTAAAGGCTGATTATTTGTGAAAAAAT
195 GAGGAGGAGAGGAATGACTAGGGCAATGAGGAGGAGGATTAAAGGCTGATTATTTGTGAAAAAAT
*
31340289 AATACTTATACCTAGGTTTACTCGGCTTGGACGACACACACATT-AAACAAGGGGTTTTTGTCAA
260 AATACTTATACCTAGGTTTACTAGGCTTGGACGACACACACATTAAAACAAGGGGTTTTTGTCAA
* *
31340353 AAAATTAAATTATTTGCAAGAGAAGGGATTTGAACTTGGGATTGATTTAAATACGATTTAAAGAG
325 AAAATTAAATTATTTGCAAGAGAAGGGATTTGAACTTGGGACTGATTTAAATACGATTTAAAGAC
* * * *
31340418 CCATTAAAAAACTGAGAAAATATATTTAAAATAATAAAAATTCTCCAAAATTCCAAATCTAGAAA
390 CCATTAAAAAACTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATTCCAAATCTAGAAA
* * *
31340483 TTTAGGTTTTTAATTGGCATGATTA-ATAAAAAAAA-TGAAGAAAGAAGAGCTCTTACCTAAGCT
455 TTTAGGTTTTTAAATGGCAAGATTATA-AAAAAAAATTGAAGAAAGAAGAGCTCTTACCCAAGCT
*
31340546 AGTTGAGAGAAACGATAATACCACTTTCTTGGCAATG
519 AGTTGAGAGAAACGATAATGCCACTTTCTTGGCAATG
* * *
31340583 TTTAGGATTGATCTTGGAGTTCAAGATTTTAGATTTGGTGCTGATTTAGATGAGGACAAAT-GAT
1 TTCAGGATCGATCTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTTAGATGAGGACAAATGGA-
*
31340647 AGCAATAGATTAAAGGGGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAGATGGTAAAA
65 AGCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAGATGGTAAAA
* * * *
31340712 TGGGAGGTGTAGGCGACAACGACGATAGAGAAAAAGAAAAAGAAAACATTAAAATTAAAGAGAAT
130 TGGGAGGTGTAGGCGACAACAACAATAGAGGAAAAG-AAAA-AAAACATTAAAATCAAAGAGAAT
* * *
31340777 GAGAGGAGGAGAGGAATGACTA-GGCAATGAGGAGAAGGACTAAATGCTGATTATTTGTGAAAAA
193 GAGAGGAGGAGAGGAATGACTAGGGCAATGAGGAGGAGGATTAAAGGCTGATTATTTGTGAAAAA
* * *
31340841 ATAATACTTATACCTAGGTTTACTAAGCTTGGACGACACACACATTAAAACAATGGGCTTTTGTC
258 ATAATACTTATACCTAGGTTTACTAGGCTTGGACGACACACACATTAAAACAAGGGGTTTTTGTC
31340906 AAAAAATTAAATTATTT-CTAA-AGAAGGGATTTGAACTTGGGACTGATTTAAATACGATTTAAA
323 AAAAAATTAAATTATTTGC-AAGAGAAGGGATTTGAACTTGGGACTGATTTAAATACGATTTAAA
* *
31340969 GACGCATTAAAAAAATGAAAAAA-A-A-TTAAAATCATCAAAATTCTCCCAAATTCCAAATCTAG
387 GACCCATTAAAAAACTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATTCCAAATCTAG
* * * * *
31341031 AAATTTAGATTTTTAATTGGCAAGATTA-ATAAAAAAA-TGAAGAAAGAAAAGCTCTAACCCAAG
452 AAATTTAGGTTTTTAAATGGCAAGATTATAAAAAAAAATTGAAGAAAGAAGAGCTCTTACCCAAG
* *
31341094 CTAGTTGAGAGAAACGACAAAT-ACACTTTCTTGGCAATG
517 CTAGTTGAGAGAAACGA-TAATGCCACTTTCTTGGCAATG
* * * * * * *
31341133 TTCAGGATCGATCTTGGGGTGCAGGATTTCAGATTAGGTGCTGATTTAAATGAAGATAAATGGAA
1 TTCAGGATCGATCTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTTAGATGAGGACAAATGGAA
* *
31341198 GCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAAAATAAAGAGATGGTAAAAT
66 GCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAGATGGTAAAAT
** * *
31341263 GGGAGGTGTAGATGACAACAACAATGGAGGCAAAGAAAAAAAACATTAAAATCAAAGAGAATGAG
131 GGGAGGTGTAGGCGACAACAACAATAGAGGAAAAGAAAAAAAACATTAAAATCAAAGAGAATGAG
* * * * *
31341328 GGGAGGAGCGGAATGAATAGGGAAATGAGGAGGAGGATTAAAGGCTGATTATTTGTGAAGAAATA
196 AGGAGGAGAGGAATGACTAGGGCAATGAGGAGGAGGATTAAAGGCTGATTATTTGTGAAAAAATA
* *
31341393 ATACTTATACCTAGGTTTACTAGGCTTGGACGACACACACATTATAACAATGTGG-TTTTGTCAA
261 ATACTTATACCTAGGTTTACTAGGCTTGGACGACACACACATTAAAACAA-GGGGTTTTTGTCAA
31341457 AAAATTAAATTATTTGCAAGA
325 AAAATTAAATTATTTGCAAGA
31341478 TAAAACAAGG
Statistics
Matches: 2279, Mismatches: 243, Indels: 80
0.88 0.09 0.03
Matches are distributed among these distances:
548 41 0.02
549 118 0.05
550 209 0.09
551 116 0.05
552 104 0.05
553 272 0.12
554 370 0.16
555 405 0.18
556 62 0.03
557 218 0.10
558 347 0.15
559 17 0.01
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (555 bp):
TTCAGGATCGATCTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTTAGATGAGGACAAATGGAA
GCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAGATGGTAAAAT
GGGAGGTGTAGGCGACAACAACAATAGAGGAAAAGAAAAAAAACATTAAAATCAAAGAGAATGAG
AGGAGGAGAGGAATGACTAGGGCAATGAGGAGGAGGATTAAAGGCTGATTATTTGTGAAAAAATA
ATACTTATACCTAGGTTTACTAGGCTTGGACGACACACACATTAAAACAAGGGGTTTTTGTCAAA
AAATTAAATTATTTGCAAGAGAAGGGATTTGAACTTGGGACTGATTTAAATACGATTTAAAGACC
CATTAAAAAACTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATTCCAAATCTAGAAAT
TTAGGTTTTTAAATGGCAAGATTATAAAAAAAAATTGAAGAAAGAAGAGCTCTTACCCAAGCTAG
TTGAGAGAAACGATAATGCCACTTTCTTGGCAATG
Found at i:31342828 original size:556 final size:554
Alignment explanation
Indices: 31341643--31345216 Score: 3858
Period size: 554 Copynumber: 6.4 Consensus size: 554
31341633 AAGTTTTTAA
*
31341643 TTGGCAATGTTTAGGATCGATCTTT-GAGTTCAAGATTTCAGATTTGGTGCTGATGTAGATGAGG
1 TTGGCAATGTTTAGGATCGAT-TTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTTAGATGA-G
* * * * *
31341707 GA-AAATGGAAGCAATAGATTAAAGGATATGGTGCACAATCGTGATGCAACAAGAAGAAGAAAAA
64 GACAAATGGAAGCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGA
* * * * * *
31341771 GATGGTAAAAGGGGTGGTGTAAGCCAGAACAACAATGGAGGAAAAGAAAAAAAA-ATTAAAATCA
129 GATGGTAAAATGGGAGGTGTAGGCGACAACAACAATGGAGGAAAGGAAAAAAAACATTAAAATCA
* * * * *
31341835 AATAGATTGAGAGGAGGAGAGGAATGAGTAGGGCAATGAGGAGGAGGATTAAAGACTAATTATTT
194 AAGAGAATGAGAGGAGGAGAGGAATGAGTAGGGAAATGAGGAGGAGGATTAAAGGCTGATTATTT
** * *
31341900 GTGAAAGAATAGCAC-TTACACCTAGGTTTACTAAGCTTGGACGACACACACATTAAAACAAGGG
259 GTGAAA-AATAATACTTTATACCTAGGTTTACTAGGCTTGGACGACACACACATTAAAACAA-GG
* * * ** * * *
31341964 GGTTTTGTC-AAAAATTTAAATTGTTTGCAAAAGAAGGGATTTGAACTCAGGATTGATTTACATT
322 GGTTTTGTCAAAAAAATTAAATTATTTGCAGAAGAAGGGATTTGAACTTGGGACTGATTTAAATA
* * * *
31342028 CGATTTGAAGACCAATTAAAAAACTAAAAAAATGTATTTAAAATCATCAAAATTCTCCCAAATTA
387 CGATTTAAAGACCCATTAAAAAACTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATT-
* * * *
31342093 CAAAAT-TTGAAATTTAGGTTTTTAATTGG-AAGGTTTAGTAAAAAAAATTGAAGAAAGCAA-AG
451 CCAAATCTTGAAATTTAGGTTTTTAATTGGCAA-GATGAAT-AAAAAAATTGAAGAAAG-AAGAG
* * * *
31342155 CTCTTACCAAAGCTAGTTCTA-AGAAACGATAGTGACACTTTC
513 CTCTTACCCAAGCTAGTT-GAGAGAAACGATAATGCCACTTTC
** * *
31342197 TTGGCAATGTTTAGGATCGACCTTGGAGGTCAATATTTCAGATTTGGTGCTGATTTAGATGAGGA
1 TTGGCAATGTTTAGGATCGATTTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTTAGATGAGGA
* *
31342262 CAAATGGAAGCAATAGATTAAAGGGGATGGTGCACAATCTTGATACAAAAAGAAGAAGAATGAGA
66 CAAATGGAAGCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAGA
*
31342327 TGGTAAAATGGGAGGTGTGGGCGACAACAACAATGGAGGAAAGGAAAAAAAACATTAAAATCAAA
131 TGGTAAAATGGGAGGTGTAGGCGACAACAACAATGGAGGAAAGGAAAAAAAACATTAAAATCAAA
* * *
31342392 GAGAATGAGAGGAGGAGATGAATGAGTAGGGAAATGAGGAGGTGGATTAAAGGCTGATCATTTGT
196 GAGAATGAGAGGAGGAGAGGAATGAGTAGGGAAATGAGGAGGAGGATTAAAGGCTGATTATTTGT
* *
31342457 GATAAAATAATACTTATATACCTAGGTTTACTAGGCTTGGATGACGCACACATTAAAACAAGTGG
261 GA-AAAATAATACTT-TATACCTAGGTTTACTAGGCTTGGACGACACACACATTAAAACAAG-GG
* *
31342522 GTTTTGACAAAAAAAATTAAATTATTTGCAGAAGAAGAGATTTGAACTTGGGACTGATTTAAATA
323 GTTTTGTC-AAAAAAATTAAATTATTTGCAGAAGAAGGGATTTGAACTTGGGACTGATTTAAATA
* * * *
31342587 TGATTTAAAGACCCATT-AAAAACTGAGAAAATATATTTAAAATCATCAAAGTTCTCCTAAATTC
387 CGATTTAAAGACCCATTAAAAAACTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATTC
*
31342651 CAAATCTAGAAATTTAGGTTTTTAATTGGCAAGATGAATAAAAAAA-TGAAGAAAGAAGAGCTCT
452 CAAATCTTGAAATTTAGGTTTTTAATTGGCAAGATGAATAAAAAAATTGAAGAAAGAAGAGCTCT
*
31342715 TACCCAAGCTAGTTGAGAGAAACGATAATGCCACTATC
517 TACCCAAGCTAGTTGAGAGAAACGATAATGCCACTTTC
* * * *
31342753 TTAGCAATGTTCAGGGTCGATTTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTT-GAAAGAGG
1 TTGGCAATGTTTAGGATCGATTTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTTAG-ATGAGG
*
31342817 ACAAATGGAAGCAATAGATTAAAGGGGATGGTGCACAATCTTGATACAAAAA-AA-AAGAAAGAG
65 ACAAATGGAAGCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAG
* *
31342880 ATGGTAAAATGGGAGGTGTAGGCAACAACAACAATGGAGGAAAGG-AAAAAATCATTAAAATCAA
130 ATGGTAAAATGGGAGGTGTAGGCGACAACAACAATGGAGGAAAGGAAAAAAAACATTAAAATCAA
* * * * *
31342944 AGAGAATGAGAGGAGGAGATGAATGAGTAGGGCAATAAGGAGGTGGGTTAAAGGCTGATTATTTG
195 AGAGAATGAGAGGAGGAGAGGAATGAGTAGGGAAATGAGGAGGAGGATTAAAGGCTGATTATTTG
* * * *
31343009 TGAGAAAATAATAC-TTATGCCTAGGTTTACTAGGATTGGATGACACACACAATAAAACAAGGGG
260 TGA-AAAATAATACTTTATACCTAGGTTTACTAGGCTTGGACGACACACACATTAAAACAAGGGG
* * *
31343073 TTTTTGTCAAAAAAAAATTAAATTGTTTGCAGGAGAAGGGATTTGAACTTGGGACTAATTTAAAT
324 -TTTTGTC--AAAAAAATTAAATTATTTGCAGAAGAAGGGATTTGAACTTGGGACTGATTTAAAT
* * ** *
31343138 ATGATTTAAAGAACCATTAAAAATTTGAAAAATATATATTTAAAATCATTAAAATTCTCCCAAAT
386 ACGATTTAAAGACCCATTAAAAAACTGAAAAA-ATATATTTAAAATCATCAAAATTCTCCCAAAT
* * * * * *
31343203 TCCAAATCTTTAAATTTAGGTTTTTAATTAGAAACATTAATAAAAAAATTGAAGAAAGAAGAGTT
450 TCCAAATCTTGAAATTTAGGTTTTTAATTGGCAAGATGAATAAAAAAATTGAAGAAAGAAGAGCT
*
31343268 CTTACCCAAGCTAGTTGAGAGAAACGATAATGTCACTTTC
515 CTTACCCAAGCTAGTTGAGAGAAACGATAATGCCACTTTC
* * * * * * *
31343308 TTGGCAATGTTCAGGATCGATCTTCGAGTTCAATATTTTAGATTTGGTGTTGATTTAGATAAGGA
1 TTGGCAATGTTTAGGATCGATTTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTTAGATGAGGA
* * * * * * *
31343373 TAAACGAAAGAAATAGATTAAAGGAGATGGTGAACAATCTTGGTACAAAAAGAAAAAGAAAGAGA
66 CAAATGGAAGCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAGA
*
31343438 TGGTAAAAGGGGAGGTGTAGGCGACAACAACAATGGAGGAAA-GAAAAAAAACATTAAAATCAAA
131 TGGTAAAATGGGAGGTGTAGGCGACAACAACAATGGAGGAAAGGAAAAAAAACATTAAAATCAAA
* * * *
31343502 GAGAATGAGAGGAGGAGAGGAATGACTTGGGAAATGAGGAGAAGGATTAAAGTCTGATTATTTGT
196 GAGAATGAGAGGAGGAGAGGAATGAGTAGGGAAATGAGGAGGAGGATTAAAGGCTGATTATTTGT
** * * *
31343567 GAAAAAATAATAC-TTATGTCTAGGTTTAGTAGGCTTGGACGACACACACATCAAAACAAGAGGT
261 G-AAAAATAATACTTTATACCTAGGTTTACTAGGCTTGGACGACACACACATTAAAACAAG-GGG
* * *
31343631 TTTTGTCAAAAAAA-TAAATTATTTGCA-AGAGAAGGGATTTGAACCTGGGACTAATTTAAGTAC
324 TTTTGTCAAAAAAATTAAATTATTTGCAGA-AGAAGGGATTTGAACTTGGGACTGATTTAAATAC
* *
31343694 GCTTTAAAGACCCATTAAAAAATTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATTCC
388 GATTTAAAGACCCATTAAAAAACTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATTCC
*
31343759 AAATCTAGAAATTTAGGTTTTTAATTGGCAAGATGAATAAAAAAA-TGAAGAAAGAAGAGCTCTT
453 AAATCTTGAAATTTAGGTTTTTAATTGGCAAGATGAATAAAAAAATTGAAGAAAGAAGAGCTCTT
*
31343823 ACCCAAGCTAGTTGAGAGAAACGATAATGCCACTATC
518 ACCCAAGCTAGTTGAGAGAAACGATAATGCCACTTTC
* * * *
31343860 TTAGCAATGTTCAGGGTCGATTTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTT-GAAAGAGG
1 TTGGCAATGTTTAGGATCGATTTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTTAG-ATGAGG
** ** ** * ** * ***
31343924 ACAAATGGAAGTTGAT-G-TTCAAGATTTTAGATTTGGTGC-TGATTTATG-TGAGGATAACTGG
65 ACAAATGGAAG-CAATAGATT-AA-A--GGAGA--TGGTGCACAATCT-TGAT-ACAAAAAGAAG
* * * ** * ** * * ** * * *
31343985 AAGCAATAGGTTATAGGAGATGGTGCACAATCT-TGATACAAAAAGAA--GAAGAAAGAGATGGT
121 AAGAAAGAGATGGTA--AAATGG-G-A-GGTGTAGGCGACAACAACAATGGAGGAAAG-GA----
* ** ** * * ** * * *
31344047 AAAAGAGGAGGTGTAGGCGAT-AACA-ACAATG-GAGGAAAGGAAAAAAAAATTAAAATCAAAGA
176 AAAA-A-AACAT-TA--AAATCAA-AGAGAATGAGAGG--AGG--AGAGGAA-T-GAGT---AGG
** ** ** *** * * *
31344109 GAATAAAAGGAGGAGAGGAATGTCTAGAGCAATGAGAAGGAG-GATTAAAGGCTGATTATTTGTA
226 GAA-ATGAGGA-G-GAGG-AT-TAAAG-GC--TGATTATTTGTGA--AAA--AT-AATACTT-T-
* ** * * *
31344173 AAAAAAATAGTACTTATACCTAGGTTTTCTAGGCTTGGACAACACAGACATTAAAACAAGGGGTT
276 --ATACCTAG--GTT-TA-CTA---------GGCTTGGACGACACACACATTAAAACAAGGGG-T
* *
31344238 TTTGTCAAAAAAA-TAAATTATTTGCTAG-AGAAGGGATTTGAACTTGGGACAGATTTAAAGACG
325 TTTGTCAAAAAAATTAAATTATTTGC-AGAAGAAGGGATTTGAACTTGGGACTGATTTAAATACG
* * *
31344301 ATTTAAAGACCCATTAAAAAACTAAAAAAATATATTTAAAATCATTAAAATTCTCCCAAATTCTA
389 ATTTAAAGACCCATTAAAAAACTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATTC-C
*
31344366 AAAT-TTGAAATTTAGGTTTTTAATTGGCAAGATTAGTAA-AAAAAAATTGAAGAAAGAAGAGAT
453 AAATCTTGAAATTTAGGTTTTTAATTGGCAAGA-T-G-AATAAAAAAATTGAAGAAAGAAGAGCT
* *
31344429 CTTACCAAAGCTAGTTCAGAGAAACGATAATGCCACTTTC
515 CTTACCCAAGCTAGTTGAGAGAAACGATAATGCCACTTTC
* * * *
31344469 TTGGCAATGTTTACGATCGATCTTGGTGTTTAAGATTTCAGATTTGGTGCTGATTTAGATGAGGA
1 TTGGCAATGTTTAGGATCGATTTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTTAGATGAGGA
*
31344534 CAAATGGAAGCAATAGATTAAAGGGGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAGA
66 CAAATGGAAGCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAGA
* *
31344599 TGGTAAAATGGGAGGTGTGGGCGACAACAACAATGGAGGAAAGG-AAAAAAATATTAAAATCAAA
131 TGGTAAAATGGGAGGTGTAGGCGACAACAACAATGGAGGAAAGGAAAAAAAACATTAAAATCAAA
* * * * *
31344663 GA-ATATGAGAGGAGGAGAGGAATTACTAGGGCAA-GAAGGAGAAGAATTAAAGGCTGATTATTT
196 GAGA-ATGAGAGGAGGAGAGGAATGAGTAGGGAAATG-AGGAGGAGGATTAAAGGCTGATTATTT
* *
31344726 GTGAAAAAATAAT-CCTTATACCTAGGTTTACTCGGCTTGGACGACACACACATT-AAACAAGGG
259 GTG-AAAAATAATACTTTATACCTAGGTTTACTAGGCTTGGACGACACACACATTAAAACAAGGG
31344789 GTTTTTGTC-AAAAAATTAAATTATTTGCA-AGAGAAGGGATTTGAACTTGGGACTGATTTAAAT
323 G-TTTTGTCAAAAAAATTAAATTATTTGCAGA-AGAAGGGATTTGAACTTGGGACTGATTTAAAT
* * *
31344852 ACGATTTAAAGACCCCTTTAAAAATTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATT
386 ACGATTTAAAGACCCATTAAAAAACTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATT
* * * *
31344917 CCAAATCTGGAAATTTAAGTTTTTAATTGGCAAGATTAATGAAAAAATTGAAGAAAGAAGAGCTC
451 CCAAATCTTGAAATTTAGGTTTTTAATTGGCAAGATGAATAAAAAAATTGAAGAAAGAAGAGCTC
* * * *
31344982 TTACCCAAGCTAATTGAGAGAAACGGTAATGGCACTTTA
516 TTACCCAAGCTAGTTGAGAGAAACGATAATGCCACTTTC
* *
31345021 TTGGCAATGTTTAGGATCGATCTTT-GAGTTTAAGATTTCAGATTTGGTGTTGATTTAGATGAGG
1 TTGGCAATGTTTAGGATCGAT-TTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTTAGATGAGG
* ** * * *
31345085 ACAAATGGCAGCAATAGATTAAAGGATTTGGTGCACAATCTTGATGCAAAAAGAAGAATAAA-AT
65 ACAAATGGAAGCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAG
* * *
31345149 ATGGTAAAAGGGGAGGTGTAGGCGACAAAAACAATGGATGAAAGG-AAAAAAACATTAAAAATCA
130 ATGGTAAAATGGGAGGTGTAGGCGACAACAACAATGGAGGAAAGGAAAAAAAACATT-AAAATCA
31345213 AAGA
194 AAGA
31345217 AAAAGGATTT
Statistics
Matches: 2541, Mismatches: 356, Indels: 248
0.81 0.11 0.08
Matches are distributed among these distances:
550 3 0.00
551 105 0.04
552 367 0.14
553 197 0.08
554 495 0.19
555 263 0.10
556 164 0.06
557 267 0.11
558 70 0.03
559 72 0.03
560 1 0.00
561 12 0.00
562 2 0.00
564 2 0.00
565 6 0.00
566 3 0.00
567 2 0.00
568 11 0.00
569 7 0.00
570 6 0.00
571 1 0.00
572 5 0.00
573 3 0.00
574 3 0.00
576 8 0.00
577 5 0.00
578 8 0.00
579 4 0.00
580 5 0.00
581 4 0.00
582 4 0.00
583 7 0.00
584 5 0.00
585 8 0.00
587 3 0.00
588 4 0.00
589 5 0.00
590 1 0.00
591 7 0.00
592 6 0.00
593 10 0.00
594 2 0.00
595 3 0.00
596 6 0.00
597 2 0.00
599 2 0.00
600 10 0.00
601 2 0.00
602 12 0.00
604 23 0.01
605 6 0.00
606 170 0.07
607 6 0.00
608 11 0.00
609 122 0.05
610 3 0.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.26
Consensus pattern (554 bp):
TTGGCAATGTTTAGGATCGATTTTGGAGTTCAAGATTTCAGATTTGGTGCTGATTTAGATGAGGA
CAAATGGAAGCAATAGATTAAAGGAGATGGTGCACAATCTTGATACAAAAAGAAGAAGAAAGAGA
TGGTAAAATGGGAGGTGTAGGCGACAACAACAATGGAGGAAAGGAAAAAAAACATTAAAATCAAA
GAGAATGAGAGGAGGAGAGGAATGAGTAGGGAAATGAGGAGGAGGATTAAAGGCTGATTATTTGT
GAAAAATAATACTTTATACCTAGGTTTACTAGGCTTGGACGACACACACATTAAAACAAGGGGTT
TTGTCAAAAAAATTAAATTATTTGCAGAAGAAGGGATTTGAACTTGGGACTGATTTAAATACGAT
TTAAAGACCCATTAAAAAACTGAAAAAATATATTTAAAATCATCAAAATTCTCCCAAATTCCAAA
TCTTGAAATTTAGGTTTTTAATTGGCAAGATGAATAAAAAAATTGAAGAAAGAAGAGCTCTTACC
CAAGCTAGTTGAGAGAAACGATAATGCCACTTTC
Found at i:31346723 original size:24 final size:24
Alignment explanation
Indices: 31346696--31346744 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
31346686 AAGTTTTTGC
31346696 TAGTTTTTTTATTCGTGTAAAATA
1 TAGTTTTTTTATTCGTGTAAAATA
31346720 TAGTTTTTTTATTCGTGTAAAATA
1 TAGTTTTTTTATTCGTGTAAAATA
31346744 T
1 T
31346745 CAAGTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.12, T:0.55
Consensus pattern (24 bp):
TAGTTTTTTTATTCGTGTAAAATA
Found at i:31347445 original size:40 final size:40
Alignment explanation
Indices: 31347391--31347816 Score: 303
Period size: 40 Copynumber: 10.8 Consensus size: 40
31347381 AAAAATTGAT
*
31347391 GCTATAGATCGAGCATTAGCGGTGCTTTTTGAAAAACACC
1 GCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACC
* * **
31347431 GCTATAGATAGAGCATTCGC-GCGCTTTTCAAAAAACACC
1 GCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACC
* * **
31347470 GCTATAGATTGAGCATTAGCGACGCTTTTTGAAAAATGCC
1 GCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACC
* * * * *
31347510 ACTATAGGTCGAGCATTAGCGGTGCTTTTTAAAAAACGCC
1 GCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACC
* * * ** * * ** * *****
31347550 GCAAAAAAATTAAGCA-CAACACCGTCATTTT-ATGTTGA--
1 GC-TATAGATCGAGCATTAGCGGCG-CTTTTTGAAAAACACC
* *
31347588 GCTTTAG-T-G-GCATTAGCTGCGCTTTTTGAAAAACACC
1 GCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACC
** * * *
31347625 GCTATAGATCGAGCATTAGTTGCACTTTTTAAAAAACGCC
1 GCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACC
* * ** *
31347665 GCTATAGGTCGACCATTAGCGGCGCTTTTTGAAAAATGCT
1 GCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACC
** * *
31347705 ATTATAGATCAAGCATTAGTGGCGCTTTTTGAAAAACACC
1 GCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACC
* *
31347745 GCTATTGATCGAGTATTAGCGGCGCTTTTTGAAAAACGA-C
1 GCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAAC-ACC
* * * *
31347785 ACTATAGGTTGACCATTAGCGGCGCTTTTTGA
1 GCTATAGATCGAGCATTAGCGGCGCTTTTTGA
31347817 CGTCCAAAAA
Statistics
Matches: 288, Mismatches: 87, Indels: 22
0.73 0.22 0.06
Matches are distributed among these distances:
34 8 0.03
35 6 0.02
36 1 0.00
37 7 0.02
38 3 0.01
39 35 0.12
40 215 0.75
41 13 0.05
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (40 bp):
GCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACC
Found at i:31347476 original size:79 final size:80
Alignment explanation
Indices: 31347391--31347551 Score: 207
Period size: 79 Copynumber: 2.0 Consensus size: 80
31347381 AAAAATTGAT
** * *
31347391 GCTATAGATCGAGCATTAGCGGTGCTTTTTGAAAAACACCGCTATAGATAGAGCATTCGC-GCGC
1 GCTATAGATCGAGCATTAGCGACGCTTTTTGAAAAACACCACTATAGATAGAGCATTAGCGGCGC
31347455 TTTTCAAAAAACACC
66 TTTTCAAAAAACACC
* ** * * *
31347470 GCTATAGATTGAGCATTAGCGACGCTTTTTGAAAAATGCCACTATAGGTCGAGCATTAGCGGTGC
1 GCTATAGATCGAGCATTAGCGACGCTTTTTGAAAAACACCACTATAGATAGAGCATTAGCGGCGC
* *
31347535 TTTTTAAAAAACGCC
66 TTTTCAAAAAACACC
31347550 GC
1 GC
31347552 AAAAAAATTA
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
79 51 0.74
80 18 0.26
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (80 bp):
GCTATAGATCGAGCATTAGCGACGCTTTTTGAAAAACACCACTATAGATAGAGCATTAGCGGCGC
TTTTCAAAAAACACC
Found at i:31347747 original size:120 final size:120
Alignment explanation
Indices: 31347597--31347816 Score: 343
Period size: 120 Copynumber: 1.8 Consensus size: 120
31347587 AGCTTTAGTG
**
31347597 GCATTAGCTGCGCTTTTTGAAAAACACCGCTATAGATCGAGCATTAGTTGCACTTTTTAAAAAAC
1 GCATTAGCTGCGCTTTTTGAAAAACACCGCTATAGATCGAGCATTAGCGGCACTTTTTAAAAAAC
* *
31347662 GCCGCTATAGGTCGACCATTAGCGGCGCTTTTTGAAAAATGCTATTATAGATCAA
66 GACACTATAGGTCGACCATTAGCGGCGCTTTTTGAAAAATGCTATTATAGATCAA
* * * *
31347717 GCATTAG-TGGCGCTTTTTGAAAAACACCGCTATTGATCGAGTATTAGCGGCGCTTTTTGAAAAA
1 GCATTAGCT-GCGCTTTTTGAAAAACACCGCTATAGATCGAGCATTAGCGGCACTTTTTAAAAAA
*
31347781 CGACACTATAGGTTGACCATTAGCGGCGCTTTTTGA
65 CGACACTATAGGTCGACCATTAGCGGCGCTTTTTGA
31347817 CGTCCAAAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
119 1 0.01
120 89 0.99
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (120 bp):
GCATTAGCTGCGCTTTTTGAAAAACACCGCTATAGATCGAGCATTAGCGGCACTTTTTAAAAAAC
GACACTATAGGTCGACCATTAGCGGCGCTTTTTGAAAAATGCTATTATAGATCAA
Found at i:31348169 original size:14 final size:13
Alignment explanation
Indices: 31348152--31348230 Score: 59
Period size: 14 Copynumber: 5.5 Consensus size: 13
31348142 GCTAAAACTG
31348152 TAAACCTTAAACCC
1 TAAACC-TAAACCC
31348166 TAAACACTAAACCC
1 TAAAC-CTAAACCC
*
31348180 TAAATCCTAAACCA
1 TAAA-CCTAAACCC
**
31348194 TAAAATCCTAAACTA
1 T-AAA-CCTAAACCC
*
31348209 TAGACACTAAACCC
1 TAAAC-CTAAACCC
31348223 TTAAACCT
1 -TAAACCT
31348231 TTAAATATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
13 1 0.02
14 34 0.63
15 19 0.35
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.22
Consensus pattern (13 bp):
TAAACCTAAACCC
Found at i:31348176 original size:21 final size:21
Alignment explanation
Indices: 31348152--31348229 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
31348142 GCTAAAACTG
*
31348152 TAAACCTTAAACCCTAAACAC
1 TAAACCCTAAACCCTAAACAC
*
31348173 TAAACCCTAAATCCTAAAC-C
1 TAAACCCTAAACCCTAAACAC
* ** *
31348193 ATAAAATCCTAAACTATAGACAC
1 -T-AAACCCTAAACCCTAAACAC
31348216 TAAACCCTTAAACC
1 TAAACCC-TAAACC
31348230 TTTAAATATA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.02
21 23 0.52
22 19 0.43
23 1 0.02
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.21
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAACAC
Found at i:31348257 original size:59 final size:59
Alignment explanation
Indices: 31348181--31348295 Score: 148
Period size: 59 Copynumber: 1.9 Consensus size: 59
31348171 ACTAAACCCT
*
31348181 AAATCCTAAACCATAAAA-TCCTAAA-CT-ATAGACACTAAACCCTTAAACCTTTAAATATA
1 AAATCCTAAACCATAAAACT-CTAAACCTGA-A-ACACTAAACCCTTAAACCCTTAAATATA
*
31348240 AAATCCTAAATCC-TAAAACTCTAAACCTGAATCACTAAACCCTTAAACCCTTAAAT
1 AAATCCTAAA-CCATAAAACTCTAAACCTGAAACACTAAACCCTTAAACCCTTAAAT
31348296 GCAAACTTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
59 43 0.86
60 6 0.12
61 1 0.02
ACGTcount: A:0.47, C:0.26, G:0.02, T:0.25
Consensus pattern (59 bp):
AAATCCTAAACCATAAAACTCTAAACCTGAAACACTAAACCCTTAAACCCTTAAATATA
Found at i:31348314 original size:152 final size:153
Alignment explanation
Indices: 31348137--31348418 Score: 442
Period size: 152 Copynumber: 1.8 Consensus size: 153
31348127 TACAAAATCC
* *
31348137 TAAATGCTAAAACTGTAAACCTTAAACCCTAAA-CACTAAACCCTAAATCCTAAACCATAAAATC
1 TAAATGC-AAAACTGTAAACCTTAAACCATAAACCA-TAAACCCTAAATCCTAAACCATAAAACC
* * * *
31348201 CTAAACTATAGACACTAAACCCTTAAACCTTTAAATATAAAATCCTAAATCCTAAAACTCTAAAC
64 CTAAACTATAGACAATAAACCCTTAAACCGTTAAATACAAAATCCTAAATCCTAAAACTATAAAC
31348266 CTGAATCACTAAACCCTTAAACCCT
129 CTGAATCACTAAACCCTTAAACCCT
* * *
31348291 TAAATGC-AAACTTTAAACTTTAAACCATAAACCATAAACCCTAAATCCTGAACCATAAAACCCT
1 TAAATGCAAAACTGTAAACCTTAAACCATAAACCATAAACCCTAAATCCTAAACCATAAAACCCT
*
31348355 TAACTATAGACAATAAACCCTTAAACCGTTAAATACAAAATCCTAAATCCTAAAACTATAAACC
66 AAACTATAGACAATAAACCCTTAAACCGTTAAATACAAAATCCTAAATCCTAAAACTATAAACC
31348419 GTAAGAATAA
Statistics
Matches: 117, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
152 108 0.92
153 2 0.02
154 7 0.06
ACGTcount: A:0.47, C:0.26, G:0.03, T:0.24
Consensus pattern (153 bp):
TAAATGCAAAACTGTAAACCTTAAACCATAAACCATAAACCCTAAATCCTAAACCATAAAACCCT
AAACTATAGACAATAAACCCTTAAACCGTTAAATACAAAATCCTAAATCCTAAAACTATAAACCT
GAATCACTAAACCCTTAAACCCT
Found at i:31348315 original size:109 final size:109
Alignment explanation
Indices: 31348124--31348332 Score: 244
Period size: 109 Copynumber: 1.9 Consensus size: 109
31348114 CTTAAATACA
* * * *
31348124 AAATACAAAATCCTAAATGCTAAAACTGTAAACCTTAAACCCTAAACACTAAACCCTAAATCCTA
1 AAATACAAAATCCTAAATCCTAAAACTCTAAACCTGAAACACTAAACACTAAACCCTAAATCCTA
* *
31348189 AACCATAAAATCCTAAACTATAGA-CACTAAACCCTTAAACCTTT
66 AACCATAAAATCCTAAACCATAAACCA-TAAACCCTTAAACCTTT
* * * *
31348233 AAATATAAAATCCTAAATCCTAAAACTCTAAACCTGAATCACTAAACCCTTAAACCCTTAAATGC
1 AAATACAAAATCCTAAATCCTAAAACTCTAAACCTGAAACACTAAACAC-TAAACCC-TAAATCC
** * *
31348298 -AAACTTTAAACT-TTAAACCATAAACCATAAACCCT
64 TAAACCATAAAATCCTAAACCATAAACCATAAACCCT
31348333 AAATCCTGAA
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
109 59 0.71
110 18 0.22
111 6 0.07
ACGTcount: A:0.47, C:0.26, G:0.02, T:0.24
Consensus pattern (109 bp):
AAATACAAAATCCTAAATCCTAAAACTCTAAACCTGAAACACTAAACACTAAACCCTAAATCCTA
AACCATAAAATCCTAAACCATAAACCATAAACCCTTAAACCTTT
Found at i:31348335 original size:21 final size:21
Alignment explanation
Indices: 31348311--31348381 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
31348301 CTTTAAACTT
31348311 TAAACCATAAACCATAAACCC
1 TAAACCATAAACCATAAACCC
*
31348332 TAAATCC-TGAACCATAAAACCC
1 TAAA-CCATAAACCAT-AAACCC
* * * *
31348354 TTAACTATAGACAATAAACCC
1 TAAACCATAAACCATAAACCC
31348375 TTAAACC
1 -TAAACC
31348382 GTTAAATACA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
21 18 0.47
22 20 0.53
ACGTcount: A:0.48, C:0.30, G:0.03, T:0.20
Consensus pattern (21 bp):
TAAACCATAAACCATAAACCC
Found at i:31348734 original size:3 final size:3
Alignment explanation
Indices: 31348726--31348751 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31348716 TATTTTAGTA
31348726 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
31348752 AAGAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:31349158 original size:114 final size:114
Alignment explanation
Indices: 31348920--31349186 Score: 301
Period size: 114 Copynumber: 2.3 Consensus size: 114
31348910 TATTACTGTG
* * **
31348920 AAAACGCCACAAAACATCTATTAAGAGATTGCAAAACGGCGTTGTTTATAGCCTTGTTATTAGTG
1 AAAACGCCACAAAA-ATCTATTAACAGATTGCAAAACGGCATCATTTATAGCCTTGTTATTAGTG
* * ** *
31348985 GTGCTTTTATAAACGCCGCAAAATGTGTGAATTATCGGTGTTTGCACCAG
65 GTGCTTTTAAAAACGCCGCAAAATGTATGAATTATCCATGTTTGCACCAA
* *
31349035 AAAACGCCACAAATATCTATTAACAGATTGCAAAACGGCATCATTTGTAGCCTTGTTATTAGTGG
1 AAAACGCCACAAAAATCTATTAACAGATTGCAAAACGGCATCATTTATAGCCTTGTTATTAGTGG
* * * * *
31349100 TTCTTTATAAAAATGCCGCAGAA-GATATGAATTA-CCATCGTTTTCA-TAA
66 TGCTTT-TAAAAACGCCGCAAAATG-TATGAATTATCCAT-GTTTGCACCAA
*
31349149 AAAATGCCACAAAAATCTATT-ACTAGATTG-AAAACGGC
1 AAAACGCCACAAAAATCTATTAAC-AGATTGCAAAACGGC
31349187 GCCGTTTTTT
Statistics
Matches: 130, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
113 10 0.08
114 80 0.62
115 40 0.31
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (114 bp):
AAAACGCCACAAAAATCTATTAACAGATTGCAAAACGGCATCATTTATAGCCTTGTTATTAGTGG
TGCTTTTAAAAACGCCGCAAAATGTATGAATTATCCATGTTTGCACCAA
Found at i:31350003 original size:22 final size:22
Alignment explanation
Indices: 31349978--31350020 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
31349968 TTTAAAGTAT
31349978 AATTAACCCTAAACTTGTAAAA
1 AATTAACCCTAAACTTGTAAAA
*
31350000 AATTAACCTTAAACTTGTAAA
1 AATTAACCCTAAACTTGTAAA
31350021 TTTATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (22 bp):
AATTAACCCTAAACTTGTAAAA
Found at i:31351354 original size:94 final size:94
Alignment explanation
Indices: 31351242--31351431 Score: 371
Period size: 94 Copynumber: 2.0 Consensus size: 94
31351232 CACGGATGTT
31351242 CACACAATCCTTTAACATGTACTTAAGAAAAGATGACTTGTAAAATATAAATTAAATTAAGTGTG
1 CACACAATCCTTTAACATGTACTTAAGAAAAGATGACTTGTAAAATATAAATTAAATTAAGTGTG
*
31351307 GACTATTGTACATCTATATTTTAACTGCA
66 GACTATTGGACATCTATATTTTAACTGCA
31351336 CACACAATCCTTTAACATGTACTTAAGAAAAGATGACTTGTAAAATATAAATTAAATTAAGTGTG
1 CACACAATCCTTTAACATGTACTTAAGAAAAGATGACTTGTAAAATATAAATTAAATTAAGTGTG
31351401 GACTATTGGACATCTATATTTTAACTGCA
66 GACTATTGGACATCTATATTTTAACTGCA
31351430 CA
1 CA
31351432 TGTGATTTGT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (94 bp):
CACACAATCCTTTAACATGTACTTAAGAAAAGATGACTTGTAAAATATAAATTAAATTAAGTGTG
GACTATTGGACATCTATATTTTAACTGCA
Found at i:31351665 original size:15 final size:15
Alignment explanation
Indices: 31351647--31351698 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
31351637 TGGATTAATG
31351647 TAATTAAATATTATT
1 TAATTAAATATTATT
31351662 TAATTAAA-A-TAGTT
1 TAATTAAATATTA-TT
*
31351676 TATTTAAATATTATT
1 TAATTAAATATTATT
31351691 TAATTAAA
1 TAATTAAA
31351699 ATAATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 2 0.06
14 10 0.31
15 18 0.56
16 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TAATTAAATATTATT
Found at i:31351860 original size:9 final size:9
Alignment explanation
Indices: 31351846--31352009 Score: 92
Period size: 9 Copynumber: 18.7 Consensus size: 9
31351836 TAATTATGTA
31351846 ATAACTTAC
1 ATAACTTAC
31351855 ATAACTTAC
1 ATAACTTAC
*
31351864 AAAACTTAC
1 ATAACTTAC
31351873 ATAA--TAC
1 ATAACTTAC
* *
31351880 ATAA-ATAT
1 ATAACTTAC
* *
31351888 ATATCATATC
1 ATAACTTA-C
31351898 ATAACTTAC
1 ATAACTTAC
31351907 ATAACTTAC
1 ATAACTTAC
31351916 ATAA--TAC
1 ATAACTTAC
* *
31351923 ATAA-ATAT
1 ATAACTTAC
* *
31351931 ATATCATATC
1 ATAACTTA-C
31351941 ATAACTTAC
1 ATAACTTAC
*
31351950 ATACCTTAC
1 ATAACTTAC
*
31351959 ATAAATGT--
1 ATAACT-TAC
* *
31351967 ATATCATATC
1 ATAACTTA-C
*
31351977 ATAACCTAC
1 ATAACTTAC
31351986 ATAACTTAC
1 ATAACTTAC
*
31351995 AAAACTTAC
1 ATAACTTAC
*
31352004 TTAACT
1 ATAACT
31352010 AACGTAATAC
Statistics
Matches: 121, Mismatches: 24, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
7 15 0.12
8 13 0.11
9 74 0.61
10 19 0.16
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:31351902 original size:43 final size:43
Alignment explanation
Indices: 31351854--31352003 Score: 194
Period size: 43 Copynumber: 3.4 Consensus size: 43
31351844 TAATAACTTA
31351854 CATAACTTACAAAACTTACATAATACATAAATATATATCATAT
1 CATAACTTACAAAACTTACATAATACATAAATATATATCATAT
*
31351897 CATAACTTACATAACTTACATAATACATAAATATATATCATAT
1 CATAACTTACAAAACTTACATAATACATAAATATATATCATAT
* * ** * * *
31351940 CATAACTTACATACCTTACATAAATGTATATCATATCATAACCTA-
1 CATAACTTACAAAACTTACAT-AATACATA-AATAT-ATATCATAT
31351985 CATAACTTACAAAACTTAC
1 CATAACTTACAAAACTTAC
31352004 TTAACTAACG
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
43 62 0.65
44 6 0.06
45 21 0.22
46 6 0.06
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (43 bp):
CATAACTTACAAAACTTACATAATACATAAATATATATCATAT
Found at i:31351970 original size:36 final size:35
Alignment explanation
Indices: 31351906--31351995 Score: 128
Period size: 36 Copynumber: 2.5 Consensus size: 35
31351896 TCATAACTTA
*
31351906 CATAACTTACATA-ATACATAAATATATATCATAT
1 CATAACTTACATACTTACATAAATATATATCATAT
*
31351940 CATAACTTACATACCTTACATAAATGTATATCATAT
1 CATAACTTACATA-CTTACATAAATATATATCATAT
*
31351976 CATAACCTACATAACTTACA
1 CATAACTTACAT-ACTTACA
31351996 AAACTTACTT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
34 13 0.26
36 36 0.72
37 1 0.02
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.33
Consensus pattern (35 bp):
CATAACTTACATACTTACATAAATATATATCATAT
Found at i:31352023 original size:79 final size:76
Alignment explanation
Indices: 31351852--31351998 Score: 186
Period size: 79 Copynumber: 1.9 Consensus size: 76
31351842 TGTAATAACT
* *
31351852 TACATAACTTACAAAACTTACATAATACATAAATATATATCATATCATAACTTACATAACTTACA
1 TACATAA--TACATAACTTACATAATACATAAATATATATCATATCATAACCTACATAACTTACA
*
31351917 TAATACATAAATA
64 AAATACATAAATA
* * * *
31351930 TATATCATATCATAACTTACATACCTTACATAAATGTATATCATATCATAACCTACATAACTTAC
1 TACATAATA-CATAACTTACATA--ATACATAAATATATATCATATCATAACCTACATAACTTAC
31351995 AAAA
63 AAAA
31351999 CTTACTTAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
76 2 0.03
77 12 0.20
78 5 0.08
79 40 0.68
ACGTcount: A:0.48, C:0.18, G:0.01, T:0.33
Consensus pattern (76 bp):
TACATAATACATAACTTACATAATACATAAATATATATCATATCATAACCTACATAACTTACAAA
ATACATAAATA
Found at i:31357982 original size:43 final size:42
Alignment explanation
Indices: 31357903--31358181 Score: 296
Period size: 43 Copynumber: 6.6 Consensus size: 42
31357893 CGGCACTTTT
* * *
31357903 CTAAATGTCAGGTTCTTTAGCGACGTTTGTATGAAAAGCGCCG
1 CTAAAGGTCACGTTCTTTAGCGGCGTTTGTA-GAAAAGCGCCG
* * * *
31357946 CCAAAGGTCACGTTCTATAGCGGCGTTTTTTAGAAAAGCGCCA
1 CTAAAGGTCACGTTCTTTAGCGGCG-TTTGTAGAAAAGCGCCG
* * *
31357989 CTAAATGTCAGGTTCTTTAGC-G-GTGTGT-GAAAAGCGCCG
1 CTAAAGGTCACGTTCTTTAGCGGCGTTTGTAGAAAAGCGCCG
* * *
31358028 CTAAAGGTCACATTCTTTAGCGACGTTTGT-GTAAAAAGCGTCG
1 CTAAAGGTCACGTTCTTTAGCGGCGTTTGTAG--AAAAGCGCCG
* * * *
31358071 CTAAATGTCATGTTCTTTAGCGGCATTTGTGTGAAAAGCGCCG
1 CTAAAGGTCACGTTCTTTAGCGGCGTTTGT-AGAAAAGCGCCG
* * *
31358114 CTAAAGGTCACGTTCTTTAGCGGTGTTTGTATGAAAAGTGCCC
1 CTAAAGGTCACGTTCTTTAGCGGCGTTTGTA-GAAAAGCGCCG
31358157 CTAAAGGTCACGTTCTTTAGCGGCG
1 CTAAAGGTCACGTTCTTTAGCGGCG
31358182 CTTTTTACAC
Statistics
Matches: 194, Mismatches: 34, Indels: 16
0.80 0.14 0.07
Matches are distributed among these distances:
39 28 0.14
40 3 0.02
41 7 0.04
42 1 0.01
43 149 0.77
44 5 0.03
45 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (42 bp):
CTAAAGGTCACGTTCTTTAGCGGCGTTTGTAGAAAAGCGCCG
Found at i:31358129 original size:125 final size:127
Alignment explanation
Indices: 31357915--31358178 Score: 345
Period size: 125 Copynumber: 2.1 Consensus size: 127
31357905 AAATGTCAGG
* * *
31357915 TTCTTTAGCGACGTTTGTATGAAAAGCGCCGCCAAAGGTCACGTTCTATAGCGGCGTTTTTTAGA
1 TTCTTTAGCGACGTTTGTATAAAAAGCGCCGCCAAAGGTCACGTTCTATAGCGGCATTTTGTAGA
* * *
31357980 AAAGCGCCACTAAATGTCAGGTTCTTTAGCGGTG-TG-TGAAAAGCGCCGCTAAAGGTCACA
66 AAAGCGCCACTAAAGGTCACGTTCTTTAGCGGTGTTGATGAAAAGCGCCCCTAAAGGTCACA
* * * * * *
31358040 TTCTTTAGCGACGTTTGTGTAAAAAGCGTCGCTAAATGTCATGTTCTTTAGCGGCATTTGTGT-G
1 TTCTTTAGCGACGTTTGTATAAAAAGCGCCGCCAAAGGTCACGTTCTATAGCGGCATTT-TGTAG
* * *
31358104 AAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGTGTTTGTATGAAAAGTGCCCCTAAAGGTCACG
65 AAAAGCGCCACTAAAGGTCACGTTCTTTAGCGGTG-TTG-ATGAAAAGCGCCCCTAAAGGTCACA
31358169 TTCTTTAGCG
1 TTCTTTAGCG
31358179 GCGCTTTTTA
Statistics
Matches: 119, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
125 84 0.71
126 2 0.02
127 2 0.02
129 31 0.26
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (127 bp):
TTCTTTAGCGACGTTTGTATAAAAAGCGCCGCCAAAGGTCACGTTCTATAGCGGCATTTTGTAGA
AAAGCGCCACTAAAGGTCACGTTCTTTAGCGGTGTTGATGAAAAGCGCCCCTAAAGGTCACA
Found at i:31358132 original size:86 final size:85
Alignment explanation
Indices: 31357903--31358180 Score: 348
Period size: 86 Copynumber: 3.3 Consensus size: 85
31357893 CGGCACTTTT
* * * *
31357903 CTAAATGTCAGGTTCTTTAGCGACGTTTGTATGAAAAGCGCCGCCAAAGGTCACGTTCTATAGCG
1 CTAAATGTCAGGTTCTTTAGCGGC-TTTGTGTGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCG
*
31357968 GCGTTT-TTTAGAAAAGCGCCA
65 GCGTTTGTATA-AAAAGCGCCA
* *
31357989 CTAAATGTCAGGTTCTTTAGCGG---TGTGTGAAAAGCGCCGCTAAAGGTCACATTCTTTAGCGA
1 CTAAATGTCAGGTTCTTTAGCGGCTTTGTGTGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGG
* * *
31358051 CGTTTGTGTAAAAAGCGTCG
66 CGTTTGTATAAAAAGCGCCA
*
31358071 CTAAATGTCATGTTCTTTAGCGGCATTTGTGTGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCG
1 CTAAATGTCAGGTTCTTTAGCGGC-TTTGTGTGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCG
* * * *
31358136 GTGTTTGTATGAAAAGTGCCC
65 GCGTTTGTATAAAAAGCGCCA
* *
31358157 CTAAAGGTCACGTTCTTTAGCGGC
1 CTAAATGTCAGGTTCTTTAGCGGC
31358181 GCTTTTTACA
Statistics
Matches: 167, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
82 69 0.41
83 3 0.02
86 95 0.57
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (85 bp):
CTAAATGTCAGGTTCTTTAGCGGCTTTGTGTGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGG
CGTTTGTATAAAAAGCGCCA
Found at i:31359901 original size:23 final size:23
Alignment explanation
Indices: 31359853--31359912 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
31359843 AGTGAATTTC
*
31359853 ATTT-AATTATTA-A-TATATTA
1 ATTTAAATTATTATATTATAATA
*
31359873 AGTTAAATTATTATATTATAATA
1 ATTTAAATTATTATATTATAATA
* *
31359896 ATTTAAAATATAATATT
1 ATTTAAATTATTATATT
31359913 GATTGTATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 3 0.09
21 8 0.25
22 1 0.03
23 20 0.62
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTTAAATTATTATATTATAATA
Found at i:31364241 original size:31 final size:32
Alignment explanation
Indices: 31364177--31364245 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
31364167 TTACAAATGA
* *
31364177 TCACTGAATTATTTGAAAGTTTTCATTTTAAG
1 TCACTGAACTATTCGAAAGTTTTCATTTTAAG
*
31364209 TCACTGAACTATTCGGAAGCTTTT-A-TTTAAG
1 TCACTGAACTATTCGAAAG-TTTTCATTTTAAG
31364240 TCACTG
1 TCACTG
31364246 GGATGTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 12 0.36
32 17 0.52
33 4 0.12
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (32 bp):
TCACTGAACTATTCGAAAGTTTTCATTTTAAG
Found at i:31367189 original size:10 final size:10
Alignment explanation
Indices: 31367174--31367225 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
31367164 TAATTTTAGG
31367174 ATTTATTTTT
1 ATTTATTTTT
*
31367184 ATTTATCTTT
1 ATTTATTTTT
* *
31367194 AATTATCTTT
1 ATTTATTTTT
*
31367204 ATTTATTTGT
1 ATTTATTTTT
31367214 ATTTATCTTTT
1 ATTTAT-TTTT
31367225 A
1 A
31367226 GAATTTAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
10 31 0.89
11 4 0.11
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:31368955 original size:30 final size:30
Alignment explanation
Indices: 31368921--31368981 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
31368911 GTGTCACACA
*
31368921 CGGGCGTGTGGATTACCCATATGGAACTGC
1 CGGGCGTGTGGACTACCCATATGGAACTGC
* *
31368951 CGGGCGTGTGGACTACCCATGTGGAATTGC
1 CGGGCGTGTGGACTACCCATATGGAACTGC
31368981 C
1 C
31368982 TAAGCCGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (30 bp):
CGGGCGTGTGGACTACCCATATGGAACTGC
Found at i:31372997 original size:16 final size:17
Alignment explanation
Indices: 31372978--31373050 Score: 60
Period size: 16 Copynumber: 4.2 Consensus size: 17
31372968 GGGGAGGAAA
31372978 AAAAAG-AAGAGAGGAG
1 AAAAAGAAAGAGAGGAG
31372994 AAAAGAGAAAGAACAGAGGAG
1 AAAA-AGAAAG---AGAGGAG
* * * *
31373015 AGAAAGGAAGAAAAGA-
1 AAAAAGAAAGAGAGGAG
31373031 AAAAAGAAAGAGAGGAG
1 AAAAAGAAAGAGAGGAG
31373048 AAA
1 AAA
31373051 GGGGAAAGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
16 16 0.37
17 9 0.21
18 3 0.07
20 5 0.12
21 10 0.23
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAGAGGAG
Found at i:31373006 original size:21 final size:22
Alignment explanation
Indices: 31372980--31373020 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
31372970 GGAGGAAAAA
*
31372980 AAAGAAGAGAGGAGA-AAAGAG
1 AAAGAACAGAGGAGAGAAAGAG
31373001 AAAGAACAGAGGAGAGAAAG
1 AAAGAACAGAGGAGAGAAAG
31373021 GAAGAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.61, C:0.02, G:0.37, T:0.00
Consensus pattern (22 bp):
AAAGAACAGAGGAGAGAAAGAG
Found at i:31373028 original size:31 final size:31
Alignment explanation
Indices: 31372992--31373083 Score: 82
Period size: 31 Copynumber: 2.9 Consensus size: 31
31372982 AGAAGAGAGG
*
31372992 AGAAAAG-AGAAAGAACAGAG-GAGAGAAAGGA
1 AGAAAAGAAAAAAGAA-AGAGAG-GAGAAAGGA
31373023 AGAAAAGAAAAAAGAAAGAGAGGAGAAAGGGGAA
1 AGAAAAGAAAAAAGAAAGAGAGGAGAAA--GG-A
* * *
31373057 AGAAAAGAAAGAA-AAATAGAGAAGAAA
1 AGAAAAGAAAAAAGAAAGAGAGGAGAAA
31373084 AGGGTGGCTG
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
31 17 0.33
32 8 0.15
33 14 0.27
34 13 0.25
ACGTcount: A:0.66, C:0.01, G:0.32, T:0.01
Consensus pattern (31 bp):
AGAAAAGAAAAAAGAAAGAGAGGAGAAAGGA
Found at i:31373065 original size:34 final size:34
Alignment explanation
Indices: 31373022--31373087 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
31373012 GAGAGAAAGG
*
31373022 AAGAAAAGAAA-AAAGAA-AGAGAGGAGAAAGGGGA
1 AAGAAAAGAAAGAAA-AATAGAGAAGA-AAAGGGGA
31373056 AAGAAAAGAAAGAAAAATAGAGAAGAAAAGGG
1 AAGAAAAGAAAGAAAAATAGAGAAGAAAAGGG
31373088 TGGCTGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 19 0.66
35 10 0.34
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.02
Consensus pattern (34 bp):
AAGAAAAGAAAGAAAAATAGAGAAGAAAAGGGGA
Found at i:31373709 original size:30 final size:30
Alignment explanation
Indices: 31373668--31373741 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
31373658 CACGCCCATA
*
31373668 TTGAA-GGCCGTGTGTCTCCCACGGCCGCC
1 TTGAATGGCCGTGTGTCTCCCACAGCCGCC
31373697 TTGAATGGCCGTGTGTCTCCCACAGCCGCC
1 TTGAATGGCCGTGTGTCTCCCACAGCCGCC
*
31373727 TCGAATGGCCGTGTG
1 TTGAATGGCCGTGTG
31373742 GATGTATCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
29 5 0.12
30 37 0.88
ACGTcount: A:0.12, C:0.34, G:0.31, T:0.23
Consensus pattern (30 bp):
TTGAATGGCCGTGTGTCTCCCACAGCCGCC
Found at i:31381877 original size:33 final size:33
Alignment explanation
Indices: 31381835--31381900 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
31381825 ATTTAGTCCC
31381835 TAAAAGATAAAAAGACATAAATAGCTCAAATTA
1 TAAAAGATAAAAAGACATAAATAGCTCAAATTA
31381868 TAAAAGATAAAAAGACATAAATAGCTCAAATTA
1 TAAAAGATAAAAAGACATAAATAGCTCAAATTA
31381901 GTAGGCTCAA
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:0.61, C:0.09, G:0.09, T:0.21
Consensus pattern (33 bp):
TAAAAGATAAAAAGACATAAATAGCTCAAATTA
Found at i:31387686 original size:10 final size:10
Alignment explanation
Indices: 31387669--31387733 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
31387659 ACTTTTCTTA
31387669 ATTT-TTATT
1 ATTTATTATT
31387678 ATTTATTA-T
1 ATTTATTATT
*
31387687 -TTTATT-TC
1 ATTTATTATT
*
31387695 ATTTTATTAGT
1 A-TTTATTATT
31387706 ATTTATTATT
1 ATTTATTATT
*
31387716 -TTATTTTATT
1 ATT-TATTATT
31387726 ATTTATTA
1 ATTTATTA
31387734 CTTTATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
8 6 0.14
9 7 0.16
10 27 0.63
11 3 0.07
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (10 bp):
ATTTATTATT
Found at i:31387687 original size:35 final size:35
Alignment explanation
Indices: 31387641--31387725 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 35
31387631 AACCCAACCT
* * * *
31387641 TTATTTTTTATTTT-TTTTACTTTTCTTAATTTTTA
1 TTATTTATTATTTTATTTCA-TTTTATTAATATTTA
*
31387676 TTATTTATTATTTTATTTCATTTTATTAGTATTTA
1 TTATTTATTATTTTATTTCATTTTATTAATATTTA
31387711 TTA-TT-TTATTTTATT
1 TTATTTATTATTTTATT
31387726 ATTTATTACT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
33 10 0.23
34 2 0.05
35 28 0.64
36 4 0.09
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (35 bp):
TTATTTATTATTTTATTTCATTTTATTAATATTTA
Found at i:31387728 original size:20 final size:20
Alignment explanation
Indices: 31387679--31387742 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
31387669 ATTTTTATTA
31387679 TTTATTATTTTATTTCATTTTA-
1 TTTATTA-TTTA-TT-ATTTTAT
*
31387701 -TTAGTATTTATTATTTTAT
1 TTTATTATTTATTATTTTAT
*
31387720 TTTATTATTTATTACTTTAT
1 TTTATTATTTATTATTTTAT
31387740 TTT
1 TTT
31387743 TGGATATTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.16
19 2 0.05
20 24 0.65
21 5 0.14
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTATTATTTATTATTTTAT
Found at i:31387738 original size:28 final size:27
Alignment explanation
Indices: 31387672--31387740 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 27
31387662 TTTCTTAATT
*
31387672 TTTATTATTTATTATTTTATTTCATTT
1 TTTATTATTTATTATTTTATTTCATTA
* *
31387699 TATTAGTATTTATTATTTTATTTTATTA
1 T-TTATTATTTATTATTTTATTTCATTA
31387727 TTTATTACTTTATT
1 TTTATTA-TTTATT
31387741 TTTGGATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 6 0.17
28 30 0.83
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (27 bp):
TTTATTATTTATTATTTTATTTCATTA
Found at i:31387741 original size:12 final size:11
Alignment explanation
Indices: 31387672--31387732 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 11
31387662 TTTCTTAATT
31387672 TTTATTATTTA
1 TTTATTATTTA
*
31387683 TTATTTTATTTCA
1 TT-TATTATTT-A
*
31387696 TTTTATTA-GTA
1 -TTTATTATTTA
31387707 TTTATTATTTTA
1 TTTATTA-TTTA
31387719 TTTTATTATTTA
1 -TTTATTATTTA
31387731 TT
1 TT
31387733 ACTTTATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
10 7 0.17
11 5 0.12
12 14 0.35
13 12 0.30
14 2 0.05
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:31389609 original size:10 final size:10
Alignment explanation
Indices: 31389594--31389645 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
31389584 TAATTTGAGG
31389594 ATTTATTTTT
1 ATTTATTTTT
*
31389604 ATTTATCTTT
1 ATTTATTTTT
* *
31389614 AATTATCTTT
1 ATTTATTTTT
*
31389624 ATTTATTTGT
1 ATTTATTTTT
31389634 ATTTATCTTTT
1 ATTTAT-TTTT
31389645 A
1 A
31389646 GAATTTAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
10 31 0.89
11 4 0.11
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:31391118 original size:70 final size:70
Alignment explanation
Indices: 31391005--31391211 Score: 310
Period size: 70 Copynumber: 3.0 Consensus size: 70
31390995 GGGAAAATCA
* * *
31391005 TATACTTCGATGCTCACATAGAGCTACGGTAGTCCACAACATATGAGGAATTACTACTAATCACT
1 TATACCTCGATGCTCACACAGAGCTACGGTAGTCCACAACATATGAGGAATTACTACCAATCACT
31391070 ATACT
66 ATACT
*
31391075 TATACCTCGATGCTCACACAGAGCTACGATAGTCCACAACATATGCA-GAATTACTACCAATCAC
1 TATACCTCGATGCTCACACAGAGCTACGGTAGTCCACAACATATG-AGGAATTACTACCAATCAC
* *
31391139 CACACT
65 TATACT
* * *
31391145 TATACCTCGATGCTCATACAGAGCTACGGTAGT-CACAACATATGTGGAATTACTACCAATCGCT
1 TATACCTCGATGCTCACACAGAGCTACGGTAGTCCACAACATATGAGGAATTACTACCAATCACT
31391209 ATA
66 ATA
31391212 TTCGTAGAAC
Statistics
Matches: 123, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
69 29 0.24
70 93 0.76
71 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (70 bp):
TATACCTCGATGCTCACACAGAGCTACGGTAGTCCACAACATATGAGGAATTACTACCAATCACT
ATACT
Found at i:31398192 original size:3 final size:3
Alignment explanation
Indices: 31398186--31398263 Score: 120
Period size: 3 Copynumber: 26.0 Consensus size: 3
31398176 TATGCTGCTG
* *
31398186 CTT CTT CTT CTT TTT CTT TTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* *
31398234 CTT CTT CTT CTT TTT CTT CTT CTT TTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
31398264 TGTTTTAGGT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
CTT
Found at i:31403023 original size:59 final size:59
Alignment explanation
Indices: 31402911--31403030 Score: 136
Period size: 59 Copynumber: 2.0 Consensus size: 59
31402901 TTAAAGTGGA
* * * *
31402911 ACATCAGTTGCCTTCTAAGTTGCTTCAGCCAGTTAAGATTCTGTTATGAAAGTGGGAAAG
1 ACATCAGCTGCCTTCT-AGTTGCTTCAGCCAGTTAAGATTCCGCTATGAAAGTGGAAAAG
* **
31402971 ACATCAGCTGCCTTCT-GTTTGCTTCATCTGGTTAAGATTCCGCTATTG-AAGTGGAAAAG
1 ACATCAGCTGCCTTCTAG-TTGCTTCAGCCAGTTAAGATTCCGCTA-TGAAAGTGGAAAAG
31403030 A
1 A
31403031 GTAACTACGG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
58 1 0.02
59 33 0.65
60 17 0.33
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.33
Consensus pattern (59 bp):
ACATCAGCTGCCTTCTAGTTGCTTCAGCCAGTTAAGATTCCGCTATGAAAGTGGAAAAG
Found at i:31404973 original size:19 final size:19
Alignment explanation
Indices: 31404949--31404986 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
31404939 TTGCAATTTA
31404949 AATTTTT-ATTTTATTTTCT
1 AATTTTTCA-TTTATTTTCT
31404968 AATTTTTCATTTATTTTCT
1 AATTTTTCATTTATTTTCT
31404987 TCTAACAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (19 bp):
AATTTTTCATTTATTTTCT
Found at i:31410088 original size:23 final size:23
Alignment explanation
Indices: 31410058--31410106 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
31410048 ATGTTTTTAC
31410058 TTTTATTTTAT-TTTAAGACTATT
1 TTTTATTTT-TCTTTAAGACTATT
**
31410081 TTTTATTTTTCTTTAAGTTTATT
1 TTTTATTTTTCTTTAAGACTATT
31410104 TTT
1 TTT
31410107 ATTAGGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTTATTTTTCTTTAAGACTATT
Found at i:31418598 original size:26 final size:26
Alignment explanation
Indices: 31418569--31418621 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
31418559 CGAATTTCTG
31418569 TTGGCTCTGCTATCAAGTTTCAGCTT
1 TTGGCTCTGCTATCAAGTTTCAGCTT
31418595 TTGGCTCTGCTATCAAGTTTCAGCTT
1 TTGGCTCTGCTATCAAGTTTCAGCTT
31418621 T
1 T
31418622 CCCGACTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (26 bp):
TTGGCTCTGCTATCAAGTTTCAGCTT
Found at i:31418953 original size:15 final size:15
Alignment explanation
Indices: 31418933--31418981 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
31418923 GGTTAAAGTT
31418933 TTTTCAATACTATGG
1 TTTTCAATACTATGG
*
31418948 TTTTCAATACTATAGTA
1 TTTTCAATACTAT-G-G
31418965 TTTTCAATACTATGG
1 TTTTCAATACTATGG
31418980 TT
1 TT
31418982 GCATCTACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 15 0.50
16 2 0.07
17 13 0.43
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (15 bp):
TTTTCAATACTATGG
Found at i:31421574 original size:20 final size:20
Alignment explanation
Indices: 31421549--31421588 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31421539 ACATGGGTAG
*
31421549 GCCACATGAGGCTGTGAGCC
1 GCCACATGAGCCTGTGAGCC
31421569 GCCACATGAGCCTGTGAGCC
1 GCCACATGAGCCTGTGAGCC
31421589 CATTTTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.15
Consensus pattern (20 bp):
GCCACATGAGCCTGTGAGCC
Found at i:31422759 original size:11 final size:11
Alignment explanation
Indices: 31422737--31422766 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
31422727 AGAATGGTTT
31422737 TTTGAGAAATGA
1 TTTGA-AAATGA
31422749 TTTGAAAATGA
1 TTTGAAAATGA
31422760 TTTGAAA
1 TTTGAAA
31422767 TAATTTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (11 bp):
TTTGAAAATGA
Found at i:31429211 original size:40 final size:40
Alignment explanation
Indices: 31429143--31429218 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
31429133 CGATACTTTA
*
31429143 TGGTATGTAGGGTTAGATAGGTCAATTTTATCCCCATATT
1 TGGTATGTAGGGATAGATAGGTCAATTTTATCCCCATATT
* * * *
31429183 TGGTTTGTAGGGATAGGTGGGTCGATTTTATCCCCA
1 TGGTATGTAGGGATAGATAGGTCAATTTTATCCCCA
31429219 CATGGTGTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.28, T:0.38
Consensus pattern (40 bp):
TGGTATGTAGGGATAGATAGGTCAATTTTATCCCCATATT
Found at i:31438905 original size:6 final size:6
Alignment explanation
Indices: 31438894--31438937 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
31438884 GAACCAATGT
*
31438894 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA- AGAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
31438938 GGGTATTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:31442768 original size:42 final size:42
Alignment explanation
Indices: 31442666--31442817 Score: 153
Period size: 43 Copynumber: 3.5 Consensus size: 42
31442656 TACAATTCTG
* * * *
31442666 ATGTCCCAGACGTGGTCTTATATGTAATCAAATATCAATGCCA
1 ATGTCCCAGACGTGGTCTTACACGAAATCAAATA-CGATGCCA
* * ***
31442709 CTGTCCCATATAAGGTCTTACACGAAATCAAATACGATGCCA
1 ATGTCCCAGACGTGGTCTTACACGAAATCAAATACGATGCCA
*
31442751 ATGTCCCAAACGTGGTCTTACACGTAAATACCAAAT-CGATGCCA
1 ATGTCCCAGACGTGGTCTTACACG-AAAT--CAAATACGATGCCA
**
31442795 ACATCCCAGACGTGGTCTTACAC
1 ATGTCCCAGACGTGGTCTTACAC
31442818 AATAATACAT
Statistics
Matches: 89, Mismatches: 17, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
42 26 0.29
43 30 0.34
44 28 0.31
45 5 0.06
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (42 bp):
ATGTCCCAGACGTGGTCTTACACGAAATCAAATACGATGCCA
Found at i:31442802 original size:44 final size:42
Alignment explanation
Indices: 31442722--31442817 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 42
31442712 TCCCATATAA
**
31442722 GGTCTTACACGAAATCAAATACGATGCCAATGTCCCAAACGT
1 GGTCTTACACGAAATCAAATACGATGCCAACATCCCAAACGT
*
31442764 GGTCTTACACGTAAATACCAAAT-CGATGCCAACATCCCAGACGT
1 GGTCTTACACG-AAAT--CAAATACGATGCCAACATCCCAAACGT
31442808 GGTCTTACAC
1 GGTCTTACAC
31442818 AATAATACAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
42 11 0.23
43 4 0.08
44 28 0.58
45 5 0.10
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (42 bp):
GGTCTTACACGAAATCAAATACGATGCCAACATCCCAAACGT
Found at i:31448964 original size:20 final size:20
Alignment explanation
Indices: 31448939--31448979 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
31448929 AGACATATGT
31448939 TTGGAACATTTTCATGTACA
1 TTGGAACATTTTCATGTACA
*
31448959 TTGGAACATTTTCGTGTACA
1 TTGGAACATTTTCATGTACA
31448979 T
1 T
31448980 CACATTCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (20 bp):
TTGGAACATTTTCATGTACA
Found at i:31451946 original size:39 final size:39
Alignment explanation
Indices: 31451892--31451968 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
31451882 TTCGAAATAC
*
31451892 ATAATTTGTTTCAAAAGTACAAACTATCATCTATACCAT
1 ATAATTTATTTCAAAAGTACAAACTATCATCTATACCAT
*
31451931 ATAATTTATTTCAAAAGTACAAACTATCATCTGTACCA
1 ATAATTTATTTCAAAAGTACAAACTATCATCTATACCA
31451969 ATGTGAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.35
Consensus pattern (39 bp):
ATAATTTATTTCAAAAGTACAAACTATCATCTATACCAT
Found at i:31462925 original size:49 final size:49
Alignment explanation
Indices: 31462751--31462966 Score: 286
Period size: 47 Copynumber: 4.6 Consensus size: 49
31462741 CCCTTCGGGA
* * * * *
31462751 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
31462798 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
31462845 CTGATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
31462892 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31462941 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
31462967 CACAATTATC
Statistics
Matches: 151, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
46 1 0.01
47 93 0.62
49 57 0.38
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:31462948 original size:96 final size:94
Alignment explanation
Indices: 31462751--31462967 Score: 299
Period size: 96 Copynumber: 2.3 Consensus size: 94
31462741 CCCTTCGGGA
* * * * *
31462751 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
*
31462816 TTTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* * * *
31462845 CTGATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCAC--ATATATAC
*
31462910 ACTTTCACATTCATCACATCGGCCATTCGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
31462941 CTTATCACATATATATACATTCACATC
1 CTTATCACATATATACACTTTCACATC
31462968 ACAATTATCC
Statistics
Matches: 106, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
94 46 0.43
96 60 0.57
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:31466336 original size:40 final size:40
Alignment explanation
Indices: 31466304--31466686 Score: 558
Period size: 40 Copynumber: 9.6 Consensus size: 40
31466294 CCAGCATGAT
* * * *
31466304 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * *
31466344 TGCTCTTCGAGG-TTTAGCACGGATATATTACTAGCACGAA
1 TGCTCTTCG-GGACTTAGCCCGGATACATCACTAGCACGAA
* *
31466384 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
31466424 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
31466464 TGCTCTTCGGGACTTAGCCC-GAGTACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGA-TACATCACTAGCACGAA
*
31466504 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
31466544 TGCTCTTCGGGACTTAGCCC-GAGTACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGA-TACATCACTAGCACGAA
*
31466584 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
31466624 TGCTCTTCGGGACTTAGCCC-GAGTACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGA-TACATCACTAGCACGAA
31466664 TGCTCTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
31466687 ACCGCTTTCC
Statistics
Matches: 310, Mismatches: 25, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
39 7 0.02
40 295 0.95
41 8 0.03
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:31473921 original size:18 final size:17
Alignment explanation
Indices: 31473862--31473921 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
31473852 AAAGAGTGAG
31473862 AAGTAAAAGTTTGAGGGA
1 AAGTAAAAGTTTGA-GGA
* *
31473880 AAATAAAAAGTTTTA-GA
1 AAGT-AAAAGTTTGAGGA
*
31473897 GAGTAAAAGTTTGAGGCA
1 AAGTAAAAGTTTGAGG-A
31473915 AAGTAAA
1 AAGTAAA
31473922 TAGGGGGAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
16 9 0.27
17 5 0.15
18 10 0.30
19 9 0.27
ACGTcount: A:0.50, C:0.02, G:0.25, T:0.23
Consensus pattern (17 bp):
AAGTAAAAGTTTGAGGA
Found at i:31477822 original size:2 final size:2
Alignment explanation
Indices: 31477817--31478618 Score: 1604
Period size: 2 Copynumber: 401.0 Consensus size: 2
31477807 TATATATATC
31477817 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31477859 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31477901 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31477943 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31477985 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478027 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478069 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478111 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478153 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478195 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478237 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478279 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478321 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478363 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478405 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478447 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478489 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478531 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478573 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
31478615 TG TG
1 TG TG
31478619 GTTATAATCT
Statistics
Matches: 800, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 800 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:31479320 original size:66 final size:66
Alignment explanation
Indices: 31479244--31479469 Score: 452
Period size: 66 Copynumber: 3.4 Consensus size: 66
31479234 TGATTGAGAC
31479244 GAATCATCATCTAAACATTGTAAATACAGACCATTGTCATCAATATAAAGCAGAAAATATATGAA
1 GAATCATCATCTAAACATTGTAAATACAGACCATTGTCATCAATATAAAGCAGAAAATATATGAA
31479309 T
66 T
31479310 GAATCATCATCTAAACATTGTAAATACAGACCATTGTCATCAATATAAAGCAGAAAATATATGAA
1 GAATCATCATCTAAACATTGTAAATACAGACCATTGTCATCAATATAAAGCAGAAAATATATGAA
31479375 T
66 T
31479376 GAATCATCATCTAAACATTGTAAATACAGACCATTGTCATCAATATAAAGCAGAAAATATATGAA
1 GAATCATCATCTAAACATTGTAAATACAGACCATTGTCATCAATATAAAGCAGAAAATATATGAA
31479441 T
66 T
31479442 GAATCATCATCTAAACATTGTAAATACA
1 GAATCATCATCTAAACATTGTAAATACA
31479470 CATAACTATC
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 160 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.27
Consensus pattern (66 bp):
GAATCATCATCTAAACATTGTAAATACAGACCATTGTCATCAATATAAAGCAGAAAATATATGAA
T
Found at i:31479467 original size:33 final size:34
Alignment explanation
Indices: 31479244--31479469 Score: 137
Period size: 33 Copynumber: 6.8 Consensus size: 34
31479234 TGATTGAGAC
31479244 GAATCATCATCTAAACATTGTAAATACAGACCATT
1 GAATCATCATCTAAACATTGTAAATACAGA-CATT
* * *
31479279 G--TCATCAATATAAAGCA--GAAAATATATGA-A-T
1 GAATCATC-ATCTAAA-CATTGTAAATACA-GACATT
31479310 GAATCATCATCTAAACATTGTAAATACAGACCATT
1 GAATCATCATCTAAACATTGTAAATACAGA-CATT
* * *
31479345 G--TCATCAATATAAAGCA--GAAAATATATGA-A-T
1 GAATCATC-ATCTAAA-CATTGTAAATACA-GACATT
31479376 GAATCATCATCTAAACATTGTAAATACAGACCATT
1 GAATCATCATCTAAACATTGTAAATACAGA-CATT
* * *
31479411 G--TCATCAATATAAAGCA--GAAAATATATGA-A-T
1 GAATCATC-ATCTAAA-CATTGTAAATACA-GACATT
31479442 GAATCATCATCTAAACATTGTAAATACA
1 GAATCATCATCTAAACATTGTAAATACA
31479470 CATAACTATC
Statistics
Matches: 146, Mismatches: 18, Indels: 56
0.66 0.08 0.25
Matches are distributed among these distances:
31 12 0.08
32 25 0.17
33 72 0.49
34 26 0.18
35 11 0.08
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.27
Consensus pattern (34 bp):
GAATCATCATCTAAACATTGTAAATACAGACATT
Found at i:31480171 original size:24 final size:24
Alignment explanation
Indices: 31480117--31480173 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
31480107 TGTGGTACAC
* *
31480117 GGCCGTATGACAACCCATGTCCTA
1 GGCCGTGTGACAACCCATGTCCCA
* *
31480141 GGCCGTGTGACAACTCGTGTCCCA
1 GGCCGTGTGACAACCCATGTCCCA
31480165 GGCCGTGTG
1 GGCCGTGTG
31480174 CATCATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.18, C:0.32, G:0.30, T:0.21
Consensus pattern (24 bp):
GGCCGTGTGACAACCCATGTCCCA
Found at i:31481149 original size:20 final size:20
Alignment explanation
Indices: 31481121--31481159 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31481111 TATGCATAAT
* * *
31481121 AGAGGCACCGAAGTGCAAAC
1 AGAGACACCAAAGTACAAAC
31481141 AGAGACACCAAAGTACAAA
1 AGAGACACCAAAGTACAAA
31481160 TCCAGTACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.23, G:0.23, T:0.05
Consensus pattern (20 bp):
AGAGACACCAAAGTACAAAC
Found at i:31484079 original size:23 final size:23
Alignment explanation
Indices: 31484049--31484098 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
31484039 TCACAAAAAC
31484049 TTAACTTTCGAACTCCAATGTCT
1 TTAACTTTCGAACTCCAATGTCT
31484072 TTAACTTTCGAACTCCAATGTCT
1 TTAACTTTCGAACTCCAATGTCT
31484095 TTAA
1 TTAA
31484099 GAAGACCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (23 bp):
TTAACTTTCGAACTCCAATGTCT
Found at i:31485981 original size:37 final size:37
Alignment explanation
Indices: 31485940--31486011 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
31485930 AATTATTTTA
31485940 ACTATGTTCTCTATTTGTATACAACAAGTTTGTACGT
1 ACTATGTTCTCTATTTGTATACAACAAGTTTGTACGT
*
31485977 ACTATGTTCTCTATTTGTGTACAACAAGTTTGTAC
1 ACTATGTTCTCTATTTGTATACAACAAGTTTGTAC
31486012 ATATAATGCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (37 bp):
ACTATGTTCTCTATTTGTATACAACAAGTTTGTACGT
Found at i:31487663 original size:46 final size:46
Alignment explanation
Indices: 31487594--31487763 Score: 202
Period size: 46 Copynumber: 3.7 Consensus size: 46
31487584 TGTAACCCGC
31487594 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCAT
* * *
31487640 CCATAAGTGAACTCGGACACAACTCAATGAGCTC-GG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGC-A--T
* *** * *
31487686 ACATCTCTTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCAT-AAGTGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCAT
31487733 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
31487764 TTCGGATGCT
Statistics
Matches: 101, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 2 0.02
46 60 0.59
47 28 0.28
48 1 0.01
49 4 0.04
50 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCAT
Found at i:31487713 original size:93 final size:93
Alignment explanation
Indices: 31487601--31487772 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
31487591 CGCCCATAAG
*
31487601 TGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACACAACTCA
1 TGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACACAACTCA
*
31487666 ATGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
* *
31487694 TGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACACAACTCA
*
31487759 ACGAGTTCGGATGC
66 ACGAGCTCGGATGC
31487773 TCAACCATCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
TGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACACAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:31495601 original size:57 final size:58
Alignment explanation
Indices: 31495461--31495604 Score: 139
Period size: 57 Copynumber: 2.5 Consensus size: 58
31495451 ACCTCATTAC
* * * * *
31495461 AAAAAGGATTTAGCTTGGACTGGTAATCCAGATATAAGTCCTCTCGAGCATATGTTAT
1 AAAAAGGATTTAGCCTGGACTGGTAATCCAGATACAAGTCCTCTAGAGCATATATCAT
** ** ** * * *
31495519 GGATTGGATTCGGCCCGGACGGGTAATCCAGAT-CAAG-CTCTTTAGAGCATATATCAT
1 AAAAAGGATTTAGCCTGGACTGGTAATCCAGATACAAGTC-CTCTAGAGCATATATCAT
31495576 AAAAAGGATTTAGCCTGGACTGGTAATCC
1 AAAAAGGATTTAGCCTGGACTGGTAATCC
31495605 CGACTAAGCT
Statistics
Matches: 63, Mismatches: 22, Indels: 3
0.72 0.25 0.03
Matches are distributed among these distances:
56 1 0.02
57 38 0.60
58 24 0.38
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (58 bp):
AAAAAGGATTTAGCCTGGACTGGTAATCCAGATACAAGTCCTCTAGAGCATATATCAT
Found at i:31506115 original size:21 final size:21
Alignment explanation
Indices: 31506082--31506130 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
31506072 TTAGAAATCA
*
31506082 AATAAAACA-ACAAA-ATTAC
1 AATAAAAAATACAAATATTAC
*
31506101 AATTAAAAAATACAAATTTTAC
1 AA-TAAAAAATACAAATATTAC
31506123 AATAAAAA
1 AATAAAAA
31506131 TTTACAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 6 0.24
21 11 0.44
22 6 0.24
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.22
Consensus pattern (21 bp):
AATAAAAAATACAAATATTAC
Found at i:31506781 original size:18 final size:20
Alignment explanation
Indices: 31506744--31506784 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
31506734 ATAATAAGTA
31506744 ATATATAATGTAGTACTATT
1 ATATATAATGTAGTACTATT
*
31506764 ATATATAAT-TATTA-TATT
1 ATATATAATGTAGTACTATT
31506782 ATA
1 ATA
31506785 GATTATGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 4 0.20
20 9 0.45
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (20 bp):
ATATATAATGTAGTACTATT
Found at i:31507037 original size:23 final size:24
Alignment explanation
Indices: 31507008--31507065 Score: 66
Period size: 28 Copynumber: 2.3 Consensus size: 24
31506998 TTATAGTATG
31507008 TGATATAGTATTA-TATAATAAAA
1 TGATATAGTATTATTATAATAAAA
31507031 TGATATATTAAGTATTATTATAATAAAA
1 TG--ATA-T-AGTATTATTATAATAAAA
31507059 -GATATAG
1 TGATATAG
31507066 CACCAATAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
23 4 0.13
24 1 0.03
25 6 0.20
26 1 0.03
27 8 0.27
28 10 0.33
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (24 bp):
TGATATAGTATTATTATAATAAAA
Found at i:31507276 original size:27 final size:28
Alignment explanation
Indices: 31507232--31507286 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
31507222 TATTTTGGAC
* * *
31507232 TTGAGTTTTGGGCTATAATTAGTTTATT
1 TTGAGTTTTGGACAATAATGAGTTTATT
31507260 TTGAG-TTTGGACAATAATGAGTTTATT
1 TTGAGTTTTGGACAATAATGAGTTTATT
31507287 ATTTGAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.25, C:0.04, G:0.22, T:0.49
Consensus pattern (28 bp):
TTGAGTTTTGGACAATAATGAGTTTATT
Found at i:31507601 original size:15 final size:16
Alignment explanation
Indices: 31507583--31507627 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
31507573 ATAAATTATT
31507583 ATATTTAAAATT-TAA
1 ATATTTAAAATTATAA
*
31507598 ATATTTATAACTTATAA
1 ATATTTA-AAATTATAA
31507615 A-ATTTAAAATTAT
1 ATATTTAAAATTAT
31507628 CTAACCCGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 13 0.50
16 9 0.35
17 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATTTAAAATTATAA
Found at i:31515380 original size:24 final size:23
Alignment explanation
Indices: 31515349--31515393 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
31515339 CCAAAATCAA
31515349 GGAACAAAAACCTGCAAAGAAAAG
1 GGAACAAAAA-CTGCAAAGAAAAG
* *
31515373 GGAACAAACACTGGAAAGAAA
1 GGAACAAAAACTGCAAAGAAA
31515394 GATCTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.58, C:0.16, G:0.22, T:0.04
Consensus pattern (23 bp):
GGAACAAAAACTGCAAAGAAAAG
Found at i:31515503 original size:2 final size:2
Alignment explanation
Indices: 31515496--31515528 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31515486 TTTGAGTAGC
31515496 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
31515529 CCCCAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:31518182 original size:76 final size:75
Alignment explanation
Indices: 31518056--31518206 Score: 257
Period size: 76 Copynumber: 2.0 Consensus size: 75
31518046 GCTTAAGAGT
* *
31518056 CTAATGAGAAAGGATTTAAAAGGCAATTAGACCCAAAATTTATTTGGGCTGGACGGCAAAGGCAT
1 CTAATGAGAAAGGATATAAAAGGCAATTAGACCCAAAAGTTATTTGGGCTGGACGGCAAAGGCAT
31518121 GAAATCAGCA
66 GAAATCAGCA
* *
31518131 NCTAATGAGAAAGGATATAAAAGGCAATTAGACCCAAAAGTTATTTGGGCTGGACGGCAAGGGTA
1 -CTAATGAGAAAGGATATAAAAGGCAATTAGACCCAAAAGTTATTTGGGCTGGACGGCAAAGGCA
31518196 TGAAATCAGCA
65 TGAAATCAGCA
31518207 GAAAAATTGA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (75 bp):
CTAATGAGAAAGGATATAAAAGGCAATTAGACCCAAAAGTTATTTGGGCTGGACGGCAAAGGCAT
GAAATCAGCA
Found at i:31519497 original size:23 final size:23
Alignment explanation
Indices: 31519471--31519515 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
31519461 TGGGTATGAG
*
31519471 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
31519494 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
31519516 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:31523510 original size:42 final size:42
Alignment explanation
Indices: 31523451--31523614 Score: 195
Period size: 42 Copynumber: 3.9 Consensus size: 42
31523441 TTAGGGTTTT
* *
31523451 TGAGATTTCGTGTAAGACCATATCTTGGATATGGTATTAATA
1 TGAGATTTCGTGTAAGACCATATCTGGGATATGGCATTAATA
**
31523493 TGAGATTTCGTGTAAGACCATATCTGGGATATGGCATTGGTA
1 TGAGATTTCGTGTAAGACCATATCTGGGATATGGCATTAATA
* * * **
31523535 TGAGACTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATA
1 TGAGATTTCGTGTAAGACCATATCTGGGATA-TGGCATTAATA
* * * *
31523578 CGAG-TTACATGTAAGACCATATTTGGGATATGGCATT
1 TGAGATTTCGTGTAAGACCATATCTGGGATATGGCATT
31523615 GGTGCGGAAC
Statistics
Matches: 104, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
41 6 0.06
42 86 0.83
43 12 0.12
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (42 bp):
TGAGATTTCGTGTAAGACCATATCTGGGATATGGCATTAATA
Found at i:31530036 original size:17 final size:16
Alignment explanation
Indices: 31530001--31530035 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
31529991 TTTAAAAGAA
31530001 TTTGGAAAATACTTTT
1 TTTGGAAAATACTTTT
31530017 TTTGGAAAATACTTTT
1 TTTGGAAAATACTTTT
31530033 TTT
1 TTT
31530036 TTCATTTGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (16 bp):
TTTGGAAAATACTTTT
Found at i:31530166 original size:29 final size:30
Alignment explanation
Indices: 31530121--31530186 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
31530111 ATTTAGATTT
* *
31530121 ATTTAATTCTATTTAATAGTACAAAAATTA
1 ATTTAATTCTATTTAATAATACAAAAACTA
* *
31530151 ATTTAATT-TATTTAATAATAGAAGAACTA
1 ATTTAATTCTATTTAATAATACAAAAACTA
31530180 ATTTAAT
1 ATTTAAT
31530187 CTAATTCTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (30 bp):
ATTTAATTCTATTTAATAATACAAAAACTA
Found at i:31535240 original size:26 final size:26
Alignment explanation
Indices: 31535184--31535234 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
31535174 AATACACTAA
* * * *
31535184 AAATATTAAAATAAATATTTTTCAAT
1 AAATATTAAAATAAACAATATCCAAT
31535210 AAATATTAAAATAAACAATATCCAA
1 AAATATTAAAATAAACAATATCCAA
31535235 ACAATAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATATTAAAATAAACAATATCCAAT
Found at i:31537126 original size:3 final size:3
Alignment explanation
Indices: 31537118--31537142 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31537108 GAATATGGAA
31537118 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
31537143 GGGGACCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Done.