Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000116.1 Hibiscus syriacus cultivar Beakdansim tig00000211_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 74943
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:302 original size:162 final size:162
Alignment explanation
Indices: 1--322 Score: 524
Period size: 162 Copynumber: 2.0 Consensus size: 162
* *
1 CTTCACAATCGTGTCCTCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTTAACAATC
1 CTTCACAATCGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATC
*
66 GTGTCAGCTCCATATTCCTTCAGAGAGTATAGACTCGAACAATCTTCAACAATCGTGTATGCTAC
66 GTGTCAGCTCCATATTCCTTCAGAGAGTATAGACTCGAACAATCTTCAACAATCGTGTACGCTAC
131 CTATCCTTCAGAGAAT-TAAGACTCGAACAAC
131 CTATCCTTCAGAGAATATAAGACTCGAACAAC
**
162 CTTCAGCAATCGTGTCCGCTCCCTATTTTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
1 CTTCA-CAATCGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
* *
227 CGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGT-CGCT
65 CGTGTCAGCTCCATATTCCTTCAGAGAGTAT-AGACTCGAACAATCTTCAACAATCGTGTACGCT
*
291 -CCTATTCCTTCAGAGAGTATAAGACTCGAACA
129 ACCTA-TCCTTCAGAGAATATAAGACTCGAACA
323 TCTTCTTCAA
Statistics
Matches: 149, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
161 9 0.06
162 99 0.66
163 41 0.28
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (162 bp):
CTTCACAATCGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATC
GTGTCAGCTCCATATTCCTTCAGAGAGTATAGACTCGAACAATCTTCAACAATCGTGTACGCTAC
CTATCCTTCAGAGAATATAAGACTCGAACAAC
Found at i:332 original size:55 final size:55
Alignment explanation
Indices: 1--327 Score: 488
Period size: 55 Copynumber: 6.1 Consensus size: 55
*
1 CTTC-ACAATCGTGTCCTCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
1 CTTCAACAATCGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
* * *
55 CTTTAACAATCGTGTCAGCTCCATATTCCTTCAGAGAGTAT-AGACTCGAACAAT
1 CTTCAACAATCGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
** * * *
109 CTTCAACAATCGTGTATGCTACCTA-TCCTTCAGAGAAT-TAAGACTCGAACAAC
1 CTTCAACAATCGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
* **
162 CTTCAGCAATCGTGTCCGCTCCCTATTTTTTCAGAGAGTATAAGACTCGAACAAT
1 CTTCAACAATCGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
*
217 CTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
1 CTTCAACAATCGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
272 CTTCAACAATCGTGT-CGCT-CCTATTCCTTCAGAGAGTATAAGACTCGAAC-AT
1 CTTCAACAATCGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
324 CTTC
1 CTTC
328 TTCAAACGGG
Statistics
Matches: 245, Mismatches: 24, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
52 7 0.03
53 76 0.31
54 49 0.20
55 113 0.46
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.29
Consensus pattern (55 bp):
CTTCAACAATCGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
Found at i:379 original size:162 final size:162
Alignment explanation
Indices: 13--387 Score: 481
Period size: 162 Copynumber: 2.3 Consensus size: 162
3 TCACAATCGT
* ** * *
13 GTCCTCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTTAACAATCGTGTCAGCTCCA
1 GTCCGCTCCCTATTTTTTAAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCAGCTCCA
*
78 TATTCCTTCAGAGAGTATAGACTCGAACAATCTTCAACAATCGTGTATGCTACCTATCCTTCAGA
66 TATTCCTTCAGAGAGTATAGACTCGAACAATCTTCAACAATCGTGTACGCTACCTATCCTTCAGA
* *
143 GAATTAAGACTCGAACAACCTTCAGCAATCGT
131 GAATTAAGACTCGAACAACCTTCAGCAAACGG
* * *
175 GTCCGCTCCCTATTTTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCC
1 GTCCGCTCCCTATTTTTTAAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCAGCTCCA
240 TATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGT-CGCT-CCTATTCCTTCA
66 TATTCCTTCAGAGAGTAT-AGACTCGAACAATCTTCAACAATCGTGTACGCTACCTA-TCCTTCA
* * **
303 GAGAGTATAAGACTCGAAC-ATCTTCTTCAAACGG
129 GAGAAT-TAAGACTCGAACAACCTTCAGCAAACGG
* * * * * *
337 GTTCGCTCCTTCTTTCTTTAAG-GAGTAT-GGAACTCAAACAATCTTCTACAA
1 GTCCGCTCCCTATTT-TTTAAGAGAGTATAAG-ACTCGAACAATCTTCAACAA
388 ACGGATTCGC
Statistics
Matches: 188, Mismatches: 20, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
161 5 0.03
162 138 0.73
163 45 0.24
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (162 bp):
GTCCGCTCCCTATTTTTTAAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCAGCTCCA
TATTCCTTCAGAGAGTATAGACTCGAACAATCTTCAACAATCGTGTACGCTACCTATCCTTCAGA
GAATTAAGACTCGAACAACCTTCAGCAAACGG
Found at i:401 original size:108 final size:108
Alignment explanation
Indices: 18--390 Score: 384
Period size: 107 Copynumber: 3.5 Consensus size: 108
8 ATCGTGTCCT
* * * *
18 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTTAACAATCGTGTCAGCTCCATATTC
1 CTCCCTATTCCTTAAGAGAGTATAAGACTCAAACAATCTTCAACAAACGTGTC-GCTCC-TATTC
* * *
83 CTTCAGAGAGTAT-AGACTCGAACAATCTTCAACAATCGTGTATG
64 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCTG
* * * * * * * *
127 CTACCTA-TCCTTCAGAGAAT-TAAGACTCGAACAACCTTCAGCAATCGTGTCCGCTCCCTATTT
1 CTCCCTATTCCTTAAGAGAGTATAAGACTCAAACAATCTTCAACAAACGTGT-CGCT-CCTATTC
* * *
190 TTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTG
64 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCTG
* * *
235 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCGCTCCTATTCCT
1 CTCCCTATTCCTTAAGAGAGTATAAGACTCAAACAATCTTCAACAAACGTGTCGCTCCTATTCCT
**
300 TCAGAGAGTATAAGACTCGAAC-ATCTTCTTCAAACGGGT-TCG
66 TCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCT-G
* * *
342 CTCCTTCT-TTCTTTAAG-GAGTAT-GGAACTCAAACAATCTTCTACAAACG
1 CTCC--CTATTCCTTAAGAGAGTATAAG-ACTCAAACAATCTTCAACAAACG
391 GATTCGCTCC
Statistics
Matches: 231, Mismatches: 24, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
106 2 0.01
107 90 0.39
108 87 0.38
109 24 0.10
110 28 0.12
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (108 bp):
CTCCCTATTCCTTAAGAGAGTATAAGACTCAAACAATCTTCAACAAACGTGTCGCTCCTATTCCT
TCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCTG
Found at i:5169 original size:21 final size:22
Alignment explanation
Indices: 5145--5192 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 22
5135 AATGCAAAGC
5145 GTCTTCAT-GTCTTTATG-AATG
1 GTCTTC-TCGTCTTTATGAAATG
5166 GTCTTCTCGTCTTTATGAAATG
1 GTCTTCTCGTCTTTATGAAATG
5188 GTCTT
1 GTCTT
5193 ATTGTGCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 1 0.04
21 15 0.60
22 9 0.36
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.48
Consensus pattern (22 bp):
GTCTTCTCGTCTTTATGAAATG
Found at i:7326 original size:2 final size:2
Alignment explanation
Indices: 7271--7308 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
7261 CATTCAATTA
7271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7309 GCTTGCATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9321 original size:3 final size:3
Alignment explanation
Indices: 9313--9350 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
9303 TAATTTGTAT
9313 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TTAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TA
9351 TTTATAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:14999 original size:30 final size:30
Alignment explanation
Indices: 14963--15019 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
14953 GTCCTTTAAA
** *
14963 ATTATTATAAATATTAATTATATTATTATT
1 ATTATTATAAATACAAATTACATTATTATT
*
14993 ATTATTATTAATACAAATTACATTATT
1 ATTATTATAAATACAAATTACATTATT
15020 TATATAGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (30 bp):
ATTATTATAAATACAAATTACATTATTATT
Found at i:16496 original size:2 final size:2
Alignment explanation
Indices: 16489--16515 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16479 TTCATGCATT
16489 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
16516 TACATTCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23216 original size:14 final size:14
Alignment explanation
Indices: 23199--23240 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
23189 GAGAAATGTT
23199 AAAAGAGAAAAAAG
1 AAAAGAGAAAAAAG
*
23213 AAAAGATAAAAAAAAG
1 AAAAG--AGAAAAAAG
23229 AAAA-AGAAAAAA
1 AAAAGAGAAAAAA
23241 TTGTAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 7 0.29
14 5 0.21
16 12 0.50
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (14 bp):
AAAAGAGAAAAAAG
Found at i:23233 original size:17 final size:15
Alignment explanation
Indices: 23206--23240 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
23196 GTTAAAAGAG
23206 AAAAAAGAAAAGATAA
1 AAAAAAGAAAAGA-AA
23222 AAAAAAGAAAAAGAAA
1 AAAAAAG-AAAAGAAA
23238 AAA
1 AAA
23241 TTGTAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAAAGAAA
Found at i:24739 original size:125 final size:125
Alignment explanation
Indices: 24511--24888 Score: 449
Period size: 125 Copynumber: 3.0 Consensus size: 125
24501 TTAGGATATG
* **
24511 TTGGGGCACGACTGAACCCACATCAGGTTGAGATGACAAGATTCAGACCAATGAGGCATGAAGAA
1 TTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAAAAGGCATGAAGAA
* * * *
24576 TGAGCCTTAGAATTTGAGGTGATGAGGCATTTTAAAGGCCCGTACCAGTATAAGACAATA
66 GGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACAATA
* * * *
24636 TTGGGGCACGACTGAACCCACGTCATGTTGAGATGACAAGATTTAAACCAAAAATGCATGAAGAA
1 TTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAAAAGGCATGAAGAA
** * * *
24701 GGAGCCTTACAATTTGAGGTGATGGGGTTTTTTGAAGGCCCATACCGGTATAAGACACTGA
66 GGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACAAT-A
* * * *
24762 -TGGGGCATGACTGCACCCACATCGTG-TGAAGATGACAAGATTCAGACCAAGAAGGCATTG-AG
1 TTGGGGCACGACTGAACCCACATCATGTTG-AGATGACAAGATTCAGACCAAAAAGGCA-TGAAG
* * * * * * *
24824 -AGCAAGCCTTACAATCTGAGATGTTGGGGCATTTTGAAGGCCCGTACCAATGTAAGATAATA
64 AAG-GAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACAATA
24886 TTG
1 TTG
24889 CGACACTAGG
Statistics
Matches: 212, Mismatches: 36, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
124 5 0.02
125 204 0.96
126 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (125 bp):
TTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAAAAGGCATGAAGAA
GGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACAATA
Found at i:26121 original size:36 final size:36
Alignment explanation
Indices: 26042--26141 Score: 121
Period size: 36 Copynumber: 2.8 Consensus size: 36
26032 CTGAAGTCTT
* * * *
26042 CACCAAATAATAGTGAAGC-GACCATCTTAAGCCTT
1 CACCAAAGAATAGTGAAGCAAACCATCTTAAGCATG
* * *
26077 CACTAAAGAGTAGTGAAGCAAACCGTCTTAAGCATG
1 CACCAAAGAATAGTGAAGCAAACCATCTTAAGCATG
*
26113 CACCAAAGAATAATGAAGCAAACCATCTT
1 CACCAAAGAATAGTGAAGCAAACCATCTT
26142 GTGTCTTCAT
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
35 16 0.30
36 37 0.70
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (36 bp):
CACCAAAGAATAGTGAAGCAAACCATCTTAAGCATG
Found at i:26742 original size:54 final size:54
Alignment explanation
Indices: 26555--27152 Score: 877
Period size: 54 Copynumber: 11.2 Consensus size: 54
26545 AGTGAAGCAA
* * *
26555 AAGAAGATTTTCGAGTTCCATACTCCCTAGAGAAAGTGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
26609 AAG-A-TTGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT-
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
26660 --GAAGATGTACGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
26712 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
26766 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTA
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
26820 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGTGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
26874 AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * *
26928 AAGAAGATTTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * * * *
26982 AAG-AGATATCCGAGTTCCATACTCCTTAAAGAAAGAAGGAGTGAACCCATTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * **
27035 AAG-AGATTTCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCTGTAAG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCC-GTTTG
* *
27089 AAGAAGATGTTCGAGTTCCATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTG
**
27144 TTGAAGATG
1 AAGAAGATG
27153 GTTCGAGTCT
Statistics
Matches: 496, Mismatches: 40, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
49 1 0.00
50 1 0.00
51 44 0.09
52 44 0.09
53 86 0.17
54 270 0.54
55 31 0.06
56 19 0.04
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (54 bp):
AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
Found at i:26824 original size:108 final size:108
Alignment explanation
Indices: 26555--27285 Score: 892
Period size: 108 Copynumber: 6.8 Consensus size: 108
26545 AGTGAAGCAA
* * * *
26555 AAGAAGATTTTCGAGTTCCATACTCCCTAGAGAAAGTGGGAGCGAACCCGTTTGAAG-A-TTGTT
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
26618 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT-
66 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
26660 --GAAGATGTACGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTTTGAAGAAGATGTC
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
26723 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
66 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
26766 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAAGAAGATGTC
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
*
26831 CGAGTTCCATACTCCCTAGAGAAAGTGGGAGCGAACCCGTTTG
66 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
26874 AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTTT
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
*
26939 CGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTTG
66 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * * * * * *
26982 AAG-AGATATCCGAGTTCCATACTCCTTAAAGAAAGAAGGAGTGAACCCATTTGAAG-AGATTTC
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* * **
27045 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCTGTAAG
66 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCC-GTTTG
* **
27089 AAGAAGATGTTCGAGTTCCATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTGTTGAAGATGG
1 AAGAAGATGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGAT-G
* * * * *
27154 TTCGAG-TCTTATACTCTCT-GCAAGAAATG-GAGAGC-AGACACGATTT-
64 TCCGAGTTC-CATACTCCCTAG--AGAAA-GAGGGAGCGA-ACCCG-TTTG
** ** * * **
27200 TTGAAGATTGTTCGAGTTTTATACTCCCTGAAAGAAAGATGGAGCGAACCCGTTTTCAGAAGATT
1 AAGAAGA-TGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-T
* *
27265 GTTCGAGTTCTATACTCCCTA
63 GTCCGAGTTCCATACTCCCTA
27286 AAAGAATAGG
Statistics
Matches: 550, Mismatches: 56, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
103 51 0.09
104 1 0.00
105 45 0.08
106 41 0.07
107 52 0.09
108 228 0.41
109 24 0.04
110 7 0.01
111 19 0.03
112 78 0.14
113 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (108 bp):
AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
Found at i:27212 original size:112 final size:111
Alignment explanation
Indices: 26557--27373 Score: 397
Period size: 108 Copynumber: 7.6 Consensus size: 111
26547 TGAAGCAAAA
* * * *
26557 GAAGATT-TTCGAGTTCCATACTCCCT-AGAGAAAGTGGGAGCGAACCCG-TTT--GAAGATTGT
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGATGGT
* * * * *
26617 TCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGC-GAACCCGTT--T-
66 TCGAGTTCTATACTCCCTAAAAG-AATAGGAAGCAG-ACACGTTGGTC
* * * * **
26660 GAAGA-TGTACGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCTGTTTGAAGAAGAT-GT
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGATGGT
* * * * * * * **
26722 CCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGC-GAACCCGTTTGAA
66 TCGAGTTCTATACTCCCTAAAAG-AATAGGAAGCAG-ACACGTTGGTC
* * * **
26768 GAAGA-TGTCCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTAAAGAAGAT-GT
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGATGGT
* * * * * * **
26830 CCGAGTTCCATACTCCCT-AGAGAA-AGTGGGAGC-GAACCCGTTTGAA
66 TCGAGTTCTATACTCCCTAAAAGAATA--GGAAGCAG-ACACGTTGGTC
* * ** *
26876 GAAGA-TGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGAT-TT
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGATGGT
* * * * * *
26938 TCGAGTTCCATACTTCCT-AGAGAAAGAGGGAGC-GAACCCGTT--T-
66 TCGAGTTCTATACTCCCTAAAAG-AATAGGAAGCAG-ACACGTTGGTC
* * * * * * * * **
26981 GAAGAGATATCCGAGTTCCATACT-CCTTAAAGAAAGAAGGAGTGAACCCATTTGAAG-AGAT--
1 GAAGA-TTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGATGG
* * * * * * ** **
27042 TTCTGAGTTCCATACTCCCT-AGAGAAAGAGGGAG-TGAACCCTGTAAGAA
65 TTC-GAGTTCTATACTCCCTAAAAG-AATAGGAAGCAG-ACAC-GTTGGTC
* *
27091 GAAGA-TGTTCGAGTTCCATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTGT-TGAAGATGG
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTT-TCAGAAGATGG
* ** * *
27154 TTCGAG-TCTTATACTCTCTGCAAGAA-ATGGAGAGCAGACACGATT-TTT
65 TTCGAGTTC-TATACTCCCTAAAAGAATA-GGA-AGCAGACACG-TTGGTC
* * *
27202 GAAGATTGTTCGAGTTTTATACTCCCTGAAAGAAAGATGGAGCGAACCCGTTTTCAGAAGATTGT
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGATGGT
27267 TCGAGTTCTATACTCCCTAAAAGAATAGGAAGCAGACACGTTGGTC
66 TCGAGTTCTATACTCCCTAAAAGAATAGGAAGCAGACACGTTGGTC
* * * * *
27313 GAAGATTGTTCAAG-TCTTATACTCTCTGAAAGAATAGA--GAGCGGACACGTTTTCCGAAGAT
1 GAAGATTGTTCGAGTTC-TATACTCCCTGAAAGAA-AGAGGGAGCGAACCCGTTTTCAGAAGAT
27374 TTTTCAAGTC
Statistics
Matches: 617, Mismatches: 59, Indels: 69
0.83 0.08 0.09
Matches are distributed among these distances:
102 1 0.00
103 43 0.07
104 2 0.00
105 51 0.08
106 49 0.08
107 44 0.07
108 209 0.34
109 28 0.05
110 36 0.06
111 62 0.10
112 88 0.14
113 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (111 bp):
GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGATGGT
TCGAGTTCTATACTCCCTAAAAGAATAGGAAGCAGACACGTTGGTC
Found at i:27334 original size:55 final size:54
Alignment explanation
Indices: 27091--27384 Score: 244
Period size: 56 Copynumber: 5.3 Consensus size: 54
27081 CCTGTAAGAA
* * * *
27091 GAAGA-TGTTCGAGT-TCCATACTCCCTGAAAGAAAGAGGGAGC-GAACCCGTTTGTT
1 GAAGATTGTTCGAGTCT-TATACTCCCTGAAAGAAAG-GAGAGCAG-ACACGTTT-TC
* * * *
27146 GAAGATGGTTCGAGTCTTATACTCTCTGCAAGAAATGGAGAGCAGACACGATTTTT
1 GAAGATTGTTCGAGTCTTATACTCCCTGAAAGAAA-GGAGAGCAGACACG-TTTTC
* *
27202 GAAGATTGTTCGAGTTTTATACTCCCTGAAAGAAA-GATGGAGC-GAACCCGTTTTC
1 GAAGATTGTTCGAGTCTTATACTCCCTGAAAGAAAGGA--GAGCAG-ACACGTTTTC
* *
27257 AGAAGATTGTTCGAGT-TCTATACTCCCTAAAAGAATAGGA-AGCAGACACGTTGGTC
1 -GAAGATTGTTCGAGTCT-TATACTCCCTGAAAGAA-AGGAGAGCAGACACGTT-TTC
* * *
27313 GAAGATTGTTCAAGTCTTATACTCTCTGAAAGAATA-GAGAGCGGACACGTTTTCC
1 GAAGATTGTTCGAGTCTTATACTCCCTGAAAGAA-AGGAGAGCAGACACGTTTT-C
* *
27368 GAAGATTTTTCAAGTCT
1 GAAGATTGTTCGAGTCT
27385 CATTTAGTTA
Statistics
Matches: 201, Mismatches: 21, Indels: 34
0.79 0.08 0.13
Matches are distributed among these distances:
54 5 0.02
55 79 0.39
56 108 0.54
57 7 0.03
58 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (54 bp):
GAAGATTGTTCGAGTCTTATACTCCCTGAAAGAAAGGAGAGCAGACACGTTTTC
Found at i:33222 original size:3 final size:3
Alignment explanation
Indices: 33214--33249 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
33204 GCATGTAAAT
33214 TAA TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TA
33250 TATTTATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:34520 original size:80 final size:82
Alignment explanation
Indices: 34412--34829 Score: 352
Period size: 80 Copynumber: 5.1 Consensus size: 82
34402 TAGAGCAATT
* * * * * *
34412 GGTTATCTGCCAACAAAGACCTTTGAGTTCAATTACACTCAGTTCAACGGCACAACATTTGCGGT
1 GGTTATCTGCC-ACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAACATTTGCAGC
*
34477 ATAGCTCAAGGCTAA-AAG
65 ATAACTCAAGGC-AAGAAG
* * ** * *
34495 GGTTATCTG-C-CAAAGACCTTCGAGTTCGAGTACAGTCAGCTTTGAGGGCACATCATTTGCAGC
1 GGTTATCTGCCACAAAGACCTTCGAGTTCGATTACACTCAGC-TCAAAGGCACAACATTTGCAGC
***
34558 ATAACTCAAGGTTGGAAG
65 ATAACTCAAGGCAAGAAG
* * * * * * * *
34576 GGTTATCTGTCAACAAAGACCTTTGAGTTCG---ACGCTCAGCTCAATGGAATATCATTTACAGC
1 GGTTATCTG-CCACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAACATTTGCAGC
* *
34638 ATAGCTTAAGGCAAGAAG
65 ATAACTCAAGGCAAGAAG
* * * * * *
34656 AGCTATATG-C-CAAAGACCTTCGAGTTCGATTACATTTAGCTCAAAAGCACATA-ATTTGCAGC
1 GGTTATCTGCCACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACA-ACATTTGCAGC
34718 ATAACTCAAGGCAAGAAG
65 ATAACTCAAGGCAAGAAG
* * *
34736 GGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAAGCGC-CATCATTTAC
1 GGTTATCTGCC-AC-AAAGACCTTCGAGTTCGATTACACTCAGCTC-AAAG-GCACAACATTTGC
*
34800 AGCATAACTCAAGGCGAGAAG
62 AGCATAACTCAAGGCAAGAAG
*
34821 GTTTATCTG
1 GGTTATCTG
34830 TCATCAAAAT
Statistics
Matches: 262, Mismatches: 57, Indels: 30
0.75 0.16 0.09
Matches are distributed among these distances:
77 17 0.06
80 103 0.39
81 46 0.18
82 1 0.00
83 10 0.04
84 45 0.17
85 38 0.15
86 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (82 bp):
GGTTATCTGCCACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAACATTTGCAGCA
TAACTCAAGGCAAGAAG
Found at i:36609 original size:21 final size:21
Alignment explanation
Indices: 36585--36666 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 21
36575 TTTATTTATC
36585 TTTATTTTTTATATATTACAT
1 TTTATTTTTTATATATTACAT
* *
36606 TTTA-TTATTAT-TATATACGT
1 TTTATTTTTTATATAT-TACAT
*
36626 TTTATTATTATTATTATATTATAT
1 TTTATT-TT-TTA-TATATTACAT
* *
36650 TTTATTATATATATATT
1 TTTATTTTTTATATATT
36667 TTATTAACTG
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
19 3 0.06
20 14 0.29
21 11 0.23
22 3 0.06
23 4 0.08
24 10 0.21
25 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (21 bp):
TTTATTTTTTATATATTACAT
Found at i:36615 original size:3 final size:3
Alignment explanation
Indices: 36607--36687 Score: 55
Period size: 3 Copynumber: 26.7 Consensus size: 3
36597 ATATTACATT
36607 TTA TTA TTA TTA TATA CGTT- TTA TTA TTA TTA TTA -TA TTA -TA TT-
1 TTA TTA TTA TTA T-TA --TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
36651 TTA TTA TATA TATA TT- TTA TTAA CTG TTA TTA TTA TT
1 TTA TTA T-TA T-TA TTA TTA TT-A TTA TTA TTA TTA TT
36688 TTTTCCTTCT
Statistics
Matches: 64, Mismatches: 4, Indels: 20
0.73 0.05 0.23
Matches are distributed among these distances:
2 10 0.16
3 41 0.64
4 11 0.17
5 1 0.02
6 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:36628 original size:20 final size:18
Alignment explanation
Indices: 36604--36672 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 18
36594 TATATATTAC
36604 ATTTTATTATTATTATAT
1 ATTTTATTATTATTATAT
36622 ACGTTTTATTATTATTATTAT
1 A--TTTTATTATTATTA-TAT
*
36643 ATTATATTTTATTATATATAT
1 ATT-T-TATTATTAT-TATAT
36664 ATTTTATTA
1 ATTTTATTA
36673 ACTGTTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
18 1 0.02
19 6 0.14
20 16 0.37
21 18 0.42
22 2 0.05
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (18 bp):
ATTTTATTATTATTATAT
Found at i:36648 original size:26 final size:25
Alignment explanation
Indices: 36607--36687 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 25
36597 ATATTACATT
36607 TTATTATTAT-TATATACGTTTTATTA
1 TTATTATTATAT-TATAC-TTTTATTA
36633 TTATTATTATATTATA-TTTTATTA
1 TTATTATTATATTATACTTTTATTA
* *
36657 TATATATATTTTATTA-ACTGTTATTA
1 T-TAT-TATTATATTATACTTTTATTA
36683 TTATT
1 TTATT
36688 TTTTCCTTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
24 10 0.20
25 7 0.14
26 31 0.63
27 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
TTATTATTATATTATACTTTTATTA
Found at i:36671 original size:21 final size:21
Alignment explanation
Indices: 36554--36671 Score: 68
Period size: 21 Copynumber: 5.5 Consensus size: 21
36544 CCTTCAGTTC
*
36554 ATATTTTAATTTT-TTTTTCATT
1 ATATTTT-ATTTTATTATT-ATT
*
36576 TTA-TTTATCTTTATT-TT-TT
1 ATATTTTAT-TTTATTATTATT
*
36595 ATATATTACATTTTATTATTATT
1 ATAT-TT-TATTTTATTATTATT
*
36618 ATATACGTTT-TATTATTATTATT
1 ATAT---TTTATTTTATTATTATT
*
36641 ATATTATATTTTATTA-TATAT
1 ATATTTTATTTTATTATTAT-T
36662 ATATTTTATT
1 ATATTTTATT
36672 AACTGTTATT
Statistics
Matches: 76, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
19 4 0.05
20 7 0.09
21 33 0.43
22 8 0.11
23 22 0.29
25 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (21 bp):
ATATTTTATTTTATTATTATT
Found at i:36686 original size:44 final size:43
Alignment explanation
Indices: 36585--36672 Score: 116
Period size: 44 Copynumber: 2.2 Consensus size: 43
36575 TTTATTTATC
36585 TTTATT-TT-TTA-TATATTACATTTTATTATTATTATATACGT
1 TTTATTATTATTATTATATTACATTTTATTATTATTATATAC-T
*
36626 TTTATTATTATTATTATATTATATTTTATTA-TA-TATATA-T
1 TTTATTATTATTATTATATTACATTTTATTATTATTATATACT
36666 TTTATTA
1 TTTATTA
36673 ACTGTTATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
40 8 0.19
41 6 0.14
42 8 0.19
43 5 0.12
44 16 0.37
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (43 bp):
TTTATTATTATTATTATATTACATTTTATTATTATTATATACT
Found at i:37113 original size:11 final size:10
Alignment explanation
Indices: 37099--37174 Score: 55
Period size: 11 Copynumber: 7.1 Consensus size: 10
37089 TATTGTTTTC
37099 TTTTTTATTAT
1 TTTTTTATT-T
*
37110 TTTTTTATACT
1 TTTTTTAT-TT
*
37121 TATTTTATTT
1 TTTTTTATTT
37131 TTTCTTTATTT
1 TTT-TTTATTT
37142 TTGTTTT-TATT
1 TT-TTTTAT-TT
* *
37153 TCTGTTATTT
1 TTTTTTATTT
37163 TTCTTTTATTT
1 TT-TTTTATTT
37174 T
1 T
37175 AGGTATTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
10 10 0.20
11 40 0.78
12 1 0.02
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:37115 original size:18 final size:18
Alignment explanation
Indices: 37081--37114 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37071 ATATAAATAT
37081 TTTTTTACTATTGTTTTC
1 TTTTTTACTATTGTTTTC
*
37099 TTTTTTATTATT-TTTT
1 TTTTTTACTATTGTTTT
37115 TATACTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTTTACTATTGTTTTC
Found at i:37126 original size:29 final size:30
Alignment explanation
Indices: 37078--37143 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
37068 TATATATAAA
* *
37078 TATTTTTTTACTATTGTTTTCTTTTTT-AT
1 TATTTTTTTACTATTATTTTATTTTTTCAT
*
37107 TATTTTTTTA-TACTTATTTTATTTTTTCTT
1 TATTTTTTTACTA-TTATTTTATTTTTTCAT
37137 TATTTTT
1 TATTTTT
37144 GTTTTTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 2 0.06
29 22 0.69
30 8 0.25
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (30 bp):
TATTTTTTTACTATTATTTTATTTTTTCAT
Found at i:37162 original size:21 final size:19
Alignment explanation
Indices: 37131--37173 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
37121 TATTTTATTT
*
37131 TTTCTTTATTTTTGTTTTTA
1 TTTCTTTATTTTT-CTTTTA
37151 TTTCTGTTATTTTTCTTTTA
1 TTTCT-TTATTTTTCTTTTA
37171 TTT
1 TTT
37174 TAGGTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.09, C:0.07, G:0.05, T:0.79
Consensus pattern (19 bp):
TTTCTTTATTTTTCTTTTA
Found at i:37219 original size:23 final size:21
Alignment explanation
Indices: 37097--37244 Score: 83
Period size: 22 Copynumber: 6.7 Consensus size: 21
37087 ACTATTGTTT
* *
37097 TCTTTTTTATTATTT-TTTTA
1 TCTTTTTTTTTATTTACTTTA
37117 TACTTATTTTATTT-TTT-CTTTA
1 T-CTT-TTTT-TTTATTTACTTTA
37139 T-TTTTGTTTTTATTT-CTGTTA
1 TCTTTT-TTTTTATTTACT-TTA
* * *
37160 T-TTTTCTTTTATTTTAGGTATTT
1 TCTTTTTTTTTA-TTTA-CT-TTA
37183 TACTTATTTTTTTATCTTACTTTA
1 T-CTT-TTTTTTTAT-TTACTTTA
*
37207 TCCTTTTTTTTTATTTTCTTTA
1 T-CTTTTTTTTTATTTACTTTA
37229 TCTTTTTTATTTATTT
1 TCTTTTTT-TTTATTT
37245 CATTTTTCTC
Statistics
Matches: 103, Mismatches: 11, Indels: 26
0.74 0.08 0.19
Matches are distributed among these distances:
19 5 0.05
20 15 0.15
21 21 0.20
22 27 0.26
23 15 0.15
24 6 0.06
25 4 0.04
26 10 0.10
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (21 bp):
TCTTTTTTTTTATTTACTTTA
Found at i:37858 original size:31 final size:31
Alignment explanation
Indices: 37822--37880 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
37812 AAAGAACATT
37822 AACAAGTTATATTCCTTAATGAACGAACTTG
1 AACAAGTTATATTCCTTAATGAACGAACTTG
*
37853 AACAAGTTATATTCCTTAATGAATGAAC
1 AACAAGTTATATTCCTTAATGAACGAAC
37881 ACGAATAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (31 bp):
AACAAGTTATATTCCTTAATGAACGAACTTG
Found at i:41453 original size:157 final size:157
Alignment explanation
Indices: 40572--44129 Score: 4907
Period size: 157 Copynumber: 22.9 Consensus size: 157
40562 AACATTACAA
* * * *
40572 TCAACTCTGTTACAATACATCTTGAATTATCATTAGTGAAAAACCT-AAATGGTCCTTTCCTACT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAA-GATCCATTCCTACT
* * *
40636 TAAAGGGCGACATGCCTAAAAATACCCGACATACAACAAAAAATACCTTGCATTATGGTACCTAT
65 TAAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTAT
* *
40701 GAAGCATAATTGCATAAGATAATTAAGT
130 GAAGCATAATTGCATAAGCTAATTAGGT
* * * * *
40729 TCAACTTTGTTACAATATATCTTGAATTATCAATAGTAAAAAACATGAAAGAACCATTCCTTCTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * *
40794 AAAGGGCGACATGTCTTAAAATAACCGACATGCAACAG-AAATA-CTTGCATTATGGTACCTATG
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
40857 AAGCATAATTGCATAAGC---TTAGGT
131 AAGCATAATTGCATAAGCTAATTAGGT
* ** * * *
40881 TTAACTTTGTTACAATACATCTTGAATTATCATTAGTGAATGACATGACAGAACCATTCCCACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * *
40946 AAAGGGTGACATGTCTAAAAATTCCCGACATACAACAGAAAAGACCTTGCATTATAGTACCTACG
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
41011 AAGCATAATTGCATAAGCTAATTAGGT
131 AAGCATAATTGCATAAGCTAATTAGGT
* * * *
41038 TTAACTTTGTTACAACACAT-TTGAATCATCATTAGTGAAAAACATGAAAGATTCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * *
41102 AAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTACGATGCC--T-
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
41164 --GCATAATTGCATAAGCTAATTTA-GT
131 AAGCATAATTGCATAAGCTAA-TTAGGT
* * *
41189 TCAACTTTGTTAAAATACATCTTGAATTATCATTAGCGACAAACATGAAAGATCCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* *
41254 AAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTGCCTATG
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
*
41319 AAGCATAATTGCATAAGGTAATTAGGT
131 AAGCATAATTGCATAAGCTAATTAGGT
* * *
41346 TGAACTTTGTTACAATCCATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCAACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * * *
41411 AAAGGGTGGCATGTCTAAAATTACTCGACATACAACATAAAATACCTTGCATTAGGGTACCTATG
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
*
41476 ACGCATAATTGCATAAGCTAATTAGGT
131 AAGCATAATTGCATAAGCTAATTAGGT
* * *
41503 TCAACTTTGTTAAAATACATCTTGAAATATCATTAATGAAAAACATGAAAGATCCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * *
41568 AAAGGATGACATGCCTAAAAATACCCGACATTCAAAAGAAAATACCTTGCATTATGGTACCTATG
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
* *
41633 AAACATAATTGCATAAGCTAAATAGGT
131 AAGCATAATTGCATAAGCTAATTAGGT
* * * * *
41660 TTAACTTTGTTACAACACATTTTGAATTATCATTAGTGCAAAACATGAAAGA-CTCATTACTACT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATC-CATTCCTACT
* *
41724 TAAAGGATGACATGTCTAAAAATACCCGACATACAACAAAAAATACCTTGCATTACT-GTACC--
65 TAAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTA-TGGTACCTA
41786 T---GCATAATTGCATAAGCTAATTAGGT
129 TGAAGCATAATTGCATAAGCTAATTAGGT
* * * * *
41812 TCAACTTTGTTACAATACATCTTCAATTATCATTAGCGAAAAACATGATAGATACATTCCTATTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * *
41877 AAAGGGTGACATGTCTAAAAATATCCGACATACAATAGAAAATACCTTGCATTATGTTACCTATG
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
* *
41942 AAG-ATAATTTCATTAGCTAATTAGGT
131 AAGCATAATTGCATAAGCTAATTAGGT
* * * *
41968 TGAACTTTGTTACAATCCATCTTGAATTATCCTTAGTAAAAAACATGAAAGATCCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * * * *
42033 AAAGGGAGGCATGTCTAAAATTACCCAACATACAACAGAAAATACCTTACATTATGGCACCTATG
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
42098 AAGCATAATTGCATAAGCTAATTAGGT
131 AAGCATAATTGCATAAGCTAATTAGGT
* * *
42125 TTAACTTTGTTACAATACATCTTGAATTATTATTAGTGAAAAAATATGAAAGATCCATTCAC-AC
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTG-AAAAACATGAAAGATCCATTC-CTAC
* * * * *
42189 CTAAAGGGTGACATGTCTAAAAATTCCTGACATACAACAGAAAAGACCTTGCATTATGGTACATA
64 TTAAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTA
*
42254 TGAAGCATAATTGCATAAGCTAATTAAGT
129 TGAAGCATAATTGCATAAGCTAATTAGGT
* * * * * *
42283 TTAACTTTGTTACAACACAT-TATGAAATATCGTTAGTGAAAAACATAAAAGATGCATTCCTACT
1 TCAACTTTGTTACAATACATCT-TGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACT
* * * *
42347 TAAAGGATTACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTACGATACCT-T
65 TAAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTAT
42411 ----CATAATTGCATAAGCTAATTAGGT
130 GAAGCATAATTGCATAAGCTAATTAGGT
* * *
42435 TCAACTTTGTTACAATACATCTTGAATTATCATTAGAGACAAACATGAAAGATCCATTCCTACTC
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * *
42500 AAAGGGTGACGTGTCTAAAAATATCCAACATACAACAGAAAATACCTTGCATTATGGTACCTATG
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
* *
42565 AAGCATAATCGCATAAGCTAATTATGT
131 AAGCATAATTGCATAAGCTAATTAGGT
* * * * *
42592 TGAACTTTGTTACAATCCATCTTAAATTATCATTTGTCAAAAACATGAAAGATCCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * * *
42657 AAAGGGTGGCATGTCTAAAATTACCCAACATACAATAGAAAATACCTTCCATTA-GTGTACCTAT
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATG-GTACCTAT
*
42721 GAAGCATAATTGCATAAGCTAATTTGGT
130 GAAGCATAATTGCATAAGCTAATTAGGT
* *
42749 TCAACTTTGTTACAATTCATCTTGAATTCTCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * *
42814 AAAGGATGACATGCCTAAAAATACCCGACATACAACATAAAATACCTTGCAGTATGGTACCTATG
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
*
42879 AAGCATAATTGCATAAGCTAATTAAGT
131 AAGCATAATTGCATAAGCTAATTAGGT
* * * * *
42906 TTAACTTTGTTGCAACACATTTTGAATTATCATTAGTGAAAAACATGAAAGATTCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * **
42971 AAAGGATGACATGTCTAAAATTACCCGATATACAACAG-AAATACCTTGCATTACAGTACC--T-
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
43032 --GCATAATTGCATAAGCTAATTAGGT
131 AAGCATAATTGCATAAGCTAATTAGGT
* * * * *
43057 TCAACTTTGTTACAATTCATCGTGAATTATCATTAGTGACAAACATGATAGATCCATTCGTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * *
43122 AAAGGGTGGCATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGTATTATGGTACCTATG
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
* * *
43187 AAGAATAACTGCATTAGCTAATTAGGT
131 AAGCATAATTGCATAAGCTAATTAGGT
* *
43214 TGAACTTTGTTACAATCCATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * *
43279 AAAGGGTGGCATGTCTAAAATTACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTAGG
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
*
43344 AAGCATAATTGCATAAGCTAATTAGCT
131 AAGCATAATTGCATAAGCTAATTAGGT
* * * *
43371 TTAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGTTTCATTCCCACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
*
43436 AAAGGGTGACATGTCTAAAAATACCTGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
* *
43501 AAGCATAATTGCATAAGCTAATAATGT
131 AAGCATAATTGCATAAGCTAATTAGGT
* * * * *
43528 TTAACTTTGTTACAACACATTTTTAATTATCATTTGTGAAAAAAACATGAAAGAAT-CATTCCTA
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTG--AAAAACATGAAAG-ATCCATTCCTA
* * *
43592 CTTAAAGGATGACATGTCTAAAAATACCCGACATACAATAGAAAATACCTTGCATTACGGTACC-
63 CTTAAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCT
*
43656 -T---GCATAATTGCATAAGCTAATTAGTT
128 ATGAAGCATAATTGCATAAGCTAATTAGGT
* * * * *
43682 TCAACTTTGTTACATTACAACTTGAATTATCATTAGCGACATACATGAAAGATCCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * *
43747 AAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAGTACTTTGCATTATTGTACCTATG
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
43812 AAGCATAATTGCATAAGCTAATTAGGT
131 AAGCATAATTGCATAAGCTAATTAGGT
* * *
43839 TGAACTTTGTTACAATCCATCTTGAATTATCATTAGTGAAAAACATTAAAGATCCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * *
43904 AAAGGGTGGCATGTCTAAAATTACCCGACATACAACATAAAATACCTTGCATTAGGGTACCTATG
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
* *
43969 AAACATAATTTCATAAGCTAATTAGGT
131 AAGCATAATTGCATAAGCTAATTAGGT
* * * *
43996 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAAAATGATAGATACATTCCTATTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * *
44061 AAAGGATGACATGCCTAAAAATACCCGTCATACAACAGAAAATACCTTGC-TT-TGTGTACCTAT
66 AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATG-GTACCTAT
44124 GAAGCA
130 GAAGCA
44130 AAAAAGCAGT
Statistics
Matches: 2991, Mismatches: 358, Indels: 105
0.87 0.10 0.03
Matches are distributed among these distances:
151 153 0.05
152 552 0.18
153 6 0.00
154 93 0.03
155 39 0.01
156 273 0.09
157 1652 0.55
158 141 0.05
159 81 0.03
160 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (157 bp):
TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
AAAGGGTGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
AAGCATAATTGCATAAGCTAATTAGGT
Found at i:42066 original size:622 final size:622
Alignment explanation
Indices: 40572--44129 Score: 5517
Period size: 622 Copynumber: 5.7 Consensus size: 622
40562 AACATTACAA
* * * * * *
40572 TCAACTCTGTTACAATACATCTTGAATTATCATTAGTGAAAAACCT-AAATGGTCCTTTCCTACT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGCGACAAACATGAAA-GATCCATTCCTACT
* * * *
40636 TAAAGGGCGACATGCCTAAAAATACCCGACATACAACAAAAAATACCTTGCATTATGGTACCTAT
65 TAAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTAT
* * * ** *
40701 GAAGCATAATTGCATAAGATAATTAAGTTCAACTTTGTTACAATATATCTTGAATTATCAATAGT
130 GAAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGT
* * * * * * *
40766 AAAAAACATGAAAGAACCATTCCTTCTTAAAGGGCGACATGTCTTAAAA-TAACCGACATGCAAC
195 GAAAAACATGAAAGATCCATTCCTACTTAAAGGGTGGCATGTC-TAAAATTACCCGACATACAAC
* *
40830 AG-AAATA-CTTGCATTATGGTACCTATGAAGCATAATTGCATAAGC---TTAGGTTTAACTTTG
259 AGAAAATACCTTGCATTAGGGTACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTG
** * * * *
40890 TTACAATACATCTTGAATTATCATTAGTGAATGACATGACAGAACCATTCCCACTTAAAGGGTGA
324 TTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGATGA
* * * * *
40955 CATGTCTAAAAATTCCCGACATACAACAGAAAAGACCTTGCATTATAGTACCTACGAAGCATAAT
389 CATGCCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATGAAGCATAAT
* *
41020 TGCATAAGCTAATTAGGTTTAACTTTGTTACAACACA-TTTGAATCATCATTAGTGAAAAACATG
454 TGCATAAGCTAATTAAGTTTAACTTTGTTACAACACATTTTGAATTATCATTAGTGAAAAACATG
41084 AAAGATTCATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACCT
519 AAAGATTCATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACCT
*
41149 TGCATTACGATGCCTGCATAATTGCATAAGCTAATTTA-GT
584 TGCATTACG-TACCTGCATAATTGCATAAGCTAA-TTAGGT
*
41189 TCAACTTTGTTAAAATACATCTTGAATTATCATTAGCGACAAACATGAAAGATCCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGCGACAAACATGAAAGATCCATTCCTACTT
*
41254 AAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTGCCTATG
66 AAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
*
41319 AAGCATAATTGCATAAGGTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGTG
131 AAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGTG
* * *
41384 AAAAACATGAAAGATCCATTCCAACTTAAAGGGTGGCATGTCTAAAATTACTCGACATACAACAT
196 AAAAACATGAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAAAATTACCCGACATACAACAG
*
41449 AAAATACCTTGCATTAGGGTACCTATGACGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTT
261 AAAATACCTTGCATTAGGGTACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTT
* * *
41514 AAAATACATCTTGAAATATCATTAATGAAAAACATGAAAGATCCATTCCTACTTAAAGGATGACA
326 ACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGATGACA
* * *
41579 TGCCTAAAAATACCCGACATTCAAAAGAAAATACCTTGCATTATGGTACCTATGAAACATAATTG
391 TGCCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATGAAGCATAATTG
* * *
41644 CATAAGCTAAATAGGTTTAACTTTGTTACAACACATTTTGAATTATCATTAGTGCAAAACATGAA
456 CATAAGCTAATTAAGTTTAACTTTGTTACAACACATTTTGAATTATCATTAGTGAAAAACATGAA
* * *
41709 AGACTCATTACTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAAAAAATACCTTG
521 AGATTCATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTG
41774 CATTACTGTACCTGCATAATTGCATAAGCTAATTAGGT
586 CATTAC-GTACCTGCATAATTGCATAAGCTAATTAGGT
* * * * *
41812 TCAACTTTGTTACAATACATCTTCAATTATCATTAGCGAAAAACATGATAGATACATTCCTATTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGCGACAAACATGAAAGATCCATTCCTACTT
* *
41877 AAAGGGTGACATGTCTAAAAATATCCGACATACAATAGAAAATACCTTGCATTATGTTACCTATG
66 AAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
* * * *
41942 AAG-ATAATTTCATTAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCCTTAGTA
131 AAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGTG
* *
42006 AAAAACATGAAAGATCCATTCCTACTTAAAGGGAGGCATGTCTAAAATTACCCAACATACAACAG
196 AAAAACATGAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAAAATTACCCGACATACAACAG
* * * *
42071 AAAATACCTTACATTATGGCACCTATGAAGCATAATTGCATAAGCTAATTAGGTTTAACTTTGTT
261 AAAATACCTTGCATTAGGGTACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTT
* * * *
42136 ACAATACATCTTGAATTATTATTAGTGAAAAAATATGAAAGATCCATTCAC-ACCTAAAGGGTGA
326 ACAATACATCTTGAATTATCATTAGTG-AAAAACATGAAAGATCCATTC-CTACTTAAAGGATGA
* * * * *
42200 CATGTCTAAAAATTCCTGACATACAACAGAAAAGACCTTGCATTATGGTACATATGAAGCATAAT
389 CATGCCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATGAAGCATAAT
* * * *
42265 TGCATAAGCTAATTAAGTTTAACTTTGTTACAACACATTATGAAATATCGTTAGTGAAAAACATA
454 TGCATAAGCTAATTAAGTTTAACTTTGTTACAACACATTTTGAATTATCATTAGTGAAAAACATG
* *
42330 AAAGATGCATTCCTACTTAAAGGATTACATGTCTAAAAATACCCGACATACAACAGAAAATACCT
519 AAAGATTCATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACCT
*
42395 TGCATTACGATACCTTCATAATTGCATAAGCTAATTAGGT
584 TGCATTACG-TACCTGCATAATTGCATAAGCTAATTAGGT
* *
42435 TCAACTTTGTTACAATACATCTTGAATTATCATTAGAGACAAACATGAAAGATCCATTCCTACTC
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGCGACAAACATGAAAGATCCATTCCTACTT
* *
42500 AAAGGGTGACGTGTCTAAAAATATCCAACATACAACAGAAAATACCTTGCATTATGGTACCTATG
66 AAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
* * * * *
42565 AAGCATAATCGCATAAGCTAATTATGTTGAACTTTGTTACAATCCATCTTAAATTATCATTTGTC
131 AAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGTG
* *
42630 AAAAACATGAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAAAATTACCCAACATACAATAG
196 AAAAACATGAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAAAATTACCCGACATACAACAG
* * *
42695 AAAATACCTTCCATTAGTGTACCTATGAAGCATAATTGCATAAGCTAATTTGGTTCAACTTTGTT
261 AAAATACCTTGCATTAGGGTACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTT
* *
42760 ACAATTCATCTTGAATTCTCATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGATGACA
326 ACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGATGACA
* *
42825 TGCCTAAAAATACCCGACATACAACATAAAATACCTTGCAGTATGGTACCTATGAAGCATAATTG
391 TGCCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATGAAGCATAATTG
*
42890 CATAAGCTAATTAAGTTTAACTTTGTTGCAACACATTTTGAATTATCATTAGTGAAAAACATGAA
456 CATAAGCTAATTAAGTTTAACTTTGTTACAACACATTTTGAATTATCATTAGTGAAAAACATGAA
* *
42955 AGATTCATTCCTACTTAAAGGATGACATGTCTAAAATTACCCGATATACAACAG-AAATACCTTG
521 AGATTCATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTG
43019 CATTACAGTACCTGCATAATTGCATAAGCTAATTAGGT
586 CATTAC-GTACCTGCATAATTGCATAAGCTAATTAGGT
* * * * *
43057 TCAACTTTGTTACAATTCATCGTGAATTATCATTAGTGACAAACATGATAGATCCATTCGTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGCGACAAACATGAAAGATCCATTCCTACTT
* *
43122 AAAGGGTGGCATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGTATTATGGTACCTATG
66 AAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
* * *
43187 AAGAATAACTGCATTAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGTG
131 AAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGTG
43252 AAAAACATGAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAAAATTACCCGACATACAACAG
196 AAAAACATGAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAAAATTACCCGACATACAACAG
* * * *
43317 AAAATACCTTGCATTATGGTACCTAGGAAGCATAATTGCATAAGCTAATTAGCTTTAACTTTGTT
261 AAAATACCTTGCATTAGGGTACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTT
* * * *
43382 ACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGTTTCATTCCCACTTAAAGGGTGACA
326 ACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGATGACA
* *
43447 TGTCTAAAAATACCTGACATACAACAGAAAATACCTTGCATTATGGTACCTATGAAGCATAATTG
391 TGCCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATGAAGCATAATTG
* *
43512 CATAAGCTAA-TAATGTTTAACTTTGTTACAACACATTTTTAATTATCATTTGTGAAAAAAACAT
456 CATAAGCTAATTAA-GTTTAACTTTGTTACAACACATTTTGAATTATCATTAGTG--AAAAACAT
* *
43576 GAAAGAATCATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAATAGAAAATACC
518 GAAAGATTCATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACC
*
43641 TTGCATTACGGTACCTGCATAATTGCATAAGCTAATTAGTT
583 TTGCATTAC-GTACCTGCATAATTGCATAAGCTAATTAGGT
* * *
43682 TCAACTTTGTTACATTACAACTTGAATTATCATTAGCGACATACATGAAAGATCCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGCGACAAACATGAAAGATCCATTCCTACTT
* * *
43747 AAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAGTACTTTGCATTATTGTACCTATG
66 AAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
43812 AAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGTG
131 AAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGTG
* *
43877 AAAAACATTAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAAAATTACCCGACATACAACAT
196 AAAAACATGAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAAAATTACCCGACATACAACAG
* *
43942 AAAATACCTTGCATTAGGGTACCTATGAAACATAATTTCATAAGCTAATTAGGTTCAACTTTGTT
261 AAAATACCTTGCATTAGGGTACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTT
* * * *
44007 ACAATACATCTTGAATTATCATTAGTGAAAAAAATGATAGATACATTCCTATTTAAAGGATGACA
326 ACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGATGACA
*
44072 TGCCTAAAAATACCCGTCATACAACAGAAAATACCTTGC-TT-TGTGTACCTATGAAGCA
391 TGCCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATG-GTACCTATGAAGCA
44130 AAAAAGCAGT
Statistics
Matches: 2683, Mismatches: 237, Indels: 35
0.91 0.08 0.01
Matches are distributed among these distances:
616 5 0.00
617 222 0.08
618 8 0.00
619 36 0.01
621 3 0.00
622 877 0.33
623 813 0.30
624 278 0.10
625 441 0.16
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (622 bp):
TCAACTTTGTTACAATACATCTTGAATTATCATTAGCGACAAACATGAAAGATCCATTCCTACTT
AAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
AAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGTG
AAAAACATGAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAAAATTACCCGACATACAACAG
AAAATACCTTGCATTAGGGTACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTT
ACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGATGACA
TGCCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATGAAGCATAATTG
CATAAGCTAATTAAGTTTAACTTTGTTACAACACATTTTGAATTATCATTAGTGAAAAACATGAA
AGATTCATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTG
CATTACGTACCTGCATAATTGCATAAGCTAATTAGGT
Found at i:52095 original size:16 final size:16
Alignment explanation
Indices: 52062--52099 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
52052 GATAAACTGA
52062 TTTATACTTAAGTATT
1 TTTATACTTAAGTATT
52078 TTTAT-CTTAATGT-TT
1 TTTATACTTAA-GTATT
52093 TTTATAC
1 TTTATAC
52100 ACCGCGAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTATACTTAAGTATT
Found at i:57478 original size:32 final size:33
Alignment explanation
Indices: 57441--57505 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
57431 TTTTGGTTGA
*
57441 GTGCAACCTACAATGTTAA-TTTTTTAACATTT
1 GTGCAACCTAAAATGTTAATTTTTTTAACATTT
57473 GTGCAACCTAAAATGTTAATTTTTTTAACATTT
1 GTGCAACCTAAAATGTTAATTTTTTTAACATTT
57506 TCGATTAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (33 bp):
GTGCAACCTAAAATGTTAATTTTTTTAACATTT
Found at i:63477 original size:19 final size:19
Alignment explanation
Indices: 63449--63499 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 19
63439 ATTATAGTCG
* *
63449 TGATTATTTTTAAATGAGT
1 TGATTTTTTTTAAATGAGC
63468 TGATTTTTTTTTTTAAATGAGC
1 TGA---TTTTTTTTAAATGAGC
63490 TGATTTTTTT
1 TGATTTTTTT
63500 AAAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 10 0.37
22 17 0.63
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.61
Consensus pattern (19 bp):
TGATTTTTTTTAAATGAGC
Found at i:63496 original size:21 final size:22
Alignment explanation
Indices: 63455--63499 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
63445 GTCGTGATTA
*
63455 TTTTTAAATGAGTTGATTTTTT
1 TTTTTAAATGAGCTGATTTTTT
63477 TTTTTAAATGAGCTGATTTTTT
1 TTTTTAAATGAGCTGATTTTTT
63499 T
1 T
63500 AAAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.02, G:0.13, T:0.62
Consensus pattern (22 bp):
TTTTTAAATGAGCTGATTTTTT
Found at i:64498 original size:30 final size:32
Alignment explanation
Indices: 64463--64536 Score: 107
Period size: 30 Copynumber: 2.4 Consensus size: 32
64453 ACCCCAAAAT
* *
64463 TTTAGATAGAATACTA-ATTTGACCTT-TAAC
1 TTTAGATAAAATACTATATTTGACCTTACAAC
*
64493 TTTAGATAAAATACTATTTTTGACCTTACAAC
1 TTTAGATAAAATACTATATTTGACCTTACAAC
64525 TTTAGATAAAAT
1 TTTAGATAAAAT
64537 GTCAATTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 15 0.38
31 9 0.23
32 15 0.38
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (32 bp):
TTTAGATAAAATACTATATTTGACCTTACAAC
Found at i:64861 original size:2 final size:2
Alignment explanation
Indices: 64854--64903 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
64844 TAATAGTTTA
64854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64896 AT AT AT AT
1 AT AT AT AT
64904 TAATAAGTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67449 original size:34 final size:34
Alignment explanation
Indices: 67384--67449 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
67374 AGATTTTGAT
*
67384 AAATTATATATTATAATTTTATCAAACTTATAAC
1 AAATTATATATTATAATTTTATCAAAATTATAAC
*
67418 AAATTATA-ATATATAA-TTTCTCAAAAATTATA
1 AAATTATATAT-TATAATTTTATC-AAAATTATA
67450 TAAATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (34 bp):
AAATTATATATTATAATTTTATCAAAATTATAAC
Found at i:67506 original size:18 final size:18
Alignment explanation
Indices: 67483--67517 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
67473 ATATAAACAT
67483 ATTATGATATAGATATAG
1 ATTATGATATAGATATAG
*
67501 ATTATGATATATATATA
1 ATTATGATATAGATATA
67518 TATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (18 bp):
ATTATGATATAGATATAG
Found at i:67514 original size:2 final size:2
Alignment explanation
Indices: 67489--67530 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
67479 ACATATTATG
* *
67489 AT AT AG AT AT AG AT -T AT GAT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
67531 TCAATGTCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (2 bp):
AT
Found at i:68374 original size:23 final size:24
Alignment explanation
Indices: 68329--68376 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
68319 TGACCACTAT
68329 CTAACCGCACGATCAAAACCCAAC
1 CTAACCGCACGATCAAAACCCAAC
68353 CTAACCGCACGATC-AAACCCAAC
1 CTAACCGCACGATCAAAACCCAAC
68376 C
1 C
68377 GATCACACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.40, C:0.44, G:0.08, T:0.08
Consensus pattern (24 bp):
CTAACCGCACGATCAAAACCCAAC
Done.