Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009614.1 Hibiscus syriacus cultivar Beakdansim tig00117000_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: 2129691
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1655362 original size:21 final size:21
Alignment explanation
Indices: 1655311--1655363 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1655301 TGATCGTTAT
*
1655311 GATGCTGATATAACACTTCAC
1 GATGCTGATGTAACACTTCAC
1655332 GATGCTGATGTAACACTTCAC
1 GATGCTGATGTAACACTTCAC
1655353 GATGCTGATGT
1 GATGCTGATGT
1655364 GGAGATCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (21 bp):
GATGCTGATGTAACACTTCAC
Found at i:1656240 original size:61 final size:61
Alignment explanation
Indices: 1656145--1656266 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
1656135 TAACTTGAGA
1656145 GAAAAGGAAGAAGGACCAAAAGTGCAATTTACCTATTTATGGCTAAAATGGATGAAAATCC
1 GAAAAGGAAGAAGGACCAAAAGTGCAATTTACCTATTTATGGCTAAAATGGATGAAAATCC
1656206 GAAAAGGAAGAAGGACCAAAAGTGCAATTTACCTATTTATGGCTAAAATGGATGAAAATCC
1 GAAAAGGAAGAAGGACCAAAAGTGCAATTTACCTATTTATGGCTAAAATGGATGAAAATCC
1656267 ATTATTTAAG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.21
Consensus pattern (61 bp):
GAAAAGGAAGAAGGACCAAAAGTGCAATTTACCTATTTATGGCTAAAATGGATGAAAATCC
Found at i:1658467 original size:30 final size:29
Alignment explanation
Indices: 1658426--1658500 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
1658416 TTATTTTTGG
** *
1658426 TATTATTATATTTAAGGTTTTAAATATTTT
1 TATT-TTATATTTAAAATTTAAAATATTTT
1658456 ATATTTTATATTTAAAATTTAAAATATTTT
1 -TATTTTATATTTAAAATTTAAAATATTTT
1658486 TATTTT-T-TTTAAAAT
1 TATTTTATATTTAAAAT
1658501 CAAATAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
27 8 0.20
28 1 0.02
29 6 0.15
30 22 0.54
31 4 0.10
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (29 bp):
TATTTTATATTTAAAATTTAAAATATTTT
Found at i:1658509 original size:29 final size:31
Alignment explanation
Indices: 1658446--1658510 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 31
1658436 TTTAAGGTTT
**
1658446 TAAATATTTTATATTTTATATTTAAAATTTA
1 TAAATATTTTATATTTTATATTTAAAATAAA
1658477 -AAATATTTT-TATTTT-T-TTTAAAATCAAA
1 TAAATATTTTATATTTTATATTTAAAAT-AAA
1658505 TAAATA
1 TAAATA
1658511 CTTAAACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
27 8 0.27
28 2 0.07
29 11 0.37
30 9 0.30
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (31 bp):
TAAATATTTTATATTTTATATTTAAAATAAA
Found at i:1661506 original size:23 final size:23
Alignment explanation
Indices: 1661487--1661552 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
1661477 AAGAAAACGA
*
1661487 AGTTCGATTAACTAAAAAAATGC
1 AGTTCGAATAACTAAAAAAATGC
*
1661510 AGTTCGAATAACTAAAACAATGC
1 AGTTCGAATAACTAAAAAAATGC
1661533 AGTTCGAATAACTAAAAAAA
1 AGTTCGAATAACTAAAAAAA
1661553 GTTACAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.23
Consensus pattern (23 bp):
AGTTCGAATAACTAAAAAAATGC
Found at i:1661711 original size:21 final size:21
Alignment explanation
Indices: 1661675--1661741 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
1661665 CACTTTGATA
1661675 ATCACCACCA-CTACCA-CAATC
1 ATCACCACCATC-ACCATCAA-C
1661696 ATCACCACCATCACCATCAAC
1 ATCACCACCATCACCATCAAC
* * * *
1661717 ATCATCAACATCATCATCATC
1 ATCACCACCATCACCATCAAC
1661738 ATCA
1 ATCA
1661742 TCTATATGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
21 36 0.90
22 4 0.10
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (21 bp):
ATCACCACCATCACCATCAAC
Found at i:1661722 original size:3 final size:3
Alignment explanation
Indices: 1661693--1661743 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
1661683 CACTACCACA
* * * * *
1661693 ATC ATC ACC ACC ATC ACC ATC AAC ATC ATC AAC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1661741 ATC
1 ATC
1661744 TATATGGCCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (3 bp):
ATC
Found at i:1662178 original size:29 final size:29
Alignment explanation
Indices: 1662157--1662295 Score: 253
Period size: 29 Copynumber: 4.8 Consensus size: 29
1662147 CATGTGATAT
1662157 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
1662187 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
1662216 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
1662245 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
1662274 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
1662296 ACATATAAAA
Statistics
Matches: 107, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.07
29 95 0.89
30 5 0.05
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:1662398 original size:15 final size:15
Alignment explanation
Indices: 1662380--1662413 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1662370 GAGGGTATAA
*
1662380 TAGTCCTTTGGGACG
1 TAGTCCTTCGGGACG
*
1662395 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
1662410 TAGT
1 TAGT
1662414 GGTCCTATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.32, T:0.35
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:1666005 original size:18 final size:18
Alignment explanation
Indices: 1665982--1666016 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1665972 AGGGATTATC
*
1665982 AGTGGTCATTTGGGACAT
1 AGTGGTCATTCGGGACAT
*
1666000 AGTGGTCCTTCGGGACA
1 AGTGGTCATTCGGGACA
1666017 AATATTCAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:1666903 original size:4 final size:4
Alignment explanation
Indices: 1666894--1667115 Score: 89
Period size: 4 Copynumber: 54.0 Consensus size: 4
1666884 ATATCCCTTC
*
1666894 AAAT AAAT AAAT AAATTT GAAAC AAAT AAAT AAAT AAATT CGAAAT AAAT
1 AAAT AAAT AAAT AAA--T -AAAT AAAT AAAT AAAT AAA-T --AAAT AAAT
* * *
1666944 AAAT GAAT AAATT CGAAAT AAAT AAAT AAAT AAATTT GAAAC AAAC AAAT
1 AAAT AAAT AAA-T --AAAT AAAT AAAT AAAT AAA--T -AAAT AAAT AAAT
* ** ** **
1666994 AAAT AATT TCA- AAAT AAAT AAAT GTAT AAAT TCA- AAAT AAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * * * * *
1667039 GAAT -AAC AAAT AAAT GAAT GAAT AAA- AAAGT CAA- AAAC AAAT AGAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT
** *
1667085 -TCT AAAT AAAT GAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1667116 TGAACAAAAT
Statistics
Matches: 163, Mismatches: 35, Indels: 40
0.68 0.15 0.17
Matches are distributed among these distances:
3 13 0.08
4 130 0.80
5 4 0.02
6 4 0.02
7 12 0.07
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:1666967 original size:69 final size:69
Alignment explanation
Indices: 1666894--1667044 Score: 241
Period size: 69 Copynumber: 2.2 Consensus size: 69
1666884 ATATCCCTTC
* * *
1666894 AAATAAATAAATAAATTTGAAACAAATAAATAAATAAATTCGAAATAAATAAATGAATAAATTCG
1 AAATAAATAAATAAATTTGAAACAAACAAATAAATAAATTCAAAATAAATAAATGAATAAATTCA
1666959 AAAT
66 AAAT
* *
1666963 AAATAAATAAATAAATTTGAAACAAACAAATAAATAATTTCAAAATAAATAAATGTATAAATTCA
1 AAATAAATAAATAAATTTGAAACAAACAAATAAATAAATTCAAAATAAATAAATGAATAAATTCA
1667028 AAAT
66 AAAT
*
1667032 AAA-AAATGAATAA
1 AAATAAATAAATAA
1667045 CAAATAAATG
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
68 9 0.12
69 67 0.88
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (69 bp):
AAATAAATAAATAAATTTGAAACAAACAAATAAATAAATTCAAAATAAATAAATGAATAAATTCA
AAAT
Found at i:1667027 original size:23 final size:23
Alignment explanation
Indices: 1666894--1667044 Score: 187
Period size: 23 Copynumber: 6.6 Consensus size: 23
1666884 ATATCCCTTC
* *
1666894 AAATAAATAAATAAATTTGAAAC
1 AAATAAATAAATAAATTCGAAAT
1666917 AAATAAATAAATAAATTCGAAAT
1 AAATAAATAAATAAATTCGAAAT
*
1666940 AAATAAATGAATAAATTCGAAAT
1 AAATAAATAAATAAATTCGAAAT
* *
1666963 AAATAAATAAATAAATTTGAAAC
1 AAATAAATAAATAAATTCGAAAT
* * *
1666986 AAACAAATAAATAATTTCAAAAT
1 AAATAAATAAATAAATTCGAAAT
** *
1667009 AAATAAATGTATAAATTCAAAAT
1 AAATAAATAAATAAATTCGAAAT
*
1667032 AAA-AAATGAATAA
1 AAATAAATAAATAA
1667045 CAAATAAATG
Statistics
Matches: 112, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
22 9 0.08
23 103 0.92
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (23 bp):
AAATAAATAAATAAATTCGAAAT
Found at i:1667048 original size:19 final size:20
Alignment explanation
Indices: 1666990--1667067 Score: 65
Period size: 19 Copynumber: 4.0 Consensus size: 20
1666980 TGAAACAAAC
**
1666990 AAATAAAT-AATTTCAAAAT
1 AAATAAATGAATAACAAAAT
*
1667009 AAATAAATGTATAAATTCAAAAT
1 AAATAAATGAAT-AA--CAAAAT
1667032 AAA-AAATGAATAAC-AAAT
1 AAATAAATGAATAACAAAAT
*
1667050 AAATGAATGAATAA-AAAA
1 AAATAAATGAATAACAAAA
1667068 GTCAAAAACA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
18 7 0.15
19 21 0.44
20 2 0.04
21 2 0.04
22 7 0.15
23 9 0.19
ACGTcount: A:0.67, C:0.04, G:0.05, T:0.24
Consensus pattern (20 bp):
AAATAAATGAATAACAAAAT
Found at i:1671235 original size:447 final size:449
Alignment explanation
Indices: 1670349--1671252 Score: 1564
Period size: 447 Copynumber: 2.0 Consensus size: 449
1670339 GAGCACACAG
1670349 TGTCGGCAGAACTCACTGCGTGAAGCTGGTGCACCGTCTGTACCCAGAGCCCAGAGGTTGACCCT
1 TGTCGGCAGAACTCACTGCGTGAAGCTGGTGCACCGTCTGT---C--AGCCCAGAGGTTGACCCT
* *
1670414 GAGCTCAACCCCGACCATATTCCACACTTGCTCCATAAGTGCCCTGATCAAATCCCAGACCCCAA
61 GAGCTCAACCCCGACCATATTCCACACATGCTCCATAAGTGCACTGATCAAATCCCAGACCCCAA
* *
1670479 GGCGGTGCAGTACGTGAGAAACGACCGGGGGACACCCATGGTTCTGGACAACAACAACTATAGAA
126 AGCGGTGCAATACGTGAGAAACGACCGGGGGACACCCATGGTTCTGGACAACAACAACTATAGAA
1670544 ACATCCTGGACAACAAGGGCTTGTTGATTGTGGACCACCAACTGGCTTATGACAAGAGGACCAGA
191 ACATCCTGGACAACAAGGGCTTGTTGATTGTGGACCACCAACTGGCTTATGACAAGAGGACCAGA
1670609 CCTTATGTGAAGAAAATGGCCAAGAGCCAAGACTATTTCTTCAAGGAGTTCTCCAGGGCCATTAC
256 CCTTATGTGAAGAAAATGGCCAAGAGCCAAGACTATTTCTTCAAGGAGTTCTCCAGGGCCATTAC
*
1670674 TCTCCTCTCCGAGAACAACCCTCTCACCCGTACCAAGGGTGATCAGGAAGCAGTGCAATCTTGCA
321 TCTCCTCTCCGAGAACAACCCTCTCACCCGTAACAAGGGTGATCAGGAAGCAGTGCAATCTTGCA
*
1670739 AACAAGCTTCACTAAAATGCTTCTTCTTCGCTAAAGAGACCCGACTGTGGCCGAATAAAATGGT
386 AACAAGCTTCACTAAAATGCTTCTTCTTCGCTAAAAAGACCCGACTGTGGCCGAATAAAATGGT
* * *
1670803 TGTCGGCAGAACTCACTGTGTGAAGCTGGTGCACCGTCTGT-A-CTCAGAGGTTGGCCCTGAGCT
1 TGTCGGCAGAACTCACTGCGTGAAGCTGGTGCACCGTCTGTCAGCCCAGAGGTTGACCCTGAGCT
*
1670866 CAACCCCGACCATATTCCACACATGCTCCATAAGTGCACTGATCAAATCCCAGTCCCCAAAGCGG
66 CAACCCCGACCATATTCCACACATGCTCCATAAGTGCACTGATCAAATCCCAGACCCCAAAGCGG
*
1670931 TGCAATACGTGAGAAACGACCGGGGGACACCCATGGTTCTGGACAACAACTACTATAGAAACATC
131 TGCAATACGTGAGAAACGACCGGGGGACACCCATGGTTCTGGACAACAACAACTATAGAAACATC
1670996 CTGGACAACAAGGGCTTGTTGATTGTGGACCACCAACTGGCTTATGACAAGAGGACCAGACCTTA
196 CTGGACAACAAGGGCTTGTTGATTGTGGACCACCAACTGGCTTATGACAAGAGGACCAGACCTTA
*
1671061 TGTGAAGAAAATGGCCAAGAGCCAAGACTATTTCTTCACGGAGTTCTCCAGGGCCATTACTCTCC
261 TGTGAAGAAAATGGCCAAGAGCCAAGACTATTTCTTCAAGGAGTTCTCCAGGGCCATTACTCTCC
* *
1671126 TCTCCGAGAGCAA-CC-CTCACCGGTAACAAGGGTGAGATCAGGAAGCAGTGCAATCTTGCAAAC
326 TCTCCGAGAACAACCCTCTCACCCGTAACAAGGGT--GATCAGGAAGCAGTGCAATCTTGCAAAC
* * *
1671189 AATCTTCACTAAAATGCTTCTTCTTCGCTAAAAAGACCCTACTGTGGCCTAATAAAATGGT
389 AAGCTTCACTAAAATGCTTCTTCTTCGCTAAAAAGACCCGACTGTGGCCGAATAAAATGGT
1671250 TGT
1 TGT
1671253 TTCTTGTCCT
Statistics
Matches: 431, Mismatches: 17, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
445 16 0.04
446 2 0.00
447 372 0.86
448 1 0.00
454 40 0.09
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.21
Consensus pattern (449 bp):
TGTCGGCAGAACTCACTGCGTGAAGCTGGTGCACCGTCTGTCAGCCCAGAGGTTGACCCTGAGCT
CAACCCCGACCATATTCCACACATGCTCCATAAGTGCACTGATCAAATCCCAGACCCCAAAGCGG
TGCAATACGTGAGAAACGACCGGGGGACACCCATGGTTCTGGACAACAACAACTATAGAAACATC
CTGGACAACAAGGGCTTGTTGATTGTGGACCACCAACTGGCTTATGACAAGAGGACCAGACCTTA
TGTGAAGAAAATGGCCAAGAGCCAAGACTATTTCTTCAAGGAGTTCTCCAGGGCCATTACTCTCC
TCTCCGAGAACAACCCTCTCACCCGTAACAAGGGTGATCAGGAAGCAGTGCAATCTTGCAAACAA
GCTTCACTAAAATGCTTCTTCTTCGCTAAAAAGACCCGACTGTGGCCGAATAAAATGGT
Found at i:1676568 original size:2 final size:2
Alignment explanation
Indices: 1676561--1676586 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1676551 GTCCAAAATT
1676561 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1676587 ATACTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1677152 original size:19 final size:19
Alignment explanation
Indices: 1677128--1677180 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
1677118 AATGACCAAC
1677128 AAAATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
1677147 AAAATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
1677166 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1677181 TCCCCAGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.51, C:0.23, G:0.17, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1677232 original size:21 final size:20
Alignment explanation
Indices: 1677127--1677303 Score: 81
Period size: 21 Copynumber: 8.8 Consensus size: 20
1677117 AAATGACCAA
**
1677127 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* **
1677146 AAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1677165 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1677185 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1677205 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1677226 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1677247 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
1677267 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1677288 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1677304 ACACATAAAT
Statistics
Matches: 121, Mismatches: 31, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
19 35 0.29
20 40 0.33
21 46 0.38
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1677436 original size:21 final size:20
Alignment explanation
Indices: 1677271--1677463 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
1677261 GATTTTCCAG
* ** *
1677271 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1677291 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1677311 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1677331 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1677351 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1677371 AATCGCAATGCGTATCCATA
1 AATCGCAACGCGTATCCGTA
1677391 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1677411 AATCGCAACG-ATAATCCGTAA
1 AATCGCAACGCGT-ATCCGT-A
1677432 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1677452 AATCGCAACGCG
1 AATCGCAACGCG
1677464 ATTTTTAAAG
Statistics
Matches: 149, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.85
21 19 0.13
22 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1677882 original size:33 final size:33
Alignment explanation
Indices: 1677843--1677913 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1677833 TTCACTTAGA
1677843 TTTCATTTCGCGGTGCGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGGTGCGATTCTCTCGTTGCGAT
* *
1677876 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGGTGCGATTCTCTCGTTGCGAT
1677909 TTTCA
1 TTTCA
1677914 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
TTTCATTTCGCGGTGCGATTCTCTCGTTGCGAT
Found at i:1678019 original size:21 final size:21
Alignment explanation
Indices: 1677993--1678069 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
1677983 TGCAGAAGAG
1677993 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
1678014 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
1678034 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
1678056 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1678070 TCGTAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.19
21 29 0.62
22 9 0.19
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:1678084 original size:33 final size:33
Alignment explanation
Indices: 1678047--1678126 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
1678037 GCAACGAGAA
*
1678047 AAATGAAAATCGCAACGAGAGAATCGTAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1678080 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
1678113 AAACCAAAATCGCA
1 AAATGAAAATCGCA
1678127 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:1678106 original size:14 final size:14
Alignment explanation
Indices: 1678054--1678110 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1678044 GAAAAATGAA
1678054 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
1678068 AATCGTAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1678087 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1678101 AATCGCAACG
1 AATCGCAACG
1678111 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1678144 original size:19 final size:19
Alignment explanation
Indices: 1678122--1678249 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
1678112 GAAACCAAAA
*
1678122 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1678141 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1678155 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1678174 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1678188 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
1678208 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
1678228 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1678248 TC
1 TC
1678250 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1678163 original size:14 final size:14
Alignment explanation
Indices: 1678144--1678200 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1678134 TTTCATTTCG
1678144 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1678158 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1678177 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1678191 CGTTGCGATT
1 CGTTGCGATT
1678201 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1678169 original size:33 final size:33
Alignment explanation
Indices: 1678127--1678249 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
1678117 CAAAATCGCA
1678127 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1678160 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1678193 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
1678234 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1678250 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1678211 original size:21 final size:21
Alignment explanation
Indices: 1678185--1678249 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1678175 CGCGTTGCGA
1678185 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1678206 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1678226 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1678247 TTC
1 TTC
1678250 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1680553 original size:12 final size:12
Alignment explanation
Indices: 1680536--1680560 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1680526 TCTTCGGGGA
1680536 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1680548 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1680560 C
1 C
1680561 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1681501 original size:20 final size:20
Alignment explanation
Indices: 1681473--1681658 Score: 223
Period size: 20 Copynumber: 9.3 Consensus size: 20
1681463 AAATTTCAGT
* * * *
1681473 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1681493 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1681513 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1681533 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
*
1681553 GTTGCGATTTATGGATACGC
1 GTTGCGATTTACGGATACGC
1681573 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1681593 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1681613 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1681633 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1681653 GTTGCG
1 GTTGCG
1681659 TACTACTTCT
Statistics
Matches: 147, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
19 3 0.02
20 142 0.97
21 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1682202 original size:20 final size:20
Alignment explanation
Indices: 1682174--1682403 Score: 241
Period size: 20 Copynumber: 11.4 Consensus size: 20
1682164 AAATTTCAGT
* * * *
1682174 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1682194 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
*
1682214 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1682234 GTTGCGATTTTACGGATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
1682255 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1682275 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1682295 ATTGCGATTTACAGATACGC
1 GTTGCGATTTACGGATACGC
* *
1682315 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1682335 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1682355 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1682375 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1682395 GTTGCGATT
1 GTTGCGATT
1682404 CTGGAAAATC
Statistics
Matches: 181, Mismatches: 22, Indels: 14
0.83 0.10 0.06
Matches are distributed among these distances:
19 4 0.02
20 157 0.87
21 18 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1683368 original size:21 final size:21
Alignment explanation
Indices: 1683339--1683385 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1683329 ATTCTGACTA
1683339 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1683360 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
1683381 TCGCA
1 TCGCA
1683386 ATACGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1683406 original size:20 final size:20
Alignment explanation
Indices: 1683381--1683512 Score: 149
Period size: 20 Copynumber: 6.5 Consensus size: 20
1683371 TTTTCCTAAT
*
1683381 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
1683401 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
1683422 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1683442 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1683462 TCGCAATGTGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1683482 TCGCAATGCGAATACG-ACTA
1 TCGCAATGCGAATACGTA-AA
1683502 TCGCAATGCGA
1 TCGCAATGCGA
1683513 TTTACATAGC
Statistics
Matches: 94, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 1 0.01
20 78 0.83
21 15 0.16
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1684104 original size:34 final size:34
Alignment explanation
Indices: 1684061--1684142 Score: 146
Period size: 34 Copynumber: 2.4 Consensus size: 34
1684051 TGAAACCGAG
*
1684061 AATGACTATCGCAACGAGTGAATCGCAATGCGAA
1 AATGACTATCGCAACGAGTGAATCGCAACGCGAA
*
1684095 AATGACTATCGTAACGAGTGAATCGCAACGCGAA
1 AATGACTATCGCAACGAGTGAATCGCAACGCGAA
1684129 AATGACTATCGCAA
1 AATGACTATCGCAA
1684143 TGCGAATTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.18
Consensus pattern (34 bp):
AATGACTATCGCAACGAGTGAATCGCAACGCGAA
Found at i:1684141 original size:20 final size:20
Alignment explanation
Indices: 1684116--1684164 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1684106 TAACGAGTGA
1684116 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1684136 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1684156 ATCGCAACG
1 ATCGCAACG
1684165 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1684242 original size:20 final size:20
Alignment explanation
Indices: 1684177--1684243 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
1684167 AGAATCGCAA
*
1684177 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGTGT
**
1684196 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
1684216 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
1684236 TGCGATTT
1 TGCGATTT
1684244 AAAGTTTCAG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 9 0.21
20 33 0.79
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.49
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGTGT
Found at i:1684251 original size:20 final size:20
Alignment explanation
Indices: 1684208--1684251 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1684198 CGATAGTCAT
** *
1684208 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
1684228 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
1684248 TTTC
1 TTTC
1684252 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:1685992 original size:22 final size:21
Alignment explanation
Indices: 1685962--1686002 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1685952 AAATTTGCTC
*
1685962 GTAATTTCACTTAGATTGCTTA
1 GTAAATTCA-TTAGATTGCTTA
*
1685984 GTAAATTCATTCGATTGCT
1 GTAAATTCATTAGATTGCT
1686003 GTTAATACTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (21 bp):
GTAAATTCATTAGATTGCTTA
Found at i:1686147 original size:20 final size:20
Alignment explanation
Indices: 1686122--1686205 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
1686112 AGAATAGTTT
1686122 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1686142 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
1686158 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
1686176 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
1686196 ACTATCGCAA
1 ACTATCGCAA
1686206 CGAAAGAATC
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 7 0.13
16 4 0.07
17 4 0.07
18 4 0.07
20 35 0.65
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1686204 original size:54 final size:54
Alignment explanation
Indices: 1686122--1686226 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 54
1686112 AGAATAGTTT
* *
1686122 ACTATCGCAATGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAATGAGAAAATG
**
1686176 ACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAATGAGAAA
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAATGAGAAA
1686227 TAAAAATTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (54 bp):
ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAATGAGAAAATG
Found at i:1686277 original size:20 final size:20
Alignment explanation
Indices: 1686252--1686298 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1686242 GATTCTCTCG
1686252 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
1686272 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
1686292 TTGCGAT
1 TTGCGAT
1686299 TTTGTTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:1686352 original size:33 final size:34
Alignment explanation
Indices: 1686272--1686362 Score: 112
Period size: 33 Copynumber: 2.7 Consensus size: 34
1686262 CAAATTCGCA
* * * *
1686272 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCGTTGCAATTCTCTCG
** *
1686306 TTGCGATTTTCA-TTTCGCATTGCAATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCAATTCTCTCG
1686339 TTGCGATAGTCATTTTCGCGTTGC
1 TTGCGATAGTCATTTTCGCGTTGC
1686363 GATTTTAAGT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
33 26 0.57
34 20 0.43
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCAATTCTCTCG
Found at i:1686876 original size:21 final size:21
Alignment explanation
Indices: 1686802--1686888 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
1686792 GCTCGACTCA
1686802 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* ** *
1686823 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** *
1686844 CCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* * *
1686865 ACTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
1686886 CCT
1 CCT
1686889 CCCAACATTC
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.21, C:0.37, G:0.20, T:0.23
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:1686882 original size:42 final size:42
Alignment explanation
Indices: 1686810--1686892 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
1686800 CACCTGTCAT
*
1686810 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
1686852 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
1686893 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:1688264 original size:14 final size:14
Alignment explanation
Indices: 1688245--1688280 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1688235 ATTGTTTAAT
1688245 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1688259 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1688273 TGATTTGT
1 TGATTTGT
1688281 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1688443 original size:33 final size:33
Alignment explanation
Indices: 1688386--1688481 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
1688376 CAGACTTTCG
1688386 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
1688420 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
1688453 CGTTGCGATAGTCATTTCTGCGTTGCGAT
1 CGTTGCGATTTTCATTTC-GCATTGCGAT
1688482 AGTCAATTTC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 34 0.60
34 23 0.40
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:1688478 original size:20 final size:19
Alignment explanation
Indices: 1688453--1688541 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 19
1688443 GCGATTCTCT
1688453 CGTTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTC-G
1688473 CGTTGCGATAGTCAATTTCG
1 CGTTGCGATAGTC-ATTTCG
*
1688493 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
* *
1688513 TGTTGAGATAGTCATATTCG
1 CGTTGCGATAGTCAT-TTCG
1688533 CGTTGCGAT
1 CGTTGCGAT
1688542 TTCCGCGTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.07
20 49 0.82
21 7 0.12
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1692025 original size:20 final size:20
Alignment explanation
Indices: 1691886--1692028 Score: 157
Period size: 20 Copynumber: 7.1 Consensus size: 20
1691876 CAGAATCTCG
1691886 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
1691906 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* *
1691926 TTGCAATAGTT--GTAATCGCA
1 TTGCGAT--TTACGTATTCGCA
*
1691946 TTGCGATTTACGTATTCACA
1 TTGCGATTTACGTATTCGCA
*
1691966 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
1691986 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
1692007 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1692027 TT
1 TT
1692029 ACGAATTAGG
Statistics
Matches: 101, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
18 2 0.02
19 1 0.01
20 81 0.80
21 15 0.15
22 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:1697758 original size:19 final size:19
Alignment explanation
Indices: 1697734--1697792 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
1697724 AAATATATAG
1697734 TCTTAATGAATCATTTATC
1 TCTTAATGAATCATTTATC
* * *
1697753 TCTTAAT-AA-AATATATAG
1 TCTTAATGAATCATTTAT-C
1697771 TCTTAATGAATCATTTATC
1 TCTTAATGAATCATTTATC
1697790 TCT
1 TCT
1697793 CAATTTTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
17 5 0.16
18 9 0.29
19 12 0.39
20 5 0.16
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.46
Consensus pattern (19 bp):
TCTTAATGAATCATTTATC
Found at i:1697762 original size:37 final size:37
Alignment explanation
Indices: 1697721--1697792 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
1697711 AGACCTAGAG
1697721 ATAAAATATATAGTCTTAATGAATCATTTATCTCTTA
1 ATAAAATATATAGTCTTAATGAATCATTTATCTCTTA
1697758 ATAAAATATATAGTCTTAATGAATCATTTATCTCT
1 ATAAAATATATAGTCTTAATGAATCATTTATCTCT
1697793 CAATTTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (37 bp):
ATAAAATATATAGTCTTAATGAATCATTTATCTCTTA
Found at i:1697776 original size:18 final size:18
Alignment explanation
Indices: 1697721--1697777 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1697711 AGACCTAGAG
1697721 ATAAAATATATAGTCTTA
1 ATAAAATATATAGTCTTA
* * *
1697739 AT-GAATCATTTATCTCTTA
1 ATAAAAT-ATATA-GTCTTA
1697758 ATAAAATATATAGTCTTA
1 ATAAAATATATAGTCTTA
1697776 AT
1 AT
1697778 GAATCATTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
17 3 0.10
18 13 0.43
19 11 0.37
20 3 0.10
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (18 bp):
ATAAAATATATAGTCTTA
Found at i:1705111 original size:19 final size:20
Alignment explanation
Indices: 1705071--1705113 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
1705061 ACTTTCTCTA
1705071 TTCCCTCTAAATTTCCCAAT
1 TTCCCTCTAAATTTCCCAAT
*
1705091 TTCCCTCTAAA-TTCTCAAT
1 TTCCCTCTAAATTTCCCAAT
1705110 TTCC
1 TTCC
1705114 AACTTTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (20 bp):
TTCCCTCTAAATTTCCCAAT
Found at i:1716457 original size:20 final size:20
Alignment explanation
Indices: 1716432--1716511 Score: 88
Period size: 20 Copynumber: 4.0 Consensus size: 20
1716422 CTATCGCAAA
*
1716432 TTCGCGTTGCGATTTTTCAT
1 TTCGCGTTGCGATTTTCCAT
* ** *
1716452 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
* *
1716473 ATCGCGTTGCGCTTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
1716493 TTCGCGTTGCGATTTTCCA
1 TTCGCGTTGCGATTTTCCA
1716512 AATTCGTTGC
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 33 0.70
21 14 0.30
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.41
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAT
Found at i:1716615 original size:6 final size:6
Alignment explanation
Indices: 1716604--1716636 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1716594 AGACATGTAT
1716604 GACCAC GACCAC GACCAC GACCAC GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1716637 CGAGACGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.30, C:0.52, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:1717160 original size:6 final size:6
Alignment explanation
Indices: 1717127--1717156 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1717117 GTCTAGTCTC
*
1717127 GGGTCG GGGTCG GGGTCG GGGTCG TGGTCG
1 GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG
1717157 TGGTAATACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.63, T:0.20
Consensus pattern (6 bp):
GGGTCG
Found at i:1717278 original size:19 final size:19
Alignment explanation
Indices: 1717254--1717300 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1717244 CAACGAATTT
1717254 TCGCAACGAATTTGAAAAA
1 TCGCAACGAATTTGAAAAA
*
1717273 TCGCAAAGAATTTGAAAAA
1 TCGCAACGAATTTGAAAAA
1717292 TCGCAACGA
1 TCGCAACGA
1717301 CAACTGTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGAAAAA
Found at i:1717341 original size:20 final size:20
Alignment explanation
Indices: 1717316--1717385 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
1717306 GTAGACTATT
1717316 GCAACGCGATTTCAAATATC
1 GCAACGCGATTTCAAATATC
* * **
1717336 GCAACGTGAAATGGAAA-ATC
1 GCAACGCG-ATTTCAAATATC
*
1717356 GCAACGCGATTTTCAACTATC
1 GCAACGCGA-TTTCAAATATC
1717377 GCAACGCGA
1 GCAACGCGA
1717386 AATACAACGC
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
19 1 0.03
20 20 0.53
21 17 0.45
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
GCAACGCGATTTCAAATATC
Found at i:1730003 original size:32 final size:31
Alignment explanation
Indices: 1729967--1730084 Score: 159
Period size: 32 Copynumber: 3.7 Consensus size: 31
1729957 GTTCTACGGA
1729967 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGAA-TACCTATGTCTTTCGAG
* *
1729999 ACATATGGACAGTATACCTATGT-TCTAC-AG
1 ACATATGGACAGAATACCTATGTCT-TTCGAG
1730029 AACATATGGACAGAATTACCTATGTCTTTCGAG
1 -ACATATGGACAGAA-TACCTATGTCTTTCGAG
*
1730062 ACATATGGACAGTATACCTATGT
1 ACATATGGACAGAATACCTATGT
1730085 TCTAAGGAAC
Statistics
Matches: 76, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
30 3 0.04
31 33 0.43
32 37 0.49
33 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (31 bp):
ACATATGGACAGAATACCTATGTCTTTCGAG
Found at i:1730020 original size:31 final size:32
Alignment explanation
Indices: 1729946--1730140 Score: 201
Period size: 31 Copynumber: 6.2 Consensus size: 32
1729936 AAGAGTCGAG
1729946 AGTATACCTATGTTCTACG-GAACATATGGAC
1 AGTATACCTATGTTCTACGAGAACATATGGAC
* *
1729977 AGAATTACCTATG-TCTTTCGAG-ACATATGGAC
1 AGTA-TACCTATGTTC-TACGAGAACATATGGAC
1730009 AGTATACCTATGTTCTAC-AGAACATATGGAC
1 AGTATACCTATGTTCTACGAGAACATATGGAC
* *
1730040 AGAATTACCTATG-TCTTTCGAG-ACATATGGAC
1 AGTA-TACCTATGTTC-TACGAGAACATATGGAC
* *
1730072 AGTATACCTATGTTCTAAG-GAACATATGGAT
1 AGTATACCTATGTTCTACGAGAACATATGGAC
* * * *
1730103 AGTTTACCTAGGTTCTTCG-GAACCTATGGAC
1 AGTATACCTATGTTCTACGAGAACATATGGAC
1730134 AGT-TACC
1 AGTATACC
1730141 GAGGATCTTT
Statistics
Matches: 138, Mismatches: 16, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
30 7 0.05
31 77 0.56
32 51 0.37
33 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (32 bp):
AGTATACCTATGTTCTACGAGAACATATGGAC
Found at i:1730024 original size:63 final size:63
Alignment explanation
Indices: 1729946--1730101 Score: 294
Period size: 63 Copynumber: 2.5 Consensus size: 63
1729936 AAGAGTCGAG
1729946 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGAC
*
1730009 AGTATACCTATGTTCTACAGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGAC
*
1730072 AGTATACCTATGTTCTAAGGAACATATGGA
1 AGTATACCTATGTTCTACGGAACATATGGA
1730102 TAGTTTACCT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 90 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (63 bp):
AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGAC
Found at i:1735879 original size:21 final size:22
Alignment explanation
Indices: 1735855--1735913 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 22
1735845 GAAGAAAAGG
*
1735855 AAAAAAGATTAA-AAAAATAAA
1 AAAAAAGATAAAGAAAAATAAA
* *
1735876 AAAAATGATAAAGAAAAATAAG
1 AAAAAAGATAAAGAAAAATAAA
* *
1735898 GAAAGA-ATAAAGAAAA
1 AAAAAAGATAAAGAAAA
1735914 CAAATCCAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (22 bp):
AAAAAAGATAAAGAAAAATAAA
Found at i:1737969 original size:33 final size:33
Alignment explanation
Indices: 1737932--1738454 Score: 697
Period size: 33 Copynumber: 16.0 Consensus size: 33
1737922 TTTGCTTGAT
* *
1737932 TCCATCACAGAAAGAGGTGGATCGCCATTTAAA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAA
* *
1737965 TCCATCACAGAAAGAGGTGAATCGACATTCACA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAA
*
1737998 TCCATCACAGAAAGAGGTGGATCGACATTAAAA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAA
* *
1738031 TCCATCAC-TAAAGAGGTGGATCG-CGTTCAAA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAA
* * * *
1738062 TCCATAATAGAAAGAGGTGGATTGACGTTCAAA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAA
1738095 TCCATCACAGAAAGAGGTGGATCGACATTTCAAA
1 TCCATCACAGAAAGAGGTGGATCGACA-TTCAAA
*
1738129 TCCATCACAGAAAGAGGTGTATCGACATTTCAAA
1 TCCATCACAGAAAGAGGTGGATCGACA-TTCAAA
*
1738163 TCCATCATAGAAAGAGGTGGATCGACATTGCAAA
1 TCCATCACAGAAAGAGGTGGATCGACATT-CAAA
* *
1738197 TCCATCACAGAAAGAGGTGAATCGACGTTCAAA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAA
* *
1738230 TCCATCGCAGAAAGAGGTGGATCAACATTCAAA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAA
1738263 T-C--CACAGAAAGAGG-GGATCGACATTTCAAA
1 TCCATCACAGAAAGAGGTGGATCGACA-TTCAAA
* *
1738293 TCCAT--CAGAAAGAAGTGGATCGATATTCAAA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAA
* *
1738324 TCCATTACAGAAAGAGGTGGATCGACGTTCAAA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAA
*
1738357 TCTATCACAGAAAGAGGTGGATCGACATTCAAA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAA
* * *
1738390 TCCATCACAAAAAGAGGTGGATTGACATT-TAA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAA
* *
1738422 TCCATCACAGAAGGAGTTGGATCGACA-TCAAA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAA
1738454 T
1 T
1738455 TTTTGCTCGA
Statistics
Matches: 431, Mismatches: 47, Indels: 25
0.86 0.09 0.05
Matches are distributed among these distances:
29 8 0.02
30 18 0.04
31 34 0.08
32 64 0.15
33 213 0.49
34 94 0.22
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (33 bp):
TCCATCACAGAAAGAGGTGGATCGACATTCAAA
Found at i:1738076 original size:97 final size:99
Alignment explanation
Indices: 1737932--1738454 Score: 697
Period size: 97 Copynumber: 5.3 Consensus size: 99
1737922 TTTGCTTGAT
* * * *
1737932 TCCATCACAGAAAGAGGTGGATCGCCATTTAAATCCATCACAGAAAGAGGTGAATCGACATTCAC
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTCAA
*
1737997 ATCCATCACAGAAAGAGGTGGATCGACATTAAAA
66 ATCCATCACAGAAAGAGGTGGATCGACATTCAAA
* * * * * *
1738031 TCCATCAC-TAAAGAGGTGGATCG-CGTTCAAATCCATAATAGAAAGAGGTGGATTGACGTTCAA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTCAA
1738094 ATCCATCACAGAAAGAGGTGGATCGACATTTCAAA
66 ATCCATCACAGAAAGAGGTGGATCGACA-TTCAAA
* *
1738129 TCCATCACAGAAAGAGGTGTATCGACATTTCAAATCCATCATAGAAAGAGGTGGATCGACATTGC
1 TCCATCACAGAAAGAGGTGGATCGACA-TTCAAATCCATCACAGAAAGAGGTGGATCGACATT-C
* *
1738194 AAATCCATCACAGAAAGAGGTGAATCGACGTTCAAA
64 AAATCCATCACAGAAAGAGGTGGATCGACATTCAAA
* *
1738230 TCCATCGCAGAAAGAGGTGGATCAACATTCAAAT-C--CACAGAAAGAGG-GGATCGACATTTCA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACA-TTCA
* *
1738291 AATCCAT--CAGAAAGAAGTGGATCGATATTCAAA
65 AATCCATCACAGAAAGAGGTGGATCGACATTCAAA
* * *
1738324 TCCATTACAGAAAGAGGTGGATCGACGTTCAAATCTATCACAGAAAGAGGTGGATCGACATTCAA
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTCAA
* * *
1738389 ATCCATCACAAAAAGAGGTGGATTGACATT-TAA
66 ATCCATCACAGAAAGAGGTGGATCGACATTCAAA
* *
1738422 TCCATCACAGAAGGAGTTGGATCGACA-TCAAAT
1 TCCATCACAGAAAGAGGTGGATCGACATTCAAAT
1738455 TTTTGCTCGA
Statistics
Matches: 372, Mismatches: 40, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
94 52 0.14
96 18 0.05
97 102 0.27
98 61 0.16
99 40 0.11
100 8 0.02
101 62 0.17
102 29 0.08
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (99 bp):
TCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTCAA
ATCCATCACAGAAAGAGGTGGATCGACATTCAAA
Found at i:1738505 original size:44 final size:43
Alignment explanation
Indices: 1738457--1738591 Score: 108
Period size: 44 Copynumber: 3.1 Consensus size: 43
1738447 CATCAAATTT
*
1738457 TTGCTCGATTCTATCACAGAAAGAGATAGATCAGCACCGACGTC
1 TTGCTCGATTCTATCACAGAATGAGATAGATCAGCACCGAC-TC
* * * * * * * **** *
1738501 TTGCTCAAATCCATCGCAGAATGAGTTGGATCAACGTTAACTT
1 TTGCTCGATTCTATCACAGAATGAGATAGATCAGCACCGACTC
* *
1738544 TTAGCTCGATTCTATCATAGAATGAGGTAGATCAGCACCGACATC
1 TT-GCTCGATTCTATCACAGAATGAGATAGATCAGCACCGAC-TC
1738589 TTG
1 TTG
1738592 TTTGATTCCA
Statistics
Matches: 63, Mismatches: 26, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
43 3 0.05
44 57 0.90
45 3 0.05
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.27
Consensus pattern (43 bp):
TTGCTCGATTCTATCACAGAATGAGATAGATCAGCACCGACTC
Found at i:1738575 original size:88 final size:88
Alignment explanation
Indices: 1738420--1738591 Score: 245
Period size: 88 Copynumber: 2.0 Consensus size: 88
1738410 ATTGACATTT
* *
1738420 AATCCATCACAGAAGGAGTTGGATCGACATCAAATTTTTGCTCGATTCTATCACAGAAAGAGATA
1 AATCCATCACAGAAGGAGTTGGATCAACATCAAATTTTAGCTCGATTCTATCACAGAAAGAGATA
*
1738485 GATCAGCACCGACGTCTTGCTCA
66 GATCAGCACCGACATCTTGCTCA
* * * * * * * *
1738508 AATCCATCGCAGAATGAGTTGGATCAACGTTAACTTTTAGCTCGATTCTATCATAGAATGAGGTA
1 AATCCATCACAGAAGGAGTTGGATCAACATCAAATTTTAGCTCGATTCTATCACAGAAAGAGATA
1738573 GATCAGCACCGACATCTTG
66 GATCAGCACCGACATCTTG
1738592 TTTGATTCCA
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 73 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (88 bp):
AATCCATCACAGAAGGAGTTGGATCAACATCAAATTTTAGCTCGATTCTATCACAGAAAGAGATA
GATCAGCACCGACATCTTGCTCA
Found at i:1740199 original size:2 final size:2
Alignment explanation
Indices: 1740192--1740248 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
1740182 TGCATGGCTA
*
1740192 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1740233 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1740249 GTTAATGTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1742282 original size:21 final size:22
Alignment explanation
Indices: 1742242--1742282 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1742232 TTAAATATTA
* *
1742242 TAAAGGTAGTACTGATACTCAT
1 TAAAGGTAGTACCGACACTCAT
1742264 TAAAGGT-GTACCGACACTC
1 TAAAGGTAGTACCGACACTC
1742283 TCTGTCCTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (22 bp):
TAAAGGTAGTACCGACACTCAT
Found at i:1744878 original size:20 final size:21
Alignment explanation
Indices: 1744853--1744904 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1744843 TTTTCCCAAT
1744853 TCGCAATGCGAA-TAAGAAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1744873 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1744894 TCGTAATGCGA
1 TCGCAATGCGA
1744905 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1744921 original size:20 final size:20
Alignment explanation
Indices: 1744893--1745026 Score: 135
Period size: 20 Copynumber: 6.7 Consensus size: 20
1744883 AATTGGGAAA
*
1744893 ATCGTAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
1744913 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1744933 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1744953 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1744974 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * * *
1744994 TTCGCAACGCAATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
1745014 TTCGCAACGCGAT
1 ATCGCAATGCGAT
1745027 TTACATAGCG
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 81 0.83
21 13 0.13
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1745611 original size:19 final size:19
Alignment explanation
Indices: 1745589--1745748 Score: 133
Period size: 19 Copynumber: 8.8 Consensus size: 19
1745579 CAAAATCACA
1745589 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
1745608 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
1745627 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
1745646 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
** **
1745660 TCACGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
1745679 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
1745693 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
* * *
1745713 TTGTGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
1745733 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1745749 AACCAAAAGA
Statistics
Matches: 112, Mismatches: 17, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
14 18 0.16
16 4 0.04
17 5 0.04
19 55 0.49
20 29 0.26
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:1745640 original size:38 final size:33
Alignment explanation
Indices: 1745589--1745723 Score: 144
Period size: 33 Copynumber: 3.9 Consensus size: 33
1745579 CAAAATCACA
*
1745589 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTC---TCTCG
1745627 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** **
1745660 TCACGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
1745693 TTGCGATAGTCATTTCCGCGTTGTGATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
1745724 ATTATCTCGT
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
33 46 0.52
34 14 0.16
36 3 0.03
38 25 0.28
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1745725 original size:20 final size:20
Alignment explanation
Indices: 1745691--1745748 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
1745681 GCGATTCTCT
**
1745691 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
* *
1745711 CGTTGTGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1745731 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1745749 AACCAAAAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1747490 original size:95 final size:89
Alignment explanation
Indices: 1747325--1747509 Score: 271
Period size: 91 Copynumber: 2.0 Consensus size: 89
1747315 TAGATTGCTT
1747325 AGTAAATTTATTCGGTTCCTGCAAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTCCTGCAAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
*
1747390 GTCTTTTTGTTTTGTCTTTTGGTTGA
66 GTC--TTTGTTTTATCTTTTGGTTGA
* * * *
1747416 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTCCTGCAAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1747481 ATTTGTCTTTGTTTTATCTTTTGGTTGA
62 ATTTGTCTTTGTTTTATCTTTTGGTTGA
1747509 A
1 A
1747510 AGTTTGAAAT
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
91 33 0.39
93 24 0.28
94 2 0.02
95 26 0.31
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (89 bp):
AGTAAATTTATTCGGTTCCTGCAAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
GTCTTTGTTTTATCTTTTGGTTGA
Found at i:1747808 original size:42 final size:42
Alignment explanation
Indices: 1747742--1747934 Score: 183
Period size: 42 Copynumber: 4.6 Consensus size: 42
1747732 TCATCCCTTA
* * * * *
1747742 AGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCG
1 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATTCCTCG
* * *
1747784 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATCCCTCA
1 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATTCCTCG
** * * * * *
1747826 AGAGTCTACTCCTATCGTTGAAGAGGCCCCTATCTTTCCTCG
1 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATTCCTCG
* * *
1747868 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCA-TCGTTG
1 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATTCCTCG
*
1747909 AAGAGGT-CCCTCCCACCATTCAAGAG
1 -AGA-GTCCCCTCCCACCGTTCAAGAG
1747935 CCCGATTCAC
Statistics
Matches: 120, Mismatches: 29, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
41 4 0.03
42 114 0.95
43 2 0.02
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (42 bp):
AGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATTCCTCG
Found at i:1747892 original size:21 final size:21
Alignment explanation
Indices: 1747868--1747934 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1747858 TCTTTCCTCG
1747868 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1747889 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1747910 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1747931 AGAG
1 AGAG
1747935 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1747913 original size:84 final size:84
Alignment explanation
Indices: 1747729--1747904 Score: 325
Period size: 84 Copynumber: 2.1 Consensus size: 84
1747719 CCCGACTCGC
*
1747729 CTGTCATCCCTTAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1747794 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* *
1747813 CTGTCATCCCTCAAGAGTCTACTCCTATCGTTGAAGAGGCCCCTATCTTTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1747878 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
1747897 CTGTCATC
1 CTGTCATC
1747905 GTTGAAGAGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.20, C:0.37, G:0.18, T:0.25
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1747934 original size:84 final size:84
Alignment explanation
Indices: 1747729--1747934 Score: 261
Period size: 84 Copynumber: 2.5 Consensus size: 84
1747719 CCCGACTCGC
* * * * * *
1747729 CTGTCATCCCTTAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCTACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1747794 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * * *
1747813 CTGTCATCCCTCAAGAGTCTACTCCTATCGTTGAAGAGGCCCCTATCTTTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCTACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1747878 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** * *
1747897 CTGTCATCGTTGAAGAGGTC-CCTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCTACTCCCACCATTCAAGAG
1747935 CCCGATTCAC
Statistics
Matches: 110, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 107 0.97
85 3 0.03
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCTACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1749308 original size:14 final size:14
Alignment explanation
Indices: 1749289--1749324 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1749279 ATTGTTTAAT
1749289 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1749303 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1749317 TGATTTGT
1 TGATTTGT
1749325 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1749468 original size:14 final size:14
Alignment explanation
Indices: 1749449--1749505 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1749439 GCGAAATGAA
1749449 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1749463 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1749482 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1749496 AATCACAACG
1 AATCGCAACG
1749506 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1749476 original size:33 final size:33
Alignment explanation
Indices: 1749431--1749520 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
1749421 AAAAAGTACT
*
1749431 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1749464 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
1749497 ATCACAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
1749521 GTTGCGATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:1749490 original size:19 final size:19
Alignment explanation
Indices: 1749431--1749491 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
1749421 AAAAAGTACT
*
1749431 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1749450 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
1749464 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1749483 ATCGCAACG
1 ATCGCAACG
1749492 AGAGAATCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1749538 original size:19 final size:19
Alignment explanation
Indices: 1749516--1749646 Score: 103
Period size: 19 Copynumber: 7.7 Consensus size: 19
1749506 CGAAATTAAA
*
1749516 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1749535 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
1749551 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1749568 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
*
1749582 TTAGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1749601 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
1749617 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1749634 TTCGCATTGCGAT
1 TTCGCATTGCGAT
1749647 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 11, Indels: 30
0.68 0.09 0.24
Matches are distributed among these distances:
14 24 0.28
16 13 0.15
17 13 0.15
19 36 0.42
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1749562 original size:33 final size:32
Alignment explanation
Indices: 1749520--1749646 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
1749510 ATTAAATTCG
1749520 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1749553 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
1749586 CATTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1749619 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1749647 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1749596 original size:66 final size:66
Alignment explanation
Indices: 1749513--1749645 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1749503 ACGCGAAATT
* *
1749513 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1749578 G
66 G
*
1749579 AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1749644 G
66 G
1749645 A
1 A
1749646 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (66 bp):
AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1751947 original size:12 final size:12
Alignment explanation
Indices: 1751932--1751956 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1751922 TTCTTCGGGA
1751932 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1751944 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1751956 C
1 C
1751957 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1752158 original size:24 final size:24
Alignment explanation
Indices: 1752131--1752184 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1752121 CTGAAACATC
* *
1752131 ATCAAAATCCGAGTATTGATCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1752155 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1752179 ATCAAA
1 ATCAAA
1752185 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1753059 original size:20 final size:20
Alignment explanation
Indices: 1753012--1753061 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1753002 GAGATAATAC
*
1753012 AAAATTGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
1753032 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
1753052 AAAATCGCAA
1 AAAATCGCAA
1753062 TCATCTTCAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:1753327 original size:20 final size:20
Alignment explanation
Indices: 1753275--1753362 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
1753265 CAACGGGGAA
*
1753275 ATCGCAACGCAAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1753295 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* ** ***
1753315 ATCGTAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
1753335 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
1753355 ATTGCAAC
1 ATCGCAAC
1753363 TAGAAAATCG
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
19 5 0.10
20 42 0.81
21 5 0.10
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1753413 original size:14 final size:14
Alignment explanation
Indices: 1753394--1753447 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1753384 GAAAATTGCA
1753394 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1753408 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
1753425 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
1753441 TTGCGAT
1 TTGCGAT
1753448 AGTCTGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1753413 original size:33 final size:34
Alignment explanation
Indices: 1753376--1753446 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 34
1753366 AAAATCGCAA
1753376 TGCGAAATGAAAATT-GCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATTCGCATTGCGATTTTCTCGT
* *** *
1753409 TGCG-ATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATTCGCATTGCGATTTTCTCGT
1753442 TGCGA
1 TGCGA
1753447 TAGTCTGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
32 5 0.16
33 26 0.84
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (34 bp):
TGCGAAATGAAAATTCGCATTGCGATTTTCTCGT
Found at i:1753573 original size:14 final size:14
Alignment explanation
Indices: 1753554--1753590 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1753544 CATCAATTAA
1753554 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1753568 ACAAATCATCTTTT
1 ACAAATCAACATTT
1753582 ACAAATCAA
1 ACAAATCAA
1753591 TTAAAGAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1755476 original size:20 final size:19
Alignment explanation
Indices: 1755453--1755520 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
1755443 GAAACTTAAA
1755453 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* * *
1755473 ATCGCAATGTGGAAATGGCT
1 ATCGCAACG-CGAAATGACT
* **
1755493 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1755512 ATCGCAACG
1 ATCGCAACG
1755521 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 14 0.36
20 24 0.62
21 1 0.03
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.18
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1755528 original size:14 final size:14
Alignment explanation
Indices: 1755509--1755566 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1755499 ATGCGAAATG
1755509 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1755523 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1755539 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1755555 AAAATCGCAACG
1 AAAATCGCAACG
1755567 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1755551 original size:32 final size:33
Alignment explanation
Indices: 1755493--1755571 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1755483 GGAAATGGCT
1755493 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1755526 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1755558 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1755572 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1755600 original size:19 final size:19
Alignment explanation
Indices: 1755578--1755659 Score: 95
Period size: 18 Copynumber: 4.6 Consensus size: 19
1755568 GAAACACAAA
1755578 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1755597 TCGCGTTGC-AATTTCATT
1 TCGCATTGCGATTTTCATT
*
1755615 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1755631 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1755648 TCGCATTGCGAT
1 TCGCATTGCGAT
1755660 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 4 0.08
17 4 0.08
18 19 0.37
19 16 0.31
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1755675 original size:39 final size:35
Alignment explanation
Indices: 1755578--1755679 Score: 95
Period size: 33 Copynumber: 2.8 Consensus size: 35
1755568 GAAACACAAA
*
1755578 TCGCATTGCGATTTTCATTTCGCGTTGC-AATTTCATT
1 TCGCATTGCGA---TCATTTCGCGTTGCGATTTTCATT
1755615 TCGCATTGCGAT--TTT-GTCGTTGCGATTTTCATT
1 TCGCATTGCGATCATTTCG-CGTTGCGATTTTCATT
1755648 TCGCATTGCGATAGCCATTTCCGCGTTGCGAT
1 TCGCATTGCGAT---CATTT-CGCGTTGCGAT
1755680 AGTCATTTTC
Statistics
Matches: 55, Mismatches: 1, Indels: 16
0.76 0.01 0.22
Matches are distributed among these distances:
31 1 0.02
32 9 0.16
33 20 0.36
34 1 0.02
37 11 0.20
38 3 0.05
39 9 0.16
40 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (35 bp):
TCGCATTGCGATCATTTCGCGTTGCGATTTTCATT
Found at i:1755678 original size:20 final size:19
Alignment explanation
Indices: 1755644--1755698 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1755634 TTGCGATTTT
*
1755644 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1755663 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1755683 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1755699 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1756200 original size:18 final size:18
Alignment explanation
Indices: 1756174--1756218 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1756164 GTCGATCAGA
*
1756174 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1756192 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1756210 TGATGGCTC
1 TGATGGCTC
1756219 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1757564 original size:20 final size:20
Alignment explanation
Indices: 1757539--1757581 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1757529 AATAGTTTCT
1757539 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
1757559 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
1757579 GAA
1 GAA
1757582 TTTGACTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1757587 original size:20 final size:20
Alignment explanation
Indices: 1757549--1757617 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
1757539 GAAAATGAAA
* **
1757549 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAATTTGACT
1757569 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
1757589 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
1757609 ATCGCAACG
1 ATCGCAACG
1757618 AGAGAATCGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:1757907 original size:22 final size:21
Alignment explanation
Indices: 1757873--1757921 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
1757863 TCTGAGAGAT
1757873 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
*
1757893 GGAGATGAGGACGGATTTCGTC
1 GGAGATGA-GACGGATTTCGCC
1757915 GGAGATG
1 GGAGATG
1757922 GGTGAGAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 6 0.23
21 1 0.04
22 19 0.73
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:1758137 original size:20 final size:20
Alignment explanation
Indices: 1758112--1758163 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1758102 ATGATGTATT
1758112 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
* *
1758132 ATCGCGTTGCAAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
1758152 ATCTCGTTGCGA
1 ATCGCGTTGCGA
1758164 TTTTGTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:1758209 original size:30 final size:30
Alignment explanation
Indices: 1758173--1758232 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1758163 ATTTTGTATT
1758173 ATCGCATTGCGATAGTAAGTATCGCATTGC
1 ATCGCATTGCGATAGTAAGTATCGCATTGC
*
1758203 ATCGCATTGCGATAGTCAGTATCGCATTGC
1 ATCGCATTGCGATAGTAAGTATCGCATTGC
1758233 GATTTTCCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (30 bp):
ATCGCATTGCGATAGTAAGTATCGCATTGC
Found at i:1758346 original size:21 final size:21
Alignment explanation
Indices: 1758306--1758346 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1758296 ACTGTAGACC
** *
1758306 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
1758327 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
1758347 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:1760131 original size:62 final size:63
Alignment explanation
Indices: 1760029--1760148 Score: 154
Period size: 62 Copynumber: 1.9 Consensus size: 63
1760019 AAGAAATTAA
* * * *
1760029 ATTTATAATTATATTTATAATTTATTATATTTTTACACAAATAACTTAATATA-ATTTCAATT
1 ATTTATAATTATATATATAATTTATAAAATTTGTACACAAATAACTTAATATATATTTCAATT
* * *
1760091 ATTTATAATT-TATATATATTTTAATAAAATTTGTATACAAATAATTTAATATATATTT
1 ATTTATAATTATATATATAATTT-ATAAAATTTGTACACAAATAACTTAATATATATTT
1760149 ATCATTTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
61 10 0.20
62 35 0.71
63 4 0.08
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (63 bp):
ATTTATAATTATATATATAATTTATAAAATTTGTACACAAATAACTTAATATATATTTCAATT
Found at i:1764477 original size:18 final size:18
Alignment explanation
Indices: 1764433--1764492 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
1764423 ATACTACTAC
1764433 TAATAATAATTATAATTTTA
1 TAATAATAATTATAA--TTA
** *
1764453 TTGTAATAATTATGATTA
1 TAATAATAATTATAATTA
*
1764471 TAATAATAATTATTATTA
1 TAATAATAATTATAATTA
1764489 TAAT
1 TAAT
1764493 GTAATATTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 22 0.65
20 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TAATAATAATTATAATTA
Found at i:1764746 original size:55 final size:55
Alignment explanation
Indices: 1764687--1764900 Score: 252
Period size: 55 Copynumber: 3.9 Consensus size: 55
1764677 TTTCGAAAAA
* * * * * *
1764687 CATGTTTGCTCCCTATTCTTTCAGAGAGTATAGGACTTGATCAATCTTCAACAAT
1 CATGTCTGCTCCCTATTCGTTCAAAGAGTATAAGACTCGAACAATCTTCAACAAT
* * *
1764742 CATGTATGCTCCCTATTTC-TTCAAAGAGTATGAGACTCGAACAATCTTCAATAAT
1 CATGTCTGCTCCCTA-TTCGTTCAAAGAGTATAAGACTCGAACAATCTTCAACAAT
* * *
1764797 CGTGTCCT-CTCTCTATTCGTTCAAAGAGTATAAGACTCGAACAGTCTTCAACAAT
1 CATGT-CTGCTCCCTATTCGTTCAAAGAGTATAAGACTCGAACAATCTTCAACAAT
* * * *
1764852 CCTGTCCGCTCTCTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTC
1 CATGTCTGCTCCCTATTCGTTCAAAGAGTATAAGACTCGAACAATCTTC
1764901 TTTTTATGGA
Statistics
Matches: 138, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
54 4 0.03
55 130 0.94
56 4 0.03
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (55 bp):
CATGTCTGCTCCCTATTCGTTCAAAGAGTATAAGACTCGAACAATCTTCAACAAT
Found at i:1764892 original size:110 final size:110
Alignment explanation
Indices: 1764699--1764900 Score: 280
Period size: 110 Copynumber: 1.8 Consensus size: 110
1764689 TGTTTGCTCC
* * * * * *
1764699 CTATTCTTTCAGAGAGTATAGGACTTGATCAATCTTCAACAATCATGTATGCTCCCTATTTCTTC
1 CTATTCGTTCAAAGAGTATAAGACTCGAACAATCTTCAACAATCATGTACGCTCCCTATTTCTTC
*
1764764 AAAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCCTCTCT
66 AAAGAGTATAAGACTCGAACAATCTTCAATAATCGTGTCCTCTCT
* * * *
1764809 CTATTCGTTCAAAGAGTATAAGACTCGAACAGTCTTCAACAATCCTGTCCGCTCTCTA-TTCGTT
1 CTATTCGTTCAAAGAGTATAAGACTCGAACAATCTTCAACAATCATGTACGCTCCCTATTTC-TT
*
1764873 CAGAGAGTATAAGACTCGAACAATCTTC
65 CAAAGAGTATAAGACTCGAACAATCTTC
1764901 TTTTTATGGA
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
109 3 0.04
110 76 0.96
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (110 bp):
CTATTCGTTCAAAGAGTATAAGACTCGAACAATCTTCAACAATCATGTACGCTCCCTATTTCTTC
AAAGAGTATAAGACTCGAACAATCTTCAATAATCGTGTCCTCTCT
Found at i:1764974 original size:54 final size:54
Alignment explanation
Indices: 1764911--1765542 Score: 818
Period size: 54 Copynumber: 11.7 Consensus size: 54
1764901 TTTTTATGGA
* * * *
1764911 TTCGTTCCCTCTTTCTCTAGGAAGTATGGAAGTCGTACATCTTCTTCAAACGGG
1 TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGG
* **
1764965 TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGACCATCTTCTTCTTACGGG
1 TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGG
* * * * * *
1765019 TTCACTCCCTCTTTCTCTAGGGAGTACAGAAACTCAAACATATTCTTCAAACGAG
1 TTCGCTCCCTCTTTCTCTAGGGAGTA-TGGAACTCGAACATCTTCTTCAAACGGG
* * * ** *
1765074 TTCACTCCATCTTTCTCTAGGGAGTATGGAACTCAAACATCTTCTTCTTACAGG
1 TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGG
* ***
1765128 TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAAACATCTTCTTTTTACGGG
1 TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGG
* *
1765182 TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTATTCAAACGGG
1 TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGG
* *
1765236 TTTGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAATGGG
1 TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGG
* * * **
1765290 TTCACTCCCTCTTGCTCTAGGGAGTATGGAACTTGAACATCTTCTTCTTACGGG
1 TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGG
* *
1765344 TTCACTCCCTCTTTCTCTAGGGAGTATGGAACTC-AGACATCTTCTTCAAATGGG
1 TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGA-ACATCTTCTTCAAACGGG
* * * *
1765398 TTCGTTCCCTCTTTCTCTAGGGAGTATGGAACTCGGACATCTTTTTCAAATGGG
1 TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGG
* * *
1765452 TTCTCTCCCTCTTTCT-TCAGGGAGTATAGAACTCGAACGTCTTCTTCAAACGGG
1 TTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAACATCTTCTTCAAACGGG
* * * *
1765506 ATCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAA
1 TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAA
1765543 TAATTTTCTT
Statistics
Matches: 507, Mismatches: 66, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
53 2 0.00
54 459 0.91
55 46 0.09
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.34
Consensus pattern (54 bp):
TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGG
Found at i:1767261 original size:125 final size:125
Alignment explanation
Indices: 1767034--1767291 Score: 383
Period size: 125 Copynumber: 2.1 Consensus size: 125
1767024 CCTTCACTAG
* * *
1767034 TGCCGCAACATCATCTTATACTGGTACGGGCCTTCAAAATGCCCCAACACCTTAAATTGTAAGGC
1 TGCCCCAACATCATCTTATACTGGTACAGGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGC
* * *
1767099 TCATTCCTAAGGCCTTCTTGGTCTGTATCTTGTCATCTCAACATGATGTGGGTTCAGTCA
66 TCATTCCTAAGGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTACAGTCA
* * *
1767159 TGCCCCAACATTATCTTA-ACTGGTACAGGTCTTCAAAATGCCCCCATCACCTCAAATTGTAAGG
1 TGCCCCAACATCATCTTATACTGGTACAGGCCTTCAAAATG-CCCCAACACCTCAAATTGTAAGG
* * * *
1767223 CTCATTCTTCATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTACAGTCG
65 CTCATTCCTAAGGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTACAGTCA
1767284 TGCCCCAA
1 TGCCCCAA
1767292 TATATCATAA
Statistics
Matches: 119, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
124 20 0.17
125 99 0.83
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (125 bp):
TGCCCCAACATCATCTTATACTGGTACAGGCCTTCAAAATGCCCCAACACCTCAAATTGTAAGGC
TCATTCCTAAGGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTACAGTCA
Found at i:1768585 original size:26 final size:26
Alignment explanation
Indices: 1768531--1768592 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
1768521 CTCATTTCCA
*
1768531 ATTT-TCTT-TTCTTTTTTTTCTATG
1 ATTTCTCTTCTTCTTTTTTTTCTATC
* *
1768555 TTTTCTTTTCTTCTTCTTTTTTCTA-C
1 ATTTCTCTTCTTCTT-TTTTTTCTATC
1768581 ATTTCTCTTCTT
1 ATTTCTCTTCTT
1768593 TCTCTTCATG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
24 3 0.10
25 3 0.10
26 15 0.50
27 9 0.30
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (26 bp):
ATTTCTCTTCTTCTTTTTTTTCTATC
Found at i:1768598 original size:26 final size:25
Alignment explanation
Indices: 1768531--1768598 Score: 59
Period size: 27 Copynumber: 2.7 Consensus size: 25
1768521 CTCATTTCCA
* *
1768531 ATTTTC-T-TTTCTTTTTTTTCTAT
1 ATTTTCTTCTTTCTCTTTTTTCTAC
* *
1768554 GTTTTCTTTTCTTCTTCTTTTTTCTAC
1 ATTTTCTTCT-TTC-TCTTTTTTCTAC
1768581 ATTTCTCTTCTTTCTCTT
1 ATTT-TCTTCTTTCTCTT
1768599 CATGATGTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
23 5 0.14
24 1 0.03
25 1 0.03
26 7 0.20
27 16 0.46
28 5 0.14
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.72
Consensus pattern (25 bp):
ATTTTCTTCTTTCTCTTTTTTCTAC
Found at i:1768817 original size:2 final size:2
Alignment explanation
Indices: 1768810--1768856 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1768800 CAACAAGGGG
1768810 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1768852 TA TA T
1 TA TA T
1768857 TTGAAGGGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1771324 original size:22 final size:22
Alignment explanation
Indices: 1771251--1771358 Score: 91
Period size: 21 Copynumber: 5.0 Consensus size: 22
1771241 CATGTTTTTA
**
1771251 TGAATGGTCTTCAT-GT-CTTTA
1 TGAATGGTCTTC-TCGTCCTTGG
**
1771272 TGAATGGTCTTCAT-GT-CTTTA
1 TGAATGGTCTTC-TCGTCCTTGG
1771293 TGAATGGTCTTCTCGTCCTTGG
1 TGAATGGTCTTCTCGTCCTTGG
* **
1771315 TGAATAGTCTTCTCGT-CTTTA
1 TGAATGGTCTTCTCGTCCTTGG
*
1771336 TGAACGGTCTTCTCGTCCTTGG
1 TGAATGGTCTTCTCGTCCTTGG
1771358 T
1 T
1771359 ATGACTGTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
20 1 0.01
21 52 0.69
22 22 0.29
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.44
Consensus pattern (22 bp):
TGAATGGTCTTCTCGTCCTTGG
Found at i:1771352 original size:21 final size:21
Alignment explanation
Indices: 1771192--1771347 Score: 208
Period size: 21 Copynumber: 7.4 Consensus size: 21
1771182 CCATGCGAAG
1771192 TGGTCTTCATGTCTTTATGAA
1 TGGTCTTCATGTCTTTATGAA
*
1771213 GGGTCTTCATGTCTTTATGAA
1 TGGTCTTCATGTCTTTATGAA
* *
1771234 GGGTCTTCATGTTTTTATGAA
1 TGGTCTTCATGTCTTTATGAA
1771255 TGGTCTTCATGTCTTTATGAA
1 TGGTCTTCATGTCTTTATGAA
1771276 TGGTCTTCATGTCTTTATGAA
1 TGGTCTTCATGTCTTTATGAA
**
1771297 TGGTCTTC-TCGTCCTTGGTGAA
1 TGGTCTTCAT-GT-CTTTATGAA
*
1771319 TAGTCTTC-TCGTCTTTATGAA
1 TGGTCTTCAT-GTCTTTATGAA
*
1771340 CGGTCTTC
1 TGGTCTTC
1771348 TCGTCCTTGG
Statistics
Matches: 122, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
20 1 0.01
21 103 0.84
22 18 0.15
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.46
Consensus pattern (21 bp):
TGGTCTTCATGTCTTTATGAA
Found at i:1775399 original size:18 final size:18
Alignment explanation
Indices: 1775355--1775414 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
1775345 ATAATACTAC
1775355 TAATAATAATTATAATTTTA
1 TAATAATAATTATAA--TTA
** *
1775375 TTGTAATAATTATGATTA
1 TAATAATAATTATAATTA
*
1775393 TAATAATAATTATTATTA
1 TAATAATAATTATAATTA
1775411 TAAT
1 TAAT
1775415 GTAATATTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 22 0.65
20 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TAATAATAATTATAATTA
Found at i:1776946 original size:23 final size:23
Alignment explanation
Indices: 1776920--1776976 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
1776910 ATTAAGCACA
* *
1776920 ATAATATATTAGGTACCGCTTAT
1 ATAATATAATAGGTACCACTTAT
* *
1776943 ATAATGTAATAGGTAGCACTTAT
1 ATAATATAATAGGTACCACTTAT
*
1776966 ATAATAAAATA
1 ATAATATAATA
1776977 AGTTAATTAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (23 bp):
ATAATATAATAGGTACCACTTAT
Found at i:1776966 original size:87 final size:86
Alignment explanation
Indices: 1776815--1777327 Score: 718
Period size: 87 Copynumber: 6.0 Consensus size: 86
1776805 TATTTAATCG
* * ** *
1776815 GAAATATTATCAAGTACAATAACATATTAGGTACCGTTTATATAATGTAATAAGTAGCACTTATA
1 GAAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATGTAATAGGTAGCACTTATA
1776880 TAATAAAATAGGTTAATTACT
66 TAATAAAATAGGTTAATTACT
* * *
1776901 AGAAACATTATTAAGCACAATAATATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTAT
1 -GAAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATGTAATAGGTAGCACTTAT
*
1776966 ATAATAAAATAAGTTAATTACT
65 ATAATAAAATAGGTTAATTACT
* * *
1776988 GGAAACATTATCAAACACAATAACATATTAGGTAACACTTATATAATGTAATAGGTAGCGCTTAT
1 -GAAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATGTAATAGGTAGCACTTAT
1777053 ATAATAAAATAGGTTAATTACT
65 ATAATAAAATAGGTTAATTACT
* * *
1777075 GAAAACATTATCAAGCAAAATAACATATTAGGTACAACTTATATAATGTAATAGGTAGCGCTTAT
1 G-AAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATGTAATAGGTAGCACTTAT
*
1777140 ATAATATAATAGGTTAATTACT
65 ATAATAAAATAGGTTAATTACT
* *
1777162 GAAAATATTATCAAG--C---AA-A-A-TAGGTACCACTTATATAATGTAATAGGTAACACTTAT
1 G-AAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATGTAATAGGTAGCACTTAT
1777219 ATAATAAAATAGGTTAATTACT
65 ATAATAAAATAGGTTAATTACT
* * * * *
1777241 GGAAATATTATCAAGCACAATAACATATTAGGTATCGCTTATATAACGTAATAGGTAGCTCTTAT
1 -GAAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATGTAATAGGTAGCACTTAT
1777306 ATAATAAAATAGGTTAATTACT
65 ATAATAAAATAGGTTAATTACT
1777328 TAATTTGTTA
Statistics
Matches: 385, Mismatches: 31, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
79 68 0.18
80 2 0.01
81 2 0.01
82 2 0.01
84 2 0.01
85 1 0.00
86 2 0.01
87 306 0.79
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (86 bp):
GAAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATGTAATAGGTAGCACTTATA
TAATAAAATAGGTTAATTACT
Found at i:1777042 original size:23 final size:23
Alignment explanation
Indices: 1777016--1777066 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1777006 AATAACATAT
**
1777016 TAGGTAACACTTATATAATGTAA
1 TAGGTAACACTTATATAATAAAA
* *
1777039 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAACACTTATATAATAAAA
1777062 TAGGT
1 TAGGT
1777067 TAATTACTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (23 bp):
TAGGTAACACTTATATAATAAAA
Found at i:1777129 original size:23 final size:23
Alignment explanation
Indices: 1777094--1777153 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
1777084 ATCAAGCAAA
* *
1777094 ATAACATATTAGGTA-CAACTTAT
1 ATAATATAATAGGTAGC-ACTTAT
* *
1777117 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCACTTAT
1777140 ATAATATAATAGGT
1 ATAATATAATAGGT
1777154 TAATTACTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (23 bp):
ATAATATAATAGGTAGCACTTAT
Found at i:1777206 original size:23 final size:23
Alignment explanation
Indices: 1777178--1777232 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
1777168 ATTATCAAGC
*
1777178 AAAATAGGTACCACTTATATAAT
1 AAAATAGGTAACACTTATATAAT
**
1777201 GTAATAGGTAACACTTATATAAT
1 AAAATAGGTAACACTTATATAAT
1777224 AAAATAGGT
1 AAAATAGGT
1777233 TAATTACTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (23 bp):
AAAATAGGTAACACTTATATAAT
Done.