Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001444.1 Hibiscus syriacus cultivar Beakdansim tig00002793_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: 2564052
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:605270 original size:17 final size:17
Alignment explanation
Indices: 605226--605280 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
605216 CTATTTTTGT
*
605226 TTTTATTTATTTA-TATA
1 TTTTATTT-TTTACTTTA
*
605243 TATTATATTTTTACTTTA
1 TTTTAT-TTTTTACTTTA
605261 TTTTATTTTTT-CTATTA
1 TTTTATTTTTTACT-TTA
605278 TTT
1 TTT
605281 GTTTTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 2 0.06
17 20 0.62
18 10 0.31
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTTTTTACTTTA
Found at i:605349 original size:36 final size:37
Alignment explanation
Indices: 605275--605359 Score: 104
Period size: 36 Copynumber: 2.3 Consensus size: 37
605265 ATTTTTTCTA
*
605275 TTATTTGTTTT-CTTAATATCATGTATATCTTTATTTT
1 TTATTTGTTTTACTTAATAT-ATATATATCTTTATTTT
* *
605312 TTATTTGTTTTACTTAGTAT-TATATATTTATTA-TTT
1 TTATTTGTTTTACTTAATATATATATATCT-TTATTTT
605348 TTATTTGTTTTA
1 TTATTTGTTTTA
605360 GTAAATACTA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
36 22 0.51
37 14 0.33
38 7 0.16
ACGTcount: A:0.22, C:0.05, G:0.06, T:0.67
Consensus pattern (37 bp):
TTATTTGTTTTACTTAATATATATATATCTTTATTTT
Found at i:605430 original size:18 final size:17
Alignment explanation
Indices: 605385--605432 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
605375 TATGTACGCA
605385 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
*
605402 TAATTTCTTTTACCTTTTT
1 TTATTT-TTTTACC-TTTT
605421 TTATTTTTTTAC
1 TTATTTTTTTAC
605433 TCCATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.27
18 10 0.38
19 9 0.35
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:608613 original size:14 final size:13
Alignment explanation
Indices: 608582--608618 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
608572 CAATCATAAC
608582 AAAAAGAG-AAAA
1 AAAAAGAGAAAAA
608594 AAAAAGAGAAAAA
1 AAAAAGAGAAAAA
608607 AACAAAG-GAAAA
1 AA-AAAGAGAAAA
608619 TTGAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 11 0.48
14 4 0.17
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAGAGAAAAA
Found at i:608618 original size:12 final size:12
Alignment explanation
Indices: 608582--608608 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
608572 CAATCATAAC
608582 AAAAAGAGAAAA
1 AAAAAGAGAAAA
608594 AAAAAGAGAAAA
1 AAAAAGAGAAAA
608606 AAA
1 AAA
608609 CAAAGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:608809 original size:69 final size:69
Alignment explanation
Indices: 608691--608828 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 69
608681 GATTCAAACT
* * *
608691 ATGAGATTGATTAAGCACAATCATTTCTGAATCACTGAACCACTTCACTCAAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCAAAGATAATAGAGCA
608756 TCAA
66 TCAA
* * * * *
608760 ATGAGATTGATCAAGCACAATCATTTTTGAATTACTGAATCACTCCACTCGAAGATAATGGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCAAAGATAATAGAGCA
608825 TCAA
66 TCAA
608829 GAGAGAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.27
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCAAAGATAATAGAGCA
TCAA
Found at i:609785 original size:32 final size:32
Alignment explanation
Indices: 609749--609866 Score: 132
Period size: 32 Copynumber: 3.7 Consensus size: 32
609739 AGAAAATGAT
*
609749 GGCATCTTTGAAGATTCAACATCAAATGTTGG
1 GGCATCTTTGTAGATTCAACATCAAATGTTGG
* * *
609781 GGCATTTTTTTAGATTTAACATCAAATGTTGG
1 GGCATCTTTGTAGATTCAACATCAAATGTTGG
* * * *
609813 GGCATTTTTTTAGATT-AACATCGAATATTGG
1 GGCATCTTTGTAGATTCAACATCAAATGTTGG
*
609844 GGCATCTTTG-GGAATTCAACATC
1 GGCATCTTTGTAG-ATTCAACATC
609867 CTGATGCGAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.01
31 24 0.32
32 50 0.67
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (32 bp):
GGCATCTTTGTAGATTCAACATCAAATGTTGG
Found at i:609831 original size:31 final size:31
Alignment explanation
Indices: 609760--609848 Score: 142
Period size: 32 Copynumber: 2.8 Consensus size: 31
609750 GCATCTTTGA
609760 AGATTCAACATCAAATGTTGGGGCATTTTTTT
1 AGATT-AACATCAAATGTTGGGGCATTTTTTT
609792 AGATTTAACATCAAATGTTGGGGCATTTTTTT
1 AGA-TTAACATCAAATGTTGGGGCATTTTTTT
* *
609824 AGATTAACATCGAATATTGGGGCAT
1 AGATTAACATCAAATGTTGGGGCAT
609849 CTTTGGGAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
31 20 0.37
32 32 0.59
33 2 0.04
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.38
Consensus pattern (31 bp):
AGATTAACATCAAATGTTGGGGCATTTTTTT
Found at i:611110 original size:36 final size:36
Alignment explanation
Indices: 611063--611167 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
611053 TCATTGAATC
* *
611063 AGTTTCACTTGAAACAAATTTTGACTCTCTTGGGAT
1 AGTTTCACTTGAAACAAATTTTGTCTCTCTTGAGAT
*
611099 AGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAT
1 AGTTTCACTTGAAACAAATTTTGTCTCTCTTGAGAT
**
611135 AGTTTTTCTTGAAACAAATTTTGTCTCTCTTGA
1 AGTTTCACTTGAAACAAATTTTGTCTCTCTTGA
611168 AACAAATTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (36 bp):
AGTTTCACTTGAAACAAATTTTGTCTCTCTTGAGAT
Found at i:611130 original size:21 final size:21
Alignment explanation
Indices: 611106--611188 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 21
611096 GATAGTTTCC
611106 CTTGAAACAAATTTTGTCTCT
1 CTTGAAACAAATTTTGTCTCT
* * *
611127 CTTG--AGATA-GTT-T-T-T
1 CTTGAAACAAATTTTGTCTCT
611142 CTTGAAACAAATTTTGTCTCT
1 CTTGAAACAAATTTTGTCTCT
* *
611163 CTTGAAACAAATTTCGTCTCC
1 CTTGAAACAAATTTTGTCTCT
611184 CTTGA
1 CTTGA
611189 GAAATTTTCT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
15 5 0.10
16 1 0.02
17 4 0.08
18 4 0.08
19 4 0.08
20 1 0.02
21 29 0.60
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
CTTGAAACAAATTTTGTCTCT
Found at i:614716 original size:20 final size:19
Alignment explanation
Indices: 614693--614729 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
614683 AGAACCCCAG
*
614693 GGGGGTATCGATTCCCCTA
1 GGGGGAATCGATTCCCCTA
614712 GGGGGAATCGATTCCCCT
1 GGGGGAATCGATTCCCCT
614730 TCAAATGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.27, G:0.32, T:0.24
Consensus pattern (19 bp):
GGGGGAATCGATTCCCCTA
Found at i:615079 original size:14 final size:14
Alignment explanation
Indices: 615060--615088 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
615050 AAGCCTAATT
615060 CTCTCCTAAGTGTC
1 CTCTCCTAAGTGTC
615074 CTCTCCTAAGTGTC
1 CTCTCCTAAGTGTC
615088 C
1 C
615089 AAAATCTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.38, G:0.14, T:0.34
Consensus pattern (14 bp):
CTCTCCTAAGTGTC
Found at i:618627 original size:22 final size:21
Alignment explanation
Indices: 618585--618624 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
618575 GAGTTTATTT
*
618585 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
618606 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
618625 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:620510 original size:20 final size:20
Alignment explanation
Indices: 620475--620528 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
620465 TGGAGCATGG
*
620475 GGGGAATCGG-TACCCTAAT
1 GGGGAATCGGTTCCCCTAAT
620494 GGGGAATCGGTTCCCCTAAT
1 GGGGAATCGGTTCCCCTAAT
620514 GGGGAATCGGTTCCC
1 GGGGAATCGGTTCCC
620529 TAGGTGTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 10 0.30
20 23 0.70
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.22
Consensus pattern (20 bp):
GGGGAATCGGTTCCCCTAAT
Found at i:621006 original size:65 final size:64
Alignment explanation
Indices: 620925--621118 Score: 232
Period size: 65 Copynumber: 3.0 Consensus size: 64
620915 TTTCAACAAT
*
620925 AAACATT-AAAA-ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAATTTCTCTTGAAACA
1 AAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA
* * * ** ** * * *
620987 AAATCTTTG-AATCTGTTTCCCTTGAAACAAATTTCATTTCACTTGAGACAGTTTCTCTTGAAAC
1 AAA-CATTGAAAAC-ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAAC
621051 A
64 A
*
621052 TAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 -AAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA
621117 AA
1 AA
621119 TTTTGTCTCC
Statistics
Matches: 104, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
62 3 0.03
63 5 0.05
64 2 0.02
65 88 0.85
66 6 0.06
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (64 bp):
AAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA
Found at i:621221 original size:36 final size:36
Alignment explanation
Indices: 621067--621221 Score: 174
Period size: 36 Copynumber: 4.4 Consensus size: 36
621057 ATTGAAAACA
* *
621067 TTTCCCTTGAAATGAA-TTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAA-CAAGTTTTGTCTCTCTTGAGACAG
* *
621103 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
** * *
621139 TTTCTTTTG--GC-AGTTTTTGTCTCTCTTGAGACAA
1 TTTCCCTTGAAACAAG-TTTTGTCTCTCTTGAGACAG
* *
621173 TTTCTCTTGAAACAAGTTTTGTATCTCTTGAGACAG
1 TTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
621209 TTTCCCTTGAAAC
1 TTTCCCTTGAAAC
621222 TTCAACCTTT
Statistics
Matches: 100, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
33 1 0.01
34 27 0.27
35 2 0.02
36 68 0.68
37 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (36 bp):
TTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
Found at i:621248 original size:30 final size:30
Alignment explanation
Indices: 621208--621327 Score: 100
Period size: 33 Copynumber: 3.7 Consensus size: 30
621198 TCTTGAGACA
* *
621208 GTTTCCCTTGAAACTTC-AACCTTTAAAATT
1 GTTTCTCTTGAAAC-ACAAACCTTTAAAATT
*
621238 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC---AAACCTTTAAAATT
621271 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAA-T
1 GTTTCTCTTGAAACAC-----AAACCTTT-AAAATT
621306 GTTTCTCTTGAAACACCAAACC
1 GTTTCTCTTGAAACA-CAAACC
621328 CTCGAGTTCG
Statistics
Matches: 78, Mismatches: 4, Indels: 15
0.80 0.04 0.15
Matches are distributed among these distances:
29 1 0.01
30 13 0.17
31 5 0.06
33 28 0.36
35 27 0.35
36 4 0.05
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.33
Consensus pattern (30 bp):
GTTTCTCTTGAAACACAAACCTTTAAAATT
Found at i:621270 original size:33 final size:34
Alignment explanation
Indices: 621225--621321 Score: 160
Period size: 35 Copynumber: 2.9 Consensus size: 34
621215 TTGAAACTTC
*
621225 AACCTTTAAAATTGTTTCTCTTGAAACAC-AAAA
1 AACCTTTGAAATTGTTTCTCTTGAAACACAAAAA
621258 AACCTTTGAAATTGTTTCTCTTGAAACACAAAAAA
1 AACCTTTGAAATTGTTTCTCTTGAAACAC-AAAAA
*
621293 AACCTTTGAAAATGTTTCTCTTGAAACAC
1 AACCTTTGAAATTGTTTCTCTTGAAACAC
621322 CAAACCCTCG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
33 28 0.47
35 32 0.53
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (34 bp):
AACCTTTGAAATTGTTTCTCTTGAAACACAAAAA
Found at i:621473 original size:81 final size:82
Alignment explanation
Indices: 621333--621573 Score: 270
Period size: 84 Copynumber: 2.9 Consensus size: 82
621323 AAACCCTCGA
* * * * * *
621333 GTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATC
1 GTTCGACTACGCTCAGC-TCTAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGTTATC
*
621398 TGTCATCAAAAGACCTTC
65 TGTCAACAAAAGACCTTC
* * * * * *
621416 -TTCGACTATGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCAAAAAGGGCTT-TA
1 GTTCGACTACGCTCAGCTCTAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGG-TTATC
* *
621479 TGCCAACCAAAGACCTTC
65 TGTCAACAAAAGACCTTC
* *
621497 GAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGAGCTAT
1 --GTTCGACTACGCTCAGCTCTAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGTTAT
*
621562 CTGTCAATAAAA
64 CTGTCAACAAAA
621574 TTGTCGAGTT
Statistics
Matches: 127, Mismatches: 26, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
81 50 0.39
82 15 0.12
83 1 0.01
84 61 0.48
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (82 bp):
GTTCGACTACGCTCAGCTCTAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGTTATCT
GTCAACAAAAGACCTTC
Found at i:621529 original size:84 final size:84
Alignment explanation
Indices: 621329--621551 Score: 265
Period size: 81 Copynumber: 2.7 Consensus size: 84
621319 CACCAAACCC
* * * * * * *
621329 TCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGT
1 TCGAGTTCGACTACGCTCAGC-TCTAAGGCACATCATTTACAGCATAGCTCAAGGCAAAAAGGGT
* * *
621394 TATCTGTCATCAAAAGACCT
65 TATATGCCAACAAAAGACCT
* * * *
621414 TC---TTCGACTATGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCAAAAAGGGCT
1 TCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTACAGCATAGCTCAAGGCAAAAAGGG-T
*
621476 T-TATGCCAACCAAAGACCT
65 TATATGCCAACAAAAGACCT
621495 TCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTACAGCATAGCTCAAGGCAA
1 TCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTACAGCATAGCTCAAGGCAA
621552 GAAGAGCTAT
Statistics
Matches: 115, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
81 50 0.43
82 15 0.13
84 48 0.42
85 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (84 bp):
TCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTACAGCATAGCTCAAGGCAAAAAGGGTT
ATATGCCAACAAAAGACCT
Found at i:622189 original size:17 final size:17
Alignment explanation
Indices: 622164--622206 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
622154 CAACCGAGCA
*
622164 AGGAGTCTAGTTGCATT
1 AGGATTCTAGTTGCATT
622181 AGGATTCTAGTTGCATT
1 AGGATTCTAGTTGCATT
622198 AGGATTCTA
1 AGGATTCTA
622207 TTGTTAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.37
Consensus pattern (17 bp):
AGGATTCTAGTTGCATT
Found at i:622689 original size:14 final size:14
Alignment explanation
Indices: 622672--622711 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
622662 TCCTCTTTTT
622672 TTATTTATATTATA
1 TTATTTATATTATA
*
622686 TTATTTTTATTATA
1 TTATTTATATTATA
622700 TATATCTTATAT
1 T-TAT-TTATAT
622712 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:622693 original size:23 final size:23
Alignment explanation
Indices: 622637--622704 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
622627 TTTTTAATTA
*
622637 TATTTTTTTTATTTATTTACTATAT
1 TATTTTTTTTATTTA--TATTATAT
*
622662 TCCTCTTTTTTTATTTATATTATAT
1 T-AT-TTTTTTTATTTATATTATAT
* *
622687 TATTTTTATTATATATAT
1 TATTTTTTTTATTTATAT
622705 CTTATATCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
23 13 0.36
24 1 0.03
25 9 0.25
26 1 0.03
27 12 0.33
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTTTTTTTATTTATATTATAT
Found at i:622852 original size:38 final size:37
Alignment explanation
Indices: 622770--622848 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
622760 ATTTACTATG
622770 TATATAT-TTTTCTTAATATTATATTTTATATGTTTT
1 TATATATATTTTCTTAATATTATATTTTATATGTTTT
*
622806 TATATATATTTTCTTAATATTCTA-TTT-T-TGTTTT
1 TATATATATTTTCTTAATATTATATTTTATATGTTTT
*
622840 TATTTATAT
1 TATATATAT
622849 ATATATATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
34 14 0.35
35 1 0.03
36 10 0.25
37 15 0.38
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.67
Consensus pattern (37 bp):
TATATATATTTTCTTAATATTATATTTTATATGTTTT
Found at i:622896 original size:16 final size:16
Alignment explanation
Indices: 622854--622896 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
622844 TATATATATA
622854 TATTATATTTTTACTT
1 TATTATATTTTTACTT
* *
622870 TATTTTATTTTTTCTAT
1 TATTATATTTTTACT-T
622887 TATTAT-TTTT
1 TATTATATTTT
622897 CTTAATATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTATATTTTTACTT
Found at i:622922 original size:58 final size:56
Alignment explanation
Indices: 622825--622937 Score: 138
Period size: 56 Copynumber: 2.0 Consensus size: 56
622815 TTTCTTAATA
* * *
622825 TTCTATTTTTGTTTTTATTTATATATATATATTATA-TTTTTACTTTATTTTATTTT
1 TTCTATTATTATTTTTATTAATATATATATATTATATTTTTTA-TTTATTTTATTTT
* * *
622881 TTCTATTATTATTTTTCTTAATATCATGTATATCTTTATTTTTTATTTATTTTATTT
1 TTCTATTATTATTTTTATTAATAT-ATATATAT-TATATTTTTTATTTATTTTATTT
622938 AGTATTATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
56 20 0.42
57 7 0.15
58 15 0.31
59 6 0.12
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (56 bp):
TTCTATTATTATTTTTATTAATATATATATATTATATTTTTTATTTATTTTATTTT
Found at i:627714 original size:22 final size:21
Alignment explanation
Indices: 627688--627743 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
627678 ATATATATTT
*
627688 TTATAAAAAGTATATGA-AATAA
1 TTATAAAAAATAT-TGATAAT-A
*
627710 TTATAAAAAATATTTATAATA
1 TTATAAAAAATATTGATAATA
627731 TTAT-AAAAATATT
1 TTATAAAAAATATT
627744 TTTTTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.29
21 7 0.23
22 15 0.48
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (21 bp):
TTATAAAAAATATTGATAATA
Found at i:627920 original size:23 final size:23
Alignment explanation
Indices: 627902--627952 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
627892 AGAAATATTA
627902 AAATAATAT-TATTTTAAATAAT
1 AAATAATATATATTTTAAATAAT
* *
627924 AATTAATATATATTTTTAAAAAAT
1 AAATAATATATA-TTTTAAATAAT
627948 AAATA
1 AAATA
627953 TTTAAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 8 0.33
23 2 0.08
24 14 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATAATATATATTTTAAATAAT
Found at i:638956 original size:30 final size:31
Alignment explanation
Indices: 638908--638969 Score: 117
Period size: 30 Copynumber: 2.0 Consensus size: 31
638898 ATTCAAATTT
638908 CTCTATAAAATAATATTTTTTTCATTAAAAA
1 CTCTATAAAATAATATTTTTTTCATTAAAAA
638939 CTCTATAAAAT-ATATTTTTTTCATTAAAAA
1 CTCTATAAAATAATATTTTTTTCATTAAAAA
638969 C
1 C
638970 AGGTCTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.45
Consensus pattern (31 bp):
CTCTATAAAATAATATTTTTTTCATTAAAAA
Found at i:643713 original size:18 final size:18
Alignment explanation
Indices: 643676--643731 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 18
643666 CACGTTAAAG
643676 GGAGAGA-GTATATCGGGCA
1 GGAGAGAGGTA-AT-GGGCA
643695 GGAGAGAGGTAATGGGCA
1 GGAGAGAGGTAATGGGCA
643713 GGAGAGAGGTAATGGGCA
1 GGAGAGAGGTAATGGGCA
643731 G
1 G
643732 AAAGAGCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 24 0.67
19 9 0.25
20 3 0.08
ACGTcount: A:0.32, C:0.07, G:0.48, T:0.12
Consensus pattern (18 bp):
GGAGAGAGGTAATGGGCA
Found at i:644261 original size:101 final size:99
Alignment explanation
Indices: 643896--644262 Score: 308
Period size: 101 Copynumber: 3.7 Consensus size: 99
643886 GGTTGTTCCC
* * ** * **
643896 TATAACCTAAACAGTTGACAATATAGGAAGGCGCTACTTATATTATTATAAATATAATTATGTTT
1 TATAACTTAAACGGTTGACAATATAAAAAGGCGCTACTTATATTGTTATAAATATAAACATGTTT
** *
643961 TGTCTTACATAATCATAATGGAAAAGTTTTCACACA
66 TGTCTTACATAA-CATAATAAAAAAGTTTT-GCACA
* * ** * * *
643997 TATAACTTAAACGGTTGACAATATAAGAAGGCGCTACCTGCATTGTTATATATTTTAACATGTTT
1 TATAACTTAAACGGTTGACAATATAAAAAGGCGCTACTTATATTGTTATAAATATAAACATGTTT
* * * * * * *
644062 T-T-TTACAGTGTA-TTAGTAAAAATGGTTTCGAACC
66 TGTCTTACA-T-AACATAATAAAAA-AGTTTTGCACA
* * ** ** * * *
644096 TATCACGTAATTGGTTGACACCATAAAAAGGCGCTACTTGTATTGTTATAAATATAACCTTGTTT
1 TATAACTTAAACGGTTGACAATATAAAAAGGCGCTACTTATATTGTTATAAATATAAACATGTTT
644161 TGTCTTACATAACCATAATAAAACAAGTTTTGCACA
66 TGTCTTACATAA-CATAATAAAA-AAGTTTTGCACA
* * * * *
644197 TATAACTTAAACGGTTGACAATATAAAAAGGTGTTACATATATTGTTATAAATTTAAACCTGTTT
1 TATAACTTAAACGGTTGACAATATAAAAAGGCGCTACTTATATTGTTATAAATATAAACATGTTT
644262 T
66 T
644263 CTATAACAGT
Statistics
Matches: 202, Mismatches: 56, Indels: 16
0.74 0.20 0.06
Matches are distributed among these distances:
99 66 0.33
100 8 0.04
101 127 0.63
102 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (99 bp):
TATAACTTAAACGGTTGACAATATAAAAAGGCGCTACTTATATTGTTATAAATATAAACATGTTT
TGTCTTACATAACATAATAAAAAAGTTTTGCACA
Found at i:644299 original size:101 final size:97
Alignment explanation
Indices: 643896--644356 Score: 280
Period size: 101 Copynumber: 4.6 Consensus size: 97
643886 GGTTGTTCCC
* * ** * * * * **
643896 TATAACCTAAACAGTTGACAATATAGGAAGGCGCTACTTATATTATTATAAATATAATTATGTTT
1 TATAACGTAAACGGTTGACAATATAAAAAGGCGCTACATGTATTGTTATAAATTTAA-CCTGTTT
* * * *
643961 TGTCTTACA-TAATCATAATGGAAAAGTTTTCACACA
65 T-T-TTACAGT-ATCTTAAT-AAAAAGGTTTCAAACA
* * * * * *
643997 TATAACTTAAACGGTTGACAATATAAGAAGGCGCTACCTGCATTGTTATATATTTTAACATGTTT
1 TATAACGTAAACGGTTGACAATATAAAAAGGCGCTACATGTATTGTTATA-AATTTAACCTGTTT
* * * * *
644062 TTTTACAGTGTATTAGTAAAAATGGTTTCGAACC
65 TTTTACAGTATCTTAATAAAAA-GGTTTCAAACA
* ** ** * *
644096 TATCACGTAATTGGTTGACACCATAAAAAGGCGCTACTTGTATTGTTATAAATATAACCTTGTTT
1 TATAACGTAAACGGTTGACAATATAAAAAGGCGCTACATGTATTGTTATAAATTTAACC-TGTTT
* * * ***
644161 TGTCTTACA-TAACCATAATAAAACAAGTTTTGCACA
65 T-T-TTACAGT-ATCTTAATAAAA-AGGTTTCAAACA
* * * *
644197 TATAACTTAAACGGTTGACAATATAAAAAGGTGTTACATATATTGTTATAAATTTAAACCTGTTT
1 TATAACGTAAACGGTTGACAATATAAAAAGGCGCTACATGTATTGTTATAAATTT-AACCTGTTT
* *
644262 TCTATAACAGTTTCTTAATAATAAAGGTTTCAAACA
65 T-T-TTACAGTATCTTAATAA-AAAGGTTTCAAACA
* * * ** * * *
644298 TATCAA-GTAAACGGTCGACACTATAAGAAGGCATTACCTGTAGTGTTATAAATATAACC
1 TAT-AACGTAAACGGTTGACAATATAAAAAGGCGCTACATGTATTGTTATAAATTTAACC
644357 CTATTTTGCT
Statistics
Matches: 277, Mismatches: 71, Indels: 25
0.74 0.19 0.07
Matches are distributed among these distances:
98 10 0.04
99 63 0.23
100 8 0.03
101 181 0.65
102 15 0.05
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (97 bp):
TATAACGTAAACGGTTGACAATATAAAAAGGCGCTACATGTATTGTTATAAATTTAACCTGTTTT
TTTACAGTATCTTAATAAAAAGGTTTCAAACA
Found at i:648649 original size:16 final size:17
Alignment explanation
Indices: 648628--648674 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
648618 TCTATTATTT
648628 ATAATTTATATATAT-A
1 ATAATTTATATATATAA
* *
648644 ATAATTTTTTTATATAA
1 ATAATTTATATATATAA
*
648661 ATAACTTA-ATATAT
1 ATAATTTATATATAT
648675 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATAATTTATATATATAA
Found at i:648882 original size:51 final size:51
Alignment explanation
Indices: 648772--648961 Score: 226
Period size: 51 Copynumber: 3.8 Consensus size: 51
648762 AGATGTACAT
* * * *
648772 ACTTACATCGGTCTAAGTACGTGTTAAGT--TACA--CTTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATTTTTTTATTTTATTC
* * *
648819 GCTTACATCGGTGTAAGTATGTATTAAGTGCTACATTTTTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATTTTTTTATTTTATTC
* * * *
648870 ACATACACCGGTGTAAGTATGTGTTAAGTGTTACACTTGTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATTTTTTTATTTTATTC
* * *
648921 ACTTACACCGGTATAAGCATATGTTAAGTGCTACATTTTTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATTTTTT
648962 GTAGTATGAA
Statistics
Matches: 120, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
47 25 0.21
49 4 0.03
51 91 0.76
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (51 bp):
ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATTTTTTTATTTTATTC
Found at i:648917 original size:102 final size:98
Alignment explanation
Indices: 648775--648961 Score: 257
Period size: 102 Copynumber: 1.9 Consensus size: 98
648765 TGTACATACT
* * * * * *
648775 TACATCGGTCTAAGTACGTGTTAAGTTACACTTTTATTTTATTCGCTTACATCGGTGTAAGTATG
1 TACACCGGTCTAAGTACGTGTTAAGTTACACTTTTATTTTATTCACTTACACCGGTATAAGCATA
648840 TATTAAGTGCTACATTTTTTTATTTTATTCACA
66 TATTAAGTGCTACATTTTTTTATTTTATTCACA
* *
648873 TACACCGGTGTAAGTATGTGTTAAGTGTTACACTTGTTTATTTTATTCACTTACACCGGTATAAG
1 TACACCGGTCTAAGTACGTGTTAA--GTTACAC-T-TTTATTTTATTCACTTACACCGGTATAAG
*
648938 CATATGTTAAGTGCTACATTTTTT
62 CATATATTAAGTGCTACATTTTTT
648962 GTAGTATGAA
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
98 21 0.28
100 7 0.09
101 1 0.01
102 47 0.62
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (98 bp):
TACACCGGTCTAAGTACGTGTTAAGTTACACTTTTATTTTATTCACTTACACCGGTATAAGCATA
TATTAAGTGCTACATTTTTTTATTTTATTCACA
Found at i:653152 original size:16 final size:17
Alignment explanation
Indices: 653131--653163 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
653121 AAGAAGTTGT
*
653131 CACCAAC-CTTCAATTC
1 CACCAACGCATCAATTC
653147 CACCAACGCATCAATTC
1 CACCAACGCATCAATTC
653164 TCGAATCAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.42, G:0.03, T:0.21
Consensus pattern (17 bp):
CACCAACGCATCAATTC
Found at i:653606 original size:153 final size:153
Alignment explanation
Indices: 653328--653633 Score: 596
Period size: 153 Copynumber: 2.0 Consensus size: 153
653318 ACCATACTCG
653328 ACGATACTCCATTACCAACTTTCTGACCAAGCTTCGACTATGGGAGAACCACTCTGCGAGAATCT
1 ACGATACTCCATTACCAACTTTCTGACCAAGCTTCGACTATGGGAGAACCACTCTGCGAGAATCT
653393 TTGATTTATCGTTCTCCACACTTCTCAATGAAACATTGTCTTCGAAAATCATTAAAATCGCATTA
66 TTGATTTATCGTTCTCCACACTTCTCAATGAAACATTGTCTTCGAAAATCATTAAAATCGCATTA
653458 CCAGCAGCTCTCATTAAGGTGAA
131 CCAGCAGCTCTCATTAAGGTGAA
653481 ACGATACTCCATTACCAAACTTTCTGACCAAGCTTCGACTAT-GGAGAACCACTCTGCGAGAATC
1 ACGATACTCCATTACC-AACTTTCTGACCAAGCTTCGACTATGGGAGAACCACTCTGCGAGAATC
653545 TTTGATTTATCGTTCTCCACACTTCTCAATGAAACATTGTCTTCGAAAATCATTAAAATCGCATT
65 TTTGATTTATCGTTCTCCACACTTCTCAATGAAACATTGTCTTCGAAAATCATTAAAATCGCATT
653610 ACCAGCAGCTCTCATTAAGGTGAA
130 ACCAGCAGCTCTCATTAAGGTGAA
653634 GCTAATGAGG
Statistics
Matches: 152, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
153 127 0.84
154 25 0.16
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (153 bp):
ACGATACTCCATTACCAACTTTCTGACCAAGCTTCGACTATGGGAGAACCACTCTGCGAGAATCT
TTGATTTATCGTTCTCCACACTTCTCAATGAAACATTGTCTTCGAAAATCATTAAAATCGCATTA
CCAGCAGCTCTCATTAAGGTGAA
Found at i:656106 original size:45 final size:39
Alignment explanation
Indices: 656022--656100 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
656012 AAGGAATTTG
656022 TGAGTTATATTACGATTAGGATTAATTATTAGTATTTTA
1 TGAGTTATATTACGATTAGGATTAATTATTAGTATTTTA
656061 TGAGTTATATTACGATTAGGATTAATTATTAGTATTTTA
1 TGAGTTATATTACGATTAGGATTAATTATTAGTATTTTA
656100 T
1 T
656101 TTTTATTAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.49
Consensus pattern (39 bp):
TGAGTTATATTACGATTAGGATTAATTATTAGTATTTTA
Found at i:659699 original size:39 final size:40
Alignment explanation
Indices: 659600--659758 Score: 136
Period size: 39 Copynumber: 4.0 Consensus size: 40
659590 TTATTTTATC
* *
659600 ATATATATATTGTATA-TAGTTTGAAAACATTTTTTAAAAAAT
1 ATATATATATTGTATAGT--TTTGAAAATA-TTTTGAAAAAAT
* * *
659642 ATATATATAATATATAGTTTTGAAAATATGTTTGAAAACAT
1 ATATATATATTGTATAGTTTTGAAAATAT-TTTGAAAAAAT
*
659683 -T-TATATATTGTATAGTTTTTAAAATATTTTGAAAATAA-
1 ATATATATATTGTATAGTTTTGAAAATATTTTGAAAA-AAT
* * *
659721 ATATA-ATA---TATAGTTTTTAAAACATTTTGAAAATAT
1 ATATATATATTGTATAGTTTTGAAAATATTTTGAAAAAAT
659757 AT
1 AT
659759 TTACGTTTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 18
0.78 0.09 0.14
Matches are distributed among these distances:
35 1 0.01
36 26 0.26
38 8 0.08
39 28 0.28
40 4 0.04
41 18 0.18
42 14 0.14
43 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (40 bp):
ATATATATATTGTATAGTTTTGAAAATATTTTGAAAAAAT
Found at i:659733 original size:36 final size:36
Alignment explanation
Indices: 659637--659755 Score: 139
Period size: 36 Copynumber: 3.2 Consensus size: 36
659627 CATTTTTTAA
*
659637 AAAATATATATATAATATATAGTTTTGAAAATATGTTTG
1 AAAATA-A-ATATAATATATAGTTTTTAAAATAT-TTTG
** * *
659676 AAAACATTTATATATTGTATAGTTTTTAAAATATTTTG
1 -AAA-ATAAATATAATATATAGTTTTTAAAATATTTTG
*
659714 AAAATAAATATAATATATAGTTTTTAAAACATTTTG
1 AAAATAAATATAATATATAGTTTTTAAAATATTTTG
659750 AAAATA
1 AAAATA
659756 TATTTACGTT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
36 34 0.50
37 3 0.04
38 4 0.06
39 22 0.32
40 3 0.04
41 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (36 bp):
AAAATAAATATAATATATAGTTTTTAAAATATTTTG
Found at i:659767 original size:29 final size:29
Alignment explanation
Indices: 659726--659817 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 29
659716 AATAAATATA
*
659726 ATATATAGTTTTTAAAACATTTTGAAAAT
1 ATATTTAGTTTTTAAAACATTTTGAAAAT
659755 ATATTTACGTTTTTAAAACATTTT-AAAAT
1 ATATTTA-GTTTTTAAAACATTTTGAAAAT
**
659784 ATA--TAGTTTAAAAAACATTTTGAGAACAT
1 ATATTTAGTTTTTAAAACATTTTGA-AA-AT
659813 ATATT
1 ATATT
659818 ATATAATTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
26 14 0.26
27 3 0.06
28 2 0.04
29 19 0.35
30 16 0.30
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (29 bp):
ATATTTAGTTTTTAAAACATTTTGAAAAT
Found at i:661465 original size:4 final size:4
Alignment explanation
Indices: 661406--661479 Score: 64
Period size: 4 Copynumber: 18.8 Consensus size: 4
661396 CCTTTTACTT
* * * *
661406 TTTA TTT- TTTA TTCA TTTG TTTT TTTA -TTA TTTT TTTA TTTA CTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA
*
661453 -GTA TATTA TTTA TTTA TTTA TTTA TTT
1 TTTA T-TTA TTTA TTTA TTTA TTTA TTT
661480 TACTAACTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
3 8 0.14
4 41 0.73
5 7 0.12
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:662640 original size:2 final size:2
Alignment explanation
Indices: 662633--662671 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
662623 CGATTAACAG
662633 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
662672 GTATTATGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:665417 original size:2 final size:2
Alignment explanation
Indices: 665410--665439 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
665400 ATAAATCCAA
665410 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
665440 TAAACAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:669532 original size:479 final size:480
Alignment explanation
Indices: 668785--669739 Score: 1734
Period size: 486 Copynumber: 2.0 Consensus size: 480
668775 ATATTATAAT
668785 ACATCTCCATTGATATTAGATTATCGTATTTATATTGTAGACGAAAAATATTTTATCTAGAATAA
1 ACATCTCCATTGATATTAGATTATCGTATTTATATTGTAGACGAAAAATATTTTATCTAGAATAA
668850 TATATTTTAAATATTTCAAAATAATCACAATTGCATTATAAATATTATTATAACAGCATTTTTAA
66 TATATTTTAAATATTTCAAAATAATCACAATTGCATTATAAATATTATTATAACAGCATTTTTAA
668915 TTTTTATTATATTTTATGTAATTTTTTATTAAAATAATTTAAAAACACTAATTGAAATATTGAAT
131 TTTTTATTATATTTTATGTAATTTTTTATTAAAATAATTTAAAAACACTAATTGAAATATTGAAT
668980 ATGTATACATGTTTATCGTCTCCCCTTATATTTATTCACTAAATATTCTATTTTAAACATGATGA
196 ATGTATACATGTTTATCGTCTCCCCTTATATTTATTCACTAAATATTCTATTTTAAACATGATGA
669045 TTGT-A-AT-ATATAAATATAATGGATTTATAT-ATT-AATGTTATGCTATTTGTATAATAAAAT
261 TTGTAATATAATATAAATATAATGGATTTATATAATTAAATGTTATGCTATTTGTATAATAAAAT
669105 AAATAAATGGTAT-GTGTCGAGACGTAAGGCAG-ATCAGAAAAGTGGAGTTGAAAAAGAGGGATA
326 AAATAAATGGTATGGTGTCGAGACGTAAGGCAGAATCAGAAAAGTGGAGTTGAAAAAGAGGGATA
669168 AAATTAGGGAAAGA-GAGAGGAGAACAAAAGTCTTTATACCGTGTTGTTACTTTCTCTCACTTTC
391 AAATTAGGGAAAGAGGAGAGGAGAA-AAAAGTCTTTATACCGTGTTGTTACTTTCTCTCACTTTC
669232 ATTGTT-TGTATTATTGGAGGGGAGAA
455 ATTGTTGTG-ATTATTGGAGGGGAGAA
669258 ACATCTCCATTGATATTAGATTATATCGGTATTTATATTGTAGACGAAAAATATTTTATCTAGAA
1 ACATCTCCATTGATATTAGA-T-TATC-GTATTTATATTGTAGACGAAAAATATTTTATCTAGAA
*
669323 TAATATATTTTAAAATATTTC-AAA-AATTACAAATTGCATTATAAAATATTATTATAACAGCAT
63 TAATATATTTT-AAATATTTCAAAATAATCAC-AATTGCATTAT-AAATATTATTATAACAGCAT
669386 TTTTAAATTTTTATTATATTTTATGTAATTTTTTATTAAAATAATTTAAAAACACTAATTGAAAT
125 TTTT-AATTTTTATTATATTTTATGTAATTTTTTATTAAAATAATTTAAAAACACTAATTGAAAT
669451 ATTGAATATGTATACCATGTTTATCGTCTCCCCTTATATTTATTCACTAAATATTCTATTTTAAA
189 ATTGAATATGTATA-CATGTTTATCGTCTCCCCTTATATTTATTCACTAAATATTCTATTTTAAA
669516 CATGATGATTGTAATATAATATAAATATAATGGATTTATATAATTAAATGTTATGCTATTTGTAT
253 CATGATGATTGTAATATAATATAAATATAATGGATTTATATAATTAAATGTTATGCTATTTGTAT
669581 AATAAAATAAATAAATGGTATGGTGTCGAGACGTAAGGCAGAATCAGAAAAGTGGAGTTGAAAAA
318 AATAAAATAAATAAATGGTATGGTGTCGAGACGTAAGGCAGAATCAGAAAAGTGGAGTTGAAAAA
669646 GAGGGATAAAATTAGGGAAAGAGGAGAGGAGAAAAAAGTCTTTATACCGTGTTGTTACTTTCTCT
383 GAGGGATAAAATTAGGGAAAGAGGAGAGGAGAAAAAAGTCTTTATACCGTGTTGTTACTTTCTCT
669711 CACTTTCATTGTTGTGATTATTGGAGGGG
448 CACTTTCATTGTTGTGATTATTGGAGGGG
669740 GAGAGAGAGA
Statistics
Matches: 464, Mismatches: 1, Indels: 21
0.95 0.00 0.04
Matches are distributed among these distances:
473 20 0.04
474 1 0.00
475 9 0.02
476 62 0.13
477 33 0.07
478 74 0.16
479 62 0.13
480 1 0.00
481 2 0.00
482 23 0.05
483 3 0.01
484 40 0.09
485 19 0.04
486 103 0.22
487 12 0.03
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (480 bp):
ACATCTCCATTGATATTAGATTATCGTATTTATATTGTAGACGAAAAATATTTTATCTAGAATAA
TATATTTTAAATATTTCAAAATAATCACAATTGCATTATAAATATTATTATAACAGCATTTTTAA
TTTTTATTATATTTTATGTAATTTTTTATTAAAATAATTTAAAAACACTAATTGAAATATTGAAT
ATGTATACATGTTTATCGTCTCCCCTTATATTTATTCACTAAATATTCTATTTTAAACATGATGA
TTGTAATATAATATAAATATAATGGATTTATATAATTAAATGTTATGCTATTTGTATAATAAAAT
AAATAAATGGTATGGTGTCGAGACGTAAGGCAGAATCAGAAAAGTGGAGTTGAAAAAGAGGGATA
AAATTAGGGAAAGAGGAGAGGAGAAAAAAGTCTTTATACCGTGTTGTTACTTTCTCTCACTTTCA
TTGTTGTGATTATTGGAGGGGAGAA
Found at i:672617 original size:24 final size:23
Alignment explanation
Indices: 672579--672637 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
672569 AAAAATGATG
*
672579 GTAATAATAATAAGATATACAATA
1 GTAA-AATAAAAAGATATACAATA
*
672603 GATAAAATAAAAAGATATATAATA
1 G-TAAAATAAAAAGATATACAATA
*
672627 GTATAATAAAA
1 GTAAAATAAAA
672638 TAAAAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.29
24 19 0.61
25 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (23 bp):
GTAAAATAAAAAGATATACAATA
Found at i:672654 original size:10 final size:10
Alignment explanation
Indices: 672639--672676 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
672629 ATAATAAAAT
672639 AAAAAACTAA
1 AAAAAACTAA
672649 AAAAAACTAA
1 AAAAAACTAA
*
672659 AATAAA-TAA
1 AAAAAACTAA
672668 AAAAAACTA
1 AAAAAACTA
672677 TAATCAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (10 bp):
AAAAAACTAA
Found at i:672670 original size:19 final size:19
Alignment explanation
Indices: 672634--672686 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
672624 ATAGTATAAT
*
672634 AAAA-TAAAA-AACTAAAA
1 AAAACTAAAATAAATAAAA
672651 AAAACTAAAATAAATAAAA
1 AAAACTAAAATAAATAAAA
*
672670 AAAACTATAATCAAATA
1 AAAACTAAAAT-AAATA
672687 TGTACAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 4 0.13
18 5 0.16
19 17 0.55
20 5 0.16
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAACTAAAATAAATAAAA
Found at i:672672 original size:20 final size:20
Alignment explanation
Indices: 672646--672686 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
672636 AATAAAAAAC
672646 TAAAAAAAACTAAAAT-AAA
1 TAAAAAAAACTAAAATCAAA
*
672665 TAAAAAAAACTATAATCAAA
1 TAAAAAAAACTAAAATCAAA
672685 TA
1 TA
672687 TGTACAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (20 bp):
TAAAAAAAACTAAAATCAAA
Found at i:674721 original size:104 final size:104
Alignment explanation
Indices: 674520--674916 Score: 683
Period size: 104 Copynumber: 3.8 Consensus size: 104
674510 GAAGTTGTTG
* *
674520 TGACAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTT
1 TGACAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATT
* *
674585 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGT
66 GCGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGT
674624 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC-ATATCCTTCAT
1 TGACAA-CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCAT
*
674688 TGCGAAGTTGAAATTGGCTTTGAATTTGAGAAATGTTTGT
65 TGCGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGT
674728 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCAT
1 TGACAA-CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCAT
*
674793 TGCGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTAT
65 TGCGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGT
*
674833 TGACAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 TGACAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATT
*
674898 GTGAAG-TGAAA-TGGCTCTG
66 GCGAAGTTGAAATTGGCTCTG
674917 GGTAAAACCT
Statistics
Matches: 282, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
102 8 0.03
103 5 0.02
104 169 0.60
105 100 0.35
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (104 bp):
TGACAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATT
GCGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGT
Found at i:674892 original size:209 final size:206
Alignment explanation
Indices: 674520--674913 Score: 682
Period size: 209 Copynumber: 1.9 Consensus size: 206
674510 GAAGTTGTTG
*
674520 TGACAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTT
1 TGACAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCATT
* *
674585 GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTG
66 GCGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
674650 AAGTTGAACTTGCGTTGTCTGGAGTCCATATCCTTCATTGCGAAGTTGAAATTGGCTTTGAATTT
131 AAGTTGAACTTGCGTTGTCTGGAGTCCATATCCTTCATTGCGAAG-TGAAA-TGGCTTTGAATTT
674715 GAGAAATGTTTGT
194 GAGAAATGTTTGT
*
674728 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCAT
1 TGACAA-CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCAT
*
674793 TGCGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTATTGACAA-CAGCGGTCCCTTCGTCGT
65 TGCGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGT
* *
674857 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTGAAATGGCT
130 GAAGTTGAACTTGCGTTGTCTGGAGTCC-ATATCCTTCATTGCGAAGTGAAATGGCT
674914 CTGGGTAAAA
Statistics
Matches: 177, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
207 5 0.03
208 57 0.32
209 115 0.65
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (206 bp):
TGACAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCATT
GCGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
AAGTTGAACTTGCGTTGTCTGGAGTCCATATCCTTCATTGCGAAGTGAAATGGCTTTGAATTTGA
GAAATGTTTGT
Found at i:675114 original size:1 final size:1
Alignment explanation
Indices: 675108--675147 Score: 62
Period size: 1 Copynumber: 40.0 Consensus size: 1
675098 TGTTTGATGA
* *
675108 TTTTTTTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
675148 GCAGATGCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:675187 original size:23 final size:23
Alignment explanation
Indices: 675157--675202 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
675147 TGCAGATGCT
675157 CCTCAACCATCTCAAGCATGTGC
1 CCTCAACCATCTCAAGCATGTGC
675180 CCTCAACCATCTCAAGCATGTGC
1 CCTCAACCATCTCAAGCATGTGC
675203 ATGAGCCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.39, G:0.13, T:0.22
Consensus pattern (23 bp):
CCTCAACCATCTCAAGCATGTGC
Found at i:675753 original size:1 final size:1
Alignment explanation
Indices: 675743--675808 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
675733 CGTTTTCCTC
* * * * * * * * *
675743 TTTTTGTTTTTTTGTTTTGTTTTTTATTTTGTTTTGTTTTGTTTTGTTTGTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
675808 T
1 T
675809 CAACTTAGGA
Statistics
Matches: 47, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (1 bp):
T
Found at i:675760 original size:5 final size:5
Alignment explanation
Indices: 675744--675808 Score: 61
Period size: 5 Copynumber: 13.8 Consensus size: 5
675734 GTTTTCCTCT
*
675744 TTTTG -TTT- TTTTG TTTTG TTTTTTA TTTTG TTTTG TTTTG TTTTG -TTTG
1 TTTTG TTTTG TTTTG TTTTG --TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
675793 TTTT- TTTT- TTTT- TTTT
1 TTTTG TTTTG TTTTG TTTT
675809 CAACTTAGGA
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
4 22 0.42
5 27 0.51
7 4 0.08
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (5 bp):
TTTTG
Found at i:675765 original size:27 final size:27
Alignment explanation
Indices: 675744--675808 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
675734 GTTTTCCTCT
675744 TTTTG-TTT-TTTTGTTTTGTTTTTTA
1 TTTTGTTTTGTTTTGTTTTGTTTTTTA
675769 TTTTGTTTTGTTTTGTTTTGTTTGTTT-
1 TTTTGTTTTGTTTTGTTTTGTTT-TTTA
*
675796 TTTT-TTTTTTTTT
1 TTTTGTTTTGTTTT
675809 CAACTTAGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 5 0.14
26 11 0.31
27 17 0.47
28 3 0.08
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (27 bp):
TTTTGTTTTGTTTTGTTTTGTTTTTTA
Found at i:675777 original size:10 final size:9
Alignment explanation
Indices: 675743--675808 Score: 75
Period size: 8 Copynumber: 7.6 Consensus size: 9
675733 CGTTTTCCTC
675743 TTTTTG-TT
1 TTTTTGTTT
675751 TTTTTGTTT
1 TTTTTGTTT
*
675760 TGTTT-TTT
1 TTTTTGTTT
*
675768 ATTTTGTTT
1 TTTTTGTTT
675777 TGTTTTGTTT
1 T-TTTTGTTT
*
675787 TGTTTGTTT
1 TTTTTGTTT
675796 TTTTT-TTT
1 TTTTTGTTT
675804 TTTTT
1 TTTTT
675809 CAACTTAGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
8 20 0.41
9 20 0.41
10 9 0.18
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:682397 original size:21 final size:22
Alignment explanation
Indices: 682351--682399 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
682341 TCTTTATTTG
* *
682351 ATCTTCTAGTATTTTTATCTTT
1 ATCTTCCAGTATTTTTAGCTTT
*
682373 -TCTTCCA-TATTTTTGGCTTT
1 ATCTTCCAGTATTTTTAGCTTT
682393 ATCTTCC
1 ATCTTCC
682400 TCGTCAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.14, C:0.20, G:0.06, T:0.59
Consensus pattern (22 bp):
ATCTTCCAGTATTTTTAGCTTT
Found at i:682920 original size:12 final size:13
Alignment explanation
Indices: 682894--682923 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
682884 ATACGAATGT
682894 AAAAACATGGAAA
1 AAAAACATGGAAA
682907 AAAAACATGGAAA
1 AAAAACATGGAAA
682920 AAAA
1 AAAA
682924 GAAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.07, G:0.13, T:0.07
Consensus pattern (13 bp):
AAAAACATGGAAA
Found at i:686294 original size:26 final size:26
Alignment explanation
Indices: 686237--686300 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
686227 AAAAATGATG
* *
686237 GTAATAATAATAAAGATATATACAATA
1 GTAATAA-AATAAAAAGATATACAATA
*
686264 G--ATAAAATAAAAAGATATATAATA
1 GTAATAAAATAAAAAGATATACAATA
686288 GTAAT-AAATAAAA
1 GTAATAAAATAAAA
686301 TAAAAAACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
24 17 0.53
25 12 0.38
26 2 0.06
27 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.08, T:0.27
Consensus pattern (26 bp):
GTAATAAAATAAAAAGATATACAATA
Found at i:686705 original size:132 final size:132
Alignment explanation
Indices: 686493--686729 Score: 313
Period size: 132 Copynumber: 1.8 Consensus size: 132
686483 ACGTATAAGG
* *
686493 TAAAATTAATAAAAAACATATAATAATATTAATTCCATATATATATATAATAGCTAAATATGGGA
1 TAAAATTAATAAAAAACATATAATAATATTAATACCATATATATATATAATAGCTAAATATGAGA
*** * *
686558 GAGAGGGAAAAATATATAATAATAATAGAAAAATTGAATAATAATCATGGCATATAAAGTAAAAT
66 GA-AAAAAAAAATATATAATAATAATAGAAAAACTAAATAATAATCATGGCATATAAAGTAAAAT
686623 AAA
130 AAA
* *
686626 TAAAGTTAAT-AAGAACATATAATAATATTAATACCATATATATA-AT-A-A-CTAAATATGAGA
1 TAAAATTAATAAAAAACATATAATAATATTAATACCATATATATATATAATAGCTAAATATGAGA
*
686686 GGAAAAAAAAAATCTATATAATAGTAATAGAAAAACTAAATAAT
66 -GAAAAAAAAAA--TATATAATAATAATAGAAAAACTAAATAAT
686730 GAAGATAAAT
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
128 17 0.19
129 3 0.03
130 28 0.31
131 2 0.02
132 32 0.35
133 9 0.10
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.28
Consensus pattern (132 bp):
TAAAATTAATAAAAAACATATAATAATATTAATACCATATATATATATAATAGCTAAATATGAGA
GAAAAAAAAAATATATAATAATAATAGAAAAACTAAATAATAATCATGGCATATAAAGTAAAATA
AA
Found at i:689647 original size:55 final size:54
Alignment explanation
Indices: 689582--689695 Score: 219
Period size: 55 Copynumber: 2.1 Consensus size: 54
689572 ATGGGTTCTT
689582 TGCTTGCCCATGAGCACAAATTCAACAAGAATGAAGAAAACACATCCTCTGAAAC
1 TGCTTGCCCATGAGCACAAATTCAACAAGAATGAAGAAAACACA-CCTCTGAAAC
689637 TGCTTGCCCATGAGCACAAATTCAACAAGAATGAAGAAAACACACCTCTGAAAC
1 TGCTTGCCCATGAGCACAAATTCAACAAGAATGAAGAAAACACACCTCTGAAAC
689691 TGCTT
1 TGCTT
689696 TTCCATCAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 15 0.25
55 44 0.75
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.19
Consensus pattern (54 bp):
TGCTTGCCCATGAGCACAAATTCAACAAGAATGAAGAAAACACACCTCTGAAAC
Found at i:701301 original size:18 final size:18
Alignment explanation
Indices: 701291--701331 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
701281 CCCGTTGACC
701291 TGACCCGACCCGACCCGT
1 TGACCCGACCCGACCCGT
701309 TGACCCGACCCGACCCGT
1 TGACCCGACCCGACCCGT
701327 TGACC
1 TGACC
701332 GGCGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.49, G:0.22, T:0.12
Consensus pattern (18 bp):
TGACCCGACCCGACCCGT
Found at i:701325 original size:23 final size:23
Alignment explanation
Indices: 701270--701325 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
701260 ACCGGTCATA
* *
701270 ACCCGACCCAACCCGTTGACCTG
1 ACCCGACCCGACCCGTTGACCCG
701293 ACCCGACCCGACCCGTTGACCCG
1 ACCCGACCCGACCCGTTGACCCG
701316 ACCCGACCCG
1 ACCCGACCCG
701326 TTGACCGGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.52, G:0.20, T:0.09
Consensus pattern (23 bp):
ACCCGACCCGACCCGTTGACCCG
Found at i:703789 original size:24 final size:24
Alignment explanation
Indices: 703762--703877 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
703752 TTCAATTTGA
703762 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
* *
703786 ATTCTGATCTAATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
703810 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
703834 ATTCTGATCTAATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
*
703858 AGTT-TGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
703878 CTGATTTATG
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
23 1 0.01
24 76 0.95
25 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:703816 original size:48 final size:48
Alignment explanation
Indices: 703762--703877 Score: 164
Period size: 48 Copynumber: 2.4 Consensus size: 48
703752 TTCAATTTGA
703762 ATTCTGATCTGATACTTGACATGGATTCTGATCTAATA-TCTGACATAG
1 ATTCTGATCTGATACTTGACATGGATTCTGATCTAATACT-TGACATAG
* * *
703810 ATTCTGATCTGATACTTGACTTGGATTCTGATCTAATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGGATTCTGATCTAATACTTGACATAG
*
703858 AGTT-TGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
703878 CTGATTTATG
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
48 59 0.95
49 3 0.05
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (48 bp):
ATTCTGATCTGATACTTGACATGGATTCTGATCTAATACTTGACATAG
Found at i:709697 original size:21 final size:20
Alignment explanation
Indices: 709601--709740 Score: 70
Period size: 21 Copynumber: 6.8 Consensus size: 20
709591 TAAAAACATA
*
709601 AAATAAAATAAAAAATATAT
1 AAATAAAATAAAAAATAAAT
**
709621 -AATAGTGATAAAAATATAAA-
1 AAATA-AAATAAAAA-ATAAAT
** * *
709641 AAATAAACCAAAGAAAAAAAC
1 AAATAAAATAAA-AAATAAAT
* * *
709662 ATATAAACTACAAAAAATAACT
1 AAATAAA--ATAAAAAATAAAT
709684 AAAATAAAATAAAAAATAAAT
1 -AAATAAAATAAAAAATAAAT
* *
709705 CAAA-GAAATAAAAAATGAAGT
1 -AAATAAAATAAAAAAT-AAAT
*
709726 AATTAAAATAAAAAA
1 AAATAAAATAAAAAA
709741 AGAAAAGGAA
Statistics
Matches: 89, Mismatches: 21, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
19 4 0.04
20 27 0.30
21 43 0.48
22 5 0.06
23 10 0.11
ACGTcount: A:0.72, C:0.05, G:0.04, T:0.19
Consensus pattern (20 bp):
AAATAAAATAAAAAATAAAT
Found at i:710982 original size:27 final size:27
Alignment explanation
Indices: 710936--710993 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
710926 GACAAAATGA
710936 AATAAAATAAAAAGTAAATAAATAA-AT
1 AATAAAATAAAAAGTAAAT-AATAATAT
*
710963 AATAATAATAAATAGT-AATAATAATAT
1 AATAA-AATAAAAAGTAAATAATAATAT
710990 AATA
1 AATA
710994 TATACTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 5 0.18
27 14 0.50
28 9 0.32
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (27 bp):
AATAAAATAAAAAGTAAATAATAATAT
Found at i:711009 original size:7 final size:7
Alignment explanation
Indices: 710956--711011 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
710946 AAAGTAAATA
*
710956 AATAAAT
1 AATATAT
710963 AATA-AT
1 AATATAT
*
710969 AATAAAT
1 AATATAT
*
710976 AGTA-AT
1 AATATAT
710982 AATAATAT
1 AAT-ATAT
710990 AATATAT
1 AATATAT
*
710997 ACTATAT
1 AATATAT
711004 AATATAT
1 AATATAT
711011 A
1 A
711012 TGTTTCAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
6 10 0.24
7 27 0.64
8 5 0.12
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (7 bp):
AATATAT
Found at i:712528 original size:16 final size:17
Alignment explanation
Indices: 712509--712541 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
712499 AAATTAAAAT
712509 GAAAGAAAAAAA-GAAA
1 GAAAGAAAAAAATGAAA
712525 GAAAGAAAAAAATGAAA
1 GAAAGAAAAAAATGAAA
712542 AGAGTTAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
GAAAGAAAAAAATGAAA
Found at i:713624 original size:5 final size:5
Alignment explanation
Indices: 713615--713656 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
713605 AAAAAAGGGC
* *
713615 AATAA CATAA AATAA AATAA AA-AA TAAAAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA -AATAA AATAA AATAA AA
713657 ATATAATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 2 0.06
5 28 0.88
6 2 0.06
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:713640 original size:7 final size:7
Alignment explanation
Indices: 713628--713683 Score: 51
Period size: 7 Copynumber: 7.6 Consensus size: 7
713618 AACATAAAAT
713628 AAAATAA
1 AAAATAA
713635 AAAATAA
1 AAAATAA
*
713642 AAAA-AT
1 AAAATAA
713648 AAAATAA
1 AAAATAA
713655 AAATATAA
1 AAA-ATAA
*
713663 TAATGATAA
1 -AA-AATAA
713672 AAAATATA
1 AAAATA-A
713680 AAAA
1 AAAA
713684 ATGAACCAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
6 5 0.12
7 18 0.45
8 11 0.28
9 6 0.15
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.20
Consensus pattern (7 bp):
AAAATAA
Found at i:713648 original size:20 final size:20
Alignment explanation
Indices: 713623--713788 Score: 81
Period size: 21 Copynumber: 8.1 Consensus size: 20
713613 GCAATAACAT
713623 AAAATAAAATAAAAAATAAA
1 AAAATAAAATAAAAAATAAA
*
713643 AAAATAAAAT-AAAAATATA
1 AAAATAAAATAAAAAATAAA
* *
713662 ATAAT--GATAAAAAATATAA
1 AAAATAAAATAAAAAATA-AA
* **
713681 AAAATGAACCAACGAAAA-AAA
1 AAAATAAAATAA--AAAATAAA
* *
713702 GAAATAAAAATTACAAAAAATAATT
1 AAAAT-AAAA-T--AAAAAATAA-A
713727 AAAATAAAATAAAAAATAAA
1 AAAATAAAATAAAAAATAAA
* * *
713747 TCAAA-GAAATAAAAAATGAAG
1 -AAAATAAAATAAAAAAT-AAA
* * *
713768 TAATTAAAATAAAAAAGAAA
1 AAAATAAAATAAAAAATAAA
713788 A
1 A
713789 GGAAAAAAAT
Statistics
Matches: 107, Mismatches: 24, Indels: 30
0.66 0.15 0.19
Matches are distributed among these distances:
17 2 0.02
18 7 0.07
19 17 0.16
20 25 0.23
21 32 0.30
22 3 0.03
23 9 0.08
24 6 0.06
25 6 0.06
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (20 bp):
AAAATAAAATAAAAAATAAA
Found at i:713876 original size:3 final size:3
Alignment explanation
Indices: 713844--713900 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
713834 AGTAAACATA
* * *
713844 AAT AAT ACT AAT ATT AAT AAA AAT -AT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
713889 AA- AAT AA- AAT AA
1 AAT AAT AAT AAT AA
713901 GACTTTAGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 6 0.14
3 35 0.80
4 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:713899 original size:26 final size:25
Alignment explanation
Indices: 713827--713900 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 25
713817 AAATGGAACA
*
713827 AATATAAAGTAAACAT-AAATAATACT
1 AATATAAA-TAAA-ATAAAATAATAAT
* *
713853 AATATTAATAAAAATATAATAATAAT
1 AATATAAAT-AAAATAAAATAATAAT
713879 AATAATAAATAAAATAAAATAA
1 AAT-ATAAATAAAATAAAATAA
713901 GACTTTAGGG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 3 0.08
26 32 0.80
27 5 0.12
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (25 bp):
AATATAAATAAAATAAAATAATAAT
Found at i:714628 original size:41 final size:41
Alignment explanation
Indices: 714567--714654 Score: 149
Period size: 41 Copynumber: 2.1 Consensus size: 41
714557 TTCCGTGATG
* *
714567 GATTCGATGATGTTTGGTTTACTGTTTTTGACGTTGGCTTC
1 GATTTGATGATGTTTGGTTTACTGTTTTCGACGTTGGCTTC
*
714608 GATTTGATGATGTTTGGTTTACTGTTTTCGATGTTGGCTTC
1 GATTTGATGATGTTTGGTTTACTGTTTTCGACGTTGGCTTC
714649 GATTTG
1 GATTTG
714655 TTCTCTGGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.12, C:0.10, G:0.27, T:0.50
Consensus pattern (41 bp):
GATTTGATGATGTTTGGTTTACTGTTTTCGACGTTGGCTTC
Found at i:714640 original size:21 final size:20
Alignment explanation
Indices: 714574--714642 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 20
714564 ATGGATTCGA
714574 TGATGTTTGGTTTACTGTTTT
1 TGATGTTTGGTTTACTG-TTT
* *
714595 TGACG-TTGGCTT-C-GATTT
1 TGATGTTTGGTTTACTG-TTT
714613 GATGATGTTTGGTTTACTGTTT
1 --TGATGTTTGGTTTACTGTTT
714635 TCGATGTT
1 T-GATGTT
714643 GGCTTCGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
18 4 0.11
19 1 0.03
20 11 0.30
21 16 0.43
22 4 0.11
23 1 0.03
ACGTcount: A:0.12, C:0.09, G:0.26, T:0.54
Consensus pattern (20 bp):
TGATGTTTGGTTTACTGTTT
Found at i:715073 original size:3 final size:3
Alignment explanation
Indices: 715065--715099 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
715055 AAAGTAAATA
*
715065 AAT AAT AAT AAT AAT AAAT ACT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A
715100 TATACTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:715080 original size:16 final size:16
Alignment explanation
Indices: 715061--715097 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
715051 ATGAAAAGTA
715061 AATAAATAATAATAAT
1 AATAAATAATAATAAT
*
715077 AATAAATACTAATAAT
1 AATAAATAATAATAAT
715093 AATAA
1 AATAA
715098 TATATACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAAATAATAATAAT
Found at i:715091 original size:19 final size:19
Alignment explanation
Indices: 715067--715106 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
715057 AGTAAATAAA
715067 TAATAATAATAATAAATAC
1 TAATAATAATAATAAATAC
*
715086 TAATAATAATAATATATAC
1 TAATAATAATAATAAATAC
715105 TA
1 TA
715107 TATATGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
TAATAATAATAATAAATAC
Found at i:715247 original size:38 final size:37
Alignment explanation
Indices: 715137--715396 Score: 243
Period size: 37 Copynumber: 7.1 Consensus size: 37
715127 TTTTAAACTT
* * * ** *
715137 TATATTTTTTCTAAAATGTTTCCAAAACTATGTATTA
1 TATAATTTTTCAAAAATATTTTAAAAACTATATATTA
*
715174 TAT-AGTTTTCAAAAATGATTTT-AAAACTATATATTA
1 TATAATTTTTCAAAAAT-ATTTTAAAAACTATATATTA
715210 TATAATTTTTCAAAAATATTTTTAAAAACTATATATTA
1 TATAATTTTTCAAAAATA-TTTTAAAAACTATATATTA
*
715248 TATAAGTTTTCAAAAATATTTTAAAAACTATATATTA
1 TATAATTTTTCAAAAATATTTTAAAAACTATATATTA
*
715285 TATATTTATTTTC-AAAATA-TTTAAAAAC--TATA-TA
1 TATA-AT-TTTTCAAAAATATTTTAAAAACTATATATTA
* * ** *
715319 TAT-ATTTCTAAAAAACCGTTTTCAAAACTATATATTA
1 TATAATTTTTCAAAAA-TATTTTAAAAACTATATATTA
* *
715356 TAT-ATATTTT-AAAAATATTTTCAAAAACTATTTAATA
1 TATAAT-TTTTCAAAAATATTTT-AAAAACTATATATTA
715393 TATA
1 TATA
715397 CAGAGAAAAT
Statistics
Matches: 186, Mismatches: 22, Indels: 29
0.78 0.09 0.12
Matches are distributed among these distances:
31 3 0.02
32 5 0.03
34 13 0.07
35 4 0.02
36 35 0.19
37 81 0.44
38 40 0.22
39 5 0.03
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (37 bp):
TATAATTTTTCAAAAATATTTTAAAAACTATATATTA
Found at i:718268 original size:35 final size:35
Alignment explanation
Indices: 718127--718276 Score: 95
Period size: 35 Copynumber: 4.5 Consensus size: 35
718117 ATTATATAAC
*
718127 AATACATTAAATAGTTATATCAATTGAAATTAATT
1 AATACATTAAATAGTTATATCAATTAAAATTAATT
** * **
718162 AATACATTAAATAG-T-TA-CAATTTCAGTTTTTAT
1 AATACATTAAATAGTTATATCAATTAAAATTAAT-T
** ** *
718195 AATATTTTTCAT--TTAATATGC-A-TAAAATT-A-C
1 AATACATTAAATAGTT-ATAT-CAATTAAAATTAATT
718226 AATACATTAAATAGTTATATCAATTAAAATTAATT
1 AATACATTAAATAGTTATATCAATTAAAATTAATT
718261 AATACATTTAAA-AGTT
1 AATACA-TTAAATAGTT
718277 TATAGAAGTT
Statistics
Matches: 83, Mismatches: 19, Indels: 26
0.65 0.15 0.20
Matches are distributed among these distances:
31 9 0.11
32 15 0.18
33 20 0.24
34 8 0.10
35 25 0.30
36 6 0.07
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (35 bp):
AATACATTAAATAGTTATATCAATTAAAATTAATT
Found at i:718598 original size:21 final size:19
Alignment explanation
Indices: 718568--718612 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
718558 TGACACATGT
718568 TTTACCTAATTAGAGATTAAA
1 TTTACCTAATTA-A-ATTAAA
*
718589 TTTACTTAATTAAATTAAA
1 TTTACCTAATTAAATTAAA
*
718608 ATTAC
1 TTTAC
718613 AGCTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.45
20 1 0.05
21 11 0.50
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (19 bp):
TTTACCTAATTAAATTAAA
Found at i:718612 original size:19 final size:21
Alignment explanation
Indices: 718569--718612 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
718559 GACACATGTT
*
718569 TTACCTAATTAGAGATTAAAT
1 TTACCTAATTAGAGATTAAAA
*
718590 TTACTTAATTA-A-ATTAAAA
1 TTACCTAATTAGAGATTAAAA
718609 TTAC
1 TTAC
718613 AGCTAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 1 0.05
21 10 0.48
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (21 bp):
TTACCTAATTAGAGATTAAAA
Found at i:719229 original size:16 final size:16
Alignment explanation
Indices: 719204--719248 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
719194 CAAGAGCCCT
719204 AGAGGTGACACTTTTG
1 AGAGGTGACACTTTTG
719220 AG-GAGTGACACTTTTG
1 AGAG-GTGACACTTTTG
719236 AGAGGTGACACTT
1 AGAGGTGACACTT
719249 GGATTAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (16 bp):
AGAGGTGACACTTTTG
Found at i:724728 original size:200 final size:200
Alignment explanation
Indices: 724385--724789 Score: 715
Period size: 200 Copynumber: 2.0 Consensus size: 200
724375 AATGTAAATG
724385 AATTTAGATAGCCATTAACTGAAACCCTATTATCAAGATAGCCAAAATCATCAAAGACTGGCATC
1 AATTTAGATAGCCATTAACTGAAACCCTATTATCAAGATAGCCAAAATCATCAAAGACTGGCATC
724450 AACTCTCACAGAAAGCAACAAGAATACATTAGATCAATGGAACCCTCGCCAGAATAAAACTCTCA
66 AACTCTCACAGAAAGCAACAAGAATACATTAGATCAATGGAACCCTCGCCAGAATAAAACTCTCA
724515 CAAAATGCAAAAATGAC-CTAAAAAGAACAATT-AAAACCCCTAAATCATATTTTAGAATGATTT
131 CAAAATGCAAAAATG-CTCTAAAAAGAACAATTGAAAA-CCCTAAATCATATTTTAGAATGATTT
724578 CCTCCCC
194 CCTCCCC
*
724585 AATTTAGATAGCCATTAACTGAAACCCTATTATCAAGATAGCCAAAATCGTCAAAGACTGGCATC
1 AATTTAGATAGCCATTAACTGAAACCCTATTATCAAGATAGCCAAAATCATCAAAGACTGGCATC
* * *
724650 AACTCTCACAGAATGCAACAGGAATTCATTAGATCAATGGAACCCTCGCCAGAATAAAACTCTCA
66 AACTCTCACAGAAAGCAACAAGAATACATTAGATCAATGGAACCCTCGCCAGAATAAAACTCTCA
* *
724715 TAAAATGCAAAAATGCTCTAAAAAGAACAATTGAAAACCCTAATTCATATTTTAGAATGATTTCC
131 CAAAATGCAAAAATGCTCTAAAAAGAACAATTGAAAACCCTAAATCATATTTTAGAATGATTTCC
*
724780 TCCCT
196 TCCCC
724785 AATTT
1 AATTT
724790 TCAGCTCTCA
Statistics
Matches: 196, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
199 1 0.01
200 191 0.97
201 4 0.02
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.24
Consensus pattern (200 bp):
AATTTAGATAGCCATTAACTGAAACCCTATTATCAAGATAGCCAAAATCATCAAAGACTGGCATC
AACTCTCACAGAAAGCAACAAGAATACATTAGATCAATGGAACCCTCGCCAGAATAAAACTCTCA
CAAAATGCAAAAATGCTCTAAAAAGAACAATTGAAAACCCTAAATCATATTTTAGAATGATTTCC
TCCCC
Found at i:736144 original size:5 final size:6
Alignment explanation
Indices: 736135--736165 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
736125 AACAAAAACA
736135 AAAAAT AAAAAT AAAAAT AAAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT
736166 TTAGCAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:736144 original size:7 final size:7
Alignment explanation
Indices: 736128--736164 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
736118 TCAATGAAAC
*
736128 AAAAACA
1 AAAAATA
736135 AAAAAT-
1 AAAAATA
736141 AAAAAT-
1 AAAAATA
736147 AAAAATA
1 AAAAATA
736154 AAAAATA
1 AAAAATA
736161 AAAA
1 AAAA
736165 TTTAGCAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAATA
Found at i:736150 original size:13 final size:12
Alignment explanation
Indices: 736135--736165 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
736125 AACAAAAACA
736135 AAAAATAAAAAT
1 AAAAATAAAAAT
736147 AAAAATAAAAAAT
1 AAAAAT-AAAAAT
736160 AAAAAT
1 AAAAAT
736166 TTAGCAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:736156 original size:19 final size:19
Alignment explanation
Indices: 736128--736165 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
736118 TCAATGAAAC
736128 AAAAACAAAAAATAAAAAT
1 AAAAACAAAAAATAAAAAT
*
736147 AAAAATAAAAAATAAAAAT
1 AAAAACAAAAAATAAAAAT
736166 TTAGCAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (19 bp):
AAAAACAAAAAATAAAAAT
Found at i:740114 original size:21 final size:21
Alignment explanation
Indices: 740089--740141 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
740079 TGGAGCGTGG
740089 GGGGAATCGGTACCCCCTCAT
1 GGGGAATCGGTACCCCCTCAT
740110 GGGGAATCGGTACCCCCTCAT
1 GGGGAATCGGTACCCCCTCAT
740131 GGGGAATCGGT
1 GGGGAATCGGT
740142 TCCCTAAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.28, G:0.34, T:0.19
Consensus pattern (21 bp):
GGGGAATCGGTACCCCCTCAT
Found at i:742539 original size:23 final size:23
Alignment explanation
Indices: 742455--742539 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
742445 CAGAACTCGT
*
742455 GGGGGTATCGATTCCC-T-AAAG
1 GGGGGTATCGGTTCCCTTCAAAG
* * *
742476 GAGGGAATCAGTTCCCATTCAAAG
1 GGGGGTATCGGTTCCC-TTCAAAG
* *
742500 GGGGG-ATTGGTTCCCCTTCAAGG
1 GGGGGTATCGGTT-CCCTTCAAAG
742523 GGGGGTATCGGTTCCCT
1 GGGGGTATCGGTTCCCT
742540 CTGCACTAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
21 12 0.24
23 21 0.42
24 17 0.34
ACGTcount: A:0.20, C:0.21, G:0.34, T:0.25
Consensus pattern (23 bp):
GGGGGTATCGGTTCCCTTCAAAG
Found at i:749776 original size:3 final size:3
Alignment explanation
Indices: 749768--749796 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
749758 GAATTGGGTT
749768 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
749797 AAACTAGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:751332 original size:20 final size:20
Alignment explanation
Indices: 751307--751347 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
751297 TAATACCGCT
751307 TGTTATTTGGTGAATCGAGC
1 TGTTATTTGGTGAATCGAGC
751327 TGTTATTTGGTGAATCGAGC
1 TGTTATTTGGTGAATCGAGC
751347 T
1 T
751348 CCATCAACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.29, T:0.41
Consensus pattern (20 bp):
TGTTATTTGGTGAATCGAGC
Found at i:764866 original size:82 final size:77
Alignment explanation
Indices: 764758--764917 Score: 207
Period size: 77 Copynumber: 2.0 Consensus size: 77
764748 TAAAGTACAT
*
764758 TGTTGAAACTTTTTATTTTCGATTTATTTTATTTTAATCATTATTT-AAAAATAATATTTTAATC
1 TGTTGAAACTTTTTATTTTCG-----TTTTA-TTTAATCATTATTTAAAAAATAATATTCTAATC
*
764822 ATTTATATTATTAATTTA
60 ACTTATATTATTAATTTA
* *
764840 TGTTGAATCTTTTT-TTATTTGTTTTATTTAATCATTATTTAAAAAATAATATTCTAATCACTTA
1 TGTTGAAACTTTTTATT-TTCGTTTTATTTAATCATTATTTAAAAAATAATATTCTAATCACTTA
764904 TATTATTAATTTA
65 TATTATTAATTTA
764917 T
1 T
764918 TACATTTTCA
Statistics
Matches: 72, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
76 14 0.19
77 40 0.56
81 2 0.03
82 16 0.22
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (77 bp):
TGTTGAAACTTTTTATTTTCGTTTTATTTAATCATTATTTAAAAAATAATATTCTAATCACTTAT
ATTATTAATTTA
Found at i:765208 original size:25 final size:26
Alignment explanation
Indices: 765162--765246 Score: 97
Period size: 25 Copynumber: 3.3 Consensus size: 26
765152 AATTTTCCTC
* *
765162 AAATCAATTAAATTTATTAAATTATA-T
1 AAAT-AATTAAATTGATAAAATTA-AGT
*
765189 TAA-AATTAAATTGATAAAA-TAAGT
1 AAATAATTAAATTGATAAAATTAAGT
765213 AAATAATTAAATTGATAAAA-TAAGT
1 AAATAATTAAATTGATAAAATTAAGT
765238 AAATAATTA
1 AAATAATTA
765247 TGACTGAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
23 1 0.02
24 5 0.10
25 44 0.85
27 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (26 bp):
AAATAATTAAATTGATAAAATTAAGT
Found at i:785763 original size:16 final size:17
Alignment explanation
Indices: 785738--785769 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
785728 TCGCCGACCG
785738 AATTTCACTATTCACGA
1 AATTTCACTATTCACGA
785755 AATTT-ACTATTCACG
1 AATTTCACTATTCACG
785770 TGAATAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (17 bp):
AATTTCACTATTCACGA
Found at i:792609 original size:35 final size:36
Alignment explanation
Indices: 792522--792627 Score: 151
Period size: 36 Copynumber: 3.0 Consensus size: 36
792512 GAAGGTGAAT
*
792522 AAGAAGAAAGAAAGGAAGCATCGGCACTTTCGATTC
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTC
792558 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTC
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTC
* ** **
792594 AAG-TGAACGGGAGGAAGCATAAGCACTTTCGATT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATT
792628 TAATTGTTCA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
35 26 0.41
36 38 0.59
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.18
Consensus pattern (36 bp):
AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTC
Found at i:793085 original size:36 final size:37
Alignment explanation
Indices: 793032--793114 Score: 114
Period size: 37 Copynumber: 2.2 Consensus size: 37
793022 TGGTAACCAA
*
793032 CTTTGAAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTT-AAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
*
793069 CTTTAAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTAAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
* *
793106 GTTGAAAAA
1 CTTTAAAAA
793115 TGATAATGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 7 0.17
37 34 0.83
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (37 bp):
CTTTAAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:793115 original size:36 final size:36
Alignment explanation
Indices: 793005--793116 Score: 108
Period size: 37 Copynumber: 3.2 Consensus size: 36
792995 TGAAAGTATT
**
793005 AAAATGGTTTTC-AAGTTTGGTAACCAACTTT-G--AA
1 AAAATGGTTTTCAAAGTTTGGTAA--ATGTTTCGTTAA
*
793039 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTAA
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCGTTAA
* * *
793075 AAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTGA
1 AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCGTTAA
793111 AAAATG
1 AAAATG
793117 ATAATGGGAT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
33 4 0.06
34 12 0.18
35 12 0.18
36 15 0.23
37 23 0.35
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (36 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCGTTAA
Found at i:798070 original size:14 final size:14
Alignment explanation
Indices: 798049--798085 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
798039 CCCTAATCTA
798049 AAACCCTAAACCAT
1 AAACCCTAAACCAT
*
798063 ACACCCTAAACCAT
1 AAACCCTAAACCAT
798077 AAACCCTAA
1 AAACCCTAA
798086 CTTAGAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.38, G:0.00, T:0.14
Consensus pattern (14 bp):
AAACCCTAAACCAT
Found at i:799278 original size:33 final size:34
Alignment explanation
Indices: 799204--799302 Score: 182
Period size: 33 Copynumber: 2.9 Consensus size: 34
799194 GGTTTCTCAA
799204 AAGCTTAGCATTTTTCACTAATAATTTTTTCACT
1 AAGCTTAGCATTTTTCACTAATAATTTTTTCACT
*
799238 AAGCTTAGCATTTTTCACTAATAATTATTTC-CT
1 AAGCTTAGCATTTTTCACTAATAATTTTTTCACT
799271 AAGCTTAGCATTTTTCACTAATAATTTTTTCA
1 AAGCTTAGCATTTTTCACTAATAATTTTTTCA
799303 AGAATAATTC
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
33 32 0.52
34 30 0.48
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.46
Consensus pattern (34 bp):
AAGCTTAGCATTTTTCACTAATAATTTTTTCACT
Found at i:800279 original size:28 final size:28
Alignment explanation
Indices: 800222--800279 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
800212 TTTTTCAGAT
* * ***
800222 AAAAAACCGGTTTTTTATCCGGTTTGAA
1 AAAAAACAGGTTTTTAATCCGGTAAAAA
800250 AAAAAACAGGTTTTTAATCCGGTAAAAA
1 AAAAAACAGGTTTTTAATCCGGTAAAAA
800278 AA
1 AA
800280 CCGGTCGTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (28 bp):
AAAAAACAGGTTTTTAATCCGGTAAAAA
Found at i:800485 original size:23 final size:22
Alignment explanation
Indices: 800459--800503 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
800449 CCGAATCGAC
800459 CGAACTATCATTTTCGAATTAAT
1 CGAACT-TCATTTTCGAATTAAT
**
800482 CGAACTTTTTTTTCGAATTAAT
1 CGAACTTCATTTTCGAATTAAT
800504 TTTCGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (22 bp):
CGAACTTCATTTTCGAATTAAT
Found at i:800601 original size:17 final size:17
Alignment explanation
Indices: 800574--800612 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
800564 AATTTACAAT
800574 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
800590 TAATTATAAATAATATC
1 TAATTATAAATAATATC
800607 TAATTA
1 TAATTA
800613 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:809112 original size:19 final size:18
Alignment explanation
Indices: 809088--809123 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
809078 CCCACTTCGT
*
809088 TTTAATGTCAAATAATATC
1 TTTAATCTCAAA-AATATC
809107 TTTAATCTCAAAAATAT
1 TTTAATCTCAAAAATAT
809124 AAAATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (18 bp):
TTTAATCTCAAAAATATC
Found at i:814501 original size:19 final size:20
Alignment explanation
Indices: 814477--814528 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
814467 TGACCAAGAG
*
814477 CATGTATCTTCATT-AAAAT
1 CATGTATTTTCATTAAAAAT
814496 CATGTATTTTCATTAAAAAAT
1 CATGTATTTTCATT-AAAAAT
814517 CATGTATTTTCA
1 CATGTATTTTCA
814529 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:818639 original size:19 final size:20
Alignment explanation
Indices: 818615--818657 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
818605 AGCATATATC
818615 TTCATT-AAAATCATGTATT
1 TTCATTAAAAATCATGTATT
818634 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGTATT
818654 TTCA
1 TTCA
818658 AATTCATCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:819181 original size:15 final size:14
Alignment explanation
Indices: 819161--819208 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 14
819151 TACTTTGATA
819161 TCATTTCTTTCTATT
1 TCATTTCTTTC-ATT
819176 TCATTTCTTATCAATT
1 TCATTTCTT-TC-ATT
819192 TCCATTTCTTTCATT
1 T-CATTTCTTTCATT
819207 TC
1 TC
819209 TTATTTCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 1 0.03
15 13 0.43
16 8 0.27
17 8 0.27
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (14 bp):
TCATTTCTTTCATT
Found at i:825894 original size:12 final size:12
Alignment explanation
Indices: 825862--825900 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
825852 AGAGCATTTT
825862 AAAAATAAAGAA
1 AAAAATAAAGAA
***
825874 AACTTTAAAGAA
1 AAAAATAAAGAA
825886 AAAAATAAAGAA
1 AAAAATAAAGAA
825898 AAA
1 AAA
825901 GAAAGAACTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (12 bp):
AAAAATAAAGAA
Found at i:825938 original size:24 final size:20
Alignment explanation
Indices: 825892--825930 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
825882 AGAAAAAAAT
825892 AAAGAAAAAGAAAGAACTTA
1 AAAGAAAAAGAAAGAACTTA
825912 AAAGAAAAAGAAAGAACTT
1 AAAGAAAAAGAAAGAACTT
825931 TAATAAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.69, C:0.05, G:0.15, T:0.10
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAACTTA
Found at i:828398 original size:2 final size:2
Alignment explanation
Indices: 828391--828422 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
828381 AAATCCTAGC
828391 GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
828423 CGATTTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:833332 original size:29 final size:28
Alignment explanation
Indices: 833290--833349 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 28
833280 TTCACCTAAC
833290 TAAATTGATGTAAGCAACGACATCAAAAT
1 TAAATTGATGTAAGCAACGACATC-AAAT
* *
833319 TAAATTGATGTAAGCAATGCCATCAAAT
1 TAAATTGATGTAAGCAACGACATCAAAT
833347 TAA
1 TAA
833350 TTTAGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (28 bp):
TAAATTGATGTAAGCAACGACATCAAAT
Found at i:838015 original size:28 final size:27
Alignment explanation
Indices: 837975--838032 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 27
837965 TTCACCTAAC
837975 TAAATTGATGTAAGCAATGACATCAAAT
1 TAAATTGATGTAAGCAATGACAT-AAAT
838003 TAAATTGATGTAAGCAATGACATAAAT
1 TAAATTGATGTAAGCAATGACATAAAT
838030 TAA
1 TAA
838033 TTTAGGTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (27 bp):
TAAATTGATGTAAGCAATGACATAAAT
Found at i:839102 original size:42 final size:42
Alignment explanation
Indices: 839010--839141 Score: 133
Period size: 42 Copynumber: 3.2 Consensus size: 42
839000 AAATAACCAA
* * * ***
839010 CAAATTCGCAACGC-AAATTCAAATTTCGCAAC-CGAGGTTC
1 CAAAATCGCAACGCGAAAGTCAAAATTCGCAACGCGATACTC
* * * * *
839050 TAAATTCGCAACGCGAAAGTCGAAATTCGGAACGCGATAGTC
1 CAAAATCGCAACGCGAAAGTCAAAATTCGCAACGCGATACTC
**
839092 CAAAATCGCAACGCGATTGTCAAAATTCGCAACGCGATACTC
1 CAAAATCGCAACGCGAAAGTCAAAATTCGCAACGCGATACTC
839134 CAAAATCG
1 CAAAATCG
839142 TAATGCATTT
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 13 0.17
41 14 0.19
42 48 0.64
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (42 bp):
CAAAATCGCAACGCGAAAGTCAAAATTCGCAACGCGATACTC
Found at i:839129 original size:21 final size:21
Alignment explanation
Indices: 839011--839139 Score: 113
Period size: 21 Copynumber: 6.2 Consensus size: 21
839001 AATAACCAAC
* *
839011 AAATTCGCAACGC-AAATTCA
1 AAATTCGCAACGCGATAGTCA
* * *
839031 AATTTCGCAAC-CGA-GGTTCT
1 AAATTCGCAACGCGATAG-TCA
* *
839051 AAATTCGCAACGCGAAAGTCG
1 AAATTCGCAACGCGATAGTCA
*
839072 AAATTCGGAACGCGATAGTCCA
1 AAATTCGCAACGCGATAGT-CA
*
839094 AAA-TCGCAACGCGATTGTCA
1 AAATTCGCAACGCGATAGTCA
*
839114 AAATTCGCAACGCGATACTCCA
1 AAATTCGCAACGCGATAGT-CA
839136 AAAT
1 AAAT
839140 CGTAATGCAT
Statistics
Matches: 88, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.01
20 28 0.32
21 48 0.55
22 11 0.12
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (21 bp):
AAATTCGCAACGCGATAGTCA
Found at i:839815 original size:7 final size:7
Alignment explanation
Indices: 839805--839832 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
839795 TCCAACTTCC
839805 AAATGTT
1 AAATGTT
839812 AAATGTT
1 AAATGTT
839819 AAATGTT
1 AAATGTT
839826 AAATGTT
1 AAATGTT
839833 TCAACTTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (7 bp):
AAATGTT
Found at i:840120 original size:12 final size:12
Alignment explanation
Indices: 840103--840129 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
840093 ATTTTGGAGT
840103 ATCGCGTTGCGA
1 ATCGCGTTGCGA
840115 ATCGCGTTGCGA
1 ATCGCGTTGCGA
840127 ATC
1 ATC
840130 TTAAAATCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (12 bp):
ATCGCGTTGCGA
Found at i:840183 original size:20 final size:19
Alignment explanation
Indices: 840115--840191 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
840105 CGCGTTGCGA
* *
840115 ATCGCGTTGCGAATCTTAAA
1 ATCGCGTTGCGAAT-TTGAG
840135 ATCGCGTTGCGAATTTG-G
1 ATCGCGTTGCGAATTTGAG
* *
840153 AACCTGGGTTGCGAAATTTGAG
1 -ATC-GCGTTGCG-AATTTGAG
840175 ATCGCGTTGCGAATTTG
1 ATCGCGTTGCGAATTTG
840192 TTGGTCATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
19 10 0.21
20 28 0.60
21 8 0.17
22 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (19 bp):
ATCGCGTTGCGAATTTGAG
Found at i:841528 original size:140 final size:139
Alignment explanation
Indices: 841316--841839 Score: 597
Period size: 140 Copynumber: 3.8 Consensus size: 139
841306 TAAATATATT
*
841316 GGCTCTAATTATTAATTCTAATTGA-TTTAATC-ATTATTGAAATGAAT-AATCGAAATGGAACC
1 GGCTCTAATTATTAATCCTAATTGATTTTAATCAATTATTG-AATGAATAAATCGAAATGGAACC
* *
841378 TCATGCATTAAGGTGAGGACCAAATAAAAAATTCACCTAAATTAAAGGACTAAAAGTTAAATTAT
65 TCAGGCATTAAGGTGAGGACCAAATAAAAAATTCACCTAAATTAAAGGACTAAAAG-TAAATTAA
*
841443 CCTAAATTGGA
129 CCTAAAGTGGA
*
841454 GGCTCTAATTATTAATCCTAATTGATTTTAATCAATTATTGAATCAAATAAAT-GAAATGGAACC
1 GGCTCTAATTATTAATCCTAATTGATTTTAATCAATTATTGAAT-GAATAAATCGAAATGGAACC
* * ** * *
841518 TCGGGCATTAAGGTGAGCACCAAATTGAAAATTTACCTAAATTAAAGGACTAAAAGTGAACTTAA
65 TCAGGCATTAAGGTGAGGACCAAATAAAAAATTCACCTAAATTAAAGGACTAAAAGT-AAATTAA
841583 CCTAAAGTGGA
129 CCTAAAGTGGA
* * * * *
841594 GGCAT-TGATTATTAGTCCTAATTGATTTTAATCAATTATTGAGTTG-ATTAATCGAAATAGAAC
1 GGC-TCTAATTATTAATCCTAATTGATTTTAATCAATTATTGA-ATGAATAAATCGAAATGGAAC
* * **
841657 CTCAGGCATTAA-ATCGAGGACCAAATAAAAAAATT-GCCTAAATTAAATAACTAAAAAG-AAAT
64 CTCAGGCATTAAGGT-GAGGACCAAAT-AAAAAATTCACCTAAATTAAAGGACT-AAAAGTAAAT
841719 TAACCTAAAGTGGA
126 TAACCTAAAGTGGA
* * *
841733 GGCTCTAAATATTAATCATAATTGATTTTAA--AATTATTGAATCGAAT-AATTGAAATGGAACC
1 GGCTCTAATTATTAATCCTAATTGATTTTAATCAATTATTGAAT-GAATAAATCGAAATGGAACC
* * ** * *
841795 T-TGGACATTAAGGTGATGACCAAATCGAATATTCTCCTAAATTAA
65 TCAGG-CATTAAGGTGAGGACCAAATAAAAAATTCACCTAAATTAA
841840 GAGTTCGGGG
Statistics
Matches: 329, Mismatches: 40, Indels: 35
0.81 0.10 0.09
Matches are distributed among these distances:
136 8 0.02
137 50 0.15
138 28 0.09
139 59 0.18
140 168 0.51
141 16 0.05
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (139 bp):
GGCTCTAATTATTAATCCTAATTGATTTTAATCAATTATTGAATGAATAAATCGAAATGGAACCT
CAGGCATTAAGGTGAGGACCAAATAAAAAATTCACCTAAATTAAAGGACTAAAAGTAAATTAACC
TAAAGTGGA
Done.