Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008374.1 Hibiscus syriacus cultivar Beakdansim tig00111131_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: 1731758
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 10
Found at i:568466 original size:40 final size:39
Alignment explanation
Indices: 568301--568514 Score: 119
Period size: 40 Copynumber: 5.3 Consensus size: 39
568291 CAGGATTCGC
* * **
568301 GTTACGAATTCAAAAATCGAGTTGCGAAAACGAAACTTGT
1 GTTACGAATTCCAAATTCGAGTTGCGAATTCGAAA-TTGT
** ** ***
568341 GTTGTGAATTTAAAAATATCGAGTTGCGAAAAAGAAATTCGT
1 GTTACGAA-TTCCAAAT-TCGAGTTGCGAATTCGAAATT-GT
* * **
568383 GTTGCGAAAATGT-CAAATTCGAGTTGTGAATTCGACTTCTGT
1 GTTACG--AAT-TCCAAATTCGAGTTGCGAATTCGAAAT-TGT
*
568425 GTTACGAATTCCAAATTCGAGTTGCAAATTCGGAAATTGT
1 GTTACGAATTCCAAATTCGAGTTGCGAATTC-GAAATTGT
* * * * *
568465 GTTGCGAAATTGGC--TTTCGTGTTGCGAATTCGAAATTGA
1 GTTACG-AATT-CCAAATTCGAGTTGCGAATTCGAAATTGT
568504 GTTACGAATTC
1 GTTACGAATTC
568515 GTTGGTTATT
Statistics
Matches: 137, Mismatches: 26, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
38 4 0.03
39 13 0.09
40 49 0.36
41 15 0.11
42 47 0.34
43 6 0.04
44 3 0.02
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.32
Consensus pattern (39 bp):
GTTACGAATTCCAAATTCGAGTTGCGAATTCGAAATTGT
Found at i:574171 original size:2 final size:2
Alignment explanation
Indices: 574164--574189 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
574154 GTAAGGTTAA
574164 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
574190 TTAATTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:574335 original size:41 final size:41
Alignment explanation
Indices: 574277--574360 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
574267 ATAATACTCA
574277 TTCACTATTTTAACCTAAACTAACAAGAATTAAGTCTAAAT
1 TTCACTATTTTAACCTAAACTAACAAGAATTAAGTCTAAAT
* *
574318 TTCATTATTTTAACCTAAACTAACCAGAATTAAGTCTAAAT
1 TTCACTATTTTAACCTAAACTAACAAGAATTAAGTCTAAAT
574359 TT
1 TT
574361 GAAAAAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.37
Consensus pattern (41 bp):
TTCACTATTTTAACCTAAACTAACAAGAATTAAGTCTAAAT
Found at i:574692 original size:20 final size:19
Alignment explanation
Indices: 574669--574744 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 19
574659 ATCCTATCAA
*
574669 TACTATAAGAATAATATCGG
1 TACTAT-AGAACAATATCGG
*
574689 TACTGTATGAACAATATCGG
1 TACTATA-GAACAATATCGG
*
574709 TACTATACGAACAATATAGG
1 TACTATA-GAACAATATCGG
*
574729 TACGTAT-GAATAATAT
1 TAC-TATAGAACAATAT
574745 TGATACCAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
19 9 0.19
20 36 0.75
21 3 0.06
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (19 bp):
TACTATAGAACAATATCGG
Found at i:574713 original size:40 final size:39
Alignment explanation
Indices: 574669--574744 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
574659 ATCCTATCAA
* *
574669 TACTATAAGAATAATATCGGTACTGTATGAACAATATCGG
1 TACTATAAGAACAATATAGGTAC-GTATGAACAATATCGG
* *
574709 TACTATACGAACAATATAGGTACGTATGAATAATAT
1 TACTATAAGAACAATATAGGTACGTATGAACAATAT
574745 TGATACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 12 0.38
40 20 0.62
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (39 bp):
TACTATAAGAACAATATAGGTACGTATGAACAATATCGG
Found at i:576440 original size:16 final size:16
Alignment explanation
Indices: 576419--576451 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
576409 CTCATTTATC
576419 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
576435 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
576451 A
1 A
576452 AAACACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:578735 original size:22 final size:21
Alignment explanation
Indices: 578704--578764 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
578694 CAGAATCCCA
* *
578704 GGGGGTATCGATTCCC-CCTG
1 GGGGGGATCGATTCCCTCATG
*
578724 TGGGGGGAATCGGTTCCCTCATG
1 -GGGGGG-ATCGATTCCCTCATG
578747 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
578765 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 16 0.47
22 15 0.44
23 3 0.09
ACGTcount: A:0.11, C:0.26, G:0.38, T:0.25
Consensus pattern (21 bp):
GGGGGGATCGATTCCCTCATG
Found at i:593197 original size:127 final size:125
Alignment explanation
Indices: 593043--593298 Score: 397
Period size: 127 Copynumber: 2.0 Consensus size: 125
593033 TTCAGTCTTT
*
593043 ATTATTTATATAATCAATTTGGTCCTAAATTAAAT-AAATTTAATAAATTAATCATTTAATTAGG
1 ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCA-TTAATCAGG
* *
593107 ATCTGACATGTGTTAGCACATGATCATGACACGTGTCATTGGTGACACATGTTACCACCTA
65 ATCTGACATGTGTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
*
593168 ATTATTTATATGCTATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTAATCAG
1 ATTATTTATAT--AATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTAATCAG
* * * * *
593233 TATCTGACATGTGTTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTA
64 GATCTGACATGTGTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
593295 ATTA
1 ATTA
593299 GAAGAAAATT
Statistics
Matches: 119, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
125 11 0.09
127 89 0.75
128 19 0.16
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (125 bp):
ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTAATCAGGA
TCTGACATGTGTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
Found at i:593777 original size:16 final size:18
Alignment explanation
Indices: 593756--593788 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
593746 ATTTCTTATT
593756 AAAATA-AAAT-ATTCAA
1 AAAATATAAATGATTCAA
593772 AAAATATAAATGATTCA
1 AAAATATAAATGATTCA
593789 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (18 bp):
AAAATATAAATGATTCAA
Found at i:593934 original size:20 final size:20
Alignment explanation
Indices: 593906--593948 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
593896 CTATATTACC
593906 TTAAATGAAGTATTTTAGAA
1 TTAAATGAAGTATTTTAGAA
*
593926 TTAATTGAAGTATTTTAGAA
1 TTAAATGAAGTATTTTAGAA
593946 TTA
1 TTA
593949 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (20 bp):
TTAAATGAAGTATTTTAGAA
Found at i:600023 original size:23 final size:23
Alignment explanation
Indices: 599993--600054 Score: 124
Period size: 23 Copynumber: 2.7 Consensus size: 23
599983 GCCCAATTTG
599993 GATCCATCTTTGCAGTACCGGGA
1 GATCCATCTTTGCAGTACCGGGA
600016 GATCCATCTTTGCAGTACCGGGA
1 GATCCATCTTTGCAGTACCGGGA
600039 GATCCATCTTTGCAGT
1 GATCCATCTTTGCAGT
600055 TTCATCACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (23 bp):
GATCCATCTTTGCAGTACCGGGA
Found at i:608871 original size:152 final size:154
Alignment explanation
Indices: 608647--609045 Score: 480
Period size: 168 Copynumber: 2.5 Consensus size: 154
608637 GCTCTTCTCA
* * * *
608647 CCTTGAGCTATGCTACAAATGATCTGCCTTTGAGTTGAGTGTAATCGAACTTGAAGGTCTTTTGT
1 CCTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGT
* * *
608712 TGGCAGATAACCCTTAT-TGC-CATGATGTGTCTTTCAGCTGAGTATAATCAAACTCGAATGTCT
66 TGGCAGATAACCCTTATATGCAAATGATGTGCCTTTCAGCTGAGTATAATCAAACTCGAAGGTCT
*
608775 TTTGTTGGCAGATAACCCTTATCG
131 TTTGTTGGCAAATAACCCTTATCG
* * *
608799 CCTTGAGCTATGCCGCAAATGATATACCTTTGAGCTAAGTGTAATCGAACTCGAAGGTCTTTTGT
1 CCTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGT
* * *
608864 TGGCAGATAACCCTTCTCGCCTTGAGCTATGATGCAAATGATGTGCCTTTGAGCTTAGTGTAATC
66 TGGCAGATAA-------C-CC-T----TAT-ATGCAAATGATGTGCCTTTCAGCTGAGTATAATC
* * *
608929 GAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTG
117 AAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTATCG
* *
608967 CCTTGAGCTATGCTGCAAATTATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGT
1 CCTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGT
609031 TGGCAGATAACCCTT
66 TGGCAGATAACCCTT
609046 CTAGCCTTGA
Statistics
Matches: 209, Mismatches: 22, Indels: 30
0.80 0.08 0.11
Matches are distributed among these distances:
152 68 0.33
154 1 0.00
158 1 0.00
159 3 0.01
160 3 0.01
161 1 0.00
165 3 0.01
167 18 0.09
168 111 0.53
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (154 bp):
CCTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGT
TGGCAGATAACCCTTATATGCAAATGATGTGCCTTTCAGCTGAGTATAATCAAACTCGAAGGTCT
TTTGTTGGCAAATAACCCTTATCG
Found at i:608874 original size:84 final size:84
Alignment explanation
Indices: 608733--609071 Score: 500
Period size: 84 Copynumber: 4.0 Consensus size: 84
608723 CCTTATTGCC
* * * * * *
608733 ATGATGTGTCTTTCAGCTGAGTATAATCAAACTCGAATGTCTTTTGTTGGCAGATAACCCTTATC
1 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTC
*
608798 GCCTTGAGCTATGCCGCAA
66 GCCTTGAGCTATGCTGCAA
* * *
608817 ATGATATACCTTTGAGCTAAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTC
1 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTC
*
608882 GCCTTGAGCTATGATGCAA
66 GCCTTGAGCTATGCTGCAA
* * *
608901 ATGATGTGCCTTTGAGCTTAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTT
1 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTC
608966 GCCTTGAGCTATGCTGCAA
66 GCCTTGAGCTATGCTGCAA
* *
608985 ATTATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTA
1 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTC
* * *
609049 GCCTTGAGTTATACTGTAA
66 GCCTTGAGCTATGCTGCAA
609068 ATGA
1 ATGA
609072 ACATGATATC
Statistics
Matches: 230, Mismatches: 25, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
83 40 0.17
84 190 0.83
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (84 bp):
ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTC
GCCTTGAGCTATGCTGCAA
Found at i:609336 original size:114 final size:114
Alignment explanation
Indices: 609127--609425 Score: 355
Period size: 114 Copynumber: 2.5 Consensus size: 114
609117 CGTTGCGAAG
* * * **
609127 TTGAACCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGTTG
1 TTGAACCTTGAATTAGATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATAAATGTTACTG
*
609192 GTGGGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATT
66 GTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATT
* *
609241 TTGAGCCTTGAATTATATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATAAATGTTACTG
1 TTGAACCTTGAATTAGATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATAAATGTTACTG
* * * *
609306 GTGAGCACGATTCCCTTCGTTGTGACGTTGAAACTGTGGATGACCCCTTCGT
66 GTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGA-CCCAT--T
* * * * *
609358 TGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTAAAATCCAATCTCAAGATGAAT
1 T-TG-A----A-CCTTGAATTAGATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATAAAT
609423 GTT
59 GTT
609426 GCTTCGAGTC
Statistics
Matches: 156, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
114 97 0.62
115 4 0.03
117 2 0.01
118 2 0.01
119 1 0.01
124 50 0.32
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (114 bp):
TTGAACCTTGAATTAGATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATAAATGTTACTG
GTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATT
Found at i:609539 original size:64 final size:64
Alignment explanation
Indices: 609431--609661 Score: 345
Period size: 64 Copynumber: 3.6 Consensus size: 64
609421 ATGTTGCTTC
* ** * *
609431 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGTTCTAAATGAAACTGGGAAGTCGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTT
* * *
609495 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAATCGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTT
* * *
609559 GAGTCCTATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTT
* *
609623 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTTACTCT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
609662 AAAATTTGCA
Statistics
Matches: 150, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 150 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (64 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTT
Found at i:609582 original size:128 final size:128
Alignment explanation
Indices: 609431--609661 Score: 381
Period size: 128 Copynumber: 1.8 Consensus size: 128
609421 ATGTTGCTTC
** * *
609431 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGTTCTAAATGAAACTGGGAAGTCGTTTGTTG
1 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTAAATGAAACTAGAAAGTCGTTTGTTG
609496 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAATCGTTTGTT
66 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAATCGTTTGTT
* * * *
609559 GAGTCCTATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAGAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTAAATGAAACTAGAAAGTCGTTTGTTG
*
609624 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTTACTCT
66 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
609662 AAAATTTGCA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
128 94 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (128 bp):
GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTAAATGAAACTAGAAAGTCGTTTGTTG
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAATCGTTTGTT
Found at i:614092 original size:20 final size:20
Alignment explanation
Indices: 614055--614092 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
614045 AAAATCAAAC
*
614055 AAAATATTAGATGGTAAAAT
1 AAAATATTAGATGCTAAAAT
614075 AAAATATT-GAATGCTAAA
1 AAAATATTAG-ATGCTAAA
614093 CAAAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (20 bp):
AAAATATTAGATGCTAAAAT
Found at i:615280 original size:12 final size:12
Alignment explanation
Indices: 615265--615289 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
615255 GCTTTTTTTC
615265 AACATGTTTGAA
1 AACATGTTTGAA
615277 AACATGTTTGAA
1 AACATGTTTGAA
615289 A
1 A
615290 TTGTGGCAGT
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (12 bp):
AACATGTTTGAA
Found at i:625902 original size:20 final size:21
Alignment explanation
Indices: 625864--625903 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
625854 TCCAGTTGTC
* *
625864 TTTAATTAAGAAAATTGTAAT
1 TTTAAATAAGAAAAATGTAAT
625885 TTTAAATAA-AAAAATGTAA
1 TTTAAATAAGAAAAATGTAA
625904 AAATAACGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
TTTAAATAAGAAAAATGTAAT
Found at i:626225 original size:16 final size:16
Alignment explanation
Indices: 626203--626236 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
626193 ATAACCGGGC
*
626203 ATAAAAAATAAATAAAT
1 ATAAAATATAAA-AAAT
626220 ATAAAATATAAAAAAT
1 ATAAAATATAAAAAAT
626236 A
1 A
626237 CATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
ATAAAATATAAAAAAT
Found at i:626652 original size:22 final size:22
Alignment explanation
Indices: 626626--626672 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
626616 ATGTTCATCC
626626 GTTTGATGAACACCACCGTGGG
1 GTTTGATGAACACCACCGTGGG
626648 GTTTGATGAACACCACCGTGGG
1 GTTTGATGAACACCACCGTGGG
626670 GTT
1 GTT
626673 CGCTGAACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (22 bp):
GTTTGATGAACACCACCGTGGG
Found at i:626679 original size:22 final size:22
Alignment explanation
Indices: 626630--626680 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
626620 TCATCCGTTT
*
626630 GATGAACACCACCGTGGGGTTT
1 GATGAACACCACCGTGGGGTTC
626652 GATGAACACCACCGTGGGGTTC
1 GATGAACACCACCGTGGGGTTC
*
626674 GCTGAAC
1 GATGAAC
626681 CCAAAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.25, G:0.31, T:0.20
Consensus pattern (22 bp):
GATGAACACCACCGTGGGGTTC
Found at i:626748 original size:20 final size:20
Alignment explanation
Indices: 626708--626749 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
626698 CTTGCCGCGT
* *
626708 CGTCGGCTGCCATTGAACGG
1 CGTCGGCCGCCATTCAACGG
*
626728 CGTCGGCCGCCATTCATCGG
1 CGTCGGCCGCCATTCAACGG
626748 CG
1 CG
626750 GCAAAACATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.36, G:0.33, T:0.19
Consensus pattern (20 bp):
CGTCGGCCGCCATTCAACGG
Found at i:627382 original size:20 final size:20
Alignment explanation
Indices: 627359--627407 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
627349 CTTGGGTCAC
627359 TGTTGGGCCATTGTAAAGTT
1 TGTTGGGCCATTGTAAAGTT
627379 TGTTGGGCCATTGTAAAGTT
1 TGTTGGGCCATTGTAAAGTT
*
627399 TGGTGGGCC
1 TGTTGGGCC
627408 TGTAAATGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.12, G:0.35, T:0.37
Consensus pattern (20 bp):
TGTTGGGCCATTGTAAAGTT
Found at i:628161 original size:82 final size:81
Alignment explanation
Indices: 628037--628374 Score: 399
Period size: 82 Copynumber: 4.1 Consensus size: 81
628027 CTGAATGAAA
* *
628037 TCGAACTCGACAATTTTATTGACAGATAGCCCTTCTTGCCTTGAGATATGCTGTAAATGATGTGC
1 TCGAACTCGA-AATTTTATTGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGC
*
628102 CTTGGAGCTGATCGTTG
65 CTTGGAGCTGAGCGTTG
* * * *
628119 TCGAACTCGACAATTTTATTGACATATAGCCCTTATTGCCTTGAGCTATGCTGTAAATGATGTTC
1 TCGAACTCGA-AATTTTATTGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGC
628184 CTTGGAGCTGAGCGTTG
65 CTTGGAGCTGAGCGTTG
** * * * * * * **
628201 TCGAACTCGAAGGTCT-TTGGCAGATACCCCTTCTAGCCTTGAGCTATACCGCAAATGATAAGCC
1 TCGAACTCGAAATTTTATTGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCC
*
628265 TTGGAGCTGAGCGTTT
66 TTGGAGCTGAGCGTTG
* ** * *
628281 TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
1 TCGAACTCGAA-AT-TTTATTGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTG
* *
628346 CCTTGGAGCTGAACGTAG
64 CCTTGGAGCTGAGCGTTG
*
628364 TCGAACCCGAA
1 TCGAACTCGAA
628375 GATCTTTTGT
Statistics
Matches: 218, Mismatches: 35, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
80 63 0.29
81 4 0.02
82 89 0.41
83 62 0.28
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (81 bp):
TCGAACTCGAAATTTTATTGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCC
TTGGAGCTGAGCGTTG
Found at i:628267 original size:80 final size:80
Alignment explanation
Indices: 628059--628381 Score: 385
Period size: 80 Copynumber: 4.0 Consensus size: 80
628049 ATTTTATTGA
* * *
628059 CAGATAGCCCTTCTTGCCTTGAGATATGCTGTAAATGATGTGCCTTGGAGCTGATCGTTGTCGAA
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTTGTCGAA
** * *
628124 CTCGACAATTTTATTGA
66 CTCGA-AGGTCT-TTGG
* * * *
628141 CATATAGCCCTTATTGCCTTGAGCTATGCTGTAAATGATGTTCCTTGGAGCTGAGCGTTGTCGAA
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTTGTCGAA
628206 CTCGAAGGTCTTTGG
66 CTCGAAGGTCTTTGG
* * * * ** *
628221 CAGATACCCCTTCTAGCCTTGAGCTATACCGCAAATGATAAGCCTTGGAGCTGAGCGTTTTCGAA
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTTGTCGAA
628286 CTCGAAGGTCTTTGGTG
66 CTCGAAGGTCTTT-G-G
* * * *
628303 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAACGTAGTCGA
1 -CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTTGTCGA
* *
628368 ACCCGAAGATCTTT
65 ACTCGAAGGTCTTT
628382 TGTGTTTTAA
Statistics
Matches: 206, Mismatches: 32, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
80 70 0.34
81 4 0.02
82 66 0.32
83 66 0.32
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.31
Consensus pattern (80 bp):
CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTTGTCGAA
CTCGAAGGTCTTTGG
Found at i:628436 original size:15 final size:15
Alignment explanation
Indices: 628418--628474 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
628408 GGTTGGTGTT
628418 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
*
628433 TCAAGAGAGACAACTTGTT
1 TC-A-AGAGA-AAC-TGTC
*
628452 TCAAGAGAAATTGTC
1 TCAAGAGAAACTGTC
628467 TCAAGAGA
1 TCAAGAGA
628475 GACAAAACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 13 0.37
16 3 0.09
17 10 0.29
18 4 0.11
19 5 0.14
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:628457 original size:19 final size:18
Alignment explanation
Indices: 628421--628513 Score: 67
Period size: 17 Copynumber: 5.3 Consensus size: 18
628411 TGGTGTTTCA
628421 AGAGAAAC-TGTCTCAAG
1 AGAGAAACTTGTCTCAAG
*
628438 AGAGACAACTTGTTTC-A-
1 AGAGA-AACTTGTCTCAAG
628455 AGAGAAA-TTGTCTCAAG
1 AGAGAAACTTGTCTCAAG
628472 AGAGACAAAACTTAGT-TCCAA-
1 AGAG---AAACTT-GTCT-CAAG
628493 A-AGAAAC-TGTCTCAAG
1 AGAGAAACTTGTCTCAAG
628509 AGAGA
1 AGAGA
628514 CGAAATTTGT
Statistics
Matches: 61, Mismatches: 2, Indels: 26
0.69 0.02 0.29
Matches are distributed among these distances:
15 11 0.18
16 6 0.10
17 21 0.34
18 4 0.07
19 5 0.08
20 5 0.08
21 4 0.07
22 5 0.08
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (18 bp):
AGAGAAACTTGTCTCAAG
Found at i:628507 original size:37 final size:34
Alignment explanation
Indices: 628414--628514 Score: 130
Period size: 34 Copynumber: 2.9 Consensus size: 34
628404 CAAAGGTTGG
* *
628414 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAACT
1 TGTTCCAAAAGAAACTGTCTCAAGAGAGACAACT
* * *
628448 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACT
1 TGTTCCAAAAGAAACTGTCTCAAGAGAGAC--AACT
628484 TAGTTCCAAAAGAAACTGTCTCAAGAGAGAC
1 T-GTTCCAAAAGAAACTGTCTCAAGAGAGAC
628515 GAAATTTGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
34 29 0.48
36 5 0.08
37 26 0.43
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.23
Consensus pattern (34 bp):
TGTTCCAAAAGAAACTGTCTCAAGAGAGACAACT
Found at i:628635 original size:138 final size:138
Alignment explanation
Indices: 628414--629042 Score: 841
Period size: 138 Copynumber: 4.5 Consensus size: 138
628404 CAAAGGTTGG
* * * *
628414 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC--AACTTGTTTCAAGAGAAATTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTAAAGAGAGA
* * *
628477 CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAATAGATTC
66 CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACAGATTC
628542 AAAGATTT
131 AAAGATTT
* * * *
628550 TGTTTCAAGGGAAATTGTCCCAAGAGAGACAAAATTTGTTTCAAGAGAGACTGTCGAAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTAAAGAGAGA
* * * *
628615 CAAAACTTAGTTCTAGAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAATGTAAAACAGATTC
66 CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACAGATTC
628680 AAAGATTT
131 AAAGATTT
* * * *
628688 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAGACAAAATTTGTTTTAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTC--AAGAG---AAA-CTGTCTAAA
* * * *
628753 GAGTGACAAACCTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTAATA-TAAAA
60 GAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAA-AGGAAAA
* *
628817 CATACTCAAAGATTT
124 CAGATTCAAAGATTT
* * *
628832 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAAAAATTGTCTAAAGAGAGT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTAAAGAGAGA
* * ** *
628897 CAAAACTTAGTTCTAAAAGAAACTATCTCAAGGGAGACAAAATTTGTTTCCAGGAAAACAAATTC
66 CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACAGATTC
*
628962 AAAGTTTT
131 AAAGATTT
* * *
628970 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTCTTTTAAGAGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTAAAGAGAGA
629035 CAAAACTT
66 CAAAACTT
629043 TGTTTTGAGT
Statistics
Matches: 432, Mismatches: 51, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
136 27 0.06
137 1 0.00
138 274 0.63
139 3 0.01
140 5 0.01
142 4 0.01
143 2 0.00
144 116 0.27
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (138 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTAAAGAGAGA
CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACAGATTC
AAAGATTT
Found at i:628731 original size:21 final size:21
Alignment explanation
Indices: 628702--628762 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
628692 TCAAGGGAAA
*
628702 TTGTCTCAAGAGAGACAAAAT
1 TTGTTTCAAGAGAGACAAAAT
*
628723 TTGTTTCAAAAGAGACAAAAT
1 TTGTTTCAAGAGAGACAAAAT
* *
628744 TTGTTTTAAGAGTGACAAA
1 TTGTTTCAAGAGAGACAAA
628763 CCTTAGTTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.30
Consensus pattern (21 bp):
TTGTTTCAAGAGAGACAAAAT
Found at i:628991 original size:282 final size:276
Alignment explanation
Indices: 628414--629042 Score: 906
Period size: 282 Copynumber: 2.3 Consensus size: 276
628404 CAAAGGTTGG
* *
628414 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC--AACTTGTTTCAAGAGAAATTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGA
* *
628477 CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAATAGATTC
66 CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGACTC
* * *
628542 AAAGATTTTGTTTCAAGGGAAATTGTCCCAAGAGAGACAAAATTTGTTTCAAGAGAGACTGTCGA
131 AAAGATTTTGTTTCAAGGGAAACTGTCCCAAGAGAGACAAAATTTGTTTCAAGAAAAACTGTCGA
* * *
628607 AAGAGAGACAAAACTTAGTTCTAGAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAATGTAAA
196 AAGAGAGACAAAACTTAGTTCTAAAAGAAACTATCTCAAGGGAGACAAAATTTGTTTAATGGAAA
*
628672 ACAGATTCAAAGATTT
261 ACAAATTCAAAGATTT
* * *
628688 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAGACAAAATTTGTTTTAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTC--AAGAG---AAA-TTGTCTCAA
* * * *
628753 GAGTGACAAACCTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTAATA-TAAAA
60 GAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAA-AGGAAAA
* *
628817 CATACTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAAAAA
124 CAGACTCAAAGATTTTGTTTCAAGGGAAACTGTCCCAAGAGAGACAAAATTTGTTTCAAGAAAAA
* * *
628882 TTGTCTAAAGAGAGTCAAAACTTAGTTCTAAAAGAAACTATCTCAAGGGAGACAAAATTTGTTTC
189 CTGTCGAAAGAGAGACAAAACTTAGTTCTAAAAGAAACTATCTCAAGGGAGACAAAATTTGTTT-
* *
628947 CA-GGAAAACAAATTCAAAGTTTT
253 AATGGAAAACAAATTCAAAGATTT
* * *
628970 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTCTTTTAAGAGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGA
629035 CAAAACTT
66 CAAAACTT
629043 TGTTTTGAGT
Statistics
Matches: 312, Mismatches: 33, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
274 28 0.09
276 27 0.09
277 3 0.01
278 5 0.02
280 5 0.02
281 3 0.01
282 239 0.77
283 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (276 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGA
CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGACTC
AAAGATTTTGTTTCAAGGGAAACTGTCCCAAGAGAGACAAAATTTGTTTCAAGAAAAACTGTCGA
AAGAGAGACAAAACTTAGTTCTAAAAGAAACTATCTCAAGGGAGACAAAATTTGTTTAATGGAAA
ACAAATTCAAAGATTT
Found at i:630566 original size:95 final size:95
Alignment explanation
Indices: 630379--630641 Score: 330
Period size: 95 Copynumber: 2.7 Consensus size: 95
630369 GGCTAGCTGA
* * * * * * * *
630379 ATCCATAAAGACGGGGCATTTAACAAATTGCTCTAGAGGGACAGCTTAATATCATTGTATAG-AT
1 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAAC-TCA-AGC-TT-TATTGTAT
*
630443 ATTATAATCACCTTTATCAGACTAGCTGAATTTT
62 ATTATAATCACCTTTATCAGACTAGCTGAATCTT
* *
630477 ATCCATAAAGCCGATGCGTTTAACCAATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
**
630542 TAATCACCTTTATCAGGTTAGCTGAATCTT
66 TAATCACCTTTATCAGACTAGCTGAATCTT
* * *
630572 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCGAGCTTTATTGTATATAT
1 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-T
630637 ATAAT
65 ATAAT
630642 ATTATAATGC
Statistics
Matches: 145, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
94 4 0.03
95 93 0.64
96 8 0.06
97 2 0.01
98 38 0.26
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (95 bp):
ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGACTAGCTGAATCTT
Found at i:634620 original size:26 final size:26
Alignment explanation
Indices: 634574--634625 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
634564 ATACAGAAGC
* *
634574 AAATAAATAAACTAGAGATGAAATAA
1 AAATAAATAAAATACAGATGAAATAA
634600 AAATGAAATAAAATACA-ATGAAATAA
1 AAAT-AAATAAAATACAGATGAAATAA
634626 TATTATATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.67, C:0.04, G:0.10, T:0.19
Consensus pattern (26 bp):
AAATAAATAAAATACAGATGAAATAA
Found at i:634869 original size:27 final size:26
Alignment explanation
Indices: 634821--634872 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
634811 ATAAATGAAA
634821 AAATATAAAAAATACGTATATATATGT
1 AAATATAAAAAATAC-TATATATATGT
634848 AAATATAAAATAATA-TATTATATAT
1 AAATATAAAA-AATACTA-TATATAT
634873 AAAAAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 2 0.09
27 17 0.74
28 4 0.17
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (26 bp):
AAATATAAAAAATACTATATATATGT
Found at i:634937 original size:2 final size:2
Alignment explanation
Indices: 634932--634968 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
634922 ACACACACAC
634932 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
634969 CACGTAAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:637285 original size:17 final size:17
Alignment explanation
Indices: 637263--637302 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
637253 TTAATATTTT
*
637263 GTATTTAATTTATTTAA
1 GTATTTAAATTATTTAA
637280 GTATTTAAATTATTTAA
1 GTATTTAAATTATTTAA
637297 -TATTTA
1 GTATTTA
637303 TTACGAACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (17 bp):
GTATTTAAATTATTTAA
Found at i:641694 original size:20 final size:20
Alignment explanation
Indices: 641666--641716 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
641656 TATGAGAACT
* *
641666 TTGCTGGAATTATTGACTCA
1 TTGCCGGAATTATTAACTCA
*
641686 TTGCCGGAATTATTAACTCG
1 TTGCCGGAATTATTAACTCA
*
641706 TTGACGGAATT
1 TTGCCGGAATT
641717 GTTGTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCCGGAATTATTAACTCA
Found at i:646850 original size:50 final size:51
Alignment explanation
Indices: 646786--646895 Score: 177
Period size: 50 Copynumber: 2.1 Consensus size: 51
646776 TTTCCCACCC
*
646786 ATTTCTCCAAAGCCACATAACGTTTTAACAAA-ACCAACAAAAAAGAAGAA
1 ATTTGTCCAAAGCCACATAACGTTTTAACAAACACCAACAAAAAAGAAGAA
*
646836 ATTTGTCCAAAGCCACATAACGTTTTCACAAATCCACCAACAAAAAAGAAGAA
1 ATTTGTCCAAAGCCACATAACGTTTTAACAAA--CACCAACAAAAAAGAAGAA
646889 ATTTGTC
1 ATTTGTC
646896 GCAAGAAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
50 30 0.55
53 25 0.45
ACGTcount: A:0.47, C:0.23, G:0.09, T:0.21
Consensus pattern (51 bp):
ATTTGTCCAAAGCCACATAACGTTTTAACAAACACCAACAAAAAAGAAGAA
Found at i:650849 original size:18 final size:19
Alignment explanation
Indices: 650802--650853 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
650792 ATGACTAACA
* *
650802 AAATCGCAATGCGATCTCT
1 AAATCGTAACGCGATCTCT
650821 AAATCGTAACGCGATCTCT
1 AAATCGTAACGCGATCTCT
650840 AAAT-GTAACGCGAT
1 AAATCGTAACGCGAT
650854 ATCCATTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 10 0.32
19 21 0.68
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (19 bp):
AAATCGTAACGCGATCTCT
Found at i:650948 original size:21 final size:21
Alignment explanation
Indices: 650905--650945 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
650895 TTGACCATCA
* *
650905 CATTGCGATTTTCGAAATCCG
1 CATTGAGATTTTAGAAATCCG
650926 CATTGAGATTTTAGATAATC
1 CATTGAGATTTTAGA-AATC
650946 GCAATACGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (21 bp):
CATTGAGATTTTAGAAATCCG
Found at i:650994 original size:20 final size:20
Alignment explanation
Indices: 650942--650994 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
650932 GATTTTAGAT
*
650942 AATCGCAATACGAATATGTA
1 AATCGCAATGCGAATATGTA
650962 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
*
650982 AATCGCAACGCGA
1 AATCGCAATGCGA
650995 TAACACGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAATGCGAATATGTA
Found at i:651028 original size:41 final size:40
Alignment explanation
Indices: 650983--651068 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
650973 GAATATGTAA
*
650983 ATCGCAACGCGA-TAACACGTGATCGCAACGCGATTCGGACT
1 ATCGCAACGCGATTAACAC-T-ATCGCAACGAGATTCGGACT
* * *
651024 ATCGCAACGCGATTCAGACTATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTAACACTATCGCAACGAGATTCGGACT
651064 ATCGC
1 ATCGC
651069 GTTGCGATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 23 0.57
41 13 0.32
42 4 0.10
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (40 bp):
ATCGCAACGCGATTAACACTATCGCAACGAGATTCGGACT
Found at i:651029 original size:20 final size:20
Alignment explanation
Indices: 651004--651068 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
650994 ATAACACGTG
*
651004 ATCGCAACGCGATTCGGACT
1 ATCGCAACGCGATTCAGACT
651024 ATCGCAACGCGATTCAGACT
1 ATCGCAACGCGATTCAGACT
* *
651044 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCAGACT
651064 ATCGC
1 ATCGC
651069 GTTGCGATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTCAGACT
Found at i:651306 original size:22 final size:21
Alignment explanation
Indices: 651238--651309 Score: 90
Period size: 22 Copynumber: 3.3 Consensus size: 21
651228 CTACGACGAC
*
651238 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCT-CGGCGAA
* *
651260 ATCCGTCCCCATTTCGGTGAA
1 ATCCGTCCCCATCTCGGCGAA
*
651281 ATCCGTCCCTATCTCTGGCGAA
1 ATCCGTCCCCATCTC-GGCGAA
651303 ATCCGTC
1 ATCCGTC
651310 TATCTCCATC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 18 0.42
22 25 0.58
ACGTcount: A:0.19, C:0.39, G:0.17, T:0.25
Consensus pattern (21 bp):
ATCCGTCCCCATCTCGGCGAA
Found at i:651758 original size:20 final size:20
Alignment explanation
Indices: 651735--651773 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
651725 TGCGATAATT
651735 ATTTTCGTATTGCGATTTTC
1 ATTTTCGTATTGCGATTTTC
*
651755 ATTTTCGTGTTGCGATTTT
1 ATTTTCGTATTGCGATTTT
651774 AAGTTTCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.13, G:0.18, T:0.56
Consensus pattern (20 bp):
ATTTTCGTATTGCGATTTTC
Found at i:651780 original size:20 final size:20
Alignment explanation
Indices: 651737--651780 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
651727 CGATAATTAT
* *
651737 TTTCGTATTGCGATTTTCAT
1 TTTCGTATTGCGATTTTAAG
*
651757 TTTCGTGTTGCGATTTTAAG
1 TTTCGTATTGCGATTTTAAG
651777 TTTC
1 TTTC
651781 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:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTATTGCGATTTTAAG
Found at i:653492 original size:18 final size:18
Alignment explanation
Indices: 653469--653520 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
653459 GATTTACTCG
653469 TAATTTCACTTAGATTAA
1 TAATTTCACTTAGATTAA
653487 TAATTTCACTTAGATTAA
1 TAATTTCACTTAGATTAA
* *
653505 CAATTTCACTTGGATT
1 TAATTTCACTTAGATT
653521 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (18 bp):
TAATTTCACTTAGATTAA
Found at i:653833 original size:20 final size:20
Alignment explanation
Indices: 653772--653930 Score: 119
Period size: 20 Copynumber: 8.6 Consensus size: 20
653762 AGAATAATAG
* *
653772 TCGCAACACGAAAATGATTA
1 TCGCAACGCGAAAATGACTA
* *
653792 TCGCAACACGAAAATGATTA
1 TCGCAACGCGAAAATGACTA
**
653812 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
* *
653832 TCGTAA--CG-AGAT-A--A
1 TCGCAACGCGAAAATGACTA
* *
653846 TCGCAATGCGAAAACGACTA
1 TCGCAACGCGAAAATGACTA
*
653866 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTA
653886 TCGCAACG-G-----GA-TA
1 TCGCAACGCGAAAATGACTA
*
653899 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
653919 TCGCAACGCGAA
1 TCGCAACGCGAA
653931 TTTAGTTTCG
Statistics
Matches: 111, Mismatches: 15, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
13 9 0.08
14 9 0.08
16 3 0.03
17 4 0.04
18 3 0.03
19 3 0.03
20 80 0.72
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:653873 original size:54 final size:53
Alignment explanation
Indices: 653790--653933 Score: 200
Period size: 54 Copynumber: 2.7 Consensus size: 53
653780 CGAAAATGAT
** * *
653790 TATCGCAACACGAAAATGATTATCGCAACGCGAATTTGACTATCGTAACGAGA
1 TATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGA
* * *
653843 TAATCGCAATGCGAAAACGACTATCGCAACGCGGAA-ATGACTATCGCAACGGGA
1 T-ATCGCAATGCGAAAATGACTATCGCAACGC-GAATTTGACTATCGCAACGAGA
653897 TATCGCAATGCGAAAATGACTATCGCAACGCGAATTT
1 TATCGCAATGCGAAAATGACTATCGCAACGCGAATTT
653934 AGTTTCGCGT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
52 3 0.04
53 31 0.39
54 42 0.53
55 3 0.04
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (53 bp):
TATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGA
Found at i:653914 original size:33 final size:33
Alignment explanation
Indices: 653864--653926 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
653854 CGAAAACGAC
*
653864 TATCGCAACGCGGAAATGACTATCGCAACGGGA
1 TATCGCAACGCGAAAATGACTATCGCAACGGGA
*
653897 TATCGCAATGCGAAAATGACTATCGCAACG
1 TATCGCAACGCGAAAATGACTATCGCAACG
653927 CGAATTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (33 bp):
TATCGCAACGCGAAAATGACTATCGCAACGGGA
Found at i:653982 original size:20 final size:20
Alignment explanation
Indices: 653957--654023 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
653947 GATTATCTCA
653957 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
*
653977 TTGCGATAGTTAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
* * ** *
653997 TTGTGATAATCATTTTCGTG
1 TTGCGATAGTCAAATTCGCG
654017 TTGCGAT
1 TTGCGAT
654024 TTTAAGTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:654033 original size:20 final size:20
Alignment explanation
Indices: 654010--654053 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
654000 TGATAATCAT
654010 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
654030 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
654050 TTTC
1 TTTC
654054 AGAAACTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:654629 original size:21 final size:21
Alignment explanation
Indices: 654534--654637 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
654524 GACTCACCTG
* **
654534 TCATCGTTCAAGAGACATCTC
1 TCATCGTTCAAGAGGCCCCTC
*
654555 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
654575 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
654596 CCA-CAGTTCAAGAGGCCCCTG
1 TCATC-GTTCAAGAGGCCCCTC
* *
654617 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
654638 CCAACATTCT
Statistics
Matches: 63, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
20 17 0.27
21 45 0.71
22 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:654630 original size:42 final size:42
Alignment explanation
Indices: 654559--654640 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
654549 CATCTCTATC
654559 GTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACA
1 GTTCAAGAGGCCCCTATCATCCCTCAAGAGGT-CCCTCCCACA
* ** *
654601 GTTCAAGAGGCCCCTGTCATCGTTGAAGAGGTCCCTCCCA
1 GTTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCA
654641 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.21
Consensus pattern (42 bp):
GTTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCACA
Found at i:656209 original size:33 final size:34
Alignment explanation
Indices: 656167--656239 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 34
656157 ATCATATTCG
* *
656167 CGTTGCGATAGTCTAATACACTTTGCGATTTT-T
1 CGTTGCGATAGTCAAATACACGTTGCGATTTTCT
* *
656200 CGTTGCGATAGTCAAATTCCCGTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACACGTTGCGATTTTCT
656234 CGTTGC
1 CGTTGC
656240 ATTACGATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
33 28 0.80
34 7 0.20
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.40
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACACGTTGCGATTTTCT
Found at i:656278 original size:20 final size:20
Alignment explanation
Indices: 656253--656437 Score: 160
Period size: 20 Copynumber: 9.8 Consensus size: 20
656243 ACGATTATCT
656253 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
656273 CGTTGCGATAGTTAAATTCA
1 CGTTGCGATAGTCAAATTCG
**
656293 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
656313 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
*
656327 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
656347 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
656367 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
656381 CGTTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
656401 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
656421 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
656438 GAATGTGTAA
Statistics
Matches: 131, Mismatches: 22, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
14 21 0.16
16 2 0.02
18 2 0.02
19 2 0.02
20 104 0.79
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:656338 original size:54 final size:54
Alignment explanation
Indices: 656275--656429 Score: 249
Period size: 54 Copynumber: 2.9 Consensus size: 54
656265 CAAATTCGCG
656275 TTGCGATAGTTAAATTCACGTTGCGATAGTCATTTTCGCATTGCGATTATCCCA
1 TTGCGATAGTTAAATTCACGTTGCGATAGTCATTTTCGCATTGCGATTATCCCA
* * *
656329 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCG
1 TTGCGATAGTTAAATTCACGTTGCGATAGTCATTTTCGCATTGCGATTATCCCA
* *
656383 TTGCGATA-TTCAAATTCACGTTGCGATAGTCATATTCGCGTTGCGAT
1 TTGCGATAGTT-AAATTCACGTTGCGATAGTCATTTTCGCATTGCGAT
656430 AGTCAAATGA
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 1 0.01
54 92 0.99
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (54 bp):
TTGCGATAGTTAAATTCACGTTGCGATAGTCATTTTCGCATTGCGATTATCCCA
Found at i:656342 original size:74 final size:73
Alignment explanation
Indices: 656200--656437 Score: 239
Period size: 74 Copynumber: 3.2 Consensus size: 73
656190 TGCGATTTTT
* ** * *
656200 CGTTGCGATAGTCAAATTCCCGTTGCGATTTTCTCGTTGCATTACGATTATCTCGTTGCGATAGT
1 CGTTGCGATAGTCAAATTCACGTTGCGATAGTCTCGTTGCATTACGATTATCCCATTGCGATAGT
656265 CAAATTCG
66 CAAATTCG
* * *
656273 CGTTGCGATAGTTAAATTCACGTTGCGATAGTCAT-TTTCGCATTGCGATTATCCCATTGCGATA
1 CGTTGCGATAGTCAAATTCACGTTGCGATAGTC-TCGTT-GCATTACGATTATCCCATTGCGATA
656337 GTCAAATTCG
64 GTCAAATTCG
** * * * * * * * *
656347 CGTTGCGATAGTCATTTTCGCATTGCGATTA-TCCCGTTGCGATATTCAAAT-TCACGTTGCGAT
1 CGTTGCGATAGTCAAATTCACGTTGCGA-TAGTCTCGTTGC-AT-TACGATTATCCCATTGCGAT
*
656410 AGTCATATTCG
63 AGTCAAATTCG
656421 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
656438 GAATGTGTAA
Statistics
Matches: 136, Mismatches: 23, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
73 33 0.24
74 97 0.71
75 6 0.04
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (73 bp):
CGTTGCGATAGTCAAATTCACGTTGCGATAGTCTCGTTGCATTACGATTATCCCATTGCGATAGT
CAAATTCG
Found at i:656623 original size:12 final size:12
Alignment explanation
Indices: 656608--656661 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
656598 AAGCCAGTTG
*
656608 TGATTGGGATTT
1 TGATTGTGATTT
* *
656620 TGATTTTGATTG
1 TGATTGTGATTT
*
656632 TGATTTTGATTT
1 TGATTGTGATTT
656644 TGATTGTGATTT
1 TGATTGTGATTT
656656 TGATTG
1 TGATTG
656662 CCTTTTGCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.17, C:0.00, G:0.26, T:0.57
Consensus pattern (12 bp):
TGATTGTGATTT
Found at i:656624 original size:6 final size:6
Alignment explanation
Indices: 656615--656660 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
656605 TTGTGATTGG
* *
656615 GATTTT GATTTT GATTGT GATTTT GATTTT GATTGT GATTTT GATT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT GATT
656661 GCCTTTTGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.00, G:0.22, T:0.61
Consensus pattern (6 bp):
GATTTT
Found at i:656631 original size:18 final size:18
Alignment explanation
Indices: 656608--656660 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
656598 AAGCCAGTTG
*
656608 TGATTGGGATTTTGATTT
1 TGATTGTGATTTTGATTT
656626 TGATTGTGATTTTGATTT
1 TGATTGTGATTTTGATTT
656644 TGATTGTGATTTTGATT
1 TGATTGTGATTTTGATT
656661 GCCTTTTGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.00, G:0.25, T:0.58
Consensus pattern (18 bp):
TGATTGTGATTTTGATTT
Found at i:658951 original size:24 final size:24
Alignment explanation
Indices: 658917--658970 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
658907 CTGAAACATC
658917 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
658941 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
658965 ATCAAA
1 ATCAAA
658971 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:659821 original size:20 final size:20
Alignment explanation
Indices: 659791--659877 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
659781 AATTAAGTGA
*
659791 TGCGTTAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
*
659811 TGTGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
**
659831 TGCGATCACGT-ATTATCGCGT
1 TGCGAT-A-GTCAGAATCGCGT
* *
659852 TGCGATAGTCCGAATTGCGT
1 TGCGATAGTCAGAATCGCGT
659872 TGCGAT
1 TGCGAT
659878 TTACATATTC
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
19 2 0.04
20 36 0.65
21 15 0.27
22 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.31
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:659978 original size:20 final size:20
Alignment explanation
Indices: 659924--659971 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
659914 GCGGATTTCA
659924 AAAATCGCAATGCGATGGTC
1 AAAATCGCAATGCGATGGTC
659944 AAAATCGCAATGCGATGGTC
1 AAAATCGCAATGCGATGGTC
659964 AAAATCGC
1 AAAATCGC
659972 GTTGCGAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAATGCGATGGTC
Found at i:660016 original size:20 final size:19
Alignment explanation
Indices: 659992--660038 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
659982 TGGAAACTGA
*
659992 ATTGCGATAATGGAGATCGC
1 ATTGCGAT-ATAGAGATCGC
* *
660012 GTTGCGATTTAGAGATCGC
1 ATTGCGATATAGAGATCGC
660031 ATTGCGAT
1 ATTGCGAT
660039 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
ATTGCGATATAGAGATCGC
Found at i:660028 original size:19 final size:19
Alignment explanation
Indices: 660004--660040 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
659994 TGCGATAATG
*
660004 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
660023 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
660041 TGTTGGTCAT
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:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:668044 original size:21 final size:21
Alignment explanation
Indices: 668020--668059 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
668010 ATAAATGCAT
*
668020 CGAAGTGCCACGTAGAATTAC
1 CGAAATGCCACGTAGAATTAC
*
668041 CGAAATGCCGCGTAGAATT
1 CGAAATGCCACGTAGAATT
668060 GCACCGTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (21 bp):
CGAAATGCCACGTAGAATTAC
Found at i:668786 original size:45 final size:45
Alignment explanation
Indices: 668735--668834 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 45
668725 GCACTATCTA
* * * *
668735 TGCATCGGTACA-TAAATCCCATTCGATATTTTTATTTTAAGGGGG
1 TGCATCGATACACT-AATCCAATTCGATATTTTTATTTTAAAGGAG
* ** *
668780 TGCATCGATACACTGATGGAATTCGATGTTTTTATTTTAAAGGAG
1 TGCATCGATACACTAATCCAATTCGATATTTTTATTTTAAAGGAG
668825 TGCATCGATA
1 TGCATCGATA
668835 TGCTTCATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 45 0.98
46 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (45 bp):
TGCATCGATACACTAATCCAATTCGATATTTTTATTTTAAAGGAG
Found at i:674635 original size:21 final size:20
Alignment explanation
Indices: 674608--674647 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
674598 TCCCCTTCAA
* *
674608 AGGGGGAATCGGTTCCCTCT
1 AGGGGGGATCGATTCCCTCT
674628 AGGGGGGATCGATTCCCTCT
1 AGGGGGGATCGATTCCCTCT
674648 GCACCAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.25, G:0.35, T:0.25
Consensus pattern (20 bp):
AGGGGGGATCGATTCCCTCT
Found at i:682580 original size:62 final size:64
Alignment explanation
Indices: 682466--682585 Score: 154
Period size: 62 Copynumber: 1.9 Consensus size: 64
682456 ACATAAATCC
** * * * *
682466 CATTCGATGTTTGTATTTTAAGGGCGTTCATCGATGCACTACTTGTGCATCGATACACTGATGG
1 CATTCGATGTTTGTATTTTAAAAGAGTGCATCGATACACTACATGTGCATCGATACACTGATGG
* *
682530 CATTCGATGTTT-T-TTTTAAAAGAGTGCATCGATACACTTCATGTTCATCGATACAC
1 CATTCGATGTTTGTATTTTAAAAGAGTGCATCGATACACTACATGTGCATCGATACAC
682586 CTTGAATAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 35 0.73
63 1 0.02
64 12 0.25
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (64 bp):
CATTCGATGTTTGTATTTTAAAAGAGTGCATCGATACACTACATGTGCATCGATACACTGATGG
Found at i:687803 original size:18 final size:18
Alignment explanation
Indices: 687771--687805 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
687761 TCAAAATTAA
687771 ATATTATTTTAAATAATT
1 ATATTATTTTAAATAATT
687789 ATATT-TTTTACAATAAT
1 ATATTATTTTA-AATAAT
687806 AACGTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTATTTTAAATAATT
Found at i:689639 original size:20 final size:20
Alignment explanation
Indices: 689614--689653 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
689604 GCAGCGCTGG
689614 TCTTATTGCCATTCTATAAA
1 TCTTATTGCCATTCTATAAA
689634 TCTTATTGCCATTCTATAAA
1 TCTTATTGCCATTCTATAAA
689654 ATTTCCCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (20 bp):
TCTTATTGCCATTCTATAAA
Found at i:690091 original size:15 final size:15
Alignment explanation
Indices: 690050--690091 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
690040 TAACCATCAC
*
690050 TAAAAAGTCATCCTCT
1 TAAAAA-TCATTCTCT
690066 TAAAAATCATTCTCT
1 TAAAAATCATTCTCT
690081 TAAAAATCATT
1 TAAAAATCATT
690092 TATTATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (15 bp):
TAAAAATCATTCTCT
Found at i:690101 original size:15 final size:15
Alignment explanation
Indices: 690050--690102 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
690040 TAACCATCAC
* *
690050 TAAAAAGTCATCCTCT
1 TAAAAA-TCATTCTAT
*
690066 TAAAAATCATTCTCT
1 TAAAAATCATTCTAT
690081 TAAAAATCATT-TAT
1 TAAAAATCATTCTAT
690095 TATAAAAT
1 TA-AAAAT
690103 GTTATAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 4 0.12
15 24 0.71
16 6 0.18
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (15 bp):
TAAAAATCATTCTAT
Found at i:699862 original size:2 final size:2
Alignment explanation
Indices: 699850--699898 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
699840 AAGGTTGAGA
699850 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
699890 A- AT AT AT AT
1 AT AT AT AT AT
699899 GAGGTCATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:700780 original size:17 final size:18
Alignment explanation
Indices: 700758--700798 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
700748 CTAAGTTCTT
*
700758 TTCTCTTTACAT-TTTTG
1 TTCTCTTTACATCTTTTA
*
700775 TTCTCTTTTCATCTTTTA
1 TTCTCTTTACATCTTTTA
700793 TTCTCT
1 TTCTCT
700799 CTCTCTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.10, C:0.22, G:0.02, T:0.66
Consensus pattern (18 bp):
TTCTCTTTACATCTTTTA
Found at i:700818 original size:16 final size:18
Alignment explanation
Indices: 700786--700818 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
700776 TCTCTTTTCA
700786 TCTTTTATTCTCTCTCTC
1 TCTTTTATTCTCTCTCTC
700804 TCTTTT-TTC-CTCTCT
1 TCTTTTATTCTCTCTCT
700819 GTTCGACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (18 bp):
TCTTTTATTCTCTCTCTC
Found at i:700870 original size:17 final size:17
Alignment explanation
Indices: 700848--700881 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
700838 TTTTTTTCTA
*
700848 TTCGAATGGGATCCTTT
1 TTCGAATCGGATCCTTT
*
700865 TTCGAATCTGATCCTTT
1 TTCGAATCGGATCCTTT
700882 CCTTTTATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.44
Consensus pattern (17 bp):
TTCGAATCGGATCCTTT
Found at i:701505 original size:3 final size:3
Alignment explanation
Indices: 701499--701576 Score: 142
Period size: 3 Copynumber: 26.7 Consensus size: 3
701489 TAATAACAGA
701499 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
701546 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
701577 ACAATTAAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.05
3 69 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:710705 original size:18 final size:19
Alignment explanation
Indices: 710684--710719 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
710674 GGTTTGTTGG
710684 GTTGTTGTT-CTCTGTTTT
1 GTTGTTGTTGCTCTGTTTT
*
710702 GTTGTTTTTGCTCTGTTT
1 GTTGTTGTTGCTCTGTTT
710720 CTGTCTCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.11, G:0.22, T:0.67
Consensus pattern (19 bp):
GTTGTTGTTGCTCTGTTTT
Found at i:711147 original size:3 final size:3
Alignment explanation
Indices: 711121--711187 Score: 107
Period size: 3 Copynumber: 21.7 Consensus size: 3
711111 TTTGGGCTTT
*
711121 ATA ATA TTA ATAA ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA AT-A ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
711168 ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
711188 GGGTAAAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 54 0.90
4 6 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:713117 original size:21 final size:22
Alignment explanation
Indices: 713070--713130 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
713060 TAAATTAAGA
*
713070 TTTATGGTTTACAGG-TTATGAG
1 TTTATAGTTTA-AGGTTTATGAG
*
713092 ATTATAGTTTAAGGTTTAT-AG
1 TTTATAGTTTAAGGTTTATGAG
* *
713113 TTTATAATTTAGGGTTTA
1 TTTATAGTTTAAGGTTTA
713131 GGGTTAAGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 20 0.61
22 13 0.39
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (22 bp):
TTTATAGTTTAAGGTTTATGAG
Found at i:717011 original size:21 final size:21
Alignment explanation
Indices: 716986--717031 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
716976 CTGAAAATAT
*
716986 TAAAAATATTAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
717007 TAAAAATAATAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
717028 TAAA
1 TAAA
717032 TTTTTATCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAA
Found at i:717612 original size:29 final size:29
Alignment explanation
Indices: 717538--717622 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 29
717528 TTAAAATTGT
*
717538 TAAATTTAAATT-CTAAATAATATTTTATA
1 TAAA-TTAAATTATTAAATAATATTTTATA
* ** *
717567 AAATATCTAAACAATTAAATAATTTTTTATA
1 TAA-AT-TAAATTATTAAATAATATTTTATA
717598 TAAATTAAATTATTAAATTAATATT
1 TAAATTAAATTATTAAA-TAATATT
717623 ATAAGTGGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
29 13 0.30
30 13 0.30
31 17 0.40
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAATTAAATTATTAAATAATATTTTATA
Found at i:717623 original size:14 final size:14
Alignment explanation
Indices: 717593--717625 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
717583 AAATAATTTT
717593 TTATATAAATTAAA
1 TTATATAAATTAAA
717607 TTAT-TAAATTAATA
1 TTATATAAATTAA-A
717621 TTATA
1 TTATA
717626 AGTGGAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATATAAATTAAA
Found at i:717826 original size:21 final size:23
Alignment explanation
Indices: 717800--717854 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
717790 ATATTGTTAT
717800 GTATCGATA-TAT-TTTTATAAA
1 GTATCGATATTATCTTTTATAAA
*
717821 GTATCGATACATTTTCTTTTATAAA
1 GTATCGAT--ATTATCTTTTATAAA
717846 GTATCGATA
1 GTATCGATA
717855 CTTTATAGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 8 0.28
23 2 0.07
24 2 0.07
25 17 0.59
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (23 bp):
GTATCGATATTATCTTTTATAAA
Found at i:718195 original size:147 final size:146
Alignment explanation
Indices: 717940--718712 Score: 1062
Period size: 147 Copynumber: 5.2 Consensus size: 146
717930 CAACATATAT
* *
717940 GGTAGGTAGTTTAATGTAATAGGTAGTGCCTATTTTTTTACCGTTTACATTATTAGCAACCTTCA
1 GGTAGGTAGTTTAATGTAATAGGTAGCGACTATTTTTTTACCGTTTACATTATTAGCAACCTTCA
* * * *
718005 AAAAAATCGGTAGGTATTTTAATATAATAGGTAGCGCCTATTTTTTTTACAGTGTACATTATTAG
66 AAAAAATCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAG
*
718070 CAACCTTCAAAAAACC
131 CAACCTTAAAAAAACC
* * *
718086 GGTAGGTATTTTAATGTAATAGGTAGCGACTATTTTTTTTACCGTTTACATTATTAACAGCCTTC
1 GGTAGGTAGTTTAATGTAATAGGTAGCGACTA-TTTTTTTACCGTTTACATTATTAGCAACCTTC
* **
718151 AAAAAAATTGGTAGGTAGTTTAATGTAATAAATAGCGCCTATTTTTTTTACCGTTTACATTATTA
65 AAAAAAATCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTA
*
718216 GCAACCTTAAAAAAAAC
130 GCAACCTTAAAAAAACC
* * * * *
718233 AGTAGGTATTTTAATGTAATAGGTAGCGCATATATTTTTTTTATCGTTTACATTATTAACAACCT
1 GGTAGGTAGTTTAATGTAATAGGTAGCG-A-CTA-TTTTTTTACCGTTTACATTATTAGCAACCT
* *
718298 TCAAAAAAATCGGTAGGTATTTTAATGTAATAGGTAGCGTCTATTTTATTTTACCGTTTACATTA
63 TCAAAAAAATCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTT-TTTTACCGTTTACATTA
** * *
718363 TTAATAATCTTTAAACAAACC
127 TTAGCAA-CCTTAAAAAAACC
* * * *
718384 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTA-TTTTTTACTGTTTATATTATTAGCAACCTTAA
1 GGTAGGTAGTTTAATGTAATAGGTAGCGACTATTTTTTTACCGTTTACATTATTAGCAACCTTCA
* * * *
718448 AAAAAACCGGTAGGTAATTTAATGTAATAGGTAGCGCATATTTTTTTTACCGTTTACTTTATTAG
66 AAAAAATCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAG
* *
718513 TAACCCTAAAAAAACC
131 CAACCTTAAAAAAACC
* * * * *
718529 GATAGATAGTTTAATGTAATAGGTAACGACTATTGTTTTACCGTTTACATTATTAGCAACCTTAA
1 GGTAGGTAGTTTAATGTAATAGGTAGCGACTATTTTTTTACCGTTTACATTATTAGCAACCTTCA
*
718594 AAAAAACCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTA
66 AAAAAATCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTA-TTTTTTTTACCGTTTACATTATTA
718659 GCAACCTTAAAAAAAACC
130 GCAACCTT-AAAAAAACC
* * * *
718677 GGTAGATATTTTAATATAATAGGTAGCGCCTATTTT
1 GGTAGGTAGTTTAATGTAATAGGTAGCGACTATTTT
718713 ATATTTCCAG
Statistics
Matches: 555, Mismatches: 64, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
145 38 0.07
146 118 0.21
147 226 0.41
148 40 0.07
149 75 0.14
150 22 0.04
151 36 0.06
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.39
Consensus pattern (146 bp):
GGTAGGTAGTTTAATGTAATAGGTAGCGACTATTTTTTTACCGTTTACATTATTAGCAACCTTCA
AAAAAATCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAG
CAACCTTAAAAAAACC
Found at i:718706 original size:75 final size:74
Alignment explanation
Indices: 717940--718712 Score: 1047
Period size: 73 Copynumber: 10.5 Consensus size: 74
717930 CAACATATAT
* *
717940 GGTAGGTAGTTTAATGTAATAGGTAGTGCCTA-TTTTTTTACCGTTTACATTATTAGCAACCTTC
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
*
718004 AAAAAAATC
66 AAAAAAACC
* * * *
718013 GGTAGGTATTTTAATATAATAGGTAGCGCCTATTTTTTTTACAGTGTACATTATTAGCAACCTT-
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
*
718077 CAAAAAACC
66 AAAAAAACC
* * * * *
718086 GGTAGGTATTTTAATGTAATAGGTAGCGACTATTTTTTTTACCGTTTACATTATTAACAGCCTTC
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
**
718151 AAAAAAATT
66 AAAAAAACC
**
718160 GGTAGGTAGTTTAATGTAATAAATAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
718225 AAAAAAA-C
66 AAAAAAACC
* * * * *
718233 AGTAGGTATTTTAATGTAATAGGTAGCGCATATATTTTTTTTATCGTTTACATTATTAACAACCT
1 GGTAGGTAGTTTAATGTAATAGGTAGCGC--CTATTTTTTTTACCGTTTACATTATTAGCAACCT
* *
718298 TCAAAAAAATC
64 TAAAAAAAACC
* * ** *
718309 GGTAGGTATTTTAATGTAATAGGTAGCGTCTATTTTATTTTACCGTTTACATTATTAATAATCTT
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTT-TTTTACCGTTTACATTATTAGCAACCTT
* *
718374 TAAACAAACC
65 AAAAAAAACC
* *
718384 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTA--TTTTTTACTGTTTATATTATTAGCAACCTTA
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
718447 AAAAAAACC
66 AAAAAAACC
* * * * *
718456 GGTAGGTAATTTAATGTAATAGGTAGCGCATATTTTTTTTACCGTTTACTTTATTAGTAACCCT-
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
718520 AAAAAAACC
66 AAAAAAACC
* * * * *
718529 GATAGATAGTTTAATGTAATAGGTAACGACTA-TTGTTTTACCGTTTACATTATTAGCAACCTTA
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
718593 AAAAAAACC
66 AAAAAAACC
718602 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAACCTT
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTA-TTTTTTTTACCGTTTACATTATTAGCAACCTT
718667 AAAAAAAACC
65 AAAAAAAACC
* * *
718677 GGTAGATATTTTAATATAATAGGTAGCGCCTATTTT
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTT
718713 ATATTTCCAG
Statistics
Matches: 614, Mismatches: 75, Indels: 21
0.86 0.11 0.03
Matches are distributed among these distances:
72 88 0.14
73 193 0.31
74 135 0.22
75 170 0.28
76 28 0.05
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.39
Consensus pattern (74 bp):
GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
AAAAAAACC
Found at i:719700 original size:21 final size:21
Alignment explanation
Indices: 719674--719717 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
719664 CGTCTCCGAA
719674 TTCGAGCAACATAATCGAATT
1 TTCGAGCAACATAATCGAATT
719695 TTCGAGCAACATAATCGAATT
1 TTCGAGCAACATAATCGAATT
719716 TT
1 TT
719718 TTTTACCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (21 bp):
TTCGAGCAACATAATCGAATT
Found at i:727727 original size:19 final size:17
Alignment explanation
Indices: 727699--727745 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
727689 GTTTAAAAGT
727699 ATCGATACTTGTAGAAAAC
1 ATCGATACTT-TAG-AAAC
* *
727718 ATCGAAACTTTTGAAAC
1 ATCGATACTTTAGAAAC
727735 ATCGATACTTT
1 ATCGATACTTT
727746 TGCAGGAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 14 0.56
18 2 0.08
19 9 0.36
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (17 bp):
ATCGATACTTTAGAAAC
Found at i:727736 original size:17 final size:17
Alignment explanation
Indices: 727714--727747 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
727704 TACTTGTAGA
727714 AAACATCGAAACTTTTG
1 AAACATCGAAACTTTTG
*
727731 AAACATCGATACTTTTG
1 AAACATCGAAACTTTTG
727748 CAGGAGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (17 bp):
AAACATCGAAACTTTTG
Found at i:728591 original size:15 final size:15
Alignment explanation
Indices: 728572--728617 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
728562 CTATGGTGTT
728572 ACATTTAATGGTATC
1 ACATTTAATGGTATC
*
728587 GCATTTAATGGTATC
1 ACATTTAATGGTATC
728602 ACATTTAATGGTATC
1 ACATTTAATGGTATC
728617 A
1 A
728618 AAGCGTCCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (15 bp):
ACATTTAATGGTATC
Found at i:731040 original size:45 final size:45
Alignment explanation
Indices: 730976--731258 Score: 379
Period size: 45 Copynumber: 6.0 Consensus size: 45
730966 TTAAATATGC
*
730976 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
731021 AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTGTATTGGCA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
731066 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
731111 AAATAAGCTTACGAGCTTATGGAATAAATGGTAA-TATATTAGTAAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT--A
731157 ATAAGCTCGTAAGCTTATGGACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 A-AA-----TAAGC-T-T--ACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
731212 AAATAAGCTTACGAGCTTATGGGATTAAATGGTTAGTATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
731258 A
1 A
731259 GAAATGTTAT
Statistics
Matches: 213, Mismatches: 11, Indels: 27
0.85 0.04 0.11
Matches are distributed among these distances:
44 8 0.04
45 127 0.60
46 26 0.12
47 3 0.01
48 1 0.00
49 5 0.02
52 5 0.02
53 1 0.00
54 3 0.01
55 2 0.01
56 24 0.11
57 8 0.04
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:731230 original size:57 final size:55
Alignment explanation
Indices: 731121--731233 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 55
731111 AAATAAGCTT
731121 ACGAGCTTATGGAATAAATGGTAATATATTAGTAAAATAAGCTCGTAAGCTTATGG
1 ACGAGCTTATGGAATAAATGGTAATATATTAGTAAAATAAGCTCG-AAGCTTATGG
*
731177 ACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACG-AGCTTATGG
1 ACGAGCTTATGGAATAAATGGTAA-TATATTAGTAAAATAAGC-T-CGAAGCTTATGG
731234 GATTAAATGG
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
56 24 0.45
57 26 0.49
58 1 0.02
59 2 0.04
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (55 bp):
ACGAGCTTATGGAATAAATGGTAATATATTAGTAAAATAAGCTCGAAGCTTATGG
Found at i:731686 original size:21 final size:21
Alignment explanation
Indices: 731660--731700 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
731650 TTGAAATTAC
*
731660 TGTAGCAGTGCATCGGTACAT
1 TGTAGCAGTGCATCGATACAT
731681 TGTAGCAGTGCATCGATACA
1 TGTAGCAGTGCATCGATACA
731701 CAGTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (21 bp):
TGTAGCAGTGCATCGATACAT
Found at i:734137 original size:30 final size:30
Alignment explanation
Indices: 734102--734197 Score: 92
Period size: 30 Copynumber: 3.1 Consensus size: 30
734092 CATAAGACCT
734102 AAAAAATATAATATAAGAAAA-AAAAAGGAA
1 AAAAAATATAA-ATAAGAAAAGAAAAAGGAA
*
734132 AAAAAA-ATAAA-AATAAAAAGATAACGAAGG-A
1 AAAAAATATAAATAA-GAAAAGA-AA--AAGGAA
*
734163 AAAAAATATAGAAAAAGAAAAGAAAAAGGAA
1 AAAAAATATA-AATAAGAAAAGAAAAAGGAA
734194 AAAA
1 AAAA
734198 CGAGAGATGA
Statistics
Matches: 55, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
27 2 0.04
28 5 0.09
29 5 0.09
30 12 0.22
31 12 0.22
32 9 0.16
33 8 0.15
34 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.12, T:0.09
Consensus pattern (30 bp):
AAAAAATATAAATAAGAAAAGAAAAAGGAA
Found at i:734162 original size:32 final size:30
Alignment explanation
Indices: 734102--734197 Score: 99
Period size: 32 Copynumber: 3.1 Consensus size: 30
734092 CATAAGACCT
*
734102 AAAAAATATAATATAAGAAAA-AAAAAGGAAA
1 AAAAAATAGAA-A-AAGAAAAGAAAAAGGAAA
734133 AAAAAATA-AAAATA-AAAAGATAACGAAGGAAA
1 AAAAAATAGAAAA-AGAAAAGA-AA--AAGGAAA
*
734165 AAAATATAGAAAAAGAAAAGAAAAAGGAAA
1 AAAAAATAGAAAAAGAAAAGAAAAAGGAAA
734195 AAA
1 AAA
734198 CGAGAGATGA
Statistics
Matches: 57, Mismatches: 1, Indels: 15
0.78 0.01 0.21
Matches are distributed among these distances:
28 5 0.09
29 3 0.05
30 14 0.25
31 8 0.14
32 17 0.30
33 10 0.18
ACGTcount: A:0.77, C:0.01, G:0.12, T:0.09
Consensus pattern (30 bp):
AAAAAATAGAAAAAGAAAAGAAAAAGGAAA
Found at i:739594 original size:24 final size:24
Alignment explanation
Indices: 739567--739620 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
739557 TCAGGGGTCG
* *
739567 GTTGTGCGTACCCACATACGCTCA
1 GTTGCGCGTACCCACAGACGCTCA
*
739591 GTTGCGTGTACCCACAGACGCTCA
1 GTTGCGCGTACCCACAGACGCTCA
*
739615 ATTGCG
1 GTTGCG
739621 TAGTAAGATT
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:0.20, C:0.31, G:0.24, T:0.24
Consensus pattern (24 bp):
GTTGCGCGTACCCACAGACGCTCA
Found at i:739621 original size:24 final size:24
Alignment explanation
Indices: 739574--739621 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
739564 TCGGTTGTGC
* *
739574 GTACCCACATACGCTCAGTTGCGT
1 GTACCCACAGACGCTCAATTGCGT
739598 GTACCCACAGACGCTCAATTGCGT
1 GTACCCACAGACGCTCAATTGCGT
739622 AGTAAGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (24 bp):
GTACCCACAGACGCTCAATTGCGT
Found at i:742029 original size:19 final size:19
Alignment explanation
Indices: 742005--742057 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
741995 AAAATGTTTA
742005 AAAGTATCGATACTTGTAG
1 AAAGTATCGATACTTGTAG
* * *
742024 AAAGTATCGAAACTTTTGG
1 AAAGTATCGATACTTGTAG
*
742043 AGGAGTATCGATACT
1 A-AAGTATCGATACT
742058 CTTGGGCTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACTTGTAG
Found at i:742062 original size:20 final size:20
Alignment explanation
Indices: 742026--742077 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
742016 ACTTGTAGAA
* *
742026 AGTATCGAAACTTTTGGAG-G
1 AGTATCGATACTCTTGG-GCG
*
742046 AGTATCGATACTCTTGGGCT
1 AGTATCGATACTCTTGGGCG
742066 AGTATCGATACT
1 AGTATCGATACT
742078 TTCAGTTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTCTTGGGCG
Found at i:743874 original size:36 final size:36
Alignment explanation
Indices: 743785--743862 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
743775 TGACTTTTCT
* * *
743785 CTTTCCTCGAATCATCAGTCACCTTCTGGTTCACCG
1 CTTTCCACGAATCATAAGTCACCTCCTGGTTCACCG
743821 CTTTCCACGAATCATAAGTCACCTCCTGGTTCACCG
1 CTTTCCACGAATCATAAGTCACCTCCTGGTTCACCG
743857 CTTTCC
1 CTTTCC
743863 TCGTGACATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.18, C:0.37, G:0.13, T:0.32
Consensus pattern (36 bp):
CTTTCCACGAATCATAAGTCACCTCCTGGTTCACCG
Found at i:743880 original size:36 final size:36
Alignment explanation
Indices: 743785--743881 Score: 115
Period size: 36 Copynumber: 2.7 Consensus size: 36
743775 TGACTTTTCT
* * * *
743785 CTTTCCTCGAATCATCAGTCACCTTCTGGTTCACCG
1 CTTTCCACGAATCATAAGCCACCTCCTGGTTCACCG
*
743821 CTTTCCACGAATCATAAGTCACCTCCTGGTTCACCG
1 CTTTCCACGAATCATAAGCCACCTCCTGGTTCACCG
* *
743857 CTTTCCTCGTGA-CATAAGCCACCTC
1 CTTTCCACG-AATCATAAGCCACCTC
743882 TCTCACTCTC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 53 0.98
37 1 0.02
ACGTcount: A:0.20, C:0.37, G:0.13, T:0.30
Consensus pattern (36 bp):
CTTTCCACGAATCATAAGCCACCTCCTGGTTCACCG
Found at i:744796 original size:31 final size:31
Alignment explanation
Indices: 744726--744798 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
744716 GAGTATTGTT
* *
744726 AAGCTCGAATCGACTCGAAAACTTTAAAATG
1 AAGCTCGACTCGACTCGAAAACTCTAAAATG
* *
744757 AAGTTCGACTCGACTCGAAAACTCTGAAATGG
1 AAGCTCGACTCGACTCGAAAACTCTAAAAT-G
744789 AA-CTCGACTC
1 AAGCTCGACTC
744799 AAAAACTCGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 33 0.92
32 3 0.08
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (31 bp):
AAGCTCGACTCGACTCGAAAACTCTAAAATG
Found at i:747898 original size:19 final size:20
Alignment explanation
Indices: 747870--747913 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
747860 TCCTTTCATT
*
747870 TTTTTTGTAT-TTATTATAC
1 TTTTTAGTATCTTATTATAC
747889 TTTTTAGTATCTTATTATAC
1 TTTTTAGTATCTTATTATAC
747909 TTTTT
1 TTTTT
747914 TATATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTAGTATCTTATTATAC
Found at i:757736 original size:28 final size:27
Alignment explanation
Indices: 757700--757761 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
757690 AATTACAAAT
* *
757700 ATATAAAATTCA-TGGTCAAAATGAAA
1 ATATAAAAATCAGTGATCAAAATGAAA
* *
757726 ATTATAAAAATCAGTGATTAAAATGTAA
1 A-TATAAAAATCAGTGATCAAAATGAAA
757754 ATATAAAA
1 ATATAAAA
757762 CCTAAAGGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 1 0.03
27 17 0.57
28 12 0.40
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (27 bp):
ATATAAAAATCAGTGATCAAAATGAAA
Found at i:759770 original size:106 final size:104
Alignment explanation
Indices: 759512--759870 Score: 424
Period size: 106 Copynumber: 3.5 Consensus size: 104
759502 GCGAAGGGGC
* *
759512 TTCCCAATTTCATAACCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCT
1 TTCCCAATTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCT
* * * *
759577 CAACTTCACGACGAAGGGGCGGTTGATTGTCAACAAACA
66 CAACTTCAAGGCGAAGGGGCGGCTGACTGTCAACAAACA
* *** * *
759616 -----ACTTTCAGAGTTAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCT
1 TTCCCAATTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCT
* * *
759676 TAACTTCATGGTGAAGGGGCGGCTGACTGTCAACAAACGA
66 CAACTTCAAGGCGAAGGGGCGGCTGACTGTCAACAAAC-A
*
759716 TTCCCCAATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGC
1 TT-CCCAATTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGC
* *
759781 TCAACTTCAAGGCGATGGGGCGGCTGACTGTCAACAAATAA
65 TCAACTTCAAGGCGAAGGGGCGGCTGACTGTCAACAAA-CA
* * * * *
759822 TTTTCCAGTTCCAGAACTAATTTCAACTTCAC-GACGAATGATATTGGAC
1 -TTCCCAATTTCAGAACCAATTTCAACTTCACAG-CGAAGGATATTGGAC
759871 TTGGAGCAAT
Statistics
Matches: 214, Mismatches: 31, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
99 84 0.39
100 1 0.00
105 1 0.00
106 126 0.59
107 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (104 bp):
TTCCCAATTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCT
CAACTTCAAGGCGAAGGGGCGGCTGACTGTCAACAAACA
Found at i:759947 original size:35 final size:35
Alignment explanation
Indices: 759899--760019 Score: 92
Period size: 35 Copynumber: 3.4 Consensus size: 35
759889 CTTGGATTTT
*
759899 AACTTCACGACGAAGGATATCCAATTCTCAGGCTC
1 AACTTCACAACGAAGGATATCCAATTCTCAGGCTC
* * *
759934 AACTTCACAACGAATGG---GCC-A--CCCACGGTTTC
1 AACTTCACAACGAA-GGATATCCAATTCTCA-GG-CTC
759966 AACTTCATAACACGACGAAGGATATCCAATTCTCAGGCTC
1 AACTTC---ACA--ACGAAGGATATCCAATTCTCAGGCTC
760006 AACTTCACAACGAA
1 AACTTCACAACGAA
760020 TGGGCCACCC
Statistics
Matches: 65, Mismatches: 7, Indels: 28
0.65 0.07 0.28
Matches are distributed among these distances:
30 3 0.05
31 2 0.03
32 9 0.14
33 2 0.03
35 21 0.32
36 4 0.06
37 8 0.12
39 2 0.03
40 9 0.14
41 2 0.03
42 3 0.05
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.21
Consensus pattern (35 bp):
AACTTCACAACGAAGGATATCCAATTCTCAGGCTC
Found at i:760021 original size:72 final size:72
Alignment explanation
Indices: 759904--760049 Score: 292
Period size: 72 Copynumber: 2.0 Consensus size: 72
759894 ATTTTAACTT
759904 CACGACGAAGGATATCCAATTCTCAGGCTCAACTTCACAACGAATGGGCCACCCACGGTTTCAAC
1 CACGACGAAGGATATCCAATTCTCAGGCTCAACTTCACAACGAATGGGCCACCCACGGTTTCAAC
759969 TTCATAA
66 TTCATAA
759976 CACGACGAAGGATATCCAATTCTCAGGCTCAACTTCACAACGAATGGGCCACCCACGGTTTCAAC
1 CACGACGAAGGATATCCAATTCTCAGGCTCAACTTCACAACGAATGGGCCACCCACGGTTTCAAC
760041 TTCATAA
66 TTCATAA
760048 CA
1 CA
760050 AAGGGAATCG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.32, C:0.31, G:0.16, T:0.21
Consensus pattern (72 bp):
CACGACGAAGGATATCCAATTCTCAGGCTCAACTTCACAACGAATGGGCCACCCACGGTTTCAAC
TTCATAA
Found at i:761665 original size:19 final size:20
Alignment explanation
Indices: 761643--761687 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
761633 CCTTTCCGTT
761643 TTTTTTGTAT-TTATTATAC
1 TTTTTTGTATCTTATTATAC
*
761662 TTTTTAGTATCTTATTATAC
1 TTTTTTGTATCTTATTATAC
761682 TTTTTT
1 TTTTTT
761688 TATATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTTTGTATCTTATTATAC
Found at i:765368 original size:14 final size:15
Alignment explanation
Indices: 765343--765374 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
765333 TATTAGTGAC
765343 TAAAACATAAATAAA
1 TAAAACATAAATAAA
765358 TAAAA-ATAAATAAA
1 TAAAACATAAATAAA
765372 TAA
1 TAA
765375 TTAAATTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (15 bp):
TAAAACATAAATAAA
Found at i:765513 original size:29 final size:29
Alignment explanation
Indices: 765479--765554 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 29
765469 AAACTATAGA
* *
765479 ATTAAATTGCAAAATATATAAAATTCA-TG
1 ATTAAAATG-AAAATATATAAAAATCAGTG
*
765508 GTTAAAAATGAAAAT-TATAAAAATCAGTG
1 ATT-AAAATGAAAATATATAAAAATCAGTG
765537 ATTAAAATGTAAAATATA
1 ATTAAAATG-AAAATATA
765555 AAACCTAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 16 0.41
29 16 0.41
30 7 0.18
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (29 bp):
ATTAAAATGAAAATATATAAAAATCAGTG
Found at i:766774 original size:3 final size:3
Alignment explanation
Indices: 766760--766836 Score: 91
Period size: 3 Copynumber: 25.0 Consensus size: 3
766750 ATTGGGTTTG
* * * * *
766760 TAA TAT TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA TATT TAT TTA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A TAA TAA
766807 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
766837 AGAGACAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
3 60 0.94
4 4 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:767441 original size:177 final size:177
Alignment explanation
Indices: 767145--767535 Score: 622
Period size: 177 Copynumber: 2.2 Consensus size: 177
767135 TAAAATTTAA
* *
767145 TTGAAAACATCCTGCACTGAAGGTCTTATGGACGGCCCGCAAGACTTACAAATCAAGAAACTCTC
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGCAAGACTTACAAATCAAGAAACCCTC
* *
767210 GAAGGCTTAGTTTTTTTGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCTT
66 GAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCTT
* *
767275 TTGAGATAATTAGTAAACCCCCGAAGGATTGGTTTCTAAAATCTCAT
131 TTGAGATAATTAGTAAACCCCCGAAGGATTGATTTCTAAAATATCAT
* * * * *
767322 TTGAAAACATCCTGCACTGAATGTCTTATGGATGGCCCGTAGGACTTATAAATCAAGATACCCTC
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGCAAGACTTACAAATCAAGAAACCCTC
* * *
767387 GGAGGCTTAGTTTCTTAGTTGTCAAGGAACTCCTTTGTTAGGCTTAGCTTCCTTTAACAGCTCTT
66 GAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCTT
*
767452 TTGAGATAATTAGTAAACCCCCGAAGGTTTGATTTCTAAAATATCAT
131 TTGAGATAATTAGTAAACCCCCGAAGGATTGATTTCTAAAATATCAT
* *
767499 TTGAAAACATCCTGCTC-GGAGGTCTTATGGATGGCCC
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCC
767536 AGAGGTCTTA
Statistics
Matches: 196, Mismatches: 18, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
176 18 0.09
177 178 0.91
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (177 bp):
TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGCAAGACTTACAAATCAAGAAACCCTC
GAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTCTT
TTGAGATAATTAGTAAACCCCCGAAGGATTGATTTCTAAAATATCAT
Found at i:768754 original size:54 final size:54
Alignment explanation
Indices: 768594--768755 Score: 270
Period size: 54 Copynumber: 3.0 Consensus size: 54
768584 ACTGGTTCAT
* *
768594 AAAACATTTGACAACACATTCATCATTTCTTGTGGCTTCTGCACAGATGTTCAC
1 AAAACATTTGACAACACATTCATCATTTCTTGTGGCTTATGCACAGATGTTCGC
* *
768648 AAAACATTTGACAACACATTCATCATTTCTTGTGGCTTTTGCATAGATGTTCGC
1 AAAACATTTGACAACACATTCATCATTTCTTGTGGCTTATGCACAGATGTTCGC
* *
768702 AAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTATGCACAGATGTTCGC
1 AAAACATTTGACAACACATTCATCATTTCTTGTGGCTTATGCACAGATGTTCGC
768756 CAGTGAAGCT
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 101 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (54 bp):
AAAACATTTGACAACACATTCATCATTTCTTGTGGCTTATGCACAGATGTTCGC
Found at i:769936 original size:9 final size:9
Alignment explanation
Indices: 769924--769974 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
769914 CCTTAGCAAC
769924 TTCTTCTCT
1 TTCTTCTCT
769933 TTCTTCTCT
1 TTCTTCTCT
*
769942 TTCTTTTTCTT
1 TTC-TTCTC-T
* *
769953 TTTTTCTTT
1 TTCTTCTCT
769962 TTCTTCT-T
1 TTCTTCTCT
769970 TTCTT
1 TTCTT
769975 TTTTTATTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
8 6 0.17
9 19 0.54
10 7 0.20
11 3 0.09
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
TTCTTCTCT
Found at i:769958 original size:14 final size:14
Alignment explanation
Indices: 769927--769977 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
769917 TAGCAACTTC
* *
769927 TTCTCTTTCTTCTCT
1 TTCTTTTTCTT-TTT
769942 TTCTTTTTCTTTTT
1 TTCTTTTTCTTTTT
*
769956 TTCTTTTTCTTCTT
1 TTCTTTTTCTTTTT
769970 TTCTTTTT
1 TTCTTTTT
769978 TTATTTGCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
14 23 0.70
15 10 0.30
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTTTTTCTTTTT
Found at i:769959 original size:23 final size:22
Alignment explanation
Indices: 769932--769979 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
769922 ACTTCTTCTC
769932 TTTC-TTCTCTTTCTTTTTCTTTT
1 TTTCTTTCTC-TTC-TTTTCTTTT
*
769955 TTTCTTTTTCTTCTTTTCTTTT
1 TTTCTTTCTCTTCTTTTCTTTT
769977 TTT
1 TTT
769980 ATTTGCTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 12 0.52
23 7 0.30
24 4 0.17
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTCTTTCTCTTCTTTTCTTTT
Found at i:772359 original size:42 final size:43
Alignment explanation
Indices: 772312--772396 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
772302 CGGTACATCA
*
772312 AACAAA-ACTTTACATATA-AGGATAGCTTTCACTCCTAACTTC
1 AACAAATA-TTTACATATAGAGGATAACTTTCACTCCTAACTTC
*
772354 AACAAATATTTACATATAGGGGATAACTTTCACTCCTAACTTC
1 AACAAATATTTACATATAGAGGATAACTTTCACTCCTAACTTC
772397 TCTAAAGCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
42 16 0.41
43 23 0.59
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (43 bp):
AACAAATATTTACATATAGAGGATAACTTTCACTCCTAACTTC
Done.