Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 33 of 51
Found at i:6643113 original size:30 final size:30
Alignment explanation
Indices: 6643078--6643146 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
6643068 TAATTTTACG
6643078 TTTTATTTTCTAAAATTTTTAGAAGCACTA
1 TTTTATTTTCTAAAATTTTTAGAAGCACTA
6643108 TTTTATTTTCTAAAATTTTTAGAAGCACTA
1 TTTTATTTTCTAAAATTTTTAGAAGCACTA
6643138 TTTTATTTT
1 TTTTATTTT
6643147 GTTTTACAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (30 bp):
TTTTATTTTCTAAAATTTTTAGAAGCACTA
Found at i:6646072 original size:21 final size:21
Alignment explanation
Indices: 6646047--6646086 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6646037 CAATGGGATT
*
6646047 AGGATTAGGAATTGGATTTTG
1 AGGATTAGGAAGTGGATTTTG
*
6646068 AGGATTCGGAAGTGGATTT
1 AGGATTAGGAAGTGGATTT
6646087 GGTTGACGGT
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:0.28, C:0.03, G:0.35, T:0.35
Consensus pattern (21 bp):
AGGATTAGGAAGTGGATTTTG
Found at i:6646615 original size:20 final size:20
Alignment explanation
Indices: 6646578--6646616 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6646568 AGATTGAGTG
* * *
6646578 GATTTTGATGTTGTTTGCAT
1 GATTTTAATGATGATTGCAT
6646598 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
6646617 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAT
Found at i:6646797 original size:21 final size:20
Alignment explanation
Indices: 6646767--6646846 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 20
6646757 AGAACCCCAT
*
6646767 GGGGGTATCGATTCCCCTGTG
1 GGGGGAATCGATTCCCCT-TG
* *
6646788 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTT---G
*
6646811 GGGGGAATCGATTCCCTCATG
1 GGGGGAATCGATTCCC-CTTG
6646832 GGGGG-ATCGATTCCC
1 GGGGGAATCGATTCCC
6646847 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 11 0.22
21 21 0.43
23 15 0.31
24 2 0.04
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTTG
Found at i:6646847 original size:20 final size:21
Alignment explanation
Indices: 6646765--6646848 Score: 73
Period size: 20 Copynumber: 4.0 Consensus size: 21
6646755 CCAGAACCCC
* *
6646765 ATGGGGGTATCGATTCCC-CT
1 ATGGGGGGATCGATTCCCTCA
* *
6646785 GTGGGGGGAATCGGTTCCCCTTCA
1 ATGGGGGG-ATCGATT-CCC-TCA
* *
6646809 AAGGGGGAATCGATTCCCTC-
1 ATGGGGGGATCGATTCCCTCA
6646829 ATGGGGGGATCGATTCCCTC
1 ATGGGGGGATCGATTCCCTC
6646849 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
20 24 0.48
21 8 0.16
22 6 0.12
23 6 0.12
24 6 0.12
ACGTcount: A:0.17, C:0.25, G:0.33, T:0.25
Consensus pattern (21 bp):
ATGGGGGGATCGATTCCCTCA
Found at i:6653885 original size:34 final size:36
Alignment explanation
Indices: 6653791--6653913 Score: 126
Period size: 37 Copynumber: 3.4 Consensus size: 36
6653781 TCAAAGTTTT
* * *
6653791 TTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAGAT
1 TTTGTTTTAAGAGAAACCGTCTCAAGAGAGACAA-AA
* ***
6653828 TTTTTTTTAAGAGAAAATATCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACCGTCTCAAGAGAGACAAAA
*
6653864 TTTGTTTT-A-AGAAACGGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACCGTCTCAAGAGAGACAAAA
*
6653898 CTTTGTTTCAAG-GAAA
1 -TTTGTTTTAAGAGAAA
6653914 ACAAATTCAA
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
34 22 0.31
35 8 0.11
36 13 0.18
37 28 0.39
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTTAAGAGAAACCGTCTCAAGAGAGACAAAA
Found at i:6653955 original size:19 final size:19
Alignment explanation
Indices: 6653931--6653981 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
6653921 CAAAGTTTTT
6653931 TTTGTTTCAAGAGAGAAAA
1 TTTGTTTCAAGAGAGAAAA
**
6653950 TTTGTTTTTA-AGAGAAAA
1 TTTGTTTCAAGAGAGAAAA
*
6653968 --TGTCTCAAGAGAGA
1 TTTGTTTCAAGAGAGA
6653982 CAAAACTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
18 8 0.31
19 8 0.31
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (19 bp):
TTTGTTTCAAGAGAGAAAA
Found at i:6656016 original size:64 final size:63
Alignment explanation
Indices: 6655931--6656090 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 63
6655921 TTGTTTAAGG
* * *
6655931 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGA-TTT
1 TGCATCGATGCACAAGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAAT-GCATTTT
6655994 A
63 A
* * * *
6655995 TGCATCGATGCATAAGGAGTGCATTGATGCATCCCCATTAAATAAAAACATCGAATGCATTTTA
1 TGCATCGATGCACAAGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATGCATTTTA
* *
6656059 TGCACCGATGCACAAGTAGTGCATCGATGCAT
1 TGCATCGATGCACAAGCAGTGCATCGATGCAT
6656091 ACATTCATTG
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 2 0.02
64 72 0.88
65 7 0.09
66 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCACAAGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATGCATTTTA
Found at i:6656781 original size:31 final size:31
Alignment explanation
Indices: 6656693--6656784 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 31
6656683 AGTCGAGGGT
*
6656693 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTATGTTCTTT-GGGACATATGGACAG
* ** * *
6656724 TATACCTATGTTCTAAGGAATATATGGACAG
1 TTTACCTATGTTCTTTGGGACATATGGACAG
* *
6656755 TTTACCTAGGTTCTTTGGGACCTATGGACA
1 TTTACCTATGTTCTTTGGGACATATGGACA
6656785 AATGCCGAGG
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
31 44 0.94
32 3 0.06
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (31 bp):
TTTACCTATGTTCTTTGGGACATATGGACAG
Found at i:6660201 original size:64 final size:63
Alignment explanation
Indices: 6660124--6660283 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 63
6660114 TTGTTTAAGG
* * *
6660124 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGA-TTT
1 TGCATCGATGCACAAGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAAT-GCATTTT
6660187 A
63 A
* *
6660188 TGCATCGATGCACAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTTA
1 TGCATCGATGCACAAGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATGCATTTTA
* *
6660252 TGCACCGATGCACAAGTAGTGCATCGATGCAT
1 TGCATCGATGCACAAGCAGTGCATCGATGCAT
6660284 ACATTCATTG
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
63 2 0.02
64 76 0.88
65 7 0.08
66 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (63 bp):
TGCATCGATGCACAAGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATGCATTTTA
Found at i:6661000 original size:30 final size:30
Alignment explanation
Indices: 6660939--6661011 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
6660929 CTAAAGAACA
* *
6660939 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
6660970 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
6661000 TCTGGATAGTTA
1 TATGGACAGTTA
6661012 TCGGGGTCTG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 26 0.74
31 9 0.26
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.36
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:6662120 original size:95 final size:94
Alignment explanation
Indices: 6661952--6662137 Score: 250
Period size: 95 Copynumber: 2.0 Consensus size: 94
6661942 ATATGTAAAT
* * * *
6661952 ACCTTTATCAGGTTAGTTGAATCTTATCCATAAAACCGGGGAGTTTAACCAATTGCCCTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATCTTATCCATAAAACAGGGCAGTTTAACCAATTGCCCTAGAGGG
6662017 AAAGCTCAAGATTTATTGTATAGTATAATC
66 AAAGCTCAAGATTTATTGTATA-TATAATC
* ** *
6662047 ACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTCAGGGCA-TTTAACCAATTGCTTTATAGG
1 ACCTTTATCAGGCTAGCTGAATCTTATCCATAAA-ACAGGGCAGTTTAACCAATTGCCCTAGAGG
*
6662111 GATAA-CTCAAGCTTTATTGTATATATA
65 GA-AAGCTCAAGATTTATTGTATATATA
6662138 TAATATTATA
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
94 4 0.05
95 69 0.86
96 7 0.09
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (94 bp):
ACCTTTATCAGGCTAGCTGAATCTTATCCATAAAACAGGGCAGTTTAACCAATTGCCCTAGAGGG
AAAGCTCAAGATTTATTGTATATATAATC
Found at i:6666343 original size:20 final size:18
Alignment explanation
Indices: 6666300--6666344 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
6666290 AAAAGAAGGT
*
6666300 AAAAATATATATAATAAA
1 AAAAATATATATAAAAAA
*
6666318 TAAAATATATATAAAAACA
1 AAAAATATATATAAAAA-A
6666337 AAGAAATA
1 AA-AAATA
6666345 AAAATAAGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
19 2 0.09
20 5 0.23
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAAATATATATAAAAAA
Found at i:6670810 original size:178 final size:178
Alignment explanation
Indices: 6670511--6670865 Score: 595
Period size: 178 Copynumber: 2.0 Consensus size: 178
6670501 AAATGAATGG
* * *
6670511 AAATCACTGAAAAAGTTGCTCGATTGTTACTCTTGGTTCCACCACTTCCTTTAACAATACATCCC
1 AAATCACTGAAAAAGTTGCTCAATTGTTACTCTTGGTTCCACCACTTCCCTTAACAAAACATCCC
* * * *
6670576 GCAAATATGACTTGTTTTTCTTCATCATCGTCGCTTGAGATTCTATAAAATTTTACTCGTTCTTT
66 GCAAATATGACTTGTTTTTCTTCATCATCATCGCTCGAAATTCTATAAAATTTTACTCATTCTTT
*
6670641 TAA-TCTTTTCACTAAAGAACCACCCAATTATACGGTGATATCGAGTGC
131 TAACT-TTTTCACTAAAGAACCACCCAATTATACGATGATATCGAGTGC
*
6670689 AAATCACTGGAAAAGTTGCTCAATTGTTACTCTTGGTTCCACCACTTCCCTTAACAAAACATCCC
1 AAATCACTGAAAAAGTTGCTCAATTGTTACTCTTGGTTCCACCACTTCCCTTAACAAAACATCCC
* *
6670754 GCAAATATGACTTGTTTTTCTTCATCATCATCGCTCGAAATTCTGTAGAATTTTACTCATTCTTT
66 GCAAATATGACTTGTTTTTCTTCATCATCATCGCTCGAAATTCTATAAAATTTTACTCATTCTTT
6670819 TAACTTTTTCACTAAAGAACCACCCAATTATACGATGATATCGAGTG
131 TAACTTTTTCACTAAAGAACCACCCAATTATACGATGATATCGAGTG
6670866 TAAGGGTGGC
Statistics
Matches: 165, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
178 164 0.99
179 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (178 bp):
AAATCACTGAAAAAGTTGCTCAATTGTTACTCTTGGTTCCACCACTTCCCTTAACAAAACATCCC
GCAAATATGACTTGTTTTTCTTCATCATCATCGCTCGAAATTCTATAAAATTTTACTCATTCTTT
TAACTTTTTCACTAAAGAACCACCCAATTATACGATGATATCGAGTGC
Found at i:6671659 original size:31 final size:31
Alignment explanation
Indices: 6671621--6671773 Score: 171
Period size: 31 Copynumber: 4.9 Consensus size: 31
6671611 TTGGGGCATA
* * *
6671621 TGGGCCTACCCAAGAAAGTTATCAGGGCCAT
1 TGGGCCTACCCAAGAAAGATCTCAGGGCCAC
*
6671652 TGGGCCTACCCAAGAAAGATCTCAGGGCCGC
1 TGGGCCTACCCAAGAAAGATCTCAGGGCCAC
* *
6671683 AGGGCCTACCCAAGAATGATCTCAGGGCCAC
1 TGGGCCTACCCAAGAAAGATCTCAGGGCCAC
* * * * **
6671714 GGGGCCTACCTAAGAAAAATCTCAAGGCTGC
1 TGGGCCTACCCAAGAAAGATCTCAGGGCCAC
* * *
6671745 AGGGCCTACCCAAGAATGATCTCGGGGCC
1 TGGGCCTACCCAAGAAAGATCTCAGGGCC
6671774 GCAGAGCTTA
Statistics
Matches: 101, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 101 1.00
ACGTcount: A:0.28, C:0.29, G:0.27, T:0.15
Consensus pattern (31 bp):
TGGGCCTACCCAAGAAAGATCTCAGGGCCAC
Found at i:6671719 original size:62 final size:62
Alignment explanation
Indices: 6671622--6671773 Score: 214
Period size: 62 Copynumber: 2.5 Consensus size: 62
6671612 TGGGGCATAT
* * * ** * *
6671622 GGGCCTACCCAAGAAAGTTATCAGGGCCATTGGGCCTACCCAAGAAAGATCTCAGGGCCGCA
1 GGGCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGAAAAATCTCAAGGCCGCA
* *
6671684 GGGCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCTAAGAAAAATCTCAAGGCTGCA
1 GGGCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGAAAAATCTCAAGGCCGCA
*
6671746 GGGCCTACCCAAGAATGATCTCGGGGCC
1 GGGCCTACCCAAGAATGATCTCAGGGCC
6671774 GCAGAGCTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 80 1.00
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (62 bp):
GGGCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGAAAAATCTCAAGGCCGCA
Found at i:6671786 original size:62 final size:62
Alignment explanation
Indices: 6671622--6671790 Score: 203
Period size: 62 Copynumber: 2.7 Consensus size: 62
6671612 TGGGGCATAT
* * * ** * * * *
6671622 GGGCCTACCCAAGAAAGTTATCAGGGCCATTGGGCCTACCCAAGAAAGATCTCAGGGCCGCA
1 GGGCCTACCCAAGAATGATCTCAGGGCCACAGAGCCTACCTAAGAAAAATCTCAAGGCCGCA
* * *
6671684 GGGCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCTAAGAAAAATCTCAAGGCTGCA
1 GGGCCTACCCAAGAATGATCTCAGGGCCACAGAGCCTACCTAAGAAAAATCTCAAGGCCGCA
* * *
6671746 GGGCCTACCCAAGAATGATCTCGGGGCCGCAGAGCTTACCTAAGA
1 GGGCCTACCCAAGAATGATCTCAGGGCCACAGAGCCTACCTAAGA
6671791 GTCACATTAG
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 93 1.00
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.15
Consensus pattern (62 bp):
GGGCCTACCCAAGAATGATCTCAGGGCCACAGAGCCTACCTAAGAAAAATCTCAAGGCCGCA
Found at i:6676799 original size:5 final size:5
Alignment explanation
Indices: 6676789--6676830 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
6676779 CATTAACTCC
6676789 TACAT TACAT TACAT TACAT TACAT TACAT TACAT TACAT TA
1 TACAT TACAT TACAT TACAT TACAT TACAT TACAT TACAT TA
6676831 GAAGCATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (5 bp):
TACAT
Found at i:6682225 original size:6 final size:6
Alignment explanation
Indices: 6682183--6682221 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
6682173 ACGGCTCGGC
*
6682183 TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCGTGG TCG
1 TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCG
6682222 TGGTAATACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.13, C:0.18, G:0.49, T:0.21
Consensus pattern (6 bp):
TCGAGG
Found at i:6682525 original size:22 final size:22
Alignment explanation
Indices: 6682500--6682554 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
6682490 TCAGGAGTTA
* *
6682500 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
6682522 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
6682544 CGGGAGTTATA
1 CAGGAGTTATA
6682555 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:6688045 original size:5 final size:5
Alignment explanation
Indices: 6688038--6688086 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
6688028 GTCCTTCCGT
* * * *
6688038 CTCGT CTCGG CTCGG CTCGG CACGG CTCGG CTCGG CACGA CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
6688087 TGGTCGTGGT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.06, C:0.41, G:0.35, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:6688063 original size:15 final size:15
Alignment explanation
Indices: 6688045--6688086 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
6688035 CGTCTCGTCT
6688045 CGGCTCGGCTCGGCA
1 CGGCTCGGCTCGGCA
6688060 CGGCTCGGCTCGGCA
1 CGGCTCGGCTCGGCA
*
6688075 CGACTCGGCTCG
1 CGGCTCGGCTCG
6688087 TGGTCGTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.07, C:0.40, G:0.38, T:0.14
Consensus pattern (15 bp):
CGGCTCGGCTCGGCA
Found at i:6688095 original size:6 final size:6
Alignment explanation
Indices: 6688084--6688114 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
6688074 ACGACTCGGC
*
6688084 TCGTGG TCGTGG TTGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
6688115 AATACGTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.13, G:0.48, T:0.39
Consensus pattern (6 bp):
TCGTGG
Found at i:6688410 original size:22 final size:22
Alignment explanation
Indices: 6688385--6688439 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
6688375 TCAGGAGTTA
* *
6688385 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
6688407 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
6688429 CGGGAGTTATA
1 CAGGAGTTATA
6688440 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:6691771 original size:19 final size:19
Alignment explanation
Indices: 6691749--6691790 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
6691739 CAATTAGAAT
6691749 TTTTAA-TTAATAAATATTA
1 TTTTAATTTAA-AAATATTA
6691768 TTTTAATTTTAAAAATATTA
1 TTTTAA-TTTAAAAATATTA
6691788 TTT
1 TTT
6691791 AATATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTAATTTAAAAATATTA
Found at i:6694404 original size:2 final size:2
Alignment explanation
Indices: 6694399--6694483 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
6694389 AAGATAAAAG
6694399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
6694441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6694483 A
1 A
6694484 GATGGTTATA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6696269 original size:18 final size:18
Alignment explanation
Indices: 6696243--6696277 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6696233 TATTAAAATA
6696243 ATTTATTTAATATTATTT
1 ATTTATTTAATATTATTT
* *
6696261 ATTTCTTTATTATTATT
1 ATTTATTTAATATTATT
6696278 AAAATATTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTATTTAATATTATTT
Found at i:6696364 original size:21 final size:23
Alignment explanation
Indices: 6696340--6696419 Score: 66
Period size: 22 Copynumber: 3.7 Consensus size: 23
6696330 TTTAAATTAA
6696340 AATTA-TTA-TAAAATATATATT
1 AATTACTTATTAAAATATATATT
* * *
6696361 AATTATTTATTAAAATA-AGAAT
1 AATTACTTATTAAAATATATATT
*
6696383 AATATAC-TA-T-CAAT-TATATT
1 AAT-TACTTATTAAAATATATATT
6696403 AATTACTTATTAAAATA
1 AATTACTTATTAAAATA
6696420 ATAATATCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 14
0.68 0.11 0.22
Matches are distributed among these distances:
19 3 0.07
20 11 0.25
21 7 0.16
22 14 0.32
23 9 0.20
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (23 bp):
AATTACTTATTAAAATATATATT
Found at i:6696459 original size:22 final size:23
Alignment explanation
Indices: 6696413--6696459 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
6696403 AATTACTTAT
6696413 TAAAATAATAATATCATTAAAATA
1 TAAAATAATAATATCA-TAAAATA
6696437 TAAAATATATAATAT-A-AAAATA
1 TAAAATA-ATAATATCATAAAATA
6696459 T
1 T
6696460 TATATTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
24 8 0.36
25 7 0.32
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
TAAAATAATAATATCATAAAATA
Found at i:6696590 original size:21 final size:19
Alignment explanation
Indices: 6696561--6696632 Score: 76
Period size: 21 Copynumber: 3.7 Consensus size: 19
6696551 TTAATAATTT
6696561 ATTATATATTATAAAATAA
1 ATTATATATTATAAAATAA
*
6696580 AGTTATAATATTATATAATAA
1 A-TTAT-ATATTATAAAATAA
6696601 A-TATA-ATTATAACAATAA
1 ATTATATATTATAA-AATAA
*
6696619 AATATTATATTATA
1 ATTA-TATATTATA
6696633 TTACTAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
17 6 0.13
18 7 0.16
19 6 0.13
20 6 0.13
21 20 0.44
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (19 bp):
ATTATATATTATAAAATAA
Found at i:6697096 original size:15 final size:15
Alignment explanation
Indices: 6697076--6697106 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6697066 CCTTTTCTAG
*
6697076 AAGGCCGATGTGATT
1 AAGGCCAATGTGATT
6697091 AAGGCCAATGTGATT
1 AAGGCCAATGTGATT
6697106 A
1 A
6697107 GACTCTCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (15 bp):
AAGGCCAATGTGATT
Found at i:6697433 original size:14 final size:15
Alignment explanation
Indices: 6697416--6697449 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
6697406 TTAACAACAT
6697416 AAAATGA-TTTCCAG
1 AAAATGATTTTCCAG
6697430 AAAAT-ATTTTCCAG
1 AAAATGATTTTCCAG
6697444 AAAATG
1 AAAATG
6697450 TATTCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 17 0.94
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (15 bp):
AAAATGATTTTCCAG
Found at i:6698368 original size:15 final size:15
Alignment explanation
Indices: 6698348--6698378 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6698338 CCTTTTCTAG
6698348 AAGGCGAATGTGATT
1 AAGGCGAATGTGATT
6698363 AAGGCGAATGTGATT
1 AAGGCGAATGTGATT
6698378 A
1 A
6698379 GACTCTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (15 bp):
AAGGCGAATGTGATT
Found at i:6706421 original size:2 final size:2
Alignment explanation
Indices: 6706414--6706448 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6706404 TTTAGTAAGT
6706414 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 T
6706449 TGGAATTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6713606 original size:57 final size:57
Alignment explanation
Indices: 6713517--6713688 Score: 272
Period size: 57 Copynumber: 3.0 Consensus size: 57
6713507 CATAACCATA
* * * * * *
6713517 CAACCCCGTCACGAACAGTAAGGCCCTGAGCACGAAGCCAAGGAACCTACAAGTATT
1 CAACCCCATCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
*
6713574 CAACCCTATCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
1 CAACCCCATCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
*
6713631 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
1 CAACCCCATCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
6713688 C
1 C
6713689 TTCCTCCAAC
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 106 1.00
ACGTcount: A:0.34, C:0.31, G:0.20, T:0.14
Consensus pattern (57 bp):
CAACCCCATCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
Found at i:6716244 original size:10 final size:10
Alignment explanation
Indices: 6716231--6716260 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
6716221 CCGTCAAATT
6716231 TTTGGTCAAC
1 TTTGGTCAAC
6716241 TTTGGTCAAC
1 TTTGGTCAAC
*
6716251 ATTGGTCAAC
1 TTTGGTCAAC
6716261 GGTCAACGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (10 bp):
TTTGGTCAAC
Found at i:6718429 original size:57 final size:57
Alignment explanation
Indices: 6718260--6718431 Score: 281
Period size: 57 Copynumber: 3.0 Consensus size: 57
6718250 CATAACCATA
* * * * *
6718260 CAACCCCGTCACGAACAGTAAGGCCCTGAGCACAAAACCAAGGAACCTACAAGTAAT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTACAAGTATT
6718317 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTACAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTACAAGTATT
* *
6718374 CAACCCCGTCACGAACAGTAAGGCTCTCAGTACAAAGCCGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTACAAGTATT
6718431 C
1 C
6718432 TTCCTCCAAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 108 1.00
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.13
Consensus pattern (57 bp):
CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTACAAGTATT
Found at i:6722172 original size:58 final size:58
Alignment explanation
Indices: 6722021--6722177 Score: 174
Period size: 60 Copynumber: 2.7 Consensus size: 58
6722011 GGAATGTTCA
**
6722021 AAAGTTTGGGGACTAATTTAGAATGAGGGTCATAGTTTGGGGATGAATTTGAAATTTT
1 AAAGTTTAAGGACTAATTTAGAATGAGGGTCATAGTTTGGGGATGAATTTGAAATTTT
* *** * *
6722079 CAAAAGTTTAAGGACCAATTTAGAATGAAAATCATATTTTGGGGGTGAATTT-ACAATATTT
1 --AAAGTTTAAGGACTAATTTAGAATGAGGGTCATAGTTTGGGGATGAATTTGA-AAT-TTT
* *
6722140 -AAGTTTAAGGATTAATTTAAAATGAGGGTCATAGTTTG
1 AAAGTTTAAGGACTAATTTAGAATGAGGGTCATAGTTTG
6722178 AGGACGTATA
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
58 31 0.39
59 1 0.01
60 45 0.56
61 3 0.04
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.36
Consensus pattern (58 bp):
AAAGTTTAAGGACTAATTTAGAATGAGGGTCATAGTTTGGGGATGAATTTGAAATTTT
Found at i:6722472 original size:29 final size:28
Alignment explanation
Indices: 6722429--6722489 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
6722419 AGAGAAATGG
* * *
6722429 ATAATTAAAATATTATATATACTACATAT
1 ATAATTAAAATATTAAATAAAATACAT-T
6722458 ATAATTATAAA-ATTAAATAAAATACATT
1 ATAATTA-AAATATTAAATAAAATACATT
6722486 ATAA
1 ATAA
6722490 GATATTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.18
29 20 0.71
30 3 0.11
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (28 bp):
ATAATTAAAATATTAAATAAAATACATT
Found at i:6724667 original size:2 final size:2
Alignment explanation
Indices: 6724660--6724699 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6724650 TTTAAAACCT
6724660 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6724700 GCACCCCTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6725167 original size:2 final size:2
Alignment explanation
Indices: 6725160--6725195 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6725150 CAAGAATAGC
6725160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6725196 TTAATTATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6726126 original size:3 final size:3
Alignment explanation
Indices: 6726120--6726154 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
6726110 ACAAAAATAC
*
6726120 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6726155 CACAACCCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6731111 original size:31 final size:31
Alignment explanation
Indices: 6731076--6731134 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
6731066 AATAGGAATA
6731076 AATGCCAACTCATATAGGAACACCTACAGAC
1 AATGCCAACTCATATAGGAACACCTACAGAC
6731107 AATGCCAACTCATATAGGAACACCTACA
1 AATGCCAACTCATATAGGAACACCTACA
6731135 ATCCAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.29, G:0.12, T:0.17
Consensus pattern (31 bp):
AATGCCAACTCATATAGGAACACCTACAGAC
Found at i:6732950 original size:8 final size:7
Alignment explanation
Indices: 6732927--6733055 Score: 63
Period size: 8 Copynumber: 17.6 Consensus size: 7
6732917 AGTAGTATTC
6732927 TATTATA
1 TATTATA
6732934 T-TTATA
1 TATTATA
6732940 TATTATA
1 TATTATA
6732947 -A-TATA
1 TATTATA
*
6732952 TATTCACA
1 TATT-ATA
6732960 -A--AGTA
1 TATTA-TA
*
6732965 TATTATT
1 TATTATA
6732972 TATTATA
1 TATTATA
*
6732979 GTGTATATA
1 -TAT-TATA
*
6732988 TAATATA
1 TATTATA
*
6732995 TAGTAATA
1 TA-TTATA
6733003 TATTAAGTA
1 TATT-A-TA
6733012 TATATATA
1 TAT-TATA
6733020 TATATATA
1 TAT-TATA
6733028 TATATATA
1 TAT-TATA
6733036 TATATATA
1 TAT-TATA
6733044 TATATATA
1 TAT-TATA
6733052 TATT
1 TATT
6733056 GGCAAAAGGT
Statistics
Matches: 98, Mismatches: 10, Indels: 28
0.72 0.07 0.21
Matches are distributed among these distances:
4 1 0.01
5 5 0.05
6 9 0.09
7 23 0.23
8 49 0.50
9 10 0.10
10 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (7 bp):
TATTATA
Found at i:6732953 original size:12 final size:12
Alignment explanation
Indices: 6732936--6733055 Score: 56
Period size: 14 Copynumber: 9.7 Consensus size: 12
6732926 CTATTATATT
6732936 TATATATTATAA
1 TATATATTATAA
*
6732948 TATATATTCACAA
1 TATATATT-ATAA
*
6732961 -AGTATATTAT-T
1 TA-TATATTATAA
6732972 TATTATAGTGTAT-A
1 TA-TATA-T-TATAA
*
6732986 TATA-ATATATAG
1 TATATAT-TATAA
*
6732998 TAATATATTA-AG
1 T-ATATATTATAA
6733010 TATATA-TAT-A
1 TATATATTATAA
6733020 TATATATATATATA
1 TATATAT-TATA-A
6733034 TATATATATATATA
1 TATATAT-TATA-A
6733048 TATATATT
1 TATATATT
6733056 GGCAAAAGGT
Statistics
Matches: 87, Mismatches: 8, Indels: 25
0.73 0.07 0.21
Matches are distributed among these distances:
10 8 0.09
11 9 0.10
12 23 0.26
13 18 0.21
14 29 0.33
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (12 bp):
TATATATTATAA
Found at i:6732989 original size:2 final size:2
Alignment explanation
Indices: 6732982--6733054 Score: 100
Period size: 2 Copynumber: 37.5 Consensus size: 2
6732972 TATTATAGTG
6732982 TA TA TA TA -A TA TA TA GTA -A TA TA T- TA -A GTA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA
6733022 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 T
6733055 TGGCAAAAGG
Statistics
Matches: 65, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.06
2 58 0.89
3 3 0.05
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6734707 original size:23 final size:23
Alignment explanation
Indices: 6734681--6734793 Score: 70
Period size: 23 Copynumber: 4.6 Consensus size: 23
6734671 TTTAAGTCTA
6734681 TATATAATATATATTTAAAAACG
1 TATATAATATATATTTAAAAACG
* *
6734704 TATATAACT-TTTTTTTAAAAA--
1 TATATAA-TATATATTTAAAAACG
* **
6734725 TATATAATATATATATTATATAATA
1 TATATAATATATAT-TTA-AAAACG
6734750 TATTATATATAGTATATTTAAAAAACATG
1 TA-TATA-ATA-TATATTT-AAAAAC--G
6734779 TATATATATATATAT
1 TATATA-ATATATAT
6734794 ATATATAGTA
Statistics
Matches: 70, Mismatches: 8, Indels: 20
0.71 0.08 0.20
Matches are distributed among these distances:
20 1 0.01
21 10 0.14
22 3 0.04
23 20 0.29
24 1 0.01
25 2 0.03
26 4 0.06
27 13 0.19
28 14 0.20
29 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (23 bp):
TATATAATATATATTTAAAAACG
Found at i:6734729 original size:2 final size:2
Alignment explanation
Indices: 6734724--6734810 Score: 76
Period size: 2 Copynumber: 45.0 Consensus size: 2
6734714 TTTTTTAAAA
6734724 AT AT AT A- AT AT AT AT AT -T AT AT A- AT AT AT -T AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * * *
6734763 AT AT TT A- AA AA AC AT GT AT AT AT AT AT AT AT AT AT AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
6734805 AT AT AT
1 AT AT AT
6734811 TTTAAAATAT
Statistics
Matches: 72, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
1 5 0.07
2 63 0.88
3 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6734735 original size:7 final size:7
Alignment explanation
Indices: 6734723--6734766 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
6734713 TTTTTTTAAA
6734723 AATATAT
1 AATATAT
6734730 AATATAT
1 AATATAT
6734737 ATATTATAT
1 A-A-TATAT
6734746 AATATAT
1 AATATAT
*
6734753 TATATAT
1 AATATAT
*
6734760 AGTATAT
1 AATATAT
6734767 TTAAAAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 24 0.75
8 2 0.06
9 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (7 bp):
AATATAT
Found at i:6734770 original size:49 final size:45
Alignment explanation
Indices: 6734730--6734820 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 45
6734720 AAAAATATAT
6734730 AATATATATAT-TATATA-ATATAT-TATA-TATAGTATATTTAAA
1 AATATATATATATATATATATATATATATAGTATA-TATATTTAAA
* * *
6734772 AA-ACATGTATATATATATATATATATATAGTATATATATTTTAA
1 AATATATATATATATATATATATATATATAGTATATATATTTAAA
6734816 AATAT
1 AATAT
6734821 GTTATAGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
41 6 0.15
42 8 0.20
43 6 0.15
44 15 0.38
45 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (45 bp):
AATATATATATATATATATATATATATATAGTATATATATTTAAA
Found at i:6734804 original size:23 final size:22
Alignment explanation
Indices: 6734724--6734810 Score: 87
Period size: 21 Copynumber: 4.2 Consensus size: 22
6734714 TTTTTTAAAA
*
6734724 ATATATAATATATATATTATAT
1 ATATATAATATATATAGTATAT
*
6734746 A-ATATATTATATATAGTATAT
1 ATATATAATATATATAGTATAT
* *
6734767 -T-TA-AA-AAACAT-GTATAT
1 ATATATAATATATATAGTATAT
6734784 ATATATATATATATATAGTATAT
1 ATATATA-ATATATATAGTATAT
6734807 ATAT
1 ATAT
6734811 TTTAAAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
17 6 0.12
18 5 0.10
19 3 0.06
20 3 0.06
21 19 0.37
22 5 0.10
23 10 0.20
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (22 bp):
ATATATAATATATATAGTATAT
Found at i:6734820 original size:21 final size:21
Alignment explanation
Indices: 6734726--6734849 Score: 69
Period size: 23 Copynumber: 5.7 Consensus size: 21
6734716 TTTTAAAAAT
* *
6734726 ATATAATATATATATTATATAAT
1 ATATAGTATATATATT-T-TAAA
6734749 ATATTA-TATATAGTATATTTAAA
1 ATA-TAGTATATA-TAT-TTTAAA
* * * *
6734772 AAACATGTATATATATATATATAT
1 ATATA-GTATATATAT-TTTA-AA
6734796 ATATAGTATATATATTTTAAA
1 ATATAGTATATATATTTTAAA
6734817 ATAT-GT-TATAGT-TTTTAAA
1 ATATAGTATATA-TATTTTAAA
6734836 ATATA-TATCATATA
1 ATATAGTAT-ATATA
6734850 GGCCTAGGAG
Statistics
Matches: 81, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
19 16 0.20
20 5 0.06
21 8 0.10
22 4 0.05
23 31 0.38
24 16 0.20
25 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.47
Consensus pattern (21 bp):
ATATAGTATATATATTTTAAA
Found at i:6734992 original size:17 final size:17
Alignment explanation
Indices: 6734972--6735005 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6734962 TGAATTAACC
6734972 GAAATTTTTTAAAATTT
1 GAAATTTTTTAAAATTT
6734989 GAAATTTTTTAAAATTT
1 GAAATTTTTTAAAATTT
6735006 TCTAAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
GAAATTTTTTAAAATTT
Found at i:6736673 original size:20 final size:20
Alignment explanation
Indices: 6736644--6736700 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
6736634 TAGATCCTTA
*
6736644 AATTAAGCCTTTTAATTCAC
1 AATTAGGCCTTTTAATTCAC
6736664 AATTAGGCCTTTTAATTCAC
1 AATTAGGCCTTTTAATTCAC
*
6736684 AATTAGGCCTTGTAATT
1 AATTAGGCCTTTTAATT
6736701 TTCTTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (20 bp):
AATTAGGCCTTTTAATTCAC
Found at i:6739525 original size:13 final size:13
Alignment explanation
Indices: 6739507--6739531 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6739497 CCTTTTTCTT
6739507 ACTTTGCATTTGC
1 ACTTTGCATTTGC
6739520 ACTTTGCATTTG
1 ACTTTGCATTTG
6739532 GCATTTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (13 bp):
ACTTTGCATTTGC
Found at i:6742428 original size:43 final size:43
Alignment explanation
Indices: 6742366--6742685 Score: 277
Period size: 43 Copynumber: 7.4 Consensus size: 43
6742356 CGACTTGAAA
* * * *
6742366 AACATTTCACCTAGCTTAACCTATGAAGGGGAGTCATCCGAGG
1 AACATTTCACTTGGCTTAACCCACGAAGGGGAGTCATCCGAGG
* * * *
6742409 AACATTTCACTTGGGTTAACCTACGAAGGGGAGTCATTCGAAG
1 AACATTTCACTTGGCTTAACCCACGAAGGGGAGTCATCCGAGG
* * ** * *
6742452 AATATTTCACCTGGCTTAACCCACGAAAAGGAGTCATCCAAGA
1 AACATTTCACTTGGCTTAACCCACGAAGGGGAGTCATCCGAGG
* * *
6742495 AATC-TTTCATTTGGCTTAACCCGCGAATGGGAGTCATCCGAGG
1 AA-CATTTCACTTGGCTTAACCCACGAAGGGGAGTCATCCGAGG
* ** ** * *
6742538 AACATTTCACATGGCTTAATTCTTGAAGGGGAGTTATCCGATG
1 AACATTTCACTTGGCTTAACCCACGAAGGGGAGTCATCCGAGG
* * * * * *
6742581 AATATTTTACTTGACTTAACCCACAAAAGGGAGTCACCCG-GAG
1 AACATTTCACTTGGCTTAACCCACGAAGGGGAGTCATCCGAG-G
* ** **
6742624 AACATTTCA-TCTGGCTTAACCCACAAAGGGGAGTCATCTAAAT
1 AACATTTCACT-TGGCTTAACCCACGAAGGGGAGTCATCCGAGG
6742667 AACATTTCACTTGGCTTAA
1 AACATTTCACTTGGCTTAA
6742686 TCTGCAAAGG
Statistics
Matches: 216, Mismatches: 55, Indels: 12
0.76 0.19 0.04
Matches are distributed among these distances:
42 2 0.01
43 213 0.99
44 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (43 bp):
AACATTTCACTTGGCTTAACCCACGAAGGGGAGTCATCCGAGG
Found at i:6742514 original size:86 final size:86
Alignment explanation
Indices: 6742366--6742747 Score: 295
Period size: 86 Copynumber: 4.4 Consensus size: 86
6742356 CGACTTGAAA
* * * * * * * *
6742366 AACATTTCACCTAGCTTAACCTATGAAGGGGAGTCATCCGAGGAACATTTCACTTGGGTTAACCT
1 AACATTTCACCTGGCTTAACCCACGAAAGGGAGTCATCCAAGAAACATTTCACTTGGCTTAACCC
* **
6742431 ACGAAGGGGAGTCATTCGAAG
66 ACAAAGGGGAGTCACCCGAAG
* * *
6742452 AATATTTCACCTGGCTTAACCCACGAAAAGGAGTCATCCAAGAAATC-TTTCATTTGGCTTAACC
1 AACATTTCACCTGGCTTAACCCACGAAAGGGAGTCATCCAAGAAA-CATTTCACTTGGCTTAACC
* * * * *
6742516 CGCGAATGGGAGTCATCCGAGG
65 CACAAAGGGGAGTCACCCGAAG
* ** ** * * * * * *
6742538 AACATTTCACATGGCTTAATTCTTGAAGGGGAGTTATCCGATG-AATATTTTACTTGACTTAACC
1 AACATTTCACCTGGCTTAACCCACGAAAGGGAGTCATCC-AAGAAACATTTCACTTGGCTTAACC
* *
6742602 CACAAAAGGGAGTCACCCGGAG
65 CACAAAGGGGAGTCACCCGAAG
* * *
6742624 AACATTTCATCTGGCTTAACCCAC-AAAGGGGAGTCATCTAA-ATAACATTTCACTTGGCTTAAT
1 AACATTTCACCTGGCTTAACCCACGAAA-GGGAGTCATCCAAGA-AACATTTCACTTGGCTTAAC
** * * *
6742687 CTGCAAAGGAGAGTGACTCGAAG
64 CCACAAAGGGGAGTCACCCGAAG
* * * * *
6742710 AACAATTCACCTGACTTAAGCCGCGAAAAGGAGTCATC
1 AACATTTCACCTGGCTTAACCCACGAAAGGGAGTCATC
6742748 TGAAGTCTGA
Statistics
Matches: 227, Mismatches: 62, Indels: 14
0.75 0.20 0.05
Matches are distributed among these distances:
85 3 0.01
86 218 0.96
87 6 0.03
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (86 bp):
AACATTTCACCTGGCTTAACCCACGAAAGGGAGTCATCCAAGAAACATTTCACTTGGCTTAACCC
ACAAAGGGGAGTCACCCGAAG
Found at i:6742600 original size:129 final size:130
Alignment explanation
Indices: 6742366--6742745 Score: 362
Period size: 129 Copynumber: 2.9 Consensus size: 130
6742356 CGACTTGAAA
* * * ** *
6742366 AACATTTCACCTAGCTTAACCTATGAAGGGGAGTCATCCGAGGAACATTTCACTTGGGTTAA-CC
1 AACATTTCATCTGGCTTAACCCACAAAGGGGAGTCATCCGAGGAACATTTCACTTGGCTTAATCC
* *
6742430 TACGAAGGGGAGTCATTCGAAGAATATTTCACCTGGCTTAACCCACGAAAA-GGAGTCATCCAAG
66 TACGAAGGGGAGTCATCCGAAGAATATTTCACCTGACTTAACCCAC-AAAAGGGAGTCA-CCAAG
6742494 A-
129 AG
* * * * * *
6742495 AATC-TTTCATTTGGCTTAACCCGCGAATGGGAGTCATCCGAGGAACATTTCACATGGCTTAATT
1 AA-CATTTCATCTGGCTTAACCCACAAAGGGGAGTCATCCGAGGAACATTTCACTTGGCTTAATC
* * * * * **
6742559 CT-TGAAGGGGAGTTATCCGATGAATATTTTACTTGACTTAACCCACAAAAGGGAGTCACCCGGA
65 CTACGAAGGGGAGTCATCCGAAGAATATTTCACCTGACTTAACCCACAAAAGGGAGTCACCAAGA
6742623 G
130 G
** **
6742624 AACATTTCATCTGGCTTAACCCACAAAGGGGAGTCATCTAAATAACATTTCACTTGGCTTAAT-C
1 AACATTTCATCTGGCTTAACCCACAAAGGGGAGTCATCCGAGGAACATTTCACTTGGCTTAATCC
* * * * * * * *
6742688 TGCAAAGGAGAGTGA-CTCGAAGAACAATTCACCTGACTTAAGCCGCGAAAA-GGAGTCA
66 TACGAAGGGGAGTCATC-CGAAGAATATTTCACCTGACTTAACCCAC-AAAAGGGAGTCA
6742746 TCTGAAGTCT
Statistics
Matches: 204, Mismatches: 39, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
128 12 0.06
129 185 0.91
130 7 0.03
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (130 bp):
AACATTTCATCTGGCTTAACCCACAAAGGGGAGTCATCCGAGGAACATTTCACTTGGCTTAATCC
TACGAAGGGGAGTCATCCGAAGAATATTTCACCTGACTTAACCCACAAAAGGGAGTCACCAAGAG
Found at i:6742985 original size:2 final size:2
Alignment explanation
Indices: 6742980--6743139 Score: 76
Period size: 2 Copynumber: 85.0 Consensus size: 2
6742970 TAATACAATT
*
6742980 TA TA TA TA T- TA TA GTA TA TA TA AA TA TA -A TA TA TA -A TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
6743020 -A AA TA TA TA TT TGA -A AA CA TA TA AA AA GA TA TG TA TA -A TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
6743060 TA TT TA TCA TA TA -A TA TA T- TA TA TA TA -A TA CA TA T- TA TT
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
6743099 TA AA AA TA TA TA TA T- TA TA T- TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6743138 TA
1 TA
6743140 ATTTAAAATA
Statistics
Matches: 122, Mismatches: 20, Indels: 32
0.70 0.11 0.18
Matches are distributed among these distances:
1 13 0.11
2 105 0.86
3 4 0.03
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:6743001 original size:18 final size:17
Alignment explanation
Indices: 6742960--6743141 Score: 80
Period size: 18 Copynumber: 10.8 Consensus size: 17
6742950 AGTGTTCTAT
* *
6742960 TATATTTATATAATACAA
1 TATATATATATAATA-TA
* *
6742978 TTTATATATATTATAGTA
1 TATATATATATAATA-TA
*
6742996 TATATAAATATAATATA
1 TATATATATATAATATA
6743013 TA-ATATA-A-AATATA
1 TATATATATATAATATA
* * * *
6743027 TATTTGA-AAACATATAAA
1 TATAT-ATATATA-ATATA
* * *
6743045 AAGATATGTATAATATA
1 TATATATATATAATATA
6743062 T-T-TATCATATAATATA
1 TATATAT-ATATAATATA
6743078 T-TATATATAATACATAT-
1 TATATATAT-ATA-ATATA
*
6743095 TAT-T-TA-AAAATATA
1 TATATATATATAATATA
*
6743109 TATATTATATTATATTATA
1 TATA-TATA-TATAATATA
6743128 TATATATATATAAT
1 TATATATATATAAT
6743142 TTAAAATATG
Statistics
Matches: 122, Mismatches: 25, Indels: 35
0.67 0.14 0.19
Matches are distributed among these distances:
13 4 0.03
14 13 0.11
15 6 0.05
16 22 0.18
17 25 0.20
18 42 0.34
19 10 0.08
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TATATATATATAATATA
Found at i:6743178 original size:33 final size:37
Alignment explanation
Indices: 6743141--6743212 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
6743131 ATATATATAA
6743141 TTTAAAATA-T-GT-TATAGTTTTTATTA-TTATTAT
1 TTTAAAATAGTAGTGTATAGTTTTTATTATTTATTAT
6743174 TTTAAAATATGTAGTGTATAGTTTTTATTATTTATTAT
1 TTTAAAATA-GTAGTGTATAGTTTTTATTATTTATTAT
6743212 T
1 T
6743213 ATTGTTGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
33 9 0.26
35 1 0.03
36 2 0.06
37 14 0.41
38 8 0.24
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (37 bp):
TTTAAAATAGTAGTGTATAGTTTTTATTATTTATTAT
Found at i:6749643 original size:201 final size:201
Alignment explanation
Indices: 6749298--6750238 Score: 1686
Period size: 201 Copynumber: 4.7 Consensus size: 201
6749288 GTAAAATTTA
*
6749298 TCGATCCTAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
* *
6749363 TAAATATACCGGTTTTATAAGAGAATAGGTCTACAACATGTATCAACACTTGTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
**
6749428 CGATACTTTTGGTCCAGAATGGCTATCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCAGAATGGCTGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
6749493 AAAGTG
196 AAAGTG
6749499 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
*
6749564 TAAATATACCGGTTTTATGAGAGAGTAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
* * *
6749629 CGATACTTTTGGTCCAGAATGGCTGCCAAAAAGGGTGAACACATAAAATGGCGATACATTTTCAA
131 CGATACTTTTGGTCCAGAATGGCTGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
6749694 AAAGTG
196 AAAGTG
* * *
6749700 TCGATCCCAGAAACATATGCATCCATAAGTATAATATAATAGGTAAATTTACAGTGTAACCAGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
*
6749765 TAAATATATCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
*
6749830 CGATACTTTTGGTCCAGAATGGTTGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCAGAATGGCTGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
6749895 AAAGTG
196 AAAGTG
* * *
6749901 TCGATCCTAGAAACATATACATCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
*
6749966 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCAACACTTGTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
* *
6750031 TGATACTTTTGGTCCAGAATGGCTGCCAAAAAGCGTGAACGCATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCAGAATGGCTGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
6750096 AAAGTG
196 AAAGTG
6750102 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
6750167 TAAATATACCGGATTTT-TGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTG
66 TAAATATACCGG-TTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTG
6750231 TCGATACT
130 TCGATACT
6750239 AATTTAAATA
Statistics
Matches: 705, Mismatches: 34, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
201 701 0.99
202 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (201 bp):
TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
CGATACTTTTGGTCCAGAATGGCTGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
AAAGTG
Found at i:6750550 original size:15 final size:17
Alignment explanation
Indices: 6750526--6750568 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
6750516 TTTCTCAAAG
*
6750526 CTCTTTTCAACC-CAAT
1 CTCTTCTCAACCACAAT
6750542 -TCTTCTCAACCACAAT
1 CTCTTCTCAACCACAAT
6750558 CTCCTTCTCAA
1 CT-CTTCTCAA
6750569 ATAAACGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 4 0.17
17 1 0.04
18 8 0.35
ACGTcount: A:0.26, C:0.40, G:0.00, T:0.35
Consensus pattern (17 bp):
CTCTTCTCAACCACAAT
Found at i:6752054 original size:14 final size:14
Alignment explanation
Indices: 6752029--6752093 Score: 112
Period size: 14 Copynumber: 4.6 Consensus size: 14
6752019 GTAATTTTTC
6752029 AATATAACCGGTATA
1 AATAT-ACCGGTATA
6752044 AATATACCGGTATA
1 AATATACCGGTATA
6752058 AATATACCGGTATA
1 AATATACCGGTATA
*
6752072 AATATACTGGTATA
1 AATATACCGGTATA
6752086 AATATACC
1 AATATACC
6752094 AGTTTTATGA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
14 43 0.90
15 5 0.10
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (14 bp):
AATATACCGGTATA
Found at i:6755312 original size:23 final size:23
Alignment explanation
Indices: 6755282--6755331 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
6755272 CGGTTAAATG
6755282 CCTATTACATTATATAAGCGCTA
1 CCTATTACATTATATAAGCGCTA
6755305 CCTATTACATTATATAAGCGCTA
1 CCTATTACATTATATAAGCGCTA
6755328 CCTA
1 CCTA
6755332 ATATGTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (23 bp):
CCTATTACATTATATAAGCGCTA
Found at i:6755353 original size:87 final size:87
Alignment explanation
Indices: 6755206--6755368 Score: 308
Period size: 87 Copynumber: 1.9 Consensus size: 87
6755196 AAATAGGTCA
*
6755206 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTCATAATATTT
6755271 CCGGTTAAATGCCTATTACATT
66 CCGGTTAAATGCCTATTACATT
*
6755293 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTCATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTCATAATATTT
6755358 CCGGTTAAATG
66 CCGGTTAAATG
6755369 ATATAACATT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTCATAATATTT
CCGGTTAAATGCCTATTACATT
Found at i:6757787 original size:2 final size:2
Alignment explanation
Indices: 6757780--6757809 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6757770 AATTTCTTCG
6757780 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
6757810 TGAATAGGTT
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:6757881 original size:43 final size:45
Alignment explanation
Indices: 6757826--6757909 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
6757816 GGTTGGAAAT
*
6757826 CTGGTAATAGCT-CAA-ACAATTTTAGGGAATAAGTTGGAAAAAA
1 CTGGTAATAGCTCCAACACAATCTTAGGGAATAAGTTGGAAAAAA
* *
6757869 CTGGTAATAGCTCCAACATAATCTTAGGTAATAAGTTGGAA
1 CTGGTAATAGCTCCAACACAATCTTAGGGAATAAGTTGGAA
6757910 GATTCCAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 12 0.33
44 3 0.08
45 21 0.58
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.27
Consensus pattern (45 bp):
CTGGTAATAGCTCCAACACAATCTTAGGGAATAAGTTGGAAAAAA
Found at i:6770277 original size:20 final size:20
Alignment explanation
Indices: 6770252--6770290 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
6770242 AGATTGTGCA
6770252 GGGGGTA-CAGATTCCCCCTG
1 GGGGGTATCA-ATTCCCCCTG
6770272 GGGGGTATCAATTCCCCCT
1 GGGGGTATCAATTCCCCCT
6770291 TAAAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (20 bp):
GGGGGTATCAATTCCCCCTG
Found at i:6770832 original size:43 final size:41
Alignment explanation
Indices: 6770767--6770847 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 41
6770757 AGCATGTTAT
* *
6770767 ATGATATGAGACTAAGTGATGAAACATAGATGATATATATATG
1 ATGATATAAGAATAAGTGATGAAACA-A-ATGATATATATATG
*
6770810 ATGATATAAGAATAAG-GCATGAATCAAATGATATATAT
1 ATGATATAAGAATAAGTG-ATGAAACAAATGATATATAT
6770848 GTTTATGTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 11 0.32
42 2 0.06
43 21 0.62
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.30
Consensus pattern (41 bp):
ATGATATAAGAATAAGTGATGAAACAAATGATATATATATG
Found at i:6771105 original size:21 final size:21
Alignment explanation
Indices: 6771058--6771117 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
6771048 AGTCGAGTGT
* *
6771058 TACATTGGTCCTACGGGAC-A
1 TACAGTGGTCCTTCGGGACAA
6771078 T--AGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTCGGGACAA
6771097 TACAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTCGGGACAA
6771118 ATTTCAGTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 14 0.40
19 2 0.06
20 1 0.03
21 18 0.51
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (21 bp):
TACAGTGGTCCTTCGGGACAA
Found at i:6774623 original size:60 final size:60
Alignment explanation
Indices: 6774530--6774652 Score: 237
Period size: 60 Copynumber: 2.0 Consensus size: 60
6774520 GTATGTTTGG
*
6774530 TCCAGCCATGGACATGAGATGTCACTTTGTCACAGATGAAACCAAATACGTCAGAACGAT
1 TCCAGCCATGGACATGAGATATCACTTTGTCACAGATGAAACCAAATACGTCAGAACGAT
6774590 TCCAGCCATGGACATGAGATATCACTTTGTCACAGATGAAACCAAATACGTCAGAACGAT
1 TCCAGCCATGGACATGAGATATCACTTTGTCACAGATGAAACCAAATACGTCAGAACGAT
6774650 TCC
1 TCC
6774653 GACCAATCAC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (60 bp):
TCCAGCCATGGACATGAGATATCACTTTGTCACAGATGAAACCAAATACGTCAGAACGAT
Found at i:6777954 original size:8 final size:8
Alignment explanation
Indices: 6777941--6777965 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6777931 TCTCTCATTT
6777941 CTCACTTC
1 CTCACTTC
6777949 CTCACTTC
1 CTCACTTC
6777957 CTCACTTC
1 CTCACTTC
6777965 C
1 C
6777966 AACCGAGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.52, G:0.00, T:0.36
Consensus pattern (8 bp):
CTCACTTC
Found at i:6778778 original size:27 final size:27
Alignment explanation
Indices: 6778715--6778779 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
6778705 TGGGCCTGAA
**
6778715 AAATAAAATAAAAATAAATAAATAAAT
1 AAATAAAATGTAAATAAATAAATAAAT
* * *
6778742 AAATATAATGTAAATAAA-AACTATAT
1 AAATAAAATGTAAATAAATAAATAAAT
6778768 AATATAAAATGT
1 AA-ATAAAATGT
6778780 GTTCTCAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 8 0.26
27 23 0.74
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (27 bp):
AAATAAAATGTAAATAAATAAATAAAT
Found at i:6778830 original size:25 final size:25
Alignment explanation
Indices: 6778796--6778854 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
6778786 AAAAATATTT
* * *
6778796 TTTTTAAAACTA-ATAATATGTACTC
1 TTTTCAAAACTATATAATATATA-TA
*
6778821 TTTTCAAAACTATATATTATATATA
1 TTTTCAAAACTATATAATATATATA
6778846 TTTTCAAAA
1 TTTTCAAAA
6778855 AATCTTTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 21 0.72
26 8 0.28
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (25 bp):
TTTTCAAAACTATATAATATATATA
Found at i:6778862 original size:38 final size:39
Alignment explanation
Indices: 6778819--6778918 Score: 152
Period size: 38 Copynumber: 2.6 Consensus size: 39
6778809 TAATATGTAC
6778819 TCTTTTCAAAACTATATATTATATATATTTTC-AAAAAA
1 TCTTTTCAAAACTATATATTATATATATTTTCAAAAAAA
6778857 TCTTTTCAAAACTATATA-T-TATATATTTTCAAAAAAAA
1 TCTTTTCAAAACTATATATTATATATATTTTC-AAAAAAA
* *
6778895 TGTTTTCAAAACTACATATTATAT
1 TCTTTTCAAAACTATATATTATAT
6778919 GTGTTATATG
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
36 11 0.20
37 1 0.02
38 40 0.71
39 1 0.02
40 3 0.05
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.44
Consensus pattern (39 bp):
TCTTTTCAAAACTATATATTATATATATTTTCAAAAAAA
Found at i:6780710 original size:5 final size:5
Alignment explanation
Indices: 6780700--6780724 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6780690 GGACTGAAAT
6780700 CAAAA CAAAA CAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA
6780725 TTTAAAGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:6782113 original size:17 final size:16
Alignment explanation
Indices: 6782092--6782124 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6782082 ATGTAGAAAT
6782092 TAAAAATATTTTAAAA
1 TAAAAATATTTTAAAA
6782108 TAAAAATATTTTAAAA
1 TAAAAATATTTTAAAA
6782124 T
1 T
6782125 TGTAAACTAT
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAAATATTTTAAAA
Found at i:6782171 original size:19 final size:20
Alignment explanation
Indices: 6782146--6782197 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
6782136 ATAAATATAT
*
6782146 AAAAATATAAAAT-T-TGGA
1 AAAAATATAAAATGTGTAGA
6782164 ACAAAATATGAAAATGTGTAGA
1 A-AAAATAT-AAAATGTGTAGA
6782186 AAAAATATAAAA
1 AAAAATATAAAA
6782198 ATCATAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 1 0.03
19 7 0.24
20 9 0.31
21 8 0.28
22 4 0.14
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.23
Consensus pattern (20 bp):
AAAAATATAAAATGTGTAGA
Found at i:6782192 original size:21 final size:18
Alignment explanation
Indices: 6782146--6782212 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 18
6782136 ATAAATATAT
*
6782146 AAAAATATAAAATTTGGA
1 AAAAATATAAAATTTAGA
6782164 ACAAAATATGAAAATGTGTAGA
1 A-AAAATAT-AAAAT-T-TAGA
* * *
6782186 AAAAATATAAAAATCATA
1 AAAAATATAAAATTTAGA
6782204 AAAAATATA
1 AAAAATATA
6782213 TATATTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 12 0.29
19 8 0.20
20 9 0.22
21 8 0.20
22 4 0.10
ACGTcount: A:0.64, C:0.03, G:0.09, T:0.24
Consensus pattern (18 bp):
AAAAATATAAAATTTAGA
Found at i:6783078 original size:58 final size:60
Alignment explanation
Indices: 6782985--6783098 Score: 153
Period size: 58 Copynumber: 1.9 Consensus size: 60
6782975 TATTTTTTTT
*
6782985 AAATAAATTATTTAATTATTATTTTTAGTTATTTTAAATATATAAATTATT-TTTTATCA
1 AAATAAATTATTAAATTATTATTTTTAGTTATTTTAAATATATAAATTATTCTTTTATCA
** * *
6783044 AAAT-AATTACTTAAATTA-TATTTTTTTTTGTTTTAAATATTTAAATTATTCTTTT
1 AAATAAATTA-TTAAATTATTATTTTTAGTTATTTTAAATATATAAATTATTCTTTT
6783099 GGTTAGATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 33 0.69
59 15 0.31
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (60 bp):
AAATAAATTATTAAATTATTATTTTTAGTTATTTTAAATATATAAATTATTCTTTTATCA
Found at i:6784890 original size:65 final size:64
Alignment explanation
Indices: 6784793--6784980 Score: 213
Period size: 65 Copynumber: 2.9 Consensus size: 64
6784783 GCATGAATCA
* * * * * *
6784793 ATGCATCGATGCACCCTTGTTTTAATT-GAACATCGAATGGCTTTTGTGTACCGATGCACATA-C
1 ATGCATCGATGCACCCATGTATT-ATTAAAACATCGAATGGATTTTATGCACCGATGCACA-AGC
6784856 T
64 T
*
6784857 ATGCATCGATGCACTCCATGTATTATTAAAACATCGAATTGATTTTATGCACCGATGCACAAGCT
1 ATGCATCGATGCAC-CCATGTATTATTAAAACATCGAATGGATTTTATGCACCGATGCACAAGCT
** *
6784922 ATGCATCGATGCACCCCGGATATT-TTAAAACATCGAATGTG-TTTTATGCATCGATGCAC
1 ATGCATCGATGCACCCATG-TATTATTAAAACATCGAATG-GATTTTATGCACCGATGCAC
6784981 CCTCAATGTA
Statistics
Matches: 108, Mismatches: 11, Indels: 10
0.84 0.09 0.08
Matches are distributed among these distances:
64 52 0.48
65 56 0.52
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACCCATGTATTATTAAAACATCGAATGGATTTTATGCACCGATGCACAAGCT
Found at i:6784996 original size:64 final size:65
Alignment explanation
Indices: 6784821--6784999 Score: 168
Period size: 65 Copynumber: 2.8 Consensus size: 65
6784811 GTTTTAATTG
* * * * * * **
6784821 AACATCGAATGGCTTTTGTGTACCGATGCACATA-CTATGCATCGATGCACTCCATG-TATTATT
1 AACATCGAATTGATTTTATGCACCGATGCACA-AGCAATGCACCGATGCAC-CCCGGATATTATT
6784884 AA
64 AA
* *
6784886 AACATCGAATTGATTTTATGCACCGATGCACAAGCTATGCATCGATGCACCCCGGATATT-TTAA
1 AACATCGAATTGATTTTATGCACCGATGCACAAGCAATGCACCGATGCACCCCGGATATTATTAA
* *** *
6784950 AACATCGAATGTG-TTTTATGCATCGATGCACCCTCAATGTACCGATGCAC
1 AACATCGAAT-TGATTTTATGCACCGATGCACAAGCAATGCACCGATGCAC
6785000 TAAGTCTTCC
Statistics
Matches: 98, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
64 48 0.49
65 50 0.51
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (65 bp):
AACATCGAATTGATTTTATGCACCGATGCACAAGCAATGCACCGATGCACCCCGGATATTATTAA
Found at i:6786947 original size:21 final size:21
Alignment explanation
Indices: 6786922--6786961 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
6786912 AAGACTTTAT
6786922 TTTCAAAA-TACAAAAATGATA
1 TTTCAAAATTA-AAAAATGATA
6786943 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
6786962 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:6790783 original size:21 final size:21
Alignment explanation
Indices: 6790759--6790815 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 21
6790749 TTGTGCATAA
6790759 TGCATCGATACACTATAAAGG
1 TGCATCGATACACTATAAAGG
* * *
6790780 TGCATCGATGCATCCCTATGAATG
1 TGCATCGAT--A-CACTATAAAGG
6790804 TGCATCGATACA
1 TGCATCGATACA
6790816 TCATGAAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 10 0.34
22 1 0.03
23 1 0.03
24 17 0.59
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (21 bp):
TGCATCGATACACTATAAAGG
Found at i:6790828 original size:21 final size:22
Alignment explanation
Indices: 6790758--6790833 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 22
6790748 TTTGTGCATA
*
6790758 ATGCATCGATACA-CTATAAAG
1 ATGCATCGATACATCTATGAAG
* *
6790779 GTGCATCGATGCATCCCTATGAATG
1 ATGCATCGATACAT--CTATGAA-G
6790804 -TGCATCGATACATC-ATGAAG
1 ATGCATCGATACATCTATGAAG
*
6790824 ATGCACCGAT
1 ATGCATCGAT
6790834 GCACTCCTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 24 0.53
22 1 0.02
24 18 0.40
25 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (22 bp):
ATGCATCGATACATCTATGAAG
Found at i:6790834 original size:45 final size:44
Alignment explanation
Indices: 6790759--6790853 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 44
6790749 TTGTGCATAA
* *
6790759 TGCATCGATACACTATAAAGGTGCATCGATGCA-TCCCTATGAATG
1 TGCATCGATACACTATAAAGATGCACCGATGCACT-CCT-TGAATG
*
6790804 TGCATCGATACA-TCATGAAGATGCACCGATGCACTCCTTGAATG
1 TGCATCGATACACT-ATAAAGATGCACCGATGCACTCCTTGAATG
6790848 TGCATC
1 TGCATC
6790854 TATGCACAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
44 13 0.29
45 31 0.69
46 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.26
Consensus pattern (44 bp):
TGCATCGATACACTATAAAGATGCACCGATGCACTCCTTGAATG
Found at i:6790851 original size:23 final size:22
Alignment explanation
Indices: 6790779--6790859 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
6790769 CACTATAAAG
6790779 GTGCATCGATGCATCCCTATGAAT
1 GTGCATCGATGCAT-CCT-TGAAT
* *
6790803 GTGCATCGATACAT-CATGAA-
1 GTGCATCGATGCATCCTTGAAT
*
6790823 GATGCACCGATGCACTCCTTGAAT
1 G-TGCATCGATGCA-TCCTTGAAT
*
6790847 GTGCATCTATGCA
1 GTGCATCGATGCA
6790860 CAGAGCCATG
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 14 0.30
22 2 0.04
23 15 0.33
24 14 0.30
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:6793435 original size:65 final size:64
Alignment explanation
Indices: 6793338--6793525 Score: 204
Period size: 65 Copynumber: 2.9 Consensus size: 64
6793328 GCATGAATCA
* * * * * *
6793338 ATGCATCGATGCACCCTTGTTTTAATT-GAACATCGAATGGCTTTTGTGTACCGATGCACATA-C
1 ATGCATCGATGCACCCATGTATT-ATTAAAACATCGAATGGATTTTATGCACCGATGCACA-AGC
6793401 T
64 T
*
6793402 ATGCATCGATGCACTCCATGTATTATTAAAACATCGAATTGATTTTATGCACCGATGCACAAGCT
1 ATGCATCGATGCAC-CCATGTATTATTAAAACATCGAATGGATTTTATGCACCGATGCACAAGCT
** * *
6793467 ATGCATCGATGCACCCCGGCTATT-TTAAAACATCGAATGTG-TTTTCTGCATCGATGCAC
1 ATGCATCGATGCACCCATG-TATTATTAAAACATCGAATG-GATTTTATGCACCGATGCAC
6793526 CCTCAATGTA
Statistics
Matches: 107, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
64 51 0.48
65 56 0.52
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACCCATGTATTATTAAAACATCGAATGGATTTTATGCACCGATGCACAAGCT
Found at i:6793541 original size:64 final size:65
Alignment explanation
Indices: 6793366--6793544 Score: 159
Period size: 65 Copynumber: 2.8 Consensus size: 65
6793356 GTTTTAATTG
* * * * * * **
6793366 AACATCGAATGGCTTTTGTGTACCGATGCACATA-CTATGCATCGATGCACTCCATG-TATTATT
1 AACATCGAATTGATTTTATGCACCGATGCACA-AGCAATGCACCGATGCAC-CCCGGCTATTATT
6793429 AA
64 AA
* *
6793431 AACATCGAATTGATTTTATGCACCGATGCACAAGCTATGCATCGATGCACCCCGGCTATT-TTAA
1 AACATCGAATTGATTTTATGCACCGATGCACAAGCAATGCACCGATGCACCCCGGCTATTATTAA
* * *** *
6793495 AACATCGAATGTG-TTTTCTGCATCGATGCACCCTCAATGTACCGATGCAC
1 AACATCGAAT-TGATTTTATGCACCGATGCACAAGCAATGCACCGATGCAC
6793545 TAAGTCTTCC
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
64 47 0.48
65 50 0.52
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (65 bp):
AACATCGAATTGATTTTATGCACCGATGCACAAGCAATGCACCGATGCACCCCGGCTATTATTAA
Found at i:6793824 original size:27 final size:27
Alignment explanation
Indices: 6793793--6793846 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
6793783 TCAAAGAGAA
6793793 AGCATCAAACCTCAAGTTTGAGCACAT
1 AGCATCAAACCTCAAGTTTGAGCACAT
6793820 AGCATCAAACCTCAAGTTTGAGCACAT
1 AGCATCAAACCTCAAGTTTGAGCACAT
6793847 TCAAGCTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (27 bp):
AGCATCAAACCTCAAGTTTGAGCACAT
Found at i:6794796 original size:24 final size:24
Alignment explanation
Indices: 6794764--6794820 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
6794754 AAAATTTAGG
6794764 AGCTCGATTGAAGCTCGAGACTCA
1 AGCTCGATTGAAGCTCGAGACTCA
*
6794788 AGCTCGATTGAAGCTTGAGACTCA
1 AGCTCGATTGAAGCTCGAGACTCA
*
6794812 AACTCGATT
1 AGCTCGATT
6794821 TTGAGCTCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (24 bp):
AGCTCGATTGAAGCTCGAGACTCA
Found at i:6794850 original size:17 final size:17
Alignment explanation
Indices: 6794830--6794862 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6794820 TTTGAGCTCG
*
6794830 ATTCAAGCTTGAACTCC
1 ATTCAAGCTCGAACTCC
6794847 ATTCAAGCTCGAACTC
1 ATTCAAGCTCGAACTC
6794863 AAACTCGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.27
Consensus pattern (17 bp):
ATTCAAGCTCGAACTCC
Found at i:6799378 original size:7 final size:7
Alignment explanation
Indices: 6799366--6799410 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
6799356 AACTTCAACA
6799366 CTAAACC
1 CTAAACC
*
6799373 CTAAACT
1 CTAAACC
*
6799380 CTAAATC
1 CTAAACC
*
6799387 TTAAACC
1 CTAAACC
6799394 CTAAACC
1 CTAAACC
*
6799401 CTAAATC
1 CTAAACC
6799408 CTA
1 CTA
6799411 TCACATAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.24
Consensus pattern (7 bp):
CTAAACC
Found at i:6799391 original size:21 final size:21
Alignment explanation
Indices: 6799367--6799407 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
6799357 ACTTCAACAC
*
6799367 TAAACCCTAAACTCTAAATCT
1 TAAACCCTAAACCCTAAATCT
6799388 TAAACCCTAAACCCTAAATC
1 TAAACCCTAAACCCTAAATC
6799408 CTATCACATA
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:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAATCT
Found at i:6799876 original size:11 final size:11
Alignment explanation
Indices: 6799860--6799922 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
6799850 GTATTATAGA
6799860 ATTTTTAATAT
1 ATTTTTAATAT
6799871 ATTTTTAA-A-
1 ATTTTTAATAT
6799880 ATTTTATAAT-T
1 ATTTT-TAATAT
**** *
6799891 ATCAACAATGT
1 ATTTTTAATAT
6799902 ATTTTTAATAT
1 ATTTTTAATAT
6799913 ATTTTTAATA
1 ATTTTTAATA
6799923 ATGCAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:6810227 original size:31 final size:31
Alignment explanation
Indices: 6810192--6810259 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
6810182 CTTTTAAAAC
6810192 TTGCAAAACAGTCCACCAATATTTAGT-TCGT
1 TTGCAAAACAGTCCACCAATATTTAGTCT-GT
* ** *
6810223 TTGCAATATGGTCCCCCAATATTTAGTCTGT
1 TTGCAAAACAGTCCACCAATATTTAGTCTGT
6810254 TTGCAA
1 TTGCAA
6810260 TATGGTCCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (31 bp):
TTGCAAAACAGTCCACCAATATTTAGTCTGT
Found at i:6810260 original size:31 final size:31
Alignment explanation
Indices: 6810202--6810268 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
6810192 TTGCAAAACA
*
6810202 GTCCACCAATATTTAGTTCGTTTGCAATATG
1 GTCCCCCAATATTTAGTTCGTTTGCAATATG
6810233 GTCCCCCAATATTTAG-TCTGTTTGCAATATG
1 GTCCCCCAATATTTAGTTC-GTTTGCAATATG
6810264 GTCCC
1 GTCCC
6810269 TGACCATTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.37
Consensus pattern (31 bp):
GTCCCCCAATATTTAGTTCGTTTGCAATATG
Found at i:6812259 original size:31 final size:31
Alignment explanation
Indices: 6812183--6812248 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
6812173 TCAAACGGTC
* *
6812183 GGGACCATATTACAAACAGACTAAATGTTGG
1 GGGACCATATTGCAAACAGACAAAATGTTGG
*
6812214 GGGACCATATTGCAAACGGACAAAATGTTGG
1 GGGACCATATTGCAAACAGACAAAATGTTGG
6812245 GGGA
1 GGGA
6812249 TTGTATTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (31 bp):
GGGACCATATTGCAAACAGACAAAATGTTGG
Found at i:6814265 original size:23 final size:22
Alignment explanation
Indices: 6814239--6814300 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 22
6814229 GTGCCATATA
*
6814239 AAATGTCCATAAGGACCACATAG
1 AAAT-TCCATAAGGACCACATAC
* * *
6814262 AAATCTCCTTAAGAACCATATAC
1 AAAT-TCCATAAGGACCACATAC
*
6814285 ATATTCCA-AAGGACCA
1 AAATTCCATAAGGACCA
6814301 AATATGTGTC
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
21 7 0.23
22 3 0.10
23 21 0.68
ACGTcount: A:0.44, C:0.24, G:0.11, T:0.21
Consensus pattern (22 bp):
AAATTCCATAAGGACCACATAC
Found at i:6816545 original size:30 final size:27
Alignment explanation
Indices: 6816481--6816545 Score: 67
Period size: 30 Copynumber: 2.3 Consensus size: 27
6816471 GTAAACACTT
6816481 AAAATATTATTATTCTATATATTTAATA
1 AAAATA-TATTATTCTATATATTTAATA
** *
6816509 TTAATATATTATTTTAGTATCATTTTAATA
1 AAAATATATTATTCTA-TAT-A-TTTAATA
6816539 AAAATAT
1 AAAATAT
6816546 TAATTATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 9 0.31
28 7 0.24
29 1 0.03
30 12 0.41
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (27 bp):
AAAATATATTATTCTATATATTTAATA
Found at i:6825086 original size:37 final size:36
Alignment explanation
Indices: 6825027--6825146 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
6825017 ATCCCATTAT
* *
6825027 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
6825062 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
6825099 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
6825134 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
6825147 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
35 35 0.45
36 8 0.10
37 34 0.44
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:6825102 original size:21 final size:20
Alignment explanation
Indices: 6825075--6825138 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
6825065 TTTTTCAAAG
6825075 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
6825095 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
6825110 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
6825130 AAATCATTT
1 AAA-CATTT
6825139 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:6829232 original size:16 final size:16
Alignment explanation
Indices: 6829208--6829240 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6829198 TATCGCCGAC
*
6829208 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
6829224 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
6829240 C
1 C
6829241 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:6829708 original size:37 final size:37
Alignment explanation
Indices: 6829650--6829769 Score: 156
Period size: 35 Copynumber: 3.3 Consensus size: 37
6829640 TCCCATTATC
* *
6829650 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
*
6829686 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
* *
6829722 A-TTTTCAAAGAAACATTTACCGAACTTTGAAAATCAT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC-T
*
6829759 TTTTTTCAAAG
1 ATTTTTCAAAG
6829770 TTGGTTACCA
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 27 0.37
36 17 0.23
37 20 0.27
38 9 0.12
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
Found at i:6835454 original size:6 final size:6
Alignment explanation
Indices: 6835443--6835468 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6835433 AGACACGTAT
6835443 GACCAC GACCAC GACCAC GACCAC GA
1 GACCAC GACCAC GACCAC GACCAC GA
6835469 GACGAGACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.46, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:6835475 original size:5 final size:5
Alignment explanation
Indices: 6835465--6835501 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
6835455 GACCACGACC
6835465 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACG-G ACG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACG
6835502 GCGGCGCGCG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.38, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:6836287 original size:42 final size:42
Alignment explanation
Indices: 6836228--6836500 Score: 474
Period size: 42 Copynumber: 6.5 Consensus size: 42
6836218 TGCGATTTTG
*
6836228 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAATTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
6836270 GACTATCGCAATGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
6836312 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
6836354 GACTATTGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
6836396 GACTATCACAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
6836438 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
6836480 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
6836501 CTATCGCAAC
Statistics
Matches: 216, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 216 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:6836551 original size:42 final size:38
Alignment explanation
Indices: 6836232--6836569 Score: 127
Period size: 42 Copynumber: 8.2 Consensus size: 38
6836222 ATTTTGGACT
* * **
6836232 ATCGCAACGAACTTGGAATAAATCGCAACGCGAATTTCGACT
1 ATCGCAACGAACTTGGACT--ATCGCAA--CGAATTTGGAAA
* * * **
6836274 ATCGCAATGAACTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAACTTGGACT--ATCGCAA--CGAATTTGGAAA
* * * * **
6836316 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGACT--ATCGCAA--CGAATTTGGAAA
* * * * **
6836358 ATTGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGACT--ATCGCAA--CGAATTTGGAAA
* * * **
6836400 ATCACAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAACTTGGACT--ATCGCAA--CGAATTTGGAAA
* * * * **
6836442 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGACT--ATCGCAA--CGAATTTGGAAA
6836484 ATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGACTATCGCAACGAATTTGG-A-AA
*
6836524 ATCGCAACGTGAATTTGGACTATCGCAACGAATTTGGAAA
1 ATCGCAAC--GAACTTGGACTATCGCAACGAATTTGGAAA
6836564 ATCGCA
1 ATCGCA
6836570 TTGCGATAGT
Statistics
Matches: 271, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
38 7 0.03
39 1 0.00
40 23 0.08
41 1 0.00
42 239 0.88
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (38 bp):
ATCGCAACGAACTTGGACTATCGCAACGAATTTGGAAA
Found at i:6836594 original size:21 final size:21
Alignment explanation
Indices: 6836565--6836617 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
6836555 ATTTGGAAAA
*
6836565 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
6836586 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
6836607 TCGCGTTGCGA
1 TCGCGTTGCGA
6836618 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:6842844 original size:3 final size:3
Alignment explanation
Indices: 6842836--6842867 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6842826 GAGTGCCACA
6842836 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
6842868 TGGGAATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:6842870 original size:56 final size:56
Alignment explanation
Indices: 6842810--6842923 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
6842800 TAACAGAGTT
6842810 TTTGGGAATATGGTGAGAGTGCCACATTCTTCTTCTTCTTCTTCTTCTTCTTCTTC
1 TTTGGGAATATGGTGAGAGTGCCACATTCTTCTTCTTCTTCTTCTTCTTCTTCTTC
6842866 TTTGGGAATATGGTGAGAGTGCCACATTCTTCTTCTTCTTCTTCTTCTTCTTCTTC
1 TTTGGGAATATGGTGAGAGTGCCACATTCTTCTTCTTCTTCTTCTTCTTCTTCTTC
6842922 TT
1 TT
6842924 CTTCTTCTTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.12, C:0.23, G:0.16, T:0.49
Consensus pattern (56 bp):
TTTGGGAATATGGTGAGAGTGCCACATTCTTCTTCTTCTTCTTCTTCTTCTTCTTC
Found at i:6842900 original size:3 final size:3
Alignment explanation
Indices: 6842892--6842933 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
6842882 GAGTGCCACA
6842892 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6842934 CATCATTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:6842975 original size:3 final size:3
Alignment explanation
Indices: 6842967--6843000 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
6842957 ATTAATGGTA
6842967 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
6843001 CATCATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:6842997 original size:67 final size:67
Alignment explanation
Indices: 6842900--6843069 Score: 279
Period size: 67 Copynumber: 2.5 Consensus size: 67
6842890 CATTCTTCTT
*
6842900 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCCATCATTTTTAAATAAAATAAAAATTAATGG
1 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCCATCATTTTTAAATAAAATAAAAATTAATGC
6842965 TA
66 TA
*
6842967 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCCATCATTTTTAAATAAAATAAAAATTAATTC
1 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCCATCATTTTTAAATAAAATAAAAATTAATGC
*
6843032 TT
66 TA
6843034 CTCTCTTTCTTCTTCTT-TCTCTTCTTCTTCTTCTTC
1 CT-TC-TTCTTCTTCTTCT-TCTTCTTCTTCTTCTTC
6843070 TTCTTCTTCT
Statistics
Matches: 97, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
67 66 0.68
68 3 0.03
69 28 0.29
ACGTcount: A:0.19, C:0.25, G:0.01, T:0.55
Consensus pattern (67 bp):
CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCCATCATTTTTAAATAAAATAAAAATTAATGC
TA
Found at i:6843046 original size:3 final size:3
Alignment explanation
Indices: 6843029--6845140 Score: 1880
Period size: 3 Copynumber: 712.0 Consensus size: 3
6843019 TAAAAATTAA
6843029 TTC TTC TCTC TTTC TTC TTC TT- TCTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC T-TC -TTC TTC TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC
6843076 TTC TTC TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6843122 TTC TTC TTTC TTC TTC -TC TTC TTC -TC TTC TTC TTC TT- TTC TT-
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6843164 TT- TTC TT- TTC TTC TTC -TC TTC TTTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC
6843207 TTTC TTC TTC TTC -TC TTC TTC TTC TT- TTC TTC TTC TTC TTC -TC
1 -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
6843250 TTC TTT TTC TTC TTC TTC -TC TTC TTC -TC TTC TTC TTC TTTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC
6843294 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6843342 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6843389 TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6843436 TTC TTC TTC -TC TTC TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC -TC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
6843481 TTC TTC TTC -TC TTA TTC TT- TTC TTC TTC TT- TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
6843526 TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
6843573 TTC TTC TTC TTC TTC TTC TTC -TC TTC TTA TT- TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* *
6843619 TTC -TC TTC GTC GTC TTC TTC TTC TTC TTC TTC TT- TTC TTTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC
* * * * *** **
6843663 TTC TTC TTC TTC TTC TT- TCTC TTC ATC ATT- TT- TTAA ATA AAA TAA
1 TTC TTC TTC TTC TTC TTC T-TC TTC TTC -TTC TTC TT-C TTC TTC TTC
*** * * * * * * * *** *** ** *** *
6843708 AAA TTA ATG TAC GATGTG TGAC TT- TTG AAA AGA TGAA GGA GTC TT-
1 TTC TTC TTC TTC --T-TC T-TC TTC TTC TTC TTC T-TC TTC TTC TTC
6843753 TTC TTC TTC TTTC TTC TTTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC -TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* *
6843800 TTC TTC TTC TTTC GTC TTC TTC TTC TTC GTC TTC TTC TTC TTC TTC
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* *
6843846 TTC TTC TT- TTC TTC TTC TTC TTC TTA TTC TTC -TC TTCC ATC ATT-
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC -TTC
** * * *** ** *** * ** * * * * *** * *
6843890 TAA ATA AAA TAA AAA TTAA TGG TAC GATGTG TGAC TT- TTGAA AAG ATG
1 TTC TTC TTC TTC TTC TT-C TTC TTC --T-TC T-TC TTC TT--C TTC TTC
*** ***
6843938 AAG GAG TTC TTTC TTC TTC TTC TTC -TC TTTC TTC TT- TT- TTC TTC
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC
*
6843982 TTC TTC TT- TTC TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC TT- TTT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6844027 TTC TT- TTC TTC TT- TT- TTC TTC -TC TT- TTC TTC -TC TTC TTTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC
6844067 TTC TTC TTC TTC TTC TTC -TC TTTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC
6844112 TTC TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
6844159 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6844207 TTC TTC TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* *
6844253 TTC TTC TTC TTC TTA TTT TTC TTC TTC TTTC TTC TTC TTC TTC TT-
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC
* *
6844298 TTC TTC TTC TTC TTC TTA TTC TTC TTC TTTC TTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC
6844344 TTC TTC TTTC TTC TTC TT- TTC -TC TT- TTC TTC TTC -TC TTC TTC
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * ** ** *** *
6844386 TTC TTC TTC TTC GTC TTC ATC ATT- TT- TTAAA TAAA TAA AAA TTAA
1 TTC TTC TTC TTC TTC TTC TTC -TTC TTC TT--C T-TC TTC TTC TT-C
** * * * * *** *** ** *** *
6844431 TGG TAC GATGTG TGAC TT- TTG AAA AGA TGAA GGA GTC TTC -TC TTC
1 TTC TTC --T-TC T-TC TTC TTC TTC TTC T-TC TTC TTC TTC TTC TTC
6844476 TTC TTC TTC TTC TTC TTC TTC -TC TTC TTC TTTC TT- TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC
*
6844520 -TC TTA TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* *
6844566 TTC TTC TTC GTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC GTC TTCC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C
* * * * *** ** *** * ** * * *
6844615 ATC ATT- TT- TTAA ATA AAA TAA AAA TTAA TGG TAC GATGTG TGAC TT-
1 TTC -TTC TTC TT-C TTC TTC TTC TTC TT-C TTC TTC --T-TC T-TC TTC
* *** *** ** *** *
6844661 TTG AAA AGA TGAA GGA GTC TTC TTC TTC TTC TTC TTC TTC TTC TT-
1 TTC TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6844706 TTC TTC TTC -TC TTC TTC TTC TTC TTC TTC TT- TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6844752 TTC TTC TTC -TC TTC TTC TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6844798 TTC TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6844845 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6844893 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6844941 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6844989 TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6845034 TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * *
6845081 TTC TTC GTC TTC TTC TTC TTC GTC TTC TTC GTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
6845129 TTC TTC GTC TTC
1 TTC TTC TTC TTC
6845141 CATCATTTTT
Statistics
Matches: 1833, Mismatches: 152, Indels: 248
0.82 0.07 0.11
Matches are distributed among these distances:
2 155 0.08
3 1587 0.87
4 85 0.05
5 6 0.00
ACGTcount: A:0.05, C:0.29, G:0.03, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:6845937 original size:23 final size:23
Alignment explanation
Indices: 6845902--6845946 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6845892 AAAAGGGTTT
* * *
6845902 GCTAGCCATTCTAGATTTTAAAA
1 GCTAACCAATCTAGATTCTAAAA
6845925 GCTAACCAATCTAGATTCTAAA
1 GCTAACCAATCTAGATTCTAAA
6845947 GAAACTATCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (23 bp):
GCTAACCAATCTAGATTCTAAAA
Found at i:6846705 original size:13 final size:14
Alignment explanation
Indices: 6846687--6846720 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
6846677 AATACATACC
6846687 AAATATAAAA-TGT
1 AAATATAAAACTGT
6846700 AAATATAAAACTGT
1 AAATATAAAACTGT
*
6846714 ATATATA
1 AAATATA
6846721 TATATTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (14 bp):
AAATATAAAACTGT
Found at i:6849041 original size:117 final size:116
Alignment explanation
Indices: 6848644--6849094 Score: 474
Period size: 117 Copynumber: 3.9 Consensus size: 116
6848634 TACAACTGTT
* * * * *
6848644 AAGGTTGATCAAGCTCTCCTATACT-AACTTCTTCTCTCTCATCTAGATGAATTCTTCTCATTTT
1 AAGGTCGAACAAGCTCTCCTATA-TGAACTTCTTCTCTCTCATCTGGATGAGTTCTTCTCATTAT
* ** * * *
6848708 GAACTCTTCCATTGGAAATGCCGATCCATCTTCTTCTATGATGGATTTGAGCA
65 GAAC-CTTCTATTGGAAATGTTGATCCAACTCCTTCTGTGATGGATTTGAGCA
* *
6848761 AAGGTCGAACAAGCTCTCCTATATGAACTTCTTCTC-CTTTAT-TCGTATGAGTTCTTCTCATTA
1 AAGGTCGAACAAGCTCTCCTATATGAACTTCTTCTCTC-TCATCT-GGATGAGTTCTTCTCATTA
* *
6848824 TGAA-C-TCTATT-GAAATGTTGATCCACCTCCTTCTGTGATGGA--TGAGCC
64 TGAACCTTCTATTGGAAATGTTGATCCAACTCCTTCTGTGATGGATTTGAGCA
* * * * *
6848872 AAGGTTGAGCAAGCTCTCCTATATGAACTTCTTATCTCCCATCTGGACGAGTTCTTCTCATTATG
1 AAGGTCGAACAAGCTCTCCTATATGAACTTCTTCTCTCTCATCTGGATGAGTTCTTCTCATTATG
* *
6848937 AACCATTCTATTGGAAATGTTTATCCAACTCCTCCTGTGATGGATTTGAGCA
66 AACC-TTCTATTGGAAATGTTGATCCAACTCCTTCTGTGATGGATTTGAGCA
* * * * *
6848989 AAGATCAAACAAACTCTCCTATATGAACTTCTTCTCAT-TCATTTGGATGAGTTCTTCTTATTAT
1 AAGGTCGAACAAGCTCTCCTATATGAACTTCTTCTC-TCTCATCTGGATGAGTTCTTCTCATTAT
* * *
6849053 GAA-CTCTCTTAATGGAAATGTTGTTCAATACT-CTTCTGTGAT
65 GAACCT-TC-TATTGGAAATGTTGATCCA-ACTCCTTCTGTGAT
6849095 AGACGAGATA
Statistics
Matches: 279, Mismatches: 40, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
111 61 0.22
112 3 0.01
113 26 0.09
114 11 0.04
115 30 0.11
116 6 0.02
117 138 0.49
118 4 0.01
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (116 bp):
AAGGTCGAACAAGCTCTCCTATATGAACTTCTTCTCTCTCATCTGGATGAGTTCTTCTCATTATG
AACCTTCTATTGGAAATGTTGATCCAACTCCTTCTGTGATGGATTTGAGCA
Found at i:6849041 original size:228 final size:228
Alignment explanation
Indices: 6848644--6849059 Score: 593
Period size: 228 Copynumber: 1.8 Consensus size: 228
6848634 TACAACTGTT
* * * * *
6848644 AAGGTTGATCAAGCTCTCCTATACTAACTTCTTCTCTCTCATCTAGATGAATTCTTCTCATTTTG
1 AAGGTTGAGCAAGCTCTCCTATACTAACTTCTTATCTCCCATCTAGACGAATTCTTCTCATTATG
* * * * * *
6848709 AACTCTTCCATTGGAAATGCCGATCCATCTTCTTCTATGATGGATTTGAGCAAAGGTCGAACAAG
66 AACTCTTCCATTGGAAATGCCGATCCAACTCCTCCTATGATGGATTTGAGCAAAGATCAAACAAA
* * *
6848774 CTCTCCTATATGAACTTCTTCTCCTTTATTCGTATGAGTTCTTCTCATTATGAACTCTATTGAAA
131 CTCTCCTATATGAACTTCTTCTCATTCATTCGGATGAGTTCTTCTCATTATGAACTCTATTGAAA
6848839 TGTTGATCCACCTCCTTCTGTGATGGATGAGCC
196 TGTTGATCCACCTCCTTCTGTGATGGATGAGCC
* *
6848872 AAGGTTGAGCAAGCTCTCCTATA-TGAACTTCTTATCTCCCATCTGGACGAGTTCTTCTCATTAT
1 AAGGTTGAGCAAGCTCTCCTATACT-AACTTCTTATCTCCCATCTAGACGAATTCTTCTCATTAT
* *** *
6848936 GAAC-CATTCTATTGGAAATGTTTATCCAACTCCTCCTGTGATGGATTTGAGCAAAGATCAAACA
65 GAACTC-TTCCATTGGAAATGCCGATCCAACTCCTCCTATGATGGATTTGAGCAAAGATCAAACA
* *
6849000 AACTCTCCTATATGAACTTCTTCTCATTCATTTGGATGAGTTCTTCTTATTATGAACTCT
129 AACTCTCCTATATGAACTTCTTCTCATTCATTCGGATGAGTTCTTCTCATTATGAACTCT
6849060 CTTAATGGAA
Statistics
Matches: 163, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
227 2 0.01
228 161 0.99
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (228 bp):
AAGGTTGAGCAAGCTCTCCTATACTAACTTCTTATCTCCCATCTAGACGAATTCTTCTCATTATG
AACTCTTCCATTGGAAATGCCGATCCAACTCCTCCTATGATGGATTTGAGCAAAGATCAAACAAA
CTCTCCTATATGAACTTCTTCTCATTCATTCGGATGAGTTCTTCTCATTATGAACTCTATTGAAA
TGTTGATCCACCTCCTTCTGTGATGGATGAGCC
Done.