Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 219 of 240
Found at i:66121239 original size:21 final size:19
Alignment explanation
Indices: 66121205--66121243 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
66121195 ATAATCCTCC
66121205 GGAAAATGGCTTAGATAGA
1 GGAAAATGGCTTAGATAGA
66121224 GGAAACATGGTCTTAGATAG
1 GGAAA-ATGG-CTTAGATAG
66121244 GGAGGCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (19 bp):
GGAAAATGGCTTAGATAGA
Found at i:66124589 original size:13 final size:13
Alignment explanation
Indices: 66124571--66124609 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
66124561 AAGAGATTCG
66124571 AGGTTCAAGGTTT
1 AGGTTCAAGGTTT
*
66124584 AGGTTCAGGGTTT
1 AGGTTCAAGGTTT
*
66124597 CGAGTTCAAGGTT
1 AG-GTTCAAGGTT
66124610 CGGGGTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.21, C:0.10, G:0.33, T:0.36
Consensus pattern (13 bp):
AGGTTCAAGGTTT
Found at i:66124611 original size:13 final size:14
Alignment explanation
Indices: 66124567--66124616 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
66124557 AACTAAGAGA
66124567 TTCGAGGTTCAAGG
1 TTCGAGGTTCAAGG
* *
66124581 TT-TAGGTTCAGGG
1 TTCGAGGTTCAAGG
66124594 TTTCGA-GTTCAAGG
1 -TTCGAGGTTCAAGG
*
66124608 TTCGGGGTT
1 TTCGAGGTT
66124617 TTGGGTTCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 13 0.46
14 14 0.50
15 1 0.04
ACGTcount: A:0.16, C:0.12, G:0.36, T:0.36
Consensus pattern (14 bp):
TTCGAGGTTCAAGG
Found at i:66124811 original size:17 final size:18
Alignment explanation
Indices: 66124779--66124816 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
66124769 GAAAAGATGT
66124779 TTATTTATAATTTAAAAAA
1 TTATTTAT-ATTTAAAAAA
*
66124798 TTATTTAT-TTTAAATAA
1 TTATTTATATTTAAAAAA
66124815 TT
1 TT
66124817 TAATTAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
19 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATTTATATTTAAAAAA
Found at i:66125850 original size:18 final size:18
Alignment explanation
Indices: 66125825--66125861 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
66125815 ATATTTTGAT
66125825 ATATATATAAATAAATATGC
1 ATATATAT-AA-AAATATGC
66125845 ATATATATAAAAATATG
1 ATATATATAAAAATATG
66125862 TACATGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 2 0.12
20 8 0.47
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (18 bp):
ATATATATAAAAATATGC
Found at i:66126246 original size:3 final size:3
Alignment explanation
Indices: 66126238--66126269 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
66126228 AATAAATAGG
66126238 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
66126270 GGACTAATTC
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:66127888 original size:97 final size:98
Alignment explanation
Indices: 66127534--66128006 Score: 785
Period size: 97 Copynumber: 4.9 Consensus size: 98
66127524 TGCGAGGAAA
* ** * * *
66127534 AGATTCGCCGTTGCGGCTTCAATCTGTTCCGCTGCGTCGCCTGGAAGTAAGATTCGCCGTTGTGG
1 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCC-AGAAGTAAGATTCGCCGTTGTGG
66127599 CTTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
65 CTTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
* * * *
66127633 AGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCGCCAGAAGTAAGATTCACCGTTGTGGC
1 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
66127698 TTCGAT-TTTTAAATT-CAATGTC-GGGAAGTG
66 TTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
*
66127728 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCACCGTTGTGGC
1 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
66127793 TTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
66 TTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
*
66127826 AGATTCGCTGTTGTAGCTTCAATCTGCT-CGCTGCATCGCCAGAAGTAAGATTCGCCGCTGTGGC
1 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
66127890 TTCGATC-TTTAAATTGCAATGTCGGGGAAGTG
66 TTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
*
66127922 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGCTGTGGC
1 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
66127987 TTCGATCTTTTAAATTGCAA
66 TTCGATCTTTTAAATTGCAA
66128007 ACTATGGTTT
Statistics
Matches: 358, Mismatches: 11, Indels: 11
0.94 0.03 0.03
Matches are distributed among these distances:
95 76 0.21
96 69 0.19
97 100 0.28
98 76 0.21
99 37 0.10
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.32
Consensus pattern (98 bp):
AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
TTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
Found at i:66140699 original size:3 final size:3
Alignment explanation
Indices: 66140691--66140728 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
66140681 AATAAATAGG
*
66140691 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
66140729 GGACTAATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:66140707 original size:12 final size:12
Alignment explanation
Indices: 66140685--66140725 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
66140675 AGTATAAATA
66140685 AATAGGTAATAAT
1 AATA-GTAATAAT
66140698 AATAGTAATAAT
1 AATAGTAATAAT
*
66140710 AATAATAATAAT
1 AATAGTAATAAT
66140722 AATA
1 AATA
66140726 ATAGGACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (12 bp):
AATAGTAATAAT
Found at i:66142553 original size:31 final size:29
Alignment explanation
Indices: 66142518--66142592 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
66142508 AACGGCTCAA
*
66142518 TGACTAAAATGTCACAATGCGATAACATAAG
1 TGACTAAAATGTAACAATGC-A-AACATAAG
* * *
66142549 TGACTAAAACGTAACATTTCAAACATAAG
1 TGACTAAAATGTAACAATGCAAACATAAG
66142578 TGACTAAAATGTAAC
1 TGACTAAAATGTAAC
66142593 CTGAGCCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 22 0.56
30 1 0.03
31 16 0.41
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (29 bp):
TGACTAAAATGTAACAATGCAAACATAAG
Found at i:66144377 original size:37 final size:37
Alignment explanation
Indices: 66144312--66144460 Score: 217
Period size: 37 Copynumber: 4.0 Consensus size: 37
66144302 CATGCATTAA
*
66144312 TCATCAATAGAATGAGACTACAAACAAGAAAGGTATAT
1 TCAT-AATAGAATGAGAATACAAACAAGAAAGGTATAT
* * *
66144350 TCATAATAGAATGAGAAAACAAGCAAGAAAGGTATGT
1 TCATAATAGAATGAGAATACAAACAAGAAAGGTATAT
* *
66144387 TCAAAATAGAATGAGAATACTAACAAGAAAGGTATAT
1 TCATAATAGAATGAGAATACAAACAAGAAAGGTATAT
* *
66144424 TCATAATCGAATGAGAATACAAACAAGAAAGCTATAT
1 TCATAATAGAATGAGAATACAAACAAGAAAGGTATAT
66144461 ATGAATTACT
Statistics
Matches: 98, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
37 94 0.96
38 4 0.04
ACGTcount: A:0.52, C:0.11, G:0.17, T:0.21
Consensus pattern (37 bp):
TCATAATAGAATGAGAATACAAACAAGAAAGGTATAT
Found at i:66144550 original size:30 final size:27
Alignment explanation
Indices: 66144516--66144570 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 27
66144506 TATGTATATT
66144516 TTTCACTTATAAATTTGTATATATAATTAA
1 TTTCACTTAT-AA-TT-TATATATAATTAA
* *
66144546 TTTCATTTGTAATTTATATATAATT
1 TTTCACTTATAATTTATATATAATT
66144571 TCATCTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.48
28 2 0.09
29 2 0.09
30 8 0.35
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (27 bp):
TTTCACTTATAATTTATATATAATTAA
Found at i:66152662 original size:37 final size:37
Alignment explanation
Indices: 66152620--66152728 Score: 139
Period size: 37 Copynumber: 2.9 Consensus size: 37
66152610 ATTAATCATC
* *
66152620 AATAGAATGAGAATAC-ACGCAAGAAAGGTATGTTCAA
1 AATAGAATGAGAATACTA-ACAAGAAAGGTATATTCAA
*
66152657 AATAGAATGAGAATACTAACAAGAAAGGTATATTCAT
1 AATAGAATGAGAATACTAACAAGAAAGGTATATTCAA
* ** *
66152694 AATCGAATGAGAATAGAAACAAGAAAGCTATATTC
1 AATAGAATGAGAATACTAACAAGAAAGGTATATTC
66152729 CTATGAATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
37 63 0.98
38 1 0.02
ACGTcount: A:0.50, C:0.10, G:0.18, T:0.21
Consensus pattern (37 bp):
AATAGAATGAGAATACTAACAAGAAAGGTATATTCAA
Found at i:66155748 original size:153 final size:152
Alignment explanation
Indices: 66155469--66156001 Score: 608
Period size: 158 Copynumber: 3.5 Consensus size: 152
66155459 CCACGGTAAG
* * * * *
66155469 AAAGGA-AAACAAGTATGCCTTTGTTTATGGTTTCAGCTTACTTATGTAGC-AAGAAAAGTGAAT
1 AAAGGAGAAAAAAGTATGCCTTTGTTTATGGTTTCAGCTTGCTTGTGTAGCAAAAAAAAATGAAT
* * * *** **
66155532 ATAAACACATATATTTAGTATGGGTTCTTGAACTTGAATTGAGCAAAGAATTAAAAAACAACAAC
66 ATAAATATATATATTTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAATT-TTAAA-AACAAC
*
66155597 AAAGAAACAAGAAAGCCATTTAAA
129 AAAGAAACAAGAAAACCATTTAAA
*
66155621 AAAGGAGAAAAATGTATGCCTTTGTTTATGGTTTCAGCTTGCTTGTGTAGCAAAAAAAAAGTGAA
1 AAAGGAGAAAAAAGTATGCCTTTGTTTATGGTTTCAGCTTGCTTGTGTAGCAAAAAAAAA-TGAA
* * *
66155686 TATAAATATATATATTTAATATGGTTTATTGAACTTAAATTGAATGAAGAATTTTAAAAACAACA
65 TATAAATATATATATTTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAATTTTAAAAACAACA
* * *
66155751 AAGAATCAAGAAAATCATTAAAA
130 AAGAAACAAGAAAACCATTTAAA
* ** * * **
66155774 AAAGGGAAAAAAAAGCGTGCCTTTATTTATGATTTTGGCTTGCTTGTGTAGCAAGAAAAGTGAAT
1 AAA-GGAGAAAAAAGTATGCCTTTGTTTATGGTTTCAGCTTGCTTGTGTAGCAA-AAAA---AA-
*
66155839 ATAAATATAAATATATATATTTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAA-TTTAAAAA
60 ATGAATATAAATATATATATTTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAATTTTAAAAA
66155903 GCGAA-AAAGAAACAAGAAAACCATTT-AA
125 -C-AACAAAGAAACAAGAAAACCATTTAAA
* * ** * *
66155931 AAAGGCGAAAAAAAGTATTCCTTTGTTTATGGTTTTGGATTGCTTGTGGAGCAAAAAAAAATGAA
1 AAAGGAG-AAAAAAGTATGCCTTTGTTTATGGTTTCAGCTTGCTTGTGTAGCAAAAAAAAATGAA
66155996 TATAAA
65 TATAAA
66156002 CAATGAACGT
Statistics
Matches: 323, Mismatches: 46, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
152 16 0.05
153 71 0.22
154 51 0.16
155 52 0.16
156 6 0.02
157 52 0.16
158 72 0.22
159 3 0.01
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (152 bp):
AAAGGAGAAAAAAGTATGCCTTTGTTTATGGTTTCAGCTTGCTTGTGTAGCAAAAAAAAATGAAT
ATAAATATATATATTTAGTATGGTTTCTTGAACTTGAATTGAATGAAGAATTTTAAAAACAACAA
AGAAACAAGAAAACCATTTAAA
Found at i:66158086 original size:21 final size:20
Alignment explanation
Indices: 66158057--66158098 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
66158047 TTTTTTAATC
*
66158057 AAGTTGAGTAAAATAAAATTT
1 AAGTCGAGTAAAAT-AAATTT
*
66158078 AAGTCGAGTTAAATAAATTT
1 AAGTCGAGTAAAATAAATTT
66158098 A
1 A
66158099 TTCGAGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.33
Consensus pattern (20 bp):
AAGTCGAGTAAAATAAATTT
Found at i:66158105 original size:19 final size:21
Alignment explanation
Indices: 66158057--66158110 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 21
66158047 TTTTTTAATC
* *
66158057 AAGTTGAGTAAAATAAAATTT
1 AAGTCGAGTTAAATAAAATTT
66158078 AAGTCGAGTTAAAT-AAATTT
1 AAGTCGAGTTAAATAAAATTT
*
66158098 -ATTCGAGTTAAAT
1 AAGTCGAGTTAAAT
66158111 TAAGAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 12 0.40
20 6 0.20
21 12 0.40
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (21 bp):
AAGTCGAGTTAAATAAAATTT
Found at i:66168535 original size:21 final size:22
Alignment explanation
Indices: 66168506--66168552 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
66168496 CAGAAGGAGT
*
66168506 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
66168528 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
66168549 GAGT
1 GAGT
66168553 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:66171407 original size:17 final size:18
Alignment explanation
Indices: 66171385--66171418 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
66171375 TTGTTTATAA
66171385 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
66171402 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
66171419 AAATTTTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:66173018 original size:15 final size:15
Alignment explanation
Indices: 66172993--66173028 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
66172983 AGAACAAAAG
*
66172993 TAAAGATTTTTTTGTT
1 TAAA-ATTTTTTTATT
66173009 TAAAATTTTTTTATT
1 TAAAATTTTTTTATT
66173024 TAAAA
1 TAAAA
66173029 GTAAAATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
TAAAATTTTTTTATT
Found at i:66173453 original size:31 final size:30
Alignment explanation
Indices: 66173386--66173453 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
66173376 TTATGAGTTT
66173386 ATTTGAATTTTTAGTTTAATTCAAGGATTA
1 ATTTGAATTTTTAGTTTAATTCAAGGATTA
*
66173416 AATTGAATTTTTA-TTTAATAT-ATAGGGATTA
1 ATTTGAATTTTTAGTTTAAT-TCA-A-GGATTA
66173447 ATTTGAA
1 ATTTGAA
66173454 CAATAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 7 0.21
30 14 0.42
31 12 0.36
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.49
Consensus pattern (30 bp):
ATTTGAATTTTTAGTTTAATTCAAGGATTA
Found at i:66186603 original size:20 final size:20
Alignment explanation
Indices: 66186564--66186603 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
66186554 CTACCCAAAT
*
66186564 CCTAGCCCAATAACAGAAAC
1 CCTAGCCCAATAACAAAAAC
66186584 CCTAGCCCAAATAA-AAAAAC
1 CCTAGCCC-AATAACAAAAAC
66186604 AAAATGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.50, C:0.33, G:0.07, T:0.10
Consensus pattern (20 bp):
CCTAGCCCAATAACAAAAAC
Found at i:66188087 original size:28 final size:27
Alignment explanation
Indices: 66188018--66188097 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
66188008 ATTGGTTCTA
*
66188018 TTTTAAATACTATTTATTT-TTTTAAT
1 TTTTATATACTATTTATTTATTTTAAT
* *
66188044 TGTTTCTATTATTATTTATTTATTGTCTAAT
1 T-TTTATA-TACTATTTATTTATT-T-TAAT
66188075 TTTTATATA-TATTCTATTTATTT
1 TTTTATATACTATT-TATTTATTT
66188098 GAAACGTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
26 1 0.02
27 4 0.09
28 16 0.36
29 12 0.27
30 6 0.14
31 5 0.11
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (27 bp):
TTTTATATACTATTTATTTATTTTAAT
Found at i:66191775 original size:3 final size:3
Alignment explanation
Indices: 66191762--66191825 Score: 119
Period size: 3 Copynumber: 21.0 Consensus size: 3
66191752 AAATATAAGA
66191762 AAT ACAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
66191808 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
66191826 CCGCGTAGTA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:66192023 original size:13 final size:12
Alignment explanation
Indices: 66192004--66192042 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
66191994 GCAAAAAGAG
66192004 AAAATAATAATA
1 AAAATAATAATA
66192016 ATAAAT-A-AATA
1 A-AAATAATAATA
66192027 AAAATAATAATA
1 AAAATAATAATA
66192039 AAAA
1 AAAA
66192043 ATAAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.17
11 6 0.25
12 10 0.42
13 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:66192033 original size:23 final size:22
Alignment explanation
Indices: 66192004--66192051 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
66191994 GCAAAAAGAG
*
66192004 AAAATAATAATAATAAATAAATA
1 AAAATAATAATAAAAAATAAA-A
66192027 AAAATAATAATAAAAAATAAAA
1 AAAATAATAATAAAAAATAAAA
66192049 AAA
1 AAA
66192052 TTGAATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAATAATAATAAAAAATAAAA
Found at i:66192034 original size:20 final size:19
Alignment explanation
Indices: 66192009--66192049 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
66191999 AAGAGAAAAT
66192009 AATAATAATAAATAAATAAA
1 AATAATAATAAA-AAATAAA
66192029 AATAATAATAAAAAATAAA
1 AATAATAATAAAAAATAAA
66192048 AA
1 AA
66192050 AATTGAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (19 bp):
AATAATAATAAAAAATAAA
Found at i:66192043 original size:13 final size:13
Alignment explanation
Indices: 66192004--66192046 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
66191994 GCAAAAAGAG
66192004 AAAATAATAATAA
1 AAAATAATAATAA
*
66192017 TAAAT-A-AAT-A
1 AAAATAATAATAA
66192027 AAAATAATAATAA
1 AAAATAATAATAA
66192040 AAAATAA
1 AAAATAA
66192047 AAAAATTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 5 0.20
11 4 0.16
12 4 0.16
13 12 0.48
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAATAATAATAA
Found at i:66192050 original size:20 final size:21
Alignment explanation
Indices: 66192004--66192050 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
66191994 GCAAAAAGAG
66192004 AAAATAATAATAATAAATAAAT
1 AAAA-AATAATAATAAATAAAT
66192026 -AAAAATAATAATAAA-AAAT
1 AAAAAATAATAATAAATAAAT
66192045 AAAAAA
1 AAAAAA
66192051 ATTGAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.17
20 17 0.71
21 3 0.12
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAAAATAATAATAAATAAAT
Found at i:66193784 original size:13 final size:13
Alignment explanation
Indices: 66193763--66193825 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
66193753 TCTTCATTCC
66193763 TTTTGAAAAATAT
1 TTTTGAAAAATAT
*
66193776 TTTTAAAAAATAT
1 TTTTGAAAAATAT
* * *
66193789 TATGGAAAAGTAT
1 TTTTGAAAAATAT
* *
66193802 TTTTGAAAAGTAA
1 TTTTGAAAAATAT
*
66193815 TTTTAAAAAAT
1 TTTTGAAAAAT
66193826 TTGAGTATTT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (13 bp):
TTTTGAAAAATAT
Found at i:66194107 original size:21 final size:19
Alignment explanation
Indices: 66194051--66194111 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
66194041 TAATTATTTA
66194051 TTAAATT-TAATTAGAATAT
1 TTAAATTATAATTA-AATAT
* *
66194070 ATAAATTATATTTAAATAT
1 TTAAATTATAATTAAATAT
66194089 TTAAATATAATAATTAAATAT
1 TTAAAT-T-ATAATTAAATAT
66194110 TT
1 TT
66194112 GTAATTAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.46
20 6 0.17
21 13 0.37
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TTAAATTATAATTAAATAT
Found at i:66195393 original size:22 final size:22
Alignment explanation
Indices: 66195365--66195408 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
66195355 TACACCAAAA
* *
66195365 TAGGTCTTTAGCGGCGTTTTTT
1 TAGGTCTTTAGCGACGCTTTTT
66195387 TAGGTCTTTAGCGACGCTTTTT
1 TAGGTCTTTAGCGACGCTTTTT
66195409 AACGCCACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.48
Consensus pattern (22 bp):
TAGGTCTTTAGCGACGCTTTTT
Found at i:66196596 original size:55 final size:55
Alignment explanation
Indices: 66196530--66196636 Score: 205
Period size: 55 Copynumber: 1.9 Consensus size: 55
66196520 AACCAGGTTA
66196530 AAGATAGAGAAAATCATAGAAAAAATTAAGGATTTGGTCCGATGATTACAGAATT
1 AAGATAGAGAAAATCATAGAAAAAATTAAGGATTTGGTCCGATGATTACAGAATT
*
66196585 AAGATAGAGAAAATCATAGAAAGAATTAAGGATTTGGTCCGATGATTACAGA
1 AAGATAGAGAAAATCATAGAAAAAATTAAGGATTTGGTCCGATGATTACAGA
66196637 CCTCTCATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.24
Consensus pattern (55 bp):
AAGATAGAGAAAATCATAGAAAAAATTAAGGATTTGGTCCGATGATTACAGAATT
Found at i:66208863 original size:72 final size:72
Alignment explanation
Indices: 66208777--66208925 Score: 298
Period size: 72 Copynumber: 2.1 Consensus size: 72
66208767 AGAAACCAAG
66208777 GCAACTAAACAGACCAAATAAATACAAGTCCATTTAGTTCACTCATTCCCAAAACTATGGCAAGA
1 GCAACTAAACAGACCAAATAAATACAAGTCCATTTAGTTCACTCATTCCCAAAACTATGGCAAGA
66208842 TGTTAAA
66 TGTTAAA
66208849 GCAACTAAACAGACCAAATAAATACAAGTCCATTTAGTTCACTCATTCCCAAAACTATGGCAAGA
1 GCAACTAAACAGACCAAATAAATACAAGTCCATTTAGTTCACTCATTCCCAAAACTATGGCAAGA
66208914 TGTTAAA
66 TGTTAAA
66208921 GCAAC
1 GCAAC
66208926 ATATGAAGCT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 77 1.00
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (72 bp):
GCAACTAAACAGACCAAATAAATACAAGTCCATTTAGTTCACTCATTCCCAAAACTATGGCAAGA
TGTTAAA
Found at i:66210411 original size:42 final size:41
Alignment explanation
Indices: 66210361--66210484 Score: 130
Period size: 42 Copynumber: 3.0 Consensus size: 41
66210351 CGGGCCAGAT
66210361 TATA-TATTAAATATATATATTTTTATTTTTAATCAAATATA
1 TATATTATTAAATATATAT-TTTTTATTTTTAATCAAATATA
* *
66210402 CT-TTTTATTAAATATATATTTTTTGGACTTTTAATCCAAAT-TA
1 -TATATTATTAAATATATATTTTTT--ATTTTTAAT-CAAATATA
* *
66210445 TATATTA-AAAATATTTATTTTTTTATTTTTAATCAAATAT
1 TATATTATTAAATATATA-TTTTTTATTTTTAATCAAATAT
66210485 TGGTCGGGCC
Statistics
Matches: 69, Mismatches: 6, Indels: 15
0.77 0.07 0.17
Matches are distributed among these distances:
40 5 0.07
41 15 0.22
42 24 0.35
43 20 0.29
44 5 0.07
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (41 bp):
TATATTATTAAATATATATTTTTTATTTTTAATCAAATATA
Found at i:66211964 original size:30 final size:32
Alignment explanation
Indices: 66211933--66212004 Score: 96
Period size: 30 Copynumber: 2.3 Consensus size: 32
66211923 TTTCTTTAAA
* *
66211933 TTTTAATTAGATTCTC-TCAAAATTTTGAAAT
1 TTTTAATTAGATTCTCATAAAAATTTTAAAAT
*
66211964 TTTTCATT--ATTCTCATAAAAATTTTAAAAT
1 TTTTAATTAGATTCTCATAAAAATTTTAAAAT
66211994 TTTTAATTAGA
1 TTTTAATTAGA
66212005 CTCCAATCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 6 0.18
30 20 0.59
31 7 0.21
32 1 0.03
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (32 bp):
TTTTAATTAGATTCTCATAAAAATTTTAAAAT
Found at i:66215087 original size:15 final size:15
Alignment explanation
Indices: 66215064--66215105 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
66215054 AATTGATCGA
*
66215064 TCAACAATAAATGCT
1 TCAAAAATAAATGCT
66215079 TCAAAAATAAATGCT
1 TCAAAAATAAATGCT
66215094 TCAAAAATAAAT
1 TCAAAAATAAAT
66215106 TGGATACTGT
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:0.55, C:0.14, G:0.05, T:0.26
Consensus pattern (15 bp):
TCAAAAATAAATGCT
Found at i:66221348 original size:9 final size:8
Alignment explanation
Indices: 66221316--66221357 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
66221306 ACATTTATAT
66221316 TAAAAAAA
1 TAAAAAAA
66221324 TAATGAAAAA
1 TAA--AAAAA
*
66221334 T-TAAAAA
1 TAAAAAAA
66221341 TAAAAAAA
1 TAAAAAAA
66221349 TAAAAAAA
1 TAAAAAAA
66221357 T
1 T
66221358 GAAACGACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
7 6 0.21
8 17 0.59
10 6 0.21
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (8 bp):
TAAAAAAA
Found at i:66223016 original size:89 final size:87
Alignment explanation
Indices: 66222908--66223076 Score: 214
Period size: 89 Copynumber: 1.9 Consensus size: 87
66222898 TTTATTCAAT
* ** *
66222908 TTTTACAATGCATAAAAAAGACTTTCAATTTTTTTCAAAAAAAGCAATTAAGCC-TTACTTTTGT
1 TTTTAAAATGCATAAAAAAGACCCTCAAATTTTTTCAAAAAAA-CAATTAAGCCTTTAC-TTT-T
* *
66222972 TTTGCATTCAATTGGGTATTTAAAC
63 TTTACACTCAATTGGGTATTTAAAC
* * * *
66222997 TTTTAAAATGCATCAAAAAGGCCCTCAAATTTTTTCAAAAAAATAATTAAGCCTTTGCTTTTTTT
1 TTTTAAAATGCATAAAAAAGACCCTCAAATTTTTTCAAAAAAACAATTAAGCCTTTACTTTTTTT
66223062 ACACTCAATTGGGTA
66 ACACTCAATTGGGTA
66223077 CTTGAACCAT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 17 0.25
88 12 0.17
89 40 0.58
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (87 bp):
TTTTAAAATGCATAAAAAAGACCCTCAAATTTTTTCAAAAAAACAATTAAGCCTTTACTTTTTTT
ACACTCAATTGGGTATTTAAAC
Found at i:66223202 original size:19 final size:19
Alignment explanation
Indices: 66223178--66223251 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
66223168 ATAAAAGTTG
*
66223178 TAAAAATAATTAAAATTTAA
1 TAAAAAT-ATAAAAATTTAA
*
66223198 TAAAAATATAAAAATTTAT
1 TAAAAATATAAAAATTTAA
* *
66223217 TAAAAATTACAAAAATCGTAA
1 TAAAAA-TATAAAAAT-TTAA
66223238 -AAAAAGTATAAAAA
1 TAAAAA-TATAAAAA
66223252 AATATAATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
19 16 0.36
20 27 0.60
21 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (19 bp):
TAAAAATATAAAAATTTAA
Found at i:66230353 original size:33 final size:33
Alignment explanation
Indices: 66230316--66230394 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
66230306 TGTGGTTATG
66230316 GAAACACGTAATTGAATTTCTTTAAAAAAAAAC
1 GAAACACGTAATTGAATTTCTTTAAAAAAAAAC
*
66230349 GAAACACGTAATTGAATTTCTTTTAAAAAAAAC
1 GAAACACGTAATTGAATTTCTTTAAAAAAAAAC
66230382 GAAACACGTAATT
1 GAAACACGTAATT
66230395 AATATAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (33 bp):
GAAACACGTAATTGAATTTCTTTAAAAAAAAAC
Found at i:66242773 original size:5 final size:5
Alignment explanation
Indices: 66242763--66242787 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
66242753 TTCGTAAAGG
66242763 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
66242788 TGCTCTAAAT
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:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:66245355 original size:14 final size:15
Alignment explanation
Indices: 66245329--66245358 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
66245319 AAAATTCAAC
66245329 TCTTTTTTAAAAAAT
1 TCTTTTTTAAAAAAT
66245344 TCTTTTTTAAAAAAT
1 TCTTTTTTAAAAAAT
66245359 AATTACCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
TCTTTTTTAAAAAAT
Found at i:66245407 original size:26 final size:27
Alignment explanation
Indices: 66245352--66245413 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
66245342 ATTCTTTTTT
**
66245352 AAAAA-ATAATTACCAAATTTAAC-TT
1 AAAAATATAATTACCAAATTTAACAAA
*
66245377 TAAAATATAATTACCAAA-TTAACAAAA
1 AAAAATATAATTACCAAATTTAAC-AAA
66245404 AAAAATATAA
1 AAAAATATAA
66245414 ATATTCATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 9 0.30
26 12 0.40
27 9 0.30
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (27 bp):
AAAAATATAATTACCAAATTTAACAAA
Found at i:66250250 original size:21 final size:20
Alignment explanation
Indices: 66250204--66250258 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
66250194 AAAATTTAAA
* *
66250204 AATA-TTTTTTTATAATTTT
1 AATACTTTTTTAATAATGTT
*
66250223 TATACTTTTTTAATAATGTT
1 AATACTTTTTTAATAATGTT
*
66250243 AATAACTTATTTAATA
1 AAT-ACTTTTTTAATA
66250259 TTTTTTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 3 0.10
20 15 0.52
21 11 0.38
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (20 bp):
AATACTTTTTTAATAATGTT
Found at i:66250688 original size:31 final size:31
Alignment explanation
Indices: 66250653--66250711 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
66250643 CAAAACAGTT
66250653 ACTGAACTA-TTCAAAATTTTTCATTTAAGTC
1 ACTGAACTATTTCAAAATTTTT-ATTTAAGTC
* *
66250684 ACTGAACTATTTGAAAGTTTTTATTTAA
1 ACTGAACTATTTCAAAATTTTTATTTAA
66250712 ATCATTAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (31 bp):
ACTGAACTATTTCAAAATTTTTATTTAAGTC
Found at i:66252529 original size:12 final size:12
Alignment explanation
Indices: 66252512--66252539 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
66252502 TTGTTATTTT
66252512 TTAATAAAAATA
1 TTAATAAAAATA
66252524 TTAATAAAAATA
1 TTAATAAAAATA
66252536 TTAA
1 TTAA
66252540 ATTTTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAATAAAAATA
Found at i:66254777 original size:156 final size:157
Alignment explanation
Indices: 66254504--66254807 Score: 348
Period size: 156 Copynumber: 1.9 Consensus size: 157
66254494 TGTCGTCAAC
* * ** * * *
66254504 GTGTTAGTCGACATCAATAATATTTTTAATATTTTTTAGTTGGTAAATTCATAAGTTAGTTTATT
1 GTGTTAGGCAACATCAATAATATTTTTAATATTTTTTAGTTGACAAATTAACAAGTTAGCTTATT
* * * * *
66254569 TGGTTAGATAGTTAAATTTTAGAGTTTTTATCTCTAAGTCTCAGGTTCGATTCCTCT-TCTACTA
66 TGGTCAAATAGTTAAATGTTAGAGATTTTATCTCTAAGTCCCAGGTTCGATTCCTCTCT-TACTA
66254633 ATA-TTTGCATTTTTTTATGCAGCTACT
130 ATATTTTGCATTTTTTTATGCAGCTACT
* *
66254660 GTGTTAGGCAACA-CAAGTAATATTTTTAATATTTTTTAGTTGACAAATTAACAATTTAGCTTCT
1 GTGTTAGGCAACATCAA-TAATATTTTTAATATTTTTTAGTTGACAAATTAACAAGTTAGCTTAT
* * * * *
66254724 TTTGTCAAAT-GATTAAATGTTA-ATGATTTTATCTTTGAGTCCCATGTTTGATTCCTCTCTTAC
65 TTGGTCAAATAG-TTAAATGTTAGA-GATTTTATCTCTAAGTCCCAGGTTCGATTCCTCTCTTAC
* *
66254787 TCATATTTTGTATTTTTTTAT
128 TAATATTTTGCATTTTTTTAT
66254808 TTCATACTGT
Statistics
Matches: 122, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
155 5 0.04
156 102 0.84
157 15 0.12
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (157 bp):
GTGTTAGGCAACATCAATAATATTTTTAATATTTTTTAGTTGACAAATTAACAAGTTAGCTTATT
TGGTCAAATAGTTAAATGTTAGAGATTTTATCTCTAAGTCCCAGGTTCGATTCCTCTCTTACTAA
TATTTTGCATTTTTTTATGCAGCTACT
Found at i:66259292 original size:19 final size:19
Alignment explanation
Indices: 66259250--66259293 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
66259240 TTAAATTTTT
66259250 CAAAAATTATTAAAAAATA
1 CAAAAATTATTAAAAAATA
* *
66259269 GAAAAA-TATTATAAAATTA
1 CAAAAATTATTA-AAAAATA
66259288 CAAAAA
1 CAAAAA
66259294 CAATATAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (19 bp):
CAAAAATTATTAAAAAATA
Found at i:66267357 original size:16 final size:18
Alignment explanation
Indices: 66267336--66267371 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
66267326 TTTTATGTGT
66267336 TATAAAT-TAA-ATAATA
1 TATAAATATAACATAATA
66267352 TATAAATATAACATAATA
1 TATAAATATAACATAATA
66267370 TA
1 TA
66267372 AAACATTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TATAAATATAACATAATA
Found at i:66270092 original size:15 final size:15
Alignment explanation
Indices: 66270075--66270107 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 15
66270065 AAGGTATAAT
66270075 AAAATATTAAAAAATA
1 AAAAT-TTAAAAAATA
66270091 AAAATTTAAAAAATA
1 AAAATTTAAAAAATA
66270106 AA
1 AA
66270108 GACATATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATTTAAAAAATA
Found at i:66273609 original size:12 final size:12
Alignment explanation
Indices: 66273592--66273633 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
66273582 CTAAAACTGA
66273592 ATTTTATTTTTT
1 ATTTTATTTTTT
* *
66273604 ATTTTATTTATA
1 ATTTTATTTTTT
66273616 ATTTTATTTATTT
1 ATTTTATTT-TTT
66273629 -TTTTA
1 ATTTTA
66273634 GCATATTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 24 0.96
13 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTTATTTTTT
Found at i:66302584 original size:76 final size:75
Alignment explanation
Indices: 66302458--66302599 Score: 203
Period size: 76 Copynumber: 1.9 Consensus size: 75
66302448 TTAACTTAGT
* * * ** ** *
66302458 TCTTTTATAACTAGAGAAGTTATAAATTAATATATAGTAAAATTGTACTTTGGCCCCCATGAAAA
1 TCTTTTATAAATAAAGAAATTATAAATTAATATATAGTAAAATTACACTTTAACCCCCATAAAAA
66302523 TTTTTTCTAG
66 TTTTTTCTAG
66302533 TCTTCTTATAAATAAAGAAATTATAAATTAATATATAGTAAAATTACACTTTAACCCCCATAAAA
1 TCTT-TTATAAATAAAGAAATTATAAATTAATATATAGTAAAATTACACTTTAACCCCCATAAAA
66302598 AT
65 AT
66302600 GAAATGATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
75 4 0.07
76 54 0.93
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (75 bp):
TCTTTTATAAATAAAGAAATTATAAATTAATATATAGTAAAATTACACTTTAACCCCCATAAAAA
TTTTTTCTAG
Found at i:66312498 original size:6 final size:6
Alignment explanation
Indices: 66312487--66312511 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
66312477 ATATTATATT
66312487 ATTAAA ATTAAA ATTAAA ATTAAA A
1 ATTAAA ATTAAA ATTAAA ATTAAA A
66312512 AATAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTAAA
Found at i:66329060 original size:27 final size:28
Alignment explanation
Indices: 66329008--66329063 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
66328998 CGTACATGTA
*
66329008 TATATAGTATTATCTTTTATTACTTTAT
1 TATATAGTATGATCTTTTATTACTTTAT
66329036 TATATAGTATGA-CTTTTAATT-CTTTAT
1 TATATAGTATGATCTTTT-ATTACTTTAT
66329063 T
1 T
66329064 TGTTTTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (28 bp):
TATATAGTATGATCTTTTATTACTTTAT
Found at i:66332926 original size:13 final size:13
Alignment explanation
Indices: 66332894--66332935 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
66332884 TAATAGTTAA
66332894 AAAAATG-T-AAG
1 AAAAATGATAAAG
66332905 AAAACATGATAAAG
1 AAAA-ATGATAAAG
*
66332919 AAAAATGATAAAT
1 AAAAATGATAAAG
66332932 AAAA
1 AAAA
66332936 GGAGTAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 4 0.15
12 3 0.11
13 13 0.48
14 7 0.26
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (13 bp):
AAAAATGATAAAG
Found at i:66345099 original size:23 final size:23
Alignment explanation
Indices: 66345071--66345161 Score: 91
Period size: 23 Copynumber: 4.1 Consensus size: 23
66345061 TGTGTAACTT
66345071 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
* * * * *
66345094 TTCATA---ATGTGT-GTAACTT
1 TTCATATTCAAGTCTCTTCACTC
* *
66345113 TTCATCTTCAAGTCTATTCACTC
1 TTCATATTCAAGTCTCTTCACTC
66345136 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
66345159 TTC
1 TTC
66345162 TAACTTTTCA
Statistics
Matches: 51, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
19 9 0.18
20 4 0.08
22 4 0.08
23 34 0.67
ACGTcount: A:0.22, C:0.26, G:0.07, T:0.45
Consensus pattern (23 bp):
TTCATATTCAAGTCTCTTCACTC
Found at i:66345111 original size:42 final size:42
Alignment explanation
Indices: 66345058--66345141 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
66345048 CTATTCATGC
*
66345058 ATGTGTGTAACTTTTCATATTCAAGTCTCTTCACTCTTCATA
1 ATGTGTGTAACTTTTCATATTCAAGTCTATTCACTCTTCATA
*
66345100 ATGTGTGTAACTTTTCATCTTCAAGTCTATTCACTCTTCATA
1 ATGTGTGTAACTTTTCATATTCAAGTCTATTCACTCTTCATA
66345142 TTCAAGTCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (42 bp):
ATGTGTGTAACTTTTCATATTCAAGTCTATTCACTCTTCATA
Found at i:66349619 original size:42 final size:42
Alignment explanation
Indices: 66349573--66349653 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
66349563 CTATTCATGC
* *
66349573 ATGTGTGTAGCTTTTCATATTCAAGTCTCTTCACTCTTCATA
1 ATGTGTGTAACTTTTCATATTCAAGTCTATTCACTCTTCATA
*
66349615 ATGTGTGTAACTTTTCATCTTCAAGTCTATTCACTCTTC
1 ATGTGTGTAACTTTTCATATTCAAGTCTATTCACTCTTC
66349654 TAACTTTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.21, C:0.22, G:0.11, T:0.46
Consensus pattern (42 bp):
ATGTGTGTAACTTTTCATATTCAAGTCTATTCACTCTTCATA
Found at i:66354155 original size:39 final size:40
Alignment explanation
Indices: 66354031--66354141 Score: 197
Period size: 40 Copynumber: 2.8 Consensus size: 40
66354021 TTTGGATTAC
* *
66354031 AAACGCCGCTAAAAATCGAGCATTAGCGGCGCAAAGAATA
1 AAACGCCGCTAAAGATCTAGCATTAGCGGCGCAAAGAATA
66354071 AAACGCCGCTAAAGATCTAGCATTAGCGGCGCAAAGAATA
1 AAACGCCGCTAAAGATCTAGCATTAGCGGCGCAAAGAATA
66354111 AAACGCCGCTAAAG-TCTAGCATTAGCGGCGC
1 AAACGCCGCTAAAGATCTAGCATTAGCGGCGC
66354142 TTCTTTTAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
39 17 0.25
40 52 0.75
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.14
Consensus pattern (40 bp):
AAACGCCGCTAAAGATCTAGCATTAGCGGCGCAAAGAATA
Found at i:66354596 original size:228 final size:228
Alignment explanation
Indices: 66354251--66354755 Score: 572
Period size: 228 Copynumber: 2.2 Consensus size: 228
66354241 AAATCTCAAG
* * * **
66354251 ACCAACACGCAACGTTCTGGTCTTGATGTATATTAGAATTAGTGGCGCTTACGAACAAACGCCGG
1 ACCAAAACGCAACGTTCTGGTCTTGATGTATACTAGAATTAGTGGCGCTTAAGAACAAACGCCAC
* * * * *
66354316 TAATGCATAGTATTAGCGGCGCTTAGCGAAAGCGCCGCAAAAGATGTTAACCAAAACGCAGAGTT
66 TAAAGCATAGTAATAGCAGCGCTTAGCGAAAGCACCGCAAAAGATCTTAACCAAAACGCAGAGTT
* * *
66354381 T-GTCTTGATGTATATTACAATTAGTGGCGCTTATAAAGAAAACGCCGCTAATGTATAGTATTAG
131 TGGTCTTGAGGTATATTACAATTAGTGGCGCTTAT-AAGAAAACGCCGCTAAAGTATAGTAGTAG
66354445 CGGCGCTGAGCGTTAAACGCCGCAAAACATCTTA
195 CGGCGCTGAGCGTTAAACGCCGCAAAACATCTTA
* * * * *
66354479 ACCAAAACGCAGCGTTTTGGTCTTGATGTATACTATAATTAGTGGCGTTTAAGGA-AAACGCCAC
1 ACCAAAACGCAACGTTCTGGTCTTGATGTATACTAGAATTAGTGGCGCTTAAGAACAAACGCCAC
* * * * * * *
66354543 TAAAGCATAGTAATAGCAGCGTTTGGTGGTAAGCACCTCAAAATATCTTAACCAAAACGCGGAGT
66 TAAAGCATAGTAATAGCAGCGCTTAG-CGAAAGCACCGCAAAAGATCTTAACCAAAACGCAGAGT
* **
66354608 TTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATTGGAAAACGCCGCTAAAGTATAGTAGTAG
130 TTGGTCTTGAGGTATATTACAATTAGTGGCGCTTATAAGAAAACGCCGCTAAAGTATAGTAGTAG
* ** * * * **
66354673 CGGTG-TTTGTG-AAAAGCGCCGGAAAGTATCTTA
195 CGGCGCTGAGCGTTAAA-CGCCGCAAAACATCTTA
* * * *
66354706 ACCAAAACGCAGA-GTT-TGGCCTTGACGTATATTAGAGTTAGTGGCGCTTA
1 ACCAAAACGCA-ACGTTCTGGTCTTGATGTATACTAGAATTAGTGGCGCTTA
66354756 TTTCAAAACG
Statistics
Matches: 230, Mismatches: 43, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
226 31 0.13
227 59 0.26
228 109 0.47
229 31 0.13
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (228 bp):
ACCAAAACGCAACGTTCTGGTCTTGATGTATACTAGAATTAGTGGCGCTTAAGAACAAACGCCAC
TAAAGCATAGTAATAGCAGCGCTTAGCGAAAGCACCGCAAAAGATCTTAACCAAAACGCAGAGTT
TGGTCTTGAGGTATATTACAATTAGTGGCGCTTATAAGAAAACGCCGCTAAAGTATAGTAGTAGC
GGCGCTGAGCGTTAAACGCCGCAAAACATCTTA
Found at i:66354714 original size:113 final size:113
Alignment explanation
Indices: 66354232--66354909 Score: 582
Period size: 113 Copynumber: 5.9 Consensus size: 113
66354222 TTTACTACAC
* * *
66354232 AGCGCCGCAAAATCTC-AAGACCAACACGCA-ACGTTCTGGTCTTGATGTATATTAGAATTAGTG
1 AGCGCCGCAAAATATCTTA-ACCAAAACGCAGA-GTT-TGGTCTTGATGTATATTAGAATTAGTG
* * * *
66354295 GCGCTTA-CGAACAAACGCCGGTAATGCATAGTATTAGCGGCGCTTAGCGAA
63 GCGCTTATAGGA-AAACGCCGCTAAAGCATAGTATTAGCGGCGCTTAGCGAA
* * *
66354346 AGCGCCGCAAAAGATGTTAACCAAAACGCAGAGTTT-GTCTTGATGTATATTACAATTAGTGGCG
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCG
* * * *
66354410 CTTATAAAGAAAACGCCGCTAATGTATAGTATTAGCGGCGCTGAGCGTTAA
66 CTTAT-AGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTAGCG--AA
* * * *
66354461 A-CGCCGCAAAACATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTATAATTAGTGGC
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAG-TTTGGTCTTGATGTATATTAGAATTAGTGGC
* * * * * * * *
66354525 GTTTA-AGGAAAACGCCACTAAAGCATAGTAATAGCAGCGTTTGGTGGTA
65 GCTTATAGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTAG-CGAA
* * * *
66354574 AGCACCTCAAAATATCTTAACCAAAACGCGGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCG
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCG
* * * * * *
66354639 CTTATTGGAAAACGCCGCTAAAGTATAGTAGTAGCGGTG-TTTGTGAAA
66 CTTATAGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTAGCG-AA
* * * * *
66354687 AGCGCCGGAAAGTATCTTAACCAAAACGCAGAGTTTGGCCTTGACGTATATTAGAGTTAGTGGCG
1 AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCG
*** * * * * * *
66354752 CTTATTTCAAAACGCCGCTAATGCTTACTATTTA-CGACGCTTTTTG-GTA
66 CTTATAGGAAAACGCCGCTAAAGCATAGTA-TTAGCGGCGC--TTAGCGAA
* * ** * * * * *
66354801 AGCGCCGCCAAAAGATATTAATGAAAACACAGCGTTTAGTTCTTGATGTATACTGGAATTAGTGG
1 AGCGCCG-CAAAATATCTTAACCAAAACGCAGAGTTT-GGTCTTGATGTATATTAGAATTAGTGG
** * * *
66354866 CGCACACAGGAAAATGCCGCTGAAGCATAGTATTAGCGGCGCTT
64 CGCTTATAGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTT
66354910 TTCCCGAAAC
Statistics
Matches: 454, Mismatches: 91, Indels: 38
0.78 0.16 0.07
Matches are distributed among these distances:
112 32 0.07
113 157 0.35
114 151 0.33
115 34 0.07
116 80 0.18
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (113 bp):
AGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCG
CTTATAGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTAGCGAA
Found at i:66355527 original size:81 final size:80
Alignment explanation
Indices: 66355349--66355516 Score: 189
Period size: 81 Copynumber: 2.1 Consensus size: 80
66355339 TTTGGTGTTA
* * * *
66355349 GGTTAGGCTTTAGGGTTTAGATTAATTAGTGTGTTTTAATTTTTATAAAATATGGTTTAAAGGTT
1 GGTTAGGATTTAGGGTTTAGATTAATTAATATGTTTTAATTTTTATAAAATAAGGTTTAAAGGTT
*
66355414 AAGGGTTAGGGATTCG
66 AAGAGTTAGGGA-TCG
* * * *
66355430 GGTTAGGATTTAGGGTTTTGATTAATTAATATTTTTTAATTTATGTATTAAATAAGGTTT-AGGG
1 GGTTAGGATTTAGGGTTTAGATTAATTAATATGTTTTAATTT-T-TATAAAATAAGGTTTAAAGG
66355494 TT-AGTAGTTAGGG-TCGG
64 TTAAG-AGTTAGGGATC-G
66355511 GGTTAG
1 GGTTAG
66355517 TGGTTTGGGT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
80 2 0.03
81 46 0.62
82 13 0.18
83 13 0.18
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (80 bp):
GGTTAGGATTTAGGGTTTAGATTAATTAATATGTTTTAATTTTTATAAAATAAGGTTTAAAGGTT
AAGAGTTAGGGATCG
Found at i:66355932 original size:15 final size:15
Alignment explanation
Indices: 66355914--66355954 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
66355904 TGGTTTTGAC
*
66355914 TTTTAGTGTTTGGGG
1 TTTTAGGGTTTGGGG
66355929 TTTTAGGGTTT-GGG
1 TTTTAGGGTTTGGGG
*
66355943 -TTTGGGGTTTGG
1 TTTTAGGGTTTGG
66355955 TTTTTGAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 9 0.39
14 4 0.17
15 10 0.43
ACGTcount: A:0.05, C:0.00, G:0.44, T:0.51
Consensus pattern (15 bp):
TTTTAGGGTTTGGGG
Found at i:66356764 original size:44 final size:44
Alignment explanation
Indices: 66356699--66356786 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
66356689 AAGCGACTGC
* *
66356699 GTTTTGACTTATAGTTAGTGGCGCTTAGTTTAAAATGCCGCAAA
1 GTTTTGACTTATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAAA
* *
66356743 GTTTTGACTTATAGTTTGTGGCGCTTTGCTTAAAACGCCGCAAA
1 GTTTTGACTTATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAAA
66356787 AATGTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (44 bp):
GTTTTGACTTATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAAA
Found at i:66358261 original size:16 final size:16
Alignment explanation
Indices: 66358236--66358271 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
66358226 GTATTTATAA
*
66358236 TTATCGATTTTCAATT
1 TTATCAATTTTCAATT
66358252 TTATCAATTTTCAATT
1 TTATCAATTTTCAATT
66358268 TTAT
1 TTAT
66358272 TTCAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.03, T:0.58
Consensus pattern (16 bp):
TTATCAATTTTCAATT
Found at i:66358695 original size:13 final size:13
Alignment explanation
Indices: 66358659--66358717 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
66358649 TTACTAAAAT
*
66358659 TTACTTTAATATA
1 TTACTTAAATATA
* *
66358672 TTAATTGAATATA
1 TTACTTAAATATA
66358685 TTACTTAAATA-A
1 TTACTTAAATATA
*
66358697 TTTACTTAAATACA
1 -TTACTTAAATATA
66358711 TTACTTA
1 TTACTTA
66358718 TTAAAATTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
12 1 0.03
13 38 0.95
14 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.47
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:66358888 original size:48 final size:49
Alignment explanation
Indices: 66358835--66358954 Score: 131
Period size: 52 Copynumber: 2.4 Consensus size: 49
66358825 CAATATTTAT
* *
66358835 TATATTTTTAAATATATTTTTAGAATTTA-AT-TTA-ACTTA-TTAATAATA
1 TATATTTTTAAGTATATTTTTAAAATTTATATCTTACA-TTACTT-A-AATA
*
66358883 TATATTGTTAAGTAATAATTTTTTAAAATTTATATCTTACATTACTTAAATA
1 TATATTTTTAAGT-AT-A-TTTTTAAAATTTATATCTTACATTACTTAAATA
66358935 TATATTTTTAAGTATATTTT
1 TATATTTTTAAGTATATTTT
66358955 ACATGACTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
48 11 0.18
49 6 0.10
50 2 0.03
51 14 0.23
52 18 0.30
53 7 0.11
54 3 0.05
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (49 bp):
TATATTTTTAAGTATATTTTTAAAATTTATATCTTACATTACTTAAATA
Found at i:66359014 original size:13 final size:13
Alignment explanation
Indices: 66358998--66359063 Score: 89
Period size: 13 Copynumber: 5.1 Consensus size: 13
66358988 TTACTAAAAT
*
66358998 TTACTTTAATATA
1 TTACTTAAATATA
*
66359011 TTACTTGAATATA
1 TTACTTAAATATA
66359024 TTACTTAAATA-A
1 TTACTTAAATATA
*
66359036 TTTACTTAAATACA
1 -TTACTTAAATATA
66359050 TTACTTAAATATA
1 TTACTTAAATATA
66359063 T
1 T
66359064 ATTACTTACT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
12 1 0.02
13 46 0.96
14 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:66359104 original size:9 final size:9
Alignment explanation
Indices: 66359090--66359360 Score: 187
Period size: 9 Copynumber: 31.4 Consensus size: 9
66359080 TAAGTATATA
*
66359090 TTACATTAC
1 TTACATAAC
66359099 TTACATAAC
1 TTACATAAC
**
66359108 TT-GTTAAAC
1 TTACAT-AAC
66359117 TTACATAA-
1 TTACATAAC
66359125 -TACATAAC
1 TTACATAAC
66359133 TTACATAA-
1 TTACATAAC
*
66359141 -TACATTAC
1 TTACATAAC
*
66359149 TTACATAGC
1 TTACATAAC
*
66359158 ATACATAAC
1 TTACATAAC
*
66359167 TTACACAAC
1 TTACATAAC
*
66359176 TTACGTAA-
1 TTACATAAC
*
66359184 -TACAAAAC
1 TTACATAAC
*
66359192 TTACGTAAC
1 TTACATAAC
66359201 TTACATAAC
1 TTACATAAC
66359210 TTACATAAC
1 TTACATAAC
*
66359219 CTACATAATAC
1 TTACAT-A-AC
*
66359230 ATA-ATAAC
1 TTACATAAC
*
66359238 TTAC--AAT
1 TTACATAAC
66359245 TTACATAAC
1 TTACATAAC
* *
66359254 ATACATTAC
1 TTACATAAC
**
66359263 TTTGATAAC
1 TTACATAAC
66359272 TTACATAAC
1 TTACATAAC
66359281 TTACATAA-
1 TTACATAAC
*
66359289 -TACACAAC
1 TTACATAAC
* *
66359297 TTAAATAGC
1 TTACATAAC
*
66359306 TTACTTAA-
1 TTACATAAC
66359314 -TACATAAC
1 TTACATAAC
66359322 TTACATAAC
1 TTACATAAC
66359331 TT--ATACAC
1 TTACATA-AC
*
66359339 GTACATAAC
1 TTACATAAC
*
66359348 TTACATAAT
1 TTACATAAC
66359357 TTAC
1 TTAC
66359361 TTAATACATA
Statistics
Matches: 199, Mismatches: 43, Indels: 40
0.71 0.15 0.14
Matches are distributed among these distances:
7 39 0.20
8 8 0.04
9 141 0.71
10 7 0.04
11 4 0.02
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.33
Consensus pattern (9 bp):
TTACATAAC
Found at i:66359135 original size:16 final size:16
Alignment explanation
Indices: 66359114--66359371 Score: 105
Period size: 16 Copynumber: 15.1 Consensus size: 16
66359104 TAACTTGTTA
66359114 AACTTACATAATACAT
1 AACTTACATAATACAT
66359130 AACTTACATAATACAT
1 AACTTACATAATACAT
*
66359146 TACTTACATAGCATACAT
1 AACTTACATA--ATACAT
* *
66359164 AACTTACACAACTTACGT
1 AACTTACATAA--TACAT
* *
66359182 AA--TACAAAACTTACGT
1 AACTTACATAA--TACAT
66359198 AACTTACATAACTTACAT
1 AACTTACATAA--TACAT
*
66359216 AACCTACATAATACATAAT
1 AACTTACATAATAC---AT
*
66359235 AACTTACA-ATTTACAT
1 AACTTACATA-ATACAT
* * **
66359251 AACATACATTACTTTGAT
1 AACTTACA-TA-ATACAT
66359269 AACTTACATAACTTACAT
1 AACTTACATAA--TACAT
* *
66359287 AA--TACACAACTTAAAT
1 AACTTACATAA--TACAT
* *
66359303 AGCTTACTTAATACAT
1 AACTTACATAATACAT
*
66359319 AACTTACATAACT-TAT
1 AACTTACATAA-TACAT
*
66359335 ACACGTACATAACTTACAT
1 A-ACTTACATAA--TACAT
* *
66359354 AATTTACTTAATACAT
1 AACTTACATAATACAT
66359370 AA
1 AA
66359372 ATATATATCA
Statistics
Matches: 189, Mismatches: 33, Indels: 40
0.72 0.13 0.15
Matches are distributed among these distances:
16 89 0.47
17 12 0.06
18 73 0.39
19 15 0.08
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.32
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:66359137 original size:339 final size:342
Alignment explanation
Indices: 66358475--66359140 Score: 1028
Period size: 339 Copynumber: 2.0 Consensus size: 342
66358465 AAAGTTAATA
66358475 TATAATTTCAATATTTATTATATTTTTAAATATATTTTTACAATTTAATTTAACTTATTAATAAT
1 TATAATTTCAATATTTATTATATTTTTAAATATATTTTTACAATTTAATTTAACTTATTAATAAT
66358540 ATATATATTGTTAAGTAATAATTTTTTTAAAATTGATATCTTACATTACTTAAATATATATTTTT
66 ATATATATTGTTAAGTAATAATTTTTTTAAAATTGATATCTTACATTACTTAAATATATATTTTT
*
66358605 AAGTATATTCTACATGACTTAGATTACTTACTAAAACATATTTTTTACTAAAATTTACTTTAATA
131 AAGTATATTCTACATGACTTACATTACTTACTAAAACATATTTTTTACTAAAATTTACTTTAATA
* ** *
66358670 TATTAATTGAATATATTACTTAAATAATTTACTTAAATACATTACTTATTAAAATTTGTTTAAAT
196 TATTAATTGAATATATTACTTAAATAATTTACTTAAATACATTACTTAATAAAATTACTTTAAAA
* * * * *
66358735 TTTAAATACATTACTTAAATATATATTACTTACTAAAATTTAAGTATATATTACATTACTTACAT
261 TTTAAATACATTACTTAAATATACATAACTTACTAAAACTTAAGCATATATTACATAACTTACAT
66358800 AACTTGTTAAAATATAT
326 AACTTGTTAAAATATAT
*
66358817 TATAATTTCAATATTTATTATATTTTTAAATATATTTTTAGAATTTAATTTAACTTATTAAT-A-
1 TATAATTTCAATATTTATTATATTTTTAAATATATTTTTACAATTTAATTTAACTTATTAATAAT
*
66358880 ATATATATTGTTAAGTAATAA-TTTTTTAAAATTTATATCTTACATTACTTAAATATATATTTTT
66 ATATATATTGTTAAGTAATAATTTTTTTAAAATTGATATCTTACATTACTTAAATATATATTTTT
*
66358944 AAGTATATTTTACATGACTTACATTACTTACTAAAACATATTTTTTACTAAAATTTACTTTAATA
131 AAGTATATTCTACATGACTTACATTACTTACTAAAACATATTTTTTACTAAAATTTACTTTAATA
* *
66359009 TATTACTTGAATATATTACTTAAATAATTTACTTAAATACATTACTTAAATATATATTACTTACT
196 TATTAATTGAATATATTACTTAAATAATTTACTTAAATACATTACTT-AATA-AAATTACTT--T
* * * *
66359074 AAAATTTAAGTATATATTACATT-ACT-TACATAACTT-GTTAAACTT-A-CATA-A-TACATAA
257 AAAATTTAA--ATACATTAC-TTAAATATACATAACTTACTAAAACTTAAGCATATATTACATAA
66359132 CTTACATAA
319 CTTACATAA
66359141 TACATTACTT
Statistics
Matches: 298, Mismatches: 19, Indels: 17
0.89 0.06 0.05
Matches are distributed among these distances:
339 166 0.56
340 25 0.08
341 10 0.03
342 62 0.21
343 15 0.05
344 8 0.03
345 10 0.03
346 2 0.01
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (342 bp):
TATAATTTCAATATTTATTATATTTTTAAATATATTTTTACAATTTAATTTAACTTATTAATAAT
ATATATATTGTTAAGTAATAATTTTTTTAAAATTGATATCTTACATTACTTAAATATATATTTTT
AAGTATATTCTACATGACTTACATTACTTACTAAAACATATTTTTTACTAAAATTTACTTTAATA
TATTAATTGAATATATTACTTAAATAATTTACTTAAATACATTACTTAATAAAATTACTTTAAAA
TTTAAATACATTACTTAAATATACATAACTTACTAAAACTTAAGCATATATTACATAACTTACAT
AACTTGTTAAAATATAT
Found at i:66359177 original size:43 final size:43
Alignment explanation
Indices: 66359118--66359356 Score: 188
Period size: 43 Copynumber: 5.6 Consensus size: 43
66359108 TTGTTAAACT
* *
66359118 TACATAA--TACATAACTTACATAATACATTACTTACATAGCA
1 TACATAACTTACATAACTTACATAATACATAACTTACATAACA
* * * * *
66359159 TACATAACTTACACAACTTACGTAATACAAAACTTACGTAACT
1 TACATAACTTACATAACTTACATAATACATAACTTACATAACA
* **
66359202 TACATAACTTACATAACCTACATAATACATAATAACTTAC--AATT
1 TACATAACTTACATAACTTACATAATAC---ATAACTTACATAACA
* * **
66359246 TACATAACATACATTACTTTGATAACTTACATAACTTACAT-A-A
1 TACATAACTTACATAACTTACATAA--TACATAACTTACATAACA
* * * *
66359289 TACACAACTTAAATAGCTTACTTAATACATAACTTACATAAC-
1 TACATAACTTACATAACTTACATAATACATAACTTACATAACA
* *
66359331 T-TATACACGTACATAACTTACATAAT
1 TACATA-ACTTACATAACTTACATAAT
66359357 TTACTTAATA
Statistics
Matches: 154, Mismatches: 32, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
41 23 0.15
42 18 0.12
43 78 0.51
44 24 0.16
46 11 0.07
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.32
Consensus pattern (43 bp):
TACATAACTTACATAACTTACATAATACATAACTTACATAACA
Found at i:66359292 original size:34 final size:32
Alignment explanation
Indices: 66359114--66359356 Score: 139
Period size: 34 Copynumber: 7.4 Consensus size: 32
66359104 TAACTTGTTA
66359114 AACTTACATAATACATAACTTACATAA--TACAT
1 AACTTACATAATACATAACTT--ATAACTTACAT
* * *
66359146 TACTTACAT-A-GCAT-AC--ATAACTTACAC
1 AACTTACATAATACATAACTTATAACTTACAT
* *
66359173 AACTTACGTAATACAAAACTTACGTAACTTACAT
1 AACTTACATAATACATAACTTA--TAACTTACAT
*
66359207 AACTTACATAACCTACATAATACATAATAACTTAC--
1 AACTTACATAA--TACAT-A-AC-TTATAACTTACAT
* *
66359242 AATTTACATAACATACATTACTTTGATAACTTACAT
1 AACTTACAT-A-ATACATAAC-TT-ATAACTTACAT
* * *
66359278 AACTTACATAATACACAACTTAAATAGCTTACTT
1 AACTTACATAATACATAACTT--ATAACTTACAT
*
66359312 AA--TACATAACTTACATAACTTATACACGTACAT
1 AACTTACATAA--TACATAACTTATA-ACTTACAT
66359345 AACTTACATAAT
1 AACTTACATAAT
66359357 TTACTTAATA
Statistics
Matches: 161, Mismatches: 25, Indels: 49
0.69 0.11 0.21
Matches are distributed among these distances:
25 4 0.02
27 11 0.07
28 1 0.01
29 4 0.02
30 5 0.03
31 1 0.01
32 19 0.12
33 13 0.08
34 55 0.34
35 21 0.13
36 13 0.08
37 10 0.06
38 2 0.01
39 2 0.01
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (32 bp):
AACTTACATAATACATAACTTATAACTTACAT
Found at i:66359308 original size:25 final size:25
Alignment explanation
Indices: 66359141--66359368 Score: 136
Period size: 25 Copynumber: 8.8 Consensus size: 25
66359131 ACTTACATAA
* *
66359141 TACATTACTTACATAGCATACATAACT
1 TACATAACTTACATA--ATACACAACT
* * *
66359168 TACACAACTTACGTAATACAAAACT
1 TACATAACTTACATAATACACAACT
* * *
66359193 TACGTAACTTACATAACTTACATAACC
1 TACATAACTTACATAA--TACACAACT
*
66359220 TACATAA--TACATAATAACTTACAATT
1 TACATAACTTACATAAT-AC--ACAACT
* * ** *
66359246 TACATAACATACATTACTTTGATAACT
1 TACATAACTTACA-TA-ATACACAACT
66359273 TACATAACTTACATAATACACAACT
1 TACATAACTTACATAATACACAACT
* * * *
66359298 TAAATAGCTTACTTAATACATAACT
1 TACATAACTTACATAATACACAACT
* * * *
66359323 TACATAACTTATACACGTACATAACT
1 TACATAACTTACATA-ATACACAACT
* *
66359349 TACATAATTTACTTAATACA
1 TACATAACTTACATAATACA
66359369 TAAATATATA
Statistics
Matches: 153, Mismatches: 38, Indels: 22
0.72 0.18 0.10
Matches are distributed among these distances:
23 1 0.01
24 2 0.01
25 70 0.46
26 32 0.21
27 41 0.27
28 4 0.03
29 2 0.01
30 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (25 bp):
TACATAACTTACATAATACACAACT
Found at i:66362328 original size:26 final size:26
Alignment explanation
Indices: 66362299--66362352 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
66362289 TAATAAAGTG
*
66362299 AACATTTTTTTAACACAGTGAGTACA
1 AACATTTTTTTAACACAATGAGTACA
66362325 AACATTTTTTTAACACAATGAGTACA
1 AACATTTTTTTAACACAATGAGTACA
66362351 AA
1 AA
66362353 AAAATATTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (26 bp):
AACATTTTTTTAACACAATGAGTACA
Found at i:66364921 original size:21 final size:21
Alignment explanation
Indices: 66364903--66364959 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
66364893 GTAGAGGCGG
* *
66364903 CAGCGAGGGAAGCAGAGGCTA
1 CAGCGAGAGAAGCAGAGGCCA
*
66364924 CAGCGAGAGAAGTAGAGGCCA
1 CAGCGAGAGAAGCAGAGGCCA
66364945 CAGCGAGAGAAGCAG
1 CAGCGAGAGAAGCAG
66364960 TGAGAGAAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.37, C:0.19, G:0.40, T:0.04
Consensus pattern (21 bp):
CAGCGAGAGAAGCAGAGGCCA
Found at i:66364966 original size:12 final size:12
Alignment explanation
Indices: 66364945--66364983 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
66364935 GTAGAGGCCA
66364945 CAGCGAGAGAAG
1 CAGCGAGAGAAG
*
66364957 CAGTGAGAGAAG
1 CAGCGAGAGAAG
*
66364969 CAGCGATAGAAG
1 CAGCGAGAGAAG
66364981 CAG
1 CAG
66364984 AGGTTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.41, C:0.15, G:0.38, T:0.05
Consensus pattern (12 bp):
CAGCGAGAGAAG
Found at i:66365507 original size:42 final size:43
Alignment explanation
Indices: 66365418--66365540 Score: 164
Period size: 42 Copynumber: 2.9 Consensus size: 43
66365408 GTTTGTGAAA
*
66365418 TAAGCGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTGACC
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTGACC
* *
66365461 -AAGCGCCGCTATA-AACATTACTTTTAGCGGCGTTTTCT-TCC
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTT-TGACC
*
66365502 TAAGCGCCGCTAAAGAACATGA-TCTTTAGCGGCGTTTTT
1 TAAGCGCCGCTAAAGAACATTACT-TTTAGCGGCGTTTTT
66365541 TTCTGTAAGC
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
41 24 0.34
42 27 0.38
43 20 0.28
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (43 bp):
TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTGACC
Found at i:66368588 original size:13 final size:13
Alignment explanation
Indices: 66368570--66368633 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
66368560 TTATTTATTG
66368570 CTTTTGAAAAGTA
1 CTTTTGAAAAGTA
*
66368583 CTTTTGAAAAGTG
1 CTTTTGAAAAGTA
* * *
66368596 CTGTGGAAAAGTG
1 CTTTTGAAAAGTA
* *
66368609 TTTTTGAGAAGTA
1 CTTTTGAAAAGTA
66368622 CTCTTT-AAAAGT
1 CT-TTTGAAAAGT
66368634 TTGGTTTAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
13 37 0.93
14 3 0.08
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.38
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:66370537 original size:19 final size:18
Alignment explanation
Indices: 66370481--66370538 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 18
66370471 ATAGCAATCA
*
66370481 AATTTTTAGTAAATAAATTT
1 AATTTTTA-T-AATAATTTT
*
66370501 AATTTTTATATTAGATTTT
1 AATTTTTATAATA-ATTTT
66370520 AATTATTTATAATAATTTT
1 AATT-TTTATAATAATTTT
66370539 TTACTTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 3 0.09
19 14 0.42
20 16 0.48
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
AATTTTTATAATAATTTT
Found at i:66370539 original size:20 final size:19
Alignment explanation
Indices: 66370498--66370538 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
66370488 AGTAAATAAA
*
66370498 TTTAATTTTTATATTAGAT
1 TTTAATTTTTATAATAGAT
66370517 TTTAATTATTTATAATA-AT
1 TTTAATT-TTTATAATAGAT
66370536 TTT
1 TTT
66370539 TTACTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTAATTTTTATAATAGAT
Found at i:66371155 original size:41 final size:41
Alignment explanation
Indices: 66371098--66371180 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
66371088 TGCCTCCAAA
66371098 GCTGACTTTTAGCACTTATGATATCTGTTCTTTCCGACAGT
1 GCTGACTTTTAGCACTTATGATATCTGTTCTTTCCGACAGT
66371139 GCTGACTTTTAGCACTTATGATATCTGTTCTTTCCGACAGT
1 GCTGACTTTTAGCACTTATGATATCTGTTCTTTCCGACAGT
66371180 G
1 G
66371181 GCTGTTTGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (41 bp):
GCTGACTTTTAGCACTTATGATATCTGTTCTTTCCGACAGT
Found at i:66372659 original size:27 final size:25
Alignment explanation
Indices: 66372629--66372681 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
66372619 TAATATTTAA
* *
66372629 TTTATAATATAATTCCATTCATCTATT
1 TTTAAAATATAATT-AATTCAT-TATT
*
66372656 TTTAAAATATTATTAATTCATTATT
1 TTTAAAATATAATTAATTCATTATT
66372681 T
1 T
66372682 GAATACATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 6 0.26
27 12 0.52
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTAAAATATAATTAATTCATTATT
Found at i:66376571 original size:51 final size:50
Alignment explanation
Indices: 66376444--66376886 Score: 370
Period size: 51 Copynumber: 8.8 Consensus size: 50
66376434 GTGAAAGTGA
* * * * **
66376444 TGGTCATGTGTGTAGTACTATGTGTAGGCTACTACGTGTACTG-GAACGAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAGAAC-TT
* * * ** * * *
66376494 AGGCCACATGTGTAGTACTAAATGAAGGCTACAATGTGTACCGAGAAGCTT
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAGAA-CTT
* * * * *
66376545 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAGAACT-T
* * * * ** *
66376596 TGGTCACATGCGTAGTACTAAGTGAAGGCTACAATATGTACCGAGAAACTT
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAG-AACTT
* ** * * *
66376647 TGGTCACGTGTGTAGTACTTTGTGAAGGCTACTACGTGAATTGATAAATGA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAGAACT-T
* * * * *
66376698 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTT
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAGAA-CTT
* * * *
66376749 TAGTCACGTATGTAGTTCTATGTGAAGGCTACTACGTGAACCGTAAAAC-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-AGAACTT
* **
66376799 TGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAAT
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-AGAACTT
* * *
66376849 TGATTACGTATGTAGTACTATGTGAAGGCTACTACGTG
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
66376887 TATCGAATGA
Statistics
Matches: 311, Mismatches: 74, Indels: 16
0.78 0.18 0.04
Matches are distributed among these distances:
49 2 0.01
50 116 0.37
51 184 0.59
52 9 0.03
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (50 bp):
TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAGAACTT
Found at i:66376636 original size:102 final size:101
Alignment explanation
Indices: 66376444--66376892 Score: 512
Period size: 102 Copynumber: 4.4 Consensus size: 101
66376434 GTGAAAGTGA
* * * * * *
66376444 TGGTCATGTGTGTAGTACTATGTGTAGGCTACTACGTGTACTGGA-ACGAAA-GGCCACATGTGT
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTG-AATCGATA-AAAATGGTCACATGTGT
*
66376507 AGTACTAAATGAAGGCTACAATGTGTACCGAGAAGCTT
64 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTT
* *
66376545 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGCGTA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAA-AATGGTCACATGTGTA
* *
66376610 GTACTAAGTGAAGGCTACAATATGTACCGAGAAACTT
65 GTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTT
* * *
66376647 TGGTCACGTGTGTAGTACTTTGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGTGTA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAA-AATGGTCACATGTGTA
* *
66376712 GTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTT
65 GTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTT
* * * * * * *
66376749 TAGTCACGTATGTAGTTCTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCACGTGTGTA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAAA-ATGGTCACATGTGTA
* * * * **
66376813 GTACTATGTGAAGGCTACTACGTGAACCGTA-AA-AAT
65 GTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTT
* * * *
66376849 TGATTACGTATGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
66376893 ATGATAATAG
Statistics
Matches: 302, Mismatches: 40, Indels: 12
0.85 0.11 0.03
Matches are distributed among these distances:
100 43 0.14
101 82 0.27
102 177 0.59
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (101 bp):
TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAAAATGGTCACATGTGTAG
TACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTT
Found at i:66377800 original size:5 final size:5
Alignment explanation
Indices: 66377790--66377837 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
66377780 TGCTTGATAA
* * *
66377790 AATGG AATGG AATGG AATGG TAT-G ACATGG AATAG TATGG AATGG AAT
1 AATGG AATGG AATGG AATGG AATGG A-ATGG AATGG AATGG AATGG AAT
66377838 ATATATATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
4 1 0.03
5 32 0.91
6 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.33, T:0.25
Consensus pattern (5 bp):
AATGG
Found at i:66377819 original size:15 final size:15
Alignment explanation
Indices: 66377796--66377838 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
66377786 ATAAAATGGA
*
66377796 ATGGAATGGAATGGT
1 ATGGAATGGAATAGT
66377811 AT-GACATGGAATAGT
1 ATGGA-ATGGAATAGT
66377826 ATGGAATGGAATA
1 ATGGAATGGAATA
66377839 TATATATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 2 0.08
15 21 0.84
16 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.33, T:0.26
Consensus pattern (15 bp):
ATGGAATGGAATAGT
Found at i:66380056 original size:21 final size:21
Alignment explanation
Indices: 66380026--66380084 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
66380016 CTCCACAATT
66380026 GTTTCTAATCTCACCGCTACA
1 GTTTCTAATCTCACCGCTACA
*
66380047 GTTTCCAATCTCACCGCTACA
1 GTTTCTAATCTCACCGCTACA
**
66380068 GTAACTAATCTCACCGC
1 GTTTCTAATCTCACCGC
66380085 CACCGCTGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.36, G:0.10, T:0.29
Consensus pattern (21 bp):
GTTTCTAATCTCACCGCTACA
Found at i:66381255 original size:35 final size:35
Alignment explanation
Indices: 66381201--66381270 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
66381191 TTAAAAGGTG
* *
66381201 GCAACACAGCAGCAGCATGC-AGGATACCAAGCATT
1 GCAACACAGCAGCAACATGCAAGTA-ACCAAGCATT
* *
66381236 GCAACACAGCTGTAACATGCAAGTAACCAAGCATT
1 GCAACACAGCAGCAACATGCAAGTAACCAAGCATT
66381271 TCATTAGCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 27 0.90
36 3 0.10
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (35 bp):
GCAACACAGCAGCAACATGCAAGTAACCAAGCATT
Found at i:66392301 original size:28 final size:29
Alignment explanation
Indices: 66392270--66392330 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
66392260 TTTTTTAATT
* *
66392270 TTTTTTAATTTGATTTTCACTTTC-TTTC
1 TTTTTTAATATAATTTTCACTTTCTTTTC
*
66392298 TTTTTTCATATAATTTTCACTTTCTTTTC
1 TTTTTTAATATAATTTTCACTTTCTTTTC
66392327 TTTT
1 TTTT
66392331 ATTGAAATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.69
Consensus pattern (29 bp):
TTTTTTAATATAATTTTCACTTTCTTTTC
Found at i:66394652 original size:27 final size:25
Alignment explanation
Indices: 66394622--66394674 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
66394612 TAATATTTAA
* *
66394622 TTTATAATATAATTCCATTCATCTATT
1 TTTAAAATATAATT-AATTCAT-TATT
*
66394649 TTTAAAATATTATTAATTCATTATT
1 TTTAAAATATAATTAATTCATTATT
66394674 T
1 T
66394675 GAATACATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 6 0.26
27 12 0.52
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTAAAATATAATTAATTCATTATT
Found at i:66396362 original size:18 final size:19
Alignment explanation
Indices: 66396331--66396387 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 19
66396321 TTTTTTAATC
66396331 ATAAATAGTA-TTAACAAAA
1 ATAAATA-TATTTAACAAAA
*
66396350 AT-AATATATTTAACTAAATT
1 ATAAATATATTTAAC-AAA-A
66396370 ATAAATATATTTAA-AAAA
1 ATAAATATATTTAACAAAA
66396388 CACGTGGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
17 2 0.06
18 9 0.28
19 8 0.25
20 2 0.06
21 11 0.34
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
ATAAATATATTTAACAAAA
Found at i:66396700 original size:14 final size:14
Alignment explanation
Indices: 66396683--66396709 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
66396673 TGTTTTATTA
66396683 TTTTTTTATAATAT
1 TTTTTTTATAATAT
66396697 TTTTTTTATAATA
1 TTTTTTTATAATA
66396710 ATAACCATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTTTATAATAT
Found at i:66396712 original size:17 final size:16
Alignment explanation
Indices: 66396678--66396709 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
66396668 TTTTATGTTT
66396678 TATTATTTTTTTATAA
1 TATTATTTTTTTATAA
66396694 TA-T-TTTTTTTATAA
1 TATTATTTTTTTATAA
66396708 TA
1 TA
66396710 ATAACCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 13 0.81
15 1 0.06
16 2 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTATTTTTTTATAA
Found at i:66398623 original size:21 final size:21
Alignment explanation
Indices: 66398597--66398661 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
66398587 GTAATTTAAC
66398597 TAAAATTCAAGTTAAACAACA
1 TAAAATTCAAGTTAAACAACA
*
66398618 TAAAATAT-ATA-TT---TAAC-
1 TAAAAT-TCA-AGTTAAACAACA
66398635 TAAAATTCAAGTTAAACAACA
1 TAAAATTCAAGTTAAACAACA
66398656 TAAAAT
1 TAAAAT
66398662 ATATATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
16 2 0.06
17 9 0.26
18 3 0.09
20 3 0.09
21 15 0.44
22 2 0.06
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.29
Consensus pattern (21 bp):
TAAAATTCAAGTTAAACAACA
Found at i:66398632 original size:38 final size:38
Alignment explanation
Indices: 66398590--66398669 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
66398580 CTTATAGGTA
66398590 ATTTAACTAAAATTCAAGTTAAACAACATAAAATATAT
1 ATTTAACTAAAATTCAAGTTAAACAACATAAAATATAT
66398628 ATTTAACTAAAATTCAAGTTAAACAACATAAAATATAT
1 ATTTAACTAAAATTCAAGTTAAACAACATAAAATATAT
66398666 ATTT
1 ATTT
66398670 TTACTTTTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.34
Consensus pattern (38 bp):
ATTTAACTAAAATTCAAGTTAAACAACATAAAATATAT
Found at i:66410256 original size:15 final size:15
Alignment explanation
Indices: 66410221--66410272 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
66410211 TTAAGAATTT
*
66410221 TATTAAATTAT-ATA
1 TATTTAATTATAATA
66410235 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
66410249 TATTTAATAATAAT-
1 TATTTAATTATAATA
66410263 TATGTTAATT
1 TAT-TTAATT
66410273 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:66410379 original size:120 final size:120
Alignment explanation
Indices: 66410166--66410508 Score: 659
Period size: 120 Copynumber: 2.9 Consensus size: 120
66410156 AGCAATAACA
*
66410166 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
66410231 TATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
66 TATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
*
66410286 ATCATATATTATGACTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
*
66410351 TATCTTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
66 TATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
66410406 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
66410471 TATATTTTAATTATAATATATTTAATAATAATTATGTT
66 TATATTTTAATTATAATATATTTAATAATAATTATGTT
66410509 TAAATATGAT
Statistics
Matches: 218, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 218 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
TATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
Found at i:66410491 original size:16 final size:16
Alignment explanation
Indices: 66410470--66410511 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
66410460 TTATTAAATT
*
66410470 ATATATTTTAATTATA
1 ATATATTTTAATAATA
66410486 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
66410501 AT-TATGTTTAA
1 ATATAT-TTTAA
66410512 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:66410496 original size:15 final size:15
Alignment explanation
Indices: 66410461--66410502 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
66410451 TTAAGAATTT
*
66410461 TATTAAATTAT-ATA
1 TATTTAATTATAATA
66410475 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
66410489 TATTTAATAATAAT
1 TATTTAATTATAAT
66410503 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:66410739 original size:45 final size:44
Alignment explanation
Indices: 66410656--66410746 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
66410646 ACCTCTATTC
* *
66410656 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACATCTATTCCATTA
*** *
66410700 CATTCAACCAAACAGTTGATTTGCTATTACACATCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACATCTATTCCATTA
66410745 CA
1 CA
66410747 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACATCTATTCCATTA
Found at i:66410746 original size:16 final size:16
Alignment explanation
Indices: 66410725--66410778 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
66410715 TTGATTTGCT
* *
66410725 ATTACACATCTATTCC
1 ATTACACCTCTAATCC
66410741 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
66410757 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
66410773 AATACA
1 ATTACA
66410779 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:66411444 original size:17 final size:15
Alignment explanation
Indices: 66411405--66411460 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
66411395 TTTAAAGATT
*
66411405 AAATTTAATTATAAA
1 AAATTAAATTATAAA
66411420 AAATTAAATTGATAAA
1 AAATTAAATT-ATAAA
*
66411436 AAATGTAAA-TATTAA
1 AAAT-TAAATTATAAA
*
66411451 AGATTAAATT
1 AAATTAAATT
66411461 TGATATTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
14 4 0.11
15 17 0.49
16 10 0.29
17 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (15 bp):
AAATTAAATTATAAA
Found at i:66412597 original size:22 final size:24
Alignment explanation
Indices: 66412565--66412611 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
66412555 TTTAGTATTT
66412565 TTTTATATTT-A-TATATTAATAA
1 TTTTATATTTAACTATATTAATAA
*
66412587 TTTTATTTTTAATCTATATTAATAA
1 TTTTATATTTAA-CTATATTAATAA
66412612 AATTTTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 1 0.05
25 11 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTATATTTAACTATATTAATAA
Found at i:66426162 original size:22 final size:19
Alignment explanation
Indices: 66426098--66426150 Score: 79
Period size: 21 Copynumber: 2.7 Consensus size: 19
66426088 TATCTTCAAG
*
66426098 GATATGCAATCTTAGATCT
1 GATATGCAATCTTAGATAT
66426117 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
66426138 GATATGCAATCTT
1 GATATGCAATCTT
66426151 GGAAGATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.42
21 18 0.58
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:66426179 original size:22 final size:22
Alignment explanation
Indices: 66426098--66426176 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 22
66426088 TATCTTCAAG
**
66426098 GATATGCAATCTTAG-ATCTGAT
1 GATATGCAATCTTAGAAGAT-AT
66426120 -ATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
66426138 GATATGCAATCTTGGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
66426160 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
66426177 GATTTAATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 2 0.04
19 14 0.30
21 12 0.26
22 8 0.17
23 11 0.23
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:66434806 original size:3 final size:3
Alignment explanation
Indices: 66434701--66434794 Score: 84
Period size: 3 Copynumber: 31.3 Consensus size: 3
66434691 GGGTATAAAT
* * * * * * *
66434701 ATA ATG ATA GTA ATA ATA ATA GTA GTA ATA ATA CTA ACA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
66434749 A-A GATA ATA ATA GTAA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA -ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
66434794 A
1 A
66434795 ACAAAATAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
2 3 0.04
3 67 0.92
4 3 0.04
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:66436781 original size:88 final size:87
Alignment explanation
Indices: 66436534--66437064 Score: 608
Period size: 88 Copynumber: 6.1 Consensus size: 87
66436524 GATCTGTAAT
* * * *
66436534 TCTTCAACCAGCTCCACTACAACCGAGAGAGGTAAGG-TT-TGTCTTCGACCTGCTTCACTGTCA
1 TCTTCAACCAGCTCCACTACAACCGAG-GAGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTCA
* ** * *
66436597 ACGCAGGAAGATAAAATCAGTTG
65 ATGCAGGAAGGCAAGATCTGTTG
* ** * *
66436620 TCTTCAACCAACTCTTCTAC-ACTCGAGAGAGGCAAGGCTT-TGTTTTCGATCTGCTTCGCTGTT
1 TCTTCAACCAGCTCCACTACAAC-CGAG-GAGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTC
* * * *
66436683 AACGTAGGAAGGCAAGATCTGCTA
64 AATGCAGGAAGGCAAGATCTGTTG
* * *
66436707 TCTTCAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGT-TTTTCGATCTACTTCGCTGTT
1 TCTTCAACCAGCTCCACTACAACCGA-GGAGGCAAGG-TTTGTGTTTTCGATCTGCTTCGCTGTC
* *
66436771 AATGCAGGAAGGCAAGATCTGCTA
64 AATGCAGGAAGGCAAGATCTGTTG
* * * *
66436795 TCTTCAACTAGCTCCACCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCA
1 TCTTCAACCAGCTCCACTACAACCGA-GGAGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTCA
*
66436860 ATGCAGGAAGGCAAGATCTTTTG
65 ATGCAGGAAGGCAAGATCTGTTG
*
66436883 TCTTCAACCAGCTCCA-TCACAACCGAAAGAGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTC
1 TCTTCAACCAGCTCCACT-ACAACCG-AGGAGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTC
* *
66436947 AATGTAGGAAGGCAAGATCTTTTG
64 AATGCAGGAAGGCAAGATCTGTTG
* *
66436971 TCTTCAACCAGCTCTA-TCACAACCGAAAGAGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTC
1 TCTTCAACCAGCTCCACT-ACAACCG-AGGAGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTC
* *
66437035 AATGTAGGAAGGCAAGATCTTTTG
64 AATGCAGGAAGGCAAGATCTGTTG
66437059 TCTTCA
1 TCTTCA
66437065 TTTATCTGTC
Statistics
Matches: 395, Mismatches: 41, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
85 2 0.01
86 30 0.08
87 71 0.18
88 290 0.73
89 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (87 bp):
TCTTCAACCAGCTCCACTACAACCGAGGAGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTCAA
TGCAGGAAGGCAAGATCTGTTG
Found at i:66436872 original size:44 final size:44
Alignment explanation
Indices: 66436824--66437050 Score: 149
Period size: 44 Copynumber: 5.2 Consensus size: 44
66436814 CAACCGAGGG
*
66436824 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGAAGGA
* * * * ** * *
66436868 AGGCAAGATCTTTTGTCTTCAACCAGC-TC-CATCACAACCGAAAG-
1 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCGC-TGTCAA-TGAAGGA
* * *
66436912 AGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTCAATGTAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGAAGGA
* * * * ** ** * *
66436956 AGGCAAGATCTTTTGTCTTCAACCAGC-TCTATCACAACCGAAAG-
1 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCGCTGTCAA-TGAAGGA
* * *
66437000 AGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTCAATGTAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGAAGGA
66437044 AGGCAAG
1 AGGCAAG
66437051 ATCTTTTGTC
Statistics
Matches: 127, Mismatches: 46, Indels: 20
0.66 0.24 0.10
Matches are distributed among these distances:
43 31 0.24
44 63 0.50
45 33 0.26
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGAAGGA
Found at i:66437005 original size:264 final size:261
Alignment explanation
Indices: 66436534--66437054 Score: 708
Period size: 264 Copynumber: 2.0 Consensus size: 261
66436524 GATCTGTAAT
* *
66436534 TCTTCAACCAGCTCCACTACAACCGAGAGAGGTAAGGTTTGTCTTCGACCTGCTTCACTGTCAAC
1 TCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTGTCTTCGACCTGCTTCACTGTCAAC
* * *
66436599 GCAGGAAGATAAAATCAGTTGTCTTCAACCAACTCTTCTACACTCGAGAGAGGCAAGGCTTTGTT
66 GCAGGAAGACAAAATCAGTTGTCTTCAACCAACTCATCTACACTCGAAAGAGGCAAGGCTTTGTT
* *
66436664 TTCGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAA
131 TTCGATCTGCTTCGCTGTCAACGTAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAA
** *
66436729 CCGATGGAGGCAAGGCTTTGT-TTTTCGATCTACTTCGCTGTTAATGCAGGAAGGCAAGATCTGC
196 CCGAAAGAGGCAAGG-TTTGTGTTTTCGATCTACTTCGCTGTCAATGCAGGAAGGCAAGATCTGC
66436793 TA
260 TA
* * *
66436795 TCTTCAACTAGCTCCACCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCA
1 TCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGG-TT-TGTCTTCGACCTGCTTCACTGTCA
* * * ** * *
66436860 ATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC-ACAAC-CGAAAGAGGCAAGGTTT
64 ACGCAGGAAGACAAAATCAGTTGTCTTCAACCAACT-CATCTAC-ACTCGAAAGAGGCAAGGCTT
* ** * *
66436923 GTGTTTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTA-
127 -TGTTTTCGATCTGCTTCGCTGTCAACGTAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCAC
* *
66436987 TCACAACCGAAAGAGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGA
191 T-ACAACCGAAAGAGGCAAGGTTTGTGTTTTCGATCTACTTCGCTGTCAATGCAGGAAGGCAAGA
66437052 TCT
255 TCT
66437055 TTTGTCTTCA
Statistics
Matches: 226, Mismatches: 27, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
261 33 0.15
262 2 0.01
263 75 0.33
264 116 0.51
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (261 bp):
TCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTGTCTTCGACCTGCTTCACTGTCAAC
GCAGGAAGACAAAATCAGTTGTCTTCAACCAACTCATCTACACTCGAAAGAGGCAAGGCTTTGTT
TTCGATCTGCTTCGCTGTCAACGTAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAA
CCGAAAGAGGCAAGGTTTGTGTTTTCGATCTACTTCGCTGTCAATGCAGGAAGGCAAGATCTGCT
A
Found at i:66437055 original size:176 final size:176
Alignment explanation
Indices: 66436534--66437064 Score: 671
Period size: 176 Copynumber: 3.0 Consensus size: 176
66436524 GATCTGTAAT
* * * * *
66436534 TCTTCAACCAGCTCCACTACAACCGAGAGAGGTAAGG-TT-TGTCTTCGACCTGCTTCACTGTCA
1 TCTTCAACCAGCTCCACTACAACCGAAAGAGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTCA
* ** * * * *
66436597 ACGCAGGAAGATAAAATCAGTTGTCTTCAACCAACTCT-TCTAC-ACTCGAGAGAGGCAAGGCTT
66 ATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTATC-ACAAC-CGAGAGAGGCAAGGTTT
* * ** *
66436660 -TGTTTTCGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTA
129 GTGTTTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTG
* ** * *
66436707 TCTTCAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGT-TTTTCGATCTACTTCGCTGTT
1 TCTTCAACCAGCTCCACTACAACCGAAAGAGGCAAGG-TTTGTGTTTTCGATCTGCTTCGCTGTC
* * * * * *
66436771 AATGCAGGAAGGCAAGATCTGCTATCTTCAACTAGCTCCACCACAACCGAGGGAGGCAAGGTTTG
65 AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTATCACAACCGAGAGAGGCAAGGTTTG
* * *
66436836 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTG
130 TGTTTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTG
66436883 TCTTCAACCAGCTCCA-TCACAACCGAAAGAGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTC
1 TCTTCAACCAGCTCCACT-ACAACCGAAAGAGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTC
* * *
66436947 AATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTG
65 AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTATCACAACCGAGAGAGGCAAGGTTTG
66437012 TGTTTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTG
130 TGTTTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTG
66437059 TCTTCA
1 TCTTCA
66437065 TTTATCTGTC
Statistics
Matches: 303, Mismatches: 47, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
173 33 0.11
175 70 0.23
176 200 0.66
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (176 bp):
TCTTCAACCAGCTCCACTACAACCGAAAGAGGCAAGGTTTGTGTTTTCGATCTGCTTCGCTGTCA
ATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTATCACAACCGAGAGAGGCAAGGTTTGT
GTTTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTG
Found at i:66438320 original size:16 final size:16
Alignment explanation
Indices: 66438299--66438354 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 16
66438289 AGCCTCTCCA
66438299 TTTTTACTTTTTCATT
1 TTTTTACTTTTTCATT
*
66438315 TTTTTATTTTTTCATCT
1 TTTTTACTTTTTCAT-T
66438332 TCTTCTT-CTTTTTCATT
1 T-TT-TTACTTTTTCATT
66438349 CTTTTT
1 -TTTTT
66438355 TTTTTGAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
16 16 0.47
17 5 0.15
18 11 0.32
19 2 0.06
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTACTTTTTCATT
Found at i:66443710 original size:12 final size:12
Alignment explanation
Indices: 66443695--66443779 Score: 89
Period size: 12 Copynumber: 6.8 Consensus size: 12
66443685 GGGTATAAAT
*
66443695 ATAATGATAGTA
1 ATAATAATAGTA
66443707 ATAATAATAGTA
1 ATAATAATAGTA
* *
66443719 GTAATAATACTA
1 ATAATAATAGTA
*
66443731 ACAATAATAGTAAA
1 ATAATAATAGT--A
66443745 GATAATAATAGTAA
1 -ATAATAATAGT-A
*
66443759 ATAATAATAATA
1 ATAATAATAGTA
66443771 ATAATAATA
1 ATAATAATA
66443780 AAATAAACAA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
12 39 0.63
13 10 0.16
14 3 0.05
15 10 0.16
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (12 bp):
ATAATAATAGTA
Found at i:66443797 original size:3 final size:3
Alignment explanation
Indices: 66443695--66443785 Score: 78
Period size: 3 Copynumber: 30.3 Consensus size: 3
66443685 GGGTATAAAT
* * * * * * *
66443695 ATA ATG ATA GTA ATA ATA ATA GTA GTA ATA ATA CTA ACA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
66443743 A-A GATA ATA ATA GTAA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA -ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
66443786 ACAAAATAAT
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
2 3 0.04
3 64 0.91
4 3 0.04
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:66453912 original size:19 final size:20
Alignment explanation
Indices: 66453883--66453932 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
66453873 GTTATTTTTA
66453883 TTTAT-TTATTTAAT-ATAT
1 TTTATATTATTTAATAATAT
66453901 TTTATATTATTT-ATAATAT
1 TTTATATTATTTAATAATAT
66453920 TTATATATT-TTTA
1 TT-TATATTATTTA
66453933 CAAATCTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 7 0.25
19 15 0.54
20 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATATTATTTAATAATAT
Found at i:66453968 original size:23 final size:24
Alignment explanation
Indices: 66453878--66453973 Score: 76
Period size: 23 Copynumber: 4.0 Consensus size: 24
66453868 AACATGTTAT
*
66453878 TTTTAT-TTATTTA-TTTAATATA
1 TTTTATATTATTTATTTTTATATA
66453900 TTTTATATTATTTATAATATTTATATA
1 TTTTATATTATTTAT--T-TTTATATA
** * *
66453927 TTTT-TACAAATCTAATTTTATA-A
1 TTTTATA-TTATTTATTTTTATATA
66453950 TTTTATATTATTTATTTTTA-ATA
1 TTTTATATTATTTATTTTTATATA
66453973 T
1 T
66453974 CATTAATTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
22 7 0.12
23 23 0.40
24 8 0.14
25 1 0.02
26 3 0.05
27 15 0.26
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTATATTATTTATTTTTATATA
Found at i:66454605 original size:24 final size:24
Alignment explanation
Indices: 66454576--66454633 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
66454566 ATTTAATTTT
* *
66454576 ACCCCTAAAAAAAATTCTAGCTTC
1 ACCCCTAAAAAAAATTATAGCTTA
* *
66454600 ACCCCTAAAGAAAATTATAGTTTA
1 ACCCCTAAAAAAAATTATAGCTTA
*
66454624 ACCCTTAAAA
1 ACCCCTAAAA
66454634 TTGATAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (24 bp):
ACCCCTAAAAAAAATTATAGCTTA
Found at i:66455200 original size:20 final size:21
Alignment explanation
Indices: 66455161--66455200 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
66455151 CTAATAATGT
*
66455161 AATTTTTAAAATTTAAATATGA
1 AATTTTTAAAA-TAAAATATGA
66455183 AATTTTTAAAA-AAAATAT
1 AATTTTTAAAATAAAATAT
66455201 AATATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
AATTTTTAAAATAAAATATGA
Found at i:66455916 original size:18 final size:18
Alignment explanation
Indices: 66455882--66455921 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
66455872 ATATATTTTC
66455882 ATTATTTTAAGTATAAAA
1 ATTATTTTAAGTATAAAA
*
66455900 TATTATTTTTA-TATAAAA
1 -ATTATTTTAAGTATAAAA
66455918 ATTA
1 ATTA
66455922 AAATTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 7 0.35
19 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTATTTTAAGTATAAAA
Found at i:66456413 original size:21 final size:21
Alignment explanation
Indices: 66456377--66456418 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
66456367 AAAGTTAGTA
* *
66456377 TTAAAGTTTCGTTAATAAATT
1 TTAAAGTTCCGATAATAAATT
*
66456398 TTAAAGTTCCGATAATTAATT
1 TTAAAGTTCCGATAATAAATT
66456419 GAACAAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (21 bp):
TTAAAGTTCCGATAATAAATT
Done.