Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 177 of 221
Found at i:52801462 original size:19 final size:19
Alignment explanation
Indices: 52801438--52801476 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
52801428 AGCTGTTGGA
52801438 TAATTTAATAAAAAATATT
1 TAATTTAATAAAAAATATT
* *
52801457 TAATTTATTAAATAATATT
1 TAATTTAATAAAAAATATT
52801476 T
1 T
52801477 TAAAAACCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATTTAATAAAAAATATT
Found at i:52804279 original size:13 final size:13
Alignment explanation
Indices: 52804238--52804281 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
52804228 AGAGAAGGAA
*
52804238 ATTTTATTTATTT
1 ATTTTATTTAATT
*
52804251 ATTATA-TTAATAT
1 ATTTTATTTAAT-T
52804264 ATTTTATTTAATT
1 ATTTTATTTAATT
52804277 ATTTT
1 ATTTT
52804282 TTCTTTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 4 0.15
13 17 0.65
14 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTATTTAATT
Found at i:52804500 original size:18 final size:18
Alignment explanation
Indices: 52804476--52804517 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
52804466 TTAAGTCAAT
52804476 TTTAAAAATAAA-AAAAA
1 TTTAAAAATAAAGAAAAA
*
52804493 TTTAAAAATAAAGAAATA
1 TTTAAAAATAAAGAAAAA
52804511 TTTAAAA
1 TTTAAAA
52804518 CTTTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
TTTAAAAATAAAGAAAAA
Found at i:52805078 original size:16 final size:17
Alignment explanation
Indices: 52805045--52805078 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
52805035 AATGTGTTAC
*
52805045 AAATTACATAAGTATAA
1 AAATAACATAAGTATAA
52805062 AAATAACATAA-TATAA
1 AAATAACATAAGTATAA
52805078 A
1 A
52805079 GTATTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATAACATAAGTATAA
Found at i:52806714 original size:14 final size:15
Alignment explanation
Indices: 52806695--52806725 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
52806685 ATAGAGGTTA
52806695 TTTTTGTTTTT-ATT
1 TTTTTGTTTTTCATT
52806709 TTTTTGTTTTTCATT
1 TTTTTGTTTTTCATT
52806724 TT
1 TT
52806726 CATTTTCGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (15 bp):
TTTTTGTTTTTCATT
Found at i:52812161 original size:25 final size:25
Alignment explanation
Indices: 52812111--52812161 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
52812101 TGAAATGACA
*
52812111 TATTTTTATGTATTAATTACATGCT
1 TATTTTTATGTATTAATTACACGCT
* *
52812136 TATTTTTATGTATTTATTACCCGCT
1 TATTTTTATGTATTAATTACACGCT
52812161 T
1 T
52812162 TGTATGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.57
Consensus pattern (25 bp):
TATTTTTATGTATTAATTACACGCT
Found at i:52819731 original size:14 final size:14
Alignment explanation
Indices: 52819712--52819741 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52819702 TGTTGTTGAA
*
52819712 AATGTTTTGAGAAG
1 AATGTTTCGAGAAG
52819726 AATGTTTCGAGAAG
1 AATGTTTCGAGAAG
52819740 AA
1 AA
52819742 ACTACAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.27, T:0.30
Consensus pattern (14 bp):
AATGTTTCGAGAAG
Found at i:52822929 original size:29 final size:29
Alignment explanation
Indices: 52822900--52822963 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 29
52822890 TAAAAACATT
*
52822900 AAAACAAATATTAAAATAACAAACAAATTA
1 AAAAC-AATATTAAAACAACAAACAAATTA
52822930 AAAACAATATTAAAACAACAAACAAATTGA
1 AAAACAATATTAAAACAACAAACAAATT-A
52822960 AAAA
1 AAAA
52822964 ATTGCTCCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.70, C:0.11, G:0.02, T:0.17
Consensus pattern (29 bp):
AAAACAATATTAAAACAACAAACAAATTA
Found at i:52824054 original size:19 final size:21
Alignment explanation
Indices: 52824029--52824084 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 21
52824019 TATTAAATAC
52824029 TTTTAAT-ATTTTTATTTAAA
1 TTTTAATCATTTTTATTTAAA
52824049 -TTTAATCATTTTTA--TAAA
1 TTTTAATCATTTTTATTTAAA
* *
52824067 TTTTATTGATTTTTATTT
1 TTTTAATCATTTTTATTT
52824085 TTTATAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 4 0.13
19 18 0.60
20 7 0.23
21 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTAATCATTTTTATTTAAA
Found at i:52830971 original size:30 final size:30
Alignment explanation
Indices: 52830937--52831019 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
52830927 TCAAACTTTT
* *
52830937 TATAAATTCATCATGTGTGAGCAACCGTGG
1 TATAAATTCAGCTTGTGTGAGCAACCGTGG
* *
52830967 TATAAAGTT-AGCTTGTGTGAGCAACCTTGT
1 TATAAA-TTCAGCTTGTGTGAGCAACCGTGG
*
52830997 TATAAAGTCAGCTTGTGTGAGCA
1 TATAAATTCAGCTTGTGTGAGCA
52831020 CTTATTCACC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 1 0.02
30 43 0.93
31 2 0.04
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (30 bp):
TATAAATTCAGCTTGTGTGAGCAACCGTGG
Found at i:52832921 original size:319 final size:319
Alignment explanation
Indices: 52832337--52832976 Score: 1088
Period size: 319 Copynumber: 2.0 Consensus size: 319
52832327 TATCCCTCAA
* * *
52832337 TTTCAATCTTCAGAACTCCAATCCTTTGTTTTCTATAATCTTCCTAGCATTAAAACCCCTTTTGA
1 TTTCAATCTTCAGAACTCCAATCCCTTATTTTCTATAATCTTCCTAGCATTAAAACCCCCTTTGA
* *
52832402 AAGCCAAGAAGAGCAGAAAGAACACCCTTAATTTCCTTTTCATTCAACTTGTGGGTTTTCTGAAT
66 AAGCCAAGAAGAGCACAAAGAACACCCTTAATTTCCTTGTCATTCAACTTGTGGGTTTTCTGAAT
* *
52832467 TTTCAATTAAACACTCCTTTTCCCCTCAATCAAGGTAATGTTTCGTTTTCCTAATAGTTTTTTAT
131 TTTCAATCAAACACTCCTTTTCCCCTCAATCAAGGTAATGTTTCATTTTCCTAATAGTTTTTTAT
** *
52832532 GAACTCTAGCTATTTAAATCGAGTTTTTTTATCAATTGAATCAAAGGTTTTGTGTAAATGCCAAA
196 GAACTCTAGCTATTTAAATCGAGTTTTTAAATCAATTGAATCAAAGCTTTTGTGTAAATGCCAAA
52832597 ATTTTGGGCGTTAATGGTGAAATTCGAGATTTTGAATAAAATCAAAT-TTTCAAAGTGTT
261 ATTTTGGGCGTTAATGGTGAAATTCGAGATTTTGAATAAAATC-AATGTTTCAAAGTGTT
* *
52832656 TTTCAATCTTCCA-AACTCTAATCCCTTATTTTCTATAATCTTCCTAGTATTAAAACCCCCTTTG
1 TTTCAATCTT-CAGAACTCCAATCCCTTATTTTCTATAATCTTCCTAGCATTAAAACCCCCTTTG
52832720 AAAGCCAAGAAGAGCACAAAGAACACCCTTAATTTCCTTGTCATTCAACTTGTGGGTTTTCTGAA
65 AAAGCCAAGAAGAGCACAAAGAACACCCTTAATTTCCTTGTCATTCAACTTGTGGGTTTTCTGAA
52832785 TTTTCAATCAAACACTCCTTTTCCCCTCAATCAAGGTAATGTTTCATTTTCCTAATAGTTTTTTT
130 TTTTCAATCAAACACTCCTTTTCCCCTCAATCAAGGTAATGTTTCATTTTCCTAATAG-TTTTTT
**
52832850 ATGAACTCTAGCTATTTAAATCGAG-TTTTAAATCAATTGAATCAAAGCTTTTGTGTAAATGCTG
194 ATGAACTCTAGCTATTTAAATCGAGTTTTTAAATCAATTGAATCAAAGCTTTTGTGTAAATGCCA
* *
52832914 GAATTTTGGGCGTTAATGGTGAAATTCGGGATTTTGAATAAAATCAATGTTTCAAAGTGTT
259 AAATTTTGGGCGTTAATGGTGAAATTCGAGATTTTGAATAAAATCAATGTTTCAAAGTGTT
52832975 TT
1 TT
52832977 CACCTCGTTT
Statistics
Matches: 302, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
318 3 0.01
319 266 0.88
320 33 0.11
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (319 bp):
TTTCAATCTTCAGAACTCCAATCCCTTATTTTCTATAATCTTCCTAGCATTAAAACCCCCTTTGA
AAGCCAAGAAGAGCACAAAGAACACCCTTAATTTCCTTGTCATTCAACTTGTGGGTTTTCTGAAT
TTTCAATCAAACACTCCTTTTCCCCTCAATCAAGGTAATGTTTCATTTTCCTAATAGTTTTTTAT
GAACTCTAGCTATTTAAATCGAGTTTTTAAATCAATTGAATCAAAGCTTTTGTGTAAATGCCAAA
ATTTTGGGCGTTAATGGTGAAATTCGAGATTTTGAATAAAATCAATGTTTCAAAGTGTT
Found at i:52834933 original size:3 final size:3
Alignment explanation
Indices: 52834892--52834917 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52834882 AAAATCAACG
52834892 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
52834918 GTAAGCAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:52836116 original size:20 final size:18
Alignment explanation
Indices: 52836086--52836133 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 18
52836076 TAGTTTTTTT
52836086 TTTATTTTTGGGCTTGTAA
1 TTTA-TTTTGGGCTTGTAA
*
52836105 TGTTTATTTTGGGTTTGTAA
1 --TTTATTTTGGGCTTGTAA
52836125 TTTATTTTG
1 TTTATTTTG
52836134 TTGGGCCTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.35
20 13 0.50
21 4 0.15
ACGTcount: A:0.15, C:0.02, G:0.21, T:0.62
Consensus pattern (18 bp):
TTTATTTTGGGCTTGTAA
Found at i:52836560 original size:54 final size:54
Alignment explanation
Indices: 52836502--52836719 Score: 188
Period size: 54 Copynumber: 4.2 Consensus size: 54
52836492 TTCAATCTAC
52836502 TCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGT
1 TCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGT
* * * ** * * *
52836556 TCCACTACAAC-GCTAGG-GGAATAAGATTTG-C------TGT--CTTCAGTCTGC
1 TCCACTGCAACTTC-AGGAAG-ATAAGATCCGCCATAATTTGTAGCTTTAATCTGT
** * * *
52836601 TCCGTTACAACTTCAGGAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGG
1 TCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGT
** * *
52836655 TATACTGTAACTTCAGGAAGATAAGATCCGCCATAATTTTTAGCTTTAATCTGT
1 TCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGT
52836709 TCCACTGCAAC
1 TCCACTGCAAC
52836720 GCCAGGGAAA
Statistics
Matches: 123, Mismatches: 28, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
45 29 0.24
46 3 0.02
47 3 0.02
52 3 0.02
53 3 0.02
54 82 0.67
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (54 bp):
TCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGT
Found at i:52836733 original size:54 final size:54
Alignment explanation
Indices: 52836614--52836735 Score: 156
Period size: 54 Copynumber: 2.3 Consensus size: 54
52836604 GTTACAACTT
* * * **
52836614 CAGGAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGGTATACTGTAACTT
1 CAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGGTACACTGCAACGC
* * *
52836668 CAGGAAGATAAGATCCGCCATAATTTTTAGCTTTAATCTGTTCCACTGCAACGC
1 CAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGGTACACTGCAACGC
52836722 CAGGGAA-ATAAGAT
1 CA-GGAAGATAAGAT
52836736 TCGTTATCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
54 55 0.93
55 4 0.07
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (54 bp):
CAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGGTACACTGCAACGC
Found at i:52836876 original size:54 final size:55
Alignment explanation
Indices: 52836813--52836983 Score: 151
Period size: 54 Copynumber: 3.3 Consensus size: 55
52836803 TGCAACTTTA
52836813 GGAAGATAAGATTCACCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAG
1 GGAAGATAAGATTCACCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAG
*** * * * * ** * * **
52836868 GGAA-ATAAGA-T-A--A-GGCTGGTGGATTCAATCTGCTCCATTGTAACTTCA-
1 GGAAGATAAGATTCACCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAG
**
52836916 GGAAGATAAGATTTGCCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAG
1 GGAAGATAAGATTCACCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAG
52836971 GGAA-ATAAGATTC
1 GGAAGATAAGATTC
52836984 GCTGCCTTCA
Statistics
Matches: 81, Mismatches: 28, Indels: 15
0.65 0.23 0.12
Matches are distributed among these distances:
48 4 0.05
49 28 0.35
50 2 0.02
52 1 0.01
53 2 0.02
54 36 0.44
55 8 0.10
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (55 bp):
GGAAGATAAGATTCACCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAG
Found at i:52836935 original size:103 final size:103
Alignment explanation
Indices: 52836772--52836981 Score: 366
Period size: 103 Copynumber: 2.0 Consensus size: 103
52836762 AATTTCCAGG
* *
52836772 AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATTCACCATAATTT
1 AGATAAGGCTGGTGGATTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCACCATAATTT
52836837 GTAGCTTTAATCTATTCCACTGCAACGCCAGGGAAATA
66 GTAGCTTTAATCTATTCCACTGCAACGCCAGGGAAATA
* * **
52836875 AGATAAGGCTGGTGGATTCAATCTGCTCCATTGTAACTTCAGGAAGATAAGATTTGCCATAATTT
1 AGATAAGGCTGGTGGATTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCACCATAATTT
52836940 GTAGCTTTAATCTATTCCACTGCAACGCCAGGGAAATA
66 GTAGCTTTAATCTATTCCACTGCAACGCCAGGGAAATA
52836978 AGAT
1 AGAT
52836982 TCGCTGCCTT
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (103 bp):
AGATAAGGCTGGTGGATTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCACCATAATTT
GTAGCTTTAATCTATTCCACTGCAACGCCAGGGAAATA
Found at i:52836952 original size:246 final size:246
Alignment explanation
Indices: 52836660--52837124 Score: 736
Period size: 246 Copynumber: 1.9 Consensus size: 246
52836650 TCTGGTATAC
* *
52836660 TGTAACTTCAGGAAGATAAGATCCGCCATAATTTTTAGCTTTAATCTGTTCCACTGCAACGCCAG
1 TGTAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAG
* * * *
52836725 GGAAATAAGATTCGTTATCTTCAGTCTGCT-TCGTTGCAATTTCCA-GGAGATAAGGCTGGTGGC
66 GGAAATAAGATTCGCTACCTTCAGTCTGCTCT-GCTGCAACTT-CAGGGAGATAAGGCTGGTGGC
* * * *
52836788 TTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATTCACCATAATTTGTAGCTTTAATCTATT
129 TTCAATCTACTCCACTGCAACATCAGGAAAATAAGATTCACCATAATTTGTAGCTTTAATCTATT
*
52836853 CCACTGCAACGCCAGGGAAATAAGATAAGGCTGGTGGATTCAATCTGCTCCAT
194 CCACTACAACGCCAGGGAAATAAGATAAGGCTGGTGGATTCAATCTGCTCCAT
**
52836906 TGTAACTTCAGGAAGATAAGATTTGCCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAG
1 TGTAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAG
* * *
52836971 GGAAATAAGATTCGCTGCCTTCAGTCTGCTCTGCTGTAACTTCAGGGAGATAAGGCTGGTGGGTT
66 GGAAATAAGATTCGCTACCTTCAGTCTGCTCTGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTT
* *
52837036 CAATCTACTCTACTGCAACATCAGGAAAATAAGATTCACCATAATTTGTAGCTTTAATCTGTTCC
131 CAATCTACTCCACTGCAACATCAGGAAAATAAGATTCACCATAATTTGTAGCTTTAATCTATTCC
52837101 ACTACAACGCCAGGGAAATAAGAT
196 ACTACAACGCCAGGGAAATAAGAT
52837125 TCATGTTTTC
Statistics
Matches: 199, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
245 2 0.01
246 196 0.98
247 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (246 bp):
TGTAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAG
GGAAATAAGATTCGCTACCTTCAGTCTGCTCTGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTT
CAATCTACTCCACTGCAACATCAGGAAAATAAGATTCACCATAATTTGTAGCTTTAATCTATTCC
ACTACAACGCCAGGGAAATAAGATAAGGCTGGTGGATTCAATCTGCTCCAT
Found at i:52837155 original size:143 final size:143
Alignment explanation
Indices: 52836875--52838795 Score: 2418
Period size: 143 Copynumber: 13.4 Consensus size: 143
52836865 CAGGGAAATA
* * * *
52836875 AGATAAGGCTGGTGGATTCAATCTGCTCCATTGTAACTTCAGGAAGATAAGATTTGCCATAATTT
1 AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTT
* * * *
52836940 GTAGCTTTAATCTATTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGTCTGCTCTGC
66 GTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGC
*
52837005 TGTAACTTCAGGG
131 TGCAACTTCAGGG
* * * * * *
52837018 AGATAAGGCTGGTGGGTTCAATCTACTCTACTGCAACATCAGGAAAATAAGATTCACCATAATTT
1 AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTT
* * * * **
52837083 GTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTC-ATGTTTTCAATCTGCTGCAT
66 GTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGC
*
52837147 TGAAAACTTCAGGG
131 TG-CAACTTCAGGG
* *
52837161 AGATAAGGTTGGTGGCTTCAATTTGCTCCACTG-AACCTTCAGGAAGATAAGA-TCTGCCATAAT
1 AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAA-CTTCAGGAAGATAAGATTC-GCCATAAT
* * * * *
52837224 TTGTAGCTTTAATCTATTCCACTACAATGTCAGGGAAATAAGATTCACTGTCTTCAGTCTGCTCT
64 TTGTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
52837289 GCTGCAACTTCAGGG
129 GCTGCAACTTCAGGG
* * * ** * *
52837304 AGATAATG-TAGGTGGCTTCAATCTGCTCCACTACAACTTTATAAAAATAAGATTCGTCATAATT
1 AGATAAGGCT-GGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATT
* *
52837368 TGTAGCTTTAATATGTTCCACTACAATGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCG
65 TGTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCG
*
52837433 CTGCAACTTCAAGG
130 CTGCAACTTCAGGG
* * *
52837447 AGATAAGACTGGTGGCTTCAATATGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTT
1 AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTT
* * * * * * * *
52837512 GCAGCTTTAATCTGTTCTACTTCAACTCCAAGGAAATAAGATTCGTTTTCTTCAGCCTGCTCCGC
66 GTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGC
* *
52837577 TGTAACTTTAGGG
131 TGCAACTTCAGGG
* * * * *
52837590 AGATAAGGCTGGTGGCTTTAATATACTCAACTGCAACTTTAGGAAGATAAGATTCGCCATAATTT
1 AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTT
* * * *
52837655 GTAGCTTTAATTTGTTCCACTGCAACGCTAAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGC
66 GTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGC
*
52837720 TACAACTTCAGGG
131 TGCAACTTCAGGG
* * * * *
52837733 AGATAAGGTTGGTGACTTCAATCTGCTCCATTGCAACTTTAGGAAGATACGATTCGCCATAATTT
1 AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTT
* * ** * * * * **
52837798 GTAGCTTTAAACT-ATCCTACTGTAATGCTAAGGAAATAAGATTCGCTATCTTCAGTCTGCTCTA
66 GTAGCTTTAATCTGTTCC-ACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCG
*
52837862 CTGCAACTTTAGGG
130 CTGCAACTTCAGGG
* *
52837876 AGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAGAAAGATAAGATTCGCCATAATTT
1 AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTT
* * * *
52837941 GTAGCTTTAATCTGTTCTACTGCAACGCCAGGGAAATAAGATTTGTTGTCTTCAGTCTGCTCCGC
66 GTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGC
52838006 TGCAACTTCAGGG
131 TGCAACTTCAGGG
* * *
52838019 AGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATTCGCCATGATTT
1 AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTT
* * * * *
52838084 GTAGCTTTAATCTATTCCACTGCAACGCTAGGGAAATAAAATTCGCTGTCTTTAGTCTGCTCCGC
66 GTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGC
*
52838149 TACAACTTCAGGG
131 TGCAACTTCAGGG
* * * * *
52838162 AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGTAACTTTAGGATGAGAAGA-TCTGTCATAATT
1 AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTC-GCCATAATT
* * * *
52838226 TGTAGCTTGAATTTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTTTGCTCCA
65 TGTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCG
** *
52838291 CTATAACTTCATGG
130 CTGCAACTTCAGGG
* ** * * * * * * *
52838305 AGATAAGGTTGGTGGCTTCGGTTTGCTCCACTTCAACTTTAGAAAGAGAAGATCCGCTATAATTT
1 AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTT
52838370 GTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGC
66 GTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGC
* *
52838435 TACAACTTTAGGG
131 TGCAACTTCAGGG
* * * * *
52838448 AGATAAGG-TCCGTGGCTTTAATCTGCTCCACTGCAACTTCAAGAAGATAAGATTAGCCATAAAT
1 AGATAAGGCT-GGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATT
* * * * *
52838512 TGTAGCTGTAATCTGTTCCACTACAATGCTAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCTG
65 TGTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCG
*
52838577 CTGCAACTTCAGGA
130 CTGCAACTTCAGGG
* * *
52838591 AGATAAAGCTGGTGGC-TCAATCTGCTCCACTGCAACTTCAGAAAGATAAGAGTCGCCATAATTT
1 AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTT
* * * ** * * * *
52838655 TTAGTTTTAATATACTCTACTATAACGCCAGGGAAATAGGATTCGCTGTCTTCAGTCTGCTCCAC
66 GTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGC
*
52838720 TGCAACTTCAGGA
131 TGCAACTTCAGGG
* * * *
52838733 AGATAAGGCTGGTGGCTTCAATCTACTCCATTGCAACTTCAGGAAGATATGATTCACCATAAT
1 AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAAT
52838796 GACTTCAATC
Statistics
Matches: 1532, Mismatches: 231, Indels: 30
0.85 0.13 0.02
Matches are distributed among these distances:
142 146 0.10
143 1362 0.89
144 24 0.02
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (143 bp):
AGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTT
GTAGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGC
TGCAACTTCAGGG
Found at i:52839717 original size:11 final size:11
Alignment explanation
Indices: 52839701--52839729 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
52839691 AGTCCAAAAA
52839701 TATTTTAATAT
1 TATTTTAATAT
52839712 TATTTTAATAT
1 TATTTTAATAT
52839723 TATTTTA
1 TATTTTA
52839730 TGTGTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTTTAATAT
Found at i:52840218 original size:28 final size:28
Alignment explanation
Indices: 52840186--52840242 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
52840176 AAAGCTCATG
52840186 TCTTAATTTTTTATTTTGATGAAGATTT
1 TCTTAATTTTTTATTTTGATGAAGATTT
52840214 TCTTAATTTTTTATTTTGATGAAGATTT
1 TCTTAATTTTTTATTTTGATGAAGATTT
52840242 T
1 T
52840243 GAAATTTGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.04, G:0.11, T:0.61
Consensus pattern (28 bp):
TCTTAATTTTTTATTTTGATGAAGATTT
Found at i:52840248 original size:27 final size:28
Alignment explanation
Indices: 52840190--52840249 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
52840180 CTCATGTCTT
**
52840190 AATTTTTTATTTTGATGAAGATTTTCTT
1 AATTTTTTATTTTGATGAAGATTTTCGA
52840218 AATTTTTTATTTTGATGAAGATTTT-GA
1 AATTTTTTATTTTGATGAAGATTTTCGA
52840245 AATTT
1 AATTT
52840250 GCCATTGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 5 0.17
28 25 0.83
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (28 bp):
AATTTTTTATTTTGATGAAGATTTTCGA
Found at i:52840894 original size:43 final size:42
Alignment explanation
Indices: 52840842--52840971 Score: 145
Period size: 43 Copynumber: 3.0 Consensus size: 42
52840832 TAGGATCTCC
* *
52840842 GATATGTGTTTTCGTGTAACAGCACGTCTGGGACATTGGCATT
1 GATATGTGTTTACGTGTAAGA-CACGTCTGGGACATTGGCATT
* * *
52840885 GACT-TGTGTTTACGTGTAAGACCCTGTCTGGGACAGTGGCATG
1 GA-TATGTGTTTACGTGTAAGACAC-GTCTGGGACATTGGCATT
* * *
52840928 GATATGTGGTTACATGTAAGACCACGTCTGGGACGTTGGCATT
1 GATATGTGTTTACGTGTAAGA-CACGTCTGGGACATTGGCATT
52840971 G
1 G
52840972 TACGAGCTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
42 3 0.04
43 66 0.92
44 3 0.04
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.32
Consensus pattern (42 bp):
GATATGTGTTTACGTGTAAGACACGTCTGGGACATTGGCATT
Found at i:52848027 original size:3 final size:3
Alignment explanation
Indices: 52847983--52848008 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52847973 AAAATCAAGG
52847983 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
52848009 ACAAGTAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:52849236 original size:20 final size:19
Alignment explanation
Indices: 52849191--52849242 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
52849181 TTTTTTTTTA
52849191 ATTTTTGGGCTTGTAATGTT
1 ATTTTTGGGCTTGTAAT-TT
*
52849211 -TATTTTGGGTTTGTAATTT
1 AT-TTTTGGGCTTGTAATTT
52849230 AGTTTTTTGGGCT
1 A--TTTTTGGGCT
52849243 CGGGAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
19 3 0.12
20 14 0.54
21 8 0.31
22 1 0.04
ACGTcount: A:0.13, C:0.04, G:0.25, T:0.58
Consensus pattern (19 bp):
ATTTTTGGGCTTGTAATTT
Found at i:52853409 original size:26 final size:26
Alignment explanation
Indices: 52853380--52853431 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
52853370 TTTTGCCAAG
52853380 TCCATTTTTCGGGCTTATATTTTTAC
1 TCCATTTTTCGGGCTTATATTTTTAC
52853406 TCCATTTTTCGGGCTTATATTTTTAC
1 TCCATTTTTCGGGCTTATATTTTTAC
52853432 CCAAATCCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.19, G:0.12, T:0.54
Consensus pattern (26 bp):
TCCATTTTTCGGGCTTATATTTTTAC
Found at i:52861148 original size:202 final size:202
Alignment explanation
Indices: 52860796--52861200 Score: 711
Period size: 202 Copynumber: 2.0 Consensus size: 202
52860786 ACAAATCTGT
* *
52860796 AATAAGAGGAATATGGTACTTATTCTTCACAATGATCTTGTTTAAAGCCTGATAATCGATGCACA
1 AATAAGAGGAATAGGGTACCTATTCTTCACAATGATCTTGTTTAAAGCCTGATAATCGATGCACA
* * * *
52860861 TTCTCAAGGACCCATCATGTTTCTTTTGAAATAGCACTGGCGCACCGTATGGGGATTTAGATGGT
66 TTCTCAAAGACCCATCATGTTTCTTTTGAAACAACACTGGCGCACCGAATGGGGATTTAGATGGT
52860926 CTAATGAATCTCGCATCCAAAAGTTCCTTCAATTGTAAGCTATTGGTAAGCTCTTGAACTCCTCG
131 CTAATGAATCTCGCATCCAAAAGTTCCTTCAATTGTAAGCTATTGGTAAGCTCTTGAACTCCTCG
52860991 GCGCTGC
196 GCGCTGC
*
52860998 AATAAGAGGAATAGGGTACCTATTCTTCACAGTGATCTTGTTTAAAGCCTGATAATCGATGCACA
1 AATAAGAGGAATAGGGTACCTATTCTTCACAATGATCTTGTTTAAAGCCTGATAATCGATGCACA
* *
52861063 TTTTCAAAGACCCATCATGTTTCTTTTGAAACAACACTGGCGCGCCGAATGGGGATTTAGATGGT
66 TTCTCAAAGACCCATCATGTTTCTTTTGAAACAACACTGGCGCACCGAATGGGGATTTAGATGGT
*
52861128 CTAATGAATCTCGTATCCAAAAGTTCCTTCAATTGTAAGCTATTGGTAAGCTCTTGAACTCCTCG
131 CTAATGAATCTCGCATCCAAAAGTTCCTTCAATTGTAAGCTATTGGTAAGCTCTTGAACTCCTCG
*
52861193 GCGTTGC
196 GCGCTGC
52861200 A
1 A
52861201 GCTCTTGCTT
Statistics
Matches: 192, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
202 192 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (202 bp):
AATAAGAGGAATAGGGTACCTATTCTTCACAATGATCTTGTTTAAAGCCTGATAATCGATGCACA
TTCTCAAAGACCCATCATGTTTCTTTTGAAACAACACTGGCGCACCGAATGGGGATTTAGATGGT
CTAATGAATCTCGCATCCAAAAGTTCCTTCAATTGTAAGCTATTGGTAAGCTCTTGAACTCCTCG
GCGCTGC
Found at i:52862394 original size:17 final size:18
Alignment explanation
Indices: 52862345--52862396 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
52862335 TACATAATCG
*
52862345 TATCTTCTAAAGATTACAT
1 TATC-TCTAAAGATCACAT
*
52862364 TAATATCT-AAGATCACA-
1 T-ATCTCTAAAGATCACAT
52862381 TATCTCTAAAGATCAC
1 TATCTCTAAAGATCAC
52862397 CTTCCATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 5 0.18
17 9 0.32
18 8 0.29
19 4 0.14
20 2 0.07
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (18 bp):
TATCTCTAAAGATCACAT
Found at i:52862418 original size:35 final size:36
Alignment explanation
Indices: 52862379--52862450 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
52862369 TCTAAGATCA
* * *
52862379 CATATCTCTA-AAGATCACCTTCCATATTTGTCAAG
1 CATATATCTAGAAAATCACCTTCCATATTTGCCAAG
* * *
52862414 CATATATTTAGAAAATCACTTTCCTTATTTGCCAAG
1 CATATATCTAGAAAATCACCTTCCATATTTGCCAAG
52862450 C
1 C
52862451 TCCAAAGATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
35 8 0.27
36 22 0.73
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (36 bp):
CATATATCTAGAAAATCACCTTCCATATTTGCCAAG
Found at i:52872804 original size:730 final size:728
Alignment explanation
Indices: 52871406--52872850 Score: 2401
Period size: 730 Copynumber: 2.0 Consensus size: 728
52871396 ACGGAACTCA
52871406 AAACGCTACGAATGAATTCAAAGGAGTCAGTCACAAATTATTTTTCAAAAATGATGGCAATCGTC
1 AAACGCTACGAATGAATTCAAAGGAGTCAGTCACAAATTATTTTTCAAAAATGATGGCAATCGTC
** ** *
52871471 AATAAGATGCGGATTTATGGTGACAAGATGGAGAACACCGCCATTGTCGAAAAAATTCTTCGATC
66 AATAAGATGCGGATCCATGGTGACAAGACAGAGAACACCGCCATTGTCGAAAAAATTCTTCAATC
* *
52871536 CTTGACGCCAAAATTCAATTATGTTGTCTGCGCCATGAAGAAGCTAATGACATTGAAGAACTCTC
131 CTTGACGCCAAAATTCAATTATGTTGTCTACGCCATGAAGAAGCTAATGACATTAAAGAACTCTC
*
52871601 AATTGATGAGCTGCAAGGTTCGTTATTGGTTCATGAGCAGAAACTCCAACGTCAAGACCAAGAGG
196 AATTGATGAGCTGCAAGGTTCGTTATTGGTTCATGAGCAGAAACTCCAACGTCAAAACCAAGAGG
*
52871666 AACAAGCATTGAAGGTAGCAATCAATCCAAAAAACCATGAACGTGGTAGAGGGAAAGGACAAGGA
261 AACAAGCATTGAAGGTAGCAACCAATCCAAAAAACCATGAACGTGGTAGAGGGAAAGGACAAGGA
*
52871731 TTCCACCAACGCAGCAACTCCAACGATCAGAAAATAGAAGGCTCTTCTTCTGATTATACGAGAAG
326 TTCCACCAACGCAGCAACTCCAACGATCAGAAAATAGAAGGCTCTTCCTCTGATTATACGAGAAG
*
52871796 TAGAGGCCGAGGACGACGTTCAACAAGTTTCAGGCCAACCGACAAGTCTAAAGTTGAATGTTTTA
391 TAGAGGCCGAGGACGACGTTCAACAAGTTTCAGGCCAACCGACAAGTCTAAAATTGAATGTTTTA
* * * *
52871861 GATATCATAAGTATGGGAACTATAAACCTGAGTGTAGAACCAATCTCGAATGACATGTGGAGACA
456 GATATCACAAGTATGGGAACTACAAACCTGAGTGTAGAACCAATCTCGAACGACATGTAGAGACA
* *
52871926 ATAAATTTTGCTGTAGAAAAGGAAGAAGGAGAGATACTCCTAATGGCATGTCAAGAGAAAGAGAC
521 ACAAATTTTGCTGTAGAAAAGGAAAAAGGAGAGATACTCCTAATGGCATGTCAAGAGAAAGAGAC
52871991 ATCTTCACCAACTTTATGGTACCTTGACACTGGTTGTAGCAACCATATATGTGGCAACAAGAAGG
586 ATCTTCACCAACTTTATGGTACCTTGACACTGGTTGTAGCAACCATATATGTGGCAACAAGAAGG
** *
52872056 CATTTTCATCAATCGATGAATCTTACTGTACCCAAGTGAAGCTTGGAAATGCCTCTACCCTTACA
651 CATTTTCATCAATCGATGAATCCCACTGTACCCAAATGAAGCTTGGAAATGCCTCTACCCTTACA
52872121 GTACCAAAATTCG
716 GTACCAAAATTCG
** *
52872134 AAACGCTACGAATGAATTCAGGGGAGTCAGTCACAAATTATTTTTCAAGAATGATGGCAATCGTC
1 AAACGCTACGAATGAATTCAAAGGAGTCAGTCACAAATTATTTTTCAAAAATGATGGCAATCGTC
* * *
52872199 AATAAGATGCGGATCCATGGTGACAAGACAGAGGATACCGCCATTGTTGAAAAAAATTCTTCAAT
66 AATAAGATGCGGATCCATGGTGACAAGACAGAGAACACCGCCATTGTCG-AAAAAATTCTTCAAT
* * *
52872264 CCTTGATGCCAAAATTTAATTATGTTGTCTACGCTATAGAAGAAGCTAATGACATTAAAGAACTC
130 CCTTGACGCCAAAATTCAATTATGTTGTCTACGCCAT-GAAGAAGCTAATGACATTAAAGAACTC
* *
52872329 TCAATTGATGAGCTGCAAGGTTCGTTATTGGTTTATGAGCAGAAACTCCAATGTCAAAACCAAGA
194 TCAATTGATGAGCTGCAAGGTTCGTTATTGGTTCATGAGCAGAAACTCCAACGTCAAAACCAAGA
*
52872394 GGAACAAGCATTGATA-GTAGCAACCAATCCAAAAAACCATGAACGTGGTAGAGGGAAAGGACGA
259 GGAACAAGCATTGA-AGGTAGCAACCAATCCAAAAAACCATGAACGTGGTAGAGGGAAAGGACAA
52872458 GGATTCCACCAACGCAGCAACTCCAACGATCAGAAAATAGAAGGCTCTTCCTCTGATTATGA-GA
323 GGATTCCACCAACGCAGCAACTCCAACGATCAGAAAATAGAAGGCTCTTCCTCTGATTAT-ACGA
* *
52872522 GAAGTAGAGGCCGAGGACGACGTTCAACAGGTTTCAGGCCAACCGACAAGTCTAAAATTGACTGT
387 GAAGTAGAGGCCGAGGACGACGTTCAACAAGTTTCAGGCCAACCGACAAGTCTAAAATTGAATGT
* * * * *
52872587 TTTAGATGTCACAAGTATGGGCACTACAAATCTGAGTGTAGAATCAATCTCGGACGACATGTAGA
452 TTTAGATATCACAAGTATGGGAACTACAAACCTGAGTGTAGAACCAATCTCGAACGACATGTAGA
* *
52872652 GATAACGAATTTTGCTGTAGAAAAGGAAAAAGGAGAGATACTCCTAATGGCATGTCAAGAGAAAG
517 GACAACAAATTTTGCTGTAGAAAAGGAAAAAGGAGAGATACTCCTAATGGCATGTCAAGAGAAAG
* * * *
52872717 TGGCATCTTCGCCAACTTTATGGTACCTTGACACTGGTTGTAGCAACCATATGTGTGGCAACAAT
582 AGACATCTTCACCAACTTTATGGTACCTTGACACTGGTTGTAGCAACCATATATGTGGCAACAA-
* *
52872782 GAA-GCATTTTCTTCAATCGATGAATCCCACTGTACCCAAATGAAGCTTGGAGATGCCTCTACCC
646 GAAGGCATTTTCATCAATCGATGAATCCCACTGTACCCAAATGAAGCTTGGAAATGCCTCTACCC
52872846 TTACA
711 TTACA
52872851 ATCATGGGAA
Statistics
Matches: 665, Mismatches: 47, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
728 104 0.16
729 47 0.07
730 509 0.77
731 5 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24
Consensus pattern (728 bp):
AAACGCTACGAATGAATTCAAAGGAGTCAGTCACAAATTATTTTTCAAAAATGATGGCAATCGTC
AATAAGATGCGGATCCATGGTGACAAGACAGAGAACACCGCCATTGTCGAAAAAATTCTTCAATC
CTTGACGCCAAAATTCAATTATGTTGTCTACGCCATGAAGAAGCTAATGACATTAAAGAACTCTC
AATTGATGAGCTGCAAGGTTCGTTATTGGTTCATGAGCAGAAACTCCAACGTCAAAACCAAGAGG
AACAAGCATTGAAGGTAGCAACCAATCCAAAAAACCATGAACGTGGTAGAGGGAAAGGACAAGGA
TTCCACCAACGCAGCAACTCCAACGATCAGAAAATAGAAGGCTCTTCCTCTGATTATACGAGAAG
TAGAGGCCGAGGACGACGTTCAACAAGTTTCAGGCCAACCGACAAGTCTAAAATTGAATGTTTTA
GATATCACAAGTATGGGAACTACAAACCTGAGTGTAGAACCAATCTCGAACGACATGTAGAGACA
ACAAATTTTGCTGTAGAAAAGGAAAAAGGAGAGATACTCCTAATGGCATGTCAAGAGAAAGAGAC
ATCTTCACCAACTTTATGGTACCTTGACACTGGTTGTAGCAACCATATATGTGGCAACAAGAAGG
CATTTTCATCAATCGATGAATCCCACTGTACCCAAATGAAGCTTGGAAATGCCTCTACCCTTACA
GTACCAAAATTCG
Found at i:52876111 original size:72 final size:72
Alignment explanation
Indices: 52875994--52876177 Score: 350
Period size: 72 Copynumber: 2.6 Consensus size: 72
52875984 ACAACTTGAC
*
52875994 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
52876059 ACTAACA
66 ACTAACA
*
52876066 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAT
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
52876131 ACTAACA
66 ACTAACA
52876138 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
52876178 AATAATAATA
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 110 1.00
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (72 bp):
AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
ACTAACA
Found at i:52880535 original size:72 final size:72
Alignment explanation
Indices: 52880418--52880601 Score: 359
Period size: 72 Copynumber: 2.6 Consensus size: 72
52880408 ACAACTTGAC
*
52880418 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
52880483 ACTAACA
66 ACTAACA
52880490 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
52880555 ACTAACA
66 ACTAACA
52880562 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
52880602 AATAATAATA
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 111 1.00
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.28
Consensus pattern (72 bp):
AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
ACTAACA
Found at i:52880610 original size:3 final size:3
Alignment explanation
Indices: 52880602--52880630 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
52880592 ATTACATCCA
52880602 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
52880631 AACATGTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:52890306 original size:60 final size:61
Alignment explanation
Indices: 52890231--52890368 Score: 156
Period size: 59 Copynumber: 2.3 Consensus size: 61
52890221 ACTATAAACT
* * * * **
52890231 AATTTATTGAGTTTTTTAGAATT-AGAACTAAATTCATAAATTTTGTAAATTTTG-AGGCTA
1 AATTTATTGAATTTTTTAAAATTCA-AACTAAAATCACAAATTTTGTAAACATTGAAGGCTA
* *
52890291 AATTTATTGAA-TTTTTAAAATTCAAACTAAAATGACAAATTTTGTAAACATTGAATGCTA
1 AATTTATTGAATTTTTTAAAATTCAAACTAAAATCACAAATTTTGTAAACATTGAAGGCTA
* *
52890351 AATTTGTTGAATATTTTA
1 AATTTATTGAATTTTTTA
52890369 TATTTAGGAT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
59 34 0.52
60 26 0.40
61 5 0.08
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (61 bp):
AATTTATTGAATTTTTTAAAATTCAAACTAAAATCACAAATTTTGTAAACATTGAAGGCTA
Found at i:52903649 original size:16 final size:16
Alignment explanation
Indices: 52903628--52903662 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
52903618 GGTTGGGGTG
*
52903628 AATGGAATAGGGCTAT
1 AATGGAATAGAGCTAT
52903644 AATGGAATAGAGCTAT
1 AATGGAATAGAGCTAT
52903660 AAT
1 AAT
52903663 AATAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
AATGGAATAGAGCTAT
Found at i:52903968 original size:22 final size:22
Alignment explanation
Indices: 52903902--52903971 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
52903892 ATTATTATTA
*
52903902 AATATAATTTAAT-AAAATAAT
1 AATATAATTTAATAAAAATCAT
* *
52903923 -ATATAATTTAA-AAACATTCTT
1 AATATAATTTAATAAA-AATCAT
*
52903944 AATACAATTTAATAAAAATCAT
1 AATATAATTTAATAAAAATCAT
52903966 AATATA
1 AATATA
52903972 TATCATATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
20 13 0.34
21 3 0.08
22 19 0.50
23 3 0.08
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATAATTTAATAAAAATCAT
Found at i:52904582 original size:22 final size:21
Alignment explanation
Indices: 52904550--52904590 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
52904540 ACCCAATAAG
*
52904550 TCTTTTTTTTTTCTTTTTTCT
1 TCTTTTTTTTTTCCTTTTTCT
52904571 TCTTGTTTTTTTTCCTTTTT
1 TCTT-TTTTTTTTCCTTTTT
52904591 ACCAGCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (21 bp):
TCTTTTTTTTTTCCTTTTTCT
Found at i:52907804 original size:15 final size:16
Alignment explanation
Indices: 52907786--52907879 Score: 54
Period size: 14 Copynumber: 5.9 Consensus size: 16
52907776 TCATTTATCG
*
52907786 TATTTTTTGTAATTT-
1 TATTTTTTATAATTTA
52907801 TA-TTTTTATAATTTA
1 TATTTTTTATAATTTA
*
52907816 TATTTTTTCCTAGATTATA
1 TATTTTTT-ATA-ATT-TA
* * *
52907835 TATATTTTCTGAATTTT
1 TATTTTTTAT-AATTTA
* *
52907852 TATATATT-T-ATTT-
1 TATTTTTTATAATTTA
52907865 TATTTTTTATAATTT
1 TATTTTTTATAATTT
52907880 TTAATGTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
13 6 0.09
14 16 0.25
15 8 0.12
16 6 0.09
17 10 0.16
18 8 0.12
19 10 0.16
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (16 bp):
TATTTTTTATAATTTA
Found at i:52907862 original size:29 final size:29
Alignment explanation
Indices: 52907830--52907898 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
52907820 TTTTCCTAGA
52907830 TTATATATATTTTCT-GAATTTTTATATAT
1 TTATATATATTTTCTAGAATTTTTA-ATAT
* * * *
52907859 TTAT-TTTATTTTTTATAATTTTTAATGT
1 TTATATATATTTTCTAGAATTTTTAATAT
*
52907887 TTATATACATTT
1 TTATATATATTT
52907899 GATTAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (29 bp):
TTATATATATTTTCTAGAATTTTTAATAT
Found at i:52908069 original size:35 final size:35
Alignment explanation
Indices: 52908030--52908112 Score: 139
Period size: 35 Copynumber: 2.4 Consensus size: 35
52908020 TAGGTACCAA
*
52908030 ATTAGGAATGAAGTGTACTTTAGATATTAAATTTG
1 ATTAGAAATGAAGTGTACTTTAGATATTAAATTTG
52908065 ATTAGAAATGAAGTGTACTTTAGATATTAAATTTG
1 ATTAGAAATGAAGTGTACTTTAGATATTAAATTTG
* *
52908100 ATTAAAAAAGAAG
1 ATTAGAAATGAAG
52908113 AATTTTTAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.36
Consensus pattern (35 bp):
ATTAGAAATGAAGTGTACTTTAGATATTAAATTTG
Found at i:52924409 original size:25 final size:25
Alignment explanation
Indices: 52924363--52924410 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
52924353 TATCCTATTT
* *
52924363 ATTTTAAATAAAAATTATATATTAA
1 ATTTAAAATAAAAATTAAATATTAA
**
52924388 ATTTAAAATAAATTTTAAATATT
1 ATTTAAAATAAAAATTAAATATT
52924411 TAATGTGTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTTAAAATAAAAATTAAATATTAA
Found at i:52932163 original size:19 final size:19
Alignment explanation
Indices: 52932139--52932177 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
52932129 TCCTTTTCTT
52932139 AAAAAAATCATAAAAGTTA
1 AAAAAAATCATAAAAGTTA
* * *
52932158 AAAAAATTTATAAATGTTA
1 AAAAAAATCATAAAAGTTA
52932177 A
1 A
52932178 GATTCGAGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAAAAATCATAAAAGTTA
Found at i:52937754 original size:31 final size:29
Alignment explanation
Indices: 52937719--52937776 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
52937709 ATAGTAATTT
*
52937719 ATTAATTTAATATTAAAGTGATTATCTTAGC
1 ATTAAATTAA-ATTAAA-TGATTATCTTAGC
* *
52937750 ATTAAATTAAATTTAATGTTTATCTTA
1 ATTAAATTAAATTAAATGATTATCTTA
52937777 TAGATAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.42
30 5 0.21
31 9 0.38
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (29 bp):
ATTAAATTAAATTAAATGATTATCTTAGC
Found at i:52940453 original size:35 final size:35
Alignment explanation
Indices: 52940403--52940648 Score: 262
Period size: 35 Copynumber: 7.0 Consensus size: 35
52940393 CATTCCACAC
*
52940403 ACCTCATTCAATTAACATCTCGCCACAACACCAAT
1 ACCTCATTCATTTAACATCTCGCCACAACACCAAT
**
52940438 ACCTCATTCATTTAACAT-TCCGCCACAAGGCCAAT
1 ACCTCATTCATTTAACATCT-CGCCACAACACCAAT
* * * * **
52940473 ACATCGTACATTTAACATCTCGACACAATGCCAAT
1 ACCTCATTCATTTAACATCTCGCCACAACACCAAT
* *
52940508 ACCTCATTAATTTAACATCCCGCCACAACACCAAT
1 ACCTCATTCATTTAACATCTCGCCACAACACCAAT
* * * ** *
52940543 ACCTTATTCATTTAACATCCCACCACAATTCCAAC
1 ACCTCATTCATTTAACATCTCGCCACAACACCAAT
* **
52940578 ACTTCATTCATTTAACAT-TCTGTTACAACACCAAT
1 ACCTCATTCATTTAACATCTC-GCCACAACACCAAT
* *
52940613 ACCTCGTTCATTTAACATCTTGCCACAACACCAAT
1 ACCTCATTCATTTAACATCTCGCCACAACACCAAT
52940648 A
1 A
52940649 TTTCATAACA
Statistics
Matches: 171, Mismatches: 36, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
34 2 0.01
35 167 0.98
36 2 0.01
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.27
Consensus pattern (35 bp):
ACCTCATTCATTTAACATCTCGCCACAACACCAAT
Found at i:52940590 original size:105 final size:105
Alignment explanation
Indices: 52940403--52940648 Score: 307
Period size: 105 Copynumber: 2.3 Consensus size: 105
52940393 CATTCCACAC
* *
52940403 ACCTCATTCAA-TTAACATCTCGCCACAACACCAATACCTCATTCATTTAACATTCCGCCACAAG
1 ACCTCATT-AATTTAACATCTCGCCACAACACCAATACCTCATTCATTTAACATCCCACCACAAG
* * **
52940467 GCCAATACATCGTACATTTAACA-TCTCGACACAATGCCAAT
65 GCCAACACATCATACATTTAACATTCT-GACACAACACCAAT
* * **
52940508 ACCTCATTAATTTAACATCCCGCCACAACACCAATACCTTATTCATTTAACATCCCACCACAATT
1 ACCTCATTAATTTAACATCTCGCCACAACACCAATACCTCATTCATTTAACATCCCACCACAAGG
* * **
52940573 CCAACACTTCATTCATTTAACATTCTGTTACAACACCAAT
66 CCAACACATCATACATTTAACATTCTGACACAACACCAAT
* * *
52940613 ACCTCGTTCATTTAACATCTTGCCACAACACCAATA
1 ACCTCATTAATTTAACATCTCGCCACAACACCAATA
52940649 TTTCATAACA
Statistics
Matches: 121, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
104 2 0.02
105 116 0.96
106 3 0.02
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.27
Consensus pattern (105 bp):
ACCTCATTAATTTAACATCTCGCCACAACACCAATACCTCATTCATTTAACATCCCACCACAAGG
CCAACACATCATACATTTAACATTCTGACACAACACCAAT
Found at i:52955541 original size:16 final size:16
Alignment explanation
Indices: 52955512--52955565 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
52955502 TTTGGTTCGC
*
52955512 TGTATTGGAATAGAGG
1 TGTAATGGAATAGAGG
* *
52955528 CGTAATGTAATAGAGG
1 TGTAATGGAATAGAGG
52955544 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
52955560 TGTAAT
1 TGTAAT
52955566 AGCAAATCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.35, C:0.02, G:0.33, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:52955915 original size:120 final size:120
Alignment explanation
Indices: 52955782--52956074 Score: 480
Period size: 120 Copynumber: 2.4 Consensus size: 120
52955772 ATCATATTTA
*
52955782 AACATAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATCAA
*
52955847 TATTCTTATATGAATTTATTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* *
52955902 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
52955967 TATTCTTATATGAATTTACTGAAATCATAATATATGATACTATAAAATATAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* * * *
52956022 AAAATAATTAATATTAAATATATT-TTATTTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTT-AAATATATAATTTAATAAAATT
52956075 TAAAATAATT
Statistics
Matches: 161, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
119 4 0.02
120 157 0.98
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:52955947 original size:14 final size:15
Alignment explanation
Indices: 52955898--52955949 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
52955888 ATAAAATATA
52955898 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
52955913 TATTAAATATATTAT
1 AATTAAATATATTAT
52955928 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
52955941 AATTTAATA
1 AATTAAATA
52955950 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:52956144 original size:26 final size:28
Alignment explanation
Indices: 52956115--52956175 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
52956105 TATGAATTTG
*
52956115 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
52956141 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
52956169 TAAAATT
1 TATAATT
52956176 ATTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:52956176 original size:91 final size:89
Alignment explanation
Indices: 52956081--52956297 Score: 281
Period size: 91 Copynumber: 2.4 Consensus size: 89
52956071 AATTTAAAAT
* * * *
52956081 AATTATAACTAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAA
1 AATTATAA-TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
52956146 TTTAATAATAATATATAATTTCATAA
64 TTTAATAATAATATATAATTTCATAA
* *
52956172 AATTATTGATAATAAATTTTTTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
1 AATTA-TAATAATAAA-TTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
**
52956237 TTTAATAATGTTATATAATTTCATAA
64 TTTAATAATAATATATAATTTCATAA
* *
52956263 ATTTCTTAATAATAAAATGTTCTTATATGAATTTA
1 AATT-ATAATAAT-AAAT-TTCTTATATGAATTTA
52956298 CTAAAATCAA
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
91 87 0.80
92 22 0.20
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (89 bp):
AATTATAATAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATT
TAATAATAATATATAATTTCATAA
Found at i:52956178 original size:44 final size:43
Alignment explanation
Indices: 52956115--52956257 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
52956105 TATGAATTTG
52956115 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTATTATTA-ATATAATTTAATAATAATA
* **
52956159 TATAATTTCATAA-AATTATTGA-TAATA-AATTTTTTTATATGAATTTA
1 TATAATTT-AAAATAATTATT-ATTAATATAA-TTTAATA-AT-AA--TA
* * **
52956206 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGTTA
1 TATAATTTAAAATAATTATTATT-AATATAATTTAATAATAATA
52956250 TATAATTT
1 TATAATTT
52956258 CATAAATTTC
Statistics
Matches: 77, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
42 2 0.03
43 8 0.10
44 28 0.36
45 6 0.08
46 4 0.05
47 18 0.23
48 9 0.12
49 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (43 bp):
TATAATTTAAAATAATTATTATTAATATAATTTAATAATAATA
Found at i:52959312 original size:12 final size:12
Alignment explanation
Indices: 52959263--52959318 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
52959253 ATCACCCAAA
52959263 AAAGTATATATT
1 AAAGTATATATT
52959275 AAA-TGATAT-TT
1 AAAGT-ATATATT
* *
52959286 AAA-TACATTTT
1 AAAGTATATATT
52959297 AAAGTATATATT
1 AAAGTATATATT
52959309 AAAGGTATAT
1 AAA-GTATAT
52959319 GTAGTTTTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 3 0.08
11 12 0.32
12 16 0.43
13 6 0.16
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (12 bp):
AAAGTATATATT
Found at i:52960278 original size:8 final size:8
Alignment explanation
Indices: 52960265--52960303 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
52960255 GTAATGAGCA
52960265 ATACAAAC
1 ATACAAAC
52960273 ATACAAAC
1 ATACAAAC
*
52960281 A-A-AACC
1 ATACAAAC
52960287 ATACAAAC
1 ATACAAAC
52960295 ATACAAAC
1 ATACAAAC
52960303 A
1 A
52960304 AGCAATCGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 4 0.15
7 2 0.07
8 21 0.78
ACGTcount: A:0.64, C:0.26, G:0.00, T:0.10
Consensus pattern (8 bp):
ATACAAAC
Found at i:52962393 original size:23 final size:25
Alignment explanation
Indices: 52962346--52962410 Score: 80
Period size: 23 Copynumber: 2.6 Consensus size: 25
52962336 AAAAATAAAA
52962346 ATTTACCAAAATATTATAACTTTTTTT
1 ATTTACCAAAATA-TATAAC-TTTTTT
52962373 ATTTACCAAAATAT-TAA-TTTTTT
1 ATTTACCAAAATATATAACTTTTTT
**
52962396 ATTTATGAAAATATA
1 ATTTACCAAAATATA
52962411 ACAAAAAACC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 18 0.51
25 3 0.09
26 1 0.03
27 13 0.37
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.49
Consensus pattern (25 bp):
ATTTACCAAAATATATAACTTTTTT
Found at i:52962603 original size:11 final size:11
Alignment explanation
Indices: 52962587--52962626 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
52962577 GGTGCTGCAG
52962587 AAAAGAAGAGA
1 AAAAGAAGAGA
52962598 AAAAG-AGAGA
1 AAAAGAAGAGA
*
52962608 AAAAGAAAAGA
1 AAAAGAAGAGA
52962619 AAAAGAAG
1 AAAAGAAG
52962627 GTATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:52962758 original size:3 final size:3
Alignment explanation
Indices: 52962752--52962786 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
52962742 AGTATTATTA
*
52962752 TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
52962787 AGTATTAAGA
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:0.03, C:0.00, G:0.29, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:52962787 original size:12 final size:12
Alignment explanation
Indices: 52962749--52962787 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
52962739 GTTAGTATTA
52962749 TTATTGTTGTTG
1 TTATTGTTGTTG
*
52962761 TTGTTGTTGTTG
1 TTATTGTTGTTG
52962773 TTATTGTTGTTG
1 TTATTGTTGTTG
52962785 TTA
1 TTA
52962788 GTATTAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.08, C:0.00, G:0.26, T:0.67
Consensus pattern (12 bp):
TTATTGTTGTTG
Found at i:52963656 original size:18 final size:18
Alignment explanation
Indices: 52963633--52963670 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
52963623 GGTTGGTGGT
52963633 GAAGAAGAAGGTGCTGGC
1 GAAGAAGAAGGTGCTGGC
* *
52963651 GAAGAAGAATGTGGTGGC
1 GAAGAAGAAGGTGCTGGC
52963669 GA
1 GA
52963671 TCATTGGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.08, G:0.45, T:0.13
Consensus pattern (18 bp):
GAAGAAGAAGGTGCTGGC
Found at i:52965940 original size:11 final size:11
Alignment explanation
Indices: 52965924--52965950 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
52965914 GCTTATGCTT
52965924 AAATTGTATCC
1 AAATTGTATCC
52965935 AAATTGTATCC
1 AAATTGTATCC
52965946 AAATT
1 AAATT
52965951 AAGTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (11 bp):
AAATTGTATCC
Found at i:52969057 original size:24 final size:25
Alignment explanation
Indices: 52969028--52969114 Score: 74
Period size: 26 Copynumber: 3.4 Consensus size: 25
52969018 ATGTACATAT
52969028 CATAACAT-AAATACGTATAATGTA
1 CATAACATAAAATACGTATAATGTA
52969052 CATAACATCAAAATA--TAT-ATGCTA
1 CATAACAT-AAAATACGTATAATG-TA
* * *
52969076 AATAAAATATTAAAATACGTATAATTTA
1 CAT--AACA-TAAAATACGTATAATGTA
52969104 CATAACATAAA
1 CATAACATAAA
52969115 TTTTTAACAT
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
23 3 0.06
24 15 0.31
25 4 0.08
26 17 0.35
27 1 0.02
28 7 0.14
29 2 0.04
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (25 bp):
CATAACATAAAATACGTATAATGTA
Found at i:52969154 original size:9 final size:9
Alignment explanation
Indices: 52969142--52969166 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52969132 TTACAAAAAA
52969142 TTTCCTTTT
1 TTTCCTTTT
52969151 TTTCCTTTT
1 TTTCCTTTT
52969160 TTTCCTT
1 TTTCCTT
52969167 CCTTCCCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTCCTTTT
Found at i:52969196 original size:18 final size:18
Alignment explanation
Indices: 52969153--52969233 Score: 53
Period size: 19 Copynumber: 4.3 Consensus size: 18
52969143 TTCCTTTTTT
52969153 TCCTTTTTTTCCTTCCTTC
1 TCCTTTTTTT-CTTCCTTC
*
52969172 -CCTCTTTTTTTTTCTCTTC
1 TCCT-TTTTTTCTTC-CTTC
52969191 TCCTTTCCTTTTCTTTCCTTC
1 TCCTTT--TTTTC-TTCCTTC
52969212 T--TTTTCTTTCTTTCC-TC
1 TCCTTTT-TTTC-TTCCTTC
52969229 TCCTT
1 TCCTT
52969234 CCTTTCTTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
17 4 0.08
18 15 0.29
19 17 0.33
20 3 0.06
21 9 0.18
22 3 0.06
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (18 bp):
TCCTTTTTTTCTTCCTTC
Found at i:52969221 original size:4 final size:4
Alignment explanation
Indices: 52969200--52969263 Score: 69
Period size: 4 Copynumber: 16.0 Consensus size: 4
52969190 CTCCTTTCCT
* * *
52969200 TTTC TTTC CTTC -TT- TTTC TTTC TTTCC TCTCC TTCC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC
52969248 TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC
52969264 CCTCTCCTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
3 4 0.08
4 44 0.83
5 4 0.08
6 1 0.02
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:52969222 original size:36 final size:35
Alignment explanation
Indices: 52969169--52969272 Score: 104
Period size: 36 Copynumber: 2.9 Consensus size: 35
52969159 TTTTCCTTCC
* *
52969169 TTCCCTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCT
1 TTCCTTCTTTTTCTTTCT-TTCTCCTTTCCTTTTCT
*
52969205 TTCCTTCTTTTTCTTTCTTTCCTCTCCTTCC-TTTCT
1 TTCCTTCTTTTTCTTTCTTT-CTC-CTTTCCTTTTCT
* *
52969241 TTCTTTCTTTCTTTCTTTCTTTC-CCTCTCCTT
1 TTCCTTC-TT-TTTCTTTCTTTCTCCTTTCCTT
52969273 CTTCCCCCCA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
35 6 0.11
36 32 0.56
37 8 0.14
38 11 0.19
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (35 bp):
TTCCTTCTTTTTCTTTCTTTCTCCTTTCCTTTTCT
Found at i:52969238 original size:18 final size:18
Alignment explanation
Indices: 52969189--52969273 Score: 64
Period size: 18 Copynumber: 4.4 Consensus size: 18
52969179 TTTTTTCTCT
52969189 TCTCCTTTCCTTTTCTTTCC
1 TCTCC-TTCC-TTTCTTTCC
* *
52969209 T-TCTTTTTCTTTCTTTCC
1 TCTC-CTTCCTTTCTTTCC
*
52969227 TCTCCTTCCTTTCTTTCTT
1 TCTCCTTCCTTTCTTTC-C
* *
52969246 TCTTTCTTTCTTTCTTTCCC
1 TC-TCCTTCCTTTCTTT-CC
52969266 TCTCCTTC
1 TCTCCTTC
52969274 TTCCCCCCAG
Statistics
Matches: 50, Mismatches: 10, Indels: 11
0.70 0.14 0.15
Matches are distributed among these distances:
18 21 0.42
19 13 0.26
20 15 0.30
21 1 0.02
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (18 bp):
TCTCCTTCCTTTCTTTCC
Found at i:52969413 original size:25 final size:26
Alignment explanation
Indices: 52969385--52969450 Score: 98
Period size: 25 Copynumber: 2.5 Consensus size: 26
52969375 TTTTTTTGGT
* *
52969385 ATATTTTGGTAATTTAAAAAAA-ATA
1 ATATTTTGGTAAATAAAAAAAAGATA
52969410 ATATTTTGGTAAATAAAAAAAAGGATA
1 ATATTTTGGTAAATAAAAAAAA-GATA
52969437 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
52969451 TTTTATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 20 0.54
27 17 0.46
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (26 bp):
ATATTTTGGTAAATAAAAAAAAGATA
Found at i:52974294 original size:44 final size:44
Alignment explanation
Indices: 52974231--52974324 Score: 170
Period size: 44 Copynumber: 2.1 Consensus size: 44
52974221 GTCTCGACTT
**
52974231 TCATTTTTGTATGCTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
52974275 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
52974319 TCATTT
1 TCATTT
52974325 ATTGAATATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (44 bp):
TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
Found at i:52974318 original size:22 final size:22
Alignment explanation
Indices: 52974249--52974319 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
52974239 GTATGCTTAT
52974249 CAAATATAAGTATTGTATTAAC
1 CAAATATAAGTATTGTATTAAC
** * *
52974271 CAAATCAT-TTTCATATG-CTT-AT
1 CAAAT-ATAAGT-AT-TGTATTAAC
52974293 CAAATATAAGTATTGTATTAAC
1 CAAATATAAGTATTGTATTAAC
52974315 CAAAT
1 CAAAT
52974320 CATTTATTGA
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
20 2 0.06
21 6 0.17
22 19 0.54
23 6 0.17
24 2 0.06
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (22 bp):
CAAATATAAGTATTGTATTAAC
Found at i:52974328 original size:21 final size:22
Alignment explanation
Indices: 52974303--52974346 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
52974293 CAAATATAAG
* *
52974303 TATTGTAT-TAACCAAATCATT
1 TATTGAATATAACCAAATAATT
52974324 TATTGAATATAACCAAATAATT
1 TATTGAATATAACCAAATAATT
52974346 T
1 T
52974347 TCATATGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (22 bp):
TATTGAATATAACCAAATAATT
Found at i:52975187 original size:7 final size:7
Alignment explanation
Indices: 52975175--52975201 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
52975165 TTGACAATTG
52975175 GTTGATA
1 GTTGATA
52975182 GTTGATA
1 GTTGATA
52975189 GTTGATA
1 GTTGATA
52975196 GTTGAT
1 GTTGAT
52975202 TGCTAATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (7 bp):
GTTGATA
Found at i:52975210 original size:7 final size:7
Alignment explanation
Indices: 52975200--52975225 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52975190 TTGATAGTTG
52975200 ATTGCTA
1 ATTGCTA
52975207 ATTGCTA
1 ATTGCTA
52975214 ATTGCTA
1 ATTGCTA
52975221 ATTGC
1 ATTGC
52975226 AGTGGCTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (7 bp):
ATTGCTA
Found at i:52977628 original size:20 final size:20
Alignment explanation
Indices: 52977572--52977628 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
52977562 ATGCAATTAG
52977572 TAATTTA-ATTATTTTATATA
1 TAATTTATATT-TTTTATATA
* ***
52977592 -AATTTTTATTAAATATATA
1 TAATTTATATTTTTTATATA
52977611 TAATTTATATTTTTTATA
1 TAATTTATATTTTTTATA
52977629 AGGTAAACCT
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TAATTTATATTTTTTATATA
Found at i:52980747 original size:48 final size:48
Alignment explanation
Indices: 52980676--52980771 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
52980666 ACTTTAAGGT
*
52980676 GCAATTTTTACACGGGAAGAAAAAGAAAAATGTTCATTGGTTTGCTTA
1 GCAATTTTTACACGGGAAGAAAAAGAAAAATGTTCATAGGTTTGCTTA
* *
52980724 GCAATTTTTATACGGGAAGAAAAAGAAAAGTGTTCATAGGTTTGCTTA
1 GCAATTTTTACACGGGAAGAAAAAGAAAAATGTTCATAGGTTTGCTTA
52980772 ATAAAATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (48 bp):
GCAATTTTTACACGGGAAGAAAAAGAAAAATGTTCATAGGTTTGCTTA
Found at i:52985064 original size:18 final size:19
Alignment explanation
Indices: 52985035--52985071 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
52985025 TGGGTAGGAA
*
52985035 ATTTTATAAAGTGTGCATC
1 ATTTTATAAAGTATGCATC
52985054 ATTTT-TAAAGTATGCATC
1 ATTTTATAAAGTATGCATC
52985072 GACATGTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (19 bp):
ATTTTATAAAGTATGCATC
Found at i:53007575 original size:39 final size:37
Alignment explanation
Indices: 53007508--53007600 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
53007498 ACCAGAATGG
* *
53007508 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG--ATAGTTGA
* *
53007547 CACCCAGTGTCTCATCGGCAAAG-CCGAAGATAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGATAGTTGA
* *
53007584 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
53007601 AATCTATTCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 21 0.46
39 22 0.48
40 3 0.07
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.22
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGATAGTTGA
Found at i:53007622 original size:38 final size:38
Alignment explanation
Indices: 53007570--53007654 Score: 152
Period size: 38 Copynumber: 2.2 Consensus size: 38
53007560 ATCGGCAAAG
*
53007570 CCGAAGATAGTTGGTACCCAGTACCTCATCGAATCTAT
1 CCGAAGAAAGTTGGTACCCAGTACCTCATCGAATCTAT
*
53007608 TCGAAGAAAGTTGGTACCCAGTACCTCATCGAATCTAT
1 CCGAAGAAAGTTGGTACCCAGTACCTCATCGAATCTAT
53007646 CCGAAGAAA
1 CCGAAGAAA
53007655 TATAGTGACA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (38 bp):
CCGAAGAAAGTTGGTACCCAGTACCTCATCGAATCTAT
Found at i:53008932 original size:8 final size:8
Alignment explanation
Indices: 53008919--53008959 Score: 73
Period size: 8 Copynumber: 5.0 Consensus size: 8
53008909 TGTTTTATAT
53008919 ATATAATA
1 ATATAATA
53008927 ATATAATA
1 ATATAATA
53008935 ATATAATA
1 ATATAATA
53008943 ATATAATTA
1 ATATAA-TA
53008952 ATATAATA
1 ATATAATA
53008960 CTTATTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 24 0.75
9 8 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:53011880 original size:26 final size:26
Alignment explanation
Indices: 53011844--53011895 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
53011834 GATGAGGTGA
53011844 TGATACCTGACTTTTGTTTATACACT
1 TGATACCTGACTTTTGTTTATACACT
53011870 TGATACCTGACTTTTGTTTATACACT
1 TGATACCTGACTTTTGTTTATACACT
53011896 GAGTATACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (26 bp):
TGATACCTGACTTTTGTTTATACACT
Found at i:53012250 original size:23 final size:26
Alignment explanation
Indices: 53012224--53012272 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
53012214 TTGTGACTTG
*
53012224 ATATT-AAATG-ATTTCGTA-TAATT
1 ATATTCAAATGTATCTCGTACTAATT
53012247 ATATTCAAATGTATCTCGTACTAATT
1 ATATTCAAATGTATCTCGTACTAATT
53012273 TGTGTATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 5 0.23
25 7 0.32
26 5 0.23
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (26 bp):
ATATTCAAATGTATCTCGTACTAATT
Found at i:53017776 original size:42 final size:42
Alignment explanation
Indices: 53017729--53017811 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
53017719 AGATCGTAAT
*
53017729 AACCTAATCTATTTATTTTGGGGATCAATTTGCACAGTTATC
1 AACCTAATCTATTTATTTTGGGGATCAATTTGCAAAGTTATC
53017771 AACCTAATCTATTTATTTTGGGGATCAATTTGCAAAGTTAT
1 AACCTAATCTATTTATTTTGGGGATCAATTTGCAAAGTTAT
53017812 ACAAATATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (42 bp):
AACCTAATCTATTTATTTTGGGGATCAATTTGCAAAGTTATC
Found at i:53018685 original size:26 final size:26
Alignment explanation
Indices: 53018638--53018715 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 26
53018628 ACATACTGCA
* *
53018638 GCTCTTTATGAG-TGTCCCGATATATG
1 GCTCTTAATGAGCT-TCCTGATATATG
53018664 GCTCTTAATGAGCTTCCTG--ATATG
1 GCTCTTAATGAGCTTCCTGATATATG
*** *
53018688 GCT-TGCTTGAACTTCCTGATATATG
1 GCTCTTAATGAGCTTCCTGATATATG
53018713 GCT
1 GCT
53018716 ATCCAGAGCT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
23 11 0.26
24 8 0.19
25 8 0.19
26 15 0.35
27 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (26 bp):
GCTCTTAATGAGCTTCCTGATATATG
Found at i:53021512 original size:25 final size:25
Alignment explanation
Indices: 53021484--53021574 Score: 69
Period size: 25 Copynumber: 3.5 Consensus size: 25
53021474 GACTTCAAGT
53021484 ATTTAAACTATTCAAAAATAACAAC
1 ATTTAAACTATTCAAAAATAACAAC
** **
53021509 ATTTAAAACCT-TTC-AATTTAACCTTTAGT
1 ATTT-AAA-CTATTCAAAAATAA-C---AAC
53021538 ATTTAAACTATTCAAAAATAACAAC
1 ATTTAAACTATTCAAAAATAACAAC
*
53021563 ATTTAAAATATT
1 ATTTAAACTATT
53021575 AAGCAATACT
Statistics
Matches: 49, Mismatches: 9, Indels: 16
0.66 0.12 0.22
Matches are distributed among these distances:
25 21 0.43
26 7 0.14
27 4 0.08
28 7 0.14
29 10 0.20
ACGTcount: A:0.48, C:0.14, G:0.01, T:0.36
Consensus pattern (25 bp):
ATTTAAACTATTCAAAAATAACAAC
Found at i:53025516 original size:29 final size:29
Alignment explanation
Indices: 53025482--53025548 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 29
53025472 GTACAGTTTG
53025482 ATACATAAACTTTGATTTTG-TGCAAATAT
1 ATACATAAACTTTGATTTTGAT-CAAATAT
*
53025511 ATACATTAAATTTTGATTTTGACTCAAATAT
1 ATACA-TAAACTTTGATTTTGA-TCAAATAT
*
53025542 GTACATA
1 ATACATA
53025549 TAATTCTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 5 0.15
30 16 0.48
31 11 0.33
32 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (29 bp):
ATACATAAACTTTGATTTTGATCAAATAT
Found at i:53025547 original size:31 final size:29
Alignment explanation
Indices: 53025482--53025560 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 29
53025472 GTACAGTTTG
*
53025482 ATACATAAACTTTGATTTTGTGCAAATAT
1 ATACATAAATTTTGATTTTGTGCAAATAT
53025511 ATACATTAAATTTTGATTTTGACT-CAAATAT
1 ATACA-TAAATTTTGATTTTG--TGCAAATAT
* *
53025542 GTACATATAATTCTGATTT
1 ATACATA-AATTTTGATTT
53025561 AATTCAATTG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
29 5 0.12
30 16 0.37
31 21 0.49
32 1 0.02
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (29 bp):
ATACATAAATTTTGATTTTGTGCAAATAT
Found at i:53029627 original size:125 final size:125
Alignment explanation
Indices: 53029423--53029649 Score: 409
Period size: 125 Copynumber: 1.8 Consensus size: 125
53029413 TAATTTCGAG
*
53029423 TTGACGTTTCTGATCAAATAGTATAAAATCGCTTCTAGAAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGAAGGATGCTATTTGAGAAGAATTTGTG
*
53029488 AAATCGCGCCCTCGTAGATGCACTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTT
66 AAATCGCGCCCTCGTAGACGCACTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTT
*
53029548 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGAAGGATGCTATTTGAGAAGAATTTGTG
* *
53029613 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
66 AAATCGCGCCCTCGTAGACGCACTTTTGCTACAGTAG
53029650 CATGTTTGGG
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
125 97 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGAAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTAGACGCACTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTT
Found at i:53032857 original size:17 final size:17
Alignment explanation
Indices: 53032788--53032857 Score: 52
Period size: 17 Copynumber: 3.9 Consensus size: 17
53032778 TATGTGAATG
* *
53032788 TAAAATTATTAACTCTA
1 TAAAATTATTAATTATA
* *
53032805 -AAATTGTATTAATGGATA
1 TAAAAT-TATTAAT-TATA
*
53032823 GTAAAATTATCAAATTATA
1 -TAAAATTAT-TAATTATA
53032842 TAAAATTATTAATTAT
1 TAAAATTATTAATTAT
53032858 TAGTAGCAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
16 4 0.10
17 12 0.30
18 11 0.28
19 6 0.15
20 7 0.17
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:53032881 original size:115 final size:115
Alignment explanation
Indices: 53032679--53032916 Score: 406
Period size: 115 Copynumber: 2.1 Consensus size: 115
53032669 TGATAAATTG
* *
53032679 TATTAACTCAAAAAATTGTATTAATGGTTAGTAAATTATCAAATTATATAAAAGTATTAATTGTT
1 TATTAACTCAAAAAATTGTATTAATGGATAGTAAATTATCAAATTATATAAAAGTATTAATTATT
*
53032744 AGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 AGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
* *
53032794 TATTAACTC-TAAAATTGTATTAATGGATAGTAAAATTATCAAATTATATAAAATTATTAATTAT
1 TATTAACTCAAAAAATTGTATTAATGGATAGT-AAATTATCAAATTATATAAAAGTATTAATTAT
*
53032858 TAGTAGCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
65 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
53032909 TATTAACT
1 TATTAACT
53032917 TAGTTTAGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
114 20 0.17
115 96 0.83
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.38
Consensus pattern (115 bp):
TATTAACTCAAAAAATTGTATTAATGGATAGTAAATTATCAAATTATATAAAAGTATTAATTATT
AGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
Found at i:53032936 original size:23 final size:22
Alignment explanation
Indices: 53032910--53033288 Score: 141
Period size: 21 Copynumber: 16.2 Consensus size: 22
53032900 ATGTAAAATT
* *
53032910 ATTAACTTAGTTTAGGGGTTTTA
1 ATTAAATTAGGTTA-GGGTTTTA
53032933 ATTAAATTAGGTTAGGGTTTTAA
1 ATTAAATTAGGTTAGGGTTTT-A
*
53032956 AGTT-AA--GGGTTAGGGTTTTA
1 A-TTAAATTAGGTTAGGGTTTTA
*
53032976 AGTT-AA--GGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGG-TTTTA
53032997 ATTAAATTAGGTTAGGGTTAGGGGTTTTA
1 ATT-AA--A--TTA-GGTTA-GGGTTTTA
53033026 ATTAAATTAGGTTAGGGTTTT-
1 ATTAAATTAGGTTAGGGTTTTA
*
53033047 A--AAGTTAAGGTTTAGGGTTTTA
1 ATTAAATT-AGG-TTAGGGTTTTA
53033069 AGTTAAGA-T---TTAGGGTTTTTA
1 A-TTAA-ATTAGGTTAGGG-TTTTA
53033090 ATTAAATTAGGTTAGAGTTAGGGTTTTA
1 ATT-AA--A--TTAG-GTTAGGGTTTTA
53033118 ATTAAATTAGGTTAGGGTTAGGGTTTTA
1 ATT-AA--A--TTA-GGTTAGGGTTTTA
53033146 ATTAAATTAGGTTAGGG-TTT-
1 ATTAAATTAGGTTAGGGTTTTA
53033166 -TTAAAGTTAAGGTTTAGGG-TTT-
1 ATTAAA-TT-AGG-TTAGGGTTTTA
*
53033188 -TTAAGTTAAGGTTTAGGGTTTTTA
1 ATTAAATT-AGG-TTAGGG-TTTTA
53033212 ATTAAATTAGGTTAGGATTAGGGTTTTA
1 ATT-AA--A--TTAGG-TTAGGGTTTTA
*
53033240 ATTAAATTAGATTAGGG-TTTA
1 ATTAAATTAGGTTAGGGTTTTA
* * *
53033261 GGGTTAAATTAGGTTAGAGTTTTT
1 --ATTAAATTAGGTTAGGGTTTTA
53033285 ATTA
1 ATTA
53033289 CATCAAATAA
Statistics
Matches: 294, Mismatches: 16, Indels: 93
0.73 0.04 0.23
Matches are distributed among these distances:
19 9 0.03
20 31 0.11
21 60 0.20
22 47 0.16
23 45 0.15
24 9 0.03
25 8 0.03
26 3 0.01
27 4 0.01
28 44 0.15
29 29 0.10
30 5 0.02
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.44
Consensus pattern (22 bp):
ATTAAATTAGGTTAGGGTTTTA
Found at i:53033015 original size:29 final size:29
Alignment explanation
Indices: 53032981--53033164 Score: 164
Period size: 28 Copynumber: 6.2 Consensus size: 29
53032971 TTTTAAGTTA
*
53032981 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGGTTTTAATTAAATTAGGTT
53033010 AGGGTTAGGGGTTTTAATTAAATTAGGTT
1 AGGGTTAGGGGTTTTAATTAAATTAGGTT
* * *
53033039 AGGGTTTTAAAGTTAAGG-TTTAGGGTT---TTAAGTT
1 AGGG--TT--AG---GGGTTTTA--ATTAAATTAGGTT
** *
53033073 AAGATTTAGGGTTTTTAATTAAATTAGGTT
1 -AGGGTTAGGGGTTTTAATTAAATTAGGTT
*
53033103 AGAGTTA-GGGTTTTAATTAAATTAGGTT
1 AGGGTTAGGGGTTTTAATTAAATTAGGTT
53033131 AGGGTTA-GGGTTTTAATTAAATTAGGTT
1 AGGGTTAGGGGTTTTAATTAAATTAGGTT
53033159 AGGGTT
1 AGGGTT
53033165 TTTAAAGTTA
Statistics
Matches: 128, Mismatches: 13, Indels: 29
0.75 0.08 0.17
Matches are distributed among these distances:
27 2 0.02
28 54 0.42
29 42 0.33
30 6 0.05
31 4 0.03
33 4 0.03
34 6 0.05
35 6 0.05
36 2 0.02
37 2 0.02
ACGTcount: A:0.29, C:0.00, G:0.28, T:0.43
Consensus pattern (29 bp):
AGGGTTAGGGGTTTTAATTAAATTAGGTT
Found at i:53033024 original size:93 final size:93
Alignment explanation
Indices: 53032921--53033136 Score: 389
Period size: 93 Copynumber: 2.3 Consensus size: 93
53032911 TTAACTTAGT
*
53032921 TTAGGGGTTTTAATTAAATTAGGTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTAAGTTAAGGGT
1 TTAGGGGTTTTAATTAAATTAGGTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTAAGTTAAGAGT
*
53032986 TAGGGTTTTTAATTAAATTAGGTTAGGG
66 TAGGGTTTTTAATTAAATTAGGTTAGAG
* *
53033014 TTAGGGGTTTTAATTAAATTAGGTTAGGGTTTTAAAGTTAAGGTTTAGGGTTTTAAGTTAAGATT
1 TTAGGGGTTTTAATTAAATTAGGTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTAAGTTAAGAGT
53033079 TAGGGTTTTTAATTAAATTAGGTTAGAG
66 TAGGGTTTTTAATTAAATTAGGTTAGAG
53033107 TTA-GGGTTTTAATTAAATTAGGTTAGGGTT
1 TTAGGGGTTTTAATTAAATTAGGTTAGGGTT
53033137 AGGGTTTTAA
Statistics
Matches: 119, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 27 0.23
93 92 0.77
ACGTcount: A:0.29, C:0.00, G:0.28, T:0.44
Consensus pattern (93 bp):
TTAGGGGTTTTAATTAAATTAGGTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTAAGTTAAGAGT
TAGGGTTTTTAATTAAATTAGGTTAGAG
Found at i:53033139 original size:121 final size:122
Alignment explanation
Indices: 53032983--53033263 Score: 487
Period size: 122 Copynumber: 2.3 Consensus size: 122
53032973 TTAAGTTAAG
53032983 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGGTTTTAATTAAATTAGGTTAGGG-TTTT
1 GGTTAGGG-TTTTAATTAAATTAGGTTAGGGTTAGGGGTTTTAATTAAATTAGGTTAGGGTTTTT
53033047 AAAGTTAAGGTTTAGGG-TTTTAAGTTAAGATTTAGGGTTTTTAATTAAATTAGGTTA
65 AAAGTTAAGGTTTAGGGTTTTTAAGTTAAGATTTAGGGTTTTTAATTAAATTAGGTTA
53033104 GAGTTAGGGTTTTAATTAAATTAGGTTAGGGTTA-GGGTTTTAATTAAATTAGGTTAGGGTTTTT
1 G-GTTAGGGTTTTAATTAAATTAGGTTAGGGTTAGGGGTTTTAATTAAATTAGGTTAGGGTTTTT
*
53033168 AAAGTTAAGGTTTAGGGTTTTTAAGTTAAGGTTTAGGGTTTTTAATTAAATTAGGTTA
65 AAAGTTAAGGTTTAGGGTTTTTAAGTTAAGATTTAGGGTTTTTAATTAAATTAGGTTA
*
53033226 GGATTAGGGTTTTAATTAAATTAGATTAGGGTTTAGGG
1 GG-TTAGGGTTTTAATTAAATTAGGTTAGGG-TTAGGG
53033264 TTAAATTAGG
Statistics
Matches: 152, Mismatches: 2, Indels: 9
0.93 0.01 0.06
Matches are distributed among these distances:
120 25 0.16
121 48 0.32
122 74 0.49
123 3 0.02
124 2 0.01
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (122 bp):
GGTTAGGGTTTTAATTAAATTAGGTTAGGGTTAGGGGTTTTAATTAAATTAGGTTAGGGTTTTTA
AAGTTAAGGTTTAGGGTTTTTAAGTTAAGATTTAGGGTTTTTAATTAAATTAGGTTA
Found at i:53033233 original size:29 final size:30
Alignment explanation
Indices: 53033200--53033265 Score: 100
Period size: 28 Copynumber: 2.3 Consensus size: 30
53033190 AAGTTAAGGT
*
53033200 TTAGGGTTTTTAATTAAATTAGGTTA-GGA
1 TTAGGGTTTTTAATTAAATTAGATTAGGGA
*
53033229 TTAGGG-TTTTAATTAAATTAGATTAGGGT
1 TTAGGGTTTTTAATTAAATTAGATTAGGGA
53033258 TTAGGGTT
1 TTAGGGTT
53033266 AAATTAGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 18 0.55
29 14 0.42
30 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (30 bp):
TTAGGGTTTTTAATTAAATTAGATTAGGGA
Found at i:53033271 original size:28 final size:28
Alignment explanation
Indices: 53033196--53033265 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 28
53033186 TTTTAAGTTA
*
53033196 AGGTTTAGGGTTTTTAATTAAATTAGGTT
1 AGGTTTAGGG-TTTTAATTAAATTAGATT
*
53033225 AGGATTAGGGTTTTAATTAAATTAGATT
1 AGGTTTAGGGTTTTAATTAAATTAGATT
53033253 AGGGTTTAGGGTT
1 A-GGTTTAGGGTT
53033266 AAATTAGGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 18 0.49
29 19 0.51
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (28 bp):
AGGTTTAGGGTTTTAATTAAATTAGATT
Found at i:53033309 original size:25 final size:25
Alignment explanation
Indices: 53033281--53033418 Score: 173
Period size: 25 Copynumber: 5.7 Consensus size: 25
53033271 AGGTTAGAGT
53033281 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
53033306 TTTTATTACATCAAAT-AA-TATC-A
1 TTTTATTACATCAAATAAACT-TCTA
** * *
53033329 --AAATAAC-TCGAAA-AAATTTCTA
1 TTTTATTACATC-AAATAAACTTCTA
53033351 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
53033376 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
53033401 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
53033419 TATCAAAATA
Statistics
Matches: 97, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
20 2 0.02
21 11 0.11
22 2 0.02
23 2 0.02
24 11 0.11
25 69 0.71
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.41
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:53033365 original size:45 final size:44
Alignment explanation
Indices: 53033291--53033472 Score: 213
Period size: 44 Copynumber: 4.0 Consensus size: 44
53033281 TTTTATTACA
*
53033291 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAA-AAATTTCTATTTTATTACATCAAATAATATCAAAATAAC
** *
53033336 TCGAAAAAATTTCTATTTTATTACATCAAATAA-ACTTCTATTTTATTAC
1 TC-AAAAAATTTCTATTTTATTACATCAAATAATA--TC-A--AAATAAC
*
53033385 ATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 -TCAAA-AAATTTCTATTTTATTACATCAAATAATATCAAAATAAC
* *
53033431 TCAAAAAATTTCTATTTTTTTACATAAAATAATATCAAAATA
1 TCAAAAAATTTCTATTTTATTACATCAAATAATATCAAAATA
53033473 TTCAAAATAT
Statistics
Matches: 117, Mismatches: 11, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
44 35 0.30
45 33 0.28
46 9 0.08
47 1 0.01
48 1 0.01
49 9 0.08
50 28 0.24
51 1 0.01
ACGTcount: A:0.47, C:0.14, G:0.01, T:0.39
Consensus pattern (44 bp):
TCAAAAAATTTCTATTTTATTACATCAAATAATATCAAAATAAC
Found at i:53033401 original size:95 final size:94
Alignment explanation
Indices: 53033281--53033462 Score: 337
Period size: 95 Copynumber: 1.9 Consensus size: 94
53033271 AGGTTAGAGT
53033281 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAAT
1 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTC-AAAAAAT
*
53033346 TTCTATTTTATTACATCAAATAAACTTCTA
65 TTCTATTTTATTACATAAAATAAACTTCTA
53033376 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATT
1 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATT
*
53033441 TCTATTTTTTTACATAAAATAA
66 TCTATTTTATTACATAAAATAA
53033463 TATCAAAATA
Statistics
Matches: 85, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
94 28 0.33
95 57 0.67
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.41
Consensus pattern (94 bp):
TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATT
TCTATTTTATTACATAAAATAAACTTCTA
Found at i:53033918 original size:18 final size:18
Alignment explanation
Indices: 53033895--53033929 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53033885 CGAAAAAGGA
*
53033895 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
53033913 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
53033930 AAACGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:53034589 original size:7 final size:7
Alignment explanation
Indices: 53034579--53034610 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
53034569 TTATATACAT
53034579 AATACTA
1 AATACTA
53034586 AATACTA
1 AATACTA
53034593 AATACTA
1 AATACTA
*
53034600 AGTACTA
1 AATACTA
53034607 AATA
1 AATA
53034611 TCAATCGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:53034818 original size:20 final size:20
Alignment explanation
Indices: 53034781--53034818 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53034771 TTTATTTTTA
*
53034781 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
53034801 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
53034819 TACCTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:53035753 original size:11 final size:12
Alignment explanation
Indices: 53035712--53035754 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
53035702 ATTTTTACGG
53035712 TTTAAAAAA-AT
1 TTTAAAAAATAT
53035723 TTTAAAAAATAT
1 TTTAAAAAATAT
* *
53035735 TTTTAAAATTA-
1 TTTAAAAAATAT
53035746 TTTAAAAAA
1 TTTAAAAAA
53035755 GGAGTTAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTTAAAAAATAT
Found at i:53035775 original size:11 final size:11
Alignment explanation
Indices: 53035759--53035789 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
53035749 AAAAAAGGAG
53035759 TTAAGAGAAAC
1 TTAAGAGAAAC
*
53035770 TTAAGAGGAAC
1 TTAAGAGAAAC
53035781 TTAAGAGAA
1 TTAAGAGAA
53035790 TTTTTGAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:53036334 original size:9 final size:9
Alignment explanation
Indices: 53036320--53036436 Score: 60
Period size: 10 Copynumber: 12.4 Consensus size: 9
53036310 CCATTGACAA
53036320 AAAAATTAT
1 AAAAATTAT
53036329 -AAAA--AT
1 AAAAATTAT
*
53036335 AAAAATCAAT
1 AAAAAT-TAT
53036345 AAAAATTTAT
1 AAAAA-TTAT
* *
53036355 TAAATTTATT
1 AAAAATTA-T
*
53036365 AAAAAAATATT
1 -AAAAATTA-T
53036376 AAAAATTAT
1 AAAAATTAT
* *
53036385 AAAAGTCAT
1 AAAAATTAT
*
53036394 AAAAGAATAT
1 AAAA-ATTAT
53036404 AAAAATTTAT
1 AAAAA-TTAT
**
53036414 AAAAACCAT
1 AAAAATTAT
53036423 AAAAAATTAT
1 -AAAAATTAT
53036433 AAAA
1 AAAA
53036437 TGCATCAAAA
Statistics
Matches: 81, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
6 2 0.02
7 4 0.05
8 4 0.05
9 22 0.27
10 41 0.51
11 8 0.10
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:53036396 original size:29 final size:29
Alignment explanation
Indices: 53036364--53036436 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
53036354 TTAAATTTAT
**
53036364 TAAAAAAATATTAAAAA-TTATAAAAGTCA
1 TAAAAAAATA-TAAAAATTTATAAAAACCA
*
53036393 TAAAAGAATATAAAAATTTATAAAAACCA
1 TAAAAAAATATAAAAATTTATAAAAACCA
*
53036422 TAAAAAATTATAAAA
1 TAAAAAAATATAAAA
53036437 TGCATCAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 6 0.16
29 32 0.84
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (29 bp):
TAAAAAAATATAAAAATTTATAAAAACCA
Found at i:53038001 original size:3 final size:3
Alignment explanation
Indices: 53037993--53038028 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
53037983 GTTGTGGTTT
53037993 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53038029 GGGTTAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53046383 original size:19 final size:19
Alignment explanation
Indices: 53046359--53046422 Score: 92
Period size: 19 Copynumber: 3.4 Consensus size: 19
53046349 GGATATGCAC
*
53046359 TCTTAGATATGATATCCAA
1 TCTTAGATATGATATACAA
* *
53046378 TTTTAGATATGATATATAA
1 TCTTAGATATGATATACAA
*
53046397 TCTTAGATATGATATGCAA
1 TCTTAGATATGATATACAA
53046416 TCTTAGA
1 TCTTAGA
53046423 ATATATGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (19 bp):
TCTTAGATATGATATACAA
Found at i:53049269 original size:24 final size:24
Alignment explanation
Indices: 53049242--53049287 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
53049232 AGAACAATCC
* *
53049242 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGAAAATGAAGGAGCAGCTT
*
53049266 CAAAAGAAAATGAATGAGCAGC
1 CAAAAGAAAATGAAGGAGCAGC
53049288 AAAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (24 bp):
CAAAAGAAAATGAAGGAGCAGCTT
Found at i:53053382 original size:132 final size:132
Alignment explanation
Indices: 53053206--53054229 Score: 1721
Period size: 132 Copynumber: 7.8 Consensus size: 132
53053196 GACAGCAAAA
** *
53053206 CAGATCGAAGATGGTAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATTC
1 CAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
53053271 TACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
66 TACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
53053336 AG
131 AG
* * *
53053338 CAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAATGGAGTACATTGAAGCTAGTAATTC
1 CAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* *
53053403 TACTTTCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
66 TACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
53053468 AG
131 AG
* * * *
53053470 TAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAATTGAGTACATTGAAGCCAGTAATTC
1 CAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
*
53053535 TACTTCCCTGAACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCT-CCTAAGCAGTAGTGG
66 TACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
53053599 AG
131 AG
*
53053601 CAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* * * *
53053666 TATTTCTCTAGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGTGG
66 TACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
53053731 AG
131 AG
* * *
53053733 CAGATCGAAGATGGAGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTAAAGCCAGTAATTC
1 CAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* *
53053798 TACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGTGG
66 TACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
53053863 AG
131 AG
53053865 CAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
*
53053930 TACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAATGG
66 TACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
53053995 AG
131 AG
* *
53053997 CAGATCGAAGATGGCGGATTTTACCTCCATGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
53054062 TACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
66 TACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
53054127 AG
131 AG
* * *
53054129 CAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGGGTACATTGAAGCCAGTAA-TC
1 CAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* * *
53054193 ATA-TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
66 -TACT-TCCCTGGACAACAGTGGAATAGATTGAAGATT
53054230 GTAAGTCCTA
Statistics
Matches: 842, Mismatches: 47, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
131 124 0.15
132 718 0.85
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (132 bp):
CAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
TACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
AG
Found at i:53053474 original size:44 final size:44
Alignment explanation
Indices: 53053287--53054158 Score: 166
Period size: 44 Copynumber: 19.8 Consensus size: 44
53053277 CCTGGACAAC
* * *
53053287 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGCAGT
* * * * * ** *
53053331 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTA-T
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCT-AAG-CAGT
* * * * * ** **
53053376 AATGGAGTACATTGAAGCTAGT-A-AT-TCTACTTTCCTGGGCAAC
1 AGTGGAGTAGATTGAAGAT-GTCAGATCT-TACCTCCCTAAGCAGT
* * *
53053419 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGCAGT
* * * **
53053463 AGTGGAGTAGATCGAAGATGGCAGATTTTACCTCCCT--GTGGTT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGCAG-T
* * * * **
53053506 ACAATTGAGTACATTGAAGCCA-GT-A-AT-TCTACTTCCCTGAA-CAAC
1 --AGTGGAGTAGATTGAAG--ATGTCAGATCT-TACCTCCCT-AAGCAGT
* * *
53053551 AGTGGAATAGATTGAAGATTTCAGATCTTATCT-CCTAAGCAGT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGCAGT
* * * * * ** *
53053594 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTA-T
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCT-AAG-CAGT
* ** * **
53053639 AGTGGAGTACATTGAAGCCA-GT-A-AT-TCTATTTCTCT-AGACAAC
1 AGTGGAGTAGATTGAAG--ATGTCAGATCT-TACCTCCCTAAG-CAGT
* * * *
53053682 AGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGCAGT
* * * * **
53053726 AGTGGAGCAGATCGAAGATG-GAGAATTTTACCTCCCT--GTGGTT
1 AGTGGAGTAGATTGAAGATGTCAG-ATCTTACCTCCCTAAGCAG-T
* * * **
53053769 ACAGTGGAGTACATT-AA-A-GCCAGTAAT-TCTACTTCCCT-AGACAAC
1 --AGTGGAGTAGATTGAAGATGTCAG--ATCT-TACCTCCCTAAG-CAGT
* * * *
53053814 AGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGCAGT
* * * * * **
53053858 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCT--GTGGTT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGCAG-T
* * * **
53053901 ACAGTGGAGTACATTGAAGCCA-GT-A-AT-TCTACTTCCCT-GGACAAC
1 --AGTGGAGTAGATTGAAG--ATGTCAGATCT-TACCTCCCTAAG-CAGT
* * *
53053946 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGCAGT
* * * * * * * ** *
53053990 AATGGAGCAGATCGAAGATGGCGGATTTTACCTCCATGTGGTTA-T
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCT-AAG-CAGT
* * * **
53054035 AGTGGAGTACATTGAAGCCA-GT-A-AT-TCTACTTCCCT-GGACAAC
1 AGTGGAGTAGATTGAAG--ATGTCAGATCT-TACCTCCCTAAG-CAGT
* * *
53054078 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGCAGT
* * * *
53054122 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCT
53054159 GTGGTTATAG
Statistics
Matches: 567, Mismatches: 189, Indels: 144
0.63 0.21 0.16
Matches are distributed among these distances:
41 4 0.01
42 20 0.04
43 135 0.24
44 293 0.52
45 100 0.18
46 11 0.02
47 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (44 bp):
AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGCAGT
Found at i:53054579 original size:19 final size:19
Alignment explanation
Indices: 53054555--53054623 Score: 120
Period size: 19 Copynumber: 3.6 Consensus size: 19
53054545 AATCTTCAGG
53054555 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
53054574 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
53054593 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
53054612 GATATGCAATCT
1 GATATGCAATCT
53054624 AAGAAGATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:53054653 original size:22 final size:21
Alignment explanation
Indices: 53054555--53054653 Score: 84
Period size: 19 Copynumber: 4.9 Consensus size: 21
53054545 AATCTTCAGG
*
53054555 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
53054574 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
53054593 GATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
53054612 GATATGCAATCTAAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
53054634 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
53054654 TTAATTTGTA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
19 46 0.68
22 12 0.18
23 10 0.15
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.37
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:53056435 original size:20 final size:20
Alignment explanation
Indices: 53056397--53056435 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53056387 TTCAAAGTTT
* *
53056397 ATAAAAGAAATTGTAAAAAG
1 ATAAAAAAAATTATAAAAAG
53056417 ATAAAAAAAATTATTAAAA
1 ATAAAAAAAATTA-TAAAA
53056436 TTTTACAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (20 bp):
ATAAAAAAAATTATAAAAAG
Found at i:53056627 original size:20 final size:20
Alignment explanation
Indices: 53056582--53056618 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53056572 AAATCTCTCC
53056582 AAAT-TACAAAATATAAAAT
1 AAATATACAAAATATAAAAT
*
53056601 AAATATACAAATTATAAA
1 AAATATACAAAATATAAA
53056619 CTTAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATATACAAAATATAAAAT
Found at i:53062138 original size:22 final size:22
Alignment explanation
Indices: 53062110--53062155 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
53062100 TACCAAATTT
53062110 GGGTTATCAGGTCTAGGGTTTA
1 GGGTTATCAGGTCTAGGGTTTA
53062132 GGGTTATCAGGTCTAGGGTTTA
1 GGGTTATCAGGTCTAGGGTTTA
53062154 GG
1 GG
53062156 TTCTTCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.09, G:0.39, T:0.35
Consensus pattern (22 bp):
GGGTTATCAGGTCTAGGGTTTA
Found at i:53064378 original size:14 final size:14
Alignment explanation
Indices: 53064359--53064388 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53064349 CAGAGTCCCT
*
53064359 TATTTCTTTTTAAA
1 TATTTCTTTCTAAA
53064373 TATTTCTTTCTAAA
1 TATTTCTTTCTAAA
53064387 TA
1 TA
53064389 CTCATTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTTCTTTCTAAA
Found at i:53077807 original size:14 final size:15
Alignment explanation
Indices: 53077790--53077827 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
53077780 ATATTTTTTC
53077790 AAAATTATTTTAC-G
1 AAAATTATTTTACTG
*
53077804 AAAAATATTTTACTG
1 AAAATTATTTTACTG
*
53077819 ACAATTATT
1 AAAATTATT
53077828 CAAATTTCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (15 bp):
AAAATTATTTTACTG
Found at i:53089801 original size:21 final size:21
Alignment explanation
Indices: 53089775--53089818 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
53089765 TATAAAGTGC
53089775 GCTGCTCATTCAACATTCATA
1 GCTGCTCATTCAACATTCATA
53089796 GCTGCTCATTCAACATTCATA
1 GCTGCTCATTCAACATTCATA
53089817 GC
1 GC
53089819 ATCTGTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (21 bp):
GCTGCTCATTCAACATTCATA
Found at i:53091951 original size:18 final size:18
Alignment explanation
Indices: 53091928--53091970 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
53091918 TTAATTTCAG
*
53091928 CATGCTGCCAGTCAAGAT
1 CATGCTGCCAATCAAGAT
*
53091946 CATGCTGTCAATCAAGAT
1 CATGCTGCCAATCAAGAT
53091964 CATGCTG
1 CATGCTG
53091971 GTCTTGCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (18 bp):
CATGCTGCCAATCAAGAT
Found at i:53096334 original size:6 final size:6
Alignment explanation
Indices: 53096323--53096350 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53096313 TGAAATTTAA
53096323 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
53096351 TCTTTATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:53099994 original size:27 final size:27
Alignment explanation
Indices: 53099931--53099995 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
53099921 CTACCATTCC
* * *
53099931 TTCAGAGTTCGCCAAACATACTATCCC
1 TTCAGTGTTTGCCAAACATACTATCCA
* * *
53099958 TTTAATGTTTGCCACACATACTATCCA
1 TTCAGTGTTTGCCAAACATACTATCCA
53099985 TTCAGTGTTTG
1 TTCAGTGTTTG
53099996 TCGATAATAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.35
Consensus pattern (27 bp):
TTCAGTGTTTGCCAAACATACTATCCA
Found at i:53100136 original size:27 final size:27
Alignment explanation
Indices: 53100106--53100157 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
53100096 TTTCCTTCTT
* **
53100106 TAGATCGCCACAAAGGCTTCCATTTCA
1 TAGATCACCACAAAAACTTCCATTTCA
*
53100133 TAGATTACCACAAAAACTTCCATTT
1 TAGATCACCACAAAAACTTCCATTT
53100158 TCTAACGTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.29
Consensus pattern (27 bp):
TAGATCACCACAAAAACTTCCATTTCA
Done.