Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold196
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: 7488280
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 125249 characters in sequence are not A, C, G, or T
File 22 of 47
Found at i:3296333 original size:4 final size:4
Alignment explanation
Indices: 3296319--3296357 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
3296309 TAAACCCATA
* *
3296319 ATAT GTAT ATAT ATAT ATAT ATAT ATAT ATAT ATTT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
3296358 CACACAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (4 bp):
ATAT
Found at i:3296333 original size:6 final size:6
Alignment explanation
Indices: 3296319--3296357 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
3296309 TAAACCCATA
* *
3296319 ATATGT ATATAT ATATAT ATATAT ATATAT ATATTT ATA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATA
3296358 CACACAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
ATATAT
Found at i:3297651 original size:20 final size:20
Alignment explanation
Indices: 3297628--3297700 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3297618 ACAATTCAAA
3297628 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3297648 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3297669 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3297689 GTATCGATACAT
1 GTATCGATACAT
3297701 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3297672 original size:21 final size:21
Alignment explanation
Indices: 3297646--3297721 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3297636 ACATGTTGCA
3297646 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3297667 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
3297687 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
3297708 ATGTATCGATACAT
1 ATGTATCGATACAT
3297722 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3297679 original size:41 final size:41
Alignment explanation
Indices: 3297628--3297721 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
3297618 ACAATTCAAA
*
3297628 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3297669 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3297710 GTATCGATACAT
1 GTATCGATACAT
3297722 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3299106 original size:24 final size:24
Alignment explanation
Indices: 3299061--3299107 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3299051 TACTGTATTT
*
3299061 AATATAATAATATTATTATTTATA
1 AATATAATAATATTAATATTTATA
*
3299085 AATATTATAATAATTAAT-TTTAT
1 AATATAATAAT-ATTAATATTTAT
3299108 TTTTTAGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AATATAATAATATTAATATTTATA
Found at i:3299934 original size:27 final size:29
Alignment explanation
Indices: 3299904--3299967 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
3299894 TTTTAGTATA
*
3299904 TATTATTTTATTTAA-TAATTTAAT-TT-T
1 TATTATTTT-TTTAATTAAATTAATATTAT
*
3299931 TATTAATTTTTTAATTAAATTAATATTAT
1 TATTATTTTTTTAATTAAATTAATATTAT
3299960 T-TTATTTT
1 TATTATTTT
3299968 GTGATATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 5 0.16
27 16 0.52
28 8 0.26
29 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TATTATTTTTTTAATTAAATTAATATTAT
Found at i:3301059 original size:97 final size:92
Alignment explanation
Indices: 3300891--3301078 Score: 254
Period size: 97 Copynumber: 2.0 Consensus size: 92
3300881 TGCATGGATT
* * *
3300891 GTAAATGTCAAACTAGAAGGATTAGACTAAGGCATTAATTATATCTGAGAATTAGATTCCTTTTG
1 GTAAATGTCAAACTAGAAGGATTAGACTAAGGCATGAATTATATCTGAGAATGAGATTCCTTTTA
3300956 GTAGAAAAAAAGAAAAGTTGATTGATC
66 GTAGAAAAAAAGAAAAGTTGATTGATC
* *
3300983 GTAAATGTCAAACT-GCAAGGATTAGACTAATGCATGAATTGTATTGTATTTGAGAATCGA-ATT
1 GTAAATGTCAAACTAG-AAGGATTAGACTAAGGCATGAA-T-TA---TATCTGAGAAT-GAGATT
3301046 CCTTTTAGTAGAAAAAAAGAAAAGTTGATTGAT
59 CCTTTTAGTAGAAAAAAAGAAAAGTTGATTGAT
3301079 TATAAGTATT
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
91 1 0.01
92 34 0.40
93 1 0.01
94 2 0.02
97 45 0.54
98 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (92 bp):
GTAAATGTCAAACTAGAAGGATTAGACTAAGGCATGAATTATATCTGAGAATGAGATTCCTTTTA
GTAGAAAAAAAGAAAAGTTGATTGATC
Found at i:3301475 original size:43 final size:43
Alignment explanation
Indices: 3301414--3301503 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 43
3301404 ATACATTGTT
3301414 CATTGTATCGATACATTCTGGGTTTTACCTAGATGTATCGATA
1 CATTGTATCGATACATTCTGGGTTTTACCTAGATGTATCGATA
*
3301457 CATTGTATCTATACATTCTGGGTTTTACCTAGATGTATCGATA
1 CATTGTATCGATACATTCTGGGTTTTACCTAGATGTATCGATA
3301500 CATT
1 CATT
3301504 TTTAATGTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (43 bp):
CATTGTATCGATACATTCTGGGTTTTACCTAGATGTATCGATA
Found at i:3302791 original size:13 final size:13
Alignment explanation
Indices: 3302773--3302798 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3302763 TGCACAAAGT
3302773 ATGTATCGATACA
1 ATGTATCGATACA
3302786 ATGTATCGATACA
1 ATGTATCGATACA
3302799 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3302801 original size:32 final size:33
Alignment explanation
Indices: 3302755--3302818 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
3302745 TAGCCAAACT
* **
3302755 TGTATCGATGCACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3302787 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3302819 TTGGCTTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3308989 original size:13 final size:13
Alignment explanation
Indices: 3308971--3308996 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3308961 ACATTTTTCT
3308971 TTGTATCGATACA
1 TTGTATCGATACA
3308984 TTGTATCGATACA
1 TTGTATCGATACA
3308997 GGGGGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3309151 original size:20 final size:20
Alignment explanation
Indices: 3309108--3309153 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3309098 AAATCTTTTG
3309108 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
3309129 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
3309149 CAAAA
1 CAAAA
3309154 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:3310794 original size:20 final size:21
Alignment explanation
Indices: 3310769--3310815 Score: 87
Period size: 20 Copynumber: 2.3 Consensus size: 21
3310759 AGAATAGATG
3310769 TATGTGCAAATAAATTTTT-A
1 TATGTGCAAATAAATTTTTGA
3310789 TATGTGCAAATAAATTTTTGA
1 TATGTGCAAATAAATTTTTGA
3310810 TATGTG
1 TATGTG
3310816 TGTAAATTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (21 bp):
TATGTGCAAATAAATTTTTGA
Found at i:3311445 original size:13 final size:13
Alignment explanation
Indices: 3311427--3311452 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3311417 TACACAAAGT
3311427 ATGTATCGATACA
1 ATGTATCGATACA
3311440 ATGTATCGATACA
1 ATGTATCGATACA
3311453 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3311450 original size:32 final size:33
Alignment explanation
Indices: 3311409--3311472 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3311399 TAGCCAAACT
**
3311409 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3311441 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3311473 TTGGCTTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3313009 original size:20 final size:19
Alignment explanation
Indices: 3312965--3313039 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
3312955 AAAAAGACAA
* * *
3312965 AATGTATTGATACATTGAAG
1 AATGTATCGATACATT-TAT
3312985 AATGTATCGATACATTTAT
1 AATGTATCGATACATTTAT
*
3313004 ACATGTATCGATACATTTTTT
1 A-ATGTATCGATACA-TTTAT
3313025 AATGTATCGATACAT
1 AATGTATCGATACAT
3313040 CTGGGTAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 3 0.06
20 41 0.84
21 5 0.10
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (19 bp):
AATGTATCGATACATTTAT
Found at i:3318456 original size:21 final size:21
Alignment explanation
Indices: 3318409--3318450 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3318399 CAAATTGACA
*
3318409 ATATTGGAGACGTGTCTGGAT
1 ATATTGGAGACGTGTCTAGAT
*
3318430 ATATTGGTGACGTGTCTAGAT
1 ATATTGGAGACGTGTCTAGAT
3318451 TCATTGATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.36
Consensus pattern (21 bp):
ATATTGGAGACGTGTCTAGAT
Found at i:3318783 original size:97 final size:97
Alignment explanation
Indices: 3318532--3318772 Score: 311
Period size: 97 Copynumber: 2.5 Consensus size: 97
3318522 AGTGAAAAAT
* * * * **
3318532 GGGGTTAGAGTATCCCCTCGGAGGAATGGGGTTGGAATGTCCCCGATGATGGTAATTTAAGCGAG
1 GGGGTTGGAGTATCCCCTCAGAGGAATAGGGTTGGAGTGTCCCCGATGATGAAAATTTAAGCGAG
*
3318597 AATAAGATTTAAATTTTGATAAGTTTAAAAGC
66 AATAAGATTTAAACTTTGATAAGTTTAAAAGC
** * * * * * *
3318629 GAAGTTGGAGTATCCACTTAGAGGAATAGGGTTGGAGTGTCCCCAATGATGACAATTTATGTGAG
1 GGGGTTGGAGTATCCCCTCAGAGGAATAGGGTTGGAGTGTCCCCGATGATGAAAATTTAAGCGAG
* *
3318694 AATAAGATTTAAACTTTGATGAGTTTAGAAGC
66 AATAAGATTTAAACTTTGATAAGTTTAAAAGC
* *
3318726 GGGGTTGGAGTATCCCCTCAGAGGAATAAGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCTCAGAGGAATAGGGTTGGAGTGTCCCCGAT
3318773 AAATAAAATT
Statistics
Matches: 121, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
97 121 1.00
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.28
Consensus pattern (97 bp):
GGGGTTGGAGTATCCCCTCAGAGGAATAGGGTTGGAGTGTCCCCGATGATGAAAATTTAAGCGAG
AATAAGATTTAAACTTTGATAAGTTTAAAAGC
Found at i:3333579 original size:61 final size:61
Alignment explanation
Indices: 3333454--3333945 Score: 507
Period size: 61 Copynumber: 8.0 Consensus size: 61
3333444 AACCTTTTAT
*
3333454 CCTTCTAGTCCTCAAAGAGC--GACGTCTTTTCCTTTTAAAG--C-CACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAAAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
3333510 CCTTCTAGTCCTTAAAAAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGATGGCA
1 CCTTCTAGTCCTCAAAAAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
3333571 ACTTCTAGTCTTCAAAAAGTAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAAAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
3333632 CATTCCAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAAAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
3333693 CCTT-TCAGTCTTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCT-AGTCCTCAAAAAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * *
3333754 CCTTTTAGTCATGAAAGAA-CAGGATGTCTTTTCTTTTTAAAGCCCACATAAGTTGGTGACA
1 CCTTCTAGTCCTCAAA-AAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * *
3333815 CCTTCCAATCCTCAAAAAGTAGGAC-AC-TTTCCTTTCAAAGCCTATACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAAAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
3333874 ACTTTTAGTCCTCAAAGAGCAGGAGACCTTTCTCTTTTTCCATCTTAAAGCCCACACAAGTTGGT
1 CCTTCTAGTCCTCAAAAAGCA-G-GA-C---GTC-TTTTCC-TTTTAAAGCCCACACAAGTTGGT
3333939 GGCA
58 GGCA
3333943 CCT
1 CCT
3333946 ATCCACTTCA
Statistics
Matches: 361, Mismatches: 56, Indels: 25
0.82 0.13 0.06
Matches are distributed among these distances:
56 18 0.05
58 20 0.06
59 41 0.11
60 5 0.01
61 243 0.67
62 3 0.01
66 1 0.00
68 5 0.01
69 25 0.07
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (61 bp):
CCTTCTAGTCCTCAAAAAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:3337377 original size:238 final size:238
Alignment explanation
Indices: 3336913--3337491 Score: 618
Period size: 238 Copynumber: 2.4 Consensus size: 238
3336903 TCTAATCTCA
* *** ** * * *
3336913 TTATTTTCGAGGGGATACTACAACCCTGGTTTTATTTTCAAAACACCAATTTTTCATAATC-GAG
1 TTATTTTCGAGGGGATACTCCAACCCCAATTTTATTCCCAAAACATCGATTTTTCACAATCAG-G
* * * ** * * *
3336977 GATATTCCAACCCCGTTATTTTCGAGGGGATACTATAACC-CCAATTTTATTTCT--AACA-CCA
65 GATACTCCAACCTCGTTATTTTCGAAGGGATACTCCAACCACGATTTTTATTTCTAAAACATCGA
* * * * * *
3337038 ATTTTCTAGAATCGGAGGGATACTTCAACCCTGTTATTTTTGAGGGGATACTCTAACCCCAGTTT
130 TTTTTC-ACAAT--TAGGGATACTCCAACCCTGTTATTTTTGAGGGGATACTCCAACCCCAGCTT
* **
3337103 TATTTTCAAAACATCAATTTTCCACCATCAGGGATACTCCAACTTTG
192 TATTTTCAAAACATCAATTTTCCACAATCAGGGATACTCCAACCCTG
* * * *
3337150 TTATTTTCGAGGGGATACTCCAACCCCAATTTTATTTCTAAAAGATCGATTTTTTACAATCAGGG
1 TTATTTTCGAGGGGATACTCCAACCCCAATTTTATTCCCAAAACATCGATTTTTCACAATCAGGG
*
3337215 ATACTCCAACCTCGTTA-TTTCTAAGGGGATACTCCAACCACGATTTTTATTTCTAAAACATCGA
66 ATACTCCAACCTCGTTATTTTCGAA-GGGATACTCCAACCACGATTTTTATTTCTAAAACATCGA
* *
3337279 TTTTTCACAATTAGGGATACTCCAA-CCTCGTTATTTTTGTGGGGATACTCCAA-CCCTGACTTT
130 TTTTTCACAATTAGGGATACTCCAACCCT-GTTATTTTTGAGGGGATACTCCAACCCCAG-CTTT
* * * ** *
3337342 A-TTTCTAAAACATCGATTTTTCATAATGGGGGATACTCTAACCCTG
193 ATTTTC-AAAACATCAATTTTCCACAATCAGGGATACTCCAACCCTG
*** * * *
3337388 TTATTTTCGAGGGGATACTCCAACCCTGGTTTTATTCCCAAAACATTGATTTTTCACCATCGGGG
1 TTATTTTCGAGGGGATACTCCAACCCCAATTTTATTCCCAAAACATCGATTTTTCACAATCAGGG
3337453 ATACTCCAACCTCGTTATTTTCGAAGGGATACTCCAACC
66 ATACTCCAACCTCGTTATTTTCGAAGGGATACTCCAACC
3337492 TTGTTTTATC
Statistics
Matches: 284, Mismatches: 48, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
236 5 0.02
237 90 0.32
238 168 0.59
239 6 0.02
240 8 0.03
241 7 0.02
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (238 bp):
TTATTTTCGAGGGGATACTCCAACCCCAATTTTATTCCCAAAACATCGATTTTTCACAATCAGGG
ATACTCCAACCTCGTTATTTTCGAAGGGATACTCCAACCACGATTTTTATTTCTAAAACATCGAT
TTTTCACAATTAGGGATACTCCAACCCTGTTATTTTTGAGGGGATACTCCAACCCCAGCTTTATT
TTCAAAACATCAATTTTCCACAATCAGGGATACTCCAACCCTG
Found at i:3337522 original size:79 final size:79
Alignment explanation
Indices: 3336864--3337508 Score: 590
Period size: 79 Copynumber: 8.2 Consensus size: 79
3336854 TTATTGATGT
* * * * * * * *
3336864 TTTTATTTCTAAAACATTGA-TTTCCACCATCGGGGATACTCTAATCTCATTATTTTCGAGGGGA
1 TTTTATTTCCAAAACATCGATTTTTCACAATCAGGGATACTCCAACCTCGTTATTTTCGAGGGGA
* **
3336928 TACTACAACCCTGG
66 TACTCCAACCCCAG
* * * * * *
3336942 TTTTATTTTCAAAACACCAATTTTTCATAATC-GAGGATATTCCAACCCCGTTATTTTCGAGGGG
1 TTTTATTTCCAAAACATCGATTTTTCACAATCAG-GGATACTCCAACCTCGTTATTTTCGAGGGG
** *
3337006 ATACTATAACCCCAA
65 ATACTCCAACCCCAG
* * * * * *
3337021 TTTTATTT-C-TAACA-CCAATTTTCTAGAATCGGAGGGATACTTCAACC-CTGTTATTTTTGAG
1 TTTTATTTCCAAAACATCGATTTTTC-ACAATC--AGGGATACTCCAACCTC-GTTATTTTCGAG
*
3337082 GGGATACTCTAACCCCAG
62 GGGATACTCCAACCCCAG
* * * * * *
3337100 TTTTATTTTCAAAACATCAATTTTCCACCATCAGGGATACTCCAACTTTGTTATTTTCGAGGGGA
1 TTTTATTTCCAAAACATCGATTTTTCACAATCAGGGATACTCCAACCTCGTTATTTTCGAGGGGA
*
3337165 TACTCCAACCCCAA
66 TACTCCAACCCCAG
* * * *
3337179 TTTTATTTCTAAAAGATCGATTTTTTACAATCAGGGATACTCCAACCTCGTTA-TTTCTAAGGGG
1 TTTTATTTCCAAAACATCGATTTTTCACAATCAGGGATACTCCAACCTCGTTATTTTC-GAGGGG
* *
3337243 ATACTCCAACCACGAT
65 ATACTCCAACC-CCAG
* * * *
3337259 TTTTATTTCTAAAACATCGATTTTTCACAATTAGGGATACTCCAACCTCGTTATTTTTGTGGGGA
1 TTTTATTTCCAAAACATCGATTTTTCACAATCAGGGATACTCCAACCTCGTTATTTTCGAGGGGA
*
3337324 TACTCCAA-CCCTG
66 TACTCCAACCCCAG
* * * ** *
3337337 ACTTTATTTCTAAAACATCGATTTTTCATAATGGGGGATACTCTAACC-CTGTTATTTTCGAGGG
1 -TTTTATTTCCAAAACATCGATTTTTCACAATCAGGGATACTCCAACCTC-GTTATTTTCGAGGG
**
3337401 GATACTCCAACCCTGG
64 GATACTCCAACCCCAG
* * * * *
3337417 TTTTATTCCCAAAACATTGATTTTTCACCATCGGGGATACTCCAACCTCGTTATTTTCGAAGGGA
1 TTTTATTTCCAAAACATCGATTTTTCACAATCAGGGATACTCCAACCTCGTTATTTTCGAGGGGA
**
3337482 TACTCCAA-CCTTG
66 TACTCCAACCCCAG
*
3337495 TTTTATCTCCAAAA
1 TTTTATTTCCAAAA
3337509 TATTAAATTT
Statistics
Matches: 469, Mismatches: 80, Indels: 36
0.80 0.14 0.06
Matches are distributed among these distances:
76 7 0.01
77 9 0.02
78 40 0.09
79 325 0.69
80 71 0.15
81 11 0.02
82 6 0.01
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.36
Consensus pattern (79 bp):
TTTTATTTCCAAAACATCGATTTTTCACAATCAGGGATACTCCAACCTCGTTATTTTCGAGGGGA
TACTCCAACCCCAG
Found at i:3337542 original size:317 final size:317
Alignment explanation
Indices: 3336942--3337520 Score: 713
Period size: 317 Copynumber: 1.8 Consensus size: 317
3336932 ACAACCCTGG
* * *
3336942 TTTTATTTTCAAAACACCAATTTTTCATAATCGAGGATATTCCAACCCCGTTATTTTCGAGGGGA
1 TTTTATTTTCAAAACACCAATTTTTCACAATAGAGGATACTCCAACCCCGTTATTTTCGAGGGGA
* *
3337007 TACTATAACCCCAATTTTATTTCTAACACCAATTTTCTAGAATCGGAGGGATACTTCAACCCTGT
66 TACTACAACCCCAACTTTATTTCTAACACCAATTTTCTAGAATCGGAGGGATACTTCAACCCTGT
* * **
3337072 TATTTTTGAGGGGATACTCTAACCCCAGTTTTATTTTCAAAACATCAATTTTCCACCATCAGGGA
131 TATTTTCGAGGGGATACTCCAACCCCAGTTTTATTCCCAAAACATCAATTTTCCACCATCAGGGA
* * * * * * *
3337137 TACTCCAACTTTGTTATTTTCGAGGGGATACTCCAACCCCAATTTTATTTCTAAAAGATCGATTT
196 TACTCCAACCTCGTTATTTTCGAAGGGATACTCCAACCCCAATTTTATCTCCAAAAGATCAAATT
3337202 TTTACAATCAGGGATACTCCAACCTCGTTATTTCTAAGGGGATACTCCAACCACGAT
261 TTTACAATCAGGGATACTCCAACCTCGTTATTTCTAAGGGGATACTCCAACCACGAT
* * * * *
3337259 TTTTA-TTTCTAAAACATCGATTTTTCACAATTAG-GGATACTCCAACCTCGTTATTTTTGTGGG
1 TTTTATTTTC-AAAACACCAATTTTTCACAA-TAGAGGATACTCCAACCCCGTTATTTTCGAGGG
* ** * * *
3337322 GATACTCCAACCCTGACTTTATTTCTAAAACATCGATTTT-TCATAAT-GG-GGGATAC-TCTAA
64 GATACTACAACCCCAACTTTATTTCT--AACACCAATTTTCT-AGAATCGGAGGGATACTTC-AA
** ** *
3337383 CCCTGTTATTTTCGAGGGGATACTCCAACCCTGGTTTTATTCCCAAAACATTGATTTTTCACCAT
125 CCCTGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTCCCAAAACATCAATTTTCCACCAT
* *** *
3337448 CGGGGATACTCCAACCTCGTTATTTTCGAAGGGATACTCCAA-CCTTGTTTTATCTCCAAAATAT
190 CAGGGATACTCCAACCTCGTTATTTTCGAAGGGATACTCCAACCCCAATTTTATCTCCAAAAGAT
*
3337512 TAAATTTTT
255 CAAATTTTT
3337521 CATCGGGGAA
Statistics
Matches: 218, Mismatches: 38, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
316 28 0.13
317 171 0.78
318 5 0.02
319 14 0.06
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.36
Consensus pattern (317 bp):
TTTTATTTTCAAAACACCAATTTTTCACAATAGAGGATACTCCAACCCCGTTATTTTCGAGGGGA
TACTACAACCCCAACTTTATTTCTAACACCAATTTTCTAGAATCGGAGGGATACTTCAACCCTGT
TATTTTCGAGGGGATACTCCAACCCCAGTTTTATTCCCAAAACATCAATTTTCCACCATCAGGGA
TACTCCAACCTCGTTATTTTCGAAGGGATACTCCAACCCCAATTTTATCTCCAAAAGATCAAATT
TTTACAATCAGGGATACTCCAACCTCGTTATTTCTAAGGGGATACTCCAACCACGAT
Found at i:3341010 original size:2 final size:2
Alignment explanation
Indices: 3341003--3341035 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3340993 TGAAAACATA
3341003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3341036 CATGCTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3342208 original size:164 final size:163
Alignment explanation
Indices: 3341625--3342293 Score: 803
Period size: 166 Copynumber: 4.0 Consensus size: 163
3341615 TTTGCAACGA
* * *
3341625 AGAAAACTCAGT-TTCTCGAAAAAAGAGGATTTTCAAAGAAAAAATTCAAAACTTT-TGAAAATG
1 AGAAAACTCCGTATT-TCGAAAAAAGA-GAATTTCAAAGAAAAAATTCAAAA-TTTATGGAAATG
* * * * *
3341688 AATTAATTTTTTAAAACA-GATTTAATATGAAATAAATAATAACATTTTATGAATTTTAAAAATC
63 AATGAA-TTTTTAAAA-ATGAATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATT
* * *
3341752 AAAAACCAAGAAAACTCCCCCCAAAAAAATTTACAGAGT
126 AAAAACCAAGAAAAAT-CCTCCGAAAAAATTTACAGAGT
* * * *
3341791 AAAAAACTTCGTATTTCGAAAAACGGAAAATTTC-AAGAAAAAAATTCAAAATTTATGGAAATGA
1 AGAAAACTCCGTATTTCGAAAAA-AGAGAATTTCAAAG-AAAAAATTCAAAATTTATGGAAATGA
* * * *
3341855 ATGAATTTCTGAAAAATAAATTAATGTGAAATAAATAATAATATTTTATGAATTTTAAAAATTAA
64 ATGAATTT-TTAAAAATGAATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAA
* *
3341920 AAACCAAGAAAAATTCTCCCGAAAAAATTTACGGAGT
128 AAACCAAGAAAAATCCT-CCGAAAAAATTTACAGAGT
* ** * * *
3341957 AGAAAAATTTGTATTTCGAAAAAA-AGGAAATTTCAAGGAAAAAATTCAAAATTAATGGAAATGG
1 AGAAAACTCCGTATTTCGAAAAAAGA-G-AATTTCAAAGAAAAAATTCAAAATTTATGGAAATGA
*
3342021 ATGAATTTTTGAAAAATGAATTAATATGAAATAAATAATAATATTTGATAAATTTTAAAAATTAA
64 ATGAATTTTT-AAAAATGAATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAA
*
3342086 AAACCAAGAAAAATCCTCCTAAAAAA-TTACAGAGT
128 AAACCAAGAAAAATCCTCCGAAAAAATTTACAGAGT
*
3342121 AGAAAACTCCGTATTTCGGAAAAAAGAGAATTTGAAAGAAAAAATTCAAAATTTATGGAAATGAA
1 AGAAAACTCCGTATTTC-GAAAAAAGAGAATTTCAAAGAAAAAATTCAAAATTTATGGAAATGAA
** * *
3342186 TGAATTTTTAAAACCCGAATTAATATAAAATAAATAATAATATTTGATG-ATTTTATAAATTAAA
65 TGAATTTTTAAAA-ATGAATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAA
* * * *
3342250 AACAAAAAAAAATCCTCTCGAAAAAATTTACGGAGA
129 AACCAAGAAAAATCCTC-CGAAAAAATTTACAGAGT
3342286 AGAAAACT
1 AGAAAACT
3342294 TTGTAATTTG
Statistics
Matches: 435, Mismatches: 52, Indels: 33
0.84 0.10 0.06
Matches are distributed among these distances:
163 33 0.08
164 103 0.24
165 43 0.10
166 250 0.57
167 6 0.01
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (163 bp):
AGAAAACTCCGTATTTCGAAAAAAGAGAATTTCAAAGAAAAAATTCAAAATTTATGGAAATGAAT
GAATTTTTAAAAATGAATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAA
CCAAGAAAAATCCTCCGAAAAAATTTACAGAGT
Found at i:3343530 original size:60 final size:60
Alignment explanation
Indices: 3343369--3344102 Score: 682
Period size: 60 Copynumber: 12.2 Consensus size: 60
3343359 TAGGCAGATA
* ** * *
3343369 AGGAAATG-CTTGACCGAATACAATCAAGCGGTGTAAGATTTGATCAAGTATC-GTC-AAGTG
1 AGGAAA-GACTTGACCGAATACAGTCAAAAGGGGTAAGATTTGATCGAGTA-CAGTCGAA-TG
* * * * * * * *
3343429 AAGAAAAACTTGATCAAATACAATCGAACAA--GGTAAGATTTGACCGAGTACAATCAAATG
1 AGGAAAGACTTGACCGAATACAGTC-AA-AAGGGGTAAGATTTGATCGAGTACAGTCGAATG
* * * * *
3343489 AGGATAGTCTTGACTGAATACAAG-CAAAAGGGGTCAA-ATTTGATTGAGTATAGTCGAATG
1 AGGAAAGACTTGACCGAATAC-AGTCAAAAGGGGT-AAGATTTGATCGAGTACAGTCGAATG
* * * * *
3343549 AGGAAAGACTTAATCGAATACAATCAAGAA-GGGTAAGCTTTGATCAAGTACAGTCGAATG
1 AGGAAAGACTTGACCGAATACAGTCAA-AAGGGGTAAGATTTGATCGAGTACAGTCGAATG
* * * * *
3343609 AGGAAAGACTTGGCCCAATACAGTTAAGAGGGGTAA-ACTTTGA-CTGAGTACAATCGAATG
1 AGGAAAGACTTGACCGAATACAGTCAAAAGGGGTAAGA-TTTGATC-GAGTACAGTCGAATG
* * * * *
3343669 AGGAAAGGCTTGACCAAATATAGTAAAAAAGGGTAAGATTTGATCGAGTATC-GTCGAATG
1 AGGAAAGACTTGACCGAATACAGTCAAAAGGGGTAAGATTTGATCGAGTA-CAGTCGAATG
* * * * * *
3343729 AGGATAGACTTAACCGAATACAGTCAAGAGGGGTAAGATTTGGTCGAGTACAGTCTAATA
1 AGGAAAGACTTGACCGAATACAGTCAAAAGGGGTAAGATTTGATCGAGTACAGTCGAATG
* * * *
3343789 AGGAAAAACTTGACCGAATATAGTTAAAAGGGGTAAGCTTTGATCGAGTACAGTCGAATG
1 AGGAAAGACTTGACCGAATACAGTCAAAAGGGGTAAGATTTGATCGAGTACAGTCGAATG
* * * *
3343849 AAGAAAGACTTGACCGAATATAGTAAAAAGGGGTAGGATTTGATCGAGTACAGTCGAATG
1 AGGAAAGACTTGACCGAATACAGTCAAAAGGGGTAAGATTTGATCGAGTACAGTCGAATG
* * * * *
3343909 AAGAAAGACTTGACCGAATACAGTCAATAGGGGTAAGCTTTGA-CTAAGTACAGTCAAATG
1 AGGAAAGACTTGACCGAATACAGTCAAAAGGGGTAAGATTTGATC-GAGTACAGTCGAATG
* * * * *
3343969 AGGAAAGACTTGACTGAATACAGTCAAAAGGGGTAAGATTTGATCAAGTATAGTCAAATA
1 AGGAAAGACTTGACCGAATACAGTCAAAAGGGGTAAGATTTGATCGAGTACAGTCGAATG
* * * ** * * *
3344029 AGGATAGACTTAACCGAATACAGTCAAGAGGGGTAATTTTTGATCCAGTATAGTCGAATA
1 AGGAAAGACTTGACCGAATACAGTCAAAAGGGGTAAGATTTGATCGAGTACAGTCGAATG
*
3344089 AGGATAGACTTGAC
1 AGGAAAGACTTGAC
3344103 TAAATATAGT
Statistics
Matches: 554, Mismatches: 99, Indels: 42
0.80 0.14 0.06
Matches are distributed among these distances:
58 2 0.00
59 10 0.02
60 529 0.95
61 13 0.02
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (60 bp):
AGGAAAGACTTGACCGAATACAGTCAAAAGGGGTAAGATTTGATCGAGTACAGTCGAATG
Found at i:3343933 original size:30 final size:30
Alignment explanation
Indices: 3343540--3344055 Score: 185
Period size: 30 Copynumber: 17.2 Consensus size: 30
3343530 GATTGAGTAT
* * *
3343540 AGTCGAATGAGGAAAGACTTAATCGAATAC
1 AGTCAAATGAGGAAAGACTTGACCGAATAC
* * * *
3343570 AATCAAGAAG-GGTAAG-CTTTGATC-AAGTAC
1 AGTCAA-ATGAGGAAAGAC-TTGACCGAA-TAC
* * *
3343600 AGTCGAATGAGGAAAGACTTGGCCCAATAC
1 AGTCAAATGAGGAAAGACTTGACCGAATAC
* * * * *
3343630 AGTTAAGA-GGGGTAA-ACTTTGACTGAGTAC
1 AGTCAA-ATGAGGAAAGAC-TTGACCGAATAC
* * * * *
3343660 AATCGAATGAGGAAAGGCTTGACCAAATAT
1 AGTCAAATGAGGAAAGACTTGACCGAATAC
** * * * *
3343690 AGT-AAAAAAGGGTAAGATTTGATCGAGTATC
1 AGTCAAATGA-GGAAAGACTTGACCGAATA-C
* * *
3343721 -GTCGAATGAGGATAGACTTAACCGAATAC
1 AGTCAAATGAGGAAAGACTTGACCGAATAC
* * * ** *
3343750 AGTCAAGA-GGGGTAAGATTTGGTCGAGTAC
1 AGTCAA-ATGAGGAAAGACTTGACCGAATAC
* * * *
3343780 AGTCTAATAAGGAAAAACTTGACCGAATAT
1 AGTCAAATGAGGAAAGACTTGACCGAATAC
* * * * * *
3343810 AGTTAAAAGGGGTAAG-CTTTGATCGAGTAC
1 AGTCAAATGAGGAAAGAC-TTGACCGAATAC
* * *
3343840 AGTCGAATGAAGAAAGACTTGACCGAATAT
1 AGTCAAATGAGGAAAGACTTGACCGAATAC
* * * * * * * *
3343870 AGTAAAAAGGGGTAGGATTTGATCGAGTAC
1 AGTCAAATGAGGAAAGACTTGACCGAATAC
* *
3343900 AGTCGAATGAAGAAAGACTTGACCGAATAC
1 AGTCAAATGAGGAAAGACTTGACCGAATAC
* * *
3343930 AGTC-AATAGGGGTAAG-CTTTGA-CTAAGTAC
1 AGTCAAAT-GAGGAAAGAC-TTGACCGAA-TAC
*
3343960 AGTCAAATGAGGAAAGACTTGACTGAATAC
1 AGTCAAATGAGGAAAGACTTGACCGAATAC
* * * * * *
3343990 AGTCAAAAGGGGTAAGATTTGATC-AAGTAT
1 AGTCAAATGAGGAAAGACTTGACCGAA-TAC
* * *
3344020 AGTCAAATAAGGATAGACTTAACCGAATAC
1 AGTCAAATGAGGAAAGACTTGACCGAATAC
3344050 AGTCAA
1 AGTCAA
3344056 GAGGGGTAAT
Statistics
Matches: 328, Mismatches: 132, Indels: 52
0.64 0.26 0.10
Matches are distributed among these distances:
29 23 0.07
30 285 0.87
31 20 0.06
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (30 bp):
AGTCAAATGAGGAAAGACTTGACCGAATAC
Found at i:3352275 original size:24 final size:26
Alignment explanation
Indices: 3352248--3352296 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
3352238 TAGCTTAGTT
3352248 TTTCT-AATTTT-TCTCTTGTTTTTC
1 TTTCTCAATTTTCTCTCTTGTTTTTC
**
3352272 TTTCTCTCTTTTCTCTCTTGTTTTT
1 TTTCTCAATTTTCTCTCTTGTTTTT
3352297 AGCTGAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 4 0.19
26 12 0.57
ACGTcount: A:0.04, C:0.20, G:0.04, T:0.71
Consensus pattern (26 bp):
TTTCTCAATTTTCTCTCTTGTTTTTC
Found at i:3354971 original size:42 final size:42
Alignment explanation
Indices: 3354925--3355041 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 42
3354915 GAGAAAGAAA
* * *
3354925 AGATAAGAGGGATGATATAAGGGGAGATCAG-AGAGATAGTAG
1 AGATAAGAGGGATGATAGAAGGAGAGAT-AGAAGAGATAATAG
* *
3354967 AGATAGGAGGGATGATAGGAGGAGAGATAGAAGAGATAATAG
1 AGATAAGAGGGATGATAGAAGGAGAGATAGAAGAGATAATAG
* * * *
3355009 AGAGATGAGGGATGATAGGAGGAGA-AGAGAAGA
1 AGATAAGAGGGATGATAGAAGGAGAGATAGAAGA
3355042 AGATGGAAGA
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 9 0.14
42 57 0.86
ACGTcount: A:0.44, C:0.01, G:0.41, T:0.14
Consensus pattern (42 bp):
AGATAAGAGGGATGATAGAAGGAGAGATAGAAGAGATAATAG
Found at i:3357933 original size:26 final size:26
Alignment explanation
Indices: 3357903--3357955 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3357893 TGCTAAGTGG
3357903 GTTATTAAGCATAAGAAAGGTAAGAT
1 GTTATTAAGCATAAGAAAGGTAAGAT
3357929 GTTATTAAGCATAAGAAAGGTAAGAT
1 GTTATTAAGCATAAGAAAGGTAAGAT
3357955 G
1 G
3357956 CTAAGTGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.04, G:0.25, T:0.26
Consensus pattern (26 bp):
GTTATTAAGCATAAGAAAGGTAAGAT
Found at i:3360968 original size:85 final size:85
Alignment explanation
Indices: 3360825--3360994 Score: 340
Period size: 85 Copynumber: 2.0 Consensus size: 85
3360815 ATTTAAGCTA
3360825 TGAATCTAGCATGAATGGTTATGTGGAGATCAGCACATAGATCATTTGTAAATTCTCCTTACACT
1 TGAATCTAGCATGAATGGTTATGTGGAGATCAGCACATAGATCATTTGTAAATTCTCCTTACACT
3360890 AAGGGAAGCATTGGAAATCC
66 AAGGGAAGCATTGGAAATCC
3360910 TGAATCTAGCATGAATGGTTATGTGGAGATCAGCACATAGATCATTTGTAAATTCTCCTTACACT
1 TGAATCTAGCATGAATGGTTATGTGGAGATCAGCACATAGATCATTTGTAAATTCTCCTTACACT
3360975 AAGGGAAGCATTGGAAATCC
66 AAGGGAAGCATTGGAAATCC
3360995 AGTTAGTGCC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (85 bp):
TGAATCTAGCATGAATGGTTATGTGGAGATCAGCACATAGATCATTTGTAAATTCTCCTTACACT
AAGGGAAGCATTGGAAATCC
Found at i:3364537 original size:20 final size:20
Alignment explanation
Indices: 3364512--3364588 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
3364502 GAAAAAAGAC
3364512 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
3364532 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
3364552 TA-CATGTATCGATACAGTGA
1 -AGAATGTATCGATACATTGA
* * *
3364572 AAAATATATCAATACAT
1 AGAATGTATCGATACAT
3364589 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:3365542 original size:32 final size:33
Alignment explanation
Indices: 3365490--3365559 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 33
3365480 TTTTTTTTTA
* * *
3365490 AAAAAAATGTGCCACTAACTTGTGTGGGCTTTG
1 AAAAGAATGTGCCACCAACTTGTATGGGCTTTG
3365523 AAAAGAAT-TGCCACCAACTTGTATGGGCTTTG
1 AAAAGAATGTGCCACCAACTTGTATGGGCTTTG
3365555 AAAAG
1 AAAAG
3365560 GTATGCCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 27 0.79
33 7 0.21
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (33 bp):
AAAAGAATGTGCCACCAACTTGTATGGGCTTTG
Found at i:3365804 original size:113 final size:114
Alignment explanation
Indices: 3365512--3366012 Score: 607
Period size: 113 Copynumber: 4.4 Consensus size: 114
3365502 CACTAACTTG
* ** * *
3365512 TGTGGGCTTTGAAAAGAATTGCCACCAACTTGTATGGGCTTTGAAAAGGTATGCCATTGACTTGT
1 TGTGGGCTTTG-AAAGGA-TGCCACTGACTTG--TGGGCTTTGAAAAGG-ATGCCACTAACTTGT
* * * * * *
3365577 CGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGGAAG-GGTGCCATTGATTT
61 GGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGAGATGCCACTGA-CT
* * * *
3365631 GTGTGGGCTTTGAAAGGGTATGCCACTGACTTATGGGCTTTG-ATAGGGTGCCACTGACTTGTGG
1 -TGTGGGCTTTGAAA-GG-ATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTAACTTGTGG
* * *
3365695 GCTTTAAAAGGGTGCCATTGTCTTGTGGTCTTTTGAAGAGATGCCACTGACT
63 GCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGAGATGCCACTGACT
* *
3365747 TGTGGGCTTTGAAAGGATGCCACTGGCATGTGGGCTTTGAAAAGG-TGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTAACTTGTGGGCT
* * * **
3365811 TTGAAAGGATGCCATTGACTTGTGATCTTTTGAAGAGATGCCACTGACT
66 TTAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGAGATGCCACTGACT
3365860 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTAACTTGTGGGCT
* * *
3365924 TTAAAAGGGTGCCACTGACTTGTGGGC-TTTGAAAAGATGCCATTAACT
66 TTAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGAGATGCCACTGACT
* * *
3365972 TGTGGGCTTTGAAAGGATGCCACTAACCTATGGGCTTTGAA
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
3366013 GAGATGAACG
Statistics
Matches: 337, Mismatches: 38, Indels: 19
0.86 0.10 0.05
Matches are distributed among these distances:
112 59 0.18
113 162 0.48
114 6 0.02
115 14 0.04
116 48 0.14
117 13 0.04
118 9 0.03
119 3 0.01
120 22 0.07
121 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (114 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTAACTTGTGGGCT
TTAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGAGATGCCACTGACT
Found at i:3366018 original size:28 final size:28
Alignment explanation
Indices: 3365512--3366012 Score: 549
Period size: 28 Copynumber: 17.5 Consensus size: 28
3365502 CACTAACTTG
* **
3365512 TGTGGGCTTTGAAAAGAATTGCCACCAACT
1 TGTGGGCTTTG-AAAGGA-TGCCACTGACT
*
3365542 TGTATGGGCTTTGAAAAGGTATGCCATTGACT
1 TG--TGGGCTTTG-AAAGG-ATGCCACTGACT
* *
3365574 TGTCGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
3365602 TGTGGGCTTTGGAAGGGTGCCATTGATTT
1 TGTGGGCTTTGAAAGGATGCCACTGA-CT
3365631 GTGTGGGCTTTGAAAGGGTATGCCACTGACT
1 -TGTGGGCTTTGAAA-GG-ATGCCACTGACT
* * *
3365662 TATGGGCTTTGATAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
3365690 TGTGGGCTTTAAAAGGGTGCCATTGTCT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
3365718 TGTGGTCTTTTG-AAGAGATGCCACTGACT
1 TGTGGGC-TTTGAAAG-GATGCCACTGACT
* *
3365747 TGTGGGCTTTGAAAGGATGCCACTGGCA
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
3365775 TGTGGGCTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
3365803 TGTGGGCTTTGAAAGGATGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
**
3365831 TGTGATCTTTTG-AAGAGATGCCACTGACT
1 TGTGGGC-TTTGAAAG-GATGCCACTGACT
3365860 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
3365888 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
3365916 TGTGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
3365944 TGTGGGCTTTGAAAAGATGCCATTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
3365972 TGTGGGCTTTGAAAGGATGCCACTAACC
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
3366000 TATGGGCTTTGAA
1 TGTGGGCTTTGAA
3366013 GAGATGAACG
Statistics
Matches: 402, Mismatches: 54, Indels: 32
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.01
28 267 0.66
29 59 0.15
30 35 0.09
31 3 0.01
32 32 0.08
33 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:3367286 original size:29 final size:30
Alignment explanation
Indices: 3367253--3367329 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
3367243 CTGGACCCCT
*
3367253 TTTTTGTTTGTTTTTTTTTTTG-TTTTTGGA
1 TTTTT-TTTGTTTTTTTTTTAGTTTTTTGGA
* * *
3367283 TTTTTTTTGTTTTTTTCTTAGTTTTTTTGT
1 TTTTTTTTGTTTTTTTTTTAGTTTTTTGGA
3367313 TTTTTTTTGTTTTTTTT
1 TTTTTTTTGTTTTTTTT
3367330 ACGATGGACG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 14 0.34
30 27 0.66
ACGTcount: A:0.03, C:0.01, G:0.12, T:0.84
Consensus pattern (30 bp):
TTTTTTTTGTTTTTTTTTTAGTTTTTTGGA
Found at i:3367288 original size:20 final size:17
Alignment explanation
Indices: 3367252--3367328 Score: 75
Period size: 17 Copynumber: 4.4 Consensus size: 17
3367242 TCTGGACCCC
*
3367252 TTTTTTG-TTTGTTTTT
1 TTTTTTGTTTTTTTTTT
***
3367268 TTTTTTGTTTTTGGATT
1 TTTTTTGTTTTTTTTTT
3367285 TTTTTTGTTTTTTTCTTAGT
1 TTTTTTGTTTTTTT-TT--T
3367305 TTTTTTGTTTTTTTTTGT
1 TTTTTTGTTTTTTTTT-T
3367323 TTTTTT
1 TTTTTT
3367329 TACGATGGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
16 7 0.14
17 17 0.34
18 9 0.18
19 2 0.04
20 15 0.30
ACGTcount: A:0.03, C:0.01, G:0.12, T:0.84
Consensus pattern (17 bp):
TTTTTTGTTTTTTTTTT
Found at i:3367297 original size:41 final size:39
Alignment explanation
Indices: 3367252--3367329 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 39
3367242 TCTGGACCCC
* * * *
3367252 TTTTTTGTTTGTTTTTTTTTTTGTTTTTGGATTTTTTTTGT
1 TTTTTTCTTAGTTTTTTTGTTT-TTTTTTG-TTTTTTTTGT
3367293 TTTTTTCTTAGTTTTTTTGTTTTTTTTTGTTTTTTTT
1 TTTTTTCTTAGTTTTTTTGTTTTTTTTTGTTTTTTTT
3367330 ACGATGGACG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 8 0.24
40 6 0.18
41 19 0.58
ACGTcount: A:0.03, C:0.01, G:0.12, T:0.85
Consensus pattern (39 bp):
TTTTTTCTTAGTTTTTTTGTTTTTTTTTGTTTTTTTTGT
Found at i:3381206 original size:31 final size:31
Alignment explanation
Indices: 3381168--3381240 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
3381158 TTGAAAAATA
*
3381168 TATCGATACATCTGGGAAAAAAGACAGAATG
1 TATCGATACATCTAGGAAAAAAGACAGAATG
*
3381199 TATCGATACATTTAGGAAAAAAGACAGAATG
1 TATCGATACATCTAGGAAAAAAGACAGAATG
3381230 TATCGATACAT
1 TATCGATACAT
3381241 GTATGAATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.23
Consensus pattern (31 bp):
TATCGATACATCTAGGAAAAAAGACAGAATG
Found at i:3381250 original size:20 final size:20
Alignment explanation
Indices: 3381225--3381300 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
3381215 AAAAAAGACA
3381225 GAATGTATCGATACATGT-AT
1 GAATGTATCGATACAT-TCAT
3381245 GAATGTATCGATACATTCAT
1 GAATGTATCGATACATTCAT
* * *
3381265 -ACATGTATGGATACATTGAA
1 GA-ATGTATCGATACATTCAT
3381285 GAATGTATCGATACAT
1 GAATGTATCGATACAT
3381301 CTGGGTAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.04
20 46 0.94
21 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (20 bp):
GAATGTATCGATACATTCAT
Found at i:3382594 original size:20 final size:20
Alignment explanation
Indices: 3382549--3382606 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
3382539 TAATTATAAT
3382549 TTAAATAAA-C-AAAACTAA
1 TTAAATAAACCAAAAACTAA
*
3382567 TGTCAAATAAACCAAAAATTAA
1 T-T-AAATAAACCAAAAACTAA
*
3382589 TTAAATATAACTAAAAAC
1 TTAAATA-AACCAAAAAC
3382607 CTCTAAGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 12 0.38
21 10 0.31
22 8 0.25
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (20 bp):
TTAAATAAACCAAAAACTAA
Found at i:3385224 original size:32 final size:30
Alignment explanation
Indices: 3385188--3385246 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
3385178 GAAATCAAAT
3385188 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
3385220 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
3385247 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:3385544 original size:13 final size:13
Alignment explanation
Indices: 3385526--3385551 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3385516 AATTTTTTTG
3385526 TGTATCGATACAT
1 TGTATCGATACAT
3385539 TGTATCGATACAT
1 TGTATCGATACAT
3385552 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3385562 original size:32 final size:34
Alignment explanation
Indices: 3385505--3385569 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
3385495 TACAAGCCAA
*
3385505 TGTATCGATACAATTTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTATTTTGTGTATCGATACAT
3385539 TGTATCGATAC-A-TATTTTGTGTATCGATACA
1 TGTATCGATACAATTATTTTGTGTATCGATACA
3385570 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 18 0.60
33 1 0.03
34 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (34 bp):
TGTATCGATACAATTATTTTGTGTATCGATACAT
Found at i:3385674 original size:20 final size:20
Alignment explanation
Indices: 3385621--3385676 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
3385611 ACATCTTTTT
*
3385621 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
3385641 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
3385660 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
3385677 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:3388129 original size:13 final size:13
Alignment explanation
Indices: 3388111--3388149 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3388101 ATAATCCCCC
*
3388111 TGTATCGATACAG
1 TGTATCGATACAA
3388124 TGTATCGATACAA
1 TGTATCGATACAA
3388137 TGTATCGATACAA
1 TGTATCGATACAA
3388150 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3393761 original size:32 final size:30
Alignment explanation
Indices: 3393725--3393783 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
3393715 GAAATCAAAT
3393725 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
3393757 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
3393784 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:3394099 original size:32 final size:34
Alignment explanation
Indices: 3394044--3394106 Score: 103
Period size: 32 Copynumber: 1.9 Consensus size: 34
3394034 CAAGCCAATG
*
3394044 TATCGATACAATTTTTTTGTGTATCGATACACTC
1 TATCGATACAATTATTTTGTGTATCGATACACTC
3394078 TATCGATAC-A-TATTTTGTGTATCGATACA
1 TATCGATACAATTATTTTGTGTATCGATACA
3394107 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 18 0.64
33 1 0.04
34 9 0.32
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (34 bp):
TATCGATACAATTATTTTGTGTATCGATACACTC
Found at i:3394190 original size:20 final size:20
Alignment explanation
Indices: 3394167--3394210 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3394157 TCATGTATTA
3394167 ATACATTGCAAC-ATGTATCG
1 ATACATTG-AACTATGTATCG
* *
3394187 ATACTTTGAACTGTGTATCG
1 ATACATTGAACTATGTATCG
3394207 ATAC
1 ATAC
3394211 TTTTAAGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (20 bp):
ATACATTGAACTATGTATCG
Found at i:3395015 original size:14 final size:15
Alignment explanation
Indices: 3394992--3395028 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
3394982 TTTTAGCTTC
*
3394992 CAAGAGAAAAAAACA
1 CAAGAAAAAAAAACA
3395007 -AAG-AAAAAAAACA
1 CAAGAAAAAAAAACA
3395020 CAAGAAAAA
1 CAAGAAAAA
3395029 GGAGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 9 0.47
14 6 0.32
15 4 0.21
ACGTcount: A:0.78, C:0.11, G:0.11, T:0.00
Consensus pattern (15 bp):
CAAGAAAAAAAAACA
Found at i:3395016 original size:13 final size:14
Alignment explanation
Indices: 3394992--3395028 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
3394982 TTTTAGCTTC
3394992 CAAGAGAAAAAAACA
1 CAAGA-AAAAAAACA
3395007 -AAGAAAAAAAACA
1 CAAGAAAAAAAACA
3395020 CAAGAAAAA
1 CAAGAAAAA
3395029 GGAGAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.78, C:0.11, G:0.11, T:0.00
Consensus pattern (14 bp):
CAAGAAAAAAAACA
Found at i:3396271 original size:21 final size:20
Alignment explanation
Indices: 3396230--3396272 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
3396220 TTTTCAATAA
* *
3396230 AATAAAATAAAAATTATATG
1 AATAAAATAAAAATAAAATG
*
3396250 AATAATAATCAAAATAAAATG
1 AATAA-AATAAAAATAAAATG
3396271 AA
1 AA
3396273 CAAACATAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (20 bp):
AATAAAATAAAAATAAAATG
Found at i:3397083 original size:153 final size:152
Alignment explanation
Indices: 3396768--3397119 Score: 421
Period size: 153 Copynumber: 2.3 Consensus size: 152
3396758 CTTTGCAACA
* * * * *
3396768 CTTTT-CAAGTCC-CTTAGGATCATCAGGCACTTTTAAGTCGATAGTAGATCTTAAGGACCTTTT
1 CTTTTCCAAGTCCTC-TAGGATCATCAGGCACTTCTAAGTTGATGGTAGACCTTAAGGACCTTCT
* * * *
3396831 AGCATTTTTCTCTCAAAACCTAGTCCTATAAAACTACCAGGTCCACTTTTACGCCGAAGGTATGA
65 AGCATTTTTCTCTCAAAACCTAGCCCTATAAAACTACCAGGTCCACTTCTACACCGAAGGTATAA
*
3396896 ATTAGGAGAAGGTTTGTTTTTAT
130 ATTAGGAGAAGGTTTATTTTTAT
* *
3396919 CTTTTCCAAGTCCTCTAGGATCA-CTGAGCACTTCTAAGTTGATGGTAGACCTTAGGGACCTTCT
1 CTTTTCCAAGTCCTCTAGGATCATCAG-GCACTTCTAAGTTGATGGTAGACCTTAAGGACCTTCT
* * * *
3396983 AGC-TTTTTGCTC-CTAAAACCTAGCCCTATGAAAACTA-CTGAGTCTACTTCTATACCGCAGGT
65 AGCATTTTT-CTCTC-AAAACCTAGCCCTAT-AAAACTACCAG-GTCCACTTCTACACCGAAGGT
*
3397045 ATAAATTAGGAGTAGGTTTATTTTTAT
126 ATAAATTAGGAGAAGGTTTATTTTTAT
* *
3397072 CTTTTCCAAGTCCTCTAAGAT-ATCCAGGCACTTCTATGTTGATGGTAG
1 CTTTTCCAAGTCCTCTAGGATCAT-CAGGCACTTCTAAGTTGATGGTAG
3397120 GTCTTAGATG
Statistics
Matches: 172, Mismatches: 20, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
151 13 0.08
152 69 0.40
153 88 0.51
154 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (152 bp):
CTTTTCCAAGTCCTCTAGGATCATCAGGCACTTCTAAGTTGATGGTAGACCTTAAGGACCTTCTA
GCATTTTTCTCTCAAAACCTAGCCCTATAAAACTACCAGGTCCACTTCTACACCGAAGGTATAAA
TTAGGAGAAGGTTTATTTTTAT
Found at i:3401057 original size:13 final size:13
Alignment explanation
Indices: 3401039--3401064 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3401029 TACACCAAGT
3401039 ATGTATCGATACA
1 ATGTATCGATACA
3401052 ATGTATCGATACA
1 ATGTATCGATACA
3401065 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3401083 original size:34 final size:32
Alignment explanation
Indices: 3401021--3401085 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
3401011 TAGCCAAACT
**
3401021 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
3401053 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
3401086 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:3403322 original size:22 final size:21
Alignment explanation
Indices: 3403295--3403346 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
3403285 TTGCAAGTTG
3403295 AAATAAAAAATTTAGCTAATG-A
1 AAATAAAAAA-TTAGCTAA-GAA
**
3403317 AAATAATGAATTAGCTAAGAA
1 AAATAAAAAATTAGCTAAGAA
3403338 AAATAAAAA
1 AAATAAAAA
3403347 CTTGCATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 16 0.64
22 8 0.32
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.23
Consensus pattern (21 bp):
AAATAAAAAATTAGCTAAGAA
Found at i:3405114 original size:15 final size:15
Alignment explanation
Indices: 3405096--3405125 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3405086 CCAAATTGAG
3405096 GAAGCTCAAAATGAA
1 GAAGCTCAAAATGAA
*
3405111 GAAGCTCCAAATGAA
1 GAAGCTCAAAATGAA
3405126 ATCGATGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAGCTCAAAATGAA
Found at i:3405121 original size:16 final size:16
Alignment explanation
Indices: 3405085--3405125 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3405075 GATAAAAATG
* *
3405085 TCCAAATTGAGGAAGC
1 TCCAAAATGAAGAAGC
3405101 T-CAAAATGAAGAAGC
1 TCCAAAATGAAGAAGC
3405116 TCC-AAATGAA
1 TCCAAAATGAA
3405126 ATCGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (16 bp):
TCCAAAATGAAGAAGC
Found at i:3407196 original size:13 final size:13
Alignment explanation
Indices: 3407178--3407202 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3407168 CATCTTTCTT
3407178 TGTATCGATACAC
1 TGTATCGATACAC
3407191 TGTATCGATACA
1 TGTATCGATACA
3407203 GGGGGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:3407366 original size:20 final size:20
Alignment explanation
Indices: 3407323--3407369 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
3407313 AAATCTTTTG
3407323 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
3407344 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
3407364 CAAAAT
1 CAAAAT
3407370 CAGCCTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:3413016 original size:52 final size:50
Alignment explanation
Indices: 3412955--3413070 Score: 162
Period size: 52 Copynumber: 2.3 Consensus size: 50
3412945 ATTGTAGAAT
* *
3412955 GTATTGATACATTT-GGGTCAAAAACCTAGAATGTATCAATACAATGAATAA
1 GTATCGATACATTTGGGGTC-AAAACCCAGAATGTATCAATACAATGAA-AA
*
3413006 CGTATCGATACATTTGGGGTCAAAACCCAGAATGTATCGATACAATGAAAA
1 -GTATCGATACATTTGGGGTCAAAACCCAGAATGTATCAATACAATGAAAA
*
3413057 ATATCGATACATTT
1 GTATCGATACATTT
3413071 TCATTCCAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
50 13 0.22
51 2 0.03
52 39 0.66
53 5 0.08
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (50 bp):
GTATCGATACATTTGGGGTCAAAACCCAGAATGTATCAATACAATGAAAA
Found at i:3414189 original size:11 final size:11
Alignment explanation
Indices: 3414173--3414220 Score: 78
Period size: 11 Copynumber: 4.4 Consensus size: 11
3414163 TGGATTTTCA
3414173 AAAAAAAAAAG
1 AAAAAAAAAAG
3414184 AAAAAAAAAAG
1 AAAAAAAAAAG
* *
3414195 AAAAAATAAGG
1 AAAAAAAAAAG
3414206 AAAAAAAAAAG
1 AAAAAAAAAAG
3414217 AAAA
1 AAAA
3414221 TTTAATTGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:3415146 original size:75 final size:75
Alignment explanation
Indices: 3415054--3415200 Score: 233
Period size: 75 Copynumber: 2.0 Consensus size: 75
3415044 ATCCTCCAGC
* ** *
3415054 TTATTTTTAGTTTGTTTT-AGTTGTTGATAAAATTGTAAAAACAACATATTCCCTATCATGTTCT
1 TTATTTTTAGTTTGTTTTGA-TTGTTAATAAAATAATAAAAACAACATATTCCCCATCATGTTCT
3415118 TCTTTTTTCGA
65 TCTTTTTTCGA
*
3415129 TTATTTTTAGTTTGTTTTGATTGTTAATAAAATAATAAAAATAACATATTCCCCATCATGTTCTT
1 TTATTTTTAGTTTGTTTTGATTGTTAATAAAATAATAAAAACAACATATTCCCCATCATGTTCTT
3415194 CTTTTTT
66 CTTTTTT
3415201 AGGCTGTTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
75 65 0.98
76 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.51
Consensus pattern (75 bp):
TTATTTTTAGTTTGTTTTGATTGTTAATAAAATAATAAAAACAACATATTCCCCATCATGTTCTT
CTTTTTTCGA
Found at i:3415219 original size:75 final size:75
Alignment explanation
Indices: 3415065--3415220 Score: 188
Period size: 75 Copynumber: 2.1 Consensus size: 75
3415055 TATTTTTAGT
* ** * * *
3415065 TTGTTTTAGTTGTTGATAAAATTGTAAAAACAACATATTCCCTATCATGTTCTTCTTTTTTCGAT
1 TTGTTTTAGTTGTTAATAAAATAATAAAAACAACATATTCCCCATCATGTTCTTCTTTTTTAGAC
* **
3415130 TATTTTTAGT
66 TATTATTAAC
* *
3415140 TTGTTTT-GATTGTTAATAAAATAATAAAAATAACATATTCCCCATCATGTTCTTCTTTTTTAGG
1 TTGTTTTAG-TTGTTAATAAAATAATAAAAACAACATATTCCCCATCATGTTCTTCTTTTTTAGA
*
3415204 CTGTTATTAAC
65 CTATTATTAAC
3415215 TTGTTT
1 TTGTTT
3415221 CAACTATTGA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
74 1 0.01
75 67 0.99
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.49
Consensus pattern (75 bp):
TTGTTTTAGTTGTTAATAAAATAATAAAAACAACATATTCCCCATCATGTTCTTCTTTTTTAGAC
TATTATTAAC
Found at i:3416261 original size:45 final size:45
Alignment explanation
Indices: 3416211--3416399 Score: 152
Period size: 45 Copynumber: 4.2 Consensus size: 45
3416201 GTTAGTCCGT
* * *
3416211 GTCAAATTC-CTTTCATATCTCATTTGATGTAATGGTTTAGCCCCA
1 GTCAAACTCACTTTCATAT-TCATTTGACGTGATGGTTTAGCCCCA
* * * * ***
3416256 GTCAAACTCATTTTCATCTTCGTTTGAAGTGATGGTTTAGCCTTG
1 GTCAAACTCACTTTCATATTCATTTGACGTGATGGTTTAGCCCCA
* **
3416301 GTCAAATTC-CTTTCATATCTTGTTTGACGTGATGGTTTA-CCCTC-
1 GTCAAACTCACTTTCATAT-TCATTTGACGTGATGGTTTAGCCC-CA
** * * *
3416345 GATCAAACTCTTTTTCATCTTCATTTGACATGATGGTTTAGCCCTA
1 G-TCAAACTCACTTTCATATTCATTTGACGTGATGGTTTAGCCCCA
3416391 GTCAAACTC
1 GTCAAACTC
3416400 TTTCTCATAT
Statistics
Matches: 114, Mismatches: 23, Indels: 14
0.75 0.15 0.09
Matches are distributed among these distances:
44 10 0.09
45 86 0.75
46 18 0.16
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (45 bp):
GTCAAACTCACTTTCATATTCATTTGACGTGATGGTTTAGCCCCA
Found at i:3416314 original size:90 final size:90
Alignment explanation
Indices: 3416211--3416396 Score: 252
Period size: 90 Copynumber: 2.1 Consensus size: 90
3416201 GTTAGTCCGT
*
3416211 GTCAAATTCCTTTCATATCTCATTTGATGTAATGGTTTAGCCC-C-AGTCAAACTCATTTTCATC
1 GTCAAATTCCTTTCATATCTCATTTGACGTAATGGTTTA-CCCTCGA-TCAAACTCATTTTCATC
* * *
3416274 TTCGTTTGA-AGTGATGGTTTAGCCTTG
64 TTCATTTGACA-TGATGGTTTAGCCCTA
** * *
3416301 GTCAAATTCCTTTCATATCTTGTTTGACGTGATGGTTTACCCTCGATCAAACTCTTTTTCATCTT
1 GTCAAATTCCTTTCATATCTCATTTGACGTAATGGTTTACCCTCGATCAAACTCATTTTCATCTT
3416366 CATTTGACATGATGGTTTAGCCCTA
66 CATTTGACATGATGGTTTAGCCCTA
3416391 GTCAAA
1 GTCAAA
3416397 CTCTTTCTCA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
89 3 0.04
90 80 0.94
91 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.41
Consensus pattern (90 bp):
GTCAAATTCCTTTCATATCTCATTTGACGTAATGGTTTACCCTCGATCAAACTCATTTTCATCTT
CATTTGACATGATGGTTTAGCCCTA
Found at i:3416400 original size:45 final size:45
Alignment explanation
Indices: 3416242--3416445 Score: 182
Period size: 45 Copynumber: 4.5 Consensus size: 45
3416232 ATTTGATGTA
* *
3416242 ATGGTTTAGCCCCAGTCAAACTCATTTTCATCTTCGTTTGA-AGTG
1 ATGGTTTAGCCCTAGTCAAACTCTTTTTCATCTTCGTTTGACA-TG
* * * * *
3416287 ATGGTTTAGCCTTGGTCAAATTC-CTTTCATATCTT-GTTTGACGTG
1 ATGGTTTAGCCCTAGTCAAACTCTTTTTC--ATCTTCGTTTGACATG
* *
3416332 ATGGTTTA-CCCTCGATCAAACTCTTTTTCATCTTCATTTGACATG
1 ATGGTTTAGCCCTAG-TCAAACTCTTTTTCATCTTCGTTTGACATG
* * * * *
3416377 ATGGTTTAGCCCTAGTCAAACTCTTTCTCATATTAGTTTAACATA
1 ATGGTTTAGCCCTAGTCAAACTCTTTTTCATCTTCGTTTGACATG
* * *
3416422 AAGGTTTAGAACCTGGTCAAACTC
1 ATGGTTTAG-CCCTAGTCAAACTC
3416446 GATGCGTCTA
Statistics
Matches: 129, Mismatches: 22, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
44 13 0.10
45 90 0.70
46 26 0.20
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (45 bp):
ATGGTTTAGCCCTAGTCAAACTCTTTTTCATCTTCGTTTGACATG
Found at i:3416428 original size:90 final size:90
Alignment explanation
Indices: 3416257--3416429 Score: 215
Period size: 90 Copynumber: 1.9 Consensus size: 90
3416247 TTAGCCCCAG
* * * * *
3416257 TCAAACTCATTTTCATCTTCGTTTGAAGTGATGGTTTAGCCTTGGTCAAATTCCTTTCATATCTT
1 TCAAACTCATTTTCATCTTCATTTGAAGTGATGGTTTAGCCCTAGTCAAACTCCTTTCATATCTA
* * * *
3416322 GTTTGACGTGATGGTTTACCCTCGA
66 GTTTAACATAAAGGTTTACCCTCGA
* *
3416347 TCAAACTCTTTTTCATCTTCATTTGACA-TGATGGTTTAGCCCTAGTCAAACTCTTTCTCATAT-
1 TCAAACTCATTTTCATCTTCATTTGA-AGTGATGGTTTAGCCCTAGTCAAACTCCTT-TCATATC
3416410 TAGTTTAACATAAAGGTTTA
64 TAGTTTAACATAAAGGTTTA
3416430 GAACCTGGTC
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
90 63 0.90
91 7 0.10
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (90 bp):
TCAAACTCATTTTCATCTTCATTTGAAGTGATGGTTTAGCCCTAGTCAAACTCCTTTCATATCTA
GTTTAACATAAAGGTTTACCCTCGA
Found at i:3418335 original size:13 final size:13
Alignment explanation
Indices: 3418312--3418352 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
3418302 AGCTTCCAAG
3418312 AGAAA-AAAAAAA
1 AGAAAGAAAAAAA
3418324 AGAAAGAAAAAAA
1 AGAAAGAAAAAAA
3418337 A-ACAAGAAAAAAA
1 AGA-AAGAAAAAAA
3418350 AGA
1 AGA
3418353 GAAAAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.23
13 19 0.73
14 1 0.04
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAAAAA
Found at i:3422570 original size:23 final size:23
Alignment explanation
Indices: 3422538--3422581 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3422528 GTATTCAACC
*
3422538 TTGGGTTATAATCTCTT-AAGAAT
1 TTGGGGTATAAT-TCTTGAAGAAT
3422561 TTGGGGTATAATTCTTGAAGA
1 TTGGGGTATAATTCTTGAAGA
3422582 GATTGAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (23 bp):
TTGGGGTATAATTCTTGAAGAAT
Found at i:3423721 original size:13 final size:13
Alignment explanation
Indices: 3423703--3423729 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3423693 TACAATGAGC
3423703 ATGTATCGATACA
1 ATGTATCGATACA
3423716 ATGTATCGATACA
1 ATGTATCGATACA
3423729 A
1 A
3423730 GGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3424851 original size:9 final size:9
Alignment explanation
Indices: 3424837--3424875 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
3424827 TCAACCATCA
3424837 AAGATGATG
1 AAGATGATG
3424846 AAGATGATG
1 AAGATGATG
*
3424855 ATGATGATG
1 AAGATGATG
3424864 ATA-ATGATG
1 A-AGATGATG
3424873 AAG
1 AAG
3424876 TTGACTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 1 0.04
9 25 0.96
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.26
Consensus pattern (9 bp):
AAGATGATG
Found at i:3424854 original size:3 final size:3
Alignment explanation
Indices: 3424839--3424873 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
3424829 AACCATCAAA
* *
3424839 GAT GAT GAA GAT GAT GAT GAT GAT GAT AAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
3424874 AGTTGACTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:3431981 original size:13 final size:13
Alignment explanation
Indices: 3431963--3431988 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3431953 ACATTATGCT
3431963 TTGTATCGATACA
1 TTGTATCGATACA
3431976 TTGTATCGATACA
1 TTGTATCGATACA
3431989 CACTTAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3432542 original size:25 final size:25
Alignment explanation
Indices: 3432514--3432567 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
3432504 TGAAGAAATT
3432514 AAGAGATTCTTATCTTAGCCTTGAA
1 AAGAGATTCTTATCTTAGCCTTGAA
3432539 AAGAGATTCTTATCTTAGCCTTGAA
1 AAGAGATTCTTATCTTAGCCTTGAA
3432564 AAGA
1 AAGA
3432568 TAAGTGTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (25 bp):
AAGAGATTCTTATCTTAGCCTTGAA
Found at i:3433517 original size:2 final size:2
Alignment explanation
Indices: 3433510--3433548 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3433500 TAGGTTATTT
3433510 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3433549 CATTCTCACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3434236 original size:3 final size:3
Alignment explanation
Indices: 3434228--3434258 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3434218 TCAATGGAAA
*
3434228 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3434259 TGTTACTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3436997 original size:13 final size:14
Alignment explanation
Indices: 3436974--3437003 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3436964 GGTCATATAT
3436974 TTAATTATTTTTAA
1 TTAATTATTTTTAA
3436988 TTAA-TATTTTTAA
1 TTAATTATTTTTAA
3437001 TTA
1 TTA
3437004 GTTTATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTAATTATTTTTAA
Found at i:3437446 original size:21 final size:21
Alignment explanation
Indices: 3437420--3437474 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
3437410 TCAAACAATT
*
3437420 TGTATCGATACAAAC-AGTAAC
1 TGTATCGATACAAACTAG-AAA
**
3437441 TGTATCGATACATTCTAGAAA
1 TGTATCGATACAAACTAGAAA
3437462 TGTATCGATACAA
1 TGTATCGATACAA
3437475 TGTATCGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (21 bp):
TGTATCGATACAAACTAGAAA
Found at i:3437478 original size:13 final size:13
Alignment explanation
Indices: 3437460--3437486 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3437450 ACATTCTAGA
3437460 AATGTATCGATAC
1 AATGTATCGATAC
3437473 AATGTATCGATAC
1 AATGTATCGATAC
3437486 A
1 A
3437487 TAAGTTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:3440678 original size:13 final size:13
Alignment explanation
Indices: 3440660--3440685 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3440650 CAATTTTTTG
3440660 TGTATCGATACAT
1 TGTATCGATACAT
3440673 TGTATCGATACAT
1 TGTATCGATACAT
3440686 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3440697 original size:32 final size:33
Alignment explanation
Indices: 3440640--3440703 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3440630 TACAAGCCAA
**
3440640 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
3440673 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
3440704 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:3440780 original size:20 final size:19
Alignment explanation
Indices: 3440755--3440813 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
3440745 ACATCTTTTT
3440755 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTG-AA
*
3440775 CATGTATCGATACTTTGAA
1 CATGTATCGATACATTGAA
* *
3440794 CTGTGTATCGATACTTTGAA
1 C-ATGTATCGATACATTGAA
3440814 GGGTTTTGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 3 0.08
20 33 0.92
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (19 bp):
CATGTATCGATACATTGAA
Found at i:3443248 original size:13 final size:13
Alignment explanation
Indices: 3443230--3443267 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
3443220 ATAATCCCCC
3443230 TGTATCGATACAG
1 TGTATCGATACAG
*
3443243 TGTATCGATACAT
1 TGTATCGATACAG
3443256 TGTATCGATACA
1 TGTATCGATACA
3443268 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:3445380 original size:15 final size:15
Alignment explanation
Indices: 3445344--3445381 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3445334 TTCATCAATT
* *
3445344 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
3445359 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
3445374 TCATTTTG
1 TCATTTTG
3445382 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:3449459 original size:13 final size:13
Alignment explanation
Indices: 3449441--3449466 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3449431 CAATTTTTTG
3449441 TGTATCGATACAT
1 TGTATCGATACAT
3449454 TGTATCGATACAT
1 TGTATCGATACAT
3449467 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3449478 original size:32 final size:33
Alignment explanation
Indices: 3449421--3449484 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3449411 TACAAGCCAA
**
3449421 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
3449454 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
3449485 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:3449568 original size:20 final size:20
Alignment explanation
Indices: 3449514--3449570 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
3449504 AATCCCAATG
*
3449514 ACATGTATCGATACATTGCA
1 ACATGTATCGATACTTTGCA
3449534 ACATGTATCGATACTTTG-A
1 ACATGTATCGATACTTTGCA
*
3449553 ACTGTGTATCGATACTTT
1 AC-ATGTATCGATACTTT
3449571 TAAGGGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 31 0.91
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (20 bp):
ACATGTATCGATACTTTGCA
Found at i:3451029 original size:79 final size:79
Alignment explanation
Indices: 3450932--3451185 Score: 321
Period size: 79 Copynumber: 3.2 Consensus size: 79
3450922 TCAATTTTTC
* * *
3450932 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTGGCTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
*
3450997 ATTAATTTCTCATA
66 ATGAATTTCTCATA
* * * ** *
3451011 ATCGGGAATACTCTAACCCCATTATTTTTGAAGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
*
3451076 ATGAATTTTTCATA
66 ATGAATTTCTCATA
* * * *
3451090 ATCGGGGGTACTCCCATCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
** *
3451155 ACCAA-TTCTCCACA
66 ATGAATTTCT-CATA
*
3451169 ATCGGGGATACTTCAAC
1 ATCGGGGATACTCCAAC
3451186 TCCGATTTTA
Statistics
Matches: 145, Mismatches: 29, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
78 3 0.02
79 142 0.98
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
ATGAATTTCTCATA
Found at i:3451197 original size:51 final size:51
Alignment explanation
Indices: 3451121--3451240 Score: 170
Period size: 51 Copynumber: 2.4 Consensus size: 51
3451111 TTATTTCCGA
*
3451121 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAA-TTCTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCT-CACAATC
* * **
3451172 GGGGATACTTCAACTCCGATTTTATTTCCAAAACACTGATTTCTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
*
3451223 GAGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
3451241 TTATTTAATC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 56 0.93
52 4 0.07
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
Found at i:3451250 original size:158 final size:158
Alignment explanation
Indices: 3451088--3451426 Score: 423
Period size: 158 Copynumber: 2.1 Consensus size: 158
3451078 GAATTTTTCA
* * * * *
3451088 TAATCGGGGGTACTCCCATCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTA-TTTCTAA
1 TAATCGAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTTC-AA
* * **
3451152 AACACCAA-TTCTCCACAATCGGGGATACTTCAACTCCGATTTTATTTCCAAAACACTGATTTCT
65 AACACCAATTTCT-CACAATCGGGGATACTTCAACCCCAACCTTATTTCCAAAACACTGATTTCT
*
3451216 CACAATCGAGGATACTCCAACCCCGTTATT
129 CACAATCGAGGATACTCCAACCCCATTATT
*
3451246 TAATCGAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTTCAAA
1 TAATCGAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTTCAAA
* *** * * *
3451311 ATATTGATTTCTCACAATCGGGGATACTTCAACCCCAACCTTATTTCTAAAATATTGATTTCTCA
66 ACACCAATTTCTCACAATCGGGGATACTTCAACCCCAACCTTATTTCCAAAACACTGATTTCTCA
* *
3451376 TAATCGGGGATACTCCAACCCCATTATTT
131 CAATCGAGGATACTCCAACCCCATTA-TT
* * *
3451405 TCA-CAAGGATACTCCAATCCCG
1 TAATCGAGGATACTCCAACCCCG
3451427 ATTTTATTTT
Statistics
Matches: 155, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
158 143 0.92
159 12 0.08
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (158 bp):
TAATCGAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTTCAAA
ACACCAATTTCTCACAATCGGGGATACTTCAACCCCAACCTTATTTCCAAAACACTGATTTCTCA
CAATCGAGGATACTCCAACCCCATTATT
Found at i:3451259 original size:28 final size:28
Alignment explanation
Indices: 3451219--3451296 Score: 115
Period size: 28 Copynumber: 2.8 Consensus size: 28
3451209 GATTTCTCAC
3451219 AATCGAGGATACTCCAACCCCGTTATTT
1 AATCGAGGATACTCCAACCCCGTTATTT
3451247 AATCGAGGATACTCCAACCCCGTTATTT
1 AATCGAGGATACTCCAACCCCGTTATTT
*
3451275 --CCGAGGGGATACTCCAACCCCG
1 AATCGA--GGATACTCCAACCCCG
3451297 GCTTTATTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 3 0.06
28 44 0.94
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (28 bp):
AATCGAGGATACTCCAACCCCGTTATTT
Found at i:3451346 original size:51 final size:51
Alignment explanation
Indices: 3451279--3451398 Score: 179
Period size: 51 Copynumber: 2.4 Consensus size: 51
3451269 TTATTTCCGA
** *
3451279 GGGGATACTCCAACCCCGGCTTTATTT-TCAAAATATTGATTTCTCACAATC
1 GGGGATACTCCAACCCCAACCTTATTTCT-AAAATATTGATTTCTCACAATC
* *
3451330 GGGGATACTTCAACCCCAACCTTATTTCTAAAATATTGATTTCTCATAATC
1 GGGGATACTCCAACCCCAACCTTATTTCTAAAATATTGATTTCTCACAATC
3451381 GGGGATACTCCAACCCCA
1 GGGGATACTCCAACCCCA
3451399 TTATTTTCAC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
51 61 0.98
52 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAACCTTATTTCTAAAATATTGATTTCTCACAATC
Found at i:3451493 original size:130 final size:130
Alignment explanation
Indices: 3451246--3451496 Score: 276
Period size: 130 Copynumber: 1.9 Consensus size: 130
3451236 CCCCGTTATT
* * *
3451246 TAATCGAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTTCAAA
1 TAATCGAGGATACTCCAACCCCATTATTTCCGAGAGGATACTCCAACCCCGACTTTATTTTCAAA
* * * * *
3451311 ATATTGATTTCTCACAATCGGGGATACTTCAACCCCAACCTTATTTCTAAAATATTGATTTCTCA
66 ACATCGATTTCTCACAATCGGGGATACTCCAACCCCAACCTTATCTCCAAAATATTGATTTCTCA
* * * *
3451376 TAATCGGGGATACTCCAACCCCATTATTTTCAC-A-AGGATACTCCAATCCCGATTTTATTTTTA
1 TAATCGAGGATACTCCAACCCCATTA-TTTC-CGAGAGGATACTCCAACCCCGACTTTATTTTCA
* * ****
3451439 AAACATCGATTT-TCCATAATCGATGG-TACTCCAACCCCGTTGTTATCTCCAAAATATT
64 AAACATCGATTTCT-CACAATCG-GGGATACTCCAACCCCAACCTTATCTCCAAAATATT
3451497 AAATTTTTCA
Statistics
Matches: 99, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
129 1 0.01
130 90 0.91
131 7 0.07
132 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (130 bp):
TAATCGAGGATACTCCAACCCCATTATTTCCGAGAGGATACTCCAACCCCGACTTTATTTTCAAA
ACATCGATTTCTCACAATCGGGGATACTCCAACCCCAACCTTATCTCCAAAATATTGATTTCTCA
Found at i:3453895 original size:16 final size:16
Alignment explanation
Indices: 3453870--3453900 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3453860 TTTTTTTCTC
3453870 TCTTTATAATCAATTT
1 TCTTTATAATCAATTT
*
3453886 TCTTTTTAATCAATT
1 TCTTTATAATCAATT
3453901 GATTGATTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (16 bp):
TCTTTATAATCAATTT
Found at i:3455888 original size:52 final size:52
Alignment explanation
Indices: 3455788--3455888 Score: 114
Period size: 52 Copynumber: 1.9 Consensus size: 52
3455778 ATAGATTTCC
** * * * * *
3455788 AAATGTATCAATACAATTTGCTTTGTATCGATACTTTCTGGGTTTTTTATCT
1 AAATGTATCAATACAATTTGCAATGTATCGATACATGCAGGCTATTTTATCT
*
3455840 AAATGTATCAATAC-ATTCTTCAATGTATCGATACATGCAGGCTATTTTA
1 AAATGTATCAATACAATT-TGCAATGTATCGATACATGCAGGCTATTTTA
3455889 CATATTTTGC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
51 3 0.08
52 37 0.93
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (52 bp):
AAATGTATCAATACAATTTGCAATGTATCGATACATGCAGGCTATTTTATCT
Found at i:3462690 original size:19 final size:20
Alignment explanation
Indices: 3462645--3462698 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
3462635 CTGCCAGTTT
*
3462645 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAA
*
3462665 TATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
3462684 CATGTATCGATACAA
1 CATGTATCGATACAA
3462699 AGCATAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:3465048 original size:42 final size:44
Alignment explanation
Indices: 3465001--3465095 Score: 124
Period size: 42 Copynumber: 2.2 Consensus size: 44
3464991 CTCACTTTTA
3465001 ATTGATACATT-ACTATACAATATCGATACATCACTCTACA-GT
1 ATTGATACATTCACTATACAATATCGATACATCACTCTACATGT
* * * * *
3465043 ATTGATAC-TTCACTGTACAGTGTCGATACATCACTGTTCATGT
1 ATTGATACATTCACTATACAATATCGATACATCACTCTACATGT
3465086 ATTGATACAT
1 ATTGATACAT
3465096 GTGAATAGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
41 2 0.04
42 32 0.71
43 10 0.22
44 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (44 bp):
ATTGATACATTCACTATACAATATCGATACATCACTCTACATGT
Found at i:3465076 original size:21 final size:21
Alignment explanation
Indices: 3465004--3465095 Score: 94
Period size: 21 Copynumber: 4.3 Consensus size: 21
3464994 ACTTTTAATT
* * *
3465004 GATACATTACTATACAATATC
1 GATACATCACTGTACAGTATC
* *
3465025 GATACATCACTCTACAGTATT
1 GATACATCACTGTACAGTATC
* *
3465046 GATACTTCACTGTACAGTGTC
1 GATACATCACTGTACAGTATC
* *
3465067 GATACATCACTGTTCATGTATT
1 GATACATCACTGTACA-GTATC
3465089 GATACAT
1 GATACAT
3465096 GTGAATAGTA
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
21 48 0.83
22 10 0.17
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (21 bp):
GATACATCACTGTACAGTATC
Found at i:3465589 original size:36 final size:32
Alignment explanation
Indices: 3465544--3465636 Score: 109
Period size: 36 Copynumber: 2.8 Consensus size: 32
3465534 CTAAGTAATT
3465544 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGGGA
1 GAGAGGTTCTATCTTAGCC-TTGAAAAAGATA---A
*
3465580 GAGAGGTTCTATCTTAGCCCATG-AAAAGATAA
1 GAGAGGTTCTATCTTAG-CCTTGAAAAAGATAA
3465612 G-GAGGTTTCTATCTTAGCCTTGAAA
1 GAGAGG-TTCTATCTTAGCCTTGAAA
3465637 GATAGTGTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
31 8 0.15
32 15 0.29
35 8 0.15
36 19 0.37
37 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (32 bp):
GAGAGGTTCTATCTTAGCCTTGAAAAAGATAA
Found at i:3466362 original size:6 final size:6
Alignment explanation
Indices: 3466351--3466387 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
3466341 TATTATTATA
*
3466351 TACATT TACATT TACATT TACATT TACAGT T-CATT TA
1 TACATT TACATT TACATT TACATT TACATT TACATT TA
3466388 TGATAGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (6 bp):
TACATT
Found at i:3469605 original size:20 final size:20
Alignment explanation
Indices: 3469582--3469655 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
3469572 ACAATTCAAA
3469582 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3469602 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3469623 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3469643 GTATCGATACATG
1 GTATCGATACATG
3469656 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3469626 original size:21 final size:21
Alignment explanation
Indices: 3469600--3469675 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
3469590 ACATGTTGCA
3469600 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3469621 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
3469641 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
3469662 ATGTATCGATACAT
1 ATGTATCGATACAT
3469676 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3469633 original size:41 final size:41
Alignment explanation
Indices: 3469582--3469675 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
3469572 ACAATTCAAA
3469582 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
3469623 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
3469664 GTATCGATACAT
1 GTATCGATACAT
3469676 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:3469732 original size:13 final size:13
Alignment explanation
Indices: 3469714--3469739 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3469704 TACAGCAAGT
3469714 ATGTATCGATACA
1 ATGTATCGATACA
3469727 ATGTATCGATACA
1 ATGTATCGATACA
3469740 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3471981 original size:21 final size:21
Alignment explanation
Indices: 3471948--3471992 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3471938 TTGCAAGTTG
*
3471948 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3471970 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3471990 AAA
1 AAA
3471993 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3475920 original size:20 final size:21
Alignment explanation
Indices: 3475841--3475919 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
3475831 AATGTCCAAA
*
3475841 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
3475861 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
3475886 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
3475906 TTGTATCGATACAT
1 ATGTATCGATACAT
3475920 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:3475924 original size:13 final size:13
Alignment explanation
Indices: 3475906--3475944 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3475896 ACATTTTTCT
3475906 TTGTATCGATACA
1 TTGTATCGATACA
3475919 TTGTATCGATACA
1 TTGTATCGATACA
*
3475932 CTGTATCGATACA
1 TTGTATCGATACA
3475945 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3478420 original size:20 final size:20
Alignment explanation
Indices: 3478397--3478470 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
3478387 ACAATTCAAA
3478397 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3478417 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3478438 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3478458 GTATCGATACATG
1 GTATCGATACATG
3478471 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3478441 original size:21 final size:21
Alignment explanation
Indices: 3478415--3478490 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
3478405 ACATGTTGCA
3478415 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3478436 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
3478456 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
3478477 ATGTATCGATACAT
1 ATGTATCGATACAT
3478491 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3478448 original size:41 final size:41
Alignment explanation
Indices: 3478397--3478490 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
3478387 ACAATTCAAA
3478397 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
3478438 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
3478479 GTATCGATACAT
1 GTATCGATACAT
3478491 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:3479495 original size:13 final size:13
Alignment explanation
Indices: 3479477--3479502 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3479467 CAATTTTTTG
3479477 TGTATCGATACAT
1 TGTATCGATACAT
3479490 TGTATCGATACAT
1 TGTATCGATACAT
3479503 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3480620 original size:80 final size:79
Alignment explanation
Indices: 3480445--3480885 Score: 313
Period size: 79 Copynumber: 5.5 Consensus size: 79
3480435 TATCCCTTGA
* * ** * *
3480445 TGAAAAATTTGATATTTTGGAGATAAAATTGGGGTTGGAGTATCCCCTAAAAAATAGC-AGGGTT
1 TGAAAAA-TTGATATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACGA-GGTT
*
3480509 GGAGTATCCTCGAA---
64 GGAGTATCC-CTAATGG
** * * * ** * *
3480523 ACAAAAATTTTAATATTTTAAAAATAAAAACAAGGTTGGAGTATCCTCTCAAAAAATAATGAGGT
1 TGAAAAA--TTGATATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCTC-AAAAATAACGAGGT
*
3480588 TGGAGTATCCCTGA-GAG
63 TGGAGTATCCCTAATG-G
* * * *
3480605 TGGAAAATTGATATTTTGAAGATAAAACCGGGGTTGGAGTATCCCCTCAGAACTAACGAGGTTGG
1 TGAAAAATTGATATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGG
3480670 AGTATCCCTAATGG
66 AGTATCCCTAATGG
* * *** * * *
3480684 TGAAAAATTGATATTTTGAAAATTAAACCGGGGTTGGAGTATCCCTTTGGAAATAATGGGGTTAG
1 TGAAAAATTGATATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGG
*
3480749 AGTATCCCCAATGG
66 AGTATCCCTAATGG
** * * * * * *
3480763 TGAAAAATCAATATTTT-AGAAATAAAACCTGGATTGGAGTATTCCTTCAGAAATAA-TAGGGTT
1 TGAAAAATTGATATTTTGA-AAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACGA-GGTT
* *
3480826 AGAGTAT-CTTCAATGG
64 GGAGTATCCCT-AATGG
* * ** *
3480842 TGAAAAAAATTAATATTTTGGAAATAAAACTAGGATTGGAGTAT
1 TG--AAAAATTGATATTTTGAAAATAAAACCGGGGTTGGAGTAT
3480886 TCCATTTTGA
Statistics
Matches: 293, Mismatches: 57, Indels: 23
0.79 0.15 0.06
Matches are distributed among these distances:
78 7 0.02
79 191 0.65
80 55 0.19
81 36 0.12
82 4 0.01
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (79 bp):
TGAAAAATTGATATTTTGAAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACGAGGTTGG
AGTATCCCTAATGG
Found at i:3482528 original size:20 final size:21
Alignment explanation
Indices: 3482503--3482554 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3482493 TTTTAGGCAG
3482503 GTATCGATACATTCACT-TAT
1 GTATCGATACATTCACTGTAT
* * *
3482523 GTATCGATGCATTTACTGTTT
1 GTATCGATACATTCACTGTAT
*
3482544 GTATTGATACA
1 GTATCGATACA
3482555 AATTGTAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (21 bp):
GTATCGATACATTCACTGTAT
Found at i:3484089 original size:13 final size:13
Alignment explanation
Indices: 3484071--3484095 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3484061 TTTCACTACG
3484071 TATCGATACAATA
1 TATCGATACAATA
3484084 TATCGATACAAT
1 TATCGATACAAT
3484096 GTACCATGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:3485106 original size:13 final size:13
Alignment explanation
Indices: 3485088--3485114 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3485078 ACAATTGAGT
3485088 ATGTATCGATACA
1 ATGTATCGATACA
3485101 ATGTATCGATACA
1 ATGTATCGATACA
3485114 A
1 A
3485115 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3493904 original size:13 final size:13
Alignment explanation
Indices: 3493886--3493912 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3493876 TACAATGAAC
3493886 ATGTATCGATACA
1 ATGTATCGATACA
3493899 ATGTATCGATACA
1 ATGTATCGATACA
3493912 A
1 A
3493913 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3494475 original size:275 final size:273
Alignment explanation
Indices: 3493947--3494496 Score: 670
Period size: 275 Copynumber: 2.0 Consensus size: 273
3493937 ATGTGTATCG
*
3493947 ATACTTTCTAGGGTTTTAACTGTTGTAGCCTAAGTCAACCTTAATGTATCGATACAAATACTTAT
1 ATACTTTCTAGGGTTTTAACTGTTGTAGCCTAAGTCAACCTTAATGTATCGATACAAATACCTAT
* *
3494012 GTATTAATACTTTAGATTATTTTTACTTGAAAACATTCGATTTAAGGTTTGAAAATACTTATATA
66 GTATCAATACTTTAGATTATTTTTACTTGAAAACATTCGATTTAAGGCTTGAAAATACTTATATA
* *
3494077 AAACTATAAAATATTATTGATATTGAAAATATCTTAGAACAAGGTTTTAGAGTATTTTTAAATGA
131 AAACTATAAAACATTATTGATATTAAAAATATCTTAGAACAAGGTTTTAGAGTATTTTTAAATGA
* * * * *
3494142 TTAAAACTTGTTTACGGTTTTTGAAATCTCTTTTCAGTTCTATTCGTAGTTTGTTATATCAAAAC
196 ATAAAACTTGTTTACGGTTTTTGAAAGCTATTTTCAGTTCTATTCATACTTTGTTATATCAAAAC
*
3494207 CAAGATCTTAACA
261 CAAGATCCTAACA
* * *
3494220 ATACTTTCTAGGGTTTTGACCT-TTGTAGCTTAAGTCAACCTTCTATGTATCGATACAAATACCT
1 ATACTTTCTAGGGTTTT-AACTGTTGTAGCCTAAGTCAACCTT-AATGTATCGATACAAATACCT
* *
3494284 ATGTATCGATACTTTA-AGTTATTTTTTACTTGAAAACATAT-GATTTCTA-GCTTGAAAA-ACA
64 ATGTATCAATACTTTAGA-TTA-TTTTTACTTGAAAACAT-TCGATTT-AAGGCTTGAAAATAC-
* * * ** *
3494345 TT-TATACTTAACTCTAAAACATCT-TTGATATTAAAAATCAT-TTTGAGTAAGGTTTTAGAGTG
124 TTATATA--AAACTATAAAACAT-TATTGATATTAAAAAT-ATCTTAGAACAAGGTTTTAGAGTA
* * * * * *
3494407 TTTTTAAGTGAATAAAACTTG-TTATGGTTTTT-CAAGGTATTTTCTAGTTTTATTCATTCTTTG
185 TTTTTAAATGAATAAAACTTGTTTACGGTTTTTGAAAGCTATTTTC-AGTTCTATTCATACTTTG
3494470 TTATATCAAAACCAAGATCCTAACA
249 TTATATCAAAACCAAGATCCTAACA
3494495 AT
1 AT
3494497 CTCCCCCTTT
Statistics
Matches: 237, Mismatches: 28, Indels: 22
0.83 0.10 0.08
Matches are distributed among these distances:
273 37 0.16
274 53 0.22
275 82 0.35
276 62 0.26
277 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (273 bp):
ATACTTTCTAGGGTTTTAACTGTTGTAGCCTAAGTCAACCTTAATGTATCGATACAAATACCTAT
GTATCAATACTTTAGATTATTTTTACTTGAAAACATTCGATTTAAGGCTTGAAAATACTTATATA
AAACTATAAAACATTATTGATATTAAAAATATCTTAGAACAAGGTTTTAGAGTATTTTTAAATGA
ATAAAACTTGTTTACGGTTTTTGAAAGCTATTTTCAGTTCTATTCATACTTTGTTATATCAAAAC
CAAGATCCTAACA
Found at i:3496718 original size:32 final size:32
Alignment explanation
Indices: 3496682--3496756 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
3496672 AAACCGTTTT
3496682 TGATGAAGATTTTGATGAAAAATG-AAAAGAAA
1 TGATGAA-ATTTTGATGAAAAATGAAAAAGAAA
** *
3496714 TGATGTAAA-TTTGATGAAATTTGAAAAAGAAT
1 TGATG-AAATTTTGATGAAAAATGAAAAAGAAA
3496746 TGATGAAATTT
1 TGATGAAATTT
3496757 AAGATTGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
31 15 0.41
32 20 0.54
33 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (32 bp):
TGATGAAATTTTGATGAAAAATGAAAAAGAAA
Found at i:3496730 original size:31 final size:31
Alignment explanation
Indices: 3496682--3496756 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
3496672 AAACCGTTTT
3496682 TGATGAAGATTTTGATGAAAAATG-AAAAGAAA
1 TGATGAA-A-TTTGATGAAAAATGAAAAAGAAA
** *
3496714 TGATGTAAATTTGATGAAATTTGAAAAAGAAT
1 TGATG-AAATTTGATGAAAAATGAAAAAGAAA
3496746 TGATGAAATTT
1 TGATGAAATTT
3496757 AAGATTGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
31 18 0.47
32 18 0.47
33 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (31 bp):
TGATGAAATTTGATGAAAAATGAAAAAGAAA
Done.