Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 134 of 208
Found at i:41064646 original size:44 final size:45
Alignment explanation
Indices: 41064483--41064699 Score: 215
Period size: 44 Copynumber: 4.8 Consensus size: 45
41064473 CAGATCATAT
* * * *
41064483 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTT-GAAGTACA
* *
41064529 CCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-ACA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTACA
* * *
41064573 GGCTACAAGTCTTATCTCTCTGAAGTTGCATTAGAGCAGGTTGAAGTA-A
1 --C-A-AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTACA
* * * **
41064622 CAAACCTTATCCCCCTGAAGTTGCAGTGGGGCAGGTTGAA-TATG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTACA
* *
41064666 CAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAG
41064700 ACTGAAGCTG
Statistics
Matches: 141, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
43 2 0.01
44 61 0.43
45 4 0.03
46 36 0.26
47 1 0.01
48 2 0.01
49 34 0.24
50 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (45 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTACA
Found at i:41064661 original size:93 final size:95
Alignment explanation
Indices: 41064488--41064699 Score: 249
Period size: 93 Copynumber: 2.3 Consensus size: 95
41064478 CATATCAAAC
* * * *
41064488 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAACCAATCTTATCTCCCTGAAGTTGC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTAAAAATAAACAAACCTTATCCCCCTGAAGTTGC
41064553 AGTGGAGCAGATTGAAGACAGGCTACAAGT
66 AGTGGAGCAGATTGAAGACAGGCTACAAGT
* * * *
41064583 CTTATCTCTCTGAAGTTGCATTAGAGCAGGTT-GAAGT-AACAAACCTTATCCCCCTGAAGTTGC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTAAAAATAAACAAACCTTATCCCCCTGAAGTTGC
* * * *
41064646 AGTGGGGCAGGTTG-A-ATA---TGCAAGT
66 AGTGGAGCAGATTGAAGACAGGCTACAAGT
* *
41064671 CTTATCTCCCTGAAGTTGCAATGGAGCAG
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAG
41064700 ACTGAAGCTG
Statistics
Matches: 102, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
88 32 0.31
91 2 0.02
92 1 0.01
93 35 0.34
94 3 0.03
95 29 0.28
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (95 bp):
CTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTAAAAATAAACAAACCTTATCCCCCTGAAGTTGC
AGTGGAGCAGATTGAAGACAGGCTACAAGT
Found at i:41064744 original size:137 final size:137
Alignment explanation
Indices: 41064483--41064734 Score: 338
Period size: 137 Copynumber: 1.9 Consensus size: 137
41064473 CAGATCATAT
*
41064483 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAAACCAATCTTATCTCCCTGAA
1 CAAACCTTATCCCCCTGAAGTTGCAGTGGAGCAGGTT-AAAATAAACCAATCTTATCTCCCTGAA
* * *
41064548 GTTGCAGTGGAGCAGATTGAAGACAGGCTACAAGTCTTATCTCTCTGAAGTTGCATTAGAGCAGG
65 GTTGCAATGGAGCAGACTGAAGACAGGCTA-AAGTCCTATCTCTCTGAAGTTGCATTAGAGCAGG
41064613 TTGAAGTAA
129 TTGAAGTAA
* * **
41064622 CAAACCTTATCCCCCTGAAGTTGCAGTGGGGCAGGTT-GAAT-ATGCAAGTCTTATCTCCCTGAA
1 CAAACCTTATCCCCCTGAAGTTGCAGTGGAGCAGGTTAAAATAAACCAA-TCTTATCTCCCTGAA
*
41064685 GTTGCAATGGAGCAGACTGAAG-C-TGCT-AA-TCCTATAC-CTCTGAAGTTGCA
65 GTTGCAATGGAGCAGACTGAAGACAGGCTAAAGTCCTAT-CTCTCTGAAGTTGCA
41064735 GTAGGTTAGA
Statistics
Matches: 102, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
132 18 0.18
133 3 0.03
135 3 0.03
136 5 0.05
137 38 0.37
139 35 0.34
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (137 bp):
CAAACCTTATCCCCCTGAAGTTGCAGTGGAGCAGGTTAAAATAAACCAATCTTATCTCCCTGAAG
TTGCAATGGAGCAGACTGAAGACAGGCTAAAGTCCTATCTCTCTGAAGTTGCATTAGAGCAGGTT
GAAGTAA
Found at i:41066471 original size:9 final size:9
Alignment explanation
Indices: 41066457--41066502 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
41066447 ACATTTTATA
41066457 ATTTTATTT
1 ATTTTATTT
41066466 ATTTTATTT
1 ATTTTATTT
41066475 ATTGTTA-TT
1 ATT-TTATTT
41066484 A--TTATTT
1 ATTTTATTT
41066491 A-TTTATTT
1 ATTTTATTT
41066499 ATTT
1 ATTT
41066503 ACGTGTCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 3 0.09
7 3 0.09
8 7 0.21
9 17 0.52
10 3 0.09
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (9 bp):
ATTTTATTT
Found at i:41066490 original size:16 final size:15
Alignment explanation
Indices: 41066464--41066493 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41066454 ATAATTTTAT
41066464 TTATTTTATTTATTG
1 TTATTTTATTTATTG
41066479 TTATTATTATTTATT
1 TTATT-TTATTTATT
41066494 TATTTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
TTATTTTATTTATTG
Found at i:41070216 original size:11 final size:11
Alignment explanation
Indices: 41070190--41070224 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
41070180 CGAAACAAGG
41070190 GAAAAGAAAGAA
1 GAAAAGAAA-AA
41070202 GAAAAGAAAAA
1 GAAAAGAAAAA
41070213 GAAAAGGAAAAA
1 GAAAA-GAAAAA
41070225 TTAGGGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:41071411 original size:23 final size:23
Alignment explanation
Indices: 41071384--41071527 Score: 122
Period size: 23 Copynumber: 6.3 Consensus size: 23
41071374 TGCCGATCAA
*
41071384 GCACTTTATGTGTCGTATTTTAG
1 GCACTTTATGTGTCGTATTTCAG
*
41071407 GCACTTTATGTGTCGTATTTTAG
1 GCACTTTATGTGTCGTATTTCAG
* *
41071430 GCAATTCATGTGTC--ATTTCAG
1 GCACTTTATGTGTCGTATTTCAG
41071451 GCAC-TTATGTGTCGTATACTGATCAG
1 GCACTTTATGTGTCGTAT--T--TCAG
*
41071477 GTACTATGTAT-TGT--TATTTCAG
1 GCACT-T-TATGTGTCGTATTTCAG
*
41071499 GCACTTTATGTGTCATACTTT-AG
1 GCACTTTATGTGTCGTA-TTTCAG
41071522 GCACTT
1 GCACTT
41071528 CGTGCATCAT
Statistics
Matches: 101, Mismatches: 7, Indels: 26
0.75 0.05 0.19
Matches are distributed among these distances:
20 11 0.11
21 13 0.13
22 10 0.10
23 45 0.45
24 5 0.05
26 10 0.10
28 4 0.04
29 3 0.03
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (23 bp):
GCACTTTATGTGTCGTATTTCAG
Found at i:41071456 original size:44 final size:43
Alignment explanation
Indices: 41071391--41071553 Score: 123
Period size: 43 Copynumber: 3.6 Consensus size: 43
41071381 CAAGCACTTT
*
41071391 ATGTGTCGTATTTTAGGCACTTTATGTGTCGTATTTTAGGCAATTC
1 ATGTGTC--ATTTCAGGCAC-TTATGTGTCGTATTTTAGGCAATTC
* *
41071437 ATGTGTCATTTCAGGCACTTATGTGTCGTATACTGATCAGGTACTATGT-
1 ATGTGTCATTTCAGGCACTTATGTGTCGTAT--T--TTAGG--CAAT-TC
* * * *
41071486 AT-TGTTATTTCAGGCACTTTATGTGTCATACTTTAGGCACTTC
1 ATGTGTCATTTCAGGCAC-TTATGTGTCGTATTTTAGGCAATTC
* **
41071529 GTGCATCATTTCAGGCACTTATGTG
1 ATGTGTCATTTCAGGCACTTATGTG
41071554 CCATTTACTG
Statistics
Matches: 94, Mismatches: 13, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
42 1 0.01
43 23 0.24
44 22 0.23
45 5 0.05
46 7 0.07
47 5 0.05
48 14 0.15
49 16 0.17
50 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.42
Consensus pattern (43 bp):
ATGTGTCATTTCAGGCACTTATGTGTCGTATTTTAGGCAATTC
Found at i:41071563 original size:92 final size:92
Alignment explanation
Indices: 41071399--41071578 Score: 261
Period size: 92 Copynumber: 2.0 Consensus size: 92
41071389 TTATGTGTCG
* * * ** *
41071399 TATTTTAGGCACTTTATGTGTCGTATTTTAGGCAATTCATGTGTCATTTCAGGCACTTATGTGTC
1 TATTTCAGGCACTTTATGTGTCATACTTTAGGCAATTCATGCATCATTTCAGGCACTTATGTGCC
*
41071464 GTATACTGATCAGGTACTATGTATTGT
66 ATATACTGATCAGGTACTATGTATTGT
* *
41071491 TATTTCAGGCACTTTATGTGTCATACTTTAGGCACTTCGTGCATCATTTCAGGCACTTATGTGCC
1 TATTTCAGGCACTTTATGTGTCATACTTTAGGCAATTCATGCATCATTTCAGGCACTTATGTGCC
* *
41071556 ATTTACTGATTAGGTACTATGTA
66 ATATACTGATCAGGTACTATGTA
41071579 CCGTTTTAGG
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
92 77 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (92 bp):
TATTTCAGGCACTTTATGTGTCATACTTTAGGCAATTCATGCATCATTTCAGGCACTTATGTGCC
ATATACTGATCAGGTACTATGTATTGT
Found at i:41076625 original size:4 final size:4
Alignment explanation
Indices: 41076616--41076643 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
41076606 TTTTCCAATG
41076616 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
41076644 TTTTTGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:41079731 original size:2 final size:2
Alignment explanation
Indices: 41079724--41079772 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
41079714 ACATATAAGA
41079724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41079766 AT AT AT A
1 AT AT AT A
41079773 ATTTCAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41080942 original size:43 final size:42
Alignment explanation
Indices: 41080881--41081029 Score: 117
Period size: 43 Copynumber: 3.5 Consensus size: 42
41080871 CAATGCGAAC
* * *
41080881 GTCCCAGAC-GTGGTCTTACATGTAATCA-ATTAATGATGCCACT
1 GTCCCAGACAG-GGTCTTACATGTAATCATA-T-ACGACGCCAAT
* *
41080924 GTCCCTGACAGGGTCTTACACGTAATCATATACGACGCCAAT
1 GTCCCAGACAGGGTCTTACATGTAATCATATACGACGCCAAT
* * * *
41080966 GTTCCAGACATGGTCTTACATGTAAATC-TCAAATCGATGCCAAT
1 GTCCCAGACAGGGTCTTACATGT-AATCAT-ATA-CGACGCCAAT
*
41081010 GTCTCAGAC-GTGGTCTTACA
1 GTCCCAGACAG-GGTCTTACA
41081030 CGATATCACA
Statistics
Matches: 86, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
42 28 0.33
43 31 0.36
44 27 0.31
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (42 bp):
GTCCCAGACAGGGTCTTACATGTAATCATATACGACGCCAAT
Found at i:41081018 original size:44 final size:43
Alignment explanation
Indices: 41080885--41081029 Score: 120
Period size: 44 Copynumber: 3.4 Consensus size: 43
41080875 GCGAACGTCC
* * * *
41080885 CAGACGTGGTCTTACATGTAATCAAT-TAAT-GATGCCACTGTCC
1 CAGACATGGTCTTACATGTAATC--TCAAATCGATGCCAATGTCT
* * * * *
41080928 CTGACAGGGTCTTACACGTAA--TCATATACGACGCCAATGT-T
1 CAGACATGGTCTTACATGTAATCTCAAAT-CGATGCCAATGTCT
41080969 CCAGACATGGTCTTACATGTAAATCTCAAATCGATGCCAATGTCT
1 -CAGACATGGTCTTACATGT-AATCTCAAATCGATGCCAATGTCT
*
41081014 CAGACGTGGTCTTACA
1 CAGACATGGTCTTACA
41081030 CGATATCACA
Statistics
Matches: 79, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
39 1 0.01
40 2 0.03
42 25 0.32
43 19 0.24
44 26 0.33
45 6 0.08
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (43 bp):
CAGACATGGTCTTACATGTAATCTCAAATCGATGCCAATGTCT
Found at i:41085204 original size:58 final size:58
Alignment explanation
Indices: 41085142--41085265 Score: 169
Period size: 58 Copynumber: 2.1 Consensus size: 58
41085132 AATTCATATT
* * * * *
41085142 ATAATAATTACATTAAGAATGTTATTAAATTATATATTA-TTTTATTAAATTGTATTTA
1 ATAATAATTACA-TAAAAATATGATTAAATTATATATTATTTTTATTAAAATATATTTA
* *
41085200 ATAATAATTATATAAAAATATGATTAAATTATTTATTATTTTTATTAAAATATATTTA
1 ATAATAATTACATAAAAATATGATTAAATTATATATTATTTTTATTAAAATATATTTA
41085258 ATAATAAT
1 ATAATAAT
41085266 ATTATTAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 22 0.38
58 36 0.62
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (58 bp):
ATAATAATTACATAAAAATATGATTAAATTATATATTATTTTTATTAAAATATATTTA
Found at i:41085493 original size:16 final size:16
Alignment explanation
Indices: 41085450--41085520 Score: 72
Period size: 16 Copynumber: 4.4 Consensus size: 16
41085440 TGAATTACTG
41085450 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
* * *
41085466 ATTATAGTTCTATTTC
1 ATTACAGCTCTATTCC
* *
41085482 ATTACAACTCTATTCA
1 ATTACAGCTCTATTCC
*
41085498 ATTACAGC-CATATTCT
1 ATTACAGCTC-TATTCC
41085514 ATTACAG
1 ATTACAG
41085521 TGAACCAAAC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
15 1 0.02
16 43 0.98
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.41
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:41089382 original size:18 final size:19
Alignment explanation
Indices: 41089359--41089397 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
41089349 TTTTATAAAT
*
41089359 TGTGAATT-ATATTTGATA
1 TGTGAATTAATATTTAATA
41089377 TGTGAATTAATATTTAATA
1 TGTGAATTAATATTTAATA
41089396 TG
1 TG
41089398 GAAGGAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (19 bp):
TGTGAATTAATATTTAATA
Found at i:41089650 original size:23 final size:23
Alignment explanation
Indices: 41089623--41089698 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
41089613 AGTGTTATTG
41089623 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
41089646 TTCAGTGGTAG-TTACGACTACAT
1 ATCAGTGGTAGCTT-CGGCTACAT
*
41089669 ATCAGTGATAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
41089692 ATCAGTG
1 ATCAGTG
41089699 TGGCACTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 2 0.04
23 42 0.91
24 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:41092959 original size:21 final size:21
Alignment explanation
Indices: 41092930--41092981 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
41092920 GTTTGGGGTG
*
41092930 TTATAGATACCCATACAATTT
1 TTATCGATACCCATACAATTT
***
41092951 TTATCGATA-CCATATTTTTT
1 TTATCGATACCCATACAATTT
41092971 TTATCGATACC
1 TTATCGATACC
41092982 AAAATTGCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (21 bp):
TTATCGATACCCATACAATTT
Found at i:41099085 original size:75 final size:75
Alignment explanation
Indices: 41098943--41099086 Score: 225
Period size: 75 Copynumber: 1.9 Consensus size: 75
41098933 GCAGAGGGGT
* *
41098943 TTTGCGCCCAGCGCTAATCGGGTTAGCCGACGATATTGAACGTGAGCCCAGCTCTAGTCGGAAAA
1 TTTGCGCCCAGCGCTAATCGGGTTAGCCGACGATATTGAACGTGAACCCAGCTCTAGTCAGAAAA
41099008 ACCAGCAATG
66 ACCAGCAATG
* * * * *
41099018 TTTGCGCCTAGCGCTAGTCGGGTTAGCCGACGATATTGAATGTGAACCCAGCTCTAGTTAGATAA
1 TTTGCGCCCAGCGCTAATCGGGTTAGCCGACGATATTGAACGTGAACCCAGCTCTAGTCAGAAAA
41099083 ACCA
66 ACCA
41099087 ACGGTGTTTG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (75 bp):
TTTGCGCCCAGCGCTAATCGGGTTAGCCGACGATATTGAACGTGAACCCAGCTCTAGTCAGAAAA
ACCAGCAATG
Found at i:41099126 original size:75 final size:75
Alignment explanation
Indices: 41098943--41099115 Score: 222
Period size: 75 Copynumber: 2.3 Consensus size: 75
41098933 GCAGAGGGGT
* * * *
41098943 TTTGCGCCCAGCGCTAATCGGGTTAGCCGACGATATTGAACGTGAGCCCAGCTCTAGTCGGAAAA
1 TTTGCGCCTAGCGCTAGTCGGGTTAGCCGACGATATTGAACGTGAACCCAGCTCTAGTCAGAAAA
*
41099008 ACCAGCAATG
66 ACCAACAATG
* * *
41099018 TTTGCGCCTAGCGCTAGTCGGGTTAGCCGACGATATTGAATGTGAACCCAGCTCTAGTTAGATAA
1 TTTGCGCCTAGCGCTAGTCGGGTTAGCCGACGATATTGAACGTGAACCCAGCTCTAGTCAGAAAA
**
41099083 ACCAACGGTG
66 ACCAACAATG
* *
41099093 TTTGCGTCC-AGTGCTAGTTGGGT
1 TTTGCG-CCTAGCGCTAGTCGGGT
41099116 ATTCCGACGA
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
75 83 0.98
76 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (75 bp):
TTTGCGCCTAGCGCTAGTCGGGTTAGCCGACGATATTGAACGTGAACCCAGCTCTAGTCAGAAAA
ACCAACAATG
Found at i:41103638 original size:21 final size:21
Alignment explanation
Indices: 41103614--41103682 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
41103604 AACTGAAACC
41103614 CATAAAGGTTAAACGGAAGCT
1 CATAAAGGTTAAACGGAAGCT
* * * * *
41103635 CAT-AAGAGCTGAACGAAAACC
1 CATAAAG-GTTAAACGGAAGCT
* *
41103656 CATAATGGTTAAACAGAAGCT
1 CATAAAGGTTAAACGGAAGCT
41103677 CA-AAAG
1 CATAAAG
41103683 AGCTGAACGG
Statistics
Matches: 33, Mismatches: 13, Indels: 5
0.65 0.25 0.10
Matches are distributed among these distances:
20 6 0.18
21 25 0.76
22 2 0.06
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.16
Consensus pattern (21 bp):
CATAAAGGTTAAACGGAAGCT
Found at i:41103655 original size:42 final size:41
Alignment explanation
Indices: 41103576--41103696 Score: 143
Period size: 42 Copynumber: 2.9 Consensus size: 41
41103566 CAGAAGCCCG
* * * * *
41103576 AAGGCTAAATAGAAGCACATAAGTGCTAAACTGAAACCCATA
1 AAGGTTAAACAGAAGCTCATAAGAGCTGAAC-GAAACCCATA
*
41103618 AAGGTTAAACGGAAGCTCATAAGAGCTGAACGAAAACCCATA
1 AAGGTTAAACAGAAGCTCATAAGAGCTGAACG-AAACCCATA
* *
41103660 ATGGTTAAACAGAAGCTCAAAAGAGCTGAACGGAAAC
1 AAGGTTAAACAGAAGCTCATAAGAGCTGAAC-GAAAC
41103697 ATATTAGGGT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 66 0.97
43 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (41 bp):
AAGGTTAAACAGAAGCTCATAAGAGCTGAACGAAACCCATA
Found at i:41105444 original size:30 final size:30
Alignment explanation
Indices: 41105410--41105466 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
41105400 TTTAGAACTT
*
41105410 GGGAATCCCGGGATTA-TTTTCAGACATCTC
1 GGGAATCCCGGGATAAGTTTT-AGACATCTC
*
41105440 GGGAATCCTGGGATAAGTTTTAGACAT
1 GGGAATCCCGGGATAAGTTTTAGACAT
41105467 ACTATCTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (30 bp):
GGGAATCCCGGGATAAGTTTTAGACATCTC
Found at i:41108272 original size:25 final size:25
Alignment explanation
Indices: 41108226--41108275 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
41108216 TGTAGGAAAC
* *
41108226 ATTTATTTTGTATTATATTTTTTAA
1 ATTTATTTTGTATTAAAATTTTTAA
41108251 ATTTATTTT-TATATAAAATTTTTAA
1 ATTTATTTTGTAT-TAAAATTTTTAA
41108276 TACGAGTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
ATTTATTTTGTATTAAAATTTTTAA
Found at i:41112180 original size:19 final size:19
Alignment explanation
Indices: 41112154--41112197 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
41112144 AGGAGGCAAG
*
41112154 AATTTTTCTTCTTTTTTTC
1 AATTTTTCTTCTGTTTTTC
*
41112173 AGTTTTTCTTCTGTTTTTC
1 AATTTTTCTTCTGTTTTTC
41112192 AATTTT
1 AATTTT
41112198 ACCTTTTGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.05, T:0.70
Consensus pattern (19 bp):
AATTTTTCTTCTGTTTTTC
Found at i:41121619 original size:88 final size:88
Alignment explanation
Indices: 41121459--41121637 Score: 277
Period size: 88 Copynumber: 2.0 Consensus size: 88
41121449 ATTTTGTATG
* *
41121459 ATATGTATGAATGAACTAGATTTGATCATTTAATAGTATAAATTGAATGTAGTTGATAGTTGTTT
1 ATATGTATGAATGAACTAGATTTGATCATTTAATAGTATAAATTGAATGTAGTTGATAGTAGTTG
41121524 CAACAACAAATGTGACACTATAA
66 CAACAACAAATGTGACACTATAA
* * *
41121547 ATATGTATGAATGAACTGGATTTGATCATTTAATAGTATAAATTGAATGTAGTTTATTGTAGTTG
1 ATATGTATGAATGAACTAGATTTGATCATTTAATAGTATAAATTGAATGTAGTTGATAGTAGTTG
*
41121612 CTTCAACAACAAATGTGGCACTATAA
66 ---CAACAACAAATGTGACACTATAA
41121638 TAACCTGTCT
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
88 60 0.73
91 22 0.27
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (88 bp):
ATATGTATGAATGAACTAGATTTGATCATTTAATAGTATAAATTGAATGTAGTTGATAGTAGTTG
CAACAACAAATGTGACACTATAA
Found at i:41122377 original size:20 final size:21
Alignment explanation
Indices: 41122345--41122383 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
41122335 AGGGACTAAA
41122345 GTGTATAAATTCTA-AAATTG
1 GTGTATAAATTCTATAAATTG
41122365 GTGTA-AAATTTCTATAAAT
1 GTGTATAAA-TTCTATAAAT
41122384 ATGAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 10 0.59
21 4 0.24
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (21 bp):
GTGTATAAATTCTATAAATTG
Found at i:41124315 original size:65 final size:65
Alignment explanation
Indices: 41124211--41124356 Score: 265
Period size: 65 Copynumber: 2.2 Consensus size: 65
41124201 ACGAGAAATG
* *
41124211 TTTGGTGTGTTGGAGAGTGTTAGCTTTATACTTTACTTTTGGGATATGTTCGACTCTATGAGTCA
1 TTTGGTGTGTTGGAGAGTGTTAGCTTTATACTTCACTTTTGGGATATGTTCAACTCTATGAGTCA
*
41124276 TTTGGTGTGTTGGAGAGTGTTAGCTTTATGCTTCACTTTTGGGATATGTTCAACTCTATGAGTCA
1 TTTGGTGTGTTGGAGAGTGTTAGCTTTATACTTCACTTTTGGGATATGTTCAACTCTATGAGTCA
41124341 TTTGGTGTGTTGGAGA
1 TTTGGTGTGTTGGAGA
41124357 TCCGTGTATC
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 78 1.00
ACGTcount: A:0.18, C:0.10, G:0.28, T:0.44
Consensus pattern (65 bp):
TTTGGTGTGTTGGAGAGTGTTAGCTTTATACTTCACTTTTGGGATATGTTCAACTCTATGAGTCA
Found at i:41148726 original size:60 final size:60
Alignment explanation
Indices: 41148653--41148770 Score: 200
Period size: 60 Copynumber: 2.0 Consensus size: 60
41148643 AAATTATATA
* *
41148653 GTTTTTCATCACAAGGCATTCATTGTGCCTTCAACCGCCATCGTTTCATCTTCTCCTCGT
1 GTTTTTCATCACAAGGAATTCATTGTGCCTTCAACCGCCATCGTTCCATCTTCTCCTCGT
* *
41148713 GTTTTTCATCACAAGGAATTCATTGTGTCTTCGACCGCCATCGTTCCATCTTCTCCTC
1 GTTTTTCATCACAAGGAATTCATTGTGCCTTCAACCGCCATCGTTCCATCTTCTCCTC
41148771 ATCATGAACT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (60 bp):
GTTTTTCATCACAAGGAATTCATTGTGCCTTCAACCGCCATCGTTCCATCTTCTCCTCGT
Found at i:41154234 original size:35 final size:36
Alignment explanation
Indices: 41154188--41154259 Score: 137
Period size: 35 Copynumber: 2.0 Consensus size: 36
41154178 TTCAACGAGT
41154188 TAGTGGAGGGACCAATTAGACATATGT-GTTGAGGC
1 TAGTGGAGGGACCAATTAGACATATGTGGTTGAGGC
41154223 TAGTGGAGGGACCAATTAGACATATGTGGTTGAGGC
1 TAGTGGAGGGACCAATTAGACATATGTGGTTGAGGC
41154259 T
1 T
41154260 CAAATGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 27 0.75
36 9 0.25
ACGTcount: A:0.28, C:0.11, G:0.35, T:0.26
Consensus pattern (36 bp):
TAGTGGAGGGACCAATTAGACATATGTGGTTGAGGC
Found at i:41155853 original size:18 final size:18
Alignment explanation
Indices: 41155818--41155852 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41155808 TTTTCATAAT
*
41155818 TTTTAAAAATATATAAAA
1 TTTTAAAAAAATATAAAA
41155836 TTTTAAAAAAAT-TAAAA
1 TTTTAAAAAAATATAAAA
41155853 AAATTCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTTTAAAAAAATATAAAA
Found at i:41159754 original size:21 final size:21
Alignment explanation
Indices: 41159715--41159764 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
41159705 ACCCACCCTA
41159715 TTTTACTTAACATATAATATTGT
1 TTTTA-TTAACATATAATATT-T
41159738 TTTCTATTAA-ATA-AATATTT
1 TTT-TATTAACATATAATATTT
41159758 TTTTATT
1 TTTTATT
41159765 TTGATAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.15
20 4 0.15
21 6 0.23
22 3 0.12
23 7 0.27
24 2 0.08
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTAACATATAATATTT
Found at i:41161424 original size:49 final size:50
Alignment explanation
Indices: 41161348--41161446 Score: 164
Period size: 49 Copynumber: 2.0 Consensus size: 50
41161338 TTCTTTCCCT
* *
41161348 ATAGCCATGTCCTAAGACTTGTGTGAA-TTAACATCTTAAATAAGCTTCA
1 ATAGCCATGTCCTAAAACTTGTATGAATTTAACATCTTAAATAAGCTTCA
*
41161397 ATAGCCATGTCCTAAAACTTGTATGAATTTAACATCTTGAATAAGCTTCA
1 ATAGCCATGTCCTAAAACTTGTATGAATTTAACATCTTAAATAAGCTTCA
41161447 GCTTTCTTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 25 0.54
50 21 0.46
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.33
Consensus pattern (50 bp):
ATAGCCATGTCCTAAAACTTGTATGAATTTAACATCTTAAATAAGCTTCA
Found at i:41161499 original size:26 final size:26
Alignment explanation
Indices: 41161470--41161556 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
41161460 GCTATCTATC
41161470 TTTCAAATATAGTAGTGAAAATTAGT
1 TTTCAAATATAGTAGTGAAAATTAGT
** * * * *
41161496 TTTCAAACT-TTCTTGATTAATTATCTATT
1 TTTCAAA-TATAGTAG-TGAA-AAT-TAGT
*
41161525 TTTCAAATATAGTAGTGAGAATTAGT
1 TTTCAAATATAGTAGTGAAAATTAGT
41161551 TTTCAA
1 TTTCAA
41161557 CCTCTTGAAG
Statistics
Matches: 43, Mismatches: 13, Indels: 10
0.65 0.20 0.15
Matches are distributed among these distances:
26 19 0.44
27 6 0.14
28 5 0.12
29 13 0.30
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (26 bp):
TTTCAAATATAGTAGTGAAAATTAGT
Found at i:41161532 original size:55 final size:55
Alignment explanation
Indices: 41161448--41161556 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 55
41161438 TAAGCTTCAG
*
41161448 CTTTCTTGATTAGCTATCTATCTTTCAAATATAGTAGTGAAAATTAGTTTTCAAA
1 CTTTCTTGATTAACTATCTATCTTTCAAATATAGTAGTGAAAATTAGTTTTCAAA
* * *
41161503 CTTTCTTGATTAATTATCTATTTTTCAAATATAGTAGTGAGAATTAGTTTTCAA
1 CTTTCTTGATTAACTATCTATCTTTCAAATATAGTAGTGAAAATTAGTTTTCAA
41161557 CCTCTTGAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (55 bp):
CTTTCTTGATTAACTATCTATCTTTCAAATATAGTAGTGAAAATTAGTTTTCAAA
Found at i:41165444 original size:13 final size:13
Alignment explanation
Indices: 41165426--41165463 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
41165416 TAGACCAAAC
41165426 TTTTCAAAAGCAA
1 TTTTCAAAAGCAA
41165439 TTTTCAAAAGCAA
1 TTTTCAAAAGCAA
41165452 TTTTCAAAAGCA
1 TTTTCAAAAGCA
41165464 TTGTTAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTTCAAAAGCAA
Found at i:41167171 original size:13 final size:13
Alignment explanation
Indices: 41167155--41167179 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41167145 TAATTTAAAA
41167155 AATAAAATTCAAT
1 AATAAAATTCAAT
41167168 AATAAAATTCAA
1 AATAAAATTCAA
41167180 AATTTAGTGA
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAAAATTCAAT
Found at i:41170447 original size:11 final size:11
Alignment explanation
Indices: 41170426--41170465 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
41170416 AGTCTGATAC
*
41170426 AAAGCCTTAAT
1 AAAGCCATAAT
*
41170437 AAAGCTATAAT
1 AAAGCCATAAT
41170448 AAAGCCATAAT
1 AAAGCCATAAT
41170459 AAAGCCA
1 AAAGCCA
41170466 AGAACATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.20
Consensus pattern (11 bp):
AAAGCCATAAT
Found at i:41172890 original size:2 final size:2
Alignment explanation
Indices: 41172883--41172915 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41172873 CAATATTCCA
41172883 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
41172916 ACAAGGAAAA
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:41177053 original size:32 final size:32
Alignment explanation
Indices: 41177014--41177112 Score: 144
Period size: 32 Copynumber: 3.1 Consensus size: 32
41177004 GCGAACTTAA
41177014 TTCGCACTTAACAAACATACTTGTGAACACAG
1 TTCGCACTTAACAAACATACTTGTGAACACAG
* * * *
41177046 TTTGCACTTAACAGACATATTTGTGAACATAG
1 TTCGCACTTAACAAACATACTTGTGAACACAG
* *
41177078 TTCGCATTTAACAAACATACTTGTGCACACAG
1 TTCGCACTTAACAAACATACTTGTGAACACAG
41177110 TTC
1 TTC
41177113 TCGTTTAGCA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.30
Consensus pattern (32 bp):
TTCGCACTTAACAAACATACTTGTGAACACAG
Found at i:41177058 original size:64 final size:64
Alignment explanation
Indices: 41176987--41177111 Score: 180
Period size: 64 Copynumber: 2.0 Consensus size: 64
41176977 GATATCCCAA
*
41176987 ACTTAACAGACA-AGCTTGCGAACTTAATTCGCACTTAACAAACATACTTGTGAACACAGTTTGC
1 ACTTAACAGACATA-CTTGCGAACATAATTCGCACTTAACAAACATACTTGTGAACACAGTTTGC
* * * * *
41177051 ACTTAACAGACATATTTGTGAACATAGTTCGCATTTAACAAACATACTTGTGCACACAGTT
1 ACTTAACAGACATACTTGCGAACATAATTCGCACTTAACAAACATACTTGTGAACACAGTT
41177112 CTCGTTTAGC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
64 53 0.98
65 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.29
Consensus pattern (64 bp):
ACTTAACAGACATACTTGCGAACATAATTCGCACTTAACAAACATACTTGTGAACACAGTTTGC
Found at i:41177774 original size:18 final size:18
Alignment explanation
Indices: 41177765--41177799 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41177755 TATTATCATG
41177765 GGTTTGCATAATAACATA
1 GGTTTGCATAATAACATA
*
41177783 GGTTTGCAGAATAACAT
1 GGTTTGCATAATAACAT
41177800 GCAACATGGG
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:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (18 bp):
GGTTTGCATAATAACATA
Found at i:41177806 original size:25 final size:25
Alignment explanation
Indices: 41177777--41177824 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
41177767 TTTGCATAAT
41177777 AACATAGGTTTGCAGAATAACATGC
1 AACATAGGTTTGCAGAATAACATGC
* *
41177802 AACATGGGTTTGCATAATAACAT
1 AACATAGGTTTGCAGAATAACAT
41177825 AGGCTCACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (25 bp):
AACATAGGTTTGCAGAATAACATGC
Found at i:41177822 original size:43 final size:43
Alignment explanation
Indices: 41177761--41177859 Score: 144
Period size: 43 Copynumber: 2.3 Consensus size: 43
41177751 CACATATTAT
* ** *
41177761 CATGGGTTTGCATAATAACATAGGTTTGCAGAATAACATGCAA
1 CATGGGTTTGCATAATAACATAGGCTCACAGAATAACATACAA
*
41177804 CATGGGTTTGCATAATAACATAGGCTCACAGAATAACATATAA
1 CATGGGTTTGCATAATAACATAGGCTCACAGAATAACATACAA
*
41177847 CATGGGTTCGCAT
1 CATGGGTTTGCAT
41177860 CAAGACCAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (43 bp):
CATGGGTTTGCATAATAACATAGGCTCACAGAATAACATACAA
Found at i:41180171 original size:17 final size:17
Alignment explanation
Indices: 41180123--41180173 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
41180113 TTCTTTTCCA
* *
41180123 TCTATCTTATTTATTGT
1 TCTATATTATTTATTAT
41180140 TCTAATATATGATTTATTAT
1 TCT-ATAT-T-ATTTATTAT
41180160 TCTATATTATTTAT
1 TCTATATTATTTAT
41180174 CTTAGTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 9 0.31
18 4 0.14
19 5 0.17
20 11 0.38
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (17 bp):
TCTATATTATTTATTAT
Found at i:41185981 original size:39 final size:39
Alignment explanation
Indices: 41185923--41185997 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
41185913 TTTAAGTCTC
*
41185923 CTTCACCGAAACTCCATAGTTTCAACTTCTCCAAGCAGA
1 CTTCACCAAAACTCCATAGTTTCAACTTCTCCAAGCAGA
**
41185962 CTTCACCAAAACTTTATAGTTTCAACTTCTCCAAGC
1 CTTCACCAAAACTCCATAGTTTCAACTTCTCCAAGC
41185998 TTCGGTCTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.31, C:0.32, G:0.08, T:0.29
Consensus pattern (39 bp):
CTTCACCAAAACTCCATAGTTTCAACTTCTCCAAGCAGA
Found at i:41187749 original size:20 final size:20
Alignment explanation
Indices: 41187726--41187794 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
41187716 TAAGTTTATT
41187726 ACAAACTTACTAAGCTTTAA
1 ACAAACTTACTAAGCTTTAA
* * *
41187746 ACAAGCTT-TTAAG-TTTATT
1 ACAAACTTACTAAGCTTTA-A
*
41187765 ACGAACTTACTAAGCTTTAA
1 ACAAACTTACTAAGCTTTAA
*
41187785 ACAAGCTTAC
1 ACAAACTTAC
41187795 CTCATTTTGG
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 4 0.11
19 10 0.27
20 19 0.51
21 4 0.11
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (20 bp):
ACAAACTTACTAAGCTTTAA
Found at i:41187757 original size:39 final size:39
Alignment explanation
Indices: 41187714--41187792 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
41187704 TAAGTTAAAG
41187714 TTTAAGTTTATTACAAACTTACTAAGCTTTAAACAAGCT
1 TTTAAGTTTATTACAAACTTACTAAGCTTTAAACAAGCT
*
41187753 TTTAAGTTTATTACGAACTTACTAAGCTTTAAACAAGCT
1 TTTAAGTTTATTACAAACTTACTAAGCTTTAAACAAGCT
41187792 T
1 T
41187793 ACCTCATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (39 bp):
TTTAAGTTTATTACAAACTTACTAAGCTTTAAACAAGCT
Found at i:41197694 original size:162 final size:163
Alignment explanation
Indices: 41197425--41197746 Score: 522
Period size: 162 Copynumber: 2.0 Consensus size: 163
41197415 GGAAAAGAAA
* *
41197425 CCAAGGCTCATTAGATGGATTTTACTACTCCAAGAATTCGACATCGAGATTCGAGACAAGAGGGG
1 CCAAGGCTCATTAGATGGATTTTACTACTCCAAGAATTCGACATCAAGATTCGAGACAAGAAGGG
* *
41197490 ATGTGAAAACTTAGTGGCTGACCATTGAAGTAGATGAAAAACACCTTGTGATGACACTCCTATAA
66 ATGCGAAAACTTAGTGGCTGACCATTGAAGTAGATGAAAAACACCTTGTGATGACACTACTATAA
*
41197555 AGGATGAGTTTCCTGATGAGGG-CTATTTTCAG
131 AGAATGAGTTTCCTGATGAGGGCCTATTTTCAG
* *
41197587 CCAAGGCTCATTAGTTGGATTTTACTGCTCCAAGAATTCGACATCAAGATTCGAGACAAGAAGGG
1 CCAAGGCTCATTAGATGGATTTTACTACTCCAAGAATTCGACATCAAGATTCGAGACAAGAAGGG
* * * *
41197652 ATGCGAAAACTTGGTGGCTGGCCACTTG-AGTAGATTAAAAACACCTTGTGATGACACTATTATA
66 ATGCGAAAACTTAGTGGCTGACCA-TTGAAGTAGATGAAAAACACCTTGTGATGACACTACTATA
41197716 AAGAATGAGTTTCCTGATGAGGGCCTATTTT
130 AAGAATGAGTTTCCTGATGAGGGCCTATTTT
41197747 TGGCCAAAAC
Statistics
Matches: 147, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
162 137 0.93
163 10 0.07
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (163 bp):
CCAAGGCTCATTAGATGGATTTTACTACTCCAAGAATTCGACATCAAGATTCGAGACAAGAAGGG
ATGCGAAAACTTAGTGGCTGACCATTGAAGTAGATGAAAAACACCTTGTGATGACACTACTATAA
AGAATGAGTTTCCTGATGAGGGCCTATTTTCAG
Found at i:41198999 original size:4 final size:4
Alignment explanation
Indices: 41198990--41199048 Score: 50
Period size: 4 Copynumber: 13.8 Consensus size: 4
41198980 CAACCTAATT
41198990 TTTA TTTA TTTA TTTA TATTAA TTTA TATTAA TTTA -TTA TTTA -TTA
1 TTTA TTTA TTTA TTTA T-TT-A TTTA T-TT-A TTTA TTTA TTTA TTTA
41199036 CTTTA TTTTA TTT
1 -TTTA -TTTA TTT
41199049 TCATGTTAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
3 6 0.13
4 22 0.47
5 15 0.32
6 4 0.09
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:41199009 original size:10 final size:10
Alignment explanation
Indices: 41198993--41199026 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
41198983 CCTAATTTTT
41198993 ATTTAT-TT-
1 ATTTATATTA
41199001 ATTTATATTA
1 ATTTATATTA
41199011 ATTTATATTA
1 ATTTATATTA
41199021 ATTTAT
1 ATTTAT
41199027 TATTTATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 6 0.25
9 2 0.08
10 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTATATTA
Found at i:41199019 original size:24 final size:25
Alignment explanation
Indices: 41198985--41199048 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
41198975 GGAGGCAACC
*
41198985 TAATTTTTATTTATTTATT-TATAT
1 TAATTTATATTTATTTATTATATAT
* *
41199009 TAATTTATATTAATTTATTATTTAT
1 TAATTTATATTTATTTATTATATAT
*
41199034 TACTTTAT-TTTATTT
1 TAATTTATATTTATTT
41199049 TCATGTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 23 0.68
25 11 0.32
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
TAATTTATATTTATTTATTATATAT
Found at i:41201734 original size:108 final size:108
Alignment explanation
Indices: 41201556--41201760 Score: 270
Period size: 108 Copynumber: 1.9 Consensus size: 108
41201546 ATTAAACAAA
* ** *
41201556 AAAATTAAGAGTGTGTTCGGCTGAGTAATTAGGGTAGAGTGCTGGGGTTGTCATTCCACTTCGTG
1 AAAATTAAGAGTGTGTTAGGCTGAGTAACGAGGGTAGAGTGCTGGGGTTGTCATTCCACTTCGCG
41201621 TCAAAAGGGCCAAAACATTCTTAACCAAAAAAAATTATAATAAT
66 TCAAAAGGGCCAAAACATTCTTAA-CAAAAAAAATTATAATAAT
* * * * *
41201665 AAAA-TAAGAGTGTGTTAGGCTGAGTAACCGA-GGTGGGGTGCTTGGTTTGTCATTCCTCTTCGC
1 AAAATTAAGAGTGTGTTAGGCTGAGTAA-CGAGGGTAGAGTGCTGGGGTTGTCATTCCACTTCGC
* * *
41201728 GTCAAAAGGGTCAATACATTCTTAAGAAAAAAA
65 GTCAAAAGGGCCAAAACATTCTTAACAAAAAAA
41201761 TACAAAAAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
107 7 0.08
108 71 0.86
109 5 0.06
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (108 bp):
AAAATTAAGAGTGTGTTAGGCTGAGTAACGAGGGTAGAGTGCTGGGGTTGTCATTCCACTTCGCG
TCAAAAGGGCCAAAACATTCTTAACAAAAAAAATTATAATAAT
Found at i:41214944 original size:14 final size:14
Alignment explanation
Indices: 41214925--41214952 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41214915 TCAATTTATT
41214925 AATGAAATATTAAA
1 AATGAAATATTAAA
41214939 AATGAAATATTAAA
1 AATGAAATATTAAA
41214953 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (14 bp):
AATGAAATATTAAA
Found at i:41224105 original size:19 final size:19
Alignment explanation
Indices: 41224081--41224124 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
41224071 TAAAAGCAAC
41224081 ACAACATCAA-CCCAAATAA
1 ACAACAT-AAGCCCAAATAA
*
41224100 ACAACATAAGTCCAAATAA
1 ACAACATAAGCCCAAATAA
41224119 ACAACA
1 ACAACA
41224125 AAAACAATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.59, C:0.27, G:0.02, T:0.11
Consensus pattern (19 bp):
ACAACATAAGCCCAAATAA
Found at i:41227536 original size:29 final size:27
Alignment explanation
Indices: 41227502--41227555 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
41227492 CCAATAATTT
*
41227502 AATTTAAGGATTCAATTGAAATATTTAGA
1 AATTTAAGAATTCAATT-AAA-ATTTAGA
*
41227531 AATTTAAGAATTGAATTAAAATTTA
1 AATTTAAGAATTCAATTAAAATTTA
41227556 ACTCGTGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 3 0.13
29 15 0.65
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (27 bp):
AATTTAAGAATTCAATTAAAATTTAGA
Found at i:41232008 original size:23 final size:23
Alignment explanation
Indices: 41231982--41232025 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
41231972 TTTTCACAAA
41231982 AAAATAATGATTTTA-TATTTTAT
1 AAAATAAT-ATTTTATTATTTTAT
*
41232005 AAAATAATTTTTTATTATTTT
1 AAAATAATATTTTATTATTTT
41232026 GAAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
AAAATAATATTTTATTATTTTAT
Found at i:41232140 original size:14 final size:15
Alignment explanation
Indices: 41232121--41232149 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41232111 ATAATAGTTA
41232121 AATTTCTTTT-TTTT
1 AATTTCTTTTCTTTT
41232135 AATTTCTTTTCTTTT
1 AATTTCTTTTCTTTT
41232150 CTTTTGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (15 bp):
AATTTCTTTTCTTTT
Found at i:41232445 original size:179 final size:180
Alignment explanation
Indices: 41232141--41232480 Score: 438
Period size: 179 Copynumber: 1.9 Consensus size: 180
41232131 TTTTAATTTC
* * *
41232141 TTTTCTTTTCTTTTGAATTGAGAAAAATAATAATTAATTTTCAATTCTAATCTCTATACTTTTTA
1 TTTTCTTTTCTTTTGAATTGAGAAAAATAATAACTAAATTTCAATTCTAATCTCTACACTTTTTA
* * * *
41232206 AATATTCTATAATAATGGTTAAATTTTAGTTTTGATCCCTATATTTAGATCAATTTTGAGATTTA
66 AAGATTATAGAATAATGGTTAAATTTTAGTTTTGATCCCTATATTTAGATCAAATTTGAGATTTA
41232271 ATCTCTATACTTCAATTTTGACATAATTTAGACATTTGTCCATTCTTTTT
131 ATCTCTATACTTCAATTTTGACATAATTTAGACATTTGTCCATTCTTTTT
** *
41232321 TTTTCTTTTCTTTTGACA-TGAG-AAAATAATGGCTAAATTTCAATTTTAATCCATCTACA-TTT
1 TTTTCTTTTCTTTTGA-ATTGAGAAAAATAATAACTAAATTTCAATTCTAAT-C-TCTACACTTT
* * * * *
41232383 TTTAAGATTATAGAA-GATGGTTGAATTTTAGTTTTGATCCCTATA-TTATGCTTAAATTTGAGA
63 TTAAAGATTATAGAATAATGGTTAAATTTTAGTTTTGATCCCTATATTTA-GATCAAATTTGAGA
* * * *
41232446 TTTAATCTTTGTACTTTAATTTTGACATGATTTAG
127 TTTAATCTCTATACTTCAATTTTGACATAATTTAG
41232481 TGCCTCAACT
Statistics
Matches: 137, Mismatches: 19, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
178 3 0.02
179 93 0.68
180 35 0.26
181 6 0.04
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.49
Consensus pattern (180 bp):
TTTTCTTTTCTTTTGAATTGAGAAAAATAATAACTAAATTTCAATTCTAATCTCTACACTTTTTA
AAGATTATAGAATAATGGTTAAATTTTAGTTTTGATCCCTATATTTAGATCAAATTTGAGATTTA
ATCTCTATACTTCAATTTTGACATAATTTAGACATTTGTCCATTCTTTTT
Found at i:41232906 original size:21 final size:21
Alignment explanation
Indices: 41232862--41232920 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
41232852 ATTATTTTTG
**
41232862 TAATATTTT-TAGAATTTTGGT
1 TAATATTTTATA-AATTTTAAT
41232883 TAATATTTTATAAATTTTAAT
1 TAATATTTTATAAATTTTAAT
*
41232904 T-A-ATTTTATAATTTTTA
1 TAATATTTTATAAATTTTA
41232921 TGCTTTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 14 0.41
20 1 0.03
21 17 0.50
22 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
TAATATTTTATAAATTTTAAT
Found at i:41234125 original size:27 final size:27
Alignment explanation
Indices: 41234048--41234159 Score: 107
Period size: 27 Copynumber: 4.1 Consensus size: 27
41234038 GAAGGATACT
* *
41234048 CTTTCATATTGTGCCACAAAGGCGTTT
1 CTTTCATATTGCGCCACAAAGGCGTTC
* *
41234075 TTTTCATATTGTGCCACAAAGGCGTTC
1 CTTTCATATTGCGCCACAAAGGCGTTC
* * *
41234102 CTTTCACATTGCGTCACAAAGGCGCTC
1 CTTTCATATTGCGCCACAAAGGCGTTC
* * * ** *
41234129 TTTTCATGTTACGTTACAAAGACGTTC
1 CTTTCATATTGCGCCACAAAGGCGTTC
41234156 CTTT
1 CTTT
41234160 AGGGTTCTTC
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (27 bp):
CTTTCATATTGCGCCACAAAGGCGTTC
Found at i:41239156 original size:26 final size:25
Alignment explanation
Indices: 41239127--41239184 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
41239117 AAATCTCAAC
*
41239127 ATTGCCTATGAAGTTAAAAAAATTCA
1 ATTGCCTATGAA-CTAAAAAAATTCA
* **
41239153 ATTGCCTGTTTACTAAAAAAATTCA
1 ATTGCCTATGAACTAAAAAAATTCA
41239178 ATTGCCT
1 ATTGCCT
41239185 GTTTACTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 19 0.68
26 9 0.32
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (25 bp):
ATTGCCTATGAACTAAAAAAATTCA
Found at i:41239175 original size:25 final size:25
Alignment explanation
Indices: 41239141--41239191 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
41239131 CCTATGAAGT
41239141 TAAAAAAATTCAATTGCCTGTTTAC
1 TAAAAAAATTCAATTGCCTGTTTAC
41239166 TAAAAAAATTCAATTGCCTGTTTAC
1 TAAAAAAATTCAATTGCCTGTTTAC
41239191 T
1 T
41239192 GAATAATTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (25 bp):
TAAAAAAATTCAATTGCCTGTTTAC
Found at i:41240954 original size:22 final size:20
Alignment explanation
Indices: 41240896--41240955 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 20
41240886 TAGCAAAACA
41240896 TAAAAATATTGAAAAATTTAT
1 TAAAAATATT-AAAAATTTAT
* *
41240917 AAATAAATATT-GAAATTTACT
1 TAA-AAATATTAAAAATTTA-T
41240938 TAAAAATAATTAAAAATT
1 TAAAAAT-ATTAAAAATT
41240956 AATCATAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
20 11 0.35
21 8 0.26
22 12 0.39
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (20 bp):
TAAAAATATTAAAAATTTAT
Found at i:41247532 original size:24 final size:24
Alignment explanation
Indices: 41247496--41247554 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
41247486 ATAAGAAGAT
41247496 GAAAGGTTTAAGGAAGATGAAAGGC
1 GAAAGG-TTAAGGAAGATGAAAGGC
* * * *
41247521 GGAAGGTTAAGGGATATGAAAGGT
1 GAAAGGTTAAGGAAGATGAAAGGC
41247545 GAAAGGTTAA
1 GAAAGGTTAA
41247555 ACATCCACTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.42, C:0.02, G:0.37, T:0.19
Consensus pattern (24 bp):
GAAAGGTTAAGGAAGATGAAAGGC
Found at i:41252437 original size:33 final size:35
Alignment explanation
Indices: 41252390--41252461 Score: 112
Period size: 33 Copynumber: 2.1 Consensus size: 35
41252380 TAATATAAAT
* *
41252390 ATAAGTAGTTCCTTAACAA-ACTTTCAAGCA-AAC
1 ATAAGTAATCCCTTAACAATACTTTCAAGCATAAC
41252423 ATAAGTAATCCCTTAACAATACTTTCAAGCATAAC
1 ATAAGTAATCCCTTAACAATACTTTCAAGCATAAC
41252458 ATAA
1 ATAA
41252462 TAGAAAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 17 0.49
34 11 0.31
35 7 0.20
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (35 bp):
ATAAGTAATCCCTTAACAATACTTTCAAGCATAAC
Found at i:41265176 original size:19 final size:19
Alignment explanation
Indices: 41265152--41265189 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41265142 ATGTATTGGT
*
41265152 ATTAGATTTTTAGAGTTTA
1 ATTAGAGTTTTAGAGTTTA
*
41265171 ATTAGAGTTTTAGGGTTTA
1 ATTAGAGTTTTAGAGTTTA
41265190 TTTGATGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (19 bp):
ATTAGAGTTTTAGAGTTTA
Found at i:41273116 original size:17 final size:17
Alignment explanation
Indices: 41273085--41273126 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
41273075 ATATGCACAT
*
41273085 TTTAGTTTTAAAAAAAA
1 TTTATTTTTAAAAAAAA
41273102 -TTATTTTTGAAAAAAAA
1 TTTATTTTT-AAAAAAAA
41273119 TTTATTTT
1 TTTATTTT
41273127 GGCATGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 8 0.36
18 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TTTATTTTTAAAAAAAA
Found at i:41280613 original size:34 final size:34
Alignment explanation
Indices: 41280570--41280637 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
41280560 GCATTTTTGA
* *
41280570 CACTGTACTGAGATGGGCTAAGG-CCAAAACTGT
1 CACTGTACTGAAAAGGGCTAAGGCCCAAAACTGT
* *
41280603 CACTGATACTGAAAAGGGCTCAGGCCCAAGACTGT
1 CACTG-TACTGAAAAGGGCTAAGGCCCAAAACTGT
41280638 TCAACTGTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 15 0.52
35 9 0.31
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (34 bp):
CACTGTACTGAAAAGGGCTAAGGCCCAAAACTGT
Found at i:41281045 original size:14 final size:14
Alignment explanation
Indices: 41281026--41281063 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
41281016 ACAATGAGGG
41281026 ATGTTTTAAAACAA
1 ATGTTTTAAAACAA
41281040 ATGTTTTAAAACAA
1 ATGTTTTAAAACAA
41281054 ATGTTTTAAA
1 ATGTTTTAAA
41281064 TGAATAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (14 bp):
ATGTTTTAAAACAA
Found at i:41286715 original size:22 final size:23
Alignment explanation
Indices: 41286671--41286716 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
41286661 GACGATTTTA
41286671 AAATAATATATAAAAAGTTGAAAAC
1 AAATAATATATAAAAA--TGAAAAC
*
41286696 AAATAATATGTAAAAA-GAAAA
1 AAATAATATATAAAAATGAAAA
41286717 TTTCAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
25 15 0.75
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22
Consensus pattern (23 bp):
AAATAATATATAAAAATGAAAAC
Found at i:41291460 original size:14 final size:14
Alignment explanation
Indices: 41291441--41291471 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41291431 TCAAAGTTTC
41291441 CAATTTTGGGTCAT
1 CAATTTTGGGTCAT
*
41291455 CAATTTTGGGTCTT
1 CAATTTTGGGTCAT
41291469 CAA
1 CAA
41291472 AGTTTCCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (14 bp):
CAATTTTGGGTCAT
Found at i:41292969 original size:51 final size:52
Alignment explanation
Indices: 41292911--41293017 Score: 135
Period size: 51 Copynumber: 2.1 Consensus size: 52
41292901 TTTCATTTTC
** * * *
41292911 ATTTTCATTTTGGAGAAAACCACATTCATTTCGAAATGATT-CTATTTCTCA
1 ATTTTCATTAAGGAGAAAACCACAATCATTTCCAAATGATTCCTATTACTCA
* * *
41292962 ATTTTCATTAAGGAGAAAACCATAATCATTTCCAAATGTTTCCTATTACTCC
1 ATTTTCATTAAGGAGAAAACCACAATCATTTCCAAATGATTCCTATTACTCA
41293014 ATTT
1 ATTT
41293018 CTATTCATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
51 35 0.74
52 12 0.26
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (52 bp):
ATTTTCATTAAGGAGAAAACCACAATCATTTCCAAATGATTCCTATTACTCA
Found at i:41294469 original size:19 final size:19
Alignment explanation
Indices: 41294442--41294484 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
41294432 AGATTAATAA
*
41294442 TTAACTAATCCTAATTAAC
1 TTAACTAATCATAATTAAC
* *
41294461 TTAATTAATTATAATTAAC
1 TTAACTAATCATAATTAAC
41294480 -TAACT
1 TTAACT
41294485 CTAACCTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAACTAATCATAATTAAC
Found at i:41298093 original size:21 final size:22
Alignment explanation
Indices: 41298067--41298119 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
41298057 CTACAACTTA
*
41298067 AAGCAGAGGCAGTAGCGAGGG-
1 AAGCAGAGGCAGTAGCAAGGGC
*
41298088 AAGCAGAGGCAGTAGTAAGGGC
1 AAGCAGAGGCAGTAGCAAGGGC
41298110 AA-CAGAGGCA
1 AAGCAGAGGCA
41298120 ACAAGAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.38, C:0.15, G:0.42, T:0.06
Consensus pattern (22 bp):
AAGCAGAGGCAGTAGCAAGGGC
Found at i:41301881 original size:46 final size:45
Alignment explanation
Indices: 41301813--41301975 Score: 132
Period size: 46 Copynumber: 3.6 Consensus size: 45
41301803 TTTTTTGTAC
* * ** *
41301813 AGGTTAAACCCTAACGATTGACCAGACACTACTATTCAATTCGTGT
1 AGGTTCAACCCTAATGGGTGACCAGACACTA-TATTCGATTCGTGT
* ** **
41301859 AGGTTCAGCCCTAATGGGTGACCA-AGCACTATTACCCGATTTATGT
1 AGGTTCAACCCTAATGGGTGACCAGA-CACTA-TATTCGATTCGTGT
* * *
41301905 AGGTTCAACCCTAATGGGTGACCTGGCAGTAT-TGTCTGATTCGTGT
1 AGGTTCAACCCTAATGGGTGACCAGACACTATAT-TC-GATTCGTGT
* *
41301951 AGGTTTAACCCTAATGGGTAACCAG
1 AGGTTCAACCCTAATGGGTGACCAG
41301976 GAATTATGAT
Statistics
Matches: 91, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
45 3 0.03
46 88 0.97
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (45 bp):
AGGTTCAACCCTAATGGGTGACCAGACACTATATTCGATTCGTGT
Found at i:41302777 original size:35 final size:35
Alignment explanation
Indices: 41302731--41302801 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
41302721 TATGCTTTGG
* *
41302731 ATTAGGTTTGAATGGTATTATTGAAATTTTAGGTC
1 ATTAGGTTTGAATGGTATGAATGAAATTTTAGGTC
*
41302766 ATTAGGTTTGAATGGTATGAATGACATTTTAGGTC
1 ATTAGGTTTGAATGGTATGAATGAAATTTTAGGTC
41302801 A
1 A
41302802 CCTTGTAGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.42
Consensus pattern (35 bp):
ATTAGGTTTGAATGGTATGAATGAAATTTTAGGTC
Found at i:41304864 original size:18 final size:17
Alignment explanation
Indices: 41304838--41304872 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
41304828 CATGTTGCAT
41304838 GCCCATGTGGGCCCACAC
1 GCCCATGT-GGCCCACAC
*
41304856 GCCCGTGTGGCCCACAC
1 GCCCATGTGGCCCACAC
41304873 AGCCAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.14, C:0.46, G:0.29, T:0.11
Consensus pattern (17 bp):
GCCCATGTGGCCCACAC
Found at i:41317190 original size:22 final size:21
Alignment explanation
Indices: 41317165--41317208 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
41317155 TGATAAACTT
41317165 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
41317187 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
41317208 T
1 T
41317209 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:41319785 original size:38 final size:38
Alignment explanation
Indices: 41319742--41319816 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
41319732 AAGTAAAATC
* *
41319742 ATGCCTAAGTTATTCTTGTAATATTAATTGTTAGATAA
1 ATGCCTAAGTTATTCTTGCAATATTAATTATTAGATAA
41319780 ATGCCTAAGTTATTCTTGCAATATTAATTATTAGATA
1 ATGCCTAAGTTATTCTTGCAATATTAATTATTAGATA
41319817 CCTAATGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (38 bp):
ATGCCTAAGTTATTCTTGCAATATTAATTATTAGATAA
Found at i:41319850 original size:23 final size:23
Alignment explanation
Indices: 41319802--41319847 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41319792 TTCTTGCAAT
* *
41319802 ATTAATTATTAGATACCTAATGA
1 ATTAATTATTAAATACATAATGA
*
41319825 ATTAATTATTAAAT-CATATTGA
1 ATTAATTATTAAATACATAATGA
41319847 A
1 A
41319848 ATTGTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (23 bp):
ATTAATTATTAAATACATAATGA
Found at i:41325539 original size:23 final size:23
Alignment explanation
Indices: 41325493--41325558 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
41325483 TTCAACTATG
* *
41325493 ATTAAACTTAATC-ACT-TTAAT
1 ATTAAATTTAATCTAATATTAAT
41325514 ATTAAATTTAATCTAATATTAAT
1 ATTAAATTTAATCTAATATTAAT
* * *
41325537 ATTAGATTAAATTTAATATTAA
1 ATTAAATTTAATCTAATATTAA
41325559 ATCTTATTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 12 0.32
22 2 0.05
23 24 0.63
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAATTTAATCTAATATTAAT
Found at i:41325607 original size:17 final size:17
Alignment explanation
Indices: 41325585--41325658 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
41325575 GTAGCTAAAC
41325585 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTTAAT
**
41325602 ATTAAATT-AATAAAAT
1 ATTAAATTAAATTTAAT
* *
41325618 ACT--ATTAAGA--GAAGT
1 ATTAAATTAA-ATTTAA-T
41325633 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTTAAT
41325650 ATTAAATTA
1 ATTAAATTA
41325659 TTAAAATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
14 5 0.11
15 4 0.09
16 10 0.23
17 23 0.52
18 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (17 bp):
ATTAAATTAAATTTAAT
Found at i:41325672 original size:48 final size:48
Alignment explanation
Indices: 41325534--41325673 Score: 176
Period size: 48 Copynumber: 2.9 Consensus size: 48
41325524 ATCTAATATT
* * **
41325534 AATATTAGATTAAATTTAATATTAAATCTTATTAAAATAAT-GT-AGCTA
1 AATATTAAATTAAATTTAATATTAAA--TTATTAAAATAATATTAAGAGA
* * *
41325582 AACATTAAATTAAATTTAATATTAAATTAATAAAATACTATTAAGAGA
1 AATATTAAATTAAATTTAATATTAAATTATTAAAATAATATTAAGAGA
*
41325630 AGTATTAAATTAAATTTAATATTAAATTATTAAAATAATATTAA
1 AATATTAAATTAAATTTAATATTAAATTATTAAAATAATATTAA
41325674 TTTATAAATG
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
46 11 0.14
47 1 0.01
48 67 0.85
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (48 bp):
AATATTAAATTAAATTTAATATTAAATTATTAAAATAATATTAAGAGA
Found at i:41339620 original size:14 final size:15
Alignment explanation
Indices: 41339598--41339674 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
41339588 CAATCAAACA
41339598 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
41339612 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
41339627 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
41339647 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
41339661 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
41339675 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:41339639 original size:20 final size:20
Alignment explanation
Indices: 41339614--41339653 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41339604 AATATTTTCC
*
41339614 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
41339634 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
41339654 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:41339659 original size:34 final size:35
Alignment explanation
Indices: 41339602--41339668 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
41339592 CAAACACCAG
*
41339602 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
41339637 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
41339669 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:41341828 original size:29 final size:29
Alignment explanation
Indices: 41341795--41341852 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
41341785 ATGCATCCAC
41341795 AACGAGTGGTTGTAACATCCCAAATGTAG
1 AACGAGTGGTTGTAACATCCCAAATGTAG
41341824 AACGAGTGGTTGTAACATCCCAAATGTAG
1 AACGAGTGGTTGTAACATCCCAAATGTAG
41341853 CGAATCCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (29 bp):
AACGAGTGGTTGTAACATCCCAAATGTAG
Found at i:41345965 original size:105 final size:103
Alignment explanation
Indices: 41345785--41346052 Score: 412
Period size: 105 Copynumber: 2.6 Consensus size: 103
41345775 TAACCGTTAT
* * *
41345785 TGGTGGATCCCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGAT-ACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACATAGCAACCCCTCGGGGG
* *
41345850 AATCAGCACATAGCAGCCCCCTTT-TCATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
41345888 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGGAATCAGCACATAGCAACCCCTCGGG
1 TGGTGGATA-CGCACTTAGCACCACCAATG-AATC-GGGGAATCAGCACATAGCAACCCCTCGGG
41345953 GGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
63 GGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* * *
41345994 TGGTGGATCACGCACATAGCACCACCCATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACATAGCAACCCCT
41346053 TTTATATACA
Statistics
Matches: 152, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
103 27 0.18
104 28 0.18
105 57 0.38
106 39 0.26
107 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (103 bp):
TGGTGGATACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACATAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:41345976 original size:28 final size:27
Alignment explanation
Indices: 41345921--41345974 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
41345911 ACCAATGAAA
41345921 TCGGGGGAATCAGCACATAGCAACCCC
1 TCGGGGGAATCAGCACATAGCAACCCC
41345948 TCGGGGGAATCAGCACATAGCAACCCC
1 TCGGGGGAATCAGCACATAGCAACCCC
41345975 CTTTCACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.33, G:0.26, T:0.11
Consensus pattern (27 bp):
TCGGGGGAATCAGCACATAGCAACCCC
Found at i:41370950 original size:44 final size:45
Alignment explanation
Indices: 41370871--41370966 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 45
41370861 TTTGCTATGC
* **
41370871 ATCCACAACAATAGGCAGATTCCATCTGCGGTGTTT-TGTTGTGT
1 ATCCACAACAATAGGCAGATTCCACCTGCAATGTTTGTGTTGTGT
*
41370915 ATCCACAAGC-ATAGGCAGATTCCACCTGTAATGTTTGTGTTGTGT
1 ATCCACAA-CAATAGGCAGATTCCACCTGCAATGTTTGTGTTGTGT
*
41370960 GTCCACA
1 ATCCACA
41370967 GCCATTGGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 30 0.67
45 15 0.33
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (45 bp):
ATCCACAACAATAGGCAGATTCCACCTGCAATGTTTGTGTTGTGT
Found at i:41376219 original size:2 final size:2
Alignment explanation
Indices: 41376212--41376238 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41376202 TGTTTTTCTC
41376212 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 A
41376239 ATGGTGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41376750 original size:24 final size:24
Alignment explanation
Indices: 41376705--41376750 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
41376695 GAAGAACTTC
* *
41376705 TTATTGTGTTTCTAGAACAAAAAA
1 TTATAGTGTTTCTAGAAAAAAAAA
**
41376729 TTATAGTGTTTCTCTAAAAAAA
1 TTATAGTGTTTCTAGAAAAAAA
41376751 GTAGAAACAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (24 bp):
TTATAGTGTTTCTAGAAAAAAAAA
Found at i:41380562 original size:30 final size:30
Alignment explanation
Indices: 41380505--41380587 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 30
41380495 GTTGCCTGCT
* * **
41380505 TCGGCAGTCATCAGCTTCTATTGGACACAA
1 TCGGCAGTCATCGGCTTCTGTCAGACACAA
*
41380535 TTGGCAGTCATCGGCTTCTGTCAGACACAA
1 TCGGCAGTCATCGGCTTCTGTCAGACACAA
* *
41380565 TCGGTAGTCATAGGCTTCTGTCA
1 TCGGCAGTCATCGGCTTCTGTCA
41380588 TATGAAATCA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (30 bp):
TCGGCAGTCATCGGCTTCTGTCAGACACAA
Found at i:41380602 original size:30 final size:30
Alignment explanation
Indices: 41380540--41380605 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
41380530 CACAATTGGC
* *
41380540 AGTCATCGGCTTCTGTCAGACACAATCGGT
1 AGTCATAGGCTTCTGTCAGACACAATCAGT
* *
41380570 AGTCATAGGCTTCTGTCATATGA-AATCAGT
1 AGTCATAGGCTTCTGTCAGA-CACAATCAGT
41380600 AGTCAT
1 AGTCAT
41380606 CAGCTTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (30 bp):
AGTCATAGGCTTCTGTCAGACACAATCAGT
Found at i:41390184 original size:16 final size:16
Alignment explanation
Indices: 41390163--41390228 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
41390153 GTTCACATAT
41390163 GGGGGTTCGCATGAAA
1 GGGGGTTCGCATGAAA
* *
41390179 GGGGGTTTGCAT-ATA
1 GGGGGTTCGCATGAAA
* *
41390194 -GGTGTTCGCATGCAA
1 GGGGGTTCGCATGAAA
*
41390209 GAAGGGTT-GCATGAAA
1 G-GGGGTTCGCATGAAA
41390225 GGGG
1 GGGG
41390229 TTCACATGCA
Statistics
Matches: 37, Mismatches: 10, Indels: 7
0.69 0.19 0.13
Matches are distributed among these distances:
14 9 0.24
15 5 0.14
16 19 0.51
17 4 0.11
ACGTcount: A:0.24, C:0.11, G:0.42, T:0.23
Consensus pattern (16 bp):
GGGGGTTCGCATGAAA
Found at i:41390219 original size:30 final size:30
Alignment explanation
Indices: 41390149--41390238 Score: 83
Period size: 30 Copynumber: 2.9 Consensus size: 30
41390139 TTTGTAGGCT
* * *
41390149 AAGGGTTCACATATGGGGGTTCGCATGAAAG
1 AAGGGTT-GCATATAGGGGTTCGCATGCAAG
* *
41390180 -GGGGTTTGCATATAGGTGTTCGCATGCAAG
1 AAGGG-TTGCATATAGGGGTTCGCATGCAAG
* *
41390210 AAGGGTTGCATGAAAGGGGTTCACATGCA
1 AAGGGTTGCAT-ATAGGGGTTCGCATGCA
41390239 TGGGTTTGCT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
30 28 0.60
31 19 0.40
ACGTcount: A:0.27, C:0.13, G:0.36, T:0.24
Consensus pattern (30 bp):
AAGGGTTGCATATAGGGGTTCGCATGCAAG
Found at i:41391753 original size:12 final size:12
Alignment explanation
Indices: 41391736--41391760 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41391726 GAACACAATT
41391736 TCAATTTTGAGA
1 TCAATTTTGAGA
41391748 TCAATTTTGAGA
1 TCAATTTTGAGA
41391760 T
1 T
41391761 TAAAGTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TCAATTTTGAGA
Found at i:41393567 original size:15 final size:15
Alignment explanation
Indices: 41393513--41393677 Score: 96
Period size: 14 Copynumber: 11.5 Consensus size: 15
41393503 ATACATAAGA
41393513 AGGGTTTGCACATAT
1 AGGGTTTGCACATAT
* *
41393528 -GGGTTTGTACCT-T
1 AGGGTTTGCACATAT
* *
41393541 A-GGTTTCACACATGT
1 AGGGTTT-GCACATAT
*
41393556 AGGGTTTGCACATAC
1 AGGGTTTGCACATAT
*
41393571 AGGGTTCGCACATAT
1 AGGGTTTGCACATAT
* * *
41393586 -GGGTTCGTACCTA-
1 AGGGTTTGCACATAT
* * *
41393599 A-GGCTCGCACTTAT
1 AGGGTTTGCACATAT
*
41393613 -GGGTTTGCACCTA-
1 AGGGTTTGCACATAT
* * *
41393626 GGGGTTCGCACATGT
1 AGGGTTTGCACATAT
*
41393641 AAGGTTTGCACATAT
1 AGGGTTTGCACATAT
*
41393656 AGGGTTTGCATATAT
1 AGGGTTTGCACATAT
41393671 -GGGTTTG
1 AGGGTTTG
41393678 TACCTAGGGC
Statistics
Matches: 114, Mismatches: 27, Indels: 19
0.71 0.17 0.12
Matches are distributed among these distances:
13 15 0.13
14 50 0.44
15 44 0.39
16 5 0.04
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (15 bp):
AGGGTTTGCACATAT
Found at i:41393624 original size:27 final size:29
Alignment explanation
Indices: 41393520--41393701 Score: 99
Period size: 29 Copynumber: 6.4 Consensus size: 29
41393510 AGAAGGGTTT
* * **
41393520 GCACATATGGGTTTGTACCT-TAGGTTTC
1 GCACATATGGGTTTGCACCTACAGGGCTC
* * * *
41393548 ACACATGTAGGGTTTGCACATACAGGGTTC
1 GCACATAT-GGGTTTGCACCTACAGGGCTC
* *
41393578 GCACATATGGGTTCGTACCTA-A-GGCTC
1 GCACATATGGGTTTGCACCTACAGGGCTC
* * *
41393605 GCACTTATGGGTTTGCACCTA-GGGGTTC
1 GCACATATGGGTTTGCACCTACAGGGCTC
* * * * * *
41393633 GCACATGTAAGGTTTGCACATATAGGGTTT
1 GCACATAT-GGGTTTGCACCTACAGGGCTC
* *
41393663 GCATATATGGGTTTGTACCT--AGGGCTC
1 GCACATATGGGTTTGCACCTACAGGGCTC
*
41393690 ACACATA-GGGTT
1 GCACATATGGGTT
41393702 CCACATAGTA
Statistics
Matches: 117, Mismatches: 32, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
26 5 0.04
27 32 0.27
28 17 0.15
29 40 0.34
30 23 0.20
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (29 bp):
GCACATATGGGTTTGCACCTACAGGGCTC
Found at i:41393669 original size:13 final size:14
Alignment explanation
Indices: 41393643--41393677 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
41393633 GCACATGTAA
*
41393643 GGTTTGCACATATAG
1 GGTTTGCATATAT-G
41393658 GGTTTGCATATATG
1 GGTTTGCATATATG
41393672 GGTTTG
1 GGTTTG
41393678 TACCTAGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.20, C:0.09, G:0.31, T:0.40
Consensus pattern (14 bp):
GGTTTGCATATATG
Found at i:41393671 original size:85 final size:85
Alignment explanation
Indices: 41393520--41393701 Score: 242
Period size: 85 Copynumber: 2.2 Consensus size: 85
41393510 AGAAGGGTTT
* * *
41393520 GCACATATGGGTTTGTACCTTAGGTTTCACACATGTAGGGTTTGCACATACAGGGTTCGCACATA
1 GCACATATGGGTTTGCACCTTAGGGTTCACACATGTAAGGTTTGCACATACAGGGTTCGCACATA
41393585 TGGGTTCGTACCTAAGGCTC
66 TGGGTTCGTACCTAAGGCTC
* * * * *
41393605 GCACTTATGGGTTTGCACC-TAGGGGTTCGCACATGTAAGGTTTGCACATATAGGGTTTGCATAT
1 GCACATATGGGTTTGCACCTTA-GGGTTCACACATGTAAGGTTTGCACATACAGGGTTCGCACAT
* *
41393669 ATGGGTTTGTACCTAGGGCTC
65 ATGGGTTCGTACCTAAGGCTC
*
41393690 ACACATA-GGGTT
1 GCACATATGGGTT
41393702 CCACATAGTA
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
84 7 0.08
85 77 0.92
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (85 bp):
GCACATATGGGTTTGCACCTTAGGGTTCACACATGTAAGGTTTGCACATACAGGGTTCGCACATA
TGGGTTCGTACCTAAGGCTC
Found at i:41394347 original size:13 final size:13
Alignment explanation
Indices: 41394331--41394355 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41394321 TTTTCTTGAA
41394331 AAAAATTCTAGGT
1 AAAAATTCTAGGT
41394344 AAAAATTCTAGG
1 AAAAATTCTAGG
41394356 GATTGAAAAG
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:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (13 bp):
AAAAATTCTAGGT
Found at i:41398083 original size:18 final size:19
Alignment explanation
Indices: 41398038--41398084 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
41398028 ATTTAAACTA
41398038 ATAAATATT-TAAAAAATT
1 ATAAATATTATAAAAAATT
*
41398056 ATAAAAATTATAAAATAATT
1 ATAAATATTATAAAA-AATT
41398076 -T-AATATTAT
1 ATAAATATTAT
41398085 TTTAAATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 15 0.60
19 6 0.24
20 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAATATTATAAAAAATT
Found at i:41403719 original size:82 final size:81
Alignment explanation
Indices: 41403618--41403953 Score: 386
Period size: 82 Copynumber: 4.1 Consensus size: 81
41403608 ACGATAGAAT
* * * * **
41403618 TAAATCCCGAAACAAAATTATTTAATTAAATCTTGTTTGGAAACAAAATCAAAATCGAATAAAAT
1 TAAATCCC-AAATAGAATTATTCAATTAATTCTCATTTGGAAACAAAATCAAAATCGAATAAAAT
*
41403683 CTTTTAAACGGCGGGAA
65 CTGTTAAACGGCGGGAA
41403700 TAAATCCCAAAGTAGAATTATTCAATTAATTCTCATTTGGAAACAAAATCAAAATCGAATAAAAT
1 TAAATCCCAAA-TAGAATTATTCAATTAATTCTCATTTGGAAACAAAATCAAAATCGAATAAAAT
41403765 CTGTTAAACGGCGGGAA
65 CTGTTAAACGGCGGGAA
* * * * * * *
41403782 TAAATCCCGAAATAGAGTTATTCAATTGATTCTTATTTTGAAATAAGATCAAAACCGAATAAAAT
1 TAAATCCC-AAATAGAATTATTCAATTAATTCTCATTTGGAAACAAAATCAAAATCGAATAAAAT
* * *
41403847 ATGTTAAACAGCGAGAA
65 CTGTTAAACGGCGGGAA
* * ** * *
41403864 TAAATCCTGAAATAAAATTATTCAATTAATTCTCGCTGGGAAACAAAATCAAAATAGAATAAAAT
1 TAAATCC-CAAATAGAATTATTCAATTAATTCTCATTTGGAAACAAAATCAAAATCGAATAAAAT
* * *
41403929 CTATTGAAA-GACAGGAA
65 CTGTT-AAACGGCGGGAA
41403946 TAAATCCC
1 TAAATCCC
41403954 GAAACAGGTT
Statistics
Matches: 213, Mismatches: 37, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
81 3 0.01
82 204 0.96
83 6 0.03
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.27
Consensus pattern (81 bp):
TAAATCCCAAATAGAATTATTCAATTAATTCTCATTTGGAAACAAAATCAAAATCGAATAAAATC
TGTTAAACGGCGGGAA
Found at i:41403788 original size:164 final size:164
Alignment explanation
Indices: 41403618--41403959 Score: 436
Period size: 164 Copynumber: 2.1 Consensus size: 164
41403608 ACGATAGAAT
* * *
41403618 TAAATCCCGAAACAAAATTATTTAATTAAATCTTGTTTGGAAACAAAATCAAAATCGAATAAAAT
1 TAAATCCCGAAACAAAATTATTCAATTAAATCTTATTTGGAAACAAAATCAAAACCGAATAAAAT
* * * * * * *
41403683 CTTTTAAACGGCGGGAATAAATCC-CAAAGTAGAATTATTCAATTAATTCTCATTTGGAAACAAA
66 ATGTTAAACAGCGAGAATAAATCCTCAAA-TAAAATTATTCAATTAATTCTCACTGGGAAACAAA
* * * *
41403747 ATCAAAATCGAATAAAATCTGTT-AAACGGCGGGAA
130 ATCAAAATAGAATAAAATCTATTGAAA-GACAGGAA
* * * * * * * *
41403782 TAAATCCCGAAATAGAGTTATTCAATTGATTCTTATTTTGAAATAAGATCAAAACCGAATAAAAT
1 TAAATCCCGAAACAAAATTATTCAATTAAATCTTATTTGGAAACAAAATCAAAACCGAATAAAAT
* *
41403847 ATGTTAAACAGCGAGAATAAATCCTGAAATAAAATTATTCAATTAATTCTCGCTGGGAAACAAAA
66 ATGTTAAACAGCGAGAATAAATCCTCAAATAAAATTATTCAATTAATTCTCACTGGGAAACAAAA
41403912 TCAAAATAGAATAAAATCTATTGAAAGACAGGAA
131 TCAAAATAGAATAAAATCTATTGAAAGACAGGAA
41403946 TAAATCCCGAAACA
1 TAAATCCCGAAACA
41403960 GGTTTTATTG
Statistics
Matches: 151, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
164 145 0.96
165 6 0.04
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.27
Consensus pattern (164 bp):
TAAATCCCGAAACAAAATTATTCAATTAAATCTTATTTGGAAACAAAATCAAAACCGAATAAAAT
ATGTTAAACAGCGAGAATAAATCCTCAAATAAAATTATTCAATTAATTCTCACTGGGAAACAAAA
TCAAAATAGAATAAAATCTATTGAAAGACAGGAA
Found at i:41404900 original size:2 final size:2
Alignment explanation
Indices: 41404893--41404926 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
41404883 GTGGGTTCTC
41404893 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41404927 GCATATCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41415878 original size:17 final size:17
Alignment explanation
Indices: 41415852--41415884 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41415842 ATGCAGCCAC
*
41415852 ATTGTGATTACATTTTT
1 ATTGTCATTACATTTTT
41415869 ATTGTCATTACATTTT
1 ATTGTCATTACATTTT
41415885 CATGTTTGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (17 bp):
ATTGTCATTACATTTTT
Found at i:41419536 original size:163 final size:162
Alignment explanation
Indices: 41419353--41419706 Score: 476
Period size: 163 Copynumber: 2.2 Consensus size: 162
41419343 ATCAATTCTG
* * * *
41419353 TTAAACGATAAGATTAAATCCCGAAACAAAATTATTTAATTAAAACTTGTTTGGAAACAAAATCA
1 TTAAACGGT-AGAATAAATCCCGAAACAAAATTATTCAATTAAAACTCGTTTGGAAACAAAATCA
**
41419418 AAATCGAATAAAATCTGTTAAATGGC-AGAATAAATCCAGAAAAAGAATTATTCAATTAATTCTC
65 AAATCGAATAAAATCTGTTAAACAGCGAGAATAAATCCAGAAAAAGAATTATTCAATTAATTCTC
* *
41419482 ATTTGGAAACAAAATCAAAATCGAATAAAATCTA
130 ACTTGGAAACAAAATAAAAATCGAA-AAAATCTA
* **
41419516 TTAAACGGTGAGAATAAATCCCGAAACATAATTATTCAATTAATTCTCGTTTGGAAACAAAATCA
1 TTAAACGGT-AGAATAAATCCCGAAACAAAATTATTCAATTAAAACTCGTTTGGAAACAAAATCA
* * * * *
41419581 AATTTGAATAAAATCTGTTAAACAGCGGGAATAAATCCCGAAACAGAATTATTCAATTAATTCTC
65 AAATCGAATAAAATCTGTTAAACAGCGAGAATAAATCCAGAAAAAGAATTATTCAATTAATTCTC
* * * *
41419646 GCTTGGAGACAAAATAAAAATGGAAAAAATCTG
130 ACTTGGAAACAAAATAAAAATCGAAAAAATCTA
*
41419679 TTGAACGGTAGGAATAAATCCCGAAACA
1 TTAAACGGTA-GAATAAATCCCGAAACA
41419707 GGTTTTATTG
Statistics
Matches: 167, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
162 1 0.01
163 111 0.66
164 55 0.33
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.27
Consensus pattern (162 bp):
TTAAACGGTAGAATAAATCCCGAAACAAAATTATTCAATTAAAACTCGTTTGGAAACAAAATCAA
AATCGAATAAAATCTGTTAAACAGCGAGAATAAATCCAGAAAAAGAATTATTCAATTAATTCTCA
CTTGGAAACAAAATAAAAATCGAAAAAATCTA
Found at i:41419571 original size:82 final size:82
Alignment explanation
Indices: 41419349--41419707 Score: 463
Period size: 82 Copynumber: 4.4 Consensus size: 82
41419339 CAAAATCAAT
* * * * * ** *
41419349 TCTGTTAAACGATAAGATTAAATCCCGAAACAAAATTATTTAATTAAAACTTGTTTGGAAACAAA
1 TCTGTTAAACGGTGAGAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTGGAAACAAA
41419414 ATCAAAATCGAATAAAA
66 ATCAAAATCGAATAAAA
* * * * *
41419431 TCTGTTAAATGG-CAGAATAAATCCAGAAAAAGAATTATTCAATTAATTCTCATTTGGAAACAAA
1 TCTGTTAAACGGTGAGAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTGGAAACAAA
41419495 ATCAAAATCGAATAAAA
66 ATCAAAATCGAATAAAA
* *
41419512 TCTATTAAACGGTGAGAATAAATCCCGAAACATAATTATTCAATTAATTCTCGTTTGGAAACAAA
1 TCTGTTAAACGGTGAGAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTGGAAACAAA
* *
41419577 ATCAAATTTGAATAAAA
66 ATCAAAATCGAATAAAA
* * * * *
41419594 TCTGTTAAACAGCGGGAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGCTTGGAGACAAA
1 TCTGTTAAACGGTGAGAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTGGAAACAAA
* *
41419659 ATAAAAATGGAA-AAAA
66 ATCAAAATCGAATAAAA
*
41419675 TCTGTTGAACGGT-AGGAATAAATCCCGAAACAG
1 TCTGTTAAACGGTGA-GAATAAATCCCGAAACAG
41419708 GTTTTATTGA
Statistics
Matches: 240, Mismatches: 35, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
81 101 0.42
82 139 0.58
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.27
Consensus pattern (82 bp):
TCTGTTAAACGGTGAGAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTGGAAACAAA
ATCAAAATCGAATAAAA
Found at i:41423452 original size:20 final size:20
Alignment explanation
Indices: 41423427--41423468 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
41423417 TTAGAGACTA
* *
41423427 AAACTTTTGAAATATTTCTG
1 AAACTTCTGAAAAATTTCTG
41423447 AAACTTCTGAAAAATTTCTG
1 AAACTTCTGAAAAATTTCTG
41423467 AA
1 AA
41423469 GCATAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (20 bp):
AAACTTCTGAAAAATTTCTG
Found at i:41433493 original size:164 final size:163
Alignment explanation
Indices: 41433233--41433589 Score: 450
Period size: 164 Copynumber: 2.2 Consensus size: 163
41433223 AATTATGTTG
* * * * * *
41433233 AACGACAGGACTAAATCTCGAAACAAAATCATTTAATTAAATCTTGTTTGGAAATAAAATCAAAA
1 AACGGCAGGAATAAATCTCGAAAC-AAATTATTCAATTAAATCTTGTTTGAAAACAAAATCAAAA
* **
41433298 TCGAATAAAATCTATTCAAAGGAGGGAATAAATCCCGAAACAGAATTATTCAATTAATTATCGTT
65 TCAAATAAAATCTATTCAAAGGAAAGAATAAATCCCGAAACAGAATTATTCAATTAATTATCGTT
*
41433363 TGGAAACAAAATCAAAATCAAATTAAATCTATTA
130 TGGAAACAAAATCAAAATCAAATAAAATCTATTA
* * *
41433397 AACGGCGGGAATAAATC-CTGAAACAGAATTATTCAATT-AATTTTAGTTTGAAAACAAAATTAA
1 AACGGCAGGAATAAATCTC-GAAACA-AATTATTCAATTAAATCTT-GTTTGAAAACAAAATCAA
* * * *
41433460 AATCAAATAAAATCTATT-AAATGACAAGAATAAATCCCGAAATAGAATTATTCAATTACTTCTC
63 AATCAAATAAAATCTATTCAAAGGA-AAGAATAAATCCCGAAACAGAATTATTCAATTAATTATC
** * *
41433524 GTTTGGAAACAAAATCAAAATGGAATAAAATCTGTTG
127 GTTTGGAAACAAAATCAAAATCAAATAAAATCTATTA
*
41433561 AACTGCAGGAATAAATCTCGAAACAAATT
1 AACGGCAGGAATAAATCTCGAAACAAATT
41433590 TTATTAAATT
Statistics
Matches: 165, Mismatches: 23, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
163 16 0.10
164 148 0.90
165 1 0.01
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (163 bp):
AACGGCAGGAATAAATCTCGAAACAAATTATTCAATTAAATCTTGTTTGAAAACAAAATCAAAAT
CAAATAAAATCTATTCAAAGGAAAGAATAAATCCCGAAACAGAATTATTCAATTAATTATCGTTT
GGAAACAAAATCAAAATCAAATAAAATCTATTA
Found at i:41433573 original size:82 final size:82
Alignment explanation
Indices: 41433230--41433589 Score: 395
Period size: 82 Copynumber: 4.4 Consensus size: 82
41433220 ATCAATTATG
* * * * * * * *
41433230 TTGAAC-GACAGGACTAAATCTCGAAACAAAATCATTTAATTAAATCTTGTTTGGAAATAAAATC
1 TTGAACTG-CAGGAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTGGAAACAAAATC
*
41433294 AAAATCGAATAAAATCTA
65 AAAATCAAATAAAATCTA
* * * *
41433312 TTCAA-AGGAGGGAATAAATCCCGAAACAGAATTATTCAATTAATTATCGTTTGGAAACAAAATC
1 TTGAACTGCA-GGAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTGGAAACAAAATC
*
41433376 AAAATCAAATTAAATCTA
65 AAAATCAAATAAAATCTA
* * * * * * * *
41433394 TTAAACGGCGGGAATAAATCCTGAAACAGAATTATTCAATTAATTTTAGTTTGAAAACAAAATTA
1 TTGAACTGCAGGAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTGGAAACAAAATCA
41433459 AAATCAAATAAAATCTA
66 AAATCAAATAAAATCTA
* * * *
41433476 TT-AAATGACAAGAATAAATCCCGAAATAGAATTATTCAATTACTTCTCGTTTGGAAACAAAATC
1 TTGAACTG-CAGGAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTGGAAACAAAATC
** *
41433540 AAAATGGAATAAAATCTG
65 AAAATCAAATAAAATCTA
*
41433558 TTGAACTGCAGGAATAAATCTCGAAACA-AATT
1 TTGAACTGCAGGAATAAATCCCGAAACAGAATT
41433590 TTATTAAATT
Statistics
Matches: 232, Mismatches: 41, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
81 8 0.03
82 219 0.94
83 5 0.02
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (82 bp):
TTGAACTGCAGGAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTGGAAACAAAATCA
AAATCAAATAAAATCTA
Found at i:41434028 original size:82 final size:82
Alignment explanation
Indices: 41433942--41434280 Score: 435
Period size: 82 Copynumber: 4.1 Consensus size: 82
41433932 CGGAAAGATG
* * * *
41433942 AAATCCCGAAACAAAATTATTTAATTAAATCTTGTTTAGAAACAAAATCAAAATCGAATAAAATC
1 AAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTAGAAACAAAATCAAAATCGAATAAAATC
**
41434007 TGTTAAACGGGGGGAAT
66 TGTTAAACGACGGGAAT
* * *
41434024 AAATCTCGAAACAGAATTATTCAATTAATTCTCGTTTGGAAACAAAATCAAAATCTAATAAAATC
1 AAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTAGAAACAAAATCAAAATCGAATAAAATC
* * *
41434089 CGTGAAACGGCGGGAAT
66 TGTTAAACGACGGGAAT
* * * * *
41434106 AAATCCCAAAACATAATTATTCAATTAATTCTCCTTTGGAAACAAAATTAAAATCGAATAAAATC
1 AAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTAGAAACAAAATCAAAATCGAATAAAATC
*
41434171 TGTTAAGCGACGGGAAT
66 TGTTAAACGACGGGAAT
* * * * *
41434188 AAATCCCGAAACAGAACTATTCAATTAATTCTTGCTTAGAAACAAAATCAAAATGGATTAAAATC
1 AAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTAGAAACAAAATCAAAATCGAATAAAATC
* * **
41434253 TGCTGAACGAAAGGAAT
66 TGTTAAACGACGGGAAT
41434270 AAATCCCGAAA
1 AAATCCCGAAA
41434281 TAGGTTTTAT
Statistics
Matches: 222, Mismatches: 35, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 222 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (82 bp):
AAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTAGAAACAAAATCAAAATCGAATAAAATC
TGTTAAACGACGGGAAT
Found at i:41434584 original size:34 final size:34
Alignment explanation
Indices: 41434538--41434612 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
41434528 GCCCTAGCCA
* * * *
41434538 CTGCCACTGCCGCATGCCTCTGCCCACCTACCTT
1 CTGCCACCGCCGCATGCCTCTACCAACCTACCCT
*
41434572 CTGCCACCGCCGCATGCCTCTACCAACCTGCCCT
1 CTGCCACCGCCGCATGCCTCTACCAACCTACCCT
41434606 CTGCCAC
1 CTGCCAC
41434613 TGCCACTGCC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.13, C:0.52, G:0.15, T:0.20
Consensus pattern (34 bp):
CTGCCACCGCCGCATGCCTCTACCAACCTACCCT
Found at i:41435600 original size:3 final size:3
Alignment explanation
Indices: 41435592--41435634 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
41435582 ATTAATCTTG
41435592 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41435635 TAGTCATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41435794 original size:10 final size:10
Alignment explanation
Indices: 41435779--41435834 Score: 57
Period size: 10 Copynumber: 6.0 Consensus size: 10
41435769 TCATAATTTT
41435779 TATATACATA
1 TATATACATA
41435789 TATATACATA
1 TATATACATA
* *
41435799 T-TTTA-ATT
1 TATATACATA
41435807 TATATACATA
1 TATATACATA
*
41435817 TATAT--GTA
1 TATATACATA
41435825 TATATACATA
1 TATATACATA
41435835 CTTACATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
8 10 0.28
9 6 0.17
10 20 0.56
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (10 bp):
TATATACATA
Found at i:41435844 original size:18 final size:17
Alignment explanation
Indices: 41435783--41435845 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
41435773 AATTTTTATA
41435783 TACATATATATACATATTT
1 TACATATATATACATA--T
*
41435802 TA-ATTTATATACATAT
1 TACATATATATACATAT
**
41435818 ATATGTATATATACATACT
1 -TACATATATATACATA-T
41435837 TACATATAT
1 TACATATAT
41435846 TTTTATATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
16 1 0.03
17 2 0.06
18 30 0.83
19 3 0.08
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.46
Consensus pattern (17 bp):
TACATATATATACATAT
Found at i:41435844 original size:87 final size:89
Alignment explanation
Indices: 41435688--41435954 Score: 272
Period size: 87 Copynumber: 3.1 Consensus size: 89
41435678 ACATGCATAC
* * * *
41435688 ATTTTTATAATATATATACGTAC-ATATTTTTTA-AGTTT-TATAA--ATATATATATACACATA
1 ATTTTTAT-ATACATATACATACAATATTTTTCATA-TTTATATAATTATATGTATATACACATA
* *
41435748 CTTTTATATATTTTATATATTTCATA
64 CTTATATATATTTTATATATTTTATA
* *
41435774 ATTTTTATATACATATATATAC-ATA-TTTT-A-ATTTATATACATATATATGTATATATACATA
1 ATTTTTATATACATATACATACAATATTTTTCATATTTATATA-AT-TATATGTATATACACATA
*
41435835 CTTACATATATTTT-TATATTTTATA
64 CTTATATATATTTTATATATTTTATA
* * * * *
41435860 ATTTTAAAATATATATACATACATATATTTTTCATATTTTTATAATTTTATGTATATACACATAC
1 ATTTTTATATACATATACATACA-ATATTTTTCATATTTATATAATTATATGTATATACACATAC
41435925 --ATATATATTTTATAT-TTTTATA
65 TTATATATATTTTATATATTTTATA
41435947 ATTTTTAT
1 ATTTTTAT
41435955 TTATTTCCTT
Statistics
Matches: 152, Mismatches: 18, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
82 3 0.02
83 6 0.04
84 5 0.03
85 14 0.09
86 36 0.24
87 50 0.33
88 6 0.04
89 21 0.14
90 3 0.02
91 8 0.05
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (89 bp):
ATTTTTATATACATATACATACAATATTTTTCATATTTATATAATTATATGTATATACACATACT
TATATATATTTTATATATTTTATA
Found at i:41439384 original size:12 final size:12
Alignment explanation
Indices: 41439369--41439410 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
41439359 TGAAAATGAC
41439369 AAAAAAAA-AAG
1 AAAAAAAAGAAG
*
41439380 AAAAAAGAGAAG
1 AAAAAAAAGAAG
*
41439392 AAAAACAAGAAG
1 AAAAAAAAGAAG
41439404 AAAAAAA
1 AAAAAAA
41439411 GGAAAATGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAG
Done.