Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 177 of 199
Found at i:56623709 original size:41 final size:41
Alignment explanation
Indices: 56623605--56623709 Score: 140
Period size: 41 Copynumber: 2.5 Consensus size: 41
56623595 TTAATTTAAA
* *
56623605 CAGATTCACCGGCACTTAGCCTATTAGGCTTAAAGCCTAATT
1 CAGA-TCACCGGCACTTAGCCTGTCAGGCTTAAAGCCTAATT
*
56623647 CAGATCACCGGCACTTAGCCTGTCAGGCTTATAA-CCTGATT
1 CAGATCACCGGCACTTAGCCTGTCAGGCTTA-AAGCCTAATT
* *
56623688 CAGATCACTGGCATTTAGCCTG
1 CAGATCACCGGCACTTAGCCTG
56623710 ATTCAAATCA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
41 51 0.89
42 6 0.11
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGTCAGGCTTAAAGCCTAATT
Found at i:56623719 original size:25 final size:25
Alignment explanation
Indices: 56623681--56623734 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
56623671 AGGCTTATAA
* *
56623681 CCTGATTCAGATCACTGGCATTTAG
1 CCTGATTCAAATCACTGGCACTTAG
56623706 CCTGATTCAAATCACTGGCACTTAG
1 CCTGATTCAAATCACTGGCACTTAG
56623731 CCTG
1 CCTG
56623735 TTAGGCTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (25 bp):
CCTGATTCAAATCACTGGCACTTAG
Found at i:56623726 original size:66 final size:66
Alignment explanation
Indices: 56623638--56623775 Score: 213
Period size: 66 Copynumber: 2.1 Consensus size: 66
56623628 TTAGGCTTAA
* * *
56623638 AGCCTAATTCAGATCACCGGCACTTAGCCTGTCAGGCTTATAACCTGATTCAGATCACTGGCATT
1 AGCCTAATTCAAATCACCGGCACTTAGCCTGTCAGGCTTATAACCTGATTCAGATCACCGGCACT
56623703 T
66 T
* * * *
56623704 AGCCTGATTCAAATCACTGGCACTTAGCCTGTTAGGCTTATAACCTGGTTCAGATCACCGGCACT
1 AGCCTAATTCAAATCACCGGCACTTAGCCTGTCAGGCTTATAACCTGATTCAGATCACCGGCACT
56623769 T
66 T
56623770 AGCCTA
1 AGCCTA
56623776 CTAGGCTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (66 bp):
AGCCTAATTCAAATCACCGGCACTTAGCCTGTCAGGCTTATAACCTGATTCAGATCACCGGCACT
T
Found at i:56623773 original size:41 final size:41
Alignment explanation
Indices: 56623703--56623910 Score: 281
Period size: 41 Copynumber: 5.1 Consensus size: 41
56623693 CACTGGCATT
* * *
56623703 TAGCCTGATTCAAATCACTGGCACTTAGCCTGTTAGGCTTA
1 TAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTA
* * *
56623744 TAACCTGGTTCAGATCACCGGCACTTAGCCTACTAGGCTTA
1 TAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTA
* * *
56623785 TAGCCTGATTCAGTTCACCGACACTTAGCTTGCTAGGCTTA
1 TAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTA
* *
56623826 TAGCTTGATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTA
1 TAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTA
* * * *
56623867 TAGCCTGGTTTAGATCACCGGCACTTAGCCTGTTAGACTTA
1 TAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTA
56623908 TAG
1 TAG
56623911 TCCGAAATGT
Statistics
Matches: 146, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 146 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (41 bp):
TAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTA
Found at i:56623813 original size:107 final size:107
Alignment explanation
Indices: 56623610--56623813 Score: 286
Period size: 107 Copynumber: 1.9 Consensus size: 107
56623600 TTAAACAGAT
*
56623610 TCACCGGCACTTAGCCTATTAGGCTTAAAGCCTAATTCAGATCACCGGCACTTAGCCTGTCAGGC
1 TCACCGGCACTTAGCCTATTAGGCTTAAAGCCTAATTCAGATCACCGGCACTTAGCCTCTCAGGC
* * *
56623675 TTATAACCTGATTCAGATCACTGGCATTTAGCCTGATTCAAA
66 TTATAACCTGATTCAGATCACCGACACTTAGCCTGATTCAAA
* * **
56623717 TCACTGGCACTTAGCCTGTTAGGCTTATAA-CCTGGTTCAGATCACCGGCACTTAGCCTACT-AG
1 TCACCGGCACTTAGCCTATTAGGCTTA-AAGCCTAATTCAGATCACCGGCACTTAGCCT-CTCAG
* *
56623780 GCTTATAGCCTGATTCAGTTCACCGACACTTAGC
64 GCTTATAACCTGATTCAGATCACCGACACTTAGC
56623814 TTGCTAGGCT
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 82 0.96
108 3 0.04
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (107 bp):
TCACCGGCACTTAGCCTATTAGGCTTAAAGCCTAATTCAGATCACCGGCACTTAGCCTCTCAGGC
TTATAACCTGATTCAGATCACCGACACTTAGCCTGATTCAAA
Found at i:56623925 original size:82 final size:81
Alignment explanation
Indices: 56623703--56623943 Score: 211
Period size: 82 Copynumber: 2.9 Consensus size: 81
56623693 CACTGGCATT
* * * * * * ** *
56623703 TAGCCTGATTCAAATCACTGGCACTTAGCCTGTTAGGCTTATAAC-CTGGTTCAGATCACCGGCA
1 TAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGACTTATAGCTC-GAAT-AGTTCACCGGCA
*
56623767 CTTAGCCTACTAGGCTTA
64 CTTAGCCTGCTAGGCTTA
* * * * *
56623785 TAGCCTGATTCAGTTCACCGACACTTAGCTTGCTAGGCTTATAGCTTGATTCAGTTCACCGGCAC
1 TAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGACTTATAGCTCGAAT-AGTTCACCGGCAC
56623850 TTAGCCTGCTAGGCTTA
65 TTAGCCTGCTAGGCTTA
* * * *
56623867 TAGCCTGGTTTAGATCACCGGCACTTAGCCTGTTAGACTTATAG-TCCGAA-ATGTTTCACCGGC
1 TAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGACTTATAGCT-CGAATA-G-TTCACCGGC
*
56623930 A-TCAAGCCTGCTAG
63 ACT-TAGCCTGCTAG
56623944 ACATAAAGTC
Statistics
Matches: 133, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
80 1 0.01
81 3 0.02
82 129 0.97
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.30
Consensus pattern (81 bp):
TAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGACTTATAGCTCGAATAGTTCACCGGCACT
TAGCCTGCTAGGCTTA
Found at i:56623942 original size:123 final size:122
Alignment explanation
Indices: 56623703--56623943 Score: 290
Period size: 123 Copynumber: 2.0 Consensus size: 122
56623693 CACTGGCATT
* *
56623703 TAGCCTGATTCAAATCACTGGCACTTAGCCTGTTAGGCTTATAACCTGGTTCAGATCACCGGCAC
1 TAGCCTGATTCAAATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGGTTCAGATCACCGGCAC
* * * *
56623768 TTAGCCTACTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAGCTTGCTAGGCTTA
66 TTAGCCTACTAGACTTATAGCCTGAAT-AGTTCACCGACACTAAGCCTGCTAGGCTTA
* ** * *
56623826 TAGCTTGATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGGTTTAGATCACCGGCAC
1 TAGCCTGATTCAAATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGGTTCAGATCACCGGCAC
** *
56623891 TTAGCCTGTTAGACTTATAGTCC-GAA-ATGTTTCACCGGCA-TCAAGCCTGCTAG
66 TTAGCCTACTAGACTTATAG-CCTGAATA-G-TTCACCGACACT-AAGCCTGCTAG
56623944 ACATAAAGTC
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
121 1 0.01
122 2 0.02
123 95 0.95
124 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.30
Consensus pattern (122 bp):
TAGCCTGATTCAAATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGGTTCAGATCACCGGCAC
TTAGCCTACTAGACTTATAGCCTGAATAGTTCACCGACACTAAGCCTGCTAGGCTTA
Found at i:56624458 original size:76 final size:78
Alignment explanation
Indices: 56624316--56624459 Score: 186
Period size: 76 Copynumber: 1.9 Consensus size: 78
56624306 ATGTACATAT
* * * *
56624316 ATACATATTCGAATCTAACATATATACATATATAATTTTATACTTACATTCGAAACAAGTACTTA
1 ATACATATTCGAATCTAACATATATACATATATAATTTCATACTTACACTCGAAACAAGCAATTA
56624381 TACTTGTATACAC
66 TACTTGTATACAC
* * * *
56624394 ATACATTTTCGAATTTAAC-TA-ATACATATATAATTTCATACTTATACTC-AATATAAGCAATT
1 ATACATATTCGAATCTAACATATATACATATATAATTTCATACTTACACTCGAA-ACAAGCAATT
56624456 ATAC
65 ATAC
56624460 ATAAATATAC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
75 2 0.04
76 36 0.63
77 2 0.04
78 17 0.30
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (78 bp):
ATACATATTCGAATCTAACATATATACATATATAATTTCATACTTACACTCGAAACAAGCAATTA
TACTTGTATACAC
Found at i:56624481 original size:76 final size:79
Alignment explanation
Indices: 56624316--56624481 Score: 173
Period size: 76 Copynumber: 2.2 Consensus size: 79
56624306 ATGTACATAT
* * * *
56624316 ATACA-TATTCGAATCTAACATATATACATATATAATTTTATACTTACATTCGAAACAAGTACTT
1 ATACATTATTCGAATCTAACATATATACATATATAATTTCATACTTACACTCGAAACAAGCAATT
* **
56624380 ATACTTGTATACAC
66 ATACATAAATACAC
* * *
56624394 ATACATT-TTCGAATTTAAC-TA-ATACATATATAATTTCATACTTATACTC-AATATAAGCAAT
1 ATACATTATTCGAATCTAACATATATACATATATAATTTCATACTTACACTCGAA-ACAAGCAAT
*
56624455 TATACATAAATATAC
65 TATACATAAATACAC
*
56624470 ATGC-TTATTCGA
1 ATACATTATTCGA
56624482 TCCAAACATA
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
75 4 0.05
76 50 0.68
77 2 0.03
78 16 0.22
79 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.38
Consensus pattern (79 bp):
ATACATTATTCGAATCTAACATATATACATATATAATTTCATACTTACACTCGAAACAAGCAATT
ATACATAAATACAC
Found at i:56626868 original size:16 final size:16
Alignment explanation
Indices: 56626847--56626916 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
56626837 TTTGGTTCGC
* *
56626847 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
56626863 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
56626879 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
56626895 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
56626911 TGTAAT
1 TGTAAT
56626917 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:56627000 original size:39 final size:43
Alignment explanation
Indices: 56626895--56627004 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
56626885 GGAATAGAGG
56626895 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
56626940 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
56626980 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
56627005 TAATGAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:56627161 original size:16 final size:16
Alignment explanation
Indices: 56627124--56627165 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
56627114 TTAGTCATAT
*
56627124 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
56627140 TT-AAATATATTATAA
1 TTAAAATATATTATAA
56627155 TTAAAATATAT
1 TTAAAATATAT
56627166 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:56627172 original size:14 final size:15
Alignment explanation
Indices: 56627133--56627174 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
56627123 TTTAAACATA
*
56627133 ATTATTATTAAATAT
1 ATTATAATTAAATAT
56627148 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
56627162 A-TATAATTTAATA
1 ATTATAATTAAATA
56627175 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:56627369 original size:26 final size:28
Alignment explanation
Indices: 56627340--56627400 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
56627330 TATGAATTTG
*
56627340 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
56627366 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
56627394 TAAAATT
1 TATAATT
56627401 ATTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:56627398 original size:47 final size:45
Alignment explanation
Indices: 56627347--56627487 Score: 112
Period size: 47 Copynumber: 3.1 Consensus size: 45
56627337 TTGTATAATT
56627347 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTA-TATTA-ATATAATTTAATAATAATATATAATTTCA
* * ** * *
56627394 TAAAATTATTGATAATAAT-T--TTTCTTATATGAATTTATACAATT--
1 TAAAATAATT-ATATTAATATAATTTAATA-AT-AATATATA-ATTTCA
*
56627438 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATT-ATATT-AATATAATTTAATAATAATATATAATTTCA
56627485 TAA
1 TAA
56627488 CATTCTTAAT
Statistics
Matches: 70, Mismatches: 14, Indels: 20
0.67 0.13 0.19
Matches are distributed among these distances:
43 5 0.07
44 15 0.21
45 14 0.20
46 12 0.17
47 18 0.26
48 6 0.09
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (45 bp):
TAAAATAATTATATTAATATAATTTAATAATAATATATAATTTCA
Found at i:56627402 original size:91 final size:89
Alignment explanation
Indices: 56627306--56627522 Score: 290
Period size: 91 Copynumber: 2.4 Consensus size: 89
56627296 AATTTAAAAT
* * * *
56627306 AATTATAACTAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAA
1 AATTATAA-TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
56627371 TTTAATAATAATATATAATTTCATAA
64 TTTAATAATAATATATAATTTCATAA
* *
56627397 AATTATTGATAATAATTTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
1 AATTA-TAATAATAA-ATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
*
56627462 TTTAATAATGATATATAATTTCATAA
64 TTTAATAATAATATATAATTTCATAA
* *
56627488 CATTCTTAATAATAAAATGTTCTTATATGAATTTA
1 AATT-ATAATAAT-AAAT-TTCTTATATGAATTTA
56627523 CTAAAATCAA
Statistics
Matches: 110, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
91 88 0.80
92 22 0.20
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.46
Consensus pattern (89 bp):
AATTATAATAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATT
TAATAATAATATATAATTTCATAA
Found at i:56627403 original size:44 final size:42
Alignment explanation
Indices: 56627340--56627482 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 42
56627330 TATGAATTTG
56627340 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTATTATTA-ATATAATTTAATAAT-ATA
* ** *
56627384 TATAATTTCATAA-AATTATTGA-TAATAATTTTTCTTATATGAATTTA
1 TATAATTT-AAAATAATTATT-ATTAAT-A-TAAT-TTA-AT-AATATA
* *
56627431 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTATTATT-AATATAATTTAATAAT-ATA
56627475 TATAATTT
1 TATAATTT
56627483 CATAACATTC
Statistics
Matches: 77, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
43 5 0.06
44 29 0.38
45 9 0.12
46 9 0.12
47 19 0.25
48 6 0.08
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (42 bp):
TATAATTTAAAATAATTATTATTAATATAATTTAATAATATA
Found at i:56630669 original size:36 final size:36
Alignment explanation
Indices: 56630625--56630709 Score: 109
Period size: 36 Copynumber: 2.3 Consensus size: 36
56630615 AGAAACGGGG
* * *
56630625 GGAGCAAATCGGTAGAAAAGAAAAGA-AAATAAACTA
1 GGAGCAAATCGGCAGAAAAGAAAA-ACAAAGAAACAA
*
56630661 GGAGCAAATCGACAGAAAAGAAAAACAAAGAAACAA
1 GGAGCAAATCGGCAGAAAAGAAAAACAAAGAAACAA
56630697 GGAAGCAAATCGG
1 GG-AGCAAATCGG
56630710 ATGAAGGTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 1 0.02
36 32 0.76
37 9 0.21
ACGTcount: A:0.58, C:0.12, G:0.24, T:0.07
Consensus pattern (36 bp):
GGAGCAAATCGGCAGAAAAGAAAAACAAAGAAACAA
Found at i:56637321 original size:12 final size:12
Alignment explanation
Indices: 56637306--56637398 Score: 60
Period size: 12 Copynumber: 7.8 Consensus size: 12
56637296 TATATTTGTG
*
56637306 TCTGTATTTGCA
1 TCTGTATCTGCA
56637318 TCTGTATCTGCA
1 TCTGTATCTGCA
* *
56637330 CCTGTATCTGTA
1 TCTGTATCTGCA
* * *
56637342 TTTGTATTTGTA
1 TCTGTATCTGCA
* * *
56637354 TATGTATATGTA
1 TCTGTATCTGCA
* * *
56637366 TATGTATTTACA
1 TCTGTATCTGCA
* *
56637378 TCTATAACTGCA
1 TCTGTATCTGCA
56637390 TCTGTATCT
1 TCTGTATCT
56637399 AAAATTTTCA
Statistics
Matches: 63, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 63 1.00
ACGTcount: A:0.23, C:0.15, G:0.14, T:0.48
Consensus pattern (12 bp):
TCTGTATCTGCA
Found at i:56637327 original size:18 final size:18
Alignment explanation
Indices: 56637306--56637372 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
56637296 TATATTTGTG
*
56637306 TCTGTATTTGCATCTGTA
1 TCTGTATTTGTATCTGTA
* **
56637324 TCTGCACCTGTATCTGTA
1 TCTGTATTTGTATCTGTA
* *
56637342 TTTGTATTTGTATATGTA
1 TCTGTATTTGTATCTGTA
* *
56637360 TATGTATATGTAT
1 TCTGTATTTGTAT
56637373 TTACATCTAT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.51
Consensus pattern (18 bp):
TCTGTATTTGTATCTGTA
Found at i:56637340 original size:6 final size:6
Alignment explanation
Indices: 56637287--56637372 Score: 55
Period size: 6 Copynumber: 14.3 Consensus size: 6
56637277 ATGTATTTAC
* * * * * * * *
56637287 ATCTGT GTCTAT ATTTGT GTCTGT ATTTGC ATCTGT ATCTGC ACCTGT
1 ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT
* * * * *
56637335 ATCTGT ATTTGT ATTTGT ATATGT ATATGT ATATGT AT
1 ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT AT
56637373 TTACATCTAT
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.51
Consensus pattern (6 bp):
ATCTGT
Found at i:56639234 original size:36 final size:35
Alignment explanation
Indices: 56639157--56639234 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 35
56639147 AAAGGAAACT
* *
56639157 AAAAATTTCTTATAATCATTTTCACCAAATATTTA
1 AAAAATTTCTAATAATCATTTTCACCAAATACTTA
* *
56639192 ATAAAATTTCTAATAATTATTATT-ACTAAATGACTTA
1 A-AAAATTTCTAATAATCATT-TTCACCAAAT-ACTTA
56639229 AAAAAT
1 AAAAAT
56639235 ATAAATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
35 1 0.03
36 28 0.78
37 7 0.19
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.41
Consensus pattern (35 bp):
AAAAATTTCTAATAATCATTTTCACCAAATACTTA
Found at i:56639714 original size:14 final size:14
Alignment explanation
Indices: 56639670--56639714 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
56639660 GCAGGGCAGC
*
56639670 AGAAAAAAAGAA-A
1 AGAAAAGAAGAAGA
* *
56639683 AGAAAAGAAAAAGG
1 AGAAAAGAAGAAGA
56639697 AGAAAAGAAGAAGA
1 AGAAAAGAAGAAGA
56639711 AGAA
1 AGAA
56639715 GAAATGGACA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AGAAAAGAAGAAGA
Found at i:56644716 original size:20 final size:19
Alignment explanation
Indices: 56644671--56644708 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
56644661 CATACAAACA
56644671 CCAGAAAAGTAAATTATTT
1 CCAGAAAAGTAAATTATTT
56644690 CCAGAAAAGTAAATTATTT
1 CCAGAAAAGTAAATTATTT
56644709 TCTAGAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
CCAGAAAAGTAAATTATTT
Found at i:56645951 original size:26 final size:26
Alignment explanation
Indices: 56645922--56645975 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
56645912 AAACATTTGT
*
56645922 AAAGGGATT-TTTGTGAAAAATGTCAA
1 AAAGGGATTAATTGTGAAAAATG-CAA
56645948 AAAGGGATTAAATTGTGAAAAATGCAA
1 AAAGGGATT-AATTGTGAAAAATGCAA
56645975 A
1 A
56645976 CTGAGTGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 9 0.36
27 4 0.16
28 12 0.48
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (26 bp):
AAAGGGATTAATTGTGAAAAATGCAA
Found at i:56646599 original size:47 final size:47
Alignment explanation
Indices: 56646546--56646671 Score: 164
Period size: 47 Copynumber: 2.7 Consensus size: 47
56646536 GAATAATACA
* *
56646546 TTGATTTGGCTACGGGCCATGGTATAGGTATTCAGAGAGGAGTTACC
1 TTGATTTGGCTACGGGCCATGGTATAGGTACTCAGAGAGAAGTTACC
* * * * *
56646593 TTGATTTGTCTACGAGG-CATAGTATAGGTACTCCGGGATAAGTTACC
1 TTGATTTGGCTACG-GGCCATGGTATAGGTACTCAGAGAGAAGTTACC
*
56646640 TTGATTTGGCTATGGGCCATGGTATAGGTACT
1 TTGATTTGGCTACGGGCCATGGTATAGGTACT
56646672 TATCGATTGA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 2 0.03
47 63 0.94
48 2 0.03
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (47 bp):
TTGATTTGGCTACGGGCCATGGTATAGGTACTCAGAGAGAAGTTACC
Found at i:56647921 original size:59 final size:59
Alignment explanation
Indices: 56647829--56647946 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
56647819 GCAGTTTCTT
* *
56647829 TGCCCCAAAAATGCCTAAGTCAGCCTAACTTGCAACGATAAAGGATTCAATAGAATTCC
1 TGCCCCAAAAACGCCTAAGTCAGCCTAACTTGCAACGACAAAGGATTCAATAGAATTCC
56647888 TGCCCCAAAAACGCCTAAGTCAGCCTAACTTGCAACGACAAAGGATTCAATAGAATTCC
1 TGCCCCAAAAACGCCTAAGTCAGCCTAACTTGCAACGACAAAGGATTCAATAGAATTCC
56647947 CTCAAGGCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.20
Consensus pattern (59 bp):
TGCCCCAAAAACGCCTAAGTCAGCCTAACTTGCAACGACAAAGGATTCAATAGAATTCC
Found at i:56652977 original size:59 final size:59
Alignment explanation
Indices: 56652885--56653001 Score: 216
Period size: 59 Copynumber: 2.0 Consensus size: 59
56652875 GCAGTTTCTT
* *
56652885 TGCCCCAAAAATGCCTAAGTCAGCCTAACTTGCAACGATAAAGGATTCAATAGAATTCC
1 TGCCCCAAAAAGGCCTAAGTCAGCCTAACTTGCAACGACAAAGGATTCAATAGAATTCC
56652944 TGCCCCAAAAAGGCCTAAGTCAGCCTAACTTGCAACGACAAAGGATTCAATAGAATTC
1 TGCCCCAAAAAGGCCTAAGTCAGCCTAACTTGCAACGACAAAGGATTCAATAGAATTC
56653002 TCTCAAGGCT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.21
Consensus pattern (59 bp):
TGCCCCAAAAAGGCCTAAGTCAGCCTAACTTGCAACGACAAAGGATTCAATAGAATTCC
Found at i:56653509 original size:13 final size:13
Alignment explanation
Indices: 56653491--56653515 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56653481 CACTTCGAAG
56653491 GACACACGGGCTA
1 GACACACGGGCTA
56653504 GACACACGGGCT
1 GACACACGGGCT
56653516 TGTGGTCGGC
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:0.28, C:0.32, G:0.32, T:0.08
Consensus pattern (13 bp):
GACACACGGGCTA
Found at i:56658687 original size:16 final size:16
Alignment explanation
Indices: 56658638--56658687 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
56658628 ATGTGTATAA
56658638 AAATTGTA-GAAAAAT
1 AAATTGTATGAAAAAT
* * *
56658653 AAAATCT-TGAATAACT
1 AAATTGTATGAA-AAAT
56658669 AAATTGTATGAAAAAT
1 AAATTGTATGAAAAAT
56658685 AAA
1 AAA
56658688 GAAAATTATC
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
15 8 0.31
16 14 0.54
17 4 0.15
ACGTcount: A:0.58, C:0.04, G:0.10, T:0.28
Consensus pattern (16 bp):
AAATTGTATGAAAAAT
Found at i:56659296 original size:18 final size:17
Alignment explanation
Indices: 56659251--56659298 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
56659241 ACTGTTATTT
* *
56659251 AATTTTTAATTTTATAA
1 AATTTTAAATTTTAAAA
*
56659268 TATTTTAAAATTTTAAAA
1 AATTTT-AAATTTTAAAA
56659286 CAATTTTAAATTT
1 -AATTTTAAATTT
56659299 GGGTATAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTTAAATTTTAAAA
Found at i:56661158 original size:105 final size:105
Alignment explanation
Indices: 56661033--56661251 Score: 244
Period size: 105 Copynumber: 2.1 Consensus size: 105
56661023 ATTATAGGTA
* ** *
56661033 ACAACATCAGGCTCAATGCCTCGCTTTATCATTGCGTCAACAAAATC-CT-CAGCTTCAGAGACC
1 ACAACATTAGGCTCAATGCCTCGCTTTATCATCACGTCAAC--AATCTCTACAGCTTCAGAAACC
* *
56661096 ATCCCTTCCTTGCAATGCGCATCAACCAATGTACTATACGTG
64 ATCCCTTCCTTGCAAAGAGCATCAACCAATGTACTATACGTG
* * * * ** * * *
56661138 ACAACATTAGGCTCAATGCCTTGTTTTCTCATCATGTCAACGGTCTCTACAGCTTTAGAAATCGT
1 ACAACATTAGGCTCAATGCCTCGCTTTATCATCACGTCAACAATCTCTACAGCTTCAGAAACCAT
* *
56661203 TCCTTCCTTGCAAAGAGCATCAACCAATGTAGTATACGTG
66 CCCTTCCTTGCAAAGAGCATCAACCAATGTACTATACGTG
*
56661243 ACAATATTA
1 ACAACATTA
56661252 AGTGAAATAT
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
103 2 0.02
104 2 0.02
105 90 0.96
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (105 bp):
ACAACATTAGGCTCAATGCCTCGCTTTATCATCACGTCAACAATCTCTACAGCTTCAGAAACCAT
CCCTTCCTTGCAAAGAGCATCAACCAATGTACTATACGTG
Found at i:56668678 original size:105 final size:105
Alignment explanation
Indices: 56668526--56668752 Score: 262
Period size: 105 Copynumber: 2.2 Consensus size: 105
56668516 ACTAATGTAT
* *
56668526 TATACGTGACAACATTAGGCTCAATGCCTCGCTTTATCATTTCGTCAACAATACCCT-CAGCTTC
1 TATACGTGACAACATCAGGCTCAATGCCTCGCTTTATCATGTCGTCAACAAT-CCCTACAGCTTC
* * *
56668590 AGAGACCATCCCTTCCTTGCAATGCGCATCAACCAATATAC-
65 AGAAACCATCCCTTCCTTGCAAAGAGCATCAACCAATA-ACG
* * * * *
56668631 TATACGTGACAACATCAGGCTCAATGCCTTGCTTTCTCATCGT-GTCAACGATCTCTACAGCTTT
1 TATACGTGACAACATCAGGCTCAATGCCTCGCTTTATCAT-GTCGTCAACAATCCCTACAGCTTC
* * * *
56668695 AGAAATCGTTCCTTCCTTGCAAAGAGCATCAATCAATAACG
65 AGAAACCATCCCTTCCTTGCAAAGAGCATCAACCAATAACG
* *
56668736 TATATGTGACAATATCA
1 TATACGTGACAACATCA
56668753 AGTGAAATAT
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
104 5 0.05
105 97 0.94
106 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (105 bp):
TATACGTGACAACATCAGGCTCAATGCCTCGCTTTATCATGTCGTCAACAATCCCTACAGCTTCA
GAAACCATCCCTTCCTTGCAAAGAGCATCAACCAATAACG
Found at i:56670600 original size:13 final size:13
Alignment explanation
Indices: 56670582--56670606 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56670572 GAAAGGGTCT
56670582 AGTCTTCTAGCTC
1 AGTCTTCTAGCTC
56670595 AGTCTTCTAGCT
1 AGTCTTCTAGCT
56670607 ATGACTTCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (13 bp):
AGTCTTCTAGCTC
Found at i:56671333 original size:20 final size:19
Alignment explanation
Indices: 56671289--56671334 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
56671279 CATCCAAACA
56671289 CTAGAAAAGCAAATCATTT
1 CTAGAAAAGCAAATCATTT
* *
56671308 CCAGAAAAGTAAATCAATTT
1 CTAGAAAAGCAAATC-ATTT
56671328 CTAGAAA
1 CTAGAAA
56671335 TCATTTTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (19 bp):
CTAGAAAAGCAAATCATTT
Found at i:56673282 original size:48 final size:47
Alignment explanation
Indices: 56673186--56673316 Score: 165
Period size: 48 Copynumber: 2.8 Consensus size: 47
56673176 GTGTGAATAA
* * *
56673186 TACCTTGATTAGGCTACGGGCCATGGTATAGGTATTCAGAGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAGAGAGAAGT
* * *
56673233 TACCTTGATTTGTCTACGGGGCCATGGTATAAGTACTCTAG-GATAAGT
1 TACCTTGATTTGGCTAC-GGGCCATGGTATAGGTACTC-AGAGAGAAGT
**
56673281 TACCTTGATTTGGCTATAGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
56673317 TATCGATTGA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
47 32 0.44
48 38 0.53
49 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAGAGAGAAGT
Found at i:56682578 original size:13 final size:14
Alignment explanation
Indices: 56682560--56682592 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
56682550 TATAATTTAA
56682560 TTTAATTTTCT-TT
1 TTTAATTTTCTATT
*
56682573 TTTAATTTTTTATT
1 TTTAATTTTCTATT
56682587 TTTAAT
1 TTTAAT
56682593 GGCTTTCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTAATTTTCTATT
Found at i:56684665 original size:23 final size:25
Alignment explanation
Indices: 56684638--56684688 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
56684628 TTATAGATTG
*
56684638 TAATATA-CTTTTT-ATTAAAATAT
1 TAATATAGCTTTTTCAATAAAATAT
*
56684661 TAATATAGCTTTTTCAATAAATTAT
1 TAATATAGCTTTTTCAATAAAATAT
56684686 TAA
1 TAA
56684689 GAAAATTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.29
24 6 0.25
25 11 0.46
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (25 bp):
TAATATAGCTTTTTCAATAAAATAT
Found at i:56684682 original size:24 final size:24
Alignment explanation
Indices: 56684638--56684688 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
56684628 TTATAGATTG
*
56684638 TAATATACTTTTTATTAAAA-TAT
1 TAATATACTTTTTAATAAAATTAT
56684661 TAATATAGCTTTTTCAAT-AAATTAT
1 TAATATA-CTTTTT-AATAAAATTAT
56684686 TAA
1 TAA
56684689 GAAAATTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 7 0.29
24 9 0.38
25 8 0.33
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (24 bp):
TAATATACTTTTTAATAAAATTAT
Found at i:56692271 original size:11 final size:10
Alignment explanation
Indices: 56692233--56692363 Score: 78
Period size: 11 Copynumber: 13.1 Consensus size: 10
56692223 GGCCTATTTT
56692233 TATTTTAAAA
1 TATTTTAAAA
56692243 T-TTTTAAAA
1 TATTTTAAAA
*
56692252 -ATTTAAAAA
1 TATTTTAAAA
56692261 GTATTTTAAAA
1 -TATTTTAAAA
56692272 GTATTTTAAAA
1 -TATTTTAAAA
**
56692283 T-TTAAAAAA
1 TATTTTAAAA
* **
56692292 AATTAAAAAA
1 TATTTTAAAA
56692302 GTATTTTAAAAA
1 -TATTTT-AAAA
56692314 TATTTT-AAA
1 TATTTTAAAA
56692323 -A--TTAAAA
1 TATTTTAAAA
* *
56692330 AATTTAAAAAA
1 TATTT-TAAAA
56692341 GTATTTTAAAA
1 -TATTTTAAAA
56692352 GTATTTTAAAA
1 -TATTTTAAAA
56692363 T
1 T
56692364 TTAAAAAAAT
Statistics
Matches: 98, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
6 2 0.02
7 3 0.03
8 2 0.02
9 24 0.24
10 12 0.12
11 47 0.48
12 8 0.08
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:56692285 original size:30 final size:30
Alignment explanation
Indices: 56692233--56692312 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
56692223 GGCCTATTTT
*
56692233 TATTTTAAAA-T-TTTTAAAAATTTAAAAAG
1 TATTTTAAAAGTATTTT-AAAATTTAAAAAA
56692262 TATTTTAAAAGTATTTTAAAATTTAAAAAA
1 TATTTTAAAAGTATTTTAAAATTTAAAAAA
* **
56692292 AATTAAAAAAGTATTTTAAAA
1 TATTTTAAAAGTATTTTAAAA
56692313 ATATTTTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 10 0.22
30 31 0.69
31 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (30 bp):
TATTTTAAAAGTATTTTAAAATTTAAAAAA
Found at i:56692305 original size:41 final size:40
Alignment explanation
Indices: 56692233--56692417 Score: 264
Period size: 40 Copynumber: 4.6 Consensus size: 40
56692223 GGCCTATTTT
** * *
56692233 TATTTTAAAATTTTTAAAAATTTAAAAAGTATTTTAAAAG
1 TATTTTAAAATTTAAAAAAATTAAAAAAGTATTTTAAAAA
56692273 TATTTTAAAATTTAAAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTT-AAAAAAATTAAAAAAGTATTTTAAAAA
* *
56692314 TATTTTAAAA-TTAAAAAATTTAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTTAAAAAAATTAAAAAAGTATTTTAAAAA
* *
56692353 TATTTTAAAATTTAAAAAAATTAAAAAAGTATGTAAAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAGTATTTTAAAAA
* *
56692393 TATTTTAAAATTTTAAAAAAGTAAA
1 TATTTTAAAATTTAAAAAAATTAAA
56692418 TATATTGCCC
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.27
40 63 0.48
41 33 0.25
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (40 bp):
TATTTTAAAATTTAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:56692338 original size:79 final size:79
Alignment explanation
Indices: 56692233--56692404 Score: 283
Period size: 79 Copynumber: 2.2 Consensus size: 79
56692223 GGCCTATTTT
*
56692233 TATTTTAAAATTTTTAAAAATTT-AAAAAGTATTTTAAAAGTATTTTAAAATTTAAAAAAAATTA
1 TATTTTAAAA--TTAAAAAATTTAAAAAAGTATTTTAAAAGTATTTTAAAATTT-AAAAAAATTA
* *
56692297 AAAAAGTATTTTAAAAA
63 AAAAAGTATGTAAAAAA
56692314 TATTTTAAAATTAAAAAATTTAAAAAAGTATTTTAAAAGTATTTTAAAATTTAAAAAAATTAAAA
1 TATTTTAAAATTAAAAAATTTAAAAAAGTATTTTAAAAGTATTTTAAAATTTAAAAAAATTAAAA
56692379 AAGTATGTAAAAAA
66 AAGTATGTAAAAAA
56692393 TATTTTAAAATT
1 TATTTTAAAATT
56692405 TTAAAAAAGT
Statistics
Matches: 87, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
79 47 0.54
80 30 0.34
81 10 0.11
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (79 bp):
TATTTTAAAATTAAAAAATTTAAAAAAGTATTTTAAAAGTATTTTAAAATTTAAAAAAATTAAAA
AAGTATGTAAAAAA
Found at i:56692340 original size:17 final size:17
Alignment explanation
Indices: 56692307--56692339 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
56692297 AAAAAGTATT
*
56692307 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
56692324 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTAAAAA
56692340 AGTATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:56692703 original size:16 final size:16
Alignment explanation
Indices: 56692682--56692715 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56692672 CATTAATTAA
**
56692682 ATTTTAAAGTTATTTT
1 ATTTTAAAAATATTTT
56692698 ATTTTAAAAATATTTT
1 ATTTTAAAAATATTTT
56692714 AT
1 AT
56692716 ATATTTGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
ATTTTAAAAATATTTT
Found at i:56698134 original size:71 final size:71
Alignment explanation
Indices: 56698018--56698159 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
56698008 TAAAATACAA
56698018 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
1 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
56698083 AAAAGG
66 AAAAGG
56698089 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
1 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
56698154 AAAAGG
66 AAAAGG
56698160 AGGAAATTGT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (71 bp):
TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
AAAAGG
Found at i:56703151 original size:10 final size:10
Alignment explanation
Indices: 56703136--56703167 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
56703126 TATATATTTC
56703136 AAAAATGTTT
1 AAAAATGTTT
56703146 AAAAATGTTT
1 AAAAATGTTT
56703156 --AAATGTTT
1 AAAAATGTTT
56703164 AAAA
1 AAAA
56703168 TTAGTGTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.40
10 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (10 bp):
AAAAATGTTT
Found at i:56705637 original size:7 final size:7
Alignment explanation
Indices: 56705625--56705664 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
56705615 AAAGTATTTT
56705625 AAAATTA
1 AAAATTA
56705632 AAAATTA
1 AAAATTA
56705639 AAAATTA
1 AAAATTA
56705646 AAAATTA
1 AAAATTA
*
56705653 AAAAATA
1 AAAATTA
56705660 AAAAT
1 AAAAT
56705665 ATATATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAATTA
Found at i:56706905 original size:17 final size:18
Alignment explanation
Indices: 56706871--56706905 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
56706861 ATTATTGATA
56706871 ATTTTTTATAATAATTAAT
1 ATTTTTTATAAT-ATTAAT
56706890 ATTTTTTATAAT-TTAA
1 ATTTTTTATAATATTAA
56706906 AATTAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
19 12 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTTATAATATTAAT
Found at i:56711861 original size:27 final size:27
Alignment explanation
Indices: 56711811--56711862 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
56711801 TAAGTTTAAT
* ***
56711811 TATTTTTATATTTTTTTTGCACTTTGA
1 TATTTTTATATATTTTTAAAACTTTGA
56711838 TATTTTTATATATTTTTAAAACTTT
1 TATTTTTATATATTTTTAAAACTTT
56711863 TACTAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (27 bp):
TATTTTTATATATTTTTAAAACTTTGA
Found at i:56712683 original size:3 final size:3
Alignment explanation
Indices: 56712675--56712705 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
56712665 CTCCTGCTTC
56712675 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
56712706 TTGATTTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:56714471 original size:33 final size:33
Alignment explanation
Indices: 56714430--56714495 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
56714420 CCTTTTAGCC
56714430 CTATCTATATTTATATATACAATTTGGTGATTT
1 CTATCTATATTTATATATACAATTTGGTGATTT
56714463 CTATCTATATTTATATATACAATTTGGTGATTT
1 CTATCTATATTTATATATACAATTTGGTGATTT
56714496 TTACAGTTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (33 bp):
CTATCTATATTTATATATACAATTTGGTGATTT
Found at i:56721552 original size:27 final size:27
Alignment explanation
Indices: 56721502--56721553 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
56721492 TAAGTTTAAT
* ***
56721502 TATTTTTATATTTTTTTTGCACTTTGA
1 TATTTTTATATATTTTTAAAACTTTGA
56721529 TATTTTTATATATTTTTAAAACTTT
1 TATTTTTATATATTTTTAAAACTTT
56721554 TACTAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (27 bp):
TATTTTTATATATTTTTAAAACTTTGA
Found at i:56722374 original size:3 final size:3
Alignment explanation
Indices: 56722366--56722396 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
56722356 CTCCTGCTTC
56722366 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
56722397 TTGATTTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:56724161 original size:33 final size:33
Alignment explanation
Indices: 56724120--56724185 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
56724110 CCTTTTAGCC
56724120 CTATCTATATTTATATATACAATTTGGTGATTT
1 CTATCTATATTTATATATACAATTTGGTGATTT
56724153 CTATCTATATTTATATATACAATTTGGTGATTT
1 CTATCTATATTTATATATACAATTTGGTGATTT
56724186 TTACAGTTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (33 bp):
CTATCTATATTTATATATACAATTTGGTGATTT
Found at i:56731237 original size:27 final size:27
Alignment explanation
Indices: 56731187--56731238 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
56731177 TAAGTTTAAT
* ***
56731187 TATTTTTATATTTTTTTTGCACTTTGA
1 TATTTTTATATATTTTTAAAACTTTGA
56731214 TATTTTTATATATTTTTAAAACTTT
1 TATTTTTATATATTTTTAAAACTTT
56731239 TACTAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (27 bp):
TATTTTTATATATTTTTAAAACTTTGA
Found at i:56732059 original size:3 final size:3
Alignment explanation
Indices: 56732051--56732081 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
56732041 CTCCTGCTTC
56732051 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
56732082 TTGATTTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:56733846 original size:33 final size:33
Alignment explanation
Indices: 56733805--56733870 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
56733795 CCTTTTAGCC
56733805 CTATCTATATTTATATATACAATTTGGTGATTT
1 CTATCTATATTTATATATACAATTTGGTGATTT
56733838 CTATCTATATTTATATATACAATTTGGTGATTT
1 CTATCTATATTTATATATACAATTTGGTGATTT
56733871 TTACAGTTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (33 bp):
CTATCTATATTTATATATACAATTTGGTGATTT
Found at i:56738887 original size:21 final size:21
Alignment explanation
Indices: 56738861--56738900 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
56738851 ATCGGTTGGA
56738861 TAAGCTCTTACGAGCTTCTGT
1 TAAGCTCTTACGAGCTTCTGT
56738882 TAAGCTCTTACGAGCTTCT
1 TAAGCTCTTACGAGCTTCT
56738901 ACTGGAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TAAGCTCTTACGAGCTTCTGT
Found at i:56746694 original size:10 final size:11
Alignment explanation
Indices: 56746670--56746699 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
56746660 CTTTATTTTA
56746670 AATTTTTAATG
1 AATTTTTAATG
56746681 AATTTTTAAT-
1 AATTTTTAATG
56746691 AATTTTTAA
1 AATTTTTAA
56746700 ATATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
AATTTTTAATG
Found at i:56747857 original size:2 final size:2
Alignment explanation
Indices: 56747850--56747932 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
56747840 ATGATAAATT
56747850 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
56747892 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
56747933 TGCATGGGTG
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56749461 original size:34 final size:35
Alignment explanation
Indices: 56749421--56749494 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 35
56749411 AGCATATATT
* *
56749421 TATACTTATCAAT-TACATGTGCCGAATGC-ACATA
1 TATACTTAT-AATCCACATATGCCGAATGCAACATA
56749455 TATACTTATAATCCACATATGCCGAATGCATACATA
1 TATACTTATAATCCACATATGCCGAATGCA-ACATA
56749491 TATA
1 TATA
56749495 TATATCCAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 3 0.09
34 23 0.66
36 9 0.26
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.32
Consensus pattern (35 bp):
TATACTTATAATCCACATATGCCGAATGCAACATA
Found at i:56749713 original size:41 final size:40
Alignment explanation
Indices: 56749663--56749790 Score: 166
Period size: 41 Copynumber: 3.1 Consensus size: 40
56749653 TTAATTTAAA
56749663 CAGATTCACTGGCACTTAGCCTGTTAGGCTTAAAGCCTGATT
1 CAGA-TCACTGGCACTTAGCCTGTTAGGCTTAAA-CCTGATT
* *
56749705 CAGATCACTGGCACTTAGCCTGCTAGGCTTATAACCTAATT
1 CAGATCACTGGCACTTAGCCTGTTAGGCTTA-AACCTGATT
* * *
56749746 CAGATCACCGACACTTAGCCTGTTAGGTTTTAAAACCTGATT
1 CAGATCACTGGCACTTAGCCTGTTAGG-CTT-AAACCTGATT
56749788 CAG
1 CAG
56749791 TACACCGGCT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 56 0.74
42 19 0.25
43 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (40 bp):
CAGATCACTGGCACTTAGCCTGTTAGGCTTAAACCTGATT
Found at i:56750433 original size:19 final size:18
Alignment explanation
Indices: 56750391--56750433 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
56750381 ATTCAATCCA
56750391 AACATATACAAATATATT
1 AACATATACAAATATATT
* *
56750409 ATACATATATATATATATGT
1 A-ACATATACAAATATAT-T
56750429 AACAT
1 AACAT
56750434 CCATACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 18 0.86
20 2 0.10
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.37
Consensus pattern (18 bp):
AACATATACAAATATATT
Found at i:56750549 original size:75 final size:78
Alignment explanation
Indices: 56750428--56750796 Score: 316
Period size: 78 Copynumber: 4.8 Consensus size: 78
56750418 TATATATATG
* * * * * * *
56750428 TAACATCCATACTTTTAA-TAAAATCCAAGAATTTATAC-TCGTATATACATACCTATTCAAACC
1 TAACATACATACTATTAACT-AAATTCAAGAACTTATTCAT-GTATATACATACATATCCAAACC
* * *
56750491 TCTTGTAAACATATA
64 TCATATAAACAAATA
* * * * *
56750506 TAACATTCA-AC-ATTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGAACTTC
1 TAACATACATACTATTAACTAAATTCAAGAACTTATTCATGTATATACATACATATCCAAACCTC
* *
56750568 ATATATATAAATA
66 ATATAAACAAATA
* * * * * *
56750581 TAACATACATACTTTTAACTAAATTCAAGAACTTATTCATGTATATACATATATATTCGAACTTT
1 TAACATACATACTATTAACTAAATTCAAGAACTTATTCATGTATATACATACATATCCAAACCTC
* *
56750646 ATATATATAAATA
66 ATATAAACAAATA
* * * * * * * * *
56750659 TAACATACATGCTTTTAAATAAATTCAAGAATTTATTCATGTATACACATATATATCCGAACTTT
1 TAACATACATACTATTAACTAAATTCAAGAACTTATTCATGTATATACATACATATCCAAACCTC
* *
56750724 ATATATATAAATA
66 ATATAAACAAATA
* * * *
56750737 TAACATACATACTTTTAACTAAGTTCAAGAACTTATACATGTATATACATATATTATCCA
1 TAACATACATACTATTAACTAAATTCAAGAACTTATTCATGTATATACATACA-TATCCA
56750797 CTAGTAGTTC
Statistics
Matches: 252, Mismatches: 33, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
75 42 0.17
76 14 0.06
77 17 0.07
78 174 0.69
79 5 0.02
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.37
Consensus pattern (78 bp):
TAACATACATACTATTAACTAAATTCAAGAACTTATTCATGTATATACATACATATCCAAACCTC
ATATAAACAAATA
Found at i:56750635 original size:78 final size:78
Alignment explanation
Indices: 56750518--56750795 Score: 459
Period size: 78 Copynumber: 3.6 Consensus size: 78
56750508 ACATTCAACA
* *
56750518 TTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGAACTTCATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
56750582 AACATACATACTT
66 AACATACATACTT
*
56750595 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATTCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
*
56750660 AACATACATGCTT
66 AACATACATACTT
* * *
56750673 TTAAATAAATTCAAGAATTTATTCATGTATACACATATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
56750738 AACATACATACTT
66 AACATACATACTT
* *
56750751 TTAACTAAGTTCAAGAACTTATACATGTATATACATATATTATCC
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATA-TATCC
56750796 ACTAGTAGTT
Statistics
Matches: 185, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
77 14 0.08
78 166 0.90
79 5 0.03
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.38
Consensus pattern (78 bp):
TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
AACATACATACTT
Found at i:56757627 original size:2 final size:2
Alignment explanation
Indices: 56757622--56757695 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
56757612 ATGCAGAGGC
56757622 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56757664 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56757696 CAAAACTGGA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56758219 original size:25 final size:25
Alignment explanation
Indices: 56758191--56758240 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
56758181 ATATCATTAG
56758191 TTAGTTGAAAATTTGAAATAATTGA
1 TTAGTTGAAAATTTGAAATAATTGA
*
56758216 TTAGTTGAAATTTTGAAATAATTGA
1 TTAGTTGAAAATTTGAAATAATTGA
56758241 CACCTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (25 bp):
TTAGTTGAAAATTTGAAATAATTGA
Found at i:56759766 original size:2 final size:2
Alignment explanation
Indices: 56759759--56759805 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
56759749 ATGATAAATT
56759759 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56759801 AG AG A
1 AG AG A
56759806 AATGCATGGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56760138 original size:2 final size:2
Alignment explanation
Indices: 56760131--56760181 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
56760121 CCAACAAAAT
56760131 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
56760173 AC AC AC AC A
1 AC AC AC AC A
56760182 AGTTTAACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:56760691 original size:32 final size:34
Alignment explanation
Indices: 56760624--56760692 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 34
56760614 GTAGTTATCG
* *
56760624 CGATACCAGGCTCTAGGTATCGTGATATCAGTAT
1 CGATACCAGGCTCTAGGTATCGCGATATCACTAT
*
56760658 CGATACCAGGCTCT-GG-GTCGCGATATCACTAT
1 CGATACCAGGCTCTAGGTATCGCGATATCACTAT
56760690 CGA
1 CGA
56760693 AGTGAGACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 16 0.50
33 2 0.06
34 14 0.44
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (34 bp):
CGATACCAGGCTCTAGGTATCGCGATATCACTAT
Found at i:56764355 original size:21 final size:21
Alignment explanation
Indices: 56764331--56764372 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
56764321 CTGTTGAAAA
56764331 AAATTCAGTTTGAAAATGGTT
1 AAATTCAGTTTGAAAATGGTT
56764352 AAATTCAGTTTGAAAATGGTT
1 AAATTCAGTTTGAAAATGGTT
56764373 TTCTTGCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (21 bp):
AAATTCAGTTTGAAAATGGTT
Found at i:56764428 original size:36 final size:36
Alignment explanation
Indices: 56764388--56764459 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
56764378 GCACAGCAAA
56764388 AATT-AAAATTTTAAAAACTGAAC-CGGTTTGTGATAT
1 AATTAAAAATTTT-AAAACTG-ACTCGGTTTGTGATAT
56764424 AATTAAAAATTTTAAAACTGACTCGGTTTGTGATAT
1 AATTAAAAATTTTAAAACTGACTCGGTTTGTGATAT
56764460 TTATAGTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 2 0.06
36 24 0.71
37 8 0.24
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (36 bp):
AATTAAAAATTTTAAAACTGACTCGGTTTGTGATAT
Found at i:56765358 original size:9 final size:10
Alignment explanation
Indices: 56765341--56765369 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
56765331 TATTTATCTT
56765341 TTTCTATTCA
1 TTTCTATTCA
56765351 TTTC-ATTCA
1 TTTCTATTCA
56765360 TTTCTATTCA
1 TTTCTATTCA
56765370 AACACGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:56768156 original size:59 final size:59
Alignment explanation
Indices: 56767996--56768634 Score: 893
Period size: 59 Copynumber: 10.8 Consensus size: 59
56767986 TGTTTATGTA
* * *
56767996 AATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATAATTGTTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
56768055 AATTAAT-AAAAA-TAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
*
56768112 AATGAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
*
56768171 AATTATTCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATATGGTTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATG--A---TTATTTATTT
*
56768235 AATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATATGTTTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATG--A---TTATTTATTT
*
56768299 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGGTTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
**
56768358 AATTGGTCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* * * * * * *
56768417 AATTAATC--GAA--CACTAATTATTCGTACAATTATTATGAAATAAGATTATTTAATT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
*** **
56768472 AATTAATTGGAAATTAATTAATTATTTGTAAAATTATTATGAAATATGATTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* *
56768531 AACTAATC--AAA--AATTAATTATTCATAAAATTATTATGAAATATGATGATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* *
56768586 AATTAATAAAAAATTAATTAATTATTCGTAAAATTATTATGAAATATGA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGA
56768635 CCCAGCATTT
Statistics
Matches: 526, Mismatches: 39, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
55 92 0.17
57 59 0.11
58 9 0.02
59 247 0.47
61 1 0.00
64 118 0.22
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (59 bp):
AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
Found at i:56768321 original size:19 final size:20
Alignment explanation
Indices: 56768297--56768334 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
56768287 GTTTATTTAT
56768297 TTAATTAATCA-AAAATTAA
1 TTAATTAATCATAAAATTAA
*
56768316 TTAATTATTCATAAAATTA
1 TTAATTAATCATAAAATTA
56768335 TTATGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAATTAATCATAAAATTAA
Found at i:56768451 original size:114 final size:115
Alignment explanation
Indices: 56767996--56768634 Score: 877
Period size: 114 Copynumber: 5.4 Consensus size: 115
56767986 TGTTTATGTA
* * *
56767996 AATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATAATTGTTTATTTAATTAA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
*
56768061 TAAAAATAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
66 T-CAAATAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* *
56768112 AATGAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
56768177 TCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATATGGTTATTTATTT
66 TC--AAA-TAATTAATTATTCATAAAATTATTATGAAATATG--A---TTATTTATTT
*
56768235 AATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATATGTTTATTTATTTA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATG--A---TTATTTATTTA
*
56768300 ATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGGTTATTTATTT
61 ATTAATC--AAA-TAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
**
56768358 AATTGGTCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
* * * * * * *
56768423 TCGAA-CACTAATTATTCGTACAATTATTATGAAATAAGATTATTTAATT
66 TCAAATAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
*** ** *
56768472 AATTAATTGGAAATTAATTAATTATTTGTAAAATTATTATGAAATATGATTATTTATTTAACTAA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
*
56768537 TCAAA-AATTAATTATTCATAAAATTATTATGAAATATGATGATTTATTT
66 TCAAATAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* *
56768586 AATTAATAAAAAATTAATTAATTATTCGTAAAATTATTATGAAATATGA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGA
56768635 CCCAGCATTT
Statistics
Matches: 469, Mismatches: 41, Indels: 28
0.87 0.08 0.05
Matches are distributed among these distances:
114 180 0.38
116 63 0.13
117 3 0.01
118 52 0.11
120 1 0.00
121 1 0.00
123 111 0.24
125 1 0.00
128 57 0.12
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (115 bp):
AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
TCAAATAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
Found at i:56768487 original size:51 final size:53
Alignment explanation
Indices: 56768377--56768592 Score: 182
Period size: 55 Copynumber: 3.9 Consensus size: 53
56768367 AAAATTAATT
* *
56768377 AATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAATCGAACAC
1 AATTATTCATAAAATTATTATGAAATAAGATTATTTAATTAATTAATCG-ACAC
* * * * *
56768431 TAATTATTCGTACAATTATTATGAAATAAGATTATTTAATTAATTAATTGGAAATT
1 -AATTATTCATAAAATTATTATGAAATAAGATTATTTAATTAATTAA-TCGACA-C
* * * * * *
56768487 AATTAATT-ATTTGTAAAATTATTATGAAATATGATTATTTATTTAACTAATCAAAAATT
1 AATT-ATTCA----TAAAATTATTATGAAATAAGATTATTTAATTAATTAATC-GACA-C
* * *
56768546 AATTATTCATAAAATTATTATGAAATATGATGATTTATTTAATTAAT
1 AATTATTCATAAAATTATTATGAAATAAGATTATTTAATTAATTAAT
56768593 AAAAAATTAA
Statistics
Matches: 136, Mismatches: 16, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
55 84 0.62
56 5 0.04
58 4 0.03
59 43 0.32
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (53 bp):
AATTATTCATAAAATTATTATGAAATAAGATTATTTAATTAATTAATCGACAC
Found at i:56768510 original size:19 final size:19
Alignment explanation
Indices: 56768466--56768507 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
56768456 ATAAGATTAT
*
56768466 TTAATTAATTAATTGGAAA
1 TTAATTAATTAATTGAAAA
*
56768485 TTAATTAATTATTTGTAAAA
1 TTAATTAATTAATTG-AAAA
56768505 TTA
1 TTA
56768508 TTATGAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (19 bp):
TTAATTAATTAATTGAAAA
Found at i:56800656 original size:18 final size:17
Alignment explanation
Indices: 56800633--56800674 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
56800623 AATCCAAGTC
56800633 AAATAAAAAAATTAAAAT
1 AAATAAAAAAA-TAAAAT
*
56800651 AAATAACTAAAATAAAAT
1 AAATAA-AAAAATAAAAT
56800669 -AATAAA
1 AAATAAA
56800675 TCAAAGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 5 0.24
18 12 0.57
19 4 0.19
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAAAAAAATAAAAT
Found at i:56800674 original size:13 final size:14
Alignment explanation
Indices: 56800633--56800674 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
56800623 AATCCAAGTC
* *
56800633 AAATAAAAAAATTA
1 AAATAAAATAACTA
56800647 AAAT-AAATAACTA
1 AAATAAAATAACTA
56800660 AAATAAAATAA-TA
1 AAATAAAATAACTA
56800673 AA
1 AA
56800675 TCAAAGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAACTA
Found at i:56802204 original size:17 final size:17
Alignment explanation
Indices: 56802182--56802234 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
56802172 AATGTATGGT
56802182 AAAATAAATTAATTACA
1 AAAATAAATTAATTACA
**
56802199 AAAAT-AA-T-A-T-GG
1 AAAATAAATTAATTACA
56802211 AAAATAAATTAATTACA
1 AAAATAAATTAATTACA
56802228 AAAATAA
1 AAAATAA
56802235 GACATTTGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
12 5 0.19
13 3 0.11
14 2 0.07
15 2 0.07
16 3 0.11
17 12 0.44
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (17 bp):
AAAATAAATTAATTACA
Found at i:56802216 original size:29 final size:30
Alignment explanation
Indices: 56802176--56802234 Score: 111
Period size: 29 Copynumber: 2.0 Consensus size: 30
56802166 GTTAATAATG
56802176 TATGGTAAAATAAATTAATTACAAAAATAA
1 TATGGTAAAATAAATTAATTACAAAAATAA
56802206 TATGG-AAAATAAATTAATTACAAAAATAA
1 TATGGTAAAATAAATTAATTACAAAAATAA
56802235 GACATTTGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (30 bp):
TATGGTAAAATAAATTAATTACAAAAATAA
Found at i:56813478 original size:15 final size:14
Alignment explanation
Indices: 56813458--56813487 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
56813448 ATAACCTTCT
56813458 AAATATTTATTATTA
1 AAATATTTA-TATTA
56813473 AAATATTTATATTA
1 AAATATTTATATTA
56813487 A
1 A
56813488 TCAAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATATTTATATTA
Found at i:56814943 original size:29 final size:27
Alignment explanation
Indices: 56814869--56814943 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
56814859 CTTTGGGTGG
*
56814869 TTTAATTTGGGGATTTTGGGTAAGGGT
1 TTTAATTTTGGGATTTTGGGTAAGGGT
* ** *
56814896 TTTGATTTTGGGAATTTTTGTTTAGGGGTT
1 TTTAATTTTGGG-A-TTTTGGGTAAGGG-T
56814926 TTTAATTTTGGAGATTTT
1 TTTAATTTTGG-GATTTT
56814944 AGGGATTTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 10 0.26
28 1 0.03
29 14 0.37
30 12 0.32
31 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.53
Consensus pattern (27 bp):
TTTAATTTTGGGATTTTGGGTAAGGGT
Found at i:56819127 original size:22 final size:22
Alignment explanation
Indices: 56819099--56819142 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
56819089 GCAACTCGAG
56819099 ATAACTTAATTTGTGGTTTAAC
1 ATAACTTAATTTGTGGTTTAAC
56819121 ATAACTTAATTTGTGGTTTAAC
1 ATAACTTAATTTGTGGTTTAAC
56819143 CTCATATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (22 bp):
ATAACTTAATTTGTGGTTTAAC
Found at i:56819840 original size:17 final size:17
Alignment explanation
Indices: 56819788--56819840 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
56819778 TATGGAAACA
* *
56819788 TAATCTTCGAGGATATG
1 TAATCTTAGAAGATATG
*
56819805 CAATCTTAGATATGATATG
1 TAATCTTAGA-A-GATATG
56819824 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
56819841 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:56819840 original size:22 final size:23
Alignment explanation
Indices: 56819812--56819856 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
56819802 ATGCAATCTT
56819812 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
56819834 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
56819857 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:56819866 original size:22 final size:23
Alignment explanation
Indices: 56819822--56819866 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
56819812 AGATATGATA
*
56819822 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
56819845 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
56819867 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:56820304 original size:3 final size:3
Alignment explanation
Indices: 56820296--56820335 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
56820286 ATTAATTTTG
*
56820296 TTA TTA TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
56820336 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:56820304 original size:15 final size:15
Alignment explanation
Indices: 56820280--56820334 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
56820270 GTTTTTAGTC
56820280 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
56820294 TGTTATTATTATTTT
1 TATTATTATTAATTT
56820309 TATTATTA-T-ATTAT
1 TATTATTATTAATT-T
56820323 ATATTATTATTA
1 -TATTATTATTA
56820335 TACCTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 5 0.16
15 24 0.75
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:56820311 original size:12 final size:12
Alignment explanation
Indices: 56820282--56820333 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
56820272 TTTTAGTCTA
56820282 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
56820294 TGTTATTATTAT
1 TTTTATTATTAT
56820306 TTTTATTATTAT
1 TTTTATTATTAT
56820318 ATTATATATTATTAT
1 -TT-T-TATTATTAT
56820333 T
1 T
56820334 ATACCTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 2 0.06
14 2 0.06
15 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:56838804 original size:3 final size:3
Alignment explanation
Indices: 56838796--56838831 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
56838786 ATACATTCCC
56838796 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
56838832 TTACAATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:56839244 original size:26 final size:28
Alignment explanation
Indices: 56839206--56839258 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 28
56839196 GGTAATTTTC
*
56839206 TTTCATTTGCTTAATCCATGAC-ATGCT
1 TTTCATTTCCTTAATCCATGACTATGCT
* *
56839233 TTTCA-TTCCTTAGTTCATGACTATGC
1 TTTCATTTCCTTAATCCATGACTATGC
56839259 AATGATTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (28 bp):
TTTCATTTCCTTAATCCATGACTATGCT
Found at i:56843830 original size:19 final size:18
Alignment explanation
Indices: 56843806--56843859 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
56843796 TTACAACTTG
56843806 AATTTAATTTAAATAATAA
1 AATTTAATTTAAA-AATAA
* * *
56843825 AATTTATTTTTAAAATTCA
1 AATTTA-ATTTAAAAATAA
56843844 AATTTAA-TTAAAAATA
1 AATTTAATTTAAAAATA
56843860 TAAAAATGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
17 7 0.25
19 15 0.54
20 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTAATTTAAAAATAA
Found at i:56854838 original size:19 final size:19
Alignment explanation
Indices: 56854810--56854852 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
56854800 TCACAACTTT
*
56854810 TTCACCTTT-CATTTATCAA
1 TTCACCTTTCCATTT-CCAA
*
56854829 TTCACTTTTCCATTTCCAA
1 TTCACCTTTCCATTTCCAA
56854848 TTCAC
1 TTCAC
56854853 ATATTTTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (19 bp):
TTCACCTTTCCATTTCCAA
Found at i:56861626 original size:20 final size:20
Alignment explanation
Indices: 56861602--56861658 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
56861592 CATAGAACAC
**
56861602 AATAATAATAATGACGTAAT
1 AATAATAATAATGACCAAAT
* * *
56861622 TATAATATTAATCACCAAAT
1 AATAATAATAATGACCAAAT
*
56861642 AATAATAACAATGACCA
1 AATAATAATAATGACCA
56861659 TATTAATTAC
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.28
Consensus pattern (20 bp):
AATAATAATAATGACCAAAT
Found at i:56867327 original size:19 final size:19
Alignment explanation
Indices: 56867290--56867329 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
56867280 ACTTTAAAAT
*
56867290 AATTAAATTCCCTATTTTC
1 AATTAAATTCCCTAATTTC
56867309 AATTAAA-TCCCTAAATTTC
1 AATTAAATTCCCT-AATTTC
56867328 AA
1 AA
56867330 AATTTTCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTAAATTCCCTAATTTC
Found at i:56873548 original size:25 final size:25
Alignment explanation
Indices: 56873514--56873563 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
56873504 TTCACTGCTT
*
56873514 CATTTTCAGTTCTAATCTCTCAACA
1 CATTTTCAGTTCTAATCTATCAACA
56873539 CATTTTCAGTTCTAATCTATCAACA
1 CATTTTCAGTTCTAATCTATCAACA
56873564 GTTTTAGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (25 bp):
CATTTTCAGTTCTAATCTATCAACA
Found at i:56879876 original size:22 final size:22
Alignment explanation
Indices: 56879825--56879879 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
56879815 ATATGAAAAT
*
56879825 CGATATGATATAAGATGTGCTC
1 CGATATGCTATAAGATGTGCTC
56879847 CGATATGCTATAAGATGTGCTC
1 CGATATGCTATAAGATGTGCTC
56879869 CGATATGCTAT
1 CGATATGCTAT
56879880 GATACATTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (22 bp):
CGATATGCTATAAGATGTGCTC
Found at i:56880224 original size:38 final size:38
Alignment explanation
Indices: 56880177--56880272 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 38
56880167 AATAAACCAT
* * *
56880177 AGTTATAAGGTAAATTTGCTATAATGCTTTCTGCTGCA
1 AGTTTTAAGGTAAATTTGCTATAATGCTGTCCGCTGCA
*
56880215 AGTTTTAAGGTCAATTTGCTATAATGCTGTCCGCTGCA
1 AGTTTTAAGGTAAATTTGCTATAATGCTGTCCGCTGCA
**
56880253 AGTTTTATTG-AAATTTGCTA
1 AGTTTTAAGGTAAATTTGCTA
56880273 AGATGTTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 9 0.18
38 42 0.82
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.41
Consensus pattern (38 bp):
AGTTTTAAGGTAAATTTGCTATAATGCTGTCCGCTGCA
Found at i:56881263 original size:25 final size:25
Alignment explanation
Indices: 56881229--56881279 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
56881219 ATTTTTAAAT
* *
56881229 TTTTATAAATTTGC-AAAAATTTATA
1 TTTTAAAAATTT-CTAAAAATATATA
56881254 TTTTAAAAATTTCTAAAAATATATA
1 TTTTAAAAATTTCTAAAAATATATA
56881279 T
1 T
56881280 AAATAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTTAAAAATTTCTAAAAATATATA
Found at i:56885878 original size:26 final size:27
Alignment explanation
Indices: 56885850--56885902 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
56885840 GGTAATTTTC
56885850 TTTCATTTGCGTCATTCATGAC-ATGCT
1 TTTC-TTTGCGTCATTCATGACTATGCT
*
56885877 TTTCTTTGCTTCATTCATGACTATGC
1 TTTCTTTGCGTCATTCATGACTATGC
56885903 AATGATTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.17, C:0.23, G:0.13, T:0.47
Consensus pattern (27 bp):
TTTCTTTGCGTCATTCATGACTATGCT
Found at i:56890322 original size:16 final size:16
Alignment explanation
Indices: 56890293--56890342 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
56890283 TTTTTACAAA
* *
56890293 TTTTTTATTGTTCATTT
1 TTTTTTAAT-TTCAGTT
56890310 TTTTTTAATTTCAGTT
1 TTTTTTAATTTCAGTT
* *
56890326 TTATTTAATTTTAGTT
1 TTTTTTAATTTCAGTT
56890342 T
1 T
56890343 GTTTAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 21 0.72
17 8 0.28
ACGTcount: A:0.18, C:0.04, G:0.06, T:0.72
Consensus pattern (16 bp):
TTTTTTAATTTCAGTT
Found at i:56890327 original size:15 final size:15
Alignment explanation
Indices: 56890309--56890348 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
56890299 ATTGTTCATT
56890309 TTTTTTTAATTTCAG
1 TTTTTTTAATTTCAG
*
56890324 TTTTATTTAATTTTAG
1 TTTT-TTTAATTTCAG
*
56890340 TTTGTTTAA
1 TTTTTTTAA
56890349 AATTTTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.68
Consensus pattern (15 bp):
TTTTTTTAATTTCAG
Found at i:56890730 original size:22 final size:22
Alignment explanation
Indices: 56890702--56890749 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
56890692 TGCCACCAAT
56890702 CCATAGCTCCATCTAATAAACG
1 CCATAGCTCCATCTAATAAACG
56890724 CCATAGCTCCATCTAATAAACG
1 CCATAGCTCCATCTAATAAACG
56890746 CCAT
1 CCAT
56890750 TGCTTGAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.33, G:0.08, T:0.23
Consensus pattern (22 bp):
CCATAGCTCCATCTAATAAACG
Found at i:56898089 original size:76 final size:76
Alignment explanation
Indices: 56897828--56898428 Score: 670
Period size: 76 Copynumber: 7.9 Consensus size: 76
56897818 AGTGAAATTT
** * * * * * *
56897828 AAAATACCTCGGCGTGCAACCCGGGGCTCAACTCACCTCTCGGATTATAAGTTGATCTTTAAAAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
*
56897893 ACA-ACAATTG-
66 ATAGA-AATTGA
* * ** * **
56897903 AAAATACGTTAGTGTGCGACCCTAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTCAAAAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
56897968 ATAGAAATT-A
66 ATAGAAATTGA
* * *
56897978 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACCTATCAGATTATGAGTTGATTTTTGAAAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
*
56898043 ATAGAAACTGA
66 ATAGAAATTGA
* * * * *
56898054 AAAATACCTCAGCGTGCGACCCGAGGCTTAGCTCACCTCTCAGATTATGAGTTGATTTTTGAAAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
56898119 ATAGAAATTGA
66 ATAGAAATTGA
** **
56898130 AAAATACCTCAACGTATGACCTAAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
56898195 ATAGAAATTG-
66 ATAGAAATTGA
* ** ** * * ** *
56898205 AAAATACATCAGTGTATGACCCGAGGCTCAACTAACTTATCAAATTATGAGTTAATTTTTGAAAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
* *
56898270 ACAGAACTTGA
66 ATAGAAATTGA
* * * * * *
56898281 AAAATACCTCAACATGCGACCTGAGGCTCGACTCACTTCTTGGATTATGAGTTTATTTTTAAAAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
*
56898346 AGAGAAATTGA
66 ATAGAAATTGA
* * * * * *
56898357 TAAATACCTCAACGTGCGACCCAAGGCTCAACTCTCTTCTTGGATTATGAATTGATTTTTGACAA
1 AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
*
56898422 ACAGAAA
66 ATAGAAA
56898429 GGAAATTATT
Statistics
Matches: 445, Mismatches: 77, Indels: 7
0.84 0.15 0.01
Matches are distributed among these distances:
75 186 0.42
76 259 0.58
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (76 bp):
AAAATACCTCAACGTGCGACCCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATTTTTGAAAA
ATAGAAATTGA
Found at i:56898228 original size:227 final size:227
Alignment explanation
Indices: 56897828--56898428 Score: 735
Period size: 227 Copynumber: 2.7 Consensus size: 227
56897818 AGTGAAATTT
* * * * * * *
56897828 AAAATACCTCGGCGTGCAACCCGGGGCTCAACTCACCTCTCGGATTATAAGTTGATCTTTAAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTTAGCTCACCTCTCGGATTATGAGTTGATTTTTAAAAA
* * **
56897893 ACA-ACAATTG-AAAATACGTTAGTGTGCGACCCT-AGGCTCAACTCACTTCTCGGATTATGAGT
66 ACAGA-AATTGAAAAATACCTCAACGTGCGA-CCTAAGGCTCAACTCACTTCTCGGATTATGAGT
** * * *
56897955 TGATTTTCAAAAAATAGAAATTAAAAATACCTCAACGTGCGACCCGAGGCTCAACTCACCTATCA
129 TGATTTTTGAAAAATAGAAATTAAAAATACATCAACGTACGACCCGAGGCTCAACTAACCTATCA
* * *
56898020 GATTATGAGTTGATTTTTGAAAAATAGAAAC-TGA
194 AATTATGAGTTAATTTTTGAAAAACAG-AACTTGA
* *
56898054 AAAATACCTCAGCGTGCGACCCGAGGCTTAGCTCACCTCTCAGATTATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTTAGCTCACCTCTCGGATTATGAGTTGATTTTTAAAAA
* **
56898119 ATAGAAATTGAAAAATACCTCAACGTATGACCTAAGGCTCAACTCACTTCTCGGATTATGAGTTG
66 ACAGAAATTGAAAAATACCTCAACGTGCGACCTAAGGCTCAACTCACTTCTCGGATTATGAGTTG
* ** * *
56898184 ATTTTTGAAAAATAGAAATTGAAAATACATCAGTGTATGACCCGAGGCTCAACTAACTTATCAAA
131 ATTTTTGAAAAATAGAAATTAAAAATACATCAACGTACGACCCGAGGCTCAACTAACCTATCAAA
56898249 TTATGAGTTAATTTTTGAAAAACAGAACTTGA
196 TTATGAGTTAATTTTTGAAAAACAGAACTTGA
* * * * * * *
56898281 AAAATACCTCAACATGCGACCTGAGGC-TCGACTCACTTCTTGGATTATGAGTTTATTTTTAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTTAG-CTCACCTCTCGGATTATGAGTTGATTTTTAAAA
* * * * * *
56898345 AAGAGAAATTGATAAATACCTCAACGTGCGACCCAAGGCTCAACTCTCTTCTTGGATTATGAATT
65 AACAGAAATTGAAAAATACCTCAACGTGCGACCTAAGGCTCAACTCACTTCTCGGATTATGAGTT
* *
56898410 GATTTTTGACAAACAGAAA
130 GATTTTTGAAAAATAGAAA
56898429 GGAAATTATT
Statistics
Matches: 322, Mismatches: 48, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
226 71 0.22
227 251 0.78
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (227 bp):
AAAATACCTCAGCGTGCGACCCGAGGCTTAGCTCACCTCTCGGATTATGAGTTGATTTTTAAAAA
ACAGAAATTGAAAAATACCTCAACGTGCGACCTAAGGCTCAACTCACTTCTCGGATTATGAGTTG
ATTTTTGAAAAATAGAAATTAAAAATACATCAACGTACGACCCGAGGCTCAACTAACCTATCAAA
TTATGAGTTAATTTTTGAAAAACAGAACTTGA
Found at i:56899328 original size:15 final size:15
Alignment explanation
Indices: 56899305--56899349 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
56899295 AATTTACTTC
*
56899305 TGTTGACTTCTGTTT
1 TGTTTACTTCTGTTT
*
56899320 TGTTTACTTTTGTTT
1 TGTTTACTTCTGTTT
56899335 T-TTTACTTCTGTTT
1 TGTTTACTTCTGTTT
56899349 T
1 T
56899350 TTCGGTACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.07, C:0.11, G:0.13, T:0.69
Consensus pattern (15 bp):
TGTTTACTTCTGTTT
Found at i:56899341 original size:14 final size:14
Alignment explanation
Indices: 56899310--56899351 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
56899300 ACTTCTGTTG
56899310 ACTTCTGTTTTGTTT
1 ACTTCTGTTTT-TTT
*
56899325 ACTTTTGTTTTTTT
1 ACTTCTGTTTTTTT
56899339 ACTTCTGTTTTTT
1 ACTTCTGTTTTTT
56899352 CGGTACTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.07, C:0.12, G:0.10, T:0.71
Consensus pattern (14 bp):
ACTTCTGTTTTTTT
Found at i:56904511 original size:14 final size:15
Alignment explanation
Indices: 56904484--56904513 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56904474 ATAACCTTCT
56904484 AAATATTTATTATTA
1 AAATATTTATTATTA
56904499 AAATATTTA-TATTA
1 AAATATTTATTATTA
56904513 A
1 A
56904514 TCAAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATATTTATTATTA
Found at i:56907357 original size:14 final size:15
Alignment explanation
Indices: 56907338--56907377 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
56907328 ACGTTGTGTA
56907338 TTTAATTTTTA-TAT
1 TTTAATTTTTAGTAT
*
56907352 TTTAATTTTTAGTTT
1 TTTAATTTTTAGTAT
*
56907367 TTTAAATTTTA
1 TTTAATTTTTA
56907378 AAATTTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTAATTTTTAGTAT
Found at i:56910677 original size:40 final size:40
Alignment explanation
Indices: 56910632--56910725 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
56910622 TTTAGCAACA
*
56910632 TTTTTGAAAAAGCGCCGCT-AATTCTCTATTTTTAGCGGCG
1 TTTTTGAAAAAGCGCCG-TGAATGCTCTATTTTTAGCGGCG
* *
56910672 TTTTTGAAGAAGCGCTGTGAATGCTCTATTTTTAGCGGCG
1 TTTTTGAAAAAGCGCCGTGAATGCTCTATTTTTAGCGGCG
*
56910712 TTTTTAAAAAAGCG
1 TTTTTGAAAAAGCG
56910726 TCGCAATAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.02
40 47 0.98
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.37
Consensus pattern (40 bp):
TTTTTGAAAAAGCGCCGTGAATGCTCTATTTTTAGCGGCG
Found at i:56911901 original size:19 final size:18
Alignment explanation
Indices: 56911874--56911910 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
56911864 TAATATATAT
56911874 ATTAAAATATTAAAATAA
1 ATTAAAATATTAAAATAA
*
56911892 ATTAACAATATTGAAATAA
1 ATTAA-AATATTAAAATAA
56911911 GTTGAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
ATTAAAATATTAAAATAA
Found at i:56912290 original size:9 final size:9
Alignment explanation
Indices: 56912261--56912294 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
56912251 TAATATTATC
*
56912261 AATAATAGC
1 AATAATAGT
56912270 AATAATAGT
1 AATAATAGT
*
56912279 AATAATATT
1 AATAATAGT
56912288 AATAATA
1 AATAATA
56912295 ATGAAAGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (9 bp):
AATAATAGT
Found at i:56913022 original size:20 final size:18
Alignment explanation
Indices: 56912997--56913033 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
56912987 CAATAATAAT
56912997 AAAAAGAAACAGAGAAATCG
1 AAAAAGAAA-AG-GAAATCG
56913017 AAAAAGAAAAGGAAATC
1 AAAAAGAAAAGGAAATC
56913034 ACCTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.68, C:0.08, G:0.19, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAAGGAAATCG
Found at i:56913626 original size:7 final size:7
Alignment explanation
Indices: 56913616--56913669 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
56913606 GAGTTATTAT
*
56913616 TTTAAGG
1 TTTATGG
56913623 TTTATGG
1 TTTATGG
*
56913630 ATTATGGG
1 TTTAT-GG
*
56913638 TTTAAGG
1 TTTATGG
*
56913645 GTTATGG
1 TTTATGG
56913652 TTTATGG
1 TTTATGG
*
56913659 TATATGG
1 TTTATGG
56913666 TTTA
1 TTTA
56913670 AAGGCTGGGG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (7 bp):
TTTATGG
Found at i:56913641 original size:22 final size:22
Alignment explanation
Indices: 56913616--56913658 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
56913606 GAGTTATTAT
*
56913616 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGGTTATGGATTATGGG
*
56913638 TTTAAGGGTTATGGTTTATGG
1 TTTAAGGGTTATGGATTATGG
56913659 TATATGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.47
Consensus pattern (22 bp):
TTTAAGGGTTATGGATTATGGG
Found at i:56913751 original size:16 final size:16
Alignment explanation
Indices: 56913730--56913762 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56913720 TAGTGTTTTC
56913730 TAATTTA-TATATTAAT
1 TAATTTATTATA-TAAT
56913746 TAATTTATTATATAAT
1 TAATTTATTATATAAT
56913762 T
1 T
56913763 GTAAAATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTTATTATATAAT
Found at i:56914666 original size:21 final size:23
Alignment explanation
Indices: 56914640--56914687 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
56914630 TTTGAAATTT
*
56914640 ATTTTTTATTTTTAT-TTT-AAA
1 ATTTTTAATTTTTATATTTCAAA
56914661 ATTTTTAATTTTTATATTTCAAA
1 ATTTTTAATTTTTATATTTCAAA
56914684 ATTT
1 ATTT
56914688 AAAATTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 14 0.58
22 3 0.12
23 7 0.29
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTTTTAATTTTTATATTTCAAA
Done.