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 175 of 208
Found at i:53486365 original size:34 final size:35
Alignment explanation
Indices: 53486303--53486369 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
53486293 CAAACACCAG
*
53486303 AAAATATTTTCCAGTAAATAATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATAATTTTACAGAAAAGT
*
53486338 AAAACATTTTCCAG-AAATCATTTTACAGAAAA
1 AAAACATTTTCCAGTAAATAATTTTACAGAAAA
53486370 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:0.49, C:0.12, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATAATTTTACAGAAAAGT
Found at i:53486376 original size:14 final size:15
Alignment explanation
Indices: 53486300--53486377 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 15
53486290 AATCAAACAC
*
53486300 CAGAAAAT-ATTTTC
1 CAGAAAATAATTTTA
*
53486314 CAGTAAATAATTTTA
1 CAGAAAATAATTTTA
*
53486329 CAGAAAAGTAAAACATTTTC
1 CAGAAAA-T---A-ATTTTA
*
53486349 CAG-AAATCATTTTA
1 CAGAAAATAATTTTA
53486363 CAGAAAAT-ATTTTA
1 CAGAAAATAATTTTA
53486377 C
1 C
53486378 TGGCAATCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
14 22 0.43
15 15 0.29
16 1 0.02
18 1 0.02
19 4 0.08
20 8 0.16
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (15 bp):
CAGAAAATAATTTTA
Found at i:53486861 original size:20 final size:22
Alignment explanation
Indices: 53486825--53486864 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
53486815 ATATATATAT
53486825 TTAAATCAAATTAAAAAATTCA
1 TTAAATCAAATTAAAAAATTCA
53486847 TTAAA-CAAA-TAAAAAATT
1 TTAAATCAAATTAAAAAATT
53486865 ATACTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 4 0.22
22 5 0.28
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (22 bp):
TTAAATCAAATTAAAAAATTCA
Found at i:53487250 original size:82 final size:78
Alignment explanation
Indices: 53487147--53487322 Score: 230
Period size: 82 Copynumber: 2.2 Consensus size: 78
53487137 GAAAAAAAAA
* * *
53487147 TTGTTCATAGAAAATTTAGATGGTGGTGAAACTGAGAGCTGA-CTGATTTTGATTCT-TGATATC
1 TTGTTCATACAAAATTTAGATGGTGGTGAAACTGAGAGCTGATC-GATTTTAATTCTCCG-TATC
53487210 TAAAAATATATAATTTATT
64 TAAAAATATA-AA---ATT
* *
53487229 TTGTTCATACAAAATTTAGATGGTGGTGAAATTGAGAGTTGATCGATTTTAATTCTCCGTATCTA
1 TTGTTCATACAAAATTTAGATGGTGGTGAAACTGAGAGCTGATCGATTTTAATTCTCCGTATCTA
*
53487294 AGAATATAAAATT
66 AAAATATAAAATT
53487307 TTGTTCATACAAAATT
1 TTGTTCATACAAAATT
53487323 AGTTATTCTA
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
78 19 0.22
81 2 0.02
82 63 0.73
83 2 0.02
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.40
Consensus pattern (78 bp):
TTGTTCATACAAAATTTAGATGGTGGTGAAACTGAGAGCTGATCGATTTTAATTCTCCGTATCTA
AAAATATAAAATT
Found at i:53488187 original size:50 final size:50
Alignment explanation
Indices: 53488124--53488219 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
53488114 ACAAATTTAG
* * * *
53488124 CCCTCAAATTTTACATATTATATCAATTT-AGTCATAATTTTAAAAATTAA
1 CCCTCAAAATTTACAAATGATATCAATTTGA-TCATAATTCTAAAAATTAA
* *
53488174 CCCTCAAAATTTACAAATGATTTCAATTTGATCCTAATTCTAAAAA
1 CCCTCAAAATTTACAAATGATATCAATTTGATCATAATTCTAAAAA
53488220 ATTCAAAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 38 0.97
51 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.39
Consensus pattern (50 bp):
CCCTCAAAATTTACAAATGATATCAATTTGATCATAATTCTAAAAATTAA
Found at i:53488415 original size:25 final size:24
Alignment explanation
Indices: 53488382--53488429 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
53488372 ATTTAAATTA
53488382 ATATTAATATTAAATAAAGATAAAT
1 ATATTAATATTAAATAAA-ATAAAT
*
53488407 ATATTAATATTAGATAAAATAAA
1 ATATTAATATTAAATAAAATAAA
53488430 AATCCCCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
ATATTAATATTAAATAAAATAAAT
Found at i:53488548 original size:25 final size:24
Alignment explanation
Indices: 53488503--53488549 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
53488493 TGGGGGCTTT
**
53488503 TTATTTTATTTAATATTAATATAA
1 TTATTTTATTTAATACAAATATAA
53488527 TTATATTTATTTAATACAAATAT
1 TTAT-TTTATTTAATACAAATAT
53488550 TAGTATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATTTTATTTAATACAAATATAA
Found at i:53514405 original size:10 final size:11
Alignment explanation
Indices: 53514389--53514421 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
53514379 TTTTGAATAA
53514389 AATATTTTTTT
1 AATATTTTTTT
53514400 -ATATTTTTTT
1 AATATTTTTTT
53514410 AATAATTTTTTT
1 AAT-ATTTTTTT
53514422 TAAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 2 0.10
12 8 0.40
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
AATATTTTTTT
Found at i:53514515 original size:27 final size:27
Alignment explanation
Indices: 53514485--53514546 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
53514475 CCTATCAGGT
53514485 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
53514512 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
53514539 AGGCGCCA
1 AGGCGCCA
53514547 TTACTAGACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.34, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:53514715 original size:49 final size:49
Alignment explanation
Indices: 53514659--53514809 Score: 193
Period size: 49 Copynumber: 3.1 Consensus size: 49
53514649 CGGGAAAAAA
*
53514659 TTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAAT
1 TTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGTAAT
*
53514708 TTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGAATATTGTAA-
1 TTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGTAAT
* ** *
53514756 -TGTCGGTAT--ATATTGTAATATTGTAATTTTTTGTATGAATATTGTAAT
1 TTTTTTGTATGAATATTGTAATATTATAA--TTTTGTATGAATATTGTAAT
*
53514804 TATTTT
1 TTTTTT
53514810 ATAATTAATT
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
45 15 0.17
47 25 0.29
49 47 0.54
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.54
Consensus pattern (49 bp):
TTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGTAAT
Found at i:53514716 original size:22 final size:24
Alignment explanation
Indices: 53514659--53514809 Score: 114
Period size: 27 Copynumber: 6.1 Consensus size: 24
53514649 CGGGAAAAAA
53514659 TTTTTTGTATGAATATTGTAATAT
1 TTTTTTGTATGAATATTGTAATAT
*
53514683 TATAATTTTGTATGAATATTG-CA-AT
1 T-T--TTTTGTATGAATATTGTAATAT
*
53514708 TTTTTTGTATGAATGTTGTAATAT
1 TTTTTTGTATGAATATTGTAATAT
*
53514732 TATAATTTTGTATGAATATTGTAATGT
1 T-T--TTTTGTATGAATATTGTAATAT
*** * *
53514759 CGGTATATATTGTAATATTGT-A-A-
1 TTTTTTGTA-TG-AATATTGTAATAT
53514782 TTTTTTGTATGAATATTGTAATTAT
1 TTTTTTGTATGAATATTGTAA-TAT
53514807 TTT
1 TTT
53514810 ATAATTAATT
Statistics
Matches: 97, Mismatches: 16, Indels: 27
0.69 0.11 0.19
Matches are distributed among these distances:
21 8 0.08
22 18 0.19
23 5 0.05
24 10 0.10
25 11 0.11
26 9 0.09
27 36 0.37
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.54
Consensus pattern (24 bp):
TTTTTTGTATGAATATTGTAATAT
Found at i:53514731 original size:30 final size:27
Alignment explanation
Indices: 53514661--53514756 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 27
53514651 GGAAAAAATT
53514661 TTTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATTATAA
*
53514688 TTTTGTATGAATATTG-CA-ATT-T--
1 TTTTGTATGAATATTGTAATATTATAA
*
53514710 TTTTGTATGAATGTTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATTATAA
53514737 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
53514757 GTCGGTATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
22 15 0.25
23 1 0.02
24 4 0.07
25 4 0.07
26 1 0.02
27 35 0.58
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (27 bp):
TTTTGTATGAATATTGTAATATTATAA
Found at i:53514874 original size:19 final size:19
Alignment explanation
Indices: 53514852--53514889 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
53514842 TATAAATTTA
*
53514852 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
53514871 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
53514890 AAATTAAATT
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:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:53516957 original size:24 final size:24
Alignment explanation
Indices: 53516929--53517004 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 24
53516919 ACTATTTAAT
*
53516929 TATTATTTTTATTTGTTGTTATTA
1 TATTATTTTTATTTGTTATTATTA
*
53516953 TATTATATTATTACTTGTTTATTATTA
1 TATTAT-TT-TTATTTG-TTATTATTA
* * *
53516980 T-TTATTATTTTTTTGTCATCATTA
1 TATTATT-TTTATTTGTTATTATTA
53517004 T
1 T
53517005 TATTTTCATT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
24 14 0.33
25 8 0.19
26 11 0.26
27 9 0.21
ACGTcount: A:0.24, C:0.04, G:0.05, T:0.67
Consensus pattern (24 bp):
TATTATTTTTATTTGTTATTATTA
Found at i:53520985 original size:51 final size:51
Alignment explanation
Indices: 53520918--53521058 Score: 156
Period size: 51 Copynumber: 2.8 Consensus size: 51
53520908 TGATAGGTCG
* * **
53520918 CATGTGTAGTACTATGTGCAGGCCACTATGCGTACCGGATAGTTTCGATCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGTAACGATCA
* * * * * *
53520969 CGTGTGTAGTACTATGTGCAGACTACTACGTGTATCGAATGGTAACGATCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGTAACGATCA
* * * *
53521020 CATGTGTAATACTATGTGTAGGCTACTATGTGAACCGAA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAA
53521059 CATCATTGAT
Statistics
Matches: 73, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 73 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (51 bp):
CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGTAACGATCA
Found at i:53521123 original size:45 final size:45
Alignment explanation
Indices: 53521053--53521147 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
53521043 TACTATGTGA
* *
53521053 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGTTGAATCC
* *
53521098 ACCGGACATCATTGATTAATGAGGTGGTTGCTATGTGTTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGTTGAATCC
53521143 ACCGA
1 ACCGA
53521148 GTATCTGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGTTGAATCC
Found at i:53523609 original size:3 final size:3
Alignment explanation
Indices: 53523601--53523693 Score: 168
Period size: 3 Copynumber: 31.0 Consensus size: 3
53523591 ATTCCCACTC
53523601 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
53523649 ATA ATA ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA ATA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53523694 CTAAAATTAA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53524357 original size:9 final size:9
Alignment explanation
Indices: 53524345--53524418 Score: 57
Period size: 9 Copynumber: 8.6 Consensus size: 9
53524335 TATTTCCCCT
53524345 TTTTTCTTC
1 TTTTTCTTC
53524354 TTTTTCTTC
1 TTTTTCTTC
* **
53524363 TTTCTCCCC
1 TTTTTCTTC
*
53524372 TGTTTCTTC
1 TTTTTCTTC
* *
53524381 TCTGT-TTC
1 TTTTTCTTC
53524389 -TTTTCTTC
1 TTTTTCTTC
53524397 TTTTGT-TTC
1 TTTT-TCTTC
53524406 -TTTTCTTC
1 TTTTTCTTC
53524414 TTTTT
1 TTTTT
53524419 ATTTTAACTT
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
7 3 0.06
8 12 0.24
9 33 0.67
10 1 0.02
ACGTcount: A:0.00, C:0.24, G:0.04, T:0.72
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:53524405 original size:17 final size:17
Alignment explanation
Indices: 53524374--53524417 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
53524364 TTCTCCCCTG
*
53524374 TTTCTTC-TCTGTTTCT
1 TTTCTTCTTTTGTTTCT
53524390 TTTCTTCTTTTGTTTCT
1 TTTCTTCTTTTGTTTCT
53524407 TTTCTTCTTTT
1 TTTCTTCTTTT
53524418 TATTTTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (17 bp):
TTTCTTCTTTTGTTTCT
Found at i:53524592 original size:17 final size:16
Alignment explanation
Indices: 53524566--53524597 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
53524556 TTAACATAAT
53524566 ATTTATAATATAATTA
1 ATTTATAATATAATTA
53524582 ATTTAATAATATAATT
1 ATTT-ATAATATAATT
53524598 TATATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTATAATATAATTA
Found at i:53524608 original size:17 final size:17
Alignment explanation
Indices: 53524570--53524625 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
53524560 CATAATATTT
*
53524570 ATAATATAATTAATTTA
1 ATAATATAATTAATATA
*
53524587 ATAATATAATTTATATA
1 ATAATATAATTAATATA
*
53524604 TTAATA-AA--AATA-A
1 ATAATATAATTAATATA
53524617 ATAATATAA
1 ATAATATAA
53524626 AAATCTAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
13 6 0.18
14 5 0.15
16 2 0.06
17 20 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATATAATTAATATA
Found at i:53528228 original size:60 final size:62
Alignment explanation
Indices: 53528101--53528243 Score: 186
Period size: 60 Copynumber: 2.3 Consensus size: 62
53528091 AGGGGTGTTG
* * *
53528101 GCCATCAGTGTCCCAACACCCCAAAAAAATATATTTTTTTTAAATTTGGTATTGAAGTGCCA
1 GCCATTAGTGTCCCAACACCCCAAAAAAATATATTTTTTTTAAATTTGGTATTAAAGTACCA
* *
53528163 GCCATTAGTGTCCCAGCACCCTAAAAAAAT-TA-TTTTTTTAAATTTGGTA-TAAAGGTACC-
1 GCCATTAGTGTCCCAACACCCCAAAAAAATATATTTTTTTTAAATTTGGTATTAAA-GTACCA
*
53528222 GACCATTAGTGTTCCAACACCC
1 G-CCATTAGTGTCCCAACACCC
53528244 AATTTTTTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
59 4 0.06
60 39 0.54
61 2 0.03
62 27 0.38
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31
Consensus pattern (62 bp):
GCCATTAGTGTCCCAACACCCCAAAAAAATATATTTTTTTTAAATTTGGTATTAAAGTACCA
Found at i:53528312 original size:53 final size:50
Alignment explanation
Indices: 53528224--53528425 Score: 176
Period size: 50 Copynumber: 3.9 Consensus size: 50
53528214 AAGGTACCGA
* * * * *
53528224 CCATTAGTGTTCCAACACCCAA-TTTTTTT-AATCTGGTACTGGGGTGCCAG
1 CCATCAGTGTCCCAGCA-CCAATTTTTTTTAAATCTGGTACTAGGGTGTC-G
* *
53528274 CCATCAGTGTCCCAGCATCCAATTTGTTTTTAAATCTGGTACAAGAGTGTCGG
1 CCATCAGTGTCCCAGCA-CCAATTT-TTTTTAAATCTGGTACTAGGGTGTC-G
* * * * *
53528327 CCATCAATGTCCTAGCACTAATTTTTTTTAAACCAGGTACTAGGGTGTCG
1 CCATCAGTGTCCCAGCACCAATTTTTTTTAAATCTGGTACTAGGGTGTCG
* * *
53528377 GCATCAGTGTCCCAACACCCAATTTTTCTTTTAATCTGGTA-TAAGGGTG
1 CCATCAGTGTCCCAGCA-CCAATTTTT-TTTAAATCTGGTACT-AGGGTG
53528426 CAGACCATCA
Statistics
Matches: 122, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
50 32 0.26
51 32 0.26
52 27 0.22
53 31 0.25
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (50 bp):
CCATCAGTGTCCCAGCACCAATTTTTTTTAAATCTGGTACTAGGGTGTCG
Found at i:53528435 original size:53 final size:51
Alignment explanation
Indices: 53528190--53528451 Score: 176
Period size: 53 Copynumber: 5.0 Consensus size: 51
53528180 ACCCTAAAAA
* * ** * *
53528190 AATTATTTTTTTAAATTTGGTATAAAGGTACCGACCATTAGTGTTCCAACACCC
1 AATT-TTTTTTT-AATCTGGTATAAGGGTGTCG-CCATCAGTGTCCCAACACCC
* * * *
53528244 AA--TTTTTTTAATCTGGTACT-GGGGTGCCAGCCATCAGTGTCCCAGCATCC
1 AATTTTTTTTTAATCTGGTA-TAAGGGTGTC-GCCATCAGTGTCCCAACACCC
* * * * * * *
53528294 AATTTGTTTTTAAATCTGGTACAAGAGTGTCGGCCATCAATGTCCTAGCA-CT
1 AATTT-TTTTTTAATCTGGTATAAGGGTGTC-GCCATCAGTGTCCCAACACCC
* * * *
53528346 AATTTTTTTTAAACCAGGTACT-AGGGTGTCGGCATCAGTGTCCCAACACCC
1 AATTTTTTTTTAATCTGGTA-TAAGGGTGTCGCCATCAGTGTCCCAACACCC
* *
53528397 AATTTTTCTTTTAATCTGGTATAAGGGTG-CAGACCATCAATGTCCTAACACCC
1 AATTTTT-TTTTAATCTGGTATAAGGGTGTC-G-CCATCAGTGTCCCAACACCC
53528450 AA
1 AA
53528452 AAAAGATATT
Statistics
Matches: 164, Mismatches: 32, Indels: 25
0.74 0.14 0.11
Matches are distributed among these distances:
50 45 0.27
51 39 0.24
52 24 0.15
53 54 0.33
54 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (51 bp):
AATTTTTTTTTAATCTGGTATAAGGGTGTCGCCATCAGTGTCCCAACACCC
Found at i:53532980 original size:7 final size:7
Alignment explanation
Indices: 53532968--53532996 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
53532958 CCCAGCTAAC
53532968 ATATAAA
1 ATATAAA
53532975 ATATAAA
1 ATATAAA
53532982 ATATAAA
1 ATATAAA
53532989 ATATAAA
1 ATATAAA
53532996 A
1 A
53532997 AAAACTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATATAAA
Found at i:53537348 original size:14 final size:14
Alignment explanation
Indices: 53537331--53537357 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53537321 ATCAAAGATT
53537331 TATTATATTATAAA
1 TATTATATTATAAA
53537345 TATTATATTATAA
1 TATTATATTATAA
53537358 GATAATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTATATTATAAA
Found at i:53538442 original size:9 final size:9
Alignment explanation
Indices: 53538428--53538462 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
53538418 TTAACTTTAA
53538428 TTAAATTAT
1 TTAAATTAT
53538437 TTAAATTAT
1 TTAAATTAT
*
53538446 TT-AATTTT
1 TTAAATTAT
53538454 TTAAATTAT
1 TTAAATTAT
53538463 AAACAAACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTAAATTAT
Found at i:53538744 original size:15 final size:15
Alignment explanation
Indices: 53538724--53538760 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
53538714 TTAAGTTCAG
53538724 TGTTTAAGGATTTGA
1 TGTTTAAGGATTTGA
*
53538739 TGTTT-AGGGTTTGA
1 TGTTTAAGGATTTGA
53538753 -GTTTAAGG
1 TGTTTAAGG
53538761 TTTAAAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 11 0.55
15 5 0.25
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (15 bp):
TGTTTAAGGATTTGA
Found at i:53538868 original size:28 final size:27
Alignment explanation
Indices: 53538833--53538889 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
53538823 GGTTTCAGAT
* * *
53538833 TTTGGATTCTATATTTTGGGTTTAGGG
1 TTTGGATTCTAGATTTAGGGTTCAGGG
*
53538860 TTTGAGATTTTAGATTTAGGGTTCAGGG
1 TTTG-GATTCTAGATTTAGGGTTCAGGG
53538888 TT
1 TT
53538890 AAAAAAACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.18, C:0.04, G:0.30, T:0.49
Consensus pattern (27 bp):
TTTGGATTCTAGATTTAGGGTTCAGGG
Found at i:53541973 original size:24 final size:24
Alignment explanation
Indices: 53541946--53541997 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
53541936 TTAGTAAGTC
*
53541946 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
53541970 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
53541994 AAAT
1 AAAT
53541998 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:53543938 original size:24 final size:24
Alignment explanation
Indices: 53543911--53543962 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
53543901 TTAGTAAGTC
*
53543911 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
53543935 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
53543959 AAAT
1 AAAT
53543963 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:53544117 original size:22 final size:22
Alignment explanation
Indices: 53544072--53544119 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
53544062 TTTCTTGCTT
* *
53544072 TTTTTTTGTTGTTTTACTATTA
1 TTTTCTTGTTGTTTTACTACTA
53544094 TTTTCTTGTTGTTTT-CTCACTA
1 TTTTCTTGTTGTTTTACT-ACTA
53544116 TTTT
1 TTTT
53544120 GCTACCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.10, C:0.10, G:0.08, T:0.71
Consensus pattern (22 bp):
TTTTCTTGTTGTTTTACTACTA
Found at i:53544330 original size:17 final size:17
Alignment explanation
Indices: 53544280--53544333 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
53544270 GGAAAATATT
53544280 TATTTTAATATTTTTAGTA
1 TATTTTAA-ATTTTTA-TA
* *
53544299 -ATTTTAAAGTATTATA
1 TATTTTAAATTTTTATA
*
53544315 TTTTTTAAATTTTTATA
1 TATTTTAAATTTTTATA
53544332 TA
1 TA
53544334 AAAAATAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
16 2 0.07
17 19 0.68
18 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (17 bp):
TATTTTAAATTTTTATA
Found at i:53544764 original size:18 final size:19
Alignment explanation
Indices: 53544731--53544767 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
53544721 TCCTCTTCCT
*
53544731 TCTTCCATATAAAAATAAA
1 TCTTCCATACAAAAATAAA
53544750 TCTTCCA-ACAAAAATAAA
1 TCTTCCATACAAAAATAAA
53544768 AATAATTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (19 bp):
TCTTCCATACAAAAATAAA
Found at i:53545896 original size:20 final size:21
Alignment explanation
Indices: 53545873--53545919 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
53545863 ACAAGAGTAA
53545873 AGATTTTAAGG-TTTA-AGGTT
1 AGATTTT-AGGATTTAGAGGTT
53545893 AGA-TTTAGGATTTAGAGGTT
1 AGATTTTAGGATTTAGAGGTT
53545913 AGGATTT
1 A-GATTT
53545920 GGATTTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 3 0.13
19 7 0.30
20 9 0.39
21 2 0.09
22 2 0.09
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.43
Consensus pattern (21 bp):
AGATTTTAGGATTTAGAGGTT
Found at i:53545956 original size:18 final size:19
Alignment explanation
Indices: 53545933--53545970 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53545923 TTTTAAGGTT
53545933 TAGGA-TTAA-GTTCTAAAA
1 TAGGATTTAAGGTT-TAAAA
53545951 TAGGATTTAAGGTTTAAAA
1 TAGGATTTAAGGTTTAAAA
53545970 T
1 T
53545971 TGGCTTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 10 0.56
20 3 0.17
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (19 bp):
TAGGATTTAAGGTTTAAAA
Found at i:53547802 original size:29 final size:29
Alignment explanation
Indices: 53547770--53547838 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
53547760 GCCCAGTAAC
*
53547770 AAATTTTAAAAATA-AAAGAAAACTCTTTA
1 AAATTTTAAAAATATAAA-AAAACTCATTA
* ** *
53547799 AAATTTAAAAAATATTTAAAAAGTCATTA
1 AAATTTTAAAAATATAAAAAAACTCATTA
53547828 AAATTTTAAAA
1 AAATTTTAAAA
53547839 TTTCTATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 32 0.97
30 1 0.03
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.33
Consensus pattern (29 bp):
AAATTTTAAAAATATAAAAAAACTCATTA
Found at i:53548262 original size:16 final size:17
Alignment explanation
Indices: 53548241--53548274 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
53548231 ATTGAATAGA
*
53548241 ATTTTTA-ATAATTTTT
1 ATTTTTATAAAATTTTT
53548257 ATTTTTATAAAATTTTT
1 ATTTTTATAAAATTTTT
53548274 A
1 A
53548275 ATAATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTATAAAATTTTT
Found at i:53553866 original size:2 final size:2
Alignment explanation
Indices: 53553859--53553884 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53553849 ATTATGGAGA
53553859 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
53553885 GGATATGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53554175 original size:71 final size:71
Alignment explanation
Indices: 53554094--53554248 Score: 186
Period size: 71 Copynumber: 2.2 Consensus size: 71
53554084 ATGACTAGCA
* * * * * *
53554094 CTGGGTGCAAAACATCGTCGGTTTATCCTACCAGTACAGGGCACAACTATTGTTGGTTTA-TCCA
1 CTGGGCGCAAAACATCGTCGGTTTAACCAACCAGTACAAGGCACAACTATTGTCGGTATACT-CA
53554158 ACCAGCG
65 ACCAGCG
* ** * *
53554165 CTGGGCGCAAAACATTGTCTTTTTAACCAACCAGTGCAAGGCACAACTATTGTCGGTATACTCGA
1 CTGGGCGCAAAACATCGTCGGTTTAACCAACCAGTACAAGGCACAACTATTGTCGGTATACTCAA
*
53554230 CTAGCG
66 CCAGCG
53554236 CTGGGCGCAAAAC
1 CTGGGCGCAAAAC
53554249 TTTACTACGG
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
71 70 0.99
72 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.25
Consensus pattern (71 bp):
CTGGGCGCAAAACATCGTCGGTTTAACCAACCAGTACAAGGCACAACTATTGTCGGTATACTCAA
CCAGCG
Found at i:53561499 original size:42 final size:42
Alignment explanation
Indices: 53561440--53561724 Score: 430
Period size: 42 Copynumber: 6.8 Consensus size: 42
53561430 AGCGTTTAAA
*
53561440 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* * * *
53561482 AAAAAACCGTCGCTAAAGAACATGTTCTTTAGCGGCGCTTTG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* *
53561524 AAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAA
1 -AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
53561567 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTA-
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* *
53561608 AGAAAAAACGCCGCTAAAGACCAT-TTTTTTAGCGGCGCTTAT
1 A-AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
53561650 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* * *
53561692 AAAAAAACGCCGCTAAAGAACATGATGTTTAGC
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGC
53561725 AGCGTTTTTT
Statistics
Matches: 225, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
41 39 0.17
42 148 0.66
43 38 0.17
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
Found at i:53561666 original size:83 final size:84
Alignment explanation
Indices: 53561441--53561724 Score: 423
Period size: 83 Copynumber: 3.4 Consensus size: 84
53561431 GCGTTTAAAA
* * *
53561441 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT-TGAAAAAACCGTCGCTAAAGAACAT
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAT-AAAAAAACGCCGCTAAAGACCAT
53561505 GTTCTTTAGCGGCGCTTTGAA-
65 GTTCTTTAGCGGCGC-TT-AAG
* *
53561526 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAAAAAAAACGCCGCTAAAGACCATG
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGACCATG
53561591 TTCTTTAGCGGCGCTTAAG
66 TTCTTTAGCGGCGCTTAAG
*
53561610 AAAAAACGCCGCTAAAGACCAT-TTTTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGACCATG
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGACCATG
53561674 TTCTTTAGCGGCGCTT-AG
66 TTCTTTAGCGGCGCTTAAG
* * *
53561692 AAAAAAACGCCGCTAAAGAACATGATGTTTAGC
1 -AAAAAACGCCGCTAAAGACCATGTTCTTTAGC
53561725 AGCGTTTTTT
Statistics
Matches: 184, Mismatches: 11, Indels: 9
0.90 0.05 0.04
Matches are distributed among these distances:
82 2 0.01
83 79 0.43
84 30 0.16
85 73 0.40
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (84 bp):
AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGACCATG
TTCTTTAGCGGCGCTTAAG
Found at i:53564119 original size:7 final size:7
Alignment explanation
Indices: 53564107--53564238 Score: 106
Period size: 7 Copynumber: 18.9 Consensus size: 7
53564097 ATAACCCAAT
53564107 CCCTAAC
1 CCCTAAC
53564114 CCCTAAC
1 CCCTAAC
*
53564121 CCTTAAC
1 CCCTAAC
53564128 CCCTAAC
1 CCCTAAC
*
53564135 CCTTAAC
1 CCCTAAC
*
53564142 CTCTAAC
1 CCCTAAC
*
53564149 CCTTAAC
1 CCCTAAC
53564156 CCCTAAC
1 CCCTAAC
*
53564163 CCTTAAC
1 CCCTAAC
**
53564170 CTTTAAC
1 CCCTAAC
*
53564177 CCTTAA-
1 CCCTAAC
53564183 CCCTAAAC
1 CCCT-AAC
**
53564191 CTTTAA-
1 CCCTAAC
53564197 CCCTAAAC
1 CCCT-AAC
*
53564205 CCTTAAC
1 CCCTAAC
* *
53564212 CCATGAC
1 CCCTAAC
*
53564219 CTCTAAC
1 CCCTAAC
53564226 CCCTAAC
1 CCCTAAC
53564233 CCCTAA
1 CCCTAA
53564239 AACTTATTTA
Statistics
Matches: 98, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
6 5 0.05
7 88 0.90
8 5 0.05
ACGTcount: A:0.30, C:0.45, G:0.01, T:0.23
Consensus pattern (7 bp):
CCCTAAC
Found at i:53564238 original size:14 final size:14
Alignment explanation
Indices: 53564110--53564234 Score: 148
Period size: 14 Copynumber: 8.9 Consensus size: 14
53564100 ACCCAATCCC
53564110 TAACCCCTAACCCT
1 TAACCCCTAACCCT
53564124 TAACCCCTAACCCT
1 TAACCCCTAACCCT
*
53564138 TAACCTCTAACCCT
1 TAACCCCTAACCCT
53564152 TAACCCCTAACCCT
1 TAACCCCTAACCCT
**
53564166 TAACCTTTAACCCT
1 TAACCCCTAACCCT
*
53564180 TAA-CCCTAAACCTT
1 TAACCCCT-AACCCT
53564194 TAA-CCCTAAACCCT
1 TAACCCCT-AACCCT
* *
53564208 TAACCCATGA-CCT
1 TAACCCCTAACCCT
53564221 CTAACCCCTAACCC
1 -TAACCCCTAACCC
53564235 CTAAAACTTA
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
13 5 0.05
14 85 0.89
15 5 0.05
ACGTcount: A:0.30, C:0.45, G:0.01, T:0.24
Consensus pattern (14 bp):
TAACCCCTAACCCT
Found at i:53564348 original size:14 final size:12
Alignment explanation
Indices: 53564337--53564375 Score: 60
Period size: 12 Copynumber: 3.1 Consensus size: 12
53564327 CTCTTAACAT
53564337 CTAACCCCTAAC
1 CTAACCCCTAAC
53564349 CTAACCCCTAACCC
1 CTAACCCCTAA--C
53564363 CTAACCCCTAAC
1 CTAACCCCTAAC
53564375 C
1 C
53564376 CCTAATCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 13 0.52
14 12 0.48
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:53564352 original size:33 final size:33
Alignment explanation
Indices: 53564315--53564380 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
53564305 TTTTATAAAT
* * *
53564315 CCTAAACCCTAACTCTTAACATCTAACCCCTAA
1 CCTAAACCCTAACCCCTAACACCTAACCCCTAA
* *
53564348 CCTAACCCCTAACCCCTAACCCCTAACCCCTAA
1 CCTAAACCCTAACCCCTAACACCTAACCCCTAA
53564381 TCTATAAACC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (33 bp):
CCTAAACCCTAACCCCTAACACCTAACCCCTAA
Found at i:53564360 original size:26 final size:26
Alignment explanation
Indices: 53564322--53564375 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
53564312 AATCCTAAAC
* * *
53564322 CCTAACTCTTAACATCTAACCCCTAA
1 CCTAACCCCTAACACCTAACCCCTAA
*
53564348 CCTAACCCCTAACCCCTAACCCCTAA
1 CCTAACCCCTAACACCTAACCCCTAA
53564374 CC
1 CC
53564376 CCTAATCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.48, G:0.00, T:0.20
Consensus pattern (26 bp):
CCTAACCCCTAACACCTAACCCCTAA
Found at i:53564376 original size:14 final size:14
Alignment explanation
Indices: 53564337--53564380 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
53564327 CTCTTAACAT
53564337 CTAACCCCTAA--C
1 CTAACCCCTAACCC
53564349 CTAACCCCTAACCC
1 CTAACCCCTAACCC
53564363 CTAACCCCTAACCC
1 CTAACCCCTAACCC
53564377 CTAA
1 CTAA
53564381 TCTATAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.37
14 19 0.63
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (14 bp):
CTAACCCCTAACCC
Found at i:53564895 original size:114 final size:114
Alignment explanation
Indices: 53564769--53564974 Score: 247
Period size: 114 Copynumber: 1.8 Consensus size: 114
53564759 GCTTTACCGA
* *
53564769 AAACGCCGCTAA-TACTATTC-TTTAGCAGCGTTTTACCATAAACGCCACTAAT-TCTAATATAC
1 AAACGCCACTAATTA-TATTCTTTTA-CAGCGTTTTACCAAAAACGCCACTAATAT-TAATATAC
*
53564831 ATCAAAACCAAACACTGCGTTTTGGTTAAGGCATTTTGCGGCGCTTCCAAAT
63 ATCAAAACCAAACACTGCGTTTTCGTTAAGGCATTTTGCGGCGCTTCCAAAT
* * *** * *
53564883 AAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTTAAAAACGCCACTAATATTAATCTACCTC
1 AAACGCCACTAATTATATTCTTTTACAGCGTTTTACCAAAAACGCCACTAATATTAATATACATC
* **
53564948 AAGACCAAACGGTGCGTTTTCGTTAAG
66 AAAACCAAACACTGCGTTTTCGTTAAG
53564975 ATATTTGCTG
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
114 69 0.91
115 7 0.09
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (114 bp):
AAACGCCACTAATTATATTCTTTTACAGCGTTTTACCAAAAACGCCACTAATATTAATATACATC
AAAACCAAACACTGCGTTTTCGTTAAGGCATTTTGCGGCGCTTCCAAAT
Found at i:53565012 original size:188 final size:188
Alignment explanation
Indices: 53564796--53565196 Score: 640
Period size: 188 Copynumber: 2.1 Consensus size: 188
53564786 TTCTTTAGCA
* *
53564796 GCGTTTTACCATAAACGCCACTAATTCTAATATACATCAAAACCAAACACTGCGTTTTGGTTAAG
1 GCGTTTTACCGTAAACGCCACTAATTCTAATATACATCAAAACCAAACACTGCGTATTGGTTAAG
* * ** *
53564861 GCATTTTGCGGCGCTTCCAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTTAAAAAC
66 GCATTTTGCGACGCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTCTAAAAAC
* * *
53564926 GCCACTAATATTAATCTACCTCAAGACCAAACGGTGCGTTTTCGTTAAGATATTTGCT
131 GCCACTAATACTAATCTACCTCAAGACCAAACGGTGCGTTTTCATTAAGATATTTGCG
* * *
53564984 GCGTTTTATCGTAAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTATTGGTTAAG
1 GCGTTTTACCGTAAACGCCACTAATTCTAATATACATCAAAACCAAACACTGCGTATTGGTTAAG
*
53565049 GTATTTTGCGACGCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTCTAAAAAC
66 GCATTTTGCGACGCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTCTAAAAAC
*
53565114 GCCACTAATACTAATCTACCTCAAGACGAAACGGTGCGTTTTCATTAAGATATTTGCG
131 GCCACTAATACTAATCTACCTCAAGACCAAACGGTGCGTTTTCATTAAGATATTTGCG
* * *
53565172 GCGCTTTACCGAAAACGCCGCTAAT
1 GCGTTTTACCGTAAACGCCACTAAT
53565197 ACTATTCTTT
Statistics
Matches: 194, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
188 194 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (188 bp):
GCGTTTTACCGTAAACGCCACTAATTCTAATATACATCAAAACCAAACACTGCGTATTGGTTAAG
GCATTTTGCGACGCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTCTAAAAAC
GCCACTAATACTAATCTACCTCAAGACCAAACGGTGCGTTTTCATTAAGATATTTGCG
Found at i:53565278 original size:227 final size:227
Alignment explanation
Indices: 53564978--53565575 Score: 848
Period size: 227 Copynumber: 2.6 Consensus size: 227
53564968 CGTTAAGATA
* * * * * ** *
53564978 TTTGCTGCGTTTTATCGTAAACGCCACTAATTCTAATATAC-CTCAAAACCAAACGCTGCGTATT
1 TTTGCGGCGTTTTATAGAAAACGCCACGAATTCTAATATACAAT-TGAACCAAACGCTGCGTTTT
*
53565042 GGTTAAGGTATTTTGCGACGCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTC
65 GGTTAAGGTATTTTGCGACGCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTT
*
53565107 TAAAAACGCCACTAATACTAATCTACCTCAAGACGAAACGGTGCGTTTTCATTAAGATATTTGCG
130 TAAAAACGCCACTAATACTAATCTACCTCAAGACAAAACGGTGCGTTTTCATTAAGATATTTGCG
53565172 GCGCTTTACCG-AAAACGCCGCTAATACTATTCT
195 GCGCTTT-CCGTAAAACGCCGCTAATACTATTCT
53565205 TTTGCGGCGTTTTATAGAAAACGCCAC-AATGTCTAATATACAATTGAACCAAACGCTGCGTTTT
1 TTTGCGGCGTTTTATAGAAAACGCCACGAAT-TCTAATATACAATTGAACCAAACGCTGCGTTTT
* ** *
53565269 GGTTAAGGTATTTTGC-AGTGCATCCAAATAAACGCCACTAATTATGTTATTTTACGGCGTTTTT
65 GGTTAAGGTATTTTGCGA-CGCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTT
* * * *
53565333 TTAAAAACGCCACTAATATTAATCTACCTCAAGATAAAATGGTGCGTTTTCCTTAAGATATTTGC
129 TTAAAAACGCCACTAATACTAATCTACCTCAAGACAAAACGGTGCGTTTTCATTAAGATATTTGC
** *
53565398 GGCGCTTTTTGTTAAACGCCGCTAATACTATTCT
194 GGCGCTTTCCGTAAAACGCCGCTAATACTATTCT
* *
53565432 TTCGCGGCGTTTTTTTATAAAAAACGCCACGAATTCTAATATACAATTGAACC-AACGCTGCGTT
1 TTTGCGGCG---TTTTATAGAAAACGCCACGAATTCTAATATACAATTGAACCAAACGCTGCGTT
* * *
53565496 TTGGTTAAGGTATTTTGCGGCGC-TTACAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTT
63 TTGGTTAAGGTATTTTGCGACGCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTT
*
53565560 TTTAGAAACGCCACTA
128 TTTAAAAACGCCACTA
53565576 GTTCTTCAGG
Statistics
Matches: 333, Mismatches: 29, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
226 5 0.02
227 205 0.62
228 53 0.16
229 31 0.09
230 36 0.11
231 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (227 bp):
TTTGCGGCGTTTTATAGAAAACGCCACGAATTCTAATATACAATTGAACCAAACGCTGCGTTTTG
GTTAAGGTATTTTGCGACGCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTT
AAAAACGCCACTAATACTAATCTACCTCAAGACAAAACGGTGCGTTTTCATTAAGATATTTGCGG
CGCTTTCCGTAAAACGCCGCTAATACTATTCT
Found at i:53565344 original size:114 final size:112
Alignment explanation
Indices: 53564996--53565580 Score: 513
Period size: 114 Copynumber: 5.1 Consensus size: 112
53564986 GTTTTATCGT
* * *
53564996 AAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTATTGGTTAAGGTATTTTGCGAC
1 AAACGCCACTAATTCTAATATACATC-AAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
* * *
53565061 GCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTCTAA
65 GC-TTACAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTTAA
* * * * * ** *
53565110 AAACGCCACTAATACTAATCTACCTCAAGACGAAACGGTGCGTTTTCATTAAGATA-TTTGCGGC
1 AAACGCCACTAATTCTAATATACATCAA-ACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
* * * * *
53565174 GCTTTACCGA-AAACGCCGCTAA-TACTATTCTTTTGCGGCG-TTTTATAGA
65 GC-TTA-CAATAAACGCCACTAATTA-TGTTCTTTTACGGCGTTTTTTTA-A
** *
53565223 AAACGCCAC-AATGTCTAATATACAATTGAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCAG
1 AAACGCCACTAAT-TCTAATATAC-ATCAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGG
* * * *
53565287 TGCATCCAAATAAACGCCACTAATTATGTTATTTTACGGCGTTTTTTTAA
64 CGCTTAC-AATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTTAA
* * ** * * ** *
53565337 AAACGCCACTAATAT-TAATCTACCTCAAGATAAAATGGTGCGTTTTCCTTAAGATA-TTTGCGG
1 AAACGCCACTAAT-TCTAATATACATCAA-ACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGG
**** * * **
53565400 CGCTTTTTGTTAAACGCCGCTAA-TACTATTCTTTCGCGGCGTTTTTTTATAAA
64 CGC-TTACAATAAACGCCACTAATTA-TGTTCTTTTACGGCG-TTTTTT-T-AA
* **
53565453 AAACGCCACGAATTCTAATATACAATTGAACC-AACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
1 AAACGCCACTAATTCTAATATAC-ATCAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
*
53565517 GCTTACAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTTAG
65 GCTTACAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTTAA
*
53565565 AAACGCCACTAGTTCT
1 AAACGCCACTAATTCT
53565581 TCAGGTTTCA
Statistics
Matches: 365, Mismatches: 84, Indels: 46
0.74 0.17 0.09
Matches are distributed among these distances:
112 29 0.08
113 113 0.31
114 129 0.35
115 58 0.16
116 34 0.09
117 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (112 bp):
AAACGCCACTAATTCTAATATACATCAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCG
CTTACAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTTAA
Found at i:53574262 original size:43 final size:43
Alignment explanation
Indices: 53574199--53574324 Score: 134
Period size: 43 Copynumber: 2.9 Consensus size: 43
53574189 AGGACTCCGA
*
53574199 TATGTGTTTTCGTGTAAGACCACGTCTGGGA-TGTCGGCATCGAC
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACAGT-GGCATCG-C
*
53574243 T-TGTGTTTTCGTGTAAGACC-CTGTCTGGGACAGTGGCATCGG
1 TATGTGTTTTCGTGTAAGACCAC-GTCTGGGACAGTGGCATCGC
* * * *
53574285 TATGTGATTACATGTAAGACCACGTCTAGGAC-GTTGGCAT
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACAG-TGGCAT
53574325 TGTACTAGTT
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
42 3 0.04
43 64 0.90
44 4 0.06
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (43 bp):
TATGTGTTTTCGTGTAAGACCACGTCTGGGACAGTGGCATCGC
Found at i:53574995 original size:14 final size:15
Alignment explanation
Indices: 53574971--53575005 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
53574961 TACTTTAATC
53574971 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
53574986 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
53575001 ATGGT
1 ATGGT
53575006 AATGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:53575326 original size:47 final size:47
Alignment explanation
Indices: 53575257--53575438 Score: 337
Period size: 47 Copynumber: 3.9 Consensus size: 47
53575247 GAGTAAATGA
*
53575257 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATTT
53575304 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATTT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATTT
53575351 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATTT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATTT
* *
53575398 ATGTATATGCTGTCAAATTTTGATGTATAAATGTAGTCCAA
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAA
53575439 ATTTTGGTGT
Statistics
Matches: 132, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 132 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (47 bp):
ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATTT
Found at i:53582631 original size:18 final size:19
Alignment explanation
Indices: 53582610--53582646 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
53582600 TTATATAAAT
*
53582610 ATATACACAACA-ATAATA
1 ATATACAAAACATATAATA
53582628 ATATACAAAACATATAATA
1 ATATACAAAACATATAATA
53582647 TAAGGTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (19 bp):
ATATACAAAACATATAATA
Found at i:53582881 original size:8 final size:8
Alignment explanation
Indices: 53582868--53582892 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53582858 AAAAACAGAG
53582868 TAAAATAT
1 TAAAATAT
53582876 TAAAATAT
1 TAAAATAT
53582884 TAAAATAT
1 TAAAATAT
53582892 T
1 T
53582893 TTTCAGACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAAAATAT
Found at i:53583106 original size:73 final size:73
Alignment explanation
Indices: 53582976--53583111 Score: 191
Period size: 73 Copynumber: 1.9 Consensus size: 73
53582966 TATTGACTTG
* * *
53582976 GGTCACACGACCAAGCCACAAGCCGGTGTGCTAGGCCGTGTAAGCATACTGACTTGCATTAATAA
1 GGTCACACGACCAAGCCACAAGCCCGTGTGCTAGGCCATGTAAGCATACTGACTTGCACTAATAA
53583041 GATGCAAT
66 GATGCAAT
* * * * **
53583049 GGTCACACGACCAAGCTACACGCCCGTGTGCTAGGCCATGTGAGCATTCTGTTTTGCACTAAT
1 GGTCACACGACCAAGCCACAAGCCCGTGTGCTAGGCCATGTAAGCATACTGACTTGCACTAAT
53583112 TAAAAGATAC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 54 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.23
Consensus pattern (73 bp):
GGTCACACGACCAAGCCACAAGCCCGTGTGCTAGGCCATGTAAGCATACTGACTTGCACTAATAA
GATGCAAT
Found at i:53584275 original size:25 final size:26
Alignment explanation
Indices: 53584214--53584337 Score: 87
Period size: 25 Copynumber: 4.9 Consensus size: 26
53584204 CATACGAGCC
* *
53584214 ATAAACGGGAAGCTCAAGAGAGCT-A
1 ATAATCGGGAAGCTCATGAGAGCTAA
* **
53584239 TTAATCAAGAAGCTCATGAGAGCTAA
1 ATAATCGGGAAGCTCATGAGAGCTAA
* *
53584265 ATAAT-GGGAAGCTCGTGAGAGATAA
1 ATAATCGGGAAGCTCATGAGAGCTAA
* * * *
53584290 GT-ATTGGGAACCTCACGAGAGAC-AA
1 ATAATCGGGAAGCTCATGAGAG-CTAA
* *
53584315 AT-ATCGGGACGCTCATAAGAGCT
1 ATAATCGGGAAGCTCATGAGAGCT
53584338 GTGGTGTGTC
Statistics
Matches: 74, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
24 3 0.04
25 66 0.89
26 5 0.07
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.19
Consensus pattern (26 bp):
ATAATCGGGAAGCTCATGAGAGCTAA
Found at i:53588632 original size:7 final size:7
Alignment explanation
Indices: 53588622--53588647 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53588612 TAAAATATTA
53588622 AATAATT
1 AATAATT
53588629 AATAATT
1 AATAATT
53588636 AATAATT
1 AATAATT
53588643 AATAA
1 AATAA
53588648 AAATATCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AATAATT
Found at i:53603050 original size:31 final size:30
Alignment explanation
Indices: 53603018--53603116 Score: 75
Period size: 31 Copynumber: 3.4 Consensus size: 30
53603008 NNNNNNNTTA
53603018 TTGTTATTATTATTACTATTATTAATTATT
1 TTGTTATTATTATTACTATTATTAATTATT
* *
53603048 ATTAGTT-TTATT-TTCCT-TT-TTATTTA-T
1 -TT-GTTATTATTATTACTATTATTAATTATT
* *
53603075 TTGTTACTATTATATTACTA-TATTAATTAGT
1 TTGTTATTA-T-TATTACTATTATTAATTATT
*
53603106 TTGATATTATT
1 TTGTTATTATT
53603117 TTCAGCTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
25 3 0.06
26 4 0.08
27 2 0.04
28 7 0.13
29 8 0.15
30 11 0.21
31 15 0.28
32 3 0.06
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (30 bp):
TTGTTATTATTATTACTATTATTAATTATT
Found at i:53604116 original size:111 final size:108
Alignment explanation
Indices: 53603987--53604191 Score: 286
Period size: 111 Copynumber: 1.9 Consensus size: 108
53603977 ATAATTTTAA
* *
53603987 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGTTGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTT-GGAAATTCGAG-AAACGTGCCCTAAGGTGCTGGATGTCGA-
* *
53604052 TTTTCTCG-TTCAACCAAATGGCTAAATATCCTTTTAAAAAAATTCG
63 -TTTCTCGTTTAAACCAAATGGCCAAATATCCTTTTAAAAAAATTCG
** * *
53604098 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGGACGTGTCCTAAGGTGCTGGATTTCGATTT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTGCTGGATGTCGATTT
*
53604163 CTCGTTTAAACCAAATTGCCAAATATCCT
66 CTCGTTTAAACCAAATGGCCAAATATCCT
53604192 CTTGAATTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
107 7 0.08
108 21 0.25
109 22 0.26
110 11 0.13
111 23 0.27
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (108 bp):
AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTGCTGGATGTCGATTT
CTCGTTTAAACCAAATGGCCAAATATCCTTTTAAAAAAATTCG
Found at i:53610164 original size:44 final size:43
Alignment explanation
Indices: 53609891--53610353 Score: 187
Period size: 44 Copynumber: 10.7 Consensus size: 43
53609881 AAGAATTGCA
*** *
53609891 GATCTTATCTCCCTGAGATTAACAACGGAGCAGATT-GAATATAG
1 GATCTTATCTCCCTGAGATT-ACAGTAGAGCAGATTAAAATA-AG
* * * * *
53609935 TAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAACCAAG
1 -GATCTTATCTCCCTGAGATTACAGTAGAGCAGATTAAAA-TAAG
* * *** *
53609980 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGA-TCGCATCAG
1 GATCTTATCTCCCTGAGA-TTACAGTAGAGCAGATTAAAATAAG
* * * * ** *
53610022 G-TCTTATTTCCCTGATATTACAGTGGAACAGACCGAAGAATTTCA-
1 GATCTTATCTCCCTGAGATTACAGTAGAGCAGA-TTAA-AA--TAAG
** **
53610067 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AG
1 GATCTTATCTCCCTGAGATTACAGTAGAGCAGATT-AAAATAAG
* * * *
53610110 TAATCCTATCTCCTTGAGATTACAGTAGAGCGGATTAAAATAAAG
1 -GATCTTATCTCCCTGAGATTACAGTAGAGCAGATTAAAAT-AAG
* * *** **
53610155 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGA-TCGTATCCG
1 GATCTTATCTCCCTGAGA-TTACAGTAGAGCAGATTAAAATAAG
* * **
53610197 G-TCTTATCTCCCTGAGATTATAGCAGAGCAGATTGAAGCT-AG
1 GATCTTATCTCCCTGAGATTACAGTAGAGCAGATT-AAAATAAG
* * * * *
53610239 TAATCCTATCTCCCTGAGATTACAATGGAGCGGATTAAAATAAAG
1 -GATCTTATCTCCCTGAGATTACAGTAGAGCAGATTAAAAT-AAG
* * * *** *
53610284 GATCTTATCTCTCTGA-AGTTACAGCAGAGTAGA-TCGCATCAG
1 GATCTTATCTCCCTGAGA-TTACAGTAGAGCAGATTAAAATAAG
* *
53610326 G-TCTTATGTCCCTGAGGTTACAGTAGAG
1 GATCTTATCTCCCTGAGATTACAGTAGAG
53610354 TAGACCGAAG
Statistics
Matches: 305, Mismatches: 88, Indels: 54
0.68 0.20 0.12
Matches are distributed among these distances:
41 71 0.23
42 13 0.04
43 19 0.06
44 142 0.47
45 27 0.09
46 33 0.11
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (43 bp):
GATCTTATCTCCCTGAGATTACAGTAGAGCAGATTAAAATAAG
Found at i:53610166 original size:175 final size:176
Alignment explanation
Indices: 53609874--53610216 Score: 571
Period size: 175 Copynumber: 2.0 Consensus size: 176
53609864 NNNNNNNNNN
*
53609874 CAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTAACAACGGAGCAGATTGAATATAGTAAT
1 CAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTAACAACGGAGCAGATTGAAGATAGTAAT
* *
53609939 CCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAACCAAGGATCTTATCTCTCTGAAGTTACAG
66 CCTATCTCCCTGAGATTACAGTAGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAG
* *
53610004 TAGAGTAGATCGCATCAGGTCTTATTTCCCTGATATTACAGTGGAA
131 TAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAA
* * *
53610050 CAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT-ACAGCGGAGCAGATTGAAGCTAGTAAT
1 CAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTAACAACGGAGCAGATTGAAGATAGTAAT
* *
53610114 CCTATCTCCTTGAGATTACAGTAGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAG
66 CCTATCTCCCTGAGATTACAGTAGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAG
* *
53610179 TAGAGTAGATCGTATCCGGTCTTATCTCCCTGAGATTA
131 TAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTA
53610217 TAGCAGAGCA
Statistics
Matches: 155, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
175 119 0.77
176 36 0.23
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (176 bp):
CAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTAACAACGGAGCAGATTGAAGATAGTAAT
CCTATCTCCCTGAGATTACAGTAGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAG
TAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAA
Found at i:53610226 original size:129 final size:129
Alignment explanation
Indices: 53610064--53610353 Score: 472
Period size: 129 Copynumber: 2.2 Consensus size: 129
53610054 CCGAAGAATT
* * *
53610064 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCTTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * *
53610129 TTACAGTAGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTA
66 TTACAATAGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCA
* *
53610193 TCCGGTCTTATCTCCCTGAGATTATAGCAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
*
53610258 TTACAATGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCA
66 TTACAATAGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCA
* * *
53610322 TCAGGTCTTATGTCCCTGAGGTTACAGTAGAG
1 TCAGGTCTTATCTCCCTGAGATTACAGCAGAG
53610354 TAGACCGAAG
Statistics
Matches: 147, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 147 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (129 bp):
TCAGGTCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAATAGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCA
Found at i:53610525 original size:44 final size:44
Alignment explanation
Indices: 53610463--53610673 Score: 264
Period size: 44 Copynumber: 4.8 Consensus size: 44
53610453 GCCACCAGTT
* *
53610463 CTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATC
1 CTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAGATC
*
53610507 CTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGT-GAATC
1 CTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAG-ATC
* * * ** * ***
53610551 TTATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCAG-TC
1 CTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAGATC
* *
53610594 CTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATC
1 CTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAGATC
*
53610638 CTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 CTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
53610674 ATCTCTCTGA
Statistics
Matches: 138, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
43 33 0.24
44 104 0.75
45 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (44 bp):
CTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAGATC
Found at i:53610596 original size:87 final size:87
Alignment explanation
Indices: 53610505--53610666 Score: 254
Period size: 87 Copynumber: 1.9 Consensus size: 87
53610495 AGATGGTAGA
* * *
53610505 TCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGT-GAATCTTATCTTCCTAAGCAGTA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAG-ATCCTATCTCCCTAAGCAGTA
53610569 GTGAAGCAGATTTAAGCCACCAG
65 GTGAAGCAGATTTAAGCCACCAG
* *
53610592 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAGATCCTATCTCCCTAAGCAGTAG
*
53610657 TGGAGCAGAT
66 TGAAGCAGAT
53610667 CGAAGACATC
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
87 67 0.99
88 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (87 bp):
TCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAGATCCTATCTCCCTAAGCAGTAG
TGAAGCAGATTTAAGCCACCAG
Found at i:53610605 original size:131 final size:131
Alignment explanation
Indices: 53610370--53610674 Score: 502
Period size: 131 Copynumber: 2.3 Consensus size: 131
53610360 GAAGAATTTC
* *** * *
53610370 AGATCTTATCTCCCTAAGCAGTAGTGGAGCCCCCTCAAAGAAACCGAATCTCATCTTCCTAAGCA
1 AGATCCTATCTCCCTAAGCAGTAGTGGAG-CAGATCGAAGACACCGAATCTCATCTTCCTAAGCA
*
53610435 GTAGTGAAGCAGATTTAAGCCACCAGTTCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATG
65 GTAGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATG
53610500 GT
130 GT
*** *
53610502 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCTAAGCAG
1 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACACCGAATCTCATCTTCCTAAGCAG
53610567 TAGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGG
66 TAGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGG
53610632 T
131 T
53610633 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACA
1 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACA
53610675 TCTCTCTGAA
Statistics
Matches: 161, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
131 133 0.83
132 28 0.17
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (131 bp):
AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACACCGAATCTCATCTTCCTAAGCAG
TAGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGG
T
Found at i:53611764 original size:13 final size:13
Alignment explanation
Indices: 53611746--53611782 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
53611736 AAGGTCACTC
*
53611746 TTTTTTATTTCGT
1 TTTTTTATTTCGA
53611759 TTTTTTATTT--A
1 TTTTTTATTTCGA
53611770 TTTTTTATTTCGA
1 TTTTTTATTTCGA
53611783 AATACAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 10 0.48
13 11 0.52
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (13 bp):
TTTTTTATTTCGA
Found at i:53612473 original size:3 final size:3
Alignment explanation
Indices: 53612467--53612506 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
53612457 TTATTTAACC
* *
53612467 TTA TTA TTG TTA TTA TTA TTA CTA TTA TTAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
53612507 GTTTTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:53612505 original size:31 final size:30
Alignment explanation
Indices: 53612467--53612571 Score: 78
Period size: 31 Copynumber: 3.5 Consensus size: 30
53612457 TTATTTAACC
53612467 TTATTATTGTTATTATTATTACTATTATTAA
1 TTATT-TTGTTATTATTATTACTATTATTAA
* *
53612498 TTATTATTAGTT-TTATT-TTCCT-TT-TTAT
1 TTATT-TT-GTTATTATTATTACTATTATTAA
*
53612526 TTA-TTTGTTACTATTATATTACTA-TATTAA
1 TTATTTTGTTATTA-T-TATTACTATTATTAA
* *
53612556 TTAGTTTGATATTATT
1 TTATTTTGTTATTATT
53612572 TTTCAGCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
25 3 0.05
26 4 0.07
27 2 0.03
28 7 0.12
29 8 0.14
30 11 0.19
31 21 0.36
32 3 0.05
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (30 bp):
TTATTTTGTTATTATTATTACTATTATTAA
Found at i:53620967 original size:132 final size:132
Alignment explanation
Indices: 53620730--53620975 Score: 404
Period size: 132 Copynumber: 1.9 Consensus size: 132
53620720 TCGAGCTGGA
*
53620730 AGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATATTTG
1 AGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATATTCG
* *
53620795 ATCTGCTCCACTACTGCTTAGGGAGATAAGACTTATAATCTTCAATCTATTCCAGTGTTGCCCAG
66 ATCTGCTCCACTACTGCTTAAGAAGATAAGACTTATAATCTTCAATCTATTCCAGTGTTGCCCAG
53620860 GG
131 GG
* * *
53620862 AGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTTAGGGAGGTAAAATCCTCCATCTTCG
1 AGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATATTCG
* *
53620927 ATCTGCTCCACTACTGCTTAAGAAGATAAGA-TCTGTAATCTTCGATCTA
66 ATCTGCTCCACTACTGCTTAAGAAGATAAGACT-TATAATCTTCAATCTA
53620976 CTTCACGCCA
Statistics
Matches: 105, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
131 1 0.01
132 104 0.99
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (132 bp):
AGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATATTCG
ATCTGCTCCACTACTGCTTAAGAAGATAAGACTTATAATCTTCAATCTATTCCAGTGTTGCCCAG
GG
Found at i:53621105 original size:89 final size:89
Alignment explanation
Indices: 53620948--53622002 Score: 1515
Period size: 89 Copynumber: 11.9 Consensus size: 89
53620938 TACTGCTTAA
* * * * *
53620948 GAAGATAAGATCTGTAATCTTCGATCTACTTCACGCCAGTATATGAAGACAAGATCTG-TTTTTC
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCT-
* *
53621012 TCGATCTACTTCGCCACCAGCATGG
65 TCGATCTGCTTCGCCACCAGTATGG
* * **
53621037 GAAGACAAGATCTGTTATATTTGATCTACTTCACGCCAGTACATGAAGACAATATCTATTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* * *
53621102 CGATCTACTCCACCACCAGTATGG
66 CGATCTGCTTCGCCACCAGTATGG
* * * *
53621126 GGAGACAAGATCTGTTGTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTTTC
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG--CTTT-
* * *
53621191 CTTCGATATACTTCGCCACTAGTATGG
63 CTTCGATCTGCTTCGCCACCAGTATGG
*
53621218 GAAGACAAGATCTGTTATCTTTAATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* * *
53621283 TGATCTGTTTCGCCACTAGTATGG
66 CGATCTGCTTCGCCACCAGTATGG
*
53621307 GAAGACAAGATCTGTTATCTTTAATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
53621372 CGATCTG-TT--CCACCAGTATGG
66 CGATCTGCTTCGCCACCAGTATGG
53621393 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* *
53621458 CGATCTGTTTCGCAACCAGTATGG
66 CGATCTGCTTCGCCACCAGTATGG
*
53621482 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* **
53621547 CGAGCTGCTTCGCCACCAACATGG
66 CGATCTGCTTCGCCACCAGTATGG
** * * * *
53621571 GAAGGTAAGATCTGGTATCTCTGATCTACTTCACACCAGTACATGAAAACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* * *
53621636 TGACCTGCTTTGCCACCAGTATGG
66 CGATCTGCTTCGCCACCAGTATGG
* * * *
53621660 GAAGGCAAGATCGGTTATCTTTGATCTACTTCACGCAAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
*
53621725 CGATCTGCTTCGCTACCAGTATGG
66 CGATCTGCTTCGCCACCAGTATGG
* * *
53621749 GAAGGCAAGATCTGTTATCTTTGACCTACTTCACGCTAGTACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
*
53621814 CGATCTGTTTCGCCACCAGTATGG
66 CGATCTGCTTCGCCACCAGTATGG
* *
53621838 GAAGACAAGATCTGTTATCTTTTACCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* * * *
53621903 TGACCTGTTTTGCCACCAGTATGG
66 CGATCTGCTTCGCCACCAGTATGG
* *
53621927 GAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
*
53621992 CGATCTACTTC
66 CGATCTGCTTC
53622003 ACGCCAATAC
Statistics
Matches: 874, Mismatches: 85, Indels: 14
0.90 0.09 0.01
Matches are distributed among these distances:
86 82 0.09
87 2 0.00
88 2 0.00
89 700 0.80
90 7 0.01
91 4 0.00
92 77 0.09
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (89 bp):
GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
CGATCTGCTTCGCCACCAGTATGG
Found at i:53623333 original size:20 final size:21
Alignment explanation
Indices: 53623310--53623357 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
53623300 TTAGCCTCTC
53623310 CATTTTT-ACTTTTCAT-TTTT
1 CATTTTTCA-TTTTCATCTTTT
53623330 CATTTTTCATTTTCATCTTTT
1 CATTTTTCATTTTCATCTTTT
53623351 CATTTTT
1 CATTTTT
53623358 TCACATCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (21 bp):
CATTTTTCATTTTCATCTTTT
Found at i:53623336 original size:14 final size:14
Alignment explanation
Indices: 53623310--53623357 Score: 64
Period size: 13 Copynumber: 3.5 Consensus size: 14
53623300 TTAGCCTCTC
*
53623310 CATTTTT-ACTTTT
1 CATTTTTCATTTTT
53623323 CATTTTTCATTTTT
1 CATTTTTCATTTTT
53623337 CA-TTTTCATCTTTT
1 CATTTTTCAT-TTTT
53623351 CATTTTT
1 CATTTTT
53623358 TCACATCACT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 14 0.45
14 13 0.42
15 4 0.13
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:53623360 original size:8 final size:7
Alignment explanation
Indices: 53623310--53623357 Score: 64
Period size: 7 Copynumber: 7.0 Consensus size: 7
53623300 TTAGCCTCTC
53623310 CATTTTT
1 CATTTTT
*
53623317 -ACTTTT
1 CATTTTT
53623323 CATTTTT
1 CATTTTT
53623330 CATTTTT
1 CATTTTT
53623337 CA-TTTT
1 CATTTTT
53623343 CATCTTTT
1 CAT-TTTT
53623351 CATTTTT
1 CATTTTT
53623358 TCACATCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
6 11 0.31
7 18 0.50
8 7 0.19
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:53634946 original size:13 final size:13
Alignment explanation
Indices: 53634928--53634953 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53634918 TGTTCAATTT
53634928 TTTACTAGAAAAC
1 TTTACTAGAAAAC
53634941 TTTACTAGAAAAC
1 TTTACTAGAAAAC
53634954 AAATCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:53637012 original size:3 final size:3
Alignment explanation
Indices: 53637004--53637042 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
53636994 ATAGAAAAAT
*
53637004 ATA ATA ATA GTA ATA ATAA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
53637043 GAAAATTGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53637048 original size:24 final size:24
Alignment explanation
Indices: 53636994--53637048 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
53636984 GTATATATAT
*
53636994 ATAG-AAA-AATATAATAATAGTA
1 ATAGAAAATAATATAATAATAATA
53637016 ATA-ATAAATAATATAATAATAATA
1 ATAGA-AAATAATATAATAATAATA
53637040 ATAGAAAAT
1 ATAGAAAAT
53637049 TGTGGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 3 0.11
23 3 0.11
24 21 0.75
25 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (24 bp):
ATAGAAAATAATATAATAATAATA
Found at i:53638369 original size:25 final size:23
Alignment explanation
Indices: 53638323--53638370 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
53638313 TGACCCCATA
53638323 ATCCTAATATATCTCTTTTATAT
1 ATCCTAATATATCTCTTTTATAT
* * *
53638346 ATCCTAATATCTATCTTTTGTAT
1 ATCCTAATATATCTCTTTTATAT
53638369 AT
1 AT
53638371 GCACGATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.52
Consensus pattern (23 bp):
ATCCTAATATATCTCTTTTATAT
Found at i:53641855 original size:6 final size:6
Alignment explanation
Indices: 53641844--53641894 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
53641834 ACAAACAGCA
53641844 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
53641892 TTT
1 TTT
53641895 AAAGCTTCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:53643448 original size:17 final size:16
Alignment explanation
Indices: 53643426--53643462 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
53643416 AAATACGCTC
53643426 TCTCTTTGCTCTTCTAT
1 TCTCTTTGCTCTT-TAT
*
53643443 TCTCTTTGTTCTTTAT
1 TCTCTTTGCTCTTTAT
53643459 TCTC
1 TCTC
53643463 CGTCTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.05, C:0.27, G:0.05, T:0.62
Consensus pattern (16 bp):
TCTCTTTGCTCTTTAT
Found at i:53649994 original size:23 final size:23
Alignment explanation
Indices: 53649963--53650013 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
53649953 ACCTACTTTC
* *
53649963 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
53649986 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
53650009 TTACA
1 TTACA
53650014 TGAACATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:53650575 original size:64 final size:64
Alignment explanation
Indices: 53650474--53650601 Score: 168
Period size: 64 Copynumber: 2.0 Consensus size: 64
53650464 TCCGGAGAGC
* * * * *
53650474 CATATAATAGGACGCTCACAAAGAGCTGTGGTATGTCCACT-ACACATGTAGGATCACTATCGAT
1 CATATAACAGGACGCTCACAAAGAGCTGCGATATGTCC-CTAACACATGCAGGATCACTACCGAT
* * *
53650538 CATATAACAGGATGCTCACAAAGAGCTGCGATATGTCCGTAACACATGCATGATCACTACCGAT
1 CATATAACAGGACGCTCACAAAGAGCTGCGATATGTCCCTAACACATGCAGGATCACTACCGAT
53650602 TGGAATGCTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 1 0.02
64 54 0.98
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (64 bp):
CATATAACAGGACGCTCACAAAGAGCTGCGATATGTCCCTAACACATGCAGGATCACTACCGAT
Found at i:53652681 original size:11 final size:12
Alignment explanation
Indices: 53652665--53652693 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
53652655 TTATATGTTC
53652665 TTGAATGAAA-G
1 TTGAATGAAATG
53652676 TTGAATGAAATG
1 TTGAATGAAATG
53652688 TTGAAT
1 TTGAAT
53652694 AATTAAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.34
Consensus pattern (12 bp):
TTGAATGAAATG
Found at i:53653132 original size:86 final size:84
Alignment explanation
Indices: 53653028--53653186 Score: 209
Period size: 86 Copynumber: 1.9 Consensus size: 84
53653018 ATATGTGTTA
* *
53653028 TCGTGTAAGACCACGTCTGGGAC-GTTGGCATCGAT-TTGAGATT-TATGTATAAGACCATGTCT
1 TCGTGTAAGACCACGTCTGGGACAG-TGGCATCGATATT--GATTACATG--TAAGACCACGTCT
53653090 GGGACATCGGCATCATATTTGATT
61 GGGACATCGGCATCATATTTGATT
53653114 TCGTGTAAGACC-CTGTCTGGGACAGTGGCATCGATATTGATTACATGTAAGACCACGTCTGGGA
1 TCGTGTAAGACCAC-GTCTGGGACAGTGGCATCGATATTGATTACATGTAAGACCACGTCTGGGA
*
53653178 CATTGGCAT
65 CATCGGCAT
53653187 TGTACGAGGT
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
84 24 0.36
85 5 0.08
86 34 0.52
87 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (84 bp):
TCGTGTAAGACCACGTCTGGGACAGTGGCATCGATATTGATTACATGTAAGACCACGTCTGGGAC
ATCGGCATCATATTTGATT
Found at i:53653134 original size:42 final size:43
Alignment explanation
Indices: 53653028--53653186 Score: 182
Period size: 42 Copynumber: 3.7 Consensus size: 43
53653018 ATATGTGTTA
* *
53653028 TCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATT
1 TCGTGTAAGACCACGTCTGGGACATTGGCATCGATATT-TGATT
* * * *
53653071 TATGTATAAGACCATGTCTGGGACATCGGCATC-ATATTTGATT
1 T-CGTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATT
*
53653114 TCGTGTAAGACC-CTGTCTGGGACAGTGGCATCGATA-TTGATT
1 TCGTGTAAGACCAC-GTCTGGGACATTGGCATCGATATTTGATT
* *
53653156 ACATGTAAGACCACGTCTGGGACATTGGCAT
1 TCGTGTAAGACCACGTCTGGGACATTGGCAT
53653187 TGTACGAGGT
Statistics
Matches: 97, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
42 57 0.59
43 12 0.12
44 28 0.29
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
TCGTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATT
Found at i:53653537 original size:17 final size:18
Alignment explanation
Indices: 53653493--53653537 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
53653483 TATGAAATTT
53653493 TGATATGAAATGTGAGTA
1 TGATATGAAATGTGAGTA
*
53653511 TGAT-TAAAATGATGA-TA
1 TGATATGAAATG-TGAGTA
53653528 T-ATATGAAAT
1 TGATATGAAAT
53653538 ATATGATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 2 0.09
17 14 0.61
18 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (18 bp):
TGATATGAAATGTGAGTA
Found at i:53657870 original size:93 final size:93
Alignment explanation
Indices: 53657757--53657942 Score: 327
Period size: 93 Copynumber: 2.0 Consensus size: 93
53657747 CACTCATGAC
*
53657757 TTTCAAAAGAAGGTATATATGCTTAGCAAATACATTAAAATGATAATTTGAAAAGCTAGTATTCA
1 TTTCAAAAGAAGGTATATATGCTTAGCAAATACAATAAAATGATAATTTGAAAAGCTAGTATTCA
*
53657822 ATATTCAATACATAGAATATTAGATATT
66 AGATTCAATACATAGAATATTAGATATT
* * *
53657850 TTTCAAAAGAAGGTATATATGCTTAGCAAATACAATCAAATGGTCATTTGAAAAGCTAGTATTCA
1 TTTCAAAAGAAGGTATATATGCTTAGCAAATACAATAAAATGATAATTTGAAAAGCTAGTATTCA
53657915 AGATTCAATACATAGAATATTAGATATT
66 AGATTCAATACATAGAATATTAGATATT
53657943 ATGTGATGTT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (93 bp):
TTTCAAAAGAAGGTATATATGCTTAGCAAATACAATAAAATGATAATTTGAAAAGCTAGTATTCA
AGATTCAATACATAGAATATTAGATATT
Found at i:53662724 original size:21 final size:22
Alignment explanation
Indices: 53662700--53662743 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
53662690 TGTTCGTGAT
* *
53662700 TTGACTCCACTTTTCAT-GGAC
1 TTGACCCCACTATTCATAGGAC
53662721 TTGACCCCACTATTCATAGGAC
1 TTGACCCCACTATTCATAGGAC
53662743 T
1 T
53662744 GACATTCTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.34
Consensus pattern (22 bp):
TTGACCCCACTATTCATAGGAC
Found at i:53683388 original size:3 final size:3
Alignment explanation
Indices: 53683380--53683411 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
53683370 AAATCAATGT
53683380 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
53683412 TAAATCGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:53687857 original size:28 final size:29
Alignment explanation
Indices: 53687825--53687898 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 29
53687815 ATTAAAAATA
*
53687825 AAAAAAATATAAAAATGGTAAAATTTTAT
1 AAAAAAATATAAAAATGCTAAAATTTTAT
*** *
53687854 AAAATTCTA-AAAAATTCTAAAATTTTAT
1 AAAAAAATATAAAAATGCTAAAATTTTAT
53687882 AAAGAAAATTATAAAAA
1 AAA-AAAA-TATAAAAA
53687899 ATATAAAGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
28 20 0.59
29 7 0.21
30 2 0.06
31 5 0.15
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAAAAATATAAAAATGCTAAAATTTTAT
Found at i:53687899 original size:10 final size:10
Alignment explanation
Indices: 53687844--53687916 Score: 51
Period size: 10 Copynumber: 7.2 Consensus size: 10
53687834 TAAAAATGGT
* *
53687844 AAAATTTTAT
1 AAAATTATAA
*
53687854 AAAATTCTAA
1 AAAATTATAA
*
53687864 AAAATTCTAA
1 AAAATTATAA
**
53687874 AATTTTATAAA
1 AAAATTAT-AA
53687885 GAAAATTATAA
1 -AAAATTATAA
53687896 AAAA-TATAA
1 AAAATTATAA
53687905 AGAAA-TATAA
1 A-AAATTATAA
53687915 AA
1 AA
53687917 TTCATAAAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
9 7 0.13
10 36 0.68
11 4 0.08
12 6 0.11
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (10 bp):
AAAATTATAA
Found at i:53687988 original size:18 final size:19
Alignment explanation
Indices: 53687945--53687989 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
53687935 TATAAAAAGA
53687945 ATCATTTTATAATTTTTCT
1 ATCATTTTATAATTTTTCT
* * *
53687964 ATAATTTT-TATTTTTTTT
1 ATCATTTTATAATTTTTCT
53687982 ATCATTTT
1 ATCATTTT
53687990 GCACCACATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (19 bp):
ATCATTTTATAATTTTTCT
Found at i:53688118 original size:10 final size:10
Alignment explanation
Indices: 53688104--53688223 Score: 88
Period size: 10 Copynumber: 12.4 Consensus size: 10
53688094 TTTTGATGCA
53688104 TTTTATAATT
1 TTTTATAATT
* *
53688114 ATTTATGATT
1 TTTTATAATT
**
53688124 TTTTATAAAA
1 TTTTATAATT
53688134 TTTTATAATT
1 TTTTATAATT
53688144 TTTTATAATT
1 TTTTATAATT
*
53688154 TTTTATAA-A
1 TTTTATAATT
*
53688163 CTTTATAATT
1 TTTTATAATT
* *
53688173 TTTCATAA-A
1 TTTTATAATT
*
53688182 TTTTATTATT
1 TTTTATAATT
* *
53688192 TCATTA-AA-A
1 T-TTTATAATT
*
53688201 TTTAATAA-T
1 TTTTATAATT
53688210 TTTTATAATT
1 TTTTATAATT
53688220 TTTT
1 TTTT
53688224 TGCTACATGT
Statistics
Matches: 81, Mismatches: 24, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
8 2 0.02
9 23 0.28
10 53 0.65
11 3 0.04
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (10 bp):
TTTTATAATT
Found at i:53688137 original size:30 final size:29
Alignment explanation
Indices: 53688103--53688190 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 29
53688093 TTTTTGATGC
*
53688103 ATTTTATAATTATTTATGATTTTTTATAAA
1 ATTTTATAATTATTTATAATTTTTTAT-AA
*
53688133 ATTTTATAATTTTTTATAATTTTTTATAA
1 ATTTTATAATTATTTATAATTTTTTATAA
*
53688162 ACTTTATAATT-TTTCATAAATTTTATTAT
1 ATTTTATAATTATTT-AT-AATTTT-TTAT
53688191 TTCATTAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
28 3 0.06
29 14 0.27
30 31 0.60
31 4 0.08
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (29 bp):
ATTTTATAATTATTTATAATTTTTTATAA
Found at i:53688156 original size:19 final size:19
Alignment explanation
Indices: 53688103--53688221 Score: 91
Period size: 19 Copynumber: 6.3 Consensus size: 19
53688093 TTTTTGATGC
* *
53688103 ATTTTATAATTATTTATGAT
1 ATTTTATAATTTTTTAT-AA
* **
53688123 TTTTTATAAAATTTTATAA
1 ATTTTATAATTTTTTATAA
*
53688142 TTTTTTATAATTTTTTATAA
1 -ATTTTATAATTTTTTATAA
* *
53688162 ACTTTATAATTTTTCATAA
1 ATTTTATAATTTTTTATAA
* *
53688181 ATTTTATTATTTCATTA-AA
1 ATTTTATAATTT-TTTATAA
*
53688200 ATTTAATAA-TTTTTAT-A
1 ATTTTATAATTTTTTATAA
53688217 ATTTT
1 ATTTT
53688222 TTTGCTACAT
Statistics
Matches: 78, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
17 8 0.10
18 2 0.03
19 36 0.46
20 32 0.41
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.61
Consensus pattern (19 bp):
ATTTTATAATTTTTTATAA
Found at i:53688576 original size:88 final size:90
Alignment explanation
Indices: 53688403--53688595 Score: 223
Period size: 88 Copynumber: 2.1 Consensus size: 90
53688393 GTTTTTTTTT
53688403 AAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGGAAAAAAAACA
1 AAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGGAAAAAAAACA
* *** **
53688468 AGGGTTTTA-TTTTTTATTTTT-AA
66 AGAGTAAGACTTAATTATTTTTGAA
* * * *
53688491 AAAGTTTGAGGG-CTTTTTTGATGCATTTTGAAAGTTTAAGTATCTAATTGAGT-GCAAAAAAAG
1 AAAGTTTGAGGGTC-TTTTTGATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGGAAAAAAAAC
*
53688554 AAGAAGTAAGAGCTTAATTTTTTTTTGAA
65 AAG-AGTAAGA-CTTAA-TTATTTTTGAA
53688583 AAAGTTTGAGGGT
1 AAAGTTTGAGGGT
53688596 GTCACATCCC
Statistics
Matches: 87, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
87 12 0.14
88 52 0.60
90 2 0.02
91 7 0.08
92 14 0.16
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (90 bp):
AAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGGAAAAAAAACA
AGAGTAAGACTTAATTATTTTTGAA
Found at i:53688871 original size:20 final size:21
Alignment explanation
Indices: 53688832--53688871 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53688822 AGTTTTAAAA
53688832 TCACCCTATATTTTCTGCCTT
1 TCACCCTATATTTTCTGCCTT
*
53688853 TCACCCTATTTTTTC-GCCT
1 TCACCCTATATTTTCTGCCT
53688872 GAATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.12, C:0.35, G:0.05, T:0.47
Consensus pattern (21 bp):
TCACCCTATATTTTCTGCCTT
Found at i:53698910 original size:27 final size:28
Alignment explanation
Indices: 53698880--53698938 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
53698870 ACACACCCGG
**
53698880 AATAATAT-AAATCCTCCTTAACACACC
1 AATAATATCAAATCCTCCCAAACACACC
*
53698907 AAT-ATATCATATCCTCCCAAACACACC
1 AATAATATCAAATCCTCCCAAACACACC
53698934 AATAA
1 AATAA
53698939 GGCATTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 4 0.15
27 22 0.81
28 1 0.04
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.24
Consensus pattern (28 bp):
AATAATATCAAATCCTCCCAAACACACC
Found at i:53699510 original size:22 final size:24
Alignment explanation
Indices: 53699469--53699512 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
53699459 TAACTAAGCT
*
53699469 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTATAACTTAATTCA
53699493 TACTTA-TTTTAT-ACTTAATT
1 TACTTACTTTTATAACTTAATT
53699513 TCTTGCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 5 0.26
24 6 0.32
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTATAACTTAATTCA
Found at i:53700113 original size:10 final size:10
Alignment explanation
Indices: 53700098--53700130 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
53700088 TTAGTTTATT
53700098 TAATATATAA
1 TAATATATAA
53700108 TAATATA-ATA
1 TAATATATA-A
53700118 TAATATATAA
1 TAATATATAA
53700128 TAA
1 TAA
53700131 AACAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.05
10 19 0.90
11 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TAATATATAA
Found at i:53700123 original size:20 final size:20
Alignment explanation
Indices: 53700098--53700143 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
53700088 TTAGTTTATT
* *
53700098 TAATATATAATAATATAATA
1 TAATATATAATAAAACAATA
53700118 TAATATATAATAAAACAATA
1 TAATATATAATAAAACAATA
53700138 T-ATATA
1 TAATATA
53700144 AAACATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TAATATATAATAAAACAATA
Found at i:53703059 original size:5 final size:5
Alignment explanation
Indices: 53703049--53703233 Score: 334
Period size: 5 Copynumber: 37.0 Consensus size: 5
53703039 TCCTTCATCA
53703049 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
* * * *
53703099 CATAT CATAT CATAT CATGT CATGT CATGT CATGT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
53703149 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
53703199 CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT
53703234 TAGAAGCAGA
Statistics
Matches: 178, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 178 1.00
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40
Consensus pattern (5 bp):
CATAT
Found at i:53712452 original size:2 final size:2
Alignment explanation
Indices: 53712445--53712471 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53712435 TTAAGAAATG
53712445 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
53712472 GATGAGATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53714023 original size:27 final size:28
Alignment explanation
Indices: 53713984--53714040 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
53713974 ATATCATTTG
* *
53713984 ACAAGTTTAAGTACT-AAATTAGATAAAA
1 ACAAGTTTAAGTA-TGAAATAAGAAAAAA
53714012 ACAAG-TTAAGTATGAAATAAGAAAAAA
1 ACAAGTTTAAGTATGAAATAAGAAAAAA
53714039 AC
1 AC
53714041 TAAATTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 1 0.04
27 20 0.77
28 5 0.19
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.23
Consensus pattern (28 bp):
ACAAGTTTAAGTATGAAATAAGAAAAAA
Found at i:53715066 original size:44 final size:44
Alignment explanation
Indices: 53715016--53715109 Score: 179
Period size: 44 Copynumber: 2.1 Consensus size: 44
53715006 TAAATGATGC
*
53715016 ACTAAATAGCATTGTTGTTAGGAGGTACTATTACATAGATGACA
1 ACTAAATAGCATTGTTGTAAGGAGGTACTATTACATAGATGACA
53715060 ACTAAATAGCATTGTTGTAAGGAGGTACTATTACATAGATGACA
1 ACTAAATAGCATTGTTGTAAGGAGGTACTATTACATAGATGACA
53715104 ACTAAA
1 ACTAAA
53715110 ACGTTGGCTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (44 bp):
ACTAAATAGCATTGTTGTAAGGAGGTACTATTACATAGATGACA
Found at i:53732104 original size:27 final size:27
Alignment explanation
Indices: 53732063--53732180 Score: 141
Period size: 27 Copynumber: 4.4 Consensus size: 27
53732053 AACACGCTAG
53732063 GAAAGGAATGCCTTTGTGGCAATATAT
1 GAAAGGAATGCCTTTGTGGCAATATAT
* *
53732090 GAAAGGAATGACTTTGTGACAATATAT
1 GAAAGGAATGCCTTTGTGGCAATATAT
* *
53732117 GGAAGGAATGTCTTTGTGGCAATATAT
1 GAAAGGAATGCCTTTGTGGCAATATAT
* * * *
53732144 G-AATGAATGCCTTCGTGGCAGA-CTCT
1 GAAAGGAATGCCTTTGTGGCA-ATATAT
53732170 GAAAGGAATGC
1 GAAAGGAATGC
53732181 ATTAACAGTG
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
26 19 0.24
27 59 0.76
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (27 bp):
GAAAGGAATGCCTTTGTGGCAATATAT
Found at i:53734541 original size:14 final size:14
Alignment explanation
Indices: 53734522--53734549 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53734512 CGCATACATA
53734522 TCAAAATATCAATC
1 TCAAAATATCAATC
53734536 TCAAAATATCAATC
1 TCAAAATATCAATC
53734550 ATCATATTAA
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:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
TCAAAATATCAATC
Found at i:53734808 original size:47 final size:48
Alignment explanation
Indices: 53734689--53734833 Score: 166
Period size: 47 Copynumber: 2.9 Consensus size: 48
53734679 CTCGTCCATT
* *
53734689 TGAAACACAATTTGTGGACAAACCACCACTGATTTGCAGATAAACTGCAAC
1 TGAAACAC--TTTGTGGACAAGCCACCAC-GATATGCAGATAAACTGCAAC
* * *
53734740 TGATAACACTTTGTGGACAAGCCACCAC-ATATGTAGATATACTGCCAC
1 TGA-AACACTTTGTGGACAAGCCACCACGATATGCAGATAAACTGCAAC
* **
53734788 TGAAACACTTTGTGGACAAGCCACCACTGATTTATAGATAAACTGC
1 TGAAACACTTTGTGGACAAGCCACCAC-GATATGCAGATAAACTGC
53734834 CACATACTTC
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
47 24 0.29
48 19 0.23
49 14 0.17
50 18 0.22
51 3 0.04
52 5 0.06
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (48 bp):
TGAAACACTTTGTGGACAAGCCACCACGATATGCAGATAAACTGCAAC
Found at i:53736822 original size:32 final size:32
Alignment explanation
Indices: 53736786--53736849 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
53736776 GTTACAACAA
53736786 AGTAAGTACTCCGAGGATCGTACCTAAGGGAT
1 AGTAAGTACTCCGAGGATCGTACCTAAGGGAT
*
53736818 AGTAAGTACTCTGAGGATCGTACCTAAGGGAT
1 AGTAAGTACTCCGAGGATCGTACCTAAGGGAT
53736850 TGCAATTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.23
Consensus pattern (32 bp):
AGTAAGTACTCCGAGGATCGTACCTAAGGGAT
Found at i:53744379 original size:50 final size:50
Alignment explanation
Indices: 53744262--53744491 Score: 205
Period size: 50 Copynumber: 4.5 Consensus size: 50
53744252 CATGCCAAAC
* ** * * * *
53744262 CCATGTCCCAGACATGGTCTTACATGAGATGTTTCTTGTAC--TACCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGTGCCAATG
* * * ** *
53744311 CCATTTCCTAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATG
* **
53744361 CCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCGGTGCCAACA
1 CCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATATCGGTGCCAATG
* *
53744411 CCATGTCCCAGACATGGTCTTACATAGGACCTCTCATAATCTCAATGATGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTGCCAATG
53744467 CCATGTCCCAGACATGGTCTTACAT
1 CCATGTCCCAGACATGGTCTTACAT
53744492 ATGATCTCTT
Statistics
Matches: 146, Mismatches: 25, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
48 1 0.01
49 31 0.21
50 79 0.54
51 1 0.01
53 2 0.01
56 32 0.22
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATG
Found at i:53754065 original size:33 final size:33
Alignment explanation
Indices: 53754027--53754116 Score: 119
Period size: 33 Copynumber: 2.7 Consensus size: 33
53754017 CTGGTGGGAT
* * *
53754027 AGTAAACATAAAATAGAGATAGTCCGCT-GAGAC
1 AGTAAACATAGAACAAAGATAGTCCGCTAG-GAC
* *
53754060 GGTAAACACAGAACAAAGATAGTCCGCTAGGAC
1 AGTAAACATAGAACAAAGATAGTCCGCTAGGAC
53754093 AGTAAACATAGAACAAAGATAGTC
1 AGTAAACATAGAACAAAGATAGTC
53754117 TATCAGGACA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
33 48 0.98
34 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.16
Consensus pattern (33 bp):
AGTAAACATAGAACAAAGATAGTCCGCTAGGAC
Found at i:53756112 original size:17 final size:15
Alignment explanation
Indices: 53756082--53756115 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
53756072 CTCCCAGACT
53756082 TAATAAAATAATAAA
1 TAATAAAATAATAAA
53756097 TAATAAAACTTAATAAA
1 TAATAAAA--TAATAAA
53756114 TA
1 TA
53756116 CAATATTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
TAATAAAATAATAAA
Found at i:53756467 original size:23 final size:23
Alignment explanation
Indices: 53756440--53756486 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
53756430 AATTTCGTCA
* *
53756440 TATTAGTTTATTATTATTATTAT
1 TATTAGTTTATCATAATTATTAT
* *
53756463 TATTATTTTCTCATAATTATTAT
1 TATTAGTTTATCATAATTATTAT
53756486 T
1 T
53756487 CGATTTTAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (23 bp):
TATTAGTTTATCATAATTATTAT
Found at i:53758349 original size:27 final size:27
Alignment explanation
Indices: 53758311--53758363 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
53758301 ATTGAATGTA
53758311 GAGGGGTTGCTAAGTGCTGATTCCCCC
1 GAGGGGTTGCTAAGTGCTGATTCCCCC
53758338 GAGGGGTTGCTAAGTGCTGATTCCCC
1 GAGGGGTTGCTAAGTGCTGATTCCCC
53758364 TATTCATCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.15, C:0.25, G:0.34, T:0.26
Consensus pattern (27 bp):
GAGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:53758384 original size:33 final size:33
Alignment explanation
Indices: 53758315--53758565 Score: 139
Period size: 33 Copynumber: 7.4 Consensus size: 33
53758305 AATGTAGAGG
*
53758315 GGTTGCTAAGTGCTGATTCCCC----C-GAGG-
1 GGTTGCTAAGTGCTGATTCCCCTATTCATAGGT
*
53758342 GGTTGCTAAGTGCTGATTCCCCTATTCATCGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCATAGGT
* * *
53758375 GGTTGCTAAGTGCTGATCCCACCATATTTTAAATGTGAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CC-TA--TT-CA--T---AGGT
*
53758418 GGTTGCTAAGTGCTGATTCCCC----C-GAGG-
1 GGTTGCTAAGTGCTGATTCCCCTATTCATAGGT
*
53758445 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCATAGGT
* * *
53758478 GGTTGCTAAGTGCTGATTCCACCACATCTGAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CC-TAT-T--CA--T--AGGT
* *
53758520 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCATAGGT
53758553 GGTTGCTAAGTGC
1 GGTTGCTAAGTGC
53758566 GAAATCCACC
Statistics
Matches: 174, Mismatches: 19, Indels: 56
0.70 0.08 0.22
Matches are distributed among these distances:
27 44 0.25
28 3 0.02
31 2 0.01
32 4 0.02
33 54 0.31
34 4 0.02
35 5 0.03
36 1 0.01
37 3 0.02
38 2 0.01
39 1 0.01
40 4 0.02
41 2 0.01
42 24 0.14
43 21 0.12
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.31
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCTATTCATAGGT
Found at i:53758450 original size:103 final size:102
Alignment explanation
Indices: 53758313--53758541 Score: 404
Period size: 103 Copynumber: 2.2 Consensus size: 102
53758303 TGAATGTAGA
53758313 GGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGT
1 GGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGT
* * *
53758378 TGCTAAGTGCTGATCCCACCATATTTTAAATGTGAAAG
66 TGCTAAGTGCTGATCCCACCACATCTGAAATGTG-AAG
*
53758416 GGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGT
1 GGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGT
*
53758481 TGCTAAGTGCTGATTCCACCACATCTGAAATGTGAAG
66 TGCTAAGTGCTGATCCCACCACATCTGAAATGTGAAG
53758518 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
53758542 GATTCATTGG
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
102 27 0.22
103 94 0.78
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (102 bp):
GGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGT
TGCTAAGTGCTGATCCCACCACATCTGAAATGTGAAG
Found at i:53765923 original size:70 final size:72
Alignment explanation
Indices: 53765784--53765952 Score: 236
Period size: 70 Copynumber: 2.3 Consensus size: 72
53765774 TGAATATAGA
* * *
53765784 GGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGCTAAGTGCTGATCCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCCC--TTCA-CGGTGGCTGCTAAGTGCTGATCCCACCGTATCTG
53765849 AAATGTGAAAG
63 AAATGTG-AAG
* *
53765860 GGGGTTGCTAAGTGCTGATTCCCC-TGA-GG-GGCTGCTAAGTGCTGATTCCACCGTATCTGAAA
1 GGGGTTGCTAAGTGCTGATTCCCCTTCACGGTGGCTGCTAAGTGCTGATCCCACCGTATCTGAAA
53765922 TGTGAAG
66 TGTGAAG
53765929 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
53765953 CAAGGGGTTG
Statistics
Matches: 88, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
69 27 0.31
70 33 0.38
71 2 0.02
73 2 0.02
76 24 0.27
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (72 bp):
GGGGTTGCTAAGTGCTGATTCCCCTTCACGGTGGCTGCTAAGTGCTGATCCCACCGTATCTGAAA
TGTGAAG
Found at i:53765972 original size:69 final size:70
Alignment explanation
Indices: 53765784--53765964 Score: 238
Period size: 69 Copynumber: 2.5 Consensus size: 70
53765774 TGAATATAGA
* * *
53765784 GGGGTTGCTAAGTGCTGATTCCCCTATTCATCGGTGGTTGCTAAGTGCTGATCCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCCC----CA-AGG-GGTTGCTAAGTGCTGATCCCACCGTATCTG
53765849 AAATGTGAAAG
60 AAATGTGAAAG
** * *
53765860 GGGGTTGCTAAGTGCTGATTCCCCTGAGGGGCTGCTAAGTGCTGATTCCACCGTATCTGAAATGT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATCCCACCGTATCTGAAATGT
53765925 G-AAG
66 GAAAG
53765929 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCT
53765965 GTGTGCTGGT
Statistics
Matches: 95, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
69 36 0.38
70 33 0.35
71 2 0.02
76 24 0.25
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.30
Consensus pattern (70 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATCCCACCGTATCTGAAATGT
GAAAG
Done.