Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 166 of 325
Found at i:52474979 original size:38 final size:39
Alignment explanation
Indices: 52474907--52475020 Score: 128
Period size: 38 Copynumber: 3.0 Consensus size: 39
52474897 TAATTTAGTT
*
52474907 TGAGTCTTTAATTATGTCATAA-CTTG-ACAACATTAATA
1 TGAGTCTTTAATTATGTCATAATC-TGAACATCATTAATA
*
52474945 TGAGT-TTTAATTATGTCATAATCTGAACATCATT-ATT
1 TGAGTCTTTAATTATGTCATAATCTGAACATCATTAATA
* * * * *
52474982 TGTGTCTTTAATTATGTCCTAGTGTGAACATCTTTAATA
1 TGAGTCTTTAATTATGTCATAATCTGAACATCATTAATA
52475021 CATGTTTTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
37 24 0.38
38 38 0.59
39 2 0.03
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (39 bp):
TGAGTCTTTAATTATGTCATAATCTGAACATCATTAATA
Found at i:52489063 original size:512 final size:512
Alignment explanation
Indices: 52488099--52489123 Score: 2014
Period size: 512 Copynumber: 2.0 Consensus size: 512
52488089 GCCATCCTAT
52488099 TCTAGACCAACTACGAGTAGCCGTGTTAGTGAGGTTAGACAAGCCTTCTATCAAATGATGAACGA
1 TCTAGACCAACTACGAGTAGCCGTGTTAGTGAGGTTAGACAAGCCTTCTATCAAATGATGAACGA
52488164 TTGGTTTAGCCAATATATTAAAACCAATCTGGCTGTACAACAACCTCCACCCCTGGTTAATCCTC
66 TTGGTTTAGCCAATATATTAAAACCAATCTGGCTGTACAACAACCTCCACCCCTGGTTAATCCTC
52488229 CACAAGCTCCTACTATGCCATCATTGAATCTGGTTCAATTAAGCAAGCCTCCGGTAGATAAGATT
131 CACAAGCTCCTACTATGCCATCATTGAATCTGGTTCAATTAAGCAAGCCTCCGGTAGATAAGATT
52488294 AGAAAATATGGGGCTGAAGAGTTTCAAGCTACAAAGAATGATGATGCTGAAAGGGACGAGTTCTG
196 AGAAAATATGGGGCTGAAGAGTTTCAAGCTACAAAGAATGATGATGCTGAAAGGGACGAGTTCTG
52488359 GTTAGAGAACACAATACGAGTATTTGATGAATTATCATTGAATCCAGAGGAATGCATAAAATGTG
261 GTTAGAGAACACAATACGAGTATTTGATGAATTATCATTGAATCCAGAGGAATGCATAAAATGTG
*
52488424 TTGTTTCATTCTTGAGAGATACAGCGTATCACTGGTGGAAAACTTTAATATCGGTAGTTCCGGGT
326 TTGTTTCACTCTTGAGAGATACAGCGTATCACTGGTGGAAAACTTTAATATCGGTAGTTCCGGGT
52488489 GAGCGAGTTCCTGGGATTTCTTTCAAGTTGAATTCCGGAAGAAATACATCAGTCAGAGATTTATC
391 GAGCGAGTTCCTGGGATTTCTTTCAAGTTGAATTCCGGAAGAAATACATCAGTCAGAGATTTATC
*
52488554 GACCAAAAATGTAAAGAGTTTCTCGAGCTTAAAAAAGGTTGTATGTCTGTTACAAAA
456 AACCAAAAATGTAAAGAGTTTCTCGAGCTTAAAAAAGGTTGTATGTCTGTTACAAAA
52488611 TCTAGACCAACTACGAGTAGCCGTGTTAGTGAGGTTAGACAAGCCTTCTATCAAATGATGAACGA
1 TCTAGACCAACTACGAGTAGCCGTGTTAGTGAGGTTAGACAAGCCTTCTATCAAATGATGAACGA
52488676 TTGGTTTAGCCAATATATTAAAACCAATCTGGCTGTACAACAACCTCCACCCCTGGTTAATCCTC
66 TTGGTTTAGCCAATATATTAAAACCAATCTGGCTGTACAACAACCTCCACCCCTGGTTAATCCTC
52488741 CACAAGCTCCTACTATGCCATCATTGAATCTGGTTCAATTAAGCAAGCCTCCGGTAGATAAGATT
131 CACAAGCTCCTACTATGCCATCATTGAATCTGGTTCAATTAAGCAAGCCTCCGGTAGATAAGATT
52488806 AGAAAATATGGGGCTGAAGAGTTTCAAGCTACAAAGAATGATGATGCTGAAAGGGACGAGTTCTG
196 AGAAAATATGGGGCTGAAGAGTTTCAAGCTACAAAGAATGATGATGCTGAAAGGGACGAGTTCTG
52488871 GTTAGAGAACACAATACGAGTATTTGATGAATTATCATTGAATCCAGAGGAATGCATAAAATGTG
261 GTTAGAGAACACAATACGAGTATTTGATGAATTATCATTGAATCCAGAGGAATGCATAAAATGTG
*
52488936 TTGTTTCACTCTTGAGAGATACAGCGTATCACTGGTGGAAAACTTTAATATCGGTAGTTTCGGGT
326 TTGTTTCACTCTTGAGAGATACAGCGTATCACTGGTGGAAAACTTTAATATCGGTAGTTCCGGGT
*
52489001 GAGCGAGTTCCTGGGATTTCTTTCAAGTTGAATTTCGGAAGAAATACATCAGTCAGAGATTTATC
391 GAGCGAGTTCCTGGGATTTCTTTCAAGTTGAATTCCGGAAGAAATACATCAGTCAGAGATTTATC
52489066 AACCAAAAATGTAAAGAGTTTCTCGAGCTTAAAAAAGGTTGTATGTCTGTTACAAAA
456 AACCAAAAATGTAAAGAGTTTCTCGAGCTTAAAAAAGGTTGTATGTCTGTTACAAAA
52489123 T
1 T
52489124 ACGAGCAGGA
Statistics
Matches: 509, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
512 509 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (512 bp):
TCTAGACCAACTACGAGTAGCCGTGTTAGTGAGGTTAGACAAGCCTTCTATCAAATGATGAACGA
TTGGTTTAGCCAATATATTAAAACCAATCTGGCTGTACAACAACCTCCACCCCTGGTTAATCCTC
CACAAGCTCCTACTATGCCATCATTGAATCTGGTTCAATTAAGCAAGCCTCCGGTAGATAAGATT
AGAAAATATGGGGCTGAAGAGTTTCAAGCTACAAAGAATGATGATGCTGAAAGGGACGAGTTCTG
GTTAGAGAACACAATACGAGTATTTGATGAATTATCATTGAATCCAGAGGAATGCATAAAATGTG
TTGTTTCACTCTTGAGAGATACAGCGTATCACTGGTGGAAAACTTTAATATCGGTAGTTCCGGGT
GAGCGAGTTCCTGGGATTTCTTTCAAGTTGAATTCCGGAAGAAATACATCAGTCAGAGATTTATC
AACCAAAAATGTAAAGAGTTTCTCGAGCTTAAAAAAGGTTGTATGTCTGTTACAAAA
Found at i:52490479 original size:32 final size:32
Alignment explanation
Indices: 52490438--52490501 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
52490428 TCGTATAGAA
52490438 TGGCTCCGACTAAATTAAAATAATTAAGCAAG
1 TGGCTCCGACTAAATTAAAATAATTAAGCAAG
52490470 TGGCTCCGACTAAATTAAAATAATTAAGCAAG
1 TGGCTCCGACTAAATTAAAATAATTAAGCAAG
52490502 AGTTAATCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.25
Consensus pattern (32 bp):
TGGCTCCGACTAAATTAAAATAATTAAGCAAG
Found at i:52494385 original size:40 final size:40
Alignment explanation
Indices: 52494330--52494421 Score: 157
Period size: 40 Copynumber: 2.3 Consensus size: 40
52494320 ACTGCATTTG
*
52494330 GCACTAAGTCTGCGATTCAAAATAGCTTCAGCTATAAATA
1 GCACTAAGTGTGCGATTCAAAATAGCTTCAGCTATAAATA
* *
52494370 GCACTAAGTGTGCGATTCAAAATAGTTTCGGCTATAAATA
1 GCACTAAGTGTGCGATTCAAAATAGCTTCAGCTATAAATA
52494410 GCACTAAGTGTG
1 GCACTAAGTGTG
52494422 TGAAATGCTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (40 bp):
GCACTAAGTGTGCGATTCAAAATAGCTTCAGCTATAAATA
Found at i:52494444 original size:40 final size:39
Alignment explanation
Indices: 52494330--52494465 Score: 134
Period size: 40 Copynumber: 3.4 Consensus size: 39
52494320 ACTGCATTTG
* *
52494330 GCACTAAGTCTGCGATTCAAAATAGCTTCAGCTATAAATA
1 GCACTAAGTGTGCGATGC-AAATAGCTTCAGCTATAAATA
* * *
52494370 GCACTAAGTGTGCGATTCAAAATAGTTTCGGCTATAAATA
1 GCACTAAGTGTGCGATGC-AAATAGCTTCAGCTATAAATA
* *
52494410 GCACTAAGTGTGTGAAATGC-TATAGCTTCAGCTAT--ATGA
1 GCACTAAGTGTGCG--ATGCAAATAGCTTCAGCTATAAAT-A
52494449 GGCACTAAGTGTGCGAT
1 -GCACTAAGTGTGCGAT
52494466 ACCGAGATAC
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
38 4 0.05
39 1 0.01
40 75 0.90
42 3 0.04
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (39 bp):
GCACTAAGTGTGCGATGCAAATAGCTTCAGCTATAAATA
Found at i:52498006 original size:64 final size:64
Alignment explanation
Indices: 52497905--52498031 Score: 218
Period size: 64 Copynumber: 2.0 Consensus size: 64
52497895 TGAAAGACTA
* * *
52497905 TAAAACATAGAAAATTAAATCAAGTAAACTATAAAGCCTAGTAAGTTCGTATGAAATTTACTCT
1 TAAAACATAGAAAAATAAACCAAGTAAACTATAAAGCCTAGTAAGTTCGTATGAAATATACTCT
*
52497969 TAAAACATAGAAAAATAAACCAAGTAAACTATAAAGCCTAGTTAGTTCGTATGAAATATACTC
1 TAAAACATAGAAAAATAAACCAAGTAAACTATAAAGCCTAGTAAGTTCGTATGAAATATACTC
52498032 AACAAATCAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (64 bp):
TAAAACATAGAAAAATAAACCAAGTAAACTATAAAGCCTAGTAAGTTCGTATGAAATATACTCT
Found at i:52498310 original size:13 final size:13
Alignment explanation
Indices: 52498292--52498321 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
52498282 TGCTTTGATT
52498292 TTGTCATTTTACC
1 TTGTCATTTTACC
52498305 TTGTCATTTTACC
1 TTGTCATTTTACC
52498318 TTGT
1 TTGT
52498322 TTATTATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.20, G:0.10, T:0.57
Consensus pattern (13 bp):
TTGTCATTTTACC
Found at i:52503334 original size:52 final size:51
Alignment explanation
Indices: 52503255--52503377 Score: 185
Period size: 52 Copynumber: 2.4 Consensus size: 51
52503245 GAGGAAGTGC
* *
52503255 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATACCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
* *
52503307 AAAAAGGCTTATACCCTAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATACCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
*
52503358 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATACCCCAGTT
52503378 ATTAACAGAG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
50 8 0.12
51 23 0.36
52 33 0.52
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTATACCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:52503352 original size:25 final size:26
Alignment explanation
Indices: 52503255--52503377 Score: 160
Period size: 26 Copynumber: 4.8 Consensus size: 26
52503245 GAGGAAGTGC
**
52503255 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
52503281 AAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* * * **
52503307 AAAAAGGCTTATACCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
52503333 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
52503358 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
52503378 ATTAACAGAG
Statistics
Matches: 85, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
25 31 0.36
26 54 0.64
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:52508177 original size:40 final size:41
Alignment explanation
Indices: 52508110--52508187 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 41
52508100 ACACATAGCT
* *
52508110 GAAGCTATCTCGATCTCGCACATTAAGTGCCATATATAGTC
1 GAAGCTATCTCGATATCGCACACTAAGTGCCATATATAGTC
*
52508151 GAAGCTATCTTGA-ATCGCACACTAAGTGCCATATATA
1 GAAGCTATCTCGATATCGCACACTAAGTGCCATATATA
52508188 TATATTTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 22 0.65
41 12 0.35
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (41 bp):
GAAGCTATCTCGATATCGCACACTAAGTGCCATATATAGTC
Found at i:52508446 original size:42 final size:42
Alignment explanation
Indices: 52508400--52508482 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
52508390 ATTCAAAATT
52508400 AACTTATTTAATCATCT-ATTCATTCAATTTAGTCCAAAACAA
1 AACTTATTTAATCATCTAATT-ATTCAATTTAGTCCAAAACAA
*
52508442 AACTTATTTAATCATCTAATTGTTCAATTTAGTCCAAAACA
1 AACTTATTTAATCATCTAATTATTCAATTTAGTCCAAAACA
52508483 CACTTTAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 36 0.92
43 3 0.08
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.39
Consensus pattern (42 bp):
AACTTATTTAATCATCTAATTATTCAATTTAGTCCAAAACAA
Found at i:52511569 original size:9 final size:9
Alignment explanation
Indices: 52511555--52511579 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52511545 TAAATTTGAT
52511555 TTTAGTTAA
1 TTTAGTTAA
52511564 TTTAGTTAA
1 TTTAGTTAA
52511573 TTTAGTT
1 TTTAGTT
52511580 TGAGTCTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (9 bp):
TTTAGTTAA
Found at i:52511667 original size:38 final size:39
Alignment explanation
Indices: 52511578--52511694 Score: 114
Period size: 39 Copynumber: 3.0 Consensus size: 39
52511568 GTTAATTTAG
* * * *
52511578 TTTGAGTCTTTAATTATTTCATAA-CTTGGACAACATTAA
1 TTTGAGTATTTAATTATGTCATAATC-TGAACATCATTAA
*
52511617 TTTGAGTTTTTAATTATGTCATAATCTGAACATCATT-A
1 TTTGAGTATTTAATTATGTCATAATCTGAACATCATTAA
* * * *
52511655 TTTGTA-TATTTAATTATGTCCTAGTTTGAACATCTTTAA
1 TTTG-AGTATTTAATTATGTCATAATCTGAACATCATTAA
52511694 T
1 T
52511695 ACATGTTTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
38 31 0.47
39 34 0.52
40 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (39 bp):
TTTGAGTATTTAATTATGTCATAATCTGAACATCATTAA
Found at i:52513822 original size:54 final size:56
Alignment explanation
Indices: 52513687--52513846 Score: 182
Period size: 56 Copynumber: 2.9 Consensus size: 56
52513677 TTTGATGACA
* * * *
52513687 TGATACATGCTAGGTCCAAGAGCTTGTGTAGCCCCGTTGAGAGGCAT-GTAATTATG
1 TGATACATGCTAGGTCCGAGAGCTTATGTAGCCCTGTTGAGAGGCGTGGTAA-TATG
* * * *
52513743 TGGTACACGCTAGGTCCGGGAGCTTATGTAGCCCTGTTCAGAGGCGTGGT-A-ATG
1 TGATACATGCTAGGTCCGAGAGCTTATGTAGCCCTGTTGAGAGGCGTGGTAATATG
* *
52513797 TGATGCATGCTAGGTCCGAGTGCTTATATGTAGCCCTGTTGAGAGGCGTG
1 TGATACATGCTAGGTCCGAGAGC-T-TATGTAGCCCTGTTGAGAGGCGTG
52513847 CTATGTCATG
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
54 21 0.24
55 1 0.01
56 63 0.72
57 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.28
Consensus pattern (56 bp):
TGATACATGCTAGGTCCGAGAGCTTATGTAGCCCTGTTGAGAGGCGTGGTAATATG
Found at i:52521422 original size:11 final size:10
Alignment explanation
Indices: 52521400--52521433 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
52521390 TTTGTACATA
52521400 ATATGCCATG
1 ATATGCCATG
52521410 ATATGCACATG
1 ATATGC-CATG
52521421 ATATGCCATG
1 ATATGCCATG
52521431 ATA
1 ATA
52521434 CATACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (10 bp):
ATATGCCATG
Found at i:52521440 original size:21 final size:20
Alignment explanation
Indices: 52521394--52521446 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
52521384 TACTGATTTG
**
52521394 TACATAATATGCCATGATATG
1 TACAT-ATATGCCATGATACA
*
52521415 CACATGATATGCCATGATACA
1 TACAT-ATATGCCATGATACA
52521436 TACATATATGC
1 TACATATATGC
52521447 ATGGCTTGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (20 bp):
TACATATATGCCATGATACA
Found at i:52521508 original size:25 final size:25
Alignment explanation
Indices: 52521480--52521546 Score: 125
Period size: 25 Copynumber: 2.7 Consensus size: 25
52521470 GAGGAAGTGC
*
52521480 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
52521505 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
52521530 AAAAGGGCTTTGCCCCA
1 AAAAGGGCTTTGCCCCA
52521547 ATTATTAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:52521806 original size:31 final size:31
Alignment explanation
Indices: 52521768--52521879 Score: 156
Period size: 31 Copynumber: 3.6 Consensus size: 31
52521758 ACCGTTTACA
52521768 GTAAAGGCTTCGACCCAGTGGTATGAATAAT
1 GTAAAGGCTTCGACCCAGTGGTATGAATAAT
*
52521799 GTAAAGGCTTC-AGCCCAGTGATATGAATAAT
1 GTAAAGGCTTCGA-CCCAGTGGTATGAATAAT
*
52521830 G-AATAGGCTTCGGCCCAGTGGTATGAATAAT
1 GTAA-AGGCTTCGACCCAGTGGTATGAATAAT
* *
52521861 GTAAAAGCTTCGGCCCAGT
1 GTAAAGGCTTCGACCCAGT
52521880 ATATTCTGAG
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
30 3 0.04
31 68 0.93
32 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (31 bp):
GTAAAGGCTTCGACCCAGTGGTATGAATAAT
Found at i:52529052 original size:25 final size:25
Alignment explanation
Indices: 52529006--52529056 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
52528996 CCCTTATAAT
* *
52529006 GTGAAAATGACCTTTTTGCCCCTAG
1 GTGAAAATGACCTTTATACCCCTAG
52529031 GTGAAAATGA-CTATTATACCCCTAG
1 GTGAAAATGACCT-TTATACCCCTAG
52529056 G
1 G
52529057 GTTATGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (25 bp):
GTGAAAATGACCTTTATACCCCTAG
Found at i:52529122 original size:11 final size:10
Alignment explanation
Indices: 52529100--52529133 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
52529090 TTTGTACATA
52529100 ATATGCCATG
1 ATATGCCATG
52529110 ATATGCACATG
1 ATATGC-CATG
52529121 ATATGCCATG
1 ATATGCCATG
52529131 ATA
1 ATA
52529134 CATACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (10 bp):
ATATGCCATG
Found at i:52529140 original size:21 final size:20
Alignment explanation
Indices: 52529094--52529146 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
52529084 TACTGATTTG
**
52529094 TACATAATATGCCATGATATG
1 TACAT-ATATGCCATGATACA
*
52529115 CACATGATATGCCATGATACA
1 TACAT-ATATGCCATGATACA
52529136 TACATATATGC
1 TACATATATGC
52529147 ATGGGTTGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (20 bp):
TACATATATGCCATGATACA
Found at i:52540889 original size:40 final size:40
Alignment explanation
Indices: 52540820--52541030 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
52540810 CATTTGAATG
* *
52540820 ATATCCGGGCTAAG-TCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
52540859 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
52540899 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * * * * *
52540939 TTATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
52540979 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
52541019 ATATCC-GGCTAA
1 ATATCCGGGCTAA
52541031 ATTCGAAGAA
Statistics
Matches: 139, Mismatches: 30, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
39 21 0.15
40 116 0.83
41 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:52540968 original size:80 final size:79
Alignment explanation
Indices: 52540824--52541038 Score: 299
Period size: 80 Copynumber: 2.7 Consensus size: 79
52540814 TGAATGATAT
* *
52540824 CCGGGCTAAG-TCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCC-GGCTAAGATCCGAAGGCATTTG
* *
52540888 TGCGAGTTGCTATAC
65 TGCGAGTTACTAAAC
*
52540903 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGACTAAGATCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGG-CTAAGATCCGAAGGCATTTG
*
52540968 TGCGAGTTACTAAAT
65 TGCGAGTTACTAAAC
* * * * *
52540983 CCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCCGGCTAA-ATTCGAAG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGCTAAGATCCGAAG
52541039 AAACTTGGGT
Statistics
Matches: 122, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
78 7 0.06
79 15 0.12
80 100 0.82
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGCTAAGATCCGAAGGCATTTGT
GCGAGTTACTAAAC
Found at i:52544288 original size:30 final size:30
Alignment explanation
Indices: 52544254--52544314 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
52544244 TCCTTAACTC
52544254 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
52544284 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
52544314 A
1 A
52544315 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:52552614 original size:40 final size:42
Alignment explanation
Indices: 52552544--52552622 Score: 101
Period size: 40 Copynumber: 1.9 Consensus size: 42
52552534 TTGAGCTTGA
**
52552544 TTCAGCTCGAATTTTAGCTCATTGTACTTGAT-CTATTTCAC
1 TTCAGCTCGAATCCTAGCTCATTGTACTTGATGCTATTTCAC
*
52552585 TTCAGCTC-AATCCTAGCTTATTG-AGCTTGATGCTATTT
1 TTCAGCTCGAATCCTAGCTCATTGTA-CTTGATGCTATTT
52552623 TATTTTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 1 0.03
40 18 0.55
41 14 0.42
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (42 bp):
TTCAGCTCGAATCCTAGCTCATTGTACTTGATGCTATTTCAC
Found at i:52555224 original size:24 final size:24
Alignment explanation
Indices: 52555193--52555244 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
52555183 TCAAGAAAAG
52555193 AAAATTGAAAACGAAAGTGAGATA
1 AAAATTGAAAACGAAAGTGAGATA
52555217 AAAATTGAAAACGAAAGTGAGATA
1 AAAATTGAAAACGAAAGTGAGATA
52555241 AAAA
1 AAAA
52555245 GTGAGTTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.62, C:0.04, G:0.19, T:0.15
Consensus pattern (24 bp):
AAAATTGAAAACGAAAGTGAGATA
Found at i:52563923 original size:42 final size:43
Alignment explanation
Indices: 52563823--52563984 Score: 152
Period size: 43 Copynumber: 3.8 Consensus size: 43
52563813 TGTGTTATCA
* * * *
52563823 TGTAAGACCACGCCTGGGACGTTGGCATCG-ACTTATGATTTACG
1 TGTAAGACCATGTCTAGGACGTTGGCATCGTAC-T-TGAATTACG
*
52563867 TGTTAGACCATGTCTAGGACGTTGGCATCGTACTTGAATT-CG
1 TGTAAGACCATGTCTAGGACGTTGGCATCGTACTTGAATTACG
* * * * *
52563909 TGTAAGACCCTGTCTGGGATAG-TGGCATCGATATTTG-ATTACA
1 TGTAAGACCATGTCTAGGA-CGTTGGCATCG-TACTTGAATTACG
* *
52563952 TGTAAGACCATGTCTAGAACGTTGGCATTGTAC
1 TGTAAGACCATGTCTAGGACGTTGGCATCGTAC
52563985 GAGCTTTCTG
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
42 32 0.33
43 35 0.36
44 27 0.28
45 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACGTTGGCATCGTACTTGAATTACG
Found at i:52568320 original size:99 final size:99
Alignment explanation
Indices: 52568141--52568334 Score: 230
Period size: 99 Copynumber: 2.0 Consensus size: 99
52568131 TGGCACACAG
* * ** * **
52568141 GCGTATGACACGACTGTGTGACCCTACTCAGTAAGTTACGTGGGTGAGGACATGGGCTGAGATGC
1 GCGTATGACACGACCGTGTGACCCTACTCAGTAAGCTACGCAGGTGAGGACATAGGCTGAGACAC
52568206 AACTGTGTATCCTTAGTTCGAAGGTTACACACGA
66 AACTGTGTATCCTTAGTTCGAAGGTTACACACGA
* * *
52568240 GCGTATGACAC-ACCCGTGTGACCCTACTCAGTGAGCTATGCAGGTGAGGACATAGGCTGGGACA
1 GCGTATGACACGA-CCGTGTGACCCTACTCAGTAAGCTACGCAGGTGAGGACATAGGCTGAGACA
* * * *
52568304 CAGGC-GTGTGTGCTTAGTTTGAAGGTTACAC
65 CA-ACTGTGTATCCTTAGTTCGAAGGTTACAC
52568335 GGCCTAGCTA
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
98 1 0.01
99 77 0.97
100 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.24
Consensus pattern (99 bp):
GCGTATGACACGACCGTGTGACCCTACTCAGTAAGCTACGCAGGTGAGGACATAGGCTGAGACAC
AACTGTGTATCCTTAGTTCGAAGGTTACACACGA
Found at i:52570478 original size:30 final size:30
Alignment explanation
Indices: 52570444--52570502 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
52570434 CAATTTTCGA
* *
52570444 GCCTAGGGGAAAAATGGTCATTTTGCCAAG
1 GCCTAGGGAAAAAATGGTCATTTTACCAAG
52570474 GCCTAGGGAAAAAATGGTCATTTTACCAA
1 GCCTAGGGAAAAAATGGTCATTTTACCAA
52570503 AGATGTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (30 bp):
GCCTAGGGAAAAAATGGTCATTTTACCAAG
Found at i:52570979 original size:46 final size:46
Alignment explanation
Indices: 52570924--52571037 Score: 142
Period size: 46 Copynumber: 2.5 Consensus size: 46
52570914 CGAGTGCTAG
*
52570924 TGTAAGACATGTCTGGGATATACATCGGCCT-CGAGATG-TAAGCCAA
1 TGTAAGACATGTCTGGGACATACATCGG-CTACGAGATGAT-AGCCAA
* * * *
52570970 TGTAAGACATGCCTGGGACATGCATCGGCTACGAGATGATAGTCAG
1 TGTAAGACATGTCTGGGACATACATCGGCTACGAGATGATAGCCAA
52571016 TGTAAGACCATGTCTGGGACAT
1 TGTAAGA-CATGTCTGGGACAT
52571038 GGAATTGGCA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
45 2 0.03
46 43 0.73
47 14 0.24
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (46 bp):
TGTAAGACATGTCTGGGACATACATCGGCTACGAGATGATAGCCAA
Found at i:52572149 original size:21 final size:21
Alignment explanation
Indices: 52572116--52572165 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
52572106 CGGGTAGGGG
* * *
52572116 ACACAGGCGTGTTACCCTTCC
1 ACACGGGCATGTTACCCCTCC
52572137 ACACGGGCATGTTACCCCTCC
1 ACACGGGCATGTTACCCCTCC
*
52572158 ATACGGGC
1 ACACGGGC
52572166 GTGTGCCCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.38, G:0.22, T:0.20
Consensus pattern (21 bp):
ACACGGGCATGTTACCCCTCC
Found at i:52579807 original size:47 final size:45
Alignment explanation
Indices: 52579696--52579875 Score: 163
Period size: 47 Copynumber: 3.9 Consensus size: 45
52579686 CACTTGTGTG
*
52579696 TGCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCCACATTATG-GA
1 TGCTAGTGTAAGACCATGTCTGGGACATGCATCGG-CAC-TGA-GAGA
* * *
52579742 AGCAAGTGTAAGACCATGTCTAGGACATGGCATCGGCACTGAGACGA
1 TGCTAGTGTAAGACCATGTCTGGGACAT-GCATCGGCACTGAGA-GA
*
52579789 GTGCTAGTGTAAGA-CATGTCTGGGACATGCATCTGCTAC-GAGATGA
1 -TGCTAGTGTAAGACCATGTCTGGGACATGCATCGGC-ACTGAGA-GA
* *
52579835 TAG-TCAATGTAAGACCATGTCTGGGACATGGCATTGGCACT
1 T-GCT-AGTGTAAGACCATGTCTGGGACAT-GCATCGGCACT
52579876 TTATCAATAT
Statistics
Matches: 111, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
45 3 0.03
46 35 0.32
47 49 0.44
48 24 0.22
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (45 bp):
TGCTAGTGTAAGACCATGTCTGGGACATGCATCGGCACTGAGAGA
Found at i:52579856 original size:94 final size:94
Alignment explanation
Indices: 52579695--52579875 Score: 269
Period size: 94 Copynumber: 1.9 Consensus size: 94
52579685 TCACTTGTGT
*
52579695 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGGAAGCAAGTGTAAGACCATG
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGGAAGCAAGTGTAAGACCATG
52579760 TCTAGGACATGGCATCGGCACTGAGACGA
66 TCTAGGACATGGCATCGGCACTGAGACGA
* *
52579789 GTGCTAGTGTAAGACATGTCTGGGACATGCATCTGCTACGA-GAT-GATAGTCAA-TGTAAGACC
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGATGGA-AG-CAAGTGTAAGACC
* *
52579851 ATGTCTGGGACATGGCATTGGCACT
63 ATGTCTAGGACATGGCATCGGCACT
52579876 TTATCAATAT
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
93 2 0.03
94 73 0.92
95 4 0.05
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (94 bp):
GTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGGAAGCAAGTGTAAGACCATG
TCTAGGACATGGCATCGGCACTGAGACGA
Found at i:52593600 original size:40 final size:40
Alignment explanation
Indices: 52593552--52593778 Score: 400
Period size: 40 Copynumber: 5.7 Consensus size: 40
52593542 GCAAACACAT
* *
52593552 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
52593592 TTGCCTTCGGGTCTTAGCCCGGATATATCATCCCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
52593632 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
52593672 TTGCCTTCGGGTCTTAGCCCGGGTATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
52593712 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
52593752 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
52593779 ATCCAATGTT
Statistics
Matches: 177, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 177 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:52603022 original size:28 final size:28
Alignment explanation
Indices: 52602990--52603054 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
52602980 ATTTACTAGA
*
52602990 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
52603018 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
52603046 ATACCCCTA
1 ATACCCCTA
52603055 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:52603261 original size:29 final size:28
Alignment explanation
Indices: 52603160--52603250 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
52603150 AGGAAGCGTC
52603160 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAATTATCTGTT
*
52603188 CTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCACTGCCACAAATTATCTGTT
*
52603216 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAATTATCTGT-T
52603245 CTGGTG
1 CTGGTG
52603251 ACTCTGTCAC
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
28 51 0.88
29 7 0.12
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAATTATCTGTT
Found at i:52603275 original size:56 final size:55
Alignment explanation
Indices: 52603160--52603275 Score: 128
Period size: 56 Copynumber: 2.1 Consensus size: 55
52603150 AGGAAGCGTC
* * *
52603160 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCAC-AATTATCTATT
* * *
52603216 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCAC-ATTTTCTATAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACAATTATCTAT-T
52603272 CTGG
1 CTGG
52603276 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
55 8 0.16
56 29 0.57
57 14 0.27
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (55 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACAATTATCTATT
Found at i:52603738 original size:19 final size:19
Alignment explanation
Indices: 52603714--52603752 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
52603704 TTTTAATTAT
* *
52603714 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
52603733 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
52603752 T
1 T
52603753 ATGATAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:52610875 original size:28 final size:28
Alignment explanation
Indices: 52610843--52610907 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
52610833 ATTTACTAGA
*
52610843 ATACCCCTATGTATGCAAAATTA-CTATT
1 ATACCCCTATGTATGCAAAATGACCT-TT
52610871 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCTTT
52610899 ATACCCCTA
1 ATACCCCTA
52610908 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCTTT
Found at i:52611108 original size:29 final size:28
Alignment explanation
Indices: 52611007--52611097 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
52610997 AGGAAGCGTC
52611007 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAATTATCTGTT
*
52611035 CTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCACTGCCACAAATTATCTGTT
*
52611063 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAATTATCTGT-T
52611092 CTGGTG
1 CTGGTG
52611098 ACTCTGTCAC
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
28 51 0.88
29 7 0.12
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAATTATCTGTT
Found at i:52611122 original size:56 final size:55
Alignment explanation
Indices: 52611007--52611122 Score: 137
Period size: 56 Copynumber: 2.1 Consensus size: 55
52610997 AGGAAGCGTC
* *
52611007 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCAC-AATTATCTGTT
* * *
52611063 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCAC-ATTTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACAATTATCTGT-T
52611119 CTGG
1 CTGG
52611123 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
55 9 0.17
56 29 0.56
57 14 0.27
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (55 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACAATTATCTGTT
Found at i:52611584 original size:19 final size:19
Alignment explanation
Indices: 52611560--52611598 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
52611550 TTTTAATTAT
* *
52611560 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
52611579 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
52611598 T
1 T
52611599 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:52621382 original size:27 final size:27
Alignment explanation
Indices: 52621325--52621435 Score: 145
Period size: 27 Copynumber: 4.1 Consensus size: 27
52621315 AGCACGACTG
* *
52621325 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
52621351 GCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
52621378 CCAGAACAGAT-ATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* * *
52621405 CCAGATCAGATAGTTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
52621432 CCAG
1 CCAG
52621436 GACGCTTCCT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 14 0.19
27 60 0.80
28 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:52624956 original size:47 final size:47
Alignment explanation
Indices: 52624594--52624936 Score: 524
Period size: 47 Copynumber: 7.2 Consensus size: 47
52624584 TTAGGATTTT
** * * * **
52624594 ATGTGATGAATGTGAATGTGTATATATGAGATGAGGCCGAATGGAAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
52624641 ATGTGATGAATGTGAACCTGTATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATG--CATATAT--GTGATAAGGCCGAATGGCCA
* *
52624692 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
52624739 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
52624786 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
52624833 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
52624880 ATGTGATGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
52624927 ATGTGATGAA
1 ATGTGATGAA
52624937 CGTGGAAGTG
Statistics
Matches: 275, Mismatches: 17, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
47 229 0.83
49 11 0.04
51 35 0.13
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:52624969 original size:47 final size:47
Alignment explanation
Indices: 52624594--52624976 Score: 384
Period size: 47 Copynumber: 8.1 Consensus size: 47
52624584 TTAGGATTTT
** * * * **
52624594 ATGTGATGAATGTGAATGTGTATATATG-AGATGAGGCCGAATGGAAA
1 ATGTGATGAATGTGAACATGCATATATGTGGA-GAAGCCGAATGGCCA
* * * *
52624641 ATGTGATGAATGTGAACCTGTATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATG--CATATATGTG-GAGAA-GCCGAATGGCCA
* * *
52624692 ATGTGATGAATGTGAACATGCGTATGTGT-GATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGGAGAA-GCCGAATGGCCA
*
52624739 ATGTGATGAATGTGAACATGCATATATGT-GATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGGAGAA-GCCGAATGGCCA
* * *
52624786 ATGTGATGAATGTGAACATGCGTATGTGT-GATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGGAGAA-GCCGAATGGCCA
*
52624833 ATGTGATGAATGTGAACATGCATATATGT-GATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGGAGAA-GCCGAATGGCCA
*
52624880 ATGTGATGAATGTGAACATGCATATATGT-GATGAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGGA-GAAGCCGAATGGCCA
* * * * * *
52624927 ATGTGATGAACGTGGAA-GTGTATATATGTGGCGAAGCTGAATGGCTA
1 ATGTGATGAATGT-GAACATGCATATATGTGGAGAAGCCGAATGGCCA
52624974 ATG
1 ATG
52624977 CGAAATGTGT
Statistics
Matches: 301, Mismatches: 27, Indels: 16
0.88 0.08 0.05
Matches are distributed among these distances:
47 251 0.83
48 5 0.02
49 13 0.04
50 1 0.00
51 31 0.10
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGGAGAAGCCGAATGGCCA
Found at i:52624969 original size:141 final size:142
Alignment explanation
Indices: 52624594--52624976 Score: 520
Period size: 141 Copynumber: 2.7 Consensus size: 142
52624584 TTAGGATTTT
** * * ** *
52624594 ATGTGATGAATGTGAATGTGTATATATGAGATGAGGCCGAATGGAAAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCCAATGTGATGAATGTGAACA
* * * *
52624659 TGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
66 TG--TATATATGTG-GAGAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGAT
52624724 AAGGCCGAATGGCCA
128 AAGGCCGAATGGCCA
*
52624739 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCCAATGTGATGAATGTGAACA
** * *
52624804 TGCGTATGTGT-GATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAG
66 TGTATATATGTGGAGAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAG
52624868 GCCGAATGGCCA
131 GCCGAATGGCCA
*
52624880 ATGTGATGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCCAATGTGATGAACGTGGAA-
1 ATGTGATGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCCAATGTGATGAATGT-GAAC
* * * *
52624944 GTGTATATATGTGGCGAA-GCTGAATGGCTAATG
65 ATGTATATATGTGGAGAAGGCCGAATGGCCAATG
52624977 CGAAATGTGT
Statistics
Matches: 212, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
141 142 0.67
142 6 0.03
143 5 0.02
145 59 0.28
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.26
Consensus pattern (142 bp):
ATGTGATGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCCAATGTGATGAATGTGAACA
TGTATATATGTGGAGAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAG
GCCGAATGGCCA
Found at i:52625015 original size:46 final size:46
Alignment explanation
Indices: 52624960--52625086 Score: 182
Period size: 46 Copynumber: 2.8 Consensus size: 46
52624950 ATATGTGGCG
*
52624960 AAGCTGAATGGCTAATGCGAAATGTGTATGAGATGAATATGAGGTA
1 AAGCCGAATGGCTAATGCGAAATGTGTATGAGATGAATATGAGGTA
* * *
52625006 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGTGGTA
1 AAGCCGAATGGCTAATGCGAAATGTGTATGAGATGAATATGAGGTA
* * * *
52625052 AAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 AAGCCGAATGGCTAATGCGAAATGTGTATGAGATG
52625087 TGTATATATA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.35, C:0.09, G:0.31, T:0.25
Consensus pattern (46 bp):
AAGCCGAATGGCTAATGCGAAATGTGTATGAGATGAATATGAGGTA
Found at i:52626982 original size:24 final size:24
Alignment explanation
Indices: 52626947--52627047 Score: 166
Period size: 24 Copynumber: 4.2 Consensus size: 24
52626937 CCAACACTGT
*
52626947 TCTCCCTAATCAACTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
*
52626971 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
*
52626995 TATCCCTTATCAACTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
*
52627019 TATCCCTTATCAACTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
52627043 TCTCC
1 TCTCC
52627048 TGACAGACTT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.26, C:0.41, G:0.01, T:0.33
Consensus pattern (24 bp):
TCTCCCTTATCAACTCCTAAATCC
Found at i:52633337 original size:27 final size:27
Alignment explanation
Indices: 52633283--52633382 Score: 132
Period size: 27 Copynumber: 3.7 Consensus size: 27
52633273 AGCACGGCTG
* *
52633283 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
52633309 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
52633336 CCAGAACAGAT-ATATCTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* *
52633363 CCAGATCAGATAGTTGTGGC
1 CCAGAACAGATAATTGTGGC
52633383 TGGCATAGCC
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
26 15 0.23
27 49 0.75
28 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:52634840 original size:24 final size:24
Alignment explanation
Indices: 52634805--52634904 Score: 155
Period size: 24 Copynumber: 4.2 Consensus size: 24
52634795 CCAACACTGT
* *
52634805 TCTCCCTAATCATCTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
*
52634829 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
*
52634853 TATCCCTTATCAACTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
*
52634877 TATCCCTTATCAACTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
52634901 TCTC
1 TCTC
52634905 TTGACAGACT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.25, C:0.40, G:0.01, T:0.34
Consensus pattern (24 bp):
TCTCCCTTATCAACTCCTAAATCC
Found at i:52636705 original size:20 final size:20
Alignment explanation
Indices: 52636677--52636716 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
52636667 GCTTGTACGG
**
52636677 GATTGCACTTTGGTGCCTCT
1 GATTGCACTTCAGTGCCTCT
*
52636697 GATTTCACTTCAGTGCCTCT
1 GATTGCACTTCAGTGCCTCT
52636717 TTTAGCATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.12, C:0.28, G:0.20, T:0.40
Consensus pattern (20 bp):
GATTGCACTTCAGTGCCTCT
Found at i:52638062 original size:20 final size:20
Alignment explanation
Indices: 52638019--52638056 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52638009 GCACACACAA
*
52638019 GTGTGCTTTGAGACATGCTC
1 GTGTGCTTTGAGACACGCTC
*
52638039 GTGTGCTTTGGGACACGC
1 GTGTGCTTTGAGACACGC
52638057 CTGTGTCCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.21, G:0.34, T:0.32
Consensus pattern (20 bp):
GTGTGCTTTGAGACACGCTC
Found at i:52657476 original size:25 final size:24
Alignment explanation
Indices: 52657448--52657518 Score: 70
Period size: 25 Copynumber: 2.9 Consensus size: 24
52657438 GGTAAGGATA
*
52657448 GTAAATGAGAAGGGAAAAAAAAGGG
1 GTAAATGAGAA-AGAAAAAAAAGGG
* *
52657473 GTAAATGGGAAAGAAAATAAAGGG
1 GTAAATGAGAAAGAAAAAAAAGGG
** *
52657497 GCTGCATAAGAAAGAAAAAAAA
1 G-TAAATGAGAAAGAAAAAAAA
52657519 ACAGTTAATG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
24 12 0.32
25 25 0.68
ACGTcount: A:0.58, C:0.03, G:0.30, T:0.10
Consensus pattern (24 bp):
GTAAATGAGAAAGAAAAAAAAGGG
Found at i:52657581 original size:32 final size:31
Alignment explanation
Indices: 52657497--52657591 Score: 113
Period size: 31 Copynumber: 3.0 Consensus size: 31
52657487 AAATAAAGGG
* * *
52657497 GCTGCATAAGAAAGAAAAAAAAACAGTTAAT
1 GCTGCGTAAGAAATAAAAAAAAATAGTTAAT
*
52657528 GCTGCGTAAGAAATAACAAAAAATAGTTAAT
1 GCTGCGTAAGAAATAAAAAAAAATAGTTAAT
52657559 GCTGTC-TAAGAACCA-AAAAAAAAATAGTTAAT
1 GCTG-CGTAAGAA--ATAAAAAAAAATAGTTAAT
52657591 G
1 G
52657592 TATTGTATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
31 37 0.66
32 18 0.32
33 1 0.02
ACGTcount: A:0.54, C:0.11, G:0.16, T:0.20
Consensus pattern (31 bp):
GCTGCGTAAGAAATAAAAAAAAATAGTTAAT
Found at i:52658683 original size:23 final size:23
Alignment explanation
Indices: 52658651--52658694 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
52658641 AAATCCCAAG
* *
52658651 AGTTATTAATATTTATTTATAAT
1 AGTTACTAATATTTAATTATAAT
*
52658674 AGTTACTAATGTTTAATTATA
1 AGTTACTAATATTTAATTATA
52658695 TTTAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (23 bp):
AGTTACTAATATTTAATTATAAT
Found at i:52661618 original size:40 final size:40
Alignment explanation
Indices: 52661421--52661604 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
52661411 CGAATGATGT
* * * *
52661421 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
52661461 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
52661501 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
52661539 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
52661580 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
52661605 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:52661626 original size:79 final size:79
Alignment explanation
Indices: 52661476--52661627 Score: 202
Period size: 79 Copynumber: 1.9 Consensus size: 79
52661466 CTAAGATCCG
* **
52661476 AAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATC
1 AAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAATC
52661541 CGGGTTAAGTCCCA
66 CGGGTTAAGTCCCA
* * *
52661555 AAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTAT
1 AAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAA
52661618 ATCC-GGTTAA
63 ATCCGGGTTAA
52661628 ATTCTGAAGG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 38 0.59
80 24 0.38
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (79 bp):
AAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAATC
CGGGTTAAGTCCCA
Found at i:52668894 original size:44 final size:43
Alignment explanation
Indices: 52668831--52668960 Score: 131
Period size: 44 Copynumber: 3.0 Consensus size: 43
52668821 CATAGGATTC
* *
52668831 CGATATGTA-ATTTCGTGTAAGACCATGTCTGGGACGTTGGCAT
1 CGATAT-TAGATTACGTGTAAGACCATGTCTGGGAAGTTGGCAT
*
52668874 CGAT-TTGAGACTTACGTGTAAGACCCTGTCTGGGATAG-TGGCAT
1 CGATATT-AGA-TTACGTGTAAGACCATGTCTGGGA-AGTTGGCAT
* * * * *
52668918 TGATATTTGATTACATGTAAGACCACGTCTGGGATGTTGGCAT
1 CGATATTAGATTACGTGTAAGACCATGTCTGGGAAGTTGGCAT
52668961 TGTACGAGCT
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
41 1 0.01
42 3 0.04
43 32 0.44
44 33 0.46
45 3 0.04
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (43 bp):
CGATATTAGATTACGTGTAAGACCATGTCTGGGAAGTTGGCAT
Found at i:52668949 original size:43 final size:44
Alignment explanation
Indices: 52668846--52668962 Score: 134
Period size: 43 Copynumber: 2.7 Consensus size: 44
52668836 TGTAATTTCG
* * * *
52668846 TGTAAGACCATGTCTGGGACGTTGGCATCGATTTGAGACTTACG
1 TGTAAGACCACGTCTGGGATGTTGGCATTGATTTGAGACTTACA
*
52668890 TGTAAGACC-CTGTCTGGGATAG-TGGCATTGATATT-TGA-TTACA
1 TGTAAGACCAC-GTCTGGGAT-GTTGGCATTGAT-TTGAGACTTACA
52668933 TGTAAGACCACGTCTGGGATGTTGGCATTG
1 TGTAAGACCACGTCTGGGATGTTGGCATTG
52668963 TACGAGCTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
42 1 0.02
43 30 0.48
44 29 0.46
45 3 0.05
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGATGTTGGCATTGATTTGAGACTTACA
Found at i:52672024 original size:43 final size:41
Alignment explanation
Indices: 52671963--52672104 Score: 212
Period size: 43 Copynumber: 3.3 Consensus size: 41
52671953 CATAGGATTT
*
52671963 TCGATATGTGATTACGTGTAAGACCATGTTTAGGACGTTAGCA
1 TCGATATGTGATTACGTGTAAGACCACGTTT-GGACGTT-GCA
*
52672006 TCGATATGTGATTCCGTGTAAGACCACGTCTTGGACGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGT-TTGGACGTT-GCA
52672049 TCGATATGTGATTACGTGTAAGACCACGTTTGGGACGTTGCCA
1 TCGATATGTGATTACGTGTAAGACCACGTTT-GGACGTTG-CA
52672092 TCGATATGTGATT
1 TCGATATGTGATT
52672105 CTGATATGTG
Statistics
Matches: 92, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
42 3 0.03
43 87 0.95
44 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (41 bp):
TCGATATGTGATTACGTGTAAGACCACGTTTGGACGTTGCA
Found at i:52672150 original size:56 final size:56
Alignment explanation
Indices: 52672066--52672239 Score: 206
Period size: 56 Copynumber: 3.1 Consensus size: 56
52672056 GTGATTACGT
*** * **
52672066 GTAAGACCACGTTTGGGACGTTGCCATCGATATGTGATTCTGATATGTGTGTGCAA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATGTGTGTGTGA
* * *
52672122 GTAAGACCACGTTTAATACATTGGCATCGATATGTAATTCCGATATGTGTGTGTGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATGTGTGTGTGA
* * * * * *
52672178 GTAAGACCACATTTACTACGTTGGCATCGGTATATG-TTATGATATGCGTGTGTGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATGTGTGTGTGA
52672233 GTAAGAC
1 GTAAGAC
52672240 TGTAATATCC
Statistics
Matches: 100, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
55 23 0.23
56 77 0.77
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (56 bp):
GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATGTGTGTGTGA
Found at i:52673568 original size:45 final size:45
Alignment explanation
Indices: 52673500--52673705 Score: 253
Period size: 45 Copynumber: 4.7 Consensus size: 45
52673490 ATATCGCACA
*
52673500 ATACTATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCAGG-GAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCC-GGTGAG
* *
52673545 ATACTATTCGGGCCTTTGCGCCTAGCAGGTTATAATGCCGGTGAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
* *
52673590 ATACTATTCGGG-CTTCGAGCCTAGCAGGCGA-AATGCCGGTGAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
* * * *
52673633 ATACTATTTGGGCTTTTGAGCCTAGCAGGCTATAATGTCGGTGAA
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
* *
52673678 ATGA-TA-TCGGG-CTTCGAGCCTAGTAGGC
1 AT-ACTATTCGGGCCTTTGAGCCTAGCAGGC
52673706 GAAATGGCAA
Statistics
Matches: 140, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
43 37 0.26
44 37 0.26
45 65 0.46
46 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (45 bp):
ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
Found at i:52673656 original size:88 final size:88
Alignment explanation
Indices: 52673499--52673711 Score: 279
Period size: 88 Copynumber: 2.4 Consensus size: 88
52673489 AATATCGCAC
* * * *
52673499 AATACTATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCAGGGAGATACTATTCGGGCCTTTGC
1 AATACTATTCG-GGCTTCGAGCCTAGCAGGCGA-AATGCCAGGGAGATACTATTCGGGCCTTTGA
*
52673564 GCCTAGCAGGTTATAATGCCGGTGA
64 GCCTAGCAGGCTATAATGCCGGTGA
* * *
52673589 GATACTATTCGGGCTTCGAGCCTAGCAGGCGAAATGCC-GGTGAGATACTATTTGGGCTTTTGAG
1 AATACTATTCGGGCTTCGAGCCTAGCAGGCGAAATGCCAGG-GAGATACTATTCGGGCCTTTGAG
*
52673653 CCTAGCAGGCTATAATGTCGGTGA
65 CCTAGCAGGCTATAATGCCGGTGA
*
52673677 AATGA-TA-TCGGGCTTCGAGCCTAGTAGGCGAAATG
1 AAT-ACTATTCGGGCTTCGAGCCTAGCAGGCGAAATG
52673712 GCAATGAATG
Statistics
Matches: 110, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
87 29 0.26
88 52 0.47
89 19 0.17
90 10 0.09
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.26
Consensus pattern (88 bp):
AATACTATTCGGGCTTCGAGCCTAGCAGGCGAAATGCCAGGGAGATACTATTCGGGCCTTTGAGC
CTAGCAGGCTATAATGCCGGTGA
Found at i:52680286 original size:44 final size:44
Alignment explanation
Indices: 52680215--52680311 Score: 160
Period size: 43 Copynumber: 2.2 Consensus size: 44
52680205 AATATCGCAC
*
52680215 AATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCTGGTGA
1 AATACTATTCGGGCCTTTGAGCCTAGCAGGC-AAAATGCTGGTGA
52680260 AATACTATTCGGG-CTTTGAGCCTAGCAGGCAAAATGCTGGTGA
1 AATACTATTCGGGCCTTTGAGCCTAGCAGGCAAAATGCTGGTGA
*
52680303 GATACTATT
1 AATACTATT
52680312 TAGGCTTTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
43 20 0.40
44 17 0.34
45 13 0.26
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (44 bp):
AATACTATTCGGGCCTTTGAGCCTAGCAGGCAAAATGCTGGTGA
Found at i:52680309 original size:43 final size:43
Alignment explanation
Indices: 52680215--52680340 Score: 162
Period size: 44 Copynumber: 2.9 Consensus size: 43
52680205 AATATCGCAC
*
52680215 AATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCTGGTGA
1 AATACTATTCGGG-CTTTGAGCCTAGCAGGC-AAAATGCTGGTGA
52680260 AATACTATTCGGGCTTTGAGCCTAGCAGGCAAAATGCTGGTGA
1 AATACTATTCGGGCTTTGAGCCTAGCAGGCAAAATGCTGGTGA
* ** * * *
52680303 GATACTATTTAGGCTTTCAAGCCTAGTAGGCGAAATGC
1 AATACTATTCGGGCTTT-GAGCCTAGCAGGCAAAATGC
52680341 CAGTGAATGA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
43 26 0.36
44 34 0.47
45 13 0.18
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (43 bp):
AATACTATTCGGGCTTTGAGCCTAGCAGGCAAAATGCTGGTGA
Found at i:52691100 original size:56 final size:56
Alignment explanation
Indices: 52690987--52691102 Score: 169
Period size: 56 Copynumber: 2.1 Consensus size: 56
52690977 GGACGTTACA
* * * * *
52690987 AAGACCACGTTTAATATGTTGGCATCGATATGTGATTCCAATATGTGTGTGCGAGT
1 AAGAACACGTTTAATACGTTGGCATCGATAGGTGATTCCAATATGTGTGTACAAGT
* *
52691043 AAGAACACGTTTAATACGTTGGCATCGATAGGTGATTCCGATATGTGTTTACAAGT
1 AAGAACACGTTTAATACGTTGGCATCGATAGGTGATTCCAATATGTGTGTACAAGT
52691099 AAGA
1 AAGA
52691103 CCTTGTCTAG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (56 bp):
AAGAACACGTTTAATACGTTGGCATCGATAGGTGATTCCAATATGTGTGTACAAGT
Found at i:52705637 original size:46 final size:46
Alignment explanation
Indices: 52705556--52705675 Score: 188
Period size: 46 Copynumber: 2.6 Consensus size: 46
52705546 GCCCATTAGC
* * *
52705556 GAACTCGGACTCAACTCAATGAGCTCAGGCGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCAGGCATTCGCATCCATAAGT
52705602 GAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCAGG-CATTCGCATCCATAAGT
*
52705648 GAACTCGGACTCAACTAAACGAGTTCAG
1 GAACTCGGACTCAACTCAACGAGTTCAG
52705676 ATGCTCAACC
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
45 2 0.03
46 65 0.96
47 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCAGGCATTCGCATCCATAAGT
Found at i:52709001 original size:35 final size:35
Alignment explanation
Indices: 52708953--52709022 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
52708943 AAAAACAGTC
**
52708953 TTGGGCCTAAGCCCAT-TACAGATTTAGATACAGAT
1 TTGGGCCTAAGCCCATCT-CAGATACAGATACAGAT
*
52708988 TTGGGCCTTAGCCCATCTCAGATACAGATACAGAT
1 TTGGGCCTAAGCCCATCTCAGATACAGATACAGAT
52709023 ATAGAGTCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (35 bp):
TTGGGCCTAAGCCCATCTCAGATACAGATACAGAT
Found at i:52709091 original size:23 final size:23
Alignment explanation
Indices: 52709061--52709119 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
52709051 TACCCCTAGC
*
52709061 CCCTACACACCATCTCCGACCAT
1 CCCTACACACCATATCCGACCAT
*
52709084 CCCTACACACCATATCTGACCAT
1 CCCTACACACCATATCCGACCAT
52709107 CCCTACACACCAT
1 CCCTACACACCAT
52709120 GTGGTGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.29, C:0.49, G:0.03, T:0.19
Consensus pattern (23 bp):
CCCTACACACCATATCCGACCAT
Found at i:52711893 original size:26 final size:26
Alignment explanation
Indices: 52711859--52711909 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
52711849 AAAGATTTAG
*
52711859 AAGGAAAGAATGAAAAGAGAAATATA
1 AAGGAAAGAAAGAAAAGAGAAATATA
* *
52711885 AAGGGAAGAAAGAAAAGGGAAATAT
1 AAGGAAAGAAAGAAAAGAGAAATAT
52711910 GTTTCGACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.27, T:0.10
Consensus pattern (26 bp):
AAGGAAAGAAAGAAAAGAGAAATATA
Found at i:52718689 original size:52 final size:52
Alignment explanation
Indices: 52718633--52718738 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
52718623 ATTTAATGAT
*
52718633 GATATATCATGTTATTATTTATAGTTAGTACATAAGACTTATACACTAATGG
1 GATATATCATGTTATTATTTATAGTTAGCACATAAGACTTATACACTAATGG
52718685 GATATATCATGTTATTATTTATAGTTAGCACATAAGACTTATACACTAATGG
1 GATATATCATGTTATTATTTATAGTTAGCACATAAGACTTATACACTAATGG
52718737 GA
1 GA
52718739 ACGGTGCATC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (52 bp):
GATATATCATGTTATTATTTATAGTTAGCACATAAGACTTATACACTAATGG
Found at i:52719131 original size:20 final size:18
Alignment explanation
Indices: 52719082--52719137 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 18
52719072 CACTTAAACA
*
52719082 ATCTACTAATATATATTTT
1 ATCTA-TAATATATATTAT
52719101 AT-TATATATATATGATCTAT
1 ATCTATA-ATATAT-AT-TAT
52719121 ATCTATAATATATATTA
1 ATCTATAATATATATTA
52719138 AAATTTGACT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
17 2 0.06
18 10 0.31
19 6 0.19
20 10 0.31
21 4 0.12
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (18 bp):
ATCTATAATATATATTAT
Found at i:52728122 original size:44 final size:44
Alignment explanation
Indices: 52727976--52728134 Score: 114
Period size: 44 Copynumber: 3.7 Consensus size: 44
52727966 AGCTCGTACA
* * * *
52727976 ATGCCAACGTCCCAGACGTGGTCTTACATGT-AATC-AAATATCA
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCTCAA-ATCG
* * * * *
52728019 ATGCC-ACTATCCCAGATAGGGTTTTACAC--AAA-ATCAAATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAAATCTCAAAT-CG
** * * * *
52728061 ATGCTGATGTTCGAGACATGGTTTTACACGTAAATCTCAAATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCTCAAATCG
52728105 ATGCCAACGTCCCAGACATGGTCTTACACG
1 ATGCCAACGTCCCAGACATGGTCTTACACG
52728135 ATAACACATA
Statistics
Matches: 85, Mismatches: 23, Indels: 15
0.69 0.19 0.12
Matches are distributed among these distances:
41 2 0.02
42 27 0.32
43 21 0.25
44 29 0.34
45 6 0.07
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (44 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCTCAAATCG
Found at i:52736032 original size:18 final size:18
Alignment explanation
Indices: 52736011--52736048 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
52736001 TATCGGAACT
52736011 AGAATCAAAATGAGAATC
1 AGAATCAAAATGAGAATC
* *
52736029 AGAATCAGAATTAGAATC
1 AGAATCAAAATGAGAATC
52736047 AG
1 AG
52736049 GTGACAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (18 bp):
AGAATCAAAATGAGAATC
Found at i:52736034 original size:6 final size:6
Alignment explanation
Indices: 52736011--52736070 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
52736001 TATCGGAACT
* * * *
52736011 AGAATC AAAATG AGAATC AGAATC AGAATT AGAATC AG-GTGAC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC
*
52736060 AGAACC AGAAT
1 AGAATC AGAAT
52736071 GTGAATGCAA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
5 1 0.02
6 36 0.88
7 3 0.07
8 1 0.02
ACGTcount: A:0.50, C:0.13, G:0.20, T:0.17
Consensus pattern (6 bp):
AGAATC
Found at i:52736359 original size:22 final size:22
Alignment explanation
Indices: 52736333--52736386 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
52736323 TGGTACACAA
52736333 CCATAATCAGGTTGGCACAAAG
1 CCATAATCAGGTTGGCACAAAG
* *
52736355 CCAT-ATGTAGGTTGGCGCAAAG
1 CCATAAT-CAGGTTGGCACAAAG
52736377 CCATAATCAG
1 CCATAATCAG
52736387 AATAATTGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 2 0.07
22 23 0.85
23 2 0.07
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.20
Consensus pattern (22 bp):
CCATAATCAGGTTGGCACAAAG
Found at i:52736930 original size:27 final size:27
Alignment explanation
Indices: 52736900--52737007 Score: 126
Period size: 27 Copynumber: 4.0 Consensus size: 27
52736890 GGGGCAAAAT
* * *
52736900 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
** *
52736927 GGTAATTCTACATTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
52736954 GATATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
52736981 AGTAATTCTACCCTACATGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
52737008 AATAATTTTG
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:52736966 original size:54 final size:53
Alignment explanation
Indices: 52736904--52737016 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 53
52736894 CAAAATGGTA
* *
52736904 ATTTTACCCCACAAGGGTATCTCGGTAATTCTACATTACAGGGGTATTTCGAT
1 ATTTTACCCCACAAGGGTATCTCAGTAATTCTACACTACAGGGGTATTTCGAT
* * * * *
52736957 ATTTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACATGGGTATTTCAAT
1 ATTT-TACCCCACAAGGGTATCTCAGTAATTCTACACTACAGGGGTATTTCGAT
52737011 AATTTT
1 -ATTTT
52737017 GTAAATCGAG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 4 0.08
54 43 0.84
55 4 0.08
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.37
Consensus pattern (53 bp):
ATTTTACCCCACAAGGGTATCTCAGTAATTCTACACTACAGGGGTATTTCGAT
Found at i:52739111 original size:6 final size:6
Alignment explanation
Indices: 52739073--52739166 Score: 77
Period size: 6 Copynumber: 15.3 Consensus size: 6
52739063 AAGAAACATT
* * * *
52739073 ATCAGA A-CTAGA ATCAAA ATGAGA ATCATA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
*
52739122 ATCAGA ATCAGA ATCAGA ATCAGGTG AT-AGA ATCAGA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
52739167 GTGAATGCAA
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
5 4 0.06
6 57 0.81
7 6 0.09
8 3 0.04
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:52739131 original size:31 final size:31
Alignment explanation
Indices: 52739094--52739166 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
52739084 AATCAAAATG
*
52739094 AGAATCATAATCAGAATCAGGTGACAGAATC
1 AGAATCAGAATCAGAATCAGGTGACAGAATC
*
52739125 AGAATCAGAATCAGAATCAGGTGATAGAATC
1 AGAATCAGAATCAGAATCAGGTGACAGAATC
52739156 AGAATCAGAAT
1 AGAATCAGAAT
52739167 GTGAATGCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.19
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTGACAGAATC
Found at i:52739454 original size:22 final size:23
Alignment explanation
Indices: 52739420--52739479 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
52739410 CCACAATAAC
52739420 GGCACACAA-CCATAAT-TAGGTT
1 GGCACA-AAGCCATAATGTAGGTT
52739442 GGCACAAAGCCAT-ATGTAGGTT
1 GGCACAAAGCCATAATGTAGGTT
* *
52739464 GACGCAAAGCCATAAT
1 GGCACAAAGCCATAAT
52739480 CAGAATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 4 0.12
22 27 0.82
23 2 0.06
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (23 bp):
GGCACAAAGCCATAATGTAGGTT
Found at i:52739626 original size:14 final size:14
Alignment explanation
Indices: 52739607--52739648 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
52739597 TAATCATATA
52739607 TTGGCACATAGCCT
1 TTGGCACATAGCCT
* *
52739621 TTGGCAAATA-CGT
1 TTGGCACATAGCCT
*
52739634 TTGGCACACAGCCT
1 TTGGCACATAGCCT
52739648 T
1 T
52739649 CGGTAACATG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (14 bp):
TTGGCACATAGCCT
Found at i:52740026 original size:27 final size:27
Alignment explanation
Indices: 52739996--52740103 Score: 126
Period size: 27 Copynumber: 4.0 Consensus size: 27
52739986 GGGGCAAAAT
* * *
52739996 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
52740023 GGTAATTCTACCCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
52740050 GATATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
52740077 TGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
52740104 AATAATTTTG
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:52740042 original size:54 final size:54
Alignment explanation
Indices: 52739984--52740097 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 54
52739974 TTTAACACCC
*
52739984 TAGGGGCAAAATGGTAATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCCTA
1 TAGGGGCAAAATGAT-ATTTCTACCCCACAAGGGTATCTCGGTAATTCTACCCTA
* *** * * *
52740038 TAGGGGTATTTTGATATTTCTACCCTACAAGGGTATTTCTGTAATTCTACCCTA
1 TAGGGGCAAAATGATATTTCTACCCCACAAGGGTATCTCGGTAATTCTACCCTA
*
52740092 CAGGGG
1 TAGGGG
52740098 TATTTCAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 4 0.08
54 46 0.92
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (54 bp):
TAGGGGCAAAATGATATTTCTACCCCACAAGGGTATCTCGGTAATTCTACCCTA
Found at i:52740098 original size:54 final size:53
Alignment explanation
Indices: 52740000--52740102 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 53
52739990 CAAAATGGTA
*
52740000 ATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTATAGGGGTATTTTGAT
1 ATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTTGAT
* * *
52740053 ATTTCTACCCTACAAGGGTATTTCTGTAATTCTACCCTACAGGGGTATTT
1 ATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTT
52740103 CAATAATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 4 0.09
54 41 0.91
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.37
Consensus pattern (53 bp):
ATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTTGAT
Found at i:52740125 original size:27 final size:27
Alignment explanation
Indices: 52740095--52740198 Score: 75
Period size: 27 Copynumber: 3.9 Consensus size: 27
52740085 TACCCTACAG
52740095 GGGTATTTCAATAATTTTGTAAATCGA
1 GGGTATTTCAATAATTTTGTAAATCGA
*** * *
52740122 GGGTAAAACGATAATTTTGTAAATCGG
1 GGGTATTTCAATAATTTTGTAAATCGA
* * ** *
52740149 GGGTACTT-AGGTAATTTTACAAGTCGA
1 GGGTATTTCA-ATAATTTTGTAAATCGA
* * *
52740176 GGGTATTTTAGTAATTTAGTAAA
1 GGGTATTTCAATAATTTTGTAAA
52740199 CTAAAGTATT
Statistics
Matches: 56, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
27 55 0.98
28 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.37
Consensus pattern (27 bp):
GGGTATTTCAATAATTTTGTAAATCGA
Found at i:52742013 original size:64 final size:64
Alignment explanation
Indices: 52741932--52742114 Score: 201
Period size: 67 Copynumber: 2.8 Consensus size: 64
52741922 AGACATTATG
* *
52741932 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
52741996 ATGTAGCTAGGTCGCATGCGTGATTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
52742061 AA
63 AA
* * * *
52742063 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAG
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAG
52742115 TCAAACTATA
Statistics
Matches: 98, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 18 0.18
64 26 0.27
66 20 0.20
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:52742054 original size:67 final size:64
Alignment explanation
Indices: 52741908--52742061 Score: 182
Period size: 67 Copynumber: 2.3 Consensus size: 64
52741898 CATCATGTGT
* * * * *
52741908 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTAC--GAGA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCATGAGGACACCATG
52741973 TAG
62 TAG
* *
52741976 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGATTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGCGTGATACCA--TG-AGGACACCATGT
52742041 AG
63 AG
52742043 ACAAGAGAGCTACGAGATA
1 ACAAGAGAGCTACGAGATA
52742062 AACTGGCTAG
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
64 25 0.33
65 3 0.04
66 4 0.05
67 30 0.40
68 13 0.17
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGCGTGATACCATGAGGACACCATGTAG
Found at i:52753129 original size:20 final size:20
Alignment explanation
Indices: 52753104--52753144 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
52753094 CTTCAGACTA
52753104 TGGACTGAATAGTGAAGGAT
1 TGGACTGAATAGTGAAGGAT
52753124 TGGACTGAATAGTGAAGGAT
1 TGGACTGAATAGTGAAGGAT
52753144 T
1 T
52753145 ATTGTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.34, T:0.27
Consensus pattern (20 bp):
TGGACTGAATAGTGAAGGAT
Found at i:52759037 original size:15 final size:15
Alignment explanation
Indices: 52759019--52759048 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52759009 AAAAAAAAGG
52759019 AAAAAAAAAATTGCA
1 AAAAAAAAAATTGCA
52759034 AAAAAAAAAATTGCA
1 AAAAAAAAAATTGCA
52759049 TACGGTCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAAAAAATTGCA
Found at i:52761285 original size:24 final size:25
Alignment explanation
Indices: 52761258--52761311 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
52761248 ATGAGTGATA
*
52761258 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
52761282 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
52761306 AAAAAA
1 AAAAAA
52761312 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:52765943 original size:13 final size:13
Alignment explanation
Indices: 52765925--52765950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52765915 AAGTAATCGA
52765925 ACACAGGCGTGTC
1 ACACAGGCGTGTC
52765938 ACACAGGCGTGTC
1 ACACAGGCGTGTC
52765951 CCTGCCGAGC
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:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACACAGGCGTGTC
Found at i:52796213 original size:40 final size:40
Alignment explanation
Indices: 52796150--52796370 Score: 247
Period size: 40 Copynumber: 5.5 Consensus size: 40
52796140 TATTCGAATG
* *
52796150 ATATCCGGGCTAAG-TCCCAAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* **
52796190 ATATCCGGACTAAGATCCGAAGGCATTTGTG-TGAGTTTCT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCT-AGTGACT
* *
52796230 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
*
52796270 ATATCCGGGCTAAG-TCTCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGATC-CGAAGGCATTTGTGCTAGTGACT
* * * *
52796310 ATATTCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
52796350 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGAT-CCGAAG
52796371 ATACTTGGGT
Statistics
Matches: 154, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
38 1 0.01
39 14 0.09
40 134 0.87
41 5 0.03
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:52804450 original size:40 final size:40
Alignment explanation
Indices: 52804390--52804610 Score: 236
Period size: 40 Copynumber: 5.5 Consensus size: 40
52804380 TATTCGAATG
*
52804390 ATATCCGGGCTAAG-TCCCAAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * * * **
52804430 ATATCCGGACTAAGATCCAAAGGCATTTGTGCGAGTTTCT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
* * *
52804470 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
52804510 ATATCCGAGCTAAG-TCTCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGATC-CGAAGGCATTTATGCTAGTGACT
* * * *
52804550 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
52804590 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGAT-CCGAAG
52804611 ATACTTGGGT
Statistics
Matches: 154, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.01
39 13 0.08
40 136 0.88
41 4 0.03
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:52804593 original size:80 final size:78
Alignment explanation
Indices: 52804390--52804610 Score: 273
Period size: 80 Copynumber: 2.8 Consensus size: 78
52804380 TATTCGAATG
* * * *
52804390 ATATCCGGGCTAAGTCCCAAAGGCATTTATGCTAGTGACTATATCCGGACTAAGATCCAAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACTATATCCGG-CTAAG-TCCGAAGGCA
* **
52804455 TTTGTGCGAGTTTCT
64 TTTATGCGAGTGACT
*
52804470 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGAGCTAAGTCTCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACTATATCCG-GCTAAGTC-CGAAGGCA
*
52804535 TTTATGCTAGTGACT
64 TTTATGCGAGTGACT
* * *
52804550 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATATCCGGCTAAATCCCGAAG
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACTATATCCGGCTAAGT-CCGAAG
52804611 ATACTTGGGT
Statistics
Matches: 124, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
79 13 0.10
80 109 0.88
81 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (78 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACTATATCCGGCTAAGTCCGAAGGCATT
TATGCGAGTGACT
Found at i:52808218 original size:38 final size:38
Alignment explanation
Indices: 52808163--52808380 Score: 298
Period size: 38 Copynumber: 5.7 Consensus size: 38
52808153 GGCCTAAAGA
*
52808163 CCCGCAGGCTAT-ATGCTGG-AATTATATCCGGGTTAAAT
1 CCCGCAGGCT-TCGTGCTGGTAA-TATATCCGGGTTAAAT
**
52808201 CCTACAGGCTTCGTGCTGGTAATATATCCGGGACTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAATATATCCGGG--TTAAAT
52808241 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
*
52808279 CCCGCAGGCTTCTTGCT-GTAATATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
*
52808316 CCCGTAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
* * * *
52808354 CCTGCAGGCCTAGTGCTGGTATTATAT
1 CCCGCAGGCTTCGTGCTGGTAATATAT
52808381 TTGGGCCTTC
Statistics
Matches: 162, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.22
38 88 0.54
39 2 0.01
40 36 0.22
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
Found at i:52808341 original size:75 final size:77
Alignment explanation
Indices: 52808163--52808380 Score: 309
Period size: 75 Copynumber: 2.8 Consensus size: 77
52808153 GGCCTAAAGA
* *
52808163 CCCGCAGGCTAT-ATGCTGG-AATTATATCCGGGTTAAATCCTACAGGCTTCGTGCTGGTAATAT
1 CCCGCAGGCT-TCGTGCTGGTAA-TATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGGTAATAT
52808226 ATCCGGGACTTAAAT
64 ATCCGGGA-TTAAAT
* *
52808241 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCTTGCT-GTAATATAT
1 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGGTAATATAT
52808305 CCGGG-TTAAAT
66 CCGGGATTAAAT
* * * *
52808316 CCCGTAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCTGCAGGCCTAGTGCTGGTATTATAT
1 CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGGTAATATAT
52808381 TTGGGCCTTC
Statistics
Matches: 127, Mismatches: 10, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
75 56 0.44
76 8 0.06
77 15 0.12
78 46 0.36
79 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (77 bp):
CCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGGTAATATAT
CCGGGATTAAAT
Found at i:52808431 original size:43 final size:43
Alignment explanation
Indices: 52808378--52808575 Score: 351
Period size: 43 Copynumber: 4.6 Consensus size: 43
52808368 GCTGGTATTA
*
52808378 TATTTGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
52808421 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
52808464 TATTCGGGCCTTCGTGCCTAGCAGGCTTTGTGCCGATGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
52808507 TATTCGGGCCTTCGTGCCTAGCAAGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
52808550 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
52808576 GTAATGCCGG
Statistics
Matches: 147, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 147 1.00
ACGTcount: A:0.11, C:0.25, G:0.33, T:0.31
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:52811203 original size:41 final size:41
Alignment explanation
Indices: 52811158--52811325 Score: 126
Period size: 41 Copynumber: 4.1 Consensus size: 41
52811148 CCTTCAGAAT
* *
52811158 CAAGCCCAATTCTTAGCACTGGCTCAAAAGCCCTTCGAGAC
1 CAAGCCCAATTATGAGCACTGGCTCAAAAGCCCTTCGAGAC
** * * *
52811199 CAAGCTCGGATTA-GACCACTGGCTCGAAGGCCCTTCG-GAAC
1 CAAGC-CCAATTATGAGCACTGGCTCAAAAGCCCTTCGAG-AC
* * ** ** *
52811240 TAAGTCCGGTTATGA-CACTGGCTTTAAAGCCCTTCGAAAC
1 CAAGCCCAATTATGAGCACTGGCTCAAAAGCCCTTCGAGAC
* ** * *
52811280 TAAGTTCAGTTATTAGCACTGGCTCAAAAGCCCTTCGAGAC
1 CAAGCCCAATTATGAGCACTGGCTCAAAAGCCCTTCGAGAC
52811321 CAAGC
1 CAAGC
52811326 TCGGATTTAG
Statistics
Matches: 99, Mismatches: 23, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
40 38 0.38
41 57 0.58
42 4 0.04
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (41 bp):
CAAGCCCAATTATGAGCACTGGCTCAAAAGCCCTTCGAGAC
Found at i:52811272 original size:40 final size:41
Alignment explanation
Indices: 52811172--52811317 Score: 145
Period size: 41 Copynumber: 3.6 Consensus size: 41
52811162 CCCAATTCTT
* * *
52811172 AGCACTGGCTCAAAAGCCCTTCGAGACCAAG-CTCGGATTA-G
1 AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTC-CAG-TTATG
* * * * *
52811213 ACCACTGGCTCGAAGGCCCTTCGGAACTAAGTCCGGTTATG
1 AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTCCAGTTATG
** * *
52811254 A-CACTGGCTTTAAAGCCCTTCGAAACTAAGTTCAGTTATT
1 AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTCCAGTTATG
52811294 AGCACTGGCTCAAAAGCCCTTCGA
1 AGCACTGGCTCAAAAGCCCTTCGA
52811318 GACCAAGCTC
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
40 36 0.41
41 50 0.57
42 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTCCAGTTATG
Found at i:52841441 original size:30 final size:29
Alignment explanation
Indices: 52841407--52841466 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
52841397 TCCTTAACTC
52841407 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGG-AAAATTACAATTTTGCCCCT
* * * *
52841437 AAACTTTTGCAATTTACACTTTTGCCCCT
1 AAACTTTGGAAAATTACAATTTTGCCCCT
52841466 A
1 A
52841467 GGCCCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (29 bp):
AAACTTTGGAAAATTACAATTTTGCCCCT
Found at i:52843685 original size:10 final size:10
Alignment explanation
Indices: 52843672--52843706 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
52843662 AAGCTTGGTT
52843672 GAGCTCAAAC
1 GAGCTCAAAC
*
52843682 GAGCTGAAAC
1 GAGCTCAAAC
*
52843692 GAACTCAAAC
1 GAGCTCAAAC
52843702 GAGCT
1 GAGCT
52843707 AAATTGAGCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.40, C:0.26, G:0.23, T:0.11
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:52845240 original size:22 final size:22
Alignment explanation
Indices: 52845215--52845259 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
52845205 AACACATCAA
52845215 AATTTTTATGTGGAAAAATTTT
1 AATTTTTATGTGGAAAAATTTT
*
52845237 AATTTTTATGTGGACAAATTTT
1 AATTTTTATGTGGAAAAATTTT
52845259 A
1 A
52845260 TCACATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (22 bp):
AATTTTTATGTGGAAAAATTTT
Found at i:52845929 original size:15 final size:15
Alignment explanation
Indices: 52845909--52845965 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 15
52845899 TTTTCTTGCC
*
52845909 TCTCTTTTCTTTTGA
1 TCTCTTTTCTTTTCA
52845924 TCTCTTTTTTCTTTTCA
1 TCTC--TTTTCTTTTCA
52845941 TCT-TTTTCTTTTC-
1 TCTCTTTTCTTTTCA
*
52845954 TC-GTTTTCTTTT
1 TCTCTTTTCTTTT
52845966 TACAAGAGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
13 11 0.29
14 10 0.26
15 4 0.11
17 13 0.34
ACGTcount: A:0.04, C:0.21, G:0.04, T:0.72
Consensus pattern (15 bp):
TCTCTTTTCTTTTCA
Found at i:52845948 original size:14 final size:13
Alignment explanation
Indices: 52845924--52845965 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
52845914 TTTCTTTTGA
52845924 TCTCTTTTTTCTTT
1 TCTC-TTTTTCTTT
52845938 TCATCTTTTTCTTT
1 TC-TCTTTTTCTTT
*
52845952 TCTCGTTTTCTTT
1 TCTCTTTTTCTTT
52845965 T
1 T
52845966 TACAAGAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.42
14 13 0.50
15 2 0.08
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (13 bp):
TCTCTTTTTCTTT
Found at i:52845966 original size:14 final size:14
Alignment explanation
Indices: 52845930--52845965 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
52845920 TTGATCTCTT
*
52845930 TTTTCTTTTCATCT
1 TTTTCTTTTCATCG
52845944 TTTTCTTTTC-TCG
1 TTTTCTTTTCATCG
52845957 TTTTCTTTT
1 TTTTCTTTT
52845966 TACAAGAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (14 bp):
TTTTCTTTTCATCG
Found at i:52850581 original size:12 final size:12
Alignment explanation
Indices: 52850539--52850575 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
52850529 GAACTCTTTT
*
52850539 TCTTTTTCTATC
1 TCTTTTTCAATC
*
52850551 TCTTCTTCAATC
1 TCTTTTTCAATC
52850563 TCTTTTTCAATC
1 TCTTTTTCAATC
52850575 T
1 T
52850576 TATTTTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.14, C:0.27, G:0.00, T:0.59
Consensus pattern (12 bp):
TCTTTTTCAATC
Found at i:52850750 original size:18 final size:17
Alignment explanation
Indices: 52850723--52850757 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
52850713 TTCTTTTCTC
52850723 GTTTTCTTTTTACAAGA
1 GTTTTCTTTTTACAAGA
52850740 GTTTTCTTTTTACAAGA
1 GTTTTCTTTTTACAAGA
52850757 G
1 G
52850758 GTTAAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.51
Consensus pattern (17 bp):
GTTTTCTTTTTACAAGA
Found at i:52857815 original size:27 final size:27
Alignment explanation
Indices: 52857756--52857981 Score: 201
Period size: 27 Copynumber: 8.4 Consensus size: 27
52857746 AAACATACAT
***
52857756 CACAT-AGAGGCAAAATAGTCATCCAAC
1 CACATAAG-GGCAAAATAGTCATTTTAC
*
52857783 CACATAAGGGCAAAATAGTTATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
*
52857810 CTCATAAGGGCAAAATCA-TCATTTTAC
1 CACATAAGGGCAAAAT-AGTCATTTTAC
* * *
52857837 CATATAAGGGCAAAATCGTCATTTTAA
1 CACATAAGGGCAAAATAGTCATTTTAC
* * *
52857864 CACATAAGGGAAAAATAGTTATTTTGC
1 CACATAAGGGCAAAATAGTCATTTTAC
* *
52857891 CACATAAGGGCAAAACCA-TCATTTTAT
1 CACATAAGGGCAAAA-TAGTCATTTTAC
* *
52857918 CACATAAGGGAAAAATCA-TCATTTTAA
1 CACATAAGGGCAAAAT-AGTCATTTTAC
* *
52857945 CATATTAA-GGCAAAATAATCATTTTAC
1 CACA-TAAGGGCAAAATAGTCATTTTAC
**
52857972 CTTATAAGGG
1 CACATAAGGG
52857982 TATTTCAGTC
Statistics
Matches: 163, Mismatches: 28, Indels: 16
0.79 0.14 0.08
Matches are distributed among these distances:
26 4 0.02
27 152 0.93
28 7 0.04
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (27 bp):
CACATAAGGGCAAAATAGTCATTTTAC
Found at i:52857868 original size:81 final size:81
Alignment explanation
Indices: 52857783--52857981 Score: 274
Period size: 81 Copynumber: 2.5 Consensus size: 81
52857773 GTCATCCAAC
* * *
52857783 CACATAAGGGCAAAATAGTTATTTTACCTCATAAGGGCAAAATCATCATTTTACCATATAAGGGC
1 CACATAAGGGCAAAATAGTTATTTTACCTCATAAGGGCAAAACCATCATTTTACCACATAAGGGA
*
52857848 AAAATCGTCATTTTAA
66 AAAATCATCATTTTAA
* * * *
52857864 CACATAAGGGAAAAATAGTTATTTTGCCACATAAGGGCAAAACCATCATTTTATCACATAAGGGA
1 CACATAAGGGCAAAATAGTTATTTTACCTCATAAGGGCAAAACCATCATTTTACCACATAAGGGA
52857929 AAAATCATCATTTTAA
66 AAAATCATCATTTTAA
* * * *
52857945 CATATTAA-GGCAAAATAATCATTTTACCTTATAAGGG
1 CACA-TAAGGGCAAAATAGTTATTTTACCTCATAAGGG
52857982 TATTTCAGTC
Statistics
Matches: 102, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
81 99 0.97
82 3 0.03
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (81 bp):
CACATAAGGGCAAAATAGTTATTTTACCTCATAAGGGCAAAACCATCATTTTACCACATAAGGGA
AAAATCATCATTTTAA
Found at i:52857993 original size:27 final size:27
Alignment explanation
Indices: 52857963--52858132 Score: 245
Period size: 27 Copynumber: 6.3 Consensus size: 27
52857953 GGCAAAATAA
* **
52857963 TCATTTTACCTTATAAGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCAG
52857990 TCATTTTACCCTATGGGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCAG
* * *
52858017 TCATATTACCCTAT-GGGATATTTTAG
1 TCATTTTACCCTATGGGGGTATTTCAG
52858043 TCATTTTACCCTATGGGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCAG
* *
52858070 TCATTTTACCATATAGGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCAG
52858097 TCATTTTACCCTATGGGGGTATTTC-G
1 TCATTTTACCCTATGGGGGTATTTCAG
52858123 ATCATTTTAC
1 -TCATTTTAC
52858133 AAGTAAATAA
Statistics
Matches: 128, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
26 24 0.19
27 104 0.81
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCAG
Found at i:52858069 original size:80 final size:80
Alignment explanation
Indices: 52857963--52858113 Score: 248
Period size: 80 Copynumber: 1.9 Consensus size: 80
52857953 GGCAAAATAA
* * *
52857963 TCATTTTACCTTATAAGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCAGTCATATTACCC
1 TCATTTTACCCTATAAGGGTATTTCAGTCATTTTACCATATAGGGGTATTTCAGTCATATTACCC
52858028 TATGGGATATTTTAG
66 TATGGGATATTTTAG
** *
52858043 TCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCATATAGGGGTATTTCAGTCATTTTACCC
1 TCATTTTACCCTATAAGGGTATTTCAGTCATTTTACCATATAGGGGTATTTCAGTCATATTACCC
52858108 TATGGG
66 TATGGG
52858114 GGTATTTCGA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (80 bp):
TCATTTTACCCTATAAGGGTATTTCAGTCATTTTACCATATAGGGGTATTTCAGTCATATTACCC
TATGGGATATTTTAG
Found at i:52858988 original size:30 final size:30
Alignment explanation
Indices: 52858903--52858999 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
52858893 TAAACTAAAA
* *
52858903 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
52858933 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
52858963 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
52858992 ATGAGCTA
1 -TGAGCTA
52859000 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:52861268 original size:30 final size:29
Alignment explanation
Indices: 52861223--52861307 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 29
52861213 TTCTTTTGTT
*
52861223 TCAATTTCTTTTTCATCTTCTTTTTCATTC
1 TCAATTTCTTTTTCAT-TTCTTTTTCAATC
52861253 TCAAATTTC-TTTTCATTCTCTTTTTCAATC
1 TC-AATTTCTTTTTCATT-TCTTTTTCAATC
*
52861283 TCATTTTCTTTTTCATTTTCTTTTT
1 TCAATTTCTTTTTCA-TTTCTTTTT
52861308 GCTTTTCAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
29 6 0.12
30 35 0.71
31 8 0.16
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.65
Consensus pattern (29 bp):
TCAATTTCTTTTTCATTTCTTTTTCAATC
Found at i:52861306 original size:5 final size:6
Alignment explanation
Indices: 52861221--52861306 Score: 50
Period size: 6 Copynumber: 14.5 Consensus size: 6
52861211 GTTTCTTTTG
* * * * * *
52861221 TTTCAA TTTCTT TTTCAT CTTCTT TTTCAT TCTCAAA TTTC-T TTTCAT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTC-AT TTTCAT TTTCAT
* * * * *
52861269 TCTCTT TTTCAA TCTCAT TTTCTT TTTCAT TTTC-T TTT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTT
52861307 TGCTTTTCAA
Statistics
Matches: 57, Mismatches: 21, Indels: 5
0.69 0.25 0.06
Matches are distributed among these distances:
5 8 0.14
6 45 0.79
7 4 0.07
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTCAT
Found at i:52861307 original size:18 final size:18
Alignment explanation
Indices: 52861258--52861313 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
52861248 CATTCTCAAA
*
52861258 TTTC-TTTTCATTCTCTT
1 TTTCATTTTCATTTTCTT
* *
52861275 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
52861293 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
52861312 TT
1 TT
52861314 CAAAGGCTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 4 0.13
18 22 0.71
19 5 0.16
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:52861314 original size:12 final size:12
Alignment explanation
Indices: 52861221--52861307 Score: 59
Period size: 12 Copynumber: 7.2 Consensus size: 12
52861211 GTTTCTTTTG
*
52861221 TTTCAATTTCTT
1 TTTCATTTTCTT
*
52861233 TTTCATCTTCTT
1 TTTCATTTTCTT
* **
52861245 TTTCATTCTCAAA
1 TTTCATTTTC-TT
*
52861258 TTTC-TTTTCAT
1 TTTCATTTTCTT
* * **
52861269 TCTCTTTTTCAA
1 TTTCATTTTCTT
*
52861281 TCTCATTTTCTT
1 TTTCATTTTCTT
52861293 TTTCATTTTCTT
1 TTTCATTTTCTT
52861305 TTT
1 TTT
52861308 GCTTTTCAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
11 4 0.07
12 51 0.86
13 4 0.07
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTCATTTTCTT
Found at i:52861325 original size:12 final size:12
Alignment explanation
Indices: 52861310--52861340 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
52861300 TTCTTTTTGC
52861310 TTTTCAAAGGCT
1 TTTTCAAAGGCT
52861322 TTTTCAAAGGCT
1 TTTTCAAAGGCT
52861334 TTTTCAA
1 TTTTCAA
52861341 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:52861398 original size:5 final size:5
Alignment explanation
Indices: 52861388--52861444 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
52861378 CTCTTGCCTC
*
52861388 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
52861435 TCTTT TCTTT
1 TCTTT TCTTT
52861445 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:52861428 original size:15 final size:14
Alignment explanation
Indices: 52861388--52861444 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
52861378 CTCTTGCCTC
*
52861388 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
52861403 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
52861418 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
52861435 TCTTTTCTTT
1 TCTTTTCTTT
52861445 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Done.