Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 160 of 284
Found at i:53622003 original size:11 final size:11
Alignment explanation
Indices: 53621989--53622019 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
53621979 AAAATGTAGA
53621989 AAAACTAAGAG
1 AAAACTAAGAG
*
53622000 AAAACTTAGAG
1 AAAACTAAGAG
53622011 AAAACTAAG
1 AAAACTAAG
53622020 CCTAAAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.61, C:0.10, G:0.16, T:0.13
Consensus pattern (11 bp):
AAAACTAAGAG
Found at i:53622003 original size:22 final size:22
Alignment explanation
Indices: 53621978--53622019 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
53621968 AAACATTAGA
53621978 AAAAATGTAGA-AAAACTAAGAG
1 AAAAAT-TAGAGAAAACTAAGAG
*
53622000 AAAACTTAGAGAAAACTAAG
1 AAAAATTAGAGAAAACTAAG
53622020 CCTAAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.62, C:0.07, G:0.17, T:0.14
Consensus pattern (22 bp):
AAAAATTAGAGAAAACTAAGAG
Found at i:53634997 original size:17 final size:16
Alignment explanation
Indices: 53634968--53635022 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 16
53634958 TGAAGTTGGG
53634968 TTAAGAAAATAATTTAA
1 TTAA-AAAATAATTTAA
53634985 TTAAAAAATTAATTTAA
1 TTAAAAAA-TAATTTAA
53635002 TTAAACTAAATAA-TTAA
1 TTAAA--AAATAATTTAA
53635019 TTAA
1 TTAA
53635023 TTTATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.11
17 25 0.71
18 3 0.09
19 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
TTAAAAAATAATTTAA
Found at i:53635002 original size:22 final size:21
Alignment explanation
Indices: 53634977--53635026 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
53634967 GTTAAGAAAA
*
53634977 TAATTTAATTAAAAAATTAATT
1 TAATTTAACTAAAAAATTAA-T
* *
53634999 TAATTAAACTAAATAATTAAT
1 TAATTTAACTAAAAAATTAAT
53635020 TAATTTA
1 TAATTTA
53635027 TATATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATTTAACTAAAAAATTAAT
Found at i:53635437 original size:21 final size:21
Alignment explanation
Indices: 53635411--53635453 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
53635401 GGTTCGCTGT
*
53635411 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
53635432 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
53635453 A
1 A
53635454 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:53635453 original size:16 final size:16
Alignment explanation
Indices: 53635434--53635466 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53635424 TGTATTGGAT
*
53635434 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
53635450 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
53635466 T
1 T
53635467 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:53635511 original size:45 final size:44
Alignment explanation
Indices: 53635445--53635539 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
53635435 GGATTAGAGG
* *
53635445 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
53635490 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
53635534 TGTAAT
1 TGTAAT
53635540 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:53635722 original size:18 final size:17
Alignment explanation
Indices: 53635701--53635735 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53635691 TTATTATTTA
*
53635701 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
53635719 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53635736 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:53635729 original size:28 final size:27
Alignment explanation
Indices: 53635659--53635731 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
53635649 TTTATTATCA
*
53635659 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
53635687 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
53635714 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
53635732 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:53637352 original size:11 final size:11
Alignment explanation
Indices: 53637338--53637364 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
53637328 AAAAATCAAT
53637338 ACAAAAGTTTC
1 ACAAAAGTTTC
53637349 ACAAAAGTTTC
1 ACAAAAGTTTC
53637360 ACAAA
1 ACAAA
53637365 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:53639628 original size:15 final size:15
Alignment explanation
Indices: 53639608--53639638 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
53639598 ATATTATGTA
53639608 TAATTGAGGTAAAAT
1 TAATTGAGGTAAAAT
53639623 TAATTGAGGTAAAAT
1 TAATTGAGGTAAAAT
53639638 T
1 T
53639639 TGAAGGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.35
Consensus pattern (15 bp):
TAATTGAGGTAAAAT
Found at i:53647277 original size:28 final size:29
Alignment explanation
Indices: 53647229--53647294 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
53647219 TTTTTCCATC
*
53647229 TTGGTACCTAAAGTTCTTTTTATTAT-AA-
1 TTGGTACCTAAAGTTCCTTTT-TTATCAAG
*
53647257 TTGGTACCT-AAGTTACCTTTTTTCTCAAG
1 TTGGTACCTAAAGTT-CCTTTTTTATCAAG
53647286 TTGGTACCT
1 TTGGTACCT
53647295 CTTTTAGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 8 0.24
28 16 0.48
29 9 0.27
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.47
Consensus pattern (29 bp):
TTGGTACCTAAAGTTCCTTTTTTATCAAG
Found at i:53647447 original size:47 final size:47
Alignment explanation
Indices: 53647394--53647487 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
53647384 GGGTCACAAG
*
53647394 TGGTACCTAAACTATTCTTATATTACATATTTTACACAAACTGTTAT
1 TGGTACCTAAACTATTCTTATATTACATATTTTACACAAAATGTTAT
53647441 TGGTACCTAAACTATTCTTATATTACATATTTTACACAAAATGTTAT
1 TGGTACCTAAACTATTCTTATATTACATATTTTACACAAAATGTTAT
53647488 ACTTGTTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (47 bp):
TGGTACCTAAACTATTCTTATATTACATATTTTACACAAAATGTTAT
Found at i:53650320 original size:17 final size:17
Alignment explanation
Indices: 53650298--53650331 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53650288 TTAGAATTGG
53650298 ATTGAGAAAATTATTTA
1 ATTGAGAAAATTATTTA
*
53650315 ATTGAGAAATTTATTTA
1 ATTGAGAAAATTATTTA
53650332 TTTAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (17 bp):
ATTGAGAAAATTATTTA
Found at i:53656431 original size:43 final size:43
Alignment explanation
Indices: 53656359--53656544 Score: 228
Period size: 43 Copynumber: 4.3 Consensus size: 43
53656349 ACCGGTAAAG
** * *
53656359 AAAAACGCCGCTAAAGACAAGGACCTTTAGCGGCGCTTTTATA
1 AAAAACGCCGCTAAAGACCTGTACTTTTAGCGGCGCTTTTATA
* * *
53656402 AAAAACGCCGCTAAATACCTGTACTTTTAGCGGCACTTTTTTA
1 AAAAACGCCGCTAAAGACCTGTACTTTTAGCGGCGCTTTTATA
* * * * **
53656445 AAAAATGCCGCTAGAGACCTTTACTTATAGCGATGCTTTTATA
1 AAAAACGCCGCTAAAGACCTGTACTTTTAGCGGCGCTTTTATA
* *
53656488 AAAAACGCCGCTAAAGACCTGTACTTTTAGCGGTGCTTTTTTA
1 AAAAACGCCGCTAAAGACCTGTACTTTTAGCGGCGCTTTTATA
*
53656531 AAAAATGCCGCTAA
1 AAAAACGCCGCTAA
53656545 TTTGCCCAGT
Statistics
Matches: 120, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 120 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACCTGTACTTTTAGCGGCGCTTTTATA
Found at i:53656476 original size:86 final size:86
Alignment explanation
Indices: 53656386--53656543 Score: 271
Period size: 86 Copynumber: 1.8 Consensus size: 86
53656376 CAAGGACCTT
* *
53656386 TAGCGGCGCTTTTATAAAAAACGCCGCTAAATACCTGTACTTTTAGCGGCACTTTTTTAAAAAAT
1 TAGCGACGCTTTTATAAAAAACGCCGCTAAAGACCTGTACTTTTAGCGGCACTTTTTTAAAAAAT
53656451 GCCGCTAGAGACCTTTACTTA
66 GCCGCTAGAGACCTTTACTTA
* **
53656472 TAGCGATGCTTTTATAAAAAACGCCGCTAAAGACCTGTACTTTTAGCGGTGCTTTTTTAAAAAAT
1 TAGCGACGCTTTTATAAAAAACGCCGCTAAAGACCTGTACTTTTAGCGGCACTTTTTTAAAAAAT
53656537 GCCGCTA
66 GCCGCTA
53656544 ATTTGCCCAG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 67 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (86 bp):
TAGCGACGCTTTTATAAAAAACGCCGCTAAAGACCTGTACTTTTAGCGGCACTTTTTTAAAAAAT
GCCGCTAGAGACCTTTACTTA
Found at i:53657452 original size:18 final size:18
Alignment explanation
Indices: 53657420--53657457 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
53657410 TACAATATAG
53657420 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
53657439 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
53657456 TA
1 TA
53657458 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:53663845 original size:477 final size:478
Alignment explanation
Indices: 53662678--53663968 Score: 2521
Period size: 478 Copynumber: 2.7 Consensus size: 478
53662668 TTAAAATCAA
53662678 ATTTTGATAAAAATTATTTTTAACTTTTAAAGACATTTAAAAATATTAAATATTAAAATCACACA
1 ATTTTGATAAAAATTATTTTTAACTTTTAAAGACATTTAAAAATATTAAATATTAAAATCACACA
53662743 TTATTAATATAACAAAATAGTAATTTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTT
66 TTATTAATATAACAAAATAGTAATTTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTT
*
53662808 TATAAGTAAATTGGAAATAAATTAAGGTTATATAAATATTCAATAGCGATAGAACTTTTTTCAAT
131 TATAAGTAAATTGGAAATAAATTAAGGTTATATAAATATTCAATAGCGATCGAACTTTTTTCAAT
53662873 TCTTCTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATAT
196 TCTTCTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATAT
53662938 CTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATAT
261 CTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATAT
*
53663003 TTAAAATAAGGAATTGACAAGCAAGCTACATATATGGTAATAAAATTAATTCATACTTATTCATA
326 TTAAAATAAGGAATGGACAAGCAAGCTACATATATGGTAATAAAATTAATTCATACTTATTCATA
53663068 CTTAAGTTGAATCAAATAATAATTAAGTTGAACCAAAATATAAAAAACTTATTCATACTTATTCA
391 CTTAAGTTGAATCAAATAATAATTAAGTTGAACCAAAATATAAAAAACTTATTCATACTTATTCA
*
53663133 TACTTTAAATAATAATTAATACT
456 TACTTCAAATAATAATTAATACT
53663156 ATTTTGATAAAAATTATTTTTAACTTTTAAAGACATTTAAAAATATTAAATATTAAAATCACACA
1 ATTTTGATAAAAATTATTTTTAACTTTTAAAGACATTTAAAAATATTAAATATTAAAATCACACA
53663221 TTATTAATATAACAAAATAGTAATTTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTT
66 TTATTAATATAACAAAATAGTAATTTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTT
53663286 TATAAGTAAATTGGAAATAAATTAAGGTTATATAAATATTCAATAGCGATCGAACTTTTTTCAAT
131 TATAAGTAAATTGGAAATAAATTAAGGTTATATAAATATTCAATAGCGATCGAACTTTTTTCAAT
53663351 TCTTCTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATAT
196 TCTTCTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATAT
53663416 CTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATAT
261 CTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATAT
53663481 TTAAAATAAGGAATGGACAAGCAAGCTACATATATGGTAATAAAATTAATTCATACTTATTCATA
326 TTAAAATAAGGAATGGACAAGCAAGCTACATATATGGTAATAAAATTAATTCATACTTATTCATA
53663546 CTTAAGTTGAATCAAATAATAATTAAGTTGAACCAAAATAT-AAAAACTTATTCATACTTATTCA
391 CTTAAGTTGAATCAAATAATAATTAAGTTGAACCAAAATATAAAAAACTTATTCATACTTATTCA
53663610 TACTTCAAATAATAATTAATACT
456 TACTTCAAATAATAATTAATACT
* *
53663633 ATTTTGATAAAAATTAGTTATAACTTTTAAAGACATTTAAAAATATTAAATATTAAAATCACACA
1 ATTTTGATAAAAATTATTTTTAACTTTTAAAGACATTTAAAAATATTAAATATTAAAATCACACA
53663698 TTATTAATATAACAAAATAGTAATTTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTT
66 TTATTAATATAACAAAATAGTAATTTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTT
53663763 TATAAGTAAATTGGAAATAAATTAAGGTTATATAAATATTCAATAGCGATCGAACTTTTTTCAAT
131 TATAAGTAAATTGGAAATAAATTAAGGTTATATAAATATTCAATAGCGATCGAACTTTTTTCAAT
53663828 TCTTCTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATAT
196 TCTTCTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATAT
*
53663893 CTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTACAATAT
261 CTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATAT
53663958 TTAAAATAAGG
326 TTAAAATAAGG
53663969 TTGGAGAGAA
Statistics
Matches: 807, Mismatches: 6, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
477 378 0.47
478 429 0.53
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (478 bp):
ATTTTGATAAAAATTATTTTTAACTTTTAAAGACATTTAAAAATATTAAATATTAAAATCACACA
TTATTAATATAACAAAATAGTAATTTGAATATAATAATATCAAGAAAGAATCGTAGTTTAATTTT
TATAAGTAAATTGGAAATAAATTAAGGTTATATAAATATTCAATAGCGATCGAACTTTTTTCAAT
TCTTCTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATAT
CTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATAT
TTAAAATAAGGAATGGACAAGCAAGCTACATATATGGTAATAAAATTAATTCATACTTATTCATA
CTTAAGTTGAATCAAATAATAATTAAGTTGAACCAAAATATAAAAAACTTATTCATACTTATTCA
TACTTCAAATAATAATTAATACT
Found at i:53664227 original size:97 final size:98
Alignment explanation
Indices: 53664103--53664293 Score: 366
Period size: 98 Copynumber: 2.0 Consensus size: 98
53664093 CTTAAGTTGA
53664103 ATCAAATAATAATTAAGTTGAACCAAAATAT-AAAAACTTATTCATACTTATTCATACTTCAAAT
1 ATCAAATAATAATTAAGTTGAACCAAAATATAAAAAACTTATTCATACTTATTCATACTTCAAAT
53664167 AATAATTAATACTATTTTGATAAAAATTATTTT
66 AATAATTAATACTATTTTGATAAAAATTATTTT
*
53664200 ATCAAATAATAATTAAGTTGAACCAAAATATAAAAAACTTATTCATACTTATTCATACTTTAAAT
1 ATCAAATAATAATTAAGTTGAACCAAAATATAAAAAACTTATTCATACTTATTCATACTTCAAAT
53664265 AATAATTAATACTATTTTGATAAAAATTA
66 AATAATTAATACTATTTTGATAAAAATTA
53664294 GTTATAACTT
Statistics
Matches: 92, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
97 31 0.34
98 61 0.66
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (98 bp):
ATCAAATAATAATTAAGTTGAACCAAAATATAAAAAACTTATTCATACTTATTCATACTTCAAAT
AATAATTAATACTATTTTGATAAAAATTATTTT
Found at i:53668596 original size:15 final size:15
Alignment explanation
Indices: 53668576--53668607 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
53668566 AAATAATAAT
*
53668576 TTATATATATTTATC
1 TTATATACATTTATC
53668591 TTATATACATTTATC
1 TTATATACATTTATC
53668606 TT
1 TT
53668608 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:53669239 original size:25 final size:25
Alignment explanation
Indices: 53669211--53669264 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
53669201 TGAAAATTAT
53669211 ACATAGTTCAACAAATGCTAATTCC
1 ACATAGTTCAACAAATGCTAATTCC
53669236 ACATAGTTCAACAAATGCTAATTCC
1 ACATAGTTCAACAAATGCTAATTCC
53669261 ACAT
1 ACAT
53669265 TCAAAATCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (25 bp):
ACATAGTTCAACAAATGCTAATTCC
Found at i:53669739 original size:41 final size:40
Alignment explanation
Indices: 53669682--53669900 Score: 305
Period size: 41 Copynumber: 5.4 Consensus size: 40
53669672 GTTATATGAC
53669682 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GT
*
53669723 TTTTAGCGGCGTTTTACCAAAAGCGTCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GT
53669764 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTC-TGT
** *
53669805 TTTTAGCGGCGTTTTACTGAAGGCGCCGCTAATGCTCTGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
* * **
53669845 TTTTAGCGGCGTTTTTTACTAAAA-CTCCGCTGTTGCTCTGT
1 TTTTAGCGGCG--TTTTACCAAAAGCGCCGCTAATGCTCTGT
*
53669886 TTTTAGTGGCGTTTT
1 TTTTAGCGGCGTTTT
53669901 TCTTAGAACG
Statistics
Matches: 164, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
39 4 0.02
40 14 0.09
41 136 0.83
42 10 0.06
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
Found at i:53669915 original size:40 final size:40
Alignment explanation
Indices: 53669682--53669931 Score: 297
Period size: 41 Copynumber: 6.1 Consensus size: 40
53669672 GTTATATGAC
*
53669682 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCTCT-GT
* *
53669723 TTTTAGCGGCGTTTTACCAAAAGCGTCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCTCT-GT
*
53669764 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTGT
1 TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCTC-TGT
* *
53669805 TTTTAGCGGCGTTTTACTGAAGGCGCCGCTAATGCTCTGT
1 TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCTCTGT
* **
53669845 TTTTAGCGGCGTTTTTTACTAAAA-CTCCGCTGTTGCTCTGT
1 TTTTAGCGGCG--TTTTACTAAAAGCGCCGCTAATGCTCTGT
* * * * *
53669886 TTTTAGTGGCGTTTTTCTTAGAA-CGCCGCTATTGCTTTGT
1 TTTTAGCGGCGTTTTAC-TAAAAGCGCCGCTAATGCTCTGT
53669926 ATTTTA
1 -TTTTA
53669932 AAATTTTTGC
Statistics
Matches: 188, Mismatches: 16, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
39 5 0.03
40 32 0.17
41 141 0.75
42 10 0.05
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCTCTGT
Found at i:53670339 original size:21 final size:21
Alignment explanation
Indices: 53670289--53670340 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
53670279 AAGCCTTAAA
**
53670289 AATTTTAAAAGAATATATCTT
1 AATTTTAATTGAATATATCTT
53670310 AATTTTAATTGAATATATCTT
1 AATTTTAATTGAATATATCTT
53670331 AATTTTAATT
1 AATTTTAATT
53670341 TTATAGCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (21 bp):
AATTTTAATTGAATATATCTT
Found at i:53670841 original size:14 final size:14
Alignment explanation
Indices: 53670822--53670851 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53670812 TTATATCGAG
53670822 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
53670836 ACCAATCCAATTCA
1 ACCAATCCAAATCA
53670850 AC
1 AC
53670852 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:53670889 original size:23 final size:22
Alignment explanation
Indices: 53670844--53670889 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
53670834 CAACCAATCC
*
53670844 AATTCAACATATTTTCAAGATA
1 AATTCAACATATTTTCAAAATA
53670866 AATTCATACATATTTAT-AAAATA
1 AATTCA-ACATATTT-TCAAAATA
53670889 A
1 A
53670890 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.37
Consensus pattern (22 bp):
AATTCAACATATTTTCAAAATA
Found at i:53671977 original size:51 final size:51
Alignment explanation
Indices: 53671919--53672022 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
53671909 TGTTTGTAAA
53671919 TAGTAAAAATCTACTAATCCCGAACTTTTTCCTTTCCTTGATATAGCTTCG
1 TAGTAAAAATCTACTAATCCCGAACTTTTTCCTTTCCTTGATATAGCTTCG
53671970 TAGTAAAAATCTACTAATCCCGAACTTTTTCCTTTCCTTGATATAGCTTCG
1 TAGTAAAAATCTACTAATCCCGAACTTTTTCCTTTCCTTGATATAGCTTCG
53672021 TA
1 TA
53672023 TTTGAATCTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.39
Consensus pattern (51 bp):
TAGTAAAAATCTACTAATCCCGAACTTTTTCCTTTCCTTGATATAGCTTCG
Found at i:53678124 original size:14 final size:14
Alignment explanation
Indices: 53678105--53678134 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53678095 TTATATCGAG
53678105 ACCAATTCAAATCA
1 ACCAATTCAAATCA
*
53678119 ACCAATTCAATTCA
1 ACCAATTCAAATCA
53678133 AC
1 AC
53678135 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
ACCAATTCAAATCA
Found at i:53686431 original size:12 final size:12
Alignment explanation
Indices: 53686414--53686439 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53686404 GTTTTGTTTC
53686414 TTTTTATTTTAT
1 TTTTTATTTTAT
53686426 TTTTTATTTTAT
1 TTTTTATTTTAT
53686438 TT
1 TT
53686440 CTATTAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:53687574 original size:6 final size:6
Alignment explanation
Indices: 53687528--53687556 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
53687518 AAAAAGAATC
53687528 AAAAGA AAAAGA AAAAGA AAAAGA AAAAG
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAG
53687557 TATAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:53695864 original size:17 final size:18
Alignment explanation
Indices: 53695842--53695887 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
53695832 ACTAGTTATA
*
53695842 GCCCGATAAATGAA-AGT
1 GCCCGATAAATGAATAAT
*
53695859 GCCCGATCAAT-AATAAT
1 GCCCGATAAATGAATAAT
53695876 GCCCGATAAATG
1 GCCCGATAAATG
53695888 GTAAATGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 22 0.92
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (18 bp):
GCCCGATAAATGAATAAT
Found at i:53698851 original size:49 final size:48
Alignment explanation
Indices: 53698716--53698970 Score: 225
Period size: 49 Copynumber: 5.2 Consensus size: 48
53698706 TTTCAAACAT
* *
53698716 GGTCTTACACTGGCTCTCAC-ATCTAAGTCGATGCCATGTCCCAAACA
1 GGTCTTACACTGGCTCTCACTATCTGAGTCGATGCCATGTCCCAGACA
* * *
53698763 AGTCTTACACTGACT-T-A-TATACATCGAGGCTGATGCCATGTCCCAGACA
1 GGTCTTACACTGGCTCTCACTAT-C-T-GAGTC-GATGCCATGTCCCAGACA
* * *
53698812 GGTCTTACACTGGCTCTCACTTATCTGTGTCGATACCATGTCCCCGACA
1 GGTCTTACACTGGCTCTCAC-TATCTGAGTCGATGCCATGTCCCAGACA
* * * * *
53698861 GGTCTTACACTAGCT-TGCA-TATCTAGAGGCCGATGCTATGTCCCAAATA
1 GGTCTTACACTGGCTCT-CACTATCT-GA-GTCGATGCCATGTCCCAGACA
* * * *
53698910 GGTTTTACACTAGCTCTCACTTATCTGTGTCGATGCCATGTCCTAGACA
1 GGTCTTACACTGGCTCTCAC-TATCTGAGTCGATGCCATGTCCCAGACA
*
53698959 AGTCTTACACTG
1 GGTCTTACACTG
53698971 ACACACACAT
Statistics
Matches: 164, Mismatches: 29, Indels: 28
0.74 0.13 0.13
Matches are distributed among these distances:
45 3 0.02
46 2 0.01
47 19 0.12
48 5 0.03
49 118 0.72
50 6 0.04
51 7 0.04
52 1 0.01
53 3 0.02
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (48 bp):
GGTCTTACACTGGCTCTCACTATCTGAGTCGATGCCATGTCCCAGACA
Found at i:53698866 original size:98 final size:97
Alignment explanation
Indices: 53698709--53698972 Score: 329
Period size: 98 Copynumber: 2.7 Consensus size: 97
53698699 CACCATGTTT
** *
53698709 CAAACATGGTCTTACACTGGCTCTCAC--ATCTAAGTCGATGCCATGTCCCAAACAAGTCTTACA
1 CAAACA-GGTCTTACACTGGCTCTCACTTATCTGTGTCGATGCCATGTCCCAGACAAGTCTTACA
* *
53698772 CTGACTT-ATATACATCGAGGCTGATGCCATGTCC
65 CTGACTTCATAT-C-TAGAGGCCGATGCCATGTCC
* * * *
53698806 CAGACAGGTCTTACACTGGCTCTCACTTATCTGTGTCGATACCATGTCCCCGACAGGTCTTACAC
1 CAAACAGGTCTTACACTGGCTCTCACTTATCTGTGTCGATGCCATGTCCCAGACAAGTCTTACAC
*
53698871 T-AGCTTGCATATCTAGAGGCCGATGCTATGTCC
66 TGA-CTT-CATATCTAGAGGCCGATGCCATGTCC
* * * *
53698904 CAAATAGGTTTTACACTAGCTCTCACTTATCTGTGTCGATGCCATGTCCTAGACAAGTCTTACAC
1 CAAACAGGTCTTACACTGGCTCTCACTTATCTGTGTCGATGCCATGTCCCAGACAAGTCTTACAC
53698969 TGAC
66 TGAC
53698973 ACACACATCA
Statistics
Matches: 143, Mismatches: 18, Indels: 11
0.83 0.10 0.06
Matches are distributed among these distances:
96 20 0.14
97 6 0.04
98 111 0.78
99 2 0.01
100 4 0.03
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (97 bp):
CAAACAGGTCTTACACTGGCTCTCACTTATCTGTGTCGATGCCATGTCCCAGACAAGTCTTACAC
TGACTTCATATCTAGAGGCCGATGCCATGTCC
Found at i:53708268 original size:20 final size:22
Alignment explanation
Indices: 53708228--53708270 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
53708218 TTGTAATTAA
53708228 ATTATTTTTATAATTACTTTTG
1 ATTATTTTTATAATTACTTTTG
*
53708250 ATTATTTTT-T-ATTATTTTTG
1 ATTATTTTTATAATTACTTTTG
53708270 A
1 A
53708271 CAGATTTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 1 0.05
22 9 0.45
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (22 bp):
ATTATTTTTATAATTACTTTTG
Found at i:53710644 original size:59 final size:59
Alignment explanation
Indices: 53709790--53710620 Score: 1646
Period size: 59 Copynumber: 14.1 Consensus size: 59
53709780 AACTTTATTT
53709790 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
1 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
53709849 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
1 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
53709908 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
1 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
53709967 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
1 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
53710026 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
1 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
53710085 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
1 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
53710144 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
1 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
53710203 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
1 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
53710262 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
1 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
53710321 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
1 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
53710380 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
1 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
53710439 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
1 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
53710498 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
1 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
*
53710557 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAAAT-AAAA
1 TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
53710615 TATTTT
1 TATTTT
53710621 TTCTTCACCA
Statistics
Matches: 771, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
58 10 0.01
59 761 0.99
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (59 bp):
TATTTTATTTGTTTTACTTTGTTAAAATTCTAGTTTTTAATCACCTCTTCAACTCAAAA
Found at i:53724650 original size:35 final size:35
Alignment explanation
Indices: 53724604--53724673 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
53724594 AAGGAAGTAA
*
53724604 AAAACCAAGTAGCAGACCGCTTGTCTAGATTGGAG
1 AAAACCAAGTAGCAGACCGCTTGTCCAGATTGGAG
53724639 AAAACCAAGTAGCAGACCGCTTGTCCAGATTGGAG
1 AAAACCAAGTAGCAGACCGCTTGTCCAGATTGGAG
53724674 CCACAAGAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (35 bp):
AAAACCAAGTAGCAGACCGCTTGTCCAGATTGGAG
Found at i:53726466 original size:22 final size:19
Alignment explanation
Indices: 53726440--53726479 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 19
53726430 ATAATCATTT
53726440 ATATATAATTATATCTATTATA
1 ATATAT-ATTA-AT-TATTATA
53726462 ATATATATTAATTATTAT
1 ATATATATTAATTATTAT
53726480 CAACTTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 4 0.22
22 6 0.33
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATATATTAATTATTATA
Found at i:53727158 original size:8 final size:8
Alignment explanation
Indices: 53727134--53727184 Score: 84
Period size: 8 Copynumber: 6.1 Consensus size: 8
53727124 TTCTCCTAAA
53727134 TTTTAATTT
1 TTTTAA-TT
53727143 TATTTAATT
1 T-TTTAATT
53727152 TTTTAATT
1 TTTTAATT
53727160 TTTTAATT
1 TTTTAATT
53727168 TTTTAATT
1 TTTTAATT
53727176 TTTTAATT
1 TTTTAATT
53727184 T
1 T
53727185 ATTGAATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
8 32 0.78
9 4 0.10
10 5 0.12
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTAATT
Found at i:53727197 original size:24 final size:24
Alignment explanation
Indices: 53727141--53727198 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
53727131 AAATTTTAAT
*
53727141 TTTATTTAATTTTTTAATTTTTTAA
1 TTTA-TTAATTTTTTAATTTTTGAA
*
53727166 TTTTTTAATTTTTTAATTTATTGAA
1 TTTATTAATTTTTTAATTT-TTGAA
53727191 -TTATTAAT
1 TTTATTAAT
53727199 AGTTTATACT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 22 0.76
25 7 0.24
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTATTAATTTTTTAATTTTTGAA
Found at i:53730042 original size:27 final size:27
Alignment explanation
Indices: 53729992--53730045 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
53729982 ATATATAATT
53729992 ATTATAAAATAATCATTTTGTAATTAA
1 ATTATAAAATAATCATTTTGTAATTAA
* *
53730019 ATTATTAACATAATGATTTT-TAATTAA
1 ATTA-TAAAATAATCATTTTGTAATTAA
53730046 TTTTATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (27 bp):
ATTATAAAATAATCATTTTGTAATTAA
Found at i:53730051 original size:28 final size:29
Alignment explanation
Indices: 53729987--53730051 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
53729977 AAAAAATATA
53729987 TAATTATTA-TAAAATAATCATTTTGTAAT
1 TAATT-TTATTAAAATAATCATTTTGTAAT
* * *
53730016 TAA-ATTATTAACATAATGATTTT-TAAT
1 TAATTTTATTAAAATAATCATTTTGTAAT
53730043 TAATTTTAT
1 TAATTTTAT
53730052 AATTACTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
27 10 0.33
28 17 0.57
29 3 0.10
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (29 bp):
TAATTTTATTAAAATAATCATTTTGTAAT
Found at i:53735927 original size:23 final size:26
Alignment explanation
Indices: 53735900--53735952 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 26
53735890 TAAATACATG
**
53735900 TTATTTTGTTTGAAT-TGA-ATGT-T
1 TTATTTTAATTGAATATGACATGTGT
53735923 TTATTTTAATTGAATATGACATGTGT
1 TTATTTTAATTGAATATGACATGTGT
53735949 TTAT
1 TTAT
53735953 GTGAATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 13 0.52
24 3 0.12
25 4 0.16
26 5 0.20
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (26 bp):
TTATTTTAATTGAATATGACATGTGT
Found at i:53736819 original size:31 final size:31
Alignment explanation
Indices: 53736781--53736851 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
53736771 TTAGGCAGAT
53736781 TGCTAATTTGTTTGGAAGCATAATATTATTA
1 TGCTAATTTGTTTGGAAGCATAATATTATTA
* *
53736812 TGCTAATTTGTTTTGAAGCATGATATTATTA
1 TGCTAATTTGTTTGGAAGCATAATATTATTA
*
53736843 TGCTTATTT
1 TGCTAATTT
53736852 AAATCAGTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.49
Consensus pattern (31 bp):
TGCTAATTTGTTTGGAAGCATAATATTATTA
Found at i:53739175 original size:27 final size:26
Alignment explanation
Indices: 53739135--53739194 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
53739125 ACATATATAT
* *
53739135 ATATCTATTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
53739161 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
53739188 ATATCTG
1 ATATCTG
53739195 GCAGCCTCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:53741771 original size:16 final size:17
Alignment explanation
Indices: 53741750--53741790 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
53741740 AAGTGGCCTT
53741750 CTATTTG-TTAAAGTGC
1 CTATTTGTTTAAAGTGC
53741766 CTATTTGTTATTAAAGTGC
1 CTATTTG-T-TTAAAGTGC
53741785 CTATTT
1 CTATTT
53741791 ATTATGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
19 15 0.68
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (17 bp):
CTATTTGTTTAAAGTGC
Found at i:53741779 original size:19 final size:19
Alignment explanation
Indices: 53741757--53741795 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
53741747 CTTCTATTTG
*
53741757 TTAAAGTGCCTATTTGTTA
1 TTAAAGTGCCTATTTATTA
53741776 TTAAAGTGCCTATTTATTA
1 TTAAAGTGCCTATTTATTA
53741795 T
1 T
53741796 GTCTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (19 bp):
TTAAAGTGCCTATTTATTA
Found at i:53742778 original size:40 final size:40
Alignment explanation
Indices: 53742714--53742824 Score: 118
Period size: 40 Copynumber: 2.8 Consensus size: 40
53742704 ACTATGTTCG
* * *
53742714 GCACTAAGTGTGC-AATTTGAAATAGCTTCGGTTATA-AATA
1 GCACTAAGTGTGCGAA-ATGGAATAGCTTCGGCTATATAA-A
* *
53742754 GCACTAAGTGTGCGAAATGGAATAGCTTTGGCTATATAAG
1 GCACTAAGTGTGCGAAATGGAATAGCTTCGGCTATATAAA
* *
53742794 GCACTAAGTGTGCGATATCGAGATAGCTTCG
1 GCACTAAGTGTGCGAAATGGA-ATAGCTTCG
53742825 ATTTATTGGA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
40 48 0.80
41 12 0.20
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (40 bp):
GCACTAAGTGTGCGAAATGGAATAGCTTCGGCTATATAAA
Found at i:53745861 original size:14 final size:15
Alignment explanation
Indices: 53745837--53745866 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
53745827 GGATATCAAA
53745837 ACAAGAATTAAGAAC
1 ACAAGAATTAAGAAC
53745852 ACAA-AATTAAGAAC
1 ACAAGAATTAAGAAC
53745866 A
1 A
53745867 AGTTAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.63, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
ACAAGAATTAAGAAC
Found at i:53753259 original size:27 final size:27
Alignment explanation
Indices: 53753229--53753406 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
53753219 ATATCGAGTC
* * * *
53753229 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
53753256 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
53753283 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
53753311 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
53753338 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
53753365 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
53753392 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53753407 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:53753368 original size:82 final size:81
Alignment explanation
Indices: 53753250--53753405 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
53753240 TGCTATATAA
*
53753250 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
53753315 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
53753332 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
53753396 CACTTAGTGC
65 CACTTAGTGC
53753406 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:53767043 original size:17 final size:17
Alignment explanation
Indices: 53767018--53767054 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
53767008 GATAAGTATA
*
53767018 CATTATCATTGCATTTT
1 CATTATCATTACATTTT
*
53767035 CATTGTCATTACATTTT
1 CATTATCATTACATTTT
53767052 CAT
1 CAT
53767055 GTTAGTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.51
Consensus pattern (17 bp):
CATTATCATTACATTTT
Found at i:53771128 original size:94 final size:94
Alignment explanation
Indices: 53770968--53771138 Score: 227
Period size: 94 Copynumber: 1.8 Consensus size: 94
53770958 GGGTTACAAT
* * * *
53770968 AACCTAAGTTTATTGATTTATGATCATGAACAATCTTCTTTGAGTTAGCTAATTTACAATCACAA
1 AACCTAAGTTCATTGATTTACGATCATGAACAATCTTCTCTAAGTTAGCTAATTTACAATCACAA
*
53771033 CTCCAAATAGCTTGCTGATTTACAATCAC
66 CTCCAAACAGCTTGCTGATTTACAATCAC
* ** ** *
53771062 AACCTAAGTTCATTGATTTACGATCATGAACAATCTT-TCCTAAGTTAGTTGGTTTATGATCGCA
1 AACCTAAGTTCATTGATTTACGATCATGAACAATCTTCT-CTAAGTTAGCTAATTTACAATCACA
53771126 ACTCCAAACAGCT
65 ACTCCAAACAGCT
53771139 CGTTGACTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
93 1 0.02
94 64 0.98
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (94 bp):
AACCTAAGTTCATTGATTTACGATCATGAACAATCTTCTCTAAGTTAGCTAATTTACAATCACAA
CTCCAAACAGCTTGCTGATTTACAATCAC
Found at i:53771155 original size:94 final size:94
Alignment explanation
Indices: 53770968--53771158 Score: 222
Period size: 94 Copynumber: 2.0 Consensus size: 94
53770958 GGGTTACAAT
* * * *
53770968 AACCTAAGTTTATTGATTTATGATCATGAACAATCTTCTTTGAGTTAGCTAATTTACAATCACAA
1 AACCTAAGTTCATTGATTTACGATCATGAACAATCTTCTCTAAGTTAGCTAATTTACAATCACAA
* * *
53771033 CTCCAAATAGCTTGCTGATTTACAATCAC
66 CTCCAAACAGCTCGCTGACTTACAATCAC
* ** ** *
53771062 AACCTAAGTTCATTGATTTACGATCATGAACAATCTT-TCCTAAGTTAGTTGGTTTATGATCGCA
1 AACCTAAGTTCATTGATTTACGATCATGAACAATCTTCT-CTAAGTTAGCTAATTTACAATCACA
* **
53771126 ACTCCAAACAGCTCGTTGACTTATGATCAC
65 ACTCCAAACAGCTCGCTGACTTACAATCAC
53771156 AAC
1 AAC
53771159 TGATATTATT
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
93 1 0.01
94 79 0.99
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (94 bp):
AACCTAAGTTCATTGATTTACGATCATGAACAATCTTCTCTAAGTTAGCTAATTTACAATCACAA
CTCCAAACAGCTCGCTGACTTACAATCAC
Found at i:53771203 original size:130 final size:130
Alignment explanation
Indices: 53771041--53771320 Score: 352
Period size: 130 Copynumber: 2.2 Consensus size: 130
53771031 AACTCCAAAT
*
53771041 AGCTTGCTGATTTACAATCACAACCTAAGTTCATTGATTTACGATCATGAACAATCTT-TCCTAA
1 AGCTTGTTGATTTACAATCACAACCTAAGTTCATTGATTTACGATCATGAACAATCTTCT-CTAA
* * * * * *
53771105 GTTAGTTGGTTTA-TGATCGCAACTCCAAACAGCTCGTTGACTTATGATCACAACTGATATTATT
65 GTTAGCTGATTTACT-ATCGCAACTCCAAACAACTCGCTAACTTATGATCACAACCGATATTATT
53771169 -A
129 AA
* * * *
53771170 AGACTTGTTGATTTA-AGATCACAGCCTAAGTTCATTGATTTACGATCATGAATAGTCTTCTCTG
1 AG-CTTGTTGATTTACA-ATCACAACCTAAGTTCATTGATTTACGATCATGAACAATCTTCTCTA
* * *
53771234 AGTTAGCTGATTTACTATTGCAACTCCAAACAACTTGCTAATTTATGATCACAACCGATATTATT
64 AGTTAGCTGATTTACTATCGCAACTCCAAACAACTCGCTAACTTATGATCACAACCGATATTATT
53771299 AA
129 AA
* *
53771301 AGCTCGTTGATTTACTATCA
1 AGCTTGTTGATTTACAATCA
53771321 TGAATAATCT
Statistics
Matches: 129, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
129 3 0.02
130 121 0.94
131 5 0.04
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (130 bp):
AGCTTGTTGATTTACAATCACAACCTAAGTTCATTGATTTACGATCATGAACAATCTTCTCTAAG
TTAGCTGATTTACTATCGCAACTCCAAACAACTCGCTAACTTATGATCACAACCGATATTATTAA
Found at i:53771388 original size:103 final size:103
Alignment explanation
Indices: 53771204--53771423 Score: 271
Period size: 103 Copynumber: 2.1 Consensus size: 103
53771194 CCTAAGTTCA
* * * *
53771204 TTGATTTACGATCATGAATAGTCTTCTCTGAGTTAGCTGATTTACTATTGCAACTCCAAACAACT
1 TTGATTTACGATCATGAATAATCTTCTCTGAGTTAGCTGACTTACGATCGCAACTCCAAACAACT
*
53771269 TGCTAATTTATGATCACAACCGATATTATTAAAGCTCG
66 TGCTAATTTATAATCACAACCGATATTATTAAAGCTCG
* * * * * *
53771307 TTGATTTACTATCATGAATAATCTTTTTTTAGTTAGTTGACTTACGATCGCAAC-CCTAAACAAT
1 TTGATTTACGATCATGAATAATCTTCTCTGAGTTAGCTGACTTACGATCGCAACTCC-AAACAAC
* * * *
53771371 TTGCTGATTTATAATCACAACTGATATTATTAATGCTCA
65 TTGCTAATTTATAATCACAACCGATATTATTAAAGCTCG
**
53771410 CAGATTTACGATCA
1 TTGATTTACGATCA
53771424 CAACCTAAGT
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
102 2 0.02
103 96 0.98
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (103 bp):
TTGATTTACGATCATGAATAATCTTCTCTGAGTTAGCTGACTTACGATCGCAACTCCAAACAACT
TGCTAATTTATAATCACAACCGATATTATTAAAGCTCG
Found at i:53771425 original size:233 final size:224
Alignment explanation
Indices: 53770968--53771490 Score: 514
Period size: 233 Copynumber: 2.3 Consensus size: 224
53770958 GGGTTACAAT
* *
53770968 AACCTAAGTTTATTGATTTATGATCATGAACAATCTTCTTTGAGTTAGCTAATTTACAATCACAA
1 AACCTAAGTTTATTGATTTACGATCATGAACAATCTTCTCTGAGTTAGCTAATTTACAATCACAA
* * * *
53771033 CTCCAAATAGCTTGCTGATTTACAATCACAACCTAAGTTCATTGATTTACGATCATGAACAATCT
66 CTCCAAACAACTTGCTAATTTACAATCACAACCTAAGCTCATTGATTTACGATCATGAACAATCT
** * * * *
53771098 TTCCTAAGTTAGTTGGTTTATGATCGCAACTCCAAACAGCTCGTTGACTTATGATCACAACTGAT
131 TTCCTAAGTTAGTTGACTTACGATCGCAACTCCAAACAACTCGCTGACTTATAATCACAACTGAT
****
53771163 ATTATTAAGACTTGTTGATTTAAGATCAC
196 ATTATTAAGACTCACAGATTTAAGATCAC
* * * * * * **
53771192 AGCCTAAGTTCATTGATTTACGATCATGAATAGTCTTCTCTGAGTTAGCTGATTTACTATTGCAA
1 AACCTAAGTTTATTGATTTACGATCATGAACAATCTTCTCTGAGTTAGCTAATTTACAATCACAA
** * *
53771257 CTCCAAACAACTTGCTAATTTATGATCACAACCGATATTATTAAAGCTCGTTGATTTACTATCAT
66 CTCCAAACAACTTGCTAATTTACAATCACAACC--------T-AAGCTCATTGATTTACGATCAT
* ** * * * *
53771322 GAATAATCTTTTTTTAGTTAGTTGACTTACGATCGCAAC-CCTAAACAATTTGCTGATTTATAAT
122 GAACAATCTTTCCTAAGTTAGTTGACTTACGATCGCAACTCC-AAACAACTCGCTGACTTATAAT
*
53771386 CACAACTGATATTATTAATG-CTCACAGATTTACGATCAC
186 CACAACTGATATTATTAA-GACTCACAGATTTAAGATCAC
* * * * * * * *
53771425 AACCTAAGTTTACTAATTTACAATCATGAAAAATTTTGTC-GAGTTAGC-ATATTTGCGATCACA
1 AACCTAAGTTTATTGATTTACGATCATGAACAATCTTCTCTGAGTTAGCTA-ATTTACAATCACA
53771488 ACT
65 ACT
53771491 TAGGTACGTT
Statistics
Matches: 237, Mismatches: 50, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
224 83 0.35
232 23 0.10
233 130 0.55
234 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (224 bp):
AACCTAAGTTTATTGATTTACGATCATGAACAATCTTCTCTGAGTTAGCTAATTTACAATCACAA
CTCCAAACAACTTGCTAATTTACAATCACAACCTAAGCTCATTGATTTACGATCATGAACAATCT
TTCCTAAGTTAGTTGACTTACGATCGCAACTCCAAACAACTCGCTGACTTATAATCACAACTGAT
ATTATTAAGACTCACAGATTTAAGATCAC
Found at i:53774824 original size:80 final size:80
Alignment explanation
Indices: 53774691--53774838 Score: 251
Period size: 80 Copynumber: 1.9 Consensus size: 80
53774681 GCAAACACCT
* *
53774691 TTGCCTTCGGGTCTTAACCCGGACATACCAACTTGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCATAACCCGGACATACCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
53774756 TATCATCTCGCATAA
66 TATCATCTCGCATAA
* **
53774771 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCATAACCCGGACATACCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
53774836 TAT
66 TAT
53774839 TTCAAATGCT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 63 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (80 bp):
TTGCCTTCGGGTCATAACCCGGACATACCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
TATCATCTCGCATAA
Found at i:53774839 original size:40 final size:40
Alignment explanation
Indices: 53774691--53774838 Score: 224
Period size: 40 Copynumber: 3.7 Consensus size: 40
53774681 GCAAACACCT
* * *
53774691 TTGCCTTCGGGTCTTAACCCGGACATACCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
* *
53774731 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
* *
53774771 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
*
53774811 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGACATAT
53774839 TTCAAATGCT
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 97 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
Found at i:53781104 original size:57 final size:58
Alignment explanation
Indices: 53780987--53781121 Score: 139
Period size: 57 Copynumber: 2.3 Consensus size: 58
53780977 GTCATACATT
* * * * ** * *
53780987 TTACAGTAGGATTACCAGTCCAGGCTAAATCCTATTTGTAACATATGCTCTAGAGAGC
1 TTACATTAGGATTACCCGTCCAGGCCAAATCCAATTTACAACATAAGCTCAAGAGAGC
* * *
53781045 TTA-A-TATGGATTACCCGTCCAGGCCAAATCCAATTTACATCCTAAGCTCAAGAGGGC
1 TTACATTA-GGATTACCCGTCCAGGCCAAATCCAATTTACAACATAAGCTCAAGAGAGC
*
53781102 TTACATTAGAATTACCCGTC
1 TTACATTAGGATTACCCGTC
53781122 TGGGCTAAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
56 2 0.03
57 44 0.70
58 15 0.24
59 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (58 bp):
TTACATTAGGATTACCCGTCCAGGCCAAATCCAATTTACAACATAAGCTCAAGAGAGC
Found at i:53782262 original size:5 final size:5
Alignment explanation
Indices: 53782252--53782279 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
53782242 TGATGCCAAC
53782252 AATAA AATAA AATAA AATAA AATAA AAT
1 AATAA AATAA AATAA AATAA AATAA AAT
53782280 TTTATTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:53788055 original size:28 final size:28
Alignment explanation
Indices: 53788013--53788066 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
53788003 GAAAAAAGCG
*
53788013 TAAAAGTATACTTTTTAGTACCCAAGGA
1 TAAAAGTATAATTTTTAGTACCCAAGGA
53788041 TAAAAGTATAATTTTTAGTACCCAAG
1 TAAAAGTATAATTTTTAGTACCCAAG
53788067 ATGTGTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (28 bp):
TAAAAGTATAATTTTTAGTACCCAAGGA
Found at i:53794241 original size:3 final size:3
Alignment explanation
Indices: 53794235--53794272 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
53794225 AATAATAATA
*
53794235 ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
53794273 ATACGAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:53795994 original size:124 final size:124
Alignment explanation
Indices: 53795850--53796093 Score: 353
Period size: 124 Copynumber: 2.0 Consensus size: 124
53795840 CCATGGCCCA
* *
53795850 AAGCCAAATCAAGGTGATTTATATCTAAAATACTGATATAATGGCCTAAAGCCAAATCAGCCGAT
1 AAGCCAAATCAAGGTAATTTATATCTAAAATACTGATATAATGGCCCAAAGCCAAATCAGCCGAT
* * ** *
53795915 ATTCATGGCCCAAATCCAAATCGGTATAACTCATACCCGAAGTGAAAATATCATGTCCG
66 ATTCATCGCCCAAAGCCAAATCCATATAACTCACACCCGAAGTGAAAATATCATGTCCG
* * *
53795974 AAGCCAAATCAAGGTAATTTATATCTGAAATACTGATATCATGGCCCAAAGCCAAATCAGTCGAT
1 AAGCCAAATCAAGGTAATTTATATCTAAAATACTGATATAATGGCCCAAAGCCAAATCAGCCGAT
* ** * *
53796039 ATTCATCGCTCGGAGCCAAATCCATATAACTCACACCTGAAGTGCAAATATCATG
66 ATTCATCGCCCAAAGCCAAATCCATATAACTCACACCCGAAGTGAAAATATCATG
53796094 GCCTGAAGGG
Statistics
Matches: 105, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
124 105 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (124 bp):
AAGCCAAATCAAGGTAATTTATATCTAAAATACTGATATAATGGCCCAAAGCCAAATCAGCCGAT
ATTCATCGCCCAAAGCCAAATCCATATAACTCACACCCGAAGTGAAAATATCATGTCCG
Found at i:53797040 original size:13 final size:13
Alignment explanation
Indices: 53797024--53797050 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53797014 CTATGTACAT
53797024 AAATGTCCAATCA
1 AAATGTCCAATCA
53797037 AAATGTCCAATCA
1 AAATGTCCAATCA
53797050 A
1 A
53797051 CTAAACAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.22
Consensus pattern (13 bp):
AAATGTCCAATCA
Found at i:53798296 original size:24 final size:24
Alignment explanation
Indices: 53798244--53798413 Score: 218
Period size: 25 Copynumber: 7.0 Consensus size: 24
53798234 GCTTTATCAT
* *
53798244 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTC
* *
53798269 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTC
*
53798293 ATAATTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TC
*
53798318 ATAACTGGGGCATAAGCCCTTCATC
1 ATAACTGGGGCATAAGCCCTT-TTC
53798343 ATAACTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TC
*
53798368 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTC
53798391 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
53798414 GCACTTCCTC
Statistics
Matches: 130, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
23 20 0.15
24 33 0.25
25 77 0.59
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTC
Found at i:53798485 original size:9 final size:9
Alignment explanation
Indices: 53798471--53798527 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
53798461 ATCTCATGTG
53798471 CATATCATA
1 CATATCATA
*
53798480 CATATCATGTG
1 CATATCA--TA
53798491 CATATCATA
1 CATATCATA
* *
53798500 CATGTCATGTG
1 CATATCA--TA
53798511 CATATCATA
1 CATATCATA
53798520 CATATCAT
1 CATATCAT
53798528 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:53798487 original size:20 final size:20
Alignment explanation
Indices: 53798459--53798529 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
53798449 GCATTTACAA
*
53798459 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
53798479 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
53798499 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
53798519 ACATATCATGT
1 ACATATCATGT
53798530 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:53798494 original size:11 final size:11
Alignment explanation
Indices: 53798464--53798518 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
53798454 TACAAACATC
53798464 TCATGTGCATA
1 TCATGTGCATA
*
53798475 TCA--TACATA
1 TCATGTGCATA
53798484 TCATGTGCATA
1 TCATGTGCATA
* *
53798495 TCA--TACATG
1 TCATGTGCATA
53798504 TCATGTGCATA
1 TCATGTGCATA
53798515 TCAT
1 TCAT
53798519 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:53798594 original size:25 final size:25
Alignment explanation
Indices: 53798566--53798613 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
53798556 ATATATAAAC
* *
53798566 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
53798591 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
53798614 CATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:53799137 original size:14 final size:14
Alignment explanation
Indices: 53799105--53799146 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
53799095 ACACCTGATT
53799105 TGCGATAT-TCCT-
1 TGCGATATCTCCTA
53799117 TGACGATATCTCCTA
1 TG-CGATATCTCCTA
*
53799132 TGCGATTTCTCCTA
1 TGCGATATCTCCTA
53799146 T
1 T
53799147 AATCAACCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 2 0.08
13 6 0.23
14 16 0.62
15 2 0.08
ACGTcount: A:0.19, C:0.26, G:0.14, T:0.40
Consensus pattern (14 bp):
TGCGATATCTCCTA
Found at i:53799835 original size:27 final size:27
Alignment explanation
Indices: 53799773--53799850 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
53799763 GGGCATATTC
53799773 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
53799800 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGGG-TATTACG
* *
53799827 GTCTTTTTACC-TAATAGGGGTATT
1 GTCATTTTACCAT-ACAGGGGTATT
53799851 TTAGTCATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.05
27 40 0.93
28 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:53800091 original size:27 final size:27
Alignment explanation
Indices: 53799896--53800147 Score: 152
Period size: 27 Copynumber: 9.3 Consensus size: 27
53799886 TCTACAAACT
*
53799896 AAGGGTATTTTAGTAATTTTGTAAACC
1 AAGGGTATTTTAGTAATTTTGTAAATC
*
53799923 AATGGTATTTCTA-TAATTTT-TAGAAAGTC
1 AAGGGTATTT-TAGTAATTTTGT--AAA-TC
*
53799952 AAGGGTATTTCT-GTAACTTTGTAAATC
1 AAGGGTATTT-TAGTAATTTTGTAAATC
* * * ** *
53799979 AGGGGTATGTTAATAATTTTACAAATT
1 AAGGGTATTTTAGTAATTTTGTAAATC
* ** *** *
53800006 GAGGGTATTTCGGTAATTTCACAAACC
1 AAGGGTATTTTAGTAATTTTGTAAATC
* **
53800033 AAGGGTATTTTGGTAATTTTACAAA-C
1 AAGGGTATTTTAGTAATTTTGTAAATC
53800059 TAAGGGTATTTTAGTAATTTTGTAAATC
1 -AAGGGTATTTTAGTAATTTTGTAAATC
* **** *
53800087 GAGGGTAAAACAGTAATTCTGTAAATC
1 AAGGGTATTTTAGTAATTTTGTAAATC
*** *
53800114 AAGGGTAAAATAGTAGTTTTGTAAATC
1 AAGGGTATTTTAGTAATTTTGTAAATC
*
53800141 GAGGGTA
1 AAGGGTA
53800148 AAACGATAAT
Statistics
Matches: 179, Mismatches: 37, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.02
27 148 0.83
28 9 0.05
29 18 0.10
30 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (27 bp):
AAGGGTATTTTAGTAATTTTGTAAATC
Found at i:53800092 original size:54 final size:54
Alignment explanation
Indices: 53799868--53800093 Score: 204
Period size: 54 Copynumber: 4.1 Consensus size: 54
53799858 TTTCATCCTA
* * * *
53799868 CAAGGGTGTTTTGGTAAATCTACAAACTAAGGGTATTTTAGTAATTTTGTAAAC
1 CAAGGGTATTTTGATAATTTTACAAACTAAGGGTATTTTAGTAATTTTGTAAAC
* * * * *
53799922 CAATGGTATTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTCT-GTAACTTTGTAAAT
1 CAAGGGTATTT-TGATAA-TTTTACAAACT-AAGGGTATTT-TAGTAATTTTGTAAAC
* * * * * ** ***
53799978 CAGGGGTATGTTAATAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTGATAATTTTACAAACTAAGGGTATTTTAGTAATTTTGTAAAC
* *
53800032 CAAGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTTAGTAATTTTGTAAAT
1 CAAGGGTATTTTGATAATTTTACAAACTAAGGGTATTTTAGTAATTTTGTAAAC
*
53800086 CGAGGGTA
1 CAAGGGTA
53800094 AAACAGTAAT
Statistics
Matches: 132, Mismatches: 34, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
54 79 0.60
55 18 0.14
56 34 0.26
57 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (54 bp):
CAAGGGTATTTTGATAATTTTACAAACTAAGGGTATTTTAGTAATTTTGTAAAC
Found at i:53800148 original size:27 final size:27
Alignment explanation
Indices: 53800070--53800255 Score: 173
Period size: 27 Copynumber: 6.9 Consensus size: 27
53800060 AAGGGTATTT
*
53800070 TAGTAATTTTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* *
53800097 CAGTAATTCTGTAAATCAAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* *
53800124 TAGTAGTTTTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* *
53800151 -CGATAATTCTGTAAATCAAGGGTAAAA
1 TAG-TAATTCTGTAAATCGAGGGTAAAA
** * *
53800178 CGGTAATTCTATAAGTCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
*
53800205 T-GATAATTATGTAAATC-AGGGGTAAAA
1 TAG-TAATTCTGTAAATCGA-GGGTAAAA
* * *
53800232 -CGATAATTCTATAAATCGGGGGTA
1 TAG-TAATTCTGTAAATCGAGGGTA
53800256 CTTTGGTAAT
Statistics
Matches: 131, Mismatches: 22, Indels: 12
0.79 0.13 0.07
Matches are distributed among these distances:
26 3 0.02
27 127 0.97
28 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (27 bp):
TAGTAATTCTGTAAATCGAGGGTAAAA
Found at i:53800218 original size:81 final size:81
Alignment explanation
Indices: 53800073--53800248 Score: 239
Period size: 81 Copynumber: 2.2 Consensus size: 81
53800063 GGTATTTTAG
* * * * *
53800073 TAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAATAGTAGTTTTGTAA
1 TAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAATAGTAATTATGTAA
53800138 ATC-GAGGGTAAAACGA
66 ATCAG-GGGTAAAACGA
* * *
53800154 TAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAGTCGAGGGTAAAAT-GATAATTATGTA
1 TAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAATAG-TAATTATGTA
53800218 AATCAGGGGTAAAACGA
65 AATCAGGGGTAAAACGA
*
53800235 TAATTCTATAAATC
1 TAATTCTGTAAATC
53800249 GGGGGTACTT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
80 1 0.01
81 82 0.98
82 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (81 bp):
TAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAATAGTAATTATGTAA
ATCAGGGGTAAAACGA
Found at i:53800232 original size:54 final size:53
Alignment explanation
Indices: 53800072--53800255 Score: 224
Period size: 54 Copynumber: 3.4 Consensus size: 53
53800062 GGGTATTTTA
* * * **
53800072 GTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAATA
1 GTAATTCTATAAATCGAGGGTAAAAGA-TAATTCTGTAAATCAAGGGTAAAACG
* * *
53800126 GTAGTTTTGTAAATCGAGGGTAAAACGATAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAA-GATAATTCTGTAAATCAAGGGTAAAACG
* * *
53800180 GTAATTCTATAAGTCGAGGGTAAAATGATAATTATGTAAATCAGGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAA-GATAATTCTGTAAATCAAGGGTAAAACG
* *
53800234 ATAATTCTATAAATCGGGGGTA
1 GTAATTCTATAAATCGAGGGTA
53800256 CTTTGGTAAT
Statistics
Matches: 115, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
54 114 0.99
55 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (53 bp):
GTAATTCTATAAATCGAGGGTAAAAGATAATTCTGTAAATCAAGGGTAAAACG
Found at i:53800282 original size:27 final size:27
Alignment explanation
Indices: 53800261--53800350 Score: 112
Period size: 27 Copynumber: 3.3 Consensus size: 27
53800251 GGGTACTTTG
*
53800261 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
*
53800288 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
* *
53800315 GTATTTTTACAAA-CTAAGCGTATTTC-
1 GTAATTTTACAAATCGAAG-GTATTTCA
53800341 GATAATTTTA
1 G-TAATTTTA
53800351 GTAAACTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
26 4 0.07
27 51 0.93
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAATCGAAGGTATTTCA
Found at i:53800293 original size:81 final size:81
Alignment explanation
Indices: 53800081--53800282 Score: 194
Period size: 81 Copynumber: 2.5 Consensus size: 81
53800071 AGTAATTTTG
* * ** * * *
53800081 TAAATCGAGGGTAAAACAGTAATTCTGTAAATC-AAGGGTAAAAT-AGTAGTTTTGTAAATCGAG
1 TAAATCAAGGGTAAAACGGTAATTCTACAAGTCGAA-GGTAAAATCA-TAATTATGTAAATCGAG
*
53800144 GGTAAAACGATAATTCTG
64 GGTAAAACGATAATTCTA
* * *
53800162 TAAATCAAGGGTAAAACGGTAATTCTATAAGTCGAGGGTAAAATGATAATTATGTAAATC-AGGG
1 TAAATCAAGGGTAAAACGGTAATTCTACAAGTCGAAGGTAAAATCATAATTATGTAAATCGA-GG
53800226 GTAAAACGATAATTCTA
65 GTAAAACGATAATTCTA
** **** *
53800243 TAAATCGGGGGTACTTTGGTAATTTTACAAGTCGAAGGTA
1 TAAATCAAGGGTAAAACGGTAATTCTACAAGTCGAAGGTA
53800283 TTTCAGTAAT
Statistics
Matches: 101, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
80 1 0.01
81 98 0.97
82 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (81 bp):
TAAATCAAGGGTAAAACGGTAATTCTACAAGTCGAAGGTAAAATCATAATTATGTAAATCGAGGG
TAAAACGATAATTCTA
Found at i:53800309 original size:81 final size:81
Alignment explanation
Indices: 53800136--53800309 Score: 172
Period size: 81 Copynumber: 2.1 Consensus size: 81
53800126 GTAGTTTTGT
* * *
53800136 AAATCGAGGGTAAAACGATAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAGTCGAGGGT
1 AAATCGAGGGTAAAACGATAATTCTATAAATCAAGGGTAAAACGGTAATTCTACAAGTCGAAGGT
* **
53800201 AAAATGATAATTATGT
66 AAAATCATAATTATAC
** **** *
53800217 AAATC-AGGGGTAAAACGATAATTCTATAAATCGGGGGTACTTTGGTAATTTTACAAGTCGAAGG
1 AAATCGA-GGGTAAAACGATAATTCTATAAATCAAGGGTAAAACGGTAATTCTACAAGTCGAAGG
** *
53800281 T-ATTTCAGTAATTTTAC
65 TAAAATCA-TAATTATAC
53800298 AAATCGAGGGTA
1 AAATCGAGGGTA
53800310 TTTCAGTATT
Statistics
Matches: 74, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
80 4 0.05
81 69 0.93
82 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (81 bp):
AAATCGAGGGTAAAACGATAATTCTATAAATCAAGGGTAAAACGGTAATTCTACAAGTCGAAGGT
AAAATCATAATTATAC
Found at i:53802819 original size:52 final size:53
Alignment explanation
Indices: 53802762--53802865 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 53
53802752 GCTAGACTTG
* * * * * *
53802762 TAGGGAATGGTTACACATAGAAAGAAGGCGTCGATTACGATGAGAC-TTTTTC
1 TAGGGAAAGGCTACACACAAAAAAAAGGCATCGATTACGATGAGACATTTTTC
* *
53802814 TAGGGAAAGGCTACACACAAAAAAAAGGCATCGATTATGATGATACATTTTT
1 TAGGGAAAGGCTACACACAAAAAAAAGGCATCGATTACGATGAGACATTTTT
53802866 TCTGGTAGCA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
52 38 0.88
53 5 0.12
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (53 bp):
TAGGGAAAGGCTACACACAAAAAAAAGGCATCGATTACGATGAGACATTTTTC
Found at i:53812901 original size:13 final size:13
Alignment explanation
Indices: 53812883--53812907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53812873 GATATAAATT
53812883 CACACAAAATAAA
1 CACACAAAATAAA
53812896 CACACAAAATAA
1 CACACAAAATAA
53812908 TTTTTAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:53813865 original size:20 final size:18
Alignment explanation
Indices: 53813840--53813886 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
53813830 TATATTTTAG
53813840 GTATGTGTGAAATCTTGATT
1 GTATGTGTGAAATCTT--TT
* *
53813860 GTATGTG-CAAATGTTTT
1 GTATGTGTGAAATCTTTT
53813877 GTATGTGTGA
1 GTATGTGTGA
53813887 GCATGTTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
19 6 0.26
20 7 0.30
ACGTcount: A:0.23, C:0.04, G:0.28, T:0.45
Consensus pattern (18 bp):
GTATGTGTGAAATCTTTT
Found at i:53814582 original size:19 final size:19
Alignment explanation
Indices: 53814558--53814597 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
53814548 ATTAATTTTG
53814558 ATCAAGTAAAATTA-AATTA
1 ATCAAGT-AAATTACAATTA
*
53814577 ATCAAGTCAATTACAATTA
1 ATCAAGTAAATTACAATTA
53814596 AT
1 AT
53814598 ATGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
ATCAAGTAAATTACAATTA
Found at i:53815087 original size:67 final size:69
Alignment explanation
Indices: 53815014--53815147 Score: 173
Period size: 67 Copynumber: 2.0 Consensus size: 69
53815004 TTTTAATAGT
* * * ** * *
53815014 TTAATATTGAATTTAATTTAATACTTATCTTAAT-AGTATT-TTTTAATTTAATATTGAAGTGAT
1 TTAATATTAAATTTAATCTAATACTTATCTTAATAAATATTATAGTAAATTAATATTAAAGTGAT
53815077 TATC
66 TATC
* *
53815081 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATAGTAAATTAATATTAAAGTGAT
1 TTAATATTAAATTTAATCTAATACTTATCTTAATAAATATTATAGTAAATTAATATTAAAGTGAT
53815146 TA
66 TA
53815148 AGTTTAATTA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
67 30 0.54
68 5 0.09
69 21 0.38
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (69 bp):
TTAATATTAAATTTAATCTAATACTTATCTTAATAAATATTATAGTAAATTAATATTAAAGTGAT
TATC
Found at i:53820190 original size:27 final size:26
Alignment explanation
Indices: 53820154--53820225 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
53820144 TTAAGAGTGC
* *
53820154 GCCACGAAGGCTTTCTTTACGGAGTT-T
1 GCCACAAAGGCTTTCTTT-CAGA-TTAT
* * *
53820181 GTCACAAAGGCATTCTTTCATATTAT
1 GCCACAAAGGCTTTCTTTCAGATTAT
53820207 GCCACAAAGGCTTTCTTTC
1 GCCACAAAGGCTTTCTTTC
53820226 CGAACATGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
25 2 0.05
26 20 0.54
27 15 0.41
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (26 bp):
GCCACAAAGGCTTTCTTTCAGATTAT
Found at i:53828169 original size:70 final size:70
Alignment explanation
Indices: 53828056--53828194 Score: 260
Period size: 70 Copynumber: 2.0 Consensus size: 70
53828046 GGGACTAAAT
* *
53828056 CCGATAAAGGGATGGAAAAAGTGGTCGAATAGCCATCGGAATCGTTCGACAACATCCGAGGTAAG
1 CCGATAAAGGGAAGGAAAAAGTGGTCGAATAGCCATCGGAATCGTTCAACAACATCCGAGGTAAG
53828121 TTTTC
66 TTTTC
53828126 CCGATAAAGGGAAGGAAAAAGTGGTCGAATAGCCATCGGAATCGTTCAACAACATCCGAGGTAAG
1 CCGATAAAGGGAAGGAAAAAGTGGTCGAATAGCCATCGGAATCGTTCAACAACATCCGAGGTAAG
53828191 TTTT
66 TTTT
53828195 TGAGTAATGG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.21
Consensus pattern (70 bp):
CCGATAAAGGGAAGGAAAAAGTGGTCGAATAGCCATCGGAATCGTTCAACAACATCCGAGGTAAG
TTTTC
Found at i:53828476 original size:40 final size:40
Alignment explanation
Indices: 53828382--53828526 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
53828372 TACTCGAATG
*
53828382 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
53828423 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
53828463 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
53828503 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
53828527 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:53836531 original size:40 final size:40
Alignment explanation
Indices: 53836437--53836581 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
53836427 TACTCGAATG
*
53836437 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
53836478 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
53836518 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
53836558 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
53836582 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:53839153 original size:48 final size:45
Alignment explanation
Indices: 53839048--53839276 Score: 154
Period size: 48 Copynumber: 4.8 Consensus size: 45
53839038 AAGGGTAAAT
* * * **
53839048 TGCCGATGCCATGTCCCAGACATGGTCTTACAGTGGCTCAT-ATGT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACACTAGCTC-TCATAA
** *
53839093 TGAGGTAGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTGTCAA
1 T--GCCA-ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTC--AT-AA
** * *
53839144 TGCCAATGCCATGTCCTGGACATGGCCTTACTCTAGCTCTCATAATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-A-A
* * * * *
53839191 TAGCCGATGCCATGTTCCAAACATGGTCTTACACTGGATCTCATAA
1 T-GCCAATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAA
* * *
53839237 TGTCGCCAATGCCATGTTCCAAATATGGTCTTACACTAGC
1 --T-GCCAATGCCATGTCCCAGACATGGTCTTACACTAGC
53839277 ACACATATCA
Statistics
Matches: 143, Mismatches: 30, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
45 1 0.01
46 3 0.02
47 5 0.03
48 130 0.91
49 2 0.01
50 1 0.01
51 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (45 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAA
Found at i:53844452 original size:49 final size:49
Alignment explanation
Indices: 53844344--53844476 Score: 162
Period size: 49 Copynumber: 2.7 Consensus size: 49
53844334 TCACATCTAA
* * *
53844344 GTCGATGCCATGTCCCAAACAGGCCTTACACTAACTTTCATATATCGAG
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTAACTCTCATATATCGAG
* * * *
53844393 GCCGAAGCCATGTCCCAGACAGGTCTTACACTAGCTCTCGCT-TATC-AG
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTAACTCTC-ATATATCGAG
*
53844441 TGTCGATGCCATGTCCTAGACAGGTCTTACACTAAC
1 -GTCGATGCCATGTCCCAGACAGGTCTTACACTAAC
53844477 ACACCTCAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
48 2 0.03
49 68 0.96
50 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (49 bp):
GTCGATGCCATGTCCCAGACAGGTCTTACACTAACTCTCATATATCGAG
Found at i:53858975 original size:29 final size:28
Alignment explanation
Indices: 53858893--53858976 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
53858883 AACACACCAG
* *
53858893 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
53858921 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
53858949 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
53858977 GCATAAAGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:53858982 original size:29 final size:27
Alignment explanation
Indices: 53858879--53858976 Score: 123
Period size: 28 Copynumber: 3.7 Consensus size: 27
53858869 AAATGTCCAA
53858879 CCAAAACACACCAG----TATAATCCT
1 CCAAAACACACCAGAATATATAATCCT
*
53858902 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAGAAT-ATATAATCCT
*
53858930 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAGAAT-ATATAATCC-T
53858959 CCAAAACACACCAGAATA
1 CCAAAACACACCAGAATA
53858977 GCATAAAGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.22
28 34 0.52
29 17 0.26
ACGTcount: A:0.47, C:0.33, G:0.04, T:0.16
Consensus pattern (27 bp):
CCAAAACACACCAGAATATATAATCCT
Found at i:53861147 original size:22 final size:22
Alignment explanation
Indices: 53861121--53861899 Score: 1449
Period size: 22 Copynumber: 35.4 Consensus size: 22
53861111 CCAGCACATA
53861121 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861143 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
***
53861165 TTCATAG-AA---TCAAGAACT
1 TTCATAGAAACTTTCAATTTCT
**
53861183 AATGAATTTAGAAACTTTCAATTTCT
1 --TTCA--TAGAAACTTTCAATTTCT
53861209 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861231 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861253 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861275 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861297 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861319 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861341 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861363 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861385 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861407 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861429 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861451 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861473 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861495 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861517 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861539 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861561 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861583 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861605 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861627 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861649 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861671 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861693 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861715 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861737 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861759 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861781 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861803 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861825 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861847 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861869 TTCATAGAAACTTTCAATTTCT
1 TTCATAGAAACTTTCAATTTCT
53861891 TTCATAGAA
1 TTCATAGAA
53861900 TCAAGAACTA
Statistics
Matches: 739, Mismatches: 10, Indels: 16
0.97 0.01 0.02
Matches are distributed among these distances:
18 6 0.01
20 2 0.00
21 2 0.00
22 719 0.97
23 2 0.00
24 2 0.00
26 6 0.01
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (22 bp):
TTCATAGAAACTTTCAATTTCT
Found at i:53869686 original size:101 final size:100
Alignment explanation
Indices: 53869507--53869688 Score: 249
Period size: 101 Copynumber: 1.8 Consensus size: 100
53869497 GAACTGTTAT
* * * * *
53869507 TTAAAAAATTGTGTAGATAAAATACAATAGGATGTTCATAGTTTAGTTAAAGTTGTATTAACTGA
1 TTAAAAAATTGTGTAGATAAAATAAAATAGGAAGTTCATAGTTCAGTTAAAATTGAATTAACTGA
* *
53869572 GAGAATGAGTCTAATTCGATCAATGGAGCTCCTAG
66 CAAAATGAGTCTAATTCGATCAATGGAGCTCCTAG
* * *
53869607 TTAAAAAATTGTGTAGTTAGAATAAAATAGGGAAGTTCATAGTTCAGTTAAAATTGAATTAATTG
1 TTAAAAAATTGTGTAGATAAAATAAAATA-GGAAGTTCATAGTTCAGTTAAAATTGAATTAACTG
53869672 ACAAAATCGA-TCTAATT
65 ACAAAAT-GAGTCTAATT
53869689 TGGTTAATCT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
100 26 0.37
101 42 0.60
102 2 0.03
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.34
Consensus pattern (100 bp):
TTAAAAAATTGTGTAGATAAAATAAAATAGGAAGTTCATAGTTCAGTTAAAATTGAATTAACTGA
CAAAATGAGTCTAATTCGATCAATGGAGCTCCTAG
Found at i:53872206 original size:3 final size:3
Alignment explanation
Indices: 53872198--53872261 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
53872188 TGATGTGTTC
*
53872198 AAT AAT AAT AAT AAT AAT AAT AAT AAT -GT AGAT AAAT ACAT AA- AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT -AAT A-AT AAT AAT
*
53872243 AAT GAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
53872262 ACTAAGGAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
2 7 0.13
3 38 0.73
4 6 0.12
5 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:53874026 original size:6 final size:6
Alignment explanation
Indices: 53874015--53874142 Score: 256
Period size: 6 Copynumber: 21.3 Consensus size: 6
53874005 TACCCATCGT
53874015 ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA
1 ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA
53874063 ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA
1 ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA
53874111 ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA AT
1 ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA AT
53874143 AATACAATTT
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 122 1.00
ACGTcount: A:0.34, C:0.33, G:0.00, T:0.34
Consensus pattern (6 bp):
ATCCTA
Found at i:53874374 original size:22 final size:23
Alignment explanation
Indices: 53874346--53874393 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
53874336 TAAATTTTTA
* *
53874346 AAATTTTT-TAAATATAAA-TAT
1 AAATTTTTAAAAATAAAAATTAT
53874367 AAATTTTTAAAAATAAAAATTAT
1 AAATTTTTAAAAATAAAAATTAT
53874390 AAAT
1 AAAT
53874394 AAAAAATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 8 0.35
23 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATTTTTAAAAATAAAAATTAT
Found at i:53877518 original size:31 final size:31
Alignment explanation
Indices: 53877480--53877540 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
53877470 TAAAATGATT
*
53877480 ATTAAATTATTCGAAAATTCTTATTTAAATG
1 ATTAAATTATTCAAAAATTCTTATTTAAATG
* *
53877511 ATTAAATTATTTAAAAATTTTTATTTAAAT
1 ATTAAATTATTCAAAAATTCTTATTTAAAT
53877541 TATTGAGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (31 bp):
ATTAAATTATTCAAAAATTCTTATTTAAATG
Found at i:53890155 original size:24 final size:26
Alignment explanation
Indices: 53890127--53890175 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
53890117 CTTGTTTTAA
* *
53890127 TATTTG-TTT-TTATGTTTTGAAATG
1 TATTTGATTTATTATATTTTAAAATG
53890151 TATTTGATTTATTATATTTTAAAAT
1 TATTTGATTTATTATATTTTAAAAT
53890176 TTTTATTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (26 bp):
TATTTGATTTATTATATTTTAAAATG
Found at i:53898233 original size:17 final size:17
Alignment explanation
Indices: 53898211--53898247 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
53898201 CTTATTCTCG
53898211 AATAAGCAATTTATCAC
1 AATAAGCAATTTATCAC
53898228 AATAAGCAATTTATCAC
1 AATAAGCAATTTATCAC
53898245 AAT
1 AAT
53898248 CATTTATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (17 bp):
AATAAGCAATTTATCAC
Found at i:53904483 original size:23 final size:23
Alignment explanation
Indices: 53904452--53904509 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
53904442 ATATAGATTA
* *
53904452 TATAGATTTTATTATAT-ATTTT
1 TATATATTTTATTATATGATTTG
53904474 TATAT-TATTTATTATATGATTTG
1 TATATAT-TTTATTATATGATTTG
53904497 TATATATTTTATT
1 TATATATTTTATT
53904510 TGTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 1 0.03
22 14 0.45
23 15 0.48
24 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (23 bp):
TATATATTTTATTATATGATTTG
Found at i:53904484 original size:22 final size:22
Alignment explanation
Indices: 53904459--53904505 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
53904449 TTATATAGAT
*
53904459 TTTATTATAT-ATTTTTATATTA
1 TTTATTATATGATTTGTATA-TA
53904481 TTTATTATATGATTTGTATATA
1 TTTATTATATGATTTGTATATA
53904503 TTT
1 TTT
53904506 TATTTGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (22 bp):
TTTATTATATGATTTGTATATA
Found at i:53916939 original size:207 final size:206
Alignment explanation
Indices: 53916577--53917458 Score: 1334
Period size: 207 Copynumber: 4.3 Consensus size: 206
53916567 GCAGATCTGG
* * * * *
53916577 CTGAAGCAAGATCCAAGATGATTTGACATCCTTGTGCTTACAAGGAAAAAATCAAAATCATAGTT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCATTGTGCTTACAAGGAACAAATCAAGA-CATAGCT
* * *
53916642 GATTTGGCTTTCACGTGCTTATGATGAAGCAAATCTAAGATGATTTGGCATATCTGTATTGTTAG
65 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
** * * * *
53916707 AGAACAAATCAAAGTTTACCGTCTCCATATTCGATGGAGAGCAGGCACATAGTAGATCTGACCTT
130 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
* *
53916772 CAGATGTTTATA
195 CAGATGATTAGA
* * *
53916784 CTGAAGCAAGATCCAAGATAATTTGGCATCATTGTGCTTACAAGGAACATATCAAGGACATAACT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCATTGTGCTTACAAGGAACAAATCAA-GACATAGCT
* *
53916849 AATTTGGCTTTCACGTGCTCACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
65 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
**
53916914 AGAACAAATTGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
130 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
53916979 CAGATGATTAGA
195 CAGATGATTAGA
* *
53916991 CTGAAGC-AG-----AGATGATTTGGCATCATTGTGTTTACAAGGAACAAATCAAAATCATAGCT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCATTGTGCTTACAAGGAACAAATCAAGA-CATAGCT
*
53917050 GATTTGGCTTTCACGTGCTTACGATAAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
65 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
53917115 AGAACAAA-CAAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGG-CTT
130 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
* *
53917178 CAGATGTTTATA
195 CAGATGATTAGA
*
53917190 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGATTTGGCATCATTGTGCTTACAAGGAACAAATC-AAGACATAGCT
*
53917255 GATTTGGCTTTCACGTGCTTGCGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
65 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * *
53917320 AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGGAGACACATAGCAGATCTGGCCTA
130 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
53917385 CAGATGATTAGA
195 CAGATGATTAGA
*
53917397 CTGAAGC-AGATCCAAGATGATTTGGCATTC-TTGTGTTTACAAGGAACAAATCGAAGACATAG
1 CTGAAGCAAGATCCAAGATGATTTGGCA-TCATTGTGCTTACAAGGAACAAATC-AAGACATAG
53917459 TAGATTTTAC
Statistics
Matches: 617, Mismatches: 46, Indels: 25
0.90 0.07 0.04
Matches are distributed among these distances:
199 20 0.03
200 53 0.09
201 113 0.18
205 114 0.18
206 106 0.17
207 210 0.34
208 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (206 bp):
CTGAAGCAAGATCCAAGATGATTTGGCATCATTGTGCTTACAAGGAACAAATCAAGACATAGCTG
ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
GAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTTC
AGATGATTAGA
Found at i:53917346 original size:406 final size:408
Alignment explanation
Indices: 53916591--53917448 Score: 1400
Period size: 406 Copynumber: 2.1 Consensus size: 408
53916581 AGCAAGATCC
* * * *
53916591 AAGATGATTTGACATCCTTGTGCTTACAAGGAAAAAATCAAAATCATAGTTGATTTGGCTTTCAC
1 AAGATGATTTGGCAT-CTTGTGTTTACAAGGAACAAATCAAAATCATAGCTGATTTGGCTTTCAC
* * *
53916656 GTGCTTATGATGAAGCAAATCTAAGATGATTTGGCATATCTGTATTGTTAGAGAACAAATCAAAG
65 GTGCTTACGATAAAGCAAATCTAAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCAAAG
* * *
53916721 TTTACCGTCTCCATATTCGATGGAGAGCAGGCACATAGTAGATCTGACCTTCAGATGTTTATACT
130 TTTACCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGACCTTCAGATGTTTATACT
*
53916786 GAAGCAAGATCCAAGATAATTTGGCATCATTGTGCTTACAAGGAACATATCAAGGACATAACTAA
195 GAAGCAAGATCCAAGATAATTTGGCATCATTGTGCTTACAAGGAACAAATCAAGGACATAACTAA
53916851 TTTGGCTTTCACGTGCTCACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAG
260 TTTGGCTTTCACGTGCTCACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAG
* *
53916916 AACAAATTGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTTCA
325 AACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTACA
53916981 GATGATTAGACTGAAGCAG
390 GATGATTAGACTGAAGCAG
53917000 -AGATGATTTGGCATCATTGTGTTTACAAGGAACAAATCAAAATCATAGCTGATTTGGCTTTCAC
1 AAGATGATTTGGCATC-TTGTGTTTACAAGGAACAAATCAAAATCATAGCTGATTTGGCTTTCAC
*
53917064 GTGCTTACGATAAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAA-CAAAG
65 GTGCTTACGATAAAGCAAATCTAAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCAAAG
** *
53917128 TTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTG-GCTTCAGATGTTTATACT
130 TTTACCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGACCTTCAGATGTTTATACT
* * * *
53917192 GAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAA-GACATAGCTG
195 GAAGCAAGATCCAAGATAATTTGGCATCATTGTGCTTACAAGGAACAAATC-AAGGACATAACTA
**
53917256 ATTTGGCTTTCACGTGCTTGCGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
259 ATTTGGCTTTCACGTGCTCACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
*
53917321 GAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGGAGACACATAGCAGATCTGGCCTAC
324 GAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTAC
53917386 AGATGATTAGACTGAAGCAG
389 AGATGATTAGACTGAAGCAG
53917406 ATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAACAAATC
1 ----AAGATGATTTGGCA-TCTTGTGTTTACAAGGAACAAATC
53917449 GAAGACATAG
Statistics
Matches: 417, Mismatches: 24, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
406 218 0.52
407 49 0.12
408 113 0.27
411 35 0.08
412 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (408 bp):
AAGATGATTTGGCATCTTGTGTTTACAAGGAACAAATCAAAATCATAGCTGATTTGGCTTTCACG
TGCTTACGATAAAGCAAATCTAAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCAAAGT
TTACCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGACCTTCAGATGTTTATACTG
AAGCAAGATCCAAGATAATTTGGCATCATTGTGCTTACAAGGAACAAATCAAGGACATAACTAAT
TTGGCTTTCACGTGCTCACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
ACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTACAG
ATGATTAGACTGAAGCAG
Found at i:53919246 original size:17 final size:17
Alignment explanation
Indices: 53919226--53919292 Score: 50
Period size: 17 Copynumber: 4.0 Consensus size: 17
53919216 TACTACATGG
*
53919226 TATATATTTTATATTAT
1 TATATATATTATATTAT
**
53919243 TATATA-AAAATACTTAT
1 TATATATATTATA-TTAT
53919260 TATAT-TATTATTATTAT
1 TATATATATTA-TATTAT
* *
53919277 TTTATATTTTAT-TTAT
1 TATATATATTATATTAT
53919293 GCATTTTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
16 7 0.18
17 26 0.67
18 6 0.15
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATATATTATATTAT
Found at i:53919396 original size:22 final size:23
Alignment explanation
Indices: 53919364--53919422 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
53919354 ATATATATAT
* *
53919364 TATAGATTTTATTTTAT-ATTTT
1 TATATATTTTATTTTATGATTTG
*
53919386 TATAT-TATTTATTATATGATTTG
1 TATATAT-TTTATTTTATGATTTG
53919409 TATATATTTTATTT
1 TATATATTTTATTT
53919423 GTAAATTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 1 0.03
22 13 0.43
23 15 0.50
24 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (23 bp):
TATATATTTTATTTTATGATTTG
Found at i:53929511 original size:46 final size:46
Alignment explanation
Indices: 53929440--53929532 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
53929430 CTTGCATGTG
* *
53929440 TTGCAGTAAGGATTTAGCCCGGACGGGTAATCCATGGTCTCAAATA
1 TTGCAGTAAGGATTTAGCCCAGACGGGTAATCCATGATCTCAAATA
53929486 TTGCAGTAAGGATTTAGCCCAGACGGGTAATCCATGATCTCAAATA
1 TTGCAGTAAGGATTTAGCCCAGACGGGTAATCCATGATCTCAAATA
53929532 T
1 T
53929533 GGAAAGGAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (46 bp):
TTGCAGTAAGGATTTAGCCCAGACGGGTAATCCATGATCTCAAATA
Found at i:53930839 original size:55 final size:55
Alignment explanation
Indices: 53930780--53930901 Score: 190
Period size: 55 Copynumber: 2.2 Consensus size: 55
53930770 GGGCGTGCAT
* * * * *
53930780 CATGGCCGTGTTAAAATGATAGTTTCGTCCATGGGCAGGCAGCACGGGCGTTTTC
1 CATGGCCGTGTTAAAATGATAGTTTCATCCACGAGCAGGCAGCACAGGCGTGTTC
53930835 CATGGCCGTGTTAAAATGATAGTTTCATCCACGAGCAGGCAGCACAGGCGTGTTC
1 CATGGCCGTGTTAAAATGATAGTTTCATCCACGAGCAGGCAGCACAGGCGTGTTC
*
53930890 CATGGCTGTGTT
1 CATGGCCGTGTT
53930902 GATAAGTCAG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (55 bp):
CATGGCCGTGTTAAAATGATAGTTTCATCCACGAGCAGGCAGCACAGGCGTGTTC
Found at i:53932402 original size:48 final size:48
Alignment explanation
Indices: 53932220--53932683 Score: 326
Period size: 48 Copynumber: 9.9 Consensus size: 48
53932210 ACATGAAAAT
* * *
53932220 ATGCCAATGCCATGTCCCAGATGTGGTCTTACATGGGATCTCACATCG
1 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATCG
* * * * * *
53932268 ATGCCAA---C--AGCCCAGCTATGGTCTTATA-CGAAGTCTCATAACG
1 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGA-TCTCATATCG
* ** * * * * ** *
53932311 GTGCTGATGCCATGTCCTAGACATGGTCTTATACAGGACCTCATATCG
1 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATCG
* *
53932359 ATGCCAATACCATATCCCAGATATGGTCTTATATGGGATCTCATA-CTG
1 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATC-G
* * ** * * *
53932407 ATGCCGATGCCTTATCTTAGATATGGTCTTACACGAGATCTCTTATCG
1 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATCG
* *
53932455 ATGCCAATGCCATATCCCAGATATGGTGTTACATGGGATCTCATATTG
1 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATCG
* * *
53932503 ATGCCGATGCCATATCCCAGATATGATCTTACACGGGATCTC-T-T--
1 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATCG
* * ** * * *
53932547 AT--CAATGCCATGTCCCAGACATGGTCTTACATGAAATCACTTAACG
1 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATCG
* * * * * *
53932593 ATGCCGAA-GCCATATCCCTGATATGGTCTTATATGAGATCACATCTTG
1 ATGCC-AATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATCG
* ** * * * *
53932641 ATGCCGATTTCATGTCCCATACATGGTCTTACATGAGATCTCA
1 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCTCA
53932684 ATACTCACAT
Statistics
Matches: 319, Mismatches: 80, Indels: 34
0.74 0.18 0.08
Matches are distributed among these distances:
42 32 0.10
43 28 0.09
44 2 0.01
45 1 0.00
46 4 0.01
47 3 0.01
48 244 0.76
49 5 0.02
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (48 bp):
ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATCG
Found at i:53932597 original size:42 final size:42
Alignment explanation
Indices: 53932507--53932597 Score: 101
Period size: 42 Copynumber: 2.2 Consensus size: 42
53932497 ATATTGATGC
* ** * *
53932507 CGATGCCATATCCCAGATATGATCTTACACGGGATCTCTTAT
1 CGATGCCATATCCCAGACATGATCTTACACGAAATCACTTAA
* * * *
53932549 CAATGCCATGTCCCAGACATGGTCTTACATGAAATCACTTAA
1 CGATGCCATATCCCAGACATGATCTTACACGAAATCACTTAA
53932591 CGATGCC
1 CGATGCC
53932598 GAAGCCATAT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (42 bp):
CGATGCCATATCCCAGACATGATCTTACACGAAATCACTTAA
Found at i:53932659 original size:138 final size:138
Alignment explanation
Indices: 53932429--53932682 Score: 330
Period size: 138 Copynumber: 1.8 Consensus size: 138
53932419 TATCTTAGAT
* * * * *
53932429 ATGGTCTTACACGAGATCTCTTATCGATGCCAATGCCATATCCCAGATATGGTGTTACATGGGAT
1 ATGGTCTTACACGAAATCACTTAACGATGCCAATGCCATATCCCAGATATGGTCTTACATGAGAT
* * *
53932494 CTCATATTGATGCCGATGCCATATCCCAGATATGATCTTACACGGGATCTCTTATCAATGCCATG
66 CACATATTGATGCCGATGCCATATCCCAGACATGATCTTACACGAGATCTCTTATCAATGCCATG
53932559 TCCCAGAC
131 TCCCAGAC
* * *
53932567 ATGGTCTTACATGAAATCACTTAACGATGCCGAA-GCCATATCCCTGATATGGTCTTATATGAGA
1 ATGGTCTTACACGAAATCACTTAACGATGCC-AATGCCATATCCCAGATATGGTCTTACATGAGA
* ** * * * *
53932631 TCACATCTTGATGCCGATTTCATGTCCCATACATGGTCTTACATGAGATCTC
65 TCACATATTGATGCCGATGCCATATCCCAGACATGATCTTACACGAGATCTC
53932683 AATACTCACA
Statistics
Matches: 97, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
138 95 0.98
139 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (138 bp):
ATGGTCTTACACGAAATCACTTAACGATGCCAATGCCATATCCCAGATATGGTCTTACATGAGAT
CACATATTGATGCCGATGCCATATCCCAGACATGATCTTACACGAGATCTCTTATCAATGCCATG
TCCCAGAC
Found at i:53937316 original size:92 final size:90
Alignment explanation
Indices: 53937146--53937316 Score: 200
Period size: 92 Copynumber: 1.9 Consensus size: 90
53937136 GATTGTGTGC
* * * *
53937146 TAGTGTAAGACATGTCTGGGGCATGCATCGGCCACAAGATGAGAGCTAGTGGAAGATATGTCTGG
1 TAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATGAAAGCTAGTGGAAGACATGTCTGG
53937211 GACAGGCATCGTCATTGAGATGGGAGT
66 GACAGG-A-CGTCATTGAGATGGGAGT
* * ** * *
53937238 TAGTGTAAGACATGTTTGGGACATGCATCAGCCTCGCGATAGACAAGCTAGTGTAAGACCTGTCT
1 TAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGAT-GA-AAGCTAGTGGAAGACATGTCT
53937303 GGGACATGG-CGTCA
64 GGGACA-GGACGTCA
53937317 GCTTGTCGTG
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
92 39 0.59
93 2 0.03
94 23 0.35
95 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (90 bp):
TAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATGAAAGCTAGTGGAAGACATGTCTGG
GACAGGACGTCATTGAGATGGGAGT
Found at i:53937393 original size:49 final size:50
Alignment explanation
Indices: 53937330--53937462 Score: 162
Period size: 49 Copynumber: 2.7 Consensus size: 50
53937320 TGTCGTGTGT
*
53937330 CAGTGTAAGACTTGTCTGGGACATGGCATCGACAC-CGATAGATGAGAGC
1 CAGTGTAAGACTTGTCTGGGACATGGCATCGACACTCGATAGATGAAAGC
* * * * * *
53937379 CAGTGTAAGACTTGTTTGGGACATGACATTGGC-CTCGCTATATGAAAGC
1 CAGTGTAAGACTTGTCTGGGACATGGCATCGACACTCGATAGATGAAAGC
* *
53937428 CAGTGTAAGACCATGTCTGGGACATGGCGTCGACA
1 CAGTGTAAGA-CTTGTCTGGGACATGGCATCGACA
53937463 TCTTAACCCA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
48 1 0.01
49 50 0.74
50 17 0.25
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (50 bp):
CAGTGTAAGACTTGTCTGGGACATGGCATCGACACTCGATAGATGAAAGC
Found at i:53945162 original size:86 final size:86
Alignment explanation
Indices: 53945017--53945188 Score: 335
Period size: 86 Copynumber: 2.0 Consensus size: 86
53945007 GATATTGGTA
*
53945017 CCTTGATATTGGGTGATTGTGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATG
1 CCTTGATATTGGATGATTGTGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATG
53945082 GGAGCTAATGTAAGACATGTC
66 GGAGCTAATGTAAGACATGTC
53945103 CCTTGATATTGGATGATTGTGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATG
1 CCTTGATATTGGATGATTGTGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATG
53945168 GGAGCTAATGTAAGACATGTC
66 GGAGCTAATGTAAGACATGTC
53945189 TGGGACATGC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.30
Consensus pattern (86 bp):
CCTTGATATTGGATGATTGTGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATG
GGAGCTAATGTAAGACATGTC
Found at i:53945241 original size:48 final size:46
Alignment explanation
Indices: 53945125--53945245 Score: 152
Period size: 46 Copynumber: 2.6 Consensus size: 46
53945115 ATGATTGTGT
* * **
53945125 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGGGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATCGAGATGCAA
* * *
53945171 GCTAATGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATAGACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATCGAGAT-G-CAA
*
53945219 GCTAGTGTAAGACCTGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
53945246 GCGTTGATAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 37 0.58
47 1 0.02
48 26 0.41
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATCGAGATGCAA
Found at i:53945417 original size:29 final size:30
Alignment explanation
Indices: 53945360--53945417 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
53945350 CTTTTAAAAA
* * *
53945360 TATTTACAAAAAGAGGCATCTAATTTTTAT
1 TATTTACAAAAAGAGGCAACCAAATTTTAT
53945390 TATTTACAAAAAGA-GCAACCAAATTTTA
1 TATTTACAAAAAGAGGCAACCAAATTTTA
53945418 AAAATAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (30 bp):
TATTTACAAAAAGAGGCAACCAAATTTTAT
Found at i:53957468 original size:42 final size:42
Alignment explanation
Indices: 53957315--53957479 Score: 156
Period size: 42 Copynumber: 3.9 Consensus size: 42
53957305 AATCATACCA
* * **
53957315 ATGCCTTATCCCAGATATGGTCTTACATGGGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * * * *
53957357 ATGCCAATAGCCTAGCTATGGTCTTACACG-ATTCTCATATCA
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * * *
53957399 ATGCCATGTCCCAAACATGATCTTACACGAAATCTCATAAT-G
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCAT-ATCG
*
53957441 ATGCCATATCCTAGATATGGTCTTACACGTAAA-CTCATA
1 ATGCCATATCCCAGATATGGTCTTACACG-AAATCTCATA
53957480 ACCCTAATGT
Statistics
Matches: 97, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
41 18 0.19
42 55 0.57
43 24 0.25
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:53958988 original size:32 final size:32
Alignment explanation
Indices: 53958952--53959016 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
53958942 GAATCCTTTC
53958952 CAGCTAAAATGGCAAAGCCAATCGATATGCTA
1 CAGCTAAAATGGCAAAGCCAATCGATATGCTA
*
53958984 CAGCTCAAATGGCAAAGCCAATCGATATGCTA
1 CAGCTAAAATGGCAAAGCCAATCGATATGCTA
53959016 C
1 C
53959017 TAACCCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (32 bp):
CAGCTAAAATGGCAAAGCCAATCGATATGCTA
Found at i:53964849 original size:40 final size:40
Alignment explanation
Indices: 53964765--53964948 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
53964755 TTGAATGCTG
* * * *
53964765 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
**
53964804 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
53964845 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
53964885 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
53964925 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
53964949 CTATGAGTTA
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.02
40 113 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:53964902 original size:80 final size:81
Alignment explanation
Indices: 53964765--53964945 Score: 230
Period size: 80 Copynumber: 2.3 Consensus size: 81
53964755 TTGAATGCTG
* *
53964765 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
53964829 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
53964845 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
53964906 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
53964925 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
53964946 ATTCTATGAG
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
79 4 0.04
80 77 0.86
81 9 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Done.