Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 174 of 204
Found at i:51912015 original size:26 final size:28
Alignment explanation
Indices: 51911986--51912045 Score: 90
Period size: 26 Copynumber: 2.2 Consensus size: 28
51911976 AATATATGAT
51911986 ATATATATTAT-TGTATA-TT-CAAGTTA
1 ATATATATTATGT-TATATTTACAAGTTA
51912012 ATATATATTATGTTATATTTACAAGTTA
1 ATATATATTATGTTATATTTACAAGTTA
51912040 ATATAT
1 ATATAT
51912046 TAAATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 15 0.48
27 3 0.10
28 13 0.42
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (28 bp):
ATATATATTATGTTATATTTACAAGTTA
Found at i:51912187 original size:16 final size:16
Alignment explanation
Indices: 51912166--51912196 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51912156 TTAAATAAAT
51912166 ATATATACAAAAATTA
1 ATATATACAAAAATTA
*
51912182 ATATATAGAAAAATT
1 ATATATACAAAAATT
51912197 CCGTGTGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (16 bp):
ATATATACAAAAATTA
Found at i:51915446 original size:14 final size:14
Alignment explanation
Indices: 51915429--51915456 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
51915419 TTGAAAACTT
51915429 CTTATTGTATACTC
1 CTTATTGTATACTC
51915443 CTTATTGTATACTC
1 CTTATTGTATACTC
51915457 TTTACGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
CTTATTGTATACTC
Found at i:51917643 original size:113 final size:113
Alignment explanation
Indices: 51917517--51917756 Score: 453
Period size: 113 Copynumber: 2.1 Consensus size: 113
51917507 ACCTCGGGAA
51917517 CAAACGATGCGTTTTGGCTAACATTTTTTGCGACGCTTACAAATAAACGCCGCTAATTGTGCTAT
1 CAAACGATGCGTTTTGGCTAACATTTTTTGCGACGCTTACAAATAAACGCCGCTAATTGTGCTAT
* *
51917582 ATAATGGCTTTTTTATATTGCGCCGCTACTGCCACTATTCGTGAAGGT
66 ATAATGGCGTTTTTATATTACGCCGCTACTGCCACTATTCGTGAAGGT
*
51917630 CAAACGATGCGTTTTGGCTAACATTTTTTGCGGCGCTTACAAATAAACGCCGCTAATTGTGCTAT
1 CAAACGATGCGTTTTGGCTAACATTTTTTGCGACGCTTACAAATAAACGCCGCTAATTGTGCTAT
51917695 ATAATGGCGTTTTTATATTACGCCGCTACTGCCACTATTCGTGAAGGT
66 ATAATGGCGTTTTTATATTACGCCGCTACTGCCACTATTCGTGAAGGT
51917743 CAAACGATGCGTTT
1 CAAACGATGCGTTT
51917757 AGTCAGTTTT
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 124 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (113 bp):
CAAACGATGCGTTTTGGCTAACATTTTTTGCGACGCTTACAAATAAACGCCGCTAATTGTGCTAT
ATAATGGCGTTTTTATATTACGCCGCTACTGCCACTATTCGTGAAGGT
Found at i:51927378 original size:58 final size:62
Alignment explanation
Indices: 51927315--51927449 Score: 179
Period size: 61 Copynumber: 2.2 Consensus size: 62
51927305 ATCACTTTAA
* * *
51927315 TATTAAATTAATATAATACTTA-T-CAAGATAAATATTAGATTAAATTT-CATATTAAAT-T
1 TATTAAATTAATATAATACTTACTACAAGATAAATATTAAATTAAATTTAAATATGAAATCT
* *
51927373 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAAATATGAAATCT
1 TATTAAATTAATATAATACTTA-CTACAAGATAAATATTAAATTAAATTTAAATATGAAATCT
*
51927436 TATTAAAATAATAT
1 TATTAAATTAATAT
51927450 TGTTTTTGGA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
58 20 0.31
60 1 0.02
61 23 0.35
62 8 0.12
63 13 0.20
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (62 bp):
TATTAAATTAATATAATACTTACTACAAGATAAATATTAAATTAAATTTAAATATGAAATCT
Found at i:51930314 original size:34 final size:35
Alignment explanation
Indices: 51930271--51930347 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 35
51930261 TTACTGGTGT
* * *
51930271 CAGGTGTCAAG-TTGAGAGGATAGATATCTTGTTA
1 CAGGTGTCAAGTTTAAGAGGATAGATATATTATTA
*
51930305 CAGGTGTCAAGTTTTAAGGGGATAGATATATTATTA
1 CAGGTGTCAAG-TTTAAGAGGATAGATATATTATTA
51930341 CAGGTGT
1 CAGGTGT
51930348 AGGCGTATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 11 0.30
36 26 0.70
ACGTcount: A:0.30, C:0.08, G:0.29, T:0.34
Consensus pattern (35 bp):
CAGGTGTCAAGTTTAAGAGGATAGATATATTATTA
Found at i:51935772 original size:31 final size:31
Alignment explanation
Indices: 51935729--51935801 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
51935719 AACTTAACTG
*
51935729 AATTACTATTAATTGAATTAACTAAAATTTTT
1 AATT-CTATTAATCGAATTAACTAAAATTTTT
* *
51935761 AATTCTATTAATCGAATTAACTGAATTTTTT
1 AATTCTATTAATCGAATTAACTAAAATTTTT
51935792 AATTCT-TTAA
1 AATTCTATTAA
51935802 CAGTTAATCG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 4 0.11
31 30 0.79
32 4 0.11
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (31 bp):
AATTCTATTAATCGAATTAACTAAAATTTTT
Found at i:51936446 original size:4 final size:4
Alignment explanation
Indices: 51936437--51936482 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
51936427 CCATCAATAA
51936437 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
51936483 TGTAGTAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:51942622 original size:17 final size:17
Alignment explanation
Indices: 51942597--51942637 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
51942587 ATTATGTAGT
*
51942597 AATACTTTTATTTTAAA
1 AATACTTTTATTTCAAA
*
51942614 AATATTTTTATTTCAAA
1 AATACTTTTATTTCAAA
51942631 AATACTT
1 AATACTT
51942638 CTGAAAAGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (17 bp):
AATACTTTTATTTCAAA
Found at i:51948170 original size:20 final size:19
Alignment explanation
Indices: 51948145--51948191 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
51948135 ATTAATTATT
51948145 TATAAAATTTAATTAGAATA
1 TATAAAATTTAATTA-AATA
* * *
51948165 TATAAACTATATTTAAATA
1 TATAAAATTTAATTAAATA
51948184 TA-AAAATT
1 TATAAAATT
51948192 AAAAATTTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 12 0.55
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TATAAAATTTAATTAAATA
Found at i:51948524 original size:22 final size:21
Alignment explanation
Indices: 51948499--51948542 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
51948489 AAGCATATGA
*
51948499 AAATGATTTGGTTATATTCAAT
1 AAATGATTTGGTTA-ATACAAT
51948521 AAATGATTTGGTTAATACAAT
1 AAATGATTTGGTTAATACAAT
51948542 A
1 A
51948543 CTTATATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
AAATGATTTGGTTAATACAAT
Found at i:51951309 original size:20 final size:21
Alignment explanation
Indices: 51951275--51951313 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
51951265 TACAAAACTT
51951275 CTCAATTTCAGTTCTAAATAA
1 CTCAATTTCAGTTCTAAATAA
*
51951296 CTCATTTTCA-TTCTAAAT
1 CTCAATTTCAGTTCTAAAT
51951314 GTTTGCTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.44
Consensus pattern (21 bp):
CTCAATTTCAGTTCTAAATAA
Found at i:51957052 original size:134 final size:130
Alignment explanation
Indices: 51956739--51957131 Score: 439
Period size: 133 Copynumber: 3.0 Consensus size: 130
51956729 ACCAAAAGGG
51956739 AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTGTGGATCCTTCATTGTTCTTAACAG
1 AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTGT-GATCCTTCATTGTT-TTAACAG
** ** * * *
51956804 CTAAAGCTTGATGTTTCTTAGACTGTTTCATGTATTTCTTTCAT-TTTTTATCCTCCCAGCCTGA
64 CTAAAGCTCAATAATGCTTAGA-TGTTTCATGTACTTCTTTCATGTTTTTA-CCTCCCAGCCTAA
*
51956868 GGAA
127 AGAA
* * *
51956872 AATTTTTTGATGCACTTAGGCGGGAACTTGAGTGAGTCTTGTTGATCCTTCATTGATTTCAACAG
1 AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTG-TGATCCTTCATTG-TTTTAACAG
* * * * *
51956937 CTGAAGCTCAAAAATGCTTAGATGGTTTCGTGTCCTTCTTTCATGTTCTTACCTTCCCAGCCTAA
64 CTAAAGCTCAATAATGCTTAGAT-GTTTCATGTACTTCTTTCATGTTTTTACC-TCCCAGCCTAA
51957002 AGAA
127 AGAA
* * * **
51957006 AATTGTTTGATGCACTTAAGCAGGAACTTGAGTGACTGTTGCTGAT-CTTTGTTGTTTTTAACAG
1 AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTG-TGATCCTTCATTG-TTTTAACAG
* * * * *
51957070 CTAAAGTTCAATAATGCTTTAGATATTTCATGTGCTTCTTTCATGTTTTTACGTCCCGGCCT
64 CTAAAGCTCAATAATGC-TTAGATGTTTCATGTACTTCTTTCATGTTTTTACCTCCCAGCCT
51957132 GTAGTTTATC
Statistics
Matches: 219, Mismatches: 35, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
132 9 0.04
133 143 0.65
134 67 0.31
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (130 bp):
AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTGTGATCCTTCATTGTTTTAACAGCT
AAAGCTCAATAATGCTTAGATGTTTCATGTACTTCTTTCATGTTTTTACCTCCCAGCCTAAAGAA
Found at i:51958589 original size:20 final size:20
Alignment explanation
Indices: 51958560--51958599 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
51958550 ATTTTTATAG
* *
51958560 AATAATATAATATTAAAATA
1 AATAAAATAAAATTAAAATA
*
51958580 AATAAAATAAAATTGAAATA
1 AATAAAATAAAATTAAAATA
51958600 TTTTTCATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (20 bp):
AATAAAATAAAATTAAAATA
Found at i:51961634 original size:6 final size:6
Alignment explanation
Indices: 51961620--51961676 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
51961610 CATCGGTGGT
* * * * * *
51961620 TGCTCC TGCTGC TGCTGT TCCTGC TGCTGC TGCTCC TGCTCC TGCTCC
1 TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC
*
51961668 TGTTGC TGC
1 TGCTGC TGC
51961677 ATAAAGGCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.00, C:0.39, G:0.25, T:0.37
Consensus pattern (6 bp):
TGCTGC
Found at i:51961643 original size:15 final size:15
Alignment explanation
Indices: 51961620--51961676 Score: 75
Period size: 15 Copynumber: 4.0 Consensus size: 15
51961610 CATCGGTGGT
51961620 TGCTCCTGCTGCTGC
1 TGCTCCTGCTGCTGC
*
51961635 TGTTCCTGCTGCTGC
1 TGCTCCTGCTGCTGC
51961650 TGCTCCTGCT-C--C
1 TGCTCCTGCTGCTGC
*
51961662 TGCTCCTGTTGCTGC
1 TGCTCCTGCTGCTGC
51961677 ATAAAGGCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
12 10 0.28
13 1 0.03
14 1 0.03
15 24 0.67
ACGTcount: A:0.00, C:0.39, G:0.25, T:0.37
Consensus pattern (15 bp):
TGCTCCTGCTGCTGC
Found at i:51963126 original size:12 final size:12
Alignment explanation
Indices: 51963109--51963133 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51963099 ATAAGCATTA
51963109 TCGGTCATGTTG
1 TCGGTCATGTTG
51963121 TCGGTCATGTTG
1 TCGGTCATGTTG
51963133 T
1 T
51963134 GAAGGTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.32, T:0.44
Consensus pattern (12 bp):
TCGGTCATGTTG
Found at i:51964419 original size:19 final size:21
Alignment explanation
Indices: 51964376--51964418 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
51964366 TTTAACTTTC
*
51964376 TTTATATATATATTTCAATTT
1 TTTATAAATATATTTCAATTT
*
51964397 TTTATAAATAT-TTTGAATTT
1 TTTATAAATATATTTCAATTT
51964417 TT
1 TT
51964419 AAAAACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTATAAATATATTTCAATTT
Found at i:51965819 original size:458 final size:458
Alignment explanation
Indices: 51965069--51965984 Score: 1832
Period size: 458 Copynumber: 2.0 Consensus size: 458
51965059 AAGTTCTACT
51965069 TTTTTTAGTAATTGGTTGCGGATGGAATTGTTAAATTTAGGGTGGGTTTGGATGGGCGATTGGGT
1 TTTTTTAGTAATTGGTTGCGGATGGAATTGTTAAATTTAGGGTGGGTTTGGATGGGCGATTGGGT
51965134 GCGGTGCGGTGCGTTTAGCTTACTTTTTGTCTCACGCTACAGTATCACTACAGTATCTAATCTCA
66 GCGGTGCGGTGCGTTTAGCTTACTTTTTGTCTCACGCTACAGTATCACTACAGTATCTAATCTCA
51965199 CCGCCATCGCTGTTTTTACACTAAACACAAGTAAACGCACCGCCCATCCAAACTCACCCTTATAC
131 CCGCCATCGCTGTTTTTACACTAAACACAAGTAAACGCACCGCCCATCCAAACTCACCCTTATAC
51965264 GGGTTAACCATAAATAAAAATATCATTAGTCAATTATTAAAAAGGGGTAGGAACGAATTTCAATA
196 GGGTTAACCATAAATAAAAATATCATTAGTCAATTATTAAAAAGGGGTAGGAACGAATTTCAATA
51965329 CTTTTTGTAGGGCATCGTATATTCTCGAATCATCGAGTCAATATTTGTACCTTTCGCCAAGCTAC
261 CTTTTTGTAGGGCATCGTATATTCTCGAATCATCGAGTCAATATTTGTACCTTTCGCCAAGCTAC
51965394 AAAGCAAAGTCTTGGGGATTTCTTCCTTTTTTTTTTCACATTTCAATCAGCAAAGACATTTTTCC
326 AAAGCAAAGTCTTGGGGATTTCTTCCTTTTTTTTTTCACATTTCAATCAGCAAAGACATTTTTCC
51965459 GTACCCATTACCTTTTTTGCAGTAACTACCACTCTTGGAAGCAAGTCTTAGATTGTCCAGAGGTA
391 GTACCCATTACCTTTTTTGCAGTAACTACCACTCTTGGAAGCAAGTCTTAGATTGTCCAGAGGTA
51965524 GAC
456 GAC
51965527 TTTTTTAGTAATTGGTTGCGGATGGAATTGTTAAATTTAGGGTGGGTTTGGATGGGCGATTGGGT
1 TTTTTTAGTAATTGGTTGCGGATGGAATTGTTAAATTTAGGGTGGGTTTGGATGGGCGATTGGGT
51965592 GCGGTGCGGTGCGTTTAGCTTACTTTTTGTCTCACGCTACAGTATCACTACAGTATCTAATCTCA
66 GCGGTGCGGTGCGTTTAGCTTACTTTTTGTCTCACGCTACAGTATCACTACAGTATCTAATCTCA
51965657 CCGCCATCGCTGTTTTTACACTAAACACAAGTAAACGCACCGCCCATCCAAACTCACCCTTATAC
131 CCGCCATCGCTGTTTTTACACTAAACACAAGTAAACGCACCGCCCATCCAAACTCACCCTTATAC
51965722 GGGTTAACCATAAATAAAAATATCATTAGTCAATTATTAAAAAGGGGTAGGAACGAATTTCAATA
196 GGGTTAACCATAAATAAAAATATCATTAGTCAATTATTAAAAAGGGGTAGGAACGAATTTCAATA
51965787 CTTTTTGTAGGGCATCGTATATTCTCGAATCATCGAGTCAATATTTGTACCTTTCGCCAAGCTAC
261 CTTTTTGTAGGGCATCGTATATTCTCGAATCATCGAGTCAATATTTGTACCTTTCGCCAAGCTAC
51965852 AAAGCAAAGTCTTGGGGATTTCTTCCTTTTTTTTTTCACATTTCAATCAGCAAAGACATTTTTCC
326 AAAGCAAAGTCTTGGGGATTTCTTCCTTTTTTTTTTCACATTTCAATCAGCAAAGACATTTTTCC
51965917 GTACCCATTACCTTTTTTGCAGTAACTACCACTCTTGGAAGCAAGTCTTAGATTGTCCAGAGGTA
391 GTACCCATTACCTTTTTTGCAGTAACTACCACTCTTGGAAGCAAGTCTTAGATTGTCCAGAGGTA
51965982 GAC
456 GAC
51965985 CACTTTATAA
Statistics
Matches: 458, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
458 458 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (458 bp):
TTTTTTAGTAATTGGTTGCGGATGGAATTGTTAAATTTAGGGTGGGTTTGGATGGGCGATTGGGT
GCGGTGCGGTGCGTTTAGCTTACTTTTTGTCTCACGCTACAGTATCACTACAGTATCTAATCTCA
CCGCCATCGCTGTTTTTACACTAAACACAAGTAAACGCACCGCCCATCCAAACTCACCCTTATAC
GGGTTAACCATAAATAAAAATATCATTAGTCAATTATTAAAAAGGGGTAGGAACGAATTTCAATA
CTTTTTGTAGGGCATCGTATATTCTCGAATCATCGAGTCAATATTTGTACCTTTCGCCAAGCTAC
AAAGCAAAGTCTTGGGGATTTCTTCCTTTTTTTTTTCACATTTCAATCAGCAAAGACATTTTTCC
GTACCCATTACCTTTTTTGCAGTAACTACCACTCTTGGAAGCAAGTCTTAGATTGTCCAGAGGTA
GAC
Found at i:51967660 original size:2 final size:2
Alignment explanation
Indices: 51967653--51967682 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
51967643 AATTTCTATT
51967653 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51967683 TATCCATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:51974333 original size:17 final size:17
Alignment explanation
Indices: 51974311--51974363 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
51974301 CATAATCAAA
51974311 CTTAACATAATTTAAGT
1 CTTAACATAATTTAAGT
*
51974328 CTTAAC---ATGT-A--
1 CTTAACATAATTTAAGT
51974339 CTTAACATAATTTAAGT
1 CTTAACATAATTTAAGT
51974356 CTTAACAT
1 CTTAACAT
51974364 GTATTGCAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
11 6 0.21
13 1 0.04
14 6 0.21
15 1 0.04
17 14 0.50
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (17 bp):
CTTAACATAATTTAAGT
Found at i:51974350 original size:28 final size:28
Alignment explanation
Indices: 51974310--51974366 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
51974300 TCATAATCAA
51974310 ACTTAACATAATTTAAGTCTTAACATGT
1 ACTTAACATAATTTAAGTCTTAACATGT
51974338 ACTTAACATAATTTAAGTCTTAACATGT
1 ACTTAACATAATTTAAGTCTTAACATGT
51974366 A
1 A
51974367 TTGCAGGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (28 bp):
ACTTAACATAATTTAAGTCTTAACATGT
Found at i:51981252 original size:2 final size:2
Alignment explanation
Indices: 51981245--51981276 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
51981235 GACAATGATA
51981245 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51981277 GTTGATCTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51984012 original size:24 final size:23
Alignment explanation
Indices: 51983985--51984054 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 23
51983975 ATTTAATCCT
51983985 TTAAAATTATAATAATATAAATTA
1 TTAAAATTATAA-AATATAAATTA
* * *
51984009 TTAAAATAATAAAAT-TATATTT
1 TTAAAATTATAAAATATAAATTA
**
51984031 TTATTATTATAAAAATATATAATT
1 TTAAAATTAT-AAAATATA-AATT
51984055 TAATTTCAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
22 12 0.33
23 8 0.22
24 13 0.36
25 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAAAATTATAAAATATAAATTA
Found at i:51984016 original size:18 final size:17
Alignment explanation
Indices: 51983990--51984026 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
51983980 ATCCTTTAAA
*
51983990 ATTATAATAATATAAATT
1 ATTAAAATAATA-AAATT
51984008 ATTAAAATAATAAAATT
1 ATTAAAATAATAAAATT
51984025 AT
1 AT
51984027 ATTTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAAATAATAAAATT
Found at i:51985625 original size:9 final size:9
Alignment explanation
Indices: 51985608--51985644 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
51985598 TGAGTTTTCG
51985608 AATTCGAAT
1 AATTCGAAT
*
51985617 AACTCGAAT
1 AATTCGAAT
51985626 AATTCGAAT
1 AATTCGAAT
51985635 AATTCGAAT
1 AATTCGAAT
51985644 A
1 A
51985645 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:51985892 original size:30 final size:31
Alignment explanation
Indices: 51985858--51985917 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
51985848 AAACCTTTTA
*
51985858 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
51985888 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
51985918 TCCCANNNNN
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:51992525 original size:32 final size:32
Alignment explanation
Indices: 51992482--51992590 Score: 168
Period size: 31 Copynumber: 3.5 Consensus size: 32
51992472 TAGAAATAAA
51992482 AAAATTTAAAAAAATTATTTTAAAAATATTTT
1 AAAATTTAAAAAAATTATTTTAAAAATATTTT
* * *
51992514 AAAA-TTAAAAAAAGTACTTTAAAACTATTTT
1 AAAATTTAAAAAAATTATTTTAAAAATATTTT
*
51992545 AAAATTTAAAAAAGTTATTTTAAAAATATTTT
1 AAAATTTAAAAAAATTATTTTAAAAATATTTT
51992577 AAAA-TTAAAAAAAT
1 AAAATTTAAAAAAAT
51992591 AAAAATATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
31 37 0.54
32 31 0.46
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (32 bp):
AAAATTTAAAAAAATTATTTTAAAAATATTTT
Found at i:51993201 original size:21 final size:21
Alignment explanation
Indices: 51993110--51993215 Score: 61
Period size: 21 Copynumber: 5.0 Consensus size: 21
51993100 TAGTCTTTTT
* * * *
51993110 ATCTTGAACCATAAGCCATGA
1 ATCTTAAACCCTAAACCTTGA
* * *
51993131 ATCTCAAACCCTAAATCTTAA
1 ATCTTAAACCCTAAACCTTGA
* * * *
51993152 ACCTCAAACTCTAAACCTAGA
1 ATCTTAAACCCTAAACCTTGA
** *
51993173 GCCCTAAACCCTAAACCTTGA
1 ATCTTAAACCCTAAACCTTGA
*
51993194 ATCTTAAA-TCTCAAACCTTGA
1 ATCTTAAACCCT-AAACCTTGA
51993215 A
1 A
51993216 CACCAATCAT
Statistics
Matches: 63, Mismatches: 21, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
20 2 0.03
21 61 0.97
ACGTcount: A:0.40, C:0.29, G:0.07, T:0.25
Consensus pattern (21 bp):
ATCTTAAACCCTAAACCTTGA
Found at i:51993257 original size:7 final size:7
Alignment explanation
Indices: 51993237--51993280 Score: 70
Period size: 7 Copynumber: 6.3 Consensus size: 7
51993227 GAACCTGATT
51993237 CCTGAAC
1 CCTGAAC
* *
51993244 TCAGAAC
1 CCTGAAC
51993251 CCTGAAC
1 CCTGAAC
51993258 CCTGAAC
1 CCTGAAC
51993265 CCTGAAC
1 CCTGAAC
51993272 CCTGAAC
1 CCTGAAC
51993279 CC
1 CC
51993281 CAAATAAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.30, C:0.43, G:0.14, T:0.14
Consensus pattern (7 bp):
CCTGAAC
Found at i:51995022 original size:24 final size:25
Alignment explanation
Indices: 51994977--51995023 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
51994967 AGATTTGCCT
51994977 ATTATAAAAAGATGATTGTTATACA
1 ATTATAAAAAGATGATTGTTATACA
* *
51995002 ATTATAACAATATG-TTGTTATA
1 ATTATAAAAAGATGATTGTTATA
51995024 GAGAGTTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (25 bp):
ATTATAAAAAGATGATTGTTATACA
Found at i:51997027 original size:20 final size:20
Alignment explanation
Indices: 51996998--51997035 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
51996988 GAAAGCTCTT
*
51996998 CGATTAGTCTCGTCGGATCC
1 CGATTAGTCTCGACGGATCC
*
51997018 CGATTTGTCTCGACGGAT
1 CGATTAGTCTCGACGGAT
51997036 GTTCTTTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.32
Consensus pattern (20 bp):
CGATTAGTCTCGACGGATCC
Found at i:52009296 original size:27 final size:25
Alignment explanation
Indices: 52009265--52009324 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 25
52009255 AATTAATATA
52009265 ATTTTAATGGTTTTAATTTTTAAAAT
1 ATTTTAAT-GTTTTAATTTTTAAAAT
*
52009291 AGTTTTTATATTTTTTAATTTTTAAAA-
1 A--TTTTA-ATGTTTTAATTTTTAAAAT
52009318 ATTTTAA
1 ATTTTAA
52009325 AAATTAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
24 1 0.03
25 5 0.17
26 1 0.03
27 1 0.03
28 20 0.67
29 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (25 bp):
ATTTTAATGTTTTAATTTTTAAAAT
Found at i:52012387 original size:20 final size:19
Alignment explanation
Indices: 52012359--52012417 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
52012349 AATTGTTAAA
*
52012359 ATTATAAAAACAATAAATTT
1 ATTA-AAAAATAATAAATTT
* *
52012379 ATTACAAAATTATAATATTT
1 ATTAAAAAATAATAA-ATTT
*
52012399 ATTAATAAATAATAAATTT
1 ATTAAAAAATAATAAATTT
52012418 CAAAAATCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 12 0.38
20 20 0.62
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTAAAAAATAATAAATTT
Found at i:52012500 original size:2 final size:2
Alignment explanation
Indices: 52012493--52012522 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52012483 ATTTAACCAA
52012493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52012523 GTGAATCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52014419 original size:16 final size:17
Alignment explanation
Indices: 52014392--52014424 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
52014382 AAGATTTACA
52014392 CAAAATAGAATTTAAAG
1 CAAAATAGAATTTAAAG
52014409 CAAAATA-AATTTAAAG
1 CAAAATAGAATTTAAAG
52014425 AGAATTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.61, C:0.06, G:0.09, T:0.24
Consensus pattern (17 bp):
CAAAATAGAATTTAAAG
Found at i:52014724 original size:6 final size:6
Alignment explanation
Indices: 52014702--52014736 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
52014692 TAAGGATTGC
52014702 TAGGGA T-GGGTA TAGGGA TAGGGA TAGGGA TAGGG
1 TAGGGA TAGGG-A TAGGGA TAGGGA TAGGGA TAGGG
52014737 GATGAAAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 3 0.11
6 21 0.78
7 3 0.11
ACGTcount: A:0.29, C:0.00, G:0.51, T:0.20
Consensus pattern (6 bp):
TAGGGA
Found at i:52018101 original size:22 final size:22
Alignment explanation
Indices: 52018062--52018163 Score: 63
Period size: 22 Copynumber: 4.7 Consensus size: 22
52018052 AAAATATTCA
*
52018062 TAAAAATTAA-TAATAATTATAT
1 TAAAAA-TAATTAAAAATTATAT
*
52018084 TAAAAATAATTAAAAATT-GA-
1 TAAAAATAATTAAAAATTATAT
* *
52018104 -AAGAAT-ATGAAAAATTATATT
1 TAAAAATAATTAAAAATTATA-T
* *
52018125 TAAAAATAAATAAAAATGA-AT
1 TAAAAATAATTAAAAATTATAT
*
52018146 TAAAGCATAATTTAAAAA
1 TAAA-AATAA-TTAAAAA
52018164 ATATTTTTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
18 9 0.15
19 6 0.10
21 9 0.15
22 23 0.38
23 14 0.23
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (22 bp):
TAAAAATAATTAAAAATTATAT
Found at i:52018195 original size:17 final size:18
Alignment explanation
Indices: 52018175--52018211 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
52018165 TATTTTTTTG
52018175 TTAAAAATAAAAAAT-AA
1 TTAAAAATAAAAAATCAA
*
52018192 TTAAAAATAAGAAATCAA
1 TTAAAAATAAAAAATCAA
52018210 TT
1 TT
52018212 TTACCAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (18 bp):
TTAAAAATAAAAAATCAA
Found at i:52036031 original size:61 final size:61
Alignment explanation
Indices: 52035935--52036280 Score: 494
Period size: 61 Copynumber: 5.7 Consensus size: 61
52035925 GATACATGGT
* * * *
52035935 TGAATTTGGCTCTAAGTAGCAGATCAGTGACCCAATTCAGCTCCTTTCATAGTTAGATAGC
1 TGAATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
* * *
52035996 TGAATTTGGCTCTCAGTAGCACAACAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
1 TGAATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
* * * *
52036057 TGAATTTCGCTATCAGTAGAATATCAGTGAGCCAATTCAGTTCCTTTCATAGTTACATAGC
1 TGAATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
* * * *
52036118 TGAATTCGGCTCTCAGTAGAATATCAGTGAGTCAATTAAGTTCCTTTCATAGTTAGATAGC
1 TGAATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
* * * * * *
52036179 TGAATTTGGCTCTAAGTAGAATATCAGTGAGTCGATTCAGCTCCTTCCATAGATACATAGC
1 TGAATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
*
52036240 TGAATTTGGCTCTCAGTAGAATATCAGTGAGTCAATTCAGC
1 TGAATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGC
52036281 CCCTATAAAA
Statistics
Matches: 258, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 258 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (61 bp):
TGAATTTGGCTCTCAGTAGAATATCAGTGAGCCAATTCAGCTCCTTTCATAGTTAGATAGC
Found at i:52037173 original size:20 final size:20
Alignment explanation
Indices: 52037136--52037174 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52037126 TTGATATTTT
**
52037136 TGGAACCATTTCCCTGTTGG
1 TGGAACCATTTCAATGTTGG
*
52037156 TGGAACCTTTTCAATGTTG
1 TGGAACCATTTCAATGTTG
52037175 ATCCAAAGGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
TGGAACCATTTCAATGTTGG
Found at i:52037875 original size:10 final size:11
Alignment explanation
Indices: 52037858--52037908 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
52037848 GGCCCATTTT
52037858 TATTTTAAAAA
1 TATTTTAAAAA
52037869 T-TTTT-AAAA
1 TATTTTAAAAA
**
52037878 T-TTAAAAAAA
1 TATTTTAAAAA
*
52037888 TATTTTTAAAA
1 TATTTTAAAAA
52037899 TATTTTAAAA
1 TATTTTAAAA
52037909 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 7 0.22
10 9 0.28
11 16 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:52037899 original size:30 final size:31
Alignment explanation
Indices: 52037858--52037949 Score: 127
Period size: 30 Copynumber: 3.0 Consensus size: 31
52037848 GGCCCATTTT
52037858 TATTTTAAAAAT-TTTTAAAATTTAAAAAAA
1 TATTTTAAAAATATTTTAAAATTTAAAAAAA
*
52037888 TATTTTTAAAATATTTTAAAA-TTAAAAAAA
1 TATTTTAAAAATATTTTAAAATTTAAAAAAA
**
52037918 T-TTAAAAAAAGTATTTTAAAATTTAAAAAAA
1 TATTTTAAAAA-TATTTTAAAATTTAAAAAAA
52037949 T
1 T
52037950 TAAAAAAGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
29 6 0.11
30 31 0.56
31 18 0.33
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (31 bp):
TATTTTAAAAATATTTTAAAATTTAAAAAAA
Found at i:52037918 original size:40 final size:39
Alignment explanation
Indices: 52037874--52037988 Score: 137
Period size: 40 Copynumber: 2.9 Consensus size: 39
52037864 AAAAATTTTT
**
52037874 AAAATTTAAAAAAATATTTTTAAAATATT-TTAAAATTAAA
1 AAAATTTAAAAAAATA-TTTTAAAAT-TTAAAAAAATTAAA
52037914 AAAATTTAAAAAAAGTATTTTAAAATTTAAAAAAATTAAA
1 AAAATTTAAAAAAA-TATTTTAAAATTTAAAAAAATTAAA
*
52037954 AAAGTATGT-AAAAAATATTTTAAAA-TTAAAAAAAT
1 AAA--ATTTAAAAAAATATTTTAAAATTTAAAAAAAT
52037989 AAATATATTT
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
39 12 0.18
40 45 0.66
41 8 0.12
42 3 0.04
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (39 bp):
AAAATTTAAAAAAATATTTTAAAATTTAAAAAAATTAAA
Found at i:52037946 original size:29 final size:30
Alignment explanation
Indices: 52037870--52037960 Score: 87
Period size: 30 Copynumber: 3.0 Consensus size: 30
52037860 TTTTAAAAAT
* *** *
52037870 TTTTAAAATTTAAAAAAATATTTTTAAAATA
1 TTTTAAAA-TTAAAAAAAAATTAAAAAAGTA
*
52037901 TTTTAAAATT-AAAAAAATTTAAAAAAAGTA
1 TTTTAAAATTAAAAAAAAATT-AAAAAAGTA
*
52037931 TTTTAAAATT-TAAAAAAATTAAAAAAGTA
1 TTTTAAAATTAAAAAAAAATTAAAAAAGTA
52037960 T
1 T
52037961 GTAAAAAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 18 0.35
30 25 0.49
31 8 0.16
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (30 bp):
TTTTAAAATTAAAAAAAAATTAAAAAAGTA
Found at i:52037969 original size:30 final size:29
Alignment explanation
Indices: 52037905--52037986 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 29
52037895 AAAATATTTT
**
52037905 AAAA-TTAAAAAAATTTAAAAAAAGTATTTT
1 AAAATTTAAAAAAA-TT-AAAAAAGTATTAA
52037935 AAAATTTAAAAAAATTAAAAAAGTATGTAA
1 AAAATTTAAAAAAATTAAAAAAGTAT-TAA
**
52037965 AAAATATT-TTAAAATTAAAAAA
1 AAAAT-TTAAAAAAATTAAAAAA
52037987 ATAAATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 10 0.22
30 24 0.53
31 11 0.24
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (29 bp):
AAAATTTAAAAAAATTAAAAAAGTATTAA
Found at i:52040027 original size:6 final size:6
Alignment explanation
Indices: 52040016--52040041 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52040006 TGTTCAGTGT
52040016 TTGAAC TTGAAC TTGAAC TTGAAC TT
1 TTGAAC TTGAAC TTGAAC TTGAAC TT
52040042 TGGAGCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (6 bp):
TTGAAC
Found at i:52041287 original size:6 final size:6
Alignment explanation
Indices: 52041278--52041302 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
52041268 AATAATTAGT
52041278 TACTAA TACTAA TACTAA TACTAA T
1 TACTAA TACTAA TACTAA TACTAA T
52041303 TAATAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (6 bp):
TACTAA
Found at i:52041335 original size:16 final size:15
Alignment explanation
Indices: 52041304--52041360 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 15
52041294 AATACTAATT
52041304 AATAATAATAGA-AAA
1 AATAATAATA-ATAAA
52041319 AATCAATAATAATAAA
1 AAT-AATAATAATAAA
*
52041335 AATAAAAATAATGTAAA
1 AATAATAATAA--TAAA
52041352 AATACATAA
1 AATA-ATAA
52041361 AAAAGGAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
15 11 0.31
16 13 0.37
17 8 0.23
18 3 0.09
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (15 bp):
AATAATAATAATAAA
Found at i:52041459 original size:15 final size:14
Alignment explanation
Indices: 52041409--52041452 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
52041399 AAGGGTAGAG
*
52041409 AAAATAATAAAAGGT
1 AAAA-AATAAAAAGT
*
52041424 ATAAAAATAAATAGT
1 A-AAAAATAAAAAGT
52041439 AAAAAATAAAAAGT
1 AAAAAATAAAAAGT
52041453 TCAAAAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 12 0.48
15 10 0.40
16 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (14 bp):
AAAAAATAAAAAGT
Found at i:52043211 original size:22 final size:22
Alignment explanation
Indices: 52043168--52043239 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
52043158 AATAACAATA
* * **
52043168 AAATAGTAATAATATAATAACG
1 AAATAGTAACAAAATAGCAACG
52043190 AAATAGTAACAAAATAGCAACG
1 AAATAGTAACAAAATAGCAACG
* ** *
52043212 AAACAACAACAAAACAGCAACG
1 AAATAGTAACAAAATAGCAACG
52043234 AAATAG
1 AAATAG
52043240 CTCATACCTA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.61, C:0.14, G:0.11, T:0.14
Consensus pattern (22 bp):
AAATAGTAACAAAATAGCAACG
Found at i:52053002 original size:50 final size:50
Alignment explanation
Indices: 52052879--52053119 Score: 236
Period size: 50 Copynumber: 4.7 Consensus size: 50
52052869 GTAAATAACA
* ** **
52052879 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTGGTA-C--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCGG
* * *
52052927 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGCTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
52052977 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * *
52053027 TGCCAACGCCATGTACCAGACATGGTCTTACATGGGACCTCTCGTAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATATC---GG
* *
52053083 TGCCAATGCCATGTTCCAAACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
52053120 TCTCATCACC
Statistics
Matches: 162, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
47 6 0.04
48 35 0.22
50 81 0.50
53 5 0.03
56 35 0.22
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:52057965 original size:39 final size:39
Alignment explanation
Indices: 52057917--52057991 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
52057907 TTATATATGA
*
52057917 AAAATAATTATTAGAAATAAAGAAATGAATAAAAAACTT
1 AAAAGAATTATTAGAAATAAAGAAATGAATAAAAAACTT
*
52057956 AAAAGAATTATTAGTAATAAAGAAATGAATAAAAAA
1 AAAAGAATTATTAGAAATAAAGAAATGAATAAAAAA
52057992 AACTTTCTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.65, C:0.01, G:0.09, T:0.24
Consensus pattern (39 bp):
AAAAGAATTATTAGAAATAAAGAAATGAATAAAAAACTT
Found at i:52061000 original size:25 final size:27
Alignment explanation
Indices: 52060971--52061033 Score: 103
Period size: 28 Copynumber: 2.4 Consensus size: 27
52060961 TTAAAAAATA
52060971 ACCAAAATAT-TAAA-TTTTTTTATTT
1 ACCAAAATATATAAATTTTTTTTATTT
52060996 ACCAAAATATTATAAATTTTTTTTATTT
1 ACCAAAATA-TATAAATTTTTTTTATTT
52061024 ACCAAAATAT
1 ACCAAAATAT
52061034 GCCAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
25 9 0.26
26 1 0.03
27 5 0.14
28 20 0.57
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (27 bp):
ACCAAAATATATAAATTTTTTTTATTT
Found at i:52061270 original size:18 final size:19
Alignment explanation
Indices: 52061211--52061265 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 19
52061201 NNNNNNNNNN
52061211 ATTAAAATAGAGTTATTAA
1 ATTAAAATAGAGTTATTAA
* * *
52061230 ATGAGAATA-ATTTATTAA
1 ATTAAAATAGAGTTATTAA
52061248 ATTAAAATAGAGTTATTA
1 ATTAAAATAGAGTTATTA
52061266 CTTAATTAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
ATTAAAATAGAGTTATTAA
Found at i:52061360 original size:37 final size:37
Alignment explanation
Indices: 52061310--52061431 Score: 235
Period size: 37 Copynumber: 3.3 Consensus size: 37
52061300 TAACTAATAT
52061310 TAGAGTTATTAAATGAGAATAGTTTATTAAATTAAAA
1 TAGAGTTATTAAATGAGAATAGTTTATTAAATTAAAA
52061347 TAGAGTTATTAAATGAGAATAGTTTATTAAATTAAAA
1 TAGAGTTATTAAATGAGAATAGTTTATTAAATTAAAA
*
52061384 TAGAGTTATTAAATGAGAATAATTTATTAAATTAAAA
1 TAGAGTTATTAAATGAGAATAGTTTATTAAATTAAAA
52061421 TAGAGTTATTA
1 TAGAGTTATTA
52061432 CTTAATTAGA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 84 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (37 bp):
TAGAGTTATTAAATGAGAATAGTTTATTAAATTAAAA
Found at i:52061436 original size:18 final size:19
Alignment explanation
Indices: 52061310--52061431 Score: 142
Period size: 18 Copynumber: 6.6 Consensus size: 19
52061300 TAACTAATAT
* *
52061310 TAGAGTTATTAAATGAGAA
1 TAGAGTTATTAAATTAAAA
*
52061329 TAG-TTTATTAAATTAAAA
1 TAGAGTTATTAAATTAAAA
* *
52061347 TAGAGTTATTAAATGAGAA
1 TAGAGTTATTAAATTAAAA
*
52061366 TAG-TTTATTAAATTAAAA
1 TAGAGTTATTAAATTAAAA
* *
52061384 TAGAGTTATTAAATGAGAA
1 TAGAGTTATTAAATTAAAA
*
52061403 TA-ATTTATTAAATTAAAA
1 TAGAGTTATTAAATTAAAA
52061421 TAGAGTTATTA
1 TAGAGTTATTA
52061432 CTTAATTAGA
Statistics
Matches: 84, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
18 45 0.54
19 39 0.46
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (19 bp):
TAGAGTTATTAAATTAAAA
Found at i:52061480 original size:92 final size:92
Alignment explanation
Indices: 52061384--52061581 Score: 369
Period size: 92 Copynumber: 2.1 Consensus size: 92
52061374 TAAATTAAAA
52061384 TAGAGTTATTAAATGAGAATAATTTATTAAATTAAAATAGAGTTATTACTTAATTAGAATTCTAA
1 TAGAGTTATTAAATGAGAATAATTTATTAAATTAAAATAGAGTTATTACTTAATTAGAATTCTAA
52061449 GTATCTTAATTATCACTTAACTAATAT
66 GTATCTTAATTATCACTTAACTAATAT
*
52061476 TAGAGTTATTAAATGAGAATAGTTTATTAAATTAAAATAGAGTTATTACTTAATTAGAATTCTAA
1 TAGAGTTATTAAATGAGAATAATTTATTAAATTAAAATAGAGTTATTACTTAATTAGAATTCTAA
52061541 GTATCTTAATTATCACTTAACTAATAT
66 GTATCTTAATTATCACTTAACTAATAT
*
52061568 TAGATTTAATTAAA
1 TAGAGTT-ATTAAA
52061582 AAATTAATAG
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
92 97 0.94
93 6 0.06
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.41
Consensus pattern (92 bp):
TAGAGTTATTAAATGAGAATAATTTATTAAATTAAAATAGAGTTATTACTTAATTAGAATTCTAA
GTATCTTAATTATCACTTAACTAATAT
Found at i:52061481 original size:55 final size:55
Alignment explanation
Indices: 52061421--52061571 Score: 158
Period size: 55 Copynumber: 3.1 Consensus size: 55
52061411 TAAATTAAAA
52061421 TAGAGTTATTACTTAATTAGAATTCTAAGTATCTTAATTATCACTTAACTAATAT
1 TAGAGTTATTACTTAATTAGAATTCTAAGTATCTTAATTATCACTTAACTAATAT
* *
52061476 TAGAGTTATTA---AATGAGAA---T-AG--T-TT-ATTA--AATTAA---A-A-
1 TAGAGTTATTACTTAATTAGAATTCTAAGTATCTTAATTATCACTTAACTAATAT
52061513 TAGAGTTATTACTTAATTAGAATTCTAAGTATCTTAATTATCACTTAACTAATAT
1 TAGAGTTATTACTTAATTAGAATTCTAAGTATCTTAATTATCACTTAACTAATAT
52061568 TAGA
1 TAGA
52061572 TTTAATTAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 36
0.65 0.04 0.32
Matches are distributed among these distances:
37 11 0.15
38 1 0.01
39 1 0.01
40 7 0.09
42 5 0.07
43 1 0.01
44 6 0.08
45 2 0.03
46 2 0.03
47 2 0.03
48 6 0.08
49 1 0.01
50 5 0.07
52 7 0.09
53 1 0.01
54 1 0.01
55 15 0.20
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (55 bp):
TAGAGTTATTACTTAATTAGAATTCTAAGTATCTTAATTATCACTTAACTAATAT
Found at i:52061485 original size:166 final size:166
Alignment explanation
Indices: 52061211--52061523 Score: 626
Period size: 166 Copynumber: 1.9 Consensus size: 166
52061201 NNNNNNNNNN
52061211 ATTAAAATAGAGTTATTAAATGAGAATAATTTATTAAATTAAAATAGAGTTATTACTTAATTAGA
1 ATTAAAATAGAGTTATTAAATGAGAATAATTTATTAAATTAAAATAGAGTTATTACTTAATTAGA
52061276 ATTCTAAGTATCTTAATTATCACTTAACTAATATTAGAGTTATTAAATGAGAATAGTTTATTAAA
66 ATTCTAAGTATCTTAATTATCACTTAACTAATATTAGAGTTATTAAATGAGAATAGTTTATTAAA
52061341 TTAAAATAGAGTTATTAAATGAGAATAGTTTATTAA
131 TTAAAATAGAGTTATTAAATGAGAATAGTTTATTAA
52061377 ATTAAAATAGAGTTATTAAATGAGAATAATTTATTAAATTAAAATAGAGTTATTACTTAATTAGA
1 ATTAAAATAGAGTTATTAAATGAGAATAATTTATTAAATTAAAATAGAGTTATTACTTAATTAGA
52061442 ATTCTAAGTATCTTAATTATCACTTAACTAATATTAGAGTTATTAAATGAGAATAGTTTATTAAA
66 ATTCTAAGTATCTTAATTATCACTTAACTAATATTAGAGTTATTAAATGAGAATAGTTTATTAAA
52061507 TTAAAATAGAGTTATTA
131 TTAAAATAGAGTTATTA
52061524 CTTAATTAGA
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
166 147 1.00
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.40
Consensus pattern (166 bp):
ATTAAAATAGAGTTATTAAATGAGAATAATTTATTAAATTAAAATAGAGTTATTACTTAATTAGA
ATTCTAAGTATCTTAATTATCACTTAACTAATATTAGAGTTATTAAATGAGAATAGTTTATTAAA
TTAAAATAGAGTTATTAAATGAGAATAGTTTATTAA
Found at i:52061514 original size:18 final size:18
Alignment explanation
Indices: 52061481--52061515 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52061471 AATATTAGAG
*
52061481 TTATTAAATGAGAATAGT
1 TTATTAAATGAAAATAGT
*
52061499 TTATTAAATTAAAATAG
1 TTATTAAATGAAAATAG
52061516 AGTTATTACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (18 bp):
TTATTAAATGAAAATAGT
Found at i:52062231 original size:27 final size:28
Alignment explanation
Indices: 52062201--52062265 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
52062191 TTTTTTTGGT
*
52062201 ATATTTTGGTAAAT-AAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
52062228 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
52062256 ATATTTTGGT
1 ATATTTTGGT
52062266 TTTTTTTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 14 0.39
28 22 0.61
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.42
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:52067991 original size:45 final size:45
Alignment explanation
Indices: 52067925--52068016 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
52067915 ACCATCACCA
52067925 CACCTCAACCTTTGACATCTTCACACTCACCTAACCTACCAAGTT
1 CACCTCAACCTTTGACATCTTCACACTCACCTAACCTACCAAGTT
*
52067970 CACCTCAACCTTTGACTTCTTCACACTCACCTAACCTACCAAGTT
1 CACCTCAACCTTTGACATCTTCACACTCACCTAACCTACCAAGTT
52068015 CA
1 CA
52068017 ACACAGGCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.28, C:0.40, G:0.04, T:0.27
Consensus pattern (45 bp):
CACCTCAACCTTTGACATCTTCACACTCACCTAACCTACCAAGTT
Found at i:52079037 original size:25 final size:24
Alignment explanation
Indices: 52079008--52079055 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
52078998 ATCATGGGAA
52079008 AAATGTG-AAGACATTGAAATGTATT
1 AAATGTGAAAGA-ATTGAAA-GTATT
52079033 AAATGTGAAAGAATTGAAAGTAT
1 AAATGTGAAAGAATTGAAAGTAT
52079056 AATATATGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
25 14 0.64
26 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.21, T:0.29
Consensus pattern (24 bp):
AAATGTGAAAGAATTGAAAGTATT
Found at i:52098852 original size:2 final size:2
Alignment explanation
Indices: 52098845--52098869 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52098835 ACTATAGGAT
52098845 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
52098870 ATACTATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:52110171 original size:31 final size:30
Alignment explanation
Indices: 52110136--52110213 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
52110126 ACCCAGAAAT
* *
52110136 TTAAATAAAATTTTTTGAATAGTTTAATGA
1 TTAAATAAAATTTTTTGAATAATTGAATGA
**
52110166 CTTAAATAAAAACTTTTGAATAATTGAATGA
1 -TTAAATAAAATTTTTTGAATAATTGAATGA
* *
52110197 TCAAATTATAATTTTTT
1 TTAAA-TAAAATTTTTT
52110214 TAATTAAGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.45
Consensus pattern (30 bp):
TTAAATAAAATTTTTTGAATAATTGAATGA
Found at i:52113561 original size:22 final size:22
Alignment explanation
Indices: 52113519--52113562 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
52113509 NNNNNATTAG
*
52113519 GTATATAATATATTACGTATAA
1 GTATATAATATATTACATATAA
*
52113541 GTATATAAT-TAGTTATATATAA
1 GTATATAATATA-TTACATATAA
52113563 CGCATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (22 bp):
GTATATAATATATTACATATAA
Found at i:52113609 original size:20 final size:19
Alignment explanation
Indices: 52113586--52113624 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
52113576 TCTATATTAT
52113586 TATATTATTAATATTATTTA
1 TATATTATTAATA-TATTTA
52113606 TATATTATTAATATATTTA
1 TATATTATTAATATATTTA
52113625 ATTTTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATTATTAATATATTTA
Found at i:52113610 original size:11 final size:11
Alignment explanation
Indices: 52113586--52113622 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
52113576 TCTATATTAT
52113586 TATATTA-TTA
1 TATATTATTTA
52113596 -ATATTATTTA
1 TATATTATTTA
*
52113606 TATATTATTAA
1 TATATTATTTA
52113617 TATATT
1 TATATT
52113623 TAATTTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
9 6 0.25
10 3 0.12
11 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TATATTATTTA
Found at i:52113634 original size:23 final size:19
Alignment explanation
Indices: 52113580--52113623 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
52113570 TTTCTTTCTA
52113580 TATTATTATATTATTAATAT
1 TATT-TTATATTATTAATAT
52113600 TATTTATATATTATTAATA-
1 TATTT-TATATTATTAATAT
52113619 TATTT
1 TATTT
52113624 AATTTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTATATTATTAATAT
Found at i:52121188 original size:15 final size:15
Alignment explanation
Indices: 52121168--52121200 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
52121158 TGCTATCAAC
52121168 ATGTCATCAACATAA
1 ATGTCATCAACATAA
52121183 ATGTCATCAACATAA
1 ATGTCATCAACATAA
52121198 ATG
1 ATG
52121201 AGTAGATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.27
Consensus pattern (15 bp):
ATGTCATCAACATAA
Found at i:52122911 original size:21 final size:22
Alignment explanation
Indices: 52122870--52122912 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
52122860 TAAATAAATG
52122870 TGTAATAAATATATGTATACATT
1 TGTAATAAATATATG-ATACATT
*
52122893 TGTAATTAATATATG-TACAT
1 TGTAATAAATATATGATACAT
52122913 ACTTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (22 bp):
TGTAATAAATATATGATACATT
Found at i:52123003 original size:19 final size:19
Alignment explanation
Indices: 52122965--52123003 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
52122955 TTAATTAAAT
*
52122965 AAAAGAAATAAAAGATAGA
1 AAAAGAAATAAAAGACAGA
52122984 AAAAGAGAATAAAA-ACAGA
1 AAAAGA-AATAAAAGACAGA
52123003 A
1 A
52123004 TAGCAAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.08
Consensus pattern (19 bp):
AAAAGAAATAAAAGACAGA
Found at i:52123059 original size:26 final size:27
Alignment explanation
Indices: 52123008--52123064 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
52122998 ACAGAATAGC
* *
52123008 AAAACGAAAATAGGGGAGAAAGGAAAG
1 AAAAAGAAAATAGGGAAGAAAGGAAAG
52123035 AAAAAGAAAA-AGGGAAGGAAA-GAAAG
1 AAAAAGAAAATAGGGAA-GAAAGGAAAG
52123061 AAAA
1 AAAA
52123065 TTAGGGAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.02
Consensus pattern (27 bp):
AAAAAGAAAATAGGGAAGAAAGGAAAG
Found at i:52123070 original size:22 final size:21
Alignment explanation
Indices: 52123027--52123073 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 21
52123017 ATAGGGGAGA
52123027 AAGGAAAGAAAAAGAAAAAGGG
1 AAGGAAAG-AAAAGAAAAAGGG
52123049 AAGGAAAG-AAAGAAAATTAGGG
1 AAGGAAAGAAAAGAAAA--AGGG
52123071 AAG
1 AAG
52123074 TTTCAAGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.35
22 15 0.65
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (21 bp):
AAGGAAAGAAAAGAAAAAGGG
Found at i:52124147 original size:37 final size:38
Alignment explanation
Indices: 52124048--52124147 Score: 94
Period size: 37 Copynumber: 2.6 Consensus size: 38
52124038 AACTTGAGTT
**
52124048 GATGAGACACTGGGTGTCATACTGTTACTTCGGATAGATTC
1 GATGAGACACTGGGTGTCA-AC--TTACTTCGGATAGAGCC
** ** * *
52124089 GATGAGGTACTGGGTACCAACTTACTTCGGCTTG-GCC
1 GATGAGACACTGGGTGTCAACTTACTTCGGATAGAGCC
52124126 GATGAGACACTGGGTGTCAACT
1 GATGAGACACTGGGTGTCAACT
52124148 ATTGCTTCGA
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
37 19 0.40
38 11 0.23
40 2 0.04
41 15 0.32
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (38 bp):
GATGAGACACTGGGTGTCAACTTACTTCGGATAGAGCC
Found at i:52127286 original size:21 final size:22
Alignment explanation
Indices: 52127262--52127310 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
52127252 TGAATGCTTA
*
52127262 ATTTATTT-TAAATAAAATTTT
1 ATTTATTTAAAAATAAAATTTT
52127283 ATTT-TTTAAAAATAAAATTTT
1 ATTTATTTAAAAATAAAATTTT
52127304 ATTTATT
1 ATTTATT
52127311 CATAGTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 20 0.80
22 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTATTTAAAAATAAAATTTT
Found at i:52128975 original size:41 final size:40
Alignment explanation
Indices: 52128859--52128975 Score: 114
Period size: 37 Copynumber: 3.0 Consensus size: 40
52128849 CCTCACCGGA
* * *
52128859 TAATTCGAAGTAATAATTTGACACCCAATGTCTCATCG-GT
1 TAATCCGAAGT-ATAAATTGACACCCAATGTCTCATCGAAT
* * * *
52128899 TAAACCGAA--ATAAATTGGCACCCAATGCCTAATCGAAT
1 TAATCCGAAGTATAAATTGACACCCAATGTCTCATCGAAT
* *
52128937 TAATCCGAAGTAGTAAATTGACACCCAGTATCTCATCGA
1 TAATCCGAAGTA-TAAATTGACACCCAATGTCTCATCGA
52128976 CTTGAAGTCG
Statistics
Matches: 60, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
37 22 0.37
38 9 0.15
40 8 0.13
41 21 0.35
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (40 bp):
TAATCCGAAGTATAAATTGACACCCAATGTCTCATCGAAT
Found at i:52129180 original size:24 final size:24
Alignment explanation
Indices: 52129135--52129181 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
52129125 TATATATACC
52129135 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
52129159 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
52129182 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:52129861 original size:4 final size:4
Alignment explanation
Indices: 52129854--52129898 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
52129844 TTTCTCCTTC
52129854 CTTT CTTT CCTTT -TTT CTTTT CTTT CTTT CTTT C-TT -TTT CTTT CT
1 CTTT CTTT -CTTT CTTT C-TTT CTTT CTTT CTTT CTTT CTTT CTTT CT
52129899 GTTTCGTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
3 7 0.19
4 21 0.58
5 8 0.22
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:52129877 original size:17 final size:19
Alignment explanation
Indices: 52129855--52129897 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
52129845 TTCTCCTTCC
52129855 TTTCTTTCCTTT-TTTC-T
1 TTTCTTTCCTTTCTTTCTT
52129872 TTTCTTT-CTTTCTTTCTT
1 TTTCTTTCCTTTCTTTCTT
52129890 TTTCTTTC
1 TTTCTTTC
52129898 TGTTTCGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 8 0.35
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTCTTTCCTTTCTTTCTT
Found at i:52134191 original size:20 final size:20
Alignment explanation
Indices: 52134157--52134198 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
52134147 AACTATTTAA
** *
52134157 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
52134177 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
52134197 AT
1 AT
52134199 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:52134827 original size:25 final size:25
Alignment explanation
Indices: 52134798--52134903 Score: 103
Period size: 25 Copynumber: 4.2 Consensus size: 25
52134788 TTCCTCATAC
*
52134798 AGGCTTTTCACAAGATTAGCTACAA
1 AGGCTTTTCACAAGATTAGCCACAA
* * *
52134823 AGGCTTTCCA-AATAATACGCCACAA
1 AGGCTTTTCACAAGATTA-GCCACAA
*
52134848 AGACTTTTCACAAGATTAGCCACAA
1 AGGCTTTTCACAAGATTAGCCACAA
52134873 AGGC-TTTC-C-AGATAATACGCCACAA
1 AGGCTTTTCACAAGAT--TA-GCCACAA
52134898 AGGCTT
1 AGGCTT
52134904 CCTAGGTAAC
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
22 4 0.06
23 1 0.02
24 11 0.17
25 44 0.67
26 6 0.09
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.24
Consensus pattern (25 bp):
AGGCTTTTCACAAGATTAGCCACAA
Found at i:52134876 original size:50 final size:50
Alignment explanation
Indices: 52134801--52134899 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
52134791 CTCATACAGG
*
52134801 CTTTTCACAAGATTAGCTACAAAGGCTTTCCAAATAATACGCCACAAAGA
1 CTTTTCACAAGATTAGCCACAAAGGCTTTCCAAATAATACGCCACAAAGA
*
52134851 CTTTTCACAAGATTAGCCACAAAGGCTTTCCAGATAATACGCCACAAAG
1 CTTTTCACAAGATTAGCCACAAAGGCTTTCCAAATAATACGCCACAAAG
52134900 GCTTCCTAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.23
Consensus pattern (50 bp):
CTTTTCACAAGATTAGCCACAAAGGCTTTCCAAATAATACGCCACAAAGA
Found at i:52144513 original size:13 final size:13
Alignment explanation
Indices: 52144484--52144536 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
52144474 TTTAAACCAA
**
52144484 ACTTTTCAAAAAT
1 ACTTTTCAAAAGC
*
52144497 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
52144510 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
52144523 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
52144536 A
1 A
52144537 TTGCCAAACT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:52149943 original size:3 final size:3
Alignment explanation
Indices: 52149935--52149959 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
52149925 TGCCAAAATC
52149935 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
52149960 TTTTGCATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:52150126 original size:383 final size:372
Alignment explanation
Indices: 52149407--52150167 Score: 1351
Period size: 383 Copynumber: 2.0 Consensus size: 372
52149397 ATTAACATTT
* *
52149407 ATTTTACTTTGTATCCACACATAAGTATTATTGTGACATTTACTACTGGAAATGTTTAAATCAAT
1 ATTTTACTTTGTATCCACACATAAGTATTATTGTGACATTTAATACTAGAAATGTTTAAATCAAT
52149472 ATGAGGTCTATAATGTCACTAAGTCAACCAAATAAATATAAATTCCAAACAATTATATGTAGCAT
66 ATGAGGTCTATAATGTCACTAAGTCAACCAAATAAATATAAATTCCAAACAATTATATGTAGCAT
52149537 TTGCTTCATGGAATAAGCCAAAATCTCTTCTTCTTCTTTTTTTTGCATTGAGTCTTGACGATTTT
131 TTGCTTCATGGAATAAGCCAAAATCTCTTCTTCTTCTTTTTTTTGCATTGAGTCTTGACGATTTT
52149602 ATCAAGAAGTAAGCAAATTAAAATCTAGTAGTGGACTTTGAATCCAATCAGAATCTATTAATAGA
196 ATCAAGAAGTAAGCAAATTAAAATCTAGTAGTGGACTTTGAATCCAATCAGAATCTATTAATAGA
52149667 AAAATTTGAGAGTGTATCTTATTTTCTAAGTGTGCAACAGGTACATAACCAATGACATTTCATAC
261 AAAATTTGAGAGTGTATCTTATTTTCTAAGTGTGCAACAGGTACATAACCAATGACATTTCATAC
*
52149732 ATAAGTTTTCTCTCTTATAAGTTCTCATCAGTAATATTTTTTCATGTA
326 ATAAGTTTTCTCTCTTATAAGTTCTCATCAGTAATA-TTTTTCACGTA
*
52149780 ATTTTACTTTGTATCCACACATAAGTATTATTGTGACATTTAATACTAGAAATGTTTAAATGAAT
1 ATTTTACTTTGTATCCACACATAAGTATTATTGTGACATTTAATACTAGAAATGTTTAAATCAAT
52149845 ATGAGGTCTATAATGTCACTAAGTCAACCAAATAAATATAAATTCCAAACAATTATATGTAGCAT
66 ATGAGGTCTATAATGTCACTAAGTCAACCAAATAAATATAAATTCCAAACAATTATATGTAGCAT
*
52149910 TTGCTTCATGGAATATGCCAAAATCTCTTCTTCTTCTTCTTCTTCTTCTTTTTTGCATTGAGTCT
131 TTGCTTCATGGAATAAGCCAAAA--------TC-TCTTCTTCTTCTT-TTTTTTGCATTGAGTCT
*
52149975 TGACGATTTTATCAAGAAGTAAGCAAATTAAACTCTAGTAGTGGACTTTGAATCCAATCAGAATC
186 TGACGATTTTATCAAGAAGTAAGCAAATTAAAATCTAGTAGTGGACTTTGAATCCAATCAGAATC
*
52150040 TATTAATAGAAAACTTTGAGAGTGTATCTTATTTTCTAAGTGTGCAACAGGTACATAACCAATGA
251 TATTAATAGAAAAATTTGAGAGTGTATCTTATTTTCTAAGTGTGCAACAGGTACATAACCAATGA
*
52150105 CATTTCATACATAAGTTTTCTCTCTTGTAAGTTCTCATCAGTAATATTTTTCACGTA
316 CATTTCATACATAAGTTTTCTCTCTTATAAGTTCTCATCAGTAATATTTTTCACGTA
52150162 ATTTTA
1 ATTTTA
52150168 ATTGAGAACT
Statistics
Matches: 370, Mismatches: 8, Indels: 11
0.95 0.02 0.03
Matches are distributed among these distances:
373 149 0.40
381 2 0.01
382 29 0.08
383 190 0.51
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (372 bp):
ATTTTACTTTGTATCCACACATAAGTATTATTGTGACATTTAATACTAGAAATGTTTAAATCAAT
ATGAGGTCTATAATGTCACTAAGTCAACCAAATAAATATAAATTCCAAACAATTATATGTAGCAT
TTGCTTCATGGAATAAGCCAAAATCTCTTCTTCTTCTTTTTTTTGCATTGAGTCTTGACGATTTT
ATCAAGAAGTAAGCAAATTAAAATCTAGTAGTGGACTTTGAATCCAATCAGAATCTATTAATAGA
AAAATTTGAGAGTGTATCTTATTTTCTAAGTGTGCAACAGGTACATAACCAATGACATTTCATAC
ATAAGTTTTCTCTCTTATAAGTTCTCATCAGTAATATTTTTCACGTA
Found at i:52152734 original size:26 final size:26
Alignment explanation
Indices: 52152705--52152781 Score: 145
Period size: 26 Copynumber: 3.0 Consensus size: 26
52152695 ATTGTCATAC
52152705 AAGAGAATTTAAAACAGTGTTGTACT
1 AAGAGAATTTAAAACAGTGTTGTACT
*
52152731 AAGAGAATTTAAAACAATGTTGTACT
1 AAGAGAATTTAAAACAGTGTTGTACT
52152757 AAGAGAATTTAAAACAGTGTTGTAC
1 AAGAGAATTTAAAACAGTGTTGTAC
52152782 AAGCTTGGTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (26 bp):
AAGAGAATTTAAAACAGTGTTGTACT
Found at i:52157602 original size:9 final size:9
Alignment explanation
Indices: 52157583--52157615 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
52157573 AATAAAACTT
52157583 AAAATTTAAC
1 AAAA-TTAAC
52157593 AAAATTAAC
1 AAAATTAAC
52157602 AAAATTAAC
1 AAAATTAAC
52157611 AAAAT
1 AAAAT
52157616 GAATTTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATTAAC
Found at i:52165240 original size:18 final size:18
Alignment explanation
Indices: 52165205--52165246 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
52165195 TTTTTTTTAT
52165205 AATGC-TTTTGCCTCAAA
1 AATGCTTTTTGCCTCAAA
*
52165222 AGTGCTTTTTGCC-CTAAA
1 AATGCTTTTTGCCTC-AAA
52165240 AATGCTT
1 AATGCTT
52165247 CTTCGAAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (18 bp):
AATGCTTTTTGCCTCAAA
Found at i:52165656 original size:143 final size:139
Alignment explanation
Indices: 52165315--52165687 Score: 448
Period size: 139 Copynumber: 2.7 Consensus size: 139
52165305 TCCCATCTTT
* * * *
52165315 ACCAGGCATATATCCTGCCTCCTCCATATGTGGAATAAGCAACTCTACAACCCCATTTGATCATT
1 ACCAGGCATATATCCTGCTTCTTCCATATGTAGAATAAGCAACTCTACAACCCCATTTGATCATA
* * * * *
52165380 TTCAGTAATTCAATTCCGTTTCTTAAGCTTCTCTTCTCTTCAAGTCCCACTTTCAAGATCATGTA
66 TTCAGTAATTCACTTCAGTTTCTTCAGCTTCTCTCCTCTTCAAGGCCCACTTTCAAGATCATGTA
**
52165445 TCAATGTAA
131 TCAATCAAA
* * * *
52165454 ACCAGGCATTTACCCTGTTTCTTCCATATGTAGAACAAGCAACT-TAACAACCCCATTTGATCAT
1 ACCAGGCATATATCCTGCTTCTTCCATATGTAGAATAAGCAACTCT-ACAACCCCATTTGATCAT
* * *
52165518 ATTCAGTACCTT-ACTTCAGTTTCTTCAGCTTCTCTCCT-TTGAAGGCCTA-TCTTCAAGATCAT
65 ATTCAGTA-ATTCACTTCAGTTTCTTCAGCTTCTCTCCTCTTCAAGGCCCACT-TTCAAGATCAT
52165580 GTATCAAACAATCAAA
128 GTAT----CAATCAAA
* * *
52165596 ACCAGGCATGTATCCTAGCTTCTTCCATATTTAGAATAAGCAACTCTATAACCCCATTTGATCAT
1 ACCAGGCATATATCCT-GCTTCTTCCATATGTAGAATAAGCAACTCTACAACCCCATTTGATCAT
*
52165661 GTTCAGTAATTCACTTCAGTTTCTTCA
65 ATTCAGTAATTCACTTCAGTTTCTTCA
52165688 AATCCCATCT
Statistics
Matches: 198, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
137 1 0.01
138 24 0.12
139 84 0.42
140 2 0.01
142 22 0.11
143 64 0.32
144 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (139 bp):
ACCAGGCATATATCCTGCTTCTTCCATATGTAGAATAAGCAACTCTACAACCCCATTTGATCATA
TTCAGTAATTCACTTCAGTTTCTTCAGCTTCTCTCCTCTTCAAGGCCCACTTTCAAGATCATGTA
TCAATCAAA
Found at i:52168057 original size:11 final size:11
Alignment explanation
Indices: 52168043--52168068 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
52168033 TTTTTAATTA
52168043 TTTAATAATAT
1 TTTAATAATAT
52168054 TTTAATAATAT
1 TTTAATAATAT
52168065 TTTA
1 TTTA
52168069 TATTATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTAATAATAT
Found at i:52169584 original size:22 final size:22
Alignment explanation
Indices: 52169522--52169593 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
52169512 TTAGTTCAAA
* **
52169522 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
52169544 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
52169566 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
52169588 CATGAG
1 CATGAG
52169594 GGTTTCTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:52169684 original size:29 final size:29
Alignment explanation
Indices: 52169642--52169698 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
52169632 AGGATTTACC
*
52169642 TTTTTAGTTTTTCATTTAATCCCACCATG
1 TTTTTAGCTTTTCATTTAATCCCACCATG
52169671 TTTTTAGCTTTTCATTTAATCCCACCAT
1 TTTTTAGCTTTTCATTTAATCCCACCAT
52169699 TGAGGATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (29 bp):
TTTTTAGCTTTTCATTTAATCCCACCATG
Found at i:52169751 original size:45 final size:44
Alignment explanation
Indices: 52169668--52169791 Score: 175
Period size: 45 Copynumber: 2.9 Consensus size: 44
52169658 TAATCCCACC
*
52169668 ATGTTTTTAGCTTTTCATTTAATCCCAC-C-ATT--GAGGATTT
1 ATGTTTTTAGCTTTTCATTTAATCCCCCTCAATTAGGAGGATTT
52169708 ATGTTTTTAGCTTTTCATTTAATCCCTCCTCAATTAGGAGGATTT
1 ATGTTTTTAGCTTTTCATTTAATCCC-CCTCAATTAGGAGGATTT
* *
52169753 ATGTTTTTAGTTTTTCATTTAATCCCGCCTGAATTAGGA
1 ATGTTTTTAGCTTTTCATTTAATCCC-CCTCAATTAGGA
52169792 TACTTCTGTT
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
40 26 0.35
41 1 0.01
42 1 0.01
43 3 0.04
45 44 0.59
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.47
Consensus pattern (44 bp):
ATGTTTTTAGCTTTTCATTTAATCCCCCTCAATTAGGAGGATTT
Found at i:52172226 original size:23 final size:22
Alignment explanation
Indices: 52172184--52172226 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
52172174 ATTTTAACAA
*
52172184 AAATTTAATTATTAAAATATAT
1 AAATTTAATTATAAAAATATAT
52172206 AAATATTAA-TATAAAAGATAT
1 AAAT-TTAATTATAAAA-ATAT
52172227 TCTTTTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATTTAATTATAAAAATATAT
Found at i:52174853 original size:42 final size:43
Alignment explanation
Indices: 52174794--52174890 Score: 137
Period size: 42 Copynumber: 2.3 Consensus size: 43
52174784 AAGCCCCAAG
* **
52174794 TTAATCTCACC-CGAATT-AGTATTTATCTTTTTATTTTTTCAT
1 TTAATCCCACCTCGAATTAAG-ATTTATCTTTTTAGCTTTTCAT
52174836 TTAATCCCACCTC-AATTAAGATTTATCTTTTTAGCTTTTCAT
1 TTAATCCCACCTCGAATTAAGATTTATCTTTTTAGCTTTTCAT
52174878 TTAATCCCACCTC
1 TTAATCCCACCTC
52174891 TTTATTTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
42 47 0.94
43 3 0.06
ACGTcount: A:0.25, C:0.23, G:0.04, T:0.48
Consensus pattern (43 bp):
TTAATCCCACCTCGAATTAAGATTTATCTTTTTAGCTTTTCAT
Found at i:52174900 original size:33 final size:33
Alignment explanation
Indices: 52174856--52174951 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 33
52174846 CTCAATTAAG
52174856 ATTTATCTTTTTAGCTTTTCATTTAATCCCACCT
1 ATTTATCTTTTTAG-TTTTCATTTAATCCCACCT
* **
52174890 CTTTA---TTTT--TTTTCATTTAATCCCA-GG
1 ATTTATCTTTTTAGTTTTCATTTAATCCCACCT
* *
52174917 ATTTATGTTTTTAGTTTTTCATTTAATCTCACCT
1 ATTTATCTTTTTAG-TTTTCATTTAATCCCACCT
52174951 A
1 A
52174952 AGTTTTATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
27 4 0.08
28 16 0.33
30 4 0.08
31 4 0.08
33 15 0.31
34 5 0.10
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.55
Consensus pattern (33 bp):
ATTTATCTTTTTAGTTTTCATTTAATCCCACCT
Found at i:52178028 original size:6 final size:6
Alignment explanation
Indices: 52178017--52178047 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
52178007 GAATATAAAC
52178017 GTATAT GTATAT GTATAT GTATAT GTATAT G
1 GTATAT GTATAT GTATAT GTATAT GTATAT G
52178048 CATACCTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (6 bp):
GTATAT
Found at i:52184632 original size:4 final size:4
Alignment explanation
Indices: 52184623--52184657 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
52184613 TATTAAAATT
52184623 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
52184658 TATTTGTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:52197154 original size:6 final size:6
Alignment explanation
Indices: 52197143--52197191 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
52197133 TCTATTTATT
52197143 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
52197191 T
1 T
52197192 CTATCCTGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TATGTA
Found at i:52198576 original size:13 final size:13
Alignment explanation
Indices: 52198558--52198583 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52198548 TTTTATTTGT
52198558 TTATTCCCACCGG
1 TTATTCCCACCGG
52198571 TTATTCCCACCGG
1 TTATTCCCACCGG
52198584 CTGAATGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.15, T:0.31
Consensus pattern (13 bp):
TTATTCCCACCGG
Found at i:52200518 original size:25 final size:25
Alignment explanation
Indices: 52200490--52200551 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
52200480 GCTGAAGCTC
52200490 TAGTTGCAATTCAAGAGGTATTTTA
1 TAGTTGCAATTCAAGAGGTATTTTA
*
52200515 TAGTTGCAATTCAAGAGGTTTTTTA
1 TAGTTGCAATTCAAGAGGTATTTTA
52200540 TAGTTGCAATTC
1 TAGTTGCAATTC
52200552 CAGTAAATTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (25 bp):
TAGTTGCAATTCAAGAGGTATTTTA
Found at i:52200978 original size:29 final size:29
Alignment explanation
Indices: 52200940--52200998 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
52200930 GGACTATATA
52200940 AATCGATAATGATTGAAATACATCAAAAT
1 AATCGATAATGATTGAAATACATCAAAAT
52200969 AATCGATAATGATTGAAATACATCAAAAT
1 AATCGATAATGATTGAAATACATCAAAAT
52200998 A
1 A
52200999 CATCAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (29 bp):
AATCGATAATGATTGAAATACATCAAAAT
Found at i:52201008 original size:29 final size:29
Alignment explanation
Indices: 52200940--52201009 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
52200930 GGACTATATA
*
52200940 AATCGATAATGATTGAAATACATCAAAAT
1 AATCGAAAATGATTGAAATACATCAAAAT
*
52200969 AATCGATAATGATTGAAATACATCAAAAT
1 AATCGAAAATGATTGAAATACATCAAAAT
52200998 ACATC-AAAATGA
1 A-ATCGAAAATGA
52201010 AATTAAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 36 0.92
30 3 0.08
ACGTcount: A:0.53, C:0.11, G:0.10, T:0.26
Consensus pattern (29 bp):
AATCGAAAATGATTGAAATACATCAAAAT
Found at i:52202061 original size:52 final size:52
Alignment explanation
Indices: 52201983--52202086 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
52201973 AGTCGTCAAG
52201983 GCACATGCTTGTTGATGAGCAAGTTGCAATGTTTTTACATATCATTTCCCAT
1 GCACATGCTTGTTGATGAGCAAGTTGCAATGTTTTTACATATCATTTCCCAT
52202035 GCACATGCTTGTTGATGAGCAAGTTGCAATGTTTTTACATATCATTTCCCAT
1 GCACATGCTTGTTGATGAGCAAGTTGCAATGTTTTTACATATCATTTCCCAT
52202087 CACCTTAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (52 bp):
GCACATGCTTGTTGATGAGCAAGTTGCAATGTTTTTACATATCATTTCCCAT
Found at i:52204887 original size:26 final size:28
Alignment explanation
Indices: 52204745--52204896 Score: 88
Period size: 28 Copynumber: 5.6 Consensus size: 28
52204735 TAATAATGTA
52204745 TATTA-TAAATTATATTTAA-TAATAAT
1 TATTATTAAATTATATTTAATTAATAAT
* *
52204771 TA-T-TTAAATTATATTTTA-TAGT-AT
1 TATTATTAAATTATATTTAATTAATAAT
* * * * *
52204795 TATATATTATGATTTTAGTAAATTCAT-AT
1 TAT-TATTA-AATTATATTTAATTAATAAT
* ** * * * *
52204824 AAGAATAAGAATTTTATTTAATTATTTAT
1 TATTATTA-AATTATATTTAATTAATAAT
52204853 TATTATTAAATTATATTTAA-TAATAAT
1 TATTATTAAATTATATTTAATTAATAAT
52204880 TATT-TTAAATTATATTT
1 TATTATTAAATTATATTT
52204897 TAGTATTATA
Statistics
Matches: 93, Mismatches: 26, Indels: 14
0.70 0.20 0.11
Matches are distributed among these distances:
24 4 0.04
25 17 0.18
26 16 0.17
27 12 0.13
28 33 0.35
29 11 0.12
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (28 bp):
TATTATTAAATTATATTTAATTAATAAT
Found at i:52204966 original size:108 final size:106
Alignment explanation
Indices: 52204745--52204960 Score: 291
Period size: 109 Copynumber: 2.0 Consensus size: 106
52204735 TAATAATGTA
52204745 TATTA-TAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATT
1 TATTATTAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATT
* *
52204809 TTAGTAAATTCATATAAGAATAAGAATTTTATTTAATTATTTAT
66 TTAGTAAATTCATATAAGAAT---AATTTTATTAAAATATTTAT
52204853 TATTATTAAATTATATTTAATAATAATTATTTTAAATTATA-TTT-TAGTATTATATATTATGAT
1 TATTATTAAATTATATTTAATAATAATTA-TTTAAATTATATTTTATAGTATTATATATTATGA-
*
52204916 TTTATTAGTAAATTTATATAAGAAT-A-TTTATTAACAAT-TTTAT
64 -TT-TTAGTAAATTCATATAAGAATAATTTTATTAA-AATATTTAT
52204959 TA
1 TA
52204961 AATTATATTT
Statistics
Matches: 99, Mismatches: 3, Indels: 14
0.85 0.03 0.12
Matches are distributed among these distances:
106 14 0.14
107 3 0.03
108 23 0.23
109 26 0.26
110 13 0.13
111 20 0.20
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (106 bp):
TATTATTAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATT
TTAGTAAATTCATATAAGAATAATTTTATTAAAATATTTAT
Found at i:52204981 original size:100 final size:105
Alignment explanation
Indices: 52204745--52204988 Score: 301
Period size: 100 Copynumber: 2.3 Consensus size: 105
52204735 TAATAATGTA
52204745 TATTA-TAAATTATATTTAATAATAATTA-TTTAAATTATATTTTATAGTATTATATATTATGAT
1 TATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGAT
*
52204808 TTTAGTAAATTCATATAAGAATAAGAATTTTATTTAATTATTTAT
66 TTTAGTAAATTCATATAAGAAT---AATTTTATTTAATCA--TAT
52204853 TATTATTAAATTATATTTAATAATAATTATTTTAAATTATA-TTT-TAGTATTATATATTATGAT
1 TATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGA-
*
52204916 TTTATTAGTAAATTTATATAAGAAT-A-TTTA-TTAA-CA-AT
65 -TT-TTAGTAAATTCATATAAGAATAATTTTATTTAATCATAT
* * *
52204954 T-TTATTAAATTATATTTTATAACAATTATGTTAAA
1 TATTATTAAATTATATTTAATAATAATTATTTTAAA
52204989 ATATGATTAA
Statistics
Matches: 126, Mismatches: 5, Indels: 18
0.85 0.03 0.12
Matches are distributed among these distances:
100 31 0.25
101 3 0.02
104 1 0.01
105 4 0.03
106 4 0.03
107 1 0.01
108 23 0.18
109 26 0.21
110 13 0.10
111 20 0.16
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (105 bp):
TATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGAT
TTTAGTAAATTCATATAAGAATAATTTTATTTAATCATAT
Found at i:52204992 original size:24 final size:25
Alignment explanation
Indices: 52204929--52204992 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
52204919 ATTAGTAAAT
52204929 TTATA-TAAGAATA-TTTATTAACAA
1 TTATATTAA-AATATTTTATTAACAA
*
52204953 TTTTATTAAATTATATTTTA-TAACAA
1 TTATATTAAA--ATATTTTATTAACAA
*
52204979 TTATGTTAAAATAT
1 TTATATTAAAATAT
52204993 GATTAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
24 9 0.27
25 3 0.09
26 17 0.52
27 4 0.12
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (25 bp):
TTATATTAAAATATTTTATTAACAA
Found at i:52205160 original size:39 final size:41
Alignment explanation
Indices: 52205115--52205220 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
52205105 TTTCCTTATG
* *
52205115 CTATTACATCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACACCTCTATTCCATTCAACCAAACAAAAGAATTAC
52205155 C-ATTACACCTCTATTCCATTACATTCAACCAAACAAAAGAATTAC
1 CTATTACACCTCTATT-C----CATTCAACCAAACAAAAGAATTAC
*
52205200 CTATTACGCCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
52205221 ACAGCGAACT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 13 0.23
40 2 0.04
41 4 0.07
44 19 0.34
45 5 0.09
46 13 0.23
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (41 bp):
CTATTACACCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:52205195 original size:44 final size:46
Alignment explanation
Indices: 52205132--52205223 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
52205122 ATCTCTATTC
*
52205132 CATTCAACCAAACACAAGAA-TACC-ATTACACCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACACCTCTATTCCATTA
*
52205176 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACACCTCTATTCCATTA
52205222 CA
1 CA
52205224 GCGAACTACC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 19 0.43
45 4 0.09
46 21 0.48
ACGTcount: A:0.40, C:0.30, G:0.03, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACACCTCTATTCCATTA
Found at i:52205236 original size:24 final size:24
Alignment explanation
Indices: 52205208--52205255 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
52205198 ACCTATTACG
*
52205208 CCTCTATTCCATTACAGCGAACTA
1 CCTCTATTACATTACAGCGAACTA
52205232 CCTCTATTACATTACAGCGAACTA
1 CCTCTATTACATTACAGCGAACTA
52205256 AACGTATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.29
Consensus pattern (24 bp):
CCTCTATTACATTACAGCGAACTA
Found at i:52210904 original size:16 final size:17
Alignment explanation
Indices: 52210883--52210928 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
52210873 GGTAAAGAGT
52210883 TAAAATAATTTAAAT-A
1 TAAAATAATTTAAATCA
* *
52210899 TAAAATAATTAAAATCT
1 TAAAATAATTTAAATCA
*
52210916 TAAAATGATTTAA
1 TAAAATAATTTAA
52210929 TTATGAATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAAATAATTTAAATCA
Found at i:52211005 original size:41 final size:41
Alignment explanation
Indices: 52210924--52211005 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
52210914 CTTAAAATGA
52210924 TTTAATTATGAATTGATCTGAACATATAACAAAAAAAATCC
1 TTTAATTATGAATTGATCTGAACATATAACAAAAAAAATCC
* * * * *
52210965 TTTAATTATGAATTTATTTGAACATGTAACCAAAATAATCC
1 TTTAATTATGAATTGATCTGAACATATAACAAAAAAAATCC
52211006 AAATTTTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.35
Consensus pattern (41 bp):
TTTAATTATGAATTGATCTGAACATATAACAAAAAAAATCC
Found at i:52217742 original size:73 final size:76
Alignment explanation
Indices: 52217585--52217747 Score: 224
Period size: 80 Copynumber: 2.1 Consensus size: 76
52217575 CTTCAACATT
** *
52217585 AATAGAAAATTTGACATTAATAAAAGGAGTTCCCTTTTAGGAAAACACAAACTAAAAAATTCCTA
1 AATAGAAAGGTTGACATTAATAAAAGGAGTTCCCTTTTAGGAAAACACAAACTAAAAAAGTCC--
52217650 TTGACGACCTAATTA
64 -TGA-GACCTAATTA
* *
52217665 AATAGAAAGGTTGATATTAATAAAAGGAGTTCTCTTTTAGGAAAACACAAACT-AAAAAGTCC-G
1 AATAGAAAGGTTGACATTAATAAAAGGAGTTCCCTTTTAGGAAAACACAAACTAAAAAAGTCCTG
52217728 -GACCTAATTA
66 AGACCTAATTA
52217738 AATAGAAAGG
1 AATAGAAAGG
52217748 ATAATTAAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
73 20 0.26
75 1 0.01
79 8 0.10
80 49 0.63
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.26
Consensus pattern (76 bp):
AATAGAAAGGTTGACATTAATAAAAGGAGTTCCCTTTTAGGAAAACACAAACTAAAAAAGTCCTG
AGACCTAATTA
Found at i:52217760 original size:21 final size:21
Alignment explanation
Indices: 52217736--52217779 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
52217726 CGGACCTAAT
*
52217736 TAAATAGAAAGGATA-ATTAAA
1 TAAATA-AAAGGATACAATAAA
*
52217757 TAAATAAAATGATACAATAAA
1 TAAATAAAAGGATACAATAAA
52217778 TA
1 TA
52217780 CTAAAGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (21 bp):
TAAATAAAAGGATACAATAAA
Found at i:52218586 original size:7 final size:7
Alignment explanation
Indices: 52218576--52218601 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52218566 CTAATTCCCC
52218576 TTCCCAT
1 TTCCCAT
52218583 TTCCCAT
1 TTCCCAT
52218590 TTCCCAT
1 TTCCCAT
52218597 TTCCC
1 TTCCC
52218602 GACCCGGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.46, G:0.00, T:0.42
Consensus pattern (7 bp):
TTCCCAT
Found at i:52220730 original size:13 final size:13
Alignment explanation
Indices: 52220712--52220859 Score: 124
Period size: 13 Copynumber: 11.5 Consensus size: 13
52220702 ATTTTTAATG
*
52220712 TAATATACTATTT
1 TAATATACTGTTT
* *
52220725 TAATATGCTGTTA
1 TAATATACTGTTT
*
52220738 TAA-A-A-T-TTG
1 TAATATACTGTTT
*
52220747 TAATATTCTGTTT
1 TAATATACTGTTT
52220760 TAATATACTGTTAT
1 TAATATACTGTT-T
* * *
52220774 AAATATATTATTT
1 TAATATACTGTTT
52220787 TAATATACTGTTT
1 TAATATACTGTTT
* *
52220800 TAGTATATTGTTAT
1 TAATATACTGTT-T
* *
52220814 AAATATACTATTT
1 TAATATACTGTTT
*
52220827 TAATATAATGTTT
1 TAATATACTGTTT
*
52220840 TAATATATTGTTT
1 TAATATACTGTTT
52220853 TAATATA
1 TAATATA
52220860 TCGTTATAAA
Statistics
Matches: 105, Mismatches: 24, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
9 5 0.05
10 2 0.02
12 2 0.02
13 77 0.73
14 19 0.18
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:52220745 original size:40 final size:38
Alignment explanation
Indices: 52220704--52220851 Score: 122
Period size: 40 Copynumber: 3.8 Consensus size: 38
52220694 AAACATTAAT
* *
52220704 TTTTAATGTAATATACTATTTTAATATGCTGTTATAAAA
1 TTTT-ATGTAATATACTGTTTTAATATACTGTTATAAAA
*
52220743 --TT-TGTAATATTCTGTTTTAATATACTGTTATAAATA
1 TTTTATGTAATATACTGTTTTAATATACTGTTATAAA-A
* * * *
52220779 TATTATTTTAATATACTGTTTTAGTATATTGTTATAAATA
1 TTTTA-TGTAATATACTGTTTTAATATACTGTTATAAA-A
** * * *
52220819 TACTATTTTAATATAATGTTTTAATATATTGTT
1 TTTTA-TGTAATATACTGTTTTAATATACTGTT
52220852 TTAATATATC
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
35 29 0.31
36 1 0.01
37 2 0.02
38 2 0.02
40 60 0.64
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.53
Consensus pattern (38 bp):
TTTTATGTAATATACTGTTTTAATATACTGTTATAAAA
Done.