Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 88 of 97
Found at i:34611404 original size:100 final size:100
Alignment explanation
Indices: 34611231--34611529 Score: 501
Period size: 100 Copynumber: 3.0 Consensus size: 100
34611221 AGATTATCCA
* *
34611231 GAAATAGTTACTACTATTATATATTTATTTACAGTGTATTTCAGTTATCATTTCTGCATGATATT
1 GAAATAGTTACTACTATTATATATTCATTTACAGTGTATTTCAGTTATCATTTCTACATGATATT
34611296 TATAACATATTAAGAGTTTTTTAGCAATCAACTAT
66 TATAACATATTAAGAGTTTTTTAGCAATCAACTAT
* * *
34611331 GAAATAGTTACTGCTATTATATATTCATTTACAGAGTATTTCTGTTATCATTTCTACATGATATT
1 GAAATAGTTACTACTATTATATATTCATTTACAGTGTATTTCAGTTATCATTTCTACATGATATT
34611396 TATAACATATTAAGAG-TTTTTAGCAATCAACTAT
66 TATAACATATTAAGAGTTTTTTAGCAATCAACTAT
* * * *
34611430 GAAATAGTTACTACTATTATATATTCATTTACAGTGTATGTCAGTTATCACTTCTACAGGTTATT
1 GAAATAGTTACTACTATTATATATTCATTTACAGTGTATTTCAGTTATCATTTCTACATGATATT
*
34611495 TATAACATATTAAGAGTTATTTAGCAATCAACTAT
66 TATAACATATTAAGAGTTTTTTAGCAATCAACTAT
34611530 AGCTTGGACC
Statistics
Matches: 185, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
99 92 0.50
100 93 0.50
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (100 bp):
GAAATAGTTACTACTATTATATATTCATTTACAGTGTATTTCAGTTATCATTTCTACATGATATT
TATAACATATTAAGAGTTTTTTAGCAATCAACTAT
Found at i:34611477 original size:99 final size:99
Alignment explanation
Indices: 34611231--34611529 Score: 499
Period size: 99 Copynumber: 3.0 Consensus size: 99
34611221 AGATTATCCA
* *
34611231 GAAATAGTTACTACTATTATATATTTATTTACAGTGTATTTCAGTTATCATTTCTGCATGATATT
1 GAAATAGTTACTACTATTATATATTCATTTACAGTGTATTTCAGTTATCATTTCTACATGATATT
34611296 TATAACATATTAAGAGTTTTTTAGCAATCAACTAT
66 TATAACATATTAAGAG-TTTTTAGCAATCAACTAT
* * *
34611331 GAAATAGTTACTGCTATTATATATTCATTTACAGAGTATTTCTGTTATCATTTCTACATGATATT
1 GAAATAGTTACTACTATTATATATTCATTTACAGTGTATTTCAGTTATCATTTCTACATGATATT
34611396 TATAACATATTAAGAGTTTTTAGCAATCAACTAT
66 TATAACATATTAAGAGTTTTTAGCAATCAACTAT
* * * *
34611430 GAAATAGTTACTACTATTATATATTCATTTACAGTGTATGTCAGTTATCACTTCTACAGGTTATT
1 GAAATAGTTACTACTATTATATATTCATTTACAGTGTATTTCAGTTATCATTTCTACATGATATT
34611495 TATAACATATTAAGAGTTATTTAGCAATCAACTAT
66 TATAACATATTAAGAGTT-TTTAGCAATCAACTAT
34611530 AGCTTGGACC
Statistics
Matches: 186, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
99 94 0.51
100 92 0.49
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (99 bp):
GAAATAGTTACTACTATTATATATTCATTTACAGTGTATTTCAGTTATCATTTCTACATGATATT
TATAACATATTAAGAGTTTTTAGCAATCAACTAT
Found at i:34623153 original size:13 final size:13
Alignment explanation
Indices: 34623133--34623165 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
34623123 CCGATCACAC
34623133 AAAAAAGAAT-GA
1 AAAAAAGAATAGA
34623145 AAGAAAAGAATAGA
1 AA-AAAAGAATAGA
34623159 AAAAAAG
1 AAAAAAG
34623166 GAACTGTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 13 0.68
14 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (13 bp):
AAAAAAGAATAGA
Found at i:34627288 original size:3 final size:3
Alignment explanation
Indices: 34627280--34627309 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
34627270 TCTCGTTCTC
*
34627280 GTT GTT GTT GTT GTT GTT GTT GTT GCT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
34627310 CTAAAGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.03, G:0.33, T:0.63
Consensus pattern (3 bp):
GTT
Found at i:34630510 original size:33 final size:33
Alignment explanation
Indices: 34630473--34630541 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
34630463 GAGTTTCAAT
34630473 TACACAGAAATACAAGACAGATTAAGCAAAACA
1 TACACAGAAATACAAGACAGATTAAGCAAAACA
*
34630506 TACACAGAAATACAAGACAGATTGAGCAAAACA
1 TACACAGAAATACAAGACAGATTAAGCAAAACA
34630539 TAC
1 TAC
34630542 TTGAAATGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (33 bp):
TACACAGAAATACAAGACAGATTAAGCAAAACA
Found at i:34630931 original size:2 final size:2
Alignment explanation
Indices: 34630924--34631037 Score: 99
Period size: 2 Copynumber: 58.5 Consensus size: 2
34630914 AATTATCCCC
* *
34630924 AT AT AT AT AT AT AT AT AT AT AC CT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * ** * * * *
34630965 AT AT AT AT AT AC AC GC NT AT AT GT AT GT TT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
34631006 AT AT AT AT AT AT A- AT AT AT AT TT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34631038 CACGCTCGCG
Statistics
Matches: 91, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
1 3 0.03
2 88 0.97
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:34635473 original size:28 final size:28
Alignment explanation
Indices: 34635442--34635534 Score: 102
Period size: 28 Copynumber: 3.2 Consensus size: 28
34635432 GATTTTAAAT
34635442 ATAAAAATTTGATTAGATATAATAAAAA
1 ATAAAAATTTGATTAGATATAATAAAAA
* *
34635470 ATAAAAA-TT-ATTTAAATTTTTAA-AANAAA
1 ATAAAAATTTGA-TTAGA--TATAATAA-AAA
34635499 TATAAAAATTTGATTAGATATAATAAAAA
1 -ATAAAAATTTGATTAGATATAATAAAAA
34635528 ATAAAAA
1 ATAAAAA
34635535 AAATTATTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
26 1 0.02
27 6 0.11
28 16 0.30
29 14 0.26
30 9 0.17
31 6 0.11
32 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.33
Consensus pattern (28 bp):
ATAAAAATTTGATTAGATATAATAAAAA
Found at i:34635502 original size:58 final size:59
Alignment explanation
Indices: 34635438--34635556 Score: 197
Period size: 58 Copynumber: 2.0 Consensus size: 59
34635428 TTAAGATTTT
34635438 AAATATAAAAATTTGATTAGATATAATAAAAAAT-AAAAATTATTTAAA-TTTTTAAAA
1 AAATATAAAAATTTGATTAGATATAATAAAAAATAAAAAATTATTTAAATTTTTTAAAA
34635495 NAAATATAAAAATTTGATTAGATATAATAAAAAATAAAAAAAATTATTTAAATTTTTTAAAA
1 -AAATATAAAAATTTGATTAGATATAATAAAAAAT--AAAAAATTATTTAAATTTTTTAAAA
34635557 CACGTAAAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
58 34 0.60
61 14 0.25
62 9 0.16
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (59 bp):
AAATATAAAAATTTGATTAGATATAATAAAAAATAAAAAATTATTTAAATTTTTTAAAA
Found at i:34635530 original size:30 final size:30
Alignment explanation
Indices: 34635438--34635536 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 30
34635428 TTAAGATTTT
34635438 AAATATAAAAATTTGATTAGATATAAT-AA
1 AAATATAAAAATTTGATTAGATATAATAAA
* * *
34635467 AAA-ATAAAAA-TT-ATTTAAATTTTTAA-AAN
1 AAATATAAAAATTTGA-TTAGA--TATAATAAA
34635496 AAATATAAAAATTTGATTAGATATAATAAA
1 AAATATAAAAATTTGATTAGATATAATAAA
*
34635526 AAATAAAAAAA
1 AAATATAAAAA
34635537 ATTATTTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
26 1 0.02
27 6 0.11
28 7 0.13
29 15 0.27
30 19 0.35
31 6 0.11
32 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.32
Consensus pattern (30 bp):
AAATATAAAAATTTGATTAGATATAATAAA
Found at i:34635556 original size:30 final size:30
Alignment explanation
Indices: 34635472--34635556 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
34635462 AATAAAAAAT
* *
34635472 AAAAATTATTTAAATTTTTAAAANAAATATA
1 AAAAATTATTTAAATTTTTTAAA-AAATAAA
* * * **
34635503 AAAATTTGA-TTAGATATAATAAAAAATAAA
1 AAAAATT-ATTTAAATTTTTTAAAAAATAAA
34635533 AAAAATTATTTAAATTTTTTAAAA
1 AAAAATTATTTAAATTTTTTAAAA
34635557 CACGTAAAGA
Statistics
Matches: 40, Mismatches: 12, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
29 1 0.03
30 23 0.57
31 15 0.38
32 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAAATTATTTAAATTTTTTAAAAAATAAA
Found at i:34647861 original size:21 final size:21
Alignment explanation
Indices: 34647823--34647880 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
34647813 AATTAATAAT
*
34647823 TTATTTAAAATATT-AATATTC
1 TTATTTATAAT-TTAAATATTC
34647844 TTATTTATAATTTAAATA--C
1 TTATTTATAATTTAAATATTC
*
34647863 -TA-TTATAATTCAAATATT
1 TTATTTATAATTTAAATATT
34647881 AATAATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 13 0.41
18 2 0.06
19 1 0.03
20 2 0.06
21 14 0.44
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTTATAATTTAAATATTC
Found at i:34652273 original size:18 final size:19
Alignment explanation
Indices: 34652249--34652292 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
34652239 CTGTTCACTG
*
34652249 ATTTAATCGATTAA-TCGA
1 ATTTAATCCATTAATTCGA
*
34652267 CTTTAATCCATTAATTCGA
1 ATTTAATCCATTAATTCGA
34652286 ATTTAAT
1 ATTTAAT
34652293 TGACTTAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (19 bp):
ATTTAATCCATTAATTCGA
Found at i:34657551 original size:26 final size:27
Alignment explanation
Indices: 34657505--34657558 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
34657495 TTTTAAATAT
* *
34657505 TTTTTATTTTTATTATATTTAATTAAA
1 TTTTTATATTTATTATATTTAATCAAA
*
34657532 TTTTTATATTT-TTATTTTTAATCAAA
1 TTTTTATATTTATTATATTTAATCAAA
34657558 T
1 T
34657559 AAACTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTTATATTTATTATATTTAATCAAA
Found at i:34660035 original size:64 final size:64
Alignment explanation
Indices: 34659967--34660780 Score: 904
Period size: 64 Copynumber: 12.7 Consensus size: 64
34659957 ATTTGATATA
* * * *
34659967 TTAACTTGTGATGTTAATTTAGTTATTCATTATATAATAATATAAATATGGGTAGCATCAATAA
1 TTAACTTGTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
* * ** * *
34660031 TTAACTTGTAATGTTAATTCAGTTATTCGTTATATAATAATATAAATATAAGTAGCATTAATAA
1 TTAACTTGTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
* * ** * * *
34660095 ATAGCTTGTGACATTAATTTAGTTATTCGTTATATGATAATATAGATATGGATAGCATCAATAG
1 TTAACTTGTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
*
34660159 TTAACTTGTGACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
1 TTAACTTGTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
* * * * * *
34660223 TTAACTCGTGATGTTAATTCAGTTATTCGTTATACAAGAAGATA-A-ATGGGGAGCATCGATAG
1 TTAACTTGTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
* * * * * *
34660285 TTAACTCT-TTATGTTAATTCTGTTATTCGTTATATAATAATATGGCTATGGGTAACTTCAATAG
1 TTAACT-TGTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
* * * * *** *
34660349 TTAACTTGTGATGTTGATTCAGTTATTCATTACACAATAATATAGATATAAATAGCACCAATAG
1 TTAACTTGTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
* * **
34660413 TTAACTCGTAACATTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
1 TTAACTTGTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
* * * *
34660477 TTAACTCGTGATGTTAATTCAGTTATTCGTTATACAATAAGATA-A-ATGGGAAGCATCAATAG
1 TTAACTTGTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
* * *
34660539 TTAACTTTTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATAGATAGCATCAATAG
1 TTAACTTGTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
* * * * *
34660603 TTAA-TTCGTGACGTTAATTCAGTTATTTGTTATATAATAATATAGACATGGGTAGTATTAATAG
1 TTAACTT-GTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
* ** * * * * * *
34660667 TTACCTCATAATGTTAATTCAATTATTCATTATATAATAATAAAACAGGTATGGGTAGTATTCAA
1 TTAACTTGTGATGTTAATTCAGTTATTCGTTATATAATAAT---ATAGATATGGGTAGCA-TCAA
*
34660732 TAA
62 TAG
* * * * *
34660735 TTAAC-TCTGATGTTAATTCAGTTACTCATTGTATAGTAATATAGAT
1 TTAACTTGTGATGTTAATTCAGTTATTCGTTATATAATAATATAGAT
34660781 GCATTATCAT
Statistics
Matches: 624, Mismatches: 114, Indels: 24
0.82 0.15 0.03
Matches are distributed among these distances:
62 107 0.17
63 6 0.01
64 460 0.74
65 1 0.00
67 41 0.07
68 9 0.01
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (64 bp):
TTAACTTGTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
Found at i:34660390 original size:190 final size:191
Alignment explanation
Indices: 34659967--34660780 Score: 902
Period size: 190 Copynumber: 4.2 Consensus size: 191
34659957 ATTTGATATA
* * * * *
34659967 TTAACTTGTGATGTTAATTTAGTTATTCATTATATAATAATATAAATATGGGTAGCATCAATAAT
1 TTAACTTGTGATGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAGT
* * * ** * **
34660032 TAACTTGTAATGTTAATTCAGTTATTCGTTATATAATAATATAAATATAAGTAGCATTAATAAAT
66 TAACTCGTAACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAGTT
* ** * * * *
34660097 AGCT-TGTGACATTAATTTAGTTATTCGTTATATGATAATATAGATATGGATAGCATCAATAG
131 AACTCT-TGATGTTAATTCAGTTATTCGTTATATAATAATAT-GATATGGGTAACATCAATAG
* * * *
34660159 TTAACTTGTGACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAGT
1 TTAACTTGTGATGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAGT
* * * * * * *
34660224 TAACTCGTGATGTTAATTCAGTTATTCGTTATACAAGAAGATA-A-ATGGGGAGCATCGATAGTT
66 TAACTCGTAACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAGTT
* * * *
34660287 AACTCTTTATGTTAATTCTGTTATTCGTTATATAATAATATGGCTATGGGTAACTTCAATAG
131 AACTCTTGATGTTAATTCAGTTATTCGTTATATAATAATAT-GATATGGGTAACATCAATAG
* * * * *
34660349 TTAACTTGTGATGTTGATTCAGTTATTCATTACACAATAATATAGATATAAATAGCACCAATAGT
1 TTAACTTGTGATGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAGT
*
34660414 TAACTCGTAACATTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAGTT
66 TAACTCGTAACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAGTT
* * * *
34660479 AACTCGTGATGTTAATTCAGTTATTCGTTATACAATAAGAT-AAATGGG-AAGCATCAATAG
131 AACTCTTGATGTTAATTCAGTTATTCGTTATATAATAATATGATATGGGTAA-CATCAATAG
* *
34660539 TTAACTTTTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATAGATAGCATCAATAGT
1 TTAACTTGTGATGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAGT
* * * * * *
34660604 TAATTCGTGACGTTAATTCAGTTATTTGTTATATAATAATATAGACATGGGTAGTATTAATAGTT
66 TAACTCGTAACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAGTT
* * * * * * * **
34660669 ACCTCATAATGTTAATTCAATTATTCATTATATAATAATAAAACAGGTATGGGTAGTATTCAATA
131 AACTCTTGATGTTAATTCAGTTATTCGTTATATAATAAT---A-TGATATGGGTAACA-TCAATA
*
34660734 A
191 G
* * * *
34660735 TTAAC-TCTGATGTTAATTCAGTTACTCATTGTATAGTAATATAGAT
1 TTAACTTGTGATGTTAATTCAGTTATTCATTATATAATAATATAGAT
34660781 GCATTATCAT
Statistics
Matches: 525, Mismatches: 86, Indels: 19
0.83 0.14 0.03
Matches are distributed among these distances:
189 2 0.00
190 314 0.60
191 3 0.01
192 151 0.29
193 1 0.00
195 42 0.08
196 12 0.02
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (191 bp):
TTAACTTGTGATGTTAATTCAGTTATTCATTATATAATAATATAGATATAGATAGCATCAATAGT
TAACTCGTAACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAGTT
AACTCTTGATGTTAATTCAGTTATTCGTTATATAATAATATGATATGGGTAACATCAATAG
Found at i:34660490 original size:254 final size:253
Alignment explanation
Indices: 34659967--34660758 Score: 1005
Period size: 254 Copynumber: 3.1 Consensus size: 253
34659957 ATTTGATATA
* * * * * * *
34659967 TTAACTTGTGATGTTAATTTAGTTATTCATTATATAATAATATAAATATGGGTAGCATCAATAAT
1 TTAACTCGTGATGTTAATTCAGTTATTCGTTATACAATAAGAT-AA-ATGGGAAGCATCAATAGT
* * * **
34660032 TAACTTGTAATGTTAATTCAGTTATTCGTTATATAATAATATAAATATAAGTAGCATT-AATAAA
64 TAACTT-TTATGTTAATTCAGTTATTCGTTATATAATAATATAGATATAGGTAGC-TTCAATAGT
* * * *
34660096 TAGCTTGTGACATTAATTTAGTTATTCGTTATATGATAATATAGATATGGATAGCATCAATAGTT
127 TAACTTGTGACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGATAGCATCAATAGTT
* *
34660161 AACTTGTGACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
192 AACTCGTAACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
* * *
34660223 TTAACTCGTGATGTTAATTCAGTTATTCGTTATACAAGAAGATAAATGGGGAGCATCGATAGTTA
1 TTAACTCGTGATGTTAATTCAGTTATTCGTTATACAATAAGATAAATGGGAAGCATCAATAGTTA
* * * * *
34660288 ACTCTTTATGTTAATTCTGTTATTCGTTATATAATAATATGGCTATGGGTAACTTCAATAGTTAA
66 ACT-TTTATGTTAATTCAGTTATTCGTTATATAATAATATAGATATAGGTAGCTTCAATAGTTAA
* * * * * ** *
34660353 CTTGTGATGTTGATTCAGTTATTCATTACACAATAATATAGATATAAATAGCACCAATAGTTAAC
130 CTTGTGACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGATAGCATCAATAGTTAAC
*
34660418 TCGTAACATTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
195 TCGTAACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
34660477 TTAACTCGTGATGTTAATTCAGTTATTCGTTATACAATAAGATAAATGGGAAGCATCAATAGTTA
1 TTAACTCGTGATGTTAATTCAGTTATTCGTTATACAATAAGATAAATGGGAAGCATCAATAGTTA
* *
34660542 ACTTTTGATGTTAATTCAGTTATTCGTTATATAATAATATAGATATAGATAGCATCAATAGTTAA
66 ACTTTT-ATGTTAATTCAGTTATTCGTTATATAATAATATAGATATAGGTAGCTTCAATAGTTAA
* * * * * *
34660607 -TTCGTGACGTTAATTCAGTTATTTGTTATATAATAATATAGACATGGGTAGTATTAATAGTTAC
130 CTT-GTGACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGATAGCATCAATAGTTAA
* * * * * * * *
34660671 CTCATAATGTTAATTCAATTATTCATTATATAATAATAAAACAGGTATGGGTAGTATTCAATAA
194 CTCGTAACGTTAATTCAGTTATTCGTTATATAATAAT---ATAGATATGGGTAGCA-TCAATAG
34660735 TTAACTC-TGATGTTAATTCAGTTA
1 TTAACTCGTGATGTTAATTCAGTTA
34660759 CTCATTGTAT
Statistics
Matches: 461, Mismatches: 67, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
253 7 0.02
254 371 0.80
255 3 0.01
256 37 0.08
257 30 0.07
258 13 0.03
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (253 bp):
TTAACTCGTGATGTTAATTCAGTTATTCGTTATACAATAAGATAAATGGGAAGCATCAATAGTTA
ACTTTTATGTTAATTCAGTTATTCGTTATATAATAATATAGATATAGGTAGCTTCAATAGTTAAC
TTGTGACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGATAGCATCAATAGTTAACT
CGTAACGTTAATTCAGTTATTCGTTATATAATAATATAGATATGGGTAGCATCAATAG
Found at i:34661491 original size:17 final size:19
Alignment explanation
Indices: 34661469--34661506 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
34661459 AGAGAATTTT
34661469 TATTTTTAT-T-TTAAAAA
1 TATTTTTATCTATTAAAAA
34661486 TATTTTTATCTATTAAAAA
1 TATTTTTATCTATTAAAAA
34661505 TA
1 TA
34661507 ATTACAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 1 0.05
19 9 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTTTATCTATTAAAAA
Found at i:34667427 original size:2 final size:2
Alignment explanation
Indices: 34667420--34667446 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34667410 TTCTTTGTAT
34667420 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
34667447 TACTTTCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34671812 original size:26 final size:26
Alignment explanation
Indices: 34671730--34671814 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 26
34671720 CATGCTTACA
* *
34671730 TGTAACAACATTTTTTTCAAAATAATG
1 TGTAATAACA-TTTTTTCAATATAATG
* * * * *
34671757 TGCAATAAAATTTTTTTAAGTATGACG
1 TGTAATAACATTTTTTCAA-TATAATG
*
34671784 TGTAATAACATTTTTTGAATATAATG
1 TGTAATAACATTTTTTCAATATAATG
34671810 TGTAA
1 TGTAA
34671815 CTTGCTCCTT
Statistics
Matches: 45, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
26 18 0.40
27 27 0.60
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (26 bp):
TGTAATAACATTTTTTCAATATAATG
Found at i:34672790 original size:36 final size:35
Alignment explanation
Indices: 34672720--34672798 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 35
34672710 ATTATTCCAA
* * *
34672720 ATTGGAGGGGTTCACACTCCCCGCCCAACAAACTC
1 ATTGAAGGCGTTCACACCCCCCGCCCAACAAACTC
* *
34672755 ATTGAAGGCGTTCACACCCCCCCTCCCTACAAACTC
1 ATTGAAGGCGTTCACA-CCCCCCGCCCAACAAACTC
34672791 ATTGAAGG
1 ATTGAAGG
34672799 GGTCTCTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
35 14 0.37
36 24 0.63
ACGTcount: A:0.27, C:0.37, G:0.18, T:0.19
Consensus pattern (35 bp):
ATTGAAGGCGTTCACACCCCCCGCCCAACAAACTC
Found at i:34674197 original size:2 final size:2
Alignment explanation
Indices: 34674190--34674263 Score: 58
Period size: 2 Copynumber: 37.0 Consensus size: 2
34674180 ACGTGTATGC
* * * * * * *
34674190 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT GT GT GT GT GT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* **
34674232 GT NC 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
34674264 GTGTGTGTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.38, C:0.01, G:0.11, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34685155 original size:23 final size:21
Alignment explanation
Indices: 34685128--34685199 Score: 62
Period size: 23 Copynumber: 3.4 Consensus size: 21
34685118 AAAATGTTCT
34685128 TTATAAGTTTAAAAAATTACATA
1 TTATAA-TTTAAAAAATTA-ATA
34685151 TTATATATTATAAAAAA-TAATA
1 TTATA-ATT-TAAAAAATTAATA
*
34685173 TT-TAAATTTTAAAAATTAAT-
1 TTAT-AATTTAAAAAATTAATA
34685193 TTA-AATT
1 TTATAATT
34685200 ATTAATATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
19 4 0.09
20 8 0.19
21 8 0.19
22 6 0.14
23 9 0.21
24 8 0.19
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (21 bp):
TTATAATTTAAAAAATTAATA
Found at i:34685188 original size:20 final size:20
Alignment explanation
Indices: 34685157--34685204 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
34685147 CATATTATAT
*
34685157 ATTATAAAAAATAATATTTAA
1 ATTATTAAAAATAA-ATTTAA
*
34685178 ATT-TTAAAAATTAATTTAA
1 ATTATTAAAAATAAATTTAA
34685197 ATTATTAA
1 ATTATTAA
34685205 TATTTGAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTATTAAAAATAAATTTAA
Found at i:34685253 original size:25 final size:26
Alignment explanation
Indices: 34685223--34685284 Score: 101
Period size: 25 Copynumber: 2.4 Consensus size: 26
34685213 CCATAATAAC
34685223 ATTTAAATTATA-AATAAAATATTAAT
1 ATTTAAATTATATAA-AAAATATTAAT
34685249 A-TTAAATTATATAAAAAATATTAAT
1 ATTTAAATTATATAAAAAATATTAAT
34685274 ATTTAAATTAT
1 ATTTAAATTAT
34685285 CAATTATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 22 0.65
26 12 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTTAAATTATATAAAAAATATTAAT
Found at i:34685445 original size:42 final size:42
Alignment explanation
Indices: 34685399--34685502 Score: 201
Period size: 41 Copynumber: 2.5 Consensus size: 42
34685389 TTTAATCATA
34685399 ATAAATAAAATATTAATATTTTTTAAATGTTATGATTAAATT
1 ATAAATAAAATATTAATATTTTTTAAATGTTATGATTAAATT
34685441 ATAAATAAAATATTAATA-TTTTTAAATGTTATGATTAAATT
1 ATAAATAAAATATTAATATTTTTTAAATGTTATGATTAAATT
34685482 ATAAATAAAATATTAATATTT
1 ATAAATAAAATATTAATATTT
34685503 AAATTATTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
41 41 0.67
42 20 0.33
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (42 bp):
ATAAATAAAATATTAATATTTTTTAAATGTTATGATTAAATT
Found at i:34685519 original size:41 final size:41
Alignment explanation
Indices: 34685399--34685941 Score: 181
Period size: 41 Copynumber: 13.2 Consensus size: 41
34685389 TTTAATCATA
* *
34685399 ATAAATAAAATATTAATATTTTTTAAA-TGTT-ATGATTAAATT
1 ATAAATAAAATATTAATA---TTTAAATTATTAATTATTAAATT
* *
34685441 ATAAATAAAATATTAATATTTTTAAA-TGTT-ATGATTAAATT
1 ATAAATAAAATATTAATA--TTTAAATTATTAATTATTAAATT
34685482 ATAAATAAAATATTAATATTTAAATTATTAATTATTAATATT
1 ATAAATAAAATATTAATATTTAAATTATTAATTATTAA-ATT
* * * ** * * *
34685524 AT-TATGGAAAGAAAAAAAGTTTGAA-T-TT-A-TAAT-AA-T
1 ATAAAT-AAAATATTAATA-TTTAAATTATTAATTATTAAATT
* **
34685560 ATATAATAAAAATATT--TTTTTAAAATTAAAAATTGATTAAAATT
1 ATA-AAT-AAAATATTAATATTT-AAATTATTAATT-ATT-AAATT
** * * **
34685604 ATTAATATTTTAATCATAATATCATTTAAATTCTTAATGT-TTAAACA
1 A-TAA-A-TAAAAT-ATTA-AT-ATTTAAATTATTAAT-TATTAAATT
* ** *
34685651 ATAAAATAAAATATAAATAAAT-AATCA-TAATAATATTTAAATT
1 AT-AAATAAAATATTAATATTTAAATTATTAAT--TA-TTAAATT
* *
34685694 AT-AATTAAATATTAATATTTTAAAATATTAATTATTAAATT
1 ATAAATAAAATATTAATA-TTTAAATTATTAATTATTAAATT
* * * *
34685735 ATAATTAAAAGATTAATATTTAAATTATAAATTATAAATATT
1 ATAAATAAAATATTAATATTTAAATTATTAATTATTAA-ATT
* * * ** *
34685777 TTAAATAAATTA-TAACAAAT-AA-TATT--TTA--AAAAT
1 ATAAATAAAATATTAATATTTAAATTATTAATTATTAAATT
* * * *
34685811 A-AAATAAAA-ATAAATAATCATAA-TA--ACATTTTTAAATT
1 ATAAATAAAATATTAATATTTA-AATTATTA-ATTATTAAATT
* * *
34685849 ATAAATAAAATATTAATATTTTAAAATATTAATGATTAAAAT
1 ATAAATAAAATATTAATA-TTTAAATTATTAATTATTAAATT
* * *
34685891 ATAAATAAAATATAAATATTTAAATGATCAATTATTAATATT
1 ATAAATAAAATATTAATATTTAAATTATTAATTATTAA-ATT
*
34685933 TTAAATAAA
1 ATAAATAAA
34685942 TTATAAATTA
Statistics
Matches: 370, Mismatches: 82, Indels: 98
0.67 0.15 0.18
Matches are distributed among these distances:
32 1 0.00
33 11 0.03
34 2 0.01
35 9 0.02
36 7 0.02
37 5 0.01
38 12 0.03
39 21 0.06
40 19 0.05
41 122 0.33
42 94 0.25
43 20 0.05
44 11 0.03
45 10 0.03
46 5 0.01
47 6 0.02
48 2 0.01
49 9 0.02
50 4 0.01
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.42
Consensus pattern (41 bp):
ATAAATAAAATATTAATATTTAAATTATTAATTATTAAATT
Found at i:34685692 original size:225 final size:223
Alignment explanation
Indices: 34685249--34685741 Score: 493
Period size: 225 Copynumber: 2.2 Consensus size: 223
34685239 AAATATTAAT
*
34685249 ATTAAATTATATAA-AAAATATTAATATTTAAATTATCAATTATTAATATTATTATAAAAAAAGA
1 ATTAAATTATA-AATAAAATATTAATATTTAAATTATTAATTATTAATATTATTATAAAAAAAGA
* * ** * ** *
34685313 AAAAATTTTAATTTTTAATTGTATATTATAAAAAATAACATTTTAATTTTAAAAATTAATTAATA
65 AAAAATTTGAATTTATAATAATATATAATAAAAAATAACATTTTAAAATTAAAAATTAATTAAAA
* * * *** * * *
34685378 TTATTTATATTTTTAATCATAATAAATAAAATATTAATATTTTTTAAATGTTATGATTAAATTAT
130 TTATTAATATTTTTAATCATAATAAATAAAATATTAATAATGTTTAAACAATATAAATAAAATAT
* *
34685443 AAATAAAATATTAATATTTTTAAATGTTATG
195 AAATAAAATATTAATATATTTAAA--TTATA
* *
34685474 ATTAAATTATAAATAAAATATTAATATTTAAATTATTAATTATTAATATTATTATGGAAAGAA-A
1 ATTAAATTATAAATAAAATATTAATATTTAAATTATTAATTATTAATATTATTAT-AAAAAAAGA
* *** *
34685538 AAAAGTTTGAATTTATAATAATATATAAT-AAAAATATTTTTTTAAAATTAAAAATTGATTAAAA
65 AAAAATTTGAATTTATAATAATATATAATAAAAAATAACATTTTAAAATTAAAAATTAATTAAAA
* ** **
34685602 TTATTAATA-TTTTAATCATAATATCATTTAA-ATTCTTAATGTTTAAACAATA-AAATAAAATA
130 TTATTAATATTTTTAATCATAATA-AATAAAATATTAATAATGTTTAAACAATATAAATAAAATA
34685664 TAAAT-AAATAATCATAATAATATTTAAATTATA
194 TAAATAAAAT-AT--TAAT-ATATTTAAATTATA
34685697 ATTAAA-TATTAATATTTTAAAATATTAAT-TATTAAATTA-TAATTA
1 ATTAAATTA-TAA-A---TAAAATATTAATAT-TTAAATTATTAATTA
34685742 AAAGATTAAT
Statistics
Matches: 223, Mismatches: 32, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
221 4 0.02
222 16 0.07
223 41 0.18
224 47 0.21
225 83 0.37
226 12 0.05
227 20 0.09
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (223 bp):
ATTAAATTATAAATAAAATATTAATATTTAAATTATTAATTATTAATATTATTATAAAAAAAGAA
AAAATTTGAATTTATAATAATATATAATAAAAAATAACATTTTAAAATTAAAAATTAATTAAAAT
TATTAATATTTTTAATCATAATAAATAAAATATTAATAATGTTTAAACAATATAAATAAAATATA
AATAAAATATTAATATATTTAAATTATA
Found at i:34685742 original size:26 final size:27
Alignment explanation
Indices: 34685713--34685776 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
34685703 TATTAATATT
34685713 TTAAAATATTAAT-TATTAAATTAT-AA
1 TTAAAATATTAATAT-TTAAATTATAAA
*
34685739 TTAAAAGATTAATATTTAAATTATAAA
1 TTAAAATATTAATATTTAAATTATAAA
34685766 TTATAAATATT
1 TTA-AAATATT
34685777 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 21 0.64
27 6 0.18
28 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
TTAAAATATTAATATTTAAATTATAAA
Found at i:34685798 original size:14 final size:13
Alignment explanation
Indices: 34685779--34685825 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
34685769 TAAATATTTT
34685779 AAATAAATTATAA
1 AAATAAATTATAA
*
34685792 CAAATAATATTTTAA
1 -AAATAA-ATTATAA
34685807 AAATAAA--ATAA
1 AAATAAATTATAA
34685818 AAATAAAT
1 AAATAAAT
34685826 AATCATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 10 0.34
13 1 0.03
14 12 0.41
15 6 0.21
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAATTATAA
Found at i:34685826 original size:26 final size:26
Alignment explanation
Indices: 34685768--34685826 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
34685758 ATTATAAATT
34685768 ATAAATATTTTAAATAAATTATAACAA
1 ATAAATATTTTAAATAAA-TATAACAA
34685795 AT-AATATTTTAAAAATAAA-ATAA-AA
1 ATAAATATTTT--AAATAAATATAACAA
34685820 ATAAATA
1 ATAAATA
34685827 ATCATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
25 4 0.14
26 16 0.55
27 2 0.07
28 7 0.24
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
ATAAATATTTTAAATAAATATAACAA
Found at i:34685869 original size:28 final size:29
Alignment explanation
Indices: 34685820--34685875 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
34685810 TAAAATAAAA
* *
34685820 ATAAATAATCATAATAACATTTTTAAATT
1 ATAAATAATAATAATAACATTTTAAAATT
* *
34685849 ATAAATAA-AATATTAATATTTTAAAAT
1 ATAAATAATAATAATAACATTTTAAAAT
34685876 ATTAATGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (29 bp):
ATAAATAATAATAATAACATTTTAAAATT
Found at i:34685887 original size:156 final size:153
Alignment explanation
Indices: 34685653--34685991 Score: 466
Period size: 156 Copynumber: 2.2 Consensus size: 153
34685643 TTTAAACAAT
* *
34685653 AAAATAAAATATAAATAAATAATCATAATAATATTTAAATTATAATTAAATATTAATATTTTAAA
1 AAAATAAAATAAAAATAAATAATCATAATAATATTTAAATTATAATAAAATATTAATATTTTAAA
* * * * *
34685718 ATATTAATTATTAAATTATAATTAAAAGATTAATATTTAAATTATAAATTATAAATATTTTAAAT
66 ATATTAATGATTAAAATATAAATAAAAGATAAATATTTAAATGATAAATTATAAATATTTTAAAT
**
34685783 AAATTATAACA-AATAATATTTTA
131 AAATTATAA-ATAATAATATTAAA
*
34685806 AAAATAAAATAAAAATAAATAATCATAATAACATTTTTAAATTATAAATAAAATATTAATATTTT
1 AAAATAAAATAAAAATAAATAATCATAAT-A-ATATTTAAATTAT-AATAAAATATTAATATTTT
* * *
34685871 AAAATATTAATGATTAAAATATAAATAAAATATAAATATTTAAATGATCAATTATTAATATTTTA
63 AAAATATTAATGATTAAAATATAAATAAAAGATAAATATTTAAATGATAAATTATAAATATTTTA
*
34685936 AATAAATTATAAATTATTAATATTAAA
128 AATAAATTATAAA-TAATAATATTAAA
34685963 AAATACTATAAATAAAAAT-AATAATCATA
1 AAA-A-TA-AAATAAAAATAAATAATCATA
34685992 TATATAATAA
Statistics
Matches: 164, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
153 28 0.17
154 1 0.01
155 13 0.08
156 87 0.53
157 12 0.07
158 1 0.01
159 12 0.07
160 10 0.06
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (153 bp):
AAAATAAAATAAAAATAAATAATCATAATAATATTTAAATTATAATAAAATATTAATATTTTAAA
ATATTAATGATTAAAATATAAATAAAAGATAAATATTTAAATGATAAATTATAAATATTTTAAAT
AAATTATAAATAATAATATTAAA
Found at i:34685889 original size:15 final size:15
Alignment explanation
Indices: 34685854--34685914 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
34685844 AAATTATAAA
34685854 TAAAATATTAATATTT
1 TAAAATATTAATA-TT
34685870 TAAAATATTAATGA-T
1 TAAAATATTAAT-ATT
34685885 TAAAATA-TAA-A--
1 TAAAATATTAATATT
*
34685896 TAAAATATAAATATT
1 TAAAATATTAATATT
34685911 TAAA
1 TAAA
34685915 TGATCAATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
11 7 0.18
12 3 0.08
13 1 0.03
14 3 0.08
15 12 0.31
16 12 0.31
17 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
TAAAATATTAATATT
Found at i:34685938 original size:42 final size:42
Alignment explanation
Indices: 34685842--34685949 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
34685832 AATAACATTT
* *
34685842 TTAAATTATAAATAAAATATTAATATTTTAAAATATTAATGA
1 TTAAATTATAAATAAAATATAAATATTTTAAAATATCAATGA
* *
34685884 TTAAAATATAAATAAAATATAAATA-TTT-AAATGATCAATTA
1 TTAAATTATAAATAAAATATAAATATTTTAAAAT-ATCAATGA
* *
34685925 TTAATATTTTAAATAAATTATAAAT
1 TTAA-ATTATAAATAAAATATAAAT
34685950 TATTAATATT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 4 0.07
41 13 0.23
42 40 0.70
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (42 bp):
TTAAATTATAAATAAAATATAAATATTTTAAAATATCAATGA
Found at i:34687144 original size:35 final size:35
Alignment explanation
Indices: 34687075--34687160 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
34687065 AATATCCCGT
* *
34687075 TTATTTTAATTGTTCCGTGTGAAGTAATACTTCAC
1 TTATTTTAATTGTTCTGTGTAAAGTAATACTTCAC
* * **
34687110 TTGTTTTAATTGTTCTGTGTAAAGTCATGTTTCAC
1 TTATTTTAATTGTTCTGTGTAAAGTAATACTTCAC
* *
34687145 TTATTCTAATTATTCT
1 TTATTTTAATTGTTCT
34687161 CATTATTCTC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (35 bp):
TTATTTTAATTGTTCTGTGTAAAGTAATACTTCAC
Found at i:34689595 original size:17 final size:17
Alignment explanation
Indices: 34689575--34689628 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 17
34689565 ACAAAATTGA
34689575 AAAAATAATAAAATATT
1 AAAAATAATAAAATATT
*
34689592 AAAAAATAA-ATAATA-T
1 -AAAAATAATAAAATATT
*
34689608 AAAAA-AATAAAAGATT
1 AAAAATAATAAAATATT
34689624 AAAAA
1 AAAAA
34689629 AAAGTTTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 2 0.06
15 9 0.29
16 7 0.23
17 5 0.16
18 8 0.26
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (17 bp):
AAAAATAATAAAATATT
Found at i:34689629 original size:17 final size:16
Alignment explanation
Indices: 34689567--34689631 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 16
34689557 CAAATAGAAC
34689567 AAAATTGAAAAAATAATA
1 AAAATT-AAAAAA-AATA
34689585 AAATATT--AAAAAATA
1 AAA-ATTAAAAAAAATA
34689600 AATAA-TATAAAAAAATA
1 AA-AATTA-AAAAAAATA
34689617 AAAGATTAAAAAAAA
1 AAA-ATTAAAAAAAA
34689632 GTTTATCTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
14 1 0.03
15 7 0.17
16 6 0.15
17 18 0.45
18 5 0.12
19 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (16 bp):
AAAATTAAAAAAAATA
Found at i:34690439 original size:9 final size:9
Alignment explanation
Indices: 34690425--34690453 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
34690415 AGCTTAGTAC
34690425 TAATATATA
1 TAATATATA
34690434 TAATATATA
1 TAATATATA
34690443 TAATATATA
1 TAATATATA
34690452 TA
1 TA
34690454 TATTTAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATATATA
Found at i:34702972 original size:39 final size:39
Alignment explanation
Indices: 34702873--34702987 Score: 142
Period size: 39 Copynumber: 2.9 Consensus size: 39
34702863 TCAGATTTTG
* * * *
34702873 TTTCCTTAGCTTGCTTTGGAGCTGAAACCCTTGGTTTCT
1 TTTCCTTAGCTTGCTTTGGAGTTGCAAGCTTTGGTTTCT
* *
34702912 TTTCCTTGGTTTGCTTTGGAGTTGCAAGCTTTGGTTTCT
1 TTTCCTTAGCTTGCTTTGGAGTTGCAAGCTTTGGTTTCT
* *
34702951 TTTCCCTT-GCTTGCTTTGGAGTTGCAGGGTTTGGTTT
1 TTT-CCTTAGCTTGCTTTGGAGTTGCAAGCTTTGGTTT
34702988 GGTTTGTTCG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
39 62 0.94
40 4 0.06
ACGTcount: A:0.09, C:0.18, G:0.25, T:0.48
Consensus pattern (39 bp):
TTTCCTTAGCTTGCTTTGGAGTTGCAAGCTTTGGTTTCT
Found at i:34705393 original size:28 final size:28
Alignment explanation
Indices: 34705342--34705400 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
34705332 AGTATTTGTA
*
34705342 TATTTTTTATTATATTCAATTAAATTTT
1 TATTTTTTATTATATTCAATTAAATTAT
* *
34705370 TATTTTTATTTTATATTGAA-TAAATTAT
1 TATTTTT-TATTATATTCAATTAAATTAT
34705398 TAT
1 TAT
34705401 GATTAATAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
TATTTTTTATTATATTCAATTAAATTAT
Found at i:34705444 original size:27 final size:27
Alignment explanation
Indices: 34705393--34705444 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
34705383 TATTGAATAA
**
34705393 ATTATTATGATTAATAGTTAATTATAT
1 ATTATTATGATTAATAAATAATTATAT
* *
34705420 ATTATTATTATTAATAAATATTTAT
1 ATTATTATGATTAATAAATAATTAT
34705445 TTGATTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
ATTATTATGATTAATAAATAATTATAT
Found at i:34706166 original size:3 final size:3
Alignment explanation
Indices: 34706158--34706192 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
34706148 TTCCACCTTA
34706158 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
34706193 CTCTCTTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:34711109 original size:21 final size:19
Alignment explanation
Indices: 34711080--34711134 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 19
34711070 TACCAAAGAG
*
34711080 GAGGTTGATGAAGATGTAGAA
1 GAGGATGATGAAGATG--GAA
34711101 GAGGATGATGAAGA-GGAA
1 GAGGATGATGAAGATGGAA
*
34711119 GAGGATGATGATGATG
1 GAGGATGATGAAGATG
34711135 CACCTTCCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 16 0.52
19 1 0.03
20 1 0.03
21 13 0.42
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.20
Consensus pattern (19 bp):
GAGGATGATGAAGATGGAA
Found at i:34715873 original size:2 final size:2
Alignment explanation
Indices: 34715866--34715898 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34715856 TTTATCTTAT
34715866 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34715899 GTATTTGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34716666 original size:29 final size:29
Alignment explanation
Indices: 34716634--34716710 Score: 154
Period size: 29 Copynumber: 2.7 Consensus size: 29
34716624 AAATATGTCG
34716634 TGTAACAACAATATTTTTTCAATATAGCA
1 TGTAACAACAATATTTTTTCAATATAGCA
34716663 TGTAACAACAATATTTTTTCAATATAGCA
1 TGTAACAACAATATTTTTTCAATATAGCA
34716692 TGTAACAACAATATTTTTT
1 TGTAACAACAATATTTTTT
34716711 TTTCAACATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (29 bp):
TGTAACAACAATATTTTTTCAATATAGCA
Found at i:34716702 original size:32 final size:32
Alignment explanation
Indices: 34716637--34716731 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 32
34716627 TATGTCGTGT
34716637 AACAACAATATTTTTTCAATATAGCATGT---
1 AACAACAATATTTTTTCAATATAGCATGTAAC
34716666 AACAACAATATTTTTTCAATATAGCATGTAAC
1 AACAACAATATTTTTTCAATATAGCATGTAAC
* * * * *
34716698 AACAATATTTTTTTTTCAACATGGCATGTAAC
1 AACAACAATATTTTTTCAATATAGCATGTAAC
34716730 AA
1 AA
34716732 TATTTTTTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
29 29 0.50
32 29 0.50
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (32 bp):
AACAACAATATTTTTTCAATATAGCATGTAAC
Found at i:34716754 original size:58 final size:56
Alignment explanation
Indices: 34716632--34716756 Score: 130
Period size: 58 Copynumber: 2.2 Consensus size: 56
34716622 TTAAATATGT
* *
34716632 CGTGTAACAACAATATTTTTTCAATATAGCATGTAACAACAATATTTTTTCAATATAG
1 CGTGTAACAACAATATTTTTTCAACATAGCATGT-A-AACAATATTTTTTCAATAGAG
* *
34716690 CATGTAACAACAATATTTTTTTTTCAACATGGCATGT-AACAATATTTTTTAACAAT-GA-
1 CGTGTAACAACAATA---TTTTTTCAACATAGCATGTAAACAATATTTTTT--CAATAGAG
34716748 CGTGTAACA
1 CGTGTAACA
34716757 TGGTTTTGTA
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
58 35 0.61
59 1 0.02
60 4 0.07
61 17 0.30
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (56 bp):
CGTGTAACAACAATATTTTTTCAACATAGCATGTAAACAATATTTTTTCAATAGAG
Found at i:34716839 original size:45 final size:45
Alignment explanation
Indices: 34716790--34716884 Score: 102
Period size: 45 Copynumber: 2.1 Consensus size: 45
34716780 AACAGTATTT
* * **
34716790 TTTTTCAACATGCCGTGTAACAATCTA-ATTATAACTTGTCACAAG
1 TTTTTCAACATGCAGTGTAACAAGC-ACACCATAACTTGTCACAAG
** * *
34716835 TTTTTGTACATGGAGTGTAACAAGCACACCATAACTTGTCATAAG
1 TTTTTCAACATGCAGTGTAACAAGCACACCATAACTTGTCACAAG
34716880 TTTTT
1 TTTTT
34716885 ATATATGGCT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
44 1 0.02
45 40 0.98
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (45 bp):
TTTTTCAACATGCAGTGTAACAAGCACACCATAACTTGTCACAAG
Found at i:34716921 original size:114 final size:114
Alignment explanation
Indices: 34716797--34717007 Score: 282
Period size: 114 Copynumber: 1.9 Consensus size: 114
34716787 TTTTTTTTCA
* * ** *
34716797 ACATGCCGTGTAACAATCTAATTATAACTTGTCACAAGTTTTTGTACATGGA-GTGTAACAAGC-
1 ACATGACGTGTAACAAGCTAACCATAACTTGTCACAAGTTTTTGTACAT-GACGTATAACAAGCT
* *
34716860 ACACCATAACTTGTCATAAGTTTTTATATATGGCTTGTCACATATTTTTAT
65 A-ACCATAACTTGTCACAAGTTTTTATACATGGCTTGTCACATATTTTTAT
* * *
34716911 ACATGACGTGTAACACGCTAACCATAACTTGTCACAGGTTTTTGTACATGACGTATAACACGCTA
1 ACATGACGTGTAACAAGCTAACCATAACTTGTCACAAGTTTTTGTACATGACGTATAACAAGCTA
* *
34716976 ACCATAGCTTGTCACAGGTTTTTATACATGGC
66 ACCATAACTTGTCACAAGTTTTTATACATGGC
34717008 GTGTAACACG
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
113 2 0.02
114 80 0.96
115 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (114 bp):
ACATGACGTGTAACAAGCTAACCATAACTTGTCACAAGTTTTTGTACATGACGTATAACAAGCTA
ACCATAACTTGTCACAAGTTTTTATACATGGCTTGTCACATATTTTTAT
Found at i:34716935 original size:69 final size:69
Alignment explanation
Indices: 34716824--34716953 Score: 176
Period size: 69 Copynumber: 1.9 Consensus size: 69
34716814 CTAATTATAA
* *
34716824 CTTGTCACAAGTTTTTGTACATGGAGTGTAACAAGCACACCATAACTTGTCATAAGTTTTTATAT
1 CTTGTCACAAGTTTTTATACATGGAGTGTAACAAGCACACCATAACTTGTCACAAGTTTTTATAT
34716889 ATGG
66 ATGG
* *
34716893 CTTGTCACATA-TTTTTATACAT-GACGTGTAACACGCTA-ACCATAACTTGTCACAGGTTTTT
1 CTTGTCACA-AGTTTTTATACATGGA-GTGTAACAAGC-ACACCATAACTTGTCACAAGTTTTT
34716954 GTACATGACG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
68 2 0.04
69 50 0.93
70 2 0.04
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (69 bp):
CTTGTCACAAGTTTTTATACATGGAGTGTAACAAGCACACCATAACTTGTCACAAGTTTTTATAT
ATGG
Found at i:34716959 original size:45 final size:45
Alignment explanation
Indices: 34716892--34717056 Score: 231
Period size: 45 Copynumber: 3.7 Consensus size: 45
34716882 TTTATATATG
*
34716892 GCTTGTCACATATTTTTATACATGACGTGTAACACGCTAACCATA
1 GCTTGTCACAGATTTTTATACATGACGTGTAACACGCTAACCATA
* * * *
34716937 ACTTGTCACAGGTTTTTGTACATGACGTATAACACGCTAACCATA
1 GCTTGTCACAGATTTTTATACATGACGTGTAACACGCTAACCATA
* * * *
34716982 GCTTGTCACAGGTTTTTATACATGGCGTGTAACACGCTAATCATT
1 GCTTGTCACAGATTTTTATACATGACGTGTAACACGCTAACCATA
* *
34717027 GTTTGTCACAGATTTTTGTACATGACGTGT
1 GCTTGTCACAGATTTTTATACATGACGTGT
34717057 CACATTTTTT
Statistics
Matches: 105, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 105 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (45 bp):
GCTTGTCACAGATTTTTATACATGACGTGTAACACGCTAACCATA
Found at i:34717069 original size:23 final size:24
Alignment explanation
Indices: 34717030--34717075 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
34717020 AATCATTGTT
34717030 TGTCACAGATTTTTGTACATGACG
1 TGTCACAGATTTTTGTACATGACG
*
34717054 TGTCACA-TTTTTTGTACATGAC
1 TGTCACAGATTTTTGTACATGAC
34717076 ATGTAACACG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (24 bp):
TGTCACAGATTTTTGTACATGACG
Found at i:34717111 original size:68 final size:69
Alignment explanation
Indices: 34716985--34717183 Score: 222
Period size: 68 Copynumber: 2.9 Consensus size: 69
34716975 AACCATAGCT
* * * * *
34716985 TGTCACAGGTTTTTATACATGGCGTGTAACACGCTAATCATTGTTTGTCACAGATTTTTGTACAT
1 TGTCACAGGTTTTTGTACATGACATGTAACACGCTAATCATGGCTTGTCACAGATTTTTGTACAT
*
34717050 GACG
66 AACG
* * * * *
34717054 TGTCACA-TTTTTTGTACATGACATGTAACACGTTAATCATGGCTTGTCATAGGTTTTTGTATAT
1 TGTCACAGGTTTTTGTACATGACATGTAACACGCTAATCATGGCTTGTCACAGATTTTTGTACAT
34717118 AACG
66 AACG
* * * * * *
34717122 TGTAACAGGTTTTTGTACATGACCTGTAATATGCTAA-CTATGACTTATCACAGATTTTTGTA
1 TGTCACAGGTTTTTGTACATGACATGTAACACGCTAATC-ATGGCTTGTCACAGATTTTTGTA
34717184 TGTGGAGTGT
Statistics
Matches: 107, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
68 57 0.53
69 50 0.47
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40
Consensus pattern (69 bp):
TGTCACAGGTTTTTGTACATGACATGTAACACGCTAATCATGGCTTGTCACAGATTTTTGTACAT
AACG
Found at i:34717149 original size:24 final size:24
Alignment explanation
Indices: 34717034--34717150 Score: 80
Period size: 24 Copynumber: 5.0 Consensus size: 24
34717024 ATTGTTTGTC
* *
34717034 ACAGATTTTTGTACATGACGTGTC
1 ACAGGTTTTTGTACATGACGTGTA
* *
34717058 ACA-TTTTTTGTACATGACATGTA
1 ACAGGTTTTTGTACATGACGTGTA
* ** * * *
34717081 ACACG--TTAAT-CATGGCTTGTC
1 ACAGGTTTTTGTACATGACGTGTA
* * *
34717102 ATAGGTTTTTGTATATAACGTGTA
1 ACAGGTTTTTGTACATGACGTGTA
*
34717126 ACAGGTTTTTGTACATGACCTGTA
1 ACAGGTTTTTGTACATGACGTGTA
34717150 A
1 A
34717151 TATGCTAACT
Statistics
Matches: 67, Mismatches: 22, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
21 11 0.16
22 3 0.04
23 23 0.34
24 30 0.45
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (24 bp):
ACAGGTTTTTGTACATGACGTGTA
Found at i:34720025 original size:15 final size:15
Alignment explanation
Indices: 34720005--34720034 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34719995 TGACTCAGAT
34720005 TTTAATTGAGAATCA
1 TTTAATTGAGAATCA
*
34720020 TTTAATTGATAATCA
1 TTTAATTGAGAATCA
34720035 ATTTGAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (15 bp):
TTTAATTGAGAATCA
Found at i:34724706 original size:7 final size:7
Alignment explanation
Indices: 34724691--34724723 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
34724681 GAAATCGTAG
*
34724691 TGGCTAC
1 TGGCAAC
34724698 TGGCAAC
1 TGGCAAC
34724705 TGGCAAC
1 TGGCAAC
34724712 TGGCAAC
1 TGGCAAC
34724719 TGGCA
1 TGGCA
34724724 GATGTGCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.18
Consensus pattern (7 bp):
TGGCAAC
Found at i:34729351 original size:18 final size:18
Alignment explanation
Indices: 34729324--34729383 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
34729314 GGGTGATGAT
*
34729324 GATGAGAGTGATTCTGAG
1 GATGAAAGTGATTCTGAG
* *
34729342 GATGAAAGTGGTTCTGAT
1 GATGAAAGTGATTCTGAG
*
34729360 GA-GGAAGATGATTCTGAG
1 GATGAAAG-TGATTCTGAG
34729378 GATGAA
1 GATGAA
34729384 GATGAGTCTG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
17 4 0.12
18 27 0.82
19 2 0.06
ACGTcount: A:0.32, C:0.05, G:0.37, T:0.27
Consensus pattern (18 bp):
GATGAAAGTGATTCTGAG
Found at i:34729384 original size:18 final size:18
Alignment explanation
Indices: 34729332--34729394 Score: 74
Period size: 18 Copynumber: 3.5 Consensus size: 18
34729322 ATGATGAGAG
34729332 TGATTCTGAGGATGAA-A
1 TGATTCTGAGGATGAAGA
* * *
34729349 GTGGTTCTGATGAGGAAGA
1 -TGATTCTGAGGATGAAGA
34729368 TGATTCTGAGGATGAAGA
1 TGATTCTGAGGATGAAGA
*
34729386 TGAGTCTGA
1 TGATTCTGA
34729395 TGAGGTCTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
18 36 0.97
19 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.35, T:0.29
Consensus pattern (18 bp):
TGATTCTGAGGATGAAGA
Found at i:34742516 original size:108 final size:108
Alignment explanation
Indices: 34742327--34742538 Score: 370
Period size: 108 Copynumber: 2.0 Consensus size: 108
34742317 TTTTAAACTT
*
34742327 CTTATTCCACATCGAGTCCTAATCATGTTTTACTTTGGACTTTTATATTATAAAAGTGAATTTCT
1 CTTATTCCACATCGAGTCCTAATCATGTTCTACTTTGGACTTTTATATTATAAAAGTGAATTTCT
* *
34742392 AGACTTTAAAATTGCAAGTAGTGCTTTGAGAGCTATAGAGAGG
66 AGACTTTAAAATTGCAAGTAATACTTTGAGAGCTATAGAGAGG
*
34742435 CTTATTCCACATCGAGTCCTAATCATGTTCTACTTTGGGCTTTTATATTATAAAAGTGAATTTCT
1 CTTATTCCACATCGAGTCCTAATCATGTTCTACTTTGGACTTTTATATTATAAAAGTGAATTTCT
* *
34742500 AGACTTTAGAATTGCAAGTAATACTTTGAGAGCTCTAGA
66 AGACTTTAAAATTGCAAGTAATACTTTGAGAGCTATAGA
34742539 AAGGGGACAT
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 98 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (108 bp):
CTTATTCCACATCGAGTCCTAATCATGTTCTACTTTGGACTTTTATATTATAAAAGTGAATTTCT
AGACTTTAAAATTGCAAGTAATACTTTGAGAGCTATAGAGAGG
Found at i:34759191 original size:54 final size:53
Alignment explanation
Indices: 34759132--34759238 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 53
34759122 TTATATTAGC
34759132 ACCACATGGGTATAAAATAATAAGTGATATTTTGACTAATAGTAATTAGTTAA
1 ACCACATGGGTATAAAATAATAAGTGATATTTTGACTAATAGTAATTAGTTAA
*
34759185 NACCACATGGGTATAAAATGATAAGTGATATTTTGACTAATAGTAATTAGTTAA
1 -ACCACATGGGTATAAAATAATAAGTGATATTTTGACTAATAGTAATTAGTTAA
34759239 CCATTAATTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.34
Consensus pattern (53 bp):
ACCACATGGGTATAAAATAATAAGTGATATTTTGACTAATAGTAATTAGTTAA
Found at i:34764052 original size:10 final size:10
Alignment explanation
Indices: 34764037--34764065 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
34764027 AATAAAAAAT
34764037 TTAAATTAAA
1 TTAAATTAAA
34764047 TTAAATTAAA
1 TTAAATTAAA
34764057 TTAAATTAA
1 TTAAATTAA
34764066 CAATAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TTAAATTAAA
Found at i:34764057 original size:15 final size:15
Alignment explanation
Indices: 34764037--34764065 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34764027 AATAAAAAAT
34764037 TTAAATTAAATTAAA
1 TTAAATTAAATTAAA
34764052 TTAAATTAAATTAA
1 TTAAATTAAATTAA
34764066 CAATAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAATTAAATTAAA
Found at i:34764076 original size:15 final size:15
Alignment explanation
Indices: 34764038--34764073 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
34764028 ATAAAAAATT
*
34764038 TAAATTAAATTAAAT
1 TAAATTAAATTAAAA
34764053 TAAATTAAATTAACAA
1 TAAATTAAATTAA-AA
34764069 TAAAT
1 TAAAT
34764074 AAAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAATTAAATTAAAA
Found at i:34764086 original size:15 final size:15
Alignment explanation
Indices: 34764070--34764131 Score: 64
Period size: 14 Copynumber: 4.5 Consensus size: 15
34764060 AATTAACAAT
34764070 AAATAAAAAATAT--
1 AAATAAAAAATATAA
*
34764083 ATA-AAAAAATA-AA
1 AAATAAAAAATATAA
*
34764096 AAATAAAAAATAAAA
1 AAATAAAAAATATAA
34764111 AAATAAAAAA-ATAA
1 AAATAAAAAATATAA
34764125 AAA-AAAA
1 AAATAAAA
34764132 TCGGGATGGC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 8 0.19
13 8 0.19
14 14 0.33
15 12 0.29
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (15 bp):
AAATAAAAAATATAA
Found at i:34764096 original size:7 final size:7
Alignment explanation
Indices: 34764086--34764128 Score: 68
Period size: 7 Copynumber: 5.9 Consensus size: 7
34764076 AAAATATATA
34764086 AAAAAAT
1 AAAAAAT
34764093 AAAAAAT
1 AAAAAAT
34764100 AAAAAAT
1 AAAAAAT
34764107 AAAAAAAT
1 -AAAAAAT
34764115 AAAAAAAT
1 -AAAAAAT
34764123 AAAAAA
1 AAAAAA
34764129 AAATCGGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 20 0.57
8 15 0.43
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:34764096 original size:8 final size:8
Alignment explanation
Indices: 34764083--34764129 Score: 80
Period size: 8 Copynumber: 6.1 Consensus size: 8
34764073 TAAAAAATAT
34764083 ATAAAAAA
1 ATAAAAAA
34764091 AT-AAAAA
1 ATAAAAAA
34764098 AT-AAAAA
1 ATAAAAAA
34764105 ATAAAAAA
1 ATAAAAAA
34764113 ATAAAAAA
1 ATAAAAAA
34764121 ATAAAAAA
1 ATAAAAAA
34764129 A
1 A
34764130 AATCGGGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 14 0.37
8 24 0.63
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
ATAAAAAA
Found at i:34765050 original size:7 final size:7
Alignment explanation
Indices: 34765047--34765080 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
34765037 AAAAAAATAA
34765047 AAAAAAT
1 AAAAAAT
34765054 AAAAAAT
1 AAAAAAT
34765061 AAAAAAT
1 AAAAAAT
34765068 ATATAAAAT
1 A-A-AAAAT
34765077 AAAA
1 AAAA
34765081 TAAAAATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 17 0.68
8 2 0.08
9 6 0.24
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
AAAAAAT
Found at i:34765051 original size:9 final size:9
Alignment explanation
Indices: 34765037--34765086 Score: 59
Period size: 9 Copynumber: 5.4 Consensus size: 9
34765027 ATTTTTAGAT
34765037 AAAAAAATA
1 AAAAAAATA
34765046 AAAAAAAT-
1 AAAAAAATA
34765054 -AAAAAATA
1 AAAAAAATA
34765062 AAAAATATATA
1 AAAAA-A-ATA
34765073 AAATAAAATA
1 AAA-AAAATA
34765083 AAAA
1 AAAA
34765087 TAGTGATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
7 7 0.19
9 13 0.36
10 7 0.19
11 7 0.19
12 2 0.06
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAAAATA
Found at i:34765059 original size:16 final size:16
Alignment explanation
Indices: 34765038--34765085 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
34765028 TTTTTAGATA
34765038 AAAAAATAAAAAAAAT
1 AAAAAATAAAAAAAAT
*
34765054 AAAAAATAAAAAATAT
1 AAAAAATAAAAAAAAT
*
34765070 ATAAAATAAAATAAAA
1 AAAAAATAAAA-AAAA
34765086 ATAGTGATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 25 0.89
17 3 0.11
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAAATAAAAAAAAT
Found at i:34765100 original size:23 final size:22
Alignment explanation
Indices: 34765051--34765111 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 22
34765041 AAATAAAAAA
34765051 AATAA-AAAATAAAAAATATAT
1 AATAATAAAATAAAAAATATAT
34765072 AA-AATAAAAT-AAAAATAGTGAT
1 AATAATAAAATAAAAAATA-T-AT
34765094 AATAATAAAATGAAAAAA
1 AATAATAAAAT-AAAAAA
34765112 AACAAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
20 9 0.26
21 8 0.24
22 4 0.12
23 8 0.24
25 5 0.15
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (22 bp):
AATAATAAAATAAAAAATATAT
Found at i:34769200 original size:18 final size:18
Alignment explanation
Indices: 34769141--34769194 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
34769131 TCCTGATTTT
34769141 AGAGGTTTTAGTTAGCCA
1 AGAGGTTTTAGTTAGCCA
*
34769159 AGAGGTTTTAGTTAGCTA
1 AGAGGTTTTAGTTAGCCA
34769177 AGAGGTTTTAGTTAGCCA
1 AGAGGTTTTAGTTAGCCA
34769195 GAAGGTGTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (18 bp):
AGAGGTTTTAGTTAGCCA
Found at i:34781687 original size:18 final size:18
Alignment explanation
Indices: 34781664--34781699 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
34781654 CCCATAGACC
34781664 CGGAGACAAGGGTAAAGA
1 CGGAGACAAGGGTAAAGA
*
34781682 CGGAGATAAGGGTAAAGA
1 CGGAGACAAGGGTAAAGA
34781700 GAAGTGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.08, G:0.39, T:0.08
Consensus pattern (18 bp):
CGGAGACAAGGGTAAAGA
Found at i:34781752 original size:43 final size:47
Alignment explanation
Indices: 34781691--34781813 Score: 164
Period size: 49 Copynumber: 2.7 Consensus size: 47
34781681 ACGGAGATAA
*
34781691 GGGTAAAGAGAAGTGTAAGGATCCCTATACC-AGAC-CA-A-ACCAG
1 GGGTAAAGAGAAGTGTAAGGATCCCTCTACCAAGACTCAGAGACCAG
* * *
34781734 GGGTAAAAAGAAGTGTAAGGATTCCTCTACCCATAGTCTCAGAGACCAG
1 GGGTAAAGAGAAGTGTAAGGATCCCTCTA-CCA-AGACTCAGAGACCAG
34781783 GGGTAAAGAGAAGTGTAAGGATCCCTCTACC
1 GGGTAAAGAGAAGTGTAAGGATCCCTCTACC
34781814 CATACCTAGG
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
43 26 0.38
44 2 0.03
46 3 0.04
47 2 0.03
48 3 0.04
49 32 0.47
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (47 bp):
GGGTAAAGAGAAGTGTAAGGATCCCTCTACCAAGACTCAGAGACCAG
Found at i:34781886 original size:29 final size:28
Alignment explanation
Indices: 34781827--34781918 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 28
34781817 ACCTAGGAAA
* ** *
34781827 ACCCATAGACCCGTGTAAGGATTGCTTT
1 ACCCATAGACCCGTGGAAGGATCCCTCT
*
34781855 ACCCATAGACCCTTTGGAAGGATCCCTCT
1 ACCCATAGACCC-GTGGAAGGATCCCTCT
* * * *
34781884 ACCTATAGACGCGCT-GAAGAATTCCTCT
1 ACCCATAGACCCG-TGGAAGGATCCCTCT
34781912 ACCCATA
1 ACCCATA
34781919 AGCCTGGACC
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
28 29 0.57
29 22 0.43
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (28 bp):
ACCCATAGACCCGTGGAAGGATCCCTCT
Found at i:34789839 original size:107 final size:104
Alignment explanation
Indices: 34789645--34789843 Score: 292
Period size: 108 Copynumber: 1.9 Consensus size: 104
34789635 GCTCTGCTTT
* * *
34789645 AAGCACAAAACAATAAATGTGAAATTTAGCACTTAGCATATGATTATGCAGTTAAGACCAAAACT
1 AAGCACAAAACAATAAACGTCAAATTTAGAACTTAGCATATGATTATGCAGTTAAGACCAAAACT
34789710 TCATCTCTAAATCTGAAAGAAATCAATTCTCTCTGATAC
66 TCATCTCTAAATCTGAAAGAAATCAATTCTCTCTGATAC
* * **
34789749 AAGCACAAAACAATAAACGCATACAAATTTTAGAACTTAGCATATGATTATGTAGTTAAGGCTGA
1 AAGCACAAAACAATAAACG--T-CAAA-TTTAGAACTTAGCATATGATTATGCAGTTAAGACCAA
34789814 AA-TTCATCTCTAAATCTGAAAGAAATCAAT
62 AACTTCATCTCTAAATCTGAAAGAAATCAAT
34789844 AGACTGCATC
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
104 18 0.21
106 1 0.01
107 31 0.37
108 34 0.40
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.28
Consensus pattern (104 bp):
AAGCACAAAACAATAAACGTCAAATTTAGAACTTAGCATATGATTATGCAGTTAAGACCAAAACT
TCATCTCTAAATCTGAAAGAAATCAATTCTCTCTGATAC
Found at i:34791114 original size:24 final size:24
Alignment explanation
Indices: 34791061--34791108 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
34791051 GTGCTGAATT
*
34791061 CAAAATAT-AAGATGTTACTATAAG
1 CAAAA-ATCAAGATGTTACCATAAG
34791085 CAAAAATCAAGATGTTACCATAAG
1 CAAAAATCAAGATGTTACCATAAG
34791109 GTAAAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (24 bp):
CAAAAATCAAGATGTTACCATAAG
Found at i:34794312 original size:30 final size:29
Alignment explanation
Indices: 34794255--34794318 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
34794245 TAAATTATTT
* * *
34794255 TTTATTTTTTTATTATGTTCAATTAAGTA
1 TTTATATTTTTATTATGATCAAATAAGTA
* *
34794284 TTTATATTTTTATTTTTGATCAAATAAGTC
1 TTTATATTTTTA-TTATGATCAAATAAGTA
34794314 TTTAT
1 TTTAT
34794319 GAATAATAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.28, C:0.05, G:0.06, T:0.61
Consensus pattern (29 bp):
TTTATATTTTTATTATGATCAAATAAGTA
Found at i:34794464 original size:33 final size:33
Alignment explanation
Indices: 34794424--34794505 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
34794414 ATATACCACG
34794424 TCATCATCAATTATAATATGTATACATGCTACA
1 TCATCATCAATTATAATATGTATACATGCTACA
34794457 TCATCATCAATTATAATATGTATACATGCTACA
1 TCATCATCAATTATAATATGTATACATGCTACA
34794490 TCATCATCAATTATAA
1 TCATCATCAATTATAA
34794506 CAAATCAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (33 bp):
TCATCATCAATTATAATATGTATACATGCTACA
Found at i:34798714 original size:3 final size:3
Alignment explanation
Indices: 34798698--34798777 Score: 58
Period size: 3 Copynumber: 26.0 Consensus size: 3
34798688 TTTTCTTCCA
*
34798698 ATT A-T ATT ATTT ATT ATT ATT ATTT ATTT ATT TTT CATT -TT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT A-TT A-TT ATT ATT -ATT ATT ATT ATT
* * *
34798745 ATC ATT ATT TTT TTT ATT ATT ATT -TT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
34798778 TTTTTATTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
2 6 0.09
3 43 0.67
4 15 0.23
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:34798739 original size:29 final size:28
Alignment explanation
Indices: 34798707--34798788 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 28
34798697 AATTATATTA
34798707 TTTATTATTATTATTTATTTATTTTTCAT
1 TTTATTATTATTATTTATTTATTTTT-AT
*
34798736 TTTATTATTATCA-TTATTT-TTTTTAT
1 TTTATTATTATTATTTATTTATTTTTAT
*
34798762 TATTATT-TTATATATTTTTTTATTTTT
1 T-TTATTATTAT-TATTTATTTATTTTT
34798789 TTATCTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
26 7 0.15
27 11 0.24
28 11 0.24
29 17 0.37
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (28 bp):
TTTATTATTATTATTTATTTATTTTTAT
Found at i:34798744 original size:32 final size:31
Alignment explanation
Indices: 34798698--34798792 Score: 102
Period size: 32 Copynumber: 3.0 Consensus size: 31
34798688 TTTTCTTCCA
* *
34798698 ATTATATTATTTATTATTATTATTTATTTATT
1 ATTATTTTA-TTATTATTATTATTTTTTTATT
* *
34798730 TTTCATTTTATTATTATCATTATTTTTTTTATT
1 ATT-ATTTTATTATTATTATTA-TTTTTTTATT
*
34798763 ATTATTTTATATATT-TTTTTATTTTTTTAT
1 ATTATTTTAT-TATTATTATTATTTTTTTAT
34798793 CTAAAAATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
31 9 0.17
32 24 0.45
33 20 0.38
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (31 bp):
ATTATTTTATTATTATTATTATTTTTTTATT
Found at i:34798768 original size:24 final size:23
Alignment explanation
Indices: 34798698--34798782 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 23
34798688 TTTTCTTCCA
* *
34798698 ATTATATTATTTATTATTATTAT
1 ATTATTTTTTTTATTATTATTAT
34798721 -TTATTTATTTTTCATTTTATTATTAT
1 ATTATTT-TTTTT-A--TTATTATTAT
*
34798747 CATTATTTTTTTTATTATTATTTT
1 -ATTATTTTTTTTATTATTATTAT
34798771 ATATATTTTTTT
1 AT-TATTTTTTT
34798783 ATTTTTTTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
22 5 0.10
23 6 0.12
24 19 0.37
26 11 0.21
27 5 0.10
28 6 0.12
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (23 bp):
ATTATTTTTTTTATTATTATTAT
Found at i:34798778 original size:9 final size:8
Alignment explanation
Indices: 34798698--34798792 Score: 63
Period size: 8 Copynumber: 11.6 Consensus size: 8
34798688 TTTTCTTCCA
*
34798698 ATTATATT
1 ATTATTTT
34798706 ATTTATTATT
1 A-TTATT-TT
34798716 ATTA-TTT
1 ATTATTTT
34798723 ATTTATTTT
1 A-TTATTTT
*
34798732 -TCATTTT
1 ATTATTTT
*
34798739 ATTATTATC
1 ATTATT-TT
34798748 ATTATTTT
1 ATTATTTT
34798756 -TT-TTATT
1 ATTATT-TT
34798763 ATTATTTT
1 ATTATTTT
34798771 ATATATTTT
1 AT-TATTTT
*
34798780 TTTATTTT
1 ATTATTTT
*
34798788 TTTAT
1 ATTAT
34798793 CTAAAAATAT
Statistics
Matches: 71, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
6 2 0.03
7 13 0.18
8 27 0.38
9 26 0.37
10 3 0.04
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTATTTT
Found at i:34798782 original size:50 final size:49
Alignment explanation
Indices: 34798698--34798792 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 49
34798688 TTTTCTTCCA
34798698 ATTATATTATTTATTATTATTATTTATTTATTTTTCATTTTATTATTATC
1 ATTATATTATTTATTATTATTATTTATTTATTTTT-ATTTTATTATTATC
* * *
34798748 ATTATTTTTTTTATTATTATT-TTATATATT-TTTTTATTTTTTTAT
1 ATTATATTATTTATTATTATTATT-TAT-TTATTTTTATTTTATTAT
34798793 CTAAAAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
49 11 0.28
50 27 0.68
51 2 0.05
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (49 bp):
ATTATATTATTTATTATTATTATTTATTTATTTTTATTTTATTATTATC
Found at i:34799249 original size:14 final size:15
Alignment explanation
Indices: 34799225--34799263 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
34799215 CCTTTTCTCT
34799225 TTTCTCTCTCTTCAC
1 TTTCTCTCTCTTCAC
34799240 TTTC-CTCTC-TCAC
1 TTTCTCTCTCTTCAC
34799253 TTTCTCTCTCT
1 TTTCTCTCTCT
34799264 AACCGCGGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.36
14 10 0.45
15 4 0.18
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTCTCTCTCTTCAC
Found at i:34799259 original size:12 final size:12
Alignment explanation
Indices: 34799229--34799262 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
34799219 TTCTCTTTTC
34799229 TCTCTCTTCACTT
1 TCTCTC-TCACTT
34799242 TCCTCTCTCACTT
1 T-CTCTCTCACTT
34799255 TCTCTCTC
1 TCTCTCTC
34799263 TAACCGCGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 8 0.40
14 5 0.25
ACGTcount: A:0.06, C:0.44, G:0.00, T:0.50
Consensus pattern (12 bp):
TCTCTCTCACTT
Found at i:34811912 original size:21 final size:20
Alignment explanation
Indices: 34811878--34811917 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
34811868 TTTGGATTAG
**
34811878 TTATTCACTGTTTCTAAATTT
1 TTATTCACAATTTC-AAATTT
34811899 TTATTCACAATTTCAAATT
1 TTATTCACAATTTCAAATT
34811918 GATAATTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.53
Consensus pattern (20 bp):
TTATTCACAATTTCAAATTT
Found at i:34820708 original size:1 final size:1
Alignment explanation
Indices: 34820702--34820728 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
34820692 ATTAATGTAA
34820702 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
34820729 ACAAGAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:34824623 original size:2 final size:2
Alignment explanation
Indices: 34824616--34824640 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34824606 TAATAATATA
34824616 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
34824641 TTTATATAGA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:34833945 original size:59 final size:59
Alignment explanation
Indices: 34833853--34833970 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
34833843 TAGTAGCAAA
34833853 GTTCTTGAATCTATTAAGTAATGATAAAGTAAACTCTTAGCTAGTTTTTGTTAATGAAT
1 GTTCTTGAATCTATTAAGTAATGATAAAGTAAACTCTTAGCTAGTTTTTGTTAATGAAT
34833912 GTTCTTGAATCTATTAAGTAATGATAAAGTAAACTCTTAGCTAGTTTTTGTTAATGAAT
1 GTTCTTGAATCTATTAAGTAATGATAAAGTAAACTCTTAGCTAGTTTTTGTTAATGAAT
34833971 TTTAAAATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.42
Consensus pattern (59 bp):
GTTCTTGAATCTATTAAGTAATGATAAAGTAAACTCTTAGCTAGTTTTTGTTAATGAAT
Found at i:34862435 original size:40 final size:40
Alignment explanation
Indices: 34862375--34862450 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
34862365 ATATGTGGGT
* *
34862375 TAGGTCCAAATGAATTTTTGTACGGCTTTAATTTATATTG
1 TAGGCCCAAATGAAATTTTGTACGGCTTTAATTTATATTG
* *
34862415 TAGGCCCAAGTGAAATTTTGTATGGCTTTAATTTAT
1 TAGGCCCAAATGAAATTTTGTACGGCTTTAATTTAT
34862451 GCTGTAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (40 bp):
TAGGCCCAAATGAAATTTTGTACGGCTTTAATTTATATTG
Found at i:34894479 original size:25 final size:25
Alignment explanation
Indices: 34894449--34894496 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
34894439 ATAATCATAT
34894449 AATTAA-ATATATTAA-AAATATATAA
1 AATTAATATA-ATTAATAAA-ATATAA
34894474 AATTAATATAATTAATAAAATAT
1 AATTAATATAATTAATAAAATAT
34894497 CTATATATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
AATTAATATAATTAATAAAATATAA
Found at i:34918740 original size:31 final size:31
Alignment explanation
Indices: 34918702--34918761 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
34918692 AAATATTTGA
*
34918702 TTAATTAATTGAATTTTTGAATCTTTATTAT
1 TTAATTAATTGAATTTGTGAATCTTTATTAT
34918733 TTAATTAATTGAATTTGTGAATCTTTATT
1 TTAATTAATTGAATTTGTGAATCTTTATT
34918762 GTCATCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (31 bp):
TTAATTAATTGAATTTGTGAATCTTTATTAT
Found at i:34919534 original size:108 final size:109
Alignment explanation
Indices: 34919345--34919555 Score: 316
Period size: 108 Copynumber: 1.9 Consensus size: 109
34919335 TAAAGTGACT
* * * *
34919345 AAATATGTTGATTTAATTACAACTTTTACAATTTACAAATATACATTCTTTTGAAATTATTCAAC
1 AAATATGTTGATTTAATTACAACTTTCACAAGTTACAAATACACATTCTTTTGAAATTATTAAAC
* *
34919410 TCTTACCCAATTTACC-TTTTATTTTAATTTAATCAAATTAGTA
66 TCTTACCCAATATACCTTTTTATTTAAATTTAATCAAATTAGTA
* *
34919453 AAATATGTTGATTTAGTTACAACTTTCACAAGTTACAAATACACATTCTTTTGCAATTATTAAAC
1 AAATATGTTGATTTAATTACAACTTTCACAAGTTACAAATACACATTCTTTTGAAATTATTAAAC
* * *
34919518 TCTTGCCTAATATACCTTTTTATTTAAATTTACTCAAA
66 TCTTACCCAATATACCTTTTTATTTAAATTTAATCAAA
34919556 ATTTCTTATA
Statistics
Matches: 91, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
108 72 0.79
109 19 0.21
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (109 bp):
AAATATGTTGATTTAATTACAACTTTCACAAGTTACAAATACACATTCTTTTGAAATTATTAAAC
TCTTACCCAATATACCTTTTTATTTAAATTTAATCAAATTAGTA
Found at i:34931067 original size:2 final size:2
Alignment explanation
Indices: 34931055--34931085 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34931045 TTGATAATAA
*
34931055 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34931086 ATGTAAGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:34931603 original size:22 final size:22
Alignment explanation
Indices: 34931563--34931604 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
34931553 GGTTACAACT
* *
34931563 CAAGAAGAGAGGGAAGAAGAAA
1 CAAGAAGAAAAGGAAGAAGAAA
*
34931585 CAAGAAGAAAAGGACGAAGA
1 CAAGAAGAAAAGGAAGAAGA
34931605 TAGGTGAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.07, G:0.33, T:0.00
Consensus pattern (22 bp):
CAAGAAGAAAAGGAAGAAGAAA
Found at i:34940016 original size:10 final size:10
Alignment explanation
Indices: 34940001--34940042 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
34939991 ATTTTTATAT
34940001 AATATTTTAA
1 AATATTTTAA
34940011 AATATTTTATA
1 AATATTTTA-A
34940022 AATTATTTTAA
1 AA-TATTTTAA
34940033 AAT-TTTTAA
1 AATATTTTAA
34940042 A
1 A
34940043 TAAATTCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 7 0.23
10 10 0.33
11 6 0.20
12 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AATATTTTAA
Found at i:34940018 original size:22 final size:22
Alignment explanation
Indices: 34939991--34940045 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
34939981 TATTAATTTT
34939991 ATTTTTATATAA-TATTTTAAA
1 ATTTTTATATAATTATTTTAAA
34940012 ATATTTTATA-AATTATTTTAAA
1 AT-TTTTATATAATTATTTTAAA
*
34940034 ATTTTTAAATAA
1 ATTTTTATATAA
34940046 ATTCATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTTATATAATTATTTTAAA
Found at i:34940035 original size:11 final size:11
Alignment explanation
Indices: 34940003--34940036 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
34939993 TTTTATATAA
34940003 TATTTTAAAA-
1 TATTTTAAAAT
34940013 TATTTTATAAAT
1 TATTTTA-AAAT
34940025 TATTTTAAAAT
1 TATTTTAAAAT
34940036 T
1 T
34940037 TTTAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.32
11 8 0.36
12 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTTAAAAT
Found at i:34941387 original size:2 final size:2
Alignment explanation
Indices: 34941380--34941422 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
34941370 TGCATTGATA
34941380 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34941420 AT A
1 AT A
34941423 GTAGTATATC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34947587 original size:2 final size:2
Alignment explanation
Indices: 34947580--34947605 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34947570 GCATGGACAG
34947580 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
34947606 TAAAAGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34952493 original size:43 final size:43
Alignment explanation
Indices: 34952442--34952528 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
34952432 GCTTTGTTTA
*
34952442 ACATCACGTTTGTCATGTTAAAAATTTATTTTTATTCAAGTGC
1 ACATCACGTTTGTCATGTCAAAAATTTATTTTTATTCAAGTGC
*
34952485 ACATCACGTTTGTCATGTCAAAAATTTGTTTTTATTCAAGTGC
1 ACATCACGTTTGTCATGTCAAAAATTTATTTTTATTCAAGTGC
34952528 A
1 A
34952529 ATATCAAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (43 bp):
ACATCACGTTTGTCATGTCAAAAATTTATTTTTATTCAAGTGC
Found at i:34962414 original size:2 final size:2
Alignment explanation
Indices: 34962407--34962452 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
34962397 CATAAAATAG
34962407 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34962449 TA TA
1 TA TA
34962453 ATTATAAAGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34971044 original size:18 final size:19
Alignment explanation
Indices: 34970998--34971044 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 19
34970988 TATAATTAGT
* *
34970998 TTTTTGAAATGTGTAAATA
1 TTTTTGAAATGTGGAAACA
34971017 TTTTTG-AATG-GGAAACA
1 TTTTTGAAATGTGGAAACA
34971034 TTTTTGAAATG
1 TTTTTGAAATG
34971045 CAACATACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 11 0.44
18 8 0.32
19 6 0.24
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (19 bp):
TTTTTGAAATGTGGAAACA
Found at i:34980665 original size:3 final size:3
Alignment explanation
Indices: 34980657--34980731 Score: 105
Period size: 3 Copynumber: 25.0 Consensus size: 3
34980647 AAGCCTCGGC
* * * *
34980657 TCT TCT TCT TCT TCT TCT TCC TCC TCT TCT TCT TCA TCT TCT ACT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
34980705 TCT TCG TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
34980732 CTCTCGTCGT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.03, C:0.36, G:0.01, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:34983665 original size:18 final size:18
Alignment explanation
Indices: 34983624--34983666 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
34983614 ATGGTTTCAG
*
34983624 AGCATGTATAGGTTCTTA
1 AGCATTTATAGGTTCTTA
34983642 AGCATTTATAGGTTCTTA
1 AGCATTTATAGGTTCTTA
34983660 AGCATTT
1 AGCATTT
34983667 TGAAGTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.42
Consensus pattern (18 bp):
AGCATTTATAGGTTCTTA
Found at i:34984112 original size:30 final size:28
Alignment explanation
Indices: 34984047--34984113 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
34984037 AGAAAAATTA
* **
34984047 AAATAAATTTTTATTTTTTATTGTGTTC
1 AAATAAATTTGTATTTTTTATTGTAATC
* *
34984075 AATTAAATTTGTATATTTTTATTTTAAATC
1 AAATAAATTTGTAT-TTTTTATTGT-AATC
34984105 AAATAAATT
1 AAATAAATT
34984114 ATTATAATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 12 0.39
29 9 0.29
30 10 0.32
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.55
Consensus pattern (28 bp):
AAATAAATTTGTATTTTTTATTGTAATC
Found at i:34992526 original size:6 final size:6
Alignment explanation
Indices: 34992515--34992544 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
34992505 CCTAGAGTAT
34992515 CCAAGA CCAAGA CCAAGA CCAAGA CCAAGA
1 CCAAGA CCAAGA CCAAGA CCAAGA CCAAGA
34992545 AATATATGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.33, G:0.17, T:0.00
Consensus pattern (6 bp):
CCAAGA
Found at i:35001128 original size:12 final size:12
Alignment explanation
Indices: 35001111--35001135 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35001101 GGTAACACAA
35001111 ATATATATATGT
1 ATATATATATGT
35001123 ATATATATATGT
1 ATATATATATGT
35001135 A
1 A
35001136 GAATAAAGAC
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATATATATATGT
Found at i:35024895 original size:21 final size:21
Alignment explanation
Indices: 35024884--35024986 Score: 109
Period size: 21 Copynumber: 4.8 Consensus size: 21
35024874 TAGGTATTGT
35024884 GTGACTAGTTTTAGGCATTAC
1 GTGACTAGTTTTAGGCATTAC
35024905 GTGACTAGTTTTAGGCATTAC
1 GTGACTAGTTTTAGGCATTAC
* * *
35024926 GTGA-TTGATTTTAGACATTGC
1 GTGACTAG-TTTTAGGCATTAC
* * *
35024947 GTGACTGGATTATAGGCATTGC
1 GTGACTAG-TTTTAGGCATTAC
*
35024969 GTGACTGATTTTTAGGCA
1 GTGACT-AGTTTTAGGCA
35024987 ATGTCTAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.03
21 40 0.57
22 28 0.40
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (21 bp):
GTGACTAGTTTTAGGCATTAC
Found at i:35025048 original size:23 final size:23
Alignment explanation
Indices: 35024996--35025066 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
35024986 AATGTCTAAA
* * *
35024996 AACTAATCACGCAAT-ACCTATC
1 AACTAGTCACGCAATGTCATATC
*
35025018 AACCAGTCACGCAATGTCATATC
1 AACTAGTCACGCAATGTCATATC
* *
35025041 AACTAGTCATGTAATGTCATATC
1 AACTAGTCACGCAATGTCATATC
35025064 AAC
1 AAC
35025067 CAATAATACA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 13 0.32
23 28 0.68
ACGTcount: A:0.38, C:0.27, G:0.10, T:0.25
Consensus pattern (23 bp):
AACTAGTCACGCAATGTCATATC
Found at i:35025134 original size:22 final size:22
Alignment explanation
Indices: 35025075--35025136 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
35025065 ACCAATAATA
* *
35025075 CAATACCTAAAAATCAGTCATG
1 CAATACCTAAAAATCGGTCAGG
*
35025097 CAATACTTAAAAATCGGTCAGG
1 CAATACCTAAAAATCGGTCAGG
* *
35025119 TAATGCCTAAAAATCGGT
1 CAATACCTAAAAATCGGT
35025137 TACGCAATGC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (22 bp):
CAATACCTAAAAATCGGTCAGG
Found at i:35025145 original size:22 final size:22
Alignment explanation
Indices: 35025075--35025153 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 22
35025065 ACCAATAATA
* *
35025075 CAATACCTAAAAATCAGTCATG
1 CAATACCTAAAAATCGGTCACG
* *
35025097 CAATACTTAAAAATCGGTCAGG
1 CAATACCTAAAAATCGGTCACG
* * *
35025119 TAATGCCTAAAAATCGGTTACG
1 CAATACCTAAAAATCGGTCACG
* *
35025141 CAATGCCTTAAAA
1 CAATACCTAAAAA
35025154 CCAACTAAAC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (22 bp):
CAATACCTAAAAATCGGTCACG
Found at i:35029191 original size:18 final size:19
Alignment explanation
Indices: 35029168--35029204 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
35029158 ATCGATATTA
35029168 GGGTGACT-ATGATTTAAT
1 GGGTGACTCATGATTTAAT
*
35029186 GGGTGATTCATGATTTAAT
1 GGGTGACTCATGATTTAAT
35029205 TTTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.41
Consensus pattern (19 bp):
GGGTGACTCATGATTTAAT
Found at i:35033049 original size:27 final size:25
Alignment explanation
Indices: 35033015--35033064 Score: 82
Period size: 27 Copynumber: 1.9 Consensus size: 25
35033005 CAAATTAATT
35033015 ATTTATATAAATATATATTATTTTTAA
1 ATTTATATAAA-ATATA-TATTTTTAA
35033042 ATTTATATAAAATATATATTTTT
1 ATTTATATAAAATATATATTTTT
35033065 GTTATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 7 0.30
26 5 0.22
27 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTTATATAAAATATATATTTTTAA
Found at i:35037386 original size:2 final size:2
Alignment explanation
Indices: 35037381--35037424 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
35037371 CCACACACAC
35037381 AT AT AT AT AT 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 AT AT AT AT AT
35037423 AT
1 AT
35037425 TAAGAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35040202 original size:57 final size:57
Alignment explanation
Indices: 35040139--35040279 Score: 142
Period size: 57 Copynumber: 2.5 Consensus size: 57
35040129 TGGAAGGGTT
** * **
35040139 AAGCAAAGACAAAGCGCAAAAAGAACCGCA-CACAGTTCAAATTCC-AGTGGAAGCGCC
1 AAGCAAAGACAAAGCGCAAAAAGAACCGCAGC-CAGAGCAAATTCCTACT-GAAGAACC
* * * * * * *
35040196 AGGCAAAAACAAAGTGCAAAAAGGACAGGAGCCAGAGCAAGTTCCTACTGAAGAACC
1 AAGCAAAGACAAAGCGCAAAAAGAACCGCAGCCAGAGCAAATTCCTACTGAAGAACC
35040253 AAGCAAAGACAAAGCGCAAAAAGAACC
1 AAGCAAAGACAAAGCGCAAAAAGAACC
35040280 TGCGAAAGAA
Statistics
Matches: 65, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
57 62 0.95
58 3 0.05
ACGTcount: A:0.48, C:0.23, G:0.22, T:0.07
Consensus pattern (57 bp):
AAGCAAAGACAAAGCGCAAAAAGAACCGCAGCCAGAGCAAATTCCTACTGAAGAACC
Found at i:35045154 original size:39 final size:39
Alignment explanation
Indices: 35045082--35045168 Score: 95
Period size: 39 Copynumber: 2.3 Consensus size: 39
35045072 CAGAGTTTCT
* * * *
35045082 TGAGGATAAATAAGAGTAATCAGGACAAGTAGAGCCTCC
1 TGAGGATAGATAACAGTAATCAAGACAAATAGAGCCTCC
* * * *
35045121 TGAGGATAGATGACAGTAATCAAGAGAAATAGAGCTTCT
1 TGAGGATAGATAACAGTAATCAAGACAAATAGAGCCTCC
35045160 TGA-GATAGA
1 TGAGGATAGA
35045169 GAAAGAAGAG
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
38 6 0.15
39 34 0.85
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.21
Consensus pattern (39 bp):
TGAGGATAGATAACAGTAATCAAGACAAATAGAGCCTCC
Found at i:35054551 original size:2 final size:2
Alignment explanation
Indices: 35054544--35054590 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
35054534 TGGAATCCTC
*
35054544 TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35054586 TA TA T
1 TA TA T
35054591 TAGTCATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35063543 original size:21 final size:21
Alignment explanation
Indices: 35063519--35063564 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
35063509 CTGTGTCTAG
35063519 ATGTCATAA-TCTCAAAGGAGA
1 ATGTCATAATTC-CAAAGGAGA
* *
35063540 ATGTCATAGTTCCAAAGGAGG
1 ATGTCATAATTCCAAAGGAGA
35063561 ATGT
1 ATGT
35063565 TATGGTCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (21 bp):
ATGTCATAATTCCAAAGGAGA
Done.