Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 4 of 199
Found at i:1051283 original size:95 final size:92
Alignment explanation
Indices: 1051175--1051361 Score: 250
Period size: 95 Copynumber: 2.0 Consensus size: 92
1051165 ATGATTTGCG
* * * *
1051175 ACTTGTAGCTTTAATCTATTCCACTGCAACTTTAGGGAAATAAGATTCGCATTTTCAA-CTTGCT
1 ACTTGTAGCTTTAATATATTCCACTACAACTTCAGGGAAATAAGATTCGCATATTCAATC-TGCT
*
1051239 CCACTGCAACTTCAGGGAGATTAGATTTGTA
65 CCACT---ACTTCAGGGAGATAAGATTTGTA
** * *
1051270 ACTTGTATTTTTAATATGTTCCACTATAACTTCAGGGAAATAAGATTCGCATATTCAATCTGCTC
1 ACTTGTAGCTTTAATATATTCCACTACAACTTCAGGGAAATAAGATTCGCATATTCAATCTGCTC
1051335 CACTACTTCAGGGAGATAAGATTTGTA
66 CACTACTTCAGGGAGATAAGATTTGTA
1051362 TCTTCAATCT
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
92 22 0.27
95 59 0.72
96 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (92 bp):
ACTTGTAGCTTTAATATATTCCACTACAACTTCAGGGAAATAAGATTCGCATATTCAATCTGCTC
CACTACTTCAGGGAGATAAGATTTGTA
Found at i:1051504 original size:133 final size:131
Alignment explanation
Indices: 1051309--1052243 Score: 890
Period size: 133 Copynumber: 7.1 Consensus size: 131
1051299 CTTCAGGGAA
* * * ** *
1051309 ATAAGATTCGCATATTCAATCTGCTCCACT---ACTTCAGGGAGATAAGATTTGTATCTTCAATC
1 ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAATC
* * * * *
1051371 TTTTCTACTGTAACTTTAGGGAGATAAGATTT-ATAGCTTTAATCTGCTCTACTGCAACTTCTTA
66 TGTTCTACTGCAACTTTA-GGAGATAAGATTTGCTATCTTTAATCTGCTCCACTGCAAC-T-TTA
1051435 -GAG
128 GGAG
* * * *
1051438 ACAAGATTTGCTATCTTCAATATGCTCTACTGCAACTTCAGGGAGATAAGATTTATGGCTTTAAT
1 ATAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAAT
* * *
1051503 CTGCTCCT-CTACAA-TTTCAGGAGATAAGATTTGCTATCTTTAATCTGCTCCACTGCAACTTCA
65 CTG-TTCTACTGCAACTTT-AGGAGATAAGATTTGCTATCTTTAATCTGCTCCACTGCAACTT-T
1051566 AGGAG
127 AGGAG
* ** * * **
1051571 ATAATATTTGTGGCTTTAATCTGCTCCACTGTAACTTCA-GGAGATAAGATTTGCT-ATTTTCAA
1 ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TGGCTTT-AA
* * ** *
1051634 TTTGCTTC-ACTACAACTTTAGGGAGATAAGATTTG-TGGCTTTAATCTGCTCGACTGCAACTTT
64 TCTG-TTCTACTGCAACTTTA-GGAGATAAGATTTGCTATCTTTAATCTGCTCCACTGCAACTTT
1051697 AGGAG
127 AGGAG
* * * *
1051702 ATAAAATTTGCTATCTTCAATCCGCTCCACTACAACTTTAGGGAGATAAGATTTGTGGCTTTAAT
1 ATAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAAT
* * * * *
1051767 CTGCTCCACTGTAACTTTAGGAGATAAGATTTGCTATCTTCAATCCGCTCCACTGCAACTTTAGG
65 CTGTTCTACTGCAACTTTAGGAGATAAGATTTGCTATCTTTAATCTGCTCCACTGCAACTTTA-G
*
1051832 GGG
129 GAG
** * * * * *
1051835 ATAAGATTTGTGCCTTTCAATTTGCTCCACTGCAACTTTAGGGGGATAATATTTATGGCTTTAAT
1 ATAAGATTTGTATC-TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAAT
* * * * * * *
1051900 CTGCTCCACTACAACTTCAAGAGATAAGATTTGCTATCTTCAATCTACTCCACTGCAACTTTAGG
65 CTGTTCTACTGCAACTTTAGGAGATAAGATTTGCTATCTTTAATCTGCTCCACTGCAACTTTA-G
1051965 GAG
129 GAG
* *
1051968 ATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAAGATTTGTGGCTTTAAT
1 ATAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAAT
* * * * *
1052033 ATGCTCCT-CTGCAACTTCAGGAGATAAGATTTGCTATCTTTAATCTGCTCTACTGCAGCTTTAG
65 CTG-TTCTACTGCAACTTTAGGAGATAAGATTTGCTATCTTTAATCTGCTCCACTGCAACTTTA-
1052097 GGAG
128 GGAG
** * * ** *
1052101 ATAAGATTTGTGGCTTTAATCTGCTCCTCTGCAACTTCA-GGAGATAAGATTTGCTATCTTCAAT
1 ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TGGCTTTAAT
** * ** * * *
1052165 CTACTCTACTGCAACTTCAGAGAGATAAGATTTG-TGGCTTTAATTTGCTCCTCTGCAACTTCAG
65 CTGTTCTACTGCAACTTTAG-GAGATAAGATTTGCTATCTTTAATCTGCTCCACTGCAACTTTA-
1052229 GGAG
128 GGAG
*
1052233 ATAGGATTTGT
1 ATAAGATTTGT
1052244 CATGATAACT
Statistics
Matches: 671, Mismatches: 109, Indels: 49
0.81 0.13 0.06
Matches are distributed among these distances:
129 8 0.01
130 16 0.02
131 62 0.09
132 226 0.34
133 353 0.53
134 6 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (131 bp):
ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAATC
TGTTCTACTGCAACTTTAGGAGATAAGATTTGCTATCTTTAATCTGCTCCACTGCAACTTTAGGA
G
Found at i:1051564 original size:88 final size:88
Alignment explanation
Indices: 1051326--1052242 Score: 1064
Period size: 88 Copynumber: 10.4 Consensus size: 88
1051316 TCGCATATTC
* ** * *
1051326 AATCTGCTCCACT---ACTTCAGGGAGATAAGATTTG-TATCTTCAATCTTTTCTACTGTAACTT
1 AATCTGCTCCACTGCAATTTCA-GGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTT
* *
1051387 TAGGGAGATAAGATTTATAGCTTT
65 TAGGGAGATAAGATTTGTGGCTTT
* * * * *
1051411 AATCTGCTCTACTGCAACTTCTTA-GAGACAAGATTTGCTATCTTCAATATGCTCTACTGCAACT
1 AATCTGCTCCACTGCAA-TT-TCAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
* *
1051475 TCAGGGAGATAAGATTTATGGCTTT
64 TTAGGGAGATAAGATTTGTGGCTTT
* * * *
1051500 AATCTGCTCCTCTACAATTTCAGGAGATAAGATTTGCTATCTTTAATCTGCTCCACTGCAACTTC
1 AATCTGCTCCACTGCAATTTCAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTT
* *
1051565 AAGGAGATAATATTTGTGGCTTT
66 AGGGAGATAAGATTTGTGGCTTT
* * * * * *
1051588 AATCTGCTCCACTGTAACTTCAGGAGATAAGATTTGCTATTTTCAATTTGCTTCACTACAACTTT
1 AATCTGCTCCACTGCAATTTCAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTT
1051653 AGGGAGATAAGATTTGTGGCTTT
66 AGGGAGATAAGATTTGTGGCTTT
* * * *
1051676 AATCTGCTCGACTGCAACTTT-AGGAGATAAAATTTGCTATCTTCAATCCGCTCCACTACAACTT
1 AATCTGCTCCACTGCAA-TTTCAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTT
1051740 TAGGGAGATAAGATTTGTGGCTTT
65 TAGGGAGATAAGATTTGTGGCTTT
* *
1051764 AATCTGCTCCACTGTAACTTT-AGGAGATAAGATTTGCTATCTTCAATCCGCTCCACTGCAACTT
1 AATCTGCTCCACTGCAA-TTTCAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTT
* *
1051828 TAGGGGGATAAGATTTGTGCCTTT
65 TAGGGAGATAAGATTTGTGGCTTT
* * * * ** * *
1051852 CAATTTGCTCCACTGCAACTTT-AGGGGGATAATATTT-ATGGCTTTAATCTGCTCCACTACAAC
1 -AATCTGCTCCACTGCAA-TTTCA-GGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAAC
* * ** *
1051915 TTCA-AGAGATAAGATTTGCTATCTTC
63 TTTAGGGAGATAAGATTTG-TGGCTTT
*
1051941 AATCTACTCCACTGCAACTTT-AGGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
1 AATCTGCTCCACTGCAA-TTTCA-GGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
*
1052005 TTAGAGAGATAAGATTTGTGGCTTT
64 TTAGGGAGATAAGATTTGTGGCTTT
* * * * * *
1052030 AATATGCTCCTCTGCAACTTCAGGAGATAAGATTTGCTATCTTTAATCTGCTCTACTGCAGCTTT
1 AATCTGCTCCACTGCAATTTCAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTT
1052095 AGGGAGATAAGATTTGTGGCTTT
66 AGGGAGATAAGATTTGTGGCTTT
* * * * *
1052118 AATCTGCTCCTCTGCAACTTCAGGAGATAAGATTTGCTATCTTCAATCTACTCTACTGCAACTTC
1 AATCTGCTCCACTGCAATTTCAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTT
*
1052183 AGAGAGATAAGATTTGTGGCTTT
66 AGGGAGATAAGATTTGTGGCTTT
* * * *
1052206 AATTTGCTCCTCTGCAACTTCAGGGAGATAGGATTTG
1 AATCTGCTCCACTGCAATTTCA-GGAGATAAGATTTG
1052243 TCATGATAAC
Statistics
Matches: 725, Mismatches: 92, Indels: 26
0.86 0.11 0.03
Matches are distributed among these distances:
85 12 0.02
87 2 0.00
88 519 0.72
89 165 0.23
90 27 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (88 bp):
AATCTGCTCCACTGCAATTTCAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTT
AGGGAGATAAGATTTGTGGCTTT
Found at i:1052221 original size:44 final size:44
Alignment explanation
Indices: 1051177--1052243 Score: 929
Period size: 44 Copynumber: 24.1 Consensus size: 44
1051167 GATTTGCGAC
** * *
1051177 TTGTAGCTTTAATCTATTCCACTGCAACTTTAGGGAAATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
1051221 TCGCA-TTTTCAA-CTTGCTCCACTGCAACTTCAGGGAGATTAGAT
1 TTGTAGCTTT-AATC-TGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * ** *
1051265 TTGTAACTTGTATTTTTAATATGTTCCACTATAACTTCAGGGAAATAAGAT
1 TTGT-A---G---CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * ** *
1051316 TCGCATATTCAATCTGCTCCACT---ACTTCAGGGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * ** * * *
1051357 TTGTATCTTCAATCTTTTCTACTGTAACTTTAGGGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * *** *
1051401 TTATAGCTTTAATCTGCTCTACTGCAACTTCTTAGAGACAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
1051445 TTGCTATCTTCAATATGCTCTACTGCAACTTCAGGGAGATAAGAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * *
1051490 TTATGGCTTTAATCTGCTCCTCTACAATTTCA-GGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * *
1051533 TTGCTATCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAATAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* *
1051578 TTGTGGCTTTAATCTGCTCCACTGTAACTTCA-GGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * *
1051621 TTGCTA-TTTTCAATTTGCTTCACTACAACTTTAGGGAGATAAGAT
1 TTG-TAGCTTT-AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
1051666 TTGTGGCTTTAATCTGCTCGACTGCAACTTTA-GGAGATAAAAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * *
1051709 TTGCTATCTTCAATCCGCTCCACTACAACTTTAGGGAGATAAGAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * *
1051754 TTGTGGCTTTAATCTGCTCCACTGTAACTTTA-GGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * *
1051797 TTGCTATCTTCAATCCGCTCCACTGCAACTTTAGGGGGATAAGAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
1051842 TTGT-GCCTTTCAATTTGCTCCACTGCAACTTTAGGGGGATAATAT
1 TTGTAG-CTTT-AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
1051887 TTATGGCTTTAATCTGCTCCACTACAACTTCA-AGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
1051930 TTGCTATCTTCAATCTACTCCACTGCAACTTTAGGGAGATAAGAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
1051975 TTGCTATCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAAGAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * *
1052020 TTGTGGCTTTAATATGCTCCTCTGCAACTTCA-GGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
1052063 TTGCTATCTTTAATCTGCTCTACTGCAGCTTTAGGGAGATAAGAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* *
1052108 TTGTGGCTTTAATCTGCTCCTCTGCAACTTCA-GGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * *
1052151 TTGCTATCTTCAATCTACTCTACTGCAACTTCAGAGAGATAAGAT
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
1052196 TTGTGGCTTTAATTTGCTCCTCTGCAACTTCAGGGAGATAGGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
1052240 TTGT
1 TTGT
1052244 CATGATAACT
Statistics
Matches: 828, Mismatches: 161, Indels: 68
0.78 0.15 0.06
Matches are distributed among these distances:
41 34 0.04
43 97 0.12
44 448 0.54
45 214 0.26
46 1 0.00
50 1 0.00
51 29 0.04
52 4 0.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (44 bp):
TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
Found at i:1055384 original size:20 final size:21
Alignment explanation
Indices: 1055342--1055387 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
1055332 TTTTTTTTGC
1055342 TTTGGGCTTGTAATAATTTTTAT
1 TTTGGGCTTGTAATAA--TTTAT
*
1055365 TTTGGGTTTGTAATAA-TTAT
1 TTTGGGCTTGTAATAATTTAT
1055385 TTT
1 TTT
1055388 TATTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
23 15 0.68
ACGTcount: A:0.22, C:0.02, G:0.17, T:0.59
Consensus pattern (21 bp):
TTTGGGCTTGTAATAATTTAT
Found at i:1056530 original size:37 final size:37
Alignment explanation
Indices: 1056469--1056614 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
1056459 TACGTATGAT
* *
1056469 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
1056504 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1056541 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
1056578 CACTTATCACTTTGTCTCTTGATCAAATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1056615 TAAAGCTATC
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 91 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:1056631 original size:46 final size:46
Alignment explanation
Indices: 1056578--1056845 Score: 331
Period size: 52 Copynumber: 5.6 Consensus size: 46
1056568 TAAGTGTAGC
* * **
1056578 CACTTATCACTTTGTCTCTTGATCAAATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
1056624 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
1056670 CACTTTTCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
1056722 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
1056774 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG-CGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
1056819 CACTTATCACTTTGTCACCTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
1056846 AGTACTCAAA
Statistics
Matches: 203, Mismatches: 12, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
45 34 0.17
46 75 0.37
49 1 0.00
50 1 0.00
51 3 0.01
52 89 0.44
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:1056740 original size:45 final size:46
Alignment explanation
Indices: 1056676--1056845 Score: 209
Period size: 45 Copynumber: 3.6 Consensus size: 46
1056666 CTATCACTTT
* *
1056676 TCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
1 TCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCCGAAGCTA
*
1056721 TCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
1 TCACTTATCACTTT---C---TCACTTGATCAGATAAGTGTAGCCGAAGCTA
* *
1056773 TCACTTATCACTTTGTCACTTGATCAGATAAGTATAG-CGAAGCTA
1 TCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCCGAAGCTA
* *
1056818 TCACTTATCACTTTGTCACCTGATCAGA
1 TCACTTATCACTTTCTCACTTGATCAGA
1056846 AGTACTCAAA
Statistics
Matches: 111, Mismatches: 7, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
45 44 0.40
46 23 0.21
52 44 0.40
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (46 bp):
TCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCCGAAGCTA
Found at i:1056789 original size:98 final size:94
Alignment explanation
Indices: 1056578--1056845 Score: 321
Period size: 98 Copynumber: 2.8 Consensus size: 94
1056568 TAAGTGTAGC
* * ** *
1056578 CACTTATCACTTTGTCTCTTGATCAAATAAGTGTAGCTAAAGCTATCACTTATCAC--TTTGTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTTGTCA
1056641 CTTGATCAGATAAGTATAGCCGAAGCTAT
66 CTTGATCAGATAAGTATAGCCGAAGCTAT
*
1056670 CACTTTTCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
* *
1056735 CCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
60 ----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
1056774 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG-CGAAGCTATCACTTATCAC--TTTGTCA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTTGTCA
*
1056836 CCTGATCAGA
66 CTTGATCAGA
1056846 AGTACTCAAA
Statistics
Matches: 153, Mismatches: 11, Indels: 25
0.81 0.06 0.13
Matches are distributed among these distances:
91 15 0.10
92 9 0.06
95 2 0.01
97 19 0.12
98 65 0.42
100 1 0.01
101 1 0.01
104 41 0.27
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (94 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTTGTCA
CTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:1064125 original size:14 final size:15
Alignment explanation
Indices: 1064098--1064126 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1064088 TTCTTTCTTT
1064098 CCTCTTTATTTTCAA
1 CCTCTTTATTTTCAA
1064113 CCTCTTT-TTTTCAA
1 CCTCTTTATTTTCAA
1064127 TTATTGCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.55
Consensus pattern (15 bp):
CCTCTTTATTTTCAA
Found at i:1064613 original size:11 final size:11
Alignment explanation
Indices: 1064597--1064624 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1064587 ATTTTAAAAA
1064597 TTAAAAATATT
1 TTAAAAATATT
1064608 TTAAAAATATT
1 TTAAAAATATT
1064619 TTAAAA
1 TTAAAA
1064625 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:1064635 original size:9 final size:9
Alignment explanation
Indices: 1064587--1064641 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
1064577 CCAAAATTTT
*
1064587 ATTTTAAAA
1 ATTTAAAAA
1064596 A-TTAAAAA
1 ATTTAAAAA
1064604 TATTTTAAAAA
1 -A-TTTAAAAA
*
1064615 TATTT-TAAA
1 -ATTTAAAAA
1064624 ATTTAAAAA
1 ATTTAAAAA
1064633 ATTTAAAAA
1 ATTTAAAAA
1064642 TAAATATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
8 10 0.26
9 17 0.44
10 3 0.08
11 9 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATTTAAAAA
Found at i:1076876 original size:24 final size:23
Alignment explanation
Indices: 1076841--1076893 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
1076831 AATTTTTAAA
**
1076841 ATTTTATTAATATTTAAAAAAAAT
1 ATTTT-TTAATAAATAAAAAAAAT
*
1076865 ATTTTTTAAATAAATAAAAATAAT
1 ATTTTTT-AATAAATAAAAAAAAT
1076889 -TTTTT
1 ATTTTT
1076894 ATATAACATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTTTTAATAAATAAAAAAAAT
Found at i:1076883 original size:22 final size:22
Alignment explanation
Indices: 1076855--1076899 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1076845 TATTAATATT
1076855 TAAA-AAAAAT-ATTTTTTAAA
1 TAAATAAAAATAATTTTTTAAA
*
1076875 TAAATAAAAATAATTTTTTATA
1 TAAATAAAAATAATTTTTTAAA
1076897 TAA
1 TAA
1076900 CATTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 6 0.27
22 12 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATAAAAATAATTTTTTAAA
Found at i:1078713 original size:24 final size:24
Alignment explanation
Indices: 1078681--1078729 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1078671 TCTATAACAT
1078681 TTATAAATTTAGATTATCATCGTA
1 TTATAAATTTAGATTATCATCGTA
*
1078705 TTATAAATTTAGATTATTATCGTA
1 TTATAAATTTAGATTATCATCGTA
1078729 T
1 T
1078730 GATTTAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (24 bp):
TTATAAATTTAGATTATCATCGTA
Found at i:1084662 original size:16 final size:17
Alignment explanation
Indices: 1084624--1084665 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
1084614 AAAAAATACT
1084624 CAAAAGTGACTAAATCA
1 CAAAAGTGACTAAATCA
1084641 -AGAAAG-GACTAAATCA
1 CA-AAAGTGACTAAATCA
1084657 CAAAAGTGA
1 CAAAAGTGA
1084666 AAAAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (17 bp):
CAAAAGTGACTAAATCA
Found at i:1088123 original size:23 final size:23
Alignment explanation
Indices: 1088092--1088142 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1088082 ACCTACTTTC
* * *
1088092 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGAGATA
1088115 TTACAGTAGTAATTTTCGAGATA
1 TTACAGTAGTAATTTTCGAGATA
1088138 TTACA
1 TTACA
1088143 TTATGTGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGAGATA
Found at i:1088816 original size:25 final size:25
Alignment explanation
Indices: 1088788--1088845 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
1088778 AAACCTTAGC
*
1088788 GTGCTCTCTGATTATTAGCACGTTA
1 GTGCTCTCTGATTATTAGCACATTA
1088813 GTGCTCTCTGATTATTAGCACATTA
1 GTGCTCTCTGATTATTAGCACATTA
1088838 GTGCTCTC
1 GTGCTCTC
1088846 CGTTTAGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACATTA
Found at i:1088886 original size:22 final size:22
Alignment explanation
Indices: 1088810--1088892 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 22
1088800 TATTAGCACG
* *
1088810 TTAGTGCTCTCTGATTATTAGCACA
1 TTAGTGCTCTCTG--TA-TAGTACT
* *
1088835 TTAGTGCTCTCCGTTTAGCTTA-T
1 TTAGTGCTCTCTGTATAG--TACT
1088858 TTA-TGCTCTCTGTATAGTACT
1 TTAGTGCTCTCTGTATAGTACT
1088879 TTAGTGCTCTCTGT
1 TTAGTGCTCTCTGT
1088893 TTAATAGTAC
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
20 2 0.04
21 4 0.08
22 25 0.52
23 4 0.08
24 1 0.02
25 12 0.25
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (22 bp):
TTAGTGCTCTCTGTATAGTACT
Found at i:1093895 original size:36 final size:33
Alignment explanation
Indices: 1093849--1093930 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 33
1093839 TTGTAAGTTA
1093849 AAAATAATTATAAATTTCTTATCTTTGCCCTCTCCCC
1 AAAA-AATTATAAATTT-TTA--TTTGCCCTCTCCCC
1093886 AAAAAATTAT-AA--TTTATTTGCCCTCTCCCC
1 AAAAAATTATAAATTTTTATTTGCCCTCTCCCC
*
1093916 AAAAAATTACAAATT
1 AAAAAATTATAAATT
1093931 AATTTTAGGC
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
30 23 0.56
31 2 0.05
32 3 0.07
33 1 0.02
35 2 0.05
36 6 0.15
37 4 0.10
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (33 bp):
AAAAAATTATAAATTTTTATTTGCCCTCTCCCC
Found at i:1095688 original size:51 final size:49
Alignment explanation
Indices: 1095618--1095787 Score: 223
Period size: 51 Copynumber: 3.3 Consensus size: 49
1095608 ACGTGACATA
* *
1095618 TTGTTAACCTTGCTAGCATGCTGATCTGTCTAATAATTAGTCTTAATTGT
1 TTGTTAACCTTGCTGGCATGCTGACCTGTCTAATAATTAGT-TTAATTGT
* *
1095668 TTGTTTAACCTTGTTGGCATGCTGACCTGTGTAATAATTAGTTTTAATTGT
1 TTG-TTAACCTTGCTGGCATGCTGACCTGTCTAATAATTAG-TTTAATTGT
* *
1095719 TTGGTTAACCTTACTGGCATGCTGACCTGTCTAAAAATTAGTTTGAATTGT
1 TT-GTTAACCTTGCTGGCATGCTGACCTGTCTAATAATTAGTTT-AATTGT
*
1095770 TCAGTTAACCTTGCTGGC
1 T-TGTTAACCTTGCTGGC
1095788 GTGCAAATCG
Statistics
Matches: 105, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
50 6 0.06
51 97 0.92
52 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (49 bp):
TTGTTAACCTTGCTGGCATGCTGACCTGTCTAATAATTAGTTTAATTGT
Found at i:1095805 original size:102 final size:103
Alignment explanation
Indices: 1095620--1095825 Score: 240
Period size: 102 Copynumber: 2.0 Consensus size: 103
1095610 GTGACATATT
* * * * *
1095620 GTTAACCTTGCTAGCATGCTGATCTGTCTAATAATTAGTCTTAATTGTTTGTTTAACCTTGTTGG
1 GTTAACCTTACTAGCATGCTGACCTGTCTAAAAATTAGTCTTAATTGTTAGTTTAACCTTGCTGG
** * * *
1095685 CATGCTGACCTGTGTAATAA-TTAGTTTTAATTGTTTG
66 CATGCAAACCTGTCTAATAACTAAATTTTAATTGTTTG
*
1095722 GTTAACCTTACTGGCATGCTGACCTGTCTAAAAATTAGT-TTGAATTGTTCAG-TTAACCTTGCT
1 GTTAACCTTACTAGCATGCTGACCTGTCTAAAAATTAGTCTT-AATTGTT-AGTTTAACCTTGCT
* *
1095785 GGCGTGCAAATC-GATCTAATAACTAAATTTTAATTGTTTG
64 GGCATGCAAACCTG-TCTAATAACTAAATTTTAATTGTTTG
1095825 G
1 G
1095826 CTAGCATGCC
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
101 3 0.03
102 67 0.77
103 17 0.20
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.41
Consensus pattern (103 bp):
GTTAACCTTACTAGCATGCTGACCTGTCTAAAAATTAGTCTTAATTGTTAGTTTAACCTTGCTGG
CATGCAAACCTGTCTAATAACTAAATTTTAATTGTTTG
Found at i:1098635 original size:16 final size:16
Alignment explanation
Indices: 1098614--1098661 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
1098604 ATTTTAAAAT
1098614 CTAAAAAGTACAATGA
1 CTAAAAAGTACAATGA
* **
1098630 CTAAAAAATA-AATTT
1 CTAAAAAGTACAATGA
*
1098645 TTAAAAAGTACAATGA
1 CTAAAAAGTACAATGA
1098661 C
1 C
1098662 CTATGGTATA
Statistics
Matches: 23, Mismatches: 8, Indels: 2
0.70 0.24 0.06
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.25
Consensus pattern (16 bp):
CTAAAAAGTACAATGA
Found at i:1101542 original size:14 final size:14
Alignment explanation
Indices: 1101523--1101551 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1101513 TTTACCAATA
1101523 TTCATCAATCAGAC
1 TTCATCAATCAGAC
1101537 TTCATCAATCAGAC
1 TTCATCAATCAGAC
1101551 T
1 T
1101552 AAGTGGTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.31
Consensus pattern (14 bp):
TTCATCAATCAGAC
Found at i:1106277 original size:127 final size:127
Alignment explanation
Indices: 1106046--1106301 Score: 363
Period size: 127 Copynumber: 2.0 Consensus size: 127
1106036 TATTAAAAGG
* *
1106046 AACATTTTAGTCCCTATACATTTCAAAAGCTAACATTTTAATCCTTGCATGTTAAGTTTGTCGTT
1 AACATTTTAGTCCCCATACATGTCAAAAGCTAACATTTTAATCCTTGCATGTTAAGTTTGTCGTT
* * * *
1106111 AAATGAATGACATGACTTAACTATTATTGACGTAACATTAAATCAAATATTAAATCAAATTA
66 AAATGAATGACATGACTTAACTATGACTGACATAACATTAAATCAAACATTAAATCAAATTA
* * *
1106173 AACATTTTAGTCCCCATACATGTGAAAAGCTGACATTTTAATCCTTGCATGTTAAGTTTGTTGTT
1 AACATTTTAGTCCCCATACATGTCAAAAGCTAACATTTTAATCCTTGCATGTTAAGTTTGTCGTT
** **
1106238 -AATGGAATGACATGACTTAAC-AGTGACTGACATCGCATTAAATCAAACATTAAATTGAATTA
66 AAAT-GAATGACATGACTTAACTA-TGACTGACATAACATTAAATCAAACATTAAATCAAATTA
1106300 AA
1 AA
1106302 AGGCTAAAAA
Statistics
Matches: 114, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
126 4 0.04
127 110 0.96
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (127 bp):
AACATTTTAGTCCCCATACATGTCAAAAGCTAACATTTTAATCCTTGCATGTTAAGTTTGTCGTT
AAATGAATGACATGACTTAACTATGACTGACATAACATTAAATCAAACATTAAATCAAATTA
Found at i:1108466 original size:7 final size:7
Alignment explanation
Indices: 1108451--1108489 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
1108441 TAAATTTAAA
*
1108451 TTCAAAT
1 TTCATAT
1108458 TTCATAT
1 TTCATAT
1108465 TTCATAT
1 TTCATAT
1108472 TTCATAT
1 TTCATAT
1108479 TTCATAT
1 TTCATAT
1108486 TTCA
1 TTCA
1108490 ACAATAACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (7 bp):
TTCATAT
Found at i:1109825 original size:17 final size:17
Alignment explanation
Indices: 1109789--1109829 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1109779 ACTCTACTTT
*
1109789 ATATATAATATAATATC
1 ATATATAATATAATAAC
1109806 ATATATAATAATAA-AAC
1 ATATATAAT-ATAATAAC
1109823 ATA-ATAA
1 ATATATAA
1109830 ATATCTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATATAATATAATAAC
Found at i:1111078 original size:18 final size:18
Alignment explanation
Indices: 1111057--1111091 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1111047 AATCAATATT
1111057 TCATTTAAAATAAAAAAA
1 TCATTTAAAATAAAAAAA
**
1111075 TCATTTGGAATAAAAAA
1 TCATTTAAAATAAAAAA
1111092 TTTTGCTTTA
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:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (18 bp):
TCATTTAAAATAAAAAAA
Found at i:1127870 original size:4 final size:4
Alignment explanation
Indices: 1127861--1127895 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1127851 GGTTTCTTAC
* *
1127861 CATA CATA CATG CATA CATA CACA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CAT
1127896 GCATGCATGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.46, C:0.29, G:0.03, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:1127878 original size:12 final size:12
Alignment explanation
Indices: 1127861--1127916 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
1127851 GGTTTCTTAC
1127861 CATACATACATG
1 CATACATACATG
**
1127873 CATACATACACA
1 CATACATACATG
1127885 CATACATACATG
1 CATACATACATG
* * *
1127897 CATGCATGCTTG
1 CATACATACATG
1127909 CATACATA
1 CATACATA
1127917 ATGATGATGA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (12 bp):
CATACATACATG
Found at i:1141505 original size:21 final size:20
Alignment explanation
Indices: 1141456--1141508 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1141446 TACAAAATCA
1141456 AAAGTATCGATACCCTTAAC
1 AAAGTATCGATACCCTTAAC
* *
1141476 AAAGTATCGATACCTTTCAC
1 AAAGTATCGATACCCTTAAC
1141496 AAAGGTATCGATA
1 AAA-GTATCGATA
1141509 TCATTTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (20 bp):
AAAGTATCGATACCCTTAAC
Found at i:1150890 original size:2 final size:2
Alignment explanation
Indices: 1150883--1150907 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1150873 GGGAATTTAG
1150883 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 T
1150908 GGAGGTCTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1153924 original size:22 final size:22
Alignment explanation
Indices: 1153899--1153940 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1153889 GCAACTGTGA
*
1153899 TTTCAGTCGAAGAAACGAGGTC
1 TTTCAGTCGAAGAAAAGAGGTC
* *
1153921 TTTCATTGGAAGAAAAGAGG
1 TTTCAGTCGAAGAAAAGAGG
1153941 GAGAAAATTC
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:0.36, C:0.12, G:0.29, T:0.24
Consensus pattern (22 bp):
TTTCAGTCGAAGAAAAGAGGTC
Found at i:1162544 original size:11 final size:11
Alignment explanation
Indices: 1162530--1162559 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1162520 AAAATAAAAA
1162530 TAAAATTATTT
1 TAAAATTATTT
*
1162541 TAAAAGTATTT
1 TAAAATTATTT
1162552 TAAAATTA
1 TAAAATTA
1162560 AAAAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:1162570 original size:8 final size:7
Alignment explanation
Indices: 1162553--1162586 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1162543 AAAGTATTTT
*
1162553 AAAATTA
1 AAAAATA
1162560 AAAAATA
1 AAAAATA
1162567 AAAAAT-
1 AAAAATA
1162573 AAAAATA
1 AAAAATA
1162580 AAAAATA
1 AAAAATA
1162587 TATATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
AAAAATA
Found at i:1162576 original size:13 final size:13
Alignment explanation
Indices: 1162560--1162586 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1162550 TTTAAAATTA
1162560 AAAAATAAAAAAT
1 AAAAATAAAAAAT
1162573 AAAAATAAAAAAT
1 AAAAATAAAAAAT
1162586 A
1 A
1162587 TATATTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:1187621 original size:36 final size:35
Alignment explanation
Indices: 1187554--1187638 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 35
1187544 TAATTTTTTT
*
1187554 AATATTTTTATAA-AAAAATTTCGCAATATTTTCATA
1 AATATTTTTA-AATAAAAATTTCGCAAGATTTT-ATA
* *
1187590 AATATTTTTAAATAATAAATTT-TCAAGATTTTTTA
1 AATATTTTTAAATAA-AAATTTCGCAAGATTTTATA
1187625 AAT-TATTTTAAATA
1 AATAT-TTTTAAATA
1187639 TACAATATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
34 1 0.02
35 16 0.37
36 20 0.47
37 6 0.14
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (35 bp):
AATATTTTTAAATAAAAATTTCGCAAGATTTTATA
Found at i:1202511 original size:20 final size:20
Alignment explanation
Indices: 1202479--1202521 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1202469 TTCAAAATAA
1202479 TTATTTTAGGTTGATA-TTAT
1 TTATTTTAGGTTGA-AGTTAT
1202499 TTATTTT-GAGTTGAAGTTAT
1 TTATTTTAG-GTTGAAGTTAT
1202519 TTA
1 TTA
1202522 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (20 bp):
TTATTTTAGGTTGAAGTTAT
Found at i:1203576 original size:20 final size:20
Alignment explanation
Indices: 1203551--1203590 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1203541 CGTAAAATGA
*
1203551 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
1203571 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
1203591 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:1203580 original size:34 final size:35
Alignment explanation
Indices: 1203536--1203602 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
1203526 CAGTAAAATA
*
1203536 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
1203570 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
1203603 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:1203606 original size:14 final size:15
Alignment explanation
Indices: 1203530--1203606 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
1203520 GATTGCCAGT
* *
1203530 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
1203544 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
1203558 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
1203578 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
1203593 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
1203607 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:1205194 original size:4 final size:4
Alignment explanation
Indices: 1205185--1205220 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
1205175 ATGTAGCTTA
*
1205185 GTAT GTAT GTAT ATAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1205221 ATTTTCTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:1212440 original size:20 final size:20
Alignment explanation
Indices: 1212415--1212453 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1212405 TGGTGAATAT
1212415 GCCAAGAGTTAAGTGGAGAC
1 GCCAAGAGTTAAGTGGAGAC
1212435 GCCAAGAGTTAAGTGGAGA
1 GCCAAGAGTTAAGTGGAGA
1212454 ACCGTCTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.36, T:0.15
Consensus pattern (20 bp):
GCCAAGAGTTAAGTGGAGAC
Found at i:1215721 original size:19 final size:18
Alignment explanation
Indices: 1215684--1215727 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1215674 TTCTTTTACA
* *
1215684 TTTTGCTTTTGATTCCTT
1 TTTTTCTTTGGATTCCTT
1215702 TTTTTCTTTGGATTCACTT
1 TTTTTCTTTGGATTC-CTT
*
1215721 TATTTCT
1 TTTTTCT
1215728 ACGGCATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.09, C:0.16, G:0.09, T:0.66
Consensus pattern (18 bp):
TTTTTCTTTGGATTCCTT
Found at i:1217307 original size:13 final size:13
Alignment explanation
Indices: 1217289--1217313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1217279 TGAAAATATT
1217289 ATTTTCATTTTCC
1 ATTTTCATTTTCC
1217302 ATTTTCATTTTC
1 ATTTTCATTTTC
1217314 AGAACACGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTCATTTTCC
Found at i:1219096 original size:17 final size:17
Alignment explanation
Indices: 1219076--1219115 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1219066 AATAAAAGGG
*
1219076 AAAGAAAGGAAAAAGAA
1 AAAGAAAAGAAAAAGAA
*
1219093 AAAGAAAAGAAGAAGAA
1 AAAGAAAAGAAAAAGAA
*
1219110 GAAGAA
1 AAAGAA
1219116 CGATTAGGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AAAGAAAAGAAAAAGAA
Found at i:1231011 original size:15 final size:15
Alignment explanation
Indices: 1230988--1231017 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1230978 TTGGAAAAAT
*
1230988 TAAATTGACTTGAAC
1 TAAAATGACTTGAAC
1231003 TAAAATGACTTGAAC
1 TAAAATGACTTGAAC
1231018 CTTAAATTAT
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:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (15 bp):
TAAAATGACTTGAAC
Found at i:1235735 original size:31 final size:32
Alignment explanation
Indices: 1235699--1235762 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1235689 AAATACAAAG
1235699 TAAACATT-TTTTTCAAATACCCTTTGTACAT
1 TAAACATTATTTTTCAAATACCCTTTGTACAT
1235730 TAAACATTATTTTTCAAATACCCTTTGTACAT
1 TAAACATTATTTTTCAAATACCCTTTGTACAT
1235762 T
1 T
1235763 TTTTTATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 8 0.25
32 24 0.75
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.45
Consensus pattern (32 bp):
TAAACATTATTTTTCAAATACCCTTTGTACAT
Found at i:1236186 original size:178 final size:175
Alignment explanation
Indices: 1235739--1236377 Score: 711
Period size: 177 Copynumber: 3.7 Consensus size: 175
1235729 TTAAACATTA
* * ** *
1235739 TTTTTCAAATACCCTTTGTACATTTTTTTATAAACCTTATTAATTTTTTCAACTT-TACCCAGTA
1 TTTTTCAAATACCCTTTGTATA-ATTTTTATAAACCTTATTAATTTTAACAACTTCT-CCCACTA
*
1235803 CTTTCTCAGGAAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGA-TGCC-AAA
64 CTTTCTCAGCAAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAA-ACTGCCAAAA
* * *
1235866 AAATGACCCAATTTCTAAATTAAAACACATAGAAAATACAAAGCAAGCAC
128 AAATGACCCAATTTCTAAATTAAAACACATA-AAAATGCAAA-CAAACAT
* * * * * * *
1235916 TTCTTCAAATACCGTTTGCAGAATATTTTACAAACCTTACTAATTTGT-ACAACTTC-CCCTCTA
1 TTTTTCAAATACCCTTTGTATAAT-TTTTATAAACCTTATTAATTT-TAACAACTTCTCCCACTA
* *
1235979 CTTTCTCAGCAAACAAACACCAGGTAATGGTGGGTAATTAAAGAGTACCACAAAACTGCCAAAAA
64 CTTTCTCAGCAAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAACTGCCAAAAA
* *
1236044 AACGACCCAATTTCTAATTTAAAACACATAAAAAATGCAAACTAAACATT
129 AATGACCCAATTTCTAAATTAAAACACAT-AAAAATGCAAAC-AAACA-T
* * *
1236094 TTTTTCAAATA-CCTTTGTATAATTTTTATTAAACCTTATTAATTTCAACAAATTCTCCGACTAC
1 TTTTTCAAATACCCTTTGTATAATTTTTA-TAAACCTTATTAATTTTAACAACTTCTCCCACTAC
* * * *
1236158 TTTCTCAGCAAACAAACACCAAGTAATGGTGAGTAATTAAAAAGTACCTCAAAGCTGCCAACAAA
65 TTTCTCAGCAAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAACTGCCAAAAAA
* *
1236223 ATGACCCAATTTCTAAATTCAAACACAT----A-G-AAA-ATAC--
130 ATGACCCAATTTCTAAATTAAAACACATAAAAATGCAAACAAACAT
** *
1236260 TTTTTCAAATACCCTTTGCTCATTTTTTTTATAAACCTTATTAAATTGTT---AACTTTTCCCAC
1 TTTTTCAAATACCCTTTG-T-ATAATTTTTATAAACCTTATT-AATT-TTAACAACTTCTCCCAC
* *
1236322 TACTTTCTCAGCAAACAAACACCAAGTAATGATGGGTAACTAAAGAGTACCTCAAA
62 TACTTTCTCAGCAAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAA
1236378 CAAGGCCATC
Statistics
Matches: 398, Mismatches: 48, Indels: 42
0.82 0.10 0.09
Matches are distributed among these distances:
166 11 0.03
167 67 0.17
168 12 0.03
169 15 0.04
170 1 0.00
171 3 0.01
172 1 0.00
173 1 0.00
175 1 0.00
176 67 0.17
177 117 0.29
178 102 0.26
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (175 bp):
TTTTTCAAATACCCTTTGTATAATTTTTATAAACCTTATTAATTTTAACAACTTCTCCCACTACT
TTCTCAGCAAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAACTGCCAAAAAAA
TGACCCAATTTCTAAATTAAAACACATAAAAATGCAAACAAACAT
Found at i:1237498 original size:13 final size:13
Alignment explanation
Indices: 1237480--1237506 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1237470 ATGAAATATT
1237480 TAATTTTTTTAGG
1 TAATTTTTTTAGG
1237493 TAATTTTTTTAGG
1 TAATTTTTTTAGG
1237506 T
1 T
1237507 CTCTAAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (13 bp):
TAATTTTTTTAGG
Found at i:1254303 original size:23 final size:24
Alignment explanation
Indices: 1254276--1254340 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 24
1254266 ATGAAAATGA
1254276 TTTTTATGATAAAAA-AATTG-GGT
1 TTTTTAT-ATAAAAATAATTGAGGT
1254299 TTTTT-TA-AATAAATAATTGAAGGT
1 TTTTTATATAA-AAATAATTG-AGGT
1254323 TTTTTATTATAAAAATAA
1 TTTTTA-TATAAAAATAA
1254341 AAAATGAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
20 2 0.06
21 4 0.11
22 6 0.17
23 5 0.14
24 8 0.23
26 8 0.23
27 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (24 bp):
TTTTTATATAAAAATAATTGAGGT
Found at i:1254794 original size:6 final size:6
Alignment explanation
Indices: 1254785--1254811 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1254775 TTGATTTTTT
1254785 TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTT
1254812 CAATCAAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:1255367 original size:22 final size:22
Alignment explanation
Indices: 1255326--1255367 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1255316 ATTTTATATT
* *
1255326 ATATAAATTAAATAATATATAA
1 ATATAAAATAAATAACATATAA
*
1255348 ATATAAAATAAATCACATAT
1 ATATAAAATAAATAACATAT
1255368 TATAAAAGTA
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:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATAAAATAAATAACATATAA
Found at i:1255505 original size:19 final size:21
Alignment explanation
Indices: 1255477--1255519 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1255467 CTCAAATCCA
1255477 TTTTTTCGAA-TC-C-TATAT
1 TTTTTTCGAACTCTCTTATAT
1255495 TTTTATTCGAACTCTCTTATAT
1 TTTT-TTCGAACTCTCTTATAT
1255517 TTT
1 TTT
1255520 AAGTGAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 4 0.19
19 6 0.29
20 2 0.10
21 1 0.05
22 8 0.38
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (21 bp):
TTTTTTCGAACTCTCTTATAT
Found at i:1271279 original size:15 final size:16
Alignment explanation
Indices: 1271259--1271296 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1271249 CTAAATCTAT
1271259 TTTAAAACACATA-A-A
1 TTTAAAAC-CATATATA
1271274 TTTAAAACCATATATA
1 TTTAAAACCATATATA
1271290 TTTAAAA
1 TTTAAAA
1271297 AAAATTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 8 0.38
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (16 bp):
TTTAAAACCATATATA
Found at i:1274233 original size:29 final size:30
Alignment explanation
Indices: 1274193--1274332 Score: 112
Period size: 29 Copynumber: 4.8 Consensus size: 30
1274183 GTGTATATTA
*
1274193 TATGCGAGCCTATAGT-CGAACCCTAGGAT
1 TATGCGAGCCTATAGTGCGAACCCTAAGAT
* * *
1274222 TATGCGAGCCTATA-TGTGAACCTTAAAAT
1 TATGCGAGCCTATAGTGCGAACCCTAAGAT
* * * * *
1274251 TATACGAGGCTATA-TGCGAACCTTAGGAA
1 TATGCGAGCCTATAGTGCGAACCCTAAGAT
* * *
1274280 CATGCAAGCCTACA-TGCGAACCCTAAG-T
1 TATGCGAGCCTATAGTGCGAACCCTAAGAT
*
1274308 ATATGCGTGCCTAT-GTGCGAACCCT
1 -TATGCGAGCCTATAGTGCGAACCCT
1274333 TGGTGCATGC
Statistics
Matches: 86, Mismatches: 22, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
28 1 0.01
29 85 0.99
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (30 bp):
TATGCGAGCCTATAGTGCGAACCCTAAGAT
Found at i:1274361 original size:34 final size:34
Alignment explanation
Indices: 1274323--1274397 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
1274313 CGTGCCTATG
* * ***
1274323 TGCGAACCCTTGGTGCATGCGTGCCTATATGTCA
1 TGCGAACCCTAGGTACATGCAAACCTATATGTCA
*
1274357 TGCGAACCCTAGGTACATGTAAACCTATATGTCA
1 TGCGAACCCTAGGTACATGCAAACCTATATGTCA
1274391 TGCGAAC
1 TGCGAAC
1274398 TTGTAAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (34 bp):
TGCGAACCCTAGGTACATGCAAACCTATATGTCA
Found at i:1276081 original size:3 final size:3
Alignment explanation
Indices: 1276067--1276116 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
1276057 AAATGACATT
* * *
1276067 TTA TTA TT- TTA TTA TTA TTG TTA TTA TTA ATA TTA TTG TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1276113 TTA T
1 TTA T
1276117 GAAATAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1276102 original size:18 final size:18
Alignment explanation
Indices: 1276070--1276111 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1276060 TGACATTTTA
*
1276070 TTATT-TTATTATTATTG
1 TTATTATTAATATTATTG
1276087 TTATTATTAATATTATTG
1 TTATTATTAATATTATTG
1276105 TTATTAT
1 TTATTAT
1276112 ATTATGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTATTATTAATATTATTG
Found at i:1277790 original size:21 final size:21
Alignment explanation
Indices: 1277766--1277874 Score: 76
Period size: 21 Copynumber: 5.2 Consensus size: 21
1277756 ACTCATATGA
1277766 GTTTCAGATTAACCCTTTTGG
1 GTTTCAGATTAACCCTTTTGG
* ** *
1277787 GTTTCAG-TTCAGCTATTTTGA
1 GTTTCAGATT-AACCCTTTTGG
* * **
1277808 GCTTCAGTTTAACCCTAATGG
1 GTTTCAGATTAACCCTTTTGG
* * * *
1277829 GTTTCAGTTTAGCTCTTTTGA
1 GTTTCAGATTAACCCTTTTGG
* *
1277850 GCTTCAGATTAACCCTTATGG
1 GTTTCAGATTAACCCTTTTGG
1277871 GTTT
1 GTTT
1277875 TCGTTTAGCA
Statistics
Matches: 62, Mismatches: 24, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
20 2 0.03
21 58 0.94
22 2 0.03
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.43
Consensus pattern (21 bp):
GTTTCAGATTAACCCTTTTGG
Found at i:1277881 original size:42 final size:42
Alignment explanation
Indices: 1277763--1277883 Score: 172
Period size: 42 Copynumber: 2.9 Consensus size: 42
1277753 TTAACTCATA
* * *
1277763 TGAGTTTCAGATTAACCCTTTTGGGTTTCAGTTCAGCTATTT
1 TGAGCTTCAGATTAACCCTTATGGGTTTCAGTTTAGCTATTT
* * *
1277805 TGAGCTTCAGTTTAACCCTAATGGGTTTCAGTTTAGCTCTTT
1 TGAGCTTCAGATTAACCCTTATGGGTTTCAGTTTAGCTATTT
1277847 TGAGCTTCAGATTAACCCTTATGGGTTTTC-GTTTAGC
1 TGAGCTTCAGATTAACCCTTATGGG-TTTCAGTTTAGC
1277884 ACTTATGTGC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
42 66 0.94
43 4 0.06
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.43
Consensus pattern (42 bp):
TGAGCTTCAGATTAACCCTTATGGGTTTCAGTTTAGCTATTT
Found at i:1283655 original size:17 final size:16
Alignment explanation
Indices: 1283631--1283668 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1283621 ATTTTTTTTG
1283631 AAAA-AATATTTATAAA
1 AAAATAATATTTA-AAA
1283647 AAAATAATATTTAAAA
1 AAAATAATATTTAAAA
*
1283663 ATAATA
1 AAAATA
1283669 CAATAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAATAATATTTAAAA
Found at i:1289587 original size:10 final size:10
Alignment explanation
Indices: 1289557--1289600 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1289547 CCAACCAATG
*
1289557 ATTTTATATT
1 ATTTTATTTT
* *
1289567 ATTATAATTT
1 ATTTTATTTT
1289577 ATTTTATTTT
1 ATTTTATTTT
1289587 ATTTTATTTAT
1 ATTTTATTT-T
1289598 ATT
1 ATT
1289601 GCATAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 24 0.86
11 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTTTATTTT
Found at i:1299865 original size:19 final size:18
Alignment explanation
Indices: 1299830--1299865 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1299820 GAATTTTTCA
*
1299830 TTAAATTAATCCTAAAAC
1 TTAAATTAAACCTAAAAC
1299848 TTAAATTAAACACTAAAA
1 TTAAATTAAAC-CTAAAA
1299866 AGTTAGCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAATTAAACCTAAAAC
Found at i:1300714 original size:19 final size:20
Alignment explanation
Indices: 1300684--1300721 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1300674 TTTAAAAATA
1300684 TTGAAAATATTTAAATTGAG
1 TTGAAAATATTTAAATTGAG
1300704 TTGAAAA-ATTTAAATTGA
1 TTGAAAATATTTAAATTGA
1300722 AGTGGAGCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (20 bp):
TTGAAAATATTTAAATTGAG
Found at i:1305797 original size:30 final size:30
Alignment explanation
Indices: 1305763--1305822 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1305753 CAAATGGTCA
1305763 TTGAACTATTTAAAAGTTTTCATTTAAGTC
1 TTGAACTATTTAAAAGTTTTCATTTAAGTC
* *
1305793 TTGAACTATTTGAAAGTTTTTATTTAAGTC
1 TTGAACTATTTAAAAGTTTTCATTTAAGTC
1305823 ACTGGATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (30 bp):
TTGAACTATTTAAAAGTTTTCATTTAAGTC
Found at i:1307546 original size:93 final size:93
Alignment explanation
Indices: 1307387--1307573 Score: 365
Period size: 93 Copynumber: 2.0 Consensus size: 93
1307377 TAAAAACGTC
1307387 ACTCAAAACACATGATATCATCAATCAAGTAATCTTATAATGAATAATTTATTAGAGTTGAATCT
1 ACTCAAAACACATGATATCATCAATCAAGTAATCTTATAATGAATAATTTATTAGAGTTGAATCT
1307452 TAATTCGACGAACATAATTATACTTATA
66 TAATTCGACGAACATAATTATACTTATA
*
1307480 ACTCAAAACACATGATATCATCAATCAAGTAATCTTATAATTAATAATTTATTAGAGTTGAATCT
1 ACTCAAAACACATGATATCATCAATCAAGTAATCTTATAATGAATAATTTATTAGAGTTGAATCT
1307545 TAATTCGACGAACATAATTATACTTATA
66 TAATTCGACGAACATAATTATACTTATA
1307573 A
1 A
1307574 TATTTAAGAA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (93 bp):
ACTCAAAACACATGATATCATCAATCAAGTAATCTTATAATGAATAATTTATTAGAGTTGAATCT
TAATTCGACGAACATAATTATACTTATA
Found at i:1313228 original size:15 final size:15
Alignment explanation
Indices: 1313208--1313242 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1313198 AAGTTAATCG
* *
1313208 AATGTGATTTTTTGT
1 AATGTGATTATTAGT
1313223 AATGTGATTATTAGT
1 AATGTGATTATTAGT
1313238 AATGT
1 AATGT
1313243 AATTGTCGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (15 bp):
AATGTGATTATTAGT
Found at i:1315333 original size:15 final size:15
Alignment explanation
Indices: 1315315--1315344 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1315305 TAGCCCAACT
*
1315315 TTATTTACTAAAATA
1 TTATTTACCAAAATA
1315330 TTATTTACCAAAATA
1 TTATTTACCAAAATA
1315345 ATACGAGTTC
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:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (15 bp):
TTATTTACCAAAATA
Found at i:1326634 original size:29 final size:30
Alignment explanation
Indices: 1326602--1326665 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
1326592 GCAATTTAAT
1326602 ACAT-AAACTTTGATTG-GATGCAACTATAC
1 ACATGAAA-TTTGATTGTGATGCAACTATAC
*
1326631 ACATGGAAATTTGATTGTGATTCAACTATAC
1 ACAT-GAAATTTGATTGTGATGCAACTATAC
1326662 ACAT
1 ACAT
1326666 TTAAAGAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 4 0.13
30 8 0.26
31 19 0.61
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (30 bp):
ACATGAAATTTGATTGTGATGCAACTATAC
Found at i:1328942 original size:3 final size:3
Alignment explanation
Indices: 1328934--1328969 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1328924 AGTCGGGTCT
1328934 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1328970 CCTTCTAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1337243 original size:16 final size:18
Alignment explanation
Indices: 1337222--1337257 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1337212 TTTAATAATA
1337222 AAAG-AAATTTGG-AAAC
1 AAAGAAAATTTGGTAAAC
1337238 AAAGAAAATTTGGTAAAC
1 AAAGAAAATTTGGTAAAC
1337256 AA
1 AA
1337258 GCCTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 8 0.44
18 6 0.33
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.19
Consensus pattern (18 bp):
AAAGAAAATTTGGTAAAC
Found at i:1346034 original size:7 final size:7
Alignment explanation
Indices: 1346010--1346043 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1346000 CTCAAACATA
1346010 TTATTTT
1 TTATTTT
* *
1346017 TAATATT
1 TTATTTT
1346024 TTATTTT
1 TTATTTT
1346031 TTATTTT
1 TTATTTT
1346038 TTATTT
1 TTATTT
1346044 AGTCATTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (7 bp):
TTATTTT
Found at i:1348641 original size:37 final size:37
Alignment explanation
Indices: 1348580--1348725 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
1348570 TACGTATGAT
*
1348580 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
* * *
1348615 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAAC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1348652 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1348689 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1348726 TAAAGCTATC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 9 0.09
36 4 0.04
37 89 0.87
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:1348768 original size:52 final size:52
Alignment explanation
Indices: 1348689--1349055 Score: 488
Period size: 52 Copynumber: 7.2 Consensus size: 52
1348679 TAAGTGTAGC
* * **
1348689 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1348742 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1348794 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
1348846 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* ** *
1348892 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
1348944 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* ** *
1348990 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1349042 CACTTTGTCACTTG
1 CACTTT-TCACTTG
1349056 ATCAGAAGTA
Statistics
Matches: 276, Mismatches: 25, Indels: 26
0.84 0.08 0.08
Matches are distributed among these distances:
46 83 0.30
49 1 0.00
52 177 0.64
53 15 0.05
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Found at i:1348865 original size:150 final size:144
Alignment explanation
Indices: 1348689--1349055 Score: 509
Period size: 150 Copynumber: 2.5 Consensus size: 144
1348679 TAAGTGTAGC
*
1348689 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
* *
1348754 GTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAG
66 GTCACTTGATCAGATAAGTGTAGCCAAAGCTACCACTTATCAC---T---TTGTCACTTGATCAG
*
1348819 ATAAGTGTAGCCGAAGCTAT
125 ATAAGTATAGCCGAAGCTAT
* ** * *
1348839 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
*
1348904 GTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGT
66 GTCACTTGATCAGATAAGTGTAGCCAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGT
1348969 ATAGCCGAAGCTAT
131 ATAGCCGAAGCTAT
* *
1348983 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTT
1349048 GTCACTTG
60 -TCACTTG
1349056 ATCAGAAGTA
Statistics
Matches: 193, Mismatches: 17, Indels: 13
0.87 0.08 0.06
Matches are distributed among these distances:
144 43 0.22
146 1 0.01
147 1 0.01
150 142 0.74
151 6 0.03
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (144 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
GTCACTTGATCAGATAAGTGTAGCCAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGT
ATAGCCGAAGCTAT
Found at i:1348876 original size:98 final size:98
Alignment explanation
Indices: 1348700--1349061 Score: 598
Period size: 98 Copynumber: 3.6 Consensus size: 98
1348690 ACTTATCACT
* *
1348700 TTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTTGTCACTTGATC
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC---T---TTGTCACTTGATC
* * *
1348765 AGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTCAC
60 AGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCAC
** *
1348804 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
1348869 GTATAGCCGAAGCTATTACTTATCACTTTCCAC
66 GTATAGCCGAAGCTATTACTTATCACTTTCCAC
1348902 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
1348967 GTATAGCCGAAGCTATTACTTATCACTTTCCAC
66 GTATAGCCGAAGCTATTACTTATCACTTTCCAC
1349000 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
1349062 AGTACTCAAA
Statistics
Matches: 249, Mismatches: 9, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
98 206 0.83
101 1 0.00
104 42 0.17
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (98 bp):
TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
GTATAGCCGAAGCTATTACTTATCACTTTCCAC
Found at i:1355075 original size:16 final size:17
Alignment explanation
Indices: 1355047--1355087 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1355037 TTTGGATCGG
*
1355047 GTTAA-TTTGAGTTTAA
1 GTTAATTTTAAGTTTAA
*
1355063 GTT-ATTTTAAGTTTAG
1 GTTAATTTTAAGTTTAA
1355079 GTTAATTTT
1 GTTAATTTT
1355088 TAGCTCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 15 0.71
17 5 0.24
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (17 bp):
GTTAATTTTAAGTTTAA
Found at i:1361114 original size:10 final size:10
Alignment explanation
Indices: 1361083--1361115 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1361073 CATCATTGTA
1361083 TTAAATT-AT
1 TTAAATTAAT
1361092 TTAAATATAAT
1 TTAAAT-TAAT
1361103 TTAAATTAAT
1 TTAAATTAAT
1361113 TTA
1 TTA
1361116 TATTTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.27
10 8 0.36
11 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTAAATTAAT
Found at i:1362985 original size:6 final size:6
Alignment explanation
Indices: 1362979--1363044 Score: 60
Period size: 6 Copynumber: 11.0 Consensus size: 6
1362969 CTCATCGTCG
* * * * * * * *
1362979 TCATCG TCATCT TCATCT TCATCT TCATCA TCGTCC TCGTCC ACATCA
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
1363027 TCATCT TCATCT TCATCT
1 TCATCT TCATCT TCATCT
1363045 ACTATCTCAT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.18, C:0.36, G:0.05, T:0.41
Consensus pattern (6 bp):
TCATCT
Found at i:1363000 original size:18 final size:18
Alignment explanation
Indices: 1362958--1363043 Score: 73
Period size: 18 Copynumber: 4.8 Consensus size: 18
1362948 GGTCTTACTT
* * *
1362958 TCTTCATCATCCTCATCG
1 TCTTCATCTTCATCATCA
* * *
1362976 TCGTCATCGTCATCTTCA
1 TCTTCATCTTCATCATCA
*
1362994 TCTTCATCTTCATCATCG
1 TCTTCATCTTCATCATCA
* * **
1363012 TCCTCGTCCACATCATCA
1 TCTTCATCTTCATCATCA
1363030 TCTTCATCTTCATC
1 TCTTCATCTTCATC
1363044 TACTATCTCA
Statistics
Matches: 50, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.17, C:0.37, G:0.06, T:0.40
Consensus pattern (18 bp):
TCTTCATCTTCATCATCA
Found at i:1363010 original size:36 final size:36
Alignment explanation
Indices: 1362958--1363043 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
1362948 GGTCTTACTT
* * * ** *
1362958 TCTTCATCATCCTCATCGTCGTCATCGTCATCTTCA
1 TCTTCATCTTCATCATCGTCCTCATCCACATCATCA
*
1362994 TCTTCATCTTCATCATCGTCCTCGTCCACATCATCA
1 TCTTCATCTTCATCATCGTCCTCATCCACATCATCA
1363030 TCTTCATCTTCATC
1 TCTTCATCTTCATC
1363044 TACTATCTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.17, C:0.37, G:0.06, T:0.40
Consensus pattern (36 bp):
TCTTCATCTTCATCATCGTCCTCATCCACATCATCA
Found at i:1363019 original size:42 final size:42
Alignment explanation
Indices: 1362958--1363044 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
1362948 GGTCTTACTT
** *
1362958 TCTTCATCATCCTCATCGTCGTCATCGTCATCTTCATCTTCA
1 TCTTCATCATCCTCATCGTCCACATCATCATCTTCATCTTCA
* *
1363000 TCTTCATCATCGTCCTCGTCCACATCATCATCTTCATCTTCA
1 TCTTCATCATCCTCATCGTCCACATCATCATCTTCATCTTCA
1363042 TCT
1 TCT
1363045 ACTATCTCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.17, C:0.37, G:0.06, T:0.40
Consensus pattern (42 bp):
TCTTCATCATCCTCATCGTCCACATCATCATCTTCATCTTCA
Found at i:1369030 original size:50 final size:50
Alignment explanation
Indices: 1368955--1369057 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
1368945 AAAAATAAGT
1368955 AAATTAGTCCCTATATATTTGATTAAAGAGTAAAGATGTCGTTCTATTAA
1 AAATTAGTCCCTATATATTTGATTAAAGAGTAAAGATGTCGTTCTATTAA
1369005 AAATTAGTCCCTATATATTTGATTAAAGAGTAAAGATGTCGTTCTATTAA
1 AAATTAGTCCCTATATATTTGATTAAAGAGTAAAGATGTCGTTCTATTAA
1369055 AAA
1 AAA
1369058 ATATATCAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (50 bp):
AAATTAGTCCCTATATATTTGATTAAAGAGTAAAGATGTCGTTCTATTAA
Found at i:1377809 original size:53 final size:54
Alignment explanation
Indices: 1377696--1377809 Score: 203
Period size: 54 Copynumber: 2.1 Consensus size: 54
1377686 ATTACAATGA
*
1377696 TATTTTCTAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATATTTTT
1 TATTTTCTAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATAATTTT
*
1377750 TATTTTCTAATTATGTAAAAAATAGACAAGATAAAAATGGTATTTCA-AATTTT
1 TATTTTCTAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATAATTTT
1377803 TATTTTC
1 TATTTTC
1377810 CAAAATTGAG
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
53 12 0.21
54 46 0.79
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (54 bp):
TATTTTCTAATTATGTAAAAAATAGACAAGATAAAAATGGGATTTCATAATTTT
Found at i:1378097 original size:47 final size:47
Alignment explanation
Indices: 1378023--1378112 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 47
1378013 AGTATTTTCT
* * *
1378023 GTCAAAATTTGCCATCAATACAGCTATGCTATCATACTAACTTTAGA
1 GTCAAAATTTACCATCAATACACCTATGCAATCATACTAACTTTAGA
* * *
1378070 GTCAAAATTTACCATCAATGCACCTATGCAATGATATTAACTT
1 GTCAAAATTTACCATCAATACACCTATGCAATCATACTAACTT
1378113 CCAGAAGCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (47 bp):
GTCAAAATTTACCATCAATACACCTATGCAATCATACTAACTTTAGA
Found at i:1380592 original size:31 final size:33
Alignment explanation
Indices: 1380568--1380633 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
1380558 TAAAAGATAT
1380568 ATTTTTATA-CTTTTT-AATTTTTAAAAATAAA
1 ATTTTTATATCTTTTTAAATTTTTAAAAATAAA
* *
1380599 ATTTTTATATTTTTTTTAAATTTTTAAAATTAAA
1 ATTTTTATA-TCTTTTTAAATTTTTAAAAATAAA
1380633 A
1 A
1380634 AAATAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 9 0.30
33 5 0.17
34 16 0.53
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (33 bp):
ATTTTTATATCTTTTTAAATTTTTAAAAATAAA
Found at i:1386850 original size:19 final size:19
Alignment explanation
Indices: 1386826--1386871 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1386816 TCACAAAAAT
1386826 AAAAAAATTAAATTTTCAA
1 AAAAAAATTAAATTTTCAA
1386845 AAAAAAATTAAATTTTCAA
1 AAAAAAATTAAATTTTCAA
*
1386864 ATAAAAAT
1 AAAAAAAT
1386872 AAGGAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAAAATTAAATTTTCAA
Found at i:1387152 original size:21 final size:21
Alignment explanation
Indices: 1387108--1387148 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1387098 TTTTCTAAAA
**
1387108 ATTTTTATGAACTTTTTATAT
1 ATTTTTATGAACTTTGAATAT
1387129 ATTTTT-TGAACTTTGAATAT
1 ATTTTTATGAACTTTGAATAT
1387149 TATTATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.59
Consensus pattern (21 bp):
ATTTTTATGAACTTTGAATAT
Found at i:1388022 original size:21 final size:20
Alignment explanation
Indices: 1387996--1388034 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1387986 TTACAATTCC
*
1387996 ATTTTAAACATAATGTTAAAA
1 ATTTTAAAAATAAT-TTAAAA
1388017 ATTTTAAAAATAATTTAA
1 ATTTTAAAAATAATTTAA
1388035 TGTAGTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
ATTTTAAAAATAATTTAAAA
Found at i:1388164 original size:21 final size:22
Alignment explanation
Indices: 1388140--1388181 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1388130 ATAATAACCA
*
1388140 TAAAATATTTTTTAAA-AATTT
1 TAAAATATATTTTAAATAATTT
1388161 TAAAATATATTTTAAATAATT
1 TAAAATATATTTTAAATAATT
1388182 AGTACAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAAAATATATTTTAAATAATTT
Found at i:1392757 original size:10 final size:10
Alignment explanation
Indices: 1392742--1392777 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1392732 CCCTCTCTAG
1392742 TATTTTTATT
1 TATTTTTATT
1392752 TATTTTT-TT
1 TATTTTTATT
*
1392761 AATTTTTATT
1 TATTTTTATT
1392771 TATTTTT
1 TATTTTT
1392778 CGTCGATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TATTTTTATT
Found at i:1397238 original size:17 final size:17
Alignment explanation
Indices: 1397216--1397249 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1397206 CTAATCAATT
1397216 CAACTAATATCATAAAA
1 CAACTAATATCATAAAA
1397233 CAACTAATATCATAAAA
1 CAACTAATATCATAAAA
1397250 TTGGAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
CAACTAATATCATAAAA
Found at i:1397985 original size:21 final size:19
Alignment explanation
Indices: 1397959--1397997 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
1397949 TTGATCAGTT
1397959 TCATTAATAATAATTAAAAAA
1 TCATTAA-AAT-ATTAAAAAA
1397980 TCATTAAAATATTAAAAA
1 TCATTAAAATATTAAAAA
1397998 TTCAGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
TCATTAAAATATTAAAAAA
Found at i:1398144 original size:11 final size:11
Alignment explanation
Indices: 1398128--1398152 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1398118 TGTTTATTAA
1398128 TTTTTAATGAT
1 TTTTTAATGAT
1398139 TTTTTAATGAT
1 TTTTTAATGAT
1398150 TTT
1 TTT
1398153 ATTTTACAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTTAATGAT
Found at i:1399883 original size:51 final size:51
Alignment explanation
Indices: 1399828--1399926 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
1399818 AATAATAAAT
*
1399828 TTAACCTTCAA-CATTTACATATTATGTCAAATTGGTCATAATTCTAAAAAA
1 TTAACCTT-AATCATTTACATATTATGTCAAATTGATCATAATTCTAAAAAA
* * * * *
1399879 TTAACCTTAATCGTTTACATATTGTTTCAATTTGATCTTAATTCTAAA
1 TTAACCTTAATCATTTACATATTATGTCAAATTGATCATAATTCTAAA
1399927 TAATATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.05
51 39 0.95
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.42
Consensus pattern (51 bp):
TTAACCTTAATCATTTACATATTATGTCAAATTGATCATAATTCTAAAAAA
Found at i:1402466 original size:25 final size:24
Alignment explanation
Indices: 1402417--1402467 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
1402407 ATGTTTACAC
** *
1402417 TTTTATTAATTTAATCTTAATTTT
1 TTTTATTAATTTAATAATAACTTT
1402441 TTTTAGTTAATTTAATAATAACTTT
1 TTTTA-TTAATTTAATAATAACTTT
1402466 TT
1 TT
1402468 AAGGAGTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTATTAATTTAATAATAACTTT
Found at i:1404852 original size:37 final size:37
Alignment explanation
Indices: 1404795--1404946 Score: 173
Period size: 37 Copynumber: 3.9 Consensus size: 37
1404785 TATGATCATT
*
1404795 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
1404830 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
1404867 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
*
1404912 TTATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
1404947 GAAGCTATCA
Statistics
Matches: 100, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
35 6 0.06
36 4 0.04
37 54 0.54
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 32 0.32
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:1404930 original size:46 final size:46
Alignment explanation
Indices: 1404863--1405131 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
1404853 TAAGTGTAGC
* **
1404863 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
1404909 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1404955 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
1405007 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
1405053 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1405105 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
1405132 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:1404982 original size:52 final size:52
Alignment explanation
Indices: 1404906--1405125 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
1404896 TAGCTAAAGC
* *
1404906 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
1404959 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
1405011 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
1405057 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1405109 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
1405126 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:1405028 original size:98 final size:98
Alignment explanation
Indices: 1404863--1405131 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
1404853 TAAGTGTAGC
* * *
1404863 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
1404928 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
1404962 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
1405027 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
1405060 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
1405125 GATCAGA
66 GATCAGA
1405132 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:1408312 original size:49 final size:49
Alignment explanation
Indices: 1408257--1408402 Score: 229
Period size: 49 Copynumber: 3.0 Consensus size: 49
1408247 TTCGTTTTCT
* *
1408257 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACAAATCACATAC
* *
1408306 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACAAATCACATAC
* *
1408355 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACA-AATCACAT
1408403 GTTCACATGT
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 82 0.93
50 6 0.07
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (49 bp):
CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACAAATCACATAC
Found at i:1409716 original size:37 final size:37
Alignment explanation
Indices: 1409659--1409810 Score: 173
Period size: 37 Copynumber: 3.9 Consensus size: 37
1409649 TATGATCATT
*
1409659 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
1409694 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
1409731 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
*
1409776 TTATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
1409811 GAAGCTATCA
Statistics
Matches: 100, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
35 6 0.06
36 4 0.04
37 54 0.54
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 32 0.32
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:1409794 original size:46 final size:46
Alignment explanation
Indices: 1409727--1409995 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
1409717 TAAGTGTAGC
* **
1409727 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
1409773 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1409819 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
1409871 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
1409917 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1409969 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
1409996 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:1409846 original size:52 final size:52
Alignment explanation
Indices: 1409770--1409989 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
1409760 TAGCTAAAGC
* *
1409770 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
1409823 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
1409875 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
1409921 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1409973 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
1409990 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:1409892 original size:98 final size:98
Alignment explanation
Indices: 1409727--1409995 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
1409717 TAAGTGTAGC
* * *
1409727 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
1409792 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
1409826 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
1409891 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
1409924 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
1409989 GATCAGA
66 GATCAGA
1409996 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:1428348 original size:19 final size:19
Alignment explanation
Indices: 1428324--1428360 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1428314 AGTCACCATA
1428324 CAAGAAAA-CAACCAAAAAG
1 CAAGAAAATCAA-CAAAAAG
1428343 CAAGAAAATCAACAAAAA
1 CAAGAAAATCAACAAAAA
1428361 TTGAAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.70, C:0.19, G:0.08, T:0.03
Consensus pattern (19 bp):
CAAGAAAATCAACAAAAAG
Found at i:1433264 original size:26 final size:26
Alignment explanation
Indices: 1433214--1433265 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1433204 TGGATATTTT
*
1433214 ATATTTTTAATTTTTTATGTGTTTAA
1 ATATTTTTAATTTTATATGTGTTTAA
*
1433240 ATATTTTTAAATTTTATA-GTTTTTAA
1 ATATTTTT-AATTTTATATGTGTTTAA
1433266 TAAATATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (26 bp):
ATATTTTTAATTTTATATGTGTTTAA
Found at i:1435148 original size:16 final size:14
Alignment explanation
Indices: 1435117--1435155 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1435107 ATATGAAGAA
1435117 TATTA-TTTTAAAT
1 TATTATTTTTAAAT
1435130 TATTATTTTTAAAT
1 TATTATTTTTAAAT
*
1435144 T-TTATTATTAAA
1 TATTATTTTTAAA
1435156 ATAAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATTTTTAAAT
Found at i:1445486 original size:214 final size:214
Alignment explanation
Indices: 1445117--1445546 Score: 797
Period size: 214 Copynumber: 2.0 Consensus size: 214
1445107 GCAATTGGTC
*
1445117 CAAATATAAAAGAAAGTGCCAAAGTTGGTGAAAATCTTCAATGTCGTAGGAGAGAGATACCTCCT
1 CAAATATAAAAGAAAGTGCCAAAGTTGGTGAAAATCTTCAATGTCGTAGGAGAGAAATACCTCCT
* *
1445182 ACTGGGCAGTTCAAACTCCTCATTTTATTCAGATAGTGGGGAGACACCATCTCAATGTAGACAAA
66 ACAGGGCAGTTCAAACTCCTCATTTTATTCAGATAGTGAGGAGACACCATCTCAATGTAGACAAA
*
1445247 GTCTGGGTTGCTCACTAAGTCCCAAATGGATGATGCTTCTGCAGTTCTTCTTGATCTTATATATG
131 GTCTGGGTTGCTCACTAAGTCCCAAATGGATGATGCTTCTGCAGTTCTCCTTGATCTTATATATG
* *
1445312 GAATCTGTTTCTCCTTGAT
196 GAATCTGTTTCACCATGAT
1445331 CAAATATAAAAGAAAGTGCCAAAGTTGGTGAAAATCTTCAATGTCGTAGGAGAGAAATACCTCCT
1 CAAATATAAAAGAAAGTGCCAAAGTTGGTGAAAATCTTCAATGTCGTAGGAGAGAAATACCTCCT
*
1445396 ACAGGGCAGTTCAAACTCCTCATTTTATTCAGATAGTGAGGATACACCATCTCAATGTAGACAAA
66 ACAGGGCAGTTCAAACTCCTCATTTTATTCAGATAGTGAGGAGACACCATCTCAATGTAGACAAA
1445461 GTCTGGGTTGCTCACTAAGTCCCAAATGGATGATGCTTCTGCAGTTCTCCTTGATCTTATATATG
131 GTCTGGGTTGCTCACTAAGTCCCAAATGGATGATGCTTCTGCAGTTCTCCTTGATCTTATATATG
1445526 GAATCTGTTTCACCATGAT
196 GAATCTGTTTCACCATGAT
1445545 CA
1 CA
1445547 TAATGTGGTT
Statistics
Matches: 209, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
214 209 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (214 bp):
CAAATATAAAAGAAAGTGCCAAAGTTGGTGAAAATCTTCAATGTCGTAGGAGAGAAATACCTCCT
ACAGGGCAGTTCAAACTCCTCATTTTATTCAGATAGTGAGGAGACACCATCTCAATGTAGACAAA
GTCTGGGTTGCTCACTAAGTCCCAAATGGATGATGCTTCTGCAGTTCTCCTTGATCTTATATATG
GAATCTGTTTCACCATGAT
Found at i:1454806 original size:12 final size:12
Alignment explanation
Indices: 1454773--1454805 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1454763 CTTCTTTTTC
1454773 TTTTATTTTTAA
1 TTTTATTTTTAA
1454785 TTTTATTTTTAA
1 TTTTATTTTTAA
1454797 TTTT-TTTTT
1 TTTTATTTTT
1454806 TTTGGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTATTTTTAA
Found at i:1462492 original size:5 final size:5
Alignment explanation
Indices: 1462473--1462507 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
1462463 AAGGCTTTGA
1462473 AAAAG -AAAG -AAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
1462508 CAAGTTACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1465144 original size:3 final size:3
Alignment explanation
Indices: 1465136--1465201 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
1465126 ATTAAGTTGG
1465136 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1465184 ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
1465202 CACATTGACT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1479839 original size:11 final size:11
Alignment explanation
Indices: 1479799--1479929 Score: 74
Period size: 11 Copynumber: 12.9 Consensus size: 11
1479789 GACCCATTTT
1479799 TATTTT-AAAA
1 TATTTTAAAAA
1479809 -ATTTTAAAAA
1 TATTTTAAAAA
**
1479819 -ATTAAAAAAA
1 TATTTTAAAAA
1479829 GTATTTTAAAAA
1 -TATTTTAAAAA
1479841 TATTTT--AAA
1 TATTTTAAAAA
1479850 -A--TTAAAAA
1 TATTTTAAAAA
* **
1479858 AATTAAAAAAA
1 TATTTTAAAAA
1479869 GTATTTTAAAAA
1 -TATTTTAAAAA
1479881 TATTTT--AAA
1 TATTTTAAAAA
1479890 -A--TTAAAAA
1 TATTTTAAAAA
**
1479898 -ATTAAAAAAA
1 TATTTTAAAAA
1479908 GTATTTTAAAAA
1 -TATTTTAAAAA
1479920 TATTTTAAAA
1 TATTTTAAAA
1479930 TTAAAAAAGT
Statistics
Matches: 93, Mismatches: 13, Indels: 29
0.69 0.10 0.21
Matches are distributed among these distances:
6 4 0.04
8 9 0.10
9 12 0.13
10 17 0.18
11 27 0.29
12 24 0.26
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:1479866 original size:39 final size:40
Alignment explanation
Indices: 1479799--1479959 Score: 247
Period size: 40 Copynumber: 4.0 Consensus size: 40
1479789 GACCCATTTT
*
1479799 TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAA-TTAAAAAAATTAAAAAAAGTATTTTAAAAA
1479841 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
1479881 TATTTTAAAATT-AAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
1479920 TATTTTAAAATTAAAAAAGTATGT-AAAAAA-TATTTTAAAA
1 TATTTTAAAATTAAAAAA--AT-TAAAAAAAGTATTTTAAAA
1479960 TTAAAAAAAT
Statistics
Matches: 114, Mismatches: 1, Indels: 9
0.92 0.01 0.07
Matches are distributed among these distances:
39 39 0.34
40 46 0.40
41 14 0.12
42 14 0.12
43 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:1479938 original size:30 final size:30
Alignment explanation
Indices: 1479895--1479967 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
1479885 TTAAAATTAA
* *
1479895 AAAATTAAAAAAAGTATTTTAAAAATATTTT
1 AAAATT-AAAAAAGTATGTAAAAAATATTTT
1479926 AAAATTAAAAAAGTATGTAAAAAATATTTT
1 AAAATTAAAAAAGTATGTAAAAAATATTTT
1479956 AAAATTAAAAAA
1 AAAATTAAAAAA
1479968 ATAAATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 34 0.85
31 6 0.15
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAATTAAAAAAGTATGTAAAAAATATTTT
Found at i:1479960 original size:40 final size:40
Alignment explanation
Indices: 1479812--1479959 Score: 223
Period size: 39 Copynumber: 3.7 Consensus size: 40
1479802 TTTAAAAATT
*
1479812 TTAAAAAAT-TAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATATTAAAAAAGTATTTTAAAAATATTTTAAAA
1479851 TTAAAAAA-ATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATATT-AAAAAAGTATTTTAAAAATATTTTAAAA
*
1479891 TTAAAAAAT-TAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATATTAAAAAAGTATTTTAAAAATATTTTAAAA
1479930 TTAAAAAAGTATGTAAAAAA-TATTTTAAAA
1 TTAAAAAA-TAT-TAAAAAAGTATTTTAAAA
1479960 TTAAAAAAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
39 45 0.45
40 38 0.38
41 11 0.11
42 6 0.06
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (40 bp):
TTAAAAAATATTAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:1479960 original size:79 final size:79
Alignment explanation
Indices: 1479812--1479959 Score: 255
Period size: 79 Copynumber: 1.9 Consensus size: 79
1479802 TTTAAAAATT
1479812 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTA
1 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTA
1479877 AAAATATTTTAAAA
66 AAAATATTTTAAAA
1479891 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAGTATGT-AAAAAA-TATT
1 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAA--AT-TAAAAAAAGTATT
1479954 TTAAAA
63 TTAAAA
1479960 TTAAAAAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
79 47 0.71
80 10 0.15
81 8 0.12
82 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (79 bp):
TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTA
AAAATATTTTAAAA
Found at i:1485579 original size:29 final size:29
Alignment explanation
Indices: 1485547--1485604 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1485537 GAATAGTTAA
* *
1485547 GTGACCATTTTATAACTTTTCACAGTTGG
1 GTGACAATTTTACAACTTTTCACAGTTGG
* *
1485576 GTGACAATTTTGCAACTTTTCATAGTTGG
1 GTGACAATTTTACAACTTTTCACAGTTGG
1485605 ATGATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (29 bp):
GTGACAATTTTACAACTTTTCACAGTTGG
Found at i:1487564 original size:29 final size:29
Alignment explanation
Indices: 1487530--1487585 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1487520 TTTGATTCTT
* *
1487530 TTTAATGGTATAGGGACTAAATTGATCCA
1 TTTAATAGTAGAGGGACTAAATTGATCCA
*
1487559 TTTAATAGTAGAGGGACTAATTTGATC
1 TTTAATAGTAGAGGGACTAAATTGATC
1487586 AGATCTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (29 bp):
TTTAATAGTAGAGGGACTAAATTGATCCA
Done.