Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold485
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: 999764
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 8
Found at i:224383 original size:17 final size:17
Alignment explanation
Indices: 224361--224452 Score: 54
Period size: 18 Copynumber: 5.7 Consensus size: 17
224351 TTTATTTTAT
224361 TATTTTAAAAAAAATTA
1 TATTTTAAAAAAAATTA
*
224378 TATTTT----ATAATTA
1 TATTTTAAAAAAAATTA
*
224391 AATTTT--AAAAAA-TA
1 TATTTTAAAAAAAATTA
* *
224405 TATTTTATTAAAAAATAA
1 TATTTTA-AAAAAAATTA
* *
224423 TAATTTAAAATAAATTTA
1 TATTTTAAAA-AAAATTA
*
224441 AATTTTAAAAAA
1 TATTTTAAAAAA
224453 TTTTATATAA
Statistics
Matches: 57, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
13 11 0.19
14 7 0.12
15 3 0.05
17 16 0.28
18 20 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TATTTTAAAAAAAATTA
Found at i:224391 original size:23 final size:24
Alignment explanation
Indices: 224347--224392 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
224337 TAGATAGAAG
*
224347 AAAATTTATTTTATTATTTTAAAA
1 AAAATTTATTTTATTATATTAAAA
224371 AAAATTATATTTTA-TA-ATTAAA
1 AAAATT-TATTTTATTATATTAAA
224393 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 8 0.40
25 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AAAATTTATTTTATTATATTAAAA
Found at i:224429 original size:18 final size:17
Alignment explanation
Indices: 224395--224429 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
224385 TAATTAAATT
*
224395 TTAAAAAATATATTTTA
1 TTAAAAAATATAATTTA
224412 TTAAAAAATAATAATTTA
1 TTAAAAAAT-ATAATTTA
224430 AAATAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAAAAATATAATTTA
Found at i:225543 original size:21 final size:21
Alignment explanation
Indices: 225502--225543 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
225492 TAATATATTT
* *
225502 TTATTTAAATTTAATTTTAAA
1 TTATATAAATTTAATTATAAA
225523 TTATATAAATTTTAA-TATAAA
1 TTATATAAA-TTTAATTATAAA
225544 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATATAAATTTAATTATAAA
Found at i:225552 original size:17 final size:16
Alignment explanation
Indices: 225514--225565 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
225504 ATTTAAATTT
* *
225514 AATTTTAAATTATATA
1 AATTTTAAATAAAATA
225530 AATTTTAATATAAAATA
1 AATTTTAA-ATAAAATA
* *
225547 ATTTTTTAATAAAATA
1 AATTTTAAATAAAATA
225563 AAT
1 AAT
225566 AGTGATTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 18 0.60
17 12 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTTTAAATAAAATA
Found at i:225929 original size:17 final size:16
Alignment explanation
Indices: 225821--225929 Score: 57
Period size: 17 Copynumber: 6.7 Consensus size: 16
225811 AGGATGAAAT
* **
225821 TTAAATTTTTAATATT
1 TTAAATTTTTAAAAAA
225837 TTAAATTTATTATAAAAA
1 TTAAATTT-TTA-AAAAA
*
225855 TTATATTATTTAACAAAA
1 TTAAATT-TTTAA-AAAA
* *
225873 TAAAATTTTTAATAAA
1 TTAAATTTTTAAAAAA
*
225889 -T--ATTTATT--ATAA
1 TTAAATTT-TTAAAAAA
225901 TTAATATTTTTAAAAAA
1 TTAA-ATTTTTAAAAAA
225918 TTAAATTATTTA
1 TTAAATT-TTTA
225930 TTTAATATTT
Statistics
Matches: 70, Mismatches: 11, Indels: 23
0.67 0.11 0.22
Matches are distributed among these distances:
12 2 0.03
13 5 0.07
14 2 0.03
15 2 0.03
16 18 0.26
17 20 0.29
18 20 0.29
19 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATTTTTAAAAAA
Found at i:225937 original size:46 final size:47
Alignment explanation
Indices: 225836--225939 Score: 117
Period size: 46 Copynumber: 2.2 Consensus size: 47
225826 TTTTTAATAT
225836 TTTAA-ATTTATTATAAAAATTATATTATTTAACAAAATAAAATTTTTA
1 TTTAATATTTATTAT--AAATTATATTATTTAACAAAATAAAATTTTTA
* * *
225884 ATAAATATTTATTAT-AATTAATATT-TTTAA-AAAATTAAATTATTTA
1 TTTAATATTTATTATAAATT-ATATTATTTAACAAAATAAAATT-TTTA
225930 TTTAATATTT
1 TTTAATATTT
225940 TAAATTTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
45 10 0.21
46 21 0.44
47 5 0.10
48 3 0.06
49 9 0.19
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (47 bp):
TTTAATATTTATTATAAATTATATTATTTAACAAAATAAAATTTTTA
Found at i:226789 original size:41 final size:41
Alignment explanation
Indices: 226729--226828 Score: 111
Period size: 41 Copynumber: 2.5 Consensus size: 41
226719 CGATGTTTTA
*
226729 ATAAATATATAAATA--ATATGAT-AGATA-CAATAACATATT
1 ATAAATATA-AAATATGATATGATGA-ATATAAATAACATATT
*
226768 -TAAATATAATTAATATGATATGATGAATATAAATATCATATT
1 ATAAATATAA--AATATGATATGATGAATATAAATAACATATT
226810 ATAAATATAAAATATGATA
1 ATAAATATAAAATATGATA
226829 CATATATATA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
37 1 0.02
38 8 0.15
39 4 0.08
41 19 0.37
42 11 0.21
43 9 0.17
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (41 bp):
ATAAATATAAAATATGATATGATGAATATAAATAACATATT
Found at i:226808 original size:20 final size:20
Alignment explanation
Indices: 226779--226820 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
226769 AAATATAATT
* *
226779 AATATGATATGATGAATATA
1 AATATCATATGATAAATATA
*
226799 AATATCATATTATAAATATA
1 AATATCATATGATAAATATA
226819 AA
1 AA
226821 ATATGATACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (20 bp):
AATATCATATGATAAATATA
Found at i:226825 original size:36 final size:36
Alignment explanation
Indices: 226733--226854 Score: 90
Period size: 36 Copynumber: 3.4 Consensus size: 36
226723 GTTTTAATAA
** *
226733 ATATATAAATAATATGATA-GATACA-ATAACATATTT
1 ATATATAAAT-ATAAAATATGATACATATAA-ATATAT
* * **
226769 AAATATAATTAATATGATATGATGA-ATATAAATATCAT
1 ATATATAAAT-ATAAAATATGAT-ACATATAAATAT-AT
*
226807 AT-TATAAATATAAAATATGATACATATATATATAT
1 ATATATAAATATAAAATATGATACATATAAATATAT
*
226842 ATATATATATATA
1 ATATATAAATATA
226855 TATATAAATT
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
35 5 0.07
36 45 0.63
37 14 0.20
38 7 0.10
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (36 bp):
ATATATAAATATAAAATATGATACATATAAATATAT
Found at i:226837 original size:2 final size:2
Alignment explanation
Indices: 226794--226860 Score: 66
Period size: 2 Copynumber: 33.5 Consensus size: 2
226784 GATATGATGA
* * * *
226794 AT AT AA AT AT CAT AT -T AT AA AT AT A- AA AT AT GAT AC 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
226836 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 A
226861 AATTACCAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
1 2 0.04
2 48 0.89
3 4 0.07
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:227837 original size:18 final size:18
Alignment explanation
Indices: 227814--227849 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
227804 TTAATTTTAT
227814 ATTTTTAT-ATATTAAATA
1 ATTTTTATCATA-TAAATA
227832 ATTTTTATCATATAAATA
1 ATTTTTATCATATAAATA
227850 TATATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTTATCATATAAATA
Found at i:228689 original size:21 final size:21
Alignment explanation
Indices: 228663--228706 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
228653 GCCGTCATTC
*
228663 TAAATTTTTTACTATTTTATA
1 TAAATTTTTTACTATTATATA
228684 TAAATTTTTTACTATTATATA
1 TAAATTTTTTACTATTATATA
228705 TA
1 TA
228707 TATATATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TAAATTTTTTACTATTATATA
Found at i:230224 original size:65 final size:65
Alignment explanation
Indices: 230112--230262 Score: 212
Period size: 65 Copynumber: 2.3 Consensus size: 65
230102 AAATGCATTG
* ** * *
230112 TTAAGTAGTTATTTAGGATATCATAAGTAAAATTCATTTCTGAATTAAGTCACTTGCTAAGATAA
1 TTAAGTAATTATTTAGGATAAAATAAGTAAAAGTCATTTCTGAATTAAATCACTTGCTAAGATAA
* * *
230177 TTAAGTAATTATTTAGGATAAAATAAGTAAAAGTCATTTTTGTATTAAATCACTTGTTAAGATAA
1 TTAAGTAATTATTTAGGATAAAATAAGTAAAAGTCATTTCTGAATTAAATCACTTGCTAAGATAA
* *
230242 TTAAGTTATTATTTATGATAA
1 TTAAGTAATTATTTAGGATAA
230263 TACTTTATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 76 1.00
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (65 bp):
TTAAGTAATTATTTAGGATAAAATAAGTAAAAGTCATTTCTGAATTAAATCACTTGCTAAGATAA
Found at i:231324 original size:3 final size:3
Alignment explanation
Indices: 231309--231360 Score: 86
Period size: 3 Copynumber: 17.0 Consensus size: 3
231299 TTTAGTCTTG
*
231309 ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
231358 ATT
1 ATT
231361 GGAATAAAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:231595 original size:40 final size:39
Alignment explanation
Indices: 231545--231622 Score: 97
Period size: 38 Copynumber: 2.0 Consensus size: 39
231535 GATAATAAAA
*
231545 TTTTATTTATTTAACATTTAATTAATAAAAAT-AAAATTTAT
1 TTTTATTTATTTAA-ATAT-ATTAA-AAAAATAAAAATTTAT
*
231586 TTTTA-TTATTTAAATATATTAAAATAATAAAAATTTA
1 TTTTATTTATTTAAATATATTAAAAAAATAAAAATTTA
231623 AATTTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
37 5 0.15
38 13 0.38
39 3 0.09
40 8 0.24
41 5 0.15
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (39 bp):
TTTTATTTATTTAAATATATTAAAAAAATAAAAATTTAT
Found at i:232686 original size:2 final size:2
Alignment explanation
Indices: 232679--232718 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
232669 TAGGCTCGGC
232679 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
232719 ATTCTGACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:233353 original size:2 final size:2
Alignment explanation
Indices: 233310--233337 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
233300 CAGAGTGCTC
233310 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
233338 AGTATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:237963 original size:27 final size:27
Alignment explanation
Indices: 237924--237992 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
237914 TAATTTTTTT
*
237924 ATATATTAAAAAAAAATATTTT-TATA
1 ATATATTTAAAAAAAATATTTTATATA
* *
237950 TTTATATTT-AAAAATATATTTTATATGA
1 -ATATATTTAAAAAAAATATTTTATAT-A
237978 ATATATTTAAAAAAA
1 ATATATTTAAAAAAA
237993 TAAATGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
26 12 0.35
27 16 0.47
28 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (27 bp):
ATATATTTAAAAAAAATATTTTATATA
Found at i:238266 original size:29 final size:28
Alignment explanation
Indices: 238233--238313 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 28
238223 AGATAAAAAA
238233 AATTAATATTAATATTTAAATTTTAAATT
1 AATTAA-ATTAATATTTAAATTTTAAATT
* *
238262 TATTAAA-TATTA-TTATAATTATATAAATT
1 AATTAAATTAATATTTA-AATT-T-TAAATT
238291 AATTAAATTAA-ATTTTAAATTTT
1 AATTAAATTAATA-TTTAAATTTT
238314 GTCATCTGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
26 3 0.07
27 8 0.19
28 3 0.07
29 19 0.45
30 6 0.14
31 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AATTAAATTAATATTTAAATTTTAAATT
Found at i:241806 original size:15 final size:14
Alignment explanation
Indices: 241759--241816 Score: 59
Period size: 15 Copynumber: 4.3 Consensus size: 14
241749 AATCATTGTG
* *
241759 ATAAACTATACAAA
1 ATAAAATATATAAA
241773 AT-AAA-A-ATAAA
1 ATAAAATATATAAA
241784 ATAAAATATATATAA
1 ATAAAATATATA-AA
*
241799 ATACAATATATAAA
1 ATAAAATATATAAA
241813 ATAA
1 ATAA
241817 TTAAAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
11 6 0.17
12 4 0.11
13 3 0.08
14 10 0.28
15 13 0.36
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAAATATATAAA
Found at i:242175 original size:32 final size:32
Alignment explanation
Indices: 242132--242246 Score: 90
Period size: 32 Copynumber: 3.4 Consensus size: 32
242122 CGATTATATC
*
242132 AAAATTAATATAAAATAAATTATTAACTTATA
1 AAAATTTATATAAAATAAATTATTAACTTATA
* *
242164 AAAATTTATATAAAATTTATAA-TACTTAAAAAATT-TT
1 AAAATTTATATAAAA--TA-AATTA-TT---AACTTATA
* * *
242201 AAAATTTATATAAAATAAATAATCAACATATA
1 AAAATTTATATAAAATAAATTATTAACTTATA
*
242233 AAAATTTATTTAAA
1 AAAATTTATATAAA
242247 TTTATAATAT
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
31 3 0.05
32 28 0.43
34 7 0.11
35 7 0.11
37 16 0.25
38 4 0.06
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (32 bp):
AAAATTTATATAAAATAAATTATTAACTTATA
Found at i:242181 original size:11 final size:10
Alignment explanation
Indices: 242159--242253 Score: 54
Period size: 11 Copynumber: 9.6 Consensus size: 10
242149 AATTATTAAC
242159 TTATAAAAAT
1 TTATAAAAAT
242169 TTATATAAAAT
1 TTATA-AAAAT
* *
242180 TTAT-AATAC
1 TTATAAAAAT
242189 TTA-AAAAAT
1 TTATAAAAAT
242198 TT-T-AAAAT
1 TTATAAAAAT
242206 TTATATAAAAT
1 TTATA-AAAAT
** * *
242217 AAATAATCAAC
1 TTATAA-AAAT
*
242228 ATATAAAAAT
1 TTATAAAAAT
**
242238 TTATTTAAAT
1 TTATAAAAAT
242248 TTATAA
1 TTATAA
242254 TATTTTAAAT
Statistics
Matches: 62, Mismatches: 16, Indels: 14
0.67 0.17 0.15
Matches are distributed among these distances:
8 7 0.11
9 12 0.19
10 19 0.31
11 24 0.39
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
TTATAAAAAT
Found at i:245109 original size:2 final size:2
Alignment explanation
Indices: 245090--245134 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
245080 AAAAATATCC
* * * *
245090 AT AT AC AT AT AT AC AT AT AT AT AT AT AT AT AT AT GT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
245132 AT A
1 AT A
245135 CTTGAATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:249347 original size:2 final size:2
Alignment explanation
Indices: 249328--249373 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
249318 GGTATGTCAC
* *
249328 AG AG AT AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
249370 AG AG
1 AG AG
249374 TTCGAAGCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.46, T:0.04
Consensus pattern (2 bp):
AG
Found at i:249643 original size:25 final size:27
Alignment explanation
Indices: 249596--249649 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
249586 ATTTAAAAAA
249596 TTATAATTATTTAAATAAATTTTATTT
1 TTATAATTATTTAAATAAATTTTATTT
* *
249623 TTAT-ATT-TTTAATTAATTTTTATTT
1 TTATAATTATTTAAATAAATTTTATTT
249648 TT
1 TT
249650 TCTAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 18 0.72
26 3 0.12
27 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTATAATTATTTAAATAAATTTTATTT
Found at i:253403 original size:2 final size:2
Alignment explanation
Indices: 253390--253431 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
253380 CCAGAAAGAA
*
253390 AT AT AA 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
253432 GTATTAATGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:253772 original size:56 final size:55
Alignment explanation
Indices: 253711--253827 Score: 132
Period size: 56 Copynumber: 2.1 Consensus size: 55
253701 AATCAAATCT
*
253711 ATCAATTGACAGT-TCAATTA-AAATCTATCTAAG-TTGAAATTAAACTAATCCATCAG
1 ATCAA-TGA-AGTATCAATTAGAAAT-TAT-TAAGTTTGAAATTAAACTAATCAATCAG
* * *
253767 ATCAATGAATTAATCAATTAGAAATTATTCAGTTTGAAATTAAACTTATCAATCAG
1 ATCAATGAAGT-ATCAATTAGAAATTATTAAGTTTGAAATTAAACTAATCAATCAG
253823 ATCAA
1 ATCAA
253828 CGAAATTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
54 2 0.04
55 6 0.11
56 41 0.77
57 4 0.08
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (55 bp):
ATCAATGAAGTATCAATTAGAAATTATTAAGTTTGAAATTAAACTAATCAATCAG
Found at i:253834 original size:27 final size:27
Alignment explanation
Indices: 253802--253854 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
253792 TATTCAGTTT
* *
253802 GAAATTAAACTTATCAATCAGATCAAC
1 GAAATTAAACTAATCAACCAGATCAAC
253829 GAAATTAAACTAATCAACCAGATCAA
1 GAAATTAAACTAATCAACCAGATCAA
253855 TGAATTGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.51, C:0.19, G:0.08, T:0.23
Consensus pattern (27 bp):
GAAATTAAACTAATCAACCAGATCAAC
Found at i:256531 original size:3 final size:3
Alignment explanation
Indices: 256523--256572 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
256513 TATGTATTAT
256523 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
256571 AT
1 AT
256573 TGTTATGCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:258170 original size:20 final size:20
Alignment explanation
Indices: 258145--258189 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
258135 AAATTCAAAT
**
258145 ATAAATTATAAAGTAATAAA
1 ATAAATTATAAAAAAATAAA
*
258165 ATAAA-TATAAAAAAATTAA
1 ATAAATTATAAAAAAATAAA
258184 ATAAAT
1 ATAAAT
258190 CTTAATTCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
ATAAATTATAAAAAAATAAA
Found at i:258290 original size:15 final size:14
Alignment explanation
Indices: 258272--258301 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
258262 ATTTATAAAA
258272 AAATTAATAAACTAT
1 AAATTAATAAA-TAT
258287 AAATTAATAAATAT
1 AAATTAATAAATAT
258301 A
1 A
258302 TATTTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTAATAAATAT
Found at i:259353 original size:23 final size:23
Alignment explanation
Indices: 259286--259353 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
259276 TTACAGATGC
* * *
259286 TTTTGGATATTTTAAATTGATTT
1 TTTTGGATATTTTATATTAATGT
* * **
259309 TTTTAGGATTTTTTGTGGTAATGT
1 TTTT-GGATATTTTATATTAATGT
259333 TTTTGGATATTTTATATTAAT
1 TTTTGGATATTTTATATTAAT
259354 TCTCTTGAGA
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
23 17 0.52
24 16 0.48
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (23 bp):
TTTTGGATATTTTATATTAATGT
Found at i:259642 original size:14 final size:14
Alignment explanation
Indices: 259625--259695 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
259615 AAAAAATATT
259625 ATAATTAAAAATTA
1 ATAATTAAAAATTA
* *
259639 ATAA-GAAATATT-
1 ATAATTAAAAATTA
*
259651 -T-TTTAAAAATATA
1 ATAATTAAAAAT-TA
259664 ATAATTAAAAATTA
1 ATAATTAAAAATTA
259678 ATCAA-TAAAAA-TA
1 AT-AATTAAAAATTA
259691 ATAAT
1 ATAAT
259696 ATTATAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
11 6 0.14
12 3 0.07
13 10 0.23
14 15 0.34
15 10 0.23
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (14 bp):
ATAATTAAAAATTA
Found at i:259647 original size:26 final size:25
Alignment explanation
Indices: 259618--259667 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
259608 AATTTTTAAA
259618 AAATATTATAATTAAAAAT-TAATAAG
1 AAATATT-T-ATTAAAAATATAATAAG
*
259644 AAATATTTTTTAAAAATATAATAA
1 AAATATTTATTAAAAATATAATAA
259668 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 7 0.32
26 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
AAATATTTATTAAAAATATAATAAG
Found at i:259725 original size:24 final size:24
Alignment explanation
Indices: 259663--259726 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
259653 TTAAAAATAT
*
259663 AATAATTAAAAAT-TAATCAATAAA
1 AATAA-TAAGAATATAATCAATAAA
* * *
259687 AATAATAATATTATAAT-AATTAA
1 AATAATAAGAATATAATCAATAAA
259710 AATGAATAAGAATATAA
1 AAT-AATAAGAATATAA
259727 GTTTAATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
23 13 0.39
24 20 0.61
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (24 bp):
AATAATAAGAATATAATCAATAAA
Found at i:260403 original size:23 final size:23
Alignment explanation
Indices: 260371--260420 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
260361 TTTTCGACAT
* *
260371 AAAATTAAAAAAATAATAATAAA
1 AAAATCAAAAAAATAAAAATAAA
*
260394 AAAATCAAAAAATTAAAAATAAA
1 AAAATCAAAAAAATAAAAATAAA
260417 AAAA
1 AAAA
260421 AAACGAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (23 bp):
AAAATCAAAAAAATAAAAATAAA
Found at i:271946 original size:9 final size:9
Alignment explanation
Indices: 271932--272008 Score: 50
Period size: 9 Copynumber: 8.2 Consensus size: 9
271922 ATGGAGAGGT
271932 TTAAATAAA
1 TTAAATAAA
*
271941 TTAAATTAA
1 TTAAATAAA
* *
271950 TTAATTGAA
1 TTAAATAAA
*
271959 TT-GATAAA
1 TTAAATAAA
*
271967 TTAATTAAGTA
1 TTAAATAA--A
271978 TTATCAATTAAA
1 TTA--AA-TAAA
271990 TT-AATAAA
1 TTAAATAAA
271998 TTAAATAAA
1 TTAAATAAA
272007 TT
1 TT
272009 GAATTGATGA
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
8 11 0.21
9 30 0.58
11 4 0.08
12 3 0.06
13 1 0.02
14 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (9 bp):
TTAAATAAA
Found at i:271951 original size:4 final size:4
Alignment explanation
Indices: 271939--272070 Score: 61
Period size: 4 Copynumber: 31.0 Consensus size: 4
271929 GGTTTAAATA
* * * *
271939 AATT AAATT AATT AATT GAATT GATA AATT AATT AAGT -ATT -ATC AATT
1 AATT -AATT AATT AATT -AATT AATT AATT AATT AATT AATT AATT AATT
* * * *
271987 AAATT AATA AATT AAATA AATT GAATT GATG AATT AAATT AATT AATT
1 -AATT AATT AATT -AATT AATT -AATT AATT AATT -AATT AATT AATT
* * *
272035 GATG AATCG AATT AATT AATAT GAATT AAATT AATT
1 AATT AAT-T AATT AATT AAT-T -AATT -AATT AATT
272071 GTTGATAAAT
Statistics
Matches: 97, Mismatches: 21, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
3 4 0.04
4 57 0.59
5 33 0.34
6 3 0.03
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.41
Consensus pattern (4 bp):
AATT
Found at i:272013 original size:22 final size:21
Alignment explanation
Indices: 271933--272034 Score: 63
Period size: 22 Copynumber: 4.9 Consensus size: 21
271923 TGGAGAGGTT
271933 TAAA-TAAATTAAATTAATTAA
1 TAAATTAAA-TAAATTAATTAA
* *
271954 TTGAATT-GATAAATTAATTAA
1 -TAAATTAAATAAATTAATTAA
*
271975 GT--ATT--ATCAATTAAATTAA
1 -TAAATTAAATAAATT-AATTAA
*
271994 TAAATTAAATAAATTGAATTGA
1 TAAATTAAATAAATT-AATTAA
* *
272016 TGAATTAAATTAATTAATT
1 TAAATTAAATAAATTAATT
272035 GATGAATCGA
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
18 7 0.11
19 9 0.14
20 3 0.05
21 17 0.26
22 28 0.43
23 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (21 bp):
TAAATTAAATAAATTAATTAA
Found at i:272022 original size:35 final size:34
Alignment explanation
Indices: 271932--272034 Score: 95
Period size: 35 Copynumber: 3.1 Consensus size: 34
271922 ATGGAGAGGT
* * * *
271932 TTAAATAAATTAAATTAATTAATTGAATTGATAAA
1 TTAAATAAATTGAATT-ATCAATTAAATTAATAAA
* *
271967 TT-AATTAA--GTATTATCAATTAAATTAATAAA
1 TTAAATAAATTGAATTATCAATTAAATTAATAAA
* *
271998 TTAAATAAATTGAATTGATGAATTAAATTAATTAA
1 TTAAATAAATTGAATT-ATCAATTAAATTAATAAA
272033 TT
1 TT
272035 GATGAATCGA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
31 17 0.31
32 8 0.15
34 9 0.17
35 20 0.37
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (34 bp):
TTAAATAAATTGAATTATCAATTAAATTAATAAA
Found at i:272036 original size:21 final size:21
Alignment explanation
Indices: 271996--272070 Score: 100
Period size: 21 Copynumber: 3.6 Consensus size: 21
271986 TAAATTAATA
*
271996 AATTAAATAAATTGAATTGATG
1 AATTAAATTAATT-AATTGATG
272018 AATTAAATTAATTAATTGATG
1 AATTAAATTAATTAATTGATG
**
272039 AATCGAATTAATTAA-T-ATG
1 AATTAAATTAATTAATTGATG
272058 AATTAAATTAATT
1 AATTAAATTAATT
272071 GTTGATAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.29
20 1 0.02
21 21 0.44
22 12 0.25
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.40
Consensus pattern (21 bp):
AATTAAATTAATTAATTGATG
Found at i:272060 original size:19 final size:21
Alignment explanation
Indices: 272000--272098 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
271990 TTAATAAATT
* *
272000 AAATAAATTGAATTGATGAATT
1 AAATTAATT-AATTGATGAATC
272022 AAATTAATTAATTGATGAATC
1 AAATTAATTAATTGATGAATC
* *
272043 GAATTAATTAA-T-ATGAATT
1 AAATTAATTAATTGATGAATC
* *
272062 AAATTAATT-GTTGATAAATC
1 AAATTAATTAATTGATGAATC
**
272082 AAAGAAATTGAATTGAT
1 AAATTAATT-AATTGAT
272099 CAGATTTAGA
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
19 15 0.24
20 13 0.21
21 21 0.34
22 13 0.21
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.37
Consensus pattern (21 bp):
AAATTAATTAATTGATGAATC
Found at i:272203 original size:16 final size:16
Alignment explanation
Indices: 272182--272215 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
272172 CTGACGAATC
*
272182 CATGAATCAAATTTAT
1 CATGAATCAAATTAAT
*
272198 CATGAATTAAATTAAT
1 CATGAATCAAATTAAT
272214 CA
1 CA
272216 ATTAGCTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (16 bp):
CATGAATCAAATTAAT
Found at i:273879 original size:3 final size:3
Alignment explanation
Indices: 273871--273898 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
273861 AAACCAGGAA
273871 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
273899 GAAGGGACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:274588 original size:11 final size:10
Alignment explanation
Indices: 274557--274604 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 10
274547 TATATAAAAA
274557 ATTTTATTAT
1 ATTTTATTAT
274567 A---TATTAT
1 ATTTTATTAT
274574 ATTTTATTAAT
1 ATTTTATT-AT
274585 ATTTTAATTAT
1 ATTTT-ATTAT
274596 ATTTTATTA
1 ATTTTATTA
274605 AAATTATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
7 7 0.21
10 9 0.27
11 14 0.42
12 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTATTAT
Found at i:274619 original size:22 final size:21
Alignment explanation
Indices: 274566--274620 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
274556 AATTTTATTA
*
274566 TATATTATATTTTATTAATAT
1 TATATTATATTTTATTAAAAT
*
274587 TTTAATTATATTTTATTAAAAT
1 TAT-ATTATATTTTATTAAAAT
274609 TATATTCATATT
1 TATATT-ATATT
274621 AAATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATATTATATTTTATTAAAAT
Found at i:275129 original size:29 final size:27
Alignment explanation
Indices: 275096--275162 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 27
275086 ACATAATTAA
*
275096 TATATTTATATTAAATTT-ATATATTT
1 TATATTTATATTAAATTTAAAATATTT
*
275122 TATTATATTATAATTATATTTAAAATATTT
1 TA-TAT-TTAT-ATTAAATTTAAAATATTT
275152 TATATTTATAT
1 TATATTTATAT
275163 ATTTTAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 2 0.06
27 5 0.14
28 8 0.23
29 11 0.31
30 9 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TATATTTATATTAAATTTAAAATATTT
Found at i:275154 original size:16 final size:15
Alignment explanation
Indices: 275135--275168 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
275125 TATATTATAA
275135 TTATATTTAAAATATT
1 TTATATTT-AAATATT
*
275151 TTATATTTATATATT
1 TTATATTTAAATATT
275166 TTA
1 TTA
275169 ATATATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATATTTAAATATT
Found at i:275187 original size:25 final size:24
Alignment explanation
Indices: 275102--275187 Score: 90
Period size: 23 Copynumber: 3.7 Consensus size: 24
275092 TTAATATATT
*
275102 TATATTA-AATTTATATATTTTAT
1 TATATTATAATTTATATATTTTAA
**
275125 TATATTATAA-TTATAT-TTAAAA
1 TATATTATAATTTATATATTTTAA
*
275147 TATTTTAT-ATTTATATATTTTAA
1 TATATTATAATTTATATATTTTAA
*
275170 TATATTAATAATTCATAT
1 TATATT-ATAATTTATAT
275188 TATATATTCA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.02
22 16 0.32
23 22 0.44
24 4 0.08
25 7 0.14
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
TATATTATAATTTATATATTTTAA
Found at i:275195 original size:45 final size:43
Alignment explanation
Indices: 275088--275195 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 43
275078 CTTAACATAC
* * *
275088 ATAATTA-ATATATTTATATTAAATTTATATATTTTATTATATT
1 ATAATTATAT-TATATATTTTAAATTTATATATTTTAATATATT
* *
275131 ATAATTATATTTAAAATATTTTATATTTATATATTTTAATATATT
1 ATAATTATA-TT-ATATATTTTAAATTTATATATTTTAATATATT
275176 AATAATTCATATTATATATT
1 -ATAATT-ATATTATATATT
275196 CACGTCACCA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
43 7 0.13
44 2 0.04
45 34 0.63
46 8 0.15
47 3 0.06
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (43 bp):
ATAATTATATTATATATTTTAAATTTATATATTTTAATATATT
Found at i:276990 original size:2 final size:2
Alignment explanation
Indices: 276979--277010 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
276969 TTCCAGTTAT
276979 TA TA TA -A 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
277011 CACCATATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:278543 original size:34 final size:34
Alignment explanation
Indices: 278498--278567 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
278488 TAACAACAAG
278498 GAAATGAAGATTTCAATGGAACTTTTGGTTGAGA
1 GAAATGAAGATTTCAATGGAACTTTTGGTTGAGA
* *
278532 GAAATGTAGATTTCAATGGACCTTTTGGTTGAGA
1 GAAATGAAGATTTCAATGGAACTTTTGGTTGAGA
278566 GA
1 GA
278568 CTGCTGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (34 bp):
GAAATGAAGATTTCAATGGAACTTTTGGTTGAGA
Found at i:279187 original size:18 final size:19
Alignment explanation
Indices: 279151--279190 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
279141 GATACGTTTA
279151 ATAAATATAAATATAATAT
1 ATAAATATAAATATAATAT
* *
279170 ATAAATAT-CATATGATAT
1 ATAAATATAAATATAATAT
279188 ATA
1 ATA
279191 TTTAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
ATAAATATAAATATAATAT
Found at i:280120 original size:13 final size:13
Alignment explanation
Indices: 280091--280136 Score: 60
Period size: 12 Copynumber: 3.6 Consensus size: 13
280081 TTTAGATAGT
280091 ATATATTTAATAAA
1 ATATATTTAA-AAA
280105 ATATATTTAAAAA
1 ATATATTTAAAAA
*
280118 ATA-AATTAAAAA
1 ATATATTTAAAAA
280130 AT-TATTT
1 ATATATTT
280137 TATATATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 13 0.45
13 6 0.21
14 10 0.34
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATATTTAAAAA
Found at i:280233 original size:20 final size:21
Alignment explanation
Indices: 280191--280255 Score: 87
Period size: 21 Copynumber: 3.0 Consensus size: 21
280181 AACATATCAT
280191 TTTATAAATTTTATTTATAAA
1 TTTATAAATTTTATTTATAAA
*
280212 TTTATAAATTTTA-TTATTAA
1 TTTATAAATTTTATTTATAAA
*
280232 TTTATAAAATAATTATTTATAAA
1 TTTAT-AAAT-TTTATTTATAAA
280255 T
1 T
280256 AAATATTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 11 0.29
21 17 0.45
22 3 0.08
23 7 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATAAATTTTATTTATAAA
Found at i:280309 original size:11 final size:11
Alignment explanation
Indices: 280293--280319 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
280283 TTTATTTATG
280293 AATATTAAAGA
1 AATATTAAAGA
280304 AATATTAAAGA
1 AATATTAAAGA
280315 AATAT
1 AATAT
280320 ATGTAAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (11 bp):
AATATTAAAGA
Found at i:280598 original size:6 final size:6
Alignment explanation
Indices: 280581--280644 Score: 55
Period size: 6 Copynumber: 10.8 Consensus size: 6
280571 AATTTTAAAC
*
280581 ATATATA ATATAA ATATAA AT-TAA ATATTAA A-ATTA ATAT-A ATATTAA
1 ATATA-A ATATAA ATATAA ATATAA ATA-TAA ATATAA ATATAA ATA-TAA
*
280629 A-ATTA ATATAA ATATA
1 ATATAA ATATAA ATATA
280645 TAAAATTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
5 15 0.31
6 22 0.46
7 11 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAA
Found at i:280599 original size:11 final size:11
Alignment explanation
Indices: 280583--280644 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
280573 TTTTAAACAT
280583 ATATAATATAA
1 ATATAATATAA
280594 ATATAA-ATTAA
1 ATATAATA-TAA
* *
280605 ATATTAAAATTA
1 ATA-TAATATAA
280617 ATATAATATTAA
1 ATATAATA-TAA
280629 A-ATTAATATAA
1 ATA-TAATATAA
280640 ATATA
1 ATATA
280645 TAAAATTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
10 1 0.02
11 23 0.55
12 17 0.40
13 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATAATATAA
Found at i:280620 original size:23 final size:23
Alignment explanation
Indices: 280592--280644 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
280582 TATATAATAT
280592 AAATATAA-ATTAAATATTAAAAT
1 AAATATAATATTAAA-ATTAAAAT
* *
280615 TAATATAATATTAAAATTAATAT
1 AAATATAATATTAAAATTAAAAT
280638 AAATATA
1 AAATATA
280645 TAAAATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATATAATATTAAAATTAAAAT
Found at i:280624 original size:17 final size:18
Alignment explanation
Indices: 280581--280651 Score: 85
Period size: 17 Copynumber: 3.9 Consensus size: 18
280571 AATTTTAAAC
*
280581 ATATATAATA-TAAATATAA
1 ATATA-AATATTAAA-ATTA
280600 AT-TAAATATTAAAATTA
1 ATATAAATATTAAAATTA
280617 ATAT-AATATTAAAATTA
1 ATATAAATATTAAAATTA
280634 ATATAAATATATAAAATT
1 ATATAAATAT-TAAAATT
280652 TATTTAATTA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
17 26 0.55
18 12 0.26
19 9 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAAATATTAAAATTA
Found at i:280688 original size:19 final size:18
Alignment explanation
Indices: 280610--280686 Score: 56
Period size: 17 Copynumber: 4.3 Consensus size: 18
280600 ATTAAATATT
280610 AAAA-TTAATATAATATT-
1 AAAATTTAATATAA-ATTA
280627 AAAA-TTAATATAAATATA
1 AAAATTTAATATAAAT-TA
*
280645 TAAAATTT-AT-TTAATTA
1 -AAAATTTAATATAAATTA
* *
280662 ATACTTATAATATAAATTA
1 AAAATT-TAATATAAATTA
280681 AAAATT
1 AAAATT
280687 ATTTATTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
16 6 0.13
17 17 0.36
18 6 0.13
19 16 0.34
20 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATTTAATATAAATTA
Found at i:283460 original size:23 final size:23
Alignment explanation
Indices: 283415--283458 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
283405 TAATTTTTTT
283415 AATATTTAATTATAAAATATATA
1 AATATTTAATTATAAAATATATA
*
283438 AATA-TTAA-TATAAATTATATA
1 AATATTTAATTATAAAATATATA
283459 TAGTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 4 0.20
23 4 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AATATTTAATTATAAAATATATA
Found at i:285677 original size:12 final size:12
Alignment explanation
Indices: 285660--285689 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
285650 TTCTTTGATA
285660 AAAAAATATAAT
1 AAAAAATATAAT
285672 AAAAAATATAAT
1 AAAAAATATAAT
285684 AAAAAA
1 AAAAAA
285690 CAAAAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAAAATATAAT
Found at i:285748 original size:6 final size:7
Alignment explanation
Indices: 285738--285768 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
285728 ATAAAATTAA
285738 AAAAATC
1 AAAAATC
285745 AAAAATC
1 AAAAATC
*
285752 AAAAATA
1 AAAAATC
285759 AAAAATC
1 AAAAATC
285766 AAA
1 AAA
285769 CAAAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATC
Found at i:285762 original size:14 final size:14
Alignment explanation
Indices: 285738--285777 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
285728 ATAAAATTAA
*
285738 AAAAATCAAAAATC
1 AAAAATAAAAAATC
285752 AAAAATAAAAAATC
1 AAAAATAAAAAATC
*
285766 AAACA-AAAAAAT
1 AAAAATAAAAAAT
285778 TGTCGAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAATAAAAAATC
Found at i:286755 original size:23 final size:24
Alignment explanation
Indices: 286699--286759 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
286689 GCAGTAAAAG
286699 AGAAGAACGAGCAGCAAAGGAGAA
1 AGAAGAACGAGCAGCAAAGGAGAA
* * *
286723 A-TAGAGCGAGTAGCAAAGGA-AA
1 AGAAGAACGAGCAGCAAAGGAGAA
286745 AGAAGAACGAGCAGC
1 AGAAGAACGAGCAGC
286760 TAAGACGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 3 0.10
23 26 0.87
24 1 0.03
ACGTcount: A:0.51, C:0.13, G:0.33, T:0.03
Consensus pattern (24 bp):
AGAAGAACGAGCAGCAAAGGAGAA
Found at i:288846 original size:162 final size:163
Alignment explanation
Indices: 288578--288907 Score: 626
Period size: 162 Copynumber: 2.0 Consensus size: 163
288568 TCAAGATCTA
288578 ACTTTTTTTATAAAAAAAATTCTTCAAAGGGATAATTACTCGACAAATCCAAACTAGTCTCTAAG
1 ACTTTTTTTATAAAAAAAATTCTTCAAAGGGATAATTACTCGACAAATCCAAACTAGTCTCTAAG
* *
288643 TTACCAGTCGATTATTTATCAATAATCGAGGACAATTATGAGATATATTATGGGTTGTCTATTTT
66 TTACCAGTCAATTATTTATCAATAATCGAAGACAATTATGAGATATATTATGGGTTGTCTATTTT
288708 CTTATTCATCATTTTTCCTTGTGTCATATCACT
131 CTTATTCATCATTTTTCCTTGTGTCATATCACT
*
288741 ACTTTTTTTATAAAAAAAA-TCTTCAAAGGGATAATTACTCGGCAAATCCAAACTAGTCTCTAAG
1 ACTTTTTTTATAAAAAAAATTCTTCAAAGGGATAATTACTCGACAAATCCAAACTAGTCTCTAAG
288805 TTACCAGTCAATTATTTATCAATAATCGAAGACAATTATGAGATATATTATGGGTTGTCTATTTT
66 TTACCAGTCAATTATTTATCAATAATCGAAGACAATTATGAGATATATTATGGGTTGTCTATTTT
288870 CTTATTCATCATTTTTCCTTGTGTCATATCACT
131 CTTATTCATCATTTTTCCTTGTGTCATATCACT
288903 ACTTT
1 ACTTT
288908 AGTCGCATGT
Statistics
Matches: 164, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
162 145 0.88
163 19 0.12
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (163 bp):
ACTTTTTTTATAAAAAAAATTCTTCAAAGGGATAATTACTCGACAAATCCAAACTAGTCTCTAAG
TTACCAGTCAATTATTTATCAATAATCGAAGACAATTATGAGATATATTATGGGTTGTCTATTTT
CTTATTCATCATTTTTCCTTGTGTCATATCACT
Found at i:290374 original size:598 final size:599
Alignment explanation
Indices: 289231--290411 Score: 1965
Period size: 598 Copynumber: 2.0 Consensus size: 599
289221 AAGAGGTACC
* **
289231 AATTTTGGGTGTTGTGGGGGTGCTAATCATTCCCCATGCGTAATCGACTCTTGGACCCTACTAAC
1 AATTTTGGGCGTTGTGGGGGTGCTAATCATTCCCCACACGTAATCGACTCTTGGACCCTACTAAC
*
289296 GAACTTTGAAATACGCAGACCATGAAATCAAGTTCTCGAGTTACGTAACTTAAAACAGTGATTTC
66 GAACTTTGAAATACGCAGACCATGAAATCAAGTTCTCGAGTTACGTAACTTAAAACAATGATTTC
* * * * *
289361 GATAGGCGTCCGGTCACACCTAGCTTAAATGATCTGTGGCGACTCCAAATCTTTGGTCATTTCGT
131 GATAGGCATCCAGTCACACCTAGCTCAAATGATCGGTGGCGACTCCAAATCTTTAGTCATTTCGT
* *
289426 GATGACCATTGAAGATCAGTTAGATGGGCGATTCATCTAATGATCTTTCTCAATTCATACATTTT
196 GATGACCATTGAAGATCAATTAGATAGGCGATTCATCTAATGATCTTTCTCAATTCATACATTTT
*
289491 CATCATGCTGTAAAAATCCCCAATCGCGGGGGATATTAAGTCAGGCACGCCTCATTTGCCCTATC
261 CATCATGCTGTAAAAATCCCCAATCGCGAGGGATATTAAGTCAGGCACGCCTCATTTGCCCTATC
* * *
289556 GCCGAGGTTGAGCGCATGTTGCGACAAACGTATTTTAGGTTGGCTAAATTATTTGCTAAGATGAG
326 ACCGAGGTCGAGCGCACGTTGCGACAAACGTATTTTAGGTTGGCTAAATTATTTGCTAAGATGAG
289621 AAACAAGCAGATAGCAATGATGGAGGTAGGCCACACATACTGTAAAACAGTCACTAATGCCATGT
391 AAACAAGCAGATAGCAATGATGGAGGTAGGCCACACATACTGTAAAACAGTCACTAATGCCATGT
* *
289686 GAGAAAATCGAAAGAAAGCTAACTCCTACTTTGTTTGTGGGTTTACGCGAATAAATCAATCTTTC
456 GAGAAAATCGAAAGAAAGCTAACTCCTACTTTATTTGTGGGTTTACGCGAACAAATCAATCTTTC
*
289751 CTAGTTGAAGATTTAGAAAACTCACAGGAA-AGAGTTGTGGCTTCGAACTACAAA-TCAATCTTT
521 CTAATTGAAGATTTAGAAAACTCACAGGAATA-AGTTGTGGCTTCGAACTACAAAGTCAATCTTT
289814 ACTAGTATAATTGAA
585 ACTAGTATAATTGAA
* * *
289829 AATTTTGGGCGTTGTGGGGGTGCTAATCCTTCCCCACACGTAATCGACTTTTGGACCCTACTAAT
1 AATTTTGGGCGTTGTGGGGGTGCTAATCATTCCCCACACGTAATCGACTCTTGGACCCTACTAAC
* * *
289894 GAACTTTGAAGTACGCAGACCATGAAATCAAGTTCTTGAGTTACGTAACTTAAAACAATGATTTT
66 GAACTTTGAAATACGCAGACCATGAAATCAAGTTCTCGAGTTACGTAACTTAAAACAATGATTTC
*
289959 GATAGGCATCCAGTCACACCTAGCTCAAATGATCGGTGGCGACTCTAAATCTTTAGTCATTTCGT
131 GATAGGCATCCAGTCACACCTAGCTCAAATGATCGGTGGCGACTCCAAATCTTTAGTCATTTCGT
*
290024 GATGACCATTGAAGATTAATTAGATAGGCGATTCATCTAATGATCTTTCTCAATTCATACATTTT
196 GATGACCATTGAAGATCAATTAGATAGGCGATTCATCTAATGATCTTTCTCAATTCATACATTTT
* * *
290089 CATCATGCTGTAAAAATTCTCAATCGCGAGGGATATTAAGTCAGGCATGCCTCATTTGCCCTATC
261 CATCATGCTGTAAAAATCCCCAATCGCGAGGGATATTAAGTCAGGCACGCCTCATTTGCCCTATC
* *
290154 ACCGGGGTCGAGCGCACGTTGCGACAAACGTATTTTAGGTTGGCTAAATTATTTGCTAAGATGGG
326 ACCGAGGTCGAGCGCACGTTGCGACAAACGTATTTTAGGTTGGCTAAATTATTTGCTAAGATGAG
* * * *
290219 GAACAAGCAGATAGCAATGATGGAGGTAGGTCACACATACTGTGAAACAGTCACTAATGCCGTGT
391 AAACAAGCAGATAGCAATGATGGAGGTAGGCCACACATACTGTAAAACAGTCACTAATGCCATGT
290284 GAGAAAATCGAAAGAAAGCTAACTCCTAAC-TTATTTGTGGGTTTACGCGAACAAATCAATCTTT
456 GAGAAAATCGAAAGAAAGCTAACTCCT-ACTTTATTTGTGGGTTTACGCGAACAAATCAATCTTT
* * *
290348 CCTAATTGAATATTTA-AAAGACTCACATGAATAAGTTGTGGCTTCGAACTACAAAGTTAATCTT
520 CCTAATTGAAGATTTAGAAA-ACTCACAGGAATAAGTTGTGGCTTCGAACTACAAAGTCAATCTT
290412 AATGAAAGGT
Statistics
Matches: 541, Mismatches: 38, Indels: 7
0.92 0.06 0.01
Matches are distributed among these distances:
597 3 0.01
598 528 0.98
599 10 0.02
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (599 bp):
AATTTTGGGCGTTGTGGGGGTGCTAATCATTCCCCACACGTAATCGACTCTTGGACCCTACTAAC
GAACTTTGAAATACGCAGACCATGAAATCAAGTTCTCGAGTTACGTAACTTAAAACAATGATTTC
GATAGGCATCCAGTCACACCTAGCTCAAATGATCGGTGGCGACTCCAAATCTTTAGTCATTTCGT
GATGACCATTGAAGATCAATTAGATAGGCGATTCATCTAATGATCTTTCTCAATTCATACATTTT
CATCATGCTGTAAAAATCCCCAATCGCGAGGGATATTAAGTCAGGCACGCCTCATTTGCCCTATC
ACCGAGGTCGAGCGCACGTTGCGACAAACGTATTTTAGGTTGGCTAAATTATTTGCTAAGATGAG
AAACAAGCAGATAGCAATGATGGAGGTAGGCCACACATACTGTAAAACAGTCACTAATGCCATGT
GAGAAAATCGAAAGAAAGCTAACTCCTACTTTATTTGTGGGTTTACGCGAACAAATCAATCTTTC
CTAATTGAAGATTTAGAAAACTCACAGGAATAAGTTGTGGCTTCGAACTACAAAGTCAATCTTTA
CTAGTATAATTGAA
Found at i:290907 original size:20 final size:21
Alignment explanation
Indices: 290869--290909 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
290859 TTTAATTTTT
*
290869 ATATTTAATTTACATATATTC
1 ATATTGAATTTACATATATTC
290890 ATATTGAATTTA-ATATATTC
1 ATATTGAATTTACATATATTC
290910 GCACAACATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (21 bp):
ATATTGAATTTACATATATTC
Found at i:291152 original size:19 final size:18
Alignment explanation
Indices: 291128--291171 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
291118 AGGTCTAAGG
*
291128 AAAAAAATAATGTAAAACT
1 AAAAAAATAAAGTAAAA-T
291147 AAAAAAA-AAAGTAAAAT
1 AAAAAAATAAAGTAAAAT
*
291164 CAAAAAAT
1 AAAAAAAT
291172 TATTTGACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 7 0.32
18 8 0.36
19 7 0.32
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAAAAATAAAGTAAAAT
Found at i:299220 original size:25 final size:25
Alignment explanation
Indices: 299186--299236 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
299176 CTCGTTTTTT
299186 TCTTTAAGTATCCATGTTCAACATC
1 TCTTTAAGTATCCATGTTCAACATC
*
299211 TCTTTAAGTATCTATGTTCAACATC
1 TCTTTAAGTATCCATGTTCAACATC
299236 T
1 T
299237 ATATGCAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (25 bp):
TCTTTAAGTATCCATGTTCAACATC
Found at i:305810 original size:37 final size:37
Alignment explanation
Indices: 305769--305842 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
305759 AGATAATAAA
*
305769 ATATTTTAATTTTATAAGTAA-A-ATTAAAAAATATTAT
1 ATATTTT-ATTTT-TAAATAATATATTAAAAAATATTAT
*
305806 ATATTTTATTTTTAAATAATATTTTAAAAAATATTAT
1 ATATTTTATTTTTAAATAATATATTAAAAAATATTAT
305843 TTTATTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 6 0.18
36 6 0.18
37 21 0.64
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (37 bp):
ATATTTTATTTTTAAATAATATATTAAAAAATATTAT
Found at i:306144 original size:19 final size:19
Alignment explanation
Indices: 306100--306137 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
306090 AAGCTTCAAG
306100 TAATAATAATTATGATAAT
1 TAATAATAATTATGATAAT
* *
306119 TAATAATTATTATTATAAT
1 TAATAATAATTATGATAAT
306138 AATTAATAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TAATAATAATTATGATAAT
Found at i:306405 original size:21 final size:22
Alignment explanation
Indices: 306373--306429 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
306363 TATTTTTATT
*
306373 TAAATTTATTTATATGTATAAA
1 TAAATTAATTTATATGTATAAA
* *
306395 TAAA-TAATTTAAATTTATAAA
1 TAAATTAATTTATATGTATAAA
306416 TAAATTAATATTAT
1 TAAATTAAT-TTAT
306430 TATTTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 18 0.62
22 8 0.28
23 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TAAATTAATTTATATGTATAAA
Found at i:306549 original size:22 final size:21
Alignment explanation
Indices: 306512--306568 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
306502 TATATTTTTA
* *
306512 ATATTTAAATTATAATATCAT
1 ATATTTAATTTTTAATATCAT
* *
306533 ATATTTTAATTTTTAATGTGAT
1 ATA-TTTAATTTTTAATATCAT
*
306555 ATATTTATTTTTTA
1 ATATTTAATTTTTA
306569 TATAATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (21 bp):
ATATTTAATTTTTAATATCAT
Found at i:307723 original size:20 final size:20
Alignment explanation
Indices: 307686--307725 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
307676 ATTATAATTT
*
307686 TTTATTAATTATTAAACTTG
1 TTTATTAATTAGTAAACTTG
307706 TTTATTAATTAAGT-AACTTG
1 TTTATTAATT-AGTAAACTTG
307726 CTAGATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (20 bp):
TTTATTAATTAGTAAACTTG
Found at i:308234 original size:16 final size:16
Alignment explanation
Indices: 308211--308257 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 16
308201 ATAATCATAA
308211 TAATATTTAATAAATTT
1 TAATATTT-ATAAATTT
308228 TAA-A-TT-TAAATTT
1 TAATATTTATAAATTT
308241 TAATATTTATAAATTT
1 TAATATTTATAAATTT
308257 T
1 T
308258 TTATTCTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 10 0.37
14 1 0.04
15 4 0.15
16 9 0.33
17 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATATTTATAAATTT
Found at i:308425 original size:2 final size:2
Alignment explanation
Indices: 308418--308444 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
308408 TTTTATAATT
308418 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
308445 GTAAAAAAGG
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:308616 original size:20 final size:20
Alignment explanation
Indices: 308580--308618 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
308570 TATTTTCACT
*
308580 TATTATAATTATGTTTAAAG
1 TATTATAATTATATTTAAAG
308600 TATTATATATT-TATTTAAA
1 TATTATA-ATTATATTTAAA
308619 TTTTAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TATTATAATTATATTTAAAG
Found at i:308646 original size:32 final size:33
Alignment explanation
Indices: 308600--308673 Score: 105
Period size: 32 Copynumber: 2.2 Consensus size: 33
308590 ATGTTTAAAG
*
308600 TATTATATATTTATTTAAATTTTAATATGTTAATA
1 TATT-TAT-TTTATTTAAATTTTAATATATTAATA
*
308635 -ATTTATTTTATTTAAATTTTAATATATTTATA
1 TATTTATTTTATTTAAATTTTAATATATTAATA
308667 TATTTAT
1 TATTTAT
308674 ACCGTATACT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
32 24 0.67
33 9 0.25
34 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (33 bp):
TATTTATTTTATTTAAATTTTAATATATTAATA
Found at i:308662 original size:16 final size:16
Alignment explanation
Indices: 308611--308664 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
308601 ATTATATATT
308611 TATTTAAATTTTAATA
1 TATTTAAATTTTAATA
* * * *
308627 T-GTTAATAATTTATTT
1 TATTTAA-ATTTTAATA
308643 TATTTAAATTTTAATA
1 TATTTAAATTTTAATA
308659 TATTTA
1 TATTTA
308665 TATATTTATA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
15 4 0.14
16 20 0.71
17 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TATTTAAATTTTAATA
Found at i:309061 original size:27 final size:26
Alignment explanation
Indices: 309030--309100 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 26
309020 GATTTAATTT
*
309030 TTTTATAAAAATATTATAATTAATA-TA
1 TTTTATAAAAA-ATTA-AATAAATATTA
309057 TTTTATAAAAAATTAAATAAATATTA
1 TTTTATAAAAAATTAAATAAATATTA
*
309083 TATTTATAATTAAATTAA
1 T-TTTATAA-AAAATTAA
309101 TTTAAATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.18
26 7 0.18
27 18 0.46
28 7 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTTATAAAAAATTAAATAAATATTA
Found at i:309107 original size:10 final size:10
Alignment explanation
Indices: 309092--309135 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
309082 ATATTTATAA
309092 TTAAATTAAT
1 TTAAATTAAT
*
309102 TTAAATTAAA
1 TTAAATTAAT
*
309112 TTATATTAAT
1 TTAAATTAAT
*
309122 TTAAATTGAT
1 TTAAATTAAT
309132 TTAA
1 TTAA
309136 TTTATTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (10 bp):
TTAAATTAAT
Found at i:309108 original size:15 final size:15
Alignment explanation
Indices: 309069--309135 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 15
309059 TTATAAAAAA
*
309069 TTAAATAAATATTATAT
1 TTAAATTAA-ATTA-AT
309086 TTATAATTAAATTAAT
1 TTA-AATTAAATTAAT
309102 TTAAATTAAATT-AT
1 TTAAATTAAATTAAT
* *
309116 ATTAATTTAAATTGAT
1 -TTAAATTAAATTAAT
309132 TTAA
1 TTAA
309136 TTTATTAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
14 2 0.04
15 24 0.53
16 7 0.16
17 7 0.16
18 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (15 bp):
TTAAATTAAATTAAT
Found at i:309737 original size:4 final size:4
Alignment explanation
Indices: 309728--309755 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
309718 GTATAGCAGC
309728 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
309756 TAAAGAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:309870 original size:4 final size:4
Alignment explanation
Indices: 309861--309886 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
309851 TACCAACATT
309861 TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA
309887 TTCTTTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:310086 original size:20 final size:18
Alignment explanation
Indices: 310061--310100 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
310051 GGATTGATTT
310061 AAATAATTATTTATTAATTA
1 AAATAA-TATTT-TTAATTA
*
310081 AAATAATATTTTTATTTA
1 AAATAATATTTTTAATTA
310099 AA
1 AA
310101 TTTAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 5 0.26
20 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATAATATTTTTAATTA
Found at i:310515 original size:20 final size:18
Alignment explanation
Indices: 310492--310544 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
310482 TTATAAAAAT
*
310492 TATATTAAATATGAAAGTAA
1 TATATTAAATAT-AAACT-A
* *
310512 TATAATAAAAATAAACTA
1 TATATTAAATATAAACTA
310530 TATATTTAAATATAA
1 TATA-TTAAATATAA
310545 TTAATATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 5 0.19
19 12 0.44
20 10 0.37
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (18 bp):
TATATTAAATATAAACTA
Found at i:311788 original size:22 final size:21
Alignment explanation
Indices: 311734--311801 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 21
311724 CCAAATTAAG
311734 TAAATAGTATTTAATAAATTAT
1 TAAATA-TATTTAATAAATTAT
* *
311756 T-TATATGTTTAATGAATATT-T
1 TAAATATATTTAAT-AA-ATTAT
*
311777 TAAATATATTTAATAAAATA-
1 TAAATATATTTAATAAATTAT
311797 TAAAT
1 TAAAT
311802 TTTAACTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
20 14 0.38
21 9 0.24
22 14 0.38
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (21 bp):
TAAATATATTTAATAAATTAT
Found at i:311854 original size:22 final size:21
Alignment explanation
Indices: 311808--311865 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
311798 AAATTTTAAC
*
311808 TTAAACTCAATTAAAATCAAA
1 TTAAACTCAAATAAAATCAAA
* *
311829 TTAAATCTCAAGTAAAATTC-AT
1 TTAAA-CTCAAATAAAA-TCAAA
311851 TTAAACTCAAATAAA
1 TTAAACTCAAATAAA
311866 TCCAAACCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 14 0.44
22 16 0.50
23 2 0.06
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (21 bp):
TTAAACTCAAATAAAATCAAA
Found at i:312350 original size:16 final size:16
Alignment explanation
Indices: 312326--312376 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
312316 ATTTTTAATT
*
312326 TTTTTATTTATATAAA
1 TTTTAATTTATATAAA
312342 TTTTAATTTAT-T-AA
1 TTTTAATTTATATAAA
*
312356 TAATTAATATTATATAAA
1 T-TTTAAT-TTATATAAA
312374 TTT
1 TTT
312377 AAAAATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 3 0.11
15 6 0.21
16 14 0.50
17 2 0.07
18 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTAATTTATATAAA
Found at i:312369 original size:32 final size:32
Alignment explanation
Indices: 312333--312411 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
312323 ATTTTTTTAT
* **
312333 TTATATAAATTTTAATTTATTAAT-AATTAATA
1 TTATATAAATTTAAAAATATT-ATGAATTAATA
*
312365 TTATATAAATTTAAAAATATTATGAATTTATA
1 TTATATAAATTTAAAAATATTATGAATTAATA
312397 TTATATTATAATTTA
1 TTATA-TA-AATTTA
312412 TTTTTATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 2 0.05
32 30 0.75
33 2 0.05
34 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (32 bp):
TTATATAAATTTAAAAATATTATGAATTAATA
Found at i:312404 original size:18 final size:16
Alignment explanation
Indices: 312381--312531 Score: 59
Period size: 16 Copynumber: 9.3 Consensus size: 16
312371 AAATTTAAAA
312381 ATATTATGAATTTATATT
1 ATATTAT-AATTTAT-TT
312399 ATATTATAATTTATTT
1 ATATTATAATTTATTT
* * *
312415 TTATTATATAATATAATT
1 ATA-T-TATAATTTATTT
312433 ATATT-TAATATTA-TT
1 ATATTATAAT-TTATTT
*
312448 A-AATATTAATTTGATTTT
1 ATATTA-TAATTT-A-TTT
* *
312466 TTATTAT-TTTTAATTT
1 ATATTATAATTT-ATTT
*
312482 -T-TTATAA-TAATTT
1 ATATTATAATTTATTT
*
312495 AATTTTATAATTTATTT
1 -ATATTATAATTTATTT
*
312512 AT-TTAT-ATAATATTT
1 ATATTATAAT-TTATTT
312527 ATATT
1 ATATT
312532 TTTTATTATA
Statistics
Matches: 103, Mismatches: 14, Indels: 34
0.68 0.09 0.23
Matches are distributed among these distances:
13 4 0.04
14 9 0.09
15 22 0.21
16 25 0.24
17 18 0.17
18 22 0.21
19 3 0.03
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (16 bp):
ATATTATAATTTATTT
Found at i:312424 original size:28 final size:28
Alignment explanation
Indices: 312393--312455 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
312383 ATTATGAATT
* *
312393 TATATTAT-ATTATAATTTATTTTTATTA
1 TATATTATAATTAT-ATTTAATATTATTA
*
312421 TATAATATAATTATATTTAATATTATTA
1 TATATTATAATTATATTTAATATTATTA
*
312449 AATATTA
1 TATATTA
312456 ATTTGATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TATATTATAATTATATTTAATATTATTA
Found at i:312483 original size:17 final size:18
Alignment explanation
Indices: 312454--312546 Score: 65
Period size: 17 Copynumber: 5.4 Consensus size: 18
312444 TATTAAATAT
* *
312454 TAATTTGATTTTTTATTA
1 TAATTTAATTTTTTATAA
*
312472 T-TTTTAATTTTTTATAA
1 TAATTTAATTTTTTATAA
312489 TAATTTAA--TTTTATAA
1 TAATTTAATTTTTTATAA
* *
312505 TTTATTT-A-TTTATATAA
1 -TAATTTAATTTTTTATAA
*
312522 T-ATTTATATTTTTTATTA
1 TAATTTA-ATTTTTTATAA
312540 T-ATTTAA
1 TAATTTAA
312547 AATTATTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
15 4 0.07
16 10 0.16
17 28 0.46
18 19 0.31
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (18 bp):
TAATTTAATTTTTTATAA
Found at i:312531 original size:21 final size:18
Alignment explanation
Indices: 312461--312545 Score: 67
Period size: 18 Copynumber: 4.9 Consensus size: 18
312451 TATTAATTTG
*
312461 ATTTTTTATTATTTTTA-
1 ATTTTTTATTATATTTAT
*
312478 ATTTTTTATAATAATTTA-
1 ATTTTTTATTAT-ATTTAT
312496 A--TTTTA-TA-ATTTAT
1 ATTTTTTATTATATTTAT
*
312510 -TTATTTATATAATATTTAT
1 ATT-TTT-TATTATATTTAT
312529 ATTTTTTATTATATTTA
1 ATTTTTTATTATATTTA
312546 AAATTATTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
13 5 0.09
15 1 0.02
16 8 0.15
17 13 0.24
18 16 0.30
19 9 0.17
20 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTTATTATATTTAT
Found at i:312544 original size:33 final size:34
Alignment explanation
Indices: 312454--312545 Score: 100
Period size: 33 Copynumber: 2.7 Consensus size: 34
312444 TATTAAATAT
* * *
312454 TAATTTGATTTTTTATTATTTTTAATTTTTTATAA
1 TAATTTAATTTTTTATTATATTT-ATTTTATATAA
*
312489 TAATTTAATTTTATAATT-TATTTA-TTTATATAA
1 TAATTTAATTTT-TTATTATATTTATTTTATATAA
312522 T-ATTTATATTTTTTATTATATTTA
1 TAATTTA-ATTTTTTATTATATTTA
312546 AAATTATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
32 9 0.18
33 20 0.41
34 1 0.02
35 15 0.31
36 4 0.08
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (34 bp):
TAATTTAATTTTTTATTATATTTATTTTATATAA
Found at i:312836 original size:16 final size:16
Alignment explanation
Indices: 312785--312836 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
312775 AATATATATT
*
312785 TATATAAATTTTAATA
1 TATAAAAATTTTAATA
* * *
312801 AATTAATAATTTAAAT-
1 TA-TAAAAATTTTAATA
312817 TATAAAAATTTTAATA
1 TATAAAAATTTTAATA
312833 TATA
1 TATA
312837 TTAGATTTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
15 11 0.41
16 6 0.22
17 10 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATAAAAATTTTAATA
Found at i:312930 original size:17 final size:17
Alignment explanation
Indices: 312864--312961 Score: 51
Period size: 17 Copynumber: 5.8 Consensus size: 17
312854 CATGATTAAA
312864 TAATTT-ATTTATAAATT
1 TAATTTAATTTA-AAATT
* * *
312881 AAATTTAA-ATAAATTT
1 TAATTTAATTTAAAATT
* *
312897 TAAATTTAAATT--GATT
1 T-AATTTAATTTAAAATT
312913 TAATTTAATTTAAAATT
1 TAATTTAATTTAAAATT
* *
312930 TTATTTATATAATAAAATT
1 TAATTTA-AT-TTAAAATT
* *
312949 TATTTTATTTTAA
1 TAATTTAATTTAA
312962 TTATAATATT
Statistics
Matches: 59, Mismatches: 15, Indels: 14
0.67 0.17 0.16
Matches are distributed among these distances:
15 9 0.15
16 7 0.12
17 26 0.44
18 5 0.08
19 12 0.20
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (17 bp):
TAATTTAATTTAAAATT
Found at i:313064 original size:4 final size:5
Alignment explanation
Indices: 313033--313069 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
313023 GTTGACTGAT
313033 TAAAA TAAAA TAAAA TAAAA TAAAA T-AAA T-AAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
313070 GAGAGAGGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:316795 original size:15 final size:15
Alignment explanation
Indices: 316775--316803 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
316765 GTCAATTAAC
316775 GTTACTCAAACTTAT
1 GTTACTCAAACTTAT
316790 GTTACTCAAACTTA
1 GTTACTCAAACTTA
316804 AGTGTCAGTG
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:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (15 bp):
GTTACTCAAACTTAT
Found at i:319435 original size:15 final size:15
Alignment explanation
Indices: 319415--319458 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
319405 TAATATTTAT
*
319415 AATTAAATTGATTCG
1 AATTAAATTGATTCA
*
319430 AATTAAATTTTATT-A
1 AATTAAA-TTGATTCA
319445 AATTAAATTGATTC
1 AATTAAATTGATTC
319459 CATTCATCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 5 0.21
15 14 0.58
16 5 0.21
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (15 bp):
AATTAAATTGATTCA
Found at i:319532 original size:22 final size:24
Alignment explanation
Indices: 319507--319558 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
319497 TAATATTTTT
319507 AAAATTTATTTA-CTTA-ATTAAA
1 AAAATTTATTTATCTTATATTAAA
* *
319529 AAAA--TATTTATTTTATATTATA
1 AAAATTTATTTATCTTATATTAAA
319551 AAAATTTA
1 AAAATTTA
319559 AAAATTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
20 6 0.25
21 3 0.12
22 13 0.54
24 2 0.08
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATTTATTTATCTTATATTAAA
Found at i:324329 original size:15 final size:15
Alignment explanation
Indices: 324311--324342 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
324301 ACATTGCCCT
324311 GACATTTGTAAAGTC
1 GACATTTGTAAAGTC
324326 GACATTTGTAAAGTC
1 GACATTTGTAAAGTC
324341 GA
1 GA
324343 GTACGAGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (15 bp):
GACATTTGTAAAGTC
Found at i:330356 original size:34 final size:34
Alignment explanation
Indices: 330312--330384 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 34
330302 CTGAACATTA
330312 ATATTTTATATAAACTTTAAGAT-TTAA-AATATT
1 ATATTTTATATAAACTTTAAGATATTAATAAT-TT
* *
330345 ATATATTTATATAAATTTTAATATATTAATAATTT
1 ATAT-TTTATATAAACTTTAAGATATTAATAATTT
330380 ATATT
1 ATATT
330385 ATTAATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 4 0.11
34 18 0.51
35 10 0.29
36 3 0.09
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (34 bp):
ATATTTTATATAAACTTTAAGATATTAATAATTT
Found at i:330384 original size:13 final size:13
Alignment explanation
Indices: 330366--330397 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
330356 TAAATTTTAA
330366 TATATTAATAATT
1 TATATTAATAATT
*
330379 TATATTATTAATT
1 TATATTAATAATT
330392 TATATT
1 TATATT
330398 TTAATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TATATTAATAATT
Found at i:331377 original size:22 final size:23
Alignment explanation
Indices: 331352--331395 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
331342 GAATCGATTA
*
331352 TATATAAT-ATATAAATTATTTT
1 TATATAATAATATAAATAATTTT
331374 TATATAATAATATAAATAATTT
1 TATATAATAATATAAATAATTT
331396 AATTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATATAATAATATAAATAATTTT
Found at i:331425 original size:17 final size:17
Alignment explanation
Indices: 331405--331453 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
331395 TAATTTTTAA
331405 AATTTTAAATTTAATTT
1 AATTTTAAATTTAATTT
* *
331422 AATTATAAATTTTATTT
1 AATTTTAAATTTAATTT
*
331439 AATTTAATAATTTAA
1 AATTTTA-AATTTAA
331454 AATATTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTTAAATTTAATTT
Found at i:331441 original size:22 final size:22
Alignment explanation
Indices: 331390--331446 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
331380 ATAATATAAA
331390 TAATTTAATTT--TTAAAATTT
1 TAATTTAATTTAATTAAAATTT
331410 TAAATTTAATTTAATTATAAATTT
1 T-AATTTAATTTAATTA-AAATTT
331434 T-ATTTAATTTAAT
1 TAATTTAATTTAAT
331447 AATTTAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 1 0.03
21 10 0.30
22 12 0.36
23 3 0.09
24 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TAATTTAATTTAATTAAAATTT
Found at i:331459 original size:22 final size:22
Alignment explanation
Indices: 331390--331462 Score: 60
Period size: 25 Copynumber: 3.1 Consensus size: 22
331380 ATAATATAAA
*
331390 TAATTTAAT-TTTTAAAAT-TT
1 TAATTTAATAATTTAAAATATT
*
331410 TAAATTTAATTTAATTATAAATTTTATT
1 T-AATTTAA--TAATT-TAAA--ATATT
331438 TAATTTAATAATTTAAAATATT
1 TAATTTAATAATTTAAAATATT
331460 TAA
1 TAA
331463 AATCCAGTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
20 1 0.02
21 7 0.17
22 7 0.17
23 1 0.02
24 6 0.14
25 9 0.21
27 8 0.19
28 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATTTAATAATTTAAAATATT
Found at i:339849 original size:28 final size:28
Alignment explanation
Indices: 339809--339867 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
339799 TCATTTCGGG
339809 CTAGGCATGATCGGATGCCTATTGAAAC
1 CTAGGCATGATCGGATGCCTATTGAAAC
339837 CTAGGCATGATCGGATGCCTATTGAAAC
1 CTAGGCATGATCGGATGCCTATTGAAAC
339865 CTA
1 CTA
339868 TGTATTGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (28 bp):
CTAGGCATGATCGGATGCCTATTGAAAC
Found at i:342250 original size:14 final size:14
Alignment explanation
Indices: 342231--342274 Score: 63
Period size: 13 Copynumber: 3.1 Consensus size: 14
342221 CCATTTCATA
342231 TTTTTTTCTTTTT-
1 TTTTTTTCTTTTTC
342244 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
*
342258 TTTCTTTCTTTCTTC
1 TTTTTTTCTTT-TTC
342273 TT
1 TT
342275 CATCTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
13 13 0.46
14 10 0.36
15 5 0.18
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:342257 original size:19 final size:21
Alignment explanation
Indices: 342233--342295 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 21
342223 ATTTCATATT
*
342233 TTTTTCTTT-TTT-TTTTTTC
1 TTTTTCTTTCTTTCTTTCTTC
342252 TTTTTCTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTTCTTC
**
342273 TTCATC-TTCTTTCTTTCTT-
1 TTTTTCTTTCTTTCTTTCTTC
342292 TTTT
1 TTTT
342296 ACAACCCATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 11 0.30
20 16 0.43
21 10 0.27
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTCTTTCTTTCTTTCTTC
Found at i:343539 original size:32 final size:31
Alignment explanation
Indices: 343493--344883 Score: 1206
Period size: 28 Copynumber: 46.8 Consensus size: 31
343483 AAAATGGTGA
* * *
343493 TTTGAAAATGGTTGCCACTAACTTGCGTGGGC
1 TTTG-AAAGGGTTGCCACTGACTTGTGTGGGC
* *
343525 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAA-GGGTTGCCACTGACTTGTGTGGGC
*
343557 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
1 TTTG-AAAGGGTTGCCACTGACTTGTGTGGGC
* *
343589 TTTGAAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAA-GGGTTGCCACTGACTTGTGTGGGC
* * *
343621 TCTGAAAAGGGTTGCCACCGACTTGTGTAGGC
1 TTTG-AAAGGGTTGCCACTGACTTGTGTGGGC
*
343653 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAA-GGGTTGCCACTGACTTGTGTGGGC
*
343685 TTTGGAATGGGTTGCCACTGACTTGTGTGGGC
1 TTT-GAAAGGGTTGCCACTGACTTGTGTGGGC
*
343717 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAA-GGGTTGCCACTGACTTGTGTGGGC
* *
343749 TTTGAAATGGGTTGCCACCGACTTGTGTGGGT
1 TTTGAAA-GGGTTGCCACTGACTTGTGTGGGC
* *
343781 TTTGAAATGGGTTGCTACCGACTTGTGTGGGC
1 TTTGAAA-GGGTTGCCACTGACTTGTGTGGGC
*
343813 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAA-GGGTTGCCACTGACTTGTGTGGGC
*
343845 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAA-GGGTTGCCACTGACTTGTGTGGGC
*
343877 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAA-GGGTTGCCACTGACTTGTGTGGGC
* *
343909 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTT-GAAAGGGTTGCCACTGACTTGTGTGGGC
*
343941 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
1 TTTG-AAAGGGTTGCCACTGACTTGTGTGGGC
**
343973 TTTGAAAAAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
*
344001 TTTGAAA-GG-TGCCACTGAC-T-CGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
* ** *
344028 TTTGAAAAGG-AACCACTGAC-T-CGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
344056 -TTGAAAGGG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
* *
344083 TTTGAAAGAG-TGCCACTGAC-T-CGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
* *
344111 TTTGAAAAGG-TGCCACTGACTTGCGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
344141 TTTGAAAGGAG-TGCCACTGACTTGTGTGGGC
1 TTTGAAAGG-GTTGCCACTGACTTGTGTGGGC
* * *
344172 TTTGATAGGG-TGCCACTAAC-T-CGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
*
344200 TTTGAAA-GGATGCCACTGAC-T-TGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
* *
344228 TTTGAAAGAG-TGCCACTGAC-T-CGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
* * * *
344256 TTTGAAAAGG-TACCACTGACTTGCGTGAGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
* *
344286 TTTAAAAGGAG-TGCCACTGACTTGTGTGAGC
1 TTTGAAAGG-GTTGCCACTGACTTGTGTGGGC
*
344317 TTTAAAAGGG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
344345 TTTGAAAGGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAAGG-GTTGCCACTGACTTGTGTGGGC
*
344374 TTTGAAAGGAG-TGCCACTGACTTGAGTGGGC
1 TTTGAAAGG-GTTGCCACTGACTTGTGTGGGC
* * *
344405 TTTAAAAAGG-TGCCACTGAC-T-TATGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
* *
344433 TTTGAAAGAG-TGCCACTGA-AT-TGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
* * *
344461 TTCGCAATGG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
* * *
344489 TTCGAAAAGG-TACCACTGAC-T-TGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
* ** * *
344517 TCTGAAAAAG-TGCCACTAAC-T-TGTGAGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
*
344545 TTTGAAAGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
* * *
344573 TTTAAAAAGAG-TGCGACTGA-TT-TGTGGGC
1 TTT-GAAAGGGTTGCCACTGACTTGTGTGGGC
*
344602 TTTGAAAAGAG-TGCCACTGAC-T-TGTGGGC
1 TTTG-AAAGGGTTGCCACTGACTTGTGTGGGC
344631 TTTGAAAGGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAAGG-GTTGCCACTGACTTGTGTGGGC
344660 TTTGAAAGGAG-TGCCACTGACTTGTGTGGGC
1 TTTGAAAGG-GTTGCCACTGACTTGTGTGGGC
*
344691 TTTAAAAGGG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
* *
344719 TTTAAAAGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
** *
344747 TTTGAAAAAG-TGCCACTGA-AT-TGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
* * * *
344775 TTCGCAATGG-TGCCATTGAC-T-TGTGGGC
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
*
344803 TTCGAAAGGG-TGCCACTGAC-T-TGTGGG-
1 TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
* *
344830 TTCTAAAAGGGTT-CCACTAAC-T-TGTGGGC
1 TT-TGAAAGGGTTGCCACTGACTTGTGTGGGC
* *
344859 TTTGAAAGGG-TGCCACGGAGTTGTG
1 TTTGAAAGGGTTGCCACTGACTTGTG
344884 GATTTTAAAA
Statistics
Matches: 1212, Mismatches: 107, Indels: 82
0.87 0.08 0.06
Matches are distributed among these distances:
27 53 0.04
28 423 0.35
29 144 0.12
30 83 0.07
31 101 0.08
32 396 0.33
33 12 0.01
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.29
Consensus pattern (31 bp):
TTTGAAAGGGTTGCCACTGACTTGTGTGGGC
Found at i:343597 original size:64 final size:59
Alignment explanation
Indices: 343493--344953 Score: 1290
Period size: 64 Copynumber: 24.7 Consensus size: 59
343483 AAAATGGTGA
* * * * *
343493 TTTGAAAATGGTTGCCACTAACTTGCGTGGGCTTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAAA-GGGTGCCACTGACTT-TGTGGGCTTTGAAA-GGG-TGCCACTGACTT-TGTGGGC
* *
343557 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAAAGGG-TGCCACTGACTT-TGTGGGCTTTGAAA-GGG-TGCCACTGACTT-TGTGGGC
* * * *
343621 TCTGAAAAGGGTTGCCACCGACTTGTGTAGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAAAGGG-TGCCACTGACTT-TGTGGGCTTTGAAA-GGG-TGCCACTGACTT-TGTGGGC
* * *
343685 TTTGGAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAAAGGG-TGCCACTGACTT-TGTGGGCTTTGAAA-GGG-TGCCACTGACTT-TGTGGGC
* * * * *
343749 TTTGAAATGGGTTGCCACCGACTTGTGTGGGTTTTGAAATGGGTTGCTACCGACTTGTGTGGGC
1 TTTGAAAAGGG-TGCCACTGACTT-TGTGGGCTTTGAAA-GGG-TGCCACTGACTT-TGTGGGC
* * *
343813 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAAAGGG-TGCCACTGACTT-TGTGGGCTTTGAAA-GGG-TGCCACTGACTT-TGTGGGC
* * * *
343877 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAAAGGG-TGCCACTGACTT-TGTGGGCTTT-GAAAGGG-TGCCACTGACTT-TGTGGGC
* **
343941 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAAGTGCCACTGAC-TTGTGGGC
1 TTTGAAAAGGG-TGCCACTGACTT-TGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGC
* * ** *
344001 TTTG-AAA-GGTGCCACTGAC-TCGTGGGCTTTGAAAAGGAACCACTGAC-TCGTGGGC
1 TTTGAAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGC
* *
344056 -TTG-AAAGGGTGCCACTGAC-TTGTGGGCTTTGAAAGAGTGCCACTGAC-TCGTGGGC
1 TTTGAAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGC
*
344111 TTTGAAAA-GGTGCCACTGACTTGCGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGC
1 TTTGAAAAGGGTGCCACTGACTT-TGTGGGCTTTGAAAGG-GTGCCACTGACTT-TGTGGGC
* * * *
344172 TTTG-ATAGGGTGCCACTAAC-TCGTGGGCTTTGAAAGGATGCCACTGAC-TTGTGGGC
1 TTTGAAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGC
* * * * * *
344228 TTTG-AAAGAGTGCCACTGAC-TCGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGC
1 TTTGAAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTT-TGTGGGC
* *
344286 TTT-AAAAGGAGTGCCACTGACTTGTGTGAGCTTTAAAAGGGTGCCACTGAC-TTGTGGGC
1 TTTGAAAAGG-GTGCCACTGACTT-TGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGC
*
344345 TTTG-AAAGGAGTGCCACTGAC-TTGTGGGCTTTGAAAGGAGTGCCACTGACTTGAGTGGGC
1 TTTGAAAAGG-GTGCCACTGACTTTGTGGGCTTTGAAAGG-GTGCCACTGACTT-TGTGGGC
* * * *
344405 TTT-AAAAAGGTGCCACTGAC-TTATGGGCTTTGAAAGAGTGCCACTGA-ATTGTGGGC
1 TTTGAAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGC
* * * * * *
344461 TTCG-CAATGGTGCCACTGAC-TTGTGGGCTTCGAAAAGGTACCACTGAC-TTGTGGGC
1 TTTGAAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGC
* * * * *
344517 TCTGAAAA-AGTGCCACTAAC-TTGTGAGCTTTGAAAGAGTGCCACTGAC-TTGTGGGC
1 TTTGAAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGC
* * * *
344573 TTTAAAAAGAGTGCGACTGA-TTTGTGGGCTTTGAAAAGAGTGCCACTGAC-TTGTGGGC
1 TTTGAAAAGGGTGCCACTGACTTTGTGGGCTTTG-AAAGGGTGCCACTGACTTTGTGGGC
344631 TTTG-AAAGGAGTGCCACTGAC-TTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGC
1 TTTGAAAAGG-GTGCCACTGACTTTGTGGGCTTTGAAAGG-GTGCCACTGACTT-TGTGGGC
* *
344691 TTT-AAAAGGGTGCCACTGA-TTTGTGGGCTTTAAAAGAGTGCCACTGAC-TTGTGGGC
1 TTTGAAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGC
* * * * * *
344747 TTTGAAAA-AGTGCCACTGA-ATTGTGGGCTTCGCAATGGTGCCATTGAC-TTGTGGGC
1 TTTGAAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGC
* * * *
344803 TTCG-AAAGGGTGCCACTGAC-TTGTGGG-TTCTAAAAGGGTTCCACTAAC-TTGTGGGC
1 TTTGAAAAGGGTGCCACTGACTTTGTGGGCTT-TGAAAGGGTGCCACTGACTTTGTGGGC
* * ** * * * *
344859 TTTG-AAAGGGTGCCACGGA-GTTGTGGATTTTAAAAGGGTGCCACAGA-GTTGTGGAC
1 TTTGAAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGC
* * * *
344915 -TT-AAAAGGGTGCCACGGA-GTTGTGGACTTTAAAAGGGTG
1 TTTGAAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAGGGTG
344954 ACACAGAGTT
Statistics
Matches: 1233, Mismatches: 121, Indels: 95
0.85 0.08 0.07
Matches are distributed among these distances:
54 6 0.00
55 115 0.09
56 299 0.24
57 67 0.05
58 130 0.11
59 119 0.10
60 45 0.04
61 44 0.04
62 9 0.01
63 6 0.00
64 390 0.32
65 3 0.00
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (59 bp):
TTTGAAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGC
Found at i:343619 original size:96 final size:89
Alignment explanation
Indices: 343505--344953 Score: 1299
Period size: 96 Copynumber: 16.3 Consensus size: 89
343495 TGAAAATGGT
* * * *
343505 TGCCACTAACTTGCGTGGGCTTTTAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTT
1 TGCCACTGACTT-TGTGGGCTTTGAAA-GGG-TGCCACTGACTT-TGTGGGCTTTGAAAAGGG-T
*
343570 GCCACCGACTTGTGTGGGCTTTGAAATGGG
61 GCCACTGACTTGTGTGGGCTTTGAAA-GGG
* * * * *
343600 TTGCCACCGACTTATGTGGGCTCTGAAAAGGGTTGCCACCGACTTGTGTAGGCTTTGAAATGGGT
1 -TGCCACTGACTT-TGTGGGCTTTG-AAAGGG-TGCCACTGACTT-TGTGGGCTTTGAAAAGGG-
* *
343665 TGCCACCGACTTGTGTGGGCTTTGGAATGGG
60 TGCCACTGACTTGTGTGGGCTTT-GAAAGGG
* *
343696 TTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 -TGCCACTGACTT-TGTGGGCTTTGAAA-GGG-TGCCACTGACTT-TGTGGGCTTTGAAAAGGG-
* *
343761 TGCCACCGACTTGTGTGGGTTTTGAAATGGG
60 TGCCACTGACTTGTGTGGGCTTTGAAA-GGG
* * * *
343792 TTGCTACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 -TGCCACTGACTT-TGTGGGCTTTGAAA-GGG-TGCCACTGACTT-TGTGGGCTTTGAAAAGGG-
*
343857 TGCCACCGACTTGTGTGGGCTTTGAAATGGG
60 TGCCACTGACTTGTGTGGGCTTTGAAA-GGG
* * *
343888 TTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGT
1 -TGCCACTGACTT-TGTGGGCTTT-GAAAGGG-TGCCACTGACTT-TGTGGGCTTTGAAAAGGG-
* **
343953 TGCCACCGACTTGTGTGGGCTTTGAAAAAG
60 TGCCACTGACTTGTGTGGGCTTTGAAAGGG
* **
343983 TGCCACTGAC-TTGTGGGCTTTGAAA-GGTGCCACTGAC-TCGTGGGCTTTGAAAA-GGAACCAC
1 TGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCAC
*
344044 TGAC-T-CGTGGGC-TTGAAAGGG
66 TGACTTGTGTGGGCTTTGAAAGGG
* *
344065 TGCCACTGAC-TTGTGGGCTTTGAAAGAGTGCCACTGAC-TCGTGGGCTTTGAAAA-GGTGCCAC
1 TGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCAC
*
344127 TGACTTGCGTGGGCTTTGAAAGGAG
66 TGACTTGTGTGGGCTTTGAAAGG-G
* * * *
344152 TGCCACTGACTTGTGTGGGCTTTGATAGGGTGCCACTAAC-TCGTGGGCTTTG-AAAGGATGCCA
1 TGCCACTGACTT-TGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCA
*
344215 CTGAC-T-TGTGGGCTTTGAAAGAG
65 CTGACTTGTGTGGGCTTTGAAAGGG
* * * * *
344238 TGCCACTGAC-TCGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGCTTT-AAAAGGAGTGCC
1 TGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTT-TGTGGGCTTTGAAAAGG-GTGCC
* *
344301 ACTGACTTGTGTGAGCTTTAAAAGGG
64 ACTGACTTGTGTGGGCTTTGAAAGGG
344327 TGCCACTGAC-TTGTGGGCTTTGAAAGGAGTGCCACTGAC-TTGTGGGCTTTG-AAAGGAGTGCC
1 TGCCACTGACTTTGTGGGCTTTGAAAGG-GTGCCACTGACTTTGTGGGCTTTGAAAAGG-GTGCC
* * *
344389 ACTGACTTGAGTGGGCTTTAAAAAGG
64 ACTGACTTGTGTGGGCTTTGAAAGGG
* * * * * *
344415 TGCCACTGAC-TTATGGGCTTTGAAAGAGTGCCACTGA-ATTGTGGGCTTCG-CAATGGTGCCAC
1 TGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCAC
* *
344477 TGAC-T-TGTGGGCTTCGAAAAGG
66 TGACTTGTGTGGGCTTTGAAAGGG
* * ** * * *
344499 TACCACTGAC-TTGTGGGCTCTGAAAAAGTGCCACTAAC-TTGTGAGCTTTG-AAAGAGTGCCAC
1 TGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCAC
* *
344561 TGAC-T-TGTGGGCTTTAAAAAGAG
66 TGACTTGTGTGGGCTTT-GAAAGGG
* *
344584 TGCGACTGA-TTTGTGGGCTTTGAAAAGAGTGCCACTGAC-TTGTGGGCTTTG-AAAGGAGTGCC
1 TGCCACTGACTTTGTGGGCTTTG-AAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGG-GTGCC
344646 ACTGAC-T-TGTGGGCTTTGAAAGGAG
64 ACTGACTTGTGTGGGCTTTGAAAGG-G
* *
344671 TGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGA-TTTGTGGGCTTT-AAAAGAGTGCCA
1 TGCCACTGACTT-TGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCA
**
344734 CTGAC-T-TGTGGGCTTTGAAAAAG
65 CTGACTTGTGTGGGCTTTGAAAGGG
* * * * * *
344757 TGCCACTGA-ATTGTGGGCTTCGCAATGGTGCCATTGAC-TTGTGGGCTTCG-AAAGGGTGCCAC
1 TGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCAC
*
344819 TGAC-T-TGTGGG-TTCTAAAAGGG
66 TGACTTGTGTGGGCTT-TGAAAGGG
* * * * * *
344841 TTCCACTAAC-TTGTGGGCTTTGAAAGGGTGCCACGGA-GTTGT-GGATTTTAAAAGGGTGCCAC
1 TGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCAC
* * * *
344903 AGA-GT-TGTGGAC-TTAAAAGGG
66 TGACTTGTGTGGGCTTTGAAAGGG
* * * *
344924 TGCCACGGA-GTTGTGGACTTTAAAAGGGTG
1 TGCCACTGACTTTGTGGGCTTTGAAAGGGTG
344954 ACACAGAGTT
Statistics
Matches: 1187, Mismatches: 125, Indels: 95
0.84 0.09 0.07
Matches are distributed among these distances:
82 32 0.03
83 81 0.07
84 215 0.18
85 40 0.03
86 89 0.07
87 130 0.11
88 105 0.09
89 106 0.09
90 12 0.01
91 3 0.00
92 10 0.01
93 1 0.00
94 9 0.01
95 7 0.01
96 338 0.28
97 9 0.01
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (89 bp):
TGCCACTGACTTTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCAC
TGACTTGTGTGGGCTTTGAAAGGG
Found at i:344683 original size:286 final size:280
Alignment explanation
Indices: 343550--345774 Score: 1247
Period size: 273 Copynumber: 7.8 Consensus size: 280
343540 CACCGACTTG
* * *
343550 TGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTAT
1 TGTGGGCTTTG-AAA-GG-TGCCACTGAC-T-TGTGGGCTTCGAAA--GG-TGCCACTGAC-T-T
* * * *
343615 GTGGGCTCTGAAAAGGGTTGCCACCGACTTGTGTAGGCTTTGAAATGGGTTGCCACCGACTTGTG
56 GTGGGCT-TG-AAAGAG-TGCCACTGACTTGTG--GGCTTTGAAA-GAG-TGCCACTGAC-T-TG
* * * * *
343680 TGGGCTTTGGAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGT
112 TGGGCTTT-AAAAGAG-TGCCACTGA-TT-TGTGGGCTTTGAAAAGGG-TGCCACTGAC-T-TGT
* * * * *
343745 GGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGTTTTGAAATGG-GTTGCTACCGACTTGTGT
170 GGGC-TTGAAA-GGG-TGCCACTGAC-T-TGTGGGCTTTGAAA-GGAG-TGCCACTGACTTGAGT
** * * * *
343809 GGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTT
228 GGGCTTT-AAAAAGG-TGCCACTGAC-T-TGTGGGCTTTGAAA-GAG-TGCCACTGA-AT
* * * *
343869 GTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTG
1 -TGTGGGCTTTGAAA--GG-TGCCACTGAC-T-TGTGGGC-TTCGAA-AGG-TGCCACTGAC-T-
* * *
343934 TGTGGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAAGTGCCACTGACTTGTGG
55 TGTGGGC-TTG-AAAGAG-TGCCACTGAC-T-TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGG
* * * ** *
343999 GCTTTGAAAG-GTGCCACTGACTCGTGGGCTTTGAAAA-GGAACCACTGACTCGTGGGCTTGAAA
115 GCTTTAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTGAAA
* *
344062 GGGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGAC-T-CGTGGGCTTTGAAAAGGTGC
180 GGGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGAGTGGGCTTTAAAAAGGTGC
*
344124 CACTGACTTGCGTGGGCTTTGAAAGGAGTGCCACTGACTT
245 CACTGACTT--GTGGGCTTTGAAA-GAGTGCCACTGA-AT
* * * *
344164 GTGTGGGCTTTGATAGGGTGCCACTAACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
1 -TGTGGGCTTTGA-AAGGTGCCACTGACTTGTGGGCTTCGAAAGG-TGCCACTGACTTGTGGGC-
* * *
344229 TTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAA-AGGTACCACTGACTTGCGTGAGCTTTAAAA
62 TTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACTT--GTGGGCTTTAAAA
*
344293 GGAGTGCCACTGACTTGTGTGAGCTTT-AAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAGT
124 -GAGTGCCACTGA-TT-TGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGC-TTGAAAGG-GT
344357 GCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGAGTGGGCTTTAAAAAGGTGCCACT
184 GCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGAGTGGGCTTTAAAAAGGTGCCACT
*
344422 GACTTATGGGCTTTGAAAGAGTGCCACTGAAT
249 GACTTGTGGGCTTTGAAAGAGTGCCACTGAAT
* * *
344454 TGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGAAAAGGTACCACTGACTTGTGGGCTC
1 TGTGGGCTTTG-AAAGGTGCCACTGACTTGTGGGCTTCG-AAAGGTGCCACTGACTTGTGGGCT-
* * *
344519 TGAAAAAGTGCCACTAACTTGTGAGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTAAAAAGAG
63 TGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTT-AAAAGAG
* *
344584 TGCGACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACT
127 TGCCACTGATTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGC-TTGAAAGG-GTGCCACT
* * *
344649 GACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGATTTG
190 GACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGAGTGGGCTTTAAAAAGGTGCCACTGACTTG
* *
344714 TGGGCTTTAAAAGAGTGCCACTGACT
255 TGGGCTTTGAAAGAGTGCCACTGAAT
* * * *
344740 TGTGGGCTTTGAAAAAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCATTGACTTGTGGGCTT
1 TGTGGGCTTTG-AAAGGTGCCACTGACTTGTGGGCTTCG-AAAGGTGCCACTGACTTGTGGGCTT
* * * * * * *
344805 CGAAAGGGTGCCACTGACTTGTGGG-TTCTAAAAGGGTTCCACTAACTTGTGGGCTTTGAAAGGG
64 -GAAAGAGTGCCACTGACTTGTGGGCTT-TGAAAGAGTGCCACTGACTTGTGGGCTTTAAAAGAG
* * * * * * * * *
344869 TGCCACGGAGTTGT-GGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
127 TGCCACTGATTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTGAAAGGGTGCCACTGA
* * * * * * * * * * *
344933 GTTGTGGACTTTAAAAGG-GTGACACAGAGTT--GTGGAC-TTAAAAGAGATGCCACGGAGTTAT
192 CTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGAGTGGGCTTTAAAA-AGGTGCCACTGACTTGT
* * * * *
344994 GGAC-TTAAAAGGGTGCCACGGAGT
256 GGGCTTTGAAAGAGTGCCACTGAAT
* * * * * * * * * *
345018 TGTGGAC-TTAAAAGGGTGCCACAGAGTTGTAGTCTT-AAAAGGGATGCCACGGAGTTGTGGACT
1 TGTGGGCTTTGAAA-GGTGCCACTGACTTGTGGGCTTCGAAA-GG-TGCCACTGACTTGTGGGCT
* * * * * * * * * * *
345081 TAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGAATGCCACGGAGTTGTGGAC-TTAAAAGAAT
63 TGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTAAAAGAGT
* * * * * * * * *
345144 GCCACGGAGTTGTAGAC-TT-AAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCACAGA
128 GCCACTGATTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTGAAAGGG-TGCCACTGA
* * * * * * * * * *
345207 GTTGTGGAC-TTAAAAGG-GTGCGACGGAGTT--GTGGAC-TTAAAAGGGTGCCACGGAGTTGTG
192 CTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGAGTGGGCTTTAAAAAGGTGCCACTGACTTGTG
* * * * *
345267 GAC-TTAAAAGAATGCCACGGAGT
257 GGCTTTGAAAGAGTGCCACTGAAT
* * * * * * * * * *
345290 TGTGGAC-TTAAAAGAATGCCA-TGGAGTTGTAGACTT-AAAAGGGTGCCACGGAGTTGTGGTCT
1 TGTGGGCTTTGAAAG-GTGCCACT-GACTTGTGGGCTTCGAAA-GGTGCCACTGACTTGTGGGCT
* * * * * * * * * * * *
345352 TAAAAGGGATGCCACAGAGTTGTGGAC-TTAAAAGGGTGCGACGGAGTTGTGGAC-TTAAAAGGG
63 TGAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTAAAAGAG
** * * * * * * *
345415 TGCCACAAAGTTGTGGAC-TT-AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGATGCCACGG
127 TGCCACTGATTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTGAAAGGG-TGCCACTG
* ** * * * * * * *
345478 AGTTGTGGATTTTAAAAGG-GTGCCACGGAGTT--GTGGAC-TT-AAAAGAATGCCACGGAGTTG
191 ACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGAGTGGGCTTTAAAAAG-GTGCCACTGACTTG
* * * * *
345538 TGGAC-TTAAAAGGGTGCCACAGAGT
255 TGGGCTTTGAAAGAGTGCCACTGAAT
* * * * * * * *
345563 TGTGGTC-TTAAAAGGGATGCCA-TAGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGAC
1 TGTGGGCTTTGAAA-GG-TGCCACT-GACTTGTGGGCTTCGAAA-GGTGCCACTGACTTGTGGGC
* * * * * * * * * * *
345625 TTAAAAGGGTGCCAC-GAAGTTGTGGAC-TTAAAAGTGTGCCACGGAGTTATGGAC-TTAAAAGG
62 TTGAAAGAGTGCCACTG-ACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTAAAAGA
* * * * * * * * *
345687 GTGCCACAGAGTTGTGGAC-TT-AAAAAGGTGCCACGGATTTGTGGACTTAAAAGGGTGCCACGG
126 GTGCCACTGATTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTGAAAGGGTGCCACTG
* * *
345750 AGTTGTGGAC-TTAAAAGG-GTGCCAC
191 ACTTGTGGGCTTTGAAAGGAGTGCCAC
345775 AGAGTTGTGG
Statistics
Matches: 1666, Mismatches: 193, Indels: 141
0.83 0.10 0.07
Matches are distributed among these distances:
271 42 0.03
272 209 0.13
273 236 0.14
274 91 0.05
275 22 0.01
276 26 0.02
277 35 0.02
278 29 0.02
279 20 0.01
281 10 0.01
282 25 0.02
283 32 0.02
284 27 0.02
285 48 0.03
286 235 0.14
287 40 0.02
288 11 0.01
289 126 0.08
290 21 0.01
291 44 0.03
292 26 0.02
293 9 0.01
294 30 0.02
295 25 0.02
296 25 0.02
297 4 0.00
298 9 0.01
299 1 0.00
300 9 0.01
301 1 0.00
302 13 0.01
303 1 0.00
304 9 0.01
305 3 0.00
306 6 0.00
307 6 0.00
308 1 0.00
309 7 0.00
310 2 0.00
311 13 0.01
312 1 0.00
313 9 0.01
314 1 0.00
315 4 0.00
316 10 0.01
317 1 0.00
318 9 0.01
319 4 0.00
320 87 0.05
321 7 0.00
322 4 0.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.27
Consensus pattern (280 bp):
TGTGGGCTTTGAAAGGTGCCACTGACTTGTGGGCTTCGAAAGGTGCCACTGACTTGTGGGCTTGA
AAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTAAAAGAGTGCC
ACTGATTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTGAAAGGGTGCCACTGACTTG
TGGGCTTTGAAAGGAGTGCCACTGACTTGAGTGGGCTTTAAAAAGGTGCCACTGACTTGTGGGCT
TTGAAAGAGTGCCACTGAAT
Found at i:345182 original size:136 final size:135
Alignment explanation
Indices: 344549--345876 Score: 1506
Period size: 136 Copynumber: 9.6 Consensus size: 135
344539 GTGAGCTTTG
* * * * * * * * *
344549 AAAGAGTGCCACTGACTTGTGGGCTTTAAAAAGAGTGCGACTGATTTGTGGGCTTTGAAAAGAGT
1 AAAGAGTGCCACGGAGTTGTGGAC-TT-AAAAGGGTGCCACAGAGTTGTGGAC-TT-AAAAGGGT
* * * * * * * * *
344614 GCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTG
62 GCCACAGAGTTGTGGAC-TTAAAAGG-GTGCCACGGAGTTGTGGAC-TTAAAAGG-GTGCCACGG
* *
344679 ACTTGTGTGGGCTTTA
123 A-GT-TGTGGAC-TTA
* * * * * * * * *
344695 AAAGGGTGCCACTGATTTGTGGGCTTTAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA-AGTG
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGAC-TT-AAAAGGGTG
* * * ** * ** * * * * *
344759 CCACTGAATTGTGGGCTTCGCAATGGTGCCATTGACTTGTGGGCTTCGAAAGGGTGCCACTGACT
63 CCACAGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGT
**
344824 TGTGGGTTCTA
126 TGTGGACT-TA
* * ** * * * * *
344835 AAAGGGTTCCACTAACTTGTGGGCTTTGAAAGGGTGCCACGGAGTTGTGGATTTTAAAAGGGTGC
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGA-CTTAAAAGGGTGC
* *
344900 CACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGACACAGAGTTG
64 CACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTG
344965 TGGACTTA
128 TGGACTTA
* *
344973 AAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
1 AAAGAG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCC
* *
345038 ACAGAGTTGTAGTCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGT
65 ACAGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGT
345103 GGACTTA
129 GGACTTA
* ** * *
345110 AAAGAATGCCACGGAGTTGTGGACTTAAAAGAATGCCACGGAGTTGTAGACTTAAAAGGGTGCCA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCA
* * * *
345175 CGGAGTTGTGGTCTTAAAAGGGATGCCACAGAGTTGTGGACTTAAAAGGGTGCGACGGAGTTGTG
66 CAGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTG
345240 GACTTA
130 GACTTA
* ** * **
345246 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGAATGCCACGGAGTTGTGGACTTAAAAGAATGCCA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCA
** * * *
345311 TGGAGTTGTAGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCACAGAGTTGTG
66 CAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTG
345376 GACTTA
130 GACTTA
* * *
345382 AAAGGGTGCGACGGAGTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTTAAAAGGGTGCCA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCA
*
345447 CAGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGATTTTAAAAGGGTGCCACGGAGTTGT
66 CAGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGT
345512 GGACTTA
129 GGACTTA
* *
345519 AAAGAATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGTCTTAAAAGGGATGCC
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGG-TGCC
* *
345584 ATAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTTGTG
65 ACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTG
345649 GACTTA
130 GACTTA
* * *
345655 AAAGTGTGCCACGGAGTTATGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGGTGCCA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCA
* * *
345720 CGGATTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGG
66 CAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGG
*
345785 ACTAA
131 ACTTA
* * * *
345790 AAAGGGTGCCATGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGATGCC
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCC
345855 ACAGAGTTGTGGACTTTAAAAG
65 ACAGAGTTGTGGAC-TTAAAAG
345877 AAAATGCCAC
Statistics
Matches: 1060, Mismatches: 108, Indels: 37
0.88 0.09 0.03
Matches are distributed among these distances:
135 115 0.11
136 432 0.41
137 182 0.17
138 85 0.08
139 55 0.05
140 73 0.07
141 1 0.00
142 12 0.01
143 26 0.02
144 23 0.02
145 31 0.03
146 25 0.02
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.25
Consensus pattern (135 bp):
AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCA
CAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGG
ACTTA
Found at i:345877 original size:27 final size:27
Alignment explanation
Indices: 344606--345876 Score: 1500
Period size: 27 Copynumber: 46.2 Consensus size: 27
344596 GTGGGCTTTG
* * * *
344606 AAAAGAGTGCCACTGACTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* * * *
344634 GAAAGGAGTGCCACTGACTTGTGGGCTTT
1 AAAAGG-GTGCCACGGAGTTGTGGAC-TT
* * * *
344663 GAAAGGAGTGCCACTGACTTGTGTGGGCTTT
1 AAAAGG-GTGCCACGGA-GT-TGTGGAC-TT
* * *
344694 AAAAGGGTGCCACTGATTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* * * *
344722 AAAAGAGTGCCACTGACTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* * * *
344750 GAAAA-AGTGCCACTGAATTGTGGGCTT
1 -AAAAGGGTGCCACGGAGTTGTGGACTT
** * ** * *
344777 CGCAATGGTGCCATTGACTTGTGGGCTT
1 -AAAAGGGTGCCACGGAGTTGTGGACTT
* * * **
344805 CGAAAGGGTGCCACTGACTTGTGGGTTCT
1 -AAAAGGGTGCCACGGAGTTGTGGACT-T
* ** * *
344834 AAAAGGGTTCCACTAACTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
344862 GAAAGGGTGCCACGGAGTTGTGGATTTT
1 AAAAGGGTGCCACGGAGTTGTGGA-CTT
*
344890 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
344917 AAAAGGGTGCCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
344945 AAAAGGGTGACACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
344972 AAAAGAGATGCCACGGAGTTATGGACTT
1 AAAAG-GGTGCCACGGAGTTGTGGACTT
345000 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
345027 AAAAGGGTGCCACAGAGTTGTAGTCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
345054 AAAAGGGATGCCACGGAGTTGTGGACTT
1 AAAAGGG-TGCCACGGAGTTGTGGACTT
345082 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
**
345109 AAAAGAATGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
** *
345136 AAAAGAATGCCACGGAGTTGTAGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
345163 AAAAGGGTGCCACGGAGTTGTGGTCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
345190 AAAAGGGATGCCACAGAGTTGTGGACTT
1 AAAAGGG-TGCCACGGAGTTGTGGACTT
*
345218 AAAAGGGTGCGACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
345245 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
**
345272 AAAAGAATGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
** * *
345299 AAAAGAATGCCATGGAGTTGTAGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
345326 AAAAGGGTGCCACGGAGTTGTGGTCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
345353 AAAAGGGATGCCACAGAGTTGTGGACTT
1 AAAAGGG-TGCCACGGAGTTGTGGACTT
*
345381 AAAAGGGTGCGACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
**
345408 AAAAGGGTGCCACAAAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
345435 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
345462 AAAAGGGATGCCACGGAGTTGTGGATTTT
1 AAAAGGG-TGCCACGGAGTTGTGGA-CTT
345491 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
**
345518 AAAAGAATGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
345545 AAAAGGGTGCCACAGAGTTGTGGTCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
**
345572 AAAAGGGATGCCATAGAGTTGTGGACTT
1 AAAAGGG-TGCCACGGAGTTGTGGACTT
345600 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
345627 AAAAGGGTGCCACGAAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
345654 AAAAGTGTGCCACGGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
345681 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
345708 AAAAAGGTGCCACGGATTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
345735 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
345762 AAAAGGGTGCCACAGAGTTGTGGACTA
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
345789 AAAAGGGTGCCATGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
*
345817 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
345844 AAAAAGATGCCACAGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
345872 AAAAG
1 AAAAG
345877 AAAATGCCAC
Statistics
Matches: 1115, Mismatches: 110, Indels: 36
0.88 0.09 0.03
Matches are distributed among these distances:
27 658 0.59
28 375 0.34
29 56 0.05
30 11 0.01
31 15 0.01
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.25
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Done.