Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 16 of 32
Found at i:2403120 original size:49 final size:49
Alignment explanation
Indices: 2403048--2403146 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
2403038 TTTCTCACGG
2403048 TAAGTATCATCCATATTGGATTATTAATGTATTTAACAGTATATATGCA
1 TAAGTATCATCCATATTGGATTATTAATGTATTTAACAGTATATATGCA
2403097 TAAGTATCATCCATATTGGATTATTAATGTATTTAACAGTATATATGCA
1 TAAGTATCATCCATATTGGATTATTAATGTATTTAACAGTATATATGCA
2403146 T
1 T
2403147 TAATTACATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.41
Consensus pattern (49 bp):
TAAGTATCATCCATATTGGATTATTAATGTATTTAACAGTATATATGCA
Found at i:2407553 original size:20 final size:22
Alignment explanation
Indices: 2407530--2407578 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
2407520 ATAATATTAT
2407530 ATTAAATTTAATAATT-AATA-
1 ATTAAATTTAATAATTAAATAC
* * *
2407550 ATTATATTTATTATTTAAATAC
1 ATTAAATTTAATAATTAAATAC
2407572 ATTAAAT
1 ATTAAAT
2407579 AAAAATATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 13 0.57
21 4 0.17
22 6 0.26
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTAAATTTAATAATTAAATAC
Found at i:2407565 original size:27 final size:31
Alignment explanation
Indices: 2407503--2407587 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 31
2407493 TTAAAATCAA
*
2407503 TTAAATATATTATTATAATAATATTATATTAAAT
1 TTAAATACATTA--ATAATAATATTATATT-AAT
*
2407537 TT-AATA-ATTAATAATTATATT-TATT-AT
1 TTAAATACATTAATAATAATATTATATTAAT
*
2407564 TTAAATACATTAAATAAAAATATT
1 TTAAATACATT-AATAATAATATT
2407588 GGTATGCATA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
27 4 0.09
28 4 0.09
29 7 0.16
30 20 0.44
32 4 0.09
33 4 0.09
34 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (31 bp):
TTAAATACATTAATAATAATATTATATTAAT
Found at i:2408241 original size:25 final size:25
Alignment explanation
Indices: 2408176--2408250 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
2408166 AAAGTTTATA
*
2408176 AATTTTAATATATTTATATAATTATATT
1 AATTTTAAT-T-TTTTTAT-ATTATATT
* * *
2408204 -ATGTTGATATTTTTATATTATATT
1 AATTTTAATTTTTTTATATTATATT
2408228 AATTTTAATTTTTTTATATTATA
1 AATTTTAATTTTTTTATATTATA
2408251 ATTATATTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
24 8 0.21
25 25 0.64
27 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (25 bp):
AATTTTAATTTTTTTATATTATATT
Found at i:2408741 original size:17 final size:17
Alignment explanation
Indices: 2408719--2408751 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2408709 AATATAATTA
2408719 TTAAATATAAAA-AAATC
1 TTAAAT-TAAAATAAATC
2408736 TTAAATTAAAATAAAT
1 TTAAATTAAAATAAAT
2408752 ATTTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAATTAAAATAAATC
Found at i:2412150 original size:21 final size:23
Alignment explanation
Indices: 2412125--2412170 Score: 78
Period size: 21 Copynumber: 2.1 Consensus size: 23
2412115 ATAAATATTT
2412125 AAGAGATAAATTATT-TTT-TAA
1 AAGAGATAAATTATTCTTTGTAA
2412146 AAGAGATAAATTATTCTTTGTAA
1 AAGAGATAAATTATTCTTTGTAA
2412169 AA
1 AA
2412171 TTTTAGGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 15 0.65
22 3 0.13
23 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (23 bp):
AAGAGATAAATTATTCTTTGTAA
Found at i:2414378 original size:12 final size:12
Alignment explanation
Indices: 2414361--2414399 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2414351 TATTAGTACC
2414361 ATTAAAATTTAA
1 ATTAAAATTTAA
*
2414373 ATTAAAATTCAGA
1 ATTAAAATTTA-A
2414386 ATTAAAATTTAA
1 ATTAAAATTTAA
2414398 AT
1 AT
2414400 ATTTAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (12 bp):
ATTAAAATTTAA
Found at i:2416287 original size:14 final size:14
Alignment explanation
Indices: 2416268--2416313 Score: 67
Period size: 14 Copynumber: 3.2 Consensus size: 14
2416258 AAGTAAATAT
2416268 AATATAAATTATTA
1 AATATAAATTATTA
2416282 AATATATAATT-TTA
1 AATATA-AATTATTA
2416296 AATATAAATATATTA
1 AATATAAAT-TATTA
2416311 AAT
1 AAT
2416314 GTAATTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.10
14 16 0.55
15 10 0.34
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATAAATTATTA
Found at i:2416290 original size:16 final size:16
Alignment explanation
Indices: 2416269--2416313 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
2416259 AGTAAATATA
2416269 ATATAAATTATTAAAT
1 ATATAAATTATTAAAT
2416285 ATAT-AATT-TT-AA-
1 ATATAAATTATTAAAT
2416297 ATATAAATATATTAAAT
1 ATATAAAT-TATTAAAT
2416314 GTAATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
12 4 0.17
13 5 0.21
14 3 0.12
15 6 0.25
16 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATAAATTATTAAAT
Found at i:2416290 original size:21 final size:20
Alignment explanation
Indices: 2416264--2416308 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2416254 ATCAAAGTAA
2416264 ATATAA-TATAAATTATTAAAT
1 ATATAATTATAAA-TA-TAAAT
*
2416285 ATATAATTTTAAATATAAAT
1 ATATAATTATAAATATAAAT
2416305 ATAT
1 ATAT
2416309 TAAATGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 8 0.36
22 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATAATTATAAATATAAAT
Found at i:2417267 original size:17 final size:17
Alignment explanation
Indices: 2417233--2417280 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
2417223 TAAATATTAC
*
2417233 ATATTTA-ATATATATA
1 ATATTTATATATTTATA
*
2417249 ATATTTATATATTTTTA
1 ATATTTATATATTTATA
*
2417266 ATATATATATATTTA
1 ATATTTATATATTTA
2417281 ATATTAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTTATATATTTATA
Found at i:2417272 original size:26 final size:24
Alignment explanation
Indices: 2417236--2417285 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 24
2417226 ATATTACATA
2417236 TTTAATATATATAATATTTATATATT
1 TTTAATATATAT-ATATTTA-ATATT
2417262 TTTAATATATATATATTTAATATT
1 TTTAATATATATATATTTAATATT
2417286 AAATACATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.21
25 7 0.29
26 12 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTAATATATATATATTTAATATT
Found at i:2417316 original size:15 final size:15
Alignment explanation
Indices: 2417233--2417316 Score: 81
Period size: 15 Copynumber: 5.8 Consensus size: 15
2417223 TAAATATTAC
2417233 ATATTTAATATATATA
1 ATATTTAATATATA-A
2417249 ATATTT-ATATAT--
1 ATATTTAATATATAA
*
2417261 -T-TTTAATATATAT
1 ATATTTAATATATAA
2417274 ATATTTAATAT-TAA
1 ATATTTAATATATAA
*
2417288 ATACATTTAATATATAC
1 AT--ATTTAATATATAA
2417305 ATATTTAATATA
1 ATATTTAATATA
2417317 AACACAAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 17
0.75 0.03 0.22
Matches are distributed among these distances:
10 3 0.05
11 7 0.12
14 5 0.09
15 24 0.41
16 15 0.26
17 4 0.07
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTTAATATATAA
Found at i:2426003 original size:25 final size:26
Alignment explanation
Indices: 2425940--2426005 Score: 64
Period size: 28 Copynumber: 2.5 Consensus size: 26
2425930 AAATTTAAAA
* * *
2425940 TTTAAATT-TATTAAATAATATTTTT
1 TTTAAATTAAATTAAATAAAATTATT
2425965 TTTAATTATATAAATT-AATAAAATTATT
1 TTTAA--AT-TAAATTAAATAAAATTATT
2425993 TTTAAATTAAATT
1 TTTAAATTAAATT
2426006 TTGCATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
25 11 0.32
26 2 0.06
27 2 0.06
28 16 0.47
29 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTAAATTAAATTAAATAAAATTATT
Found at i:2426968 original size:3 final size:3
Alignment explanation
Indices: 2426960--2426993 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2426950 TTAAATAATT
2426960 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2426994 AAAATTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2439981 original size:16 final size:17
Alignment explanation
Indices: 2439952--2439985 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2439942 AGGGAAAAGT
2439952 AAAATAAAATAAAATTA
1 AAAATAAAATAAAATTA
*
2439969 AAAATTAAA-AAAATTA
1 AAAATAAAATAAAATTA
2439985 A
1 A
2439986 GAAAAAGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATAAAATAAAATTA
Found at i:2440582 original size:20 final size:20
Alignment explanation
Indices: 2440543--2440582 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2440533 AGTTTGATAA
* **
2440543 TAATATTTTATTAATTAAAT
1 TAATATTTAATTAAAAAAAT
2440563 TAATATTTAATTAAAAAAAT
1 TAATATTTAATTAAAAAAAT
2440583 ATATGATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATATTTAATTAAAAAAAT
Found at i:2440711 original size:24 final size:24
Alignment explanation
Indices: 2440664--2440711 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2440654 TATATATAAA
* *
2440664 AATATAAATATTCATAAATTAAAT
1 AATAAAAATATTCATAAATCAAAT
* *
2440688 AATAAAAATATTTATAGATCAAAT
1 AATAAAAATATTCATAAATCAAAT
2440712 TAGATTATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
AATAAAAATATTCATAAATCAAAT
Found at i:2443788 original size:2 final size:2
Alignment explanation
Indices: 2443781--2443805 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2443771 TACAACAATA
2443781 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
2443806 ACTTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2444778 original size:92 final size:92
Alignment explanation
Indices: 2444651--2444846 Score: 268
Period size: 92 Copynumber: 2.1 Consensus size: 92
2444641 CATATCGGTA
*
2444651 AGTATTATTTGTTTCGATTGATAGCTATTAATTAATATAAGATTTAAAATTTTTTTTATTAT-TT
1 AGTATTATTTGTTTCGATTGATAGCTATTAATTAATATAAGATTT-AAATTTTTTATATTATGTT
* *
2444715 CATTTATTTAATTTTTTAATTACCTTCT
65 CACTTATTTAATTTTTTAATTAACTTCT
* * * ** *
2444743 AGTATTATTTGTTTGGATTGATAGTTATTAGTTAATATAAGATTTTGATTTTTTATATTATGTTT
1 AGTATTATTTGTTTCGATTGATAGCTATTAATTAATATAAGATTTAAATTTTTTATATTATGTTC
*
2444808 ACTTATTTAATTTTTTAATTAACTTTT
66 ACTTATTTAATTTTTTAATTAACTTCT
* *
2444835 ATTATTTTTTGT
1 AGTATTATTTGT
2444847 CATATATATT
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
91 13 0.14
92 78 0.86
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.59
Consensus pattern (92 bp):
AGTATTATTTGTTTCGATTGATAGCTATTAATTAATATAAGATTTAAATTTTTTATATTATGTTC
ACTTATTTAATTTTTTAATTAACTTCT
Found at i:2446957 original size:2 final size:2
Alignment explanation
Indices: 2446946--2446984 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2446936 AGATAACAGA
2446946 AT AT -T 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
2446985 GCAGAGATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2451056 original size:2 final size:2
Alignment explanation
Indices: 2451049--2451080 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2451039 AGGCAATCAA
2451049 AG 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
2451081 TAACTTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2452155 original size:8 final size:9
Alignment explanation
Indices: 2452095--2452218 Score: 53
Period size: 9 Copynumber: 14.0 Consensus size: 9
2452085 ATTAGCATTT
2452095 AATTAATTA
1 AATTAATTA
*
2452104 AATTAATTT
1 AATTAATTA
*
2452113 TATT--TTA
1 AATTAATTA
*
2452120 AATT-TTTAA
1 AATTAATT-A
*
2452129 TAATTAAATA
1 -AATTAATTA
2452139 AATTAATTA
1 AATTAATTA
2452148 AATT-ATTA
1 AATTAATTA
*
2452156 AAAT-A-TA
1 AATTAATTA
* *
2452163 TAAGTAATAA
1 -AATTAATTA
*
2452173 AAATAATTA
1 AATTAATTA
*
2452182 AATTAAATAA
1 AATT-AATTA
* *
2452192 AATCAATCA
1 AATTAATTA
* *
2452201 ATTTAATTT
1 AATTAATTA
2452210 AATTAATTA
1 AATTAATTA
2452219 TAAATTTGAT
Statistics
Matches: 85, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
7 7 0.08
8 13 0.15
9 51 0.60
10 13 0.15
11 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (9 bp):
AATTAATTA
Found at i:2452258 original size:23 final size:23
Alignment explanation
Indices: 2452226--2452303 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
2452216 TTATAAATTT
*
2452226 GATAAGATAATTGAGTGATAATA
1 GATAATATAATTGAGTGATAATA
*
2452249 GATATTATAATT-A-T-A-AATTTA
1 GATAATATAATTGAGTGATAA--TA
*
2452270 G-TAAGATAATTGAGTGATAATA
1 GATAATATAATTGAGTGATAATA
2452292 GATAATATAATT
1 GATAATATAATT
2452304 ATAAAAAAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
19 2 0.05
20 9 0.21
21 5 0.12
22 5 0.12
23 20 0.47
24 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.37
Consensus pattern (23 bp):
GATAATATAATTGAGTGATAATA
Found at i:2452261 original size:43 final size:43
Alignment explanation
Indices: 2452209--2452308 Score: 168
Period size: 43 Copynumber: 2.3 Consensus size: 43
2452199 CAATTTAATT
2452209 TAAT-TAATTATAAATTT-GATAAGATAATTGAGTGATAATAGA
1 TAATATAATTATAAATTTAG-TAAGATAATTGAGTGATAATAGA
*
2452251 TATTATAATTATAAATTTAGTAAGATAATTGAGTGATAATAGA
1 TAATATAATTATAAATTTAGTAAGATAATTGAGTGATAATAGA
2452294 TAATATAATTATAAA
1 TAATATAATTATAAA
2452309 AAAGATAGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
42 3 0.06
43 50 0.93
44 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (43 bp):
TAATATAATTATAAATTTAGTAAGATAATTGAGTGATAATAGA
Found at i:2455678 original size:14 final size:15
Alignment explanation
Indices: 2455651--2455679 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2455641 GATAAAAATT
2455651 AATAAAAACAAGAAA
1 AATAAAAACAAGAAA
2455666 AATAAAAAC-AGAAA
1 AATAAAAACAAGAAA
2455680 TGTGTTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (15 bp):
AATAAAAACAAGAAA
Found at i:2461774 original size:131 final size:131
Alignment explanation
Indices: 2461510--2461754 Score: 318
Period size: 131 Copynumber: 1.9 Consensus size: 131
2461500 ATTATTTATG
* * * * * *
2461510 TAACATGGCATATTGGCGAAAAAATAAATTGCACAATCTCTCCACGACATTTAGATTCTTTAAGA
1 TAACATGGCACATTGGCGAAAAAAGAAATTGCACAACCTCTCCACAACATTTAGACTCTTCAAGA
* *
2461575 CAGTAACACCAAAATCCAAATTTAGAAACTAAATTCAAGACCAGAAAAAAAACACTCAAAATCAA
66 CAGTAACAACAAAATCCAAATTTAGAAACTAAATTCAAGACCACAAAAAAAACACT-AAAATCAA
2461640 AC
130 AC
* * * *
2461642 TAACATGGCACGTTGGC-AAAAAAGAAATTGCATAACCTCTCCATAACATTTAGACTCTTCGAGA
1 TAACATGGCACATTGGCGAAAAAAGAAATTGCACAACCTCTCCACAACATTTAGACTCTTCAAGA
*
2461706 CATTAACAACAAAATCCAAATTTAAGAAA-TAAA-TCATA-ACCACAAAAAA
66 CAGTAACAACAAAATCCAAATTT-AGAAACTAAATTCA-AGACCACAAAAAA
2461755 CTTGATACTT
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
130 13 0.13
131 65 0.66
132 20 0.20
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.22
Consensus pattern (131 bp):
TAACATGGCACATTGGCGAAAAAAGAAATTGCACAACCTCTCCACAACATTTAGACTCTTCAAGA
CAGTAACAACAAAATCCAAATTTAGAAACTAAATTCAAGACCACAAAAAAAACACTAAAATCAAA
C
Found at i:2463769 original size:1 final size:1
Alignment explanation
Indices: 2463763--2463790 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
2463753 GAGACTTCAA
2463763 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
2463791 AAAAGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2470322 original size:3 final size:3
Alignment explanation
Indices: 2470314--2470344 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2470304 TGGTTGAAGG
*
2470314 TTA TTA TTA TTA TTA TTA TTA TTA TTC TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2470345 ACACACTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2475913 original size:12 final size:12
Alignment explanation
Indices: 2475893--2475928 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2475883 AAAAGGAAAC
*
2475893 ATATATATATAT
1 ATATGTATATAT
*
2475905 ATATGTATATGT
1 ATATGTATATAT
2475917 ATATGTATATAT
1 ATATGTATATAT
2475929 TTCTTTAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:2476515 original size:3 final size:3
Alignment explanation
Indices: 2476507--2476531 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2476497 AACATAAAGC
2476507 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
2476532 GAGGAGGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2479039 original size:2 final size:2
Alignment explanation
Indices: 2479032--2479065 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2479022 ACATACATGC
* *
2479032 AT AT AT AT AT AT AT AT GT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2479066 GTTTATATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2479047 original size:10 final size:10
Alignment explanation
Indices: 2479032--2479065 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
2479022 ACATACATGC
*
2479032 ATATATATAT
1 ATATATGTAT
2479042 ATATATGTAT
1 ATATATGTAT
2479052 ATATATGTAT
1 ATATATGTAT
2479062 ATAT
1 ATAT
2479066 GTTTATATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
ATATATGTAT
Found at i:2479057 original size:20 final size:20
Alignment explanation
Indices: 2479039--2479149 Score: 95
Period size: 20 Copynumber: 5.6 Consensus size: 20
2479029 TGCATATATA
* *
2479039 TATATATATGTATATATATG
1 TATATATATATATATGTATG
* *
2479059 TATATATGTTTATATGCT-TG
1 TATATATATATATATG-TATG
*
2479079 TATA-ATATA-AAACTGTCATG
1 TATATATATATATA-TGT-ATG
2479099 TATATATATATATATGTATG
1 TATATATATATATATGTATG
* * *
2479119 TATGTATGTATGTATGTATG
1 TATATATATATATATGTATG
2479139 TATA-ATATATA
1 TATATATATATA
2479150 ACTATTGTAT
Statistics
Matches: 72, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
18 3 0.04
19 10 0.14
20 48 0.67
21 9 0.12
22 2 0.03
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.48
Consensus pattern (20 bp):
TATATATATATATATGTATG
Found at i:2479108 original size:4 final size:4
Alignment explanation
Indices: 2479096--2479141 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
2479086 TAAAACTGTC
* * *
2479096 ATGT ATAT ATAT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
2479142 AATATATAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:2479141 original size:60 final size:60
Alignment explanation
Indices: 2479039--2479152 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
2479029 TGCATATATA
* *
2479039 TATATATATGTATATATATGTATATATGTTTATATGCTTGTATAATATAAAACTGTCATG
1 TATATATATATATATATATGTATATATGTATATATGCTTGTATAATATAAAACTGTCATG
* * * *
2479099 TATATATATATATATGTATGTATGTATGTATGTATG-TATGTATAATATATAACT
1 TATATATATATATATATATGTATATATGTATATATGCT-TGTATAATATAAAACT
2479153 ATTGTATTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 1 0.02
60 46 0.98
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (60 bp):
TATATATATATATATATATGTATATATGTATATATGCTTGTATAATATAAAACTGTCATG
Found at i:2480238 original size:2 final size:2
Alignment explanation
Indices: 2480231--2480264 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2480221 ATACTAACTG
2480231 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2480265 ATATGTAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2482634 original size:28 final size:28
Alignment explanation
Indices: 2482577--2482638 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
2482567 AAAATAATGG
*
2482577 TTTTTTTTTCAAATAAAGAAGCGATGAGT
1 TTTTTTTTTCAAATAAAGAA-CGATCAGT
2482606 TTTTTTTTTCAAATAAAAGATA-GA-CAGT
1 TTTTTTTTTCAAAT-AAAGA-ACGATCAGT
2482634 TTTTT
1 TTTTT
2482639 CAAATTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.27
29 16 0.53
30 5 0.17
31 1 0.03
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (28 bp):
TTTTTTTTTCAAATAAAGAACGATCAGT
Found at i:2483515 original size:3 final size:3
Alignment explanation
Indices: 2483507--2483548 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2483497 TTCTTGTTTG
2483507 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2483549 CTTGTGTCCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2485509 original size:11 final size:11
Alignment explanation
Indices: 2485493--2485517 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2485483 TAATTTTAGC
2485493 AAAAAAGAAAA
1 AAAAAAGAAAA
2485504 AAAAAAGAAAA
1 AAAAAAGAAAA
2485515 AAA
1 AAA
2485518 GAGCGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:2486079 original size:22 final size:22
Alignment explanation
Indices: 2486037--2486081 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2486027 AGAAAAATAA
* *
2486037 TAAATTAAATATTTAAAAATTT
1 TAAATTAAATAATAAAAAATTT
2486059 TAAATT-AATAATAAAATAATTT
1 TAAATTAAATAATAAAA-AATTT
2486081 T
1 T
2486082 TAAACAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAATTAAATAATAAAAAATTT
Found at i:2487714 original size:2 final size:2
Alignment explanation
Indices: 2487707--2487732 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2487697 TACTTTGATA
2487707 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
2487733 TAAATATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2487779 original size:5 final size:5
Alignment explanation
Indices: 2487769--2487799 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
2487759 TACAAACACA
2487769 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
2487800 TTGTATGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:2490602 original size:18 final size:18
Alignment explanation
Indices: 2490558--2490607 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
2490548 TCATTAAAAT
2490558 ATTAA-TAA-TATATAAA
1 ATTAATTAATTATATAAA
*
2490574 ATT-ATAAAATTATATAAA
1 ATTAAT-TAATTATATAAA
*
2490592 ATTAATTAATTTTATA
1 ATTAATTAATTATATA
2490608 TTAATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
15 1 0.04
16 3 0.11
17 2 0.07
18 19 0.70
19 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTAATTAATTATATAAA
Found at i:2490859 original size:18 final size:18
Alignment explanation
Indices: 2490836--2490870 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2490826 CATTACCTGA
2490836 AAATATATATAGATATAC
1 AAATATATATAGATATAC
*
2490854 AAATATATATATATATA
1 AAATATATATAGATATA
2490871 TATGATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (18 bp):
AAATATATATAGATATAC
Found at i:2490969 original size:16 final size:17
Alignment explanation
Indices: 2490954--2491048 Score: 56
Period size: 17 Copynumber: 5.5 Consensus size: 17
2490944 ATTTTAAAAT
2490954 TTATATAAAA-A-TAAA
1 TTATATAAAATATTAAA
2490969 TTAT-TAAAATATTAAAA
1 TTATATAAAATATT-AAA
* *
2490986 TTATATAAATTATAAAA
1 TTATATAAAATATTAAA
* *
2491003 TAATTTAAATATAATTATAA
1 TTATATAAA-AT-ATTA-AA
*
2491023 -TATAATATAATATTTAAA
1 TTAT-ATAAAATA-TTAAA
2491041 TTAT-TAAA
1 TTATATAAA
2491049 TTTATGTATA
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
14 5 0.08
15 5 0.08
16 1 0.02
17 20 0.33
18 11 0.18
19 13 0.22
20 5 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTATATAAAATATTAAA
Found at i:2490986 original size:17 final size:17
Alignment explanation
Indices: 2490966--2491048 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 17
2490956 ATATAAAAAT
2490966 AAATTATTAAAATATTA
1 AAATTATTAAAATATTA
*
2490983 AAATTATATAAATTA-TA
1 AAATTAT-TAAAATATTA
*
2491000 AAATAATTTAAATATAATTA
1 AAATTA-TTAAA-AT-ATTA
* * * *
2491020 TAATATAATATAATATTT
1 AAAT-TATTAAAATATTA
2491038 AAATTATTAAA
1 AAATTATTAAA
2491049 TTTATGTATA
Statistics
Matches: 49, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
17 23 0.47
18 14 0.29
19 3 0.06
20 8 0.16
21 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTATTAAAATATTA
Found at i:2491046 original size:27 final size:26
Alignment explanation
Indices: 2490964--2491046 Score: 78
Period size: 29 Copynumber: 3.0 Consensus size: 26
2490954 TTATATAAAA
* *
2490964 ATAAATTATTAAAATATTAAAATTA-T
1 ATAAA-TAATAAAATATTTAAATTATT
*
2490990 ATAAATTATAAAATAATTTAAATATAATT
1 ATAAATAATAAAAT-ATTTAAAT-T-ATT
*
2491019 ATAATATAATATAATATTTAAATTATT
1 ATAA-ATAATAAAATATTTAAATTATT
2491046 A
1 A
2491047 AATTTATGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
25 7 0.15
26 12 0.26
27 5 0.11
28 2 0.04
29 13 0.28
30 8 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAAATAATAAAATATTTAAATTATT
Found at i:2491698 original size:22 final size:22
Alignment explanation
Indices: 2491670--2491761 Score: 62
Period size: 22 Copynumber: 3.9 Consensus size: 22
2491660 TTTTACTTTC
2491670 ATTTTATTATTTAAAAAATATT
1 ATTTTATTATTTAAAAAATATT
* *
2491692 ATTTTA-TA-TTAATAATTATAT
1 ATTTTATTATTTAAAAAATAT-T
2491713 ATTTTATAATTAATTTAAATAAAAATATT
1 A-TTT-T-ATT-ATTT--A-AAAAATATT
* *
2491742 ATTTTATTAATTAAATAATA
1 ATTTTATTATTTAAAAAATA
2491762 ATTTAATATT
Statistics
Matches: 54, Mismatches: 6, Indels: 20
0.68 0.08 0.25
Matches are distributed among these distances:
20 9 0.17
21 4 0.07
22 15 0.28
23 2 0.04
24 1 0.02
25 4 0.07
26 4 0.07
27 3 0.06
28 3 0.06
29 3 0.06
30 6 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTTATTATTTAAAAAATATT
Found at i:2491740 original size:26 final size:25
Alignment explanation
Indices: 2491711--2491759 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
2491701 TAATAATTAT
2491711 ATATT-TTATAATTAATTTAAATAAAA
1 ATATTATT-TAATTAA-TTAAATAAAA
*
2491737 ATATTATTTTATTAATTAAATAA
1 ATATTATTTAATTAATTAAATAA
2491760 TAATTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 8 0.38
26 11 0.52
27 2 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATTATTTAATTAATTAAATAAAA
Found at i:2491778 original size:50 final size:50
Alignment explanation
Indices: 2491683--2491780 Score: 121
Period size: 50 Copynumber: 2.0 Consensus size: 50
2491673 TTATTATTTA
* *
2491683 AAAAATATTATTTTATATTAATAATTATATATTTTATAATTAATTTAAAT
1 AAAAATATTATTTTATATTAATAATAATATATTTAATAATTAATTTAAAT
*
2491733 AAAAATATTA-TTT-TATTAATTAAATAATA-ATTTAATATTTAAATTTAA
1 AAAAATATTATTTTATATTAA-T-AATAATATATTTAATAATT-AATTTAA
2491781 TAATTATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
48 6 0.14
49 13 0.31
50 23 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (50 bp):
AAAAATATTATTTTATATTAATAATAATATATTTAATAATTAATTTAAAT
Found at i:2491782 original size:24 final size:24
Alignment explanation
Indices: 2491750--2491800 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
2491740 TTATTTTATT
2491750 AATTAAATAATAATTT-AATATTTA
1 AATTAAATAATAATTTAAAT-TTTA
* *
2491774 AATTTAATAATTATTTAAATTTTA
1 AATTAAATAATAATTTAAATTTTA
2491798 AAT
1 AAT
2491801 AGATTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTAAATAATAATTTAAATTTTA
Found at i:2492483 original size:17 final size:17
Alignment explanation
Indices: 2492458--2492492 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2492448 CCCGCCCCCA
2492458 TCAAATTTTAATTTTAT
1 TCAAATTTTAATTTTAT
*
2492475 TCAACTTTTAATTTTAT
1 TCAAATTTTAATTTTAT
2492492 T
1 T
2492493 TTAATCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (17 bp):
TCAAATTTTAATTTTAT
Found at i:2493404 original size:2 final size:2
Alignment explanation
Indices: 2493397--2493434 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2493387 ACTATACAGC
2493397 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
2493435 CACCCATTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2494280 original size:2 final size:2
Alignment explanation
Indices: 2494267--2494300 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2494257 CAGAGATAAT
*
2494267 GA GA GT GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2494301 TGGGAAAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
GA
Found at i:2499551 original size:18 final size:18
Alignment explanation
Indices: 2499526--2499574 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
2499516 AATTAATTTA
2499526 AAAT-TTATATAATTATT
1 AAATATTATATAATTATT
*
2499543 AAATATTAT-TTATATATT
1 AAATATTATATAAT-TATT
2499561 -AATATT-TATAATTA
1 AAATATTATATAATTA
2499575 AATTTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 3 0.11
17 16 0.59
18 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATATTATATAATTATT
Found at i:2499579 original size:12 final size:14
Alignment explanation
Indices: 2499549--2499580 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2499539 TATTAAATAT
2499549 TATTTATATATTAA
1 TATTTATATATTAA
2499563 TATTTATA-ATTAA
1 TATTTATATATTAA
2499576 -ATTTA
1 TATTTA
2499581 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.28
13 5 0.28
14 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTTATATATTAA
Found at i:2499616 original size:21 final size:20
Alignment explanation
Indices: 2499572--2499621 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
2499562 ATATTTATAA
*
2499572 TTAAATTTAAATAAAAAAAAT
1 TTAAA-TTATATAAAAAAAAT
* *
2499593 TTATATTATATAAATAATAAT
1 TTAAATTATATAAA-AAAAAT
2499614 TTAAATTA
1 TTAAATTA
2499622 AATTAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAATTATATAAAAAAAAT
Found at i:2499623 original size:47 final size:45
Alignment explanation
Indices: 2499543--2499644 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 45
2499533 TATAATTATT
*
2499543 AAATATTATTTATATATTAATATTTATAATTAAATTTAAA-TAAAAA
1 AAAT-TTATTTATATAATAATATTTATAATTAAA-TTAAATTAAAAA
**
2499589 AAATTTATATTATATAAATAATAATTTA-AATTAAATTAAATTTTAAA
1 AAATTTAT-TTATAT-AATAAT-ATTTATAATTAAATTAAATTAAAAA
2499636 AAATTTATT
1 AAATTTATT
2499645 AAAATCTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
45 4 0.08
46 16 0.33
47 24 0.49
48 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (45 bp):
AAATTTATTTATATAATAATATTTATAATTAAATTAAATTAAAAA
Found at i:2500610 original size:23 final size:23
Alignment explanation
Indices: 2500584--2500667 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
2500574 TATTTATAAA
2500584 TATTTTTTTTATATTTTTATATT
1 TATTTTTTTTATATTTTTATATT
*
2500607 TATTTTATTTTTTA-TTTTA-ATT
1 TATTTT-TTTTATATTTTTATATT
* **
2500629 AATTTTTAATATTATTTTTATA-T
1 TATTTTTTTTA-TATTTTTATATT
**
2500652 TATTTTTCGTATATTT
1 TATTTTTTTTATATTT
2500668 AAAGTATTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
21 2 0.04
22 15 0.31
23 25 0.51
24 7 0.14
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.73
Consensus pattern (23 bp):
TATTTTTTTTATATTTTTATATT
Found at i:2500617 original size:17 final size:17
Alignment explanation
Indices: 2500595--2500646 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2500585 ATTTTTTTTA
2500595 TATTTTTATATTTATTT
1 TATTTTTATATTTATTT
*
2500612 TATTTTT-TATTTTAATT
1 TATTTTTATA-TTTATTT
*
2500629 AATTTTTA-ATATTATTT
1 TATTTTTATAT-TTATTT
2500646 T
1 T
2500647 TATATTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
16 3 0.11
17 25 0.89
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TATTTTTATATTTATTT
Found at i:2500647 original size:13 final size:11
Alignment explanation
Indices: 2500583--2500658 Score: 63
Period size: 11 Copynumber: 7.0 Consensus size: 11
2500573 ATATTTATAA
2500583 ATATT-TTTTT
1 ATATTATTTTT
2500593 -TA-TATTTTT
1 ATATTATTTTT
2500602 ATATT-TATTTT
1 ATATTAT-TTTT
* *
2500613 ATTTTTTATTTT
1 ATATTAT-TTTT
2500625 A-ATTAATTTTT
1 ATATT-ATTTTT
2500636 AATATTATTTTT
1 -ATATTATTTTT
2500648 ATATTATTTTT
1 ATATTATTTTT
2500659 CGTATATTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
8 1 0.02
9 7 0.13
10 3 0.05
11 26 0.47
12 15 0.27
13 3 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:2500788 original size:10 final size:12
Alignment explanation
Indices: 2500750--2500793 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
2500740 TTAGTATCAT
*
2500750 TTTTATATTATT
1 TTTTATATTATA
2500762 TTTTATATTATA
1 TTTTATATTATA
2500774 TTTTA-ATTA-A
1 TTTTATATTATA
2500784 TTTTAT-TTAT
1 TTTTATATTAT
2500794 GTTGTGTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 9 0.31
11 4 0.14
12 16 0.55
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTATATTATA
Found at i:2501376 original size:11 final size:11
Alignment explanation
Indices: 2501360--2501452 Score: 56
Period size: 11 Copynumber: 8.8 Consensus size: 11
2501350 TACATTTTGC
2501360 ATTTATATTAT
1 ATTTATATTAT
2501371 ATTTATATTAT
1 ATTTATATTAT
* *
2501382 TTTTGTA-TAT
1 ATTTATATTAT
*
2501392 -TATTATATTTT
1 AT-TTATATTAT
*
2501403 AATTAT-TT-T
1 ATTTATATTAT
*
2501412 -TTTATATTGT
1 ATTTATATTAT
*
2501422 ATTTATATTGT
1 ATTTATATTAT
2501433 ATCTTA-ATTCAT
1 AT-TTATATT-AT
2501445 -TTTATATT
1 ATTTATATT
2501453 TTCATAGTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
8 4 0.06
9 4 0.06
10 13 0.20
11 41 0.62
12 4 0.06
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:2501383 original size:27 final size:26
Alignment explanation
Indices: 2501353--2501430 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 26
2501343 ATTATGATAC
2501353 ATTTTGCATTTATATTATATTTATATT
1 ATTTTG-ATTTATATTATATTTATATT
*
2501380 ATTTTTG-TATATTATTATATTT-TAATT
1 A-TTTTGATTTA-TATTATATTTAT-ATT
*
2501407 ATTTT--TTTATATTGTATTTATATT
1 ATTTTGATTTATATTATATTTATATT
2501431 GTATCTTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
24 12 0.27
25 4 0.09
26 8 0.18
27 15 0.34
28 5 0.11
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (26 bp):
ATTTTGATTTATATTATATTTATATT
Found at i:2501506 original size:17 final size:18
Alignment explanation
Indices: 2501480--2501521 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
2501470 TTAACTTCAA
*
2501480 ATTT-AATTACATAAAAT
1 ATTTAAATTACAAAAAAT
2501497 -TTTAAATTACAAAAAAT
1 ATTTAAATTACAAAAAAT
2501514 ATTTAAAT
1 ATTTAAAT
2501522 AAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 12 0.55
18 7 0.32
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTTAAATTACAAAAAAT
Found at i:2506148 original size:39 final size:39
Alignment explanation
Indices: 2506088--2506193 Score: 149
Period size: 39 Copynumber: 2.7 Consensus size: 39
2506078 CCTGGTCATT
* * *
2506088 CTGAAAGAGAAATCACGTTATCTGAGCTAAGGAGGGCTC
1 CTGAAAGAGAAGTCACATTATCTGAGCTAAGGAGGCCTC
* *
2506127 CTGAAAGAGAAGTTACATTATCTGAACTAAGGAGGCCTC
1 CTGAAAGAGAAGTCACATTATCTGAGCTAAGGAGGCCTC
* *
2506166 CGGAAAGAGAAGTCACATTATCTAAGCT
1 CTGAAAGAGAAGTCACATTATCTGAGCT
2506194 TCGGAAAGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.22
Consensus pattern (39 bp):
CTGAAAGAGAAGTCACATTATCTGAGCTAAGGAGGCCTC
Found at i:2513616 original size:20 final size:22
Alignment explanation
Indices: 2513572--2513620 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
2513562 TGAATTTTGA
2513572 ATTTAAAAATATAACTTAATAT
1 ATTTAAAAATATAACTTAATAT
* *
2513594 ATTTAATAA-ATAA-TTAATTT
1 ATTTAAAAATATAACTTAATAT
2513614 A-TTAAAA
1 ATTTAAAA
2513621 TTTTAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.21
20 7 0.29
21 4 0.17
22 8 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTAAAAATATAACTTAATAT
Found at i:2513658 original size:17 final size:18
Alignment explanation
Indices: 2513633--2513667 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2513623 TTAAAATAAA
*
2513633 TATTTTAAATTTA-ATTT
1 TATTATAAATTTATATTT
2513650 TATTATAAATTTATATTT
1 TATTATAAATTTATATTT
2513668 AAAAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTATAAATTTATATTT
Found at i:2514108 original size:30 final size:29
Alignment explanation
Indices: 2514074--2514161 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 29
2514064 TGTGTAGTTA
2514074 ATTATTATTTATATATAATTATATAAAAAT
1 ATTATTATTTATATATAATT-TATAAAAAT
2514104 ATTATATATTTATATA-AATTT-T-AAAAT
1 ATTAT-TATTTATATATAATTTATAAAAAT
* *
2514131 ATTACTAATTTATTTTATAATTTA-AAAAAT
1 ATTA-TTATTTA-TATATAATTTATAAAAAT
2514161 A
1 A
2514162 AATTTAATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
27 14 0.28
28 5 0.10
29 6 0.12
30 15 0.30
31 10 0.20
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTATTATTTATATATAATTTATAAAAAT
Found at i:2514156 original size:28 final size:27
Alignment explanation
Indices: 2514074--2514143 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 27
2514064 TGTGTAGTTA
2514074 ATTAT-TATTTATATATAATTATATAAAAAT
1 ATTATATATTTATATA-AATT-T-T-AAAAT
2514104 ATTATATATTTATATAAATTTTAAAAT
1 ATTATATATTTATATAAATTTTAAAAT
2514131 ATTACTA-ATTTAT
1 ATTA-TATATTTAT
2514144 TTTATAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
27 15 0.39
28 3 0.08
29 1 0.03
30 9 0.24
31 10 0.26
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTATATATTTATATAAATTTTAAAAT
Found at i:2514175 original size:22 final size:23
Alignment explanation
Indices: 2514148--2514198 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
2514138 ATTTATTTTA
2514148 TAATTTAAAAAATAAATTTA-AT
1 TAATTTAAAAAATAAATTTATAT
* *
2514170 TAATTTATAAATTAAATTTATAT
1 TAATTTAAAAAATAAATTTATAT
2514193 TAATTT
1 TAATTT
2514199 TATTTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATTTAAAAAATAAATTTATAT
Found at i:2514222 original size:24 final size:23
Alignment explanation
Indices: 2514195--2514243 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
2514185 ATTTATATTA
*
2514195 ATTTTAT-TTTATTATATATTAATT
1 ATTTTATATTTA-TACATA-TAATT
2514219 ATTTTATATTTATACATATAATT
1 ATTTTATATTTATACATATAATT
2514242 AT
1 AT
2514244 AATAAGAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 12 0.52
25 4 0.17
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTATATTTATACATATAATT
Found at i:2514508 original size:4 final size:4
Alignment explanation
Indices: 2514499--2514525 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2514489 TTTCGTGTAA
2514499 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
2514526 AATAAAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2514954 original size:2 final size:2
Alignment explanation
Indices: 2514949--2514977 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2514939 GAGATTTGAC
2514949 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2514978 AACATGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2517003 original size:10 final size:10
Alignment explanation
Indices: 2516988--2517032 Score: 63
Period size: 10 Copynumber: 4.3 Consensus size: 10
2516978 ATCACACCTG
2516988 TATATACATA
1 TATATACATA
2516998 TATATACATATA
1 TATATAC--ATA
2517010 TATATACATA
1 TATATACATA
*
2517020 TATATATATA
1 TATATACATA
2517030 TAT
1 TAT
2517033 GTATAGGCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 22 0.69
12 10 0.31
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (10 bp):
TATATACATA
Found at i:2517037 original size:6 final size:6
Alignment explanation
Indices: 2516988--2517037 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
2516978 ATCACACCTG
* * * *
2516988 TATATA CATATA TATACA TATATA TATACA TATATA TATATA TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
2517036 TA
1 TA
2517038 GGCTGTTCTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (6 bp):
TATATA
Found at i:2519492 original size:19 final size:19
Alignment explanation
Indices: 2519470--2519533 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
2519460 ATAATATAAA
2519470 TATATAAATATTTAAATTT
1 TATATAAATATTTAAATTT
* * *
2519489 TATAT-GATACATTAAAATT
1 TATATAAATA-TTTAAATTT
2519508 TATATAAAT-TTATAATATTT
1 TATATAAATATT-TAA-ATTT
2519528 TATATA
1 TATATA
2519534 TAATTATATT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
18 4 0.11
19 20 0.57
20 11 0.31
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TATATAAATATTTAAATTT
Found at i:2519540 original size:20 final size:19
Alignment explanation
Indices: 2519458--2519541 Score: 65
Period size: 20 Copynumber: 4.6 Consensus size: 19
2519448 ATAAAAAATA
*
2519458 ATATAA-TATAAA-TATAT
1 ATATAATTATAAATTTTAT
*
2519475 AAAT-ATT-TAAATTTTAT
1 ATATAATTATAAATTTTAT
2519492 ATGATACATTA-AAA-TTTAT
1 AT-ATA-ATTATAAATTTTAT
2519511 ATA-AATTTATAATATTTTAT
1 ATATAA-TTATAA-ATTTTAT
2519531 ATATAATTATA
1 ATATAATTATA
2519542 TTTATAAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 19
0.71 0.04 0.25
Matches are distributed among these distances:
16 6 0.11
17 13 0.25
18 5 0.09
19 8 0.15
20 19 0.36
21 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (19 bp):
ATATAATTATAAATTTTAT
Found at i:2522292 original size:17 final size:18
Alignment explanation
Indices: 2522272--2522314 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2522262 ATTTTTACTT
*
2522272 ATTAAATTTAT-TTATAA
1 ATTAAATTTATATCATAA
2522289 ATTAAA-TTATATCATAA
1 ATTAAATTTATATCATAA
*
2522306 TTTAAATTT
1 ATTAAATTT
2522315 TTTTTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 4 0.18
17 16 0.73
18 2 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTAAATTTATATCATAA
Found at i:2522459 original size:21 final size:22
Alignment explanation
Indices: 2522417--2522460 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2522407 AATTTATAAT
**
2522417 TTAAATAAAATATTTTTTATTA
1 TTAAATAAAATATTTTAAATTA
*
2522439 TTAAATTAAA-ATTTTAAATTA
1 TTAAATAAAATATTTTAAATTA
2522460 T
1 T
2522461 ATTAAATCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAATAAAATATTTTAAATTA
Found at i:2522521 original size:24 final size:23
Alignment explanation
Indices: 2522451--2522522 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 23
2522441 AAATTAAAAT
*
2522451 TTTAAA-TTAT-ATTAAA-TCAA
1 TTTAAATTTATAAATAAATTCAA
*
2522471 TTTAAATTTATAAA-AAATATAATA
1 TTTAAATTTATAAATAAAT-TCA-A
*
2522495 TTTAATTTTTATAAATAAATTCAA
1 TTTAA-ATTTATAAATAAATTCAA
2522519 TTTA
1 TTTA
2522523 TCAAATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 6 0.15
21 7 0.17
22 1 0.02
23 2 0.05
24 11 0.27
25 10 0.24
26 4 0.10
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTAAATTTATAAATAAATTCAA
Found at i:2524645 original size:2 final size:2
Alignment explanation
Indices: 2524638--2524683 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2524628 AGGCTTGATT
2524638 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2524680 TA TA
1 TA TA
2524684 GGTATTTTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2525321 original size:26 final size:24
Alignment explanation
Indices: 2525292--2525371 Score: 81
Period size: 26 Copynumber: 3.2 Consensus size: 24
2525282 GATGGGAGTT
*
2525292 TTTTTTTTTCTCTCTAAACTAAGATA
1 TTTTTTTTT-TCT-TAAAATAAGATA
*
2525318 TTTTAATTTTTTCTTAAAATGAGATA
1 TTTT--TTTTTTCTTAAAATAAGATA
* *
2525344 TTTTTATTTT-TTAAAATAAAATA
1 TTTTTTTTTTCTTAAAATAAGATA
2525367 TTTTT
1 TTTTT
2525372 CGCCATTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
23 16 0.34
24 5 0.11
26 18 0.38
27 3 0.06
28 5 0.11
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTTTTTTTCTTAAAATAAGATA
Found at i:2525367 original size:23 final size:24
Alignment explanation
Indices: 2525326--2525371 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2525316 TATTTTAATT
* *
2525326 TTTTCTTAAAATGAGATATTTTTA
1 TTTTCTTAAAATAAAATATTTTTA
2525350 TTTT-TTAAAATAAAATATTTTT
1 TTTTCTTAAAATAAAATATTTTT
2525372 CGCCATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTCTTAAAATAAAATATTTTTA
Found at i:2527316 original size:545 final size:545
Alignment explanation
Indices: 2526287--2527377 Score: 2182
Period size: 545 Copynumber: 2.0 Consensus size: 545
2526277 GAGCCTCAAA
2526287 AAACGGCTAGCCATCGCCGTTGCTTGAGACTTTTCAGGTCATAATTTATTTATCTGTTTTTTTTT
1 AAACGGCTAGCCATCGCCGTTGCTTGAGACTTTTCAGGTCATAATTTATTTATCTGTTTTTTTTT
2526352 TCCTTTTAATATCAATTAAATGTGCTTTCGGCATTAACGAGGAAAATATTAATTTTTATATAAAT
66 TCCTTTTAATATCAATTAAATGTGCTTTCGGCATTAACGAGGAAAATATTAATTTTTATATAAAT
2526417 TATTGTCAAAAAGGTTTAAAGATTTCTAAATTTTTAAGCCACAGTTAAATATACAGAGCAAATGT
131 TATTGTCAAAAAGGTTTAAAGATTTCTAAATTTTTAAGCCACAGTTAAATATACAGAGCAAATGT
2526482 TATTAACTTTATATGTCTTTTGGCCAACTTATTAATTTCTATATTAAGGGTATATTGAATTAGAA
196 TATTAACTTTATATGTCTTTTGGCCAACTTATTAATTTCTATATTAAGGGTATATTGAATTAGAA
2526547 ACTTGCTTTGAGAGGGTACAAAGATCTGTACTATTTCAGTACACAAGCTTCGTTACTTTAGTTGC
261 ACTTGCTTTGAGAGGGTACAAAGATCTGTACTATTTCAGTACACAAGCTTCGTTACTTTAGTTGC
2526612 TTACTAGCTACAACATGTAATTTGATGATGAGAGGAGACCATATTCCTGCTTTGCTAAAAATTGG
326 TTACTAGCTACAACATGTAATTTGATGATGAGAGGAGACCATATTCCTGCTTTGCTAAAAATTGG
2526677 CCATTTGTTTTTGGCCCTTCAATAAAATCCCTATGTTGATAAAAGCTTCAACCTGCAGGAAAATG
391 CCATTTGTTTTTGGCCCTTCAATAAAATCCCTATGTTGATAAAAGCTTCAACCTGCAGGAAAATG
2526742 CCCTCAAGGAGTATCCATCTCAACTGCCCAATCCTAACCATATCTCCATTCTTCCCTACCATAGT
456 CCCTCAAGGAGTATCCATCTCAACTGCCCAATCCTAACCATATCTCCATTCTTCCCTACCATAGT
2526807 GTCCATGGCCCGATTCTTTTAAGTT
521 GTCCATGGCCCGATTCTTTTAAGTT
2526832 AAACGGCTAGCCATCGCCGTTGCTTGAGACTTTTCAGGTCATAATTTATTTATCTGTTTTTTTTT
1 AAACGGCTAGCCATCGCCGTTGCTTGAGACTTTTCAGGTCATAATTTATTTATCTGTTTTTTTTT
2526897 TCCTTTTAATATCAATTAAATGTGCTTTCGGCATTAACGAGGAAAATATTAATTTTTATATAAAT
66 TCCTTTTAATATCAATTAAATGTGCTTTCGGCATTAACGAGGAAAATATTAATTTTTATATAAAT
2526962 TATTGTCAAAAAGGTTTAAAGATTTCTAAATTTTTAAGCCACAGTTAAATATACAGAGCAAATGT
131 TATTGTCAAAAAGGTTTAAAGATTTCTAAATTTTTAAGCCACAGTTAAATATACAGAGCAAATGT
2527027 TATTAACTTTATATGTCTTTTGGCCAACTTATTAATTTCTATATTAAGGGTATATTGAATTAGAA
196 TATTAACTTTATATGTCTTTTGGCCAACTTATTAATTTCTATATTAAGGGTATATTGAATTAGAA
2527092 ACTTGCTTTGAGAGGGTACAAAGATCTGTACTATTTCAGTACACAAGCTTCGTTACTTTAGTTGC
261 ACTTGCTTTGAGAGGGTACAAAGATCTGTACTATTTCAGTACACAAGCTTCGTTACTTTAGTTGC
2527157 TTACTAGCTACAACATGTAATTTGATGATGAGAGGAGACCATATTCCTGCTTTGCTAAAAATTGG
326 TTACTAGCTACAACATGTAATTTGATGATGAGAGGAGACCATATTCCTGCTTTGCTAAAAATTGG
2527222 CCATTTGTTTTTGGCCCTTCAATAAAATCCCTATGTTGATAAAAGCTTCAACCTGCAGGAAAATG
391 CCATTTGTTTTTGGCCCTTCAATAAAATCCCTATGTTGATAAAAGCTTCAACCTGCAGGAAAATG
2527287 CCCTCAAGGAGTATCCATCTCAACTGCCCAATCCTAACCATATCTCCATTCTTCCCTACCATAGT
456 CCCTCAAGGAGTATCCATCTCAACTGCCCAATCCTAACCATATCTCCATTCTTCCCTACCATAGT
2527352 GTCCATGGCCCGATTCTTTTAAGTT
521 GTCCATGGCCCGATTCTTTTAAGTT
2527377 A
1 A
2527378 TTTGTCTGGA
Statistics
Matches: 546, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
545 546 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (545 bp):
AAACGGCTAGCCATCGCCGTTGCTTGAGACTTTTCAGGTCATAATTTATTTATCTGTTTTTTTTT
TCCTTTTAATATCAATTAAATGTGCTTTCGGCATTAACGAGGAAAATATTAATTTTTATATAAAT
TATTGTCAAAAAGGTTTAAAGATTTCTAAATTTTTAAGCCACAGTTAAATATACAGAGCAAATGT
TATTAACTTTATATGTCTTTTGGCCAACTTATTAATTTCTATATTAAGGGTATATTGAATTAGAA
ACTTGCTTTGAGAGGGTACAAAGATCTGTACTATTTCAGTACACAAGCTTCGTTACTTTAGTTGC
TTACTAGCTACAACATGTAATTTGATGATGAGAGGAGACCATATTCCTGCTTTGCTAAAAATTGG
CCATTTGTTTTTGGCCCTTCAATAAAATCCCTATGTTGATAAAAGCTTCAACCTGCAGGAAAATG
CCCTCAAGGAGTATCCATCTCAACTGCCCAATCCTAACCATATCTCCATTCTTCCCTACCATAGT
GTCCATGGCCCGATTCTTTTAAGTT
Found at i:2534075 original size:166 final size:167
Alignment explanation
Indices: 2533612--2534106 Score: 940
Period size: 167 Copynumber: 3.0 Consensus size: 167
2533602 CTTTAATTAG
2533612 AAACATAATTCAAATATTACCCCATAGTCTCCACACTTATGAACTAACAAAATTCACATAAGAGC
1 AAACATAATTCAAATATTACCCCATAGTCTCCACACTTATGAACTAACAAAATTCACATAAGAGC
* *
2533677 AGGACTATTTCCCAGTGCTTACATCCAATTCAAAACAACAAAACCACTTTATATGAAGAAAAAAA
66 AGGACTATTTCCCAGTGCTTAAATCCAATTCAAAACAACAAAACCACTTTATATGATG-AAAAAA
2533742 AAAACCCACCAAAATATTACACAAAAAT-AAAAAAAAT
130 AAAACCCACCAAAATATTACACAAAAATAAAAAAAAAT
2533779 AAACATAATTCAAATATTACCCCATAGTCTCCACACTTATGAACTAACAAAATTCACATAAGAGC
1 AAACATAATTCAAATATTACCCCATAGTCTCCACACTTATGAACTAACAAAATTCACATAAGAGC
2533844 AGGACTATTTCCCAGTGCTTAAATCCAATTCAAAACAACAAAACCACTTTATATGATGAAAAAAA
66 AGGACTATTTCCCAGTGCTTAAATCCAATTCAAAACAACAAAACCACTTTATATGATGAAAAAAA
2533909 AAACCCACCAAAATATTACACAAAAATAAAAAAAAAT
131 AAACCCACCAAAATATTACACAAAAATAAAAAAAAAT
*
2533946 AAACATAATTCAAATATTACCCCATAGTCTCCACACTTATGAACAAACAAAATTCACATAAGAGC
1 AAACATAATTCAAATATTACCCCATAGTCTCCACACTTATGAACTAACAAAATTCACATAAGAGC
2534011 AGGACTATTTCCCAGTGCTTAAATCCAATTCAAAACAACAAAACCACTTTATATGATGAAAAAAA
66 AGGACTATTTCCCAGTGCTTAAATCCAATTCAAAACAACAAAACCACTTTATATGATGAAAAAAA
2534076 AAACCCACCAAAATATTACACAAAAA-AAAAA
131 AAACCCACCAAAATATTACACAAAAATAAAAA
2534107 TATTGAAATA
Statistics
Matches: 324, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
166 39 0.12
167 285 0.88
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (167 bp):
AAACATAATTCAAATATTACCCCATAGTCTCCACACTTATGAACTAACAAAATTCACATAAGAGC
AGGACTATTTCCCAGTGCTTAAATCCAATTCAAAACAACAAAACCACTTTATATGATGAAAAAAA
AAACCCACCAAAATATTACACAAAAATAAAAAAAAAT
Found at i:2537257 original size:23 final size:23
Alignment explanation
Indices: 2537231--2537274 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2537221 TATATTTAAA
* *
2537231 AAATATATTTTAAATTTAAATTT
1 AAATATATATTAAATATAAATTT
2537254 AAATATATATTAAATATAAAT
1 AAATATATATTAAATATAAAT
2537275 GTTTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATATATATTAAATATAAATTT
Found at i:2543490 original size:6 final size:6
Alignment explanation
Indices: 2543458--2543502 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
2543448 TCAAGTAAAG
* * *
2543458 CATTTC CAGTTC CAGTTC CATTTC CATTTC CATATC CATTTC CAT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CAT
2543503 ATCAATATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.20, C:0.33, G:0.04, T:0.42
Consensus pattern (6 bp):
CATTTC
Found at i:2543510 original size:18 final size:18
Alignment explanation
Indices: 2543474--2543511 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2543464 CAGTTCCAGT
* *
2543474 TCCATTTCCATTTCCATA
1 TCCATTTCCATATCAATA
2543492 TCCATTTCCATATCAATA
1 TCCATTTCCATATCAATA
2543510 TC
1 TC
2543512 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCATTTCCATATCAATA
Found at i:2543520 original size:2 final size:2
Alignment explanation
Indices: 2543513--2543573 Score: 68
Period size: 2 Copynumber: 30.5 Consensus size: 2
2543503 ATCAATATCA
* * * * * *
2543513 AT AT AT AT AT AT AT AT AT AT AT GT GT GT GT GT GT 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
2543555 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
2543574 CAGAGTTGCT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2546090 original size:2 final size:2
Alignment explanation
Indices: 2546083--2546127 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2546073 TATTAAATCT
2546083 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2546125 TA T
1 TA T
2546128 TGGAATCTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2546266 original size:2 final size:2
Alignment explanation
Indices: 2546259--2546287 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2546249 TTTTATACCA
2546259 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2546288 ATCATATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2550597 original size:2 final size:2
Alignment explanation
Indices: 2550590--2550635 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2550580 AGTTAGGCAA
2550590 AG AG AG AG AG AG 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
2550632 AG AG
1 AG AG
2550636 GCTTGGGCTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2551412 original size:12 final size:12
Alignment explanation
Indices: 2551395--2551420 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2551385 TAACTTTTTT
2551395 TCTTTAAAACTG
1 TCTTTAAAACTG
2551407 TCTTTAAAACTG
1 TCTTTAAAACTG
2551419 TC
1 TC
2551421 AATGATTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (12 bp):
TCTTTAAAACTG
Found at i:2553717 original size:25 final size:24
Alignment explanation
Indices: 2553643--2553718 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 24
2553633 AATGAAAACT
* *
2553643 AAAATTAAATAAGCAA-TT-AATA
1 AAAATTAAATTATCAAGTTAAATA
* *
2553665 AAAATAAAATTAT-TAGTATAAAATA
1 AAAATTAAATTATCAAGT-T-AAATA
*
2553690 AAAATTAAATTATCAAGTTAAATG
1 AAAATTAAATTATCAAGTTAAATA
2553714 AAAAT
1 AAAAT
2553719 CAATCTTATC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
21 1 0.02
22 11 0.26
23 1 0.02
24 9 0.21
25 17 0.40
26 3 0.07
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (24 bp):
AAAATTAAATTATCAAGTTAAATA
Found at i:2555073 original size:50 final size:50
Alignment explanation
Indices: 2554952--2555091 Score: 181
Period size: 50 Copynumber: 2.8 Consensus size: 50
2554942 GAAGTGGTCG
* * * *
2554952 TAATTGTTGACGATTCTTCACAAACTTTTGACAATAGAGAGAGGTGGCCG
1 TAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTAGCCA
* *
2555002 TAATTGTTGACGATTCTTCACCAACCTTTAACAATAGAGAGAGGTAGCTA
1 TAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTAGCCA
* * * * *
2555052 TAATTATTGACGAATCTTCACCGATCTTTGATAATAGAGA
1 TAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGA
2555092 AATGTGATCG
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 78 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Consensus pattern (50 bp):
TAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTAGCCA
Found at i:2555106 original size:50 final size:50
Alignment explanation
Indices: 2554949--2555112 Score: 170
Period size: 50 Copynumber: 3.3 Consensus size: 50
2554939 TATGAAGTGG
* *
2554949 TCGTAATTGTTGACGATTCTTCA-CAAACTTTTGACAATAGAGAGAGGTGG
1 TCGTAATTATTGACGATTCTTCACCAAAC-TTTGACAATAGAGAGAGGTGA
* * * *
2554999 CCGTAATTGTTGACGATTCTTCACCAACCTTTAACAATAGAGAGAGGT-A
1 TCGTAATTATTGACGATTCTTCACCAAACTTTGACAATAGAGAGAGGTGA
* * * * * * * *
2555048 GCTATAATTATTGACGAATCTTCACCGATCTTTGATAATAGAGAAATGTGA
1 TC-GTAATTATTGACGATTCTTCACCAAACTTTGACAATAGAGAGAGGTGA
2555099 TCGTAATTATTGAC
1 TCGTAATTATTGAC
2555113 TCTAAGTATA
Statistics
Matches: 95, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
49 1 0.01
50 88 0.93
51 6 0.06
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (50 bp):
TCGTAATTATTGACGATTCTTCACCAAACTTTGACAATAGAGAGAGGTGA
Found at i:2555291 original size:13 final size:13
Alignment explanation
Indices: 2555275--2555299 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2555265 TAAATACTTA
2555275 TTTTTTATTTTAT
1 TTTTTTATTTTAT
2555288 TTTTTTATTTTA
1 TTTTTTATTTTA
2555300 ACTGTAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTATTTTAT
Found at i:2558475 original size:4 final size:5
Alignment explanation
Indices: 2558445--2558480 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
2558435 TACACGAACG
2558445 AAACC AAACC AAACC AAACC AAACC -AACC -AACC AAA
1 AAACC AAACC AAACC AAACC AAACC AAACC AAACC AAA
2558481 GCATGTTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.61, C:0.39, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACC
Found at i:2562056 original size:2 final size:2
Alignment explanation
Indices: 2562049--2562083 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2562039 AACGAACTTT
2562049 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2562084 GCTACAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2562493 original size:3 final size:3
Alignment explanation
Indices: 2562487--2562520 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2562477 GTTATTTATT
2562487 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2562521 ATTTATACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2562983 original size:2 final size:2
Alignment explanation
Indices: 2562976--2563014 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2562966 ATGATCTGGT
2562976 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2563015 TGACGACTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2563827 original size:3 final size:3
Alignment explanation
Indices: 2563819--2563843 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2563809 TGGAAAGTAC
2563819 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
2563844 AGTGATGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:2567317 original size:3 final size:3
Alignment explanation
Indices: 2567309--2567351 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2567299 ATCATATGAT
2567309 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2567352 AGTCAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2568100 original size:2 final size:2
Alignment explanation
Indices: 2568093--2568122 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2568083 TTTGAAGATT
2568093 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
2568123 ATTTTGGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2569700 original size:30 final size:30
Alignment explanation
Indices: 2569640--2569722 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 30
2569630 AATTTTAATC
*
2569640 TAAATTTTTATATATTT-A-TTATAATCAAA
1 TAAATTTTTA-ATTTTTAATTTATAATCAAA
* *
2569669 TAAATTTTTAATTTTTAATTTATATTTAAA
1 TAAATTTTTAATTTTTAATTTATAATCAAA
**
2569699 TAAA-TCATAATTTTTAATTT-TAAT
1 TAAATTTTTAATTTTTAATTTATAAT
2569723 AAACTTTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
28 8 0.17
29 25 0.54
30 13 0.28
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
TAAATTTTTAATTTTTAATTTATAATCAAA
Found at i:2571022 original size:4 final size:4
Alignment explanation
Indices: 2571013--2571039 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2571003 TCATACCTAA
2571013 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
2571040 ACCCTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2572952 original size:27 final size:27
Alignment explanation
Indices: 2572915--2572995 Score: 83
Period size: 32 Copynumber: 2.9 Consensus size: 27
2572905 TTTAATTTTA
* *
2572915 TTTAAATTATTTTATATTTATATAATT
1 TTTAAAATATTTTATATTTATATAAAT
2572942 TTTAAAATATTATTAATTTATATTATATAAAT
1 TTTAAAATATT-TT-A--TAT-TTATATAAAT
*
2572974 TTTAAAATA-TTTATATATATAT
1 TTTAAAATATTTTATATTTATAT
2572996 TATACTTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
26 5 0.11
27 13 0.28
28 2 0.04
29 2 0.04
30 2 0.04
31 4 0.09
32 18 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTAAAATATTTTATATTTATATAAAT
Found at i:2572968 original size:38 final size:38
Alignment explanation
Indices: 2572889--2573047 Score: 95
Period size: 38 Copynumber: 4.2 Consensus size: 38
2572879 TTTCATCGTG
* * *
2572889 TATATTTTATAATATTTTTAATTTTATTTAAATTATTT
1 TATATTTTATAATATTTTAAATATTATTTAAATTATAT
*
2572927 TATATTTATATAAT-TTTTAAAATATTA-TTAATTTATAT
1 TATATTT-TATAATATTTT-AAATATTATTTAAATTATAT
* * *
2572965 TATATAAATTT-TAAAATATTTATATA-TATATTATACTTATAT
1 TATAT---TTTATAATAT-TTTAAATATTAT-TTA-AATTATAT
* *
2573007 TATA-TTTATATTATATT--ATATT-TTT--ATTATAT
1 TATATTTTATAATATTTTAAATATTATTTAAATTATAT
2573039 TATATTTTA
1 TATATTTTA
2573048 ATTTTTTATA
Statistics
Matches: 97, Mismatches: 11, Indels: 31
0.70 0.08 0.22
Matches are distributed among these distances:
32 10 0.10
33 4 0.04
35 2 0.02
36 4 0.04
37 1 0.01
38 30 0.31
39 21 0.22
40 6 0.06
41 8 0.08
42 11 0.11
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (38 bp):
TATATTTTATAATATTTTAAATATTATTTAAATTATAT
Found at i:2572977 original size:32 final size:33
Alignment explanation
Indices: 2572920--2572984 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
2572910 TTTTATTTAA
* *
2572920 ATTATTTTATATTTATATAATTTTTAAAATATT
1 ATTAATTTATATTTATATAAATTTTAAAATATT
2572953 ATTAATTTATA-TTATATAAATTTTAAAATATT
1 ATTAATTTATATTTATATAAATTTTAAAATATT
2572985 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 20 0.67
33 10 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
ATTAATTTATATTTATATAAATTTTAAAATATT
Found at i:2573005 original size:11 final size:10
Alignment explanation
Indices: 2572984--2573083 Score: 85
Period size: 11 Copynumber: 9.4 Consensus size: 10
2572974 TTTAAAATAT
2572984 TTATATATATA
1 TTATAT-TATA
2572995 TTATACTTATA
1 TTATA-TTATA
2573006 TTATATTTATA
1 TTATA-TTATA
2573017 TTATATTATA
1 TTATATTATA
*
2573027 TTTTTATTATA
1 -TTATATTATA
*
2573038 TTATATTTTAA
1 TTATATTAT-A
*
2573049 TT-TTTTATA
1 TTATATTATA
*
2573058 ATATATTATA
1 TTATATTATA
*
2573068 GTTAATATTATT
1 -TT-ATATTATA
2573080 TTAT
1 TTAT
2573084 TCAATTAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
9 2 0.03
10 24 0.33
11 39 0.53
12 8 0.11
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (10 bp):
TTATATTATA
Found at i:2573009 original size:5 final size:5
Alignment explanation
Indices: 2572984--2573083 Score: 85
Period size: 5 Copynumber: 18.8 Consensus size: 5
2572974 TTTAAAATAT
*
2572984 TTATA TATATA TTATA CTTATA TTATA TTTATA TTATA TTATA TTTTTA
1 TTATA T-TATA TTATA -TTATA TTATA -TTATA TTATA TTATA -TTATA
* * * *
2573033 TTATA TTATA TTTTAA TT-TT TTATA ATATA TTATA GTTAATA TTATT
1 TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA -TT-ATA TTATA
2573080 TTAT
1 TTAT
2573084 TCAATTAAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 16
0.77 0.08 0.16
Matches are distributed among these distances:
4 2 0.03
5 48 0.61
6 26 0.33
7 3 0.04
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:2573061 original size:23 final size:21
Alignment explanation
Indices: 2572980--2573061 Score: 69
Period size: 21 Copynumber: 3.7 Consensus size: 21
2572970 AAATTTTAAA
*
2572980 ATATTTATATATATATTATACTT
1 ATATTTTTATA-ATATTATA-TT
2573003 ATATTATATT-T-ATATTATATT
1 ATATT-T-TTATAATATTATATT
*
2573024 ATATTTTTATTATATTATATT
1 ATATTTTTATAATATTATATT
*
2573045 TTAATTTTTTATAATAT
1 AT-A-TTTTTATAATAT
2573062 ATTATAGTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
19 2 0.04
20 2 0.04
21 18 0.36
22 9 0.18
23 16 0.32
24 2 0.04
25 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATTTTTATAATATTATATT
Found at i:2573293 original size:14 final size:15
Alignment explanation
Indices: 2573268--2573297 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2573258 TGTTTGATAA
2573268 TTTGATAATAATTTT
1 TTTGATAATAATTTT
2573283 TTTGA-AATAATTTT
1 TTTGATAATAATTTT
2573297 T
1 T
2573298 AATTAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TTTGATAATAATTTT
Found at i:2573727 original size:15 final size:16
Alignment explanation
Indices: 2573703--2573755 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
2573693 ATGAATTAGG
2573703 ATTTAGTTTATTATTTT
1 ATTTA-TTTATTATTTT
2573720 -TTTATTTATTATTTT
1 ATTTATTTATTATTTT
*
2573735 AATATATTTATTATTATT
1 -ATTTATTTATTATT-TT
2573753 ATT
1 ATT
2573756 ATTCACATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 11 0.35
16 4 0.13
17 14 0.45
18 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (16 bp):
ATTTATTTATTATTTT
Found at i:2573728 original size:12 final size:11
Alignment explanation
Indices: 2573709--2573758 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
2573699 TAGGATTTAG
*
2573709 TTTATTATTTT
1 TTTATTATTAT
2573720 TTTATTTATTAT
1 TTTA-TTATTAT
*
2573732 TTTAATA-TA-
1 TTTATTATTAT
2573741 TTTATTATTAT
1 TTTATTATTAT
2573752 TATTATT
1 T-TTATT
2573759 CACATGCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
9 6 0.19
10 4 0.12
11 7 0.22
12 15 0.47
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTATTATTAT
Found at i:2575076 original size:29 final size:29
Alignment explanation
Indices: 2575022--2575077 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2575012 TTTAATATTT
* *
2575022 ATATATAATATATGTTAAAATATAAAAAG
1 ATATATAAAATATGTTAAAAGATAAAAAG
* *
2575051 ATATATAAAATATTTTAAAAGGTAAAA
1 ATATATAAAATATGTTAAAAGATAAAA
2575078 TAATTATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (29 bp):
ATATATAAAATATGTTAAAAGATAAAAAG
Found at i:2576963 original size:16 final size:16
Alignment explanation
Indices: 2576942--2576972 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2576932 TGTTCATACT
*
2576942 TTAATTATAATAAATA
1 TTAATTAAAATAAATA
2576958 TTAATTAAAATAAAT
1 TTAATTAAAATAAAT
2576973 CAAAATTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAATTAAAATAAATA
Found at i:2580467 original size:2 final size:2
Alignment explanation
Indices: 2580460--2580485 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2580450 TTAAAGGTCA
2580460 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
2580486 GAAAGAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.