Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 29 of 29
Found at i:5029849 original size:68 final size:67
Alignment explanation
Indices: 5029733--5029950 Score: 301
Period size: 67 Copynumber: 3.2 Consensus size: 67
5029723 TGGTAAAAAC
* * *
5029733 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
5029798 AT
66 AT
* * *
5029800 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
5029865 AAT
65 AAT
* * * * * * * *
5029868 CTCTATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGATAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
5029933 AT
66 AT
5029935 CACCATTTAATCAACA
1 CACCATTTAATCAACA
5029951 GTTGACAGCT
Statistics
Matches: 131, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
67 70 0.53
68 61 0.47
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:5031281 original size:6 final size:7
Alignment explanation
Indices: 5031255--5031280 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5031245 TTGCTTAAGC
5031255 AAAAAAT
1 AAAAAAT
5031262 AAAAAAT
1 AAAAAAT
5031269 AAAAAAT
1 AAAAAAT
5031276 AAAAA
1 AAAAA
5031281 TCACAATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:5034550 original size:22 final size:21
Alignment explanation
Indices: 5034520--5034572 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
5034510 TTTTTTAAGT
5034520 TATTATATACTTAAT-TCATTGAA
1 TATT-TATACTTAATAT-ATT-AA
*
5034543 TATTTATATTTAATATATTAA
1 TATTTATACTTAATATATTAA
5034564 TAATTTATA
1 T-ATTTATA
5034573 AATTTATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.11
22 19 0.70
23 5 0.19
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTTATACTTAATATATTAA
Found at i:5034594 original size:19 final size:20
Alignment explanation
Indices: 5034563--5034622 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
5034553 TAATATATTA
5034563 ATAATTT-ATAAATTTATAT
1 ATAATTTAATAAATTTATAT
*
5034582 ATTA-TTAATAAATTTAATAAT
1 ATAATTTAATAAATTT-AT-AT
5034603 ATAATTTAATTAAATTTATA
1 ATAATTTAA-TAAATTTATA
5034623 AAAAAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 2 0.06
19 11 0.32
20 2 0.06
21 6 0.18
22 6 0.18
23 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAATTTAATAAATTTATAT
Found at i:5034623 original size:22 final size:21
Alignment explanation
Indices: 5034563--5034639 Score: 79
Period size: 22 Copynumber: 3.7 Consensus size: 21
5034553 TAATATATTA
5034563 ATAATTT-ATAAATTTAT-AT
1 ATAATTTAATAAATTTATAAT
*
5034582 ATTA-TTAATAAATTTAATAAT
1 ATAATTTAATAAATTT-ATAAT
*
5034603 ATAATTTAATTAAATTTATAAA
1 ATAATTTAA-TAAATTTATAAT
*
5034625 AAAATTTAATGAAAT
1 ATAATTTAAT-AAAT
5034640 AATATCGTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
18 2 0.04
19 11 0.23
20 2 0.04
21 6 0.12
22 20 0.42
23 7 0.15
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (21 bp):
ATAATTTAATAAATTTATAAT
Found at i:5041383 original size:2 final size:2
Alignment explanation
Indices: 5041376--5041405 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5041366 TCATTGTCAT
5041376 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
5041406 GCATACATCA
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:5043428 original size:16 final size:16
Alignment explanation
Indices: 5043391--5043426 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5043381 AAAAGAAAAA
*
5043391 ATTTCATTTTTTATGT
1 ATTTTATTTTTTATGT
5043407 ATTTTATTTTTTAT-T
1 ATTTTATTTTTTATGT
5043422 ATTTT
1 ATTTT
5043427 TAAACAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (16 bp):
ATTTTATTTTTTATGT
Found at i:5043694 original size:35 final size:34
Alignment explanation
Indices: 5043645--5043735 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 34
5043635 AATATTTATT
5043645 ATAAAT-TAATTTTTAATATATATT-TTATTATTAAA
1 ATAAATATAA-TTTTAATATATATTATT-TT-TTAAA
5043680 ATAAATATAATTTTAATA-AT-TTATTTTTTAAA
1 ATAAATATAATTTTAATATATATTATTTTTTAAA
*
5043712 ATAATATATAATTTTTATAGTATA
1 ATAA-ATATAATTTTAATA-TATA
5043736 AAAATTAAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
32 9 0.18
33 17 0.35
34 4 0.08
35 16 0.33
36 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (34 bp):
ATAAATATAATTTTAATATATATTATTTTTTAAA
Found at i:5043708 original size:50 final size:50
Alignment explanation
Indices: 5043616--5043710 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
5043606 TTGTTATTAA
* *
5043616 ATTTTATTTTAACATAAATAATATTTATTATAAATTAATTTTTAATATAT
1 ATTTTATTTTAAAATAAATAATATTTATAATAAATTAATTTTTAATATAT
* *
5043666 ATTTTATTATTAAAATAAAT-ATAATTT-TAATAATTTATTTTTTAA
1 ATTTTATT-TTAAAATAAATAAT-ATTTATAATAAATTAATTTTTAA
5043711 AATAATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
50 25 0.64
51 14 0.36
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (50 bp):
ATTTTATTTTAAAATAAATAATATTTATAATAAATTAATTTTTAATATAT
Found at i:5043954 original size:16 final size:15
Alignment explanation
Indices: 5043933--5043968 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
5043923 GAAAAATCCG
5043933 TTTTTTATCCTTTTT
1 TTTTTTATCCTTTTT
5043948 ATTTTTTATCCTTTTT
1 -TTTTTTATCCTTTTT
5043964 TTTTT
1 TTTTT
5043969 AAATAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTATCCTTTTT
Found at i:5044270 original size:30 final size:32
Alignment explanation
Indices: 5044208--5044422 Score: 204
Period size: 31 Copynumber: 6.3 Consensus size: 32
5044198 TTTAATATAT
*
5044208 ATTTTATTATTTAAAATAAATATAACTTTAATA
1 ATTTTATTATTTAATATAAATATAA-TTTAATA
5044241 A-TTTATT-TTTAATATAAATATAATTTAATA
1 ATTTTATTATTTAATATAAATATAATTTAATA
* *
5044271 ATTTATAATTCTTATCTAATATAAATATAATTTGATTTA
1 ATTT-T-A---TTATTTAATATAAATATAATTT-A-ATA
5044310 TATTTTATTATTTAATATAAATAT-ATTTAATA
1 -ATTTTATTATTTAATATAAATATAATTTAATA
**
5044342 ATTTTTAATTATTATTCAATATAAATATATATTTTTTA
1 A-TTTT-ATTA-T-TT-AATATAAATATA-ATTTAATA
*
5044380 CATTTTATTATTTAATATAAATATATTTTAATA
1 -ATTTTATTATTTAATATAAATATAATTTAATA
5044413 ATTTT-TTATT
1 ATTTTATTATT
5044423 ATTTATCATA
Statistics
Matches: 154, Mismatches: 10, Indels: 38
0.76 0.05 0.19
Matches are distributed among these distances:
30 8 0.05
31 23 0.15
32 18 0.12
33 12 0.08
34 17 0.11
35 20 0.13
36 14 0.09
37 22 0.14
38 12 0.08
39 4 0.03
40 4 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (32 bp):
ATTTTATTATTTAATATAAATATAATTTAATA
Found at i:5044351 original size:71 final size:70
Alignment explanation
Indices: 5044242--5044449 Score: 266
Period size: 71 Copynumber: 3.0 Consensus size: 70
5044232 ACTTTAATAA
* *
5044242 TTTATT-TTTAATATAAATATAATTTAATAATTTATAATTCTTA-TCTAATATAAATATA-ATTT
1 TTTATTATTTAATATAAATAT-ATTTAATAATTTTTAATTATTATTC-AATATAAATATATATTT
*
5044304 GATTTATAT
64 --TTTACAT
5044313 TTTATTATTTAATATAAATATATTTAATAATTTTTAATTATTATTCAATATAAATATATATTTTT
1 TTTATTATTTAATATAAATATATTTAATAATTTTTAATTATTATTCAATATAAATATATATTTTT
5044378 TACAT
66 TACAT
* *
5044383 TTTATTATTTAATATAAATATATTTTAATAATTTTTTATTATT-TATC-ATATATATATAT-TTC
1 TTTATTATTTAATATAAATATA-TTTAATAATTTTTAATTATTAT-TCAATATAAATATATATT-
5044445 TTTTA
63 TTTTA
5044450 ATCAAATATT
Statistics
Matches: 126, Mismatches: 5, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
69 2 0.02
70 45 0.36
71 59 0.47
72 20 0.16
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (70 bp):
TTTATTATTTAATATAAATATATTTAATAATTTTTAATTATTATTCAATATAAATATATATTTTT
TACAT
Found at i:5044397 original size:34 final size:33
Alignment explanation
Indices: 5044208--5044443 Score: 193
Period size: 34 Copynumber: 6.9 Consensus size: 33
5044198 TTTAATATAT
*
5044208 ATTTTATTATTTAAAATAAATATA-ACTTTAATA
1 ATTTTATTATTTAATATAAATATATA-TTTAATA
5044241 A-TTTATT-TTTAATATAAATATA-ATTTAATA
1 ATTTTATTATTTAATATAAATATATATTTAATA
* *
5044271 ATTTATAATTCTTATCTAATATAAATATA-ATTTGATTTA
1 ATTT-T-A---TTATTTAATATAAATATATATTT-A-ATA
5044310 TATTTTATTATTTAATAT-AA-ATATATTTAATA
1 -ATTTTATTATTTAATATAAATATATATTTAATA
**
5044342 ATTTTTAATTATTATTCAATATAAATATATATTTTTTA
1 A-TTTT-ATTA-T-TT-AATATAAATATATATTTAATA
5044380 CATTTTATTATTTAATATAAATATAT-TTTAATA
1 -ATTTTATTATTTAATATAAATATATATTTAATA
*
5044413 ATTTTTTATTATTT-ATCATATATATATATTT
1 A--TTTTATTATTTAAT-ATAAATATATATTT
5044444 CTTTTAATCA
Statistics
Matches: 170, Mismatches: 10, Indels: 44
0.76 0.04 0.20
Matches are distributed among these distances:
30 8 0.05
31 18 0.11
32 14 0.08
33 17 0.10
34 40 0.24
35 17 0.10
36 8 0.05
37 24 0.14
38 16 0.09
39 4 0.02
40 4 0.02
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (33 bp):
ATTTTATTATTTAATATAAATATATATTTAATA
Found at i:5044441 original size:36 final size:34
Alignment explanation
Indices: 5044196--5044443 Score: 204
Period size: 36 Copynumber: 7.1 Consensus size: 34
5044186 TTAATTTTTA
* *
5044196 ATTTTAATATATATTTTATTATTTAAAATAAATAT
1 ATTTTAATA-ATTTTTTATTATTTAATATAAATAT
*
5044231 AACTTTAATAA---TTTATT-TTTAATATAAATAT
1 -ATTTTAATAATTTTTTATTATTTAATATAAATAT
* * *
5044262 AATTTAATAATTTATAATTCTTATCTAATATAAATAT
1 ATTTTAATAATTT-T--TTATTATTTAATATAAATAT
* * * *
5044299 AATTTGATTTATATTTTATTATTTAATATAAATAT
1 -ATTTTAATAATTTTTTATTATTTAATATAAATAT
*
5044334 A-TTTAATAATTTTTAATTATTATTCAATATAAATAT
1 ATTTTAATAA-TTTT--TTATTATTTAATATAAATAT
**
5044370 ATATTTTTTACA--TTTTATTATTTAATATAAATAT
1 AT-TTTAATA-ATTTTTTATTATTTAATATAAATAT
*
5044404 ATTTTAATAATTTTTTATTATTTATCATATATATAT
1 ATTTTAATAATTTTTTATTATTTA--ATATAAATAT
5044440 ATTT
1 ATTT
5044444 CTTTTAATCA
Statistics
Matches: 171, Mismatches: 23, Indels: 36
0.74 0.10 0.16
Matches are distributed among these distances:
30 9 0.05
31 13 0.08
32 7 0.04
33 10 0.06
34 38 0.22
35 19 0.11
36 47 0.27
37 14 0.08
38 13 0.08
39 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (34 bp):
ATTTTAATAATTTTTTATTATTTAATATAAATAT
Found at i:5046323 original size:36 final size:35
Alignment explanation
Indices: 5046282--5046511 Score: 219
Period size: 36 Copynumber: 6.7 Consensus size: 35
5046272 ATTTTTAATT
*
5046282 TTTAATATATATTTTATTATTTAAAATAAATATAA
1 TTTAATATATATTTTATTATTTAATATAAATATAA
*
5046317 CTTT-A-ATA-A-TTTATT-TTTTA-ATAAATATAA
1 -TTTAATATATATTTTATTATTTAATATAAATATAA
* * * *
5046347 TTTAATAATTTATAATTCTTATCTAATATAAATATAA
1 TTTAAT-ATATAT-TTTATTATTTAATATAAATATAA
5046384 TTTTAATATATATTTTATTATTTAATATAAATATAA
1 -TTTAATATATATTTTATTATTTAATATAAATATAA
* *
5046420 TTTAATA-ATTTTAATTATTATTCAATATAAATATATA
1 TTTAATATATATT--TTATTATTTAATATAAATATA-A
* * *
5046457 TTT--TTTACATTTTATTATTTAATATAAATATAT
1 TTTAATATATATTTTATTATTTAATATAAATATAA
*
5046490 TTTAATA-ATTTTTTATTATTTA
1 TTTAATATATATTTTATTATTTA
5046512 TCATATATAT
Statistics
Matches: 159, Mismatches: 20, Indels: 32
0.75 0.09 0.15
Matches are distributed among these distances:
29 3 0.02
30 11 0.07
31 4 0.03
32 8 0.05
33 5 0.03
34 40 0.25
35 14 0.09
36 49 0.31
37 19 0.12
38 6 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (35 bp):
TTTAATATATATTTTATTATTTAATATAAATATAA
Found at i:5046336 original size:15 final size:15
Alignment explanation
Indices: 5046312--5046363 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
5046302 TTAAAATAAA
5046312 TATAACTTTAATAATT
1 TATAA-TTTAATAATT
** *
5046328 TATTTTTTAATAA-A
1 TATAATTTAATAATT
5046342 TATAATTTAATAATT
1 TATAATTTAATAATT
5046357 TATAATT
1 TATAATT
5046364 CTTATCTAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 11 0.38
15 15 0.52
16 3 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TATAATTTAATAATT
Found at i:5046352 original size:14 final size:14
Alignment explanation
Indices: 5046306--5046354 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
5046296 TATTATTTAA
5046306 AATAAATATAACTTT
1 AATAAATATAA-TTT
* **
5046321 AATAATTTATTTTTT
1 AATAA-ATATAATTT
5046336 AATAAATATAATTT
1 AATAAATATAATTT
5046350 AATAA
1 AATAA
5046355 TTTATAATTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 11 0.41
15 13 0.48
16 3 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAAATATAATTT
Found at i:5046398 original size:103 final size:104
Alignment explanation
Indices: 5046281--5046511 Score: 292
Period size: 103 Copynumber: 2.2 Consensus size: 104
5046271 AATTTTTAAT
* *
5046281 TTTTAATATATATTTTATTATTTAAAATAAATATAACTTTAATAA-TTTATTTTTTAATAAATAT
1 TTTTAATATATATTTTATTATTTAAAATAAATATAA-TTTAATAATTTTAATTATTAATAAATAT
* *
5046345 -AATTTAATAATTTATA-A-TTCTTATCTAATATAAATATAA
65 AAATAT-ATAATTTATACATTTATTATCTAATATAAATAT-A
* * *
5046384 TTTTAATATATATTTTATTATTTAATATAAATATAATTTAATAATTTTAATTATTATTCAATATA
1 TTTTAATATATATTTTATTATTTAAAATAAATATAATTTAATAATTTTAATTATTAATAAATATA
* * *
5046449 AATATATATTTTTTACATTTTATTATTTAATATAAATATA
66 AATATATAATTTATACA-TTTATTATCTAATATAAATATA
*
5046489 TTTTAATA-ATTTTTTATTATTTA
1 TTTTAATATATATTTTATTATTTA
5046512 TCATATATAT
Statistics
Matches: 112, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
102 8 0.07
103 58 0.52
104 19 0.17
105 9 0.08
106 18 0.16
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (104 bp):
TTTTAATATATATTTTATTATTTAAAATAAATATAATTTAATAATTTTAATTATTAATAAATATA
AATATATAATTTATACATTTATTATCTAATATAAATATA
Found at i:5046496 original size:70 final size:70
Alignment explanation
Indices: 5046337--5046537 Score: 246
Period size: 70 Copynumber: 2.8 Consensus size: 70
5046327 TTATTTTTTA
* *
5046337 ATAAATATAATTTAATAATTTATAATTCTTA-TCTAATATAAATATA-ATTTTAATATATATTTT
1 ATAAATATAATTTAATAATTT-TAATTATTATTC-AATATAAATATATATTTT--T-TACATTTT
5046400 ATTATTTAAT
61 ATTATTTAAT
5046410 ATAAATATAATTTAATAATTTTAATTATTATTCAATATAAATATATATTTTTTACATTTTATTAT
1 ATAAATATAATTTAATAATTTTAATTATTATTCAATATAAATATATATTTTTTACATTTTATTAT
5046475 TTAAT
66 TTAAT
* * *
5046480 ATAAATATATTTTAATAATTTTTTATTATT-TATCATATATATATATATACTTATTTTA
1 ATAAATATAATTTAATAA-TTTTAATTATTAT-TCA-ATATAAATATATA-TT-TTTTA
5046538 ATTAAATATT
Statistics
Matches: 116, Mismatches: 5, Indels: 13
0.87 0.04 0.10
Matches are distributed among these distances:
70 35 0.30
71 14 0.12
72 32 0.28
73 30 0.26
74 5 0.04
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (70 bp):
ATAAATATAATTTAATAATTTTAATTATTATTCAATATAAATATATATTTTTTACATTTTATTAT
TTAAT
Found at i:5046549 original size:13 final size:14
Alignment explanation
Indices: 5046533--5046567 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
5046523 TATATACTTA
5046533 TTTTAATTAAATAT
1 TTTTAATTAAATAT
*
5046547 TTTTAA-TAATTAT
1 TTTTAATTAAATAT
5046560 TTTTAATT
1 TTTTAATT
5046568 TTTATCTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTAATTAAATAT
Found at i:5050329 original size:28 final size:28
Alignment explanation
Indices: 5050298--5050356 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
5050288 AATAAAAACA
5050298 AAAAATGATATGAACATAT-AAATATATC
1 AAAAATGATATGAA-ATATAAAATATATC
* * * *
5050326 AAAATTTATATTAAATATAAAATATTTC
1 AAAAATGATATGAAATATAAAATATATC
5050354 AAA
1 AAA
5050357 TACAATTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAAATGATATGAAATATAAAATATATC
Found at i:5052234 original size:29 final size:31
Alignment explanation
Indices: 5052186--5052260 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
5052176 ATAATAAAAT
5052186 TTTTTAAAAGATTACGGATG-A-TAAATATAA
1 TTTTTAAAAG-TTACGGATGAATTAAATATAA
* *
5052216 TTTTTAAAAGTTATGGATGAATTAAATGTAA
1 TTTTTAAAAGTTACGGATGAATTAAATATAA
5052247 TTTTTAAAAGTTAC
1 TTTTTAAAAGTTAC
5052261 AGATAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.20
30 11 0.28
31 21 0.52
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.41
Consensus pattern (31 bp):
TTTTTAAAAGTTACGGATGAATTAAATATAA
Found at i:5052417 original size:23 final size:23
Alignment explanation
Indices: 5052391--5052458 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
5052381 CAAATTTTTT
5052391 TAAAAAAAATTAATTATTTAATA
1 TAAAAAAAATTAATTATTTAATA
** * *
5052414 TAAAAATTATTAATAAATT-ATA
1 TAAAAAAAATTAATTATTTAATA
5052436 -AAAATAAATATTAATTATTTAAT
1 TAAAA-AAA-ATTAATTATTTAAT
5052459 TATTATATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
21 4 0.12
22 4 0.12
23 24 0.71
24 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAAAAAAATTAATTATTTAATA
Found at i:5052425 original size:19 final size:21
Alignment explanation
Indices: 5052395--5052440 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
5052385 TTTTTTTAAA
* *
5052395 AAAAATTAATTATTTAA-TAT
1 AAAAATTAATTAATAAATTAT
5052415 AAAAATT-ATTAATAAATTAT
1 AAAAATTAATTAATAAATTAT
5052435 AAAAAT
1 AAAAAT
5052441 AAATATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATTAATTAATAAATTAT
Found at i:5053189 original size:25 final size:24
Alignment explanation
Indices: 5053146--5053211 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
5053136 TCATTTATTA
*
5053146 ATATTTTTAATAAAA-ATTAATAGT
1 ATATGTTTAA-AAAATATTAATAGT
*
5053170 ATATGATTTAAAAAATATTAATATT
1 ATATG-TTTAAAAAATATTAATAGT
*
5053195 TTATGTTT-AAAAATATT
1 ATATGTTTAAAAAATATT
5053212 TAATTTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 9 0.24
24 11 0.30
25 17 0.46
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (24 bp):
ATATGTTTAAAAAATATTAATAGT
Found at i:5053203 original size:24 final size:25
Alignment explanation
Indices: 5053151--5053221 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
5053141 TATTAATATT
* *
5053151 TTTAATAAAA-ATTAATAGTATATGA
1 TTTAA-AAAATATTAATATTTTATGA
5053176 TTTAAAAAATATTAATATTTTATG-
1 TTTAAAAAATATTAATATTTTATGA
*
5053200 TTT-AAAAATATTTAATTTTTTA
1 TTTAAAAAATA-TTAATATTTTA
5053222 ACATAATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.17
24 17 0.41
25 17 0.41
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
TTTAAAAAATATTAATATTTTATGA
Found at i:5053206 original size:23 final size:24
Alignment explanation
Indices: 5053151--5053221 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
5053141 TATTAATATT
* * *
5053151 TTTAATAAAAATTAATAGTATATGA
1 TTTAA-AAATATTAATATTTTATGA
5053176 TTTAAAAAATATTAATATTTTATG-
1 TTT-AAAAATATTAATATTTTATGA
*
5053200 TTTAAAAATATTTAATTTTTTA
1 TTTAAAAATA-TTAATATTTTA
5053222 ACATAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 7 0.17
24 13 0.32
25 18 0.45
26 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TTTAAAAATATTAATATTTTATGA
Found at i:5053981 original size:6 final size:6
Alignment explanation
Indices: 5053972--5053997 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5053962 TCTCTGGTGG
5053972 CTGTGA CTGTGA CTGTGA CTGTGA CT
1 CTGTGA CTGTGA CTGTGA CTGTGA CT
5053998 ATATCTGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.19, G:0.31, T:0.35
Consensus pattern (6 bp):
CTGTGA
Found at i:5054328 original size:23 final size:25
Alignment explanation
Indices: 5054292--5054337 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
5054282 TTATTATTTA
*
5054292 AAAATTTTAAAAT-AT-TCATTAAT
1 AAAATCTTAAAATAATATCATTAAT
*
5054315 AAAATCTTATAATAATATCATTA
1 AAAATCTTAAAATAATATCATTA
5054338 CATCCGTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 2 0.11
25 6 0.32
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAATCTTAAAATAATATCATTAAT
Found at i:5055676 original size:24 final size:23
Alignment explanation
Indices: 5055628--5055676 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
5055618 CAATTTTTTA
* *
5055628 AAATAAAAAATAATATATTATTT
1 AAATAAAAAATAATAAAATATTT
5055651 AAATAAAATAATAA-AAAATATCTT
1 AAATAAAA-AATAATAAAATAT-TT
5055675 AA
1 AA
5055677 TATATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATAAAAAATAATAAAATATTT
Found at i:5056845 original size:21 final size:20
Alignment explanation
Indices: 5056802--5056845 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5056792 AGTTATATTT
* *
5056802 TTTCATCTAAAAATGTATTA
1 TTTCATCTAAAAATGCATCA
*
5056822 TTTCATCTAACCAATGCATCA
1 TTTCATCTAA-AAATGCATCA
5056843 TTT
1 TTT
5056846 ATTCAAAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (20 bp):
TTTCATCTAAAAATGCATCA
Found at i:5057700 original size:19 final size:20
Alignment explanation
Indices: 5057678--5057737 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 20
5057668 TTTAAATATC
5057678 ATATAAAAATATGAT-ATAA
1 ATATAAAAATATGATAATAA
* **
5057697 ATAT-AATATATTTTAATAA
1 ATATAAAAATATGATAATAA
* *
5057716 ATATAAAAAAATCATAA-AA
1 ATATAAAAATATGATAATAA
5057735 ATA
1 ATA
5057738 ATATAATATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
18 7 0.22
19 17 0.53
20 8 0.25
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
ATATAAAAATATGATAATAA
Found at i:5058010 original size:3 final size:3
Alignment explanation
Indices: 5058002--5058026 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5057992 ATTTAAAGGA
5058002 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
5058027 GAATAAGGGC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5058355 original size:2 final size:2
Alignment explanation
Indices: 5058348--5058402 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
5058338 TGTCTGTCTG
5058348 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
5058390 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
5058403 GGAGGATTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5058551 original size:2 final size:2
Alignment explanation
Indices: 5058544--5058575 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5058534 AAATAAATTA
5058544 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
5058576 TAGAAACAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5061802 original size:2 final size:2
Alignment explanation
Indices: 5061797--5061826 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5061787 TGAAAAAAAA
5061797 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
5061827 GAAGTAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5062386 original size:3 final size:3
Alignment explanation
Indices: 5062378--5062415 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5062368 GTAAATATAT
5062378 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
5062416 TAGCAGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5067535 original size:144 final size:142
Alignment explanation
Indices: 5067371--5067634 Score: 357
Period size: 144 Copynumber: 1.8 Consensus size: 142
5067361 TTCTAAGTTA
*
5067371 AAATAACATAAGTTAAACATAAATATTTAAATTTAAATTTTAATATGATTATCAATAATAACATA
1 AAATAACATAAGTTAAACATAAATATTTAAACTTAAATTTTAATATGATTATCAATAATAACAT-
* * *
5067436 AAAAGTATTGATTCTTACTCTTAACGTTAAGATAATATTAATTAATTATAATTAATCTTAAAAAA
65 -AAAGCATTGATTCTAACTCTCAACGTTAAGATAATATTAATTAATTATAATTAATCTTAAAAAA
5067501 AAGTATTTAAGTCG
129 AAGTATTTAAGTCG
* * ** * * *
5067515 AAATAACATAAGTTAAACATAAGTGTTTAGGCTTATATTTTGATATGGTTATCAATAATAACATA
1 AAATAACATAAGTTAAACATAAATATTTAAACTTAAATTTTAATATGATTATCAATAATAACATA
** ** * *
5067580 AAGCATTGATTCTAACTCTCAACGTTGTGATGGTATTAATTAATTGTAGTTAATC
66 AAGCATTGATTCTAACTCTCAACGTTAAGATAATATTAATTAATTATAATTAATC
5067635 AAACTTTGTA
Statistics
Matches: 103, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
142 47 0.46
144 56 0.54
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (142 bp):
AAATAACATAAGTTAAACATAAATATTTAAACTTAAATTTTAATATGATTATCAATAATAACATA
AAGCATTGATTCTAACTCTCAACGTTAAGATAATATTAATTAATTATAATTAATCTTAAAAAAAA
GTATTTAAGTCG
Found at i:5068600 original size:32 final size:32
Alignment explanation
Indices: 5068564--5068629 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
5068554 TAAATATCAA
5068564 ATAAATATATGAATAT-GTAAAAATTTATATAT
1 ATAAAT-TATGAATATAGTAAAAATTTATATAT
* * * *
5068596 ATAAATTATTAATATATTAAAATTTTATTTAT
1 ATAAATTATGAATATAGTAAAAATTTATATAT
5068628 AT
1 AT
5068630 TTATAATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 8 0.28
32 21 0.72
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (32 bp):
ATAAATTATGAATATAGTAAAAATTTATATAT
Found at i:5068623 original size:19 final size:20
Alignment explanation
Indices: 5068601--5068642 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
5068591 TATATATAAA
5068601 TTATTAATATATTA-AA-ATT
1 TTATTAATAT-TTATAATATT
*
5068620 TTATTTATATTTATAATATT
1 TTATTAATATTTATAATATT
5068640 TTA
1 TTA
5068643 AATATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 3 0.15
19 11 0.55
20 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATTAATATTTATAATATT
Found at i:5068648 original size:20 final size:19
Alignment explanation
Indices: 5068589--5068653 Score: 55
Period size: 20 Copynumber: 3.5 Consensus size: 19
5068579 TGTAAAAATT
*
5068589 TATATATATAAATTATT-AA
1 TATATTTATAAATT-TTAAA
**
5068608 TATA-TTA-AAATTTTATT
1 TATATTTATAAATTTTAAA
5068625 TATATTTATAATATTTTAAA
1 TATATTTATAA-ATTTTAAA
*
5068645 TATAATTAT
1 TATATTTAT
5068654 CATATATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
16 2 0.06
17 9 0.25
18 5 0.14
19 6 0.17
20 14 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATATTTATAAATTTTAAA
Found at i:5068673 original size:29 final size:29
Alignment explanation
Indices: 5068641--5068700 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
5068631 TATAATATTT
*
5068641 TAAATATAAT-TATCATATATAAAAATATA
1 TAAATATAATATA-AATATATAAAAATATA
*
5068670 TAAATATAATATAAATATATAAATATATA
1 TAAATATAATATAAATATATAAAAATATA
5068699 TA
1 TA
5068701 CATTACGCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
TAAATATAATATAAATATATAAAAATATA
Found at i:5068687 original size:19 final size:18
Alignment explanation
Indices: 5068655--5068700 Score: 74
Period size: 19 Copynumber: 2.5 Consensus size: 18
5068645 TATAATTATC
*
5068655 ATATATAAAAATATATAA
1 ATATATATAAATATATAA
5068673 ATATAATATAAATATATAA
1 ATAT-ATATAAATATATAA
5068692 ATATATATA
1 ATATATATA
5068701 CATTACGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATATATATAAATATATAA
Found at i:5071430 original size:19 final size:20
Alignment explanation
Indices: 5071402--5071461 Score: 77
Period size: 19 Copynumber: 3.0 Consensus size: 20
5071392 TATTTCTGTC
*
5071402 AAGAAAGAAAGAAAAAAAA-
1 AAGAAGGAAAGAAAAAAAAG
5071421 AAGAAGGAAAGGAAAAAAAAAG
1 AAGAAGGAAA-G-AAAAAAAAG
*
5071443 AAAAAGGAAAGAAAAAAAA
1 AAGAAGGAAAGAAAAAAAA
5071462 TTATGTATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 9 0.25
20 9 0.25
21 9 0.25
22 9 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (20 bp):
AAGAAGGAAAGAAAAAAAAG
Found at i:5072298 original size:14 final size:14
Alignment explanation
Indices: 5072279--5072331 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
5072269 CTCAATTCAT
5072279 AATATTTTTATATA
1 AATATTTTTATATA
* *
5072293 AATATTTATATATT
1 AATATTTTTATATA
5072307 AATAATTCATTTTATATA
1 AAT-A-T--TTTTATATA
5072325 AATATTT
1 AATATTT
5072332 ACATGTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
AATATTTTTATATA
Found at i:5072416 original size:24 final size:24
Alignment explanation
Indices: 5072375--5072428 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
5072365 TTTTTGTGCC
5072375 ATATTATATTTTAATTAT-TTTCTA
1 ATATTATATTTTAATTATATTTC-A
*
5072399 ATATTATATTTGT-GTTATATTTCA
1 ATATTATATTT-TAATTATATTTCA
5072423 AT-TTAT
1 ATATTAT
5072429 CTTATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.15
24 18 0.67
25 5 0.19
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (24 bp):
ATATTATATTTTAATTATATTTCA
Found at i:5082171 original size:3 final size:3
Alignment explanation
Indices: 5082163--5082197 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5082153 GACAGCAGTA
5082163 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5082198 GGCAAGAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5085077 original size:50 final size:50
Alignment explanation
Indices: 5085002--5085102 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
5084992 TTGTCGAAAA
5085002 GAAAGACAAATTGGCTCCACTTTATCAGGTACATTACTTATCTCCTTTTG
1 GAAAGACAAATTGGCTCCACTTTATCAGGTACATTACTTATCTCCTTTTG
5085052 GAAAGACAAATTGGCTCCACTTTATCAGGTACATTACTTATCTCCTTTTG
1 GAAAGACAAATTGGCTCCACTTTATCAGGTACATTACTTATCTCCTTTTG
5085102 G
1 G
5085103 TGCTTGATCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (50 bp):
GAAAGACAAATTGGCTCCACTTTATCAGGTACATTACTTATCTCCTTTTG
Found at i:5087988 original size:2 final size:2
Alignment explanation
Indices: 5087981--5088008 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5087971 TAAGCCAAAC
5087981 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
5088009 CTAGCAGATG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5088634 original size:20 final size:20
Alignment explanation
Indices: 5088611--5088664 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
5088601 TATTTTTTTA
*
5088611 TTATTTAATATATTAGAAAT
1 TTATTTAATATATTACAAAT
* * *
5088631 TTATATAATATTTTACATAT
1 TTATTTAATATATTACAAAT
* *
5088651 ATATTTTATATATT
1 TTATTTAATATATT
5088665 TATGTATTAA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTATTTAATATATTACAAAT
Found at i:5088697 original size:20 final size:19
Alignment explanation
Indices: 5088629--5088713 Score: 71
Period size: 20 Copynumber: 4.2 Consensus size: 19
5088619 TATATTAGAA
*
5088629 ATTTATATAATATTTTACAT
1 ATTTATATAATATTTTA-TT
* * *
5088649 ATATATTTTATATATTTATGT
1 ATTTATATAATAT-TTTAT-T
*
5088670 ATTAATATAATATTTGTATT
1 ATTTATATAATATTT-TATT
*
5088690 ATTTATATTATATTTTAATT
1 ATTTATATAATATTTT-ATT
5088710 ATTT
1 ATTT
5088714 TTATGTCATG
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
19 1 0.02
20 33 0.65
21 17 0.33
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTATATAATATTTTATT
Found at i:5088857 original size:57 final size:57
Alignment explanation
Indices: 5088789--5088904 Score: 151
Period size: 57 Copynumber: 2.0 Consensus size: 57
5088779 ATTAATTTAA
* * ** * *
5088789 TTATTCGTTTATTTATATTTTAATACTTTTGTATATTTTTATCATATTTATGTTATT
1 TTATTCATTTATTTACATTTTAATACTTTCATATATTCTTATCATATTCATGTTATT
* * *
5088846 TTATTCATTTATTTACATTTTGATACTTTCATATATTCTTATTATGTTCATGTTATT
1 TTATTCATTTATTTACATTTTAATACTTTCATATATTCTTATCATATTCATGTTATT
5088903 TT
1 TT
5088905 TATGTTATGT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (57 bp):
TTATTCATTTATTTACATTTTAATACTTTCATATATTCTTATCATATTCATGTTATT
Found at i:5092174 original size:24 final size:22
Alignment explanation
Indices: 5092140--5092184 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
5092130 TACATATATA
*
5092140 TATTTAGATAATGATAATTTATTT
1 TATTTAAATAAT--TAATTTATTT
5092164 TATTTAAATAATTAATTTATT
1 TATTTAAATAATTAATTTATT
5092185 AACGTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
24 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
TATTTAAATAATTAATTTATTT
Found at i:5092308 original size:22 final size:22
Alignment explanation
Indices: 5092283--5092329 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
5092273 TTAAAAAAAC
5092283 TATGTTATAATTTTTGATGCAT
1 TATGTTATAATTTTTGATGCAT
5092305 TATGTTATAATTTTTGATGCAT
1 TATGTTATAATTTTTGATGCAT
5092327 TAT
1 TAT
5092330 TATATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.55
Consensus pattern (22 bp):
TATGTTATAATTTTTGATGCAT
Found at i:5105911 original size:14 final size:14
Alignment explanation
Indices: 5105892--5105919 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5105882 TCTATTAATG
5105892 TTATTTAAGACGAT
1 TTATTTAAGACGAT
5105906 TTATTTAAGACGAT
1 TTATTTAAGACGAT
5105920 GAGGTTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
TTATTTAAGACGAT
Found at i:5106115 original size:12 final size:12
Alignment explanation
Indices: 5106091--5106130 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5106081 TAGTGAAAAA
*
5106091 ATATATGTATGT
1 ATATATATATGT
*
5106103 ATTTATATATGT
1 ATATATATATGT
*
5106115 ATATATATATAT
1 ATATATATATGT
5106127 ATAT
1 ATAT
5106131 GTATGAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (12 bp):
ATATATATATGT
Found at i:5107797 original size:2 final size:2
Alignment explanation
Indices: 5107790--5107821 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5107780 CCAGGTTTCG
5107790 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5107822 CCCCCATTTG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5109577 original size:21 final size:21
Alignment explanation
Indices: 5109457--5109602 Score: 63
Period size: 21 Copynumber: 6.9 Consensus size: 21
5109447 TACGAATATA
*
5109457 TTATTAAA-TTATATCAAAAG
1 TTATTAAATTTATATCAAAAT
* *
5109477 TT-GTAAAGATTATTAT-AAAAT
1 TTATTAAA-TTTA-TATCAAAAT
* * *
5109498 TTATTAAAATTATATAAAAAA
1 TTATTAAATTTATATCAAAAT
* *
5109519 TTA-CAAATATTATATTACAAAAG
1 TTATTAAAT-TTATA-T-CAAAAT
* * *
5109542 TTACT-GATTACATATCAAAAT
1 TTATTAAATT-TATATCAAAAT
5109563 TTATTAAATTTATAT-AAAAT
1 TTATTAAATTTATATCAAAAT
*
5109583 ATTATTCGAA-TTATATCAAA
1 -TTATT-AAATTTATATCAAA
5109603 TGATGTTGAA
Statistics
Matches: 96, Mismatches: 16, Indels: 26
0.70 0.12 0.19
Matches are distributed among these distances:
19 4 0.04
20 13 0.14
21 49 0.51
22 18 0.19
23 12 0.12
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.40
Consensus pattern (21 bp):
TTATTAAATTTATATCAAAAT
Found at i:5109747 original size:21 final size:21
Alignment explanation
Indices: 5109717--5109807 Score: 91
Period size: 21 Copynumber: 4.4 Consensus size: 21
5109707 TTAGTAAAGG
* *
5109717 TTATCCAAATTGCATTAAAAA
1 TTATCAAAATTACATTAAAAA
5109738 CTT-TCAAAATTACA-TAAAAA
1 -TTATCAAAATTACATTAAAAA
*
5109758 TTATCAAATTTATC-TTAAAAA
1 TTATCAAAATTA-CATTAAAAA
*
5109779 TTATCAAAATTATATTAAAAA
1 TTATCAAAATTACATTAAAAA
*
5109800 CTA-CAAAA
1 TTATCAAAA
5109808 AAAAAAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
19 2 0.03
20 19 0.32
21 36 0.61
22 2 0.03
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTACATTAAAAA
Found at i:5123456 original size:2 final size:2
Alignment explanation
Indices: 5123449--5123475 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5123439 TGAGTCCGCC
5123449 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 A
5123476 CACACACAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5124355 original size:14 final size:15
Alignment explanation
Indices: 5124336--5124373 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
5124326 ATAAAATCTA
5124336 TTTAAATATTAAAT-
1 TTTAAATATTAAATC
*
5124350 TTTAAATTTTAAATC
1 TTTAAATATTAAATC
5124365 TCTTAAATA
1 T-TTAAATA
5124374 ATATTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 1 0.05
16 6 0.30
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAAATATTAAATC
Found at i:5136818 original size:20 final size:20
Alignment explanation
Indices: 5136776--5136823 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
5136766 AATTAAAATA
* *
5136776 TTAATAAAAATAAAATTATT
1 TTAAAAAAAATAAAATTACT
5136796 TTATAAAAAAATAAAA-TACT
1 TTA-AAAAAAATAAAATTACT
5136816 TTAAAAAA
1 TTAAAAAA
5136824 TATTTTATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.20
20 9 0.36
21 11 0.44
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAAAAAAATAAAATTACT
Found at i:5142057 original size:2 final size:2
Alignment explanation
Indices: 5142045--5142094 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
5142035 CAAACATCAA
*
5142045 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
5142086 AT AT AT AT A
1 AT AT AT AT A
5142095 CAGAAAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5145024 original size:2 final size:2
Alignment explanation
Indices: 5145017--5145047 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5145007 GAAGCAAATA
5145017 AT 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 AT A
5145048 CACACACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5145052 original size:2 final size:2
Alignment explanation
Indices: 5145047--5145072 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5145037 ATATATATAT
5145047 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
5145073 TATTAACCTA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5145382 original size:2 final size:2
Alignment explanation
Indices: 5145377--5145408 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
5145367 TATATCTGTG
5145377 TA TA TA TA TA TA T- TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5145409 CACAATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5145397 original size:15 final size:15
Alignment explanation
Indices: 5145377--5145408 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5145367 TATATCTGTG
5145377 TATATATATATATTA
1 TATATATATATATTA
5145392 TATATATATATATTA
1 TATATATATATATTA
5145407 TA
1 TA
5145409 CACAATTTTC
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATTA
Found at i:5145408 original size:13 final size:13
Alignment explanation
Indices: 5145377--5145402 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5145367 TATATCTGTG
5145377 TATATATATATAT
1 TATATATATATAT
5145390 TATATATATATAT
1 TATATATATATAT
5145403 ATTATACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:5147444 original size:2 final size:2
Alignment explanation
Indices: 5147437--5147485 Score: 75
Period size: 2 Copynumber: 25.0 Consensus size: 2
5147427 AGGTTCCAAA
5147437 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG ATG A- AG A-
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG
5147478 AG AG AG AG
1 AG AG AG AG
5147486 TGACAAGGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (2 bp):
AG
Found at i:5147918 original size:2 final size:2
Alignment explanation
Indices: 5147911--5147935 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5147901 TGCCTCTTCC
5147911 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
5147936 ACCCTCATCC
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:5148713 original size:18 final size:17
Alignment explanation
Indices: 5148684--5148719 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5148674 ATATAAATAA
5148684 TAAAATGTTAATTAAAT
1 TAAAATGTTAATTAAAT
*
5148701 TAAAATAGTTAATTTAAT
1 TAAAAT-GTTAATTAAAT
5148719 T
1 T
5148720 TAATTTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAAATGTTAATTAAAT
Found at i:5152460 original size:2 final size:2
Alignment explanation
Indices: 5152453--5152492 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5152443 TTCCAATCCT
5152453 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5152493 ATTTTTCATC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5153126 original size:13 final size:13
Alignment explanation
Indices: 5153108--5153137 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5153098 TGAACTAGGG
*
5153108 TTTTAAGTTTTTT
1 TTTTAAATTTTTT
5153121 TTTTAAATTTTTT
1 TTTTAAATTTTTT
5153134 TTTT
1 TTTT
5153138 TTTGGTGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (13 bp):
TTTTAAATTTTTT
Found at i:5153700 original size:12 final size:12
Alignment explanation
Indices: 5153679--5153717 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5153669 TAGCCTTGCA
*
5153679 GCAGCTACAGCT
1 GCAGCAACAGCT
*
5153691 GCAGCAACAGCA
1 GCAGCAACAGCT
*
5153703 GCAGCAGCAGCT
1 GCAGCAACAGCT
5153715 GCA
1 GCA
5153718 TATGGGAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.31, C:0.33, G:0.28, T:0.08
Consensus pattern (12 bp):
GCAGCAACAGCT
Found at i:5156605 original size:2 final size:2
Alignment explanation
Indices: 5156600--5156638 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
5156590 TACATTTCAA
5156600 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5156639 AAATAGGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5156643 original size:14 final size:14
Alignment explanation
Indices: 5156598--5156643 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
5156588 AATACATTTC
5156598 AAATAT-ATATAT-
1 AAATATAATATATA
*
5156610 ATATATATATATATA
1 AAATATA-ATATATA
*
5156625 TAATATAATATATA
1 AAATATAATATATA
5156639 AAATA
1 AAATA
5156644 GGCATAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 5 0.19
14 17 0.63
15 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATAATATATA
Found at i:5159855 original size:25 final size:25
Alignment explanation
Indices: 5159827--5159876 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5159817 GGCTTTATCA
5159827 ACTAACATGTTTTAGGAACTTTTTT
1 ACTAACATGTTTTAGGAACTTTTTT
5159852 ACTAACATGTTTTAGGAACTTTTTT
1 ACTAACATGTTTTAGGAACTTTTTT
5159877 GGGGGTACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (25 bp):
ACTAACATGTTTTAGGAACTTTTTT
Found at i:5163818 original size:51 final size:51
Alignment explanation
Indices: 5163737--5163841 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
5163727 ACCTGAAGAT
*
5163737 TCTCAGGGGTATATAATATACTTATCTTCAACAAGATGATAAAGCCTTGGG
1 TCTCAGGGGTATATAATATACTTATATTCAACAAGATGATAAAGCCTTGGG
5163788 TCTCAGGGGTATATAATATACTTATATTCAACAAGATGATAAAGCCTTGGG
1 TCTCAGGGGTATATAATATACTTATATTCAACAAGATGATAAAGCCTTGGG
5163839 TCT
1 TCT
5163842 TTTACTGCCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Consensus pattern (51 bp):
TCTCAGGGGTATATAATATACTTATATTCAACAAGATGATAAAGCCTTGGG
Found at i:5165904 original size:22 final size:23
Alignment explanation
Indices: 5165879--5165934 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
5165869 TTATTTATAT
5165879 TATATTTATATTTTAAAA-A-TA
1 TATATTTATATTTTAAAATATTA
* *
5165900 GTATAATTATTTTTTAAAATATTA
1 -TATATTTATATTTTAAAATATTA
5165924 TATATTTATAT
1 TATATTTATAT
5165935 AAATTTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 16 0.57
23 10 0.36
24 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TATATTTATATTTTAAAATATTA
Found at i:5165948 original size:14 final size:14
Alignment explanation
Indices: 5165929--5165978 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 14
5165919 TATTATATAT
5165929 TTATATAAATTTTA
1 TTATATAAATTTTA
5165943 TTATATTAATAATTTTTA
1 TTATA-T-A-AA-TTTTA
5165961 TTATATAAA-TTTA
1 TTATATAAATTTTA
5165974 TTATA
1 TTATA
5165979 ATTAATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.28
14 5 0.16
15 3 0.09
16 2 0.06
17 3 0.09
18 10 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTATATAAATTTTA
Found at i:5165967 original size:20 final size:22
Alignment explanation
Indices: 5165919--5165967 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 22
5165909 TTTTTTAAAA
5165919 TATTATATATTTATATAAATTT
1 TATTATATATTTATATAAATTT
*
5165941 TA-T-TATA-TTA-ATAATTTT
1 TATTATATATTTATATAAATTT
5165959 TATTATATA
1 TATTATATA
5165968 AATTTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 9 0.38
19 4 0.17
20 8 0.33
21 1 0.04
22 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTATATATTTATATAAATTT
Found at i:5165981 original size:74 final size:72
Alignment explanation
Indices: 5165862--5166005 Score: 175
Period size: 74 Copynumber: 2.0 Consensus size: 72
5165852 TCACCGTCTA
*
5165862 ATAAATTTTATTTATATTATATTTATATTTTAAAAATAGTATAATTATTTTTTAAAATA-TTATA
1 ATAAATTTTATTTATATTATATTTATATTTTAAAAATAGTATAATTAATTTTTAAAATATTTATA
5165926 TATTTAT
66 TATTTAT
* ** * *
5165933 ATAAATTTTA-TTATATTAATAATTTTTATTATATAAATTTATTATAATTAATTTTTAATATATT
1 ATAAATTTTATTTATATT-AT-ATTTATATT-T-TAAAAATAGTATAATTAATTTTTAAAATATT
*
5165997 TTTATATTT
62 TATATATTT
5166006 TTATTTTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
70 7 0.11
71 12 0.20
72 8 0.13
73 1 0.02
74 24 0.39
75 9 0.15
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (72 bp):
ATAAATTTTATTTATATTATATTTATATTTTAAAAATAGTATAATTAATTTTTAAAATATTTATA
TATTTAT
Found at i:5165985 original size:29 final size:31
Alignment explanation
Indices: 5165929--5165995 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
5165919 TATTATATAT
5165929 TTATATAAATTTTATTATATTAATAATTTTTA
1 TTATATAAATTTTATTATA-TAATAATTTTTA
*
5165961 TTATATAAA-TTTATTATA-ATTAATTTTTA
1 TTATATAAATTTTATTATATAATAATTTTTA
*
5165990 ATATAT
1 TTATAT
5165996 TTTTATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 15 0.45
31 9 0.27
32 9 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
TTATATAAATTTTATTATATAATAATTTTTA
Found at i:5166007 original size:19 final size:20
Alignment explanation
Indices: 5165972--5166051 Score: 63
Period size: 22 Copynumber: 3.9 Consensus size: 20
5165962 TATATAAATT
*
5165972 TATTATAATTAATTTTTAATA
1 TATTTTAATT-ATTTTTAATA
* * *
5165993 TATTTTTA-TATTTTTATTT
1 TATTTTAATTATTTTTAATA
*
5166012 TATTTTAATTATTTTTATTTTA
1 TATTTTAATTATTTTTA--ATA
* *
5166034 TATTTAAATTATATTTAA
1 TATTTTAATTATTTTTAA
5166052 AATTATTAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
19 15 0.32
20 9 0.19
21 6 0.13
22 17 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTTTAATTATTTTTAATA
Found at i:5167072 original size:23 final size:22
Alignment explanation
Indices: 5167030--5167074 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
5167020 AATTTTGAGA
**
5167030 CATAATATTATTTTTTAAATTT
1 CATAATATTATTTTAAAAATTT
5167052 CATATATATTATTTTAAAAATTT
1 CATA-ATATTATTTTAAAAATTT
5167075 TTCAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
CATAATATTATTTTAAAAATTT
Found at i:5167401 original size:3 final size:3
Alignment explanation
Indices: 5167393--5167432 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5167383 TGCTTTCATT
5167393 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5167433 ATTTAATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5168461 original size:2 final size:2
Alignment explanation
Indices: 5168454--5168480 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5168444 ATACTATGAA
5168454 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 A
5168481 AAATAATAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5174292 original size:2 final size:2
Alignment explanation
Indices: 5174287--5174313 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5174277 GATATATGTG
5174287 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 A
5174314 AAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5174320 original size:2 final size:2
Alignment explanation
Indices: 5174315--5174345 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5174305 ATATATATAA
5174315 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5174346 AATGCGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5182420 original size:1 final size:1
Alignment explanation
Indices: 5182416--5182440 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
5182406 TTTTTTTTTT
5182416 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
5182441 CAACCAAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:5182703 original size:20 final size:21
Alignment explanation
Indices: 5182664--5182703 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5182654 GGGGGGGGGT
*
5182664 AAGCAGAACTTGAAGAAAGCA
1 AAGCAGAACGTGAAGAAAGCA
*
5182685 AAGCAGAA-GTGAAGCAAGC
1 AAGCAGAACGTGAAGAAAGC
5182704 TCGCTTAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.15, G:0.28, T:0.07
Consensus pattern (21 bp):
AAGCAGAACGTGAAGAAAGCA
Found at i:5184165 original size:17 final size:16
Alignment explanation
Indices: 5184116--5184210 Score: 51
Period size: 15 Copynumber: 6.1 Consensus size: 16
5184106 AGGATGTATT
5184116 TGATAATTTT-ATATA
1 TGATAATTTTAATATA
*
5184131 TGA-AATTCTAATAAATA
1 TGATAATTTTAAT--ATA
5184148 TGATATATTTTAATATA
1 TGATA-ATTTTAATATA
* *
5184165 TCAT--TTTTATATACA
1 TGATAATTTTA-ATATA
*
5184180 T-ATTATATTT-ATA-A
1 TGATAAT-TTTAATATA
*
5184194 TTATAATTTTAATATA
1 TGATAATTTTAATATA
5184210 T
1 T
5184211 TTATATGATT
Statistics
Matches: 63, Mismatches: 5, Indels: 23
0.69 0.05 0.25
Matches are distributed among these distances:
14 17 0.27
15 20 0.32
16 3 0.05
17 15 0.24
18 1 0.02
19 7 0.11
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (16 bp):
TGATAATTTTAATATA
Found at i:5190694 original size:42 final size:42
Alignment explanation
Indices: 5190642--5190752 Score: 170
Period size: 42 Copynumber: 2.6 Consensus size: 42
5190632 TTTTGTGAAC
* * * *
5190642 ATGGCGGTGCTCATCTTTGGAGTGCTCTGCCTCATCATGATG
1 ATGGTGGTGCTCATCTTTGGAGTGCTCAGCCGCATCATCATG
5190684 ATGGTGGTGCTCATCTTTGGAGTGCTCAGCCGCATCATCATG
1 ATGGTGGTGCTCATCTTTGGAGTGCTCAGCCGCATCATCATG
5190726 ATGGTGGTGCTCAGTC-TTGGAGTGCTC
1 ATGGTGGTGCTCA-TCTTTGGAGTGCTC
5190753 CTCAGGATGG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 62 0.97
43 2 0.03
ACGTcount: A:0.14, C:0.23, G:0.31, T:0.32
Consensus pattern (42 bp):
ATGGTGGTGCTCATCTTTGGAGTGCTCAGCCGCATCATCATG
Found at i:5190847 original size:6 final size:6
Alignment explanation
Indices: 5190831--5190897 Score: 80
Period size: 6 Copynumber: 11.2 Consensus size: 6
5190821 GACCGTGGTC
* * * * * *
5190831 ACCATG GCCATG ACCATG GCTATG AACATG AGCATG ACCATG AGCATG
1 ACCATG ACCATG ACCATG ACCATG ACCATG ACCATG ACCATG ACCATG
5190879 ACCATG ACCATG ACCATG A
1 ACCATG ACCATG ACCATG A
5190898 TCGTGGCCCA
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (6 bp):
ACCATG
Found at i:5191949 original size:2 final size:2
Alignment explanation
Indices: 5191942--5191978 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5191932 CAAGGAGCTA
*
5191942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5191979 AAGTAGGGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 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):
AT
Found at i:5194545 original size:21 final size:22
Alignment explanation
Indices: 5194519--5194586 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
5194509 TTATTAATTT
*
5194519 AATAAAAAATTATAATT-TAAA
1 AATAAAAAATAATAATTATAAA
5194540 AATAAAAAATAATAATTATAAA
1 AATAAAAAATAATAATTATAAA
* * * *
5194562 TATTAAAATTAAAAATTCATAAA
1 AATAAAAAATAATAATT-ATAAA
5194585 AA
1 AA
5194587 CCATTATCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 16 0.41
22 17 0.44
23 6 0.15
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAAAAAATAATAATTATAAA
Found at i:5194546 original size:19 final size:19
Alignment explanation
Indices: 5194508--5194546 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5194498 ATTATTTATT
*
5194508 ATTATTAATTTAATAAAAA
1 ATTATTAATTTAAAAAAAA
5194527 ATTA-TAATTTAAAAATAAA
1 ATTATTAATTTAAAAA-AAA
5194546 A
1 A
5194547 AATAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTATTAATTTAAAAAAAA
Found at i:5204253 original size:24 final size:24
Alignment explanation
Indices: 5204226--5204295 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
5204216 ACTGTAAATT
*
5204226 TAAAATATTTAAATAGATTTTATA
1 TAAAATATTTAAATAAATTTTATA
* * *
5204250 TAAAATGTATAAATATAA-ATTATA
1 TAAAATATTTAAATA-AATTTTATA
*
5204274 TAAAA-AATTAATATAAATTTTA
1 TAAAATATTTAA-ATAAATTTTA
5204296 AAAAGTAACA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
23 5 0.14
24 29 0.83
25 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (24 bp):
TAAAATATTTAAATAAATTTTATA
Found at i:5204879 original size:18 final size:18
Alignment explanation
Indices: 5204849--5204912 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
5204839 GCGGATGAAT
5204849 ATTTTAATT-TTAATTTTA
1 ATTTT-ATTATTAATTTTA
* *
5204867 ATTTTATTATTAAATTAA
1 ATTTTATTATTAATTTTA
5204885 ATTATT-TTATTATATTTT-
1 ATT-TTATTATTA-ATTTTA
5204903 ATTTTATTAT
1 ATTTTATTAT
5204913 AAATATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 5 0.13
18 28 0.74
19 5 0.13
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTATTATTAATTTTA
Found at i:5217729 original size:36 final size:36
Alignment explanation
Indices: 5217682--5217755 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
5217672 CTCCATGAGT
5217682 TATAAAAAAATCTAAATAAAGAGATTAAAACAAGTG
1 TATAAAAAAATCTAAATAAAGAGATTAAAACAAGTG
**
5217718 TATAAAAAAATCTAAATAAAGTTATTAAAACAAGTG
1 TATAAAAAAATCTAAATAAAGAGATTAAAACAAGTG
5217754 TA
1 TA
5217756 CCTACATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.26
Consensus pattern (36 bp):
TATAAAAAAATCTAAATAAAGAGATTAAAACAAGTG
Found at i:5218211 original size:3 final size:3
Alignment explanation
Indices: 5218205--5218231 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5218195 TTCTCTTTTT
5218205 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
5218232 ATCCTTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Done.