Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 60 of 82
Found at i:21629671 original size:24 final size:24
Alignment explanation
Indices: 21629626--21629677 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
21629616 TTTTTGTTGT
* *
21629626 TTTTTTAAAATATATAATAATA-A
1 TTTTTTAAAATATAAAAAAATATA
*
21629649 TTTTTTAAATTAATAAAAAAATATA
1 TTTTTTAAAAT-ATAAAAAAATATA
21629674 TTTT
1 TTTT
21629678 AGTCCTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 10 0.42
24 9 0.38
25 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTTTTAAAATATAAAAAAATATA
Found at i:21636122 original size:28 final size:29
Alignment explanation
Indices: 21636081--21636140 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
21636071 GTCTATGGGC
21636081 AATTTTTCAATTTT-GGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
21636109 AATTTTTGATTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
21636139 AA
1 AA
21636141 ATATCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
30 15 0.56
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:21644547 original size:16 final size:17
Alignment explanation
Indices: 21644528--21644580 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
21644518 TTTATGATGA
21644528 TTAAAATTTATTA-ATT
1 TTAAAATTTATTATATT
*
21644544 TTAAATTTTATTATATT
1 TTAAAATTTATTATATT
* *
21644561 TGATAAATATTATGATATT
1 TTA-AAAT-TTATTATATT
21644580 T
1 T
21644581 ACGATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 12 0.40
17 5 0.17
18 3 0.10
19 10 0.33
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (17 bp):
TTAAAATTTATTATATT
Found at i:21644567 original size:19 final size:17
Alignment explanation
Indices: 21644528--21644580 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 17
21644518 TTTATGATGA
*
21644528 TTAAAATTTATTA-ATT
1 TTAAATTTTATTATATT
21644544 TTAAATTTTATTATATT
1 TTAAATTTTATTATATT
* *
21644561 TGATAAATATTATGATATT
1 T--TAAATTTTATTATATT
21644580 T
1 T
21644581 ACGATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 12 0.39
17 4 0.13
19 15 0.48
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (17 bp):
TTAAATTTTATTATATT
Found at i:21649049 original size:19 final size:19
Alignment explanation
Indices: 21649005--21649041 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
21648995 CCATTTGACT
21649005 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
21649024 TATTGGAGTATGATTTGA
1 TATTGGAGTATGATTTGA
21649042 AGTTTGGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:21652332 original size:35 final size:36
Alignment explanation
Indices: 21652250--21652337 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 36
21652240 TCTCACTAGC
21652250 TCATGTGCACTCTCACACCGCACATAGCTAGAATCA
1 TCATGTGCACTCTCACACCGCACATAGCTAGAATCA
* * ** * *
21652286 TCCTGTACACTCTCATGCCGCATA-AGGTA-ATATCA
1 TCATGTGCACTCTCACACCGCACATAGCTAGA-ATCA
*
21652321 TCATGTGCACTCCCACA
1 TCATGTGCACTCTCACA
21652338 TTGCACATGG
Statistics
Matches: 40, Mismatches: 11, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
34 1 0.03
35 20 0.50
36 19 0.47
ACGTcount: A:0.28, C:0.33, G:0.14, T:0.25
Consensus pattern (36 bp):
TCATGTGCACTCTCACACCGCACATAGCTAGAATCA
Found at i:21652359 original size:39 final size:37
Alignment explanation
Indices: 21652323--21652527 Score: 147
Period size: 39 Copynumber: 5.5 Consensus size: 37
21652313 TAATATCATC
* *
21652323 ATGTGCACTCCCACATTGCACATGGCATATATTATCAGT
1 ATGTGCACTCACACA--GCACATGGCATATATCATCAGT
* * * * *
21652362 GTGTGCACTCACACAACACA--CCA-CTATCA-CCGT
1 ATGTGCACTCACACAGCACATGGCATATATCATCAGT
*
21652395 CATGTGCACTCCCACATCGCACATGGCATATATCATCAGT
1 -ATGTGCACTCACACA--GCACATGGCATATATCATCAGT
* * * *
21652435 GTGTGCACTCACACAACACA--CCA-CTATCATC-GT
1 ATGTGCACTCACACAGCACATGGCATATATCATCAGT
*
21652468 CATGTGCACTCCCACACCGCACATGGCATATATCATCAGT
1 -ATGTGCACT--CACACAGCACATGGCATATATCATCAGT
* *
21652508 GTGTGCACTCACACAACACA
1 ATGTGCACTCACACAGCACA
21652528 CCACTATCAC
Statistics
Matches: 126, Mismatches: 26, Indels: 30
0.69 0.14 0.16
Matches are distributed among these distances:
33 5 0.04
34 32 0.25
35 4 0.03
36 13 0.10
37 17 0.13
38 4 0.03
39 46 0.37
40 5 0.04
ACGTcount: A:0.29, C:0.34, G:0.14, T:0.23
Consensus pattern (37 bp):
ATGTGCACTCACACAGCACATGGCATATATCATCAGT
Found at i:21652401 original size:34 final size:34
Alignment explanation
Indices: 21652363--21652556 Score: 126
Period size: 34 Copynumber: 5.4 Consensus size: 34
21652353 ATTATCAGTG
*
21652363 TGTGCACTCACACAACACACCACTATCACCGTCA
1 TGTGCACTCACACAACACACCACTATCACAGTCA
* * * * *
21652397 TGTGCACTCCCACATCGCACATGGCATATATCATCAGT-G
1 TGTGCACTCACACA--ACACA--CCA-CTATCA-CAGTCA
21652436 TGTGCACTCACACAACACACCACTATCATC-GTCA
1 TGTGCACTCACACAACACACCACTATCA-CAGTCA
** * * *
21652470 TGTGCACTCCCACACCGCACATGGCATATATCATCAGT-G
1 TGTGCACT--CACACAACACA--CCA-CTATCA-CAGTCA
21652509 TGTGCACTCACACAACACACCACTATCACTA-TCA
1 TGTGCACTCACACAACACACCACTATCAC-AGTCA
*
21652543 TGTGCACTCCCACA
1 TGTGCACTCACACA
21652557 TTGCACACGC
Statistics
Matches: 123, Mismatches: 22, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
33 4 0.03
34 47 0.38
35 4 0.03
36 13 0.11
37 13 0.11
38 4 0.03
39 33 0.27
40 5 0.04
ACGTcount: A:0.29, C:0.37, G:0.12, T:0.22
Consensus pattern (34 bp):
TGTGCACTCACACAACACACCACTATCACAGTCA
Found at i:21652403 original size:73 final size:73
Alignment explanation
Indices: 21652321--21652563 Score: 423
Period size: 73 Copynumber: 3.3 Consensus size: 73
21652311 GGTAATATCA
* *
21652321 TCATGTGCACTCCCACATTGCACATGGCATATATTATCAGTGTGTGCACTCACACAACACACCAC
1 TCATGTGCACTCCCACATCGCACATGGCATATATCATCAGTGTGTGCACTCACACAACACACCAC
21652386 TATCACCG
66 TATCACCG
21652394 TCATGTGCACTCCCACATCGCACATGGCATATATCATCAGTGTGTGCACTCACACAACACACCAC
1 TCATGTGCACTCCCACATCGCACATGGCATATATCATCAGTGTGTGCACTCACACAACACACCAC
*
21652459 TATCATCG
66 TATCACCG
*
21652467 TCATGTGCACTCCCACACCGCACATGGCATATATCATCAGTGTGTGCACTCACACAACACACCAC
1 TCATGTGCACTCCCACATCGCACATGGCATATATCATCAGTGTGTGCACTCACACAACACACCAC
**
21652532 TATCACTA
66 TATCACCG
*
21652540 TCATGTGCACTCCCACATTGCACA
1 TCATGTGCACTCCCACATCGCACA
21652564 CGCACGGTTA
Statistics
Matches: 161, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 161 1.00
ACGTcount: A:0.29, C:0.35, G:0.13, T:0.23
Consensus pattern (73 bp):
TCATGTGCACTCCCACATCGCACATGGCATATATCATCAGTGTGTGCACTCACACAACACACCAC
TATCACCG
Found at i:21653372 original size:15 final size:13
Alignment explanation
Indices: 21653350--21653389 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
21653340 AGGATGAAGT
21653350 AAGAAAAGAAAAGC
1 AAGAAAAGAAAA-C
21653364 AACGAAAAGAAAAC
1 AA-GAAAAGAAAAC
*
21653378 AAGGAAAGAAAA
1 AAGAAAAGAAAA
21653390 ATGAAAAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 9 0.38
14 5 0.21
15 10 0.42
ACGTcount: A:0.72, C:0.07, G:0.20, T:0.00
Consensus pattern (13 bp):
AAGAAAAGAAAAC
Found at i:21654254 original size:39 final size:39
Alignment explanation
Indices: 21654206--21654299 Score: 152
Period size: 39 Copynumber: 2.4 Consensus size: 39
21654196 CAAGGAAGCT
*
21654206 TCCAATAGAGAACAATACATAAGAAAACCAAGATAGGGA
1 TCCAGTAGAGAACAATACATAAGAAAACCAAGATAGGGA
* *
21654245 TCCAGTAGAGAACAATACATCAGAAAACCATGATAGGGA
1 TCCAGTAGAGAACAATACATAAGAAAACCAAGATAGGGA
*
21654284 TCCAGCAGAGAACAAT
1 TCCAGTAGAGAACAAT
21654300 TCTAATGATA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.49, C:0.18, G:0.19, T:0.14
Consensus pattern (39 bp):
TCCAGTAGAGAACAATACATAAGAAAACCAAGATAGGGA
Found at i:21655456 original size:24 final size:23
Alignment explanation
Indices: 21655412--21655456 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
21655402 ATATAGTAAC
*
21655412 AAAAAAATTTAAGAAGGAATTTA
1 AAAAAAATTTAAGAAGAAATTTA
21655435 AAAAAGAATTTAAAGAA-AAATT
1 AAAAA-AATTT-AAGAAGAAATT
21655457 ACTGTCACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 9 0.47
25 5 0.26
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.24
Consensus pattern (23 bp):
AAAAAAATTTAAGAAGAAATTTA
Found at i:21656399 original size:8 final size:8
Alignment explanation
Indices: 21656386--21656415 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
21656376 AAAAATTATA
21656386 TTAAAATT
1 TTAAAATT
21656394 TTAAAATT
1 TTAAAATT
*
21656402 TTAATATT
1 TTAAAATT
21656410 TTAAAA
1 TTAAAA
21656416 ATAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTAAAATT
Found at i:21657027 original size:69 final size:70
Alignment explanation
Indices: 21656905--21657039 Score: 245
Period size: 69 Copynumber: 1.9 Consensus size: 70
21656895 ATTCATTATT
* *
21656905 TTTTATATTATATTATTTATATTGAAAAGAGGACCATGTGAAACACGGGTGTCAGCCATGGCATC
1 TTTTATATTATATTATTTATATTGAAAAGAGGAACATGTGAAACAAGGGTGTCAGCCATGGCATC
21656970 AATAA
66 AATAA
21656975 TTTTATATTATATTATTTATATTG-AAAGAGGAACATGTGAAACAAGGGTGTCAGCCATGGCATC
1 TTTTATATTATATTATTTATATTGAAAAGAGGAACATGTGAAACAAGGGTGTCAGCCATGGCATC
21657039 A
66 A
21657040 TCATTGTTGA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
69 39 0.62
70 24 0.38
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (70 bp):
TTTTATATTATATTATTTATATTGAAAAGAGGAACATGTGAAACAAGGGTGTCAGCCATGGCATC
AATAA
Found at i:21661952 original size:14 final size:14
Alignment explanation
Indices: 21661931--21661964 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
21661921 TCTTGTTAGT
21661931 TAAATTTTAGTTAA
1 TAAATTTTAGTTAA
*
21661945 TTAATTTTAGTTAA
1 TAAATTTTAGTTAA
21661959 TAAATT
1 TAAATT
21661965 AATTTTGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (14 bp):
TAAATTTTAGTTAA
Found at i:21665154 original size:2 final size:2
Alignment explanation
Indices: 21665149--21665174 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21665139 TTGGTTTTAA
21665149 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
21665175 TTTTTTCTTC
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:21672054 original size:24 final size:23
Alignment explanation
Indices: 21672014--21672064 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
21672004 ATTTCTTTCT
21672014 AATT-GAGTACCTCATGT-CACTC
1 AATTGGAGTACCTCATGTCCAC-C
*
21672036 AATTGGAGTCACCTGATGTCCACC
1 AATTGGAGT-ACCTCATGTCCACC
21672060 AATTG
1 AATTG
21672065 TCTCATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 4 0.16
23 4 0.16
24 14 0.56
25 3 0.12
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (23 bp):
AATTGGAGTACCTCATGTCCACC
Found at i:21673825 original size:253 final size:248
Alignment explanation
Indices: 21673121--21674130 Score: 1049
Period size: 250 Copynumber: 4.1 Consensus size: 248
21673111 TCATATACAA
* * **
21673121 TTTTATCCTTATTATTATTTATTTTAAAATTAAAATTTGTAAATCGTTAAATACTTTTAGTTTGA
1 TTTTATCTTTATTATTATTTATTTTTAAATTAAAATTTGTAAATCGTTAAATA-TTTTAACTTGA
*
21673186 AAATATAAATTTTAATATTTTTTTCATT-AAATTAGATTTTTGTGACTTAATTGACCTATTACAT
65 AAATATAAATTTAAATATTTTTTTCATTAAAATTAGATTTTTGTGACTTAATTGACCTATTACAT
* * ** * * * * *
21673250 TAACTTTTACACATTTACGTTAAAATGTTTAAATATGTTTGTTCCATCTTTATGAGTTTTTACGT
130 TAACTCTCACACATTTATATTAAGAT-TTTAAATATATTTGTTTCACCTTTATGAG-TTTTACAT
** * *
21673315 CAATTCTTACAA-TTTTACGTCATA--CTTTTCAAAAAGTGACTTTTAATAATAATTAT
193 CAATTCTTA-AAGTTTTACGTCA-AGGCTTTTCAATGAGAG-CTTTTAACAATAATTAT
* * *
21673371 TTTTATCTTTATTATTATTTATTTTTAAATTAAAATTTATAAATCGTTAAATACTTTTAGCTCGA
1 TTTTATCTTTATTATTATTTATTTTTAAATTAAAATTTGTAAATCGTTAAATA-TTTTAACTTGA
* ***
21673436 AAATATAAATTTAAATATTTTTTTCATTAAAATTATATTTTTGTGACTTAATTGACCTATTATGG
65 AAATATAAATTTAAATATTTTTTTCATTAAAATTAGATTTTTGTGACTTAATTGACCTATTACAT
* * * * * * * *
21673501 TAACTCTCATACATTTATGTTTAGATTTTAAA-AGTAATTGTTTGACTTTTATGAATTTTCATAT
130 TAACTCTCACACATTTATATTAAGATTTTAAATA-TATTTGTTTCACCTTTATGAGTTTT-ACAT
* *
21673565 TAATTCTTAAAGTTTTACGTCAAGGCTTTTCGATGAGAGCTTTTAACAATAATTAT
193 CAATTCTTAAAGTTTTACGTCAAGGCTTTTCAATGAGAGCTTTTAACAATAATTAT
*
21673621 TTTTATCTTTATTATTATTTATTTTTAAAATTAAAATTTGTAAATCTTTAAAT-TTTCTGAACTT
1 TTTTATCTTTATTATTATTTATTTTT-AAATTAAAATTTGTAAATCGTTAAATATTT-T-AACTT
* * * * * *
21673685 GAGAATATAAATTTAAATGTTTAGTTTTCATTAAAATTAGATTTTTATGACTTAGTTGACTTATA
63 GAAAATATAAATTTAAATATTT--TTTTCATTAAAATTAGATTTTTGTGACTTAATTGACCTATT
* *
21673750 ACATTAACTCTCACACATTTATATTAAGGTTTTAAATATTTTTGTTTCACCTTTATGAGTTCTTA
126 ACATTAACTCTCACACATTTATATTAAGATTTTAAATATATTTGTTTCACCTTTATGAGTT-TTA
* * ** * * *
21673815 CATCAATTCTTACAGCTTTATATTAAGGCTTTTTAATAGAAAG-TTTTAACAATAATTAT
190 CATCAATTCTTAAAGTTTTACGTCAAGGCTTTTCAAT-GAGAGCTTTTAACAATAATTAT
*
21673874 TTTTATCTTTATTATTATTTATTTTTAAATTAAAATTTGTAAATCGTTAAATACTTTTAA-TCAG
1 TTTTATCTTTATTATTATTTATTTTTAAATTAAAATTTGTAAATCGTTAAATA-TTTTAACT-TG
* * *
21673938 AGAATATAAATTTAAAAAATTTTTTT-ATTAAAATTAGATTTTTGTGACTTATTTGACC---T--
64 AAAATATAAATTT-AAATATTTTTTTCATTAAAATTAGATTTTTGTGACTTAATTGACCTATTAC
* * * **
21673997 GTTAACTTTCACACATTTATATTAAGATTTT-AA-ATA--TGCTT-A---TTATGAGTTTTTATG
128 ATTAACTCTCACACATTTATATTAAGATTTTAAATATATTTGTTTCACCTTTATGAG-TTTTACA
* * * ** * * **
21674054 TCAATTTTTACAA-TTTTATGTTAAACCTTTTCAATTACAATTTTTAACAATAATTAT
192 TCAATTCTTA-AAGTTTTACGTCAAGGCTTTTCAATGAGAGCTTTTAACAATAATTAT
21674111 TTTTATCTTTATTATTATTT
1 TTTTATCTTTATTATTATTT
21674131 CTTAGAAAGT
Statistics
Matches: 650, Mismatches: 89, Indels: 55
0.82 0.11 0.07
Matches are distributed among these distances:
236 2 0.00
237 72 0.11
238 3 0.00
240 1 0.00
241 4 0.01
243 2 0.00
244 2 0.00
245 28 0.04
249 11 0.02
250 199 0.31
251 114 0.18
252 41 0.06
253 161 0.25
254 10 0.02
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (248 bp):
TTTTATCTTTATTATTATTTATTTTTAAATTAAAATTTGTAAATCGTTAAATATTTTAACTTGAA
AATATAAATTTAAATATTTTTTTCATTAAAATTAGATTTTTGTGACTTAATTGACCTATTACATT
AACTCTCACACATTTATATTAAGATTTTAAATATATTTGTTTCACCTTTATGAGTTTTACATCAA
TTCTTAAAGTTTTACGTCAAGGCTTTTCAATGAGAGCTTTTAACAATAATTAT
Found at i:21678706 original size:16 final size:18
Alignment explanation
Indices: 21678674--21678706 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21678664 TAATGAATGA
21678674 AAAAAGAGAAAGTAAAAT
1 AAAAAGAGAAAGTAAAAT
21678692 AAAAAGA-AAAG-AAAA
1 AAAAAGAGAAAGTAAAA
21678707 CATAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (18 bp):
AAAAAGAGAAAGTAAAAT
Found at i:21678711 original size:18 final size:18
Alignment explanation
Indices: 21678674--21678711 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
21678664 TAATGAATGA
*
21678674 AAAAAGAGAAAGTAAAAT
1 AAAAAGAGAAAGAAAAAT
21678692 AAAAAGA-AAAGAAAACAT
1 AAAAAGAGAAAGAAAA-AT
21678710 AA
1 AA
21678712 TAATTAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.76, C:0.03, G:0.13, T:0.08
Consensus pattern (18 bp):
AAAAAGAGAAAGAAAAAT
Found at i:21678720 original size:17 final size:15
Alignment explanation
Indices: 21678700--21678733 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
21678690 ATAAAAAGAA
21678700 AAGAAAACATAATAATT
1 AAGAAAA-ATAA-AATT
21678717 AAGAAAAATAAAATT
1 AAGAAAAATAAAATT
21678732 AA
1 AA
21678734 ATACGAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 4 0.24
17 7 0.41
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (15 bp):
AAGAAAAATAAAATT
Found at i:21679105 original size:16 final size:16
Alignment explanation
Indices: 21679084--21679122 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
21679074 AGATTATATT
21679084 AATATTTTATAAT-AAA
1 AATATTTT-TAATGAAA
21679100 AATATTTTTAATGAAA
1 AATATTTTTAATGAAA
*
21679116 GATATTT
1 AATATTT
21679123 GATATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (16 bp):
AATATTTTTAATGAAA
Found at i:21688261 original size:58 final size:57
Alignment explanation
Indices: 21688144--21688263 Score: 168
Period size: 58 Copynumber: 2.1 Consensus size: 57
21688134 AAGGTCTCAT
* *
21688144 CTTTGCATGCATAGCATTTATTAAATCGCATAAAATAAATCTATCACATGCATATTA
1 CTTTGCATGCATAGCATTTATTAAATCGCATAAAATAAATCTATCACATGCAAACTA
* * * **
21688201 CTTTGCATTGCATAGCATTTCTTAAATTGCATAAAATAAATCTATCAGATTTAAACTA
1 CTTTGCA-TGCATAGCATTTATTAAATCGCATAAAATAAATCTATCACATGCAAACTA
21688259 CTTTG
1 CTTTG
21688264 AATGATCATC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 7 0.13
58 48 0.87
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.38
Consensus pattern (57 bp):
CTTTGCATGCATAGCATTTATTAAATCGCATAAAATAAATCTATCACATGCAAACTA
Found at i:21692200 original size:13 final size:13
Alignment explanation
Indices: 21692182--21692206 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21692172 ATTTTCAAAA
21692182 ATTTTATAAAATT
1 ATTTTATAAAATT
21692195 ATTTTATAAAAT
1 ATTTTATAAAAT
21692207 CCCATTTTCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:21708796 original size:28 final size:28
Alignment explanation
Indices: 21708755--21708818 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
21708745 AAATTTTTTG
*
21708755 AAAATTACACTTTTG-CCCATATAAAGTGA
1 AAAATTACACTTTTGCCCCA-A-AAACTGA
*
21708784 AAAATTACATTTTTGCCCCAAAAACTGA
1 AAAATTACACTTTTGCCCCAAAAACTGA
21708812 AAAATTA
1 AAAATTA
21708819 TCCATAGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 13 0.41
29 15 0.47
30 4 0.12
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (28 bp):
AAAATTACACTTTTGCCCCAAAAACTGA
Found at i:21720121 original size:11 final size:11
Alignment explanation
Indices: 21720105--21720134 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21720095 AAGGGTCATT
21720105 GAGAAAATCAA
1 GAGAAAATCAA
21720116 GAGAAAATCAA
1 GAGAAAATCAA
*
21720127 GATAAAAT
1 GAGAAAAT
21720135 ATTTTATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (11 bp):
GAGAAAATCAA
Found at i:21720149 original size:138 final size:137
Alignment explanation
Indices: 21720005--21720260 Score: 406
Period size: 137 Copynumber: 1.9 Consensus size: 137
21719995 GAGAAAATTG
* *
21720005 AGAGAATTGAGGTGTAAGTGGAGAGGAGGAAGAAGAGAGAATTGAGGTGTGGTGTGTTGAGAATG
1 AGAGAATTGAGGTGTAAGTGGAAAAGAGGAAGAAGAGAGAATTGAGGTGTGGT-TGTTGAGAATG
* * * * *
21720070 AA-TGTAGCGGCTTATATTTATAGGGAAGGGTCATTGAGAAAATCAAGAGAAAATCAAGATAAAA
65 AACAG-AGAGGCTGATATTTATAGGGAAGGGTCACTGAAAAAATCAAGAGAAAATCAAGATAAAA
21720134 TATTTTATA
129 TATTTTATA
21720143 AGAGAATTGAGGTGTAAGTGGAAAAGAGGAAGAAGAGAGAATTGAGGTGTGGTTGTTGAGAATGA
1 AGAGAATTGAGGTGTAAGTGGAAAAGAGGAAGAAGAGAGAATTGAGGTGTGGTTGTTGAGAATGA
* *
21720208 ACAGGGAGGCTGATATTTATAGGGAAGGGTCACTGAAAAAATCAAGATAAAAT
66 ACAGAGAGGCTGATATTTATAGGGAAGGGTCACTGAAAAAATCAAGAGAAAAT
21720261 ATTTTATAAC
Statistics
Matches: 108, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
137 56 0.52
138 52 0.48
ACGTcount: A:0.40, C:0.04, G:0.33, T:0.23
Consensus pattern (137 bp):
AGAGAATTGAGGTGTAAGTGGAAAAGAGGAAGAAGAGAGAATTGAGGTGTGGTTGTTGAGAATGA
ACAGAGAGGCTGATATTTATAGGGAAGGGTCACTGAAAAAATCAAGAGAAAATCAAGATAAAATA
TTTTATA
Found at i:21720412 original size:108 final size:108
Alignment explanation
Indices: 21720221--21720434 Score: 320
Period size: 108 Copynumber: 2.0 Consensus size: 108
21720211 GGGAGGCTGA
* * * **
21720221 TATTTATAGGGAAGGGTCACTGAAAAAATCAAGATAAAATATTTTATAACGTTATAAAAATAACT
1 TATTTATAGGAAAGGGTCACTGAAAAAATCAAAATAAAATATTCTATAACACTATAAAAATAACT
* *
21720286 TATAAAATAATCTAAAAGATAAAATCAATAATTGATTCAATAG
66 TATAAAATAATCTAAAAGACAAAATCAATAACTGATTCAATAG
* * *
21720329 TATTTATAGGAAAGGGTTATTGAGAAAATCAAAATAAAATATTCTATAACACTATAAAAATAACT
1 TATTTATAGGAAAGGGTCACTGAAAAAATCAAAATAAAATATTCTATAACACTATAAAAATAACT
* *
21720394 TATAAAATAATCTGAAAGACCAAATCAATAACTGATTCAAT
66 TATAAAATAATCTAAAAGACAAAATCAATAACTGATTCAAT
21720435 CAAAGACTAA
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
108 94 1.00
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (108 bp):
TATTTATAGGAAAGGGTCACTGAAAAAATCAAAATAAAATATTCTATAACACTATAAAAATAACT
TATAAAATAATCTAAAAGACAAAATCAATAACTGATTCAATAG
Found at i:21720681 original size:204 final size:204
Alignment explanation
Indices: 21720307--21720700 Score: 666
Period size: 204 Copynumber: 1.9 Consensus size: 204
21720297 CTAAAAGATA
21720307 AAATCAATAATTGATTCAATAGTATTTATAGGAAAGGGTTATTGAGAAAATCAAAATAAAATATT
1 AAATCAATAATTGATTCAATAGTATTTATAGGAAAGGGTTATTGAGAAAATCAAAATAAAATATT
21720372 CTATAACACTATAAAAATAACTTATAAAATAATCTGAAAGACCAAATCAATAACTGATTCAATCA
66 CTATAACACTATAAAAATAACTTATAAAATAATCTGAAAGACCAAATCAATAACTGATTCAATCA
* *
21720437 AAGACTAATTCTTTTTTCACCATGGTAAAAAGATTGAATAAAGATAAGGTAAAAATAAAACTGAC
131 AAGACTAACTCTTTTTTCACCATGGTAAAAAGACTGAATAAAGATAAGGTAAAAA-AAAACTGAC
21720502 CATCAAGACC
195 CATCAAGACC
*
21720512 AAATCAATAATTGATTCAATAGTATTTATAGGAAATGGTTACTT-AGAAAATCAAAATAAAATAT
1 AAATCAATAATTGATTCAATAGTATTTATAGGAAAGGGTTA-TTGAGAAAATCAAAATAAAATAT
** *
21720576 TCTATAATGCTATAAAAA-AGCTTATAAAATAATCTGAAAGACCAAATCAATAACTGATTCAATC
65 TCTATAACACTATAAAAATAACTTATAAAATAATCTGAAAGACCAAATCAATAACTGATTCAATC
* * * *
21720640 AAAGACTAACTCTTTTTTCACCATGGTGAAAGGACTGAATAATGGTAAGGTAAAAAAAAAC
130 AAAGACTAACTCTTTTTTCACCATGGTAAAAAGACTGAATAAAGATAAGGTAAAAAAAAAC
21720701 ATTGATCGTC
Statistics
Matches: 178, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
203 5 0.03
204 95 0.53
205 76 0.43
206 2 0.01
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.28
Consensus pattern (204 bp):
AAATCAATAATTGATTCAATAGTATTTATAGGAAAGGGTTATTGAGAAAATCAAAATAAAATATT
CTATAACACTATAAAAATAACTTATAAAATAATCTGAAAGACCAAATCAATAACTGATTCAATCA
AAGACTAACTCTTTTTTCACCATGGTAAAAAGACTGAATAAAGATAAGGTAAAAAAAAACTGACC
ATCAAGACC
Found at i:21727252 original size:23 final size:26
Alignment explanation
Indices: 21727207--21727258 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
21727197 TGTTATTGTG
*
21727207 TTGTGATGATTGCCATGTCGCTATTA
1 TTGTGATGATTGCCATGTCGCTATGA
21727233 TTGTGATGATTGCC-T-T-GCTATGA
1 TTGTGATGATTGCCATGTCGCTATGA
21727256 TTG
1 TTG
21727259 CAGTCAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 9 0.36
24 1 0.04
25 1 0.04
26 14 0.56
ACGTcount: A:0.17, C:0.13, G:0.25, T:0.44
Consensus pattern (26 bp):
TTGTGATGATTGCCATGTCGCTATGA
Found at i:21729449 original size:82 final size:82
Alignment explanation
Indices: 21729304--21729456 Score: 220
Period size: 82 Copynumber: 1.9 Consensus size: 82
21729294 ATATATTATA
* * **
21729304 TAAAATTATTGTCTATTATGAATATTTTTATAATTGAGAGAGGGGGATTCGAATTCTGGTCTTTA
1 TAAAATTATTGTCCATTATAAATATTTTTATAATTGAGAGAGGGGGATTCGAATTCTAATCTTTA
*
21729369 GGCAGAGGATTATACAT
66 GACAGAGGATTATACAT
*
21729386 TAAAATTATTGTCCATTATAAATATTTTTATAATT-AGGGGAGGGGGATTCGAA-TCTTAATCTT
1 TAAAATTATTGTCCATTATAAATATTTTTATAATTGA-GAGAGGGGGATTCGAATTC-TAATCTT
21729449 TAGACAGA
64 TAGACAGA
21729457 ATATTATATA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
81 3 0.05
82 60 0.95
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (82 bp):
TAAAATTATTGTCCATTATAAATATTTTTATAATTGAGAGAGGGGGATTCGAATTCTAATCTTTA
GACAGAGGATTATACAT
Found at i:21730461 original size:15 final size:14
Alignment explanation
Indices: 21730432--21730466 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
21730422 AAATTCAAAG
*
21730432 AAAAAGAGAAAAAT
1 AAAAAGAAAAAAAT
21730446 AAAAAGAAAAAGAAT
1 AAAAAGAAAAA-AAT
21730461 AAAAAG
1 AAAAAG
21730467 GAATAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (14 bp):
AAAAAGAAAAAAAT
Found at i:21731447 original size:25 final size:25
Alignment explanation
Indices: 21731413--21731460 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
21731403 AAAATAATAA
21731413 TAATAAAAAAATATATTTTTTAAAT
1 TAATAAAAAAATATATTTTTTAAAT
21731438 TAATAAAAAAATATATTTTTTAA
1 TAATAAAAAAATATATTTTTTAA
21731461 TTTTTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TAATAAAAAAATATATTTTTTAAAT
Found at i:21738437 original size:28 final size:28
Alignment explanation
Indices: 21738406--21738496 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 28
21738396 GCAGGGTTTG
21738406 ACATAAACAACTTTAAAATCAATTTGAA
1 ACATAAACAACTTTAAAATCAATTTGAA
** **
21738434 ACATAAACAAC--T--CCTC-ATCCGAA
1 ACATAAACAACTTTAAAATCAATTTGAA
* *
21738457 GCTTAAACAACTTTAAAATCAATTTGAA
1 ACATAAACAACTTTAAAATCAATTTGAA
*
21738485 AAATAAACAACT
1 ACATAAACAACT
21738497 CCTTATCCGA
Statistics
Matches: 45, Mismatches: 13, Indels: 10
0.66 0.19 0.15
Matches are distributed among these distances:
23 14 0.31
24 2 0.04
25 1 0.02
26 1 0.02
27 2 0.04
28 25 0.56
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.25
Consensus pattern (28 bp):
ACATAAACAACTTTAAAATCAATTTGAA
Found at i:21738485 original size:51 final size:51
Alignment explanation
Indices: 21738409--21738635 Score: 211
Period size: 51 Copynumber: 4.6 Consensus size: 51
21738399 GGGTTTGACA
*
21738409 TAAACAACTTTAAAATCAATTTGAAACATAAACAACTCCTCATCCGAAGCT
1 TAAACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAAGCT
* *
21738460 TAAACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTTATCCGAGGC-
1 TAAACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAAGCT
** * * *
21738510 TCCACAACTTT----T-AATTTGAAGAAT-AACAACTCCTCAACC-AAGGTT
1 TAAACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAA-GCT
* ** * * * *
21738555 TAGACAACTTTAGCATCAATTT-AAAGAATAAGCAACTCTTCATCCTAGGCT
1 TAAACAACTTTAAAATCAATTTGAAA-AATAAACAACTCCTCATCCGAAGCT
* *
21738606 TAGACAGCTTTAACAATCAATTTGAAAAAT
1 TAAACAACTTTAA-AATCAATTTGAAAAAT
21738636 TAGTAACATC
Statistics
Matches: 143, Mismatches: 21, Indels: 23
0.76 0.11 0.12
Matches are distributed among these distances:
43 1 0.01
44 14 0.10
45 20 0.14
46 1 0.01
49 3 0.02
50 17 0.12
51 72 0.50
52 12 0.08
53 3 0.02
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (51 bp):
TAAACAACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAAGCT
Found at i:21738605 original size:95 final size:96
Alignment explanation
Indices: 21738426--21738605 Score: 226
Period size: 95 Copynumber: 1.9 Consensus size: 96
21738416 CTTTAAAATC
*
21738426 AATTTGAAACATAAACAACTCCTCATCCGAAGCTTAAACAACTTTAAAATCAATTTGAAAAATAA
1 AATTTGAAACATAAACAACTCCTCAACCGAAGCTTAAACAACTTTAAAATCAATTTGAAAAATAA
21738491 ACAACTCCTTATCCGAGGCTCCACAACTTTT
66 ACAACTCCTTATCCGAGGCTCCACAACTTTT
* * **
21738522 AATTTGAAGA-AT-AACAACTCCTCAACC-AAGGTTTAGACAACTTTAGCATCAATTT-AAAGAA
1 AATTTGAA-ACATAAACAACTCCTCAACCGAA-GCTTAAACAACTTTAAAATCAATTTGAAA-AA
* *
21738583 TAAGCAACT-CTTCATCCTAGGCT
63 TAAACAACTCCTT-ATCCGAGGCT
21738606 TAGACAGCTT
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
94 8 0.11
95 54 0.74
96 10 0.14
97 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (96 bp):
AATTTGAAACATAAACAACTCCTCAACCGAAGCTTAAACAACTTTAAAATCAATTTGAAAAATAA
ACAACTCCTTATCCGAGGCTCCACAACTTTT
Found at i:21744771 original size:11 final size:11
Alignment explanation
Indices: 21744753--21744786 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
21744743 CCCTTTTTGG
21744753 TCTT-TTTTTT
1 TCTTCTTTTTT
21744763 TCTTCTTTTTT
1 TCTTCTTTTTT
21744774 TCTTCTTCTTTT
1 TCTTCTT-TTTT
21744786 T
1 T
21744787 TATTTATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.18
11 13 0.59
12 5 0.23
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TCTTCTTTTTT
Found at i:21744772 original size:14 final size:14
Alignment explanation
Indices: 21744753--21744787 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
21744743 CCCTTTTTGG
21744753 TCTTTTTTT-TTCT
1 TCTTTTTTTCTTCT
21744766 TCTTTTTTTCTTCT
1 TCTTTTTTTCTTCT
21744780 TCTTTTTT
1 TCTTTTTT
21744788 ATTTATTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TCTTTTTTTCTTCT
Found at i:21746590 original size:15 final size:15
Alignment explanation
Indices: 21746546--21746630 Score: 59
Period size: 15 Copynumber: 5.5 Consensus size: 15
21746536 ATAAAACAAT
21746546 AATAATAATAAA-AGA
1 AATAA-AATAAATAGA
*
21746561 AATAAATAGAAAATAGA
1 AATAAA-A-TAAATAGA
*
21746578 AATAAAATGAATAGTGA
1 AATAAAATAAATA--GA
* *
21746595 AAT-AAGTAAATAAA
1 AATAAAATAAATAGA
21746609 AATAAAATACAATA-A
1 AATAAAATA-AATAGA
21746624 AATAAAA
1 AATAAAA
21746631 AATTAAAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
14 5 0.09
15 22 0.39
16 15 0.27
17 14 0.25
ACGTcount: A:0.71, C:0.01, G:0.08, T:0.20
Consensus pattern (15 bp):
AATAAAATAAATAGA
Found at i:21747578 original size:19 final size:20
Alignment explanation
Indices: 21747550--21747624 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 20
21747540 TAATTTATTA
21747550 TTTTTCAATTAAGATTTAAG
1 TTTTTCAATTAAGATTTAAG
*
21747570 TTTTT-AATTGAACAGTAATTATATG
1 TTTTTCAATT--A-AG--ATT-TAAG
21747595 CTTTTTCAATTAAGATTTAAG
1 -TTTTTCAATTAAGATTTAAG
21747616 TTTTT-AATT
1 TTTTTCAATT
21747625 GAACAGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 17
0.70 0.03 0.27
Matches are distributed among these distances:
19 8 0.18
20 10 0.22
21 4 0.09
22 5 0.11
24 5 0.11
25 4 0.09
26 5 0.11
27 4 0.09
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.52
Consensus pattern (20 bp):
TTTTTCAATTAAGATTTAAG
Found at i:21747605 original size:27 final size:26
Alignment explanation
Indices: 21747570--21747643 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 26
21747560 AAGATTTAAG
21747570 TTTTTAATTGAACAGTAATTATATGC
1 TTTTTAATTGAACAGTAATTATATGC
*
21747596 TTTTTCAATT--A-AG--ATT-TAAG-
1 TTTTT-AATTGAACAGTAATTATATGC
21747616 TTTTTAATTGAACAGTAATTATATGC
1 TTTTTAATTGAACAGTAATTATATGC
21747642 TT
1 TT
21747644 ACTACAATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 16
0.68 0.04 0.29
Matches are distributed among these distances:
19 4 0.11
20 5 0.13
21 4 0.11
22 5 0.13
24 5 0.13
25 4 0.11
26 7 0.18
27 4 0.11
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.49
Consensus pattern (26 bp):
TTTTTAATTGAACAGTAATTATATGC
Found at i:21747606 original size:46 final size:46
Alignment explanation
Indices: 21747550--21747643 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
21747540 TAATTTATTA
21747550 TTTTTCAATTAAGATTTAAGTTTTTAATTGAACAGTAATTATATGC
1 TTTTTCAATTAAGATTTAAGTTTTTAATTGAACAGTAATTATATGC
21747596 TTTTTCAATTAAGATTTAAGTTTTTAATTGAACAGTAATTATATGC
1 TTTTTCAATTAAGATTTAAGTTTTTAATTGAACAGTAATTATATGC
21747642 TT
1 TT
21747644 ACTACAATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (46 bp):
TTTTTCAATTAAGATTTAAGTTTTTAATTGAACAGTAATTATATGC
Found at i:21747786 original size:43 final size:43
Alignment explanation
Indices: 21747722--21747803 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
21747712 CCTATTCTTT
21747722 AAGCAGAGAGAACATACACCTATTAATGAGTCAAATGCTTTTA
1 AAGCAGAGAGAACATACACCTATTAATGAGTCAAATGCTTTTA
** *
21747765 AAGCAGAGA-AATCATGTACCTATTAATGAGTTAAATGCT
1 AAGCAGAGAGAA-CATACACCTATTAATGAGTCAAATGCT
21747804 CGAATATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 2 0.06
43 33 0.94
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (43 bp):
AAGCAGAGAGAACATACACCTATTAATGAGTCAAATGCTTTTA
Found at i:21751478 original size:2 final size:2
Alignment explanation
Indices: 21751471--21751500 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21751461 AAATTTTCAT
*
21751471 TA TA TA TA TA GA 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
21751501 ATGTCATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:21752238 original size:26 final size:26
Alignment explanation
Indices: 21752202--21752253 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
21752192 TTTGACTATA
21752202 CATATGATTACAAATGGTAAAAGTAG
1 CATATGATTACAAATGGTAAAAGTAG
21752228 CATATGATTACAAATGGTAAAAGTAG
1 CATATGATTACAAATGGTAAAAGTAG
21752254 GGCAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (26 bp):
CATATGATTACAAATGGTAAAAGTAG
Found at i:21753537 original size:168 final size:167
Alignment explanation
Indices: 21753073--21753668 Score: 425
Period size: 171 Copynumber: 3.6 Consensus size: 167
21753063 GTTTTTAGCG
* * * * * * * * *
21753073 ATAAAGATTATGAGAATAAATAAGTT-ATTGCAAAACATGTTACCGATTCTCATTCAAAATCACT
1 ATAAAGATTCTGAAAATAAATAAATTGCTT-CAAACCATATCACAGATTCTAATTCAAAATCACT
* * * * * * * * * *
21753137 TCTCAGATAA-T-TTTATCAATTGAGTAAACATGCTGCTATTACATATTATTTTG-GGATAAATT
65 TTTTAGACAACTATTTATCAATTGAATCAACATGTTGTTAATACATATTATCTTGACG-TAAATT
* * * * ** *
21753199 TCGTCTATGA--TC-TCTTCTT-TTTTTGTAT-TTAATG
129 CCATCCATGATCTCTTCTTCTTCTTTTTTTATCTTGGTA
* * * * * * *
21753233 ATAAAAATTCTGAAAATAAATAAATTACTTTAAACCATGTCACAGATTCTACTTCAGAATCATTT
1 ATAAAGATTCTGAAAATAAATAAATTGCTTCAAACCATATCACAGATTCTAATTCAAAATCACTT
* * * * *
21753298 TTTAGACAACTAATTTATGAATTGAGTCAACATGTTGTTAATACATATTATTTTGAGGTAAATTT
66 TTTAGACAACT-ATTTATCAATTGAATCAACATGTTGTTAATACATATTATCTTGACGTAAATTC
* * * *
21753363 CATCCATGATCTTTTTTCTTTTTTTTTTTTTGTCTTTGGTA
130 CATCCATGATC--TCTTCTTCTTCTTTTTTTATC-TTGGTA
* * *
21753404 ATAAAGATTCTGAGAATAAATAAGTTGCTTCAAACCATATCACTA-ATTCTAATTCAAAATTACT
1 ATAAAGATTCTGAAAATAAATAAATTGCTTCAAACCATATCAC-AGATTCTAATTCAAAATCACT
* * * *
21753468 TTTTATATAA-T-TTTATCAATTGAATCAACATGTTAG-TAATATATATTATCTTGCCGTAAATT
65 TTTTAGACAACTATTTATCAATTGAATCAACATGTT-GTTAATACATATTATCTTGACGTAAATT
*
21753530 CCATCCATGATCTCTTCTTCTTCTTTTTTTATCTTGGTG
129 CCATCCATGATCTCTTCTTCTTCTTTTTTTATCTTGGTA
* * * * * * * * *
21753569 ATAAAGATTTTAAAAATAAATAAATTGTTTCAAATCATTTCAC-CATTATAACTCAAAACCAC-T
1 ATAAAGATTCTGAAAATAAATAAATTGCTTCAAACCATATCACAGATTCTAATTCAAAATCACTT
* * * *
21753632 TCTGGTACAAC--TTTACCAGTTGAATCAACATGTTGTT
66 TTTAG-ACAACTATTTATCAATTGAATCAACATGTTGTT
21753669 GCTATGTGTT
Statistics
Matches: 346, Mismatches: 71, Indels: 34
0.77 0.16 0.08
Matches are distributed among these distances:
160 55 0.16
161 3 0.01
163 55 0.16
164 41 0.12
165 41 0.12
166 17 0.05
167 1 0.00
168 60 0.17
169 8 0.02
170 1 0.00
171 63 0.18
172 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (167 bp):
ATAAAGATTCTGAAAATAAATAAATTGCTTCAAACCATATCACAGATTCTAATTCAAAATCACTT
TTTAGACAACTATTTATCAATTGAATCAACATGTTGTTAATACATATTATCTTGACGTAAATTCC
ATCCATGATCTCTTCTTCTTCTTTTTTTATCTTGGTA
Found at i:21772868 original size:3 final size:3
Alignment explanation
Indices: 21772860--21772885 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
21772850 TTCACAGGGG
21772860 CAA CAA CAA CAA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CA
21772886 GTAACAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:21777743 original size:46 final size:46
Alignment explanation
Indices: 21777670--21777762 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
21777660 AGAACCAGAG
*
21777670 TTTTAAGTGAAACAAAGAAAACCAAACACCAAACAACATAGTATAA
1 TTTTAAATGAAACAAAGAAAACCAAACACCAAACAACATAGTATAA
* **
21777716 TTTTAAATGAAACAAAGATAATTAAACACCAAACAACATAGTATAA
1 TTTTAAATGAAACAAAGAAAACCAAACACCAAACAACATAGTATAA
21777762 T
1 T
21777763 CTTACCTGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.22
Consensus pattern (46 bp):
TTTTAAATGAAACAAAGAAAACCAAACACCAAACAACATAGTATAA
Found at i:21777761 original size:25 final size:25
Alignment explanation
Indices: 21777693--21777762 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 25
21777683 AAAGAAAACC
21777693 AAACACCAAACAACATAGTATAATTT
1 AAACACCAAACAACATAGTATAA-TT
* **
21777719 TAA-ATGAAAC-A-A-AG-ATAATT
1 AAACACCAAACAACATAGTATAATT
21777739 AAACACCAAACAACATAGTATAAT
1 AAACACCAAACAACATAGTATAAT
21777763 CTTACCTGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 11
0.66 0.12 0.22
Matches are distributed among these distances:
20 4 0.12
21 9 0.27
22 3 0.09
23 2 0.06
24 3 0.09
25 10 0.30
26 2 0.06
ACGTcount: A:0.57, C:0.16, G:0.06, T:0.21
Consensus pattern (25 bp):
AAACACCAAACAACATAGTATAATT
Found at i:21788117 original size:8 final size:8
Alignment explanation
Indices: 21788104--21788129 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
21788094 ACTGACCACC
21788104 AATCATGA
1 AATCATGA
21788112 AATCATGA
1 AATCATGA
21788120 AATCATGA
1 AATCATGA
21788128 AA
1 AA
21788130 GATTACTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.23
Consensus pattern (8 bp):
AATCATGA
Found at i:21794684 original size:38 final size:37
Alignment explanation
Indices: 21794621--21794742 Score: 144
Period size: 38 Copynumber: 3.3 Consensus size: 37
21794611 GCTAACAGTA
* *
21794621 GGTGGTGCCCTGGATGCAATAGATTATGGAGTCGATGTG
1 GGTGGTGCCC-GGATGC-ATTGATTATGGGGTCGATGTG
21794660 GGTGGTGCCTCGGATGCATTGATTATGGGGTCGATGTG
1 GGTGGTGCC-CGGATGCATTGATTATGGGGTCGATGTG
*
21794698 GGTGGTGCCCCGGA--CA-T-ATAATTGGGGTCGATGTG
1 GGTGGTG-CCCGGATGCATTGATTA-TGGGGTCGATGTG
21794733 GGTGGTGCCC
1 GGTGGTGCCC
21794743 TGTATGTGTA
Statistics
Matches: 77, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
34 6 0.08
35 21 0.27
36 2 0.03
38 30 0.39
39 17 0.22
40 1 0.01
ACGTcount: A:0.16, C:0.16, G:0.41, T:0.28
Consensus pattern (37 bp):
GGTGGTGCCCGGATGCATTGATTATGGGGTCGATGTG
Found at i:21796163 original size:66 final size:66
Alignment explanation
Indices: 21796057--21796190 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
21796047 ACATTGTTAT
21796057 TGCTTGTGTAGCTATGTATAACTACATCTGAAAATTACCTATTACTGATACTCTCTTGGAGCAGG
1 TGCTTGTGTAGCTATGTATAACTACATCTGAAAATTACCTATTACTGATACTCTCTTGGAGCAGG
21796122 C
66 C
21796123 TGCTTGTGTAGCTATGTATAACTACATCTGAAAATTACCTATTACTGATACTCTCTTGGAGCAGG
1 TGCTTGTGTAGCTATGTATAACTACATCTGAAAATTACCTATTACTGATACTCTCTTGGAGCAGG
21796188 C
66 C
21796189 TG
1 TG
21796191 ATAATGAAGG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (66 bp):
TGCTTGTGTAGCTATGTATAACTACATCTGAAAATTACCTATTACTGATACTCTCTTGGAGCAGG
C
Found at i:21800835 original size:17 final size:17
Alignment explanation
Indices: 21800813--21800847 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21800803 CAATCTCCTA
21800813 AGAACATGCTTTGGTAG
1 AGAACATGCTTTGGTAG
21800830 AGAACATGCTTTGGTAG
1 AGAACATGCTTTGGTAG
21800847 A
1 A
21800848 TTTAGTAGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (17 bp):
AGAACATGCTTTGGTAG
Found at i:21804379 original size:32 final size:32
Alignment explanation
Indices: 21804338--21804403 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
21804328 GCTTGGATCC
21804338 AACTAAACATATTTTAAGTTATAAAATTATTA
1 AACTAAACATATTTTAAGTTATAAAATTATTA
21804370 AACTAAACATATTTTAAGTTATAAAATTATTA
1 AACTAAACATATTTTAAGTTATAAAATTATTA
21804402 AA
1 AA
21804404 TTTCACGTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (32 bp):
AACTAAACATATTTTAAGTTATAAAATTATTA
Found at i:21804402 original size:16 final size:16
Alignment explanation
Indices: 21804351--21804402 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
21804341 TAAACATATT
21804351 TTAAGTTATAAAATTA
1 TTAAGTTATAAAATTA
**
21804367 TTAAACTA-AACATATT-
1 TTAAGTTATAA-A-ATTA
21804383 TTAAGTTATAAAATTA
1 TTAAGTTATAAAATTA
21804399 TTAA
1 TTAA
21804403 ATTTCACGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 5 0.18
16 18 0.64
17 5 0.18
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (16 bp):
TTAAGTTATAAAATTA
Found at i:21804614 original size:14 final size:15
Alignment explanation
Indices: 21804589--21804617 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21804579 TAGACTTTTA
21804589 TAATTAATAATTAAT
1 TAATTAATAATTAAT
21804604 TAATT-ATAATTAAT
1 TAATTAATAATTAAT
21804618 CAAAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATTAATAATTAAT
Found at i:21804847 original size:12 final size:12
Alignment explanation
Indices: 21804832--21804857 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21804822 TTAATTTTTT
21804832 AAAAATTATTTA
1 AAAAATTATTTA
21804844 AAAAATTATTTA
1 AAAAATTATTTA
21804856 AA
1 AA
21804858 TATGTTGTCA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAAATTATTTA
Found at i:21813238 original size:17 final size:16
Alignment explanation
Indices: 21813215--21813260 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
21813205 TTATTTCTAA
21813215 ATAAAAGACAATTGTA-
1 ATAAAAGACAATT-TAT
*
21813231 ATTAAAAGACAAATTAT
1 A-TAAAAGACAATTTAT
21813248 ATAAAAGACAATT
1 ATAAAAGACAATT
21813261 AATGTCTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.26
Consensus pattern (16 bp):
ATAAAAGACAATTTAT
Found at i:21825929 original size:55 final size:55
Alignment explanation
Indices: 21825845--21825990 Score: 249
Period size: 55 Copynumber: 2.7 Consensus size: 55
21825835 ATGTTTACAT
* *
21825845 TGCTTGGGTCTATTC-TTTGGGCCAAACTGATCAAATGGTTGGTCCAGCCCATTAC
1 TGCTTGGGTCGA-TCGTTTGGGCCAAACTGATCAAATGGTTGGTCCAGCCCATTAA
21825900 TGCTTGGGTCGATCGTTTGGGCCAAACTGATCAAATGGTTGGTCCAGCCCATTAA
1 TGCTTGGGTCGATCGTTTGGGCCAAACTGATCAAATGGTTGGTCCAGCCCATTAA
*
21825955 TGCTTGGGTCGATTGTTTGGGCCAAACTGATCAAAT
1 TGCTTGGGTCGATCGTTTGGGCCAAACTGATCAAAT
21825991 TGGTCCAATC
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
54 2 0.02
55 85 0.98
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (55 bp):
TGCTTGGGTCGATCGTTTGGGCCAAACTGATCAAATGGTTGGTCCAGCCCATTAA
Found at i:21827505 original size:88 final size:88
Alignment explanation
Indices: 21827350--21827520 Score: 229
Period size: 88 Copynumber: 1.9 Consensus size: 88
21827340 GGATTTTCAT
* * *
21827350 TTTGTGTGTGTAATTGAAACTAAAATGTGAGTAAATTAGTTTAGTTGTGTTTTGAGTTTACTAGT
1 TTTGTCTGTGTAATTGAAACTAAAATGTGAATAAATTAGTTTAGTTGTATTTTGAGTTTACTAGT
21827415 TTGTGTTTGGA-AACAACAGATTC
66 TTGTGTTT-GACAACAACAGATTC
* * * * * *
21827438 TTTGTCTGTGTATTTGAAATTCAAATGTTAATAAATTAGTTTTGTTGTATTTTGAGTTTGC-AGG
1 TTTGTCTGTGTAATTGAAACTAAAATGTGAATAAATTAGTTTAGTTGTATTTTGAGTTTACTA-G
21827502 TTTGTGTTTGACAACAACA
65 TTTGTGTTTGACAACAACA
21827521 AATTTTAACT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
87 3 0.04
88 69 0.96
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.45
Consensus pattern (88 bp):
TTTGTCTGTGTAATTGAAACTAAAATGTGAATAAATTAGTTTAGTTGTATTTTGAGTTTACTAGT
TTGTGTTTGACAACAACAGATTC
Found at i:21828976 original size:28 final size:28
Alignment explanation
Indices: 21828914--21828985 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
21828904 CATTAAAATG
* * *
21828914 TAACAA-AATGTTTTTTAATATGTCGTA
1 TAACAACAATATTTTTTAACATGGCGTA
*
21828941 TAACAACAATATTTTTTAACATGGCGTG
1 TAACAACAATATTTTTTAACATGGCGTA
*
21828969 TAATAACAATATTTTTT
1 TAACAACAATATTTTTT
21828986 TTTCAACATA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 6 0.15
28 33 0.85
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (28 bp):
TAACAACAATATTTTTTAACATGGCGTA
Found at i:21829104 original size:52 final size:52
Alignment explanation
Indices: 21829048--21829148 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
21829038 TGTACATGAC
* * *
21829048 ATGTAACAACAATATTTTTTTTCAATATGGTGTGTAACAACCTAACTATAGA
1 ATGTAACAACAATATTTTTTTTCAACATGGCGTGTAACAACCAAACTATAGA
*
21829100 ATGTAACAACAGTATTTTTTTTCAACATGGCGTGTAACAACCAAACTAT
1 ATGTAACAACAATATTTTTTTTCAACATGGCGTGTAACAACCAAACTAT
21829149 GGCTTGACAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (52 bp):
ATGTAACAACAATATTTTTTTTCAACATGGCGTGTAACAACCAAACTATAGA
Found at i:21829293 original size:66 final size:67
Alignment explanation
Indices: 21829125--21829323 Score: 294
Period size: 66 Copynumber: 3.0 Consensus size: 67
21829115 TTTTTTTCAA
* * *
21829125 CATGGCGTGTAACAACCAAACTATGGCTTGACACATATTTTTGTACATGACGTGTAACAACCCTA
1 CATGACGTGTAACAACCAAACCATGGCTTGACACATATTTTTGTACATGGCGTGTAACAA-CCTA
21829190 A-T
65 ACT
*
21829192 CATGACGTGTAACAACCAAACCATGGCTTGACACATATTTTTGTACATGGCATGTAACAACCTAA
1 CATGACGTGTAACAACCAAACCATGGCTTGACACATATTTTTGTACATGGCGTGTAACAACCTAA
21829257 CT
66 CT
* * * * *
21829259 -ATGCCGTGTAACAATCTAACCATGACTTGTCACATATTTTTGTACATGGCGTGTAACAACCTAA
1 CATGACGTGTAACAACCAAACCATGGCTTGACACATATTTTTGTACATGGCGTGTAACAACCTAA
21829323 C
66 C
21829324 CATAGCTTAT
Statistics
Matches: 121, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
66 64 0.53
67 57 0.47
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (67 bp):
CATGACGTGTAACAACCAAACCATGGCTTGACACATATTTTTGTACATGGCGTGTAACAACCTAA
CT
Found at i:21829337 original size:45 final size:45
Alignment explanation
Indices: 21829263--21829372 Score: 168
Period size: 45 Copynumber: 2.4 Consensus size: 45
21829253 CTAACTATGC
*
21829263 CGTGTAACAATCTAACCATGACTTGTCACATATTTTTGTACATGG
1 CGTGTAACAATCTAACCATGACTTATCACATATTTTTGTACATGG
*
21829308 CGTGTAACAACCTAACCAT-AGCTTATCACATATTTTTGTACATGG
1 CGTGTAACAATCTAACCATGA-CTTATCACATATTTTTGTACATGG
* *
21829353 TGTATAACAATCTAACCATG
1 CGTGTAACAATCTAACCATG
21829373 GCGCGTAACA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
44 1 0.02
45 57 0.98
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.34
Consensus pattern (45 bp):
CGTGTAACAATCTAACCATGACTTATCACATATTTTTGTACATGG
Found at i:21830766 original size:8 final size:8
Alignment explanation
Indices: 21830753--21830795 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
21830743 TTTACATAAA
21830753 TTTTTTCT
1 TTTTTTCT
21830761 TTTTTTCT
1 TTTTTTCT
*
21830769 TTTTTCCT
1 TTTTTTCT
*
21830777 TTTTCT-T
1 TTTTTTCT
21830784 TTTTTTCT
1 TTTTTTCT
21830792 TTTT
1 TTTT
21830796 CATGGGTCGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTTCT
Found at i:21830771 original size:15 final size:15
Alignment explanation
Indices: 21830753--21830796 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
21830743 TTTACATAAA
21830753 TTTTTTCTTTTT-TT
1 TTTTTTCTTTTTCTT
21830767 CTTTTTTCCTTTTTCTT
1 -TTTTTT-CTTTTTCTT
21830784 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
21830797 ATGGGTCGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 13 0.48
16 12 0.44
17 2 0.07
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTCTTTTTCTT
Found at i:21830795 original size:7 final size:7
Alignment explanation
Indices: 21830753--21830787 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
21830743 TTTACATAAA
21830753 TTTTTTC
1 TTTTTTC
21830760 TTTTTTTC
1 -TTTTTTC
21830768 TTTTTTC
1 TTTTTTC
*
21830775 CTTTTTC
1 TTTTTTC
21830782 TTTTTT
1 TTTTTT
21830788 TTCTTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:21836208 original size:35 final size:35
Alignment explanation
Indices: 21836169--21836255 Score: 102
Period size: 35 Copynumber: 2.5 Consensus size: 35
21836159 AACATTGTTT
* * * **
21836169 AATTAAGTTGTTGTGCTTAATTAATTAAATTATTC
1 AATTAAGTTATTGGGCCTAATTAATTAAATTAAAC
* *
21836204 AATTAAATTATTGGGCCTAATTGATTAAATTAAAC
1 AATTAAGTTATTGGGCCTAATTAATTAAATTAAAC
21836239 AATTAAGTTAATTGGGC
1 AATTAAGTT-ATTGGGC
21836256 TTCTTAAGGA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 36 0.84
36 7 0.16
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (35 bp):
AATTAAGTTATTGGGCCTAATTAATTAAATTAAAC
Found at i:21836209 original size:13 final size:13
Alignment explanation
Indices: 21836191--21836215 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21836181 GTGCTTAATT
21836191 AATTAAATTATTC
1 AATTAAATTATTC
21836204 AATTAAATTATT
1 AATTAAATTATT
21836216 GGGCCTAATT
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTAAATTATTC
Found at i:21837979 original size:16 final size:16
Alignment explanation
Indices: 21837936--21837981 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
21837926 TTCAAATAAA
21837936 ATATCTGTTGAAAAATT
1 ATATCTGTTG-AAAATT
* *
21837953 -TGTAT-TTGAAAATT
1 ATATCTGTTGAAAATT
21837967 ATATCTGTTGAAAAT
1 ATATCTGTTGAAAAT
21837982 AAGAAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
14 6 0.26
15 6 0.26
16 11 0.48
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.43
Consensus pattern (16 bp):
ATATCTGTTGAAAATT
Found at i:21839170 original size:5 final size:5
Alignment explanation
Indices: 21839160--21839189 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
21839150 TAAGAAGGGA
*
21839160 TGCCT TGCCT TGCCT TGCCT TGCCA TGCCT
1 TGCCT TGCCT TGCCT TGCCT TGCCT TGCCT
21839190 GCTCCCCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.03, C:0.40, G:0.20, T:0.37
Consensus pattern (5 bp):
TGCCT
Found at i:21840862 original size:26 final size:26
Alignment explanation
Indices: 21840748--21840864 Score: 89
Period size: 27 Copynumber: 4.3 Consensus size: 26
21840738 TTAAAATAAA
*
21840748 AAAATATTAAAATAAAATATATAATAT
1 AAAA-ATTAAAATTAAATATATAATAT
*
21840775 AAGAATTAGAAATTAAA-ATA-AAGTAT
1 AAAAATTA-AAATTAAATATATAA-TAT
* *
21840801 AAGAAATTAAAATTTATATATATAGGTCA-
1 AA-AAATTAAAA-TTAAATATATA-AT-AT
21840830 AAGAAATTAAAA-TAACATATATAATAT
1 AA-AAATTAAAATTAA-ATATATAATAT
21840857 AAAAATTA
1 AAAAATTA
21840865 TATTAAAAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
25 2 0.03
26 22 0.30
27 24 0.33
28 10 0.14
29 14 0.19
30 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (26 bp):
AAAAATTAAAATTAAATATATAATAT
Found at i:21840932 original size:27 final size:29
Alignment explanation
Indices: 21840865--21840935 Score: 74
Period size: 33 Copynumber: 2.4 Consensus size: 29
21840855 ATAAAAATTA
*
21840865 TATTAAAAATAAAAATAAAATATATAATAC
1 TATTAAAAATAAAAATAAAATATAT-AGAC
*
21840895 TATAATAAAAAATAAAAATAAAATGTAT-GAC
1 TAT--T-AAAAATAAAAATAAAATATATAGAC
21840926 -ATTAAAAATA
1 TATTAAAAATA
21840936 TATTTAAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
27 7 0.19
28 1 0.03
30 5 0.14
31 2 0.06
32 1 0.03
33 20 0.56
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (29 bp):
TATTAAAAATAAAAATAAAATATATAGAC
Found at i:21848206 original size:2 final size:2
Alignment explanation
Indices: 21848199--21848229 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21848189 GACATCACGG
21848199 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
21848230 TGCATATGTG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:21849871 original size:21 final size:18
Alignment explanation
Indices: 21849845--21849892 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 18
21849835 TTTATATTAT
21849845 AATATTTTTAATGTTGAAAAA
1 AATATTTTT-ATG--GAAAAA
*
21849866 AATATTTTTATGGTAAAA
1 AATATTTTTATGGAAAAA
21849884 AATATTTTT
1 AATATTTTT
21849893 TTAAAACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 14 0.54
20 3 0.12
21 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (18 bp):
AATATTTTTATGGAAAAA
Found at i:21849884 original size:20 final size:20
Alignment explanation
Indices: 21849845--21849895 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
21849835 TTTATATTAT
* *
21849845 AATATTTTTAATGTTGAAAAA
1 AATATTTTT-ATGGTAAAAAA
21849866 AATATTTTTATGGTAAAAAA
1 AATATTTTTATGGTAAAAAA
* *
21849886 TATTTTTTTA
1 AATATTTTTA
21849896 AAACAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (20 bp):
AATATTTTTATGGTAAAAAA
Found at i:21857619 original size:55 final size:55
Alignment explanation
Indices: 21857500--21857609 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 55
21857490 AATCAAAAGT
21857500 CACTCATTA-TTTTTTTGTCCACATGTTGAGATGGAAACTAAAAAATATAATGTA
1 CACTCATTATTTTTTTTGTCCACATGTTGAGATGGAAACTAAAAAATATAATGTA
21857554 NCACTCATTATTTTTTTTGTCCACATGTTGAGATGGAAACTAAAAAATATAATGTA
1 -CACTCATTATTTTTTTTGTCCACATGTTGAGATGGAAACTAAAAAATATAATGTA
21857610 ATCTTATTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 9 0.17
56 45 0.83
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (55 bp):
CACTCATTATTTTTTTTGTCCACATGTTGAGATGGAAACTAAAAAATATAATGTA
Found at i:21857775 original size:21 final size:20
Alignment explanation
Indices: 21857746--21857788 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
21857736 TATTTTATTT
21857746 AATAAAATAAAAAATTAATTA
1 AATAAAAT-AAAAATTAATTA
* *
21857767 AATATAATAAAAATTATTTA
1 AATAAAATAAAAATTAATTA
21857787 AA
1 AA
21857789 CTTTTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAAAATAAAAATTAATTA
Found at i:21860373 original size:21 final size:21
Alignment explanation
Indices: 21860347--21860393 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
21860337 TTATGCATAA
*
21860347 TATTTAAGAGAATTCTTAAAT
1 TATTTAAAAGAATTCTTAAAT
21860368 TATTTAAAAGAATTCTTAAAT
1 TATTTAAAAGAATTCTTAAAT
21860389 TATTT
1 TATTT
21860394 TTAAAAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (21 bp):
TATTTAAAAGAATTCTTAAAT
Found at i:21860590 original size:13 final size:13
Alignment explanation
Indices: 21860572--21860601 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
21860562 TCACATGTCT
*
21860572 TCATATTACATCA
1 TCATATCACATCA
21860585 TCATATCACATCA
1 TCATATCACATCA
21860598 TCAT
1 TCAT
21860602 CTATTATGAT
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:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (13 bp):
TCATATCACATCA
Found at i:21861074 original size:21 final size:22
Alignment explanation
Indices: 21861036--21861096 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
21861026 TAGTCAAAGA
*
21861036 TAAATCGATTTTAA-GGTT-TT
1 TAAATCGAGTTTAAGGGTTCTT
*
21861056 ATGAATCGA-TTTAAGGGTTCTT
1 -TAAATCGAGTTTAAGGGTTCTT
21861078 TAAATCGAGTTT-AGGGTTC
1 TAAATCGAGTTTAAGGGTTC
21861097 ACTAAACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 5 0.14
21 25 0.71
22 5 0.14
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (22 bp):
TAAATCGAGTTTAAGGGTTCTT
Found at i:21861343 original size:31 final size:31
Alignment explanation
Indices: 21861267--21861343 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
21861257 TGAATCTATC
21861267 TTAAG-GTTTTCTTGAATTGAATTAAACCAGT
1 TTAAGAGTTTT-TTGAATTGAATTAAACCAGT
* ** *
21861298 TTAAGAG-TTTTTGAATTGAGTTGGACTAGT
1 TTAAGAGTTTTTTGAATTGAATTAAACCAGT
21861328 TTAAGAGTTTTTTGAA
1 TTAAGAGTTTTTTGAA
21861344 CAAAAGCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 23 0.57
31 16 0.40
32 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (31 bp):
TTAAGAGTTTTTTGAATTGAATTAAACCAGT
Found at i:21862206 original size:25 final size:25
Alignment explanation
Indices: 21862172--21862222 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
21862162 TAATTTGGGT
21862172 TGTCAACTTCTTTGAGCTATATTCC
1 TGTCAACTTCTTTGAGCTATATTCC
21862197 TGTCAACTTCTTTGAGCTATATTCC
1 TGTCAACTTCTTTGAGCTATATTCC
21862222 T
1 T
21862223 ACTCATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.45
Consensus pattern (25 bp):
TGTCAACTTCTTTGAGCTATATTCC
Found at i:21867903 original size:17 final size:18
Alignment explanation
Indices: 21867881--21867914 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
21867871 TAATAATAAT
21867881 TAATTAATTA-TTAATTA
1 TAATTAATTATTTAATTA
*
21867898 TAATTATTTATTTAATT
1 TAATTAATTATTTAATT
21867915 TAAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TAATTAATTATTTAATTA
Found at i:21868586 original size:18 final size:19
Alignment explanation
Indices: 21868565--21868610 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
21868555 TGGGTTTTAT
21868565 TTTTAGTTTGT-TTTGTTC
1 TTTTAGTTTGTCTTTGTTC
* *
21868583 TTTTACTTT-TCTTTTTTC
1 TTTTAGTTTGTCTTTGTTC
*
21868601 TTTTGGTTTG
1 TTTTAGTTTG
21868611 ACAAGCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.04, C:0.09, G:0.13, T:0.74
Consensus pattern (19 bp):
TTTTAGTTTGTCTTTGTTC
Found at i:21881421 original size:13 final size:13
Alignment explanation
Indices: 21881403--21881429 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21881393 TTAATGTTAG
21881403 ATTAAGACTGATT
1 ATTAAGACTGATT
21881416 ATTAAGACTGATT
1 ATTAAGACTGATT
21881429 A
1 A
21881430 CAATGTGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ATTAAGACTGATT
Found at i:21888916 original size:23 final size:23
Alignment explanation
Indices: 21888886--21888931 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
21888876 AAACCCAACA
21888886 GCATGTGCTGGAAAGTGGGCTGG
1 GCATGTGCTGGAAAGTGGGCTGG
21888909 GCATGTGCTGGAAAGTGGGCTGG
1 GCATGTGCTGGAAAGTGGGCTGG
21888932 TTGGGAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.48, T:0.22
Consensus pattern (23 bp):
GCATGTGCTGGAAAGTGGGCTGG
Found at i:21900658 original size:45 final size:45
Alignment explanation
Indices: 21900545--21900651 Score: 151
Period size: 45 Copynumber: 2.4 Consensus size: 45
21900535 ATATGGTTAA
*
21900545 GTTGTTACACGCCATGTACAAAAACATGTGACAAACCATGATTAG
1 GTTGTTACACGTCATGTACAAAAACATGTGACAAACCATGATTAG
* * * * *
21900590 GTTATCACACATCATGTACAAAAACATGTGATAAGCCATGATTAG
1 GTTGTTACACGTCATGTACAAAAACATGTGACAAACCATGATTAG
*
21900635 GTTGTTACATGTCATGT
1 GTTGTTACACGTCATGT
21900652 TAAAAAAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (45 bp):
GTTGTTACACGTCATGTACAAAAACATGTGACAAACCATGATTAG
Found at i:21900688 original size:52 final size:52
Alignment explanation
Indices: 21900626--21900733 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 52
21900616 TGTGATAAGC
* *
21900626 CATGATTAGGTTGTTACATGTCATGTTAAAAAAAAATACTGTTGTTTCACCT
1 CATGATTAGGTTGTTACACGTCATGTTAAAAAAAAATACTGTTGTTACACCT
* * *
21900678 CATGGTTAGGTTGTTACACGTCATGTTGAAAAAAAATACTGTTGTTACACGT
1 CATGATTAGGTTGTTACACGTCATGTTAAAAAAAAATACTGTTGTTACACCT
21900730 CATG
1 CATG
21900734 TACACAAACA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (52 bp):
CATGATTAGGTTGTTACACGTCATGTTAAAAAAAAATACTGTTGTTACACCT
Found at i:21900822 original size:25 final size:26
Alignment explanation
Indices: 21900744--21900828 Score: 127
Period size: 26 Copynumber: 3.3 Consensus size: 26
21900734 TACACAAACA
* *
21900744 TGTTATACGTCATACTTAAAAAAGGT
1 TGTTACACGTCATAGTTAAAAAAGGT
*
21900770 TGTTACACGTCATGGTTAAAAAAGGT
1 TGTTACACGTCATAGTTAAAAAAGGT
*
21900796 TGTTACACGTAATAGTT-AAAAAGGT
1 TGTTACACGTCATAGTTAAAAAAGGT
21900821 TGTTACAC
1 TGTTACAC
21900829 ACTATGTTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
25 16 0.30
26 38 0.70
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (26 bp):
TGTTACACGTCATAGTTAAAAAAGGT
Found at i:21900856 original size:33 final size:29
Alignment explanation
Indices: 21900819--21900917 Score: 96
Period size: 29 Copynumber: 3.3 Consensus size: 29
21900809 AGTTAAAAAG
*
21900819 GTTGTTACACACTATGTTGAAAAAAAATATATT
1 GTTGTTACACACCATGTTG---AAAAA-ATATT
*
21900852 GTTGTTACACGCCATGTTGAAAAAATATT
1 GTTGTTACACACCATGTTGAAAAAATATT
* *
21900881 GTTGTTACACGA-CATATT-CAAAAATATT
1 GTTGTTACAC-ACCATGTTGAAAAAATATT
21900909 -TTGTTACAC
1 GTTGTTACAC
21900918 TTTAATGCCT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
27 9 0.15
28 9 0.15
29 20 0.33
30 5 0.08
33 17 0.28
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (29 bp):
GTTGTTACACACCATGTTGAAAAAATATT
Found at i:21900912 original size:27 final size:29
Alignment explanation
Indices: 21900841--21900917 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
21900831 TATGTTGAAA
* *
21900841 AAAAATATATTGTTGTTACACGCCATGTTG
1 AAAAA-ATATTGTTGTTACACGACATATTG
21900871 AAAAAATATTGTTGTTACACGACATATT-
1 AAAAAATATTGTTGTTACACGACATATTG
*
21900899 CAAAAATATT-TTGTTACAC
1 AAAAAATATTGTTGTTACAC
21900918 TTTAATGCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 9 0.20
28 9 0.20
29 21 0.48
30 5 0.11
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (29 bp):
AAAAAATATTGTTGTTACACGACATATTG
Found at i:21904533 original size:35 final size:36
Alignment explanation
Indices: 21904487--21904569 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 36
21904477 CATAACTAGA
*
21904487 ATCATCCTGTGCACTCCCACACCGCACAA-GGCA-AT
1 ATCATCATGTGCACTCCCACACCGCA-AATGGCATAT
* **
21904522 ATCATCATGTGCACTCTCACATTGCAAATGGCATAT
1 ATCATCATGTGCACTCCCACACCGCAAATGGCATAT
21904558 ATCATCAGTGTG
1 ATCATCA-TGTG
21904570 TGCACTCACA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 2 0.05
35 26 0.63
36 9 0.22
37 4 0.10
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (36 bp):
ATCATCATGTGCACTCCCACACCGCAAATGGCATAT
Found at i:21904628 original size:52 final size:52
Alignment explanation
Indices: 21904549--21904700 Score: 277
Period size: 52 Copynumber: 2.9 Consensus size: 52
21904539 CACATTGCAA
21904549 ATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCACGCAC
1 ATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCACGCAC
* *
21904601 ATGGCATATATCATTAGTGTGTACACTCACACAGCACACCACTATCACGCAC
1 ATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCACGCAC
*
21904653 ATGCCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCAC
1 ATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCAC
21904701 CGTCTATGCA
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 95 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (52 bp):
ATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCACGCAC
Found at i:21906153 original size:21 final size:22
Alignment explanation
Indices: 21906099--21906155 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
21906089 GTTATAAAAG
* *
21906099 AATATAATTACTATTATATATA
1 AATATATTTACTTTTATATATA
* *
21906121 TATATATATACTTTTA-ATATA
1 AATATATTTACTTTTATATATA
21906142 AATATATTTACTTT
1 AATATATTTACTTT
21906156 CTATTTTGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATATTTACTTTTATATATA
Found at i:21907257 original size:5 final size:5
Alignment explanation
Indices: 21907207--21907241 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
21907197 GACATGTATC
*
21907207 ATTAT ATTAT ATTGT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
21907242 GTGCTACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:21909500 original size:21 final size:23
Alignment explanation
Indices: 21909460--21909519 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
21909450 TATATTAACA
* * *
21909460 ATATATAGTAATATACTATATTGT
1 ATATATACTAAT-TAATATACTGT
21909484 -TATATA-TAATTAATATACTGT
1 ATATATACTAATTAATATACTGT
21909505 ATAGTATACTAATTA
1 ATA-TATACTAATTA
21909520 GTAAATAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
21 9 0.29
22 6 0.19
23 10 0.32
24 6 0.19
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (23 bp):
ATATATACTAATTAATATACTGT
Found at i:21910293 original size:13 final size:13
Alignment explanation
Indices: 21910277--21910321 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
21910267 TTAATATCAC
21910277 ATTTTTTATTTTT
1 ATTTTTTATTTTT
* *
21910290 ATTTTTTATTATA
1 ATTTTTTATTTTT
*
21910303 ATTTTATATATTTT
1 ATTTTTTAT-TTTT
21910317 ATTTT
1 ATTTT
21910322 CATTTTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 19 0.73
14 7 0.27
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTTTATTTTT
Found at i:21910749 original size:2 final size:2
Alignment explanation
Indices: 21910710--21910735 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21910700 ATTAATTTCA
21910710 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
21910736 TAAAAGAAAT
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:21914553 original size:28 final size:23
Alignment explanation
Indices: 21914490--21914553 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
21914480 AGTTCAAAGA
*
21914490 TTATGTTTT-ATGAAATGAATAG
1 TTATATTTTCATGAAATGAATAG
*
21914512 TTTTATTTTCATGAAATGAATAG
1 TTATATTTTCATGAAATGAATAG
*
21914535 TTATATTTTCATAAAATGA
1 TTATATTTTCATGAAATGA
21914554 TTAAAACAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 7 0.19
23 30 0.81
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (23 bp):
TTATATTTTCATGAAATGAATAG
Found at i:21917772 original size:15 final size:15
Alignment explanation
Indices: 21917748--21917782 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
21917738 CAATTAACTT
21917748 TTAATAAAAATTAAA
1 TTAATAAAAATTAAA
*
21917763 TTAATCAAAATTAAA
1 TTAATAAAAATTAAA
*
21917778 ATAAT
1 TTAAT
21917783 GGTCCGAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAATAAAAATTAAA
Found at i:21919257 original size:2 final size:2
Alignment explanation
Indices: 21919246--21919278 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
21919236 TCTCTCTCTC
*
21919246 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21919279 CTATNCTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21919308 original size:2 final size:2
Alignment explanation
Indices: 21919303--21919363 Score: 79
Period size: 2 Copynumber: 30.5 Consensus size: 2
21919293 TCTCTCTCTC
* * *
21919303 TA TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TC TA TC
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21919346 TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA T
21919364 CAACATAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.94
3 2 0.04
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:21924068 original size:2 final size:2
Alignment explanation
Indices: 21924063--21924090 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21924053 ATATACATAT
21924063 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
21924091 TCCTTTACAT
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):
AG
Found at i:21937137 original size:2 final size:2
Alignment explanation
Indices: 21937125--21937179 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
21937115 ACTGTTTGTG
* *
21937125 TA TA TA CA TA TA TA TA TA TA TA TG 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
*
21937167 TA TA TT TA TA TA T
1 TA TA TA TA TA TA T
21937180 TTTCCTTCAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21943681 original size:34 final size:34
Alignment explanation
Indices: 21943643--21943721 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 34
21943633 CTCGATTTAA
*
21943643 GGGTGTCGCCAGTTAGGAATAGAGGGCTTTAAAG
1 GGGTGTCGCCAGTTAGGAATAGAGAGCTTTAAAG
*
21943677 GGGTGCCGCCAGTTAGGAATAGAGAGCTTTAAAG
1 GGGTGTCGCCAGTTAGGAATAGAGAGCTTTAAAG
*
21943711 GGTTGTCGCCA
1 GGGTGTCGCCA
21943722 TTTGGGTAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.25, C:0.15, G:0.37, T:0.23
Consensus pattern (34 bp):
GGGTGTCGCCAGTTAGGAATAGAGAGCTTTAAAG
Found at i:21943873 original size:130 final size:130
Alignment explanation
Indices: 21943640--21943900 Score: 423
Period size: 130 Copynumber: 2.0 Consensus size: 130
21943630 AGGCTCGATT
* *
21943640 TAAGGGTGTCGCCAGTTAGGAATAGAGGGCTTTAAAGGGGTGCCGCCAGTTAGGAATAGAGAGCT
1 TAAGGGTGTCGCCAGTTAGGAATACAGGGCTTTAAAGGGGTGCCGCCAGTTAAGAATAGAGAGCT
* *
21943705 TTAAAGGGTTGTCGCCATTTGGGTAGAGAGAGAAAGGTTCGGCGTTAGAGTAAGAGAGGAAAAGC
66 TTAAAGGGGTGTCGCCATTTGAGTAGAGAGAGAAAGGTTCGGCGTTAGAGTAAGAGAGGAAAAGC
* * * *
21943770 TAAGGGTGTCGGCGGTTAGGAATACAGGGCTTTAAAGGGGTGCTGCCGGTTAAGAATAGAGAGCT
1 TAAGGGTGTCGCCAGTTAGGAATACAGGGCTTTAAAGGGGTGCCGCCAGTTAAGAATAGAGAGCT
* * *
21943835 TTAAAGGGGTGTCGCCGTTTGAGTAGAGAGAGAAAGGTTTGGCGTTGGAGTAAGAGAGGAAAAGC
66 TTAAAGGGGTGTCGCCATTTGAGTAGAGAGAGAAAGGTTCGGCGTTAGAGTAAGAGAGGAAAAGC
21943900 T
1 T
21943901 TTGGGTCATC
Statistics
Matches: 120, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 120 1.00
ACGTcount: A:0.29, C:0.11, G:0.38, T:0.22
Consensus pattern (130 bp):
TAAGGGTGTCGCCAGTTAGGAATACAGGGCTTTAAAGGGGTGCCGCCAGTTAAGAATAGAGAGCT
TTAAAGGGGTGTCGCCATTTGAGTAGAGAGAGAAAGGTTCGGCGTTAGAGTAAGAGAGGAAAAGC
Found at i:21943903 original size:28 final size:27
Alignment explanation
Indices: 21943850--21943904 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
21943840 GGGGTGTCGC
* *
21943850 CGTTTGAGTAGAGAGAGAAAGGTTTGG
1 CGTTGGAGTAGAGAGAGAAAGCTTTGG
21943877 CGTTGGAGTA-AGAGAGGAAAAGCTTTGG
1 CGTTGGAGTAGAGAGA-G-AAAGCTTTGG
21943905 GTCATCTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 10 0.42
28 9 0.38
ACGTcount: A:0.31, C:0.05, G:0.40, T:0.24
Consensus pattern (27 bp):
CGTTGGAGTAGAGAGAGAAAGCTTTGG
Found at i:21959630 original size:2 final size:2
Alignment explanation
Indices: 21959623--21959662 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
21959613 GAAGAATTAT
*
21959623 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21959663 GCTCTTTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:21961518 original size:40 final size:40
Alignment explanation
Indices: 21961463--21961541 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
21961453 TTGACTATTT
*
21961463 TTCACCTTAGTGGGGTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
* *
21961503 TTCACCTTAGTGGGGTTTTCAATCTCGCCACGATTGGTG
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTG
21961542 TTTTTTATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
Found at i:21962955 original size:141 final size:140
Alignment explanation
Indices: 21962709--21962989 Score: 553
Period size: 141 Copynumber: 2.0 Consensus size: 140
21962699 GAAGAAGAAG
21962709 TCATGGAAGAACCTAGCCTAGAAGAAGTAGATGATGAGCTAGAAATATTCAATAATGAAGAGATA
1 TCATGGAAGAACCTAGCCTAGAAGAAGTAGATGATGAGCTAGAAATATTCAATAATGAAGAGATA
21962774 GAAGAAGTCTCTGCTGACCATGGAGAAGCTCTTGTTGTACGTCGTAACCTTAACACTGCTATGAT
66 GAAGAAGTCTCTGCTGACCATGGAGAAGCTCTTGTTGTACGTCGTAACCTTAACACTGCTATGAT
21962839 GACAGAAGAT
131 GACAGAAGAT
21962849 NTCATGGAAGAACCTAGCCTAGAAGAAGTAGATGATGAGCTAGAAATATTCAATAATGAAGAGAT
1 -TCATGGAAGAACCTAGCCTAGAAGAAGTAGATGATGAGCTAGAAATATTCAATAATGAAGAGAT
21962914 AGAAGAAGTCTCTGCTGACCATGGAGAAGCTCTTGTTGTACGTCGTAACCTTAACACTGCTATGA
65 AGAAGAAGTCTCTGCTGACCATGGAGAAGCTCTTGTTGTACGTCGTAACCTTAACACTGCTATGA
21962979 TGACAGAAGAT
130 TGACAGAAGAT
21962990 GAAAGTTGGC
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 140 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.24
Consensus pattern (140 bp):
TCATGGAAGAACCTAGCCTAGAAGAAGTAGATGATGAGCTAGAAATATTCAATAATGAAGAGATA
GAAGAAGTCTCTGCTGACCATGGAGAAGCTCTTGTTGTACGTCGTAACCTTAACACTGCTATGAT
GACAGAAGAT
Found at i:21966193 original size:5 final size:5
Alignment explanation
Indices: 21966183--21966208 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
21966173 TTTAAGATTA
21966183 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
21966209 TGTTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:21966611 original size:40 final size:40
Alignment explanation
Indices: 21966556--21966633 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
21966546 TTGGCTATTT
*
21966556 TTCACCTTAGTGGGGTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
*
21966596 TTCACCTTAGTGGGGTTTTCAACCTCGCCACGATTGGT
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGT
21966634 ATTTTTCATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
Found at i:21971392 original size:21 final size:21
Alignment explanation
Indices: 21971366--21971412 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
21971356 AAGTTGATAC
21971366 TCCAAATCCAATAAATAGCAA
1 TCCAAATCCAATAAATAGCAA
*
21971387 TCCAAATCCAATAAATATCAA
1 TCCAAATCCAATAAATAGCAA
21971408 TCCAA
1 TCCAA
21971413 TTGCCGTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.51, C:0.26, G:0.02, T:0.21
Consensus pattern (21 bp):
TCCAAATCCAATAAATAGCAA
Found at i:21972131 original size:13 final size:14
Alignment explanation
Indices: 21972110--21972142 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
21972100 GATATTATTG
*
21972110 TATATATTGTAAA-
1 TATAGATTGTAAAT
21972123 TATAGATTGTAAAT
1 TATAGATTGTAAAT
21972137 TATAGA
1 TATAGA
21972143 AATTCAATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (14 bp):
TATAGATTGTAAAT
Found at i:21974221 original size:2 final size:2
Alignment explanation
Indices: 21974214--21974257 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
21974204 CATATGCAAC
*
21974214 TA TA TA TA TA -A TA TA TA T- TA TA TA TA TA TA TA TA GTA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
21974255 TA T
1 TA T
21974258 TAACAAANTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 2 0.05
2 33 0.89
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:21974229 original size:9 final size:9
Alignment explanation
Indices: 21974215--21974257 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
21974205 ATATGCAACT
21974215 ATATATATA
1 ATATATATA
*
21974224 ATATATATT
1 ATATATATA
21974233 ATATATATA
1 ATATATATA
21974242 TATATAGTATA
1 -ATATA-TATA
21974253 A-ATAT
1 ATATAT
21974258 TAACAAANTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 1 0.03
9 19 0.63
10 6 0.20
11 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (9 bp):
ATATATATA
Found at i:21974230 original size:11 final size:11
Alignment explanation
Indices: 21974214--21974257 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
21974204 CATATGCAAC
21974214 TATATATATAA
1 TATATATATAA
21974225 TATATATTATATA
1 TATATA-TATA-A
*
21974238 TATATATATAG
1 TATATATATAA
*
21974249 TATAAATAT
1 TATATATAT
21974258 TAACAAANTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 14 0.48
12 8 0.28
13 7 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (11 bp):
TATATATATAA
Found at i:21974323 original size:2 final size:2
Alignment explanation
Indices: 21974316--21974349 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
21974306 CATATGCAAC
21974316 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
21974350 ACATCTTAAA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21977259 original size:81 final size:80
Alignment explanation
Indices: 21977118--21977285 Score: 327
Period size: 81 Copynumber: 2.1 Consensus size: 80
21977108 TAGTTTATAT
21977118 AAATTGATATATATATATATATATATATATTATGTGTACTATTAATTTGATCTTTTGATCAATTT
1 AAATTGATATATATATATATATATATATATTATGTGTACTATTAATTTGATCTTTTGATCAATTT
21977183 AGTCTAAAAATTTTA
66 AGTCTAAAAATTTTA
21977198 AAATTGNATATATATATATATATATATATATTATGTGTACTATTAATTTGATCTTTTGATCAATT
1 AAATTG-ATATATATATATATATATATATATTATGTGTACTATTAATTTGATCTTTTGATCAATT
21977263 TAGTCTAAAAATTTTA
65 TAGTCTAAAAATTTTA
21977279 AAATTGA
1 AAATTGA
21977286 AAATCGATCA
Statistics
Matches: 87, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
80 7 0.08
81 80 0.92
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (80 bp):
AAATTGATATATATATATATATATATATATTATGTGTACTATTAATTTGATCTTTTGATCAATTT
AGTCTAAAAATTTTA
Done.