Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 66 of 75
Found at i:21390487 original size:6 final size:6
Alignment explanation
Indices: 21390450--21390533 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
21390440 GGCATTGTTT
* * ** * * *
21390450 ATGATG AAGATG AAGATG ATGATG GGGCTG ATGGTG ATGGTG ATGATG
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG
* * *
21390498 ATGATG ATGATGG AAG-TG ATGATG GTGATG GTGATG
1 ATGATG ATGAT-G ATGATG ATGATG ATGATG ATGATG
21390534 CATGCAACAC
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
5 3 0.05
6 58 0.91
7 3 0.05
ACGTcount: A:0.29, C:0.01, G:0.42, T:0.29
Consensus pattern (6 bp):
ATGATG
Found at i:21390508 original size:15 final size:15
Alignment explanation
Indices: 21390450--21390533 Score: 62
Period size: 15 Copynumber: 5.6 Consensus size: 15
21390440 GGCATTGTTT
* *
21390450 ATGATGAAGATGAAG
1 ATGATGATGATGATG
** *
21390465 ATGATGATGGGGCTG
1 ATGATGATGATGATG
* *
21390480 ATGGTGATGGTGATG
1 ATGATGATGATGATG
21390495 ATGATGATGATGATGG
1 ATGATGATGATGAT-G
* *
21390511 AAG-TGATGATGGTG
1 ATGATGATGATGATG
*
21390525 ATGGTGATG
1 ATGATGATG
21390534 CATGCAACAC
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
14 3 0.06
15 48 0.89
16 3 0.06
ACGTcount: A:0.29, C:0.01, G:0.42, T:0.29
Consensus pattern (15 bp):
ATGATGATGATGATG
Found at i:21392972 original size:2 final size:2
Alignment explanation
Indices: 21392965--21392997 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
21392955 AATGATACTA
21392965 AT AT AT AT -T AT AT AT AT A- AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21392998 GAATAAGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21392981 original size:11 final size:11
Alignment explanation
Indices: 21392965--21392994 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21392955 AATGATACTA
21392965 ATATATATTAT
1 ATATATATTAT
*
21392976 ATATATAATAT
1 ATATATATTAT
21392987 ATATATAT
1 ATATATAT
21392995 ATAGAATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATATATATTAT
Found at i:21393226 original size:95 final size:94
Alignment explanation
Indices: 21393080--21393257 Score: 216
Period size: 95 Copynumber: 1.9 Consensus size: 94
21393070 TAACTAATTG
** * * * *
21393080 TATTATAAAAGTAGATACAAAATTATTTCATATTAAATTGTAACGACTAAATCTCAAAT-TCGAG
1 TATTATAAAAGTAGATACAAAATTACGTCAAATTAAATTATAACGACTAAATCTCAAATCT-AAA
21393144 TATAATAAAAGGACCAAAATCACAATTTGA
65 TATAATAAAAGGACCAAAATCACAATTTGA
* * * *
21393174 TATTATAAAAGTAGATGAGAAGATTACGTCAAATTAAATTATAGA-GACTAAATTTCATATCTAA
1 TATTATAAAAGTAGAT-ACAAAATTACGTCAAATTAAATTATA-ACGACTAAATCTCAAATCTAA
*
21393238 ATATAGTAAAAGGACCAAAA
64 ATATAATAAAAGGACCAAAA
21393258 CCAATCCCTT
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
94 16 0.23
95 52 0.74
96 2 0.03
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (94 bp):
TATTATAAAAGTAGATACAAAATTACGTCAAATTAAATTATAACGACTAAATCTCAAATCTAAAT
ATAATAAAAGGACCAAAATCACAATTTGA
Found at i:21393609 original size:22 final size:21
Alignment explanation
Indices: 21393584--21393644 Score: 52
Period size: 22 Copynumber: 2.8 Consensus size: 21
21393574 TAAAACTTAG
21393584 TTTAATAATTTATTTTAATATT
1 TTTAATAATTTATTTT-ATATT
* *
21393606 TTTATTATATTGATGTATTATATT
1 TTTAATA-ATTTAT-T-TTATATT
*
21393630 TTTTA-AATTTATTTT
1 TTTAATAATTTATTTT
21393645 TGTATAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
20 2 0.06
21 1 0.03
22 11 0.35
23 6 0.19
24 9 0.29
25 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (21 bp):
TTTAATAATTTATTTTATATT
Found at i:21394259 original size:34 final size:34
Alignment explanation
Indices: 21394211--21394278 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
21394201 AGAGAAATAT
21394211 AAAGGGCAGACCCCCCAAAAAAAAAAAAAAAGTA
1 AAAGGGCAGACCCCCCAAAAAAAAAAAAAAAGTA
*
21394245 AAAGGGCAGCCCCCCCAAAAAAAAAAAAAAAGTA
1 AAAGGGCAGACCCCCCAAAAAAAAAAAAAAAGTA
21394279 GAACTGAGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.60, C:0.22, G:0.15, T:0.03
Consensus pattern (34 bp):
AAAGGGCAGACCCCCCAAAAAAAAAAAAAAAGTA
Found at i:21414270 original size:20 final size:20
Alignment explanation
Indices: 21414224--21414261 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21414214 ATAATTCGTT
21414224 AAAAAATAAATCTTAATTTA
1 AAAAAATAAATCTTAATTTA
21414244 AAGAAAATAAA-CTTAATT
1 AA-AAAATAAATCTTAATT
21414262 ATCTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAAAATAAATCTTAATTTA
Found at i:21415987 original size:17 final size:16
Alignment explanation
Indices: 21415951--21415988 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
21415941 AGTCTTAGTA
*
21415951 ATATATTACTTTTATT
1 ATATATTACATTTATT
*
21415967 ATATATTAGATTTATT
1 ATATATTACATTTATT
21415983 -TATATT
1 ATATATT
21415989 TTTTAATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (16 bp):
ATATATTACATTTATT
Found at i:21421754 original size:34 final size:35
Alignment explanation
Indices: 21421696--21421762 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
21421686 CAAACACCAG
21421696 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
21421731 AAAATATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
21421763 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:21422007 original size:22 final size:23
Alignment explanation
Indices: 21421979--21422024 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
21421969 ATATATCGAA
21421979 CTGAATCCAAGT-TGAATTAATT
1 CTGAATCCAAGTGTGAATTAATT
**
21422001 CTGAATCCATTTGTGAATTAATT
1 CTGAATCCAAGTGTGAATTAATT
21422024 C
1 C
21422025 ACTTGTGACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (23 bp):
CTGAATCCAAGTGTGAATTAATT
Found at i:21425033 original size:9 final size:9
Alignment explanation
Indices: 21424972--21425045 Score: 55
Period size: 9 Copynumber: 7.9 Consensus size: 9
21424962 ATTTGGAAAA
21424972 TTTTATAA-
1 TTTTATAAT
21424980 TTTTATAAT
1 TTTTATAAT
21424989 TATTCTAT-AT
1 T-TT-TATAAT
21424999 TTTT-TCAACT
1 TTTTAT-AA-T
*
21425009 TTTAATACATT
1 TTTTATA-A-T
21425020 TTTTATAAT
1 TTTTATAAT
*
21425029 TTTTATAGT
1 TTTTATAAT
21425038 TTTTATAA
1 TTTTATAA
21425046 AATAAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
7 1 0.02
8 9 0.17
9 20 0.38
10 11 0.21
11 12 0.23
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:21426293 original size:29 final size:28
Alignment explanation
Indices: 21426247--21426405 Score: 156
Period size: 29 Copynumber: 5.4 Consensus size: 28
21426237 CGATTTTATT
** *
21426247 TTTTTAAAATTTGTATTTTGACCCCTCAA
1 TTTTTAAAA-TTACATTTTGACCCCTAAA
* *
21426276 TTTTTAAAAATTGCATTTTGACCTCTAAA
1 TTTTT-AAAATTACATTTTGACCCCTAAA
*
21426305 CTTTCTTAAAATTACATTTTTACCCCTAAA
1 -TTT-TTAAAATTACATTTTGACCCCTAAA
* * *
21426335 TTTTTTAAATTATATTTTAACCCCTAAA
1 TTTTTAAAATTACATTTTGACCCCTAAA
*
21426363 TTTTTTGAAATTACATTTTGACCCCTAAA
1 -TTTTTAAAATTACATTTTGACCCCTAAA
*
21426392 CTTTCTCAAAATTA
1 -TTT-TTAAAATTA
21426406 TGTTTCGGTC
Statistics
Matches: 110, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
28 22 0.20
29 52 0.47
30 34 0.31
31 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.46
Consensus pattern (28 bp):
TTTTTAAAATTACATTTTGACCCCTAAA
Found at i:21426642 original size:16 final size:17
Alignment explanation
Indices: 21426623--21426656 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
21426613 TTTCAGCAGC
21426623 AAAAGAAAGAGGA-AAG
1 AAAAGAAAGAGGAGAAG
21426639 AAAAGAAAGAGGAGAAG
1 AAAAGAAAGAGGAGAAG
21426656 A
1 A
21426657 GGAGAGGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (17 bp):
AAAAGAAAGAGGAGAAG
Found at i:21426755 original size:10 final size:11
Alignment explanation
Indices: 21426742--21426802 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 11
21426732 GAAGAGGGAA
21426742 AAAG-AGAAAG
1 AAAGAAGAAAG
*
21426752 AAAGAAGGAAG
1 AAAGAAGAAAG
21426763 -AAGAAGAAAG
1 AAAGAAGAAAG
21426773 AAA-AAG-AA-
1 AAAGAAGAAAG
21426781 AAAGAA-AAAG
1 AAAGAAGAAAG
21426791 -AAGAAG-AAG
1 AAAGAAGAAAG
21426800 AAA
1 AAA
21426803 AAAATTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
8 3 0.07
9 14 0.33
10 18 0.43
11 7 0.17
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
AAAGAAGAAAG
Found at i:21426767 original size:3 final size:3
Alignment explanation
Indices: 21426753--21426801 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
21426743 AAGAGAAAGA
* * *
21426753 AAG AAGG AAG AAG AAG AAAG AAA AAG AAA AAG AAA AAG AAG AAG AAG
1 AAG AA-G AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
21426800 AA
1 AA
21426802 AAAAATTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:21426814 original size:31 final size:33
Alignment explanation
Indices: 21426739--21426806 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
21426729 GGTGAAGAGG
*
21426739 GAAAAAGAGAAAGAAAGAAGGAAGAAGAAGAAA
1 GAAAAAGAAAAAGAAAGAAGGAAGAAGAAGAAA
21426772 GAAAAAGAAAAAGAAA-AA-GAAGAAGAAGAAA
1 GAAAAAGAAAAAGAAAGAAGGAAGAAGAAGAAA
21426803 -AAAA
1 GAAAA
21426807 TTTAAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 4 0.12
31 13 0.38
32 2 0.06
33 15 0.44
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (33 bp):
GAAAAAGAAAAAGAAAGAAGGAAGAAGAAGAAA
Found at i:21427108 original size:12 final size:13
Alignment explanation
Indices: 21427080--21427112 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
21427070 GCAGCAAGCC
*
21427080 AGAAAAAACAAAG
1 AGAAAAAACAAAA
21427093 AGAAAAAA-AAAA
1 AGAAAAAACAAAA
21427105 AGAAAAAA
1 AGAAAAAA
21427113 GCCAAGTCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (13 bp):
AGAAAAAACAAAA
Found at i:21427542 original size:18 final size:20
Alignment explanation
Indices: 21427500--21427550 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 20
21427490 CTTCTTGTTT
*
21427500 TTTTAAAAAAAATCCTCGTG
1 TTTTCAAAAAAATCCTCGTG
*
21427520 TTTTCAAAAAAAT-CTCTTG
1 TTTTCAAAAAAATCCTCGTG
21427539 -TTTCAAAAAAAT
1 TTTTCAAAAAAAT
21427551 ATTGTCTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 12 0.41
19 5 0.17
20 12 0.41
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (20 bp):
TTTTCAAAAAAATCCTCGTG
Found at i:21427555 original size:16 final size:17
Alignment explanation
Indices: 21427521--21427562 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
21427511 ATCCTCGTGT
*
21427521 TTTCAAAAAAATCTCTTG
1 TTTCAAAAAAA-CTATTG
21427539 TTTCAAAAAAA-TATTG
1 TTTCAAAAAAACTATTG
*
21427555 TCTCAAAA
1 TTTCAAAA
21427563 TTCTCGTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 11 0.50
18 11 0.50
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (17 bp):
TTTCAAAAAAACTATTG
Found at i:21434534 original size:12 final size:12
Alignment explanation
Indices: 21434517--21434542 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21434507 ATTCTAGCCG
21434517 AATTTATTCACA
1 AATTTATTCACA
21434529 AATTTATTCACA
1 AATTTATTCACA
21434541 AA
1 AA
21434543 CTAGGACAGT
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:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTTATTCACA
Found at i:21434930 original size:5 final size:5
Alignment explanation
Indices: 21434920--21434963 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
21434910 AAGATGATAG
* *
21434920 TATTT TATTT TATTT TATTT TACTT AAGTTT TATTT TACTTT TA
1 TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT TA-TTT TA
21434964 ACATATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
5 25 0.76
6 8 0.24
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (5 bp):
TATTT
Found at i:21438429 original size:19 final size:20
Alignment explanation
Indices: 21438400--21438440 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
21438390 ACCATTGTTT
*
21438400 TTTCTATTGTTTTACTATTA
1 TTTCTATTGTTATACTATTA
*
21438420 TTTC-ATTGTTATATTATTA
1 TTTCTATTGTTATACTATTA
21438439 TT
1 TT
21438441 ATATTATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTCTATTGTTATACTATTA
Found at i:21438431 original size:11 final size:11
Alignment explanation
Indices: 21438424--21438453 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21438414 CTATTATTTC
21438424 ATTGTTATATT
1 ATTGTTATATT
*
21438435 ATTATTATATT
1 ATTGTTATATT
21438446 ATTGTTAT
1 ATTGTTAT
21438454 TGTTTGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (11 bp):
ATTGTTATATT
Found at i:21440959 original size:26 final size:27
Alignment explanation
Indices: 21440914--21440970 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
21440904 AATTTTAAAA
** * *
21440914 TATTTTTAAAATACTTTTTTTATTTTT
1 TATTTTTAAAATACAATTTTTAGTGTT
21440941 TATTTTTAAAATA-AATTTTTAGTGTT
1 TATTTTTAAAATACAATTTTTAGTGTT
21440967 TATT
1 TATT
21440971 AAAAAAATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (27 bp):
TATTTTTAAAATACAATTTTTAGTGTT
Found at i:21443474 original size:25 final size:25
Alignment explanation
Indices: 21443445--21443497 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
21443435 TAAGAGCTAT
*
21443445 ATGATTTACAAGGATTATAAATTAC
1 ATGATTTACAAGGATTATAAACTAC
* *
21443470 ATGATTTACATGGTTTATAAACTAC
1 ATGATTTACAAGGATTATAAACTAC
21443495 ATG
1 ATG
21443498 GAATACATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (25 bp):
ATGATTTACAAGGATTATAAACTAC
Found at i:21443504 original size:25 final size:25
Alignment explanation
Indices: 21443445--21443506 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
21443435 TAAGAGCTAT
* * * *
21443445 ATGATTTACAAGGATTATAAATTAC
1 ATGATATACATGGTTTATAAACTAC
*
21443470 ATGATTTACATGGTTTATAAACTAC
1 ATGATATACATGGTTTATAAACTAC
21443495 ATGGA-ATACATG
1 AT-GATATACATG
21443507 ATTTTCATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 30 0.94
26 2 0.06
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (25 bp):
ATGATATACATGGTTTATAAACTAC
Found at i:21473784 original size:28 final size:28
Alignment explanation
Indices: 21473753--21473812 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
21473743 AAAAGCCCTT
*
21473753 TTTTTTTA-AATTTACCGAAATGGGCCGA
1 TTTTTTGATAATTTACCGAAATGGGCC-A
* *
21473781 TTTTTTGATTATTTACCGGAATGGGCCA
1 TTTTTTGATAATTTACCGAAATGGGCCA
21473809 TTTT
1 TTTT
21473813 CCGCGAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.45
Consensus pattern (28 bp):
TTTTTTGATAATTTACCGAAATGGGCCA
Found at i:21473879 original size:42 final size:42
Alignment explanation
Indices: 21473820--21473925 Score: 167
Period size: 42 Copynumber: 2.5 Consensus size: 42
21473810 TTTCCGCGAA
* *
21473820 ATCGCGTCCATGTCAGCGCGATGTCAGGGTACGTGTCAGGAC
1 ATCGCGTCCACGTCAGCGCGATGCCAGGGTACGTGTCAGGAC
* *
21473862 ATCGCGTCCACGTCAGCGCGATGCCAGTGTATGTGTCAGGAC
1 ATCGCGTCCACGTCAGCGCGATGCCAGGGTACGTGTCAGGAC
*
21473904 ATCGCGTCCACGTCAGAGCGAT
1 ATCGCGTCCACGTCAGCGCGAT
21473926 TTGCTTACAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.20, C:0.28, G:0.31, T:0.21
Consensus pattern (42 bp):
ATCGCGTCCACGTCAGCGCGATGCCAGGGTACGTGTCAGGAC
Found at i:21477213 original size:23 final size:21
Alignment explanation
Indices: 21477189--21477231 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
21477179 AACTCTTATA
21477189 TATATATAAGAAGGAGAATAT
1 TATATATAAGAAGGAGAATAT
21477210 TATATATAAGAAGGAGAATAT
1 TATATATAAGAAGGAGAATAT
21477231 T
1 T
21477232 TAGGGTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (21 bp):
TATATATAAGAAGGAGAATAT
Found at i:21480858 original size:9 final size:9
Alignment explanation
Indices: 21480831--21480877 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
21480821 ACAATTAATT
*
21480831 AATTTTTAA
1 AATTATTAA
*
21480840 AATT-TAAA
1 AATTATTAA
*
21480848 AATAATTAAA
1 AATTATT-AA
21480858 AATTATTAA
1 AATTATTAA
21480867 AATTATTAA
1 AATTATTAA
21480876 AA
1 AA
21480878 ATAAAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 6 0.19
9 18 0.56
10 8 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AATTATTAA
Found at i:21480858 original size:10 final size:10
Alignment explanation
Indices: 21480843--21480881 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
21480833 TTTTTAAAAT
21480843 TTAAAAATAA
1 TTAAAAATAA
*
21480853 TTAAAAATTA
1 TTAAAAATAA
*
21480863 TT-AAAATTA
1 TTAAAAATAA
21480872 TTAAAAATAA
1 TTAAAAATAA
21480882 AAATTTCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TTAAAAATAA
Found at i:21486763 original size:14 final size:14
Alignment explanation
Indices: 21486744--21486771 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21486734 AGTCAAAATA
21486744 CGGTCGGGTCGGGT
1 CGGTCGGGTCGGGT
21486758 CGGTCGGGTCGGGT
1 CGGTCGGGTCGGGT
21486772 GGCGCCTATC
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:0.00, C:0.21, G:0.57, T:0.21
Consensus pattern (14 bp):
CGGTCGGGTCGGGT
Found at i:21495593 original size:29 final size:30
Alignment explanation
Indices: 21495545--21495605 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
21495535 AATATGAGCC
* * *
21495545 TAGAGTTTTATCCCATCTCTCTTATATTTG
1 TAGAGTTTTATCCAAGCTCTCCTATATTTG
21495575 TAGA-TTTTATCCAAGCTCTCCTATATTTG
1 TAGAGTTTTATCCAAGCTCTCCTATATTTG
21495604 TA
1 TA
21495606 AATGACTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.48
Consensus pattern (30 bp):
TAGAGTTTTATCCAAGCTCTCCTATATTTG
Found at i:21503488 original size:3 final size:3
Alignment explanation
Indices: 21503480--21503507 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
21503470 AATAAATCCT
21503480 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
21503508 GGCTGGTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:21514741 original size:2 final size:2
Alignment explanation
Indices: 21514734--21514762 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21514724 TCCCATTATT
21514734 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21514763 TNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21516079 original size:12 final size:12
Alignment explanation
Indices: 21516062--21516087 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21516052 GTCTTATTCT
21516062 GGATTCAGATTA
1 GGATTCAGATTA
21516074 GGATTCAGATTA
1 GGATTCAGATTA
21516086 GG
1 GG
21516088 GTCGCCTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (12 bp):
GGATTCAGATTA
Found at i:21518214 original size:2 final size:2
Alignment explanation
Indices: 21518207--21518238 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21518197 AACACATTTC
21518207 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
21518239 TNNNNNNNNN
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:21528025 original size:31 final size:31
Alignment explanation
Indices: 21527960--21528026 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
21527950 AAAAGAATTA
* *
21527960 AATTTGACCATTAACCTTTCAGAAAGAGTCG
1 AATTTGACCATCAACCTTTCAAAAAGAGTCG
* * * *
21527991 AATTTGACCATCAGCCTTTTAAAAATAGTTG
1 AATTTGACCATCAACCTTTCAAAAAGAGTCG
21528022 AATTT
1 AATTT
21528027 TTTTAAATGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (31 bp):
AATTTGACCATCAACCTTTCAAAAAGAGTCG
Found at i:21529720 original size:31 final size:31
Alignment explanation
Indices: 21529684--21529750 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
21529674 ATTTAGCGGA
21529684 GAGTGACCAAAATAGAAAC-GATCTAAAATGT
1 GAGTGACCAAAATA-AAACTGATCTAAAATGT
*
21529715 GAGTGACCAAAGTAAAACTGATCTAAAATGT
1 GAGTGACCAAAATAAAACTGATCTAAAATGT
*
21529746 TAGTG
1 GAGTG
21529751 GTTAAATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (31 bp):
GAGTGACCAAAATAAAACTGATCTAAAATGT
Found at i:21535389 original size:21 final size:20
Alignment explanation
Indices: 21535363--21535403 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
21535353 AAGATGCAAC
21535363 AAACAATACTTTATAGAAATT
1 AAACAAT-CTTTATAGAAATT
* *
21535384 AAACAATTTTTCTAGAAATT
1 AAACAATCTTTATAGAAATT
21535404 CATAGGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (20 bp):
AAACAATCTTTATAGAAATT
Found at i:21537406 original size:21 final size:22
Alignment explanation
Indices: 21537364--21537412 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
21537354 TAACAGTTAA
21537364 CTAACTATAACTACCATAACTG
1 CTAACTATAACTACCATAACTG
21537386 CTAACTATTAACTA-C-TAACTG
1 CTAACTA-TAACTACCATAACTG
21537407 CTAACT
1 CTAACT
21537413 GTCACAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.46
22 8 0.31
23 6 0.23
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.31
Consensus pattern (22 bp):
CTAACTATAACTACCATAACTG
Found at i:21541908 original size:14 final size:14
Alignment explanation
Indices: 21541885--21541921 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
21541875 TCCATGGCAG
21541885 AAACACAAACAAGA
1 AAACACAAACAAGA
*
21541899 AAACATAAACAAGA
1 AAACACAAACAAGA
21541913 AAACACAAA
1 AAACACAAA
21541922 GAAGGCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.73, C:0.19, G:0.05, T:0.03
Consensus pattern (14 bp):
AAACACAAACAAGA
Found at i:21542095 original size:7 final size:7
Alignment explanation
Indices: 21542062--21542111 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
21542052 TTAACAGTTA
21542062 ACTAACT
1 ACTAACT
21542069 A-TAACT
1 ACTAACT
21542075 ACCATAACT
1 A-C-TAACT
*
21542084 GCTAACT
1 ACTAACT
21542091 ACTAACT
1 ACTAACT
21542098 ACTAACT
1 ACTAACT
*
21542105 GCTAACT
1 ACTAACT
21542112 GTCACAATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
6 6 0.16
7 25 0.68
8 1 0.03
9 5 0.14
ACGTcount: A:0.40, C:0.28, G:0.04, T:0.28
Consensus pattern (7 bp):
ACTAACT
Found at i:21542105 original size:21 final size:22
Alignment explanation
Indices: 21542063--21542111 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
21542053 TAACAGTTAA
21542063 CTAACTATAACTACCATAACTG
1 CTAACTATAACTACCATAACTG
21542085 CTAACTACTAACTA-C-TAACTG
1 CTAACTA-TAACTACCATAACTG
21542106 CTAACT
1 CTAACT
21542112 GTCACAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.46
22 8 0.31
23 6 0.23
ACGTcount: A:0.39, C:0.29, G:0.04, T:0.29
Consensus pattern (22 bp):
CTAACTATAACTACCATAACTG
Found at i:21543050 original size:18 final size:18
Alignment explanation
Indices: 21543011--21543059 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
21543001 GCCCATATAA
*
21543011 TAAAATATATTT--ATTT
1 TAAAATATTTTTAAATTT
* *
21543027 TTAAATTTTTTTAAATTT
1 TAAAATATTTTTAAATTT
21543045 TAAAATATTTTTAAA
1 TAAAATATTTTTAAA
21543060 ATACTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 9 0.35
18 17 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAAAATATTTTTAAATTT
Found at i:21554814 original size:14 final size:15
Alignment explanation
Indices: 21554785--21554818 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
21554775 GTTATGATTA
21554785 TATGAGCATATGAGT
1 TATGAGCATATGAGT
*
21554800 TATGA-CATTTGAGT
1 TATGAGCATATGAGT
21554814 TATGA
1 TATGA
21554819 TGCTGTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (15 bp):
TATGAGCATATGAGT
Found at i:21561343 original size:96 final size:97
Alignment explanation
Indices: 21561186--21561372 Score: 367
Period size: 96 Copynumber: 1.9 Consensus size: 97
21561176 TGAATGATTG
21561186 GAGTAAGAGGTATATATGTTTCGAATGATGGGATTTCAAAGAATGTGTAAATGACTATTTTGAGC
1 GAGTAAGAGGTATATATGTTTCGAATGATGGGATTTCAAAGAATGTGTAAATGACTATTTTGAGC
21561251 CGTGTTTTATATGGT-ATGCCTTGTATGATAT
66 CGTGTTTTATATGGTAATGCCTTGTATGATAT
21561282 GAGTAAGAGGTATATATGTTTCGAATGATGGGATTTCAAAGAATGTGTAAATGACTATTTTGAGC
1 GAGTAAGAGGTATATATGTTTCGAATGATGGGATTTCAAAGAATGTGTAAATGACTATTTTGAGC
21561347 CGTGTTTTATATGGTAATGCCTTGTA
66 CGTGTTTTATATGGTAATGCCTTGTA
21561373 ACCTTATTCC
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 80 0.89
97 10 0.11
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.38
Consensus pattern (97 bp):
GAGTAAGAGGTATATATGTTTCGAATGATGGGATTTCAAAGAATGTGTAAATGACTATTTTGAGC
CGTGTTTTATATGGTAATGCCTTGTATGATAT
Found at i:21561716 original size:14 final size:14
Alignment explanation
Indices: 21561699--21561725 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21561689 TATGAGCTTA
21561699 AGGTTTTGAGTTTG
1 AGGTTTTGAGTTTG
21561713 AGGTTTTGAGTTT
1 AGGTTTTGAGTTT
21561726 CGAGTACGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (14 bp):
AGGTTTTGAGTTTG
Found at i:21568671 original size:13 final size:13
Alignment explanation
Indices: 21568653--21568678 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21568643 ATTTATATGG
21568653 ATCAAGATGCTAA
1 ATCAAGATGCTAA
21568666 ATCAAGATGCTAA
1 ATCAAGATGCTAA
21568679 CTAAAAAAAA
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:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ATCAAGATGCTAA
Found at i:21579105 original size:7 final size:7
Alignment explanation
Indices: 21579095--21579134 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
21579085 AGTATTGAGG
*
21579095 ATTGAAA
1 ATTGGAA
21579102 ATTGGAA
1 ATTGGAA
21579109 ATTGGAA
1 ATTGGAA
21579116 ATTGGAA
1 ATTGGAA
21579123 ATTGGAA
1 ATTGGAA
21579130 ATTGG
1 ATTGG
21579135 GATTGAAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (7 bp):
ATTGGAA
Found at i:21579641 original size:31 final size:30
Alignment explanation
Indices: 21579599--21579663 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
21579589 TTTTAAAAAT
* ** *
21579599 TTGTTATTTTAGTCATTCTTGTTAGATAAG
1 TTGTTATTTTAGTCACTCCCGTTAGACAAG
21579629 TTGTTAATTTTAGTCACTCCCGTTAGACAAG
1 TTGTT-ATTTTAGTCACTCCCGTTAGACAAG
21579660 TTGT
1 TTGT
21579664 CCAATTTAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (30 bp):
TTGTTATTTTAGTCACTCCCGTTAGACAAG
Found at i:21579672 original size:31 final size:31
Alignment explanation
Indices: 21579604--21579678 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
21579594 AAAATTTGTT
* ** * *
21579604 ATTTTAGTCATTCTTGTTAGATAAGTTGTTA
1 ATTTTAGTCACTCCCGTTAGACAAGTTGTCA
21579635 ATTTTAGTCACTCCCGTTAGACAAGTTGTCCA
1 ATTTTAGTCACTCCCGTTAGACAAGTTGT-CA
*
21579667 A-TTTAGTTACTC
1 ATTTTAGTCACTC
21579679 TACCATTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 35 0.95
32 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (31 bp):
ATTTTAGTCACTCCCGTTAGACAAGTTGTCA
Found at i:21580905 original size:2 final size:2
Alignment explanation
Indices: 21580898--21580922 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21580888 NNNTTTAATT
21580898 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
21580923 TAATGTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21581561 original size:55 final size:55
Alignment explanation
Indices: 21581500--21581607 Score: 162
Period size: 55 Copynumber: 2.0 Consensus size: 55
21581490 CAACTTCTTC
* * * * *
21581500 TTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATGTTAGAATACTGT
1 TTCTTTTGAATCAATTATTTATATATTTAAATCAATTATTATCTTAGAATACTGT
*
21581555 TTCTTTTGAATCGATTATTTATATATTTAAATCAATTATTATCTTAGAATACT
1 TTCTTTTGAATCAATTATTTATATATTTAAATCAATTATTATCTTAGAATACT
21581608 ACTTTTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (55 bp):
TTCTTTTGAATCAATTATTTATATATTTAAATCAATTATTATCTTAGAATACTGT
Found at i:21581640 original size:37 final size:36
Alignment explanation
Indices: 21581584--21581655 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
21581574 TATATATTTA
*
21581584 AATCAATTATTATCTTAGAATACTACTTTTTTTTTTG
1 AATCAATTATTATCTTAGAATACTA-TTTTTCTTTTG
* *
21581621 AATCGATTATTATGC-TAGAATATTATTTTTCTTTT
1 AATCAATTATTAT-CTTAGAATACTATTTTTCTTTT
21581656 AACTTGATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 9 0.29
37 21 0.68
38 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (36 bp):
AATCAATTATTATCTTAGAATACTATTTTTCTTTTG
Found at i:21582563 original size:2 final size:2
Alignment explanation
Indices: 21582558--21582584 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21582548 TATGTGTGTG
21582558 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
21582585 CATTTTCGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21583591 original size:15 final size:16
Alignment explanation
Indices: 21583565--21583594 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
21583555 TCTTAAGCAT
21583565 CTCAGTGAAGATGACA
1 CTCAGTGAAGATGACA
21583581 CTCAG-GAAGATGAC
1 CTCAGTGAAGATGAC
21583595 GATACCTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.17
Consensus pattern (16 bp):
CTCAGTGAAGATGACA
Found at i:21589041 original size:12 final size:12
Alignment explanation
Indices: 21589024--21589052 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
21589014 ATTTGTGACC
21589024 ATAAATGATCCA
1 ATAAATGATCCA
21589036 ATAAATGATCCA
1 ATAAATGATCCA
21589048 ATAAA
1 ATAAA
21589053 GATTCTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (12 bp):
ATAAATGATCCA
Found at i:21598397 original size:16 final size:16
Alignment explanation
Indices: 21598378--21598431 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
21598368 ACACACATGA
21598378 CGAACAACATAAATGG
1 CGAACAACATAAATGG
** *
21598394 CGAACAGTATAATTGG
1 CGAACAACATAAATGG
* *
21598410 TGAACAACATAAATGT
1 CGAACAACATAAATGG
21598426 CGAACA
1 CGAACA
21598432 GTTTAATTAG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.19
Consensus pattern (16 bp):
CGAACAACATAAATGG
Found at i:21598447 original size:32 final size:32
Alignment explanation
Indices: 21598378--21598447 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
21598368 ACACACATGA
*
21598378 CGAACAACATAAATGGCGAACAGTATAATTGG
1 CGAACAACATAAATGGCGAACAGTATAATTAG
* * *
21598410 TGAACAACATAAATGTCGAACAGTTTAATTAG
1 CGAACAACATAAATGGCGAACAGTATAATTAG
21598442 CGAACA
1 CGAACA
21598448 CACGTGGCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (32 bp):
CGAACAACATAAATGGCGAACAGTATAATTAG
Found at i:21610154 original size:19 final size:19
Alignment explanation
Indices: 21610127--21610163 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21610117 TTTTGTGTTA
21610127 GTTTATTTATATTTTATTG
1 GTTTATTTATATTTTATTG
* *
21610146 GTTTTTTTATTTTTTATT
1 GTTTATTTATATTTTATT
21610164 AATTAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (19 bp):
GTTTATTTATATTTTATTG
Found at i:21620568 original size:76 final size:76
Alignment explanation
Indices: 21620485--21620636 Score: 279
Period size: 76 Copynumber: 2.0 Consensus size: 76
21620475 TTTGTTTTAA
*
21620485 CCAAAAATATATATAAAAATTTCGGTT-ATTCAGTTAAACCGACCGAATTAACCGAAAAAATTTT
1 CCAAAAATACATATAAAAATTTCGGTTAATTCAGTT-AACCGACCGAATTAACCGAAAAAATTTT
21620549 GTTTGGTTAAAT
65 GTTTGGTTAAAT
21620561 CCAAAAATACATATAAAAATTTCGGTTAATTCAGTTAACCGACCGAATTAACCGAAAAAATTTTG
1 CCAAAAATACATATAAAAATTTCGGTTAATTCAGTTAACCGACCGAATTAACCGAAAAAATTTTG
21620626 TTTGGTTAAAT
66 TTTGGTTAAAT
21620637 TTTTTTGAAA
Statistics
Matches: 74, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
76 66 0.89
77 8 0.11
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (76 bp):
CCAAAAATACATATAAAAATTTCGGTTAATTCAGTTAACCGACCGAATTAACCGAAAAAATTTTG
TTTGGTTAAAT
Found at i:21620638 original size:15 final size:15
Alignment explanation
Indices: 21620618--21620664 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
21620608 TTAACCGAAA
21620618 AAATTTTGTTTGGTT
1 AAATTTTGTTTGGTT
***
21620633 AAATTTT-TTTGAAA
1 AAATTTTGTTTGGTT
21620647 AAATTTTGGTTTGGTT
1 AAATTTT-GTTTGGTT
21620663 AA
1 AA
21620665 CGGTTAACGG
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
14 11 0.46
15 7 0.29
16 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (15 bp):
AAATTTTGTTTGGTT
Found at i:21629939 original size:42 final size:42
Alignment explanation
Indices: 21629893--21629982 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
21629883 ATTCTAGGAA
* *
21629893 TATTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGAGAAT
1 TATTTTATCTTATCTTTTAGTAGTTGATTAGAATAAGAGAAT
* *
21629935 TATTTTCTCTTATGTTTTAGTAGTTGATTAGAATAAGAGAAT
1 TATTTTATCTTATCTTTTAGTAGTTGATTAGAATAAGAGAAT
21629977 TATTTT
1 TATTTT
21629983 TCCAATTAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.52
Consensus pattern (42 bp):
TATTTTATCTTATCTTTTAGTAGTTGATTAGAATAAGAGAAT
Found at i:21634442 original size:50 final size:50
Alignment explanation
Indices: 21634336--21634448 Score: 126
Period size: 50 Copynumber: 2.3 Consensus size: 50
21634326 GACACACCAC
* *
21634336 AGCTCATATGAGCTTACCGATTTGCAGCTCGTGGGAGCTTACTGATTCTA
1 AGCTCGTATGAGCTTACCGATTTGCAGCTCGTAGGAGCTTACTGATTCTA
* *
21634386 AACTCGTATGAGCTTACCGTTATTT-CAGCTGGTAGGAGCTTA-TCG-TT-TA
1 AGCTCGTATGAGCTTACCG--ATTTGCAGCTCGTAGGAGCTTACT-GATTCTA
21634435 TAGCTCGTATGAGC
1 -AGCTCGTATGAGC
21634449 ATACATGTAC
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
49 2 0.04
50 32 0.59
51 16 0.30
52 4 0.07
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (50 bp):
AGCTCGTATGAGCTTACCGATTTGCAGCTCGTAGGAGCTTACTGATTCTA
Found at i:21634448 original size:24 final size:26
Alignment explanation
Indices: 21634388--21634448 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
21634378 TGATTCTAAA
*
21634388 CTCGTATGAGCTTACCGTTATTTCAG
1 CTCGTATGAGCTTACCGTTATATCAG
* * *
21634414 CTGGTAGGAGCTTATCGTT-TAT-AG
1 CTCGTATGAGCTTACCGTTATATCAG
21634438 CTCGTATGAGC
1 CTCGTATGAGC
21634449 ATACATGTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
24 11 0.38
25 2 0.07
26 16 0.55
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (26 bp):
CTCGTATGAGCTTACCGTTATATCAG
Found at i:21639678 original size:33 final size:33
Alignment explanation
Indices: 21639640--21639718 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 33
21639630 CAACTATAAG
21639640 TGCCGAATGCACATAT-TCACT-TATACCCACCTA
1 TGCCGAATGCACATATAT-A-TATATACCCACCTA
*
21639673 TGCCGAATGCATACATATATATATATATCCACCTA
1 TGCCGAATGC--ACATATATATATATACCCACCTA
*
21639708 TGCTGAATGCA
1 TGCCGAATGCA
21639719 TACATATACA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
33 11 0.28
34 1 0.03
35 27 0.68
36 1 0.03
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (33 bp):
TGCCGAATGCACATATATATATATACCCACCTA
Found at i:21639985 original size:41 final size:41
Alignment explanation
Indices: 21639920--21640078 Score: 171
Period size: 41 Copynumber: 3.9 Consensus size: 41
21639910 TTTAAACGGA
* * * *
21639920 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTCTAATTCCG
1 TTCACCGGCACTT-AGCCTGCTAGGCTTATAGTCTGATTCAG
* *
21639961 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGTCTGATTCAG
* * *
21640002 TTCACCGGCACTTAGCCTGCT-GGACGTATAGTCCGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGG-CTTATAGTCTGATTCAG
* *
21640043 TTCATCGGCACTTAGCCTGCTA-GATGTATAGTCTGA
1 TTCACCGGCACTTAGCCTGCTAGGCT-TATAGTCTGA
21640079 ACAATTTCAC
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.03
41 96 0.97
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAGTCTGATTCAG
Found at i:21640354 original size:21 final size:23
Alignment explanation
Indices: 21640303--21640357 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
21640293 ATATATAACC
*
21640303 TCGGACGATGGAAAATCGACTTACC
1 TCGGACGATGGAAAATCGA--TACA
21640328 TCGGACGATGGAAAATCGA-A-A
1 TCGGACGATGGAAAATCGATACA
21640349 TCGGACGAT
1 TCGGACGAT
21640358 TATTCGACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 9 0.31
22 1 0.03
25 19 0.66
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (23 bp):
TCGGACGATGGAAAATCGATACA
Found at i:21641284 original size:13 final size:13
Alignment explanation
Indices: 21641266--21641290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21641256 CAATCAAATG
21641266 CACACAAAATAAA
1 CACACAAAATAAA
21641279 CACACAAAATAA
1 CACACAAAATAA
21641291 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:21646859 original size:33 final size:31
Alignment explanation
Indices: 21646821--21646897 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 31
21646811 CAACTATAAG
21646821 TGCCGAATGCACATAT-TCACTTATACCCACCTA
1 TGCCGAATGCACATATAT-A--TATACCCACCTA
*
21646854 TGCCGAATGCATACATATATATATATCCACCTA
1 TGCCGAATGC--ACATATATATATACCCACCTA
21646887 TGCCGAATGCA
1 TGCCGAATGCA
21646898 TTCATATACA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
31 1 0.03
33 31 0.77
35 7 0.17
36 1 0.03
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (31 bp):
TGCCGAATGCACATATATATATACCCACCTA
Found at i:21646898 original size:33 final size:33
Alignment explanation
Indices: 21646842--21646905 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
21646832 CATATTCACT
21646842 TATACCCACCTATGCCGAATGCATACATATATA
1 TATACCCACCTATGCCGAATGCATACATATATA
* *
21646875 TATATCCACCTATGCCGAATGCATTCATATA
1 TATACCCACCTATGCCGAATGCATACATATA
21646906 CACACTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.27, G:0.09, T:0.30
Consensus pattern (33 bp):
TATACCCACCTATGCCGAATGCATACATATATA
Found at i:21647753 original size:41 final size:41
Alignment explanation
Indices: 21647108--21647730 Score: 1124
Period size: 41 Copynumber: 15.2 Consensus size: 41
21647098 TGGCACTGCA
* * * * *
21647108 CCTGATAGGCTTATAGTCTAATTCCGTTCACCGGCACTTAG
1 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
* *
21647149 CCTGCTAGGCCTATAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
21647190 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
21647231 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
21647272 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
21647313 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
21647354 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
21647395 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
21647436 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
21647477 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
21647518 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
21647559 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
21647600 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
21647641 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
* * *
21647682 CCTGCT-GGACGTATAGTCC-GATTCAATTCACCGGCACTTAG
1 CCTGCTAGG-CTTGTAG-CCTGATTCAGTTCACCGGCACTTAG
21647723 CCTGCTAG
1 CCTGCTAG
21647731 ACGTATAGTC
Statistics
Matches: 569, Mismatches: 10, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
40 2 0.00
41 564 0.99
42 3 0.01
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (41 bp):
CCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAG
Found at i:21649557 original size:13 final size:13
Alignment explanation
Indices: 21649539--21649563 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21649529 CAATCAAATG
21649539 CACACAAAATAAA
1 CACACAAAATAAA
21649552 CACACAAAATAA
1 CACACAAAATAA
21649564 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:21652771 original size:19 final size:19
Alignment explanation
Indices: 21652725--21652772 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
21652715 GTATATATTT
21652725 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
21652743 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
21652762 TAAGTTTTATT
1 TAAATTTTATT
21652773 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:21659374 original size:18 final size:18
Alignment explanation
Indices: 21659351--21659388 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
21659341 AACTTTCCTA
* *
21659351 AATAAATCAGTAGAATCC
1 AATAAAGCAGCAGAATCC
21659369 AATAAAGCAGCAGAATCC
1 AATAAAGCAGCAGAATCC
21659387 AA
1 AA
21659389 GTTTAAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.18, G:0.13, T:0.16
Consensus pattern (18 bp):
AATAAAGCAGCAGAATCC
Found at i:21663790 original size:20 final size:20
Alignment explanation
Indices: 21663767--21663809 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
21663757 TAAAATATAT
*
21663767 TATAAATAATATAGT-ATAGA
1 TATAAAT-ATATAATGATAGA
*
21663787 TATAGATATATAATGATAGA
1 TATAAATATATAATGATAGA
21663807 TAT
1 TAT
21663810 TGATAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (20 bp):
TATAAATATATAATGATAGA
Found at i:21668079 original size:38 final size:38
Alignment explanation
Indices: 21668021--21668139 Score: 134
Period size: 38 Copynumber: 3.1 Consensus size: 38
21668011 CGGGTACCCA
* * *
21668021 ATAACACACCATTTTACTCATAAGAGTTA-TCTCATTCG
1 ATAACACGCCAGTTTGCTCATAAGAGTTATTC-CATTCG
* * *
21668059 ATAACACGCCAGTTTGCTCATAAGAGCTATTCCA-CCTA
1 ATAACACGCCAGTTTGCTCATAAGAGTTATTCCATTC-G
* *
21668097 ATATCACGCCTGTTTGCTCATAAGAGTTATTCCATTCG
1 ATAACACGCCAGTTTGCTCATAAGAGTTATTCCATTCG
21668135 ATAAC
1 ATAAC
21668140 GCAAATATAT
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
37 1 0.02
38 62 0.94
39 3 0.05
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (38 bp):
ATAACACGCCAGTTTGCTCATAAGAGTTATTCCATTCG
Found at i:21671307 original size:180 final size:181
Alignment explanation
Indices: 21670996--21671321 Score: 537
Period size: 180 Copynumber: 1.8 Consensus size: 181
21670986 TTTAAGAAAT
* *
21670996 TTAGTCATGGTATATATATATGTATGTGTAGTAATTTTGATATCTGGATGTATTTTTGTTGTGGA
1 TTAGTCATGGTATATATATATG-ATGTGTAGTAATTTTGATATATGGATGTATTTTGGTTGTGGA
* * * * *
21671061 TTGATCATGATGATAAATGTTAGGTATATTTGGTCTATTAAGTGACGCAATTGAGAAGCGTGATA
65 TTGATCATGATAATAAAGGTTAGATATATTTGGTCTATTAAGTGACACAATTGAGAAGCATGATA
21671126 GGTGGGTCATTCTATGATAGGTTGCACTGATTAATTCGGTTTATGTGATGGA
130 GGTGGGTCATTCTATGATAGGTTGCACTGATTAATTCGGTTTATGTGATGGA
* *
21671178 TTAGTCATTGTATATATATATG-TGTGTGGTAATTTTGATATATGGATGTATTTTGGTTGTGGAT
1 TTAGTCATGGTATATATATATGATGTGTAGTAATTTTGATATATGGATGTATTTTGGTTGTGGAT
* *
21671242 TGATCATGATAATAAAGGTTAGATATATTTGGTCTATTAAGTGACATAATTGAGAAGTATGATAG
66 TGATCATGATAATAAAGGTTAGATATATTTGGTCTATTAAGTGACACAATTGAGAAGCATGATAG
21671307 GTGGGTCATTCTATG
131 GTGGGTCATTCTATG
21671322 TGTGAGATGA
Statistics
Matches: 133, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
180 112 0.84
182 21 0.16
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.42
Consensus pattern (181 bp):
TTAGTCATGGTATATATATATGATGTGTAGTAATTTTGATATATGGATGTATTTTGGTTGTGGAT
TGATCATGATAATAAAGGTTAGATATATTTGGTCTATTAAGTGACACAATTGAGAAGCATGATAG
GTGGGTCATTCTATGATAGGTTGCACTGATTAATTCGGTTTATGTGATGGA
Found at i:21671728 original size:105 final size:106
Alignment explanation
Indices: 21671542--21671752 Score: 388
Period size: 105 Copynumber: 2.0 Consensus size: 106
21671532 TTTGACAAAT
21671542 GATAAAAATTAACTCGATTACTATGTGAGGTGAATTATGATTTGGGTAGCACATCTATATTCTAC
1 GATAAAAATTAACTCGATTACTATGTGAGGTGAATTATGATTTGGGTAGCACATCTATATTCTAC
21671607 AATAATAGATAAAATATATTTATGTCATG-GTGAATGGTTA
66 AATAATAGATAAAATATATTTATGTCATGTGTGAATGGTTA
*
21671647 GATAAAAATTAACTCGATTACTATGTGAGGTGAATTATGATTTGGGTAGCACATCTATATTCTGC
1 GATAAAAATTAACTCGATTACTATGTGAGGTGAATTATGATTTGGGTAGCACATCTATATTCTAC
* *
21671712 AATAATAGATAGAATATATTTATGTCATGTGTGATTGGTTA
66 AATAATAGATAAAATATATTTATGTCATGTGTGAATGGTTA
21671753 AACACTTGGG
Statistics
Matches: 102, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
105 92 0.90
106 10 0.10
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.37
Consensus pattern (106 bp):
GATAAAAATTAACTCGATTACTATGTGAGGTGAATTATGATTTGGGTAGCACATCTATATTCTAC
AATAATAGATAAAATATATTTATGTCATGTGTGAATGGTTA
Found at i:21672340 original size:46 final size:48
Alignment explanation
Indices: 21672261--21672357 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 48
21672251 GCAACCCAAT
21672261 AAGTAATAAAGTGACCCTGCTCCCAAACACAT-GGGG-GGCTTATAGA
1 AAGTAATAAAGTGACCCTGCTCCCAAACACATGGGGGAGGCTTATAGA
* * *
21672307 AAGTAATAAAGTGGCCTTGC-CCCTAAACGCATGGGGGACGGCTTATAGA
1 AAGTAATAAAGTGACCCTGCTCCC-AAACACATGGGGGA-GGCTTATAGA
21672356 AA
1 AA
21672358 AAATAGTGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
45 3 0.07
46 25 0.57
47 4 0.09
49 12 0.27
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.20
Consensus pattern (48 bp):
AAGTAATAAAGTGACCCTGCTCCCAAACACATGGGGGAGGCTTATAGA
Found at i:21672602 original size:21 final size:20
Alignment explanation
Indices: 21672559--21672603 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
21672549 GATTTACATG
*
21672559 ATGAATGTAGAATCATAGGT
1 ATGAATGTAGAATCATAGAT
* *
21672579 ATGATATGTAGAATTATATAT
1 ATGA-ATGTAGAATCATAGAT
21672600 ATGA
1 ATGA
21672604 CATAATGTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36
Consensus pattern (20 bp):
ATGAATGTAGAATCATAGAT
Found at i:21674990 original size:24 final size:23
Alignment explanation
Indices: 21674955--21674999 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
21674945 TCACATCATT
*
21674955 TTCTCTTTCTCTTCTTCCTCTCC
1 TTCTCTTCCTCTTCTTCCTCTCC
21674978 TTCTCCTTCCTCTTCTTCCTCT
1 TTCT-CTTCCTCTTCTTCCTCT
21675000 ATTTCTTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (23 bp):
TTCTCTTCCTCTTCTTCCTCTCC
Found at i:21675005 original size:24 final size:23
Alignment explanation
Indices: 21674954--21675019 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
21674944 CTCACATCAT
* *
21674954 TTTCTCTTTCTCTTCTTCCTCTC
1 TTTCTCTTCCTCTTCTTCCTCTA
*
21674977 CTTCTCCTTCCTCTTCTTCCTCTA
1 TTTCT-CTTCCTCTTCTTCCTCTA
* *
21675001 TTTCTTCTGCTTCTTCTTC
1 TTTC-TCTTCCTCTTCTTC
21675020 ATCTGCTTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
23 4 0.11
24 30 0.86
25 1 0.03
ACGTcount: A:0.02, C:0.39, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTCTCTTCCTCTTCTTCCTCTA
Found at i:21675024 original size:15 final size:15
Alignment explanation
Indices: 21675006--21675034 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21674996 CTCTATTTCT
21675006 TCTGCTTCTTCTTCA
1 TCTGCTTCTTCTTCA
21675021 TCTGCTTCTTCTTC
1 TCTGCTTCTTCTTC
21675035 TGCTTTGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.34, G:0.07, T:0.55
Consensus pattern (15 bp):
TCTGCTTCTTCTTCA
Found at i:21675029 original size:24 final size:24
Alignment explanation
Indices: 21674963--21675032 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
21674953 TTTTCTCTTT
* * *
21674963 CTCTTCTTCCTCTCCTTCTCCTTC
1 CTCTTCTTCCTCTACTTCTTCTGC
*
21674987 CTCTTCTTCCTCTATTTCTTCTGC
1 CTCTTCTTCCTCTACTTCTTCTGC
* * *
21675011 TTCTTCTTCATCTGCTTCTTCT
1 CTCTTCTTCCTCTACTTCTTCT
21675033 TCTGCTTTGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.03, C:0.40, G:0.03, T:0.54
Consensus pattern (24 bp):
CTCTTCTTCCTCTACTTCTTCTGC
Found at i:21678532 original size:29 final size:28
Alignment explanation
Indices: 21678500--21678554 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
21678490 TTAGAGATTG
*
21678500 GATCAATTTAATATTTCTACTATTAAATA
1 GATCAATTTAAT-CTTCTACTATTAAATA
*
21678529 GATCAATTTAATCTTGTACTATTAAA
1 GATCAATTTAATCTTCTACTATTAAA
21678555 AAGAATCCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (28 bp):
GATCAATTTAATCTTCTACTATTAAATA
Found at i:21680729 original size:2 final size:2
Alignment explanation
Indices: 21680722--21680749 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21680712 TGGGTACTTG
21680722 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
21680750 TTACACACAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:21684553 original size:16 final size:17
Alignment explanation
Indices: 21684520--21684556 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
21684510 TAATTTTGGT
*
21684520 AAAATAATTTGATAAAA
1 AAAATAATTTCATAAAA
*
21684537 AAAATTATTTCATAAAA
1 AAAATAATTTCATAAAA
21684554 AAA
1 AAA
21684557 GCTATCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (17 bp):
AAAATAATTTCATAAAA
Found at i:21688953 original size:27 final size:27
Alignment explanation
Indices: 21688913--21688988 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
21688903 TAGTATTGGC
*
21688913 GCCTATCTCAGAGGCGCCAATGGTGGT
1 GCCTATCTGAGAGGCGCCAATGGTGGT
* * **
21688940 GCCTATCTGGGAGGCGCCATTATTGGT
1 GCCTATCTGAGAGGCGCCAATGGTGGT
21688967 GCC-ATACTGAGAGGCGCCAATG
1 GCCTAT-CTGAGAGGCGCCAATG
21688989 CTCTGATTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 2 0.05
27 38 0.95
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.22
Consensus pattern (27 bp):
GCCTATCTGAGAGGCGCCAATGGTGGT
Found at i:21689082 original size:22 final size:21
Alignment explanation
Indices: 21689054--21689098 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
21689044 CGGAAGAAAT
21689054 AAGAAGGAA-GAAAGCAGAAGAA
1 AAGAAGGAAGGAAA--AGAAGAA
21689076 AAGAAGGAAGGAAAAGAAGAA
1 AAGAAGGAAGGAAAAGAAGAA
21689097 AA
1 AA
21689099 AAATAAGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.41
22 9 0.41
23 4 0.18
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (21 bp):
AAGAAGGAAGGAAAAGAAGAA
Found at i:21689101 original size:24 final size:22
Alignment explanation
Indices: 21689046--21689106 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
21689036 TACAGAAACG
*
21689046 GAAG-AAATAAGAAGGAAGAAA
1 GAAGAAAAAAAGAAGGAAGAAA
* *
21689067 GCAGAAGAAAAGAAGGAAGGAAAA
1 GAAGAAAAAAAGAAGGAA-G-AAA
*
21689091 GAAGAAAAAAATAAGG
1 GAAGAAAAAAAGAAGG
21689107 TATTTTGGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.10
22 11 0.35
23 1 0.03
24 16 0.52
ACGTcount: A:0.66, C:0.02, G:0.30, T:0.03
Consensus pattern (22 bp):
GAAGAAAAAAAGAAGGAAGAAA
Found at i:21694119 original size:16 final size:15
Alignment explanation
Indices: 21694088--21694129 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
21694078 ACAAAATCAA
*
21694088 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
21694103 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
21694119 ATAAAAATTAA
1 ATAAAAGTTAA
21694130 ATGAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:21694860 original size:3 final size:3
Alignment explanation
Indices: 21694854--21694900 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
21694844 TTTTTTTTCT
*
21694854 TTC TTC TTC TTC TT- TTC TTC TTC TTC TTC TTC TCC TTC -TC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
21694900 T
1 T
21694901 CCTTTCTCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:21694872 original size:14 final size:14
Alignment explanation
Indices: 21694853--21694900 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
21694843 TTTTTTTTTC
21694853 TTTCTTCTTCTTCT
1 TTTCTTCTTCTTCT
21694867 TTTCTTCTTCTTC-
1 TTTCTTCTTCTTCT
*
21694880 -TTCTTCTCCTTCT
1 TTTCTTCTTCTTCT
*
21694893 CTTCTTCT
1 TTTCTTCT
21694901 CCTTTCTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 11 0.35
14 20 0.65
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTCTTCTTCTTCT
Found at i:21694876 original size:17 final size:17
Alignment explanation
Indices: 21694848--21694900 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
21694838 TTACCTTTTT
21694848 TTTTCTTTCTTCTTCTTC
1 TTTTC-TTCTTCTTCTTC
21694866 TTTTCTTCTTCTTCTTC
1 TTTTCTTCTTCTTCTTC
*
21694883 TTCTCCTTC-TCTTCTTC
1 TT-TTCTTCTTCTTCTTC
21694900 T
1 T
21694901 CCTTTCTCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 23 0.70
18 10 0.30
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTCTTCTTCTTCTTC
Found at i:21694901 original size:14 final size:14
Alignment explanation
Indices: 21694850--21694909 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
21694840 ACCTTTTTTT
*
21694850 TTCT-TTCTTCTTC
1 TTCTCTTCTTCTCC
* *
21694863 TTCTTTTCTTCTTC
1 TTCTCTTCTTCTCC
21694877 -T-TCTTCTTCTCC
1 TTCTCTTCTTCTCC
21694889 TTCTCTTCTTCTCC
1 TTCTCTTCTTCTCC
21694903 TTTCTCT
1 -TTCTCT
21694910 CTTTTTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
12 9 0.22
13 6 0.15
14 20 0.49
15 6 0.15
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (14 bp):
TTCTCTTCTTCTCC
Found at i:21694910 original size:17 final size:17
Alignment explanation
Indices: 21694849--21694923 Score: 68
Period size: 17 Copynumber: 4.4 Consensus size: 17
21694839 TACCTTTTTT
*
21694849 TTTCTTTCTTCTTCTTC
1 TTTCTCTCTTCTTCTTC
21694866 TTT-TCTTCTTCTTCTTC
1 TTTCTC-TCTTCTTCTTC
*
21694883 TTCTCCTTCTCTTCTTCTCC
1 TT-T-C-TCTCTTCTTCTTC
21694903 TTTCTCTCTT-TT-TT-
1 TTTCTCTCTTCTTCTTC
21694917 TTTCTCT
1 TTTCTCT
21694924 ACCATGTGGC
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
14 7 0.14
15 1 0.02
16 3 0.06
17 22 0.44
18 2 0.04
19 1 0.02
20 12 0.24
21 2 0.04
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCTCTCTTCTTCTTC
Found at i:21702285 original size:31 final size:31
Alignment explanation
Indices: 21702247--21702305 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
21702237 CTTTACAGCC
21702247 TAGTGACTTAAA-TAAATATTTTTGAATAGTT
1 TAGTGACTTAAATTAAA-ATTTTTGAATAGTT
21702278 TAGTGACTTAAATTAAAATTTTTGAATA
1 TAGTGACTTAAATTAAAATTTTTGAATA
21702306 ATTTTGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (31 bp):
TAGTGACTTAAATTAAAATTTTTGAATAGTT
Found at i:21702322 original size:31 final size:32
Alignment explanation
Indices: 21702259--21702323 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
21702249 GTGACTTAAA
* * *
21702259 TAAATATTTTTGAATAGTTTAGTGACTTAAAT
1 TAAATATTTTTGAATAATTTAGTGAATCAAAT
* *
21702291 TAAA-ATTTTTGAATAATTTTGTTAATCAAAT
1 TAAATATTTTTGAATAATTTAGTGAATCAAAT
21702322 TA
1 TA
21702324 TAACTTTGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (32 bp):
TAAATATTTTTGAATAATTTAGTGAATCAAAT
Found at i:21709967 original size:23 final size:22
Alignment explanation
Indices: 21709917--21709974 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
21709907 CATTTTAATC
*
21709917 AAAATTTTATTTTAATTTTTATA
1 AAAATTTT-TTTTAATTTTTACA
*
21709940 TAAATTTTTTTTATATTTTTACA
1 AAAATTTTTTTTA-ATTTTTACA
*
21709963 AAAATTATTTTT
1 AAAATTTTTTTT
21709975 CACTCACATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
AAAATTTTTTTTAATTTTTACA
Found at i:21709973 original size:22 final size:22
Alignment explanation
Indices: 21709923--21709973 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
21709913 AATCAAAATT
* *
21709923 TTATTTTAATTTTTATATAAAT
1 TTATTTTAATTTTTACATAAAA
*
21709945 TTTTTTTATATTTTTACA-AAAA
1 TTATTTTA-ATTTTTACATAAAA
21709967 TTATTTT
1 TTATTTT
21709974 TCACTCACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTTTAATTTTTACATAAAA
Found at i:21710013 original size:6 final size:6
Alignment explanation
Indices: 21710002--21710041 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
21709992 ACAATTTACC
21710002 TATCTA TATCTA TATCTA TATCTA TAT-TA CCTATCTA TAT
1 TATCTA TATCTA TATCTA TATCTA TATCTA --TATCTA TAT
21710042 ACTTAGTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 2 0.06
6 24 0.77
7 3 0.10
8 2 0.06
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
TATCTA
Found at i:21711332 original size:22 final size:23
Alignment explanation
Indices: 21711307--21711350 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
21711297 GATCAGTCCA
21711307 TTTTTATT-TACTTTTTA-ATATG
1 TTTTTATTCTA-TTTTTATATATG
21711329 TTTTTATTCTATTTTTATATAT
1 TTTTTATTCTATTTTTATATAT
21711351 TATGTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTTTATTCTATTTTTATATATG
Found at i:21711498 original size:31 final size:31
Alignment explanation
Indices: 21711460--21711534 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
21711450 TTAATATAAT
* *
21711460 ATTTGGTACTTGAACTTAATACTTTTTCCTA
1 ATTTGGTACTTAAACTTAACACTTTTTCCTA
* * * *
21711491 ATTTGGTACCTAAAGTTAGCACTTTTTCTTA
1 ATTTGGTACTTAAACTTAACACTTTTTCCTA
*
21711522 ATTTGATACTTAA
1 ATTTGGTACTTAA
21711535 TCTTTTTTGG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (31 bp):
ATTTGGTACTTAAACTTAACACTTTTTCCTA
Found at i:21711586 original size:32 final size:31
Alignment explanation
Indices: 21711550--21711617 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 31
21711540 TTTGGGATCC
*
21711550 AATTTGATATTTAAACTTACTTTTTTTT-TTCT
1 AATTTGATAATTAAACTT--TTTTTTTTGTTCT
* *
21711582 AATTTGGTAATTAATCTTTTTTTTTTGTTCT
1 AATTTGATAATTAAACTTTTTTTTTTGTTCT
21711613 -ATTTG
1 AATTTG
21711618 GTACTTCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 13 0.41
31 4 0.12
32 15 0.47
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (31 bp):
AATTTGATAATTAAACTTTTTTTTTTGTTCT
Found at i:21711768 original size:24 final size:23
Alignment explanation
Indices: 21711724--21711768 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
21711714 TTTTATTTTA
*
21711724 TTTTATTTTATATGTTCAATTAC
1 TTTTATTTTATATATTCAATTAC
* *
21711747 TTTTAATTTTATTTATTTAATT
1 TTTT-ATTTTATATATTCAATT
21711769 CATTATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTATTTTATATATTCAATTAC
Found at i:21714796 original size:6 final size:6
Alignment explanation
Indices: 21714787--21714825 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
21714777 TCATCACCAT
* * *
21714787 CATCAC CATCAC CATCAC CATCAC CGTTAC AATCAC CAT
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CAT
21714826 GATAGTGGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.44, G:0.03, T:0.21
Consensus pattern (6 bp):
CATCAC
Found at i:21715610 original size:26 final size:27
Alignment explanation
Indices: 21715566--21715620 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
21715556 ATTGCTGCAA
**
21715566 TTTTTTTTTAAAAGTGCAAC-ATCACT
1 TTTTTTTTTAAAACAGCAACAATCACT
*
21715592 TTTTTTTTTACAACAGCAACAATCACT
1 TTTTTTTTTAAAACAGCAACAATCACT
21715619 TT
1 TT
21715621 CCATTTGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.45
Consensus pattern (27 bp):
TTTTTTTTTAAAACAGCAACAATCACT
Found at i:21727722 original size:23 final size:23
Alignment explanation
Indices: 21727682--21727755 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
21727672 TGGTGGGAGC
*
21727682 TTATTGACAC-TTGGTGCGATTG
1 TTATTGGCACTTTGGTGCGATTG
21727704 TTATTGGCACTTTGGTGCGATTG
1 TTATTGGCACTTTGGTGCGATTG
* * * * *
21727727 ATACTAGCACTTTGATGCGATTA
1 TTATTGGCACTTTGGTGCGATTG
21727750 TTATTG
1 TTATTG
21727756 TGGAGTGTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 9 0.21
23 33 0.79
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42
Consensus pattern (23 bp):
TTATTGGCACTTTGGTGCGATTG
Found at i:21728423 original size:87 final size:87
Alignment explanation
Indices: 21728277--21728436 Score: 268
Period size: 87 Copynumber: 1.8 Consensus size: 87
21728267 AAGAGCATGT
*
21728277 TTATAAATCATTTGGATAACTAATTTTGACACTTGATTTGTATATGCATTGCTTTCAAATCATGT
1 TTATAAATCATTTGGATAACTAATTATGACACTTGATTTGTATATGCATTGCTTTCAAATCATGT
21728342 TAGAACCATTGAGCTCTTTTGC
66 TAGAACCATTGAGCTCTTTTGC
* *
21728364 TTATAAATTATTTGGATAACTAAATTATG-TACTTGATTTGTATATGCATTGCTTTCAAATCATG
1 TTATAAATCATTTGGATAACT-AATTATGACACTTGATTTGTATATGCATTGCTTTCAAATCATG
*
21728428 TTAGCACCA
65 TTAGAACCA
21728437 CTAATTCTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
87 62 0.91
88 6 0.09
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (87 bp):
TTATAAATCATTTGGATAACTAATTATGACACTTGATTTGTATATGCATTGCTTTCAAATCATGT
TAGAACCATTGAGCTCTTTTGC
Found at i:21760848 original size:23 final size:23
Alignment explanation
Indices: 21760762--21760851 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 23
21760752 GTGATCTCAA
* *
21760762 CACTTCGGTACTTCATGTTATAG
1 CACTTCGGTGCTTCGTGTTATAG
* * *
21760785 CACTTTGGTGCTTTGTGATATAG
1 CACTTCGGTGCTTCGTGTTATAG
* * *
21760808 CACATT-TGTGCTTCGTGTTACAT
1 CAC-TTCGGTGCTTCGTGTTATAG
*
21760831 CACTTCGGTGCTTTGTGTTAT
1 CACTTCGGTGCTTCGTGTTAT
21760852 CCAATATGTT
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
22 2 0.04
23 48 0.92
24 2 0.04
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (23 bp):
CACTTCGGTGCTTCGTGTTATAG
Found at i:21761224 original size:20 final size:21
Alignment explanation
Indices: 21761181--21761224 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 21
21761171 TAAAAAGTAA
21761181 TAAA-TAAGTATGATAATAAG
1 TAAATTAAGTATGATAATAAG
21761201 -AAATTAAG-ATGA-AATAAGG
1 TAAATTAAGTATGATAATAA-G
21761220 TAAAT
1 TAAAT
21761225 AAACAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.16, T:0.27
Consensus pattern (21 bp):
TAAATTAAGTATGATAATAAG
Found at i:21763855 original size:41 final size:41
Alignment explanation
Indices: 21763781--21763875 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
21763771 AAGAAAAGAT
* * *
21763781 TTTGCAACTTCAACATGGCTAGAGGATGGCCCAT-TCCGAAC
1 TTTGCAACTTCAACATGACTAGAGGATGACCCATCT-AGAAC
21763822 TTTGCAACTTCAACATGACTAGAGGA-GAACCCATCTAGAAC
1 TTTGCAACTTCAACATGACTAGAGGATG-ACCCATCTAGAAC
*
21763863 TTTGCAACATCAA
1 TTTGCAACTTCAA
21763876 AACGGTTTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 1 0.02
41 46 0.96
42 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (41 bp):
TTTGCAACTTCAACATGACTAGAGGATGACCCATCTAGAAC
Found at i:21767177 original size:18 final size:18
Alignment explanation
Indices: 21767156--21767193 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
21767146 ACACTACTCA
21767156 TACTCCTACTACTAATCC
1 TACTCCTACTACTAATCC
**
21767174 TACTCCTACTTTTAATCC
1 TACTCCTACTACTAATCC
21767192 TA
1 TA
21767194 TGTAAATCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.39
Consensus pattern (18 bp):
TACTCCTACTACTAATCC
Found at i:21810230 original size:129 final size:130
Alignment explanation
Indices: 21810000--21810258 Score: 511
Period size: 129 Copynumber: 2.0 Consensus size: 130
21809990 AGTTAATCTT
21810000 CCTTACTTTTATTTGGATAACAATTAAAATAAAATAAAGGGAAGTGTTCTAGAGTTCCTTTTCTT
1 CCTTACTTTTATTTGGATAACAATTAAAATAAAATAAAGGGAAGTGTTCTAGAGTTCCTTTTCTT
21810065 CAAAACTCTTATGCCTTATTTGGTTAGGAAAAAAATTATTTATTATATTTATA-TATAATAATTA
66 CAAAACTCTTATGCCTTATTTGGTTAGGAAAAAAATTATTTATTATATTTATATTATAATAATTA
21810129 CCTTACTTTTATTTGGATAACAATTAAAATAAAATAAAGGGAAGTGTTCTAGAGTTCCTTTTCTT
1 CCTTACTTTTATTTGGATAACAATTAAAATAAAATAAAGGGAAGTGTTCTAGAGTTCCTTTTCTT
21810194 CAAAACTCTTATGCCTTATTTGGTTAGGAAAAAAATTATTTATTATATTTATATTATAATAATTA
66 CAAAACTCTTATGCCTTATTTGGTTAGGAAAAAAATTATTTATTATATTTATATTATAATAATTA
21810259 GAAATAAAAT
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
129 118 0.91
130 11 0.09
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (130 bp):
CCTTACTTTTATTTGGATAACAATTAAAATAAAATAAAGGGAAGTGTTCTAGAGTTCCTTTTCTT
CAAAACTCTTATGCCTTATTTGGTTAGGAAAAAAATTATTTATTATATTTATATTATAATAATTA
Found at i:21818122 original size:18 final size:18
Alignment explanation
Indices: 21818099--21818134 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21818089 TTGATCCTAC
21818099 TAAAAAATATAAAAAAAT
1 TAAAAAATATAAAAAAAT
* *
21818117 TAAAAATTTTAAAAAAAT
1 TAAAAAATATAAAAAAAT
21818135 ATAGTTCAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAAATATAAAAAAAT
Found at i:21818308 original size:18 final size:18
Alignment explanation
Indices: 21818285--21818319 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21818275 AATCTCCTCC
21818285 ACCTTAATGACTCTTCAT
1 ACCTTAATGACTCTTCAT
*
21818303 ACCTTAATGATTCTTCA
1 ACCTTAATGACTCTTCA
21818320 CACACTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.40
Consensus pattern (18 bp):
ACCTTAATGACTCTTCAT
Found at i:21819609 original size:28 final size:28
Alignment explanation
Indices: 21819578--21819637 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
21819568 TTAAGGAAAA
*
21819578 AAAATCTAATTTATCATTCTCCTACTAG
1 AAAATCTAATTTATCAATCTCCTACTAG
* * *
21819606 AAAATTTAATTTATCAATCTGCTATTAG
1 AAAATCTAATTTATCAATCTCCTACTAG
21819634 AAAA
1 AAAA
21819638 GAGTAGGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (28 bp):
AAAATCTAATTTATCAATCTCCTACTAG
Done.