Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 8 of 135
Found at i:3462465 original size:40 final size:40
Alignment explanation
Indices: 3462373--3462468 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 40
3462363 ATGATGGATG
* ** * *
3462373 AAAGTCGATCAACGGCGGACAAAGTCGATCAACGGCGGAC
1 AAAGGCGATCAACGGTAGACAAAATCGATCAACGACGGAC
* * *
3462413 AAAGTCGGTCAACGGTAGACAAAATCGATCAACGACGGTC
1 AAAGGCGATCAACGGTAGACAAAATCGATCAACGACGGAC
* *
3462453 AACGGCTATCAACGGT
1 AAAGGCGATCAACGGT
3462469 GGTCTTGAGG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.35, C:0.24, G:0.27, T:0.14
Consensus pattern (40 bp):
AAAGGCGATCAACGGTAGACAAAATCGATCAACGACGGAC
Found at i:3462869 original size:83 final size:83
Alignment explanation
Indices: 3462633--3463157 Score: 756
Period size: 83 Copynumber: 6.3 Consensus size: 83
3462623 TAAATATAAA
* *
3462633 ATATGATAAAAATTGTAATATAA-AAAAAGGTTTTATTTAAAGATATAAAATTAATAAATAATGT
1 ATATTATAAAAATTGTAATATAATAAAAA-ATTTTATTTAAAGATATAAAATTAATAAATAATGT
*
3462697 ATTGTAAAATCAACACATT
65 ATTGTCAAATCAACACATT
* *
3462716 ATATGATAAAAATTGTAATATAAATTAATAAA-TTTATTTAAAGATATAAAATTAATAAATAATG
1 ATATTATAAAAATTGTAATAT-AA-TAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATG
3462780 TATTGTCAAATCAACACATT
64 TATTGTCAAATCAACACATT
* * *
3462800 ATATTATAAAAATTATAATATAATAAAAAATTTTATTTAAAGAAATAAAATTAATAAATATTGTA
1 ATATTATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
3462865 TTGTCAAATCAACACATT
66 TTGTCAAATCAACACATT
*
3462883 ATATTATAAAAATTGTAATATAATAAAAAA-ATTATTTAAAGATATAAAATTAATAAATAATGTA
1 ATATTATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
* *
3462947 TTATCAAGTCAACACATT
66 TTGTCAAATCAACACATT
* *
3462965 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATTATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
3463030 TTGTCAAATCAACACATT
66 TTGTCAAATCAACACATT
* * * *
3463048 ATATTATAAAAATTATAATATAAT-AATAATTTGTACTTTAAATATA-AAAATTTGATAAATAAT
1 ATATTATAAAAATTGTAATATAATAAAAAATTT-TA-TTTAAAGATATAAAA-TTAATAAATAAT
* * *
3463111 GTATTGTCAAATTAATACAAT
63 GTATTGTCAAATCAACACATT
*
3463132 AT-TTGATATAAATTGTAATATAATAA
1 ATATT-ATAAAAATTGTAATATAATAA
3463158 CTATCTTTTT
Statistics
Matches: 402, Mismatches: 30, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
82 89 0.22
83 180 0.45
84 128 0.32
85 1 0.00
86 4 0.01
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (83 bp):
ATATTATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTA
TTGTCAAATCAACACATT
Found at i:3462993 original size:165 final size:165
Alignment explanation
Indices: 3462633--3463157 Score: 802
Period size: 165 Copynumber: 3.2 Consensus size: 165
3462623 TAAATATAAA
* *
3462633 ATATGATAAAAATTGTAATATAA-AAAAAGGTTTTATTTAAAGATATAAAATTAATAAATAATGT
1 ATATGATAAAAATTGTAATATAATAAAAA-ATTTTATTTAAAGATATAAAATTAATAAATATTGT
* *
3462697 ATTGTAAAATCAACACATTATATGATAAAAATTGTAATATAAATTAATAAATTTATTTAAAGATA
65 ATTGTCAAATCAACACATTATATTATAAAAATTGTAATAT-AA-TAATAAATTTATTTAAAGATA
3462762 TAAAATTAATAAATAATGTATTGTCAAATCAACACATT
128 TAAAATTAATAAATAATGTATTGTCAAATCAACACATT
* * *
3462800 ATATTATAAAAATTATAATATAATAAAAAATTTTATTTAAAGAAATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
* *
3462865 TTGTCAAATCAACACATTATATTATAAAAATTGTAATATAATAAAAAAATTATTTAAAGATATAA
66 TTGTCAAATCAACACATTATATTATAAAAATTGTAATATAATAATAAATTTATTTAAAGATATAA
* *
3462930 AATTAATAAATAATGTATTATCAAGTCAACACATT
131 AATTAATAAATAATGTATTGTCAAATCAACACATT
3462965 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
* * *
3463030 TTGTCAAATCAACACATTATATTATAAAAATTATAATATAATAATAATTTGTACTTTAAATATA-
66 TTGTCAAATCAACACATTATATTATAAAAATTGTAATATAATAATAAATT-TA-TTTAAAGATAT
* * * *
3463094 AAAATTTGATAAATAATGTATTGTCAAATTAATACAAT
129 AAAA-TTAATAAATAATGTATTGTCAAATCAACACATT
* *
3463132 ATTTGATATAAATTGTAATATAATAA
1 ATATGATAAAAATTGTAATATAATAA
3463158 CTATCTTTTT
Statistics
Matches: 327, Mismatches: 27, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
165 163 0.50
166 8 0.02
167 151 0.46
168 5 0.02
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (165 bp):
ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
TTGTCAAATCAACACATTATATTATAAAAATTGTAATATAATAATAAATTTATTTAAAGATATAA
AATTAATAAATAATGTATTGTCAAATCAACACATT
Found at i:3467197 original size:61 final size:61
Alignment explanation
Indices: 3467066--3467338 Score: 294
Period size: 61 Copynumber: 4.6 Consensus size: 61
3467056 AGGAGAAGTT
* * * * *
3467066 GGTGTCGGCCATTTGATGACCAACATCCAAAAAAATTTGAATTTTTTTTCTCTAG-AACAGGG
1 GGTGTCGGCCATTTGATGGCCAACA-CAAAAAAAATTT-AAATTTTTTTCTCGAGAAATAGGG
* *
3467128 GGTATCGGCCATTTGATGGCCAACACAAAAAAAATTTAAATTTTTTTCTCGAGAAATAGGA
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTAAATTTTTTTCTCGAGAAATAGGG
*** ** *
3467189 GGTGTCGGCCATGCAATGGCCAACAC-CCAAAAA--TACAATTTTTTT-T--TGAAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTA-AATTTTTTTCTCGAGAAATAGGG
3467245 GGTGTCGGCCA-TTGATGGCCAACACAAAAAAAATTT-AATTTTTTTCTCGAGAAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTAAATTTTTTTCTCGAGAAATAGGG
*** **
3467304 GGTGTCGGCCATGCAATGGCCAACACCCAAAAAAT
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAAT
3467339 ACTTTTTTTC
Statistics
Matches: 176, Mismatches: 26, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
55 11 0.06
56 33 0.19
57 1 0.01
58 4 0.02
59 29 0.16
60 37 0.21
61 38 0.22
62 23 0.13
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (61 bp):
GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTAAATTTTTTTCTCGAGAAATAGGG
Found at i:3467277 original size:56 final size:59
Alignment explanation
Indices: 3467066--3467439 Score: 291
Period size: 56 Copynumber: 6.4 Consensus size: 59
3467056 AGGAGAAGTT
* * ** *
3467066 GGTGTCGGCCATTTG-ATGACCAACATCCAAAAAAATTTGAATTTTTTTTCTCTAG-AACAGGG
1 GGTGTCGGCCA-TTGCATGGCCAACA--CAAAAAAAATACAA-TTTTTTTCTC-AGAAATAGGG
* *
3467128 GGTATCGGCCATTTG-ATGGCCAACACAAAAAAAATTTA-AATTTTTTTCTCGAGAAATAGGA
1 GGTGTCGGCCA-TTGCATGGCCAACACAAAAAAAA--TACAATTTTTTTCTC-AGAAATAGGG
** *
3467189 GGTGTCGGCCA-TGCAATGGCCAACAC-CCAAAAATACAATTTTTTT-T-TGAAATAGGG
1 GGTGTCGGCCATTGC-ATGGCCAACACAAAAAAAATACAATTTTTTTCTCAGAAATAGGG
**
3467245 GGTGTCGGCCATTG-ATGGCCAACACAAAAAAAATTTAATTTTTTTCTCGAGAAATAGGG
1 GGTGTCGGCCATTGCATGGCCAACACAAAAAAAATACAATTTTTTTCTC-AGAAATAGGG
** * *
3467304 GGTGTCGGCCA-TGCAATGGCCAACACCCAAAAAATAC--TTTTTTTC-AAGAAATAGAG
1 GGTGTCGGCCATTGC-ATGGCCAACACAAAAAAAATACAATTTTTTTCTCAGAAATAGGG
** ** * *
3467360 GGTGTCGGTTA-TGCAATGGCCAACAC-CTAAAAATGCAA-ATTTTT-T--GAAATAGGG
1 GGTGTCGGCCATTGC-ATGGCCAACACAAAAAAAATACAATTTTTTTCTCAGAAATAGGG
*
3467414 GGTGTCGGCCATTGCATGACCAACAC
1 GGTGTCGGCCATTGCATGGCCAACAC
3467440 CCAAAAATTT
Statistics
Matches: 263, Mismatches: 32, Indels: 42
0.78 0.09 0.12
Matches are distributed among these distances:
54 27 0.10
55 22 0.08
56 72 0.27
57 3 0.01
58 13 0.05
59 31 0.12
60 43 0.16
61 28 0.11
62 24 0.09
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (59 bp):
GGTGTCGGCCATTGCATGGCCAACACAAAAAAAATACAATTTTTTTCTCAGAAATAGGG
Found at i:3467308 original size:115 final size:115
Alignment explanation
Indices: 3467124--3467461 Score: 399
Period size: 115 Copynumber: 3.0 Consensus size: 115
3467114 TCTCTAGAAC
* *
3467124 AGGGGGTATCGGCCATTTGATGGCCAACACAAAAAAAATTTAAATTTTTTTCTCGAGAAATAGGA
1 AGGGGGTGTCGGCCA-TTGATGGCCAACACAAAAAAAATTT-AATTTTTTTCTCGAGAAATAGGG
3467189 GGTGTCGGCCATGCAATGGCCAACACCCAAAAATACAATTTTTTTTTGAAAT
64 GGTGTCGGCCATGCAATGGCCAACACCCAAAAATACAATTTTTTTTTGAAAT
3467241 AGGGGGTGTCGGCCATTGATGGCCAACACAAAAAAAATTTAATTTTTTTCTCGAGAAATAGGGGG
1 AGGGGGTGTCGGCCATTGATGGCCAACACAAAAAAAATTTAATTTTTTTCTCGAGAAATAGGGGG
**
3467306 TGTCGGCCATGCAATGGCCAACACCCAAAAAATAC--TTTTTTTCAAGAAAT
66 TGTCGGCCATGCAATGGCCAACACCC-AAAAATACAATTTTTTT-TTGAAAT
* ** ** ** *
3467356 AGAGGGTGTCGGTTA-TGCAATGGCCAACAC-CTAAAAATGCAA-ATTTTT-T---GAAATAGGG
1 AGGGGGTGTCGGCCATTG--ATGGCCAACACAAAAAAAATTTAATTTTTTTCTCGAGAAATAGGG
* **
3467414 GGTGTCGGCCATTGC-ATGACCAACACCCAAAAATTTTAATTTTTTTTT
64 GGTGTCGGCCA-TGCAATGGCCAACACCCAAAAA-TACAATTTTTTTTT
3467462 TGACAAAAAG
Statistics
Matches: 196, Mismatches: 17, Indels: 22
0.83 0.07 0.09
Matches are distributed among these distances:
109 5 0.03
110 33 0.17
111 3 0.02
112 7 0.04
113 1 0.01
114 14 0.07
115 75 0.38
116 44 0.22
117 14 0.07
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (115 bp):
AGGGGGTGTCGGCCATTGATGGCCAACACAAAAAAAATTTAATTTTTTTCTCGAGAAATAGGGGG
TGTCGGCCATGCAATGGCCAACACCCAAAAATACAATTTTTTTTTGAAAT
Found at i:3475020 original size:15 final size:15
Alignment explanation
Indices: 3474971--3475021 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
3474961 TTGCCTTAGG
*
3474971 TTACATTTTAATTAT
1 TTACATTTTAATTAA
* * *
3474986 TTATATTTGAA-AAA
1 TTACATTTTAATTAA
*
3475000 TTACATTTTAATTAC
1 TTACATTTTAATTAA
3475015 TTACATT
1 TTACATT
3475022 ATCATTTTGT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (15 bp):
TTACATTTTAATTAA
Found at i:3475172 original size:18 final size:18
Alignment explanation
Indices: 3475149--3475191 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3475139 GAATAAGTTT
3475149 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
3475167 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
3475185 TTAATTA
1 TTAATTA
3475192 CATCTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:3477407 original size:23 final size:23
Alignment explanation
Indices: 3477379--3477478 Score: 148
Period size: 23 Copynumber: 4.3 Consensus size: 23
3477369 ACACTAGCGC
3477379 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
3477402 GTTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
3477425 GCTCTCTGATTAGTACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
3477448 GCTCTCTGCTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
3477471 GCTCTCTG
1 GCTCTCTG
3477479 TTGCCTGGCA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
22 1 0.01
23 67 0.97
24 1 0.01
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:3501642 original size:26 final size:26
Alignment explanation
Indices: 3501612--3501701 Score: 171
Period size: 26 Copynumber: 3.5 Consensus size: 26
3501602 AAATTAATGC
3501612 CATATTAAACTAAATACCATACTGTA
1 CATATTAAACTAAATACCATACTGTA
3501638 CATATTAAACTAAATACCATACTGTA
1 CATATTAAACTAAATACCATACTGTA
*
3501664 CATATTAAACCAAATACCATACTGTA
1 CATATTAAACTAAATACCATACTGTA
3501690 CATATTAAACTA
1 CATATTAAACTA
3501702 CAAAAGTAGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 62 1.00
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (26 bp):
CATATTAAACTAAATACCATACTGTA
Found at i:3504029 original size:21 final size:20
Alignment explanation
Indices: 3503986--3504025 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3503976 TTATTACATC
* *
3503986 TTTTTTAATTATGATTTAAA
1 TTTTTTAAATATGATTAAAA
*
3504006 TTTTTTAAATATTATTAAAA
1 TTTTTTAAATATGATTAAAA
3504026 ATTTATTGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTTTAAATATGATTAAAA
Found at i:3504978 original size:12 final size:12
Alignment explanation
Indices: 3504917--3504982 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
3504907 TAAAGAAGAG
3504917 AAGAAAGATGACA
1 AAGAAAGATGA-A
* * *
3504930 AA-AAGGACGAC
1 AAGAAAGATGAA
3504941 AAGAAAGATGAA
1 AAGAAAGATGAA
* **
3504953 GAGAAAGACAAA
1 AAGAAAGATGAA
*
3504965 AAGAAGGATGAA
1 AAGAAAGATGAA
3504977 AAGAAA
1 AAGAAA
3504983 TGATTATCAA
Statistics
Matches: 38, Mismatches: 14, Indels: 3
0.69 0.25 0.05
Matches are distributed among these distances:
11 2 0.05
12 34 0.89
13 2 0.05
ACGTcount: A:0.64, C:0.06, G:0.26, T:0.05
Consensus pattern (12 bp):
AAGAAAGATGAA
Found at i:3514228 original size:2 final size:2
Alignment explanation
Indices: 3514221--3514276 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
3514211 CAATGGTTTA
3514221 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3514263 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
3514277 TAGTTTATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3514524 original size:7 final size:7
Alignment explanation
Indices: 3514508--3514556 Score: 57
Period size: 7 Copynumber: 7.1 Consensus size: 7
3514498 AACTTCTAAC
3514508 TTAATT-
1 TTAATTA
3514514 TTAATTA
1 TTAATTA
3514521 TTAATTA
1 TTAATTA
3514528 TTAATTA
1 TTAATTA
*
3514535 TTAAATA
1 TTAATTA
*
3514542 -TAGATTT
1 TTA-ATTA
3514549 TTAATTA
1 TTAATTA
3514556 T
1 T
3514557 ATTTAACTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 8 0.22
7 26 0.72
8 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (7 bp):
TTAATTA
Found at i:3514977 original size:38 final size:38
Alignment explanation
Indices: 3514926--3515004 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
3514916 GTTTGAAGCT
3514926 TAAAAATGACACTATTGAGAAAAGTATTTAATTTTTAA
1 TAAAAATGACACTATTGAGAAAAGTATTTAATTTTTAA
3514964 TAAAAATGACACTATTGAGAAAAGTATTTAATTTTTAA
1 TAAAAATGACACTATTGAGAAAAGTATTTAATTTTTAA
3515002 TAA
1 TAA
3515005 TAAAAAAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.37
Consensus pattern (38 bp):
TAAAAATGACACTATTGAGAAAAGTATTTAATTTTTAA
Found at i:3518058 original size:18 final size:19
Alignment explanation
Indices: 3518035--3518072 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3518025 CCGAAGATTG
3518035 TAATTCATG-TCTT-TCTCA
1 TAATTCA-GCTCTTGTCTCA
3518053 TAATTCAGCTCTTGTCTCA
1 TAATTCAGCTCTTGTCTCA
3518072 T
1 T
3518073 TTCTTCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 11 0.61
19 6 0.33
ACGTcount: A:0.21, C:0.24, G:0.08, T:0.47
Consensus pattern (19 bp):
TAATTCAGCTCTTGTCTCA
Found at i:3529247 original size:30 final size:30
Alignment explanation
Indices: 3529212--3529276 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
3529202 TTTTATTTTA
* * *
3529212 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAACTTTGTTACTATTTTAGAGACAT
3529242 TTGTTAACTTTGTTACTATTTTAGAGACAT
1 TTGTTAACTTTGTTACTATTTTAGAGACAT
3529272 TTGTT
1 TTGTT
3529277 TGTTAAGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.06, G:0.15, T:0.55
Consensus pattern (30 bp):
TTGTTAACTTTGTTACTATTTTAGAGACAT
Found at i:3532977 original size:12 final size:12
Alignment explanation
Indices: 3532949--3532991 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
3532939 TCTTTCATTG
*
3532949 CTCGAATCCCGAA
1 CTCGAAT-CCAAA
3532962 CTCGAATCCAAA
1 CTCGAATCCAAA
3532974 CTCGAA-CCTAAA
1 CTCGAATCC-AAA
3532986 CTCGAA
1 CTCGAA
3532992 ACCTTTCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 2 0.07
12 19 0.68
13 7 0.25
ACGTcount: A:0.37, C:0.35, G:0.12, T:0.16
Consensus pattern (12 bp):
CTCGAATCCAAA
Found at i:3537746 original size:6 final size:6
Alignment explanation
Indices: 3537735--3537794 Score: 84
Period size: 6 Copynumber: 10.0 Consensus size: 6
3537725 GACTCGAAAC
* * *
3537735 CAGAAG CAGAAG CGGAAG CGGAAG CAGAAG CAGAAG CAGAAG CGGAAG
1 CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG CAGAAG
*
3537783 CGGAAG CAGAAG
1 CAGAAG CAGAAG
3537795 AAACAGAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.43, C:0.17, G:0.40, T:0.00
Consensus pattern (6 bp):
CAGAAG
Found at i:3537762 original size:24 final size:24
Alignment explanation
Indices: 3537735--3537794 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
3537725 GACTCGAAAC
*
3537735 CAGAAGCAGAAGCGGAAGCGGAAG
1 CAGAAGCAGAAGCAGAAGCGGAAG
3537759 CAGAAGCAGAAGCAGAAGCGGAAG
1 CAGAAGCAGAAGCAGAAGCGGAAG
*
3537783 CGGAAGCAGAAG
1 CAGAAGCAGAAG
3537795 AAACAGAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.43, C:0.17, G:0.40, T:0.00
Consensus pattern (24 bp):
CAGAAGCAGAAGCAGAAGCGGAAG
Found at i:3549219 original size:31 final size:31
Alignment explanation
Indices: 3549191--3549251 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
3549181 TTGATAATCT
*
3549191 AATAACTTAAATGAATTTTTTTAAATAATTC
1 AATAACTTAAATAAATTTTTTTAAATAATTC
* * * *
3549222 AATGATTTTAATAAATTTTTTTGAATAATT
1 AATAACTTAAATAAATTTTTTTAAATAATT
3549252 AACAATCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (31 bp):
AATAACTTAAATAAATTTTTTTAAATAATTC
Found at i:3549271 original size:32 final size:31
Alignment explanation
Indices: 3549200--3549273 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
3549190 TAATAACTTA
*
3549200 AATGAATTTTTTTAAATAATTCAATGATTTT
1 AATGAATTTTTTTAAATAATTCAATCATTTT
* *
3549231 AATAAATTTTTTTGAATAATTAACAATCA-TTT
1 AATGAATTTTTTTAAATAATT--CAATCATTTT
*
3549263 CATGAATTTTT
1 AATGAATTTTT
3549274 AAAGTTAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 19 0.53
32 12 0.33
33 5 0.14
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (31 bp):
AATGAATTTTTTTAAATAATTCAATCATTTT
Found at i:3550479 original size:18 final size:18
Alignment explanation
Indices: 3550429--3550479 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
3550419 GTAAAAAAAA
*
3550429 TTTAAATTAGTAT-ATAT
1 TTTAAATTAATATGATAT
* * *
3550446 ATT-AATAAAGATGATAT
1 TTTAAATTAATATGATAT
3550463 TTTAAATTAATATGATA
1 TTTAAATTAATATGATA
3550480 AAAATATTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 3
0.71 0.20 0.09
Matches are distributed among these distances:
16 6 0.24
17 8 0.32
18 11 0.44
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (18 bp):
TTTAAATTAATATGATAT
Found at i:3558270 original size:23 final size:22
Alignment explanation
Indices: 3558222--3558270 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 22
3558212 TTATATAAAT
3558222 ATATTTAAATAATTTTTTATGCA
1 ATATTTAAATAATTTTTTAT-CA
3558245 ATATTTAAATAAATTTTATTAT-A
1 ATATTTAAAT-AATTTT-TTATCA
3558268 ATA
1 ATA
3558271 ATTCATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 14 0.58
24 6 0.25
25 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
ATATTTAAATAATTTTTTATCA
Found at i:3560167 original size:23 final size:23
Alignment explanation
Indices: 3559995--3560155 Score: 157
Period size: 23 Copynumber: 6.9 Consensus size: 23
3559985 CGAAGTACTT
3559995 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
*
3560021 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * * *
3560043 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
3560065 AATCAGTAGGCACACGAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
* *
3560089 AACAGTAGGCACACAAAATGCGA
1 AACAGTAAGCACACAAAGTGCGA
3560112 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
3560135 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
3560156 TGAACGGTAA
Statistics
Matches: 116, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
22 19 0.16
23 75 0.65
24 3 0.03
26 14 0.12
27 5 0.04
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:3560828 original size:13 final size:13
Alignment explanation
Indices: 3560810--3560836 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3560800 ATTTTCAAAG
3560810 TTAACCCTCTGAT
1 TTAACCCTCTGAT
3560823 TTAACCCTCTGAT
1 TTAACCCTCTGAT
3560836 T
1 T
3560837 CTGTCCAATC
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:0.22, C:0.30, G:0.07, T:0.41
Consensus pattern (13 bp):
TTAACCCTCTGAT
Found at i:3563032 original size:61 final size:59
Alignment explanation
Indices: 3562967--3563084 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 59
3562957 AAAAAATAAA
* * * * *
3562967 AAATAGTATCTCAATATTAATT-TTATAAAAATAAAGTTTAATAATTGTAATATCTAATCAT
1 AAATAGTATCT-AA-AATAATTAGTAT-AAAATAAACTTAAATAATTATAATATCTAATCAT
3563028 AAATAGTATCTAAAATAATTAGGTATAAAATAAACTTAAATAATTATAATATCTAAT
1 AAATAGTATCTAAAATAATTA-GTATAAAATAAACTTAAATAATTATAATATCTAAT
3563085 ACGAATTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
59 6 0.12
60 30 0.60
61 14 0.28
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (59 bp):
AAATAGTATCTAAAATAATTAGTATAAAATAAACTTAAATAATTATAATATCTAATCAT
Found at i:3591400 original size:18 final size:19
Alignment explanation
Indices: 3591360--3591400 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
3591350 TTAAAATATG
*
3591360 TTTTTGAGTCAAAAAATAA
1 TTTTTAAGTCAAAAAATAA
*
3591379 -TTTTAAGT-AAAAATTAA
1 TTTTTAAGTCAAAAAATAA
3591396 TTTTT
1 TTTTT
3591401 TCTTCTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (19 bp):
TTTTTAAGTCAAAAAATAA
Found at i:3591436 original size:13 final size:14
Alignment explanation
Indices: 3591418--3591446 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3591408 TTTTTTACTA
3591418 TAAAAA-TATTTTT
1 TAAAAAGTATTTTT
3591431 TAAAAAGTATTTTT
1 TAAAAAGTATTTTT
3591445 TA
1 TA
3591447 TCATAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (14 bp):
TAAAAAGTATTTTT
Found at i:3599827 original size:6 final size:6
Alignment explanation
Indices: 3599816--3599841 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3599806 AAGACCTGAC
3599816 TTTGGT TTTGGT TTTGGT TTTGGT TT
1 TTTGGT TTTGGT TTTGGT TTTGGT TT
3599842 GCAGTCTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (6 bp):
TTTGGT
Found at i:3600491 original size:25 final size:24
Alignment explanation
Indices: 3600462--3600508 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
3600452 ATCATGAAAG
3600462 TTTTTATA-TTAAAAATTAAATTATA
1 TTTTT-TACTTAAAAA-TAAATTATA
3600487 TTTTTTACTTAAAAATAAATTA
1 TTTTTTACTTAAAAATAAATTA
3600509 ATTAATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTTTTACTTAAAAATAAATTATA
Found at i:3600517 original size:24 final size:25
Alignment explanation
Indices: 3600470--3600517 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
3600460 AGTTTTTATA
*
3600470 TTAAAAATTAAATTATATTTTTTAC
1 TTAAAAATTAAATTATATTATTTAC
3600495 TTAAAAA-TAAATTA-ATTAATTTA
1 TTAAAAATTAAATTATATT-ATTTA
3600518 TAAATGTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 11 0.52
25 7 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TTAAAAATTAAATTATATTATTTAC
Found at i:3607242 original size:15 final size:14
Alignment explanation
Indices: 3607210--3607251 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
3607200 AAAAAAATTC
3607210 AAAAATATATATAAT
1 AAAAATATATA-AAT
*
3607225 AAAAATATATAAGTT
1 AAAAATATATAA-AT
3607240 AAAAAT-TATAAA
1 AAAAATATATAAA
3607252 ATAATTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
AAAAATATATAAAT
Found at i:3608069 original size:16 final size:15
Alignment explanation
Indices: 3608048--3608121 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 15
3608038 TCAAACATAT
3608048 TTAAAATATTAAATA
1 TTAAAATATTAAATA
*
3608063 TTGAAAATATAAAAGTA
1 TT-AAAATATTAAA-TA
*
3608080 TTAAAATTATTATTCATGCA
1 TTAAAA-TATTA--AAT--A
3608100 TCTAAAATATTAAATA
1 T-TAAAATATTAAATA
3608116 TTAAAA
1 TTAAAA
3608122 ATTTTCATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
15 7 0.15
16 16 0.34
17 8 0.17
18 3 0.06
19 1 0.02
20 7 0.15
21 5 0.11
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (15 bp):
TTAAAATATTAAATA
Found at i:3611369 original size:60 final size:60
Alignment explanation
Indices: 3611288--3611421 Score: 171
Period size: 60 Copynumber: 2.2 Consensus size: 60
3611278 AGTTGGTGAC
* * * * *
3611288 CAAAAATGAAAAAATTGAATAGTTAAGTGACCATTCTGTAACTTTTCATAGTTGATTGAT
1 CAAAAAAGAAAAAATTGAATAGTTAAGTAACCATTCTGTAACTTATCATAATTGAATGAT
** * *
3611348 -AAAAAAGAACAAAATTGAATAGTTAAGTAATTATTTTGTAACTTATCATAATTTAATGAT
1 CAAAAAAGAA-AAAATTGAATAGTTAAGTAACCATTCTGTAACTTATCATAATTGAATGAT
3611408 CAAAAAAGAAAAAA
1 CAAAAAAGAAAAAA
3611422 AACATAGTCA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 8 0.13
60 46 0.73
61 9 0.14
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (60 bp):
CAAAAAAGAAAAAATTGAATAGTTAAGTAACCATTCTGTAACTTATCATAATTGAATGAT
Found at i:3611890 original size:31 final size:29
Alignment explanation
Indices: 3611849--3611930 Score: 76
Period size: 31 Copynumber: 2.7 Consensus size: 29
3611839 AATCTCAAAA
* *
3611849 TTATATATAAATTATGATTTAATGTGTAA-TT
1 TTATACATAAATT-TGATTT--TATGTAATTT
3611880 TTATACATAAACTTTGATTTTATGTAATTT
1 TTATACATAAA-TTTGATTTTATGTAATTT
*
3611910 TTATACACGAAATTTTGATTT
1 TTATACA-TAAA-TTTGATTT
3611931 GATCAAATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
29 6 0.14
30 9 0.20
31 27 0.61
32 2 0.05
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (29 bp):
TTATACATAAATTTGATTTTATGTAATTT
Found at i:3611905 original size:29 final size:31
Alignment explanation
Indices: 3611873--3611930 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3611863 TGATTTAATG
*
3611873 TGTAA-TTTTATACA-TAAACTTTGATTTTA
1 TGTAATTTTTATACACGAAACTTTGATTTTA
*
3611902 TGTAATTTTTATACACGAAATTTTGATTT
1 TGTAATTTTTATACACGAAACTTTGATTT
3611931 GATCAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
30 9 0.36
31 11 0.44
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.52
Consensus pattern (31 bp):
TGTAATTTTTATACACGAAACTTTGATTTTA
Found at i:3616501 original size:16 final size:18
Alignment explanation
Indices: 3616476--3616513 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
3616466 ATAAATTTAA
3616476 TTTTATTAATATGTTT-T
1 TTTTATTAATATGTTTGT
3616493 TTTTA-TAATATGTTTGT
1 TTTTATTAATATGTTTGT
3616510 TTTT
1 TTTT
3616514 TTTTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (18 bp):
TTTTATTAATATGTTTGT
Found at i:3618881 original size:16 final size:16
Alignment explanation
Indices: 3618854--3618887 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
3618844 TATTTGTGAG
3618854 TTTTAATTAAAT-TTA
1 TTTTAATTAAATCTTA
3618869 TTTTAACTTAAATCTTA
1 TTTTAA-TTAAATCTTA
3618886 TT
1 TT
3618888 ACATGTTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTAATTAAATCTTA
Found at i:3619310 original size:35 final size:34
Alignment explanation
Indices: 3619244--3619324 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 34
3619234 CTTTGAATCA
*
3619244 TCAACCTTGAACTTAAACTTTAGATTCTAAAC-C
1 TCAACCTTGAACTTAAACCTTAGATTCTAAACTC
3619277 TCAAACCTTGAATCTTAAACCTTAGA-TCTTAAACTC
1 TC-AACCTTGAA-CTTAAACCTTAGATTC-TAAACTC
*
3619313 TCGACCTTGAAC
1 TCAACCTTGAAC
3619325 CTTGAGTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
33 2 0.05
34 12 0.29
35 25 0.60
36 3 0.07
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.32
Consensus pattern (34 bp):
TCAACCTTGAACTTAAACCTTAGATTCTAAACTC
Found at i:3624245 original size:6 final size:6
Alignment explanation
Indices: 3624234--3624273 Score: 71
Period size: 6 Copynumber: 6.5 Consensus size: 6
3624224 GCTGCTTGAA
3624234 AAATCC AAATCC AAATCC AAATCC AAATCC AAAATCC AAA
1 AAATCC AAATCC AAATCC AAATCC AAATCC -AAATCC AAA
3624274 AGATTCAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.55, C:0.30, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATCC
Found at i:3629818 original size:15 final size:16
Alignment explanation
Indices: 3629783--3629821 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
3629773 GTCGTAAAAA
3629783 TATAATTTATCATTTT
1 TATAATTTATCATTTT
*
3629799 AATAATTTAT-ATTTT
1 TATAATTTATCATTTT
3629814 TATAATTT
1 TATAATTT
3629822 TTAAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATCATTTT
Found at i:3629861 original size:29 final size:31
Alignment explanation
Indices: 3629809--3629873 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 31
3629799 AATAATTTAT
* *
3629809 ATTTTTATAATTTTTAAAATATTAAATTA-A
1 ATTTTCATAATTTTTAAAATATTAAAATATA
3629839 ATTTTCATAATTTTTAAAA-ATTAAAATATA
1 ATTTTCATAATTTTTAAAATATTAAAATATA
3629869 ATTTT
1 ATTTT
3629874 ATTATTACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 8 0.25
30 24 0.75
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (31 bp):
ATTTTCATAATTTTTAAAATATTAAAATATA
Found at i:3635233 original size:21 final size:20
Alignment explanation
Indices: 3635205--3635246 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
3635195 CTACGTTTTT
3635205 TTTAC-TTTAATTTTTACTAA
1 TTTACTTTTAATTTTTA-TAA
*
3635225 TTTAGCTTTTTATTTTTATAA
1 TTTA-CTTTTAATTTTTATAA
3635246 T
1 T
3635247 GTTTTTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 5 0.26
22 10 0.53
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTACTTTTAATTTTTATAA
Found at i:3635564 original size:21 final size:21
Alignment explanation
Indices: 3635534--3635573 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3635524 TTTTTAAAAA
* *
3635534 ATATTTATATTATATTATATT
1 ATATTAATATAATATTATATT
*
3635555 ATATTAATATAATTTTATA
1 ATATTAATATAATATTATA
3635574 CAATTTTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTAATATAATATTATATT
Found at i:3659050 original size:26 final size:26
Alignment explanation
Indices: 3659014--3659067 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3659004 CATAAGCATC
3659014 TTACCAGTCAAGTTAGCCGTCTTTTG
1 TTACCAGTCAAGTTAGCCGTCTTTTG
3659040 TTACCAGTCAAGTTAGCCGTCTTTTG
1 TTACCAGTCAAGTTAGCCGTCTTTTG
3659066 TT
1 TT
3659068 TTAACTTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (26 bp):
TTACCAGTCAAGTTAGCCGTCTTTTG
Found at i:3660033 original size:24 final size:21
Alignment explanation
Indices: 3660002--3660047 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
3659992 ATTCGAATAC
3660002 ATTTTAATTATTAATTTATTTAT
1 ATTTTAATTATT-ATTT-TTTAT
*
3660025 ATTTGTAATTGTTATTTTTTAT
1 ATTT-TAATTATTATTTTTTAT
3660047 A
1 A
3660048 AATATCCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 8 0.38
24 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (21 bp):
ATTTTAATTATTATTTTTTAT
Found at i:3660377 original size:3 final size:3
Alignment explanation
Indices: 3660369--3660395 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3660359 TTGAGAAATA
3660369 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
3660396 CCCAACGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3674073 original size:2 final size:2
Alignment explanation
Indices: 3674066--3674107 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3674056 TTATTATTAT
3674066 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3674108 AAATTAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3674384 original size:29 final size:30
Alignment explanation
Indices: 3674320--3674392 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 30
3674310 AATTCTAAAA
3674320 TTATACATGAATTATGATTTAATGTGCAATT
1 TTATACATGAATTATGATTT-ATGTGCAATT
* * *
3674351 GTATACGTGAACTT-TGATTT-TGTGTAATT
1 TTATACATGAA-TTATGATTTATGTGCAATT
3674380 TTATACATGAATT
1 TTATACATGAATT
3674393 TTTTATTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.06
29 17 0.47
31 15 0.42
32 2 0.06
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.47
Consensus pattern (30 bp):
TTATACATGAATTATGATTTATGTGCAATT
Found at i:3678271 original size:10 final size:9
Alignment explanation
Indices: 3678253--3678277 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3678243 CTCTCAGAAT
3678253 AAGAAAAAA
1 AAGAAAAAA
3678262 AAGAAAAAA
1 AAGAAAAAA
3678271 AAGAAAA
1 AAGAAAA
3678278 GAGATTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:3679392 original size:3 final size:3
Alignment explanation
Indices: 3679386--3679417 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3679376 ACAACCAAGT
3679386 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3679418 AAAAAGAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3684133 original size:32 final size:31
Alignment explanation
Indices: 3684093--3684152 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
3684083 ATTAACTGTG
*
3684093 TATTATGATCAAAACGTTACAAATTAAATAA
1 TATTATGATCAAAACGTAACAAATTAAATAA
* * *
3684124 TATTAATGATCGAAATGTAATAAATTAAA
1 TATT-ATGATCAAAACGTAACAAATTAAA
3684153 ATTCAGTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 4 0.17
32 20 0.83
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (31 bp):
TATTATGATCAAAACGTAACAAATTAAATAA
Found at i:3693698 original size:168 final size:168
Alignment explanation
Indices: 3693420--3693724 Score: 556
Period size: 168 Copynumber: 1.8 Consensus size: 168
3693410 ATTTACGATT
* * *
3693420 TGAAATATCGAAGTTGTGAGCTCAAAATTACCATTCTCGATCATACTAAAAATAAACCAATTAGT
1 TGAAATATCAAAGTTGTGACCTCAAAATTACCATTCCCGATCATACTAAAAATAAACCAATTAGT
*
3693485 AAGTCTTCATTTTATTTGGATTTAATTGCAATTTACCAAAATCTAAAGAGTTTCACATCATTTCT
66 AAGTCCTCATTTTATTTGGATTTAATTGCAATTTACCAAAATCTAAAGAGTTTCACATCATTTCT
3693550 ATTATTACCAAAATATTAAAAAATTAATATTTACAGTC
131 ATTATTACCAAAATATTAAAAAATTAATATTTACAGTC
*
3693588 TGAAATATCAAAGTTGTGACCTCAAAATTACCATTCCCGATCATATTAAAAATAAACCAATTAGT
1 TGAAATATCAAAGTTGTGACCTCAAAATTACCATTCCCGATCATACTAAAAATAAACCAATTAGT
*
3693653 AAGTCCTCATTTTATTTGGATTTAATTTCAATTTACCAAAATCTAAAGAGTTTCACATCATTTCT
66 AAGTCCTCATTTTATTTGGATTTAATTGCAATTTACCAAAATCTAAAGAGTTTCACATCATTTCT
3693718 ATTATTA
131 ATTATTA
3693725 TGCCATTTAA
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
168 131 1.00
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (168 bp):
TGAAATATCAAAGTTGTGACCTCAAAATTACCATTCCCGATCATACTAAAAATAAACCAATTAGT
AAGTCCTCATTTTATTTGGATTTAATTGCAATTTACCAAAATCTAAAGAGTTTCACATCATTTCT
ATTATTACCAAAATATTAAAAAATTAATATTTACAGTC
Found at i:3694905 original size:25 final size:25
Alignment explanation
Indices: 3694852--3694898 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
3694842 GTTGAATCCA
3694852 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAATTCTAAAAAGATAATTAG
*
3694877 AATTAAA-TCTAAATA-ATAATTA
1 AATTAAATTCTAAAAAGATAATTA
3694899 CCTAATTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 7 0.33
25 7 0.33
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTAG
Found at i:3702611 original size:15 final size:15
Alignment explanation
Indices: 3702588--3702618 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3702578 AATTGGATTA
*
3702588 AATACTTTTTTTTTG
1 AATAATTTTTTTTTG
3702603 AATAATTTTTTTTTG
1 AATAATTTTTTTTTG
3702618 A
1 A
3702619 GTTTTTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (15 bp):
AATAATTTTTTTTTG
Found at i:3703875 original size:29 final size:30
Alignment explanation
Indices: 3703841--3703907 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
3703831 AGATCAAATA
3703841 ATGTATAAAATTGCACA-AAATCAAAGTTC
1 ATGTATAAAATTGCACATAAATCAAAGTTC
* * *
3703870 ATGTATATAATTGCACATTAAATCATAGTTG
1 ATGTATAAAATTGCACA-TAAATCAAAGTTC
3703901 ATGTATA
1 ATGTATA
3703908 GTTTTGTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 16 0.48
31 17 0.52
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.34
Consensus pattern (30 bp):
ATGTATAAAATTGCACATAAATCAAAGTTC
Found at i:3708199 original size:3 final size:3
Alignment explanation
Indices: 3708191--3708216 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3708181 ATAAGATTCC
3708191 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
3708217 CTATACTTAT
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:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:3715521 original size:7 final size:7
Alignment explanation
Indices: 3715509--3715539 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3715499 AAATGTATAA
3715509 AAATATT
1 AAATATT
3715516 AAATATT
1 AAATATT
3715523 AAATATT
1 AAATATT
*
3715530 AACTATT
1 AAATATT
3715537 AAA
1 AAA
3715540 ATAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (7 bp):
AAATATT
Found at i:3715712 original size:6 final size:6
Alignment explanation
Indices: 3715703--3715730 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3715693 TATCATACTT
3715703 AATCCA AATCCA AATCCA AATCCA AATC
1 AATCCA AATCCA AATCCA AATCCA AATC
3715731 TGACCGATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (6 bp):
AATCCA
Found at i:3717064 original size:2 final size:2
Alignment explanation
Indices: 3717057--3717090 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3717047 CATATGCATA
3717057 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3717091 CAGTGAAGTT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3723099 original size:58 final size:57
Alignment explanation
Indices: 3723035--3723153 Score: 175
Period size: 58 Copynumber: 2.1 Consensus size: 57
3723025 AAAAGGAATT
* *
3723035 GTTTATGAGTATTATTTAGGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
1 GTTTATGAGTATTATTTAAGAATAAAATTATATTTGGATTTAAAAA-ATTTGGGCTTA
* * * *
3723093 GTTTATGAGTGTTTTTTAAGAATGAAATTATATTTGGGTTTAAAAAATTTGGGCTTA
1 GTTTATGAGTATTATTTAAGAATAAAATTATATTTGGATTTAAAAAATTTGGGCTTA
3723150 GTTT
1 GTTT
3723154 GTTGATGGGT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
57 14 0.25
58 41 0.75
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (57 bp):
GTTTATGAGTATTATTTAAGAATAAAATTATATTTGGATTTAAAAAATTTGGGCTTA
Found at i:3741226 original size:17 final size:17
Alignment explanation
Indices: 3741206--3741252 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
3741196 TGACAAGAAT
3741206 TCTCTACGAACAAAAAC
1 TCTCTACGAACAAAAAC
3741223 TCTCTACGAACAAAAAC
1 TCTCTACGAACAAAAAC
*
3741240 TCTCAACGAACAA
1 TCTCTACGAACAA
3741253 GTTTTCCACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.47, C:0.30, G:0.06, T:0.17
Consensus pattern (17 bp):
TCTCTACGAACAAAAAC
Found at i:3744469 original size:23 final size:23
Alignment explanation
Indices: 3744297--3744457 Score: 148
Period size: 23 Copynumber: 6.9 Consensus size: 23
3744287 CGAAGTACTT
3744297 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
*
3744323 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * * *
3744345 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * *
3744367 AATCAATAGGCACACGAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
*
3744391 AACAGTAGGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
3744414 AACAATAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
3744437 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
3744458 TGAACGGTAA
Statistics
Matches: 114, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
22 19 0.17
23 73 0.64
24 3 0.03
26 14 0.12
27 5 0.04
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:3751205 original size:17 final size:18
Alignment explanation
Indices: 3751167--3751207 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3751157 CTTTACTTTT
* *
3751167 ATTTTATTTTACCACTAA
1 ATTTTATTTTAACACAAA
3751185 ATTTTATTTTAACA-AAA
1 ATTTTATTTTAACACAAA
3751202 ATTTTA
1 ATTTTA
3751208 GTCACCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTATTTTAACACAAA
Found at i:3773407 original size:21 final size:21
Alignment explanation
Indices: 3773382--3773422 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3773372 AAATTATGGG
3773382 GGGTTTAGGTTTTGG-CTTTTT
1 GGGTTTA-GTTTTGGTCTTTTT
*
3773403 GGGTTTATTTTTGGTCTTTT
1 GGGTTTAGTTTTGGTCTTTT
3773423 GTTGACTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.05, C:0.05, G:0.29, T:0.61
Consensus pattern (21 bp):
GGGTTTAGTTTTGGTCTTTTT
Found at i:3774395 original size:16 final size:16
Alignment explanation
Indices: 3774370--3774401 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3774360 TGAATTCGAT
3774370 TCGATATGGAATAAGA
1 TCGATATGGAATAAGA
*
3774386 TCGATTTGGAATAAGA
1 TCGATATGGAATAAGA
3774402 ATAAGAGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.25, T:0.28
Consensus pattern (16 bp):
TCGATATGGAATAAGA
Found at i:3774768 original size:7 final size:7
Alignment explanation
Indices: 3774750--3774785 Score: 63
Period size: 7 Copynumber: 5.0 Consensus size: 7
3774740 AATAAAAAAT
3774750 TATTAAA
1 TATTAAA
3774757 TTATTAAA
1 -TATTAAA
3774765 TATTAAA
1 TATTAAA
3774772 TATTAAA
1 TATTAAA
3774779 TATTAAA
1 TATTAAA
3774786 ATAAAACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATTAAA
Found at i:3784990 original size:2 final size:2
Alignment explanation
Indices: 3784983--3785016 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
3784973 AAAGGCAAAC
3784983 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
3785017 GTGAAACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3786843 original size:13 final size:14
Alignment explanation
Indices: 3786817--3786845 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3786807 ATCATATTAC
3786817 TACTAAAAATAAAT
1 TACTAAAAATAAAT
3786831 TACTAAAAA-AAAT
1 TACTAAAAATAAAT
3786844 TA
1 TA
3786846 GGTGAAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (14 bp):
TACTAAAAATAAAT
Found at i:3788615 original size:18 final size:17
Alignment explanation
Indices: 3788585--3788618 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3788575 TATTTGATTT
*
3788585 TTTAAAATTATTTTTTA
1 TTTAAAATAATTTTTTA
3788602 TTTAAGAATAATTTTTT
1 TTTAA-AATAATTTTTT
3788619 TAAAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTAAAATAATTTTTTA
Found at i:3788626 original size:15 final size:16
Alignment explanation
Indices: 3788582--3788628 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
3788572 CCATATTTGA
* *
3788582 TTTTTTAAAATTATTT
1 TTTTTTAAAAATATAT
*
3788598 TTTATTTAAGAATA-AT
1 TTT-TTTAAAAATATAT
3788614 TTTTTTAAAAATATA
1 TTTTTTAAAAATATA
3788629 ATATACTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 9 0.36
16 8 0.32
17 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTTTTTAAAAATATAT
Found at i:3790374 original size:130 final size:128
Alignment explanation
Indices: 3790138--3790396 Score: 473
Period size: 130 Copynumber: 2.0 Consensus size: 128
3790128 TCTTACCCGT
*
3790138 TTCGGCTTTTCCCAAATTCAATCTCAAATTACTAATTAGCTTTTTTTTTTAAGTTATATAAAACA
1 TTCGCCTTTTCCCAAATTCAATCTCAAATTACTAATTAGCTTTTTTTTTTAAGTTATATAAAACA
*
3790203 ATTACAAGTATAAAGAATACGTATATGAATAATTATCATTAAAATTAGATATTATAAAAATAA
66 ATTACAAGTATAAAGAATACGTATACGAATAATTATCATTAAAATTAGATATTATAAAAATAA
3790266 TTCGCCTTTTCCCAAATTCAATCTCAAATTACTAATTAGCTTTTTTTTTTTTAAGTTATATAAAA
1 TTCGCCTTTTCCCAAATTCAATCTCAAATTACTAATTAGC--TTTTTTTTTTAAGTTATATAAAA
*
3790331 CAATTACGAGTATAAAGAATACGTATACGAATAATTATCATTAAAATTAGATATTATAAAAATAA
64 CAATTACAAGTATAAAGAATACGTATACGAATAATTATCATTAAAATTAGATATTATAAAAATAA
3790396 T
1 T
3790397 AATTAGTTTC
Statistics
Matches: 126, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
128 39 0.31
130 87 0.69
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (128 bp):
TTCGCCTTTTCCCAAATTCAATCTCAAATTACTAATTAGCTTTTTTTTTTAAGTTATATAAAACA
ATTACAAGTATAAAGAATACGTATACGAATAATTATCATTAAAATTAGATATTATAAAAATAA
Found at i:3790842 original size:20 final size:19
Alignment explanation
Indices: 3790817--3790866 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
3790807 TATATTATTT
*
3790817 ATATTTTATAATTTTTTATA
1 ATATTTTATAA-TTTTAATA
*
3790837 ATATTTGAATAATTTTAATA
1 ATATTT-TATAATTTTAATA
*
3790857 AAATTTTATA
1 ATATTTTATA
3790867 TTTATCTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 3 0.12
20 18 0.72
21 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATATTTTATAATTTTAATA
Found at i:3795604 original size:21 final size:21
Alignment explanation
Indices: 3795580--3795620 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3795570 AATTCAAATC
* *
3795580 GAGTCGAGTGAAATGAAATTT
1 GAGTCAAGTCAAATGAAATTT
*
3795601 GAGTCAAGTCAAATTAAATT
1 GAGTCAAGTCAAATGAAATT
3795621 GAATGAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (21 bp):
GAGTCAAGTCAAATGAAATTT
Found at i:3796896 original size:37 final size:37
Alignment explanation
Indices: 3796855--3796933 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
3796845 GATATTTTTT
* *
3796855 AATTTGGT-TCTAATTTTTTAGCTCAATTTGGTATATA
1 AATTTGGTACCTAATTTTTT-GCTCAATTTGGTACATA
* * *
3796892 AATTTGGTACCTAATTTTTTTCTTAATTTGGTACCTA
1 AATTTGGTACCTAATTTTTTGCTCAATTTGGTACATA
3796929 AATTT
1 AATTT
3796934 TTTGGGGACC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 26 0.72
38 10 0.28
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.52
Consensus pattern (37 bp):
AATTTGGTACCTAATTTTTTGCTCAATTTGGTACATA
Found at i:3816109 original size:46 final size:46
Alignment explanation
Indices: 3816048--3816139 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
3816038 CATGTATAGG
3816048 AAACAAGAAAAAATTATATCATATTTCCCATTTCAGCTTCAAATAA
1 AAACAAGAAAAAATTATATCATATTTCCCATTTCAGCTTCAAATAA
*
3816094 AAACAAGAAAGAATTATATCATATTTCCCATTTCAGCTTCAAATAA
1 AAACAAGAAAAAATTATATCATATTTCCCATTTCAGCTTCAAATAA
3816140 CAGATGCATC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.30
Consensus pattern (46 bp):
AAACAAGAAAAAATTATATCATATTTCCCATTTCAGCTTCAAATAA
Found at i:3818573 original size:27 final size:27
Alignment explanation
Indices: 3818542--3818598 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
3818532 AAATTAAAGG
* * **
3818542 TAAATTTATCATTATACTTTTCTTTTA
1 TAAATTTACCACTATACTTTAATTTTA
3818569 TAAATTTACCACTATACTTTAATTTTA
1 TAAATTTACCACTATACTTTAATTTTA
3818596 TAA
1 TAA
3818599 TAAAGTTTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (27 bp):
TAAATTTACCACTATACTTTAATTTTA
Found at i:3818792 original size:17 final size:18
Alignment explanation
Indices: 3818762--3818795 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3818752 AAAATTAATG
3818762 AAAATAATTATTTTATAA
1 AAAATAATTATTTTATAA
3818780 AAAATAATT-TTTTATA
1 AAAATAATTATTTTATA
3818796 TATATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATAATTATTTTATAA
Found at i:3823156 original size:26 final size:25
Alignment explanation
Indices: 3823128--3823177 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3823118 TCGTACAATT
*
3823128 TTTTTTTATTTCGGTGAAATAAAAC
1 TTTTTTTATTTCGATGAAATAAAAC
3823153 TTTTTTTATTTCGATGAAATAAAAC
1 TTTTTTTATTTCGATGAAATAAAAC
3823178 AAATGCACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (25 bp):
TTTTTTTATTTCGATGAAATAAAAC
Found at i:3826269 original size:13 final size:15
Alignment explanation
Indices: 3826253--3826290 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
3826243 TTAAGTTAAA
3826253 TTATTAAAATT-A-T
1 TTATTAAAATTAAGT
*
3826266 TTATTAAATTTAAGT
1 TTATTAAAATTAAGT
3826281 TTATTAAAAT
1 TTATTAAAAT
3826291 ATTATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 10 0.48
14 1 0.05
15 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTATTAAAATTAAGT
Found at i:3835126 original size:58 final size:57
Alignment explanation
Indices: 3835057--3835184 Score: 154
Period size: 58 Copynumber: 2.2 Consensus size: 57
3835047 TACAAATAAA
* * * *
3835057 AAAAATATTTTTTT-GA-GTGATTGCCATCTAATGG-TCTATACCATTTTTTTTAAGATTT
1 AAAAATATTTTTTTGGATGT-A-TGCCACCCAATGGCT-TACACCATTTTTTTCAA-ATTT
*
3835115 AAAAATATTTTTTTGGATGTATGTCACCCAATGGCTTACACCATTTTTTTCAAATTT
1 AAAAATATTTTTTTGGATGTATGCCACCCAATGGCTTACACCATTTTTTTCAAATTT
3835172 AAAAATATTTTTT
1 AAAAATATTTTTT
3835185 AAATGTTTAC
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
57 17 0.27
58 39 0.63
59 4 0.06
60 2 0.03
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (57 bp):
AAAAATATTTTTTTGGATGTATGCCACCCAATGGCTTACACCATTTTTTTCAAATTT
Found at i:3835202 original size:56 final size:58
Alignment explanation
Indices: 3835096--3835203 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 58
3835086 AATGGTCTAT
* ** **
3835096 ACCATTTTTTTTAAGATTTAAAAATATTTTTTTGGATGTATGTCACCCAATGGCTTAC
1 ACCATTTTTTTCAAGATTTAAAAATATTTTTTTAAATGTATACCACCCAATGGCTTAC
* *
3835154 ACCATTTTTTTCAA-ATTTAAAAATA-TTTTTTAAATGTTTACCATCCAATG
1 ACCATTTTTTTCAAGATTTAAAAATATTTTTTTAAATGTATACCACCCAATG
3835204 ACAAATTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
56 19 0.44
57 11 0.26
58 13 0.30
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.45
Consensus pattern (58 bp):
ACCATTTTTTTCAAGATTTAAAAATATTTTTTTAAATGTATACCACCCAATGGCTTAC
Found at i:3835471 original size:57 final size:55
Alignment explanation
Indices: 3835410--3835612 Score: 167
Period size: 57 Copynumber: 3.6 Consensus size: 55
3835400 TTATGCAGAT
*
3835410 CATTAAATGACAAACACTTAAAAAAATATTTTTAAATTTAAAAAAGATAGTGTAGAC
1 CATTAAATGACAAACACTTAAAAAAATATTTTTAAATTTAAAAAA-AT-GTGTAGGC
** * * * *
3835467 CATTAGGTGATAAATA-TAAAAAATAATATTTTTAAATTTAGGAAAAATGGTGTAGGC
1 CATTAAATGACAAACACTTAAAAA-AATATTTTTAAATTTA-AAAAAAT-GTGTAGGC
*** * * * *
3835524 CATTGGGTGACGAACAC-TCAAAAAATATTTTTAAATCTGAAAAAAATGATATAGGC
1 CATTAAATGACAAACACTTAAAAAAATATTTTTAAAT-TTAAAAAAATG-TGTAGGC
* * **
3835580 CATTCAATAACAAACACCCAAAAAAATATTTTT
1 CATTAAATGACAAACACTTAAAAAAATATTTTT
3835613 GAGAACCTAA
Statistics
Matches: 116, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
55 1 0.01
56 43 0.37
57 68 0.59
58 4 0.03
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (55 bp):
CATTAAATGACAAACACTTAAAAAAATATTTTTAAATTTAAAAAAATGTGTAGGC
Found at i:3857822 original size:6 final size:6
Alignment explanation
Indices: 3857811--3857847 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
3857801 ATTGGTACTT
3857811 GTGTCA GTGTCA GTGTCA GTGTCA GTGTCA GTGTCA G
1 GTGTCA GTGTCA GTGTCA GTGTCA GTGTCA GTGTCA G
3857848 AGCCAATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.35, T:0.32
Consensus pattern (6 bp):
GTGTCA
Found at i:3862707 original size:3 final size:3
Alignment explanation
Indices: 3862699--3862735 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3862689 TATTTAGGAG
3862699 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3862736 TATCTTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3866581 original size:6 final size:6
Alignment explanation
Indices: 3866564--3866607 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
3866554 ATTAATAACT
* * *
3866564 TAAATAA TAAATA TAAATA TATATA TAAATA TATATA TATATA T
1 TAAAT-A TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA T
3866608 TAATCCATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
TAAATA
Found at i:3866587 original size:2 final size:2
Alignment explanation
Indices: 3866574--3866607 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3866564 TAAATAATAA
* *
3866574 AT AT AA AT AT AT AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3866608 TAATCCATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3866589 original size:12 final size:12
Alignment explanation
Indices: 3866564--3866607 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
3866554 ATTAATAACT
*
3866564 TAAATAATAAATA
1 TAAAT-ATATATA
3866577 TAAATATATATA
1 TAAATATATATA
3866589 TAAATATATATA
1 TAAATATATATA
*
3866601 TATATAT
1 TAAATAT
3866608 TAATCCATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 24 0.83
13 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATATATATA
Found at i:3867702 original size:29 final size:28
Alignment explanation
Indices: 3867647--3867702 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
3867637 ATTTTTTTAA
**
3867647 TTTTATATTATTATTTTAGTATTAAATT
1 TTTTATATTATTATTTTAGTAAAAAATT
3867675 TTTTATATATATTATTATT-GTAAAAAAT
1 TTTTATAT-TATTATT-TTAGTAAAAAAT
3867703 CCTCATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.33
29 14 0.58
30 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (28 bp):
TTTTATATTATTATTTTAGTAAAAAATT
Found at i:3870813 original size:22 final size:20
Alignment explanation
Indices: 3870786--3870825 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3870776 TTTATGATTG
3870786 AATTTGGAATTAATTCTAATTA
1 AATTT-GAATTAATT-TAATTA
*
3870808 AATTTGAATTTATTTAAT
1 AATTTGAATTAATTTAAT
3870826 AATTTTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (20 bp):
AATTTGAATTAATTTAATTA
Found at i:3870859 original size:26 final size:26
Alignment explanation
Indices: 3870810--3870859 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3870800 TCTAATTAAA
**
3870810 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
*
3870836 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
3870860 GCAAATGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:3873382 original size:13 final size:13
Alignment explanation
Indices: 3873366--3873393 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3873356 TAATTTGCCA
3873366 TTTTAAAAAATAT
1 TTTTAAAAAATAT
3873379 TTTTAAAAAATAT
1 TTTTAAAAAATAT
3873392 TT
1 TT
3873394 AATATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAAAAAATAT
Found at i:3873414 original size:17 final size:17
Alignment explanation
Indices: 3873385--3873432 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
3873375 ATATTTTTAA
3873385 AAAATATTT-AATATAT
1 AAAATATTTAAATATAT
3873401 AAAATATTTAAATATAT
1 AAAATATTTAAATATAT
* *
3873418 CAAATGAATTAAATA
1 AAAAT-ATTTAAATA
3873433 AAATAATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.32
17 11 0.39
18 8 0.29
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AAAATATTTAAATATAT
Found at i:3874208 original size:16 final size:17
Alignment explanation
Indices: 3874178--3874210 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3874168 CTTACAATAA
*
3874178 TTAAATAACATTTAAAT
1 TTAAACAACATTTAAAT
3874195 TTAAACAACA-TTAAAT
1 TTAAACAACATTTAAAT
3874211 GAATTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAACAACATTTAAAT
Found at i:3875486 original size:11 final size:11
Alignment explanation
Indices: 3875454--3875488 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
3875444 TATGAAAATT
3875454 TTAAAATT-AA
1 TTAAAATTAAA
3875464 TTAAAAATTAAA
1 TT-AAAATTAAA
3875476 TTAAAATTAAA
1 TTAAAATTAAA
3875487 TT
1 TT
3875489 GTAAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 17 0.74
12 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAAATTAAA
Found at i:3876523 original size:37 final size:37
Alignment explanation
Indices: 3876482--3876553 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
3876472 ATTTCATGTG
*
3876482 TTATTATTA-ATTAATTTTAAAATATATATTT-TATTAT
1 TTATT-TTATATTAATTTTAAAA-ACATATTTATATTAT
*
3876519 TTATTTTATGTTAATTTTAAAAACATATTTATATT
1 TTATTTTATATTAATTTTAAAAACATATTTATATT
3876554 CTAAATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 10 0.32
37 21 0.68
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (37 bp):
TTATTTTATATTAATTTTAAAAACATATTTATATTAT
Found at i:3883032 original size:21 final size:19
Alignment explanation
Indices: 3882990--3883036 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
3882980 GCTTTTTTTC
* *
3882990 AAAATATTTTTTAATGTCA
1 AAAATATTTTTAAATCTCA
3883009 AAAATATTTTTAAAAATCTCA
1 AAAATATTTTT--AAATCTCA
3883030 AAAATAT
1 AAAATAT
3883037 CTAATTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
21 13 0.54
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATATTTTTAAATCTCA
Found at i:3883090 original size:18 final size:17
Alignment explanation
Indices: 3882990--3883090 Score: 62
Period size: 18 Copynumber: 5.6 Consensus size: 17
3882980 GCTTTTTTTC
*
3882990 AAAATATTTTTTAATGTCA
1 AAAATA-TTTTT-ATCTCA
3883009 AAAATATTTTTAAAAATCTCA
1 AAAATATTTTT----ATCTCA
* * *
3883030 AAAATA-TCTAAT-TTA
1 AAAATATTTTTATCTCA
*
3883045 ATAATATTTTTATCTCA
1 AAAATATTTTTATCTCA
*
3883062 AAAGTAATTTTTATCTCA
1 AAAAT-ATTTTTATCTCA
*
3883080 AAAATACTTTT
1 AAAATATTTTT
3883091 GAGTAGTACT
Statistics
Matches: 64, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
15 7 0.11
16 6 0.09
17 10 0.16
18 21 0.33
19 6 0.09
20 2 0.03
21 12 0.19
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (17 bp):
AAAATATTTTTATCTCA
Found at i:3887216 original size:14 final size:16
Alignment explanation
Indices: 3887197--3887233 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
3887187 GGTTTTTTTG
3887197 TAAAAAAATAA-T-AT
1 TAAAAAAATAATTAAT
*
3887211 TAAAAAATTAATTAAT
1 TAAAAAAATAATTAAT
3887227 TAAAAAA
1 TAAAAAA
3887234 GTGGAGTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 10 0.50
15 1 0.05
16 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAAAAATAATTAAT
Found at i:3887403 original size:31 final size:31
Alignment explanation
Indices: 3887362--3887433 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
3887352 AAATATTTTT
*
3887362 ATAAATTTTAAATTTTATAATTAAATCATCA
1 ATAATTTTTAAATTTTATAATTAAATCATCA
* **
3887393 ATAATTTTTAAATTTTATAATTAATTCATTG
1 ATAATTTTTAAATTTTATAATTAAATCATCA
3887424 ATAATTTTTA
1 ATAATTTTTA
3887434 TAGTTAAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (31 bp):
ATAATTTTTAAATTTTATAATTAAATCATCA
Found at i:3903919 original size:56 final size:56
Alignment explanation
Indices: 3903795--3903918 Score: 142
Period size: 57 Copynumber: 2.2 Consensus size: 56
3903785 GACACCCAAA
* * * * * *
3903795 CAAATTAAAAAATATTTTTTTGGTGTTTGTCATCCAATGACCTATATCATTTTTTT
1 CAAATTTAAAAATAATTTTTTGGTGTTTGCCATCCAATGACCTACACCATTCTTTT
* *
3903851 CAAATTTAAAAATAATTTTTTGTGTGTTTGCCATCTAATGATCTACACCA-TCTTTT
1 CAAATTTAAAAATAATTTTTTG-GTGTTTGCCATCCAATGACCTACACCATTCTTTT
*
3903907 CGAGATTTAAAA
1 C-AAATTTAAAA
3903919 TTTTAAAATT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
56 26 0.46
57 31 0.54
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (56 bp):
CAAATTTAAAAATAATTTTTTGGTGTTTGCCATCCAATGACCTACACCATTCTTTT
Found at i:3914250 original size:20 final size:21
Alignment explanation
Indices: 3914225--3914264 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3914215 AATTCAAGTT
3914225 AATTACAACGTTAT-TTTTTA
1 AATTACAACGTTATCTTTTTA
*
3914245 AATTACAAGGTTATCTTTTT
1 AATTACAACGTTATCTTTTT
3914265 TTTTTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
AATTACAACGTTATCTTTTTA
Found at i:3923005 original size:75 final size:75
Alignment explanation
Indices: 3922868--3923546 Score: 1034
Period size: 75 Copynumber: 9.1 Consensus size: 75
3922858 GCGGATAGCT
* * * * * * * *
3922868 AGGAGGAGTGGGAGAGCTTTGAGAAGGGTTCAGTCCGGTTGGTACTTTTCTCTTTACATTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
*
3922933 TATAATTGGA
66 TATAACTGGA
* * * *
3922943 AAGAGAAGTAGGAGAACTCTGAGAAGGGTTCGGCCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
3923008 TATAACTGGA
66 TATAACTGGA
* *
3923018 AGGAGGGGTAGGAGAACTTTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
3923083 TATAACTGGA
66 TATAACTGGA
3923093 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
*
3923158 TATAGCTGGA
66 TATAACTGGA
3923168 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
*
3923233 TATAAGTGGA
66 TATAACTGGA
* *
3923243 AGGAGGGGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACATTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
3923308 TATAACTGGA
66 TATAACTGGA
* *
3923318 AGGAGGAGTAGGAGAACTCTGACAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
*
3923383 TATAATTGGA
66 TATAACTGGA
* *
3923393 AGGAGGGGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTAAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
*
3923458 TATAACTAGA
66 TATAACTGGA
* * * ** * * * *
3923468 AGGAGGAGTAGGAGAACTCTGTGTAGGGCTCGGTCCACTTGGTACTTTTCTCTTTACGATGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
* *
3923533 TATCACTAGA
66 TATAACTGGA
3923543 AGGA
1 AGGA
3923547 TCATGAAGTA
Statistics
Matches: 556, Mismatches: 48, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 556 1.00
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (75 bp):
AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
TATAACTGGA
Found at i:3923967 original size:127 final size:127
Alignment explanation
Indices: 3923727--3924617 Score: 1193
Period size: 127 Copynumber: 7.0 Consensus size: 127
3923717 GAAGTAAAAG
* * * * *
3923727 TATGATTGATGGTAGGAAACAGAGTACAATGCATTATATTTATATGAACATATTTTCAAATAGAA
1 TATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
** *
3923792 TCCAAGAATCGAACATTTTTAAGAAAATATTTTGTGCAGATTTCTATTTCCATTTTTGATGA
66 TCCAAGAATCGAACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
* * * *
3923854 TATGTTTGATGATAGGAAAAAGAGTACACTACATTATATTTATATGAACAAATTTTCAATTAGAA
1 TATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
* * * * *
3923919 TCCAAGAATAGGAA-ATTTTTTAGAAAATATTTAATGCAAATTTTTATTTCCATTTTTTATAA
66 TCCAAGAAT-CGAACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
* * * *
3923981 AATATTTGATGGTAAGAAAGAGAGTATAATACATTATATTTATATGAACAGATTTTCAATTAGAA
1 TATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
* * * * *
3924046 TCCAAGAAT-AAGACATTTTTGAGAAAATGTTTAATGCAGATTTTTATTTCCATTTCTGATAA
66 TCCAAGAATCGA-ACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
3924108 TATGTTT-ATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
1 TATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
* * *
3924172 TCCAAGAATCAAACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTTCATTTTCGATAA
66 TCCAAGAATCGAACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
*
3924234 TATGTTT-ATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAAATAGAA
1 TATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
**
3924298 TCCAAGAATCGAACATTTTTAAGAAAATATTTTGTGCAGATTTCTATTTCCATTTTTGATAA
66 TCCAAGAATCGAACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
* * * * *
3924360 TATGATTGATGGTAGG-AAGTAGAGTATAGTACATTATATATT-TATGAACATATTTTCAATTAA
1 TATGTTTGATGGTAGGAAAG-AGAGTACAATACATTATAT-TTATATGAACAGATTTTCAATTAG
* * * *
3924423 AATCTAAGAAT-GAAATATTTTTTAGAAAATATTTAATGCAGATTTCTATTTCTATTTTTGATAA
64 AATCCAAGAATCG-AACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
* * * * * *
3924487 TATATTTGATGGTAGGAAATAGAATATAATACGTTATATTTATATGGACAGATTTTCAATTAGAA
1 TATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
* * * * * * *
3924552 TCCAAAAATCAAACATTGTTAGAAAAAATATATAATGGAGATTTCTATTTCTATTTTTGATAA
66 TCCAAGAATCGAACATTTTTA-AGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
3924615 TAT
1 TAT
3924618 TGATATCAAG
Statistics
Matches: 677, Mismatches: 75, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
125 1 0.00
126 241 0.36
127 387 0.57
128 48 0.07
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (127 bp):
TATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
TCCAAGAATCGAACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
Found at i:3934811 original size:75 final size:75
Alignment explanation
Indices: 3934688--3935666 Score: 1442
Period size: 75 Copynumber: 13.1 Consensus size: 75
3934678 GCGGATAGCT
* * * *
3934688 AGGAGGAGTAGGAGAACTCTGGGAAGGGTTCGGTCCAGTCGGTACTTTTCTCTTTACATTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
3934753 TATAACTGGA
66 TATAACTGGA
* * *
3934763 AGGAGGAGTAGGAGAGCTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTTACATTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
3934828 TATAACTGGA
66 TATAACTGGA
* *
3934838 AGAAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCTGGTCGGTACTTTTCTCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
3934903 TATAACTGGA
66 TATAACTGGA
* * *
3934913 AGGAGGAGTAGGAGAACTCAGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTTTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
3934978 TATAACTGGA
66 TATAACTGGA
* * * *
3934988 AGGAGGAGTAGGAGAACTCTGCGTAGGGCTT-GGTCCGGTCGGTACTTTCCTCTTCACATTGAAA
1 AGGAGGAGTAGGAGAACTCTGAGAAGGG-TTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAA
*
3935052 TTATAACTAGA
65 TTATAACTGGA
* * *
3935063 AGGAGGAGTAGGAGAACTCTGCGTAAGGCTT-GGTCCGGTCGGTACTTTCCTCTTCACGTTGAAA
1 AGGAGGAGTAGGAGAACTCTGAG-AAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAA
3935127 TTATAACTGGA
65 TTATAACTGGA
* * * * *
3935138 AGGAAGAGTAAGAGAACTCTGAGAAGGGTTCGGTCCGATCGATACTTTTCTCTTCACGTTAAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
*
3935203 TATAAGTGGA
66 TATAACTGGA
3935213 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
*
3935278 TATAACTTGA
66 TATAACTGGA
* * *
3935288 AGGAGGGGTAGGAGAACTCTGAGAAGAGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
*
3935353 TATAAGTGGA
66 TATAACTGGA
* * *
3935363 AGGAGGGGTAGGAGAACTTTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCCCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
*
3935428 TATAGCTGGA
66 TATAACTGGA
* *
3935438 AGGAGGAGTAGGAGAACTTTGAGAAGGGTTCGGTCCGGTCGGTACTTTCCTCTTCACGTTGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
3935503 TATAACTGGA
66 TATAACTGGA
* * * *
3935513 AGGAGGAGTAGGAGAACTCTGCGTAGGGCTCGGTCCGGTCGGTAC-TTTCTTCTTCACGTTAAAA
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTC-TCTTCACGTTGAAA
*
3935577 TTATAACTAGA
65 TTATAACTGGA
* * * ** * * *
3935588 AGGAGGAGTAGGAGAACTCTGTGTAGGGCTCGGTCCACTTGGTACTTTTCTCTTTACGATGAAAT
1 AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
* *
3935653 TATCACTAGA
66 TATAACTGGA
3935663 AGGA
1 AGGA
3935667 TCATGAAGTA
Statistics
Matches: 830, Mismatches: 69, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
74 9 0.01
75 812 0.98
76 9 0.01
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (75 bp):
AGGAGGAGTAGGAGAACTCTGAGAAGGGTTCGGTCCGGTCGGTACTTTTCTCTTCACGTTGAAAT
TATAACTGGA
Found at i:3936087 original size:127 final size:127
Alignment explanation
Indices: 3935847--3936737 Score: 1195
Period size: 127 Copynumber: 7.0 Consensus size: 127
3935837 GAAGTAAAAG
* * * * *
3935847 TATGATTGATGGTAGGAAACAGAGTACAATGCATTATATTTATATGAACATATTTTCAAATAGAA
1 TATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
* ** *
3935912 TCCAAGAATCGAACATTTTTAAGAAAATATTTTGTGCAGATTTCTATTTCCATTTTTGATGA
66 TCCAAGAATAGAACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
* * * *
3935974 TATGTTTGATGATAGGAAAAAGAGTACACTACATTATATTTATATGAACAAATTTTCAATTAGAA
1 TATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
* * * * *
3936039 TCCAAGAATAGAAAATTTTTTAGAAAATATTTAATGCAAATTTTTATTTCCATTTTTTATAA
66 TCCAAGAATAGAACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
* * *
3936101 TATTTTTGATGGTAAGAAAGAGAGTATAATACATTATATTTATATGAACAGATTTTCAATTAGAA
1 TATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
* * * *
3936166 TCCAAGAATA-AGACATTTTTGAGAAAATGTTTAATGCAGATTTTTATTTCCATTTCTGATAA
66 TCCAAGAATAGA-ACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
3936228 TATGTTT-ATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
1 TATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
* *
3936292 TCCAAGAATCA-AACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTTCATTTTCGATAA
66 TCCAAGAAT-AGAACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
*
3936354 TATGTTT-ATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAAATAGAA
1 TATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
* **
3936418 TCCAAGAATCGAACATTTTTAAGAAAATATTTTGTGCAGATTTCTATTTCCATTTTTGATAA
66 TCCAAGAATAGAACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
* * * * *
3936480 TATGATTGATGGTAGG-AAGTAGAGTATAGTACATTATATATT-TATGAACATATTTTCAATTAA
1 TATGTTTGATGGTAGGAAAG-AGAGTACAATACATTATAT-TTATATGAACAGATTTTCAATTAG
* * * *
3936543 AATCTAAGAAT-GAAATATTTTTTAGAAAATATTTAATGCAGATTTCTATTTCTATTTTTGATAA
64 AATCCAAGAATAG-AACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
* * * * * *
3936607 TATATTTGATGGTAGGAAATAGAATATAATACGTTATATTTATATGGACAGATTTTCAATTAGAA
1 TATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
* * * * * *
3936672 TCCAAAAATCA-AACATTGTTAGAAAAAATATATAATGGAGATTTCTATTTCTATTTTTGATAA
66 TCCAAGAAT-AGAACATTTTTA-AGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
3936735 TAT
1 TAT
3936738 TGATATCAAG
Statistics
Matches: 679, Mismatches: 73, Indels: 23
0.88 0.09 0.03
Matches are distributed among these distances:
126 240 0.35
127 394 0.58
128 45 0.07
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (127 bp):
TATGTTTGATGGTAGGAAAGAGAGTACAATACATTATATTTATATGAACAGATTTTCAATTAGAA
TCCAAGAATAGAACATTTTTAAGAAAATATTTAATGCAGATTTCTATTTCCATTTTTGATAA
Found at i:3959878 original size:17 final size:17
Alignment explanation
Indices: 3959852--3959885 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3959842 AATTGAATAT
*
3959852 TTAATTTTTAATATTTC
1 TTAATATTTAATATTTC
*
3959869 TTAATATTTAATTTTTC
1 TTAATATTTAATATTTC
3959886 AATTTAAAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAATATTTAATATTTC
Found at i:3965201 original size:220 final size:220
Alignment explanation
Indices: 3964819--3965262 Score: 834
Period size: 220 Copynumber: 2.0 Consensus size: 220
3964809 AAACAAACCA
*
3964819 AATTATATTTATTTGTTAGAGCAGTGGCGTAGCTAGGATGCTGGCAATGCTCCTGTTTTTTAAAA
1 AATTATATTTATTTGTTAGAGCAGTGACGTAGCTAGGATGCTGGCAATGCTCCTGTTTTTTAAAA
* *
3964884 TAAAAATTTTAATTTTAAAATTTTAAATTGATAAAGATAAAAGTGTATTTTAACCCCTAAAATGG
66 TAAAAATTTTAATTTTAAAATTTTAAATTGATAAAGATAAAAGTATATTTTAACCCCTAAAATGA
*
3964949 TAAGATTTGATTTAATTCTTTAAAGATTATAAATATATAAACTATTAAAATGATGAAATTATATT
131 TAAGATTTGATTTAATTCTTTAAAAATTATAAATATATAAACTATTAAAATGATGAAATTATATT
*
3965014 TTTACTATTGTAAAAATTACTATTT
196 TTTACTATCGTAAAAATTACTATTT
3965039 AATTATATTTATTTGTTAGAGCAGTGACGTAGCTAGGATGCTGGCAATGCTCCTGTTTTTTAAAA
1 AATTATATTTATTTGTTAGAGCAGTGACGTAGCTAGGATGCTGGCAATGCTCCTGTTTTTTAAAA
3965104 TAAAAATTTTAATTTTAAAATTTTAAATTGATAAAGATAAAAGTATATTTTAACCCCTAAAATGA
66 TAAAAATTTTAATTTTAAAATTTTAAATTGATAAAGATAAAAGTATATTTTAACCCCTAAAATGA
3965169 TAAGATTTGATTTAATTCTTTAAAAATTATAAATATATAAACTATTAAAATGATGAAATTATATT
131 TAAGATTTGATTTAATTCTTTAAAAATTATAAATATATAAACTATTAAAATGATGAAATTATATT
*
3965234 TTTAGTATCGTAAAAATTACTATTT
196 TTTACTATCGTAAAAATTACTATTT
3965259 AATT
1 AATT
3965263 TCAGCCTTTA
Statistics
Matches: 218, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
220 218 1.00
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.41
Consensus pattern (220 bp):
AATTATATTTATTTGTTAGAGCAGTGACGTAGCTAGGATGCTGGCAATGCTCCTGTTTTTTAAAA
TAAAAATTTTAATTTTAAAATTTTAAATTGATAAAGATAAAAGTATATTTTAACCCCTAAAATGA
TAAGATTTGATTTAATTCTTTAAAAATTATAAATATATAAACTATTAAAATGATGAAATTATATT
TTTACTATCGTAAAAATTACTATTT
Found at i:3967330 original size:87 final size:89
Alignment explanation
Indices: 3967219--3967396 Score: 333
Period size: 87 Copynumber: 2.0 Consensus size: 89
3967209 TACTAATATT
3967219 TGATTTTTTAATTTTTTTTATTCTATTAATCTTGGAAATTAGATAATGATATAAAGCTTGTTATT
1 TGATTTTTTAATTTTTTTTATTCTATTAATCTTGGAAATTAGATAATGATATAAAGCTTGTTATT
3967284 TCAACAAGCATTAAAAG-AGGTGA
66 TCAACAAGCATTAAAAGAAGGTGA
3967307 TGATTTTTTAA-TTTTTTTATTCTATTAATCTTGGAAATTAGATAATGATATAAAGCTTGTTATT
1 TGATTTTTTAATTTTTTTTATTCTATTAATCTTGGAAATTAGATAATGATATAAAGCTTGTTATT
*
3967371 TTAACAAGCATTAAAAGAAGGTGA
66 TCAACAAGCATTAAAAGAAGGTGA
3967395 TG
1 TG
3967397 GAAGTGCTTC
Statistics
Matches: 88, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
87 69 0.78
88 19 0.22
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (89 bp):
TGATTTTTTAATTTTTTTTATTCTATTAATCTTGGAAATTAGATAATGATATAAAGCTTGTTATT
TCAACAAGCATTAAAAGAAGGTGA
Found at i:3974446 original size:18 final size:18
Alignment explanation
Indices: 3974423--3974472 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
3974413 CCCACCTTCT
*
3974423 GGTGGAGGCGGAGGCGGC
1 GGTGGAGGAGGAGGCGGC
* *
3974441 GGTGGAGGAGGTGGCGGT
1 GGTGGAGGAGGAGGCGGC
*
3974459 GGTGGAGGTGGAGG
1 GGTGGAGGAGGAGG
3974473 TGGAGGAGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.12, C:0.08, G:0.68, T:0.12
Consensus pattern (18 bp):
GGTGGAGGAGGAGGCGGC
Found at i:3974456 original size:15 final size:15
Alignment explanation
Indices: 3974432--3974490 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
3974422 TGGTGGAGGC
*
3974432 GGAGGCGGCGGTGGA
1 GGAGGTGGCGGTGGA
*
3974447 GGAGGTGGCGGTGGT
1 GGAGGTGGCGGTGGA
*
3974462 GGAGGTGGAGGTGGA
1 GGAGGTGGCGGTGGA
*
3974477 GGAGGTGGGGGTGG
1 GGAGGTGGCGGTGG
3974491 GGGTAGCACT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.12, C:0.05, G:0.69, T:0.14
Consensus pattern (15 bp):
GGAGGTGGCGGTGGA
Found at i:3980930 original size:16 final size:16
Alignment explanation
Indices: 3980905--3980950 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 16
3980895 TAAAATTGAA
3980905 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
*
3980922 ATTTTAATAA---ATT
1 ATATTAATAATTTATT
3980935 ATATTAATAATTTATT
1 ATATTAATAATTTATT
3980951 GTATGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
13 12 0.50
16 8 0.33
17 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:3980961 original size:29 final size:30
Alignment explanation
Indices: 3980905--3980962 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
3980895 TAAAATTGAA
* *
3980905 ATATTAAATAATTTATTATTTTAATAAATT
1 ATATTAAATAATTTATTATATGAATAAATT
* *
3980935 ATATT-AATAATTTATTGTATGATTAAAT
1 ATATTAAATAATTTATTATATGAATAAAT
3980963 ATAAATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
ATATTAAATAATTTATTATATGAATAAATT
Found at i:3991428 original size:3 final size:3
Alignment explanation
Indices: 3991420--3991449 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3991410 GATAATTACA
3991420 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
3991450 AATAATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:4004703 original size:19 final size:19
Alignment explanation
Indices: 4004679--4004715 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4004669 AAATGTCACA
4004679 TAGTCTGCTGCTACTTCCG
1 TAGTCTGCTGCTACTTCCG
4004698 TAGTCTGCTGCTACTTCC
1 TAGTCTGCTGCTACTTCC
4004716 ATTTGGCCGA
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:0.11, C:0.32, G:0.19, T:0.38
Consensus pattern (19 bp):
TAGTCTGCTGCTACTTCCG
Found at i:4014804 original size:35 final size:35
Alignment explanation
Indices: 4014781--4014857 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 35
4014771 TTTTTATATT
4014781 AAATTTAATAAAATTAATAATTAAATTCAAAAATTA
1 AAATTTAA-AAAATTAATAATTAAATTCAAAAATTA
* * *
4014817 AAATTTAAAAAATAAAAAATTAAATTCCTAAAAATAA
1 AAATTTAAAAAATTAATAATTAAATT-C-AAAAATTA
4014854 AAAT
1 AAAT
4014858 ATAATGATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 16 0.44
36 9 0.25
37 11 0.31
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (35 bp):
AAATTTAAAAAATTAATAATTAAATTCAAAAATTA
Found at i:4014837 original size:22 final size:21
Alignment explanation
Indices: 4014809--4014856 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
4014799 AATTAAATTC
4014809 AAAAATTAAAATT-TAAAAAATA
1 AAAAATT-AAATTCT-AAAAATA
4014831 AAAAATTAAATTCCTAAAAATA
1 AAAAATTAAATT-CTAAAAATA
4014853 AAAA
1 AAAA
4014857 TATAATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.21
22 18 0.75
23 1 0.04
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAAATTAAATTCTAAAAATA
Found at i:4016799 original size:3 final size:3
Alignment explanation
Indices: 4016791--4016816 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4016781 TTTTATATGA
4016791 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
4016817 AGTACGTGGG
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:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:4030659 original size:15 final size:15
Alignment explanation
Indices: 4030641--4030688 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
4030631 TTTTCTCAAA
* *
4030641 TTACGTTTTAGTCAC
1 TTACATTTTAATCAC
4030656 TTACATTTTAAAT-A-
1 TTACATTTT-AATCAC
4030670 TTACATTTTAATCAC
1 TTACATTTTAATCAC
4030685 TTAC
1 TTAC
4030689 GTTACCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 3 0.11
14 10 0.36
15 13 0.46
16 2 0.07
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (15 bp):
TTACATTTTAATCAC
Done.