Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 10 of 128
Found at i:2990985 original size:88 final size:89
Alignment explanation
Indices: 2990885--2991203 Score: 392
Period size: 88 Copynumber: 3.6 Consensus size: 89
2990875 ACAGATATTG
* * * * * * *
2990885 GATTTGTCGCTTCAATCTGCTCCACTGCAACTTCAGGGAAACT-GGATTTG-TAGCTTCAATCTG
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGA-TAAGATTCGCTATCTTCAATCTG
*
2990948 CTCCATTGCAACTTCAGGGAGATAA
65 CTCCACTGCAACTTCAGGGAGATAA
* * * *
2990973 GATTTTTAGCTTCAATTTGCTCTACTGTAACTTTAGAGAGATAAGATTCGCTATCTTCAATCTGC
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAAGATTCGCTATCTTCAATCTGC
*
2991038 TCTACTGCAACTTCAGGGAGATAA
66 TCCACTGCAACTTCAGGGAGATAA
* * *
2991062 GGTTTGTAGCTTCAATCTGCTCTACTACAACTTTAGAGAGATAAGA-TCGCTATCTTCAATCTGC
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAAGATTCGCTATCTTCAATCTGC
* * * * *
2991126 TGCACTACAAATTTAAGGAGATAA
66 TCCACTGCAACTTCAGGGAGATAA
* * *
2991150 GATTTGTAGCATCAATCTGCTCCACTGCAACTTTAGAGAGATAATATTGGCTAT
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAAGATTCGCTAT
2991204 GATGATTTCA
Statistics
Matches: 198, Mismatches: 30, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
87 1 0.01
88 115 0.58
89 82 0.41
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (89 bp):
GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAAGATTCGCTATCTTCAATCTGC
TCCACTGCAACTTCAGGGAGATAA
Found at i:2991050 original size:133 final size:132
Alignment explanation
Indices: 2990893--2991193 Score: 349
Period size: 133 Copynumber: 2.3 Consensus size: 132
2990883 TGGATTTGTC
* * *
2990893 GCTTCAATCTGCTCCACTGCAACTTCAGGGA-A-ACTGGATTTGTAGCTTCAATCTGCTCCATTG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA-AGG-TTTGTAGCTTCAATCTGCTCCACTA
* *** * ** *
2990956 CAACTTCAGGGAGATAAGATTTTTAGCTTCAATTTGCT-CTACTGTAACTTT-AGAGAGATAAGA
64 CAACTTCAGAGAGATAAGATCGCTAGCTTCAATCTGCTGC-ACTACAAATTTAAG-GAGATAAGA
2991019 TTCGCTA
127 TTCG-TA
* * *
2991026 TCTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGGTTTGTAGCTTCAATCTGCTCTACTACA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAGCTTCAATCTGCTCCACTACA
* * *
2991091 ACTTTAGAGAGATAAGATCGCTATCTTCAATCTGCTGCACTACAAATTTAAGGAGATAAGATTTG
66 ACTTCAGAGAGATAAGATCGCTAGCTTCAATCTGCTGCACTACAAATTTAAGGAGATAAGATTCG
2991156 TA
131 TA
* * *
2991158 GCATCAATCTGCTCCACTGCAACTTTAGAGAGATAA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
2991194 TATTGGCTAT
Statistics
Matches: 142, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
132 33 0.23
133 102 0.72
134 6 0.04
135 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (132 bp):
GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAGCTTCAATCTGCTCCACTACA
ACTTCAGAGAGATAAGATCGCTAGCTTCAATCTGCTGCACTACAAATTTAAGGAGATAAGATTCG
TA
Found at i:2991191 original size:44 final size:44
Alignment explanation
Indices: 2990885--2991193 Score: 327
Period size: 44 Copynumber: 7.0 Consensus size: 44
2990875 ACAGATATTG
* * * * *
2990885 GATTTGTCGCTTCAATCTGCTCCACTGCAACTTCAGGGAAACT-G
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGA-TAA
* * *
2990929 GATTTGTAGCTTCAATCTGCTCCATTGCAACTTCAGGGAGATAA
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAA
* * * *
2990973 GATTTTTAGCTTCAATTTGCTCTACTGTAACTTTAGAGAGATAA
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAA
* * * * *
2991017 GATTCGCTATCTTCAATCTGCTCTACTGCAACTTCAGGGAGATAA
1 GATTTG-TAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAA
* * *
2991062 GGTTTGTAGCTTCAATCTGCTCTACTACAACTTTAGAGAGATAA
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAA
* * * * *
2991106 GA-TCGCTATCTTCAATCTGCTGCACTACAAATTTA-AGGAGATAA
1 GATTTG-TAGCTTCAATCTGCTCCACTGCAACTTTAGA-GAGATAA
*
2991150 GATTTGTAGCATCAATCTGCTCCACTGCAACTTTAGAGAGATAA
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAA
2991194 TATTGGCTAT
Statistics
Matches: 223, Mismatches: 36, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
43 4 0.02
44 179 0.80
45 40 0.18
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAA
Found at i:3001647 original size:20 final size:20
Alignment explanation
Indices: 3001604--3001645 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3001594 TAATGAGAGT
3001604 AAATGAAATAGAAAATAATG
1 AAATGAAATAGAAAATAATG
3001624 AAATGCAAAT-GAAAATAA-G
1 AAATG-AAATAGAAAATAATG
3001643 AAA
1 AAA
3001646 ATTTGAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.14, T:0.17
Consensus pattern (20 bp):
AAATGAAATAGAAAATAATG
Found at i:3004368 original size:6 final size:6
Alignment explanation
Indices: 3004320--3004366 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
3004310 AATAATAGCA
*
3004320 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAA TAATA
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATA
3004367 ATCATATTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TAATAT
Found at i:3004373 original size:18 final size:18
Alignment explanation
Indices: 3004320--3004385 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 18
3004310 AATAATAGCA
* *
3004320 TAATATTAATATTAATAT
1 TAATAATAATAATAATAT
* *
3004338 TAATATTAATATTAATAT
1 TAATAATAATAATAATAT
*
3004356 TAATAATAATAATCATAT
1 TAATAATAATAATAATAT
*
3004374 TAGTAATAATAA
1 TAATAATAATAA
3004386 ATAAACGAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TAATAATAATAATAATAT
Found at i:3004614 original size:4 final size:4
Alignment explanation
Indices: 3004605--3004629 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3004595 ATAAAGAAGT
3004605 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
3004630 TAATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:3004639 original size:23 final size:23
Alignment explanation
Indices: 3004594--3004636 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3004584 TGTGTATAAC
*
3004594 AATAAAGAAGTAATAAATAAATA
1 AATAAAGAAATAATAAATAAATA
*
3004617 AATAAATAAATAAT-AATAAA
1 AATAAAGAAATAATAAATAAA
3004637 ATAGTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (23 bp):
AATAAAGAAATAATAAATAAATA
Found at i:3004785 original size:8 final size:8
Alignment explanation
Indices: 3004765--3004869 Score: 60
Period size: 8 Copynumber: 13.8 Consensus size: 8
3004755 AGAATTAAAA
3004765 TAAA-AAG
1 TAAATAAG
3004772 TAAATAAG
1 TAAATAAG
*
3004780 TGAATAA-
1 TAAATAAG
* *
3004787 TATATAAA
1 TAAATAAG
3004795 TAAATAAG
1 TAAATAAG
**
3004803 TAAATGGG
1 TAAATAAG
*
3004811 TAAATAAA
1 TAAATAAG
*
3004819 TGAATAAAG
1 TAAAT-AAG
3004828 T-AA-AAG
1 TAAATAAG
*
3004834 -GAAT-AG
1 TAAATAAG
* *
3004840 TGAATAAA
1 TAAATAAG
*
3004848 TATATAAG
1 TAAATAAG
3004856 TAAATAAG
1 TAAATAAG
3004864 TAAATA
1 TAAATA
3004870 GATGAATAAA
Statistics
Matches: 74, Mismatches: 17, Indels: 13
0.71 0.16 0.12
Matches are distributed among these distances:
6 7 0.09
7 13 0.18
8 51 0.69
9 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (8 bp):
TAAATAAG
Found at i:3011297 original size:20 final size:20
Alignment explanation
Indices: 3011272--3011311 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3011262 TGCATACAGC
3011272 TTGTATGCATACTGCAGCAA
1 TTGTATGCATACTGCAGCAA
**
3011292 TTGTATGCATGTTGCAGCAA
1 TTGTATGCATACTGCAGCAA
3011312 CATATTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGTATGCATACTGCAGCAA
Found at i:3011357 original size:21 final size:20
Alignment explanation
Indices: 3011324--3011366 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
3011314 TATTTTCTGT
* * *
3011324 TTTAGTTGCAATGTATTTAG
1 TTTAGTTGAAATGAACTTAG
3011344 TTTAGTTGAAAATGAACTTAG
1 TTTAGTTG-AAATGAACTTAG
3011365 TT
1 TT
3011367 GTTGTTGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.47
Consensus pattern (20 bp):
TTTAGTTGAAATGAACTTAG
Found at i:3024857 original size:29 final size:28
Alignment explanation
Indices: 3024815--3024874 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
3024805 AATGGCCAAC
* *
3024815 CATGTTGCTGTTATGTTTTTGTTAAAGTG
1 CATGTTGCTATTATGATTTTGTT-AAGTG
*
3024844 CATGTTGCTATTATGATTTTGTTGAGTG
1 CATGTTGCTATTATGATTTTGTTAAGTG
3024872 CAT
1 CAT
3024875 ACAGCATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.18, C:0.08, G:0.23, T:0.50
Consensus pattern (28 bp):
CATGTTGCTATTATGATTTTGTTAAGTG
Found at i:3026309 original size:23 final size:22
Alignment explanation
Indices: 3026248--3026328 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
3026238 GATCTGCAAA
* *
3026248 GCCTTAGTGGCATATTTTGTGAG
1 GCCTT-GTGGCATATTTTGTAAT
* **
3026271 GCTTGTGTGGTGTATTTTGTAAT
1 GCCT-TGTGGCATATTTTGTAAT
**
3026294 GCCTATGTGGCATATTCAGTAAT
1 GCCT-TGTGGCATATTTTGTAAT
3026317 GCCTTCGTGGCA
1 GCCTT-GTGGCA
3026329 AAAATCTAGT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
22 1 0.02
23 43 0.96
24 1 0.02
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (22 bp):
GCCTTGTGGCATATTTTGTAAT
Found at i:3027645 original size:31 final size:31
Alignment explanation
Indices: 3027605--3027811 Score: 138
Period size: 31 Copynumber: 6.7 Consensus size: 31
3027595 CAACAATATC
* *
3027605 TATATTCATATACGAATCAAATTCGGAAATG
1 TATAATCATATACAAATCAAATTCGGAAATG
* *
3027636 TATAATCATATACAAATC-AATTTGGCAATG
1 TATAATCATATACAAATCAAATTCGGAAATG
* * ** * **
3027666 AATAACCATATATGAATCAAGTTTAGAAATG
1 TATAATCATATACAAATCAAATTCGGAAATG
* *
3027697 TATAATCATATACAAATCAAATTC-TACATTG
1 TATAATCATATACAAATCAAATTCGGA-AATG
* * * *
3027728 TATAACCATATACGAAT-TAATTCGGCAACT-
1 TATAATCATATACAAATCAAATTCGG-AAATG
** *
3027758 TATCTTCATATACAAATCAATTTC-GACAATG
1 TATAATCATATACAAATCAAATTCGGA-AATG
* *
3027789 TATAA-CTATAAACAATTCAAATT
1 TATAATC-ATATACAAATCAAATT
3027812 TAGCAATATA
Statistics
Matches: 132, Mismatches: 36, Indels: 16
0.72 0.20 0.09
Matches are distributed among these distances:
29 1 0.01
30 47 0.36
31 83 0.63
32 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (31 bp):
TATAATCATATACAAATCAAATTCGGAAATG
Found at i:3027685 original size:61 final size:61
Alignment explanation
Indices: 3027611--3027811 Score: 212
Period size: 61 Copynumber: 3.3 Consensus size: 61
3027601 TATCTATATT
* *
3027611 CATATACGAATCAAATTCGGAAATGTATAATCATATACAAATCAATTTGGCAATGAATAAC
1 CATATACGAATCAAATTCGGAAATGTATAATCATATACAAATCAATTTGACAATGTATAAC
* * ** *
3027672 CATATATGAATCAAGTTTAGAAATGTATAATCATATACAAATCAAATTCT-ACATTGTATAAC
1 CATATACGAATCAAATTCGGAAATGTATAATCATATACAAATC-AATT-TGACAATGTATAAC
* * **
3027734 CATATACGAAT-TAATTCGGCAACT-TATCTTCATATACAAATCAATTTCGACAATGTATAAC
1 CATATACGAATCAAATTCGG-AAATGTATAATCATATACAAATCAATTT-GACAATGTATAAC
* *
3027795 TATAAAC-AATTCAAATT
1 CATATACGAA-TCAAATT
3027812 TAGCAATATA
Statistics
Matches: 114, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
59 1 0.01
60 6 0.05
61 76 0.67
62 30 0.26
63 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.32
Consensus pattern (61 bp):
CATATACGAATCAAATTCGGAAATGTATAATCATATACAAATCAATTTGACAATGTATAAC
Found at i:3027827 original size:26 final size:25
Alignment explanation
Indices: 3027798--3027848 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3027788 GTATAACTAT
*
3027798 AAACAATTCAAATTTAGCAATATATA
1 AAACAA-TCAAATTCAGCAATATATA
*
3027824 AAACAATCAAATTCGGCAATATATA
1 AAACAATCAAATTCAGCAATATATA
3027849 TATCTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.53, C:0.14, G:0.06, T:0.27
Consensus pattern (25 bp):
AAACAATCAAATTCAGCAATATATA
Found at i:3028378 original size:25 final size:25
Alignment explanation
Indices: 3028349--3028400 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
3028339 AAAATTGGTA
*
3028349 AGACATTTTCCATT-TTTCTCTAAGC
1 AGACATTTTCCATTCTCT-TCTAAGC
3028374 AGACATTTTCCATTCTCTTCTAAGC
1 AGACATTTTCCATTCTCTTCTAAGC
3028399 AG
1 AG
3028401 CAGACATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (25 bp):
AGACATTTTCCATTCTCTTCTAAGC
Found at i:3030462 original size:32 final size:32
Alignment explanation
Indices: 3030426--3030512 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
3030416 ACAACTTTTT
* * *
3030426 CAGAAAATATTTTCAGGAAATCTGCCAAACAG
1 CAGAAAATATTTTCAGCAAATCTACCAAACAC
* *
3030458 CAGAAAATATTTTACA-CAGATTTACCAAACAC
1 CAGAAAATATTTT-CAGCAAATCTACCAAACAC
*
3030490 CAGAAAATATTTTCGAGTAAATC
1 CAGAAAATATTTTC-AGCAAATC
3030513 ATTTTACAGA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
31 1 0.02
32 38 0.86
33 5 0.11
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.25
Consensus pattern (32 bp):
CAGAAAATATTTTCAGCAAATCTACCAAACAC
Found at i:3030530 original size:20 final size:20
Alignment explanation
Indices: 3030505--3030544 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3030495 AATATTTTCG
*
3030505 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
3030525 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
3030545 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:3030547 original size:34 final size:35
Alignment explanation
Indices: 3030493--3030559 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
3030483 CAAACACCAG
* *
3030493 AAAATATTTTCGAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3030528 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
3030560 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:3030551 original size:14 final size:14
Alignment explanation
Indices: 3030528--3030567 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3030518 ACAGAAAAGT
*
3030528 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
3030542 AAATCATTTTACGG
1 AAAACATTTTACAG
3030556 AAAACATTTTAC
1 AAAACATTTTAC
3030568 TGCCAATCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:3034534 original size:14 final size:14
Alignment explanation
Indices: 3034515--3034543 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3034505 CAACACCTTA
3034515 AGCAATCCTTGTTG
1 AGCAATCCTTGTTG
3034529 AGCAATCCTTGTTG
1 AGCAATCCTTGTTG
3034543 A
1 A
3034544 ACCAATATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (14 bp):
AGCAATCCTTGTTG
Found at i:3035156 original size:23 final size:23
Alignment explanation
Indices: 3035130--3035177 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
3035120 CTCCTTCAAG
*
3035130 TTAATAGCCACATTTCATAAGAC
1 TTAATAGCCACATTTAATAAGAC
3035153 TTAATAGCCACATTTAATAAGAC
1 TTAATAGCCACATTTAATAAGAC
3035176 TT
1 TT
3035178 GCCAATTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (23 bp):
TTAATAGCCACATTTAATAAGAC
Found at i:3036725 original size:14 final size:14
Alignment explanation
Indices: 3036706--3036733 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3036696 CTGAAATTGT
3036706 TGTTAAAATCATTA
1 TGTTAAAATCATTA
3036720 TGTTAAAATCATTA
1 TGTTAAAATCATTA
3036734 AAAATGTTGA
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:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TGTTAAAATCATTA
Found at i:3042934 original size:39 final size:39
Alignment explanation
Indices: 3042868--3042947 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
3042858 GGAGTTAAGC
* *
3042868 TACAAGTTGGCCAATGAAAAGGTAAGAAAGACTTCGAGG
1 TACAAGTTGGCCAATGAAAAAGCAAGAAAGACTTCGAGG
* *
3042907 TACAGGTTGGCCTATGAAAAAGCAAGAAAGACTTCGAGG
1 TACAAGTTGGCCAATGAAAAAGCAAGAAAGACTTCGAGG
3042946 TA
1 TA
3042948 ATTTATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.28, T:0.19
Consensus pattern (39 bp):
TACAAGTTGGCCAATGAAAAAGCAAGAAAGACTTCGAGG
Found at i:3043298 original size:20 final size:19
Alignment explanation
Indices: 3043275--3043319 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3043265 TTTATTATTA
3043275 TTTAACATTTTATATAAATT
1 TTTAA-ATTTTATATAAATT
* *
3043295 TTTAGAATTTTATGTAATTT
1 TTTA-AATTTTATATAAATT
3043315 TTTAA
1 TTTAA
3043320 TTTAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTAAATTTTATATAAATT
Found at i:3043322 original size:18 final size:20
Alignment explanation
Indices: 3043281--3043318 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3043271 ATTATTTAAC
3043281 ATTTTATATAAATTTTTAGA
1 ATTTTATATAAATTTTTAGA
* *
3043301 ATTTTATGTAATTTTTTA
1 ATTTTATATAAATTTTTA
3043319 ATTTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
ATTTTATATAAATTTTTAGA
Found at i:3043878 original size:21 final size:21
Alignment explanation
Indices: 3043841--3043889 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
3043831 TCCAAGCTTC
3043841 TTCCATTTTCCTCTATC-TCTT
1 TTCC-TTTTCCTCTATCGTCTT
*
3043862 TTCCTTTTCCTTTTATCGTTCTT
1 TTCCTTTTCC-TCTATCG-TCTT
3043885 TTCCT
1 TTCCT
3043890 CTTATTCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 9 0.38
23 9 0.38
ACGTcount: A:0.06, C:0.31, G:0.02, T:0.61
Consensus pattern (21 bp):
TTCCTTTTCCTCTATCGTCTT
Found at i:3045064 original size:24 final size:24
Alignment explanation
Indices: 3045037--3045094 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
3045027 GGGTTGGATC
*
3045037 TGATTATGTATATGAATATGCATT
1 TGATTATGTATATAAATATGCATT
* *
3045061 TGATTTTGTATCTAAATATGCATT
1 TGATTATGTATATAAATATGCATT
* *
3045085 CGATTCTGTA
1 TGATTATGTA
3045095 CTTGAACTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.47
Consensus pattern (24 bp):
TGATTATGTATATAAATATGCATT
Found at i:3046926 original size:20 final size:19
Alignment explanation
Indices: 3046881--3046919 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 19
3046871 AATATTACAA
3046881 AAATAAAAAAAATCTAAAG
1 AAATAAAAAAAATCTAAAG
3046900 AATATAAAAAAGAATCTAAA
1 AA-ATAAAAAA-AATCTAAA
3046920 ATAATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 8 0.44
21 8 0.44
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (19 bp):
AAATAAAAAAAATCTAAAG
Found at i:3053187 original size:21 final size:21
Alignment explanation
Indices: 3053163--3053204 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3053153 CTTTTTGTTC
*
3053163 AATTAATTATCGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
**
3053184 AATTTCTTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
3053205 TACTAACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:3057080 original size:53 final size:53
Alignment explanation
Indices: 3056996--3057100 Score: 147
Period size: 53 Copynumber: 2.0 Consensus size: 53
3056986 GAGATTCAAG
* *
3056996 TTAATAGCTACATTTAATAAAGCTTGACAATTGGAAGACGGTAATAATAATTT
1 TTAATAGCCACATTTAATAAAGCTTGACAATTGGAAGACGGTAATAAAAATTT
** * * *
3057049 TTAATAGCCACATTTAATACGGTTTGGCAATTGGAAGATGGTAATAAAAATT
1 TTAATAGCCACATTTAATAAAGCTTGACAATTGGAAGACGGTAATAAAAATT
3057101 GTTGCCACGA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (53 bp):
TTAATAGCCACATTTAATAAAGCTTGACAATTGGAAGACGGTAATAAAAATTT
Found at i:3057311 original size:15 final size:16
Alignment explanation
Indices: 3057286--3057315 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3057276 TTAGATTAGT
3057286 TTTTATTTTAAAATAA
1 TTTTATTTTAAAATAA
3057302 TTTT-TTTTAAAATA
1 TTTTATTTTAAAATA
3057316 TAATACACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTATTTTAAAATAA
Found at i:3057449 original size:36 final size:40
Alignment explanation
Indices: 3057389--3057475 Score: 119
Period size: 38 Copynumber: 2.2 Consensus size: 40
3057379 TAAAAAGTAT
* *
3057389 TTATATTAAAAAACACTACCATAAATATAAT-ATTTTTTA
1 TTATATTAAAAAACACTACAATAAATATAATAATATTTTA
3057428 TTATATTAAAAAA-AC-A-AATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTACAATAAATATAAT-AATATTTTA
3057466 TTATATTAAA
1 TTATATTAAA
3057476 TATAAATGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
36 11 0.25
37 1 0.02
38 19 0.43
39 13 0.30
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (40 bp):
TTATATTAAAAAACACTACAATAAATATAATAATATTTTA
Found at i:3057629 original size:21 final size:21
Alignment explanation
Indices: 3057605--3057646 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3057595 CATTTTTTCC
*
3057605 TTTTATAA-TTAATATAATATT
1 TTTTATAACATAATAT-ATATT
3057626 TTTTATAACATAATATATATT
1 TTTTATAACATAATATATATT
3057647 CGGGCCAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATAACATAATATATATT
Found at i:3057897 original size:12 final size:12
Alignment explanation
Indices: 3057882--3057924 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
3057872 CCTTAACAAA
3057882 ATTTTTAAAATT
1 ATTTTTAAAATT
*
3057894 ATTTTCAAAATT
1 ATTTTTAAAATT
3057906 ACTTTTTTAAAAATT
1 A--TTTTT-AAAATT
3057921 ATTT
1 ATTT
3057925 GGTTTGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 12 0.46
13 3 0.12
14 4 0.15
15 7 0.27
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTTTAAAATT
Found at i:3060706 original size:664 final size:664
Alignment explanation
Indices: 3059438--3060730 Score: 2552
Period size: 664 Copynumber: 1.9 Consensus size: 664
3059428 TTATTTCTGC
*
3059438 AAGGTGCAAAGTTAATGGACGATTATGATCAATAAAACAGCTATGATTAAAGAAATTTTCGGCTC
1 AAGGTGCAAAGTTAACGGACGATTATGATCAATAAAACAGCTATGATTAAAGAAATTTTCGGCTC
3059503 TTGTTGTAAGGTTCCAGGCATGTTGCTTTCGAGTTTCACAAATTGTTCTTTAATGGTAAGCTTGA
66 TTGTTGTAAGGTTCCAGGCATGTTGCTTTCGAGTTTCACAAATTGTTCTTTAATGGTAAGCTTGA
3059568 TTATTGATTTCACTTGGGGAATAAAATATAGTAAAACCAGAATCAATTGAAAATCTAAATTCAAC
131 TTATTGATTTCACTTGGGGAATAAAATATAGTAAAACCAGAATCAATTGAAAATCTAAATTCAAC
3059633 ACGTTGCGGATAATATAAATCTTGATAGATTCAGTAAATAAATTGTATGATTTTTATTTACTTAT
196 ACGTTGCGGATAATATAAATCTTGATAGATTCAGTAAATAAATTGTATGATTTTTATTTACTTAT
3059698 TTATTTATTTATTACAGGCTTCACCCATTTCAGCTCAAGCTTCCCGGTAATCAGAGTAAACTATT
261 TTATTTATTTATTACAGGCTTCACCCATTTCAGCTCAAGCTTCCCGGTAATCAGAGTAAACTATT
3059763 GACTCTTTATTAGCAATCTGAAGTTCATACGAACTACCAAATTCAAAACTAAAAACTAGAAGAGA
326 GACTCTTTATTAGCAATCTGAAGTTCATACGAACTACCAAATTCAAAACTAAAAACTAGAAGAGA
3059828 AAAATGGCCAATAGCGTACGTGATATTCATTGAAGTGGATAATGCTCTCTTAGTAAGCATCAGGA
391 AAAATGGCCAATAGCGTACGTGATATTCATTGAAGTGGATAATGCTCTCTTAGTAAGCATCAGGA
3059893 TTTGCCAGGAGGTAGGCTTCAATGGCCTTGAACATTCCCAATGCCTTTTCTTTGCCTGCCTTGAT
456 TTTGCCAGGAGGTAGGCTTCAATGGCCTTGAACATTCCCAATGCCTTTTCTTTGCCTGCCTTGAT
3059958 TCCCTCTTCCTTGAGCTCAAACTCACCAACGGTGTAATACTTGCTACTAGTCTTGCATAGAGATC
521 TCCCTCTTCCTTGAGCTCAAACTCACCAACGGTGTAATACTTGCTACTAGTCTTGCATAGAGATC
3060023 CCCCATCCGGAGAGGCCTCCAATTTCGTCTCGTAAGTGATTTTCCCGAGTCCAGCTCAATAATTT
586 CCCCATCCGGAGAGGCCTCCAATTTCGTCTCGTAAGTGATTTTCCCGAGTCCAGCTCAATAATTT
3060088 GCTACTGGGGCTCT
651 GCTACTGGGGCTCT
*
3060102 AAGGTGCAAAGTTAACGGACGATTATGATTC-GTAAAACAGCTATGATTAAAGAAATTTTCGGCT
1 AAGGTGCAAAGTTAACGGACGATTATGA-TCAATAAAACAGCTATGATTAAAGAAATTTTCGGCT
3060166 CTTGTTGTAAGGTTCCAGGCATGTTGCTTTCGAGTTTCACAAATTGTTCTTTAATGGTAAGCTTG
65 CTTGTTGTAAGGTTCCAGGCATGTTGCTTTCGAGTTTCACAAATTGTTCTTTAATGGTAAGCTTG
3060231 ATTATTGATTTCACTTGGGGAATAAAATATAGTAAAACCAGAATCAATTGAAAATCTAAATTCAA
130 ATTATTGATTTCACTTGGGGAATAAAATATAGTAAAACCAGAATCAATTGAAAATCTAAATTCAA
3060296 CACGTTGCGGATAATATAAATCTTGATAGATTCAGTAAATAAATTGTATGATTTTTATTTACTTA
195 CACGTTGCGGATAATATAAATCTTGATAGATTCAGTAAATAAATTGTATGATTTTTATTTACTTA
3060361 TTTATTTATTTATTACAGGCTTCACCCATTTCAGCTCAAGCTTCCCGGTAATCAGAGTAAACTAT
260 TTTATTTATTTATTACAGGCTTCACCCATTTCAGCTCAAGCTTCCCGGTAATCAGAGTAAACTAT
3060426 TGACTCTTTATTAGCAATCTGAAGTTCATACGAACTACCAAATTCAAAACTAAAAACTAGAAGAG
325 TGACTCTTTATTAGCAATCTGAAGTTCATACGAACTACCAAATTCAAAACTAAAAACTAGAAGAG
3060491 AAAAATGGCCAATAGCGTACGTGATATTCATTGAAGTGGATAATGCTCTCTTAGTAAGCATCAGG
390 AAAAATGGCCAATAGCGTACGTGATATTCATTGAAGTGGATAATGCTCTCTTAGTAAGCATCAGG
3060556 ATTTGCCAGGAGGTAGGCTTCAATGGCCTTGAACATTCCCAATGCCTTTTCTTTGCCTGCCTTGA
455 ATTTGCCAGGAGGTAGGCTTCAATGGCCTTGAACATTCCCAATGCCTTTTCTTTGCCTGCCTTGA
3060621 TTCCCTCTTCCTTGAGCTCAAACTCACCAACGGTGTAATACTTGCTACTAGTCTTGCATAGAGAT
520 TTCCCTCTTCCTTGAGCTCAAACTCACCAACGGTGTAATACTTGCTACTAGTCTTGCATAGAGAT
3060686 CCCCCATCCGGAGAGGCCTCCAATTTCGTCTCGTAAGTGATTTTC
585 CCCCCATCCGGAGAGGCCTCCAATTTCGTCTCGTAAGTGATTTTC
3060731 TCAAGCTTGT
Statistics
Matches: 626, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
664 624 1.00
665 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (664 bp):
AAGGTGCAAAGTTAACGGACGATTATGATCAATAAAACAGCTATGATTAAAGAAATTTTCGGCTC
TTGTTGTAAGGTTCCAGGCATGTTGCTTTCGAGTTTCACAAATTGTTCTTTAATGGTAAGCTTGA
TTATTGATTTCACTTGGGGAATAAAATATAGTAAAACCAGAATCAATTGAAAATCTAAATTCAAC
ACGTTGCGGATAATATAAATCTTGATAGATTCAGTAAATAAATTGTATGATTTTTATTTACTTAT
TTATTTATTTATTACAGGCTTCACCCATTTCAGCTCAAGCTTCCCGGTAATCAGAGTAAACTATT
GACTCTTTATTAGCAATCTGAAGTTCATACGAACTACCAAATTCAAAACTAAAAACTAGAAGAGA
AAAATGGCCAATAGCGTACGTGATATTCATTGAAGTGGATAATGCTCTCTTAGTAAGCATCAGGA
TTTGCCAGGAGGTAGGCTTCAATGGCCTTGAACATTCCCAATGCCTTTTCTTTGCCTGCCTTGAT
TCCCTCTTCCTTGAGCTCAAACTCACCAACGGTGTAATACTTGCTACTAGTCTTGCATAGAGATC
CCCCATCCGGAGAGGCCTCCAATTTCGTCTCGTAAGTGATTTTCCCGAGTCCAGCTCAATAATTT
GCTACTGGGGCTCT
Found at i:3070938 original size:50 final size:49
Alignment explanation
Indices: 3070816--3071008 Score: 208
Period size: 50 Copynumber: 3.9 Consensus size: 49
3070806 TAATAACATT
* ** * * *
3070816 CCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCTTGTAC-TG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAT-CGTG
* * * *
3070865 CCAACGCCATATCCCAGATATGGTCTTACATGGGACTTCTCATATCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATC-GTG
* * ** *
3070915 CCCATGCCATGTCCCAGACATGGTCTTACGGGAGACCTCTCATCTCGATG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCG-TG
*
3070965 CCAACGCCATGTCCCAGACATGCTCTTACATGAGACCTCTCATA
1 CCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATA
3071009 ATCTCAATGA
Statistics
Matches: 117, Mismatches: 24, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
48 1 0.01
49 37 0.32
50 79 0.68
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (49 bp):
CCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGTG
Found at i:3070993 original size:100 final size:99
Alignment explanation
Indices: 3070821--3071008 Score: 245
Period size: 100 Copynumber: 1.9 Consensus size: 99
3070811 ACATTCCAAA
* * * * *
3070821 GCCATGTCCCAGACATGGTCTTACATGAGATGTTTCTTGTACTGCCAACGCCATATCCCAGATAT
1 GCCATGTCCCAGACATGGTCTTACAGGAGATCTATCTCGTACTGCCAACGCCATATCCCAGACAT
* * *
3070886 GGTCTTACATGGGACTTCTCATATCGGTGCCCAT
66 GCTCTTACATGAGACCTCTCATATCGGTGCCCAT
* *
3070920 GCCATGTCCCAGACATGGTCTTACGGGAGACCTCTCATCTCG-A-TGCCAACGCCATGTCCCAGA
1 GCCATGTCCCAGACATGGTCTTACAGGAGA--TCT-ATCTCGTACTGCCAACGCCATATCCCAGA
3070983 CATGCTCTTACATGAGACCTCTCATA
63 CATGCTCTTACATGAGACCTCTCATA
3071009 ATCTCAATGA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
99 28 0.37
100 41 0.54
101 3 0.04
102 4 0.05
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (99 bp):
GCCATGTCCCAGACATGGTCTTACAGGAGATCTATCTCGTACTGCCAACGCCATATCCCAGACAT
GCTCTTACATGAGACCTCTCATATCGGTGCCCAT
Found at i:3072534 original size:25 final size:25
Alignment explanation
Indices: 3072506--3072553 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3072496 CAAAGCTACA
*
3072506 AGCTTAGCGAGAAGTGCGAGCTCTG
1 AGCTTAGCAAGAAGTGCGAGCTCTG
**
3072531 AGCTTAGCAAGTGGTGCGAGCTC
1 AGCTTAGCAAGAAGTGCGAGCTC
3072554 ATCAAAAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (25 bp):
AGCTTAGCAAGAAGTGCGAGCTCTG
Found at i:3072729 original size:16 final size:16
Alignment explanation
Indices: 3072708--3072743 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3072698 AGACAGTAAG
*
3072708 CAAAGTGCGAGCCTGT
1 CAAAGTGCGAGCCTAT
*
3072724 CAAAGTGTGAGCCTAT
1 CAAAGTGCGAGCCTAT
3072740 CAAA
1 CAAA
3072744 TTGCAAGCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.19
Consensus pattern (16 bp):
CAAAGTGCGAGCCTAT
Found at i:3082869 original size:43 final size:43
Alignment explanation
Indices: 3082769--3082997 Score: 255
Period size: 43 Copynumber: 5.3 Consensus size: 43
3082759 TTATTTGAAA
3082769 AAACGCCGCTAAAGAACATGATCTTTAGC-AGCGC-TTTTCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGA-CGCTTTTTCCAC
* *
3082811 AAACACCGCTAAAGAACATGATCTTTAGCGACGCTTTTTTCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTTCCAC
* * * *
3082854 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTTCCAC
* *** * * * *
3082897 AAACGCCACTAAAGGTTAAGTTCTTTAACGACGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTTCCAC
* * * * * *
3082940 AAATGCCGCTAAAAAACCTGACCTTTAGCGGCGCTTTTTCCAA
1 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTTCCAC
3082983 AAACGCCGCTAAAGA
1 AAACGCCGCTAAAGA
3082998 TCATAAAAAA
Statistics
Matches: 151, Mismatches: 34, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
42 31 0.21
43 120 0.79
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTTTCCAC
Found at i:3082962 original size:86 final size:85
Alignment explanation
Indices: 3082769--3082997 Score: 296
Period size: 86 Copynumber: 2.7 Consensus size: 85
3082759 TTATTTGAAA
* * * * *
3082769 AAACGCCGCTAAAGAACATGATCTTTAGCAGCGCTTTTCCACAAACACCGCTAAAGAACATGATC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGAACAAGATC
* **
3082834 TTTAGCGACGCTTTTTTCAC
66 TTTAACGACGCTTTTCCCAC
* *** *
3082854 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAAAAACGCCACTAAAGGTTAAGTT
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTT-CCAAAAACGCCGCTAAAGAACAAGAT
3082919 CTTTAACGACGCTTTTCCCAC
65 CTTTAACGACGCTTTTCCCAC
* * *
3082940 AAATGCCGCTAAAAAACCTGACCTTTAGCGGCGCTTTTTCCAAAAACGCCGCTAAAGA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGC-TTTTCCAAAAACGCCGCTAAAGA
3082998 TCATAAAAAA
Statistics
Matches: 124, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
85 36 0.29
86 84 0.68
87 4 0.03
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (85 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGAACAAGATC
TTTAACGACGCTTTTCCCAC
Found at i:3089455 original size:25 final size:26
Alignment explanation
Indices: 3089427--3089478 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3089417 AATGCCTACA
*
3089427 AAATA-ACATCAGCACAAAGCCTGCT
1 AAATATACACCAGCACAAAGCCTGCT
* *
3089452 AAATATACACCGGTACAAAGCCTGCT
1 AAATATACACCAGCACAAAGCCTGCT
3089478 A
1 A
3089479 CACCCTAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.17
Consensus pattern (26 bp):
AAATATACACCAGCACAAAGCCTGCT
Found at i:3090793 original size:27 final size:26
Alignment explanation
Indices: 3090758--3090839 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 26
3090748 GTGACAGATG
3090758 TGAAATATTATCCATTAAGGGAT-AGA
1 TGAAATATTATCCATTAAGGGATGA-A
*
3090784 TGATAATATTATCCCTTAAGGGATGAA
1 TGA-AATATTATCCATTAAGGGATGAA
* *
3090811 TGACATATTATCCCATGAA-GGATGAA
1 TGAAATATTAT-CCATTAAGGGATGAA
3090837 TGA
1 TGA
3090840 TTAGTTCAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
26 20 0.41
27 28 0.57
28 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (26 bp):
TGAAATATTATCCATTAAGGGATGAA
Found at i:3093883 original size:39 final size:39
Alignment explanation
Indices: 3093818--3093915 Score: 133
Period size: 39 Copynumber: 2.5 Consensus size: 39
3093808 TTAGGACACC
* * *
3093818 GACATTAAGCCTGGTAGACATTAAGTCTGAAAATTTCATT
1 GACAATAAGCCTGCTAGA-ATTAAGTCTGAAAATTTCACT
*
3093858 GGCAATAAGCCTGCTAGAATTAAGTCTGAAAATTTCACT
1 GACAATAAGCCTGCTAGAATTAAGTCTGAAAATTTCACT
* *
3093897 GATAATAAGCTTGCTAGAA
1 GACAATAAGCCTGCTAGAA
3093916 ACAGAACCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 36 0.71
40 15 0.29
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (39 bp):
GACAATAAGCCTGCTAGAATTAAGTCTGAAAATTTCACT
Found at i:3100744 original size:25 final size:25
Alignment explanation
Indices: 3100680--3100749 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
3100670 ATGTACATGT
* *
3100680 ATGCTCACACAAGCAGTGAATTAGA
1 ATGCTCACACAAGCTGTGAATCAGA
**
3100705 ATGCTCACATGAGCTGTGAATCAGA
1 ATGCTCACACAAGCTGTGAATCAGA
*
3100730 ATGCTCACACAAGCTATGAA
1 ATGCTCACACAAGCTGTGAA
3100750 AATGAGCCTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.21
Consensus pattern (25 bp):
ATGCTCACACAAGCTGTGAATCAGA
Found at i:3101497 original size:15 final size:15
Alignment explanation
Indices: 3101477--3101506 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3101467 CATTTTTGTC
3101477 ACATTTTTAATGATT
1 ACATTTTTAATGATT
3101492 ACATTTTTAATGATT
1 ACATTTTTAATGATT
3101507 TCTATATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (15 bp):
ACATTTTTAATGATT
Found at i:3107560 original size:10 final size:11
Alignment explanation
Indices: 3107533--3107562 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3107523 TTTTCTAACA
3107533 GGGTTTTAAAT
1 GGGTTTTAAAT
3107544 GGGTTTTAAAT
1 GGGTTTTAAAT
*
3107555 GGTTTTTA
1 GGGTTTTA
3107563 GATTTCGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (11 bp):
GGGTTTTAAAT
Found at i:3118895 original size:17 final size:15
Alignment explanation
Indices: 3118868--3118902 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
3118858 TTGAGTCAAG
3118868 AAAACAAAAGAAGAAA
1 AAAACAAAAGAA-AAA
3118884 AAAACGAAAAGAAAAA
1 AAAAC-AAAAGAAAAA
3118900 AAA
1 AAA
3118903 TAGAGAACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAACAAAAGAAAAA
Found at i:3127049 original size:32 final size:33
Alignment explanation
Indices: 3127008--3127074 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 33
3126998 AATAAATGTG
3127008 AATACCTTGAGGGTGCATCGAG-ACCTTATAGT
1 AATACCTTGAGGGTGCATCGAGAACCTTATAGT
3127040 AATACCTTGAGGGTGCATCGAGAACCTTATAGT
1 AATACCTTGAGGGTGCATCGAGAACCTTATAGT
3127073 AA
1 AA
3127075 ATGGGCATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 22 0.65
33 12 0.35
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (33 bp):
AATACCTTGAGGGTGCATCGAGAACCTTATAGT
Found at i:3130751 original size:27 final size:27
Alignment explanation
Indices: 3130707--3130759 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
3130697 TCATCGATTC
3130707 ATATAACCATTCCGTAT-ATCTATTTCT
1 ATATAACCATTCCGTATAATC-ATTTCT
*
3130734 ATATAACCAATT-CTTATAATCATTTC
1 ATATAACC-ATTCCGTATAATCATTTC
3130760 ACATAATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (27 bp):
ATATAACCATTCCGTATAATCATTTCT
Found at i:3130765 original size:13 final size:13
Alignment explanation
Indices: 3130749--3130773 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3130739 ACCAATTCTT
3130749 ATAATCATTTCAC
1 ATAATCATTTCAC
3130762 ATAATCATTTCA
1 ATAATCATTTCA
3130774 TATAGCGATT
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:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATCATTTCAC
Found at i:3131997 original size:13 final size:13
Alignment explanation
Indices: 3131979--3132007 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3131969 TGACTTCTTC
3131979 TTTTTTTCTTTAA
1 TTTTTTTCTTTAA
3131992 TTTTTTTCTTTAA
1 TTTTTTTCTTTAA
3132005 TTT
1 TTT
3132008 ATTATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTCTTTAA
Found at i:3137123 original size:23 final size:22
Alignment explanation
Indices: 3137087--3137143 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
3137077 AATATTTTTA
*
3137087 TAAAATTAACATAAAGTAATAT
1 TAAAATTAAAATAAAGTAATAT
* *
3137109 TAAAATTAATAATAACGTACTAT
1 TAAAATTAA-AATAAAGTAATAT
*
3137132 TATAAAGTAAAA
1 TA-AAATTAAAA
3137144 CTTTCACATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 9 0.31
23 14 0.48
24 6 0.21
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (22 bp):
TAAAATTAAAATAAAGTAATAT
Found at i:3141648 original size:25 final size:25
Alignment explanation
Indices: 3141620--3141692 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 25
3141610 TATACTTATT
* *
3141620 CGAGCTGTAGATCGATATGCTCTTA
1 CGAGCTATAAATCGATATGCTCTTA
* *
3141645 CGAGATATAAATCGGTATGCTCTTA
1 CGAGCTATAAATCGATATGCTCTTA
3141670 CGAGCTATAAATC-AGTATGCTCT
1 CGAGCTATAAATCGA-TATGCTCT
3141693 CCCAAGCTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (25 bp):
CGAGCTATAAATCGATATGCTCTTA
Found at i:3141700 original size:25 final size:25
Alignment explanation
Indices: 3141635--3141700 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
3141625 TGTAGATCGA
* * * *
3141635 TATGCTCTTACGAGATATAAATCGG
1 TATGCTCTCACAAGCTATAAATCAG
* *
3141660 TATGCTCTTACGAGCTATAAATCAG
1 TATGCTCTCACAAGCTATAAATCAG
*
3141685 TATGCTCTCCCAAGCT
1 TATGCTCTCACAAGCT
3141701 GTGGAGTATC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (25 bp):
TATGCTCTCACAAGCTATAAATCAG
Found at i:3142796 original size:19 final size:20
Alignment explanation
Indices: 3142755--3142796 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3142745 ACATATTAAC
*
3142755 ATATGTGTAATTAAAAACTA
1 ATATGTGTAATTAAAAACCA
*
3142775 ATATGTGTAATT-CAAACCA
1 ATATGTGTAATTAAAAACCA
3142794 ATA
1 ATA
3142797 AAATTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (20 bp):
ATATGTGTAATTAAAAACCA
Found at i:3143661 original size:13 final size:13
Alignment explanation
Indices: 3143643--3143673 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3143633 TTAACGTCTT
3143643 ATTCTTTTTTATA
1 ATTCTTTTTTATA
3143656 ATTCTTTTTTATA
1 ATTCTTTTTTATA
*
3143669 GTTCT
1 ATTCT
3143674 ATTAATTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.10, G:0.03, T:0.68
Consensus pattern (13 bp):
ATTCTTTTTTATA
Found at i:3143838 original size:25 final size:25
Alignment explanation
Indices: 3143804--3143857 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
3143794 ATTTTTTTAG
*
3143804 AACTTTGTTTTTAGTTTCCCACTCA
1 AACTTTGTTTTTAGTTTCACACTCA
*
3143829 AACTTTGTTTTTAGTTTCACACTTA
1 AACTTTGTTTTTAGTTTCACACTCA
3143854 AACT
1 AACT
3143858 CTGATCAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.48
Consensus pattern (25 bp):
AACTTTGTTTTTAGTTTCACACTCA
Found at i:3145786 original size:25 final size:25
Alignment explanation
Indices: 3145758--3145817 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
3145748 CTTCTCCCAG
*
3145758 TTAAACTCTATTTTTAGTTTC-CTTC
1 TTAAACTCTATTTTTAGTTTCAC-AC
*
3145783 TTAAACTCTTTTTTTAGTTTCACAC
1 TTAAACTCTATTTTTAGTTTCACAC
3145808 TTAAACTCTA
1 TTAAACTCTA
3145818 ATTAATGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.03, T:0.52
Consensus pattern (25 bp):
TTAAACTCTATTTTTAGTTTCACAC
Found at i:3146389 original size:21 final size:20
Alignment explanation
Indices: 3146352--3146390 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3146342 AATATTATGC
*
3146352 CTAATTTTTATTATTTTAAT
1 CTAATTTATATTATTTTAAT
*
3146372 CTAATATTATATTTTTTTA
1 CTAAT-TTATATTATTTTA
3146391 TTTTAGTTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
CTAATTTATATTATTTTAAT
Found at i:3150272 original size:18 final size:17
Alignment explanation
Indices: 3150242--3150287 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
3150232 TAGTATTAAA
* *
3150242 TATTTTTTATTTACTTTT
1 TATTTTTT-TTTACCTTG
3150260 TATATTTTTTTTACCTTG
1 TAT-TTTTTTTTACCTTG
3150278 TATTTTTTTT
1 TATTTTTTTT
3150288 GTTTGATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 13 0.52
19 5 0.20
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (17 bp):
TATTTTTTTTTACCTTG
Found at i:3153850 original size:39 final size:40
Alignment explanation
Indices: 3153721--3153853 Score: 144
Period size: 40 Copynumber: 3.3 Consensus size: 40
3153711 AAACAGGCTT
* ** * *
3153721 TTAGCGGCGTTTGGACAAAAAACGCCACTAAAAATCGAGCA
1 TTAGCGGCGTTT-TACGGAAAACGCCGCTAAAAATCAAGCA
* * *
3153762 TTAGCGGCGCTTTACGTAAAACGCCGCTAAAGATCAAGCA
1 TTAGCGGCGTTTTACGGAAAACGCCGCTAAAAATCAAGCA
* *
3153802 TTAGCGGCGTTTCTA-GGAAAGCGCCGCTAAAAAT-TAGCA
1 TTAGCGGCGTTT-TACGGAAAACGCCGCTAAAAATCAAGCA
3153841 TTAGCGGCGTTTT
1 TTAGCGGCGTTTT
3153854 TTAGAAAAAC
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
38 1 0.01
39 16 0.20
40 49 0.62
41 13 0.16
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.23
Consensus pattern (40 bp):
TTAGCGGCGTTTTACGGAAAACGCCGCTAAAAATCAAGCA
Found at i:3153873 original size:39 final size:39
Alignment explanation
Indices: 3153738--3153873 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 39
3153728 CGTTTGGACA
* * *
3153738 AAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTT-TACG
1 AAAAACGCCGCTAAAAAT-TAGCATTAGCGGCGTTTCTA-G
* * *
3153778 TAAAACGCCGCTAAAGATCAAGCATTAGCGGCGTTTCTAG
1 AAAAACGCCGCTAAAAAT-TAGCATTAGCGGCGTTTCTAG
* * *
3153818 GAAAGCGCCGCTAAAAATTAGCATTAGCGGCGTTTTTTAG
1 AAAAACGCCGCTAAAAATTAGCATTAGCGGCG-TTTCTAG
*
3153858 AAAAACGCTGC-AAAAA
1 AAAAACGCCGCTAAAAA
3153874 GTCTAAGCCC
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 18 0.22
40 61 0.75
41 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATTAGCATTAGCGGCGTTTCTAG
Found at i:3153994 original size:41 final size:41
Alignment explanation
Indices: 3153906--3154011 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 41
3153896 TTGTACCTTA
**
3153906 CAGATCTTTAGCGGCG-TTTTGAAAAAAAGTGCCGCTAATGCT
1 CAGATCTTTAGCGGCGTTTTTG--AAAAAGCACCGCTAATGCT
*
3153948 CAGATCTTTAGCGGCGTTTTTGAGAAAGCACCGCTAATGCT
1 CAGATCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCT
3153989 CAGATCTTTAGCGGCGTTTTTGA
1 CAGATCTTTAGCGGCGTTTTTGA
3154012 NNNNNNNNNN
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
41 39 0.65
42 16 0.27
43 5 0.08
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (41 bp):
CAGATCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCT
Found at i:3154832 original size:17 final size:16
Alignment explanation
Indices: 3154799--3154832 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3154789 ATATTAGATT
*
3154799 TAAAAAAATTAATAAA
1 TAAAAAAATTAACAAA
3154815 TAAAAAAATGTAACAAA
1 TAAAAAAAT-TAACAAA
3154832 T
1 T
3154833 TGATACGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAAAATTAACAAA
Found at i:3156219 original size:5 final size:5
Alignment explanation
Indices: 3156209--3156237 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3156199 AGTGGGTATG
3156209 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
3156238 TGCAGTCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:3161257 original size:43 final size:42
Alignment explanation
Indices: 3161074--3161353 Score: 255
Period size: 43 Copynumber: 6.6 Consensus size: 42
3161064 TTTTTCAAAA
* ** * *
3161074 GTCAT-GTTTTTAGCGGCGTTTGTTAAAAAGCGTCGCTAAAA
1 GTCATGGTCTTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAG
* * * *
3161115 GTCA---TCTTTATTGTGGCGTTTGTTGTATAAGCGTCGCTAAAG
1 GTCATGGTCTTTA--GCGGCGTTTG-TGGAAAAGCGCCGCTAAAG
* * * ** * *
3161157 GTCGTGGCCTTCAATGGCGTTTTTTGGGAAAAGCGTCGCTAAAG
1 GTCATGGTCTTTAGCGGCG-TTTGT-GGAAAAGCGCCGCTAAAG
* *
3161201 ATCGTGG-CTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAG
1 GTCATGGTC-TTTAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAG
3161244 GTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAG
1 GTCATGGTCTTTAGCGGCGTTTGTGG-AAAAGCGCCGCTAAAG
* * *
3161287 GTCATGGTCTTTAGCGGCGTTTGTGGGATAAGCGCTGCTAAAA
1 GTCATGGTCTTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAG
3161330 GTCATGGTCTTTAGCGGCGTTTGT
1 GTCATGGTCTTTAGCGGCGTTTGT
3161354 TTCTAAAAAC
Statistics
Matches: 202, Mismatches: 24, Indels: 24
0.81 0.10 0.10
Matches are distributed among these distances:
39 5 0.02
41 13 0.06
42 20 0.10
43 125 0.62
44 35 0.17
45 4 0.02
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (42 bp):
GTCATGGTCTTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAG
Found at i:3161311 original size:86 final size:85
Alignment explanation
Indices: 3161074--3161353 Score: 284
Period size: 86 Copynumber: 3.3 Consensus size: 85
3161064 TTTTTCAAAA
* * * *
3161074 GTCAT-GTTTTTAGCGGCGTTTGT-TAAAAAGCGTCGCTAAAAGTCA---TCTTTATTGTGGCGT
1 GTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGGTCTTTA--GCGGCGT
* *
3161134 TTGTTGTATAAGCGTCGCTAAAG
64 TTG-TGGATAAGCGCCGCTAAAG
* * * ** * * * *
3161157 GTCGTGGCCTTCAATGGCGTTTTTTGGGAAAAGCGTCGCTAAAGATCGTGG-CTTTTAGCGGCGT
1 GTCATGGTCTTTAGCGGCG-TTTGTGGAAAAAGCGTCGCTAAAGGTCATGGTC-TTTAGCGGCGT
*
3161221 TTGTGAGAAAAGCGCCGCTAAAG
64 TTGTG-GATAAGCGCCGCTAAAG
*
3161244 GTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTT
1 GTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTT
* *
3161309 GTGGGATAAGCGCTGCTAAAA
66 GT-GGATAAGCGCCGCTAAAG
3161330 GTCATGGTCTTTAGCGGCGTTTGT
1 GTCATGGTCTTTAGCGGCGTTTGT
3161354 TTCTAAAAAC
Statistics
Matches: 158, Mismatches: 29, Indels: 17
0.77 0.14 0.08
Matches are distributed among these distances:
83 4 0.03
84 8 0.05
85 4 0.03
86 98 0.62
87 39 0.25
88 1 0.01
89 4 0.03
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (85 bp):
GTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTT
GTGGATAAGCGCCGCTAAAG
Found at i:3161327 original size:129 final size:126
Alignment explanation
Indices: 3161070--3161353 Score: 306
Period size: 129 Copynumber: 2.2 Consensus size: 126
3161060 ATATTTTTTC
* * * *
3161070 AAAAGTCATGTTTTTAGCGGCGTTTGTTAAAAAGCGTCGCTAAAAGTCATCTTTATTGTGGCGTT
1 AAAAGTCATGGTTTTAGCGGCGTTTGTGAAAAAGCGCCGCTAAAAGTCATCTTTA-TGCGGCGTT
* * * * * * *
3161135 TGTTGTATAAGCGTCGCTAAAGGTCGTGGCCTTCAATGGCGTTTTTTGGGAAAAGCGTCGCT
65 TGTGGAAAAAGCGCCGCTAAAGGTCATGGCCTTCAACGGCGTTTTGTGGGAAAAGCGTCGCT
* *
3161197 -AAAGATCGTGGCTTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTTTA-GCG
1 AAAAG-TCATGG-TTTTAGCGGCGTTTGTGA-AAAAGCGCCGCTAAAAGTCA---TCTTTATGCG
* * * *
3161260 GCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCG-TTTGTGGGATAAGCG-CT
60 GCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGCCTTCAACGGCGTTTTGTGGGAAAAGCGTC-
3161323 GCT
124 GCT
3161326 AAAAGTCATGGTCTTTAGCGGCGTTTGT
1 AAAAGTCATGGT-TTTAGCGGCGTTTGT
3161354 TTCTAAAAAC
Statistics
Matches: 130, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
126 4 0.03
127 4 0.03
128 19 0.15
129 54 0.42
130 43 0.33
132 6 0.05
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (126 bp):
AAAAGTCATGGTTTTAGCGGCGTTTGTGAAAAAGCGCCGCTAAAAGTCATCTTTATGCGGCGTTT
GTGGAAAAAGCGCCGCTAAAGGTCATGGCCTTCAACGGCGTTTTGTGGGAAAAGCGTCGCT
Found at i:3162611 original size:14 final size:14
Alignment explanation
Indices: 3162592--3162622 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3162582 CAAATCGAGC
3162592 ATTTAAAAGATGAA
1 ATTTAAAAGATGAA
3162606 ATTTAAAAGATGAA
1 ATTTAAAAGATGAA
3162620 ATT
1 ATT
3162623 CATGTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (14 bp):
ATTTAAAAGATGAA
Found at i:3166242 original size:227 final size:227
Alignment explanation
Indices: 3165847--3166267 Score: 797
Period size: 227 Copynumber: 1.9 Consensus size: 227
3165837 AAATAGGGCC
3165847 GATCCTCCATCATCCATGTTTTTCTTTATTTCATTAGTTATAATGTCTCAGCCCTTCTTCCCCTT
1 GATCCTCCATCATCCATGTTTTTCTTTATTTCATTAGTTATAATGTCTCAGCCCTTCTTCCCCTT
*
3165912 GGGATTGGCTCCCACCACCCATAGTAGCCTCCTATAGCTGTTAGTGTAAGGCTACTCAATCATCT
66 GGGATTGGCCCCCACCACCCATAGTAGCCTCCTATAGCTGTTAGTGTAAGGCTACTCAATCATCT
* *
3165977 TCACACTGAGTTTTGGGGGGTAACTTTAGAGTATCTCTTTTCAGAACAGACAGCAAATGATCCAT
131 TCACACTGAGTTATGGGGGGTAACTTTAGAGTATCTCTTTTCAGAACAGACAGCAAAGGATCCAT
3166042 CAATTCTTGACAAATAGGGCCGAAGGTGGTTA
196 CAATTCTTGACAAATAGGGCCGAAGGTGGTTA
*
3166074 GATCCTCCATCATCCATGTTTTTCTTTGTTTCATTAGTTATAATGTCTCAGCCCTTCTTCCCCTT
1 GATCCTCCATCATCCATGTTTTTCTTTATTTCATTAGTTATAATGTCTCAGCCCTTCTTCCCCTT
*
3166139 GGGATTGGCCCCCACCACCCATAGTAGCCTCCTATAGCTGTTAGTGTACGGCTACTCAATCATCT
66 GGGATTGGCCCCCACCACCCATAGTAGCCTCCTATAGCTGTTAGTGTAAGGCTACTCAATCATCT
3166204 TCACACTGAGTTATGGGGGGTAACTTTAGAGTATCTCTTTTCAGAACAGACAGCAAAGGATCCA
131 TCACACTGAGTTATGGGGGGTAACTTTAGAGTATCTCTTTTCAGAACAGACAGCAAAGGATCCA
3166268 ATCGGCTATC
Statistics
Matches: 189, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
227 189 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (227 bp):
GATCCTCCATCATCCATGTTTTTCTTTATTTCATTAGTTATAATGTCTCAGCCCTTCTTCCCCTT
GGGATTGGCCCCCACCACCCATAGTAGCCTCCTATAGCTGTTAGTGTAAGGCTACTCAATCATCT
TCACACTGAGTTATGGGGGGTAACTTTAGAGTATCTCTTTTCAGAACAGACAGCAAAGGATCCAT
CAATTCTTGACAAATAGGGCCGAAGGTGGTTA
Found at i:3168599 original size:16 final size:16
Alignment explanation
Indices: 3168549--3168599 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
3168539 AGGATTACCT
*
3168549 ATTACGCCTCTATTCT
1 ATTACGCCTCTATTCC
*
3168565 ATTACGCCTCTATTTC
1 ATTACGCCTCTATTCC
3168581 ATTACAG-CTCTATTCC
1 ATTAC-GCCTCTATTCC
3168597 ATT
1 ATT
3168600 TACCAAACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 30 0.97
17 1 0.03
ACGTcount: A:0.22, C:0.29, G:0.06, T:0.43
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:3168638 original size:72 final size:73
Alignment explanation
Indices: 3168520--3168671 Score: 297
Period size: 72 Copynumber: 2.1 Consensus size: 73
3168510 GCCCCATTCC
3168520 TTCCATTTAACCAAACAAAAGGATTACCTATTACGCCTCTATTCTATTACGCCTCTATTTCATTA
1 TTCCATTTAACCAAACAAAAGGATTACCTATTACGCCTCTATTCTATTACGCCTCTATTTCATTA
3168585 CAGCTCTA
66 CAGCTCTA
3168593 TTCCATTT-ACCAAACAAAAGGATTACCTATTACGCCTCTATTCTATTACGCCTCTATTTCATTA
1 TTCCATTTAACCAAACAAAAGGATTACCTATTACGCCTCTATTCTATTACGCCTCTATTTCATTA
3168657 CAGCTCTA
66 CAGCTCTA
3168665 TTCCATT
1 TTCCATT
3168672 ACAACGAACC
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 71 0.90
73 8 0.10
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.37
Consensus pattern (73 bp):
TTCCATTTAACCAAACAAAAGGATTACCTATTACGCCTCTATTCTATTACGCCTCTATTTCATTA
CAGCTCTA
Found at i:3168674 original size:16 final size:17
Alignment explanation
Indices: 3168621--3168674 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 17
3168611 AGGATTACCT
*
3168621 ATTAC-GCCTCTATTCT
1 ATTACAGCCTCTATTCC
*
3168637 ATTAC-GCCTCTATTTC
1 ATTACAGCCTCTATTCC
3168653 ATTACAG-CTCTATTCC
1 ATTACAGCCTCTATTCC
3168669 ATTACA
1 ATTACA
3168675 ACGAACCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 33 0.97
17 1 0.03
ACGTcount: A:0.24, C:0.30, G:0.06, T:0.41
Consensus pattern (17 bp):
ATTACAGCCTCTATTCC
Found at i:3168957 original size:26 final size:26
Alignment explanation
Indices: 3168917--3168983 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 26
3168907 CAAATACTTT
*
3168917 TTAAATAAACTAAAAACCC-ATCCCAAA
1 TTAAA-AAA-TAAAAACCCAAACCCAAA
3168944 TATAAAAAAT-AAAACCCAAACCCAAA
1 T-TAAAAAATAAAAACCCAAACCCAAA
* *
3168970 TTAATAAGTAAAAA
1 TTAAAAAATAAAAA
3168984 TTTATAATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 13 0.38
26 13 0.38
27 4 0.12
28 4 0.12
ACGTcount: A:0.61, C:0.19, G:0.01, T:0.18
Consensus pattern (26 bp):
TTAAAAAATAAAAACCCAAACCCAAA
Found at i:3169292 original size:20 final size:20
Alignment explanation
Indices: 3169269--3169378 Score: 73
Period size: 20 Copynumber: 5.4 Consensus size: 20
3169259 AAAAATTACA
3169269 AAAAAATTAAAATAATTTTT
1 AAAAAATTAAAATAATTTTT
* *
3169289 AAAAATTTAAAATAAATTTT
1 AAAAAATTAAAATAATTTTT
*
3169309 --AAAATTCAAAAT-ATTTAT
1 AAAAAATT-AAAATAATTTTT
* * *
3169327 AAAAATTTCAAATTTTATTTTTT
1 AAAAAATT-AAA--ATAATTTTT
* * *
3169350 AAAAAATTATAAAAAAATGTT
1 AAAAAATTA-AAATAATTTTT
3169371 AAAAAATT
1 AAAAAATT
3169379 TTCTAAAAGA
Statistics
Matches: 68, Mismatches: 15, Indels: 13
0.71 0.16 0.14
Matches are distributed among these distances:
18 9 0.13
19 5 0.07
20 27 0.40
21 12 0.18
22 2 0.03
23 13 0.19
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (20 bp):
AAAAAATTAAAATAATTTTT
Found at i:3169294 original size:19 final size:19
Alignment explanation
Indices: 3169270--3169333 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
3169260 AAAATTACAA
3169270 AAAAATTAAAATAATTTTT
1 AAAAATTAAAATAATTTTT
*
3169289 AAAAATTTAAAATAAATTTT
1 AAAAA-TTAAAATAATTTTT
*
3169309 -AAAATTCAAAAT-ATTTAT
1 AAAAATT-AAAATAATTTTT
3169327 AAAAATT
1 AAAAATT
3169334 TCAAATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 6 0.15
19 20 0.51
20 13 0.33
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTAAAATAATTTTT
Found at i:3171139 original size:16 final size:17
Alignment explanation
Indices: 3171086--3171139 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 17
3171076 AGGATTACCT
*
3171086 ATTAC-GCCTCTATTCT
1 ATTACAGCCTCTATTCC
*
3171102 ATTAC-GCCTCTATTTC
1 ATTACAGCCTCTATTCC
3171118 ATTACAG-CTCTATTCC
1 ATTACAGCCTCTATTCC
3171134 ATTACA
1 ATTACA
3171140 ACGAACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 33 0.97
17 1 0.03
ACGTcount: A:0.24, C:0.30, G:0.06, T:0.41
Consensus pattern (17 bp):
ATTACAGCCTCTATTCC
Found at i:3171422 original size:26 final size:26
Alignment explanation
Indices: 3171382--3171448 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 26
3171372 CAAATACTTT
*
3171382 TTAAATAAACTAAAAACCC-ATCCCAAA
1 TTAAA-AAA-TAAAAACCCAAACCCAAA
3171409 TATAAAAAAT-AAAACCCAAACCCAAA
1 T-TAAAAAATAAAAACCCAAACCCAAA
* *
3171435 TTAATAAGTAAAAA
1 TTAAAAAATAAAAA
3171449 TTTATAATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 13 0.38
26 13 0.38
27 4 0.12
28 4 0.12
ACGTcount: A:0.61, C:0.19, G:0.01, T:0.18
Consensus pattern (26 bp):
TTAAAAAATAAAAACCCAAACCCAAA
Found at i:3171757 original size:20 final size:20
Alignment explanation
Indices: 3171734--3171843 Score: 73
Period size: 20 Copynumber: 5.4 Consensus size: 20
3171724 AAAAATTACA
3171734 AAAAAATTAAAATAATTTTT
1 AAAAAATTAAAATAATTTTT
* *
3171754 AAAAATTTAAAATAAATTTT
1 AAAAAATTAAAATAATTTTT
*
3171774 --AAAATTCAAAAT-ATTTAT
1 AAAAAATT-AAAATAATTTTT
* * *
3171792 AAAAATTTCAAATTTTATTTTTT
1 AAAAAATT-AAA--ATAATTTTT
* * *
3171815 AAAAAATTATAAAAAAATGTT
1 AAAAAATTA-AAATAATTTTT
3171836 AAAAAATT
1 AAAAAATT
3171844 TTCTAAAAGA
Statistics
Matches: 68, Mismatches: 15, Indels: 13
0.71 0.16 0.14
Matches are distributed among these distances:
18 9 0.13
19 5 0.07
20 27 0.40
21 12 0.18
22 2 0.03
23 13 0.19
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (20 bp):
AAAAAATTAAAATAATTTTT
Found at i:3171759 original size:19 final size:19
Alignment explanation
Indices: 3171735--3171798 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
3171725 AAAATTACAA
3171735 AAAAATTAAAATAATTTTT
1 AAAAATTAAAATAATTTTT
*
3171754 AAAAATTTAAAATAAATTTT
1 AAAAA-TTAAAATAATTTTT
*
3171774 -AAAATTCAAAAT-ATTTAT
1 AAAAATT-AAAATAATTTTT
3171792 AAAAATT
1 AAAAATT
3171799 TCAAATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 6 0.15
19 20 0.51
20 13 0.33
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTAAAATAATTTTT
Found at i:3184434 original size:25 final size:25
Alignment explanation
Indices: 3184406--3184456 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3184396 ACAATAAACA
*
3184406 CGAATTCTCTAAAAAGCCTTTGTGG
1 CGAATTCTCTAAAAAGCCTATGTGG
**
3184431 CGAATTCTCTGGAAAGCCTATGTGG
1 CGAATTCTCTAAAAAGCCTATGTGG
3184456 C
1 C
3184457 TACCTCTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (25 bp):
CGAATTCTCTAAAAAGCCTATGTGG
Found at i:3192049 original size:46 final size:46
Alignment explanation
Indices: 3191979--3192072 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
3191969 GGTTTAAGAG
* *
3191979 ACCTCGACTCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGAAACCTTGGTATATGATGA
*
3192025 ACCTCGACCCACTATCAAGGATGATAGAAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGAAACCTTGGTATATGATGA
3192071 AC
1 AC
3192073 ACCACACTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAAGAATGATAGAAACCTTGGTATATGATGA
Found at i:3192581 original size:22 final size:21
Alignment explanation
Indices: 3192556--3192599 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
3192546 AGAGCATAAA
*
3192556 AATGCTCTTTAAGAACTCCTTT
1 AATGATCTTTAAG-ACTCCTTT
* *
3192578 AATGATGTTTAAGCCTCCTTT
1 AATGATCTTTAAGACTCCTTT
3192599 A
1 A
3192600 TAACAACCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (21 bp):
AATGATCTTTAAGACTCCTTT
Found at i:3199116 original size:12 final size:14
Alignment explanation
Indices: 3199098--3199129 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
3199088 TGCCTGTGTG
3199098 ATTTTTCTGT-TTT
1 ATTTTTCTGTCTTT
3199111 -TTTTTCTGTCTTT
1 ATTTTTCTGTCTTT
3199124 ATTTTT
1 ATTTTT
3199130 ATAGGCCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.53
13 3 0.18
14 5 0.29
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.78
Consensus pattern (14 bp):
ATTTTTCTGTCTTT
Found at i:3201232 original size:45 final size:46
Alignment explanation
Indices: 3201142--3201232 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
3201132 TTTAAAAGAA
* *
3201142 CTCGACCCATTATCAAGAATGATAGGAACCTTGGTATATAATGAAC
1 CTCGACCCACTATCAAGAATGATAGAAACCTTGGTATATAATGAAC
* *
3201188 CTCGACCCACTATCAAGGATGAT-GAAACCTTGGTATATGATGAAC
1 CTCGACCCACTATCAAGAATGATAGAAACCTTGGTATATAATGAAC
3201233 GCCACACTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 20 0.49
46 21 0.51
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (46 bp):
CTCGACCCACTATCAAGAATGATAGAAACCTTGGTATATAATGAAC
Found at i:3205267 original size:6 final size:6
Alignment explanation
Indices: 3205256--3205281 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3205246 ATCATTGCAC
3205256 AAAGAA AAAGAA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AA
3205282 TTAAAATATA
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:3207181 original size:15 final size:15
Alignment explanation
Indices: 3207161--3207191 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3207151 AAAACAACAT
*
3207161 AACTCTTGGCCTTTC
1 AACTCTTGACCTTTC
3207176 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
3207191 A
1 A
3207192 CTTACATAAC
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:0.19, C:0.32, G:0.10, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:3212073 original size:15 final size:14
Alignment explanation
Indices: 3212035--3212074 Score: 71
Period size: 14 Copynumber: 2.8 Consensus size: 14
3212025 TAAACCTCGA
3212035 AACCCAAAAATAAG
1 AACCCAAAAATAAG
3212049 AACCCAAAAATAAG
1 AACCCAAAAATAAG
3212063 AACCCACAAAAT
1 AACCCA-AAAAT
3212075 TCCTTGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.62, C:0.25, G:0.05, T:0.07
Consensus pattern (14 bp):
AACCCAAAAATAAG
Found at i:3214204 original size:30 final size:30
Alignment explanation
Indices: 3214168--3214228 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3214158 TAGATTTCAA
* * * **
3214168 GAGCCACATGGGTTGGGCACATGCCCATGT
1 GAGCCACACGGGCTGGACACACACCCATGT
3214198 GAGCCACACGGGCTGGACACACACCCATGT
1 GAGCCACACGGGCTGGACACACACCCATGT
3214228 G
1 G
3214229 CTAGCCCGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (30 bp):
GAGCCACACGGGCTGGACACACACCCATGT
Found at i:3218157 original size:42 final size:42
Alignment explanation
Indices: 3218110--3218249 Score: 271
Period size: 42 Copynumber: 3.3 Consensus size: 42
3218100 GGTGTAAAAA
*
3218110 CATGGCCATGTGAGACACACGGCCTGGACACACGTACGTGTC
1 CATGGCCATGTGAGACACACGGCCTGGACACACGTGCGTGTC
3218152 CATGGCCATGTGAGACACACGGCCTGGACACACGTGCGTGTC
1 CATGGCCATGTGAGACACACGGCCTGGACACACGTGCGTGTC
3218194 CATGGCCATGTGAGACACACGGCCTGGACACACGTGCGTGTC
1 CATGGCCATGTGAGACACACGGCCTGGACACACGTGCGTGTC
3218236 CATGGCCATGTGAG
1 CATGGCCATGTGAG
3218250 TTCTGGGACT
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 97 1.00
ACGTcount: A:0.22, C:0.30, G:0.31, T:0.17
Consensus pattern (42 bp):
CATGGCCATGTGAGACACACGGCCTGGACACACGTGCGTGTC
Found at i:3220366 original size:18 final size:19
Alignment explanation
Indices: 3220343--3220383 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
3220333 ATTTTATTTG
*
3220343 TTTTTCTTTTTA-GTTTTC
1 TTTTTCTTTTTATGTTTAC
3220361 TTTTTCTTTTTATGTTTAC
1 TTTTTCTTTTTATGTTTAC
3220380 TTTT
1 TTTT
3220384 ATTTTTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.78
Consensus pattern (19 bp):
TTTTTCTTTTTATGTTTAC
Found at i:3220415 original size:5 final size:6
Alignment explanation
Indices: 3220343--3220415 Score: 56
Period size: 6 Copynumber: 11.7 Consensus size: 6
3220333 ATTTTATTTG
* * * * * * *
3220343 TTTTTC TTTTTA GTTTTC TTTTTC TTTTTA TGTTTA CTTTTA TTTTTG
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
3220391 TTTTTA GTTGTTTTA TTTTTA TTTT
1 TTTTTA --T-TTTTA TTTTTA TTTT
3220416 CTTAAATTTC
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
6 46 0.87
7 1 0.02
8 1 0.02
9 5 0.09
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:3222247 original size:30 final size:30
Alignment explanation
Indices: 3222211--3222271 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
3222201 TAGATTTCAG
* * *
3222211 GAGCCACACGGGTTGGGCACACACCTATGT
1 GAGCCACACGGGCTGGACACACACCCATGT
3222241 GAGCCACACGGGCTGGACACACACCCATGT
1 GAGCCACACGGGCTGGACACACACCCATGT
3222271 G
1 G
3222272 CCAGCCCGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.33, G:0.30, T:0.13
Consensus pattern (30 bp):
GAGCCACACGGGCTGGACACACACCCATGT
Found at i:3224053 original size:9 final size:8
Alignment explanation
Indices: 3224041--3224097 Score: 51
Period size: 9 Copynumber: 6.4 Consensus size: 8
3224031 CTTTTAAATT
3224041 TTTTTTTCA
1 TTTTTTT-A
3224050 TTTTTTTA
1 TTTTTTTA
3224058 GTTTTTTTA
1 -TTTTTTTA
3224067 TTTTATTTA
1 TTTT-TTTA
*
3224076 TTTATTTAAA
1 TTT-TTT-TA
3224086 TTTATTTTA
1 TTT-TTTTA
3224095 TTT
1 TTT
3224098 AGTATTAATC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
8 5 0.12
9 28 0.67
10 9 0.21
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTTTTA
Found at i:3224062 original size:17 final size:18
Alignment explanation
Indices: 3224042--3224075 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3224032 TTTTAAATTT
3224042 TTTTTTCATTTT-TTTAG
1 TTTTTTCATTTTATTTAG
*
3224059 TTTTTTTATTTTATTTA
1 TTTTTTCATTTTATTTA
3224076 TTTATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTTTCATTTTATTTAG
Found at i:3227171 original size:43 final size:43
Alignment explanation
Indices: 3227121--3227306 Score: 225
Period size: 43 Copynumber: 4.3 Consensus size: 43
3227111 GTTTTTAGAA
*
3227121 ACAAACGCCGCTAAAGACTCAGACCATTAGCGGCACTTTTCCC
1 ACAAACGCCGCTAAAGACTCAGACCATTAGCGGCGCTTTTCCC
* ** *
3227164 ACAAACGCCGCTAAAGACTAAGACCATTAGTAGCGCTTTTCCA
1 ACAAACGCCGCTAAAGACTCAGACCATTAGCGGCGCTTTTCCC
* *
3227207 AAAAACGTCGCTAAAGAC-CAAGACCATTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACTC-AGACCATTAGCGGCGCTTTTCCC
* * * * *
3227250 ACAAACGCCGCTATAGA-TCAAACCTTTAGCGGCGCTTCTCGCG
1 ACAAACGCCGCTAAAGACTCAGACCATTAGCGGCGCTTTTC-CC
3227293 A-AAACGCCGCTAAA
1 ACAAACGCCGCTAAA
3227307 AACATAACCT
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
42 30 0.25
43 91 0.75
ACGTcount: A:0.32, C:0.31, G:0.18, T:0.19
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGACTCAGACCATTAGCGGCGCTTTTCCC
Found at i:3227626 original size:43 final size:43
Alignment explanation
Indices: 3227553--3227643 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
3227543 ACATATGCAA
* * *
3227553 GGTAATAAAACATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAACATACAATACATTATCTTAATCAAGGAAATCTT
* *
3227596 GGTAATAAAAGATATAATACATATAT-TTAATCAAGGAAATCTT
1 GGTAATAAAACATACAATACAT-TATCTTAATCAAGGAAATCTT
3227639 -GTAAT
1 GGTAAT
3227644 GAACTCAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 5 0.12
43 35 0.83
44 2 0.05
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (43 bp):
GGTAATAAAACATACAATACATTATCTTAATCAAGGAAATCTT
Found at i:3229233 original size:31 final size:31
Alignment explanation
Indices: 3229198--3229256 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
3229188 TAAAAGCACC
*
3229198 TGGGTTAAAAACAAACACAGACGAGACTACT
1 TGGGTTAAAAACAAACACAAACGAGACTACT
3229229 TGGGTTAAAAACAAACACAAACGAGACT
1 TGGGTTAAAAACAAACACAAACGAGACT
3229257 CTATCACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (31 bp):
TGGGTTAAAAACAAACACAAACGAGACTACT
Found at i:3230669 original size:148 final size:149
Alignment explanation
Indices: 3230497--3230778 Score: 451
Period size: 149 Copynumber: 1.9 Consensus size: 149
3230487 TTTAAATGAT
* ** * *
3230497 TTTTGCGGCGTTTTTATTATAAACGCCGCTATTGTTTACC-TTAGCGGTGTTTTTCATAAAAGCG
1 TTTTGCGGCGTTTTTATTAAAAACGCCGCTATTGCCTACCTTTAGCGGCGTTTTTCATAAAAGCA
*
3230561 CCGCAAAAAAAAATCATTTTGAAAAAAATTACGTCGTTTTGCTATGCTATGCTAAAAGGGGGCTA
66 CCGCAAAAAAAAATCATTTTGAAAAAAACTACGTCGTTTTGCTATGCTATGCTAAAAGGGGGCTA
3230626 TTTTTTAAAAGTAAAATTA
131 TTTTTTAAAAGTAAAATTA
* *
3230645 TTTTGTGGCGTTTTT-TATAAAAACGCCGCTATTGCCTACCTTTAGTGGCGTTTTTCATAAAAGC
1 TTTTGCGGCGTTTTTAT-TAAAAACGCCGCTATTGCCTACCTTTAGCGGCGTTTTTCATAAAAGC
* *
3230709 ACCGCAAAAAAAATTCATTTTGAACAAAACTACGTCGTTTTGCTATGCTATGCTAAAAGGGGGCT
65 ACCGCAAAAAAAAATCATTTTGAAAAAAACTACGTCGTTTTGCTATGCTATGCTAAAAGGGGGCT
3230774 ATTTT
130 ATTTT
3230779 AGCGGCGTTC
Statistics
Matches: 122, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
147 1 0.01
148 34 0.28
149 87 0.71
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (149 bp):
TTTTGCGGCGTTTTTATTAAAAACGCCGCTATTGCCTACCTTTAGCGGCGTTTTTCATAAAAGCA
CCGCAAAAAAAAATCATTTTGAAAAAAACTACGTCGTTTTGCTATGCTATGCTAAAAGGGGGCTA
TTTTTTAAAAGTAAAATTA
Found at i:3230808 original size:91 final size:91
Alignment explanation
Indices: 3230685--3230869 Score: 343
Period size: 91 Copynumber: 2.0 Consensus size: 91
3230675 ATTGCCTACC
* *
3230685 TTTAGTGGCGTTTTTCATAAAAGCACCGCAAAAAAAATTCATTTTGAACAAAACTACGTCGTTTT
1 TTTAGCGGCGTTCTTCATAAAAGCACCGCAAAAAAAATTCATTTTGAACAAAACTACGTCGTTTT
3230750 GCTATGCTATGCTAAAAGGGGGCTAT
66 GCTATGCTATGCTAAAAGGGGGCTAT
*
3230776 TTTAGCGGCGTTCTTCATAAAAGCGCCGCAAAAAAAATTCATTTTGAACAAAACTACGTCGTTTT
1 TTTAGCGGCGTTCTTCATAAAAGCACCGCAAAAAAAATTCATTTTGAACAAAACTACGTCGTTTT
3230841 GCTATGCTATGCTAAAAGGGGGCTAT
66 GCTATGCTATGCTAAAAGGGGGCTAT
3230867 TTT
1 TTT
3230870 TTAAAAGTAA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (91 bp):
TTTAGCGGCGTTCTTCATAAAAGCACCGCAAAAAAAATTCATTTTGAACAAAACTACGTCGTTTT
GCTATGCTATGCTAAAAGGGGGCTAT
Found at i:3232378 original size:73 final size:73
Alignment explanation
Indices: 3232251--3232405 Score: 229
Period size: 73 Copynumber: 2.1 Consensus size: 73
3232241 TATTTTTTTG
* * * * *
3232251 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATATTTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAGATTATTTTGCGGCGCTTAC
* *
3232316 TTAAAAAT
66 TCAAAAAC
*
3232324 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTATTTTGCGGCGCTTAC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAGATTATTTTGCGGCGCTTAC
3232389 TCAAAAAC
66 TCAAAAAC
*
3232397 GCTGCTAAA
1 GCCGCTAAA
3232406 GCCCTAAGCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (73 bp):
GCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAGATTATTTTGCGGCGCTTAC
TCAAAAAC
Found at i:3232509 original size:114 final size:115
Alignment explanation
Indices: 3232305--3232874 Score: 470
Period size: 114 Copynumber: 4.7 Consensus size: 115
3232295 ATATTTTTTT
* *
3232305 GCGGCGCTTTCTTAAAAATGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
* * *
3232370 GTTATTTTGCGGCGC-TTACTCAAAAACGCTGCTAAAGCCCTAAGCATTA
66 GTTTTTTTGCGGCGCTTTCCTCAAAAACGCCGCTAAAGCCCTAAGCATTA
* * * *
3232419 GCGGCGCATTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTTGGCTTAT
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
* * **
3232484 GTTTTTTTGCGGCGCTTTCCT-AAAAACGCCGCTAAATCCCCAAAAGCTCACAAA
66 GTTTTTTTGCGGCGCTTTCCTCAAAAACGCCGCTAAA-GCCC-TAAG--CA-TTA
* *** * * *
3232538 ACGGCG-TGGTTGGGCTTAGGTTATTTTGCGGCGCTTACTTAAAAACGCCGCTAAAGCCCCGAAA
1 GCGGCGCT--TT---CTTA----A--AAAC-GC-C--GC-T-AAATC-CC-CGAAAG--------
* * * * *
3232602 GCTCATAAAACGACGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTT-CTTAAAAACGCCGCTAAA
39 -CTCACAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCCTCAAAAACGCCGCTAAA
*
3232666 GACCTAAGCATTA
103 GCCCTAAGCATTA
* * *
3232679 GCGACGCTTTCTTAAAAACGCCGCTAAAGCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
* *
3232744 GTTTTTTTGCGGCGCTTT-TTCAAAAACGTCGCTAAAGCCCTGAA-CATTA
66 GTTTTTTTGCGGCGCTTTCCTCAAAAACGCCGCTAAAGCCCT-AAGCATTA
* * * *
3232793 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAATGGCGTCATTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
3232858 G-TTTTTTGCGGCGCTTT
66 GTTTTTTTGCGGCGCTTT
3232875 TTGGAAAACG
Statistics
Matches: 368, Mismatches: 51, Indels: 75
0.74 0.10 0.15
Matches are distributed among these distances:
113 16 0.04
114 210 0.57
115 9 0.02
116 3 0.01
118 2 0.01
119 6 0.02
120 2 0.01
123 9 0.02
124 2 0.01
125 4 0.01
126 1 0.00
127 2 0.01
129 2 0.01
130 4 0.01
131 2 0.01
133 2 0.01
134 1 0.00
135 4 0.01
136 2 0.01
137 9 0.02
140 2 0.01
141 5 0.01
142 3 0.01
144 3 0.01
145 4 0.01
146 59 0.16
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (115 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAG
GTTTTTTTGCGGCGCTTTCCTCAAAAACGCCGCTAAAGCCCTAAGCATTA
Found at i:3232510 original size:73 final size:73
Alignment explanation
Indices: 3232419--3232665 Score: 395
Period size: 73 Copynumber: 3.4 Consensus size: 73
3232409 CTAAGCATTA
*
3232419 GCGGCGCATTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTTGGCTTAT
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTTGGCTTAT
3232484 GTTTTTTT
66 GTTTTTTT
* * * * * *
3232492 GCGGCGCTTTCCTAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTGGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTTGGCTTAT
*
3232557 GTTATTTT
66 GTTTTTTT
* * *
3232565 GCGGCGCTTACTTAAAAACGCCGCTAAAGCCCCGAAAGCTCATAAAACGACGTCGTTTGGCTTAT
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTTGGCTTAT
3232630 GTTTTTTT
66 GTTTTTTT
3232638 GCGGCGCTTTCTTAAAAACGCCGCTAAA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAA
3232666 GACCTAAGCA
Statistics
Matches: 155, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 155 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (73 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTTGGCTTAT
GTTTTTTT
Found at i:3232566 original size:187 final size:187
Alignment explanation
Indices: 3232251--3232596 Score: 611
Period size: 187 Copynumber: 1.9 Consensus size: 187
3232241 TATTTTTTTG
*
3232251 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATATTTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTTGGCTTATATTTTTTTGCGGCGCTTTC
* * *
3232316 TTAAAAATGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTATTTTGCG
66 CTAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTATTTTGCG
*
3232381 GCGCTTACTCAAAAACGCTGCTAAAGCCCTAAGCATTAGCGGCGCATTCTTAAAAAC
131 GCGCTTACTCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCATTCTTAAAAAC
*
3232438 GCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTTGGCTTATATTTTTTTGCGGCGCTTTC
* *
3232503 CTAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTGGTTGGGCTTAGGTTATTTTGCG
66 CTAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTATTTTGCG
*
3232568 GCGCTTACTTAAAAACGCCGCTAAAGCCC
131 GCGCTTACTCAAAAACGCCGCTAAAGCCC
3232597 CGAAAGCTCA
Statistics
Matches: 150, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
187 150 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (187 bp):
GCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTTGGCTTATATTTTTTTGCGGCGCTTTC
CTAAAAACGCCGCTAAATCCCCAAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTATTTTGCG
GCGCTTACTCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCATTCTTAAAAAC
Found at i:3232714 original size:260 final size:260
Alignment explanation
Indices: 3232251--3232779 Score: 790
Period size: 260 Copynumber: 2.0 Consensus size: 260
3232241 TATTTTTTTG
* * * * *
3232251 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATATTTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAGATTATTTTGCGGCGCTTAC
* * *
3232316 TTAAAAATGCCGCTAAATCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTATTTTGCG
66 TTAAAAACGCCGCTAAAGCCCCGAAAGCTCACAAAACGACATCGTTGGGCTTAGGTTATTTTGCG
* * *
3232381 GCGCTTACTCAAAAACGCTGCTAAAGCCCTAAGCATTAGCGGCGCATTCTTAAAAACGCCGCTAA
131 GCGCTTACTCAAAAACGCCGCTAAAGACCTAAGCATTAGCGACGCATTCTTAAAAACGCCGCTAA
* * * *
3232446 ATCCCCGAAAGCTCACAAAACGACGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC-CTAAAAA
196 AGCCCCGAAAGCTCACAAAACGACATCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTC-AAAAA
3232510 C
260 C
* *
3232511 GCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTGGTTGGGCTTAGGTTATTTTGCGGCGCTTAC
1 GCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAGATTATTTTGCGGCGCTTAC
* * * * *
3232576 TTAAAAACGCCGCTAAAGCCCCGAAAGCTCATAAAACGACGTCGTTTGGCTTATGTTTTTTTGCG
66 TTAAAAACGCCGCTAAAGCCCCGAAAGCTCACAAAACGACATCGTTGGGCTTAGGTTATTTTGCG
* * *
3232641 GCGCTTTCTTAAAAACGCCGCTAAAGACCTAAGCATTAGCGACGCTTTCTTAAAAACGCCGCTAA
131 GCGCTTACTCAAAAACGCCGCTAAAGACCTAAGCATTAGCGACGCATTCTTAAAAACGCCGCTAA
* *
3232706 AGCCCCGAAAGCTCACAAAACGGCATCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTTTCAAAAAC
196 AGCCCCGAAAGCTCACAAAACGACATCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAAC
*
3232771 GTCGCTAAA
1 GCCGCTAAA
3232780 GCCCTGAACA
Statistics
Matches: 240, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
260 239 1.00
261 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (260 bp):
GCCGCTAAATCCCCAAAAGCTCACAAAACGGCGTCGTTGGGCTTAGATTATTTTGCGGCGCTTAC
TTAAAAACGCCGCTAAAGCCCCGAAAGCTCACAAAACGACATCGTTGGGCTTAGGTTATTTTGCG
GCGCTTACTCAAAAACGCCGCTAAAGACCTAAGCATTAGCGACGCATTCTTAAAAACGCCGCTAA
AGCCCCGAAAGCTCACAAAACGACATCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAAC
Found at i:3232977 original size:12 final size:12
Alignment explanation
Indices: 3232960--3232985 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3232950 TTTTTTATCC
3232960 AAACGCCGCTAA
1 AAACGCCGCTAA
3232972 AAACGCCGCTAA
1 AAACGCCGCTAA
3232984 AA
1 AA
3232986 GCCTGTTTTG
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:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:3234240 original size:18 final size:19
Alignment explanation
Indices: 3234217--3234256 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
3234207 ACTCTTATAA
3234217 TATATTTTATA-TAAAATT
1 TATATTTTATATTAAAATT
*
3234235 TATATTTTGTATTAAAATT
1 TATATTTTATATTAAAATT
3234254 TAT
1 TAT
3234257 TTTAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TATATTTTATATTAAAATT
Found at i:3238701 original size:33 final size:33
Alignment explanation
Indices: 3238664--3238731 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
3238654 ACCAAAATAT
*
3238664 AATTTTGTTAAGTCCAAAAAGGATACTAACCAA
1 AATTTTGTTAAGCCCAAAAAGGATACTAACCAA
3238697 AATTTTGTTAAGCCCAAAAAGGATACTAACCAA
1 AATTTTGTTAAGCCCAAAAAGGATACTAACCAA
3238730 AA
1 AA
3238732 AGTTACTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (33 bp):
AATTTTGTTAAGCCCAAAAAGGATACTAACCAA
Found at i:3239951 original size:16 final size:16
Alignment explanation
Indices: 3239925--3239964 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3239915 TGTATGTACA
*
3239925 AAAAAAAATTACATAT
1 AAAATAAATTACATAT
* *
3239941 AGAATAAATTATATAT
1 AAAATAAATTACATAT
3239957 AAAATAAA
1 AAAATAAA
3239965 AAAATTGTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (16 bp):
AAAATAAATTACATAT
Found at i:3240014 original size:14 final size:15
Alignment explanation
Indices: 3239972--3240018 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
3239962 AAAAAAATTG
3239972 TATA-TATATATAAAA
1 TATATTATATA-AAAA
*
3239987 TGATATTCTATAAAAA
1 T-ATATTATATAAAAA
3240003 TAT-TTATATAAAAA
1 TATATTATATAAAAA
3240017 TA
1 TA
3240019 CAAAATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 12 0.43
15 3 0.11
16 8 0.29
17 5 0.18
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
TATATTATATAAAAA
Found at i:3245842 original size:15 final size:16
Alignment explanation
Indices: 3245822--3245851 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3245812 AGGTAAACTT
3245822 CGCGAATGGC-AAGTA
1 CGCGAATGGCTAAGTA
3245837 CGCGAATGGCTAAGT
1 CGCGAATGGCTAAGT
3245852 TGAGCGAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.20, G:0.33, T:0.17
Consensus pattern (16 bp):
CGCGAATGGCTAAGTA
Found at i:3252874 original size:14 final size:13
Alignment explanation
Indices: 3252827--3252886 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 13
3252817 CATATAGTTT
3252827 TTATATTATTAATA
1 TTATATTATT-ATA
* *
3252841 TTA-ATTATAAAA
1 TTATATTATTATA
3252853 GGTTATATTATGTATA
1 --TTATATTAT-TATA
*
3252869 TTATATTATTATG
1 TTATATTATTATA
3252882 TTATA
1 TTATA
3252887 ATAAAAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
12 2 0.05
13 13 0.35
14 15 0.41
15 5 0.14
16 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
TTATATTATTATA
Found at i:3254094 original size:41 final size:41
Alignment explanation
Indices: 3253812--3254078 Score: 507
Period size: 41 Copynumber: 6.5 Consensus size: 41
3253802 ATCTGAGATT
* * *
3253812 TTCAGGCTTAATGCCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
3253853 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
3253894 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
3253935 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
3253976 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
3254017 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
3254058 TTCAGACTTTATGTCTAGCAG
1 TTCAGACTTTATGTCTAGCAG
3254079 GCTTTGTGCC
Statistics
Matches: 223, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 223 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (41 bp):
TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
Found at i:3254153 original size:123 final size:122
Alignment explanation
Indices: 3253812--3254133 Score: 432
Period size: 123 Copynumber: 2.6 Consensus size: 122
3253802 ATCTGAGATT
* * * * *
3253812 TTCAGGCTTAATGCCTAGCAGACTTGATGTCGGTGAATTACTTCAGACTTTATGTCTAGCAGACT
1 TTCAGACTTTATGTCTAGCAGACTTGATGCCGGTGAATTAC-TCAGACTTTATGCCTAGCAGACT
* *
3253877 TGATGTCGGTGAATTACTTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
65 TGATGCCGGTGAATTACTACAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
* *
3253935 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTACTTCAGACTTTATGTCTAGCAGACT
1 TTCAGACTTTATGTCTAGCAGACTTGATGCCGGTGAATTAC-TCAGACTTTATGCCTAGCAGACT
* *
3254000 TGATGTCGGTGAATTACTTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
65 TGATGCCGGTGAATTACTACAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
* * * * *
3254058 TTCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAAATGTA-TCGGGCTTTGTGCCTAGCAGG
1 TTCAGACTTTATGTCTAGCAGAC-TTGATGCCGGTG-AAT-TACTCAGACTTTATGCCTAGCAGA
*
3254121 CTTTATGCCGGTG
63 CTTGATGCCGGTG
3254134 TTTTATACAA
Statistics
Matches: 184, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
123 176 0.96
124 6 0.03
125 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (122 bp):
TTCAGACTTTATGTCTAGCAGACTTGATGCCGGTGAATTACTCAGACTTTATGCCTAGCAGACTT
GATGCCGGTGAATTACTACAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
Found at i:3259718 original size:415 final size:415
Alignment explanation
Indices: 3258948--3259780 Score: 1621
Period size: 415 Copynumber: 2.0 Consensus size: 415
3258938 AGATTTGGCT
*
3258948 GCTCCTATAGTATTTGGAGAAACATTGGTCGACTATCTCTCAGGATACAACACGATGATCAAAGC
1 GCTCCTATAGTACTTGGAGAAACATTGGTCGACTATCTCTCAGGATACAACACGATGATCAAAGC
3259013 AGTAGCACTTCTGTAGCAATCAACAAACAAACGTTGTCTATTTCTATCACCAAAACGTTGAAAAA
66 AGTAGCACTTCTGTAGCAATCAACAAACAAACGTTGTCTATTTCTATCACCAAAACGTTGAAAAA
*
3259078 TATGGAGAGGAAAAAAAGAATTTTGAGAGAAAATAATCTCGGTTTGAGAGAGTGAAATTTTTTAG
131 TATGGAGAGGAAAAAAAGAATTTTGAGAGAAAATAATCTCGGTTTGAGAGAGTGAAATTTTTGAG
3259143 CAATAATTCAAAAGAAGTCTTAGCCTTTTATAGCCATTCAAAGAGGAGGAATTTTTGGAAATATC
196 CAATAATTCAAAAGAAGTCTTAGCCTTTTATAGCCATTCAAAGAGGAGGAATTTTTGGAAATATC
3259208 CATGTATAAGGAGACAAAATTTGCATTAAAGGGGTAATTAAATCCATTTGATTAAAATCAAATTA
261 CATGTATAAGGAGACAAAATTTGCATTAAAGGGGTAATTAAATCCATTTGATTAAAATCAAATTA
3259273 AATTGATTAGAATAAAATAATATTAGGATATATGTCCTTTTATATCAGATTTTGTATATATTTGC
326 AATTGATTAGAATAAAATAATATTAGGATATATGTCCTTTTATATCAGATTTTGTATATATTTGC
3259338 TGAGGAAAAATAAATTTCGTGTTGG
391 TGAGGAAAAATAAATTTCGTGTTGG
3259363 GCTCCTATAGTACTTGGAGAAACATTGGTCGACTATCTCTCAGGATACAACACGATGATCAAAGC
1 GCTCCTATAGTACTTGGAGAAACATTGGTCGACTATCTCTCAGGATACAACACGATGATCAAAGC
3259428 AGTAGCACTTCTGTAGCAATCAACAAACAAACGTTGTCTATTTCTATCACCAAAACGTTGAAAAA
66 AGTAGCACTTCTGTAGCAATCAACAAACAAACGTTGTCTATTTCTATCACCAAAACGTTGAAAAA
3259493 TATGGAGAGGAAAAAAAGAATTTTGAGAGAAAATAATCTCGGTTTGAGAGAGTGAAATTTTTGAG
131 TATGGAGAGGAAAAAAAGAATTTTGAGAGAAAATAATCTCGGTTTGAGAGAGTGAAATTTTTGAG
* *
3259558 CAATAATTCAAAAGAAGTCTTATCCTTTTATAGCCATTCAAAGAGGAGGAATTTTTTGAAATATC
196 CAATAATTCAAAAGAAGTCTTAGCCTTTTATAGCCATTCAAAGAGGAGGAATTTTTGGAAATATC
3259623 CATGTATAAGGAGACAAAATTTGCATTAAAGGGGTAATTAAATCCATTTGATTAAAATCAAATTA
261 CATGTATAAGGAGACAAAATTTGCATTAAAGGGGTAATTAAATCCATTTGATTAAAATCAAATTA
3259688 AATTGATTAGAATAAAATAATATTAGGATATATGTCCTTTTATATCAGATTTTGTATATATTTGC
326 AATTGATTAGAATAAAATAATATTAGGATATATGTCCTTTTATATCAGATTTTGTATATATTTGC
*
3259753 TGAGGAAAAATAAATTTCGTTTTGG
391 TGAGGAAAAATAAATTTCGTGTTGG
3259778 GCT
1 GCT
3259781 AAAATATCCA
Statistics
Matches: 413, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
415 413 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (415 bp):
GCTCCTATAGTACTTGGAGAAACATTGGTCGACTATCTCTCAGGATACAACACGATGATCAAAGC
AGTAGCACTTCTGTAGCAATCAACAAACAAACGTTGTCTATTTCTATCACCAAAACGTTGAAAAA
TATGGAGAGGAAAAAAAGAATTTTGAGAGAAAATAATCTCGGTTTGAGAGAGTGAAATTTTTGAG
CAATAATTCAAAAGAAGTCTTAGCCTTTTATAGCCATTCAAAGAGGAGGAATTTTTGGAAATATC
CATGTATAAGGAGACAAAATTTGCATTAAAGGGGTAATTAAATCCATTTGATTAAAATCAAATTA
AATTGATTAGAATAAAATAATATTAGGATATATGTCCTTTTATATCAGATTTTGTATATATTTGC
TGAGGAAAAATAAATTTCGTGTTGG
Found at i:3265171 original size:27 final size:28
Alignment explanation
Indices: 3265122--3265175 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
3265112 TAAAGATCAT
3265122 GACCTTTAGCGGCACTTTTGTCACAAAC
1 GACCTTTAGCGGCACTTTTGTCACAAAC
* *
3265150 GACCTTTAG-TGCGCTTTTGTCACAAA
1 GACCTTTAGCGGCACTTTTGTCACAAA
3265176 TGCCGCTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (28 bp):
GACCTTTAGCGGCACTTTTGTCACAAAC
Found at i:3265224 original size:24 final size:25
Alignment explanation
Indices: 3265179--3265231 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
3265169 TCACAAATGC
*
3265179 CGCTAAAGAACATAACCTTTAGCGG
1 CGCTAAAGAACATAACCTTTAGCGA
*
3265204 CGCTATAGAACA-AACCTTTAGCGA
1 CGCTAAAGAACATAACCTTTAGCGA
3265228 CGCT
1 CGCT
3265232 TCTCGTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (25 bp):
CGCTAAAGAACATAACCTTTAGCGA
Done.