Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 122 of 193
Found at i:38574486 original size:30 final size:29
Alignment explanation
Indices: 38574445--38574762 Score: 148
Period size: 29 Copynumber: 10.8 Consensus size: 29
38574435 TTTTTGACTC
*
38574445 TCGAGGGTAAAAAAGTAATTTTGGAAAAAA
1 TCGAGGGTAAAAATGTAATTTTGG-AAAAA
* * *
38574475 TCGAGGTTAAAAATG-AGATTTTGGAAGAT
1 TCGAGGGTAAAAATGTA-ATTTTGGAAAAA
* **
38574504 TCGGGGGTAAAAATGGTAATTTTTGGTGAAA
1 TCGAGGGTAAAAAT-GTAA-TTTTGGAAAAA
* * * **
38574535 TCGAGGTTAAAAATGGAATTTTAGAAAGT
1 TCGAGGGTAAAAATGTAATTTTGGAAAAA
* * **
38574564 TTGGGGGT-AAAATGGTAATTTTGGTGAAA
1 TCGAGGGTAAAAAT-GTAATTTTGGAAAAA
* * **
38574593 TC-AGGGTTAAAAATGGAATTTTAGAAAGT
1 TCGAGGG-TAAAAATGTAATTTTGGAAAAA
* * **
38574622 TTGGGGGT-AAAATGGTAATTTTTGGTGAAA
1 TCGAGGGTAAAAAT-GTAA-TTTTGGAAAAA
* * **
38574652 TCG-GGGTTACAAATGGAATTTTGGAAAGT
1 TCGAGGG-TAAAAATGTAATTTTGGAAAAA
* **
38574681 TCAAGGGT-AAAATGGTAATTTTGGTGAAA
1 TCGAGGGTAAAAAT-GTAATTTTGGAAAAA
* * **
38574710 TCG-GGGTTAAAAATGGAATTTTGGTAAGT
1 TCGAGGG-TAAAAATGTAATTTTGGAAAAA
*
38574739 TCGGGGGT-AAAATGGTAATTTTGG
1 TCGAGGGTAAAAAT-GTAATTTTGG
38574763 TGAGTTCAGG
Statistics
Matches: 207, Mismatches: 63, Indels: 37
0.67 0.21 0.12
Matches are distributed among these distances:
28 25 0.12
29 102 0.49
30 56 0.27
31 24 0.12
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.32
Consensus pattern (29 bp):
TCGAGGGTAAAAATGTAATTTTGGAAAAA
Found at i:38574512 original size:59 final size:58
Alignment explanation
Indices: 38574449--38574765 Score: 424
Period size: 58 Copynumber: 5.4 Consensus size: 58
38574439 TGACTCTCGA
** **
38574449 GGGTAAAAAAGTAATTTTGGAAAAAATCGAGGTTAAAAAT-GAGATTTTGG-AAGATTCGG
1 GGGTAAAATGGTAATTTTGG-TGAAATCGAGGTTAAAAATGGA-ATTTTGGAAAG-TTCGG
* *
38574508 GGGTAAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTTGG
1 GGGT-AAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGG
* *
38574568 GGGTAAAATGGTAATTTTGGTGAAATC-AGGGTTAAAAATGGAATTTTAGAAAGTTTGG
1 GGGTAAAATGGTAATTTTGGTGAAATCGA-GGTTAAAAATGGAATTTTGGAAAGTTCGG
* * **
38574626 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTACAAATGGAATTTTGGAAAGTTCAA
1 GGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGG
* *
38574685 GGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGTAAGTTCGG
1 GGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGG
38574743 GGGTAAAATGGTAATTTTGGTGA
1 GGGTAAAATGGTAATTTTGGTGA
38574766 GTTCAGGGAC
Statistics
Matches: 235, Mismatches: 16, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
57 1 0.00
58 119 0.51
59 65 0.28
60 39 0.17
61 11 0.05
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.32
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGG
Found at i:38574575 original size:29 final size:29
Alignment explanation
Indices: 38574493--38574760 Score: 164
Period size: 29 Copynumber: 9.1 Consensus size: 29
38574483 AAAAATGAGA
*
38574493 TTTTGGAAGATTCGGGGGTAAAAATGGTAATT
1 TTTTGAAAG-TTCGGGGGT-AAAATGGTAA-T
* *
38574525 TTTGGTGAAA--TCGAGGTTAAAAATGG-AAT
1 TTT--TGAAAGTTCGGGGGT-AAAATGGTAAT
* *
38574554 TTTAGAAAGTTTGGGGGTAAAATGGTAAT
1 TTTTGAAAGTTCGGGGGTAAAATGGTAAT
* *
38574583 TTTGGTGAAA--TCAGGGTTAAAAATGG-AAT
1 TTT--TGAAAGTTCGGGGGT-AAAATGGTAAT
* *
38574612 TTTAGAAAGTTTGGGGGTAAAATGGTAATT
1 TTTTGAAAGTTCGGGGGTAAAATGGTAA-T
*
38574642 TTTGGTGAAA--TCGGGGTTACAAATGG-AAT
1 TTT--TGAAAGTTCGGGGGTA-AAATGGTAAT
* **
38574671 TTTGGAAAGTTCAAGGGTAAAATGGTAAT
1 TTTTGAAAGTTCGGGGGTAAAATGGTAAT
*
38574700 TTTGGTGAAA--TCGGGGTTAAAAATGG-AAT
1 TTT--TGAAAGTTCGGGGGT-AAAATGGTAAT
* *
38574729 TTTGGTAAGTTCGGGGGTAAAATGGTAAT
1 TTTTGAAAGTTCGGGGGTAAAATGGTAAT
38574758 TTT
1 TTT
38574761 GGTGAGTTCA
Statistics
Matches: 183, Mismatches: 29, Indels: 51
0.70 0.11 0.19
Matches are distributed among these distances:
27 15 0.08
28 27 0.15
29 73 0.40
30 29 0.16
31 28 0.15
32 7 0.04
34 4 0.02
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
TTTTGAAAGTTCGGGGGTAAAATGGTAAT
Found at i:38574668 original size:117 final size:116
Alignment explanation
Indices: 38574448--38574765 Score: 426
Period size: 117 Copynumber: 2.7 Consensus size: 116
38574438 TTGACTCTCG
** ** *
38574448 AGGGTAAAAAAGTAATTTTGGAAAAAATC-GAGGTTAAAAAT-GAGATTTTGGAAGATTCGGGGG
1 AGGGTAAAATGGTAATTTTGG-TGAAATCAG-GGTTAAAAATGGA-ATTTTGAAAG-TTCGGGGG
**
38574511 TAAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTTG
62 T-AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCA
* *
38574567 GGGGTAAAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTAA
1 AGGGTAAAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTT-GAAAGTTCGGGGGTAA
* * *
38574632 AATGGTAATTTTTGGTGAAATCGGGGTTACAAATGGAATTTTGGAAAGTTCA
65 AATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCA
* *
38574684 AGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGTAAGTTCGGGGGTAA
1 AGGGTAAAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTT-GAAAGTTCGGGGGTAA
38574749 AATGGTAA-TTTTGGTGA
65 AATGGTAATTTTTGGTGA
38574766 GTTCAGGGAC
Statistics
Matches: 179, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
116 9 0.05
117 117 0.65
118 28 0.16
119 25 0.14
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.32
Consensus pattern (116 bp):
AGGGTAAAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGAAAGTTCGGGGGTAAA
ATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCA
Found at i:38576574 original size:29 final size:29
Alignment explanation
Indices: 38576542--38576636 Score: 108
Period size: 29 Copynumber: 3.2 Consensus size: 29
38576532 CCTGAACTCA
38576542 CCAAAATTACCATTTTACCCTCGAACTTT
1 CCAAAATTACCATTTTACCCTCGAACTTT
38576571 CCAAAATT-CCATTTTTAACCCT-G-A-TTT
1 CCAAAATTACCA-TTTT-ACCCTCGAACTTT
*
38576598 CACCAAAAATTACCATTTTACCCTCGAACCTT
1 --CC-AAAATTACCATTTTACCCTCGAACTTT
38576630 CCAAAAT
1 CCAAAAT
38576637 CTCATTTTTA
Statistics
Matches: 56, Mismatches: 1, Indels: 18
0.75 0.01 0.24
Matches are distributed among these distances:
27 3 0.05
28 4 0.07
29 25 0.45
30 18 0.32
31 4 0.07
32 2 0.04
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.33
Consensus pattern (29 bp):
CCAAAATTACCATTTTACCCTCGAACTTT
Found at i:38576634 original size:30 final size:30
Alignment explanation
Indices: 38576544--38576635 Score: 104
Period size: 30 Copynumber: 3.1 Consensus size: 30
38576534 TGAACTCACC
38576544 AAAATTACCATTTTACCCTCGAACTTTCC-
1 AAAATTACCATTTTACCCTCGAACTTTCCA
38576573 AAAATT-CCATTTTTAACCCT-G-A-TTTCACCA
1 AAAATTACCA-TTTT-ACCCTCGAACTTT--CCA
*
38576603 AAAATTACCATTTTACCCTCGAACCTTCCA
1 AAAATTACCATTTTACCCTCGAACTTTCCA
38576633 AAA
1 AAA
38576636 TCTCATTTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 17
0.75 0.01 0.24
Matches are distributed among these distances:
27 3 0.06
28 4 0.08
29 18 0.34
30 22 0.42
31 4 0.08
32 2 0.04
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (30 bp):
AAAATTACCATTTTACCCTCGAACTTTCCA
Found at i:38576683 original size:59 final size:58
Alignment explanation
Indices: 38576539--38576649 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 58
38576529 GTCCCTGAAC
*
38576539 TCACCAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCTGATT
1 TCACCAAAATTACCATTTTACCCTCGAACCTTCCAAAATTCCATTTTTAACCCTGATT
38576597 TCACCAAAAATTACCATTTTACCCTCGAACCTTCCAAAA-TCTCATTTTTAACC
1 TCACC-AAAATTACCATTTTACCCTCGAACCTTCCAAAATTC-CATTTTTAACC
38576650 TCGATTTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
58 7 0.14
59 43 0.86
ACGTcount: A:0.32, C:0.31, G:0.03, T:0.34
Consensus pattern (58 bp):
TCACCAAAATTACCATTTTACCCTCGAACCTTCCAAAATTCCATTTTTAACCCTGATT
Found at i:38584384 original size:23 final size:23
Alignment explanation
Indices: 38584345--38584398 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
38584335 TATTTTAATC
38584345 TTAAATTT--ATTTAAATTCAAT
1 TTAAATTTAAATTTAAATTCAAT
* *
38584366 TTAAATTTAAATTTGAATTTAAT
1 TTAAATTTAAATTTAAATTCAAT
38584389 TTAAATTTAA
1 TTAAATTTAA
38584399 TGTTATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 8 0.28
23 21 0.72
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAAATTTAAATTTAAATTCAAT
Found at i:38584396 original size:11 final size:11
Alignment explanation
Indices: 38584338--38584399 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
38584328 TCAAATTTAT
38584338 TTTAATCTTAAA
1 TTTAAT-TTAAA
38584350 TTT-ATTTAAA
1 TTTAATTTAAA
*
38584360 TTCAATTTAAA
1 TTTAATTTAAA
*
38584371 TTTAAATTTGAA
1 TTT-AATTTAAA
38584383 TTTAATTTAAA
1 TTTAATTTAAA
38584394 TTTAAT
1 TTTAAT
38584400 GTTATTATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
10 7 0.16
11 24 0.55
12 13 0.30
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:38584396 original size:17 final size:15
Alignment explanation
Indices: 38584331--38584415 Score: 80
Period size: 17 Copynumber: 5.1 Consensus size: 15
38584321 TTGAAAATCA
*
38584331 AATTTATTTTAATCTT
1 AATTTATTTAAAT-TT
*
38584347 AAATTTATTTAAATTC
1 -AATTTATTTAAATTT
38584363 AATTTAAATTTAAATTT
1 AATTT--ATTTAAATTT
38584380 GAATTTAATTTAAATTT
1 -AATTT-ATTTAAATTT
38584397 AATGTTATTATAAATTT
1 AAT-TTATT-TAAATTT
38584414 AA
1 AA
38584416 AAAGAAAGTC
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
15 5 0.08
16 7 0.12
17 43 0.72
18 5 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
AATTTATTTAAATTT
Found at i:38584416 original size:6 final size:6
Alignment explanation
Indices: 38584345--38584398 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
38584335 TATTTTAATC
* *
38584345 TTAAAT TT--AT TTAAA- TTCAAT TTAAAT TTAAAT TTGAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
38584389 TTAAAT TTAA
1 TTAAAT TTAA
38584399 TGTTATTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
4 4 0.10
5 9 0.22
6 28 0.68
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:38584461 original size:14 final size:14
Alignment explanation
Indices: 38584442--38584501 Score: 90
Period size: 14 Copynumber: 4.5 Consensus size: 14
38584432 CATGGCCCTG
38584442 GGCCCAATTACAAT
1 GGCCCAATTACAAT
*
38584456 GGCCCAATTACAAA
1 GGCCCAATTACAAT
38584470 GGCCCAATT--AA-
1 GGCCCAATTACAAT
38584481 GGCCCAATTACAAT
1 GGCCCAATTACAAT
38584495 GGCCCAA
1 GGCCCAA
38584502 ATGGCCCAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
11 9 0.21
12 2 0.05
13 2 0.05
14 29 0.69
ACGTcount: A:0.37, C:0.30, G:0.17, T:0.17
Consensus pattern (14 bp):
GGCCCAATTACAAT
Found at i:38584490 original size:25 final size:27
Alignment explanation
Indices: 38584442--38584501 Score: 88
Period size: 25 Copynumber: 2.3 Consensus size: 27
38584432 CATGGCCCTG
38584442 GGCCCAATTACAATGGCCCAATTACAAA
1 GGCCCAATTA-AATGGCCCAATTACAAA
*
38584470 GGCCCAATT-AA-GGCCCAATTACAAT
1 GGCCCAATTAAATGGCCCAATTACAAA
38584495 GGCCCAA
1 GGCCCAA
38584502 ATGGCCCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 20 0.65
26 2 0.06
28 9 0.29
ACGTcount: A:0.37, C:0.30, G:0.17, T:0.17
Consensus pattern (27 bp):
GGCCCAATTAAATGGCCCAATTACAAA
Found at i:38584643 original size:15 final size:15
Alignment explanation
Indices: 38584623--38584653 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38584613 GCCTATGCCG
38584623 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
38584638 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
38584653 C
1 C
38584654 CATCCACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.55, G:0.13, T:0.13
Consensus pattern (15 bp):
CTGCCACCACCAGCT
Found at i:38586453 original size:30 final size:30
Alignment explanation
Indices: 38586244--38586445 Score: 280
Period size: 30 Copynumber: 6.5 Consensus size: 30
38586234 CCCTAAATTG
38586244 TCCAGAAATTACATTTTGACCCCAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
*
38586275 TCCAAAATTCCATTTTGACCCCAAAACTTTTT
1 TCCAAAATTACATTTTGACCCCAAAAC--TTT
* * *
38586307 TCCAAAATTATATTTTTTGACCACGAAACTTT
1 TCCAAAATTACA--TTTTGACCCCAAAACTTT
*
38586339 ACCAAAATTACATTTTGACCCCAAAAACTTT
1 TCCAAAATTACATTTTGACCCC-AAAACTTT
38586370 TCCAAAATTACATTTT-ACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
38586399 TCCAAAAATTATATTTTGACCCCAAAACTTT
1 TCC-AAAATTACATTTTGACCCCAAAACTTT
38586430 TCCAAAATTACATTTT
1 TCCAAAATTACATTTT
38586446 TAACCCAATT
Statistics
Matches: 152, Mismatches: 12, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
29 11 0.07
30 60 0.39
31 42 0.28
32 26 0.17
34 13 0.09
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:38586516 original size:58 final size:57
Alignment explanation
Indices: 38586434--38586650 Score: 275
Period size: 57 Copynumber: 3.8 Consensus size: 57
38586424 AACTTTTCCA
* *
38586434 AAATTACATTTTTAA-CCCAATTTCACCG-AAATTACCATTTTACCCCTGAATCTTTT
1 AAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCC-GAATCTTTT
* *
38586490 AAAATTCCATTTTTAA-CTCGATTTTCATCGAAAATTACCATTTTA-CCCGAATC-TTT
1 -AAATTCCATTTTTAACCCCGA-TTTCACCGAAAATTACCATTTTACCCCGAATCTTTT
** * *
38586546 AAATTTTATTTTTAACCCCGATTTCACTGAAAATTACCATTTTACCCCCGAATATTTT
1 AAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTA-CCCCGAATCTTTT
*
38586604 AAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTGCCCC
1 AAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCC
38586651 CGGGTATCCA
Statistics
Matches: 140, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
55 34 0.24
56 11 0.08
57 43 0.31
58 38 0.27
59 14 0.10
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (57 bp):
AAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCGAATCTTTT
Found at i:38586674 original size:58 final size:58
Alignment explanation
Indices: 38586440--38586687 Score: 197
Period size: 58 Copynumber: 4.3 Consensus size: 58
38586430 TCCAAAATTA
* * * * ** *
38586440 CATTTTTAA-CCCAATTTCAC-CGAAATTACCATTTTACCCCTGAATCTTTTAAAATTC
1 CATTTTTAACCCCGATTTCACTCAAAATTACCATTTTACCCCCGAATATCAT-AAATCC
* * * **
38586497 CATTTTTAA-CTCGATTTTCA-TCGAAAATTACCATTTTA--CCCGAATCT-TTAAATTT
1 CATTTTTAACCCCGA-TTTCACTC-AAAATTACCATTTTACCCCCGAATATCATAAATCC
* * ** *
38586552 TATTTTTAACCCCGATTTCACTGAAAATTACCATTTTACCCCCGAATATTTTAAATTC
1 CATTTTTAACCCCGATTTCACTCAAAATTACCATTTTACCCCCGAATATCATAAATCC
* ** *
38586610 CATTTTTAACCCCGATTTCAC-CAAAATTACCATTTTGCCCCCGGGTATCCATAAGTCC
1 CATTTTTAACCCCGATTTCACTCAAAATTACCATTTTACCCCCGAATAT-CATAAATCC
* *
38586668 CGTTTTTCACCCCGATTTCA
1 CATTTTTAACCCCGATTTCA
38586688 TCATTTATCA
Statistics
Matches: 161, Mismatches: 21, Indels: 17
0.81 0.11 0.09
Matches are distributed among these distances:
55 33 0.20
56 7 0.04
57 51 0.32
58 56 0.35
59 14 0.09
ACGTcount: A:0.29, C:0.27, G:0.06, T:0.38
Consensus pattern (58 bp):
CATTTTTAACCCCGATTTCACTCAAAATTACCATTTTACCCCCGAATATCATAAATCC
Found at i:38598652 original size:68 final size:68
Alignment explanation
Indices: 38598535--38599277 Score: 982
Period size: 68 Copynumber: 10.9 Consensus size: 68
38598525 TCTCACATCG
38598535 TTCCC-TGAAATTGAAGTAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCA
1 TTCCCTTGAAATTG-A--AGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCA
38598599 ACGTCA
63 ACGTCA
*
38598605 TTCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAATG
1 TTCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAACG
38598670 TCA
66 TCA
* **
38598673 -TCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTCCATCTCTGAAATTGAAGTAAGAGC-ATT
1 TTCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAACG
38598736 TCA
66 TCA
* *
38598739 TCTCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
1 T-TCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAAC
38598804 -TCA
65 GTCA
* * *
38598807 TTCCTCTTGAAAATTGAAGTAGAGTTGATATCAAGTCTTT-ATCTCTGAAATTGAAGTAAGAGCA
1 TTCC-CTTG-AAATTGAAGTAGAGTGGATAACACGT-TTTCATCTCTGAAATTGAAGTAAGAGCA
38598871 ACGTCA
63 ACGTCA
*
38598877 TTCCCTTGAAAATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAAT
1 TTCCCTTG-AAATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAAC
38598942 GTCA
65 GTCA
* **
38598946 -TCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTCCATCTCTGAAATTGAAGTAAGAGCAATT
1 TTCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAACG
38599010 TCA
66 TCA
*
38599013 -TCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCT-AAATTG-AGTAAGAGCAAC
1 TTCC-CTTGAAATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAAC
38599075 GTCA
65 GTCA
* *
38599079 -TCCTCTTGAAATTGAAGTAGAGCTGGATAGCAAGTCTTT-ATCTCTGAAATTGAAGTAAGAGCA
1 TTCC-CTTGAAATTGAAGTAGAG-TGGATAACACGT-TTTCATCTCTGAAATTGAAGTAAGAGCA
38599142 ACGTC-
63 ACGTCA
* * * * *
38599147 GTCCTCTTGAAATTGAAGTAGAGTTGGATATA-A--ATCTCTAT-TCTGAAATTGGAGTAAAAAG
1 TTCC-CTTGAAATTGAAGTAGAG-TGGATA-ACACGTTTTC-ATCTCTGAAATTGAAGT-AAGAG
38599208 CAACGTCA
61 CAACGTCA
* * *
38599216 TCCCCTCGAAATTGAAATAGAGTGGATAACACGTCTTT-AT-TCTGAAATTGAAGTAAGAGCAA
1 TTCCCTTGAAATTGAAGTAGAGTGGATAACACGT-TTTCATCTCTGAAATTGAAGTAAGAGCAA
38599278 GATCTTCCTA
Statistics
Matches: 610, Mismatches: 39, Indels: 51
0.87 0.06 0.07
Matches are distributed among these distances:
66 44 0.07
67 171 0.28
68 217 0.36
69 153 0.25
70 17 0.03
71 8 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (68 bp):
TTCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAACG
TCA
Found at i:38598794 original size:135 final size:136
Alignment explanation
Indices: 38598552--38599277 Score: 1005
Period size: 135 Copynumber: 5.4 Consensus size: 136
38598542 AAATTGAAGT
* *
38598552 AGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAACGTCAT-TCCCTTGAAA
1 AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCTCTCTTGAAA
* *
38598616 TTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAATGTCATCCCTTGA
66 TTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCTTGA
38598681 AATTGA
131 AATTGA
**
38598687 AGTAGAGTGGATAACACGT-TTCCATCTCTGAAATTGAAGTAAGAGC-ATTTCATCTCTCTTGAA
1 AGTAGAGTGGATAACACGTCTT-CATCTCTGAAATTGAAGTAAGAGCAACGTCATCTCTCTTGAA
38598750 ATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC-TCATTCCTCT
65 ATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCA-TCC-CT
38598814 TGAAAATTGA
128 TG-AAATTGA
* * * * *
38598824 AGTAGAGTTGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCAT-TCCCTTGAAA
1 AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCTCTCTTG-AA
* *
38598888 ATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAATGTCATCCCTTG
65 ATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCTTG
38598953 AAATTGA
130 AAATTGA
**
38598960 AGTAGAGTGGATAACACGT-TTCCATCTCTGAAATTGAAGTAAGAGCAATTTCATC-CTCTTGAA
1 AGTAGAGTGGATAACACGTCTT-CATCTCTGAAATTGAAGTAAGAGCAACGTCATCTCTCTTGAA
38599023 ATTGAAGTAGAGTGGATAACACGTCTTCATCTCT-AAATTG-AGTAAGAGCAACGTCATCCTCTT
65 ATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCC-CTT
38599086 GAAATTGA
129 GAAATTGA
* * * *
38599094 AGTAGAGCTGGATAGCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCGTC-CTCTTGAA
1 AGTAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCTCTCTTGAA
* * *
38599158 ATTGAAGTAGAGTTGGATATA-A-ATC-TCTAT-TCTGAAATTGGAGTAAAAAGCAACGTCATCC
65 ATTGAAGTAGAG-TGGATA-ACACGTCTTC-ATCTCTGAAATTGAAGT-AAGAGCAACGTCAT-C
*
38599219 CCTCGAAATTGA
125 CCTTGAAATTGA
* *
38599231 AATAGAGTGGATAACACGTCTTTAT-TCTGAAATTGAAGTAAGAGCAA
1 AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
38599278 GATCTTCCTA
Statistics
Matches: 535, Mismatches: 35, Indels: 42
0.87 0.06 0.07
Matches are distributed among these distances:
133 18 0.03
134 39 0.07
135 234 0.44
136 89 0.17
137 86 0.16
138 66 0.12
139 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (136 bp):
AGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCTCTCTTGAAA
TTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCTTGA
AATTGA
Found at i:38598821 original size:32 final size:32
Alignment explanation
Indices: 38598785--38598896 Score: 95
Period size: 32 Copynumber: 3.3 Consensus size: 32
38598775 TTCATCTCTG
38598785 AAATTGAAGTAAGAGCAACTCATTCCTCTTGA
1 AAATTGAAGTAAGAGCAACTCATTCCTCTTGA
* * **
38598817 AAATTGAAGTAGAGTTGATATCAAGTC-TTTATCTCTG-
1 AAATTGAAGTA-A---G--AGCAACTCATTCCTCT-TGA
38598854 AAATTGAAGTAAGAGCAACGTCATTCC-CTTGA
1 AAATTGAAGTAAGAGCAAC-TCATTCCTCTTGA
38598886 AAATTGAAGTA
1 AAATTGAAGTA
38598897 GAGTGGATAA
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
31 6 0.10
32 26 0.42
33 4 0.06
36 2 0.03
37 16 0.26
38 8 0.13
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (32 bp):
AAATTGAAGTAAGAGCAACTCATTCCTCTTGA
Found at i:38598955 original size:30 final size:31
Alignment explanation
Indices: 38598914--38599166 Score: 124
Period size: 31 Copynumber: 7.7 Consensus size: 31
38598904 TAACACGTTT
38598914 TCAT-CTC-TGAAATTGAAGTAAGAGCAATG
1 TCATCCTCTTGAAATTGAAGTAAGAGCAATG
** *
38598943 TCATCC-CTTGAAATTGAAGTAGAGTGGATAACACG
1 TCATCCTCTTGAAATTGAAGTA-A---GAGCA-ATG
* *
38598978 T-TTCCATCTCTGAAATTGAAGTAAGAGCAATT
1 TCATCC-TCT-TGAAATTGAAGTAAGAGCAATG
** *
38599010 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACACG
1 TCATCCTCTTGAAATTGAAGTA-A---GAGCA-ATG
* * *
38599046 TCTTCATCTCT-AAATTG-AGTAAGAGCAACG
1 TCATCCTCT-TGAAATTGAAGTAAGAGCAATG
38599076 TCATCCTCTTGAAATTGAAGTAGAGCTGGATAGCAA-G
1 TCATCCTCTTGAAATTGAAGTA-A----G--AGCAATG
* ** *
38599113 TCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATCCTCT-TGAAATTGAAGTAAGAGCAATG
*
38599145 TCGTCCTCTTGAAATTGAAGTA
1 TCATCCTCTTGAAATTGAAGTA
38599167 GAGTTGGATA
Statistics
Matches: 171, Mismatches: 25, Indels: 54
0.68 0.10 0.22
Matches are distributed among these distances:
29 6 0.04
30 30 0.18
31 39 0.23
32 14 0.08
33 7 0.04
34 7 0.04
35 10 0.06
36 18 0.11
37 22 0.13
38 18 0.11
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (31 bp):
TCATCCTCTTGAAATTGAAGTAAGAGCAATG
Found at i:38599038 original size:273 final size:269
Alignment explanation
Indices: 38598552--38599306 Score: 1134
Period size: 273 Copynumber: 2.8 Consensus size: 269
38598542 AAATTGAAGT
*
38598552 AGTAGAGTGGATAACACGT-TTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATTCCCTTGAAA
1 AGTAGAGTGGATAACAAGTCTTT-ATCTCTGAAATTGAAGTAAGAGCAACGTCATTCCCTTGAAA
38598616 TTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAATGTCATCCCTTGA
65 TTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAATGTCATCCCTTGA
38598681 AATTGAAGTAGAGTGGATAACACGTTTCCATCTCTGAAATTGAAGTAAGAGC-ATTTCATCTCTC
130 AATTGAAGTAGAGTGGATAACACGTTTCCATCTCTGAAATTGAAGTAAGAGCAATTTCATC-CTC
38598745 TTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC-TCATT
194 TTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCT-AAATTG-AGTAAGAGCAACGTCA-T
38598809 CCTCTTGAAAATTGA
256 CCTCTTG-AAATTGA
* *
38598824 AGTAGAGTTGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATTCCCTTGAAAA
1 AGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATTCCCTTG-AAA
38598889 TTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAATGTCATCCCTTGA
65 TTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAATGTCATCCCTTGA
38598954 AATTGAAGTAGAGTGGATAACACGTTTCCATCTCTGAAATTGAAGTAAGAGCAATTTCATCCTCT
130 AATTGAAGTAGAGTGGATAACACGTTTCCATCTCTGAAATTGAAGTAAGAGCAATTTCATCCTCT
38599019 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTAAATTGAGTAAGAGCAACGTCATCCTC
195 TGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTAAATTGAGTAAGAGCAACGTCATCCTC
38599084 TTGAAATTGA
260 TTGAAATTGA
* *
38599094 AGTAGAGCTGGATAGCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTC-GTCCTCTTGAA
1 AGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATTCC-CTTGAA
* * * * *
38599158 ATTGAAGTAGAGTTGGATATA-A--ATCTCTAT-TCTGAAATTGGAGTAAAAAGCAACGTCATCC
64 ATTGAAGTAGAG-TGGATA-ACACGTTTTC-ATCTCTGAAATTGAAGT-AAGAGCAATGTCAT-C
* * *
38599219 CCTCGAAATTGAAATAGAGTGGATAACACGTCTT-TAT-TCTGAAATTGAAGTAAGAGCAAGATC
124 CCTTGAAATTGAAGTAGAGTGGATAACACGT-TTCCATCTCTGAAATTGAAGTAAGAGC-A-AT-
*
38599282 TTCCTATCCTCTAGAAATTGAAGTA
185 TT-C-ATCCTCTTGAAATTGAAGTA
38599307 AAATTGGATA
Statistics
Matches: 451, Mismatches: 15, Indels: 31
0.91 0.03 0.06
Matches are distributed among these distances:
269 16 0.04
270 65 0.14
271 107 0.24
272 68 0.15
273 167 0.37
274 9 0.02
275 19 0.04
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (269 bp):
AGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATTCCCTTGAAAT
TGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAAGAGCAATGTCATCCCTTGAA
ATTGAAGTAGAGTGGATAACACGTTTCCATCTCTGAAATTGAAGTAAGAGCAATTTCATCCTCTT
GAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTAAATTGAGTAAGAGCAACGTCATCCTCT
TGAAATTGA
Found at i:38599644 original size:11 final size:11
Alignment explanation
Indices: 38599621--38599682 Score: 72
Period size: 11 Copynumber: 5.5 Consensus size: 11
38599611 TCAAATTTAT
38599621 TTTAATCTTAAA
1 TTTAAT-TTAAA
*
38599633 TTTATTTTAAA
1 TTTAATTTAAA
*
38599644 TTCAATTT-AA
1 TTTAATTTAAA
*
38599654 TTTAAATTTGAA
1 TTT-AATTTAAA
38599666 TTTAATTTAAA
1 TTTAATTTAAA
38599677 TTTAAT
1 TTTAAT
38599683 GTTATTATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
10 4 0.09
11 29 0.67
12 10 0.23
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:38599651 original size:33 final size:32
Alignment explanation
Indices: 38599614--38599699 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 32
38599604 TTGAAAATCA
* *
38599614 AATTTATTTTAATCTTAAATTTATTTTAAATTC
1 AATTTATTTAAAT-TTAAATTTAATTTAAATTC
* *
38599647 AATTTAATTTAAATTTGAATTTAATTTAAATTT
1 AATTT-ATTTAAATTTAAATTTAATTTAAATTC
38599680 AATGTTATTATAAATTTAAA
1 AAT-TTATT-TAAATTTAAA
38599700 GAAAGTCCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 27 0.60
34 18 0.40
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (32 bp):
AATTTATTTAAATTTAAATTTAATTTAAATTC
Found at i:38599667 original size:6 final size:5
Alignment explanation
Indices: 38599614--38599682 Score: 57
Period size: 5 Copynumber: 12.6 Consensus size: 5
38599604 TTGAAAATCA
* * *
38599614 AATTT ATTTT AATCTT AAATTT ATTTT AAATTC AATTT AATTT AAATTT
1 AATTT AATTT AAT-TT -AATTT AATTT -AATTT AATTT AATTT -AATTT
38599663 GAATTT AATTT AAATTT AAT
1 -AATTT AATTT -AATTT AAT
38599683 GTTATTATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
5 27 0.52
6 22 0.42
7 3 0.06
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (5 bp):
AATTT
Found at i:38599679 original size:17 final size:16
Alignment explanation
Indices: 38599631--38599698 Score: 84
Period size: 17 Copynumber: 4.1 Consensus size: 16
38599621 TTTAATCTTA
* *
38599631 AATTTATTTTAAATTC
1 AATTTAATTTAAATTT
38599647 AATTTAATTTAAATTT
1 AATTTAATTTAAATTT
38599663 GAATTTAATTTAAATTT
1 -AATTTAATTTAAATTT
38599680 AATGTT-ATTATAAATTT
1 AAT-TTAATT-TAAATTT
38599697 AA
1 AA
38599699 AGAAAGTCCA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
16 20 0.43
17 27 0.57
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (16 bp):
AATTTAATTTAAATTT
Found at i:38599731 original size:20 final size:21
Alignment explanation
Indices: 38599706--38599765 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 21
38599696 TAAAGAAAGT
38599706 CCAATTACAATGGCC-AGGGC
1 CCAATTACAATGGCCAAGGGC
38599726 CCAATTACAATGGCCAATTAAGGGC
1 CCAATTACAATGGCC----AAGGGC
38599751 CCAATTACAATGGCC
1 CCAATTACAATGGCC
38599766 CAAATGGCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 15 0.43
25 20 0.57
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.18
Consensus pattern (21 bp):
CCAATTACAATGGCCAAGGGC
Found at i:38599740 original size:14 final size:14
Alignment explanation
Indices: 38599723--38599768 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
38599713 CAATGGCCAG
38599723 GGCCCAATTACAAT
1 GGCCCAATTACAAT
*
38599737 GG-CCAATT--AAG
1 GGCCCAATTACAAT
38599748 GGCCCAATTACAAT
1 GGCCCAATTACAAT
38599762 GGCCCAA
1 GGCCCAA
38599769 ATGGCCAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 4 0.15
12 6 0.22
13 6 0.22
14 11 0.41
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (14 bp):
GGCCCAATTACAAT
Found at i:38599914 original size:15 final size:15
Alignment explanation
Indices: 38599894--38599924 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38599884 GCCTATGCCG
38599894 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
38599909 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
38599924 C
1 C
38599925 CATCCACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.55, G:0.13, T:0.13
Consensus pattern (15 bp):
CTGCCACCACCAGCT
Found at i:38601790 original size:30 final size:30
Alignment explanation
Indices: 38601532--38601786 Score: 350
Period size: 30 Copynumber: 8.4 Consensus size: 30
38601522 AATTGTCGAG
*
38601532 AAATTACATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
38601562 AAATTACATTTTAAACCCCAAAACTTTTCCA
1 AAATTACATTTT-GACCCCAAAACTTTTCCA
* * *
38601593 AAATTATTATTTTTGACCCCGAAACTTTACCA
1 AAATTA-CA-TTTTGACCCCAAAACTTTTCCA
38601625 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
38601655 AAATTACATTTTGACCCTAAAACTTTACCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
** *
38601685 AAATTATTTTTTTGA-CCCTAAACTTTTCCA
1 AAATTA-CATTTTGACCCCAAAACTTTTCCA
* *
38601715 AAATTACATTTTGACCCCGAAACTTTACCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
38601745 AAATTACATTTTAACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
38601775 AAATTACATTTT
1 AAATTACATTTT
38601787 AACCTCGATT
Statistics
Matches: 197, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
29 6 0.03
30 136 0.69
31 29 0.15
32 22 0.11
33 4 0.02
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTTCCA
Found at i:38601815 original size:60 final size:58
Alignment explanation
Indices: 38601559--38602047 Score: 323
Period size: 60 Copynumber: 8.3 Consensus size: 58
38601549 TAAAACTTTT
* *
38601559 CCAAAATTA-CATTTTAAACCCCAAAACTTTTCCAAAATTATTATTTTTGACCCCGAAACTTTA
1 CCAAAATTACCATTTT-AACCCCAAAACTTTTCCAAAATTA-CA-TTTTAACCCCG--A-TTTA
* * **
38601622 CCAAAATTA-CATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTA
1 CCAAAATTACCATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCC--CGA-TTTA
*** * * *
38601682 CCAAAATTATTTTTTTGA-CCCTAAACTTTTCCAAAATTACATTTTGACCCCGAAACTTTA
1 CCAAAATTACCATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCCCG--A-TTTA
*
38601742 CCAAAATTA-CATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCTCGATTTCA
1 CCAAAATTACCATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCCCGATTT-A
* * * *
38601800 CCGAAAATTACCATTTT-ACCCCTGAATCTTTT---AAATT-CTGTTTTTAACCTCGATTTCA
1 CC-AAAATTACCATTTTAACCCC-AAAACTTTTCCAAAATTAC--ATTTTAACCCCGATTT-A
* ** * **
38601858 TCGAAAATTTACCATTTT-ACCCC-CGATTTTTTTAAAATT-CTATTTTTAACCCCGATTTA
1 -CCAAAA-TTACCATTTTAACCCCAAAACTTTTCCAAAATTAC-A-TTTTAACCCCGATTTA
* *
38601917 TCCAAAATTACCATTTTTACCCCCAAA-TCTTT--AAAATT-CTATTTTAACCCCGATTTTA
1 -CCAAAATTACCATTTTAACCCCAAAACT-TTTCCAAAATTAC-ATTTTAACCCCGA-TTTA
* * * * *
38601975 CCGAAAATTACCATTTTACCCCCGAATCTTTT--AAAATTCCATTTTTAATCCCGATTTA
1 CC-AAAATTACCATTTTAACCCCAAAACTTTTCCAAAATTACA-TTTTAACCCCGATTTA
38602033 -CAAAATTACCATTTT
1 CCAAAATTACCATTTT
38602048 GCCCCCGGGT
Statistics
Matches: 366, Mismatches: 34, Indels: 59
0.80 0.07 0.13
Matches are distributed among these distances:
56 15 0.04
57 27 0.07
58 82 0.22
59 59 0.16
60 138 0.38
61 7 0.02
62 23 0.06
63 15 0.04
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (58 bp):
CCAAAATTACCATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAACCCCGATTTA
Found at i:38601815 original size:90 final size:89
Alignment explanation
Indices: 38601532--38601821 Score: 361
Period size: 90 Copynumber: 3.2 Consensus size: 89
38601522 AATTGTCGAG
*
38601532 AAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTAAACCCCAAAACTTTTCCAAAAT
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTT-AACCCCAAAACTTTTCCAAAAT
* *
38601597 TATTATTTTTGACCCCGAAACTTTACCA
65 TATTA-TTTTAACCTCG--ACTTTACCA
* * *
38601625 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTACCAAAATT
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATT
* * ** *
38601690 ATTTTTTTGACCCTAAACTTTTCCA
66 ATTATTTT-AACCTCGACTTTACCA
* *
38601715 AAATTACATTTTGACCCCGAAACTTTACCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATT
1 AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATT
*
38601780 A-CATTTTAACCTCGA-TTTCACCGA
66 ATTATTTTAACCTCGACTTT-ACC-A
38601804 AAATTACCATTTT-ACCCC
1 AAATTA-CATTTTGACCCC
38601822 TGAATCTTTT
Statistics
Matches: 171, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
87 3 0.02
88 7 0.04
89 16 0.09
90 75 0.44
91 4 0.02
92 25 0.15
93 41 0.24
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (89 bp):
AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATT
ATTATTTTAACCTCGACTTTACCA
Found at i:38601879 original size:59 final size:58
Alignment explanation
Indices: 38601738--38602054 Score: 357
Period size: 58 Copynumber: 5.5 Consensus size: 58
38601728 ACCCCGAAAC
* * * *
38601738 TTTACC-AAAATTA-CATTTTAACCCCAAAACTTTTCCAAAATTAC-A-TTTTAACCTCGA
1 TTTACCGAAAATTACCATTTTACCCCCGAATCTTTT--AAAATT-CTATTTTTAACCCCGA
* * *
38601795 TTTCACCGAAAATTACCATTTTACCCCTGAATCTTTT-AAATTCTGTTTTTAACCTCGA
1 TTT-ACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCTATTTTTAACCCCGA
* * *
38601853 TTTCATCGAAAATTTACCATTTTACCCCCGATTTTTTTAAAATTCTATTTTTAACCCCGA
1 TTT-ACCGAAAA-TTACCATTTTACCCCCGAATCTTTTAAAATTCTATTTTTAACCCCGA
*
38601913 TTTATCC-AAAATTACCATTTTTACCCCCAAATC-TTTAAAATTCTA-TTTTAACCCCGA
1 TTTA-CCGAAAATTACCA-TTTTACCCCCGAATCTTTTAAAATTCTATTTTTAACCCCGA
* *
38601970 TTTTACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAATCCCGA
1 -TTTACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCTATTTTTAACCCCGA
*
38602029 TTTA-C-AAAATTACCATTTTGCCCCCG
1 TTTACCGAAAATTACCATTTTACCCCCG
38602055 GGTATCCATA
Statistics
Matches: 228, Mismatches: 19, Indels: 27
0.83 0.07 0.10
Matches are distributed among these distances:
56 21 0.09
57 37 0.16
58 73 0.32
59 57 0.25
60 40 0.18
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (58 bp):
TTTACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCTATTTTTAACCCCGA
Found at i:38601910 original size:29 final size:29
Alignment explanation
Indices: 38601872--38602031 Score: 119
Period size: 29 Copynumber: 5.5 Consensus size: 29
38601862 AAATTTACCA
* *
38601872 TTTTACCCCCGATTTTTTTAAAATTCTAT
1 TTTTAACCCCGATTTTTTTAAAATTCCAT
* **
38601901 TTTTAACCCCGATTTATCCAAAATTACCAT
1 TTTTAACCCCGATTTTTTTAAAATT-CCAT
* ** * *
38601931 TTTT-ACCCCCAAATCTTTAAAATTCTA-
1 TTTTAACCCCGATTTTTTTAAAATTCCAT
***
38601958 TTTTAACCCCGATTTTACCGAAAATTACCA-
1 TTTTAACCCCGATTTT-TTTAAAATT-CCAT
* * *
38601988 TTTTACCCCCGAATCTTTTAAAATTCCAT
1 TTTTAACCCCGATTTTTTTAAAATTCCAT
*
38602017 TTTTAATCCCGATTT
1 TTTTAACCCCGATTT
38602032 ACAAAATTAC
Statistics
Matches: 96, Mismatches: 30, Indels: 10
0.71 0.22 0.07
Matches are distributed among these distances:
27 4 0.04
28 12 0.12
29 58 0.60
30 22 0.23
ACGTcount: A:0.29, C:0.25, G:0.04, T:0.42
Consensus pattern (29 bp):
TTTTAACCCCGATTTTTTTAAAATTCCAT
Found at i:38606279 original size:37 final size:37
Alignment explanation
Indices: 38606175--38606281 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 37
38606165 ATCAATCAAC
**
38606175 ATCATTTCCTATCCTCTTGAAATTGAAGT-AGAGTTAG
1 ATCATTT-CTATCCTCTTGAAATTGAAGTAAGAGCAAG
38606212 ATAACAAGTCTT-TAT-CTC-TGAAATTGAAGTAAGAGCAAG
1 AT--C-A-T-TTCTATCCTCTTGAAATTGAAGTAAGAGCAAG
38606251 ATCATTTCTATCCTCTTGAAATTGAAGTAAG
1 ATCATTTCTATCCTCTTGAAATTGAAGTAAG
38606282 CTGGATATCA
Statistics
Matches: 59, Mismatches: 2, Indels: 18
0.75 0.03 0.23
Matches are distributed among these distances:
34 2 0.03
35 4 0.07
36 4 0.07
37 18 0.31
38 12 0.20
39 12 0.20
40 4 0.07
41 1 0.02
42 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (37 bp):
ATCATTTCTATCCTCTTGAAATTGAAGTAAGAGCAAG
Found at i:38606315 original size:76 final size:76
Alignment explanation
Indices: 38606175--38606327 Score: 247
Period size: 76 Copynumber: 2.0 Consensus size: 76
38606165 ATCAATCAAC
*
38606175 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTAGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
38606240 GTAAGAGCAAG
66 GTAAGAGCAAG
* *
38606251 ATCATTT-CTATCCTCTTGAAATTGAAGTA-AGCTGGATATCAAGTCTTTATCTCTCTGAAATTG
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTA--TCTCTGAAATTG
38606314 AAGTAAGAGCAAG
64 AAGTAAGAGCAAG
38606327 A
1 A
38606328 CAGAGCATCA
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
74 17 0.24
75 22 0.31
76 33 0.46
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (76 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAG
Found at i:38606404 original size:89 final size:88
Alignment explanation
Indices: 38606251--38607056 Score: 638
Period size: 76 Copynumber: 9.9 Consensus size: 88
38606241 TAAGAGCAAG
*
38606251 ATCATTTCTATCCTCTTGAAATTGAAGTAAGCTGGATATCAAGTCTTTATCTCTCTGAAATTGAA
1 ATCATTTCTATCCTCTTGAAATTGAAGTAAGCTGGATAACAAGTCTTTA-CTCTCTGAAATTGAA
38606316 GTAAGAGCAAGACAGAGCATCAAC
65 GTAAGAGCAAGACAGAGCATCAAC
*
38606340 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTA-TCTCTGAAATTGA
1 ATCATTT-CTATCCTCTTGAAATTGAAGTA-AGCTGGATAACAAGTCTTTACTCTCTGAAATTGA
38606404 AGT-A-AG--AG-CA-AG-AT---C
64 AGTAAGAGCAAGACAGAGCATCAAC
* *
38606419 AT--TTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTA-TCTCTGAAATTGAA
1 ATCATTTCTATCCTCTTGAAATTGAAGTA-AGCTGGATAACAAGTCTTTACTCTCTGAAATTGAA
38606481 GT-A-AG--AG-CA-AG-AT---C
65 GTAAGAGCAAGACAGAGCATCAAC
* * *
38606495 AT--TTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTA-TCTCTGAAATTGAA
1 ATCATTTCTATCCTCTTGAAATTGAAGT-AAGCTGGATAACAAGTCTTTACTCTCTGAAATTGAA
38606557 GT-A-AG--AG-CA-AG-AT---C
65 GTAAGAGCAAGACAGAGCATCAAC
* * *
38606571 AT--TTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTATTTA-TCTCTGAAATTGAA
1 ATCATTTCTATCCTCTTGAAATTGAAGTA-AGCTGGATAACAAGTCTTTACTCTCTGAAATTGAA
38606633 GT-A-AG--A-ACA-AG-AT---C
65 GTAAGAGCAAGACAGAGCATCAAC
* * *
38606647 AT--TTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA-TCTCTGAAAATGAA
1 ATCATTTCTATCCTCTTGAAATTGAAGT-AAGCTGGATAACAAGTCTTTACTCTCTG-AAAT--T
38606709 GTAAGTAAGAGCAAGACAGAGCATCAAC
62 G-AAGTAAGAGCAAGACAGAGCATCAAC
*
38606737 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTA-TCTCTGAAATTGA
1 ATCATTT-CTATCCTCTTGAAATTGAAGTA-AGCTGGATAACAAGTCTTTACTCTCTGAAATTGA
38606801 AGT-A-AG--AG-CA-AG-AT---C
64 AGTAAGAGCAAGACAGAGCATCAAC
* * * *
38606816 -T-TTTCCTATCCTCTTGAAATTGAAATAAAGCTGGATATCAAGTCTTTATCTCTCTGAAATTGA
1 ATCATTTCTATCCTCTTGAAATTGAAGT-AAGCTGGATAACAAGTCTTTA-CTCTCTGAAATTGA
*
38606879 AGTAAGAGCAAGTCAGAGCATCAAC
64 AGTAAGAGCAAGACAGAGCATCAAC
* * * *
38606904 ATCATTTCCTATCCTCTTGAAGTTGAAGTAGAGTTGAATAACAAGTCTTTA-TCTTTGAAATTGA
1 ATCATTT-CTATCCTCTTGAAATTGAAGTA-AGCTGGATAACAAGTCTTTACTCTCTGAAATTGA
*
38606968 AGT-A-AG--AG-CA-AG-AT---T
64 AGTAAGAGCAAGACAGAGCATCAAC
* * * *
38606983 AT--TTCCTATCCTCTTGAAATTGAAGTAAAGTTGGACATCAAGTCTTTA-TCTCTGAAATTGAA
1 ATCATTTCTATCCTCTTGAAATTGAAGT-AAGCTGGATAACAAGTCTTTACTCTCTGAAATTGAA
38607045 GTAAGAGCAAGA
65 GTAAGAGCAAGA
38607057 TCATCTCCTA
Statistics
Matches: 632, Mismatches: 38, Indels: 102
0.82 0.05 0.13
Matches are distributed among these distances:
75 1 0.00
76 350 0.55
77 15 0.02
78 19 0.03
79 8 0.01
80 8 0.01
81 1 0.00
82 10 0.02
83 8 0.01
84 9 0.01
85 11 0.02
86 2 0.00
87 8 0.01
88 4 0.01
89 43 0.07
90 29 0.05
91 54 0.09
92 7 0.01
93 45 0.07
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (88 bp):
ATCATTTCTATCCTCTTGAAATTGAAGTAAGCTGGATAACAAGTCTTTACTCTCTGAAATTGAAG
TAAGAGCAAGACAGAGCATCAAC
Found at i:38606466 original size:76 final size:76
Alignment explanation
Indices: 38606340--38607111 Score: 857
Period size: 76 Copynumber: 9.7 Consensus size: 76
38606330 GAGCATCAAC
38606340 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
38606405 GTAAGAGCAAG
66 GTAAGAGCAAG
38606416 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
38606481 GTAAGAGCAAG
66 GTAAGAGCAAG
* * * *
38606492 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
38606557 GTAAGAGCAAG
66 GTAAGAGCAAG
*
38606568 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTATTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
*
38606633 GTAAGAACAAG
66 GTAAGAGCAAG
* * * *
38606644 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAAATGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTG-AAAT--T
38606709 GTAAGTAAGAGCAAG
63 G-AAGTAAGAGCAAG
** * ****
38606724 A-CAGAGCATCAACATCATTTCCT-ATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTT
1 ATC--A-TTTC--C-T-A--TCCTCTTGAAATTG-A-----AGTAGAGTTGGATAACAAGTCTTT
38606787 ATCTCTGAAATTGAAGTAAGAGCAAG
51 ATCTCTGAAATTGAAGTAAGAGCAAG
* * * * *
38606813 ATCTTTTCCTATCCTCTTGAAATTGAAATAAAGCTGGATATCAAGTCTTTATCTCTCTGAAATTG
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTA--TCTCTGAAATTG
38606878 AAGTAAGAGCAAG
64 AAGTAAGAGCAAG
** ** * *
38606891 -TCAGAGCATCAACATCATTTCCTATCCTCTTGAAGTTGAAGTAGAGTTGAATAACAAGTCTTTA
1 ATC--A-TTTC--C-T-A--TCC--T-CT-TGAAAT-TGAAGTAGAGTTGGATAACAAGTCTTTA
*
38606955 TCTTTGAAATTGAAGTAAGAGCAAG
52 TCTCTGAAATTGAAGTAAGAGCAAG
* * * *
38606980 ATTATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGACATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
38607045 GTAAGAGCAAG
66 GTAAGAGCAAG
* * ** * *
38607056 ATCATCTCCTATCCTCTTAAAATTGAAGTAGAGCCGGATATCAAGACTTTATCTCT
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCT
38607112 CTGAAGCTAT
Statistics
Matches: 588, Mismatches: 70, Indels: 76
0.80 0.10 0.10
Matches are distributed among these distances:
76 388 0.66
77 9 0.02
78 27 0.05
79 3 0.01
80 15 0.03
81 9 0.02
82 7 0.01
83 3 0.01
84 4 0.01
85 3 0.01
86 4 0.01
87 8 0.01
88 7 0.01
89 40 0.07
90 6 0.01
91 23 0.04
92 4 0.01
93 28 0.05
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (76 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAG
Found at i:38606965 original size:167 final size:165
Alignment explanation
Indices: 38606568--38607056 Score: 809
Period size: 167 Copynumber: 2.9 Consensus size: 165
38606558 TAAGAGCAAG
*
38606568 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTATTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
* *
38606633 GTAAGAACAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCT
66 GTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCT
*
38606698 CTGAAAATGAAGTAAGTAAGAGCAAGACAGAGCATCAAC
131 CTG-AAAT--TG-AAGTAAGAGCAAGACAGAGCATCAAC
38606737 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
*
38606802 GTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAATAAAGCTGGATATCAAGTCTTTATCT
66 GTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA--T
*
38606867 CTCTGAAATTGAAGTAAGAGCAAGTCAGAGCATCAAC
129 CTCTGAAATTGAAGTAAGAGCAAGACAGAGCATCAAC
* * *
38606904 ATCATTTCCTATCCTCTTGAAGTTGAAGTAGAGTTGAATAACAAGTCTTTATCTTTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
* *
38606969 GTAAGAGCAAGAT-TATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGACATCAAGTCTTTATC
66 GTAAGAGCAAGATCT-TTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATC
38607033 TCTGAAATTGAAGTAAGAGCAAGA
130 TCTGAAATTGAAGTAAGAGCAAGA
38607057 TCATCTCCTA
Statistics
Matches: 304, Mismatches: 13, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
165 25 0.08
166 1 0.00
167 144 0.47
168 1 0.00
169 123 0.40
170 4 0.01
171 6 0.02
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (165 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCT
CTGAAATTGAAGTAAGAGCAAGACAGAGCATCAAC
Found at i:38607000 original size:38 final size:38
Alignment explanation
Indices: 38606958--38607089 Score: 130
Period size: 38 Copynumber: 3.5 Consensus size: 38
38606948 GTCTTTATCT
* *
38606958 TTGAAATTGAAGTAAGAGCAAGATTATTTCCTATCCTC
1 TTGAAATTGAAGTAAGAGCAAGATCATCTCCTATCCTC
*** *
38606996 TTGAAATTGAAGTAA-AGTTGGA-CATCAAGTCTTTAT-CTC
1 TTGAAATTGAAGTAAGAGCAAGATCATC---TC-CTATCCTC
38607035 -TGAAATTGAAGTAAGAGCAAGATCATCTCCTATCCTC
1 TTGAAATTGAAGTAAGAGCAAGATCATCTCCTATCCTC
*
38607072 TTAAAATTGAAGT-AGAGC
1 TTGAAATTGAAGTAAGAGC
38607090 CGGATATCAA
Statistics
Matches: 75, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
36 5 0.07
37 14 0.19
38 40 0.53
39 9 0.12
40 7 0.09
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (38 bp):
TTGAAATTGAAGTAAGAGCAAGATCATCTCCTATCCTC
Found at i:38607411 original size:17 final size:17
Alignment explanation
Indices: 38607389--38607461 Score: 67
Period size: 17 Copynumber: 4.4 Consensus size: 17
38607379 ACTTTATGTT
*
38607389 TTAATTTTGAATTTAAA
1 TTAATTTTAAATTTAAA
* *
38607406 TTAATTTTTAATTT-AT
1 TTAATTTTAAATTTAAA
* **
38607422 TTAAATTTAAATTTATT
1 TTAATTTTAAATTTAAA
*
38607439 TTAAATTTAAATTTAAA
1 TTAATTTTAAATTTAAA
*
38607456 TAAATT
1 TTAATT
38607462 CAAAATTAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
16 13 0.28
17 33 0.72
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (17 bp):
TTAATTTTAAATTTAAA
Found at i:38607452 original size:33 final size:33
Alignment explanation
Indices: 38607388--38607478 Score: 92
Period size: 33 Copynumber: 2.8 Consensus size: 33
38607378 GACTTTATGT
* * * * *
38607388 TTTAATTTTGAATTTAAATTAATTTTTAATTTA
1 TTTAAATTTAAATTTAATTTAAATTTAAATTTA
*
38607421 TTTAAATTTAAATTTATTTTAAATTTAAATTTA
1 TTTAAATTTAAATTTAATTTAAATTTAAATTTA
** * *
38607454 AATAAATTCAAAATTAATTTAAATT
1 TTTAAATTTAAATTTAATTTAAATT
38607479 CAAAATTAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (33 bp):
TTTAAATTTAAATTTAATTTAAATTTAAATTTA
Found at i:38607467 original size:23 final size:23
Alignment explanation
Indices: 38607420--38607477 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
38607410 TTTTTAATTT
** **
38607420 ATTTAAATTTAAATTTATTTTAA
1 ATTTAAATTTAAATAAATTCAAA
38607443 ATTTAAATTTAAATAAATTCAAA
1 ATTTAAATTTAAATAAATTCAAA
38607466 A-TT-AATTTAAAT
1 ATTTAAATTTAAAT
38607478 TCAAAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 9 0.29
22 2 0.06
23 20 0.65
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTAAATTTAAATAAATTCAAA
Found at i:38607486 original size:17 final size:17
Alignment explanation
Indices: 38607415--38607487 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 17
38607405 ATTAATTTTT
* *
38607415 AATTTATTTAAATTTAA
1 AATTAATTTAAATTCAA
* * *
38607432 ATTTATTTTAAATTTAA
1 AATTAATTTAAATTCAA
* *
38607449 ATTTAA-ATAAATTCAA
1 AATTAATTTAAATTCAA
38607465 AATTAATTTAAATTCAA
1 AATTAATTTAAATTCAA
38607482 AATTAA
1 AATTAA
38607488 AACATAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
16 13 0.28
17 34 0.72
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAATTTAAATTCAA
Found at i:38607488 original size:33 final size:33
Alignment explanation
Indices: 38607423--38607488 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
38607413 TTAATTTATT
* * * * *
38607423 TAAATTTAAATTTATTTTAAATTTAAATTTAAA
1 TAAATTCAAAATTAATTTAAATTCAAAATTAAA
38607456 TAAATTCAAAATTAATTTAAATTCAAAATTAAA
1 TAAATTCAAAATTAATTTAAATTCAAAATTAAA
38607489 ACATAAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (33 bp):
TAAATTCAAAATTAATTTAAATTCAAAATTAAA
Found at i:38609462 original size:16 final size:16
Alignment explanation
Indices: 38609430--38609467 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
38609420 AATTCCATTG
38609430 CTTTTC-CTTTATCTT
1 CTTTTCTCTTTATCTT
38609445 CTTTTCTCTTTAAT-TT
1 CTTTTCTCTTT-ATCTT
38609461 CTTTTCT
1 CTTTTCT
38609468 TTTTTTATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 13 0.62
17 2 0.10
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (16 bp):
CTTTTCTCTTTATCTT
Found at i:38615184 original size:26 final size:26
Alignment explanation
Indices: 38615138--38615189 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
38615128 TTGTTAAAAC
**
38615138 TTTTTAAAAGAAAACTCAAGAGAATT
1 TTTTTAAAAGAAAACAAAAGAGAATT
38615164 TTTTTAAAAG-AAACAAAAAGAGAATT
1 TTTTTAAAAGAAAAC-AAAAGAGAATT
38615190 ATATTAACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.54, C:0.06, G:0.12, T:0.29
Consensus pattern (26 bp):
TTTTTAAAAGAAAACAAAAGAGAATT
Found at i:38615326 original size:4 final size:4
Alignment explanation
Indices: 38615317--38615347 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
38615307 ACAACTTATC
*
38615317 AACT AACT AACT AACT AACT AACT AATT AAC
1 AACT AACT AACT AACT AACT AACT AACT AAC
38615348 ATGAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
AACT
Found at i:38615931 original size:2 final size:2
Alignment explanation
Indices: 38615924--38615977 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
38615914 CCCACTTTAA
*
38615924 AT AT AT AT AT AG AT AT AT AT A- AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38615964 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
38615978 TTTATGGTAG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:38615950 original size:17 final size:17
Alignment explanation
Indices: 38615924--38615977 Score: 92
Period size: 17 Copynumber: 3.2 Consensus size: 17
38615914 CCCACTTTAA
*
38615924 ATAT-ATATATAGATAT
1 ATATAATATATATATAT
38615940 ATATAATATATATATAT
1 ATATAATATATATATAT
38615957 ATATAATATATATATAT
1 ATATAATATATATATAT
38615974 ATAT
1 ATAT
38615978 TTTATGGTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
16 4 0.11
17 32 0.89
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
ATATAATATATATATAT
Found at i:38627561 original size:27 final size:27
Alignment explanation
Indices: 38627531--38627595 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
38627521 CCTCTGTGGC
*
38627531 GAACTCTGAAGGAACGATATTTATGGT
1 GAACTCTGAAGGAACGACATTTATGGT
*
38627558 GAACTCTGAAGTAACGACATTTATGGT
1 GAACTCTGAAGGAACGACATTTATGGT
* *
38627585 AAACTATGAAG
1 GAACTCTGAAG
38627596 AAATGGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (27 bp):
GAACTCTGAAGGAACGACATTTATGGT
Found at i:38629742 original size:20 final size:20
Alignment explanation
Indices: 38629705--38629748 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
38629695 GAATTTAAGG
38629705 ATTTTATAAAACTAAATT-A
1 ATTTTATAAAACTAAATTCA
* *
38629724 ATTTTATTAAATCTCAATTCA
1 ATTTTA-TAAAACTAAATTCA
38629745 ATTT
1 ATTT
38629749 AATTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 10 0.48
21 5 0.24
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTTATAAAACTAAATTCA
Found at i:38642820 original size:22 final size:22
Alignment explanation
Indices: 38642775--38642820 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
38642765 GAGGTTAAGA
*
38642775 AGAAAAGAAGAGAGATTGATAAG
1 AGAAAAGAAGAGAGA-TGAGAAG
38642798 AGAAAAGAGAGAGAGA-GAGAAG
1 AGAAAAGA-AGAGAGATGAGAAG
38642820 A
1 A
38642821 CTGAAAATAT
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:0.59, C:0.00, G:0.35, T:0.07
Consensus pattern (22 bp):
AGAAAAGAAGAGAGATGAGAAG
Found at i:38651386 original size:46 final size:46
Alignment explanation
Indices: 38651319--38651410 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
38651309 CAAAAATAAA
38651319 GATTAAAAAGAAATCAATAATCAAGAAGGCTATAAAAGAAGAGCAT
1 GATTAAAAAGAAATCAATAATCAAGAAGGCTATAAAAGAAGAGCAT
38651365 GATTAAAAAGAAATCAATAATCAAGAAGGCTATAAAAGAAGAGCAT
1 GATTAAAAAGAAATCAATAATCAAGAAGGCTATAAAAGAAGAGCAT
38651411 ATCTTCGTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (46 bp):
GATTAAAAAGAAATCAATAATCAAGAAGGCTATAAAAGAAGAGCAT
Found at i:38653457 original size:17 final size:19
Alignment explanation
Indices: 38653423--38653457 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
38653413 ATTTTTTACA
38653423 TTATTTGTTTCTCTTTATT
1 TTATTTGTTTCTCTTTATT
38653442 TTATTT-TTTC-CTTTAT
1 TTATTTGTTTCTCTTTAT
38653458 CTTTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.74
Consensus pattern (19 bp):
TTATTTGTTTCTCTTTATT
Found at i:38653462 original size:19 final size:19
Alignment explanation
Indices: 38653423--38653469 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
38653413 ATTTTTTACA
38653423 TTATTTGTTTCTCTTTA-TT
1 TTATTT-TTTCTCTTTATTT
38653442 TTATTTTTTC-CTTTATCTTT
1 TTATTTTTTCTCTTTA--TTT
38653462 TTATTTTT
1 TTATTTTT
38653470 ATAATGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.20
18 4 0.16
19 6 0.24
20 10 0.40
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.77
Consensus pattern (19 bp):
TTATTTTTTCTCTTTATTT
Found at i:38653471 original size:31 final size:30
Alignment explanation
Indices: 38653399--38653471 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
38653389 TTTTTAACTA
*
38653399 TTTTA-TTTCATTTTATTTTTTACATTATT
1 TTTTATTTTTATTTTATTTTTTACATTATT
* * * *
38653428 TGTTTCTCTTTATTTTATTTTTTCCTTTATCT
1 T-TTTATTTTTATTTTATTTTTTACATTAT-T
38653460 TTTTATTTTTAT
1 TTTTATTTTTAT
38653472 AATGTTAAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
29 1 0.03
30 3 0.09
31 28 0.82
32 2 0.06
ACGTcount: A:0.15, C:0.10, G:0.01, T:0.74
Consensus pattern (30 bp):
TTTTATTTTTATTTTATTTTTTACATTATT
Found at i:38654096 original size:25 final size:25
Alignment explanation
Indices: 38654049--38654096 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
38654039 TATATATTGC
* *
38654049 ATATAGAAATAATTATATTTATTCG
1 ATATAAAAATAATTATATGTATTCG
38654074 ATATAAAAATAAATTA-ATGTATT
1 ATATAAAAAT-AATTATATGTATT
38654097 TATTTCTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (25 bp):
ATATAAAAATAATTATATGTATTCG
Found at i:38654200 original size:29 final size:32
Alignment explanation
Indices: 38654167--38654236 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
38654157 CGATCAAAAT
*
38654167 TTCATATATAT-AATT-CA-ACTAAATTAAAG
1 TTCATATATATAAATTGCACACTAAATCAAAG
*
38654196 TTCATATAT-TAAATTGCACATTAAATCAAAG
1 TTCATATATATAAATTGCACACTAAATCAAAG
*
38654227 TTCATGTATA
1 TTCATATATA
38654237 ATTTTAAGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 1 0.03
29 13 0.38
30 2 0.06
31 18 0.53
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (32 bp):
TTCATATATATAAATTGCACACTAAATCAAAG
Found at i:38655340 original size:31 final size:31
Alignment explanation
Indices: 38655281--38655340 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
38655271 AAAATTTCAA
* * *
38655281 AATGTTTTAATTGAGTTTTTGAACTATAAAT
1 AATGTTTTAATTAAGTTCTTAAACTATAAAT
*
38655312 AATGTTTTAATTAAGTTCTTAAATTATAA
1 AATGTTTTAATTAAGTTCTTAAACTATAA
38655341 GTATTTGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.48
Consensus pattern (31 bp):
AATGTTTTAATTAAGTTCTTAAACTATAAAT
Found at i:38660020 original size:195 final size:195
Alignment explanation
Indices: 38659656--38660028 Score: 559
Period size: 195 Copynumber: 1.9 Consensus size: 195
38659646 TTAAAAAGTT
*
38659656 CAAGCACATTCCATTTTCATTTCAAGTGGTTTCAATCCAACGCAACCTGACCTATAATAATTAAT
1 CAAGCACATTCCATTTTCATTTCAAGTGGTTTCAATCCAACACAACCTGACCTATAATAATTAAT
* * *
38659721 AATATAAGATATCCTTCCAAGAAATCATGTCAAGGTACATTTAGTATGTGTTATCTCTCCATCCC
66 AATATAAGATATCCTTCCAAGAAATCACGTCAAGGTACATTTAGTATGTGCTACCTCTCCATCCC
* *
38659786 TTGAGCACAAGTAAGCTTAAAGCGAATTAAACACAACCACAAGAATATCTTTTATGCAAAAAGCA
131 TAGAGCACAAGTAAGCTTAAAGCGAATCAAACACAACCACAAGAATATCTTTTATGCAAAAAGCA
* * * *
38659851 CAAGCACATTCCATTTTCATTTCAAGTGGTTTCAATCCGACACAACTTTACCTATAATAATTAGT
1 CAAGCACATTCCATTTTCATTTCAAGTGGTTTCAATCCAACACAACCTGACCTATAATAATTAAT
* * * *
38659916 AATATAAGATATCCTTCCAAGAAATTACGTCATGGTGCATTTAGTATGTGCTCCCTCTCCATCCC
66 AATATAAGATATCCTTCCAAGAAATCACGTCAAGGTACATTTAGTATGTGCTACCTCTCCATCCC
* * * * *
38659981 TAGGGCACAAAG-AAGTTTTAAGTGAATCAAACTCAACCACAAGAATAT
131 TAGAGCAC-AAGTAAGCTTAAAGCGAATCAAACACAACCACAAGAATAT
38660029 GTCTTTTTAT
Statistics
Matches: 158, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
195 155 0.98
196 3 0.02
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (195 bp):
CAAGCACATTCCATTTTCATTTCAAGTGGTTTCAATCCAACACAACCTGACCTATAATAATTAAT
AATATAAGATATCCTTCCAAGAAATCACGTCAAGGTACATTTAGTATGTGCTACCTCTCCATCCC
TAGAGCACAAGTAAGCTTAAAGCGAATCAAACACAACCACAAGAATATCTTTTATGCAAAAAGCA
Found at i:38665090 original size:29 final size:28
Alignment explanation
Indices: 38665035--38665094 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
38665025 TTTTTAAAAA
*
38665035 ATATTTTTTTAATATTTAATAATTTTAT
1 ATATTTTTTTAATATTGAATAATTTTAT
*
38665063 ATATTTTTTTATTTATTGAA-AATGTTTAT
1 ATATTTTTTTA-ATATTGAATAAT-TTTAT
38665092 ATA
1 ATA
38665095 ATCATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (28 bp):
ATATTTTTTTAATATTGAATAATTTTAT
Found at i:38666890 original size:16 final size:17
Alignment explanation
Indices: 38666858--38666890 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38666848 CGTCATTTCC
*
38666858 TTCCTAAATTTCCAATA
1 TTCCTAAATTGCCAATA
38666875 TTCCTAAA-TGCCAATA
1 TTCCTAAATTGCCAATA
38666891 CAATTTGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (17 bp):
TTCCTAAATTGCCAATA
Found at i:38669970 original size:25 final size:26
Alignment explanation
Indices: 38669913--38669983 Score: 117
Period size: 25 Copynumber: 2.8 Consensus size: 26
38669903 AATTTAGTAG
38669913 TTAGTAGGTGAAAGATCAAGAGTTTT
1 TTAGTAGGTGAAAGATCAAGAGTTTT
*
38669939 TTAGTAGATGAAAGATCAAGAG-TTT
1 TTAGTAGGTGAAAGATCAAGAGTTTT
*
38669964 TTAGTAGGTGAAAGGTCAAG
1 TTAGTAGGTGAAAGATCAAG
38669984 GGTCAAATCT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 21 0.50
26 21 0.50
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (26 bp):
TTAGTAGGTGAAAGATCAAGAGTTTT
Found at i:38672103 original size:24 final size:25
Alignment explanation
Indices: 38672034--38672097 Score: 94
Period size: 26 Copynumber: 2.6 Consensus size: 25
38672024 AATTTAGTAG
*
38672034 TTAGTAGGTGAAAGATCAAGAGTTTT
1 TTAGTAGGTGAAAGATCAAAAG-TTT
*
38672060 TTAGTAGATGAAAGATCAAAAG-TT
1 TTAGTAGGTGAAAGATCAAAAGTTT
38672084 TTAGTAGGTGAAAG
1 TTAGTAGGTGAAAG
38672098 GCCAAAGGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
24 15 0.43
26 20 0.57
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.31
Consensus pattern (25 bp):
TTAGTAGGTGAAAGATCAAAAGTTT
Found at i:38682651 original size:14 final size:15
Alignment explanation
Indices: 38682632--38682662 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
38682622 GGGTTTAGAA
38682632 TTTGTAAATGGA-TT
1 TTTGTAAATGGACTT
38682646 TTTGTAAATGGACTT
1 TTTGTAAATGGACTT
38682661 TT
1 TT
38682663 AAGTAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (15 bp):
TTTGTAAATGGACTT
Found at i:38688666 original size:13 final size:11
Alignment explanation
Indices: 38688641--38688680 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
38688631 CAATTAAATC
38688641 TTTTCTTTTTT
1 TTTTCTTTTTT
38688652 TTTTCTTGATTTT
1 TTTTCTT--TTTT
*
38688665 TTTCCTTTTTT
1 TTTTCTTTTTT
38688676 TTTTC
1 TTTTC
38688681 GAATAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 15 0.60
13 10 0.40
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:38689605 original size:6 final size:6
Alignment explanation
Indices: 38689594--38689659 Score: 80
Period size: 6 Copynumber: 10.8 Consensus size: 6
38689584 GCATAATAAC
* *
38689594 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATGAAA ATGAAA ATGAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT-AAAA
*
38689643 ATGAAAA A-AATA ATAAA
1 AT-AAAA ATAAAA ATAAA
38689660 TGCACTATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
5 4 0.07
6 39 0.72
7 11 0.20
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:38693587 original size:23 final size:24
Alignment explanation
Indices: 38693544--38693589 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
38693534 AGTTGGATCC
*
38693544 AAATTAAATTTTAAAAGATAATTA
1 AAATTAAATTCTAAAAGATAATTA
38693568 AAATTAAA-TCTAAACA-ATAATT
1 AAATTAAATTCTAAA-AGATAATT
38693590 CCTTAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATTAAATTCTAAAAGATAATTA
Found at i:38694243 original size:6 final size:6
Alignment explanation
Indices: 38694232--38694259 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
38694222 CAAAAAGAAA
38694232 GAAGAT GAAGAT GAAGAT GAAGAT GAAG
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAG
38694260 GAGAGAGGTG
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:0.00, G:0.36, T:0.14
Consensus pattern (6 bp):
GAAGAT
Found at i:38697091 original size:21 final size:21
Alignment explanation
Indices: 38697067--38697106 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38697057 TATTTTTTTA
*
38697067 AAGTTAAAAATTAAAATTATT
1 AAGTTAAAAAATAAAATTATT
38697088 AAGTTAAAAAATAAAATTA
1 AAGTTAAAAAATAAAATTA
38697107 CGTCATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
AAGTTAAAAAATAAAATTATT
Found at i:38697104 original size:69 final size:67
Alignment explanation
Indices: 38697024--38697155 Score: 174
Period size: 69 Copynumber: 1.9 Consensus size: 67
38697014 TTTAAATAAA
** * * * *
38697024 AAAAAAGAAAATTACGTTGTTTTAATGAATGTTTATTTTTTTAAAGTTAAAAATTAAAATTATTA
1 AAAAAAGAAAATTACGTCATTTTAATAAATGTTTA-TCTATT-AAGTTAAAAAGTAAAATTATTA
38697089 AGTT
64 AGTT
* *
38697093 AAAAAATAAAATTACGTCATTTTGATAAATGTTTATCTATTAAGTTAAAAAGTAAAATTATTA
1 AAAAAAGAAAATTACGTCATTTTAATAAATGTTTATCTATTAAGTTAAAAAGTAAAATTATTA
38697156 TATTATTTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
67 21 0.38
68 4 0.07
69 30 0.55
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (67 bp):
AAAAAAGAAAATTACGTCATTTTAATAAATGTTTATCTATTAAGTTAAAAAGTAAAATTATTAAG
TT
Found at i:38713911 original size:18 final size:17
Alignment explanation
Indices: 38713888--38713921 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
38713878 TATGTCAATG
38713888 TAAAATAAATTTATTTTA
1 TAAAAT-AATTTATTTTA
*
38713906 TAAAATGATTTATTTT
1 TAAAATAATTTATTTT
38713922 TTTTAATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TAAAATAATTTATTTTA
Found at i:38716400 original size:643 final size:645
Alignment explanation
Indices: 38715227--38716414 Score: 1749
Period size: 643 Copynumber: 1.8 Consensus size: 645
38715217 ACTGTGCCGC
* * * * *
38715227 AGAGTGTAAGGGTCTCCATCATTATTTCTTGTTCATTGTGGGGACTTCCATGAGCGTTCGGGAGC
1 AGAGTGTAAGGGTCTCCATCATTACTTATTATTCATTGTGGGGACTTCCATGAGCGTCCAGGAGC
* * *
38715292 ATTGTCATTGTTTCACTTTCTACATTTAATTGATGGTTGATTATTGATTAAATTGTGTTTATTGC
66 ATTGTCATTGTTGCACTTTCTACATTTAATTGATGGTTGATTATTGATTAAATTGTGTTGATCGC
* * * * * *
38715357 GCAATAGAGTATTGTCATTGTTGATGCTTGCATCATTTTCATTGATCATTTGGTTCAGTTAGACA
131 ACAAGAGAGTATTGTCATTGTTGACGCTTGCACCATTTTCATTGACCATTTGGTTCAATTAGACA
* *
38715422 CTCTTGTGTCCGAATATCTTTCCTTCTTGTGTTACTTGGGCAAAATGATTTAATGAACTTGAACA
196 CTCTTGTGTCCGAATATCTTTCCTCCTTCTGTTACTTGGGCAAAATGATTTAATGAACTTGAACA
38715487 TTGAATCAAAACACTATCCTTATTTATTTATTGAATGTCTTATATTATTTTATTGTTATTTTAAA
261 TTGAATCAAAACACTATCCTTATTTATTTATTGAATGTC---T-TTA--TTATTG-T-TTTTAAA
* *
38715552 TGTTATTTTGTGATTGATTCATCACTATATTGTATCTCTGGAAATTTTTATTGAATGTTATTTTC
318 TGTTATTTTGTGACTGATTCATCACTATATTGTATCTCTGGAAATTTTTATTGAATGTTAATTTC
* *
38715617 ACTCTTCGAATTATTACATAAACATATATATTTGTATTTGATTAGGATGCTTTTATTTTTAACCA
383 ACTCTTCGAATTATTACATAAACATATATAGTTGTATTTGATTAGAATGCTTTTATTTTTAACCA
*
38715682 TATGCATTAGTAGTTTAAAATGTTTTAGATCTCCACCAAGCATTGAAAAGCTCAACATGTGGGTT
448 TATGCATTAGTAGTTTAAAATGTTTTAGATCTCCACCAAGCACTGAAAAGCTCAACATGTGGGTT
* *
38715747 ATTAATTTCGTGCGCATGTCACATTACAATTTTACTTTTATTATTTTAAAATTTTTAAAAAGCAT
513 ATTAATTTCGTGCGCAGGTAACATTACAATTTTACTTTTATTATTTTAAAATTTTTAAAAAGCAT
38715812 AAATGAAATTTTTTTTATTTTAGAGGGTATGGGTCTCTATCAGTCCTCTAGATGCGCCACTGTGT
578 AAATGAAATTTTTTTTATTTTAGAGGGTATGGGTCTCTATCAGTCCTCTAGATGCGCCACTGTGT
38715877 TGT
643 TGT
* * * *
38715880 AGAGTGTAGGGGTCTCCATCATTGCTTATTATTCATTGTGGGGACTTCCTTGAGTGTCCAGGAGC
1 AGAGTGTAAGGGTCTCCATCATTACTTATTATTCATTGTGGGGACTTCCATGAGCGTCCAGGAGC
** * * * *
38715945 ATTGTCATTGTTGCGTTTTGC-GCATTTAGTTGATGGTTGGTTATTGATTAAGTTGTGTTGATCG
66 ATTGTCATTGTTGCACTTT-CTACATTTAATTGATGGTTGATTATTGATTAAATTGTGTTGATCG
* * *
38716009 CACAAGGGAGTATTGTTATTGTTGGCGCTTGCACCATTTTCATTGACCATTTGGTGTTCAATTAG
130 CACAAGAGAGTATTGTCATTGTTGACGCTTGCACCATTTTCATTGACCATTT-G-GTTCAATTAG
*
38716074 ACACT-TGTGTGTTCGAATATCTTTCCTCCTTCTGTTACTTGGGCAAAATGATTTAATGAACTTG
193 ACACTCT-TGTGTCCGAATATCTTTCCTCCTTCTGTTACTTGGGCAAAATGATTTAATGAACTTG
* * *
38716138 AACATTGAATCGAAAGACTATCTTTATTTATTTATTGAATGTC-TTA-TATTG-TTTT-AATGTT
257 AACATTGAATCAAAACACTATCCTTATTTATTTATTGAATGTCTTTATTATTGTTTTTAAATGTT
* * * * *
38716199 ATTTTGTGACTGATTCATGATTGTATTGTGTCTCTGGAAATTTTTATTGAATGTTAATTTCATTC
322 ATTTTGTGACTGATTCATCACTATATTGTATCTCTGGAAATTTTTATTGAATGTTAATTTCACTC
* * * *
38716264 TTCGAATTATTACATAAATATATATGGTTGTGTTTGATTAGAATGCTTTTATTTTTAACTATATG
387 TTCGAATTATTACATAAACATATATAGTTGTATTTGATTAGAATGCTTTTATTTTTAACCATATG
* * * *
38716329 TATTATTAGTTTAAAATGTTTTGGATCTCCACCAAGCACTGAAAAGCTCAGCATGTGGGTTATTA
452 CATTAGTAGTTTAAAATGTTTTAGATCTCCACCAAGCACTGAAAAGCTCAACATGTGGGTTATTA
38716394 ATTTCGTGCGCAGGTAACATT
517 ATTTCGTGCGCAGGTAACATT
38716415 TGGATTGAAT
Statistics
Matches: 478, Mismatches: 53, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
643 202 0.42
644 4 0.01
647 5 0.01
650 3 0.01
653 153 0.32
654 3 0.01
655 108 0.23
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.44
Consensus pattern (645 bp):
AGAGTGTAAGGGTCTCCATCATTACTTATTATTCATTGTGGGGACTTCCATGAGCGTCCAGGAGC
ATTGTCATTGTTGCACTTTCTACATTTAATTGATGGTTGATTATTGATTAAATTGTGTTGATCGC
ACAAGAGAGTATTGTCATTGTTGACGCTTGCACCATTTTCATTGACCATTTGGTTCAATTAGACA
CTCTTGTGTCCGAATATCTTTCCTCCTTCTGTTACTTGGGCAAAATGATTTAATGAACTTGAACA
TTGAATCAAAACACTATCCTTATTTATTTATTGAATGTCTTTATTATTGTTTTTAAATGTTATTT
TGTGACTGATTCATCACTATATTGTATCTCTGGAAATTTTTATTGAATGTTAATTTCACTCTTCG
AATTATTACATAAACATATATAGTTGTATTTGATTAGAATGCTTTTATTTTTAACCATATGCATT
AGTAGTTTAAAATGTTTTAGATCTCCACCAAGCACTGAAAAGCTCAACATGTGGGTTATTAATTT
CGTGCGCAGGTAACATTACAATTTTACTTTTATTATTTTAAAATTTTTAAAAAGCATAAATGAAA
TTTTTTTTATTTTAGAGGGTATGGGTCTCTATCAGTCCTCTAGATGCGCCACTGTGTTGT
Found at i:38717180 original size:94 final size:94
Alignment explanation
Indices: 38717046--38717243 Score: 380
Period size: 94 Copynumber: 2.1 Consensus size: 94
38717036 TTTGCTTAGT
*
38717046 AGTCACATCTTTTGAATCTCATTTTATTTTTATTGGATTAACAATATGTGTCAATCTTTCTCTTG
1 AGTCACATTTTTTGAATCTCATTTTATTTTTATTGGATTAACAATATGTGTCAATCTTTCTCTTG
38717111 AGAATTTCATTGTATTAGTTGCCTCATCG
66 AGAATTTCATTGTATTAGTTGCCTCATCG
38717140 AGTCACATTTTTTGAATCTCATTTTATTTTTATTGGATTAACAATATGTGTCAATCTTTCTCTTG
1 AGTCACATTTTTTGAATCTCATTTTATTTTTATTGGATTAACAATATGTGTCAATCTTTCTCTTG
38717205 AGAATTTCATTGTATTAGTTGCCTCATCG
66 AGAATTTCATTGTATTAGTTGCCTCATCG
38717234 AGTCAC-TTTT
1 AGTCACATTTT
38717244 CTTTAATAAA
Statistics
Matches: 103, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
93 4 0.04
94 99 0.96
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (94 bp):
AGTCACATTTTTTGAATCTCATTTTATTTTTATTGGATTAACAATATGTGTCAATCTTTCTCTTG
AGAATTTCATTGTATTAGTTGCCTCATCG
Found at i:38718799 original size:2 final size:2
Alignment explanation
Indices: 38718792--38718853 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
38718782 TGTTGTGATG
38718792 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
38718834 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
38718854 GAAAAGGATA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38733674 original size:14 final size:14
Alignment explanation
Indices: 38733655--38733682 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38733645 ATTTATATTT
38733655 AAATTATTTTTTTA
1 AAATTATTTTTTTA
38733669 AAATTATTTTTTTA
1 AAATTATTTTTTTA
38733683 TGTATACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AAATTATTTTTTTA
Found at i:38735795 original size:21 final size:21
Alignment explanation
Indices: 38735766--38735807 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
38735756 TTATTTCATA
*
38735766 AATCTTATTTATA-TTTTAATT
1 AATCATATTT-TAGTTTTAATT
38735787 AATCATATTTTAGTTTTAATT
1 AATCATATTTTAGTTTTAATT
38735808 CATCTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (21 bp):
AATCATATTTTAGTTTTAATT
Found at i:38736901 original size:20 final size:20
Alignment explanation
Indices: 38736876--38736913 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
38736866 ATAGTGAAAA
38736876 ATCATATAATAGGTAAATTT
1 ATCATATAATAGGTAAATTT
38736896 ATCATATAATAGGTAAAT
1 ATCATATAATAGGTAAAT
38736914 CTTACCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (20 bp):
ATCATATAATAGGTAAATTT
Found at i:38740282 original size:59 final size:57
Alignment explanation
Indices: 38740209--38740493 Score: 251
Period size: 59 Copynumber: 4.9 Consensus size: 57
38740199 TACCAAGGGT
* *
38740209 AAAATGGTAATTTTGGACA-TTTAGGGGTAAAATGGTAATTTTGGGAAAGTTCGGGGTCA
1 AAAATGG-AATTTTGGAAAGTTTAGGGGTAAAAT-GTAATTTTGGGAAAGTT-GAGGTCA
* ** * *
38740268 AAAATGGAATTTTTGGACA-TCCAAGGGTAAAATGGTAATTTTTGG-AAGTTTTGAGGTCA
1 AAAATGGAA-TTTTGGAAAGTTTAGGGGTAAAAT-GTAATTTTGGGAAAG--TTGAGGTCA
* ** * *
38740327 AAATTGGAATTTTTGG-AAGTTCGGGGGTAAAAATGTAATTTTTTGAGAAA-TTGGGGTCA
1 AAAATGGAA-TTTTGGAAAGTTTAGGGGT-AAAATGTAA--TTTTGGGAAAGTTGAGGTCA
* *
38740386 AAAATGGAATTTTGGAAAGTTTGAGGGGGAAAATGTAATTTTGGAGAAA-TTGAGGT-T
1 AAAATGGAATTTTGGAAAGTTT-AGGGGTAAAATGTAATTTTGG-GAAAGTTGAGGTCA
* *
38740443 AAAATAGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAGTT
1 AAAATGGAATTTTGGAAAGTTTAGGGGT-AAAATGTAATTTTGGGAAAGTT
38740494 TAGGGACCTT
Statistics
Matches: 190, Mismatches: 23, Indels: 28
0.79 0.10 0.12
Matches are distributed among these distances:
56 9 0.05
57 42 0.22
58 22 0.12
59 99 0.52
60 11 0.06
61 5 0.03
62 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (57 bp):
AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGTAATTTTGGGAAAGTTGAGGTCA
Found at i:38740307 original size:29 final size:29
Alignment explanation
Indices: 38740191--38740313 Score: 119
Period size: 29 Copynumber: 4.3 Consensus size: 29
38740181 AAAATAAGAC
*
38740191 TTTTTGGATA-CCAAGGGTAAAATGGTAA
1 TTTTTGGACATCCAAGGGTAAAATGGTAA
** *
38740219 -TTTTGGACATTTAGGGGTAAAATGGTAA
1 TTTTTGGACATCCAAGGGTAAAATGGTAA
* * * *
38740247 TTTTGGGAAAGTTC-GGGGTCAAAAATGG-AA
1 TTTTTGGACA-TCCAAGGGT--AAAATGGTAA
38740277 TTTTTGGACATCCAAGGGTAAAATGGTAA
1 TTTTTGGACATCCAAGGGTAAAATGGTAA
38740306 TTTTTGGA
1 TTTTTGGA
38740314 AGTTTTGAGG
Statistics
Matches: 77, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
27 8 0.10
28 22 0.29
29 24 0.31
30 16 0.21
31 7 0.09
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.33
Consensus pattern (29 bp):
TTTTTGGACATCCAAGGGTAAAATGGTAA
Found at i:38740490 original size:30 final size:30
Alignment explanation
Indices: 38740205--38740498 Score: 185
Period size: 29 Copynumber: 10.1 Consensus size: 30
38740195 TGGATACCAA
*
38740205 GGGT-AAAATGGTAA-TTTTGGACA-TTTAG
1 GGGTAAAAAT-GTAATTTTTGGAAAGTTTAG
* *
38740233 GGGT-AAAATGGTAATTTTGGGAAAG-TTCG
1 GGGTAAAAAT-GTAATTTTTGGAAAGTTTAG
* * ** *
38740262 GGGTCAAAAATGGAATTTTTGGACA-TCCAA
1 GGGT-AAAAATGTAATTTTTGGAAAGTTTAG
*
38740292 GGGT-AAAATGGTAATTTTTGG-AAGTTTTG
1 GGGTAAAAAT-GTAATTTTTGGAAAGTTTAG
* * * **
38740321 AGGTCAAAATTGGAATTTTTGG-AAGTTCGG
1 GGGT-AAAAATGTAATTTTTGGAAAGTTTAG
38740351 GGGTAAAAATGTAATTTTTTGAGAAA--TT-G
1 GGGTAAAAATGTAA-TTTTTG-GAAAGTTTAG
*
38740380 GGGTCAAAAATGGAA-TTTTGGAAAGTTTGAG
1 GGGT-AAAAATGTAATTTTTGGAAAGTTT-AG
* *
38740411 GGG-GAAAATGTAA-TTTTGGAGAA-ATT-G
1 GGGTAAAAATGTAATTTTTGGA-AAGTTTAG
* *
38740438 AGGTTAAAATAG-AA-TTTTGGAAAGTTTAG
1 GGGTAAAAAT-GTAATTTTTGGAAAGTTTAG
38740467 GGGTAAAAATGTAATTTTTGGAAAGTTTAG
1 GGGTAAAAATGTAATTTTTGGAAAGTTTAG
38740497 GG
1 GG
38740499 ACCTTTAGGG
Statistics
Matches: 208, Mismatches: 34, Indels: 46
0.72 0.12 0.16
Matches are distributed among these distances:
27 9 0.04
28 42 0.20
29 72 0.35
30 69 0.33
31 14 0.07
32 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.33
Consensus pattern (30 bp):
GGGTAAAAATGTAATTTTTGGAAAGTTTAG
Found at i:38740891 original size:11 final size:11
Alignment explanation
Indices: 38740875--38740905 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
38740865 TTGAGGCGGG
38740875 TCGGGTCGGAT
1 TCGGGTCGGAT
38740886 TCGGGTCGGAT
1 TCGGGTCGGAT
38740897 TCGGGTCGG
1 TCGGGTCGG
38740906 CCATGGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.06, C:0.19, G:0.48, T:0.26
Consensus pattern (11 bp):
TCGGGTCGGAT
Found at i:38741443 original size:17 final size:17
Alignment explanation
Indices: 38741403--38741508 Score: 115
Period size: 17 Copynumber: 6.2 Consensus size: 17
38741393 TATAATAAGT
38741403 TTTAAATTTAAATATAAA
1 TTTAAATTTAAA-ATAAA
* * *
38741421 TCTAAATTTATATTAAA
1 TTTAAATTTAAAATAAA
*
38741438 TTTAAACTTT-AAACAAA
1 TTTAAA-TTTAAAATAAA
38741455 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
38741472 TTTATATTCAAAATAAA
1 TTTAAATTTAAAATAAA
**
38741489 TTTAACCTTAAAATAAA
1 TTTAAATTTAAAATAAA
38741506 TTT
1 TTT
38741509 TAAAATGAGT
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
16 3 0.04
17 56 0.78
18 13 0.18
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:38741468 original size:7 final size:6
Alignment explanation
Indices: 38741403--38741493 Score: 66
Period size: 6 Copynumber: 15.8 Consensus size: 6
38741393 TATAATAAGT
* * *
38741403 TTTAAA TTTAAA TATAAA TCTAAA TTTATA -TTAAA TTTAAA CTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
* * * * *
38741451 --CAAA TTTAAA TTTAAA -ATAAA TTTATA TTCAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
38741494 CCTTAAAATA
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
4 3 0.05
5 11 0.17
6 44 0.69
7 6 0.09
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:38742518 original size:209 final size:209
Alignment explanation
Indices: 38742041--38743469 Score: 1945
Period size: 209 Copynumber: 6.9 Consensus size: 209
38742031 ATTTGGTTTT
* * * *
38742041 CTTCT-TAGTATCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATTTCATTAGGAAGCTAA
1 CTTCTCTA-TATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAA
* * * * *
38742105 CCATTTTATTGCTTCGACCTGCTTCTTAGTATCTCACCAGAAAACTGGGGTTCAAAGATTTGCTC
65 CCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
* * * *
38742170 GCATTGAGCC-----TC---GAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTC
130 ACTTTGAGCCTTGTTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTC
38742227 ACTTGTTTCAA-TCG
195 ACTTGTTTCAATTCG
* * * * *
38742241 CTTCTCTGTATCTCATCAGAAAGACGAATTTGGTCTACCTCTCAGTATCGCATCAGGAAGTTAAC
1 CTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAAC
* * **
38742306 CATTTTATTGCTTTGACCAGCTTCTCAGTATCTCATCAGGAATTTGGGGTTCGAAGATTTGCTCA
66 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* * * * *
38742371 CTTTGAGCCTTGTTTCATTGATTTGATCTACTTTTCTGTAGCTCATCAGGAAGATTATCGCCTCA
131 CTTTGAGCCTTGTTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCA
38742436 CTTGTTTCAATTCG
196 CTTGTTTCAATTCG
* * * *
38742450 CTTCTCTATGTCTCATTAGGAAGACGAATTTGGTCCACCTCTCAGTATCTAATCAGAAAGCTAAC
1 CTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAAC
* * * *
38742515 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGAGGTTTGAAGATTTACTCA
66 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* * * * * * * * *
38742580 CATTGAGCGTAG-GT--TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCT
131 CTTTGAGCCTTGTTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCA
*
38742642 CTTGTTTCAATCCG
196 CTTGTTTCAATTCG
* *
38742656 CTTCCCTATATCTCATTAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAAC
1 CTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAAC
* * * * *
38742721 CATTTTATTGCTTCGACCCGCTTCTCAATATCTCATCAAGAATCCGGGGTTCGAAGATTTGCTCA
66 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* * * *
38742786 ATTTGAGCCTTGTTTCATTGATTTGATTTACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCA
131 CTTTGAGCCTTGTTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCA
38742851 CTTGTTTCAATTCG
196 CTTGTTTCAATTCG
* * *
38742865 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACCTCTTAGTATCTCATGAGGAAGCTAAC
1 CTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAAC
38742930 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
66 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* * * ** * ** *** *
38742995 CATCGAG-CGTGGGT--TTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACCATATCG
131 CTTTGAGCCTTGTTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCA
*
38743057 CTTGTTTCAATCCG
196 CTTGTTTCAATTCG
* * *
38743071 CTTCCCTATATCTCATTAGGAAGACGAATTTGGTCCACCTCTTAGTATCTCATCAGGAAGCTAAC
1 CTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAAC
* * *
38743136 CATTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAAGAATCTGGGGTTCGAAGATTTGCTCA
66 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* * * * *
38743201 ATTTGAGCCTTATTTCATTGATTTGATTTACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCA
131 CTTTGAGCCTTGTTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCA
38743266 CTTGTTTCAATTCG
196 CTTGTTTCAATTCG
* * *
38743280 CTTCTTTGTATCTCATCAGGAAGACGAATTTGGTCCACCTCTTAGTATCTCATCAGGAAGCTAAC
1 CTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAAC
38743345 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
66 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* *
38743410 CTTTGAGCCTTGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCG
131 CTTTGAGCCTTGTTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCG
38743470 TGTCGCTGTT
Statistics
Matches: 1062, Mismatches: 151, Indels: 23
0.86 0.12 0.02
Matches are distributed among these distances:
200 118 0.11
201 1 0.00
205 2 0.00
206 354 0.33
207 4 0.00
208 54 0.05
209 529 0.50
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (209 bp):
CTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAAC
CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
CTTTGAGCCTTGTTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCA
CTTGTTTCAATTCG
Found at i:38742833 original size:415 final size:414
Alignment explanation
Indices: 38742048--38743468 Score: 2204
Period size: 415 Copynumber: 3.4 Consensus size: 414
38742038 TTTCTTCTTA
* * * *
38742048 GTATCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATTTCATTAGGAAGCTAACCATTTTA
1 GTATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAACCATTTTA
* * * * * *
38742113 TTGCTTCGACCTGCTTCTTAGTATCTCACCAGAAAACTGGGGTTCAAAGATTTGCTCGCATTGAG
66 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAG
* * * * * * *
38742178 C----CTCGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAAT
131 CGTGGTTTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAAT
* * * * * * *
38742239 -CGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTCTACCTCTCAGTATCGCATCAGGAAGTT
196 CCGCTTCCCTATATCTCATTAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCT
* * * *
38742303 AACCATTTTATTGCTTTGACCAGCTTCTCAGTATCTCATCAGGAATTTGGGGTTCGAAGATTTGC
261 AACCATTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAAGAATCTGGGGTTCGAAGATTTGC
* * * * *
38742368 TCACTTTGAGCCTTGTTTCATTGATTTGATCTACTTTTCTGTAGCTCATCAGGAAGATTATCGCC
326 TCAATTTGAGCCTTGTTTCATTGATTTGATTTACTTCTCTGTATCTCATCAGGAAGATGATCGCC
38742433 TCACTTGTTTCAATTCGCTTCTCT
391 TCACTTGTTTCAATTCGCTTCTCT
* * * * *
38742457 ATGTCTCATTAGGAAGACGAATTTGGTCCACCTCTCAGTATCTAATCAGAAAGCTAACCATTTTA
1 GTATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAACCATTTTA
* * * *
38742522 TTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGAGGTTTGAAGATTTACTCACATTGAG
66 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAG
* *
38742587 CGTAGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCTCTTGTTTCAA
131 CGT-GGTTTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAA
38742652 TCCGCTTCCCTATATCTCATTAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGC
195 TCCGCTTCCCTATATCTCATTAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGC
* *
38742717 TAACCATTTTATTGCTTCGACCCGCTTCTCAATATCTCATCAAGAATCCGGGGTTCGAAGATTTG
260 TAACCATTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAAGAATCTGGGGTTCGAAGATTTG
38742782 CTCAATTTGAGCCTTGTTTCATTGATTTGATTTACTTCTCTGTATCTCATCAGGAAGATGATCGC
325 CTCAATTTGAGCCTTGTTTCATTGATTTGATTTACTTCTCTGTATCTCATCAGGAAGATGATCGC
38742847 CTCACTTGTTTCAATTCGCTTCTCT
390 CTCACTTGTTTCAATTCGCTTCTCT
* *
38742872 GTATCTCATCAGGAAGACGAATTTGGTCCACCTCTTAGTATCTCATGAGGAAGCTAACCATTTTA
1 GTATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAACCATTTTA
*
38742937 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAG
66 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAG
* * * *
38743002 CGTGGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACCATATCGCTTGTTTCAA
131 CGT-GGTTTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAA
*
38743067 TCCGCTTCCCTATATCTCATTAGGAAGACGAATTTGGTCCACCTCTTAGTATCTCATCAGGAAGC
195 TCCGCTTCCCTATATCTCATTAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGC
38743132 TAACCATTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAAGAATCTGGGGTTCGAAGATTTG
260 TAACCATTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAAGAATCTGGGGTTCGAAGATTTG
*
38743197 CTCAATTTGAGCCTTATTTCATTGATTTGATTTACTTCTCTGTATCTCATCAGGAAGATGATCGC
325 CTCAATTTGAGCCTTGTTTCATTGATTTGATTTACTTCTCTGTATCTCATCAGGAAGATGATCGC
*
38743262 CTCACTTGTTTCAATTCGCTTCTTT
390 CTCACTTGTTTCAATTCGCTTCTCT
*
38743287 GTATCTCATCAGGAAGACGAATTTGGTCCACCTCTTAGTATCTCATCAGGAAGCTAACCATTTTA
1 GTATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAACCATTTTA
*
38743352 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAG
66 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAG
* * *
38743417 CCTTGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACC
131 -CGTG-GT--TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACC
38743469 GTGTCGCTGT
Statistics
Matches: 927, Mismatches: 75, Indels: 11
0.92 0.07 0.01
Matches are distributed among these distances:
409 112 0.12
414 51 0.06
415 722 0.78
416 3 0.00
418 39 0.04
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (414 bp):
GTATCTCATCAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCTAACCATTTTA
TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAG
CGTGGTTTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAAT
CCGCTTCCCTATATCTCATTAGGAAGACGAATTTGGTCCACCTCTCAGTATCTCATCAGGAAGCT
AACCATTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAAGAATCTGGGGTTCGAAGATTTGC
TCAATTTGAGCCTTGTTTCATTGATTTGATTTACTTCTCTGTATCTCATCAGGAAGATGATCGCC
TCACTTGTTTCAATTCGCTTCTCT
Found at i:38755113 original size:59 final size:58
Alignment explanation
Indices: 38755050--38755270 Score: 250
Period size: 59 Copynumber: 3.7 Consensus size: 58
38755040 TACCCGGGGC
* * *
38755050 AAAATGGTAATTTTGGACATTCAAGGGTAAAATGGTAATTTTGGGAAAG-TTCGAGGTCA
1 AAAATGG-AATTTTGGACATTCGAGGGTAAAATGGTAATTTT-TGAAAGTTTTGAGGTCA
* * * * *
38755109 AAAATGGAATTTTTGGACATCCGAGAGTAAAAAGGTAATTTTTGAAAGTTTTGGGGTTA
1 AAAATGGAA-TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTCA
* *
38755168 AAAATAGAATTTATGGACATTCGGGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTCA
1 AAAATGGAATTT-TGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTCA
**
38755227 AAAATGGAATTTTTGGATGTTCG-GGGATAAGAAT-GTAATTTTTG
1 AAAATGGAA-TTTTGGACATTCGAGGG-TAA-AATGGTAATTTTTG
38755271 GAAAAATCAA
Statistics
Matches: 138, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
58 13 0.09
59 119 0.86
60 6 0.04
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTCA
Found at i:38755148 original size:29 final size:28
Alignment explanation
Indices: 38755050--38755152 Score: 93
Period size: 29 Copynumber: 3.6 Consensus size: 28
38755040 TACCCGGGGC
* *
38755050 AAAATGGTAA-TTTTGGACATTCAAGGGT
1 AAAAAGGTAATTTTTGGACATTCGA-GGT
* * *
38755078 AAAATGGTAATTTTGGGAAAGTTCGAGGT
1 AAAAAGGTAATTTTTGGACA-TTCGAGGT
*
38755107 CAAAAATGG-AATTTTTGGACATCCGAGAGT
1 -AAAAA-GGTAATTTTTGGACATTCGAG-GT
38755137 AAAAAGGTAATTTTTG
1 AAAAAGGTAATTTTTG
38755153 AAAGTTTTGG
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
28 12 0.19
29 28 0.45
30 20 0.32
31 2 0.03
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (28 bp):
AAAAAGGTAATTTTTGGACATTCGAGGT
Found at i:38755179 original size:30 final size:30
Alignment explanation
Indices: 38755136--38755424 Score: 100
Period size: 30 Copynumber: 9.8 Consensus size: 30
38755126 CATCCGAGAG
38755136 TAAAAA-GGTAATTTTTGAAAGTTTTGGGGT
1 TAAAAATGG-AATTTTTGAAAGTTTTGGGGT
* * * * *
38755166 TAAAAATAGAATTTATGGACA--TTCGGGGG
1 TAAAAATGGAATTT-TTGAAAGTTTTGGGGT
*
38755195 T-AAAATGGTAATTTTTGAAAGTTTTGAGGT
1 TAAAAATGG-AATTTTTGAAAGTTTTGGGGT
* * * * *
38755225 CAAAAATGGAATTTTTGGATG-TTCGGGGA
1 TAAAAATGGAATTTTTGAAAGTTTTGGGGT
* * ** ***
38755254 TAAGAATGTAATTTTTGGAAA-AATCAAGGT
1 TAAAAATGGAATTTTT-GAAAGTTTTGGGGT
* * * * *
38755284 CAAAAATAGAA-TTTTAAAAG-TTTGAGTT
1 TAAAAATGGAATTTTTGAAAGTTTTGGGGT
* * *
38755312 TAAAAATGTAATTTTTGGAGAA--ATTAGGGT
1 TAAAAATGGAATTTTT-GA-AAGTTTTGGGGT
* * **
38755342 CAAAAATGGAATTTTAGAAAGTTTAAGGG-
1 TAAAAATGGAATTTTTGAAAGTTTTGGGGT
* * *
38755371 TAAAAATGTAATTTTTTGAGAA--ATCGGGGT
1 TAAAAATGGAA-TTTTTGA-AAGTTTTGGGGT
**
38755401 TAAAAATGGAATTTTAAAAAGTTT
1 TAAAAATGGAATTTTTGAAAGTTT
38755425 GAGGGGTAAA
Statistics
Matches: 182, Mismatches: 58, Indels: 38
0.65 0.21 0.14
Matches are distributed among these distances:
28 29 0.16
29 58 0.32
30 79 0.43
31 16 0.09
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (30 bp):
TAAAAATGGAATTTTTGAAAGTTTTGGGGT
Found at i:38755207 original size:29 final size:28
Alignment explanation
Indices: 38755045--38755209 Score: 102
Period size: 28 Copynumber: 5.7 Consensus size: 28
38755035 TTGAATACCC
* *
38755045 GGGGCAAAATGGTAATTTTGGACATTCA
1 GGGGTAAAATGGTAATTTTGGACATTCG
* *
38755073 AGGGTAAAATGGTAATTTTGGGAAAGTTC-
1 GGGGTAAAATGGTAATTTT-GGACA-TTCG
* *
38755102 GAGGTCAAAAATGG-AATTTTTGGACATCCG
1 GGGGT--AAAATGGTAA-TTTTGGACATTCG
* * * * * *
38755132 AGAGTAAAAAGGTAATTTTTGAAAGTTTTG
1 GGGGTAAAATGGTAATTTTGGACA--TTCG
* *
38755162 GGGTTAAAAATAG-AATTTATGGACATTCG
1 GGGGT-AAAATGGTAATTT-TGGACATTCG
38755191 GGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
38755210 TGAAAGTTTT
Statistics
Matches: 100, Mismatches: 25, Indels: 24
0.67 0.17 0.16
Matches are distributed among these distances:
28 37 0.37
29 23 0.23
30 20 0.20
31 20 0.20
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTGGACATTCG
Found at i:38755289 original size:118 final size:117
Alignment explanation
Indices: 38755058--38755298 Score: 281
Period size: 118 Copynumber: 2.1 Consensus size: 117
38755048 GCAAAATGGT
38755058 AATTTTGGACATTCAAGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAATGGAATTTTT
1 AATTTTGGACATTCAAGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAATGGAATTTTT
** *** *
38755123 GGACATCCGAGAGTAAAAAGGTAATTTTTGAAAGTTTTGGGGTTAAAAATAG
66 GGACATCCGAGAGTAAAAAGGTAATTTTTGAAAGAATCAAGGTCAAAAATAG
** * *
38755175 AATTTATGGACATTCGGGGGTAAAATGGTAATTTT-TGAAAGTTTTGAGGTCAAAAATGGAATTT
1 AATTT-TGGACATTCAAGGGTAAAATGGTAATTTTGGGAAAG-TTCGAGGTCAAAAATGGAATTT
** * * * *
38755239 TTGGATGTTCG-GGGATAAGAATGTAATTTTTGGAAA-AATCAAGGTCAAAAATAG
64 TTGGACATCCGAGAG-TAAAAAGGTAATTTTT-GAAAGAATCAAGGTCAAAAATAG
38755293 AATTTT
1 AATTTT
38755299 AAAAGTTTGA
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
117 13 0.12
118 87 0.84
119 4 0.04
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (117 bp):
AATTTTGGACATTCAAGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAATGGAATTTTT
GGACATCCGAGAGTAAAAAGGTAATTTTTGAAAGAATCAAGGTCAAAAATAG
Found at i:38755346 original size:29 final size:30
Alignment explanation
Indices: 38755313--38755394 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 30
38755303 GTTTGAGTTT
*
38755313 AAAAATGTAATTTTTGGAGAAATT-AGGGTC
1 AAAAATGTAATTTTT-GAGAAATTAAGGGTA
*
38755343 AAAAATGGAA-TTTT-AGAAAGTTTAAGGGT-
1 AAAAATGTAATTTTTGAGAAA--TTAAGGGTA
38755372 AAAAATGTAATTTTTTGAGAAAT
1 AAAAATGTAA-TTTTTGAGAAAT
38755395 CGGGGTTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
27 5 0.11
29 15 0.34
30 15 0.34
31 4 0.09
32 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.21, T:0.34
Consensus pattern (30 bp):
AAAAATGTAATTTTTGAGAAATTAAGGGTA
Found at i:38755444 original size:59 final size:59
Alignment explanation
Indices: 38755222--38755436 Score: 245
Period size: 59 Copynumber: 3.6 Consensus size: 59
38755212 AAAGTTTTGA
*** * * * * *
38755222 GGTCAAAAATGGAATTTTTGGATGTTCG-GGGATAAGAATGTAATTTTTGGAAAAATCAA
1 GGTCAAAAATGGAATTTTAAAAAGTTTGAGGG-TAAAAATGTAATTTTTGGAGAAATCAG
* ** *
38755281 GGTCAAAAATAGAATTTT-AAAAGTTTGAGTTTAAAAATGTAATTTTTGGAGAAATTAG
1 GGTCAAAAATGGAATTTTAAAAAGTTTGAGGGTAAAAATGTAATTTTTGGAGAAATCAG
* * * *
38755339 GGTCAAAAATGGAATTTTAGAAAGTTTAAGGGTAAAAATGTAATTTTTTGAGAAATCGG
1 GGTCAAAAATGGAATTTTAAAAAGTTTGAGGGTAAAAATGTAATTTTTGGAGAAATCAG
*
38755398 GGTTAAAAATGGAATTTTAAAAAGTTTGAGGGGTAAAAA
1 GGTCAAAAATGGAATTTTAAAAAGTTTGA-GGGTAAAAA
38755437 AGCATTTTAC
Statistics
Matches: 131, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
58 45 0.34
59 77 0.59
60 9 0.07
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (59 bp):
GGTCAAAAATGGAATTTTAAAAAGTTTGAGGGTAAAAATGTAATTTTTGGAGAAATCAG
Found at i:38757103 original size:17 final size:17
Alignment explanation
Indices: 38757063--38757167 Score: 113
Period size: 17 Copynumber: 6.2 Consensus size: 17
38757053 TATAATAAGT
38757063 TTTAAATTTAAATATAAA
1 TTTAAATTTAAA-ATAAA
* * *
38757081 TCTAAATTTATATTAAA
1 TTTAAATTTAAAATAAA
* *
38757098 TTTAAATTTTAAACAAA
1 TTTAAATTTAAAATAAA
38757115 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
38757132 TTTATATTCAAAATAAA
1 TTTAAATTTAAAATAAA
**
38757149 TTTAACCTT-AAATAAA
1 TTTAAATTTAAAATAAA
38757165 TTT
1 TTT
38757168 TAAAATGAGT
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
16 10 0.14
17 51 0.72
18 10 0.14
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:38757110 original size:7 final size:6
Alignment explanation
Indices: 38757063--38757153 Score: 66
Period size: 6 Copynumber: 15.8 Consensus size: 6
38757053 TATAATAAGT
* * *
38757063 TTTAAA TTTAAA TATAAA TCTAAA TTTATA -TTAAA TTTAAA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
* * * * *
38757111 --CAAA TTTAAA TTTAAA -ATAAA TTTATA TTCAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
38757154 CCTTAAATAA
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
4 3 0.05
5 11 0.17
6 44 0.69
7 6 0.09
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:38763413 original size:28 final size:28
Alignment explanation
Indices: 38763382--38763442 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
38763372 AAAATGAGAC
*
38763382 TTTGGATACTCGGGGGCAAAATGGTAAT
1 TTTGGATACTCGAGGGCAAAATGGTAAT
* * * *
38763410 TTTGAATTCTCGAGGGCACAGTGGTAAT
1 TTTGGATACTCGAGGGCAAAATGGTAAT
38763438 TTTGG
1 TTTGG
38763443 GAAATTTGGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.11, G:0.31, T:0.33
Consensus pattern (28 bp):
TTTGGATACTCGAGGGCAAAATGGTAAT
Found at i:38763685 original size:30 final size:30
Alignment explanation
Indices: 38763635--38763726 Score: 100
Period size: 29 Copynumber: 3.1 Consensus size: 30
38763625 TGGATATCGT
* * *
38763635 AAAAAATAAATTTTT-AAAATTT-CGGGATC
1 AAAAAAGAAATTTTTGGAAATTTAAGGG-TC
*
38763664 AAAAAAGGAATTTTTGGAAATTTAAGGGTC
1 AAAAAAGAAATTTTTGGAAATTTAAGGGTC
* *
38763694 AAAAATGAAATTTTTGG-AAGTTAAGGGTC
1 AAAAAAGAAATTTTTGGAAATTTAAGGGTC
38763723 AAAA
1 AAAA
38763727 TGGAATTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.52
30 23 0.43
31 3 0.06
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.30
Consensus pattern (30 bp):
AAAAAAGAAATTTTTGGAAATTTAAGGGTC
Found at i:38763697 original size:29 final size:28
Alignment explanation
Indices: 38763665--38763747 Score: 107
Period size: 29 Copynumber: 3.0 Consensus size: 28
38763655 TTCGGGATCA
*
38763665 AAAAAGGAATTTTTGGAAATTTAAGGGTC
1 AAAAAGGAATTTTTGG-AAGTTAAGGGTC
*
38763694 AAAAATGAAATTTTTGGAAGTTAAGGGTC
1 AAAAA-GGAATTTTTGGAAGTTAAGGGTC
*
38763723 AAAATGGAATTTTT--AAGTTAAGGGT
1 AAAAAGGAATTTTTGGAAGTTAAGGGT
38763748 AATTTTTAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 11 0.22
28 8 0.16
29 20 0.41
30 10 0.20
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (28 bp):
AAAAAGGAATTTTTGGAAGTTAAGGGTC
Found at i:38763747 original size:26 final size:28
Alignment explanation
Indices: 38763636--38763747 Score: 95
Period size: 28 Copynumber: 4.0 Consensus size: 28
38763626 GGATATCGTA
* * **
38763636 AAAAAT-AAATTTTTAAAATTTCGGGATC
1 AAAAATGAAATTTTTGAAGTTAAGGG-TC
* * *
38763664 AAAAAAGGAATTTTTGGAAATTTAAGGGTC
1 AAAAATGAAATTTTT-G-AAGTTAAGGGTC
38763694 AAAAATGAAATTTTTGGAAGTTAAGGGTC
1 AAAAATGAAATTTTT-GAAGTTAAGGGTC
*
38763723 -AAAATGGAATTTTT-AAGTTAAGGGT
1 AAAAATGAAATTTTTGAAGTTAAGGGT
38763748 AATTTTTAGA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
26 11 0.15
28 18 0.25
29 18 0.25
30 17 0.24
31 7 0.10
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.33
Consensus pattern (28 bp):
AAAAATGAAATTTTTGAAGTTAAGGGTC
Found at i:38763788 original size:29 final size:29
Alignment explanation
Indices: 38763747--38763963 Score: 138
Period size: 29 Copynumber: 7.6 Consensus size: 29
38763737 AAGTTAAGGG
* *
38763747 TAATTTTTAGAAGTTTTGGGGTCAAAAATT
1 TAATTTTTGGAAGTTTTGGGGT-AAAAATA
* *
38763777 TAA-TTTTGGAAG-TTTAGGGTAAAAGTA
1 TAATTTTTGGAAGTTTTGGGGTAAAAATA
* * *
38763804 TAA-TTTTGGAAGTTTCGAGGTTAAAATA
1 TAATTTTTGGAAGTTTTGGGGTAAAAATA
* * * *
38763832 CAATTTTTGAAAGTTTAGGGGTAAAAATG
1 TAATTTTTGGAAGTTTTGGGGTAAAAATA
* * * *
38763861 TAATTTTTAGAAG-TTTAGGGTTAAAATG
1 TAATTTTTGGAAGTTTTGGGGTAAAAATA
** * * *
38763889 T-ATTTTTCAAAAGTTTTAGGGTTAAAACA
1 TAATTTTT-GGAAGTTTTGGGGTAAAAATA
* * * * *
38763918 TAATTTTTAGAAGTTTCGAGGTCAAAATG
1 TAATTTTTGGAAGTTTTGGGGTAAAAATA
*
38763947 TAATTTTTTTGAAGTTT
1 TAA-TTTTTGGAAGTTT
38763964 CTAGAAGTTC
Statistics
Matches: 149, Mismatches: 32, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
27 23 0.15
28 36 0.24
29 69 0.46
30 21 0.14
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.41
Consensus pattern (29 bp):
TAATTTTTGGAAGTTTTGGGGTAAAAATA
Found at i:38763810 original size:57 final size:55
Alignment explanation
Indices: 38763747--38763953 Score: 202
Period size: 57 Copynumber: 3.7 Consensus size: 55
38763737 AAGTTAAGGG
* * * * *
38763747 TAATTTTTAGAAGTTTTGGGGTCAAAAATTTAATTTTGGAAGTTTAGGGTAAAAGTA
1 TAATTTTTAGAAGTTTCGAGGT-TAAAATGTAATTTTGAAAGTTTAGGGTAAAA-TA
* ** *
38763804 TAA-TTTTGGAAGTTTCGAGGTTAAAATACAATTTTTGAAAGTTTAGGGGTAAAAATG
1 TAATTTTTAGAAGTTTCGAGGTTAAAATGTAA-TTTTGAAAGTTTA-GGGT-AAAATA
* * * *
38763861 TAATTTTTAGAAGTTTAG-GGTTAAAATGTATTTTTCAAAAGTTTTAGGGTTAAAACA
1 TAATTTTTAGAAGTTTCGAGGTTAAAATGTAATTTT-GAAAG-TTTAGGG-TAAAATA
*
38763918 TAATTTTTAGAAGTTTCGAGGTCAAAATGTAATTTT
1 TAATTTTTAGAAGTTTCGAGGTTAAAATGTAATTTT
38763954 TTTGAAGTTT
Statistics
Matches: 123, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
55 7 0.06
56 31 0.25
57 49 0.40
58 36 0.29
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.41
Consensus pattern (55 bp):
TAATTTTTAGAAGTTTCGAGGTTAAAATGTAATTTTGAAAGTTTAGGGTAAAATA
Found at i:38763924 original size:86 final size:84
Alignment explanation
Indices: 38763747--38763963 Score: 226
Period size: 86 Copynumber: 2.5 Consensus size: 84
38763737 AAGTTAAGGG
* * *
38763747 TAATTTTTAGAAGTTTTGGGGTCAAAAATTTAA-TTTTGGAAGTTTAGGGTAAAAGTATAATTTT
1 TAATTTTTAGAAGTTTAGGGGT-AAAAATGTAATTTTTAGAAGTTTAGGGTAAAAGTAT-ATTTT
** * *
38763811 GGAAGTTTCGAGGTTAAAATA
64 AAAAGTTTAGAGGTTAAAACA
*
38763832 CAATTTTT-GAAAGTTTAGGGGTAAAAATGTAATTTTTAGAAGTTTAGGGTTAAAATGTAT-TTT
1 TAATTTTTAG-AAGTTTAGGGGTAAAAATGTAATTTTTAGAAGTTTAGGG-TAAAA-GTATATTT
38763895 TCAAAAGTTTTAG-GGTTAAAACA
63 T-AAAAG-TTTAGAGGTTAAAACA
* * * *
38763918 TAATTTTTAGAAGTTTCGAGGTCAAAATGTAATTTTTTTGAAGTTT
1 TAATTTTTAGAAGTTTAGGGGTAAAAATGTAA-TTTTTAGAAGTTT
38763964 CTAGAAGTTC
Statistics
Matches: 111, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
84 10 0.09
85 37 0.33
86 43 0.39
87 21 0.19
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.41
Consensus pattern (84 bp):
TAATTTTTAGAAGTTTAGGGGTAAAAATGTAATTTTTAGAAGTTTAGGGTAAAAGTATATTTTAA
AAGTTTAGAGGTTAAAACA
Found at i:38764303 original size:32 final size:33
Alignment explanation
Indices: 38764253--38764323 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
38764243 AATTATTGGG
* *
38764253 CCAAATTAAAATTAATT-AAAAGTATGAAAAGGA
1 CCAAATTAAAATTAATTAAAAAATACG-AAAGGA
*
38764286 CCAAATTGAAA-TAATTAAAAAATACGAAAGGA
1 CCAAATTAAAATTAATTAAAAAATACGAAAGGA
38764318 CCAAAT
1 CCAAAT
38764324 GCATAAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 17 0.50
33 17 0.50
ACGTcount: A:0.58, C:0.10, G:0.11, T:0.21
Consensus pattern (33 bp):
CCAAATTAAAATTAATTAAAAAATACGAAAGGA
Found at i:38765969 original size:19 final size:17
Alignment explanation
Indices: 38765945--38765991 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 17
38765935 CAAATTTAAT
38765945 TAAATTTAAATTAAAAAGA
1 TAAATTTAAATT-AAAA-A
*
38765964 TAAATTTAAATTTAAAA
1 TAAATTTAAATTAAAAA
38765981 TAAATTTAAAT
1 TAAATTTAAAT
38765992 CAATTTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 12 0.44
18 3 0.11
19 12 0.44
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTAAAAA
Found at i:38766435 original size:92 final size:92
Alignment explanation
Indices: 38766277--38766970 Score: 1129
Period size: 92 Copynumber: 7.5 Consensus size: 92
38766267 GATGTCGAGG
* *
38766277 CTTCATCTTGCTCTTACTACAACTTCAGAGAGAGATAAAGACTTGTTATCCAACTTTACTGCAAC
1 CTTCATCTTGCTCTTACTACAACTTC--AGAGAGATAAAGACTTGCTATCCAACTTTACTACAAC
* * *
38766342 TTCAAGAGGAAAAGAATTGATGTTTGAAG
64 TTCAAGAGGATAGGAATTGATGTTTGAAA
*
38766371 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAAATTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
* * * * * *
38766436 CAAGAGAATTGGGATTAACGTTTGAAG
66 CAAGAGGATAGGAATTGATGTTTGAAA
* *
38766463 CTTCATCTTACTCTTACTACAACTTCAGAGAGAT-AAGACTTGCTATCCAACTTCACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
*
38766527 CAAGAGGATAGGAATTGATGTTTGAAG
66 CAAGAGGATAGGAATTGATGTTTGAAA
38766554 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
*
38766619 CAAGAGGATAGGTATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
* *
38766646 CTTCATCTTGCTATTACTACAACTTCAGAGAGATAAAGACTTGCTATCCCACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
* *
38766711 CAAGAGGATAGGGATGGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
38766738 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
38766803 CAAGAGGATAGGAATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
* * *
38766830 ATTCATCTTACTCTTACTAGAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
*
38766895 CAAGAGGATAGGGATTGATGTTTGAAA
66 CAAGAGGATAGGAATTGATGTTTGAAA
38766922 CTTCATCTTGCTCTTACTACAACTTCAGAGAAAGATAAAGACTTGCTAT
1 CTTCATCTTGCTCTTACTACAACTTCAGAG--AGATAAAGACTTGCTAT
38766971 TTTGATCTGA
Statistics
Matches: 560, Mismatches: 37, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
91 83 0.15
92 434 0.77
94 43 0.08
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (92 bp):
CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTT
CAAGAGGATAGGAATTGATGTTTGAAA
Found at i:38766901 original size:276 final size:275
Alignment explanation
Indices: 38766278--38766970 Score: 1143
Period size: 275 Copynumber: 2.5 Consensus size: 275
38766268 ATGTCGAGGC
* *
38766278 TTCATCTTGCTCTTACTACAACTTCAGAGAGAGATAAAGACTTGTTATCCAACTTTACTGCAACT
1 TTCATCTTGCTCTTACTACAACTTC--AGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* * *
38766343 TCAAGAGGAAAAGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAA
64 TCAAGAGGATAGGAATTGATGTTTGAAACTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAA
* * *
38766408 GACTTGCTATCCAAATTTACTACAACTTCAAGAGAATTGGGATTAACGTTTGAAGCTTCATCTTA
129 GACTTGCTATCCAAATTTACTACAACTTCAAGAGAATAGGGATGAACGTTTGAAACTTCATCTTA
38766473 CTCTTACTACAACTTCAGAGAGATAAGACTTGCTATCCAACTTCACTACAACTTCAAGAGGATAG
194 CTCTTACTACAACTTCAGAGAGATAAGACTTGCTATCCAACTTCACTACAACTTCAAGAGGATAG
**
38766538 GAATTGATGTTTGAAGC
259 GAATTGATGTTTGAAAA
38766555 TTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
1 TTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
* *
38766620 AAGAGGATAGGTATTGATGTTTGAAACTTCATCTTGCTATTACTACAACTTCAGAGAGATAAAGA
66 AAGAGGATAGGAATTGATGTTTGAAACTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGA
* * * * * *
38766685 CTTGCTATCCCACTTTACTACAACTTCAAGAGGATAGGGATGGATGTTTGAAACTTCATCTTGCT
131 CTTGCTATCCAAATTTACTACAACTTCAAGAGAATAGGGATGAACGTTTGAAACTTCATCTTACT
*
38766750 CTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGG
196 CTTACTACAACTTCAGAGAGAT-AAGACTTGCTATCCAACTTCACTACAACTTCAAGAGGATAGG
38766815 AATTGATGTTTGAAAA
260 AATTGATGTTTGAAAA
* *
38766831 TTCATCTTACTCTTACTAGAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
1 TTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
*
38766896 AAGAGGATAGGGATTGATGTTTGAAACTTCATCTTGCTCTTACTACAACTTCAGAGAAAGATAAA
66 AAGAGGATAGGAATTGATGTTTGAAACTTCATCTTGCTCTTACTACAACTTCAGAG--AGATAAA
38766961 GACTTGCTAT
129 GACTTGCTAT
38766971 TTTGATCTGA
Statistics
Matches: 390, Mismatches: 23, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
275 176 0.45
276 172 0.44
277 25 0.06
278 17 0.04
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (275 bp):
TTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTC
AAGAGGATAGGAATTGATGTTTGAAACTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGA
CTTGCTATCCAAATTTACTACAACTTCAAGAGAATAGGGATGAACGTTTGAAACTTCATCTTACT
CTTACTACAACTTCAGAGAGATAAGACTTGCTATCCAACTTCACTACAACTTCAAGAGGATAGGA
ATTGATGTTTGAAAA
Found at i:38777865 original size:28 final size:29
Alignment explanation
Indices: 38777834--38777895 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
38777824 AAAATGAGAC
38777834 TTTGGA-TACTCG-GGGGCAAAATGATAAT
1 TTTGGACT-CTCGAGGGGCAAAATGATAAT
* *
38777862 TTTGGACTCTCGAGGGGCACAATGGTAAT
1 TTTGGACTCTCGAGGGGCAAAATGATAAT
38777891 TTTGG
1 TTTGG
38777896 GAAATTTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 10 0.33
29 20 0.67
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.31
Consensus pattern (29 bp):
TTTGGACTCTCGAGGGGCAAAATGATAAT
Found at i:38777979 original size:30 final size:28
Alignment explanation
Indices: 38777906--38777981 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 28
38777896 GAAATTTGAG
*
38777906 GTTAAAAATGAAA-TTTTAGAAATTCAA
1 GTTAAAAATGAAATTTTTAGAAAATCAA
*** *
38777933 GGGCAAAATGGTAATTTTTAGAAAAATCAA
1 GTTAAAAAT-GAAATTTTTAG-AAAATCAA
38777963 GATTAAAAATGAAATTTTT
1 G-TTAAAAATGAAATTTTT
38777982 GGACATTTGG
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
27 6 0.17
28 3 0.08
29 6 0.17
30 16 0.44
31 5 0.14
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (28 bp):
GTTAAAAATGAAATTTTTAGAAAATCAA
Found at i:38778007 original size:29 final size:29
Alignment explanation
Indices: 38777975--38778068 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
38777965 TTAAAAATGA
38777975 AATTTTTGGACATTTGGGGGTAAAATGGT
1 AATTTTTGGACATTTGGGGGTAAAATGGT
** * ** *** *
38778004 AATTTTAAGAAAAATCCAGATAAAAATGG-
1 AATTTTTGGACATTTGGGGGT-AAAATGGT
*
38778033 AATTTTTGGACATTCGGGGGTAAAATGGT
1 AATTTTTGGACATTTGGGGGTAAAATGGT
*
38778062 AAATTTT
1 AATTTTT
38778069 AGAAAAATCA
Statistics
Matches: 43, Mismatches: 20, Indels: 4
0.64 0.30 0.06
Matches are distributed among these distances:
28 7 0.16
29 29 0.67
30 7 0.16
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.34
Consensus pattern (29 bp):
AATTTTTGGACATTTGGGGGTAAAATGGT
Found at i:38778017 original size:59 final size:58
Alignment explanation
Indices: 38777907--38778089 Score: 244
Period size: 58 Copynumber: 3.1 Consensus size: 58
38777897 AAATTTGAGG
* * ** *
38777907 TTAAAAATGAAA-TTTTAGAAATTCAAGGGCAAAATGGTAATTTTTAGAAAAATCAAGA
1 TTAAAAATGAAATTTTTGGACATTCGGGGGTAAAATGGTAA-TTTTAGAAAAATCAAGA
* *
38777965 TTAAAAATGAAATTTTTGGACATTTGGGGGTAAAATGGTAATTTTAAGAAAAATCCAGA
1 TTAAAAATGAAATTTTTGGACATTCGGGGGTAAAATGGTAATTTT-AGAAAAATCAAGA
*
38778024 -TAAAAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAAATTTTAGAAAAATCAAGA
1 TTAAAAATGAAATTTTTGGACATTCGGGGGTAAAATGGT-AATTTTAGAAAAATCAAGA
*
38778082 TAAAAAAT
1 TTAAAAAT
38778090 AAAAATGGAA
Statistics
Matches: 110, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
58 64 0.58
59 46 0.42
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (58 bp):
TTAAAAATGAAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTAGAAAAATCAAGA
Found at i:38778188 original size:29 final size:29
Alignment explanation
Indices: 38778114--38778493 Score: 252
Period size: 29 Copynumber: 12.9 Consensus size: 29
38778104 AGATATTCGA
* * *
38778114 GGGT-AAAATGATAATTTTCGAAAGTTTCG
1 GGGTAAAAATG-TAATTTTTGGAAGTTTAG
* * *
38778143 GGATCAAAAATGAAATTTTTGGAATTTTAG
1 GGGT-AAAAATGTAATTTTTGGAAGTTTAG
* *
38778173 GGGTAAAAACT-TAATTTTTGGAAATTTAA
1 GGGTAAAAA-TGTAATTTTTGGAAGTTTAG
* * *
38778202 GGGTCAAAAATGGAATGTTTGGAAGTTCAG
1 GGGT-AAAAATGTAATTTTTGGAAGTTTAG
* ** *
38778232 GGGTAAAAATGAAATTTTTACAAGTTTCG
1 GGGTAAAAATGTAATTTTTGGAAGTTTAG
* *
38778261 GGGTCAAAAATGGAATTTTTGAAAGTTTAG
1 GGGT-AAAAATGTAATTTTTGGAAGTTTAG
**
38778291 GGGTAAAAACATAATTTTTGGAAGTTTTA-
1 GGGTAAAAATGTAATTTTTGGAAG-TTTAG
* * * *
38778320 GGGTTAAAATGCAATTTTTGAAAG-TTCG
1 GGGTAAAAATGTAATTTTTGGAAGTTTAG
**
38778348 AGGGTAAAAACATAATTTTTGGAAGTTTCA-
1 -GGGTAAAAATGTAATTTTTGGAAGTTT-AG
* * * *
38778378 AGGTCAAGATGTAATTTTTTAGAAGTTTTA-
1 GGGTAAAAATGTAA-TTTTTGGAAG-TTTAG
* * *
38778408 AGGTTAAAATGTAATTTTTAGAAGTTTCA-
1 GGGTAAAAATGTAATTTTTGGAAGTTT-AG
* * * *
38778437 AGGTTAAAATGTAATTTTTTAGAAGTTTTG
1 GGGTAAAAATGTAA-TTTTTGGAAGTTTAG
* *
38778467 GGGTCAAAATGTAATTTTGGAGAAGTT
1 GGGTAAAAATGTAATTTTTG-GAAGTT
38778494 CGAGGGTCAA
Statistics
Matches: 280, Mismatches: 54, Indels: 33
0.76 0.15 0.09
Matches are distributed among these distances:
27 2 0.01
28 3 0.01
29 143 0.51
30 123 0.44
31 9 0.03
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTAG
Found at i:38778188 original size:59 final size:57
Alignment explanation
Indices: 38778125--38778376 Score: 215
Period size: 59 Copynumber: 4.3 Consensus size: 57
38778115 GGTAAAATGA
* *
38778125 TAATTTTCGAAAGTTTCGGGATCAAAAATGAAATTTTTGGAATTTTAGGGGTAAAAACT
1 TAATTTT-GAAAGTTTCGGG-TCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAACT
* * *
38778184 TAATTTTTGGAAA-TTTAAGGGTCAAAAATGGAATGTTTGGAAGTTCAGGGGTAAAAA-T
1 TAA-TTTT-GAAAGTTT-CGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAACT
* * * *
38778242 GAAATTTTTACAAGTTTCGGGGTCAAAAATGGAATTTTTGAAAGTTTAGGGGTAAAAACA
1 -TAATTTTGA-AAGTTTC-GGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAACT
* * * * * * *
38778302 TAATTTTTGGAAGTTTTAGGGT-TAAAATGCAATTTTTGAAAG-TTCGAGGGTAAAAACA
1 TAA-TTTTGAAAG-TTTCGGGTCAAAAATGGAATTTTTGGAAGTTTAG-GGGTAAAAACT
*
38778360 TAATTTTTGGAAGTTTC
1 TAA-TTTTGAAAGTTTC
38778377 AAGGTCAAGA
Statistics
Matches: 162, Mismatches: 21, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
57 7 0.04
58 49 0.30
59 88 0.54
60 18 0.11
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.35
Consensus pattern (57 bp):
TAATTTTGAAAGTTTCGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAACT
Found at i:38778432 original size:59 final size:59
Alignment explanation
Indices: 38778237--38778506 Score: 206
Period size: 59 Copynumber: 4.6 Consensus size: 59
38778227 TTCAGGGGTA
* * ** * * * *
38778237 AAAATGAAATTTTTACAAGTTTCGGGGTCAAAAATGGAATTTTTGA-AAG-TTTAGGGGTA
1 AAAATGTAATTTTTAGAAGTTTCAAGGTC-AAAATGTAATTTTTTAGAAGTTTTA-AGGTC
** * * * * * * ** * *
38778296 AAAACATAATTTTTGGAAGTTTTAGGGTTAAAATGCAATTTTTGA-AAGTTCGAGGGTA
1 AAAATGTAATTTTTAGAAGTTTCAAGGTCAAAATGTAATTTTTTAGAAGTTTTAAGGTC
** * * *
38778354 AAAACATAATTTTTGGAAGTTTCAAGGTCAAGATGTAATTTTTTAGAAGTTTTAAGGTT
1 AAAATGTAATTTTTAGAAGTTTCAAGGTCAAAATGTAATTTTTTAGAAGTTTTAAGGTC
* **
38778413 AAAATGTAATTTTTAGAAGTTTCAAGGTTAAAATGTAATTTTTTAGAAGTTTTGGGGTC
1 AAAATGTAATTTTTAGAAGTTTCAAGGTCAAAATGTAATTTTTTAGAAGTTTTAAGGTC
* *
38778472 AAAATGTAATTTTGGAGAAG-TTCGAGGGTCAAAAT
1 AAAATGTAATTTT-TAGAAGTTTC-AAGGTCAAAAT
38778507 ACAATTTCTA
Statistics
Matches: 175, Mismatches: 32, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
58 62 0.35
59 99 0.57
60 14 0.08
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.37
Consensus pattern (59 bp):
AAAATGTAATTTTTAGAAGTTTCAAGGTCAAAATGTAATTTTTTAGAAGTTTTAAGGTC
Found at i:38780496 original size:6 final size:6
Alignment explanation
Indices: 38780466--38780537 Score: 57
Period size: 6 Copynumber: 13.0 Consensus size: 6
38780456 AATATTACGT
* **
38780466 TTTAAA -TT-AA TTCAAA TTT-AA -TTAAA TTTAAA TTTAAA AATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
38780510 TTTAAA --TCAA TTTAAA TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
38780538 ATCAAAGCTT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
4 7 0.14
5 7 0.14
6 36 0.72
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:38780537 original size:28 final size:27
Alignment explanation
Indices: 38780466--38780533 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
38780456 AATATTACGT
* *
38780466 TTTAAA-TTAATTCAAATTTAATTAAA
1 TTTAAATTTAATTTAAATTTAAATAAA
** *
38780492 TTTAAATTTAAAAATAAATTTAAATCAA
1 TTTAAATTT-AATTTAAATTTAAATAAA
38780520 TTTAAATTTAATTT
1 TTTAAATTTAATTT
38780534 TAAAATCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
26 6 0.18
27 5 0.15
28 22 0.67
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (27 bp):
TTTAAATTTAATTTAAATTTAAATAAA
Found at i:38782343 original size:2 final size:2
Alignment explanation
Indices: 38782336--38782361 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38782326 TATAGATTTC
38782336 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
38782362 TCAATATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38784868 original size:80 final size:80
Alignment explanation
Indices: 38784734--38784894 Score: 286
Period size: 80 Copynumber: 2.0 Consensus size: 80
38784724 AGTCCGGATC
* *
38784734 TCATCTGATAAGGATGCTATCACTTCATGTTGTTGGAGTGAAACACCTGGCAAATGCTTTTCCTT
1 TCATCAGATAAGGATGCTATCACCTCATGTTGTTGGAGTGAAACACCTGGCAAATGCTTTTCCTT
38784799 GTTGATAAGCATTAG
66 GTTGATAAGCATTAG
* *
38784814 TCATCAGATAAGGATGCTATCACCTCATGTTGTTGGAGTGAAACACCTGTCAAATGCTTTTCTTT
1 TCATCAGATAAGGATGCTATCACCTCATGTTGTTGGAGTGAAACACCTGGCAAATGCTTTTCCTT
38784879 GTTGATAAGCATTAG
66 GTTGATAAGCATTAG
38784894 T
1 T
38784895 TCTTCCGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (80 bp):
TCATCAGATAAGGATGCTATCACCTCATGTTGTTGGAGTGAAACACCTGGCAAATGCTTTTCCTT
GTTGATAAGCATTAG
Found at i:38795370 original size:80 final size:80
Alignment explanation
Indices: 38795236--38795396 Score: 277
Period size: 80 Copynumber: 2.0 Consensus size: 80
38795226 ATCCGGAAGA
* *
38795236 ACTAATGCTTATCAACAAAGAAAAGCATTTGACAGGTGTTTCACTCCAATAACATGAGGTGATAG
1 ACTAATGCTTATCAACAAAGAAAAGCATTTGACAGGTGTTTCACTCCAACAACATGAAGTGATAG
*
38795301 CATCCTTATCTGATG
66 CATCCTTATCAGATG
* *
38795316 ACTAATGCTTATCAACAAGGAAAAGCATTTGCCAGGTGTTTCACTCCAACAACATGAAGTGATAG
1 ACTAATGCTTATCAACAAAGAAAAGCATTTGACAGGTGTTTCACTCCAACAACATGAAGTGATAG
38795381 CATCCTTATCAGATG
66 CATCCTTATCAGATG
38795396 A
1 A
38795397 GATCCGGACT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (80 bp):
ACTAATGCTTATCAACAAAGAAAAGCATTTGACAGGTGTTTCACTCCAACAACATGAAGTGATAG
CATCCTTATCAGATG
Found at i:38797831 original size:5 final size:5
Alignment explanation
Indices: 38797811--38797848 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
38797801 AAGTGCTTAG
*
38797811 AAGAA AA-AA AAGAA AAAAA AAGAA AAGAA AAGAA AAGA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGA
38797849 GATTTGCCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAGAA
Done.