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 124 of 193
Found at i:39184483 original size:21 final size:22
Alignment explanation
Indices: 39184459--39184517 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
39184449 TAGAAGCATG
**
39184459 ACTTGTTTCGGTAGAAGTTA-C
1 ACTTGTTTCGGTAGAAACTATC
39184480 ACTT-TTATCGGTA-AAACTATC
1 ACTTGTT-TCGGTAGAAACTATC
*
39184501 ACTTGTATCGGTAGAAA
1 ACTTGTTTCGGTAGAAA
39184518 TCTGCACTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 6 0.19
21 21 0.68
22 4 0.13
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36
Consensus pattern (22 bp):
ACTTGTTTCGGTAGAAACTATC
Found at i:39187506 original size:28 final size:29
Alignment explanation
Indices: 39187394--39187630 Score: 131
Period size: 28 Copynumber: 8.3 Consensus size: 29
39187384 CTCGAACCTT
* *
39187394 TACAGAAATATAGCTCAT-TCGAGCCAAAA
1 TACAG-AATATCGCTCTTATCGAGCCAAAA
* * **
39187423 T-CAGATTATTGCTCGCACTCGAGCCAAAA
1 TACAGAATATCGCTCTTA-TCGAGCCAAAA
*
39187452 TACGGAATATCGCTCTTAT-GAGCCAAAA
1 TACAGAATATCGCTCTTATCGAGCCAAAA
* *
39187480 CACAGAATATCGCTCTT-TCGAGTCAAAA
1 TACAGAATATCGCTCTTATCGAGCCAAAA
* ** * * *
39187508 TACATAATAAAAGCTCATA-CGATCCAGAA
1 TACAGAAT-ATCGCTCTTATCGAGCCAAAA
* * *
39187537 TATAGAGTTAT-GCTCTT-TTGAGCCAAAA
1 TACAGA-ATATCGCTCTTATCGAGCCAAAA
* *
39187565 TACAAAATAAT-GCTCATA-CGAGCCAAAA
1 TACAGAAT-ATCGCTCTTATCGAGCCAAAA
39187593 TACA-AAGTTAT-GCTCTTA-CGAGCCAAAA
1 TACAGAA--TATCGCTCTTATCGAGCCAAAA
39187621 TATC-GAATAT
1 TA-CAGAATAT
39187631 TTTTTAAGTC
Statistics
Matches: 160, Mismatches: 34, Indels: 30
0.71 0.15 0.13
Matches are distributed among these distances:
27 15 0.09
28 97 0.61
29 36 0.22
30 12 0.08
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (29 bp):
TACAGAATATCGCTCTTATCGAGCCAAAA
Found at i:39187606 original size:56 final size:56
Alignment explanation
Indices: 39187441--39187622 Score: 181
Period size: 56 Copynumber: 3.2 Consensus size: 56
39187431 TTGCTCGCAC
** * * *
39187441 TCGAGCCAAAATACGGAAT-ATCGCTCTTATGAGCCAAAACACAGAA--TATCGCTCTT
1 TCGAGCCAAAATACAAAATAAT-GCTCATACGAGCCAAAATACA-AAGTTAT-GCTCTT
* * * * * * *
39187497 TCGAGTCAAAATACATAATAAAAGCTCATACGATCCAGAATATAGAGTTATGCTCTT
1 TCGAGCCAAAATACAAAAT-AATGCTCATACGAGCCAAAATACAAAGTTATGCTCTT
*
39187554 TTGAGCCAAAATACAAAATAATGCTCATACGAGCCAAAATACAAAGTTATGCTCTT
1 TCGAGCCAAAATACAAAATAATGCTCATACGAGCCAAAATACAAAGTTATGCTCTT
*
39187610 ACGAGCCAAAATA
1 TCGAGCCAAAATA
39187623 TCGAATATTT
Statistics
Matches: 101, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
56 60 0.59
57 37 0.37
58 4 0.04
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (56 bp):
TCGAGCCAAAATACAAAATAATGCTCATACGAGCCAAAATACAAAGTTATGCTCTT
Found at i:39187869 original size:19 final size:19
Alignment explanation
Indices: 39187845--39187889 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
39187835 CTCATTCAAC
39187845 ATGAAATTTAAATCATTTT
1 ATGAAATTTAAATCATTTT
* *
39187864 ATGAAA-TTAAGTCCTTTT
1 ATGAAATTTAAATCATTTT
39187882 -TGAAATTT
1 ATGAAATTT
39187890 TATAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 12 0.52
19 6 0.26
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (19 bp):
ATGAAATTTAAATCATTTT
Found at i:39189054 original size:65 final size:65
Alignment explanation
Indices: 39188978--39189108 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
39188968 GTAATTCAAC
39188978 AATAATCATACATTCACATACAGCAATATAATTCCATACAGTTGGCTTGAAAACATATGTTAGAT
1 AATAATCATACATTCACATACAGCAATATAATTCCATACAGTTGGCTTGAAAACATATGTTAGAT
* *
39189043 AATAATCATACATTCACATACATCAATATAATTCCATATAGTTGGCTTGAAAACATATGTTAGAT
1 AATAATCATACATTCACATACAGCAATATAATTCCATACAGTTGGCTTGAAAACATATGTTAGAT
39189108 A
1 A
39189109 CTTTAAAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (65 bp):
AATAATCATACATTCACATACAGCAATATAATTCCATACAGTTGGCTTGAAAACATATGTTAGAT
Found at i:39190727 original size:26 final size:26
Alignment explanation
Indices: 39190696--39190797 Score: 100
Period size: 26 Copynumber: 4.0 Consensus size: 26
39190686 CTGCGAAAAG
39190696 TCACCGGCTCAAGGCCTGCTATTTAA
1 TCACCGGCTCAAGGCCTGCTATTTAA
* * * *
39190722 TCACCGACTTAAGGCCTACTGTTTAA
1 TCACCGGCTCAAGGCCTGCTATTTAA
* * * *
39190748 TCATCGGCTCGAGGCTTGCTA--AAA
1 TCACCGGCTCAAGGCCTGCTATTTAA
*
39190772 GTCACCGGCTCAAGGCCCGCTATTTA
1 -TCACCGGCTCAAGGCCTGCTATTTA
39190798 TCTCTTATTT
Statistics
Matches: 56, Mismatches: 17, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
24 2 0.04
25 17 0.30
26 36 0.64
27 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (26 bp):
TCACCGGCTCAAGGCCTGCTATTTAA
Found at i:39192943 original size:26 final size:25
Alignment explanation
Indices: 39192935--39193126 Score: 98
Period size: 25 Copynumber: 7.6 Consensus size: 25
39192925 TAGAGTTTAG
39192935 CTCTTACGAGCCCAAACAGAATATTA
1 CTCTTACGAG-CCAAACAGAATATTA
** * **
39192961 CTCTTACGAGCCAGTCAAAATATCG
1 CTCTTACGAGCCAAACAGAATATTA
* * * * * **
39192986 TTCTTGCGAGCTAGATAGAATATCG
1 CTCTTACGAGCCAAACAGAATATTA
* * *
39193011 CTCTTACGAGCCAGACATAATATTG
1 CTCTTACGAGCCAAACAGAATATTA
* * * **
39193036 CTCTTATGAGTCAAATAGAATATGG
1 CTCTTACGAGCCAAACAGAATATTA
* * * * *
39193061 CACTTACGAGCTAGAGAGAATACTA
1 CTCTTACGAGCCAAACAGAATATTA
* *
39193086 CTCTCACGAGCCAGACAGAATATTTA
1 CTCTTACGAGCCAAACAGAATA-TTA
*
39193112 CT-TTACCGAACCAAA
1 CTCTTA-CGAGCCAAA
39193127 ATCCAGAATT
Statistics
Matches: 124, Mismatches: 40, Indels: 4
0.74 0.24 0.02
Matches are distributed among these distances:
25 103 0.83
26 21 0.17
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.26
Consensus pattern (25 bp):
CTCTTACGAGCCAAACAGAATATTA
Found at i:39193054 original size:50 final size:49
Alignment explanation
Indices: 39192934--39193071 Score: 132
Period size: 50 Copynumber: 2.7 Consensus size: 49
39192924 ATAGAGTTTA
* ** *
39192934 GCTCTTACGAGCCCAAACAGAATATTACTCTTACGAGCCAGTCAAAATATC
1 GCTCTTACGAG--CAAATAGAATATCGCTCTTACGAGCCAGACAAAATATC
* * * * *
39192985 GTTCTTGCGAGCTAGATAGAATATCGCTCTTACGAGCCAGACATAATATT
1 GCTCTTACGAGC-AAATAGAATATCGCTCTTACGAGCCAGACAAAATATC
* * *
39193035 GCTCTTATGAGTCAAATAGAATATGGCACTTACGAGC
1 GCTCTTACGAG-CAAATAGAATATCGCTCTTACGAGC
39193072 TAGAGAGAAT
Statistics
Matches: 70, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
49 1 0.01
50 59 0.84
51 10 0.14
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (49 bp):
GCTCTTACGAGCAAATAGAATATCGCTCTTACGAGCCAGACAAAATATC
Found at i:39193057 original size:25 final size:25
Alignment explanation
Indices: 39192914--39193071 Score: 102
Period size: 25 Copynumber: 6.2 Consensus size: 25
39192904 TTTAGCTTAA
* * *
39192914 ACGAGCCAAGATAGAGTTTAGCTCTT
1 ACGAGCCAA-ATAGAATATCGCTCTT
* **
39192940 ACGAGCCCAAACAGAATATTACTCTT
1 ACGAG-CCAAATAGAATATCGCTCTT
* * *
39192966 ACGAGCC-AGTCAAAATATCGTTCTT
1 ACGAGCCAAAT-AGAATATCGCTCTT
* * *
39192991 GCGAGCTAGATAGAATATCGCTCTT
1 ACGAGCCAAATAGAATATCGCTCTT
* * * *
39193016 ACGAGCCAGACATAATATTGCTCTT
1 ACGAGCCAAATAGAATATCGCTCTT
* * * *
39193041 ATGAGTCAAATAGAATATGGCACTT
1 ACGAGCCAAATAGAATATCGCTCTT
39193066 ACGAGC
1 ACGAGC
39193072 TAGAGAGAAT
Statistics
Matches: 98, Mismatches: 31, Indels: 7
0.72 0.23 0.05
Matches are distributed among these distances:
24 1 0.01
25 71 0.72
26 22 0.22
27 4 0.04
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (25 bp):
ACGAGCCAAATAGAATATCGCTCTT
Found at i:39198789 original size:17 final size:18
Alignment explanation
Indices: 39198767--39198808 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
39198757 AATTATTGTT
39198767 AAAATATAAA-TTTAAAA
1 AAAATATAAAGTTTAAAA
*
39198784 AAAATA-AAAGTTTCAAA
1 AAAATATAAAGTTTAAAA
39198801 AAAATATA
1 AAAATATA
39198809 TATAGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 18 0.82
18 1 0.05
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAATATAAAGTTTAAAA
Found at i:39202887 original size:18 final size:18
Alignment explanation
Indices: 39202866--39202923 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
39202856 CTCCACAGGC
39202866 TCTTCTTCAGGATCTTCT
1 TCTTCTTCAGGATCTTCT
* * *
39202884 TCTT-TCTCAAGATCCTAT
1 TCTTCT-TCAGGATCTTCT
*
39202902 TCTTCCTCAGGATCTTCT
1 TCTTCTTCAGGATCTTCT
39202920 TCTT
1 TCTT
39202924 TAACAGAATC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
17 1 0.03
18 30 0.97
ACGTcount: A:0.14, C:0.29, G:0.09, T:0.48
Consensus pattern (18 bp):
TCTTCTTCAGGATCTTCT
Found at i:39215160 original size:192 final size:191
Alignment explanation
Indices: 39214833--39215414 Score: 894
Period size: 192 Copynumber: 3.0 Consensus size: 191
39214823 AGCATTGAAA
* *
39214833 CAATGCTTTGTAGCGGTCCCATGTTGTGTGTAAATTCTCATCATCAAGTTGATGATATGCAGTGA
1 CAATGCTTTGTAGCGCTCCCATGTTGTGTGTAAATTCTCATCATCGAGTTGATGATATGCAGTGA
* * * * *
39214898 TGTCATTTCACAACCTTGCATTCATTGTTGGGGGATTAAATCGTAAGAAAAATTACGTTGCTAAA
66 TGTCATTTCGCAACCTTGCATTCATTGTTGGCGGATTAAATCGTAAGACAAACTGCGTTGCTAAA
39214963 GCATTCCATGATGTAATAGATCCAGTCGGCAATCCTAAAAACCATGTTCGAGCTTTTCCCTG
131 GCATTCCATGATGTAATAGATCCAG-CGGCAATCCTAAAAACCATGTTCGAGCTTTTCCCTG
* * * *
39215025 CAATGCTTTGTAGAGCTCCCATGTTGTGTGTAAATTCTGATTATCGAGTTGATGATATGTAGTGA
1 CAATGCTTTGTAGCGCTCCCATGTTGTGTGTAAATTCTCATCATCGAGTTGATGATATGCAGTGA
**
39215090 TGTCATTTCGCAACCTTGCATTCATTGTTGATGGATTAAATCGTAAGACAAACTGCGTTGCTAAA
66 TGTCATTTCGCAACCTTGCATTCATTGTTGGCGGATTAAATCGTAAGACAAACTGCGTTGCTAAA
* * *
39215155 GCATTCCACGATGTAATAGATCCAGCTGGCAATCCTAAAAATCATGTTCAAGCTTTTCCCTG
131 GCATTCCATGATGTAATAGATCCAGC-GGCAATCCTAAAAACCATGTTCGAGCTTTTCCCTG
* * *
39215217 CATTGCTTTGTAGCGCTCCCATGTTGTGTGTAAATTCTCATCATCGAGTTGATGATGTGCAGTAA
1 CAATGCTTTGTAGCGCTCCCATGTTGTGTGTAAATTCTCATCATCGAGTTGATGATATGCAGTGA
* *
39215282 TGTCATTTCGCAACCTTGCATTCATTATCGGCGGATTAAATCGTAAGACAAACTGCGTTGCTAAA
66 TGTCATTTCGCAACCTTGCATTCATTGTTGGCGGATTAAATCGTAAGACAAACTGCGTTGCTAAA
* * * * *
39215347 GTATTCCATGATGTAATAGATCCAACCGGTAATCCTAAAAAACCATGTTTGAGCTTTTCCCTA
131 GCATTCCATGATGTAATAGATCC-AGCGGCAATCCT-AAAAACCATGTTCGAGCTTTTCCCTG
39215410 CAATG
1 CAATG
39215415 AATAAGGAAA
Statistics
Matches: 352, Mismatches: 35, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
191 1 0.00
192 323 0.92
193 28 0.08
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (191 bp):
CAATGCTTTGTAGCGCTCCCATGTTGTGTGTAAATTCTCATCATCGAGTTGATGATATGCAGTGA
TGTCATTTCGCAACCTTGCATTCATTGTTGGCGGATTAAATCGTAAGACAAACTGCGTTGCTAAA
GCATTCCATGATGTAATAGATCCAGCGGCAATCCTAAAAACCATGTTCGAGCTTTTCCCTG
Found at i:39220165 original size:6 final size:6
Alignment explanation
Indices: 39220150--39220181 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
39220140 TGTTCACCAC
*
39220150 TTCTGA TTCTGG TTCTGG TTCTGG TTCTGG TT
1 TTCTGG TTCTGG TTCTGG TTCTGG TTCTGG TT
39220182 TCGATTCTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.16, G:0.28, T:0.53
Consensus pattern (6 bp):
TTCTGG
Found at i:39221281 original size:41 final size:41
Alignment explanation
Indices: 39221207--39221478 Score: 244
Period size: 41 Copynumber: 6.7 Consensus size: 41
39221197 AAATGCCGTA
* * * * **
39221207 AAAGGT-AGAGCAATAGTGACACTTATGGGAAAGCGCCATT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCT
* * *
39221247 AAAGGTCAGAGCAATAGCGGTGCTTCTGCAAAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCT
* *** * *
39221288 AAAGGTCAAAGCAATAGCGAAACTTTTGTG-CAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATG-GAAAAGCGCCGCT
* * ** *
39221329 AAAGGTCAAAGCAATAGCGACGCTTATGGGCAAGCGCCGCC
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCT
*
39221370 AAAGGTCAGAGCAATAGCAGCGCTTATGGGAAAA-CGCCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTAT-GGAAAAGCGCCGCT
* * * ** *
39221411 AAAGGTCAGAGCAATAGCGGCGCTTTTGTACAAGCATCGGT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCT
* *
39221452 AAAGGTCAGAGCATTAGCGGTGCTTAT
1 AAAGGTCAGAGCAATAGCGGCGCTTAT
39221479 TCGAAACGCC
Statistics
Matches: 191, Mismatches: 36, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
40 11 0.06
41 176 0.92
42 4 0.02
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.18
Consensus pattern (41 bp):
AAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCT
Found at i:39221374 original size:123 final size:123
Alignment explanation
Indices: 39221207--39221470 Score: 325
Period size: 123 Copynumber: 2.2 Consensus size: 123
39221197 AAATGCCGTA
* ** * *
39221207 AAAGGT-AGAGCAATAGTGACACTTATGGGAAAGCGCCATTAAAGGTCAGAGCAATAGCGGTGCT
1 AAAGGTCAGAGCAATAGCGACACTTATGGGAAAGCGCCACCAAAGGTCAGAGCAATAGCAGCGCT
* * *
39221271 TCT-GCAAAAGCGCCGCTAAAGGTCAAAGCAATAGCGAAACTTTTGTGCAAGCGCCGCT
66 TATGGCAAAA-CGCCGCTAAAGGTCAAAGCAATAGCGAAACTTTTGTACAAGCACCGCT
* * * *
39221329 AAAGGTCAAAGCAATAGCGACGCTTATGGGCAAGCGCCGCCAAAGGTCAGAGCAATAGCAGCGCT
1 AAAGGTCAGAGCAATAGCGACACTTATGGGAAAGCGCCACCAAAGGTCAGAGCAATAGCAGCGCT
* * *** * *
39221394 TATGGGAAAACGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTTTGTACAAGCATCGGT
66 TATGGCAAAACGCCGCTAAAGGTCAAAGCAATAGCGAAACTTTTGTACAAGCACCGCT
*
39221452 AAAGGTCAGAGCATTAGCG
1 AAAGGTCAGAGCAATAGCG
39221471 GTGCTTATTC
Statistics
Matches: 119, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
122 6 0.05
123 108 0.91
124 5 0.04
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.17
Consensus pattern (123 bp):
AAAGGTCAGAGCAATAGCGACACTTATGGGAAAGCGCCACCAAAGGTCAGAGCAATAGCAGCGCT
TATGGCAAAACGCCGCTAAAGGTCAAAGCAATAGCGAAACTTTTGTACAAGCACCGCT
Found at i:39221408 original size:82 final size:82
Alignment explanation
Indices: 39221207--39221470 Score: 280
Period size: 82 Copynumber: 3.2 Consensus size: 82
39221197 AAATGCCGTA
* * ** *
39221207 AAAGGT-AGAGCAATAGTGACACTTATGGGAAAGCGCCATTAAAGGTCAGAGCAATAGCGGTGCT
1 AAAGGTCAGAGCAATAGCGACACTTATGGGAAAACGCCGCTAAAGGTCAGAGCAATAGCGGCGCT
* *
39221271 TCTGCAAAAGCGCCGCT
66 TATGCACAAGCGCCGCT
* * * * * * * *
39221288 AAAGGTCAAAGCAATAGCGAAACTTTTGTGCAAGCGCCGCTAAAGGTCAAAGCAATAGCGACGCT
1 AAAGGTCAGAGCAATAGCGACACTTATGGGAAAACGCCGCTAAAGGTCAGAGCAATAGCGGCGCT
** *
39221353 TATGGGCAAGCGCCGCC
66 TATGCACAAGCGCCGCT
*
39221370 AAAGGTCAGAGCAATAGC-AGCGCTTATGGGAAAACGCCGCTAAAGGTCAGAGCAATAGCGGCGC
1 AAAGGTCAGAGCAATAGCGA-CACTTATGGGAAAACGCCGCTAAAGGTCAGAGCAATAGCGGCGC
* * ** *
39221434 TTTTGTACAAGCATCGGT
65 TTATGCACAAGCGCCGCT
*
39221452 AAAGGTCAGAGCATTAGCG
1 AAAGGTCAGAGCAATAGCG
39221471 GTGCTTATTC
Statistics
Matches: 147, Mismatches: 33, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
81 7 0.05
82 140 0.95
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.17
Consensus pattern (82 bp):
AAAGGTCAGAGCAATAGCGACACTTATGGGAAAACGCCGCTAAAGGTCAGAGCAATAGCGGCGCT
TATGCACAAGCGCCGCT
Found at i:39222310 original size:31 final size:31
Alignment explanation
Indices: 39222275--39222335 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
39222265 GTCATGTTTT
*
39222275 TAACACCAACAATACGAAGCTATCTTATTTA
1 TAACACCAACAATAAGAAGCTATCTTATTTA
*
39222306 TAACACCAACTATAAGAAGCTATCTTATTT
1 TAACACCAACAATAAGAAGCTATCTTATTT
39222336 TGCTTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (31 bp):
TAACACCAACAATAAGAAGCTATCTTATTTA
Found at i:39246502 original size:32 final size:32
Alignment explanation
Indices: 39246456--39246529 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
39246446 GTGTCCAGAT
*
39246456 CGTGTGCGATGCTTCTTTGCTTTTCCCATGCC
1 CGTGTGCGAGGCTTCTTTGCTTTTCCCATGCC
39246488 CGTGTGCGAGGCTTCTTTGCTTTTCCCATGCC
1 CGTGTGCGAGGCTTCTTTGCTTTTCCCATGCC
39246520 CGTGTGCGAG
1 CGTGTGCGAG
39246530 CTCGTGTGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.07, C:0.30, G:0.27, T:0.36
Consensus pattern (32 bp):
CGTGTGCGAGGCTTCTTTGCTTTTCCCATGCC
Found at i:39252890 original size:33 final size:33
Alignment explanation
Indices: 39252852--39252920 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
39252842 GAGAGCTTTC
39252852 TTATTTTTGCTTTTAAGCTTTTGAGAAATTATT
1 TTATTTTTGCTTTTAAGCTTTTGAGAAATTATT
*
39252885 TTATTTTTGCTTTTAAGCTTTTGAGAAATTGTT
1 TTATTTTTGCTTTTAAGCTTTTGAGAAATTATT
39252918 TTA
1 TTA
39252921 CATTATGGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.58
Consensus pattern (33 bp):
TTATTTTTGCTTTTAAGCTTTTGAGAAATTATT
Found at i:39253660 original size:37 final size:37
Alignment explanation
Indices: 39253619--39253690 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
39253609 ACTCAAATTC
* *
39253619 ACTTTCACACAA-TACTTTTTAAAAGTAATGAGAAAAT
1 ACTTTCACACAACT-CTTTTTAAAAGCAACGAGAAAAT
* *
39253656 ACTTTCGCGCAACTCTTTTTAAAAGCAACGAGAAA
1 ACTTTCACACAACTCTTTTTAAAAGCAACGAGAAA
39253691 CTAAACCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 29 0.97
38 1 0.03
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (37 bp):
ACTTTCACACAACTCTTTTTAAAAGCAACGAGAAAAT
Found at i:39254225 original size:13 final size:13
Alignment explanation
Indices: 39254207--39254232 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39254197 CAAAAAAAAA
39254207 AAAGAGAAATAAT
1 AAAGAGAAATAAT
39254220 AAAGAGAAATAAT
1 AAAGAGAAATAAT
39254233 GTAAAAGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAGAGAAATAAT
Found at i:39260976 original size:57 final size:58
Alignment explanation
Indices: 39260847--39261154 Score: 290
Period size: 57 Copynumber: 5.3 Consensus size: 58
39260837 AAAATTTTAG
* * * * * *
39260847 GGGTAAAAATGTTATTTTTGGAGAGTTTGAGGTAAAAATATGATTTTTGAGAAGTTCGA
1 GGGTAAAAATGTGATTTTTGGA-AGTTGGGGGCAAAAATGTGATTTTTTAGAAGTTCGA
*
39260906 -GGTAAAAATGTGATTTTTGGAAGTTCGGGGGCAAAAATGT-ATTTTTTAGAAGATCGA
1 GGGTAAAAATGTGATTTTTGGAAGTT-GGGGGCAAAAATGTGATTTTTTAGAAGTTCGA
* * *
39260963 GGGT-AAAATGTGATTTTTGAAAGTTCGAGGGCAAAAATGTGA-TTTTTAGAAGTTCAA
1 GGGTAAAAATGTGATTTTTGGAAGTT-GGGGGCAAAAATGTGATTTTTTAGAAGTTCGA
* * *
39261020 GGGT--AAATGTGATTTTTGGAAGTTTGGGAGCAAAAATGT-AATTTTTAGAAGTT-TA
1 GGGTAAAAATGTGATTTTTGGAAG-TTGGGGGCAAAAATGTGATTTTTTAGAAGTTCGA
* * ** * * *
39261075 GGGGTAAAAATGTAATTTTTAGAAGTTGGAGGGCAAATGTGTAATTTTTGAGAAGTTTGGA
1 -GGGTAAAAATGTGATTTTTGGAAGTTGG-GGGCAAAAATGTGATTTTTTAGAAG-TTCGA
* *
39261136 GGGGTTAAAATGTAATTTT
1 -GGGTAAAAATGTGATTTT
39261155 AGAAAAGTTT
Statistics
Matches: 213, Mismatches: 24, Indels: 22
0.82 0.09 0.08
Matches are distributed among these distances:
55 2 0.01
56 45 0.21
57 76 0.36
58 59 0.28
59 10 0.05
60 2 0.01
61 19 0.09
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (58 bp):
GGGTAAAAATGTGATTTTTGGAAGTTGGGGGCAAAAATGTGATTTTTTAGAAGTTCGA
Found at i:39261117 original size:29 final size:29
Alignment explanation
Indices: 39260851--39261158 Score: 204
Period size: 29 Copynumber: 10.7 Consensus size: 29
39260841 TTTTAGGGGT
* * * *
39260851 AAAAATGTTATTTTTGGAGAGTTTGA-GGT
1 AAAAATGTAATTTTTAGA-AGTTGGAGGGC
* * * *
39260880 AAAAATATGATTTTTGAGAAGTTCGA-GGT
1 AAAAATGTAATTTTT-AGAAGTTGGAGGGC
* *
39260909 AAAAATGTGATTTTTGGAAGTTCGG-GGGC
1 AAAAATGTAATTTTTAGAAGTT-GGAGGGC
* * *
39260938 AAAAATGTATTTTTTAGAAGATCGAGGG-
1 AAAAATGTAATTTTTAGAAGTTGGAGGGC
* * *
39260966 TAAAATGTGATTTTT-GAAAGTTCGAGGGC
1 AAAAATGTAATTTTTAG-AAGTTGGAGGGC
* **
39260995 AAAAATGTGATTTTTAGAAGTTCAAGGG-
1 AAAAATGTAATTTTTAGAAGTTGGAGGGC
* * * *
39261023 -TAAATGTGATTTTTGGAAGTTTGG-GAGC
1 AAAAATGTAATTTTTAGAAG-TTGGAGGGC
* *
39261051 AAAAATGTAATTTTTAGAAGTT-TAGGGGT
1 AAAAATGTAATTTTTAGAAGTTGGA-GGGC
39261080 AAAAATGTAATTTTTAGAAGTTGGAGGGC
1 AAAAATGTAATTTTTAGAAGTTGGAGGGC
** *
39261109 AAATGTGTAATTTTTGAGAAGTTTGGAGGGGT
1 AAAAATGTAATTTTT-AGAAG-TTGGA-GGGC
*
39261141 TAAAATGTAA-TTTTAGAA
1 AAAAATGTAATTTTTAGAA
39261159 AAGTTTAGGG
Statistics
Matches: 225, Mismatches: 38, Indels: 31
0.77 0.13 0.11
Matches are distributed among these distances:
27 20 0.09
28 33 0.15
29 140 0.62
30 13 0.06
31 9 0.04
32 10 0.04
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAAATGTAATTTTTAGAAGTTGGAGGGC
Found at i:39261118 original size:58 final size:58
Alignment explanation
Indices: 39260822--39261154 Score: 304
Period size: 58 Copynumber: 5.7 Consensus size: 58
39260812 GTTTGGGGTT
* * * * * *
39260822 AAAATGTAATTTTGGAAAATTTTAGGGGTAAAAATGTTATTTTTGGAGAGTTTGA-GGTA
1 AAAATGTAATTTT-TAGAAGTTTAGGGGTAAAAATGTGATTTTTGGA-AGTTGGAGGGCA
* * * *
39260881 AAAATATGATTTTTGAGAAG-TTCGAGGTAAAAATGTGATTTTTGGAAGTTCGG-GGGCA
1 AAAATGTAATTTTT-AGAAGTTTAGGGGTAAAAATGTGATTTTTGGAAGTT-GGAGGGCA
* * * * *
39260939 AAAATGTATTTTTTAGAAG-ATCGAGGGT-AAAATGTGATTTTTGAAAGTTCGAGGGCA
1 AAAATGTAATTTTTAGAAGTTTAG-GGGTAAAAATGTGATTTTTGGAAGTTGGAGGGCA
* * * *
39260996 AAAATGTGATTTTTAGAAGTTCAAGGGT--AAATGTGATTTTTGGAAGTTTGG-GAGCA
1 AAAATGTAATTTTTAGAAGTTTAGGGGTAAAAATGTGATTTTTGGAAG-TTGGAGGGCA
* *
39261052 AAAATGTAATTTTTAGAAGTTTAGGGGTAAAAATGTAATTTTTAGAAGTTGGAGGGCA
1 AAAATGTAATTTTTAGAAGTTTAGGGGTAAAAATGTGATTTTTGGAAGTTGGAGGGCA
** * *
39261110 AATGTGTAATTTTTGAGAAGTTTGGAGGGGTTAAAATGTAATTTT
1 AAAATGTAATTTTT-AGAAGTTT--AGGGGTAAAAATGTGATTTT
39261155 AGAAAAGTTT
Statistics
Matches: 226, Mismatches: 35, Indels: 24
0.79 0.12 0.08
Matches are distributed among these distances:
56 47 0.21
57 65 0.29
58 73 0.32
59 22 0.10
61 19 0.08
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (58 bp):
AAAATGTAATTTTTAGAAGTTTAGGGGTAAAAATGTGATTTTTGGAAGTTGGAGGGCA
Found at i:39261171 original size:30 final size:30
Alignment explanation
Indices: 39261052--39261227 Score: 123
Period size: 30 Copynumber: 5.9 Consensus size: 30
39261042 TTTGGGAGCA
*
39261052 AAAATGTAATTTTTAG--AAGTTTAGGGGTA
1 AAAATGTAA-TTTTAGAAAAGTTTAGGGGTC
*
39261081 AAAATGTAATTTTTAG--AAG-TT-GGAGGGC
1 AAAATGTAA-TTTTAGAAAAGTTTAGG-GGTC
* * * *
39261109 AAATGTGTAATTTTTGAGAAGTTTGGAGGGGTT
1 AAA-ATGTAATTTTAGAAAAGTTT--AGGGGTC
*
39261142 AAAATGTAATTTTAGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTC
* * * *
39261172 AAAATATAATTTTGGAAAAATTTAAGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTC
* * *
39261202 AAAATGTGATTTTTGGAAAG-TTAGGG
1 AAAATGTAATTTTAGAAAAGTTTAGGG
39261228 ACCTTTGGGC
Statistics
Matches: 119, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
27 2 0.02
28 12 0.10
29 29 0.24
30 50 0.42
31 2 0.02
32 17 0.14
33 5 0.04
34 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTAGAAAAGTTTAGGGGTC
Found at i:39262998 original size:17 final size:17
Alignment explanation
Indices: 39262978--39263014 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
39262968 AATTAAATTT
39262978 TAAATTTAAACTCAAAA
1 TAAATTTAAACTCAAAA
* *
39262995 TAAATTTAAATTTAAAA
1 TAAATTTAAACTCAAAA
39263012 TAA
1 TAA
39263015 TTCAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAATTTAAACTCAAAA
Found at i:39263023 original size:7 final size:7
Alignment explanation
Indices: 39262996--39263037 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
39262986 AACTCAAAAT
39262996 AAATTT-
1 AAATTTA
39263002 AAATTTA
1 AAATTTA
39263009 AAATAATTCA
1 AAAT--TT-A
39263019 AAATTTA
1 AAATTTA
39263026 AAATTTA
1 AAATTTA
39263033 AAATT
1 AAATT
39263038 GAATTTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.19
7 17 0.53
8 2 0.06
9 2 0.06
10 5 0.16
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:39265787 original size:2 final size:2
Alignment explanation
Indices: 39265780--39265807 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39265770 TAAACATCAA
39265780 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
39265808 CATCCATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39266179 original size:24 final size:24
Alignment explanation
Indices: 39266147--39266197 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
39266137 GCAAGTTCAT
*
39266147 TACGTTTACGCTCGTCAACATGAA
1 TACGTTTACGCTAGTCAACATGAA
*
39266171 TACGTTTACGCTAGTCAGCATGAA
1 TACGTTTACGCTAGTCAACATGAA
39266195 TAC
1 TAC
39266198 ATATTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (24 bp):
TACGTTTACGCTAGTCAACATGAA
Found at i:39280230 original size:17 final size:17
Alignment explanation
Indices: 39280208--39280254 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
39280198 ATATATTACT
39280208 TAATAATAATATTATAA
1 TAATAATAATATTATAA
* *
39280225 TAATAATAATATTTTAT
1 TAATAATAATATTATAA
39280242 TATATAATAATAT
1 TA-ATAATAATAT
39280255 AAAATATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATAATAATATTATAA
Found at i:39292824 original size:17 final size:17
Alignment explanation
Indices: 39292802--39292836 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
39292792 TCCAACATAC
*
39292802 ACTATATTATTTATTTT
1 ACTATATCATTTATTTT
39292819 ACTATATCATTTATTTT
1 ACTATATCATTTATTTT
39292836 A
1 A
39292837 AAAAATACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (17 bp):
ACTATATCATTTATTTT
Found at i:39296035 original size:14 final size:13
Alignment explanation
Indices: 39295981--39296041 Score: 54
Period size: 14 Copynumber: 4.6 Consensus size: 13
39295971 GATAGTTATA
*
39295981 TATAGTATATTTG
1 TATATTATATTTG
*
39295994 -ATATGAT-TATTG
1 TATATTATAT-TTG
39296006 TATATTATATTGTG
1 TATATTATATT-TG
*
39296020 TATTTTGATATTTG
1 TATATT-ATATTTG
39296034 TATATTAT
1 TATATTAT
39296042 GAATGTATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
11 1 0.03
12 8 0.21
13 9 0.24
14 15 0.39
15 5 0.13
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (13 bp):
TATATTATATTTG
Found at i:39298736 original size:20 final size:19
Alignment explanation
Indices: 39298687--39298736 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
39298677 AAAAAATTAT
39298687 AAAAATA-AAAA-TCAATA
1 AAAAATATAAAATTCAATA
* * *
39298704 AATATTATTAAATTTCAATA
1 AAAAATA-TAAAATTCAATA
39298724 AAAAATATAAAAT
1 AAAAATATAAAAT
39298737 ATATTTAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
17 5 0.21
19 8 0.33
20 11 0.46
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAATATAAAATTCAATA
Found at i:39298796 original size:20 final size:19
Alignment explanation
Indices: 39298773--39298834 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
39298763 AACAAATTGT
*
39298773 AAAATTGTAAAAGATTTAGA
1 AAAATTGTAAAA-ATTTATA
*
39298793 AAAATTGTAAAATTTTATA
1 AAAATTGTAAAAATTTATA
**
39298812 AAAATCATAAAAATTTATA
1 AAAATTGTAAAAATTTATA
39298831 AAAA
1 AAAA
39298835 GCACCAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 25 0.68
20 12 0.32
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (19 bp):
AAAATTGTAAAAATTTATA
Found at i:39298823 original size:28 final size:28
Alignment explanation
Indices: 39298766--39298826 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
39298756 ATTAGAAAAC
* *
39298766 AAATTGTAAAATTGTAAAAGATTTAGAA
1 AAATTGTAAAATTGTAAAAGAATCAGAA
* *
39298794 AAATTGTAAAATTTTATAAA-AATCATAA
1 AAATTGTAAAATTGTA-AAAGAATCAGAA
39298822 AAATT
1 AAATT
39298827 TATAAAAAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (28 bp):
AAATTGTAAAATTGTAAAAGAATCAGAA
Found at i:39298843 original size:19 final size:20
Alignment explanation
Indices: 39298801--39298844 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
39298791 GAAAAATTGT
* *
39298801 AAAATTTTATAAAAATCATA
1 AAAATTTTATAAAAAGCACA
39298821 AAAA-TTTATAAAAAGCACCA
1 AAAATTTTATAAAAAGCA-CA
39298841 AAAA
1 AAAA
39298845 GATTCATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAATTTTATAAAAAGCACA
Found at i:39299016 original size:20 final size:19
Alignment explanation
Indices: 39298991--39299033 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
39298981 ATAATTTTTT
39298991 TTTTTTACAAA-TTTTATATA
1 TTTTTT-CAAATTTTTATA-A
*
39299011 TTTTTTTAAATTTTTATAA
1 TTTTTTCAAATTTTTATAA
39299030 TTTT
1 TTTT
39299034 CTTATGACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTCAAATTTTTATAA
Found at i:39299021 original size:19 final size:18
Alignment explanation
Indices: 39298999--39299130 Score: 79
Period size: 19 Copynumber: 6.9 Consensus size: 18
39298989 TTTTTTTTAC
39298999 AAATTTTATATATTTTTTT
1 AAATTTTATA-ATTTTTTT
*
39299018 AAATTTTTATAATTTTCTT
1 AAA-TTTTATAATTTTTTT
* * **
39299037 ATGACTTTATAA-AATTTT
1 A-AATTTTATAATTTTTTT
* *
39299055 ATAATTTTTTACGATTTTTGT
1 A-AATTTTATA--ATTTTTTT
39299076 AAAGTTTTATAATTTTTTT
1 AAA-TTTTATAATTTTTTT
*
39299095 ATAATTTTTTACA-TTTTTT
1 A-AATTTTATA-ATTTTTTT
*
39299114 ACAATTTTCTAATTTTT
1 A-AATTTTATAATTTTT
39299131 AATAATTTTT
Statistics
Matches: 87, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
18 12 0.14
19 51 0.59
20 14 0.16
21 10 0.11
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
AAATTTTATAATTTTTTT
Found at i:39299026 original size:8 final size:9
Alignment explanation
Indices: 39298992--39299149 Score: 65
Period size: 9 Copynumber: 16.6 Consensus size: 9
39298982 TAATTTTTTT
*
39298992 TTTTTACAA
1 TTTTTATAA
*
39299001 ATTTTATATA
1 TTTTTATA-A
*
39299011 TTTTTTTAAA
1 TTTTTAT-AA
39299021 TTTTTATAA
1 TTTTTATAA
*
39299030 TTTTCTTATGA
1 -TTT-TTATAA
*
39299041 -CTTTATAAA
1 TTTTTAT-AA
*
39299050 ATTTTATAA
1 TTTTTATAA
39299059 TTTTT-TACGA
1 TTTTTATA--A
*
39299069 TTTTTGTAAA
1 TTTTTAT-AA
*
39299079 GTTTTATAA
1 TTTTTATAA
39299088 TTTTTTTATAA
1 --TTTTTATAA
39299099 TTTTT-TACA
1 TTTTTATA-A
39299108 TTTTT-TACA
1 TTTTTATA-A
* *
39299117 ATTTTCTAA
1 TTTTTATAA
39299126 TTTTTAATAA
1 TTTTT-ATAA
39299136 TTTTT-TAA
1 TTTTTATAA
39299144 TATTTT
1 T-TTTT
39299150 TATTAAAAAT
Statistics
Matches: 117, Mismatches: 16, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
8 12 0.10
9 46 0.39
10 43 0.37
11 15 0.13
12 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:39299049 original size:29 final size:29
Alignment explanation
Indices: 39299012--39299123 Score: 100
Period size: 29 Copynumber: 3.8 Consensus size: 29
39299002 TTTTATATAT
*
39299012 TTTTTTAAATTTTTATAATTTTCTTATGA
1 TTTTATAAATTTTTATAATTTTCTTATGA
* * *
39299041 CTTTATAAAATTTTATAATTTT-TTACGA
1 TTTTATAAATTTTTATAATTTTCTTATGA
* * * *
39299069 TTTTTGTAAAGTTTTATAATTTTTTTATAA
1 -TTTTATAAATTTTTATAATTTTCTTATGA
* * *
39299099 TTTTTTACATTTTTTACAATTTTCT
1 TTTTATA-AATTTTTATAATTTTCT
39299124 AATTTTTAAT
Statistics
Matches: 66, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
28 5 0.08
29 44 0.67
30 17 0.26
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (29 bp):
TTTTATAAATTTTTATAATTTTCTTATGA
Found at i:39299094 original size:11 final size:11
Alignment explanation
Indices: 39299080--39299104 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39299070 TTTTGTAAAG
39299080 TTTTATAATTT
1 TTTTATAATTT
39299091 TTTTATAATTT
1 TTTTATAATTT
39299102 TTT
1 TTT
39299105 ACATTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:39299192 original size:15 final size:15
Alignment explanation
Indices: 39299174--39299203 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
39299164 ATTTTATAAC
39299174 TTTTATTTATTTTTAT
1 TTTTA-TTATTTTTAT
39299190 TTTTATTATTTTTA
1 TTTTATTATTTTTA
39299204 GCCACATGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTATTATTTTTAT
Found at i:39301693 original size:26 final size:24
Alignment explanation
Indices: 39301647--39301701 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
39301637 ATCCTTTTTT
*
39301647 TTTTATCTTGTTTTAAATTAATCG
1 TTTTATCTTGTTTTAAATTAATCC
* *
39301671 TTTTATTTTGTTTTATTATTTAATCC
1 TTTTATCTTGTTTTA--AATTAATCC
39301697 TTTTA
1 TTTTA
39301702 GCTACTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 14 0.54
26 12 0.46
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.65
Consensus pattern (24 bp):
TTTTATCTTGTTTTAAATTAATCC
Found at i:39302397 original size:35 final size:35
Alignment explanation
Indices: 39302358--39302428 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
39302348 TGGTGGCGAC
*
39302358 TCCATTTTCGATTTTAAAATGAAATTCAGGACTTT
1 TCCATTTTCGATTTTAAAATGAAATTCAAGACTTT
*
39302393 TCCATTTTCGGTTTTAAAATGAAATTCAAGACTTT
1 TCCATTTTCGATTTTAAAATGAAATTCAAGACTTT
39302428 T
1 T
39302429 TCAAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (35 bp):
TCCATTTTCGATTTTAAAATGAAATTCAAGACTTT
Found at i:39305274 original size:23 final size:23
Alignment explanation
Indices: 39305248--39305387 Score: 125
Period size: 23 Copynumber: 6.3 Consensus size: 23
39305238 TGCTGGGCAG
39305248 CAGAGAGCACACAAAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
*
39305271 CAGAGAGTACACAAA--G-T--A
1 CAGAGAGCACACAAAGTGCTAAA
* *
39305289 C--TGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
39305310 CAGAGAGCAC-CGAAGTGCTCATAA
1 CAGAGAGCACACAAAGTGCT-A-AA
* *
39305334 CAAAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
39305357 CAGAAATCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
39305380 CAGAGAGC
1 CAGAGAGC
39305388 GCGCTAGTGT
Statistics
Matches: 92, Mismatches: 15, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
16 10 0.11
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 8 0.09
23 49 0.53
24 11 0.12
25 7 0.08
ACGTcount: A:0.44, C:0.24, G:0.21, T:0.11
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:39307747 original size:3 final size:3
Alignment explanation
Indices: 39307739--39307776 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
39307729 GGAAGTCAAA
*
39307739 AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
39307777 AATGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39308465 original size:21 final size:21
Alignment explanation
Indices: 39308428--39308506 Score: 67
Period size: 20 Copynumber: 3.9 Consensus size: 21
39308418 CACCCAAAGG
*
39308428 AAAAAAAAGTAAAGAAAAAAT
1 AAAAAAAAGAAAAGAAAAAAT
*
39308449 AAAAAAAA-AAAACG-AAAAAG
1 AAAAAAAAGAAAA-GAAAAAAT
* * *
39308469 AAGAGAAAGAAGAGAAAAAA-
1 AAAAAAAAGAAAAGAAAAAAT
*
39308489 AAAAGAAA-AAAAGAAAAA
1 AAAAAAAAGAAAAGAAAAA
39308507 GGAGAGGTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
19 9 0.19
20 22 0.46
21 17 0.35
ACGTcount: A:0.82, C:0.01, G:0.14, T:0.03
Consensus pattern (21 bp):
AAAAAAAAGAAAAGAAAAAAT
Found at i:39308466 original size:13 final size:12
Alignment explanation
Indices: 39308427--39308505 Score: 59
Period size: 13 Copynumber: 6.0 Consensus size: 12
39308417 TCACCCAAAG
39308427 GAAAAAAAAGTAAA
1 GAAAAAAAA--AAA
39308441 GAAAAAATAAAAA
1 GAAAAAA-AAAAA
*
39308454 AAAAAAACGAAAAA
1 GAAAAAA--AAAAA
* * *
39308468 GAAGAGAAAGAA
1 GAAAAAAAAAAA
39308480 GAGAAAAAAAAAA
1 GA-AAAAAAAAAA
39308493 GAAAAAAAGAAAA
1 GAAAAAAA-AAAA
39308506 AGGAGAGGTC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
12 12 0.23
13 22 0.42
14 16 0.31
15 2 0.04
ACGTcount: A:0.81, C:0.01, G:0.15, T:0.03
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:39308489 original size:30 final size:30
Alignment explanation
Indices: 39308451--39308512 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
39308441 GAAAAAATAA
*
39308451 AAAAAAAAAACGAAAAAGAAGAGAAAGAAGAG
1 AAAAAAAAAA-GAAAAA-AAGAAAAAGAAGAG
*
39308483 AAAAAAAAAAGAAAAAAAGAAAAAGGAGAG
1 AAAAAAAAAAGAAAAAAAGAAAAAGAAGAG
39308513 GTCAAGGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 12 0.43
31 6 0.21
32 10 0.36
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (30 bp):
AAAAAAAAAAGAAAAAAAGAAAAAGAAGAG
Found at i:39308497 original size:9 final size:9
Alignment explanation
Indices: 39308427--39308506 Score: 56
Period size: 9 Copynumber: 8.7 Consensus size: 9
39308417 TCACCCAAAG
39308427 GAAAAAAAA
1 GAAAAAAAA
*
39308436 GTAAAGAAAA
1 G-AAAAAAAA
*
39308446 -AATAAAAA
1 GAAAAAAAA
*
39308454 -AAAAAAAC
1 GAAAAAAAA
39308462 GAAAAAGAAGA
1 GAAAAA-AA-A
* *
39308473 GAAAGAAGA
1 GAAAAAAAA
39308482 GAAAAAAAA
1 GAAAAAAAA
*
39308491 AAGAAAAAAA
1 GA-AAAAAAA
39308501 GAAAAA
1 GAAAAA
39308507 GGAGAGGTCA
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
8 12 0.22
9 19 0.35
10 18 0.33
11 5 0.09
ACGTcount: A:0.81, C:0.01, G:0.15, T:0.03
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:39309016 original size:112 final size:112
Alignment explanation
Indices: 39308819--39309045 Score: 319
Period size: 112 Copynumber: 2.0 Consensus size: 112
39308809 AAATTTTTCG
* *
39308819 TTTTTAATCTTTTCATACAAACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAAC
1 TTTTTAATCTTTTCATACAAACGAGATTTGCCTCCAATAAAATTCAAATTTATCCACCTTACAAC
* * *
39308884 TCTGTTCAAGCATGTTTGCATTGAAATAACGGTTAGTGGACTAATGA
66 CCTGTTCAAGCATGTTTGCATTGAAATAACGGTTAGCGGACTAACGA
* *** * * *
39308931 TTTTTAATCTTTTCATTCACGTGAGATTTGTCTCCAATAAAATTCAAATTTATCTACTTTACAAC
1 TTTTTAATCTTTTCATACAAACGAGATTTGCCTCCAATAAAATTCAAATTTATCCACCTTACAAC
* * *
39308996 CCTGTTCAAGCATTTTTGCATTGAAATAATGGTTAGCGGTCTAACGA
66 CCTGTTCAAGCATGTTTGCATTGAAATAACGGTTAGCGGACTAACGA
39309043 TTT
1 TTT
39309046 AAGGAATAAA
Statistics
Matches: 100, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
112 100 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (112 bp):
TTTTTAATCTTTTCATACAAACGAGATTTGCCTCCAATAAAATTCAAATTTATCCACCTTACAAC
CCTGTTCAAGCATGTTTGCATTGAAATAACGGTTAGCGGACTAACGA
Found at i:39309540 original size:49 final size:49
Alignment explanation
Indices: 39309470--39309674 Score: 248
Period size: 49 Copynumber: 4.2 Consensus size: 49
39309460 TATTGAATCA
** *
39309470 TATACCCTAGAAGACATGAAGAGATAGATTGAAGCCGCAACGACGAACCT
1 TATACCCTAG-AGATGTGAAGAGAAAGATTGAAGCCGCAACGACGAACCT
* * * *
39309520 GATACCTTAGAGATGTGAAGAGAAAGATTGAAGCCACAATGACGAACCT
1 TATACCCTAGAGATGTGAAGAGAAAGATTGAAGCCGCAACGACGAACCT
* * * * * *
39309569 TATACCCTAGAGATGTGGAGGGAAAGGTTGAAGCTGCAATGACAAACCT
1 TATACCCTAGAGATGTGAAGAGAAAGATTGAAGCCGCAACGACGAACCT
* * * *
39309618 TATACCCTAAAGATGTGAAGAGAAAGATTAAAGTCGCAACGACGAATCT
1 TATACCCTAGAGATGTGAAGAGAAAGATTGAAGCCGCAACGACGAACCT
39309667 TATACCCT
1 TATACCCT
39309675 GAAAATGAGG
Statistics
Matches: 130, Mismatches: 25, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
49 122 0.94
50 8 0.06
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.20
Consensus pattern (49 bp):
TATACCCTAGAGATGTGAAGAGAAAGATTGAAGCCGCAACGACGAACCT
Found at i:39309698 original size:98 final size:97
Alignment explanation
Indices: 39309495--39309701 Score: 238
Period size: 98 Copynumber: 2.1 Consensus size: 97
39309485 ATGAAGAGAT
* * * * *
39309495 AGATTGAAGCCGCAACGACGAACCTGATACCTTAGAGATGTGAAGAGAAAGATTGAAGCCACAAT
1 AGATTGAAGCCGCAACGACAAACCTGATACCCTAAAGATGTGAAGAGAAAGATTAAAGCCACAAC
* *
39309560 GACGAACCTTATACCCTAGAGATGTGGAGGGAA
66 GACGAACCTTATACCCTAGAAATGAGGA-GGAA
* * * * * *
39309593 AGGTTGAAGCTGCAATGACAAACCTTATACCCTAAAGATGTGAAGAGAAAGATTAAAGTCGCAAC
1 AGATTGAAGCCGCAACGACAAACCTGATACCCTAAAGATGTGAAGAGAAAGATTAAAGCCACAAC
*
39309658 GACGAATCTTATACCCT-GAAAATGAGGA-GAA
66 GACGAACCTTATACCCTAG-AAATGAGGAGGAA
39309689 GCAGATTGAAGCC
1 --AGATTGAAGCC
39309702 ACACAGACGA
Statistics
Matches: 90, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
96 3 0.03
97 1 0.01
98 86 0.96
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (97 bp):
AGATTGAAGCCGCAACGACAAACCTGATACCCTAAAGATGTGAAGAGAAAGATTAAAGCCACAAC
GACGAACCTTATACCCTAGAAATGAGGAGGAA
Found at i:39310367 original size:50 final size:50
Alignment explanation
Indices: 39310304--39310512 Score: 172
Period size: 50 Copynumber: 4.2 Consensus size: 50
39310294 CATTATCTCT
* *
39310304 CTGAAGTTTCAGTAGAGCAAGATGAAGCTACAAAATCAAATCCTATGTCC
1 CTGAAGTTACAGTAGAGCAAGATGAAGCTACAAAATCAAATCCTATATCC
* * * * * *
39310354 ATGAAGTTACAGTACAGTAGGATGAAGCTAAAAAACCAAATCCTATATCC
1 CTGAAGTTACAGTAGAGCAAGATGAAGCTACAAAATCAAATCCTATATCC
* * ** * * *
39310404 CTAAAGTTGCAGT-GAGTTAGATTAAAG-T-CATGAAATCAAATCTTTATCTCC
1 CTGAAGTTACAGTAGAGCAAGA-TGAAGCTACA--AAATCAAATC-CTATATCC
* * * * *
39310455 CTAAAGCTACAGTGGAGCAAGATGAAGCTACAACATCAAATCATATATCC
1 CTGAAGTTACAGTAGAGCAAGATGAAGCTACAAAATCAAATCCTATATCC
*
39310505 TTGAAGTT
1 CTGAAGTT
39310513 GTAGTGGATT
Statistics
Matches: 122, Mismatches: 30, Indels: 14
0.73 0.18 0.08
Matches are distributed among these distances:
48 1 0.01
49 6 0.05
50 76 0.62
51 30 0.25
52 7 0.06
53 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (50 bp):
CTGAAGTTACAGTAGAGCAAGATGAAGCTACAAAATCAAATCCTATATCC
Found at i:39310408 original size:151 final size:151
Alignment explanation
Indices: 39310225--39310512 Score: 364
Period size: 151 Copynumber: 1.9 Consensus size: 151
39310215 TGGAATGGAG
* * * * * *
39310225 TGAAGTTATAAAACCAAATCCTATATCCCTAAAGTTACAGTG-GATTGGGTTGAAG-CTACGAAG
1 TGAAGCTAAAAAACCAAATCCTATATCCCTAAAGTTACAGTGAG-TTAGATTAAAGTC-ACGAAA
* * * * * * *
39310288 GCGAATCATTATCTCTCTGAAGTTTCAGTAGAGCAAGATGAAGCTACAAAATCAAATCCTATGTC
64 GCAAATCATTATCTCCCTAAAGCTACAGTAGAGCAAGATGAAGCTACAAAATCAAATCATATATC
39310353 CATGAAGTTACAGTACAGTAGGA
129 CATGAAGTTACAGTACAGTAGGA
* * *
39310376 TGAAGCTAAAAAACCAAATCCTATATCCCTAAAGTTGCAGTGAGTTAGATTAAAGTCATGAAATC
1 TGAAGCTAAAAAACCAAATCCTATATCCCTAAAGTTACAGTGAGTTAGATTAAAGTCACGAAAGC
* * * *
39310441 AAATCTTTATCTCCCTAAAGCTACAGTGGAGCAAGATGAAGCTACAACATCAAATCATATATCCT
66 AAATCATTATCTCCCTAAAGCTACAGTAGAGCAAGATGAAGCTACAAAATCAAATCATATATCCA
39310506 TGAAGTT
131 TGAAGTT
39310513 GTAGTGGATT
Statistics
Matches: 115, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
151 113 0.98
152 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (151 bp):
TGAAGCTAAAAAACCAAATCCTATATCCCTAAAGTTACAGTGAGTTAGATTAAAGTCACGAAAGC
AAATCATTATCTCCCTAAAGCTACAGTAGAGCAAGATGAAGCTACAAAATCAAATCATATATCCA
TGAAGTTACAGTACAGTAGGA
Found at i:39311011 original size:14 final size:15
Alignment explanation
Indices: 39310992--39311021 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
39310982 TTATTATTTT
39310992 ATAAATAT-AAATAA
1 ATAAATATAAAATAA
39311006 ATAAATATAAAATAA
1 ATAAATATAAAATAA
39311021 A
1 A
39311022 ATTAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAATATAAAATAA
Found at i:39313335 original size:58 final size:58
Alignment explanation
Indices: 39313245--39313361 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
39313235 GAGTAGCCTT
39313245 CAATTCAAAAAAAGGGTTTTATAAATAGTAAAACAGATATAAAATGTAGTTTGACCAA
1 CAATTCAAAAAAAGGGTTTTATAAATAGTAAAACAGATATAAAATGTAGTTTGACCAA
39313303 CAATTCAAAAAAAGGGTTTTATAAATAGTAAAACAGATATAAAATGTAGTTTGACCAA
1 CAATTCAAAAAAAGGGTTTTATAAATAGTAAAACAGATATAAAATGTAGTTTGACCAA
39313361 C
1 C
39313362 TCCATTAACA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.27
Consensus pattern (58 bp):
CAATTCAAAAAAAGGGTTTTATAAATAGTAAAACAGATATAAAATGTAGTTTGACCAA
Found at i:39313456 original size:14 final size:14
Alignment explanation
Indices: 39313437--39313463 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39313427 TACCAAAACT
39313437 TTTAAGTTTTTTAC
1 TTTAAGTTTTTTAC
39313451 TTTAAGTTTTTTA
1 TTTAAGTTTTTTA
39313464 TCATTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTAAGTTTTTTAC
Found at i:39316027 original size:80 final size:80
Alignment explanation
Indices: 39315887--39316044 Score: 244
Period size: 80 Copynumber: 2.0 Consensus size: 80
39315877 CGTTGGGCAC
* * * * *
39315887 AAATCGTTGGTTAATCCAACTAGAGTTGGGCTCATTTATTGCGGTTAATCCGCTAGGCACTGGGT
1 AAATCGTTGGTTAATCCAACTAGAGCTAGGCTCACTTATCGCGGTTAATCCGCTAAGCACTGGGT
39315952 GCCATGAATTGACAG
66 GCCATGAATTGACAG
* * *
39315967 AAATTGTTGGTTAATCCAACTAGAGCTAGGCTCACTTATCGCGTTTTATCCGCTAAGCACTGGGT
1 AAATCGTTGGTTAATCCAACTAGAGCTAGGCTCACTTATCGCGGTTAATCCGCTAAGCACTGGGT
39316032 GCCATGAATTGAC
66 GCCATGAATTGAC
39316045 GGATTTGATT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 70 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (80 bp):
AAATCGTTGGTTAATCCAACTAGAGCTAGGCTCACTTATCGCGGTTAATCCGCTAAGCACTGGGT
GCCATGAATTGACAG
Found at i:39320625 original size:24 final size:24
Alignment explanation
Indices: 39320583--39320628 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
39320573 CCACCCATGC
*
39320583 GCACACATGCACACTCACTCACAT
1 GCACACATGCACACGCACTCACAT
**
39320607 GCACACATGCATGCGCACTCAC
1 GCACACATGCACACGCACTCAC
39320629 TCGCTCGCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.41, G:0.13, T:0.15
Consensus pattern (24 bp):
GCACACATGCACACGCACTCACAT
Found at i:39320630 original size:32 final size:32
Alignment explanation
Indices: 39320592--39320700 Score: 110
Period size: 32 Copynumber: 3.2 Consensus size: 32
39320582 CGCACACATG
* *
39320592 CACACTCACTCACATGCACACATGCATGCGCA
1 CACACTCACTCACATGCACACACGCATGCACA
* * * * *
39320624 CTCACTCGCTCGCTTTCTCACAACACACGCATGCACA
1 CACACTCACTCAC---AT-GCA-CACACGCATGCACA
39320661 CACACTCACTCACATGCACACACGCATGCACA
1 CACACTCACTCACATGCACACACGCATGCACA
39320693 CACACTCA
1 CACACTCA
39320701 TTTTTTAAAG
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
32 32 0.53
33 2 0.03
34 1 0.02
35 1 0.02
36 2 0.03
37 22 0.37
ACGTcount: A:0.30, C:0.43, G:0.10, T:0.17
Consensus pattern (32 bp):
CACACTCACTCACATGCACACACGCATGCACA
Found at i:39320663 original size:12 final size:12
Alignment explanation
Indices: 39320646--39320695 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
39320636 CTTTCTCACA
39320646 ACACACGCATGC
1 ACACACGCATGC
*
39320658 ACACACAC-T-C
1 ACACACGCATGC
*
39320668 ACTCA--CATGC
1 ACACACGCATGC
39320678 ACACACGCATGC
1 ACACACGCATGC
39320690 ACACAC
1 ACACAC
39320696 ACTCATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
8 1 0.03
9 1 0.03
10 10 0.32
11 1 0.03
12 18 0.58
ACGTcount: A:0.36, C:0.44, G:0.10, T:0.10
Consensus pattern (12 bp):
ACACACGCATGC
Found at i:39320665 original size:14 final size:14
Alignment explanation
Indices: 39320646--39320697 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
39320636 CTTTCTCACA
39320646 ACACACGCATGCAC
1 ACACACGCATGCAC
* *
39320660 ACACACTCACTCACATGC
1 ACACACGCA-T-GCA--C
39320678 ACACACGCATGCAC
1 ACACACGCATGCAC
39320692 ACACAC
1 ACACAC
39320698 TCATTTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 15 0.50
15 1 0.03
16 4 0.13
17 1 0.03
18 9 0.30
ACGTcount: A:0.37, C:0.44, G:0.10, T:0.10
Consensus pattern (14 bp):
ACACACGCATGCAC
Found at i:39321746 original size:54 final size:54
Alignment explanation
Indices: 39321637--39321739 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 54
39321627 AATATACCTA
* * *
39321637 TTTCATCGCAATCAGAGGCTATGAATGTTGATAATCAGGTAATATGAACAATCT
1 TTTCATCGCAATCAGAGGATATGAATGTTGAGAATCAGGTAACATGAACAATCT
* * **
39321691 TTTCATCTCAATCAGAGTATATGGCTGTTGAGAATCAGGTAACATGAAC
1 TTTCATCGCAATCAGAGGATATGAATGTTGAGAATCAGGTAACATGAAC
39321740 TTTCTTTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (54 bp):
TTTCATCGCAATCAGAGGATATGAATGTTGAGAATCAGGTAACATGAACAATCT
Found at i:39331025 original size:19 final size:19
Alignment explanation
Indices: 39330974--39331045 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
39330964 ATTACAAAAA
39330974 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
**
39330993 CAAAAATTTTAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
39331013 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
39331032 AAAAATTCCAAAAT
1 AAAAATT-CAAAAT
39331046 TTATATTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
18 4 0.09
19 17 0.39
20 23 0.52
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:39331073 original size:16 final size:16
Alignment explanation
Indices: 39331001--39331076 Score: 62
Period size: 16 Copynumber: 4.4 Consensus size: 16
39330991 TTCAAAAATT
*
39331001 TTAAATAATTTTTAAAA
1 TTAAA-AATTTATAAAA
39331018 TTCAAAATATTTATAAAAA
1 TT-AAAA-ATTTAT-AAAA
* ***
39331037 TTCCAAAATTTATATTT
1 TT-AAAAATTTATAAAA
39331054 TTAAAAATTTATAAAA
1 TTAAAAATTTATAAAA
39331070 TTAAAAA
1 TTAAAAA
39331077 AATCTAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
16 17 0.36
17 6 0.13
18 14 0.30
19 10 0.21
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAAAATTTATAAAA
Found at i:39331108 original size:52 final size:52
Alignment explanation
Indices: 39330995--39331112 Score: 130
Period size: 52 Copynumber: 2.2 Consensus size: 52
39330985 ATAATTTTCA
* * * * * * *
39330995 AAAATTTTAAATAATTTTTAAAATTCAAAATATTTATAAAAATTCCAAAATTT
1 AAAATTTTAAA-AATTTATAAAATTAAAAAAATCTAAAAAAATTACAAAAGTT
* *
39331048 ATATTTTTAAAAATTTATAAAATTAAAAAAATCTAAAAAAATATAC-AAAGTT
1 AAAATTTTAAAAATTTATAAAATTAAAAAAATCTAAAAAAAT-TACAAAAGTT
39331100 AAAATTTTAAAAA
1 AAAATTTTAAAAA
39331113 AAAATTAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
52 42 0.79
53 11 0.21
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (52 bp):
AAAATTTTAAAAATTTATAAAATTAAAAAAATCTAAAAAAATTACAAAAGTT
Found at i:39343844 original size:17 final size:17
Alignment explanation
Indices: 39343824--39343862 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
39343814 GACATGGGCG
*
39343824 TGTGGGACACATGAGCA
1 TGTGGGACACACGAGCA
*
39343841 TGTGGGACACACGAGCG
1 TGTGGGACACACGAGCA
39343858 TGTGG
1 TGTGG
39343863 AAGAACCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.18, G:0.41, T:0.18
Consensus pattern (17 bp):
TGTGGGACACACGAGCA
Found at i:39344998 original size:22 final size:22
Alignment explanation
Indices: 39344970--39345021 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
39344960 AACAATTACG
*
39344970 TCGCGACGTCGAGCCTTTGCCA
1 TCGCGACGTCGAGCCCTTGCCA
*
39344992 TCGCGACGTTGAGCCCTTGCCA
1 TCGCGACGTCGAGCCCTTGCCA
*
39345014 TTGCGACG
1 TCGCGACG
39345022 AGACTTAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.13, C:0.35, G:0.29, T:0.23
Consensus pattern (22 bp):
TCGCGACGTCGAGCCCTTGCCA
Found at i:39348357 original size:20 final size:20
Alignment explanation
Indices: 39348321--39348358 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39348311 TATTTGTTCT
*
39348321 AAATATTTAACATGAAAAAA
1 AAATATTTAACAAGAAAAAA
39348341 AAATATTTTAA-AAGAAAA
1 AAATA-TTTAACAAGAAAA
39348359 TTTACAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (20 bp):
AAATATTTAACAAGAAAAAA
Found at i:39348718 original size:18 final size:18
Alignment explanation
Indices: 39348692--39348739 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
39348682 TAAATTGTTA
*
39348692 AAAAAATAAATTTTATTT
1 AAAAAATAAAATTTATTT
*
39348710 AAAATATAAAATTTATTT
1 AAAAAATAAAATTTATTT
39348728 AAAAAA-AAAATT
1 AAAAAATAAAATT
39348740 ATAATATTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAAATAAAATTTATTT
Found at i:39349562 original size:20 final size:21
Alignment explanation
Indices: 39349531--39349572 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
39349521 GATCAATATG
39349531 GGATTAAAATTAACTTTTAAT
1 GGATTAAAATTAACTTTTAAT
*
39349552 GGATT-AAATTAATTTTTAAT
1 GGATTAAAATTAACTTTTAAT
39349572 G
1 G
39349573 AAAATAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (21 bp):
GGATTAAAATTAACTTTTAAT
Found at i:39350844 original size:64 final size:66
Alignment explanation
Indices: 39350767--39350899 Score: 182
Period size: 68 Copynumber: 2.0 Consensus size: 66
39350757 TAAAATATAT
* *
39350767 ATTTAATTAATTCATATCTTA-TATAT-AATATTTGCATATAATATAA-TTCAATGCATATATAA
1 ATTTAATTAATTCATATCTTATTATATAAATATTTACACATAATATAACTT-AATGCATATATAA
39350829 AA
65 AA
* *
39350831 ATTTAATTAATTCATATTTTATTTATATAAAATATTTACACATAATATAACTTAGTGCATATATA
1 ATTTAATTAATTCATATCTTA-TTATAT-AAATATTTACACATAATATAACTTAATGCATATATA
39350896 AAA
64 AAA
39350899 A
1 A
39350900 GATTTATTCA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
64 20 0.33
66 5 0.08
68 33 0.55
69 2 0.03
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (66 bp):
ATTTAATTAATTCATATCTTATTATATAAATATTTACACATAATATAACTTAATGCATATATAAA
A
Found at i:39352454 original size:21 final size:19
Alignment explanation
Indices: 39352423--39352461 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
39352413 ATACTCTTTC
39352423 ATATAATATATATTATTAT
1 ATATAATATATATTATTAT
39352442 ATATCAATAATATATTATTA
1 ATAT-AAT-ATATATTATTA
39352462 ATACTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 3 0.17
21 11 0.61
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATAATATATATTATTAT
Found at i:39356268 original size:19 final size:20
Alignment explanation
Indices: 39356229--39356271 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
39356219 TAAATTAGAA
39356229 AAAAATAATTATGAATCATT
1 AAAAATAATTATGAATCATT
* *
39356249 AAAAATAATTTTTAAT-ATT
1 AAAAATAATTATGAATCATT
39356268 AAAA
1 AAAA
39356272 GTAAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAATAATTATGAATCATT
Found at i:39357193 original size:13 final size:13
Alignment explanation
Indices: 39357177--39357201 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39357167 ATAATTAAAA
39357177 ATAATATCATTAG
1 ATAATATCATTAG
39357190 ATAATATCATTA
1 ATAATATCATTA
39357202 ATTTATTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
ATAATATCATTAG
Found at i:39360679 original size:9 final size:9
Alignment explanation
Indices: 39360665--39360691 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
39360655 TACTTTCTCT
39360665 CAAAGAATA
1 CAAAGAATA
39360674 CAAAGAATA
1 CAAAGAATA
39360683 CAAAGAATA
1 CAAAGAATA
39360692 GAATGGAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (9 bp):
CAAAGAATA
Found at i:39361764 original size:40 final size:40
Alignment explanation
Indices: 39361715--39361937 Score: 232
Period size: 40 Copynumber: 5.6 Consensus size: 40
39361705 ATTTACAATG
* *
39361715 CTGGCAGTGACACTATAAACACTACGATATTACAACTGAA
1 CTGGCAGTGACACTGTAAACACTGCGATATTACAACTGAA
* * * * *
39361755 CAGGAAGTGACACTGTAAATACTGTGATATTAAAACTGAA
1 CTGGCAGTGACACTGTAAACACTGCGATATTACAACTGAA
* *
39361795 -TGGGCAGTGACACTGTAAACATTGTGATATTACAACTGAA
1 CT-GGCAGTGACACTGTAAACACTGCGATATTACAACTGAA
* * * * *
39361835 CTGGCATTGACACTGTAAACACTGCAATACTACCACTAAA
1 CTGGCAGTGACACTGTAAACACTGCGATATTACAACTGAA
* * * *
39361875 TTGGCAGTGACACTGTAAACACTGCGATATCATAACTAAA
1 CTGGCAGTGACACTGTAAACACTGCGATATTACAACTGAA
*** *
39361915 CTCTAAGTGACACTGTAATCACT
1 CTGGCAGTGACACTGTAAACACT
39361938 TAAATGCTAC
Statistics
Matches: 150, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
40 149 0.99
41 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (40 bp):
CTGGCAGTGACACTGTAAACACTGCGATATTACAACTGAA
Found at i:39364346 original size:103 final size:103
Alignment explanation
Indices: 39364159--39364366 Score: 346
Period size: 103 Copynumber: 2.0 Consensus size: 103
39364149 TGTTCGTTAA
* * *
39364159 AAAAAAGATGGTAGGATGAGAATGTGTATCTATTACCGTTAGTTAAATAAGTTAACAATAAAGAA
1 AAAAAAGACGGTAGGATGAGAATGTGTATCGATTACCATTAGTTAAATAAGTTAACAATAAAGAA
*
39364224 CAAGTACCTATTACCGAGAATTGATGATTTGTTTGATT
66 CAAGTACCTATCACCGAGAATTGATGATTTGTTTGATT
*
39364262 AAAAAAGACGGTAGGATGAGAATGTGTATCGATTACCATTAGTTAAATAAGTTAACAATGAAGAA
1 AAAAAAGACGGTAGGATGAGAATGTGTATCGATTACCATTAGTTAAATAAGTTAACAATAAAGAA
*
39364327 CAAGTATCC-ATCACTGAGAATTGATGATTTGTTTGATT
66 CAAGTA-CCTATCACCGAGAATTGATGATTTGTTTGATT
39364365 AA
1 AA
39364367 TTCCGTGGAG
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 96 0.98
104 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (103 bp):
AAAAAAGACGGTAGGATGAGAATGTGTATCGATTACCATTAGTTAAATAAGTTAACAATAAAGAA
CAAGTACCTATCACCGAGAATTGATGATTTGTTTGATT
Found at i:39370446 original size:22 final size:22
Alignment explanation
Indices: 39370403--39370446 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
39370393 TCTTCGATGA
*
39370403 TTCTGATTTTTGTTATCTATCT
1 TTCTGATTTTTGTTATCAATCT
* * *
39370425 TTCTGTTTTTTTTTTTCAATCT
1 TTCTGATTTTTGTTATCAATCT
39370447 CTTAGCAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.11, C:0.14, G:0.07, T:0.68
Consensus pattern (22 bp):
TTCTGATTTTTGTTATCAATCT
Found at i:39380031 original size:14 final size:15
Alignment explanation
Indices: 39380004--39380053 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
39379994 CAATGCGATG
39380004 ATGTAA-ATGATTAAA
1 ATGTAAGAT-ATTAAA
*
39380019 ATGTAATAT-TTAAA
1 ATGTAAGATATTAAA
**
39380033 AAATAAGATATTAAA
1 ATGTAAGATATTAAA
39380048 ATGTAA
1 ATGTAA
39380054 ACTGAGTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 11 0.39
15 15 0.54
16 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (15 bp):
ATGTAAGATATTAAA
Found at i:39385748 original size:2 final size:2
Alignment explanation
Indices: 39385741--39385765 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39385731 ATAATGAAAG
39385741 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39385766 AACTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39406328 original size:69 final size:68
Alignment explanation
Indices: 39406165--39406402 Score: 217
Period size: 69 Copynumber: 3.5 Consensus size: 68
39406155 CATTATCAAG
* * *
39406165 GGAGAGCTAGGAACAGAATCTGCAAAAATAGACGAGCTT-TGCCCCTTGAACAAGTTATCCGCAT
1 GGAGAGCTAGGAACAGAATCTGCAAAAATAG-CGA-ATTCTTCCCCTTGAACAAGTTATCTGCAT
*
39406229 AGACA
64 AGGCA
* * * * * *
39406234 GGAGAGCTTGGAATAGATTCTGCAAATATGGCCGAATTCTTCCCCTTGAACATGTTATCTGCATA
1 GGAGAGCTAGGAACAGAATCTGCAAAAATAG-CGAATTCTTCCCCTTGAACAAGTTATCTGCATA
39406299 GGCA
65 GGCA
* * ** * * * * * *
39406303 GGAGTGCTAGGAACAGAATCAGCAAAAATAGATAAGCTCTTTCCCTTGCACACGATATCTGCAGA
1 GGAGAGCTAGGAACAGAATCTGCAAAAATAGCGAA-TTCTTCCCCTTGAACAAGTTATCTGCATA
39406368 GGCA
65 GGCA
* * * *
39406372 GGGGTGCTCGGAACAGAATCCGCAAAAATAG
1 GGAGAGCTAGGAACAGAATCTGCAAAAATAG
39406403 ACGATCTTTT
Statistics
Matches: 138, Mismatches: 29, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
68 4 0.03
69 134 0.97
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (68 bp):
GGAGAGCTAGGAACAGAATCTGCAAAAATAGCGAATTCTTCCCCTTGAACAAGTTATCTGCATAG
GCA
Found at i:39406415 original size:69 final size:67
Alignment explanation
Indices: 39406289--39406468 Score: 182
Period size: 69 Copynumber: 2.6 Consensus size: 67
39406279 TTGAACATGT
* * * * * *
39406289 TATCTGCATAGGCAGGAGTGCTAGGAACAGAATCAGCAAAAATAGATAAGCTCTTTCCCTTGCAC
1 TATCTGCAGAGGCAGGGGTGCTCGGAACAGAATCCGCAAAAATAGACAAGCTCTTTCCCATGCA-
39406354 ACGA
65 AC-A
* * * *
39406358 TATCTGCAGAGGCAGGGGTGCTCGGAACAGAATCCGCAAAAATAGACGATCTTTTTCCCATGGAA
1 TATCTGCAGAGGCAGGGGTGCTCGGAACAGAATCCGCAAAAATAGACAAGCTCTTTCCCATGCAA
39406423 CA
66 CA
* * *
39406425 TGTCACTTG-TGTAGGCAGGGGTGCTCGGAACAGAATCCTCAAAA
1 TAT--C-TGCAG-AGGCAGGGGTGCTCGGAACAGAATCCGCAAAA
39406469 GTGAACGGGC
Statistics
Matches: 94, Mismatches: 13, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
67 3 0.03
68 2 0.02
69 56 0.60
70 33 0.35
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (67 bp):
TATCTGCAGAGGCAGGGGTGCTCGGAACAGAATCCGCAAAAATAGACAAGCTCTTTCCCATGCAA
CA
Found at i:39407121 original size:1 final size:1
Alignment explanation
Indices: 39407117--39407152 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
39407107 AGGAAAAAGC
39407117 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
39407153 ACAAAACTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:39449122 original size:16 final size:18
Alignment explanation
Indices: 39449101--39449133 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
39449091 ATATAAAAAT
39449101 TTTAAAT-T-ATTTTTAC
1 TTTAAATATAATTTTTAC
39449117 TTTAAATATAATTTTTA
1 TTTAAATATAATTTTTA
39449134 TCATCATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAAATATAATTTTTAC
Found at i:39450894 original size:16 final size:16
Alignment explanation
Indices: 39450875--39450905 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39450865 GCTGTCAACC
39450875 TTCAAAAAACTTCATT
1 TTCAAAAAACTTCATT
39450891 TTCAAAAAACTTCAT
1 TTCAAAAAACTTCAT
39450906 GTCTTCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (16 bp):
TTCAAAAAACTTCATT
Found at i:39455192 original size:33 final size:34
Alignment explanation
Indices: 39455155--39455219 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
39455145 TATACAGAGA
*
39455155 AATTTTTCAT-CAATTTTTACTTCTTTTCTCTGC
1 AATTTTTCATCCAATTTTGACTTCTTTTCTCTGC
* * *
39455188 AATTTTTCTTCCAATTTTGATTTGTTTTCTCT
1 AATTTTTCATCCAATTTTGACTTCTTTTCTCT
39455220 TCAAGAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 9 0.33
34 18 0.67
ACGTcount: A:0.17, C:0.18, G:0.05, T:0.60
Consensus pattern (34 bp):
AATTTTTCATCCAATTTTGACTTCTTTTCTCTGC
Found at i:39455630 original size:2 final size:2
Alignment explanation
Indices: 39455623--39455657 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39455613 CTGTACAGTG
39455623 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39455658 TAAGGTCAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39462809 original size:153 final size:154
Alignment explanation
Indices: 39462530--39462809 Score: 454
Period size: 153 Copynumber: 1.8 Consensus size: 154
39462520 TTGAAAGCTC
* * * * *
39462530 TTGAAAAGGATATTCGATTGGCGTGAATCACGAAAATCACACTTAACACGTTAAAGCGCGATTTT
1 TTGAAAAGGATATTCAATTCGCATGAATCACGAAAATCACACTTAACACGTTAAAACGCGATTCT
* *
39462595 TTCGAAGTTTTCACACGAAAGGACATTGCCTCGTTTTAAAATTATTTGTGATATAGATATATAAA
66 TTCGAAGTTTTCACACGAAAGGACATTGCCTCGCTTTAAAATTATTTGTAATATAGATATATAAA
39462660 AATTGAAGGATGTTTCGGGAACTT
131 AATTGAAGGATGTTTCGGGAACTT
* *
39462684 TTGAAGAGGATATTCAATTCGCATGAATTACGAAAATCACACTTAACACGTTAAAACGCGA-TCT
1 TTGAAAAGGATATTCAATTCGCATGAATCACGAAAATCACACTTAACACGTTAAAACGCGATTCT
* *
39462748 TTCGAAGTTTTCACACGACAGGACATTGTCTCGCTTTAAAATTATTTGTAATATAGATATAT
66 TTCGAAGTTTTCACACGAAAGGACATTGCCTCGCTTTAAAATTATTTGTAATATAGATATAT
39462810 GTTTTGAGAA
Statistics
Matches: 115, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
153 60 0.52
154 55 0.48
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (154 bp):
TTGAAAAGGATATTCAATTCGCATGAATCACGAAAATCACACTTAACACGTTAAAACGCGATTCT
TTCGAAGTTTTCACACGAAAGGACATTGCCTCGCTTTAAAATTATTTGTAATATAGATATATAAA
AATTGAAGGATGTTTCGGGAACTT
Found at i:39463394 original size:59 final size:58
Alignment explanation
Indices: 39463327--39463801 Score: 528
Period size: 59 Copynumber: 8.1 Consensus size: 58
39463317 GAATTTCGGA
* * *
39463327 GGGGTAAAAAT-GTAATTTTTGGTTAAATCGGGCTCAAAAATGGAATTTTGGAAAGTTT
1 GGGGT-AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
* ** * * * *
39463385 AAGCATAAAATAGTATTTTTTTGGTGAAAAT-GGGGTTAAAAAT-GAGATTTTGGAAGGTTCG
1 -GGGGTAAAATGGTA-ATTTTTGGTG-AAATCGGGGTTAAAAATGGA-ATTTTGGAAAGTT-T
* * * * *
39463446 GGGGTAAAATAGTAATTTTTGGTGAAATCGGGGGTAAAAATGGGATTTTGGAAGGTTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
* * * *
39463504 GGGGGAAAATGGTAATTTTTTAGTGAAATCAGGGTTAAAAATGAAATTTTGGAAAGTTT
1 GGGGTAAAATGGTAA-TTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
* * *
39463563 GGGGTTAAAATGGCAATTTTGGGTAAAATCGGGGTTAAAAAT-GAAGTTTTGGAAAGTTT
1 GGGG-TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAA-TTTTGGAAAGTTT
* *
39463622 GGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTT-AAAATGGAATTTTGGAAAGTTT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
*
39463679 AGGGGTAAAATGGTAATTTTGGGTGAAATCGGGGGTTAAAAATGGAATTTTGGAAAGTTT
1 -GGGGTAAAATGGTAATTTTTGGTGAAATC-GGGGTTAAAAATGGAATTTTGGAAAGTTT
*** * * *
39463739 AATTGTAAAATGGTAATTTTGGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTT
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
39463798 GGGG
1 GGGG
39463802 ACTAGAGAGT
Statistics
Matches: 356, Mismatches: 46, Indels: 29
0.83 0.11 0.07
Matches are distributed among these distances:
57 18 0.05
58 83 0.23
59 151 0.42
60 100 0.28
61 4 0.01
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
Found at i:39463448 original size:29 final size:29
Alignment explanation
Indices: 39463416--39463512 Score: 87
Period size: 29 Copynumber: 3.3 Consensus size: 29
39463406 TGGTGAAAAT
*
39463416 GGGGTTAAAAATGAGATTTTGGAAGGTTC
1 GGGGGTAAAAATGAGATTTTGGAAGGTTC
*
39463445 GGGGGT-AAAAT-AGTAATTTTTGGTGAA--ATC
1 GGGGGTAAAAATGAG--A-TTTT-G-GAAGGTTC
*
39463475 GGGGGTAAAAATGGGATTTTGGAAGGTTC
1 GGGGGTAAAAATGAGATTTTGGAAGGTTC
39463504 GGGGG-AAAA
1 GGGGGTAAAA
39463513 TGGTAATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
27 5 0.09
28 10 0.18
29 17 0.31
30 13 0.24
31 6 0.11
32 4 0.07
ACGTcount: A:0.32, C:0.03, G:0.37, T:0.28
Consensus pattern (29 bp):
GGGGGTAAAAATGAGATTTTGGAAGGTTC
Found at i:39463466 original size:30 final size:30
Alignment explanation
Indices: 39463432--39463523 Score: 86
Period size: 30 Copynumber: 3.1 Consensus size: 30
39463422 AAAAATGAGA
39463432 TTTTGGAAGGTTCGGGGGTAAAATAGTAAT
1 TTTTGGAAGGTTCGGGGGTAAAATAGTAAT
* **
39463462 TTTTGGTGAA--ATCGGGGGTAAAA-ATGGGA-
1 TTTT-G-GAAGGTTCGGGGGTAAAATA-GTAAT
*
39463491 TTTTGGAAGGTTCGGGGG-AAAATGGTAAT
1 TTTTGGAAGGTTCGGGGGTAAAATAGTAAT
39463520 TTTT
1 TTTT
39463524 TAGTGAAATC
Statistics
Matches: 48, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
27 3 0.06
28 7 0.15
29 16 0.33
30 18 0.38
31 1 0.02
32 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.35, T:0.34
Consensus pattern (30 bp):
TTTTGGAAGGTTCGGGGGTAAAATAGTAAT
Found at i:39463567 original size:29 final size:28
Alignment explanation
Indices: 39463535--39463738 Score: 130
Period size: 29 Copynumber: 7.0 Consensus size: 28
39463525 AGTGAAATCA
39463535 GGGTTAAAAATGAAATTTTGGAAAGTTTG
1 GGGTT-AAAATGAAATTTTGGAAAGTTTG
* * *
39463564 GGGTTAAAATGGCAATTTTGGGTAAA-ATCG
1 GGGTTAAAAT-GAAATTTT-GG-AAAGTTTG
*
39463594 GGGTTAAAAATGAAGTTTTGGAAAGTTTG
1 GGGTT-AAAATGAAATTTTGGAAAGTTTG
* * *
39463623 GGG-TAAAATGGTAATTTTTGGTAAA-ATCG
1 GGGTTAAAAT-G-AAATTTTGG-AAAGTTTG
* *
39463652 AGGTTAAAATGGAATTTTGGAAAGTTTAG
1 GGGTTAAAATGAAATTTTGGAAAGTTT-G
* **
39463681 GGG-TAAAATGGTAATTTTGGGTGAAA-TCGG
1 GGGTTAAAAT-GAAATTTT--G-GAAAGTTTG
*
39463711 GGGTTAAAAATGGAATTTTGGAAAGTTT
1 GGGTT-AAAATGAAATTTTGGAAAGTTT
39463739 AATTGTAAAA
Statistics
Matches: 135, Mismatches: 22, Indels: 36
0.70 0.11 0.19
Matches are distributed among these distances:
27 8 0.06
28 28 0.21
29 44 0.33
30 28 0.21
31 18 0.13
32 9 0.07
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (28 bp):
GGGTTAAAATGAAATTTTGGAAAGTTTG
Found at i:39463693 original size:176 final size:173
Alignment explanation
Indices: 39463326--39463801 Score: 539
Period size: 176 Copynumber: 2.7 Consensus size: 173
39463316 TGAATTTCGG
* * *
39463326 AGGGGTAAAAAT-GTAATTTTTGGTTAAATCGGGCTCAAAAATGGAATTTTGGAAAGTTTAAGCA
1 AGGGGT-AAAATGGTAATTTTTGGTGAAATCGGG-TTAAAAATGGAATTTTGGAAAGTTT-AGCT
* * * * *
39463390 TAAAATAGTATTTTTTTGGTGAAAAT-GGGGTTAAAAATG-AGATTTTGGAAGGTTCGGGGGTAA
63 TAAAATGGTA-ATTTTGGGT-AAAATCGGGGTTAAAAATGAAG-TTTTGGAAAGTT-TGGGGTAA
* * *
39463453 AATAGTAATTTTTGGTGAAATCGGGGGTAAAAATGGGATTTTGGAAGGTT
124 AATAGTAATTTTTGGTAAAATCGGAGGTAAAAATGGAATTTTGGAAGGTT
* * * * * *
39463503 CGGGGGAAAATGGTAATTTTTTAGTGAAATCAGGGTTAAAAATGAAATTTTGGAAAGTTTGGGGT
1 AGGGGTAAAATGGTAA-TTTTTGGTGAAATC-GGGTTAAAAATGGAATTTTGGAAAGTTT-AGCT
* *
39463568 TAAAATGGCAATTTTGGGTAAAATCGGGGTTAAAAATGAAGTTTTGGAAAGTTTGGGGTAAAATG
63 TAAAATGGTAATTTTGGGTAAAATCGGGGTTAAAAATGAAGTTTTGGAAAGTTTGGGGTAAAATA
* *
39463633 GTAATTTTTGGTAAAATC-GAGGTTAAAATGGAATTTTGGAAAGTTT
128 GTAATTTTTGGTAAAATCGGAGGTAAAAATGGAATTTTGG-AAGGTT
* **
39463679 AGGGGTAAAATGGTAATTTTGGGTGAAATCGGGGGTTAAAAATGGAATTTTGGAAAGTTTAATTG
1 AGGGGTAAAATGGTAATTTTTGGTGAAATC--GGGTTAAAAATGGAATTTTGGAAAGTTTAGCT-
* * *
39463744 TAAAATGGTAATTTTGGGTGAAATCGAGGTCAAAAATGGAA-TTTTGGAAAGTTTGGGG
63 TAAAATGGTAATTTTGGGTAAAATCGGGGTTAAAAAT-GAAGTTTTGGAAAGTTTGGGG
39463802 ACTAGAGAGT
Statistics
Matches: 255, Mismatches: 35, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
175 31 0.12
176 133 0.52
177 42 0.16
178 46 0.18
179 3 0.01
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (173 bp):
AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGTTAAAAATGGAATTTTGGAAAGTTTAGCTTAA
AATGGTAATTTTGGGTAAAATCGGGGTTAAAAATGAAGTTTTGGAAAGTTTGGGGTAAAATAGTA
ATTTTTGGTAAAATCGGAGGTAAAAATGGAATTTTGGAAGGTT
Found at i:39476130 original size:38 final size:38
Alignment explanation
Indices: 39476085--39477349 Score: 1029
Period size: 38 Copynumber: 35.6 Consensus size: 38
39476075 AAGAGCAACG
39476085 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
39476123 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
** *
39476161 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACAACG
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
* * *
39476199 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACTCATCC
1 TCAT-CCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
* * **
39476238 TCGTCTC-TGAAATTGAAGTA-A---GAGCA-ACG---
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
39476267 TCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCT
1 TCATCC-CTTGAAATTGAAGTAGAG-TGGATAACACGTCT
* * ** *
39476307 TGATCTC-TGAAATTGAAGTA-A---GAGCA-ACGTCA
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
* * *
39476339 TC--CCCTTGAAACTGAAGTAGAGTGGGTAATACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
* * **
39476375 TGATCTC-TGAAATTGAAGTA-A---GAGCA-ACG---
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
39476404 TCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCT
1 TCATCC-CTTGAAATTGAAGTAGAG-TGGATAACACGTCT
* ** *
39476444 TCATCTC-TGAAATTGAAGTA-A---GAGCA-ACGTCA
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
39476476 TC--CCCTTGAAATTGAAGTAGAGTGGATAACACGTCA
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
39476512 TC--CCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
* ** *
39476548 TCATCTC-TGAAATTGAAGTA-A---GAGCA-ACGTCA
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
39476580 TC--CCCTTGAAATTGAAGTAGAGTGGATAAAACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
39476616 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
39476654 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
* * *
39476692 TCATCCCTTGAAATTGAAGTAGAGTGGATAACTCATCC
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
* * **
39476730 TCGTCTC-TGAAATTGAAGTA-A---GAGCA-ACG---
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
39476759 TCATCCTCTTGAAATTGAAGTAGAGTTGGATAA-AGAGTCT
1 TCATCC-CTTGAAATTGAAGTAGAG-TGGATAACA-CGTCT
* * * *
39476799 TGATCTC-TGAAATTGAAGTA-AG-AG-T-A-ACGTCA
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
* * *
39476831 TC--CCCTTGAAACTGAAGTAGAGTGGGTAATACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
* * **
39476867 TGATCTC-TGAAATTGAAGTA-A---GAGCA-ACG---
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
39476896 TCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCT
1 TCATCC-CTTGAAATTGAAGTAGAG-TGGATAACACGTCT
* ** *
39476936 TCATCTC-TGAAATTGAAGTA-A---GAGCA-ACGTCA
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
39476968 TC--CCCTTGAAATTGAAGTAGAGTGGATAACACG---
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
39477001 TCATCCCTTTGAAATTGAAGTAGAGTGGATAACACGTCT
1 TCATCCC-TTGAAATTGAAGTAGAGTGGATAACACGTCT
* ** *
39477040 TCATCTC-TGAAATTGAAGTA-A---GAGCA-ACGTCA
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
39477072 TC--CCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
39477108 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
39477146 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
** *
39477184 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACAACG
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
* * *
39477222 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACTCATCC
1 TCAT-CCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
* * **
39477261 TCGTCTC-TGAAATTGAAGTA-A---GAGCA-ACG---
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
*
39477290 TCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCT
1 TCATCC-CTTGAAATTGAAGTAGAG-TGGATAACACGTCT
* *
39477330 TAATCTC-TGAAATTGAAGTA
1 TCATCCCTTGAAATTGAAGTA
39477350 AGAGCAACGT
Statistics
Matches: 989, Mismatches: 129, Indels: 218
0.74 0.10 0.16
Matches are distributed among these distances:
29 20 0.02
30 17 0.02
31 141 0.14
32 56 0.06
33 33 0.03
34 2 0.00
35 19 0.02
36 123 0.12
37 103 0.10
38 374 0.38
39 79 0.08
40 22 0.02
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (38 bp):
TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCT
Found at i:39476331 original size:69 final size:68
Alignment explanation
Indices: 39476194--39476998 Score: 860
Period size: 69 Copynumber: 11.6 Consensus size: 68
39476184 GTGGATAACA
* *
39476194 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACTCA-TCCTCG-TCTCTGAAATTGAAGT
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAAC-AAGT-CTTGATCTCTGAAATTGAAGT
39476257 AAGAG
64 AAGAG
*
39476262 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTGATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTGATCTCTGAAATTGAAGTA
39476327 AGAG
65 AGAG
* * * *
39476331 CAACGTCATCCCCTTGAAACTGAAGTAGAGTGGGTAATACGTCTTGATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAGTAA
39476396 GAG
66 GAG
* *
39476399 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTGATCTCTGAAATTGAAGTA
39476464 AGAG
65 AGAG
* * ***
39476468 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCATCCCCT-TGAAATTGAAGTAG
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAGTA-
*
39476532 AGTGGAT
65 A---GAG
* * ** * * * ***
39476539 AACACGTCTTCATCTCTGAAATTGAAGTA-AG-AG-CAAC--GTCATCCCCT-TGAAATTGAAGT
1 CA-ACGTCATCCCCT-TGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAGT
*
39476598 AGAGTGGATA
64 A-A---GA-G
* * * * *
39476608 AAACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAG
1 CAACGTCATC--CCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTC-TGAAATTGAAG
*
39476673 TAGAGTGGAT
63 TA-A---GAG
* * * *
39476683 AACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACTCA-TCCTCG-TCTCTGAAATTGA
1 CA-ACGTCATC--CCCTTGAAATTGAAGTAGAGTGGATAAC-AAGT-CTTGATCTCTGAAATTGA
39476746 AGTAAGAG
61 AGTAAGAG
*
39476754 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAA-AGAGTCTTGATCTCTGAAATTGAAGT
1 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACA-AGTCTTGATCTCTGAAATTGAAGT
39476818 AAGAG
64 AAGAG
* * * * *
39476823 TAACGTCATCCCCTTGAAACTGAAGTAGAGTGGGTAATACGTCTTGATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAGTAA
39476888 GAG
66 GAG
* *
39476891 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTGATCTCTGAAATTGAAGTA
39476956 AGAG
65 AGAG
39476960 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACA
39476999 CGTCATCCCT
Statistics
Matches: 648, Mismatches: 60, Indels: 58
0.85 0.08 0.08
Matches are distributed among these distances:
67 13 0.02
68 244 0.38
69 256 0.40
70 14 0.02
71 8 0.01
72 14 0.02
73 13 0.02
74 7 0.01
75 15 0.02
76 62 0.10
77 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (68 bp):
CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAGTAA
GAG
Found at i:39476383 original size:137 final size:136
Alignment explanation
Indices: 39476123--39477022 Score: 933
Period size: 137 Copynumber: 6.4 Consensus size: 136
39476113 TAACACGTCT
* *
39476123 TCATCC-CTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTG
1 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTC-TGAAATTGAAGTA-A---
* * * * *
39476187 GATAACACAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACTCATCCTCGTCTCTGAAATT
61 G---A-GCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATT
39476252 GAAGTAAGAGCAACG
122 GAAGTAAGAGCAACG
*
39476267 TCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTGATCTCTGAAATTGAAGTAAGAGC
1 TCATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGC
* * * *
39476332 AACGTCATCCCCTTGAAACTGAAGTAGAGTGGGTAATACGTCTTGATCTCTGAAATTGAAGTAAG
65 AACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAG
39476397 AGCAACG
130 AGCAACG
39476404 TCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGC
1 TCATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGC
* **
39476469 AACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCATCCCCT-TGAAATTGAAGTAGA
65 AACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTA-A
**
39476533 GTGGATAACACG
129 ---GAGCA-ACG
* * * * * **
39476545 TCTTCATCTCTGAAATTGAAGTA-AG-AG-CAAC--GTCATCCCCT-TGAAATTGAAGTAGAGTG
1 TCATCCTCT-TGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA-A---
** * *
39476604 GATAAAACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATT
61 GA-GCAACGTCATC--CCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTC-TGAAATT
**
39476669 GAAGTAGAGTGGATAACACG
122 GAAGTA-A---GAGCA-ACG
* * *
39476689 TCTTCATCC-CTTGAAATTGAAGTAGAGTGGATAACTCA-TCCTCGTCTCTGAAATTGAAGTAAG
1 ---TCATCCTCTTGAAATTGAAGTAGAGTGGATAAC-AAGTCTTCATCTCTGAAATTGAAGTAAG
* * *
39476752 AGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAA-AGAGTCTTGATCTCTGAAATTGAA
62 AGCAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACA-CGTCTTCATCTCTGAAATTGAA
*
39476816 GTAAGAGTAACG
125 GTAAGAGCAACG
* * * * * *
39476828 TCATCCCCTTGAAACTGAAGTAGAGTGGGTAATACGTCTTGATCTCTGAAATTGAAGTAAGAGCA
1 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCA
* *
39476893 ACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAG
66 ACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTCATCTCTGAAATTGAAGTAAG
39476958 AGCAACG
130 AGCAACG
* * * * *
39476965 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCATC-CCTTTGAAATTGAAGTA
1 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
39477023 GAGTGGATAA
Statistics
Matches: 655, Mismatches: 69, Indels: 72
0.82 0.09 0.09
Matches are distributed among these distances:
135 13 0.02
136 42 0.06
137 325 0.50
138 5 0.01
139 6 0.01
140 14 0.02
141 13 0.02
142 49 0.07
143 1 0.00
144 67 0.10
145 60 0.09
146 30 0.05
147 7 0.01
148 3 0.00
150 7 0.01
151 13 0.02
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (136 bp):
TCATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCA
ACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGA
GCAACG
Found at i:39476999 original size:492 final size:492
Alignment explanation
Indices: 39476075--39477215 Score: 2196
Period size: 492 Copynumber: 2.3 Consensus size: 492
39476065 CATTTTCTGC
39476075 AAGAGCAACGTCAT-CCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTG
1 AAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTG
** *
39476139 AAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACAACGTCATC
66 AAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCAT-
39476204 CCCTTGAAATTGAAGTAGAGTGGATAACTCATCCTCGTCTCTGAAATTGAAGTAAGAGCAACGTC
130 CCCTTGAAATTGAAGTAGAGTGGATAACTCATCCTCGTCTCTGAAATTGAAGTAAGAGCAACGTC
39476269 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTGATCTCTGAAATTGAAGTAAGAGCAA
195 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTGATCTCTGAAATTGAAGTAAGAGCAA
39476334 CGTCATCCCCTTGAAACTGAAGTAGAGTGGGTAATACGTCTTGATCTCTGAAATTGAAGTAAGAG
260 CGTCATCCCCTTGAAACTGAAGTAGAGTGGGTAATACGTCTTGATCTCTGAAATTGAAGTAAGAG
39476399 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
325 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
39476464 AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCATCCCCTTGAAATTGAAG
390 AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCATCCCCTTGAAATTGAAG
39476529 TAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGT
455 TAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGT
*
39476567 AAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAAAACGTCTTCATCCCTTGAAATTG
1 AAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTG
39476632 AAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATC
66 AAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATC
39476697 CCTTGAAATTGAAGTAGAGTGGATAACTCATCCTCGTCTCTGAAATTGAAGTAAGAGCAACGTCA
131 CCTTGAAATTGAAGTAGAGTGGATAACTCATCCTCGTCTCTGAAATTGAAGTAAGAGCAACGTCA
*
39476762 TCCTCTTGAAATTGAAGTAGAGTTGGATAA-AGAGTCTTGATCTCTGAAATTGAAGTAAGAGTAA
196 TCCTCTTGAAATTGAAGTAGAGTTGGATAACA-AGTCTTGATCTCTGAAATTGAAGTAAGAGCAA
39476826 CGTCATCCCCTTGAAACTGAAGTAGAGTGGGTAATACGTCTTGATCTCTGAAATTGAAGTAAGAG
260 CGTCATCCCCTTGAAACTGAAGTAGAGTGGGTAATACGTCTTGATCTCTGAAATTGAAGTAAGAG
39476891 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
325 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTA
*
39476956 AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCATCCCTTTGAAATTGAAG
390 AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCATCCCCTTGAAATTGAAG
39477021 TAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGT
455 TAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGT
39477059 AAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTG
1 AAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTG
39477124 AAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATC
66 AAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATC
39477189 CCTTGAAATTGAAGTAGAGTGGATAAC
131 CCTTGAAATTGAAGTAGAGTGGATAAC
39477216 ACAACGTCAT
Statistics
Matches: 640, Mismatches: 7, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
491 1 0.00
492 529 0.83
493 110 0.17
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (492 bp):
AAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTG
AAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATC
CCTTGAAATTGAAGTAGAGTGGATAACTCATCCTCGTCTCTGAAATTGAAGTAAGAGCAACGTCA
TCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTGATCTCTGAAATTGAAGTAAGAGCAAC
GTCATCCCCTTGAAACTGAAGTAGAGTGGGTAATACGTCTTGATCTCTGAAATTGAAGTAAGAGC
AACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAA
GAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCATCCCCTTGAAATTGAAGT
AGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGT
Found at i:39477358 original size:69 final size:69
Alignment explanation
Indices: 39477217--39477425 Score: 269
Period size: 69 Copynumber: 3.0 Consensus size: 69
39477207 GTGGATAACA
* * **
39477217 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAACTCA-TCCTCGTCTCTGAAATTGAAGT
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTTGGATAAC-AAGTCTTAATCTCTGAAATTGAAGT
39477280 AAGAG
65 AAGAG
*
39477285 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTAATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTAATCTCTGAAATTGAAGTA
39477350 AGAG
66 AGAG
* * * * * * * * *
39477354 CAACGTCGTCCCCTTTAAATCGAAATAGAGTTGGATAACACGCCTTTATTTCAGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTAATCTCTGAAATTGAAGTA
39477419 AGAG
66 AGAG
39477423 CAA
1 CAA
39477426 GATCATTTCC
Statistics
Matches: 124, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
68 30 0.24
69 94 0.76
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (69 bp):
CAACGTCATCCCCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTAATCTCTGAAATTGAAGTA
AGAG
Found at i:39477787 original size:6 final size:6
Alignment explanation
Indices: 39477769--39477870 Score: 77
Period size: 6 Copynumber: 17.0 Consensus size: 6
39477759 TTAAATTGAT
* *
39477769 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAATA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AA-A TTTAAA
* ** * *
39477816 TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA TTAAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TT-TAAA
39477865 TTTAAA
1 TTTAAA
39477871 AGTCCAAAGT
Statistics
Matches: 77, Mismatches: 11, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 47 0.61
7 14 0.18
8 4 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:39477799 original size:17 final size:15
Alignment explanation
Indices: 39477773--39477837 Score: 78
Period size: 17 Copynumber: 4.1 Consensus size: 15
39477763 ATTGATTTTA
39477773 AATTTATTTAAATTT
1 AATTTATTTAAATTT
39477788 AGATTTATTTTAAATTT
1 A-ATTTA-TTTAAATTT
*
39477805 AA-ATATTTAAATTT
1 AATTTATTTAAATTT
39477819 AATTTGAATTTAAATTT
1 AATTT--ATTTAAATTT
39477836 AA
1 AA
39477838 ATAAAAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.26
15 4 0.09
16 6 0.14
17 22 0.51
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
AATTTATTTAAATTT
Found at i:39477815 original size:31 final size:31
Alignment explanation
Indices: 39477777--39477840 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
39477767 ATTTTAAATT
*
39477777 TATTTAAATTTAGATTT-ATTTTAAATTTAAA
1 TATTTAAATTTA-ATTTGAATTTAAATTTAAA
39477808 TATTTAAATTTAATTTGAATTTAAATTTAAA
1 TATTTAAATTTAATTTGAATTTAAATTTAAA
39477839 TA
1 TA
39477841 AAAATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
TATTTAAATTTAATTTGAATTTAAATTTAAA
Found at i:39477823 original size:11 final size:11
Alignment explanation
Indices: 39477759--39477839 Score: 64
Period size: 11 Copynumber: 7.5 Consensus size: 11
39477749 GACTTTTGAG
* *
39477759 TTAAATTGATT
1 TTAAATTTAAT
39477770 TTAAATTT-AT
1 TTAAATTTAAT
39477780 TTAAATTTAGAT
1 TTAAATTTA-AT
*
39477792 TT-ATTTTAAAT
1 TTAAATTT-AAT
39477803 TTAAA--T-AT
1 TTAAATTTAAT
39477811 TTAAATTTAAT
1 TTAAATTTAAT
*
39477822 TTGAATTTAAAT
1 TTAAATTT-AAT
39477834 TTAAAT
1 TTAAAT
39477840 AAAAATTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
8 7 0.12
10 11 0.20
11 24 0.43
12 14 0.25
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:39477849 original size:42 final size:40
Alignment explanation
Indices: 39477769--39477859 Score: 101
Period size: 42 Copynumber: 2.2 Consensus size: 40
39477759 TTAAATTGAT
* ** * *
39477769 TTTAAATTTATTTAAATTTAGATTTATTTTAAATTTAAATA
1 TTTAAATTTATTTAAATTTAAATTTAAATAAAAATTAAA-A
*
39477810 TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAA
1 TTTAAATTT-ATTTAAATTTAAATTTAAATAAAAATTAAAA
39477851 TATTAAATT
1 T-TTAAATT
39477860 AAAAATTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 11 0.26
42 31 0.74
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (40 bp):
TTTAAATTTATTTAAATTTAAATTTAAATAAAAATTAAAA
Found at i:39478054 original size:20 final size:20
Alignment explanation
Indices: 39478029--39478088 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
39478019 GTGCCTACTG
*
39478029 CTGCTGGCCACCAGCTCCAT
1 CTGCTGACCACCAGCTCCAT
*
39478049 CTGCTGACTACCAGCTCCAT
1 CTGCTGACCACCAGCTCCAT
39478069 CTGCTGACCACCAAGCTCCA
1 CTGCTGACCACC-AGCTCCA
39478089 CCATGCCCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 29 0.81
21 7 0.19
ACGTcount: A:0.20, C:0.43, G:0.17, T:0.20
Consensus pattern (20 bp):
CTGCTGACCACCAGCTCCAT
Found at i:39478587 original size:9 final size:9
Alignment explanation
Indices: 39478573--39478671 Score: 74
Period size: 9 Copynumber: 10.3 Consensus size: 9
39478563 AAATGAGGTT
39478573 TAATATTAA
1 TAATATTAA
*
39478582 TAATATTAT
1 TAATATTAA
39478591 TAATGGCATTAA
1 TAAT---ATTAA
39478603 TAATATTAA
1 TAATATTAA
*
39478612 TAATATTAT
1 TAATATTAA
39478621 TAATGGCATTAA
1 TAAT---ATTAA
39478633 TAATATTAA
1 TAATATTAA
**
39478642 TAACGGTT-A
1 TAA-TATTAA
*
39478651 TAATATCAA
1 TAATATTAA
*
39478660 TAATAATAA
1 TAATATTAA
39478669 TAA
1 TAA
39478672 ATTTATTTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
8 1 0.01
9 52 0.73
10 2 0.03
12 16 0.23
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.40
Consensus pattern (9 bp):
TAATATTAA
Found at i:39478608 original size:30 final size:30
Alignment explanation
Indices: 39478573--39478644 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
39478563 AAATGAGGTT
39478573 TAATATTAATAATATTATTAATGGCATTAA
1 TAATATTAATAATATTATTAATGGCATTAA
39478603 TAATATTAATAATATTATTAATGGCATTAA
1 TAATATTAATAATATTATTAATGGCATTAA
39478633 TAATATTAATAA
1 TAATATTAATAA
39478645 CGGTTATAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (30 bp):
TAATATTAATAATATTATTAATGGCATTAA
Found at i:39478622 original size:21 final size:21
Alignment explanation
Indices: 39478576--39478640 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
39478566 TGAGGTTTAA
* **
39478576 TATTAATAATATTATTAATGG
1 TATTAATAATATTAATAATAT
*
39478597 CATTAATAATATTAATAATAT
1 TATTAATAATATTAATAATAT
***
39478618 TATTAATGGCATTAATAATAT
1 TATTAATAATATTAATAATAT
39478639 TA
1 TA
39478641 ATAACGGTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (21 bp):
TATTAATAATATTAATAATAT
Found at i:39478940 original size:15 final size:15
Alignment explanation
Indices: 39478922--39478977 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
39478912 TAAAAAAACA
*
39478922 AAAGAAAGAAAAGGG
1 AAAGAAAGAAAAGAG
39478937 AAAGAAA-AAATAGAG
1 AAAGAAAGAAA-AGAG
39478952 AACA-AAAGAAAAGAG
1 AA-AGAAAGAAAAGAG
39478967 AAAG-AAGAAAA
1 AAAGAAAGAAAA
39478978 AGGAAAGGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
14 11 0.31
15 21 0.58
16 4 0.11
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (15 bp):
AAAGAAAGAAAAGAG
Found at i:39478978 original size:15 final size:15
Alignment explanation
Indices: 39478930--39478984 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
39478920 CAAAAGAAAG
*
39478930 AAAAGGGAAAGAA-A
1 AAAAGAGAAAGAAGA
*
39478944 AAATAGAGAACAAAAG-
1 AAA-AGAGAA-AGAAGA
39478960 AAAAGAGAAAGAAGA
1 AAAAGAGAAAGAAGA
39478975 AAAAG-GAAAG
1 AAAAGAGAAAG
39478985 GGCGACTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 12 0.35
15 16 0.47
16 6 0.18
ACGTcount: A:0.71, C:0.02, G:0.25, T:0.02
Consensus pattern (15 bp):
AAAAGAGAAAGAAGA
Found at i:39479706 original size:30 final size:30
Alignment explanation
Indices: 39479670--39480166 Score: 685
Period size: 30 Copynumber: 16.6 Consensus size: 30
39479660 AACAATCTAG
39479670 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
**
39479700 AAATTACATTTTGACCTTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
39479730 AAATTATATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
39479760 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* * *
39479790 AAATTATATTTTAACCTCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
39479820 AAATTACATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* * * *
39479850 AAATTATACTTTAACCCCAAAACTTATCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
39479880 AAATTACATTTTAACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* * *
39479910 AAATTATATTTTAACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* * *
39479940 AAATTACATTTTAACCCTAAAACTTTACCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
39479970 AAATTATATTTTGACCCCAAAACTTTTCTA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* **
39480000 AAATTATATTTTGACCCTGAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
39480030 AAATTACATTTTGACCCTAAAA-TTTCTCTA
1 AAATTACATTTTGACCCCAAAACTTT-TCCA
*
39480060 AAATTACATTTTGACCCCGAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
39480090 AAATTATATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
39480120 AAATTACATTTTGACCCCAAAAC-TTTCAA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
39480149 AAATTACCATTTT-ACCCC
1 AAATTA-CATTTTGACCCC
39480167 TCGAATCTTC
Statistics
Matches: 419, Mismatches: 45, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
29 19 0.05
30 397 0.95
31 3 0.01
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTTCCA
Found at i:39484278 original size:6 final size:6
Alignment explanation
Indices: 39484267--39484382 Score: 77
Period size: 6 Copynumber: 20.0 Consensus size: 6
39484257 TATAATAATT
* *
39484267 TTTAAA TTTAAA -ATAAA TTTAGAA -TTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
39484313 GTTTAAT TTTAAA TTTAAA -TTAGAA -ATAAA TCTAAA TTTAAA -TCAAA
1 -TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA
*
39484360 TTT-AA TCTTAAA -ATAAA TTTAAA
1 TTTAAA T-TTAAA TTTAAA TTTAAA
39484383 AGTGCCCGAT
Statistics
Matches: 87, Mismatches: 13, Indels: 20
0.73 0.11 0.17
Matches are distributed among these distances:
5 27 0.31
6 51 0.59
7 9 0.10
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:39484292 original size:18 final size:17
Alignment explanation
Indices: 39484253--39484382 Score: 77
Period size: 17 Copynumber: 7.1 Consensus size: 17
39484243 ATTGGGTTTC
* *
39484253 AATTTATAATAATTTTTA
1 AATTTAAAATAA-ATTTA
39484271 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
*
39484288 GAATTAAATTAAATTCAAATTTA
1 -AA-T---TTAAAAT-AAATTTA
**
39484311 AAGTTTAATTTTAAATTTA
1 AA-TTTAA-AATAAATTTA
*
39484330 AA-TTAGAAATAAATCTA
1 AATTTA-AAATAAATTTA
39484347 AATTT-AAATCAAATTT-
1 AATTTAAAAT-AAATTTA
39484363 AATCTTAAAATAAATTTA
1 AAT-TTAAAATAAATTTA
39484381 AA
1 AA
39484383 AGTGCCCGAT
Statistics
Matches: 90, Mismatches: 9, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
16 7 0.08
17 29 0.32
18 22 0.24
19 14 0.16
20 2 0.02
22 9 0.10
23 7 0.08
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.42
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:39484311 original size:12 final size:12
Alignment explanation
Indices: 39484270--39484364 Score: 54
Period size: 11 Copynumber: 7.7 Consensus size: 12
39484260 AATAATTTTT
*
39484270 AAATTTAAAAT-
1 AAATTTAAATTC
39484281 AAATTTAGAATT-
1 AAATTTA-AATTC
39484293 AAA-TTAAATTC
1 AAATTTAAATTC
*
39484304 AAATTTAAAGTTT
1 AAATTTAAA-TTC
* *
39484317 AATTTTAAATTT
1 AAATTTAAATTC
*
39484329 AAATTAGAAATAAATC
1 AAATT-TAAAT---TC
39484345 TAAATTTAAA-TC
1 -AAATTTAAATTC
39484357 AAATTTAA
1 AAATTTAA
39484365 TCTTAAAATA
Statistics
Matches: 68, Mismatches: 7, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
10 4 0.06
11 21 0.31
12 20 0.29
13 14 0.21
16 4 0.06
17 5 0.07
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (12 bp):
AAATTTAAATTC
Found at i:39484311 original size:17 final size:16
Alignment explanation
Indices: 39484268--39484382 Score: 79
Period size: 17 Copynumber: 6.7 Consensus size: 16
39484258 ATAATAATTT
*
39484268 TTAAATTTAAAATAAA
1 TTAAATTTAAATTAAA
39484284 TTTAGAA-TTAAATTAAA
1 -TTA-AATTTAAATTAAA
*
39484301 TTCAAATTTAAAGTTTAATT
1 TT-AAATTTAAA--TTAA-A
39484321 TTAAATTTAAATTAGAA
1 TTAAATTTAAATTA-AA
* *
39484338 ATAAATCTAAATTTAAA
1 TTAAATTTAAA-TTAAA
* *
39484355 TCAAATTTAATCTTAAA
1 TTAAATTTAA-ATTAAA
*
39484372 ATAAATTTAAA
1 TTAAATTTAAA
39484383 AGTGCCCGAT
Statistics
Matches: 77, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
16 4 0.05
17 52 0.68
18 6 0.08
19 13 0.17
20 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:39507441 original size:19 final size:20
Alignment explanation
Indices: 39507414--39507457 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
39507404 TAACTTAATT
*
39507414 AATTCTTTACT-TTTATTTTA
1 AATTCTTTACTCATT-TTTTA
39507434 AATT-TTTACTCATTTTTTA
1 AATTCTTTACTCATTTTTTA
39507453 AATTC
1 AATTC
39507458 AAAATGTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.61
Consensus pattern (20 bp):
AATTCTTTACTCATTTTTTA
Found at i:39507945 original size:3 final size:3
Alignment explanation
Indices: 39507937--39507966 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
39507927 ATTTCATTCC
39507937 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
39507967 TTGGAACCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:39511003 original size:140 final size:140
Alignment explanation
Indices: 39510751--39511031 Score: 562
Period size: 140 Copynumber: 2.0 Consensus size: 140
39510741 TTAGAAATTA
39510751 GAGAATAAAACTGGTTGAATTTTGGTCAGTAGATTTATGATATTCAAATCTATTTCATAAAAAAA
1 GAGAATAAAACTGGTTGAATTTTGGTCAGTAGATTTATGATATTCAAATCTATTTCATAAAAAAA
39510816 TTGAACTATAAAATAAAAGAACAAAATTAAATAATAGAAGAAGAGAAACAAAAGCTTTTGATTGG
66 TTGAACTATAAAATAAAAGAACAAAATTAAATAATAGAAGAAGAGAAACAAAAGCTTTTGATTGG
39510881 TGCAGACGAT
131 TGCAGACGAT
39510891 GAGAATAAAACTGGTTGAATTTTGGTCAGTAGATTTATGATATTCAAATCTATTTCATAAAAAAA
1 GAGAATAAAACTGGTTGAATTTTGGTCAGTAGATTTATGATATTCAAATCTATTTCATAAAAAAA
39510956 TTGAACTATAAAATAAAAGAACAAAATTAAATAATAGAAGAAGAGAAACAAAAGCTTTTGATTGG
66 TTGAACTATAAAATAAAAGAACAAAATTAAATAATAGAAGAAGAGAAACAAAAGCTTTTGATTGG
39511021 TGCAGACGAT
131 TGCAGACGAT
39511031 G
1 G
39511032 CAAGTAAAGA
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 141 1.00
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (140 bp):
GAGAATAAAACTGGTTGAATTTTGGTCAGTAGATTTATGATATTCAAATCTATTTCATAAAAAAA
TTGAACTATAAAATAAAAGAACAAAATTAAATAATAGAAGAAGAGAAACAAAAGCTTTTGATTGG
TGCAGACGAT
Found at i:39516554 original size:19 final size:19
Alignment explanation
Indices: 39516532--39516575 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
39516522 CTATAACAAC
*
39516532 ATTTTATTAT-AATAATTAA
1 ATTTTATTATGAA-AATCAA
39516551 A-TTTATTATGAAAATCAA
1 ATTTTATTATGAAAATCAA
39516569 ATTTTAT
1 ATTTTAT
39516576 GTTATTGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
ATTTTATTATGAAAATCAA
Done.