Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 67 of 168
Found at i:19454879 original size:22 final size:22
Alignment explanation
Indices: 19454844--19454908 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
19454834 CTTTGATTAC
*
19454844 TAGCACGTCAGTGCTCTCTG-A
1 TAGCACATCAGTGCTCTCTGTA
*
19454865 TTAGCACATCTGTGCTCTCTGTA
1 -TAGCACATCAGTGCTCTCTGTA
*
19454888 TAGCACTTCAGTGCTCTCTGT
1 TAGCACATCAGTGCTCTCTGT
19454909 TCATTAGTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 37 0.97
23 1 0.03
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.35
Consensus pattern (22 bp):
TAGCACATCAGTGCTCTCTGTA
Found at i:19456464 original size:22 final size:22
Alignment explanation
Indices: 19456436--19456478 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
19456426 CGCACCAGTA
*
19456436 TATGAGAGCCCTTTGTGGGACG
1 TATGAGAGCCCTTTATGGGACG
19456458 TATGAGAGCCCTTTATGGGAC
1 TATGAGAGCCCTTTATGGGAC
19456479 ATATTGAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.28
Consensus pattern (22 bp):
TATGAGAGCCCTTTATGGGACG
Found at i:19462921 original size:21 final size:21
Alignment explanation
Indices: 19462895--19462949 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
19462885 TCTTAAGGTC
19462895 AAATTTTTACATCTACTTTGT
1 AAATTTTTACATCTACTTTGT
* *
19462916 AAA-TTTTAAAGCTACTTTGT
1 AAATTTTTACATCTACTTTGT
19462936 AAATTTTTACATCT
1 AAATTTTTACATCT
19462950 TAAAAATACT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (21 bp):
AAATTTTTACATCTACTTTGT
Found at i:19475160 original size:2 final size:2
Alignment explanation
Indices: 19475153--19475203 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
19475143 TCCTACAATA
19475153 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19475195 AT AT AT AT A
1 AT AT AT AT A
19475204 AGAACTAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19487372 original size:50 final size:49
Alignment explanation
Indices: 19487252--19487429 Score: 184
Period size: 50 Copynumber: 3.6 Consensus size: 49
19487242 CATGCCAAAG
* * *
19487252 CCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTA-C--TACCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGA-G-TTCTTATATCGGTGCC-ATA
* *
19487301 CCATATCCCAGATATGGTCTTACATGGGAGTTCTTATATCGGTGCTCATA
1 CCATGTCCCAGACATGGTCTTACATGGGAGTTCTTATATCGGTGC-CATA
** * * *
19487351 CCATGTCCCAGACATGGTCTTACGGGGGAGCTCTCATCTCGGTGCCA-A
1 CCATGTCCCAGACATGGTCTTACATGGGAGTTCTTATATCGGTGCCATA
19487399 CGCCATGTCCCAGACATGGTCTTACATGGGA
1 --CCATGTCCCAGACATGGTCTTACATGGGA
19487430 TCTCTTTACC
Statistics
Matches: 109, Mismatches: 14, Indels: 11
0.81 0.10 0.08
Matches are distributed among these distances:
47 7 0.06
48 3 0.03
49 29 0.27
50 69 0.63
51 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (49 bp):
CCATGTCCCAGACATGGTCTTACATGGGAGTTCTTATATCGGTGCCATA
Found at i:19490987 original size:20 final size:20
Alignment explanation
Indices: 19490939--19490998 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
19490929 GATTTAGGGG
* *
19490939 AAAATAAGAAAATAAGAAATTT
1 AAAATAA-AAAATAA-ATATTC
19490961 AAGAATAAAAAATAAATATTC
1 AA-AATAAAAAATAAATATTC
* *
19490982 AAAATAATAACTAAATA
1 AAAATAAAAAATAAATA
19490999 AAGAAAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 13 0.39
21 6 0.18
22 9 0.27
23 5 0.15
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAATAAAAAATAAATATTC
Found at i:19498619 original size:14 final size:14
Alignment explanation
Indices: 19498600--19498632 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
19498590 TAACATAGTA
19498600 TAACAAGCTAACAG
1 TAACAAGCTAACAG
19498614 TAACAAGCTAACAG
1 TAACAAGCTAACAG
19498628 TAACA
1 TAACA
19498633 TAGTATAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.21, G:0.12, T:0.15
Consensus pattern (14 bp):
TAACAAGCTAACAG
Found at i:19502956 original size:21 final size:21
Alignment explanation
Indices: 19502922--19502962 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19502912 CTATTTAAGC
*
19502922 CTTGAGACAAGTGACCTTTGT
1 CTTGAGACAAGTGAACTTTGT
* *
19502943 CTTGAGATAGGTGAACTTTG
1 CTTGAGACAAGTGAACTTTG
19502963 AAGCTAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (21 bp):
CTTGAGACAAGTGAACTTTGT
Found at i:19504727 original size:19 final size:18
Alignment explanation
Indices: 19504681--19504728 Score: 87
Period size: 18 Copynumber: 2.6 Consensus size: 18
19504671 AAAACTTTAG
19504681 GAGACCCAAAAGATTAAA
1 GAGACCCAAAAGATTAAA
19504699 GAGACCCAAAAGATTAAA
1 GAGACCCAAAAGATTAAA
19504717 GAGACCCCAAAA
1 GAGA-CCCAAAA
19504729 TAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 22 0.76
19 7 0.24
ACGTcount: A:0.54, C:0.21, G:0.17, T:0.08
Consensus pattern (18 bp):
GAGACCCAAAAGATTAAA
Found at i:19514904 original size:100 final size:99
Alignment explanation
Indices: 19514773--19514960 Score: 277
Period size: 100 Copynumber: 1.9 Consensus size: 99
19514763 ATTGAAGCCA
** * * *
19514773 CAACGGCGAATCTTGTTTCCCTCGCGGTGTAGTGGAACTGATTGAAGTTACGACGGCGAATCTTG
1 CAACGGCGAATCTTACTTCCCTCGAGGTGTAGTGGAACGGATTGAAGCTACGACGGCGAATCTTG
*
19514838 TTTCCCCAATACTGCAATTAAAAATATTAAAGTTG
66 TTT-CCCAACACTGCAATTAAAAATATTAAAGTTG
* *
19514873 CAACGGTGAATCTTACTTCCCTGGAGGTGTAGTGGAACGGATTGAAGCTACGACGGCGAATCTTG
1 CAACGGCGAATCTTACTTCCCTCGAGGTGTAGTGGAACGGATTGAAGCTACGACGGCGAATCTTG
* *
19514938 TTTCCCAACATTGCAATTTAAAA
66 TTTCCCAACACTGCAATTAAAAA
19514961 GACTGAAGAT
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 17 0.22
100 61 0.78
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (99 bp):
CAACGGCGAATCTTACTTCCCTCGAGGTGTAGTGGAACGGATTGAAGCTACGACGGCGAATCTTG
TTTCCCAACACTGCAATTAAAAATATTAAAGTTG
Found at i:19514934 original size:50 final size:50
Alignment explanation
Indices: 19514753--19514943 Score: 159
Period size: 50 Copynumber: 3.8 Consensus size: 50
19514743 TTGGCATTAC
* *
19514753 AGTGGAACGGATTGAAGCCACAACGGCGAATCTTGTTTCCCTCGCGGTGT
1 AGTGGAACGGATTGAAGCTACAACGGCGAATCTTGTTTCCCTCGAGGTGT
* * * * ** *
19514803 AGTGGAACTGATTGAAGTTACGACGGCGAATCTTGTTTCCC-CAATACTGC
1 AGTGGAACGGATTGAAGCTACAACGGCGAATCTTGTTTCCCTCGA-GGTGT
* ** *** * * * * ** *
19514853 AATTAAAAATATTAAAGTTGCAACGGTGAATCTTACTTCCCTGGAGGTGT
1 AGTGGAACGGATTGAAGCTACAACGGCGAATCTTGTTTCCCTCGAGGTGT
*
19514903 AGTGGAACGGATTGAAGCTACGACGGCGAATCTTGTTTCCC
1 AGTGGAACGGATTGAAGCTACAACGGCGAATCTTGTTTCCC
19514944 AACATTGCAA
Statistics
Matches: 100, Mismatches: 39, Indels: 4
0.70 0.27 0.03
Matches are distributed among these distances:
49 1 0.01
50 98 0.98
51 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (50 bp):
AGTGGAACGGATTGAAGCTACAACGGCGAATCTTGTTTCCCTCGAGGTGT
Found at i:19515172 original size:45 final size:45
Alignment explanation
Indices: 19515103--19515265 Score: 168
Period size: 45 Copynumber: 3.6 Consensus size: 45
19515093 GATCACATCT
* * *
19515103 AGTCCTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAGCG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCA
* *
19515148 AGTGTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCA
* * * ** *
19515193 AGTCTTATC-CCCTTGAAATTACAGTGGGGCAGACTAAATAAA-CA
1 AGTCTTATCTCCC-TGAAGTTGCAGTGGAGCAGACCCAAGAAAGCA
* * * *
19515237 AATCCTATCTCCCTAAAGTTGTAGTGGAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
19515266 TGAATTCTAG
Statistics
Matches: 98, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
44 23 0.23
45 75 0.77
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCA
Found at i:19516853 original size:21 final size:21
Alignment explanation
Indices: 19516815--19516854 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19516805 TTATAATCTA
*
19516815 TATATATATATATCTATTTTT
1 TATATATATACATCTATTTTT
* *
19516836 TATATATGTACATGTATTT
1 TATATATATACATCTATTT
19516855 ATATTTTTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TATATATATACATCTATTTTT
Found at i:19516858 original size:31 final size:30
Alignment explanation
Indices: 19516799--19516858 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
19516789 TATATGTAAT
*
19516799 TATTTTTTATAATCTATATATATATATATC
1 TATTTTTTATAATCTACATATATATATATC
* * *
19516829 TATTTTTTATATATGTACATGTATTTATAT
1 TATTTTTTATA-ATCTACATATATATATAT
19516859 TTTTTCTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.58
Consensus pattern (30 bp):
TATTTTTTATAATCTACATATATATATATC
Found at i:19517289 original size:13 final size:14
Alignment explanation
Indices: 19517253--19517292 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
19517243 GGTCATTTTT
19517253 TTTATATTAGTTTCG
1 TTTATATTA-TTTCG
19517268 TTTAT-TTATTT-G
1 TTTATATTATTTCG
19517280 TTTATATTATTTC
1 TTTATATTATTTC
19517293 TATGCCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.26
13 9 0.39
14 3 0.13
15 5 0.22
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (14 bp):
TTTATATTATTTCG
Found at i:19517323 original size:15 final size:15
Alignment explanation
Indices: 19517303--19517332 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19517293 TATGCCATTA
19517303 TTGTATTTATTATTG
1 TTGTATTTATTATTG
*
19517318 TTGTATTTGTTATTG
1 TTGTATTTATTATTG
19517333 CTACATTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (15 bp):
TTGTATTTATTATTG
Found at i:19517904 original size:28 final size:28
Alignment explanation
Indices: 19517868--19517925 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
19517858 TTTTAACTCT
*
19517868 TGACATTAAGGCGCTAATTAATCAACTA
1 TGACATTAAGACGCTAATTAATCAACTA
19517896 TGACATTAAGACGCTAATTAATCAACTA
1 TGACATTAAGACGCTAATTAATCAACTA
19517924 TG
1 TG
19517926 TACCAATTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (28 bp):
TGACATTAAGACGCTAATTAATCAACTA
Found at i:19526567 original size:27 final size:27
Alignment explanation
Indices: 19526537--19526634 Score: 106
Period size: 27 Copynumber: 3.6 Consensus size: 27
19526527 TCAGAGTTTG
**
19526537 CCACAAAGGCATTTCTTTTTTATTACA
1 CCACAAAGGCATTTCTTTCATATTACA
* ***
19526564 CCACAAAGGCTTTTCTTTCATATTGTG
1 CCACAAAGGCATTTCTTTCATATTACA
* *
19526591 CCACAAAGGCTTTTCTTTCATACTACA
1 CCACAAAGGCATTTCTTTCATATTACA
* *
19526618 TCGCAAAGGCATTTCTT
1 CCACAAAGGCATTTCTT
19526635 CCCTAACGTG
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (27 bp):
CCACAAAGGCATTTCTTTCATATTACA
Found at i:19539335 original size:50 final size:50
Alignment explanation
Indices: 19539231--19539347 Score: 137
Period size: 50 Copynumber: 2.3 Consensus size: 50
19539221 AGGTCCCACG
* * * * **
19539231 TAAGACCATGTCTGGGACATGGCGTTGGTACCGAGATGAGAGGTCCTCTA
1 TAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAACTCCTCTA
* *
19539281 TAAGACCATGTCTGGGACATGGCATGGGCACCGATACGAGAACT-CTCATC
1 TAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAACTCCTC-TA
*
19539331 TAAGACCATATCTGGGA
1 TAAGACCATGTCTGGGA
19539348 TATGACATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 3 0.05
50 54 0.95
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAACTCCTCTA
Found at i:19539636 original size:20 final size:20
Alignment explanation
Indices: 19539611--19539649 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
19539601 TGAGTTATTT
19539611 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
19539631 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
19539650 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:19546939 original size:50 final size:50
Alignment explanation
Indices: 19546881--19547010 Score: 161
Period size: 50 Copynumber: 2.6 Consensus size: 50
19546871 TATTGAGGTT
* * * *
19546881 ATGAGAGGTCCCACGTAAGACCATGTTTGGGACATGGCGTTGGTACCAAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
* *
19546931 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
** * * *
19546981 ATGAGAACTCTCATGTAAGACCATATCTGG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGG
19547011 AATTTGGCAT
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
Found at i:19549518 original size:30 final size:30
Alignment explanation
Indices: 19549482--19549572 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
19549472 GGTGAAATAA
* * *
19549482 GTTGCTCACACAATCTTACATTATATTAGG
1 GTTGCTCACACAATCTGACATTATATCAAG
* *
19549512 GTTGCTCATACAAGCTGACATTATATCAAG
1 GTTGCTCACACAATCTGACATTATATCAAG
* * *
19549542 GTTGCTTACACAATATGAAATTTATATCAAG
1 GTTGCTCACACAATCTGACA-TTATATCAAG
19549573 TTACCTGTTC
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 40 0.80
31 10 0.20
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (30 bp):
GTTGCTCACACAATCTGACATTATATCAAG
Found at i:19558610 original size:28 final size:28
Alignment explanation
Indices: 19558579--19558647 Score: 120
Period size: 28 Copynumber: 2.5 Consensus size: 28
19558569 ATTTTATCAC
*
19558579 ATTATTTTTTATTTGGCAGTTTTACTGT
1 ATTATTTATTATTTGGCAGTTTTACTGT
19558607 ATTATTTATTATTTGGCAGTTTTACTGT
1 ATTATTTATTATTTGGCAGTTTTACTGT
*
19558635 ATTATTTAATATT
1 ATTATTTATTATT
19558648 GATGGTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.23, C:0.06, G:0.12, T:0.59
Consensus pattern (28 bp):
ATTATTTATTATTTGGCAGTTTTACTGT
Found at i:19559009 original size:3 final size:3
Alignment explanation
Indices: 19558996--19559029 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
19558986 TATTTCTAAG
*
19558996 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19559030 TGGTTTTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19579974 original size:24 final size:25
Alignment explanation
Indices: 19579945--19580000 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
19579935 AGAGTTACCC
*
19579945 ATTAAGCTCACATGAGCTTTCTGTT
1 ATTAAGCTCACATGAGCTTCCTGTT
***
19579970 -TTAAGCTTTTATGAGCTTCCTGTT
1 ATTAAGCTCACATGAGCTTCCTGTT
19579994 ATTAAGC
1 ATTAAGC
19580001 ACGGATAAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (25 bp):
ATTAAGCTCACATGAGCTTCCTGTT
Found at i:19580033 original size:25 final size:25
Alignment explanation
Indices: 19580005--19580052 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
19579995 TTAAGCACGG
19580005 ATAAGCTT-CTCGTTACATGGCTCAC
1 ATAAGCTTCCT-GTTACATGGCTCAC
*
19580030 ATAAGCTTCCTGTTATATGGCTC
1 ATAAGCTTCCTGTTACATGGCTC
19580053 GAGAGAGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (25 bp):
ATAAGCTTCCTGTTACATGGCTCAC
Found at i:19587340 original size:16 final size:16
Alignment explanation
Indices: 19587303--19587339 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
19587293 TGAAGCTTCC
*
19587303 ATTTTTAGTTTGCAAA
1 ATTTTTAGTGTGCAAA
19587319 ATTTTTAGTGT-CAAA
1 ATTTTTAGTGTGCAAA
19587334 ATTTTT
1 ATTTTT
19587340 TGTTGCCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (16 bp):
ATTTTTAGTGTGCAAA
Found at i:19589246 original size:72 final size:72
Alignment explanation
Indices: 19589158--19589301 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
19589148 AAATATTTTA
*
19589158 AAATGAATTTCATGTTTGTATATCTTTCAAATATATAATTATATATTTTATAAGGGTAGGGCTTA
1 AAATGAATTTCATGTTTGTATATCTTTCAAATATATAATTATATATTTTATAACGGTAGGGCTTA
19589223 ATGGTTG
66 ATGGTTG
19589230 AAATGAATTTCATGTTTGTATATCTTTCAAATATATAATTATATATTTTATAACGGTAGGGCTTA
1 AAATGAATTTCATGTTTGTATATCTTTCAAATATATAATTATATATTTTATAACGGTAGGGCTTA
19589295 ATGGTTG
66 ATGGTTG
19589302 TCCAAGGATT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.44
Consensus pattern (72 bp):
AAATGAATTTCATGTTTGTATATCTTTCAAATATATAATTATATATTTTATAACGGTAGGGCTTA
ATGGTTG
Found at i:19591716 original size:14 final size:16
Alignment explanation
Indices: 19591691--19591722 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19591681 CATTTCACTA
19591691 TTATGTCATTTT-TAT
1 TTATGTCATTTTATAT
19591706 TTATGTC-TTTTATAT
1 TTATGTCATTTTATAT
19591721 TT
1 TT
19591723 TGCATGCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (16 bp):
TTATGTCATTTTATAT
Found at i:19598827 original size:46 final size:46
Alignment explanation
Indices: 19598752--19598839 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
19598742 AAAAGTATAG
*
19598752 TGTGGGCCTAAGCCCATTACAATATCAGAATCAGAAATAGAATACA
1 TGTGGGCCTAAGCCCACTACAATATCAGAATCAGAAATAGAATACA
* * *
19598798 TGTGGGCCTAAGCCTACTACAGTGA-CAGAATCAGTAATAGAA
1 TGTGGGCCTAAGCCCACTACAAT-ATCAGAATCAGAAATAGAA
19598840 ATGCAATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 36 0.97
47 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (46 bp):
TGTGGGCCTAAGCCCACTACAATATCAGAATCAGAAATAGAATACA
Found at i:19599118 original size:32 final size:31
Alignment explanation
Indices: 19599063--19599168 Score: 108
Period size: 31 Copynumber: 3.4 Consensus size: 31
19599053 GAATGGATAC
* *
19599063 AAGCCATAAGTACAGTAATATGATTGGCACA
1 AAGCCATCAGTACAGTAATATGATCGGCACA
*
19599094 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTA-CAGTAATATGATCGGCACA
* * *
19599126 CAA--CATCAGTAACGGTAATATGATCGACATA
1 -AAGCCATCAGT-ACAGTAATATGATCGGCACA
*
19599157 AAGCCATTAGTA
1 AAGCCATCAGTA
19599169 ACATCGCAGC
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
30 2 0.03
31 34 0.55
32 24 0.39
33 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.22
Consensus pattern (31 bp):
AAGCCATCAGTACAGTAATATGATCGGCACA
Found at i:19599221 original size:26 final size:26
Alignment explanation
Indices: 19599171--19599221 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
19599161 CATTAGTAAC
19599171 ATCGCAGCAAAGCTGCCAGCAATAGT
1 ATCGCAGCAAAGCTGCCAGCAATAGT
*
19599197 ATCGCAGCAAAGCTGCCAGTAATAG
1 ATCGCAGCAAAGCTGCCAGCAATAG
19599222 AATATGTGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAGCAATAGT
Found at i:19599381 original size:24 final size:24
Alignment explanation
Indices: 19599347--19599402 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
19599337 CAGAATTAGA
* * *
19599347 CATTTAAATCACAAACAAATCAGT
1 CATTTACATCACAAACAAACCAAT
*
19599371 CATTTACATCACAGACAAACCAAT
1 CATTTACATCACAAACAAACCAAT
19599395 CATTTACA
1 CATTTACA
19599403 CTCGAGGGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.25
Consensus pattern (24 bp):
CATTTACATCACAAACAAACCAAT
Found at i:19599476 original size:27 final size:27
Alignment explanation
Indices: 19599439--19599864 Score: 284
Period size: 27 Copynumber: 15.6 Consensus size: 27
19599429 CTCTAGAAGC
* *
19599439 ATTACGATCATTTTACCTTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * * *
19599466 ATTTCGGTCATTTAATCCTATAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * ** *
19599493 ATTACAGTTATTTTACCCTACAAAGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
** **
19599520 ATTACAATCATTTTACCCTATGGGGGGT
1 ATTACGGTCATTTTACCCTA-CAGGGGT
* * *
19599548 -TTTCAGTTATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
19599574 ATTACGATCATTTTACCTTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
19599601 ATTACAGTCATTTTACCCTACGGGGGGC
1 ATTACGGTCATTTTACCCTAC-AGGGGT
**
19599629 ATTACGGTCATTTTACCCTATGGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
** * * *
19599656 -TTGTTGGTCATTTTACCTTACAGGCGC
1 ATT-ACGGTCATTTTACCCTACAGGGGT
* *
19599683 ATTACAGTCATTTTACCCTA-TGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
19599709 GAGGGCATTACGCTCACTTTACCCTA-TGGGGT
1 ------ATTACGGTCATTTTACCCTACAGGGGT
* * * * * *
19599741 TTTTCGATTATTTTACCCTATAGGAGT
1 ATTACGGTCATTTTACCCTACAGGGGT
**
19599768 ATTACGGTCATTTTACCCTATGGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
19599795 TTTTCGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
19599822 ATTACGGTCATTTTACCTTGCAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
*
19599849 ATTACGATCATTTTAC
1 ATTACGGTCATTTTAC
19599865 AAATATTGGC
Statistics
Matches: 307, Mismatches: 80, Indels: 24
0.75 0.19 0.06
Matches are distributed among these distances:
26 25 0.08
27 231 0.75
28 28 0.09
32 23 0.07
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:19603117 original size:20 final size:20
Alignment explanation
Indices: 19603074--19603121 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
19603064 TTTAGCTTGG
* ** *
19603074 TTCAGCTCACTTAATTTTAT
1 TTCAGCTCACATAAGCTTAA
19603094 TTCAGCTCACATAAGCTTAA
1 TTCAGCTCACATAAGCTTAA
19603114 TTCAGCTC
1 TTCAGCTC
19603122 GTTTGAGCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (20 bp):
TTCAGCTCACATAAGCTTAA
Found at i:19608369 original size:19 final size:19
Alignment explanation
Indices: 19608347--19608386 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
19608337 AATAATTTTG
19608347 ATCAAATAAAATT-AAATTA
1 ATCAAAT-AAATTAAAATTA
*
19608366 ATCAAATCAATTAAAATTA
1 ATCAAATAAATTAAAATTA
19608385 AT
1 AT
19608387 ACAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:19608946 original size:25 final size:25
Alignment explanation
Indices: 19608899--19608948 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
19608889 TTTATCTTGT
* **
19608899 AGATAAACATTATTTTATTTTAATA
1 AGATAAACATTATATTAAATTAATA
*
19608924 AGATAAATATTATATTAAATTAATA
1 AGATAAACATTATATTAAATTAATA
19608949 TTAAAGTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (25 bp):
AGATAAACATTATATTAAATTAATA
Found at i:19610427 original size:20 final size:20
Alignment explanation
Indices: 19610391--19610486 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
19610381 GAAATGCTAT
* *
19610391 ACAGAGGCACC-ACAGTGCGA
1 ACAGAGACACCGA-AGTGCAA
19610411 ACAGAGACACCGAAGTG-AA
1 ACAGAGACACCGAAGTGCAA
*
19610430 AGCAGAGCCACCGAA-TGCAA
1 A-CAGAGACACCGAAGTGCAA
* * *
19610450 ATAGAGGCACCAAAGTGCAA
1 ACAGAGACACCGAAGTGCAA
* *
19610470 TCAGAGACACTGAAGTG
1 ACAGAGACACCGAAGTG
19610487 TAATACAGTA
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
19 14 0.23
20 46 0.75
21 1 0.02
ACGTcount: A:0.41, C:0.24, G:0.27, T:0.08
Consensus pattern (20 bp):
ACAGAGACACCGAAGTGCAA
Found at i:19613364 original size:22 final size:22
Alignment explanation
Indices: 19613322--19613370 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
19613312 ATTTCTTTAT
*
19613322 TTAATTGATTCATAATGATTAA
1 TTAATTGATTCATAATAATTAA
*
19613344 TTAATTGATT-GTAATAAATTAA
1 TTAATTGATTCATAAT-AATTAA
*
19613366 ATAAT
1 TTAAT
19613371 AATTCAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (22 bp):
TTAATTGATTCATAATAATTAA
Found at i:19619478 original size:27 final size:27
Alignment explanation
Indices: 19619459--19619563 Score: 149
Period size: 27 Copynumber: 3.9 Consensus size: 27
19619449 ATACCTCTGG
*
19619459 AGGGTAAAATG-TCTGAAATACCCCCAA
1 AGGGTAAAATGAT-TGAAATACCCCTAA
19619486 AGGGTAAAATGATTGAAATACCCCTAA
1 AGGGTAAAATGATTGAAATACCCCTAA
*
19619513 AGGGTAAAATGATTGAAATACCCCCAA
1 AGGGTAAAATGATTGAAATACCCCTAA
* * *
19619540 AAGTTAAAATGACTGAAATACCCC
1 AGGGTAAAATGATTGAAATACCCC
19619564 ATATGGTAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
27 71 0.99
28 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (27 bp):
AGGGTAAAATGATTGAAATACCCCTAA
Found at i:19619517 original size:54 final size:54
Alignment explanation
Indices: 19619459--19619563 Score: 167
Period size: 54 Copynumber: 1.9 Consensus size: 54
19619449 ATACCTCTGG
* *
19619459 AGGGTAAAATG-TCTGAAATACCCCCAAAGGGTAAAATGATTGAAATACCCCTAA
1 AGGGTAAAATGAT-TGAAATACCCCCAAAAGGTAAAATGACTGAAATACCCCTAA
*
19619513 AGGGTAAAATGATTGAAATACCCCCAAAAGTTAAAATGACTGAAATACCCC
1 AGGGTAAAATGATTGAAATACCCCCAAAAGGTAAAATGACTGAAATACCCC
19619564 ATATGGTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 46 0.98
55 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (54 bp):
AGGGTAAAATGATTGAAATACCCCCAAAAGGTAAAATGACTGAAATACCCCTAA
Found at i:19619573 original size:26 final size:26
Alignment explanation
Indices: 19619459--19619589 Score: 145
Period size: 27 Copynumber: 4.9 Consensus size: 26
19619449 ATACCTCTGG
*
19619459 AGGGTAAAATGTCTGAAATACCCCCAA
1 AGGGTAAAATGACTGAAATA-CCCCAA
*
19619486 AGGGTAAAATGATTGAAATACCCCTAA
1 AGGGTAAAATGACTGAAATACCCC-AA
*
19619513 AGGGTAAAATGATTGAAATACCCCCAA
1 AGGGTAAAATGACTGAAATA-CCCCAA
* * *
19619540 AAGTTAAAATGACTGAAATACCCCAT
1 AGGGTAAAATGACTGAAATACCCCAA
* * **
19619566 ATGGTAAAATAACTGTTATACCCC
1 AGGGTAAAATGACTGAAATACCCC
19619590 TAGGAGATGA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
26 28 0.31
27 59 0.65
28 4 0.04
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (26 bp):
AGGGTAAAATGACTGAAATACCCCAA
Found at i:19627632 original size:40 final size:40
Alignment explanation
Indices: 19627586--19627692 Score: 133
Period size: 40 Copynumber: 2.7 Consensus size: 40
19627576 ATAACACATA
*
19627586 AATATTGTGGACAAGCCACCAGTATTGCAAATAAGCTATC
1 AATATTGTGGACAAGCCACCAGTATTGCAAATAAACTATC
* * * * *
19627626 AGTATTGTGGACAAGCCACCAATAATGCAGATAAACTGTC
1 AATATTGTGGACAAGCCACCAGTATTGCAAATAAACTATC
** *
19627666 AATATTGCAGACAAGCTACCAGTATTG
1 AATATTGTGGACAAGCCACCAGTATTG
19627693 TGGACAAGCC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (40 bp):
AATATTGTGGACAAGCCACCAGTATTGCAAATAAACTATC
Found at i:19627641 original size:20 final size:20
Alignment explanation
Indices: 19627595--19627715 Score: 71
Period size: 20 Copynumber: 6.0 Consensus size: 20
19627585 AAATATTGTG
*
19627595 GACAAGCCACCAGTATTGCA
1 GACAAGCTACCAGTATTGCA
* * * **
19627615 AATAAGCTATCAGTATTGTG
1 GACAAGCTACCAGTATTGCA
* * *
19627635 GACAAGCCACCAATAATGCA
1 GACAAGCTACCAGTATTGCA
* * ** *
19627655 GATAAACTGTCAATATTGCA
1 GACAAGCTACCAGTATTGCA
**
19627675 GACAAGCTACCAGTATTGTG
1 GACAAGCTACCAGTATTGCA
* * *
19627695 GACAAGCCAACAGTAATGCA
1 GACAAGCTACCAGTATTGCA
19627715 G
1 G
19627716 GTAAACTGTC
Statistics
Matches: 69, Mismatches: 32, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (20 bp):
GACAAGCTACCAGTATTGCA
Found at i:19627701 original size:60 final size:60
Alignment explanation
Indices: 19627608--19627776 Score: 239
Period size: 60 Copynumber: 2.8 Consensus size: 60
19627598 AAGCCACCAG
* *
19627608 TATTGCAAATAAGCTATCAGTATTGTGGACAAGCCACCAATAATGCAGATAAACTGTCAA
1 TATTGCAAACAAGCTACCAGTATTGTGGACAAGCCACCAATAATGCAGATAAACTGTCAA
* * * *
19627668 TATTGCAGACAAGCTACCAGTATTGTGGACAAGCCAACAGTAATGCAGGTAAACTGTCAA
1 TATTGCAAACAAGCTACCAGTATTGTGGACAAGCCACCAATAATGCAGATAAACTGTCAA
* * * * *
19627728 TATTGTAAACAAGCTACTAATATTATTGACAAGCCACCAATAATGCAGA
1 TATTGCAAACAAGCTACCAGTATTGTGGACAAGCCACCAATAATGCAGA
19627777 CAAGCTACTA
Statistics
Matches: 94, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 94 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (60 bp):
TATTGCAAACAAGCTACCAGTATTGTGGACAAGCCACCAATAATGCAGATAAACTGTCAA
Found at i:19675064 original size:9 final size:9
Alignment explanation
Indices: 19674997--19675066 Score: 54
Period size: 9 Copynumber: 7.3 Consensus size: 9
19674987 TGATAGTTTC
*
19674997 TTCTTCTTA
1 TTCTTCTTT
*
19675006 TTCTTCTTC
1 TTCTTCTTT
19675015 TTCTTCTTTT
1 TTCTTC-TTT
19675025 TTCTT-TTT
1 TTCTTCTTT
19675033 TTCTT-TTT
1 TTCTTCTTT
19675041 GTCATCTTATCTTT
1 -T--TC-T-TCTTT
19675055 TTCTTCTTT
1 TTCTTCTTT
19675064 TTC
1 TTC
19675067 GTTTGATTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
8 11 0.21
9 23 0.44
10 8 0.15
11 4 0.08
12 1 0.02
13 2 0.04
14 3 0.06
ACGTcount: A:0.04, C:0.21, G:0.01, T:0.73
Consensus pattern (9 bp):
TTCTTCTTT
Found at i:19678722 original size:18 final size:18
Alignment explanation
Indices: 19678699--19678736 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
19678689 CGACTAAGAA
19678699 TGACAAGGTGGTCATAGT
1 TGACAAGGTGGTCATAGT
19678717 TGACAAGGTGGTCATAGT
1 TGACAAGGTGGTCATAGT
19678735 TG
1 TG
19678737 GTGAGCGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.34, T:0.29
Consensus pattern (18 bp):
TGACAAGGTGGTCATAGT
Found at i:19682837 original size:30 final size:30
Alignment explanation
Indices: 19682803--19682872 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
19682793 TATAAATTAA
*
19682803 ATAATAAATAATTAAAAATTTAT-AAAATTC
1 ATAATAAATAA-TAAAAACTTATAAAAATTC
*
19682833 ATAATAGAA-AATATAAACTTATAAAAATTC
1 ATAATA-AATAATAAAAACTTATAAAAATTC
*
19682863 A-AAAAAATAA
1 ATAATAAATAA
19682873 AAATCATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 2 0.06
29 14 0.41
30 16 0.47
31 2 0.06
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.30
Consensus pattern (30 bp):
ATAATAAATAATAAAAACTTATAAAAATTC
Found at i:19682909 original size:27 final size:27
Alignment explanation
Indices: 19682853--19682929 Score: 83
Period size: 25 Copynumber: 3.0 Consensus size: 27
19682843 ATATAAACTT
19682853 ATAAAA-ATTC-AAAAAAATAAAAATC
1 ATAAAATATTCAAAAAAAATAAAAATC
*
19682878 ATAAAATATTCAAAAAAAATTCAAAAT-
1 ATAAAATATTCAAAAAAAA-TAAAAATC
*
19682905 GTAAAATA-T-AAAAAAATATAAAAAT
1 ATAAAATATTCAAAAAAA-ATAAAAAT
19682930 TCAAAAACAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
25 19 0.42
26 6 0.13
27 14 0.31
28 6 0.13
ACGTcount: A:0.70, C:0.05, G:0.01, T:0.23
Consensus pattern (27 bp):
ATAAAATATTCAAAAAAAATAAAAATC
Found at i:19683567 original size:24 final size:24
Alignment explanation
Indices: 19683522--19683567 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
19683512 ACATAGGGAG
* * *
19683522 AAAACAACAAGAAAATAACATTCA
1 AAAACAAAAAAAAAAGAACATTCA
*
19683546 AAAACAAAAAAAAAAGAGCATT
1 AAAACAAAAAAAAAAGAACATT
19683568 TTTTTTTTCC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.70, C:0.13, G:0.07, T:0.11
Consensus pattern (24 bp):
AAAACAAAAAAAAAAGAACATTCA
Found at i:19690337 original size:24 final size:21
Alignment explanation
Indices: 19690305--19690364 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 21
19690295 AGAGCAGACC
*
19690305 AGTTACATATGCAGAAGCAATTTCT
1 AGTT-CATATGCAGAA-C-ATAT-T
*
19690330 AGTTCATATACAGAACATATT
1 AGTTCATATGCAGAACATATT
19690351 AGATTCATATGCAG
1 AG-TTCATATGCAG
19690365 TTATTCCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 3 0.10
22 13 0.42
23 1 0.03
24 10 0.32
25 4 0.13
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (21 bp):
AGTTCATATGCAGAACATATT
Found at i:19690939 original size:42 final size:42
Alignment explanation
Indices: 19690866--19690976 Score: 159
Period size: 42 Copynumber: 2.6 Consensus size: 42
19690856 ACGGCTTGGA
* * *
19690866 CACACGCTCATGTCCTTGCCCGTGTGGCTCACATGGCCTAGG
1 CACACGCCCATGTCCTTGCCCATGTGACTCACATGGCCTAGG
* * *
19690908 CACATGCCCATGTCCTTGCTCATGTGACTCACATGGCCTGGG
1 CACACGCCCATGTCCTTGCCCATGTGACTCACATGGCCTAGG
19690950 CACACGCCCATGTCCTCTGCCCATGTG
1 CACACGCCCATGTCCT-TGCCCATGTG
19690977 GTTTCAAAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 51 0.85
43 9 0.15
ACGTcount: A:0.15, C:0.37, G:0.23, T:0.24
Consensus pattern (42 bp):
CACACGCCCATGTCCTTGCCCATGTGACTCACATGGCCTAGG
Found at i:19693429 original size:15 final size:16
Alignment explanation
Indices: 19693401--19693430 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19693391 CGACACTCAA
19693401 TTTAATGAACTCTTGG
1 TTTAATGAACTCTTGG
19693417 TTTAATG-ACTCTTG
1 TTTAATGAACTCTTG
19693431 CAACCGAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (16 bp):
TTTAATGAACTCTTGG
Found at i:19704566 original size:53 final size:53
Alignment explanation
Indices: 19704437--19704645 Score: 250
Period size: 53 Copynumber: 4.0 Consensus size: 53
19704427 GGCACTAAAG
* * *
19704437 AAGACCATATCGTGTAAGACAGTAACTAGTGGGTTATGGTATCATATGG---A
1 AAGACCATATCGTGTAAGACTGTAACTTGTGGGTTATGGCATCATATGGAAAA
* * *
19704487 AAGATCATATCGTGTAAGAAC-ATAACTTGTGAGTTATGGCATCATATGGAAAA
1 AAGACCATATCGTGTAAG-ACTGTAACTTGTGGGTTATGGCATCATATGGAAAA
* * *
19704540 AAGACCATATCGTGTCAGACTGTAACTGGTGGGTTATGGCATCATATGGAAAG
1 AAGACCATATCGTGTAAGACTGTAACTTGTGGGTTATGGCATCATATGGAAAA
* * *
19704593 AAGATCATATCATGTAAGA-TCGTAACTTGTGGGTTATGACATCATAT-GAAAA
1 AAGACCATATCGTGTAAGACT-GTAACTTGTGGGTTATGGCATCATATGGAAAA
19704645 A
1 A
19704646 CATTTAAGGA
Statistics
Matches: 136, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
50 41 0.30
51 2 0.01
52 8 0.06
53 85 0.62
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (53 bp):
AAGACCATATCGTGTAAGACTGTAACTTGTGGGTTATGGCATCATATGGAAAA
Found at i:19725065 original size:21 final size:21
Alignment explanation
Indices: 19725031--19725105 Score: 125
Period size: 21 Copynumber: 3.6 Consensus size: 21
19725021 AGTCTATGGT
*
19725031 CAAGCTAG-GTCTAAGAAAGA
1 CAAGCTTGAGTCTAAGAAAGA
19725051 CAAGCTTGAGTCTAAGAAAGA
1 CAAGCTTGAGTCTAAGAAAGA
19725072 CAAGCTTGAGTCTAAGAAAGA
1 CAAGCTTGAGTCTAAGAAAGA
*
19725093 CAAACTTGAGTCT
1 CAAGCTTGAGTCT
19725106 TCTGAGTTCA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
20 7 0.13
21 45 0.87
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (21 bp):
CAAGCTTGAGTCTAAGAAAGA
Found at i:19726393 original size:14 final size:15
Alignment explanation
Indices: 19726369--19726397 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19726359 TTTTTCTGTG
19726369 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
19726384 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
19726398 AGTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:19726635 original size:28 final size:28
Alignment explanation
Indices: 19726589--19726645 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
19726579 TATAGTTTTT
19726589 ATAATAATTATAAAGGTTATAATAATAA
1 ATAATAATTATAAAGGTTATAATAATAA
*
19726617 ATAATATATTATAAA-GTTATTATAATAA
1 ATAATA-ATTATAAAGGTTATAATAATAA
19726645 A
1 A
19726646 AACAAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATAATTATAAAGGTTATAATAATAA
Found at i:19727593 original size:43 final size:42
Alignment explanation
Indices: 19727532--19727659 Score: 150
Period size: 43 Copynumber: 3.0 Consensus size: 42
19727522 ATAGGACTCT
* *
19727532 GATATCTGATTTCGTGTAAGACCACGTTTGGGACGTCGGCATC
1 GATATCTGATTACGTGTAAGACCACGTCTGGGACGT-GGCATC
*
19727575 GATATCTGATTACGTGTAAGACC-CTGTCTGGGATAGTGGCATC
1 GATATCTGATTACGTGTAAGACCAC-GTCTGGGA-CGTGGCATC
* * * *
19727618 AATATGTGATTACATATAAGACCACGTCTGGGACGATGGCAT
1 GATATCTGATTACGTGTAAGACCACGTCTGGGACG-TGGCAT
19727660 TGTACGAGCT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
42 2 0.03
43 68 0.93
44 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (42 bp):
GATATCTGATTACGTGTAAGACCACGTCTGGGACGTGGCATC
Found at i:19733063 original size:29 final size:28
Alignment explanation
Indices: 19733008--19733063 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
19732998 TTGGCTTATC
* *
19733008 ATTTTTGTCAAAACATTCAAGTCTTAAT
1 ATTTTTGTCAAAACATTCAAATATTAAT
* *
19733036 ATTTTTGTCTAAATCATTTAAATATTAA
1 ATTTTTGTC-AAAACATTCAAATATTAA
19733064 ATAAATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (28 bp):
ATTTTTGTCAAAACATTCAAATATTAAT
Found at i:19737895 original size:17 final size:18
Alignment explanation
Indices: 19737868--19737903 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
19737858 TTTAGTTATA
19737868 TTTAGTTTTCGATATGTT
1 TTTAGTTTTCGATATGTT
19737886 TTTA-TTTTCGATATGTT
1 TTTAGTTTTCGATATGTT
19737903 T
1 T
19737904 CATTTAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.17, C:0.06, G:0.14, T:0.64
Consensus pattern (18 bp):
TTTAGTTTTCGATATGTT
Found at i:19739142 original size:17 final size:17
Alignment explanation
Indices: 19739120--19739155 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
19739110 TTTGATTTTG
19739120 TTTTACTATTATTAAAA
1 TTTTACTATTATTAAAA
*
19739137 TTTTACTATTATTGAAA
1 TTTTACTATTATTAAAA
19739154 TT
1 TT
19739156 AGTATTGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTACTATTATTAAAA
Found at i:19743137 original size:19 final size:20
Alignment explanation
Indices: 19743104--19743143 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19743094 AAATACAATC
* *
19743104 AAAACAAT-ATTTTTTTATA
1 AAAACAATAAATTTTCTATA
19743123 AAAACAATAAATTTTCTATA
1 AAAACAATAAATTTTCTATA
19743143 A
1 A
19743144 CTTGCACAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAACAATAAATTTTCTATA
Found at i:19750054 original size:16 final size:15
Alignment explanation
Indices: 19750019--19750054 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
19750009 CAAAATCAAG
19750019 ATTTTTACAACATTC
1 ATTTTTACAACATTC
*
19750034 ATTTTTACAATATTC
1 ATTTTTACAACATTC
19750049 ATTTTT
1 ATTTTT
19750055 GTTTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTTACAACATTC
Found at i:19750361 original size:24 final size:24
Alignment explanation
Indices: 19750334--19750379 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
19750324 ATATATATTG
*
19750334 TTTTTAAATAAATTTGTTAATTCA
1 TTTTTAAATAAATTAGTTAATTCA
*
19750358 TTTTTAATTAAATTAGTTAATT
1 TTTTTAAATAAATTAGTTAATT
19750380 ACCATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTTAAATAAATTAGTTAATTCA
Found at i:19751889 original size:19 final size:20
Alignment explanation
Indices: 19751865--19751903 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19751855 AATGATTAGC
*
19751865 AAAAAAA-TTCTTTAAAAAT
1 AAAAAAATTTCTATAAAAAT
19751884 AAAAAAATTTCTATAAAAAT
1 AAAAAAATTTCTATAAAAAT
19751904 TTAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAAATTTCTATAAAAAT
Found at i:19753275 original size:22 final size:22
Alignment explanation
Indices: 19753250--19753291 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19753240 ATTACATAAC
19753250 TATAATTTTAAAAAATAAATTT
1 TATAATTTTAAAAAATAAATTT
* *
19753272 TATAGTTTTAGAAAATAAAT
1 TATAATTTTAAAAAATAAAT
19753292 AAATTTCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
TATAATTTTAAAAAATAAATTT
Found at i:19753677 original size:5 final size:5
Alignment explanation
Indices: 19753667--19753691 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
19753657 CGGAACACTT
19753667 GAGCC GAGCC GAGCC GAGCC GAGCC
1 GAGCC GAGCC GAGCC GAGCC GAGCC
19753692 ATTTCATGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.40, T:0.00
Consensus pattern (5 bp):
GAGCC
Found at i:19759521 original size:2 final size:2
Alignment explanation
Indices: 19759514--19759539 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19759504 ATTTATACAA
19759514 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
19759540 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19762842 original size:15 final size:14
Alignment explanation
Indices: 19762801--19762848 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
19762791 TGATTTGTGT
19762801 AAACTTAATTAATC
1 AAACTTAATTAATC
* *
19762815 AAAATTAATTTAATT
1 AAACTTAA-TTAATC
19762830 AAACTTTAATTAATC
1 AAAC-TTAATTAATC
19762845 AAAC
1 AAAC
19762849 CATAATCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 7 0.25
15 17 0.61
16 4 0.14
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (14 bp):
AAACTTAATTAATC
Found at i:19763623 original size:36 final size:36
Alignment explanation
Indices: 19763540--19763628 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 36
19763530 TCTATTAAAA
* * * *
19763540 AAACAAAAAACTCATCACATTCAAAGAACAAATAAC
1 AAACAAAGAACCCAGCACATTCAAACAACAAATAAC
* *
19763576 AAACAATAAAGAACCCAGCATATTCAAACAACAAGTAAC
1 AAAC---AAAGAACCCAGCACATTCAAACAACAAATAAC
19763615 AAACAAAGAACCCA
1 AAACAAAGAACCCA
19763629 AAATATTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
36 14 0.32
39 30 0.68
ACGTcount: A:0.60, C:0.24, G:0.06, T:0.11
Consensus pattern (36 bp):
AAACAAAGAACCCAGCACATTCAAACAACAAATAAC
Found at i:19765895 original size:176 final size:178
Alignment explanation
Indices: 19765460--19765930 Score: 411
Period size: 169 Copynumber: 2.7 Consensus size: 178
19765450 ATTTTAATCC
* ** * * *
19765460 AAATTATATCAAAATTAAAGTATAGAGATTAAATCTCAAA-TTTGAGCGAAATATAGGGATCAAA
1 AAATTATGTCAAAAAAAAAGTATAGAAATTAAATCT-AAACTTTAAGAGAAATATAGGGATCAAA
* * * * * * * *
19765524 AATAAAATTTTACCATTATTATATAATC-TTAAAAATGTAGATG-GATTATAATTG-AATTTAGC
65 AATAAAATTTAACCATTCTCATATAATCATGAAATA-GTAGA-GAG-TTAAAACTGAAATTTAGA
* ** *
19765586 CATTATTTTCTCATG-C------CCA-AAA-GAAAAGAATGGATAGGTGTCT
127 CATTATTTTTTCATGTCAAAAGAAAAGAAAGGAAAAGAATGGACAGGTGTCT
** ** * * *
19765629 AAATTATGTCAAAATTAAAGTATAGGGATTTAATCTAAACTTTGAGAGTAATATAGGGATCAAAA
1 AAATTATGTCAAAAAAAAAGTATAGAAATTAAATCTAAACTTTAAGAGAAATATAGGGATCAAAA
* * *
19765694 ATCAAATTTAACCATTCTCATATAATTTCA-GAAA-GGTAGAGA-TTAAAATTGAAATTTAGACA
66 ATAAAATTTAACCATTCTCATATAA--TCATGAAATAGTAGAGAGTTAAAACTGAAATTTAGACA
*
19765756 TTATTTTTTCATGTCAAAAGAAAAGAAAGGAAAAGATTGGACAGGTGTCT
129 TTATTTTTTCATGTCAAAAGAAAAGAAAGGAAAAGAATGGACAGGTGTCT
* * * *
19765806 AAATTATGT-AAAAAAAAAGTTTAGAAATTAAATATTAAA-TTTAAGTGAAATATAGGGATTAAA
1 AAATTATGTCAAAAAAAAAGTATAGAAATTAAAT-CTAAACTTTAAGAGAAATATAGGGATCAAA
* * * *
19765869 ATTAAAATTTAATCATTTTTATATAATCATGAAATAGTAGAGAGGTTAAAACTGAAATTTAG
65 AATAAAATTTAACCATTCTCATATAATCATGAAATAGTAGAGA-GTTAAAACTGAAATTTAG
19765931 CCTCTTTTCC
Statistics
Matches: 246, Mismatches: 36, Indels: 31
0.79 0.12 0.10
Matches are distributed among these distances:
167 8 0.03
168 25 0.10
169 83 0.34
171 5 0.02
174 3 0.01
175 5 0.02
176 69 0.28
177 32 0.13
178 16 0.07
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.33
Consensus pattern (178 bp):
AAATTATGTCAAAAAAAAAGTATAGAAATTAAATCTAAACTTTAAGAGAAATATAGGGATCAAAA
ATAAAATTTAACCATTCTCATATAATCATGAAATAGTAGAGAGTTAAAACTGAAATTTAGACATT
ATTTTTTCATGTCAAAAGAAAAGAAAGGAAAAGAATGGACAGGTGTCT
Found at i:19768155 original size:19 final size:20
Alignment explanation
Indices: 19768120--19768176 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
19768110 ATTTCTTTTA
* *
19768120 TATATTATAAAAGTATTATT
1 TATATTCTAAAATTATTATT
19768140 TA-ATTCTAAAATTATTATT
1 TATATTCTAAAATTATTATT
*
19768159 TATTCTTCTAAAATTATT
1 TA-TATTCTAAAATTATT
19768177 CACTATCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.53
20 2 0.06
21 13 0.41
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (20 bp):
TATATTCTAAAATTATTATT
Found at i:19773568 original size:39 final size:39
Alignment explanation
Indices: 19773500--19773663 Score: 220
Period size: 39 Copynumber: 4.2 Consensus size: 39
19773490 AGGAGTACCA
* * *
19773500 AAGTACAACAGGGGCACATATATACGAACAAGGGTACTG
1 AAGTACAACAGGGGCACGTATGTGCGAACAAGGGTACTG
* * *
19773539 AAGTACAACAGGAGCACGTATGTGTGAACAGGGGTACTG
1 AAGTACAACAGGGGCACGTATGTGCGAACAAGGGTACTG
* * **
19773578 AAGTACAACAAGGGCATGTATGTGCGAACAAGTATACTG
1 AAGTACAACAGGGGCACGTATGTGCGAACAAGGGTACTG
* *
19773617 AAGTACAACAGGGGCACGTATGTGCGAACAGGGGTACCG
1 AAGTACAACAGGGGCACGTATGTGCGAACAAGGGTACTG
19773656 AAGTACAA
1 AAGTACAA
19773664 TAGTTATCTA
Statistics
Matches: 106, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 106 1.00
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.16
Consensus pattern (39 bp):
AAGTACAACAGGGGCACGTATGTGCGAACAAGGGTACTG
Found at i:19778494 original size:26 final size:26
Alignment explanation
Indices: 19778465--19778518 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
19778455 TTAGAAACTC
19778465 ATTTGAAATGAATTAATTGCATATAT
1 ATTTGAAATGAATTAATTGCATATAT
19778491 ATTTGAAATGAATTAATTGCATATAT
1 ATTTGAAATGAATTAATTGCATATAT
19778517 AT
1 AT
19778519 GCTGAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (26 bp):
ATTTGAAATGAATTAATTGCATATAT
Found at i:19782146 original size:19 final size:19
Alignment explanation
Indices: 19782122--19782159 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19782112 AGAAGATAAG
19782122 TTGAACTGAGTAAATCGTA
1 TTGAACTGAGTAAATCGTA
19782141 TTGAACTGAGTAAATCGTA
1 TTGAACTGAGTAAATCGTA
19782160 ATTTATCCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
TTGAACTGAGTAAATCGTA
Found at i:19789950 original size:32 final size:32
Alignment explanation
Indices: 19789909--19789974 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
19789899 TTTGCTATTA
19789909 AGTACTTGGTGACTAAGAAAGACGCCAAATCC
1 AGTACTTGGTGACTAAGAAAGACGCCAAATCC
*
19789941 AGTACTTGGTGACTAAGAAAGACGCTAAATCC
1 AGTACTTGGTGACTAAGAAAGACGCCAAATCC
19789973 AG
1 AG
19789975 ATTAGTTCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (32 bp):
AGTACTTGGTGACTAAGAAAGACGCCAAATCC
Found at i:19798108 original size:118 final size:118
Alignment explanation
Indices: 19797900--19798132 Score: 376
Period size: 118 Copynumber: 2.0 Consensus size: 118
19797890 AACCAAGGCT
* *
19797900 CAAAATTGAATGATATGGTTATTTCGATATCAACGACTAAATTGAATAAAATGTAAAAATTTAGA
1 CAAAATTGAAAGATATGATTATTTCGATATCAACGACTAAATTGAATAAAATGTAAAAATTTAGA
* * *
19797965 GGTATCAAAAAATAAGATTTTTTAGGTTCATTCATGTCATGGTATAATGTGTA
66 GGTATCAAAAAATAAGATTATTTAGGTTCATCCATGTCATGGCATAATGTGTA
* * * * *
19798018 CAAAATTGAAAGATATGATTATTTCGATTTTAATGACTAAATTGAATAAAATGTAAAACTTTAGG
1 CAAAATTGAAAGATATGATTATTTCGATATCAACGACTAAATTGAATAAAATGTAAAAATTTAGA
19798083 GGTATCAAAAAATAAGATTATTTAGGTTCATCCATGTCATGGCATAATGT
66 GGTATCAAAAAATAAGATTATTTAGGTTCATCCATGTCATGGCATAATGT
19798133 ATAAATGTTT
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 105 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (118 bp):
CAAAATTGAAAGATATGATTATTTCGATATCAACGACTAAATTGAATAAAATGTAAAAATTTAGA
GGTATCAAAAAATAAGATTATTTAGGTTCATCCATGTCATGGCATAATGTGTA
Found at i:19800628 original size:5 final size:5
Alignment explanation
Indices: 19800615--19800653 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
19800605 ACCCTCTCTT
* * *
19800615 TTCTC TTCTG TTCTC TTCTT TTCTC TTTTC TTCTC TTCT
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCT
19800654 TCTCCTCCTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.67
Consensus pattern (5 bp):
TTCTC
Found at i:19800636 original size:20 final size:20
Alignment explanation
Indices: 19800611--19800654 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
19800601 CCGAACCCTC
*
19800611 TCTTTTCTCTTCTGTTCTCT
1 TCTTTTCTCTTCTCTTCTCT
*
19800631 TCTTTTCTCTTTTCTTCTCT
1 TCTTTTCTCTTCTCTTCTCT
19800651 TCTT
1 TCTT
19800655 CTCCTCCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (20 bp):
TCTTTTCTCTTCTCTTCTCT
Found at i:19801446 original size:28 final size:28
Alignment explanation
Indices: 19801414--19801520 Score: 133
Period size: 28 Copynumber: 3.8 Consensus size: 28
19801404 ACTGTACTGG
19801414 TTACTGTATTGGGCTAAGGCCCACACTA
1 TTACTGTATTGGGCTAAGGCCCACACTA
**
19801442 TTACTGTATTGGGCTAAGGCCTTCACTA
1 TTACTGTATTGGGCTAAGGCCCACACTA
* * * *
19801470 TTATTGTATTAGGCTAAGGCCCACATTG
1 TTACTGTATTGGGCTAAGGCCCACACTA
* * *
19801498 TTATTGTTTTGGGGTAAGGCCCA
1 TTACTGTATTGGGCTAAGGCCCA
19801521 TATTGTACTG
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 68 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTA
Found at i:19802863 original size:27 final size:27
Alignment explanation
Indices: 19802832--19802892 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
19802822 TGCAAGGTTC
19802832 GCCACAGAGGCTATCCCTTCATCATT-T
1 GCCACAGAGGCTATCCCTTCA-CATTAT
* * * *
19802859 TCCACAAAGGCTTTCCTTTCACATTAT
1 GCCACAGAGGCTATCCCTTCACATTAT
19802886 GCCACAG
1 GCCACAG
19802893 GGTGTTCCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.25, C:0.33, G:0.13, T:0.30
Consensus pattern (27 bp):
GCCACAGAGGCTATCCCTTCACATTAT
Found at i:19822469 original size:20 final size:20
Alignment explanation
Indices: 19822424--19822469 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
19822414 AGAGATAAAG
19822424 AATAAAAATCAGAAAATCAA
1 AATAAAAATCAGAAAATCAA
*
19822444 ATTAAAAAT-AGCAAAAAT-AA
1 AATAAAAATCAG--AAAATCAA
19822464 AATAAA
1 AATAAA
19822470 GCAAAGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.09
20 15 0.68
21 5 0.23
ACGTcount: A:0.72, C:0.07, G:0.04, T:0.17
Consensus pattern (20 bp):
AATAAAAATCAGAAAATCAA
Found at i:19824420 original size:25 final size:22
Alignment explanation
Indices: 19824366--19824420 Score: 56
Period size: 26 Copynumber: 2.3 Consensus size: 22
19824356 AATTTCAATT
19824366 AAAAATTTATTTAATAATTAAA
1 AAAAATTTATTTAATAATTAAA
*
19824388 AATTAAATTTATTATAAATATTTAAA
1 AA--AAATTTATT-T-AATAATTAAA
19824414 ACAAAAT
1 A-AAAAT
19824421 ATTAATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 2 0.07
24 9 0.33
25 5 0.19
26 10 0.37
27 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATTTATTTAATAATTAAA
Found at i:19830157 original size:23 final size:23
Alignment explanation
Indices: 19830128--19830189 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
19830118 GCCCGGCCCG
* *
19830128 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAATTAAAATTAAAACTAA
*
19830151 TTTTTAAATAAAATTAAAACTAA
1 TTTTTAATTAAAATTAAAACTAA
*
19830174 TTGTT-ATTAAAATTAA
1 TTTTTAATTAAAATTAA
19830190 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 10 0.29
23 24 0.71
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTTTAATTAAAATTAAAACTAA
Found at i:19830202 original size:16 final size:16
Alignment explanation
Indices: 19830165--19830204 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
19830155 TAAATAAAAT
* *
19830165 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
19830181 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
19830197 TAAAATTA
1 TAAAATTA
19830205 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:19830310 original size:9 final size:9
Alignment explanation
Indices: 19830277--19830304 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
19830267 TTTATCAAAT
19830277 TATTAATTG
1 TATTAATTG
19830286 TATTAATTG
1 TATTAATTG
19830295 TATTAATTG
1 TATTAATTG
19830304 T
1 T
19830305 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:19830315 original size:68 final size:68
Alignment explanation
Indices: 19830193--19830402 Score: 379
Period size: 68 Copynumber: 3.1 Consensus size: 68
19830183 AAATTAATTG
* *
19830193 TTAGTAAAATTATCAAATTATTAATTG--TTAATTATATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
19830256 TGA
66 TGA
19830259 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
19830324 TGA
66 TGA
*
19830327 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
19830392 TGA
66 TGA
19830395 TTAGTAAA
1 TTAGTAAA
19830403 ACAAACTTGA
Statistics
Matches: 139, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
66 26 0.19
68 113 0.81
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:19830357 original size:9 final size:9
Alignment explanation
Indices: 19830345--19830372 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
19830335 TTTATCAAAT
19830345 TATTAATTG
1 TATTAATTG
19830354 TATTAATTG
1 TATTAATTG
19830363 TATTAATTG
1 TATTAATTG
19830372 T
1 T
19830373 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:19830489 original size:24 final size:22
Alignment explanation
Indices: 19830460--19830503 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 22
19830450 AAATAAACTT
19830460 AAAATAAAAAAATATTATATTTTA
1 AAAAT-AAAAAATA-TATATTTTA
19830484 AAAATAAAAAATATATATTT
1 AAAATAAAAAATATATATTT
19830504 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAATAAAAAATATATATTTTA
Found at i:19830611 original size:31 final size:33
Alignment explanation
Indices: 19830576--19830646 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 33
19830566 ATTTTTTAAA
*
19830576 CGGGCCTAAAATTTTGCCC-AA-GCCCATATTT
1 CGGGCCTAAAATTTTACCCAAACGCCCATATTT
* *
19830607 CGGGCCTATATTTTTACCCAAACCCGCCCATATTT
1 CGGGCCTAAAATTTTACCCAAA--CGCCCATATTT
19830642 CGGGC
1 CGGGC
19830647 GGGCCGTCGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 16 0.48
32 2 0.06
35 15 0.45
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (33 bp):
CGGGCCTAAAATTTTACCCAAACGCCCATATTT
Found at i:19831350 original size:64 final size:64
Alignment explanation
Indices: 19831249--19831380 Score: 237
Period size: 64 Copynumber: 2.1 Consensus size: 64
19831239 TCAATCGGAA
19831249 ATGTCGCATCTTAATTTCGAATATATTTATATGAAAAATTAATTTATTGGAAATACCAATCAAC
1 ATGTCGCATCTTAATTTCGAATATATTTATATGAAAAATTAATTTATTGGAAATACCAATCAAC
* * *
19831313 ATGTCGTATCTTAATTTTGAATATATTTATATGAAAAATTAATTTATTGGAAATAGCAATCAAC
1 ATGTCGCATCTTAATTTCGAATATATTTATATGAAAAATTAATTTATTGGAAATACCAATCAAC
19831377 ATGT
1 ATGT
19831381 TTGTTAGGTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (64 bp):
ATGTCGCATCTTAATTTCGAATATATTTATATGAAAAATTAATTTATTGGAAATACCAATCAAC
Found at i:19831451 original size:11 final size:12
Alignment explanation
Indices: 19831422--19831455 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
19831412 TTGAATGAAG
*
19831422 AAATAAATAAAT
1 AAATAATTAAAT
19831434 AAATAATTAAAT
1 AAATAATTAAAT
19831446 -AATAATTAAA
1 AAATAATTAAA
19831456 AGAGATCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATAATTAAAT
Found at i:19832640 original size:17 final size:17
Alignment explanation
Indices: 19832609--19832641 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19832599 ATAAAAATTC
19832609 CCCAACAACATTAGAAG
1 CCCAACAACATTAGAAG
19832626 CCCAA-AACATATAGAA
1 CCCAACAACAT-TAGAA
19832642 CATACTACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.52, C:0.27, G:0.09, T:0.12
Consensus pattern (17 bp):
CCCAACAACATTAGAAG
Found at i:19844907 original size:23 final size:23
Alignment explanation
Indices: 19844881--19844931 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
19844871 TCTAAAGCAA
* *
19844881 TTGTGGCATTTTCTGTAAAGCCT
1 TTGTGGCATGTTCTATAAAGCCT
* **
19844904 TTGTAGTGTGTTCTATAAAGCCT
1 TTGTGGCATGTTCTATAAAGCCT
19844927 TTGTG
1 TTGTG
19844932 ACGTATTTTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.45
Consensus pattern (23 bp):
TTGTGGCATGTTCTATAAAGCCT
Found at i:19844961 original size:23 final size:23
Alignment explanation
Indices: 19844935--19844986 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
19844925 CTTTGTGACG
* *
19844935 TATTTTGTGATGCTTGTGTGGCA
1 TATTTTGTAATGCCTGTGTGGCA
19844958 TATTTTGTAATGCCTGTGTGGCA
1 TATTTTGTAATGCCTGTGTGGCA
19844981 TATTTT
1 TATTTT
19844987 ATAGCGCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.15, C:0.10, G:0.25, T:0.50
Consensus pattern (23 bp):
TATTTTGTAATGCCTGTGTGGCA
Found at i:19854159 original size:35 final size:35
Alignment explanation
Indices: 19854092--19854167 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
19854082 GTTATCGGCT
* * *
19854092 AGTCCTTCAAGGTGACACCGTGATGACAGTATATA
1 AGTCCTTCAAGGTGACACCATGATAACAGTATACA
* *
19854127 AGTCCTTCGAGGTGACACCATG-TAAACGGTATACA
1 AGTCCTTCAAGGTGACACCATGAT-AACAGTATACA
19854162 AGTCCT
1 AGTCCT
19854168 ATGAGGAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 1 0.03
35 34 0.97
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (35 bp):
AGTCCTTCAAGGTGACACCATGATAACAGTATACA
Found at i:19865857 original size:16 final size:16
Alignment explanation
Indices: 19865836--19865878 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
19865826 TTATAATTTA
19865836 TTAAATAAAA-ACTAT
1 TTAAATAAAATACTAT
*
19865851 CTTAAATAAAATATTAT
1 -TTAAATAAAATACTAT
19865868 TTAAATAAAAT
1 TTAAATAAAAT
19865879 GTTTAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAATAAAATACTAT
Found at i:19881545 original size:49 final size:48
Alignment explanation
Indices: 19881492--19881608 Score: 110
Period size: 49 Copynumber: 2.4 Consensus size: 48
19881482 TCATTATTTA
* * *
19881492 GCTCTTATGAGCTTCACGTTTA-TGGCTCGTATAAGCTTTCTGATTAATG
1 GCTCTTATGAGCTTC-CGTTTATTGGCTCGCATAAGCTTCCCGATT-ATG
** * *** *
19881541 GCTCTTCGGAGCTACCCAATATTGGCTCGCATGAGCTTCCCGATTATG
1 GCTCTTATGAGCTTCCGTTTATTGGCTCGCATAAGCTTCCCGATTATG
19881589 GCTCTTATGAGCTTCTCGTT
1 GCTCTTATGAGCTTC-CGTT
19881609 ACATGGTTCA
Statistics
Matches: 50, Mismatches: 16, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
48 18 0.36
49 32 0.64
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (48 bp):
GCTCTTATGAGCTTCCGTTTATTGGCTCGCATAAGCTTCCCGATTATG
Found at i:19881681 original size:25 final size:26
Alignment explanation
Indices: 19881570--19881681 Score: 78
Period size: 25 Copynumber: 4.5 Consensus size: 26
19881560 TATTGGCTCG
* *
19881570 CATGAGCTTCCCGAT-TATGGCTCTT-
1 CATGAGCTTCCTGTTATATGGCT-TTA
* *
19881595 -ATGAGCTT-CTCGTTACATGG-TTCA
1 CATGAGCTTCCT-GTTATATGGCTTTA
*
19881619 CATGAGCTTCTTGTTATATGGCTTTA
1 CATGAGCTTCCTGTTATATGGCTTTA
* *
19881645 -AAGAGCTACCTGTTATAT-GC-TTA
1 CATGAGCTTCCTGTTATATGGCTTTA
19881668 CATGAGCATTCCTG
1 CATGAGC-TTCCTG
19881682 AATATGAATT
Statistics
Matches: 67, Mismatches: 12, Indels: 16
0.71 0.13 0.17
Matches are distributed among these distances:
23 5 0.07
24 18 0.27
25 40 0.60
26 4 0.06
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (26 bp):
CATGAGCTTCCTGTTATATGGCTTTA
Found at i:19883848 original size:12 final size:12
Alignment explanation
Indices: 19883831--19883856 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19883821 AGGATATGCA
19883831 ATCTTAGATATG
1 ATCTTAGATATG
19883843 ATCTTAGATATG
1 ATCTTAGATATG
19883855 AT
1 AT
19883857 ATGCAATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATCTTAGATATG
Found at i:19883905 original size:21 final size:23
Alignment explanation
Indices: 19883861--19883905 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
19883851 TATGATATGC
*
19883861 AATCTTAGAAGATATTATTTTGT
1 AATCTTAGAAGATATTAATTTGT
19883884 AATCTTAG-AGAT-TTAATTTGT
1 AATCTTAGAAGATATTAATTTGT
19883905 A
1 A
19883906 GATACCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 4 0.19
23 8 0.38
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (23 bp):
AATCTTAGAAGATATTAATTTGT
Found at i:19884217 original size:3 final size:3
Alignment explanation
Indices: 19884209--19884247 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
19884199 TGTTATTAAG
* *
19884209 TTA TTA TTA TTA TTT TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19884248 CTATATATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19884403 original size:17 final size:17
Alignment explanation
Indices: 19884372--19884415 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
19884362 CATAACTTTT
*
19884372 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
19884388 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
19884405 ATATACATTTT
1 ATATACATTTT
19884416 TTATTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:19884631 original size:30 final size:31
Alignment explanation
Indices: 19884579--19884636 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
19884569 TATTTGTTTA
*
19884579 TATATATATGTAATTATCTTTTT-TATAATC
1 TATATATATGTAATAATCTTTTTATATAATC
19884609 TATATATATGTATATAAT-TTTTTATATA
1 TATATATATGTA-ATAATCTTTTTATATA
19884637 TGTACATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (31 bp):
TATATATATGTAATAATCTTTTTATATAATC
Found at i:19888156 original size:6 final size:6
Alignment explanation
Indices: 19888131--19888212 Score: 60
Period size: 6 Copynumber: 13.2 Consensus size: 6
19888121 TTTCTCTTGA
* *
19888131 TTTTTC TTCTTT- TCTTTC TTTTTC TTTTTC ATTTTT- ATTTTC TTTTTC
1 TTTTTC TT-TTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC
* * *
19888179 CTTTTC TTTTGTC TCTTTAC TCATTTC TTTTTC T
1 TTTTTC TTTT-TC T-TTTTC T-TTTTC TTTTTC T
19888213 CTCAATTGTT
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
5 7 0.12
6 32 0.53
7 18 0.30
8 3 0.05
ACGTcount: A:0.05, C:0.20, G:0.01, T:0.74
Consensus pattern (6 bp):
TTTTTC
Found at i:19888171 original size:13 final size:12
Alignment explanation
Indices: 19888120--19888188 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
19888110 ACTCAATTTC
* *
19888120 TTTTCTCTTGAT
1 TTTTCTTTTTAT
19888132 TTTTCTTCTTT-T
1 TTTTCTT-TTTAT
* *
19888144 CTTTCTTTTTCT
1 TTTTCTTTTTAT
19888156 TTTTCATTTTTA-
1 TTTTC-TTTTTAT
**
19888168 TTTTCTTTTTCC
1 TTTTCTTTTTAT
19888180 TTTTCTTTT
1 TTTTCTTTT
19888189 GTCTCTTTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
11 8 0.17
12 32 0.68
13 7 0.15
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.77
Consensus pattern (12 bp):
TTTTCTTTTTAT
Found at i:19888551 original size:23 final size:23
Alignment explanation
Indices: 19888513--19888563 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
19888503 GTAGGGAGTT
* *
19888513 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
19888536 TGTAATACCCCAAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
*
19888559 AGTAA
1 TGTAA
19888564 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCAAAAATTACTAC
Found at i:19891043 original size:50 final size:50
Alignment explanation
Indices: 19890989--19891269 Score: 287
Period size: 50 Copynumber: 5.6 Consensus size: 50
19890979 TGTGAGCCAG
*
19890989 TGTAAGACCATGCCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
* *
19891039 TGTAAGACCATGTCTCGGACATGGTGTTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
* *
19891089 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCC
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
** * * * * * **
19891139 CATAAGACGATGTCTAGGACATGGC-ATGAGCACCAATATGAGAACTCCCA
1 TGTAAGACCATGTCTGGGACATGGCGTTG-GCACCGAGATGAGAGGTCCCA
* * * * * * * * * * ** *
19891189 TGTAAGACCATATCTAGGATATGACATTGACAGC-ACAGGAAACATCCAA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
*
19891238 TGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCA
19891270 TGTTATTATC
Statistics
Matches: 191, Mismatches: 38, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
49 37 0.19
50 152 0.80
51 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
Found at i:19892785 original size:23 final size:23
Alignment explanation
Indices: 19892758--19892808 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
19892748 GGGGGAGAAA
*
19892758 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
19892781 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
19892804 AGTAA
1 TGTAA
19892809 GAAAATATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:19897894 original size:20 final size:20
Alignment explanation
Indices: 19897866--19897906 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19897856 AGGTAATTTA
* *
19897866 AATTGAGCTTAAATGAGCTG
1 AATTAAGCTCAAATGAGCTG
*
19897886 AATTAAGCTCAAGTGAGCTG
1 AATTAAGCTCAAATGAGCTG
19897906 A
1 A
19897907 TCGGAGCTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (20 bp):
AATTAAGCTCAAATGAGCTG
Found at i:19899928 original size:18 final size:19
Alignment explanation
Indices: 19899888--19899930 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
19899878 GACCTCGATG
*
19899888 ACTGAAAAAGGGTCGTGTC
1 ACTGAAAAAGGGTCGTGTA
*
19899907 ACTGAAAAAGGGTTGT-TA
1 ACTGAAAAAGGGTCGTGTA
19899925 ACTGAA
1 ACTGAA
19899931 CTACCTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.23
Consensus pattern (19 bp):
ACTGAAAAAGGGTCGTGTA
Found at i:19902045 original size:17 final size:17
Alignment explanation
Indices: 19902025--19902077 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
19902015 AATGACAATG
19902025 TGTGAGCTGTGCTTATA
1 TGTGAGCTGTGCTTATA
* * *
19902042 TGTGTGTTGCGCTTATA
1 TGTGAGCTGTGCTTATA
** *
19902059 TACGAGCTGTGTTTATA
1 TGTGAGCTGTGCTTATA
19902076 TG
1 TG
19902078 CTAGCTTTGT
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.17, C:0.11, G:0.28, T:0.43
Consensus pattern (17 bp):
TGTGAGCTGTGCTTATA
Found at i:19902083 original size:17 final size:17
Alignment explanation
Indices: 19902063--19902146 Score: 78
Period size: 17 Copynumber: 4.9 Consensus size: 17
19902053 CTTATATACG
19902063 AGCTGTGTTTATATGCT
1 AGCTGTGTTTATATGCT
* *
19902080 AGCTTTGTTTATATGCA
1 AGCTGTGTTTATATGCT
* * **
19902097 AGTTGTGTTTATAAGAG
1 AGCTGTGTTTATATGCT
*
19902114 AGCTGTGTTTCTATGCT
1 AGCTGTGTTTATATGCT
* * *
19902131 AACTATGTTCATATGC
1 AGCTGTGTTTATATGC
19902147 AAACTGTTTC
Statistics
Matches: 51, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (17 bp):
AGCTGTGTTTATATGCT
Found at i:19902180 original size:34 final size:34
Alignment explanation
Indices: 19902141--19902264 Score: 115
Period size: 34 Copynumber: 3.6 Consensus size: 34
19902131 AACTATGTTC
**
19902141 ATATGCAAACTGTTTCAATGTGTGGATTGTGTAA
1 ATATGCAAACTGTGACAATGTGTGGATTGTGTAA
* * * * **
19902175 ATATGCTACCTATGACAATGTGCGTG-TTGTGTTT
1 ATATGCAAACTGTGACAATGTGTG-GATTGTGTAA
* * **
19902209 ATATGTAAACTGTGTCAATGTGTGGAACGTGTAA
1 ATATGCAAACTGTGACAATGTGTGGATTGTGTAA
*
19902243 ATATGCAAGCTGTGACAATGTG
1 ATATGCAAACTGTGACAATGTG
19902265 CGTGTTATGT
Statistics
Matches: 67, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
33 1 0.01
34 65 0.97
35 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.35
Consensus pattern (34 bp):
ATATGCAAACTGTGACAATGTGTGGATTGTGTAA
Found at i:19902227 original size:68 final size:68
Alignment explanation
Indices: 19902134--19902287 Score: 227
Period size: 68 Copynumber: 2.3 Consensus size: 68
19902124 CTATGCTAAC
* * ** *
19902134 TATGTTCATATGCAAACTGTTTCAATGTGTGGATTGTGTAAATATGCTACCTATGACAATGTGCG
1 TATGTTTATATGCAAACTGTGTCAATGTGTGGAACGTGTAAATATGCAACCTATGACAATGTGCG
19902199 TGT
66 TGT
* * * *
19902202 TGTGTTTATATGTAAACTGTGTCAATGTGTGGAACGTGTAAATATGCAAGCTGTGACAATGTGCG
1 TATGTTTATATGCAAACTGTGTCAATGTGTGGAACGTGTAAATATGCAACCTATGACAATGTGCG
19902267 TGT
66 TGT
19902270 TATGTTTATATGCAAACT
1 TATGTTTATATGCAAACT
19902288 CTCACTGTAA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 75 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (68 bp):
TATGTTTATATGCAAACTGTGTCAATGTGTGGAACGTGTAAATATGCAACCTATGACAATGTGCG
TGT
Found at i:19902281 original size:34 final size:34
Alignment explanation
Indices: 19902134--19902287 Score: 98
Period size: 34 Copynumber: 4.5 Consensus size: 34
19902124 CTATGCTAAC
* ** *
19902134 TATGTTCATATGCAAACTGTTTCAATGTGTG-GAT
1 TATGTTTATATGCAAACTGTGACAATGTGCGTG-T
* ** * * *
19902168 TGTGTAAATATGCTACCTATGACAATGTGCGTGT
1 TATGTTTATATGCAAACTGTGACAATGTGCGTGT
* * * *
19902202 TGTGTTTATATGTAAACTGTGTCAATGT--GTGG
1 TATGTTTATATGCAAACTGTGACAATGTGCGTGT
* ** *
19902234 AACGTGTAAATATGCAAGCTGTGACAATGTGCGTGT
1 TA--TGTTTATATGCAAACTGTGACAATGTGCGTGT
19902270 TATGTTTATATGCAAACT
1 TATGTTTATATGCAAACT
19902288 CTCACTGTAA
Statistics
Matches: 86, Mismatches: 29, Indels: 10
0.69 0.23 0.08
Matches are distributed among these distances:
32 3 0.03
34 78 0.91
35 1 0.01
36 4 0.05
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (34 bp):
TATGTTTATATGCAAACTGTGACAATGTGCGTGT
Found at i:19902489 original size:26 final size:26
Alignment explanation
Indices: 19902437--19902489 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
19902427 TGTTTATGTA
* *
19902437 CGAGCTTTTTGTAAAGTAATTACGTG
1 CGAGCTCTTTGTAAAGTAATTAAGTG
19902463 CGAGCTCTTTGTAAAGT-ATCTAAGTG
1 CGAGCTCTTTGTAAAGTAAT-TAAGTG
19902489 C
1 C
19902490 TGGTCTGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (26 bp):
CGAGCTCTTTGTAAAGTAATTAAGTG
Found at i:19902710 original size:27 final size:27
Alignment explanation
Indices: 19902680--19902756 Score: 145
Period size: 27 Copynumber: 2.9 Consensus size: 27
19902670 CAAGATGTAG
19902680 AATGGATTCAAGCCATGCAAGATACAA
1 AATGGATTCAAGCCATGCAAGATACAA
19902707 AATGGATTCAAGCCATGCAAGATACAA
1 AATGGATTCAAGCCATGCAAGATACAA
*
19902734 AATGGATTCAAGACATGCAAGAT
1 AATGGATTCAAGCCATGCAAGAT
19902757 GAGCTCTAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.19
Consensus pattern (27 bp):
AATGGATTCAAGCCATGCAAGATACAA
Found at i:19905816 original size:14 final size:14
Alignment explanation
Indices: 19905797--19905825 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19905787 AATGGCCTAT
19905797 AGTTTACGCGGGAA
1 AGTTTACGCGGGAA
19905811 AGTTTACGCGGGAA
1 AGTTTACGCGGGAA
19905825 A
1 A
19905826 TATAAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (14 bp):
AGTTTACGCGGGAA
Found at i:19906753 original size:12 final size:12
Alignment explanation
Indices: 19906736--19906760 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19906726 TGTAAATGAA
19906736 TCATTTCCATTT
1 TCATTTCCATTT
19906748 TCATTTCCATTT
1 TCATTTCCATTT
19906760 T
1 T
19906761 GGAAATCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Done.