Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 63 of 144
Found at i:19106314 original size:18 final size:18
Alignment explanation
Indices: 19106291--19106328 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
19106281 TCTTACATGA
19106291 AAATCTCGTATCGATGCC
1 AAATCTCGTATCGATGCC
19106309 AAATCTCGTATCGATGCC
1 AAATCTCGTATCGATGCC
19106327 AA
1 AA
19106329 TAGCCCAGCT
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:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (18 bp):
AAATCTCGTATCGATGCC
Found at i:19106370 original size:43 final size:43
Alignment explanation
Indices: 19106309--19106442 Score: 171
Period size: 43 Copynumber: 3.1 Consensus size: 43
19106299 TATCGATGCC
**
19106309 AAATCTCGTATCGATGCCAATAGCCCAGCTATGGTCTTACACG
1 AAATCTCAAATCGATGCCAATAGCCCAGCTATGGTCTTACACG
* **
19106352 AAATCTCAAATCGATGCCAATAGCCTAGCTATGGTCTTTTACG
1 AAATCTCAAATCGATGCCAATAGCCCAGCTATGGTCTTACACG
* * * *
19106395 AAATCTCAAATCAATGCCAATAGCACAGAC-ATGGTCTGACATG
1 AAATCTCAAATCGATGCCAATAGCCCAG-CTATGGTCTTACACG
19106438 AAATC
1 AAATC
19106443 ACACCTCGGA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 77 0.99
44 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (43 bp):
AAATCTCAAATCGATGCCAATAGCCCAGCTATGGTCTTACACG
Found at i:19116303 original size:4 final size:4
Alignment explanation
Indices: 19116296--19116325 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
19116286 TTTTAATGCT
*
19116296 TTTA TTTA TTTA TTTA TTTA CTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
19116326 ATTGGGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:19116436 original size:24 final size:25
Alignment explanation
Indices: 19116387--19116436 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
19116377 GTTATAACTT
19116387 TTTTTTATTTACCAAAAAATATATAA
1 TTTTTTATTTACC-AAAAATATATAA
19116413 TTTTTTATTTACC-AAAATATATAA
1 TTTTTTATTTACCAAAAATATATAA
19116437 AAAAAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 11 0.46
26 13 0.54
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTTTTATTTACCAAAAATATATAA
Found at i:19116454 original size:16 final size:16
Alignment explanation
Indices: 19116433--19116465 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
19116423 ACCAAAATAT
19116433 ATAAAAAAAACAAAAA
1 ATAAAAAAAACAAAAA
*
19116449 ATAAAAAAAATAAAAA
1 ATAAAAAAAACAAAAA
19116465 A
1 A
19116466 ACAGAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (16 bp):
ATAAAAAAAACAAAAA
Found at i:19116456 original size:18 final size:18
Alignment explanation
Indices: 19116425--19116479 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
19116415 TTTTATTTAC
* *
19116425 CAAAATATATAAAAAAAA
1 CAAAAAATAAAAAAAAAA
*
19116443 CAAAAAATAAAAAAAATA
1 CAAAAAATAAAAAAAAAA
*
19116461 -AAAAAACAGAAAAAAAAA
1 CAAAAAATA-AAAAAAAAA
19116479 C
1 C
19116480 CTGAACTGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 7 0.23
18 23 0.77
ACGTcount: A:0.82, C:0.07, G:0.02, T:0.09
Consensus pattern (18 bp):
CAAAAAATAAAAAAAAAA
Found at i:19116549 original size:27 final size:27
Alignment explanation
Indices: 19116519--19116585 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
19116509 AGGGAAGCAG
19116519 GTTGGCGGCACCAAACAAGGGATCCCT
1 GTTGGCGGCACCAAACAAGGGATCCCT
***
19116546 GTTGGCGGCACCAATGGAGGGATCCCT
1 GTTGGCGGCACCAAACAAGGGATCCCT
19116573 GTTGGCGGCACCA
1 GTTGGCGGCACCA
19116586 CCCTTGAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.21, C:0.28, G:0.34, T:0.16
Consensus pattern (27 bp):
GTTGGCGGCACCAAACAAGGGATCCCT
Found at i:19116655 original size:18 final size:17
Alignment explanation
Indices: 19116632--19116802 Score: 70
Period size: 18 Copynumber: 9.8 Consensus size: 17
19116622 GAAGGAGAGG
19116632 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
19116650 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
19116667 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
*
19116683 GGAAAGAAAGAAACAGAA
1 GG-AAGAAAGAAAAAGAA
** *
19116701 GGAAAGAAAAGGAAAGGGGA
1 GG-AAG-AAA-GAAAAAGAA
*
19116721 GGAAAGAAAGAAAAATAA
1 GG-AAGAAAGAAAAAGAA
19116739 -G--GAAAGAAAAAGAAA
1 GGAAGAAAGAAAAAG-AA
*
19116754 GG-AGAAGAGACAAAAAAA
1 GGAAGAA-AGA-AAAAGAA
* * *
19116772 GAAAG-AAGAAGAAGAG
1 GGAAGAAAGAAAAAGAA
*
19116788 GGAAGGAAGGAAAAA
1 GGAA-GAAAGAAAAA
19116803 AAGAAAATAA
Statistics
Matches: 117, Mismatches: 21, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
14 10 0.09
15 11 0.09
16 12 0.10
17 12 0.10
18 35 0.30
19 25 0.21
20 12 0.10
ACGTcount: A:0.65, C:0.01, G:0.33, T:0.01
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:19116665 original size:10 final size:10
Alignment explanation
Indices: 19116634--19116784 Score: 53
Period size: 10 Copynumber: 15.1 Consensus size: 10
19116624 AGGAGAGGGG
*
19116634 AAGAAGAAGA
1 AAGAAAAAGA
19116644 AAGAAAGGAAGA
1 AAGAAA--AAGA
19116656 AAGAAAAAGA
1 AAGAAAAAGA
* *
19116666 AGGAAAAGGA
1 AAGAAAAAGA
* * *
19116676 AAGGAGAGGA
1 AAGAAAAAGA
19116686 AAG--AAAGA
1 AAGAAAAAGA
* * *
19116694 AACAGAAGGA
1 AAGAAAAAGA
*
19116704 AAGAAAAGGA
1 AAGAAAAAGA
*** *
19116714 AAGGGGAGGA
1 AAGAAAAAGA
19116724 AAG--AAAGA
1 AAGAAAAAGA
*
19116732 AA-AATAAGGA
1 AAGAA-AAAGA
19116742 AAGAAAAAGA
1 AAGAAAAAGA
*
19116752 AAGGAGAAGAGA
1 AA-GA-AAAAGA
19116764 CAA-AAAAAGA
1 -AAGAAAAAGA
*
19116774 AAGAAGAAGA
1 AAGAAAAAGA
19116784 A
1 A
19116785 GAGGGAAGGA
Statistics
Matches: 107, Mismatches: 22, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
8 10 0.09
9 2 0.02
10 73 0.68
11 5 0.05
12 15 0.14
13 2 0.02
ACGTcount: A:0.67, C:0.01, G:0.31, T:0.01
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:19116710 original size:38 final size:38
Alignment explanation
Indices: 19116652--19116809 Score: 154
Period size: 38 Copynumber: 4.3 Consensus size: 38
19116642 GAAAGAAAGG
19116652 AAGAAAGAAAAAGAA-G---GAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
* *
19116686 AAGAAAGAAACAGAAGGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
* *
19116724 AAGAAAGAAAAATAAGGAAAGAAAAAGAAAGGAGAAGAGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAG-AG-GA
* *
19116764 CAA-AAA-AAGAAAGAA-G-AAGAAGAGGGAAGGA-AGGA
1 -AAGAAAGAA-AAAGAAGGAAAGAAAAGGAAAGGAGAGGA
*
19116799 AAAAAAGAAAA
1 AAGAAAGAAAA
19116810 TAAGATAATT
Statistics
Matches: 104, Mismatches: 10, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
34 16 0.15
35 8 0.08
36 4 0.04
38 59 0.57
39 5 0.05
40 10 0.10
41 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.32, T:0.01
Consensus pattern (38 bp):
AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
Found at i:19118750 original size:17 final size:17
Alignment explanation
Indices: 19118728--19118763 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
19118718 ATGGGGTAAG
19118728 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
19118745 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
19118762 AT
1 AT
19118764 TACATCTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:19119770 original size:15 final size:14
Alignment explanation
Indices: 19119730--19119758 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19119720 TTTTTGTATC
19119730 AATTTAATTATTCT
1 AATTTAATTATTCT
19119744 AATTTAATTATTCT
1 AATTTAATTATTCT
19119758 A
1 A
19119759 GTTTTAGTTA
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:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:19122280 original size:18 final size:18
Alignment explanation
Indices: 19122254--19122291 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
19122244 ATCCCAATGA
*
19122254 TCGCCACCACATTCTTCT
1 TCGCAACCACATTCTTCT
19122272 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
19122290 TC
1 TC
19122292 ACCACCAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.42, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:19122298 original size:18 final size:18
Alignment explanation
Indices: 19122257--19122298 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
19122247 CCAATGATCG
*
19122257 CCACCACATTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
19122275 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
19122293 CCACCA
1 CCACCA
19122299 ACCATATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:19123335 original size:81 final size:81
Alignment explanation
Indices: 19123176--19123334 Score: 304
Period size: 81 Copynumber: 2.0 Consensus size: 81
19123166 ATTATACAAA
19123176 ACAATAACAATAACATAATCAATTATTTTTAAAAAAATACCTTATTTTTCTCTTCTCTTTCTCTC
1 ACAATAACAATAACATAATCAATTATTTTTAAAAAAATACCTTATTTTTCTCTTCTCTTTCTCTC
19123241 TTTTTCTCTTTTTTTC
66 TTTTTCTCTTTTTTTC
19123257 ACAATAACAATAACATAATCAATTATTTTTAAAAAAATACCTTATTTTTCTCTTCTC-TT-TCTC
1 ACAATAACAATAACATAATCAATTATTTTTAAAAAAATACCTTATTTTTCTCTTCTCTTTCTCTC
19123320 TTTTTCTCTTTTTTT
66 TTTTTCTCTTTTTTT
19123335 TCGCAGCACC
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
79 19 0.24
80 2 0.03
81 57 0.73
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (81 bp):
ACAATAACAATAACATAATCAATTATTTTTAAAAAAATACCTTATTTTTCTCTTCTCTTTCTCTC
TTTTTCTCTTTTTTTC
Found at i:19123500 original size:27 final size:27
Alignment explanation
Indices: 19123440--19123508 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
19123430 GGTTGGCAGG
* *
19123440 ATTGGTGTCGCCAACAGGGATTCCTCC
1 ATTGGTGCCGCCAACAGGGATCCCTCC
* **
19123467 ATAGGTGCCGCCAACAGGGATCCCTTG
1 ATTGGTGCCGCCAACAGGGATCCCTCC
*
19123494 TTTGGTGCCGCCAAC
1 ATTGGTGCCGCCAAC
19123509 CTACTTCCCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (27 bp):
ATTGGTGCCGCCAACAGGGATCCCTCC
Found at i:19123756 original size:3 final size:3
Alignment explanation
Indices: 19123750--19123780 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
19123740 TTTTATGCCT
19123750 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
19123781 CTTCTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19123790 original size:11 final size:10
Alignment explanation
Indices: 19123750--19123790 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
19123740 TTTTATGCCT
19123750 TTATTA-TTA
1 TTATTATTTA
19123759 TTATTA-TTA
1 TTATTATTTA
19123768 TTATTATTTA
1 TTATTATTTA
*
19123778 TTACTTCTTTA
1 TTA-TTATTTA
19123789 TT
1 TT
19123791 TTTTATAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 15 0.52
10 6 0.21
11 8 0.28
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATTATTTA
Found at i:19124015 original size:17 final size:18
Alignment explanation
Indices: 19123993--19124026 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19123983 TTAGTTATTT
*
19123993 ATTATTACTA-TAATATG
1 ATTATTAATATTAATATG
19124010 ATTATTAATATTAATAT
1 ATTATTAATATTAATAT
19124027 TAATATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTATTAATATTAATATG
Found at i:19124033 original size:29 final size:29
Alignment explanation
Indices: 19123995--19124051 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
19123985 AGTTATTTAT
*
19123995 TATTACTATAAT-ATGATTATTAATATTAA
1 TATTAATATAATAAT-ATTATTAATATTAA
*
19124024 TATTAATATAATAATATTATTATTATTA
1 TATTAATATAATAATATTATTAATATTA
19124052 TAGTATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (29 bp):
TATTAATATAATAATATTATTAATATTAA
Found at i:19124040 original size:20 final size:20
Alignment explanation
Indices: 19124015--19124053 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19124005 ATATGATTAT
19124015 TAATATTAATATTAATATAA
1 TAATATTAATATTAATATAA
* *
19124035 TAATATTATTATTATTATA
1 TAATATTAATATTAATATA
19124054 GTATTCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATATTAATATTAATATAA
Found at i:19127403 original size:225 final size:225
Alignment explanation
Indices: 19127104--19127537 Score: 832
Period size: 225 Copynumber: 1.9 Consensus size: 225
19127094 TTAATTTATA
*
19127104 AAACCAAACTCTAAATAATTCAGCAAGAAACTTGTAACCCCCTAAACTCGGCCTAGACATTATGG
1 AAACCAAACTCTAAACAATTCAGCAAGAAACTTGTAACCCCCTAAACTCGGCCTAGACATTATGG
**
19127169 CTGAATCTCGAAGATCACATTGGCCAGGATGATGGCACAGAAAATTATTTAACTATTTTCTCTTG
66 CCAAATCTCGAAGATCACATTGGCCAGGATGATGGCACAGAAAATTATTTAACTATTTTCTCTTG
*
19127234 ACAAACATCATTATTTAAAATCGTCATTTTGATTTGCTTAAGAAAAGCCAAGTAGTGTCTATAAA
131 ACAAACATCATTATTTAAAATCATCATTTTGATTTGCTTAAGAAAAGCCAAGTAGTGTCTATAAA
19127299 TTTTCTTTTCAAAACTCTAAATAATTCAGC
196 TTTTCTTTTCAAAACTCTAAATAATTCAGC
19127329 AAACCAAACTCTAAACAATTCAGCAAGAAACTTGTAACCCCCTAAACTCGGCCTAGACATTATGG
1 AAACCAAACTCTAAACAATTCAGCAAGAAACTTGTAACCCCCTAAACTCGGCCTAGACATTATGG
19127394 CCAAATCTCGAAGATCACATTGGCCAGGATGATGGCACAGAAAATTATTTAACTATTTTCTCTTG
66 CCAAATCTCGAAGATCACATTGGCCAGGATGATGGCACAGAAAATTATTTAACTATTTTCTCTTG
19127459 ACAAACATCATTATTTAAAATCATCATTTTGATTTGCTTAAGAAAAGCCAAGTAGTGTCTATAAA
131 ACAAACATCATTATTTAAAATCATCATTTTGATTTGCTTAAGAAAAGCCAAGTAGTGTCTATAAA
19127524 TTTTCTTTTCAAAA
196 TTTTCTTTTCAAAA
19127538 GAAATTGTCA
Statistics
Matches: 205, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
225 205 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.31
Consensus pattern (225 bp):
AAACCAAACTCTAAACAATTCAGCAAGAAACTTGTAACCCCCTAAACTCGGCCTAGACATTATGG
CCAAATCTCGAAGATCACATTGGCCAGGATGATGGCACAGAAAATTATTTAACTATTTTCTCTTG
ACAAACATCATTATTTAAAATCATCATTTTGATTTGCTTAAGAAAAGCCAAGTAGTGTCTATAAA
TTTTCTTTTCAAAACTCTAAATAATTCAGC
Found at i:19128245 original size:21 final size:20
Alignment explanation
Indices: 19128206--19128246 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
19128196 ATCCAATAAC
*
19128206 ACACCAATAATGTAGTCAAG
1 ACACCAATAATGCAGTCAAG
*
19128226 ACACCAGATAATGCATTCAAG
1 ACACCA-ATAATGCAGTCAAG
19128247 CTTCCAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.20
Consensus pattern (20 bp):
ACACCAATAATGCAGTCAAG
Found at i:19131580 original size:21 final size:20
Alignment explanation
Indices: 19131537--19131595 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 20
19131527 AAAAACAAAC
19131537 ATATTAAAACTATATATGCTTAAT
1 ATATTAAAACTATA-A---TTAAT
*
19131561 ATGTTTAAAACTATAATTAAT
1 AT-ATTAAAACTATAATTAAT
19131582 ATATTAAAACTATA
1 ATATTAAAACTATA
19131596 TAAGACAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 11 0.34
21 7 0.22
24 3 0.09
25 11 0.34
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (20 bp):
ATATTAAAACTATAATTAAT
Found at i:19132519 original size:13 final size:13
Alignment explanation
Indices: 19132501--19132526 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19132491 TATATTATGT
19132501 TATAAATTATAGA
1 TATAAATTATAGA
19132514 TATAAATTATAGA
1 TATAAATTATAGA
19132527 AAATTAAAAA
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
TATAAATTATAGA
Found at i:19143655 original size:17 final size:17
Alignment explanation
Indices: 19143635--19143671 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19143625 TATTAAATTC
*
19143635 AATAATATATTTCCAAT
1 AATAATATAATTCCAAT
*
19143652 AATAATTTAATTCCAAT
1 AATAATATAATTCCAAT
19143669 AAT
1 AAT
19143672 CACGTTTCTT
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:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAATATAATTCCAAT
Found at i:19143949 original size:23 final size:23
Alignment explanation
Indices: 19143877--19143952 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
19143867 CGCACGAGGT
*
19143877 GCCTGAAATACGACACATAAAGC
1 GCCTGATATACGACACATAAAGC
*
19143900 GCATGATATACGACACATAAAGC
1 GCCTGATATACGACACATAAAGC
* *
19143923 GCCTGATATATGACACATAAAGT
1 GCCTGATATACGACACATAAAGC
19143946 GCCTGAT
1 GCCTGAT
19143953 CGGCAAAGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.20
Consensus pattern (23 bp):
GCCTGATATACGACACATAAAGC
Found at i:19144211 original size:21 final size:22
Alignment explanation
Indices: 19144182--19144246 Score: 89
Period size: 21 Copynumber: 3.0 Consensus size: 22
19144172 CAGAAGCAGT
*
19144182 ATACGACACATAAAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
* *
19144204 AT-CGACACACATGGTGCCT-A
1 ATACGACACATATAGTGCCTGA
19144224 ATACGACACATATAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
19144246 A
1 A
19144247 CCTAAAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 3 0.08
21 29 0.81
22 4 0.11
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:19151565 original size:151 final size:151
Alignment explanation
Indices: 19151289--19151565 Score: 410
Period size: 151 Copynumber: 1.8 Consensus size: 151
19151279 AAATTGGATC
*
19151289 CGGGCGCTGGTCATAAGTTCTACCAGTGGCTGGGTATACCGGTATATGTTGCGGATACCTGACAG
1 CGGGCGCTGGTCATAAGTTCTACCAGTGGCTGGGTATACCGGCATATGTTGCGGATACCTGACAG
** * * * * *
19151354 CTTGTGTGAGCAGCACTGAGTAGTAATGAATGACCAATAGCTTGTGTGAGCAGGCCCGTGATGCG
66 CTTGTGTGAGCAGCACTGAGTAGTAACAAAAGACCAACAACTTATGTGAGCAGACCCGTGATGCG
19151419 AAACTGTGATTAATGTGAACT
131 AAACTGTGATTAATGTGAACT
* * * * *
19151440 CGGGTGCTGGTCTTAAGTTCTACTAGTGGTTGGGTATACCGGCATATGTTGCGGATACTTGACAG
1 CGGGCGCTGGTCATAAGTTCTACCAGTGGCTGGGTATACCGGCATATGTTGCGGATACCTGACAG
** *
19151505 CTTGTGTGAGCAGCACTGAGTAGTAACAAAAGACTGACAACTTATGTGAGCAGACTCGTGA
66 CTTGTGTGAGCAGCACTGAGTAGTAACAAAAGACCAACAACTTATGTGAGCAGACCCGTGA
19151566 AAGTGAATAG
Statistics
Matches: 110, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
151 110 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (151 bp):
CGGGCGCTGGTCATAAGTTCTACCAGTGGCTGGGTATACCGGCATATGTTGCGGATACCTGACAG
CTTGTGTGAGCAGCACTGAGTAGTAACAAAAGACCAACAACTTATGTGAGCAGACCCGTGATGCG
AAACTGTGATTAATGTGAACT
Found at i:19162719 original size:50 final size:50
Alignment explanation
Indices: 19162608--19162793 Score: 209
Period size: 50 Copynumber: 3.8 Consensus size: 50
19162598 CACATATCGG
* * * * *
19162608 TGCCAATGCCATGTCCCAGACATGCTCTTACACTGGCGCTCATC--TCGA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCAGTCCA
* * *
19162656 -GCCGATGCCATGTCCCAAACATGGT-TTGACACTGGCTCTCCTTAGTCCA
1 TGCCGATGCCATGTCCCAGACATGGTCTT-ACACTGGCACTCCTCAGTCCA
* * * **
19162705 TGCCGATGCCATGTCCCAGACATGGTCTTAAACTAGCACTCCTCGGTCTG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCAGTCCA
*
19162755 TGCCGATGCCATGTCCCAGACATAGTCTTACACTGGCAC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCAC
19162794 ACTCACTGCC
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
46 2 0.02
47 34 0.30
49 3 0.03
50 74 0.64
51 2 0.02
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.25
Consensus pattern (50 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCAGTCCA
Found at i:19162806 original size:100 final size:97
Alignment explanation
Indices: 19162608--19162806 Score: 222
Period size: 97 Copynumber: 2.0 Consensus size: 97
19162598 CACATATCGG
* * *
19162608 TGCCAATGCCATGTCCCAGACATGCTCTTACACTGGCGCTCATCTCGAGCCGATGCCATGTCCCA
1 TGCCAATGCCATGTCCCAGACATGCTCTTAAACTAGCACTCATCTCGAGCCGATGCCATGTCCCA
* * * * *
19162673 AACATGGTTTGACACTGGCTCTCCTTAGTCCA
66 AACATAGTTTGACACTGGCACTACTCACTCCA
* * * *
19162705 TGCCGATGCCATGTCCCAGACATGGTCTTAAACTAGCACTCCTCGGTCTGTGCCGATGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGCTCTTAAACTAGCACTCATC--TC-GAGCCGATGCCATGTC
*
19162770 CCAGACATAGTCTT-ACACTGGCAC-ACTCACTGCCA
63 CCAAACATAGT-TTGACACTGGCACTACTCACT-CCA
19162805 TG
1 TG
19162807 GTCCAACCAT
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
97 38 0.45
99 6 0.07
100 38 0.45
101 2 0.02
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (97 bp):
TGCCAATGCCATGTCCCAGACATGCTCTTAAACTAGCACTCATCTCGAGCCGATGCCATGTCCCA
AACATAGTTTGACACTGGCACTACTCACTCCA
Found at i:19172127 original size:50 final size:50
Alignment explanation
Indices: 19172016--19172201 Score: 209
Period size: 50 Copynumber: 3.8 Consensus size: 50
19172006 CACATATCGG
* * * * *
19172016 TGCCAATGCCATGTCCCAGACATGCTCTTACACTGGCGCTCATC--TCGA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCAGTCCA
* * *
19172064 -GCCGATGCCATGTCCCAAACATGGT-TTGACACTGGCTCTCCTTAGTCCA
1 TGCCGATGCCATGTCCCAGACATGGTCTT-ACACTGGCACTCCTCAGTCCA
* * * **
19172113 TGCCGATGCCATGTCCCAGACATGGTCTTAAACTAGCACTCCTCGGTCTG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCAGTCCA
*
19172163 TGCCGATGCCATGTCCCAGACATAGTCTTACACTGGCAC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCAC
19172202 ACTCACTGCC
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
46 2 0.02
47 34 0.30
49 3 0.03
50 74 0.64
51 2 0.02
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.25
Consensus pattern (50 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCAGTCCA
Found at i:19172214 original size:100 final size:97
Alignment explanation
Indices: 19172016--19172214 Score: 222
Period size: 97 Copynumber: 2.0 Consensus size: 97
19172006 CACATATCGG
* * *
19172016 TGCCAATGCCATGTCCCAGACATGCTCTTACACTGGCGCTCATCTCGAGCCGATGCCATGTCCCA
1 TGCCAATGCCATGTCCCAGACATGCTCTTAAACTAGCACTCATCTCGAGCCGATGCCATGTCCCA
* * * * *
19172081 AACATGGTTTGACACTGGCTCTCCTTAGTCCA
66 AACATAGTTTGACACTGGCACTACTCACTCCA
* * * *
19172113 TGCCGATGCCATGTCCCAGACATGGTCTTAAACTAGCACTCCTCGGTCTGTGCCGATGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGCTCTTAAACTAGCACTCATC--TC-GAGCCGATGCCATGTC
*
19172178 CCAGACATAGTCTT-ACACTGGCAC-ACTCACTGCCA
63 CCAAACATAGT-TTGACACTGGCACTACTCACT-CCA
19172213 TG
1 TG
19172215 GTCCAACCAT
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
97 38 0.45
99 6 0.07
100 38 0.45
101 2 0.02
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (97 bp):
TGCCAATGCCATGTCCCAGACATGCTCTTAAACTAGCACTCATCTCGAGCCGATGCCATGTCCCA
AACATAGTTTGACACTGGCACTACTCACTCCA
Found at i:19177308 original size:89 final size:89
Alignment explanation
Indices: 19177157--19177377 Score: 343
Period size: 89 Copynumber: 2.5 Consensus size: 89
19177147 TGGTGTTTTC
* * *
19177157 GATCTGCTATCTTCAGTCTGCTCCGCTGCAAACTCAAGGAGGCAAGGCTGGTGTCTTCGATCTAT
1 GATCTGCTATCTTCAGTCTGCTCCGCTGCAAACTCAAGGAGGCAAGGATAGTGTCTTCGATCTAC
*
19177222 TTCGCTGCCAATACAGGAAGACAA
66 TTCGCTGCCAATACAGAAAGACAA
* * * *
19177246 GATCTGCTATATTCATTCTGCTCTGCTGCAAACTCAAGGAGGCAAGGATAGTGTCTTCGATCTGC
1 GATCTGCTATCTTCAGTCTGCTCCGCTGCAAACTCAAGGAGGCAAGGATAGTGTCTTCGATCTAC
19177311 TTCGCTGCCAATACAGAAAGACAA
66 TTCGCTGCCAATACAGAAAGACAA
* * *
19177335 GATCTGCTATCGTCAGTCTGCTCCGCTGCATACTCAGGGAGGC
1 GATCTGCTATCTTCAGTCTGCTCCGCTGCAAACTCAAGGAGGC
19177378 TAGGCTGGAT
Statistics
Matches: 118, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 118 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (89 bp):
GATCTGCTATCTTCAGTCTGCTCCGCTGCAAACTCAAGGAGGCAAGGATAGTGTCTTCGATCTAC
TTCGCTGCCAATACAGAAAGACAA
Found at i:19177318 original size:44 final size:44
Alignment explanation
Indices: 19177173--19177318 Score: 113
Period size: 44 Copynumber: 3.3 Consensus size: 44
19177163 CTATCTTCAG
* * *
19177173 TCTGCTCCGCTGCAAACTCAAGGAGGCAAGGCTGGTGTCTTCGA
1 TCTGCTTCGCTGCAAACTCAAGGAGGCAAGGATAGTGTCTTCGA
** * * * * *
19177217 TCTATTTCGCTGCCAA-T-ACAGGAAGACAA-GATCTGCTATATTC-A
1 TCTGCTTCGCTGCAAACTCA-AGG-AGGCAAGGAT-AG-TGTCTTCGA
19177261 TTCTGC-TCTGCTGCAAACTCAAGGAGGCAAGGATAGTGTCTTCGA
1 -TCTGCTTC-GCTGCAAACTCAAGGAGGCAAGGATAGTGTCTTCGA
19177306 TCTGCTTCGCTGC
1 TCTGCTTCGCTGC
19177319 CAATACAGAA
Statistics
Matches: 75, Mismatches: 16, Indels: 22
0.66 0.14 0.19
Matches are distributed among these distances:
42 1 0.01
43 6 0.08
44 36 0.48
45 24 0.32
46 7 0.09
47 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.27
Consensus pattern (44 bp):
TCTGCTTCGCTGCAAACTCAAGGAGGCAAGGATAGTGTCTTCGA
Found at i:19177462 original size:44 final size:42
Alignment explanation
Indices: 19177393--19177644 Score: 202
Period size: 44 Copynumber: 5.8 Consensus size: 42
19177383 TGGATGCGAT
* ** *
19177393 TGCTCTACTACAACTTCAGAAAGATAATATCTGTGATTTTAATC
1 TGCTCCACTACAACTTCAGGGAGATAAGAT-TG-GATTTTAATC
* * * *
19177437 CGCTCCACTACAACTTCAGGGAGATAGGGTTGGTTTCTTTAATC
1 TGCTCCACTACAACTTCAGGGAGATAAGATTGG-AT-TTTAATC
** * *
19177481 TGCTCCACTGTAACTTCAGGGAGATAAGATTGGTTTATTCAGTC
1 TGCTCCACTACAACTTCAGGGAGATAAGATTGGATT-TT-AATC
** ** *
19177525 TGCTCCACTGTAACTTCAAAGAGATAAGATCTATGATTTTAATC
1 TGCTCCACTACAACTTCAGGGAGATAAGAT-T-GGATTTTAATC
* * *
19177569 CGCTCCACTATAACTTTAGGGAGAT-AGATTGGATTCTTTAATC
1 TGCTCCACTACAACTTCAGGGAGATAAGATTGGA-T-TTTAATC
*
19177612 TGCTCCACTGCAACTTCTA-GGAGATAAGATTGG
1 TGCTCCACTACAACTTC-AGGGAGATAAGATTGG
19177645 TTTATTCAGT
Statistics
Matches: 169, Mismatches: 29, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
41 2 0.01
42 4 0.02
43 37 0.22
44 120 0.71
45 3 0.02
46 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (42 bp):
TGCTCCACTACAACTTCAGGGAGATAAGATTGGATTTTAATC
Found at i:19177638 original size:87 final size:88
Alignment explanation
Indices: 19177474--19177641 Score: 239
Period size: 87 Copynumber: 1.9 Consensus size: 88
19177464 GGTTGGTTTC
* * * * *
19177474 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGTTTATTCAGTCTGCTCCACTGTAAC
1 TTTAATCCGCTCCACTATAACTTCAGGGAGATAAGATTGGATTATTCAATCTGCTCCACTGCAAC
19177539 TTCAAAGAGATAAGATCTATGAT
66 TTCAAAGAGATAAGATCTATGAT
* * *
19177562 TTTAATCCGCTCCACTATAACTTTAGGGAGAT-AGATTGGATTCTTTAATCTGCTCCACTGCAAC
1 TTTAATCCGCTCCACTATAACTTCAGGGAGATAAGATTGGATTATTCAATCTGCTCCACTGCAAC
* *
19177626 TTCTAGGAGATAAGAT
66 TTCAAAGAGATAAGAT
19177642 TGGTTTATTC
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
87 41 0.59
88 29 0.41
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (88 bp):
TTTAATCCGCTCCACTATAACTTCAGGGAGATAAGATTGGATTATTCAATCTGCTCCACTGCAAC
TTCAAAGAGATAAGATCTATGAT
Found at i:19177671 original size:131 final size:132
Alignment explanation
Indices: 19177404--19177684 Score: 397
Period size: 131 Copynumber: 2.1 Consensus size: 132
19177394 GCTCTACTAC
* * *
19177404 AACTTCAGAA-AGATAATATCTGTGATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGGTT
1 AACTTCA-AAGAGATAAGATCTATGATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATT
* * *
19177468 GGTTTCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGTTTATTCAGTCTGCTCCAC
65 GGATTCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAGTCTACTCCAC
*
19177533 TGT
130 TGG
* *
19177536 AACTTCAAAGAGATAAGATCTATGATTTTAATCCGCTCCACTATAACTTTAGGGAGATA-GATTG
1 AACTTCAAAGAGATAAGATCTATGATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTG
***
19177600 GATTCTTTAATCTGCTCCACTGCAACTTCTA-GGAGATAAGATTGGTTTATTCAGTCTACTTTGC
66 GATTCTTTAATCTGCTCCACTGCAACTTC-AGGGAGATAAGATTGGTTTATTCAGTCTACTCCAC
19177664 TGG
130 TGG
**
19177667 AACTTCAGGGAGATAAGA
1 AACTTCAAAGAGATAAGA
19177685 CTGGATGCGA
Statistics
Matches: 133, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
131 80 0.60
132 53 0.40
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (132 bp):
AACTTCAAAGAGATAAGATCTATGATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTG
GATTCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAGTCTACTCCACT
GG
Found at i:19178225 original size:72 final size:72
Alignment explanation
Indices: 19178103--19178238 Score: 175
Period size: 72 Copynumber: 1.9 Consensus size: 72
19178093 ATTCGCTACC
* ** * * *
19178103 TTTAGCTTTAATCTGTTTCACTGTAACGCCAAGAAGATAGGATTCACTACCTTCAGCTTTAATCC
1 TTTAGCTTTAATCTATGCCACTGCAACGCCAAGAAGACAAGATTCACTACCTTCAGCTTTAATCC
19178168 GCTCCAT
66 GCTCCAT
* * *
19178175 TTTAGCTTTAATCTATGCCACTGCAACGCCAGGGAA-ACAAGATTCGCTACCTTTAGCTTTAATC
1 TTTAGCTTTAATCTATGCCACTGCAACGCCA-AGAAGACAAGATTCACTACCTTCAGCTTTAATC
19178239 TGTTCCACTG
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
72 51 0.94
73 3 0.06
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (72 bp):
TTTAGCTTTAATCTATGCCACTGCAACGCCAAGAAGACAAGATTCACTACCTTCAGCTTTAATCC
GCTCCAT
Found at i:19178251 original size:51 final size:51
Alignment explanation
Indices: 19178175--19178278 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
19178165 TCCGCTCCAT
19178175 TTTAGCTTTAATCTATGCCACTGCAACGCCAGGGAAACAAGATTCGCTACC
1 TTTAGCTTTAATCTATGCCACTGCAACGCCAGGGAAACAAGATTCGCTACC
* * * * * *
19178226 TTTAGCTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAGATTTGCTGCC
1 TTTAGCTTTAATCTATGCCACTGCAACGCCAGGGAAACAAGATTCGCTACC
19178277 TT
1 TT
19178279 CAGTCTTAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (51 bp):
TTTAGCTTTAATCTATGCCACTGCAACGCCAGGGAAACAAGATTCGCTACC
Found at i:19178650 original size:24 final size:24
Alignment explanation
Indices: 19178618--19178675 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
19178608 CAGATTGCCC
*
19178618 CCACTGTAATCTTCAAGGTTTAAT
1 CCACTGTAATCTTCAAGGTTCAAT
19178642 CCACTGTAATCTTCAAGGTTCAAT
1 CCACTGTAATCTTCAAGGTTCAAT
19178666 CCACTGTAAT
1 CCACTGTAAT
19178676 TTTGGGACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (24 bp):
CCACTGTAATCTTCAAGGTTCAAT
Found at i:19192710 original size:37 final size:37
Alignment explanation
Indices: 19192669--19192844 Score: 298
Period size: 37 Copynumber: 4.8 Consensus size: 37
19192659 TTTGAGTACT
19192669 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
19192706 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
19192743 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
19192780 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
19192817 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
19192845 TAGCTTCAGC
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:19192916 original size:45 final size:46
Alignment explanation
Indices: 19192807--19192930 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
19192797 GTGATAAGTG
* *
19192807 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
19192853 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
19192898 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
19192931 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:19199617 original size:30 final size:30
Alignment explanation
Indices: 19199572--19199653 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
19199562 TGTATTTATG
* * *
19199572 GAAATTCAAATATATGGTTATCAAATAATA
1 GAAAATCAAAGATATGGGTATCAAATAATA
* * *
19199602 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAATCAAAGATATGGGTATCAAATAATA
*
19199632 GAAAATAAAAGATATGGGTATC
1 GAAAATCAAAGATATGGGTATC
19199654 GAGATATTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (30 bp):
GAAAATCAAAGATATGGGTATCAAATAATA
Found at i:19199815 original size:2 final size:2
Alignment explanation
Indices: 19199808--19199854 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
19199798 AAGGCATTGT
19199808 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19199850 TC TC T
1 TC TC T
19199855 TTGTAAATTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:19204044 original size:248 final size:248
Alignment explanation
Indices: 19203599--19204094 Score: 974
Period size: 248 Copynumber: 2.0 Consensus size: 248
19203589 TGATTCTGAT
* *
19203599 TATGCCGGTGATTTGGACAAACGAAGATCAACCACTGGTTATGTGTTTACTCTTGCTGGAGGACC
1 TATGCCAGTGATTTGGACAAACGAAGATCAACCACTGGTTATGTGTTTACACTTGCTGGAGGACC
19203664 AATAAGTTGGAAGTCTACACTGCAGTCTACAGTTGCGTTGTCAACCACAGAAGCTGAATACATGG
66 AATAAGTTGGAAGTCTACACTGCAGTCTACAGTTGCGTTGTCAACCACAGAAGCTGAATACATGG
19203729 CTGTAACAGAGGCTGTAAAGGAAGCTATTTGGTTACAAGGTATGGTTAAAACCTTGGGATTGGTC
131 CTGTAACAGAGGCTGTAAAGGAAGCTATTTGGTTACAAGGTATGGTTAAAACCTTGGGATTGGTC
19203794 CAGGAGCATATTAATGTGTATTGTGATAGTCAAAGTGCTATTCATTTAGCAAA
196 CAGGAGCATATTAATGTGTATTGTGATAGTCAAAGTGCTATTCATTTAGCAAA
19203847 TATGCCAGTGATTTGGACAAACGAAGATCAACCACTGGTTATGTGTTTACACTTGCTGGAGGACC
1 TATGCCAGTGATTTGGACAAACGAAGATCAACCACTGGTTATGTGTTTACACTTGCTGGAGGACC
19203912 AATAAGTTGGAAGTCTACACTGCAGTCTACAGTTGCGTTGTCAACCACAGAAGCTGAATACATGG
66 AATAAGTTGGAAGTCTACACTGCAGTCTACAGTTGCGTTGTCAACCACAGAAGCTGAATACATGG
19203977 CTGTAACAGAGGCTGTAAAGGAAGCTATTTGGTTACAAGGTATGGTTAAAACCTTGGGATTGGTC
131 CTGTAACAGAGGCTGTAAAGGAAGCTATTTGGTTACAAGGTATGGTTAAAACCTTGGGATTGGTC
19204042 CAGGAGCATATTAATGTGTATTGTGATAGTCAAAGTGCTATTCATTTAGCAAA
196 CAGGAGCATATTAATGTGTATTGTGATAGTCAAAGTGCTATTCATTTAGCAAA
19204095 GAATCAAGTC
Statistics
Matches: 246, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
248 246 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (248 bp):
TATGCCAGTGATTTGGACAAACGAAGATCAACCACTGGTTATGTGTTTACACTTGCTGGAGGACC
AATAAGTTGGAAGTCTACACTGCAGTCTACAGTTGCGTTGTCAACCACAGAAGCTGAATACATGG
CTGTAACAGAGGCTGTAAAGGAAGCTATTTGGTTACAAGGTATGGTTAAAACCTTGGGATTGGTC
CAGGAGCATATTAATGTGTATTGTGATAGTCAAAGTGCTATTCATTTAGCAAA
Found at i:19207100 original size:15 final size:17
Alignment explanation
Indices: 19207068--19207101 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
19207058 AGGTTCGGTT
19207068 TAGGATAGAAACAAAGG
1 TAGGATAGAAACAAAGG
19207085 TAGGATA-AAA-AAAGG
1 TAGGATAGAAACAAAGG
19207100 TA
1 TA
19207102 ATTGATGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.56, C:0.03, G:0.26, T:0.15
Consensus pattern (17 bp):
TAGGATAGAAACAAAGG
Found at i:19210180 original size:12 final size:12
Alignment explanation
Indices: 19210151--19210223 Score: 53
Period size: 12 Copynumber: 6.1 Consensus size: 12
19210141 TCTTCACTCG
*
19210151 TTTCTTTTACAA
1 TTTCTTTTTCAA
**
19210163 ACTCTTTTTCAA
1 TTTCTTTTTCAA
*
19210175 TTTCTTTTTCCACTC
1 TTTCTTTTT-CA--A
19210190 TTTCTTTTTC--
1 TTTCTTTTTCAA
*
19210200 -TTCTCTTTCAA
1 TTTCTTTTTCAA
19210211 TTTCTTTTTCAA
1 TTTCTTTTTCAA
19210223 T
1 T
19210224 CTCAATTTCT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 8 0.17
12 27 0.57
13 2 0.04
14 1 0.02
15 9 0.19
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:19211705 original size:15 final size:17
Alignment explanation
Indices: 19211673--19211706 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
19211663 AGGTTCAATT
19211673 TAGGATAGAAACAAAGG
1 TAGGATAGAAACAAAGG
19211690 TAGGATA-AAA-AAAGG
1 TAGGATAGAAACAAAGG
19211705 TA
1 TA
19211707 ATTGATGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.56, C:0.03, G:0.26, T:0.15
Consensus pattern (17 bp):
TAGGATAGAAACAAAGG
Found at i:19213587 original size:18 final size:18
Alignment explanation
Indices: 19213561--19213612 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
19213551 GATTGTCAAG
*
19213561 TAAAGAAATCATGTGAAA
1 TAAATAAATCATGTGAAA
19213579 TAAATAAATCATGTGAAA
1 TAAATAAATCATGTGAAA
19213597 TAAATAAATCATGTGA
1 TAAATAAATCATGTGA
19213613 CAAGATGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.54, C:0.06, G:0.13, T:0.27
Consensus pattern (18 bp):
TAAATAAATCATGTGAAA
Found at i:19215773 original size:20 final size:19
Alignment explanation
Indices: 19215750--19215801 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
19215740 ATATTATATG
*
19215750 TTTATATTTTATTTTTAATA
1 TTTATATTTTATGTTTAA-A
*
19215770 TTTATATTTAATGTTTAAA
1 TTTATATTTTATGTTTAAA
*
19215789 ATTATATTATTAT
1 TTTATATT-TTAT
19215802 ATATTATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTATATTTTATGTTTAAA
Found at i:19215935 original size:2 final size:2
Alignment explanation
Indices: 19215928--19215956 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19215918 TAGTTATGTT
19215928 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 T
19215957 TCTTAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19217243 original size:14 final size:14
Alignment explanation
Indices: 19217215--19217261 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
19217205 TGTCATGTAA
19217215 TTATTTTAGTT-ATG
1 TTATTTTA-TTCATG
19217229 TTATTTTATTCATG
1 TTATTTTATTCATG
* * *
19217243 TCATTATAATCATG
1 TTATTTTATTCATG
19217257 TTATT
1 TTATT
19217262 AATTGTGCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 2 0.07
14 26 0.93
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.60
Consensus pattern (14 bp):
TTATTTTATTCATG
Found at i:19227315 original size:21 final size:22
Alignment explanation
Indices: 19227281--19227321 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
19227271 TTAAAACTTT
19227281 TTATTTAATATT-AAATATTAC
1 TTATTTAATATTAAAATATTAC
* *
19227302 TTATTTATTTTTAAAATATT
1 TTATTTAATATTAAAATATT
19227322 TAAATATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATTTAATATTAAAATATTAC
Found at i:19239525 original size:323 final size:322
Alignment explanation
Indices: 19238917--19239572 Score: 909
Period size: 323 Copynumber: 2.0 Consensus size: 322
19238907 TTGGAATGAT
* * * * *
19238917 GTTTGGGTTTGGTAGATTGGTTCTCTTCGAGGGTTTTATATAGGTCGCAATCAACCGGATGATAT
1 GTTTGGGTTTGGTAGATTGGTCCTCTTCAAGGGTTTTATACAGGTCGCAATCAACCAGATGATAC
* * * * *
19238982 TTTAAGAGTATGTGATTTGGTAAACGGAAATGGTTGTTGGGATTGGTCTCGTCTATTCTCGCTAT
66 TTTAAAAGTATGTGATTTGGTAAACGAAAATGGTTGTTGGGACTGGCCTCATCTATTCTCGCTAT
* * *
19239047 TATCGGTTAATATTGTTACACAAATAGCATCTATTGTGCCCATTTCCTGTTATATAGGTCAGGAC
131 TATCGATTAATATTGTTACACAAATAGCATCTATTGTG-CCATTTCCTGTGATATAAGTCAGGAC
* * *
19239112 TGGTTAGCTTGGAGATGGATGAAGAAAGACGATTTTTCCATAGCGAAAAGGTTTAAAAATATGTA
195 TGGTTAGCTTGAAAATGGATGAAGAAAGACGATTTTTCCACAGCGAAAAGGTTTAAAAATATGTA
** * * *
19239177 TCAGGGGGAATTGCGCCTACTAATATTTGGAGGCTGATTTGGAAGGTGAAAACACCTCAAAGA
260 TCACCGGGAATAGCGCATACTAATATTTGAAGGCTGATTTGGAAGGTGAAAACACCTCAAAGA
** * * *
19239240 GTTTGGGTTTGGTAGATTGGTCCTCTTCAAGGGTTTTATACAGGTCGCGGTCAGCTAGATGATGC
1 GTTTGGGTTTGGTAGATTGGTCCTCTTCAAGGGTTTTATACAGGTCGCAATCAACCAGATGATAC
*
19239305 TTTAAAAGTATGTGATTTGGTAGACGAAAATGGTTGTTGGGACTGGCCTCATCTATTCTCGCTAT
66 TTTAAAAGTATGTGATTTGGTAAACGAAAATGGTTGTTGGGACTGGCCTCATCTATTCTCGCTAT
* * * * *
19239370 TATCGATTAATATTGTTATATAAATAGCATCTATTGTG-CATTTTTCTAGTGATGTAAGTTAGGA
131 TATCGATTAATATTGTTACACAAATAGCATCTATTGTGCCA-TTTCCT-GTGATATAAGTCAGGA
* * * *
19239434 TTGGTTAGCTTGAAAATGGATGAAGAAAGATGTTTTTTCCACAGCGAAAAGGTTTAGAAATATGT
194 CTGGTTAGCTTGAAAATGGATGAAGAAAGACGATTTTTCCACAGCGAAAAGGTTTAAAAATATGT
* * * **
19239499 ATCACCGGGAATAGGGCATGCTAATATTTGAAGGTTGATTTGGAAGGTGAAAATGCCTCAAAGA
259 ATCACCGGGAATAGCGCATACTAATATTTGAAGGCTGATTTGGAAGGTGAAAACACCTCAAAGA
19239563 GTTTGGGTTT
1 GTTTGGGTTT
19239573 TGATCTAGTT
Statistics
Matches: 290, Mismatches: 41, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
321 2 0.01
322 5 0.02
323 283 0.98
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.35
Consensus pattern (322 bp):
GTTTGGGTTTGGTAGATTGGTCCTCTTCAAGGGTTTTATACAGGTCGCAATCAACCAGATGATAC
TTTAAAAGTATGTGATTTGGTAAACGAAAATGGTTGTTGGGACTGGCCTCATCTATTCTCGCTAT
TATCGATTAATATTGTTACACAAATAGCATCTATTGTGCCATTTCCTGTGATATAAGTCAGGACT
GGTTAGCTTGAAAATGGATGAAGAAAGACGATTTTTCCACAGCGAAAAGGTTTAAAAATATGTAT
CACCGGGAATAGCGCATACTAATATTTGAAGGCTGATTTGGAAGGTGAAAACACCTCAAAGA
Found at i:19240496 original size:29 final size:28
Alignment explanation
Indices: 19240464--19240529 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
19240454 ACCAAAAAAA
19240464 GCCGTTTTTTTCAAAATTTACCGAAATGG
1 GCCGTTTTTTT-AAAATTTACCGAAATGG
* ** *
19240493 GCCGATTTTTTATCATTTACCGGAATGG
1 GCCGTTTTTTTAAAATTTACCGAAATGG
*
19240521 GCCATTTTT
1 GCCGTTTTT
19240530 CGCGAAATTG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
28 21 0.68
29 10 0.32
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (28 bp):
GCCGTTTTTTTAAAATTTACCGAAATGG
Found at i:19241634 original size:39 final size:39
Alignment explanation
Indices: 19241580--19241654 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
19241570 ATAAAAAAGC
*
19241580 CTTATATCATGATTTAGTTCATATATTATATTTGTTAAA
1 CTTATATAATGATTTAGTTCATATATTATATTTGTTAAA
19241619 CTTATATAATGATTTAGTTCATATATTATATTTGTT
1 CTTATATAATGATTTAGTTCATATATTATATTTGTT
19241655 TTCCCAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.53
Consensus pattern (39 bp):
CTTATATAATGATTTAGTTCATATATTATATTTGTTAAA
Found at i:19246714 original size:14 final size:13
Alignment explanation
Indices: 19246694--19246734 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
19246684 ATAAATTTAA
19246694 ATTTAAAAAAATT
1 ATTTAAAAAAATT
19246707 ATTTTAAAAAAATT
1 A-TTTAAAAAAATT
*
19246721 AATTAAAAATAATT
1 ATTTAAAAA-AATT
19246735 TATAATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATTTAAAAAAATT
Found at i:19247267 original size:39 final size:39
Alignment explanation
Indices: 19247132--19247268 Score: 159
Period size: 40 Copynumber: 3.4 Consensus size: 39
19247122 TGTTTGGACA
**
19247132 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTACG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCG-TTTTTG
* * * *
19247172 TAAAACGCCACTAAAGATCGAGCATTAGCGGCGCTTTTTC
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCG-TTTTTG
*
19247212 AAAATCGCCGCTAAAAAT-GAGCATTAGCGGCGTTTCTTGG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTT-TT-G
*
19247252 AAAAACGCCGCAAAAAA
1 AAAAACGCCGCTAAAAA
19247269 CCCTAAGCCC
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
38 3 0.04
39 16 0.20
40 63 0.77
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTG
Found at i:19247375 original size:41 final size:41
Alignment explanation
Indices: 19247306--19247516 Score: 249
Period size: 41 Copynumber: 5.3 Consensus size: 41
19247296 CCTTTCGGGG
**
19247306 CTTTAGCGGCGTTTTTTAAAAAAGCGCCGCTAATGCTCAGAT
1 CTTTAGCGGCG-TTTTTGGAAAAGCGCCGCTAATGCTCAGAT
* *
19247348 CTTTAGCGGCATTTTT-GAAAATGCGCCGCTAATGCAC-GAT
1 CTTTAGCGGCGTTTTTGGAAAA-GCGCCGCTAATGCTCAGAT
* * *
19247388 CTTTAGTGGCGTTTTTGGGAAAGCGCCGCTAATGCTTAGAT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAT
*
19247429 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAAAT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAT
* *
19247470 CTTTAGC-G-G----TGGAAAAGCGCTGCTAATGCTCAGTT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAT
*
19247505 CTTTAGTGGCGT
1 CTTTAGCGGCGT
19247517 CGTTAAAAAA
Statistics
Matches: 147, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
35 29 0.20
36 1 0.01
37 1 0.01
39 1 0.01
40 35 0.24
41 70 0.48
42 10 0.07
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAT
Found at i:19247495 original size:35 final size:35
Alignment explanation
Indices: 19247407--19247510 Score: 109
Period size: 35 Copynumber: 2.8 Consensus size: 35
19247397 CGTTTTTGGG
* *
19247407 AAAGCGCCGCTAATGCTTAGATCTTTAGCGGCGTTTTTGGA
1 AAAGCGCCGCTAATGCTCAAATCTTTAGC-G-G----TGGA
19247448 AAAGCGCCGCTAATGCTCAAATCTTTAGCGGTGGA
1 AAAGCGCCGCTAATGCTCAAATCTTTAGCGGTGGA
* **
19247483 AAAGCGCTGCTAATGCTCAGTTCTTTAG
1 AAAGCGCCGCTAATGCTCAAATCTTTAG
19247511 TGGCGTCGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
35 29 0.50
39 1 0.02
40 1 0.02
41 27 0.47
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (35 bp):
AAAGCGCCGCTAATGCTCAAATCTTTAGCGGTGGA
Found at i:19247888 original size:20 final size:21
Alignment explanation
Indices: 19247851--19247894 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
19247841 TATCATTATA
*
19247851 GTTTAGGGTTTAATATATATG
1 GTTTAGGGTATAATATATATG
19247872 GTTTAGGGTAT-ATATATATG
1 GTTTAGGGTATAATATATATG
19247892 GTT
1 GTT
19247895 AATTTAGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (21 bp):
GTTTAGGGTATAATATATATG
Found at i:19247971 original size:14 final size:14
Alignment explanation
Indices: 19247943--19248013 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
19247933 AAGGTTTATA
19247943 GATTATGGAATTAGG
1 GATTATGG-ATTAGG
19247958 GATTATGGATTAGG
1 GATTATGGATTAGG
*
19247972 GATTCT-GATTTAAGG
1 GATTATGGA-TT-AGG
* *
19247987 G-TTGT-GATTAAG
1 GATTATGGATTAGG
*
19247999 GTTTATGGATTAGG
1 GATTATGGATTAGG
19248013 G
1 G
19248014 GTTAGGGGTC
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
12 3 0.06
13 7 0.15
14 25 0.53
15 12 0.26
ACGTcount: A:0.27, C:0.01, G:0.34, T:0.38
Consensus pattern (14 bp):
GATTATGGATTAGG
Found at i:19248145 original size:7 final size:7
Alignment explanation
Indices: 19248133--19248189 Score: 50
Period size: 7 Copynumber: 8.7 Consensus size: 7
19248123 TAAATAATGT
19248133 TTAGGGG
1 TTAGGGG
19248140 TTAGGGG
1 TTAGGGG
*
19248147 TTAGGGA
1 TTAGGGG
*
19248154 TTTGGGG
1 TTAGGGG
*
19248161 -T-CGGG
1 TTAGGGG
19248166 TTA-GGG
1 TTAGGGG
19248172 TTA-GGG
1 TTAGGGG
*
19248178 TTAGGGT
1 TTAGGGG
19248185 TTAGG
1 TTAGG
19248190 ATTTAGATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
5 3 0.07
6 14 0.33
7 25 0.60
ACGTcount: A:0.14, C:0.02, G:0.51, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:19248174 original size:6 final size:6
Alignment explanation
Indices: 19248137--19248185 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
19248127 TAATGTTTAG
* * *
19248137 GGGTTA GGGGTTA GGGATTT GGGGTC GGGTTA GGGTTA GGGTTA GGGTT
1 GGGTTA -GGGTTA GGG-TTA GGGTTA GGGTTA GGGTTA GGGTTA GGGTT
19248186 TAGGATTTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
6 25 0.69
7 11 0.31
ACGTcount: A:0.12, C:0.02, G:0.53, T:0.33
Consensus pattern (6 bp):
GGGTTA
Found at i:19248195 original size:101 final size:101
Alignment explanation
Indices: 19248075--19248262 Score: 322
Period size: 101 Copynumber: 1.9 Consensus size: 101
19248065 TCTAGTGTCA
* *
19248075 GGTTAGGGTTTAGGGTTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAATGTTTAGGGG
1 GGTTAGGGTTTAGGATTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAAGGTTTAGGGG
19248140 TTAGGGGTTAGGGATTTGGGGTCGGGTTAGGGTTAG
66 TTAGGGGTTAGGGATTTGGGGTCGGGTTAGGGTTAG
*
19248176 GGTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAGGTTTAGGGG
1 GGTTAGGGTTTAGGATTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAAGGTTTAGGGG
* * *
19248241 TTAGTGGTTTGGGGTTTGGGGT
66 TTAGGGGTTAGGGATTTGGGGT
19248263 TAAGAGCTAG
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 81 1.00
ACGTcount: A:0.23, C:0.01, G:0.32, T:0.44
Consensus pattern (101 bp):
GGTTAGGGTTTAGGATTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAAGGTTTAGGGG
TTAGGGGTTAGGGATTTGGGGTCGGGTTAGGGTTAG
Found at i:19249841 original size:30 final size:30
Alignment explanation
Indices: 19249807--19249870 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
19249797 CTGTTCTTGC
19249807 TTTTGGTAGTCTAATTATTGGTTTTCCTCT
1 TTTTGGTAGTCTAATTATTGGTTTTCCTCT
19249837 TTTTGGTAGTCTAATTATTGGTTTTCCTCT
1 TTTTGGTAGTCTAATTATTGGTTTTCCTCT
19249867 TTTT
1 TTTT
19249871 CTTTTATTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.59
Consensus pattern (30 bp):
TTTTGGTAGTCTAATTATTGGTTTTCCTCT
Found at i:19252513 original size:5 final size:5
Alignment explanation
Indices: 19252503--19252529 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
19252493 GATTCTTGGT
19252503 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
19252530 GGCAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:19254203 original size:43 final size:43
Alignment explanation
Indices: 19254150--19254264 Score: 140
Period size: 43 Copynumber: 2.7 Consensus size: 43
19254140 AATCTTATAG
* * * *
19254150 CGGCATTTGTAATAGAAGCGCCACTAAAGGTCCTAGTTTTTAA
1 CGGCGTTTGTAACAGAAGCGCCGCTAAAGGTCCTAGTCTTTAA
* * * *
19254193 CGGCGTTTGTAACAAAAGCGCCGCTAAAGGTCTTGGTCTTTAG
1 CGGCGTTTGTAACAGAAGCGCCGCTAAAGGTCCTAGTCTTTAA
* *
19254236 CGGCGTTTGTGAGAGAAGCGCCGCTAAAG
1 CGGCGTTTGTAACAGAAGCGCCGCTAAAG
19254265 ACTAAAGGTC
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (43 bp):
CGGCGTTTGTAACAGAAGCGCCGCTAAAGGTCCTAGTCTTTAA
Found at i:19254302 original size:50 final size:50
Alignment explanation
Indices: 19254216--19254400 Score: 148
Period size: 43 Copynumber: 4.0 Consensus size: 50
19254206 AAAAGCGCCG
*
19254216 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGA
1 CTAAAGGTCTTGGTCTTTAGCGACGTTTGTGAGAGAAGCGCCGCTAAAGA
* *
19254266 CTAAAGGTCTTGGTCTTTAGCGACGATTT-TGGGAGAAGTG--GC----G-
1 CTAAAGGTCTTGGTCTTTAGCGACG-TTTGTGAGAGAAGCGCCGCTAAAGA
* * * * *
19254309 CTAAAGGTTTTGATCTTTAGCGGCGTTTGTGGGAGAA--G-CG-T--CG-
1 CTAAAGGTCTTGGTCTTTAGCGACGTTTGTGAGAGAAGCGCCGCTAAAGA
* * * *
19254352 CTAAAGGTCTTGGTCTTTAGCGGCATTTGTGGGAGAAGCGCCGTTAAAG
1 CTAAAGGTCTTGGTCTTTAGCGACGTTTGTGAGAGAAGCGCCGCTAAAG
19254401 GTCTTGGTCT
Statistics
Matches: 114, Mismatches: 10, Indels: 23
0.78 0.07 0.16
Matches are distributed among these distances:
41 1 0.01
42 4 0.04
43 65 0.57
44 1 0.01
45 1 0.01
46 2 0.02
47 1 0.01
48 2 0.02
49 1 0.01
50 33 0.29
51 3 0.03
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.29
Consensus pattern (50 bp):
CTAAAGGTCTTGGTCTTTAGCGACGTTTGTGAGAGAAGCGCCGCTAAAGA
Found at i:19254314 original size:43 final size:44
Alignment explanation
Indices: 19254266--19254416 Score: 218
Period size: 43 Copynumber: 3.5 Consensus size: 44
19254256 CCGCTAAAGA
* * *
19254266 CTAAAGGTCTTGGTCTTTAGCGACGATTT-TGGGAGAAGTGGCG
1 CTAAAGGTCTTGGTCTTTAGCGGCGATTTGTGGGAGAAGCGCCG
* * *
19254309 CTAAAGGTTTTGATCTTTAGCGGCG-TTTGTGGGAGAAGCGTCG
1 CTAAAGGTCTTGGTCTTTAGCGGCGATTTGTGGGAGAAGCGCCG
19254352 CTAAAGGTCTTGGTCTTTAGCGGC-ATTTGTGGGAGAAGCGCCG
1 CTAAAGGTCTTGGTCTTTAGCGGCGATTTGTGGGAGAAGCGCCG
*
19254395 TTAAAGGTCTTGGTCTTTAGCG
1 CTAAAGGTCTTGGTCTTTAGCG
19254417 CCGTTTTTTC
Statistics
Matches: 97, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
42 3 0.03
43 94 0.97
ACGTcount: A:0.19, C:0.15, G:0.34, T:0.32
Consensus pattern (44 bp):
CTAAAGGTCTTGGTCTTTAGCGGCGATTTGTGGGAGAAGCGCCG
Found at i:19254681 original size:3 final size:3
Alignment explanation
Indices: 19254673--19254710 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
19254663 CAAAATGAAA
19254673 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
19254711 TCATGCATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19255565 original size:24 final size:24
Alignment explanation
Indices: 19255490--19255565 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
19255480 TTATGTCCTT
* *
19255490 ATTCCGGCCTCTCACGAAATAGCC
1 ATTCCAGCCTCTCACGGAATAGCC
* * **
19255514 ATTCAAGACTACCATCAAAGAATAGCC
1 ATTCCAGCCT--C-TCACGGAATAGCC
19255541 ATTCCAGCCTCTCACGGAATAGCC
1 ATTCCAGCCTCTCACGGAATAGCC
19255565 A
1 A
19255566 CCAGAGTTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
24 19 0.49
25 1 0.03
26 1 0.03
27 18 0.46
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.20
Consensus pattern (24 bp):
ATTCCAGCCTCTCACGGAATAGCC
Found at i:19259545 original size:14 final size:14
Alignment explanation
Indices: 19259528--19259559 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
19259518 GTGGACGACC
19259528 GGAGGTGGATCGGT
1 GGAGGTGGATCGGT
*
19259542 GGAGGTGGATTGGT
1 GGAGGTGGATCGGT
19259556 GGAG
1 GGAG
19259560 ATGAAGGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.03, G:0.59, T:0.22
Consensus pattern (14 bp):
GGAGGTGGATCGGT
Found at i:19271729 original size:24 final size:24
Alignment explanation
Indices: 19271702--19271752 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
19271692 AGATTTAGTA
*
19271702 TTTATTAGCATTAAATATTTGATG
1 TTTATTAGCATAAAATATTTGATG
* * *
19271726 TTTATTAGTATAAAATCTTTGTTG
1 TTTATTAGCATAAAATATTTGATG
19271750 TTT
1 TTT
19271753 CTTTCCATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTATTAGCATAAAATATTTGATG
Found at i:19282142 original size:56 final size:56
Alignment explanation
Indices: 19282056--19282188 Score: 221
Period size: 56 Copynumber: 2.4 Consensus size: 56
19282046 AAAAATGACT
* *
19282056 GTTACAATATAGTAGTTGGAACTTGATCATTATATTATGATCGTTGGAATCTCTTC
1 GTTACAATATAGTAGTTGGAACTTGATCATTATAATATGACCGTTGGAATCTCTTC
* *
19282112 GTTACAATATAGTAGTTGGAACTTGATCATTATAATGTGACCGTTGGAATCTTTTC
1 GTTACAATATAGTAGTTGGAACTTGATCATTATAATATGACCGTTGGAATCTCTTC
*
19282168 GTTACAATATAGTTGTTGGAA
1 GTTACAATATAGTAGTTGGAA
19282189 TCTAATTATT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 72 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (56 bp):
GTTACAATATAGTAGTTGGAACTTGATCATTATAATATGACCGTTGGAATCTCTTC
Found at i:19282185 original size:28 final size:28
Alignment explanation
Indices: 19282056--19282191 Score: 93
Period size: 28 Copynumber: 4.9 Consensus size: 28
19282046 AAAAATGACT
*
19282056 GTTACAATATAGTAGTTGGAA-CTTGATC
1 GTTACAATATAGTAGTTGGAATCTT-TTC
* * * * *
19282084 ATTATATTAT-GATCGTTGGAATCTCTTC
1 GTTACAATATAG-TAGTTGGAATCTTTTC
*
19282112 GTTACAATATAGTAGTTGGAA-CTTGATC
1 GTTACAATATAGTAGTTGGAATCTT-TTC
* * *
19282140 ATTATAATGT-G-ACCGTTGGAATCTTTTC
1 GTTACAATATAGTA--GTTGGAATCTTTTC
*
19282168 GTTACAATATAGTTGTTGGAATCT
1 GTTACAATATAGTAGTTGGAATCT
19282192 AATTATTACA
Statistics
Matches: 79, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
26 1 0.01
27 4 0.05
28 67 0.85
29 7 0.09
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (28 bp):
GTTACAATATAGTAGTTGGAATCTTTTC
Found at i:19285944 original size:22 final size:22
Alignment explanation
Indices: 19285881--19285934 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
19285871 AAATTTGTCA
* *
19285881 AAAATAAATTA-AAAATT-ATG
1 AAAATTAATTATAAAATTAATT
*
19285901 AAAATTTATTATAAAATTAATT
1 AAAATTAATTATAAAATTAATT
19285923 AAAATTAATTAT
1 AAAATTAATTAT
19285935 GATAATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 9 0.32
21 6 0.21
22 13 0.46
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AAAATTAATTATAAAATTAATT
Found at i:19288870 original size:25 final size:26
Alignment explanation
Indices: 19288842--19288896 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
19288832 CAATTTGTAT
* *
19288842 AAAATATTAA-TAATTTAATAAATTG
1 AAAATATTAATTAACTAAATAAATTG
*
19288867 AAAA-ATTAATTAACTAAATAAATTT
1 AAAATATTAATTAACTAAATAAATTG
19288892 AAAAT
1 AAAAT
19288897 TTAGGAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (26 bp):
AAAATATTAATTAACTAAATAAATTG
Found at i:19289636 original size:22 final size:22
Alignment explanation
Indices: 19289611--19289652 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19289601 TGCAAAGTTG
19289611 ATAAT-AAT-TAA-TATATATT
1 ATAATAAATATAATTATATATT
19289630 ATAATAAATATAATTATATATT
1 ATAATAAATATAATTATATATT
19289652 A
1 A
19289653 GTTATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 3 0.15
21 3 0.15
22 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAATAAATATAATTATATATT
Found at i:19289639 original size:16 final size:15
Alignment explanation
Indices: 19289614--19289647 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
19289604 AAAGTTGATA
*
19289614 ATAATTAATATATATT
1 ATAATAAATATA-ATT
19289630 ATAATAAATATAATT
1 ATAATAAATATAATT
19289645 ATA
1 ATA
19289648 TATTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:19292283 original size:15 final size:15
Alignment explanation
Indices: 19292263--19292299 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
19292253 GCTTTGATGT
19292263 TATATATAAAACATA
1 TATATATAAAACATA
*
19292278 TATATATAAAGCATA
1 TATATATAAAACATA
*
19292293 AATATAT
1 TATATAT
19292300 GAATATTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (15 bp):
TATATATAAAACATA
Found at i:19294085 original size:43 final size:42
Alignment explanation
Indices: 19294028--19294136 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
19294018 AATGCCAACA
* * *
19294028 TCCCAGAC-GTGGTCTTACATGTAATCAAATAACGATGCCACTG
1 TCCCAGACAG-GGTCTTACACGTAATCAAAT-ACGACGCCAATG
* *
19294071 TCCCAGACAGGGTCTTACACGTGATCATATACGACGCCAATG
1 TCCCAGACAGGGTCTTACACGTAATCAAATACGACGCCAATG
* **
19294113 TCCCAAACATTGTCTTACACGTAA
1 TCCCAGACAGGGTCTTACACGTAA
19294137 ATCTCAAATC
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
42 30 0.54
43 25 0.45
44 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (42 bp):
TCCCAGACAGGGTCTTACACGTAATCAAATACGACGCCAATG
Found at i:19300627 original size:27 final size:28
Alignment explanation
Indices: 19300585--19300641 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
19300575 TTAATTAAAA
19300585 TTAAATATTTTAATAATGTA-ATTATATT
1 TTAAATATTTTAATAAT-TATATTATATT
*
19300613 TTAATTATTTT-ATAATTATATTATATT
1 TTAAATATTTTAATAATTATATTATATT
19300640 TT
1 TT
19300642 TCGACAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 2 0.07
27 15 0.56
28 10 0.37
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (28 bp):
TTAAATATTTTAATAATTATATTATATT
Found at i:19300636 original size:11 final size:11
Alignment explanation
Indices: 19300603--19300637 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
19300593 TTTAATAATG
*
19300603 TAATTATATTT
1 TAATTATATTA
*
19300614 TAATTATTTTA
1 TAATTATATTA
19300625 TAATTATATTA
1 TAATTATATTA
19300636 TA
1 TA
19300638 TTTTTCGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TAATTATATTA
Found at i:19302073 original size:18 final size:18
Alignment explanation
Indices: 19302050--19302090 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
19302040 ACAAAACGTA
19302050 AATAAAGAACACCTACAG
1 AATAAAGAACACCTACAG
19302068 AATAAAGAACACCTACAG
1 AATAAAGAACACCTACAG
19302086 AATAA
1 AATAA
19302091 CACAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.59, C:0.20, G:0.10, T:0.12
Consensus pattern (18 bp):
AATAAAGAACACCTACAG
Found at i:19312040 original size:67 final size:67
Alignment explanation
Indices: 19311932--19312063 Score: 228
Period size: 67 Copynumber: 2.0 Consensus size: 67
19311922 GTTTATATTA
**
19311932 CAGGGGATTTAGCCTGGACTGGTAATCCTTCTGTAAGAAATGAGGTTCACAGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCACAGGAGTGTGCTCTCT
19311997 TG
66 TG
* *
19311999 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCACAGGAGTGTGCTCTCT
19312064 GAATTGGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (67 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCACAGGAGTGTGCTCTCT
TG
Found at i:19313135 original size:22 final size:23
Alignment explanation
Indices: 19313091--19313135 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
19313081 GTTCGTAATG
* *
19313091 CAAAAATCTGTCTATTAGTAATA
1 CAAAAATCTGACTATTAGCAATA
*
19313114 CAAAAATCTGACTGTTA-CAATA
1 CAAAAATCTGACTATTAGCAATA
19313136 TGATCGTTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (23 bp):
CAAAAATCTGACTATTAGCAATA
Found at i:19313180 original size:27 final size:28
Alignment explanation
Indices: 19313118--19313199 Score: 139
Period size: 27 Copynumber: 3.0 Consensus size: 28
19313108 GTAATACAAA
* *
19313118 AATCTGACTGTTACAATATGATCGTTGG
1 AATCTGACCGTTACAATATAATCGTTGG
19313146 AATCTGACCGTTACAATATAATC-TTGG
1 AATCTGACCGTTACAATATAATCGTTGG
19313173 AATCTGACCGTTACAATATAATCGTTG
1 AATCTGACCGTTACAATATAATCGTTG
19313200 CAATATGATT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
27 27 0.53
28 24 0.47
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (28 bp):
AATCTGACCGTTACAATATAATCGTTGG
Found at i:19313203 original size:14 final size:14
Alignment explanation
Indices: 19313131--19313208 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
19313121 CTGACTGTTA
19313131 CAATATGATCGTTG
1 CAATATGATCGTTG
* * * *
19313145 GAATCTGACCGTTA
1 CAATATGATCGTTG
*
19313159 CAATATAATC-TTG
1 CAATATGATCGTTG
* * * *
19313172 GAATCTGACCGTTA
1 CAATATGATCGTTG
*
19313186 CAATATAATCGTTG
1 CAATATGATCGTTG
19313200 CAATATGAT
1 CAATATGAT
19313209 TGTCGAATTT
Statistics
Matches: 43, Mismatches: 20, Indels: 2
0.66 0.31 0.03
Matches are distributed among these distances:
13 8 0.19
14 35 0.81
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (14 bp):
CAATATGATCGTTG
Found at i:19325824 original size:16 final size:16
Alignment explanation
Indices: 19325793--19325831 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
19325783 ACATTTAATT
*
19325793 ATATTTTAAAAATAAA
1 ATATTATAAAAATAAA
* *
19325809 ATGTTATAAAACTAAA
1 ATATTATAAAAATAAA
19325825 ATATTAT
1 ATATTAT
19325832 TATTGTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (16 bp):
ATATTATAAAAATAAA
Found at i:19330740 original size:52 final size:48
Alignment explanation
Indices: 19330721--19330923 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
19330711 TGACAAGTGG
* *
19330721 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
19330767 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
19330819 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
19330865 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
19330911 AAAGTGATAAGTG
1 AAAGTGATAAGTG
19330924 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:19330775 original size:98 final size:98
Alignment explanation
Indices: 19330655--19330923 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
19330645 TTTGAGTACT
*
19330655 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
19330720 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
19330753 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
19330818 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
19330851 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
19330916 GATAAGTG
65 GAAAAGTG
19330924 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:19330931 original size:37 final size:37
Alignment explanation
Indices: 19330887--19331032 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
19330877 GATAGCTTTA
*
19330887 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
19330924 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
19330961 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
19330998 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
19331033 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:19341225 original size:50 final size:50
Alignment explanation
Indices: 19341115--19341359 Score: 258
Period size: 50 Copynumber: 4.8 Consensus size: 50
19341105 ATTTGGGTAA
* *
19341115 AGAGATCCC-TGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* *
19341170 AGAGGTCCCATGTAAGACTATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
19341220 AGAGGTCTCATGTAAGACCTTGTCTAGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
19341270 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
19341320 AGAACTCCCATGTAAGACCATATCTGAGATATGACATTGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
19341360 TAGCACAAGA
Statistics
Matches: 162, Mismatches: 27, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
50 120 0.74
53 3 0.02
55 9 0.06
56 30 0.19
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:19344788 original size:27 final size:27
Alignment explanation
Indices: 19344719--19344788 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
19344709 AGTCTGTCGA
* * *
19344719 GACAGTAAACATAGGGTAGTCCCCTAG
1 GACACTAAACATGGGGAAGTCCCCTAG
*
19344746 GACACTAAACACGGGGAAGTCCACC-AG
1 GACACTAAACATGGGGAAGTCC-CCTAG
19344773 GACA-TAAAACATGGGG
1 GACACT-AAACATGGGG
19344789 TTACACTTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 1 0.03
27 33 0.92
28 2 0.06
ACGTcount: A:0.37, C:0.23, G:0.27, T:0.13
Consensus pattern (27 bp):
GACACTAAACATGGGGAAGTCCCCTAG
Found at i:19351597 original size:13 final size:13
Alignment explanation
Indices: 19351579--19351603 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19351569 AATTGCTTAT
19351579 CAAATGCATATAC
1 CAAATGCATATAC
19351592 CAAATGCATATA
1 CAAATGCATATA
19351604 TATTTAATAT
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:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
CAAATGCATATAC
Found at i:19351849 original size:41 final size:41
Alignment explanation
Indices: 19351789--19351919 Score: 131
Period size: 41 Copynumber: 3.2 Consensus size: 41
19351779 TGATTCGGTA
* * * *
19351789 CACCGGCTTTTAGCTTGCTAGACTTATAGTCCG-A-AATGTAT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCCGAATAAT-T-T
*
19351830 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATAATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCCGAATAATTT
* * * * *
19351871 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCCGAATAATTT
*
19351912 CACTGGCA
1 CACCGGCA
19351920 ATAAATCAGA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
41 73 0.94
42 2 0.03
43 3 0.04
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACGTATAGTCCGAATAATTT
Found at i:19353261 original size:25 final size:24
Alignment explanation
Indices: 19353229--19353278 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
19353219 TCTTTATTTG
*
19353229 TTTAATTATAATA-TTATAATATAA
1 TTTAATTATAACATTTATAAT-TAA
19353253 TTTATATTATAACATTTATAATTAA
1 TTTA-ATTATAACATTTATAATTAA
19353278 T
1 T
19353279 ATAAAACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 12 0.52
26 7 0.30
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTAATTATAACATTTATAATTAA
Found at i:19353293 original size:21 final size:21
Alignment explanation
Indices: 19353247--19353293 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
19353237 TAATATTATA
* *
19353247 ATATAATTTATATTATAACAT
1 ATATAATTAATATTAAAACAT
*
19353268 TTATAATTAATA-TAAAACTAT
1 ATATAATTAATATTAAAAC-AT
19353289 ATATA
1 ATATA
19353294 TTATACACAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATAATTAATATTAAAACAT
Found at i:19355573 original size:65 final size:63
Alignment explanation
Indices: 19355447--19355586 Score: 194
Period size: 65 Copynumber: 2.2 Consensus size: 63
19355437 TTTAATAAAT
* *
19355447 TTAATATTTAAT-TTAATTTAATACTTATCTTGATAGTATTTTATTAATTTAATATTAAAGTAA
1 TTAA-ATTTAATATTAATTTAATACTTATCCTGATAGTATTATATTAATTTAATATTAAAGTAA
* *
19355510 TT-ATTTTAATATTAAATTTAATCACTTATCCTGATATGTATTATATTAATTTAATATTGAAGTA
1 TTAAATTTAATATT-AATTTAAT-ACTTATCCTGATA-GTATTATATTAATTTAATATTAAAGTA
19355574 A
63 A
19355575 TTAAATTTAATA
1 TTAAATTTAATA
19355587 ATAGTTGAAC
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
61 6 0.09
62 3 0.04
63 10 0.15
64 12 0.18
65 28 0.42
66 8 0.12
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (63 bp):
TTAAATTTAATATTAATTTAATACTTATCCTGATAGTATTATATTAATTTAATATTAAAGTAA
Found at i:19356858 original size:8 final size:8
Alignment explanation
Indices: 19356845--19356884 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
19356835 ATGCACAACC
19356845 CTTTCTCT
1 CTTTCTCT
19356853 C-TT-TCT
1 CTTTCTCT
19356859 CTTTCTCT
1 CTTTCTCT
19356867 C--TCTCT
1 CTTTCTCT
19356873 CTTTCTCT
1 CTTTCTCT
19356881 CTTT
1 CTTT
19356885 GTGTAACACC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 10 0.36
7 4 0.14
8 14 0.50
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (8 bp):
CTTTCTCT
Found at i:19356864 original size:14 final size:14
Alignment explanation
Indices: 19356845--19356884 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
19356835 ATGCACAACC
19356845 CTTTCTCTCTTTCT
1 CTTTCTCTCTTTCT
*
19356859 CTTTCTCTCTCTCT
1 CTTTCTCTCTTTCT
19356873 CTTTCTCTCTTT
1 CTTTCTCTCTTT
19356885 GTGTAACACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (14 bp):
CTTTCTCTCTTTCT
Found at i:19358868 original size:20 final size:22
Alignment explanation
Indices: 19358843--19358887 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
19358833 CTTGGGAGGT
*
19358843 GGATATTGCCATACC-C-AAAG
1 GGATATCGCCATACCACTAAAG
*
19358863 GGATATCGCGATACCACTAAAG
1 GGATATCGCCATACCACTAAAG
19358885 GGA
1 GGA
19358888 ATCCTTGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 1 0.05
22 7 0.33
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (22 bp):
GGATATCGCCATACCACTAAAG
Found at i:19362971 original size:21 final size:23
Alignment explanation
Indices: 19362942--19362988 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
19362932 TAAAATAGGG
* *
19362942 AAAAAAACAAAAAGAAAAAGCATT
1 AAAACAACAAAAA-AAATAGCATT
19362966 AAAACAACAAAAAAAATAGCATT
1 AAAACAACAAAAAAAATAGCATT
19362989 TTTTTGTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.72, C:0.11, G:0.06, T:0.11
Consensus pattern (23 bp):
AAAACAACAAAAAAAATAGCATT
Found at i:19364976 original size:2 final size:2
Alignment explanation
Indices: 19364971--19365019 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
19364961 CACACACACA
19364971 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
19365013 CT CT CT C
1 CT CT CT C
19365020 CCCATGATGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:19366026 original size:22 final size:23
Alignment explanation
Indices: 19366000--19366042 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
19365990 AATTTAAATT
19366000 TTAAAAT-CTAAAAAGAAAAAAA
1 TTAAAATACTAAAAAGAAAAAAA
* *
19366022 TTAAATTACTAAAAATAAAAA
1 TTAAAATACTAAAAAGAAAAA
19366043 TAATAAACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (23 bp):
TTAAAATACTAAAAAGAAAAAAA
Found at i:19367045 original size:13 final size:14
Alignment explanation
Indices: 19367027--19367055 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19367017 TTATGTCTTT
19367027 TTTTTAAT-ATTTA
1 TTTTTAATAATTTA
19367040 TTTTTAATAATTTA
1 TTTTTAATAATTTA
19367054 TT
1 TT
19367056 ATATTCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTAATAATTTA
Found at i:19368563 original size:24 final size:24
Alignment explanation
Indices: 19368531--19368613 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
19368521 TTAAGTAGTG
19368531 ATACATAATAAATTTAAAATAATA
1 ATACATAATAAATTTAAAATAATA
* * * *
19368555 ATACGTAATAAACTTATAATAAAA
1 ATACATAATAAATTTAAAATAATA
* *
19368579 ATACATTATAATTTTAAAA-AAGTA
1 ATACATAATAAATTTAAAATAA-TA
19368603 ATA-ATATATAA
1 ATACATA-ATAA
19368614 CGTTTGAGAA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
23 4 0.09
24 42 0.91
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (24 bp):
ATACATAATAAATTTAAAATAATA
Found at i:19372591 original size:24 final size:24
Alignment explanation
Indices: 19372555--19372608 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
19372545 TATTTCTAGA
** *
19372555 ATATTTAGTATTTATTAGTATAAT
1 ATATTTAACATTTATTAGCATAAT
19372579 ATATTTAACATTTATTAGCATAAT
1 ATATTTAACATTTATTAGCATAAT
*
19372603 TTATTT
1 ATATTT
19372609 GACCTACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (24 bp):
ATATTTAACATTTATTAGCATAAT
Found at i:19376579 original size:14 final size:14
Alignment explanation
Indices: 19376560--19376597 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
19376550 CCAGAAAAGT
19376560 AAATTATTTTCCAG
1 AAATTATTTTCCAG
*
19376574 AAATTATTTTCCGG
1 AAATTATTTTCCAG
*
19376588 AAAATATTTT
1 AAATTATTTT
19376598 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (14 bp):
AAATTATTTTCCAG
Found at i:19377249 original size:18 final size:17
Alignment explanation
Indices: 19377226--19377261 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
19377216 TTTTTAAATG
19377226 TGAATTTAGTAATATGAT
1 TGAATTTAGTAATA-GAT
19377244 TGAATTTAGTAATAGAT
1 TGAATTTAGTAATAGAT
19377261 T
1 T
19377262 TAACTTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (17 bp):
TGAATTTAGTAATAGAT
Found at i:19398585 original size:15 final size:16
Alignment explanation
Indices: 19398560--19398594 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
19398550 AAATAACAAG
*
19398560 AAGAAAGGAAGGAAGA
1 AAGAAAGGAAGGAAAA
19398576 AAGAAA-GAAGGAAAA
1 AAGAAAGGAAGGAAAA
19398591 AAGA
1 AAGA
19398595 TAGGCTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
AAGAAAGGAAGGAAAA
Found at i:19400300 original size:3 final size:3
Alignment explanation
Indices: 19400294--19400324 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
19400284 CATCATCATC
19400294 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
19400325 ATTCCATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:19408535 original size:9 final size:9
Alignment explanation
Indices: 19408521--19408548 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
19408511 TGAGTTTTCG
19408521 AATTCGAAT
1 AATTCGAAT
19408530 AATTCGAAT
1 AATTCGAAT
19408539 AATTCGAAT
1 AATTCGAAT
19408548 A
1 A
19408549 TCAAACTATA
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:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:19410073 original size:20 final size:20
Alignment explanation
Indices: 19410039--19410080 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
19410029 AACTGTTTAA
** *
19410039 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
19410059 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
19410079 AT
1 AT
19410081 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:19411515 original size:13 final size:11
Alignment explanation
Indices: 19411480--19411509 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
19411470 GCCCATATTA
19411480 AATTTTTATAT
1 AATTTTTATAT
*
19411491 TATTTTTATAT
1 AATTTTTATAT
19411502 AATTTTTA
1 AATTTTTA
19411510 AGTATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
AATTTTTATAT
Found at i:19416329 original size:46 final size:46
Alignment explanation
Indices: 19416251--19416819 Score: 385
Period size: 46 Copynumber: 12.4 Consensus size: 46
19416241 ACTCATTTGT
* * ** *
19416251 ACACCTCAATCTGCAGCACTCAAACA-CTTCAATTTACAATATTTAA
1 ACACTTCAATTTGCAGCACTTTAACATC-TCAATTTACAACATTTAA
* * * * * *
19416297 GCACTTCATTTTGCAGCACTGTAACATCTCAATTAACAACGTTTAT
1 ACACTTCAATTTGCAGCACTTTAACATCTCAATTTACAACATTTAA
* * * * ** * * *
19416343 ACACTTTAATTTACAACAATAAAACATCTCAATTTCCAGCAATTAA
1 ACACTTCAATTTGCAGCACTTTAACATCTCAATTTACAACATTTAA
* * * * * *
19416389 ACAGTTCAATTTGTAGTAGTTAAACA-CTTTAATTTACAACATTTAA
1 ACACTTCAATTTGCAGCACTTTAACATC-TCAATTTACAACATTTAA
* * * * *
19416435 ACACTTCAATTCGCAACACTTTAACATCTCAATTAACAACGTTTAT
1 ACACTTCAATTTGCAGCACTTTAACATCTCAATTTACAACATTTAA
* ** * ** * * **
19416481 ACACCTCAATTTATAGCAATAAAACATATCAATTTCCAACAACT-A
1 ACACTTCAATTTGCAGCACTTTAACATCTCAATTTACAACATTTAA
* *
19416526 ACACTTCAATTTGCAGTACTTAAACA-CTTCAATTTACAACATTTAA
1 ACACTTCAATTTGCAGCACTTTAACATC-TCAATTTACAACATTTAA
**
19416572 ACACTTCAATTTGCAGTGCTTTAACA-CTTCAATTTACAACATTTAA
1 ACACTTCAATTTGCAGCACTTTAACATC-TCAATTTACAACATTTAA
* * * * * * ** *
19416618 GCACTTCATTTTGCAACATTTTAACATCTCAATTAATAATGTTTAT
1 ACACTTCAATTTGCAGCACTTTAACATCTCAATTTACAACATTTAA
* * * ** * * **
19416664 ACACCTCAATTTACAGCAATAAAACATCTCAATTTCCAGCAACTAA
1 ACACTTCAATTTGCAGCACTTTAACATCTCAATTTACAACATTTAA
* * * *
19416710 ACACTTCAACTTGCAGTACTTAAACA-CTTCAATTTACAATATTTAA
1 ACACTTCAATTTGCAGCACTTTAACATC-TCAATTTACAACATTTAA
* * * *
19416756 ACACTTCAATTTGCAGCACTTTAACATCTCAGTTAACAACGTTTAT
1 ACACTTCAATTTGCAGCACTTTAACATCTCAATTTACAACATTTAA
* * *
19416802 ACACCTAAATTTACAGCA
1 ACACTTCAATTTGCAGCA
19416820 ATAAAAAATC
Statistics
Matches: 391, Mismatches: 124, Indels: 16
0.74 0.23 0.03
Matches are distributed among these distances:
45 35 0.09
46 352 0.90
47 4 0.01
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (46 bp):
ACACTTCAATTTGCAGCACTTTAACATCTCAATTTACAACATTTAA
Found at i:19416434 original size:23 final size:23
Alignment explanation
Indices: 19416272--19416767 Score: 249
Period size: 23 Copynumber: 21.6 Consensus size: 23
19416262 TGCAGCACTC
*
19416272 AAACACTTCAATTTACAATATTT
1 AAACACTTCAATTTACAACATTT
* * * * *
19416295 AAGCACTTCATTTTGCAGCACTGT
1 AAACACTTCAATTTACAACA-TTT
* *
19416319 -AACA-TCTCAATTAACAACGTTT
1 AAACACT-TCAATTTACAACATTT
* * * *
19416341 ATACACTTTAATTTACAACAATA
1 AAACACTTCAATTTACAACATTT
* * *
19416364 AAACA-TCTCAATTTCCAGCAATT
1 AAACACT-TCAATTTACAACATTT
* ** ** *
19416387 AAACAGTTCAATTTGTAGTAGTT
1 AAACACTTCAATTTACAACATTT
*
19416410 AAACACTTTAATTTACAACATTT
1 AAACACTTCAATTTACAACATTT
**
19416433 AAACACTTCAATTCGCAACACTTT
1 AAACACTTCAATTTACAACA-TTT
* *
19416457 -AACA-TCTCAATTAACAACGTTT
1 AAACACT-TCAATTTACAACATTT
* * * * * *
19416479 ATACACCTCAATTTATAGCAATA
1 AAACACTTCAATTTACAACATTT
* **
19416502 AAACA-TATCAATTTCCAACAACT
1 AAACACT-TCAATTTACAACATTT
* ** *
19416525 -AACACTTCAATTTGCAGTACTT
1 AAACACTTCAATTTACAACATTT
19416547 AAACACTTCAATTTACAACATTT
1 AAACACTTCAATTTACAACATTT
* *
19416570 AAACACTTCAATTTGCAGTGC-TTT
1 AAACACTTCAATTTACA--ACATTT
19416594 -AACACTTCAATTTACAACATTT
1 AAACACTTCAATTTACAACATTT
* * *
19416616 AAGCACTTCATTTTGCAACATTT
1 AAACACTTCAATTTACAACATTT
* * * **
19416639 TAACA-TCTCAATTAATAATGTTT
1 AAACACT-TCAATTTACAACATTT
* * * * *
19416662 ATACACCTCAATTTACAGCAATA
1 AAACACTTCAATTTACAACATTT
* * **
19416685 AAACA-TCTCAATTTCCAGCAACT
1 AAACACT-TCAATTTACAACATTT
* * ** *
19416708 AAACACTTCAACTTGCAGTACTT
1 AAACACTTCAATTTACAACATTT
*
19416731 AAACACTTCAATTTACAATATTT
1 AAACACTTCAATTTACAACATTT
19416754 AAACACTTCAATTT
1 AAACACTTCAATTT
19416768 GCAGCACTTT
Statistics
Matches: 348, Mismatches: 104, Indels: 42
0.70 0.21 0.09
Matches are distributed among these distances:
21 1 0.00
22 27 0.08
23 308 0.89
24 11 0.03
25 1 0.00
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
AAACACTTCAATTTACAACATTT
Found at i:19416504 original size:138 final size:137
Alignment explanation
Indices: 19416251--19416582 Score: 466
Period size: 138 Copynumber: 2.4 Consensus size: 137
19416241 ACTCATTTGT
* * * * * * * * *
19416251 ACACCTCAATCTGCAGCACTCAAACACTTCAATTTACAATATTTAAGCACTTCATTTTGCAGCAC
1 ACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTTAAACACTTCAATTCGCAACAC
* * *
19416316 TGTAACATCTCAATTAACAACGTTTATACACTTTAATTTACAACAATAAAACATCTCAATTTCCA
66 TGTAACATCTCAATTAACAACGTTTATACACCTCAATTTACAACAATAAAACATATCAATTTCCA
* *
19416381 GCAATTAA
131 ACAACT-A
* * * *
19416389 ACAGTTCAATTTGTAGTAGTTAAACACTTTAATTTACAACATTTAAACACTTCAATTCGCAACAC
1 ACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTTAAACACTTCAATTCGCAACAC
* * *
19416454 TTTAACATCTCAATTAACAACGTTTATACACCTCAATTTATAGCAATAAAACATATCAATTTCCA
66 TGTAACATCTCAATTAACAACGTTTATACACCTCAATTTACAACAATAAAACATATCAATTTCCA
19416519 ACAACTA
131 ACAACTA
19416526 ACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTTAAACACTTCAATT
1 ACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTTAAACACTTCAATT
19416583 TGCAGTGCTT
Statistics
Matches: 169, Mismatches: 25, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
137 54 0.32
138 115 0.68
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (137 bp):
ACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTTAAACACTTCAATTCGCAACAC
TGTAACATCTCAATTAACAACGTTTATACACCTCAATTTACAACAATAAAACATATCAATTTCCA
ACAACTA
Done.