Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 20 of 230
Found at i:5562304 original size:45 final size:45
Alignment explanation
Indices: 5562252--5562398 Score: 161
Period size: 45 Copynumber: 3.2 Consensus size: 45
5562242 TTTCTCAGTT
5562252 TGAACAATCTGTCACCCTAGATTGCCCAGCAACGGTGAATCTATG
1 TGAACAATCTGTCACCCTAGATTGCCCAGCAACGGTGAATCTATG
* ** * * * * *
5562297 TGAACAATTTACCACCTTAGGTTGCCC-GACAACGATGATTTTCTCAGTT
1 TGAACAATCTGTCACCCTAGATTGCCCAG-CAACGGTGA--ATCT-A-TG
*
5562346 TGAACAATCTGTCACCCTAGATTGCCCAGCAAGGGTGAATCTATG
1 TGAACAATCTGTCACCCTAGATTGCCCAGCAACGGTGAATCTATG
5562391 TGAACAAT
1 TGAACAAT
5562399 TTACCACCTT
Statistics
Matches: 79, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
44 1 0.01
45 39 0.49
46 1 0.01
47 6 0.08
48 1 0.01
49 30 0.38
50 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (45 bp):
TGAACAATCTGTCACCCTAGATTGCCCAGCAACGGTGAATCTATG
Found at i:5562385 original size:94 final size:94
Alignment explanation
Indices: 5562224--5562433 Score: 402
Period size: 94 Copynumber: 2.2 Consensus size: 94
5562214 ACATCCCGGA
*
5562224 TTGCCCGACAACAATGATTTTCTCAGTTTGAACAATCTGTCACCCTAGATTGCCCAGCAACGGTG
1 TTGCCCGACAACGATGATTTTCTCAGTTTGAACAATCTGTCACCCTAGATTGCCCAGCAACGGTG
5562289 AATCTATGTGAACAATTTACCACCTTAGG
66 AATCTATGTGAACAATTTACCACCTTAGG
*
5562318 TTGCCCGACAACGATGATTTTCTCAGTTTGAACAATCTGTCACCCTAGATTGCCCAGCAAGGGTG
1 TTGCCCGACAACGATGATTTTCTCAGTTTGAACAATCTGTCACCCTAGATTGCCCAGCAACGGTG
5562383 AATCTATGTGAACAATTTACCACCTTAGG
66 AATCTATGTGAACAATTTACCACCTTAGG
5562412 TTGCCCGACAACGATGATTTTC
1 TTGCCCGACAACGATGATTTTC
5562434 AACAAATAAT
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 114 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (94 bp):
TTGCCCGACAACGATGATTTTCTCAGTTTGAACAATCTGTCACCCTAGATTGCCCAGCAACGGTG
AATCTATGTGAACAATTTACCACCTTAGG
Found at i:5562416 original size:45 final size:45
Alignment explanation
Indices: 5562264--5562417 Score: 157
Period size: 45 Copynumber: 3.3 Consensus size: 45
5562254 AACAATCTGT
5562264 CACCCTAGATTGCCCAGCAACGGTGAATCTATGTGAACAATTTAC
1 CACCCTAGATTGCCCAGCAACGGTGAATCTATGTGAACAATTTAC
* * * * * * **
5562309 CACCTTAGGTTGCCC-GACAACGATGATTTTCTCAGTTTGAACAATCTGT
1 CACCCTAGATTGCCCAG-CAACGGTGA--ATCT-A-TGTGAACAATTTAC
*
5562358 CACCCTAGATTGCCCAGCAAGGGTGAATCTATGTGAACAATTTAC
1 CACCCTAGATTGCCCAGCAACGGTGAATCTATGTGAACAATTTAC
* *
5562403 CACCTTAGGTTGCCC
1 CACCCTAGATTGCCC
5562418 GACAACGATG
Statistics
Matches: 84, Mismatches: 19, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
44 1 0.01
45 44 0.52
46 1 0.01
47 6 0.07
48 1 0.01
49 30 0.36
50 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (45 bp):
CACCCTAGATTGCCCAGCAACGGTGAATCTATGTGAACAATTTAC
Found at i:5562617 original size:7 final size:7
Alignment explanation
Indices: 5562605--5562629 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5562595 AATTTCATAC
5562605 CAATTAT
1 CAATTAT
5562612 CAATTAT
1 CAATTAT
5562619 CAATTAT
1 CAATTAT
5562626 CAAT
1 CAAT
5562630 CAAATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (7 bp):
CAATTAT
Found at i:5565295 original size:20 final size:20
Alignment explanation
Indices: 5565258--5565296 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5565248 TAGTTTTAAT
* *
5565258 GAACACCGATATCAAATTGG
1 GAACACCAATACCAAATTGG
*
5565278 GAACACCAATACCGAATTG
1 GAACACCAATACCAAATTG
5565297 AAACTACCCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (20 bp):
GAACACCAATACCAAATTGG
Found at i:5569431 original size:18 final size:19
Alignment explanation
Indices: 5569398--5569435 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
5569388 AGACTCCAGG
*
5569398 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
5569417 TCTGATT-TCTTCAATCAT
1 TCTGATTCTCTTCAATCAT
5569435 T
1 T
5569436 GCTTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:5574323 original size:2 final size:2
Alignment explanation
Indices: 5574316--5574345 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5574306 ACAGATTAAA
*
5574316 AC AC AC AC AC AC AC AC AC AC AC AC AG AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5574346 TAGAGAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.47, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5574494 original size:21 final size:21
Alignment explanation
Indices: 5574465--5574507 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5574455 AAAGTAAGCT
*
5574465 TATTGCAACGCGTTTGTGATC
1 TATTACAACGCGTTTGTGATC
5574486 TATTACAACGCGTTTGTGATC
1 TATTACAACGCGTTTGTGATC
5574507 T
1 T
5574508 TTAGAACCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TATTACAACGCGTTTGTGATC
Found at i:5575747 original size:19 final size:19
Alignment explanation
Indices: 5575706--5575747 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5575696 AAAGGAGGGC
* *
5575706 TAAGTTAGAAAATAGAAAT
1 TAAGTTAAAAAATAGAAAA
5575725 TAAGTTAAAAAATA-AATAA
1 TAAGTTAAAAAATAGAA-AA
5575744 TAAG
1 TAAG
5575748 CTCTGCATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (19 bp):
TAAGTTAAAAAATAGAAAA
Found at i:5576593 original size:16 final size:16
Alignment explanation
Indices: 5576572--5576602 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5576562 CAAAAAGTAG
5576572 CCCAAAAGTATTTTTT
1 CCCAAAAGTATTTTTT
5576588 CCCAAAAGTATTTTT
1 CCCAAAAGTATTTTT
5576603 GAGAAGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (16 bp):
CCCAAAAGTATTTTTT
Found at i:5582183 original size:24 final size:24
Alignment explanation
Indices: 5582156--5582235 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 24
5582146 CAAGGCATTT
5582156 TTTTCCTTTTTTATTTACTTATTA
1 TTTTCCTTTTTTATTTACTTATTA
*
5582180 --TT--TTATTTATTTACCTATACTTA
1 TTTTCCTTTTTTATTTA-CT-TA-TTA
* * *
5582203 TTTTCATTTATTATTTATTTATTA
1 TTTTCCTTTTTTATTTACTTATTA
5582227 TTATTCCTT
1 TT-TTCCTT
5582236 CAATCTTTGC
Statistics
Matches: 43, Mismatches: 5, Indels: 15
0.68 0.08 0.24
Matches are distributed among these distances:
20 10 0.23
21 2 0.05
22 4 0.09
23 3 0.07
24 5 0.12
25 9 0.21
26 1 0.02
27 9 0.21
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTCCTTTTTTATTTACTTATTA
Found at i:5582190 original size:20 final size:24
Alignment explanation
Indices: 5582165--5582214 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 24
5582155 TTTTTCCTTT
5582165 TTTATTTA-CT-TA-TTATTTT-A
1 TTTATTTACCTATACTTATTTTCA
5582185 TTTATTTACCTATACTTATTTTCA
1 TTTATTTACCTATACTTATTTTCA
5582209 TTTATT
1 TTTATT
5582215 ATTTATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.31
21 2 0.08
22 2 0.08
23 7 0.27
24 7 0.27
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTATTTACCTATACTTATTTTCA
Found at i:5582507 original size:15 final size:15
Alignment explanation
Indices: 5582469--5582510 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
5582459 CTACTACTAT
*
5582469 TATTATTAATATTAC
1 TATTATTATTATTAC
5582484 TATTATTATTATTAC
1 TATTATTATTATTAC
* *
5582499 TGTTGTTATTAT
1 TATTATTATTAT
5582511 ATTTTTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:5588676 original size:16 final size:14
Alignment explanation
Indices: 5588614--5588678 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 14
5588604 GAATAAGAAT
5588614 AATAAATAA-AATAA
1 AATAAA-AATAATAA
*
5588628 AATAAAAAATTAGTAA
1 AAT-AAAAA-TAATAA
5588644 AATAAAAATAAATAA
1 AATAAAAAT-AATAA
*
5588659 TATAACAAATAAT-A
1 AATAA-AAATAATAA
5588673 AATAAA
1 AATAAA
5588679 TAAAATAAGC
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 1 0.02
14 11 0.26
15 19 0.45
16 11 0.26
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (14 bp):
AATAAAAATAATAA
Found at i:5588677 original size:23 final size:22
Alignment explanation
Indices: 5588643--5588686 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
5588633 AAAATTAGTA
*
5588643 AAATAAAAATAAATAATATAAC
1 AAATAAAAATAAATAAAATAAC
5588665 AAATAATAAATAAATAAAATAA
1 AAATAA-AAATAAATAAAATAA
5588687 GCATAATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (22 bp):
AAATAAAAATAAATAAAATAAC
Found at i:5588684 original size:16 final size:16
Alignment explanation
Indices: 5588605--5588686 Score: 65
Period size: 19 Copynumber: 4.6 Consensus size: 16
5588595 AAAATCTGAG
5588605 AATAAGAATAATAAATAA
1 AATAA-AATAATAAAT-A
* *
5588623 AATAAAATAAAAAATT
1 AATAAAATAATAAATA
*
5588639 AGTAAAATAAAAATAAATA
1 AATAAAAT---AATAAATA
5588658 ATATAACAAATAATAAATA
1 A-AT-A-AAATAATAAATA
5588677 AATAAAATAA
1 AATAAAATAA
5588687 GCATAATGGG
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
16 13 0.25
17 10 0.19
18 7 0.13
19 16 0.31
20 1 0.02
21 1 0.02
22 4 0.08
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.23
Consensus pattern (16 bp):
AATAAAATAATAAATA
Found at i:5593661 original size:28 final size:28
Alignment explanation
Indices: 5593630--5593720 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 28
5593620 TAAAAAATCG
5593630 TAAAAAAATTATAAAATATATAGAAATA
1 TAAAAAAATTATAAAATATATAGAAATA
* *
5593658 TAAAAAAATTATAAAATTTTATA-AAGTCA
1 TAAAAAAATTATAAAA-TATATAGAAAT-A
* * *
5593687 TAAGAAAATTATACAAAATGTAAAGAAATA
1 TAAAAAAATTAT--AAAATATATAGAAATA
5593717 TAAA
1 TAAA
5593721 TTTCGTAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 19 0.37
29 17 0.33
30 8 0.16
31 7 0.14
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (28 bp):
TAAAAAAATTATAAAATATATAGAAATA
Found at i:5593944 original size:10 final size:10
Alignment explanation
Indices: 5593929--5594003 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 10
5593919 AAAAAAAATC
5593929 TAATTTTTAA
1 TAATTTTTAA
5593939 TAATTTTTAA
1 TAATTTTTAA
5593949 T--TTTTT-A
1 TAATTTTTAA
*
5593956 T-ATTTTTAT
1 TAATTTTTAA
**
5593965 TAAAATTTAA
1 TAATTTTTAA
* *
5593975 TATTTTTTTA
1 TAATTTTTAA
**
5593985 TAAAATTTAA
1 TAATTTTTAA
*
5593995 TATTTTTTA
1 TAATTTTTA
5594004 TTTTTTATAA
Statistics
Matches: 47, Mismatches: 15, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
7 2 0.04
8 10 0.21
9 1 0.02
10 34 0.72
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:5593951 original size:17 final size:16
Alignment explanation
Indices: 5593929--5593963 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5593919 AAAAAAAATC
5593929 TAATTTTTAATAATTTT
1 TAATTTTTAAT-ATTTT
*
5593946 TAATTTTTTATATTTT
1 TAATTTTTAATATTTT
5593962 TA
1 TA
5593964 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TAATTTTTAATATTTT
Found at i:5593988 original size:20 final size:21
Alignment explanation
Indices: 5593958--5594002 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
5593948 ATTTTTTATA
5593958 TTTTTATTAAAATTTAATATT
1 TTTTTATTAAAATTTAATATT
5593979 TTTTTA-TAAAATTTAATATT
1 TTTTTATTAAAATTTAATATT
5593999 TTTT
1 TTTT
5594003 ATTTTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTATTAAAATTTAATATT
Found at i:5593994 original size:27 final size:26
Alignment explanation
Indices: 5593964--5594014 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5593954 TATATTTTTA
5593964 TTAAAATTTAATATTTTTTTATAAAAT
1 TTAAAATTTAATA-TTTTTTATAAAAT
* **
5593991 TTAATATTTTTTATTTTTTATAAA
1 TTAAAATTTAATATTTTTTATAAA
5594015 TAAGAGCAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TTAAAATTTAATATTTTTTATAAAAT
Found at i:5594124 original size:85 final size:86
Alignment explanation
Indices: 5594021--5594181 Score: 218
Period size: 86 Copynumber: 1.9 Consensus size: 86
5594011 TAAATAAGAG
* * * *
5594021 CAGGGGCTTAATTTC-TTTTTTAAAAAATTTTGAGGGTCTTTTTTATACATTTTG-AAAGTTCAA
1 CAGGGGCTTAATTGCTTTTTTTAAAAAAGTTTGAGGGCCTTTTTGATACA-TTTGAAAAGTTCAA
5594084 GTACTCAATTGAGTGAAAAAAA
65 GTACTCAATTGAGTGAAAAAAA
* * * *
5594106 CAGGGGCTTTATTGCTTTTTTTGAAGAAGTTTGAGGGCCTTTTTGATGCATTTGAAAAGTTCAAG
1 CAGGGGCTTAATTGCTTTTTTTAAAAAAGTTTGAGGGCCTTTTTGATACATTTGAAAAGTTCAAG
*
5594171 TGCTCAATTGA
66 TACTCAATTGA
5594182 ATACAAAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
85 17 0.26
86 48 0.74
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (86 bp):
CAGGGGCTTAATTGCTTTTTTTAAAAAAGTTTGAGGGCCTTTTTGATACATTTGAAAAGTTCAAG
TACTCAATTGAGTGAAAAAAA
Found at i:5597629 original size:195 final size:194
Alignment explanation
Indices: 5597097--5597630 Score: 536
Period size: 195 Copynumber: 2.7 Consensus size: 194
5597087 TAAGAAATCG
* * * * **
5597097 ATCTTCATTAAATCTTATGCTGTTCTTAATATTGCACGTGTTTTGCAAA-GAAAAATCTTATAAT
1 ATCTTCATTTATTCTTATGCAGTTCTTAATATTACACGTGTTTTGCAAATG-TCAATCTTATAAT
* * * * * * *
5597161 TTATTTAATTTATTGGCTTCAAAGATAAATTATTGTATTCATTCATTCATACGCAATTCTT-AAT
65 TTATTTAATTTATAGGATTCAAATATAAATTATTGTATTCATTCATTCATATGTAGTTCTTAAAA
** * * ** *
5597225 GTTACACATACTTGTGAAGATTGATCCTATAATTGAATTGATTTTTATTGTTAAAATACATACCA
130 G-TACACATGTTTGTGAAGATCGATCATATAATTGAATTGATTTTTAGAGTTAAAATACAAACCA
5597290 T
194 T
* * * * * * * * *
5597291 AGTCCTCATTTGTTCTTAAGCAATTCTTAATATTACATGTGTTTTGCTAATATCGATATTATAAT
1 A-TCTTCATTTATTCTTATGCAGTTCTTAATATTACACGTGTTTTGCAAATGTCAATCTTATAAT
* * * * *
5597356 TTATTTAATTTA-CGAGATTCAAATATAAATTATTGTCTTCATTTATTCATATGTAGTTCTCAAT
65 TTATTTAATTTATAG-GATTCAAATATAAATTATTGTATTCATTCATTCATATGTAGTTCTTAAA
* * * * * *
5597420 ATTACACGTGTTTGTGAAGATCGATGATTTAATTGATTTGATTTTTAGAGTTCAAATACAAACCA
129 AGTACACATGTTTGTGAAGATCGATCATATAATTGAATTGATTTTTAGAGTTAAAATACAAACCA
5597485 T
194 T
* * *
5597486 CATCTTCATTTATTCTTATGCGGTTCTTAATATTACAGGTGTTTTACAAATGTCAATCTTATAAT
1 -ATCTTCATTTATTCTTATGCAGTTCTTAATATTACACGTGTTTTGCAAATGTCAATCTTATAAT
* * * * ** *
5597551 TTGTTTAATTTATAGGATTAAAATAGAAATTATTATGGTCATTCATTCAT-TGTTAGTTTTTAAA
65 TTATTTAATTTATAGGATTCAAATATAAATTATTGTATTCATTCATTCATATG-TAGTTCTTAAA
5597615 AGTACACATGTTTGTG
129 AGTACACATGTTTGTG
5597631 CAAACGAATT
Statistics
Matches: 270, Mismatches: 63, Indels: 13
0.78 0.18 0.04
Matches are distributed among these distances:
194 4 0.01
195 263 0.97
196 3 0.01
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (194 bp):
ATCTTCATTTATTCTTATGCAGTTCTTAATATTACACGTGTTTTGCAAATGTCAATCTTATAATT
TATTTAATTTATAGGATTCAAATATAAATTATTGTATTCATTCATTCATATGTAGTTCTTAAAAG
TACACATGTTTGTGAAGATCGATCATATAATTGAATTGATTTTTAGAGTTAAAATACAAACCAT
Found at i:5598157 original size:26 final size:26
Alignment explanation
Indices: 5598124--5598173 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
5598114 GAGTTGTCCA
*
5598124 AAAATCACATATATGGTTATGAATCC
1 AAAATCACATATATAGTTATGAATCC
*
5598150 AAAATCACATATTTAGTTATGAAT
1 AAAATCACATATATAGTTATGAAT
5598174 ATGTCCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (26 bp):
AAAATCACATATATAGTTATGAATCC
Found at i:5598677 original size:26 final size:26
Alignment explanation
Indices: 5598648--5598700 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
5598638 AGCAAAGTTG
*
5598648 TCCAAAATCACATATATGGTTATGAA
1 TCCAAAATCACATATATGATTATGAA
*
5598674 TCCAAAATCACATATTTGATTATGAA
1 TCCAAAATCACATATATGATTATGAA
5598700 T
1 T
5598701 ATGTCCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (26 bp):
TCCAAAATCACATATATGATTATGAA
Found at i:5599008 original size:12 final size:12
Alignment explanation
Indices: 5598991--5599020 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
5598981 ATTGAAAAGG
5598991 AAATATAATTAA
1 AAATATAATTAA
5599003 AAATATAATTAA
1 AAATATAATTAA
5599015 AAATAT
1 AAATAT
5599021 TTAACTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATATAATTAA
Found at i:5599082 original size:15 final size:16
Alignment explanation
Indices: 5599052--5599084 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5599042 ATATTAATGC
*
5599052 TATTTAATTTTTAAAA
1 TATTTAATTATTAAAA
5599068 TATTTAA-TATTAAAA
1 TATTTAATTATTAAAA
5599083 TA
1 TA
5599085 ACAGAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTTAATTATTAAAA
Found at i:5599102 original size:18 final size:18
Alignment explanation
Indices: 5599079--5599113 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5599069 ATTTAATATT
5599079 AAAATAACAGAAA-AATTC
1 AAAATAA-AGAAATAATTC
5599097 AAAATAAAGAAATAATT
1 AAAATAAAGAAATAATT
5599114 TATTTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.20
Consensus pattern (18 bp):
AAAATAAAGAAATAATTC
Found at i:5602471 original size:27 final size:26
Alignment explanation
Indices: 5602441--5602491 Score: 93
Period size: 27 Copynumber: 1.9 Consensus size: 26
5602431 TATAAACACA
5602441 GATAATAATATTTAATAAATTTTTTTG
1 GATAATAATATTTAAT-AATTTTTTTG
5602468 GATAATAATATTTAATAATTTTTT
1 GATAATAATATTTAATAATTTTTT
5602492 GACTCAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (26 bp):
GATAATAATATTTAATAATTTTTTTG
Found at i:5606533 original size:12 final size:11
Alignment explanation
Indices: 5606516--5606549 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
5606506 AAATAGGGAG
5606516 AAAATAGCAAA
1 AAAATAGCAAA
5606527 TAAAATAGCAAA
1 -AAAATAGCAAA
*
5606539 AAAGTAGCAAA
1 AAAATAGCAAA
5606550 CTTTTTTATC
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:0.68, C:0.09, G:0.12, T:0.12
Consensus pattern (11 bp):
AAAATAGCAAA
Found at i:5609313 original size:11 final size:11
Alignment explanation
Indices: 5609297--5609321 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5609287 TTTTATACTA
5609297 AATAAAAGAAT
1 AATAAAAGAAT
5609308 AATAAAAGAAT
1 AATAAAAGAAT
5609319 AAT
1 AAT
5609322 CTTGATGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (11 bp):
AATAAAAGAAT
Found at i:5610958 original size:27 final size:28
Alignment explanation
Indices: 5610921--5610974 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
5610911 AATTTGTAAC
*
5610921 GTTATTTGGTAAC-GTTTATTTTTAATA
1 GTTATTCGGTAACAGTTTATTTTTAATA
* *
5610948 GTTATTCGGTAACATTTTCTTTTTAAT
1 GTTATTCGGTAACAGTTTATTTTTAAT
5610975 TTGTAACGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.24, C:0.07, G:0.13, T:0.56
Consensus pattern (28 bp):
GTTATTCGGTAACAGTTTATTTTTAATA
Found at i:5613752 original size:6 final size:6
Alignment explanation
Indices: 5613737--5613765 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5613727 GATTGAGCAC
5613737 AAAA-A AAAAGA AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
5613766 GTTTACTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:5622875 original size:38 final size:38
Alignment explanation
Indices: 5622816--5622921 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
5622806 CATTTTTAAG
*
5622816 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
5622853 AATATGCATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
5622891 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
5622922 TACGTATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.35
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:5623314 original size:19 final size:17
Alignment explanation
Indices: 5623290--5623406 Score: 59
Period size: 16 Copynumber: 6.9 Consensus size: 17
5623280 TAATATTAGA
5623290 AAAATATATATAATAGTGT
1 AAAATATATATAATA-T-T
5623309 AAAATATAACTAATAATATT
1 AAAATAT-A-T-ATAATATT
*
5623329 AAAATATATACAATGA-T
1 AAAATATATATAAT-ATT
* * *
5623346 AATATATATAAAAGA-T
1 AAAATATATATAATATT
* *
5623362 -ATATGTATAT-ATAATT
1 AAAATATATATAAT-ATT
*
5623378 -ATATA-ATATAATATT
1 AAAATATATATAATATT
5623393 AAAATATA-ATAATA
1 AAAATATATATAATA
5623407 CGACATAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
14 1 0.01
15 16 0.20
16 19 0.24
17 17 0.21
18 2 0.03
19 8 0.10
20 9 0.11
21 2 0.03
22 6 0.08
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (17 bp):
AAAATATATATAATATT
Found at i:5623619 original size:3 final size:3
Alignment explanation
Indices: 5623604--5623645 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
5623594 AAGCATAAAC
* *
5623604 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5623646 CATTGGAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5623803 original size:6 final size:6
Alignment explanation
Indices: 5623761--5623794 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
5623751 ATAAAAATAT
*
5623761 ATACTA ATACATA ATAGTA ATACTA ATACTA ATA
1 ATACTA ATAC-TA ATACTA ATACTA ATACTA ATA
5623795 ATACTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (6 bp):
ATACTA
Found at i:5624295 original size:11 final size:11
Alignment explanation
Indices: 5624279--5624314 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
5624269 GAAAAAAAAA
5624279 GAAGAGAGAGG
1 GAAGAGAGAGG
*
5624290 GAAGAGAGAAG
1 GAAGAGAGAGG
5624301 GAAGAGAGAAGG
1 GAAGAGAG-AGG
5624313 GA
1 GA
5624315 GGGGGGAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAGG
Found at i:5624396 original size:15 final size:17
Alignment explanation
Indices: 5624376--5624412 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
5624366 AGGTAAAAAA
*
5624376 TTTATTTTTTGT-T-TT
1 TTTATTTGTTGTATATT
5624391 TTTATTTGTTGTATATT
1 TTTATTTGTTGTATATT
5624408 TTTAT
1 TTTAT
5624413 GTTAAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.58
16 1 0.05
17 7 0.37
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (17 bp):
TTTATTTGTTGTATATT
Found at i:5626846 original size:25 final size:25
Alignment explanation
Indices: 5626812--5626861 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5626802 ACTACAATAG
5626812 GTTAATTACTTGACATAATTTTCAC
1 GTTAATTACTTGACATAATTTTCAC
5626837 GTTAATTACTTGACATAATTTTCAC
1 GTTAATTACTTGACATAATTTTCAC
5626862 AAACTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (25 bp):
GTTAATTACTTGACATAATTTTCAC
Found at i:5632033 original size:99 final size:99
Alignment explanation
Indices: 5631751--5632047 Score: 312
Period size: 99 Copynumber: 3.0 Consensus size: 99
5631741 AGCTCAGCTT
* * * *
5631751 GAAGGCTACTTCCAATATGACCATTGAGA-TGATTTGTTTGAACTGAGTTAACCCTATGCTCCGA
1 GAAGGCTACTTCCAATATGACTATT-AAACTGATTTGCTTGAACTGAGTTAACCCTATGTTCCGA
* * *
5631815 GGAAACTGGTTGAGA-AGTATAAATTCCGTCTTCTG
65 GCAAACTGGTTGA-ACAGTATAAACTCCATCTTCTG
* * * * * * *
5631850 GAAGGCTATTTCTAATATGACTATTGAACTTATTTTCTTGAA-TCGAGTTAACCCTATATCCCGA
1 GAAGGCTACTTCCAATATGACTATTAAACTGATTTGCTTGAACT-GAGTTAACCCTATGTTCCGA
* * *
5631914 GCAAACCGATTGAACCGTATAAACTCCATCTTCTG
65 GCAAACTGGTTGAACAGTATAAACTCCATCTTCTG
* * * * *
5631949 GTAGGCTACTTCCAATATGATTATTAAACTGGTTTGCTTGAACTGAGTTAACCCTAGGTTCTGAG
1 GAAGGCTACTTCCAATATGACTATTAAACTGATTTGCTTGAACTGAGTTAACCCTATGTTCCGAG
* * * *
5632014 TAAATTGGTTGATCTGTATAAACTCCATCTTCTG
66 CAAACTGGTTGAACAGTATAAACTCCATCTTCTG
5632048 AGAGCCTTTC
Statistics
Matches: 159, Mismatches: 35, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
98 3 0.02
99 155 0.97
100 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (99 bp):
GAAGGCTACTTCCAATATGACTATTAAACTGATTTGCTTGAACTGAGTTAACCCTATGTTCCGAG
CAAACTGGTTGAACAGTATAAACTCCATCTTCTG
Found at i:5632137 original size:16 final size:16
Alignment explanation
Indices: 5632116--5632148 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5632106 AGTGTAATTT
5632116 AAATTATTTATATCTG
1 AAATTATTTATATCTG
5632132 AAATTATTTATATCTG
1 AAATTATTTATATCTG
5632148 A
1 A
5632149 TAGGCATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
AAATTATTTATATCTG
Found at i:5638373 original size:9 final size:10
Alignment explanation
Indices: 5638339--5638382 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
5638329 TAGTATTTGG
5638339 AAAATTTAAA
1 AAAATTTAAA
* *
5638349 ATGATTTTCAAA
1 A-AAATTT-AAA
5638361 AAAATTTAAA
1 AAAATTTAAA
5638371 AAAATTTAAA
1 AAAATTTAAA
5638381 AA
1 AA
5638383 TTAAATCGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 16 0.57
11 8 0.29
12 4 0.14
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:5640429 original size:96 final size:96
Alignment explanation
Indices: 5640314--5640506 Score: 386
Period size: 96 Copynumber: 2.0 Consensus size: 96
5640304 AGGTGAGAGG
5640314 CAAGCAAGTAAGGCAATACTTTTGTGTAGGTGACTTTAGTTTTAAATGTGGTTTAAAGGCAAGGT
1 CAAGCAAGTAAGGCAATACTTTTGTGTAGGTGACTTTAGTTTTAAATGTGGTTTAAAGGCAAGGT
5640379 GGGACTATACTTTGGGAATAGATTTTATAAA
66 GGGACTATACTTTGGGAATAGATTTTATAAA
5640410 CAAGCAAGTAAGGCAATACTTTTGTGTAGGTGACTTTAGTTTTAAATGTGGTTTAAAGGCAAGGT
1 CAAGCAAGTAAGGCAATACTTTTGTGTAGGTGACTTTAGTTTTAAATGTGGTTTAAAGGCAAGGT
5640475 GGGACTATACTTTGGGAATAGATTTTATAAA
66 GGGACTATACTTTGGGAATAGATTTTATAAA
5640506 C
1 C
5640507 TAATTGCGGA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (96 bp):
CAAGCAAGTAAGGCAATACTTTTGTGTAGGTGACTTTAGTTTTAAATGTGGTTTAAAGGCAAGGT
GGGACTATACTTTGGGAATAGATTTTATAAA
Found at i:5648951 original size:313 final size:310
Alignment explanation
Indices: 5648285--5649173 Score: 1138
Period size: 313 Copynumber: 2.9 Consensus size: 310
5648275 ATTTCACAAG
* * *
5648285 TTCATCATTTCGCATTCAATTATAATGTTTTTCTCATTTCCATAATCCAAGTTTATGACTGCCTT
1 TTCATCATTTCGC-TTCAATTATACTATTTTTCTCATTTTCATAATCCAAGTTTATGACTGCCTT
* * *
5648350 -CTCAACAATTTCGTCTCCAACATTCATACCTCCTTTAAATCGATAAATGACTAAATAAAATATA
65 AC-CAACAATGTCGTCTCCAACATTCATACCTCCCTTAAATCGATAAATGACTAAATGAAA-ATA
* * * *
5648414 ACTCTAAACATCAAAGTGGTTAAAAAAACT-------TAAGAAAATAGTATAATCTAGCTTAATC
128 ACTTTAGATATCAAAGTGGTTAAAAAAACTAACACAATAAGAAAA-AGTATAATTTAGCTTAATC
*
5648472 ATTAGTAAAAGCTTAATTACATTATACAAGAAAACTAAACCTCCAACTATACCAAAAATAACATC
192 ATTAGTAAAAGCTTAATTACATTATAAAAGAAAACTAAACCTCCAACTATACCAAAAATAACATC
* * * *
5648537 CTTAACGTCACATGATAAGTTCCATATTCAAATTTTACAAGTCCATGGATAACA
257 CATAACATCACATGATAAGTTCCAAATTCAAATGTTACAAGTCCATGGATAACA
* * *
5648591 TTCATCATTTCACCTTCAATTATACTATTTTTCTCATTTTGATAATCCAGGTTTATGACTGCCTT
1 TTCATCATTTC-GCTTCAATTATACTATTTTTCTCATTTTCATAATCCAAGTTTATGACTGCCTT
** *
5648656 ACCAACAATGTCGTCTCCAACATTCATACCTCCCCAAAATTGATAAATGACTAAATGAAACATAA
65 ACCAACAATGTCGTCTCCAACATTCATACCTCCCTTAAATCGATAAATGACTAAATGAAA-ATAA
* * *
5648721 CTTTAGATATAAAAGTGGTTAAAAAAACTAACACAATAAGAAAACGGTATAATTTAGCTTAATTA
129 CTTTAGATATCAAAGTGGTTAAAAAAACTAACACAATAAGAAAA-AGTATAATTTAGCTTAATCA
** * * *
5648786 TTAAAAAAAGCTTAATCACATTATAAAAGAAAACTACACCTCCAATTATACCAAAAA-AACATCC
193 TTAGTAAAAGCTTAATTACATTATAAAAGAAAACTAAACCTCCAACTATACCAAAAATAACATCC
* *
5648850 ATAACATCACATGATAAGTTCGAAATTCAAATGTTACAAGTCTATGGATAACA
258 ATAACATCACATGATAAGTTCCAAATTCAAATGTTACAAGTCCATGGATAACA
* * * * *
5648903 TTCATTATTTCGTCTTCAATTATACCTTTTTTTCTCGTTTTCATAATCCAAATTTATGACTACAC
1 TTCATCATTTCG-CTTCAATTATA-CTATTTTTCTCATTTTCATAATCCAAGTTTATGACTGC-C
* * *
5648968 -TACCAACAATGTTGTCTGCAACATTCGTACCTCCCTTAAATCGATAAATGACTAAATGAAAAGT
63 TTACCAACAATGTCGTCTCCAACATTCATACCTCCCTTAAATCGATAAATGACTAAATGAAAA-T
* * *
5649032 AACTTTAGATATCAAAGTGGCTT-TAAAAATTAACACAATAA-AAAAAGTATAATTTAACTTAAT
127 AACTTTAGATATCAAAGTGG-TTAAAAAAACTAACACAATAAGAAAAAGTATAATTTAGCTTAAT
* * * *
5649095 CATTAGTAAAA-CTTTAATTATATTATAATAGAAAACTAAACTTCTAACTATACCAAAAATAACA
191 CATTAGTAAAAGC-TTAATTACATTATAAAAGAAAACTAAACCTCCAACTATACCAAAAATAACA
* *
5649159 TCAACAACATCACAT
255 TCCATAACATCACAT
5649174 AATATTGGAA
Statistics
Matches: 503, Mismatches: 64, Indels: 26
0.85 0.11 0.04
Matches are distributed among these distances:
306 138 0.27
307 2 0.00
310 1 0.00
311 63 0.13
312 97 0.19
313 199 0.40
314 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (310 bp):
TTCATCATTTCGCTTCAATTATACTATTTTTCTCATTTTCATAATCCAAGTTTATGACTGCCTTA
CCAACAATGTCGTCTCCAACATTCATACCTCCCTTAAATCGATAAATGACTAAATGAAAATAACT
TTAGATATCAAAGTGGTTAAAAAAACTAACACAATAAGAAAAAGTATAATTTAGCTTAATCATTA
GTAAAAGCTTAATTACATTATAAAAGAAAACTAAACCTCCAACTATACCAAAAATAACATCCATA
ACATCACATGATAAGTTCCAAATTCAAATGTTACAAGTCCATGGATAACA
Found at i:5649807 original size:36 final size:36
Alignment explanation
Indices: 5649760--5649883 Score: 194
Period size: 36 Copynumber: 3.4 Consensus size: 36
5649750 ATCGTTTACG
*
5649760 GTACTATTCACGTATATGGCACTATTCATGTATACA
1 GTACTATTCACGTATATGGCACTATTCACGTATACA
* *
5649796 GTACTATTCACGTTTATGGCACTATTCACGTATACG
1 GTACTATTCACGTATATGGCACTATTCACGTATACA
* *
5649832 GTACTATTCACATATACGGCACTATTCACGTATACA
1 GTACTATTCACGTATATGGCACTATTCACGTATACA
*
5649868 GTACTGTTCACGTATA
1 GTACTATTCACGTATA
5649884 CAGTAGTTGG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 79 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (36 bp):
GTACTATTCACGTATATGGCACTATTCACGTATACA
Found at i:5649888 original size:18 final size:18
Alignment explanation
Indices: 5649756--5649884 Score: 159
Period size: 18 Copynumber: 7.2 Consensus size: 18
5649746 TACGATCGTT
5649756 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* * *
5649774 TATGGCACTATTCATGTA
1 TACGGTACTATTCACGTA
* *
5649792 TACAGTACTATTCACGTT
1 TACGGTACTATTCACGTA
* *
5649810 TATGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
5649828 TACGGTACTATTCACATA
1 TACGGTACTATTCACGTA
*
5649846 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
5649864 TACAGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
5649882 TAC
1 TAC
5649885 AGTAGTTGGG
Statistics
Matches: 91, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 91 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:5661663 original size:56 final size:56
Alignment explanation
Indices: 5661571--5661681 Score: 127
Period size: 56 Copynumber: 2.0 Consensus size: 56
5661561 TAGAGTATTC
* ** * *
5661571 TAATTATATTTTTTAATTTTAGTGTAAACGAGAATTAAAATA-ATTACATTTAAATG
1 TAATTATATTTTTTAATATTAAAGTAAACAAGAATTAAAATATATAAC-TTTAAATG
* *
5661627 TAATTAT-TTTTTTAATATTAAAGTAAAACAATAATTAATATATATAACTTTAAAT
1 TAATTATATTTTTTAATATTAAAGT-AAACAAGAATTAAAATATATAACTTTAAAT
5661682 TATTAAAGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
55 14 0.30
56 28 0.61
57 4 0.09
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (56 bp):
TAATTATATTTTTTAATATTAAAGTAAACAAGAATTAAAATATATAACTTTAAATG
Found at i:5669302 original size:20 final size:20
Alignment explanation
Indices: 5669277--5669318 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5669267 AAAAACTAAG
5669277 AAAATAGTATAATTTAGCTT
1 AAAATAGTATAATTTAGCTT
5669297 AAAATAGTATAATTTAGCTT
1 AAAATAGTATAATTTAGCTT
5669317 AA
1 AA
5669319 TCATTAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.38
Consensus pattern (20 bp):
AAAATAGTATAATTTAGCTT
Found at i:5669335 original size:18 final size:19
Alignment explanation
Indices: 5669312--5669350 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
5669302 AGTATAATTT
5669312 AGCTTAA-T-CATTAGTAAA
1 AGCTTAATTACATTA-TAAA
5669330 AGCTTAATTACATTATAAA
1 AGCTTAATTACATTATAAA
5669349 AG
1 AG
5669351 AAAACTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (19 bp):
AGCTTAATTACATTATAAA
Found at i:5669698 original size:312 final size:309
Alignment explanation
Indices: 5669302--5670025 Score: 1044
Period size: 312 Copynumber: 2.3 Consensus size: 309
5669292 AGCTTAAAAT
*
5669302 AGTATAATTTAGCTTAATCATTAGTAAAAGCTTAATTACATTATAAAAGAAAACTAAACCTCCAA
1 AGTATAATTTAGCTTAATCATTAGTAAAAGCTTAATTATATTAT-AAAGAAAACTAAACCTCCAA
*
5669367 CTATACCAAAAATAACATCCATAACATCACATGATAAGTTCAAAATTCAAATTTTACAAGTCCAT
65 CTATACCAAAAATAACATCCATAACATCACATGATAAGTTCAAAATTCAAATTTCACAAGTCCAT
* * * *
5669432 GGATAACATTCATCATTTCACCTTCAACTATACTATTTTTCTCATTTTGATAATCCAGGTTTAT-
130 AGATAACATTCATCATTTCGCCTTCAATTATACTATTTTTCTCATTTTCATAATCCAGGTTTATG
* * *
5669496 ACCTGCCCTACCAACAATGTCATCTCCAACAGTCGTACCTCCCCTCAATTGATAAATGACTAAAT
195 A-CTGCCCTACCAACAATGTCGTCTCCAACATTCGTACCTCCCCTAAATTGATAAATGACTAAAT
*
5669561 GAAATGTAACTTTAGATATAAAAGTGGTTAAAAAATTAACACAATAAGAAA
259 GAAATGTAACTTTAGATATCAAAGTGGTTAAAAAATTAACACAATAAGAAA
5669612 ACGGTATAATTTAGCTTAATCATTAG-AAAAGGCTTAATTATATTATAAAGGAAAACTAAACCTC
1 A--GTATAATTTAGCTTAATCATTAGTAAAA-GCTTAATTATATTATAAA-GAAAACTAAACCTC
* ** *
5669676 CAATTATACCAAAAATAACATCCATAACATCACATGATAAGTTTGAAATTCAAATTTCACAATTC
62 CAACTATACCAAAAATAACATCCATAACATCACATGATAAGTTCAAAATTCAAATTTCACAAGTC
* * **
5669741 CTTAGATAACATTCATCATTTTGCCTTCAATTATACT-TCTTTTCTCATTTTCATAATCCAAATT
127 CATAGATAACATTCATCATTTCGCCTTCAATTATACTAT-TTTTCTCATTTTCATAATCCAGGTT
* * * ***
5669805 TATGACTACTCTACCAACAATGTTGTCTCCAACATTCGTACCTCCCCTAAACCAATAAATGACTA
191 TATGACTGCCCTACCAACAATGTCGTCTCCAACATTCGTACCTCCCCTAAATTGATAAATGACTA
* **
5669870 AATGAAAAGTAACTTTAGATATCAAAGTGGTTTTCAAAATTAACACAATAA-AAA
256 AATGAAATGTAACTTTAGATATCAAAGTGG-TTAAAAAATTAACACAATAAGAAA
* *
5669924 AGTACAATTTAGCTTAATCATTAGTAAAA-CTTTAATTATATTATAATAGAAAACTAAACTTCCA
1 AGTATAATTTAGCTTAATCATTAGTAAAAGC-TTAATTATATTATAA-AGAAAACTAAACCTCCA
* *
5669988 ACTATACCAAAAATAACATCGATAACATCACATAATAA
64 ACTATACCAAAAATAACATCCATAACATCACATGATAA
5670026 TGTCATTTTT
Statistics
Matches: 372, Mismatches: 32, Indels: 20
0.88 0.08 0.05
Matches are distributed among these distances:
309 1 0.00
310 88 0.24
311 13 0.03
312 251 0.67
313 19 0.05
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (309 bp):
AGTATAATTTAGCTTAATCATTAGTAAAAGCTTAATTATATTATAAAGAAAACTAAACCTCCAAC
TATACCAAAAATAACATCCATAACATCACATGATAAGTTCAAAATTCAAATTTCACAAGTCCATA
GATAACATTCATCATTTCGCCTTCAATTATACTATTTTTCTCATTTTCATAATCCAGGTTTATGA
CTGCCCTACCAACAATGTCGTCTCCAACATTCGTACCTCCCCTAAATTGATAAATGACTAAATGA
AATGTAACTTTAGATATCAAAGTGGTTAAAAAATTAACACAATAAGAAA
Found at i:5673038 original size:12 final size:13
Alignment explanation
Indices: 5673015--5673041 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5673005 GATGAGAGGC
5673015 TTAGATTTTTTTT
1 TTAGATTTTTTTT
5673028 TTAGATTTTTTTT
1 TTAGATTTTTTTT
5673041 T
1 T
5673042 GTTTGAGGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (13 bp):
TTAGATTTTTTTT
Found at i:5673313 original size:25 final size:25
Alignment explanation
Indices: 5673282--5673408 Score: 148
Period size: 26 Copynumber: 5.0 Consensus size: 25
5673272 TTTTATCATC
5673282 ATTTATTTTAAGTTTTATATATATT
1 ATTTATTTTAAGTTTTATATATATT
5673307 ATTTATTTTAAGTTTTATATATATT
1 ATTTATTTTAAGTTTTATATATATT
*
5673332 ATTTATTTTAAGCTGTTT-TACATATT
1 ATTTATTTTAAG-T-TTTATATATATT
* * * *
5673358 ATTTATTTAAATTTCTTTTATATGTT
1 ATTTATTTTAAGTT-TTATATATATT
* *
5673384 ATTTATTGTAAATTATTATATATAT
1 ATTTATTTTAAGTT-TTATATATAT
5673409 ATCTTTCAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.01
25 40 0.46
26 43 0.49
27 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.61
Consensus pattern (25 bp):
ATTTATTTTAAGTTTTATATATATT
Found at i:5673496 original size:38 final size:39
Alignment explanation
Indices: 5673454--5673551 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 39
5673444 TATATGTTAT
*
5673454 TTTTTATTATTTATTTTAAATTGTTTTATTGT-TTTG-TA-
1 TTTTTATTATTTATTTT-AATTGTTTTATT-TATTTGAAAC
* *
5673492 TTTTTAGT-TTT-TTTT-A-TGTTTTGTTTATTTGAAAC
1 TTTTTATTATTTATTTTAATTGTTTTATTTATTTGAAAC
5673527 TTTTTATTATTTATTTTGAATTGTT
1 TTTTTATTATTTATTTT-AATTGTT
5673552 CTTACAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
32 1 0.02
33 12 0.25
34 2 0.04
35 7 0.15
36 7 0.15
37 7 0.15
38 7 0.15
39 1 0.02
40 4 0.08
ACGTcount: A:0.19, C:0.01, G:0.09, T:0.70
Consensus pattern (39 bp):
TTTTTATTATTTATTTTAATTGTTTTATTTATTTGAAAC
Found at i:5674176 original size:15 final size:16
Alignment explanation
Indices: 5674158--5674192 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5674148 AAAATATTTC
*
5674158 AAAAAAA-AGGAAAAG
1 AAAAAAAGAGAAAAAG
5674173 AAAAAAAGAGAAAAAG
1 AAAAAAAGAGAAAAAG
5674189 AAAA
1 AAAA
5674193 GGAAAGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAGAAAAAG
Found at i:5675156 original size:44 final size:44
Alignment explanation
Indices: 5675093--5675309 Score: 123
Period size: 44 Copynumber: 4.7 Consensus size: 44
5675083 CATGGTGAAT
* *
5675093 CTTATTTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGC
* * * * * * **
5675137 CTTATCTTCCTGAAGTTGCAGCGGAGCAAACTGAAGACAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CCAGC
* * * * **
5675182 CTTATGTCCCTGACGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC--C--ACCA--GC
* * *
5675232 GGATCTTATCTTCCTGAAGTTACAGTGGAGTAGATTGAAGCCACCAG-
1 ----CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGC
*
5675279 CTTAATCTCCCT-ACAGTTGCAGCGGAGCAGA
1 CTT-ATCTCCCTGA-AGTTGCAGTGGAGCAGA
5675310 CTAAGGACAG
Statistics
Matches: 124, Mismatches: 36, Indels: 26
0.67 0.19 0.14
Matches are distributed among these distances:
43 4 0.03
44 53 0.43
45 30 0.24
47 1 0.01
48 2 0.02
49 1 0.01
50 2 0.02
52 1 0.01
54 30 0.24
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGC
Found at i:5675349 original size:143 final size:141
Alignment explanation
Indices: 5675091--5675546 Score: 595
Period size: 143 Copynumber: 3.2 Consensus size: 141
5675081 ATCATGGTGA
*
5675091 ATCTTAT-TTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTTCCTGAAGTTG
1 ATCTTATCTT-CCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAG-CTTATCTCCCT-AAGTTG
* * * * *
5675155 CAGCGGAGCAAACTGAAGACAGCGAATCTTATGTCCCTGACGTTGCAGTGGAACAGATTAAAGCT
63 CAGCGGAGCAGACTGAAGACAGTGAATCTTATTTCCCTGAAGTTGTAGTGGAACAGATTAAAGCT
5675220 ACAAATTATGGCGG
128 ACAAATTATGGCGG
* * *
5675234 ATCTTATCTTCCTGAAGTTACAGTGGAGTAGATTGAAGCCACCAGCTTAATCTCCCTACAGTTGC
1 ATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCTT-ATCTCCCTA-AGTTGC
* ** *
5675299 AGCGGAGCAGACT-AAGGACAGTGAATCTCATTTCCCTGGTGTTGTAGTGGAACATATTAAAGCT
64 AGCGGAGCAGACTGAA-GACAGTGAATCTTATTTCCCTGAAGTTGTAGTGGAACAGATTAAAGCT
5675363 ACAAATTATGGCGG
128 ACAAATTATGGCGG
* *
5675377 ATCTTATCTTCCTTAAGTTGCAGTGGAGCAGATTGAAGCCAGC--CTTATCTCCCTAAAGTTGCA
1 ATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCTTATCTCCCT-AAGTTGCA
* * * *
5675440 GCGGAGTAGACTGAAGACAGTAAATCTTATTTCCTTGAAGTTGTAGTGGAACAGATTAAAGCTAT
65 GCGGAGCAGACTGAAGACAGTGAATCTTATTTCCCTGAAGTTGTAGTGGAACAGATTAAAGCTAC
5675505 AAATTA---CGG
130 AAATTATGGCGG
**
5675514 ATCTTATC-TCTCTAAAGTTGCAGTAAAGCAGAT
1 ATCTTATCTTC-CTAAAGTTGCAGTGGAGCAGAT
5675547 CATATCAAAC
Statistics
Matches: 279, Mismatches: 27, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
136 2 0.01
137 30 0.11
140 75 0.27
141 6 0.02
142 6 0.02
143 158 0.57
144 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (141 bp):
ATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCTTATCTCCCTAAGTTGCAG
CGGAGCAGACTGAAGACAGTGAATCTTATTTCCCTGAAGTTGTAGTGGAACAGATTAAAGCTACA
AATTATGGCGG
Found at i:5675709 original size:44 final size:44
Alignment explanation
Indices: 5675603--5675817 Score: 191
Period size: 44 Copynumber: 4.8 Consensus size: 44
5675593 ATAAACCAAT
* * *
5675603 CTTATCTCCCTGAAGTTGTAGTGGAGCAGATAGAAGATGGGCTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-TAA-A---GCTACAAAC
* *
5675652 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAC
* * * * *
5675696 CTTATCTCCCTGAAGTT-CAGTAGAGCAGGTTAAAGATACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAC
* * * * *
5675739 CTTATCTCTCTAAAGTTGTAGTGGAGCAGATTGAAGCTACTAATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC-AAAC
* * * *
5675784 C-TATTTTCTTGAAGTTGCAGTGGAGCAGACTAAA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
5675818 ACAGTGAATC
Statistics
Matches: 134, Mismatches: 30, Indels: 9
0.77 0.17 0.05
Matches are distributed among these distances:
43 34 0.25
44 66 0.49
45 2 0.01
47 1 0.01
48 2 0.01
49 29 0.22
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAC
Found at i:5675797 original size:87 final size:88
Alignment explanation
Indices: 5675649--5675811 Score: 204
Period size: 87 Copynumber: 1.9 Consensus size: 88
5675639 ATGGGCTACA
* *
5675649 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCACAAACCTTATCTCCCTGAAGTT-
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTG
5675713 CAGTAGAGCAGGTTAAAGATACC
66 CAGTAGAGCAGGTTAAAGATACC
* * * * * * * *
5675736 AATCTTATCTCTCTAAAGTTGTAGTGGAGCAGATTGAAGCTACTAATCC-TATTTTCTTGAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAC-AAACCTTATCTCCCTGAAGTT
*
5675800 GCAGTGGAGCAG
65 GCAGTAGAGCAG
5675812 ACTAAAACAG
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
87 49 0.78
88 14 0.22
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (88 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTG
CAGTAGAGCAGGTTAAAGATACC
Found at i:5677436 original size:26 final size:26
Alignment explanation
Indices: 5677387--5677455 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
5677377 AGTTTTATAT
* * *
5677387 ATATTATTTATTTTAAGCTGTTTTCC
1 ATATTATTTATTTAAAGCTCTTTTAC
** *
5677413 ATATTATTTATTTAAATTTCTTTTAT
1 ATATTATTTATTTAAAGCTCTTTTAC
*
5677439 ATGTTATTTATTGTAAA
1 ATATTATTTATT-TAAA
5677456 CTATTATATA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
26 31 0.89
27 4 0.11
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (26 bp):
ATATTATTTATTTAAAGCTCTTTTAC
Found at i:5677486 original size:17 final size:17
Alignment explanation
Indices: 5677464--5677497 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5677454 AACTATTATA
*
5677464 TATATATCTTTCAAATT
1 TATATATATTTCAAATT
*
5677481 TATATATATTTTAAATT
1 TATATATATTTCAAATT
5677498 GTTTTATATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATATATTTCAAATT
Found at i:5677486 original size:19 final size:17
Alignment explanation
Indices: 5677462--5677497 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
5677452 TAAACTATTA
5677462 TATATATATCTTTCAAATT
1 TATATATAT-TTT-AAATT
5677481 TATATATATTTTAAATT
1 TATATATATTTTAAATT
5677498 GTTTTATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 9 0.53
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATATATTTTAAATT
Found at i:5677527 original size:25 final size:24
Alignment explanation
Indices: 5677499--5677562 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
5677489 TTTTAAATTG
*
5677499 TTTTATATGTTTTTTTCTTTATTTA
1 TTTTATATGTTTTTTT-GTTATTTA
* *
5677524 TTTTAAATTGTTTTATTGTTATTTA
1 TTTTATA-TGTTTTTTTGTTATTTA
5677549 TTTT-TA-GTTTTTTT
1 TTTTATATGTTTTTTT
5677563 ATATTTTGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
22 7 0.21
24 1 0.03
25 17 0.52
26 8 0.24
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (24 bp):
TTTTATATGTTTTTTTGTTATTTA
Found at i:5677563 original size:25 final size:25
Alignment explanation
Indices: 5677517--5677607 Score: 73
Period size: 25 Copynumber: 3.8 Consensus size: 25
5677507 GTTTTTTTCT
5677517 TTATTTATTTTAAATTGTTTTATTG
1 TTATTTATTTTAAATTGTTTTATTG
* * * *
5677542 TTATTTATTTTTAGTTTTTTTATATT
1 TTATTTATTTTAAATTGTTTTAT-TG
* * *
5677568 TTGTTTATTTGAAACT-TTTTA---
1 TTATTTATTTTAAATTGTTTTATTG
*
5677589 TTATTTATTTTGAATTGTT
1 TTATTTATTTTAAATTGTT
5677608 CTTACAAATC
Statistics
Matches: 51, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
21 12 0.24
22 2 0.04
25 25 0.49
26 12 0.24
ACGTcount: A:0.22, C:0.01, G:0.08, T:0.69
Consensus pattern (25 bp):
TTATTTATTTTAAATTGTTTTATTG
Found at i:5680885 original size:99 final size:98
Alignment explanation
Indices: 5680642--5680935 Score: 295
Period size: 99 Copynumber: 3.0 Consensus size: 98
5680632 CATCTTCGAG
* * * * * *
5680642 GCTACTTCCAACATGACCGTT-AAGTGTTTTTTCTTGAAGTGAGTTAACCTTACACTCCTAGTAA
1 GCTACTTCCAATATGACCGTTAAATTG-ATTTTCTTGAACTGAGTTAACCCTACACTCCAAGTAA
* * * *
5680706 ACCGATTTAGCTATATAAACTCCATCTTTTGGGAG
65 ACCGATTAAG-TTTATAAACTCCATCTTTTGGAAA
* * *** * ** *
5680741 GCTACTTCCAATATGACCATTGAGATT-ATTGAATTGAACTAAGTTAACCCTACGTTTCAAGTAA
1 GCTACTTCCAATATGACCGTT-AAATTGATTTTCTTGAACTGAGTTAACCCTACACTCCAAGTAA
* * *
5680805 ATCGATTGAGTTGTATATACTCCATCTTTTGGAAA
65 ACCGATTAAGTT-TATAAACTCCATCTTTTGGAAA
* * * *
5680840 GCTACTTCCAATATGACTGTTAAATTGATTTTCTTCAACTGAGTTAACCCTGCACTCCGAGTAAA
1 GCTACTTCCAATATGACCGTTAAATTGATTTTCTTGAACTGAGTTAACCCTACACTCCAAGTAAA
5680905 CCGATTAAGTCTTATAAACTCCATCTTTTGG
66 CCGATTAAGT-TTATAAACTCCATCTTTTGG
5680936 GAGCATTTCT
Statistics
Matches: 153, Mismatches: 37, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
98 5 0.03
99 145 0.95
100 1 0.01
101 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (98 bp):
GCTACTTCCAATATGACCGTTAAATTGATTTTCTTGAACTGAGTTAACCCTACACTCCAAGTAAA
CCGATTAAGTTTATAAACTCCATCTTTTGGAAA
Found at i:5689231 original size:4 final size:4
Alignment explanation
Indices: 5689217--5689248 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
5689207 TTAATTGAGA
5689217 AATT AATTT AATT AATT AATT AATT AATT AAT
1 AATT AA-TT AATT AATT AATT AATT AATT AAT
5689249 ATTTTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:5690048 original size:21 final size:21
Alignment explanation
Indices: 5690024--5690067 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5690014 GAGGTCAAGG
* *
5690024 GGCATTAGAAGAGCTAGTCTA
1 GGCATAAGAAGAGCTAGGCTA
*
5690045 GGCATAAGAGGAGCTAGGCTA
1 GGCATAAGAAGAGCTAGGCTA
5690066 GG
1 GG
5690068 TTAATTGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.14, G:0.36, T:0.18
Consensus pattern (21 bp):
GGCATAAGAAGAGCTAGGCTA
Found at i:5693782 original size:3 final size:3
Alignment explanation
Indices: 5693774--5693808 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5693764 ATACAGATGT
5693774 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
5693809 CAAAGGAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5695869 original size:120 final size:121
Alignment explanation
Indices: 5695725--5695968 Score: 481
Period size: 121 Copynumber: 2.0 Consensus size: 121
5695715 ATTTTATCTA
5695725 TTTAACTCAAAAAACTTTAATATTTATAAAAATGAATTTAATTT-AAAATATTTATTAAAATAAT
1 TTTAACTCAAAAAACTTTAATATTTATAAAAATGAATTTAATTTAAAAATATTTATTAAAATAAT
5695789 TTGAAATGAACAGTAAATTTAAGTTTTAAGAACCCAATGGCCGACACTACTTAGTG
66 TTGAAATGAACAGTAAATTTAAGTTTTAAGAACCCAATGGCCGACACTACTTAGTG
5695845 TTTAACTCAAAAAACTTTAATATTTATAAAAATGAATTTAATTTAAAAATATTTATTAAAATAAT
1 TTTAACTCAAAAAACTTTAATATTTATAAAAATGAATTTAATTTAAAAATATTTATTAAAATAAT
5695910 TTGAAATGAACAGTAAATTTAAGTTTTAAGAACCCAATGGCCGACACTACTTAGTG
66 TTGAAATGAACAGTAAATTTAAGTTTTAAGAACCCAATGGCCGACACTACTTAGTG
5695966 TTT
1 TTT
5695969 TGGCCCCATT
Statistics
Matches: 123, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
120 44 0.36
121 79 0.64
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (121 bp):
TTTAACTCAAAAAACTTTAATATTTATAAAAATGAATTTAATTTAAAAATATTTATTAAAATAAT
TTGAAATGAACAGTAAATTTAAGTTTTAAGAACCCAATGGCCGACACTACTTAGTG
Found at i:5699147 original size:87 final size:84
Alignment explanation
Indices: 5699049--5699326 Score: 234
Period size: 90 Copynumber: 3.1 Consensus size: 84
5699039 AATATTTAAT
* * * *
5699049 AAAAAGTATATAATTCGAATAAGTAATAGTACGCAAAAAATTAAATTTACAGATACAATAAAATA
1 AAAAA-TATA-AATTC-AATAA-TAATAATACGCAATAAATTAAATTTACACATACAAAAAAATA
5699114 CAAACATTCTACAATATTAATACAC
62 CAAACATTCTA-AA-ATTAATACAC
* * * * ** * *
5699139 AAAAATATAAAATTCAAAAAAAATAATACGCACTAAATTAAATTTAAACACCCAACAAACTACAA
1 AAAAATAT-AAATTCAATAATAATAATACGCAATAAATTAAATTTACACATACAAAAAAATACAA
**
5699204 ACAGATGGGTAAAATTAATACAC
65 AC--AT-TCTAAAATTAATACAC
* * * *
5699227 GAAAATTTTAAATTCAAACTACAT-ATAATACGGAATAAATTAAATTTACATATACAAAAAAATA
1 -AAAAATATAAATTC-AA-TA-ATAATAATACGCAATAAATTAAATTTACACATACAAAAAAATA
5699291 CAAACATTCTAAGAAATTAATACAC
62 CAAACATTCT-A-AAATTAATACAC
*
5699316 GAAAATATAAA
1 AAAAATATAAA
5699327 AATGAAACCT
Statistics
Matches: 148, Mismatches: 30, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
87 38 0.26
88 31 0.21
89 32 0.22
90 46 0.31
91 1 0.01
ACGTcount: A:0.56, C:0.13, G:0.06, T:0.25
Consensus pattern (84 bp):
AAAAATATAAATTCAATAATAATAATACGCAATAAATTAAATTTACACATACAAAAAAATACAAA
CATTCTAAAATTAATACAC
Found at i:5699166 original size:90 final size:86
Alignment explanation
Indices: 5699078--5699327 Score: 250
Period size: 90 Copynumber: 2.8 Consensus size: 86
5699068 TAAGTAATAG
* * * *
5699078 TACGCAAAAAATTAAATTTACAGATACAATAAAATACAAACATTCTACAATATTAATACACAAAA
1 TACGCAATAAATTAAATTTACACATACAAAAAAATACAAACATTCTA-AA-ATTAATACACGAAA
5699143 ATATAAAATTCAAAAAAAATA-A
64 ATATAAAATTCAAAAAAAATATA
* * ** * * **
5699165 TACGCACTAAATTAAATTTAAACACCCAACAAACTACAAACAGATGGGTAAAATTAATACACGAA
1 TACGCAATAAATTAAATTTACACATACAAAAAAATACAAAC--AT-TCTAAAATTAATACACGAA
* * ** *
5699230 AATTTTAAATTCAAACTACATATAA
63 AATATAAAATTCAAAAAAAATAT-A
* *
5699255 TACGGAATAAATTAAATTTACATATACAAAAAAATACAAACATTCTAAGAAATTAATACACGAAA
1 TACGCAATAAATTAAATTTACACATACAAAAAAATACAAACATTCT-A-AAATTAATACACGAAA
5699320 ATATAAAA
64 ATATAAAA
5699328 ATGAAACCTT
Statistics
Matches: 128, Mismatches: 28, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
87 34 0.27
88 32 0.25
89 26 0.20
90 36 0.28
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.24
Consensus pattern (86 bp):
TACGCAATAAATTAAATTTACACATACAAAAAAATACAAACATTCTAAAATTAATACACGAAAAT
ATAAAATTCAAAAAAAATATA
Found at i:5699711 original size:27 final size:28
Alignment explanation
Indices: 5699671--5699747 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 28
5699661 AATTCGATTG
*
5699671 TACACTACGAAAAACTCTCATTT-ACAA
1 TACACTACAAAAAACTCTCATTTGACAA
* * **
5699698 TCCACTACAAAAAA-ACTCATTTGATGA
1 TACACTACAAAAAACTCTCATTTGACAA
* *
5699725 TATACTACAAAATACTCTCATTT
1 TACACTACAAAAAACTCTCATTT
5699748 TGATGGCTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
26 7 0.18
27 25 0.64
28 7 0.18
ACGTcount: A:0.43, C:0.23, G:0.04, T:0.30
Consensus pattern (28 bp):
TACACTACAAAAAACTCTCATTTGACAA
Found at i:5700160 original size:109 final size:106
Alignment explanation
Indices: 5699956--5700165 Score: 253
Period size: 109 Copynumber: 2.0 Consensus size: 106
5699946 ACTTGGTGCC
* * *
5699956 GGCCGGCACCCAATTTTTTTTAAATACACTGGTGCCAGCCATCAGTATTCCAAAATAAAAAAATG
1 GGCCGGCACCCAATTTTTTTTAAATACACTAGTGCCAGCCATCAGTATCCCAAAAAAAAAAAATG
* * *
5700021 CATTGGAAGCCGAAAATTGTACTTGGTGCCGACCATGTAAT
66 CATTGGAAGCCGAAAATTATACCTGCTGCCGACCATGTAAT
* * * * *
5700062 GGCCGTCACCTAATTTTTTTTTAAATATACTAGTGCC-GACCATTAGTGTCCCAAAGTAAAAAAA
1 GGCCGGCACCCAA-TTTTTTTTAAATACACTAGTGCCAG-CCATCAGTATCCCAAA--AAAAAAA
*
5700126 AATGCATTGGGAA-CCGAAAATTATACCTGCTGCCGGCCAT
62 AATGCATT-GGAAGCCGAAAATTATACCTGCTGCCGACCAT
5700166 TTACTGCCAA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
106 12 0.14
107 34 0.39
109 37 0.43
110 4 0.05
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (106 bp):
GGCCGGCACCCAATTTTTTTTAAATACACTAGTGCCAGCCATCAGTATCCCAAAAAAAAAAAATG
CATTGGAAGCCGAAAATTATACCTGCTGCCGACCATGTAAT
Found at i:5700571 original size:14 final size:15
Alignment explanation
Indices: 5700548--5700595 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
5700538 TAAATTTAAA
5700548 TTTTAGTTTTGATAT
1 TTTTAGTTTTGATAT
* *
5700563 TTTTA-TTTTCATAA
1 TTTTAGTTTTGATAT
5700577 TTTTAGTTTTGATAT
1 TTTTAGTTTTGATAT
5700592 TTTT
1 TTTT
5700596 TAGATTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.69
Consensus pattern (15 bp):
TTTTAGTTTTGATAT
Found at i:5702261 original size:24 final size:24
Alignment explanation
Indices: 5702229--5702288 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
5702219 GCGAAAGGTC
* *
5702229 ATTTTTTTATTTTCTTTATTTTCG
1 ATTTTTTTATTTTCTTTATATTCA
*** *
5702253 ATTTTTTTAAACTGTTTATATTCA
1 ATTTTTTTATTTTCTTTATATTCA
5702277 ATTTTTTTATTT
1 ATTTTTTTATTT
5702289 CCCTTTGTTT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (24 bp):
ATTTTTTTATTTTCTTTATATTCA
Found at i:5703039 original size:12 final size:14
Alignment explanation
Indices: 5703022--5703060 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
5703012 TACTTTATGT
5703022 TTTTATTATTA-C-
1 TTTTATTATTATCA
5703034 TTTTATTATTATCA
1 TTTTATTATTATCA
5703048 TTTTATTTATTAT
1 TTTTA-TTATTAT
5703061 TTATTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.46
13 1 0.04
14 5 0.21
15 7 0.29
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTATTATCA
Found at i:5703044 original size:15 final size:15
Alignment explanation
Indices: 5703023--5703085 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 15
5703013 ACTTTATGTT
5703023 TTTATTATTACTTTTA
1 TTTATTATTA-TTTTA
*
5703039 -TTATTATCATTTTA
1 TTTATTATTATTTTA
5703053 TTTATTATTTATTTATA
1 TTTATTA-TTATTT-TA
*
5703070 TCTTTTTATATATTTT
1 T-TTATTAT-TATTTT
5703086 TAAACTCTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 5 0.13
15 14 0.36
16 5 0.13
17 5 0.13
18 10 0.26
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTATTATTTTA
Found at i:5703071 original size:25 final size:27
Alignment explanation
Indices: 5703022--5703087 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 27
5703012 TACTTTATGT
5703022 TTTTA-TTATTACTTT-TATTATTATCA
1 TTTTATTTATTA-TTTATATTATTATCA
*
5703048 TTTTATTTATTATTTAT-TTA-TATCT
1 TTTTATTTATTATTTATATTATTATCA
*
5703073 TTTTATATATT-TTTA
1 TTTTATTTATTATTTA
5703088 AACTCTAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
24 4 0.11
25 14 0.39
26 11 0.31
27 7 0.19
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTATTTATTATTTATATTATTATCA
Found at i:5710213 original size:6 final size:6
Alignment explanation
Indices: 5710198--5710249 Score: 81
Period size: 6 Copynumber: 8.8 Consensus size: 6
5710188 ACTTCACTTG
5710198 AAAA-A AAAAGA AAAAGA AAAAGA AAATAGA AAAA-A AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAA-AGA AAAAGA AAAAGA AAAAGA
5710245 AAAAG
1 AAAAG
5710250 GAGAGGCCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
5 9 0.20
6 29 0.66
7 6 0.14
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:5714620 original size:143 final size:143
Alignment explanation
Indices: 5714359--5714913 Score: 813
Period size: 143 Copynumber: 3.9 Consensus size: 143
5714349 GATTGAAATC
* * * * * *
5714359 ATTATGGCGAATCTTATCTTCCTGAAGTTTCAGTCGAGCAGATTGAAGCCACTAGCCTTATCTCT
1 ATTATGGCGGATATTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * *
5714424 TTGAAGTTGTAGCGGAGTAGACTGAAGACAGCGAATCTTATTTCCTTGACGTTGCAGTGGAACAA
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGCGTTGCAGTGGAACAA
*
5714489 ATTAAAGTTACAA
131 ATTAAAGCTACAA
* *
5714502 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGGCGGATATTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * *
5714567 CTGAAGTTTCAGCGAAGCAAACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGCGTTGCAGTGGAACAA
5714632 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * *
5714645 ATTATGGCAGATATTATCTTCCTGAAGTTGTAGTGGAGCAGATTGAAGCCACCAGCCCTATCTCC
1 ATTATGGCGGATATTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * *
5714710 CTGAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCTCTGGCGTTGCAGTAGAATAA
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGCGTTGCAGTGGAACAA
5714775 ATTAAAGCTACAA
131 ATTAAAGCTACAA
* * * **
5714788 ATTATGGTGGATATGATCTTCCTGAAGTTGCAGTGGAGTAGATTGAATTCACCAGCCTTATCTCC
1 ATTATGGCGGATATTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* *
5714853 CTGAAGTTGCAGCGGAGCAGATTGAAGACAACGAATCTTATTTCCCTAGCGTTGCAGTGGA
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGCGTTGCAGTGGA
5714914 GCAGATTGAA
Statistics
Matches: 372, Mismatches: 40, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
143 372 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (143 bp):
ATTATGGCGGATATTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
CTGAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGCGTTGCAGTGGAACAA
ATTAAAGCTACAA
Found at i:5714875 original size:44 final size:44
Alignment explanation
Indices: 5714803--5714955 Score: 164
Period size: 44 Copynumber: 3.5 Consensus size: 44
5714793 GGTGGATATG
* * * **
5714803 ATCTTCCTGAAGTTGCAGTGGAGTAGATTGAATTCACCAGCCTT
1 ATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGACACCAGCCTT
* **
5714847 ATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGACAACGAATCTT
1 ATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGAC-ACCAGCCTT
* * * * *
5714892 ATTTCCCT-AGCGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTT
1 ATCTCCCTGA-AGTTGCAGCGGAGCAGATTGAAGACACCAGCCTT
5714936 ATCTCCCTGAAGTTGCAGCG
1 ATCTCCCTGAAGTTGCAGCG
5714956 AAACAAACTA
Statistics
Matches: 88, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
44 52 0.59
45 36 0.41
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (44 bp):
ATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGACACCAGCCTT
Found at i:5714942 original size:232 final size:232
Alignment explanation
Indices: 5714671--5715095 Score: 570
Period size: 232 Copynumber: 1.8 Consensus size: 232
5714661 TCTTCCTGAA
* * * * *
5714671 GTTGTAGTGGAGCAGATTGAAGCCACCAGCCCTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAA
1 GTTGCAGTGGAGCAGATTGAAGCCACCAGCCCTATCTCCCTGAAGTTGCAGCGAAACAAACTAAA
* * * * **
5714736 GACAA-CGAATCTTATTTCTCTGGCGTTGC-AGTAGAATA-AATTAAAGCTACAAATTATGGTGG
66 GA-AAGCGAATCTTATTTCCCTAGC-TTGCTAATAGAACAGAA-TAAAGCTACAAATTATGGCAG
* * * * *
5714798 ATATGATCTTCCTGAAGTTGCAGTGGAGTAGATTGAA-TTCACCAGCCTTATCTCCCTGAAGTTG
128 ATATGATCTTCCTAAAGTTGCAGTGGAGCAAATTGAAGCT-ACCAGCCTTATCTCACTGAAGTTG
5714862 CAGCGGAGCAGATTGAAGACAACGAATCTTATTTCCCTAGC
192 CAGCGGAGCAGATTGAAGACAACGAATCTTATTTCCCTAGC
* *
5714903 GTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCCCTGAAGTTGCAGCGAAACAAACTAAA
1 GTTGCAGTGGAGCAGATTGAAGCCACCAGCCCTATCTCCCTGAAGTTGCAGCGAAACAAACTAAA
* * * *
5714968 GAAAGCGAATCTTATTTCCCTAGCTTTCTAATGGAACAGAATAAAGTTACAAATTATGGCAGATC
66 GAAAGCGAATCTTATTTCCCTAGCTTGCTAATAGAACAGAATAAAGCTACAAATTATGGCAGATA
* *
5715033 TTATCTTCCTAAAGTTGCAGTGGAGCAAATTGAAGCTACCAGTCTTATCTCACTGAAGTTGCA
131 TGATCTTCCTAAAGTTGCAGTGGAGCAAATTGAAGCTACCAGCCTTATCTCACTGAAGTTGCA
5715096 ATGGGTTAGG
Statistics
Matches: 165, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
231 5 0.03
232 157 0.95
233 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (232 bp):
GTTGCAGTGGAGCAGATTGAAGCCACCAGCCCTATCTCCCTGAAGTTGCAGCGAAACAAACTAAA
GAAAGCGAATCTTATTTCCCTAGCTTGCTAATAGAACAGAATAAAGCTACAAATTATGGCAGATA
TGATCTTCCTAAAGTTGCAGTGGAGCAAATTGAAGCTACCAGCCTTATCTCACTGAAGTTGCAGC
GGAGCAGATTGAAGACAACGAATCTTATTTCCCTAGC
Found at i:5714977 original size:89 final size:89
Alignment explanation
Indices: 5714814--5714991 Score: 259
Period size: 89 Copynumber: 2.0 Consensus size: 89
5714804 TCTTCCTGAA
* ** * * * * *
5714814 GTTGCAGTGGAGTAGATTGAATTCACCAGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAA
1 GTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGAAACAAACTAAA
5714879 GACAACGAATCTTATTTCCCTAGC
66 GACAACGAATCTTATTTCCCTAGC
*
5714903 GTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCCCTGAAGTTGCAGCGAAACAAACTAAA
1 GTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGAAACAAACTAAA
5714968 GA-AAGCGAATCTTATTTCCCTAGC
66 GACAA-CGAATCTTATTTCCCTAGC
5714992 TTTCTAATGG
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 2 0.03
89 77 0.97
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.25
Consensus pattern (89 bp):
GTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGAAACAAACTAAA
GACAACGAATCTTATTTCCCTAGC
Found at i:5715960 original size:2 final size:2
Alignment explanation
Indices: 5715955--5715981 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5715945 CAAAAAACTG
5715955 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5715982 GGCCTCCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5716486 original size:12 final size:14
Alignment explanation
Indices: 5716469--5716507 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
5716459 CACTTTATGT
5716469 TTTTATTATTA-C-
1 TTTTATTATTATCA
5716481 TTTTATTATTATCA
1 TTTTATTATTATCA
5716495 TTTTATTTATTAT
1 TTTTA-TTATTAT
5716508 TTATCTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.46
13 1 0.04
14 5 0.21
15 7 0.29
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTATTATCA
Found at i:5716491 original size:15 final size:15
Alignment explanation
Indices: 5716470--5716508 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
5716460 ACTTTATGTT
5716470 TTTATTATTACTTTTA
1 TTTATTATTA-TTTTA
*
5716486 -TTATTATCATTTTA
1 TTTATTATTATTTTA
5716500 TTTATTATT
1 TTTATTATT
5716509 TATCTATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATTATTATTTTA
Found at i:5732189 original size:21 final size:21
Alignment explanation
Indices: 5732163--5732203 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5732153 ATCTGCTCAA
* *
5732163 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5732184 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5732204 TTGCTCATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5735544 original size:2 final size:2
Alignment explanation
Indices: 5735537--5735561 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5735527 TTGCAAACCC
5735537 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
5735562 ATCAATCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5752995 original size:16 final size:16
Alignment explanation
Indices: 5752974--5753041 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
5752964 TTTGGTTCGC
5752974 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5752990 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
5753006 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
*
5753022 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
5753038 TGTA
1 TGTA
5753042 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:5753081 original size:45 final size:41
Alignment explanation
Indices: 5753022--5753131 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 41
5753012 GGATTAGAGG
*
5753022 TGTATTGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGG-T
* * ***
5753064 GAATGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGT
1 ---TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
5753107 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
5753132 TAATGGAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
39 20 0.36
40 2 0.04
43 1 0.02
44 11 0.20
45 22 0.39
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (41 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
Found at i:5753294 original size:16 final size:16
Alignment explanation
Indices: 5753257--5753298 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5753247 TTAATCATAT
*
5753257 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
5753273 TT-AAATATATTATAA
1 TTAAAATATATTATAA
5753288 TTAAAATATAT
1 TTAAAATATAT
5753299 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:5753305 original size:14 final size:15
Alignment explanation
Indices: 5753266--5753307 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5753256 TTTAAACATA
*
5753266 ATTATTATTAAATAT
1 ATTATAATTAAATAT
5753281 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
5753295 A-TATAATTTAATA
1 ATTATAATTAAATA
5753308 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:5753399 original size:120 final size:121
Alignment explanation
Indices: 5753255--5753523 Score: 456
Period size: 120 Copynumber: 2.2 Consensus size: 121
5753245 ATTTAATCAT
5753255 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
5753320 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA-GATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATG-TA
5753376 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
5753440 ATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACTATAAAATGTA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATGTA
* *
5753496 ATTTGAA-ATAATTAATATTAAATA-ATTA
1 ATTTAAACATAATTATTATTAAATATATTA
5753524 ATGTTGACAA
Statistics
Matches: 142, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
119 4 0.03
120 131 0.92
121 7 0.05
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATGTA
Found at i:5753416 original size:16 final size:16
Alignment explanation
Indices: 5753373--5753418 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5753363 ACTATAAAAG
*
5753373 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
5753389 ATTATT-AAATATATT
1 ATAATTAAAATATATT
5753404 ATAATTAAAATATAT
1 ATAATTAAAATATAT
5753419 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:5753425 original size:14 final size:15
Alignment explanation
Indices: 5753373--5753427 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
5753363 ACTATAAAAG
5753373 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
5753389 ATTATTAAATATATT
1 ATAATTAAATATATT
5753404 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
5753417 ATAATTTAATA
1 ATAATTAAATA
5753428 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:5753490 original size:61 final size:61
Alignment explanation
Indices: 5753305--5753492 Score: 181
Period size: 61 Copynumber: 3.1 Consensus size: 61
5753295 ATATAATTTA
* * *
5753305 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
** * * * * * * * *
5753366 ATAAAA--GATAAT--TTAACATAATTATTAT-TAAATATATTATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTATTAAAATCATAATATATGATACT
5753424 AATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
5753486 ATAAAAT
1 ATAAAAT
5753493 GTAATTTGAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
57 1 0.01
58 2 0.02
59 32 0.34
60 14 0.15
61 41 0.44
62 2 0.02
63 2 0.02
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (61 bp):
ATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTAAAATCATAATATATGATACT
Found at i:5757334 original size:19 final size:19
Alignment explanation
Indices: 5757298--5757337 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5757288 CAGATAATAC
*
5757298 TAACATATTTTAATTAATT
1 TAACATATTTTAAATAATT
5757317 TAAC-TATTTTAACATAATT
1 TAACATATTTTAA-ATAATT
5757336 TA
1 TA
5757338 TACTTAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (19 bp):
TAACATATTTTAAATAATT
Found at i:5767004 original size:104 final size:104
Alignment explanation
Indices: 5766824--5767030 Score: 414
Period size: 104 Copynumber: 2.0 Consensus size: 104
5766814 GGGAAAAGGC
5766824 TGCACTCCAAACAACCATCAAATTTGCACACGTGACACTTATTCATAACTTCTCTCGGTTGTAAT
1 TGCACTCCAAACAACCATCAAATTTGCACACGTGACACTTATTCATAACTTCTCTCGGTTGTAAT
5766889 ACCATAGAAATAGAAGAAGAACCTTCGGCAACAACCAAT
66 ACCATAGAAATAGAAGAAGAACCTTCGGCAACAACCAAT
5766928 TGCACTCCAAACAACCATCAAATTTGCACACGTGACACTTATTCATAACTTCTCTCGGTTGTAAT
1 TGCACTCCAAACAACCATCAAATTTGCACACGTGACACTTATTCATAACTTCTCTCGGTTGTAAT
5766993 ACCATAGAAATAGAAGAAGAACCTTCGGCAACAACCAA
66 ACCATAGAAATAGAAGAAGAACCTTCGGCAACAACCAA
5767031 GGTATTGAAA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.24
Consensus pattern (104 bp):
TGCACTCCAAACAACCATCAAATTTGCACACGTGACACTTATTCATAACTTCTCTCGGTTGTAAT
ACCATAGAAATAGAAGAAGAACCTTCGGCAACAACCAAT
Found at i:5771646 original size:50 final size:50
Alignment explanation
Indices: 5771570--5771666 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
5771560 TATGATAAAA
* * *
5771570 GATGATAAAAATTGTTATGAATAGCCATCTCGCTTGAGGAGCCTCCTTGT
1 GATGATAAAAATTGTTATGAAAAGCCACCTCGCTTGAGGAACCTCCTTGT
*
5771620 GATGATAATAATTGTTATGAAAAGCCACCTCGCTTGAGGAACCTCCT
1 GATGATAAAAATTGTTATGAAAAGCCACCTCGCTTGAGGAACCTCCT
5771667 CGTCAGCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (50 bp):
GATGATAAAAATTGTTATGAAAAGCCACCTCGCTTGAGGAACCTCCTTGT
Found at i:5772232 original size:30 final size:30
Alignment explanation
Indices: 5772186--5772309 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
5772176 TTTTATTATG
*
5772186 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
5772217 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
5772247 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
5772277 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
5772307 CCA
1 CCA
5772310 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:5772241 original size:15 final size:15
Alignment explanation
Indices: 5772196--5772303 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
5772186 CCAATATCTC
5772196 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
5772211 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
5772226 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
5772241 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
5772256 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
5772271 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
5772286 GATACCCATATCTTT
1 GATACCCATATCTTT
5772301 GAT
1 GAT
5772304 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:5776921 original size:30 final size:30
Alignment explanation
Indices: 5776875--5776998 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
5776865 TTTTATTATG
*
5776875 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
5776906 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
5776936 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
5776966 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
5776996 CCA
1 CCA
5776999 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:5776930 original size:15 final size:15
Alignment explanation
Indices: 5776885--5776992 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
5776875 CCAATATCTC
5776885 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
5776900 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
5776915 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
5776930 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
5776945 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
5776960 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
5776975 GATACCCATATCTTT
1 GATACCCATATCTTT
5776990 GAT
1 GAT
5776993 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:5780506 original size:41 final size:41
Alignment explanation
Indices: 5780456--5780615 Score: 119
Period size: 41 Copynumber: 3.9 Consensus size: 41
5780446 CTGGCGGTTT
* *
5780456 CTCACAAACGCCACTAAAAGACCCACCATTAGCGGCGTATA
1 CTCAAAAACGCCGCTAAAAGACCCACCATTAGCGGCGTATA
* * ** ** * *
5780497 CTCAAAAACGCCGGTAAAAGTCATAGAATTTGCGGCTCTATTA
1 CTCAAAAACGCCGCTAAAAGACCCACCATTAGCGGC-GTA-TA
* *
5780540 -T-AAAAACGCCGC-AAAAAACCCTACCATTAGTGGCGTATA
1 CTCAAAAACGCCGCTAAAAGACCC-ACCATTAGCGGCGTATA
* * * * *
5780579 CTCAAAAACGCCGTTAAAGGTCTCAGCATTAGCGGCG
1 CTCAAAAACGCCGCTAAAAGACCCACCATTAGCGGCG
5780616 CTAATATTGA
Statistics
Matches: 86, Mismatches: 27, Indels: 12
0.69 0.22 0.10
Matches are distributed among these distances:
39 2 0.02
40 8 0.09
41 66 0.77
42 8 0.09
43 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (41 bp):
CTCAAAAACGCCGCTAAAAGACCCACCATTAGCGGCGTATA
Found at i:5780614 original size:82 final size:82
Alignment explanation
Indices: 5780461--5780637 Score: 214
Period size: 82 Copynumber: 2.2 Consensus size: 82
5780451 GGTTTCTCAC
*
5780461 AAACGCCACTAAAAGACCCACCATTAGCGGCGTATACTCAAAAACGCCGGTAAAAGTCATAGAAT
1 AAACGCCACTAAAAAACCCACCATTAGCGGCGTATACTCAAAAACGCCGGTAAAAGTCATAGAAT
*
5780526 TTGCGGCTCTATTATAA
66 TAGCGGCTCTATTATAA
* * * * *
5780543 AAACGCCGC-AAAAAACCCTACCATTAGTGGCGTATACTCAAAAACGCCGTTAAAGGTC-TCAGC
1 AAACGCCACTAAAAAACCC-ACCATTAGCGGCGTATACTCAAAAACGCCGGTAAAAGTCAT-AGA
* * **
5780606 ATTAGCGGCGCTAATATTG
64 ATTAGCGGCTCTATTATAA
*
5780625 AAACACCACTAAA
1 AAACGCCACTAAA
5780638 GCCCTTCGAA
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
81 9 0.11
82 67 0.85
83 3 0.04
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (82 bp):
AAACGCCACTAAAAAACCCACCATTAGCGGCGTATACTCAAAAACGCCGGTAAAAGTCATAGAAT
TAGCGGCTCTATTATAA
Found at i:5791251 original size:32 final size:32
Alignment explanation
Indices: 5791210--5791270 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
5791200 CCTGATTCCG
5791210 TTCACCGGCATTAAGCCTGCTAGATGTATTAT
1 TTCACCGGCATTAAGCCTGCTAGATGTATTAT
5791242 TTCACCGGCATTAAGCCTGCTAGATGTAT
1 TTCACCGGCATTAAGCCTGCTAGATGTAT
5791271 AATCTGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (32 bp):
TTCACCGGCATTAAGCCTGCTAGATGTATTAT
Found at i:5791294 original size:40 final size:40
Alignment explanation
Indices: 5791239--5791420 Score: 310
Period size: 40 Copynumber: 4.5 Consensus size: 40
5791229 CTAGATGTAT
* *
5791239 TATTTCACCGGCATTAAGCCTGCTAGATGTATAATCTGAA
1 TATTTCACCGGCATTAAGCCTGCTAGACGTATAGTCTGAA
* *
5791279 TATTTCATCAGCATTAAGCCTGCTAGACGTATAGTCTGAA
1 TATTTCACCGGCATTAAGCCTGCTAGACGTATAGTCTGAA
*
5791319 TATTTCACCGGCATTAAGCCTGCTAGACGTATAGTTTGAA
1 TATTTCACCGGCATTAAGCCTGCTAGACGTATAGTCTGAA
5791359 TATTTCACCGGCATTAAGCCTGCTAGACGTATAGTCTGAA
1 TATTTCACCGGCATTAAGCCTGCTAGACGTATAGTCTGAA
*
5791399 TATTTCACCGACATTAAGCCTG
1 TATTTCACCGGCATTAAGCCTG
5791421 TTAGGCACAA
Statistics
Matches: 133, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 133 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (40 bp):
TATTTCACCGGCATTAAGCCTGCTAGACGTATAGTCTGAA
Found at i:5800990 original size:19 final size:19
Alignment explanation
Indices: 5800964--5801011 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
5800954 TTTTCTCACT
*
5800964 CTTT-TTTCATTTTTTTC-C
1 CTTTCTTTC-TTTATTTCTC
5800982 CTTTCTTTCTTTATTTCTC
1 CTTTCTTTCTTTATTTCTC
*
5801001 CTTTCCTTCTT
1 CTTTCTTTCTT
5801012 CTGCTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (19 bp):
CTTTCTTTCTTTATTTCTC
Found at i:5817405 original size:41 final size:42
Alignment explanation
Indices: 5817360--5817439 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 42
5817350 ATATTGGGGA
* *
5817360 CACACGGTCT-ATCAACATGCCTGTGTG-CAAGCCGTGTGTCT
1 CACACGGTCTGATC-ACACGCCCGTGTGACAAGCCGTGTGTCT
*
5817401 CACACGGTCTGATCACACGCCCGTGTGACATGCCGTGTG
1 CACACGGTCTGATCACACGCCCGTGTGACAAGCCGTGTG
5817440 GACTCAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 21 0.62
42 13 0.38
ACGTcount: A:0.19, C:0.31, G:0.26, T:0.24
Consensus pattern (42 bp):
CACACGGTCTGATCACACGCCCGTGTGACAAGCCGTGTGTCT
Found at i:5818176 original size:6 final size:6
Alignment explanation
Indices: 5818160--5818194 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
5818150 GGAATACACC
* *
5818160 GTAATA GTAACA ATAACA GTAACA GTAACA GTAAC
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAAC
5818195 GATACACAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.20
Consensus pattern (6 bp):
GTAACA
Found at i:5819896 original size:16 final size:15
Alignment explanation
Indices: 5819875--5819922 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
5819865 GATGGGAATA
5819875 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
5819891 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
5819906 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
5819922 A
1 A
5819923 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:5819905 original size:8 final size:8
Alignment explanation
Indices: 5819871--5819922 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
5819861 CAATGATGGG
*
5819871 AATAATAA
1 AATATTAA
5819879 AATATATAA
1 AATAT-TAA
5819888 AATA-TAA
1 AATATTAA
5819895 AATATTAA
1 AATATTAA
*
5819903 AATATCAA
1 AATATTAA
*
5819911 AATATTAG
1 AATATTAA
5819919 AATA
1 AATA
5819923 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:5819922 original size:24 final size:24
Alignment explanation
Indices: 5819870--5819926 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
5819860 ACAATGATGG
*
5819870 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
5819894 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
5819918 GAATAATAA
1 GAATAATAA
5819927 TAATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:5820084 original size:23 final size:22
Alignment explanation
Indices: 5820033--5820086 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
5820023 ATACTACATC
5820033 AATATGTACATAT-ATA--AAA
1 AATATGTACATATAATATTAAA
**
5820052 AATAAATACATGATAATATTAAA
1 AATATGTACAT-ATAATATTAAA
5820075 AATATGTACATA
1 AATATGTACATA
5820087 ATATAGTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 3 0.11
22 1 0.04
23 12 0.44
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
AATATGTACATATAATATTAAA
Found at i:5820133 original size:22 final size:24
Alignment explanation
Indices: 5820049--5820134 Score: 81
Period size: 25 Copynumber: 3.7 Consensus size: 24
5820039 TACATATATA
* *
5820049 AAAAATAAATACATGATAATA--TT
1 AAAAATATATACATAAT-ATAGGTT
*
5820072 AAAAATATGTACATAATATAGTGTT
1 AAAAATATATACATAATATAG-GTT
*
5820097 AAAAATACATACATAATATA-GTT
1 AAAAATATATACATAATATAGGTT
*
5820120 -AAGATATATACATAA
1 AAAAATATATACATAA
5820135 GATAACATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
22 16 0.30
23 17 0.32
25 20 0.38
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAAATATATACATAATATAGGTT
Found at i:5820184 original size:25 final size:25
Alignment explanation
Indices: 5820156--5820287 Score: 91
Period size: 25 Copynumber: 5.6 Consensus size: 25
5820146 AAAAAAATAT
5820156 ATATATAAATAATATAATATTAAAG
1 ATATATAAATAATATAATATTAAAG
* * *
5820181 ATATATAAATAAAATAGTA-TAATAT
1 ATATATAAATAATATAATATTAA-AG
** * *
5820206 ATATATACGTAATATAAAATTTAA-
1 ATATATAAATAATATAATATTAAAG
** *
5820230 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATAAATAATATAATATTAAAG
*
5820252 A-ATATATATAATATAATATT-AAG
1 ATATATAAATAATATAATATTAAAG
*
5820275 AAATAT-AATAATA
1 ATATATAAATAATA
5820288 ACAAAAAAAT
Statistics
Matches: 84, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
21 3 0.04
22 13 0.15
23 24 0.29
24 9 0.11
25 33 0.39
26 2 0.02
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (25 bp):
ATATATAAATAATATAATATTAAAG
Found at i:5820185 original size:23 final size:23
Alignment explanation
Indices: 5820158--5820287 Score: 63
Period size: 22 Copynumber: 5.5 Consensus size: 23
5820148 AAAAATATAT
5820158 ATATAAATAATATAATATTAAAG
1 ATATAAATAATATAATATTAAAG
* * *
5820181 ATATATA-AATAAAATAGTATAATAT
1 ATATAAATAATATAATA-T-TAA-AG
* *
5820206 ATATATACGTAATATAAAATTTAAA-
1 ATATA-A-ATAATATAATA-TTAAAG
** *
5820231 ATATACCTAATAT-AT-TAAAAG
1 ATATAAATAATATAATATTAAAG
*
5820252 AATATATATAATATAATATT-AAG
1 -ATATAAATAATATAATATTAAAG
*
5820275 AAATATAATAATA
1 ATATA-AATAATA
5820288 ACAAAAAAAT
Statistics
Matches: 79, Mismatches: 17, Indels: 22
0.67 0.14 0.19
Matches are distributed among these distances:
20 4 0.05
22 24 0.30
23 24 0.30
24 4 0.05
25 11 0.14
26 1 0.01
27 3 0.04
28 8 0.10
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (23 bp):
ATATAAATAATATAATATTAAAG
Found at i:5820186 original size:16 final size:15
Alignment explanation
Indices: 5820149--5820205 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 15
5820139 ACATGTAAAA
5820149 AAAATATAT-ATA-T
1 AAAATATATAATATT
5820162 -AAATAATATAATATT
1 AAAAT-ATATAATATT
5820177 AAAGATATATAA-A-T
1 AAA-ATATATAATATT
5820191 AAAATAGTATAATAT
1 AAAATA-TATAATAT
5820206 ATATATACGT
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
12 4 0.11
13 7 0.19
14 12 0.33
15 3 0.08
16 8 0.22
17 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (15 bp):
AAAATATATAATATT
Found at i:5820802 original size:30 final size:30
Alignment explanation
Indices: 5820766--5820970 Score: 329
Period size: 30 Copynumber: 6.8 Consensus size: 30
5820756 TAGGTACAAG
*
5820766 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
5820796 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
5820826 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* * *
5820856 TGGTGGTGGAAAAAGAGTGGTTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
5820886 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
5820916 TGGTGGTGGAAAATGTGTGCCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
5820946 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
5820971 TGAGAAAAGT
Statistics
Matches: 159, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 159 1.00
ACGTcount: A:0.22, C:0.03, G:0.48, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:5821736 original size:14 final size:14
Alignment explanation
Indices: 5821717--5821766 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
5821707 GATTTGATTT
*
5821717 TTGAAAAATATAAA
1 TTGAAAAATAGAAA
*
5821731 TTGAAAAAACAGAAA
1 TTG-AAAAATAGAAA
*
5821746 TTGAAAAGTAGAAA
1 TTGAAAAATAGAAA
5821760 TT-AAAAA
1 TTGAAAAA
5821767 GACCTCAGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 4 0.13
14 14 0.47
15 12 0.40
ACGTcount: A:0.64, C:0.02, G:0.12, T:0.22
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Done.