Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397270.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_55.0, whole genome shotgun sequence
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: 4719911
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 90628 characters in sequence are not A, C, G, or T
File 9 of 10
Found at i:3414065 original size:25 final size:25
Alignment explanation
Indices: 3414031--3414084 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
3414021 AACAGGTGAT
3414031 AGGTTGGTGGCTCTGTTTCCTTTTA
1 AGGTTGGTGGCTCTGTTTCCTTTTA
3414056 AGGTTGGTGGCTCTGTTTCCTTTTA
1 AGGTTGGTGGCTCTGTTTCCTTTTA
3414081 AGGT
1 AGGT
3414085 CATAGGGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.09, C:0.15, G:0.30, T:0.46
Consensus pattern (25 bp):
AGGTTGGTGGCTCTGTTTCCTTTTA
Found at i:3414877 original size:12 final size:12
Alignment explanation
Indices: 3414860--3414884 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3414850 GACCTACACT
3414860 TAACATTAGGCC
1 TAACATTAGGCC
3414872 TAACATTAGGCC
1 TAACATTAGGCC
3414884 T
1 T
3414885 GTACCAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (12 bp):
TAACATTAGGCC
Found at i:3430012 original size:2 final size:2
Alignment explanation
Indices: 3430005--3430037 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3429995 TTGCTTGCTT
3430005 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3430038 TATATATCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3431184 original size:26 final size:24
Alignment explanation
Indices: 3431121--3431174 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
3431111 TTCACAGTAG
3431121 TTTTTGTTAAGAAATTTGTGTCAT
1 TTTTTGTTAAGAAATTTGTGTCAT
3431145 TTTTTGTTAAGAAATTTGTGTCAT
1 TTTTTGTTAAGAAATTTGTGTCAT
3431169 TCTTTT
1 T-TTTT
3431175 TTCTGTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.22, C:0.06, G:0.15, T:0.57
Consensus pattern (24 bp):
TTTTTGTTAAGAAATTTGTGTCAT
Found at i:3436349 original size:78 final size:78
Alignment explanation
Indices: 3436167--3436632 Score: 652
Period size: 78 Copynumber: 6.0 Consensus size: 78
3436157 TTTCGGAGAG
* * *
3436167 ACATCTTGTGTTTTAGATTTGCTTTTCCCCCAATCACCCCACTCAGTTT-C--CATTGTACTGGT
1 ACATCTTGTGTTTTAGATTTGCTTGTCCCCCAATCACACCACTCAGTTTGCTTCGTTGTACTGGT
3436229 CACAGCTGCTGCA
66 CACAGCTGCTGCA
* * * *
3436242 ACATCTTGTGTTTTAGATTTGCTTTTCCCCCAATCACCCCACTCCGTTTGCTTCATTGTACTGGT
1 ACATCTTGTGTTTTAGATTTGCTTGTCCCCCAATCACACCACTCAGTTTGCTTCGTTGTACTGGT
3436307 CACAGCTGCTGCA
66 CACAGCTGCTGCA
* * * * * *
3436320 GCATCTTGTGTTTTAGATTTACCTGTCCCCCAATCACACCACTCATTTTGCTCCGCTGTACTGGT
1 ACATCTTGTGTTTTAGATTTGCTTGTCCCCCAATCACACCACTCAGTTTGCTTCGTTGTACTGGT
*
3436385 CACAGTTGCTGCA
66 CACAGCTGCTGCA
*
3436398 ACATCTTGTGTTTTAGATTTGCTTGTCCCCCAATCACACCAGTCA-TTCTGCTTCGTTGTACTGG
1 ACATCTTGTGTTTTAGATTTGCTTGTCCCCCAATCACACCACTCAGTT-TGCTTCGTTGTACTGG
*
3436462 TCACAGCTACTGCA
65 TCACAGCTGCTGCA
* * * ** *
3436476 ACTTCTTGTGTTTTAGATTTGCTTGTCCCCCAATCACACCACTCAGTTTTCTTTGTTACACTAGT
1 ACATCTTGTGTTTTAGATTTGCTTGTCCCCCAATCACACCACTCAGTTTGCTTCGTTGTACTGGT
3436541 CACAGCTGCTGCA
66 CACAGCTGCTGCA
* * * *
3436554 GCATCTTGTGTTTTAGATTTGCTTGTTCCCCAATCACACCACTCACTTTGCTTCGTTGTACCGGT
1 ACATCTTGTGTTTTAGATTTGCTTGTCCCCCAATCACACCACTCAGTTTGCTTCGTTGTACTGGT
*
3436619 CACAGCTGCCGCA
66 CACAGCTGCTGCA
3436632 A
1 A
3436633 ATTTGTCACC
Statistics
Matches: 346, Mismatches: 40, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
75 48 0.14
76 1 0.00
77 2 0.01
78 293 0.85
79 2 0.01
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.36
Consensus pattern (78 bp):
ACATCTTGTGTTTTAGATTTGCTTGTCCCCCAATCACACCACTCAGTTTGCTTCGTTGTACTGGT
CACAGCTGCTGCA
Found at i:3448093 original size:2 final size:2
Alignment explanation
Indices: 3448086--3448122 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3448076 TTTTCTGTTT
3448086 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3448123 TTTATAGAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3449683 original size:21 final size:21
Alignment explanation
Indices: 3449649--3449698 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3449639 GATTTTCAAA
3449649 ATTTCAAA-ATTTTTTAAACTTT
1 ATTT-AAATATTTTTTAAA-TTT
*
3449671 -TTTAAATATTTTTTTAATTT
1 ATTTAAATATTTTTTAAATTT
3449691 ATTTAAAT
1 ATTTAAAT
3449699 GAATTTAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTAAATATTTTTTAAATTT
Found at i:3456984 original size:28 final size:28
Alignment explanation
Indices: 3456950--3457003 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
3456940 GATTGAAATT
* * *
3456950 TTATTTATGTTTGGTGTAATGTATTTGC
1 TTATTTATATATGGTATAATGTATTTGC
*
3456978 TTATTTATATATGGTATAATTTATTT
1 TTATTTATATATGGTATAATGTATTT
3457004 ATTTGTAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.24, C:0.02, G:0.15, T:0.59
Consensus pattern (28 bp):
TTATTTATATATGGTATAATGTATTTGC
Found at i:3457569 original size:7 final size:7
Alignment explanation
Indices: 3457557--3457582 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3457547 TGTTTTTTTA
3457557 AATATTT
1 AATATTT
3457564 AATATTT
1 AATATTT
3457571 AATATTT
1 AATATTT
3457578 AATAT
1 AATAT
3457583 AATTAAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AATATTT
Found at i:3465617 original size:176 final size:177
Alignment explanation
Indices: 3465291--3465650 Score: 499
Period size: 176 Copynumber: 2.0 Consensus size: 177
3465281 ATGGATGAAG
* * * * **
3465291 TTTATCACTGGTATGTCAATTGGTATTTGTTACATGACGTTTAAGTCAACATACAATATGTCGGT
1 TTTATCACTCGTATGTCAATTGGTATTTGTCACATGACATTTAAGTCAACATACAATATATCGAC
* * * * * *
3465356 GAAGAAATAGATTTAAAGTAAATTTGAAATATATATTATGAAAGAGAAATTGAGTTTTTTGAGTT
66 GAAGAAATAAATTTAAAGTAAATTTAAAATATATATTATGAAAGAAAAATCGAATTTTTTGAATT
* *
3465421 ATGGACAAAAATTAATAATAAA-AGAAGACTAAAGACTAATATAACAA
131 ACGGACAAAAATGAATAATAAACA-AAGACTAAAGACTAATATAACAA
* *
3465468 TTTATCACTCG-ATGTTAATTTGTATTTGTCACATGACATTTAAGTCAACATACAATATATCGAC
1 TTTATCACTCGTATGTCAATTGGTATTTGTCACATGACATTTAAGTCAACATACAATATATCGAC
3465532 GAAGAAATAAATTTAAAGTAAATTTAAAATATATATTATGAAAGAAAAATCGAATTTTTTGAATT
66 GAAGAAATAAATTTAAAGTAAATTTAAAATATATATTATGAAAGAAAAATCGAATTTTTTGAATT
*** * * *
3465597 ACGGATGGAAATGGATAATAAACAAAGATTAAGGACTAATATAACAA
131 ACGGACAAAAATGAATAATAAACAAAGACTAAAGACTAATATAACAA
3465644 TTTATCA
1 TTTATCA
3465651 TGATCTGCTG
Statistics
Matches: 160, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
176 149 0.93
177 11 0.07
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.33
Consensus pattern (177 bp):
TTTATCACTCGTATGTCAATTGGTATTTGTCACATGACATTTAAGTCAACATACAATATATCGAC
GAAGAAATAAATTTAAAGTAAATTTAAAATATATATTATGAAAGAAAAATCGAATTTTTTGAATT
ACGGACAAAAATGAATAATAAACAAAGACTAAAGACTAATATAACAA
Found at i:3466373 original size:13 final size:13
Alignment explanation
Indices: 3466355--3466391 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
3466345 TAGATTTTCT
3466355 TATCATCCTCTAA
1 TATCATCCTCTAA
3466368 TATCATCCTCTAA
1 TATCATCCTCTAA
3466381 TATCACTCCTC
1 TATCA-TCCTC
3466392 ACATGTAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.27, C:0.35, G:0.00, T:0.38
Consensus pattern (13 bp):
TATCATCCTCTAA
Found at i:3477114 original size:21 final size:21
Alignment explanation
Indices: 3477073--3477134 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
3477063 CCTCCAATAT
* * *
3477073 ATCTTCAAAACCTCTAAGTAC
1 ATCTTCAAAATCTTTAGGTAC
*
3477094 CTCTTCAAAA-CTTTCAGGTAC
1 ATCTTCAAAATCTTT-AGGTAC
3477115 ATCTTCAAAATCTTTAGGTA
1 ATCTTCAAAATCTTTAGGTA
3477135 ACATTGGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 3 0.09
21 28 0.80
22 4 0.11
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (21 bp):
ATCTTCAAAATCTTTAGGTAC
Found at i:3482195 original size:340 final size:338
Alignment explanation
Indices: 3481802--3482814 Score: 977
Period size: 350 Copynumber: 2.9 Consensus size: 338
3481792 NNNNNNNNNN
* * * * * * *
3481802 TTATAATATATATACCATTATTTATATAAACCTATAACT-TATATACTTAAAGAG-AGCTTTTGA
1 TTATAATATATATAACTTTGTTTATATAAACTTATAA-TATATAAACCTAAAGAGAAG-TTGTGA
* * **
3481865 GATTAAAATAGTTTTGGAATC-TAACTATTTTTTTTAATTTCATGTAATTAAGGACAAA-TCCAT
64 GATTAGAATA-TTTTGGAAACGTAGTTATTTTTTTTAATTTCATGTAATTAAGGACAAACT-CAT
* * * *
3481928 ATAGTGAATTAAATTAATTCATGAAACTATTATTATTAATTAATTTGTAATGTCTTTCAATATAT
127 ATAGTTAATTAAATTAATTCATGAAACTATAATTATTAATTAACTTGTAATGTCTTTTAATATAT
*
3481993 ATAGTTTATATATTGTGTTAATTTATAAGAAATAT-ATTACTATTATATATATACTAAAATATTT
192 ATAGTTTATATATTGTGTTCATTTATAAGAAATATAATTACTATTATATATATA-TAAAATATTT
* * *
3482057 TTAGTCTATATATACTTTAAATATAAACATATTTATTTTTTATTTTGCATTAACATTACAAATTT
256 TTAGTGTATATATACTTTAAATATAAACATATTTATTTTATATTTTG--TTAACATTACAAAATT
*
3482122 ATAACTTATAAAATT-ATTA-A
319 ATAACTCAT--AATTAATTACA
* *
3482142 TTATAATATATATAACTTTGTCTGTATAAACTTATAATATATAAACCTAAAGAGAAGTTGTGAGA
1 TTATAATATATATAACTTTGTTTATATAAACTTATAATATATAAACCTAAAGAGAAGTTGTGAGA
* * * * *
3482207 TTAGAATAATTCT-GAAACGTAGTTATTTTTTTTAATTTTATGTAATTAAGAACAAACTCGTACA
66 TTAGAAT-ATTTTGGAAACGTAGTTATTTTTTTTAATTTCATGTAATTAAGGACAAACTCATATA
*
3482271 GTTAATTAAATTAATTCATGAAACTATAATTATTAATTAACTTGTAAAGTCTTTTAATATATATA
130 GTTAATTAAATTAATTCATGAAACTATAATTATTAATTAACTTGTAATGTCTTTTAATATATATA
* * * *
3482336 ATTTATATATAT-TAAGCTCATTTATAAGGAATATAATTACTATTATATATATATATATATGAGT
195 GTTTATATAT-TGT--GTTCATTTATAAGAAATATAATTACTATTATATATATATA-AAAT-A-T
* * *********
3482400 GTGTGTCT-GTGTGTATGTACTTTAAATATAAACATATTTACTNNNNNNNNNNTGTTAACATTAC
254 -T-T-T-TAGTGTATATATACTTTAAATATAAACATATTTA-T-TTTATATTTTGTTAACATTAC
*
3482464 AAAAATTATAACTCATTATTAATTACA
313 -AAAATTATAACTCATAATTAATTACA
* * * *
3482491 ATATATATATATATATA-TTTGTTTATATAAACTTATAACATATAAATCTAAAGGGAAGTTGTGA
1 TTATA-ATATATATA-ACTTTGTTTATATAAACTTATAATATATAAACCTAAAGAGAAGTTGTGA
* * * * * *
3482555 GATTAGAATAATTTGGAAACTTAGTTATTTTTTTTAATTTCTTATAATTAAGGATAAACTTATAT
64 GATTAGAATATTTTGGAAACGTAGTTATTTTTTTTAATTTCATGTAATTAAGGACAAACTCATAT
* * * **********
3482620 AATTAATTAAATTAATTAATGAAACTATGANNNNNNNNNNACTTGTAATGTCTTTTAATATATAT
129 AGTTAATTAAATTAATTCATGAAACTATAATTATTAATTAACTTGTAATGTCTTTTAATATATAT
* * *
3482685 ACGTTATATATATTGAGTTCATTTATAAGAAATATAATCACTATTATATATGTATATTAAAATAC
194 A-GTT-TATATATTGTGTTCATTTATAAGAAATATAATTACTATTATATA--TATA-TAAAATAT
* * * * * *
3482750 TTTTAGTGTACACACACTTTAAATATAAATATATTTACTTTATATTTTGTGTTAACATTTCAAAA
254 TTTTAGTGTATATATACTTTAAATATAAACATATTTATTTTATA-TTT-TGTTAACATTACAAAA
3482815 GCCATAGCTA
Statistics
Matches: 542, Mismatches: 98, Indels: 60
0.77 0.14 0.09
Matches are distributed among these distances:
339 5 0.01
340 167 0.31
341 5 0.01
342 18 0.03
343 21 0.04
344 1 0.00
345 1 0.00
346 6 0.01
347 42 0.08
348 45 0.08
349 24 0.04
350 186 0.34
351 5 0.01
352 14 0.03
353 2 0.00
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.43
Consensus pattern (338 bp):
TTATAATATATATAACTTTGTTTATATAAACTTATAATATATAAACCTAAAGAGAAGTTGTGAGA
TTAGAATATTTTGGAAACGTAGTTATTTTTTTTAATTTCATGTAATTAAGGACAAACTCATATAG
TTAATTAAATTAATTCATGAAACTATAATTATTAATTAACTTGTAATGTCTTTTAATATATATAG
TTTATATATTGTGTTCATTTATAAGAAATATAATTACTATTATATATATATAAAATATTTTTAGT
GTATATATACTTTAAATATAAACATATTTATTTTATATTTTGTTAACATTACAAAATTATAACTC
ATAATTAATTACA
Found at i:3489143 original size:14 final size:13
Alignment explanation
Indices: 3489121--3489171 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
3489111 GCTTTAAAGC
*
3489121 AAACCCTAAACCTT
1 AAACTCTAAACC-T
*
3489135 AAACTCTAATCCT
1 AAACTCTAAACCT
3489148 AAAC-CTTAAACCCT
1 AAACTC-TAAA-CCT
3489162 AAACTCTAAA
1 AAACTCTAAA
3489172 ATCTTAAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 1 0.03
13 8 0.26
14 21 0.68
15 1 0.03
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (13 bp):
AAACTCTAAACCT
Found at i:3489150 original size:20 final size:20
Alignment explanation
Indices: 3489125--3489163 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3489115 TAAAGCAAAC
*
3489125 CCTAAACCTTAAACTCTAAT
1 CCTAAACCTTAAACCCTAAT
3489145 CCTAAACCTTAAACCCTAA
1 CCTAAACCTTAAACCCTAA
3489164 ACTCTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (20 bp):
CCTAAACCTTAAACCCTAAT
Found at i:3491768 original size:12 final size:12
Alignment explanation
Indices: 3491747--3491791 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
3491737 CAAGCAATCA
* *
3491747 CCTTTTCCTCGG
1 CCTTTGCCTCAG
3491759 CCTTTGCCTCAG
1 CCTTTGCCTCAG
3491771 CCTTTGCCTCAG
1 CCTTTGCCTCAG
*
3491783 CCTTGGCCT
1 CCTTTGCCT
3491792 TGTGCATCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.04, C:0.42, G:0.18, T:0.36
Consensus pattern (12 bp):
CCTTTGCCTCAG
Found at i:3494072 original size:11 final size:11
Alignment explanation
Indices: 3494045--3494075 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
3494035 GAACCCTAGG
3494045 TATAAATTTTT
1 TATAAATTTTT
3494056 TA-AAATTTTT
1 TATAAATTTTT
3494066 TATAAATTTT
1 TATAAATTTT
3494076 CCATCCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATAAATTTTT
Found at i:3498017 original size:31 final size:31
Alignment explanation
Indices: 3497982--3498076 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 31
3497972 AGTTCTAATC
3497982 AATATATGTAGTTCGTTTTATAGAATATTAA
1 AATATATGTAGTTCGTTTTATAGAATATTAA
* * ** * ** * *
3498013 AATATA-ATATTTCAATTTGT--TCTAAT-C
1 AATATATGTAGTTCGTTTTATAGAATATTAA
3498040 AATATATGTAGTTCGTTTTATAGAATATTAA
1 AATATATGTAGTTCGTTTTATAGAATATTAA
3498071 AATATA
1 AATATA
3498077 ATATATCAAT
Statistics
Matches: 42, Mismatches: 18, Indels: 8
0.62 0.26 0.12
Matches are distributed among these distances:
27 6 0.14
28 12 0.29
30 12 0.29
31 12 0.29
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.45
Consensus pattern (31 bp):
AATATATGTAGTTCGTTTTATAGAATATTAA
Found at i:3498063 original size:58 final size:58
Alignment explanation
Indices: 3497973--3498089 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
3497963 TGATCATCGA
*
3497973 GTTCTAATCAATATATGTAGTTCGTTTTATAGAATATTAAAATATAATATTTCAATTT
1 GTTCTAATCAATATATGTAGTTCGTTTTATAGAATATTAAAATATAATATATCAATTT
3498031 GTTCTAATCAATATATGTAGTTCGTTTTATAGAATATTAAAATATAATATATCAATTT
1 GTTCTAATCAATATATGTAGTTCGTTTTATAGAATATTAAAATATAATATATCAATTT
3498089 G
1 G
3498090 GATATGTCTA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.45
Consensus pattern (58 bp):
GTTCTAATCAATATATGTAGTTCGTTTTATAGAATATTAAAATATAATATATCAATTT
Found at i:3505268 original size:37 final size:37
Alignment explanation
Indices: 3505219--3505297 Score: 133
Period size: 37 Copynumber: 2.2 Consensus size: 37
3505209 CTATTATTAT
*
3505219 AATTT-TTTTATGACTTAAGTACGTAATGTTCTTCAC
1 AATTTATTTTATGACTTAAGTACGTAATGTTCATCAC
*
3505255 AATTTATTTTATGACTTGAGTACGTAATGTTCATCAC
1 AATTTATTTTATGACTTAAGTACGTAATGTTCATCAC
3505292 AATTTA
1 AATTTA
3505298 GACTCATCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 5 0.12
37 35 0.88
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (37 bp):
AATTTATTTTATGACTTAAGTACGTAATGTTCATCAC
Found at i:3517552 original size:18 final size:21
Alignment explanation
Indices: 3517510--3517553 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 21
3517500 TCAGCCTTTC
*
3517510 TTTTCTTTTTTCTCTCTCTCA
1 TTTTCTTTTTTCTCTCTCGCA
3517531 TTTTC-TTTTTC-CT-TCGCA
1 TTTTCTTTTTTCTCTCTCGCA
3517549 TTTTC
1 TTTTC
3517554 CCTCATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 6 0.27
21 5 0.23
ACGTcount: A:0.05, C:0.27, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTCTTTTTTCTCTCTCGCA
Found at i:3530209 original size:16 final size:18
Alignment explanation
Indices: 3530183--3530221 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3530173 TTGAAGTTCG
*
3530183 TAATATATTTATGAA-CT
1 TAATATATTTATAAATCT
3530200 TAAT-TATTTATAAATCT
1 TAATATATTTATAAATCT
3530217 TAATA
1 TAATA
3530222 AATGTGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (18 bp):
TAATATATTTATAAATCT
Found at i:3562978 original size:859 final size:861
Alignment explanation
Indices: 3561307--3563074 Score: 1892
Period size: 859 Copynumber: 2.0 Consensus size: 861
3561297 TTTTGAGTTG
* * * * * * *
3561307 TGTGATCTTGTGACAAATGATATCAGATCTTATTTTACTATTCATTAAAGTGAGACCTTCTCATA
1 TGTGATCTTGTAACAAATGGTATCAGAACTTACTTAACCATTAATTAAAGTGAGACCTTCTCATA
* * * *
3561372 AGAAATAATAAGATCAAGATAAGTCTCCACCAAAGTAATCCTTCTTTTCCATGTGTAAAAGAATC
66 AGAAATAATAAGATCAAGATAAGTCCCCACCAAAATAATCCTACTCTTCCATGTGTAAAAGAATC
** * *
3561437 AATGCAACAAAAATCTCACATCAAAAGAAATAAGATGAGTCTTAAACTTATAAGTCAAACCTTCT
131 AACACAACAAAAATCTCACATCAAAAGAAATAAGATGAGTCTCAAACTTATAAGTAAAACCTTCT
* * * * *
3561502 TGCATCTAATACACATGTATTTTGAGTCAAAACTACCTCTCGACTTTCGATTTGTAATTTTTAGT
196 T-CACCTAATAAACATGTATTTTAAGTCAAAACTACCTCTCGACTTTCGACTTGTAATTTTTAAT
** * * *
3561567 ATTTTTTTTACCCTTAAAGTCATTTTGGCCTAATTTTTCATAAGTTTTCATATAAAAAAAAACGA
260 ACATTTTTTACCCTTAAAGTCATTTCGACCTAATCTTTCATAAGTTTTCATATAAAAAAAAAC-A
* * * * * * * *
3561632 TAAATTCAATATAATCAAAATTTAACTTAAATTGTCAAGTTGGTATAAAAAATTTATTTTAAATT
324 TAAATTCAATAGAATCAAAATTTAACTCAAATTATCAAGTTAGAAGAAAAAAATGATTTTAAATT
* * * *
3561697 TGATTTGATTATTAAATCATTATGTTTGATAAGAAGTTGATAACTTAAATAATAGTAATCTTGTA
389 TGATATGATTATTAAATCATCATGTTTGACAAGAA---GATAACATAAATAATAGTAATCTTGTA
* * * * * * * * *
3561762 TTTAATAAGTGATCGATAAATCATAAGGTGACTATCTCATATTTGGTAAAAAGTCAGTATCTTAC
451 TTTAATAAATAAACAACAAATCATAAGCTGACAATCTCATATTTAGTAAAAAGTCAGTACCTTAC
* * * * *
3561827 TTTGCAATGATTTATGTCACTAAGAAGTGATATAATTTTCAACAAGATTGATGAAATAATGTTTT
516 TTAGCAATGATTTATATCACTAAGAAGTGATAT-ATTTT--ACAAGA-TCATAAAATAATCTTTT
* * * ** *
3561892 CGCCAAATGTAATAATTTATGAAATTAAGTACGAACCATTATAATTGTTATTATATTGTGTTAAA
577 CACCAAATGTAATAATTCATGAAATTAAGTACGAACAATTATAATTGTTATTATATCATATTAAA
* * * *
3561957 ATATTCTTCTCGTATAATTTTAAAATATATTGCATGCTACTTTTTATATTTAAATATAATTTTTA
642 ATATTCTTCTCATATAACTTCAAAATATATTACATGCTACTTTTTATATTTAAATATAATTTTTA
* * * *
3562022 ATTTTCTAAAAAATTTATCATTATTATAATAATTTCAATTTCGTTTTAAACTAATACTTTGTATC
707 ATTTTCTAAAAAAGTTATCATTATTATAATAATCTCAATTTCATTTTAAACTAAGACTTTGTATC
* * * * *
3562087 ATGAATTTCATATCAATAAAAGAAAAGATGATCTTGACCTTCTAAGTAATGATATTCTTT-GACC
772 AT-AATCTCATATCAATAAAAGAAAAGATGATCTTGACCTTATAAATAATGAT-TACTTTCAACC
* * * *
3562151 GAATA-ATCATGTTTTTTGAGTTAAAAA
835 AAATAGA-CATGTCTTTTAAATTAAAAA
* * * * * * *
3562178 TGTGATCATGTTACAAATGGTATCAGAACTTACTTAACCCTTAATTGAAGTGAGATCTTCTTATG
1 TGTGATCTTGTAACAAATGGTATCAGAACTTACTTAACCATTAATTAAAGTGAGACCTTCTCATA
* * * **
3562243 AGAGATAATAGGGTTGAGATAAGTCCCCACCAAAATAGATACC-ACTCTTCCATGTGTGAAAA-A
66 AGAAATAATAAGATCAAGATAAGTCCCCACCAAAATA-AT-CCTACTCTTCCATGTGT-AAAAGA
* * * * * *
3562306 ATCAACACAACAAAAATCTCACATTAAAATATATAAGATGAGTCTCGAACTTTTAAGTAAAACAT
128 ATCAACACAACAAAAATCTCACATCAAAAGAAATAAGATGAGTCTCAAACTTATAAGTAAAACCT
* *
3562371 T-TCTCTACCTAATAAACATGTATTTTAAGTCAAAATTA-CTTTCAGACGTTT-GACTTGTAATT
193 TCT-TC-ACCTAATAAACATGTATTTTAAGTCAAAACTACCTCTC-GAC-TTTCGACTTGTAATT
* * *
3562433 TTTAATACATTTTTTACTCTTAAAGTTATTTCGATCTAATCTTTCATAAGTTTTCATATAAAAAA
254 TTTAATACATTTTTTACCCTTAAAGTCATTTCGACCTAATCTTTCATAAGTTTTCATATAAAAAA
*
3562498 AATAC-TAAATTTGAA-AGAATCAAAATTTAACTCAAATTATCAAGTTAGAAGAAAAAAATGATT
319 AA-ACATAAA-TTCAATAGAATCAAAATTTAACTCAAATTATCAAGTTAGAAGAAAAAAATGATT
* * ** *
3562561 TTAAAATTT-ATATGATTATTAGATCATCATGTTTGGCAAGAA-ATAA-ATAGCTTATAGTAATC
382 TT-AAATTTGATATGATTATTAAATCATCATGTTTGACAAGAAGATAACATAAATAATAGTAATC
*
3562623 TTGTATTTAATAAATAAACAACAAATCATGAA-CTGGCAATCTCATATTTAG-AAAGCAA-TCAG
446 TTGTATTTAATAAATAAACAACAAATCAT-AAGCTGACAATCTCATATTTAGTAAA--AAGTCAG
* ** * * *** **
3562685 TGCCTTACTTAGTGATGATTTATATTATTTTTTAA-TGATAT-TTTT-CTTG-TCATAAAATAAT
508 TACCTTACTTAGCAATGATTTATATCA-CTAAGAAGTGATATATTTTACAAGATCATAAAATAAT
* * * * *
3562746 CTTTTCATCAAATGTAATAATTCCTGAAATTATGTATGAACAATTATAGTTGTTATTATATCATA
572 CTTTTCACCAAATGTAATAATTCATGAAATTAAGTACGAACAATTATAATTGTTATTATATCATA
* * *
3562811 TTAAAATATTCTTCTCATCTAACTTCAAAATATATTACATGCTCCTTTTTATATTTATATATAAT
637 TTAAAATATTCTTCTCATATAACTTCAAAATATATTACATGCTACTTTTTATATTTAAATATAAT
*
3562876 TTTTATTTTTCTAAAAAAGTTATCATTATTATAATAA-CTCTAATTTCATTTTAAA-TCAAGACT
702 TTTTAATTTTCTAAAAAAGTTATCATTATTATAATAATCTC-AATTTCATTTTAAACT-AAGAC-
* ** *
3562939 TTATGT-TGCAT-ATCTCATATTAATAAAA-AATGGGATGATCTTGAGCTTATAAATAATGATTA
764 TT-TGTAT-CATAATCTCATATCAATAAAAGAA-AAGATGATCTTGACCTTATAAATAATGATTA
*
3563001 CTTTCAACTAAATAGACATGTCTTTTAAATTAAAAA
826 CTTTCAACCAAATAGACATGTCTTTTAAATTAAAAA
* * **
3563037 TATGATCTTGCAACAAATGGTATCAGAGTTTACTTAAC
1 TGTGATCTTGTAACAAATGGTATCAGAACTTACTTAAC
3563075 TATTTATTGA
Statistics
Matches: 742, Mismatches: 133, Indels: 56
0.80 0.14 0.06
Matches are distributed among these distances:
858 10 0.01
859 267 0.36
860 4 0.01
861 8 0.01
864 4 0.01
865 3 0.00
866 81 0.11
867 11 0.01
871 162 0.22
872 181 0.24
873 11 0.01
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.39
Consensus pattern (861 bp):
TGTGATCTTGTAACAAATGGTATCAGAACTTACTTAACCATTAATTAAAGTGAGACCTTCTCATA
AGAAATAATAAGATCAAGATAAGTCCCCACCAAAATAATCCTACTCTTCCATGTGTAAAAGAATC
AACACAACAAAAATCTCACATCAAAAGAAATAAGATGAGTCTCAAACTTATAAGTAAAACCTTCT
TCACCTAATAAACATGTATTTTAAGTCAAAACTACCTCTCGACTTTCGACTTGTAATTTTTAATA
CATTTTTTACCCTTAAAGTCATTTCGACCTAATCTTTCATAAGTTTTCATATAAAAAAAAACATA
AATTCAATAGAATCAAAATTTAACTCAAATTATCAAGTTAGAAGAAAAAAATGATTTTAAATTTG
ATATGATTATTAAATCATCATGTTTGACAAGAAGATAACATAAATAATAGTAATCTTGTATTTAA
TAAATAAACAACAAATCATAAGCTGACAATCTCATATTTAGTAAAAAGTCAGTACCTTACTTAGC
AATGATTTATATCACTAAGAAGTGATATATTTTACAAGATCATAAAATAATCTTTTCACCAAATG
TAATAATTCATGAAATTAAGTACGAACAATTATAATTGTTATTATATCATATTAAAATATTCTTC
TCATATAACTTCAAAATATATTACATGCTACTTTTTATATTTAAATATAATTTTTAATTTTCTAA
AAAAGTTATCATTATTATAATAATCTCAATTTCATTTTAAACTAAGACTTTGTATCATAATCTCA
TATCAATAAAAGAAAAGATGATCTTGACCTTATAAATAATGATTACTTTCAACCAAATAGACATG
TCTTTTAAATTAAAAA
Found at i:3576201 original size:113 final size:114
Alignment explanation
Indices: 3576061--3576336 Score: 358
Period size: 113 Copynumber: 2.4 Consensus size: 114
3576051 AAAATATCTT
* * * * *
3576061 TTGTTGATAAATATGTGGTTTTAAAGAATGAATTAATTATTTTAAGGTACACAATTTGGGGTTTA
1 TTGTTGATAAATTTGTGGTTTT-AAGAATGAATTAGTCATTTTAAGGTACACAACTTGGGATTTA
* * *
3576126 TTATTCTCGATTCGGAATTAAGGAGGTAATATG-TG-AAAGCATCTGTTG
65 TTATTCTCAATTCGAAATTAAGGAGGTAATATGACGAAAAGCATCTGTTG
* * * *
3576174 TTGTTGATAAATTTATCGTTTTCAAGAATGAATTAGTCATTTTAAGGTACATAACTTGTGATTTA
1 TTGTTGATAAATTTGTGGTTTT-AAGAATGAATTAGTCATTTTAAGGTACACAACTTGGGATTTA
* * * *
3576239 TTATTCTCAATTTGAAATTAAGGAGGTAATATGACGACAAAGTATTTTTTG
65 TTATTCTCAATTCGAAATTAAGGAGGTAATATGACGA-AAAGCATCTGTTG
*
3576290 TTGTTGATAAATTTGTGGTTTTAATAATGAATTAGTCATTTTAAGGT
1 TTGTTGATAAATTTGTGGTTTTAAGAATGAATTAGTCATTTTAAGGT
3576337 TTTGATAAAA
Statistics
Matches: 140, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
113 85 0.61
114 1 0.01
115 24 0.17
116 30 0.21
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (114 bp):
TTGTTGATAAATTTGTGGTTTTAAGAATGAATTAGTCATTTTAAGGTACACAACTTGGGATTTAT
TATTCTCAATTCGAAATTAAGGAGGTAATATGACGAAAAGCATCTGTTG
Found at i:3579069 original size:21 final size:19
Alignment explanation
Indices: 3579052--3579088 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3579042 AAAATTTTAA
*
3579052 ATAAAATTTTCTCTATTTT
1 ATAAAATTATCTCTATTTT
*
3579071 ATTAAATTATCTCTATTT
1 ATAAAATTATCTCTATTT
3579089 AGCTCGTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (19 bp):
ATAAAATTATCTCTATTTT
Found at i:3590500 original size:4 final size:4
Alignment explanation
Indices: 3590491--3590521 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
3590481 TTTCTCCCCC
3590491 AAAT AAAT -AAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
3590522 CCTTTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:3594521 original size:72 final size:73
Alignment explanation
Indices: 3594398--3594540 Score: 207
Period size: 72 Copynumber: 2.0 Consensus size: 73
3594388 AATGGGTACC
* *
3594398 TTGATAACCTTATATCTAATTCCAAACCGGAAATATATATTAAAATTATTTCAAGAAATGAACAT
1 TTGATAACCTTATATCAAATTCCAAACCGGAAATATACATTAAAATTATTTCAAGAAATGAACAT
3594463 GTAGGCAT
66 GTAGGCAT
* * * * * *
3594471 TTGATATCCTTATATCAAATTCGAAA-CTGAAATATGCATTAACATTATTTCAAGGAATGAACAT
1 TTGATAACCTTATATCAAATTCCAAACCGGAAATATACATTAAAATTATTTCAAGAAATGAACAT
3594535 GTAGGC
66 GTAGGC
3594541 CTTTAGTTAG
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
72 39 0.63
73 23 0.37
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.33
Consensus pattern (73 bp):
TTGATAACCTTATATCAAATTCCAAACCGGAAATATACATTAAAATTATTTCAAGAAATGAACAT
GTAGGCAT
Found at i:3613985 original size:8 final size:8
Alignment explanation
Indices: 3613972--3613996 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3613962 GTATAAAGCG
3613972 AAATATTT
1 AAATATTT
3613980 AAATATTT
1 AAATATTT
3613988 AAATATTT
1 AAATATTT
3613996 A
1 A
3613997 TTGGAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AAATATTT
Found at i:3614478 original size:33 final size:33
Alignment explanation
Indices: 3614441--3614544 Score: 172
Period size: 33 Copynumber: 3.2 Consensus size: 33
3614431 CATCATGGAA
3614441 TTTAGGTTCTATGTTCATTTTAGATGCAATTTC
1 TTTAGGTTCTATGTTCATTTTAGATGCAATTTC
* * *
3614474 TTTAGGTTTTATGTTAATTTTAGATGCAACTTC
1 TTTAGGTTCTATGTTCATTTTAGATGCAATTTC
*
3614507 TTTAGATTCTATGTTCATTTTAGATGCAATTTC
1 TTTAGGTTCTATGTTCATTTTAGATGCAATTTC
3614540 TTTAG
1 TTTAG
3614545 AAGAAATCAT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.52
Consensus pattern (33 bp):
TTTAGGTTCTATGTTCATTTTAGATGCAATTTC
Found at i:3614530 original size:18 final size:18
Alignment explanation
Indices: 3614441--3614531 Score: 59
Period size: 18 Copynumber: 5.4 Consensus size: 18
3614431 CATCATGGAA
*
3614441 TTTAGGTTCTATGTTCAT
1 TTTAGATTCTATGTTCAT
* *
3614459 TTTAGATGCAAT-TTC--
1 TTTAGATTCTATGTTCAT
* * *
3614474 TTTAGGTTTTATGTTAAT
1 TTTAGATTCTATGTTCAT
* **
3614492 TTTAGATGC-AACTTC--
1 TTTAGATTCTATGTTCAT
3614507 TTTAGATTCTATGTTCAT
1 TTTAGATTCTATGTTCAT
3614525 TTTAGAT
1 TTTAGAT
3614532 GCAATTTCTT
Statistics
Matches: 50, Mismatches: 17, Indels: 12
0.63 0.22 0.15
Matches are distributed among these distances:
15 16 0.32
16 6 0.12
17 6 0.12
18 22 0.44
ACGTcount: A:0.23, C:0.10, G:0.14, T:0.53
Consensus pattern (18 bp):
TTTAGATTCTATGTTCAT
Found at i:3618831 original size:11 final size:12
Alignment explanation
Indices: 3618807--3618835 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3618797 GTATAAAATG
3618807 ATTATTTTTATA
1 ATTATTTTTATA
3618819 ATTATTTTT-TA
1 ATTATTTTTATA
3618830 ATTATT
1 ATTATT
3618836 CTTCATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
ATTATTTTTATA
Found at i:3623180 original size:35 final size:35
Alignment explanation
Indices: 3623134--3623204 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
3623124 TCGGCGTTTG
3623134 AAATTGAATCTTATAAATCTAAAGGTCATTATGCA
1 AAATTGAATCTTATAAATCTAAAGGTCATTATGCA
3623169 AAATTGAATCTTATAAATCTAAAGGTCATTATGCA
1 AAATTGAATCTTATAAATCTAAAGGTCATTATGCA
3623204 A
1 A
3623205 TGACCTTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (35 bp):
AAATTGAATCTTATAAATCTAAAGGTCATTATGCA
Found at i:3647173 original size:28 final size:28
Alignment explanation
Indices: 3647140--3647262 Score: 113
Period size: 28 Copynumber: 4.4 Consensus size: 28
3647130 AACATATTTC
* *
3647140 TTTTGTTACTC-CCTTTATATAATTTCTA
1 TTTTGTTACACACCTTGA-ATAATTTCTA
* * ** *
3647168 TTTTGTTATACACATTTTATAATTTATA
1 TTTTGTTACACACCTTGAATAATTTCTA
* * *
3647196 TTTCGTTTCACACCTTGACTAATTTCTA
1 TTTTGTTACACACCTTGAATAATTTCTA
* * *
3647224 TTTTGTTACACGCCCTGACTAATTTCTA
1 TTTTGTTACACACCTTGAATAATTTCTA
3647252 TTTTGTTACAC
1 TTTTGTTACAC
3647263 TCCATACCTT
Statistics
Matches: 77, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
28 73 0.95
29 4 0.05
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.51
Consensus pattern (28 bp):
TTTTGTTACACACCTTGAATAATTTCTA
Found at i:3660456 original size:16 final size:16
Alignment explanation
Indices: 3660435--3660469 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3660425 ACGACAAAGC
*
3660435 AAAAAAGGAAAGAAGA
1 AAAAAAAGAAAGAAGA
*
3660451 AAAAAAAGAAAGAATA
1 AAAAAAAGAAAGAAGA
3660467 AAA
1 AAA
3660470 GATTACGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAAAAAGAAAGAAGA
Found at i:3662166 original size:23 final size:23
Alignment explanation
Indices: 3662140--3662185 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3662130 ATTAATTACC
*
3662140 TAAAAAACAATTGGCATAATGCT
1 TAAAAAACAATGGGCATAATGCT
**
3662163 TAAAATGCAATGGGCATAATGCT
1 TAAAAAACAATGGGCATAATGCT
3662186 CAAATATATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (23 bp):
TAAAAAACAATGGGCATAATGCT
Found at i:3662279 original size:28 final size:27
Alignment explanation
Indices: 3662223--3662283 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 27
3662213 AAATTTAAAT
3662223 AAATTTTTATTTTTTTATTACATTCAATC
1 AAATTTTTATTTTTTTATT--ATTCAATC
*
3662252 AAATTTTCGTATTTTTTTATT-TTGAATC
1 AAATTTT--TATTTTTTTATTATTCAATC
3662280 AAAT
1 AAAT
3662284 AAACTCTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 10 0.34
29 7 0.24
31 12 0.41
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.57
Consensus pattern (27 bp):
AAATTTTTATTTTTTTATTATTCAATC
Found at i:3664995 original size:16 final size:16
Alignment explanation
Indices: 3664974--3665004 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3664964 TCACCCAATG
*
3664974 GTTAAATATATAAATA
1 GTTAAAAATATAAATA
3664990 GTTAAAAATATAAAT
1 GTTAAAAATATAAAT
3665005 GGAGGGAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
GTTAAAAATATAAATA
Found at i:3670047 original size:19 final size:20
Alignment explanation
Indices: 3670015--3670072 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
3670005 CCTCGTACTC
3670015 AAATATAAAAATAAT-TAAT
1 AAATATAAAAATAATATAAT
3670034 AAAT-TAAAATATAATATAAT
1 AAATATAAAA-ATAATATAAT
*
3670054 AAAAAAATAAAAATAATAT
1 --AAATATAAAAATAATAT
3670073 TTAATTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 5 0.15
19 9 0.27
20 4 0.12
22 10 0.30
23 5 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATATAAAAATAATATAAT
Found at i:3670061 original size:24 final size:23
Alignment explanation
Indices: 3670015--3670087 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 23
3670005 CCTCGTACTC
* * *
3670015 AAATATAAAAATAATTAATAAATTA
1 AAATAT-AATATAA-TAAAAAAATA
3670040 AAATATAATATAATAAAAAAATA
1 AAATATAATATAATAAAAAAATA
*
3670063 AAA-ATAATATTTAATTAAAAAATA
1 AAATATAATA--TAATAAAAAAATA
3670087 A
1 A
3670088 TCGAATCTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 6 0.14
23 11 0.26
24 19 0.45
25 6 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATATAATATAATAAAAAAATA
Found at i:3671827 original size:38 final size:38
Alignment explanation
Indices: 3671776--3671849 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
3671766 CACATTCTGG
3671776 GTAAAAGAACAATCAATAATAAAATGCATAGTATTCAC
1 GTAAAAGAACAATCAATAATAAAATGCATAGTATTCAC
*
3671814 GTAAAAGAACAATCAATATTAAAATGCATAGTATTC
1 GTAAAAGAACAATCAATAATAAAATGCATAGTATTC
3671850 TATTTTGGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.26
Consensus pattern (38 bp):
GTAAAAGAACAATCAATAATAAAATGCATAGTATTCAC
Found at i:3676708 original size:28 final size:28
Alignment explanation
Indices: 3676668--3676738 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
3676658 GCATATCAAG
* *
3676668 AAGTAGATGAATACTTGTAATCCACCAA
1 AAGTAGATGAATAATTGTAACCCACCAA
*
3676696 AAGTAGATGAATAATTTTAACCCACCAA
1 AAGTAGATGAATAATTGTAACCCACCAA
* *
3676724 AAGTGGATAAATAAT
1 AAGTAGATGAATAAT
3676739 GAAAAGAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (28 bp):
AAGTAGATGAATAATTGTAACCCACCAA
Found at i:3679554 original size:85 final size:85
Alignment explanation
Indices: 3679411--3679580 Score: 313
Period size: 85 Copynumber: 2.0 Consensus size: 85
3679401 TGAAGTAATG
* *
3679411 ATGAATATTCCTCTATTATTGGTGTCATATCGACTTCATTGAACACAAAATACCAGTAAGAAGGA
1 ATGAATATTCCTCTATTATTGGTCTCATATCAACTTCATTGAACACAAAATACCAGTAAGAAGGA
3679476 TCCCAAAACTAAGTGATTGC
66 TCCCAAAACTAAGTGATTGC
*
3679496 ATGAATATTCCTCTATTATTGGTCTCATATCAACTTCATTGAACACAAAATACTAGTAAGAAGGA
1 ATGAATATTCCTCTATTATTGGTCTCATATCAACTTCATTGAACACAAAATACCAGTAAGAAGGA
3679561 TCCCAAAACTAAGTGATTGC
66 TCCCAAAACTAAGTGATTGC
3679581 CTTAAGTAGC
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (85 bp):
ATGAATATTCCTCTATTATTGGTCTCATATCAACTTCATTGAACACAAAATACCAGTAAGAAGGA
TCCCAAAACTAAGTGATTGC
Found at i:3688545 original size:86 final size:87
Alignment explanation
Indices: 3688399--3688571 Score: 231
Period size: 86 Copynumber: 2.0 Consensus size: 87
3688389 ATCATAGTAA
* * * *
3688399 TTTTAACAATATTGGTTAAACAGACTTACTTAGATGAAGTCAACTGTTATGTAAAAAAG-CCTTT
1 TTTTAACAATATTAGTTAAACAGACTTACTTAGATGAAGTCAAATGTTAAGCAAAAAAGCCCTTT
* **
3688463 GGGGTTTCCTTTAAATATAGTT
66 GAGCCTTCCTTTAAATATAGTT
* * **
3688485 TTTTAATAATATTAGTTAAACAGACTTACTTAGATGAAGTTAAATGTTAAGCAAGTAAGCCCTTT
1 TTTTAACAATATTAGTTAAACAGACTTACTTAGATGAAGTCAAATGTTAAGCAAAAAAGCCCTTT
*
3688550 GAGCCTTCTTTTAAATATAGTT
66 GAGCCTTCCTTTAAATATAGTT
3688572 ATAGATTTAT
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
86 51 0.69
87 23 0.31
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.39
Consensus pattern (87 bp):
TTTTAACAATATTAGTTAAACAGACTTACTTAGATGAAGTCAAATGTTAAGCAAAAAAGCCCTTT
GAGCCTTCCTTTAAATATAGTT
Found at i:3699402 original size:29 final size:29
Alignment explanation
Indices: 3699365--3699519 Score: 117
Period size: 29 Copynumber: 5.5 Consensus size: 29
3699355 GATTTTGAAT
*
3699365 ATGACGTGTAACAATAATATTTTTTCAAC
1 ATGATGTGTAACAATAATATTTTTTCAAC
* * *
3699394 ATGATGTGTAATAACAGTATTGTTTTTCAAC
1 ATGATGTGTAACAATAATA-T-TTTTTCAAC
* * *
3699425 ATCAGGTGTAACAAT-AT-TTTTTTTAACC
1 ATGATGTGTAACAATAATATTTTTTCAA-C
* *
3699453 ATAATGTGTAAC-AT-AT-TTTTGT--AC
1 ATGATGTGTAACAATAATATTTTTTCAAC
* * *
3699477 ATGACGTGTAATAATAATATTTTTTTAAC
1 ATGATGTGTAACAATAATATTTTTTCAAC
*
3699506 ATGATGTATAACAA
1 ATGATGTGTAACAA
3699520 CCTAATCATA
Statistics
Matches: 98, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
24 10 0.10
25 3 0.03
26 2 0.02
27 21 0.21
28 12 0.12
29 28 0.29
30 2 0.02
31 20 0.20
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.41
Consensus pattern (29 bp):
ATGATGTGTAACAATAATATTTTTTCAAC
Found at i:3699447 original size:28 final size:28
Alignment explanation
Indices: 3699370--3699472 Score: 84
Period size: 28 Copynumber: 3.6 Consensus size: 28
3699360 TGAATATGAC
* *
3699370 GTGTAACAATAATATTTTTTCAACATGATG
1 GTGTAACAAT-ATTTTTTTTCAACAT-AAG
* * * *
3699400 TGTAATAACAGTATTGTTTTTCAACATCAG
1 -GT-GTAACAATATTTTTTTTCAACATAAG
*
3699430 GTGTAACAATATTTTTTTT-AACCATAAT
1 GTGTAACAATATTTTTTTTCAA-CATAAG
3699458 GTGTAAC-ATATTTTT
1 GTGTAACAATATTTTT
3699473 GTACATGACG
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
27 10 0.17
28 25 0.42
29 2 0.03
30 1 0.02
31 15 0.25
32 6 0.10
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.44
Consensus pattern (28 bp):
GTGTAACAATATTTTTTTTCAACATAAG
Found at i:3699654 original size:69 final size:68
Alignment explanation
Indices: 3699573--3699707 Score: 189
Period size: 69 Copynumber: 2.0 Consensus size: 68
3699563 CTTAACCATA
* * * * *
3699573 GCGTGTCACACGTTTTTATACATGACGTGTAATAACCTAATCATGGCATATAACATGTTTTTGTA
1 GCGTGTCACACGTTTTTATACATAACGTGTAACAACCT-ACCATGACATATAACATGTTTCTGTA
3699638 CATG
65 CATG
* * *
3699642 GCGTGTCACACGTTTTTGTACATAACGTGTAACAATCTACCATGACATGTAACATGTTTCTGTAC
1 GCGTGTCACACGTTTTTATACATAACGTGTAACAACCTACCATGACATATAACATGTTTCTGTAC
3699707 A
66 A
3699708 CGGTGTGTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
68 24 0.41
69 34 0.59
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (68 bp):
GCGTGTCACACGTTTTTATACATAACGTGTAACAACCTACCATGACATATAACATGTTTCTGTAC
ATG
Found at i:3703880 original size:2 final size:2
Alignment explanation
Indices: 3703873--3703918 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3703863 TAGTGCGGCA
3703873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3703915 AT AT
1 AT AT
3703919 TCTCCATAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3710146 original size:36 final size:37
Alignment explanation
Indices: 3710106--3710182 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 37
3710096 AATTAAACAT
*
3710106 AACCTTTACATAGTAC-CTTTCAAGAGGATCAAGCAC
1 AACCTTTACACAGTACTCTTTCAAGAGGATCAAGCAC
* * *
3710142 AACC-TTACACATTGCTTTTTCAAGAGGATCAAGCAC
1 AACCTTTACACAGTACTCTTTCAAGAGGATCAAGCAC
3710178 AACCT
1 AACCT
3710183 CTTTGTCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 8 0.23
36 27 0.77
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (37 bp):
AACCTTTACACAGTACTCTTTCAAGAGGATCAAGCAC
Found at i:3711914 original size:16 final size:16
Alignment explanation
Indices: 3711893--3711931 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
3711883 TTAATAAATT
*
3711893 ATTAATTTATCGATTA
1 ATTAATATATCGATTA
*
3711909 ATTAATATCTCGATTA
1 ATTAATATATCGATTA
3711925 ATTAATA
1 ATTAATA
3711932 AATTTTCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (16 bp):
ATTAATATATCGATTA
Found at i:3726465 original size:3 final size:3
Alignment explanation
Indices: 3726457--3726481 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3726447 AGGTGTCGCG
3726457 GCA GCA GCA GCA GCA GCA GCA GCA G
1 GCA GCA GCA GCA GCA GCA GCA GCA G
3726482 TGGCTGTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.36, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:3753891 original size:31 final size:31
Alignment explanation
Indices: 3753856--3753914 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3753846 TATAAGAGTT
* *
3753856 TATTTGATTCAAAATAAAAATATAAAAAATA
1 TATTTGACTCAAAATAAAAATACAAAAAATA
3753887 TATTTGACTCAAAATAAAAATACAAAAA
1 TATTTGACTCAAAATAAAAATACAAAAA
3753915 CTTAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.29
Consensus pattern (31 bp):
TATTTGACTCAAAATAAAAATACAAAAAATA
Found at i:3754215 original size:14 final size:14
Alignment explanation
Indices: 3754196--3754229 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3754186 AAGAAAAGAG
3754196 AAAAAAAAAGGAAA
1 AAAAAAAAAGGAAA
*
3754210 AAAAAAAGAGGAAA
1 AAAAAAAAAGGAAA
3754224 AAAAAA
1 AAAAAA
3754230 GGCAAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGGAAA
Found at i:3754236 original size:11 final size:12
Alignment explanation
Indices: 3754183--3754238 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
3754173 AAGAAAACAG
*
3754183 GGAAAGAAAAGA
1 GGAAAAAAAAGA
3754195 -GAAAAAAAA-A
1 GGAAAAAAAAGA
3754205 GGAAAAAAAAAAGA
1 GG--AAAAAAAAGA
3754219 GGAAAAAAAA-A
1 GGAAAAAAAAGA
3754230 GGCAAAAAA
1 GG-AAAAAA
3754239 GAAAAAGGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
10 1 0.03
11 12 0.32
12 14 0.37
13 8 0.21
14 3 0.08
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (12 bp):
GGAAAAAAAAGA
Found at i:3754238 original size:14 final size:13
Alignment explanation
Indices: 3754196--3754247 Score: 63
Period size: 12 Copynumber: 3.9 Consensus size: 13
3754186 AAGAAAAGAG
3754196 AAAAAAAAAGGAA
1 AAAAAAAAAGGAA
3754209 AAAAAAAAGAGG--
1 AAAAAAAA-AGGAA
3754221 AAAAAAAAAGGCAA
1 AAAAAAAAAGG-AA
3754235 AAAAGAAAAAGGA
1 AAAA-AAAAAGGA
3754248 GAGGAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 3 0.09
12 8 0.24
13 8 0.24
14 8 0.24
15 7 0.21
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGGAA
Found at i:3757496 original size:13 final size:13
Alignment explanation
Indices: 3757478--3757502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3757468 GCCCTTTGCT
3757478 AATGCTTATTTGG
1 AATGCTTATTTGG
3757491 AATGCTTATTTG
1 AATGCTTATTTG
3757503 CAAGATTATG
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:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
AATGCTTATTTGG
Found at i:3768610 original size:12 final size:12
Alignment explanation
Indices: 3768587--3768627 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
3768577 GATCTCATTC
3768587 TTTTATTTTTTTA
1 TTTTA-TTTTTTA
3768600 TTTTATTTTTTA
1 TTTTATTTTTTA
* *
3768612 TTTAATTATTTA
1 TTTTATTTTTTA
3768624 TTTT
1 TTTT
3768628 TAAGGGCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 20 0.80
13 5 0.20
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:3768612 original size:20 final size:19
Alignment explanation
Indices: 3768587--3768628 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3768577 GATCTCATTC
**
3768587 TTTTATTTTTTTATTTTATT
1 TTTTATTTAATTA-TTTATT
3768607 TTTTATTTAATTATTTATT
1 TTTTATTTAATTATTTATT
3768626 TTT
1 TTT
3768629 AAGGGCGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTATTTAATTATTTATT
Found at i:3792328 original size:21 final size:21
Alignment explanation
Indices: 3792302--3792343 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3792292 TACTTATGAC
3792302 CCATGCCATTG-GAGTTAATTG
1 CCATGCCATTGAG-GTTAATTG
3792323 CCATGCCATTGAGGTTAATTG
1 CCATGCCATTGAGGTTAATTG
3792344 TGATTTATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (21 bp):
CCATGCCATTGAGGTTAATTG
Found at i:3811703 original size:32 final size:32
Alignment explanation
Indices: 3811662--3811724 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3811652 CGTGAGCTAA
*
3811662 CCCATCCCAAATGTAGCAGGCGCCATTAAGTC
1 CCCATCCCAAATGTAGCAGGCACCATTAAGTC
3811694 CCCATCCCAAATGTAGCAGGCACCATTAAGT
1 CCCATCCCAAATGTAGCAGGCACCATTAAGT
3811725 ATTAAAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.19
Consensus pattern (32 bp):
CCCATCCCAAATGTAGCAGGCACCATTAAGTC
Found at i:3814357 original size:17 final size:17
Alignment explanation
Indices: 3814335--3814370 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3814325 TCAGCTTTGA
3814335 TTGCATTTCAATTTCAT
1 TTGCATTTCAATTTCAT
*
3814352 TTGCATTTCAGTTTCAT
1 TTGCATTTCAATTTCAT
3814369 TT
1 TT
3814371 TGACGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.17, G:0.08, T:0.56
Consensus pattern (17 bp):
TTGCATTTCAATTTCAT
Found at i:3820521 original size:10 final size:11
Alignment explanation
Indices: 3820497--3820526 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3820487 TAAACATGTT
3820497 AAAAATGTGCG
1 AAAAATGTGCG
*
3820508 AAAAATGTGCA
1 AAAAATGTGCG
3820519 AAAAATGT
1 AAAAATGT
3820527 TTAAAGGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (11 bp):
AAAAATGTGCG
Found at i:3821560 original size:2 final size:2
Alignment explanation
Indices: 3821553--3821582 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3821543 TCGGTTTGTC
3821553 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3821583 GAATATAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3826709 original size:29 final size:30
Alignment explanation
Indices: 3826660--3826740 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 30
3826650 TCTGCTTTTT
* *
3826660 CCTTATTCTCTTATACTTGTTCATGTACAA
1 CCTTATTCTCTTGTACCTGTTCATGTACAA
**
3826690 CCTT-TTCTCTTGTACCTGTTCATAAAC-A
1 CCTTATTCTCTTGTACCTGTTCATGTACAA
* **
3826718 GCTTCCTCTCTTGTACCTGTTCA
1 CCTTATTCTCTTGTACCTGTTCA
3826741 CGTATAACTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 4 0.09
29 36 0.82
30 4 0.09
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (30 bp):
CCTTATTCTCTTGTACCTGTTCATGTACAA
Found at i:3829364 original size:2 final size:2
Alignment explanation
Indices: 3829359--3829388 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3829349 ATATAGTAAC
3829359 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3829389 GATTTGCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3844952 original size:17 final size:17
Alignment explanation
Indices: 3844930--3844965 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3844920 TTTAGATTAT
*
3844930 TTACAATTATATTTTTC
1 TTACAATTATATTTCTC
3844947 TTACAATTATATTTCTC
1 TTACAATTATATTTCTC
3844964 TT
1 TT
3844966 TTTTTGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.58
Consensus pattern (17 bp):
TTACAATTATATTTCTC
Found at i:3847012 original size:21 final size:21
Alignment explanation
Indices: 3846986--3847029 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3846976 TGTTTATCAC
3846986 TTACATAAACGGAATTTGCCA
1 TTACATAAACGGAATTTGCCA
*
3847007 TTACATAAATGGAATTTGCCA
1 TTACATAAACGGAATTTGCCA
3847028 TT
1 TT
3847030 GGCTAGCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (21 bp):
TTACATAAACGGAATTTGCCA
Found at i:3863772 original size:2 final size:2
Alignment explanation
Indices: 3863765--3863791 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3863755 NNNNNNNNNN
3863765 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 T
3863792 TAAAATACAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3864496 original size:20 final size:21
Alignment explanation
Indices: 3864465--3864504 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3864455 AACGCTTTTA
*
3864465 AGTTTAGTTAGTTTTGATCTT
1 AGTTTAGTTAGTTTTAATCTT
3864486 AGTTT-GTTAGTTTTAATCT
1 AGTTTAGTTAGTTTTAATCT
3864505 CATTTTCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.17, T:0.57
Consensus pattern (21 bp):
AGTTTAGTTAGTTTTAATCTT
Found at i:3865023 original size:18 final size:17
Alignment explanation
Indices: 3864996--3865030 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3864986 TTTAGTTATC
3864996 ATTTGATTAATTATAAAA
1 ATTTGATTAATT-TAAAA
*
3865014 ATTTGTTTAATTTAAAA
1 ATTTGATTAATTTAAAA
3865031 TAAAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
ATTTGATTAATTTAAAA
Found at i:3872196 original size:15 final size:16
Alignment explanation
Indices: 3872176--3872205 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3872166 GGAATACAAC
3872176 AGAAACTGA-AGAAAA
1 AGAAACTGAGAGAAAA
3872191 AGAAACTGAGAGAAA
1 AGAAACTGAGAGAAA
3872206 CTCCAGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.07, G:0.23, T:0.07
Consensus pattern (16 bp):
AGAAACTGAGAGAAAA
Found at i:3879857 original size:23 final size:23
Alignment explanation
Indices: 3879831--3879876 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3879821 TGACTTCCTT
3879831 ATTTACATCATCCATGAATAAGA
1 ATTTACATCATCCATGAATAAGA
3879854 ATTTACATCATCCATGAATAAGA
1 ATTTACATCATCCATGAATAAGA
3879877 CTGTAATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (23 bp):
ATTTACATCATCCATGAATAAGA
Found at i:3881136 original size:15 final size:14
Alignment explanation
Indices: 3881099--3881135 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
3881089 TTAAAAACAG
*
3881099 TATTAAAATATATA
1 TATTAAAATAAATA
3881113 TAATTAAAATAAATA
1 T-ATTAAAATAAATA
3881128 TATTAAAA
1 TATTAAAA
3881136 AACTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TATTAAAATAAATA
Found at i:3890218 original size:12 final size:12
Alignment explanation
Indices: 3890201--3890226 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3890191 ATATATATAA
3890201 TATAATTACTTT
1 TATAATTACTTT
3890213 TATAATTACTTT
1 TATAATTACTTT
3890225 TA
1 TA
3890227 CCTATTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
TATAATTACTTT
Found at i:3892221 original size:20 final size:19
Alignment explanation
Indices: 3892159--3892222 Score: 56
Period size: 22 Copynumber: 3.1 Consensus size: 19
3892149 TAGTGAAAAA
*
3892159 TAAAAAATTTAAGCATAATAT
1 TAAAAAATTTAA--ATAATTT
*
3892180 TAAAAAAGTATATAAATTATTT
1 TAAAAAA-T-T-TAAATAATTT
3892202 TAAAAAATTTAAATAAATTT
1 TAAAAAATTTAAAT-AATTT
3892222 T
1 T
3892223 TATTTTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
19 5 0.14
20 6 0.17
21 8 0.22
22 13 0.36
23 1 0.03
24 3 0.08
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (19 bp):
TAAAAAATTTAAATAATTT
Found at i:3897240 original size:28 final size:30
Alignment explanation
Indices: 3897179--3897234 Score: 89
Period size: 28 Copynumber: 1.9 Consensus size: 30
3897169 AATCAAGTCA
*
3897179 TTATATTTTTATTTTAAGTCAAATAAGTTG
1 TTATATTTTTATTTTAAGTCAAATAAATTG
3897209 TTATATTTTT-TTTT-AGTCAAATAAAT
1 TTATATTTTTATTTTAAGTCAAATAAAT
3897235 CTTTATGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 11 0.44
29 4 0.16
30 10 0.40
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (30 bp):
TTATATTTTTATTTTAAGTCAAATAAATTG
Found at i:3899464 original size:18 final size:18
Alignment explanation
Indices: 3899429--3899487 Score: 70
Period size: 17 Copynumber: 3.3 Consensus size: 18
3899419 AAAACATATG
*
3899429 AATAAATAGAATAGAAATA
1 AATAAATA-AATATAAATA
3899448 AATAAATAAATATAAAT-
1 AATAAATAAATATAAATA
3899465 AATAATATAAAT-TAAA-A
1 AATAA-ATAAATATAAATA
3899482 AATAAA
1 AATAAA
3899488 AAAACTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
16 1 0.03
17 14 0.38
18 14 0.38
19 8 0.22
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (18 bp):
AATAAATAAATATAAATA
Found at i:3899471 original size:12 final size:14
Alignment explanation
Indices: 3899430--3899485 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
3899420 AAACATATGA
3899430 ATAAATAGAATAGAA-
1 ATAAATA-AATA-AAT
3899445 ATAAATAAATAAAT
1 ATAAATAAATAAAT
3899459 ATAAAT-AAT-AAT
1 ATAAATAAATAAAT
3899471 ATAAATTAAA-AAAT
1 ATAAA-TAAATAAAT
3899485 A
1 A
3899486 AAAAAACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 8 0.22
13 6 0.16
14 16 0.43
15 7 0.19
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (14 bp):
ATAAATAAATAAAT
Found at i:3899487 original size:30 final size:29
Alignment explanation
Indices: 3899430--3899487 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
3899420 AAACATATGA
3899430 ATAAATAGAATAGAAATAAATAAATAAAT
1 ATAAATAGAATAGAAATAAATAAATAAAT
* *
3899459 ATAAATAATAATATAAATTAAA-AAATAAA
1 ATAAAT-AGAATAGAAA-TAAATAAATAAA
3899488 AAAACTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.24
30 15 0.60
31 4 0.16
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (29 bp):
ATAAATAGAATAGAAATAAATAAATAAAT
Found at i:3901838 original size:3 final size:3
Alignment explanation
Indices: 3901832--3901870 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
3901822 TTTAATATAT
*
3901832 ATA ATA ATA ACA ATA ATAA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA AT
3901871 TTTTTCGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3901856 original size:19 final size:19
Alignment explanation
Indices: 3901832--3901869 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3901822 TTTAATATAT
3901832 ATAATAATAACAATAATAA
1 ATAATAATAACAATAATAA
*
3901851 ATAATAATAATAATAATAA
1 ATAATAATAACAATAATAA
3901870 TTTTTTCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAATAATAACAATAATAA
Found at i:3907234 original size:23 final size:23
Alignment explanation
Indices: 3907189--3907235 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3907179 AATAATAATT
** * *
3907189 TTAATTTATTTTTTTATTTTCAA
1 TTAATTTATTTAATAATTCTCAA
3907212 TTAATTTATTTAATAATTCTCAA
1 TTAATTTATTTAATAATTCTCAA
3907235 T
1 T
3907236 AGCTATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (23 bp):
TTAATTTATTTAATAATTCTCAA
Found at i:3917192 original size:36 final size:36
Alignment explanation
Indices: 3917152--3917223 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3917142 TATGTATGTA
3917152 AGCATTCTAGTTGGCGAATTCTTGATATGCAAGGTT
1 AGCATTCTAGTTGGCGAATTCTTGATATGCAAGGTT
3917188 AGCATTCTAGTTGGCGAATTCTTGATATGCAAGGTT
1 AGCATTCTAGTTGGCGAATTCTTGATATGCAAGGTT
3917224 GGCTGCTACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (36 bp):
AGCATTCTAGTTGGCGAATTCTTGATATGCAAGGTT
Found at i:3923523 original size:24 final size:26
Alignment explanation
Indices: 3923495--3923549 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
3923485 ATACTCATTT
*
3923495 CAAAGAAGATGGA-AAATAGATA-AA
1 CAAAGAAGATGGATAAAGAGATAGAA
*
3923519 CAAAG-AGATGGATAGAGAGATAGAA
1 CAAAGAAGATGGATAAAGAGATAGAA
3923544 CAAAGA
1 CAAAGA
3923550 TTATAGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 7 0.27
24 12 0.46
25 7 0.27
ACGTcount: A:0.58, C:0.05, G:0.25, T:0.11
Consensus pattern (26 bp):
CAAAGAAGATGGATAAAGAGATAGAA
Found at i:3930730 original size:51 final size:51
Alignment explanation
Indices: 3930650--3930783 Score: 178
Period size: 51 Copynumber: 2.6 Consensus size: 51
3930640 CATGCTATTC
* * * * *
3930650 CTCCAACTCAGAGGCAGATGAATCCTCCTCTTCTGAAGAACTCGATAATTT
1 CTCCGACTCAGAGACGGTTGAATCTTCCTCTTCTGAAGAACTCGATAATTT
* * * *
3930701 CTCCGACTCGGAGACGGTTGAATCTTCCTCTTCTGAAGACCTTGGTAATTT
1 CTCCGACTCAGAGACGGTTGAATCTTCCTCTTCTGAAGAACTCGATAATTT
*
3930752 CTCTGACTCAGAGACGGTTGAATCTTCCTCTT
1 CTCCGACTCAGAGACGGTTGAATCTTCCTCTT
3930784 TGTCTTGATC
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 72 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (51 bp):
CTCCGACTCAGAGACGGTTGAATCTTCCTCTTCTGAAGAACTCGATAATTT
Found at i:3930918 original size:144 final size:144
Alignment explanation
Indices: 3930719--3930993 Score: 390
Period size: 144 Copynumber: 1.9 Consensus size: 144
3930709 CGGAGACGGT
** * *
3930719 TGAATCTTCCTCTTCTGAAGACCTTGGTAATTTCTCTGACTCAGAGACGGTTGAATCTTCCTCTT
1 TGAATCTTCCTCTTCTGAAGACAATGGTAATTTCTCCGACTCAGAGACGGATGAATCTTCCTCTT
** * * * *
3930784 TGTCTTGATCTGTTGACTCACTA-CTATTGAAATATTCCCTCCACCACATTGTCTTTTCAGGATT
66 TGTCTTGATCCATTGACTCACTATC-ATCGAAACATTCCCTCCACCACATTCTCTTCTCAGGATT
3930848 CAATTCAAAGGGAGA
130 CAATTCAAAGGGAGA
* *
3930863 TGAATCTTCGTCTTCTGAAGATAATGGTAATTTCTCCGACTCAGAGACGGATGAATCTTCCTCTT
1 TGAATCTTCCTCTTCTGAAGACAATGGTAATTTCTCCGACTCAGAGACGGATGAATCTTCCTCTT
** * *
3930928 TGTCTTGATCCATTGACTCGTTATCATCGAAACATTCCCTCCCCCACATTCTCTTCTGAGGATTC
66 TGTCTTGATCCATTGACTCACTATCATCGAAACATTCCCTCCACCACATTCTCTTCTCAGGATTC
3930993 A
131 A
3930994 TTTCTAGCGA
Statistics
Matches: 114, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
144 113 0.99
145 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (144 bp):
TGAATCTTCCTCTTCTGAAGACAATGGTAATTTCTCCGACTCAGAGACGGATGAATCTTCCTCTT
TGTCTTGATCCATTGACTCACTATCATCGAAACATTCCCTCCACCACATTCTCTTCTCAGGATTC
AATTCAAAGGGAGA
Found at i:3958086 original size:6 final size:6
Alignment explanation
Indices: 3958077--3958141 Score: 64
Period size: 6 Copynumber: 11.3 Consensus size: 6
3958067 GACCTTGACA
*
3958077 AGGATG AGGATG ATGATG AGGATG AGGAT- --GATG AGGATG AGGATG
1 AGGATG AGGATG AGGATG AGGATG AGGATG AGGATG AGGATG AGGATG
* * * *
3958122 ATGAGG ATGATG ATGATG AG
1 AGGATG AGGATG AGGATG AG
3958142 AACCAAGAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
3 3 0.06
6 47 0.94
ACGTcount: A:0.34, C:0.00, G:0.45, T:0.22
Consensus pattern (6 bp):
AGGATG
Found at i:3958091 original size:9 final size:9
Alignment explanation
Indices: 3958079--3958140 Score: 76
Period size: 9 Copynumber: 7.2 Consensus size: 9
3958069 CCTTGACAAG
3958079 GATGAGGAT
1 GATGAGGAT
* *
3958088 GATGATGAG
1 GATGAGGAT
3958097 GATGAGGAT
1 GATGAGGAT
3958106 GATGA-G--
1 GATGAGGAT
3958112 GATGAGGAT
1 GATGAGGAT
3958121 GATGAGGAT
1 GATGAGGAT
*
3958130 GATGATGAT
1 GATGAGGAT
3958139 GA
1 GA
3958141 GAACCAAGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 5 0.11
7 1 0.02
8 1 0.02
9 38 0.84
ACGTcount: A:0.34, C:0.00, G:0.44, T:0.23
Consensus pattern (9 bp):
GATGAGGAT
Found at i:3958108 original size:15 final size:15
Alignment explanation
Indices: 3958088--3958141 Score: 99
Period size: 15 Copynumber: 3.6 Consensus size: 15
3958078 GGATGAGGAT
3958088 GATGATGAGGATGAG
1 GATGATGAGGATGAG
3958103 GATGATGAGGATGAG
1 GATGATGAGGATGAG
*
3958118 GATGATGAGGATGAT
1 GATGATGAGGATGAG
3958133 GATGATGAG
1 GATGATGAG
3958142 AACCAAGAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.44, T:0.22
Consensus pattern (15 bp):
GATGATGAGGATGAG
Found at i:3992263 original size:24 final size:23
Alignment explanation
Indices: 3992227--3992272 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
3992217 TACAATAATC
*
3992227 TTATCCTAATATAATTAGGATATG
1 TTATCCTAATATAACTA-GATATG
* *
3992251 TTATCTTAGTATAACTAGATAT
1 TTATCCTAATATAACTAGATAT
3992273 AAAGATCTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (23 bp):
TTATCCTAATATAACTAGATATG
Found at i:3995473 original size:23 final size:23
Alignment explanation
Indices: 3995445--3995494 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
3995435 ATTAAATTAA
* *
3995445 TAAAAAAAATTTATTTAAATTTTT
1 TAAAAATAATTTA-ATAAATTTTT
*
3995469 TAAAAATAATTTAATAACTTTTT
1 TAAAAATAATTTAATAAATTTTT
3995492 TAA
1 TAA
3995495 GTATTATACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAAAATAATTTAATAAATTTTT
Found at i:3998039 original size:48 final size:47
Alignment explanation
Indices: 3997859--3998048 Score: 195
Period size: 48 Copynumber: 3.9 Consensus size: 47
3997849 AGGAGATGAG
* * **
3997859 AAAGAATCATCCAGTTTCTTACTTGGTATGAAGTGCTCTGGAAAGAGA
1 AAAGAATCATCCACTTTCTTACTTGGTATGGAGTGCTCTGGAAAG-CC
* * *
3997907 AAAGAATCATCCAATCTCTCATCACTTGGTGTGGA--GCTCTGTAGAAAGCC
1 AAAGAATCATCC-A-CTTTC-TTACTTGGTATGGAGTGCTCTG--GAAAGCC
* **
3997957 AAAAAATTCATCCGGTTTCTTACTTGGTATGGAGTGCTCTGGAAAGCC
1 AAAGAA-TCATCCACTTTCTTACTTGGTATGGAGTGCTCTGGAAAGCC
*
3998005 AAAGGAATCATCCACTTTCTTACTTGGTATGGAGTGTTCTGGAA
1 AAA-GAATCATCCACTTTCTTACTTGGTATGGAGTGCTCTGGAA
3998049 TGCTAAAAGA
Statistics
Matches: 116, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
48 68 0.59
49 12 0.10
50 14 0.12
51 22 0.19
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (47 bp):
AAAGAATCATCCACTTTCTTACTTGGTATGGAGTGCTCTGGAAAGCC
Found at i:4008660 original size:4 final size:4
Alignment explanation
Indices: 4008651--4008687 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
4008641 GTGATAATGA
4008651 AATT AATT AATT AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT A
4008688 CAACTGATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
AATT
Found at i:4023944 original size:29 final size:28
Alignment explanation
Indices: 4023910--4023976 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
4023900 ATAAAATATT
4023910 TCATAAAAT-ATGAAAATTTAAAATTATAA
1 TCATAAAATCATGAAAATTT-AAA-TATAA
*
4023939 TCATAAAAATCATTAAAATTTAAATATAA
1 TCAT-AAAATCATGAAAATTTAAATATAA
*
4023968 TAATAAAAT
1 TCATAAAAT
4023977 TTAATATTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 5 0.15
29 12 0.35
30 8 0.24
31 9 0.26
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (28 bp):
TCATAAAATCATGAAAATTTAAATATAA
Found at i:4034554 original size:29 final size:29
Alignment explanation
Indices: 4034499--4034555 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
4034489 GTTAACAAAA
**
4034499 GCATTCATGCTCCACCATGAATGTTCATG
1 GCATTCATGCTCCACCATGAACATTCATG
4034528 GCATTCATGCTCCACCATGAACATTCAT
1 GCATTCATGCTCCACCATGAACATTCAT
4034556 CTATAGGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (29 bp):
GCATTCATGCTCCACCATGAACATTCATG
Found at i:4044576 original size:28 final size:29
Alignment explanation
Indices: 4044503--4044577 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
4044493 AGAAAAAGTG
*
4044503 TATGTTATAAAAAGAGTTAATTAACATATAA
1 TATGTTATAAAAA-A-TTAATTAACATAGAA
* * * *
4044534 TATGTTATGATAAATT-ATTGATATAGAA
1 TATGTTATAAAAAATTAATTAACATAGAA
4044562 TATGTTATAAAAAATT
1 TATGTTATAAAAAATT
4044578 TAAATTTATA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 23 0.62
29 2 0.05
30 1 0.03
31 11 0.30
ACGTcount: A:0.48, C:0.01, G:0.11, T:0.40
Consensus pattern (29 bp):
TATGTTATAAAAAATTAATTAACATAGAA
Found at i:4045653 original size:41 final size:41
Alignment explanation
Indices: 4045601--4045678 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
4045591 GTTGTTCTTC
*
4045601 AATATACTTAGTTGATTAAGTGGTTTGATTTATACATTCAA
1 AATATACTTAGTTGATTAAGTAGTTTGATTTATACATTCAA
*
4045642 AATATACTTAGTTGATTAAGTAGTTTGATTTGTACAT
1 AATATACTTAGTTGATTAAGTAGTTTGATTTATACAT
4045679 AGGGTAGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.45
Consensus pattern (41 bp):
AATATACTTAGTTGATTAAGTAGTTTGATTTATACATTCAA
Found at i:4045986 original size:13 final size:13
Alignment explanation
Indices: 4045970--4045995 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4045960 TAGATTTTAA
4045970 ATTAGTTTTAATT
1 ATTAGTTTTAATT
4045983 ATTAGTTTTAATT
1 ATTAGTTTTAATT
4045996 TTTCTTATTA
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
ATTAGTTTTAATT
Found at i:4046825 original size:13 final size:13
Alignment explanation
Indices: 4046807--4046834 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4046797 TGACGGCCAG
4046807 AGGCATGTAGTCA
1 AGGCATGTAGTCA
4046820 AGGCATGTAGTCA
1 AGGCATGTAGTCA
4046833 AG
1 AG
4046835 TCTAGGAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.21
Consensus pattern (13 bp):
AGGCATGTAGTCA
Found at i:4050891 original size:21 final size:22
Alignment explanation
Indices: 4050865--4050911 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
4050855 CTAGTTGGTT
4050865 TTGAAATTAATTATAATGGCA-
1 TTGAAATTAATTATAATGGCAC
4050886 TTGAAATTAATTATAATGGCAC
1 TTGAAATTAATTATAATGGCAC
4050908 TTGA
1 TTGA
4050912 TGTCACATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (22 bp):
TTGAAATTAATTATAATGGCAC
Found at i:4052099 original size:23 final size:23
Alignment explanation
Indices: 4052073--4052127 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
4052063 TATACTTGTG
4052073 TCCTTCATTATAAACAAACTTCT
1 TCCTTCATTATAAACAAACTTCT
4052096 TCCTTCATTATAAACAAACTTCT
1 TCCTTCATTATAAACAAACTTCT
*
4052119 TCCGTCATT
1 TCCTTCATT
4052128 GAAAGACTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.27, G:0.02, T:0.40
Consensus pattern (23 bp):
TCCTTCATTATAAACAAACTTCT
Found at i:4053157 original size:17 final size:17
Alignment explanation
Indices: 4053135--4053167 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4053125 ACATATCATA
4053135 TATTGTAGTTTCTTATG
1 TATTGTAGTTTCTTATG
4053152 TATTGTAGTTTCTTAT
1 TATTGTAGTTTCTTAT
4053168 TACATTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.61
Consensus pattern (17 bp):
TATTGTAGTTTCTTATG
Found at i:4073834 original size:35 final size:35
Alignment explanation
Indices: 4073783--4073868 Score: 127
Period size: 35 Copynumber: 2.5 Consensus size: 35
4073773 CAATATCAAG
* * *
4073783 GTGGTATTCTTACCCCCATAGTGGGCTTTATTCAT
1 GTGGTATTCTTACCCCCATAGTAGACTCTATTCAT
*
4073818 GTGGTATTCTTTCCCCCATAGTAGACTCTATTCAT
1 GTGGTATTCTTACCCCCATAGTAGACTCTATTCAT
*
4073853 GTGGTATTATTACCCC
1 GTGGTATTCTTACCCC
4073869 AACGATGGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (35 bp):
GTGGTATTCTTACCCCCATAGTAGACTCTATTCAT
Found at i:4073952 original size:34 final size:34
Alignment explanation
Indices: 4073853--4073956 Score: 136
Period size: 35 Copynumber: 3.0 Consensus size: 34
4073843 CTCTATTCAT
*
4073853 GTGGTATTATTACCCCAACGATGGGCGATAATCAA
1 GTGGTATTATTACCCC-ACGATGGGCAATAATCAA
* *
4073888 GGGGTATTCTTACCCTCACGATGGGCAATAATCAA
1 GTGGTATTATTACCC-CACGATGGGCAATAATCAA
* * *
4073923 GTGGTATTTTTTCCCCACGTTGGGCAATAATCAA
1 GTGGTATTATTACCCCACGATGGGCAATAATCAA
4073957 TATTCATGAG
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
34 18 0.30
35 42 0.69
36 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (34 bp):
GTGGTATTATTACCCCACGATGGGCAATAATCAA
Found at i:4081760 original size:12 final size:11
Alignment explanation
Indices: 4081735--4081772 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4081725 TTTTCACACA
4081735 TCTTTCTC-TC
1 TCTTTCTCTTC
*
4081745 TCTTTCTTTTTC
1 TCTTTC-TCTTC
4081757 TCTTTCTCTTC
1 TCTTTCTCTTC
4081768 TCTTT
1 TCTTT
4081773 TATTCTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 6 0.25
11 10 0.42
12 8 0.33
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (11 bp):
TCTTTCTCTTC
Found at i:4085224 original size:42 final size:42
Alignment explanation
Indices: 4085177--4085259 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
4085167 ATTTGATTGA
*
4085177 TTGAAAAATGCTCAATGGTAGTGATATATAGTAACTTTTAGG
1 TTGAAAAATGCTCAATGGTAGTAATATATAGTAACTTTTAGG
* *
4085219 TTGAAAAATGCTTAATGGTAGTAATTTATAGTAACTTTTAG
1 TTGAAAAATGCTCAATGGTAGTAATATATAGTAACTTTTAG
4085260 CTAGGAATGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (42 bp):
TTGAAAAATGCTCAATGGTAGTAATATATAGTAACTTTTAGG
Found at i:4098124 original size:208 final size:208
Alignment explanation
Indices: 4097636--4098258 Score: 1034
Period size: 208 Copynumber: 3.0 Consensus size: 208
4097626 GTACTTAGTC
*
4097636 TGAACTGAATTCCTACTGCTCTTGAAAACAGCATAATCATTTTTGTCCTCAATTATCATTATCTA
1 TGAACTGAATTCCTCCTGCTCTTGAAAACAGCATAATCATTTTTGTCCTCAATTATCATTATCTA
* * *
4097701 CAATATCTTAGGTGTACAGCATTGACCAATTTATAACTGATAAGAAACATGCTATGCTGAGTTTC
66 CAATATCTTAGGTGTACAGCATTGACCAATTTATAGCTGATAAGAAACATGATATGCTGAATTTC
* *
4097766 CATCTCCTCAATTTTCAA-TTTTACCATGAGACAGTATTATCCACAAATCATTAGGCATCGGATA
131 CATCTCCTCAATTTTCAATTTTTACTATGAGACAGTATTATCCACAAATCATTAGGCATAGGATA
4097830 ATGAAAAGGAGGG
196 ATGAAAAGGAGGG
* * * * * ** * *
4097843 TGAAGTGAATTCCTCCTGCCCTTGAAAACGGCATAAACCTTTTCATCCTCCATTATGATTATCTA
1 TGAACTGAATTCCTCCTGCTCTTGAAAACAGCATAATCATTTTTGTCCTCAATTATCATTATCTA
*
4097908 CAATATCTTAGGTGTACAGCATTGATCAATTTATAGCTGATAAGAAACATGATATGCTGAATTTC
66 CAATATCTTAGGTGTACAGCATTGACCAATTTATAGCTGATAAGAAACATGATATGCTGAATTTC
4097973 CATCTCCTCAATTTTCAATTTTTACTATCG-GACAGTATTATCCACAAATCATTAGGCATAGGAT
131 CATCTCCTCAATTTTCAATTTTTACTAT-GAGACAGTATTATCCACAAATCATTAGGCATAGGAT
4098037 AATGAAAAGGAGGG
195 AATGAAAAGGAGGG
4098051 TGAACTGAATTCCTCCTGCTCTTGAAAACAGCATAATCATTTTTGTCCTCAATTATCATTATCTA
1 TGAACTGAATTCCTCCTGCTCTTGAAAACAGCATAATCATTTTTGTCCTCAATTATCATTATCTA
* **
4098116 CAATATCTTAGGTGTACAGCATTGACCAATTTATAGCTGATAAGAAACATGTTACACTGAATTTC
66 CAATATCTTAGGTGTACAGCATTGACCAATTTATAGCTGATAAGAAACATGATATGCTGAATTTC
* *
4098181 CATCTCCTCAATTTTCAATTTTTACTATGAGACAGTATTATCTACAAATCGTTAGGCATAGGATA
131 CATCTCCTCAATTTTCAATTTTTACTATGAGACAGTATTATCCACAAATCATTAGGCATAGGATA
4098246 ATGAAAAGGAGGG
196 ATGAAAAGGAGGG
4098259 GGCTATGTGA
Statistics
Matches: 382, Mismatches: 31, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
207 135 0.35
208 246 0.64
209 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (208 bp):
TGAACTGAATTCCTCCTGCTCTTGAAAACAGCATAATCATTTTTGTCCTCAATTATCATTATCTA
CAATATCTTAGGTGTACAGCATTGACCAATTTATAGCTGATAAGAAACATGATATGCTGAATTTC
CATCTCCTCAATTTTCAATTTTTACTATGAGACAGTATTATCCACAAATCATTAGGCATAGGATA
ATGAAAAGGAGGG
Found at i:4112607 original size:2 final size:2
Alignment explanation
Indices: 4112600--4112624 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4112590 GGGTTTAGAA
4112600 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4112625 CAAGTGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4118137 original size:3 final size:3
Alignment explanation
Indices: 4118125--4118178 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
4118115 ATTACATGTA
*
4118125 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4118172 TAT TAT T
1 TAT TAT T
4118179 CAAAAACATT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:4120464 original size:2 final size:2
Alignment explanation
Indices: 4120457--4120485 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4120447 TTGCACATAC
4120457 AT 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 AT A
4120486 CAGGTTTTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4121540 original size:66 final size:66
Alignment explanation
Indices: 4121434--4121558 Score: 250
Period size: 66 Copynumber: 1.9 Consensus size: 66
4121424 TAACCTTCTC
4121434 TGATAGTTTCTATGACTAAGGAGAATTACATGGGATTAATAGGTTTCTATATATAACTTCCTTTT
1 TGATAGTTTCTATGACTAAGGAGAATTACATGGGATTAATAGGTTTCTATATATAACTTCCTTTT
4121499 T
66 T
4121500 TGATAGTTTCTATGACTAAGGAGAATTACATGGGATTAATAGGTTTCTATATATAACTT
1 TGATAGTTTCTATGACTAAGGAGAATTACATGGGATTAATAGGTTTCTATATATAACTT
4121559 ACTTACCCAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.41
Consensus pattern (66 bp):
TGATAGTTTCTATGACTAAGGAGAATTACATGGGATTAATAGGTTTCTATATATAACTTCCTTTT
T
Found at i:4125756 original size:24 final size:25
Alignment explanation
Indices: 4125729--4125786 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 25
4125719 CACAAAACTC
*
4125729 AAAAAATTTAATCGTAAT-TTG-GTG
1 AAAAAATTAAATCG-AATCTTGAGTG
4125753 AAAATAA-TAAATCGAATCTTGAAGTG
1 AAAA-AATTAAATCGAATCTTG-AGTG
4125779 AAAAAATT
1 AAAAAATT
4125787 CGACAAACGA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
23 3 0.11
24 13 0.46
25 4 0.14
26 8 0.29
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (25 bp):
AAAAAATTAAATCGAATCTTGAGTG
Found at i:4129635 original size:6 final size:6
Alignment explanation
Indices: 4129624--4129658 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
4129614 TGCATTACAC
*
4129624 TCACAT TCACAT TCAACAT TCTCAT TCACAT TCAC
1 TCACAT TCACAT TC-ACAT TCACAT TCACAT TCAC
4129659 TATTAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (6 bp):
TCACAT
Found at i:4129644 original size:13 final size:12
Alignment explanation
Indices: 4129624--4129658 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
4129614 TGCATTACAC
4129624 TCACATTCACAT
1 TCACATTCACAT
*
4129636 TCAACATTCTCAT
1 TC-ACATTCACAT
4129649 TCACATTCAC
1 TCACATTCAC
4129659 TATTAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (12 bp):
TCACATTCACAT
Found at i:4133843 original size:16 final size:16
Alignment explanation
Indices: 4133822--4133853 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4133812 CACTTACTAA
4133822 AATGAAGTGTGACCAT
1 AATGAAGTGTGACCAT
4133838 AATGAAGTGTGACCAT
1 AATGAAGTGTGACCAT
4133854 TGTTTGCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (16 bp):
AATGAAGTGTGACCAT
Found at i:4162264 original size:6 final size:6
Alignment explanation
Indices: 4162253--4162285 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
4162243 AAGTTGAGGA
*
4162253 TGCTAC TGCTAC TGCTAC TGCTAC TGCTGC TGC
1 TGCTAC TGCTAC TGCTAC TGCTAC TGCTAC TGC
4162286 AGCTGCTGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.12, C:0.33, G:0.21, T:0.33
Consensus pattern (6 bp):
TGCTAC
Found at i:4183202 original size:3 final size:3
Alignment explanation
Indices: 4183194--4183220 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4183184 ATCAGGAAGA
4183194 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
4183221 TGCTTTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:4189163 original size:15 final size:15
Alignment explanation
Indices: 4189102--4189168 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
4189092 AAGTTAACAT
*
4189102 TATAAA-TTATAAAA
1 TATAAATTTATAATA
*
4189116 TTATTAA-TTATAATA
1 -TATAAATTTATAATA
**
4189131 TATATAATTT-TGTTTA
1 TATA-AATTTAT-AATA
4189147 TATAAATTTATAATA
1 TATAAATTTATAATA
4189162 TATAAAT
1 TATAAAT
4189169 CTAAAGAGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
14 3 0.07
15 29 0.71
16 9 0.22
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (15 bp):
TATAAATTTATAATA
Found at i:4190257 original size:26 final size:26
Alignment explanation
Indices: 4190205--4190257 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
4190195 TTTTAATTAA
* *
4190205 AGATAATTTTGCCAACAAAAGCGGAT
1 AGATAATTTTGCCAACAAAAACAGAT
* * *
4190231 AGATAATTTTGTCATCAAAAATAGAT
1 AGATAATTTTGCCAACAAAAACAGAT
4190257 A
1 A
4190258 AAGAACTTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.28
Consensus pattern (26 bp):
AGATAATTTTGCCAACAAAAACAGAT
Found at i:4190305 original size:18 final size:18
Alignment explanation
Indices: 4190273--4190311 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4190263 CTTAACCCAC
* *
4190273 TAACCCATGAGAAGTAGA
1 TAACCCATCAAAAGTAGA
*
4190291 TAACCCATCAAAAGTGGA
1 TAACCCATCAAAAGTAGA
4190309 TAA
1 TAA
4190312 ATACTTTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (18 bp):
TAACCCATCAAAAGTAGA
Found at i:4190332 original size:28 final size:28
Alignment explanation
Indices: 4190292--4190370 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
4190282 AGAAGTAGAT
4190292 AACCCATCAAAAGTGGATAAATACTTTC
1 AACCCATCAAAAGTGGATAAATACTTTC
*** *
4190320 AACCCATCAAAAGCAAATGAATACTTTC
1 AACCCATCAAAAGTGGATAAATACTTTC
* *
4190348 AACCTACCAAAAGTGGATAAATA
1 AACCCATCAAAAGTGGATAAATA
4190371 ATGAAAAGAC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.47, C:0.22, G:0.10, T:0.22
Consensus pattern (28 bp):
AACCCATCAAAAGTGGATAAATACTTTC
Done.