Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 99 of 295
Found at i:29319084 original size:176 final size:174
Alignment explanation
Indices: 29318794--29319363 Score: 802
Period size: 176 Copynumber: 3.2 Consensus size: 174
29318784 CTTGGGGCTT
* * * * * *
29318794 AAATATGCTCCATTGCCGATATATATGGAGATAAGATTCGCC-TCTTTCGATCTGTTCCGCTACT
1 AAATCTGCTCCATTGCCG--ATACATGGAGATAAGATTCACCATC-TTCGATCTGCTCCGCTGCA
* * * * * * *
29318858 GCTT-AGAGAAATAAGATCTTCAATCTTTAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTT
63 ACTTCAGGGAGATAAGATCTTCAATCATTAGTCTGCTTTCTTGCTACCTCAGAAAGATAAGACTC
* * *
29318922 ATGCTTCAACTATTCTCTTGCTACCTCAGAGAAATAAGGCTGGTGGCTT
128 ATTCTTCAACT-TTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGG-TA
* *
29318971 AAATCTGCTCCATTGCTGATACATGGAGATAAGATTCACCATCTTCGATTTGCTCCGCTGCAACT
1 AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGATCTGCTCCGCTGCAACT
* * *
29319036 TCAGGGAGATAAAATCTTCAATCCTCAGTCTGCTTTCTTGCTACCTCAGAAAGATAAGACTCATT
66 TCAGGGAGATAAGATCTTCAATCATTAGTCTGCTTTCTTGCTACCTCAGAAAGATAAGACTCATT
29319101 CTTCAACTTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGTA
131 CTTCAACTT--TCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGTA
*
29319147 AAATCTGCTCCATTGTCGATACATGGAGATAAGATTCACCATCTTCGATCTGCTCCGCTGCAACT
1 AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGATCTGCTCCGCTGCAACT
* *
29319212 TCAGGGAGATAAGATCTTCAATCATTAGTCTACTTTCTTGCTACCTCAGAAAGTTAAGACTCATT
66 TCAGGGAGATAAGATCTTCAATCATTAGTCTGCTTTCTTGCTACCTCAGAAAGATAAGACTCATT
* * *
29319277 CTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTAGTAGTA
131 CTTCAA-CT-TTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGTA
29319323 AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCA
1 AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCA
29319364 ATCTACTAAT
Statistics
Matches: 355, Mismatches: 32, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
175 39 0.11
176 266 0.75
177 50 0.14
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (174 bp):
AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGATCTGCTCCGCTGCAACT
TCAGGGAGATAAGATCTTCAATCATTAGTCTGCTTTCTTGCTACCTCAGAAAGATAAGACTCATT
CTTCAACTTTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGTA
Found at i:29319192 original size:88 final size:87
Alignment explanation
Indices: 29319097--29319363 Score: 192
Period size: 88 Copynumber: 3.0 Consensus size: 87
29319087 AGATAAGACT
29319097 CATTCTTCAACTTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGTAAAATCTGCTCCATTG
1 CATTCTTCAACTTGCTCTCTTGCTACCTCAGAGAGATAAGGCT-GT-GTAAAATCTGCTCCATTG
29319162 TCGATACATGGAGATAAGATTCAC
64 TCGATACATGGAGATAAGATTCAC
* * * * * * * * *
29319186 CA-TCTTCGA-TCTGCTC-CGCTGCAACTTCAGGGAGATAA-GATCT-T-CAATCATTAGTCTAC
1 CATTCTTCAACT-TGCTCTC-TTGCTACCTCAGAGAGATAAGGCTGTGTAAAATC--T-G-CTCC
* * * * * * *
29319245 TTTCTTGCTACCT-CAGA-AAG-TTAAGAC
60 ATTGTCGATACATGGAGATAAGATT--CAC
*
29319272 TCATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTAGTAGTAAAATCTGCTCCATT
1 -CATTCTTCAACTTGCTCTCTTGCTACCTCAGAGAGATAAGGCT-GT-GTAAAATCTGCTCCATT
*
29319337 GCCGATACATGGAGATAAGATTCAC
63 GTCGATACATGGAGATAAGATTCAC
29319362 CA
1 CA
29319364 ATCTACTAAT
Statistics
Matches: 124, Mismatches: 34, Indels: 40
0.63 0.17 0.20
Matches are distributed among these distances:
83 4 0.03
84 3 0.02
85 4 0.03
86 7 0.06
87 17 0.14
88 54 0.44
89 17 0.14
90 7 0.06
91 4 0.03
92 3 0.02
93 4 0.03
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (87 bp):
CATTCTTCAACTTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGTGTAAAATCTGCTCCATTGTC
GATACATGGAGATAAGATTCAC
Found at i:29320963 original size:12 final size:12
Alignment explanation
Indices: 29320946--29320970 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29320936 GTATCCATTC
29320946 TGCTTCATCTAA
1 TGCTTCATCTAA
29320958 TGCTTCATCTAA
1 TGCTTCATCTAA
29320970 T
1 T
29320971 TTTAATTCTG
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:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (12 bp):
TGCTTCATCTAA
Found at i:29336344 original size:22 final size:24
Alignment explanation
Indices: 29336308--29336353 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
29336298 TTTTTTAAAT
29336308 TTTTAATTAAATAAATATATTTTA
1 TTTTAATTAAATAAATATATTTTA
29336332 TTTT-ATT-AATAAATATATTTTA
1 TTTTAATTAAATAAATATATTTTA
29336354 AAAATCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 15 0.68
23 3 0.14
24 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTAATTAAATAAATATATTTTA
Found at i:29337419 original size:16 final size:16
Alignment explanation
Indices: 29337394--29337435 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
29337384 CAATGGTTTT
*
29337394 TGGAAGCAAAGCAAAA
1 TGGAAACAAAGCAAAA
29337410 TGGAAACAAAGCAAAA
1 TGGAAACAAAGCAAAA
29337426 TGGAAACAAA
1 TGGAAACAAA
29337436 TATTGGCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.60, C:0.12, G:0.21, T:0.07
Consensus pattern (16 bp):
TGGAAACAAAGCAAAA
Found at i:29348599 original size:16 final size:16
Alignment explanation
Indices: 29348580--29348618 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
29348570 GTTTGGTTCA
*
29348580 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
29348596 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
29348612 TTGTAAT
1 CTGTAAT
29348619 AAGTAATTCA
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:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:29356552 original size:17 final size:18
Alignment explanation
Indices: 29356530--29356570 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
29356520 AAAATAAAAC
* *
29356530 ATTAAAAA-TATGTTTTA
1 ATTAAAAATTATCTTTAA
29356547 ATTAAAAATTATCTTTAA
1 ATTAAAAATTATCTTTAA
29356565 ATTAAA
1 ATTAAA
29356571 TAGAGAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTAAAAATTATCTTTAA
Found at i:29359997 original size:20 final size:20
Alignment explanation
Indices: 29359974--29360012 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
29359964 CATGAAAAAA
*
29359974 GAGAAAATTCAAAAAATTAT
1 GAGAAAATTAAAAAAATTAT
29359994 GAGAAAATTAAAAAAATTA
1 GAGAAAATTAAAAAAATTA
29360013 ACAATAAAAA
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:0.64, C:0.03, G:0.10, T:0.23
Consensus pattern (20 bp):
GAGAAAATTAAAAAAATTAT
Found at i:29360779 original size:26 final size:26
Alignment explanation
Indices: 29360750--29360803 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
29360740 CTTGTGCCCT
29360750 TCAATTATTTGCTCATTAGTGAAGTC
1 TCAATTATTTGCTCATTAGTGAAGTC
29360776 TCAATTATTTGCTCATTAGTGAAGTC
1 TCAATTATTTGCTCATTAGTGAAGTC
29360802 TC
1 TC
29360804 CATTTTCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (26 bp):
TCAATTATTTGCTCATTAGTGAAGTC
Found at i:29366707 original size:18 final size:19
Alignment explanation
Indices: 29366684--29366719 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29366674 AACTTGGCAC
*
29366684 CATAA-TCATTTAATTTAA
1 CATAATTCAATTAATTTAA
29366702 CATAATTCAATTAATTTA
1 CATAATTCAATTAATTTA
29366720 CTAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (19 bp):
CATAATTCAATTAATTTAA
Found at i:29373125 original size:41 final size:41
Alignment explanation
Indices: 29373068--29373150 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
29373058 ATAATGAATG
29373068 ATAAGTCTAATCTTTAGTACATAAGAAATTTACTTCTAAAC
1 ATAAGTCTAATCTTTAGTACATAAGAAATTTACTTCTAAAC
*
29373109 ATAAGTCTAATCTTTAGTACATAAGAATTTTACTTCTAAAC
1 ATAAGTCTAATCTTTAGTACATAAGAAATTTACTTCTAAAC
29373150 A
1 A
29373151 AGATAACAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.37
Consensus pattern (41 bp):
ATAAGTCTAATCTTTAGTACATAAGAAATTTACTTCTAAAC
Found at i:29373132 original size:20 final size:20
Alignment explanation
Indices: 29373068--29373133 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
29373058 ATAATGAATG
29373068 ATAAGTCTAATCTTTAGTAC
1 ATAAGTCTAATCTTTAGTAC
* *
29373088 ATAAG--AAATTTACTTCTA-AAC
1 ATAAGTCTAA--T-CTT-TAGTAC
29373109 ATAAGTCTAATCTTTAGTAC
1 ATAAGTCTAATCTTTAGTAC
29373129 ATAAG
1 ATAAG
29373134 AATTTTACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 16 0.46
21 11 0.31
22 2 0.06
23 2 0.06
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (20 bp):
ATAAGTCTAATCTTTAGTAC
Found at i:29373225 original size:6 final size:7
Alignment explanation
Indices: 29373197--29373224 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
29373187 AGAAGAGAGC
29373197 ATAAAAA
1 ATAAAAA
29373204 ATAAAAA
1 ATAAAAA
29373211 ATAAAAA
1 ATAAAAA
29373218 ATAAAAA
1 ATAAAAA
29373225 TGATTCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
ATAAAAA
Found at i:29378949 original size:27 final size:27
Alignment explanation
Indices: 29378919--29378996 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 27
29378909 GACTAATCGA
* *
29378919 GCCTTTCTCTGAGGCGCAAATGGTTGT
1 GCCTATCTCAGAGGCGCAAATGGTTGT
29378946 GCCTATCTCAGAGGCGCAAATGGTTGT
1 GCCTATCTCAGAGGCGCAAATGGTTGT
* * *
29378973 GCCTATCCCAGATGTGCAAATGGT
1 GCCTATCTCAGAGGCGCAAATGGT
29378997 GGGGCCCACA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (27 bp):
GCCTATCTCAGAGGCGCAAATGGTTGT
Found at i:29382437 original size:33 final size:33
Alignment explanation
Indices: 29382395--29382458 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
29382385 ATGAACTTGA
* *
29382395 GCCAGGAGGAGTGGAGTACGGCGATTGATACGG
1 GCCAGGAGGAGTGGAGTACGACGATAGATACGG
29382428 GCCAGGAGGAGTGGAGTACGACGATAGATAC
1 GCCAGGAGGAGTGGAGTACGACGATAGATAC
29382459 AGGTCGGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.28, C:0.16, G:0.42, T:0.14
Consensus pattern (33 bp):
GCCAGGAGGAGTGGAGTACGACGATAGATACGG
Found at i:29385052 original size:15 final size:15
Alignment explanation
Indices: 29385016--29385058 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
29385006 AATATATGAT
* *
29385016 ATGATATGATATGAT
1 ATGATATGATATAAC
29385031 ATGATATGATATAAC
1 ATGATATGATATAAC
* *
29385046 ATTATATAATATA
1 ATGATATGATATA
29385059 GTAAGAGGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.40
Consensus pattern (15 bp):
ATGATATGATATAAC
Found at i:29385058 original size:5 final size:5
Alignment explanation
Indices: 29385009--29385042 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
29384999 AATTACTAAT
29385009 ATATG ATATG ATATG ATATG ATATG ATATG ATAT
1 ATATG ATATG ATATG ATATG ATATG ATATG ATAT
29385043 AACATTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
ATATG
Found at i:29388647 original size:40 final size:40
Alignment explanation
Indices: 29388603--29388681 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
29388593 AAAACACACC
29388603 AATTTGGCACCTAGTGCCTCATCGGAT-AATTCGAAGTAAT
1 AATTTGGCACCTAGTGCCTCATCGGATGAA-TCGAAGTAAT
* * * *
29388643 AATTTGTCACCTAGTGTCTTATCGGCTGAATCGAAGTAA
1 AATTTGGCACCTAGTGCCTCATCGGATGAATCGAAGTAA
29388682 ATTGGCACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.94
41 2 0.06
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (40 bp):
AATTTGGCACCTAGTGCCTCATCGGATGAATCGAAGTAAT
Found at i:29389638 original size:20 final size:20
Alignment explanation
Indices: 29389613--29389671 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
29389603 AACTTTTCTC
29389613 CTTTCTTTCTCCTTTTCTTT
1 CTTTCTTTCTCCTTTTCTTT
* *
29389633 CTTTCTTTC-CCCTTTGTTT
1 CTTTCTTTCTCCTTTTCTTT
*
29389652 CGTTCTATTCT-CTTTTCTTT
1 CTTTCT-TTCTCCTTTTCTTT
29389672 TTCTATTCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 13 0.41
20 19 0.59
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (20 bp):
CTTTCTTTCTCCTTTTCTTT
Found at i:29389789 original size:20 final size:19
Alignment explanation
Indices: 29389755--29389793 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
29389745 ATTAATAAGC
29389755 AATACATATTTTATTATTA
1 AATACATATTTTATTATTA
*
29389774 AATATATATGTTTATTATTA
1 AATACATAT-TTTATTATTA
29389794 TTACACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (19 bp):
AATACATATTTTATTATTA
Found at i:29391918 original size:11 final size:11
Alignment explanation
Indices: 29391902--29391927 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29391892 CATGACGCAC
29391902 AAAATAAAACT
1 AAAATAAAACT
29391913 AAAATAAAACT
1 AAAATAAAACT
29391924 AAAA
1 AAAA
29391928 AGCGAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAAAACT
Found at i:29393427 original size:30 final size:31
Alignment explanation
Indices: 29393391--29393474 Score: 145
Period size: 30 Copynumber: 2.7 Consensus size: 31
29393381 TCAATCTCAG
29393391 CATATACTGGGCCGAAGCCTTTAT-ATTATT
1 CATATACTGGGCCGAAGCCTTTATCATTATT
29393421 CATATACTGGGCCGAAGCCTTT-TCATTATT
1 CATATACTGGGCCGAAGCCTTTATCATTATT
29393451 CATATCACTGGGCCGAAGCCTTTA
1 CATAT-ACTGGGCCGAAGCCTTTA
29393475 CTGCAACAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
29 1 0.02
30 33 0.65
31 17 0.33
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (31 bp):
CATATACTGGGCCGAAGCCTTTATCATTATT
Found at i:29393777 original size:24 final size:26
Alignment explanation
Indices: 29393693--29393788 Score: 135
Period size: 26 Copynumber: 3.8 Consensus size: 26
29393683 CTCTTTTAAT
* *
29393693 AACTGGGGCAAAAGCCCTTTTTGATA
1 AACTGGGGCAAAAGCCCTTTTCGGTA
*
29393719 AACTGGAGCAAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAAGCCCTTTTCGGTA
29393745 AACTGGGGC-AAAGCCCTTTTCGGT-
1 AACTGGGGCAAAAGCCCTTTTCGGTA
*
29393769 AACTGGGGC-ATAGCCCTTTT
1 AACTGGGGCAAAAGCCCTTTT
29393789 GCACTTCCTC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 19 0.29
25 15 0.23
26 31 0.48
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (26 bp):
AACTGGGGCAAAAGCCCTTTTCGGTA
Found at i:29393958 original size:25 final size:25
Alignment explanation
Indices: 29393921--29393969 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
29393911 ATAATTAAAC
* **
29393921 CCTAGAGGTAAAATGGTCATTTTTA
1 CCTAGAGGCAAAACAGTCATTTTTA
*
29393946 CCTAGGGGCAAAACAGTCATTTTT
1 CCTAGAGGCAAAACAGTCATTTTT
29393970 CATATTATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (25 bp):
CCTAGAGGCAAAACAGTCATTTTTA
Found at i:29402652 original size:22 final size:22
Alignment explanation
Indices: 29402626--29402669 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29402616 GTTCGTAAGG
29402626 TCTGAATTACATAAAATAAACC
1 TCTGAATTACATAAAATAAACC
29402648 TCTGAATTACATAAAATAAACC
1 TCTGAATTACATAAAATAAACC
29402670 CCGAATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.27
Consensus pattern (22 bp):
TCTGAATTACATAAAATAAACC
Found at i:29404139 original size:16 final size:17
Alignment explanation
Indices: 29404113--29404144 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29404103 AAATTTTTAA
29404113 AAAAGAATAAAATAAAT
1 AAAAGAATAAAATAAAT
29404130 AAAA-AATAAAATAAA
1 AAAAGAATAAAATAAA
29404145 ATCTGATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAAGAATAAAATAAAT
Found at i:29407522 original size:33 final size:31
Alignment explanation
Indices: 29407451--29407537 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 31
29407441 ATTCAGATAA
* *
29407451 ATGGGCCTACACACCCGTGTGGCTTGCTCGT
1 ATGGGCCCACACACCCGTGTGGCTTACTCGT
* *
29407482 ATAGGCCCACACACCCAGTTTGGTCTTACTCGT
1 ATGGGCCCACACACCC-GTGTGG-CTTACTCGT
* **
29407515 GTGGGCCCACACGTCCGTGTGGC
1 ATGGGCCCACACACCCGTGTGGC
29407538 CCATATGCAT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
31 15 0.33
32 10 0.22
33 20 0.44
ACGTcount: A:0.15, C:0.33, G:0.28, T:0.24
Consensus pattern (31 bp):
ATGGGCCCACACACCCGTGTGGCTTACTCGT
Found at i:29408166 original size:20 final size:20
Alignment explanation
Indices: 29408117--29408177 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
29408107 GTGAAAAGGG
29408117 AATTTTTG-AAGAACAATAA
1 AATTTTTGAAAGAACAATAA
** *
29408136 AATTTAGGAAAGAA-AGTCAA
1 AATTTTTGAAAGAACAAT-AA
*
29408156 AATTTTTGAAA-AAGAATAA
1 AATTTTTGAAAGAACAATAA
29408175 AAT
1 AAT
29408178 AAATAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.56, C:0.03, G:0.13, T:0.28
Consensus pattern (20 bp):
AATTTTTGAAAGAACAATAA
Found at i:29408191 original size:16 final size:17
Alignment explanation
Indices: 29408165--29408196 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29408155 AAATTTTTGA
29408165 AAAAGAATAAAATAAAT
1 AAAAGAATAAAATAAAT
29408182 AAAA-AATAAAATAAA
1 AAAAGAATAAAATAAA
29408197 ATTTGATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAAGAATAAAATAAAT
Found at i:29419766 original size:20 final size:20
Alignment explanation
Indices: 29419741--29419778 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29419731 ACTTAGAAGG
29419741 ACTTCTATAC-ATACAAGTCC
1 ACTTCTAT-CGATACAAGTCC
29419761 ACTTCTATCGATACAAGT
1 ACTTCTATCGATACAAGT
29419779 TTGCTTCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (20 bp):
ACTTCTATCGATACAAGTCC
Found at i:29430884 original size:25 final size:25
Alignment explanation
Indices: 29430856--29430934 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
29430846 CTAATGGCCG
29430856 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ***
29430881 ATGTGAT-AAGGCCTAA-TGT-CCG
1 ATGTGATGAATGTGAAAGTGTATAT
29430903 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
*
29430928 GTGTGAT
1 ATGTGAT
29430935 AAGGCCTAAT
Statistics
Matches: 36, Mismatches: 15, Indels: 6
0.63 0.26 0.11
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 8 0.22
25 13 0.36
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:29430906 original size:47 final size:47
Alignment explanation
Indices: 29430840--29431124 Score: 428
Period size: 47 Copynumber: 6.1 Consensus size: 47
29430830 GAAATGATAG
29430840 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
29430887 TAAGGCCTAATGTCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
29430934 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
29430981 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
29431028 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * * *
29431074 CAGGGCCGAGTGGCCAACGTGATGGATGCGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
29431121 TAAG
1 TAAG
29431125 TCCCGAAGGG
Statistics
Matches: 219, Mismatches: 18, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
46 40 0.18
47 179 0.82
ACGTcount: A:0.32, C:0.10, G:0.31, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:29431299 original size:37 final size:37
Alignment explanation
Indices: 29431243--29431321 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
29431233 CCGAGCTCTA
* *
29431243 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
29431280 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
29431317 AAGAC
1 AAGAC
29431322 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:29436406 original size:20 final size:20
Alignment explanation
Indices: 29436381--29436418 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29436371 TATTTAGGGA
29436381 AAAAATTTTCT-AAGTTTTGT
1 AAAAA-TTTCTAAAGTTTTGT
29436401 AAAAATTTCTAAAGTTTT
1 AAAAATTTCTAAAGTTTT
29436419 TGGTTTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (20 bp):
AAAAATTTCTAAAGTTTTGT
Found at i:29438332 original size:138 final size:137
Alignment explanation
Indices: 29438055--29438310 Score: 350
Period size: 138 Copynumber: 1.9 Consensus size: 137
29438045 AATATATGTG
**
29438055 ATTGAATGTTTTATGATATATTTAAATTAATGAATGTTATGATGTTTGAATATTTCTAATTGTAC
1 ATTGAATGGCTTATGATATATTTAAATTAATGAATGTTATGATGTTTGAATATTTCTAATTGTAC
** * * * *
29438120 GATAATACTTTGTAACCCTAATTCAACGATGGAGGCAGGTTAGGGGTGTTACATTTATATGAAAT
66 GATAATACTCCGTAACCCTAATCCAACGACGGAGGCAAGTTAGGGGTGTTACATTGATATGAAAT
** *
29438185 GTATGTA
131 CCATCTA
* * * *
29438192 ATTGAATGGCTTATGATATATTTAAATTATTGAATGTTATGGTGTTTGAATATTTTTTTATTGTA
1 ATTGAATGGCTTATGATATATTTAAATTAATGAATGTTATGATGTTTGAATA-TTTCTAATTGTA
* *
29438257 CGGTAATACTCCGTAACCCTAATCCAGCGACGGAGGCAAGTTAGGGGTGTTACA
65 CGATAATACTCCGTAACCCTAATCCAACGACGGAGGCAAGTTAGGGGTGTTACA
29438311 GTTCGAGTTT
Statistics
Matches: 105, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
137 48 0.46
138 57 0.54
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (137 bp):
ATTGAATGGCTTATGATATATTTAAATTAATGAATGTTATGATGTTTGAATATTTCTAATTGTAC
GATAATACTCCGTAACCCTAATCCAACGACGGAGGCAAGTTAGGGGTGTTACATTGATATGAAAT
CCATCTA
Found at i:29438827 original size:2 final size:2
Alignment explanation
Indices: 29438815--29438883 Score: 81
Period size: 2 Copynumber: 36.0 Consensus size: 2
29438805 AAAAAGACAA
* * *
29438815 AG AG AG A- AG AG AG AG AG AG AG AG AG AG -G GG GG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
29438855 AG AG -G GG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29438884 TTGGAAATGA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
1 3 0.05
2 57 0.95
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29441012 original size:23 final size:23
Alignment explanation
Indices: 29440986--29441029 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
29440976 TCAAATTGAC
29440986 TTTGATTCTACT-TATCAATAAAT
1 TTTGATTC-ACTATATCAATAAAT
*
29441009 TTTGATTCACTATGTCAATAA
1 TTTGATTCACTATATCAATAA
29441030 TTAAATCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (23 bp):
TTTGATTCACTATATCAATAAAT
Found at i:29441143 original size:31 final size:31
Alignment explanation
Indices: 29441062--29441148 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
29441052 TTAATGAGCT
* *
29441062 AAATAAAAA-TATTTGAATAATTAAATAAGTA
1 AAATAAAAACT-TTTCAATAATTTAATAAGTA
*
29441093 AAATAAAAACTTTTCAATAATTTAATAATTA
1 AAATAAAAACTTTTCAATAATTTAATAAGTA
* * *
29441124 AGATATAAA-TTTATTAATAATTTAA
1 AAATAAAAACTTT-TCAATAATTTAA
29441149 AGAATTAGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.06
31 44 0.92
32 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.38
Consensus pattern (31 bp):
AAATAAAAACTTTTCAATAATTTAATAAGTA
Found at i:29444133 original size:25 final size:25
Alignment explanation
Indices: 29444105--29444156 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
29444095 TATTAACTAA
29444105 AGAACTGAACTTAAATAGAGAAAAG
1 AGAACTGAACTTAAATAGAGAAAAG
29444130 AGAACTGAACTTAAATAGAGAAAAG
1 AGAACTGAACTTAAATAGAGAAAAG
29444155 AG
1 AG
29444157 TCCTAATCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.56, C:0.08, G:0.21, T:0.15
Consensus pattern (25 bp):
AGAACTGAACTTAAATAGAGAAAAG
Found at i:29444235 original size:42 final size:42
Alignment explanation
Indices: 29444176--29444261 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
29444166 TAATTAGGAC
29444176 AATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAGAA
1 AATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAGAA
* *
29444218 AATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAATAA
1 AATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAGAA
29444260 AA
1 AA
29444262 ATATTCCTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (42 bp):
AATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAGAA
Found at i:29444282 original size:43 final size:42
Alignment explanation
Indices: 29444176--29444283 Score: 103
Period size: 42 Copynumber: 2.5 Consensus size: 42
29444166 TAATTAGGAC
* * * *
29444176 AATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAGAA
1 AATAGTTCCCTGAATATAATAAACTACTAAAACATAAAAAAA
* * * *
29444218 AATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAATAAA
1 AATAGTTCCCTGAATATAATAAACTACTAAAACATAAAA-AAA
29444261 AATA-TT-CCTAGAATATGAATAAA
1 AATAGTTCCCT-GAATAT-AATAAA
29444284 ACTTATTTAC
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
41 3 0.05
42 43 0.74
43 12 0.21
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.30
Consensus pattern (42 bp):
AATAGTTCCCTGAATATAATAAACTACTAAAACATAAAAAAA
Found at i:29444308 original size:19 final size:18
Alignment explanation
Indices: 29444286--29444325 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
29444276 TGAATAAAAC
*
29444286 TTATTTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
29444305 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
29444323 TTA
1 TTA
29444326 AAATATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:29448675 original size:18 final size:19
Alignment explanation
Indices: 29448637--29448676 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
29448627 TGAATAAAAC
*
29448637 TTATTTACCTAAATGAAAT
1 TTATCTACCTAAATGAAAT
29448656 TTATCTACCTAAAT-AAAT
1 TTATCTACCTAAATGAAAT
29448674 TTA
1 TTA
29448677 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (19 bp):
TTATCTACCTAAATGAAAT
Found at i:29460125 original size:36 final size:36
Alignment explanation
Indices: 29460078--29460152 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
29460068 CCTTGTCCAA
29460078 AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
1 AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
29460114 AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
1 AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
29460150 AAG
1 AAG
29460153 ATTCCATTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (36 bp):
AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
Found at i:29472747 original size:15 final size:15
Alignment explanation
Indices: 29472729--29472757 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29472719 GACCACGACC
29472729 ATAGCCACCATGACT
1 ATAGCCACCATGACT
29472744 ATAGCCACCATGAC
1 ATAGCCACCATGAC
29472758 ACTGACCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (15 bp):
ATAGCCACCATGACT
Found at i:29476384 original size:43 final size:42
Alignment explanation
Indices: 29476260--29476384 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 42
29476250 TGATTACATG
* * *
29476260 TAAGACCATGTCTGGGACATTGGCATTGTATTGTGATTACGTG
1 TAAGACCATGTCTGGGACATTGGCATCGTA-TGTGATTTCGTA
* * **
29476303 TAAGACCATGTCTAGGACATTGGTATCGTTATAAGATTTCGTA
1 TAAGACCATGTCTGGGACATTGGCATCG-TATGTGATTTCGTA
* * *
29476346 TAAGACCCTGTCTGGGATAGTGGCATCGATATGTGATTT
1 TAAGACCATGTCTGGGACATTGGCATCG-TATGTGATTT
29476385 TCGAGTATCC
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
43 64 0.97
44 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACATTGGCATCGTATGTGATTTCGTA
Found at i:29479608 original size:14 final size:15
Alignment explanation
Indices: 29479575--29479610 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
29479565 TCTAACCTTG
29479575 TTTAATATAGCATAT
1 TTTAATATAGCATAT
*
29479590 ATTAATATA-CATAT
1 TTTAATATAGCATAT
29479604 TTTAATA
1 TTTAATA
29479611 GCATGAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (15 bp):
TTTAATATAGCATAT
Found at i:29479898 original size:59 final size:59
Alignment explanation
Indices: 29479825--29479986 Score: 159
Period size: 59 Copynumber: 2.7 Consensus size: 59
29479815 ATATATATAT
* *
29479825 TAATTTAGCATCTAAACTATTTTTTACT-CAATTTAGTACCTGAACTTGACA-CTTTTTTC
1 TAATTTAGTATCTAAA-T-TTTTTTACTCCAATTTAGTACCTAAACTTGACATCTTTTTTC
* * * *
29479884 TAATTTAGTATCT-AATTTTTTTTCTCCCAATTTGGTACCTAAACTTGGCATTTTTTTTC
1 TAATTTAGTATCTAAATTTTTTTACT-CCAATTTAGTACCTAAACTTGACATCTTTTTTC
* * * * * *
29479943 TAATTTGGTACCTAAGTTTTTTTAGGTTCAATTTGGTACCTAAA
1 TAATTTAGTATCTAAATTTTTTTA-CTCCAATTTAGTACCTAAA
29479987 TTTATTAAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
56 8 0.09
57 1 0.01
58 22 0.26
59 30 0.35
60 24 0.28
61 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (59 bp):
TAATTTAGTATCTAAATTTTTTTACTCCAATTTAGTACCTAAACTTGACATCTTTTTTC
Found at i:29479977 original size:60 final size:58
Alignment explanation
Indices: 29479851--29479986 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 58
29479841 CTATTTTTTA
* * * *
29479851 CTCAATTTAGTACCTGAACTTGACACTTTTTTCTAATTTAGTATCTAATTTTTTTTCT
1 CTCAATTTGGTACCTAAACTTGACACTTTTTTCTAATTTAGTACCTAATTTTTTTGCT
* * * * *
29479909 CCCAATTTGGTACCTAAACTTGGCATTTTTTTTCTAATTTGGTACCTAAGTTTTTTTAGGT
1 CTCAATTTGGTACCTAAACTTGACA-CTTTTTTCTAATTTAGTACCTAA-TTTTTTT-GCT
29479970 -TCAATTTGGTACCTAAA
1 CTCAATTTGGTACCTAAA
29479987 TTTATTAAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
58 21 0.32
59 20 0.31
60 23 0.35
61 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (58 bp):
CTCAATTTGGTACCTAAACTTGACACTTTTTTCTAATTTAGTACCTAATTTTTTTGCT
Found at i:29480457 original size:31 final size:30
Alignment explanation
Indices: 29480405--29480526 Score: 147
Period size: 31 Copynumber: 3.9 Consensus size: 30
29480395 AAAAGATTAA
* *
29480405 GTACCAACTTAAGAAAAAAGTGTCAAGTTTAG
1 GTACCAAATT-AGGAAAAAGTGTCAAGTTT-G
29480437 GTACCAAATTAGGAAAAAGTGT-ATAGTTTG
1 GTACCAAATTAGGAAAAAGTGTCA-AGTTTG
*
29480467 AGTACCAAATTAGGAAAAACTGTCAAGTTTGG
1 -GTACCAAATTAGGAAAAAGTGTCAAGTTT-G
* *
29480499 GTGCCAAATTAGGAAAAAGTATCAAGTT
1 GTACCAAATTAGGAAAAAGTGTCAAGTT
29480527 CATATACCAA
Statistics
Matches: 80, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
30 2 0.03
31 67 0.84
32 11 0.14
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (30 bp):
GTACCAAATTAGGAAAAAGTGTCAAGTTTG
Found at i:29480664 original size:15 final size:14
Alignment explanation
Indices: 29480648--29480686 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
29480638 GAATTTAGAT
29480648 TTTAAAATTTTATA
1 TTTAAAATTTTATA
* *
29480662 TTTGAAATTTTTTA
1 TTTAAAATTTTATA
29480676 TTTATAAATTT
1 TTTA-AAATTT
29480687 ATAATTTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TTTAAAATTTTATA
Found at i:29480811 original size:12 final size:12
Alignment explanation
Indices: 29480794--29480819 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29480784 TAAATTCAAG
29480794 TTTTAAAATTAT
1 TTTTAAAATTAT
29480806 TTTTAAAATTAT
1 TTTTAAAATTAT
29480818 TT
1 TT
29480820 ATTTATATTA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTAAAATTAT
Found at i:29481641 original size:82 final size:82
Alignment explanation
Indices: 29481504--29481654 Score: 284
Period size: 82 Copynumber: 1.8 Consensus size: 82
29481494 ACGAATTCTA
*
29481504 GAAAACATAACAAACAAAGTTCAAATGAATTTGTGAGTTACTAATATAACATACCATTTATGAAT
1 GAAAACATAACAAACAAAGTTCAAATGAATTAGTGAGTTACTAATATAACATACCATTTATGAAT
29481569 TTATGAATTTATACCTG
66 TTATGAATTTATACCTG
*
29481586 GAAAACATAACAAACTAAGTTCAAATGAATTAGTGAGTTACTAATATAACATACCATTTATGAAT
1 GAAAACATAACAAACAAAGTTCAAATGAATTAGTGAGTTACTAATATAACATACCATTTATGAAT
29481651 TTAT
66 TTAT
29481655 AAGTTAGAAC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 67 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (82 bp):
GAAAACATAACAAACAAAGTTCAAATGAATTAGTGAGTTACTAATATAACATACCATTTATGAAT
TTATGAATTTATACCTG
Found at i:29485532 original size:38 final size:39
Alignment explanation
Indices: 29485460--29485534 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 39
29485450 TTTAAAATTT
* * *
29485460 TAAAAATTAAAAAAAATTGTAAAAATTATATTTAAAAAG
1 TAAAAAGTAAAAAAAATTATAAAAAATATATTTAAAAAG
*
29485499 TAAAAAGT-AAAAAAATTATAAAAAA-ATATTTTAAAA
1 TAAAAAGTAAAAAAAATTATAAAAAATATATTTAAAAA
29485535 TTTTAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 10 0.31
38 15 0.47
39 7 0.22
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (39 bp):
TAAAAAGTAAAAAAAATTATAAAAAATATATTTAAAAAG
Found at i:29485542 original size:39 final size:39
Alignment explanation
Indices: 29485449--29485543 Score: 113
Period size: 39 Copynumber: 2.4 Consensus size: 39
29485439 TTAATTAATT
* * *
29485449 TTTTAAAATTTTAAAAATTAAAAAAAATTGTAAAAATTA
1 TTTTAAAATTTTAAAAAGTAAAAAAAATTATAAAAAATA
**
29485488 TATTTAAAA-AGTAAAAAGT-AAAAAAATTATAAAAAAATA
1 T-TTTAAAATTTTAAAAAGTAAAAAAAATTAT-AAAAAATA
29485527 TTTTAAAATTTTAAAAA
1 TTTTAAAATTTTAAAAA
29485544 TTAATTAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
38 17 0.37
39 22 0.48
40 7 0.15
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (39 bp):
TTTTAAAATTTTAAAAAGTAAAAAAAATTATAAAAAATA
Found at i:29486032 original size:6 final size:6
Alignment explanation
Indices: 29486014--29486045 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
29486004 CTTCAAATTA
29486014 TCCTTT ATCCTTT TCCTTT TCCTTT TCCTTT T
1 TCCTTT -TCCTTT TCCTTT TCCTTT TCCTTT T
29486046 ATGGTCTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (6 bp):
TCCTTT
Found at i:29491154 original size:21 final size:22
Alignment explanation
Indices: 29491106--29491156 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
29491096 TAACATAATT
29491106 TATTTT-A-AAATTTTTATTGA
1 TATTTTAACAAATTTTTATTGA
*
29491126 TGTTTTAACAAATTTTT-TT-A
1 TATTTTAACAAATTTTTATTGA
29491146 TATTATTAACA
1 TATT-TTAACA
29491157 CATAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 9 0.35
21 9 0.35
22 8 0.31
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (22 bp):
TATTTTAACAAATTTTTATTGA
Found at i:29491241 original size:6 final size:7
Alignment explanation
Indices: 29491193--29491239 Score: 71
Period size: 7 Copynumber: 7.0 Consensus size: 7
29491183 AACTTTAAAC
29491193 CTTGAAT
1 CTTGAAT
*
29491200 ATTGAAT
1 CTTGAAT
29491207 CTTGAAT
1 CTTGAAT
29491214 CTTGAAT
1 CTTGAAT
29491221 CTTGAAT
1 CTTGAAT
29491228 -TTGAAT
1 CTTGAAT
29491234 -TTGAAT
1 CTTGAAT
29491240 TTTAAACTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
6 12 0.32
7 26 0.68
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.45
Consensus pattern (7 bp):
CTTGAAT
Found at i:29491658 original size:13 final size:13
Alignment explanation
Indices: 29491637--29491669 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
29491627 GACTTAAAAG
*
29491637 TATTTTATATATA
1 TATTATATATATA
29491650 TATTATATATATA
1 TATTATATATATA
29491663 TA-TATAT
1 TATTATAT
29491670 GAAGCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATATATATA
Found at i:29498161 original size:21 final size:20
Alignment explanation
Indices: 29498120--29498161 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
29498110 ACAATTGTAA
*
29498120 TTTCATTTATTAAACATTAT
1 TTTCATTTATAAAACATTAT
*
29498140 TTTCATTTAATAAAATATTAT
1 TTTCATTT-ATAAAACATTAT
29498161 T
1 T
29498162 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTCATTTATAAAACATTAT
Found at i:29499546 original size:29 final size:30
Alignment explanation
Indices: 29499493--29499552 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
29499483 TCCGAGCCTT
*
29499493 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGTAAAAATTTA
* *
29499523 GGGGCAAAATTGTAATTTTG-AAAAATTTA
1 GGGGCAAAAATGTAATTATGTAAAAATTTA
29499552 G
1 G
29499553 AGTCGAGGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGTAAAAATTTA
Found at i:29499780 original size:13 final size:13
Alignment explanation
Indices: 29499762--29499793 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
29499752 TTTCCAGCAA
29499762 TTATGAATTTATT
1 TTATGAATTTATT
29499775 TTATGAATTTATT
1 TTATGAATTTATT
*
29499788 TGATGA
1 TTATGA
29499794 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:29500001 original size:50 final size:50
Alignment explanation
Indices: 29499888--29500129 Score: 279
Period size: 50 Copynumber: 4.7 Consensus size: 50
29499878 ATTTGGGTAA
* * *
29499888 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
29499944 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * *
29499994 AGAGGTCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * *
29500044 AGAGGTCCCCTATAAGACCATGTCTAGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
29500094 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
29500130 TTTGGCATGT
Statistics
Matches: 162, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 88 0.54
51 28 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.24
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:29500077 original size:100 final size:103
Alignment explanation
Indices: 29499888--29500137 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 103
29499878 ATTTGGGTAA
29499888 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* * *
29499953 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTAGGACATGGCATGGGCACC-ATCACG
* * * *
29499994 AGAGGTCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
29500056 TAAGACCATGTCTAGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTAGGACATGGCATGGGCACCATCACG
* *
29500094 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
29500138 GTTATTATCA
Statistics
Matches: 130, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 38 0.29
105 2 0.02
106 39 0.30
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTAGGACATGGCATGGGCACCATCACG
Found at i:29505125 original size:2 final size:2
Alignment explanation
Indices: 29505118--29505142 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29505108 AAACCCCGGG
29505118 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
29505143 AGAGAGAGAG
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:29510026 original size:39 final size:40
Alignment explanation
Indices: 29509963--29510052 Score: 112
Period size: 39 Copynumber: 2.2 Consensus size: 40
29509953 TGAAAAGTAT
29509963 TTATATTAAAAAAATCAACCATAAATATAATAAATGTCTTA
1 TTATATTAAAAAAATCAA-CATAAATATAATAAATGTCTTA
* * *
29510004 TTATATTAAAAAACAT-AA-ATAAATATAATAATTTTTTTA
1 TTATATTAAAAAA-ATCAACATAAATATAATAAATGTCTTA
*
29510043 TTGTATTAAA
1 TTATATTAAA
29510053 TATAATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 27 0.61
41 15 0.34
42 2 0.05
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (40 bp):
TTATATTAAAAAAATCAACATAAATATAATAAATGTCTTA
Found at i:29511041 original size:6 final size:7
Alignment explanation
Indices: 29511026--29511050 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29511016 AATAAAACGA
29511026 TTTTCTT
1 TTTTCTT
29511033 TTTTCTT
1 TTTTCTT
29511040 TTTTCTT
1 TTTTCTT
29511047 TTTT
1 TTTT
29511051 TGTTTCATTA
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:29514088 original size:6 final size:6
Alignment explanation
Indices: 29514077--29514115 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
29514067 AATTATTATA
29514077 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TAT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TAT
29514116 ATTAAATTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TATTTT
Found at i:29515206 original size:48 final size:47
Alignment explanation
Indices: 29515144--29515271 Score: 152
Period size: 48 Copynumber: 2.7 Consensus size: 47
29515134 GTCTGAGTGA
* *
29515144 TACCTTGATTTGGCTGTGGGCCATGGTATAGGTATTTCAGAGAGGAGT
1 TACCTTGATTTGGCTGTGGGCCATGGTATAGGTA-ATCAGAGAGAAGT
* * * * *
29515192 TACCTTGATTTGGCTGTAGGCCATGTTATAGGTAATCCGGGATAAGT
1 TACCTTGATTTGGCTGTGGGCCATGGTATAGGTAATCAGAGAGAAGT
*
29515239 TACCTTGATTTGG-T-TAGGGCCTTGGTATAGGTA
1 TACCTTGATTTGGCTGT-GGGCCATGGTATAGGTA
29515272 CTTATCGATT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
45 1 0.01
46 15 0.22
47 21 0.30
48 32 0.46
ACGTcount: A:0.21, C:0.13, G:0.30, T:0.35
Consensus pattern (47 bp):
TACCTTGATTTGGCTGTGGGCCATGGTATAGGTAATCAGAGAGAAGT
Found at i:29523815 original size:27 final size:26
Alignment explanation
Indices: 29523785--29523846 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
29523775 AGATAATTAA
29523785 AATAAAATCCTAAAT-TTGAATAATCCT
1 AATAAAAT-CTAAATATT-AATAATCCT
* * *
29523812 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTAAATATTAATAATCCT
29523839 AATAAAAT
1 AATAAAAT
29523847 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAAAATCTAAATATTAATAATCCT
Found at i:29524430 original size:9 final size:9
Alignment explanation
Indices: 29524416--29524450 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
29524406 TTAGTACTTA
29524416 TTTTTTTTC
1 TTTTTTTTC
29524425 -TTTTTTTC
1 TTTTTTTTC
29524433 TTTTTTTTC
1 TTTTTTTTC
29524442 TCTTTTTTT
1 T-TTTTTTT
29524451 TATTATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 9 0.38
10 7 0.29
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:29526843 original size:22 final size:22
Alignment explanation
Indices: 29526818--29526862 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
29526808 TGAAAAGTGG
29526818 TGTTTGGCTGCAGGTGTAGGGT
1 TGTTTGGCTGCAGGTGTAGGGT
29526840 TGTTTGGCTGCAGGTGTAGGGT
1 TGTTTGGCTGCAGGTGTAGGGT
29526862 T
1 T
29526863 AGTCTAGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.09, C:0.09, G:0.44, T:0.38
Consensus pattern (22 bp):
TGTTTGGCTGCAGGTGTAGGGT
Found at i:29526874 original size:22 final size:21
Alignment explanation
Indices: 29526818--29526875 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
29526808 TGAAAAGTGG
*
29526818 TGTTTGGCTGCAGGTGTAGGGT
1 TGTTAGGC-GCAGGTGTAGGGT
*
29526840 TGTTTGGCTGCAGGTGTAGGGT
1 TGTTAGGC-GCAGGTGTAGGGT
29526862 TAGTCTAGG-GCAGG
1 T-GT-TAGGCGCAGG
29526876 AATAAGGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
22 28 0.85
23 2 0.06
24 3 0.09
ACGTcount: A:0.12, C:0.10, G:0.45, T:0.33
Consensus pattern (21 bp):
TGTTAGGCGCAGGTGTAGGGT
Found at i:29533499 original size:20 final size:20
Alignment explanation
Indices: 29533461--29533508 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
29533451 TAAATTCTAA
* **
29533461 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
29533481 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
29533501 AAA-ATAAA
1 AAAGATAAA
29533509 ATCCTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:29533533 original size:27 final size:26
Alignment explanation
Indices: 29533503--29533564 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
29533493 AGATAATTAA
29533503 AATAAAATCCTAAAT-TTGAATAATCCT
1 AATAAAAT-CTAAATATT-AATAATCCT
* * *
29533530 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTAAATATTAATAATCCT
29533557 AATAAAAT
1 AATAAAAT
29533565 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAAAATCTAAATATTAATAATCCT
Found at i:29535570 original size:19 final size:18
Alignment explanation
Indices: 29535543--29535579 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
29535533 TAATTAAAGG
29535543 GGTTAATTTTTTTAAAATT
1 GGTTAA-TTTTTTAAAATT
*
29535562 GGTTTATTTTTTAAAATT
1 GGTTAATTTTTTAAAATT
29535580 AATAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (18 bp):
GGTTAATTTTTTAAAATT
Found at i:29536939 original size:18 final size:18
Alignment explanation
Indices: 29536916--29537198 Score: 162
Period size: 18 Copynumber: 15.3 Consensus size: 18
29536906 GAATAATTAT
29536916 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
29536934 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
29536952 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
*
29536970 TTATTCAGTATCGATCAATTGATCGG
1 TTATTCAGTA---A-C-A--G-TCAG
* *
29536996 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
*
29537014 TTATTCAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * *
29537031 ATATTCAGTAACTATTAAG
1 TTATTCAGTAAC-AGTCAG
*
29537050 TTATTCAGTAGCAGTCA-
1 TTATTCAGTAACAGTCAG
* *
29537067 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAG
* *
29537086 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* *
29537104 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
29537122 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAGTC-AG
* * *
29537140 ATATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
29537158 TTA-TCTGGTAACAGTCAA
1 TTATTC-AGTAACAGTCAG
* *
29537176 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
29537194 TTATT
1 TTATT
29537199 TTATACCTTT
Statistics
Matches: 200, Mismatches: 47, Indels: 36
0.71 0.17 0.13
Matches are distributed among these distances:
17 18 0.09
18 146 0.73
19 20 0.10
21 2 0.01
22 1 0.00
23 2 0.01
26 11 0.05
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:29536958 original size:36 final size:36
Alignment explanation
Indices: 29536916--29537198 Score: 189
Period size: 36 Copynumber: 7.6 Consensus size: 36
29536906 GAATAATTAT
* *
29536916 TTATTCAGTAACAGTCAGTTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * * * *
29536952 TTATTCAATAATAACCAGTTATTCAGTATCGATCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* *
29536988 TTGATCGGTTATCCAGTAACAGTCAATTATTCAGTAA-AATCAGA
1 TT-A-----T-T-CAGTAACAATCAGTTATTCAGTAACAATCA-A
* * * *
29537032 -TATTCAGTAACTATTAAGTTATTCAGTAGCAGTC-A
1 TTATTCAGTAAC-AATCAGTTATTCAGTAACAATCAA
* **
29537067 TTCATTCAGTGACAATCAGTTATTCAGTAATGATCAA
1 TT-ATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * *
29537104 TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATC-AA
* * * * *
29537141 -TATCCAGTAACAGTCAATTA-TCTGGTAACAGTCAA
1 TTATTCAGTAACAATCAGTTATTC-AGTAACAATCAA
*
29537176 TTATTCAGTAATAATCAGTTATT
1 TTATTCAGTAACAATCAGTTATT
29537199 TTATACCTTT
Statistics
Matches: 188, Mismatches: 41, Indels: 35
0.71 0.16 0.13
Matches are distributed among these distances:
35 12 0.06
36 129 0.69
37 20 0.11
42 2 0.01
43 6 0.03
44 19 0.10
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (36 bp):
TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
Found at i:29537131 original size:72 final size:71
Alignment explanation
Indices: 29536997--29537198 Score: 221
Period size: 72 Copynumber: 2.8 Consensus size: 71
29536987 ATTGATCGGT
* * *
29536997 TATCCAGTAACAGTCAATTATTCAGTAAAATCAGA-TATTCAGTAACTATTAAGTTATTCAGTAG
1 TATCCAGTAACAATCAATTATTCAGTAAAATCA-ATTATTCAGTAA-TATTCAGTTATTCAGTAA
*
29537061 CAGTC-AT
64 CAGTCTAA
* * * *
29537068 TCATTCAGTGACAATCAGTTATTCAGTAATGATCAATTATTCAGTAATATTCAGTTATTCAGTAA
1 T-ATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATTCAGTAA
29537133 CAGTCTAA
64 CAGTCTAA
* * * *
29537141 TATCCAGTAACAGTCAATTA-TCTGGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 TATCCAGTAACAATCAATTATTC-AGTAA-AATCAATTATTCAGTAATATTCAGTTATT
29537199 TTATACCTTT
Statistics
Matches: 109, Mismatches: 17, Indels: 9
0.81 0.13 0.07
Matches are distributed among these distances:
71 3 0.03
72 90 0.83
73 16 0.15
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (71 bp):
TATCCAGTAACAATCAATTATTCAGTAAAATCAATTATTCAGTAATATTCAGTTATTCAGTAACA
GTCTAA
Found at i:29537640 original size:45 final size:45
Alignment explanation
Indices: 29537366--29537650 Score: 417
Period size: 45 Copynumber: 6.3 Consensus size: 45
29537356 ATCTAGAATA
* * * *
29537366 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* *
29537411 ATAACGGTAACAGTAACAATATTCGACACACAAAGTGTCGAATCG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
*
29537456 GTAACGGTAACAGTAACAATATTCGACACACATAGTGCCGAATCG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* *
29537501 GCAACGGTAACAGTAACAATATTCGACACACAAAGTGTCGAATCG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* * *
29537546 ATAACGGTAGCAGTAACAATATTCGACACACAAAGTGTCGAATCG
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* * *
29537591 GTAACAGTAGCAGTAACAATATTCGACACACAAAGTGCCGAATCA
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* *
29537636 GTAACAGTAGCAGTA
1 GTAACGGTAACAGTA
29537651 GCAGTAACAG
Statistics
Matches: 221, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 221 1.00
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (45 bp):
GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
Found at i:29537650 original size:135 final size:135
Alignment explanation
Indices: 29537361--29537650 Score: 467
Period size: 135 Copynumber: 2.2 Consensus size: 135
29537351 AACAAATCTA
*
29537361 GAAT-AGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCGATAACGGTAACAGT
1 GAATCAGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCGATAACGGTAACAGT
* *
29537425 AACAATATTCGACACACAAAGTGTCGAATCGGTAACGGTAACAGTAACAATATTCGACACACATA
66 AACAATATTCGACACACAAAGTGTCGAATCGGTAACAGTAACAGTAACAATATTCGACACACAAA
29537490 GTGCC
131 GTGCC
* * * * *
29537495 GAATCGGCAACGGTAACAGTAACAATATTCGACACACAAAGTG-TCGAATCGATAACGGTAGCAG
1 GAATCAGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCT-GAATCGATAACGGTAACAG
*
29537559 TAACAATATTCGACACACAAAGTGTCGAATCGGTAACAGTAGCAGTAACAATATTCGACACACAA
65 TAACAATATTCGACACACAAAGTGTCGAATCGGTAACAGTAACAGTAACAATATTCGACACACAA
29537624 AGTGCC
130 AGTGCC
*
29537630 GAATCAGTAACAGTAGCAGTA
1 GAATCAGTAACAGTAACAGTA
29537651 GCAGTAACAG
Statistics
Matches: 141, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
134 5 0.04
135 136 0.96
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.19
Consensus pattern (135 bp):
GAATCAGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCGATAACGGTAACAGT
AACAATATTCGACACACAAAGTGTCGAATCGGTAACAGTAACAGTAACAATATTCGACACACAAA
GTGCC
Found at i:29539311 original size:9 final size:9
Alignment explanation
Indices: 29539293--29539327 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
29539283 TTTCTTTTTC
*
29539293 ATTTCTTTT
1 ATTTCATTT
29539302 ATTTCATTT
1 ATTTCATTT
29539311 ATTTC-TTT
1 ATTTCATTT
29539319 ATTTCATTT
1 ATTTCATTT
29539328 CTTTTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (9 bp):
ATTTCATTT
Found at i:29539319 original size:17 final size:18
Alignment explanation
Indices: 29539293--29539339 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
29539283 TTTCTTTTTC
29539293 ATTTCTTTTATTTCATTT
1 ATTTCTTTTATTTCATTT
29539311 ATTTC-TTTATTTCATTT
1 ATTTCTTTTATTTCATTT
* *
29539328 CTTTTTTTTATT
1 ATTTCTTTTATT
29539340 ATTAAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTCTTTTATTTCATTT
Found at i:29539362 original size:23 final size:23
Alignment explanation
Indices: 29539334--29539386 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
29539324 ATTTCTTTTT
29539334 TTTATTATTAAACTATTATAATA
1 TTTATTATTAAACTATTATAATA
29539357 TTTATTATTAAACTATTATAATA
1 TTTATTATTAAACTATTATAATA
29539380 TTTATTA
1 TTTATTA
29539387 ATACATATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTATTATTAAACTATTATAATA
Found at i:29540605 original size:27 final size:27
Alignment explanation
Indices: 29540546--29540607 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
29540536 AGTTTGTTTC
*
29540546 ATTGAAAATGATTTTTGAAAAATGATT
1 ATTGAAAATGATTTTTGAAAAATAATT
29540573 ATTGAAAATGATTTTTGAAAAATAATT
1 ATTGAAAATGATTTTTGAAAAATAATT
29540600 -TCTGAAAA
1 AT-TGAAAA
29540608 ATAACTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.47, C:0.02, G:0.13, T:0.39
Consensus pattern (27 bp):
ATTGAAAATGATTTTTGAAAAATAATT
Found at i:29540611 original size:14 final size:14
Alignment explanation
Indices: 29540550--29540609 Score: 86
Period size: 14 Copynumber: 4.4 Consensus size: 14
29540540 TGTTTCATTG
29540550 AAAATGATTTTTGA
1 AAAATGATTTTTGA
*
29540564 AAAATGATTATTG-
1 AAAATGATTTTTGA
29540577 AAAATGATTTTTGA
1 AAAATGATTTTTGA
* *
29540591 AAAATAATTTCTGA
1 AAAATGATTTTTGA
29540605 AAAAT
1 AAAAT
29540610 AACTTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
13 12 0.29
14 29 0.71
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (14 bp):
AAAATGATTTTTGA
Found at i:29541168 original size:14 final size:13
Alignment explanation
Indices: 29541140--29541175 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
29541130 ATATTTATAT
29541140 TTATTAAAA-TTA
1 TTATTAAAATTTA
29541152 TTACTTAAAATTTA
1 TTA-TTAAAATTTA
29541166 TTATTAAAAT
1 TTATTAAAAT
29541176 AAAATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 13 0.59
14 6 0.27
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
TTATTAAAATTTA
Found at i:29541295 original size:13 final size:12
Alignment explanation
Indices: 29541241--29541292 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
29541231 TATAATATTT
29541241 TAATAATTTTAA
1 TAATAATTTTAA
* *
29541253 T-TTTATTTTAA
1 TAATAATTTTAA
29541264 TAATAAATTTTAA
1 TAAT-AATTTTAA
29541277 GTAATAATTTTAA
1 -TAATAATTTTAA
29541290 TAA
1 TAA
29541293 ATATAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 9 0.27
12 5 0.15
13 15 0.45
14 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
TAATAATTTTAA
Found at i:29542496 original size:54 final size:55
Alignment explanation
Indices: 29542432--29542538 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 55
29542422 TCAATTTTGA
*
29542432 GTGTTG-TTTTTTTTTATATGAAAGGAATGAAGATAAGGACAATAGGAAAGGTGG
1 GTGTTGTTTTTTTTTTATATGAAAGGAATGAAGATAAGGAAAATAGGAAAGGTGG
29542486 GTGTTGTTTTTTTTTTATATGAAAGGAATGAAGATAAGGAAAATAGGAAAGGT
1 GTGTTGTTTTTTTTTTATATGAAAGGAATGAAGATAAGGAAAATAGGAAAGGT
29542539 AATCATTTTC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 6 0.12
55 45 0.88
ACGTcount: A:0.36, C:0.01, G:0.28, T:0.35
Consensus pattern (55 bp):
GTGTTGTTTTTTTTTTATATGAAAGGAATGAAGATAAGGAAAATAGGAAAGGTGG
Found at i:29544229 original size:17 final size:18
Alignment explanation
Indices: 29544197--29544234 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
29544187 GCAAAACGTG
*
29544197 CCACACGTGTATGTT-AC
1 CCACACGTGTAGGTTAAC
*
29544214 CCACACGTGTCGGTTAAC
1 CCACACGTGTAGGTTAAC
29544232 CCA
1 CCA
29544235 TGCACTGTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (18 bp):
CCACACGTGTAGGTTAAC
Found at i:29547803 original size:15 final size:15
Alignment explanation
Indices: 29547783--29547815 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29547773 CTGAAGGTTA
29547783 ACTTGTTTTGAGAAT
1 ACTTGTTTTGAGAAT
*
29547798 ACTTGTTTTGAGAGT
1 ACTTGTTTTGAGAAT
29547813 ACT
1 ACT
29547816 AACTGATCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.45
Consensus pattern (15 bp):
ACTTGTTTTGAGAAT
Found at i:29552859 original size:14 final size:14
Alignment explanation
Indices: 29552840--29552869 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29552830 TTATATCGAG
29552840 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
29552854 ACCAATCCAATTCA
1 ACCAATCCAAATCA
29552868 AC
1 AC
29552870 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:29555509 original size:25 final size:27
Alignment explanation
Indices: 29555475--29555526 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
29555465 AATTGGTAAA
*
29555475 ATTTTTCTATCA-AT-ATTTTCATACG
1 ATTTTCCTATCATATAATTTTCATACG
29555500 ATTTTCCTATCATATCAATTTTCATAC
1 ATTTTCCTATCATAT-AATTTTCATAC
29555527 AAAAATATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 2 0.09
28 10 0.43
ACGTcount: A:0.29, C:0.19, G:0.02, T:0.50
Consensus pattern (27 bp):
ATTTTCCTATCATATAATTTTCATACG
Found at i:29565373 original size:172 final size:172
Alignment explanation
Indices: 29565081--29565425 Score: 681
Period size: 172 Copynumber: 2.0 Consensus size: 172
29565071 GAATTTGATC
29565081 AACCTAGCATGCGACGAGACTAGTTGGGTGATTGATACTGGTGCATCACTTCATGTCACGTCGAG
1 AACCTAGCATGCGACGAGACTAGTTGGGTGATTGATACTGGTGCATCACTTCATGTCACGTCGAG
*
29565146 GAAGGAATTCTTCACATCTTATACTCCTGGTGATTTTGGGGTATTGAAGATGGGTAATGATGGTT
66 GAAGGAATTCTTCACATCTTATACTCCTGGTGATTTTGGGGTATTGAAAATGGGTAATGATGGTT
29565211 TGGTTTCGGTTATTGGTATGGGAGATGTTAGCTTGGTAAGTA
131 TGGTTTCGGTTATTGGTATGGGAGATGTTAGCTTGGTAAGTA
29565253 AACCTAGCATGCGACGAGACTAGTTGGGTGATTGATACTGGTGCATCACTTCATGTCACGTCGAG
1 AACCTAGCATGCGACGAGACTAGTTGGGTGATTGATACTGGTGCATCACTTCATGTCACGTCGAG
29565318 GAAGGAATTCTTCACATCTTATACTCCTGGTGATTTTGGGGTATTGAAAATGGGTAATGATGGTT
66 GAAGGAATTCTTCACATCTTATACTCCTGGTGATTTTGGGGTATTGAAAATGGGTAATGATGGTT
29565383 TGGTTTCGGTTATTGGTATGGGAGATGTTAGCTTGGTAAGTA
131 TGGTTTCGGTTATTGGTATGGGAGATGTTAGCTTGGTAAGTA
29565425 A
1 A
29565426 CAATGGAACA
Statistics
Matches: 172, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
172 172 1.00
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (172 bp):
AACCTAGCATGCGACGAGACTAGTTGGGTGATTGATACTGGTGCATCACTTCATGTCACGTCGAG
GAAGGAATTCTTCACATCTTATACTCCTGGTGATTTTGGGGTATTGAAAATGGGTAATGATGGTT
TGGTTTCGGTTATTGGTATGGGAGATGTTAGCTTGGTAAGTA
Found at i:29574276 original size:47 final size:47
Alignment explanation
Indices: 29574210--29574333 Score: 144
Period size: 47 Copynumber: 2.6 Consensus size: 47
29574200 TTACATAATA
* * * *
29574210 ATGCCATAGCCCAGCTATGGTCTTACAC-GTAATCACATATCTC-ACTG
1 ATGCCATATCCCAGATATGGTCTTACACAGT-AGCACATATCACAAC-G
* * *
29574257 ATGTCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAACG
1 ATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAACG
*
29574304 ATGCCATATCCCAGATATGGTCTTATACAG
1 ATGCCATATCCCAGATATGGTCTTACACAG
29574334 AAATCACTTG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 63 0.94
48 4 0.06
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (47 bp):
ATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAACG
Found at i:29574392 original size:31 final size:31
Alignment explanation
Indices: 29574357--29574565 Score: 292
Period size: 31 Copynumber: 6.7 Consensus size: 31
29574347 CTTGTCACTT
* *
29574357 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* ** *
29574388 GTAGCTGGTGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
29574419 GTAGCCGAAGCTACCACTTTTTACTGGTCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
29574450 GTAGCCGAAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
29574481 GTAGCAGAAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
29574512 GTAGCTGAAACTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
29574543 GTAGCTGAAGCTACCACTTTTCA
1 GTAGCCGAAGCTACCACTTTTCA
29574566 GTTGTCATTT
Statistics
Matches: 158, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 158 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:29574649 original size:50 final size:51
Alignment explanation
Indices: 29574543--29574671 Score: 181
Period size: 50 Copynumber: 2.5 Consensus size: 51
29574533 CACTGATCAG
* * * * * *
29574543 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTGCCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGCCATTAATCAGATAAGT
29574594 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTCC-TTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTG-CCATTAATCAGATAAGT
29574644 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
29574672 TTCCATGGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
50 45 0.64
51 25 0.36
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTGCCATTAATCAGATAAGT
Found at i:29580865 original size:20 final size:21
Alignment explanation
Indices: 29580817--29580885 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
29580807 CGAATTTTCT
* * * *
29580817 TTTTACAAAATTAAAATTTTC
1 TTTTAAAAAATCAAAACTTTA
* *
29580838 TTTAAAAAAATCAGAACTTT-
1 TTTTAAAAAATCAAAACTTTA
29580858 TTTT-AAAAATCAAAACTTTA
1 TTTTAAAAAATCAAAACTTTA
29580878 TTTTAAAA
1 TTTTAAAA
29580886 TAGTTGAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 14 0.36
20 7 0.18
21 18 0.46
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (21 bp):
TTTTAAAAAATCAAAACTTTA
Found at i:29580886 original size:19 final size:19
Alignment explanation
Indices: 29580816--29580885 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 19
29580806 TCGAATTTTC
*
29580816 TTTTTACAAAATTAAAA-TT
1 TTTTTA-AAAATCAAAACTT
*
29580835 TTCTTTAAAAAAATCAGAACTT
1 TT-TTT--AAAAATCAAAACTT
29580857 TTTTTAAAAATCAAAACTT
1 TTTTTAAAAATCAAAACTT
29580876 TATTTTAAAA
1 T-TTTTAAAA
29580886 TAGTTGAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
19 16 0.37
20 11 0.26
21 11 0.26
22 5 0.12
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (19 bp):
TTTTTAAAAATCAAAACTT
Found at i:29580917 original size:22 final size:22
Alignment explanation
Indices: 29580892--29580939 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
29580882 AAAATAGTTG
*
29580892 AAAAAGATCAAAACTTTCTTTT
1 AAAAAGATCAAAACTTTCCTTT
** *
29580914 AAAAATTTTAAAACTTTCCTTT
1 AAAAAGATCAAAACTTTCCTTT
29580936 AAAA
1 AAAA
29580940 TGAGTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAAAGATCAAAACTTTCCTTT
Found at i:29580986 original size:52 final size:50
Alignment explanation
Indices: 29580858--29581140 Score: 149
Period size: 52 Copynumber: 5.6 Consensus size: 50
29580848 TCAGAACTTT
* * ** *
29580858 TTTTAAAAATCAAAACTTTAT--TTTAAAATAGTTGAAAAAGATCAAAACTTTC
1 TTTTAAAAATCTAAACTTT-TCCTTTAAAATAG-T-AAAAA-AACAAATTTTTA
*
29580910 TTTTAAAAATTTTAAAAC-TTTCCTTTAAAATGAGTAAAAAAACAAATTTTTA
1 TTTTAAAAA-TCT-AAACTTTTCCTTTAAAAT-AGTAAAAAAACAAATTTTTA
* *
29580962 TTTTAAAAATCTAAACTTTCTCCTTTAAAA-A--AAAAGAATC-ACTATTTT-
1 TTTTAAAAATCTAAACTTT-TCCTTTAAAATAGTAAAA-AAACAAAT-TTTTA
* ** * * **
29581010 TCTTAAAAATC-AAAGCTTTTATTTTGAGATAGTTAAAAAAAATCAAAACTTTA
1 TTTTAAAAATCTAAA-CTTTTCCTTTAAAATAG-T-AAAAAAA-CAAATTTTTA
* * * *
29581063 -TTTAAAAATTTAAAC-TTTCCTTTGAAATGACTAAAAAAACATATTTTTA
1 TTTTAAAAATCTAAACTTTTCCTTTAAAAT-AGTAAAAAAACAAATTTTTA
* *
29581112 TTTTTAAAATCTAAA-ATTTCTCTTTAAAA
1 TTTTAAAAATCTAAACTTTTC-CTTTAAAA
29581141 AAAATCAAAA
Statistics
Matches: 178, Mismatches: 30, Indels: 47
0.70 0.12 0.18
Matches are distributed among these distances:
47 9 0.05
48 21 0.12
49 14 0.08
50 28 0.16
51 24 0.13
52 55 0.31
53 12 0.07
54 13 0.07
55 2 0.01
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (50 bp):
TTTTAAAAATCTAAACTTTTCCTTTAAAATAGTAAAAAAACAAATTTTTA
Found at i:29581098 original size:150 final size:150
Alignment explanation
Indices: 29580809--29581144 Score: 433
Period size: 150 Copynumber: 2.3 Consensus size: 150
29580799 ACGGTGGTCG
*
29580809 AATTTTCT-TTTTACAAAAT-TAAAATTT-TCTTTAAAAAAATCAG-A--AC--TTTTTTTAAAA
1 AATTTT-TATTTTA-AAAATCTAAAATTTCTCTTTAAAAAAA-AAGAATCACTATTTTTTTAAAA
* * *
29580866 ATCAAAACTTTATTTTAAAATAGTTGAAAAAGATCAAAACTTTCTTTTAAAAATTTTAAAACTTT
63 ATCAAAACTTTATTTTAAAATAGTTAAAAAAAATCAAAACTTTCATTTAAAAATTTTAAAACTTT
*
29580931 CCTTTAAAATGAGTAAAAAAACA
128 CCTTTAAAATGACTAAAAAAACA
*
29580954 AATTTTTATTTTAAAAATCTAAACTTTCTCCTTTAAAAAAAAAGAATCACTATTTTTCTTAAAAA
1 AATTTTTATTTTAAAAATCTAAAATTTCT-CTTTAAAAAAAAAGAATCACTATTTTT-TTAAAAA
* * *
29581019 TCAAAGCTTTTATTTTGAGATAGTTAAAAAAAATCAAAACTTT-ATTTAAAAA-TTT-AAACTTT
64 TCAAAAC-TTTATTTTAAAATAGTTAAAAAAAATCAAAACTTTCATTTAAAAATTTTAAAACTTT
*
29581081 CCTTTGAAATGACTAAAAAAACA
128 CCTTTAAAATGACTAAAAAAACA
* *
29581104 TATTTTTATTTTTAAAATCTAAAATTTCTCTTTAAAAAAAA
1 AATTTTTATTTTAAAAATCTAAAATTTCTCTTTAAAAAAAA
29581145 TCAAAACTTT
Statistics
Matches: 167, Mismatches: 13, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
144 6 0.04
145 18 0.11
146 3 0.02
147 12 0.07
149 14 0.08
150 54 0.32
151 8 0.05
152 21 0.13
153 31 0.19
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (150 bp):
AATTTTTATTTTAAAAATCTAAAATTTCTCTTTAAAAAAAAAGAATCACTATTTTTTTAAAAATC
AAAACTTTATTTTAAAATAGTTAAAAAAAATCAAAACTTTCATTTAAAAATTTTAAAACTTTCCT
TTAAAATGACTAAAAAAACA
Found at i:29581495 original size:12 final size:12
Alignment explanation
Indices: 29581475--29581508 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29581465 TAATAACATT
*
29581475 TAATAATAATGG
1 TAATAATAATGA
*
29581487 TAGTAATAATGA
1 TAATAATAATGA
29581499 TAATAATAAT
1 TAATAATAAT
29581509 TTGCGTCCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (12 bp):
TAATAATAATGA
Found at i:29582444 original size:10 final size:10
Alignment explanation
Indices: 29582431--29582465 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
29582421 CTTTTATCTT
*
29582431 TCTTTAATTA
1 TCTTTATTTA
29582441 TCTTTATTTA
1 TCTTTATTTA
*
29582451 TCTGTATTTA
1 TCTTTATTTA
29582461 TCTTT
1 TCTTT
29582466 TAGAATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.20, C:0.11, G:0.03, T:0.66
Consensus pattern (10 bp):
TCTTTATTTA
Found at i:29583233 original size:40 final size:38
Alignment explanation
Indices: 29583187--29583264 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 38
29583177 CGGAATTTCA
*
29583187 ATCAAAACTTTTAATTCTGTTTTTATTTTATTTTTTCCAG
1 ATCAAAACTTTTAATTCTGTTTTT-TTAT-TTTTTTCCAG
29583227 ATCAAAACTTTTAATTCTGTTTTTTTATTTTTTTCCAG
1 ATCAAAACTTTTAATTCTGTTTTTTTATTTTTTTCCAG
29583265 GTACGCAGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 10 0.27
39 3 0.08
40 24 0.65
ACGTcount: A:0.24, C:0.13, G:0.05, T:0.58
Consensus pattern (38 bp):
ATCAAAACTTTTAATTCTGTTTTTTTATTTTTTTCCAG
Found at i:29589619 original size:20 final size:19
Alignment explanation
Indices: 29589581--29589620 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29589571 TATTATTATT
*
29589581 TTTTATCATTTCAATTCAA
1 TTTTATCATTTCAAATCAA
*
29589600 TTTTATCATTTATAAATCAA
1 TTTTATCATTT-CAAATCAA
29589620 T
1 T
29589621 GTATTTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTATCATTTCAAATCAA
Found at i:29591248 original size:33 final size:33
Alignment explanation
Indices: 29591206--29591277 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
29591196 TTTACACATG
* *
29591206 TATATTTTTATTACCATACAATTATCTACTATT
1 TATATTTTTATTACCACACAATTATCTACCATT
29591239 TATATTTTTATTACCACACAATTATCTACCATT
1 TATATTTTTATTACCACACAATTATCTACCATT
29591272 TA-ATTT
1 TATATTT
29591278 ATTTAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
32 4 0.11
33 33 0.89
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (33 bp):
TATATTTTTATTACCACACAATTATCTACCATT
Found at i:29593665 original size:29 final size:29
Alignment explanation
Indices: 29593623--29593697 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
29593613 GAAATATTTT
*
29593623 CATGGCCCGAAGCCAAAACATCTGATATG
1 CATGGCCCAAAGCCAAAACATCTGATATG
*
29593652 CATGGCCCAAAGCCAAAACATTTGATATG
1 CATGGCCCAAAGCCAAAACATCTGATATG
*
29593681 CATGGCCCAAAGTCAAA
1 CATGGCCCAAAGCCAAA
29593698 TCAGTATAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (29 bp):
CATGGCCCAAAGCCAAAACATCTGATATG
Found at i:29597620 original size:6 final size:6
Alignment explanation
Indices: 29597588--29597617 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
29597578 CTCACGAGGA
*
29597588 CCCACC CCCACC CCCACC CCCACC ACCACC
1 CCCACC CCCACC CCCACC CCCACC CCCACC
29597618 ACCGCGTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.80, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCACC
Found at i:29597819 original size:6 final size:6
Alignment explanation
Indices: 29597804--29597872 Score: 97
Period size: 6 Copynumber: 11.5 Consensus size: 6
29597794 TTTGAGTCCC
29597804 TTTA-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-T
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
29597850 TTTATT TTCTCTT ATTTATT TTT
1 TTTATT TT-TATT -TTTATT TTT
29597873 GAAGACTTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
5 9 0.16
6 41 0.71
7 6 0.10
8 2 0.03
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:29598884 original size:4 final size:4
Alignment explanation
Indices: 29598877--29598963 Score: 165
Period size: 4 Copynumber: 21.8 Consensus size: 4
29598867 CTTAAAAAAA
*
29598877 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAA ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
29598925 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
29598964 TTAGTAGTAA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 81 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:29602217 original size:21 final size:23
Alignment explanation
Indices: 29602170--29602223 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
29602160 TATTCAAGAT
**
29602170 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
29602193 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
29602214 AAAAT-ATATA
1 AAAATAATATA
29602224 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:29602472 original size:17 final size:15
Alignment explanation
Indices: 29602432--29602477 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
29602422 ATATAAATAG
*
29602432 AAATAAAAATATAAT
1 AAATAGAAATATAAT
29602447 AAATAGAAATATAAT
1 AAATAGAAATATAAT
29602462 AATAGTAGAAATATAA
1 AA-A-TAGAAATATAA
29602478 ATAGATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:29602487 original size:14 final size:13
Alignment explanation
Indices: 29602447--29602548 Score: 59
Period size: 14 Copynumber: 7.2 Consensus size: 13
29602437 AAAATATAAT
29602447 AAATAGA-AATATA
1 AAATAGATAA-ATA
*
29602460 ATAATAGTAGAAATA
1 A-AATAG-ATAAATA
29602475 TAAATAGATAAATA
1 -AAATAGATAAATA
29602489 AAATTAGATAAATA
1 AAA-TAGATAAATA
29602503 ATAATAGTATTAGAATA
1 A-AATAG-A-TA-AATA
29602520 ACAA-A-ATAAATA
1 A-AATAGATAAATA
29602532 TAAATAGA-AACATA
1 -AAATAGATAA-ATA
29602546 AAA
1 AAA
29602549 ATAATAGCAA
Statistics
Matches: 74, Mismatches: 2, Indels: 26
0.73 0.02 0.25
Matches are distributed among these distances:
12 6 0.08
13 13 0.18
14 30 0.41
15 12 0.16
16 6 0.08
17 7 0.09
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (13 bp):
AAATAGATAAATA
Found at i:29602506 original size:29 final size:30
Alignment explanation
Indices: 29602442--29602571 Score: 76
Period size: 29 Copynumber: 4.5 Consensus size: 30
29602432 AAATAAAAAT
29602442 ATAATAAATAGAAATATAATAATAGTAGAA
1 ATAATAAATAGAAATATAATAATAGTAGAA
*
29602472 AT-ATAAATAGATAA-ATAA-AATTAG-ATAA
1 ATAATAAATAGA-AATATAATAA-TAGTAGAA
* * * * ** *
29602500 ATAAT-AATAGTATTAGAATAACAAAATAA
1 ATAATAAATAGAAATATAATAATAGTAGAA
* * * *
29602529 AT-ATAAATAGAAACATAAAAATAATAGCA
1 ATAATAAATAGAAATATAATAATAGTAGAA
*
29602558 ATAATATAT-GAAAT
1 ATAATAAATAGAAAT
29602572 TAGTTAATTT
Statistics
Matches: 75, Mismatches: 17, Indels: 17
0.69 0.16 0.16
Matches are distributed among these distances:
27 1 0.01
28 18 0.24
29 47 0.63
30 9 0.12
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (30 bp):
ATAATAAATAGAAATATAATAATAGTAGAA
Found at i:29605853 original size:18 final size:18
Alignment explanation
Indices: 29605812--29605847 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29605802 ACAGTGGGTG
29605812 AAATTAGGTTTTCAAGTC
1 AAATTAGGTTTTCAAGTC
29605830 AAATTAGGTTTTCAAGTC
1 AAATTAGGTTTTCAAGTC
29605848 TTATTAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (18 bp):
AAATTAGGTTTTCAAGTC
Found at i:29619205 original size:16 final size:17
Alignment explanation
Indices: 29619171--29619205 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29619161 GTTTTGTCCA
*
29619171 TTTATGGTTTTGGACTT
1 TTTATGGTTTTGAACTT
29619188 TTTATGGTTTT-AACTT
1 TTTATGGTTTTGAACTT
29619204 TT
1 TT
29619206 CTAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.14, C:0.06, G:0.17, T:0.63
Consensus pattern (17 bp):
TTTATGGTTTTGAACTT
Found at i:29619282 original size:20 final size:19
Alignment explanation
Indices: 29619257--29619297 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
29619247 TGTGATATTT
29619257 AAATATATAGA-TATAAAATA
1 AAATATATA-ACTAT-AAATA
29619277 AAATATATAACTATAAATA
1 AAATATATAACTATAAATA
29619296 AA
1 AA
29619298 GTGATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AAATATATAACTATAAATA
Found at i:29624050 original size:22 final size:22
Alignment explanation
Indices: 29624024--29624084 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 22
29624014 CTTTTTAGTT
29624024 TTTTATATATTTATATATATA-A
1 TTTTATA-ATTTATATATATACA
29624046 -TTT-TAATTTATATAT-TACA
1 TTTTATAATTTATATATATACA
* *
29624065 TATTACAAATTTATATATAT
1 TTTTA-TAATTTATATATAT
29624085 TTCAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 2 0.06
19 11 0.34
20 4 0.12
21 3 0.09
22 11 0.34
23 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTATAATTTATATATATACA
Found at i:29624077 original size:27 final size:27
Alignment explanation
Indices: 29624025--29624077 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
29624015 TTTTTAGTTT
* * *
29624025 TTTATATATTTATATATATAATTTTAA
1 TTTATATATTCATATATACAAATTTAA
29624052 TTTATATATTACATAT-TACAAATTTA
1 TTTATATATT-CATATATACAAATTTA
29624078 TATATATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTATATATTCATATATACAAATTTAA
Done.