Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 22 of 250
Found at i:6319938 original size:12 final size:12
Alignment explanation
Indices: 6319923--6319955 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6319913 ATTTCTTAAA
6319923 TTTTAACAATTT
1 TTTTAACAATTT
*
6319935 TTTTAAAAATTT
1 TTTTAACAATTT
6319947 TTTT-ACAAT
1 TTTTAACAAT
6319956 CTTCTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTAACAATTT
Found at i:6320022 original size:19 final size:19
Alignment explanation
Indices: 6319998--6320042 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
6319988 ATATTTCAAA
6319998 AATTTTAGT-AATT-TTTAAT
1 AATTTTA-TAAATTATTT-AT
6320017 AATTTTATAAATTATTTAT
1 AATTTTATAAATTATTTAT
6320036 AATTTTA
1 AATTTTA
6320043 CGTTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.04
19 20 0.83
20 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
AATTTTATAAATTATTTAT
Found at i:6326709 original size:18 final size:21
Alignment explanation
Indices: 6326679--6326732 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
6326669 TTAACTATAT
6326679 AAATAAA-TAATTT-T-TTTA
1 AAATAAATTAATTTATATTTA
6326697 AAA-AAATTAATTTAATATTTA
1 AAATAAATTAATTT-ATATTTA
6326718 AAATAAATTAATTTA
1 AAATAAATTAATTTA
6326733 CTTATTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 3 0.10
18 9 0.29
20 1 0.03
21 8 0.26
22 10 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATAAATTAATTTATATTTA
Found at i:6333381 original size:18 final size:19
Alignment explanation
Indices: 6333345--6333383 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
6333335 TATGACAACG
6333345 AATGATATGAATGTATATA
1 AATGATATGAATGTATATA
6333364 AATGA-ATGATATGT-TATA
1 AATGATATGA-ATGTATATA
6333382 AA
1 AA
6333384 CGCTCGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (19 bp):
AATGATATGAATGTATATA
Found at i:6335262 original size:21 final size:21
Alignment explanation
Indices: 6335238--6335290 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
6335228 TTGAATTGAT
*
6335238 TCGAGTGAAATGAAATTCGAA
1 TCGAGTGAAATGAAATTCAAA
6335259 TCGAGTGAAATGAAATTCAAA
1 TCGAGTGAAATGAAATTCAAA
6335280 TCGAGTGAAAT
1 TCGAGTGAAAT
6335291 TGTTAGAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (21 bp):
TCGAGTGAAATGAAATTCAAA
Found at i:6335588 original size:18 final size:20
Alignment explanation
Indices: 6335567--6335608 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
6335557 AAATTTTGAA
*
6335567 AATTTTATAAA-TA-TTTTG
1 AATTTTAGAAATTATTTTTG
6335585 AATTTTAGAAATTATTTTTG
1 AATTTTAGAAATTATTTTTG
6335605 AATT
1 AATT
6335609 ATTTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 2 0.10
20 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
AATTTTAGAAATTATTTTTG
Found at i:6336465 original size:29 final size:29
Alignment explanation
Indices: 6336423--6336484 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
6336413 TGAACAGGTT
6336423 GTGTGTCTCACACGGCATTAGACACACCC
1 GTGTGTCTCACACGGCATTAGACACACCC
* * *
6336452 GTGTGTCTTACACGGTATTAGACACGCCC
1 GTGTGTCTCACACGGCATTAGACACACCC
6336481 GTGT
1 GTGT
6336485 ATCTAAGCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (29 bp):
GTGTGTCTCACACGGCATTAGACACACCC
Found at i:6337627 original size:44 final size:41
Alignment explanation
Indices: 6337579--6337677 Score: 119
Period size: 41 Copynumber: 2.4 Consensus size: 41
6337569 GGATCAATCC
* *
6337579 CGCACACTTAGTGCCATCTCAAATAACCTAAGCTATCTCGGTAT
1 CGCACACTTAGTGCC--CTCAAATAACCGAAGCTATCTC-GAAT
* * *
6337623 CGCACACTTAGTG-CCTCATATAGCCGAAGCTATTTCGAAT
1 CGCACACTTAGTGCCCTCAAATAACCGAAGCTATCTCGAAT
6337663 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
6337678 GAACATAGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
40 16 0.33
41 19 0.39
43 1 0.02
44 13 0.27
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.26
Consensus pattern (41 bp):
CGCACACTTAGTGCCCTCAAATAACCGAAGCTATCTCGAAT
Found at i:6337675 original size:40 final size:41
Alignment explanation
Indices: 6337579--6337677 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 41
6337569 GGATCAATCC
* *
6337579 CGCACACTTAGTGCCATCTCAAATAACCTAAGCTATCTCGGTAT
1 CGCACACTTAGTG-C--CTCAAATAACCGAAGCTATCTCGGAAT
* * *
6337623 CGCACACTTAGTGCCTCATATAGCCGAAGCTATTTC-GAAT
1 CGCACACTTAGTGCCTCAAATAACCGAAGCTATCTCGGAAT
6337663 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
6337678 GAACATAGTC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 18 0.36
41 18 0.36
43 1 0.02
44 13 0.26
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.26
Consensus pattern (41 bp):
CGCACACTTAGTGCCTCAAATAACCGAAGCTATCTCGGAAT
Found at i:6340518 original size:20 final size:20
Alignment explanation
Indices: 6340495--6340534 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
6340485 TCAAATAGAA
*
6340495 GTAATGCAGTAGATGAAAAC
1 GTAATGCAGCAGATGAAAAC
6340515 GTAATGCAGCAGATGAAAAC
1 GTAATGCAGCAGATGAAAAC
6340535 ATCTTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.25, T:0.17
Consensus pattern (20 bp):
GTAATGCAGCAGATGAAAAC
Found at i:6340757 original size:26 final size:26
Alignment explanation
Indices: 6340710--6340759 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
6340700 TTCATCATGA
* *
6340710 CACAAATTCTCAATAAATAAGTTCAT
1 CACAAATTCTCAACAAACAAGTTCAT
* *
6340736 CACAAATTCTTAACGAACAAGTTC
1 CACAAATTCTCAACAAACAAGTTC
6340760 TCCACCTCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (26 bp):
CACAAATTCTCAACAAACAAGTTCAT
Found at i:6348419 original size:42 final size:40
Alignment explanation
Indices: 6348372--6348525 Score: 155
Period size: 42 Copynumber: 3.7 Consensus size: 40
6348362 CGAGAGTATG
6348372 TGTAAGACCATATCTAGGATATGGCATCATTATGAGACTTCA
1 TGTAAGACCATATCTAGGATATGGCATCA-TATGAGA-TTCA
* *
6348414 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCG
1 TGTAAGACCATATCTAGGATATGGCATC-ATATGAGA-TTCA
* * * * * * *
6348456 TGTAAGACCATAGCTGGGCTATTGGCATGGAAACGAGATCCCA
1 TGTAAGACCATATCTAGGATA-TGGCAT-CATATGAGAT-TCA
*
6348499 TGTAAGACTATATCTAGGATATGGCAT
1 TGTAAGACCATATCTAGGATATGGCAT
6348526 TGCTGTGGTA
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
42 63 0.67
43 31 0.33
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (40 bp):
TGTAAGACCATATCTAGGATATGGCATCATATGAGATTCA
Found at i:6351364 original size:12 final size:12
Alignment explanation
Indices: 6351347--6351374 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6351337 TTAGGTAGTT
6351347 ACACAGCCTAGC
1 ACACAGCCTAGC
6351359 ACACAGCCTAGC
1 ACACAGCCTAGC
6351371 ACAC
1 ACAC
6351375 GGGCGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.43, G:0.14, T:0.07
Consensus pattern (12 bp):
ACACAGCCTAGC
Found at i:6354996 original size:20 final size:20
Alignment explanation
Indices: 6354971--6355008 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6354961 TTTATTTTAT
6354971 ATTTTTATATATATATTTGA
1 ATTTTTATATATATATTTGA
*
6354991 ATTTTTATATATTTATTT
1 ATTTTTATATATATATTT
6355009 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (20 bp):
ATTTTTATATATATATTTGA
Found at i:6356206 original size:17 final size:17
Alignment explanation
Indices: 6356184--6356220 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
6356174 TAAGAAAGAA
6356184 TAATTAAAAATTTTAAT
1 TAATTAAAAATTTTAAT
**
6356201 TAATTAAATTTTTTAAT
1 TAATTAAAAATTTTAAT
6356218 TAA
1 TAA
6356221 AAATCTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATTAAAAATTTTAAT
Found at i:6358891 original size:117 final size:120
Alignment explanation
Indices: 6358655--6358909 Score: 389
Period size: 117 Copynumber: 2.1 Consensus size: 120
6358645 TTATTAAATT
6358655 TTAATA-AGATTATTATT-AAATATAATTTAATAAAAATAAAAAGTAAATAATTTAATCATATTT
1 TTAATATA-ATTATTATTAAAATATAATTTAATAAAAATAAAAAGTAAATAATTTAATCATATTT
* *
6358718 TAACATAATTATTATTAAATACAATTTAATAAAATGATATATAATTTGAAATCATTA
65 TAACATAA-TATTATTAAATACAATTTAATAAAATAATATATAATTTGAAAACATTA
* *
6358775 TTAATATAATTATTATTAAAATATGAA-TTAATAAAAATCATAA-TAAATAATTTAATCATATTT
1 TTAATATAATTATTATTAAAATAT-AATTTAATAAAAATAAAAAGTAAATAATTTAATCATATTT
6358838 TAACAT-A-ATTATTAAATACAATTTAATAAAATAATATATAATTT-AATAACATTA
65 TAACATAATATTATTAAATACAATTTAATAAAATAATATATAATTTGAA-AACATTA
6358892 TTAATATAATTATTATTA
1 TTAATATAATTATTATTA
6358910 TTTTAGGTAT
Statistics
Matches: 127, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
116 2 0.02
117 60 0.47
119 1 0.01
120 41 0.32
121 21 0.17
122 2 0.02
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (120 bp):
TTAATATAATTATTATTAAAATATAATTTAATAAAAATAAAAAGTAAATAATTTAATCATATTTT
AACATAATATTATTAAATACAATTTAATAAAATAATATATAATTTGAAAACATTA
Found at i:6366779 original size:5 final size:5
Alignment explanation
Indices: 6366769--6366855 Score: 53
Period size: 5 Copynumber: 17.8 Consensus size: 5
6366759 TATAGTGCAT
*
6366769 AATAA AATAA AAT-A AATAA AA-AA AGTAA AAGTAA AA-AA AA-AA ACA-AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AA-TAA AATAA AATAA A-ATAA
* *
6366816 AACAA AA-ACA AA-AA AATAAAA AATAA AAAAA AATAA AATA
1 AATAA AATA-A AATAA AAT--AA AATAA AATAA AATAA AATA
6366856 TAAAACTAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
4 19 0.28
5 40 0.58
6 5 0.07
7 5 0.07
ACGTcount: A:0.83, C:0.03, G:0.02, T:0.11
Consensus pattern (5 bp):
AATAA
Found at i:6366805 original size:1 final size:1
Alignment explanation
Indices: 6366801--6366853 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
6366791 AAGTAAAAGT
* * * * * *
6366801 AAAAAAAAAAACAAAAACAAAAACAAAAAAATAAAAAATAAAAAAAAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6366854 TATAAAACTA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.89, C:0.06, G:0.00, T:0.06
Consensus pattern (1 bp):
A
Found at i:6366853 original size:17 final size:16
Alignment explanation
Indices: 6366772--6366853 Score: 76
Period size: 17 Copynumber: 4.9 Consensus size: 16
6366762 AGTGCATAAT
*
6366772 AAAATAAAATAAATAAA
1 AAAAAAAAATAAA-AAA
*
6366789 AAAAGTAAAAGTAAAAAA
1 AAAA--AAAAATAAAAAA
*
6366807 AAAAACAAAA-ACAAAA
1 AAAAA-AAAATAAAAAA
*
6366823 ACAAAAAAATAAAAAA
1 AAAAAAAAATAAAAAA
6366839 TAAAAAAAAATAAAA
1 -AAAAAAAAATAAAA
6366854 TATAAAACTA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
15 4 0.08
16 15 0.28
17 20 0.38
18 7 0.13
19 7 0.13
ACGTcount: A:0.84, C:0.04, G:0.02, T:0.10
Consensus pattern (16 bp):
AAAAAAAAATAAAAAA
Found at i:6374509 original size:62 final size:62
Alignment explanation
Indices: 6374433--6374556 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
6374423 GGGATTAGTT
6374433 CCCATGGTTTTTGAAAACACTATAGAATCGATATAAACAATGAACATGATGAATGAATCGAA
1 CCCATGGTTTTTGAAAACACTATAGAATCGATATAAACAATGAACATGATGAATGAATCGAA
6374495 CCCATGGTTTTTGAAAACACTATAGAATCGATATAAACAATGAACATGATGAATGAATCGAA
1 CCCATGGTTTTTGAAAACACTATAGAATCGATATAAACAATGAACATGATGAATGAATCGAA
6374557 AGTATAGAGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.26
Consensus pattern (62 bp):
CCCATGGTTTTTGAAAACACTATAGAATCGATATAAACAATGAACATGATGAATGAATCGAA
Found at i:6380898 original size:25 final size:26
Alignment explanation
Indices: 6380855--6380905 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
6380845 ACAGAGGACA
6380855 TATGCCCATTTGAACAGGCCGTGTGT
1 TATGCCCATTTGAACAGGCCGTGTGT
*
6380881 TATGCCCGTTT-AACAGGCCGTGTGT
1 TATGCCCATTTGAACAGGCCGTGTGT
6380906 CTCACACGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (26 bp):
TATGCCCATTTGAACAGGCCGTGTGT
Found at i:6386983 original size:20 final size:20
Alignment explanation
Indices: 6386958--6387004 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
6386948 GATATGATAT
*
6386958 ACATGAT-TGAGATGATATGC
1 ACATGATATG-GATGAAATGC
*
6386978 ACATGATATGTATGAAATGC
1 ACATGATATGGATGAAATGC
6386998 ACATGAT
1 ACATGAT
6387005 GAATTCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (20 bp):
ACATGATATGGATGAAATGC
Found at i:6387112 original size:24 final size:26
Alignment explanation
Indices: 6387054--6387112 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
6387044 GAGGAAGTGC
6387054 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
6387080 AAAAGGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
6387103 AAAAGAGGCT
1 AAAAG-GGCT
6387113 AGGCCTCCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.16
24 9 0.28
25 8 0.25
26 10 0.31
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:6387122 original size:25 final size:25
Alignment explanation
Indices: 6387054--6387122 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
6387044 GAGGAAGTGC
*
6387054 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGC-TAGGCCCCAGTTTATTG
**
6387080 AAAAGGGCTTTGCCCCAG-TTATT-
1 AAAAGGGCTAGGCCCCAGTTTATTG
6387103 AAAAGAGGCTAGGCCTCCAG
1 AAAAG-GGCTAGGCC-CCAG
6387123 ATATATGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 5 0.13
24 12 0.32
25 13 0.34
26 8 0.21
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (25 bp):
AAAAGGGCTAGGCCCCAGTTTATTG
Found at i:6392212 original size:43 final size:43
Alignment explanation
Indices: 6392093--6392229 Score: 204
Period size: 42 Copynumber: 3.2 Consensus size: 43
6392083 ATATCCCGTA
* * *
6392093 ATAATATCCTATAATATCCAATTAGGAATCAAATTGCTAAGAG
1 ATAATATCCTACAATATCCCATTAGGAATAAAATTGCTAAGAG
*
6392136 ATAATATCCTAC-ATATCCCATTAGGAATTAAATTGCTAAGAG
1 ATAATATCCTACAATATCCCATTAGGAATAAAATTGCTAAGAG
* *
6392178 ATAATATCCTACAATATCCCATTAGAAATAAAATTGCTAAAAAG
1 ATAATATCCTACAATATCCCATTAGGAATAAAATTGCT-AAGAG
6392222 ATAATATC
1 ATAATATC
6392230 TCATAATAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
42 40 0.47
43 34 0.40
44 12 0.14
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (43 bp):
ATAATATCCTACAATATCCCATTAGGAATAAAATTGCTAAGAG
Found at i:6395113 original size:22 final size:23
Alignment explanation
Indices: 6395086--6395128 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
6395076 TATAACTTTC
6395086 TTTTGGA-T-AAATATTTATAAAA
1 TTTTGGATTAAAAT-TTTATAAAA
6395108 TTTTGGATTAAAATTTTATAA
1 TTTTGGATTAAAATTTTATAA
6395129 CATAAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (23 bp):
TTTTGGATTAAAATTTTATAAAA
Found at i:6395848 original size:23 final size:23
Alignment explanation
Indices: 6395822--6395867 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
6395812 GGTGATAAAA
* * *
6395822 GTATGCAAATGTAATAATAATAT
1 GTATACAAATGTAACAAAAATAT
*
6395845 GTATACAATTGTAACAAAAATAT
1 GTATACAAATGTAACAAAAATAT
6395868 TTAATTATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.33
Consensus pattern (23 bp):
GTATACAAATGTAACAAAAATAT
Found at i:6397738 original size:47 final size:47
Alignment explanation
Indices: 6397656--6397745 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 47
6397646 CCTTGTGTCT
** * *
6397656 CGTACTGTTACTGTTACTTCGGTTTAATCCAATGAGGTACTGAGTAC
1 CGTACTGTTACTGTTACTTCGGTCAAAGCCAATGAGGCACTGAGTAC
*
6397703 CGTACTGTTACTGTTTACTTCGG-CAAAGCCGATGAGGCACTGA
1 CGTACTGTTACTG-TTACTTCGGTCAAAGCCAATGAGGCACTGA
6397746 ATGTCGTACT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
47 28 0.76
48 9 0.24
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (47 bp):
CGTACTGTTACTGTTACTTCGGTCAAAGCCAATGAGGCACTGAGTAC
Found at i:6397754 original size:47 final size:47
Alignment explanation
Indices: 6397655--6397756 Score: 116
Period size: 47 Copynumber: 2.2 Consensus size: 47
6397645 ACCTTGTGTC
** * * *
6397655 TCGTACTGTTACTGTTACTTCGGTTTAATCCAATGAGGTACTGAGTA
1 TCGTACTGTTACTGTTACTTCGGTCAAAGCCAATGAGGCACTGAATA
* * *
6397702 CCGTACTGTTACTGTTTACTTCGG-CAAAGCCGATGAGGCACTGAATG
1 TCGTACTGTTACTG-TTACTTCGGTCAAAGCCAATGAGGCACTGAATA
6397749 TCGTACTG
1 TCGTACTG
6397757 GTGTGTTGGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
47 36 0.80
48 9 0.20
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (47 bp):
TCGTACTGTTACTGTTACTTCGGTCAAAGCCAATGAGGCACTGAATA
Found at i:6398254 original size:39 final size:40
Alignment explanation
Indices: 6398197--6398273 Score: 104
Period size: 39 Copynumber: 1.9 Consensus size: 40
6398187 ATTGAAAGAC
*
6398197 TAAAGTTACTGAATAACTAA-TGATTACTGAATGATTATAT
1 TAAAGTTACTGAACAACTAATTG-TTACTGAATGATTATAT
* *
6398237 TAAAG-TACTGAACAACTAATTGTTATTGATTGATTAT
1 TAAAGTTACTGAACAACTAATTGTTACTGAATGATTAT
6398274 GAATAGAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 26 0.79
40 7 0.21
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (40 bp):
TAAAGTTACTGAACAACTAATTGTTACTGAATGATTATAT
Found at i:6404829 original size:16 final size:16
Alignment explanation
Indices: 6404801--6404866 Score: 71
Period size: 16 Copynumber: 4.0 Consensus size: 16
6404791 CCATACTAAT
6404801 CATA-AATCTCATGTAA
1 CATATAATC-CATGTAA
6404817 CATATAATCCATGTAAA
1 CATATAATCCATGT-AA
*
6404834 CCTTATAATCCATGTAA
1 -CATATAATCCATGTAA
* *
6404851 CATGTAATTCATGTAA
1 CATATAATCCATGTAA
6404867 GGTATATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
16 22 0.51
17 8 0.19
18 13 0.30
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (16 bp):
CATATAATCCATGTAA
Found at i:6404882 original size:34 final size:34
Alignment explanation
Indices: 6404809--6404890 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
6404799 ATCATAAATC
*
6404809 TCATGTAACATATAATCCATGTAAACCTTATAAT
1 TCATGTAACATGTAATCCATGTAAACCTTATAAT
* * ** *
6404843 CCATGTAACATGTAATTCATGT-AAGGTATATTAT
1 TCATGTAACATGTAATCCATGTAAACCT-TATAAT
6404877 TCATGTAACATGTA
1 TCATGTAACATGTA
6404891 CTCTATGTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
33 3 0.08
34 37 0.93
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.37
Consensus pattern (34 bp):
TCATGTAACATGTAATCCATGTAAACCTTATAAT
Found at i:6405113 original size:23 final size:23
Alignment explanation
Indices: 6405073--6405180 Score: 123
Period size: 23 Copynumber: 4.7 Consensus size: 23
6405063 AGCTGAATGA
6405073 TAAGCTCCGT-AGAGCTGAAACGG
1 TAAGCTCC-TAAGAGCTGAAACGG
* *
6405096 TAAGCCCCTAAG-GACTGAAACTG
1 TAAGCTCCTAAGAG-CTGAAACGG
*
6405119 TAAGCTCCGAAGAGCTG-AACGG
1 TAAGCTCCTAAGAGCTGAAACGG
*
6405141 TAAGCTCATAAGAGCTGAAACGG
1 TAAGCTCCTAAGAGCTGAAACGG
* *
6405164 TAAGCTCATACGAGCTG
1 TAAGCTCCTAAGAGCTG
6405181 TGGTGAGTCT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
22 21 0.29
23 51 0.70
24 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (23 bp):
TAAGCTCCTAAGAGCTGAAACGG
Found at i:6405159 original size:45 final size:46
Alignment explanation
Indices: 6405049--6405170 Score: 137
Period size: 45 Copynumber: 2.7 Consensus size: 46
6405039 GCCGATAAAA
* *
6405049 GGTAAGCTCA-ATTGAGCTG-AA-TGATAAGCTCCGTAGAGCTGAAAC
1 GGTAAGCTCATA-AGAGCTGAAACTG-TAAGCTCCGAAGAGCTGAAAC
* *
6405094 GGTAAGCCCCTAAG-GACTGAAACTGTAAGCTCCGAAGAGCTG-AAC
1 GGTAAGCTCATAAGAG-CTGAAACTGTAAGCTCCGAAGAGCTGAAAC
*
6405139 GGTAAGCTCATAAGAGCTGAAACGGTAAGCTC
1 GGTAAGCTCATAAGAGCTGAAACTGTAAGCTC
6405171 ATACGAGCTG
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
44 1 0.02
45 42 0.65
46 20 0.31
47 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (46 bp):
GGTAAGCTCATAAGAGCTGAAACTGTAAGCTCCGAAGAGCTGAAAC
Found at i:6408160 original size:26 final size:24
Alignment explanation
Indices: 6408119--6408168 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
6408109 GTCATCACTA
* *
6408119 ACTAAAAATTAATTTATAATAATT
1 ACTAAAAAATAATTTAAAATAATT
6408143 ACTAACAAAATAACTTTAAAATAATT
1 ACTAA-AAAATAA-TTTAAAATAATT
6408169 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 6 0.27
26 11 0.50
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (24 bp):
ACTAAAAAATAATTTAAAATAATT
Found at i:6408331 original size:10 final size:10
Alignment explanation
Indices: 6408316--6408341 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6408306 TCTACTATCC
6408316 TTTTTTCTTT
1 TTTTTTCTTT
6408326 TTTTTTCTTT
1 TTTTTTCTTT
6408336 TTTTTT
1 TTTTTT
6408342 TCTTCTCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:6408337 original size:11 final size:11
Alignment explanation
Indices: 6408316--6408345 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
6408306 TCTACTATCC
6408316 TTTTTTC-TTT
1 TTTTTTCTTTT
6408326 TTTTTTCTTTT
1 TTTTTTCTTTT
6408337 TTTTTTCTT
1 TTTTTTCTT
6408346 CTCCTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:6408834 original size:42 final size:42
Alignment explanation
Indices: 6408775--6408859 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
6408765 CCTCTATCCC
6408775 TCAAACATCCTATACTCGTATCTAATGGGACATACATATTAT
1 TCAAACATCCTATACTCGTATCTAATGGGACATACATATTAT
*
6408817 TCAAACATCCTATACTCGTATCTAATTGGACATACATATTAT
1 TCAAACATCCTATACTCGTATCTAATGGGACATACATATTAT
6408859 T
1 T
6408860 TTCAAATTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.35
Consensus pattern (42 bp):
TCAAACATCCTATACTCGTATCTAATGGGACATACATATTAT
Found at i:6409175 original size:13 final size:13
Alignment explanation
Indices: 6409157--6409181 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6409147 AATCATGAAG
6409157 TTTCCACAATAAC
1 TTTCCACAATAAC
6409170 TTTCCACAATAA
1 TTTCCACAATAA
6409182 TCACTCTGCA
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:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (13 bp):
TTTCCACAATAAC
Found at i:6415095 original size:19 final size:20
Alignment explanation
Indices: 6415071--6415109 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
6415061 TTTATGAAAA
6415071 TATTTTCTAATTT-ATTTTC
1 TATTTTCTAATTTCATTTTC
*
6415090 TATTTTCTATTTTCATTTTC
1 TATTTTCTAATTTCATTTTC
6415110 AAAAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTTCTAATTTCATTTTC
Found at i:6419595 original size:14 final size:14
Alignment explanation
Indices: 6419576--6419605 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6419566 CATCTCCATG
6419576 TTTCTCTACTTTCA
1 TTTCTCTACTTTCA
6419590 TTTCTCTACTTTCA
1 TTTCTCTACTTTCA
6419604 TT
1 TT
6419606 CTCCACAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.27, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTCTCTACTTTCA
Found at i:6419961 original size:65 final size:65
Alignment explanation
Indices: 6419857--6419991 Score: 218
Period size: 65 Copynumber: 2.1 Consensus size: 65
6419847 TTTCTAACTT
*
6419857 CATTTTCATAGTCACATAGGCTATTAAACTCATAGCTTACCCTTCCATTTATTACCTTCAGTGCC
1 CATTTCCATAGTCACATAGGCTATTAAACTCATAGCTTACCCTTCCATTTATTACCTTCAGTGCC
* *
6419922 CATTTCCATAGTC-CTATAGGCTATTAAACTCATAGCTTACCCTTGCATTTATTTCCTTCAGTGC
1 CATTTCCATAGTCAC-ATAGGCTATTAAACTCATAGCTTACCCTTCCATTTATTACCTTCAGTGC
*
6419986 T
65 C
6419987 CATTT
1 CATTT
6419992 TCTAGCCCTA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
64 1 0.02
65 64 0.98
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (65 bp):
CATTTCCATAGTCACATAGGCTATTAAACTCATAGCTTACCCTTCCATTTATTACCTTCAGTGCC
Found at i:6427320 original size:93 final size:93
Alignment explanation
Indices: 6427208--6427378 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
6427198 GCCCATAAGT
* * *
6427208 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
6427273 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
6427301 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
6427366 CGAGTTCGGATGC
66 CGAGCTCGGATGC
6427379 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:6427375 original size:46 final size:46
Alignment explanation
Indices: 6427200--6427375 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
6427190 TGTAACCCGC
* *
6427200 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
6427246 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** * *
6427292 ACATCTCTCGAACTCGAACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
6427339 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
6427376 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 69 0.63
47 31 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:6436653 original size:11 final size:11
Alignment explanation
Indices: 6436639--6436678 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
6436629 TATTTTCTCC
6436639 CTATTTTGCTA
1 CTATTTTGCTA
*
6436650 CTATTTTACTA
1 CTATTTTGCTA
* *
6436661 TTATGTTGCTA
1 CTATTTTGCTA
6436672 CTATTTT
1 CTATTTT
6436679 ATTATTATTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:6436684 original size:22 final size:22
Alignment explanation
Indices: 6436644--6436686 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
6436634 TCTCCCTATT
6436644 TTGCTACTATTTTACTATTATG
1 TTGCTACTATTTTACTATTATG
*
6436666 TTGCTACTATTTTATTATTAT
1 TTGCTACTATTTTACTATTAT
6436687 TATTTGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (22 bp):
TTGCTACTATTTTACTATTATG
Found at i:6437534 original size:13 final size:13
Alignment explanation
Indices: 6437516--6437540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6437506 ATAAACTGTA
6437516 ATATACATACATG
1 ATATACATACATG
6437529 ATATACATACAT
1 ATATACATACAT
6437541 ATTTTAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (13 bp):
ATATACATACATG
Found at i:6437576 original size:16 final size:16
Alignment explanation
Indices: 6437555--6437586 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6437545 TAAACAATGC
*
6437555 TAAACATAACATACAT
1 TAAACACAACATACAT
6437571 TAAACACAACATACAT
1 TAAACACAACATACAT
6437587 ACTTAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (16 bp):
TAAACACAACATACAT
Found at i:6457674 original size:24 final size:25
Alignment explanation
Indices: 6457646--6457709 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
6457636 TCAACTGAAT
* * *
6457646 TCGCACACATAGTGCTA-ATTAAGC
1 TCGCACACATAGTGCCATACTAAAC
6457670 TCGCACACATAGTGCCATACTAAAC
1 TCGCACACATAGTGCCATACTAAAC
6457695 -CGCACACATAGTGCC
1 TCGCACACATAGTGCC
6457710 TGAAATTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 31 0.86
25 5 0.14
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (25 bp):
TCGCACACATAGTGCCATACTAAAC
Found at i:6457862 original size:24 final size:24
Alignment explanation
Indices: 6457835--6457936 Score: 105
Period size: 24 Copynumber: 4.0 Consensus size: 24
6457825 GAATATAAAA
6457835 TCTGCACACAAAGTGACATTTAAT
1 TCTGCACACAAAGTGACATTTAAT
* * * *
6457859 TCTGCACACATAGTGCCAATCAAATAAAA
1 TCTGCACACAAAGTG---A-C-ATTTAAT
6457888 TCTGCACACAAAGTGACATTTAAT
1 TCTGCACACAAAGTGACATTTAAT
*
6457912 TCCGCACACAAAGTGACATTATAAT
1 TCTGCACACAAAGTGACATT-TAAT
6457937 AAGGCAATTT
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
24 37 0.59
25 5 0.08
26 1 0.02
27 1 0.02
28 1 0.02
29 18 0.29
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (24 bp):
TCTGCACACAAAGTGACATTTAAT
Found at i:6457938 original size:53 final size:53
Alignment explanation
Indices: 6457829--6457929 Score: 175
Period size: 53 Copynumber: 1.9 Consensus size: 53
6457819 CAAATAGAAT
* * *
6457829 ATAAAATCTGCACACAAAGTGACATTTAATTCTGCACACATAGTGCCAATCAA
1 ATAAAATCTGCACACAAAGTGACATTTAATTCCGCACACAAAGTGACAATCAA
6457882 ATAAAATCTGCACACAAAGTGACATTTAATTCCGCACACAAAGTGACA
1 ATAAAATCTGCACACAAAGTGACATTTAATTCCGCACACAAAGTGACA
6457930 TTATAATAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.43, C:0.23, G:0.12, T:0.23
Consensus pattern (53 bp):
ATAAAATCTGCACACAAAGTGACATTTAATTCCGCACACAAAGTGACAATCAA
Found at i:6477642 original size:24 final size:23
Alignment explanation
Indices: 6477586--6477702 Score: 101
Period size: 23 Copynumber: 4.9 Consensus size: 23
6477576 GACTCACCTT
* *
6477586 AGCTCGTATGAGCTTACCGATATATC
1 AGCTCGTAAGAGCTTACTG-T-T-TC
*
6477612 AGCTCGTAAGAGCTTATTGTTCTC
1 AGCTCGTAAGAGCTTACTGTT-TC
* *
6477636 AGCTCGTATGAGCTTACTATTTC
1 AGCTCGTAAGAGCTTACTGTTTC
* * *
6477659 AGCTCATTAGAGCTTACCGTTTC
1 AGCTCGTAAGAGCTTACTGTTTC
*
6477682 AGCTC-AATAGAGCTTACTGTT
1 AGCTCGTA-AGAGCTTACTGTT
6477703 CATAGCTCGA
Statistics
Matches: 75, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
23 37 0.49
24 21 0.28
25 1 0.01
26 16 0.21
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (23 bp):
AGCTCGTAAGAGCTTACTGTTTC
Found at i:6489411 original size:17 final size:17
Alignment explanation
Indices: 6489389--6489421 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
6489379 TTTAAATAAA
6489389 TAAATAAATTTCTCAAT
1 TAAATAAATTTCTCAAT
6489406 TAAATAAATTTCTCAA
1 TAAATAAATTTCTCAA
6489422 CCCAATTCTA
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:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATAAATTTCTCAAT
Found at i:6492975 original size:25 final size:27
Alignment explanation
Indices: 6492914--6492984 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 27
6492904 ATATTTTCTC
6492914 AAAATTTTACTAGAGGTAAAATCATCA
1 AAAATTTTACTAGAGGTAAAATCATCA
* * *
6492941 AAAATTTTACCAG-GGTAAAATCGT-T
1 AAAATTTTACTAGAGGTAAAATCATCA
*
6492966 AAAATTTTACTAGCGGTAA
1 AAAATTTTACTAGAGGTAA
6492985 TATGGGGATG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
25 12 0.31
26 15 0.38
27 12 0.31
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (27 bp):
AAAATTTTACTAGAGGTAAAATCATCA
Found at i:6495673 original size:18 final size:20
Alignment explanation
Indices: 6495650--6495689 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
6495640 TAGTCTTCCA
6495650 TTGAA-TAAT-TTTTTATAT
1 TTGAATTAATATTTTTATAT
*
6495668 TTGAATTGATATTTTTATAT
1 TTGAATTAATATTTTTATAT
6495688 TT
1 TT
6495690 AAACTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 3 0.16
20 11 0.58
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (20 bp):
TTGAATTAATATTTTTATAT
Found at i:6496493 original size:90 final size:90
Alignment explanation
Indices: 6496331--6496531 Score: 233
Period size: 90 Copynumber: 2.2 Consensus size: 90
6496321 TGCTTTCTAA
* * * * * * *
6496331 CCTCGAAGAGTGTGTGATCAAATAATTAAAATTTGGCTAAGTGACTTAGAAGGCTAGCATTCGAT
1 CCTCAAAGGGTGTGTGCTCAAATAATTAAAATTTGGCTAACTGACTTAAAAGGCTACCATACGAT
* * * *
6496396 TTGCTATTAACTTATCGAGAAGTAC
66 CTGCTATTAACCTAGCAAGAAGTAC
* * *
6496421 CCTCAAAGGGTGTGTGCTCAAATTATTAAAATTTGGCTAACTGCCTTAAAAGGCTACCA-ACGGC
1 CCTCAAAGGGTGTGTGCTCAAATAATTAAAATTTGGCTAACTGACTTAAAAGGCTACCATAC-GA
*
6496485 TCTGCTATTAACCTAGCAAGTAGTAC
65 TCTGCTATTAACCTAGCAAGAAGTAC
*
6496511 CCTCGAAAGGGCGTGTGCTCA
1 CCTC-AAAGGGTGTGTGCTCA
6496532 TATATGAATT
Statistics
Matches: 93, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
89 1 0.01
90 77 0.83
91 15 0.16
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (90 bp):
CCTCAAAGGGTGTGTGCTCAAATAATTAAAATTTGGCTAACTGACTTAAAAGGCTACCATACGAT
CTGCTATTAACCTAGCAAGAAGTAC
Found at i:6497588 original size:14 final size:15
Alignment explanation
Indices: 6497562--6497617 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 15
6497552 TTTCCCAAAA
6497562 TAAATATAA-TTT-AT
1 TAAAT-TAATTTTAAT
6497576 TAAATTAATTTTAAT
1 TAAATTAATTTTAAT
6497591 T-AATTAATTTTTCAAT
1 TAAATTAA-TTTT-AAT
6497607 TAAA-TAATTTT
1 TAAATTAATTTT
6497618 CTAAACTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.08
14 14 0.38
15 11 0.30
16 7 0.19
17 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TAAATTAATTTTAAT
Found at i:6497609 original size:16 final size:15
Alignment explanation
Indices: 6497578--6497617 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
6497568 TAATTTATTA
6497578 AATTAA-TTTTAATT
1 AATTAATTTTTAATT
6497592 AATTAATTTTTCAATT
1 AATTAATTTTT-AATT
*
6497608 AAATAATTTT
1 AATTAATTTT
6497618 CTAAACTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.26
15 4 0.17
16 13 0.57
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTAATTTTTAATT
Found at i:6500075 original size:31 final size:31
Alignment explanation
Indices: 6500010--6500076 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
6500000 CTATGTGTCA
*
6500010 GTGTTTATATTGTATCAGGCACAATGTGTCG
1 GTGTTTATATTGTATCAGGCACAATGTATCG
* * * * *
6500041 GTGTTTATATTTTATTAGGTACTATGTATTG
1 GTGTTTATATTGTATCAGGCACAATGTATCG
6500072 GTGTT
1 GTGTT
6500077 GGACACCTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.21, C:0.07, G:0.24, T:0.48
Consensus pattern (31 bp):
GTGTTTATATTGTATCAGGCACAATGTATCG
Found at i:6507437 original size:18 final size:18
Alignment explanation
Indices: 6507414--6507460 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
6507404 TCATCAGAAT
6507414 AGCTCACCAAGAA-CTACA
1 AGCTCACCAA-AATCTACA
* *
6507432 AGCTCACTAAAATGTACA
1 AGCTCACCAAAATCTACA
6507450 AGCTCACCAAA
1 AGCTCACCAAA
6507461 TGTGTGAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.45, C:0.30, G:0.11, T:0.15
Consensus pattern (18 bp):
AGCTCACCAAAATCTACA
Found at i:6507649 original size:2 final size:2
Alignment explanation
Indices: 6507642--6507669 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6507632 CCAAGTTGTA
6507642 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
6507670 TAGTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6509008 original size:24 final size:24
Alignment explanation
Indices: 6508976--6509022 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
6508966 ACACCATCAA
6508976 GTACTAAACTTGTTACAAATGTTG
1 GTACTAAACTTGTTACAAATGTTG
*
6509000 GTACTAAACTTGTTATAAATGTT
1 GTACTAAACTTGTTACAAATGTT
6509023 CTTTTAGTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (24 bp):
GTACTAAACTTGTTACAAATGTTG
Found at i:6511910 original size:17 final size:17
Alignment explanation
Indices: 6511856--6511932 Score: 77
Period size: 18 Copynumber: 4.4 Consensus size: 17
6511846 TCACCAGAAC
6511856 AGCTCACCAAGAACT-ACG
1 AGCTCACCAA-AA-TGACG
6511874 AGCTCACCAAAATGTACG
1 AGCTCACCAAAATG-ACG
6511892 AGCTCACCAAATATG-CG
1 AGCTCACCAAA-ATGACG
* * *
6511909 AGCTCACCAAGATCACA
1 AGCTCACCAAAATGACG
6511926 AGCTCAC
1 AGCTCAC
6511933 TAACACTGCG
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
16 3 0.06
17 22 0.42
18 24 0.46
19 3 0.06
ACGTcount: A:0.38, C:0.32, G:0.16, T:0.14
Consensus pattern (17 bp):
AGCTCACCAAAATGACG
Found at i:6512126 original size:3 final size:3
Alignment explanation
Indices: 6512118--6512175 Score: 107
Period size: 3 Copynumber: 19.0 Consensus size: 3
6512108 AAGCCAAGTT
6512118 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
6512164 TTA TTA TTA TTA
1 TTA TTA TTA TTA
6512176 GCTTATTTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6513510 original size:5 final size:5
Alignment explanation
Indices: 6513500--6513546 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
6513490 TTATGTTTTA
6513500 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
6513547 AAACTAAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:6514863 original size:19 final size:15
Alignment explanation
Indices: 6514817--6514858 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
6514807 CGATGAATTT
*
6514817 ATTGAATTTATATTG
1 ATTGAAATTATATTG
6514832 ATTGAAATTATATTG
1 ATTGAAATTATATTG
6514847 ATTG-AATTATAT
1 ATTGAAATTATAT
6514859 AATATATATG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (15 bp):
ATTGAAATTATATTG
Found at i:6515261 original size:23 final size:23
Alignment explanation
Indices: 6515231--6515316 Score: 83
Period size: 23 Copynumber: 4.0 Consensus size: 23
6515221 GCTTTACCGA
* *
6515231 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
6515254 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
6515275 TC-GGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
6515296 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
6515317 ACTGATCAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
20 17 0.32
21 17 0.32
22 1 0.02
23 18 0.34
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:6515282 original size:20 final size:22
Alignment explanation
Indices: 6515243--6515316 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 22
6515233 AGGCACTTTA
6515243 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAGGCACCTCG
6515266 TGTGTCGTA-TC-GGCACCTCG
1 TGTGTCGTATTCAGGCACCTCG
* * **
6515286 TGTGTCGT-TTTAGGCACTTTA
1 TGTGTCGTATTCAGGCACCTCG
6515307 TGTGTCGTAT
1 TGTGTCGTAT
6515317 ACTGATCAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
20 18 0.41
21 16 0.36
22 1 0.02
23 9 0.20
ACGTcount: A:0.12, C:0.22, G:0.27, T:0.39
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACCTCG
Found at i:6516464 original size:14 final size:15
Alignment explanation
Indices: 6516445--6516477 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6516435 TAGGGACAAC
*
6516445 TAAAAAT-TTTGTAT
1 TAAAAATATTTGAAT
6516459 TAAAAATATTTGAAT
1 TAAAAATATTTGAAT
6516474 TAAA
1 TAAA
6516478 CTATTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
TAAAAATATTTGAAT
Found at i:6516826 original size:13 final size:12
Alignment explanation
Indices: 6516791--6516829 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
6516781 TTTAATAATA
6516791 TAATAAATTA-T
1 TAATAAATTATT
6516802 TAATACAATTATT
1 TAATA-AATTATT
6516815 TCAATAAATTATT
1 T-AATAAATTATT
6516828 TA
1 TA
6516830 TTAATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.20
12 6 0.24
13 10 0.40
14 4 0.16
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (12 bp):
TAATAAATTATT
Found at i:6519355 original size:18 final size:18
Alignment explanation
Indices: 6519329--6519367 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6519319 ACAAATGTTT
*
6519329 TATAGTATAATATATTAA
1 TATAGTATAATATATAAA
* *
6519347 TATATTATACTATATAAA
1 TATAGTATAATATATAAA
6519365 TAT
1 TAT
6519368 GAATATTTGT
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:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (18 bp):
TATAGTATAATATATAAA
Found at i:6520024 original size:19 final size:19
Alignment explanation
Indices: 6520000--6520036 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
6519990 AAAACAGAAT
6520000 ATGGAC-ATGTGAAATTTGC
1 ATGGACAATGT-AAATTTGC
6520019 ATGGACAATGTAAATTTG
1 ATGGACAATGTAAATTTG
6520037 TCTTTAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.32
Consensus pattern (19 bp):
ATGGACAATGTAAATTTGC
Found at i:6523527 original size:43 final size:44
Alignment explanation
Indices: 6523479--6523566 Score: 142
Period size: 43 Copynumber: 2.0 Consensus size: 44
6523469 TTTGCTGGCG
* *
6523479 TGGCTACAGGCTTGCAGTCTTTCATTCTGAATTTA-TTTAAAAT
1 TGGCTACAGGCTTGCAATCCTTCATTCTGAATTTATTTTAAAAT
*
6523522 TGGCTACATGCTTGCAATCCTTCATTCTGAATTTATTTTAAAAT
1 TGGCTACAGGCTTGCAATCCTTCATTCTGAATTTATTTTAAAAT
6523566 T
1 T
6523567 TGTTTTGCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 32 0.78
44 9 0.22
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (44 bp):
TGGCTACAGGCTTGCAATCCTTCATTCTGAATTTATTTTAAAAT
Found at i:6524678 original size:40 final size:41
Alignment explanation
Indices: 6524619--6524704 Score: 138
Period size: 40 Copynumber: 2.1 Consensus size: 41
6524609 GCAAAAATTG
*
6524619 TAAAACACAGAGCAATAGCGGCGTTTTTGGTAAAACGCCGC
1 TAAAACACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* *
6524660 TAAAA-ACCGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAACACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
6524700 TAAAA
1 TAAAA
6524705 GTCATATAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 37 0.88
41 5 0.12
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (41 bp):
TAAAACACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
Found at i:6524801 original size:17 final size:18
Alignment explanation
Indices: 6524774--6524807 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6524764 CTAAAATAGT
*
6524774 AAACTCCTAAACCCTAAC
1 AAACTCCTAAACACTAAC
6524792 AAAC-CCTAAACACTAA
1 AAACTCCTAAACACTAA
6524808 ATTATAACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (18 bp):
AAACTCCTAAACACTAAC
Found at i:6524831 original size:54 final size:55
Alignment explanation
Indices: 6524716--6524831 Score: 135
Period size: 54 Copynumber: 2.1 Consensus size: 55
6524706 TCATATAACT
* * * *
6524716 CCTAAAATCCTAAACCCCAAAAAAATCATAAACACTAATTTATAACCCCTAAAAT
1 CCTAAACTCCTAAACCCCAAAAAAACCATAAACACTAAATTATAACCCCTAAAAC
** * * * *
6524771 AGTAAACTCCTAAA-CCCTAACAAACCCTAAACACTAAATTATAACCTCTAAAAC
1 CCTAAACTCCTAAACCCCAAAAAAACCATAAACACTAAATTATAACCCCTAAAAC
6524825 CCTAAAC
1 CCTAAAC
6524832 GCCGCAATAG
Statistics
Matches: 49, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
54 38 0.78
55 11 0.22
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.21
Consensus pattern (55 bp):
CCTAAACTCCTAAACCCCAAAAAAACCATAAACACTAAATTATAACCCCTAAAAC
Found at i:6525345 original size:24 final size:24
Alignment explanation
Indices: 6525318--6525366 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
6525308 CGTATATTTG
6525318 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
6525342 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
6525366 T
1 T
6525367 GTTATTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TTAAAAGTTTATATAAAAATTAAT
Found at i:6538483 original size:15 final size:15
Alignment explanation
Indices: 6538463--6538493 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6538453 CTTTCGATCC
6538463 TTACGCTTCTTCTCT
1 TTACGCTTCTTCTCT
6538478 TTACGCTTCTTCTCT
1 TTACGCTTCTTCTCT
6538493 T
1 T
6538494 CATCTGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.32, G:0.06, T:0.55
Consensus pattern (15 bp):
TTACGCTTCTTCTCT
Found at i:6539795 original size:50 final size:50
Alignment explanation
Indices: 6539698--6539819 Score: 154
Period size: 50 Copynumber: 2.4 Consensus size: 50
6539688 GATGAGTGTG
* * * * *
6539698 GGACAATTTGCCACGTCGTGACGAGGAATCCCTTCACCAAGATGAGGCCA
1 GGACAGTTTGTCACGTCGTGACAAGGAATCCCATCACCAAGACGAGGCCA
* * *
6539748 GGACAGTTTGTCACGTCGTGACAAGGAATCCCATCATCACGACGAGGCCG
1 GGACAGTTTGTCACGTCGTGACAAGGAATCCCATCACCAAGACGAGGCCA
* *
6539798 GGATAGTTTGTCACATCGTGAC
1 GGACAGTTTGTCACGTCGTGAC
6539820 GAGAAACCCT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.20
Consensus pattern (50 bp):
GGACAGTTTGTCACGTCGTGACAAGGAATCCCATCACCAAGACGAGGCCA
Found at i:6540339 original size:19 final size:18
Alignment explanation
Indices: 6540306--6540341 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6540296 TTATATTAGT
*
6540306 TAAACATGTTTAATTAAA
1 TAAACATGATTAATTAAA
6540324 TAAACTATGATTAATTAA
1 TAAAC-ATGATTAATTAA
6540342 TTTTTAATTA
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:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (18 bp):
TAAACATGATTAATTAAA
Found at i:6542378 original size:8 final size:8
Alignment explanation
Indices: 6542365--6542392 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
6542355 GTATTTATTA
6542365 TATTTTAT
1 TATTTTAT
6542373 TATTTTAT
1 TATTTTAT
6542381 TATTTTAT
1 TATTTTAT
6542389 TATT
1 TATT
6542393 CTGAATTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTTTAT
Found at i:6548560 original size:31 final size:31
Alignment explanation
Indices: 6548522--6548589 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
6548512 TGAAATGTTA
6548522 TTAGGTTGTTCTTAGAACTAGGCATAAAATG
1 TTAGGTTGTTCTTAGAACTAGGCATAAAATG
6548553 TTAGGTTGTTCTTAGAACTAGGCATAAAATG
1 TTAGGTTGTTCTTAGAACTAGGCATAAAATG
6548584 TTAGGT
1 TTAGGT
6548590 GTTAATTCAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.37
Consensus pattern (31 bp):
TTAGGTTGTTCTTAGAACTAGGCATAAAATG
Found at i:6551114 original size:28 final size:28
Alignment explanation
Indices: 6551055--6551115 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
6551045 TTGGTGTCGA
* * *
6551055 TTTTGTATCATGTTTAAATTATCAGATC
1 TTTTGTATCATGTTTAAAGTATAAAATC
*
6551083 TTTTGTATCATGTTTAAAAGTATAAAATT
1 TTTTGTATCATGTTT-AAAGTATAAAATC
6551112 TTTT
1 TTTT
6551116 TTTGATTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (28 bp):
TTTTGTATCATGTTTAAAGTATAAAATC
Found at i:6553837 original size:13 final size:13
Alignment explanation
Indices: 6553821--6553854 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
6553811 ATTATTAATG
*
6553821 TAATTTATTATTT
1 TAATTAATTATTT
*
6553834 TAATAAATTATTT
1 TAATTAATTATTT
6553847 TAATTAAT
1 TAATTAAT
6553855 AAATTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAATTAATTATTT
Found at i:6553872 original size:16 final size:16
Alignment explanation
Indices: 6553843--6553884 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
6553833 TTAATAAATT
*
6553843 ATTTTAATTAAT-A-A
1 ATTTTAAATAATAATA
6553857 ATTTTAAA-AATAATA
1 ATTTTAAATAATAATA
6553872 ATTTTAAATAATA
1 ATTTTAAATAATA
6553885 TGTTTCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.12
14 8 0.33
15 9 0.38
16 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTTAAATAATAATA
Found at i:6553929 original size:15 final size:15
Alignment explanation
Indices: 6553909--6553960 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
6553899 ATTCAATTTC
6553909 AATATTTTAATAATA
1 AATATTTTAATAATA
*
6553924 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
6553943 AATATATTAATAATA
1 AATATTTTAATAATA
6553958 AAT
1 AAT
6553961 TGTTATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 13 0.43
16 2 0.07
17 4 0.13
18 1 0.03
19 10 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:6568189 original size:12 final size:12
Alignment explanation
Indices: 6568174--6568230 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
6568164 TCCCTCCTCT
*
6568174 CTTTCCTCTACC
1 CTTTCCTCCACC
* * *
6568186 CTTTCCACCGCT
1 CTTTCCTCCACC
*
6568198 CTTTCCTCCGCC
1 CTTTCCTCCACC
*
6568210 CTTTCCTCTACC
1 CTTTCCTCCACC
*
6568222 CCTTCCTCC
1 CTTTCCTCC
6568231 CTCCGTTCAC
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.05, C:0.54, G:0.04, T:0.37
Consensus pattern (12 bp):
CTTTCCTCCACC
Found at i:6571019 original size:25 final size:25
Alignment explanation
Indices: 6570985--6571032 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
6570975 TGTCAGCTAT
6570985 AGTTTAGGTTAGTAGCTTATGAACA
1 AGTTTAGGTTAGTAGCTTATGAACA
6571010 AGTTTAGGTTAGTAGCTTATGAA
1 AGTTTAGGTTAGTAGCTTATGAA
6571033 GATGATATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (25 bp):
AGTTTAGGTTAGTAGCTTATGAACA
Found at i:6572018 original size:104 final size:104
Alignment explanation
Indices: 6571909--6572102 Score: 372
Period size: 104 Copynumber: 1.9 Consensus size: 104
6571899 TCATTAGAAA
6571909 AAAAAAACAAAAATGTAAATGTTTCATAT-TGATGAAGAAGGTTATATAGCACCAAATTGTCCTA
1 AAAAAAACAAAAATGTAAATGTTTCATATATGATGAAGAAGGTTATATAGCACCAAATTGTCCTA
6571973 ATAAGGGAAAAAGTGCAAGAAAAATTTCTAAAAAAATCT
66 ATAAGGGAAAAAGTGCAAGAAAAATTTCTAAAAAAATCT
*
6572012 AAAAAAATAAAAATGTAAATGTTTCATATATGATGAAGAAGGTTATATAGCACCAAATTGTCCTA
1 AAAAAAACAAAAATGTAAATGTTTCATATATGATGAAGAAGGTTATATAGCACCAAATTGTCCTA
6572077 ATAAGGGAAAAAGTGCAAGAAAAATT
66 ATAAGGGAAAAAGTGCAAGAAAAATT
6572103 ATTAAAACAC
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
103 28 0.31
104 61 0.69
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (104 bp):
AAAAAAACAAAAATGTAAATGTTTCATATATGATGAAGAAGGTTATATAGCACCAAATTGTCCTA
ATAAGGGAAAAAGTGCAAGAAAAATTTCTAAAAAAATCT
Found at i:6572733 original size:15 final size:15
Alignment explanation
Indices: 6572713--6572741 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6572703 AGCCAAATTG
6572713 CTTTATATCTATTAA
1 CTTTATATCTATTAA
6572728 CTTTATATCTATTA
1 CTTTATATCTATTA
6572742 CAGATATTTT
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:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (15 bp):
CTTTATATCTATTAA
Found at i:6573974 original size:15 final size:15
Alignment explanation
Indices: 6573954--6573983 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6573944 ACAAATTAAG
*
6573954 GAATTATTAGAAAAA
1 GAATTAATAGAAAAA
6573969 GAATTAATAGAAAAA
1 GAATTAATAGAAAAA
6573984 ACTAATAGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (15 bp):
GAATTAATAGAAAAA
Found at i:6577784 original size:3 final size:3
Alignment explanation
Indices: 6577776--6577882 Score: 65
Period size: 3 Copynumber: 33.7 Consensus size: 3
6577766 AGAAAATGAC
* * **
6577776 AAT AAT AAT AAT AAT AAT ACT AAT AAC AAT AAT AA- AGAT AGC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* * *
6577821 AAT AAAT AA- AAA AAGT AAT AAAT AAGT ATGT GAAT AAAT AAC AAT AAT
1 AAT -AAT AAT AAT AA-T AAT -AAT AA-T A-AT -AAT -AAT AAT AAT AAT
6577869 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
6577883 AAGAAATAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
2 3 0.04
3 61 0.75
4 16 0.20
5 1 0.01
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:6577841 original size:16 final size:16
Alignment explanation
Indices: 6577820--6577898 Score: 54
Period size: 16 Copynumber: 4.8 Consensus size: 16
6577810 AAGATAGCAA
6577820 TAATAAATAAAAAAAG
1 TAATAAATAAAAAAAG
** *
6577836 TAATAAAT-AAGTATG
1 TAATAAATAAAAAAAG
*
6577851 TGAATAAATAACAATAA-
1 T-AATAAATAA-AAAAAG
*
6577868 TAATAATAATAATAAAAG
1 TAAT-A-AATAAAAAAAG
*
6577886 AAATAAATAAAAA
1 TAATAAATAAAAA
6577899 TATAAACAAG
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
15 5 0.10
16 25 0.52
17 7 0.15
18 11 0.23
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.24
Consensus pattern (16 bp):
TAATAAATAAAAAAAG
Found at i:6579451 original size:44 final size:44
Alignment explanation
Indices: 6579351--6579980 Score: 334
Period size: 44 Copynumber: 13.7 Consensus size: 44
6579341 CTTCGATCCA
* * * * * *
6579351 CTCCAATGCAACCTCAGGGAAATAAAACTTGTAG-CTTCAATTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGT-GTCTTCAATCTG
* ** * * *
6579395 TTCCGTTGCAACTCCAGGGAGGTGAGATTTGTGTCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTGTCTTCAATCTG
* * * * *
6579439 CTCCACTACAACTTCAGGGAGATAAGATTTGTTTAATTTTAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTGT--CTTCAATCTG
* * * * *
6579485 CACCACTACAACTTCAGGGAGATAAGGTTTGTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTGTCTTCAATCTG
* *
6579529 CTCCACTGTAACTTC-GGAGAGATAGGATTTGTAGGCTGTCTTCAATCTG
1 CTCCACTGCAACTTCAGG-GAGATAAGA-TT-T--G-TGTCTTCAATCTG
* *
6579578 CTCCACTGCAACTTCAGAGAGATAAGATTTGTAGCCTATTTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGT-G----TCTTCAATCTG
* *
6579627 CTCCACTGCAACTTCAGGGAGATAAGATTTGTGTGATTTTAA-CTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTGT--CTTCAATC-TG
* * * * **
6579673 CTCCATTGCAACTTTAGGGAGATATGATTTATAACTCGTAGCTTTGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-TT-T--GT-GT--CTTCAATCTG
* * * * ** * * *
6579724 TTCCACTACAACTTCAGCGAAATAAGATCCGCTATCTTCAGTTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TGTCTTCAATCTG
* * ** * *
6579769 CTCCACTGCAACTTGAGGGAG-TAAAGACTTGTAACTTTAACCTG
1 CTCCACTGCAACTTCAGGGAGAT-AAGATTTGTGTCTTCAATCTG
* * * *
6579813 CTCCAATGCATCTTCAGGGAGATAAGGTTTGTGACTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTGTCTTCAATCTG
* ** * * *
6579857 CTCCATTGCAACTTCAAAGAGATAAGATTCGCCATGATAACTTCGATATG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG---TG-T--CTTCAATCTG
* * * *
6579907 CTTCACTGCAACTTTCAGGGAGATAAAATTTGTGGCTTCAATATG
1 CTCCACTGCAAC-TTCAGGGAGATAAGATTTGTGTCTTCAATCTG
* *
6579952 CTCCACTACAAC-TCTAGGGAGGTAAGATT
1 CTCCACTGCAACTTC-AGGGAGATAAGATT
6579981 CGCCATAATG
Statistics
Matches: 445, Mismatches: 106, Indels: 70
0.72 0.17 0.11
Matches are distributed among these distances:
43 5 0.01
44 166 0.37
45 52 0.12
46 69 0.16
47 6 0.01
48 8 0.02
49 74 0.17
50 21 0.05
51 43 0.10
52 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTGTGTCTTCAATCTG
Found at i:6584040 original size:33 final size:32
Alignment explanation
Indices: 6584003--6584115 Score: 129
Period size: 32 Copynumber: 3.5 Consensus size: 32
6583993 TAGAGGAATA
*
6584003 TTGTTATCATTTAACAAAAATTAAAGTTGATAT
1 TTGTTATCATTTCAC-AAAATTAAAGTTGATAT
* *
6584036 TTGTTATCACTTCACAAAATTGAAGTTG-TAAT
1 TTGTTATCATTTCACAAAATTAAAGTTGAT-AT
* * *
6584068 TTGTTACCATTTCACAAAATGAAAGCTGATAT
1 TTGTTATCATTTCACAAAATTAAAGTTGATAT
* *
6584100 TTATCATCATTTCACA
1 TTGTTATCATTTCACA
6584116 TAACCACACG
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
31 1 0.01
32 52 0.78
33 14 0.21
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (32 bp):
TTGTTATCATTTCACAAAATTAAAGTTGATAT
Found at i:6585369 original size:23 final size:24
Alignment explanation
Indices: 6585339--6585388 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
6585329 TTAAATAAAA
*
6585339 TAAGAGATTGCTTGCAAGTCAA-T
1 TAAGAGATTGCTTACAAGTCAAGT
6585362 TAAGAGATTGCTTACAAGTCAAGT
1 TAAGAGATTGCTTACAAGTCAAGT
6585386 TAA
1 TAA
6585389 ACAAAATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (24 bp):
TAAGAGATTGCTTACAAGTCAAGT
Found at i:6595426 original size:10 final size:10
Alignment explanation
Indices: 6595402--6595494 Score: 65
Period size: 10 Copynumber: 9.7 Consensus size: 10
6595392 AGCATTTAAT
6595402 TAATTTTTTA
1 TAATTTTTTA
6595412 T--TTTTTTA
1 TAATTTTTTA
*
6595420 TAATTTTTAA
1 TAATTTTTTA
*
6595430 TAATTTTTAA
1 TAATTTTTTA
6595440 TAA--TTTTA
1 TAATTTTTTA
*
6595448 -ATTTTTTTA
1 TAATTTTTTA
*
6595457 AAATAATTTTTA
1 TAAT--TTTTTA
6595469 TAATTTTTCT-
1 TAATTTTT-TA
*
6595479 GAATTTTTTA
1 TAATTTTTTA
6595489 -AATTTT
1 TAATTTT
6595495 AAAAAATTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
7 1 0.01
8 12 0.18
9 12 0.18
10 33 0.49
11 1 0.01
12 9 0.13
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:6599227 original size:15 final size:14
Alignment explanation
Indices: 6599193--6599223 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6599183 AAAATATTCT
*
6599193 AAATATTTTTAATA
1 AAATATTTTTAAAA
6599207 AAATATTTTTAAAA
1 AAATATTTTTAAAA
6599221 AAA
1 AAA
6599224 ATATATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATATTTTTAAAA
Found at i:6605800 original size:6 final size:6
Alignment explanation
Indices: 6605789--6605815 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6605779 CACAAAAAAA
6605789 AATTAT AATTAT AATTAT AATTAT AAT
1 AATTAT AATTAT AATTAT AATTAT AAT
6605816 AAAAACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:6606029 original size:9 final size:9
Alignment explanation
Indices: 6606017--6606068 Score: 68
Period size: 9 Copynumber: 5.7 Consensus size: 9
6606007 TATTAAAAAC
6606017 GAGAGAGTT
1 GAGAGAGTT
*
6606026 GAGAGACTT
1 GAGAGAGTT
*
6606035 GAGAGGGTTT
1 GAGAGAG-TT
*
6606045 GAGAGAATT
1 GAGAGAGTT
6606054 GAGAGAGTT
1 GAGAGAGTT
6606063 GAGAGA
1 GAGAGA
6606069 AGGATGTGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
9 29 0.81
10 7 0.19
ACGTcount: A:0.35, C:0.02, G:0.42, T:0.21
Consensus pattern (9 bp):
GAGAGAGTT
Found at i:6606048 original size:19 final size:18
Alignment explanation
Indices: 6606017--6606069 Score: 79
Period size: 19 Copynumber: 2.9 Consensus size: 18
6606007 TATTAAAAAC
*
6606017 GAGAGAGTTGAGAGACTT
1 GAGAGAGTTGAGAGAATT
*
6606035 GAGAGGGTTTGAGAGAATT
1 GAGAGAG-TTGAGAGAATT
6606054 GAGAGAGTTGAGAGAA
1 GAGAGAGTTGAGAGAA
6606070 GGATGTGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.36, C:0.02, G:0.42, T:0.21
Consensus pattern (18 bp):
GAGAGAGTTGAGAGAATT
Found at i:6607481 original size:26 final size:23
Alignment explanation
Indices: 6607432--6607492 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
6607422 TGATTTAAAC
*
6607432 AAATACTCATATTTATATAATTA
1 AAATATTCATATTTATATAATTA
*
6607455 AAATATTCATATTTTATACTATGTTA
1 AAATATTCATA-TTTATA-TA-ATTA
6607481 AAATATGTCATA
1 AAATAT-TCATA
6607493 AGTCTTTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 10 0.31
24 6 0.19
25 2 0.06
26 9 0.28
27 5 0.16
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (23 bp):
AAATATTCATATTTATATAATTA
Found at i:6607878 original size:11 final size:11
Alignment explanation
Indices: 6607862--6607886 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6607852 ACTATAAAAC
6607862 ATTTATTAATA
1 ATTTATTAATA
6607873 ATTTATTAATA
1 ATTTATTAATA
6607884 ATT
1 ATT
6607887 ATAATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTATTAATA
Found at i:6608024 original size:18 final size:18
Alignment explanation
Indices: 6607991--6608029 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6607981 ATTTATTTAT
* *
6607991 TAAAATAAAATTTTAATA
1 TAAAATAAAATATTAAAA
*
6608009 TAAAATAATATATTAAAA
1 TAAAATAAAATATTAAAA
6608027 TAA
1 TAA
6608030 TATTTTATTA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAATAAAATATTAAAA
Found at i:6612596 original size:18 final size:18
Alignment explanation
Indices: 6612562--6612616 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
6612552 TTTTTTAAAA
6612562 TATAAAT-TTTGGAATTT
1 TATAAATATTTGGAATTT
*
6612579 TATAAATATTTTGAATTT
1 TATAAATATTTGGAATTT
*
6612597 TAAAAATTATTTGGAATTT
1 TATAAA-TATTTGGAATTT
6612616 T
1 T
6612617 TTTTTGTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 7 0.21
18 14 0.42
19 12 0.36
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TATAAATATTTGGAATTT
Found at i:6612728 original size:10 final size:10
Alignment explanation
Indices: 6612713--6612740 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
6612703 TGAGTTACTC
6612713 GAATTATTTG
1 GAATTATTTG
6612723 GAATTATTTG
1 GAATTATTTG
6612733 GAATTATT
1 GAATTATT
6612741 CGAGTTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (10 bp):
GAATTATTTG
Found at i:6616489 original size:17 final size:18
Alignment explanation
Indices: 6616467--6616508 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
6616457 GGATTTGACG
* *
6616467 TTTGACAAAC-TTTATGT
1 TTTGACAAACATTAAGGT
*
6616484 TTTGACGAACATTAAGGT
1 TTTGACAAACATTAAGGT
6616502 TTTGACA
1 TTTGACA
6616509 GACTCTTCTG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (18 bp):
TTTGACAAACATTAAGGT
Found at i:6622904 original size:28 final size:28
Alignment explanation
Indices: 6622872--6622943 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
6622862 TCAGTTTGCG
* * *
6622872 ACAAAGGCTATTCTTTTTAGAGTTCACC
1 ACAAAGGTTATTCTTTTCAAAGTTCACC
**
6622900 ACAAAGGTTATTCTTTTCAAAGTTTGCC
1 ACAAAGGTTATTCTTTTCAAAGTTCACC
*
6622928 ACAATGGTTATTCTTT
1 ACAAAGGTTATTCTTT
6622944 ATTGTCGTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (28 bp):
ACAAAGGTTATTCTTTTCAAAGTTCACC
Found at i:6625343 original size:20 final size:20
Alignment explanation
Indices: 6625318--6625365 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
6625308 TAAATTCTAA
* *
6625318 AAAGATAAATACATTTAATT
1 AAAGATAAATAAATATAATT
6625338 AAAGATAAATAAATATAATT
1 AAAGATAAATAAATATAATT
6625358 AAA-ATAAA
1 AAAGATAAA
6625366 ATCCTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (20 bp):
AAAGATAAATAAATATAATT
Found at i:6625409 original size:15 final size:15
Alignment explanation
Indices: 6625389--6625418 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6625379 ATAATCCTAA
*
6625389 TAATTATCTTAATAT
1 TAATTATCCTAATAT
6625404 TAATTATCCTAATAT
1 TAATTATCCTAATAT
6625419 AAATAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:6625429 original size:5 final size:5
Alignment explanation
Indices: 6625414--6625443 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
6625404 TAATTATCCT
6625414 AATATA AATAA AATAA AATAA AATAA AATA
1 AATA-A AATAA AATAA AATAA AATAA AATA
6625444 GAGTCTTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AATAA
Found at i:6628941 original size:28 final size:28
Alignment explanation
Indices: 6628896--6628996 Score: 125
Period size: 28 Copynumber: 3.6 Consensus size: 28
6628886 TAAGAATTTT
*
6628896 CCACAAAGGC-ATCCTTTTCAGAGTTCG
1 CCACAAAGGCTATTCTTTTCAGAGTTCG
*
6628923 TCACACAA-GCTATTCTTTTCAGAGTTCG
1 CCACA-AAGGCTATTCTTTTCAGAGTTCG
* *
6628951 CCACAAAGGCTATTCTTTTCAGGGTTCC
1 CCACAAAGGCTATTCTTTTCAGAGTTCG
* *
6628979 CCACAAGGGCCATTCTTT
1 CCACAAAGGCTATTCTTT
6628997 ACTGTTGGGT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 8 0.12
28 56 0.88
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (28 bp):
CCACAAAGGCTATTCTTTTCAGAGTTCG
Found at i:6635388 original size:16 final size:17
Alignment explanation
Indices: 6635350--6635392 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
6635340 GGTTTAAAAT
* *
6635350 TATTCTCAATAATTTAA
1 TATTTTCAATAATATAA
6635367 TA-TTTCAA-AATATAA
1 TATTTTCAATAATATAA
6635382 TATTTTCAATA
1 TATTTTCAATA
6635393 TGGATTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.36
16 11 0.50
17 3 0.14
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTTTCAATAATATAA
Found at i:6638249 original size:26 final size:24
Alignment explanation
Indices: 6638174--6638255 Score: 94
Period size: 24 Copynumber: 3.3 Consensus size: 24
6638164 TCTCTCTAAA
*
6638174 AAAACTAACCCTAGCCCATGGCCC
1 AAAACTAACCCTAACCCATGGCCC
* **
6638198 AAAA-TACAACAAAACCCATGGCCC
1 AAAACTA-ACCCTAACCCATGGCCC
6638222 AAAACTAACCCTAACCCAAATGGCCC
1 AAAACTAACCCTAACCC--ATGGCCC
6638248 AAAACTAA
1 AAAACTAA
6638256 ACCAATTTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
23 2 0.04
24 28 0.60
25 2 0.04
26 15 0.32
ACGTcount: A:0.45, C:0.35, G:0.09, T:0.11
Consensus pattern (24 bp):
AAAACTAACCCTAACCCATGGCCC
Found at i:6641038 original size:3 final size:3
Alignment explanation
Indices: 6641032--6641080 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
6641022 TTGTTCCCTT
6641032 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6641080 T
1 T
6641081 ATACTTTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6651629 original size:10 final size:10
Alignment explanation
Indices: 6651616--6651641 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6651606 TTTGGACTTT
6651616 TTTTTGTTTA
1 TTTTTGTTTA
6651626 TTTTTGTTTA
1 TTTTTGTTTA
6651636 TTTTTG
1 TTTTTG
6651642 GGTTTTGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.12, T:0.81
Consensus pattern (10 bp):
TTTTTGTTTA
Found at i:6658439 original size:13 final size:13
Alignment explanation
Indices: 6658418--6658478 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
6658408 TTGGCAATGT
6658418 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
*
6658431 TTTTAAAAAGTGC
1 TTTTGAAAAGTGC
** *
6658444 CGTGGAAAAGTGC
1 TTTTGAAAAGTGC
*
6658457 TTTTGAGAAGTGC
1 TTTTGAAAAGTGC
6658470 TTTTGAAAA
1 TTTTGAAAA
6658479 TTTTGATTTA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.34
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:6661060 original size:19 final size:19
Alignment explanation
Indices: 6661036--6661075 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6661026 TCAAATTTAA
*
6661036 TTTTAATATTATTGAGTTT
1 TTTTAATATTATTGACTTT
* *
6661055 TTTTAATTTTTTTGACTTT
1 TTTTAATATTATTGACTTT
6661074 TT
1 TT
6661076 ATGAGTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (19 bp):
TTTTAATATTATTGACTTT
Found at i:6669730 original size:2 final size:2
Alignment explanation
Indices: 6669723--6669749 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6669713 GCGAATTTTA
6669723 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
6669750 TTTTGTTGAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6670290 original size:30 final size:30
Alignment explanation
Indices: 6670254--6670312 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
6670244 TATGCCATAG
6670254 TTGAATGAATAATTTATTGTATAAAGATAT
1 TTGAATGAATAATTTATTGTATAAAGATAT
*
6670284 TTGAATGAATAATTTGTTGTATAAAGATA
1 TTGAATGAATAATTTATTGTATAAAGATA
6670313 CTTTTATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (30 bp):
TTGAATGAATAATTTATTGTATAAAGATAT
Done.