Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 18 of 105
Found at i:3789042 original size:14 final size:16
Alignment explanation
Indices: 3789012--3789044 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
3789002 TTTTTAAAAA
3789012 ATTATAATTATTTTAT
1 ATTATAATTATTTTAT
3789028 ATTATAA-TA-TTTAT
1 ATTATAATTATTTTAT
3789042 ATT
1 ATT
3789045 TTTAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 2 0.12
16 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATAATTATTTTAT
Found at i:3792696 original size:23 final size:23
Alignment explanation
Indices: 3792646--3792692 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
3792636 AAAAATTTAG
* *
3792646 ATAAAAATTTTTAGTTAAAATTC
1 ATAAAAATTTTTAGTTAAAAATA
*
3792669 ATAAAATTTTTTA-TTAAAAATA
1 ATAAAAATTTTTAGTTAAAAATA
3792691 AT
1 AT
3792693 TAAATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAAAAATTTTTAGTTAAAAATA
Found at i:3792697 original size:22 final size:23
Alignment explanation
Indices: 3792646--3792698 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
3792636 AAAAATTTAG
* * *
3792646 ATAAAAATTTTTAGTTAAAATTC
1 ATAAAATTTTTTAGTTAAAAATA
3792669 ATAAAATTTTTTA-TTAAAAATA
1 ATAAAATTTTTTAGTTAAAAATA
*
3792691 ATTAAATT
1 ATAAAATT
3792699 AAAAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAAAATTTTTTAGTTAAAAATA
Found at i:3793126 original size:3 final size:3
Alignment explanation
Indices: 3793118--3793160 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3793108 TTGAATTTTT
3793118 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3793161 TAAAGGGTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3808253 original size:22 final size:22
Alignment explanation
Indices: 3808222--3808267 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3808212 TATAAAATCC
3808222 AAATTGAAGAAACTATGGAAAA
1 AAATTGAAGAAACTATGGAAAA
* *
3808244 AAATTTAAGAAATTATGGAAAA
1 AAATTGAAGAAACTATGGAAAA
3808266 AA
1 AA
3808268 TTAAAATAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.61, C:0.02, G:0.15, T:0.22
Consensus pattern (22 bp):
AAATTGAAGAAACTATGGAAAA
Found at i:3808611 original size:2 final size:2
Alignment explanation
Indices: 3808599--3808632 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3808589 TTCCTTTCTT
*
3808599 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3808633 AAACCAGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3809611 original size:24 final size:24
Alignment explanation
Indices: 3809575--3809631 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
3809565 GGGAAATCCT
*
3809575 CAAATTCTGTACCAGTAGTTGACA
1 CAAATTCTATACCAGTAGTTGACA
3809599 CAAATTCTATACCAGTAGTTGACA
1 CAAATTCTATACCAGTAGTTGACA
3809623 CAAATTCTA
1 CAAATTCTA
3809632 AAGCTGCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (24 bp):
CAAATTCTATACCAGTAGTTGACA
Found at i:3815052 original size:20 final size:20
Alignment explanation
Indices: 3815027--3815068 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3815017 ACAGAAATGA
3815027 AAACAATAATAAAAGGTGCT
1 AAACAATAATAAAAGGTGCT
* *
3815047 AAACAATGATACAAGGTGCT
1 AAACAATAATAAAAGGTGCT
3815067 AA
1 AA
3815069 CCTAAGTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.19
Consensus pattern (20 bp):
AAACAATAATAAAAGGTGCT
Found at i:3825078 original size:36 final size:35
Alignment explanation
Indices: 3825038--3825109 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 35
3825028 ATTCTTGTAT
3825038 TTTATAAAAATTTAAAATTTA-ATTTTTATATTATAA
1 TTTATAAAAATTTAAAATTTACATTTTT-TATT-TAA
* **
3825074 TTTATACAAATTTAATTTTTACATTTTTTATTTAA
1 TTTATAAAAATTTAAAATTTACATTTTTTATTTAA
3825109 T
1 T
3825110 AATTTTAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 4 0.12
36 22 0.69
37 6 0.19
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (35 bp):
TTTATAAAAATTTAAAATTTACATTTTTTATTTAA
Found at i:3825417 original size:13 final size:12
Alignment explanation
Indices: 3825391--3825415 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3825381 TCCTTTAATA
3825391 TAAAAATATTTT
1 TAAAAATATTTT
3825403 TAAAAATATTTT
1 TAAAAATATTTT
3825415 T
1 T
3825416 TATATGTAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAAATATTTT
Found at i:3826353 original size:26 final size:26
Alignment explanation
Indices: 3826315--3826364 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
3826305 TAAAATTTTC
3826315 AATATTGTAACAGAATATTATGACCA
1 AATATTGTAACAGAATATTATGACCA
*
3826341 AATATTGTGACAGAATATTATGAC
1 AATATTGTAACAGAATATTATGAC
3826365 AATTTTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (26 bp):
AATATTGTAACAGAATATTATGACCA
Found at i:3826364 original size:13 final size:13
Alignment explanation
Indices: 3826324--3826365 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
3826314 CAATATTGTA
3826324 ACAGAATATTATG
1 ACAGAATATTATG
*
3826337 ACCA-AATATTGTG
1 A-CAGAATATTATG
3826350 ACAGAATATTATG
1 ACAGAATATTATG
3826363 ACA
1 ACA
3826366 ATTTTAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 2 0.08
13 21 0.84
14 2 0.08
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (13 bp):
ACAGAATATTATG
Found at i:3827079 original size:30 final size:29
Alignment explanation
Indices: 3827017--3827116 Score: 80
Period size: 30 Copynumber: 3.4 Consensus size: 29
3827007 TTATTATACA
* * *
3827017 AAATAATTCTTAAAC-TTTAATTT-CACCC
1 AAATAAGTCTTTAACATTTAATTTGTA-CC
**
3827045 AAATAAGTCTTTAATTTTTAATTTGTATCC
1 AAATAAGTCTTTAACATTTAATTTGTA-CC
*
3827075 AAATAAG-CTATTAACATTTATTTTGTACC
1 AAATAAGTCT-TTAACATTTAATTTGTACC
3827104 TAAATAAGCTCTT
1 -AAATAAG-TCTT
3827117 AATATAAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
28 12 0.21
29 12 0.21
30 31 0.53
31 1 0.02
32 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (29 bp):
AAATAAGTCTTTAACATTTAATTTGTACC
Found at i:3829940 original size:15 final size:16
Alignment explanation
Indices: 3829909--3829941 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3829899 AAATAAAAAT
*
3829909 ATATATATGTTATAAA
1 ATATATATGTGATAAA
3829925 ATATATA-GTGATAAA
1 ATATATATGTGATAAA
3829940 AT
1 AT
3829942 TGTATTGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (16 bp):
ATATATATGTGATAAA
Found at i:3841532 original size:6 final size:6
Alignment explanation
Indices: 3841517--3841564 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
3841507 ATGTGTGAAC
* * *
3841517 TTTTTT TTTTTG TTTTTG TTTTTG ATTTGTTT TTTTTT TTTTTG TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG -TTT-TTG TTTTTG TTTTTG TTTT
3841565 GTTGAAAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 29 0.78
7 6 0.16
8 2 0.05
ACGTcount: A:0.02, C:0.00, G:0.10, T:0.88
Consensus pattern (6 bp):
TTTTTG
Found at i:3843187 original size:17 final size:18
Alignment explanation
Indices: 3843165--3843199 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
3843155 GAGGACCGGT
3843165 CTGCCGTCGTCG-TCGTC
1 CTGCCGTCGTCGTTCGTC
3843182 CTGCCGTCGTCGTTCGTC
1 CTGCCGTCGTCGTTCGTC
3843200 GGTCATCGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.00, C:0.40, G:0.29, T:0.31
Consensus pattern (18 bp):
CTGCCGTCGTCGTTCGTC
Found at i:3843772 original size:12 final size:12
Alignment explanation
Indices: 3843750--3843802 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
3843740 AAGGTAGAAG
3843750 AAAAAGA-GAAA
1 AAAAAGAGGAAA
3843761 AAAAAGAGGAAAGA
1 AAAAAGAGG-AA-A
*
3843775 AAAAAGAAAGAAA
1 AAAAAG-AGGAAA
*
3843788 AAAAATAGGAAA
1 AAAAAGAGGAAA
3843800 AAA
1 AAA
3843803 TTTAAATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 7 0.20
12 9 0.26
13 8 0.23
14 9 0.26
15 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (12 bp):
AAAAAGAGGAAA
Found at i:3843790 original size:11 final size:12
Alignment explanation
Indices: 3843747--3843789 Score: 63
Period size: 11 Copynumber: 3.7 Consensus size: 12
3843737 CATAAGGTAG
3843747 AAGAAAAAGAGA
1 AAGAAAAAGAGA
3843759 AA-AAAAAGAGGA
1 AAGAAAAAGA-GA
3843771 AAGAAAAA-AGA
1 AAGAAAAAGAGA
3843782 AAGAAAAA
1 AAGAAAAA
3843790 AAATAGGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 17 0.59
12 7 0.24
13 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAGA
Found at i:3846337 original size:58 final size:57
Alignment explanation
Indices: 3846247--3846519 Score: 316
Period size: 58 Copynumber: 4.7 Consensus size: 57
3846237 CTTTTGTACA
* **
3846247 AGAAAAATTGATACTTTCAACTTCTCTTCAAAATATTTTTTAGAAAACTTTAATTTCG
1 AGAAAAATTGATACTTTCAACTTTTCCCCAAAATATTTTTT-GAAAACTTTAATTTCG
*
3846305 AGAAAAATTGATACTTTTC-ACTTTTCCCCAAAAATATTTTTTGGAAACTTTAATTTCG
1 AGAAAAATTGATAC-TTTCAACTTTTCCCC-AAAATATTTTTTGAAAACTTTAATTTCG
* * * * ** * * **
3846363 AGGAAAGTTGATACTTTCAACTTTTTCTCAAAACCTTTTTAGAAAA-TTTATTTTTA
1 AGAAAAATTGATACTTTCAACTTTTCCCCAAAATATTTTTTGAAAACTTTAATTTCG
* *
3846419 AGAAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTGAAAACTTTAATTTCG
1 AGAAAAATTGATACTTTCAAC-TTTTCCCCAAAATATTTTTTGAAAACTTTAATTTCG
* *
3846477 AGAAAAATTGATACTTTCCACTTTTCCCAAAAAATATATTTTT
1 AGAAAAATTGATACTTTCAACTTTTCCC-CAAAATAT-TTTTT
3846520 TTAATTTTAT
Statistics
Matches: 181, Mismatches: 27, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
56 26 0.14
57 43 0.24
58 91 0.50
59 21 0.12
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (57 bp):
AGAAAAATTGATACTTTCAACTTTTCCCCAAAATATTTTTTGAAAACTTTAATTTCG
Found at i:3846455 original size:114 final size:117
Alignment explanation
Indices: 3846247--3846501 Score: 358
Period size: 114 Copynumber: 2.2 Consensus size: 117
3846237 CTTTTGTACA
* * *
3846247 AGAAAAATTGATACTTTCAAC-TTCTCTTCAAAATATTTTTTAGAAAACTTTAATTTCGAGAAAA
1 AGAAAAATTGATACTTTCAACTTTTTCTTCAAAATACTTTTTAGAAAACTTTAATTTCAAGAAAA
*
3846311 ATTGATACTTTTCACTTTTCCCCAAAAATATTTTTTGGAAACTTTAATTTCG
66 ATTGATACTTTTCACTTTTCCCCAAAAATATTTTTTGAAAACTTTAATTTCG
* * * * *
3846363 AGGAAAGTTGATACTTTCAACTTTTTC-TCAAAA-CCTTTTTAGAAAA-TTTATTTTTAAGAAAA
1 AGAAAAATTGATACTTTCAACTTTTTCTTCAAAATACTTTTTAGAAAACTTTAATTTCAAGAAAA
**
3846425 ATTGATAC-TTTCAACTTTTTTCCAAAAATATTTTTTGAAAACTTTAATTTCG
66 ATTGATACTTTTC-ACTTTTCCCCAAAAATATTTTTTGAAAACTTTAATTTCG
*
3846477 AGAAAAATTGATACTTTCCACTTTT
1 AGAAAAATTGATACTTTCAACTTTT
3846502 CCCAAAAAAT
Statistics
Matches: 123, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
113 4 0.03
114 79 0.64
115 11 0.09
116 25 0.20
117 4 0.03
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (117 bp):
AGAAAAATTGATACTTTCAACTTTTTCTTCAAAATACTTTTTAGAAAACTTTAATTTCAAGAAAA
ATTGATACTTTTCACTTTTCCCCAAAAATATTTTTTGAAAACTTTAATTTCG
Found at i:3846564 original size:6 final size:5
Alignment explanation
Indices: 3846536--3846618 Score: 64
Period size: 5 Copynumber: 15.8 Consensus size: 5
3846526 TTATTTAAAG
*
3846536 AAAAT AAAAT --AAT AAAAT AAAAAT GAAAAT AAAAT AAAGA- AAAGT
1 AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAAT AAA-AT AAAAT
*
3846581 TAAAT AAAAAT AAAAAT AAAAT AAAGAT AAAAAT AAAA
1 AAAAT -AAAAT -AAAAT AAAAT AAA-AT -AAAAT AAAA
3846619 GAATATTAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
3 3 0.05
5 34 0.52
6 25 0.38
7 3 0.05
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:3846566 original size:17 final size:17
Alignment explanation
Indices: 3846536--3846618 Score: 89
Period size: 17 Copynumber: 4.9 Consensus size: 17
3846526 TTATTTAAAG
3846536 AAAATAAAATAATAAAATA
1 AAAAT-AAA-AATAAAATA
*
3846555 AAAATGAAAATAAAAT-
1 AAAATAAAAATAAAATA
* * *
3846571 -AAAGAAAAGTTAAATA
1 AAAATAAAAATAAAATA
3846587 AAAATAAAAATAAAATA
1 AAAATAAAAATAAAATA
*
3846604 AAGATAAAAATAAAA
1 AAAATAAAAATAAAA
3846619 GAATATTAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
15 11 0.21
17 35 0.66
18 2 0.04
19 5 0.09
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAATAAAAATAAAATA
Found at i:3846664 original size:17 final size:17
Alignment explanation
Indices: 3846583--3846673 Score: 63
Period size: 15 Copynumber: 5.7 Consensus size: 17
3846573 AGAAAAGTTA
3846583 AATAA-AAATAA-AAAT
1 AATAATAAATAATAAAT
*
3846598 AA-AATAAA-GATAAA-
1 AATAATAAATAATAAAT
* * *
3846612 AATAAAAGAATATTAAAC
1 AATAATA-AATAATAAAT
*
3846630 AATTATAATATAAT-AAT
1 AATAATAA-ATAATAAAT
3846647 AATAATAAATAATAAAT
1 AATAATAAATAATAAAT
3846664 -A-AATAAATAA
1 AATAATAAATAA
3846674 AACGAATAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
14 5 0.08
15 20 0.34
16 8 0.14
17 17 0.29
18 9 0.15
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.25
Consensus pattern (17 bp):
AATAATAAATAATAAAT
Found at i:3846666 original size:11 final size:11
Alignment explanation
Indices: 3846588--3846674 Score: 51
Period size: 11 Copynumber: 7.9 Consensus size: 11
3846578 AGTTAAATAA
3846588 AAATAA-AAAT
1 AAATAATAAAT
*
3846598 AAAATAA-AGAT
1 -AAATAATAAAT
3846609 AAA-AATAAA-
1 AAATAATAAAT
* *
3846618 AGAATATTAAAC
1 A-AATAATAAAT
3846630 AATTATAATATAAT
1 AA--ATAATA-AAT
3846644 -AATAAT-AAT
1 AAATAATAAAT
3846653 AAATAATAAAT
1 AAATAATAAAT
3846664 AAATAAATAAA
1 AAAT-AATAAA
3846675 ACGAATAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
9 6 0.10
10 13 0.21
11 27 0.44
12 7 0.11
13 6 0.10
14 2 0.03
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.25
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:3847151 original size:87 final size:88
Alignment explanation
Indices: 3846998--3847157 Score: 189
Period size: 87 Copynumber: 1.8 Consensus size: 88
3846988 CTAAACCTCG
** * * * **** *
3846998 AAGAACTCCGGTTGAATCTTCATCGGATTCTGGAAATTTTCATTGAAATTTGAGTTTTTCGTCG-
1 AAGAACTCCGGTTGAATCTTCATCGGATTCTAAAAATTCTCATCGAAAATTGAGCAGCTCGCCGA
3847062 AAAGTTCATCGAAAAGTTGGTCA
66 AAAGTTCATCGAAAAGTTGGTCA
* *
3847085 AAGAACTCCGGTTGAATCTTCATC-GATTTCTAAAAATTCTCATCGAAAATTGGGCAGCTGGCCG
1 AAGAACTCCGGTTGAATCTTCATCGGA-TTCTAAAAATTCTCATCGAAAATTGAGCAGCTCGCCG
3847149 AAAAGTTCA
65 AAAAGTTCA
3847158 AACTTGACCG
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
86 2 0.03
87 49 0.83
88 8 0.14
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (88 bp):
AAGAACTCCGGTTGAATCTTCATCGGATTCTAAAAATTCTCATCGAAAATTGAGCAGCTCGCCGA
AAAGTTCATCGAAAAGTTGGTCA
Found at i:3847548 original size:18 final size:17
Alignment explanation
Indices: 3847525--3847578 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
3847515 AAAAAAATTG
3847525 AAAGAAGAAAATAAAATA
1 AAAGAA-AAAATAAAATA
*
3847543 AAAGAAAATAA-AAGATA
1 AAAGAAAA-AATAAAATA
*
3847560 AAATAAAAAATAAAGATA
1 AAAGAAAAAATAAA-ATA
3847578 A
1 A
3847579 TATATTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 2 0.07
17 16 0.53
18 12 0.40
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.13
Consensus pattern (17 bp):
AAAGAAAAAATAAAATA
Found at i:3847564 original size:12 final size:12
Alignment explanation
Indices: 3847535--3847578 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
3847525 AAAGAAGAAA
3847535 ATAAAATAAAAG
1 ATAAAATAAAAG
3847547 --AAAATAAAAG
1 ATAAAATAAAAG
*
3847557 ATAAAATAAAAA
1 ATAAAATAAAAG
3847569 ATAAAGATAA
1 ATAAA-ATAA
3847579 TATATTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 10 0.36
12 14 0.50
13 4 0.14
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:3847601 original size:4 final size:4
Alignment explanation
Indices: 3847560--3847774 Score: 66
Period size: 4 Copynumber: 55.8 Consensus size: 4
3847550 ATAAAAGATA
* * * * *
3847560 AAAT AAA- AAAT AAAG ATAAT ATAT TAAT TAAT AGAT AAAT -AAT -AAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
3847606 AAAT ATATAT TAAC AGAT AAAT -AAT AACAT --AT AAAT AGAT AAAT AAAT
1 AAAT A-A-AT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT
* * * * * * *
3847654 ATAT AAAT ATAT TAAC AGAT -AA- AAAT ATCAT TAAT AAAT AGTAAT -AAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT A--AAT AAAT
* * *
3847702 AAAT AAAT AAAT AAAT AAGT -TAT AAA- AAAT -AA- AAAT ACA- AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
3847745 ACAA- GAA- AAAT AAAT AAAT AAAT AAAT AAA
1 A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
3847775 AACTGGCCTA
Statistics
Matches: 151, Mismatches: 38, Indels: 44
0.65 0.16 0.19
Matches are distributed among these distances:
2 2 0.01
3 32 0.21
4 101 0.67
5 11 0.07
6 5 0.03
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:3847604 original size:32 final size:29
Alignment explanation
Indices: 3847562--3847632 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
3847552 AAAAGATAAA
* *
3847562 ATAAAAAATAAAGATAATATATTAATTAATAG
1 ATAAATAATAAAGA-AATATA-T-ATTAACAG
*
3847594 ATAAATAAT-AATAAATATATATTAACAG
1 ATAAATAATAAAGAAATATATATTAACAG
3847622 ATAAATAATAA
1 ATAAATAATAA
3847633 CATATAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 16 0.46
29 2 0.06
30 6 0.17
31 3 0.09
32 8 0.23
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (29 bp):
ATAAATAATAAAGAAATATATATTAACAG
Found at i:3847617 original size:28 final size:28
Alignment explanation
Indices: 3847577--3847718 Score: 88
Period size: 28 Copynumber: 5.1 Consensus size: 28
3847567 AAATAAAGAT
3847577 AATATATTAATTAATAGATAAATAATAATA
1 AATATA-T-ATTAATAGATAAATAATAATA
*
3847607 AATATATATTAACAGAT--A-AATAAT-
1 AATATATATTAATAGATAAATAATAATA
*
3847631 AACATATA--AATAGATAAATAA-ATATA
1 AATATATATTAATAGATAAATAATA-ATA
* *
3847657 TAA-ATATATTAACAGATAAA-AATATCATT
1 -AATATATATTAATAGATAAATAATA--ATA
* *
3847686 AATAAATAGTAATA-ATAAATAAATAAATA
1 AATATATATTAATAGATAAAT-AAT-AATA
3847715 AATA
1 AATA
3847719 AGTTATAAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 29
0.69 0.08 0.23
Matches are distributed among these distances:
22 6 0.07
24 9 0.10
25 10 0.11
26 6 0.07
27 4 0.05
28 26 0.30
29 17 0.19
30 9 0.10
31 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.32
Consensus pattern (28 bp):
AATATATATTAATAGATAAATAATAATA
Found at i:3847628 original size:22 final size:22
Alignment explanation
Indices: 3847603--3847658 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
3847593 GATAAATAAT
*
3847603 AATAAATATATATTAACAGATA
1 AATAAATATATATAAACAGATA
* *
3847625 AAT-AATAACATATAAATAGATA
1 AATAAAT-ATATATAAACAGATA
3847647 AATAAATATATA
1 AATAAATATATA
3847659 AATATATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 3 0.11
22 22 0.79
23 3 0.11
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (22 bp):
AATAAATATATATAAACAGATA
Found at i:3847649 original size:8 final size:7
Alignment explanation
Indices: 3847560--3847773 Score: 63
Period size: 7 Copynumber: 29.9 Consensus size: 7
3847550 ATAAAAGATA
*
3847560 AAATAAA
1 AAATAAT
3847567 AAATAA-
1 AAATAAT
*
3847573 AGATAAT
1 AAATAAT
*
3847580 ATATTAAT
1 A-AATAAT
*
3847588 TAATAGAT
1 AAATA-AT
3847596 AAATAAT
1 AAATAAT
3847603 -AATAAAT
1 AAAT-AAT
* *
3847610 ATATATT
1 AAATAAT
*
3847617 AACA-GAT
1 AA-ATAAT
3847624 AAATAAT
1 AAATAAT
3847631 AACAT-AT
1 AA-ATAAT
3847638 AAATAGAT
1 AAATA-AT
3847646 AAATAA-
1 AAATAAT
*
3847652 ATAT-AT
1 AAATAAT
3847658 AAATATAT
1 AAATA-AT
* *
3847666 TAACAGAT
1 AAATA-AT
3847674 AAA-AAT
1 AAATAAT
*
3847680 ATCATTAAT
1 A--AATAAT
*
3847689 AAATAGT
1 AAATAAT
3847696 -AATAAT
1 AAATAAT
3847702 AAATAAAT
1 AAAT-AAT
3847710 AAATAAAT
1 AAAT-AAT
* *
3847718 AAGTTAT
1 AAATAAT
*
3847725 AAAAAAT
1 AAATAAT
3847732 AAA-AAT
1 AAATAAT
3847738 ACAA-AAT
1 A-AATAAT
*
3847745 ACAAGAA-
1 A-AATAAT
3847752 AAATAAAT
1 AAAT-AAT
3847760 AAATAAAT
1 AAAT-AAT
3847768 AAATAA
1 AAATAA
3847774 AAACTGGCCT
Statistics
Matches: 157, Mismatches: 28, Indels: 44
0.69 0.12 0.19
Matches are distributed among these distances:
5 1 0.01
6 31 0.20
7 61 0.39
8 60 0.38
9 4 0.03
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.28
Consensus pattern (7 bp):
AAATAAT
Found at i:3847649 original size:50 final size:51
Alignment explanation
Indices: 3847582--3847710 Score: 162
Period size: 50 Copynumber: 2.6 Consensus size: 51
3847572 AAGATAATAT
*
3847582 ATTAATTAATAGATAAATAATAATAAATATATATTAACAGATAAATAATAAC
1 ATTAATAAATAGATAAATAATAATAAATATATATTAACAGATAAA-AATAAC
*
3847634 A-T-ATAAATAGATAAATAA-ATATATAA-ATATATTAACAGATAAAAATATC
1 ATTAATAAATAGATAAATAATA-ATA-AATATATATTAACAGATAAAAATAAC
3847683 ATTAATAAATAG-T-AATAATAAATAAATA
1 ATTAATAAATAGATAAATAAT-AATAAATA
3847711 AATAAATAAG
Statistics
Matches: 68, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
49 14 0.21
50 41 0.60
51 12 0.18
52 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (51 bp):
ATTAATAAATAGATAAATAATAATAAATATATATTAACAGATAAAAATAAC
Found at i:3847681 original size:18 final size:18
Alignment explanation
Indices: 3847604--3847687 Score: 54
Period size: 18 Copynumber: 4.8 Consensus size: 18
3847594 ATAAATAATA
*
3847604 ATAAATATATATTAACAG
1 ATAAAAATATATTAACAG
*
3847622 AT--AAATA-A-TAACAT
1 ATAAAAATATATTAACAG
* *
3847636 ATAAATAGATA-AATAA-AT
1 ATAAA-A-ATATATTAACAG
*
3847654 ATATAAATATATTAACAG
1 ATAAAAATATATTAACAG
3847672 ATAAAAATATCATTAA
1 ATAAAAATAT-ATTAA
3847688 TAAATAGTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
14 7 0.13
15 1 0.02
16 8 0.15
17 6 0.12
18 22 0.42
19 8 0.15
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.31
Consensus pattern (18 bp):
ATAAAAATATATTAACAG
Found at i:3847705 original size:26 final size:25
Alignment explanation
Indices: 3847672--3847769 Score: 71
Period size: 25 Copynumber: 3.9 Consensus size: 25
3847662 ATATTAACAG
* *
3847672 ATAAAAATATCATTAATAAAT-AGTA
1 ATAAAAATA-AATAAATAAATAAGTA
*
3847697 ATAATAAATAAATAAATAAATAAGTT
1 ATAA-AAATAAATAAATAAATAAGTA
3847723 ATAAAAA-ATAA-AAATACAA-AA-TACA
1 ATAAAAATA-AATAAATA-AATAAGT--A
*
3847748 AGAAAAATAAATAAATAAATAA
1 ATAAAAATAAATAAATAAATAA
3847770 ATAAAAACTG
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
23 1 0.02
24 8 0.14
25 30 0.51
26 20 0.34
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (25 bp):
ATAAAAATAAATAAATAAATAAGTA
Found at i:3848026 original size:46 final size:44
Alignment explanation
Indices: 3847954--3848099 Score: 178
Period size: 42 Copynumber: 3.4 Consensus size: 44
3847944 TTGATCAAAA
3847954 CTCCTCTAAGT-AGAGGCTCAATGACTTTGAAAAAACATAAATAAAG
1 CTCCTCTAA-TCAGAGGCTCAATGACTTTG-AAAAA-ATAAATAAAG
* *
3848000 CTCCTCTAATCAGAGGCTCAACGACTTTG--AAAATGAATAAAG
1 CTCCTCTAATCAGAGGCTCAATGACTTTGAAAAAATAAATAAAG
* * *
3848042 CTCCTCTAAACAGAGGCTCAATAACTTT-AAAAAATAAAT--GG
1 CTCCTCTAATCAGAGGCTCAATGACTTTGAAAAAATAAATAAAG
3848083 CTCCTCTAATCAGAGGC
1 CTCCTCTAATCAGAGGC
3848100 ATCACAACTT
Statistics
Matches: 89, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
41 17 0.19
42 34 0.38
43 11 0.12
45 1 0.01
46 26 0.29
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (44 bp):
CTCCTCTAATCAGAGGCTCAATGACTTTGAAAAAATAAATAAAG
Found at i:3848121 original size:41 final size:40
Alignment explanation
Indices: 3847995--3848128 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 40
3847985 AAAACATAAA
*
3847995 TAAA-GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAATG
1 TAAATGCTCCTCTAATCAGAGGCTCAACAACTTTGAAAA-G
* * * *
3848035 AATAAA-GCTCCTCTAAACAGAGGCTCAATAACTTTAAAAAA
1 --TAAATGCTCCTCTAATCAGAGGCTCAACAACTTTGAAAAG
*
3848076 TAAATGGCTCCTCTAATCAGAGGCATC-ACAACTTTGGAAAG
1 TAAAT-GCTCCTCTAATCAGAGGC-TCAACAACTTTGAAAAG
3848117 TAAATTGCTCCT
1 TAAA-TGCTCCT
3848129 TGACAATCAT
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
39 4 0.05
41 37 0.47
42 37 0.47
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (40 bp):
TAAATGCTCCTCTAATCAGAGGCTCAACAACTTTGAAAAG
Found at i:3854026 original size:15 final size:15
Alignment explanation
Indices: 3853995--3854045 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
3853985 TATTCCGTCT
*
3853995 TTCTTTTTTCTTGGCC
1 TTCTTTCTTC-TGGCC
3854011 TTCTTTCTTCTGGCC
1 TTCTTTCTTCTGGCC
*
3854026 TTCTTTCTTCTAG-C
1 TTCTTTCTTCTGGCC
3854040 TTCTTT
1 TTCTTT
3854046 AATATTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.21
15 17 0.52
16 9 0.27
ACGTcount: A:0.02, C:0.27, G:0.10, T:0.61
Consensus pattern (15 bp):
TTCTTTCTTCTGGCC
Found at i:3859676 original size:6 final size:6
Alignment explanation
Indices: 3859661--3859704 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
3859651 ATAAAATAAT
* *
3859661 AAAATA AAAATG AAAATA AAAAT- AAAATA AAGATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
3859705 GAATATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:3859680 original size:17 final size:16
Alignment explanation
Indices: 3859649--3859704 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 16
3859639 TTATTTAAGG
3859649 AAATAAAATAATAAAATAA
1 AAATAAAAT-A-AAAAT-A
3859668 AAATGAAAATAAAAATA
1 AAAT-AAAATAAAAATA
3859685 AAATAAAGATAAAAATA
1 AAATAAA-ATAAAAATA
3859702 AAA
1 AAA
3859705 GAATATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.09
17 17 0.49
18 5 0.14
19 5 0.14
20 5 0.14
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.18
Consensus pattern (16 bp):
AAATAAAATAAAAATA
Found at i:3859688 original size:23 final size:23
Alignment explanation
Indices: 3859649--3859704 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
3859639 TTATTTAAGG
*
3859649 AAATAAAATAATAAAATAAAAATGA
1 AAAT-AAA-AATAAAATAAAAATAA
*
3859674 AAATAAAAATAAAATAAAGATAA
1 AAATAAAAATAAAATAAAAATAA
3859697 AAATAAAA
1 AAATAAAA
3859705 GAATATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 22 0.76
24 3 0.10
25 4 0.14
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.18
Consensus pattern (23 bp):
AAATAAAAATAAAATAAAAATAA
Found at i:3860658 original size:6 final size:6
Alignment explanation
Indices: 3860634--3860705 Score: 78
Period size: 6 Copynumber: 12.0 Consensus size: 6
3860624 TTATTTAAAG
*
3860634 AAAAT- AAAATAA TAAAATA AAAATA AAAATA AAAAT- AAAATA AAGAT-
1 AAAATA AAAAT-A -AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
3860681 AAAATA AAGATA AAAATA AAGAATA
1 AAAATA AAAATA AAAATA AA-AATA
3860706 TTAAACAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
5 14 0.25
6 33 0.58
7 5 0.09
8 5 0.09
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:3860660 original size:11 final size:11
Alignment explanation
Indices: 3860634--3860705 Score: 81
Period size: 11 Copynumber: 6.1 Consensus size: 11
3860624 TTATTTAAAG
3860634 AAAATAAAATAAT
1 AAAAT-AAA-AAT
3860647 AAAATAAAAAT
1 AAAATAAAAAT
3860658 AAAAATAAAAAT
1 -AAAATAAAAAT
*
3860670 AAAATAAAGAT
1 AAAATAAAAAT
*
3860681 AAAATAAAGAT
1 AAAATAAAAAT
3860692 AAAAATAAAGAAT
1 -AAAATAAA-AAT
3860705 A
1 A
3860706 TTAAACAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
11 24 0.44
12 23 0.43
13 7 0.13
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:3860664 original size:17 final size:17
Alignment explanation
Indices: 3860634--3860700 Score: 82
Period size: 17 Copynumber: 3.8 Consensus size: 17
3860624 TTATTTAAAG
3860634 AAAATAAAATAATAAAATA
1 AAAAT-AAA-AATAAAATA
3860653 AAAATAAAAATAAAA-A
1 AAAATAAAAATAAAATA
*
3860669 TAAAATAAAGATAAAATA
1 -AAAATAAAAATAAAATA
*
3860687 AAGATAAAAATAAA
1 AAAATAAAAATAAA
3860701 GAATATTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
16 1 0.02
17 33 0.77
18 4 0.09
19 5 0.12
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAATAAAAATAAAATA
Found at i:3860674 original size:23 final size:23
Alignment explanation
Indices: 3860634--3860705 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 23
3860624 TTATTTAAAG
3860634 AAAATAAAATAATAAAATAAAAATA
1 AAAAT-AAA-AATAAAATAAAAATA
*
3860659 AAAATAAAAATAAAATAAAGAT-
1 AAAATAAAAATAAAATAAAAATA
*
3860681 AAAATAAAGATAAAAATAAAGAATA
1 AAAATAAAAAT-AAAATAAA-AATA
3860706 TTAAACAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.24
23 21 0.51
24 5 0.12
25 5 0.12
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (23 bp):
AAAATAAAAATAAAATAAAAATA
Found at i:3861037 original size:21 final size:22
Alignment explanation
Indices: 3861003--3861047 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
3860993 TTTCTCAGAA
*
3861003 TCCCTTCTCCTCTTCTCTCTCT
1 TCCCTTCTCCTCTTCTCTCCCT
*
3861025 TCCCTTCT-TTCTTCTCTCCCT
1 TCCCTTCTCCTCTTCTCTCCCT
3861046 TC
1 TC
3861048 TCTCTAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (22 bp):
TCCCTTCTCCTCTTCTCTCCCT
Found at i:3861546 original size:12 final size:12
Alignment explanation
Indices: 3861526--3861555 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3861516 GAAGGAAGAA
3861526 AAAAAATAAAAT
1 AAAAAATAAAAT
*
3861538 AAAAGATAAAAT
1 AAAAAATAAAAT
3861550 AAAAAA
1 AAAAAA
3861556 AAAGATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:3861548 original size:17 final size:17
Alignment explanation
Indices: 3861528--3861563 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3861518 AGGAAGAAAA
*
3861528 AAAATAAAATAAAAGAT
1 AAAATAAAAAAAAAGAT
3861545 AAAATAAAAAAAAAGAT
1 AAAATAAAAAAAAAGAT
3861562 AA
1 AA
3861564 TATATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAATAAAAAAAAAGAT
Found at i:3861602 original size:28 final size:30
Alignment explanation
Indices: 3861562--3861617 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
3861552 AAAAAAAGAT
*
3861562 AATATATTAATTAAGAGATAAATAATAATA
1 AATATATTAATTAACAGATAAATAATAATA
*
3861592 AATATA-T-ATTAACAGTTAAATAATAA
1 AATATATTAATTAACAGATAAATAATAA
3861618 CGCATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
29 1 0.04
30 6 0.25
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (30 bp):
AATATATTAATTAACAGATAAATAATAATA
Found at i:3861638 original size:4 final size:4
Alignment explanation
Indices: 3861621--3861746 Score: 64
Period size: 4 Copynumber: 31.2 Consensus size: 4
3861611 ATAATAACGC
* * * * * *
3861621 ATAA ATAG ATAA ATAA ATAT ATAA ATAT ATTA ATAG ATAA A-AA TATAC
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA -ATAA
* *
3861669 ATTA ATAA ATAGTA AT-A ATAA ATAA ATAA AT-T ATAA A-AA ATACAA
1 ATAA ATAA ATA--A ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT--AA
* * *
3861714 ATAC A-AA ATACA AGAA AAAA ATAA ATAA ATAA A
1 ATAA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA A
3861747 AATTGGCCTA
Statistics
Matches: 90, Mismatches: 21, Indels: 22
0.68 0.16 0.17
Matches are distributed among these distances:
3 12 0.13
4 67 0.74
5 4 0.04
6 7 0.08
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:3868868 original size:16 final size:17
Alignment explanation
Indices: 3868849--3868886 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3868839 TATTCACATT
3868849 TAAAAA-ATTAACAAC-A
1 TAAAAATATTAA-AACAA
3868865 TAAAAATATTAAAACAA
1 TAAAAATATTAAAACAA
3868882 TAAAA
1 TAAAA
3868887 TCATTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAAATATTAAAACAA
Found at i:3881774 original size:176 final size:175
Alignment explanation
Indices: 3881371--3881936 Score: 691
Period size: 175 Copynumber: 3.2 Consensus size: 175
3881361 ATTTTAACCC
* * *
3881371 ATTTTATAAGCATTAGCTTTTGGTGGGTATATTATCAATTTCTTTTATAGATATATTTTGCTTAT
1 ATTTTATAAGCATTAGCTTTTGGTGGTTATGTTATCAATTTCTTTTATAGATATATTTTGGTTAT
* *
3881436 ACCTAATAATCCTTTTGGAAATGTTGACTCTTGTCTTCTTTTGCTTGATATTCTCTCATTTTAGG
66 CCCTAATAATCCTTTTGGAAATGTTGACTCTTGTCTTCTTTTGCTTGATATTCTCTCACTTTAGG
* * * * **
3881501 GAAATGAGATTTAGCTTTTGGTGGA-TATATGACACAT-T-T-AAA-CCT
131 GAAATGAGA-TT--C--TTGTTGAATTCTATGTCACATCTATCAAATATT
* *
3881546 ATTTTATAAGCATTAGCTTTTGATGGATA-GATTATCAATTTCTTTTATAGATATATTTTGGTTA
1 ATTTTATAAGCATTAGCTTTTGGTGGTTATG-TTATCAATTTCTTTTATAGATATATTTTGGTTA
* *
3881610 TCCCTACTAATCCTTTGGGAAATGTTGACTCTTGTCTTCTTTTGCTTTGATATTCTCTCACTTTA
65 TCCCTAATAATCCTTTTGGAAATGTTGACTCTTGTCTTCTTTTGC-TTGATATTCTCTCACTTTA
*
3881675 GGGAAAGGAGATTCTTGTTGAATTCTATGTCA-ATCTATCAGAATATT
129 GGGAAATGAGATTCTTGTTGAATTCTATGTCACATCTATCA-AATATT
* * *
3881722 ATTTTATAAGCATTAGCTTTTGGTGGTTATGTTATTAATTTCTTGTATAGATAGATTTTGGTTAT
1 ATTTTATAAGCATTAGCTTTTGGTGGTTATGTTATCAATTTCTTTTATAGATATATTTTGGTTAT
* * * * *
3881787 CTCC-AATACTCCTTTTTGAAATGTTAATTCTTGTCTTCTTTTGCTTGATATTCTCTCACCTTAG
66 C-CCTAATAATCCTTTTGGAAATGTTGACTCTTGTCTTCTTTTGCTTGATATTCTCTCACTTTAG
* * * * *
3881851 GGAGATGAGATTCTTGTTTAATTCTATAT-ATACCTATCACAATATT
130 GGAAATGAGATTCTTGTTGAATTCTATGTCACATCTATCA-AATATT
* * *
3881897 ATTTTATAAGCATTTGCTTTTGGTGGTTATATAATCAATT
1 ATTTTATAAGCATTAGCTTTTGGTGGTTATGTTATCAATT
3881937 GTCTGGGATC
Statistics
Matches: 343, Mismatches: 37, Indels: 22
0.85 0.09 0.05
Matches are distributed among these distances:
171 8 0.02
172 8 0.02
173 2 0.01
174 2 0.01
175 198 0.58
176 122 0.36
177 3 0.01
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.47
Consensus pattern (175 bp):
ATTTTATAAGCATTAGCTTTTGGTGGTTATGTTATCAATTTCTTTTATAGATATATTTTGGTTAT
CCCTAATAATCCTTTTGGAAATGTTGACTCTTGTCTTCTTTTGCTTGATATTCTCTCACTTTAGG
GAAATGAGATTCTTGTTGAATTCTATGTCACATCTATCAAATATT
Found at i:3882232 original size:16 final size:16
Alignment explanation
Indices: 3882200--3882243 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
3882190 CAAAATCTAC
* *
3882200 TTTTTATTTTTTGTTTG
1 TTTTTATTTTAT-TTGG
3882217 TCTTTTATTTTATTTGG
1 T-TTTTATTTTATTTGG
3882234 TTTTTATTTT
1 TTTTTATTTT
3882244 TTATTAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 9 0.38
17 5 0.21
18 10 0.42
ACGTcount: A:0.09, C:0.02, G:0.09, T:0.80
Consensus pattern (16 bp):
TTTTTATTTTATTTGG
Found at i:3882246 original size:18 final size:17
Alignment explanation
Indices: 3882200--3882248 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
3882190 CAAAATCTAC
*
3882200 TTTTTATTTTTTGTTTG
1 TTTTTATTTTTTATTTG
3882217 TCTTTTA--TTTTATTTGG
1 T-TTTTATTTTTTATTT-G
3882234 TTTTTATTTTTTATT
1 TTTTTATTTTTTATT
3882249 AGATAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
16 12 0.44
17 3 0.11
18 12 0.44
ACGTcount: A:0.10, C:0.02, G:0.08, T:0.80
Consensus pattern (17 bp):
TTTTTATTTTTTATTTG
Found at i:3882621 original size:29 final size:26
Alignment explanation
Indices: 3882564--3882625 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 26
3882554 TCATTTGACA
**
3882564 TTTTTTTTTCTTTTACTTTTTGTCAT
1 TTTTTTTTTCTTTTACTTTTTAACAT
*
3882590 TTTTTTTCGTTCTTTTAGTTTTTAACAT
1 TTTTTTT--TTCTTTTACTTTTTAACAT
3882618 TTTTTTTT
1 TTTTTTTT
3882626 AATTAGATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 8 0.26
28 23 0.74
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.76
Consensus pattern (26 bp):
TTTTTTTTTCTTTTACTTTTTAACAT
Found at i:3882871 original size:15 final size:15
Alignment explanation
Indices: 3882828--3882926 Score: 52
Period size: 15 Copynumber: 6.7 Consensus size: 15
3882818 AATATAAAAA
3882828 TATATTT-TAT-TAT
1 TATATTTATATATAT
3882841 T-TATTTAT-T-T-T
1 TATATTTATATATAT
3882852 TATATTTATATATAT
1 TATATTTATATATAT
*
3882867 TATATTAATATTAATAGAGT
1 TATATT--TA-T-ATATA-T
3882887 TATTATTTA-ATATAT
1 TA-TATTTATATATAT
* *
3882902 TAT-TTTAATAAAAAT
1 TATATTT-ATATATAT
3882917 TATATTTATA
1 TATATTTATA
3882927 CATAATTAAG
Statistics
Matches: 68, Mismatches: 4, Indels: 26
0.69 0.04 0.27
Matches are distributed among these distances:
11 2 0.03
12 14 0.21
13 6 0.09
14 3 0.04
15 20 0.29
16 7 0.10
17 2 0.03
18 1 0.01
19 6 0.09
20 3 0.04
21 4 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TATATTTATATATAT
Found at i:3883190 original size:22 final size:23
Alignment explanation
Indices: 3883149--3883192 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
3883139 AGGTCTTTTC
*
3883149 TTTTTTTTAGTTTTAGCTATTTGG
1 TTTTTTTTAATTTTA-CTATTTGG
3883173 TTTTTTTTAATTTT-CTATTT
1 TTTTTTTTAATTTTACTATTT
3883193 TTAGCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
24 13 0.68
ACGTcount: A:0.14, C:0.05, G:0.09, T:0.73
Consensus pattern (23 bp):
TTTTTTTTAATTTTACTATTTGG
Found at i:3884127 original size:21 final size:22
Alignment explanation
Indices: 3884092--3884132 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3884082 AAGATGAACG
*
3884092 AAATTTTTTTATATTATTAAGA
1 AAATTCTTTTATATTATTAAGA
*
3884114 AAATTCTTTT-TATTTTTAA
1 AAATTCTTTTATATTATTAA
3884133 TTTTAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
AAATTCTTTTATATTATTAAGA
Found at i:3885100 original size:12 final size:12
Alignment explanation
Indices: 3885082--3885115 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3885072 AAAGAAAAAA
3885082 TTATTTTCTTTT
1 TTATTTTCTTTT
*
3885094 TTCTTTTCTTTT
1 TTATTTTCTTTT
3885106 TTATTTTCTT
1 TTATTTTCTT
3885116 CTCTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (12 bp):
TTATTTTCTTTT
Found at i:3887571 original size:54 final size:54
Alignment explanation
Indices: 3887487--3887597 Score: 195
Period size: 54 Copynumber: 2.1 Consensus size: 54
3887477 CATTTTCTAT
** *
3887487 TTTGCTTTCAAGCATTTATATTGCTTCTCGTACATAGGTATGAAAATTTATTGC
1 TTTGCTTTCAAGCATTTATATTGCACCTCGTACATAGGTATGAAAACTTATTGC
3887541 TTTGCTTTCAAGCATTTATATTGCACCTCGTACATAGGTATGAAAACTTATTGC
1 TTTGCTTTCAAGCATTTATATTGCACCTCGTACATAGGTATGAAAACTTATTGC
3887595 TTT
1 TTT
3887598 TGTCGTTTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.43
Consensus pattern (54 bp):
TTTGCTTTCAAGCATTTATATTGCACCTCGTACATAGGTATGAAAACTTATTGC
Found at i:3888757 original size:3 final size:3
Alignment explanation
Indices: 3888749--3888788 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3888739 TCATTAAAAG
3888749 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3888789 AAATCATATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3889013 original size:6 final size:6
Alignment explanation
Indices: 3889002--3889054 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
3888992 AAAAGTGTTG
* * *
3889002 ATTTTA ATTTTA ATTTGA ATTTTG ATCTTTAA ATTTTTA TTTTTA ATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA AT-TTT-A A-TTTTA ATTTTA ATTTTA
3889053 AT
1 AT
3889055 ATTTTTGGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 29 0.76
7 4 0.11
8 4 0.11
9 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (6 bp):
ATTTTA
Found at i:3889052 original size:20 final size:20
Alignment explanation
Indices: 3889002--3889060 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
3888992 AAAAGTGTTG
*
3889002 ATTTTAATTTT-AA-TTTGA
1 ATTTTAATTTTAAATTTTTA
*
3889020 ATTTTGATCTTTAAATTTTTA
1 ATTTTAAT-TTTAAATTTTTA
*
3889041 TTTTTAATTTTAATATTTTT
1 ATTTTAATTTTAA-ATTTTT
3889061 GGTTTAATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 7 0.21
19 3 0.09
20 7 0.21
21 16 0.48
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (20 bp):
ATTTTAATTTTAAATTTTTA
Found at i:3890516 original size:79 final size:78
Alignment explanation
Indices: 3890454--3890617 Score: 220
Period size: 79 Copynumber: 2.1 Consensus size: 78
3890444 TTTGATTAAT
* ** *
3890454 ATATTTGCATGATTATTGCATGCTTATTTTTATGTGATTTATTATATTTGTGTTTGATTTTTGCA
1 ATATTT-CAT-ATTATTGCATGATTATTTTTACATGATTTATTATATTTATGTTTGATTTTTGCA
3890519 TAATAATTATTACATA
64 TAAT-ATTATTACATA
* *
3890535 ATATTTTATATTATTGCATGATTATTTTTACATGATTTATTATATTTATGTTTGATTTTTGTATA
1 ATATTTCATATTATTGCATGATTATTTTTACATGATTTATTATATTTATGTTTGATTTTTGCATA
* *
3890600 ATAATTATTGCATG
66 AT-ATTATTACATA
3890614 ATAT
1 ATAT
3890618 AGTTTTGCAT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
79 67 0.89
80 2 0.03
81 6 0.08
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (78 bp):
ATATTTCATATTATTGCATGATTATTTTTACATGATTTATTATATTTATGTTTGATTTTTGCATA
ATATTATTACATA
Found at i:3890553 original size:34 final size:34
Alignment explanation
Indices: 3890514--3890580 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
3890504 TGTTTGATTT
3890514 TTGCATAATAATTATTACATAATATT-TTATATTA
1 TTGCATAATAATTATTACATAAT-TTATTATATTA
* * * *
3890548 TTGCATGATTATTTTTACATGATTTATTATATT
1 TTGCATAATAATTATTACATAATTTATTATATT
3890581 TATGTTTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 2 0.07
34 26 0.93
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (34 bp):
TTGCATAATAATTATTACATAATTTATTATATTA
Found at i:3890739 original size:17 final size:18
Alignment explanation
Indices: 3890717--3890750 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3890707 TAATTTTTTT
3890717 ATATGAT-TTTTATATTG
1 ATATGATATTTTATATTG
*
3890734 ATATGATATTTTTTATT
1 ATATGATATTTTATATT
3890751 ACTGCATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (18 bp):
ATATGATATTTTATATTG
Found at i:3898335 original size:38 final size:39
Alignment explanation
Indices: 3898284--3898378 Score: 88
Period size: 37 Copynumber: 2.5 Consensus size: 39
3898274 AAATATCCAT
* * * *
3898284 TTTAGTTTGCAAAAGTCAAAAG-CTCAATTGAGCAGTAC
1 TTTATTTTTCAAAAGTCAAAAGTCTCAATGGAGCAATAC
* *** *
3898322 TTTATTTTTCAAAA-T-TAAAGTCTTGGTGGAGGAATAC
1 TTTATTTTTCAAAAGTCAAAAGTCTCAATGGAGCAATAC
3898359 TTTATTTTTCAAAAGTCAAA
1 TTTATTTTTCAAAAGTCAAA
3898379 GCATTGCTGG
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
36 4 0.09
37 25 0.57
38 13 0.30
39 2 0.05
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (39 bp):
TTTATTTTTCAAAAGTCAAAAGTCTCAATGGAGCAATAC
Found at i:3898483 original size:39 final size:38
Alignment explanation
Indices: 3898317--3898485 Score: 137
Period size: 39 Copynumber: 4.3 Consensus size: 38
3898307 TCAATTGAGC
* *
3898317 AGTACTTTATTTTTCAAAA-TTAAAGTCTTGGTGGAGGA
1 AGTACTTTATTTTTCAAAAGTTAAAGCCTTGGTGGA-AA
* * * * *
3898355 A-TACTTTATTTTTCAAAAGTCAAAGCATTGCTGGCGGAG
1 AGTACTTTATTTTTCAAAAGTTAAAGCCTTGGT-G-GAAA
* * **
3898394 TGCTTTGCTTTATTTTTCAAAAGTTAAAGCCCCGGT-GAAA
1 AG---TACTTTATTTTTCAAAAGTTAAAGCCTTGGTGGAAA
*
3898434 GAGTATTTTATTTTTCAAAAAGTTAAAGCCTTGGTGGAAA
1 -AGTACTTTATTTTTC-AAAAGTTAAAGCCTTGGTGGAAA
3898474 AGTACTTTATTT
1 AGTACTTTATTT
3898486 AAAGTTTCAA
Statistics
Matches: 99, Mismatches: 22, Indels: 19
0.71 0.16 0.14
Matches are distributed among these distances:
37 17 0.17
38 21 0.21
39 28 0.28
40 7 0.07
41 1 0.01
43 25 0.25
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (38 bp):
AGTACTTTATTTTTCAAAAGTTAAAGCCTTGGTGGAAA
Found at i:3898607 original size:38 final size:38
Alignment explanation
Indices: 3898479--3898609 Score: 172
Period size: 38 Copynumber: 3.4 Consensus size: 38
3898469 GGAAAAGTAC
* * *
3898479 TTTATTTAAAGTTTCAAGTCTTAGTTATGGGGGAGCAT
1 TTTATTTAAAGTTTTAAGCCTTAGTTGTGGGGGAGCAT
* * *
3898517 TTTATTTAAAGTTTGAAGCCTTTGTTGTGGGGGAGTAT
1 TTTATTTAAAGTTTTAAGCCTTAGTTGTGGGGGAGCAT
* * * *
3898555 TTTGTTTAAAGTTTTAAGCCTCAGTTGTGGAGGAACAT
1 TTTATTTAAAGTTTTAAGCCTTAGTTGTGGGGGAGCAT
3898593 TTTATTTAAAGTTTTAA
1 TTTATTTAAAGTTTTAA
3898610 AACCTCTATT
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 80 1.00
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.44
Consensus pattern (38 bp):
TTTATTTAAAGTTTTAAGCCTTAGTTGTGGGGGAGCAT
Found at i:3899283 original size:24 final size:22
Alignment explanation
Indices: 3899246--3899297 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
3899236 CGTAGACAAT
*
3899246 AAGCAATAGGTAAACAGAAGCAAC
1 AAGCAATAAGTAAAC--AAGCAAC
* *
3899270 AAGCAATAATTAAACAAGCAAT
1 AAGCAATAAGTAAACAAGCAAC
3899292 AAGCAA
1 AAGCAA
3899298 ATTGGCATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.48
24 13 0.52
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (22 bp):
AAGCAATAAGTAAACAAGCAAC
Found at i:3902521 original size:17 final size:16
Alignment explanation
Indices: 3902501--3902532 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
3902491 AAAAGTAAAA
3902501 CAAATTTAAAAACAAAC
1 CAAA-TTAAAAACAAAC
3902518 CAAATTAAAAACAAA
1 CAAATTAAAAACAAA
3902533 AACCCAAGTC
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:0.69, C:0.16, G:0.00, T:0.16
Consensus pattern (16 bp):
CAAATTAAAAACAAAC
Found at i:3907761 original size:94 final size:94
Alignment explanation
Indices: 3907600--3907782 Score: 303
Period size: 94 Copynumber: 1.9 Consensus size: 94
3907590 GTAGTGGACC
* * * * * *
3907600 ATATTACAACATCATGAGTAATTATATACTAAGCTATGACGTCATTTTTACTTCCAGAATCGTAG
1 ATATTACAAAATAACGAGTAATTATATAATAAGCTATGACGACATTTTTACTGCCAGAATCGTAG
*
3907665 CAACTTTATTAATCCGATCCATATGTACT
66 CAACTTTATTAATCCAATCCATATGTACT
3907694 ATATTACAAAATAACGAGTAATTATATAATAAGCTATGACGACATTTTTACTGCCAGAATCGTAG
1 ATATTACAAAATAACGAGTAATTATATAATAAGCTATGACGACATTTTTACTGCCAGAATCGTAG
3907759 CAACTTTATTAATCCAATCCATAT
66 CAACTTTATTAATCCAATCCATAT
3907783 AATCGGTTCT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 82 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.34
Consensus pattern (94 bp):
ATATTACAAAATAACGAGTAATTATATAATAAGCTATGACGACATTTTTACTGCCAGAATCGTAG
CAACTTTATTAATCCAATCCATATGTACT
Found at i:3923547 original size:23 final size:23
Alignment explanation
Indices: 3923499--3923547 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
3923489 TTAATATTTA
*
3923499 AATAATAAAATTAATATAATAAT
1 AATAATAAAATTAAAATAATAAT
* *
3923522 AATAA-AAAAGTTAAAATCATATT
1 AATAATAAAA-TTAAAATAATAAT
3923545 AAT
1 AAT
3923548 TAAAGCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AATAATAAAATTAAAATAATAAT
Found at i:3925049 original size:3 final size:3
Alignment explanation
Indices: 3925041--3925092 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
3925031 CATACATACA
*
3925041 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3925089 TAT T
1 TAT T
3925093 GCCAGCCGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3927650 original size:15 final size:15
Alignment explanation
Indices: 3927630--3927672 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
3927620 TTGTTGAGCT
3927630 TTTGTTGGTTATATA
1 TTTGTTGGTTATATA
3927645 TTTGTT-G--A-A-A
1 TTTGTTGGTTATATA
3927655 TTTGTTGGTTATATA
1 TTTGTTGGTTATATA
3927670 TTT
1 TTT
3927673 TTATTGGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 10
0.70 0.00 0.30
Matches are distributed among these distances:
10 7 0.30
11 2 0.09
12 1 0.04
13 1 0.04
14 2 0.09
15 10 0.43
ACGTcount: A:0.21, C:0.00, G:0.19, T:0.60
Consensus pattern (15 bp):
TTTGTTGGTTATATA
Found at i:3927664 original size:25 final size:25
Alignment explanation
Indices: 3927595--3927672 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
3927585 ATTTGTTGAA
*
3927595 ATTTGTTTAAA-TT-TTGGTTATAT
1 ATTTGTTGAAATTTGTTGGTTATAT
**
3927618 ATTTGTTGAGCTTTTGTTGGTTATAT
1 ATTTGTTGA-AATTTGTTGGTTATAT
3927644 ATTTGTTGAAATTTGTTGGTTATAT
1 ATTTGTTGAAATTTGTTGGTTATAT
3927669 ATTT
1 ATTT
3927673 TTATTGGATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
23 8 0.17
25 20 0.43
26 19 0.40
ACGTcount: A:0.22, C:0.01, G:0.18, T:0.59
Consensus pattern (25 bp):
ATTTGTTGAAATTTGTTGGTTATAT
Found at i:3931164 original size:13 final size:13
Alignment explanation
Indices: 3931146--3931171 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3931136 CAGTGGGCTG
3931146 AGTTAGATGATGA
1 AGTTAGATGATGA
3931159 AGTTAGATGATGA
1 AGTTAGATGATGA
3931172 TCTTATTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
AGTTAGATGATGA
Found at i:3934234 original size:12 final size:12
Alignment explanation
Indices: 3934217--3934241 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3934207 AAATTTTTTA
3934217 TATTTATAATTT
1 TATTTATAATTT
3934229 TATTTATAATTT
1 TATTTATAATTT
3934241 T
1 T
3934242 TTGATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTATAATTT
Found at i:3934408 original size:20 final size:20
Alignment explanation
Indices: 3934385--3934422 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3934375 AGTTAAAAAT
3934385 ATTAAAA-TAAATAATTAATA
1 ATTAAAATTAAA-AATTAATA
3934405 ATTAAAATTAAAAATTAA
1 ATTAAAATTAAAAATTAA
3934423 AACTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
ATTAAAATTAAAAATTAATA
Found at i:3934420 original size:13 final size:13
Alignment explanation
Indices: 3934397--3934431 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3934387 TAAAATAAAT
*
3934397 AATTAATAATTAA
1 AATTAAAAATTAA
3934410 AATTAAAAATTAA
1 AATTAAAAATTAA
*
3934423 AACTAAAAA
1 AATTAAAAA
3934432 AGGGGAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (13 bp):
AATTAAAAATTAA
Found at i:3934688 original size:17 final size:18
Alignment explanation
Indices: 3934658--3934693 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3934648 ATATAATATT
3934658 TATAAAATATTATTTTAA
1 TATAAAATATTATTTTAA
*
3934676 TATAAATTA-TATTTTAA
1 TATAAAATATTATTTTAA
3934693 T
1 T
3934694 TATATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATAAAATATTATTTTAA
Found at i:3934697 original size:18 final size:19
Alignment explanation
Indices: 3934657--3934697 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
3934647 AATATAATAT
3934657 TTATAAAATATTATTTTAA
1 TTATAAAATATTATTTTAA
*
3934676 -TATAAATTA-TATTTTAA
1 TTATAAAATATTATTTTAA
3934693 TTATA
1 TTATA
3934698 TATAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATAAAATATTATTTTAA
Found at i:3937683 original size:442 final size:442
Alignment explanation
Indices: 3936629--3937951 Score: 2484
Period size: 442 Copynumber: 3.0 Consensus size: 442
3936619 CAAAATCTTG
3936629 TTAAGGAGATCCCTCCCATT-CCCAGAGCCGCTAGCAATCGCCCATTGTTTTAC-AGTGCCGTGT
1 TTAAGGAGATCCCTCCCATTCCCCAGAGCCGCTAGCAATCGCCCATTGTTTTACGA-TGCCGTGT
3936692 CAAACTTGTCAAGGAGAGCCCCTAGCATTCCTCCGTTGTATATCATCTTCATCTCTCTCATTCCA
65 CAAACTTGTCAAGGAGAGCCCCTAGCATTCCTCCGTTGTATATCATCTTCATCTCTCTCATTCCA
3936757 CTCTTTCCAAAATCCCTTCTTTAAAATCTGGACATCCATCGCCAACTGATTTCCCCTTACACCTC
130 CTCTTTCCAAAATCCCTTCTTTAAAATCTGGACATCCATCGCCAACTGATTTCCCCTTACACCTC
3936822 CGTTCGCCTGCCGGTATCTCTCTCACTTCTCTCCCTAGTTTCATATCTTTTGGCCTCCAAACAAG
195 CGTTCGCCTGCCGGTATCTCTCTCACTTCTCTCCCTAGTTTCATATCTTTTGGCCTCCAAACAAG
*
3936887 GTATGTTTGTCTGTTCAGTTACCTAAAAGCCAAAATGTTTTTACAGTTCTATTAACAAAATTTTT
260 GTATGTTTGTCTGTTCAGTTACCTAAAAGCCAAAATGTTTTTACAGTTCTATCAACAAAATTTTT
3936952 GCTTTTTTTGGGAGGATAAATCATAAACAAGTTTTTTTTTCCCTTTAATTCGATAGATTGATAAT
325 GCTTTTTTTGGGAGGATAAATCATAAACAAGTTTTTTTTTCCCTTTAATTCGATAGATTGATAAT
3937017 TATGGTTAAAGTTGTGTTATTTGGAATATGTTAAATATTGGATTTTTTTTTTTT
390 TATGGTTAAAGTTGTGTTATTTGGAATATGTTAAATATTGGA-TTTTTTTTTTT
3937071 TTAAGGAGATCCCTCCCATTCCCCAGAGCCGCTAGCAATCGCCCATTGTTTTACGATGCCGTGTC
1 TTAAGGAGATCCCTCCCATTCCCCAGAGCCGCTAGCAATCGCCCATTGTTTTACGATGCCGTGTC
3937136 AAACTTGTCAAGGAGAGCCCCTAGCATTCCTCCGTTGTATATCATCTTCATCTCTCTCATTCCAC
66 AAACTTGTCAAGGAGAGCCCCTAGCATTCCTCCGTTGTATATCATCTTCATCTCTCTCATTCCAC
3937201 TCTTTCCAAAATCCCTTCTTTAAAAATCTGGACA-CCATCGCCAACTGATTTCCCCTTACACCTC
131 TCTTTCCAAAATCCCTTCTTT-AAAATCTGGACATCCATCGCCAACTGATTTCCCCTTACACCTC
3937265 CGTTCGCCTGCCGGTATCTCTCTCACTTCTCT-CCT-GTTTCATATCTTTTGGCCTCCAAACAAG
195 CGTTCGCCTGCCGGTATCTCTCTCACTTCTCTCCCTAGTTTCATATCTTTTGGCCTCCAAACAAG
3937328 GTATGTTTGTCTGTTCAGTTTACCTAAAAAGCCAAAATGTTTTTACAGTTCTAATCAACAAAATT
260 GTATGTTTGTCTGTTCAG-TTACCT-AAAAGCCAAAATGTTTTTACAGTTCT-ATCAACAAAATT
* *
3937393 TTTGCTTGTTTTGGGAGTATAAATCATAAACAAGTTTTTTTTTCCCTTTAATTCGATAGATTGAT
322 TTTGCTTTTTTTGGGAGGATAAATCATAAACAAGTTTTTTTTTCCCTTTAATTCGATAGATTGAT
3937458 AATTATGGTTAAAGTTGTGGTTATTTGGAATATGTTAAATATT-GATTTTTTTTTTT
387 AATTATGGTTAAAGTTGT-GTTATTTGGAATATGTTAAATATTGGATTTTTTTTTTT
3937514 TTAAGGAGAT-CCTCCCATTCCCCAGAGCCGCTAGCAATCGCCCATTGTTTTACGATGCCGTGTC
1 TTAAGGAGATCCCTCCCATTCCCCAGAGCCGCTAGCAATCGCCCATTGTTTTACGATGCCGTGTC
3937578 AAACTTGTCAAGGAGAGCCCCTAGCATTCCTCCGTTGTATATCATCTTCATCTCTCTCATTCCAC
66 AAACTTGTCAAGGAGAGCCCCTAGCATTCCTCCGTTGTATATCATCTTCATCTCTCTCATTCCAC
*
3937643 TCTTTCCAAAATCCCTTCTTTAAAATCTGTACATCCATCGCCAACTGATTTCCCCTTACACCTCC
131 TCTTTCCAAAATCCCTTCTTTAAAATCTGGACATCCATCGCCAACTGATTTCCCCTTACACCTCC
3937708 GTTCGCCTGCCGGTATCTCTCTCACTTCTCTCCCTAGTTTCATATCTTTTGGCCTCCAAACAAGG
196 GTTCGCCTGCCGGTATCTCTCTCACTTCTCTCCCTAGTTTCATATCTTTTGGCCTCCAAACAAGG
3937773 TATGTTTGTCTGTTCAGTTACCTAAAAGCCAAAATGTTTTTACAGTTCTATCAACAAAATTTTTG
261 TATGTTTGTCTGTTCAGTTACCTAAAAGCCAAAATGTTTTTACAGTTCTATCAACAAAATTTTTG
3937838 CTTTTTTTGGGAGGATAAATCATAAACAAG--TTTTTTTCCCTTTAATTCGATAGATTGATAATT
326 CTTTTTTTGGGAGGATAAATCATAAACAAGTTTTTTTTTCCCTTTAATTCGATAGATTGATAATT
3937901 ATGGTTAAAGTTGTGTTATTTGGAATATGTTAAATATTGGATTTTTTTTTT
391 ATGGTTAAAGTTGTGTTATTTGGAATATGTTAAATATTGGATTTTTTTTTT
3937952 GTCTTGTATT
Statistics
Matches: 864, Mismatches: 6, Indels: 25
0.97 0.01 0.03
Matches are distributed among these distances:
438 24 0.03
439 59 0.07
441 101 0.12
442 257 0.30
443 246 0.28
444 153 0.18
445 24 0.03
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (442 bp):
TTAAGGAGATCCCTCCCATTCCCCAGAGCCGCTAGCAATCGCCCATTGTTTTACGATGCCGTGTC
AAACTTGTCAAGGAGAGCCCCTAGCATTCCTCCGTTGTATATCATCTTCATCTCTCTCATTCCAC
TCTTTCCAAAATCCCTTCTTTAAAATCTGGACATCCATCGCCAACTGATTTCCCCTTACACCTCC
GTTCGCCTGCCGGTATCTCTCTCACTTCTCTCCCTAGTTTCATATCTTTTGGCCTCCAAACAAGG
TATGTTTGTCTGTTCAGTTACCTAAAAGCCAAAATGTTTTTACAGTTCTATCAACAAAATTTTTG
CTTTTTTTGGGAGGATAAATCATAAACAAGTTTTTTTTTCCCTTTAATTCGATAGATTGATAATT
ATGGTTAAAGTTGTGTTATTTGGAATATGTTAAATATTGGATTTTTTTTTTT
Found at i:3940295 original size:37 final size:38
Alignment explanation
Indices: 3940244--3940319 Score: 127
Period size: 37 Copynumber: 2.0 Consensus size: 38
3940234 TTTTTTGAGC
*
3940244 ATATTCTATTCATTAGTTGTGTTATATTTATTTGTGTT
1 ATATTCTATTCATTAGTTGTATTATATTTATTTGTGTT
*
3940282 ATATT-TATTCATTAGTTGTATTATGTTTATTTGTGTT
1 ATATTCTATTCATTAGTTGTATTATATTTATTTGTGTT
3940319 A
1 A
3940320 ATTAATTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 31 0.86
38 5 0.14
ACGTcount: A:0.22, C:0.04, G:0.13, T:0.61
Consensus pattern (38 bp):
ATATTCTATTCATTAGTTGTATTATATTTATTTGTGTT
Found at i:3940333 original size:18 final size:18
Alignment explanation
Indices: 3940307--3940346 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3940297 TTGTATTATG
*
3940307 TTTATTTGTGTTAATTAA
1 TTTAGTTGTGTTAATTAA
3940325 TTTAGTTGTGTTAATTAA
1 TTTAGTTGTGTTAATTAA
3940343 TTTA
1 TTTA
3940347 AATCATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (18 bp):
TTTAGTTGTGTTAATTAA
Found at i:3940383 original size:18 final size:18
Alignment explanation
Indices: 3940250--3940383 Score: 54
Period size: 18 Copynumber: 7.7 Consensus size: 18
3940240 GAGCATATTC
* *
3940250 TATTCATTAGTTGTGTTA
1 TATTTATTATTTGTGTTA
3940268 TA--T-TTATTTGTGTTA
1 TATTTATTATTTGTGTTA
*
3940283 TATTTATTCATTAGT-TGTA
1 TATTTATT-ATTTGTGT-TA
*
3940302 TTATGT-TTATTTGTGTTA
1 -TATTTATTATTTGTGTTA
* *
3940320 -ATTAATTTAGTTGTGTTA
1 TATTTA-TTATTTGTGTTA
*** *
3940338 -A-TTA--ATTTAAATCA
1 TATTTATTATTTGTGTTA
3940352 TATTATATTTATTTGTGTTA
1 TATT-TA-TTATTTGTGTTA
3940372 TATTTATTATTT
1 TATTTATTATTT
3940384 TTATTAAATT
Statistics
Matches: 83, Mismatches: 18, Indels: 30
0.63 0.14 0.23
Matches are distributed among these distances:
14 5 0.06
15 14 0.17
16 3 0.04
17 5 0.06
18 30 0.36
19 12 0.14
20 14 0.17
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.60
Consensus pattern (18 bp):
TATTTATTATTTGTGTTA
Found at i:3940387 original size:15 final size:15
Alignment explanation
Indices: 3940260--3940290 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3940250 TATTCATTAG
3940260 TTGTGTTATATTTAT
1 TTGTGTTATATTTAT
3940275 TTGTGTTATATTTAT
1 TTGTGTTATATTTAT
3940290 T
1 T
3940291 CATTAGTTGT
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:0.19, C:0.00, G:0.13, T:0.68
Consensus pattern (15 bp):
TTGTGTTATATTTAT
Found at i:3941109 original size:35 final size:35
Alignment explanation
Indices: 3941063--3941134 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
3941053 CGAGGATTAG
3941063 TTGTTAGTTATTATATTTTCATTTGAATCATCCAA
1 TTGTTAGTTATTATATTTTCATTTGAATCATCCAA
3941098 TTGTTAGTTATTATATTTTCATTTGAATCATCCAA
1 TTGTTAGTTATTATATTTTCATTTGAATCATCCAA
3941133 TT
1 TT
3941135 TCTCTTATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (35 bp):
TTGTTAGTTATTATATTTTCATTTGAATCATCCAA
Found at i:3941871 original size:11 final size:11
Alignment explanation
Indices: 3941855--3941884 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
3941845 ATTACAACTT
3941855 CCATCTCCCAA
1 CCATCTCCCAA
3941866 CCATCTCCCAA
1 CCATCTCCCAA
3941877 CCATCTCC
1 CCATCTCC
3941885 TAACTTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.57, G:0.00, T:0.20
Consensus pattern (11 bp):
CCATCTCCCAA
Found at i:3947180 original size:28 final size:28
Alignment explanation
Indices: 3947127--3947181 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3947117 TGGTAAATAA
*
3947127 TATTATCCTTTTTAACTAATTCATTTTT
1 TATTATCCTTTTTAAATAATTCATTTTT
*
3947155 TATTATCTTTTTTAAATATATT-ATTTT
1 TATTATCCTTTTTAAATA-ATTCATTTT
3947182 ATGAGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (28 bp):
TATTATCCTTTTTAAATAATTCATTTTT
Found at i:3952238 original size:9 final size:9
Alignment explanation
Indices: 3952224--3952256 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
3952214 AACATCATAC
*
3952224 AAATATTAT
1 AAATATCAT
3952233 AAATATCAT
1 AAATATCAT
3952242 AAATATCAT
1 AAATATCAT
3952251 AAATAT
1 AAATAT
3952257 TATGTCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (9 bp):
AAATATCAT
Found at i:3952353 original size:21 final size:21
Alignment explanation
Indices: 3952329--3952406 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
3952319 ACTTTAGCAT
*
3952329 ATCATACAAATATATTAATAA
1 ATCACACAAATATATTAATAA
*
3952350 ATCACACAAATAAACATATT-ATCA
1 ATCACACAAAT----ATATTAATAA
* * *
3952374 ATCATATAAATATATTAACAA
1 ATCACACAAATATATTAATAA
3952395 ATCACACAAATA
1 ATCACACAAATA
3952407 AATTTATTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
20 5 0.11
21 22 0.50
24 12 0.27
25 5 0.11
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATCACACAAATATATTAATAA
Found at i:3954173 original size:12 final size:12
Alignment explanation
Indices: 3954146--3954186 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
3954136 CTTTGACCAA
3954146 TAAAATC-AAAT
1 TAAAATCAAAAT
3954157 TAAAATCAAAAT
1 TAAAATCAAAAT
* *
3954169 CAAAATTAAAAT
1 TAAAATCAAAAT
3954181 TAAAAT
1 TAAAAT
3954187 TAAGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAAATCAAAAT
Found at i:3954176 original size:18 final size:17
Alignment explanation
Indices: 3954147--3954186 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
3954137 TTTGACCAAT
3954147 AAAATCAAATTAAAATC
1 AAAATCAAATTAAAATC
*
3954164 AAAATCAAAATTAAAATT
1 AAAATC-AAATTAAAATC
3954182 AAAAT
1 AAAAT
3954187 TAAGATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAATCAAATTAAAATC
Found at i:3954187 original size:6 final size:6
Alignment explanation
Indices: 3954153--3954189 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
3954143 CAATAAAATC
* *
3954153 AAATTA AAATCA AAATCA AAATTA AAATTA AAATTA A
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA A
3954190 GATTTTTGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (6 bp):
AAATTA
Found at i:3954482 original size:45 final size:45
Alignment explanation
Indices: 3954428--3954513 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
3954418 ATTAGAAAAC
3954428 TTTTAAAAAATAAAATACTCCTCCACCT-ATGCTTCAACTTTTTTT
1 TTTTAAAAAATAAAATACTCCTCCA-CTGATGCTTCAACTTTTTTT
* *
3954473 TTTTGAAAAATAAAATACTCTTCCACTGATGCTTCAACTTT
1 TTTTAAAAAATAAAATACTCCTCCACTGATGCTTCAACTTT
3954514 GGAAAATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 2 0.05
45 36 0.95
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.41
Consensus pattern (45 bp):
TTTTAAAAAATAAAATACTCCTCCACTGATGCTTCAACTTTTTTT
Found at i:3954521 original size:37 final size:37
Alignment explanation
Indices: 3954474--3954568 Score: 111
Period size: 37 Copynumber: 2.5 Consensus size: 37
3954464 ACTTTTTTTT
*
3954474 TTTGAAAAATAAAATACTCTTCCACTGATGCTTCAAC
1 TTTGAAAAATAAAATACTCTTCCACTGAGGCTTCAAC
* * *
3954511 TTTGGAAAATAAAATAC-CTTTCCATTGAGGTTTCAAC
1 TTTGAAAAATAAAATACTC-TTCCACTGAGGCTTCAAC
**
3954548 TCTAAAAAAATAAAATACTCT
1 T-TTGAAAAATAAAATACTCT
3954569 CCCATAATTG
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
36 1 0.02
37 32 0.67
38 14 0.29
39 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (37 bp):
TTTGAAAAATAAAATACTCTTCCACTGAGGCTTCAAC
Found at i:3955004 original size:22 final size:22
Alignment explanation
Indices: 3954961--3955050 Score: 85
Period size: 22 Copynumber: 4.1 Consensus size: 22
3954951 ATACATGAAA
*
3954961 GTCTTGGAGATTATG-TCTAGAG
1 GTCTTGAAGATTATGCTC-AGAG
*
3954983 GTTTTGAAGATTATGCTCAGAG
1 GTCTTGAAGATTATGCTCAGAG
* * * *
3955005 ATCTT-ACAAATTATGCCCAGAA
1 GTCTTGA-AGATTATGCTCAGAG
*
3955027 GTCTTGAAGATTATGCTCAAAG
1 GTCTTGAAGATTATGCTCAGAG
3955049 GT
1 GT
3955051 TTTGCAAATC
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
21 1 0.02
22 49 0.92
23 3 0.06
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (22 bp):
GTCTTGAAGATTATGCTCAGAG
Found at i:3955079 original size:111 final size:112
Alignment explanation
Indices: 3954877--3955085 Score: 246
Period size: 111 Copynumber: 1.9 Consensus size: 112
3954867 CAAGGTCTTA
* * * * * *
3954877 AAGATTATGCCAAGAGGTCTTACAAATCAATGCCCGGAGGTTTTGGAGATTACGCCTGAAGGTTT
1 AAGATTATGCCAAGAGATCTTACAAATCAATGCCCAGAAGTCTTGAAGATTACGCCTAAAGGTTT
*
3954942 TATAAATCAATACATGAAAGTCTTGGAGATTATGTCTAGAGGTTTTG
66 TACAAATCAATACATGAAAGTCTTGGAGATTATGTCTAGAGGTTTTG
* *
3954989 AAGATTATGCTC-AGAGATCTTACAAAT-TATGCCCAGAAGTCTTGAAGATTATG-CTCAAAGGT
1 AAGATTATGC-CAAGAGATCTTACAAATCAATGCCCAGAAGTCTTGAAGATTACGCCT-AAAGGT
* * * *
3955051 TTTGCAAATCAATGCCT-AAAGGTGTTGGAGATTAT
64 TTTACAAATCAATACATGAAA-GTCTTGGAGATTAT
3955086 TCCCAAAAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
110 5 0.06
111 51 0.63
112 24 0.30
113 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (112 bp):
AAGATTATGCCAAGAGATCTTACAAATCAATGCCCAGAAGTCTTGAAGATTACGCCTAAAGGTTT
TACAAATCAATACATGAAAGTCTTGGAGATTATGTCTAGAGGTTTTG
Found at i:3955085 original size:45 final size:45
Alignment explanation
Indices: 3954990--3955177 Score: 161
Period size: 45 Copynumber: 4.2 Consensus size: 45
3954980 GAGGTTTTGA
* * * *
3954990 AGATTATGCTCAGAGATCTTACAAAT-TATGCCCAGAA-GTCTT-G
1 AGATTATGCTCAAAGATCTTACAAATCAATGCCTA-AAGGTGTTAG
* * * *
3955033 AAGATTATGCTCAAAGGTTTTGCAAATCAATGCCTAAAGGTGTTGG
1 -AGATTATGCTCAAAGATCTTACAAATCAATGCCTAAAGGTGTTAG
* * * * * *
3955079 AGATTATTCCCAAAAATCTTACAAATCAATGCTTGAAGGTTTTAG
1 AGATTATGCTCAAAGATCTTACAAATCAATGCCTAAAGGTGTTAG
* * *
3955124 AGATTATGCTCAGAGATCTTACAAATCAATGCAC-GAA-GTTTTAG
1 AGATTATGCTCAAAGATCTTACAAATCAATGC-CTAAAGGTGTTAG
3955168 AGATTATGCT
1 AGATTATGCT
3955178 TGGAGGTTTT
Statistics
Matches: 118, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
44 41 0.35
45 76 0.64
46 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (45 bp):
AGATTATGCTCAAAGATCTTACAAATCAATGCCTAAAGGTGTTAG
Found at i:3955127 original size:156 final size:156
Alignment explanation
Indices: 3954834--3955131 Score: 332
Period size: 156 Copynumber: 1.9 Consensus size: 156
3954824 TCATACTCAG
* * *
3954834 AGATTATGTCCGAAGATCTTACAAATCATGCTTCAAGGTCTTAAAGATTATGCCAAGAGGTCTTA
1 AGATTATGTCAGAAGATCTTACAAATCATGCTCCAAAGTCTTAAAGATTATGCCAAGAGGTCTTA
** * ** ** * *
3954899 CAAATCAATGCCCGGAGGTTTTGGAGATTACGCCTGAAGGTTTTATAAATCAATACATGAAAGTC
66 CAAATCAATGCCCAAAGGTGTTGGAGATTACGCCCAAAAATCTTACAAATCAATACATGAAAGTC
*
3954964 TTGGAGATTATGTCTAGAGGTTTTGA
131 TTAGAGATTATGTCTAGAGGTTTTGA
* * *
3954990 AGATTATGCTCAG-AGATCTTACAAATTATGC-CCAGAAGTCTTGAAGATTATGCTCAA-AGGTT
1 AGATTATG-TCAGAAGATCTTACAAATCATGCTCCA-AAGTCTTAAAGATTATGC-CAAGAGGTC
* * ** * * *
3955052 TTGCAAATCAATGCCTAAAGGTGTTGGAGATTATTCCCAAAAATCTTACAAATCAATGCTTGAAG
63 TTACAAATCAATGCCCAAAGGTGTTGGAGATTACGCCCAAAAATCTTACAAATCAATACATGAAA
*
3955117 GTTTTAGAGATTATG
128 GTCTTAGAGATTATG
3955132 CTCAGAGATC
Statistics
Matches: 115, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
155 2 0.02
156 107 0.93
157 6 0.05
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (156 bp):
AGATTATGTCAGAAGATCTTACAAATCATGCTCCAAAGTCTTAAAGATTATGCCAAGAGGTCTTA
CAAATCAATGCCCAAAGGTGTTGGAGATTACGCCCAAAAATCTTACAAATCAATACATGAAAGTC
TTAGAGATTATGTCTAGAGGTTTTGA
Found at i:3955176 original size:21 final size:22
Alignment explanation
Indices: 3955152--3955196 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
3955142 TTACAAATCA
3955152 ATGC-ACGAAGTTTTAGAGATT
1 ATGCTACGAAGTTTTAGAGATT
** *
3955173 ATGCTTGGAGGTTTTAGAGATT
1 ATGCTACGAAGTTTTAGAGATT
3955195 AT
1 AT
3955197 TCTTCTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.38
Consensus pattern (22 bp):
ATGCTACGAAGTTTTAGAGATT
Found at i:3955485 original size:18 final size:18
Alignment explanation
Indices: 3955462--3955496 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3955452 ATACAATTCA
3955462 TGAATGCAGTAAATGTAG
1 TGAATGCAGTAAATGTAG
* *
3955480 TGAATGCTGTGAATGTA
1 TGAATGCAGTAAATGTA
3955497 ATGCAAGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (18 bp):
TGAATGCAGTAAATGTAG
Found at i:3955612 original size:18 final size:18
Alignment explanation
Indices: 3955565--3955669 Score: 63
Period size: 18 Copynumber: 5.8 Consensus size: 18
3955555 CAAAATATTC
* *
3955565 AAGGTTCCAATATTCGCTA
1 AAGGTTTCAAGATTCGC-A
3955584 AA-G-TTCTAAGATTCGCA
1 AAGGTTTC-AAGATTCGCA
* *
3955601 TAGGTTTCAAGATTTGCA
1 AAGGTTTCAAGATTCGCA
* * ** * *
3955619 CATGTCCCAAAATTTGCA
1 AAGGTTTCAAGATTCGCA
*
3955637 AAGG-TTCAAAGATTCGAA
1 AAGGTTTC-AAGATTCGCA
3955655 AAGGTTTCAAGATTC
1 AAGGTTTCAAGATTC
3955670 AAAAATATCC
Statistics
Matches: 65, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
17 5 0.08
18 52 0.80
19 8 0.12
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (18 bp):
AAGGTTTCAAGATTCGCA
Found at i:3955674 original size:18 final size:18
Alignment explanation
Indices: 3955636--3955674 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3955626 CAAAATTTGC
*
3955636 AAAGGTTCAAAGATTCGA
1 AAAGGTTCAAAGATTCAA
3955654 AAAGGTTTC-AAGATTCAA
1 AAAGG-TTCAAAGATTCAA
3955672 AAA
1 AAA
3955675 TATCCCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.23
Consensus pattern (18 bp):
AAAGGTTCAAAGATTCAA
Found at i:3955842 original size:37 final size:36
Alignment explanation
Indices: 3955783--3955899 Score: 148
Period size: 37 Copynumber: 3.2 Consensus size: 36
3955773 CACCTTCACT
*
3955783 ATTCACATTAAAAAATTTTAGAGATTCGCATTTAAG
1 ATTCACATTAAAAAATATTAGAGATTCGCATTTAAG
* * *
3955819 ATTCACATTAAAAAAATCTTAGAGATTCACATTCAAG
1 ATTCACATT-AAAAAATATTAGAGATTCGCATTTAAG
* *
3955856 ATTCACATTCAAAAATATTAGAAATAT-GCATTTAAG
1 ATTCACATTAAAAAATATTAGAGAT-TCGCATTTAAG
3955892 A-TCACATT
1 ATTCACATT
3955900 CGAAAGTCCA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
35 7 0.10
36 30 0.42
37 34 0.48
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (36 bp):
ATTCACATTAAAAAATATTAGAGATTCGCATTTAAG
Found at i:3955859 original size:13 final size:13
Alignment explanation
Indices: 3955841--3955867 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3955831 AAAATCTTAG
3955841 AGATTCACATTCA
1 AGATTCACATTCA
3955854 AGATTCACATTCA
1 AGATTCACATTCA
3955867 A
1 A
3955868 AAATATTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (13 bp):
AGATTCACATTCA
Found at i:3956405 original size:70 final size:70
Alignment explanation
Indices: 3956321--3956479 Score: 169
Period size: 70 Copynumber: 2.3 Consensus size: 70
3956311 AAAGTTAAAA
* * * ** *
3956321 ATTTAAATGA-TCACCAAATGATGCAAATACATGGTTCTAACTATGATGCAAATGCAATATTC-A
1 ATTTAAAT-ACTCACCAAATGATGC-AATACATAGTACAAAAAATGATGCAAATACAATATTCAA
3956384 AATAATG
64 AATAATG
* * * * * *
3956391 ATTTATATACTCACCAAACGATTCAATGCATAGTACAAAAAATGATGCAAATATACTATTCAAAA
1 ATTTAAATACTCACCAAATGATGCAATACATAGTACAAAAAATGATGCAAATACAATATTCAAAA
3956456 TAATG
66 TAATG
*
3956461 ATTTAAATATTCACCAAAT
1 ATTTAAATACTCACCAAAT
3956480 AATATAGATG
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
69 29 0.40
70 43 0.60
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (70 bp):
ATTTAAATACTCACCAAATGATGCAATACATAGTACAAAAAATGATGCAAATACAATATTCAAAA
TAATG
Found at i:3957648 original size:5 final size:5
Alignment explanation
Indices: 3957625--3957685 Score: 65
Period size: 5 Copynumber: 12.6 Consensus size: 5
3957615 TTTTTCTACA
* **
3957625 TTTTCC TTTT- TTCTC TTTTC TTTTC TTTTC TTTTC -TTTC TTTT- TTCCC
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
3957673 TTTTC TTTTC TTT
1 TTTTC TTTTC TTT
3957686 CATGTTTTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
4 9 0.20
5 33 0.72
6 4 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:3959301 original size:145 final size:148
Alignment explanation
Indices: 3959137--3959438 Score: 389
Period size: 145 Copynumber: 2.0 Consensus size: 148
3959127 AATTGGATAA
* * * * *
3959137 AAATATATATGTAAATATATGTATGCAATGCA-AAGTGAAAAATAAGGATTCATATCCAAAACTA
1 AAATATATATATAAATATATATATGCAATACATAA-TGAAAAACAAGAATTCATATCCAAAACTA
*
3959201 TGCACAAAATT-AA-AAAGATTTTCCCAAGCT-AATAAAATAATGTACATACAAAAA-TATTTAC
65 TGCACAAAATTAAAGAAAGATTTTCCCAA-ATAAATAAAATAATGTACATACAAAAATTATTTAC
*
3959262 ATGGAGAAAAATGTATATGC
129 ATGGAGAAAAATGTATATAC
*
3959282 AAATATATATATATATATATATATGCAATACATAATGAAAAACAAGAATTCATATCCAAAACTAT
1 AAATATATATATAAATATATATATGCAATACATAATGAAAAACAAGAATTCATATCCAAAACTAT
* * * * *
3959347 GTACAAAATTACAAAGGCAAAGATTTTTCCAAATAAATGAAATAATTTACATACAAAAATTTTTT
66 GCACAAAATT--AAA-G-AAAGATTTTCCCAAATAAATAAAATAATGTACATACAAAAATTATTT
*
3959412 ACATGGATAAAAATGTATATAC
127 ACATGGAGAAAAATGTATATAC
3959434 AAATA
1 AAATA
3959439 CATGTTTGCA
Statistics
Matches: 134, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
145 65 0.49
146 2 0.01
148 2 0.01
150 1 0.01
151 35 0.26
152 29 0.22
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (148 bp):
AAATATATATATAAATATATATATGCAATACATAATGAAAAACAAGAATTCATATCCAAAACTAT
GCACAAAATTAAAGAAAGATTTTCCCAAATAAATAAAATAATGTACATACAAAAATTATTTACAT
GGAGAAAAATGTATATAC
Found at i:3959475 original size:140 final size:133
Alignment explanation
Indices: 3959305--3959803 Score: 494
Period size: 140 Copynumber: 3.7 Consensus size: 133
3959295 TATATATATA
*
3959305 TGCAATACATAATGAAAAACAAGAATTCATATCCAAAACTATGTACAAAATTACAAAGGCAAAGA
1 TGCAATACATAGTGAAAAACAAGAATTCATATCCAAAACTATGTACAAAATTA-AAAGGCAAAGA
* * * *
3959370 TTTTTCCAAATAAATGAAATAATTTACATACAAAAATTTTTTACATGGATAAAAATGTATATACA
65 TTTTTCCAAACAAATGAAATAATGTACATACAAAAA-TATTTACATGGAT----ATGTATATGCA
3959435 AATACATGTT
125 AATACATG-T
* * * *
3959445 TGCAATATATAGTGAAAAACAAGAAGTCATATCCAAAACTATGTATAGAATTGAAAAGGCAAAGA
1 TGCAATACATAGTGAAAAACAAGAATTCATATCCAAAACTATGTACAAAATT-AAAAGGCAAAGA
* * * * * *
3959510 TTTTTTCAAATAAATGAAATAATATACATACAAAGATGTTTACATAGATGTATGTATATGCAAAT
65 TTTTTCCAAACAAATGAAATAATGTACATACAAAAATATTTACATGGA--TATGTATATGCAAAT
3959575 ACATG-
128 ACATGT
* * * * * * * *
3959580 T--AATGCATGGT-AATAACAAGAATTCATATTCAAAGCTATGTACAAAACTGAAAAAGCAAAAA
1 TGCAATACATAGTGAAAAACAAGAATTCATATCCAAAACTATGTACAAAA-TTAAAAGGCAAAGA
** * * * *
3959642 TTCTCCCCAAACAAATGAAATAATGTACATATAAAAATATTTAAATGG--AGGTATATGCAAAAA
65 TT-TTTCCAAACAAATGAAATAATGTACATACAAAAATATTTACATGGATATGTATATGCAAATA
3959705 CATGT
129 CATGT
* * * * *
3959710 AGCAATACAAAGTG-AAAACAAAAATT-ATATCCAAAACTATGTACAAAATTGAAAGGCAAATA-
1 TGCAATACATAGTGAAAAACAAGAATTCATATCCAAAACTATGTACAAAATTAAAAGGCAAAGAT
* *
3959772 TTTTCTGAAACAAATGAAATAATGTAGATACA
66 TTTTC-CAAACAAATGAAATAATGTACATACA
3959804 GTGATGTCTA
Statistics
Matches: 297, Mismatches: 52, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
128 2 0.01
129 41 0.14
130 10 0.03
131 20 0.07
132 59 0.20
133 43 0.14
135 1 0.00
137 18 0.06
139 10 0.03
140 91 0.31
141 2 0.01
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.27
Consensus pattern (133 bp):
TGCAATACATAGTGAAAAACAAGAATTCATATCCAAAACTATGTACAAAATTAAAAGGCAAAGAT
TTTTCCAAACAAATGAAATAATGTACATACAAAAATATTTACATGGATATGTATATGCAAATACA
TGT
Found at i:3959950 original size:22 final size:22
Alignment explanation
Indices: 3959922--3959993 Score: 144
Period size: 22 Copynumber: 3.3 Consensus size: 22
3959912 GAAATGGAAT
3959922 AATGCATGAATGAATGCATGTA
1 AATGCATGAATGAATGCATGTA
3959944 AATGCATGAATGAATGCATGTA
1 AATGCATGAATGAATGCATGTA
3959966 AATGCATGAATGAATGCATGTA
1 AATGCATGAATGAATGCATGTA
3959988 AATGCA
1 AATGCA
3959994 ATAAGAAGGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.26
Consensus pattern (22 bp):
AATGCATGAATGAATGCATGTA
Found at i:3960088 original size:38 final size:39
Alignment explanation
Indices: 3960040--3960118 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 39
3960030 CAATAAAAGA
*
3960040 AAAGGATTAGTA-AACATAATATATACAAGGAATAATAT
1 AAAGGATTAGTAGAACATAATATATACAAGGAACAATAT
* *
3960078 AAAGGGTTAGTATGCACATAATATATACAAGGAACAATAT
1 AAAGGATTAGTA-GAACATAATATATACAAGGAACAATAT
3960118 A
1 A
3960119 TAAATTTACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 11 0.31
40 25 0.69
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (39 bp):
AAAGGATTAGTAGAACATAATATATACAAGGAACAATAT
Found at i:3961693 original size:25 final size:24
Alignment explanation
Indices: 3961663--3961733 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 24
3961653 ACAAATTTAA
3961663 ATAAAATTTCTCACTTAAAAATTT-T
1 ATAAAATTTCT-A-TTAAAAATTTCT
*
3961688 ATAAAAATTTACTATTTAAAATTTCT
1 AT-AAAATTT-CTATTAAAAATTTCT
3961714 AT-AAATTTCATTATTAAAAA
1 ATAAAATTTC--TATTAAAAA
3961734 ATTAATATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
23 1 0.03
24 6 0.15
25 19 0.49
26 11 0.28
27 2 0.05
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAAAATTTCTATTAAAAATTTCT
Found at i:3963142 original size:42 final size:43
Alignment explanation
Indices: 3962974--3963179 Score: 287
Period size: 43 Copynumber: 4.9 Consensus size: 43
3962964 AAATTGTTTC
* * *
3962974 TCTAAATAGAGGCACCACAAC-TTTGAAAAAATAAAT-GCTCC
1 TCTAAATAGAGGCAACAAAACTTTTGAAAAAATAAATGGCTCA
* * * *
3963015 TCTAAACAGAGGCAATAGAAC-TTTG-AAAAATAAATGGCTCT
1 TCTAAATAGAGGCAACAAAACTTTTGAAAAAATAAATGGCTCA
*
3963056 TCCAAATAGAGGCAACAAAACTTTTGAAAAAATAAATGGCTCA
1 TCTAAATAGAGGCAACAAAACTTTTGAAAAAATAAATGGCTCA
3963099 TCTAAATAGAGGCAACAAAACTTTTG-AAAAATAAATGGCTCA
1 TCTAAATAGAGGCAACAAAACTTTTGAAAAAATAAATGGCTCA
* *
3963141 TCTAAATAAAGGCAACAGAACTTTTGAAAAAATAAATGG
1 TCTAAATAGAGGCAACAAAACTTTTGAAAAAATAAATGG
3963180 TAACCTTTGA
Statistics
Matches: 148, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
40 10 0.07
41 42 0.28
42 44 0.30
43 52 0.35
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.23
Consensus pattern (43 bp):
TCTAAATAGAGGCAACAAAACTTTTGAAAAAATAAATGGCTCA
Found at i:3963154 original size:85 final size:84
Alignment explanation
Indices: 3962974--3963179 Score: 299
Period size: 85 Copynumber: 2.5 Consensus size: 84
3962964 AAATTGTTTC
* * * * *
3962974 TCTAAATAGAGGCACCACAAC-TTTGAAAAAATAAAT-GCTCCTCTAAACAGAGGCAATAGAACT
1 TCTAAATAGAGGCAACAAAACTTTTGAAAAAATAAATGGCTCATCTAAACAGAGGCAACAAAACT
*
3963037 TTGAAAAATAAATGGCTCT
66 TTGAAAAATAAATGGCTCA
* *
3963056 TCCAAATAGAGGCAACAAAACTTTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAACAAAACT
1 TCTAAATAGAGGCAACAAAACTTTTGAAAAAATAAATGGCTCATCTAAACAGAGGCAACAAAAC-
3963121 TTTGAAAAATAAATGGCTCA
65 TTTGAAAAATAAATGGCTCA
* *
3963141 TCTAAATAAAGGCAACAGAACTTTTGAAAAAATAAATGG
1 TCTAAATAGAGGCAACAAAACTTTTGAAAAAATAAATGG
3963180 TAACCTTTGA
Statistics
Matches: 110, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
82 18 0.16
83 15 0.14
84 22 0.20
85 55 0.50
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.23
Consensus pattern (84 bp):
TCTAAATAGAGGCAACAAAACTTTTGAAAAAATAAATGGCTCATCTAAACAGAGGCAACAAAACT
TTGAAAAATAAATGGCTCA
Found at i:3963231 original size:42 final size:42
Alignment explanation
Indices: 3963184--3963370 Score: 266
Period size: 42 Copynumber: 4.4 Consensus size: 42
3963174 AAATGGTAAC
*
3963184 CTTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAACATAA
1 CTTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAACAGAA
*
3963226 CTTTGAAAAAATAAATGGCTCATCTAAATAGAGACAACAGAA
1 CTTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAACAGAA
* *
3963268 CTTTTGGAAAAATAAATGGCTCTTCTAAATAGAGGCAACAGAA
1 C-TTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAACAGAA
* * * * *
3963311 CTTTGGAAAAATTAATTGCTTATCTAAATAGAGGCAACCACAA
1 CTTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAA-CAGAA
*
3963354 CTTTGAAAAATTAAATG
1 CTTTGAAAAAATAAATG
3963371 CTTCTTGACA
Statistics
Matches: 129, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
42 73 0.57
43 56 0.43
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (42 bp):
CTTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAACAGAA
Found at i:3963238 original size:64 final size:64
Alignment explanation
Indices: 3963121--3963243 Score: 212
Period size: 65 Copynumber: 1.9 Consensus size: 64
3963111 CAACAAAACT
3963121 TTTGAAAAATAAATGGCTCATCTAAATAAAGGCAACAGAACTTTTGAAAAAATAAATGGTAACC
1 TTTGAAAAATAAATGGCTCATCTAAATAAAGGCAACAGAACTTTTGAAAAAATAAATGGTAACC
* *
3963185 TTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAACATAAC-TTTGAAAAAATAAATGG
1 TTTG-AAAAATAAATGGCTCATCTAAATAAAGGCAACAGAACTTTTGAAAAAATAAATGG
3963244 CTCATCTAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
64 21 0.38
65 35 0.62
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (64 bp):
TTTGAAAAATAAATGGCTCATCTAAATAAAGGCAACAGAACTTTTGAAAAAATAAATGGTAACC
Found at i:3963264 original size:107 final size:107
Alignment explanation
Indices: 3963078--3963286 Score: 366
Period size: 107 Copynumber: 2.0 Consensus size: 107
3963068 CAACAAAACT
3963078 TTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAACAAAACTTTTGAAAAATAAATGGCTCATC
1 TTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAACAAAACTTTTGAAAAATAAATGGCTCATC
*
3963143 TAAATAAAGGCAACAGAACTTTTGAAAAAATAAATGGTAACC
66 TAAATAAAGACAACAGAACTTTTGAAAAAATAAATGGTAACC
*
3963185 TTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAACATAAC-TTTGAAAAAATAAATGGCTCAT
1 TTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAACAAAACTTTTG-AAAAATAAATGGCTCAT
* *
3963249 CTAAATAGAGACAACAGAACTTTTGGAAAAATAAATGG
65 CTAAATAAAGACAACAGAACTTTTGAAAAAATAAATGG
3963287 CTCTTCTAAA
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
106 4 0.04
107 93 0.96
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.24
Consensus pattern (107 bp):
TTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAACAAAACTTTTGAAAAATAAATGGCTCATC
TAAATAAAGACAACAGAACTTTTGAAAAAATAAATGGTAACC
Found at i:3963289 original size:85 final size:85
Alignment explanation
Indices: 3963184--3963370 Score: 261
Period size: 85 Copynumber: 2.2 Consensus size: 85
3963174 AAATGGTAAC
* *
3963184 CTTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAACATAACTTTGAAAAAATAAATGGCTCAT
1 CTTTGGAAAAATAAATGGCTCATCTAAATAGAGGCAACAGAACTTTGAAAAAATAAATGGCTCAT
*
3963249 CTAAATAGAGACAA-CAGAA
66 CTAAATAGAGACAACCACAA
* * * * *
3963268 CTTTTGGAAAAATAAATGGCTCTTCTAAATAGAGGCAACAGAACTTTGGAAAAATTAATTGCTTA
1 C-TTTGGAAAAATAAATGGCTCATCTAAATAGAGGCAACAGAACTTTGAAAAAATAAATGGCTCA
*
3963333 TCTAAATAGAGGCAACCACAA
65 TCTAAATAGAGACAACCACAA
3963354 CTTT-GAAAAATTAAATG
1 CTTTGGAAAAA-TAAATG
3963371 CTTCTTGACA
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
84 7 0.08
85 79 0.87
86 5 0.05
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (85 bp):
CTTTGGAAAAATAAATGGCTCATCTAAATAGAGGCAACAGAACTTTGAAAAAATAAATGGCTCAT
CTAAATAGAGACAACCACAA
Done.