Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, 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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 17 of 77
Found at i:3050534 original size:126 final size:123
Alignment explanation
Indices: 3050405--3050838 Score: 376
Period size: 126 Copynumber: 3.5 Consensus size: 123
3050395 TTTTGCCCAA
* * * *
3050405 AGGTCTTAAAAATTATACTTGAAGGTCTTAGAGATTATGCTCGAAGGTCTTACAAATTTTAAAAT
1 AGGTCTTGAAAATTATGCTCGAAGGTCTTAGAAATTATGCTCGAAGGTCTTACAAATTTTAAAAT
* *
3050470 TTTTGTATGCTCCTCTAATCAGAGGCATTAAAACTGTAAAAATTTAAAATGTTTTATTTG
66 TTTTGAATGCTCCTCTAATCAGAGGCATTGAAACT-TAAAAATTTAAAATGTTTTA-TTG
* * * * * *
3050530 AAGGTCTTGAAAATTATGCTTGGAGGTC-TAGAAAGTATGC-CCAGAGGTCTTACAAATCTCAAA
1 -AGGTCTTGAAAATTATGCTCGAAGGTCTTAGAAATTATGCTCGA-AGGTCTTACAAATTTTAAA
* * * * * * * **
3050593 ATCTTTGAATGCTCTTTTCAATCTGAGGCATTGAAACTTTAACAATTAAAAAAAAGTTTTGGCT-
64 ATTTTTGAATGCTCCTCT-AATCAGAGGCATTGAAAC-TTAAAAATT--TAAAATGTTTT-ATTG
* * * * * *
3050657 AGAGTTTTGAAAATTATGCTCGAAAGTCTTAGAAATTATGCTCAAAGATCTTACAAA-TCTCAAA
1 AG-GTCTTGAAAATTATGCTCGAAGGTCTTAGAAATTATGCTCGAAGGTCTTACAAATTTTAAAA
* * * *
3050721 TCTTTT-AATGCTTCTCCAATCAGAGGCATTGAAACTTTAAAATTTAAAATGTTTTGCATAG
65 T-TTTTGAATGCTCCTCTAATCAGAGGCATTGAAACTTAAAAATTTAAAATGTTTT--ATTG
* * * * *
3050782 AGGTCTTGAAAATTATGCCCGAAGATCTTA-AAGATTATGTTTGGAGGTCTTACAAAT
1 AGGTCTTGAAAATTATGCTCGAAGGTCTTAGAA-ATTATGCTCGAAGGTCTTACAAAT
3050839 CTCAAAAAGG
Statistics
Matches: 241, Mismatches: 53, Indels: 29
0.75 0.16 0.09
Matches are distributed among these distances:
123 11 0.05
124 44 0.18
125 50 0.21
126 66 0.27
127 33 0.14
128 35 0.15
129 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (123 bp):
AGGTCTTGAAAATTATGCTCGAAGGTCTTAGAAATTATGCTCGAAGGTCTTACAAATTTTAAAAT
TTTTGAATGCTCCTCTAATCAGAGGCATTGAAACTTAAAAATTTAAAATGTTTTATTG
Found at i:3050692 original size:22 final size:22
Alignment explanation
Indices: 3050667--3050714 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3050657 AGAGTTTTGA
*
3050667 AAATTATGCTCGAAAG-TCTTAG
1 AAATTATGCTC-AAAGATCTTAC
3050689 AAATTATGCTCAAAGATCTTAC
1 AAATTATGCTCAAAGATCTTAC
3050711 AAAT
1 AAAT
3050715 CTCAAATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (22 bp):
AAATTATGCTCAAAGATCTTAC
Found at i:3050856 original size:42 final size:42
Alignment explanation
Indices: 3050807--3050887 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
3050797 TGCCCGAAGA
** *
3050807 TCTTAAAGATTATGTTTGGAGGTCTTACAAATCTCAAAAAGG
1 TCTTAAAGATTATACTTAGAGGTCTTACAAATCTCAAAAAGG
3050849 TCTTAAAGATTATACTTAGAGGTCTTACAAATCTCAAAA
1 TCTTAAAGATTATACTTAGAGGTCTTACAAATCTCAAAA
3050888 TCTTTGAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (42 bp):
TCTTAAAGATTATACTTAGAGGTCTTACAAATCTCAAAAAGG
Found at i:3051541 original size:41 final size:43
Alignment explanation
Indices: 3051496--3051692 Score: 150
Period size: 44 Copynumber: 4.6 Consensus size: 43
3051486 GTCTTTCTTG
**
3051496 TGATGCAGATACAAGTGATGTAAATGTGAATGTC-TTTTTC-A
1 TGATGCAGATACAAGTGATGTAAATGCAAATGTCTTTTTTCTA
* * **
3051537 TGATGCA-AGTATAGGTGATAAAAATGCAAATGTCTTTTTTCTTA
1 TGATGCAGA-TACAAGTGATGTAAATGCAAATGTCTTTTTTC-TA
* * * * *
3051581 TGATGTAGGTGCTAGTGATGTAAATGCAAATGTCTTTTTTCTTG
1 TGATGCAGATACAAGTGATGTAAATGCAAATGTCTTTTTTC-TA
* ** * *
3051625 TGATGCAGATGCAAGTGATACAAATGCAAAT-TTTTTTTTCATG
1 TGATGCAGATACAAGTGATGTAAATGCAAATGTCTTTTTTC-TA
** * *
3051668 TGATGTGGATGCAAGTGATGCAAAT
1 TGATGCAGATACAAGTGATGTAAAT
3051693 ACGAATGCAA
Statistics
Matches: 126, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
40 1 0.01
41 26 0.21
42 6 0.05
43 32 0.25
44 61 0.48
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (43 bp):
TGATGCAGATACAAGTGATGTAAATGCAAATGTCTTTTTTCTA
Found at i:3051606 original size:44 final size:44
Alignment explanation
Indices: 3051558--3051692 Score: 175
Period size: 44 Copynumber: 3.1 Consensus size: 44
3051548 TAGGTGATAA
* * *
3051558 AAATGCAAATGTCTTTTTTCTTATGATGTAGGTGCTAGTGATGT
1 AAATGCAAATGTCTTTTTTCTTGTGATGTAGGTGCAAGTGATGC
* * *
3051602 AAATGCAAATGTCTTTTTTCTTGTGATGCAGATGCAAGTGATAC
1 AAATGCAAATGTCTTTTTTCTTGTGATGTAGGTGCAAGTGATGC
* *
3051646 AAATGCAAAT-TTTTTTTTCATGTGATGT-GGATGCAAGTGATGC
1 AAATGCAAATGTCTTTTTTCTTGTGATGTAGG-TGCAAGTGATGC
3051689 AAAT
1 AAAT
3051693 ACGAATGCAA
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 1 0.01
43 30 0.38
44 48 0.61
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.39
Consensus pattern (44 bp):
AAATGCAAATGTCTTTTTTCTTGTGATGTAGGTGCAAGTGATGC
Found at i:3051845 original size:86 final size:86
Alignment explanation
Indices: 3051683--3052013 Score: 322
Period size: 86 Copynumber: 3.9 Consensus size: 86
3051673 TGGATGCAAG
** * * * * * * * * * *
3051683 TGATGCAAATACGAATGCAAATGTCTTTCTCAAGATGTACATGCAAGTGTAAATACAAGTTATAC
1 TGATGCAAATGTGAATGCAAATATTTTTCTCATGATGCACATGTAAGTATGAATGCAAGTGATGC
* * *
3051748 AAATGCAAATGTCTTTTTTTA
66 AAATGCGAATGTCATTTATTA
** * * * * * *
3051769 TGATATAGATATGAATGTAAATATCTTTCTCATGATGCATATGTAAGTATGAATGCGAGTGATGC
1 TGATGCAAATGTGAATGCAAATATTTTTCTCATGATGCACATGTAAGTATGAATGCAAGTGATGC
* *
3051834 AAATGCGAATGTCCTTTATTG
66 AAATGCGAATGTCATTTATTA
** * *
3051855 TGATGCAAATGTGAATGCAAATATTTTTCTCATGATGCACATACAAGTATGAATGTAAGTGATAC
1 TGATGCAAATGTGAATGCAAATATTTTTCTCATGATGCACATGTAAGTATGAATGCAAGTGATGC
* **
3051920 -AATGTGAATGTCATTTCCTA
66 AAATGCGAATGTCATTTATTA
* * **
3051940 TGATGCAAATGTGAATGCAAATGTTTTTCTCATAATGCACATGTAAGTACAAATGCAAGTGATGC
1 TGATGCAAATGTGAATGCAAATATTTTTCTCATGATGCACATGTAAGTATGAATGCAAGTGATGC
*
3052005 AAATACGAA
66 AAATGCGAA
3052014 GACTCTTTTT
Statistics
Matches: 197, Mismatches: 47, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
85 72 0.37
86 125 0.63
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (86 bp):
TGATGCAAATGTGAATGCAAATATTTTTCTCATGATGCACATGTAAGTATGAATGCAAGTGATGC
AAATGCGAATGTCATTTATTA
Found at i:3054210 original size:14 final size:14
Alignment explanation
Indices: 3054191--3054253 Score: 76
Period size: 14 Copynumber: 4.6 Consensus size: 14
3054181 TTCCTCTTTA
* *
3054191 TTTTTGTTTTCATT
1 TTTTTGTTTTTACT
3054205 TTTTTGTTTTTTACT
1 TTTTTG-TTTTTACT
3054220 TTTTTGTTTTTA-T
1 TTTTTGTTTTTACT
*
3054233 TTTGT-TTTTTACT
1 TTTTTGTTTTTACT
3054246 TTTTTGTT
1 TTTTTGTT
3054254 GCAACCATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
12 6 0.14
13 10 0.24
14 14 0.33
15 12 0.29
ACGTcount: A:0.06, C:0.05, G:0.08, T:0.81
Consensus pattern (14 bp):
TTTTTGTTTTTACT
Found at i:3056570 original size:25 final size:26
Alignment explanation
Indices: 3056535--3056588 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
3056525 AATATTTTAT
*
3056535 AATTATCAAATGATGAGATTCTT-AGA
1 AATTATCAAATGAT-AAATTCTTAAGA
*
3056561 AATT-TCAAATGGTAAATTCTTAAGA
1 AATTATCAAATGATAAATTCTTAAGA
3056586 AAT
1 AAT
3056589 CTCTAGGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 14 0.56
26 4 0.16
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.35
Consensus pattern (26 bp):
AATTATCAAATGATAAATTCTTAAGA
Found at i:3056824 original size:56 final size:54
Alignment explanation
Indices: 3056709--3056895 Score: 206
Period size: 56 Copynumber: 3.5 Consensus size: 54
3056699 AAATAAAGAA
* * * *
3056709 AAAATATTTCTAAATTGACCAAAATGGTGAAAATTTTAGAAAT-----TAAAAG
1 AAAATATTTCTAAATTGACCCAAATGGTAAAAAATTTAGAAATCCAAAAAAAAG
3056758 AAAATATTTCTAAATTGACCCAAATGGTAAAAAATTTAGAAATCCAACAAAAAAAG
1 AAAATATTTCTAAATTGACCCAAATGGTAAAAAATTTAGAAATCC-A-AAAAAAAG
* * * * * *
3056814 AGAGA-ATTTCTAAGTAGGCCCAAATGGTGAAAAATTTAGAAATTCAAAAAAAAG
1 A-AAATATTTCTAAATTGACCCAAATGGTAAAAAATTTAGAAATCCAAAAAAAAG
*
3056868 AAAATATTTCTAATTTGACCCAAATGGT
1 AAAATATTTCTAAATTGACCCAAATGGT
3056896 GGAATAATTA
Statistics
Matches: 115, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
49 40 0.35
53 2 0.02
54 29 0.25
55 1 0.01
56 41 0.36
57 2 0.02
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (54 bp):
AAAATATTTCTAAATTGACCCAAATGGTAAAAAATTTAGAAATCCAAAAAAAAG
Found at i:3060857 original size:10 final size:10
Alignment explanation
Indices: 3060839--3060923 Score: 51
Period size: 9 Copynumber: 9.2 Consensus size: 10
3060829 ACCACTAATG
*
3060839 GATGGAAAAA
1 GATGAAAAAA
3060849 GATGAAAAAA
1 GATGAAAAAA
* *
3060859 TA-AAAAAAA
1 GATGAAAAAA
3060868 GA-GAAAAAA
1 GATGAAAAAA
3060877 -A-GAAAAAA
1 GATGAAAAAA
* *
3060885 AAT-AAAAGA
1 GATGAAAAAA
3060894 -ATGGAAAAAA
1 GAT-GAAAAAA
*
3060904 GATG-AAAAT
1 GATGAAAAAA
3060913 GA-GAAAAAA
1 GATGAAAAAA
3060922 GA
1 GA
3060924 AAAACTAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
8 11 0.18
9 31 0.52
10 16 0.27
11 2 0.03
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (10 bp):
GATGAAAAAA
Found at i:3060868 original size:19 final size:19
Alignment explanation
Indices: 3060844--3060911 Score: 72
Period size: 18 Copynumber: 3.7 Consensus size: 19
3060834 TAATGGATGG
3060844 AAAAAGATGAAAAAATAAA
1 AAAAAGATGAAAAAATAAA
3060863 AAAAAGA-GAAAAAA-AGAA
1 AAAAAGATGAAAAAATA-AA
**
3060881 AAAAA-AT-AAAAGAATGGA
1 AAAAAGATGAAAA-AATAAA
3060899 AAAAAGATGAAAA
1 AAAAAGATGAAAA
3060912 TGAGAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
17 6 0.15
18 22 0.54
19 9 0.22
20 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (19 bp):
AAAAAGATGAAAAAATAAA
Found at i:3060918 original size:18 final size:18
Alignment explanation
Indices: 3060844--3060923 Score: 58
Period size: 19 Copynumber: 4.4 Consensus size: 18
3060834 TAATGGATGG
*
3060844 AAAAAGATGAAAAAAT-AAA
1 AAAAAGATG--AAAATGAGA
**
3060863 AAAAAGA-GAAAAAAAGA
1 AAAAAGATGAAAATGAGA
* *
3060880 AAAAAAATAAAAGAATG-GA
1 AAAAAGAT-GAA-AATGAGA
3060899 AAAAAGATGAAAATGAGA
1 AAAAAGATGAAAATGAGA
3060917 AAAAAGA
1 AAAAAGA
3060924 AAAACTAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
16 4 0.08
17 12 0.25
18 12 0.25
19 18 0.38
20 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.07
Consensus pattern (18 bp):
AAAAAGATGAAAATGAGA
Found at i:3062292 original size:21 final size:21
Alignment explanation
Indices: 3062225--3062304 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 21
3062215 TTTTGAGTTC
* *
3062225 TCAAATGAGAATCTGTGAATT
1 TCAAATGAGAATCTTTAAATT
* *
3062246 TTAAATGAGAAT-TTTCAAA-C
1 TCAAATGAGAATCTTT-AAATT
*
3062266 TCAAATGAGAAGCTTTAAATT
1 TCAAATGAGAATCTTTAAATT
*
3062287 TCAAATAAGAATCTTTAA
1 TCAAATGAGAATCTTTAA
3062305 GTTGTGAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
20 15 0.32
21 32 0.68
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (21 bp):
TCAAATGAGAATCTTTAAATT
Found at i:3062350 original size:79 final size:79
Alignment explanation
Indices: 3062263--3062489 Score: 339
Period size: 79 Copynumber: 2.9 Consensus size: 79
3062253 AGAATTTTCA
* * *
3062263 AACTCAAATGAGAAGCTTTAAATTTCAAATAAGAATCTTTAAGTTGTGAAACCCAAAATTTGTTA
1 AACTCAAATGAGAATCTTTGAATTTCAAATAAGAATCTTTAAGGTGTGAAACCCAAAATTTGTTA
*
3062328 AATATGACTCTTTG
66 AATATGAATCTTTG
* * *
3062342 AACTCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTAAGGTGTGAATCCCAAAATTTGTTG
1 AACTCAAATGAGAATCTTTGAATTTCAAATAAGAATCTTTAAGGTGTGAAACCCAAAATTTGTTA
*
3062407 AATGTGAATCTTTG
66 AATATGAATCTTTG
* *
3062421 AACAT-AAATAAGAATCTTTGAATTTCAAATAAGAATCTTTGAGGTGTGAAACCCTAAAATTTGT
1 AAC-TCAAATGAGAATCTTTGAATTTCAAATAAGAATCTTTAAGGTGTGAAACCC-AAAATTTGT
3062485 TAAAT
64 TAAAT
3062490 GTAAGCCTTT
Statistics
Matches: 133, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
79 119 0.89
80 14 0.11
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (79 bp):
AACTCAAATGAGAATCTTTGAATTTCAAATAAGAATCTTTAAGGTGTGAAACCCAAAATTTGTTA
AATATGAATCTTTG
Found at i:3062359 original size:20 final size:21
Alignment explanation
Indices: 3062336--3062381 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
3062326 TAAATATGAC
3062336 TCTTTGAA-CTCAAATGAGAA
1 TCTTTGAATCTCAAATGAGAA
*
3062356 TCTTTGAATTTCAAATGAGAA
1 TCTTTGAATCTCAAATGAGAA
3062377 TCTTT
1 TCTTT
3062382 AAGGTGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (21 bp):
TCTTTGAATCTCAAATGAGAA
Found at i:3062437 original size:20 final size:21
Alignment explanation
Indices: 3062412--3062462 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
3062402 TGTTGAATGT
3062412 GAATCTTTGAACAT-AAATAA
1 GAATCTTTGAACATCAAATAA
**
3062432 GAATCTTTGAATTTCAAATAA
1 GAATCTTTGAACATCAAATAA
3062453 GAATCTTTGA
1 GAATCTTTGA
3062463 GGTGTGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (21 bp):
GAATCTTTGAACATCAAATAA
Found at i:3063026 original size:8 final size:8
Alignment explanation
Indices: 3063013--3063055 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
3063003 TAATTTTGCT
3063013 AATAAAAA
1 AATAAAAA
3063021 AATAAAAA
1 AATAAAAA
*
3063029 GAT-AAAA
1 AATAAAAA
3063036 AATAAAAA
1 AATAAAAA
*
3063044 AATGAAAA
1 AATAAAAA
3063052 AATA
1 AATA
3063056 GGTAGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (8 bp):
AATAAAAA
Found at i:3063037 original size:15 final size:16
Alignment explanation
Indices: 3063017--3063055 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
3063007 TTTGCTAATA
*
3063017 AAAAAATAAAAAGAT-
1 AAAAAATAAAAAAATG
3063032 AAAAAATAAAAAAATG
1 AAAAAATAAAAAAATG
3063048 AAAAAATA
1 AAAAAATA
3063056 GGTAGTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (16 bp):
AAAAAATAAAAAAATG
Found at i:3064157 original size:53 final size:54
Alignment explanation
Indices: 3064099--3064252 Score: 247
Period size: 53 Copynumber: 2.8 Consensus size: 54
3064089 ACAAATAAAG
* * *
3064099 AAAAAGTATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAATCCAAC-AAA
1 AAAAAGAATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGAAATCCAACAAAA
3064152 AAAAAGAATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGAAATCCAACAAAA
1 AAAAAGAATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGAAATCCAACAAAA
*
3064206 AAAGAGAGAATTTCTAAATAGGCCCAAATGGTGAAAAGTTTAGAAAT
1 AAA-A-AGAATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGAAAT
3064253 AATGACCTAA
Statistics
Matches: 94, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
53 47 0.50
54 6 0.06
55 1 0.01
56 40 0.43
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.23
Consensus pattern (54 bp):
AAAAAGAATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGAAATCCAACAAAA
Found at i:3069058 original size:3 final size:3
Alignment explanation
Indices: 3069050--3069085 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
3069040 ATTACCACTG
3069050 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
3069086 GAAAGAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3069069 original size:14 final size:14
Alignment explanation
Indices: 3069050--3069076 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3069040 ATTACCACTG
3069050 TTATTATTATTATA
1 TTATTATTATTATA
3069064 TTATTATTATTAT
1 TTATTATTATTAT
3069077 TATTTATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:3069072 original size:17 final size:16
Alignment explanation
Indices: 3069050--3069085 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
3069040 ATTACCACTG
3069050 TTATTATTATTATATTA
1 TTATTATTATTAT-TTA
3069067 TTATTATTATTATTTA
1 TTATTATTATTATTTA
3069083 TTA
1 TTA
3069086 GAAAGAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTATTATTATTTA
Found at i:3069739 original size:17 final size:19
Alignment explanation
Indices: 3069717--3069751 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
3069707 CATAAAATAT
3069717 AATATT-TTTTT-AAAACA
1 AATATTGTTTTTCAAAACA
3069734 AATATTGTTTTTCAAAAC
1 AATATTGTTTTTCAAAAC
3069752 TCATTCTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (19 bp):
AATATTGTTTTTCAAAACA
Found at i:3072291 original size:143 final size:141
Alignment explanation
Indices: 3072088--3072474 Score: 472
Period size: 143 Copynumber: 2.7 Consensus size: 141
3072078 TCATTTTTGA
* * *
3072088 GATTTTAAAATGC-CAAAAATTATGAAATATTATAAAATTAAGATTTGAAAAGTTTCATGAAAAT
1 GATTTT-AAATGCACAAAAATCATGAAATATTATAAAATTAAAATCT-AAAAGTTTCATGAAAAT
* * * *
3072152 TCGAGCTCATAAAGGTCAAATTATGAAAATACCTTTGTAGGGGTATTTTGGTAATTTGATATTTT
64 TCGAGCTCA-AAAGGTCAAATTATGAAAATACCTTTATAGGGGTATTTTGGTAATTTCACATTAT
3072217 TAGGGTACTG-CTAT
128 TAGGGTAC-GACTAT
* * * * * *
3072231 GATTTTAAATGCACAAAAAATCATGAAATATTATGAAATTAATATCTCAAAGTTTAATGAAGATA
1 GATTTTAAATGCAC-AAAAATCATGAAATATTATAAAATTAAAATCTAAAAGTTTCATGAAAATT
*
3072296 CGAGCTCGAAAAGGTTAAATTATGAAAATACCTTTATAGGGGTATTTTGGTAATTTCACATTATT
65 CGAGCTC-AAAAGGTCAAATTATGAAAATACCTTTATAGGGGTATTTTGGTAATTTCACATTATT
*
3072361 AGGGTACGACTGT
129 AGGGTACGACTAT
* * * *
3072374 GATTTCAAATGCACCAAACATCATGAAATATTATAAAATTAAAATCTAAAAATGTTCATTAAAAT
1 GATTTTAAATGCA-CAAAAATCATGAAATATTATAAAATTAAAATCTAAAAGT-TTCATGAAAAT
** *
3072439 TAAAGCTTGAAAAGGTCAAATTATGAAAATATCCTT
64 TCGAGC-TCAAAAGGTCAAATTATGAAAATA-CCTT
3072475 GATAAAAATA
Statistics
Matches: 208, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
142 7 0.03
143 134 0.64
144 62 0.30
145 5 0.02
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.34
Consensus pattern (141 bp):
GATTTTAAATGCACAAAAATCATGAAATATTATAAAATTAAAATCTAAAAGTTTCATGAAAATTC
GAGCTCAAAAGGTCAAATTATGAAAATACCTTTATAGGGGTATTTTGGTAATTTCACATTATTAG
GGTACGACTAT
Found at i:3076540 original size:3 final size:3
Alignment explanation
Indices: 3076534--3076564 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3076524 GCAGTAAATA
3076534 AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3076565 AAAATCTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3076546 original size:12 final size:11
Alignment explanation
Indices: 3076529--3076566 Score: 58
Period size: 12 Copynumber: 3.3 Consensus size: 11
3076519 ATGATGCAGT
3076529 AAATAAATAATA
1 AAAT-AATAATA
3076541 AAATAATAATA
1 AAATAATAATA
3076552 ATAATAATAATA
1 A-AATAATAATA
3076564 AAA
1 AAA
3076567 AATCTGTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATAATAATA
Found at i:3077175 original size:17 final size:17
Alignment explanation
Indices: 3077154--3077190 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3077144 GAAAAAAATT
*
3077154 TAAAAATT-AAATTTTA
1 TAAAAATTAAAATTCTA
3077170 TAAAAATTAAAATTCTA
1 TAAAAATTAAAATTCTA
3077187 TAAA
1 TAAA
3077191 TTTATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAATTAAAATTCTA
Found at i:3077262 original size:18 final size:18
Alignment explanation
Indices: 3077241--3077404 Score: 123
Period size: 18 Copynumber: 8.8 Consensus size: 18
3077231 TTCCTTAATT
*
3077241 ATTTTTGAATTTTTAAAA
1 ATTTTTAAATTTTTAAAA
*
3077259 ATTTTCTAAAATTTTTAGAA
1 ATTTT-T-AAATTTTTAAAA
* *
3077279 TTTTTTAAATGTTTAAAA
1 ATTTTTAAATTTTTAAAA
* * *
3077297 ATTTTTAAAAGTTTTAGAG
1 ATTTTT-AAATTTTTAAAA
*
3077316 TTTTTTCAAAATTTTTAAAA
1 ATTTTT--AAATTTTTAAAA
* * *
3077336 TTTTTTAAATATATTAAAC
1 ATTTTTAAAT-TTTTAAAA
*
3077355 A-TTTTAAATTTTTAAAT
1 ATTTTTAAATTTTTAAAA
* *
3077372 TTTTTTAAAATTTTAAAA
1 ATTTTTAAATTTTTAAAA
*
3077390 GTTTTTAGAATTTTT
1 ATTTTTA-AATTTTT
3077405 TAATTTTTTA
Statistics
Matches: 115, Mismatches: 24, Indels: 13
0.76 0.16 0.09
Matches are distributed among these distances:
17 6 0.05
18 52 0.45
19 27 0.23
20 30 0.26
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTTTTAAATTTTTAAAA
Found at i:3077268 original size:11 final size:9
Alignment explanation
Indices: 3077248--3077567 Score: 133
Period size: 10 Copynumber: 33.2 Consensus size: 9
3077238 ATTATTTTTG
3077248 AATTTTTAAA
1 AATTTTT-AA
3077258 AATTTTCTAA
1 AATTTT-TAA
*
3077268 AATTTTTAG
1 AATTTTTAA
*
3077277 AATTTTTTA
1 AATTTTTAA
*
3077286 AATGTTTAAA
1 AAT-TTTTAA
3077296 AATTTTTAA
1 AATTTTTAA
*
3077305 AAGTTTTAGA
1 AATTTTTA-A
**
3077315 GTTTTTTCAA
1 AATTTTT-AA
3077325 AATTTTTAA
1 AATTTTTAA
*
3077334 AATTTTTTA
1 AATTTTTAA
*
3077343 AATATATTAA
1 AAT-TTTTAA
3077353 ACA-TTTT-A
1 A-ATTTTTAA
3077361 AATTTTTAA
1 AATTTTTAA
*
3077370 ATTTTTTTAA
1 A-ATTTTTAA
3077380 AA-TTTTAA
1 AATTTTTAA
*
3077388 AAGTTTTTAG
1 AA-TTTTTAA
*
3077398 AATTTTTTA
1 AATTTTTAA
*
3077407 ATTTTTTAAGA
1 AATTTTT-A-A
*
3077418 AATTTTTTAG
1 AA-TTTTTAA
*
3077428 AATTCGTTTGA
1 AATT--TTTAA
*
3077439 ATTTTTTGAA
1 AATTTTT-AA
* *
3077449 ACTTTTTTGA
1 A-ATTTTTAA
*
3077459 AATTATTTTA
1 AATT-TTTAA
* *
3077469 TATTATTTAG
1 AATT-TTTAA
*
3077479 AATTATTGAA
1 AATT-TTTAA
*
3077489 AATTTGTTAG
1 AATTT-TTAA
3077499 AATTTTTAA
1 AATTTTTAA
* *
3077508 AGTTGTTGATA
1 AATT-TTTA-A
*
3077519 ATTTTTTAA
1 AATTTTTAA
**
3077528 TTTTTTTGAA
1 AATTTTT-AA
**
3077538 TTTTTTTAA
1 AATTTTTAA
3077547 TAATTTTTAA
1 -AATTTTTAA
*
3077557 AAATTTTAA
1 AATTTTTAA
3077566 AA
1 AA
3077568 ACTTTGCTGG
Statistics
Matches: 237, Mismatches: 49, Indels: 49
0.71 0.15 0.15
Matches are distributed among these distances:
7 1 0.00
8 14 0.06
9 86 0.36
10 109 0.46
11 22 0.09
12 5 0.02
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.55
Consensus pattern (9 bp):
AATTTTTAA
Found at i:3077403 original size:9 final size:8
Alignment explanation
Indices: 3077241--3077412 Score: 74
Period size: 9 Copynumber: 18.8 Consensus size: 8
3077231 TTCCTTAATT
*
3077241 ATTTTTGA
1 ATTTTTAA
3077249 ATTTTTAAAA
1 ATTTTT--AA
3077259 ATTTTCTAAA
1 ATTTT-T-AA
3077269 ATTTTTAGA
1 ATTTTTA-A
3077278 ATTTTTTAA
1 A-TTTTTAA
*
3077287 ATGTTTAAAA
1 AT-TTT-TAA
3077297 ATTTTTAAA
1 ATTTTT-AA
*
3077306 AGTTTTAGA
1 ATTTTTA-A
*
3077315 GTTTTTTCAAA
1 -ATTTTT--AA
3077326 ATTTTTAAA
1 ATTTTT-AA
3077335 ATTTTTTAA
1 A-TTTTTAA
*
3077344 ATATATTAA
1 AT-TTTTAA
*
3077353 ACATTTTAA
1 A-TTTTTAA
3077362 ATTTTTAA
1 ATTTTTAA
3077370 ATTTTTTTAAA
1 A--TTTTT-AA
*
3077381 ATTTTAAA
1 ATTTTTAA
3077389 AGTTTTTAGA
1 A-TTTTTA-A
*
3077399 ATTTTTTA
1 ATTTTTAA
3077407 ATTTTT
1 ATTTTT
3077413 TAAGAAATTT
Statistics
Matches: 130, Mismatches: 14, Indels: 40
0.71 0.08 0.22
Matches are distributed among these distances:
8 27 0.21
9 52 0.40
10 45 0.35
11 5 0.04
12 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (8 bp):
ATTTTTAA
Found at i:3077405 original size:20 final size:19
Alignment explanation
Indices: 3077248--3077646 Score: 152
Period size: 20 Copynumber: 19.8 Consensus size: 19
3077238 ATTATTTTTG
* *
3077248 AATTTTTAAAAATTTTCTAA
1 AATTTTT-AGAATTTTTTAA
3077268 AATTTTTAGAATTTTTT-A
1 AATTTTTAGAATTTTTTAA
* * *
3077286 AATGTTTAAAAATTTTTAA
1 AATTTTTAGAATTTTTTAA
* *
3077305 AAGTTTTAGAGTTTTTTCAA
1 AATTTTTAGAATTTTTT-AA
*
3077325 AATTTTTAAAATTTTTTAA
1 AATTTTTAGAATTTTTTAA
** *
3077344 ATATATTAAACATTTTAAATTTTTAA
1 A-AT-TT-----TTAGAATTTTTTAA
* *
3077370 ATTTTTTTA-AA-ATTTTAA
1 A-ATTTTTAGAATTTTTTAA
3077388 AAGTTTTTAGAATTTTTT-A
1 AA-TTTTTAGAATTTTTTAA
* *
3077407 ATTTTTTAAGAAATTTTTTAG
1 AATTTTT-AG-AATTTTTTAA
3077428 AATTCGTTT-GAATTTTTTGAA
1 AATT--TTTAGAATTTTTT-AA
* *
3077449 ACTTTTTTGAAATTATTTT-A
1 AATTTTTAG-AATT-TTTTAA
* * *
3077469 TATTATTTAGAATTATTGAA
1 AATT-TTTAGAATTTTTTAA
3077489 AATTTGTTAGAA-TTTTTAA
1 AATTT-TTAGAATTTTTTAA
* * *
3077508 AGTTGTTGATAATTTTTT-A
1 AATT-TTTAGAATTTTTTAA
* *
3077527 ATTTTTTTGAATTTTTTTAA
1 AATTTTTAGAA-TTTTTTAA
* * *
3077547 TAATTTTTAAAAATTTTAAA
1 -AATTTTTAGAATTTTTTAA
* *
3077567 AACTTTGCTGGAATTTTTTAA
1 AA-TTT-TTAGAATTTTTTAA
*
3077588 AATTTATTTAGAATTTTTT-T
1 AA-TT-TTTAGAATTTTTTAA
3077608 AA-TTTTAGAATAATTTTTACA
1 AATTTTTAGAAT--TTTTTA-A
*
3077629 ATTTATGTTAGAATTTTT
1 AATT-T-TTAGAATTTTT
3077647 CAAATTTTGA
Statistics
Matches: 283, Mismatches: 57, Indels: 76
0.68 0.14 0.18
Matches are distributed among these distances:
17 8 0.03
18 38 0.13
19 67 0.24
20 83 0.29
21 50 0.18
22 10 0.04
23 4 0.01
24 7 0.02
25 2 0.01
26 14 0.05
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (19 bp):
AATTTTTAGAATTTTTTAA
Found at i:3077602 original size:11 final size:10
Alignment explanation
Indices: 3077242--3077646 Score: 90
Period size: 10 Copynumber: 41.4 Consensus size: 10
3077232 TCCTTAATTA
3077242 TTTTT-GAAT
1 TTTTTAGAAT
* *
3077251 TTTTAAAAAT
1 TTTTTAGAAT
* *
3077261 TTTCTA-AAA
1 TTTTTAGAAT
3077270 TTTTTAGAAT
1 TTTTTAGAAT
3077280 TTTTTA-AA-
1 TTTTTAGAAT
* * *
3077288 TGTTTAAAAA
1 TTTTTAGAAT
*
3077298 TTTTTA-AAA
1 TTTTTAGAAT
* *
3077307 GTTTTAGAGT
1 TTTTTAGAAT
*
3077317 TTTTTCA-AAA
1 TTTTT-AGAAT
*
3077327 TTTTTAAAAT
1 TTTTTAGAAT
3077337 TTTTTA-AAT
1 TTTTTAGAAT
* * *
3077346 ATATTA-AAC
1 TTTTTAGAAT
*
3077355 ATTTTA-AA-
1 TTTTTAGAAT
3077363 TTTTTA-AATT
1 TTTTTAGAA-T
3077373 TTTTTA-AA-
1 TTTTTAGAAT
* * *
3077381 ATTTTAAAAG
1 TTTTTAGAAT
3077391 TTTTTAGAAT
1 TTTTTAGAAT
3077401 TTTTT--AAT
1 TTTTTAGAAT
3077409 TTTTTAAGAAAT
1 TTTTT-AG-AAT
3077421 TTTTTAGAAT
1 TTTTTAGAAT
*
3077431 TCGTTT-GAAT
1 T-TTTTAGAAT
3077441 TTTTT-GAAACT
1 TTTTTAG-AA-T
3077452 TTTTT-GAAAT
1 TTTTTAG-AAT
*
3077462 TATTTTA-TAT
1 T-TTTTAGAAT
*
3077472 TATTTAGAAT
1 TTTTTAGAAT
* * *
3077482 TATTGAAAAT
1 TTTTTAGAAT
*
3077492 TTGTTAGAA-
1 TTTTTAGAAT
3077501 TTTTTA-AAGT
1 TTTTTAGAA-T
* * *
3077511 TGTTGATAAT
1 TTTTTAGAAT
3077521 TTTTT--AAT
1 TTTTTAGAAT
*
3077529 TTTTTTGAATT
1 TTTTTAGAA-T
*
3077540 TTTTTA-ATAA
1 TTTTTAGA-AT
* *
3077550 TTTTTAAAAA
1 TTTTTAGAAT
* *
3077560 TTTTAAAAACT
1 TTTTTAGAA-T
** *
3077571 TTGCTGGAAT
1 TTTTTAGAAT
*
3077581 TTTTTAAAAT
1 TTTTTAGAAT
3077591 TTATTTAGAAT
1 TT-TTTAGAAT
*
3077602 TTTTT-TAA-
1 TTTTTAGAAT
3077610 -TTTTAGAAT
1 TTTTTAGAAT
*
3077619 AATTTTTACAAT
1 --TTTTTAGAAT
3077631 TTATGTTAGAAT
1 TT-T-TTAGAAT
3077643 TTTT
1 TTTT
3077647 CAAATTTTGA
Statistics
Matches: 299, Mismatches: 59, Indels: 75
0.69 0.14 0.17
Matches are distributed among these distances:
7 4 0.01
8 37 0.12
9 57 0.19
10 132 0.44
11 45 0.15
12 24 0.08
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (10 bp):
TTTTTAGAAT
Found at i:3077652 original size:21 final size:20
Alignment explanation
Indices: 3077581--3077653 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 20
3077571 TTGCTGGAAT
3077581 TTTTTAAAATTTAT-TTAGAA
1 TTTTT-AAATTTATGTTAGAA
* * *
3077601 TTTTTTTAATTT-TAG-AATAA
1 -TTTTTAAATTTAT-GTTAGAA
3077621 TTTTTACAATTTATGTTAGAA
1 TTTTTA-AATTTATGTTAGAA
3077642 TTTTTCAAATTT
1 TTTTT-AAATTT
3077654 TGAAAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
19 6 0.15
20 14 0.35
21 19 0.47
22 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTTAAATTTATGTTAGAA
Found at i:3078099 original size:34 final size:34
Alignment explanation
Indices: 3078050--3078129 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 34
3078040 ACATTTTACA
* * **
3078050 GCATTTGTATATGAAAAATGTCACTATATTAATG
1 GCATTTGCATCTGAAAAACATCACTATATTAATG
* **
3078084 GCGTTTGCATCTGAAAAACATTGCTATATTAATG
1 GCATTTGCATCTGAAAAACATCACTATATTAATG
*
3078118 GCATTTGTATCT
1 GCATTTGCATCT
3078130 TTGAAATGCA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (34 bp):
GCATTTGCATCTGAAAAACATCACTATATTAATG
Found at i:3081013 original size:63 final size:60
Alignment explanation
Indices: 3080940--3081303 Score: 191
Period size: 63 Copynumber: 5.8 Consensus size: 60
3080930 TTTAGGTAAA
*
3080940 AAAAACACCTTCAATAATCTCTTAAATTTTTTAGAGAGGATTATTGAAGGTATTTTTTTTGCC
1 AAAAA-ACCTTCAATAATCTCTTAAATTTTTTAGAAAGGATTATTGAAGGTATTTTTTTT--C
* * * *
3081003 AAAAATACCTTCAATAATCCCCTCTAATTTTTTTA-AGAA-GATTATTTG-AGGTGTTTTTTTAC
1 AAAAA-ACCTTCAATAAT-CTCT-TAAATTTTTTAGA-AAGGATTA-TTGAAGGTATTTTTTTTC
* * * * *** **
3081065 AAAAAGCGCATTCAATAATCTTCTTAAA-TTTTGATGAAAAGATTATTGAAAGCGCTTTTGATC
1 AAAAAAC-C-TTCAATAATC-TCTTAAATTTTTTA-GAAAGGATTATTGAAGGTATTTTTTTTC
* * * * * * * *
3081128 AAAAAAGCCTTCAATAATCCCTTCTAATTTTATA-AAAGAAATTATTGATGATGTTTTTTGATC
1 AAAAAA-CCTTCAATAATCTCTT-AAATTTTTTAGAAAG-GATTATTGAAGGTATTTTTT-TTC
* * ** * *
3081191 AAAAATGCCTTCAATAATCATATCCAATTTTTTAGAAGGGATTATTGAAGGTATTTTTTTGTA
1 AAAAA-ACCTTCAATAATC-TCTTAAATTTTTTAGAAAGGATTATTGAAGGTATTTTTTT-TC
* * **
3081254 AAAAAAGGCATTCAATAATCTCCTT-CATTTTTTATGATGGGATTATTGAA
1 AAAAAA--CCTTCAATAATCT-CTTAAATTTTTTA-GAAAGGATTATTGAA
3081304 AGCGTTTTGT
Statistics
Matches: 229, Mismatches: 48, Indels: 47
0.71 0.15 0.15
Matches are distributed among these distances:
61 12 0.05
62 41 0.18
63 111 0.48
64 51 0.22
65 14 0.06
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (60 bp):
AAAAAACCTTCAATAATCTCTTAAATTTTTTAGAAAGGATTATTGAAGGTATTTTTTTTC
Found at i:3081257 original size:125 final size:121
Alignment explanation
Indices: 3080947--3081287 Score: 293
Period size: 125 Copynumber: 2.7 Consensus size: 121
3080937 AAAAAAAACA
*
3080947 CCTTCAATAATCTCTTAAATTTTTTAG-AGAGGATTATTGAAGGTATTTTTTTTGCCAAAAATA-
1 CCTTCAATAATCT-TCAAATTTTTTAGAAG-GGATTATTGAAGGTA-TTTTTTTG-CAAAAA-AG
* ** * *
3081010 CCTTCAATAATCCCCTCTAATTTTTTTAAGAAGATTATTTGAGGTGTTTTTTTACAAAAAG
61 CCTTCAATAATCCCTTCTAATTTTTAAAAGAAGATTATTTGAGATGTTTTTTGACAAAAAG
* ** * **
3081071 CGCATTCAATAATCTTCTTAAA-TTTTGATGAAAAGATTATTGAAAGCG-CTTTTGAT-CAAAAA
1 C-C-TTCAATAATCTTC--AAATTTTTTA-GAAGGGATTATTG-AAG-GTATTTTTTTGCAAAAA
3081133 AGCCTTCAATAATCCCTTCTAATTTTATAAAAGAA-ATTA-TTGATGATGTTTTTTGATCAAAAA
59 AGCCTTCAATAATCCCTTCTAATTTT-TAAAAGAAGATTATTTGA-GATGTTTTTTGA-CAAAAA
3081196 TG
121 -G
* *
3081198 CCTTCAATAATCATATCCAATTTTTTAGAAGGGATTATTGAAGGTATTTTTTTGTAAAAAAAGGC
1 CCTTCAATAATC-T-TCAAATTTTTTAGAAGGGATTATTGAAGGTATTTTTTTG-CAAAAAA-GC
* *
3081263 ATTCAATAATCTCCTTC-ATTTTTTA
62 CTTCAATAATC-CCTTCTAATTTTTA
3081288 TGATGGGATT
Statistics
Matches: 174, Mismatches: 22, Indels: 40
0.74 0.09 0.17
Matches are distributed among these distances:
123 1 0.01
124 14 0.08
125 68 0.39
126 43 0.25
127 38 0.22
128 9 0.05
129 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (121 bp):
CCTTCAATAATCTTCAAATTTTTTAGAAGGGATTATTGAAGGTATTTTTTTGCAAAAAAGCCTTC
AATAATCCCTTCTAATTTTTAAAAGAAGATTATTTGAGATGTTTTTTGACAAAAAG
Found at i:3081991 original size:63 final size:62
Alignment explanation
Indices: 3081848--3082015 Score: 173
Period size: 62 Copynumber: 2.7 Consensus size: 62
3081838 TTTTATGAGC
* * * *
3081848 GATTATTTAAGGTGTTTTTTGCTTGAAACACTTTCAATAAT-CCTTCATAAAAAATTGGAAGA
1 GATTA-TTAAAGTGTTTTTTGCATAAAACACTTTCAATAATCCCTTCATAAAAAATTGAAAGA
* ** *
3081910 GATTATTAAAGACGTTTTTTGCATAAAACACCATCAATAATCCCTTCATAAAAAA-T-AAAGGG
1 GATTATTAAAG-TGTTTTTTGCATAAAACACTTTCAATAATCCCTTCATAAAAAATTGAAA-GA
3081972 GATTATTGAAAGTGTTTTTTTGACCA-AAAACACTTTCAATAATC
1 GATTATT-AAAGTG-TTTTTTG--CATAAAACACTTTCAATAATC
3082016 ATCTAAATTT
Statistics
Matches: 88, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
61 7 0.08
62 39 0.44
63 24 0.27
64 16 0.18
65 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (62 bp):
GATTATTAAAGTGTTTTTTGCATAAAACACTTTCAATAATCCCTTCATAAAAAATTGAAAGA
Found at i:3082101 original size:62 final size:64
Alignment explanation
Indices: 3082030--3082171 Score: 155
Period size: 62 Copynumber: 2.2 Consensus size: 64
3082020 AAATTTTTTA
* * * **
3082030 AGAGAATTATTGAAGGCATTTTCTAT-AGAAAATGCCTTCAATAATTGCTT-T-TATTTTCTATG
1 AGAGGATTATTCAAGGCATTATCTATCA-AAAACACCTTCAATAATTGCTTATCTATTTTCTATG
* * * * *
3082092 AGAGGATTATTCAAAGCATTATCTATCAAAAACACTTTCAATAATTTCTTATCTTTTTTTTATG
1 AGAGGATTATTCAAGGCATTATCTATCAAAAACACCTTCAATAATTGCTTATCTATTTTCTATG
*
3082156 AAAGGATTATTCAAGG
1 AGAGGATTATTCAAGG
3082172 TGTTTTCTGC
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
62 40 0.62
63 2 0.03
64 23 0.35
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (64 bp):
AGAGGATTATTCAAGGCATTATCTATCAAAAACACCTTCAATAATTGCTTATCTATTTTCTATG
Found at i:3084478 original size:314 final size:314
Alignment explanation
Indices: 3083855--3084481 Score: 850
Period size: 314 Copynumber: 2.0 Consensus size: 314
3083845 TGGTCATGAT
* * *
3083855 GTTTTAAAAAATTGTTGTTTTCTTTTATTAGTAGTGGTGAAAATTGGCTTTAGATCTAAAGATCC
1 GTTTTAAAAAATTGTTGTTTTATTTTATTAGTAGTGGTGAAAAATGACTTTAGATCTAAAGATCC
* * *
3083920 ACATATTTGAAAAGGTTACAAAGTACAACAAAACCAAATATTATTGACTAATTATTTTTTAGCAA
66 ACACATTTCAAAAGGTTACAAAGTACAACAAAACCAAATATTATTGACTAATTATTTTTTAGAAA
* *
3083985 GTCAAATCTTTCACTTTCTTTTATTTATTTACGATTGTTTTTGTTGATGATTCATGAGTTACTAC
131 GTCAAATCTTTCACTTTCTTTTATTTATTTACGATTATTTTTGTTGATGATTCATAAGTTACTAC
** * * *
3084050 ATATTGAGACAAGTTTGAACAAATTTAAATATTTCCATTTTTATTTTGAGTTAAACTCAAACTAA
196 ATATCAAGACAAGTTTGAACAAACTTAAATATCTCAATTTTTATTTTGAGTTAAACTCAAACTAA
* * * * *
3084115 AAAATAAAATTTGATGAGTTAGAGTTGAATTTAGAGCCTTGAGTTTGGAGTGAC
261 AAAATAAAATTCGATGAGCTAAAGTTGAATTTAGAACCTTGAATTTGGAGTGAC
* * *
3084169 GTTTTAAAAGATTGTTGTTTTATTTTATTAGTAGTGGTGAAAAATGACTTTAGATCTAAGGATGC
1 GTTTTAAAAAATTGTTGTTTTATTTTATTAGTAGTGGTGAAAAATGACTTTAGATCTAAAGATCC
* * *
3084234 ACACA-TTCAAAGAGGTTATAAAGTACAACAAAACCAAATATTATTGGCTGATTA-TTTTTAGAA
66 ACACATTTCAAA-AGGTTACAAAGTACAACAAAACCAAATATTATTGACTAATTATTTTTTAGAA
** *
3084297 AGTCAAATCTTTTGCTTTCTTTTATTTATTTATGATTATTTTTGTTGATGGA-TCATAAGTTTAC
130 AGTCAAATCTTTCACTTTCTTTTATTTATTTACGATTATTTTTGTTGAT-GATTCATAAG-TTAC
* *** * * * * *
3084361 TTCATATCAAGGTGAGTTTGAGCAAACTTGAGTATCTCAATTTTTATTTTGAG-TAAATTCAAAT
193 TACATATCAAGACAAGTTTGAACAAACTTAAATATCTCAATTTTTATTTTGAGTTAAACTCAAAC
3084425 TAAAAAAACTAAAATTCGATGAGCTAAAGTTGAATTTA-AACCTTGAATTTGGAGTGA
258 T-AAAAAA-TAAAATTCGATGAGCTAAAGTTGAATTTAGAACCTTGAATTTGGAGTGA
3084482 AACTTAAGCT
Statistics
Matches: 272, Mismatches: 36, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
313 74 0.27
314 172 0.63
315 26 0.10
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (314 bp):
GTTTTAAAAAATTGTTGTTTTATTTTATTAGTAGTGGTGAAAAATGACTTTAGATCTAAAGATCC
ACACATTTCAAAAGGTTACAAAGTACAACAAAACCAAATATTATTGACTAATTATTTTTTAGAAA
GTCAAATCTTTCACTTTCTTTTATTTATTTACGATTATTTTTGTTGATGATTCATAAGTTACTAC
ATATCAAGACAAGTTTGAACAAACTTAAATATCTCAATTTTTATTTTGAGTTAAACTCAAACTAA
AAAATAAAATTCGATGAGCTAAAGTTGAATTTAGAACCTTGAATTTGGAGTGAC
Found at i:3084889 original size:21 final size:22
Alignment explanation
Indices: 3084822--3084893 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 22
3084812 GAAAATATGA
*
3084822 ATGTACATATAGTT-TAAATTG
1 ATGTACATATAGTTCTTAATTG
* * * * *
3084843 ATTATACATATATTTCCT-GTTA
1 A-TGTACATATAGTTCTTAATTG
3084865 ATGTACATATA-TTCTTAATTG
1 ATGTACATATAGTTCTTAATTG
3084886 ATGTACAT
1 ATGTACAT
3084894 TTTATACCCA
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 4 0.11
21 20 0.53
22 14 0.37
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (22 bp):
ATGTACATATAGTTCTTAATTG
Found at i:3098983 original size:13 final size:13
Alignment explanation
Indices: 3098965--3098995 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3098955 TCATATTTTT
3098965 CTAAAATGAAACC
1 CTAAAATGAAACC
*
3098978 CTAAAATGAAATC
1 CTAAAATGAAACC
3098991 CTAAA
1 CTAAA
3098996 CTATAAGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (13 bp):
CTAAAATGAAACC
Found at i:3099099 original size:19 final size:20
Alignment explanation
Indices: 3099053--3099106 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
3099043 TTAAAACCCC
3099053 AAATGAAACCCTAAAATCTT
1 AAATGAAACCCTAAAATCTT
* *
3099073 AAGA-GAAACCCT-TAATTTT
1 AA-ATGAAACCCTAAAATCTT
3099092 AAATGAAACCCTAAA
1 AAATGAAACCCTAAA
3099107 CCCTAAGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.04
19 15 0.54
20 11 0.39
21 1 0.04
ACGTcount: A:0.50, C:0.19, G:0.07, T:0.24
Consensus pattern (20 bp):
AAATGAAACCCTAAAATCTT
Found at i:3101508 original size:40 final size:39
Alignment explanation
Indices: 3101464--3101577 Score: 165
Period size: 40 Copynumber: 2.8 Consensus size: 39
3101454 ACTTTTTCAT
*
3101464 ATTTATCCTTTGCTCATCCATCACGGCATTAGTGCTTAAA
1 ATTTATCCTTTGCTCATACATCAC-GCATTAGTGCTTAAA
*
3101504 ATTTACCCTTTGCTCATACATCATCGCATTAGTGCTTAAA
1 ATTTATCCTTTGCTCATACATCA-CGCATTAGTGCTTAAA
* *
3101544 ATTTATCCCTTGCTCATACATCACCGCACTAGTG
1 ATTTATCCTTTGCTCATACATCA-CGCATTAGTG
3101578 GTCCCAACAG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 66 0.99
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.36
Consensus pattern (39 bp):
ATTTATCCTTTGCTCATACATCACGCATTAGTGCTTAAA
Found at i:3112880 original size:21 final size:21
Alignment explanation
Indices: 3112855--3112895 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3112845 GTTGAGCTAG
* * *
3112855 TTTTCTTTTTAATTTTGTGAT
1 TTTTCTATTAAATCTTGTGAT
3112876 TTTTCTATTAAATCTTGTGA
1 TTTTCTATTAAATCTTGTGA
3112896 AAAACTTGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (21 bp):
TTTTCTATTAAATCTTGTGAT
Found at i:3119549 original size:18 final size:19
Alignment explanation
Indices: 3119528--3119572 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3119518 GGAGCTGGGT
3119528 TTAGGGTTT-G-GTTTGAGA
1 TTAGGGTTTAGAGTTTG-GA
3119546 TTA-GGTTTAGAGTTTGGA
1 TTAGGGTTTAGAGTTTGGA
3119564 TTAGGGTTT
1 TTAGGGTTT
3119573 TAAGTAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.21
18 9 0.38
19 10 0.42
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.47
Consensus pattern (19 bp):
TTAGGGTTTAGAGTTTGGA
Found at i:3122906 original size:49 final size:49
Alignment explanation
Indices: 3122811--3122907 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 49
3122801 ATGCATTTTT
* * * ** **
3122811 CATGTATCAATATTTATATTTTTACCAATGACATTTTTGTTGTTTGCTA
1 CATGCATCAATATTTACATTATTACCAATGACATCCTTGTAATTTGCTA
* *
3122860 CATGCATCAATATTTACATTATTAGCAATGGCATCCTTGTAATTTGCT
1 CATGCATCAATATTTACATTATTACCAATGACATCCTTGTAATTTGCT
3122908 TCTGTCACTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.45
Consensus pattern (49 bp):
CATGCATCAATATTTACATTATTACCAATGACATCCTTGTAATTTGCTA
Found at i:3123146 original size:92 final size:91
Alignment explanation
Indices: 3122930--3123117 Score: 245
Period size: 92 Copynumber: 2.1 Consensus size: 91
3122920 ATTTTCCATA
* * * * * * *
3122930 AAACC-CCAAATTCCAAACCTTAAACCTTAAACCACCCATGAAACCTTCACTCACCCATGCTATG
1 AAACCACCAAATTCAAAACCTAAAACCCTAAATCACCCATGAAACCTTCAATCACCCATACCATG
3122994 AAACCATAAATCCTCCTTGAAAACCT
66 AAACCATAAATCCTCCTTGAAAACCT
* * * *
3123020 AATCCACCTAAATTCCAAACCTTAAACCCTAAATCACCTATGAAACCTTCAATCACCCATACCAT
1 AAACCACC-AAATTCAAAACCTAAAACCCTAAATCACCCATGAAACCTTCAATCACCCATACCAT
*
3123085 G-AACCATAAATCCTCCTTGAAACCCT
65 GAAACCATAAATCCTCCTTGAAAACCT
3123111 AAACCAC
1 AAACCAC
3123118 ACTTAAAACA
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
90 4 0.05
91 32 0.37
92 51 0.59
ACGTcount: A:0.39, C:0.36, G:0.04, T:0.21
Consensus pattern (91 bp):
AAACCACCAAATTCAAAACCTAAAACCCTAAATCACCCATGAAACCTTCAATCACCCATACCATG
AAACCATAAATCCTCCTTGAAAACCT
Found at i:3123160 original size:7 final size:6
Alignment explanation
Indices: 3123148--3123201 Score: 58
Period size: 6 Copynumber: 8.8 Consensus size: 6
3123138 CATGAAATCT
3123148 TAAACCC TAAACC -AAACC TAAACCC TAAA-C TAAACC TAAACCC TAAACC
1 TAAA-CC TAAACC TAAACC TAAA-CC TAAACC TAAACC TAAA-CC TAAACC
*
3123197 AAAAC
1 TAAAC
3123202 TTAGACCCCA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.24
6 16 0.38
7 16 0.38
ACGTcount: A:0.52, C:0.35, G:0.00, T:0.13
Consensus pattern (6 bp):
TAAACC
Found at i:3123169 original size:11 final size:12
Alignment explanation
Indices: 3123148--3123201 Score: 58
Period size: 13 Copynumber: 4.4 Consensus size: 12
3123138 CATGAAATCT
3123148 TAAACCCTAAACC
1 TAAA-CCTAAACC
3123161 -AAACCTAAACCC
1 TAAACCTAAA-CC
3123173 TAAA-CTAAACC
1 TAAACCTAAACC
3123184 TAAACCCTAAACC
1 TAAA-CCTAAACC
*
3123197 AAAAC
1 TAAAC
3123202 TTAGACCCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
11 12 0.33
12 11 0.31
13 13 0.36
ACGTcount: A:0.52, C:0.35, G:0.00, T:0.13
Consensus pattern (12 bp):
TAAACCTAAACC
Found at i:3123171 original size:18 final size:18
Alignment explanation
Indices: 3123148--3123249 Score: 107
Period size: 18 Copynumber: 5.6 Consensus size: 18
3123138 CATGAAATCT
3123148 TAAACCCTAAACCAAACC
1 TAAACCCTAAACCAAACC
*
3123166 TAAACCCTAAACTAAACC
1 TAAACCCTAAACCAAACC
*
3123184 TAAACCCTAAACCAAAACT
1 TAAACCCTAAACC-AAACC
* * *
3123203 TAGACCCCAAA-CTAACC
1 TAAACCCTAAACCAAACC
* *
3123220 TTAAACCCTAATCTAAATCC
1 -TAAACCCTAAACCAAA-CC
3123240 TAAACCCTAA
1 TAAACCCTAA
3123250 CTTAGACCCA
Statistics
Matches: 68, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
17 3 0.04
18 38 0.56
19 25 0.37
20 2 0.03
ACGTcount: A:0.47, C:0.34, G:0.01, T:0.18
Consensus pattern (18 bp):
TAAACCCTAAACCAAACC
Found at i:3123225 original size:37 final size:37
Alignment explanation
Indices: 3123146--3123246 Score: 125
Period size: 37 Copynumber: 2.7 Consensus size: 37
3123136 CCCATGAAAT
*
3123146 CTTAAACCCTAAACCAAACCTAAACCCTAAACTAAAC
1 CTTAAACCCTAAACCAAACCTAAACCCCAAACTAAAC
* *
3123183 C-TAAACCCTAAACCAAAACTTAGACCCCAAACT-AAC
1 CTTAAACCCTAAACC-AAACCTAAACCCCAAACTAAAC
* *
3123219 CTTAAACCCTAATCTAAATCCTAAACCC
1 CTTAAACCCTAAACCAAA-CCTAAACCC
3123247 TAACTTAGAC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
36 20 0.37
37 34 0.63
ACGTcount: A:0.46, C:0.36, G:0.01, T:0.18
Consensus pattern (37 bp):
CTTAAACCCTAAACCAAACCTAAACCCCAAACTAAAC
Found at i:3123270 original size:28 final size:29
Alignment explanation
Indices: 3123238--3123293 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
3123228 TAATCTAAAT
*
3123238 CCTAAACCCTAACTTAGACCC-AAACCAA
1 CCTAAACCCTAACCTAGACCCTAAACCAA
3123266 CCTAAACCCTAACCTAGACCCTAAACCA
1 CCTAAACCCTAACCTAGACCCTAAACCA
3123294 CCCCTTGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.41, C:0.41, G:0.04, T:0.14
Consensus pattern (29 bp):
CCTAAACCCTAACCTAGACCCTAAACCAA
Found at i:3123860 original size:13 final size:13
Alignment explanation
Indices: 3123842--3123869 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3123832 TTTTCGATGG
3123842 GTAGTTAATTTTT
1 GTAGTTAATTTTT
3123855 GTAGTTAATTTTT
1 GTAGTTAATTTTT
3123868 GT
1 GT
3123870 TATTTGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (13 bp):
GTAGTTAATTTTT
Found at i:3123957 original size:17 final size:16
Alignment explanation
Indices: 3123935--3123976 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
3123925 TAAAACATTG
3123935 GAAATTATTTATTATTT
1 GAAATTATTTATTA-TT
*
3123952 GAAATTGTTTATTATT
1 GAAATTATTTATTATT
*
3123968 AAAATTATT
1 GAAATTATT
3123977 AATGTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (16 bp):
GAAATTATTTATTATT
Found at i:3127537 original size:23 final size:23
Alignment explanation
Indices: 3127484--3127537 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
3127474 AGTTTTTTAC
* *
3127484 TAAAATTTTTTTAATCATAACTA
1 TAAAAATTTTTTAATCACAACTA
* * *
3127507 CAATAATTTTTTAATCACAATTA
1 TAAAAATTTTTTAATCACAACTA
3127530 TAAAAATT
1 TAAAAATT
3127538 ATTATTATTA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAAAATTTTTTAATCACAACTA
Found at i:3128495 original size:21 final size:21
Alignment explanation
Indices: 3128455--3128506 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
3128445 AATAATTTTT
* * *
3128455 AAATAAGATTATTTGGTAAAC
1 AAATAAAATTATTTAGTAAAA
* *
3128476 AACTAAAATTATTTATTAAAA
1 AAATAAAATTATTTAGTAAAA
3128497 AAATAAAATT
1 AAATAAAATT
3128507 TATAATTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (21 bp):
AAATAAAATTATTTAGTAAAA
Found at i:3128778 original size:21 final size:20
Alignment explanation
Indices: 3128748--3128787 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3128738 AGTTATAATT
*
3128748 TGAATAAATTTAAAATTATC
1 TGAATAAATTAAAAATTATC
3128768 TGAATTAAATTAAAAATTAT
1 TGAA-TAAATTAAAAATTAT
3128788 TTATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (20 bp):
TGAATAAATTAAAAATTATC
Found at i:3128879 original size:2 final size:2
Alignment explanation
Indices: 3128867--3128901 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3128857 ATGTATGTTG
*
3128867 AT AT AT A- AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3128902 TAGATTTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3134497 original size:22 final size:22
Alignment explanation
Indices: 3134469--3134512 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3134459 CTAAATCTTC
*
3134469 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
3134491 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
3134513 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:3137975 original size:18 final size:18
Alignment explanation
Indices: 3137949--3137983 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3137939 TAATCCATGA
*
3137949 GAACCAGAAGCTTTACCT
1 GAACCAGAAACTTTACCT
*
3137967 GAACTAGAAACTTTACC
1 GAACCAGAAACTTTACC
3137984 CAAAGAACAT
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:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (18 bp):
GAACCAGAAACTTTACCT
Found at i:3138214 original size:23 final size:25
Alignment explanation
Indices: 3138159--3138217 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
3138149 AAAGGGTTCG
* * *
3138159 GCAATGAAGGCCTAAACAGGATTCG
1 GCAATGAAGGCCTAAACAGAAGTCA
3138184 GCAATGAAGGCCTAAA-A-AAGTCA
1 GCAATGAAGGCCTAAACAGAAGTCA
3138207 GCAATGAAGGC
1 GCAATGAAGGC
3138218 TGAAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 14 0.45
24 1 0.03
25 16 0.52
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.14
Consensus pattern (25 bp):
GCAATGAAGGCCTAAACAGAAGTCA
Found at i:3138392 original size:22 final size:22
Alignment explanation
Indices: 3138364--3138407 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3138354 CTAAATCTTC
*
3138364 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
3138386 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
3138408 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:3142929 original size:19 final size:19
Alignment explanation
Indices: 3142907--3142945 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3142897 ACATGACAAG
* *
3142907 ATTAATCAATTTAGACACA
1 ATTAACCAATTTAAACACA
*
3142926 ATTAACCCATTTAAACACA
1 ATTAACCAATTTAAACACA
3142945 A
1 A
3142946 ATAAGTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.21, G:0.03, T:0.28
Consensus pattern (19 bp):
ATTAACCAATTTAAACACA
Found at i:3143605 original size:53 final size:52
Alignment explanation
Indices: 3143494--3143605 Score: 163
Period size: 53 Copynumber: 2.1 Consensus size: 52
3143484 GTTCTTGTAC
*
3143494 GGATAAAATATGTGATATAGAGGTAGAAGAAAATCTTACAACAGTTCTTACAG
1 GGATAAAATATGTGATATAGAGGTAGAAGAAAATCTTACAACAG-TCTTAAAG
*
3143547 GGATAAAATATGTGATCTAGAGGTAGAAGAAAATCTTACAAACAG-CTTGAAAG
1 GGATAAAATATGTGATATAGAGGTAGAAGAAAATCTTAC-AACAGTCTT-AAAG
*
3143600 TGATAA
1 GGATAA
3143606 TTTACTTTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
52 3 0.06
53 46 0.85
54 5 0.09
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (52 bp):
GGATAAAATATGTGATATAGAGGTAGAAGAAAATCTTACAACAGTCTTAAAG
Found at i:3144785 original size:2 final size:2
Alignment explanation
Indices: 3144778--3144813 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3144768 GGAGAGGTGA
3144778 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3144814 GAAGTAAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3146417 original size:24 final size:27
Alignment explanation
Indices: 3146388--3146444 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 27
3146378 GCTCTTGAAA
3146388 TTTATAATTTTATT-T-AAATAAAT-T
1 TTTATAATTTTATTATAAAATAAATAT
*
3146412 TTTATAGTTTTATTATACAAATAAATAT
1 TTTATAATTTTATTATA-AAATAAATAT
3146440 TTTAT
1 TTTAT
3146445 TTTTAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 13 0.46
25 1 0.04
27 8 0.29
28 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTATAATTTTATTATAAAATAAATAT
Found at i:3146466 original size:30 final size:29
Alignment explanation
Indices: 3146387--3146532 Score: 126
Period size: 30 Copynumber: 5.0 Consensus size: 29
3146377 AGCTCTTGAA
* *
3146387 ATTTATAATTT-TATTTAAATAAATTTTT
1 ATTTTTAATTTATATCTAAATAAATTTTT
3146415 ATAGTTTT-A-TTATA-C-AAATAAATATTTT
1 AT--TTTTAATTTATATCTAAATAAAT-TTTT
*
3146443 ATTTTTAATTTATATCTAAATAAATTTGTA
1 ATTTTTAATTTATATCTAAATAAATTT-TT
*
3146473 ACTTTTAATTTATAT-TCAAATAAATTTTT
1 ATTTTTAATTTATATCT-AAATAAATTTTT
* *
3146502 AATCTATAATTTATA-CTTAAATAAATTTTT
1 -ATTTTTAATTTATATC-TAAATAAATTTTT
3146532 A
1 A
3146533 ATATAAATTA
Statistics
Matches: 97, Mismatches: 8, Indels: 25
0.75 0.06 0.19
Matches are distributed among these distances:
26 4 0.04
27 9 0.09
28 15 0.15
29 9 0.09
30 59 0.61
31 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (29 bp):
ATTTTTAATTTATATCTAAATAAATTTTT
Found at i:3146479 original size:56 final size:59
Alignment explanation
Indices: 3146390--3146529 Score: 157
Period size: 60 Copynumber: 2.4 Consensus size: 59
3146380 TCTTGAAATT
* * * *
3146390 TATAATTT-TATTTAAATAAATTTTTATAGTTTT-A-TTATA-CAAATAAATATTTT-ATT
1 TATAATTTATACTTAAATAAATTTGTA-ACTTTTAATTTATATCAAATAAAT-TTTTAATC
*
3146446 TTTAATTTATA-TCTAAATAAATTTGTAACTTTTAATTTATATTCAAATAAATTTTTAATC
1 TATAATTTATACT-TAAATAAATTTGTAACTTTTAATTTATA-TCAAATAAATTTTTAATC
3146506 TATAATTTATACTTAAATAAATTT
1 TATAATTTATACTTAAATAAATTT
3146530 TTAATATAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 12
0.81 0.06 0.14
Matches are distributed among these distances:
56 13 0.18
57 16 0.23
58 5 0.07
59 4 0.06
60 32 0.45
61 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (59 bp):
TATAATTTATACTTAAATAAATTTGTAACTTTTAATTTATATCAAATAAATTTTTAATC
Found at i:3154766 original size:21 final size:21
Alignment explanation
Indices: 3154742--3154804 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
3154732 AAAAACCATG
*
3154742 AATTTAAAACCCCAAATCCTA
1 AATTTAAAACCCCAAACCCTA
* *
3154763 AA-TTAAAA-TCCTAACCCTA
1 AATTTAAAACCCCAAACCCTA
*
3154782 AATCTT-AAACCCTAAACCCTA
1 AAT-TTAAAACCCCAAACCCTA
3154803 AA
1 AA
3154805 CCTAAACTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
19 10 0.30
20 9 0.27
21 14 0.42
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.24
Consensus pattern (21 bp):
AATTTAAAACCCCAAACCCTA
Found at i:3154898 original size:8 final size:8
Alignment explanation
Indices: 3154876--3154920 Score: 62
Period size: 8 Copynumber: 6.1 Consensus size: 8
3154866 CTTAAACCTT
3154876 AACCCT-A
1 AACCCTAA
3154883 AA-CCTAA
1 AACCCTAA
3154890 AACCCT-A
1 AACCCTAA
3154897 AA-CCTAA
1 AACCCTAA
3154904 AACCCTAA
1 AACCCTAA
3154912 AACCCTAA
1 AACCCTAA
3154920 A
1 A
3154921 TCCTACCTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
6 6 0.18
7 11 0.32
8 17 0.50
ACGTcount: A:0.51, C:0.36, G:0.00, T:0.13
Consensus pattern (8 bp):
AACCCTAA
Found at i:3154935 original size:7 final size:7
Alignment explanation
Indices: 3154775--3154912 Score: 115
Period size: 7 Copynumber: 20.3 Consensus size: 7
3154765 TTAAAATCCT
*
3154775 AACCCTA
1 AACCTTA
*
3154782 AATCTTA
1 AACCTTA
*
3154789 AACCCTA
1 AACCTTA
*
3154796 AACCCTA
1 AACCTTA
3154803 AACC-TA
1 AACCTTA
3154809 AA-CTTA
1 AACCTTA
*
3154815 AACCCT-
1 AACCTTA
3154821 AACCTTA
1 AACCTTA
*
3154828 AACATTAA
1 AACCTT-A
*
3154836 AACC-AA
1 AACCTTA
3154842 AACCTTA
1 AACCTTA
*
3154849 AATCTTA
1 AACCTTA
3154856 AACCTTA
1 AACCTTA
3154863 AACCTTA
1 AACCTTA
3154870 AACCTT-
1 AACCTTA
*
3154876 AACCCTA
1 AACCTTA
*
3154883 AACCTAA
1 AACCTTA
*
3154890 AACCCTA
1 AACCTTA
*
3154897 AACCTAA
1 AACCTTA
*
3154904 AACCCTA
1 AACCTTA
3154911 AA
1 AA
3154913 ACCCTAAATC
Statistics
Matches: 104, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
5 1 0.01
6 23 0.22
7 76 0.73
8 4 0.04
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (7 bp):
AACCTTA
Found at i:3155991 original size:16 final size:16
Alignment explanation
Indices: 3155970--3156000 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3155960 AAATTTTGAA
3155970 AAAAAATAAAAAATGG
1 AAAAAATAAAAAATGG
3155986 AAAAAATAAAAAATG
1 AAAAAATAAAAAATG
3156001 TTTTGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (16 bp):
AAAAAATAAAAAATGG
Found at i:3156095 original size:65 final size:60
Alignment explanation
Indices: 3155968--3156098 Score: 138
Period size: 65 Copynumber: 2.1 Consensus size: 60
3155958 GAAAATTTTG
*
3155968 AAAAAAAATAAAAAATGGAAAAAATAAAAAATGTTTTGATTTTAATTTCCCCGTTTTCAAA
1 AAAAAAAATAAAAAATGGAAAAAATAAAAAATGTTTTGATTTTAATTTCCCCG-TTTAAAA
* * ** **
3156029 AAAGAAAATAAAATAAATTGAAAAAATGAAAATGGTGTTTTGATTTTAATTTCTTTC-TTTAAAA
1 AAAAAAAAT-AAA-AAATGGAAAAAAT-AAAA-AATGTTTTGATTTTAATTTC-CCCGTTTAAAA
3156093 AAAAAA
1 AAAAAA
3156099 TGTGTGTGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
61 8 0.14
62 3 0.05
63 12 0.21
64 15 0.26
65 18 0.32
66 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (60 bp):
AAAAAAAATAAAAAATGGAAAAAATAAAAAATGTTTTGATTTTAATTTCCCCGTTTAAAA
Found at i:3156150 original size:25 final size:25
Alignment explanation
Indices: 3156122--3156176 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
3156112 CAATTCATGC
*
3156122 ATATTTTAATTATGTCATTTCATT-T
1 ATATTTTAATTATGTCAATT-ATTAT
3156147 ATATTTTAATTATGTCAATTATTAT
1 ATATTTTAATTATGTCAATTATTAT
3156172 ATATT
1 ATATT
3156177 GTTGTTACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 3 0.11
25 25 0.89
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (25 bp):
ATATTTTAATTATGTCAATTATTAT
Found at i:3157063 original size:38 final size:38
Alignment explanation
Indices: 3157001--3157075 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
3156991 GATTGAGAAT
** *
3157001 AATAAGATAATACATGTACCTTATCTCATGCTCATCAA
1 AATAAGATAATACATCCACCTTATCTCATGCACATCAA
** *
3157039 AATAAGATAATACATCCATTTTATCTTATGCACATCA
1 AATAAGATAATACATCCACCTTATCTCATGCACATCA
3157076 TAGATAGTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (38 bp):
AATAAGATAATACATCCACCTTATCTCATGCACATCAA
Found at i:3157087 original size:34 final size:34
Alignment explanation
Indices: 3157043--3157107 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
3157033 CATCAAAATA
*
3157043 AGATAATACATCCATTTTATCTT-ATGCACATCAT
1 AGATAATACATCCATTCTAT-TTCATGCACATCAT
* *
3157077 AGATAGTACATGCATTCTATTTCATGCACAT
1 AGATAATACATCCATTCTATTTCATGCACAT
3157108 GTTAATAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 2 0.07
34 25 0.93
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (34 bp):
AGATAATACATCCATTCTATTTCATGCACATCAT
Found at i:3157150 original size:37 final size:37
Alignment explanation
Indices: 3157043--3157152 Score: 95
Period size: 37 Copynumber: 3.1 Consensus size: 37
3157033 CATCAAAATA
* * *
3157043 AGATAATACATCCATTTTATCTT-ATGCACATC---AT
1 AGATAGTACATACATTCTAT-TTCATGCACATCTTAAT
* *
3157077 AGATAGTACATGCATTCTATTTCATGCACATGTTAAT
1 AGATAGTACATACATTCTATTTCATGCACATCTTAAT
* **
3157114 AGATGGTACATACATTCT-TTCTCATGCATGTCTTAAT
1 AGATAGTACATACATTCTATT-TCATGCACATCTTAAT
3157151 AG
1 AG
3157153 GTAACACATG
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
33 2 0.03
34 25 0.40
36 2 0.03
37 33 0.53
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (37 bp):
AGATAGTACATACATTCTATTTCATGCACATCTTAAT
Found at i:3163063 original size:2 final size:2
Alignment explanation
Indices: 3163058--3163088 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3163048 AAATCCTGTC
3163058 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3163089 TTTAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3180195 original size:160 final size:160
Alignment explanation
Indices: 3179895--3180198 Score: 379
Period size: 160 Copynumber: 1.9 Consensus size: 160
3179885 CAACCAACGG
*
3179895 ATAGGTAAGAAAATTAAAAAATACAAGTCTATACTAATGGATGTTAAGTGTTGGTATAAGTAAAG
1 ATAGGTAAGAAAATTAAAAAATACAAGTCTATACAAATGGATGTTAAGTGTTGGTATAAGTAAAG
* * * * *
3179960 AAAATTATAAGTCTATATTAACGAATGTTAACTATTATTATAAGTAAAAATAATTAAAACATACA
66 AAAATTATAAATATATATTAACGAACGTTAACCATCATTATAAGTAAAAATAATTAAAACATACA
3180025 AGTCTATACTGACAACCGTTAACTGCTGGT
131 AGTCTATACTGACAACCGTTAACTGCTGGT
* *
3180055 ATAGGTAAGAAAATTAAAACATACAAGTCTATACAAAT-GAGTTTTAAGCT-TTGGTATAAGT-A
1 ATAGGTAAGAAAATTAAAAAATACAAGTCTATACAAATGGA-TGTTAAG-TGTTGGTATAAGTAA
* * *
3180117 AGAAAAATTATAAATATATATACTGAC-AAGCGTTAACCATCA-TATAGGTAAGAAA-AATTCAA
64 AG-AAAATTATAAATATATAT--TAACGAA-CGTTAACCATCATTATAAGTAA-AAATAATTAAA
* *
3180179 ACATATAA-TTTATACTGACA
124 ACATACAAGTCTATACTGACA
3180199 GGTGCTAACT
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
159 5 0.04
160 80 0.65
161 24 0.19
162 15 0.12
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.30
Consensus pattern (160 bp):
ATAGGTAAGAAAATTAAAAAATACAAGTCTATACAAATGGATGTTAAGTGTTGGTATAAGTAAAG
AAAATTATAAATATATATTAACGAACGTTAACCATCATTATAAGTAAAAATAATTAAAACATACA
AGTCTATACTGACAACCGTTAACTGCTGGT
Found at i:3183438 original size:18 final size:19
Alignment explanation
Indices: 3183417--3183455 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
3183407 TTTTATTTCA
3183417 TCTTTTCA-TTT-TTTTCTT
1 TCTTTTCACTTTATTTT-TT
3183435 TCTTTTCACTTTATTTTTT
1 TCTTTTCACTTTATTTTTT
3183454 TC
1 TC
3183456 ATTCTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (19 bp):
TCTTTTCACTTTATTTTTT
Found at i:3187335 original size:55 final size:53
Alignment explanation
Indices: 3187269--3187400 Score: 131
Period size: 55 Copynumber: 2.4 Consensus size: 53
3187259 GACTTATATA
* ** * *
3187269 TTTTAATTTTTCTTATCTATACAGACTCTTAGCA-TTTGTCAGTATAAAATTGTATT
1 TTTTAA-TTTTCTTA-CTATAC-GACGCTTAG-AGACTGTCAATATAAAATTGTATG
*
3187325 TTTTAATTTTCTTACTTATATCGACGGTTAGAGACTGTCAATATAAAATTGTATG
1 TTTTAATTTTCTTAC-TATA-CGACGCTTAGAGACTGTCAATATAAAATTGTATG
*
3187380 CTTTAATTTTCTTACCTATAC
1 TTTTAATTTTCTTA-CTATAC
3187401 CAACGGTTAG
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
54 3 0.05
55 54 0.83
56 8 0.12
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.48
Consensus pattern (53 bp):
TTTTAATTTTCTTACTATACGACGCTTAGAGACTGTCAATATAAAATTGTATG
Found at i:3187407 original size:55 final size:55
Alignment explanation
Indices: 3187305--3187413 Score: 164
Period size: 55 Copynumber: 2.0 Consensus size: 55
3187295 TCTTAGCATT
* ** * * *
3187305 TGTCAGTATAAAATTGTATTTTTTAATTTTCTTACTTATATCGACGGTTAGAGAC
1 TGTCAATATAAAATTGTATGCTTTAATTTTCTTACCTATACCAACGGTTAGAGAC
3187360 TGTCAATATAAAATTGTATGCTTTAATTTTCTTACCTATACCAACGGTTAGAGA
1 TGTCAATATAAAATTGTATGCTTTAATTTTCTTACCTATACCAACGGTTAGAGA
3187414 TTGTTTGTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (55 bp):
TGTCAATATAAAATTGTATGCTTTAATTTTCTTACCTATACCAACGGTTAGAGAC
Found at i:3195526 original size:65 final size:62
Alignment explanation
Indices: 3195441--3195592 Score: 144
Period size: 65 Copynumber: 2.4 Consensus size: 62
3195431 TACAAAAAAT
* * * * **
3195441 TAAATGGGGTTATTGAAGGCATTTCAAGGC-CAAAAATACCTTGAATAATTTTTTTCTAAATTTT
1 TAAA-GGGATTATTCAAGGCATTT--AGGCTAAAAAATACCTTCAATAATCCTTTTC--AATTTT
3195505 TA
61 TA
* *
3195507 TAAAGGGATTATTCAAGGCATGTTTGGCTAAAAAATGCCTTCAATAATCCTTTTCAATTTTTA
1 TAAAGGGATTATTCAAGGCAT-TTAGGCTAAAAAATACCTTCAATAATCCTTTTCAATTTTTA
* **
3195570 TGAAGTAATTATTCAAGGCATTT
1 TAAAGGGATTATTCAAGGCATTT
3195593 TTGCCTAAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
62 2 0.03
63 26 0.36
64 3 0.04
65 36 0.49
66 6 0.08
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (62 bp):
TAAAGGGATTATTCAAGGCATTTAGGCTAAAAAATACCTTCAATAATCCTTTTCAATTTTTA
Found at i:3195601 original size:63 final size:64
Alignment explanation
Indices: 3195472--3195617 Score: 179
Period size: 63 Copynumber: 2.3 Consensus size: 64
3195462 TTTCAAGGCC
* ** * *
3195472 AAAAATACCTTGAATAATTTTTTTCTAAATTTTTATAAAGGGATTATTCAAGGCATGTTTGGCTA
1 AAAAATGCCTTGAATAATCCTTTTC-AAATTTTTATAAAGGAATTATTCAAGGCATGTTTGCCTA
* * * *
3195537 AAAAATGCCTTCAATAATCCTTTTC-AATTTTTATGAAGTAATTATTCAAGGCATTTTTGCCTA
1 AAAAATGCCTTGAATAATCCTTTTCAAATTTTTATAAAGGAATTATTCAAGGCATGTTTGCCTA
*
3195600 AAAAACG-CTTGAATAATC
1 AAAAATGCCTTGAATAATC
3195618 ACTTACAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
62 10 0.14
63 39 0.56
65 21 0.30
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (64 bp):
AAAAATGCCTTGAATAATCCTTTTCAAATTTTTATAAAGGAATTATTCAAGGCATGTTTGCCTA
Found at i:3195617 original size:190 final size:186
Alignment explanation
Indices: 3195264--3195693 Score: 460
Period size: 190 Copynumber: 2.3 Consensus size: 186
3195254 TGGCATTTGA
* * * *
3195264 TTATTCAAGGCATTTACGGCCAAAAACACCTTGAATAATCTTCAAAATTTTTTTATAGAGGATTA
1 TTATTAAAGGCATTTAAGGCCAAAAACACCTTGAATAATCTTCAAAATTTTTATAAAGAGGATTA
* * * * *
3195329 TTGAAGGCATTTTTTGTCAAAAACGCCTTCAATAATCCCTCATTTTTTATGAAGGAGATTATTCA
66 TTCAAGGCATGTTTGGTAAAAAACGCCTTCAATAATCCCTCAATTTTTATGAAGGAGATTATTCA
** * * * *
3195394 AGGTGTTTTAGCCCATAAATCACTTTTAATAATC-CTTTACAAAAAATTAAATGGGG
131 AGGCATTTTAGCCCAAAAAACACTTTGAATAATCAC-TTACAAAAAATTAAATGAGG
* * * *
3195450 TTATTGAAGGCATTTCAAGGCCAAAAATACCTTGAATAATTTTTTTCTAAATTTTTATAAAG-GG
1 TTATTAAAGGCATTT-AAGGCCAAAAACACCTTGAATAA---TCTTCAAAATTTTTATAAAGAGG
* * *
3195514 ATTATTCAAGGCATGTTTGGCTAAAAAATGCCTTCAATAATCCTTTTCAATTTTTATGAAGTA-A
62 ATTATTCAAGGCATGTTTGG-TAAAAAACGCCTTCAATAATCC--CTCAATTTTTATGAAGGAGA
* * *
3195578 TTATTCAAGGCATTTTTGCCTAAAAAACGC-TTGAATAATCACTTACAAAAAATTAAATGAGG
124 TTATTCAAGGCATTTTAGCCCAAAAAACACTTTGAATAATCACTTACAAAAAATTAAATGAGG
* * *
3195640 TTATTAAAGGCCTTCTAA--CCAGAAACACTTTGAATAATC-TCATTAAATTTTTAT
1 TTATTAAAGGCATT-TAAGGCCAAAAACACCTTGAATAATCTTCA--AAATTTTTAT
3195694 GAGTAGATTA
Statistics
Matches: 202, Mismatches: 31, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
184 2 0.01
185 1 0.00
186 24 0.12
187 21 0.10
188 16 0.08
189 19 0.09
190 78 0.39
191 26 0.13
192 15 0.07
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (186 bp):
TTATTAAAGGCATTTAAGGCCAAAAACACCTTGAATAATCTTCAAAATTTTTATAAAGAGGATTA
TTCAAGGCATGTTTGGTAAAAAACGCCTTCAATAATCCCTCAATTTTTATGAAGGAGATTATTCA
AGGCATTTTAGCCCAAAAAACACTTTGAATAATCACTTACAAAAAATTAAATGAGG
Found at i:3201279 original size:20 final size:20
Alignment explanation
Indices: 3201250--3201290 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
3201240 CTTTTCTCTC
3201250 TTTTATTTTTTTGCTCTTTTT
1 TTTTATTTTTTTGC-CTTTTT
3201271 TTTTATTTTTTTGCCTTTTT
1 TTTTATTTTTTTGCCTTTTT
3201291 CTTAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.80
Consensus pattern (20 bp):
TTTTATTTTTTTGCCTTTTT
Found at i:3202140 original size:12 final size:12
Alignment explanation
Indices: 3202124--3202165 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
3202114 TTTGCTATTT
3202124 TTTTTCATTTTTG
1 TTTTT-ATTTTTG
*
3202137 TTTTTATTTTTA
1 TTTTTATTTTTG
3202149 TTTTTATTTTTG
1 TTTTTATTTTTG
*
3202161 GTTTT
1 TTTTT
3202166 GTTAGATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.10, C:0.02, G:0.07, T:0.81
Consensus pattern (12 bp):
TTTTTATTTTTG
Found at i:3202146 original size:5 final size:6
Alignment explanation
Indices: 3202124--3202159 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
3202114 TTTGCTATTT
*
3202124 TTTTTCA TTTTTG TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTT-A TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
3202160 GGTTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:3203396 original size:231 final size:232
Alignment explanation
Indices: 3202536--3203488 Score: 774
Period size: 235 Copynumber: 4.0 Consensus size: 232
3202526 TTGGTGGGAA
** * * * * *
3202536 GTGACGTTATAATTTTGTCACCAATTTAAAATTTTATCTATGA-CAATTTT-TTTGATAGATTTT
1 GTGACGTTATAATTTCATCACCAATTTAAAATTTTATCTGTGATGAATTTTATCTAATAAATTTT
* * ** **
3202599 AGGA-AGCGTTATTAATTTTTGTCACAAATTGAACACTTTAGTTAACTATTAACAACATTGCAAT
66 A-GATA--GTTATTAATTTTT-TCACAAATTGAACACTTTACTCAACTATTAATGACATTAAAAT
** ** * * * * * **
3202663 TTAATCACGTTAATGTATGGTGGTATCTAATGATAACATAAATGTCACAAACTTTTACTGCCAAA
127 TTTGTCAAATCAATGTATGGTGTTATATGATGATAACATAAATCTCACAAACTTTTACCACCAAA
* * * * *
3202728 TTTATTTGGTGAAAAATTTTTTTGTGATATTTTTTTATTTTAG
192 -TAATTTGATGAGAAATTTTTTTATGACA-TTTTTTATTTTAG
* * ** ** * * * *
3202771 ATGATGTT-TAAATTTTGTCATTAATTTAAAATTCTATTTGTGACT-AATTTTTTCTAATAGATT
1 GTGACGTTAT-AATTTCATCACCAATTTAAAATTTTATCTGTGA-TGAATTTTATCTAATAAATT
* * * * * * * **
3202834 TTAGGTGACATTATCAATTTTTGTCACAAATGGAACACTTTAGTTAACTATTAATAACATTGCAA
64 TTAGAT-A-GTTATTAATTTTT-TCACAAATTGAACACTTTACTCAACTATTAATGACATTAAAA
** * * * * * * *
3202899 TTTCATCACCATTATTTTATGGTATTATATGATGATAACATAAATGTCACAAACTTTTACCATCA
126 TTTTGTCA-AATCAATGTATGGTGTTATATGATGATAACATAAATCTCACAAACTTTTACCACCA
* * * * *** *
3202964 ATTTTATTTGGTTA-AAATTTTTTTGTGATGTTTTTTTTTTTTTATTTTAA
190 A-ATAATTTGATGAGAAA-TTTTTT-T-ATG----ACATTTTTTATTTTAG
* * * * *
3203014 GTGAAGTTATAATTTCATCACTAATTTAAAATTTTATCTGTGATGAATTTTTTCTGATAGATTTT
1 GTGACGTTATAATTTCATCACCAATTTAAAATTTTATCTGTGATGAATTTTATCTAATAAATTTT
* * * **
3203079 AGATGACGTTATTAATTTTTTTACAAATTGAATATTTTACTCAACTATTAATGACATTGCAATTT
66 AGAT-A-GTTATTAATTTTTTCACAAATTGAACACTTTACTCAACTATTAATGACATTAAAATTT
** *
3203144 TGTCACTTCAATGTATGGTGTTATATGATGATAACATAAATCTCACAAATTTTTACCACCAAATT
129 TGTCAAATCAATGTATGGTGTTATATGATGATAACATAAATCTCACAAACTTTTACCACCAAA-T
*
3203209 TATTTGATGAGAAATTTTTTTATGACATTTTTTATTTTAG
193 AATTTGATGAGAAATTTTTTTATGACATTTTTTATTTTAG
* ** *
3203249 GTGACGTTGTAATTTTGTCACCAATTTAAAATTTTGTCTGTGATGAATTTTAT-TAATAAATTTT
1 GTGACGTTATAATTTCATCACCAATTTAAAATTTTATCTGTGATGAATTTTATCTAATAAATTTT
* *
3203313 -GAT-GTTATTAATTTTTGTCACAAATTGAACACTTTAGTTAACTATTAATGACATTAAAATTTT
66 AGATAGTTATTAATTTTT-TCACAAATTGAACACTTTACTCAACTATTAATGACATTAAAATTTT
* * * ***
3203376 G-CTAAATCAATGTTTGGTGTTATATGATGATAACATAAATGTGACAAACTTTTACCGTTAAATA
130 GTC-AAATCAATGTATGGTGTTATATGATGATAACATAAATCTCACAAACTTTTACCACCAAATA
* *
3203440 ATTTGATGAGAAATTTTTTTGTGACATTTTTTATTCTAG
194 ATTTGATGAGAAATTTTTTTATGACATTTTTTATTTTAG
3203479 GTGACGTTAT
1 GTGACGTTAT
3203489 TTATCTATCA
Statistics
Matches: 602, Mismatches: 95, Indels: 47
0.81 0.13 0.06
Matches are distributed among these distances:
230 61 0.10
231 90 0.15
233 3 0.00
234 10 0.02
235 92 0.15
236 7 0.01
237 75 0.12
238 64 0.11
239 4 0.01
240 3 0.00
241 64 0.11
242 45 0.07
243 82 0.14
244 2 0.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (232 bp):
GTGACGTTATAATTTCATCACCAATTTAAAATTTTATCTGTGATGAATTTTATCTAATAAATTTT
AGATAGTTATTAATTTTTTCACAAATTGAACACTTTACTCAACTATTAATGACATTAAAATTTTG
TCAAATCAATGTATGGTGTTATATGATGATAACATAAATCTCACAAACTTTTACCACCAAATAAT
TTGATGAGAAATTTTTTTATGACATTTTTTATTTTAG
Found at i:3205260 original size:133 final size:133
Alignment explanation
Indices: 3205022--3205287 Score: 496
Period size: 133 Copynumber: 2.0 Consensus size: 133
3205012 TTGTTCAAAA
*
3205022 TACTTGAAATAATTAGGAATAAAAGTTTGATTTCTATTATGTTTGGTTTCTATTCCGTTTTGCAC
1 TACTTGAAATAATTAGGAATAAAAGTTTGATTTCTATTATGTTTGGTTTCTATTCCGTTCTGCAC
3205087 TCTATTGACAACGGTAGAGACAAAGAAATTGGCAACGGTGGGCATTTACCATATGCTTGCCATGC
66 TCTATTGACAACGGTAGAGACAAAGAAATTGGCAACGGTGGGCATTTACCATATGCTTGCCATGC
3205152 TTT
131 TTT
* *
3205155 TACTTGAAATAATTAGGAATAAAATTTTGATTTCTATTATGTTTGGTTTTTATTCCGTTCTGCAC
1 TACTTGAAATAATTAGGAATAAAAGTTTGATTTCTATTATGTTTGGTTTCTATTCCGTTCTGCAC
*
3205220 TCTATTGACAACGGTAGAGACAAAGAAATTGGCAATGGTGGGCATTTACCATATGCTTGCCATGC
66 TCTATTGACAACGGTAGAGACAAAGAAATTGGCAACGGTGGGCATTTACCATATGCTTGCCATGC
3205285 TTT
131 TTT
3205288 GGTTAGTTGA
Statistics
Matches: 129, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 129 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38
Consensus pattern (133 bp):
TACTTGAAATAATTAGGAATAAAAGTTTGATTTCTATTATGTTTGGTTTCTATTCCGTTCTGCAC
TCTATTGACAACGGTAGAGACAAAGAAATTGGCAACGGTGGGCATTTACCATATGCTTGCCATGC
TTT
Found at i:3211358 original size:16 final size:16
Alignment explanation
Indices: 3211337--3211369 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3211327 CATGATATTC
3211337 ATGAATAGAATAAATG
1 ATGAATAGAATAAATG
*
3211353 ATGAATAGTATAAATG
1 ATGAATAGAATAAATG
3211369 A
1 A
3211370 ATGACAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (16 bp):
ATGAATAGAATAAATG
Found at i:3211589 original size:18 final size:18
Alignment explanation
Indices: 3211563--3211600 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3211553 GGGGTTAAGG
* *
3211563 TTTAGGGTTTCATGGAAA
1 TTTAAGGTTTCATAGAAA
3211581 TTTAAGGTTTCATAGAAA
1 TTTAAGGTTTCATAGAAA
3211599 TT
1 TT
3211601 ATGCTTGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (18 bp):
TTTAAGGTTTCATAGAAA
Found at i:3216359 original size:24 final size:24
Alignment explanation
Indices: 3216328--3216386 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
3216318 CATAAAATGG
*
3216328 GAGAGAACCTATCCTAGAAAGGGA
1 GAGAGAACCTATCCTAGAAAGGAA
3216352 GAGAGAACCTATCCTAGAAAGGAA
1 GAGAGAACCTATCCTAGAAAGGAA
*
3216376 GAGCGAACCTA
1 GAGAGAACCTA
3216387 ACCAATCGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.42, C:0.19, G:0.27, T:0.12
Consensus pattern (24 bp):
GAGAGAACCTATCCTAGAAAGGAA
Found at i:3217913 original size:14 final size:14
Alignment explanation
Indices: 3217894--3217921 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3217884 TTGATTTATT
3217894 TTAACTTTATTTGA
1 TTAACTTTATTTGA
3217908 TTAACTTTATTTGA
1 TTAACTTTATTTGA
3217922 CTAAGTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
TTAACTTTATTTGA
Found at i:3226644 original size:13 final size:13
Alignment explanation
Indices: 3226622--3226783 Score: 102
Period size: 13 Copynumber: 12.4 Consensus size: 13
3226612 TTGATTTTGA
*
3226622 GGTTTC-ATTTAT
1 GGTTTCGATTTAG
3226634 GGTTTCGATTTAG
1 GGTTTCGATTTAG
**
3226647 GGTTTTAATTTTAG
1 GGTTTCGA-TTTAG
3226661 GGTTTCGATTT-G
1 GGTTTCGATTTAG
* *
3226673 GGTTTCAATTTTAA
1 GGTTTCGA-TTTAG
*
3226687 GATTTC-AGTTTAG
1 GGTTTCGA-TTTAG
*
3226700 GGTTTCAATTTAG
1 GGTTTCGATTTAG
**
3226713 GGTTTTAATTTTA-
1 GGTTTCGA-TTTAG
*
3226726 GGTTTTGATTTAAG
1 GGTTTCGATTT-AG
* *
3226740 GCTTT-AACTTTAG
1 GGTTTCGA-TTTAG
3226753 GGTTTTC-ATTTAG
1 GG-TTTCGATTTAG
*
3226766 GGTTTTGATTTAG
1 GGTTTCGATTTAG
3226779 GGTTT
1 GGTTT
3226784 TAATTTTACA
Statistics
Matches: 121, Mismatches: 17, Indels: 23
0.75 0.11 0.14
Matches are distributed among these distances:
12 20 0.17
13 69 0.57
14 32 0.26
ACGTcount: A:0.19, C:0.06, G:0.23, T:0.52
Consensus pattern (13 bp):
GGTTTCGATTTAG
Found at i:3226717 original size:66 final size:64
Alignment explanation
Indices: 3226615--3226791 Score: 212
Period size: 66 Copynumber: 2.7 Consensus size: 64
3226605 TAGAGTTTTG
* * * *
3226615 ATTTTGAGGTTTCATTTATGGTTTCGATTTAGGGTTTTAATTTTAGGGTTTCGATTT-GGGTTTC
1 ATTTTAAGATTTCATTTAGGGTTTCGATTTAGGGTTTTAATTTTA-GGTTTCGATTTAGGCTTT-
3226679 A
64 A
* *
3226680 ATTTTAAGATTTCAGTTTAGGGTTTCAATTTAGGGTTTTAATTTTAGGTTTTGATTTAAGGCTTT
1 ATTTTAAGATTTCA-TTTAGGGTTTCGATTTAGGGTTTTAATTTTAGGTTTCGATTT-AGGCTTT
3226745 A
64 A
* * * *
3226746 ACTTTAGGGTTTTCATTTAGGGTTTTGATTTAGGGTTTTAATTTTA
1 ATTTTA-AGATTTCATTTAGGGTTTCGATTTAGGGTTTTAATTTTA
3226792 CAACTTTGAA
Statistics
Matches: 97, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
65 22 0.23
66 64 0.66
67 11 0.11
ACGTcount: A:0.20, C:0.05, G:0.22, T:0.53
Consensus pattern (64 bp):
ATTTTAAGATTTCATTTAGGGTTTCGATTTAGGGTTTTAATTTTAGGTTTCGATTTAGGCTTTA
Found at i:3226752 original size:40 final size:40
Alignment explanation
Indices: 3226708--3226791 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
3226698 AGGGTTTCAA
3226708 TTTAGGGTTTTAATTTTA-GGTTTTGATTTAAGGCTTTAAC
1 TTTAGGGTTTTAA-TTTAGGGTTTTGATTTAAGGCTTTAAC
* * * *
3226748 TTTAGGGTTTTCATTTAGGGTTTTGATTTAGGGTTTTAAT
1 TTTAGGGTTTTAATTTAGGGTTTTGATTTAAGGCTTTAAC
3226788 TTTA
1 TTTA
3226792 CAACTTTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 4 0.10
40 35 0.90
ACGTcount: A:0.20, C:0.04, G:0.21, T:0.55
Consensus pattern (40 bp):
TTTAGGGTTTTAATTTAGGGTTTTGATTTAAGGCTTTAAC
Found at i:3226784 original size:13 final size:13
Alignment explanation
Indices: 3226641--3226789 Score: 131
Period size: 13 Copynumber: 11.3 Consensus size: 13
3226631 TATGGTTTCG
3226641 ATTTAGGGTTTTA
1 ATTTAGGGTTTTA
**
3226654 ATTTTAGGGTTTCG
1 A-TTTAGGGTTTTA
*
3226668 ATTT-GGGTTTCA
1 ATTTAGGGTTTTA
* * *
3226680 ATTTTAAGATTTCA
1 A-TTTAGGGTTTTA
* *
3226694 GTTTAGGGTTTCA
1 ATTTAGGGTTTTA
3226707 ATTTAGGGTTTTA
1 ATTTAGGGTTTTA
*
3226720 ATTTTA-GGTTTTG
1 A-TTTAGGGTTTTA
* *
3226733 ATTTAAGGCTTTA
1 ATTTAGGGTTTTA
*
3226746 ACTTTAGGGTTTTC
1 A-TTTAGGGTTTTA
*
3226760 ATTTAGGGTTTTG
1 ATTTAGGGTTTTA
3226773 ATTTAGGGTTTTA
1 ATTTAGGGTTTTA
3226786 ATTT
1 ATTT
3226790 TACAACTTTG
Statistics
Matches: 112, Mismatches: 18, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
12 12 0.11
13 69 0.62
14 31 0.28
ACGTcount: A:0.21, C:0.05, G:0.22, T:0.52
Consensus pattern (13 bp):
ATTTAGGGTTTTA
Found at i:3231295 original size:15 final size:15
Alignment explanation
Indices: 3231259--3231305 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
3231249 CAAAACAAAA
3231259 AATTTGTTTAACTTG
1 AATTTGTTTAACTTG
3231274 -A-TTGTTTAACTTG
1 AATTTGTTTAACTTG
*
3231287 AATTTGTTTAACTTA
1 AATTTGTTTAACTTG
3231302 AATT
1 AATT
3231306 GAACATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 12 0.41
14 2 0.07
15 15 0.52
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.53
Consensus pattern (15 bp):
AATTTGTTTAACTTG
Found at i:3239727 original size:18 final size:18
Alignment explanation
Indices: 3239706--3239745 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3239696 TCCTAATGAC
3239706 ATTGATGGTTTTGGTGAT
1 ATTGATGGTTTTGGTGAT
* *
3239724 ATTGGTTGTTTTGGTGAT
1 ATTGATGGTTTTGGTGAT
3239742 ATTG
1 ATTG
3239746 GTTTTGCCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.53
Consensus pattern (18 bp):
ATTGATGGTTTTGGTGAT
Found at i:3239729 original size:15 final size:15
Alignment explanation
Indices: 3239711--3239751 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 15
3239701 ATGACATTGA
3239711 TGGTTTTGGTGATAT
1 TGGTTTTGGTGATAT
3239726 TGGTTGTTTTGGTGATAT
1 T-G--GTTTTGGTGATAT
3239744 TGGTTTTG
1 TGGTTTTG
3239752 CCTAGTTGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.30
16 1 0.04
17 1 0.04
18 14 0.61
ACGTcount: A:0.10, C:0.00, G:0.34, T:0.56
Consensus pattern (15 bp):
TGGTTTTGGTGATAT
Found at i:3239746 original size:18 final size:18
Alignment explanation
Indices: 3239713--3239748 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3239703 GACATTGATG
3239713 GTTTTGGTGATATTGGTT
1 GTTTTGGTGATATTGGTT
3239731 GTTTTGGTGATATTGGTT
1 GTTTTGGTGATATTGGTT
3239749 TTGCCTAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.33, T:0.56
Consensus pattern (18 bp):
GTTTTGGTGATATTGGTT
Found at i:3239936 original size:22 final size:22
Alignment explanation
Indices: 3239911--3239963 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
3239901 TGATCGAAAG
3239911 TTTTGATTT-GACAAAACAAAAA
1 TTTTG-TTTAGACAAAACAAAAA
3239933 TTTTGTTTAGACAAAACAAAAA
1 TTTTGTTTAGACAAAACAAAAA
3239955 TTTTGTTTA
1 TTTTGTTTA
3239964 ACTTGAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (22 bp):
TTTTGTTTAGACAAAACAAAAA
Found at i:3250268 original size:166 final size:167
Alignment explanation
Indices: 3249994--3250327 Score: 616
Period size: 166 Copynumber: 2.0 Consensus size: 167
3249984 AACGTGAAGC
*
3249994 ATCAATATGCCAAATTCCAGAACCTTATTGCAGCCTTCAACATCTGATCATTAGGTTTCACCATC
1 ATCAATATGCCAAATTCCAAAACCTTATTGCAGCCTTCAACATCTGATCATTAGGTTTCACCATC
**
3250059 AATAATAGGGTAATGTCTCCATACTTCGCTATGAAAGAGGTTTTCCTTTTT-GGTCCCATTGACT
66 AATAATAGGGTAATGTCAACATACTTCGCTATGAAAGAGGTTTTCCTTTTTGGGTCCCATTGACT
3250123 TCAAATTCCCCCCAAATCTACTATATCATTCCATCTT
131 TCAAATTCCCCCCAAATCTACTATATCATTCCATCTT
* *
3250160 ATCAATATGCCAAATTCTAAAACCTTATTGTAGCCTTCAACATCTGATCATTAGGTTTCACCATC
1 ATCAATATGCCAAATTCCAAAACCTTATTGCAGCCTTCAACATCTGATCATTAGGTTTCACCATC
3250225 AATAATAGGGTAATGTCAACATACTTCGCTATGAAAGAGGTTTTCCTTTTTGGGTCCCATTGACT
66 AATAATAGGGTAATGTCAACATACTTCGCTATGAAAGAGGTTTTCCTTTTTGGGTCCCATTGACT
3250290 TCAAATTCCCCCCAAATCTACTATATCATTCCATCTT
131 TCAAATTCCCCCCAAATCTACTATATCATTCCATCTT
3250327 A
1 A
3250328 AGTCTATATA
Statistics
Matches: 162, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
166 111 0.69
167 51 0.31
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.34
Consensus pattern (167 bp):
ATCAATATGCCAAATTCCAAAACCTTATTGCAGCCTTCAACATCTGATCATTAGGTTTCACCATC
AATAATAGGGTAATGTCAACATACTTCGCTATGAAAGAGGTTTTCCTTTTTGGGTCCCATTGACT
TCAAATTCCCCCCAAATCTACTATATCATTCCATCTT
Found at i:3250687 original size:25 final size:24
Alignment explanation
Indices: 3250659--3250728 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 24
3250649 TTTTAAATCC
3250659 CTTTTTCATTTTTTCATTTATTCCA
1 CTTTTT-ATTTTTTCATTTATTCCA
* * * *
3250684 CTTTTGTTTTTTTTCCTTTTTTCCCCT
1 CTTTT-TATTTTTTCATTTATT--CCA
*
3250711 CTTTTTATTATTTCATTT
1 CTTTTTATTTTTTCATTT
3250729 TTTCTTTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
25 17 0.49
26 11 0.31
27 7 0.20
ACGTcount: A:0.10, C:0.20, G:0.01, T:0.69
Consensus pattern (24 bp):
CTTTTTATTTTTTCATTTATTCCA
Found at i:3258850 original size:31 final size:31
Alignment explanation
Indices: 3258789--3258850 Score: 72
Period size: 32 Copynumber: 2.0 Consensus size: 31
3258779 TCTGTGCATA
*
3258789 CAAATAAAGAAAATATCAAGATGTATAAAAG
1 CAAATAAAGAAAATATCAAGATGTACAAAAG
* **
3258820 CAAATGAAAGTAAATATTTAGAT-TACAAAAG
1 CAAAT-AAAGAAAATATCAAGATGTACAAAAG
3258851 AGTAAAGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 12 0.46
32 14 0.54
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.23
Consensus pattern (31 bp):
CAAATAAAGAAAATATCAAGATGTACAAAAG
Found at i:3263936 original size:21 final size:20
Alignment explanation
Indices: 3263912--3263950 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3263902 AATATCTATC
3263912 TAAAAATATATCGAAATTTAT
1 TAAAAATATATC-AAATTTAT
* *
3263933 TAAAATTTTATCAAATTT
1 TAAAAATATATCAAATTT
3263951 TACAGATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (20 bp):
TAAAAATATATCAAATTTAT
Found at i:3264361 original size:228 final size:228
Alignment explanation
Indices: 3263919--3264365 Score: 541
Period size: 228 Copynumber: 2.0 Consensus size: 228
3263909 ATCTAAAAAT
* * *
3263919 ATATCGAAATTTATTAAAATTTTATCAAATTTTACAGATATGATCTATTAACAAGACTTTTCAAT
1 ATATCGAAATTTATTAAAATTTTATCAAATTTTACAGACATGATCTATGAACAAAACTTTTCAAT
* * * * * *
3263984 CTATCAATTTTAATTTTTTATTTTAATTTTTATTTAATCGTTTCTGATAAGGAATTTTGCAAATT
66 CTATCAATTTTAATTTTTTATTTTAACTTTTATTTAATCATTTCTAATAAGAAATTTTACAAACT
* * * * * *
3264049 TCACCTAAAGAATTTCATCTAAAATTCTTTCATGTTAAAGAGGCCAAAAACAGAACATTTTATCC
131 TCACCTAAAAAAATTCATCTAAAATTATTTCATGTGAAAGAGGCAAAAAACAGAACATGTTATCC
3264114 CAATTCAATTTTATTATTTCCATTCCTTTAGTG
196 CAATTCAATTTTATTATTTCCATTCCTTTAGTG
* * * *
3264147 ATATCGAAATTTATTAAAATTTT-TACAAATTTTGCATACATGATTTATGAACAAAACTTTTTAA
1 ATATCGAAATTTATTAAAATTTTAT-CAAATTTTACAGACATGATCTATGAACAAAACTTTTCAA
* * *
3264211 TTTATCGATTTTAA-TTTTTATTTTAACTTTTATTTAATCATTTCTAATAA-AATATTTTACCAA
65 TCTATCAATTTTAATTTTTTATTTTAACTTTTATTTAATCATTTCTAATAAGAA-ATTTTACAAA
* *
3264274 CTTCATCTAAAAAAAATTCAT-TTAAA-TATTTC-TGATGAAGGAGAGGCAAAAAAACA-AATCA
129 CTTCACCT-AAAAAAATTCATCTAAAATTATTTCATG-TGAA--AGAGGC-AAAAAACAGAA-CA
*
3264335 TGTTATCCCAATTCAA-TTTGTTATTTCCATT
188 TGTTATCCCAATTCAATTTTATTATTTCCATT
3264366 TCTTCAGCAA
Statistics
Matches: 186, Mismatches: 25, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
225 2 0.01
226 9 0.05
227 52 0.28
228 99 0.53
229 24 0.13
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (228 bp):
ATATCGAAATTTATTAAAATTTTATCAAATTTTACAGACATGATCTATGAACAAAACTTTTCAAT
CTATCAATTTTAATTTTTTATTTTAACTTTTATTTAATCATTTCTAATAAGAAATTTTACAAACT
TCACCTAAAAAAATTCATCTAAAATTATTTCATGTGAAAGAGGCAAAAAACAGAACATGTTATCC
CAATTCAATTTTATTATTTCCATTCCTTTAGTG
Found at i:3266383 original size:35 final size:35
Alignment explanation
Indices: 3266332--3266399 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
3266322 CCATTGTAAG
* *
3266332 AAAGCTGCATAAAGAAAATCCTAAAATGATTCTAT
1 AAAGATGCATAAAGAAAACCCTAAAATGATTCTAT
*
3266367 AAAGATGCATAAAGAAAACCCTAAAATTATTCT
1 AAAGATGCATAAAGAAAACCCTAAAATGATTCT
3266400 CCATGACCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (35 bp):
AAAGATGCATAAAGAAAACCCTAAAATGATTCTAT
Found at i:3266730 original size:2 final size:2
Alignment explanation
Indices: 3266723--3266751 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3266713 ATTGAATCAA
3266723 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3266752 AAGTGAGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3267217 original size:23 final size:23
Alignment explanation
Indices: 3267175--3267396 Score: 191
Period size: 23 Copynumber: 10.0 Consensus size: 23
3267165 ATAAATTAAA
3267175 ATAATACTATATAA-AAATAATATT
1 ATAATA-TAT-TAATAAATAATATT
*
3267199 ATAATATATTCATAAAT-A-A-T
1 ATAATATATTAATAAATAATATT
*
3267219 AT--TATATTAATAAATAATATA
1 ATAATATATTAATAAATAATATT
* *
3267240 ATAA-ATATTATTAATTTAAT-TT
1 ATAATATATTAATAA-ATAATATT
* *
3267262 AAAATAT-TATAATAAATAATAAT
1 ATAATATAT-TAATAAATAATATT
3267285 AT-AT-TATTAATAAATAATA-T
1 ATAATATATTAATAAATAATATT
* *
3267305 AAAATATTATTAATAAATAATAAT
1 ATAATA-TATTAATAAATAATATT
*
3267329 ATGATATATTAATAAATAATA-T
1 ATAATATATTAATAAATAATATT
* *
3267351 AAAATATTATTAATAAATAATAAT
1 ATAATA-TATTAATAAATAATATT
*
3267375 ATGATATATTAATAAATAATAT
1 ATAATATATTAATAAATAATAT
3267397 AAAATAATAA
Statistics
Matches: 162, Mismatches: 19, Indels: 35
0.75 0.09 0.16
Matches are distributed among these distances:
18 12 0.07
19 1 0.01
20 6 0.04
21 18 0.11
22 29 0.18
23 80 0.49
24 16 0.10
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (23 bp):
ATAATATATTAATAAATAATATT
Found at i:3267219 original size:15 final size:15
Alignment explanation
Indices: 3267199--3267411 Score: 71
Period size: 16 Copynumber: 14.3 Consensus size: 15
3267189 AAATAATATT
*
3267199 ATAATATATTCATAA
1 ATAATATATTAATAA
3267214 ATAATATTATATTAATAA
1 AT-A-A-TATATTAATAA
3267232 AT-A-ATA-TAATAA
1 ATAATATATTAATAA
3267244 AT-AT-TATTAATTTAA
1 ATAATATATTAA--TAA
* *
3267259 TTTAAAATATT-AT-A
1 -ATAATATATTAATAA
*
3267273 ATAA-ATAATAAT--
1 ATAATATATTAATAA
3267285 AT-AT-TATTAATAA
1 ATAATATATTAATAA
*
3267298 ATAATATA-AAATATTA
1 ATAATATATTAATA--A
* *
3267314 TTAATA-AATAATAA
1 ATAATATATTAATAA
*
3267328 TATGATATATTAATAA
1 -ATAATATATTAATAA
*
3267344 ATAATATA-AAATATTA
1 ATAATATATTAATA--A
* *
3267360 TTAATA-AATAATAA
1 ATAATATATTAATAA
*
3267374 TATGATATATTAATAA
1 -ATAATATATTAATAA
*
3267390 ATAATATAAAATAATAA
1 ATAATAT--ATTAATAA
3267407 ATAAT
1 ATAAT
3267412 TTTATTTTAA
Statistics
Matches: 149, Mismatches: 21, Indels: 54
0.67 0.09 0.24
Matches are distributed among these distances:
11 7 0.05
12 17 0.11
13 13 0.09
14 13 0.09
15 32 0.21
16 36 0.24
17 15 0.10
18 16 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (15 bp):
ATAATATATTAATAA
Found at i:3267226 original size:18 final size:18
Alignment explanation
Indices: 3267173--3267421 Score: 79
Period size: 18 Copynumber: 13.9 Consensus size: 18
3267163 TTATAAATTA
*
3267173 AAATAATACTATA-TAA-
1 AAATAATATTATATTAAT
3267189 AAATAATATTATAATATATTCAT
1 AAATAATATTAT-AT-TA---AT
3267212 AAATAATATTATATTAAT
1 AAATAATATTATATTAAT
3267230 --A-AATA--ATA-TAAT
1 AAATAATATTATATTAAT
*
3267242 AAATATTATTA-ATTTAATT
1 AAATAATATTATA-TTAA-T
* *
3267261 TAA-AATATTATAATAA-
1 AAATAATATTATATTAAT
3267277 ATAATAATA-TATTATTAAT
1 A-AATAATATTA-TATTAAT
3267296 AAATAATATAAAATATTATTAAT
1 AAATAATAT----TA-TATTAAT
*
3267319 AAATAATAATATGA-TATAT
1 AAATAATATTAT-ATTA-AT
* *
3267338 TAATAA-ATAATA-T-A-
1 AAATAATATTATATTAAT
* *
3267352 AAATATTATTA-ATAAAT
1 AAATAATATTATATTAAT
3267369 -AATAATATGATATATTAAT
1 AAATAATAT--TATATTAAT
* *
3267388 AAATAATA-TAAAATAAT
1 AAATAATATTATATTAAT
* *
3267405 AAATAATTTTATTTTAA
1 AAATAATATTATATTAA
3267422 GTATTTTTAT
Statistics
Matches: 174, Mismatches: 23, Indels: 70
0.65 0.09 0.26
Matches are distributed among these distances:
12 4 0.02
13 3 0.02
14 6 0.03
15 11 0.06
16 21 0.12
17 22 0.13
18 43 0.25
19 22 0.13
20 7 0.04
21 2 0.01
22 3 0.02
23 30 0.17
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (18 bp):
AAATAATATTATATTAAT
Found at i:3267239 original size:33 final size:32
Alignment explanation
Indices: 3267199--3267350 Score: 100
Period size: 30 Copynumber: 4.7 Consensus size: 32
3267189 AAATAATATT
3267199 ATAATATATTCATAAATAATATTATATTAATAA
1 ATAATATATT-ATAAATAATATTATATTAATAA
* *
3267232 ATAATATA--ATAAATATTATTA-ATTTAATTTA
1 ATAATATATTATAAATAATATTATA-TTAA-TAA
* * *
3267263 A-AATATTATAATAAATAATAATATATT-ATTA
1 ATAATA-TATTATAAATAATATTATATTAATAA
* * *
3267294 ATAA-ATAATATAAAATATTATTAATAAATAATAA
1 ATAATATATTAT-AAATAATATT-AT-ATTAATAA
*
3267328 TATGATATATTAATAAATAATAT
1 -ATAATATATT-ATAAATAATAT
3267351 AAAATATTAT
Statistics
Matches: 92, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
29 1 0.01
30 24 0.26
31 18 0.20
32 5 0.05
33 23 0.25
34 4 0.04
35 3 0.03
36 12 0.13
37 2 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (32 bp):
ATAATATATTATAAATAATATTATATTAATAA
Found at i:3267282 original size:3 final size:3
Alignment explanation
Indices: 3267270--3267411 Score: 54
Period size: 3 Copynumber: 48.7 Consensus size: 3
3267260 TTAAAATATT
* * *
3267270 ATA ATAA ATA ATA AT- ATA TTA TTA ATAA ATA AT- ATA A-A ATA TTA
1 ATA AT-A ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
* * *
3267314 TTA ATAA ATA ATA AT- ATG AT- ATA TTA ATAA ATA AT- ATA A-A ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
* * * *
3267357 TTA TTA ATAA ATA ATA AT- ATG AT- ATA TTA ATAA ATA AT- ATA A-A
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
3267400 ATA ATAA ATA AT
1 ATA AT-A ATA AT
3267412 TTTATTTTAA
Statistics
Matches: 111, Mismatches: 10, Indels: 36
0.71 0.06 0.23
Matches are distributed among these distances:
2 22 0.20
3 68 0.61
4 21 0.19
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:3267383 original size:26 final size:24
Alignment explanation
Indices: 3267223--3267402 Score: 197
Period size: 23 Copynumber: 8.0 Consensus size: 24
3267213 AATAATATTA
3267223 TATTAATAAATAAT-ATAATAAATAT
1 TATTAATAAATAATAAT-A-AAATAT
* *
3267248 TATTAAT--TTAAT-TTAAAATAT
1 TATTAATAAATAATAATAAAATAT
3267269 TA-TAATAAATAATAAT---ATAT
1 TATTAATAAATAATAATAAAATAT
3267289 TATTAATAAATAAT-ATAAAATAT
1 TATTAATAAATAATAATAAAATAT
**
3267312 TATTAATAAATAATAATATGATA-
1 TATTAATAAATAATAATAAAATAT
3267335 TATTAATAAATAAT-ATAAAATAT
1 TATTAATAAATAATAATAAAATAT
**
3267358 TATTAATAAATAATAATATGATA-
1 TATTAATAAATAATAATAAAATAT
3267381 TATTAATAAATAAT-ATAAAATA
1 TATTAATAAATAATAATAAAATA
3267403 ATAAATAATT
Statistics
Matches: 133, Mismatches: 12, Indels: 23
0.79 0.07 0.14
Matches are distributed among these distances:
20 12 0.09
21 19 0.14
22 17 0.13
23 66 0.50
24 12 0.09
25 7 0.05
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (24 bp):
TATTAATAAATAATAATAAAATAT
Found at i:3267496 original size:16 final size:16
Alignment explanation
Indices: 3267488--3267543 Score: 52
Period size: 17 Copynumber: 3.8 Consensus size: 16
3267478 TTTGAATATT
3267488 AATAATTTTAATAATA
1 AATAATTTTAATAATA
*
3267504 AATAA-TTT--CAAT-
1 AATAATTTTAATAATA
3267516 -AT-ATTTTAATAATA
1 AATAATTTTAATAATA
3267530 AATAATTTTTAATA
1 AATAA-TTTTAATA
3267544 TTTTAATAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 13
0.67 0.04 0.28
Matches are distributed among these distances:
10 1 0.03
11 5 0.16
13 6 0.19
15 5 0.16
16 6 0.19
17 8 0.26
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
AATAATTTTAATAATA
Found at i:3267521 original size:26 final size:26
Alignment explanation
Indices: 3267488--3267551 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
3267478 TTTGAATATT
3267488 AATA-ATTTTAATAATAAATAATTTC
1 AATATATTTTAATAATAAATAATTTC
*
3267513 AATATATTTTAATAATAAATAATTTT
1 AATATATTTTAATAATAAATAATTTC
*
3267539 TA-ATATTTTAATA
1 AATATATTTTAATA
3267552 GATATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 15 0.42
26 21 0.58
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:3267543 original size:10 final size:9
Alignment explanation
Indices: 3267486--3267551 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
3267476 CTTTTGAATA
3267486 TTAATAATT
1 TTAATAATT
3267495 TTAATAA--
1 TTAATAATT
*
3267502 TAAATAATT
1 TTAATAATT
*
3267511 TCAATATATT
1 TTAATA-ATT
3267521 TTAATAA--
1 TTAATAATT
*
3267528 TAAATAATTT
1 TTAATAA-TT
3267538 TTAAT-ATT
1 TTAATAATT
3267546 TTAATA
1 TTAATA
3267552 GATATATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
7 12 0.27
8 7 0.16
9 14 0.31
10 12 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (9 bp):
TTAATAATT
Found at i:3267885 original size:21 final size:20
Alignment explanation
Indices: 3267860--3267905 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3267850 AAAATTAATC
*
3267860 AAAATTTTAATA-AAAATATA
1 AAAATTTAAATATAAAAT-TA
3267880 ATAAATTTAAATATAAAATTA
1 A-AAATTTAAATATAAAATTA
3267901 AAAAT
1 AAAAT
3267906 ACGTGAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATTTAAATATAAAATTA
Done.