Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3349.1
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: 139127
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.28
Warning! 20314 characters in sequence are not A, C, G, or T
Found at i:6516 original size:27 final size:27
Alignment explanation
Indices: 6499--6650 Score: 216
Period size: 27 Copynumber: 5.6 Consensus size: 27
6489 ATATTAAGTC
* *
6499 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
6526 CGCACACTTAGTGCTACATAATTAAACT
1 CGCACACTTAGTGCTACATAA-TCAACT
*
6554 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
6581 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
6609 CGCACACTTAGTGCTACA-AAGTCAATT
1 CGCACACTTAGTGCTACATAA-TCAACT
6636 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
6651 GCACAATTTA
Statistics
Matches: 115, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
27 66 0.57
28 49 0.43
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:6561 original size:28 final size:28
Alignment explanation
Indices: 6499--6671 Score: 199
Period size: 27 Copynumber: 6.2 Consensus size: 28
6489 ATATTAAGTC
* * *
6499 CGCACACTCAGTGCTATATAA-TCAACT
1 CGCACACTTAGTGCTACATAATTAAACT
6526 CGCACACTTAGTGCTACATAATTAAACT
1 CGCACACTTAGTGCTACATAATTAAACT
* *
6554 CGCACACTTAGTGCTACAT-AGTCAACT
1 CGCACACTTAGTGCTACATAATTAAACT
* *
6581 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATTAAACT
* * *
6609 CGCACACTTAGTGCTACA-AAGTCAATT
1 CGCACACTTAGTGCTACATAATTAAACT
* * *
6636 CGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAA-TTAAACT
6665 CGCACAC
1 CGCACAC
6672 GTAGCGCCAA
Statistics
Matches: 123, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 65 0.53
28 48 0.39
29 10 0.08
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATTAAACT
Found at i:6579 original size:55 final size:55
Alignment explanation
Indices: 6499--6671 Score: 247
Period size: 55 Copynumber: 3.1 Consensus size: 55
6489 ATATTAAGTC
* * *
6499 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATTAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATTAAACT
* *
6554 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATTAAACT
* * * * *
6609 CGCACACTTAGTGCTACAAAGTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAA-TTAAACT
6665 CGCACAC
1 CGCACAC
6672 GTAGCGCCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 93 0.89
56 12 0.11
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.25
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATTAAACT
Found at i:9925 original size:92 final size:92
Alignment explanation
Indices: 9768--9950 Score: 339
Period size: 92 Copynumber: 2.0 Consensus size: 92
9758 GAACTTGGCA
9768 AACAAATCATTCAAAGCTTGGAAGAGAGCTTCTCGAGTCACTCCTCCCTGATCAACTATTACTGG
1 AACAAATCATTCAAAGCTTGGAAGAGAGCTTCTCGAGTCACTCCTCCCTGATCAACTATTACTGG
*
9833 CCTATTCTCAGATGGCGCTGCCCCTTC
66 CCTATTCTCAGATAGCGCTGCCCCTTC
* *
9860 AACAAATCATTCAAAGCTTGGAAGAGAGCTTCTCGAGTCACTCCTCCCTGATTAACTGTTACTGG
1 AACAAATCATTCAAAGCTTGGAAGAGAGCTTCTCGAGTCACTCCTCCCTGATCAACTATTACTGG
9925 CCTATTCTCAGATAGCGCTGCCCCTT
66 CCTATTCTCAGATAGCGCTGCCCCTT
9951 TCACGGGAGC
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (92 bp):
AACAAATCATTCAAAGCTTGGAAGAGAGCTTCTCGAGTCACTCCTCCCTGATCAACTATTACTGG
CCTATTCTCAGATAGCGCTGCCCCTTC
Found at i:11133 original size:46 final size:48
Alignment explanation
Indices: 11045--11147 Score: 138
Period size: 46 Copynumber: 2.2 Consensus size: 48
11035 TACATGAATT
* * * *
11045 ATTCCTGTCTCTAATGCCATATATATATAATATGGGCTTACATGGCTC
1 ATTCCTGTCTCCAAAGCCATATATATATAATATGGACCTACATGGCTC
*
11093 ATTCCTGTCTCCAAAGCCATATA-A-CTAATATGGACCTACATGGCTC
1 ATTCCTGTCTCCAAAGCCATATATATATAATATGGACCTACATGGCTC
*
11139 ATTTCTGTC
1 ATTCCTGTC
11148 CTGTCCTGTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
46 27 0.55
47 1 0.02
48 21 0.43
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (48 bp):
ATTCCTGTCTCCAAAGCCATATATATATAATATGGACCTACATGGCTC
Found at i:14044 original size:28 final size:28
Alignment explanation
Indices: 14012--14067 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
14002 GGTGTTTGCA
**
14012 ATACTATTAGTGGATAAGTGTATGGTAT
1 ATACTATTAGCAGATAAGTGTATGGTAT
*
14040 ATACTATTAGCAGATAAGTTTATGGTAT
1 ATACTATTAGCAGATAAGTGTATGGTAT
14068 TGCATAACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.39
Consensus pattern (28 bp):
ATACTATTAGCAGATAAGTGTATGGTAT
Found at i:21784 original size:285 final size:285
Alignment explanation
Indices: 21274--21844 Score: 1133
Period size: 285 Copynumber: 2.0 Consensus size: 285
21264 GGATTCAAAG
*
21274 TCGGCTATTTAAATGAATTGGAAAAAATGCTAGACAAAGTTTTACCCCATGCTATGTTGAAGGCT
1 TCGGCTATTTAAATGAATTGGAAAAAATGCTAGAAAAAGTTTTACCCCATGCTATGTTGAAGGCT
21339 AAACCTAATCTTGAATCGAGTTATAAGACATTGAAAAGGGATTAGTCAATCGTTTATGACATTCT
66 AAACCTAATCTTGAATCGAGTTATAAGACATTGAAAAGGGATTAGTCAATCGTTTATGACATTCT
21404 TAGTGGAAAAAATAATAGCAGCTTTGGTTGGGATGAGCATAGGCAGCTTGCTGTTGCTTAAGATG
131 TAGTGGAAAAAATAATAGCAGCTTTGGTTGGGATGAGCATAGGCAGCTTGCTGTTGCTTAAGATG
21469 CGATGTGGAACTCATATATAAATGTAAGAATTATTTCAAGTCTTTATTATCTTATTTTGATCAAA
196 CGATGTGGAACTCATATATAAATGTAAGAATTATTTCAAGTCTTTATTATCTTATTTTGATCAAA
21534 CTTATATCTAATATAAATTCCTCAT
261 CTTATATCTAATATAAATTCCTCAT
21559 TCGGCTATTTAAATGAATTGGAAAAAATGCTAGAAAAAGTTTTACCCCATGCTATGTTGAAGGCT
1 TCGGCTATTTAAATGAATTGGAAAAAATGCTAGAAAAAGTTTTACCCCATGCTATGTTGAAGGCT
21624 AAACCTAATCTTGAATCGAGTTATAAGACATTGAAAAGGGATTAGTCAATCGTTTATGACATTCT
66 AAACCTAATCTTGAATCGAGTTATAAGACATTGAAAAGGGATTAGTCAATCGTTTATGACATTCT
21689 TAGTGGAAAAAATAATAGCAGCTTTGGTTGGGATGAGCATAGGCAGCTTGCTGTTGCTTAAGATG
131 TAGTGGAAAAAATAATAGCAGCTTTGGTTGGGATGAGCATAGGCAGCTTGCTGTTGCTTAAGATG
21754 CGATGTGGAACTCATATATAAATGTAAGAATTATTTCAAGTCTTTATTATCTTATTTTGATCAAA
196 CGATGTGGAACTCATATATAAATGTAAGAATTATTTCAAGTCTTTATTATCTTATTTTGATCAAA
21819 CTTATATCTAATATAAATTCCTCAT
261 CTTATATCTAATATAAATTCCTCAT
21844 T
1 T
21845 TTTATAGAGT
Statistics
Matches: 285, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
285 285 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (285 bp):
TCGGCTATTTAAATGAATTGGAAAAAATGCTAGAAAAAGTTTTACCCCATGCTATGTTGAAGGCT
AAACCTAATCTTGAATCGAGTTATAAGACATTGAAAAGGGATTAGTCAATCGTTTATGACATTCT
TAGTGGAAAAAATAATAGCAGCTTTGGTTGGGATGAGCATAGGCAGCTTGCTGTTGCTTAAGATG
CGATGTGGAACTCATATATAAATGTAAGAATTATTTCAAGTCTTTATTATCTTATTTTGATCAAA
CTTATATCTAATATAAATTCCTCAT
Found at i:22879 original size:17 final size:17
Alignment explanation
Indices: 22857--22889 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22847 ATTAAGAATG
22857 TTATTAAATCATATTTT
1 TTATTAAATCATATTTT
*
22874 TTATTAAATTATATTT
1 TTATTAAATCATATTT
22890 AATAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTAAATCATATTTT
Found at i:23157 original size:16 final size:16
Alignment explanation
Indices: 23132--23175 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
23122 ACAATTAAAT
23132 TATT-TATTACATA-TC
1 TATTCTATTACA-AGTC
23147 TATTCTATTACAAGTC
1 TATTCTATTACAAGTC
*
23163 TATTCCATTACAA
1 TATTCTATTACAA
23176 CTATATTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.34, C:0.18, G:0.02, T:0.45
Consensus pattern (16 bp):
TATTCTATTACAAGTC
Found at i:27954 original size:17 final size:17
Alignment explanation
Indices: 27918--27953 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
27908 AATATTAAAA
*
27918 TTTAATTATTTTTCATT
1 TTTAATTATTTATCATT
27935 TTTAA-TATTTATCATT
1 TTTAATTATTTATCATT
27951 TTT
1 TTT
27954 TGCCACATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTAATTATTTATCATT
Found at i:28044 original size:20 final size:20
Alignment explanation
Indices: 28015--28052 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28005 TTTAAAAATA
*
28015 GTTAACTTTAATGATCAACC
1 GTTAAATTTAATGATCAACC
*
28035 GTTAAATTTAATGGTCAA
1 GTTAAATTTAATGATCAA
28053 AAAGCCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (20 bp):
GTTAAATTTAATGATCAACC
Found at i:37487 original size:39 final size:39
Alignment explanation
Indices: 37443--37679 Score: 429
Period size: 39 Copynumber: 6.1 Consensus size: 39
37433 ATTATATTAT
* *
37443 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
37482 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
37521 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
37560 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
37599 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
37638 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
37677 CAG
1 CAG
37680 TGTCTTGCAT
Statistics
Matches: 190, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 190 1.00
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:43345 original size:39 final size:39
Alignment explanation
Indices: 43285--43635 Score: 531
Period size: 39 Copynumber: 9.0 Consensus size: 39
43275 ATTATATTAT
* * * *
43285 AGCACAAAGCCTGTGGGACTTTAACACGGATACATTTCC
1 AGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCC
* * *
43324 AGCAGGAAGCCTGCGGGACTTTGGCCCGGATACATTTCT
1 AGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCC
* * *
43363 AGCATGAAGCCTGCGAGACTTTAGTCCGGATACATTTCC
1 AGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCC
* *
43402 AGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTCC
1 AGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCC
*
43441 AGCACGAAGCCTACGGGACTTTAGCCCGGATACATTTCC
1 AGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCC
* * *
43480 AGCACGAAACCTGCGGGACTTTGGCCCGGATATATTTCC
1 AGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCC
43519 AGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCC
1 AGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCC
**
43558 AGCACGAAGCCTGTAGGACTTTAGCCCGGATACATTTCC
1 AGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCC
43597 AGCACGAAGCCTGCGGGACTTTAGCCCGGATACACTTTC
1 AGCACGAAGCCTGCGGGACTTTAGCCCGGATACA-TTTC
43636 AGTGACTTGA
Statistics
Matches: 280, Mismatches: 31, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
39 276 0.99
40 4 0.01
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (39 bp):
AGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCC
Found at i:47385 original size:39 final size:39
Alignment explanation
Indices: 47341--47690 Score: 619
Period size: 39 Copynumber: 9.0 Consensus size: 39
47331 ATTATATTAT
* *
47341 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
47380 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
47419 CAGCACAAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
47458 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
47497 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
47536 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
47575 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
47614 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
47653 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
47691 TCAGTGTCTT
Statistics
Matches: 299, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 299 1.00
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:74316 original size:19 final size:18
Alignment explanation
Indices: 74288--74326 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
74278 TGAAATAACT
**
74288 AAAAATAAATTTAAATAA
1 AAAAATAAATAAAAATAA
74306 AAAAATGAAATAAAAATAA
1 AAAAAT-AAATAAAAATAA
74325 AA
1 AA
74327 TGAATTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
AAAAATAAATAAAAATAA
Found at i:76672 original size:40 final size:40
Alignment explanation
Indices: 76415--76670 Score: 399
Period size: 40 Copynumber: 6.4 Consensus size: 40
76405 AAACCAAGTA
* *
76415 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
76454 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
76494 CCTTCGGGACTTAGCCCGGTTTTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
76534 CCTTCGGGACTTAGCCCGGACATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
76574 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
76614 CCTTCGGGACTTAGCCCAGATATAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
76654 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
76671 AGTTATCGTC
Statistics
Matches: 203, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
39 15 0.07
40 188 0.93
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:81135 original size:24 final size:24
Alignment explanation
Indices: 81091--81136 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
81081 AGCTGATCGC
*
81091 TTGGGTTTTCGATCATCTCTTCGG
1 TTGGGGTTTCGATCATCTCTTCGG
*
81115 TTGGGGTTT-GATTATCGTCTTC
1 TTGGGGTTTCGATCATC-TCTTC
81137 CCACTCGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (24 bp):
TTGGGGTTTCGATCATCTCTTCGG
Found at i:85776 original size:18 final size:18
Alignment explanation
Indices: 85753--85817 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
85743 TTTTTGGAAA
85753 TAAATACCAATTTTAAAG
1 TAAATACCAATTTTAAAG
*
85771 TAAATACTGATATTTTTGGAAA-
1 TAAATAC-CA-A-TTTT--AAAG
*
85793 TAAATACCGATTTTAAAG
1 TAAATACCAATTTTAAAG
85811 TAAATAC
1 TAAATAC
85818 TTTTTGGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
17 3 0.08
18 14 0.37
19 5 0.13
20 2 0.05
21 4 0.11
22 7 0.18
23 3 0.08
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.35
Consensus pattern (18 bp):
TAAATACCAATTTTAAAG
Found at i:85793 original size:40 final size:40
Alignment explanation
Indices: 85738--85818 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
85728 TGCTATAAAA
85738 TGATATTTTTGGAAATAAATACCAATTTTAAAGTAAATAC
1 TGATATTTTTGGAAATAAATACCAATTTTAAAGTAAATAC
*
85778 TGATATTTTTGGAAATAAATACCGATTTTAAAGTAAATAC
1 TGATATTTTTGGAAATAAATACCAATTTTAAAGTAAATAC
85818 T
1 T
85819 TTTTGGATAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.38
Consensus pattern (40 bp):
TGATATTTTTGGAAATAAATACCAATTTTAAAGTAAATAC
Found at i:85796 original size:22 final size:22
Alignment explanation
Indices: 85738--85799 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 22
85728 TGCTATAAAA
85738 TGATATTTTTGGAAATAAATAC
1 TGATATTTTTGGAAATAAATAC
*
85760 -CA-A-TTTT--AAAGTAAATAC
1 TGATATTTTTGGAAA-TAAATAC
85778 TGATATTTTTGGAAATAAATAC
1 TGATATTTTTGGAAATAAATAC
85800 CGATTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
17 3 0.09
18 7 0.22
19 5 0.16
20 2 0.06
21 5 0.16
22 7 0.22
23 3 0.09
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (22 bp):
TGATATTTTTGGAAATAAATAC
Found at i:113266 original size:42 final size:42
Alignment explanation
Indices: 113219--113298 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
113209 TGGCCCATAG
113219 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
113261 GCCCATTTCAATATCACATGTAATGTCAATGAATGTAT
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTAT
113299 ACCAACCAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:113440 original size:25 final size:25
Alignment explanation
Indices: 113406--113475 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
113396 ATCTTTTAAT
* *
113406 AATTGAGGCAAAGCCCTTTTTGATA
1 AATTGGGGCAAAGCCCTTTTGGATA
113431 AATTGGGGCAAAGCCCTTTTGGATA
1 AATTGGGGCAAAGCCCTTTTGGATA
* * *
113456 AACTGGGGCATAGCTCTTTT
1 AATTGGGGCAAAGCCCTTTT
113476 AGCACTTCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (25 bp):
AATTGGGGCAAAGCCCTTTTGGATA
Found at i:113451 original size:24 final size:24
Alignment explanation
Indices: 113398--113475 Score: 86
Period size: 25 Copynumber: 3.2 Consensus size: 24
113388 GGCCTAGCAT
* *
113398 CTTTTAAT-AATTGAGGCAAAGCC
1 CTTTTGATAAATTGGGGCAAAGCC
113421 CTTTTTGATAAATTGGGGCAAAGCC
1 C-TTTTGATAAATTGGGGCAAAGCC
* * *
113446 CTTTTGGATAAACTGGGGCATAGCT
1 CTTTT-GATAAATTGGGGCAAAGCC
113471 CTTTT
1 CTTTT
113476 AGCACTTCCT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
23 1 0.02
24 10 0.21
25 36 0.77
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (24 bp):
CTTTTGATAAATTGGGGCAAAGCC
Found at i:113709 original size:27 final size:27
Alignment explanation
Indices: 113679--113896 Score: 312
Period size: 27 Copynumber: 8.1 Consensus size: 27
113669 GGGCAAAATG
* * * *
113679 GTAATTTTACCCTATAAGGGTATCTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
113706 GTAATTCTACCCTAAAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
*
113733 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
113760 GTAGTTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
113787 GTAGTTCTACCCTATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
*
113814 GTAATTCTACCCTATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
113841 GTAATTCTACCCTA-AGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
*
113867 GTAATTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
113894 GTA
1 GTA
113897 TTTTACGAAT
Statistics
Matches: 179, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
26 26 0.15
27 153 0.85
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:113965 original size:27 final size:27
Alignment explanation
Indices: 113937--114075 Score: 208
Period size: 27 Copynumber: 5.2 Consensus size: 27
113927 CACAAATTAG
*
113937 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
113964 GGGTATTTTGGTAATTTTATAAACTAA
1 GGGTATTTTGGTAATTTTACAAACCAA
*
113991 GGGTATTTTAGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
*
114018 TGGTATTTTGGTAATTTTACAAACC-A
1 GGGTATTTTGGTAATTTTACAAACCAA
**
114044 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
114071 GGGTA
1 GGGTA
114076 AAACGATAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
26 23 0.23
27 77 0.77
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:113979 original size:54 final size:53
Alignment explanation
Indices: 113921--114075 Score: 211
Period size: 54 Copynumber: 2.9 Consensus size: 53
113911 GGTTTTTCGA
* * *
113921 TAATTTCACAAATTAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGG
1 TAATTTTACAAACTA-GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGG
* * *
113975 TAATTTTATAAACTAAGGGTATTTTAGTAATTTTACAAACCAATGGTATTTTGG
1 TAATTTTACAAACT-AGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGG
* **
114029 TAATTTTACAAACCAGGGTATTTTGGTAATTTTGTAAACCAAGGGTA
1 TAATTTTACAAACTAGGGTATTTTGGTAATTTTACAAACCAAGGGTA
114076 AAACGATAAT
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
53 29 0.33
54 58 0.66
55 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (53 bp):
TAATTTTACAAACTAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGG
Found at i:114085 original size:27 final size:27
Alignment explanation
Indices: 114026--114345 Score: 336
Period size: 27 Copynumber: 11.9 Consensus size: 27
114016 AATGGTATTT
* * ***
114026 TGGTAATTTTACAAA-CCAGGGTATTT
1 TGGTAATTTTATAAATCGAGGGTAAAA
* * *
114052 TGGTAATTTTGTAAACCAAGGGTAAAA
1 TGGTAATTTTATAAATCGAGGGTAAAA
* * * *
114079 CGATAATTCTGTAAATCGAGGGTAAAA
1 TGGTAATTTTATAAATCGAGGGTAAAA
*
114106 TAGTAATTTTATAAATCGAGGGTAAAA
1 TGGTAATTTTATAAATCGAGGGTAAAA
114133 TGGTAATTTTATAAATCGAGGGTAAAA
1 TGGTAATTTTATAAATCGAGGGTAAAA
**
114160 TGGTAATTTTATAAATTAAGGGTAAAA
1 TGGTAATTTTATAAATCGAGGGTAAAA
* * **
114187 TAGTAATTTTGTAAATTAAGGGTAAAA
1 TGGTAATTTTATAAATCGAGGGTAAAA
* *
114214 CGGTAATTCTATAAATCGAGGGTAAAA
1 TGGTAATTTTATAAATCGAGGGTAAAA
*
114241 TGGTAATTCTATAAATCGAGGGTAAAA
1 TGGTAATTTTATAAATCGAGGGTAAAA
* * *
114268 CGGTAATTCTATAAATCAAGGGTAAAA
1 TGGTAATTTTATAAATCGAGGGTAAAA
* * ***
114295 TGGTAATTTTGTAAATCGGGGGTACTT
1 TGGTAATTTTATAAATCGAGGGTAAAA
* * *
114322 TGATAATTTTACAAGTCGAGGGTA
1 TGGTAATTTTATAAATCGAGGGTA
114346 TTTCAGTAAT
Statistics
Matches: 250, Mismatches: 43, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
26 13 0.05
27 237 0.95
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (27 bp):
TGGTAATTTTATAAATCGAGGGTAAAA
Found at i:114355 original size:27 final size:27
Alignment explanation
Indices: 114214--114465 Score: 167
Period size: 27 Copynumber: 9.4 Consensus size: 27
114204 AAGGGTAAAA
* * **
114214 CGGTAATTCTATAAATCGAGGGTAAAAT
1 CGGTAATTTTACAAATCGAGGGT-ATTT
* * ***
114242 -GGTAATTCTATAAATCGAGGGTAAAA
1 CGGTAATTTTACAAATCGAGGGTATTT
* * * **
114268 CGGTAATTCTATAAATCAAGGGTAAAAT
1 CGGTAATTTTACAAATCGAGGGT-ATTT
** *
114296 -GGTAATTTTGTAAATCGGGGGTACTTT
1 CGGTAATTTTACAAATCGAGGGTA-TTT
* *
114323 -GATAATTTTACAAGTCGAGGGTATTT
1 CGGTAATTTTACAAATCGAGGGTATTT
* *
114349 CAGTAATTTTAC-AATCGACGGT-TTT
1 CGGTAATTTTACAAATCGAGGGTATTT
*
114374 CGGTAATTTTATAAATC-AGGGGTACTTT
1 CGGTAATTTTACAAATCGA-GGGTA-TTT
* * *
114402 -GGTAATTTTACAAGTCCAAGGTATTT
1 CGGTAATTTTACAAATCGAGGGTATTT
*
114428 CAGTAATTTTACAAATCGAGGGTATTT
1 CGGTAATTTTACAAATCGAGGGTATTT
*
114455 TGGTAATTTTA
1 CGGTAATTTTA
114466 GTAAACTAAA
Statistics
Matches: 184, Mismatches: 30, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
25 14 0.08
26 25 0.14
27 138 0.75
28 7 0.04
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (27 bp):
CGGTAATTTTACAAATCGAGGGTATTT
Found at i:114355 original size:81 final size:81
Alignment explanation
Indices: 114052--114470 Score: 328
Period size: 81 Copynumber: 5.2 Consensus size: 81
114042 CAGGGTATTT
* * * * * * **
114052 TGGTAATTTTGTAAACCAAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAAT-AGTAATTTT
1 TGGTAATTTTATAAATCGAGGGTAAAATGGTAATTTTACAAATCGAGGGT-AAATCAGTAATTTT
114116 ATAAATCGAGGGTAAAA
65 ATAAATCGAGGGTAAAA
* **
114133 TGGTAATTTTATAAATCGAGGGTAAAATGGTAATTTTATAAATTAAGGGTAAAAT-AGTAATTTT
1 TGGTAATTTTATAAATCGAGGGTAAAATGGTAATTTTACAAATCGAGGGT-AAATCAGTAATTTT
* **
114197 GTAAATTAAGGGTAAAA
65 ATAAATCGAGGGTAAAA
* * * * * * *
114214 CGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTA
1 TGGTAATTTTATAAATCGAGGGTAAAATGGTAATTTTACAAATCGAGGGTAAATCAGTAATTTTA
*
114279 TAAATCAAGGGTAAAA
66 TAAATCGAGGGTAAAA
* * *** * * **
114295 TGGTAATTTTGTAAATCGGGGGTACTTTGATAATTTTACAAGTCGAGGGTATTTCAGTAATTTTA
1 TGGTAATTTTATAAATCGAGGGTAAAATGGTAATTTTACAAATCGAGGGTAAATCAGTAATTTTA
* * **
114360 -CAATCGACGGT--TT
66 TAAATCGAGGGTAAAA
*** * * * **
114373 TCGGTAATTTTATAAATC-AGGGGTACTTTGGTAATTTTACAAGTCCAAGGTATTTCAGTAATTT
1 T-GGTAATTTTATAAATCGA-GGGTAAAATGGTAATTTTACAAATCGAGGGTAAATCAGTAATTT
* ***
114437 TACAAATCGAGGGTATTT
64 TATAAATCGAGGGTAAAA
114455 TGGTAATTTTAGTAAA
1 TGGTAATTTTA-TAAA
114471 CTAAAGTATT
Statistics
Matches: 281, Mismatches: 50, Indels: 13
0.82 0.15 0.04
Matches are distributed among these distances:
78 1 0.00
79 58 0.21
80 20 0.07
81 195 0.69
82 7 0.02
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.35
Consensus pattern (81 bp):
TGGTAATTTTATAAATCGAGGGTAAAATGGTAATTTTACAAATCGAGGGTAAATCAGTAATTTTA
TAAATCGAGGGTAAAA
Found at i:114399 original size:79 final size:81
Alignment explanation
Indices: 114296--114470 Score: 264
Period size: 79 Copynumber: 2.2 Consensus size: 81
114286 AGGGTAAAAT
* * * *
114296 GGTAATTTTGTAAATCGGGGGTACTTTGATAATTTTACAAGTCGAGGGTATTTCAGTAATTTTAC
1 GGTAATTTTATAAATCAGGGGTACTTTGATAATTTTACAAGTCCAAGGTATTTCAGTAATTTTAC
114361 -AATCGACGGT-TTTC
66 AAATCGACGGTATTTC
*
114375 GGTAATTTTATAAATCAGGGGTACTTTGGTAATTTTACAAGTCCAAGGTATTTCAGTAATTTTAC
1 GGTAATTTTATAAATCAGGGGTACTTTGATAATTTTACAAGTCCAAGGTATTTCAGTAATTTTAC
* *
114440 AAATCGAGGGTATTTT
66 AAATCGACGGTATTTC
114456 GGTAATTTTAGTAAA
1 GGTAATTTTA-TAAA
114471 CTAAAGTATT
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
79 60 0.70
80 9 0.10
81 13 0.15
82 4 0.05
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (81 bp):
GGTAATTTTATAAATCAGGGGTACTTTGATAATTTTACAAGTCCAAGGTATTTCAGTAATTTTAC
AAATCGACGGTATTTC
Found at i:115646 original size:25 final size:25
Alignment explanation
Indices: 115612--115697 Score: 145
Period size: 25 Copynumber: 3.4 Consensus size: 25
115602 TTTCTACATT
115612 AAAGCCCTTTTTGATAAACTGGGGC
1 AAAGCCCTTTTTGATAAACTGGGGC
*
115637 AAAGCCCTTTTTGATAAACTAGGGC
1 AAAGCCCTTTTTGATAAACTGGGGC
*
115662 AAAGCCCTTTTCGATAAACTGGGGC
1 AAAGCCCTTTTTGATAAACTGGGGC
*
115687 ATAGCCCTTTT
1 AAAGCCCTTTT
115698 AGAACTTCCT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (25 bp):
AAAGCCCTTTTTGATAAACTGGGGC
Found at i:115930 original size:27 final size:27
Alignment explanation
Indices: 115900--116068 Score: 187
Period size: 27 Copynumber: 6.3 Consensus size: 27
115890 GGGGCAAAAT
* * *
115900 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
115927 GGTAATTCTACCCTAC-AGGGATATTTC
1 GGTAATTCTACCCTACAAGGG-TATTTC
* *
115954 GGTAGTTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* ** *
115981 GATGGTTCTACCTTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
116008 GGTAGTTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
116035 GGTAATTTTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
116062 AGTAATT
1 GGTAATT
116069 AAATTTCAAA
Statistics
Matches: 123, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
26 4 0.03
27 116 0.94
28 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:116047 original size:54 final size:54
Alignment explanation
Indices: 115908--116061 Score: 211
Period size: 54 Copynumber: 2.9 Consensus size: 54
115898 ATGGTAATTT
* * * *
115908 TACCCCACAAGGGTATCTCGGTAATTCTACCCTAC-AGGGATATTTCGGTAGTTC
1 TACCCTACAGGGGTATTTCGGTAATTCTACCTTACAAGGG-TATTTCGGTAGTTC
* **
115962 TACCCTACAGGGGTATTTCGATGGTTCTACCTTACAAGGGTATTTCGGTAGTTC
1 TACCCTACAGGGGTATTTCGGTAATTCTACCTTACAAGGGTATTTCGGTAGTTC
* *
116016 TACCCTACAGGGGTATTTCGGTAATTTTACCTTACAGGGGTATTTC
1 TACCCTACAGGGGTATTTCGGTAATTCTACCTTACAAGGGTATTTC
116062 AGTAATTAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
54 83 0.95
55 4 0.05
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (54 bp):
TACCCTACAGGGGTATTTCGGTAATTCTACCTTACAAGGGTATTTCGGTAGTTC
Found at i:116428 original size:27 final size:27
Alignment explanation
Indices: 116343--116429 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 27
116333 GTATTTCAGT
* * *
116343 ATTTTACGAATC-GAGGTTTTTTCGATA
1 ATTTTACAAATCAGAGGTATTTTGGA-A
* * * *
116370 ATTTCACAAATTAGGGGTATTTTGGTA
1 ATTTTACAAATCAGAGGTATTTTGGAA
116397 ATTTTACAAATCAGAGGTATTTTGGAA
1 ATTTTACAAATCAGAGGTATTTTGGAA
116424 ATTTTA
1 ATTTTA
116430 TAAACATTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
27 39 0.81
28 9 0.19
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (27 bp):
ATTTTACAAATCAGAGGTATTTTGGAA
Found at i:116439 original size:38 final size:38
Alignment explanation
Indices: 116397--116472 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
116387 TATTTTGGTA
* * *
116397 ATTTTACAAATC-AGAGGTATTTTGGAAATTTTATAAAC
1 ATTTTACAAACCAAG-GGTATTTTAGAAATTTTACAAAC
* *
116435 ATTTTATAAACCAAGGGTATTTTAGTAATTTTACAAAC
1 ATTTTACAAACCAAGGGTATTTTAGAAATTTTACAAAC
116473 CAAGGGTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 30 0.94
39 2 0.06
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (38 bp):
ATTTTACAAACCAAGGGTATTTTAGAAATTTTACAAAC
Found at i:116467 original size:27 final size:27
Alignment explanation
Indices: 116435--116534 Score: 155
Period size: 27 Copynumber: 3.7 Consensus size: 27
116425 TTTTATAAAC
* *
116435 ATTTTATAAACCAAGGGTATTTTAGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
116462 ATTTTACAAACCAAGGGTATTTTGGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
*
116489 ATTTTACAAACCAGGGGTATTTTGGTA
1 ATTTTACAAACCAAGGGTATTTTGGTA
**
116516 ATTTTGTAAACCAAGGGTA
1 ATTTTACAAACCAAGGGTA
116535 AAATAATAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (27 bp):
ATTTTACAAACCAAGGGTATTTTGGTA
Found at i:116544 original size:27 final size:27
Alignment explanation
Indices: 116514--116804 Score: 249
Period size: 27 Copynumber: 10.8 Consensus size: 27
116504 GGTATTTTGG
* * * *
116514 TAATTTTGTAAACCAAGGGTAAAATAA
1 TAATTTTATAAATCGAGGGTAAAATGA
* * *
116541 TAATTCTGTAAATCGAGGGTAAAACGA
1 TAATTTTATAAATCGAGGGTAAAATGA
*
116568 TAATTTTATAAATCGAGGGTAAAATGG
1 TAATTTTATAAATCGAGGGTAAAATGA
* *
116595 TAATTCTATAAATCGAGGGTAAAATGG
1 TAATTTTATAAATCGAGGGTAAAATGA
* * *
116622 TAATTTTATAAATTGAGGATAAAACGA
1 TAATTTTATAAATCGAGGGTAAAATGA
* * * *
116649 TAACTTTGTAAATCGAGGGTAAAACGG
1 TAATTTTATAAATCGAGGGTAAAATGA
* * *
116676 TAATTCTATAAATTGAGGGTAAAATGG
1 TAATTTTATAAATCGAGGGTAAAATGA
* ** * *
116703 TAATTCTATAAATCGAAAGAAAAACGA
1 TAATTTTATAAATCGAGGGTAAAATGA
* * * * *
116730 TAATTCTATAAATTGAAGGTGAAATGG
1 TAATTTTATAAATCGAGGGTAAAATGA
* * * *
116757 TAATTCTGTAAATCGAGGGTAAAACGG
1 TAATTTTATAAATCGAGGGTAAAATGA
* * *
116784 TAATTCTGTAAATCGGGGGTA
1 TAATTTTATAAATCGAGGGTA
116805 CTTTTATACT
Statistics
Matches: 221, Mismatches: 43, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 221 1.00
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.30
Consensus pattern (27 bp):
TAATTTTATAAATCGAGGGTAAAATGA
Found at i:116561 original size:54 final size:54
Alignment explanation
Indices: 116511--116804 Score: 302
Period size: 54 Copynumber: 5.4 Consensus size: 54
116501 AGGGGTATTT
* * * *
116511 TGGTAATTTTGTAAACCAAGGGTAAAATAATAATTCTGTAAATCGAGGGTAAAA
1 TGGTAATTTTATAAATCGAGGGTAAAATGATAATTCTGTAAATCGAGGGTAAAA
* * * *
116565 CGATAATTTTATAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAA
1 TGGTAATTTTATAAATCGAGGGTAAAATGATAATTCTGTAAATCGAGGGTAAAA
* * *
116619 TGGTAATTTTATAAATTGAGGATAAAACGATAACTT-TGTAAATCGAGGGTAAAA
1 TGGTAATTTTATAAATCGAGGGTAAAATGATAA-TTCTGTAAATCGAGGGTAAAA
* * * * * ** *
116673 CGGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTATAAATCGAAAGAAAAA
1 TGGTAATTTTATAAATCGAGGGTAAAATGATAATTCTGTAAATCGAGGGTAAAA
* * * * * * *
116727 CGATAATTCTATAAATTGAAGGTGAAATGGTAATTCTGTAAATCGAGGGTAAAA
1 TGGTAATTTTATAAATCGAGGGTAAAATGATAATTCTGTAAATCGAGGGTAAAA
* * * *
116781 CGGTAATTCTGTAAATCGGGGGTA
1 TGGTAATTTTATAAATCGAGGGTA
116805 CTTTTATACT
Statistics
Matches: 201, Mismatches: 37, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
53 2 0.01
54 197 0.98
55 2 0.01
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.30
Consensus pattern (54 bp):
TGGTAATTTTATAAATCGAGGGTAAAATGATAATTCTGTAAATCGAGGGTAAAA
Found at i:116852 original size:81 final size:81
Alignment explanation
Indices: 116766--116939 Score: 219
Period size: 81 Copynumber: 2.1 Consensus size: 81
116756 GTAATTCTGT
* * * *
116766 AAATCGAGGGTAAAACGGTAATTCTG-TAAATC-GGGGGTACTTTTATACTTTTTACAAGTCGAG
1 AAATCGAGGGTAAAACGGTAATT-TGATAAA-CGGGGGGTACGTTGATA-ATTTTACAAGTCGAA
116829 GGTATTTCAGTAATTTTAC
63 GGTATTTCAGTAATTTTAC
* *** *
116848 -AATCGACGGTATTTCGGTAATTTGATAAACGGGGGGTACGTTGGTAATTTTACAAGTCGAAGGT
1 AAATCGAGGGTAAAACGGTAATTTGATAAACGGGGGGTACGTTGATAATTTTACAAGTCGAAGGT
116912 ATTTCAGTAATTTTAC
66 ATTTCAGTAATTTTAC
116928 AAATCGAGGGTA
1 AAATCGAGGGTA
116940 TTTCGGTAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
80 35 0.44
81 44 0.56
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.34
Consensus pattern (81 bp):
AAATCGAGGGTAAAACGGTAATTTGATAAACGGGGGGTACGTTGATAATTTTACAAGTCGAAGGT
ATTTCAGTAATTTTAC
Found at i:116912 original size:27 final size:27
Alignment explanation
Indices: 116890--116953 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
116880 GGGGTACGTT
*
116890 GGTAATTTTACAAGTCGAAGGTATTTC
1 GGTAATTTTACAAATCGAAGGTATTTC
* *
116917 AGTAATTTTACAAATCGAGGGTATTTC
1 GGTAATTTTACAAATCGAAGGTATTTC
116944 GGTAATTTTA
1 GGTAATTTTA
116954 GTAAACTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
GGTAATTTTACAAATCGAAGGTATTTC
Found at i:116939 original size:54 final size:53
Alignment explanation
Indices: 116815--116953 Score: 165
Period size: 54 Copynumber: 2.6 Consensus size: 53
116805 CTTTTATACT
* * * *
116815 TTTTACAAGTCGAGGGTATTTCAGTAATTTTACAATCGACGGTATTTCGGTAA
1 TTTTACAAATCGAGGGTATTTCGGTAATTTTACAATCGAAGGTATTTCAGTAA
* * * *
116868 TTTGATAAA-CGGGGGGTACGTT-GGTAATTTTACAAGTCGAAGGTATTTCAGTAA
1 TTTTACAAATC-GAGGGTA-TTTCGGTAATTTTACAA-TCGAAGGTATTTCAGTAA
116922 TTTTACAAATCGAGGGTATTTCGGTAATTTTA
1 TTTTACAAATCGAGGGTATTTCGGTAATTTTA
116954 GTAAACTAAA
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
52 1 0.01
53 26 0.38
54 41 0.59
55 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (53 bp):
TTTTACAAATCGAGGGTATTTCGGTAATTTTACAATCGAAGGTATTTCAGTAA
Found at i:120074 original size:23 final size:21
Alignment explanation
Indices: 120046--120094 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
120036 TAAAAAAGGG
120046 TAATAAAT-AAATAGATAAATAGA
1 TAATAAATAAAATAG-T-AATA-A
120069 TAAT-AATAAAATAGTAATAA
1 TAATAAATAAAATAGTAATAA
120089 TAATAA
1 TAATAA
120095 TGAAGGCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 5 0.21
21 5 0.21
22 4 0.17
23 10 0.42
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (21 bp):
TAATAAATAAAATAGTAATAA
Found at i:120086 original size:14 final size:15
Alignment explanation
Indices: 120062--120091 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
120052 ATAAATAGAT
120062 AAATAGATAATAATA
1 AAATAGATAATAATA
120077 AAATAG-TAATAATA
1 AAATAGATAATAATA
120091 A
1 A
120092 TAATGAAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (15 bp):
AAATAGATAATAATA
Found at i:120253 original size:5 final size:4
Alignment explanation
Indices: 120130--120294 Score: 92
Period size: 4 Copynumber: 41.8 Consensus size: 4
120120 CGATGATAGA
* * * * *
120130 AAAT AAAA AAAT AAA- ATAT AAA- AAAT GAAG GAAT -AAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * * *
120175 AAAT AAAT ACAAG GATT AAAAT AAA- AAAT AAA- ATAT AAAT GAAT AAAT
1 AAAT AAAT A-AAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
120223 AAGT AAAT GAAC AAAT AAAT AAAT AAAAT AAA- AGGAA- CAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT A--AAT AAAT AAAT AAAT
* *
120272 AAAC AAGT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAA
120295 AGAATTAAAA
Statistics
Matches: 121, Mismatches: 29, Indels: 22
0.70 0.17 0.13
Matches are distributed among these distances:
3 16 0.13
4 95 0.79
5 10 0.08
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:120265 original size:41 final size:42
Alignment explanation
Indices: 120193--120296 Score: 133
Period size: 41 Copynumber: 2.5 Consensus size: 42
120183 ACAAGGATTA
* * *
120193 AAATAAA-AAATAAAATATAAATGAATAAATAAGTAAATGAAC
1 AAATAAATAAATAAAATA-AAAGGAATAAATAAATAAATAAAC
*
120235 AAATAAATAAATAAAATAAAAGGAA-CAATAAATAAATAAAC
1 AAATAAATAAATAAAATAAAAGGAATAAATAAATAAATAAAC
*
120276 AAGTAAATAAAT-AAATAAAAG
1 AAATAAATAAATAAAATAAAAG
120297 AATTAAAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 9 0.16
41 24 0.43
42 13 0.23
43 10 0.18
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (42 bp):
AAATAAATAAATAAAATAAAAGGAATAAATAAATAAATAAAC
Found at i:121524 original size:13 final size:14
Alignment explanation
Indices: 121508--121536 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
121498 TGTAAATGGA
121508 ATTTGGACTTT-TT
1 ATTTGGACTTTATT
121521 ATTTGGACTTTATT
1 ATTTGGACTTTATT
121535 AT
1 AT
121537 ATTTTTGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59
Consensus pattern (14 bp):
ATTTGGACTTTATT
Found at i:123007 original size:30 final size:30
Alignment explanation
Indices: 122967--123025 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
122957 TTTACGAGCC
* *
122967 TAGGGACCAAAGTGCAAATATGTAAAAGTT
1 TAGGGACCAAAATGCAAATATGAAAAAGTT
* * *
122997 TAGGGGCCAAAATGTAAATTTGAAAAAGT
1 TAGGGACCAAAATGCAAATATGAAAAAGT
123026 ATGATTTATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (30 bp):
TAGGGACCAAAATGCAAATATGAAAAAGTT
Found at i:135219 original size:2 final size:2
Alignment explanation
Indices: 135212--135245 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
135202 AGTCCTTGCA
*
135212 AG AG AG AG AG AG AA 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
135246 GAATCTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Done.