Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 11 of 226
Found at i:3899854 original size:21 final size:21
Alignment explanation
Indices: 3899830--3899871 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3899820 ATTATAAGAT
3899830 AATTACAATATTCATACAAAA
1 AATTACAATATTCATACAAAA
3899851 AATTACAATATTCATACAAAA
1 AATTACAATATTCATACAAAA
3899872 TACTAATCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (21 bp):
AATTACAATATTCATACAAAA
Found at i:3900779 original size:21 final size:21
Alignment explanation
Indices: 3900755--3900846 Score: 59
Period size: 21 Copynumber: 4.4 Consensus size: 21
3900745 ATATAGGGAG
*
3900755 AATTAAATTATTATTAAACT-T
1 AATTAAATTAATATTAAA-TAT
**
3900776 AATTACTTTAATATTAAATAT
1 AATTAAATTAATATTAAATAT
* *
3900797 TATTAAATTAATA-AAAATACT
1 AATTAAATTAATATTAAATA-T
3900818 -ATTAACA-TAGATATTAAAT-T
1 AATTAA-ATTA-ATATTAAATAT
3900838 AAATTAAAT
1 -AATTAAAT
3900847 ATTAAATCTA
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
20 14 0.25
21 32 0.58
22 9 0.16
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (21 bp):
AATTAAATTAATATTAAATAT
Found at i:3902078 original size:10 final size:9
Alignment explanation
Indices: 3902047--3902075 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
3902037 TACTGCTCAT
3902047 CCACTTCCC
1 CCACTTCCC
3902056 CCACTTCCC
1 CCACTTCCC
3902065 CCACTTCCC
1 CCACTTCCC
3902074 CC
1 CC
3902076 CACATATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.69, G:0.00, T:0.21
Consensus pattern (9 bp):
CCACTTCCC
Found at i:3906021 original size:13 final size:13
Alignment explanation
Indices: 3906003--3906028 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3905993 ACTTAAAAAG
3906003 GTACCAAATTCAA
1 GTACCAAATTCAA
3906016 GTACCAAATTCAA
1 GTACCAAATTCAA
3906029 AATCTTCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
GTACCAAATTCAA
Found at i:3928805 original size:21 final size:21
Alignment explanation
Indices: 3928781--3928822 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3928771 ATCGTGAAAG
*
3928781 AAGGATTGGAGACGGCGGAGA
1 AAGGACTGGAGACGGCGGAGA
*
3928802 AAGGGCTGGAGACGGCGGAGA
1 AAGGACTGGAGACGGCGGAGA
3928823 GAGGGATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.50, T:0.07
Consensus pattern (21 bp):
AAGGACTGGAGACGGCGGAGA
Found at i:3928827 original size:21 final size:21
Alignment explanation
Indices: 3928787--3928827 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3928777 AAAGAAGGAT
3928787 TGGAGACGGCGGAGAAAGGGC
1 TGGAGACGGCGGAGAAAGGGC
*
3928808 TGGAGACGGCGGAGAGAGGG
1 TGGAGACGGCGGAGAAAGGG
3928828 ATCTTTACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.56, T:0.05
Consensus pattern (21 bp):
TGGAGACGGCGGAGAAAGGGC
Found at i:3945950 original size:60 final size:60
Alignment explanation
Indices: 3945870--3946001 Score: 219
Period size: 60 Copynumber: 2.2 Consensus size: 60
3945860 ATTGTAATTT
* * *
3945870 TTTTTGTTTTTATAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAA
1 TTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
*
3945930 TTTTTGTGTTTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
1 TTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
*
3945990 TTGTTGTGTTTA
1 TTTTTGTGTTTA
3946002 GTTTAGTATT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (60 bp):
TTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAA
Found at i:3946443 original size:20 final size:22
Alignment explanation
Indices: 3946390--3946444 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
3946380 ATAGGCGCGA
*
3946390 ATTAATTTTTTATATTAAAAAT
1 ATTAATTTTTTATAATAAAAAT
*
3946412 ATT-TTTTGTTTA-AAT-AAAAT
1 ATTAATTT-TTTATAATAAAAAT
3946432 ATTAATTTTTTAT
1 ATTAATTTTTTAT
3946445 TTTTATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
20 12 0.44
21 8 0.30
22 7 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTAATTTTTTATAATAAAAAT
Found at i:3947282 original size:39 final size:38
Alignment explanation
Indices: 3947165--3947293 Score: 106
Period size: 36 Copynumber: 3.4 Consensus size: 38
3947155 GATCCGATTG
* *
3947165 AAACACGAGAATTTCTTGTTTTGAAAACACGAGAATTTTA
1 AAACACGAG-ATTT-TTTTTTTGAAAACACGAAAATTTTA
** * * *
3947205 TGACA-TA-ATATTTTTTTT-AAAAC-C-AAAATTTATG
1 AAACACGAGATTTTTTTTTTGAAAACACGAAAATTT-TA
3947239 AAACACGAGATTTTTTTTTTGAAAACACGAAAATTTTCA
1 AAACACGAGATTTTTTTTTTGAAAACACGAAAATTTT-A
*
3947278 AAACACCGAAATTTTT
1 AAACA-CGAGATTTTT
3947294 GAAAACAAGA
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
33 6 0.09
34 5 0.07
35 6 0.09
36 16 0.24
37 8 0.12
38 2 0.03
39 13 0.19
40 12 0.18
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.36
Consensus pattern (38 bp):
AAACACGAGATTTTTTTTTTGAAAACACGAAAATTTTA
Found at i:3947300 original size:35 final size:35
Alignment explanation
Indices: 3947254--3947389 Score: 150
Period size: 35 Copynumber: 3.9 Consensus size: 35
3947244 CGAGATTTTT
**
3947254 TTTTTGAAAACACGAAAATTTTCAAAACACCGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
* ** *
3947289 TTTTTGAAAACAAGAGGATTTTTGAAATA-CGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCG-AAA
* *
3947324 ATTTTGAAAACACGAAAATTTTTGAAACACGGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
*
3947359 TTTTTG-AAACACAAAAATTTTTAGAAGACAC
1 TTTTTGAAAACACGAAAATTTTT-GAA-ACAC
3947390 TAAAAATTTT
Statistics
Matches: 83, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
34 17 0.20
35 61 0.73
36 5 0.06
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
Found at i:3947380 original size:18 final size:17
Alignment explanation
Indices: 3947254--3947404 Score: 117
Period size: 17 Copynumber: 8.5 Consensus size: 17
3947244 CGAGATTTTT
*
3947254 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACAAAAA
** **
3947272 TTTTCAAAACACCGAAA
1 TTTTTGAAACACAAAAA
*
3947289 TTTTTGAAA-ACAAGAGGA
1 TTTTTGAAACACAA-A-AA
*
3947307 TTTTTGAAATACGAAAAA
1 TTTTTGAAACAC-AAAAA
*
3947325 -TTTTGAAAACACGAAAA
1 TTTTTG-AAACACAAAAA
**
3947342 TTTTTGAAACACGGAAA
1 TTTTTGAAACACAAAAA
3947359 TTTTTGAAACACAAAAA
1 TTTTTGAAACACAAAAA
3947376 TTTTTAGAAGACACTAAAAA
1 TTTTT-GAA-ACAC-AAAAA
*
3947396 TTTTGGAAA
1 TTTTTGAAA
3947405 ATGGATTTTT
Statistics
Matches: 108, Mismatches: 16, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
16 2 0.02
17 56 0.52
18 29 0.27
19 10 0.09
20 11 0.10
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.29
Consensus pattern (17 bp):
TTTTTGAAACACAAAAA
Found at i:3947615 original size:20 final size:19
Alignment explanation
Indices: 3947577--3947623 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
3947567 GAATATATTT
3947577 TTTTTGAAACACGAGAAAAA
1 TTTTTGAAACACG-GAAAAA
*
3947597 TTTTTGAAGGCAC-GAAAAA
1 TTTTTGAA-ACACGGAAAAA
3947616 -TTTTGAAA
1 TTTTTGAAA
3947624 AATAGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 7 0.29
19 6 0.25
20 8 0.33
21 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (19 bp):
TTTTTGAAACACGGAAAAA
Found at i:3947996 original size:8 final size:8
Alignment explanation
Indices: 3947983--3948078 Score: 99
Period size: 8 Copynumber: 12.0 Consensus size: 8
3947973 TTGAAACTCT
3947983 TTTTTTTC
1 TTTTTTTC
3947991 TTTTTTTC
1 TTTTTTTC
3947999 TTCTTTTTTCC
1 -T-TTTTTT-C
*
3948010 TTTTTTCC
1 TTTTTTTC
3948018 TTTTTTTC
1 TTTTTTTC
*
3948026 -TCTTTTC
1 TTTTTTTC
3948033 TTTTTTTC
1 TTTTTTTC
*
3948041 -TTCTTTC
1 TTTTTTTC
3948048 TTTTTTTC
1 TTTTTTTC
3948056 -TTTTTTC
1 TTTTTTTC
* *
3948063 TTTCTCTC
1 TTTTTTTC
3948071 TTTTTTTC
1 TTTTTTTC
3948079 CTGGCCTGCT
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
7 19 0.26
8 39 0.54
9 6 0.08
10 7 0.10
11 1 0.01
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTTC
Found at i:3948035 original size:15 final size:15
Alignment explanation
Indices: 3947980--3948076 Score: 108
Period size: 15 Copynumber: 6.5 Consensus size: 15
3947970 GAATTGAAAC
*
3947980 TCTTTTTT-TTCTTT
1 TCTTTTTTCTTTTTT
*
3947994 T-TTTCTTCTTTTTT
1 TCTTTTTTCTTTTTT
*
3948008 CCTTTTTTCCTTTTTT
1 TCTTTTTT-CTTTTTT
*
3948024 TCTCTTTTCTTTTTT
1 TCTTTTTTCTTTTTT
*
3948039 TCTTCTTTCTTTTTT
1 TCTTTTTTCTTTTTT
* *
3948054 TCTTTTTTCTTTCTC
1 TCTTTTTTCTTTTTT
3948069 TCTTTTTT
1 TCTTTTTT
3948077 TCCTGGCCTG
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
13 5 0.07
14 6 0.09
15 45 0.65
16 13 0.19
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TCTTTTTTCTTTTTT
Found at i:3948067 original size:23 final size:22
Alignment explanation
Indices: 3947980--3948078 Score: 96
Period size: 23 Copynumber: 4.5 Consensus size: 22
3947970 GAATTGAAAC
*
3947980 TCTTTTTTT-TCTTTTTTTC-T
1 TCTTTTTTTCTTTTTTTTTCTT
* *
3948000 TCTTTTTTCCTTTTTTCCTTTTTT
1 TCTTTTTTTCTTTTTT--TTTCTT
*
3948024 TC-TCTTTTCTTTTTTTCTTCTT
1 TCTTTTTTTCTTTTTTT-TTCTT
*
3948046 TCTTTTTTTCTTTTTTCTTTCTC
1 TCTTTTTTTCTTTTTT-TTTCTT
3948069 TCTTTTTTTC
1 TCTTTTTTTC
3948079 CTGGCCTGCT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
20 8 0.12
21 6 0.09
22 6 0.09
23 40 0.62
24 4 0.06
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (22 bp):
TCTTTTTTTCTTTTTTTTTCTT
Found at i:3948238 original size:30 final size:31
Alignment explanation
Indices: 3948204--3948269 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
3948194 GGGCCTTTTC
* *
3948204 TTTTTGGGCTGCTTTTTTTTGTTTTG-GTT-T
1 TTTTTGGGCTGATTTGTTTT-TTTTGTGTTGT
*
3948234 TTTTTGGGTTGATTTGTTTTTTTTGTGTTGT
1 TTTTTGGGCTGATTTGTTTTTTTTGTGTTGT
3948265 TTTTT
1 TTTTT
3948270 TTTAATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.16
30 20 0.65
31 6 0.19
ACGTcount: A:0.02, C:0.03, G:0.23, T:0.73
Consensus pattern (31 bp):
TTTTTGGGCTGATTTGTTTTTTTTGTGTTGT
Found at i:3948249 original size:20 final size:19
Alignment explanation
Indices: 3948230--3948272 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3948220 TTTTGTTTTG
3948230 GTTTTTTTTGGGTTGATTT
1 GTTTTTTTTGGGTTGATTT
*
3948249 GTTTTTTTTGTGTTG-TTT
1 GTTTTTTTTGGGTTGATTT
3948267 -TTTTTT
1 GTTTTTT
3948273 AATTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 3 0.13
19 14 0.61
ACGTcount: A:0.02, C:0.00, G:0.21, T:0.77
Consensus pattern (19 bp):
GTTTTTTTTGGGTTGATTT
Found at i:3948272 original size:15 final size:15
Alignment explanation
Indices: 3948216--3948272 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
3948206 TTTGGGCTGC
* *
3948216 TTTTTTTTGTTTTGG
1 TTTTTTTTGTGTTGT
*
3948231 TTTTTTTTGGGTTGATTT
1 TTTTTTTTGTGTTG---T
3948249 GTTTTTTTTGTGTTGT
1 -TTTTTTTTGTGTTGT
3948265 TTTTTTTT
1 TTTTTTTT
3948273 AATTAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 20 0.59
16 1 0.03
19 13 0.38
ACGTcount: A:0.02, C:0.00, G:0.19, T:0.79
Consensus pattern (15 bp):
TTTTTTTTGTGTTGT
Found at i:3948385 original size:10 final size:10
Alignment explanation
Indices: 3948375--3948424 Score: 75
Period size: 10 Copynumber: 5.1 Consensus size: 10
3948365 TTAAATTTTT
* *
3948375 TTCTTTTTTT
1 TTCTTTCTTC
3948385 TTCTTTCTTC
1 TTCTTTCTTC
3948395 TTCTTTCTTC
1 TTCTTTCTTC
3948405 TTCTTTCTTC
1 TTCTTTCTTC
3948415 TTCTTT-TTC
1 TTCTTTCTTC
3948424 T
1 T
3948425 CCTCCTACAC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
9 4 0.11
10 34 0.89
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (10 bp):
TTCTTTCTTC
Found at i:3948525 original size:10 final size:10
Alignment explanation
Indices: 3948490--3948539 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
3948480 ACGCCGGTAC
3948490 TCTT-TCTTT
1 TCTTCTCTTT
* *
3948499 TCTTCTCCTC
1 TCTTCTCTTT
3948509 T-TTCTCTTT
1 TCTTCTCTTT
3948518 TCTTCTCTTT
1 TCTTCTCTTT
*
3948528 TCTTCTTTTT
1 TCTTCTCTTT
3948538 TC
1 TC
3948540 CTTCGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:3948537 original size:19 final size:19
Alignment explanation
Indices: 3948494--3948536 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
3948484 CGGTACTCTT
3948494 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
3948513 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
3948530 TTCTTTT
1 -TCTTTT
3948537 TTCCTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:3948843 original size:30 final size:30
Alignment explanation
Indices: 3948803--3948904 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
3948793 ACTTAGGATT
*
3948803 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
3948833 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
3948863 AAAATAAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
3948893 AAAATGCAATTT
1 AAAATGAAATTT
3948905 TTATTTTTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 2 0.03
30 58 0.97
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:3948925 original size:14 final size:15
Alignment explanation
Indices: 3948900--3948934 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
3948890 GTCAAAATGC
3948900 AATTTTTATTTTTAA
1 AATTTTTATTTTTAA
*
3948915 AATTTTT-TTTTTGA
1 AATTTTTATTTTTAA
3948929 AATTTT
1 AATTTT
3948935 GAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
AATTTTTATTTTTAA
Found at i:3956669 original size:18 final size:17
Alignment explanation
Indices: 3956632--3956670 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
3956622 TTTTTTATTT
3956632 TAAAATTTTTATTAAAA
1 TAAAATTTTTATTAAAA
3956649 TAAAATTTTAATATT-AAA
1 TAAAATTTT--TATTAAAA
3956667 TAAA
1 TAAA
3956671 TATTAATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 7 0.35
19 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTTTATTAAAA
Found at i:3956671 original size:17 final size:19
Alignment explanation
Indices: 3956641--3956677 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
3956631 TTAAAATTTT
*
3956641 TATTAAAATAAAATTTTAA
1 TATTAAAATAAAATATTAA
3956660 TATT-AAAT-AAATATTAA
1 TATTAAAATAAAATATTAA
3956677 T
1 T
3956678 GTAATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TATTAAAATAAAATATTAA
Found at i:3960068 original size:24 final size:24
Alignment explanation
Indices: 3960041--3960092 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3960031 TTAGTAAGTC
*
3960041 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3960065 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3960089 AAAT
1 AAAT
3960093 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3962038 original size:24 final size:24
Alignment explanation
Indices: 3962011--3962062 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3962001 TTAGTAAGTC
*
3962011 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3962035 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3962059 AAAT
1 AAAT
3962063 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3967177 original size:38 final size:38
Alignment explanation
Indices: 3967128--3967204 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
3967118 AAAATAACCT
3967128 AAAAATTAAGTGACCAAAATAAGTAACAACATGATATA
1 AAAAATTAAGTGACCAAAATAAGTAACAACATGATATA
3967166 AAAAATTAAGTGACCAAAATAAGTAACAACATGATATA
1 AAAAATTAAGTGACCAAAATAAGTAACAACATGATATA
3967204 A
1 A
3967205 CATGTACAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.21
Consensus pattern (38 bp):
AAAAATTAAGTGACCAAAATAAGTAACAACATGATATA
Found at i:3972144 original size:36 final size:35
Alignment explanation
Indices: 3972062--3972147 Score: 106
Period size: 33 Copynumber: 2.5 Consensus size: 35
3972052 CAACAATAAC
*
3972062 AACAA-AATAATAAAATAAGAGTTATATAATATCT
1 AACAATAATAACAAAATAAGAGTTATATAATATCT
* * *
3972096 -A-AATAAAAACAAAATGAGATTTATATAATATCT
1 AACAATAATAACAAAATAAGAGTTATATAATATCT
3972129 AAACAATAATAACAAAATA
1 -AACAATAATAACAAAATA
3972148 TTAACAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
32 2 0.05
33 26 0.62
35 1 0.02
36 13 0.31
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.27
Consensus pattern (35 bp):
AACAATAATAACAAAATAAGAGTTATATAATATCT
Found at i:3972147 original size:11 final size:11
Alignment explanation
Indices: 3972133--3972168 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
3972123 ATATCTAAAC
3972133 AATAATAACAA
1 AATAATAACAA
*
3972144 AATATTAACAA
1 AATAATAACAA
*
3972155 TATAATAACAA
1 AATAATAACAA
3972166 AAT
1 AAT
3972169 GACAGTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (11 bp):
AATAATAACAA
Found at i:3973805 original size:26 final size:27
Alignment explanation
Indices: 3973769--3973830 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
3973759 GGCCCGGCCC
* * *
3973769 ATTTTAAAAAT-AAACATTAACAAATT
1 ATTTTAAAAATAAAAAATAAAAAAATT
3973795 ATTTTAAAAATAAAAAATAAAAAAATT
1 ATTTTAAAAATAAAAAATAAAAAAATT
3973822 ATTTTAAAA
1 ATTTTAAAA
3973831 GTATTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 11 0.34
27 21 0.66
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (27 bp):
ATTTTAAAAATAAAAAATAAAAAAATT
Found at i:3974848 original size:11 final size:11
Alignment explanation
Indices: 3974834--3974879 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
3974824 TTTATTGTTG
*
3974834 TTTTTTTATTA
1 TTTTGTTATTA
* *
3974845 TTTTGTTGTAA
1 TTTTGTTATTA
3974856 TTTTGTTATTA
1 TTTTGTTATTA
*
3974867 TATTGTTATTA
1 TTTTGTTATTA
3974878 TT
1 TT
3974880 CTATTGTTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.72
Consensus pattern (11 bp):
TTTTGTTATTA
Found at i:3974852 original size:19 final size:21
Alignment explanation
Indices: 3974826--3974873 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
3974816 AAATATTTTT
3974826 TATTGTTGT-TTTT-TTATTA
1 TATTGTTGTATTTTGTTATTA
*
3974845 TTTTGTTGTAATTTTGTTATTA
1 TATTGTTGT-ATTTTGTTATTA
3974867 TATTGTT
1 TATTGTT
3974874 ATTATTCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.33
21 4 0.17
22 12 0.50
ACGTcount: A:0.17, C:0.00, G:0.12, T:0.71
Consensus pattern (21 bp):
TATTGTTGTATTTTGTTATTA
Found at i:3974884 original size:14 final size:14
Alignment explanation
Indices: 3974861--3974890 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3974851 TGTAATTTTG
3974861 TTATTATATTGTTA
1 TTATTATATTGTTA
*
3974875 TTATTCTATTGTTA
1 TTATTATATTGTTA
3974889 TT
1 TT
3974891 GTTTAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (14 bp):
TTATTATATTGTTA
Found at i:3982862 original size:45 final size:45
Alignment explanation
Indices: 3982791--3982879 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 45
3982781 TATCGTTTAA
3982791 TTAATTGTTTATTATTATATTATTATATA-ATCAA-TAATATTATTG
1 TTAATTGTTTATTATTATATTATTATA-ACAT-AATTAATATTATTG
*
3982836 TTAATGTGTTTATT-TTGT-TTATTTATAACATAATTAATATTATT
1 TTAAT-TGTTTATTATTATATTA-TTATAACATAATTAATATTATT
3982880 TATATTTGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
44 6 0.15
45 25 0.64
46 8 0.21
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (45 bp):
TTAATTGTTTATTATTATATTATTATAACATAATTAATATTATTG
Found at i:3983556 original size:26 final size:27
Alignment explanation
Indices: 3983502--3983558 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
3983492 AATTTTAAAA
* *
3983502 TATTTTTAAAATAATTTTTTTTATTTT
1 TATTTTTAAAATAATTTTTTTGATGTT
*
3983529 TATTTTTAAAAT-ATTTTTTTGGTGTT
1 TATTTTTAAAATAATTTTTTTGATGTT
3983555 TATT
1 TATT
3983559 AAAAATAGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (27 bp):
TATTTTTAAAATAATTTTTTTGATGTT
Found at i:3989971 original size:18 final size:19
Alignment explanation
Indices: 3989948--3989992 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
3989938 AAATGTACTA
3989948 ATTAATTT-TTTGGACCAC
1 ATTAATTTCTTTGGACCAC
*
3989966 ATTAATTTCTTTGGACGAC
1 ATTAATTTCTTTGGACCAC
3989985 ATTAATTT
1 ATTAATTT
3989993 AAGATCTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (19 bp):
ATTAATTTCTTTGGACCAC
Found at i:3993554 original size:22 final size:20
Alignment explanation
Indices: 3993513--3993554 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3993503 ACAAACATAT
3993513 TAAATAAGAACAAGATTGAA
1 TAAATAAGAACAAGATTGAA
*
3993533 TAAATAATTAACAATGATTGAA
1 TAAATAA-GAACAA-GATTGAA
3993555 ACAATTGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 5 0.26
22 7 0.37
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.26
Consensus pattern (20 bp):
TAAATAAGAACAAGATTGAA
Found at i:3996217 original size:7 final size:7
Alignment explanation
Indices: 3996205--3996231 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3996195 GTATAATATA
3996205 AACCAAT
1 AACCAAT
3996212 AACCAAT
1 AACCAAT
3996219 AACCAAT
1 AACCAAT
3996226 AACCAA
1 AACCAA
3996232 ATCCCTCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.30, G:0.00, T:0.11
Consensus pattern (7 bp):
AACCAAT
Found at i:4001544 original size:11 final size:12
Alignment explanation
Indices: 4001528--4001556 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4001518 TTTAATTCTC
4001528 TTTTTTCT-GCT
1 TTTTTTCTGGCT
4001539 TTTTTTCTGGCT
1 TTTTTTCTGGCT
4001551 TTTTTT
1 TTTTTT
4001557 TTTTTGCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (12 bp):
TTTTTTCTGGCT
Found at i:4003823 original size:18 final size:17
Alignment explanation
Indices: 4003784--4003826 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
4003774 ATGTTTATAT
4003784 GTATATATATATTACAA
1 GTATATATATATTACAA
*
4003801 -AATATATATATGTACAA
1 GTATATATATAT-TACAA
4003818 GTATATATA
1 GTATATATA
4003827 AAAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 10 0.45
17 5 0.23
18 7 0.32
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (17 bp):
GTATATATATATTACAA
Found at i:4005591 original size:44 final size:44
Alignment explanation
Indices: 4005537--4005694 Score: 169
Period size: 44 Copynumber: 3.6 Consensus size: 44
4005527 GATGTGATCT
* * * *
4005537 GCTCTACTGCAACTTCAGAGAGATAAGATCAATC-ATTTGAACCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATCGATTT-AATCC
* *
4005581 GCTCCACTGCAACTTCAGGGAGATAAAATCTA-CTACTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATCGA-TTTAATCC
* * * * *
4005625 GCTCCTCTGCAACTTCAGGGAGATAGGAT-TATCGGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTATC-GATTTAATCC
4005669 GCTCCACTGCAACTTCAGGGAGATAA
1 GCTCCACTGCAACTTCAGGGAGATAA
4005695 AATTTGTACC
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
43 3 0.03
44 90 0.94
45 3 0.03
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATCTATCGATTTAATCC
Found at i:4005708 original size:44 final size:43
Alignment explanation
Indices: 4005581--4005791 Score: 165
Period size: 44 Copynumber: 4.8 Consensus size: 43
4005571 ATTTGAACCC
** * *
4005581 GCTCCACTGCAACTTCAGGGAGATAAAATCTACTACTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAAAT-TTGTACTTCAATCT
* ** *
4005625 GCTCCTCTGCAACTTCAGGGAGATAGGATTATCG-GCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAAATT-T-GTACTTCAATCT
*
4005669 GCTCCACTGCAACTTCAGGGAGATAAAATTTGTACCTTCAATTT
1 GCTCCACTGCAACTTCAGGGAGATAAAATTTGTA-CTTCAATCT
* * * * * * *
4005713 GCCCCACTGCATCTTCAGGGGGATAAGACTTTGGTTCTTCGATCC
1 GCTCCACTGCAACTTCAGGGAGATAA-AATTT-GTACTTCAATCT
* * **
4005758 ACTCCACTGTAA-TATCAGGGAGATAGGATTTGTA
1 GCTCCACTGCAACT-TCAGGGAGATAAAATTTGTA
4005792 ACTCGTAACT
Statistics
Matches: 130, Mismatches: 30, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
42 1 0.01
43 4 0.03
44 95 0.73
45 28 0.22
46 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGGAGATAAAATTTGTACTTCAATCT
Found at i:4005940 original size:25 final size:25
Alignment explanation
Indices: 4005912--4005961 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
4005902 CTTGGGGCGT
* *
4005912 AAGATTCGCTGATGTAGCTTTAATC
1 AAGATTCACCGATGTAGCTTTAATC
*
4005937 AAGATTCACCGATGTGGCTTTAATC
1 AAGATTCACCGATGTAGCTTTAATC
4005962 TTTTTAACTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (25 bp):
AAGATTCACCGATGTAGCTTTAATC
Found at i:4005966 original size:125 final size:125
Alignment explanation
Indices: 4005824--4006311 Score: 807
Period size: 125 Copynumber: 3.9 Consensus size: 125
4005814 GATTCGTCAT
* * * ** *
4005824 TGTGGCTTTAATCTTTTTAACTGCAATATCGGAGAAATAAGATTCACCAATTTGGCTTTAATCTG
1 TGTGGCTTTAATCTTTTTAACTGCAATGTAGGGGAAGCAAGATTCACCAATGTGGCTTTAATCTG
* *
4005889 TTCCACTGTATCGCTTGGGGCGTAAGATTCGCTGATGTAGCTTTAATCAAGATTCACCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
*
4005949 TGTGGCTTTAATCTTTTTAACTGCAATGTAGGGGAAGCAAGATTCACCAATTTGGCTTTAATCTG
1 TGTGGCTTTAATCTTTTTAACTGCAATGTAGGGGAAGCAAGATTCACCAATGTGGCTTTAATCTG
4006014 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
* *
4006074 TGTGGCTTTAATCTTTTTAACTGCAATGTAGGGGAAGCAAGATTCACCGATGTGGTTTTAATCTG
1 TGTGGCTTTAATCTTTTTAACTGCAATGTAGGGGAAGCAAGATTCACCAATGTGGCTTTAATCTG
*
4006139 TTCCACTGCATCGTTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
66 TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
* *
4006199 TGTGGCTTTAATCTTTTTAACTGCAATGTAGGGGAAGCAAGATTCACCGATGTGGTTTTAATCTG
1 TGTGGCTTTAATCTTTTTAACTGCAATGTAGGGGAAGCAAGATTCACCAATGTGGCTTTAATCTG
* * *
4006264 TTCCACTGCACCGCCTGAGAG-GTAAGATTCGCTGTTGTAGCTTTAATC
66 TTCCACTGCATCGCTTG-GGGCGTAAGATTCGCTGTTGTAGCTTTAATC
4006312 TTTTTTAACC
Statistics
Matches: 347, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
125 345 0.99
126 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (125 bp):
TGTGGCTTTAATCTTTTTAACTGCAATGTAGGGGAAGCAAGATTCACCAATGTGGCTTTAATCTG
TTCCACTGCATCGCTTGGGGCGTAAGATTCGCTGTTGTAGCTTTAATCAAGATTCACCGA
Found at i:4006250 original size:50 final size:49
Alignment explanation
Indices: 4006186--4006363 Score: 169
Period size: 50 Copynumber: 3.6 Consensus size: 49
4006176 TAGCTTTAAT
* *
4006186 CAAGATTCACCGATGTGGCTTTAATCTTTTTAACTGCAATGTAGGGGAAG
1 CAAGATTCACCGATGTGGCTTTAATCTTTTTAACTGCAATGTA-GAGAGG
* * ** **
4006236 CAAGATTCACCGATGTGGTTTTAATCTGTTCCACTGCACCGCCT-GAGAGG
1 CAAGATTCACCGATGTGGCTTTAATCTTTTTAACTGCAATG--TAGAGAGG
* * * * * *
4006286 TAAGATTCGCTGTTGTAGCTTTAATCTTTTTTAACCGCAATGTCAGAGAGG
1 CAAGATTCACCGATGTGGCTTTAATC-TTTTTAACTGCAATGT-AGAGAGG
*
4006337 CAAGATTCACCGTTGTGGCTTTAATCT
1 CAAGATTCACCGATGTGGCTTTAATCT
4006364 ATTCCACTGC
Statistics
Matches: 99, Mismatches: 24, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
49 1 0.01
50 60 0.61
51 37 0.37
52 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (49 bp):
CAAGATTCACCGATGTGGCTTTAATCTTTTTAACTGCAATGTAGAGAGG
Found at i:4006361 original size:101 final size:100
Alignment explanation
Indices: 4006203--4006523 Score: 376
Period size: 100 Copynumber: 3.2 Consensus size: 100
4006193 CACCGATGTG
* *
4006203 GCTTTAATCTTTTTAACTGCAATGT-AGGGGAAGCAAGATTCACCGATGTGGTTTTAATCTGTTC
1 GCTTTAATCTTTTTAACTGCAATGTCA-GGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTC
*
4006267 CACTGCACCGCCTGAGAGGTAAGATTCGCTGTTGTA
65 CACTGCACCGCCTGAGAGATAAGATTCGCTGTTGTA
* * * *
4006303 GCTTTAATCTTTTTTAACCGCAATGTCAGAGAGGCAAGATTCACCGTTGTGGCTTTAATCTATTC
1 GCTTTAATC-TTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTC
* * *
4006368 CACTGCACCGCTTGGGAGATAAGATTCGCTGATGTA
65 CACTGCACCGCCTGAGAGATAAGATTCGCTGTTGTA
* * * * ** * *
4006404 GCTTCAATCTTTTTAAATGCAATGTCAGGGAAGTAAGATCCATTGTTGTAGCTTCAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* * * * *
4006469 ACTACAACG-CTAGAAAAATAAGATCCGCTGTTGTA
66 ACTGCACCGCCT-GAGAGATAAGATTCGCTGTTGTA
* *
4006504 GCCTTAATCCTTTTAACTGC
1 GCTTTAATCTTTTTAACTGC
4006524 CAGGGAAATA
Statistics
Matches: 184, Mismatches: 34, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
99 1 0.01
100 95 0.52
101 87 0.47
102 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (100 bp):
GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
ACTGCACCGCCTGAGAGATAAGATTCGCTGTTGTA
Found at i:4006669 original size:50 final size:50
Alignment explanation
Indices: 4006604--4006835 Score: 261
Period size: 50 Copynumber: 4.6 Consensus size: 50
4006594 CGGGGAAACA
4006604 ATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAG
1 ATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAG
* * ** * *** *
4006654 ATCCGCTGTTGTAGCTTCAATTTTTTTAATTGCAATGTTAGGGAAGTAAG
1 ATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAG
* *
4006704 ATCCGCTGTTGTAGCTTCAATCTGTTCCACTACAACACTAGAAAAGTAAG
1 ATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAG
** * * ** *
4006754 ATCCGCTGTTGTAGCTTCAATCT-TCTTAATTGTAA-TGTCAGGGAAGTAAG
1 ATCCGCTGTTGTAGCTTCAATCTGT-TCCACTGCAACACT-AGGAAAGTAAG
*
4006804 ATCCGCTATTGTAGCTTCAATCTGTTCCACTG
1 ATCCGCTGTTGTAGCTTCAATCTGTTCCACTG
4006836 TTGTAGCTTC
Statistics
Matches: 146, Mismatches: 33, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
49 2 0.01
50 143 0.98
51 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (50 bp):
ATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAG
Found at i:4006725 original size:100 final size:100
Alignment explanation
Indices: 4006604--4006835 Score: 401
Period size: 100 Copynumber: 2.3 Consensus size: 100
4006594 CGGGGAAACA
*
4006604 ATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGC
1 ATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGAAAAGTAAGATCCGCTGTTGTAGC
* * *
4006669 TTCAATTTTTTTAATTGCAATGTTAGGGAAGTAAG
66 TTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAG
*
4006704 ATCCGCTGTTGTAGCTTCAATCTGTTCCACTACAACACTAGAAAAGTAAGATCCGCTGTTGTAGC
1 ATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGAAAAGTAAGATCCGCTGTTGTAGC
*
4006769 TTCAATCTTCTTAATTGTAATGTCAGGGAAGTAAG
66 TTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAG
*
4006804 ATCCGCTATTGTAGCTTCAATCTGTTCCACTG
1 ATCCGCTGTTGTAGCTTCAATCTGTTCCACTG
4006836 TTGTAGCTTC
Statistics
Matches: 124, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 124 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (100 bp):
ATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGAAAAGTAAGATCCGCTGTTGTAGC
TTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAG
Found at i:4006880 original size:74 final size:74
Alignment explanation
Indices: 4006759--4006909 Score: 266
Period size: 74 Copynumber: 2.0 Consensus size: 74
4006749 GTAAGATCCG
* *
4006759 CTGTTGTAGCTTCAATCTTCTTAATTGTAATGTCAGGGAAGTAAGATCCGCTATTGTAGCTTCAA
1 CTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGAGAAGTAAGATCCGCTATTGTAGCTTCAA
4006824 TCTGTTCCA
66 TCTGTTCCA
* *
4006833 CTGTTGTAGCTTCAATCTTCTTGATTGCAATGTCAGAGAAGTAAGATCCGCTGTTGTAGCTTCAA
1 CTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGAGAAGTAAGATCCGCTATTGTAGCTTCAA
4006898 TCTGTTCCA
66 TCTGTTCCA
4006907 CTG
1 CTG
4006910 CAACGCTAGG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (74 bp):
CTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGAGAAGTAAGATCCGCTATTGTAGCTTCAA
TCTGTTCCA
Found at i:4006892 original size:50 final size:50
Alignment explanation
Indices: 4006833--4006962 Score: 158
Period size: 50 Copynumber: 2.6 Consensus size: 50
4006823 ATCTGTTCCA
* *
4006833 CTGTTGTAGCTTCAATCTTCTTGATTGCAATG-TCA-GAGAAGTAAGATCCG
1 CTGTTGTAGCTTCAATCTTCTTAATTGCAACGCT-AGGA-AAGTAAGATCCG
** * *
4006883 CTGTTGTAGCTTCAATCTGT-TCCACTGCAACGCTAGGAAAGTAAGATCTG
1 CTGTTGTAGCTTCAATCT-TCTTAATTGCAACGCTAGGAAAGTAAGATCCG
4006933 CTGTTGTAGCTTCAATCTTCTTAATTGCAA
1 CTGTTGTAGCTTCAATCTTCTTAATTGCAA
4006963 ACTATGGTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
49 1 0.01
50 63 0.93
51 4 0.06
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (50 bp):
CTGTTGTAGCTTCAATCTTCTTAATTGCAACGCTAGGAAAGTAAGATCCG
Found at i:4009243 original size:6 final size:6
Alignment explanation
Indices: 4009211--4009314 Score: 56
Period size: 6 Copynumber: 17.8 Consensus size: 6
4009201 TCTTTTTCTC
* * * * *
4009211 ATTTTC ATTTTC ATTTTG ATCTTG ATTTTG ATTTT- -TTCTTC TTTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATT-TTG ATTTTG
* * * * * *
4009258 TTTTTT ATTTTT ATTTTTG A-TTT- -TTTTC ATTTTC ATTTTG ACTTTG
1 ATTTTG ATTTTG A-TTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
4009304 ATTTTG ATTTT
1 ATTTTG ATTTT
4009315 TTCTTCTTTC
Statistics
Matches: 81, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
4 5 0.06
5 5 0.06
6 64 0.79
7 7 0.09
ACGTcount: A:0.13, C:0.08, G:0.08, T:0.71
Consensus pattern (6 bp):
ATTTTG
Found at i:4009342 original size:76 final size:74
Alignment explanation
Indices: 4009203--4009398 Score: 311
Period size: 76 Copynumber: 2.6 Consensus size: 74
4009193 TTCTTCTTTC
* * * * *
4009203 TTTTTCTCATTTTCATTTTCATTTTGATCTTGATTTTGATTTTTTCTTCTTTTTGTTTTTTATTT
1 TTTTTTTCATTTTCATTTTGACTTTGATTTTGATTTT-TTTTTTTCTTCTTTTTGTTTTTTATTT
4009268 TTATTTTTGA
65 TTATTTTTGA
4009278 TTTTTTTCATTTTCATTTTGACTTTGATTTTGATTTTTTCTTCTTTCTTCTTTTTGTTTTTTATT
1 TTTTTTTCATTTTCATTTTGACTTTGATTTTGATTTTTT-TT-TTTCTTCTTTTTGTTTTTTATT
4009343 TTTATTTTTGA
64 TTTATTTTTGA
4009354 TTTTTTTCATTTTCATTTTGACTTTGATTTTGATTTTTCTTTTTT
1 TTTTTTTCATTTTCATTTTGACTTTGATTTTGATTTTT-TTTTTT
4009399 TTCCCTTTTT
Statistics
Matches: 113, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
74 1 0.01
75 38 0.34
76 73 0.65
77 1 0.01
ACGTcount: A:0.11, C:0.09, G:0.07, T:0.73
Consensus pattern (74 bp):
TTTTTTTCATTTTCATTTTGACTTTGATTTTGATTTTTTTTTTTCTTCTTTTTGTTTTTTATTTT
TATTTTTGA
Found at i:4014135 original size:18 final size:17
Alignment explanation
Indices: 4014096--4014138 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
4014086 ATGTTTATAT
4014096 GTATATATATATTACAA
1 GTATATATATATTACAA
*
4014113 -AATATATATATGTACAA
1 GTATATATATAT-TACAA
4014130 GTATATATA
1 GTATATATA
4014139 AAAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 10 0.45
17 5 0.23
18 7 0.32
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (17 bp):
GTATATATATATTACAA
Found at i:4014148 original size:14 final size:14
Alignment explanation
Indices: 4014098--4014166 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 14
4014088 GTTTATATGT
4014098 ATATATATATTACAAA
1 ATATATATA-TA-AAA
* *
4014114 ATATATATATGTACA
1 ATATATATAT-AAAA
*
4014129 A-GTATATATAAAA
1 ATATATATATAAAA
*
4014142 ATATATATATAAAT
1 ATATATATATAAAA
*
4014156 ATATGTATATA
1 ATATATATATA
4014167 TCTATAAAGC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
13 3 0.07
14 27 0.63
15 4 0.09
16 9 0.21
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (14 bp):
ATATATATATAAAA
Found at i:4014164 original size:12 final size:12
Alignment explanation
Indices: 4014116--4014164 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
4014106 ATTACAAAAT
*
4014116 ATATATATGTACA
1 ATATATATATA-A
*
4014129 AGTATATATAAAA
1 A-TATATATATAA
4014142 ATATATATATAA
1 ATATATATATAA
*
4014154 ATATATGTATA
1 ATATATATATA
4014165 TATCTATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 20 0.65
13 3 0.10
14 8 0.26
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (12 bp):
ATATATATATAA
Found at i:4019883 original size:15 final size:16
Alignment explanation
Indices: 4019863--4019903 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
4019853 GCAAGCAATC
4019863 ACAGCAACCCGGGTA-
1 ACAGCAACCCGGGTAG
*
4019878 ACAGC-ACCAGGGTAG
1 ACAGCAACCCGGGTAG
4019893 AGCAGCAACCC
1 A-CAGCAACCC
4019904 TTCCACATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 8 0.38
15 6 0.29
16 4 0.19
17 3 0.14
ACGTcount: A:0.34, C:0.34, G:0.27, T:0.05
Consensus pattern (16 bp):
ACAGCAACCCGGGTAG
Found at i:4024314 original size:21 final size:22
Alignment explanation
Indices: 4024288--4024330 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4024278 ATGAGCTTAG
*
4024288 AAAATTAT-CAAAATATTATTA
1 AAAATTATAAAAAATATTATTA
4024309 AAAATTATAAAAAATATTATTA
1 AAAATTATAAAAAATATTATTA
4024331 TTTTTAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATTATAAAAAATATTATTA
Found at i:4024795 original size:9 final size:9
Alignment explanation
Indices: 4024732--4024796 Score: 53
Period size: 10 Copynumber: 7.0 Consensus size: 9
4024722 ATAATCATTA
4024732 TTTATAATT
1 TTTATAATT
4024741 TCTTATAATT
1 T-TTATAATT
*
4024751 CTTAATAATT
1 -TTTATAATT
4024761 TTTA-AATAT
1 TTTATAAT-T
* *
4024770 TTTTTTATAT
1 TTTATAAT-T
4024780 TTT-TAATT
1 TTTATAATT
4024788 TTTATAATT
1 TTTATAATT
4024797 ATGCAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
8 7 0.15
9 16 0.35
10 22 0.48
11 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTATAATT
Found at i:4025737 original size:2 final size:2
Alignment explanation
Indices: 4025730--4025766 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
4025720 TTCTTTTGTA
4025730 AT AT AT AT -T AT AT AT GAT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
4025767 TTTAAAGATC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 28 0.88
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4025751 original size:10 final size:9
Alignment explanation
Indices: 4025730--4025767 Score: 58
Period size: 10 Copynumber: 4.0 Consensus size: 9
4025720 TTCTTTTGTA
4025730 ATATATATT
1 ATATATATT
4025739 ATATATGATT
1 ATATAT-ATT
4025749 ATATATATAT
1 ATATATAT-T
4025759 ATATATATT
1 ATATATATT
4025768 TTAAAGATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
ATATATATT
Found at i:4026003 original size:22 final size:22
Alignment explanation
Indices: 4025978--4026029 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
4025968 TAAACAAGAA
*
4025978 AAAAATATCTTATACATCAAAC
1 AAAAATATCTAATACATCAAAC
* *
4026000 AAAATTATCTAATACATTAAAC
1 AAAAATATCTAATACATCAAAC
*
4026022 AACAATAT
1 AAAAATAT
4026030 TACTTCATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAATATCTAATACATCAAAC
Found at i:4027011 original size:48 final size:48
Alignment explanation
Indices: 4026940--4027035 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
4026930 CTTCTCCTTC
4026940 CTTCGACACCATATCCTTAAGTTTACAATCCATTACTGGTCTGTCCAT
1 CTTCGACACCATATCCTTAAGTTTACAATCCATTACTGGTCTGTCCAT
4026988 CTTCGACACCATATCCTTAAGTTTACAATCCATTACTGGTCTGTCCAT
1 CTTCGACACCATATCCTTAAGTTTACAATCCATTACTGGTCTGTCCAT
4027036 GGTAGGTACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.29, G:0.10, T:0.35
Consensus pattern (48 bp):
CTTCGACACCATATCCTTAAGTTTACAATCCATTACTGGTCTGTCCAT
Found at i:4030770 original size:32 final size:30
Alignment explanation
Indices: 4030732--4030810 Score: 104
Period size: 32 Copynumber: 2.6 Consensus size: 30
4030722 GAGCACAAAT
4030732 TTTTTTTAAAATTTTTTATCTTACTTTATA
1 TTTTTTTAAAATTTTTTATCTTACTTTATA
**
4030762 TATATTTTTTTAATTTTTTATCTTACTTTATA
1 T-T-TTTTTAAAATTTTTTATCTTACTTTATA
* *
4030794 TTTTTTTAGATTTTTTT
1 TTTTTTTAAAATTTTTT
4030811 TGAAATTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 13 0.31
31 2 0.05
32 27 0.64
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (30 bp):
TTTTTTTAAAATTTTTTATCTTACTTTATA
Found at i:4030811 original size:32 final size:32
Alignment explanation
Indices: 4030732--4030794 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 32
4030722 GAGCACAAAT
4030732 TTTTTTTAAAATTTTTTATCTTACTTTATATATA
1 TTTTTTT--AATTTTTTATCTTACTTTATATATA
4030766 TTTTTTTAATTTTTTATCTTACTTTATAT
1 TTTTTTTAATTTTTTATCTTACTTTATAT
4030795 TTTTTTAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 22 0.76
34 7 0.24
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.68
Consensus pattern (32 bp):
TTTTTTTAATTTTTTATCTTACTTTATATATA
Found at i:4030820 original size:29 final size:29
Alignment explanation
Indices: 4030762--4030832 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 29
4030752 TTACTTTATA
**
4030762 TATATTTTTTTA-ATTTTTTATCTTACTT
1 TATATTTTTTTAGATTTTTTATCAAACTT
* * *
4030790 TATATTTTTTTAGATTTTTTTTGAAATTT
1 TATATTTTTTTAGATTTTTTATCAAACTT
*
4030819 TATAATTTTTTAGA
1 TATATTTTTTTAGA
4030833 AAATATAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 12 0.33
29 24 0.67
ACGTcount: A:0.25, C:0.03, G:0.04, T:0.68
Consensus pattern (29 bp):
TATATTTTTTTAGATTTTTTATCAAACTT
Found at i:4033341 original size:29 final size:29
Alignment explanation
Indices: 4033308--4033365 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
4033298 GGCCACTACA
*
4033308 CCCTCAGGAAGATAAAAAAATAATACTAG
1 CCCTCAAGAAGATAAAAAAATAATACTAG
*
4033337 CCCTCAAGAAGATTAAAAAATAATACTAG
1 CCCTCAAGAAGATAAAAAAATAATACTAG
4033366 TTTAATAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (29 bp):
CCCTCAAGAAGATAAAAAAATAATACTAG
Found at i:4047226 original size:25 final size:25
Alignment explanation
Indices: 4047172--4047227 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
4047162 AAATCGTGAC
*
4047172 AATTAAAAAAATTAGTATAATAGTA
1 AATTTAAAAAATTAGTATAATAGTA
4047197 AATTTAAAAAATTAGTATAATAGTA
1 AATTTAAAAAATTAGTATAATAGTA
4047222 AATTTA
1 AATTTA
4047228 GTCCTCAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (25 bp):
AATTTAAAAAATTAGTATAATAGTA
Found at i:4048126 original size:25 final size:25
Alignment explanation
Indices: 4048098--4048153 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
4048088 AGTTGAGGAC
4048098 TAAATTTACTATTATACTAATTTTT
1 TAAATTTACTATTATACTAATTTTT
4048123 TAAATTTACTATTATACTAATTTTT
1 TAAATTTACTATTATACTAATTTTT
*
4048148 TTAATT
1 TAAATT
4048154 GTCACGATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (25 bp):
TAAATTTACTATTATACTAATTTTT
Found at i:4050080 original size:21 final size:19
Alignment explanation
Indices: 4050054--4050097 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
4050044 TCGGCCCGGT
4050054 TTTTAATAAACACAAAAAATA
1 TTTTAA-AAACA-AAAAAATA
*
4050075 TTTTAAAAATAAAAAAATA
1 TTTTAAAAACAAAAAAATA
4050094 TTTT
1 TTTT
4050098 TAAAGTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.55
20 4 0.18
21 6 0.27
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
TTTTAAAAACAAAAAAATA
Found at i:4050098 original size:20 final size:21
Alignment explanation
Indices: 4050053--4050101 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
4050043 CTCGGCCCGG
4050053 TTTTTAATAAACACAAAAAATA
1 TTTTTAA-AAACACAAAAAATA
*
4050075 -TTTTAAAAATA-AAAAAATA
1 TTTTTAAAAACACAAAAAATA
4050094 TTTTTAAA
1 TTTTTAAA
4050102 GTATTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 8 0.32
20 11 0.44
21 6 0.24
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (21 bp):
TTTTTAAAAACACAAAAAATA
Found at i:4070943 original size:23 final size:23
Alignment explanation
Indices: 4070905--4071083 Score: 171
Period size: 23 Copynumber: 7.7 Consensus size: 23
4070895 CTACCCTGTT
* *
4070905 TTGGACAGCTTTTATACATCAAA
1 TTGGACAGCATATATACATCAAA
* *
4070928 TCGGACAGCATATATATATACCAAA
1 TTGGACAGCATATATACAT--CAAA
*
4070953 TTGGACAGCATATATACACCAAA
1 TTGGACAGCATATATACATCAAA
*
4070976 TTGGACAGCATATATAAATCAAA
1 TTGGACAGCATATATACATCAAA
* * *
4070999 TTGGACAACATTTATACA-CCAA
1 TTGGACAGCATATATACATCAAA
* *
4071021 TTGGACAACATATATACACCAAA
1 TTGGACAGCATATATACATCAAA
* * * *
4071044 TTGAACAACATTTTATACACCAAA
1 TTGGACAGCA-TATATACATCAAA
* *
4071068 TTGAACAGAATATATA
1 TTGGACAGCATATATA
4071084 TATACCGAAT
Statistics
Matches: 132, Mismatches: 20, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
22 20 0.15
23 72 0.55
24 20 0.15
25 20 0.15
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (23 bp):
TTGGACAGCATATATACATCAAA
Found at i:4071015 original size:46 final size:46
Alignment explanation
Indices: 4070905--4071083 Score: 216
Period size: 48 Copynumber: 3.8 Consensus size: 46
4070895 CTACCCTGTT
* * * *
4070905 TTGGACAGCTTTTATACATCAAATCGGACAGCATATATATATACCAAA
1 TTGGACAACATTTATACACCAAATTGGACAGCATATATA-A-ACCAAA
* * *
4070953 TTGGACAGCATATATACACCAAATTGGACAGCATATATAAATCAAA
1 TTGGACAACATTTATACACCAAATTGGACAGCATATATAAACCAAA
* *
4070999 TTGGACAACATTTATACACC-AATTGGACAACATATATACACCAAA
1 TTGGACAACATTTATACACCAAATTGGACAGCATATATAAACCAAA
* * *
4071044 TTGAACAACATTTTATACACCAAATTGAACAGAATATATA
1 TTGGACAACA-TTTATACACCAAATTGGACAGCATATATA
4071084 TATACCGAAT
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
45 31 0.27
46 33 0.29
47 16 0.14
48 35 0.30
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (46 bp):
TTGGACAACATTTATACACCAAATTGGACAGCATATATAAACCAAA
Found at i:4072127 original size:42 final size:43
Alignment explanation
Indices: 4072028--4072145 Score: 150
Period size: 42 Copynumber: 2.8 Consensus size: 43
4072018 AGCTCGTACA
* * *
4072028 ATGCCAACGTCCCAAAC-GTGGTATTACATGTAATTAAATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACATGTAATTAAATATCG
* * *
4072071 ATGCCACTGTCCCAGACAGGGTCTTACACGTAATTATATA-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACATGTAATTAAATATCG
*
4072113 ATGCCAATGTCCCAGACATGGTCTTACATGTAA
1 ATGCCAATGTCCCAGACAGGGTCTTACATGTAA
4072146 ATCTCAAATC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 32 0.49
43 32 0.49
44 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACATGTAATTAAATATCG
Found at i:4076099 original size:51 final size:51
Alignment explanation
Indices: 4076023--4076283 Score: 403
Period size: 51 Copynumber: 5.3 Consensus size: 51
4076013 CGGATCACAT
*
4076023 TTATCACTTGTCACTTGTCCCTGATCAAATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCAC
* *
4076074 TTATCACTTGTTACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCAC
*
4076125 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCAC
4076176 TTATCACTTGTCACTTGTCACTGAT-AAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAA-ATAAGTGTAGCTAAAGCTACCAC
* *
4076227 -T-T-A----TCACTTGTCACTGATCAATTAAGTGTAGTTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCAC
4076271 TTATCACTTGTCA
1 TTATCACTTGTCA
4076284 TGTAACACCC
Statistics
Matches: 194, Mismatches: 7, Indels: 18
0.89 0.03 0.08
Matches are distributed among these distances:
44 36 0.19
45 3 0.02
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 2 0.01
51 149 0.77
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCAC
Found at i:4079739 original size:41 final size:41
Alignment explanation
Indices: 4079621--4079731 Score: 186
Period size: 41 Copynumber: 2.7 Consensus size: 41
4079611 TTAAAGTCTA
* *
4079621 ATTCAGTTCACCGGCACTTAGCCTTCTAGGCTTATAGGCTG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
4079662 ATTCAGTTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
4079703 ATTCAATTCACCGGCACTTAGCCTGCTAG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAG
4079732 ACATATAGTC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (41 bp):
ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:4079754 original size:41 final size:40
Alignment explanation
Indices: 4079627--4079759 Score: 158
Period size: 41 Copynumber: 3.2 Consensus size: 40
4079617 TCTAATTCAG
* * *
4079627 TTCACCGGCACTTAGCCTTCTAGGCTTATAGGCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT-AA
*
4079668 TTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT-AA
* * * *
4079709 TTCACCGGCACTTAGCCTGCTAGACATATAGTCTGAATAA
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTAA
*
4079749 TTTCACTGGCA
1 -TTCACCGGCA
4079760 ATAAATCCGA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 2 0.02
41 79 0.98
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (40 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTAA
Found at i:4081532 original size:13 final size:13
Alignment explanation
Indices: 4081514--4081538 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4081504 ACCAACGATA
4081514 AAATTTTCACACG
1 AAATTTTCACACG
4081527 AAATTTTCACAC
1 AAATTTTCACAC
4081539 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:4084935 original size:19 final size:19
Alignment explanation
Indices: 4084923--4084960 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4084913 TACCAGAATA
4084923 CCAGCTAACTACCACAACT
1 CCAGCTAACTACCACAACT
*
4084942 GCAGCTAACTACCACAACT
1 CCAGCTAACTACCACAACT
4084961 ACTTTCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.39, G:0.08, T:0.16
Consensus pattern (19 bp):
CCAGCTAACTACCACAACT
Found at i:4087873 original size:22 final size:20
Alignment explanation
Indices: 4087831--4087882 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
4087821 ATTAGTATAA
4087831 TTATAAATTTTTAAATAAAG
1 TTATAAATTTTTAAATAAAG
*
4087851 TTTTTAAATTTTTGAAA-ATAAG
1 -TTATAAATTTTT-AAATA-AAG
4087873 TTATAAATTT
1 TTATAAATTT
4087883 CAATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (20 bp):
TTATAAATTTTTAAATAAAG
Found at i:4093165 original size:31 final size:32
Alignment explanation
Indices: 4093113--4093174 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
4093103 ATGTGATGCG
* *
4093113 TGTTTATTTATATATAAATAAAAAGTAATTAT
1 TGTTTATTTAAATATAAATAAAAAATAATTAT
*
4093145 TGTTTA-TTAAATATATATAAAAAATAATTA
1 TGTTTATTTAAATATAAATAAAAAATAATTA
4093175 AATACATTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (32 bp):
TGTTTATTTAAATATAAATAAAAAATAATTAT
Found at i:4096398 original size:21 final size:21
Alignment explanation
Indices: 4096372--4096412 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4096362 AGACGAGCAA
* *
4096372 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
4096393 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
4096413 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:4110866 original size:8 final size:8
Alignment explanation
Indices: 4110855--4110889 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
4110845 CCAATATCTA
*
4110855 ATTATCAT
1 ATTATCAC
*
4110863 ATTAGCAC
1 ATTATCAC
4110871 ATTATCAC
1 ATTATCAC
4110879 ATTATCAC
1 ATTATCAC
4110887 ATT
1 ATT
4110890 TATACATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (8 bp):
ATTATCAC
Found at i:4111691 original size:9 final size:8
Alignment explanation
Indices: 4111674--4111716 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 8
4111664 GTCGTGCGTC
4111674 TCTTTCTT
1 TCTTTCTT
*
4111682 TTTCTTCTT
1 TCT-TTCTT
4111691 TCTATTCTT
1 TCT-TTCTT
4111700 TCTTTCTTT
1 TCTTTC-TT
4111709 TCTTTCTT
1 TCTTTCTT
4111717 ATTTCGTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (8 bp):
TCTTTCTT
Found at i:4111692 original size:13 final size:14
Alignment explanation
Indices: 4111674--4111716 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
4111664 GTCGTGCGTC
4111674 TCTTTCTTTTTC-T
1 TCTTTCTTTTTCTT
*
4111687 TCTTTC-TATTCTT
1 TCTTTCTTTTTCTT
4111700 TCTTTC-TTTTCTT
1 TCTTTCTTTTTCTT
4111713 TCTT
1 TCTT
4111717 ATTTCGTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 4 0.15
13 23 0.85
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (14 bp):
TCTTTCTTTTTCTT
Found at i:4111693 original size:4 final size:4
Alignment explanation
Indices: 4111674--4111716 Score: 50
Period size: 4 Copynumber: 10.0 Consensus size: 4
4111664 GTCGTGCGTC
*
4111674 TCTT TCTT TTTCT TCTT TCTAT TCTT TCTT TCTTT TCTT TCTT
1 TCTT TCTT TCT-T TCTT TCT-T TCTT TCTT TC-TT TCTT TCTT
4111717 ATTTCGTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 23 0.68
5 11 0.32
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:4118234 original size:16 final size:17
Alignment explanation
Indices: 4118198--4118234 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
4118188 AATTTTATTT
4118198 TAATAATAATTTTTAAA
1 TAATAATAATTTTTAAA
4118215 -AATAATAA-TTTTAAA
1 TAATAATAATTTTTAAA
4118230 TAATA
1 TAATA
4118235 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATAATAATTTTTAAA
Found at i:4119873 original size:19 final size:19
Alignment explanation
Indices: 4119836--4119886 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
4119826 TAAAACAGTA
*
4119836 ATAAATTTTAGAAATAATAT
1 ATAAATTTTA-AAAAAATAT
4119856 -TAAATTTTAATAAAAATAT
1 ATAAATTTTAA-AAAAATAT
*
4119875 AAAAATTTTAAA
1 ATAAATTTTAAA
4119887 TTTTATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.04
19 17 0.63
20 9 0.33
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
ATAAATTTTAAAAAAATAT
Found at i:4119957 original size:19 final size:19
Alignment explanation
Indices: 4119872--4119963 Score: 73
Period size: 19 Copynumber: 4.8 Consensus size: 19
4119862 TTAATAAAAA
*
4119872 TATAAAAATT-TTAAATTT
1 TATAAAAATTGTAAAATTT
**
4119890 TATTAAAAATTAG-AATTTTT
1 TA-TAAAAATT-GTAAAATTT
**
4119910 TATAAAAATTGTAAAA-AA
1 TATAAAAATTGTAAAATTT
*
4119928 TATATATAATTGTAAAATTT
1 TATA-AAAATTGTAAAATTT
*
4119948 TATAAAAATTATAAAA
1 TATAAAAATTGTAAAA
4119964 AATTAACAAC
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
18 7 0.12
19 39 0.70
20 10 0.18
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TATAAAAATTGTAAAATTT
Found at i:4120199 original size:58 final size:58
Alignment explanation
Indices: 4120127--4120237 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
4120117 CGAAATTTAT
* * *
4120127 ATTTCTTTACATTTTGTAT-TGTTTTCTTACGA-CTTTATAAAATTTTATAATTTTTTGC
1 ATTTCTATACATTTTATATAT-TTTT-TTACGATCTTTATAAAATTTTACAATTTTTTGC
* *
4120185 ATTTCTATATATTTTATATATTTTTTTACGATTTTTATAAAATTTTACAATTT
1 ATTTCTATACATTTTATATATTTTTTTACGATCTTTATAAAATTTTACAATTT
4120238 CATATATATT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 6 0.13
58 39 0.85
59 1 0.02
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (58 bp):
ATTTCTATACATTTTATATATTTTTTTACGATCTTTATAAAATTTTACAATTTTTTGC
Found at i:4120268 original size:19 final size:19
Alignment explanation
Indices: 4120195--4120267 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
4120185 ATTTCTATAT
*
4120195 ATTTTATATATTTTTTTACG
1 ATTTT-TATATTATTTTACG
**
4120215 ATTTTTATAAAATTTTAC-
1 ATTTTTATATTATTTTACG
* *
4120233 AATTTCATATATATTTTACG
1 ATTTTTATAT-TATTTTACG
4120253 ATTTTTATATT-TTTT
1 ATTTTTATATTATTTT
4120268 TCTAATTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
18 11 0.26
19 18 0.43
20 13 0.31
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTTTTATATTATTTTACG
Found at i:4124824 original size:44 final size:43
Alignment explanation
Indices: 4124775--4124857 Score: 116
Period size: 42 Copynumber: 1.9 Consensus size: 43
4124765 AATTAATTGG
4124775 AAAGTAATAATATTTATAAA-AATAATATTTTAAT-TAAAATAAAT
1 AAAGTAATAATA---ATAAACAATAATATTTTAATGTAAAATAAAT
*
4124819 AAAGTAATAATAATAAACAATCATATTTTAATGTAAAAT
1 AAAGTAATAATAATAAACAATAATATTTTAATGTAAAAT
4124858 GGAGTGGTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
41 5 0.14
42 13 0.36
43 6 0.17
44 12 0.33
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (43 bp):
AAAGTAATAATAATAAACAATAATATTTTAATGTAAAATAAAT
Found at i:4135919 original size:23 final size:22
Alignment explanation
Indices: 4135867--4135919 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
4135857 TCCACGTCTT
*
4135867 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
4135889 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
4135912 TTTCTTTT
1 TTTCTTTT
4135920 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:4140124 original size:23 final size:23
Alignment explanation
Indices: 4140097--4140141 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4140087 AATATTTAAA
*
4140097 ATTTAAATAAT-TTTTTATTTTT
1 ATTTTAATAATATTTTTATTTTT
* *
4140119 ATTTTAGTAGTATTTTTATTTTT
1 ATTTTAATAATATTTTTATTTTT
4140142 TAAAATTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (23 bp):
ATTTTAATAATATTTTTATTTTT
Found at i:4140615 original size:22 final size:23
Alignment explanation
Indices: 4140590--4140632 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4140580 AAATATTTAA
4140590 TAAAAAATTT-ATAATATAAATG
1 TAAAAAATTTAATAATATAAATG
* *
4140612 TAAATATTTTAATAATATAAA
1 TAAAAAATTTAATAATATAAA
4140633 CAGATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAAAAATTTAATAATATAAATG
Found at i:4140899 original size:18 final size:18
Alignment explanation
Indices: 4140868--4140911 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
4140858 TTAAAAATTG
*
4140868 ATTTTATTAGAAAATATTCA
1 ATTTT-TTAGAAAAT-TTAA
4140888 ATTTTTTA-AAAATTTAA
1 ATTTTTTAGAAAATTTAA
4140905 ATTTTTT
1 ATTTTTT
4140912 TTGATAAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 5 0.22
19 3 0.13
20 5 0.22
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTTTTAGAAAATTTAA
Found at i:4141759 original size:13 final size:13
Alignment explanation
Indices: 4141738--4141801 Score: 74
Period size: 13 Copynumber: 4.9 Consensus size: 13
4141728 AATTTTTCAT
4141738 TACTTTTGAAAAG
1 TACTTTTGAAAAG
*
4141751 TATTTTTGAAAAG
1 TACTTTTGAAAAG
* * *
4141764 TGCTGTGGAAAAG
1 TACTTTTGAAAAG
*
4141777 TACTTTTGAGAAG
1 TACTTTTGAAAAG
*
4141790 TGCTTTTGAAAA
1 TACTTTTGAAAA
4141802 ATTTGAGTGT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:4141800 original size:26 final size:26
Alignment explanation
Indices: 4141740--4141801 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
4141730 TTTTTCATTA
*
4141740 CTTTTGAAAAGTATTTTTGAAAAGTG
1 CTTTTGAAAAGTACTTTTGAAAAGTG
* * *
4141766 CTGTGGAAAAGTACTTTTGAGAAGTG
1 CTTTTGAAAAGTACTTTTGAAAAGTG
4141792 CTTTTGAAAA
1 CTTTTGAAAA
4141802 ATTTGAGTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (26 bp):
CTTTTGAAAAGTACTTTTGAAAAGTG
Found at i:4141987 original size:15 final size:14
Alignment explanation
Indices: 4141967--4141996 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
4141957 AACTTATTGT
4141967 TAATATTTTAATATA
1 TAATATTTTAA-ATA
4141982 TAATATTTTAAATA
1 TAATATTTTAAATA
4141996 T
1 T
4141997 TTCTAAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATATTTTAAATA
Found at i:4144869 original size:17 final size:18
Alignment explanation
Indices: 4144847--4144880 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4144837 TTCTTCATTG
4144847 CTTTTCAAAG-AAAAGCA
1 CTTTTCAAAGTAAAAGCA
*
4144864 CTTTTCCAAGTAAAAGC
1 CTTTTCAAAGTAAAAGC
4144881 TCGTTTCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (18 bp):
CTTTTCAAAGTAAAAGCA
Found at i:4159263 original size:2 final size:2
Alignment explanation
Indices: 4159256--4159285 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4159246 CGATGAATGT
4159256 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4159286 ACCAGTTTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4162501 original size:16 final size:16
Alignment explanation
Indices: 4162464--4162503 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
4162454 TTAATAAAAT
* *
4162464 TAAAACTAATTATTAT
1 TAAAATTAATTATTAG
*
4162480 TAAAATTAATTGTTAG
1 TAAAATTAATTATTAG
4162496 TAAAATTA
1 TAAAATTA
4162504 TCAATTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTATTAG
Found at i:4162531 original size:16 final size:15
Alignment explanation
Indices: 4162506--4162536 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
4162496 TAAAATTATC
4162506 AATTTATTAATTGTT
1 AATTTATTAATTGTT
4162521 AATTGTATTAATTGTT
1 AATT-TATTAATTGTT
4162537 GTAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (15 bp):
AATTTATTAATTGTT
Found at i:4162582 original size:59 final size:59
Alignment explanation
Indices: 4162506--4162653 Score: 271
Period size: 59 Copynumber: 2.5 Consensus size: 59
4162496 TAAAATTATC
* *
4162506 AATTTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AATTTATCAAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
4162564 AATTTATCAAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AATTTATCAAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
4162623 AATTTATCAAATTATTAATTGTATTAATTGT
1 AATTTATCAAATTATTAATTGTATTAATTGT
4162654 ATTAATTGTT
Statistics
Matches: 87, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
58 7 0.08
59 80 0.92
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (59 bp):
AATTTATCAAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
Found at i:4162647 original size:9 final size:9
Alignment explanation
Indices: 4162635--4162662 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
4162625 TTTATCAAAT
4162635 TATTAATTG
1 TATTAATTG
4162644 TATTAATTG
1 TATTAATTG
4162653 TATTAATTG
1 TATTAATTG
4162662 T
1 T
4162663 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:4179099 original size:26 final size:26
Alignment explanation
Indices: 4179051--4179101 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4179041 CACCATGTAT
*
4179051 CAATTTTTTTTATCAAATCTAATAAA
1 CAATTTTTTTTATAAAATCTAATAAA
*
4179077 CAATTTGTTTTTGTAAAAT-TAATAA
1 CAATTT-TTTTTATAAAATCTAATAA
4179102 TTTATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (26 bp):
CAATTTTTTTTATAAAATCTAATAAA
Found at i:4179150 original size:26 final size:27
Alignment explanation
Indices: 4179104--4179162 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
4179094 ATTAATAATT
*
4179104 TATTTTTAGTTAAAAATAGAATATATA
1 TATTTTTAGTTAAAAATAGAATATACA
*
4179131 TATTTTTA-TTATTAAA-AGAATATACA
1 TATTTTTAGTTA-AAAATAGAATATACA
4179157 TATTTT
1 TATTTT
4179163 AACATTAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 18 0.62
27 11 0.38
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (27 bp):
TATTTTTAGTTAAAAATAGAATATACA
Found at i:4184339 original size:16 final size:16
Alignment explanation
Indices: 4184296--4184331 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4184286 TGATTAAGAA
*
4184296 ATTATTATTATATTAC
1 ATTATTATAATATTAC
*
4184312 ATTATTATAATATTAT
1 ATTATTATAATATTAC
4184328 ATTA
1 ATTA
4184332 ATTAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATTATAATATTAC
Found at i:4184369 original size:16 final size:15
Alignment explanation
Indices: 4184339--4184381 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
4184329 TTAATTAAAT
*
4184339 AATAAAAAAACGTAA
1 AATAAAAAAAAGTAA
4184354 AATAAAAATAAAGTAA
1 AATAAAAA-AAAGTAA
*
4184370 AAGAAAGAAAAA
1 AATAAA-AAAAA
4184382 AAGCAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.33
16 14 0.58
17 2 0.08
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (15 bp):
AATAAAAAAAAGTAA
Found at i:4185090 original size:3 final size:3
Alignment explanation
Indices: 4185082--4185107 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4185072 GTGAGGTAAG
4185082 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
4185108 GTGGGAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4185274 original size:23 final size:25
Alignment explanation
Indices: 4185258--4185317 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 25
4185248 TGGATTAATT
4185258 ATTG-ATTG-AAAGGTGGAAAAATG
1 ATTGAATTGAAAAGGTGGAAAAATG
**
4185281 ATTGAATTGAAAAGGTGAGAATTTATG
1 ATTGAATTGAAAAGGTG-GAA-AAATG
4185308 ATTGAATTGA
1 ATTGAATTGA
4185318 GATTATATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 4 0.13
24 4 0.13
25 7 0.23
26 3 0.10
27 13 0.42
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.32
Consensus pattern (25 bp):
ATTGAATTGAAAAGGTGGAAAAATG
Found at i:4188107 original size:13 final size:13
Alignment explanation
Indices: 4188083--4188116 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
4188073 CCCTCATTGG
4188083 TATCACAATTATAT
1 TATCA-AATTATAT
4188097 TATCAAATTATAT
1 TATCAAATTATAT
*
4188110 CATCAAA
1 TATCAAA
4188117 ATATCATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TATCAAATTATAT
Found at i:4195259 original size:16 final size:16
Alignment explanation
Indices: 4195238--4195269 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4195228 CCCTTAGTCA
*
4195238 TGATTATTTAATTAAT
1 TGATTAGTTAATTAAT
4195254 TGATTAGTTAATTAAT
1 TGATTAGTTAATTAAT
4195270 CACCTCTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (16 bp):
TGATTAGTTAATTAAT
Found at i:4203707 original size:19 final size:18
Alignment explanation
Indices: 4203668--4203722 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
4203658 AAAAAATAAT
*
4203668 AAATAATAAATTTTAGAAA
1 AAATATTAAATTTTA-AAA
*
4203687 AATTATTAAATTTTAATAA
1 AAATATTAAATTTTAA-AA
* *
4203706 AAATATAAAAATTTAAA
1 AAATATTAAATTTTAAA
4203723 TTTTATTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 2 0.07
19 28 0.93
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AAATATTAAATTTTAAAA
Found at i:4204059 original size:45 final size:44
Alignment explanation
Indices: 4204001--4204086 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 44
4203991 TTTCTTACGA
* * *
4204001 TTTTATAAAATTTTATATTTCTATATACTTTATAATTTTTAAGAT
1 TTTTATAAAATTTTACAATTATATATA-TTTATAATTTTTAAGAT
* *
4204046 TTTTATAAGATTTTACAATTATATATATTTTTAATTTTTAA
1 TTTTATAAAATTTTACAATTATATATATTTATAATTTTTAA
4204087 TAAATTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 13 0.36
45 23 0.64
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.58
Consensus pattern (44 bp):
TTTTATAAAATTTTACAATTATATATATTTATAATTTTTAAGAT
Found at i:4204100 original size:27 final size:29
Alignment explanation
Indices: 4204064--4204131 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
4204054 GATTTTACAA
*
4204064 TTATATATATTTTTAA-TTTTTAATAAATT
1 TTATA-ATATTTTGAATTTTTTAATAAATT
*
4204093 TT-TAATA-TTTGAATTTTTTATTAAATT
1 TTATAATATTTTGAATTTTTTAATAAATT
4204120 TTGATAATATTT
1 TT-ATAATATTT
4204132 ATAGCTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
26 5 0.15
27 17 0.52
28 2 0.06
29 7 0.21
30 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (29 bp):
TTATAATATTTTGAATTTTTTAATAAATT
Found at i:4206787 original size:18 final size:18
Alignment explanation
Indices: 4206760--4206802 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4206750 CCAAAAGGAT
*
4206760 AAAGACAAAGACAAAAAC
1 AAAGATAAAGACAAAAAC
* *
4206778 AAAGATAAAGATAAAAAT
1 AAAGATAAAGACAAAAAC
4206796 AAAGATA
1 AAAGATA
4206803 GAGAGGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.07, G:0.12, T:0.09
Consensus pattern (18 bp):
AAAGATAAAGACAAAAAC
Found at i:4212011 original size:33 final size:35
Alignment explanation
Indices: 4211916--4212012 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
4211906 TTAATATTTT
*
4211916 AATATATGAAATATAAATTTTAAATATTT--TTAAGC
1 AATATAT-AAAT-TATATTTTAAATATTTAATTAAGC
* *
4211951 AATAAATATTAATTAT-TTATAAA-ATTTAATT-AG-
1 AAT--ATATAAATTATATTTTAAATATTTAATTAAGC
4211984 AATATATAAATTATATTTTAAATATTTAA
1 AATATATAAATTATATTTTAAATATTTAA
4212013 ATATAACCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.20
32 6 0.12
33 13 0.25
34 8 0.16
35 7 0.14
36 3 0.06
37 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (35 bp):
AATATATAAATTATATTTTAAATATTTAATTAAGC
Found at i:4214629 original size:21 final size:22
Alignment explanation
Indices: 4214603--4214645 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4214593 ATAAATAAAT
4214603 ATTAATTTATTA-ATATTTTAA
1 ATTAATTTATTAGATATTTTAA
*
4214624 ATTAATTTTTTATGATATTTTA
1 ATTAATTTATTA-GATATTTTA
4214646 TTATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTAATTTATTAGATATTTTAA
Found at i:4214648 original size:21 final size:20
Alignment explanation
Indices: 4214602--4214657 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 20
4214592 AATAAATAAA
*
4214602 TATTAATTTATTA-ATATTT
1 TATTAATTTTTTATATATTT
4214621 TAAATTAATTTTTTATGATATTT
1 T--ATTAATTTTTTAT-ATATTT
4214644 TATT-ATTTTATTAT
1 TATTAATTTT-TTAT
4214658 TTTATTTAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.03
20 5 0.16
21 18 0.58
23 7 0.23
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TATTAATTTTTTATATATTT
Done.