Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008824.1 Hibiscus syriacus cultivar Beakdansim tig00111996_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4603428
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 19
Found at i:4111628 original size:21 final size:21
Alignment explanation
Indices: 4111568--4111631 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
4111558 TTTCATATAC
* * *
4111568 ATTTACCAAAGTAATTTACCT
1 ATTTACCAAGGTAATTCATCT
*
4111589 ATTTACCAAGGTACTTCATCT
1 ATTTACCAAGGTAATTCATCT
4111610 ATTTACCAAGGTAATTCATCT
1 ATTTACCAAGGTAATTCATCT
4111631 A
1 A
4111632 CTTCCACTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (21 bp):
ATTTACCAAGGTAATTCATCT
Found at i:4112571 original size:90 final size:89
Alignment explanation
Indices: 4112418--4112594 Score: 282
Period size: 90 Copynumber: 2.0 Consensus size: 89
4112408 CCTAACACAC
* *
4112418 CCTTTTATAGCCAAGTCACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATG
1 CCTTTTATAGCCAAGTCACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
* *
4112483 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
* * *
4112507 CCTTTTATATCCAAGTTACCCTAATTATATTAAGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTCACCCTAATCATATT-AGGATTTTATTATTTCAAATTAATTAAATCTAT
4112572 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
4112595 TTCAGGATTA
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 28 0.35
90 52 0.65
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTCACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:4114613 original size:14 final size:14
Alignment explanation
Indices: 4114594--4114621 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4114584 TTTAAGGATT
4114594 GATGGTGATGGAAA
1 GATGGTGATGGAAA
4114608 GATGGTGATGGAAA
1 GATGGTGATGGAAA
4114622 TAGTATCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
GATGGTGATGGAAA
Found at i:4115784 original size:22 final size:22
Alignment explanation
Indices: 4115744--4115785 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4115734 AAATATGTGG
*
4115744 TTCATAATAATATCTTCATACA
1 TTCATAATAATATCATCATACA
4115766 TTCATAAT-ATCATCATCATA
1 TTCATAATAAT-ATCATCATA
4115786 ACTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATATCATCATACA
Found at i:4119341 original size:19 final size:19
Alignment explanation
Indices: 4119317--4119379 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
4119307 GTATTTGTAT
4119317 ATGGAATATTGTTATGGTG
1 ATGGAATATTGTTATGGTG
* * * *
4119336 ATGGAAGA-AG-TATTTGTAT
1 ATGGAATATTGTTA-TGGT-G
4119355 ATGGAATATTGTTATGGTG
1 ATGGAATATTGTTATGGTG
4119374 ATGGAA
1 ATGGAA
4119380 GAAGGAAGTA
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
17 2 0.06
18 4 0.12
19 20 0.62
20 4 0.12
21 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.30, T:0.38
Consensus pattern (19 bp):
ATGGAATATTGTTATGGTG
Found at i:4119353 original size:38 final size:38
Alignment explanation
Indices: 4119302--4119383 Score: 164
Period size: 38 Copynumber: 2.2 Consensus size: 38
4119292 AAATGATTTA
4119302 AAGAAGTATTTGTATATGGAATATTGTTATGGTGATGG
1 AAGAAGTATTTGTATATGGAATATTGTTATGGTGATGG
4119340 AAGAAGTATTTGTATATGGAATATTGTTATGGTGATGG
1 AAGAAGTATTTGTATATGGAATATTGTTATGGTGATGG
4119378 AAGAAG
1 AAGAAG
4119384 GAAGTATGGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (38 bp):
AAGAAGTATTTGTATATGGAATATTGTTATGGTGATGG
Found at i:4130667 original size:10 final size:10
Alignment explanation
Indices: 4130639--4130677 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
4130629 CTCAGCTCCT
4130639 CAGCTACTCTCC
1 CAGCTACT-T-C
4130651 CAGCTACTTC
1 CAGCTACTTC
*
4130661 GAGCTACTTC
1 CAGCTACTTC
4130671 CAGCTAC
1 CAGCTAC
4130678 CTCTAGTCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 1 0.04
12 8 0.32
ACGTcount: A:0.21, C:0.41, G:0.13, T:0.26
Consensus pattern (10 bp):
CAGCTACTTC
Found at i:4137687 original size:19 final size:20
Alignment explanation
Indices: 4137646--4137696 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
4137636 GAAACCCCTT
*
4137646 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
4137666 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
4137685 TGAAAATGCATG
1 TGAAAATACATG
4137697 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:4138626 original size:30 final size:31
Alignment explanation
Indices: 4138585--4138644 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
4138575 ACATGTTGCC
**
4138585 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
4138616 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
4138645 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:4140589 original size:40 final size:40
Alignment explanation
Indices: 4140543--4140664 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
4140533 ACCGTAGTGC
4140543 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
4140583 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
4140623 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
4140663 TA
1 TA
4140665 TAAACCTGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:4146201 original size:27 final size:27
Alignment explanation
Indices: 4146171--4146227 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
4146161 CAGGAGAAAC
4146171 CTCAGAGTCATCACTAGATTAAAAAAT
1 CTCAGAGTCATCACTAGATTAAAAAAT
4146198 CTCAGAGTCATCACTAGATTAAAAAAT
1 CTCAGAGTCATCACTAGATTAAAAAAT
4146225 CTC
1 CTC
4146228 TTCTGAATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (27 bp):
CTCAGAGTCATCACTAGATTAAAAAAT
Found at i:4147388 original size:48 final size:47
Alignment explanation
Indices: 4147322--4147500 Score: 172
Period size: 53 Copynumber: 3.8 Consensus size: 47
4147312 TATAAAATCC
*
4147322 CTTACCATTT--ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
4147367 CTTACCGTTTAAAATTCCATAAGCTCGTAAGCTTAAAATTGTTTTTCCAATATA
1 CTTACCATTT-AAATTCCATAAGCTCGTAAGCTT---A---TTTTACCAAAATA
* *
4147421 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTA-TTTACCCATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
4147467 CTTGCCA-TT--ATTCCAAAAGCTCATAAGCTTATTT
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTT
4147501 GTATGCTTAC
Statistics
Matches: 114, Mismatches: 10, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
43 20 0.18
44 2 0.02
45 11 0.10
46 16 0.14
48 20 0.18
50 1 0.01
51 1 0.01
53 23 0.20
54 20 0.18
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.37
Consensus pattern (47 bp):
CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:4147649 original size:40 final size:40
Alignment explanation
Indices: 4147605--4147726 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
4147595 ACCGTAGTGC
* *
4147605 TACACATAAGGTCGTGTCTACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
4147645 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
4147685 TACACATAAGGCCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
4147725 TA
1 TA
4147727 TAAACCTGCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:4152666 original size:6 final size:6
Alignment explanation
Indices: 4152652--4152681 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
4152642 CTTGTATCTC
*
4152652 GACCGT GACCAT GACCAT GACCAT GACCAT
1 GACCAT GACCAT GACCAT GACCAT GACCAT
4152682 AGGTCTTCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (6 bp):
GACCAT
Found at i:4153303 original size:27 final size:27
Alignment explanation
Indices: 4153273--4153329 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
4153263 CTGGAGAAAC
4153273 CTCAGAGTCATCACTAGATTAAAAAAT
1 CTCAGAGTCATCACTAGATTAAAAAAT
4153300 CTCAGAGTCATCACTAGATTAAAAAAT
1 CTCAGAGTCATCACTAGATTAAAAAAT
4153327 CTC
1 CTC
4153330 TTCTGAATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (27 bp):
CTCAGAGTCATCACTAGATTAAAAAAT
Found at i:4154495 original size:48 final size:47
Alignment explanation
Indices: 4154429--4154606 Score: 170
Period size: 52 Copynumber: 3.8 Consensus size: 47
4154419 TATAAAATCC
*
4154429 CTTACCATTT--ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
4154474 CTTACCGTTTAAAATTCCATAAGCTCGTAAGCTTATAATTTTTTTCCAATATA
1 CTTACCATTT-AAATTCCATAAGCTCGTAAGC-T-T-A--TTTTACCAAAATA
* *
4154527 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTA-TTTACCCATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
** * *
4154573 CTTGTCA-TT--ATTCCAAAAGCTCATAAGCTTATTT
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTT
4154607 GTATGCTTAC
Statistics
Matches: 113, Mismatches: 11, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
43 20 0.18
44 2 0.02
45 11 0.10
46 15 0.13
48 18 0.16
49 2 0.02
50 2 0.02
51 2 0.02
52 21 0.19
53 20 0.18
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (47 bp):
CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:4154804 original size:40 final size:40
Alignment explanation
Indices: 4154711--4154833 Score: 219
Period size: 40 Copynumber: 3.0 Consensus size: 40
4154701 ACCGTAGTGC
*
4154711 TACACATAAGGTCGTGCCCACCATATACACCGAAGTTTTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAG-TGTAT
4154752 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
4154792 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
4154832 TA
1 TA
4154834 TAAACCTGCA
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
40 45 0.56
41 35 0.44
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:4165147 original size:30 final size:30
Alignment explanation
Indices: 4165113--4165184 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
4165103 AGGAAAGCTC
*
4165113 AACTTAGTTGGAGGAACTAACATGTAACTG
1 AACTTAGCTGGAGGAACTAACATGTAACTG
* * *
4165143 AACTTAGCTGGAGGAGCTAGCATGTAGCTG
1 AACTTAGCTGGAGGAACTAACATGTAACTG
4165173 AACTTAGCTGGA
1 AACTTAGCTGGA
4165185 AGAGAGCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (30 bp):
AACTTAGCTGGAGGAACTAACATGTAACTG
Found at i:4166478 original size:21 final size:21
Alignment explanation
Indices: 4166436--4166494 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
4166426 GAATCCCCTT
4166436 TGAAAATACATGATTGTTTTTA
1 TGAAAATACATGATT-TTTTTA
4166458 TGAAAATACATGATTTTTTTA
1 TGAAAATACATGATTTTTTTA
4166479 TGAAAATACATGATTT
1 TGAAAATACATGATTT
4166495 AAATGAAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (21 bp):
TGAAAATACATGATTTTTTTA
Found at i:4175586 original size:18 final size:16
Alignment explanation
Indices: 4175552--4175594 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
4175542 AACTTGTTGT
4175552 TTTTTCTTTCAACTTC
1 TTTTTCTTTCAACTTC
*
4175568 TTTTTCTTTGCAATTTTC
1 TTTTTCTTT-CAA-CTTC
4175586 TTTTTCTTT
1 TTTTTCTTT
4175595 TCTTATCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 3 0.12
18 12 0.50
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (16 bp):
TTTTTCTTTCAACTTC
Found at i:4180949 original size:19 final size:20
Alignment explanation
Indices: 4180907--4180949 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4180897 GAAACCCCTT
*
4180907 TGAAAACACATGATTTTCAA
1 TGAAAACACATAATTTTCAA
*
4180927 TGAAAATACATAATTTT-AA
1 TGAAAACACATAATTTTCAA
4180946 TGAA
1 TGAA
4180950 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATAATTTTCAA
Found at i:4185027 original size:28 final size:28
Alignment explanation
Indices: 4184963--4185019 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
4184953 TAGAAGCACG
4184963 ACACACATTGGTGCAATTTAAAGGAGTA
1 ACACACATTGGTGCAATTTAAAGGAGTA
4184991 ACACACATTGGTGCAATTTAAAGGAGTA
1 ACACACATTGGTGCAATTTAAAGGAGTA
4185019 A
1 A
4185020 TTGGCATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (28 bp):
ACACACATTGGTGCAATTTAAAGGAGTA
Found at i:4186253 original size:16 final size:17
Alignment explanation
Indices: 4186232--4186271 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
4186222 AAATTACAAT
*
4186232 AAGAAAATGATAA-GAA
1 AAGAAAATGAAAATGAA
*
4186248 AAGAAAATGAAAATGCA
1 AAGAAAATGAAAATGAA
4186265 AAGAAAA
1 AAGAAAA
4186272 AGAAGTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.70, C:0.03, G:0.17, T:0.10
Consensus pattern (17 bp):
AAGAAAATGAAAATGAA
Found at i:4186574 original size:111 final size:110
Alignment explanation
Indices: 4186380--4186808 Score: 574
Period size: 111 Copynumber: 3.9 Consensus size: 110
4186370 TACAGGGAAG
* * * * * * *
4186380 ATTGAATCATGGTAGACTTGTCCCATTATCACTCATGTAATATCAAATCTTGAAAGAGAGGGATT
1 ATTGAATCAGGGTAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAGAGA-GGATA
* *
4186445 TGTTCCACTTCTTTTGAGGGAATATCAGATCTGGGAAAGTTGATTA
65 TGTTCCACTTCTTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
* *
4186491 ATTGAATCAGGGTAGATTTGTTCCACTTTCACT-AAGGGAATATCAAATCTTGAAAGAGAGAGAT
1 ATTGAATCAGGGTAGACTTGTTCCACTGTCACTCAA-GGAATATCAAATCTTGAAAGAGAG-GAT
* * *
4186555 ATATTCCGCTTCTTCTGAGGGAATATCAGATATGGGAAAGTTGATTC
64 ATGTTCCACTTCTTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
** * *
4186602 ATTGAATCAGGGTAGACTTGTTCTGCTGTCACTCAATGAATATCAAATCTTGAAAGAGACGGATC
1 ATTGAATCAGGGTAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAGAGA-GGATA
* * *
4186667 TGTTCCGCTTCCTCTGAGAGAATATCAGATCTGGGAAAGTTGATTC
65 TGTTCCACTTCTTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
* *
4186713 ATTGAAT-ACGGGTAGACTTGTTCCGCTGTCACTCAAGGAATATCAAATCTTGAAAAAGAGTGAT
1 ATTGAATCA-GGGTAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAGAGAG-GAT
4186777 ATGTTCCACTTCTTCTGAAGGGAATATCAGAT
64 ATGTTCCACTTCTTCTG-AGGGAATATCAGAT
4186809 AGATGGTTTT
Statistics
Matches: 281, Mismatches: 30, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
110 4 0.01
111 261 0.93
112 16 0.06
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (110 bp):
ATTGAATCAGGGTAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAGAGAGGATAT
GTTCCACTTCTTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
Found at i:4186932 original size:34 final size:34
Alignment explanation
Indices: 4186858--4186932 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
4186848 ATGGCCCAAA
*
4186858 GGATTTAAGCATCATGCTCGAAAGACTTACATAT
1 GGATTTGAGCATCATGCTCGAAAGACTTACATAT
* * * *
4186892 GAATTTGATCATCATGCTTGGAAGACTTAC-TGAT
1 GGATTTGAGCATCATGCTCGAAAGACTTACAT-AT
4186926 GGATTTG
1 GGATTTG
4186933 CTTCACTACA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 1 0.03
34 33 0.97
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (34 bp):
GGATTTGAGCATCATGCTCGAAAGACTTACATAT
Found at i:4186980 original size:113 final size:113
Alignment explanation
Indices: 4186810--4187045 Score: 346
Period size: 113 Copynumber: 2.1 Consensus size: 113
4186800 ATATCAGATA
* * ** * *
4186810 GATGGTTTTTCTTCACTATTCTTCTGTGAAGGCTTAAAATGGCCCAAAGGATTTAAGCATCATGC
1 GATGGATTTGCTTCACTACACTTCGGTGAAGGATTAAAATGGCCCAAAGGATTTAAGCATCATGC
* **
4186875 TCGAAAGACTTACATATGAATTTGATCATCATGCTTGGAAGACTTACT
66 TCGAAAGACTTACAAATGAATTTGATCATCATGCTCAGAAGACTTACT
* *
4186923 GATGGATTTGCTTCACTACACTTCGGTGAAGGATTAAGATGGTCCAAAGGATTTAAGCATCATGC
1 GATGGATTTGCTTCACTACACTTCGGTGAAGGATTAAAATGGCCCAAAGGATTTAAGCATCATGC
* * *
4186988 TCGAAAGACTTACAAATGGATTTGATCATCATGCTCAGATGACTTATT
66 TCGAAAGACTTACAAATGAATTTGATCATCATGCTCAGAAGACTTACT
4187036 GATGGATTTG
1 GATGGATTTG
4187046 ATCATCATGC
Statistics
Matches: 109, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
113 109 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (113 bp):
GATGGATTTGCTTCACTACACTTCGGTGAAGGATTAAAATGGCCCAAAGGATTTAAGCATCATGC
TCGAAAGACTTACAAATGAATTTGATCATCATGCTCAGAAGACTTACT
Found at i:4187018 original size:34 final size:34
Alignment explanation
Indices: 4186971--4187243 Score: 399
Period size: 34 Copynumber: 8.0 Consensus size: 34
4186961 ATGGTCCAAA
* * **
4186971 GGATTTAAGCATCATGCTCGAAAGACTTACAAAT
1 GGATTTGATCATCATGCTCGAAAGACTTACTGAT
* *
4187005 GGATTTGATCATCATGCTC-AGATGACTTATTGAT
1 GGATTTGATCATCATGCTCGA-AAGACTTACTGAT
4187039 GGATTTGATCATCATGCTCGAAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGAAAGACTTACTGAT
*
4187073 GGATTTAATCATCATGCTC-ATAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGA-AAGACTTACTGAT
*
4187107 GGATTTGATCATCATGCTCTAAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGAAAGACTTACTGAT
*
4187141 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGAAAGACTTACTGAT
*
4187175 GGATTTGATCATCATGCTC-AGAAGACGTACTGAT
1 GGATTTGATCATCATGCTCGA-AAGACTTACTGAT
*
4187209 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGAAAGACTTACTGAT
4187243 G
1 G
4187244 ACCCGAAGGA
Statistics
Matches: 217, Mismatches: 16, Indels: 12
0.89 0.07 0.05
Matches are distributed among these distances:
33 2 0.01
34 213 0.98
35 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (34 bp):
GGATTTGATCATCATGCTCGAAAGACTTACTGAT
Found at i:4188673 original size:5 final size:5
Alignment explanation
Indices: 4188663--4188692 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
4188653 TTAGGCTCAC
4188663 AATCA AATCA AATCA AATCA AATCA AATCA
1 AATCA AATCA AATCA AATCA AATCA AATCA
4188693 TAAACATGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AATCA
Found at i:4192744 original size:15 final size:14
Alignment explanation
Indices: 4192703--4192744 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
4192693 GTGGGTAGCT
*
4192703 GGTACGAACTATCG
1 GGTACGAACTGTCG
*
4192717 GGTACGAAATGTCG
1 GGTACGAACTGTCG
4192731 GGTACCGAACTGTC
1 GGTA-CGAACTGTC
4192745 TGAGTACAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.21
Consensus pattern (14 bp):
GGTACGAACTGTCG
Found at i:4195471 original size:2 final size:2
Alignment explanation
Indices: 4195464--4195494 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4195454 ATTCATATGA
4195464 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4195495 CATTACACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4196025 original size:105 final size:105
Alignment explanation
Indices: 4195843--4196049 Score: 414
Period size: 105 Copynumber: 2.0 Consensus size: 105
4195833 AATATTTCTC
4195843 AAACTGATTTCTTTGAGGGGGTTTTCTTTTTTTTTATTCGTCTTCCTTCTCCCTTTTTTGTTCAG
1 AAACTGATTTCTTTGAGGGGGTTTTCTTTTTTTTTATTCGTCTTCCTTCTCCCTTTTTTGTTCAG
4195908 GACTCCCTCTCTTTATTTCTTTTCTCTCCACCGAATCTTT
66 GACTCCCTCTCTTTATTTCTTTTCTCTCCACCGAATCTTT
4195948 AAACTGATTTCTTTGAGGGGGTTTTCTTTTTTTTTATTCGTCTTCCTTCTCCCTTTTTTGTTCAG
1 AAACTGATTTCTTTGAGGGGGTTTTCTTTTTTTTTATTCGTCTTCCTTCTCCCTTTTTTGTTCAG
4196013 GACTCCCTCTCTTTATTTCTTTTCTCTCCACCGAATC
66 GACTCCCTCTCTTTATTTCTTTTCTCTCCACCGAATC
4196050 CTTTGTCGTC
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.12, C:0.25, G:0.12, T:0.52
Consensus pattern (105 bp):
AAACTGATTTCTTTGAGGGGGTTTTCTTTTTTTTTATTCGTCTTCCTTCTCCCTTTTTTGTTCAG
GACTCCCTCTCTTTATTTCTTTTCTCTCCACCGAATCTTT
Found at i:4196368 original size:3 final size:3
Alignment explanation
Indices: 4196360--4196386 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4196350 TGTAAAAATA
4196360 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
4196387 GTATTAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4198810 original size:2 final size:2
Alignment explanation
Indices: 4198803--4198865 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
4198793 CTATAGTTAC
*
4198803 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4198845 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
4198866 TAGTTATTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4201012 original size:21 final size:21
Alignment explanation
Indices: 4200964--4201013 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
4200954 TGCTGCCATG
* *
4200964 ATATGTAAATGATATGCAAAC
1 ATATATAAATGATATGAAAAC
4200985 ATA-ATAAATGAATAT-AAAAC
1 ATATATAAATG-ATATGAAAAC
4201005 ATATATAAA
1 ATATATAAA
4201014 CATAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (21 bp):
ATATATAAATGATATGAAAAC
Found at i:4204190 original size:19 final size:20
Alignment explanation
Indices: 4204151--4204200 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
4204141 GAAACCCCTT
4204151 TGAAAATACATGATTTTTTAA
1 TGAAAATACATGA-TTTTTAA
4204172 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
4204191 TGAAGATACA
1 TGAAAATACA
4204201 AGCTCTTGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 15 0.54
21 13 0.46
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:4212876 original size:27 final size:29
Alignment explanation
Indices: 4212841--4212905 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
4212831 CTTTTCTTTT
* *
4212841 ATTTGCTTTTC-TTCTTTTTGAGTGC-TGA
1 ATTT-CTTTTCTTTCTTTTGGAGTGCTTCA
4212869 ATTTC-TTTCTTTCTTTTGGAGTGCTTCA
1 ATTTCTTTTCTTTCTTTTGGAGTGCTTCA
4212897 ATTTCTTTT
1 ATTTCTTTT
4212906 ATGATTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.12
27 14 0.44
28 11 0.34
29 3 0.09
ACGTcount: A:0.11, C:0.15, G:0.14, T:0.60
Consensus pattern (29 bp):
ATTTCTTTTCTTTCTTTTGGAGTGCTTCA
Found at i:4219757 original size:20 final size:21
Alignment explanation
Indices: 4219713--4219758 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
4219703 GTCCAAAGCT
*
4219713 CTCCTCCAGCTAACGTGCTAG
1 CTCCTCCAGCTAACGTGCAAG
4219734 CTCCTCCAGCTAA-GTTG-AAG
1 CTCCTCCAGCTAACG-TGCAAG
4219754 CTCCT
1 CTCCT
4219759 TAAGTTATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.26
Consensus pattern (21 bp):
CTCCTCCAGCTAACGTGCAAG
Found at i:4223388 original size:23 final size:22
Alignment explanation
Indices: 4223361--4223413 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
4223351 AAAATCAGAC
* *
4223361 AAGAAAGTGAAGCACTCAAAAG
1 AAGAAAATCAAGCACTCAAAAG
*
4223383 AAAGAAAAATCCAGCACTCAAAAG
1 -AAG-AAAATCAAGCACTCAAAAG
4223407 AAGAAAA
1 AAGAAAA
4223414 CAGCAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 6 0.23
24 16 0.62
ACGTcount: A:0.60, C:0.15, G:0.17, T:0.08
Consensus pattern (22 bp):
AAGAAAATCAAGCACTCAAAAG
Found at i:4224659 original size:22 final size:24
Alignment explanation
Indices: 4224629--4224676 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
4224619 GGTGATCCAC
*
4224629 AAGGCATGT-CCT-TTGACATTTCA
1 AAGGCATGTACCTCTTGA-AATTCA
4224652 AAGG-ATGTACCTCTTGAAATTCA
1 AAGGCATGTACCTCTTGAAATTCA
4224675 AA
1 AA
4224677 AGAATGTGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 4 0.18
23 14 0.64
24 4 0.18
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (24 bp):
AAGGCATGTACCTCTTGAAATTCA
Found at i:4235496 original size:24 final size:24
Alignment explanation
Indices: 4235468--4235519 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
4235458 AAAGGCGTGA
*
4235468 CTCTTTGTGATTCATAAGACATGT
1 CTCTTTGTGATTCACAAGACATGT
* * *
4235492 CTCTTTGTGGTTCACATGATATGT
1 CTCTTTGTGATTCACAAGACATGT
4235516 CTCT
1 CTCT
4235520 GGATGTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.44
Consensus pattern (24 bp):
CTCTTTGTGATTCACAAGACATGT
Found at i:4244919 original size:16 final size:15
Alignment explanation
Indices: 4244888--4244932 Score: 65
Period size: 16 Copynumber: 3.0 Consensus size: 15
4244878 ATTGGAGTGC
*
4244888 AAGAAGAAGAG-AAA
1 AAGAAGAAAAGAAAA
4244902 AAGAAGAAAAGAATAA
1 AAGAAGAAAAGAA-AA
4244918 AAGAAGAAAAGAAAA
1 AAGAAGAAAAGAAAA
4244933 GAAAAAGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 10 0.36
15 3 0.11
16 15 0.54
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAGAAGAAAAGAAAA
Found at i:4244931 original size:21 final size:21
Alignment explanation
Indices: 4244888--4244944 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
4244878 ATTGGAGTGC
* *
4244888 AAGAAGAAGAGAAAAAGAAGAA
1 AAGAAAAAGAGAAGAA-AAGAA
4244910 AAGAATAAA-AGAAGAAAAGAA
1 AAGAA-AAAGAGAAGAAAAGAA
4244931 AAGAAAAAGAGAAG
1 AAGAAAAAGAGAAG
4244945 TTCAAAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 3 0.10
21 15 0.48
22 11 0.35
23 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (21 bp):
AAGAAAAAGAGAAGAAAAGAA
Found at i:4244940 original size:16 final size:16
Alignment explanation
Indices: 4244899--4244940 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4244889 AGAAGAAGAG
4244899 AAAAAGAAGAAAAGAAT
1 AAAAA-AAGAAAAGAAT
*
4244916 AAAAGAAGAAAAGAA-
1 AAAAAAAGAAAAGAAT
4244931 AAGAAAAAGA
1 AA-AAAAAGA
4244941 GAAGTTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 16 0.73
17 4 0.18
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (16 bp):
AAAAAAAGAAAAGAAT
Found at i:4248807 original size:19 final size:18
Alignment explanation
Indices: 4248751--4248807 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
4248741 TCCGCAGCCA
4248751 TCTTTATCCTTTCTT-TATT
1 TCTTT-TCC-TTCTTATATT
* *
4248770 TCATTTCATTCTTATTATT
1 TCTTTTCCTTCTTA-TATT
4248789 TCTTTTCCTTACTTATATT
1 TCTTTTCCTT-CTTATATT
4248808 ATTACCCCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
17 5 0.16
18 2 0.06
19 20 0.65
20 4 0.13
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (18 bp):
TCTTTTCCTTCTTATATT
Found at i:4251312 original size:24 final size:21
Alignment explanation
Indices: 4251277--4251319 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
4251267 GGCACATTCT
*
4251277 TTTGAATTTCAAGAGGTACATCA
1 TTTGAATGTCAA-AGG-ACATCA
4251300 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
4251320 GTATCACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCA
Found at i:4252674 original size:23 final size:25
Alignment explanation
Indices: 4252635--4252688 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
4252625 TTCTTTTCTC
4252635 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
4252660 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
4252683 TTTCTT
1 TTTCTT
4252689 TGCTGGATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:4259708 original size:16 final size:16
Alignment explanation
Indices: 4259676--4259707 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4259666 ATTTATAAAC
4259676 TAAATAATATAAGATA
1 TAAATAATATAAGATA
4259692 TAAAT-ATATAA-ATA
1 TAAATAATATAAGATA
4259706 TA
1 TA
4259708 TGGTTCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 6 0.38
16 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
TAAATAATATAAGATA
Found at i:4263061 original size:14 final size:14
Alignment explanation
Indices: 4263042--4263071 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4263032 TTTAAGGATT
4263042 GATGGTGATGGAAA
1 GATGGTGATGGAAA
4263056 GATGGTGATGGAAA
1 GATGGTGATGGAAA
4263070 GA
1 GA
4263072 GTATCTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.43, T:0.20
Consensus pattern (14 bp):
GATGGTGATGGAAA
Found at i:4264232 original size:22 final size:22
Alignment explanation
Indices: 4264192--4264233 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4264182 AAATATATGG
*
4264192 TTCATAATAATATCTTCATACA
1 TTCATAATAATATCATCATACA
4264214 TTCATAAT-ATCATCATCATA
1 TTCATAATAAT-ATCATCATA
4264234 ACTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATATCATCATACA
Found at i:4265080 original size:11 final size:12
Alignment explanation
Indices: 4265064--4265107 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
4265054 AGCCCCTACT
4265064 TAATTTTT-TCA
1 TAATTTTTCTCA
4265075 TAATTTTTCTC-
1 TAATTTTTCTCA
4265086 T--TTTTTC-CA
1 TAATTTTTCTCA
4265095 TAATTTTTCTCA
1 TAATTTTTCTCA
4265107 T
1 T
4265108 CATATATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
8 1 0.04
9 7 0.25
11 15 0.54
12 5 0.18
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (12 bp):
TAATTTTTCTCA
Found at i:4265096 original size:20 final size:19
Alignment explanation
Indices: 4265067--4265105 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
4265057 CCCTACTTAA
4265067 TTTTTTCATAATTTTTCTC
1 TTTTTTCATAATTTTTCTC
4265086 TTTTTTCCATAATTTTTCTC
1 TTTTTT-CATAATTTTTCTC
4265106 ATCATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTCATAATTTTTCTC
Found at i:4268584 original size:14 final size:14
Alignment explanation
Indices: 4268567--4268594 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4268557 GCTAAGGATT
4268567 GATGGTGATGGAAA
1 GATGGTGATGGAAA
4268581 GATGGTGATGGAAA
1 GATGGTGATGGAAA
4268595 TAGTATCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
GATGGTGATGGAAA
Found at i:4271474 original size:21 final size:21
Alignment explanation
Indices: 4271450--4271492 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
4271440 GGTGATCTAG
4271450 GGAATCTTGTGGTGCAGCCTT
1 GGAATCTTGTGGTGCAGCCTT
4271471 GGAATCTTGTGGTGCAGCCTT
1 GGAATCTTGTGGTGCAGCCTT
4271492 G
1 G
4271493 TGCATGGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.35, T:0.33
Consensus pattern (21 bp):
GGAATCTTGTGGTGCAGCCTT
Found at i:4284125 original size:5 final size:5
Alignment explanation
Indices: 4284115--4284156 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
4284105 CTCTTTTGAA
**
4284115 TTTCT TTTCT TTTCT TTTCT TTTCT GAT-T TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
4284157 GTCTTTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 2 0.06
5 30 0.94
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:4284148 original size:14 final size:15
Alignment explanation
Indices: 4284115--4284153 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
4284105 CTCTTTTGAA
**
4284115 TTTCTTTTCTTTTCT
1 TTTCTTTTCTGATCT
4284130 TTTCTTTTCTGAT-T
1 TTTCTTTTCTGATCT
4284144 TTTCTTTTCT
1 TTTCTTTTCT
4284154 TTTGTCTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTTCTGATCT
Found at i:4301040 original size:19 final size:19
Alignment explanation
Indices: 4301014--4301067 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
4301004 AACTTCTCTT
4301014 TTTCTTTTCTTTTTTTCTAA
1 TTTCTTTTCTTTTTTTCT-A
* *
4301034 TTT-TTTTCTTTTTGTCTT
1 TTTCTTTTCTTTTTTTCTA
4301052 TTTCTTTTCTTTTTTT
1 TTTCTTTTCTTTTTTT
4301068 GCTTTGCACG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.10
19 24 0.80
20 3 0.10
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTCTTTTCTTTTTTTCTA
Found at i:4303217 original size:20 final size:19
Alignment explanation
Indices: 4303192--4303229 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
4303182 ACAATAACAA
4303192 CATCATCTACATTTCATCAT
1 CATCATCTACA-TTCATCAT
*
4303212 CATCATCTTCATTCATCA
1 CATCATCTACATTCATCA
4303230 AGACCATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (19 bp):
CATCATCTACATTCATCAT
Found at i:4305272 original size:21 final size:21
Alignment explanation
Indices: 4305229--4305272 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4305219 AGATGAACTA
*
4305229 TGGCTTTGCAACAATGTTGCT
1 TGGCTTTGCAACAATGTTCCT
*
4305250 TGGCTTTGTAACAAAT-TTCCT
1 TGGCTTTGCAAC-AATGTTCCT
4305271 TG
1 TG
4305273 ATTTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (21 bp):
TGGCTTTGCAACAATGTTCCT
Found at i:4305335 original size:21 final size:21
Alignment explanation
Indices: 4305310--4305352 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4305300 CATCAAGGTC
4305310 TTTGTAGAAGCCATGAAATCT
1 TTTGTAGAAGCCATGAAATCT
* * *
4305331 TTTGTCGAGGCCATGAATTCT
1 TTTGTAGAAGCCATGAAATCT
4305352 T
1 T
4305353 GCAAGGATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (21 bp):
TTTGTAGAAGCCATGAAATCT
Found at i:4308174 original size:22 final size:22
Alignment explanation
Indices: 4308148--4308191 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4308138 CATCAAGGTC
4308148 TTTGTAGAAGCCATGAAATCCT
1 TTTGTAGAAGCCATGAAATCCT
* *
4308170 TTTGTAGAGGCCATGAATTCCT
1 TTTGTAGAAGCCATGAAATCCT
4308192 GCAAGGATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (22 bp):
TTTGTAGAAGCCATGAAATCCT
Found at i:4315166 original size:16 final size:15
Alignment explanation
Indices: 4315142--4315216 Score: 54
Period size: 16 Copynumber: 5.1 Consensus size: 15
4315132 ATTTTATATG
4315142 TTATAATATATAATTA
1 TTAT-ATATATAATTA
4315158 TTATCATATAT-A-TA
1 TTAT-ATATATAATTA
4315172 -TATATATAT-A-TA
1 TTATATATATAATTA
* *
4315184 TTATATCTATAGTTA
1 TTATATATATAATTA
4315199 TTATGATA-ATAACTTA
1 TTAT-ATATATAA-TTA
4315215 TT
1 TT
4315217 CATTAATATG
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
12 9 0.18
13 11 0.22
14 2 0.04
15 10 0.20
16 17 0.35
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.51
Consensus pattern (15 bp):
TTATATATATAATTA
Found at i:4315168 original size:2 final size:2
Alignment explanation
Indices: 4315143--4315194 Score: 51
Period size: 2 Copynumber: 28.0 Consensus size: 2
4315133 TTTTATATGT
4315143 TA TA -A TA TA TA -A T- TA T- TA TCA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
*
4315182 TA T- TA TA TC TA TA
1 TA TA TA TA TA TA TA
4315195 GTTATTATGA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
1 5 0.12
2 35 0.83
3 2 0.05
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4319959 original size:5 final size:5
Alignment explanation
Indices: 4319949--4319974 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4319939 CTTCAACTTC
4319949 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
4319975 CTTTTTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:4324588 original size:11 final size:10
Alignment explanation
Indices: 4324557--4324610 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
4324547 CTCTTTTGAA
*
4324557 TTTCTTTTCT
1 TTTCTTTTTT
*
4324567 TTTCTGATTTT
1 TTTCT-TTTTT
4324578 TTTCTTCTTTT
1 TTTCTT-TTTT
*
4324589 TGTCTTTTTCT
1 TTTCTTTTT-T
4324600 TTTCTTTTTT
1 TTTCTTTTTT
4324610 T
1 T
4324611 GCACTCCAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
10 10 0.28
11 26 0.72
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.80
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:4324604 original size:19 final size:19
Alignment explanation
Indices: 4324557--4324608 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
4324547 CTCTTTTGAA
4324557 TTTCTTTTCTTTTCTGATTT
1 TTTCTTTTCTTTT-TGATTT
*
4324577 TTT-TCTTCTTTTTG-TCTT
1 TTTCTTTTCTTTTTGAT-TT
4324595 TTTCTTTTCTTTTT
1 TTTCTTTTCTTTTT
4324609 TTGCACTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 1 0.04
18 7 0.25
19 17 0.61
20 3 0.11
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (19 bp):
TTTCTTTTCTTTTTGATTT
Found at i:4330846 original size:28 final size:28
Alignment explanation
Indices: 4330784--4330846 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
4330774 AAATAAAATC
* * *
4330784 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAAATCAAGCACTCAAAAAGA
*
4330812 A-AGAAAGAAAATCCAGCACTCAAAAAGA
1 AGA-AAAGAAAATCAAGCACTCAAAAAGA
4330840 AGAAAAG
1 AGAAAAG
4330847 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 27 0.93
29 1 0.03
ACGTcount: A:0.60, C:0.14, G:0.17, T:0.08
Consensus pattern (28 bp):
AGAAAAGAAAATCAAGCACTCAAAAAGA
Found at i:4330850 original size:15 final size:15
Alignment explanation
Indices: 4330839--4330867 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4330829 ACTCAAAAAG
4330839 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
4330854 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
4330868 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:4333598 original size:11 final size:13
Alignment explanation
Indices: 4333566--4333595 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4333556 TGGCCAAAGA
4333566 TGAAAAGGTATGT
1 TGAAAAGGTATGT
4333579 TGAAAAGGTATG-
1 TGAAAAGGTATGT
4333591 TGAAA
1 TGAAA
4333596 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:4335546 original size:91 final size:91
Alignment explanation
Indices: 4335398--4335570 Score: 283
Period size: 91 Copynumber: 1.9 Consensus size: 91
4335388 CCCATGTGCC
*
4335398 TTGCATATGACCAGCCCCCATGCGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGCGCCTTGCATATGGATCATTTAGGCGCCAAGATGAAGAGTTCT
4335463 CTCCCTATTCAGCCAAGCTATGTGTT
66 CTCCCTATTCAGCCAAGCTATGTGTT
* * * * *
4335489 TTGCATGTGATCAGCCCCTATGTGCCTTGCATATGGTTCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGCGCCTTGCATATGGATCATTTAGGCGCCAAGATGAAGAGTTCT
*
4335554 CTCCCTATTCGGCCAAG
66 CTCCCTATTCAGCCAAG
4335571 TATCAACTAC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 75 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (91 bp):
TTGCATATGACCAGCCCCCATGCGCCTTGCATATGGATCATTTAGGCGCCAAGATGAAGAGTTCT
CTCCCTATTCAGCCAAGCTATGTGTT
Found at i:4340776 original size:34 final size:32
Alignment explanation
Indices: 4340704--4340777 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 32
4340694 CTTGGCTTGC
* *
4340704 TTTCTTTTTGAATTTTTCTTTTTCTTTTCTTT
1 TTTCTTTTTGAATTTTTCTTCTTCTTTTATTT
*
4340736 TCTTCTTTTCTG-ATTTTTGTCTCTTCTTTTATGTT
1 T-TTCTTTT-TGAATTTTTCT-TCTTCTTTTAT-TT
4340771 TTTCTTT
1 TTTCTTT
4340778 CTTTTTGCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
32 1 0.03
33 14 0.40
34 17 0.49
35 3 0.09
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.74
Consensus pattern (32 bp):
TTTCTTTTTGAATTTTTCTTCTTCTTTTATTT
Found at i:4341075 original size:19 final size:19
Alignment explanation
Indices: 4341044--4341094 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
4341034 AGGGAATAAT
4341044 AATATAAGTAATGAAATGA
1 AATATAAGTAATGAAATGA
4341063 AATATTAAG-AATGAAATGA
1 AATA-TAAGTAATGAAATGA
*
4341082 AATA-AAGAAATGA
1 AATATAAGTAATGA
4341095 TAGAGATGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.10
18 5 0.17
19 18 0.60
20 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.24
Consensus pattern (19 bp):
AATATAAGTAATGAAATGA
Found at i:4342573 original size:20 final size:19
Alignment explanation
Indices: 4342537--4342575 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
4342527 AGTAAAGATG
**
4342537 TGAAAACATATGTTATGCA
1 TGAAAACATATAATATGCA
4342556 TGAAAATCATATAATATGCA
1 TGAAAA-CATATAATATGCA
4342576 AGTGAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (19 bp):
TGAAAACATATAATATGCA
Found at i:4348573 original size:19 final size:20
Alignment explanation
Indices: 4348549--4348597 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
4348539 TATCCTTTAT
4348549 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
4348568 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
4348588 -TATTATTATT
1 TTATT-TTATT
4348598 CCCTTTACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:4348880 original size:8 final size:8
Alignment explanation
Indices: 4348867--4348899 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
4348857 CAAAAAGAAG
4348867 AGAAAAGA
1 AGAAAAGA
4348875 AGAAAAGA
1 AGAAAAGA
4348883 AGAAAAGA
1 AGAAAAGA
4348891 AGAAAAGA
1 AGAAAAGA
4348899 A
1 A
4348900 AAGAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:4348883 original size:13 final size:13
Alignment explanation
Indices: 4348859--4348906 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
4348849 TTGGAGTGCA
*
4348859 AAAAGAAGAGAA-
1 AAAAGAAAAGAAG
4348871 AAGAAGAAAAGAAG
1 AA-AAGAAAAGAAG
4348885 AAAAGAAGAA-AAG
1 AAAAGAA-AAGAAG
4348898 AAAAGAAAA
1 AAAAGAAAA
4348907 AGAGAAGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 4 0.12
13 24 0.75
14 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAGAAG
Found at i:4348909 original size:16 final size:16
Alignment explanation
Indices: 4348859--4348909 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
4348849 TTGGAGTGCA
*
4348859 AAAAGAAGAGAAAAGAAG
1 AAAAGAAAAG-AAA-AAG
*
4348877 AAAAGAAGAA-AAGAAG
1 AAAAGAA-AAGAAAAAG
4348893 AAAAGAAAAGAAAAAG
1 AAAAGAAAAGAAAAAG
4348909 A
1 A
4348910 GAAGTTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 2 0.07
16 16 0.57
17 2 0.07
18 7 0.25
19 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:4353019 original size:13 final size:13
Alignment explanation
Indices: 4352983--4353032 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
4352973 ATGCAAAGCA
*
4352983 AAAAAAAGAAGAG
1 AAAAAAAGAAAAG
*
4352996 AAAAATCAGAAAAG
1 AAAAA-AAGAAAAG
* *
4353010 AAGAAAAGAACAG
1 AAAAAAAGAAAAG
4353023 AAAAAAAGAA
1 AAAAAAAGAA
4353033 GTTCAAAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:4353025 original size:18 final size:18
Alignment explanation
Indices: 4352986--4353032 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
4352976 CAAAGCAAAA
4352986 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGA-AAAAATCAG
4353005 AAAAGAAGAAAAGAA-CAG
1 AAAAGAAGAAAA-AATCAG
*
4353023 AAAAAAAGAA
1 AAAAGAAGAA
4353033 GTTCAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.74, C:0.04, G:0.19, T:0.02
Consensus pattern (18 bp):
AAAAGAAGAAAAAATCAG
Found at i:4356891 original size:19 final size:20
Alignment explanation
Indices: 4356867--4356915 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
4356857 TATCCTTTAT
4356867 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
4356886 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
4356906 -TATTATTATT
1 TTATT-TTATT
4356916 CCCTTTACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:4357107 original size:23 final size:23
Alignment explanation
Indices: 4357077--4357124 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
4357067 CAGTACAAGT
*
4357077 GCCTTACATCAAGTGGTATCAGA
1 GCCTTACATCAAGTGGAATCAGA
*
4357100 GCCTTACATCAATTGGAATCAGA
1 GCCTTACATCAAGTGGAATCAGA
4357123 GC
1 GC
4357125 ATTGGTGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (23 bp):
GCCTTACATCAAGTGGAATCAGA
Found at i:4358980 original size:12 final size:13
Alignment explanation
Indices: 4358950--4358981 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
4358940 TGGCCAAAGA
4358950 TGAAAGGGTATGT
1 TGAAAGGGTATGT
4358963 TGAAAGGGTATG-
1 TGAAAGGGTATGT
4358975 TGAAAGG
1 TGAAAGG
4358982 TGTTTAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.34, C:0.00, G:0.41, T:0.25
Consensus pattern (13 bp):
TGAAAGGGTATGT
Found at i:4365818 original size:91 final size:91
Alignment explanation
Indices: 4365652--4365823 Score: 213
Period size: 91 Copynumber: 1.9 Consensus size: 91
4365642 CCCATGAGCC
* * **
4365652 TTGCATATGACCAACCCCCATGTGCCTTGCATGTGGATCATTTAGGTACCAAGATGAAGAGTTCT
1 TTGCATATGACCAACCCCCATGTGCCTTGCATATGGATCATTTAGGCACCAAGATGAAGACATCT
4365717 CACCCTATTCGGCCAAGCCATGTGTT
66 CACCCTATTCGGCCAAGCCATGTGTT
* * * * * *
4365743 TTGCATGTGATCAGCCCCCATGTGCCTTGCATATGGTTTATTTAGGCGCCAAGATGAATGACCAT
1 TTGCATATGACCAACCCCCATGTGCCTTGCATATGGATCATTTAGGCACCAAGATGAA-GA-CAT
*
4365808 CT-ATCC-ATTCGGCCAA
64 CTCACCCTATTCGGCCAA
4365824 TCACCATTAC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
91 60 0.88
92 5 0.07
93 3 0.04
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (91 bp):
TTGCATATGACCAACCCCCATGTGCCTTGCATATGGATCATTTAGGCACCAAGATGAAGACATCT
CACCCTATTCGGCCAAGCCATGTGTT
Found at i:4369430 original size:13 final size:13
Alignment explanation
Indices: 4369412--4369436 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4369402 TGGCTAAAGA
4369412 TGAAAAGGTATGT
1 TGAAAAGGTATGT
4369425 TGAAAAGGTATG
1 TGAAAAGGTATG
4369437 CGAAAGGTGT
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:0.00, G:0.32, T:0.28
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:4376224 original size:9 final size:9
Alignment explanation
Indices: 4376212--4376251 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
4376202 TTTTTTGAAA
4376212 TTTTGGCTT
1 TTTTGGCTT
4376221 TTTTGGCTT
1 TTTTGGCTT
* *
4376230 TTTTTGTTT
1 TTTTGGCTT
*
4376239 TTTTGCCTT
1 TTTTGGCTT
4376248 TTTT
1 TTTT
4376252 TTGGCCTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.00, C:0.10, G:0.15, T:0.75
Consensus pattern (9 bp):
TTTTGGCTT
Found at i:4376232 original size:10 final size:10
Alignment explanation
Indices: 4376212--4376265 Score: 60
Period size: 11 Copynumber: 5.5 Consensus size: 10
4376202 TTTTTTGAAA
4376212 TTTTGGC-TT
1 TTTTGGCTTT
4376221 TTTTGGCTTT
1 TTTTGGCTTT
4376231 TTTT-G-TTT
1 TTTTGGCTTT
*
4376239 TTTTGCCTTTT
1 TTTTGGC-TTT
4376250 TTTTGGCCTTT
1 TTTTGG-CTTT
4376261 TTTTG
1 TTTTG
4376266 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 7 0.18
9 8 0.21
10 6 0.16
11 16 0.42
12 1 0.03
ACGTcount: A:0.00, C:0.11, G:0.17, T:0.72
Consensus pattern (10 bp):
TTTTGGCTTT
Found at i:4376234 original size:19 final size:19
Alignment explanation
Indices: 4376212--4376272 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
4376202 TTTTTTGAAA
4376212 TTTTGGCTTTTTTGGCTTT
1 TTTTGGCTTTTTTGGCTTT
* *
4376231 TTTT-GTTTTTTTGCCTTTT
1 TTTTGGCTTTTTTGGC-TTT
*
4376250 TTTTGGCCTTTTTTTG-TTT
1 TTTTGG-CTTTTTTGGCTTT
4376269 TTTT
1 TTTT
4376273 TTTTTTTGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 9 0.26
19 18 0.53
20 1 0.03
21 6 0.18
ACGTcount: A:0.00, C:0.10, G:0.15, T:0.75
Consensus pattern (19 bp):
TTTTGGCTTTTTTGGCTTT
Found at i:4376251 original size:12 final size:12
Alignment explanation
Indices: 4376236--4376264 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4376226 GCTTTTTTTG
4376236 TTTTTTT-GCCT
1 TTTTTTTGGCCT
4376247 TTTTTTTGGCCT
1 TTTTTTTGGCCT
4376259 TTTTTT
1 TTTTTT
4376265 GTTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (12 bp):
TTTTTTTGGCCT
Found at i:4376262 original size:38 final size:37
Alignment explanation
Indices: 4376212--4376289 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
4376202 TTTTTTGAAA
*
4376212 TTTTGG-CTTTTTTGGCTTTTTTTGTTTTTTTGCCTTTT
1 TTTTGGCCTTTTTTGG-TTTTTTT-TTTTTTTGCATTTT
* *
4376250 TTTTGGCCTTTTTTTGTTTTTTTTTTTTTTGTATTTT
1 TTTTGGCCTTTTTTGGTTTTTTTTTTTTTTGCATTTT
4376287 TTT
1 TTT
4376290 GAAAAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 15 0.42
38 13 0.36
39 8 0.22
ACGTcount: A:0.01, C:0.08, G:0.13, T:0.78
Consensus pattern (37 bp):
TTTTGGCCTTTTTTGGTTTTTTTTTTTTTTGCATTTT
Found at i:4376276 original size:15 final size:16
Alignment explanation
Indices: 4376258--4376289 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
4376248 TTTTTTGGCC
4376258 TTTTTTTGT-TTTTTT
1 TTTTTTTGTATTTTTT
4376273 TTTTTTTGTATTTTTT
1 TTTTTTTGTATTTTTT
4376289 T
1 T
4376290 GAAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.91
Consensus pattern (16 bp):
TTTTTTTGTATTTTTT
Found at i:4396294 original size:19 final size:20
Alignment explanation
Indices: 4396270--4396312 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4396260 AGGATTTATC
*
4396270 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
4396289 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
4396309 TTCA
1 TTCA
4396313 AAGGGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:4397331 original size:16 final size:16
Alignment explanation
Indices: 4397294--4397351 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
4397284 GAGTTGTAAG
4397294 TTATCTTCACTTTC-TTA
1 TTAT-TTCA-TTTCTTTA
*
4397311 CTATTTCATTTCTTTA
1 TTATTTCATTTCTTTA
* *
4397327 TTATTTCATCT-TTTC
1 TTATTTCATTTCTTTA
4397342 TTATTTCATT
1 TTATTTCATT
4397352 ACCATATTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 16 0.46
16 16 0.46
17 3 0.09
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTTCATTTCTTTA
Found at i:4400448 original size:19 final size:20
Alignment explanation
Indices: 4400424--4400466 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4400414 AGCATTTATC
*
4400424 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
4400443 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
4400463 TTCA
1 TTCA
4400467 AAGGGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:4405648 original size:35 final size:36
Alignment explanation
Indices: 4405601--4405668 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
4405591 ATTTATAAGT
4405601 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
4405636 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
4405669 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:4410794 original size:18 final size:18
Alignment explanation
Indices: 4410771--4410808 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4410761 TCTTCACTTT
*
4410771 TTCTTTGTT-TTTTTATTC
1 TTCTTT-TTCTTTTCATTC
4410789 TTCTTTTTCTTTTCATTC
1 TTCTTTTTCTTTTCATTC
4410807 TT
1 TT
4410809 TTGCACTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (18 bp):
TTCTTTTTCTTTTCATTC
Found at i:4411304 original size:35 final size:36
Alignment explanation
Indices: 4411257--4411324 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
4411247 ATTTATAAGT
4411257 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
4411292 TGGTGA-AGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATA-ATATAGGCGTGATAATGGTGATGGA
4411325 CAGATTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
34 1 0.03
35 19 0.61
36 11 0.35
ACGTcount: A:0.31, C:0.03, G:0.37, T:0.29
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:4418801 original size:35 final size:36
Alignment explanation
Indices: 4418754--4418821 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
4418744 ATTTATAAGT
4418754 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
4418789 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
4418822 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:4419186 original size:20 final size:20
Alignment explanation
Indices: 4419161--4419216 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
4419151 GAAACCCCTT
4419161 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTGA
*
4419181 TGAAAATGCATGATTTTTGA
1 TGAAAATACATGATTTTTGA
4419201 TGAAAATACATGATTT
1 TGAAAATACATGATTT
4419217 AAATGAAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (20 bp):
TGAAAATACATGATTTTTGA
Found at i:4421799 original size:9 final size:9
Alignment explanation
Indices: 4421785--4421820 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
4421775 TTTTTAGTAT
4421785 AAAAATAAA
1 AAAAATAAA
4421794 AAAAAT-AA
1 AAAAATAAA
4421802 AAAAATAAA
1 AAAAATAAA
*
4421811 AAAATTAAA
1 AAAAATAAA
4421820 A
1 A
4421821 CCTTAGCAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAATAAA
Found at i:4421803 original size:8 final size:8
Alignment explanation
Indices: 4421785--4421820 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
4421775 TTTTTAGTAT
4421785 AAAAATAAA
1 AAAAAT-AA
4421794 AAAAATAA
1 AAAAATAA
4421802 AAAAATAA
1 AAAAATAA
*
4421810 AAAAATTA
1 AAAAATAA
4421818 AAA
1 AAA
4421821 CCTTAGCAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAAATAA
Found at i:4421807 original size:17 final size:17
Alignment explanation
Indices: 4421785--4421820 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
4421775 TTTTTAGTAT
4421785 AAAAATAAAAAAAATAA
1 AAAAATAAAAAAAATAA
*
4421802 AAAAATAAAAAAATTAA
1 AAAAATAAAAAAAATAA
4421819 AA
1 AA
4421821 CCTTAGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAAATAAAAAAAATAA
Found at i:4422831 original size:35 final size:37
Alignment explanation
Indices: 4422784--4422856 Score: 114
Period size: 35 Copynumber: 2.0 Consensus size: 37
4422774 ATTTATAAGT
*
4422784 TGGTGATAATATAGGCGTGA-TATGGTGATGGA-ATA
1 TGGTGATAATATAGGCGTGACAATGGTGATGGACATA
*
4422819 TGGTGATGATATAGGCGTGACAATGGTGATGGACATA
1 TGGTGATAATATAGGCGTGACAATGGTGATGGACATA
4422856 T
1 T
4422857 TGTATCTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 19 0.56
36 11 0.32
37 4 0.12
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.30
Consensus pattern (37 bp):
TGGTGATAATATAGGCGTGACAATGGTGATGGACATA
Found at i:4425047 original size:23 final size:24
Alignment explanation
Indices: 4425000--4425047 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
4424990 AACTCTTGGC
*
4425000 ACTTCAACTGACGCTTCTCTTTGA
1 ACTTCAACTGACGCTTATCTTTGA
4425024 ACTTCAAAC-GACG-TTATCTTTGA
1 ACTTC-AACTGACGCTTATCTTTGA
4425047 A
1 A
4425048 ACATCAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
24 9 0.41
25 3 0.14
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.35
Consensus pattern (24 bp):
ACTTCAACTGACGCTTATCTTTGA
Found at i:4428702 original size:5 final size:5
Alignment explanation
Indices: 4428688--4428722 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
4428678 GTGCTTCAAC
*
4428688 TTTC- TTTCT TTTCT TTTCT TTTCT TTGCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
4428723 CTTTTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:4432279 original size:19 final size:20
Alignment explanation
Indices: 4432255--4432297 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4432245 AGCATTTATC
*
4432255 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
4432274 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
4432294 TTCA
1 TTCA
4432298 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:4432683 original size:36 final size:35
Alignment explanation
Indices: 4432636--4432743 Score: 130
Period size: 35 Copynumber: 3.1 Consensus size: 35
4432626 AGATACTACG
*
4432636 TATAATATCACCATCTTCCATCT-CATTTTTCACGCC
1 TATAACATCACCATCTTCCATCTCCA--TTTCACGCC
*
4432672 TATAACATCACCATCTTCCAT-TACCATTGCACGCC
1 TATAACATCACCATCTTCCATCT-CCATTTCACGCC
* * *
4432707 TATATCATTACCATCTTCTATCTCCATTTCACGCC
1 TATAACATCACCATCTTCCATCTCCATTTCACGCC
4432742 TA
1 TA
4432744 AATAACCACC
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
35 40 0.63
36 21 0.33
37 2 0.03
ACGTcount: A:0.26, C:0.34, G:0.04, T:0.36
Consensus pattern (35 bp):
TATAACATCACCATCTTCCATCTCCATTTCACGCC
Found at i:4432787 original size:11 final size:11
Alignment explanation
Indices: 4432771--4432797 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
4432761 TACCATCTAT
4432771 TCATCCTTCAA
1 TCATCCTTCAA
4432782 TCATCCTTCAA
1 TCATCCTTCAA
4432793 TCATC
1 TCATC
4432798 ATCAAGGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.00, T:0.37
Consensus pattern (11 bp):
TCATCCTTCAA
Found at i:4440365 original size:19 final size:20
Alignment explanation
Indices: 4440341--4440389 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
4440331 TATACTTTCT
4440341 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
4440360 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
4440380 -TATTATTATT
1 TTATT-TTATT
4440390 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:4440681 original size:8 final size:8
Alignment explanation
Indices: 4440668--4440700 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
4440658 GAGAAAATTT
*
4440668 AGAAAATA
1 AGAAAAGA
4440676 AGAAAAGA
1 AGAAAAGA
4440684 AGAAAAGA
1 AGAAAAGA
4440692 AGAAAAGA
1 AGAAAAGA
4440700 A
1 A
4440701 AAGAAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (8 bp):
AGAAAAGA
Found at i:4440691 original size:13 final size:12
Alignment explanation
Indices: 4440675--4440714 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 12
4440665 TTTAGAAAAT
4440675 AAGAAAAGAAGAA
1 AAGAAAA-AAGAA
4440688 AAGAAGAAAAGAA
1 AAGAA-AAAAGAA
4440701 AAGAAAAAGAGAA
1 AAGAAAAA-AGAA
4440714 A
1 A
4440715 GCAAGCCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 20 0.80
14 2 0.08
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAGAA
Found at i:4441295 original size:19 final size:20
Alignment explanation
Indices: 4441271--4441319 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
4441261 TATCATTTCT
4441271 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
4441290 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
4441310 -TATTATTATT
1 TTATT-TTATT
4441320 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:4443364 original size:14 final size:14
Alignment explanation
Indices: 4443345--4443372 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4443335 GGGGATGGAG
4443345 GATGGTGATGGAAA
1 GATGGTGATGGAAA
4443359 GATGGTGATGGAAA
1 GATGGTGATGGAAA
4443373 TAATATCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
GATGGTGATGGAAA
Found at i:4452752 original size:21 final size:21
Alignment explanation
Indices: 4452711--4452753 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4452701 CTTAGGAGTC
*
4452711 TCTTCTTTCTCTTTTTGTTTT
1 TCTTCTTTCTCTTTTTCTTTT
4452732 TCTTCTTTCT-TTTTCTCTTTT
1 TCTTCTTTCTCTTTT-TCTTTT
4452753 T
1 T
4452754 GTTGCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (21 bp):
TCTTCTTTCTCTTTTTCTTTT
Found at i:4459930 original size:3 final size:3
Alignment explanation
Indices: 4459922--4459967 Score: 65
Period size: 3 Copynumber: 14.7 Consensus size: 3
4459912 AATTTAAATG
*
4459922 TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TATT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT TAT TA
4459968 CAAAACCCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:4468980 original size:16 final size:17
Alignment explanation
Indices: 4468959--4468995 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
4468949 GTAAGTTATC
4468959 TTCATTTTC-TTACTAT
1 TTCATTTTCTTTACTAT
*
4468975 TTCA-TTTCTTTATTAT
1 TTCATTTTCTTTACTAT
4468991 TTCAT
1 TTCAT
4468996 CTTTTCTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCATTTTCTTTACTAT
Found at i:4469007 original size:15 final size:16
Alignment explanation
Indices: 4468972--4469010 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
4468962 ATTTTCTTAC
*
4468972 TATTTCATTTCTTTAT
1 TATTTCATCTCTTTAT
*
4468988 TATTTCATCT-TTTCT
1 TATTTCATCTCTTTAT
4469003 TATTTCAT
1 TATTTCAT
4469011 TACCATCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTCATCTCTTTAT
Found at i:4475648 original size:13 final size:13
Alignment explanation
Indices: 4475626--4475655 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4475616 ACTAAACACC
4475626 TTTC-ACATACCT
1 TTTCAACATACCT
4475638 TTTCAACATACCT
1 TTTCAACATACCT
4475651 TTTCA
1 TTTCA
4475656 TCTTTGGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:4478699 original size:2 final size:2
Alignment explanation
Indices: 4478692--4478726 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4478682 AGTTATTTTC
4478692 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4478727 CCTATAGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4480053 original size:19 final size:20
Alignment explanation
Indices: 4480029--4480068 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
4480019 TATCATTTCT
4480029 TTATTTCATTTT-ATT-CTTA
1 TTATTT-ATTTTCATTACTTA
4480048 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
4480068 T
1 T
4480069 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:4480071 original size:19 final size:19
Alignment explanation
Indices: 4480025--4480071 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
4480015 TCTCTATCAT
4480025 TTCTT-TATTTCATTTT-A
1 TTCTTATATTTCATTTTCA
4480042 TTCTTATTATTT-ATTTTCA
1 TTCTTA-TATTTCATTTTCA
4480061 TTACTTATATT
1 TT-CTTATATT
4480072 ATTATCCGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.19
18 5 0.19
19 12 0.46
20 4 0.15
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (19 bp):
TTCTTATATTTCATTTTCA
Found at i:4480382 original size:13 final size:12
Alignment explanation
Indices: 4480334--4480382 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 12
4480324 AAATTAGAGT
4480334 GAAAAAAG-AAA
1 GAAAAAAGAAAA
4480345 GAAAAATCAGAAAA
1 GAAAAA--AGAAAA
4480359 GAAGAAAAGAAAA
1 GAA-AAAAGAAAA
4480372 GAAAAAGAGAA
1 GAAAAA-AGAA
4480383 GTTCAAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 6 0.18
12 3 0.09
13 15 0.45
14 6 0.18
15 3 0.09
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (12 bp):
GAAAAAAGAAAA
Done.