Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000913.1 Hibiscus syriacus cultivar Beakdansim tig00001818_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: 1610646
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:214878 original size:18 final size:19
Alignment explanation
Indices: 214855--214904 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
214845 GTCATTTTTG
214855 GTATCGATACTCAAGG-GA
1 GTATCGATACTCAAGGAGA
214873 GTATCGATAC-CAAGGATAGA
1 GTATCGATACTCAAGG--AGA
214893 GTATCGATACTC
1 GTATCGATACTC
214905 CCAATAGGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.18
18 10 0.36
20 12 0.43
21 1 0.04
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (19 bp):
GTATCGATACTCAAGGAGA
Found at i:215267 original size:16 final size:16
Alignment explanation
Indices: 215246--215284 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
215236 TAATTTCATT
215246 ACAACTAAAAATAGAA
1 ACAACTAAAAATAGAA
215262 ACAACTAAAAATAGAA
1 ACAACTAAAAATAGAA
215278 ACAACTA
1 ACAACTA
215285 GGACTACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.67, C:0.15, G:0.05, T:0.13
Consensus pattern (16 bp):
ACAACTAAAAATAGAA
Found at i:220110 original size:18 final size:18
Alignment explanation
Indices: 220087--220128 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
220077 CCGACTGTTA
220087 TACCGTTTACTGACTTTT
1 TACCGTTTACTGACTTTT
220105 TACCGTTTACTGACTTTT
1 TACCGTTTACTGACTTTT
220123 TACCGT
1 TACCGT
220129 ATTCAGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.17, C:0.24, G:0.12, T:0.48
Consensus pattern (18 bp):
TACCGTTTACTGACTTTT
Found at i:221272 original size:3 final size:3
Alignment explanation
Indices: 221264--221305 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
221254 CAGCCTCAAA
221264 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
221306 TGGAAACCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:223559 original size:30 final size:28
Alignment explanation
Indices: 223506--223576 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 28
223496 AAACACTCAA
223506 AATATTATTATTTTATATATTTAATATT
1 AATATTATTATTTTATATATTTAATATT
**
223534 AATA-TATTATTTTAGTATCATTTTAATAAA
1 AATATTATTATTTTA-TAT-A-TTTAATATT
223564 AATATTAATTATT
1 AATATT-ATTATT
223577 AAATTATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 10 0.28
28 7 0.19
29 1 0.03
30 11 0.31
31 1 0.03
32 6 0.17
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
AATATTATTATTTTATATATTTAATATT
Found at i:223738 original size:10 final size:10
Alignment explanation
Indices: 223673--223731 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
223663 TTTAATAATA
223673 TATAATAAAT
1 TATAATAAAT
223683 TATTAATAAAT
1 TA-TAATAAAT
*
223694 T-TAATATTATT
1 TATAATA--AAT
*
223705 TATTAAT-TAT
1 TA-TAATAAAT
223715 TATAATAAAT
1 TATAATAAAT
223725 TATAATA
1 TATAATA
223732 TAATATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
9 9 0.23
10 14 0.36
11 12 0.31
13 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TATAATAAAT
Found at i:225692 original size:8 final size:8
Alignment explanation
Indices: 225674--225723 Score: 50
Period size: 7 Copynumber: 6.2 Consensus size: 8
225664 ACCTTGACTG
225674 AAAAAAT-
1 AAAAAATA
225681 AAAAAATA
1 AAAAAATA
225689 AAAAAAT-
1 AAAAAATA
*
225696 TAAAAATGA
1 AAAAAAT-A
*
225705 AATAAATA
1 AAAAAATA
225713 AATAAAATA
1 AA-AAAATA
225722 AA
1 AA
225724 TAATATTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 13 0.37
8 10 0.29
9 12 0.34
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (8 bp):
AAAAAATA
Found at i:225694 original size:15 final size:16
Alignment explanation
Indices: 225674--225714 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
225664 ACCTTGACTG
225674 AAAAAATAAAAAAT-A
1 AAAAAATAAAAAATGA
*
225689 AAAAAATTAAAAATGA
1 AAAAAATAAAAAATGA
*
225705 AATAAATAAA
1 AAAAAATAAA
225715 TAAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (16 bp):
AAAAAATAAAAAATGA
Found at i:225713 original size:4 final size:4
Alignment explanation
Indices: 225677--225726 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
225667 TTGACTGAAA
* *
225677 AAAT AAA- AAAT AAAA AAAT TAA- AAAT GAAAT AAAT AAAT AAAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT -AAAT AAAT
225725 AA
1 AA
225727 TATTATGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 5 0.13
4 25 0.66
5 8 0.21
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:225720 original size:13 final size:13
Alignment explanation
Indices: 225684--225726 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
225674 AAAAAATAAA
225684 AAATAAA-AAAAT
1 AAATAAATAAAAT
* *
225696 TAA-AAATGAAAT
1 AAATAAATAAAAT
225708 AAATAAATAAAAT
1 AAATAAATAAAAT
225721 AAATAA
1 AAATAA
225727 TATTATGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
11 3 0.12
12 8 0.32
13 14 0.56
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:225723 original size:24 final size:22
Alignment explanation
Indices: 225675--225728 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 22
225665 CCTTGACTGA
*
225675 AAAAATAAAAAATAAAAAAATT
1 AAAAATAAAAAATAAAAAAAAT
*
225697 AAAAATGAAATAAATAAATAAAAT
1 AAAAAT-AAA-AAATAAAAAAAAT
225721 AAATAATA
1 AAA-AATA
225729 TTATGTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 6 0.22
23 3 0.11
24 15 0.56
25 3 0.11
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (22 bp):
AAAAATAAAAAATAAAAAAAAT
Found at i:225898 original size:35 final size:35
Alignment explanation
Indices: 225782--226188 Score: 359
Period size: 35 Copynumber: 11.4 Consensus size: 35
225772 TTTTTAAAAC
** * *
225782 ATACGTTTTCAAAATAATTTAAAAAAACCATATATT
1 ATACGTTTTCAAAACCATTT-TAAAAACTATATATT
* *
225818 ATACGTTTTCAAAACCATTTCGAAAAA-TGTAT-TAT
1 ATACGTTTTCAAAACCATTT-TAAAAACTATATAT-T
* * *
225853 ATATGTTTTCAAAACCATTTTTAAAACTATACATT
1 ATACGTTTTCAAAACCATTTTAAAAACTATATATT
* ** *
225888 ATACGCTTTCAAAATTATTTTAAAAACTATATACT
1 ATACGTTTTCAAAACCATTTTAAAAACTATATATT
* * * *
225923 ATATGTTTTCAAAATCGTTTTTAAAACTATATATT
1 ATACGTTTTCAAAACCATTTTAAAAACTATATATT
* * * ** *
225958 ATGCATTTTTAAAATTATTTTAAAAACTATATACT
1 ATACGTTTTCAAAACCATTTTAAAAACTATATATT
* * *
225993 ATATGCTTTCAAAACCATTTTAAAAACTACATATT
1 ATACGTTTTCAAAACCATTTTAAAAACTATATATT
*
226028 ATACGTTTTCAAAACTATTTTTTAAAAAATCTATATATT
1 ATACGTTTTCAAAACCA--TTTT-AAAAA-CTATATATT
* ** *
226067 ATATGTTTTCAAAATTATTTTAAAAACTATATACT
1 ATACGTTTTCAAAACCATTTTAAAAACTATATATT
* *
226102 ATATGTTTTCAAGACCATTTTAAAAACTATATATT
1 ATACGTTTTCAAAACCATTTTAAAAACTATATATT
* ** *
226137 ATACGTTTTTAAAAATAAGTTTCCAAAAACTATATATT
1 ATACG-TTTTCAAAACCA-TTT-TAAAAACTATATATT
**
226175 ATATATTTTCAAAA
1 ATACGTTTTCAAAA
226189 ACTATATTTG
Statistics
Matches: 300, Mismatches: 61, Indels: 19
0.79 0.16 0.05
Matches are distributed among these distances:
34 5 0.02
35 194 0.65
36 37 0.12
37 19 0.06
38 22 0.07
39 23 0.08
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.42
Consensus pattern (35 bp):
ATACGTTTTCAAAACCATTTTAAAAACTATATATT
Found at i:226214 original size:109 final size:109
Alignment explanation
Indices: 225804--226193 Score: 393
Period size: 109 Copynumber: 3.7 Consensus size: 109
225794 AATAATTTAA
* * ** * * *
225804 AAAAACCATATATTATACGTTTTC-AAAACCA-TTTCGAAAAATGTAT-TA-TATATGTTTTCAA
1 AAAAACTACATATTATACGTTTTCAAAAATAAGTTTCAAAAAATCTATATATTATATATTTTCAA
* * * * * **
225865 AACCATTTTTAAAACTATACATTATACGCTTTCAAAATTATTTT
66 AACTATTTTAAAAACTATATACTATATGCTTTCAAAACCATTTT
* * * * ** ** *
225909 AAAAACTATATACTATATGTTTTC-AAAAT-CGTTT-TTAAAA-CTATATATTATGCATTTTTAA
1 AAAAACTACATATTATACGTTTTCAAAAATAAGTTTCAAAAAATCTATATATTATATATTTTCAA
*
225970 AATTATTTTAAAAACTATATACTATATGCTTTCAAAACCATTTT
66 AACTATTTTAAAAACTATATACTATATGCTTTCAAAACCATTTT
* ** * *
226014 AAAAACTACATATTATACGTTTTCAAAACTATTTTTTAAAAAATCTATATATTATATGTTTTCAA
1 AAAAACTACATATTATACGTTTTCAAAAATAAGTTTCAAAAAATCTATATATTATATATTTTCAA
* * *
226079 AATTATTTTAAAAACTATATACTATATGTTTTCAAGACCATTTT
66 AACTATTTTAAAAACTATATACTATATGCTTTCAAAACCATTTT
* * *
226123 AAAAACTATATATTATACGTTTTTAAAAATAAGTTTCCAAAAA-CTATATATTATATATTTTCAA
1 AAAAACTACATATTATACGTTTTCAAAAATAAGTTTCAAAAAATCTATATATTATATATTTTC-A
226187 AAACTAT
65 AAACTAT
226194 ATTTGAAATT
Statistics
Matches: 234, Mismatches: 43, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
103 3 0.01
104 6 0.03
105 94 0.40
106 4 0.02
107 3 0.01
108 22 0.09
109 102 0.44
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (109 bp):
AAAAACTACATATTATACGTTTTCAAAAATAAGTTTCAAAAAATCTATATATTATATATTTTCAA
AACTATTTTAAAAACTATATACTATATGCTTTCAAAACCATTTT
Found at i:226543 original size:18 final size:18
Alignment explanation
Indices: 226520--226557 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
226510 CATTCGTCAT
226520 GAAGTTGAGTCGATCTTG
1 GAAGTTGAGTCGATCTTG
226538 GAAGTTGAGTCGATCTTG
1 GAAGTTGAGTCGATCTTG
226556 GA
1 GA
226558 TGTTTCGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.34, T:0.32
Consensus pattern (18 bp):
GAAGTTGAGTCGATCTTG
Found at i:234664 original size:24 final size:24
Alignment explanation
Indices: 234621--234682 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
234611 TACAATAATA
*
234621 TGTACTTTTACAGCAGACGA-CACT
1 TGTACTTTTACAGCACACGAGC-CT
* *
234645 TGTACTTTTATAGCTCACGAGCCT
1 TGTACTTTTACAGCACACGAGCCT
* *
234669 TGTGCTTTTGCAGC
1 TGTACTTTTACAGC
234683 GAATGAGTCC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
24 30 0.97
25 1 0.03
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.35
Consensus pattern (24 bp):
TGTACTTTTACAGCACACGAGCCT
Found at i:239541 original size:35 final size:35
Alignment explanation
Indices: 239424--239788 Score: 265
Period size: 35 Copynumber: 10.4 Consensus size: 35
239414 TTTTTAAAAC
* * *
239424 ATACATTTTCAAAATCC--TTTAAAAACCATATATT
1 ATACGTTTTCAAAA-CCATTTTTAAAACTATATATT
*** *
239458 ATACGTTTTCAAAACCATTCCGAAAAATATATTATAT
1 ATACGTTTTCAAAACCATTTTTAAAACTATA-TAT-T
*
239495 ATA--TTTTCAAAACCATTTTTAAAACTATACATT
1 ATACGTTTTCAAAACCATTTTTAAAACTATATATT
* ** *
239528 ATACGTTTCCAAAATTA-TTTTAAAACTATATACT
1 ATACGTTTTCAAAACCATTTTTAAAACTATATATT
* * *
239562 ATATGTTTTCAAACCCGTTTTTAAAACTATATATT
1 ATACGTTTTCAAAACCATTTTTAAAACTATATATT
** * *
239597 ATACGTTTTCAAAATTA-ATTTAAAACTATATACT
1 ATACGTTTTCAAAACCATTTTTAAAACTATATATT
* * * *
239631 ATATGATTTCAAAACCATTTTAAAAACTATATAAT
1 ATACGTTTTCAAAACCATTTTTAAAACTATATATT
* * *
239666 ATACATTTTCAAAACTATTTTTTTAAAAAGCTATACATT
1 ATACGTTTTCAAAACCA--TTTTT-AAAA-CTATATATT
* * ** * * * *
239705 TTATGTTTTCAAAATTATTTTAAAAACTGTCTACT
1 ATACGTTTTCAAAACCATTTTTAAAACTATATATT
* * * *
239740 ATATGTTTTCAAAATCATTTTAAAAACTATATGTT
1 ATACGTTTTCAAAACCATTTTTAAAACTATATATT
* *
239775 ATACATTTTTAAAA
1 ATACGTTTTCAAAA
239789 ATAAGTTTCC
Statistics
Matches: 257, Mismatches: 62, Indels: 23
0.75 0.18 0.07
Matches are distributed among these distances:
33 6 0.02
34 69 0.27
35 139 0.54
36 7 0.03
37 12 0.05
38 4 0.02
39 20 0.08
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (35 bp):
ATACGTTTTCAAAACCATTTTTAAAACTATATATT
Found at i:239571 original size:69 final size:70
Alignment explanation
Indices: 239429--239771 Score: 286
Period size: 69 Copynumber: 4.9 Consensus size: 70
239419 AAAACATACA
* * * ** **
239429 TTTTCAAAATCC--TTTAAAAACCATATATTATACGTTTTCAAAACCATTCCGAAAAA-TATATT
1 TTTTCAAAA-CCATTTTAAAAACTATACATTATACGTTTCCAAAATTATT-TTAAAAACTATA-T
*
239491 A-TATATA
63 ACTATATG
*
239498 TTTTCAAAACCATTTTTAAAACTATACATTATACGTTTCCAAAATTATTTT-AAAACTATATACT
1 TTTTCAAAACCATTTTAAAAACTATACATTATACGTTTCCAAAATTATTTTAAAAACTATATACT
239562 ATATG
66 ATATG
* * * * * *
239567 TTTTCAAACCCGTTTTTAAAACTATATATTATACGTTTTCAAAATTAATTT-AAAACTATATACT
1 TTTTCAAAACCATTTTAAAAACTATACATTATACGTTTCCAAAATTATTTTAAAAACTATATACT
239631 ATATG
66 ATATG
* * * * * *
239636 ATTTCAAAACCATTTTAAAAACTATATAATATACATTTTCAAAACTATTTTTTTAAAAAGCTATA
1 TTTTCAAAACCATTTTAAAAACTATACATTATAC-GTTTCCAAA--ATTATTTTAAAAA-CTATA
* * *
239701 CATTTTATG
62 TACTATATG
** * * * * *
239710 TTTTCAAAATTATTTTAAAAACTGT-CTACTATATGTTTTCAAAATCATTTTAAAAACTATAT
1 TTTTCAAAACCATTTTAAAAACTATAC-ATTATACGTTTCCAAAATTATTTTAAAAACTATAT
239772 GTTATACATT
Statistics
Matches: 224, Mismatches: 40, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
68 8 0.04
69 111 0.50
70 41 0.18
71 11 0.05
72 6 0.03
73 10 0.04
74 37 0.17
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.42
Consensus pattern (70 bp):
TTTTCAAAACCATTTTAAAAACTATACATTATACGTTTCCAAAATTATTTTAAAAACTATATACT
ATATG
Found at i:239803 original size:109 final size:107
Alignment explanation
Indices: 239584--239826 Score: 315
Period size: 109 Copynumber: 2.3 Consensus size: 107
239574 ACCCGTTTTT
*
239584 AAAACTATATATTATACGTTTTCAAAATTAATTTAAAACTATATACTATATGATTTCAAAACCAT
1 AAAACTATATATTATATGTTTTCAAAATTAATTTAAAACTATATACTATATGATTTCAAAACCAT
* ** **
239649 TTTAAAAACTATATAATATACATTTTCAAAACTATTTTTTTA
66 TTTAAAAACTATATAATATACATTTTCAAAAATAAGTTTCCA
* * * * * * *
239691 AAAAGCTATACATTTTATGTTTTCAAAATTATTTTAAAAACTGTCTACTATATGTTTTCAAAATC
1 AAAA-CTATATATTATATGTTTTCAAAATTAATTT-AAAACTATATACTATATGATTTCAAAACC
** *
239756 ATTTTAAAAACTATATGTTATACATTTTTAAAAATAAGTTTCCA
64 ATTTTAAAAACTATATAATATACATTTTCAAAAATAAGTTTCCA
*
239800 AAAACTATATATTATATATTTTCAAAA
1 AAAACTATATATTATATGTTTTCAAAA
239827 ACTATATTTG
Statistics
Matches: 115, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
107 4 0.03
108 46 0.40
109 65 0.57
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (107 bp):
AAAACTATATATTATATGTTTTCAAAATTAATTTAAAACTATATACTATATGATTTCAAAACCAT
TTTAAAAACTATATAATATACATTTTCAAAAATAAGTTTCCA
Found at i:249233 original size:2 final size:2
Alignment explanation
Indices: 249221--249253 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
249211 ACTACGATTG
*
249221 AC AC TC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
249254 TTTTAGAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.48, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:261575 original size:30 final size:30
Alignment explanation
Indices: 261541--261612 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
261531 CAATATTCTA
*
261541 AGCTTTGCTAAGC-TTCACCCTCTCTCTAAT
1 AGCTTTGCTAAGCTTTCACCAT-TCTCTAAT
***
261571 AGCTTTGCTAAGCTTTTTTCATTCTCTAAT
1 AGCTTTGCTAAGCTTTCACCATTCTCTAAT
261601 AGCTTTGCTAAG
1 AGCTTTGCTAAG
261613 TTATTTCTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 33 0.89
31 4 0.11
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (30 bp):
AGCTTTGCTAAGCTTTCACCATTCTCTAAT
Found at i:276208 original size:2 final size:2
Alignment explanation
Indices: 276201--276234 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
276191 TATGAAATGC
276201 AT AT AT AT AT AT AT AT 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
276235 CAGAATTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:276328 original size:52 final size:52
Alignment explanation
Indices: 276261--276381 Score: 129
Period size: 52 Copynumber: 2.3 Consensus size: 52
276251 GAGATTGGAG
* * * *
276261 TTTTAATTATTGGAGTCGCTGTTAATGGAGTATTAGGGGTTA-GGGAGTTATA
1 TTTTTATTATCGGAGTCGCTGTTAATAGAGTATCAGGGGTTAGGGGA-TTATA
** * * *
276313 TTTTTATTATCGGAGTCATTGTTATTAGAGTATCGGGGGTTAGGGGATTGTA
1 TTTTTATTATCGGAGTCGCTGTTAATAGAGTATCAGGGGTTAGGGGATTATA
*
276365 -TTTTACTATCGGAGTCG
1 TTTTTATTATCGGAGTCG
276382 TTATTGGAGT
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
51 15 0.26
52 38 0.67
53 4 0.07
ACGTcount: A:0.22, C:0.07, G:0.30, T:0.41
Consensus pattern (52 bp):
TTTTTATTATCGGAGTCGCTGTTAATAGAGTATCAGGGGTTAGGGGATTATA
Found at i:294733 original size:2 final size:2
Alignment explanation
Indices: 294726--294773 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
294716 GTTTCGTACA
294726 AT AT AT AT AT AT AT AT AT AT AT AT 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 AT AT
294768 AT AT AT
1 AT AT AT
294774 TAAGGGTGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:295329 original size:2 final size:2
Alignment explanation
Indices: 295322--295350 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
295312 ATGCATAATT
295322 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
295351 CGGAAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:295507 original size:50 final size:52
Alignment explanation
Indices: 295376--295508 Score: 148
Period size: 52 Copynumber: 2.6 Consensus size: 52
295366 GGGATTGGAG
* * *
295376 TTTTAATTATCAGAGTCGTTGTTAATGGAGTATCGGGGGTTAGGGAGTTATA
1 TTTTTATTATCAGAGTCGTTGTTAATGGAGTATCGCGGGTTAGGGAGTAATA
* * *
295428 TTTTTATTATCAGGGTCGTTTTTATTGGAGTATC-CGGGTTAGGG-G-AATGCA
1 TTTTTATTATCAGAGTCGTTGTTAATGGAGTATCGCGGGTTAGGGAGTAAT--A
**
295479 -TTTTATTATCAGAGTCACTGTTAATGGAGT
1 TTTTTATTATCAGAGTCGTTGTTAATGGAGT
295509 CGTTATTAGA
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
49 2 0.03
50 26 0.38
51 10 0.15
52 30 0.44
ACGTcount: A:0.23, C:0.08, G:0.28, T:0.41
Consensus pattern (52 bp):
TTTTTATTATCAGAGTCGTTGTTAATGGAGTATCGCGGGTTAGGGAGTAATA
Found at i:296874 original size:12 final size:13
Alignment explanation
Indices: 296857--296885 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
296847 TTTATTTGCG
296857 AAAATTAAAA-TT
1 AAAATTAAAATTT
296869 AAAATTAAAATTT
1 AAAATTAAAATTT
296882 AAAA
1 AAAA
296886 AACTTGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:297047 original size:8 final size:8
Alignment explanation
Indices: 297034--297066 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
297024 AAGGAAAAAG
297034 AAAATAAT
1 AAAATAAT
297042 AAAATAAT
1 AAAATAAT
297050 AAAATAAT
1 AAAATAAT
297058 AAAA-AAT
1 AAAATAAT
297065 AA
1 AA
297067 TAATGAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAATAAT
Found at i:297055 original size:16 final size:15
Alignment explanation
Indices: 297028--297066 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
297018 ATGAAGAAGG
*
297028 AAAAAGAAAATAATA
1 AAAAATAAAATAATA
297043 AAATAATAAAATAATA
1 AAA-AATAAAATAATA
297059 AAAAATAA
1 AAAAATAA
297067 TAATGAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAAATAAAATAATA
Found at i:298502 original size:5 final size:5
Alignment explanation
Indices: 298494--298562 Score: 50
Period size: 5 Copynumber: 14.0 Consensus size: 5
298484 AAACAAAAAC
* * * * * *
298494 AAATG AAATT AAATT AAATT AAATT AA-TA AAATG AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* * *
298543 AAATA ATATT ATATA AAATA
1 AAATA AAATA AAATA AAATA
298563 TATAATATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
4 3 0.05
5 52 0.95
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (5 bp):
AAATA
Found at i:298537 original size:15 final size:15
Alignment explanation
Indices: 298494--298548 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
298484 AAACAAAAAC
* *
298494 AAATGAAATTAAATT
1 AAATGAAATAAAATA
* *
298509 AAATTAAAT-TAATA
1 AAATGAAATAAAATA
298523 AAATGAAATAAAATA
1 AAATGAAATAAAATA
*
298538 AAATAAAATAA
1 AAATGAAATAA
298549 TATTATATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 11 0.33
15 22 0.67
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (15 bp):
AAATGAAATAAAATA
Found at i:298571 original size:5 final size:5
Alignment explanation
Indices: 298519--298562 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
298509 AAATTAAATT
* * * *
298519 AATAA AATGA AATAA AATAA AATAA AATAA TATTA TATAA AATA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATA
298563 TATAATATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (5 bp):
AATAA
Found at i:298680 original size:33 final size:35
Alignment explanation
Indices: 298642--298738 Score: 108
Period size: 35 Copynumber: 2.7 Consensus size: 35
298632 CATAGTTTCC
*
298642 AAAATGTTTTTAAAAATATATATA-AGTTTCA-AA
1 AAAATGTTTTTAAAAATATATATATAATTTCACAA
* *
298675 AAAATGTCTTTAAAACTATATATATATAATTTTACAA
1 AAAATGTTTTTAAAA--ATATATATATAATTTCACAA
* *
298712 AAAATATTTTTAAAACTATATACTATA
1 AAAATGTTTTTAAAAATATATA-TATA
298739 TATGTTTTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
33 14 0.26
35 15 0.28
36 9 0.17
37 15 0.28
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (35 bp):
AAAATGTTTTTAAAAATATATATATAATTTCACAA
Found at i:298714 original size:37 final size:35
Alignment explanation
Indices: 298657--298906 Score: 184
Period size: 38 Copynumber: 6.6 Consensus size: 35
298647 GTTTTTAAAA
*
298657 ATATATATAAGTTTCAAAAAAATGTCTTT-AAAACTAT
1 ATATATATAATTTTC--AAAAATGT-TTTAAAAACTAT
* *
298694 ATATATATAATTTTACAAAAAATATTTTTAAAACTAT
1 ATATATATAATTTT-C-AAAAATGTTTTAAAAACTAT
*
298731 ATACTATATATGTTTTC-AAAATGTTTTAAAAACTAT
1 ATA-TATATA-ATTTTCAAAAATGTTTTAAAAACTAT
* *
298767 ATAATATTTAAACGTTTTC-AAAATGTTTTCAAAACTAT
1 AT-ATATAT-AA--TTTTCAAAAATGTTTTAAAAACTAT
298805 ATATTATATACGTATTTTC-AAAATGTTTTTAGAAAAACTAT
1 ATA-TATATA---ATTTTCAAAAATG-TTTT--AAAAACTAT
* *
298846 ATAATATATAAATGTTTTCAAACATGTTTTCAAAACTAT
1 AT-ATATAT-AA--TTTTCAAAAATGTTTTAAAAACTAT
298885 ATATTATATATATTTTCAAAAA
1 ATA-TATATA-ATTTTCAAAAA
298907 CCATTTGCAA
Statistics
Matches: 178, Mismatches: 13, Indels: 44
0.76 0.06 0.19
Matches are distributed among these distances:
36 26 0.15
37 45 0.25
38 50 0.28
39 25 0.14
40 1 0.01
41 24 0.13
42 7 0.04
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.42
Consensus pattern (35 bp):
ATATATATAATTTTCAAAAATGTTTTAAAAACTAT
Found at i:298732 original size:35 final size:34
Alignment explanation
Indices: 298642--298769 Score: 104
Period size: 36 Copynumber: 3.6 Consensus size: 34
298632 CATAGTTTCC
* *
298642 AAAATGTTTTTAAAA--ATATATATAAGTTTCAA
1 AAAATATTTTTAAAACTATATATATAATTTTCAA
298674 AAAA-ATGTCTTTAAAACTATATATATATAATTTTACAA
1 AAAATAT-T-TTTAAAAC--TATATATATAATTTT-CAA
298712 AAAATATTTTTAAAACTATATACTATATATGTTTTC--
1 AAAATATTTTTAAAACTATATA-TATA-A--TTTTCAA
* *
298748 AAAATGTTTTAAAAACTATATA
1 AAAATATTTTTAAAACTATATA
298770 ATATTTAAAC
Statistics
Matches: 80, Mismatches: 4, Indels: 20
0.77 0.04 0.19
Matches are distributed among these distances:
31 1 0.01
32 5 0.06
33 7 0.09
35 6 0.08
36 24 0.30
37 22 0.28
38 9 0.11
39 6 0.08
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.41
Consensus pattern (34 bp):
AAAATATTTTTAAAACTATATATATAATTTTCAA
Found at i:298739 original size:38 final size:36
Alignment explanation
Indices: 298637--298931 Score: 203
Period size: 37 Copynumber: 7.9 Consensus size: 36
298627 TATTACATAG
* *
298637 TTTCCAAAATGTTTTT-AAA--A-AT-ATATATAAG
1 TTTCAAAAATGTTTTTAAAACTATATAATATATAAT
*
298668 TTTCAAAAAAATGTCTTTAAAACTATAT-ATATATAAT
1 TTTC--AAAAATGTTTTTAAAACTATATAATATATAAT
* * *
298705 TTTACAAAAAATATTTTTAAAACTATATACTATATATGT
1 TTT-C-AAAAATGTTTTTAAAACTATATAATATATA-AT
* *
298744 TTTC-AAAATGTTTTAAAAACTATATAATATTTAAACGT
1 TTTCAAAAATGTTTTTAAAACTATATAATATAT-AA--T
* *
298782 TTTC-AAAATGTTTTCAAAACTATATATTATATACGTAT
1 TTTCAAAAATGTTTTTAAAACTATATAATATATA---AT
298820 TTTC-AAAATGTTTTTAGAAAAACTATATAATATATAAATGT
1 TTTCAAAAATGTTTTT---AAAACTATATAATATAT-AA--T
* * *
298861 TTTCAAACATGTTTTCAAAACTATATATTATATATAT
1 TTTCAAAAATGTTTTTAAAACTATATAATATATA-AT
*** **
298898 TTTCAAAAACCATTTGCAAACTATATAATATATA
1 TTTCAAAAATGTTTTTAAAACTATATAATATATA
298932 GACGTATATG
Statistics
Matches: 214, Mismatches: 27, Indels: 40
0.76 0.10 0.14
Matches are distributed among these distances:
31 4 0.02
33 10 0.05
34 3 0.01
36 25 0.12
37 64 0.30
38 54 0.25
39 22 0.10
40 1 0.00
41 21 0.10
42 10 0.05
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (36 bp):
TTTCAAAAATGTTTTTAAAACTATATAATATATAAT
Found at i:298881 original size:39 final size:38
Alignment explanation
Indices: 298675--298894 Score: 218
Period size: 38 Copynumber: 5.8 Consensus size: 38
298665 AAGTTTCAAA
*
298675 AAAATGTCTTT-AAAACTATAT-ATATAT-AAT-TTTAC
1 AAAATGT-TTTAAAAACTATATAATATATAAATGTTTTC
* * *
298710 AAAAAATATTTTTAAAACTATATACTATAT--ATGTTTTC
1 --AAAATGTTTTAAAAACTATATAATATATAAATGTTTTC
* *
298748 AAAATGTTTTAAAAACTATATAATATTTAAACGTTTTC
1 AAAATGTTTTAAAAACTATATAATATATAAATGTTTTC
* * ** *
298786 AAAATGTTTTCAAAACTATATATTATATACGTATTTTC
1 AAAATGTTTTAAAAACTATATAATATATAAATGTTTTC
298824 AAAATGTTTTTAGAAAAACTATATAATATATAAATGTTTTC
1 AAAATG-TTTT--AAAAACTATATAATATATAAATGTTTTC
* *
298865 AAACATGTTTTCAAAACTATATATTATATA
1 AAA-ATGTTTTAAAAACTATATAATATATA
298895 TATTTTCAAA
Statistics
Matches: 152, Mismatches: 22, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
36 27 0.18
37 18 0.12
38 53 0.35
39 21 0.14
41 30 0.20
42 3 0.02
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (38 bp):
AAAATGTTTTAAAAACTATATAATATATAAATGTTTTC
Found at i:299949 original size:106 final size:106
Alignment explanation
Indices: 299764--300347 Score: 913
Period size: 106 Copynumber: 5.5 Consensus size: 106
299754 CTATTCCAAT
* ** * * * *
299764 TCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGAAAATTGTTTATTGACAACCA
1 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
*
299829 GCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * * *
299870 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATCGGGAAATTATTTATTGACAACCA
1 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
299935 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * * *
299976 TCCATTATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCA
1 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
*
300041 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
*
300082 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAACCA
1 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
* * *
300147 GCGGTCCCTTCGTTGTGAAGTTGAATTTGCGTTGTCTTGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* *
300188 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCA
1 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
* * *
300253 GCGATCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
300294 TCCAATATCCTTC---GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATT
1 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATT
300348 CGTGAATTTG
Statistics
Matches: 439, Mismatches: 39, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
103 39 0.09
106 400 0.91
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (106 bp):
TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
Found at i:304182 original size:8 final size:8
Alignment explanation
Indices: 304169--304207 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
304159 AAGGAAAAAG
304169 AAAATAAT
1 AAAATAAT
304177 AAAATAAT
1 AAAATAAT
304185 AAAATAAT
1 AAAATAAT
304193 AAAA-AAT
1 AAAATAAT
304200 AATAATAA
1 AA-AATAA
304208 AAGATTAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 5 0.17
8 22 0.76
9 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATAAT
Found at i:304190 original size:16 final size:15
Alignment explanation
Indices: 304163--304207 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
304153 ATGAAGAAGG
*
304163 AAAAAGAAAATAATA
1 AAAAATAAAATAATA
304178 AAATAATAAAATAATA
1 AAA-AATAAAATAATA
304194 AAAAATAATAATAA
1 AAAAATAA-AATAA
304208 AAGATTAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 8 0.30
16 19 0.70
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (15 bp):
AAAAATAAAATAATA
Found at i:305644 original size:5 final size:5
Alignment explanation
Indices: 305632--305691 Score: 79
Period size: 5 Copynumber: 12.4 Consensus size: 5
305622 AAAAAAAACC
* * *
305632 AAAAT -AAAT TAAAT TAA-T AAAAT AAAAT TAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
305680 AAAAT AAAAT AA
1 AAAAT AAAAT AA
305692 TATGATATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
4 7 0.14
5 43 0.86
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (5 bp):
AAAAT
Found at i:305873 original size:38 final size:36
Alignment explanation
Indices: 305751--306053 Score: 221
Period size: 38 Copynumber: 8.1 Consensus size: 36
305741 TATATACTTT
* * * *
305751 AAAAAAGTTTTCAAAACTATATATTACAT-AGTTTC
1 AAAAATGTTTTTAAAACTATATATTATATAATTTTC
*
305786 CAAAATGTTTTT-AAA--A-ATATTATATAAGTTTTC
1 AAAAATGTTTTTAAAACTATATATTATATAA-TTTTC
*
305819 AAAAAAAATGTCTTTAAAACTATATATTATATAATTTTAC
1 ---AAAAATGTTTTTAAAACTATATATTATATAATTTT-C
* *
305859 AAAAAATGTTTTT-AAACTATATACTATATATGTTTTC
1 -AAAAATGTTTTTAAAACTATATATTATATA-ATTTTC
* *
305896 -AAAATG-TTTTAAAACTATATAATATTTAAACGTTTTC
1 AAAAATGTTTTTAAAACTATATATTATAT-AA--TTTTC
*
305933 -AAAATGTTTTCAAAACTATATATTATATACATATTTTC
1 AAAAATGTTTTTAAAACTATATATTATAT--A-ATTTTC
* *
305971 -AAAATGTTTTCAAAAAAACTATATAATATATAAATGTTTTC
1 AAAAATGTTTT---TAAAACTATATATTATAT-AA--TTTTC
* *
306012 AAACATGTTTTCAAAACTATATATTATATATATTTTC
1 AAAAATGTTTTTAAAACTATATATTATATA-ATTTTC
306049 AAAAA
1 AAAAA
306054 CCATTTGCAA
Statistics
Matches: 219, Mismatches: 24, Indels: 48
0.75 0.08 0.16
Matches are distributed among these distances:
31 8 0.04
32 2 0.01
33 4 0.02
34 7 0.03
35 29 0.13
36 11 0.05
37 40 0.18
38 50 0.23
39 24 0.11
40 14 0.06
41 21 0.10
42 9 0.04
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (36 bp):
AAAAATGTTTTTAAAACTATATATTATATAATTTTC
Found at i:305876 original size:37 final size:36
Alignment explanation
Indices: 305751--306053 Score: 230
Period size: 37 Copynumber: 8.1 Consensus size: 36
305741 TATATACTTT
* * *
305751 AAAAAAGTTTTCAAAACTATATATTACAT-A-GTTTC
1 AAAAATGTTTT-AAAACTATATATTATATAATTTTTC
* * *
305786 CAAAATGTTTTTAAA--A-ATATTATATAAGTTTTC
1 AAAAATGTTTTAAAACTATATATTATATAATTTTTC
*
305819 AAAAAAAATGTCTTTAAAACTATATATTATATAATTTTAC
1 ---AAAAATGT-TTTAAAACTATATATTATATAATTTTTC
* *
305859 AAAAAATGTTTTTAAACTATATACTATAT-ATGTTTTC
1 -AAAAATGTTTTAAAACTATATATTATATAAT-TTTTC
* * *
305896 -AAAATGTTTTAAAACTATATAATATTTAAACGTTTTC
1 AAAAATGTTTTAAAACTATATATTATAT-AA-TTTTTC
305933 -AAAATGTTTTCAAAACTATATATTATATACATATTTTC
1 AAAAATGTTTT-AAAACTATATATTATATA-AT-TTTTC
*
305971 -AAAATGTTTTCAAAAAAACTATATAATATATAAATGTTTTC
1 AAAAATGTTTT----AAAACTATATATTATAT-AAT-TTTTC
*
306012 AAACATGTTTTCAAAACTATATATTATAT-ATATTTTC
1 AAAAATGTTTT-AAAACTATATATTATATAAT-TTTTC
306049 AAAAA
1 AAAAA
306054 CCATTTGCAA
Statistics
Matches: 220, Mismatches: 27, Indels: 40
0.77 0.09 0.14
Matches are distributed among these distances:
31 8 0.04
32 2 0.01
33 4 0.02
34 3 0.01
35 33 0.15
36 9 0.04
37 56 0.25
38 40 0.18
39 17 0.08
40 15 0.07
41 23 0.10
42 10 0.05
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (36 bp):
AAAAATGTTTTAAAACTATATATTATATAATTTTTC
Found at i:306469 original size:15 final size:15
Alignment explanation
Indices: 306451--306491 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
306441 TTCTCCTCTT
306451 CTTCTTCCTCTTCTA
1 CTTCTTCCTCTTCTA
306466 CTTCTTCCTCTTCTA
1 CTTCTTCCTCTTCTA
306481 CTTCTTCCTCT
1 CTTCTTCCTCT
306492 GCATAACCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (15 bp):
CTTCTTCCTCTTCTA
Found at i:307303 original size:24 final size:24
Alignment explanation
Indices: 307271--307328 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
307261 AGCAGAAGAA
*
307271 GAAGAAGAGAGACAGAAATATGTT
1 GAAGAAGAGAGACAAAAATATGTT
*
307295 GAAGAAGAGAGAGAAAAATATGTT
1 GAAGAAGAGAGACAAAAATATGTT
307319 GAAGAAGAGA
1 GAAGAAGAGA
307329 TAACGTTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.53, C:0.02, G:0.31, T:0.14
Consensus pattern (24 bp):
GAAGAAGAGAGACAAAAATATGTT
Found at i:308211 original size:2 final size:2
Alignment explanation
Indices: 308204--308228 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
308194 TGCCGAAGTA
308204 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
308229 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:313040 original size:29 final size:30
Alignment explanation
Indices: 312993--313053 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
312983 TTTTGGTCCT
**
312993 TAAACTTTTCAAAGTTTATACTTTAGCCAC
1 TAAACTTTTCAAAACTTATACTTTAGCCAC
* *
313023 TAAAC-TTTCAAAACTTATATTTTAGTCAC
1 TAAACTTTTCAAAACTTATACTTTAGCCAC
313052 TA
1 TA
313054 GATAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (30 bp):
TAAACTTTTCAAAACTTATACTTTAGCCAC
Found at i:324196 original size:64 final size:63
Alignment explanation
Indices: 324108--324317 Score: 221
Period size: 65 Copynumber: 3.3 Consensus size: 63
324098 TGCACTAAGA
* * *
324108 GTGCAACGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGG-TG
* ** *
324172 GTGCATCGATGCATCAAATACATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGT-
*
324236 T
63 G
*
324237 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTAAT-TCCATG-GTGCATCGATGCATGGA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAA--AATATCCA-GAGTGCATCGATGCATGG-
324299 TTG
62 -TG
*
324302 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
324318 CTCTGAAAAA
Statistics
Matches: 121, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 47 0.39
65 65 0.54
66 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTG
Found at i:325414 original size:3 final size:3
Alignment explanation
Indices: 325406--325433 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
325396 AGTCGGAGCT
325406 GGA GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA G
325434 CACGAGAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:332788 original size:19 final size:19
Alignment explanation
Indices: 332764--332819 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
332754 TTGGACCCTT
*
332764 AGTGCATCGGTGCACTAAG
1 AGTGCATCGATGCACTAAG
*
332783 AGTGCATCGATGCA-TTA-
1 AGTGCATCGATGCACTAAG
*
332800 AGTGCATTCGATGCATTAAG
1 AGTGCA-TCGATGCACTAAG
332820 TGCATTCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 6 0.19
18 10 0.32
19 15 0.48
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAG
Found at i:332812 original size:18 final size:18
Alignment explanation
Indices: 332783--332826 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
332773 GTGCACTAAG
332783 AGTGCA-TCGATGCATTA
1 AGTGCATTCGATGCATTA
332800 AGTGCATTCGATGCATTA
1 AGTGCATTCGATGCATTA
332818 AGTGCATTC
1 AGTGCATTC
332827 AATGTTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (18 bp):
AGTGCATTCGATGCATTA
Found at i:346533 original size:9 final size:10
Alignment explanation
Indices: 346514--346538 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
346504 TTTATACGAC
346514 AAAATGAAAA
1 AAAATGAAAA
346524 AAAATGAAAA
1 AAAATGAAAA
346534 AAAAT
1 AAAAT
346539 ATGCTACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (10 bp):
AAAATGAAAA
Found at i:354465 original size:4 final size:4
Alignment explanation
Indices: 354440--354651 Score: 153
Period size: 4 Copynumber: 51.2 Consensus size: 4
354430 GGCGGTAATT
* ** *
354440 TTTA TTTTA TTTT TTGTA TTTA TTTA TTTA TTT- TGAA TTTA TATA TTTA
1 TTTA -TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* ** *
354489 TATA TTTA TTT- TTTA TTTA TTTA TTT- TGGA TTTA TTTA TTTA TTCAA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA
* * * *
354536 CTTGAA TTTA TTTA TTTA TTTCGAA TTTA TTTG TTTG TTTA TTTA GTTA
1 -TT-TA TTTA TTTA TTTA TTT---A TTTA TTTA TTTA TTTA TTTA TTTA
** * *
354585 TTT- TGAA TTTA TTTA TTTG TTTA TTTCAAA ATTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT---A TTTA TTTA TTTA TTTA TTTA
354635 TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA T
354652 GTGAAGGGAT
Statistics
Matches: 165, Mismatches: 29, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
3 6 0.04
4 138 0.84
5 10 0.06
6 4 0.02
7 7 0.04
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:354494 original size:27 final size:27
Alignment explanation
Indices: 354456--354514 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
354446 TTATTTTTTG
*
354456 TATTTATTTATTTATTTTGAATTTATA
1 TATTTATATATTTATTTTGAATTTATA
** *
354483 TATTTATATATTTATTTTTTATTTATT
1 TATTTATATATTTATTTTGAATTTATA
354510 TATTT
1 TATTT
354515 TGGATTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (27 bp):
TATTTATATATTTATTTTGAATTTATA
Found at i:354567 original size:23 final size:21
Alignment explanation
Indices: 354440--354651 Score: 132
Period size: 23 Copynumber: 9.9 Consensus size: 21
354430 GGCGGTAATT
* *
354440 TTTATTTTATTTTTTGTATTTA
1 TTTATTTAATTTATT-TATTTA
* *
354462 TTTATTTATTTTGAATTTATATA
1 TTTATTTAATTT--ATTTATTTA
*
354485 TTTATAT-ATTTATTT-TTTA
1 TTTATTTAATTTATTTATTTA
*
354504 TTTATTTATTTTGGATTTATTTA
1 TTTATTTAATTT--ATTTATTTA
* *
354527 TTTATTCAACTTGAATTTATTTA
1 TTTATTTAA-TT-TATTTATTTA
* *
354550 TTTATTTCGAATTTATTTGTTTG
1 TTTATTT--AATTTATTTATTTA
* **
354573 TTTATTT-AGTTATTT-TGAA
1 TTTATTTAATTTATTTATTTA
*
354592 TTTATTT-ATTTGTTTATTTCAAA
1 TTTATTTAATTTATTTATTT---A
*
354615 ATTATTT-ATTTATTTATTTA
1 TTTATTTAATTTATTTATTTA
354635 TTTATTT-ATTTATTTAT
1 TTTATTTAATTTATTTAT
354652 GTGAAGGGAT
Statistics
Matches: 149, Mismatches: 27, Indels: 30
0.72 0.13 0.15
Matches are distributed among these distances:
19 23 0.15
20 32 0.21
22 17 0.11
23 69 0.46
24 6 0.04
25 2 0.01
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTATTTAATTTATTTATTTA
Found at i:354977 original size:3 final size:3
Alignment explanation
Indices: 354969--355022 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
354959 ATACACGTTG
354969 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
355017 TTA TTA
1 TTA TTA
355023 ATGTTTTTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:361016 original size:60 final size:60
Alignment explanation
Indices: 360916--361035 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 60
360906 TAGATTGGTT
* * * *
360916 TTTAAACTTTTGAATATTTTAATTTCATCCTCAAAATATGACTCTCATTCTAAATTAGTC
1 TTTAAAATTTTGAACATTTTAATTTCATCCTCAAAATATGACACCCATTCTAAATTAGTC
* *
360976 TTTAAAATTTTGAACATTTTAATTTCAT-CTCTAAACTATGACACCCTTTCTAAATTAGTC
1 TTTAAAATTTTGAACATTTTAATTTCATCCTC-AAAATATGACACCCATTCTAAATTAGTC
361036 CCCAAACTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 3 0.06
60 50 0.94
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.44
Consensus pattern (60 bp):
TTTAAAATTTTGAACATTTTAATTTCATCCTCAAAATATGACACCCATTCTAAATTAGTC
Found at i:361047 original size:60 final size:60
Alignment explanation
Indices: 360919--361070 Score: 162
Period size: 60 Copynumber: 2.5 Consensus size: 60
360909 ATTGGTTTTT
* * * ***
360919 AAACTTTTGAATATTTTAATTTCATCCTCAAAATATGACTCTCATTCTAAATTAGTCTTT
1 AAACTTTTGAACATTTTAATTTCATCCTCAAAATATGACACCCATTCTAAATTAGTCCCC
* * *
360979 AAAATTTTGAACATTTTAATTTCAT-CTCTAAACTATGACACCCTTTCTAAATTAGTCCCC
1 AAACTTTTGAACATTTTAATTTCATCCTC-AAAATATGACACCCATTCTAAATTAGTCCCC
* * ** *
361039 AAACTTTTGGATATTCCAATTTCATCCCCAAA
1 AAACTTTTGAACATTTTAATTTCATCCTCAAA
361071 TTCATCCAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
59 3 0.04
60 70 0.93
61 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (60 bp):
AAACTTTTGAACATTTTAATTTCATCCTCAAAATATGACACCCATTCTAAATTAGTCCCC
Found at i:361274 original size:61 final size:60
Alignment explanation
Indices: 361198--361336 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 60
361188 TATGTGATGT
* *
361198 ATAGTTT-GGGATGAAATTGTAATGATC-AAAAAGTTTGAGGACCAATTTAGAATAAAAGTC
1 ATAGTTTAGGAATGAAATTGAAATG-TCTAAAAA-TTTGAGGACCAATTTAGAATAAAAGTC
* * * * * * *
361258 ATAGTTTAGGAATGAAATTGAAATGTCTAGATATTTGATGACTAATTTAGAATGATATTC
1 ATAGTTTAGGAATGAAATTGAAATGTCTAAAAATTTGAGGACCAATTTAGAATAAAAGTC
*
361318 ATAGTTTAGGTATGAAATT
1 ATAGTTTAGGAATGAAATT
361337 AGAATATTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 49 0.73
61 18 0.27
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (60 bp):
ATAGTTTAGGAATGAAATTGAAATGTCTAAAAATTTGAGGACCAATTTAGAATAAAAGTC
Found at i:367145 original size:14 final size:14
Alignment explanation
Indices: 367126--367171 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
367116 TCGGTGAGAG
367126 GAGAGAAAAAAAAT
1 GAGAGAAAAAAAAT
367140 GAGAGAACAAAAAAT
1 GAGAGAA-AAAAAAT
*
367155 CGA-AGGAAAAAAA-
1 -GAGAGAAAAAAAAT
367168 GAGA
1 GAGA
367172 AATCCTTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 2 0.07
13 1 0.04
14 13 0.46
15 10 0.36
16 2 0.07
ACGTcount: A:0.67, C:0.04, G:0.24, T:0.04
Consensus pattern (14 bp):
GAGAGAAAAAAAAT
Found at i:368133 original size:30 final size:29
Alignment explanation
Indices: 368091--368310 Score: 173
Period size: 30 Copynumber: 7.4 Consensus size: 29
368081 CCTAAGTTTC
*
368091 TATTTTTTCTATTTTAGTCCTTTAAATGTT
1 TATTTTTGCTATTTTAGTCCTTTAAAT-TT
*
368121 TGTTTTTGCTATTTTAGTCC-TTAAAGTTTT
1 TATTTTTGCTATTTTAGTCCTTTAAA--TTT
* * * *
368151 TATTTGTACAATTCTAGTCCTTTAAATTT
1 TATTTTTGCTATTTTAGTCCTTTAAATTT
* * *
368180 CTATTTTTTCTATTTTATTCCTTTAAGTTCT
1 -TATTTTTGCTATTTTAGTCCTTTAAATT-T
* *
368211 TATTTATGCTATTTTAGTCCTTT-GATTT
1 TATTTTTGCTATTTTAGTCCTTTAAATTT
* *
368239 TATGTTCTT--TATTTTAATCCTTTAAGTTTT
1 TAT-TT-TTGCTATTTTAGTCCTTTAA-ATTT
* *
368269 TATTTTTGCTA-TTTAGGTCC-TCAAGTTT
1 TATTTTTGCTATTTTA-GTCCTTTAAATTT
368297 CTATTTTTGCTATT
1 -TATTTTTGCTATT
368311 CTGGTCCTCA
Statistics
Matches: 151, Mismatches: 25, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
28 22 0.15
29 32 0.21
30 90 0.60
31 7 0.05
ACGTcount: A:0.19, C:0.12, G:0.09, T:0.60
Consensus pattern (29 bp):
TATTTTTGCTATTTTAGTCCTTTAAATTT
Found at i:368155 original size:60 final size:59
Alignment explanation
Indices: 368083--368282 Score: 217
Period size: 60 Copynumber: 3.4 Consensus size: 59
368073 TTTTAGTTCC
* *
368083 TAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAATGTT-TGTTTTTGCTATTTTAGTCCTT
1 TAAGTTTTTATTTTTGCTATTTTAGTCCTTTAAAT-TTATGTTTTT-CTATTTTAGTCCTT
* * * * * *
368143 AAAGTTTTTATTTGTACAATTCTAGTCCTTTAAATTTCTAT-TTTTTCTATTTTATTCCTT
1 TAAGTTTTTATTTTTGCTATTTTAGTCCTTTAAA-TT-TATGTTTTTCTATTTTAGTCCTT
* * * * * *
368203 TAAGTTCTTATTTATGCTATTTTAGTCCTTTGATTTTATGTTCTT-TATTTTAATCCTT
1 TAAGTTTTTATTTTTGCTATTTTAGTCCTTTAAATTTATGTTTTTCTATTTTAGTCCTT
368261 TAAGTTTTTATTTTTGCTATTT
1 TAAGTTTTTATTTTTGCTATTT
368283 AGGTCCTCAA
Statistics
Matches: 117, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
58 35 0.30
59 6 0.05
60 68 0.58
61 7 0.06
62 1 0.01
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.61
Consensus pattern (59 bp):
TAAGTTTTTATTTTTGCTATTTTAGTCCTTTAAATTTATGTTTTTCTATTTTAGTCCTT
Found at i:368240 original size:14 final size:13
Alignment explanation
Indices: 368220--368262 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
368210 TTATTTATGC
368220 TATTTTAGTCCTT
1 TATTTTAGTCCTT
*
368233 TGATTTTATGTTCTT
1 T-ATTTTA-GTCCTT
*
368248 TATTTTAATCCTT
1 TATTTTAGTCCTT
368261 TA
1 TA
368263 AGTTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 7 0.28
14 12 0.48
15 6 0.24
ACGTcount: A:0.19, C:0.12, G:0.07, T:0.63
Consensus pattern (13 bp):
TATTTTAGTCCTT
Found at i:368289 original size:58 final size:59
Alignment explanation
Indices: 368083--368359 Score: 201
Period size: 58 Copynumber: 4.7 Consensus size: 59
368073 TTTTAGTTCC
* * * * *
368083 TAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAATGTT-TGTTT-TTGCTATTTTAGTCCTT
1 TAAGTTTTTATTTATGCTA-TTTAGTCCTTTAAAT-TTCTATTTCTT-CTATTTTAATCCTT
* * * * * *
368143 AAAGTTTTTATTTGTACAATTCTAGTCCTTTAAATTTCTATTTTTTCTATTTTATTCCTT
1 TAAGTTTTTATTTATGCTATT-TAGTCCTTTAAATTTCTATTTCTTCTATTTTAATCCTT
* *
368203 TAAGTTCTTATTTATGCTATTTTAGTCCTTT-GATTT-TATGTTCTT-TATTTTAATCCTT
1 TAAGTTTTTATTTATGCTA-TTTAGTCCTTTAAATTTCTAT-TTCTTCTATTTTAATCCTT
* * * * **
368261 TAAGTTTTTATTTTTGCTATTTAGGTCC-TCAAGTTTCTATTT-TTGCTATTCTGGTCC-T
1 TAAGTTTTTATTTATGCTATTTA-GTCCTTTAAATTTCTATTTCTT-CTATTTTAATCCTT
* * * * * *
368319 CAAGTTTTTGTTAATCCTATTTTGTCCTTTAAATTTTTATT
1 TAAGTTTTTATTTATGCTATTTAGTCCTTTAAATTTCTATT
368360 GTTTTTTTTA
Statistics
Matches: 174, Mismatches: 32, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
57 11 0.06
58 69 0.40
59 23 0.13
60 67 0.39
61 4 0.02
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.59
Consensus pattern (59 bp):
TAAGTTTTTATTTATGCTATTTAGTCCTTTAAATTTCTATTTCTTCTATTTTAATCCTT
Found at i:368316 original size:29 final size:29
Alignment explanation
Indices: 368262--368325 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
368252 TTAATCCTTT
*
368262 AAGTTTTTATTTTTGCTATTTAGGTCCTC
1 AAGTTTCTATTTTTGCTATTTAGGTCCTC
368291 AAGTTTCTATTTTTGCTATTCT-GGTCCTC
1 AAGTTTCTATTTTTGCTATT-TAGGTCCTC
368320 AAGTTT
1 AAGTTT
368326 TTGTTAATCC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 32 0.97
30 1 0.03
ACGTcount: A:0.17, C:0.16, G:0.14, T:0.53
Consensus pattern (29 bp):
AAGTTTCTATTTTTGCTATTTAGGTCCTC
Found at i:370186 original size:15 final size:14
Alignment explanation
Indices: 370153--370196 Score: 58
Period size: 12 Copynumber: 3.3 Consensus size: 14
370143 GGATTAACAT
370153 TTTTGCATC-TGCA
1 TTTTGCATCTTGCA
370166 -TTTGCATCTTTGCA
1 TTTTGCATC-TTGCA
370180 TTTTGCATC-TGCA
1 TTTTGCATCTTGCA
370193 TTTT
1 TTTT
370197 ATTTTTAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 8 0.29
13 8 0.29
14 4 0.14
15 8 0.29
ACGTcount: A:0.14, C:0.20, G:0.14, T:0.52
Consensus pattern (14 bp):
TTTTGCATCTTGCA
Found at i:371497 original size:90 final size:89
Alignment explanation
Indices: 371345--371517 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
371335 ACACACCCTT
371345 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
371410 ATTAATTAGAATTTAATAATCCTC
66 ATTAATTAAAATTAAATAATCCTC
* *
371434 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTGAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
371499 AATTAATTAAAATTAAATA
65 AATTAATTAAAATTAAATA
371518 TTCGGGATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 30 0.38
90 49 0.62
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.44
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTAAAATTAAATAATCCTC
Found at i:380331 original size:174 final size:174
Alignment explanation
Indices: 380041--380377 Score: 584
Period size: 174 Copynumber: 1.9 Consensus size: 174
380031 CAACCTACGC
* * * *
380041 TGACTATACATTCCATGGCACTACTATACACTTGCACTTGACCATACACTGCCTTTCAGTAACGT
1 TGACTATACATTCCATGGCACTACCATACACTTGCACTTAACCAGACACTGCCTTCCAGTAACGT
380106 AAAATCTTAAACAAAAGATGACCTAATGATTATTAATAACTCATAATAGGAAATGAGAAGCAAAC
66 AAAATCTTAAACAAAAGATGACCTAATGATTATTAATAACTCATAATAGGAAATGAGAAGCAAAC
380171 AATTTATTAGGCAGATTCTCTAAAGGGAAGAAGCAAACAAAGGG
131 AATTTATTAGGCAGATTCTCTAAAGGGAAGAAGCAAACAAAGGG
380215 TGACTATACATTCCATGGCACTACCATACACTTGCACTTAACCAGACACTGCCTTCCAGTAACGT
1 TGACTATACATTCCATGGCACTACCATACACTTGCACTTAACCAGACACTGCCTTCCAGTAACGT
* * * * *
380280 AAAGTCTTAAACAAAGGGTGACCTAATGGTTATTAATAACTCATAATAGGAACTGAGAAGCAAAC
66 AAAATCTTAAACAAAAGATGACCTAATGATTATTAATAACTCATAATAGGAAATGAGAAGCAAAC
*
380345 AATTTATTAGGCAGATTCTCTAAAGGGGAGAAG
131 AATTTATTAGGCAGATTCTCTAAAGGGAAGAAG
380378 TCACAAAAAT
Statistics
Matches: 153, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
174 153 1.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (174 bp):
TGACTATACATTCCATGGCACTACCATACACTTGCACTTAACCAGACACTGCCTTCCAGTAACGT
AAAATCTTAAACAAAAGATGACCTAATGATTATTAATAACTCATAATAGGAAATGAGAAGCAAAC
AATTTATTAGGCAGATTCTCTAAAGGGAAGAAGCAAACAAAGGG
Found at i:383360 original size:21 final size:22
Alignment explanation
Indices: 383329--383385 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
383319 CAATTGGTTA
383329 TTAGTAAAAAATAATAATATT-T
1 TTAG-AAAAAATAATAATATTAT
383351 TTAGAAAAAATACA-AATATTAT
1 TTAGAAAAAATA-ATAATATTAT
*
383373 TT-TAAAAAATAAT
1 TTAGAAAAAATAAT
383386 TAAAAAACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 1 0.03
21 22 0.71
22 8 0.26
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (22 bp):
TTAGAAAAAATAATAATATTAT
Found at i:386504 original size:53 final size:53
Alignment explanation
Indices: 386407--386507 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 53
386397 ACATTATCTG
*
386407 TAAAATAAGTAACTAATAGAAGAAAACTCAGATTTCAGGGTGGGCACGATCAA
1 TAAAATAAGTAACTAATAGAAGAAAACTCAGATTTCAGGATGGGCACGATCAA
* * * * * *
386460 TAAAATAAGTCACTAATCGAAGAAAATTTAGATTTTAGTATGGGCACG
1 TAAAATAAGTAACTAATAGAAGAAAACTCAGATTTCAGGATGGGCACG
386508 TGGCCACCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 41 1.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.25
Consensus pattern (53 bp):
TAAAATAAGTAACTAATAGAAGAAAACTCAGATTTCAGGATGGGCACGATCAA
Found at i:389159 original size:16 final size:16
Alignment explanation
Indices: 389135--389166 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
389125 ATCTAGTTTT
*
389135 CCCGGGTACCCGGTTA
1 CCCGAGTACCCGGTTA
389151 CCCGAGTACCCGGTTA
1 CCCGAGTACCCGGTTA
389167 GTTTTTAATT
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:0.16, C:0.38, G:0.28, T:0.19
Consensus pattern (16 bp):
CCCGAGTACCCGGTTA
Found at i:389490 original size:16 final size:16
Alignment explanation
Indices: 389452--389491 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
389442 ACCCGGAAGT
389452 TCCGGGTACCCGAAAA
1 TCCGGGTACCCGAAAA
389468 T-CGGGTACCCGAAAA
1 TCCGGGTACCCGAAAA
389483 TCCGGGTAC
1 TCCGGGTAC
389492 TCGGATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.15
Consensus pattern (16 bp):
TCCGGGTACCCGAAAA
Found at i:391074 original size:65 final size:66
Alignment explanation
Indices: 390936--391081 Score: 154
Period size: 65 Copynumber: 2.2 Consensus size: 66
390926 AGCTATTTTA
* * * *
390936 TGTACCGATGCACAACCATGCATCGATACACTCCTATTTTTTTTATTGAAAACATCGAATACATT
1 TGTACCGATACACAACCATGCATCGATACACTCCTA--TATCTTATTGAAAACATCGAATACAAT
*
391001 TTG
64 TAG
* **
391004 TGTACCGATACACATCCTATGCATCGATACACTCCTGA-ATCTT-TTG-AAACATCGAATGTAAT
1 TGTACCGATACACAACC-ATGCATCGATACACTCCT-ATATCTTATTGAAAACATCGAATACAAT
391066 TAG
64 TAG
*
391069 TGTACCTATACAC
1 TGTACCGATACAC
391082 CCCAAGTGTA
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
65 27 0.40
66 3 0.04
67 3 0.04
68 15 0.22
69 18 0.27
70 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (66 bp):
TGTACCGATACACAACCATGCATCGATACACTCCTATATCTTATTGAAAACATCGAATACAATTA
G
Found at i:391163 original size:21 final size:21
Alignment explanation
Indices: 391139--391196 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
391129 ATTTTACACT
391139 GAGTGTACCGATACACCTTGA
1 GAGTGTACCGATACACCTTGA
391160 GAGTGTACCGATACACCTTGA
1 GAGTGTACCGATACACCTTGA
*
391181 GAGTGTACCAATACAC
1 GAGTGTACCGATACAC
391197 ACACGCTCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
GAGTGTACCGATACACCTTGA
Found at i:397290 original size:13 final size:14
Alignment explanation
Indices: 397272--397318 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 14
397262 AAATTTAAAA
397272 TTATTATATAT-TT
1 TTATTATATATATT
397285 TTATTATATATATT
1 TTATTATATATATT
*
397299 TTATTGAAAATATATT
1 TTATT--ATATATATT
397315 TTAT
1 TTAT
397319 CATTTTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 11 0.37
14 7 0.23
16 12 0.40
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TTATTATATATATT
Found at i:397296 original size:15 final size:16
Alignment explanation
Indices: 397271--397300 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
397261 AAAATTTAAA
397271 ATTATTATATATTTTT
1 ATTATTATATATTTTT
397287 ATTA-TATATATTTT
1 ATTATTATATATTTT
397301 ATTGAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTATTATATATTTTT
Found at i:397339 original size:27 final size:26
Alignment explanation
Indices: 397309--397363 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
397299 TTATTGAAAA
397309 TATAT-TTTATCATTTTCTTTAAAATTT
1 TATATGTTTAT-ATTTTC-TTAAAATTT
*
397336 TATATGTTTATTTTTTCTTAAAATTT
1 TATATGTTTATATTTTCTTAAAATTT
397362 TA
1 TA
397364 AAAATTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 11 0.42
27 10 0.38
28 5 0.19
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (26 bp):
TATATGTTTATATTTTCTTAAAATTT
Found at i:408012 original size:21 final size:20
Alignment explanation
Indices: 407971--408049 Score: 70
Period size: 22 Copynumber: 3.7 Consensus size: 20
407961 ATCCCTCAAT
*
407971 ATATTATTTTT-TTCAATTAA
1 ATATTATTTTTATTGAA-TAA
407991 ATCATTATTTTTATTGAATAAAA
1 AT-ATTATTTTTATTGAAT--AA
*
408014 ATAATATTTTTATTGAATAAAA
1 ATATTATTTTTATTGAAT--AA
*
408036 ATAATATTTTTATT
1 ATATTATTTTTATT
408050 ATTTCAGGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.04
21 10 0.19
22 37 0.70
23 4 0.08
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
ATATTATTTTTATTGAATAA
Found at i:408021 original size:22 final size:22
Alignment explanation
Indices: 407996--408049 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
407986 ATTAAATCAT
407996 TATTTTTATTGAATAAAAATAA
1 TATTTTTATTGAATAAAAATAA
408018 TATTTTTATTGAATAAAAATAA
1 TATTTTTATTGAATAAAAATAA
408040 TATTTTTATT
1 TATTTTTATT
408050 ATTTCAGGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TATTTTTATTGAATAAAAATAA
Found at i:408329 original size:18 final size:18
Alignment explanation
Indices: 408306--408347 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
408296 CCACACTAAA
408306 ATTTTAAAATTGTTATAT
1 ATTTTAAAATTGTTATAT
* * *
408324 ATTTTAGATTTTTTATAT
1 ATTTTAAAATTGTTATAT
408342 ATTTTA
1 ATTTTA
408348 TATTAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATTTTAAAATTGTTATAT
Found at i:408814 original size:15 final size:15
Alignment explanation
Indices: 408794--408831 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
408784 GTTTATTTCA
408794 GAATGATTAAGTTTT
1 GAATGATTAAGTTTT
408809 GAATGATTAAGTTTT
1 GAATGATTAAGTTTT
*
408824 AAATGATT
1 GAATGATT
408832 CAAATGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (15 bp):
GAATGATTAAGTTTT
Found at i:410618 original size:4 final size:4
Alignment explanation
Indices: 410593--410641 Score: 71
Period size: 4 Copynumber: 11.8 Consensus size: 4
410583 CTATAACAAA
*
410593 TTTG TTTTG TCTTG TGTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG -TTTG T-TTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
410642 TTCTTTGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
4 33 0.80
5 8 0.20
ACGTcount: A:0.00, C:0.02, G:0.24, T:0.73
Consensus pattern (4 bp):
TTTG
Found at i:410890 original size:16 final size:16
Alignment explanation
Indices: 410871--410902 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
410861 TCCACTTGTG
410871 GAATCTGAGGAAGACA
1 GAATCTGAGGAAGACA
410887 GAATCTGAGGAAGACA
1 GAATCTGAGGAAGACA
410903 CGCCACTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.31, T:0.12
Consensus pattern (16 bp):
GAATCTGAGGAAGACA
Found at i:411773 original size:24 final size:24
Alignment explanation
Indices: 411741--411790 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
411731 TTCTTAGTAG
411741 GACATTTGAATTATAAGGTTAACA
1 GACATTTGAATTATAAGGTTAACA
411765 GACATTTGAATTATAAGGTTAACA
1 GACATTTGAATTATAAGGTTAACA
411789 GA
1 GA
411791 ATCATTATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (24 bp):
GACATTTGAATTATAAGGTTAACA
Found at i:416726 original size:20 final size:20
Alignment explanation
Indices: 416698--416735 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
416688 GGCCGTTTCT
*
416698 AGCCATTGGGGATGATTTGG
1 AGCCATTGGGGATAATTTGG
*
416718 AGCCGTTGGGGATAATTT
1 AGCCATTGGGGATAATTT
416736 TTCTGCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (20 bp):
AGCCATTGGGGATAATTTGG
Found at i:416900 original size:98 final size:98
Alignment explanation
Indices: 416718--416921 Score: 345
Period size: 98 Copynumber: 2.1 Consensus size: 98
416708 GATGATTTGG
* * **
416718 AGCCGTTGGGGATAATTTTTCTGCAAAATAAAACTGCCCAGGACATGGAGTATCGGTACTCCTTT
1 AGCCGTTAGGGATAATTTTTCTGCAAAATAAAACTGCCCAGGACAGGGAGTATCAATACTCCTTT
*
416783 AATGAGTATCGATATTTCCTTTATAAATAAACT
66 AATGAGTATCGATAATTCCTTTATAAATAAACT
* *
416816 AGTCGTTAGGGATAATTTTTCTGTAAAATAAAACTGCCCAGGACAGGGAGTATCAATACTCCTTT
1 AGCCGTTAGGGATAATTTTTCTGCAAAATAAAACTGCCCAGGACAGGGAGTATCAATACTCCTTT
416881 AATGAGTATCGATAATTCCTTTATAAATAAACT
66 AATGAGTATCGATAATTCCTTTATAAATAAACT
416914 AGCCGTTA
1 AGCCGTTA
416922 CTAGACGTTG
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (98 bp):
AGCCGTTAGGGATAATTTTTCTGCAAAATAAAACTGCCCAGGACAGGGAGTATCAATACTCCTTT
AATGAGTATCGATAATTCCTTTATAAATAAACT
Found at i:418498 original size:20 final size:21
Alignment explanation
Indices: 418469--418512 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
418459 CTCAAAATCA
*
418469 TTTTTCAAAATTTC-ATTTTGC
1 TTTTTCAAAA-TCCAATTTTGC
418490 TTTTT-AAAATCCAATTTTGC
1 TTTTTCAAAATCCAATTTTGC
418510 TTT
1 TTT
418513 CAAGAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 14 0.67
21 5 0.24
ACGTcount: A:0.25, C:0.14, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTTTCAAAATCCAATTTTGC
Found at i:425549 original size:60 final size:58
Alignment explanation
Indices: 425417--425554 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 58
425407 GTATATACAT
* * *
425417 ATAGTTTGGGATGAAATTGAAATATTTCAAAATTTTGGGACTAGTTTAGAATTAAGGTC
1 ATAGTTTGGGATGAAATTGAAATATTTCAAAAGTTTGGGACTAATATAGAATTAA-GTC
*
425476 ATAATTTGAGGATGAAATTGAAATA-TTCAAAAGTTTGAGGACTAATATAGAATGATAA-TC
1 ATAGTTTG-GGATGAAATTGAAATATTTCAAAAGTTTG-GGACTAATATAGAAT--TAAGTC
*
425536 ATTGTTTAGGGATGAAATT
1 ATAGTTT-GGGATGAAATT
425555 AGAGTATTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
59 18 0.26
60 46 0.68
61 1 0.01
62 3 0.04
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (58 bp):
ATAGTTTGGGATGAAATTGAAATATTTCAAAAGTTTGGGACTAATATAGAATTAAGTC
Found at i:427635 original size:21 final size:22
Alignment explanation
Indices: 427609--427651 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
427599 ATAATCTCTT
* *
427609 GCATGTC-TGAACCTACAACAA
1 GCATGTCATCAACATACAACAA
427630 GCATGTCATCAACATACAACAA
1 GCATGTCATCAACATACAACAA
427652 TAAAATAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.19
Consensus pattern (22 bp):
GCATGTCATCAACATACAACAA
Found at i:433379 original size:17 final size:17
Alignment explanation
Indices: 433357--433461 Score: 79
Period size: 17 Copynumber: 6.1 Consensus size: 17
433347 AATTAAGAGT
433357 TAGTTTATTAAATGAAC
1 TAGTTTATTAAATGAAC
*
433374 TAGTTTGA-TGAATGAAC
1 TAGTTT-ATTAAATGAAC
433391 TAGTTTAATT-AATGAAC
1 TAGTTT-ATTAAATGAAC
* *
433408 TAACTTTATTCAATGAAC
1 T-AGTTTATTAAATGAAC
* ** * *
433426 TAGATGCTTGAATGAAG
1 TAGTTTATTAAATGAAC
* *
433443 TAGCTTACTAAATGAAC
1 TAGTTTATTAAATGAAC
433460 TA
1 TA
433462 AATATGCATA
Statistics
Matches: 69, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
17 55 0.80
18 14 0.20
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (17 bp):
TAGTTTATTAAATGAAC
Found at i:433422 original size:18 final size:18
Alignment explanation
Indices: 433384--433427 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
433374 TAGTTTGATG
*
433384 AATGAACT-AGTTTAATT
1 AATGAACTAACTTTAATT
433401 AATGAACTAACTTT-ATT
1 AATGAACTAACTTTAATT
433418 CAATGAACTA
1 -AATGAACTA
433428 GATGCTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTAATT
Found at i:433438 original size:52 final size:52
Alignment explanation
Indices: 433360--433462 Score: 127
Period size: 52 Copynumber: 2.0 Consensus size: 52
433350 TAAGAGTTAG
* * *
433360 TTTATTAAATGAACTAGTTTGATGAATGAACTAGTTTAATTAATGAACTAAC
1 TTTATTAAATGAACTAGTATGATGAATGAACTAGCTTAATAAATGAACTAAC
* * * *
433412 TTTATTCAATGAACTAG-ATGCTTGAATGAAGTAGCTTACTAAATGAACTAA
1 TTTATTAAATGAACTAGTATG-ATGAATGAACTAGCTTAATAAATGAACTAA
433463 ATATGCATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 2 0.05
52 41 0.95
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (52 bp):
TTTATTAAATGAACTAGTATGATGAATGAACTAGCTTAATAAATGAACTAAC
Found at i:434629 original size:18 final size:19
Alignment explanation
Indices: 434574--434631 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 19
434564 AATGTGCTCA
434574 TTTTC-ACTCTCAA-TTCT
1 TTTTCAACTCTCAATTTCT
434591 CTTTTCAATGCTCTCAATTTCT
1 -TTTTCAA--CTCTCAATTTCT
434613 TTTTCAACTCT-AATTTCT
1 TTTTCAACTCTCAATTTCT
434631 T
1 T
434632 CTTCTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
18 13 0.36
19 5 0.14
21 14 0.39
22 4 0.11
ACGTcount: A:0.19, C:0.26, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTCAACTCTCAATTTCT
Found at i:436258 original size:17 final size:17
Alignment explanation
Indices: 436236--436324 Score: 85
Period size: 17 Copynumber: 5.2 Consensus size: 17
436226 AATTAAGAGT
*
436236 TAGTTTATTAAATGAAC
1 TAGTTTATTGAATGAAC
436253 TAGTTTGA-TGAATGAAC
1 TAGTTT-ATTGAATGAAC
436270 TAGTTT-TATGAATGAAC
1 TAGTTTAT-TGAATGAAC
436287 TAGTTTAATT-AATGAAC
1 TAGTTT-ATTGAATGAAC
* * *
436304 TAACTTTATTCAATAAAC
1 T-AGTTTATTGAATGAAC
436322 TAG
1 TAG
436325 ATGCATGAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
17 47 0.77
18 13 0.21
19 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (17 bp):
TAGTTTATTGAATGAAC
Found at i:436301 original size:21 final size:17
Alignment explanation
Indices: 436246--436305 Score: 93
Period size: 17 Copynumber: 3.5 Consensus size: 17
436236 TAGTTTATTA
*
436246 AATGAACTAGTTTGATG
1 AATGAACTAGTTTTATG
436263 AATGAACTAGTTTTATG
1 AATGAACTAGTTTTATG
* *
436280 AATGAACTAGTTTAATT
1 AATGAACTAGTTTTATG
436297 AATGAACTA
1 AATGAACTA
436306 ACTTTATTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (17 bp):
AATGAACTAGTTTTATG
Found at i:436312 original size:34 final size:34
Alignment explanation
Indices: 436246--436312 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
436236 TAGTTTATTA
* **
436246 AATGAACTAGTTTGATGAATGAACTAGTTTTATG
1 AATGAACTAGTTTAATGAATGAACTAACTTTATG
*
436280 AATGAACTAGTTTAATTAATGAACTAACTTTAT
1 AATGAACTAGTTTAATGAATGAACTAACTTTAT
436313 TCAATAAACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (34 bp):
AATGAACTAGTTTAATGAATGAACTAACTTTATG
Found at i:448440 original size:23 final size:24
Alignment explanation
Indices: 448384--448440 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
448374 ACTTAAATTT
* *
448384 TTTTTGAGTCGAGTCGAGTTTATAA
1 TTTTTGAGTCGAATCGAG-TTAGAA
*
448409 ATTTTGAGTCGAATCGAG-TAGAA
1 TTTTTGAGTCGAATCGAGTTAGAA
448432 TTTTTGAGT
1 TTTTTGAGT
448441 TTTTATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 12 0.43
25 16 0.57
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (24 bp):
TTTTTGAGTCGAATCGAGTTAGAA
Found at i:449650 original size:18 final size:19
Alignment explanation
Indices: 449627--449662 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
449617 GATGTTATTT
449627 TCATTTGGAATT-AGAGAA
1 TCATTTGGAATTGAGAGAA
*
449645 TCATTTGTAATTGAGAGA
1 TCATTTGGAATTGAGAGA
449663 GATTTCACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (19 bp):
TCATTTGGAATTGAGAGAA
Found at i:454704 original size:26 final size:27
Alignment explanation
Indices: 454666--454718 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
454656 ATTGGTGTCA
*
454666 GGTGGAGGATAT-ATATTTTCGGGTTG
1 GGTGGAGGATATAAAATTTTCGGGTTG
*
454692 GGTGGAGGTTATAAAATTTTCGGGTTG
1 GGTGGAGGATATAAAATTTTCGGGTTG
454719 AGTAGGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.21, C:0.04, G:0.38, T:0.38
Consensus pattern (27 bp):
GGTGGAGGATATAAAATTTTCGGGTTG
Found at i:454927 original size:15 final size:15
Alignment explanation
Indices: 454904--454938 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
454894 ATAAGATTAG
*
454904 TTTGATTGTTTTGAT
1 TTTGGTTGTTTTGAT
*
454919 TTTGGTTGTTTTGGT
1 TTTGGTTGTTTTGAT
454934 TTTGG
1 TTTGG
454939 AAATCTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.00, G:0.29, T:0.66
Consensus pattern (15 bp):
TTTGGTTGTTTTGAT
Found at i:457703 original size:35 final size:35
Alignment explanation
Indices: 457643--457740 Score: 160
Period size: 35 Copynumber: 2.7 Consensus size: 35
457633 ATTTTAGACA
457643 CTTAATTATTATTATTTTAAAATTATACTAAAATGT
1 CTTAATTATTATT-TTTTAAAATTATACTAAAATGT
457679 CTTAATTATTATTTTTTAAAATTATACTAAAATGT
1 CTTAATTATTATTTTTTAAAATTATACTAAAATGT
* *
457714 CTTAATTACTTATTTTTTTAAGTTATA
1 CTTAATTA-TTATTTTTTAAAATTATA
457741 GTAACTTACA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 30 0.51
36 29 0.49
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (35 bp):
CTTAATTATTATTTTTTAAAATTATACTAAAATGT
Found at i:459414 original size:41 final size:41
Alignment explanation
Indices: 459368--459445 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
459358 ACAGACCTTG
* * *
459368 AATATTTCATTTCCAGAATCTGTTTTCAATGAAACAAACTA
1 AATATTTCATTTCCAAAACCTGCTTTCAATGAAACAAACTA
459409 AATATTTCATTTCCAAAACCTGCTTTCAATGAAACAA
1 AATATTTCATTTCCAAAACCTGCTTTCAATGAAACAA
459446 GCAGACCCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (41 bp):
AATATTTCATTTCCAAAACCTGCTTTCAATGAAACAAACTA
Found at i:460002 original size:2 final size:2
Alignment explanation
Indices: 459993--460039 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
459983 TATATATTCT
459993 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
460034 TA TA TA
1 TA TA TA
460040 GAGGGGTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:466750 original size:17 final size:18
Alignment explanation
Indices: 466706--466751 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
466696 GGTCCTGAAT
466706 CGACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACC
*
466724 CTACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACC
466742 CGA-CCGTTGA
1 CGACCCGTTGA
466752 TCGGTGCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.17, C:0.46, G:0.22, T:0.15
Consensus pattern (18 bp):
CGACCCGTTGACCCGACC
Found at i:466815 original size:29 final size:29
Alignment explanation
Indices: 466754--466906 Score: 112
Period size: 29 Copynumber: 5.3 Consensus size: 29
466744 ACCGTTGATC
* *** *
466754 GGTGCTATTCTGGGAATTAATTTGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
*
466783 GGTGTTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* ** ** *
466812 GGTGCTATTTTGATAAAAAAATTC-AAA-A
1 GGTGCTATTCTG-GGAATTAATTCGAAATG
* * * * *
466840 AGTGATATTATGGGAATTAATTCAAAATT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
466869 GGTGCTATTTTGGGAATTAATTCGAAAAG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
466898 GGTGCTATT
1 GGTGCTATT
466907 TTTGTAATTA
Statistics
Matches: 94, Mismatches: 27, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
27 7 0.07
28 12 0.13
29 68 0.72
30 7 0.07
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.39
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:466907 original size:29 final size:28
Alignment explanation
Indices: 466783--466935 Score: 119
Period size: 29 Copynumber: 5.4 Consensus size: 28
466773 ATTTGGTTTT
* * *
466783 GGTGTTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTC-AAAAG
** **
466812 GGTGCTATTTTGATAAAAAAATTCAAAA-
1 GGTGCTATTTTG-GGAATTAATTCAAAAG
* * * *
466840 AGTGATATTATGGGAATTAATTCAAAATT
1 GGTGCTATTTTGGGAATTAATTCAAAA-G
466869 GGTGCTATTTTGGGAATTAATTCGAAAAG
1 GGTGCTATTTTGGGAATTAATTC-AAAAG
* * * * *
466898 GGTGCTATTTTTGTAATTATTTTAAAAA
1 GGTGCTATTTTGGGAATTAATTCAAAAG
466926 GGTGCTATTT
1 GGTGCTATTT
466936 GTGTAAAATG
Statistics
Matches: 97, Mismatches: 23, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
27 11 0.11
28 23 0.24
29 52 0.54
30 11 0.11
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (28 bp):
GGTGCTATTTTGGGAATTAATTCAAAAG
Found at i:474019 original size:11 final size:11
Alignment explanation
Indices: 473994--474030 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
473984 GAAATCTGGA
473994 AACCGG-TTT-
1 AACCGGTTTTG
474003 AACCGGTTTTG
1 AACCGGTTTTG
474014 AACCGGTTTTG
1 AACCGGTTTTG
474025 -ACCGGT
1 AACCGGT
474031 CCTGACCCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 6 0.23
10 9 0.35
11 11 0.42
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:474065 original size:21 final size:21
Alignment explanation
Indices: 474039--474078 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
474029 GTCCTGACCC
474039 GACCCGTTGACCCGACCCGTT
1 GACCCGTTGACCCGACCCGTT
474060 GACCCGTTGACCCGACCCG
1 GACCCGTTGACCCGACCCG
474079 ACCGTTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.45, G:0.25, T:0.15
Consensus pattern (21 bp):
GACCCGTTGACCCGACCCGTT
Found at i:474078 original size:13 final size:13
Alignment explanation
Indices: 474033--474065 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
474023 TGACCGGTCC
474033 TGACCCGACCCGT
1 TGACCCGACCCGT
474046 TGACCCGACCCGT
1 TGACCCGACCCGT
474059 TGACCCG
1 TGACCCG
474066 TTGACCCGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.45, G:0.24, T:0.15
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:474197 original size:29 final size:29
Alignment explanation
Indices: 474139--474247 Score: 94
Period size: 29 Copynumber: 3.7 Consensus size: 29
474129 GGTAAAAAAA
* * * *
474139 AATTTCAAAAAAGTGATATTATGGGGAATT
1 AATTTCAAAAGAGTGCTATT-TTGGAAATT
*
474169 AA-TTCAAAATTAGTGCTATTTTGGAAATT
1 AATTTCAAAA-GAGTGCTATTTTGGAAATT
* * *
474198 AATTTGAAAAGGGTGCTATTTTGGTAATT
1 AATTTCAAAAGAGTGCTATTTTGGAAATT
* * *
474227 ATTTTAAAAAGGGTGCTATTT
1 AATTTCAAAAGAGTGCTATTT
474248 GTGTAAAATG
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
29 51 0.76
30 16 0.24
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (29 bp):
AATTTCAAAAGAGTGCTATTTTGGAAATT
Found at i:474253 original size:29 final size:29
Alignment explanation
Indices: 474181--474247 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
474171 TTCAAAATTA
* *
474181 GTGCTATTTTGGAAATTAATTTGAAAAGG
1 GTGCTATTTTGGTAATTAATTTAAAAAGG
*
474210 GTGCTATTTTGGTAATTATTTTAAAAAGG
1 GTGCTATTTTGGTAATTAATTTAAAAAGG
474239 GTGCTATTT
1 GTGCTATTT
474248 GTGTAAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.43
Consensus pattern (29 bp):
GTGCTATTTTGGTAATTAATTTAAAAAGG
Found at i:476516 original size:16 final size:18
Alignment explanation
Indices: 476490--476526 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
476480 TTTTTATAAA
476490 TTTTAAGTTTCTTA-ATT
1 TTTTAAGTTTCTTAGATT
476507 TTTTAA-TTTCTTAGATT
1 TTTTAAGTTTCTTAGATT
476524 TTT
1 TTT
476527 ATTTTTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTAAGTTTCTTAGATT
Found at i:476558 original size:17 final size:17
Alignment explanation
Indices: 476490--476558 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 17
476480 TTTTTATAAA
476490 TTTTAAGTTTCTTA-ATT
1 TTTTAA-TTTCTTATATT
*
476507 TTTTAATTTCTTAGA-T
1 TTTTAATTTCTTATATT
***
476523 TTTT-ATTT-TTATCCA
1 TTTTAATTTCTTATATT
476538 TTTTAATTTCTTATATT
1 TTTTAATTTCTTATATT
476555 TTTT
1 TTTT
476559 TAATCTCATA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
14 3 0.07
15 8 0.19
16 16 0.38
17 15 0.36
ACGTcount: A:0.22, C:0.07, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTAATTTCTTATATT
Found at i:484425 original size:25 final size:25
Alignment explanation
Indices: 484397--484461 Score: 130
Period size: 25 Copynumber: 2.6 Consensus size: 25
484387 AAGATTTCTT
484397 GAAGAGAGAGAAAGAAAGAAAGTTG
1 GAAGAGAGAGAAAGAAAGAAAGTTG
484422 GAAGAGAGAGAAAGAAAGAAAGTTG
1 GAAGAGAGAGAAAGAAAGAAAGTTG
484447 GAAGAGAGAGAAAGA
1 GAAGAGAGAGAAAGA
484462 GATTTTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.06
Consensus pattern (25 bp):
GAAGAGAGAGAAAGAAAGAAAGTTG
Found at i:496183 original size:11 final size:11
Alignment explanation
Indices: 496160--496202 Score: 77
Period size: 11 Copynumber: 3.8 Consensus size: 11
496150 CTGTAATTAT
496160 TATTTATATATA
1 TATTTA-ATATA
496172 TATTTAATATA
1 TATTTAATATA
496183 TATTTAATATA
1 TATTTAATATA
496194 TATTTAATA
1 TATTTAATA
496203 ATAATAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 25 0.81
12 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:496206 original size:3 final size:3
Alignment explanation
Indices: 496198--496267 Score: 113
Period size: 3 Copynumber: 22.7 Consensus size: 3
496188 AATATATATT
*
496198 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
496246 TAA TAA TAGGA TAA TAA TAA TA
1 TAA TAA TA--A TAA TAA TAA TA
496268 TGGATAAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 60 0.95
5 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:496832 original size:113 final size:113
Alignment explanation
Indices: 496587--497140 Score: 1008
Period size: 113 Copynumber: 4.9 Consensus size: 113
496577 AGAATTATGC
* *
496587 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
496652 TATGAAC-TTCTCTGGAAAAGCT-ACTCCATCAAGTGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGA-TCCATCAAGTGATGAATTCAGGT
496699 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
496764 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGT
496812 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
496877 TATGAACTTTCTTTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGT
*
496925 AACAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
496990 TATGAAC-TTCTCTGGAAAAGCT-ACTCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGA-TCCATCAAGTGATGAATTCAGGT
497037 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
497102 TATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATG
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATG
497141 GATTTGAATC
Statistics
Matches: 429, Mismatches: 8, Indels: 9
0.96 0.02 0.02
Matches are distributed among these distances:
111 1 0.00
112 178 0.41
113 248 0.58
114 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGT
Found at i:496849 original size:225 final size:225
Alignment explanation
Indices: 496587--497144 Score: 1014
Period size: 225 Copynumber: 2.5 Consensus size: 225
496577 AGAATTATGC
* *
496587 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
496652 TATGAAC-TTCTCTGGAAAAGCT-ACTCCATCAAGTGATGGATTCAGGTAAAAGGTTGAACAAGT
66 TATGAACTTTCTCTGGAAAAGCTGA-TCCATCAAGTGATGGATTCAGGTAAAAGGTTGAACAAGT
496715 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGG
496780 AAAAGCTGA-TCCATCAAGTGATGAATTCAGGT
194 AAAAGCT-ACTCCATCAAGTGATGAATTCAGGT
496812 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
496877 TATGAACTTTCTTTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGTAACAGGTTGAACAAGTT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTCAGGTAAAAGGTTGAACAAGTT
496942 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAA
497007 AAGCTACTCCATCAAGTGATGAATTCAGGT
196 AAGCTACTCCATCAAGTGATGAATTCAGGT
497037 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
497102 TATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGGATT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATT
497145 TGAATCTTTG
Statistics
Matches: 322, Mismatches: 8, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
224 1 0.00
225 213 0.66
226 107 0.33
227 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (225 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTCAGGTAAAAGGTTGAACAAGTT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAA
AAGCTACTCCATCAAGTGATGAATTCAGGT
Found at i:498085 original size:83 final size:83
Alignment explanation
Indices: 497946--498191 Score: 458
Period size: 83 Copynumber: 3.0 Consensus size: 83
497936 TACTATGAGT
497946 AAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACT
1 AAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACT
*
498010 TCCAGAATATGCTATTAGC
65 TCCAGAAGATGCTATTAGC
498029 AAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
1 AAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
498094 CCAGAAGATGCTATTAGC
66 CCAGAAGATGCTATTAGC
*
498112 AAATTCATCTTCCAAATTCAATGATTAGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
1 AAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
498177 CCAGAAGATGCTATT
66 CCAGAAGATGCTATT
498192 GAGTCTCCTT
Statistics
Matches: 160, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
83 158 0.99
84 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (83 bp):
AAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTT
CCAGAAGATGCTATTAGC
Found at i:498220 original size:188 final size:188
Alignment explanation
Indices: 498021--498379 Score: 666
Period size: 188 Copynumber: 1.9 Consensus size: 188
498011 CCAGAATATG
*
498021 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
498085 AGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGATTAGTTCTGTCCAA
65 AGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGATTAGTTCTGTCCAA
498150 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTA
130 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTA
498209 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
* * *
498274 GAACACTTCCAGAATATGCTATTAGCAAATTCATCTTCCAAATTTAATGATTGGTTCTGTCCAAC
66 GAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGATTAGTTCTGTCCAAC
498339 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
131 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
498380 AGCAAATTCA
Statistics
Matches: 166, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
187 2 0.01
188 164 0.99
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.30
Consensus pattern (188 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGATTAGTTCTGTCCAAC
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTA
Found at i:498233 original size:105 final size:105
Alignment explanation
Indices: 498104--498296 Score: 343
Period size: 105 Copynumber: 1.8 Consensus size: 105
498094 CCAGAAGATG
*
498104 CTATTAGCAAATTCATCTTCCAAATTCAATGATTAGTTCTGTCC-AACCAGATCAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTAGTTCTG-CCAAACCAGATCAGATAACTCAA
498168 AGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTA
65 AGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTA
*
498209 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAACCAGATCAGATAACTCAAA
*
498274 GAACACTTCCAGAATATGCTATT
66 GAACACTTCCAGAAGATGCTATT
498297 AGCAAATTCA
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
104 2 0.02
105 82 0.98
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.31
Consensus pattern (105 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTA
Done.