Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 115 of 160
Found at i:21648908 original size:9 final size:9
Alignment explanation
Indices: 21648891--21648959 Score: 66
Period size: 9 Copynumber: 7.2 Consensus size: 9
21648881 AAAGAAATTT
*
21648891 TTTTTAAAA
1 TTTTAAAAA
21648900 TTTTAAAAA
1 TTTTAAAAA
21648909 TTTTTAAAAAA
1 -TTTT-AAAAA
*
21648920 TTCTAAAAA
1 TTTTAAAAA
*
21648929 TTCTAAAAA
1 TTTTAAAAA
*
21648938 TATTCAAAAAA
1 T-TT-TAAAAA
21648949 TTTTAAAAA
1 TTTTAAAAA
21648958 TT
1 TT
21648960 CAAAAAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
9 30 0.59
10 10 0.20
11 11 0.22
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:21648919 original size:20 final size:19
Alignment explanation
Indices: 21648896--21648957 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
21648886 AATTTTTTTT
21648896 AAAATTTTAAAAATTTTTAA
1 AAAATTTTAAAAA-TTTTAA
* *
21648916 AAAATTCTAAAAATTCTAA
1 AAAATTTTAAAAATTTTAA
**
21648935 AAATATTCAAAAAATTTTAA
1 AAA-ATTTTAAAAATTTTAA
21648955 AAA
1 AAA
21648958 TTCAAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.22
20 29 0.78
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTTTAAAAATTTTAA
Found at i:21648930 original size:29 final size:29
Alignment explanation
Indices: 21648896--21648970 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
21648886 AATTTTTTTT
* * *
21648896 AAAATTTTAAAAATTTTTAAAAAATTCTA
1 AAAATTCTAAAAATATTCAAAAAATTCTA
*
21648925 AAAATTCTAAAAATATTCAAAAAATTTTA
1 AAAATTCTAAAAATATTCAAAAAATTCTA
*
21648954 AAAATTC-AAAAAAATTC
1 AAAATTCTAAAAATATTC
21648971 CAAATGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 9 0.22
29 32 0.78
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAATTCTAAAAATATTCAAAAAATTCTA
Found at i:21648958 original size:20 final size:19
Alignment explanation
Indices: 21648904--21648966 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
21648894 TTAAAATTTT
*
21648904 AAAAATTTTTAAAAAATTC
1 AAAAAATTTTAAAAAATTC
* *
21648923 TAAAAATTCTAAAAATATTC
1 AAAAAATTTTAAAAA-ATTC
21648943 AAAAAATTTT-AAAAATTC
1 AAAAAATTTTAAAAAATTC
21648961 AAAAAA
1 AAAAAA
21648967 ATTCCAAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
18 10 0.26
19 16 0.42
20 12 0.32
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAAATTTTAAAAAATTC
Found at i:21648965 original size:9 final size:9
Alignment explanation
Indices: 21648914--21648966 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
21648904 AAAAATTTTT
21648914 AAAAAATTC
1 AAAAAATTC
*
21648923 TAAAAATTC
1 AAAAAATTC
21648932 TAAAAATATTC
1 -AAAAA-ATTC
*
21648943 AAAAAATTT
1 AAAAAATTC
*
21648952 TAAAAATTC
1 AAAAAATTC
21648961 AAAAAA
1 AAAAAA
21648967 ATTCCAAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 23 0.64
10 9 0.25
11 4 0.11
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAAAATTC
Found at i:21650491 original size:10 final size:10
Alignment explanation
Indices: 21650467--21650512 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
21650457 CTTTTCTTAG
21650467 AATTTTTATAA
1 AATTTTT-TAA
*
21650478 AATTTTTTAG
1 AATTTTTTAA
21650488 AATTTTTT--
1 AATTTTTTAA
21650496 AATTTTTTAA
1 AATTTTTTAA
21650506 AATTTTT
1 AATTTTT
21650513 ATAATTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
8 8 0.25
10 17 0.53
11 7 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:21655903 original size:3 final size:3
Alignment explanation
Indices: 21655895--21655929 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
21655885 TATTTATTTA
*
21655895 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
21655930 AATATAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:21656696 original size:27 final size:29
Alignment explanation
Indices: 21656665--21656719 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
21656655 CAATTTTTCG
*
21656665 ACATGGAACA-A-ATTAAAAAAAAAATGA
1 ACATGGAACATATAATAAAAAAAAAATGA
* *
21656692 ACATGTAACATATAATAAGAAAAAAATG
1 ACATGGAACATATAATAAAAAAAAAATG
21656720 TTTGGTTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 9 0.39
28 1 0.04
29 13 0.57
ACGTcount: A:0.64, C:0.07, G:0.11, T:0.18
Consensus pattern (29 bp):
ACATGGAACATATAATAAAAAAAAAATGA
Found at i:21662306 original size:23 final size:23
Alignment explanation
Indices: 21662248--21662317 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
21662238 CATGACTGTT
* *
21662248 TATTTTGAATAGACAAATAT-TGTC
1 TATTTTGAATAGAC--TTATCTATC
*
21662272 TATTTTTTAATAGACTTATCTATC
1 TA-TTTTGAATAGACTTATCTATC
*
21662296 TATTTTGAATAGACTTAACTAT
1 TATTTTGAATAGACTTATCTAT
21662318 TTATCTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 21 0.54
24 7 0.18
25 11 0.28
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (23 bp):
TATTTTGAATAGACTTATCTATC
Found at i:21663030 original size:20 final size:19
Alignment explanation
Indices: 21663005--21663054 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
21662995 AGCTTAAACT
21663005 GTAAAAAAATATGAA-AAAA
1 GTAAAAAAATAT-AAGAAAA
*
21663024 GGTAAAAAATTATAAGAAAA
1 -GTAAAAAAATATAAGAAAA
*
21663044 ATAAAAAAATA
1 GTAAAAAAATA
21663055 AAAAAATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (19 bp):
GTAAAAAAATATAAGAAAA
Found at i:21663042 original size:22 final size:20
Alignment explanation
Indices: 21663005--21663060 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 20
21662995 AGCTTAAACT
*
21663005 GTAAAAAAATATGAAAAAAG
1 GTAAAAAAATAAGAAAAAAG
21663025 GTAAAAAATTATAAG-AAAAA-
1 GTAAAAAA--ATAAGAAAAAAG
21663045 -TAAAAAAATAA-AAAAA
1 GTAAAAAAATAAGAAAAA
21663061 TACATAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
17 8 0.25
19 7 0.22
20 8 0.25
21 5 0.16
22 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (20 bp):
GTAAAAAAATAAGAAAAAAG
Found at i:21663049 original size:17 final size:16
Alignment explanation
Indices: 21663006--21663062 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 16
21662996 GCTTAAACTG
21663006 TAAAAAAATATGAAAAAA
1 TAAAAAAATA--AAAAAA
21663024 GGTAAAAAATTATAAGAAAAA
1 --TAAAAAA--ATAA-AAAAA
21663045 TAAAAAAATAAAAAAA
1 TAAAAAAATAAAAAAA
21663061 TA
1 TA
21663063 CATAATTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 7 0.21
17 4 0.12
19 7 0.21
20 8 0.24
21 5 0.15
22 3 0.09
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (16 bp):
TAAAAAAATAAAAAAA
Found at i:21663057 original size:7 final size:8
Alignment explanation
Indices: 21663006--21663062 Score: 51
Period size: 8 Copynumber: 6.2 Consensus size: 8
21662996 GCTTAAACTG
21663006 TAAAAAAA
1 TAAAAAAA
21663014 TATGAAAAAA
1 TA--AAAAAA
21663024 GGTAAAAAATTA
1 --TAAAAAA--A
21663036 TAAGAAAAA
1 TAA-AAAAA
21663045 TAAAAAAA
1 TAAAAAAA
21663053 TAAAAAAA
1 TAAAAAAA
21663061 TA
1 TA
21663063 CATAATTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
8 17 0.40
9 4 0.10
10 14 0.33
11 4 0.10
12 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (8 bp):
TAAAAAAA
Found at i:21663741 original size:219 final size:217
Alignment explanation
Indices: 21663180--21663744 Score: 603
Period size: 219 Copynumber: 2.6 Consensus size: 217
21663170 TCATAATTAG
* * **
21663180 TAATATGACAAATAAGAATTTAGA-AAAGAAA-TAT-ACAAGAGGTATAAAAGACACTCATATAA
1 TAATATGACAAATAATAA-TTAGAGAAAAAAAGTATCA-AAGAGAAATAAAAGACACTCATATAA
* *
21663242 CCTCTCATCCTTAAAAGAGATAGAAAATCATAAGTCACAAGAAAATTAAAAGTAAAAAATATAAA
64 -CTCTCATCCTTAAAAGTGATA-AAAATCATAAGTCACAAGAAAATAAAAAGTAAAAAATATAAA
*
21663307 TGTTACAAAATCGAAAATTTGATCAATAAATTTTAACAGATAATAGATTTAAAGAAAATGAATAC
127 TGTTACAAAATCGAAAATTTGATCAATAAATTTTAACAAATAATAGATTTAAAGAAAATGAATAC
* *
21663372 AAGAAAATCAAAGTCAATAATTCAAG
192 AAGAAAATCAAAGTCAATAAATCAAA
* *
21663398 TAATATGACAAATAATAATTAGGAGAAAAAAAGTATCAAAGAGAAATGAAAGAAACTCATATAAC
1 TAATATGACAAATAATAATTA-GAGAAAAAAAGTATCAAAGAGAAATAAAAGACACTCATATAAC
* * * * * * *
21663463 TCTCATTCTTAAAAGAT-ATAAAACACCATAAATTAGAAAAAAATATAAAGTAAAAAATATAAAT
65 TCTCATCCTTAAAAG-TGATAAAA-ATCATAAGTCACAAGAAAATAAAAAGTAAAAAATATAAAT
* * * * * * *
21663527 GTTACAAAATC-AAAGGTTTGATTAATCAAA-TTTCACAAATAATAGTTTTAAATAAATTGAGTA
128 GTTACAAAATCGAAA-ATTTGATCAAT-AAATTTTAACAAATAATAGATTTAAAGAAAATGAATA
21663590 CAAGAAAATCAAAAGTCAA-AAATCAAAA
191 CAAGAAAATC-AAAGTCAATAAATC-AAA
* * * *
21663618 TAATATGATAAATAATAATT-GA-AAGGAAAAGGTGT-AATAGA-AACATAAAATACACTCATAT
1 TAATATGACAAATAATAATTAGAGAA--AAAAAGTATCAA-AGAGAA-ATAAAAGACACTCATAT
* * * * *
21663679 AACTCTCACCCTTAAAAGTGATAAAAGATCATAAGTCATATGAAAATAAAAAATATAAAATATAA
62 AACTCTCATCCTTAAAAGTGATAAAA-ATCATAAGTCACAAGAAAATAAAAAGTAAAAAATATAA
21663744 A
126 A
21663745 AAGTTAATAG
Statistics
Matches: 289, Mismatches: 43, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
217 5 0.02
218 32 0.11
219 194 0.67
220 57 0.20
221 1 0.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (217 bp):
TAATATGACAAATAATAATTAGAGAAAAAAAGTATCAAAGAGAAATAAAAGACACTCATATAACT
CTCATCCTTAAAAGTGATAAAAATCATAAGTCACAAGAAAATAAAAAGTAAAAAATATAAATGTT
ACAAAATCGAAAATTTGATCAATAAATTTTAACAAATAATAGATTTAAAGAAAATGAATACAAGA
AAATCAAAGTCAATAAATCAAA
Found at i:21664015 original size:18 final size:19
Alignment explanation
Indices: 21663992--21664031 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
21663982 AAACAAAATT
*
21663992 ATTTCA-AAATTTTTATGA
1 ATTTCATAAATTTTTATAA
*
21664010 ATTTCATATATTTTTATAA
1 ATTTCATAAATTTTTATAA
21664029 ATT
1 ATT
21664032 ATTAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTTCATAAATTTTTATAA
Found at i:21664533 original size:32 final size:32
Alignment explanation
Indices: 21664495--21664590 Score: 97
Period size: 32 Copynumber: 3.0 Consensus size: 32
21664485 TTGTCAAAAA
*
21664495 TTATATCATTTTAAAAAATTAACTAAAAATTT
1 TTATATCATTTTAAAAAATTAAATAAAAATTT
** *
21664527 TTATATCGGTTTAAAAAATTAAATAAAAA-CT
1 TTATATCATTTTAAAAAATTAAATAAAAATTT
* * **
21664558 CTATATCATGTTAAAATAA-TATGTAAAAATTT
1 TTATATCATTTTAAAA-AATTAAATAAAAATTT
21664590 T
1 T
21664591 CAAAAATAGA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
31 21 0.42
32 29 0.58
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (32 bp):
TTATATCATTTTAAAAAATTAAATAAAAATTT
Found at i:21664771 original size:17 final size:18
Alignment explanation
Indices: 21664744--21664785 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
21664734 ATATTTAATA
21664744 TTTTA-AAAAATAA-ATT
1 TTTTATAAAAATAATATT
21664760 TTTTATAAAAATAATATT
1 TTTTATAAAAATAATATT
*
21664778 TTTAATAA
1 TTTTATAA
21664786 TTTTTTTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.22
17 8 0.35
18 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTTATAAAAATAATATT
Found at i:21665381 original size:21 final size:21
Alignment explanation
Indices: 21665357--21665396 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
21665347 TAAATTTATA
21665357 ATTTATGTA-AAAAAATTTGGC
1 ATTTAT-TACAAAAAATTTGGC
*
21665378 ATTTATTACAAAATATTTG
1 ATTTATTACAAAAAATTTG
21665397 AGTTTTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (21 bp):
ATTTATTACAAAAAATTTGGC
Found at i:21668778 original size:2 final size:2
Alignment explanation
Indices: 21668773--21668798 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21668763 TGTGTGTGTG
21668773 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
21668799 AGTTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21670377 original size:21 final size:21
Alignment explanation
Indices: 21670330--21670378 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
21670320 TAAGAAAAAA
21670330 AAAAATAAACAAATAAAATAC
1 AAAAATAAACAAATAAAATAC
** *
21670351 TTAAATAAATAAA-AAAATACC
1 AAAAATAAACAAATAAAATA-C
21670372 AAAAATA
1 AAAAATA
21670379 TTCGAAAATG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.18
Consensus pattern (21 bp):
AAAAATAAACAAATAAAATAC
Found at i:21671199 original size:20 final size:20
Alignment explanation
Indices: 21671169--21671207 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
21671159 ATAATTTAAT
21671169 TTAAAAAAATAAAA-AAAAG
1 TTAAAAAAATAAAATAAAAG
21671188 TTAAACAAAATAAAATAAAA
1 TTAAA-AAAATAAAATAAAA
21671208 TAAAACAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 9 0.50
21 4 0.22
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (20 bp):
TTAAAAAAATAAAATAAAAG
Found at i:21671999 original size:16 final size:15
Alignment explanation
Indices: 21671963--21671991 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21671953 CAAAAACTTT
21671963 CAAAAATTAAAATTA
1 CAAAAATTAAAATTA
21671978 CAAAAATTAAAATT
1 CAAAAATTAAAATT
21671992 TTGAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (15 bp):
CAAAAATTAAAATTA
Found at i:21672405 original size:3 final size:3
Alignment explanation
Indices: 21672397--21672423 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
21672387 ATCTAAAAAC
21672397 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
21672424 AACGTAACTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:21673559 original size:3 final size:3
Alignment explanation
Indices: 21673544--21673581 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
21673534 ATTAATGTGT
* *
21673544 ATA ATA GTA ATA ATA ATA ACA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
21673582 TTCGATTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:21673678 original size:2 final size:2
Alignment explanation
Indices: 21673671--21673703 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
21673661 GAGATAACTA
*
21673671 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21673704 AAATTGTTTT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:21674100 original size:2 final size:2
Alignment explanation
Indices: 21674093--21674132 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
21674083 TTTCTCCCAA
21674093 AT AT AT AT CA- AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT A
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21674133 AAGGATAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 32 0.91
3 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:21674269 original size:170 final size:164
Alignment explanation
Indices: 21673974--21674277 Score: 387
Period size: 169 Copynumber: 1.8 Consensus size: 164
21673964 TCAAGAGATG
* *
21673974 AGAGAGACAAGTAAAAATAAAAAAAATTTAATCTCATCCATTTGATCTATTGAAATCAAAAGTTT
1 AGAGAGACAAGTAAAAATAAAAAAAATTTAATCTCATCCATTTGATCTATTAAAATCAAAAGGTT
* * *** * **
21674039 AAAAAAAATATAAAACTAAAAAAGTTTTATATTGTGTAAGTTTATTTCTCCCAAATATATATCAA
66 AAAAAAAATATAAAACTAAAAAAATTTTACACCATGTAAATTTATCCCTCCCAAATATATAT--A
21674104 TATATATATATATATATAATATATATATAAAGGATA
129 TATATATATATATATATAATATATATATAAAGGATA
**
21674140 AGAGAGACAAGTAAAAATAGGAAAAAATAGTTTAATCTCAT-TTTTTGAATCTATTAAAATC-AA
1 AGAGAGACAAGTAAAAATA--AAAAAA-A-TTTAATCTCATCCATTTG-ATCTATTAAAATCAAA
* * *
21674203 TGGTTAAAAAAAATATAAAACTAAAAAAATTTTACACCATGTAAATTTATCCCTTCTCATATATA
61 AGGTTAAAAAAAATATAAAACTAAAAAAATTTTACACCATGTAAATTTATCCC-TCCCAAATATA
21674268 TATATATATA
125 TATATATATA
21674278 AATAATCAAG
Statistics
Matches: 117, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
166 19 0.16
168 13 0.11
169 50 0.43
170 35 0.30
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34
Consensus pattern (164 bp):
AGAGAGACAAGTAAAAATAAAAAAAATTTAATCTCATCCATTTGATCTATTAAAATCAAAAGGTT
AAAAAAAATATAAAACTAAAAAAATTTTACACCATGTAAATTTATCCCTCCCAAATATATATATA
TATATATATATATATAATATATATATAAAGGATA
Found at i:21674644 original size:30 final size:29
Alignment explanation
Indices: 21674594--21674706 Score: 86
Period size: 30 Copynumber: 3.7 Consensus size: 29
21674584 AATCCAAAAT
* *
21674594 TTTTTCCTTCTTTTCCTTTTTTCTTTTTTAA
1 TTTTCCCTTATTTT-CTTTTTTCTTTTTT-A
*
21674625 TTTTCCCTTATTTTATTTTTTGCTTCTTTT-
1 TTTTCCCTTATTTTCTTTTTT-CTT-TTTTA
* * * *
21674655 TCTTCCCTCATTTTCTTTCTTT-ATTTTCA
1 TTTTCCCTTATTTTCTTT-TTTCTTTTTTA
21674684 TTTTTCCCTTATTCTTCTTTTTT
1 -TTTTCCCTTATT-TTCTTTTTT
21674707 TTAAATAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
28 3 0.05
29 1 0.02
30 34 0.52
31 24 0.36
32 4 0.06
ACGTcount: A:0.07, C:0.21, G:0.01, T:0.71
Consensus pattern (29 bp):
TTTTCCCTTATTTTCTTTTTTCTTTTTTA
Found at i:21674654 original size:16 final size:16
Alignment explanation
Indices: 21674592--21674654 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
21674582 TTAATCCAAA
21674592 ATTTTTTCCTTCTTTT
1 ATTTTTTCCTTCTTTT
*
21674608 CCTTTTTT-CTT-TTTT
1 -ATTTTTTCCTTCTTTT
* * *
21674623 AATTTTCCCTTATTTT
1 ATTTTTTCCTTCTTTT
*
21674639 ATTTTTTGCTTCTTTT
1 ATTTTTTCCTTCTTTT
21674655 TCTTCCCTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
14 4 0.11
15 7 0.19
16 19 0.53
17 6 0.17
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.73
Consensus pattern (16 bp):
ATTTTTTCCTTCTTTT
Found at i:21674785 original size:22 final size:20
Alignment explanation
Indices: 21674753--21674795 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
21674743 TTTTTTGAAC
* *
21674753 TTTTTTGAAAACTTAATTTA
1 TTTTTTGAAAAATAAATTTA
21674773 TTTTTTGTTAAAAATAAATTTA
1 TTTTTTG--AAAAATAAATTTA
21674795 T
1 T
21674796 CTCTTAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTTTTGAAAAATAAATTTA
Found at i:21682191 original size:42 final size:42
Alignment explanation
Indices: 21682149--21682230 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
21682139 ATACTTTAAT
*
21682149 TTAAAATATTAAATTA-A-TAAAAA-TATTATATTTATGAATAA
1 TTAAAATA-TAAATTATAGTAAAAAGTAATAT-TTTATGAATAA
* *
21682190 TTAAGATATAATTTATAGTAAAAAGTAATATTTTATGAATA
1 TTAAAATATAAATTATAGTAAAAAGTAATATTTTATGAATA
21682231 TTATACTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
40 6 0.17
41 8 0.23
42 16 0.46
43 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.41
Consensus pattern (42 bp):
TTAAAATATAAATTATAGTAAAAAGTAATATTTTATGAATAA
Found at i:21690623 original size:26 final size:26
Alignment explanation
Indices: 21690574--21690644 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 26
21690564 GAAAAACTAG
* *
21690574 TAAAATTAAATAAAAAAATTTAAAAA
1 TAAAATAAAATAAAAAAATATAAAAA
21690600 TAAAATAAAATAAAATAAA-AT--AAA
1 TAAAATAAAATAAAA-AAATATAAAAA
21690624 TGAAAATGAAAATGAAAAAAA
1 T-AAAAT-AAAAT-AAAAAAA
21690645 AGAAACCTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
24 4 0.10
25 5 0.13
26 23 0.59
27 7 0.18
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (26 bp):
TAAAATAAAATAAAAAAATATAAAAA
Found at i:21690632 original size:6 final size:5
Alignment explanation
Indices: 21690574--21690645 Score: 60
Period size: 5 Copynumber: 14.0 Consensus size: 5
21690564 GAAAAACTAG
* *
21690574 TAAAA TTAAA TAAAA -AAATT TAAAAA TAAAA TAAAA TAAAA TAAAA T-AAA
1 TAAAA TAAAA TAAAA TAAA-A T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA
21690624 TGAAAA TGAAAA TGAAAA -AAAA
1 T-AAAA T-AAAA T-AAAA TAAAA
21690646 GAAACCTACG
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
4 11 0.19
5 28 0.48
6 16 0.28
7 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:21691058 original size:21 final size:21
Alignment explanation
Indices: 21691032--21691074 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
21691022 AATCCCAACT
21691032 CCATAAACCTAAAACTAAATC
1 CCATAAACCTAAAACTAAATC
**
21691053 CCATAAACCTAAATTTAAATC
1 CCATAAACCTAAAACTAAATC
21691074 C
1 C
21691075 AGAATCTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (21 bp):
CCATAAACCTAAAACTAAATC
Found at i:21691471 original size:3 final size:3
Alignment explanation
Indices: 21691458--21691638 Score: 148
Period size: 3 Copynumber: 62.3 Consensus size: 3
21691448 AATAAAAAAG
*
21691458 AAT AA- AAT AAT AAT AAT AAT AAT AAT AACC AAGT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AA-T AAT AAT AAT AAT
* * *
21691503 AAT AACC AAGT -AT CAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AGT
1 AAT AA-T AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
21691548 -AT AAC AAT AAT AAA AAT AAT AA- AGT -AT AAT AAT AAT GAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* **
21691593 AAT -AT AAT AA- AAT AAT AAT AGT AAT AAT GGT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21691638 A
1 A
21691639 TACTATATCA
Statistics
Matches: 143, Mismatches: 23, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
2 14 0.10
3 125 0.87
4 4 0.03
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:21691496 original size:22 final size:22
Alignment explanation
Indices: 21691470--21691529 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
21691460 TAAAATAATA
21691470 ATAATAATAATAATAACCAAGT
1 ATAATAATAATAATAACCAAGT
21691492 ATAATAATAATAATAACCAAGT
1 ATAATAATAATAATAACCAAGT
*
21691514 ATCATAATAATAATAA
1 ATAATAATAATAATAA
21691530 TAATAATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.28
Consensus pattern (22 bp):
ATAATAATAATAATAACCAAGT
Found at i:21691496 original size:28 final size:27
Alignment explanation
Indices: 21691464--21691620 Score: 133
Period size: 28 Copynumber: 5.7 Consensus size: 27
21691454 AAAGAATAAA
21691464 ATAATAATAATAATAATAATAACCAAGT
1 ATAATAATAATAATAATAATAA-CAAGT
* *
21691492 ATAATAATAATAATAACCAAGTATC-A-T
1 ATAATAATAATAATAA-TAA-TAACAAGT
*
21691519 AATAATAATAATAATAATAATAATAAAGT
1 -ATAATAATAATAATAATAATAA-CAAGT
* *
21691548 ATAACAATAATAAAAATAAT-A-AAGT
1 ATAATAATAATAATAATAATAACAAGT
* * * *
21691573 ATAATAATAATGATGATAATAATATAAT
1 ATAATAATAATAATAATAATAACA-AGT
* *
21691601 AAAATAATAATAGTAATAAT
1 ATAATAATAATAATAATAAT
21691621 GGTAATAATA
Statistics
Matches: 104, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
25 20 0.19
26 3 0.03
27 5 0.05
28 70 0.67
29 4 0.04
30 2 0.02
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (27 bp):
ATAATAATAATAATAATAATAACAAGT
Found at i:21691551 original size:25 final size:24
Alignment explanation
Indices: 21691458--21691638 Score: 117
Period size: 25 Copynumber: 7.4 Consensus size: 24
21691448 AATAAAAAAG
21691458 AATAA-AAT-AATAATAATAATAAT
1 AATAATAATAAAT-ATAATAATAAT
* *
21691481 AATAACCAAGTATA-ATAATAATAAT
1 AATAA-TAA-TAAATATAATAATAAT
*
21691506 AACCAAGT-ATCATAATAATAATAATAAT
1 AA-TAA-TAAT-A-AAT-ATAATAATAAT
*
21691534 AATAATAATAAAGTATAACAATAAT
1 AATAATAATAAA-TATAATAATAAT
*
21691559 AAAAATAATAAAGTATAATAATAAT
1 AATAATAATAAA-TATAATAATAAT
* *
21691584 GATGATAAT-AATATAATAA-AAT
1 AATAATAATAAATATAATAATAAT
* **
21691606 AATAATAGT-AATAATGGTAATAAT
1 AATAATAATAAAT-ATAATAATAAT
21691630 AAT-ATAATA
1 AATAATAATA
21691639 TACTATATCA
Statistics
Matches: 126, Mismatches: 18, Indels: 27
0.74 0.11 0.16
Matches are distributed among these distances:
22 12 0.10
23 22 0.17
24 9 0.07
25 58 0.46
26 7 0.06
27 5 0.04
28 13 0.10
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (24 bp):
AATAATAATAAATATAATAATAAT
Found at i:21691655 original size:37 final size:36
Alignment explanation
Indices: 21691458--21691638 Score: 123
Period size: 37 Copynumber: 5.1 Consensus size: 36
21691448 AATAAAAAAG
* *
21691458 AATAAAATAAT-A-ATAATAATAATAATAACCAAGTAT
1 AATAAAATAATAATATAATAATGATAATAA-TAA-TAT
* * *
21691494 AATAATAATAATAACCA-AGT-ATCATAATAATAATAAT
1 AATAA-AATAATAA-TATAATAATGATAATAATAAT-AT
**
21691531 AATAATAATAATAA-AGT-ATAACAATAATAA-AA-AT
1 AATAA-AATAATAATA-TAATAATGATAATAATAATAT
* *
21691565 AATAAAGT-AT-A-ATAATAATGATGATAATAATAT
1 AATAAAATAATAATATAATAATGATAATAATAATAT
*
21691598 AATAAAATAATAATAGTAATAATGGTAATAATAATAT
1 AATAAAATAATAATA-TAATAATGATAATAATAATAT
21691635 AATA
1 AATA
21691639 TACTATATCA
Statistics
Matches: 117, Mismatches: 13, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
30 1 0.01
31 12 0.10
32 4 0.03
33 11 0.09
34 9 0.08
35 2 0.02
36 10 0.09
37 55 0.47
38 10 0.09
39 2 0.02
40 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (36 bp):
AATAAAATAATAATATAATAATGATAATAATAATAT
Found at i:21691656 original size:10 final size:10
Alignment explanation
Indices: 21691520--21691709 Score: 88
Period size: 12 Copynumber: 18.1 Consensus size: 10
21691510 AAGTATCATA
21691520 ATAATAATAAT
1 ATAAT-ATAAT
21691531 AATAATAATAAT
1 -ATAAT-ATAAT
*
21691543 A-AAGTATAACA
1 ATAA-TATAA-T
*
21691554 ATAATA-AAA
1 ATAATATAAT
21691563 ATAATA-AAGT
1 ATAATATAA-T
21691573 ATAATAATAAT
1 ATAAT-ATAAT
*
21691584 GATGATAATAAT
1 -ATAAT-ATAAT
21691596 ATAATA-AA-
1 ATAATATAAT
*
21691604 ATAATAATAGT
1 ATAAT-ATAAT
*
21691615 AATAATGGTAAT
1 -ATAAT-ATAAT
21691627 AATAATATAAT
1 -ATAATATAAT
*
21691638 ATACTATATCAT
1 ATA--ATATAAT
21691650 ATAATAT-AT
1 ATAATATAAT
*
21691659 -TAATATACT
1 ATAATATAAT
*
21691668 ATACTATAAT
1 ATAATATAAT
*
21691678 AGTAAGATAAT
1 A-TAATATAAT
* *
21691689 AAAATATCAT
1 ATAATATAAT
21691699 ATAATATAAT
1 ATAATATAAT
21691709 A
1 A
21691710 ATAGTTCACA
Statistics
Matches: 142, Mismatches: 20, Indels: 34
0.72 0.10 0.17
Matches are distributed among these distances:
8 11 0.08
9 15 0.11
10 45 0.32
11 23 0.16
12 48 0.34
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (10 bp):
ATAATATAAT
Found at i:21691663 original size:54 final size:50
Alignment explanation
Indices: 21691554--21691712 Score: 123
Period size: 49 Copynumber: 3.2 Consensus size: 50
21691544 AAGTATAACA
* * * *
21691554 ATAATAAAAATAATA-AAGTATAATAATAATGATGATAATAATAT-A-ATAAA
1 ATAATAATAATACTATAA-TATAATAATAA-GATAATAA-AATATCATATAAT
* * * *
21691604 ATAATAATAGTA--ATAATGGTAATAATAATATAATATACTATATCATATAAT
1 ATAATAATAATACTATAAT-ATAATAATAAGATAATA-A-AATATCATATAAT
* * *
21691655 ATATTAAT-ATACTATACTATAATAGTAAGATAATAAAATATCATATAAT
1 ATAATAATAATACTATAATATAATAATAAGATAATAAAATATCATATAAT
21691704 ATAATAATA
1 ATAATAATA
21691713 GTTCACAAAC
Statistics
Matches: 85, Mismatches: 16, Indels: 16
0.73 0.14 0.14
Matches are distributed among these distances:
48 7 0.08
49 35 0.41
50 14 0.16
51 25 0.29
52 4 0.05
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (50 bp):
ATAATAATAATACTATAATATAATAATAAGATAATAAAATATCATATAAT
Found at i:21693642 original size:28 final size:28
Alignment explanation
Indices: 21693611--21693669 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
21693601 TAAGTCTCGC
*
21693611 TTTTGCTTTTTT-TTTCTATTTTTTCTTG
1 TTTTGATTTTTTATTT-TATTTTTTCTTG
* *
21693639 TTTTTATTTTTTATTTTATTTTTTTTTG
1 TTTTGATTTTTTATTTTATTTTTTCTTG
21693667 TTT
1 TTT
21693670 GTACATCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.83
Consensus pattern (28 bp):
TTTTGATTTTTTATTTTATTTTTTCTTG
Found at i:21698849 original size:20 final size:21
Alignment explanation
Indices: 21698801--21698851 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
21698791 ATTTAATCCC
21698801 AACTCCAAAAACCTAAAACTA
1 AACTCCAAAAACCTAAAACTA
* *
21698822 AACCCCAAAAACCTAAATCTA
1 AACTCCAAAAACCTAAAACTA
21698843 AA-TCCAAAA
1 AACTCCAAAA
21698852 TGCTCAGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (21 bp):
AACTCCAAAAACCTAAAACTA
Found at i:21699249 original size:3 final size:3
Alignment explanation
Indices: 21699231--21699332 Score: 74
Period size: 3 Copynumber: 36.3 Consensus size: 3
21699221 AATAAAAAAG
* *
21699231 AAT AA- AAT AA- AAT AAT AAT AAT AAT AAT AAT AA- AGT -AT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * **
21699275 AAT GAT GAT AAT AAT -AT AAT AA- GAT AAT AGT AGT AAT AAT GGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21699321 AAT AAT -AT AAT A
1 AAT AAT AAT AAT A
21699333 TACTATATCA
Statistics
Matches: 78, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
2 11 0.14
3 67 0.86
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21699287 original size:34 final size:35
Alignment explanation
Indices: 21699241--21699327 Score: 108
Period size: 34 Copynumber: 2.5 Consensus size: 35
21699231 AATAAAATAA
*
21699241 AATAATAATAATAATAATAATAA-AGT-ATAATAGT
1 AATAATGATAATAATAATAATAAGA-TAATAATAGT
* *
21699275 AATGATGATAATAAT-ATAATAAGATAATAGTAGT
1 AATAATGATAATAATAATAATAAGATAATAATAGT
*
21699309 AATAATGGTAATAATAATA
1 AATAATGATAATAATAATA
21699328 TAATATACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 8 0.18
34 34 0.76
35 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.32
Consensus pattern (35 bp):
AATAATGATAATAATAATAATAAGATAATAATAGT
Found at i:21699295 original size:5 final size:5
Alignment explanation
Indices: 21699231--21699403 Score: 70
Period size: 5 Copynumber: 32.8 Consensus size: 5
21699221 AATAAAAAAG
* *
21699231 AATAA AATAA AATAAT AATAAT AATAAT AATA- AAGTAT AATAGT AATGAT
1 AATAT AATAT AAT-AT AAT-AT AAT-AT AATAT AA-TAT AATA-T AAT-AT
* * * *
21699281 GATAAT AATAT -A-AT AAGAT AATAGT AGTAAT AATGGT AATAAT AATAT
1 AAT-AT AATAT AATAT AATAT AATA-T AAT-AT AAT-AT AAT-AT AATAT
* * *
21699329 AATAT ACTATAT CATAT AATAT -AT-T AATAT ACTAT ACTAT AATAGT
1 AATAT A--ATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA-T
* *
21699375 -CTGAT AATAT AATAT CATAT AATAT AATA
1 AAT-AT AATAT AATAT AATAT AATAT AATA
21699404 ATAGTACACA
Statistics
Matches: 133, Mismatches: 19, Indels: 32
0.72 0.10 0.17
Matches are distributed among these distances:
3 3 0.02
4 8 0.06
5 70 0.53
6 46 0.35
7 6 0.05
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:21699686 original size:96 final size:101
Alignment explanation
Indices: 21699580--21699766 Score: 258
Period size: 103 Copynumber: 1.9 Consensus size: 101
21699570 GAAAAATCAT
*
21699580 TCTAATTATAAAAAAAAATC-TAAT-AAAAA-T-ATTTAAATTAAAATTTATAAATAA-TAATAA
1 TCTAATTATAAAAAAAAATCATAATAAAAAATTAATTTAAATTAAAATTTATAAAAAATTAATAA
* *
21699640 TAATATTTTAATCAATCACTTTTAGCACTTTTCAAA
66 AAAGATTTTAATCAATCACTTTTAGCACTTTTCAAA
** *
21699676 TCTAATTATAAAAAAAGGTCTAATAATAAAAAATTAATTTAAATTAAAATTTATAAAAAATTACT
1 TCTAATTATAAAAAAAAATC--ATAATAAAAAATTAATTTAAATTAAAATTTATAAAAAATTAAT
*
21699741 AAAAAGATTTTAATTAATCACTTTTA
64 AAAAAGATTTTAATCAATCACTTTTA
21699767 ATATTTTTTG
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
96 18 0.23
99 4 0.05
100 5 0.06
101 1 0.01
102 23 0.30
103 26 0.34
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (101 bp):
TCTAATTATAAAAAAAAATCATAATAAAAAATTAATTTAAATTAAAATTTATAAAAAATTAATAA
AAAGATTTTAATCAATCACTTTTAGCACTTTTCAAA
Found at i:21700825 original size:2 final size:2
Alignment explanation
Indices: 21700812--21700842 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21700802 TATTCAGATA
*
21700812 AT AT AT AC 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
21700843 ATTATACCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:21705937 original size:21 final size:22
Alignment explanation
Indices: 21705897--21705997 Score: 82
Period size: 22 Copynumber: 4.7 Consensus size: 22
21705887 ACTTAAATAT
*
21705897 AATTAGT-ATAATTTAATAGT-
1 AATTAGTGATAACTTAATAGTA
*
21705917 AATTA-TCGATAACTTATTAGTA
1 AATTAGT-GATAACTTAATAGTA
*
21705939 AATTAGTGATAACTTAATAGCA
1 AATTAGTGATAACTTAATAGTA
** * * *
21705961 AACAAATGATAATTTAATAGTT
1 AATTAGTGATAACTTAATAGTA
* *
21705983 AATAATTGATAACTT
1 AATTAGTGATAACTT
21705998 TTTAGTGAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 5 0.08
21 11 0.17
22 46 0.72
23 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.39
Consensus pattern (22 bp):
AATTAGTGATAACTTAATAGTA
Found at i:21705949 original size:22 final size:21
Alignment explanation
Indices: 21705886--21705958 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 21
21705876 AATAATTAAA
21705886 AACTTAAATA-TAATTAGT-AT
1 AACTT-AATAGTAATTAGTGAT
*
21705906 AATTTAATAGTAATTA-TCGAT
1 AACTTAATAGTAATTAGT-GAT
*
21705927 AACTTATTAGTAAATTAGTGAT
1 AACTTAATAGT-AATTAGTGAT
21705949 AACTTAATAG
1 AACTTAATAG
21705959 CAAACAAATG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 5 0.11
20 10 0.23
21 11 0.25
22 17 0.39
23 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (21 bp):
AACTTAATAGTAATTAGTGAT
Found at i:21706187 original size:22 final size:22
Alignment explanation
Indices: 21706097--21706202 Score: 68
Period size: 22 Copynumber: 4.8 Consensus size: 22
21706087 CTAAATAAAG
* ** *
21706097 GATAACTTAACAAAAAATAAGT
1 GATAACTTAATAGTAAATTAGT
* * * *
21706119 GATAACTTAATCGTTATTTATT
1 GATAACTTAATAGTAAATTAGT
* * * * * *
21706141 GATAAATTAGTAATAACTCAAT
1 GATAACTTAATAGTAAATTAGT
21706163 GATAACTTAATAGTAAATTAGT
1 GATAACTTAATAGTAAATTAGT
* *
21706185 GATAATTTATTAGTAAAT
1 GATAACTTAATAGTAAAT
21706203 CAGTTTCAAC
Statistics
Matches: 60, Mismatches: 24, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (22 bp):
GATAACTTAATAGTAAATTAGT
Found at i:21706362 original size:22 final size:22
Alignment explanation
Indices: 21706234--21706756 Score: 182
Period size: 22 Copynumber: 23.7 Consensus size: 22
21706224 GAATTGATAT
* *
21706234 TAGTAAATCATAAATAATTTAG
1 TAGTAAATCATTAATAATTTAA
* * * *
21706256 TAATAAAT-AATGATAATTTAG
1 TAGTAAATCATTAATAATTTAA
* * *
21706277 TAGTAAATAATTGAT-AGTTAA
1 TAGTAAATCATTAATAATTTAA
*
21706298 GTAGTTAATCATTGAA-AATTTAA
1 -TAGTAAATCATT-AATAATTTAA
*
21706321 -AGTTAA--ATTAATGTAATTTAA
1 TAGTAAATCATTAA--TAATTTAA
*
21706342 TAGTAAATTATTAATAATTTAA
1 TAGTAAATCATTAATAATTTAA
* *
21706364 TAATAAATCA-TACATTATTTAA
1 TAGTAAATCATTA-ATAATTTAA
* *
21706386 TA-TAAATCAGTAATAATTTGA
1 TAGTAAATCATTAATAATTTAA
* * * *
21706407 TAGTGAATTATAAATAATTTAG
1 TAGTAAATCATTAATAATTTAA
* * * *
21706429 TAATAAATCAATGATAATTTTA
1 TAGTAAATCATTAATAATTTAA
* * *
21706451 TAGTAAATAATCAA-AAATTAA
1 TAGTAAATCATTAATAATTTAA
* * * *
21706472 GTAGTAAATCAATGATAATATAG
1 -TAGTAAATCATTAATAATTTAA
* **
21706495 TAGTAAAT-A-TACAGCAATACAA
1 TAGTAAATCATTA-A-TAATTTAA
* *
21706517 TAGTAAATCATTGATAATTTAG
1 TAGTAAATCATTAATAATTTAA
* **
21706539 TAGTAAATTAGTTAATCGTTGATAA
1 TAGTAAATCA-TTAATAATT--TAA
* * *
21706564 CTTTTTAGTAAATTATCT-ATAAATTAG
1 -----TAGTAAATCAT-TAATAATTTAA
* *
21706591 TAGCAAATCAGTT-ATAAATT--
1 TAGTAAATCA-TTAATAATTTAA
** *
21706611 TA-TAAATCATTAATAACATAG
1 TAGTAAATCATTAATAATTTAA
* * **
21706632 TGGTAAATTAACAATAATTTAA
1 TAGTAAATCATTAATAATTTAA
* *
21706654 TAG-AAATCATTCATAATTTGA
1 TAGTAAATCATTAATAATTTAA
* *
21706675 TAGTAAATCTTTAATAACTTAA
1 TAGTAAATCATTAATAATTTAA
* * * * *
21706697 T-GAAAAATTATTCATAAATTAG
1 TAG-TAAATCATTAATAATTTAA
* * *
21706719 TAATAAATCATTGATAATTTAG
1 TAGTAAATCATTAATAATTTAA
21706741 TAGTAAATCATTAATA
1 TAGTAAATCATTAATA
21706757 GCCTAGTAAT
Statistics
Matches: 366, Mismatches: 99, Indels: 72
0.68 0.18 0.13
Matches are distributed among these distances:
18 4 0.01
19 14 0.04
20 3 0.01
21 77 0.21
22 224 0.61
23 19 0.05
24 6 0.02
25 2 0.01
27 2 0.01
29 4 0.01
30 11 0.03
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (22 bp):
TAGTAAATCATTAATAATTTAA
Found at i:21706563 original size:30 final size:30
Alignment explanation
Indices: 21706517--21706578 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
21706507 AGCAATACAA
21706517 TAGTAAATCATTGATAA-TTTAGTAGTAAAT
1 TAGTAAATCATTGATAACTTT-GTAGTAAAT
* * *
21706547 TAGTTAATCGTTGATAACTTTTTAGTAAAT
1 TAGTAAATCATTGATAACTTTGTAGTAAAT
21706577 TA
1 TA
21706579 TCTATAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.44
Consensus pattern (30 bp):
TAGTAAATCATTGATAACTTTGTAGTAAAT
Found at i:21706726 original size:44 final size:43
Alignment explanation
Indices: 21706644--21706785 Score: 99
Period size: 44 Copynumber: 3.3 Consensus size: 43
21706634 GTAAATTAAC
* * * *
21706644 AATAATTTAATAGAAATCATTCATAATTTGATAGTAAATCTTT
1 AATAACTTAATAAAAATCATTCATAATTAGATAATAAATCTTT
* *
21706687 AATAACTTAATGAAAAATTATTCATAAATTAG-TAATAAATCATT
1 AATAACTTAAT-AAAAATCATTCAT-AATTAGATAATAAATCTTT
* * * * * ** **
21706731 GATAATTTAGTAGTAAATCATTAATAGCCTAG-TAATAAATCACT
1 AATAACTTAATA-AAAATCATTCATA-ATTAGATAATAAATCTTT
21706775 AATAACTTAAT
1 AATAACTTAAT
21706786 TATATTGATA
Statistics
Matches: 77, Mismatches: 18, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
43 12 0.16
44 60 0.78
45 5 0.06
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.37
Consensus pattern (43 bp):
AATAACTTAATAAAAATCATTCATAATTAGATAATAAATCTTT
Found at i:21707095 original size:22 final size:22
Alignment explanation
Indices: 21707068--21707147 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
21707058 AAAACAAATA
* *
21707068 ATAACTTAATAGTTAATTATTG
1 ATAACTTAATAGTAAATTAATG
* *
21707090 ATAACTTAATAATAAATCAATG
1 ATAACTTAATAGTAAATTAATG
* *
21707112 ATAATTTAATAGTAAATTAGTG
1 ATAACTTAATAGTAAATTAATG
21707134 ATAACTTAATAGTA
1 ATAACTTAATAGTA
21707148 TATCAGTTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (22 bp):
ATAACTTAATAGTAAATTAATG
Found at i:21707242 original size:22 final size:22
Alignment explanation
Indices: 21707173--21707244 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
21707163 ATTAAATGAT
21707173 AAATTTAGTA-TAAATCATTAA
1 AAATTTAGTAGTAAATCATTAA
* *
21707194 CAACTTAGTAGTAAATCAATT-A
1 AAATTTAGTAGTAAATC-ATTAA
* *
21707216 TAATTTAGTAGTTAATCATTAA
1 AAATTTAGTAGTAAATCATTAA
21707238 AAATTTA
1 AAATTTA
21707245 AAGGTAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
21 11 0.26
22 28 0.67
23 3 0.07
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (22 bp):
AAATTTAGTAGTAAATCATTAA
Found at i:21707322 original size:22 final size:22
Alignment explanation
Indices: 21707271--21707330 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
21707261 ACTTAGTAAT
*
21707271 AATAAATCATCGATAACTTAAT
1 AATAAATCATCGATAACTTAAA
* *
21707293 AGTTAATCAGT-GATAACTTAAA
1 AATAAATCA-TCGATAACTTAAA
*
21707315 AATAAATCATGGATAA
1 AATAAATCATCGATAA
21707331 TTTATATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (22 bp):
AATAAATCATCGATAACTTAAA
Found at i:21707517 original size:66 final size:67
Alignment explanation
Indices: 21707447--21707584 Score: 172
Period size: 66 Copynumber: 2.1 Consensus size: 67
21707437 AATATGGTAG
* * * *
21707447 TAAATTCA-TAATAAAATAATTGTAAATCATTAATAATTTAAATGTAAATTATTAATAACTTAAT
1 TAAATTCAGTAATAAAATAATTGCAAATCAATAATAATTTAAATGTAAATCAGTAATAACTTAAT
21707511 AA
66 AA
** * * * *
21707513 TAAA-TCAGTAATAATTTAGTTGCAAATCAATAATAATTTAATTGTAAATCAGTAATAATTTTAT
1 TAAATTCAGTAATAAAATAATTGCAAATCAATAATAATTTAAATGTAAATCAGTAATAACTTAAT
21707577 AA
66 AA
21707579 TAAATT
1 TAAATT
21707585 AGTTAATCAT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
65 3 0.05
66 56 0.93
67 1 0.02
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (67 bp):
TAAATTCAGTAATAAAATAATTGCAAATCAATAATAATTTAAATGTAAATCAGTAATAACTTAAT
AA
Found at i:21707571 original size:22 final size:22
Alignment explanation
Indices: 21707446--21707573 Score: 132
Period size: 22 Copynumber: 5.8 Consensus size: 22
21707436 TAATATGGTA
**
21707446 GTAAATTCA-TAATAAAATAATT
1 GTAAA-TCAGTAATAATTTAATT
* *
21707468 GTAAATCATTAATAATTTAAAT
1 GTAAATCAGTAATAATTTAATT
* * * *
21707490 GTAAATTATTAATAACTTAATA
1 GTAAATCAGTAATAATTTAATT
* *
21707512 ATAAATCAGTAATAATTTAGTT
1 GTAAATCAGTAATAATTTAATT
* *
21707534 GCAAATCAATAATAATTTAATT
1 GTAAATCAGTAATAATTTAATT
21707556 GTAAATCAGTAATAATTT
1 GTAAATCAGTAATAATTT
21707574 TATAATAAAT
Statistics
Matches: 86, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
21 3 0.03
22 83 0.97
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.39
Consensus pattern (22 bp):
GTAAATCAGTAATAATTTAATT
Found at i:21707593 original size:30 final size:30
Alignment explanation
Indices: 21707559--21707615 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
21707549 TTTAATTGTA
*
21707559 AATCAGTAATAATTTTATAATAAATTAGTT
1 AATCAGTAATAACTTTATAATAAATTAGTT
* * *
21707589 AATCATTGATAACTTTATAATTAATTA
1 AATCAGTAATAACTTTATAATAAATTA
21707616 TCAATAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (30 bp):
AATCAGTAATAACTTTATAATAAATTAGTT
Found at i:21707622 original size:22 final size:21
Alignment explanation
Indices: 21707597--21707694 Score: 81
Period size: 22 Copynumber: 4.4 Consensus size: 21
21707587 TTAATCATTG
*
21707597 ATAACTTTATAATTAATTATCA
1 ATAA-TTTATAATAAATTATCA
* * *
21707619 ATAAATTAATAAAAAAATTAAT-T
1 AT-AATTTAT-AATAAATT-ATCA
21707642 ATAACTTTATAATAAATTATCA
1 ATAA-TTTATAATAAATTATCA
* *
21707664 ATAATTTAGTAGTAAATCATCA
1 ATAATTTA-TAATAAATTATCA
21707686 ATAATTTAT
1 ATAATTTAT
21707695 TAGTAAATCA
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
21 7 0.11
22 38 0.62
23 14 0.23
24 2 0.03
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (21 bp):
ATAATTTATAATAAATTATCA
Found at i:21707770 original size:22 final size:22
Alignment explanation
Indices: 21707664--21707798 Score: 105
Period size: 22 Copynumber: 6.2 Consensus size: 22
21707654 TAAATTATCA
* **
21707664 ATAATTTAGTAGTAAATCATCA
1 ATAATTTTGTAGTAAATCATTG
*
21707686 ATAATTTAT-TAGTAAATCATTT
1 ATAATTT-TGTAGTAAATCATTG
* * ** **
21707708 ATAACTTAGTAGTACTTCAAAG
1 ATAATTTTGTAGTAAATCATTG
* *
21707730 CTAATTTAGTAGTAAATCATTG
1 ATAATTTTGTAGTAAATCATTG
**
21707752 ATAATTTTGTAGTGTATCATTG
1 ATAATTTTGTAGTAAATCATTG
21707774 ATAGA--TTGTAGTAAATCATTG
1 ATA-ATTTTGTAGTAAATCATTG
21707795 ATAA
1 ATAA
21707799 AATAATATTA
Statistics
Matches: 88, Mismatches: 22, Indels: 8
0.75 0.19 0.07
Matches are distributed among these distances:
20 1 0.01
21 17 0.19
22 69 0.78
23 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (22 bp):
ATAATTTTGTAGTAAATCATTG
Found at i:21708140 original size:22 final size:22
Alignment explanation
Indices: 21708106--21708160 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
21708096 ATCATAAGTT
*
21708106 ATCAAAAGATTACTAAAATTAC
1 ATCAAAAGATTACCAAAATTAC
* * **
21708128 ATCAAGAGGTTACCAAAATTTT
1 ATCAAAAGATTACCAAAATTAC
21708150 ATC-AAAGATTA
1 ATCAAAAGATTA
21708161 TTAAAATTGT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29
Consensus pattern (22 bp):
ATCAAAAGATTACCAAAATTAC
Found at i:21708243 original size:21 final size:21
Alignment explanation
Indices: 21708219--21708275 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
21708209 AACTAACTTT
21708219 GAAAGTTATCAAAATTGTATC
1 GAAAGTTATCAAAATTGTATC
* * *
21708240 GAAAGCTA-CTGAAATTTTATC
1 GAAAGTTATC-AAAATTGTATC
21708261 -AAAGGTTATCAAAAT
1 GAAA-GTTATCAAAAT
21708276 CAAAATTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
20 4 0.14
21 23 0.82
22 1 0.04
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (21 bp):
GAAAGTTATCAAAATTGTATC
Found at i:21708336 original size:26 final size:29
Alignment explanation
Indices: 21708283--21708336 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
21708273 AATCAAAATT
* *
21708283 ATATAAAAAATTATCAAATTTTACTTATA
1 ATATAAAAAATTATCAAATTTAAATTATA
21708312 ATATAAAAAA-TA-CAAA-TTAAATTAT
1 ATATAAAAAATTATCAAATTTAAATTAT
21708337 TAGCATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 7 0.30
27 4 0.17
28 2 0.09
29 10 0.43
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (29 bp):
ATATAAAAAATTATCAAATTTAAATTATA
Found at i:21708366 original size:69 final size:68
Alignment explanation
Indices: 21708280--21708423 Score: 159
Period size: 69 Copynumber: 2.1 Consensus size: 68
21708270 CAAAATCAAA
21708280 ATTA-TATAAAAAATTATCAAATTTTACTTATAATATA-AAAAAT-ACAAATTAAATTATTAGCA
1 ATTATTATAAAAAATTATCAAATTTTA-TTATAATATACAAAAATCA-AAATTAAATTATT-GCA
*
21708342 TTTATC
63 ATTATC
* * ** * * *
21708348 ATTATTATCAAAAGTTATCAGGTTTTATTATATTATACTAAAATCAAAATTAAATTATTGGAATT
1 ATTATTATAAAAAATTATCAAATTTTATTATAATATACAAAAATCAAAATTAAATTATTGCAATT
*
21708413 ATT
66 ATC
21708416 ATTATTAT
1 ATTATTAT
21708424 TATTATTATT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
68 27 0.42
69 36 0.56
70 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (68 bp):
ATTATTATAAAAAATTATCAAATTTTATTATAATATACAAAAATCAAAATTAAATTATTGCAATT
ATC
Found at i:21708418 original size:3 final size:3
Alignment explanation
Indices: 21708410--21708450 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
21708400 AATTATTGGA
21708410 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
21708451 AGTATAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:21714090 original size:26 final size:27
Alignment explanation
Indices: 21714058--21714110 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
21714048 CGACTATCAA
*
21714058 TTTTTCTTTATT-TTTTTA-TTTTATTT
1 TTTTTCTTT-TTAGTTTTATTTTTATTT
21714084 TTTTTCTTTTTAGTTTTATTTTTATTT
1 TTTTTCTTTTTAGTTTTATTTTTATTT
21714111 ATTGAGTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 2 0.08
26 14 0.58
27 8 0.33
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (27 bp):
TTTTTCTTTTTAGTTTTATTTTTATTT
Found at i:21716923 original size:20 final size:20
Alignment explanation
Indices: 21716882--21716938 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
21716872 AATTGTATTA
*
21716882 TTTTAA-TAAAAA-ATTATTT
1 TTTTAATTAAAAAGA-TATCT
21716901 TTTTAATTAAAAAGATATCT
1 TTTTAATTAAAAAGATATCT
*
21716921 TTTTGAATCATAAAAGAT
1 TTTT-AATTA-AAAAGAT
21716939 GAATTAATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 6 0.19
20 14 0.44
21 5 0.16
22 7 0.22
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (20 bp):
TTTTAATTAAAAAGATATCT
Found at i:21716923 original size:21 final size:20
Alignment explanation
Indices: 21716877--21716938 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 20
21716867 TCTTTAATTG
*
21716877 TATTATTTTAA-TAAAAA-A
1 TATTTTTTTAATTAAAAAGA
21716895 TTATTTTTTTAATTAAAAAGA
1 -TATTTTTTTAATTAAAAAGA
* *
21716916 TATCTTTTTGAATCATAAAAGA
1 TAT-TTTTTTAATTA-AAAAGA
21716938 T
1 T
21716939 GAATTAATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 10 0.28
20 9 0.25
21 10 0.28
22 7 0.19
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
TATTTTTTTAATTAAAAAGA
Found at i:21717676 original size:23 final size:23
Alignment explanation
Indices: 21717629--21717676 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
21717619 ATCTCAATTT
*
21717629 ATTCTCTCTCTAAAACTAAATCA
1 ATTCTCTCTCTAAAACTAAACCA
* *
21717652 ATTCTCTCTCTAAATCTAGACCA
1 ATTCTCTCTCTAAAACTAAACCA
21717675 AT
1 AT
21717677 CATCAAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.35
Consensus pattern (23 bp):
ATTCTCTCTCTAAAACTAAACCA
Found at i:21717800 original size:21 final size:21
Alignment explanation
Indices: 21717774--21717817 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
21717764 TTTTCATCTC
*
21717774 AATTCAT-TTTTTTCCTCTAAA
1 AATTCATCTTTTCT-CTCTAAA
21717795 AATTCATCTTTTCTCTCTAAA
1 AATTCATCTTTTCTCTCTAAA
21717816 AA
1 AA
21717818 CTTTACTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTCATCTTTTCTCTCTAAA
Found at i:21718701 original size:18 final size:19
Alignment explanation
Indices: 21718678--21718713 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
21718668 TTTTAGAAAG
21718678 AAAAAATAAATTA-AAATA
1 AAAAAATAAATTATAAATA
21718696 AAAAAATAAATTATAAAT
1 AAAAAATAAATTATAAAT
21718714 TATAAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAAATAAATTATAAATA
Found at i:21721981 original size:2 final size:2
Alignment explanation
Indices: 21721974--21722007 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
21721964 TCTTGCAAGC
21721974 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
21722008 GTATGTATGT
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:21726932 original size:26 final size:27
Alignment explanation
Indices: 21726874--21726927 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
21726864 TAATTATTTT
*
21726874 AATATAAAAAATAATAAATATTATATA
1 AATATTAAAAATAATAAATATTATATA
*
21726901 AATATTAAAATTAA-AAATATATATATA
1 AATATTAAAAATAATAAATAT-TATATA
21726928 GTATTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
AATATTAAAAATAATAAATATTATATA
Found at i:21728632 original size:18 final size:17
Alignment explanation
Indices: 21728609--21728657 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
21728599 TAAAAATATT
21728609 TAAATAATCTTATATAAA
1 TAAATAATCTTATAT-AA
*
21728627 TAAAT-ATAATTATATAA
1 TAAATAAT-CTTATATAA
*
21728644 TAAATAATCATATA
1 TAAATAATCTTATA
21728658 ATTACATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATAATCTTATATAA
Found at i:21728660 original size:23 final size:21
Alignment explanation
Indices: 21728622--21728669 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 21
21728612 ATAATCTTAT
*
21728622 ATAAATAAATATAATTATATA
1 ATAAATAAATATAATTACATA
21728643 ATAAATAATCATATAATTACATA
1 ATAAATAA--ATATAATTACATA
21728666 ATAA
1 ATAA
21728670 TTACTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 8 0.33
23 16 0.67
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAATAAATATAATTACATA
Found at i:21729496 original size:17 final size:17
Alignment explanation
Indices: 21729476--21729527 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
21729466 AACATTTTAG
21729476 TTTTTCCAACATAATTT
1 TTTTTCCAACATAATTT
***
21729493 TTTTGAAAACATAATTT
1 TTTTTCCAACATAATTT
21729510 TATTTTCACACACATAAT
1 T-TTTTC-CA-ACATAAT
21729528 GAATGTATGA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 15 0.58
18 3 0.12
19 1 0.04
20 7 0.27
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (17 bp):
TTTTTCCAACATAATTT
Found at i:21730771 original size:6 final size:6
Alignment explanation
Indices: 21730760--21730784 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21730750 CCACAGCCCG
21730760 TAGACA TAGACA TAGACA TAGACA T
1 TAGACA TAGACA TAGACA TAGACA T
21730785 TAGTGTTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (6 bp):
TAGACA
Found at i:21734982 original size:30 final size:30
Alignment explanation
Indices: 21734946--21735005 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
21734936 AGGCTAGATA
21734946 CCACTGAGTTCTCATGCAACTATTTTAAAT
1 CCACTGAGTTCTCATGCAACTATTTTAAAT
21734976 CCACTGAGTTCTCATGCAACTATTTTAAAT
1 CCACTGAGTTCTCATGCAACTATTTTAAAT
21735006 TCTTTCTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (30 bp):
CCACTGAGTTCTCATGCAACTATTTTAAAT
Found at i:21739315 original size:17 final size:19
Alignment explanation
Indices: 21739290--21739327 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
21739280 TAGCAGCTGC
*
21739290 AAAAGACAAAA-AAAA-AA
1 AAAAAACAAAACAAAACAA
21739307 AAAAAACAAAACAAAACAA
1 AAAAAACAAAACAAAACAA
21739326 AA
1 AA
21739328 GCAAGATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 4 0.22
19 4 0.22
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (19 bp):
AAAAAACAAAACAAAACAA
Found at i:21740444 original size:21 final size:19
Alignment explanation
Indices: 21740405--21740447 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
21740395 TCTTGTAAGA
*
21740405 AAAACAGTAATTCTTTATT
1 AAAACAGTAATTATTTATT
21740424 AAAACAGTAATAATATTTATT
1 AAAACAGTAAT--TATTTATT
21740445 AAA
1 AAA
21740448 TGTAGAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
21 10 0.48
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (19 bp):
AAAACAGTAATTATTTATT
Found at i:21750840 original size:30 final size:31
Alignment explanation
Indices: 21750787--21750851 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
21750777 AAATTCCTTA
* *
21750787 AAAAATGATACTATAAAAATT-AAATTTTTT
1 AAAAATAATACTACAAAAATTAAAATTTTTT
* *
21750817 AAAAATAATATTACAAAATTTAAAATTTTTT
1 AAAAATAATACTACAAAAATTAAAATTTTTT
21750848 AAAA
1 AAAA
21750852 GTACAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (31 bp):
AAAAATAATACTACAAAAATTAAAATTTTTT
Found at i:21751610 original size:10 final size:10
Alignment explanation
Indices: 21751564--21751627 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
21751554 AAACTTAACC
21751564 AATTCAAAAA
1 AATTCAAAAA
**
21751574 AA-TCTTAAA
1 AATTCAAAAA
* *
21751583 ATTTTAACAAA
1 AATTCAA-AAA
21751594 AATTTCAAAAA
1 AA-TTCAAAAA
21751605 AATTCAAAAA
1 AATTCAAAAA
*
21751615 AATTTAAAAA
1 AATTCAAAAA
21751625 AAT
1 AAT
21751628 AAAATTTTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
9 6 0.14
10 23 0.55
11 9 0.21
12 4 0.10
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (10 bp):
AATTCAAAAA
Found at i:21751730 original size:19 final size:19
Alignment explanation
Indices: 21751692--21751749 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
21751682 AAAATGAAAA
*
21751692 TAAAAAATCT-AAAACTTTT
1 TAAAAATTCTCAAAA-TTTT
*
21751711 TAAAAATTGTCAAATATTTT
1 TAAAAATTCTCAAA-ATTTT
*
21751731 TAAAAATTCTGAAAATTTT
1 TAAAAATTCTCAAAATTTT
21751750 AAATTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 13 0.39
20 19 0.58
21 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (19 bp):
TAAAAATTCTCAAAATTTT
Found at i:21751916 original size:17 final size:17
Alignment explanation
Indices: 21751896--21752036 Score: 54
Period size: 19 Copynumber: 7.9 Consensus size: 17
21751886 ATTTTTCAGA
21751896 ATTTTTTTAAAATTTTT
1 ATTTTTTTAAAATTTTT
** *
21751913 ATTTTTTTTTAATTTTAAA
1 ATTTTTTTAAAATTTT--T
* *
21751932 ATTTTTTAAAAGATTTTAG
1 ATTTTTTTAAA-ATTTT-T
* *
21751951 ATTTCTTT--AATTTTC
1 ATTTTTTTAAAATTTTT
***
21751966 AGTTTTTTATTCTATTTTT
1 A-TTTTTT-TAAAATTTTT
* * *
21751985 GAATTTTTAAGAAAATTTT
1 -ATTTTTTTA-AAATTTTT
*
21752004 ATTTTTATTAAAATTTTC
1 ATTTTT-TTAAAATTTTT
21752022 ATTTTTTT-AAATTTT
1 ATTTTTTTAAAATTTT
21752037 AAAATCTTTT
Statistics
Matches: 91, Mismatches: 23, Indels: 21
0.67 0.17 0.16
Matches are distributed among these distances:
15 1 0.01
16 17 0.19
17 18 0.20
18 17 0.19
19 32 0.35
20 6 0.07
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.64
Consensus pattern (17 bp):
ATTTTTTTAAAATTTTT
Found at i:21751920 original size:36 final size:38
Alignment explanation
Indices: 21751880--21751964 Score: 88
Period size: 36 Copynumber: 2.3 Consensus size: 38
21751870 ATGTTTAAGA
* * *
21751880 TTTTTAATTTTTCAGAATTTTTTTAAAA-TTTTTA-TTTT
1 TTTTTAATTTTT-A-AAATTTTTTAAAAGATTTTAGATTT
21751918 TTTTTAA-TTTTAAAATTTTTTAAAAGATTTTAGA-TT
1 TTTTTAATTTTTAAAATTTTTTAAAAGATTTTAGATTT
*
21751954 TCTTTAATTTT
1 TTTTTAATTTT
21751965 CAGTTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
35 12 0.30
36 14 0.35
37 7 0.17
38 7 0.17
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (38 bp):
TTTTTAATTTTTAAAATTTTTTAAAAGATTTTAGATTT
Found at i:21751960 original size:55 final size:54
Alignment explanation
Indices: 21751896--21752049 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
21751886 ATTTTTCAGA
* *
21751896 ATTTTTTTAAAATTTTTATTTTTTTTTAATTTTAAAATTTTTTAA-AAGATTTT
1 ATTTTTTTAAAATTTTCATTTTTTTTTAATTTTAAAATTTTTTAAGAAAATTTT
* **
21751949 AGATTTCTTT--AATTTTCAGTTTTTTATTCT-ATTTTTGAA-TTTTTAAGAAAATTTT
1 --ATTTTTTTAAAATTTTCA-TTTTTT-TT-TAATTTTAAAATTTTTTAAGAAAATTTT
*
21752004 ATTTTTATTAAAATTTTCA-TTTTTTTAAATTTTAAAATCTTTTTAA
1 ATTTTT-TTAAAATTTTCATTTTTTTTTAATTTTAAAAT-TTTTTAA
21752050 CTTTGGGATT
Statistics
Matches: 80, Mismatches: 9, Indels: 20
0.73 0.08 0.18
Matches are distributed among these distances:
53 21 0.26
54 20 0.25
55 30 0.38
56 9 0.11
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (54 bp):
ATTTTTTTAAAATTTTCATTTTTTTTTAATTTTAAAATTTTTTAAGAAAATTTT
Found at i:21752009 original size:18 final size:18
Alignment explanation
Indices: 21751987--21752027 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
21751977 CTATTTTTGA
21751987 ATTTTTAAGAAAATTTT-
1 ATTTTTAAGAAAATTTTC
**
21752004 ATTTTTATTAAAATTTTC
1 ATTTTTAAGAAAATTTTC
21752022 ATTTTT
1 ATTTTT
21752028 TTAAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTTTAAGAAAATTTTC
Found at i:21752035 original size:16 final size:17
Alignment explanation
Indices: 21751996--21752037 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
21751986 AATTTTTAAG
21751996 AAAATTTTATTTTTATT
1 AAAATTTTATTTTTATT
21752013 AAAATTTTCATTTTT-TT
1 AAAATTTT-ATTTTTATT
21752030 -AAATTTTA
1 AAAATTTTA
21752038 AAATCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.04
16 7 0.29
17 10 0.42
18 6 0.25
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
AAAATTTTATTTTTATT
Found at i:21752118 original size:9 final size:9
Alignment explanation
Indices: 21752104--21752164 Score: 70
Period size: 9 Copynumber: 6.7 Consensus size: 9
21752094 TGAATGGTTA
21752104 AAAATTTTT
1 AAAATTTTT
21752113 AAAA-TTTT
1 AAAATTTTT
*
21752121 AGAATTTTT
1 AAAATTTTT
*
21752130 AAAGTTTTT
1 AAAATTTTT
*
21752139 AAAAATGTTT
1 -AAAATTTTT
21752149 AAAATTTTTT
1 AAAA-TTTTT
21752159 AAAATT
1 AAAATT
21752165 CTTTTGAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 7 0.16
9 21 0.49
10 15 0.35
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (9 bp):
AAAATTTTT
Found at i:21752120 original size:27 final size:26
Alignment explanation
Indices: 21752081--21752142 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
21752071 TTTAAGATTT
* * *
21752081 TTTTTTAATTTTTTGAATGGTTAAAAA
1 TTTTTAAAATTTTAGAAT-GTTAAAAA
* * *
21752108 TTTTTAAAATTTTAGAATTTTTAAAG
1 TTTTTAAAATTTTAGAATGTTAAAAA
21752134 TTTTTAAAA
1 TTTTTAAAA
21752143 ATGTTTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (26 bp):
TTTTTAAAATTTTAGAATGTTAAAAA
Found at i:21752174 original size:11 final size:10
Alignment explanation
Indices: 21752101--21752177 Score: 63
Period size: 10 Copynumber: 8.0 Consensus size: 10
21752091 TTTTGAATGG
*
21752101 TTAAAAATTT
1 TTAAAATTTT
21752111 TTAAAA--TT
1 TTAAAATTTT
*
21752119 TTAGAA-TTT
1 TTAAAATTTT
*
21752128 TT-AAAGTTT
1 TTAAAATTTT
* *
21752137 TTAAAAATGT
1 TTAAAATTTT
21752147 TTAAAATTTT
1 TTAAAATTTT
21752157 TTAAAATTCTT
1 TTAAAATT-TT
*
21752168 TTGAAATTTT
1 TTAAAATTTT
21752178 CTTTTAATAC
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
8 9 0.16
9 9 0.16
10 29 0.52
11 9 0.16
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (10 bp):
TTAAAATTTT
Found at i:21752817 original size:3 final size:3
Alignment explanation
Indices: 21752811--21752846 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
21752801 AATAATAATA
21752811 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
21752847 GAGCCAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:21753082 original size:93 final size:93
Alignment explanation
Indices: 21752923--21753115 Score: 291
Period size: 93 Copynumber: 2.1 Consensus size: 93
21752913 CCCTTAGTTA
** * * *
21752923 TATGTATTGGATTTGAATCTCAATTCTGTTGGATACTATCTCTAAAGGGTAATTTACATGAACTA
1 TATGTATTGGATTTGAATCTCAAACCTATTGGATACCATCTCTAAAGGATAATTTACATGAACTA
* *
21752988 ACTAAACTATGTTTTGGGTTTATTATT-T
66 ACTAAACTAAGTTTT-GGATTATTATTAT
*
21753016 TATGTATTGGATTTGAATCTCAAACCTATTGGATACCATCTCTAAAGGATAATTTGCATGAACTA
1 TATGTATTGGATTTGAATCTCAAACCTATTGGATACCATCTCTAAAGGATAATTTACATGAACTA
21753081 ACTAAACTAAGTTTTGGATTATTATTAT
66 ACTAAACTAAGTTTTGGATTATTATTAT
21753109 TAT-TATT
1 TATGTATT
21753116 ATTATTATTA
Statistics
Matches: 91, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
92 14 0.15
93 77 0.85
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (93 bp):
TATGTATTGGATTTGAATCTCAAACCTATTGGATACCATCTCTAAAGGATAATTTACATGAACTA
ACTAAACTAAGTTTTGGATTATTATTAT
Found at i:21753106 original size:3 final size:3
Alignment explanation
Indices: 21753098--21753129 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
21753088 TAAGTTTTGG
21753098 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
21753130 AAAGTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:21756302 original size:50 final size:50
Alignment explanation
Indices: 21756179--21756312 Score: 133
Period size: 50 Copynumber: 2.7 Consensus size: 50
21756169 TTGCATTTGT
* * * * *
21756179 ATAATTGTTTGAATCATTCATTTGTGTTATTTAGGGAATTTATAAACTAC
1 ATAATTGTTTGAATCATGCATTTGTATCATTTGGGGAATATATAAACTAC
* * * * * * * *
21756229 GTAATTGTGTGGATAATGTATTTGCATCATTTGGGGAATATATAAATTGC
1 ATAATTGTTTGAATCATGCATTTGTATCATTTGGGGAATATATAAACTAC
* *
21756279 ATAATTGTTTGTATCATGCATTTGTATCTTTTGG
1 ATAATTGTTTGAATCATGCATTTGTATCATTTGG
21756313 TGAGAATTTA
Statistics
Matches: 64, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (50 bp):
ATAATTGTTTGAATCATGCATTTGTATCATTTGGGGAATATATAAACTAC
Found at i:21756358 original size:46 final size:45
Alignment explanation
Indices: 21756297--21756413 Score: 153
Period size: 45 Copynumber: 2.6 Consensus size: 45
21756287 TTGTATCATG
* * * * * *
21756297 CATTTGTATCTTTTGGTGAGAATTTAAATTATTATTTTGAATATTC
1 CATTTGCATCATTTGGTGAGCATTTAAATCATT-GTTTGAATATTA
*
21756343 CATTTGCATCATTTGGTGAGCATCTAAATCATTGTTTGAATATTA
1 CATTTGCATCATTTGGTGAGCATTTAAATCATTGTTTGAATATTA
*
21756388 CATTTGCATCATTTAGTGAGCATTTA
1 CATTTGCATCATTTGGTGAGCATTTA
21756414 GATCTTTGAC
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
45 34 0.55
46 28 0.45
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (45 bp):
CATTTGCATCATTTGGTGAGCATTTAAATCATTGTTTGAATATTA
Found at i:21757141 original size:43 final size:44
Alignment explanation
Indices: 21757066--21757183 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 44
21757056 ATACCTCTTT
** * *
21757066 GAATTTTCAAATGTGAATAATTGTATTCTAGATGCGAATCTCTA
1 GAATTTTCAAATGTGAATTTTTGAATTTTAGATGCGAATCTCTA
**
21757110 -AATTTTCAAATGTGAATTTTTGAATTTTAGATTTGAATCTCTA
1 GAATTTTCAAATGTGAATTTTTGAATTTTAGATGCGAATCTCTA
* * *
21757153 GAGTTTTTCAAGA-GTGAAATTTTAAATTTTA
1 GA-ATTTTCAA-ATGTGAATTTTTGAATTTTA
21757184 CATGTGGATC
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
43 37 0.60
44 1 0.02
45 23 0.37
46 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (44 bp):
GAATTTTCAAATGTGAATTTTTGAATTTTAGATGCGAATCTCTA
Found at i:21757430 original size:20 final size:19
Alignment explanation
Indices: 21757405--21757494 Score: 62
Period size: 20 Copynumber: 4.6 Consensus size: 19
21757395 TTTGAATATG
21757405 AATCTTTGAAATTATTTGCA
1 AATCTTT-AAATTATTTGCA
*
21757425 AATCTTTACA--A-TTGCAA
1 AATCTTTAAATTATTTGC-A
*
21757442 AAT-TTTAAATTTCATTTGTA
1 AATCTTTAAA-TT-ATTTGCA
* *
21757462 AATCTTTGAAATTATTTACG
1 AATCTTT-AAATTATTTGCA
21757482 AATCTTTACAATT
1 AATCTTTA-AATT
21757495 GAAATTTTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
16 9 0.16
17 5 0.09
19 3 0.05
20 27 0.49
21 8 0.15
22 3 0.05
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (19 bp):
AATCTTTAAATTATTTGCA
Found at i:21757471 original size:57 final size:57
Alignment explanation
Indices: 21757405--21757524 Score: 188
Period size: 57 Copynumber: 2.1 Consensus size: 57
21757395 TTTGAATATG
*
21757405 AATCTTTGAAATTATTTGCAAATCTTTACAATTGCAAAATTTT-AAATTTCATTTGTA
1 AATCTTTGAAATTATTTACAAATCTTTACAATTG-AAAATTTTGAAATTTCATTTGTA
* * *
21757462 AATCTTTGAAATTATTTACGAATCTTTACAATTGAAATTTTTGAAATTTCATTTGTG
1 AATCTTTGAAATTATTTACAAATCTTTACAATTGAAAATTTTGAAATTTCATTTGTA
21757519 AATCTT
1 AATCTT
21757525 GGAACTCTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
56 7 0.12
57 51 0.88
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (57 bp):
AATCTTTGAAATTATTTACAAATCTTTACAATTGAAAATTTTGAAATTTCATTTGTA
Found at i:21757559 original size:151 final size:151
Alignment explanation
Indices: 21757389--21757683 Score: 545
Period size: 151 Copynumber: 2.0 Consensus size: 151
21757379 CTTTGAATAT
*
21757389 TTGGTTTTTGAATATGAATCTTTGAAATTATTTGCAAATCTTTACAATTGCAAAATTTTAAATTT
1 TTGGTTTTCGAATATGAATCTTTGAAATTATTTGCAAATCTTTACAATTGCAAAATTTTAAATTT
*
21757454 CATTTGTAAATCTTTGAAATTATTTACGAATCTTTACAATTGAAATTTTTGAAATTTCATTTGTG
66 CATTTGTAAATCTTTGAAATTATTTACGAATCTTTACAATTGAAAATTTTGAAATTTCATTTGTG
21757519 AATCTTGGAACTCTTGCATAA
131 AATCTTGGAACTCTTGCATAA
* *
21757540 TTGGTTTTCGAATATGAATCTTTGAAATTATTTGCGAATCTTTACAATTGTAAAATTTTAAATTT
1 TTGGTTTTCGAATATGAATCTTTGAAATTATTTGCAAATCTTTACAATTGCAAAATTTTAAATTT
*
21757605 CATTTGTAAATCTTTGAAATTATTTATGAATCTTTACAATTGAAAATTTTGAAATTTCATTTGTG
66 CATTTGTAAATCTTTGAAATTATTTACGAATCTTTACAATTGAAAATTTTGAAATTTCATTTGTG
21757670 AATCTTGGAACTCT
131 AATCTTGGAACTCT
21757684 AGTGATCTTT
Statistics
Matches: 139, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
151 139 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (151 bp):
TTGGTTTTCGAATATGAATCTTTGAAATTATTTGCAAATCTTTACAATTGCAAAATTTTAAATTT
CATTTGTAAATCTTTGAAATTATTTACGAATCTTTACAATTGAAAATTTTGAAATTTCATTTGTG
AATCTTGGAACTCTTGCATAA
Found at i:21757617 original size:57 final size:57
Alignment explanation
Indices: 21757556--21757675 Score: 197
Period size: 57 Copynumber: 2.1 Consensus size: 57
21757546 TTCGAATATG
*
21757556 AATCTTTGAAATTATTTGCGAATCTTTACAATTGTAAAATTTT-AAATTTCATTTGTA
1 AATCTTTGAAATTATTTACGAATCTTTACAATTG-AAAATTTTGAAATTTCATTTGTA
* *
21757613 AATCTTTGAAATTATTTATGAATCTTTACAATTGAAAATTTTGAAATTTCATTTGTG
1 AATCTTTGAAATTATTTACGAATCTTTACAATTGAAAATTTTGAAATTTCATTTGTA
21757670 AATCTT
1 AATCTT
21757676 GGAACTCTAG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
56 8 0.14
57 51 0.86
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.47
Consensus pattern (57 bp):
AATCTTTGAAATTATTTACGAATCTTTACAATTGAAAATTTTGAAATTTCATTTGTA
Found at i:21757629 original size:20 final size:19
Alignment explanation
Indices: 21757556--21757645 Score: 53
Period size: 20 Copynumber: 4.6 Consensus size: 19
21757546 TTCGAATATG
**
21757556 AATCTTTGAAATTATTTGCG
1 AATCTTT-AAATTATTTGTA
*
21757576 AATCTTTACA--A-TTGTAA
1 AATCTTTAAATTATTTGT-A
21757593 AAT-TTTAAATTTCATTTGTA
1 AATCTTTAAA-TT-ATTTGTA
* *
21757613 AATCTTTGAAATTATTTATG
1 AATCTTT-AAATTATTTGTA
21757633 AATCTTTACAATT
1 AATCTTTA-AATT
21757646 GAAAATTTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
16 8 0.15
17 4 0.07
19 3 0.05
20 28 0.51
21 9 0.16
22 3 0.05
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.48
Consensus pattern (19 bp):
AATCTTTAAATTATTTGTA
Found at i:21757709 original size:35 final size:36
Alignment explanation
Indices: 21757661--21757738 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 36
21757651 TTTTGAAATT
**
21757661 TCATTTGTGAATCTTGGAACTCTAGTGA-TCTTTGA
1 TCATTTGAAAATCTTGGAACTCTAGTGAGTCTTTGA
* * *
21757696 TCATTTGAAAATCTTTGAACTCTTGTGAGTTTTTGA
1 TCATTTGAAAATCTTGGAACTCTAGTGAGTCTTTGA
*
21757732 TCTTTTG
1 TCATTTG
21757739 TGAATCTCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 24 0.67
36 12 0.33
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (36 bp):
TCATTTGAAAATCTTGGAACTCTAGTGAGTCTTTGA
Found at i:21757745 original size:36 final size:35
Alignment explanation
Indices: 21757661--21757765 Score: 113
Period size: 36 Copynumber: 2.9 Consensus size: 35
21757651 TTTTGAAATT
* *
21757661 TCATTTGTGAATCTTGGAACTCTAGTGATCTTTGA
1 TCATTTGTGAATCTTTGAACTCTTGTGATCTTTGA
** *
21757696 TCATTTGAAAATCTTTGAACTCTTGTGAGTTTTTGA
1 TCATTTGTGAATCTTTGAACTCTTGTGA-TCTTTGA
* *
21757732 TCTTTTGTGAATCTCT-AATCTCTTGTGAATCTTT
1 TCATTTGTGAATCTTTGAA-CTCTTGTG-ATCTTT
21757766 AAACTTTTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
35 26 0.46
36 30 0.53
37 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (35 bp):
TCATTTGTGAATCTTTGAACTCTTGTGATCTTTGA
Found at i:21757752 original size:18 final size:18
Alignment explanation
Indices: 21757731--21757775 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
21757721 TGAGTTTTTG
21757731 ATCTTTTGTGAATCTCTA
1 ATCTTTTGTGAATCTCTA
* *
21757749 ATCTCTTGTGAATCTTTA
1 ATCTTTTGTGAATCTCTA
*
21757767 AACTTTTGT
1 ATCTTTTGT
21757776 TTATTTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (18 bp):
ATCTTTTGTGAATCTCTA
Found at i:21757969 original size:22 final size:22
Alignment explanation
Indices: 21757944--21757997 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 22
21757934 GAGTGAACCG
21757944 TTAAATTTCAAATTATGAATCT
1 TTAAATTTCAAATTATGAATCT
* *
21757966 TTAAAAATTTCAAATTGTGAATTT
1 TT--AAATTTCAAATTATGAATCT
*
21757990 TTTAATTT
1 TTAAATTT
21757998 TAGCATATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 7 0.26
24 20 0.74
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (22 bp):
TTAAATTTCAAATTATGAATCT
Found at i:21763549 original size:52 final size:49
Alignment explanation
Indices: 21763448--21763549 Score: 114
Period size: 52 Copynumber: 2.0 Consensus size: 49
21763438 TTGACAATTG
* * * *
21763448 AAAATTTTTATCTAGAAAAGGCTCTTCTATGTAGAGGTTTAACAGCTTT
1 AAAATTTTTATCTAGAAAAGGCTCTTCTATGTAAAGGCTCAACAACTTT
* * *
21763497 AAAATTTTTCATCTTGAAAAGGGGTTCTTTTATGTAAAGGCTCAACAACTTT
1 AAAATTTTT-ATCTAGAAAA--GGCTCTTCTATGTAAAGGCTCAACAACTTT
21763549 A
1 A
21763550 GAAAAAATTC
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
49 9 0.21
50 9 0.21
52 25 0.58
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (49 bp):
AAAATTTTTATCTAGAAAAGGCTCTTCTATGTAAAGGCTCAACAACTTT
Found at i:21763653 original size:54 final size:53
Alignment explanation
Indices: 21763463--21763930 Score: 264
Period size: 54 Copynumber: 9.0 Consensus size: 53
21763453 TTTTATCTAG
* * * * * * *
21763463 AAAAGGCTCTTCTATGTAGAGGTTTAACAGCTTT--AAAATTTTTCATCTTGA
1 AAAAGGCTCCTCTAGGTAGAGGCTCAACAACTTTAAAAAAATTCTCATCTTGA
* * * * * *
21763514 AAAGGGGTTCTTTTATGTAAAGGCTCAACAACTTTAGAAAAAATTCTCATCTTGA
1 AAA-AGGCTCCTCTAGGTAGAGGCTCAACAACTTTA-AAAAAATTCTCATCTTGA
* * * *
21763569 AAAAGACTCC-CTTAGGTAGAGACTCTACAACTTTAAAAAAAAATCTCATCTTGA
1 AAAAGGCTCCTC-TAGGTAGAGGCTCAACAACTTT-AAAAAAATTCTCATCTTGA
* * * * * * *
21763623 AAAAAGCTCCTCTAGTTAGTGGTTCAACAACTTT---AAAATTCTTATATGGA
1 AAAAGGCTCCTCTAGGTAGAGGCTCAACAACTTTAAAAAAATTCTCATCTTGA
* * * * * *
21763673 AAAGGGCTCATCTATGTAGATGCTTAATAACTTT--AAAAATTCTCATCTTGA
1 AAAAGGCTCCTCTAGGTAGAGGCTCAACAACTTTAAAAAAATTCTCATCTTGA
* * * **
21763724 AAAAGGCTCCTTTAGGTAAAGGCTCAACAACTTAAAAAAAAAAACTCATCTTGA
1 AAAAGGCTCCTCTAGGTAGAGGCTCAACAACTT-TAAAAAAATTCTCATCTTGA
* * * * *
21763778 AAAAGGCTCTTATAAGTAGAGGCTAAACAACTTT---AAAATTCTTAT-TTG-
1 AAAAGGCTCCTCTAGGTAGAGGCTCAACAACTTTAAAAAAATTCTCATCTTGA
* * * * * * * * *
21763826 AAAAGGCCTGCTTTATGTTGAGGCTTAATAACTTT--AAAAATTTTTATCTTAA
1 AAAAGG-CTCCTCTAGGTAGAGGCTCAACAACTTTAAAAAAATTCTCATCTTGA
* ** * * *
21763878 AAAAGACTTATCTAGGTAGAAGCTTAACAATTTTAAACAAAATTCTTCATCTT
1 AAAAGGCTCCTCTAGGTAGAGGCTCAACAACTTTAAA-AAAATTC-TCATCTT
21763931 TTCTCGAAAC
Statistics
Matches: 315, Mismatches: 83, Indels: 34
0.73 0.19 0.08
Matches are distributed among these distances:
48 6 0.02
49 24 0.08
50 54 0.17
51 63 0.20
52 29 0.09
53 1 0.00
54 112 0.36
55 26 0.08
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (53 bp):
AAAAGGCTCCTCTAGGTAGAGGCTCAACAACTTTAAAAAAATTCTCATCTTGA
Found at i:21763894 original size:154 final size:155
Alignment explanation
Indices: 21763463--21763895 Score: 460
Period size: 155 Copynumber: 2.8 Consensus size: 155
21763453 TTTTATCTAG
* * * * * * *
21763463 AAAAGGCTCTTCTATGTAGAGGTTTAACAGCTTTAAAATTTTTCATCTTGAAAAGGGGTTCTTTT
1 AAAAGGCTCTTCTAAGTAGAGGTTAAACAACTTTAAAATTCTT-ATATTGAAAA-GGGCTCATTT
* * * * *
21763528 ATGTAAAGGCTCAACAACTTTAGAAAAAATTCTCATCTTGAAAAAGAC-TCCCTTAGGTAGAGAC
64 ATGTAGAGGCTTAATAACTTT---AAAAATTCTCATCTTGAAAAAGACTTCTC-TAGGTAAAGAC
* * *
21763592 TCTACAACTTTAAAAAAAAATCTCATCTTGA
125 TCAACAACTTAAAAAAAAAAACTCATCTTGA
* * * * * *
21763623 AAAAAGCTCCTCT-AGTTAGTGGTTCAACAACTTTAAAATTCTTATATGGAAAAGGGCTCATCTA
1 AAAAGGCTCTTCTAAG-TAGAGGTTAAACAACTTTAAAATTCTTATATTGAAAAGGGCTCATTTA
* * * * *
21763687 TGTAGATGCTTAATAACTTTAAAAATTCTCATCTTGAAAAAGGCTCCTTTAGGTAAAGGCTCAAC
65 TGTAGAGGCTTAATAACTTTAAAAATTCTCATCTTGAAAAAGACTTCTCTAGGTAAAGACTCAAC
21763752 AACTTAAAAAAAAAAACTCATCTTGA
130 AACTTAAAAAAAAAAACTCATCTTGA
* * *
21763778 AAAAGGCTCTTATAAGTAGAGGCTAAACAACTTTAAAATTCTTAT-TTGAAAAGGCCTGC-TTTA
1 AAAAGGCTCTTCTAAGTAGAGGTTAAACAACTTTAAAATTCTTATATTGAAAAGGGCT-CATTTA
* * * * *
21763841 TGTTGAGGCTTAATAACTTTAAAAATTTTTATCTTAAAAAAGACTTATCTAGGTA
65 TGTAGAGGCTTAATAACTTTAAAAATTCTCATCTTGAAAAAGACTTCTCTAGGTA
21763896 GAAGCTTAAC
Statistics
Matches: 226, Mismatches: 43, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
154 59 0.26
155 97 0.43
156 3 0.01
158 24 0.11
159 9 0.04
160 34 0.15
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (155 bp):
AAAAGGCTCTTCTAAGTAGAGGTTAAACAACTTTAAAATTCTTATATTGAAAAGGGCTCATTTAT
GTAGAGGCTTAATAACTTTAAAAATTCTCATCTTGAAAAAGACTTCTCTAGGTAAAGACTCAACA
ACTTAAAAAAAAAAACTCATCTTGA
Found at i:21771271 original size:18 final size:16
Alignment explanation
Indices: 21771250--21771283 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
21771240 ATATTATTTT
21771250 TTAAATATAATTATATAA
1 TTAAATA-AA-TATATAA
21771268 TTAAATAAATATATAA
1 TTAAATAAATATATAA
21771284 AAAAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAATAAATATATAA
Found at i:21771281 original size:24 final size:24
Alignment explanation
Indices: 21771264--21771316 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
21771254 ATATAATTAT
21771264 ATAATTAAATAAATATATAAAAAA
1 ATAATTAAATAAATATATAAAAAA
*
21771288 ATAATTAAATAAATA-ATGAAAAA
1 ATAATTAAATAAATATATAAAAAA
21771311 ATAATT
1 ATAATT
21771317 TTTATATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
ATAATTAAATAAATATATAAAAAA
Found at i:21771289 original size:12 final size:11
Alignment explanation
Indices: 21771264--21771315 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
21771254 ATATAATTAT
*
21771264 ATAATTAAATAA
1 ATAA-TAAAAAA
21771276 ATATATAAAAAA
1 ATA-ATAAAAAA
*
21771288 ATAATTAAATAA
1 ATAA-TAAAAAA
*
21771300 ATAATGAAAAA
1 ATAATAAAAAA
21771311 ATAAT
1 ATAAT
21771316 TTTTATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
11 11 0.32
12 22 0.65
13 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
ATAATAAAAAA
Found at i:21771299 original size:16 final size:16
Alignment explanation
Indices: 21771256--21771300 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
21771246 TTTTTTAAAT
**
21771256 ATAATTATATAATTAA
1 ATAATTATATAAAAAA
*
21771272 ATAAATATATAAAAAA
1 ATAATTATATAAAAAA
*
21771288 ATAATTAAATAAA
1 ATAATTATATAAA
21771301 TAATGAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATTATATAAAAAA
Found at i:21775650 original size:18 final size:18
Alignment explanation
Indices: 21775627--21775664 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
21775617 TGAAATTTTG
*
21775627 TTTATTTTTTATTATCTT
1 TTTATTATTTATTATCTT
*
21775645 TTTATTATTTATTTTCTT
1 TTTATTATTTATTATCTT
21775663 TT
1 TT
21775665 GTTATTCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTATTATTTATTATCTT
Found at i:21775675 original size:18 final size:17
Alignment explanation
Indices: 21775627--21775677 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
21775617 TGAAATTTTG
* *
21775627 TTTATTTTTTATTATCTT
1 TTTATTATTTATTTTC-T
21775645 TTTATTATTTATTTTCT
1 TTTATTATTTATTTTCT
*
21775662 TTTGTTATTCTATTTT
1 TTTATTATT-TATTTT
21775678 ATTTAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 9 0.31
18 20 0.69
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTATTATTTATTTTCT
Found at i:21777289 original size:1 final size:1
Alignment explanation
Indices: 21777242--21777276 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
21777232 TTGGCTGTGG
21777242 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
21777277 ACGATGGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:21777654 original size:15 final size:16
Alignment explanation
Indices: 21777634--21777675 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
21777624 GGGGGTGGCC
21777634 TTTTTGTTTTTT-CCT
1 TTTTTGTTTTTTACCT
21777649 TTTTTGTTTTTTAGCCT
1 TTTTTGTTTTTTA-CCT
21777666 TTATTTGTTT
1 TT-TTTGTTT
21777676 GTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.50
17 5 0.21
18 7 0.29
ACGTcount: A:0.05, C:0.10, G:0.10, T:0.76
Consensus pattern (16 bp):
TTTTTGTTTTTTACCT
Found at i:21779280 original size:21 final size:21
Alignment explanation
Indices: 21779255--21779305 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
21779245 TGAAATATGG
* *
21779255 ATTTTATTTTTTTAATAAATA
1 ATTTTATTTGTTTAACAAATA
* *
21779276 ATTTTAGTTGTTTACCAAATA
1 ATTTTATTTGTTTAACAAATA
*
21779297 ACTTTATTT
1 ATTTTATTT
21779306 AAAAAAATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (21 bp):
ATTTTATTTGTTTAACAAATA
Done.