Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 60 of 64
Found at i:10021343 original size:28 final size:27
Alignment explanation
Indices: 10021301--10021353 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
10021291 TATAACATGT
*
10021301 CTATCCTCAAGGAAGAAAAGATCTTATG
1 CTATCCTCAAAGAAGAAAAGA-CTTATG
*
10021329 CTATCTTCAAAGAAGAAAAGACTTA
1 CTATCCTCAAAGAAGAAAAGACTTA
10021354 AAAAAACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (27 bp):
CTATCCTCAAAGAAGAAAAGACTTATG
Found at i:10033482 original size:24 final size:24
Alignment explanation
Indices: 10033433--10033482 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
10033423 CTATTTGGGT
* *
10033433 TAAAATTTTATTTTATTTTATTAA
1 TAAAATTTAATTTTATTTTATAAA
10033457 TAAAATTTAATTTTTATTTTA-AAA
1 TAAAATTTAA-TTTTATTTTATAAA
10033481 TA
1 TA
10033483 TATTTGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TAAAATTTAATTTTATTTTATAAA
Found at i:10039033 original size:20 final size:20
Alignment explanation
Indices: 10039008--10039061 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 20
10038998 ATTAATAAGA
*
10039008 TATTTTTTAATATAAAATCT
1 TATTTTTTAATATAAAATAT
*
10039028 TA-TTTTT-ATATAAATTAT
1 TATTTTTTAATATAAAATAT
*
10039046 TATTTTTAAATATAAA
1 TATTTTTTAATATAAA
10039062 CATAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 11 0.38
19 9 0.31
20 9 0.31
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTTTTTAATATAAAATAT
Found at i:10039038 original size:18 final size:18
Alignment explanation
Indices: 10039002--10039053 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
10038992 TCCGAAATTA
* *
10039002 ATAAGATATT-TTTTAAT
1 ATAAAATATTATTTTTAT
*
10039019 ATAAAATCTTATTTTTAT
1 ATAAAATATTATTTTTAT
*
10039037 ATAAATTATTATTTTTA
1 ATAAAATATTATTTTTA
10039054 AATATAAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
ATAAAATATTATTTTTAT
Found at i:10041742 original size:26 final size:29
Alignment explanation
Indices: 10041705--10041770 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 29
10041695 TTGATATATT
10041705 TATTAA-ATAAATATTT-TTAATAAA-AA-
1 TATTAACA-AAATATTTATTAATAAATAAG
* *
10041731 TATTAACAAAATTTTTATTATTAAATAAG
1 TATTAACAAAATATTTATTAATAAATAAG
10041760 TATTAATCAAA
1 TATTAA-CAAA
10041771 TTTGAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 13 0.39
27 8 0.24
28 2 0.06
29 6 0.18
30 4 0.12
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (29 bp):
TATTAACAAAATATTTATTAATAAATAAG
Found at i:10042312 original size:16 final size:16
Alignment explanation
Indices: 10042291--10042324 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10042281 TCGATTTAAT
*
10042291 TTTAAATTAATCAAAA
1 TTTAAAATAATCAAAA
*
10042307 TTTAAAATAATTAAAA
1 TTTAAAATAATCAAAA
10042323 TT
1 TT
10042325 CTCATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAAATAATCAAAA
Found at i:10042535 original size:19 final size:19
Alignment explanation
Indices: 10042511--10042552 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
10042501 TCACTTAGGG
10042511 TTATTACACCTACGTTGGA
1 TTATTACACCTACGTTGGA
*
10042530 TTATTACACCTATGTTGGA
1 TTATTACACCTACGTTGGA
10042549 TTAT
1 TTAT
10042553 CTTTATGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (19 bp):
TTATTACACCTACGTTGGA
Found at i:10042919 original size:24 final size:24
Alignment explanation
Indices: 10042892--10042940 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
10042882 TTAATAATTT
*
10042892 AAAATATAATATA-AATATGATATA
1 AAAATAAAATA-AGAATATGATATA
10042916 AAAATAAAATAAGAATATGATATA
1 AAAATAAAATAAGAATATGATATA
10042940 A
1 A
10042941 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (24 bp):
AAAATAAAATAAGAATATGATATA
Found at i:10042940 original size:13 final size:12
Alignment explanation
Indices: 10042891--10042940 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
10042881 TTTAATAATT
*
10042891 TAAAATATAATA
1 TAAAATATGATA
10042903 T-AAATATGATA
1 TAAAATATGATA
* *
10042914 TAAAA-ATAAAA
1 TAAAATATGATA
10042925 TAAGAATATGATA
1 TAA-AATATGATA
10042938 TAA
1 TAA
10042941 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
11 17 0.57
12 6 0.20
13 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (12 bp):
TAAAATATGATA
Found at i:10043063 original size:32 final size:32
Alignment explanation
Indices: 10043027--10043093 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
10043017 TATGTTACGT
* *
10043027 AATTTTCATGTAAAATATAATACAAATATATA
1 AATTTTAATATAAAATATAATACAAATATATA
*** *
10043059 AATTTTAATATTTTATATAATATAAATATATA
1 AATTTTAATATAAAATATAATACAAATATATA
10043091 AAT
1 AAT
10043094 CATCAAATCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (32 bp):
AATTTTAATATAAAATATAATACAAATATATA
Found at i:10044895 original size:16 final size:17
Alignment explanation
Indices: 10044858--10044895 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
10044848 TATCGAATAC
10044858 ATTAAAAATAAAATTTT
1 ATTAAAAATAAAATTTT
10044875 ATTAAAAATAAAATTTT
1 ATTAAAAATAAAATTTT
10044892 -TTAA
1 ATTAA
10044896 TCTTATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTAAAAATAAAATTTT
Found at i:10046456 original size:17 final size:18
Alignment explanation
Indices: 10046429--10046463 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
10046419 AATTTTTATA
*
10046429 AGATATAAATATTAAAAT
1 AGATATAAATATAAAAAT
10046447 AGATAT-AATATAAAAAT
1 AGATATAAATATAAAAAT
10046464 TTAAAGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
AGATATAAATATAAAAAT
Found at i:10046457 original size:23 final size:21
Alignment explanation
Indices: 10046431--10046483 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
10046421 TTTTTATAAG
10046431 ATATAAATATTAAAATAGATATA
1 ATATAAATATT-AAA-AGATATA
* *
10046454 ATATAAAAATTTAAAGATATA
1 ATATAAATATTAAAAGATATA
10046475 A-A-AAATATT
1 ATATAAATATT
10046484 TTATCCTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 6 0.22
20 1 0.04
21 8 0.30
22 2 0.07
23 10 0.37
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (21 bp):
ATATAAATATTAAAAGATATA
Found at i:10053798 original size:32 final size:33
Alignment explanation
Indices: 10053738--10053799 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
10053728 TAATTTATAA
*
10053738 TTTTATAATTTAAAATATGACTTAAATTTAATT
1 TTTTATAATTGAAAATATGACTTAAATTTAATT
*
10053771 TTTTATAA-TGAAAAT-TGATTTATAATTTA
1 TTTTATAATTGAAAATATGACTTA-AATTTA
10053800 CTTAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 6 0.23
32 12 0.46
33 8 0.31
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (33 bp):
TTTTATAATTGAAAATATGACTTAAATTTAATT
Found at i:10058739 original size:253 final size:253
Alignment explanation
Indices: 10058247--10058741 Score: 832
Period size: 252 Copynumber: 2.0 Consensus size: 253
10058237 TTTAAATTTC
10058247 GTTAATTCAATCATCTTAATAACTTACAAGTTATTGTCCTAAAATGCTAACTTGTCATGTCTAAA
1 GTTAATTCAATCATCTTAATAACTTACAAGTTATTGTCCTAAAATGCTAACTTGTCATGTCTAAA
* * **
10058312 ATAATTAATCTAACTGTTAATTCAATTTAAGAAATCAATTTTAATATTTTAAAGTTGATTTCGGA
66 ATAATTAATCTAACTGTTAATTCAATTTAAGAAATCAATTTTAATATTTTAAAATTAATTTCAAA
* * * *
10058377 TAATTTAAATCTAAAACTTCCATCATATAAGTATAAATAATATTATCCAAATACTTTTAATTTCA
131 TAATCTAAATCCAAAACTTCCATCATATAAATATAAATAATATTATCCAAATACTTTTAATCTCA
10058442 TCTTTAACTTTTCAACTTTTAAGTATTTACTTCGATTGTTTTTTTTTTTTAATTTTAT
196 TCTTTAACTTTTCAACTTTTAAGTATTTACTTCGATTGTTTTTTTTTTTTAATTTTAT
* *
10058500 GTTAATTCAATCATCTTAATAACTTACAAGTTATTGTCTTAAAATGTTAACTTGTCATGTCTAAA
1 GTTAATTCAATCATCTTAATAACTTACAAGTTATTGTCCTAAAATGCTAACTTGTCATGTCTAAA
* * *
10058565 ATAATTAATCTAACTGTTAGTTCAATTTGAG-AATCAATTTTAATTTTTTAAAATTAATTTCAAA
66 ATAATTAATCTAACTGTTAATTCAATTTAAGAAATCAATTTTAATATTTTAAAATTAATTTCAAA
* *
10058629 TGATCTAAATCCAAAATTTCCATCATATAAATATAAATAATATTATCCAAATACTTTTAATCTCA
131 TAATCTAAATCCAAAACTTCCATCATATAAATATAAATAATATTATCCAAATACTTTTAATCTCA
*
10058694 TCTTTAACTTTTTAACTTTTAAGTATTTACTTCGATT-TTTTTTTTTTT
196 TCTTTAACTTTTCAACTTTTAAGTATTTACTTCGATTGTTTTTTTTTTT
10058742 AAATCGATCT
Statistics
Matches: 226, Mismatches: 16, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
251 11 0.05
252 123 0.54
253 92 0.41
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (253 bp):
GTTAATTCAATCATCTTAATAACTTACAAGTTATTGTCCTAAAATGCTAACTTGTCATGTCTAAA
ATAATTAATCTAACTGTTAATTCAATTTAAGAAATCAATTTTAATATTTTAAAATTAATTTCAAA
TAATCTAAATCCAAAACTTCCATCATATAAATATAAATAATATTATCCAAATACTTTTAATCTCA
TCTTTAACTTTTCAACTTTTAAGTATTTACTTCGATTGTTTTTTTTTTTTAATTTTAT
Found at i:10065306 original size:14 final size:15
Alignment explanation
Indices: 10065278--10065306 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10065268 CAGGTTAACA
10065278 TGTTTAACAATGATT
1 TGTTTAACAATGATT
10065293 TGTTTAAC-ATGATT
1 TGTTTAACAATGATT
10065307 CTTTTTTGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (15 bp):
TGTTTAACAATGATT
Found at i:10066902 original size:16 final size:17
Alignment explanation
Indices: 10066867--10066904 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
10066857 AATATGTTTT
* *
10066867 AATATTTTATTTAAATA
1 AATATTTTATATAAAAA
10066884 AATATTTT-TATAAAAA
1 AATATTTTATATAAAAA
10066900 AATAT
1 AATAT
10066905 CTGACAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATTTTATATAAAAA
Found at i:10068687 original size:12 final size:12
Alignment explanation
Indices: 10068672--10068696 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10068662 TATTTTTTAT
10068672 TATATATTATAA
1 TATATATTATAA
10068684 TATATATTATAA
1 TATATATTATAA
10068696 T
1 T
10068697 TAAAGGCAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATATTATAA
Found at i:10072012 original size:24 final size:23
Alignment explanation
Indices: 10071984--10072032 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
10071974 ATATATATAT
10071984 ATTTATATAATTATAACATTATTA
1 ATTTATATAATTATAACATT-TTA
*
10072008 ATTTATATAATTATAATATTTTA
1 ATTTATATAATTATAACATTTTA
10072031 AT
1 AT
10072033 AATATTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTATATAATTATAACATTTTA
Found at i:10072500 original size:13 final size:13
Alignment explanation
Indices: 10072482--10072506 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10072472 AAGAAATTTC
10072482 TTTTTTTTTTTTG
1 TTTTTTTTTTTTG
10072495 TTTTTTTTTTTT
1 TTTTTTTTTTTT
10072507 TACAAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.04, T:0.96
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:10072759 original size:31 final size:30
Alignment explanation
Indices: 10072700--10072775 Score: 120
Period size: 31 Copynumber: 2.6 Consensus size: 30
10072690 CTAATAAATT
*
10072700 AACATGATTAATTAC--TTTTTTGGTCAAC
1 AACATGATTAATTACTTTTTTTTGGCCAAC
10072728 AACATGATTAATTACTTTTCTTTTGGCCAAC
1 AACATGATTAATTACTTTT-TTTTGGCCAAC
10072759 AACATGATTAATTACTT
1 AACATGATTAATTACTT
10072776 AAATAAATAG
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 15 0.34
30 2 0.05
31 27 0.61
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (30 bp):
AACATGATTAATTACTTTTTTTTGGCCAAC
Found at i:10082584 original size:2 final size:2
Alignment explanation
Indices: 10082577--10082606 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10082567 CTATATTTGA
10082577 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
10082607 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:10082611 original size:2 final size:2
Alignment explanation
Indices: 10082606--10082630 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10082596 TCTCTCTCTC
10082606 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 T
10082631 CATTAAAGCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10088180 original size:26 final size:25
Alignment explanation
Indices: 10088150--10088207 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
10088140 GATTAATCGA
10088150 TAAATAAAAATATTTTTAATT-ATATT
1 TAAATAAAAATA--TTTAATTAATATT
* *
10088176 TAAATGTAACATATTTAATTAATATT
1 TAAAT-AAAAATATTTAATTAATATT
10088202 TAAATA
1 TAAATA
10088208 TTTAATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
25 7 0.26
26 15 0.56
27 5 0.19
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
TAAATAAAAATATTTAATTAATATT
Found at i:10088208 original size:19 final size:21
Alignment explanation
Indices: 10088186--10088224 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
10088176 TAAATGTAAC
10088186 ATATTTAA-TTAAT-ATTTAA
1 ATATTTAATTTAATGATTTAA
10088205 ATATTTAATTTAATGATTTA
1 ATATTTAATTTAATGATTTA
10088225 CTCATGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 5 0.28
21 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (21 bp):
ATATTTAATTTAATGATTTAA
Found at i:10089146 original size:8 final size:8
Alignment explanation
Indices: 10089133--10089187 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
10089123 ATAATGAATT
10089133 ATTATATA
1 ATTATATA
10089141 ATTATATA
1 ATTATATA
10089149 A-T-TATA
1 ATTATATA
*
10089155 ATTAAATA
1 ATTATATA
*
10089163 ATTA-AAA
1 ATTATATA
10089170 TATTATATA
1 -ATTATATA
10089179 TATTATATA
1 -ATTATATA
10089188 TTTTAATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
6 5 0.12
7 4 0.10
8 20 0.50
9 11 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
ATTATATA
Found at i:10089156 original size:14 final size:14
Alignment explanation
Indices: 10089137--10089185 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
10089127 TGAATTATTA
10089137 TATAATTATATAAT
1 TATAATTATATAAT
*
10089151 TATAATTAAATAAT
1 TATAATTATATAAT
*
10089165 TAAAATATTATATATAT
1 T-ATA-ATTATATA-AT
10089182 TATA
1 TATA
10089186 TATTTTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 14 0.50
15 2 0.07
16 9 0.32
17 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATAATTATATAAT
Found at i:10089257 original size:12 final size:12
Alignment explanation
Indices: 10089240--10089278 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10089230 TCTACTTAAA
10089240 TATATTAAAATT
1 TATATTAAAATT
*
10089252 TATATTAAAATAA
1 TATATTAAAAT-T
*
10089265 TATATAAAAATT
1 TATATTAAAATT
10089277 TA
1 TA
10089279 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATTAAAATT
Found at i:10092480 original size:19 final size:19
Alignment explanation
Indices: 10092458--10092514 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
10092448 TACTTTATAT
10092458 TAAATAT-ATTTTAATTGAA
1 TAAATATAATTTTAATT-AA
*
10092477 TAAATATAATTTTTATTAA
1 TAAATATAATTTTAATTAA
* * *
10092496 TAAATTTTATTCTAATTAA
1 TAAATATAATTTTAATTAA
10092515 AATTTAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 24 0.75
20 8 0.25
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TAAATATAATTTTAATTAA
Found at i:10095577 original size:16 final size:16
Alignment explanation
Indices: 10095556--10095591 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
10095546 TGGAGGGTGG
10095556 TTAGTTAGTTAGT-TAA
1 TTAGTTAGTTA-TATAA
10095572 TTAGTTAGTTATATAA
1 TTAGTTAGTTATATAA
10095588 TTAG
1 TTAG
10095592 AGTGAGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (16 bp):
TTAGTTAGTTATATAA
Found at i:10096405 original size:79 final size:79
Alignment explanation
Indices: 10096274--10096439 Score: 332
Period size: 79 Copynumber: 2.1 Consensus size: 79
10096264 GGTTGGATAT
10096274 TTTGTTTTATGTCGGGCTCAAGTTTTGTTATGTTCTTCCTTCCTGTTATCCCTTTAGGGTTTTTC
1 TTTGTTTTATGTCGGGCTCAAGTTTTGTTATGTTCTTCCTTCCTGTTATCCCTTTAGGGTTTTTC
10096339 ATGTGATGAGCCCC
66 ATGTGATGAGCCCC
10096353 TTTGTTTTATGTCGGGCTCAAGTTTTGTTATGTTCTTCCTTCCTGTTATCCCTTTAGGGTTTTTC
1 TTTGTTTTATGTCGGGCTCAAGTTTTGTTATGTTCTTCCTTCCTGTTATCCCTTTAGGGTTTTTC
10096418 ATGTGATGAGCCCC
66 ATGTGATGAGCCCC
10096432 TTTGTTTT
1 TTTGTTTT
10096440 TGGCTTACAT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 87 1.00
ACGTcount: A:0.11, C:0.19, G:0.20, T:0.50
Consensus pattern (79 bp):
TTTGTTTTATGTCGGGCTCAAGTTTTGTTATGTTCTTCCTTCCTGTTATCCCTTTAGGGTTTTTC
ATGTGATGAGCCCC
Found at i:10102215 original size:19 final size:16
Alignment explanation
Indices: 10102185--10102228 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 16
10102175 AAAATGTTTT
*
10102185 ATTTTTAATTTTGAGTTA
1 ATTTTAAATTTTGA--TA
10102203 ATATTTAAATTTTGATA
1 AT-TTTAAATTTTGATA
10102220 ATTTTAAAT
1 ATTTTAAAT
10102229 ATATAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.29
17 4 0.17
18 2 0.08
19 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
ATTTTAAATTTTGATA
Found at i:10106126 original size:20 final size:20
Alignment explanation
Indices: 10106103--10106153 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
10106093 TTTAATAATC
* *
10106103 AGATAAATTTTAGAAAAATT
1 AGATAAATTATAAAAAAATT
10106123 AGATAAA-TATAAAAAAATT
1 AGATAAATTATAAAAAAATT
*
10106142 AAATAAA-TATAA
1 AGATAAATTATAA
10106154 TTACAGATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (20 bp):
AGATAAATTATAAAAAAATT
Found at i:10106140 original size:19 final size:19
Alignment explanation
Indices: 10106116--10106153 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
10106106 TAAATTTTAG
*
10106116 AAAAATTAGATAAATATAA
1 AAAAATTAAATAAATATAA
10106135 AAAAATTAAATAAATATAA
1 AAAAATTAAATAAATATAA
10106154 TTACAGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (19 bp):
AAAAATTAAATAAATATAA
Found at i:10109598 original size:12 final size:12
Alignment explanation
Indices: 10109581--10109616 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
10109571 AACTGGGGCC
*
10109581 TCTGGTTCTGCT
1 TCTGGTTCCGCT
10109593 TCTGGTTCCGCT
1 TCTGGTTCCGCT
10109605 TCTGGTTCCGCT
1 TCTGGTTCCGCT
10109617 GCTACCTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.25, T:0.44
Consensus pattern (12 bp):
TCTGGTTCCGCT
Found at i:10111729 original size:63 final size:63
Alignment explanation
Indices: 10111624--10111746 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 63
10111614 ACGAGCTTGG
* * * *
10111624 AGATTGAGTTTTAACCACTGACAAGTAGGGTATTAAAGCAGGTCTTAGACCATTCGACCCTGA
1 AGATTGAGTCTCAACCACTGACAAGTAGGGTATCAAAACAGGTCTTAGACCATTCGACCCTGA
* * *
10111687 AGATTGAGTCTCAACCACTGACAAGTGGGGTATCAAAACAGGTCTTAGACCGTTTGACCC
1 AGATTGAGTCTCAACCACTGACAAGTAGGGTATCAAAACAGGTCTTAGACCATTCGACCC
10111747 ACGTCAAGCG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (63 bp):
AGATTGAGTCTCAACCACTGACAAGTAGGGTATCAAAACAGGTCTTAGACCATTCGACCCTGA
Found at i:10112033 original size:196 final size:193
Alignment explanation
Indices: 10111689--10112170 Score: 615
Period size: 196 Copynumber: 2.5 Consensus size: 193
10111679 GACCCTGAAG
* * * *
10111689 ATTGAGTCTCAACCACTGACAAGTGGGGTATCAAAACAGGTCTTAGACCGTTTGACCCACGTCAA
1 ATTGAGTCTCGACCACTGACAAGTGGGGTATCAAAGCAGGTCTTAGACCATTCGACCCACGTCAA
* * * * * * * *
10111754 GCGCCTTGAAAGAGATAGACAGGGTGCAAGCAGGGTGGCTAGCCTCCGTGATGAGGGCGTCACAA
66 GCGTCTTGAGAGAGGTAGGCAGGGTGCAAGCAGGATGACCAACCTCCGTGATGAGGGCGTCACAA
* * *
10111819 GGTTGACAAATGGTATCAAAGCAAGTTCTAGACCGCATGTTTGGGTATTAGAGCTGTACGAGCTT
131 GGTTGACAAATAGTATCAAAGCAAGTCCTAGACCGCATGTTTGGGTATTAGAGC----CAAGCTT
10111884 GA
192 GA
* * * * *
10111886 A-TGAGTCTCGACTACTGACAAGTAGGGTATCAAAGCATGTCCTAAACCATTCGACCCACGTCAA
1 ATTGAGTCTCGACCACTGACAAGTGGGGTATCAAAGCAGGTCTTAGACCATTCGACCCACGTCAA
* * *
10111950 GCATCTCGAGAGAGGTAGGCAGGGTGCAGGCAGGATGACCAACCTCCGTGATGAGGGCGTCACAA
66 GCGTCTTGAGAGAGGTAGGCAGGGTGCAAGCAGGATGACCAACCTCCGTGATGAGGGCGTCACAA
*
10112015 GGTTGACAAGTAGTATCAAAGCAAGTCCTAGACCGCATGTTTGGGTATTAGAGCCAAGCTTGA
131 GGTTGACAAATAGTATCAAAGCAAGTCCTAGACCGCATGTTTGGGTATTAGAGCCAAGCTTGA
* * * * *
10112078 ATGTTGAGTCTCGGCCATTGACAAGTGGGGTATCAAAGTAGGTCTTAGATCATTCAACCCACGTC
1 A--TTGAGTCTCGACCACTGACAAGTGGGGTATCAAAGCAGGTCTTAGACCATTCGACCCACGTC
* * *
10112143 AAACGTCTTGAGAGAGGTATGCAAGGTG
64 AAGCGTCTTGAGAGAGGTAGGCAGGGTG
10112171 GGGTATCAAA
Statistics
Matches: 243, Mismatches: 39, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
192 9 0.04
195 74 0.30
196 159 0.65
197 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (193 bp):
ATTGAGTCTCGACCACTGACAAGTGGGGTATCAAAGCAGGTCTTAGACCATTCGACCCACGTCAA
GCGTCTTGAGAGAGGTAGGCAGGGTGCAAGCAGGATGACCAACCTCCGTGATGAGGGCGTCACAA
GGTTGACAAATAGTATCAAAGCAAGTCCTAGACCGCATGTTTGGGTATTAGAGCCAAGCTTGA
Found at i:10112102 original size:454 final size:456
Alignment explanation
Indices: 10111228--10112434 Score: 1392
Period size: 454 Copynumber: 2.6 Consensus size: 456
10111218 GCCGTACGAG
* * *
10111228 CCTGGAGATTGAGTCTCAACCACTGACAAGTGGGGTATTAAAGTAGGTCTTAGACCGTTCGACCC
1 CCTGAAGATTGAGTCTCAACCACTGACAAGTGGGGTATCAAAGCAGGTCTTAGACCGTTCGACCC
**
10111293 ACGTCAAGCGCCTTGAAAGAGGTAGGCAGCCTGCAGGCAGGGTGGCCAGCCTCCGTGATGAGGGC
66 ACGTCAAGCGCCTTGAAAGAGGTAGGCAGGGTGCAGGCAGGGTGGCCAGCCTCCGTGATGAGGGC
* * *
10111358 GTTACAAGGTTGACAAGTGGTATCAAAGCAAGTTCTAGACTGCATGTTTGGGTATTAGAGCTGTC
131 GTCACAAGGTTGACAAGTGGTATCAAAGCAAGTTCTAGACCGCATGTTTGGGTATTAGAGCTGTA
*
10111423 CGAGC----TGAGTCTCGGCTACTGACAAGTGGGGTATCAAAGCAGGTCCTAAACCGTTCGACCC
196 CGAGCTGAATGAGTCTCGGCTACTGACAAGTAGGGTATCAAAGCAGGTCCTAAACCGTTCGACCC
* * * ***
10111484 ATGACAAGCGTCTCGAGAGAGGTAAGCAGGGTGTCCTAGACCGTTTAACCCACGTAAAGCGCCTC
261 ATGTCAAGCATCTCGAGAGAGGTAGGCAGGGTGTCCTAGACCGACCAACCCACGTAAAGCGCCTC
* * * *
10111549 AAGAGAGGTTGACAAGTGGTATCAAAGCAAGTGTTGAACCGCATGTTTGAGTATTATAGAGCTGT
326 AACAGAGGTTGACAAGTAGTATCAAAGCAAGTCTAGAACCGCATGTTTGAGTATTATAGAGC--T
* * * * *
10111614 ACGAGCTTGGAGATTGAGTTTTAACCACTGACAAGTAGGGTATTAAAGCAGGTCTTAGACCATTC
389 -CAAGCTTGAAGATTGAGTCTCAACCACTGACAAGTAGGGTATCAAAGCAGGTCTTAGACCATTC
*
10111679 GA-C
453 AACC
* *
10111682 CCTGAAGATTGAGTCTCAACCACTGACAAGTGGGGTATCAAAACAGGTCTTAGACCGTTTGACCC
1 CCTGAAGATTGAGTCTCAACCACTGACAAGTGGGGTATCAAAGCAGGTCTTAGACCGTTCGACCC
* * * *
10111747 ACGTCAAGCGCCTTGAAAGAGATAGACAGGGTGCAAGCAGGGTGGCTAGCCTCCGTGATGAGGGC
66 ACGTCAAGCGCCTTGAAAGAGGTAGGCAGGGTGCAGGCAGGGTGGCCAGCCTCCGTGATGAGGGC
*
10111812 GTCACAAGGTTGACAAATGGTATCAAAGCAAGTTCTAGACCGCATGTTTGGGTATTAGAGCTGTA
131 GTCACAAGGTTGACAAGTGGTATCAAAGCAAGTTCTAGACCGCATGTTTGGGTATTAGAGCTGTA
* * *
10111877 CGAGCTTGAATGAGTCTCGACTACTGACAAGTAGGGTATCAAAGCATGTCCTAAACCATTCGACC
196 CGAGC-TGAATGAGTCTCGGCTACTGACAAGTAGGGTATCAAAGCAGGTCCTAAACCGTTCGACC
* * *
10111942 CACGTCAAGCATCTCGAGAGAGGTAGGCAGGGTG-CAGGC-AGGA-TGACCAACCTC-CGTGATG
260 CATGTCAAGCATCTCGAGAGAGGTAGGCAGGGTGTC---CTA-GACCGACCAACC-CACGT-A-A
* * *
10112003 AGGGCGTC-ACA-AGGTTGACAAGTAGTATCAAAGCAAGTCCTAG-ACCGCATGTTTGGGTA-T-
318 AGCGCCTCAACAGAGGTTGACAAGTAGTATCAAAGCAAGT-CTAGAACCGCATGTTTGAGTATTA
** * * *
10112063 TAGAGC-CAAGCTTGAATG-TTGAGTCTCGGCCATTGACAAGTGGGGTATCAAAGTAGGTCTTAG
382 TAGAGCTCAAGCTTGAA-GATTGAGTCTCAACCACTGACAAGTAGGGTATCAAAGCAGGTCTTAG
*
10112126 ATCATTCAACC
446 ACCATTCAACC
* * ** *** * * *
10112137 CACGTCAAACGTCTTGAG--AGAGGTA-TG-CAAGGTGGGGTATCAAAGCAGATCCTAGACCATT
1 C-C-T-GAA-G-ATTGAGTCTCAACCACTGACAA-GTGGGGTATCAAAGCAGGTCTTAGACCGTT
* * * * * * *
10112198 CGACCCACGTCAAGTGTCTCGAGAGAGGTAGGCAGGGTGCAGGTAGAGTGACCAGCCTCCGTGAT
60 CGACCCACGTCAAGCGCCTTGAAAGAGGTAGGCAGGGTGCAGGCAGGGTGGCCAGCCTCCGTGAT
* * * * *
10112263 GAGGGCATCACAAGGTTGATAAGTGGTATCAAAGCAAGTCCTAGACCACATGTTTGGGTATTAAA
125 GAGGGCGTCACAAGGTTGACAAGTGGTATCAAAGCAAGTTCTAGACCGCATGTTTGGGTATTAGA
* * * *
10112328 GCTGTACGAGCCTGAATGTTGAGTCTCGGCCACTGATAAGTAGGGTATCAAAGCAGGTCTTAAAT
190 GCTGTACGAG-CTGAA---TGAGTCTCGGCTACTGACAAGTAGGGTATCAAAGCAGGTCCTAAAC
* *
10112393 CGTTCGACCCATGTCAAGCATATTGAGAGAGGTAGGCAGGGT
251 CGTTCGACCCATGTCAAGCATCTCGAGAGAGGTAGGCAGGGT
10112435 AACCATCCTC
Statistics
Matches: 642, Mismatches: 86, Indels: 44
0.83 0.11 0.06
Matches are distributed among these distances:
454 237 0.37
455 3 0.00
456 4 0.01
457 155 0.24
458 12 0.02
459 83 0.13
460 133 0.21
461 9 0.01
462 6 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (456 bp):
CCTGAAGATTGAGTCTCAACCACTGACAAGTGGGGTATCAAAGCAGGTCTTAGACCGTTCGACCC
ACGTCAAGCGCCTTGAAAGAGGTAGGCAGGGTGCAGGCAGGGTGGCCAGCCTCCGTGATGAGGGC
GTCACAAGGTTGACAAGTGGTATCAAAGCAAGTTCTAGACCGCATGTTTGGGTATTAGAGCTGTA
CGAGCTGAATGAGTCTCGGCTACTGACAAGTAGGGTATCAAAGCAGGTCCTAAACCGTTCGACCC
ATGTCAAGCATCTCGAGAGAGGTAGGCAGGGTGTCCTAGACCGACCAACCCACGTAAAGCGCCTC
AACAGAGGTTGACAAGTAGTATCAAAGCAAGTCTAGAACCGCATGTTTGAGTATTATAGAGCTCA
AGCTTGAAGATTGAGTCTCAACCACTGACAAGTAGGGTATCAAAGCAGGTCTTAGACCATTCAAC
C
Found at i:10112208 original size:66 final size:66
Alignment explanation
Indices: 10112102--10112236 Score: 180
Period size: 66 Copynumber: 2.0 Consensus size: 66
10112092 CCATTGACAA
* * * * * *
10112102 GTGGGGTATCAAAGTAGGTCTTAGATCATTCAACCCACGTCAAACGTCTTGAGAGAGGTATGCAA
1 GTGGGGTATCAAAGCAGATCCTAGACCATTCAACCCACGTCAAACGTCTCGAGAGAGGTAGGCAA
10112167 G
66 G
* ** *
10112168 GTGGGGTATCAAAGCAGATCCTAGACCATTCGACCCACGTCAAGTGTCTCGAGAGAGGTAGGCAG
1 GTGGGGTATCAAAGCAGATCCTAGACCATTCAACCCACGTCAAACGTCTCGAGAGAGGTAGGCAA
10112233 G
66 G
10112234 GTG
1 GTG
10112237 CAGGTAGAGT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.21
Consensus pattern (66 bp):
GTGGGGTATCAAAGCAGATCCTAGACCATTCAACCCACGTCAAACGTCTCGAGAGAGGTAGGCAA
G
Found at i:10115149 original size:21 final size:21
Alignment explanation
Indices: 10115094--10115150 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
10115084 TAAAATAATA
10115094 TTATT-TAAT-TTAATCCTATT
1 TTATTATAATCTT-ATCCTATT
* *
10115114 TATAATATCATCTTATCCTATT
1 T-TATTATAATCTTATCCTATT
10115136 TTATTATAATCTTAT
1 TTATTATAATCTTAT
10115151 ATACCAAGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.03
21 15 0.50
22 12 0.40
23 2 0.07
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTATAATCTTATCCTATT
Found at i:10115578 original size:6 final size:6
Alignment explanation
Indices: 10115567--10115593 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
10115557 TCTTAAGTTG
10115567 GAACAT GAACAT GAACAT GAACAT GAA
1 GAACAT GAACAT GAACAT GAACAT GAA
10115594 ATGCTGGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.19, T:0.15
Consensus pattern (6 bp):
GAACAT
Found at i:10137439 original size:3 final size:3
Alignment explanation
Indices: 10137431--10137466 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
10137421 AACTCATCTG
10137431 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10137467 CACAAGAAAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10138481 original size:27 final size:28
Alignment explanation
Indices: 10138451--10138510 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
10138441 ATAGATAAAC
* * *
10138451 TATAAATGTAGATATATATATTAT-GAT
1 TATAAATATAGAGATATAGATTATAGAT
*
10138478 TATAAATATATAGATATAGATTATAGAT
1 TATAAATATAGAGATATAGATTATAGAT
10138506 TATAA
1 TATAA
10138511 TAATTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (28 bp):
TATAAATATAGAGATATAGATTATAGAT
Found at i:10138487 original size:21 final size:21
Alignment explanation
Indices: 10138462--10138502 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10138452 ATAAATGTAG
*
10138462 ATATATATAT-TATGATTATAA
1 ATATATAGATATA-GATTATAA
10138483 ATATATAGATATAGATTATA
1 ATATATAGATATAGATTATA
10138503 GATTATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
ATATATAGATATAGATTATAA
Found at i:10138979 original size:34 final size:36
Alignment explanation
Indices: 10138941--10139018 Score: 94
Period size: 34 Copynumber: 2.3 Consensus size: 36
10138931 AATTGATAAT
10138941 ATTTTTAAATTTAAAAATAAA-TA-AAT-TATTTAAA
1 ATTTTTAAATTT-AAAATAAATTATAATATATTTAAA
*
10138975 A-TTTTAAA-TTAAAATAAATTATATTATATTTAAA
1 ATTTTTAAATTTAAAATAAATTATAATATATTTAAA
*
10139009 ATTTTAAAAT
1 ATTTTTAAAT
10139019 AAATTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
31 8 0.22
32 4 0.11
33 9 0.24
34 10 0.27
35 6 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (36 bp):
ATTTTTAAATTTAAAATAAATTATAATATATTTAAA
Found at i:10139005 original size:27 final size:26
Alignment explanation
Indices: 10138936--10139048 Score: 95
Period size: 29 Copynumber: 4.2 Consensus size: 26
10138926 TAATCAATTG
* *
10138936 ATAATATT-TTTAAATTTAAAAAT-AA
1 ATAA-ATTATTTAAATTTTAAATTAAA
10138961 ATAAATTATTTAAAATTTTAAATTAAA
1 ATAAATTATTT-AAATTTTAAATTAAA
* *
10138988 ATAAATTATATTATATTTAAAATTTTAAA
1 ATAAATTAT-TTAAATTTTAAA--TTAAA
* *
10139017 ATAAATTATTTTAAATTATATATTTAAA
1 ATAAATTA-TTTAAATTTTA-AATTAAA
10139045 ATAA
1 ATAA
10139049 TCTTAATAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
24 3 0.04
25 7 0.10
26 10 0.14
27 19 0.26
28 11 0.15
29 20 0.28
30 2 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATAAATTATTTAAATTTTAAATTAAA
Found at i:10139035 original size:34 final size:36
Alignment explanation
Indices: 10138967--10139046 Score: 101
Period size: 34 Copynumber: 2.3 Consensus size: 36
10138957 ATAAATAAAT
* *
10138967 TATTTAAAATTTTAAATTAAAATAAATTATA-T-TA
1 TATTTAAAATTTTAAAATAAAATAAATTAAATTATA
* **
10139001 TATTTAAAATTTTAAAATAAATTATTTTAAATTATA
1 TATTTAAAATTTTAAAATAAAATAAATTAAATTATA
10139037 TATTTAAAAT
1 TATTTAAAAT
10139047 AATCTTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 26 0.67
35 1 0.03
36 12 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
TATTTAAAATTTTAAAATAAAATAAATTAAATTATA
Found at i:10139809 original size:10 final size:10
Alignment explanation
Indices: 10139781--10139818 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
10139771 TTTAATAATT
10139781 TAAAATATAA
1 TAAAATATAA
10139791 TACAAATATAA
1 TA-AAATATAA
*
10139802 TAAAATATAT
1 TAAAATATAA
10139812 TAAAATA
1 TAAAATA
10139819 ATATAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (10 bp):
TAAAATATAA
Found at i:10141955 original size:2 final size:2
Alignment explanation
Indices: 10141942--10141973 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
10141932 CAAAGTTTAC
*
10141942 AT AT AT AA 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
10141974 TTTGGTAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10144164 original size:16 final size:16
Alignment explanation
Indices: 10144143--10144174 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10144133 TTTTAATTAA
10144143 TTAATTATATATTTAT
1 TTAATTATATATTTAT
*
10144159 TTAATTTTATATTTAT
1 TTAATTATATATTTAT
10144175 ACTAAAAATA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTAATTATATATTTAT
Found at i:10145409 original size:14 final size:14
Alignment explanation
Indices: 10145354--10145415 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
10145344 TTATTCGAAC
*
10145354 TAAATTTAA-ATAT
1 TAAATTTAATAAAT
* *
10145367 TAAATATATTAAAT
1 TAAATTTAATAAAT
* * *
10145381 AAAAATTAAAAAAAT
1 -TAAATTTAATAAAT
10145396 TAAATTTAATAAAT
1 TAAATTTAATAAAT
10145410 TAAATT
1 TAAATT
10145416 AAATTCGAAT
Statistics
Matches: 36, Mismatches: 11, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
13 7 0.19
14 20 0.56
15 9 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAATTTAATAAAT
Found at i:10146664 original size:18 final size:17
Alignment explanation
Indices: 10146624--10146678 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
10146614 TTTGATCTAG
*
10146624 TATATTTA-TTATTTAT
1 TATATTTATTTAATTAT
10146640 TATTATTTATTTAATTAT
1 TA-TATTTATTTAATTAT
* *
10146658 ATATATTTATATAATTTT
1 -TATATTTATTTAATTAT
10146676 TAT
1 TAT
10146679 TAAATTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
16 2 0.06
17 9 0.27
18 20 0.61
19 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATTTATTTAATTAT
Found at i:10146727 original size:23 final size:25
Alignment explanation
Indices: 10146701--10146749 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
10146691 AAATAATATT
10146701 AAAAATAATATTTTA-T-ATTTTAA
1 AAAAATAATATTTTATTAATTTTAA
* *
10146724 AAAATTATTATTTTATTAATTTTAA
1 AAAAATAATATTTTATTAATTTTAA
10146749 A
1 A
10146750 TTGAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 13 0.59
24 1 0.05
25 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AAAAATAATATTTTATTAATTTTAA
Found at i:10152751 original size:17 final size:17
Alignment explanation
Indices: 10152731--10152768 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
10152721 AATTTGTTTT
10152731 TATTTAGTATTTTAAAA
1 TATTTAGTATTTTAAAA
*
10152748 TATTAAGTATTTTAAAA
1 TATTTAGTATTTTAAAA
10152765 -ATTT
1 TATTT
10152769 TGAAAATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
TATTTAGTATTTTAAAA
Found at i:10166677 original size:13 final size:12
Alignment explanation
Indices: 10166658--10166693 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
10166648 TCGTATCATA
10166658 TTTATATTATAT
1 TTTATATTATAT
10166670 TATTATATTATAT
1 T-TTATATTATAT
*
10166683 TTTAAATTATA
1 TTTATATTATA
10166694 AATAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:10166682 original size:24 final size:24
Alignment explanation
Indices: 10166621--10166693 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
10166611 TTAAAATTTT
*
10166621 TTATTATATCATTTTTATATT-T-
1 TTATTATATCATATTTATATTATA
*
10166643 TTAATTCGTATCATATTTATATTATA
1 TT-ATT-ATATCATATTTATATTATA
* *
10166669 TTATTATATTATATTTTAAATTATA
1 TTATTATATCATA-TTTATATTATA
10166694 AATAAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
22 2 0.05
23 3 0.07
24 20 0.49
25 14 0.34
26 2 0.05
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (24 bp):
TTATTATATCATATTTATATTATA
Found at i:10168423 original size:21 final size:24
Alignment explanation
Indices: 10168378--10168430 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
10168368 ATTTTTTTTG
*
10168378 TTTTTATATATTGTTTTAATAAGA
1 TTTTTATATATTGTTTAAATAAGA
10168402 TTTTTA-ATA-TGTTTAAAT-AGA
1 TTTTTATATATTGTTTAAATAAGA
*
10168423 TTTATATA
1 TTTTTATA
10168431 AAATAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 8 0.31
22 9 0.35
23 3 0.12
24 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTTTATATATTGTTTAAATAAGA
Found at i:10168466 original size:9 final size:10
Alignment explanation
Indices: 10168447--10168491 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
10168437 TTATTTTTAT
10168447 TTTATAAAAA
1 TTTATAAAAA
10168457 TTTA-AAAAA
1 TTTATAAAAA
*
10168466 TCTATAAAAA
1 TTTATAAAAA
*
10168476 TTAATAAAAA
1 TTTATAAAAA
*
10168486 TATATA
1 TTTATA
10168492 TTTAGATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (10 bp):
TTTATAAAAA
Found at i:10168473 original size:19 final size:20
Alignment explanation
Indices: 10168449--10168491 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
10168439 ATTTTTATTT
* *
10168449 TATAAAAATTTA-AAAAATC
1 TATAAAAATTAATAAAAATA
10168468 TATAAAAATTAATAAAAATA
1 TATAAAAATTAATAAAAATA
10168488 TATA
1 TATA
10168492 TTTAGATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
TATAAAAATTAATAAAAATA
Found at i:10169317 original size:21 final size:21
Alignment explanation
Indices: 10169269--10169320 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
10169259 GTCAAGTATA
10169269 TAATTAAAATATTAAAAACAT
1 TAATTAAAATATTAAAAACAT
* *
10169290 TATATTAATATTTTAAAAA-ATT
1 TA-ATTAAAATATTAAAAACA-T
10169312 TAATTAAAA
1 TAATTAAAA
10169321 ATAATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TAATTAAAATATTAAAAACAT
Found at i:10171256 original size:13 final size:12
Alignment explanation
Indices: 10171238--10171275 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
10171228 CACAAGATAT
10171238 AAATATAATATAA
1 AAATATAATA-AA
10171251 AAATATAAT-AA
1 AAATATAATAAA
10171262 AAATAATAATAAA
1 AAAT-ATAATAAA
10171275 A
1 A
10171276 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.26
12 5 0.22
13 12 0.52
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATATAATAAA
Found at i:10171312 original size:40 final size:42
Alignment explanation
Indices: 10171256--10171354 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 42
10171246 TATAAAAATA
* * **
10171256 TAATAAAAATAATAATAAAATTTAAAATTT-TATTAATA-AT
1 TAATATAAATTATAATAAAATAAAAAATTTATATTAATATAT
**
10171296 TATATATAAATT-TAATAAAATAAAAAATTTATATTTTTATAT
1 TA-ATATAAATTATAATAAAATAAAAAATTTATATTAATATAT
10171338 TAATATAAATTATAATA
1 TAATATAAATTATAATA
10171355 CATAATTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
40 18 0.37
41 22 0.45
42 9 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (42 bp):
TAATATAAATTATAATAAAATAAAAAATTTATATTAATATAT
Found at i:10172160 original size:30 final size:30
Alignment explanation
Indices: 10172124--10172183 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
10172114 ATGTCAATTT
*
10172124 CTATATATACATATGAATGAAATTTGTGTA
1 CTATATATACAGATGAATGAAATTTGTGTA
10172154 CTATATATACAGATGAATGAAATTTGTGTA
1 CTATATATACAGATGAATGAAATTTGTGTA
10172184 GTTGCCATGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (30 bp):
CTATATATACAGATGAATGAAATTTGTGTA
Found at i:10177717 original size:18 final size:18
Alignment explanation
Indices: 10177694--10177731 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
10177684 AGGAGTCCTG
10177694 AATCCCATATCGAATATA
1 AATCCCATATCGAATATA
10177712 AATCCCATATCGAATATA
1 AATCCCATATCGAATATA
10177730 AA
1 AA
10177732 AGGAGGGTCA
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:0.47, C:0.21, G:0.05, T:0.26
Consensus pattern (18 bp):
AATCCCATATCGAATATA
Found at i:10194164 original size:3 final size:3
Alignment explanation
Indices: 10194156--10194181 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10194146 TTTAAATAAA
10194156 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
10194182 CAAGGGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:10194855 original size:21 final size:22
Alignment explanation
Indices: 10194829--10194872 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
10194819 AATTAATATT
10194829 ATAAAATA-TTTTTAAATTATA
1 ATAAAATATTTTTTAAATTATA
10194850 ATAAAATATTTTTTAAATTATA
1 ATAAAATATTTTTTAAATTATA
10194872 A
1 A
10194873 ATTTATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAAATATTTTTTAAATTATA
Found at i:10195681 original size:21 final size:21
Alignment explanation
Indices: 10195656--10195713 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
10195646 TATTTAATTT
10195656 ATTTTAAATATAA-AAATTTTA
1 ATTTT-AATATAATAAATTTTA
*
10195677 ATTTTAATTTAATAAATTTT-
1 ATTTTAATATAATAAATTTTA
10195697 ATTATTCAAT-TAATAAA
1 ATT-TT-AATATAATAAA
10195714 AAATTAATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 9 0.27
21 21 0.64
22 3 0.09
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTTAATATAATAAATTTTA
Found at i:10196401 original size:22 final size:21
Alignment explanation
Indices: 10196371--10196416 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
10196361 TATAATTTTT
* * *
10196371 TATTTTAATCAAATAATTGTAA
1 TATTATAATAAAATAAAT-TAA
10196393 TATTATAATAAAATAAATTAA
1 TATTATAATAAAATAAATTAA
10196414 TAT
1 TAT
10196417 ATTATTCATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
TATTATAATAAAATAAATTAA
Found at i:10197516 original size:13 final size:13
Alignment explanation
Indices: 10197498--10197533 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
10197488 ACGATTAACG
*
10197498 ATTGATTCGGACA
1 ATTGATTCGAACA
10197511 ATTGATTCGAACA
1 ATTGATTCGAACA
10197524 ATTGATTCGA
1 ATTGATTCGA
10197534 TCACCGTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (13 bp):
ATTGATTCGAACA
Found at i:10197775 original size:14 final size:14
Alignment explanation
Indices: 10197725--10197776 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
10197715 ATTATATTTT
10197725 ATATAAAAATAATATA
1 ATATAAAAAT-ATA-A
* *
10197741 TTATAATTAATAT-A
1 ATATAA-AAATATAA
10197755 ATATAAAAATATAA
1 ATATAAAAATATAA
10197769 ATATAAAA
1 ATATAAAA
10197777 TTTTTAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 5 0.17
14 15 0.50
16 7 0.23
17 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATATAAAAATATAA
Found at i:10198199 original size:22 final size:21
Alignment explanation
Indices: 10198165--10198210 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
10198155 AAAATTTGAT
*
10198165 TTTTTATATTATTTTAATATAA
1 TTTTTATATTATTTAAATA-AA
10198187 TTTTTAGTA-TATTTAAATAAA
1 TTTTTA-TATTATTTAAATAAA
10198208 TTT
1 TTT
10198211 AAGTATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 15 0.68
23 2 0.09
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTTATATTATTTAAATAAA
Found at i:10198215 original size:20 final size:21
Alignment explanation
Indices: 10198177--10198217 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
10198167 TTTATATTAT
* *
10198177 TTTAATATAATTTTTAGTATA
1 TTTAATATAAATTTAAGTATA
10198198 TTTAA-ATAAATTTAAGTATA
1 TTTAATATAAATTTAAGTATA
10198218 AAATAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TTTAATATAAATTTAAGTATA
Found at i:10208104 original size:12 final size:12
Alignment explanation
Indices: 10208079--10208121 Score: 54
Period size: 10 Copynumber: 3.7 Consensus size: 12
10208069 TTTAAAAAAA
10208079 TTTAAATATA--
1 TTTAAATATATT
10208089 TTTAAATATATT
1 TTTAAATATATT
*
10208101 TTTAAATAAATAT
1 TTTAAATATAT-T
10208114 TTTAAATA
1 TTTAAATA
10208122 AAACATTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 10 0.34
12 10 0.34
13 9 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTAAATATATT
Found at i:10208159 original size:24 final size:24
Alignment explanation
Indices: 10208105--10208161 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
10208095 TATATTTTTA
*
10208105 AATAAATATTTTAAATAAAACATT
1 AATAAATTTTTTAAATAAAACATT
*
10208129 ACA-AAATTTTTTAAAT-AAATATT
1 A-ATAAATTTTTTAAATAAAACATT
10208152 AATTAAATTT
1 AA-TAAATTT
10208162 GAATTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 7 0.25
24 19 0.68
25 1 0.04
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
AATAAATTTTTTAAATAAAACATT
Found at i:10208221 original size:30 final size:28
Alignment explanation
Indices: 10208172--10208243 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 28
10208162 GAATTATAAA
10208172 TATT-ATTTTTAATAA-TTTT-TTATATAT
1 TATTAATTTTTAATAATTTTTATTA-AT-T
10208199 TATTAATTTTTATATCAATTTTTATTAATT
1 TATTAATTTTTA-AT-AATTTTTATTAATT
10208229 TATTAATTTATTAAT
1 TATTAATTT-TTAAT
10208244 TTAAAGTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
27 4 0.10
28 7 0.18
29 2 0.05
30 14 0.36
31 9 0.23
32 3 0.08
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (28 bp):
TATTAATTTTTAATAATTTTTATTAATT
Found at i:10208232 original size:8 final size:8
Alignment explanation
Indices: 10208219--10208246 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
10208209 TATATCAATT
10208219 TTTATTAA
1 TTTATTAA
10208227 TTTATTAA
1 TTTATTAA
10208235 TTTATTAA
1 TTTATTAA
10208243 TTTA
1 TTTA
10208247 AAGTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTATTAA
Found at i:10208509 original size:2 final size:2
Alignment explanation
Indices: 10208502--10208535 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10208492 GATCCCCACG
10208502 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
10208536 TTCTTTTTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:10219966 original size:17 final size:17
Alignment explanation
Indices: 10219944--10219976 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10219934 TATATATAAA
10219944 ATAAAAATAAAAATTAC
1 ATAAAAATAAAAATTAC
*
10219961 ATAAAAGTAAAAATTA
1 ATAAAAATAAAAATTA
10219977 AATTTAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
ATAAAAATAAAAATTAC
Found at i:10219979 original size:22 final size:22
Alignment explanation
Indices: 10219939--10219990 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
10219929 ACATATATAT
10219939 ATAAAATAAAAATAAAAA-TTA
1 ATAAAATAAAAATAAAAATTTA
*
10219960 CATAAAAGTAAAAAT-TAAATTTA
1 -ATAAAA-TAAAAATAAAAATTTA
10219983 ATAAAATA
1 ATAAAATA
10219991 TATATAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 2 0.07
22 15 0.56
23 10 0.37
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
ATAAAATAAAAATAAAAATTTA
Found at i:10220470 original size:30 final size:32
Alignment explanation
Indices: 10220417--10220476 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
10220407 ATATTTTTTT
*
10220417 ATAAAAAAAAGATGCAATCTGAAAATAAAAAA
1 ATAAAAAAAAGATGAAATCTGAAAATAAAAAA
* *
10220449 ATAAAAAAATGAT-AAAT-TGAAACTAAAA
1 ATAAAAAAAAGATGAAATCTGAAAATAAAA
10220477 GTTGGAGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.40
31 3 0.12
32 12 0.48
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.18
Consensus pattern (32 bp):
ATAAAAAAAAGATGAAATCTGAAAATAAAAAA
Found at i:10223831 original size:19 final size:19
Alignment explanation
Indices: 10223794--10223830 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
10223784 TTCTCAAAAA
*
10223794 ATTTATTTTATTTTGTTTT
1 ATTTATTTTATTTAGTTTT
10223813 ATTTATTTT-TTTAGTTTT
1 ATTTATTTTATTTAGTTTT
10223831 TTTTCAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.78
Consensus pattern (19 bp):
ATTTATTTTATTTAGTTTT
Found at i:10224416 original size:11 final size:12
Alignment explanation
Indices: 10224392--10224422 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
10224382 TCGAATTTTG
10224392 AAAAATTTTCAA
1 AAAAATTTTCAA
*
10224404 AAAAATTTTAAA
1 AAAAATTTTCAA
10224416 AAAAATT
1 AAAAATT
10224423 ACAAAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAATTTTCAA
Found at i:10225031 original size:89 final size:87
Alignment explanation
Indices: 10224905--10225228 Score: 296
Period size: 89 Copynumber: 3.7 Consensus size: 87
10224895 TATGACTTTG
* * *
10224905 AAAAATAAATAAAGTTCATCTAAATAGAGGCTCAACAACTTTAAAAAATAAATAAAGCTATTCTA
1 AAAAATAAATAAAGCTCATCTAAACAGAGACTCAACAACTTTAAAAAATAAATAAAGCT-TTCTA
* *
10224970 AATAGAGGCTCAAGGACTTTAAAA
65 AACAGAGGCTCAAGAACTTT-AAA
* * * *
10224994 AAAAATAAATAAAGCTCCTCTAAACAGAGATTTAACAACATTAAAAAATAAATAAAGCTCTTCTA
1 AAAAATAAATAAAGCTCATCTAAACAGAGACTCAACAACTTTAAAAAATAAATAAAGCT-TTCTA
* *
10225059 AACAGAGACTC-AGTAACTTTAGA
65 AACAGAGGCTCAAG-AACTTTAAA
** * * ** * * * * *
10225082 AAATGTAAGTAAAGCTCCTCTACGCA-AAAGCTTAACAACTTTGAAAAATAAGTAAAGCTTCTTT
1 AAAAATAAATAAAGCTCATCTAAACAGAGA-CTCAACAACTTTAAAAAATAAATAAAGCTT-TCT
* * *
10225146 AAGCAGAGGCTTAATAAC-TTAAA
64 AAACAGAGGCTCAAGAACTTTAAA
* * * *
10225169 AAAAA-AAATAAAGCTCATTTAAACAAAGGCTCAACAACTTTAAAAAAATAAATAAGGCTT
1 AAAAATAAATAAAGCTCATCTAAACAGAGACTCAACAACTTT-AAAAAATAAATAAAGCTT
10225229 CTTTTTAATC
Statistics
Matches: 188, Mismatches: 41, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
86 26 0.14
87 26 0.14
88 64 0.34
89 72 0.38
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (87 bp):
AAAAATAAATAAAGCTCATCTAAACAGAGACTCAACAACTTTAAAAAATAAATAAAGCTTTCTAA
ACAGAGGCTCAAGAACTTTAAA
Found at i:10225085 original size:43 final size:43
Alignment explanation
Indices: 10224899--10225223 Score: 247
Period size: 43 Copynumber: 7.4 Consensus size: 43
10224889 ATGCTCTATG
* * * * *
10224899 ACTTTGAAAAATAAATAAAGTTCATCTAAATAGAGGCTCAACA
1 ACTTTAAAAAATAAATAAAGCTCCTCTAAACAGAGACTCAACA
** * * **
10224942 ACTTTAAAAAATAAATAAAGCTATTCTAAATAGAGGCTCAAGG
1 ACTTTAAAAAATAAATAAAGCTCCTCTAAACAGAGACTCAACA
* *
10224985 ACTTTAAAAAAAAATAAATAAAGCTCCTCTAAACAGAGATTTAACA
1 ACTTT---AAAAAATAAATAAAGCTCCTCTAAACAGAGACTCAACA
* * **
10225031 ACATTAAAAAATAAATAAAGCTCTTCTAAACAGAGACTCAGTA
1 ACTTTAAAAAATAAATAAAGCTCCTCTAAACAGAGACTCAACA
* * ** * *
10225074 ACTTTAGAAAATGTAAGTAAAGCTCCTCTACGCA-AAAGCTTAACA
1 ACTTTA-AAAA-ATAAATAAAGCTCCTCTAAACAGAGA-CTCAACA
* * * * * * * *
10225119 ACTTTGAAAAATAAGTAAAGCTTCTTTAAGCAGAGGCTTAATA
1 ACTTTAAAAAATAAATAAAGCTCCTCTAAACAGAGACTCAACA
* * * * * *
10225162 ACTTAAAAAAAAAAATAAAGCTCATTTAAACAAAGGCTCAACA
1 ACTTTAAAAAATAAATAAAGCTCCTCTAAACAGAGACTCAACA
10225205 ACTTTAAAAAAATAAATAA
1 ACTTT-AAAAAATAAATAA
10225224 GGCTTCTTTT
Statistics
Matches: 224, Mismatches: 50, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
43 141 0.63
44 23 0.10
45 26 0.12
46 34 0.15
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.25
Consensus pattern (43 bp):
ACTTTAAAAAATAAATAAAGCTCCTCTAAACAGAGACTCAACA
Found at i:10227280 original size:13 final size:13
Alignment explanation
Indices: 10227262--10227287 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10227252 AAAAAATTAA
10227262 TTAGTTTTTTATT
1 TTAGTTTTTTATT
10227275 TTAGTTTTTTATT
1 TTAGTTTTTTATT
10227288 GAAAATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
TTAGTTTTTTATT
Found at i:10227530 original size:56 final size:56
Alignment explanation
Indices: 10227423--10227537 Score: 133
Period size: 56 Copynumber: 2.1 Consensus size: 56
10227413 TTTTATTTTA
** * ****
10227423 TTTTATTTCTAAATTTTTCATTATTTTGGTCTATTTAGAAATTTTCTTTTTATAAG
1 TTTTATTTCTAAATTTTTCACCATTTGGGTCTATTTAGAAAAAAACTTTTTATAAG
* *
10227479 TTTTATTTTTAAATTTTTCACCATTTGGGTCTATTTAGAAAAAAAAC-TTTTATTAG
1 TTTTATTTCTAAATTTTTCACCATTTGGGTCTATTTAG-AAAAAAACTTTTTATAAG
10227535 TTT
1 TTT
10227538 CTTAATCTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
56 45 0.92
57 4 0.08
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.57
Consensus pattern (56 bp):
TTTTATTTCTAAATTTTTCACCATTTGGGTCTATTTAGAAAAAAACTTTTTATAAG
Found at i:10228024 original size:26 final size:24
Alignment explanation
Indices: 10227995--10228058 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 24
10227985 TAAATTTAGA
*
10227995 AAAAATTTCTCATATAGGAATTTTAT
1 AAAAATTTCTCAT-TAGAAATTTT-T
*
10228021 AAAAATTTAC-CATTTGAAATTTTT
1 AAAAATTT-CTCATTAGAAATTTTT
10228045 AAAAATTTCATCAT
1 AAAAATTTC-TCAT
10228059 CGAATAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
23 1 0.03
24 9 0.27
25 11 0.33
26 11 0.33
27 1 0.03
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (24 bp):
AAAAATTTCTCATTAGAAATTTTT
Found at i:10230539 original size:3 final size:3
Alignment explanation
Indices: 10230531--10230564 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
10230521 TTAAGTTTAG
10230531 TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
10230565 AGTTTGAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:10230648 original size:19 final size:19
Alignment explanation
Indices: 10230624--10230666 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
10230614 TAAAATCAAA
* *
10230624 TTATATATTTTTTTATTTT
1 TTATATATTTTTTAAATTT
10230643 TTATATATTTTTTAAATTT
1 TTATATATTTTTTAAATTT
10230662 TTATA
1 TTATA
10230667 AAATAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATATATTTTTTAAATTT
Found at i:10230666 original size:17 final size:19
Alignment explanation
Indices: 10230624--10230666 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
10230614 TAAAATCAAA
**
10230624 TTATATATTTTTTTATTTT
1 TTATATATTTTTTTAAATT
10230643 TTATATA-TTTTTTAAATT
1 TTATATATTTTTTTAAATT
10230661 TT-TATA
1 TTATATA
10230667 AAATAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 11 0.50
19 7 0.32
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATATATTTTTTTAAATT
Found at i:10231762 original size:2 final size:2
Alignment explanation
Indices: 10231755--10231798 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
10231745 GGGAGTAAAT
* *
10231755 TA TA TA TA TA AA TA TA TA TA TA TA TT 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
10231797 TA
1 TA
10231799 AATCCTGTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10232313 original size:26 final size:26
Alignment explanation
Indices: 10232283--10232333 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
10232273 CAAATAAAAT
*
10232283 TTTTTAATAAATTATTTAAATTGAATA
1 TTTTGAAT-AATTATTTAAATTGAATA
* *
10232310 TTTTGGATAATTGTTTAAATTGAA
1 TTTTGAATAATTATTTAAATTGAA
10232334 ATCAATATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (26 bp):
TTTTGAATAATTATTTAAATTGAATA
Found at i:10233322 original size:2 final size:2
Alignment explanation
Indices: 10233315--10233343 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10233305 GTTCAATCAA
10233315 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10233344 CACACCGCTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10235463 original size:23 final size:23
Alignment explanation
Indices: 10235437--10235484 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
10235427 CAAACTCGCA
* *
10235437 ATCTTTAAATATCAATTTTAACG
1 ATCTCTAAATATCAACTTTAACG
10235460 ATCTCTAAATATCAACTTTAACG
1 ATCTCTAAATATCAACTTTAACG
10235483 AT
1 AT
10235485 ATATCAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.40
Consensus pattern (23 bp):
ATCTCTAAATATCAACTTTAACG
Found at i:10237293 original size:18 final size:18
Alignment explanation
Indices: 10237267--10237301 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10237257 AAAAAATTAA
*
10237267 AAATATAATTTATAATTT
1 AAATATAATTAATAATTT
*
10237285 AAATTTAATTAATAATT
1 AAATATAATTAATAATT
10237302 ATTCATCAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATATAATTAATAATTT
Found at i:10237438 original size:20 final size:19
Alignment explanation
Indices: 10237413--10237468 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
10237403 GTAATGAAAC
10237413 ATTTTCATTTATTAATTTTT
1 ATTTTCATTT-TTAATTTTT
* *
10237433 ATTTTCAATTTTAATCTTT
1 ATTTTCATTTTTAATTTTT
*
10237452 ATTAATCATTTTTAATT
1 ATT-TTCATTTTTAATT
10237469 AAAAACTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTCATTTTTAATTTTT
Found at i:10237452 original size:19 final size:20
Alignment explanation
Indices: 10237413--10237454 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
10237403 GTAATGAAAC
* *
10237413 ATTTTCATTTATTAATTTTT
1 ATTTTCAATTATTAATCTTT
10237433 ATTTTCAATT-TTAATCTTT
1 ATTTTCAATTATTAATCTTT
10237452 ATT
1 ATT
10237455 AATCATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTCAATTATTAATCTTT
Found at i:10238867 original size:21 final size:23
Alignment explanation
Indices: 10238827--10238878 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
10238817 TATTTTTTAT
*
10238827 TTTTATATATTATTTTAATAAAA
1 TTTTATATATTATTTAAATAAAA
10238850 TTTTA-ATA-TATTTAAAT-AAA
1 TTTTATATATTATTTAAATAAAA
*
10238870 TTATATATA
1 TTTTATATA
10238879 ATAATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 3 0.12
23 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTATATATTATTTAAATAAAA
Found at i:10238935 original size:52 final size:53
Alignment explanation
Indices: 10238836--10238936 Score: 125
Period size: 52 Copynumber: 1.9 Consensus size: 53
10238826 TTTTTATATA
* * * * *
10238836 TTATTTTAATAAAATTTTAATATATTTAAATAAATTATATATAATAATTATTT
1 TTATTTTAATAAAAATTTAAAATATCTAAATAAATAAAATATAATAATTATTT
*
10238889 TTATTTT-ATAAAAATTTAAAATATCTAAATTAATAAAA-ATATATAATT
1 TTATTTTAATAAAAATTTAAAATATCTAAATAAATAAAATATA-ATAATT
10238937 CGATTATATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
51 3 0.07
52 31 0.76
53 7 0.17
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (53 bp):
TTATTTTAATAAAAATTTAAAATATCTAAATAAATAAAATATAATAATTATTT
Found at i:10239023 original size:130 final size:130
Alignment explanation
Indices: 10238874--10239141 Score: 509
Period size: 130 Copynumber: 2.1 Consensus size: 130
10238864 AATAAATTAT
*
10238874 ATATAATAATTATTTTTATTTTATAAAAATTTAAAATATCTAAATTAATAAAAATATATAATTCG
1 ATATAATAATTATTTTTATTTTATAAAAATTTAAAATATATAAATTAATAAAAATATATAATTCG
*
10238939 ATTATATTCCAATTTTTTAATTTTTCACATTCCGATTTAAAATTTCATTTAAATTTAATATATAC
66 ATTATATTCAAATTTTTTAATTTTTCACATTCCGATTTAAAATTTCATTTAAATTTAATATATAC
10239004 ATATAATAATTATTTTTATTTTATAAAAATTTAAAATATATAAATTAATAAAAATATATAATTCG
1 ATATAATAATTATTTTTATTTTATAAAAATTTAAAATATATAAATTAATAAAAATATATAATTCG
10239069 ATTATATTCAAATTTTTTAATTTTTCACATTCCGATTTAAAATTTCATTTAAATTTAATATATAC
66 ATTATATTCAAATTTTTTAATTTTTCACATTCCGATTTAAAATTTCATTTAAATTTAATATATAC
*
10239134 ATTTAATA
1 ATATAATA
10239142 TCTAAAGTTA
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 135 1.00
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.48
Consensus pattern (130 bp):
ATATAATAATTATTTTTATTTTATAAAAATTTAAAATATATAAATTAATAAAAATATATAATTCG
ATTATATTCAAATTTTTTAATTTTTCACATTCCGATTTAAAATTTCATTTAAATTTAATATATAC
Found at i:10240809 original size:56 final size:56
Alignment explanation
Indices: 10240704--10240809 Score: 124
Period size: 56 Copynumber: 1.9 Consensus size: 56
10240694 TTTTAATTTT
* * ****
10240704 TTATATTATTTTAATAAAAATTATAATATATTTAAATAAATTTGTATATAAAATAA
1 TTATATTATTTTAATAAAAATTAAAATATATATAAATAAATAAAAATATAAAATAA
* *
10240760 TTATTTTATTTT-ATAAAATTTTAAAATATATATAAATAAATAAAAATATA
1 TTATATTATTTTAATAAAA-ATTAAAATATATATAAATAAATAAAAATATA
10240810 TAATTAAGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
55 6 0.15
56 35 0.85
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (56 bp):
TTATATTATTTTAATAAAAATTAAAATATATATAAATAAATAAAAATATAAAATAA
Found at i:10240886 original size:13 final size:12
Alignment explanation
Indices: 10240855--10240912 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
10240845 TCTTGATCTA
*
10240855 AAATTTAAT-CT
1 AAATTTAATATT
10240866 AAATTTAATATAT
1 AAATTTAATAT-T
*
10240879 ATATTTAATATT
1 AAATTTAATATT
10240891 AAATTTAA-ATTT
1 AAATTTAATA-TT
*
10240903 AAATTAAATA
1 AAATTTAATA
10240913 AAATATTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 10 0.26
12 17 0.44
13 12 0.31
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
AAATTTAATATT
Found at i:10240920 original size:18 final size:18
Alignment explanation
Indices: 10240865--10240937 Score: 67
Period size: 18 Copynumber: 4.0 Consensus size: 18
10240855 AAATTTAATC
* *
10240865 TAAATTTAATATATATATT
1 TAAATTAAATA-AAATATT
**
10240884 TAATATTAAATTTAA-ATT
1 TAA-ATTAAATAAAATATT
10240902 TAAATTAAATAAAATATT
1 TAAATTAAATAAAATATT
* *
10240920 TAAATCAAATCAAATATT
1 TAAATTAAATAAAATATT
10240938 ATATTTTAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
17 9 0.20
18 25 0.57
19 4 0.09
20 6 0.14
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATTAAATAAAATATT
Found at i:10241379 original size:15 final size:15
Alignment explanation
Indices: 10241356--10241390 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10241346 CCATACTCTG
*
10241356 CAAAACAAAACAAAT
1 CAAACCAAAACAAAT
*
10241371 CAAACCAAACCAAAT
1 CAAACCAAAACAAAT
10241386 CAAAC
1 CAAAC
10241391 ACTTTGTTTT
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:0.66, C:0.29, G:0.00, T:0.06
Consensus pattern (15 bp):
CAAACCAAAACAAAT
Found at i:10251853 original size:17 final size:16
Alignment explanation
Indices: 10251827--10251862 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
10251817 TTCTTACTGA
*
10251827 TTTTTGTATATCAATTT
1 TTTTTATATAT-AATTT
10251844 TTTTTATATATAATTT
1 TTTTTATATATAATTT
10251860 TTT
1 TTT
10251863 CTAATATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTTTATATATAATTT
Found at i:10251869 original size:15 final size:17
Alignment explanation
Indices: 10251833--10251869 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
10251823 CTGATTTTTG
*
10251833 TATATCAATTTTTTTTA
1 TATATCAATTTTTTCTA
10251850 TATAT-AATTTTTTCTA
1 TATATCAATTTTTTCTA
10251866 -ATAT
1 TATAT
10251870 TTGATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 10 0.53
17 5 0.26
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATCAATTTTTTCTA
Found at i:10255280 original size:6 final size:6
Alignment explanation
Indices: 10255269--10255293 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
10255259 ATTATATATT
10255269 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
10255294 GCTAATTATG
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:10255737 original size:20 final size:19
Alignment explanation
Indices: 10255695--10255741 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
10255685 AAGACACCTA
*
10255695 TTTTGTATTTTATTTTCTC
1 TTTTTTATTTTATTTTCTC
10255714 TTTTTTATTATTATTTT-T-
1 TTTTTTATT-TTATTTTCTC
10255732 TTTTTT-TTTT
1 TTTTTTATTTT
10255742 TCTTGTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 2 0.08
18 6 0.23
19 9 0.35
20 7 0.27
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTTTTATTTTATTTTCTC
Found at i:10264101 original size:2 final size:2
Alignment explanation
Indices: 10264094--10264119 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10264084 CATTAACTGC
10264094 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
10264120 CCCAACGGAA
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):
AT
Found at i:10264360 original size:15 final size:15
Alignment explanation
Indices: 10264340--10264370 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10264330 ACAACAGTGA
10264340 AGAAAAAAATAATCC
1 AGAAAAAAATAATCC
*
10264355 AGAAAAATATAATCC
1 AGAAAAAAATAATCC
10264370 A
1 A
10264371 ACACTGGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.13, G:0.06, T:0.16
Consensus pattern (15 bp):
AGAAAAAAATAATCC
Found at i:10278016 original size:17 final size:17
Alignment explanation
Indices: 10277972--10278007 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
10277962 ATTCAAATCG
10277972 AATTATATATATATATTT
1 AATT-TATATATATATTT
10277990 AATTTATATATAT-TTT
1 AATTTATATATATATTT
10278006 AA
1 AA
10278008 ATTTTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 9 0.50
18 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTATATATATATTT
Found at i:10278590 original size:30 final size:29
Alignment explanation
Indices: 10278537--10278601 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
10278527 TTAGCTTCTA
* * *
10278537 ATTTATTTAATATTATTAATATAATTTAT
1 ATTTATCTAAAATCATTAATATAATTTAT
10278566 ATTTATCTAAAATCATTAAATATAATTTAT
1 ATTTATCTAAAATCATT-AATATAATTTAT
*
10278596 AATTAT
1 ATTTAT
10278602 TCACATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (29 bp):
ATTTATCTAAAATCATTAATATAATTTAT
Found at i:10279315 original size:7 final size:6
Alignment explanation
Indices: 10279274--10279311 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
10279264 AATAAAATAA
* *
10279274 AAATTT -AATTC AAATTC AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAA
10279312 ATTTTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (6 bp):
AAATTT
Found at i:10282610 original size:14 final size:14
Alignment explanation
Indices: 10282581--10282625 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
10282571 AACAATAAAT
*
10282581 AAATTATAACCAAAC
1 AAATT-TAAACAAAC
10282596 AAATTTAAACAAAC
1 AAATTTAAACAAAC
*
10282610 AAATCCTAAACAAAC
1 AAAT-TTAAACAAAC
10282625 A
1 A
10282626 TAAATGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 12 0.44
15 15 0.56
ACGTcount: A:0.62, C:0.20, G:0.00, T:0.18
Consensus pattern (14 bp):
AAATTTAAACAAAC
Found at i:10282745 original size:11 final size:11
Alignment explanation
Indices: 10282709--10282738 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
10282699 GTATTATTAT
*
10282709 AAATGAACAAC
1 AAATGAATAAC
10282720 AAATGAATAAC
1 AAATGAATAAC
10282731 AAATGAAT
1 AAATGAAT
10282739 TATAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.17
Consensus pattern (11 bp):
AAATGAATAAC
Found at i:10287341 original size:18 final size:19
Alignment explanation
Indices: 10287320--10287357 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
10287310 TATATTTTAT
*
10287320 TTATAT-TTTATATAAAAA
1 TTATATATTAATATAAAAA
10287338 TTATATATTAATATAAAAA
1 TTATATATTAATATAAAAA
10287357 T
1 T
10287358 ATAAAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTATATATTAATATAAAAA
Found at i:10290706 original size:20 final size:20
Alignment explanation
Indices: 10290668--10290706 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10290658 AGGTAATCAA
*
10290668 AAATTAAATTTTGATTATTT
1 AAATTAAATTTTGAATATTT
10290688 AAATTAAAATTTT-AATATT
1 AAATT-AAATTTTGAATATT
10290707 AATCTCTGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
AAATTAAATTTTGAATATTT
Found at i:10294920 original size:33 final size:33
Alignment explanation
Indices: 10294847--10294923 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
10294837 ATATTATATG
* ***
10294847 TATATTATATATAAATAGTTTAAAATTTTAATA
1 TATATTATATATAAATAGTATAAAATAAAAATA
10294880 -ATAATTATATATAAAT-GTGATAAAATAAAAATA
1 TAT-ATTATATATAAATAGT-ATAAAATAAAAATA
10294913 TATATTATATA
1 TATATTATATA
10294924 ATTTTGTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
32 4 0.11
33 31 0.84
34 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (33 bp):
TATATTATATATAAATAGTATAAAATAAAAATA
Found at i:10295794 original size:12 final size:12
Alignment explanation
Indices: 10295777--10295816 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
10295767 CTGTGGATTT
10295777 GGGTTAGGGCTA
1 GGGTTAGGGCTA
*
10295789 GGGTTAGGG-TT
1 GGGTTAGGGCTA
*
10295800 GGGTTGGGGCTA
1 GGGTTAGGGCTA
10295812 GGGTT
1 GGGTT
10295817 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.10, C:0.05, G:0.55, T:0.30
Consensus pattern (12 bp):
GGGTTAGGGCTA
Found at i:10300381 original size:3 final size:3
Alignment explanation
Indices: 10300373--10300416 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
10300363 GCAAAGAAAA
*
10300373 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GGT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
10300417 AGGGTTCAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Done.