Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 9 of 130
Found at i:2529770 original size:22 final size:22
Alignment explanation
Indices: 2529726--2529787 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
2529716 TTATCCCAGT
*
2529726 TGATTCTATAAGACCTCCGAGCA
1 TGATTCT-TAAGACCTCCAAGCA
*
2529749 TGATTCTTAAAACCTCCAAGCA
1 TGATTCTTAAGACCTCCAAGCA
2529771 TGACTTC-TAAGACCTCC
1 TGA-TTCTTAAGACCTCC
2529788 GGGTATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
22 25 0.71
23 10 0.29
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (22 bp):
TGATTCTTAAGACCTCCAAGCA
Found at i:2530195 original size:102 final size:101
Alignment explanation
Indices: 2530083--2530394 Score: 299
Period size: 102 Copynumber: 3.0 Consensus size: 101
2530073 CAAGTTAACT
* * * *
2530083 TTATTCTCTAACTCGCGGTTTAATCCCGATCTCTTTATTCTTCGATTCGCTATTCAATCCTAATC
1 TTATTTTCTAACTCGTGGTTTAATCCCGATCTTTTTATTCTCCGATTCGCTATTCAATCCTAATC
2530148 TCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTG
66 TCTTTAATTTAAAATCA-AGTTTAATCTCGATTGTTG
* ** * ** * *
2530185 TTATTTTCTAACTCGTGATTTAATCTTGATCTTTTTATTCTCCGATTCACGGTTTAATCCCAATC
1 TTATTTTCTAACTCGTGGTTTAATCCCGATCTTTTTATTCTCCGATTCGCTATTCAATCCTAATC
** **
2530250 TCTTTAATTTGAACCTGTAGTTTAATCTCGATTGTTG
66 TCTTTAATTT-AAAATCAAGTTTAATCTCGATTGTTG
* * * * * *
2530287 TTGTCATCTTCTGACTCATGGTTTAATCCCAAACTTTTTATTCTCCGATT-G-TCATTTCAATCT
1 -T-T-ATTTTCTAACTCGTGGTTTAATCCCGATCTTTTTATTCTCCGATTCGCT-A-TTCAATCC
* * *
2530350 TGATCTCTTTTAATTTAAAAT-ATGTTT-ATCTCGATTGTTA
61 TAATCTC-TTTAATTTAAAATCAAGTTTAATCTCGATTGTTG
2530390 TTATT
1 TTATT
2530395 CTTGAAAATG
Statistics
Matches: 166, Mismatches: 37, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
100 2 0.01
101 1 0.01
102 83 0.50
103 16 0.10
104 5 0.03
105 51 0.31
106 8 0.05
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (101 bp):
TTATTTTCTAACTCGTGGTTTAATCCCGATCTTTTTATTCTCCGATTCGCTATTCAATCCTAATC
TCTTTAATTTAAAATCAAGTTTAATCTCGATTGTTG
Found at i:2530755 original size:22 final size:23
Alignment explanation
Indices: 2530713--2530756 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2530703 AAATAATAAT
*
2530713 AATTTAAATTTATTTAAAAAATA
1 AATTTAAATTTATTAAAAAAATA
*
2530736 AATTTAATTTTA-TAAAAAAAT
1 AATTTAAATTTATTAAAAAAAT
2530757 GAAAAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTTAAATTTATTAAAAAAATA
Found at i:2531113 original size:16 final size:15
Alignment explanation
Indices: 2531073--2531133 Score: 65
Period size: 14 Copynumber: 4.1 Consensus size: 15
2531063 CCCTTAAATT
2531073 AAATCCCAAACTCC-A
1 AAATCCCAAAC-CCTA
2531088 AAA-CCCAAACCCTA
1 AAATCCCAAACCCTA
*
2531102 AAATCTCCAAACTCTA
1 AAATC-CCAAACCCTA
*
2531118 AAAT-CAAAACCCTA
1 AAATCCCAAACCCTA
2531132 AA
1 AA
2531134 CCTTCCATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.05
14 21 0.52
15 4 0.10
16 13 0.32
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (15 bp):
AAATCCCAAACCCTA
Found at i:2531114 original size:30 final size:29
Alignment explanation
Indices: 2531073--2531133 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
2531063 CCCTTAAATT
*
2531073 AAATCCCAAACTCCAAAACCCAAACCCTA
1 AAATCCCAAACTCCAAAACCAAAACCCTA
* *
2531102 AAATCTCCAAACTCTAAAATCAAAACCCTA
1 AAATC-CCAAACTCCAAAACCAAAACCCTA
2531132 AA
1 AA
2531134 CCTTCCATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (29 bp):
AAATCCCAAACTCCAAAACCAAAACCCTA
Found at i:2543284 original size:30 final size:30
Alignment explanation
Indices: 2543222--2543286 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
2543212 ATGATCAGCC
* * *
2543222 TTCTCATACTTAGTTAATTTAGCTAGACCT
1 TTCTGATACTTAGTTAACTTAGCTACACCT
* *
2543252 TTCTGATACTTAGTTAACTTAGGTACATCT
1 TTCTGATACTTAGTTAACTTAGCTACACCT
2543282 TTCTG
1 TTCTG
2543287 CACTCAGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (30 bp):
TTCTGATACTTAGTTAACTTAGCTACACCT
Found at i:2551288 original size:25 final size:25
Alignment explanation
Indices: 2551260--2551327 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 25
2551250 AATCATATTA
2551260 ATTTTTAATAATATAAAATTTAATG
1 ATTTTTAATAATATAAAATTTAATG
* *
2551285 ATTTTTAAT--TCATAAAAGTTAATT
1 ATTTTTAATAAT-ATAAAATTTAATG
* * *
2551309 ATTATTAACAAAATAAAAT
1 ATTTTTAATAATATAAAAT
2551328 AATTTCAATC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
23 1 0.03
24 18 0.53
25 15 0.44
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (25 bp):
ATTTTTAATAATATAAAATTTAATG
Found at i:2552781 original size:12 final size:13
Alignment explanation
Indices: 2552748--2552803 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
2552738 AATAACTCAA
2552748 AATAATAAAATTAT
1 AATAA-AAAATTAT
2552762 AATAAAAAATTA-
1 AATAAAAAATTAT
*
2552774 AATCAAAAAATTTT
1 AAT-AAAAAATTAT
* *
2552788 AA-AAATAATAAT
1 AATAAAAAATTAT
2552800 AATA
1 AATA
2552804 CCTGAATCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
12 12 0.34
13 16 0.46
14 7 0.20
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (13 bp):
AATAAAAAATTAT
Found at i:2561339 original size:31 final size:31
Alignment explanation
Indices: 2561301--2561360 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2561291 TATTTTATTC
2561301 TTTATTTATAAATA-AAATAAAATTTATTTTA
1 TTTATTTATAAATACAAAT-AAATTTATTTTA
**
2561332 TTTATTTATATTTACAAATAAATTTATTT
1 TTTATTTATAAATACAAATAAATTTATTT
2561361 AATATTCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (31 bp):
TTTATTTATAAATACAAATAAATTTATTTTA
Found at i:2562475 original size:14 final size:14
Alignment explanation
Indices: 2562455--2562487 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2562445 TAAATATTAA
2562455 TTTTAATA-AAATT
1 TTTTAATATAAATT
2562468 TATTTAATATAAATT
1 T-TTTAATATAAATT
2562483 TTTTA
1 TTTTA
2562488 TAATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 11 0.61
15 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTAATATAAATT
Found at i:2594375 original size:23 final size:23
Alignment explanation
Indices: 2594322--2594371 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
2594312 AAATAATAAT
2594322 TATTATAATTATAATTTAAAAAA
1 TATTATAATTATAATTTAAAAAA
* *
2594345 TATCATAATTATGA-TTAAAAAA
1 TATTATAATTATAATTTAAAAAA
2594367 TATTA
1 TATTA
2594372 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TATTATAATTATAATTTAAAAAA
Found at i:2594378 original size:13 final size:13
Alignment explanation
Indices: 2594360--2594391 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2594350 TAATTATGAT
2594360 TAAAAAATATTAA
1 TAAAAAATATTAA
*
2594373 TAAAAAATATTAT
1 TAAAAAATATTAA
2594386 TAAAAA
1 TAAAAA
2594392 TAATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAAAATATTAA
Found at i:2597493 original size:29 final size:27
Alignment explanation
Indices: 2597448--2597501 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
2597438 AATTGAATCA
*
2597448 TTTTATGTTTTAAATAAATTTTTATAT
1 TTTTATGTTTTAAATAAAATTTTATAT
2597475 TTTTATTGTATTTAAATAAAATTTTAT
1 TTTTA-TGT-TTTAAATAAAATTTTAT
2597502 TTCAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 5 0.21
28 3 0.12
29 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTTATGTTTTAAATAAAATTTTATAT
Found at i:2597518 original size:18 final size:16
Alignment explanation
Indices: 2597483--2597522 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
2597473 ATTTTTATTG
*
2597483 TATTTAAATAAAATTT
1 TATTTAAATAAAAATT
2597499 TATTTCAAATAAAAAATT
1 TATTT-AAAT-AAAAATT
2597517 TATTTA
1 TATTTA
2597523 TGTTAAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.24
17 5 0.24
18 11 0.52
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTAAATAAAAATT
Found at i:2610187 original size:14 final size:13
Alignment explanation
Indices: 2610164--2610193 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
2610154 TACAAATTAA
2610164 TAAATAAAAAATT
1 TAAATAAAAAATT
2610177 TAAATTAAAAAATT
1 TAAA-TAAAAAATT
2610191 TAA
1 TAA
2610194 CAACAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATAAAAAATT
Found at i:2610602 original size:31 final size:30
Alignment explanation
Indices: 2610539--2610634 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 30
2610529 TTTTAAATTA
* *
2610539 TAAAATT-ATTA-ATTAATATAATATT--T
1 TAAAATTAATTATGTTAATATTATATTAAT
* * *
2610565 TAAAAATTATTTAT-TTATTATGTATTATTATT
1 T-AAAATTAATTATGTTAATAT-TA-TATTAAT
2610597 TAAAATTAATTATGTTAATATTATATTAAT
1 TAAAATTAATTATGTTAATATTATATTAAT
2610627 TAATAATT
1 TAA-AATT
2610635 TTATAATTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
26 1 0.02
27 6 0.11
28 9 0.16
29 1 0.02
30 13 0.24
31 17 0.31
32 8 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
TAAAATTAATTATGTTAATATTATATTAAT
Found at i:2610663 original size:27 final size:27
Alignment explanation
Indices: 2610618--2610693 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 27
2610608 ATGTTAATAT
* * *
2610618 TATATT-AATTAATAATTTTATAATTTA
1 TATATTAAATTAA-ATTTTTAAAACTTA
2610645 TATATTAAATTAAATTTTTTAAAACTTA
1 TATATTAAATTAAA-TTTTTAAAACTTA
* *
2610673 AATATTAAATTAAATATTTAA
1 TATATTAAATTAAATTTTTAA
2610694 TTTAAACTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 13 0.31
28 29 0.69
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (27 bp):
TATATTAAATTAAATTTTTAAAACTTA
Found at i:2610698 original size:13 final size:13
Alignment explanation
Indices: 2610644--2610706 Score: 56
Period size: 13 Copynumber: 4.5 Consensus size: 13
2610634 TTTATAATTT
2610644 ATATATTAAATTAA
1 ATAT-TTAAATTAA
*
2610658 ATTTTTTAAAACTTAA
1 A-TATTT-AAA-TTAA
2610674 ATA-TTAAATTAA
1 ATATTTAAATTAA
*
2610686 ATATTTAATTTAA
1 ATATTTAAATTAA
2610699 ACTATTTA
1 A-TATTTA
2610707 GAGGTAACTA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
12 7 0.17
13 12 0.29
14 11 0.27
15 6 0.15
16 5 0.12
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTTAAATTAA
Found at i:2613250 original size:21 final size:22
Alignment explanation
Indices: 2613221--2613261 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2613211 TTGGGGTCGA
* *
2613221 GAAGATGGTGAGATTCGGAAGG
1 GAAGATGGTGAAAGTCGGAAGG
2613243 GAAG-TGGTGAAAGTCGGAA
1 GAAGATGGTGAAAGTCGGAA
2613262 CTTTGGAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.34, C:0.05, G:0.44, T:0.17
Consensus pattern (22 bp):
GAAGATGGTGAAAGTCGGAAGG
Found at i:2617013 original size:19 final size:19
Alignment explanation
Indices: 2616989--2617026 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2616979 AATTGGATCA
* *
2616989 AATTAAATATTATATCTTT
1 AATTAAAAATTACATCTTT
2617008 AATTAAAAATTACATCTTT
1 AATTAAAAATTACATCTTT
2617027 GAATCGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTAAAAATTACATCTTT
Found at i:2619813 original size:26 final size:26
Alignment explanation
Indices: 2619777--2619828 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2619767 TTTCTGATCC
2619777 CCGATGCTTAGAAAATGGGTTCAGTT
1 CCGATGCTTAGAAAATGGGTTCAGTT
2619803 CCGATGCTTAGAAAATGGGTTCAGTT
1 CCGATGCTTAGAAAATGGGTTCAGTT
2619829 AGAAGCTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (26 bp):
CCGATGCTTAGAAAATGGGTTCAGTT
Found at i:2626074 original size:23 final size:23
Alignment explanation
Indices: 2626024--2626077 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
2626014 TTTAATTAAT
*
2626024 TTAAAATATTAAATGATTTGTTAA
1 TTAAAATATTAAA-GATTTGATAA
2626048 -TAAAATATTAAA-ATTTGATAA
1 TTAAAATATTAAAGATTTGATAA
2626069 CTTAAAATA
1 -TTAAAATA
2626078 AAAAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 8 0.30
23 19 0.70
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (23 bp):
TTAAAATATTAAAGATTTGATAA
Found at i:2628142 original size:20 final size:20
Alignment explanation
Indices: 2628117--2628154 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2628107 TAATTATGTC
2628117 AAAATAGATTAACTGTATTT
1 AAAATAGATTAACTGTATTT
* *
2628137 AAAATATATTATCTGTAT
1 AAAATAGATTAACTGTAT
2628155 CTGCCAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (20 bp):
AAAATAGATTAACTGTATTT
Found at i:2628203 original size:23 final size:23
Alignment explanation
Indices: 2628172--2628215 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2628162 AATATATATT
*
2628172 ATTTATATAATAAAATATTTAATC
1 ATTTATATAAAAAAAT-TTTAATC
2628196 ATTT-TATAAAAAAATTTTAA
1 ATTTATATAAAAAAATTTTAA
2628216 GACAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTTATATAAAAAAATTTTAATC
Found at i:2634287 original size:24 final size:24
Alignment explanation
Indices: 2634253--2634301 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2634243 GGGTGGAAAC
2634253 TTCTTGCGAATAGGAAGAATACAA
1 TTCTTGCGAATAGGAAGAATACAA
*
2634277 TTCTTGTGAATAGGAAGAATACAA
1 TTCTTGCGAATAGGAAGAATACAA
2634301 T
1 T
2634302 AGCTTCTGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (24 bp):
TTCTTGCGAATAGGAAGAATACAA
Found at i:2635879 original size:3 final size:3
Alignment explanation
Indices: 2635871--2635899 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2635861 ACGTTAAAGT
2635871 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
2635900 TTGATGCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:2643402 original size:24 final size:24
Alignment explanation
Indices: 2643375--2643435 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
2643365 AATATAATTT
2643375 TAATATAAATA-AAAAATAAAATCA
1 TAATATAAATATAAAAAT-AAATCA
* * *
2643399 TAAT-TATATATTAAAATAATTCA
1 TAATATAAATATAAAAATAAATCA
*
2643422 TAAAATAAATATAA
1 TAATATAAATATAA
2643436 CAACATAGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
23 13 0.45
24 16 0.55
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (24 bp):
TAATATAAATATAAAAATAAATCA
Found at i:2644800 original size:28 final size:27
Alignment explanation
Indices: 2644744--2644801 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
2644734 TTAATTAATA
*
2644744 AAATATTATTTTTATTTAATTTTAATTT
1 AAATATTATTTTTA-TAAATTTTAATTT
*
2644772 AAATATATATTTTTA-AAATTATTATTTT
1 AAATAT-TATTTTTATAAATT-TTAATTT
2644800 AA
1 AA
2644802 TTTCTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 4 0.15
28 14 0.54
29 8 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
AAATATTATTTTTATAAATTTTAATTT
Found at i:2645364 original size:42 final size:42
Alignment explanation
Indices: 2645317--2645406 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
2645307 TTAATCTAAG
*
2645317 ATTTAATTCAATTAATTTATATAATCATCTTTAAAAAATGAC
1 ATTTAATTCAATTAATTTATATAATCATCTTTAAAAAATAAC
* * *
2645359 ATTTAATTCAATTGATTTATATAATCGTTTTTAAAAAATAAC
1 ATTTAATTCAATTAATTTATATAATCATCTTTAAAAAATAAC
2645401 ATTTAA
1 ATTTAA
2645407 CAAGTTTGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (42 bp):
ATTTAATTCAATTAATTTATATAATCATCTTTAAAAAATAAC
Found at i:2648178 original size:6 final size:6
Alignment explanation
Indices: 2648158--2648200 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
2648148 ATAATAAAAT
*
2648158 ATTTTA ATTTATTA ATTTTA ATTTTTA ATTTTA ATTTTT ATTT
1 ATTTTA A-TT-TTA ATTTTA A-TTTTA ATTTTA ATTTTA ATTT
2648201 ACTCATTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
6 19 0.58
7 10 0.30
8 4 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
ATTTTA
Found at i:2648185 original size:7 final size:7
Alignment explanation
Indices: 2648159--2648197 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
2648149 TAATAAAATA
2648159 TTTTAAT
1 TTTTAAT
2648166 TTATTAA-
1 TT-TTAAT
2648173 TTTTAAT
1 TTTTAAT
2648180 TTTTAA-
1 TTTTAAT
2648186 TTTTAAT
1 TTTTAAT
2648193 TTTTA
1 TTTTA
2648198 TTTACTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 10 0.34
7 15 0.52
8 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTAAT
Found at i:2648187 original size:13 final size:13
Alignment explanation
Indices: 2648158--2648197 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
2648148 ATAATAAAAT
2648158 ATTTTAATTTATTA
1 ATTTTAATTT-TTA
2648172 ATTTTAATTTTTA
1 ATTTTAATTTTTA
2648185 ATTTTAATTTTTA
1 ATTTTAATTTTTA
2648198 TTTACTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTAATTTTTA
Found at i:2648658 original size:21 final size:20
Alignment explanation
Indices: 2648633--2648720 Score: 56
Period size: 21 Copynumber: 4.2 Consensus size: 20
2648623 AGCGTATTAA
2648633 ATTTAAAATTTAATTTAATTG
1 ATTTAAAA-TTAATTTAATTG
*
2648654 ATTTATATAATT-ATTT--TTT
1 ATTTA-A-AATTAATTTAATTG
* *
2648673 ATTTAAAAATAATTAATATATTAA
1 ATTTAAAATTAATT--TA-ATT-G
2648697 ATTTAAAATTTAATTTAATTG
1 ATTTAAAA-TTAATTTAATTG
2648718 ATT
1 ATT
2648721 CATATAATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 20
0.68 0.06 0.26
Matches are distributed among these distances:
17 3 0.06
18 4 0.08
19 7 0.13
20 1 0.02
21 12 0.23
22 6 0.12
23 6 0.12
24 8 0.15
25 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTAAAATTAATTTAATTG
Found at i:2648766 original size:59 final size:62
Alignment explanation
Indices: 2648630--2648768 Score: 203
Period size: 64 Copynumber: 2.3 Consensus size: 62
2648620 GTTAGCGTAT
* *
2648630 TAAATTTAAAATTTAATTTAATTGATTTATATAATTATTTTTTATTTAAAAATAATTAATATAT
1 TAAATTTAAAATTTAATTTAATTGATTCATATAATTATTTTTTA--TAAAAATAATTAATATAA
2648694 TAAATTTAAAATTTAATTTAATTGATTCATATAATTATTTTTTA-AAAAATAA-T-ATATAA
1 TAAATTTAAAATTTAATTTAATTGATTCATATAATTATTTTTTATAAAAATAATTAATATAA
* *
2648753 TAATTTTATAATTTAA
1 TAAATTTAAAATTTAA
2648769 ATTTTAGCAT
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
59 19 0.27
60 1 0.01
61 8 0.11
64 43 0.61
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (62 bp):
TAAATTTAAAATTTAATTTAATTGATTCATATAATTATTTTTTATAAAAATAATTAATATAA
Found at i:2652123 original size:9 final size:10
Alignment explanation
Indices: 2652101--2652135 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
2652091 CAGGGAAGGG
*
2652101 AAGAAGGAAA
1 AAGAAAGAAA
2652111 AAGAAAG-AA
1 AAGAAAGAAA
2652120 AAGAAAGAAA
1 AAGAAAGAAA
2652130 AAGAAA
1 AAGAAA
2652136 AATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:2652153 original size:14 final size:14
Alignment explanation
Indices: 2652134--2652173 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
2652124 AAGAAAAAGA
2652134 AAAAT-ATATATAAT
1 AAAATAATA-ATAAT
2652148 AAAATAATAATAAT
1 AAAATAATAATAAT
2652162 AATAATAATAAT
1 AA-AATAATAAT
2652174 GAAAAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:2652156 original size:3 final size:3
Alignment explanation
Indices: 2652143--2652173 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2652133 AAAAATATAT
2652143 ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2652174 GAAAAAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2652361 original size:27 final size:27
Alignment explanation
Indices: 2652331--2652409 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
2652321 GATAATTTCT
*
2652331 TTTAATTAAAAATTAAATAATTTTAAA
1 TTTAATTAAAAATCAAATAATTTTAAA
* * *
2652358 TTTATTTAAATATCAAA-ATTATTTAAA
1 TTTAATTAAAAATCAAATAAT-TTTAAA
*
2652385 TTATAATTGAAAATCAAATCAATTT
1 TT-TAATTAAAAATCAAAT-AATTT
2652410 AGATATATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
26 2 0.05
27 22 0.55
28 12 0.30
29 2 0.05
30 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (27 bp):
TTTAATTAAAAATCAAATAATTTTAAA
Found at i:2652479 original size:21 final size:21
Alignment explanation
Indices: 2652453--2652503 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2652443 TATGGTATGG
* *
2652453 ATTTTATTTTTTTAATAAATA
1 ATTTTATTTGTTTAACAAATA
*
2652474 ATTTTATTTGTTTACCAAATA
1 ATTTTATTTGTTTAACAAATA
*
2652495 ATCTTATTT
1 ATTTTATTT
2652504 AAAATTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTTATTTGTTTAACAAATA
Found at i:2653432 original size:642 final size:627
Alignment explanation
Indices: 2652212--2653481 Score: 1985
Period size: 642 Copynumber: 2.0 Consensus size: 627
2652202 GATTTATCTA
* *
2652212 ATATATATATATATATATTATATAACAATATACACAAACTAGTTTGTCATATAAGCGTTTATGTG
1 ATATATATATATATATATTATATAACAACATACACAAACTAATTTGTCATATAAGCGTTTATGTG
2652277 GACAACTCTTTTAAATGACACATAAGTAGTTTTTAAAAGAATAAGATAATTTCTTTTAATTAAAA
66 GACAACTCTTTTAAATGACACATAAGTAGTTTTTAAAAGAATAAGATAATTTCTTTTAATTAAAA
* *
2652342 ATTAAATAATTTTAAATTTATTTAAATATCAAAATTATTTAAATTATAATTGAAAATCAAATCAA
131 ATTAAATAATTTTAAATTTACTCAAATATCAAAATTATTTAAATTATAATTGAAAATCAAATCAA
* * *
2652407 TTTAGATATATATATTCTAAAATTAAATATATGAAATATGGTATGGATTTTATTTTTTTAATAAA
196 TTCAGATATATATATTCTAAAATTAAAAATATGAAATATGGAATGG----TATTTTTTTAATAAA
* **
2652472 TAATTTTATTTGTTTACCAAATAATCTTATTTAAAATTTTATTTACTTATCAAAATCTTTCAAAC
257 TAATTTTAGTTGTTTACCAAATAATCTTATTTAAAAAATTATTTACTTATCAAAATCTTTCAAAC
* * *
2652537 ATATTTAAAAATTACAACGATTAAGTTTATCCAAATATTTCAACCATATTTTTTTTATCTTGATT
322 ATATTTAAAAATTACAAAGATTAAGTTTATCCAAATATTTCAACAATATTTTTTTTATCTTAATT
2652602 TAAAAAATTTACGTAAAACATTAAAAATTCAAATAATTTTATGTAAGATTTTAAGAATTTTAAAA
387 TAAAAAATTTACGTAAAACATTAAAAATTCAAATAATTTTATGTAAGATTTTAAGAATTTTAAAA
2652667 ATTTTCATCTTAAATCTTTAAATAATAAGATTACCAAAATGATTATATCTATTTGAACTCTAATT
452 ATTTTCATCTTAAATCTTTAAATAATAAGATTACCAAAATGATTATATCTATTTGAACTCTAATT
*
2652732 ATCAAATTTATATTTAAAATAAATGCAAAAAATTTAATATTATCTATATTACTTATTATATCCAT
517 ATCAAATTTATATTTAAAATAAATGCAAAAAATTTAATATTATCTATATCACTTATTATATCCAT
2652797 TTTAAATTTTAAAAAATTAATTTAAAAAGT-ATCTATTTAATCTAAT
582 TTTAAATTTTAAAAAATTAATTTAAAAA-TAATCTATTTAATCTAAT
2652843 ATATATATATATATATATTATATAACAACATACACAAA-TAAATTTGTCATATAAGCGTTTATGT
1 ATATATATATATATATATTATATAACAACATACACAAACT-AATTTGTCATATAAGCGTTTATGT
* * * * *
2652907 GGAGAATTCTTTTAAATGACACATAGGTAGTGTTTTAAAAGAATAAGATAGTTTCTTTTAATTAC
65 GGACAACTCTTTTAAATGACACATAAGTAGT-TTTTAAAAGAATAAGATAATTTCTTTTAATTAA
* *
2652972 AAATTAAATAATTTTAAATTTACTCAAATATCAAAATTATTTAAATTATAATTGAAAATTAAATT
129 AAATTAAATAATTTTAAATTTACTCAAATATCAAAATTATTTAAATTATAATTGAAAATCAAATC
2653037 AATTCAGATATATATATTCTAAAATTAAAAATATGAAATATGGAATGG-ATTTTTTTAATAAATA
194 AATTCAGATATATATATTCTAAAATTAAAAATATGAAATATGGAATGGTATTTTTTTAATAAATA
2653101 ATTTTAGTTGTTTACCAAATAATCTTATTTAAAAAATTATTTACTTATCAAAATCTTTCAAACAT
259 ATTTTAGTTGTTTACCAAATAATCTTATTTAAAAAATTATTTACTTATCAAAATCTTTCAAACAT
*
2653166 ATTTAAAAATTACAAAGATTAAGTTTATTCAAATATTTCAACAATA-TTTTTTTATCTTAATTTA
324 ATTTAAAAATTACAAAGATTAAGTTTATCCAAATATTTCAACAATATTTTTTTTATC-----TT-
* * *
2653230 AAAAATTCTCTTTTAAAAAATTTTATGTAAGACATTAAAAATTCAAGTAATTTTATGTAAG--TT
383 ---AA------TTTAAAAAA-TTTACGTAAAACATTAAAAATTCAAATAATTTTATGTAAGATTT
* * *
2653293 TATGAAATTTTAAAAAATTTTCATCTTAAATCTTTAAATAATAAGATTATCAAAATGATTATATT
438 TAAG-AATTTT-AAAAATTTTCATCTTAAATCTTTAAATAATAAGATTACCAAAATGATTATATC
** * *
2653358 TATTTGAACTCTAATTATCACTTTTATATTTAAAATAAATGCAACAAATTTAATATTATCTTTAT
501 TATTTGAACTCTAATTATCAAATTTATATTTAAAATAAATGCAAAAAATTTAATATTATCTATAT
2653423 CACTTATTATATCCATTTTAAATTTTAAAAAATTAATTTAAAAATAATCTATTTAATCT
566 CACTTATTATATCCATTTTAAATTTTAAAAAATTAATTTAAAAATAATCTATTTAATCT
2653482 TAATTTCACT
Statistics
Matches: 586, Mismatches: 32, Indels: 31
0.90 0.05 0.05
Matches are distributed among these distances:
626 10 0.02
627 121 0.21
630 1 0.00
631 90 0.15
632 137 0.23
635 1 0.00
640 5 0.01
641 16 0.03
642 205 0.35
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (627 bp):
ATATATATATATATATATTATATAACAACATACACAAACTAATTTGTCATATAAGCGTTTATGTG
GACAACTCTTTTAAATGACACATAAGTAGTTTTTAAAAGAATAAGATAATTTCTTTTAATTAAAA
ATTAAATAATTTTAAATTTACTCAAATATCAAAATTATTTAAATTATAATTGAAAATCAAATCAA
TTCAGATATATATATTCTAAAATTAAAAATATGAAATATGGAATGGTATTTTTTTAATAAATAAT
TTTAGTTGTTTACCAAATAATCTTATTTAAAAAATTATTTACTTATCAAAATCTTTCAAACATAT
TTAAAAATTACAAAGATTAAGTTTATCCAAATATTTCAACAATATTTTTTTTATCTTAATTTAAA
AAATTTACGTAAAACATTAAAAATTCAAATAATTTTATGTAAGATTTTAAGAATTTTAAAAATTT
TCATCTTAAATCTTTAAATAATAAGATTACCAAAATGATTATATCTATTTGAACTCTAATTATCA
AATTTATATTTAAAATAAATGCAAAAAATTTAATATTATCTATATCACTTATTATATCCATTTTA
AATTTTAAAAAATTAATTTAAAAATAATCTATTTAATCTAAT
Found at i:2657303 original size:13 final size:13
Alignment explanation
Indices: 2657285--2657311 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2657275 TGTTGGTCAA
2657285 TCTGTTAAAACTT
1 TCTGTTAAAACTT
2657298 TCTGTTAAAACTT
1 TCTGTTAAAACTT
2657311 T
1 T
2657312 GAAAGCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (13 bp):
TCTGTTAAAACTT
Found at i:2665020 original size:23 final size:23
Alignment explanation
Indices: 2664989--2665036 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2664979 GTTTTCCTAT
2664989 TTTTAGGGGTGTCCAGA-AGAAAA
1 TTTTAGGGGTGTCCA-ACAGAAAA
*
2665012 TTTTGGGGGTGTCCAACAGAAAA
1 TTTTAGGGGTGTCCAACAGAAAA
2665035 TT
1 TT
2665037 CTCCTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.29
Consensus pattern (23 bp):
TTTTAGGGGTGTCCAACAGAAAA
Found at i:2667391 original size:19 final size:17
Alignment explanation
Indices: 2667369--2667406 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
2667359 CAACACTTTG
2667369 TTTTGTTTTTGTTTTGTTT
1 TTTTGTTTTT-TTTT-TTT
2667388 TTTTGTTTTTTTTTTTT
1 TTTTGTTTTTTTTTTTT
2667405 TT
1 TT
2667407 CTGCTAGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (17 bp):
TTTTGTTTTTTTTTTTT
Found at i:2667399 original size:11 final size:11
Alignment explanation
Indices: 2667365--2667406 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
2667355 TTAGCAACAC
*
2667365 TTTGTTTTGTT
1 TTTGTTTTTTT
2667376 TTTGTTTTGTTTT
1 TTTG-TTT-TTTT
2667389 TTTGTTTTTTT
1 TTTGTTTTTTT
2667400 TTT-TTTT
1 TTTGTTTT
2667407 CTGCTAGTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.14
11 11 0.39
12 6 0.21
13 7 0.25
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (11 bp):
TTTGTTTTTTT
Found at i:2667404 original size:13 final size:13
Alignment explanation
Indices: 2667369--2667404 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2667359 CAACACTTTG
*
2667369 TTTTGTTTTTGTT
1 TTTTTTTTTTGTT
*
2667382 TTGTTTTTTTGTT
1 TTTTTTTTTTGTT
2667395 TTTTTTTTTT
1 TTTTTTTTTT
2667405 TTCTGCTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTGTT
Found at i:2671753 original size:24 final size:24
Alignment explanation
Indices: 2671707--2671762 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
2671697 ATAATATTTG
* *
2671707 ATTTTTATAATATTAAATATAATT
1 ATTTTTAAAATATTAAAAATAATT
2671731 ATTTTTAAAAT-TTAAAAATTAATT
1 ATTTTTAAAATATTAAAAA-TAATT
*
2671755 ATTATTAA
1 ATTTTTAA
2671763 TAAAATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTTTAAAATATTAAAAATAATT
Found at i:2676383 original size:21 final size:22
Alignment explanation
Indices: 2676350--2676402 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
2676340 AATCAAAAAA
* * *
2676350 TTAAGATATAATTAAAT-AAAT
1 TTAATATAAAATTAAATCAAAC
2676371 TTAATATAAAATTAAATCAAAC
1 TTAATATAAAATTAAATCAAAC
2676393 TTATATATAA
1 TTA-ATATAA
2676403 TGAAGCTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 15 0.56
22 6 0.22
23 6 0.22
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
TTAATATAAAATTAAATCAAAC
Found at i:2679230 original size:4 final size:4
Alignment explanation
Indices: 2679221--2679255 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
2679211 TGCCAGTTAG
*
2679221 ATAC ATAC ATAC ATAC ATAC CTAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
2679256 TAACTAACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:2682960 original size:17 final size:17
Alignment explanation
Indices: 2682938--2682976 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2682928 TAAATTATTC
2682938 TTTAATTAATAAAATAT-
1 TTTAATT-ATAAAATATA
*
2682955 TTTAATTTTAAAATATA
1 TTTAATTATAAAATATA
2682972 TTTAA
1 TTTAA
2682977 AAAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAATTATAAAATATA
Found at i:2688034 original size:5 final size:5
Alignment explanation
Indices: 2688024--2688082 Score: 118
Period size: 5 Copynumber: 11.8 Consensus size: 5
2688014 TCGTACAATC
2688024 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
2688074 AACAT AACA
1 AACAT AACA
2688083 GATTATCATG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 54 1.00
ACGTcount: A:0.61, C:0.20, G:0.00, T:0.19
Consensus pattern (5 bp):
AACAT
Found at i:2696568 original size:6 final size:6
Alignment explanation
Indices: 2696557--2696584 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2696547 TTGCAATATC
2696557 AAATCT AAATCT AAATCT AAATCT AAAT
1 AAATCT AAATCT AAATCT AAATCT AAAT
2696585 TTATTGTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATCT
Found at i:2699373 original size:20 final size:19
Alignment explanation
Indices: 2699336--2699373 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2699326 TGAAAATTTT
*
2699336 TTTGGGGCCATTGAAAAAC
1 TTTGGGGCCATAGAAAAAC
2699355 TTTGGGGCCAATAGAAAAA
1 TTTGGGGCC-ATAGAAAAA
2699374 AATTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (19 bp):
TTTGGGGCCATAGAAAAAC
Found at i:2699400 original size:15 final size:16
Alignment explanation
Indices: 2699375--2699404 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2699365 ATAGAAAAAA
2699375 ATTTAAATTTAATTTG
1 ATTTAAATTTAATTTG
2699391 ATTT-AATTTAATTT
1 ATTTAAATTTAATTT
2699405 ATGGTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
ATTTAAATTTAATTTG
Found at i:2700080 original size:21 final size:21
Alignment explanation
Indices: 2700042--2700081 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2700032 TAAAAGTTTT
*
2700042 TTCTTTTCTAATTATTTTGGA
1 TTCTTTTATAATTATTTTGGA
2700063 TTCTTTTATGAATT-TTTTG
1 TTCTTTTAT-AATTATTTTG
2700082 ACAAAGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.65
Consensus pattern (21 bp):
TTCTTTTATAATTATTTTGGA
Found at i:2700471 original size:13 final size:12
Alignment explanation
Indices: 2700437--2700483 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
2700427 TAATCACAAC
2700437 TCTTTTTA-TTT
1 TCTTTTTATTTT
2700448 TCTTTTTATTTT
1 TCTTTTTATTTT
*
2700460 TGTTTTTGATTTT
1 TCTTTTT-ATTTT
2700473 T-TATTTTATTT
1 TCT-TTTTATTT
2700484 CCATTTCCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 8 0.25
12 14 0.44
13 10 0.31
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.81
Consensus pattern (12 bp):
TCTTTTTATTTT
Found at i:2700513 original size:3 final size:3
Alignment explanation
Indices: 2700507--2700545 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2700497 TTTTTGTGTT
2700507 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2700546 AAAGAGTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2700656 original size:21 final size:21
Alignment explanation
Indices: 2700602--2700659 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
2700592 GTATATATTT
*
2700602 TTACATGATTA-TTA-ATTAA
1 TTACATGATAATTTATATTAA
**
2700621 TTACATGATGTTTTATATTAA
1 TTACATGATAATTTATATTAA
*
2700642 TTGCATGATAATTTATAT
1 TTACATGATAATTTATAT
2700660 ATTATATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 9 0.28
20 3 0.09
21 20 0.62
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (21 bp):
TTACATGATAATTTATATTAA
Found at i:2700700 original size:19 final size:19
Alignment explanation
Indices: 2700678--2700714 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2700668 ATTGCATAAT
**
2700678 TATATTATTTTTGTATGAC
1 TATATTATAATTGTATGAC
2700697 TATATTATAATTGTATGA
1 TATATTATAATTGTATGA
2700715 TATTATTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.54
Consensus pattern (19 bp):
TATATTATAATTGTATGAC
Found at i:2709313 original size:59 final size:59
Alignment explanation
Indices: 2709247--2709367 Score: 233
Period size: 59 Copynumber: 2.1 Consensus size: 59
2709237 ATGAGTCTCC
2709247 AAAATTGATTTAGTGAATAATATTCATAAGAAGAAGAAAAAAAAAATGTAGTAGAGAAG
1 AAAATTGATTTAGTGAATAATATTCATAAGAAGAAGAAAAAAAAAATGTAGTAGAGAAG
*
2709306 AAAATTGATTTAGTGAATAATATTCATAAGAAGAAGAAAAAAAATATGTAGTAGAGAAG
1 AAAATTGATTTAGTGAATAATATTCATAAGAAGAAGAAAAAAAAAATGTAGTAGAGAAG
2709365 AAA
1 AAA
2709368 GAACAATGAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.56, C:0.02, G:0.18, T:0.24
Consensus pattern (59 bp):
AAAATTGATTTAGTGAATAATATTCATAAGAAGAAGAAAAAAAAAATGTAGTAGAGAAG
Found at i:2709413 original size:64 final size:64
Alignment explanation
Indices: 2709333--2709461 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
2709323 TAATATTCAT
2709333 AAGAAGAAGAAAAAAAATATGTAGTAGAGAAGAAAGAACAATGATGCATAAAATTAACTTTTAA
1 AAGAAGAAGAAAAAAAATATGTAGTAGAGAAGAAAGAACAATGATGCATAAAATTAACTTTTAA
2709397 AAGAAGAAGAAAAAAAATATGTAGTAGAGAAGAAAGAACAATGATGCATAAAATTAACTTTTAA
1 AAGAAGAAGAAAAAAAATATGTAGTAGAGAAGAAAGAACAATGATGCATAAAATTAACTTTTAA
2709461 A
1 A
2709462 GATTCTTCGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.58, C:0.05, G:0.17, T:0.20
Consensus pattern (64 bp):
AAGAAGAAGAAAAAAAATATGTAGTAGAGAAGAAAGAACAATGATGCATAAAATTAACTTTTAA
Found at i:2710072 original size:3 final size:3
Alignment explanation
Indices: 2710064--2710095 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2710054 AAAGGAAACA
2710064 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2710096 TGAAAGAAAG
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2712490 original size:22 final size:23
Alignment explanation
Indices: 2712465--2712512 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
2712455 TTCTCTCTAA
2712465 TTTAATTTAAT-TTTCTAATT-AT
1 TTTAATTTAATCTTT-TAATTCAT
*
2712487 TTT-ATTTTATCTTTTAATTCAT
1 TTTAATTTAATCTTTTAATTCAT
2712509 TTTA
1 TTTA
2712513 TTATATCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTAATTTAATCTTTTAATTCAT
Found at i:2712513 original size:22 final size:21
Alignment explanation
Indices: 2712480--2712520 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2712470 TTTAATTTTC
*
2712480 TAATTATTTTATTTTATCTTT
1 TAATTATTTTATTATATCTTT
2712501 TAATTCATTTTATTATATCT
1 TAATT-ATTTTATTATATCT
2712521 CTTGTAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (21 bp):
TAATTATTTTATTATATCTTT
Found at i:2712927 original size:2 final size:2
Alignment explanation
Indices: 2712920--2712950 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2712910 TTCCTTGGGC
2712920 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2712951 ACTTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2716079 original size:24 final size:19
Alignment explanation
Indices: 2716029--2716067 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2716019 ATATGGTCCT
2716029 TTTTTATAAAATTAAATTA
1 TTTTTATAAAATTAAATTA
2716048 TTTTTATAAAATTAAATTA
1 TTTTTATAAAATTAAATTA
2716067 T
1 T
2716068 AGTGTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTTATAAAATTAAATTA
Found at i:2724279 original size:2 final size:2
Alignment explanation
Indices: 2724274--2724314 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2724264 CGTGTGTGTG
2724274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2724315 TTTGAACCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2725586 original size:77 final size:77
Alignment explanation
Indices: 2725481--2725632 Score: 241
Period size: 77 Copynumber: 2.0 Consensus size: 77
2725471 ATAGAATAAC
* * * * *
2725481 ACTATCAATCAAATGATTATAGATATGAGAGATTGGAGGACCAACGTCCTCTAAGAAAGGCGAAG
1 ACTATCAATCAAATGATCAGAGATATGAGAGATTGGAGGACCAACGTCCCCCAAGAAAGGCGAAA
2725546 GAGGCAATAAAT
66 GAGGCAATAAAT
* *
2725558 ACTATCAATCAAATGATCAGAGATATGAGAGATTGGGGGACCAACGTCCCCCAAGAGAGGCGAAA
1 ACTATCAATCAAATGATCAGAGATATGAGAGATTGGAGGACCAACGTCCCCCAAGAAAGGCGAAA
2725623 GAGGCAATAA
66 GAGGCAATAA
2725633 CGTGGCTATA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (77 bp):
ACTATCAATCAAATGATCAGAGATATGAGAGATTGGAGGACCAACGTCCCCCAAGAAAGGCGAAA
GAGGCAATAAAT
Found at i:2731628 original size:37 final size:36
Alignment explanation
Indices: 2731556--2731637 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 36
2731546 ATTTTTATAT
2731556 TGATATAAATTATAATATATAATTTTTATAAAAAATA
1 TGATATAAATTATAATATATAATTTTTAT-AAAAATA
*
2731593 TGATATAAATATATAA-ATTTTAATATTTTAT-AAAATA
1 TGATATAAAT-TATAATA-TATAAT-TTTTATAAAAATA
2731630 TGAATATA
1 TG-ATATA
2731638 TAAATCATGA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
37 19 0.47
38 15 0.38
39 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (36 bp):
TGATATAAATTATAATATATAATTTTTATAAAAATA
Found at i:2743031 original size:3 final size:3
Alignment explanation
Indices: 2743025--2743052 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2743015 GGAGGAAATT
2743025 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2743053 GCCGAGGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2747255 original size:16 final size:15
Alignment explanation
Indices: 2747234--2747263 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
2747224 ATTGATAAAA
2747234 CTCTTTCTTTTTTTTT
1 CTCTTT-TTTTTTTTT
2747250 CTCTTTTTTTTTTT
1 CTCTTTTTTTTTTT
2747264 GGTGGCAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
CTCTTTTTTTTTTTT
Found at i:2748506 original size:16 final size:16
Alignment explanation
Indices: 2748485--2748522 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2748475 TGAGTTTCAA
2748485 TTTTTCT-TCCTGTTTT
1 TTTTTCTCT-CTGTTTT
*
2748501 TTTTTCTCTCTTTTTT
1 TTTTTCTCTCTGTTTT
2748517 TTTTTC
1 TTTTTC
2748523 AGATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTCTCTCTGTTTT
Found at i:2748589 original size:27 final size:27
Alignment explanation
Indices: 2748564--2748615 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
2748554 GTGTAAATTA
2748564 TTTT-ATA-TAAATTAATTTCAATAAT
1 TTTTAATAGTAAATTAATTTCAATAAT
** *
2748589 TTTTAATAGTTTATTAATTTCATTAAT
1 TTTTAATAGTAAATTAATTTCAATAAT
2748616 ATCAATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 4 0.18
26 3 0.14
27 15 0.68
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTTAATAGTAAATTAATTTCAATAAT
Found at i:2754770 original size:32 final size:32
Alignment explanation
Indices: 2754734--2754794 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
2754724 AAGAGGAACC
*
2754734 AAATGTCATGTCACTCAAATATGAATTATGAG
1 AAATGTCAAGTCACTCAAATATGAATTATGAG
* * *
2754766 AAATGTCAAGTCATTCGAATTTGAATTAT
1 AAATGTCAAGTCACTCAAATATGAATTAT
2754795 AAATAGCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (32 bp):
AAATGTCAAGTCACTCAAATATGAATTATGAG
Found at i:2757742 original size:22 final size:24
Alignment explanation
Indices: 2757714--2757763 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2757704 AATTTAATTA
2757714 TTTAAAT-A-ACATAAATAATTTT
1 TTTAAATCATACATAAATAATTTT
*
2757736 TTTAAATCATATATAAATAATTTT
1 TTTAAATCATACATAAATAATTTT
2757760 TTTA
1 TTTA
2757764 CTCATATAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 7 0.28
23 1 0.04
24 17 0.68
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTAAATCATACATAAATAATTTT
Found at i:2757768 original size:23 final size:24
Alignment explanation
Indices: 2757724--2757771 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
2757714 TTTAAATAAC
2757724 ATAAATAATTTTTTTAAATCATAT
1 ATAAATAATTTTTTTAAATCATAT
*
2757748 ATAAATAATTTTTTT-ACTCATAT
1 ATAAATAATTTTTTTAAATCATAT
2757771 A
1 A
2757772 AGACCCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (24 bp):
ATAAATAATTTTTTTAAATCATAT
Found at i:2764994 original size:17 final size:16
Alignment explanation
Indices: 2764938--2764994 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 16
2764928 GCAAATATGT
*
2764938 TAATAAATTACAAAAAA
1 TAATAAAATA-AAAAAA
2764955 TAA-AAACATTAAAAAAA
1 TAATAAA-A-TAAAAAAA
2764972 TGAATAAAATAAAAAATA
1 T-AATAAAATAAAAAA-A
2764990 TAATA
1 TAATA
2764995 CGAAAAGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
16 3 0.09
17 21 0.62
18 7 0.21
19 3 0.09
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (16 bp):
TAATAAAATAAAAAAA
Found at i:2766108 original size:20 final size:20
Alignment explanation
Indices: 2766067--2766115 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
2766057 TTATTCGAAA
2766067 TTTAA-TTTTAATTTGATGAG
1 TTTAATTTTTAATTT-ATGAG
2766087 TTTTAATTTTTAATTT-TGAG
1 -TTTAATTTTTAATTTATGAG
2766107 TTTAATTTT
1 TTTAATTTT
2766116 AAATAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.33
20 4 0.15
21 5 0.19
22 9 0.33
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (20 bp):
TTTAATTTTTAATTTATGAG
Found at i:2768780 original size:14 final size:14
Alignment explanation
Indices: 2768745--2768779 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2768735 TGATATTAAA
2768745 AAATTTTAAAATTT
1 AAATTTTAAAATTT
*
2768759 AAATTTTAACATTT
1 AAATTTTAAAATTT
2768773 ATAATTT
1 A-AATTT
2768780 ATTTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (14 bp):
AAATTTTAAAATTT
Found at i:2773761 original size:3 final size:3
Alignment explanation
Indices: 2773753--2773778 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2773743 AAATCAATGT
2773753 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
2773779 GGGAAGATGA
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2775613 original size:12 final size:12
Alignment explanation
Indices: 2775595--2775626 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2775585 GTTTCCCAGT
2775595 GGAATGCCTGGA
1 GGAATGCCTGGA
*
2775607 GGTATGCCTGGA
1 GGAATGCCTGGA
2775619 GGAATGCC
1 GGAATGCC
2775627 CGGTGGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.41, T:0.19
Consensus pattern (12 bp):
GGAATGCCTGGA
Found at i:2775640 original size:24 final size:24
Alignment explanation
Indices: 2775565--2775641 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
2775555 CAGTAGTAAA
*
2775565 CCTGGAGGCATGCCTGGTGGGTTTC
1 CCTGGAGGAATGCCTGGT-GGTTTC
* * * * *
2775590 CC-AGTGGAATGCCTGGAGGTATG
1 CCTGGAGGAATGCCTGGTGGTTTC
*
2775613 CCTGGAGGAATGCCCGGTGGTTTC
1 CCTGGAGGAATGCCTGGTGGTTTC
2775637 CCTGG
1 CCTGG
2775642 TAGCATGCCA
Statistics
Matches: 39, Mismatches: 12, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
23 6 0.15
24 31 0.79
25 2 0.05
ACGTcount: A:0.13, C:0.23, G:0.39, T:0.25
Consensus pattern (24 bp):
CCTGGAGGAATGCCTGGTGGTTTC
Found at i:2776960 original size:22 final size:23
Alignment explanation
Indices: 2776934--2776981 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2776924 CCTGTGAGAG
2776934 TTTT-ATGCT-TTGTCAAATGGTT
1 TTTTAATGCTCTTGTC-AATGGTT
*
2776956 TTTTAATGTTCTTGTCAATGGTT
1 TTTTAATGCTCTTGTCAATGGTT
2776979 TTT
1 TTT
2776982 GTTGCAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 14 0.61
24 5 0.22
ACGTcount: A:0.17, C:0.08, G:0.17, T:0.58
Consensus pattern (23 bp):
TTTTAATGCTCTTGTCAATGGTT
Found at i:2778328 original size:2 final size:2
Alignment explanation
Indices: 2778321--2778346 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2778311 TCAGAAATTA
2778321 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
2778347 TGCTTTGTAG
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:2781898 original size:27 final size:27
Alignment explanation
Indices: 2781857--2781911 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
2781847 TTTGTGACAA
* *
2781857 TCATGTAGTAGTGAATGCCATTATAAT
1 TCATGTAATAATGAATGCCATTATAAT
*
2781884 TCATGTAATAATGAATGTCATTATAAT
1 TCATGTAATAATGAATGCCATTATAAT
2781911 T
1 T
2781912 AAGTACATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (27 bp):
TCATGTAATAATGAATGCCATTATAAT
Found at i:2782079 original size:2 final size:2
Alignment explanation
Indices: 2782067--2782105 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2782057 AAAACACTTC
* * *
2782067 TA TA TA AA TA TA TA TA AA TA CA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2782106 TCTTTGTGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2792735 original size:30 final size:30
Alignment explanation
Indices: 2792701--2792776 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
2792691 TATATCAAAG
* *
2792701 ATTTATTTAAATATAAATTAAAAGTTAAAT
1 ATTTATTTAAATATAAAATAAAAGTTAAAA
* * *
2792731 ATTTATTTGAATATAAAATGAAATTTAAAA
1 ATTTATTTAAATATAAAATAAAAGTTAAAA
2792761 ATTTATTTAAATATAA
1 ATTTATTTAAATATAA
2792777 TACAAGTACA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (30 bp):
ATTTATTTAAATATAAAATAAAAGTTAAAA
Found at i:2795661 original size:24 final size:27
Alignment explanation
Indices: 2795629--2795687 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
2795619 GAATACATAA
2795629 TTTATAATTATT-TATAA-ATA-TTTAT
1 TTTA-AATTATTATATAATATATTTTAT
2795654 TTTAAATTATTAAATATAATATATTTTAT
1 TTTAAATTATT--ATATAATATATTTTAT
2795683 TTTAA
1 TTTAA
2795688 TATGTGAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 7 0.24
25 4 0.14
27 5 0.17
28 3 0.10
29 10 0.34
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTAAATTATTATATAATATATTTTAT
Found at i:2796356 original size:21 final size:21
Alignment explanation
Indices: 2796330--2796409 Score: 65
Period size: 24 Copynumber: 3.7 Consensus size: 21
2796320 TTTTTAAATG
**
2796330 AAAAAATTTTAAATTTTATAA
1 AAAAAATTTTAAATTAAATAA
2796351 AAAAAA-TTTAAA-TAAATAA
1 AAAAAATTTTAAATTAAATAA
* *
2796370 AAATAAATTTGAAATTAGATTAA
1 AAA-AAATTTTAAATTA-AATAA
*
2796393 AAATTAAATTTAAAATT
1 AAA--AAATTTTAAATT
2796410 TCTTAATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
19 8 0.16
20 9 0.18
21 11 0.22
22 2 0.04
23 7 0.14
24 12 0.24
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
AAAAAATTTTAAATTAAATAA
Found at i:2796415 original size:23 final size:23
Alignment explanation
Indices: 2796348--2796409 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
2796338 TTAAATTTTA
*
2796348 TAAAAA-AAATTT-AAA-TA-AA
1 TAAAAATAAATTTAAAATTAGAT
*
2796367 TAAAAATAAATTTGAAATTAGAT
1 TAAAAATAAATTTAAAATTAGAT
2796390 TAAAAATTAAATTTAAAATT
1 TAAAAA-TAAATTTAAAATT
2796410 TCTTAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 6 0.17
20 6 0.17
21 3 0.08
22 2 0.06
23 7 0.19
24 12 0.33
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (23 bp):
TAAAAATAAATTTAAAATTAGAT
Found at i:2799372 original size:27 final size:27
Alignment explanation
Indices: 2799319--2799372 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2799309 ACATAAAATA
* * *
2799319 TTATAATATTATTTAATTTTATTTTAT
1 TTATAATATCATTTAATTTAATCTTAT
*
2799346 TTATAATATCATTTTATTTAATCTTAT
1 TTATAATATCATTTAATTTAATCTTAT
2799373 CATAATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (27 bp):
TTATAATATCATTTAATTTAATCTTAT
Found at i:2799380 original size:21 final size:20
Alignment explanation
Indices: 2799332--2799383 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
2799322 TAATATTATT
*
2799332 TAATTTTATTTTATTTATAA
1 TAATTTTATTTAATTTATAA
*
2799352 TATCATTTTATTTAATCTTATCA
1 TA--ATTTTATTTAAT-TTATAA
2799375 TAATTTTAT
1 TAATTTTAT
2799384 ATACAAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.07
21 7 0.26
22 11 0.41
23 7 0.26
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATTTTATTTAATTTATAA
Found at i:2799642 original size:29 final size:30
Alignment explanation
Indices: 2799582--2799642 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
2799572 AATTTACACC
* * **
2799582 TAAATAAGTTCTTAACTTTGAATTCGTATT
1 TAAATAAATTCTTAACTATGAATTAATATT
*
2799612 TAAATAAATTCTTAAC-ATGAATTAATTTT
1 TAAATAAATTCTTAACTATGAATTAATATT
2799641 TA
1 TA
2799643 TTTGAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (30 bp):
TAAATAAATTCTTAACTATGAATTAATATT
Found at i:2809782 original size:20 final size:22
Alignment explanation
Indices: 2809746--2809797 Score: 81
Period size: 21 Copynumber: 2.4 Consensus size: 22
2809736 CTCGAAATTA
2809746 ATAAAATATTAATTTTTAAAAT
1 ATAAAATATTAATTTTTAAAAT
2809768 ATAAAATATT-ATTTTT-AAAT
1 ATAAAATATTAATTTTTAAAAT
2809788 ATAAATATAT
1 ATAAA-ATAT
2809798 AAATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.31
21 10 0.34
22 10 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAAAATATTAATTTTTAAAAT
Found at i:2810188 original size:29 final size:28
Alignment explanation
Indices: 2810156--2810219 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 28
2810146 TAAGTAAGTC
2810156 TTTATATTT-TTATCGTATTCAAATAAATT
1 TTTATATTTATT-T-GTATTCAAATAAATT
2810185 TTTATTATTTAATTTGTATTCAAATAAATT
1 TTTA-TATTT-ATTTGTATTCAAATAAATT
2810215 TTTAT
1 TTTAT
2810220 TTGAAACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
29 5 0.16
30 24 0.75
31 1 0.03
32 2 0.06
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTATATTTATTTGTATTCAAATAAATT
Found at i:2810220 original size:16 final size:16
Alignment explanation
Indices: 2810171--2810220 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
2810161 ATTTTTATCG
2810171 TATTCAAATAAATTTT
1 TATTCAAATAAATTTT
* * *
2810187 TATT--ATTTAATTTG
1 TATTCAAATAAATTTT
2810201 TATTCAAATAAATTTT
1 TATTCAAATAAATTTT
2810217 TATT
1 TATT
2810221 TGAAACAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 11 0.42
16 15 0.58
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (16 bp):
TATTCAAATAAATTTT
Found at i:2810274 original size:21 final size:22
Alignment explanation
Indices: 2810245--2810296 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
2810235 ATTTATATTA
*
2810245 AAAATTTATTTAAATA-AAATT
1 AAAAGTTATTTAAATATAAATT
*
2810266 AAAAGTTATTTAGATATAAATT
1 AAAAGTTATTTAAATATAAATT
*
2810288 AAAGGTTAT
1 AAAAGTTAT
2810297 GAATTTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (22 bp):
AAAAGTTATTTAAATATAAATT
Found at i:2810305 original size:30 final size:30
Alignment explanation
Indices: 2810271--2810344 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
2810261 AAATTAAAAG
*
2810271 TTATTTAGATATAAATTAAAGGTT-ATGAAT
1 TTATTTAGATATAAATTAAAGGTTAAT-AAC
* ** *
2810301 TTATTTAAATGCAAATTAAAGTTTAATAAC
1 TTATTTAGATATAAATTAAAGGTTAATAAC
*
2810331 TTATTTAGGTATAA
1 TTATTTAGATATAA
2810345 CAAAACTACA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
30 32 0.94
31 2 0.06
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (30 bp):
TTATTTAGATATAAATTAAAGGTTAATAAC
Found at i:2810660 original size:36 final size:36
Alignment explanation
Indices: 2810620--2810693 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 36
2810610 TAACTAATAT
* *
2810620 ATCAAAATTAAAAGTTAATTGCTAAGTAGCTTTTTA
1 ATCAAAATTAAAAGTTAATTACTAAGTAACTTTTTA
* *
2810656 ATCAAAATTAAAAGTTAATTATTAAGTAATTTTTTA
1 ATCAAAATTAAAAGTTAATTACTAAGTAACTTTTTA
2810692 AT
1 AT
2810694 TAAGATACGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (36 bp):
ATCAAAATTAAAAGTTAATTACTAAGTAACTTTTTA
Found at i:2813939 original size:13 final size:13
Alignment explanation
Indices: 2813917--2813960 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2813907 ACGAATATCT
2813917 ATATTGAATTTAAA
1 ATATT-AATTTAAA
**
2813931 ATATTAATTTTTA
1 ATATTAATTTAAA
*
2813944 ATTTTAATTTAAA
1 ATATTAATTTAAA
2813957 ATAT
1 ATAT
2813961 ATAAATATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
ATATTAATTTAAA
Found at i:2815726 original size:52 final size:52
Alignment explanation
Indices: 2815642--2815769 Score: 161
Period size: 52 Copynumber: 2.5 Consensus size: 52
2815632 TATAAGCATA
*
2815642 CAAACTTATCTATTAAGAATCAT-TTTTCTCTTAGAATTATTCTTCTGCAAGT
1 CAAACTTGTCTATTAAGAAT-ATCTTTTCTCTTAGAATTATTCTTCTGCAAGT
* * * *
2815694 CAAACTTGCCTATTAAGAATATCTTTTTTCTTAGAATTTTTTTTCTGCAAGT
1 CAAACTTGTCTATTAAGAATATCTTTTCTCTTAGAATTATTCTTCTGCAAGT
**
2815746 C-TTCTTGTCTATTAAGTAATATCT
1 CAAACTTGTCTATTAAG-AATATCT
2815770 AAAAAATCTT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
51 14 0.21
52 52 0.79
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (52 bp):
CAAACTTGTCTATTAAGAATATCTTTTCTCTTAGAATTATTCTTCTGCAAGT
Found at i:2816270 original size:12 final size:11
Alignment explanation
Indices: 2816230--2816270 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
2816220 TTTTTTGACC
2816230 AAAA-AAAC-A
1 AAAATAAACAA
2816239 AAAATAAACAA
1 AAAATAAACAA
2816250 AAAATTAAACTAA
1 AAAA-TAAAC-AA
2816263 AAAATAAA
1 AAAATAAA
2816271 AATACAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.14
10 4 0.14
11 5 0.18
12 9 0.32
13 6 0.21
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.12
Consensus pattern (11 bp):
AAAATAAACAA
Found at i:2817345 original size:14 final size:14
Alignment explanation
Indices: 2817326--2817364 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2817316 GCACCCAAGC
* *
2817326 AAAAAATAAAAATT
1 AAAAAAAAAAAACT
2817340 AAAAAAAAAAAACT
1 AAAAAAAAAAAACT
2817354 AAAACAAAAAA
1 AAAA-AAAAAA
2817365 GTCCATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAAAAAAAAACT
Found at i:2821306 original size:15 final size:15
Alignment explanation
Indices: 2821280--2821345 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
2821270 ATTCACAAAT
*
2821280 GAGTTTAAGGTTTTA
1 GAGTTTAGGGTTTTA
* *
2821295 GGGTTTAGGGTTTAAA
1 GAGTTTAGGGTTT-TA
* *
2821311 GAGTTT-TGATTTTA
1 GAGTTTAGGGTTTTA
2821325 G-GATTTAGGGTTTTA
1 GAG-TTTAGGGTTTTA
2821340 GAGTTT
1 GAGTTT
2821346 TGATTTTAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
13 1 0.03
14 5 0.13
15 25 0.66
16 7 0.18
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (15 bp):
GAGTTTAGGGTTTTA
Found at i:2821352 original size:29 final size:30
Alignment explanation
Indices: 2821290--2821359 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 30
2821280 GAGTTTAAGG
*
2821290 TTTTAGGGTTTAGGGTTTAAAGAGTTTTGA
1 TTTTAGGATTTAGGGTTTAAAGAGTTTTGA
*
2821320 TTTTAGGATTTAGGGTTT-TAGAGTTTTGA
1 TTTTAGGATTTAGGGTTTAAAGAGTTTTGA
2821349 TTTTAGGATTT
1 TTTTAGGATTT
2821360 GAAGTTTAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 21 0.55
30 17 0.45
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.51
Consensus pattern (30 bp):
TTTTAGGATTTAGGGTTTAAAGAGTTTTGA
Found at i:2821366 original size:29 final size:28
Alignment explanation
Indices: 2821290--2821374 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 28
2821280 GAGTTTAAGG
* *
2821290 TTTTAGGGTTTAGGGTTTAAAGAGTTTTGA
1 TTTTAGGATTTAGAGTTT--AGAGTTTTGA
*
2821320 TTTTAGGATTTAGGGTTTTAGAGTTTTGA
1 TTTTAGGATTTAGAG-TTTAGAGTTTTGA
*
2821349 TTTTAGGATTT-GAAGTTTAGGGTTTT
1 TTTTAGGATTTAG-AGTTTAGAGTTTT
2821375 AAATTTTTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
28 11 0.22
29 22 0.44
30 14 0.28
31 3 0.06
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (28 bp):
TTTTAGGATTTAGAGTTTAGAGTTTTGA
Found at i:2821804 original size:3 final size:3
Alignment explanation
Indices: 2821798--2821867 Score: 95
Period size: 3 Copynumber: 23.3 Consensus size: 3
2821788 TTTAAATCAA
* * * * *
2821798 TAT TAT TAT TAT TAT TGT TGT TGT TGT TGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2821846 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
2821868 TACTAATTAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2822058 original size:20 final size:19
Alignment explanation
Indices: 2822035--2822087 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
2822025 AAAATTTATT
2822035 AATTATCATGCAATAATAGC
1 AATTATCATGCAATAATA-C
*
2822055 AATTAT-AT-AAAT-ATAC
1 AATTATCATGCAATAATAC
2822071 AA-TATCATGCAATAATA
1 AATTATCATGCAATAATA
2822088 TAAAATACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 3 0.11
16 5 0.18
17 6 0.21
18 6 0.21
19 2 0.07
20 6 0.21
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (19 bp):
AATTATCATGCAATAATAC
Found at i:2822288 original size:24 final size:25
Alignment explanation
Indices: 2822237--2822296 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
2822227 GATCATTCAA
*
2822237 ATATAATATTA-ATCATGCAATAAC
1 ATATAATATCATATCATGCAATAAC
*
2822261 ATATAATATCATATCATGCAAT-AT
1 ATATAATATCATATCATGCAATAAC
*
2822285 ATATAAAATCAT
1 ATATAATATCAT
2822297 GCAATAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 22 0.69
25 10 0.31
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (25 bp):
ATATAATATCATATCATGCAATAAC
Found at i:2822430 original size:32 final size:32
Alignment explanation
Indices: 2822389--2822616 Score: 113
Period size: 32 Copynumber: 7.7 Consensus size: 32
2822379 TAACAATGTA
2822389 AATCATGCAAATAAACATATAATTAAATATAT
1 AATCATGCAAATAAACATATAATTAAATATAT
*
2822421 AATCATGCAAACAAA-A-AT-A-T---T-TA-
1 AATCATGCAAATAAACATATAATTAAATATAT
* * * *
2822444 AACCATGCAAATAAATATACAATTTAATATAT
1 AATCATGCAAATAAACATATAATTAAATATAT
* *
2822476 AATCATGC-AAT-CACATGAATAAATAAAT-TAAT
1 AATCATGCAAATAAACAT--ATAATTAAATAT-AT
* * * * *
2822508 AATCACGCAATTAGACATGCT-TTTAAATATAT
1 AATCATGCAAATAAACAT-ATAATTAAATATAT
*
2822540 AATCATGCAAAT---GATA-ACA-T---TA-AT
1 AATCATGCAAATAAACATATA-ATTAAATATAT
*
2822564 AATCATGCAAATAAACATACAATTAAATATAT
1 AATCATGCAAATAAACATATAATTAAATATAT
* *
2822596 AATCTTGCAAATAAAAATATA
1 AATCATGCAAATAAACATATA
2822617 TAAACCATTC
Statistics
Matches: 144, Mismatches: 26, Indels: 52
0.65 0.12 0.23
Matches are distributed among these distances:
23 13 0.09
24 17 0.12
25 4 0.03
26 1 0.01
27 5 0.03
28 4 0.03
29 3 0.02
30 6 0.04
31 9 0.06
32 74 0.51
33 4 0.03
34 4 0.03
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (32 bp):
AATCATGCAAATAAACATATAATTAAATATAT
Found at i:2822455 original size:55 final size:55
Alignment explanation
Indices: 2822387--2822802 Score: 254
Period size: 55 Copynumber: 7.3 Consensus size: 55
2822377 ATTAACAATG
*
2822387 TAAATCATGCAAATAAACATATAATTAAATATATAATCATGCAAACAAAAATATT
1 TAAATCATGCAAATAAACATATAATTAAATATATAATCATGCAAATAAAAATATT
* * * *
2822442 TAAACCATGCAAATAAATATACAATTTAATATATAATCATGCAATCACATGAATAAATAAATT
1 TAAATCATGCAAATAAACATATAATTAAATATATAATCATGC-A--A-AT-AA-AAAT--ATT
* * * * * * * * *
2822505 AATAATCACGCAATTAGACATGCT-TTTAAATATATAATCATGCAAATGATAACATT
1 TA-AATCATGCAAATAAACAT-ATAATTAAATATATAATCATGCAAATAAAAATATT
* * * *
2822561 AATAATCATGCAAATAAACATACAATTAAATATATAATCTTGCAAATAAAAATATA
1 TA-AATCATGCAAATAAACATATAATTAAATATATAATCATGCAAATAAAAATATT
* * * * *
2822617 TAAACCATTCAAAT-AA-ATATACATATAAATTTATAATCATGCAAATAACAATATA
1 TAAATCATGCAAATAAACATATA-AT-TAAATATATAATCATGCAAATAAAAATATT
* * * * *
2822672 TGAATCATGC-AAT---CATGTAAATAATAATATATAAACCATGCAAAATATGCAATTAA-ATA
1 TAAATCATGCAAATAAACATAT-AATTA-AATATAT-AATCATGC-AAATA---AA--AATATT
* ** * *
2822731 TATAATTATGCAAATAAACATGCAATTAAATATATAATTATGCAAATAAATATATT
1 TA-AATCATGCAAATAAACATATAATTAAATATATAATCATGCAAATAAAAATATT
*
2822787 AATAATCATGCAAATA
1 TA-AATCATGCAAATA
2822803 TATTAATAAT
Statistics
Matches: 278, Mismatches: 54, Indels: 57
0.71 0.14 0.15
Matches are distributed among these distances:
52 1 0.00
53 15 0.05
54 15 0.05
55 88 0.32
56 65 0.23
57 2 0.01
58 4 0.01
59 6 0.02
60 18 0.06
61 14 0.05
62 7 0.03
63 9 0.03
64 34 0.12
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.31
Consensus pattern (55 bp):
TAAATCATGCAAATAAACATATAATTAAATATATAATCATGCAAATAAAAATATT
Found at i:2822564 original size:56 final size:55
Alignment explanation
Indices: 2822498--2822662 Score: 156
Period size: 56 Copynumber: 3.0 Consensus size: 55
2822488 ACATGAATAA
* * * **
2822498 ATAAATTAATAATCACGCAATTAGACATGCTTTTAAATATATAATCATGCAAATG
1 ATAAATTAATAATCACGCAAATAAACATACAATTAAATATATAATCATGCAAATG
* *
2822553 ATAACATTAATAATCATGCAAATAAACATACAATTAAATATATAATCTTGCAAAT-
1 ATAA-ATTAATAATCACGCAAATAAACATACAATTAAATATATAATCATGCAAATG
* * ** * *
2822608 A-AAAATATATAAACCATTCAAATAAATATAC-ATATAAATTTATAATCATGCAAAT
1 ATAAATTA-AT-AATCACGCAAATAAACATACAAT-TAAATATATAATCATGCAAAT
2822663 AACAATATAT
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
53 3 0.03
54 6 0.06
55 41 0.44
56 43 0.46
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.32
Consensus pattern (55 bp):
ATAAATTAATAATCACGCAAATAAACATACAATTAAATATATAATCATGCAAATG
Found at i:2822694 original size:31 final size:31
Alignment explanation
Indices: 2822651--2822714 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
2822641 ATAAATTTAT
* *
2822651 AATCATGCAAATAACAATATATGAATCATGC
1 AATCATGCAAATAACAATATATAAACCATGC
* *
2822682 AATCATGTAAATAATAATATATAAACCATGC
1 AATCATGCAAATAACAATATATAAACCATGC
2822713 AA
1 AA
2822715 AATATGCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.52, C:0.14, G:0.08, T:0.27
Consensus pattern (31 bp):
AATCATGCAAATAACAATATATAAACCATGC
Found at i:2822742 original size:20 final size:20
Alignment explanation
Indices: 2822717--2822785 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 20
2822707 CCATGCAAAA
2822717 TATGCAATTAAATATATAAT
1 TATGCAATTAAATATATAAT
2822737 TATGC-----AA-ATA-AA-
1 TATGCAATTAAATATATAAT
*
2822749 CATGCAATTAAATATATAAT
1 TATGCAATTAAATATATAAT
*
2822769 TATGCAAATAAATATAT
1 TATGCAATTAAATATAT
2822786 TAATAATCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 16
0.67 0.05 0.28
Matches are distributed among these distances:
12 4 0.11
13 2 0.05
14 3 0.08
15 2 0.05
17 2 0.05
18 3 0.08
19 2 0.05
20 20 0.53
ACGTcount: A:0.52, C:0.07, G:0.06, T:0.35
Consensus pattern (20 bp):
TATGCAATTAAATATATAAT
Found at i:2822754 original size:32 final size:32
Alignment explanation
Indices: 2822718--2822780 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
2822708 CATGCAAAAT
2822718 ATGCAATTAAATATATAATTATGCAAATAAAC
1 ATGCAATTAAATATATAATTATGCAAATAAAC
2822750 ATGCAATTAAATATATAATTATGCAAATAAA
1 ATGCAATTAAATATATAATTATGCAAATAAA
2822781 TATATTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32
Consensus pattern (32 bp):
ATGCAATTAAATATATAATTATGCAAATAAAC
Found at i:2822791 original size:44 final size:43
Alignment explanation
Indices: 2822743--2822832 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 43
2822733 TAATTATGCA
*
2822743 AATAAACATGCAATTAAA-TATATAATT-ATGCAAATAAATATATT
1 AATAAACATGCAAATAAATTA-ATAATTCA--CAAATAAATATATT
* *
2822787 AATAATCATGCAAATATATTAATAATTCACAAATAAATATATT
1 AATAAACATGCAAATAAATTAATAATTCACAAATAAATATATT
2822830 AAT
1 AAT
2822833 CATGCAAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 17 0.41
44 21 0.51
45 3 0.07
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (43 bp):
AATAAACATGCAAATAAATTAATAATTCACAAATAAATATATT
Found at i:2822801 original size:20 final size:20
Alignment explanation
Indices: 2822778--2822841 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
2822768 TTATGCAAAT
2822778 AAATATATTAATAATCATGC
1 AAATATATTAATAATCATGC
2822798 AAATATATTAATAATTCA--C
1 AAATATATTAATAA-TCATGC
* *
2822817 AAATAAATATATTAATCATGC
1 AAATATAT-TAATAATCATGC
2822838 AAAT
1 AAAT
2822842 GTAATATTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 11 0.29
20 19 0.50
21 8 0.21
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.34
Consensus pattern (20 bp):
AAATATATTAATAATCATGC
Found at i:2822824 original size:23 final size:20
Alignment explanation
Indices: 2822757--2822832 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
2822747 AACATGCAAT
*
2822757 TAAATATA-TAATTATGCAAA
1 TAAATATATTAATAAT-CAAA
**
2822777 TAAATATATTAATAATCATG
1 TAAATATATTAATAATCAAA
*
2822797 CAAATATATTAATAATTCACAAA
1 TAAATATATTAATAA-T--CAAA
2822820 TAAATATATTAAT
1 TAAATATATTAAT
2822833 CATGCAAATG
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 24 0.53
21 7 0.16
23 14 0.31
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.37
Consensus pattern (20 bp):
TAAATATATTAATAATCAAA
Found at i:2824988 original size:15 final size:17
Alignment explanation
Indices: 2824968--2824999 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2824958 TCTCACATAC
2824968 AAAAAA-TAAA-ATTTT
1 AAAAAATTAAATATTTT
2824983 AAAAAATTAAATATTTT
1 AAAAAATTAAATATTTT
2825000 TTATAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAAAATTAAATATTTT
Found at i:2825017 original size:21 final size:21
Alignment explanation
Indices: 2824991--2825034 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2824981 TTAAAAAATT
*
2824991 AAATATTTTTTATAAT-TTAAA
1 AAATATTTATTA-AATGTTAAA
2825012 AAATATTTATTAAATGTTAAA
1 AAATATTTATTAAATGTTAAA
2825033 AA
1 AA
2825035 GAAAAAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AAATATTTATTAAATGTTAAA
Found at i:2829731 original size:7 final size:7
Alignment explanation
Indices: 2829719--2829753 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
2829709 TGATATTAAA
2829719 AAATTTT
1 AAATTTT
2829726 AAATTTT
1 AAATTTT
*
2829733 AAAATTT
1 AAATTTT
2829740 AAATTTT
1 AAATTTT
2829747 AACATTT
1 AA-ATTT
2829754 AACATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (7 bp):
AAATTTT
Done.