Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 12 of 26
Found at i:1990663 original size:10 final size:10
Alignment explanation
Indices: 1990648--1990717 Score: 77
Period size: 10 Copynumber: 7.0 Consensus size: 10
1990638 ATTGAAAAGG
1990648 ATATATATAT
1 ATATATATAT
*
1990658 ATATATATAG
1 ATATATATAT
* **
1990668 ATAGATAGGT
1 ATATATATAT
* *
1990678 ATAGATAGAT
1 ATATATATAT
*
1990688 AAATATATAT
1 ATATATATAT
1990698 ATATATATAT
1 ATATATATAT
1990708 ATATATATAT
1 ATATATATAT
1990718 TTGATTTCCT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (10 bp):
ATATATATAT
Found at i:1993165 original size:2 final size:2
Alignment explanation
Indices: 1993153--1993184 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1993143 ACTATTCCAT
1993153 TA TA TA T- 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 T
1993185 GTTAAGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1993340 original size:4 final size:4
Alignment explanation
Indices: 1993331--1993356 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1993321 GCAATGATAA
1993331 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
1993357 TTTGATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:1995898 original size:15 final size:15
Alignment explanation
Indices: 1995878--1995910 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1995868 TCCAAAGAAT
1995878 GCTCTCAACATTCTA
1 GCTCTCAACATTCTA
1995893 GCTCTCAACATTCTA
1 GCTCTCAACATTCTA
1995908 GCT
1 GCT
1995911 GGTGGTACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.33, G:0.09, T:0.33
Consensus pattern (15 bp):
GCTCTCAACATTCTA
Found at i:1996322 original size:14 final size:14
Alignment explanation
Indices: 1996305--1996358 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
1996295 TTATAAATTT
1996305 AAATTATTAATTAA
1 AAATTATTAATTAA
1996319 AAA-TATTTAATT--
1 AAATTA-TTAATTAA
* *
1996331 AAATT-TAAATAAA
1 AAATTATTAATTAA
1996344 AAATTATTAATTAA
1 AAATTATTAATTAA
1996358 A
1 A
1996359 TAATAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
11 4 0.13
12 3 0.10
13 8 0.26
14 16 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTATTAATTAA
Found at i:1996353 original size:25 final size:26
Alignment explanation
Indices: 1996303--1996364 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
1996293 ATTTATAAAT
* *
1996303 TTAAATTATTAATTAAAAATATTTAA
1 TTAAATTATAAATAAAAAATATTTAA
1996329 TTAAATT-TAAATAAAAAAT-TATTAA
1 TTAAATTATAAATAAAAAATAT-TTAA
*
1996354 TTAAATAATAA
1 TTAAATTATAA
1996365 TTTAAATCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 1 0.03
25 20 0.65
26 10 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
TTAAATTATAAATAAAAAATATTTAA
Found at i:1999697 original size:13 final size:12
Alignment explanation
Indices: 1999671--1999705 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1999661 AATTGCTTTT
1999671 AAAATTTATCAAA
1 AAAATTTAT-AAA
*
1999684 AAAGTTTATAAA
1 AAAATTTATAAA
1999696 AAAATTTATA
1 AAAATTTATA
1999706 TATTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (12 bp):
AAAATTTATAAA
Found at i:2001251 original size:25 final size:23
Alignment explanation
Indices: 2001222--2001274 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
2001212 TAATTTTTTA
*
2001222 ATATTTACACTATAATATTACATAT
1 ATATTTACA-TATAAAATTA-ATAT
**
2001247 ATATTTTTATATAAAATTAATAT
1 ATATTTACATATAAAATTAATAT
2001270 ATATT
1 ATATT
2001275 ATTTAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.36
24 9 0.36
25 7 0.28
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATTTACATATAAAATTAATAT
Found at i:2001286 original size:26 final size:24
Alignment explanation
Indices: 2001232--2001289 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 24
2001222 ATATTTACAC
*
2001232 TATAATATTACATATATATTTTTA
1 TATAAAATTACATATATATTTTTA
2001256 TATAAAATTA-ATATATATTATTTAA
1 TATAAAATTACATATATATT-TTT-A
2001281 TAATAAAAT
1 T-ATAAAAT
2001290 GAGCTAAGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 9 0.30
24 12 0.40
25 2 0.07
26 7 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TATAAAATTACATATATATTTTTA
Found at i:2002006 original size:33 final size:32
Alignment explanation
Indices: 2001947--2002029 Score: 84
Period size: 33 Copynumber: 2.6 Consensus size: 32
2001937 TTTATGCGTC
* *
2001947 ATAATGAT-TATTTAT-TTACATAAATTTAA-
1 ATAATTATATATTTATATTAAATAAATTTAAT
*
2001976 ATATATTA-ATAATTTATATTAAATAAAATTTGAT
1 ATA-ATTATAT-ATTTATATTAAAT-AAATTTAAT
2002010 ATAATTATATATTTATATTA
1 ATAATTATATATTTATATTA
2002030 TATTTTAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
29 3 0.07
30 4 0.09
31 6 0.14
32 5 0.11
33 21 0.48
34 5 0.11
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (32 bp):
ATAATTATATATTTATATTAAATAAATTTAAT
Found at i:2002033 original size:11 final size:11
Alignment explanation
Indices: 2002017--2002066 Score: 70
Period size: 11 Copynumber: 4.7 Consensus size: 11
2002007 GATATAATTA
2002017 TATATTTATAT
1 TATATTTATAT
2002028 TATATTT-TAAT
1 TATATTTAT-AT
2002039 T-T-TTTATAT
1 TATATTTATAT
2002048 TATATTTATAT
1 TATATTTATAT
2002059 TATATTTA
1 TATATTTA
2002067 AAGTTATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
9 6 0.17
10 4 0.11
11 25 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATATTTATAT
Found at i:2002662 original size:14 final size:14
Alignment explanation
Indices: 2002601--2002670 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 14
2002591 TAATATAAAG
*
2002601 ATATA-TTATTATA
1 ATATATTTATTTTA
* *
2002614 TTATATATATTTTA
1 ATATATTTATTTTA
*
2002628 ATAATATTCAAATTTTA
1 AT-ATATT--TATTTTA
2002645 ATATATTTTATTTT-
1 ATATA-TTTATTTTA
2002659 ATATATTTATTT
1 ATATATTTATTT
2002671 AAATTAATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 11 0.24
14 12 0.27
15 9 0.20
16 3 0.07
17 10 0.22
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (14 bp):
ATATATTTATTTTA
Found at i:2003181 original size:18 final size:18
Alignment explanation
Indices: 2003154--2003189 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2003144 TTATATTTAT
*
2003154 TTTTAAATTTTTTTAATA
1 TTTTAAATTTATTTAATA
*
2003172 TTTTATATTTATTTAATA
1 TTTTAAATTTATTTAATA
2003190 ATAAAATATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTAAATTTATTTAATA
Found at i:2003472 original size:2 final size:2
Alignment explanation
Indices: 2003465--2003501 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2003455 TGAGAAAATA
2003465 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2003502 CGTGTGGGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2003753 original size:4 final size:5
Alignment explanation
Indices: 2003721--2003768 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
2003711 TAATTTAAAA
*
2003721 AAATT AAATTTT AAATT AAATT AAATT -AATT AATTT AAATTT AAATT
1 AAATT AAA--TT AAATT AAATT AAATT AAATT AAATT AAA-TT AAATT
2003768 A
1 A
2003769 TTATTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 4 0.11
5 23 0.62
6 5 0.14
7 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (5 bp):
AAATT
Found at i:2003771 original size:19 final size:18
Alignment explanation
Indices: 2003721--2003775 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
2003711 TAATTTAAAA
*
2003721 AAATTAAATT-TTAAATT
1 AAATTAAATTATTAATTT
2003738 AAATTAAATTAATTAATTT
1 AAATTAAATT-ATTAATTT
2003757 AAATTTAAATTATT-ATTT
1 AAA-TTAAATTATTAATTT
2003775 A
1 A
2003776 TTTTATTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 10 0.29
18 5 0.15
19 12 0.35
20 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTAAATTATTAATTT
Found at i:2004264 original size:17 final size:18
Alignment explanation
Indices: 2004224--2004264 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2004214 ATATTTGATT
2004224 TTAATATTAAAAAATTAA
1 TTAATATTAAAAAATTAA
*
2004242 TATAATA-TAAAAATTTAA
1 T-TAATATTAAAAAATTAA
2004260 TTAAT
1 TTAAT
2004265 TTTTTCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 12 0.57
19 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAATATTAAAAAATTAA
Found at i:2004664 original size:3 final size:3
Alignment explanation
Indices: 2004658--2004695 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2004648 ATTATTTATT
2004658 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2004696 TTAAAGAGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2005138 original size:2 final size:2
Alignment explanation
Indices: 2005131--2005166 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2005121 TTCATAGGTG
2005131 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2005167 CATTCTCCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2005255 original size:134 final size:131
Alignment explanation
Indices: 2005020--2005264 Score: 400
Period size: 132 Copynumber: 1.8 Consensus size: 131
2005010 TATTTTCTGC
*
2005020 ATATATATATATATATATTATCCCATTTGTTGCTAAAAATAATATTATATATATTTTCTTTTATT
1 ATATATATATATATACATTATCCCATTTGTTGCTAAAAATAATATTATATATATTTTCTTTTATT
* * * *
2005085 TGAGGGTTAGAGTGGTCGCAGCTCGAATGGGAGATTTTCATAGGTGTATATATATATATATATAT
66 TGAGGGCTAAAGTGGTCGCAGCTCGAATGGCAGA-TTTCACAGGTGTATATATATATATATATAT
2005150 AT
130 AT
*
2005152 ATATATATATATATACATTCTCCCATTTGTTGCTAAAAATAATATTATATGTATATTTTCTTTTA
1 ATATATATATATATACATTATCCCATTTGTTGCTAAAAATAATATTATA--TATATTTTCTTTTA
*
2005217 TTTGAGGGCTAAAGTGGTCGCAGCTCGAATGGCTGATTTCACAGGTGT
64 TTTGAGGGCTAAAGTGGTCGCAGCTCGAATGGCAGATTTCACAGGTGT
2005265 GGGATAAATA
Statistics
Matches: 104, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
132 47 0.45
133 11 0.11
134 46 0.44
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.42
Consensus pattern (131 bp):
ATATATATATATATACATTATCCCATTTGTTGCTAAAAATAATATTATATATATTTTCTTTTATT
TGAGGGCTAAAGTGGTCGCAGCTCGAATGGCAGATTTCACAGGTGTATATATATATATATATATA
T
Found at i:2005587 original size:20 final size:20
Alignment explanation
Indices: 2005542--2005617 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 20
2005532 ATAGAATAGT
2005542 TATAATT-ATATTATTAAATT-
1 TATAATTAAT-TTATT-AATTA
2005562 TAATAATTAATTTATTAATTA
1 T-ATAATTAATTTATTAATTA
** *
2005583 TATAAAAAATTATATAAATATA
1 TATAATTAATT-TATTAAT-TA
*
2005605 TAAAATTAATTTA
1 TATAATTAATTTA
2005618 CTTTTATACT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 13 0.29
21 20 0.44
22 12 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATAATTAATTTATTAATTA
Found at i:2005932 original size:2 final size:2
Alignment explanation
Indices: 2005889--2005917 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2005879 TATATTACCG
2005889 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
2005918 ATTATTGATT
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:2009091 original size:29 final size:28
Alignment explanation
Indices: 2009063--2009144 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 28
2009053 AATAAAAAAT
2009063 TAAAAATATTTTTAT-ATTAATATTTAAA
1 TAAAAATATTTTTATAATTAA-ATTTAAA
2009091 T----ATA-TTTTATAATTAAATTTAAA
1 TAAAAATATTTTTATAATTAAATTTAAA
*
2009114 TAAAAATATTTTTAATTATTAAATATTAAA
1 TAAAAATATTTTT-ATAATTAAAT-TTAAA
2009144 T
1 T
2009145 TTATTGAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
23 14 0.31
24 8 0.18
27 3 0.07
28 5 0.11
29 9 0.20
30 6 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TAAAAATATTTTTATAATTAAATTTAAA
Found at i:2009097 original size:53 final size:54
Alignment explanation
Indices: 2009040--2009149 Score: 122
Period size: 53 Copynumber: 2.1 Consensus size: 54
2009030 TTATGTATAT
*
2009040 TATTTTTATCATT-AATAAAAAATTAAAAATATTTTT-A-TATT-AATATTTAAATA
1 TATTTTTATAATTAAAT-AAAAA-TAAAAATATTTTTAATTATTAAATA-TTAAATA
** *
2009093 TA-TTTTATAATTAAATTTAAATAAAAATATTTTTAATTATTAAATATTAAATT
1 TATTTTTATAATTAAATAAAAATAAAAATATTTTTAATTATTAAATATTAAATA
2009146 TATT
1 TATT
2009150 GAATTAGGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
51 13 0.27
52 13 0.27
53 17 0.35
54 5 0.10
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (54 bp):
TATTTTTATAATTAAATAAAAATAAAAATATTTTTAATTATTAAATATTAAATA
Found at i:2009135 original size:23 final size:23
Alignment explanation
Indices: 2009063--2009138 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 23
2009053 AATAAAAAAT
* **
2009063 TAAAAATATTTTTATATTAATATT
1 TAAAAATATTTTTA-ATTATTAAA
*
2009087 TAAATATATTTTATAATTAAATTTAAA
1 TAAAAATATTTT-TAATT--A-TTAAA
2009114 TAAAAATATTTTTAATTATTAAA
1 TAAAAATATTTTTAATTATTAAA
2009137 TA
1 TA
2009139 TTAAATTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
23 7 0.16
24 15 0.35
25 2 0.05
26 6 0.14
27 13 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAAAATATTTTTAATTATTAAA
Found at i:2009964 original size:19 final size:18
Alignment explanation
Indices: 2009935--2009972 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2009925 TATTTTTATT
2009935 TAAATATATTAAAAATTA
1 TAAATATATTAAAAATTA
*
2009953 TAAATAATATTATAAATTA
1 TAAAT-ATATTAAAAATTA
2009972 T
1 T
2009973 TATATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATATATTAAAAATTA
Found at i:2013833 original size:2 final size:2
Alignment explanation
Indices: 2013826--2013855 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2013816 TCCTAAATAT
2013826 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2013856 CATTCTTCTT
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):
TC
Found at i:2016064 original size:21 final size:23
Alignment explanation
Indices: 2016011--2016072 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 23
2016001 TATGACATAG
*
2016011 TTATTTAAATTTATTTAGTTATAA
1 TTATTTTAATTTATTTAG-TATAA
2016035 TTAATTTTTAATTT-TTTA-TATAA
1 TT-A-TTTTAATTTATTTAGTATAA
2016058 TTATTTTAAATTTAT
1 TTATTTT-AATTTAT
2016073 AACATTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
21 4 0.12
22 6 0.18
23 8 0.24
24 2 0.06
25 5 0.15
26 8 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTATTTTAATTTATTTAGTATAA
Found at i:2016758 original size:24 final size:25
Alignment explanation
Indices: 2016714--2016760 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
2016704 AATATACTAT
*
2016714 TTATAAAAACTTTTTTAAAATATAA
1 TTATAAAAACTTTTTAAAAATATAA
2016739 TTAT-AAAA-TTTTTAACAAATAT
1 TTATAAAAACTTTTTAA-AAATAT
2016761 CTATAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
TTATAAAAACTTTTTAAAAATATAA
Found at i:2020445 original size:3 final size:3
Alignment explanation
Indices: 2020437--2020462 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2020427 GCCAAAGAAA
2020437 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
2020463 ATTATTATTT
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:2021570 original size:2 final size:2
Alignment explanation
Indices: 2021565--2021608 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2021555 GCTATATAAA
*
2021565 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2021607 AT
1 AT
2021609 GCATTGCAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2022289 original size:18 final size:17
Alignment explanation
Indices: 2022268--2022301 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2022258 CAGGAAAAAA
2022268 AAAAAAAACACAAAAAGG
1 AAAAAAAAC-CAAAAAGG
*
2022286 AAAAAGAACCAAAAAG
1 AAAAAAAACCAAAAAG
2022302 AGAAGAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAAACCAAAAAGG
Found at i:2024761 original size:61 final size:61
Alignment explanation
Indices: 2024666--2024785 Score: 213
Period size: 61 Copynumber: 2.0 Consensus size: 61
2024656 GATGGAATCC
* * *
2024666 GATAAATAAAAGAGACAAGAATATTAACCTGGGAGTGATAGGTTCCTTTATGTATGTTTCT
1 GATAAATAAAAGAGAAAAGAATATTAACCTGGGAGTGATAGGCTCCTTTATGAATGTTTCT
2024727 GATAAATAAAAGAGAAAAGAATATTAACCTGGGAGTGATAGGCTCCTTTATGAATGTTT
1 GATAAATAAAAGAGAAAAGAATATTAACCTGGGAGTGATAGGCTCCTTTATGAATGTTT
2024786 TTATGCTTGA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (61 bp):
GATAAATAAAAGAGAAAAGAATATTAACCTGGGAGTGATAGGCTCCTTTATGAATGTTTCT
Found at i:2034693 original size:16 final size:15
Alignment explanation
Indices: 2034672--2034701 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2034662 TTAATTTAAT
2034672 TTTTTTTTGTTAAAAG
1 TTTTTTTT-TTAAAAG
2034688 TTTTTTTTTTAAAA
1 TTTTTTTTTTAAAA
2034702 ATTATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
TTTTTTTTTTAAAAG
Found at i:2035406 original size:2 final size:2
Alignment explanation
Indices: 2035399--2035424 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2035389 TATCAACTCT
2035399 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2035425 CACTATGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2035852 original size:7 final size:7
Alignment explanation
Indices: 2035840--2035886 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
2035830 GATTGAAAAA
2035840 TAAATTT
1 TAAATTT
2035847 TAAATTT
1 TAAATTT
2035854 TAAATTT
1 TAAATTT
2035861 TAAATATTT
1 T-AA-ATTT
*
2035870 TAAATAT
1 TAAATTT
2035877 T-AATTT
1 TAAATTT
2035883 TAAA
1 TAAA
2035887 ATATTTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 5 0.14
7 21 0.60
8 4 0.11
9 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TAAATTT
Found at i:2035859 original size:14 final size:14
Alignment explanation
Indices: 2035840--2035886 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 14
2035830 GATTGAAAAA
2035840 TAAATTTTAAATTT
1 TAAATTTTAAATTT
2035854 TAAATTTTAAATATTT
1 TAAATTTT-AA-ATTT
*
2035870 TAAATATT-AATTT
1 TAAATTTTAAATTT
2035883 TAAA
1 TAAA
2035887 ATATTTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 8 0.27
14 9 0.30
15 2 0.07
16 11 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAAATTTTAAATTT
Found at i:2035871 original size:16 final size:15
Alignment explanation
Indices: 2035841--2035893 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 15
2035831 ATTGAAAAAT
2035841 AAATTTTAAATTTT-
1 AAATTTTAAATTTTA
*
2035855 AAATTTTAAATATTTT
1 AAATTTTAAAT-TTTA
*
2035871 AAATATT-AATTTTA
1 AAATTTTAAATTTTA
2035885 AAATATTTA
1 AAAT-TTTA
2035894 TATAAATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 18 0.56
15 8 0.25
16 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AAATTTTAAATTTTA
Found at i:2035873 original size:23 final size:23
Alignment explanation
Indices: 2035843--2035912 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
2035833 TGAAAAATAA
2035843 ATTTTAAATTTTAAATTTTAAAT
1 ATTTTAAATTTTAAATTTTAAAT
*
2035866 ATTTTAAATATT-AATTTTAAAAT
1 ATTTTAAATTTTAAATTTT-AAAT
*
2035889 ATTTATATAAATTTAAA-TTTAAAT
1 ATTT-TA-AATTTTAAATTTTAAAT
2035913 TCGAAGTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 6 0.15
23 19 0.47
24 6 0.15
25 7 0.17
26 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTTAAATTTTAAATTTTAAAT
Found at i:2037200 original size:2 final size:2
Alignment explanation
Indices: 2037195--2037222 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2037185 ATCTTCATAC
2037195 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2037223 TGGCTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2041705 original size:30 final size:30
Alignment explanation
Indices: 2041662--2041728 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
2041652 TAGAGTTAAT
* *
2041662 TTTATTGACATAA-TTGATTAATAA-TAAAAG
1 TTTAATGACATAATTTGA-TAA-AATTAAAAA
*
2041692 TTTAATGATATAATTTGATAAAATTAAAAA
1 TTTAATGACATAATTTGATAAAATTAAAAA
2041722 TTTAATG
1 TTTAATG
2041729 TTTGTATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 2 0.06
30 26 0.81
31 4 0.12
ACGTcount: A:0.48, C:0.01, G:0.09, T:0.42
Consensus pattern (30 bp):
TTTAATGACATAATTTGATAAAATTAAAAA
Found at i:2046095 original size:22 final size:22
Alignment explanation
Indices: 2046067--2046125 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
2046057 TCAGCAGCTG
2046067 AGAAAGAAGGAAAAAGAAAGAA-
1 AGAAAGAAGGAAAAAGAAA-AAT
* *
2046089 AGAAAGAAAGAAAGCAGAAAAAT
1 AGAAAGAAGGAAA-AAGAAAAAT
2046112 AGAAA-AAGGAAAAA
1 AGAAAGAAGGAAAAA
2046126 ATTCAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 20 0.65
23 10 0.32
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.02
Consensus pattern (22 bp):
AGAAAGAAGGAAAAAGAAAAAT
Found at i:2046216 original size:32 final size:34
Alignment explanation
Indices: 2046142--2046240 Score: 89
Period size: 33 Copynumber: 2.9 Consensus size: 34
2046132 AAAAATTATG
* *
2046142 TATTTATATTTGTAT-TATTTTTTATAT-GTAAAA
1 TATTTAT-TTTATATATATTTTTTATATATTAAAA
2046175 TATTATATTTT-TATATATTTTTTATATATTAATAA
1 TATT-TATTTTATATATATTTTTTATATATTAA-AA
*
2046210 TTTATTT-TATTATATATATATTTTTATATAT
1 --TATTTATTTTATATATAT-TTTTTATATAT
2046241 GTATATTCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
32 3 0.05
33 19 0.34
34 6 0.11
35 5 0.09
36 8 0.14
37 15 0.27
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (34 bp):
TATTTATTTTATATATATTTTTTATATATTAAAA
Found at i:2046231 original size:16 final size:16
Alignment explanation
Indices: 2046212--2046267 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
2046202 ATTAATAATT
2046212 TATTTTATTATATATA
1 TATTTTATTATATATA
*
2046228 TATTTT-TATATATGTA
1 TATTTTAT-TATATATA
* *
2046244 TATTCATATTGTATATA
1 TATT-TTATTATATATA
2046261 TTATTTT
1 -TATTTT
2046268 TAAATAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
15 1 0.03
16 17 0.55
17 8 0.26
18 5 0.16
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (16 bp):
TATTTTATTATATATA
Found at i:2046240 original size:37 final size:36
Alignment explanation
Indices: 2046157--2046243 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 36
2046147 ATATTTGTAT
2046157 TATTTTT-TATATGTAAAATATTATATTTTTATATA
1 TATTTTTATATATGTAAAATATTATATTTTTATATA
*
2046192 T-TTTTTATATAT-TAATAAT-TTATTTTATTATATATA
1 TATTTTTATATATGTAA-AATATTATATT-TT-TATATA
2046228 TATTTTTATATATGTA
1 TATTTTTATATATGTA
2046244 TATTCATATT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
34 14 0.31
35 11 0.24
36 7 0.16
37 11 0.24
38 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (36 bp):
TATTTTTATATATGTAAAATATTATATTTTTATATA
Found at i:2046278 original size:13 final size:13
Alignment explanation
Indices: 2046262--2046298 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
2046252 TTGTATATAT
2046262 TATTTTTAAATAA
1 TATTTTTAAATAA
2046275 TA-TTTTAAATAA
1 TATTTTTAAATAA
2046287 -ATTTTATAAATA
1 TATTTT-TAAATA
2046299 TAATATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.05
12 13 0.59
13 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TATTTTTAAATAA
Found at i:2046374 original size:8 final size:8
Alignment explanation
Indices: 2046350--2046448 Score: 64
Period size: 8 Copynumber: 12.1 Consensus size: 8
2046340 TATATAAATT
2046350 TTTATATA
1 TTTATATA
2046358 -TTATATA
1 TTTATATA
*
2046365 TTTATTTA
1 TTTATATA
2046373 TTTATAT-
1 TTTATATA
2046380 TTTAATATA
1 TTT-ATATA
*
2046389 TTCATATA
1 TTTATATA
2046397 TTCGTATCATA
1 TT--TAT-ATA
2046408 TTTATATTA
1 TTTATA-TA
*
2046417 TTTTTCATA
1 TTTAT-ATA
*
2046426 -TTATGT-
1 TTTATATA
2046432 TTTA-ATA
1 TTTATATA
2046439 TTTTATATA
1 -TTTATATA
2046448 T
1 T
2046449 ATGTTGAGTT
Statistics
Matches: 71, Mismatches: 8, Indels: 24
0.69 0.08 0.23
Matches are distributed among these distances:
6 1 0.01
7 14 0.20
8 32 0.45
9 16 0.23
10 3 0.04
11 5 0.07
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (8 bp):
TTTATATA
Found at i:2046382 original size:31 final size:32
Alignment explanation
Indices: 2046337--2046398 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
2046327 AATAAAATAA
*
2046337 ATTTATATAAATTTTTATATATT-ATATATTT
1 ATTTATATAAATTTTAATATATTCATATATTT
* *
2046368 ATTTATTTATATTTTAATATATTCATATATT
1 ATTTATATAAATTTTAATATATTCATATATT
2046399 CGTATCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (32 bp):
ATTTATATAAATTTTAATATATTCATATATTT
Found at i:2046672 original size:17 final size:17
Alignment explanation
Indices: 2046640--2046673 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2046630 TATTCATGTT
*
2046640 ATTTTTTATATGTTTTA
1 ATTTTTTATATATTTTA
*
2046657 ATTTTTTATTTATTTTA
1 ATTTTTTATATATTTTA
2046674 TGTTCATATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTTTATATATTTTA
Found at i:2047129 original size:25 final size:24
Alignment explanation
Indices: 2047077--2047163 Score: 79
Period size: 25 Copynumber: 3.5 Consensus size: 24
2047067 TCCCCTTTTC
*
2047077 TTTAATATTTAAACTTGT-TTTAGTA
1 TTTAA-ATTTAAACTT-TATTTATTA
2047102 TTTTAAAATTTAAA-TTTATTTATTA
1 -TTT-AAATTTAAACTTTATTTATTA
* * *
2047127 TTTATATTAAAATTTTATATTATTA
1 TTTAAATTTAAACTTTAT-TTATTA
2047152 TTTAAATTTAAA
1 TTTAAATTTAAA
2047164 TTAAATAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
23 7 0.13
24 9 0.17
25 24 0.46
26 10 0.19
27 2 0.04
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTAAATTTAAACTTTATTTATTA
Found at i:2047147 original size:19 final size:20
Alignment explanation
Indices: 2047120--2047160 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
2047110 TTTAAATTTA
2047120 TTTATTATT-TATATTAAAAT
1 TTTATTATTAT-TATTAAAAT
*
2047140 TTTA-TATTATTATTTAAAT
1 TTTATTATTATTATTAAAAT
2047159 TT
1 TT
2047161 AAATTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTATTATTATTATTAAAAT
Found at i:2047164 original size:25 final size:24
Alignment explanation
Indices: 2047107--2047165 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 24
2047097 TAGTATTTTA
2047107 AAATTTAAA-TTTATTTATTATTT
1 AAATTTAAATTTTATTTATTATTT
* *
2047130 ATATTAAAATTTTATATTATTATTT
1 AAATTTAAATTTTAT-TTATTATTT
2047155 AAATTTAAATT
1 AAATTTAAATT
2047166 AAATAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 7 0.23
24 5 0.17
25 18 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
AAATTTAAATTTTATTTATTATTT
Found at i:2047175 original size:25 final size:25
Alignment explanation
Indices: 2047122--2047180 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
2047112 TAAATTTATT
* ** *
2047122 TATTATTTATATTAAAATTTTATAT
1 TATTATTTAAATTAAAATTAAATAA
*
2047147 TATTATTTAAATTTAAATTAAATAA
1 TATTATTTAAATTAAAATTAAATAA
*
2047172 TATTTTTTA
1 TATTATTTA
2047181 TTCGATATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTATTTAAATTAAAATTAAATAA
Found at i:2048106 original size:11 final size:11
Alignment explanation
Indices: 2048092--2048141 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
2048082 AATCGAACAA
2048092 TAAACGAGTTT
1 TAAACGAGTTT
*
2048103 TAAATGAGTTT
1 TAAACGAGTTT
* *
2048114 TAAACAATTTAT
1 TAAACGAGTT-T
*
2048126 TAAACGAGCTT
1 TAAACGAGTTT
2048137 TAAAC
1 TAAAC
2048142 AATTCATAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
11 23 0.74
12 8 0.26
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (11 bp):
TAAACGAGTTT
Found at i:2048156 original size:22 final size:23
Alignment explanation
Indices: 2048102--2048158 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
2048092 TAAACGAGTT
* *
2048102 TTAAATGAGTTTTAAACAATTTA
1 TTAAATGAGCTTTAAACAATTCA
*
2048125 TTAAACGAGCTTTAAACAATTCA
1 TTAAATGAGCTTTAAACAATTCA
2048148 -TAAATGAGCTT
1 TTAAATGAGCTT
2048159 GTTAGTGAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 10 0.33
23 20 0.67
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (23 bp):
TTAAATGAGCTTTAAACAATTCA
Found at i:2048594 original size:15 final size:15
Alignment explanation
Indices: 2048551--2048594 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
2048541 TTTTTAAATT
2048551 ATTAAATAATAATTTAA
1 ATTAAA-AA-AATTTAA
**
2048568 ATTAAATCAATTTAA
1 ATTAAAAAAATTTAA
2048583 ATTAAAAAAATT
1 ATTAAAAAAATT
2048595 ATGCCTAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 17 0.74
17 6 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAAAAAATTTAA
Found at i:2049488 original size:28 final size:28
Alignment explanation
Indices: 2049430--2049488 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
2049420 AATTTTCATC
* *
2049430 ATTTATATATTAATATAATTTTTGTTGA
1 ATTTATATAATAATATAATTTTTATTGA
*
2049458 ATTTATTTAATAATATAATTATTTATT-A
1 ATTTATATAATAATATAATT-TTTATTGA
2049486 ATT
1 ATT
2049489 GATTGCTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (28 bp):
ATTTATATAATAATATAATTTTTATTGA
Found at i:2049836 original size:16 final size:15
Alignment explanation
Indices: 2049810--2049849 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 15
2049800 TTTAATATTT
2049810 ATAAAATTTATAATTAA
1 ATAAAA-TTATAATT-A
2049827 ATAAAATTATAATTA
1 ATAAAATTATAATTA
2049842 ATAAAATT
1 ATAAAATT
2049850 TATTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.39
16 8 0.35
17 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAAATTATAATTA
Found at i:2049852 original size:16 final size:17
Alignment explanation
Indices: 2049810--2049852 Score: 72
Period size: 16 Copynumber: 2.6 Consensus size: 17
2049800 TTTAATATTT
2049810 ATAAAATTTATAATTAA
1 ATAAAATTTATAATTAA
2049827 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
2049842 ATAAAATTTAT
1 ATAAAATTTAT
2049853 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.28
16 12 0.48
17 6 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:2050279 original size:23 final size:23
Alignment explanation
Indices: 2050227--2050279 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2050217 GAAACACGAA
* *
2050227 ATGAACACAACATAGAAAATAAT
1 ATGAATACAACATAAAAAATAAT
*
2050250 -TAAAATACAACATAAAAAATAAT
1 AT-GAATACAACATAAAAAATAAT
2050273 ATGAATA
1 ATGAATA
2050280 TAATACAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 1 0.04
23 22 0.92
24 1 0.04
ACGTcount: A:0.64, C:0.09, G:0.06, T:0.21
Consensus pattern (23 bp):
ATGAATACAACATAAAAAATAAT
Found at i:2051134 original size:58 final size:59
Alignment explanation
Indices: 2051055--2051167 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
2051045 CAATTTTTTT
* * *
2051055 AATTAAATCATTATAACAAATTATG-AAAAAATGTCACGAATTGAGATATGATACATTA
1 AATTAAATCATTATAAAAAATTATGTAAAAAATGTCACGAATGGAGATACGATACATTA
* * *
2051113 AATTAAATTATTA-AGAAAAATTATGTAAAATATGTCATGAATGGAGATACGATAC
1 AATTAAATCATTATA-AAAAATTATGTAAAAAATGTCACGAATGGAGATACGATAC
2051168 GAATATGACA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 1 0.02
58 21 0.45
59 25 0.53
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (59 bp):
AATTAAATCATTATAAAAAATTATGTAAAAAATGTCACGAATGGAGATACGATACATTA
Found at i:2051593 original size:22 final size:22
Alignment explanation
Indices: 2051568--2051609 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2051558 ATGAATTGAG
*
2051568 ATATAA-TACAAACTCAACATAT
1 ATATAATTA-AAACACAACATAT
2051590 ATATAATTAAAACACAACAT
1 ATATAATTAAAACACAACAT
2051610 GAAAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (22 bp):
ATATAATTAAAACACAACATAT
Found at i:2051915 original size:9 final size:9
Alignment explanation
Indices: 2051901--2051955 Score: 60
Period size: 9 Copynumber: 6.2 Consensus size: 9
2051891 TAAATACAAA
2051901 TTTTTTTCT
1 TTTTTTTCT
2051910 TTTTTTTC-
1 TTTTTTTCT
2051918 TTTTTTTCT
1 TTTTTTTCT
* **
2051927 CCTTCCTT-T
1 -TTTTTTTCT
2051936 TTTTTTTCT
1 TTTTTTTCT
2051945 TTTTTTTCT
1 TTTTTTTCT
2051954 TT
1 TT
2051956 CTTTCTCTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 12 0.32
9 21 0.57
10 4 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:2052859 original size:23 final size:22
Alignment explanation
Indices: 2052806--2052859 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
2052796 TTAAATTTTA
*
2052806 ATATAATTATATATTTTAAAAAT
1 ATATAA-TATAAATTTTAAAAAT
* *
2052829 ATAAAATATAAATTTATAAACAT
1 ATATAATATAAATTT-TAAAAAT
*
2052852 CTATAATA
1 ATATAATA
2052860 ATTTTAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATAATATAAATTTTAAAAAT
Found at i:2053112 original size:9 final size:9
Alignment explanation
Indices: 2053098--2053133 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
2053088 AAGATTATCT
2053098 AATCGTTGC
1 AATCGTTGC
2053107 AATCGTTGC
1 AATCGTTGC
*
2053116 AATCTTTGC
1 AATCGTTGC
*
2053125 AATCTTTGC
1 AATCGTTGC
2053134 GATATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (9 bp):
AATCGTTGC
Found at i:2056690 original size:20 final size:20
Alignment explanation
Indices: 2056665--2056716 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
2056655 ATGGCATCGA
*
2056665 AAATTTGATTGCCTAAAGTC
1 AAATTTGATTGCCCAAAGTC
*
2056685 AAATTTGATTACCCAAAGTC
1 AAATTTGATTGCCCAAAGTC
2056705 AAATTTGATTGC
1 AAATTTGATTGC
2056717 GATAAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (20 bp):
AAATTTGATTGCCCAAAGTC
Found at i:2059700 original size:20 final size:20
Alignment explanation
Indices: 2059675--2059726 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2059665 AAAACCCAGA
2059675 TGTATCGATACAATATTCTT
1 TGTATCGATACAATATTCTT
* *
2059695 TGTATCGACACAATGTTCTT
1 TGTATCGATACAATATTCTT
* *
2059715 TATTTCGATACA
1 TGTATCGATACA
2059727 TGAGTTACAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATATTCTT
Found at i:2062377 original size:20 final size:20
Alignment explanation
Indices: 2062327--2062366 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
2062317 TATATTAATG
*
2062327 ATAAAATATTTT--AATTTT
1 ATAAATTATTTTAAAATTTT
2062345 ATAAATTATTTTAAAATTTT
1 ATAAATTATTTTAAAATTTT
2062365 AT
1 AT
2062367 TATATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
20 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAAATTATTTTAAAATTTT
Found at i:2062631 original size:34 final size:34
Alignment explanation
Indices: 2062556--2062631 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 34
2062546 ATTTATAAAT
2062556 TTATAAATATCTATAATAATTTTAAATTTATCAC
1 TTATAAATATCTATAATAATTTTAAATTTATCAC
* * *
2062590 TAAATAAATATCTGAT-A-AATTTATAATTTTATTAC
1 T-TATAAATATCT-ATAATAATTT-TAAATTTATCAC
2062625 TTATAAA
1 TTATAAA
2062632 ATTTAAATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
34 11 0.31
35 22 0.63
36 2 0.06
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (34 bp):
TTATAAATATCTATAATAATTTTAAATTTATCAC
Found at i:2063196 original size:20 final size:19
Alignment explanation
Indices: 2063171--2063224 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
2063161 CTACCACTAT
2063171 TTGTATCGATACATG-GTATA
1 TTGTATCGATACATGAG-A-A
*
2063191 TTGTATGGATACATGAAGAA
1 TTGTATCGATACATG-AGAA
2063211 TTGTATCGATACAT
1 TTGTATCGATACAT
2063225 TGTCCCAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 28 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:2064561 original size:13 final size:13
Alignment explanation
Indices: 2064543--2064567 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2064533 AAACTTTATC
2064543 CTACTACCCTATT
1 CTACTACCCTATT
2064556 CTACTACCCTAT
1 CTACTACCCTAT
2064568 CAGTTAGCGG
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:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (13 bp):
CTACTACCCTATT
Found at i:2065622 original size:14 final size:16
Alignment explanation
Indices: 2065591--2065622 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2065581 TATTTATTTA
2065591 TAAATATAAATAACTT
1 TAAATATAAATAACTT
2065607 TAAATA-AAATAA-TT
1 TAAATATAAATAACTT
2065621 TA
1 TA
2065623 TTTATATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 6 0.38
16 6 0.38
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATATAAATAACTT
Found at i:2079667 original size:15 final size:15
Alignment explanation
Indices: 2079644--2079673 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2079634 TTTTTAATTT
*
2079644 TTATTAATTAAATCA
1 TTATAAATTAAATCA
2079659 TTATAAATTAAATCA
1 TTATAAATTAAATCA
2079674 ATAATATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (15 bp):
TTATAAATTAAATCA
Found at i:2081365 original size:16 final size:15
Alignment explanation
Indices: 2081344--2081376 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
2081334 ATTGGACATG
2081344 TTAGATTAATTTTAAA
1 TTAGATTAA-TTTAAA
2081360 TTAGATTAATTTAAA
1 TTAGATTAATTTAAA
2081375 TT
1 TT
2081377 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
TTAGATTAATTTAAA
Found at i:2081605 original size:16 final size:15
Alignment explanation
Indices: 2081580--2081624 Score: 74
Period size: 15 Copynumber: 3.0 Consensus size: 15
2081570 AATTATAATA
2081580 TTTTTTATTTAAATT
1 TTTTTTATTTAAATT
2081595 TTTTTTAATTTAAA-T
1 TTTTTT-ATTTAAATT
2081610 TTTTTTATTTAAATT
1 TTTTTTATTTAAATT
2081625 ATTAATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.25
15 14 0.50
16 7 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTTATTTAAATT
Found at i:2081620 original size:19 final size:20
Alignment explanation
Indices: 2081593--2081635 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
2081583 TTTATTTAAA
2081593 TTTTTTTT-AATT-TAAATT
1 TTTTTTTTAAATTATAAATT
*
2081611 TTTTTATTTAAATTATTAATT
1 TTTTT-TTTAAATTATAAATT
2081632 TTTT
1 TTTT
2081636 ATTAAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 3 0.14
20 4 0.19
21 9 0.43
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTTTTAAATTATAAATT
Found at i:2082196 original size:14 final size:14
Alignment explanation
Indices: 2082177--2082228 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 14
2082167 GATTTAAATT
*
2082177 TTTTAAAATTTATA
1 TTTTAAAATTTAAA
2082191 TTTTAATAATTTAAA
1 TTTTAA-AATTTAAA
*
2082206 TTTAAATAATTTTAAA
1 TTTTAA-AA-TTTAAA
2082222 TTTTAAA
1 TTTTAAA
2082229 TTAATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 6 0.18
15 16 0.48
16 11 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTTAAAATTTAAA
Found at i:2082203 original size:22 final size:21
Alignment explanation
Indices: 2082178--2082268 Score: 66
Period size: 23 Copynumber: 4.3 Consensus size: 21
2082168 ATTTAAATTT
2082178 TTTAAAATTTATATTTTAATAA
1 TTTAAAATTTATATTTTAA-AA
2082200 TTT-AAATTTAAATAATTTT-AAA
1 TTTAAAATTT--AT-ATTTTAAAA
* * *
2082222 TTTTAAATTAATTTTTTAAAA
1 TTTAAAATTTATATTTTAAAA
2082243 TTATTAAAA-TT-TA-TTTAAAA
1 -T-TTAAAATTTATATTTTAAAA
2082263 TTTAAA
1 TTTAAA
2082269 TTAATTATTT
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
18 5 0.09
19 1 0.02
20 11 0.19
21 12 0.21
22 10 0.18
23 13 0.23
24 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAAAATTTATATTTTAAAA
Found at i:2082208 original size:21 final size:20
Alignment explanation
Indices: 2082182--2082270 Score: 74
Period size: 20 Copynumber: 4.2 Consensus size: 20
2082172 AAATTTTTTA
2082182 AAATTTATATTTTAATAATTT
1 AAATTTATATTTTAA-AATTT
*
2082203 AAATTTAAATAATTTTAAATTTT
1 AAATTT--AT-ATTTTAAAATTT
* *
2082226 AAATTAATTTTTTAAAATTATT
1 AAATTTATATTTTAAAA-T-TT
*
2082248 AAAATT-TA-TTTAAAATTT
1 AAATTTATATTTTAAAATTT
2082266 AAATT
1 AAATT
2082271 AATTATTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
18 6 0.11
19 1 0.02
20 14 0.25
21 10 0.18
22 6 0.11
23 11 0.20
24 7 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTTATATTTTAAAATTT
Found at i:2082213 original size:15 final size:15
Alignment explanation
Indices: 2082183--2082235 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
2082173 AATTTTTTAA
* *
2082183 AATTTATATTTTAAT
1 AATTTAAATTTAAAT
2082198 AATTTAAATTTAAAT
1 AATTTAAATTTAAAT
2082213 AATTTTAAATTTTAAATT
1 AA-TTTAAA-TTTAAA-T
2082231 AATTT
1 AATTT
2082236 TTTAAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 15 0.45
16 6 0.18
17 9 0.27
18 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTAAATTTAAAT
Found at i:2082262 original size:11 final size:11
Alignment explanation
Indices: 2082231--2082266 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2082221 ATTTTAAATT
2082231 AATTT-TTTAA
1 AATTTATTTAA
2082241 AA-TTA-TTAA
1 AATTTATTTAA
2082250 AATTTATTTAA
1 AATTTATTTAA
2082261 AATTTA
1 AATTTA
2082267 AATTAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 8 0.35
10 5 0.22
11 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTATTTAA
Found at i:2082282 original size:23 final size:22
Alignment explanation
Indices: 2082191--2082283 Score: 72
Period size: 23 Copynumber: 4.3 Consensus size: 22
2082181 AAAATTTATA
*
2082191 TTTTAATAATTTAAATTTAA-ATAA
1 TTTTAA-AATTTAAA-TTAATAT-T
*
2082215 TTTTAAATTTTAAATT-A-ATT
1 TTTTAAAATTTAAATTAATATT
*
2082235 TTTTAAAA-TT--ATTAAAATT
1 TTTTAAAATTTAAATTAATATT
2082254 TATTTAAAATTTAAATTAATTATT
1 T-TTTAAAATTTAAATTAA-TATT
2082278 TTTTAA
1 TTTTAA
2082284 TCAAATTAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
17 3 0.05
18 1 0.02
19 6 0.10
20 14 0.24
21 5 0.09
22 2 0.03
23 17 0.29
24 10 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTAAAATTTAAATTAATATT
Found at i:2083182 original size:17 final size:17
Alignment explanation
Indices: 2083160--2083196 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2083150 TAAATTCAAA
2083160 AATATTTATTTAT-TTAT
1 AATATTT-TTTATATTAT
2083177 AATATTTTTTATATTAT
1 AATATTTTTTATATTAT
2083194 AAT
1 AAT
2083197 TTATGTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATATTTTTTATATTAT
Found at i:2084070 original size:20 final size:20
Alignment explanation
Indices: 2084012--2084074 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 20
2084002 AAAAAATATT
* *
2084012 TTTATAAGTTTATAAATTTTT
1 TTTATAAATTT-TAAATTTTA
* *
2084033 TTTAAAAAATTT-AA-TTTA
1 TTTATAAATTTTAAATTTTA
2084051 TTTATAAATTTTAAATTTTA
1 TTTATAAATTTTAAATTTTA
2084071 TTTA
1 TTTA
2084075 ATTAATTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 13 0.38
19 4 0.12
20 9 0.26
21 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTATAAATTTTAAATTTTA
Found at i:2084083 original size:20 final size:20
Alignment explanation
Indices: 2084024--2084086 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
2084014 TATAAGTTTA
* *
2084024 TAAATTTTTTTTAAAAAATT
1 TAAATTTTATTTAATAAATT
2084044 T-AA-TTTATTT-ATAAATTT
1 TAAATTTTATTTAATAAA-TT
*
2084062 TAAATTTTATTTAATTAATT
1 TAAATTTTATTTAATAAATT
2084082 TAAAT
1 TAAAT
2084087 AAATAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 4 0.11
18 9 0.25
19 4 0.11
20 15 0.42
21 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TAAATTTTATTTAATAAATT
Found at i:2087950 original size:19 final size:20
Alignment explanation
Indices: 2087904--2087951 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
2087894 TATAAATATA
2087904 TTTA-ATTTTAAAAATTTAT
1 TTTATATTTTAAAAATTTAT
2087923 TTATATATTTTAAAAA-TTAT
1 TT-TATATTTTAAAAATTTAT
2087943 TTTATATTT
1 TTTATATTT
2087952 ATATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.33
20 8 0.30
21 10 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATATTTTAAAAATTTAT
Found at i:2088941 original size:29 final size:27
Alignment explanation
Indices: 2088895--2088956 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 27
2088885 TTGGACAACG
* * *
2088895 TATTAAAATTTATATATATATATATAA
1 TATTAAAATTTAAATATAAAAATATAA
2088922 TATTATAAATTTAAAATATAAAAATATAA
1 TATTA-AAATTT-AAATATAAAAATATAA
2088951 TATTAA
1 TATTAA
2088957 TATGATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 5 0.17
28 7 0.23
29 18 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TATTAAAATTTAAATATAAAAATATAA
Found at i:2088956 original size:21 final size:21
Alignment explanation
Indices: 2088926--2088979 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
2088916 ATATAATATT
2088926 ATAAAT-TTAAAAT-ATAAAA
1 ATAAATATTAAAATGATAAAA
* *
2088945 ATATAATATTAATATGATATAA
1 ATA-AATATTAAAATGATAAAA
*
2088967 ATACATATTAAAA
1 ATAAATATTAAAA
2088980 AATTTATGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.11
20 3 0.11
21 14 0.50
22 8 0.29
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAAATATTAAAATGATAAAA
Found at i:2089612 original size:16 final size:15
Alignment explanation
Indices: 2089587--2089625 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2089577 ATATTTAATA
*
2089587 ATTTTTTAAAAATTT
1 ATTTTTTAAAAAATT
2089602 ATTTATTTAAAAAATT
1 ATTT-TTTAAAAAATT
*
2089618 ATATTTTA
1 ATTTTTTA
2089626 TATTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTTTAAAAAATT
Found at i:2089658 original size:12 final size:11
Alignment explanation
Indices: 2089630--2089662 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2089620 ATTTTATATT
2089630 TATAT-TTAAA
1 TATATATTAAA
2089640 TATATATTAAA
1 TATATATTAAA
2089651 TATAATATTAAA
1 TAT-ATATTAAA
2089663 AAAAAAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 5 0.24
11 8 0.38
12 8 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TATATATTAAA
Found at i:2094716 original size:29 final size:30
Alignment explanation
Indices: 2094663--2094719 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
2094653 CCAATAGAAT
*
2094663 TAAATTAAATAATTATAATTTTTTAATTTA
1 TAAATTAAATAATTATAATTATTTAATTTA
2094693 TAAATTAAA-AATTA-AATATATTTAATT
1 TAAATTAAATAATTATAAT-TATTTAATT
2094720 ATTTCTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 3 0.12
29 13 0.52
30 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TAAATTAAATAATTATAATTATTTAATTTA
Found at i:2095778 original size:16 final size:15
Alignment explanation
Indices: 2095757--2095790 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2095747 GATATTTTTA
*
2095757 TTATTATTATTATTAT
1 TTATTATAATTA-TAT
2095773 TTATTATAATTATAT
1 TTATTATAATTATAT
2095788 TTA
1 TTA
2095791 AAAATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATTATAATTATAT
Found at i:2095812 original size:31 final size:31
Alignment explanation
Indices: 2095762--2095848 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 31
2095752 TTTTATTATT
2095762 ATTATTAT-TATTTATTATAATTATATTTAA-AA
1 ATTATTATATATTTA-TATAA-TAT-TTTAATAA
2095794 A-TATTATATATTTATATAA-ATTTTAATAA
1 ATTATTATATATTTATATAATATTTTAATAA
2095823 ATTAATTATAT-TGTTATATAATATTT
1 ATT-ATTATATAT-TTATATAATATTT
2095849 GTATTATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
28 5 0.10
29 5 0.10
30 2 0.04
31 26 0.53
32 11 0.22
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (31 bp):
ATTATTATATATTTATATAATATTTTAATAA
Found at i:2095813 original size:21 final size:21
Alignment explanation
Indices: 2095774--2095813 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2095764 TATTATTATT
*
2095774 TATTATAATTATATTTAAAAA
1 TATTATAATTATATATAAAAA
2095795 TATTATATATT-TATATAAA
1 TATTATA-ATTATATATAAA
2095814 TTTTAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTATAATTATATATAAAAA
Found at i:2096354 original size:21 final size:21
Alignment explanation
Indices: 2096330--2096371 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2096320 TGACCGATAT
*
2096330 AGATTTCTAATCTCAAGTTGA
1 AGATTTCTAATATCAAGTTGA
2096351 AGATTTCTAATATCAAGTTGA
1 AGATTTCTAATATCAAGTTGA
2096372 GGGAACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (21 bp):
AGATTTCTAATATCAAGTTGA
Found at i:2103175 original size:15 final size:15
Alignment explanation
Indices: 2103152--2103188 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
2103142 CGTCGTCGAG
*
2103152 AAGATGAACAAGAAC
1 AAGAAGAACAAGAAC
2103167 AAGAAGAACAAGAAC
1 AAGAAGAACAAGAAC
2103182 AAGAAGA
1 AAGAAGA
2103189 CAACCCCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.65, C:0.11, G:0.22, T:0.03
Consensus pattern (15 bp):
AAGAAGAACAAGAAC
Found at i:2103892 original size:16 final size:15
Alignment explanation
Indices: 2103865--2103895 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2103855 AATAGTAAAA
2103865 TAATTTATTTAAATT
1 TAATTTATTTAAATT
2103880 TAATTTAATTTAAATT
1 TAATTT-ATTTAAATT
2103896 GAGTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TAATTTATTTAAATT
Found at i:2104251 original size:2 final size:2
Alignment explanation
Indices: 2104244--2104269 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2104234 GGCTTTAAAT
2104244 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2104270 CCTAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2105003 original size:22 final size:21
Alignment explanation
Indices: 2104949--2105022 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 21
2104939 ATCTCAAGTA
2104949 CAAATTTAAATTATTATTTAT
1 CAAATTTAAATTATTATTTAT
*
2104970 CAAATTAAAAATTATT-TTTAAT
1 CAAATT-TAAATTATTATTT-AT
* * **
2104992 TAATATTTAAATTTTTATAAAT
1 CAA-ATTTAAATTATTATTTAT
2105014 C-AATTTAAA
1 CAAATTTAAA
2105023 ATAAAAATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
20 7 0.17
21 10 0.24
22 21 0.50
23 4 0.10
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
CAAATTTAAATTATTATTTAT
Found at i:2105264 original size:14 final size:13
Alignment explanation
Indices: 2105243--2105285 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
2105233 ATTTAATTTT
2105243 ATTA-ATTTAAACA
1 ATTATATTTAAA-A
2105256 ATTATATTTAAAA
1 ATTATATTTAAAA
*
2105269 ATAATATTTAATAA
1 ATTATATTTAA-AA
2105283 ATT
1 ATT
2105286 TTAAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTATATTTAAAA
Found at i:2106281 original size:16 final size:16
Alignment explanation
Indices: 2106262--2106313 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
2106252 AATAATTATT
2106262 TATATTAAAATTTTAA
1 TATATTAAAATTTTAA
*
2106278 TATATTAATAATTTATAT
1 TATATTAA-AATTT-TAA
*
2106296 TATA-T-AAATTTAAA
1 TATATTAAAATTTTAA
2106310 TATA
1 TATA
2106314 ATTATTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 5 0.16
15 5 0.16
16 9 0.29
17 6 0.19
18 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATTAAAATTTTAA
Found at i:2106286 original size:32 final size:32
Alignment explanation
Indices: 2106250--2106313 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
2106240 TTCATATTTT
*
2106250 TTAATAA-TTAT-TTATATTAAAATTTTAATATA
1 TTAATAATTTATATTATA-T-AAATTTAAATATA
2106282 TTAATAATTTATATTATATAAATTTAAATATA
1 TTAATAATTTATATTATATAAATTTAAATATA
2106314 ATTATTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 19 0.66
33 5 0.17
34 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
TTAATAATTTATATTATATAAATTTAAATATA
Found at i:2106296 original size:29 final size:29
Alignment explanation
Indices: 2106253--2106327 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
2106243 ATATTTTTTA
*
2106253 ATAATTATTTATATTA-A-AATTTTAATAT
1 ATAATTATTTATATTATATAAATTTAA-AT
*
2106281 ATTAATAATTTATATTATATAAATTTAAAT
1 A-TAATTATTTATATTATATAAATTTAAAT
*
2106311 ATAATTATTTATTTTAT
1 ATAATTATTTATATTAT
2106328 GTATTAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.03
29 28 0.70
30 4 0.10
31 7 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
ATAATTATTTATATTATATAAATTTAAAT
Found at i:2106336 original size:32 final size:31
Alignment explanation
Indices: 2106254--2106336 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 31
2106244 TATTTTTTAA
* *
2106254 TAATTATTTATATTA--AAATTTTAATATAT
1 TAATAATTTATATTATTAAATTTAAATATAT
2106283 TAATAATTTATATTATATAAATTTAAATATAAT
1 TAATAATTTATATTAT-TAAATTTAAATAT-AT
* *
2106316 TATTTATTT-TATGTATTAAAT
1 TAATAATTTATAT-TATTAAAT
2106337 ATTTTTTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
29 14 0.31
32 19 0.42
33 12 0.27
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
TAATAATTTATATTATTAAATTTAAATATAT
Found at i:2106785 original size:15 final size:17
Alignment explanation
Indices: 2106753--2106790 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
2106743 TAAAATTTGA
2106753 TATAAAATATATTTATT
1 TATAAAATATATTTATT
*
2106770 TTTAAAA-ATA-TTATT
1 TATAAAATATATTTATT
2106785 TATAAA
1 TATAAA
2106791 TTAATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 10 0.53
16 3 0.16
17 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATAAAATATATTTATT
Found at i:2113526 original size:26 final size:27
Alignment explanation
Indices: 2113491--2113547 Score: 100
Period size: 26 Copynumber: 2.2 Consensus size: 27
2113481 GCGGATGCAC
2113491 TAAG-ACCTCACTGAAAAGAGAACC-T
1 TAAGAACCTCACTGAAAAGAGAACCTT
2113516 TAAGAACCTCACTGAAAAGAGAACCTT
1 TAAGAACCTCACTGAAAAGAGAACCTT
2113543 TAAGA
1 TAAGA
2113548 CAGGAAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 4 0.13
26 20 0.67
27 6 0.20
ACGTcount: A:0.46, C:0.21, G:0.16, T:0.18
Consensus pattern (27 bp):
TAAGAACCTCACTGAAAAGAGAACCTT
Found at i:2117290 original size:13 final size:13
Alignment explanation
Indices: 2117272--2117311 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
2117262 ATATAAAATA
2117272 ATAAAAATATTAT
1 ATAAAAATATTAT
2117285 ATAAAAATATT-T
1 ATAAAAATATTAT
*
2117297 -TTAAAAT-TTAT
1 ATAAAAATATTAT
2117308 ATAA
1 ATAA
2117312 TATAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
10 2 0.09
11 7 0.30
12 3 0.13
13 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAAAAATATTAT
Found at i:2117328 original size:20 final size:20
Alignment explanation
Indices: 2117305--2117409 Score: 63
Period size: 18 Copynumber: 5.7 Consensus size: 20
2117295 TTTTAAAATT
2117305 TATATAATATAAATTATTAA
1 TATATAATATAAATTATTAA
2117325 TATAT--TA-AAATTATTAA
1 TATATAATATAAATTATTAA
*
2117342 -AAAT-ATATAATATT-TTAA
1 TATATAATATAA-ATTATTAA
2117360 -ATATAAT-TATAA-T-TTAA
1 TATATAATATA-AATTATTAA
* *
2117377 TAAAAAATATAAA-TA-TAA
1 TATATAATATAAATTATTAA
*
2117395 TATAAAAATATAAAT
1 TAT-ATAATATAAAT
2117410 AATAATTAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.04
17 17 0.24
18 27 0.39
19 18 0.26
20 5 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATAATATAAATTATTAA
Found at i:2117403 original size:19 final size:19
Alignment explanation
Indices: 2117374--2117415 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
2117364 AATTATAATT
2117374 TAATAAAAAATATAAAT-A
1 TAATAAAAAATATAAATAA
2117392 TAATATAAAAATATAAATAA
1 TAATA-AAAAATATAAATAA
2117412 TAAT
1 TAAT
2117416 TAATTATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.23
19 12 0.55
20 5 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
TAATAAAAAATATAAATAA
Found at i:2117425 original size:59 final size:56
Alignment explanation
Indices: 2117264--2117443 Score: 163
Period size: 59 Copynumber: 3.2 Consensus size: 56
2117254 TACAAAATAT
* * * *
2117264 ATAAAATAATAAAAATATTATATAAAAATATTTTTAA-AATTTATATAA-TATAAATTA
1 ATAAAA-AATATAAATATTATATAAAAATA--TATAATAATTAATATAATTATAATTTA
* * * *
2117321 TTAATATAT-TAAA-ATTAT-TAAAAATATATAATATTTTAAATATAATTATAATTTA
1 ATAAAAAATATAAATATTATATAAAAATATATAATA-ATT-AATATAATTATAATTTA
* *
2117376 ATAAAAAATATAAATATAATATAAAAATATAAATAATAATTAATTATAATTATAATGTA
1 ATAAAAAATATAAATATTATATAAAAATAT--ATAATAATTAA-TATAATTATAATTTA
2117435 ATAAAAAAT
1 ATAAAAAAT
2117444 TTATTTTTTA
Statistics
Matches: 99, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
51 4 0.04
52 1 0.01
53 10 0.10
54 11 0.11
55 17 0.17
56 6 0.06
57 8 0.08
58 11 0.11
59 25 0.25
60 6 0.06
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (56 bp):
ATAAAAAATATAAATATTATATAAAAATATATAATAATTAATATAATTATAATTTA
Found at i:2117554 original size:16 final size:17
Alignment explanation
Indices: 2117533--2117573 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
2117523 TTTATATTTT
*
2117533 TTAATTATATTTAAA-A
1 TTAATTATAATTAAATA
*
2117549 TTAATTATAATTAAATT
1 TTAATTATAATTAAATA
2117566 TTAATTAT
1 TTAATTAT
2117574 TAAAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAATTATAATTAAATA
Found at i:2120942 original size:55 final size:55
Alignment explanation
Indices: 2120866--2120975 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
2120856 CGAATGATTT
2120866 TCTTTTTCTTGTAGTTATTCTACTAATGGATTATCATCCTCAAAAATATGATCAA
1 TCTTTTTCTTGTAGTTATTCTACTAATGGATTATCATCCTCAAAAATATGATCAA
2120921 TCTTTTTCTTGTAGTTATTCTACTAATGGATTATCATCCTCAAAAATATGATCAA
1 TCTTTTTCTTGTAGTTATTCTACTAATGGATTATCATCCTCAAAAATATGATCAA
2120976 GGCTGATAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (55 bp):
TCTTTTTCTTGTAGTTATTCTACTAATGGATTATCATCCTCAAAAATATGATCAA
Found at i:2121930 original size:21 final size:21
Alignment explanation
Indices: 2121904--2121946 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2121894 AAGGTACAAT
2121904 ACTTTTACTAAAAGCTCATAA
1 ACTTTTACTAAAAGCTCATAA
*
2121925 ACTTTTACTAAAGGCTCATAA
1 ACTTTTACTAAAAGCTCATAA
2121946 A
1 A
2121947 AGTTTATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.33
Consensus pattern (21 bp):
ACTTTTACTAAAAGCTCATAA
Found at i:2121952 original size:21 final size:21
Alignment explanation
Indices: 2121907--2121952 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2121897 GTACAATACT
**
2121907 TTTACTAAAAGCTCATAAACT
1 TTTACTAAAAGCTCATAAAAG
*
2121928 TTTACTAAAGGCTCATAAAAG
1 TTTACTAAAAGCTCATAAAAG
2121949 TTTA
1 TTTA
2121953 TCATTTCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (21 bp):
TTTACTAAAAGCTCATAAAAG
Found at i:2123249 original size:21 final size:21
Alignment explanation
Indices: 2123211--2123251 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2123201 AGATAAAAAT
*
2123211 TCATCTTTTCTTTTTTTGCTG
1 TCATCTTTTCTTTATTTGCTG
2123232 TCAT-TTTTCTTTAATTTGCT
1 TCATCTTTTCTTT-ATTTGCT
2123252 TTTTTTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.10, C:0.17, G:0.07, T:0.66
Consensus pattern (21 bp):
TCATCTTTTCTTTATTTGCTG
Found at i:2123783 original size:16 final size:16
Alignment explanation
Indices: 2123764--2123794 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2123754 ATAAAATCAT
2123764 AAATTAATAAATAATA
1 AAATTAATAAATAATA
*
2123780 AAATTAATATATAAT
1 AAATTAATAAATAAT
2123795 TATTAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTAATAAATAATA
Found at i:2123955 original size:3 final size:3
Alignment explanation
Indices: 2123947--2123995 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
2123937 TATGTATTAT
2123947 ATA ATA ATA ATA 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 ATA ATA ATA ATA
2123995 A
1 A
2123996 AAATCTAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2124375 original size:19 final size:21
Alignment explanation
Indices: 2124286--2124377 Score: 67
Period size: 20 Copynumber: 4.7 Consensus size: 21
2124276 TTTATTATTT
2124286 AATTA-AAAATAATAAAAATATA
1 AATTATAAAATAAT--AAATATA
*
2124308 AA-TACCAAAATAA-AAAT-T-
1 AATTA-TAAAATAATAAATATA
*
2124326 -ATTATAAAAT-TTAAATATA
1 AATTATAAAATAATAAATATA
2124345 AATTATAAAATAATAAA-ATA
1 AATTATAAAATAATAAATATA
*
2124365 AA-TATATAATAAT
1 AATTATAAAATAAT
2124378 TATATACATT
Statistics
Matches: 58, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
17 10 0.17
18 3 0.05
19 11 0.19
20 19 0.33
21 6 0.10
22 2 0.03
23 7 0.12
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AATTATAAAATAATAAATATA
Found at i:2124496 original size:15 final size:15
Alignment explanation
Indices: 2124476--2124504 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2124466 TATCACTATT
2124476 ATTTATAAAAAAATA
1 ATTTATAAAAAAATA
2124491 ATTTATAAAAAAAT
1 ATTTATAAAAAAAT
2124505 TAAAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATTTATAAAAAAATA
Found at i:2125120 original size:11 final size:11
Alignment explanation
Indices: 2125104--2125129 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2125094 TTGGTATTGT
2125104 TTTTGTTTTTA
1 TTTTGTTTTTA
2125115 TTTTGTTTTTA
1 TTTTGTTTTTA
2125126 TTTT
1 TTTT
2125130 AGATTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTGTTTTTA
Done.