Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007825.1 Hibiscus syriacus cultivar Beakdansim tig00110163_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2082551
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:10038 original size:5 final size:5
Alignment explanation
Indices: 10028--10053 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
10018 TGACTTAGAA
10028 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
10054 AATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:10271 original size:42 final size:42
Alignment explanation
Indices: 10202--10291 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
10192 TTTACCCTAA
**
10202 ACCCGACCCGACCCGAACAGTGTATTTTTAAAAAAAAACCCG
1 ACCCGACCCGACCCGAACAGTAAATTTTTAAAAAAAAACCCG
* ** *
10244 ACCCGACCCGACCCGAACCCG-AAATTTTTTTAAAAAAATCCG
1 ACCCGACCCGACCCGAA-CAGTAAATTTTTAAAAAAAAACCCG
10286 ACCCGA
1 ACCCGA
10292 TCGGGTCGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 39 0.95
43 2 0.05
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (42 bp):
ACCCGACCCGACCCGAACAGTAAATTTTTAAAAAAAAACCCG
Found at i:10723 original size:168 final size:169
Alignment explanation
Indices: 10424--10818 Score: 735
Period size: 168 Copynumber: 2.4 Consensus size: 169
10414 TCGAGGGAGT
10424 TCTGTTTCCTATCA-TTTAATTTGAATTCAACATAAAACAAATTAATTCTCAATTATAGGTTAAG
1 TCTGTTTCCTATCATTTTAATTTGAATTCAACATAAAACAAATTAATTCTCAATTATAGGTTAAG
*
10488 GTTTAGGTTTAGATATTTTATATAAATTCTATACATATTTTTAATTAATTATTTTTTTATTTTAC
66 GTTTAGGTTTAGATATTTTATATAAATTCTATACATATTTTTAATTAATTATTTTTTTACTTTAC
10553 TCAAGTTGTTTACACAATTTAATTAATCATGAAATTAGA
131 TCAAGTTGTTTACACAATTTAATTAATCATGAAATTAGA
*
10592 TCTGTTTCCTATCATTTTAATTTGAATTCAACATAAAACAAATTAATTATCAATTATAGGTTAAG
1 TCTGTTTCCTATCATTTTAATTTGAATTCAACATAAAACAAATTAATTCTCAATTATAGGTTAAG
10657 GTTTAGGTTTAGATATTTTATATAAATTCTATACATA-TTTTAATTAATTATTTTTTTACTTTAC
66 GTTTAGGTTTAGATATTTTATATAAATTCTATACATATTTTTAATTAATTATTTTTTTACTTTAC
10721 TCAAGTTGTTTACACAATTTAATTAATCATGAAATTAGA
131 TCAAGTTGTTTACACAATTTAATTAATCATGAAATTAGA
*
10760 TCTGTTTCCTATCATTTTAATTTG-ATTCAACATAAAACAAATTAA-TCTCAATTGTAGGT
1 TCTGTTTCCTATCATTTTAATTTGAATTCAACATAAAACAAATTAATTCTCAATTATAGGT
10819 GGTGGATAAG
Statistics
Matches: 222, Mismatches: 4, Indels: 4
0.97 0.02 0.02
Matches are distributed among these distances:
166 12 0.05
167 21 0.09
168 103 0.46
169 86 0.39
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (169 bp):
TCTGTTTCCTATCATTTTAATTTGAATTCAACATAAAACAAATTAATTCTCAATTATAGGTTAAG
GTTTAGGTTTAGATATTTTATATAAATTCTATACATATTTTTAATTAATTATTTTTTTACTTTAC
TCAAGTTGTTTACACAATTTAATTAATCATGAAATTAGA
Found at i:13467 original size:27 final size:23
Alignment explanation
Indices: 13418--13478 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
13408 CTTATATCTA
13418 TTAGATTTAAATAAATAAATTAT
1 TTAGATTTAAATAAATAAATTAT
*
13441 TTAGATTTAAATAAATAAATGAT
1 TTAGATTTAAATAAATAAATTAT
*
13464 TTATATTTAAATAAA
1 TTAGATTTAAATAAA
13479 CTTTATAACC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
TTAGATTTAAATAAATAAATTAT
Found at i:16207 original size:27 final size:26
Alignment explanation
Indices: 16147--16208 Score: 63
Period size: 27 Copynumber: 2.2 Consensus size: 26
16137 CCAAGCCTTT
*
16147 TACTTTACTCTTTCCTATTTTGCTCAC
1 TACTTTACTC-TTCCTATTTTACTCAC
16174 TAAACTTTACTC-TCCTATTTTACTCATC
1 T--ACTTTACTCTTCCTATTTTACTCA-C
16202 GTACTTT
1 -TACTTT
16209 CAATTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
27 19 0.63
28 1 0.03
29 10 0.33
ACGTcount: A:0.19, C:0.27, G:0.03, T:0.50
Consensus pattern (26 bp):
TACTTTACTCTTCCTATTTTACTCAC
Found at i:23365 original size:112 final size:111
Alignment explanation
Indices: 23128--23365 Score: 359
Period size: 111 Copynumber: 2.1 Consensus size: 111
23118 GATACTTATA
* *
23128 ATAAAGTATCGACACTATCAACATATCTGGTAGTGCTTTACCTGTTTTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGT
* * *
23193 TTGTCATTTGTTTACCTGTTATATTGTTATTGATCGATACAGTTTT
66 TTGTCATTTGTTTACATGTTATATTGTTATAGATCAATACAGTTTT
* * * *
23239 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGG-
* * *
23304 TTTGTCATTTTTTTACATGTTATATTGTTATAGATCAATATATTTTT
65 TTTGTCATTTGTTTACATGTTATATTGTTATAGATCAATACAGTTTT
23351 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
23366 AAACCGACAA
Statistics
Matches: 114, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
111 58 0.51
112 56 0.49
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (111 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGT
TTGTCATTTGTTTACATGTTATATTGTTATAGATCAATACAGTTTT
Found at i:24686 original size:38 final size:33
Alignment explanation
Indices: 24606--24684 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
24596 TTAAAATACA
* * *
24606 CGACCAGACCCGAATATCACACTTTAAAAAAAC
1 CGACCCGACCCGAATATCAAACTTAAAAAAAAC
**
24639 CGACCCGACCCGAATATCAAACTTAAAAAAATT
1 CGACCCGACCCGAATATCAAACTTAAAAAAAAC
24672 CGACCCGACCCGA
1 CGACCCGACCCGA
24685 CCTCGAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.33, G:0.11, T:0.14
Consensus pattern (33 bp):
CGACCCGACCCGAATATCAAACTTAAAAAAAAC
Found at i:24713 original size:33 final size:32
Alignment explanation
Indices: 24542--24717 Score: 110
Period size: 32 Copynumber: 5.3 Consensus size: 32
24532 AAAACCTGAC
*
24542 CCGACCCGACCC-AATTTTTTTTTAAAAAAAT
1 CCGACCCGACCCGAATTATTTTTTAAAAAAAT
* * *
24573 CCGACCCGATCCTGAATT-TTTTTTTAAAATA-
1 CCGACCCGA-CCCGAATTATTTTTTAAAAAAAT
* ***
24604 CACGACCAGACCCGAATATCACACTTTAAAAAAA-
1 C-CGACCCGACCCGAAT-T-ATTTTTTAAAAAAAT
***
24638 CCGACCCGACCCGAA-TATCAAACTTAAAAAAATT
1 CCGACCCGACCCGAATTAT--TTTTTAAAAAAA-T
24672 CGACCCGACCCGACCTCGAATTATTTTTTAAAAAAAT
1 ----CCGACCCGACC-CGAATTATTTTTTAAAAAAAT
24709 CCGACCCGA
1 CCGACCCGA
24718 ATACGTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
30 1 0.01
31 17 0.15
32 31 0.28
33 26 0.23
34 9 0.08
37 1 0.01
38 20 0.18
39 4 0.04
40 3 0.03
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (32 bp):
CCGACCCGACCCGAATTATTTTTTAAAAAAAT
Found at i:25653 original size:23 final size:23
Alignment explanation
Indices: 25627--25674 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
25617 ATAAAGTACA
*
25627 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
25650 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
25673 AT
1 AT
25675 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:26081 original size:21 final size:22
Alignment explanation
Indices: 26056--26107 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
26046 ACACTTTACA
*
26056 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
26079 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
26102 ATATAA
1 ATATAA
26108 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:26092 original size:23 final size:23
Alignment explanation
Indices: 26066--26128 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
26056 ATATAACCAC
26066 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
26089 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
26112 TACCTATTACATCATAT
1 TACCTATTACATTATAT
26129 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:26588 original size:39 final size:39
Alignment explanation
Indices: 26530--26618 Score: 142
Period size: 39 Copynumber: 2.3 Consensus size: 39
26520 ACTCAAGTTG
*
26530 TAGATTTTGATTTCCTTTTGCTTGGCATCATATGAGATT
1 TAGATTTTGATTTCCTTTTGCTTGGCACCATATGAGATT
* * *
26569 TGGATTTTGATTTCTTTTTGCTTGGCACCATATGAGCTT
1 TAGATTTTGATTTCCTTTTGCTTGGCACCATATGAGATT
26608 TAGATTTTGAT
1 TAGATTTTGAT
26619 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.49
Consensus pattern (39 bp):
TAGATTTTGATTTCCTTTTGCTTGGCACCATATGAGATT
Found at i:26900 original size:18 final size:18
Alignment explanation
Indices: 26877--26913 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
26867 CGAAATATAT
26877 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
26895 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
26913 A
1 A
26914 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:27258 original size:25 final size:25
Alignment explanation
Indices: 27208--27258 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
27198 TTTTTCCAAA
* *
27208 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATATTCAAT
*
27233 TAATGTACCCACAACAATATTTAAT
1 TAATGTACCCACAACAATATTCAAT
27258 T
1 T
27259 GATTTGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATATTCAAT
Found at i:27552 original size:21 final size:22
Alignment explanation
Indices: 27527--27578 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
27517 ACACTTTACA
*
27527 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
27550 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
27573 ATATAA
1 ATATAA
27579 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:27563 original size:23 final size:23
Alignment explanation
Indices: 27537--27599 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
27527 ATATAACCAC
27537 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
27560 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
27583 TACCTATTACATCATAT
1 TACCTATTACATTATAT
27600 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:27943 original size:25 final size:25
Alignment explanation
Indices: 27886--27951 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
27876 CACTCAAAAG
*
27886 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
27911 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
27936 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
27952 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:30271 original size:17 final size:18
Alignment explanation
Indices: 30249--30291 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
30239 ATATATCCGG
30249 TATCATT-TTACCGGTTT
1 TATCATTGTTACCGGTTT
30266 TATCATTTTGTTACCGGTTT
1 TATCA--TTGTTACCGGTTT
30286 TATCAT
1 TATCAT
30292 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 1 0.04
19 2 0.09
20 15 0.65
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (18 bp):
TATCATTGTTACCGGTTT
Found at i:30281 original size:20 final size:20
Alignment explanation
Indices: 30254--30300 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
30244 TCCGGTATCA
30254 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
30273 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
30294 TTTTACC
1 TTTTACC
30301 TGTTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:30452 original size:20 final size:20
Alignment explanation
Indices: 30422--30469 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
30412 CACTTTTAAA
*
30422 TTTACCGGTTTTATCAT-TT
1 TTTACCTGTTTTATCATATT
30441 TGTTACCTGTTTTATCATATT
1 T-TTACCTGTTTTATCATATT
30462 TTTACCTG
1 TTTACCTG
30470 GTATATCGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 22 0.85
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.56
Consensus pattern (20 bp):
TTTACCTGTTTTATCATATT
Found at i:30476 original size:20 final size:20
Alignment explanation
Indices: 30433--30482 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
30423 TTACCGGTTT
* *
30433 TATCATTTTGTTACCTGTTT
1 TATCATTTTGTTACCTGGTA
30453 TATCATATTT-TTACCTGGTA
1 TATCAT-TTTGTTACCTGGTA
*
30473 TATCGTTTTG
1 TATCATTTTG
30483 GATCGATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 19 0.76
21 3 0.12
ACGTcount: A:0.18, C:0.14, G:0.12, T:0.56
Consensus pattern (20 bp):
TATCATTTTGTTACCTGGTA
Found at i:48144 original size:19 final size:20
Alignment explanation
Indices: 48115--48152 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
48105 AGAAATTTGT
48115 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
48135 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
48153 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:48195 original size:63 final size:62
Alignment explanation
Indices: 48120--48278 Score: 194
Period size: 63 Copynumber: 2.5 Consensus size: 62
48110 TTTGTTGAAG
* * * *
48120 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATATCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATACCCTCA
** ** *
48183 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATACCCTCA
48246 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
48279 GCCTCCATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 79 0.94
64 5 0.06
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATACCCTCA
Found at i:49643 original size:121 final size:121
Alignment explanation
Indices: 49493--49977 Score: 880
Period size: 121 Copynumber: 4.0 Consensus size: 121
49483 CGAGGGTCTA
* *
49493 TGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
49558 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
49614 TGTGGTCCTTTGTGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
49679 GATCTCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
49735 TTTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
49800 GATCTCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
49856 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* **
49921 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
49977 T
1 T
49978 ATTATATGGC
Statistics
Matches: 352, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 352 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (121 bp):
TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:49692 original size:59 final size:59
Alignment explanation
Indices: 49629--49813 Score: 150
Period size: 59 Copynumber: 3.1 Consensus size: 59
49619 TCCTTTGTGA
49629 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCTCTAG
1 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCTCTAG
* * * * * * * *
49688 CATATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT-TTTGGTCCTTT
1 CATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACTTGAT-CTCT
*
49746 GGG
58 -AG
49749 ACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCTCTAG
1 -CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCTCTAG
49809 CATAT
1 CATAT
49814 GTATATGATT
Statistics
Matches: 91, Mismatches: 18, Indels: 34
0.64 0.13 0.24
Matches are distributed among these distances:
57 6 0.07
58 6 0.07
59 22 0.24
60 14 0.15
61 14 0.15
62 17 0.19
63 6 0.07
64 6 0.07
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (59 bp):
CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCTCTAG
Found at i:49861 original size:18 final size:18
Alignment explanation
Indices: 49838--49873 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
49828 AGGAATGATA
49838 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
*
49856 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
49874 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:50052 original size:23 final size:23
Alignment explanation
Indices: 49984--50044 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
49974 CATTATTATA
*
49984 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
50007 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
50030 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
50045 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:53860 original size:19 final size:20
Alignment explanation
Indices: 53831--53868 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
53821 AGAAATTTGT
53831 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
53851 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
53869 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:53912 original size:63 final size:62
Alignment explanation
Indices: 53837--53994 Score: 192
Period size: 63 Copynumber: 2.5 Consensus size: 62
53827 TTGTTGAAGG
* * * *
53837 TGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCAA
1 TGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCAA
** ** *
53900 TGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCAG
1 TGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCAA
53963 TGCATCGATGCATCAGGAGTGCATCGATGCAT
1 TGCATCGATGCAT-AGGAGTGCATCGATGCAT
53995 GCCTCCATTA
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 78 0.94
64 5 0.06
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (62 bp):
TGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCAA
Found at i:55335 original size:18 final size:18
Alignment explanation
Indices: 55312--55347 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
55302 AGGAATGATA
55312 TGTGGT-CTTTCGGGACAT
1 TGTGGTCCTTT-GGGACAT
55330 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTTGGGACAT
55348 ATATGTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.11, C:0.17, G:0.33, T:0.39
Consensus pattern (18 bp):
TGTGGTCCTTTGGGACAT
Found at i:55368 original size:121 final size:121
Alignment explanation
Indices: 55209--55693 Score: 907
Period size: 121 Copynumber: 4.0 Consensus size: 121
55199 CGAGGGTCTA
*
55209 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
55274 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCTTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
55330 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
55395 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
55451 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
55516 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
55572 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* * **
55637 GACCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
55693 T
1 T
55694 ATTATATGGC
Statistics
Matches: 357, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 357 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:55408 original size:59 final size:59
Alignment explanation
Indices: 55224--55529 Score: 165
Period size: 59 Copynumber: 5.1 Consensus size: 59
55214 TCCTTCGGGA
55224 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
1 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
* * * * * * * *
55283 CATATGTATATGATTCTTAAGGAATGATATGTG--GTCT-TTCG-G-GACAT--TGTGGTCCTTT
1 CATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGTCTGGT-GAGACACATACT-TGATCC-CT
*
55341 GGG
58 -AG
55344 ACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
1 -CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
* * * * * * *
55404 CATATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTT
1 CATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCC-C
*
55461 TGGG
57 T-AG
55465 ACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
1 -CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
55525 CATAT
1 CATAT
55530 GTATATGATT
Statistics
Matches: 177, Mismatches: 34, Indels: 72
0.63 0.12 0.25
Matches are distributed among these distances:
57 12 0.07
58 12 0.07
59 43 0.24
60 24 0.14
61 24 0.14
62 38 0.21
63 12 0.07
64 12 0.07
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (59 bp):
CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
Found at i:55456 original size:18 final size:18
Alignment explanation
Indices: 55433--55468 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55423 AGGAATGATA
55433 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
*
55451 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
55469 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:55577 original size:18 final size:18
Alignment explanation
Indices: 55554--55589 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55544 AGGAATGATA
55554 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
*
55572 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
55590 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:55768 original size:23 final size:23
Alignment explanation
Indices: 55700--55760 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
55690 CATTATTATA
*
55700 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
55723 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
55746 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
55761 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:56970 original size:60 final size:58
Alignment explanation
Indices: 56897--57022 Score: 155
Period size: 59 Copynumber: 2.1 Consensus size: 58
56887 CCAATATAAT
* * **
56897 TATGTGTTTATTTTTAGGTACTAA-GATATTAGGAGATGTACATACTTACACCGGTGTAAG
1 TATGTGTTTA-TTTTAGGCACCAATG-TATTAAAAGATGTACATACTTACACCGGTG-AAG
* **
56957 TATGTGTTTATTTTAGGCGCCAATGTATTAAAAGATGTACATACTTACATTGGTGAAG
1 TATGTGTTTATTTTAGGCACCAATGTATTAAAAGATGTACATACTTACACCGGTGAAG
57015 TATGTGTT
1 TATGTGTT
57023 AATTGCTACA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
58 11 0.19
59 36 0.62
60 11 0.19
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (58 bp):
TATGTGTTTATTTTAGGCACCAATGTATTAAAAGATGTACATACTTACACCGGTGAAG
Found at i:67196 original size:140 final size:140
Alignment explanation
Indices: 67032--67285 Score: 364
Period size: 140 Copynumber: 1.8 Consensus size: 140
67022 AATCTTAATC
** * * * * * *
67032 GATTTTAATCAATTATTGAATCGAATAATCGTAATGGAACCTCGGGCATTAAGGCGATAATCAAA
1 GATTTTAATCAATTATTGAATCGAATAATCAAAATGGAAACTCGGACATTAAGACAAGAACCAAA
* * * *
67097 TCGGATATTCACCTAAATTAAGGGACTAAAAGTGAAATTAGTCTAAAGTACATGCTCTGATCATT
66 TCGAATATTCACCAAAATTAAGGGACTAAAAGTGAAATTAATATAAAGTACATGCTCTGATCATT
67162 CATCCTAGGT
131 CATCCTAGGT
* *
67172 GATTTTAATCAATTATTGAATCGAATAATTAAAATGGAAACTCGGACATTAAGACAAGGACCAAA
1 GATTTTAATCAATTATTGAATCGAATAATCAAAATGGAAACTCGGACATTAAGACAAGAACCAAA
* *
67237 TCGAATATTCACCAAAATTAAGGGAGTAAAAGTGTAATTAATATAAAGT
66 TCGAATATTCACCAAAATTAAGGGACTAAAAGTGAAATTAATATAAAGT
67286 GGGCTCTAAT
Statistics
Matches: 98, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
140 98 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (140 bp):
GATTTTAATCAATTATTGAATCGAATAATCAAAATGGAAACTCGGACATTAAGACAAGAACCAAA
TCGAATATTCACCAAAATTAAGGGACTAAAAGTGAAATTAATATAAAGTACATGCTCTGATCATT
CATCCTAGGT
Found at i:68981 original size:38 final size:38
Alignment explanation
Indices: 68939--69013 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 38
68929 TTTTTTTAAC
* *
68939 AAATTGAAAAATATTTATAT-ATTTTCTTTAAAAAATTT
1 AAATTCAAAAA-ACTTATATAATTTTCTTTAAAAAATTT
* * *
68977 AAATTCATAAAACTTATATAATTTTTTTTATAAAATT
1 AAATTCAAAAAACTTATATAATTTTCTTTAAAAAATT
69014 AAAAATATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 7 0.23
38 24 0.77
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (38 bp):
AAATTCAAAAAACTTATATAATTTTCTTTAAAAAATTT
Found at i:69024 original size:37 final size:37
Alignment explanation
Indices: 68953--69025 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 37
68943 TGAAAAATAT
* *
68953 TTATATATTTTCTTTAAAAAATTTAAATTCATAAAAC
1 TTATATATTTTCTTTAAAAAATTAAAAATCATAAAAC
* *
68990 TTATATAATTTTTTTTATAAAATTAAAAAT-ATAAAA
1 TTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAAA
69026 AGGTTTAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 12 0.39
38 19 0.61
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
TTATATATTTTCTTTAAAAAATTAAAAATCATAAAAC
Found at i:69449 original size:18 final size:20
Alignment explanation
Indices: 69406--69451 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
69396 GTTTGGTTTA
*
69406 AGGAATATAAGATTACCAGT
1 AGGAATAAAAGATTACCAGT
*
69426 AAGAATAAAAGATTACCA-T
1 AGGAATAAAAGATTACCAGT
69445 -GGAATAA
1 AGGAATAA
69452 GATTACTGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 6 0.26
19 1 0.04
20 16 0.70
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.22
Consensus pattern (20 bp):
AGGAATAAAAGATTACCAGT
Found at i:71310 original size:25 final size:25
Alignment explanation
Indices: 71229--71327 Score: 78
Period size: 25 Copynumber: 3.9 Consensus size: 25
71219 TTATAATTTT
* *
71229 TATATTTTTTTATAGTTTAAATTGA
1 TATAATTTATTATAGTTTAAATTGA
* *
71254 TATAATTTA-TATA-TAATAATATT-T
1 TATAATTTATTATAGT-TTAA-ATTGA
*
71278 TTTGAATTTATTATAGTTTAAATTGA
1 TAT-AATTTATTATAGTTTAAATTGA
*
71304 TATAATTTATATATAAGTGTAAAT
1 TATAATTTAT-TAT-AGTTTAAAT
71328 ATTATTTAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
23 1 0.02
24 9 0.16
25 26 0.46
26 12 0.21
27 9 0.16
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (25 bp):
TATAATTTATTATAGTTTAAATTGA
Found at i:73067 original size:6 final size:6
Alignment explanation
Indices: 73056--73109 Score: 108
Period size: 6 Copynumber: 9.0 Consensus size: 6
73046 CGCTCCATCA
73056 TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC
1 TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC
73104 TGCTTC
1 TGCTTC
73110 ATCATCCGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.00, C:0.33, G:0.17, T:0.50
Consensus pattern (6 bp):
TGCTTC
Found at i:74563 original size:2 final size:2
Alignment explanation
Indices: 74556--74585 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
74546 TAAGGATCAA
74556 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
74586 TGAGGGAATC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84494 original size:11 final size:11
Alignment explanation
Indices: 84478--84539 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
84468 AAAATTACAT
84478 TATTAAAAATA
1 TATTAAAAATA
84489 TATTAAAAATACA
1 TATTAAAAAT--A
* *
84502 CTATTGATAAT-
1 -TATTAAAAATA
84513 TA-TAAAAA-A
1 TATTAAAAATA
84522 -ATTAAAAATA
1 TATTAAAAATA
84532 TATTAAAA
1 TATTAAAA
84540 TTCTATAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
8 1 0.03
9 10 0.25
10 3 0.08
11 17 0.43
13 1 0.03
14 8 0.20
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:84602 original size:7 final size:7
Alignment explanation
Indices: 84587--84650 Score: 58
Period size: 7 Copynumber: 9.3 Consensus size: 7
84577 CCTTGTAATG
84587 AACCATA
1 AACCATA
*
84594 AACCTTA
1 AACCATA
*
84601 AACCCTA
1 AACCATA
*
84608 AAACATA
1 AACCATA
84615 AACCAT-
1 AACCATA
* *
84621 ACCCTTA
1 AACCATA
*
84628 AACTATA
1 AACCATA
84635 AACCATA
1 AACCATA
*
84642 AACCTTA
1 AACCATA
84649 AA
1 AA
84651 TTATACTTTC
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
6 4 0.09
7 40 0.91
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (7 bp):
AACCATA
Found at i:84629 original size:27 final size:28
Alignment explanation
Indices: 84587--84650 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
84577 CCTTGTAATG
*
84587 AACCATAAACCTTAAACCCTAAAACATA
1 AACCATAAACCTTAAACCATAAAACATA
* * *
84615 AACCAT-ACCCTTAAACTATAAACCATA
1 AACCATAAACCTTAAACCATAAAACATA
*
84642 AACCTTAAA
1 AACCATAAA
84651 TTATACTTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (28 bp):
AACCATAAACCTTAAACCATAAAACATA
Found at i:84630 original size:19 final size:20
Alignment explanation
Indices: 84602--84641 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
84592 TAAACCTTAA
84602 ACCCTAAAAC-ATAAACCAT
1 ACCCTAAAACTATAAACCAT
*
84621 ACCCTTAAACTATAAACCAT
1 ACCCTAAAACTATAAACCAT
84641 A
1 A
84642 AACCTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (20 bp):
ACCCTAAAACTATAAACCAT
Found at i:84635 original size:20 final size:21
Alignment explanation
Indices: 84591--84655 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
84581 GTAATGAACC
* *
84591 ATAAACCTTAAACCCTAAAAC-
1 ATAAACCAT-AACCCTTAAACT
84612 ATAAACCAT-ACCCTTAAACT
1 ATAAACCATAACCCTTAAACT
* *
84632 ATAAACCATAAACCTTAAATT
1 ATAAACCATAACCCTTAAACT
84653 ATA
1 ATA
84656 CTTTCATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.24
20 9 0.24
21 20 0.53
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
ATAAACCATAACCCTTAAACT
Found at i:86483 original size:13 final size:13
Alignment explanation
Indices: 86432--86483 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
86422 GTCATAAATC
*
86432 TATGACGCGCATT
1 TATGACGCACATT
* *
86445 GATGACACACATT
1 TATGACGCACATT
*
86458 TATGACTCACATT
1 TATGACGCACATT
*
86471 TATGACGCGCATT
1 TATGACGCACATT
86484 GAGCGTCATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:86706 original size:44 final size:45
Alignment explanation
Indices: 86654--86780 Score: 163
Period size: 44 Copynumber: 2.9 Consensus size: 45
86644 CGTTTTTAGC
86654 AGAAACGCCGCAAAACATCAATACCTACTGCGGCGTTTGTA-AAA
1 AGAAACGCCGCAAAACATCAATACCTACTGCGGCGTTTGTAGAAA
* **
86698 AGAAACGCCGCAAAACATCAACACCTACTGCGGCGTTT-TAGTGA
1 AGAAACGCCGCAAAACATCAATACCTACTGCGGCGTTTGTAGAAA
* * *
86742 A-AAACGCCGCTAAACATC-ATAACCTATTGAGGCGTTTGT
1 AGAAACGCCGCAAAACATCAAT-ACCTACTGCGGCGTTTGT
86781 CTGAAAAACG
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
42 1 0.01
43 32 0.44
44 40 0.55
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (45 bp):
AGAAACGCCGCAAAACATCAATACCTACTGCGGCGTTTGTAGAAA
Found at i:86786 original size:43 final size:43
Alignment explanation
Indices: 86656--87036 Score: 340
Period size: 43 Copynumber: 8.8 Consensus size: 43
86646 TTTTTAGCAG
* * * * **
86656 AAACGCCGCAAAACATCAATACCTACTGCGGCGTTTGTAAAAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTATGAA
* * *
86699 GAAACGCCGCAAAACATCAACACCTACTGCGGCGTTT-TAGTGAA
1 -AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTA-TGAA
* * *
86743 AAACGCCGCTAAACATCATA-ACCTATTGAGGCGTTTGTCTGAA
1 AAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTGTATGAA
* * * * * * *
86786 AAACGCTGCTAAATATTAACACATATTACGACGTTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTATGAA
* * *
86829 AAACGCCGCTAAATATCAACACCTATTGCGTCATTTATAT-AA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTATGAA
* * * *
86871 TAAACGCCACTAAATATCGACACCTATTGCGGCATTTGTCTGAA
1 -AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTATGAA
* * * *
86915 AAACGCTGCTAAATATTAACACCTATTGCGGTGGTTT-TATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGG-CGTTTGTATGAA
* * * *
86958 AAACGTCGCTAAATATCAACACCTATTGCAGCGTTTGTCA-CAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT-ATGAA
* * *
87001 AAACGCCGCTAAATATCAATATCTATTGCGGTGTTT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
87037 TTTGTGAAAA
Statistics
Matches: 279, Mismatches: 49, Indels: 19
0.80 0.14 0.05
Matches are distributed among these distances:
42 6 0.02
43 228 0.82
44 45 0.16
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTATGAA
Found at i:86896 original size:129 final size:129
Alignment explanation
Indices: 86700--86986 Score: 382
Period size: 129 Copynumber: 2.2 Consensus size: 129
86690 TTGTAAAAAG
* * * * *
86700 AAACGCCGCAAAACATCAACACCTACTGCGGCGTTTTAGTGAAAAACGCCGCTAAACATCATAAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCATTTTAGTGAAAAACGCCACTAAACATCATAAC
* *
86765 CTATTGAGGCGTTTGTCTGAAAAACGCTGCTAAATATTAACACATATTACGACGTTTTTATGAC
66 CTATTGAGGCATTTGTCTGAAAAACGCTGCTAAATATTAACACATATTACGACGGTTTTATGAC
* *
86829 AAACGCCGCTAAATATCAACACCTATTGCGTCATTTATA-T-AATAAACGCCACTAAATATCGA-
1 AAACGCCGCTAAATATCAACACCTATTGCGGCATTT-TAGTGAA-AAACGCCACTAAACATC-AT
* * * * **
86891 CACCTATTGCGGCATTTGTCTGAAAAACGCTGCTAAATATTAACACCTATTGCGGTGGTTTTATG
63 AACCTATTGAGGCATTTGTCTGAAAAACGCTGCTAAATATTAACACATATTACGACGGTTTTATG
86956 AC
128 AC
*
86958 AAACGTCGCTAAATATCAACACCTATTGC
1 AAACGCCGCTAAATATCAACACCTATTGC
86987 AGCGTTTGTC
Statistics
Matches: 139, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
128 2 0.01
129 134 0.96
130 3 0.02
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27
Consensus pattern (129 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCATTTTAGTGAAAAACGCCACTAAACATCATAAC
CTATTGAGGCATTTGTCTGAAAAACGCTGCTAAATATTAACACATATTACGACGGTTTTATGAC
Found at i:87005 original size:129 final size:129
Alignment explanation
Indices: 86700--87031 Score: 377
Period size: 129 Copynumber: 2.6 Consensus size: 129
86690 TTGTAAAAAG
* * * * * * *
86700 AAACGCCGCAAAACATCAACACCTACTGCGGCGTTT-TAGTGAA-AAACGCCGCTAAACATCATA
1 AAACGCCGCTAAATATCAACACCTATTGCGTCATTTATA-T-AACAAACGCCACTAAATATCA-A
* * *
86763 -ACCTATTGAGGCGTTTGTCTGAAAAACGCTGCTAAATATTAACACATATTACGACGTTTTTATG
63 CACCTATTGCGGCATTTGTCTGAAAAACGCTGCTAAATATTAACACATATTACGACGGTTTTATG
86827 AC
128 AC
* *
86829 AAACGCCGCTAAATATCAACACCTATTGCGTCATTTATATAATAAACGCCACTAAATATCGACAC
1 AAACGCCGCTAAATATCAACACCTATTGCGTCATTTATATAACAAACGCCACTAAATATCAACAC
* * **
86894 CTATTGCGGCATTTGTCTGAAAAACGCTGCTAAATATTAACACCTATTGCGGTGGTTTTATGAC
66 CTATTGCGGCATTTGTCTGAAAAACGCTGCTAAATATTAACACATATTACGACGGTTTTATGAC
* * * * * *
86958 AAACGTCGCTAAATATCAACACCTATTGCAG-CGTTTGTCA-CACAAACGCCGCTAAATATCAAT
1 AAACGCCGCTAAATATCAACACCTATTGC-GTCATTTAT-ATAACAAACGCCACTAAATATCAAC
*
87021 ATCTATTGCGG
64 ACCTATTGCGG
87032 TGTTTTTTGT
Statistics
Matches: 174, Mismatches: 24, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
128 3 0.02
129 167 0.96
130 4 0.02
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27
Consensus pattern (129 bp):
AAACGCCGCTAAATATCAACACCTATTGCGTCATTTATATAACAAACGCCACTAAATATCAACAC
CTATTGCGGCATTTGTCTGAAAAACGCTGCTAAATATTAACACATATTACGACGGTTTTATGAC
Found at i:87322 original size:2 final size:2
Alignment explanation
Indices: 87315--87357 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
87305 TTTCGTAAAT
87315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
87357 T
1 T
87358 TGTAGATTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:90919 original size:23 final size:23
Alignment explanation
Indices: 90893--90943 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
90883 AAACGAGCTT
* *
90893 GAGCTCAAAGTCGAGCTTGAATC
1 GAGCTCAAAATCGAGCTTCAATC
*
90916 GAGCTCAAAATCGATCTTCAATC
1 GAGCTCAAAATCGAGCTTCAATC
90939 GAGCT
1 GAGCT
90944 ATTGAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
GAGCTCAAAATCGAGCTTCAATC
Found at i:91108 original size:16 final size:16
Alignment explanation
Indices: 91087--91144 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
91077 TGAGTTCGAG
* *
91087 TCGAGCTTGGCAATAC
1 TCGAGCTCGACAATAC
91103 TCGAGCTCGACAATAC
1 TCGAGCTCGACAATAC
91119 TCGAGCTCGACAATAC
1 TCGAGCTCGACAATAC
91135 TCGAGCTCGA
1 TCGAGCTCGA
91145 TTCGACTCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (16 bp):
TCGAGCTCGACAATAC
Found at i:91153 original size:32 final size:32
Alignment explanation
Indices: 91081--91153 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 32
91071 AGTTTTTGAG
* * *
91081 TTCGAGTCGAGCTTGGCAATACTCGAGCTCGA
1 TTCGACTCGAGCTCGACAATACTCGAGCTCGA
****
91113 CAATACTCGAGCTCGACAATACTCGAGCTCGA
1 TTCGACTCGAGCTCGACAATACTCGAGCTCGA
91145 TTCGACTCG
1 TTCGACTCG
91154 TTTAAACCCC
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (32 bp):
TTCGACTCGAGCTCGACAATACTCGAGCTCGA
Found at i:92287 original size:29 final size:29
Alignment explanation
Indices: 92245--92333 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
92235 TACCGGGGGT
*
92245 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
***
92274 AGGTCGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
92303 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
92332 AG
1 AG
92334 CCAACGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:92601 original size:29 final size:29
Alignment explanation
Indices: 92540--92623 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
92530 ATGAATCCTT
** * **
92540 GGTCGCCCCGAGTGCATGGCGACCTCCTT
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
* *
92569 GGTCGCCGGGCGTGCATGGCGACCTAGGA
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
*
92598 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCGCCGGGAGTGCATGGCGACCTA
92624 TGGTTGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.18
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCATGGCGACCTACGA
Found at i:96401 original size:20 final size:20
Alignment explanation
Indices: 96376--96447 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
96366 AACACGTTAG
96376 GCATCCGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAGA
96396 GCATCCGAGGCCATCCGAACGA
1 GCATCCGAGGCCATCCG-A-GA
* * *
96418 GCTATACGAGGGCATCCGAGG
1 GC-ATCCGAGGCCATCCGAGA
*
96439 GCAACCGAG
1 GCATCCGAG
96448 CGAGCTATGC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 22 0.50
21 4 0.09
22 5 0.11
23 13 0.30
ACGTcount: A:0.26, C:0.32, G:0.32, T:0.10
Consensus pattern (20 bp):
GCATCCGAGGCCATCCGAGA
Found at i:96439 original size:10 final size:10
Alignment explanation
Indices: 96375--96472 Score: 70
Period size: 10 Copynumber: 9.2 Consensus size: 10
96365 CAACACGTTA
96375 GGCATCCGAG
1 GGCATCCGAG
*
96385 GCCATCCGAG
1 GGCATCCGAG
*
96395 AGCATCCGAG
1 GGCATCCGAG
*
96405 GCCATCCGAACG
1 GGCATCCG-A-G
* *
96417 AGCTATACGAG
1 GGC-ATCCGAG
96428 GGCATCCGAG
1 GGCATCCGAG
*
96438 GGCAACCGAG
1 GGCATCCGAG
*
96448 CGAGCTATGCGAG
1 -G-GC-ATCCGAG
*
96461 GGAATCCGAG
1 GGCATCCGAG
96471 GG
1 GG
96473 AAGCCGAGCG
Statistics
Matches: 67, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
10 46 0.69
11 6 0.09
12 6 0.09
13 9 0.13
ACGTcount: A:0.26, C:0.29, G:0.36, T:0.10
Consensus pattern (10 bp):
GGCATCCGAG
Found at i:96472 original size:33 final size:33
Alignment explanation
Indices: 96398--96484 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
96388 ATCCGAGAGC
* * * *
96398 ATCCGAGGCCATCCGAACGAGCTATACGAGGGC
1 ATCCGAGGGCAACCGAGCGAGCTATACGAGGGA
*
96431 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
1 ATCCGAGGGCAACCGAGCGAGCTATACGAGGGA
96464 ATCCGAGGG-AAGCCGAGCGAG
1 ATCCGAGGGCAA-CCGAGCGAG
96485 GGTAGGTCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.04
33 46 0.96
ACGTcount: A:0.28, C:0.26, G:0.37, T:0.09
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAGCGAGCTATACGAGGGA
Found at i:96615 original size:29 final size:29
Alignment explanation
Indices: 96573--96629 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
96563 GAGCAAGGGT
96573 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
96602 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
96630 GACCAACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.32, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:99858 original size:3 final size:3
Alignment explanation
Indices: 99850--99892 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
99840 CATAGAGATG
99850 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
99893 CAACGGAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:109133 original size:21 final size:22
Alignment explanation
Indices: 109103--109151 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
109093 AGGGAATCAA
109103 TCCCCCTTG-A-GGGAACCGAT
1 TCCCCCTTGAAGGGGAACCGAT
109123 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCC-TTGAAGGGGAACCGAT
109146 TCCCCC
1 TCCCCC
109152 CACAGGGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.23
21 3 0.12
22 1 0.04
23 16 0.62
ACGTcount: A:0.18, C:0.39, G:0.22, T:0.20
Consensus pattern (22 bp):
TCCCCCTTGAAGGGGAACCGAT
Found at i:109160 original size:21 final size:21
Alignment explanation
Indices: 109134--109173 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
109124 CCCCCTTTGA
*
109134 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
109155 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
109174 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:114244 original size:21 final size:21
Alignment explanation
Indices: 114218--114262 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
114208 AAGTTGGTCG
114218 AACCTCATACAAGCATGTATA
1 AACCTCATACAAGCATGTATA
* *
114239 AACCTCATGCAATCATGTATA
1 AACCTCATACAAGCATGTATA
114260 AAC
1 AAC
114263 AATTTCAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.24
Consensus pattern (21 bp):
AACCTCATACAAGCATGTATA
Found at i:122172 original size:15 final size:15
Alignment explanation
Indices: 122154--122249 Score: 63
Period size: 15 Copynumber: 6.5 Consensus size: 15
122144 AAAAGAAATT
122154 TTAAAAAATGATAAA
1 TTAAAAAATGATAAA
* *
122169 TTAAAAAGATAAAAAA
1 TTAAAAA-ATGATAAA
*
122185 TTAAAAATAAGAT--A
1 TTAAAAA-ATGATAAA
* ** *
122199 TTAAAATATCCTACA
1 TTAAAAAATGATAAA
*
122214 TTAAAAGATGAT-AA
1 TTAAAAAATGATAAA
* *
122228 TTAAAAAATCATAAT
1 TTAAAAAATGATAAA
122243 TTAAAAA
1 TTAAAAA
122250 TTCCTAATTA
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
13 2 0.03
14 18 0.30
15 25 0.42
16 15 0.25
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.28
Consensus pattern (15 bp):
TTAAAAAATGATAAA
Found at i:122246 original size:29 final size:28
Alignment explanation
Indices: 122157--122250 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 28
122147 AGAAATTTTA
* * *
122157 AAAAATGATAAATTAAAAAGATAAAAAATT
1 AAAAATGAT-AATTAAAAA-ATCATAATTT
* *
122187 AAAAATAAGAT-ATTAAAATATCCTACA-TT
1 AAAAAT--GATAATTAAAAAATCATA-ATTT
122216 AAAAGATGATAATTAAAAAATCATAATTT
1 AAAA-ATGATAATTAAAAAATCATAATTT
122245 AAAAAT
1 AAAAAT
122251 TCCTAATTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
28 6 0.12
29 27 0.52
30 16 0.31
32 3 0.06
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (28 bp):
AAAAATGATAATTAAAAAATCATAATTT
Found at i:130861 original size:14 final size:14
Alignment explanation
Indices: 130817--130863 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
130807 CCAAAAAAAA
*
130817 AAAAACACACATAC
1 AAAAACACACACAC
* *
130831 AAAACCA-AC-CCC
1 AAAAACACACACAC
130843 AAAAACACACACAC
1 AAAAACACACACAC
130857 AAAAACA
1 AAAAACA
130864 AGAAGTGTGC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
12 7 0.27
13 4 0.15
14 15 0.58
ACGTcount: A:0.64, C:0.34, G:0.00, T:0.02
Consensus pattern (14 bp):
AAAAACACACACAC
Found at i:133111 original size:121 final size:123
Alignment explanation
Indices: 132886--133133 Score: 482
Period size: 121 Copynumber: 2.0 Consensus size: 123
132876 CTGCTCTTGA
132886 TATTGTCAAGAAAAGCTCAACAATCTTTTTCAGTTAGTTTTCTTGTGACAAGTGGAACCCCCAAG
1 TATTGTCAAGAAAAGCTCAACAATCTTTTTCAGTTAGTTTTCTTGTGACAAGTGGAACCCCCAAG
132951 TAGCGAACATGCAGTGTACCATGTTTAAAATCAGAATAATTGATGATAGAATCAAAAT
66 TAGCGAACATGCAGTGTACCATGTTTAAAATCAGAATAATTGATGATAGAATCAAAAT
133009 TATT-TCAAG-AAAGCTCAACAATCTTTTTCAGTTAGTTTTCTTGTGACAAGTGGAACCCCCAAG
1 TATTGTCAAGAAAAGCTCAACAATCTTTTTCAGTTAGTTTTCTTGTGACAAGTGGAACCCCCAAG
133072 TAGCGAACATGCAGTGTACCATGTTTAAAATCAGAATAATTGATGATAGAATCAAAAT
66 TAGCGAACATGCAGTGTACCATGTTTAAAATCAGAATAATTGATGATAGAATCAAAAT
133130 TATT
1 TATT
133134 AGCAGAGATA
Statistics
Matches: 125, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
121 116 0.93
122 5 0.04
123 4 0.03
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (123 bp):
TATTGTCAAGAAAAGCTCAACAATCTTTTTCAGTTAGTTTTCTTGTGACAAGTGGAACCCCCAAG
TAGCGAACATGCAGTGTACCATGTTTAAAATCAGAATAATTGATGATAGAATCAAAAT
Found at i:138747 original size:21 final size:21
Alignment explanation
Indices: 138723--138783 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
138713 AATTTTGAAA
138723 AAATGGTTTTCAAAGTTTGAT
1 AAATGGTTTTCAAAGTTTGAT
138744 AAAT-G-TTTC----TTTGA-
1 AAATGGTTTTCAAAGTTTGAT
*
138758 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGAT
138779 AAATG
1 AAATG
138784 TTTCTTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 14
0.68 0.02 0.30
Matches are distributed among these distances:
14 4 0.12
15 6 0.19
16 4 0.12
19 4 0.12
20 5 0.16
21 9 0.28
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGAT
Found at i:138761 original size:35 final size:36
Alignment explanation
Indices: 138688--138822 Score: 161
Period size: 35 Copynumber: 3.8 Consensus size: 36
138678 TGAAAGTATT
***
138688 AAAATGGTTTTC-AAGTTTGGT-AATCAAT-TTTGAA
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-A
*
138722 AAAATGGTTTTCAAAGTTTGATAAATGTTTCTTTG-
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
138757 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
* * *
138793 AAAATAGTTTTTCAAAATTTGGTAGATGTT
1 AAAAT-GGTTTTCAAAGTTTGGTAAATGTT
138823 GTTGAAAAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
34 12 0.14
35 42 0.48
36 9 0.10
37 25 0.28
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
Found at i:143439 original size:36 final size:35
Alignment explanation
Indices: 143325--143444 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 35
143315 TGGTAACCAA
143325 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAAT-GTTTTCAAAGTTTGGTAAATGTTT
*
143362 CTTTGAAAATTGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTCAAAGTTTGGTAAATGTTT
*
143397 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-G-TTTTCAAAGTTTGGTAAATGTTT
*
143434 -GTTGAAAAATG
1 CTTTGAAAAATG
143445 ATAATGGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
35 35 0.45
36 15 0.19
37 27 0.35
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (35 bp):
CTTTGAAAAATGTTTTCAAAGTTTGGTAAATGTTT
Found at i:150020 original size:16 final size:16
Alignment explanation
Indices: 150001--150053 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
149991 GCAATACAAA
*
150001 CTGAATTTAACCTAGT
1 CTGAATTTAACCCAGT
*** **
150017 CTGAAAGCAACCCAAA
1 CTGAATTTAACCCAGT
150033 CTGAATTTAACCCAGT
1 CTGAATTTAACCCAGT
150049 CTGAA
1 CTGAA
150054 AGCAACCCAA
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.25
Consensus pattern (16 bp):
CTGAATTTAACCCAGT
Found at i:150026 original size:32 final size:32
Alignment explanation
Indices: 149990--150068 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 32
149980 CGAAACCGAT
* *
149990 AGCAATACAAACTGAATTTAACCTAGTCTGAA
1 AGCAACACAAACTGAATTTAACCCAGTCTGAA
*
150022 AGCAACCCAAACTGAATTTAACCCAGTCTGAA
1 AGCAACACAAACTGAATTTAACCCAGTCTGAA
*
150054 AGCAACCCAAA-TGAA
1 AGCAACACAAACTGAA
150069 AATTAATCCG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 4 0.09
32 40 0.91
ACGTcount: A:0.44, C:0.24, G:0.13, T:0.19
Consensus pattern (32 bp):
AGCAACACAAACTGAATTTAACCCAGTCTGAA
Found at i:150060 original size:16 final size:16
Alignment explanation
Indices: 150009--150062 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
149999 AACTGAATTT
*
150009 AACCTAGTCTGAAAGC
1 AACCCAGTCTGAAAGC
** ***
150025 AACCCAAACTGAATTT
1 AACCCAGTCTGAAAGC
150041 AACCCAGTCTGAAAGC
1 AACCCAGTCTGAAAGC
150057 AACCCA
1 AACCCA
150063 AATGAAAATT
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.41, C:0.30, G:0.13, T:0.17
Consensus pattern (16 bp):
AACCCAGTCTGAAAGC
Found at i:150539 original size:75 final size:75
Alignment explanation
Indices: 150414--150756 Score: 360
Period size: 75 Copynumber: 4.5 Consensus size: 75
150404 TATATATATA
* ** * *
150414 TATATATTATATAG-TTTGCAAATGATTTTTGAAAATACGTATATAATATATAGTTTTTAAAATA
1 TATATAATATATAGTTTTG-AAAACATTTTTGAAAATATGTATATATTATATAGTTTTTAAAATA
150478 TTTTTGAAAAC
65 TTTTTGAAAAC
* *
150489 TATATAATATATAGTTTTGAAAACATTTTAGAAAATATGTATATATTATATGGTTTTTAAAATCA
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAATATGTATATATTATATAGTTTTTAAAAT-A
150554 TTTTTGAAAAC
65 TTTTTGAAAAC
* *
150565 TTATATAATATATAGGTTTTTAAAATATTTTTGAAAACATATG-ATATA-TA-ATA-TTTTTAAA
1 -TATATAATATATA-GTTTTGAAAACATTTTTG-AAA-ATATGTATATATTATATAGTTTTTAAA
*
150626 ACATTTTTGAAAAC
62 ATATTTTTGAAAAC
* *
150640 -ATATAATATATAAGTTTTGAAAACATTTTCGAAAACA--TATATATTATATAGTTTTTAAAACA
1 TATATAATATAT-AGTTTTGAAAACATTTTTGAAAATATGTATATATTATATAGTTTTT-AAA-A
* *
150702 TTTTTTTTGAAAATA
63 -TATTTTTGAAAA-C
* * *
150717 TATATAATATATAATTTTTAAAAATATTTTTTGAAAATAT
1 TATATAATATAT-AGTTTTGAAAACA-TTTTTGAAAATAT
150757 ATTATTTTGA
Statistics
Matches: 226, Mismatches: 24, Indels: 31
0.80 0.09 0.11
Matches are distributed among these distances:
70 5 0.02
71 4 0.02
72 6 0.03
73 31 0.14
74 4 0.02
75 64 0.28
76 35 0.15
77 15 0.07
78 39 0.17
79 18 0.08
80 5 0.02
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (75 bp):
TATATAATATATAGTTTTGAAAACATTTTTGAAAATATGTATATATTATATAGTTTTTAAAATAT
TTTTGAAAAC
Found at i:150577 original size:38 final size:38
Alignment explanation
Indices: 150414--150753 Score: 312
Period size: 39 Copynumber: 8.9 Consensus size: 38
150404 TATATATATA
* ** * *
150414 TATATATTATATAG-TTTGCAAATGATTTTTGAAAATACG
1 TATATAATATATAGTTTTTAAAATCATTTTTG-AAA-ACT
150453 TATATAATATATAGTTTTTAAAAT-ATTTTTGAAAAC-
1 TATATAATATATAGTTTTTAAAATCATTTTTGAAAACT
* * *
150489 TATATAATATATAGTTTTGAAAA-CATTTTAGAAAATAT
1 TATATAATATATAGTTTTTAAAATCATTTTTGAAAA-CT
* *
150527 GTATATATTATATGGTTTTTAAAATCATTTTTGAAAACT
1 -TATATAATATATAGTTTTTAAAATCATTTTTGAAAACT
*
150566 TATATAATATATAGGTTTTTAAAAT-ATTTTTGAAAACA
1 TATATAATATATA-GTTTTTAAAATCATTTTTGAAAACT
150604 TATGAT-ATATAATA-TTTTTAAAA-CATTTTTGAAAAC-
1 TAT-ATAATAT-ATAGTTTTTAAAATCATTTTTGAAAACT
* * *
150640 -ATATAATATATAAGTTTTGAAAA-CATTTTCGAAAACA
1 TATATAATATAT-AGTTTTTAAAATCATTTTTGAAAACT
*
150677 TATATATTATATAGTTTTTAAAA-CATTTTTTTTGAAAA-T
1 TATATAATATATAGTTTTTAAAATCA---TTTTTGAAAACT
*
150716 ATATATAATATATAATTTTTAAAAAT-ATTTTTTGAAAA
1 -TATATAATATATAGTTTTT-AAAATCA-TTTTTGAAAA
150754 TATATTATTT
Statistics
Matches: 258, Mismatches: 22, Indels: 42
0.80 0.07 0.13
Matches are distributed among these distances:
34 4 0.02
35 7 0.03
36 52 0.20
37 35 0.14
38 43 0.17
39 68 0.26
40 44 0.17
41 5 0.02
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (38 bp):
TATATAATATATAGTTTTTAAAATCATTTTTGAAAACT
Found at i:150632 original size:151 final size:152
Alignment explanation
Indices: 150433--150758 Score: 427
Period size: 151 Copynumber: 2.1 Consensus size: 152
150423 TATAGTTTGC
* *
150433 AAATGATTTTTG-AAAATACGTATATAATATATAGTTTTTAAAATATTTTTGAAAACTATATAAT
1 AAAT-ATTTTTGAAAAATATGTATATAATATATAGTTTTTAAAACATTTTTGAAAAC-ATATAAT
* *
150497 ATAT-AGTTTTGAAAACATTTTAGAAAATATGTATATATTATATGGTTTTTAAAATCA-TTTTTG
64 ATATAAGTTTTGAAAACATTTTAGAAAACA--TATATATTATATAGTTTTTAAAA-CATTTTTTG
*
150560 AAAACT-TATATAATATATAGGTTTTT-A
126 AAAA-TATATATAATATATA-ATTTTTAA
150587 AAATATTTTTGAAAACATATG-ATAT-ATA-ATA-TTTTTAAAACATTTTTGAAAACATATAATA
1 AAATATTTTTGAAAA-ATATGTATATAATATATAGTTTTTAAAACATTTTTGAAAACATATAATA
*
150648 TATAAGTTTTGAAAACATTTTCGAAAACATATATATTATATAGTTTTTAAAACATTTTTTTTGAA
65 TATAAGTTTTGAAAACATTTTAGAAAACATATATATTATATAGTTTTTAAAACA--TTTTTTGAA
150713 AATATATATAATATATAATTTTTAA
128 AATATATATAATATATAATTTTTAA
150738 AAATATTTTTTGAAAATATAT
1 AAATA-TTTTTGAAAA-ATAT
150759 TATTTTGAAA
Statistics
Matches: 156, Mismatches: 7, Indels: 20
0.85 0.04 0.11
Matches are distributed among these distances:
148 2 0.01
149 22 0.14
150 17 0.11
151 73 0.47
152 17 0.11
153 10 0.06
154 11 0.07
155 4 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (152 bp):
AAATATTTTTGAAAAATATGTATATAATATATAGTTTTTAAAACATTTTTGAAAACATATAATAT
ATAAGTTTTGAAAACATTTTAGAAAACATATATATTATATAGTTTTTAAAACATTTTTTGAAAAT
ATATATAATATATAATTTTTAA
Found at i:150753 original size:13 final size:13
Alignment explanation
Indices: 150691--150778 Score: 52
Period size: 14 Copynumber: 6.4 Consensus size: 13
150681 TATTATATAG
*
150691 TTTTTAAAACATTT
1 TTTTTAAAA-ATAT
*
150705 TTTTTGAAAATA-
1 TTTTTAAAAATAT
* * * *
150717 TATATAATATATAA
1 TTTTTAA-AAATAT
150731 TTTTTAAAAATAT
1 TTTTTAAAAATAT
150744 TTTTTGAAAATATAT
1 TTTTT-AAAA-ATAT
*
150759 TATTTTGAAAAACAT
1 T-TTTT-AAAAATAT
150774 TTTTT
1 TTTTT
150779 TAGGGTTTTG
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
12 4 0.07
13 15 0.26
14 21 0.36
15 9 0.16
16 9 0.16
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.52
Consensus pattern (13 bp):
TTTTTAAAAATAT
Found at i:150758 original size:15 final size:14
Alignment explanation
Indices: 150731--150778 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
150721 TAATATATAA
150731 TTTTT-AAAAATAT
1 TTTTTGAAAAATAT
150744 TTTTTGAAAATATAT
1 TTTTTGAAAA-ATAT
*
150759 TATTTTGAAAAACAT
1 T-TTTTGAAAAATAT
150774 TTTTT
1 TTTTT
150779 TAGGGTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 5 0.16
14 8 0.26
15 9 0.29
16 9 0.29
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (14 bp):
TTTTTGAAAAATAT
Found at i:150758 original size:30 final size:30
Alignment explanation
Indices: 150722--150778 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
150712 AAATATATAT
* *
150722 AATATATAATTTTTAAAAATATTTTTTGAA
1 AATATATAATTTTGAAAAACATTTTTTGAA
*
150752 AATATATTATTTTGAAAAACATTTTTT
1 AATATATAATTTTGAAAAACATTTTTT
150779 TAGGGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (30 bp):
AATATATAATTTTGAAAAACATTTTTTGAA
Found at i:150817 original size:2 final size:2
Alignment explanation
Indices: 150810--150843 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
150800 AAAGCATTTA
150810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
150844 TATTTATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:151049 original size:16 final size:15
Alignment explanation
Indices: 151028--151057 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
151018 GTCGGCCGGA
151028 ATCCCGGGACTGACCC
1 ATCCCGGGA-TGACCC
151044 ATCCCGGGATGACC
1 ATCCCGGGATGACC
151058 GGCCAAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (15 bp):
ATCCCGGGATGACCC
Found at i:152072 original size:14 final size:13
Alignment explanation
Indices: 152055--152161 Score: 56
Period size: 15 Copynumber: 7.6 Consensus size: 13
152045 ATTTCCTTCA
152055 TATTATTTTTATTT
1 TATT-TTTTTATTT
152069 TATTTCTTTTAAATTT
1 TATTT-TTTT--ATTT
152085 TATCTTTTTTA-TT
1 TAT-TTTTTTATTT
*
152098 TATTTATTT-TTT
1 TATTTTTTTATTT
* *
152110 AATCTTTTTCTTTTT
1 TAT-TTTTT-TATTT
**
152125 TCCCTTTTTTATTT
1 T-ATTTTTTTATTT
*
152139 TATTTTTATCTATTG
1 TATTTTT-T-TATTT
152154 TATTTTTT
1 TATTTTTT
152162 CCTCTTTGAC
Statistics
Matches: 72, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
12 9 0.12
13 14 0.19
14 17 0.24
15 19 0.26
16 11 0.15
17 2 0.03
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.75
Consensus pattern (13 bp):
TATTTTTTTATTT
Found at i:152096 original size:30 final size:31
Alignment explanation
Indices: 152060--152125 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
152050 CTTCATATTA
152060 TTTTTATTTTATTT-CTTTTAAAT-TTTATCT
1 TTTTTA-TTTATTTACTTTTAAATCTTTATCT
* * *
152090 TTTTTATTTATTTATTTTTTAATCTTTTTCT
1 TTTTTATTTATTTACTTTTAAATCTTTATCT
152121 TTTTT
1 TTTTT
152126 CCCTTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 7 0.23
30 13 0.42
31 11 0.35
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (31 bp):
TTTTTATTTATTTACTTTTAAATCTTTATCT
Found at i:152103 original size:24 final size:26
Alignment explanation
Indices: 152066--152118 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
152056 ATTATTTTTA
*
152066 TTTTATTTCTTTTAAATTTT-ATCTT
1 TTTTATTTCATTTAAATTTTAATCTT
**
152091 TTTTATTT-ATTTATTTTTTAATCTT
1 TTTTATTTCATTTAAATTTTAATCTT
152116 TTT
1 TTT
152119 CTTTTTTCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTATTTCATTTAAATTTTAATCTT
Found at i:152145 original size:36 final size:37
Alignment explanation
Indices: 152096--152168 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
152086 ATCTTTTTTA
* *
152096 TTTATTTATTTTTTAATCT-TTTTCTTTTTTCC-CTTT
1 TTTATTTATTTTTT-ATCTATTGTATTTTTTCCTCTTT
152132 TTTATTT-TATTTTTATCTATTGTATTTTTTCCTCTTT
1 TTTATTTAT-TTTTTATCTATTGTATTTTTTCCTCTTT
152169 GACTTGTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 5 0.16
36 23 0.72
37 4 0.12
ACGTcount: A:0.12, C:0.12, G:0.01, T:0.74
Consensus pattern (37 bp):
TTTATTTATTTTTTATCTATTGTATTTTTTCCTCTTT
Found at i:152241 original size:24 final size:26
Alignment explanation
Indices: 152189--152245 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
152179 TTTTTATTTA
152189 TTTTTCTTCTTCTTCACTTATTAATT
1 TTTTTCTTCTTCTTCACTTATTAATT
* *
152215 TTTTTCATTCTT-TTGACTTATTATTT
1 TTTTTC-TTCTTCTTCACTTATTAATT
152241 TTTTT
1 TTTTT
152246 GTTTTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 23 0.82
27 5 0.18
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTTCTTCTTCTTCACTTATTAATT
Found at i:157077 original size:146 final size:145
Alignment explanation
Indices: 156759--157050 Score: 431
Period size: 146 Copynumber: 2.0 Consensus size: 145
156749 TTTTAACCCG
* * * *
156759 ATAAATGAGTAAAAGTGATTGAATAGTTTATTGTTATTATATATTTGTTAGCAATATGATGAATA
1 ATAAATGAGTAAAAGTGAAT-AATAATTTATTGTTATTATATATTTGTTAACAATATAATGAATA
* * * *
156824 GTAAAACGATGCATGTTTTATTCTCTTTTTACATTATATTACCAGTTAATCACCACCTTTGATAA
65 GTAAAACGATGCATGTTTTATTCTCTTTTTACAATATATTACCAATTAATCACCACATTTAATAA
156889 TAGTTTAATAACCACA
130 TAGTTTAATAACCACA
*
156905 ATAAATGAGTAAAAGTGACTGAATAATTTATTGTTATTATATATTTGTTAACAATATAATGAATA
1 ATAAATGAGTAAAAGTGAAT-AATAATTTATTGTTATTATATATTTGTTAACAATATAATGAATA
* * ** *
156970 GTAAAATGATGCATGTTTTATTCCTTTTTTTGTAATATATTACTAATTAATCACCACATTTAATA
65 GTAAAACGATGCATGTTTTATT-CTCTTTTTACAATATATTACCAATTAATCACCACATTTAATA
157035 ATAGTTTAATAACCAC
129 ATAGTTTAATAACCAC
157051 CAGTACCACA
Statistics
Matches: 132, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
146 82 0.62
147 50 0.38
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (145 bp):
ATAAATGAGTAAAAGTGAATAATAATTTATTGTTATTATATATTTGTTAACAATATAATGAATAG
TAAAACGATGCATGTTTTATTCTCTTTTTACAATATATTACCAATTAATCACCACATTTAATAAT
AGTTTAATAACCACA
Found at i:157414 original size:11 final size:11
Alignment explanation
Indices: 157398--157423 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
157388 ACAAATATTA
157398 AAAATTTTAGT
1 AAAATTTTAGT
157409 AAAATTTTAGT
1 AAAATTTTAGT
157420 AAAA
1 AAAA
157424 GCATTAAATT
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAATTTTAGT
Found at i:157465 original size:52 final size:52
Alignment explanation
Indices: 157356--157468 Score: 138
Period size: 52 Copynumber: 2.2 Consensus size: 52
157346 TAAACCAAGT
* ***
157356 TAAAATTTTAGTAAAAGCATTAAATTTAAAATACAAATATTAAAAATTTTAG
1 TAAAATTTTAGTAAAAGCATTAAATTTAAAATACAAACATTAAAAATCCGAG
* * * *
157408 TAAAATTTTAGTAAAAGCATTAAATTTATAAT-TAAACATTAAACATCCGAT
1 TAAAATTTTAGTAAAAGCATTAAATTTAAAATACAAACATTAAAAATCCGAG
*
157459 TAAAAATTTA
1 TAAAATTTTA
157469 ATGGAGAATG
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
51 21 0.40
52 31 0.60
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.36
Consensus pattern (52 bp):
TAAAATTTTAGTAAAAGCATTAAATTTAAAATACAAACATTAAAAATCCGAG
Found at i:157843 original size:32 final size:32
Alignment explanation
Indices: 157791--157873 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
157781 TGAAATGAAC
* *
157791 CGAAAATCAACTGATTCGATATTAACCCGACT
1 CGAAAATCAACCGATCCGATATTAACCCGACT
* *
157823 CGAATATCAACCGATCCGATATTAACCCGAAT
1 CGAAAATCAACCGATCCGATATTAACCCGACT
* * *
157855 GGAAAAACAACCGACCCGA
1 CGAAAATCAACCGATCCGA
157874 AAATTGACCC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.18
Consensus pattern (32 bp):
CGAAAATCAACCGATCCGATATTAACCCGACT
Found at i:157852 original size:16 final size:16
Alignment explanation
Indices: 157806--157852 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
157796 ATCAACTGAT
157806 TCGATATTAACCCGAC
1 TCGATATTAACCCGAC
*
157822 TCGAATATCAA-CCGA-
1 TCG-ATATTAACCCGAC
157837 TCCGATATTAACCCGA
1 T-CGATATTAACCCGA
157853 ATGGAAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 7 0.27
16 13 0.50
17 6 0.23
ACGTcount: A:0.34, C:0.30, G:0.13, T:0.23
Consensus pattern (16 bp):
TCGATATTAACCCGAC
Found at i:158730 original size:50 final size:51
Alignment explanation
Indices: 158638--158743 Score: 135
Period size: 50 Copynumber: 2.1 Consensus size: 51
158628 GATAAATTTT
* ** * *
158638 AATAAAAAATTATATTTTATTCGAACTCGTCATCCTGGCGTGACGAGTTCG
1 AATAAAAAATTATATTTTATTCAAACTCGTCATCCTAACGTGACGAATTCC
*
158689 AATAAAAAA-TATTTTTTATTCAAACTCGTCA-CCTCAACGTGACGAATTCC
1 AATAAAAAATTATATTTTATTCAAACTCGTCATCCT-AACGTGACGAATTCC
158739 AATAA
1 AATAA
158744 TACTGTAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 3 0.06
50 36 0.75
51 9 0.19
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (51 bp):
AATAAAAAATTATATTTTATTCAAACTCGTCATCCTAACGTGACGAATTCC
Found at i:160240 original size:18 final size:18
Alignment explanation
Indices: 160217--160251 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
160207 TCCCTGTAAA
160217 ACTTTTTTTTTACCTTTT
1 ACTTTTTTTTTACCTTTT
*
160235 ACTTTTTTTTTATCTTT
1 ACTTTTTTTTTACCTTT
160252 GTGGGGTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.74
Consensus pattern (18 bp):
ACTTTTTTTTTACCTTTT
Found at i:162121 original size:65 final size:65
Alignment explanation
Indices: 162017--162147 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
162007 TTCATTTGTT
162017 CTTTCGAGAAAAATTCTGCCACAAGCCTCAACCTCAACCACGAGCCTGAGCCAAGTCAAGACAGA
1 CTTTCGAGAAAAATTCTGCCACAAGCCTCAACCTCAACCACGAGCCTGAGCCAAGTCAAGACAGA
162082 CTTTCGAGAAAAATTCTGCCACAAGCCTCAACCTCAACCACGAGCCTGAGCCAAGTCAAGACAGA
1 CTTTCGAGAAAAATTCTGCCACAAGCCTCAACCTCAACCACGAGCCTGAGCCAAGTCAAGACAGA
162147 C
1 C
162148 GACTGTGCAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.35, C:0.33, G:0.17, T:0.15
Consensus pattern (65 bp):
CTTTCGAGAAAAATTCTGCCACAAGCCTCAACCTCAACCACGAGCCTGAGCCAAGTCAAGACAGA
Found at i:163516 original size:2 final size:2
Alignment explanation
Indices: 163509--163540 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
163499 GGGGTGACAG
163509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
163541 TAATAACTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:165283 original size:2 final size:2
Alignment explanation
Indices: 165276--165317 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
165266 CAAATAGGCT
* * *
165276 GA GA GA GA GA GG GA GA GA GA GG GA GA GA GA GG GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
165318 TTTTGGTAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (2 bp):
GA
Found at i:165293 original size:10 final size:10
Alignment explanation
Indices: 165278--165316 Score: 78
Period size: 10 Copynumber: 3.9 Consensus size: 10
165268 AATAGGCTGA
165278 GAGAGAGAGG
1 GAGAGAGAGG
165288 GAGAGAGAGG
1 GAGAGAGAGG
165298 GAGAGAGAGG
1 GAGAGAGAGG
165308 GAGAGAGAG
1 GAGAGAGAG
165317 ATTTTGGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (10 bp):
GAGAGAGAGG
Found at i:166858 original size:25 final size:24
Alignment explanation
Indices: 166824--166876 Score: 88
Period size: 25 Copynumber: 2.2 Consensus size: 24
166814 AATGATATAT
166824 ATATATATATATAAGTTGTCAAATG
1 ATATATATATATAAGTTGTCAAA-G
*
166849 ATATATATATATAGGTTGTCAAAG
1 ATATATATATATAAGTTGTCAAAG
166873 ATAT
1 ATAT
166877 GCATTGAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (24 bp):
ATATATATATATAAGTTGTCAAAG
Found at i:172977 original size:15 final size:16
Alignment explanation
Indices: 172957--172986 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
172947 GGAGAAAATA
172957 ATATATACA-TATTAT
1 ATATATACATTATTAT
172972 ATATATACATTATTA
1 ATATATACATTATTA
172987 ATTCAATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATATACATTATTAT
Found at i:178164 original size:3 final size:3
Alignment explanation
Indices: 178156--178203 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
178146 ATTTGTAAAT
* **
178156 TAA TAA TAA TAG TAA TAA TAA TAA TAA CGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
178204 CGATAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:178209 original size:12 final size:12
Alignment explanation
Indices: 178173--178209 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
178163 AATAGTAATA
178173 ATAATAATAACG
1 ATAATAATAACG
178185 ATAATAAT-A--
1 ATAATAATAACG
178194 ATAATAATAACG
1 ATAATAATAACG
178206 ATAA
1 ATAA
178210 AAAACCCGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.36
10 1 0.05
11 1 0.05
12 12 0.55
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (12 bp):
ATAATAATAACG
Found at i:178419 original size:43 final size:42
Alignment explanation
Indices: 178358--178652 Score: 238
Period size: 43 Copynumber: 6.8 Consensus size: 42
178348 TGTTGGGGAC
* * * *
178358 GACACTGCTCTTACGTGATGAAGAGTTTGGGTCGTCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAGTCT-GGTCATCTAAAGGT
*
178401 GACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAG-TC-TGGTCATCTAAAGGT
* * * * * *
178445 GATAACACAGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGT
1 G---ACACGGCTCCTACGTGATGAAGA-GTCTGGTCATCTAAAGGT
* * *
178491 GACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCT---GAT
1 GACACGGCTCCTACGTGATGAAGAG-TCTGGTCATCTAAAGGT
* *
178531 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAG-TCTGGTCATCTAAAGGT
* * * * *
178574 GATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT-ATGGTT
1 G---ACACGGCTCCTACGTGATGAAGA-GTCTGGTCATCTAAAGG-T
178620 GACACGGCTCCTACGTGATGAAGAGATCTGGTC
1 GACACGGCTCCTACGTGATGAAGAG-TCTGGTC
178653 TGGGGATGAC
Statistics
Matches: 201, Mismatches: 35, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
40 34 0.17
42 2 0.01
43 81 0.40
44 14 0.07
45 4 0.02
46 43 0.21
47 22 0.11
48 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (42 bp):
GACACGGCTCCTACGTGATGAAGAGTCTGGTCATCTAAAGGT
Found at i:178592 original size:129 final size:130
Alignment explanation
Indices: 178400--178680 Score: 465
Period size: 129 Copynumber: 2.2 Consensus size: 130
178390 CGTCTAAAGG
178400 TGACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACAGTTCCTACGTG
1 TGACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACAGTTCCTACGTG
* *
178465 ATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCTGA
66 ATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCAGCGGA
* *
178530 TGACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
1 TGACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACAGTTCCTACGTG
* * * *
178594 ATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCTGGGGA
66 ATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCAGCGGA
* *
178659 TGACACGGTTCCTACATGATGA
1 TGACACGGCTCCTACGTGATGA
178681 GGACGGCTGG
Statistics
Matches: 140, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
129 112 0.80
130 28 0.20
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (130 bp):
TGACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACAGTTCCTACGTG
ATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCAGCGGA
Found at i:178608 original size:86 final size:82
Alignment explanation
Indices: 178492--178690 Score: 215
Period size: 83 Copynumber: 2.4 Consensus size: 82
178482 TCTAAGGGTG
* *
178492 ACACGGCTCCTACGTGATGAGGA-GATCTGGTCAGC-T-GATGACACGGCTCATACGTGATGAAG
1 ACACGGTTCCTACGTGATGAGGACG-GCTGGTCAGCATGGATGACACGGCTCATACGTGATGAAG
* *
178554 AGTTCTGGCCATCTAAAGGTGATA
65 AGATCTGG---TCT---GGGGATA
* * * *
178578 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAG
1 ACACGGTTCCTACGTGATGAGGACGGCTGGTCAGC-ATGGATGACACGGCTCATACGTGATGAAG
*
178643 AGATCTGGTCTGGGGATG
65 AGATCTGGTCTGGGGATA
*
178661 ACACGGTTCCTACATGATGAGGACGGCTGG
1 ACACGGTTCCTACGTGATGAGGACGGCTGG
178691 CCATCTTTAG
Statistics
Matches: 99, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
83 34 0.34
86 32 0.32
87 1 0.01
88 1 0.01
89 31 0.31
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (82 bp):
ACACGGTTCCTACGTGATGAGGACGGCTGGTCAGCATGGATGACACGGCTCATACGTGATGAAGA
GATCTGGTCTGGGGATA
Found at i:178614 original size:46 final size:45
Alignment explanation
Indices: 178400--178683 Score: 195
Period size: 40 Copynumber: 6.6 Consensus size: 45
178390 CGTCTAAAGG
* ** **
178400 TGACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAGGAGAGC-TGGTTATCT-AAGGTGA
* * *
178447 TAACACAGTTCCTACGTGATGAGGACG-GCTGGTTATCTAAGG-G-
1 TGACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTAAGGTGA
* *
178490 TGACACGGCTCCTACGTGATGAGGAGATCTGG---TC--AGCTGA
1 TGACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTAAGGTGA
* * ** **
178530 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCT-AAGGTGA
* * *
178576 TAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT--
1 TGACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTAAGGTGA
* * *
178619 TGACACGGCTCCTACGTGATGAAGAGATCTGG---TCT--GGGGA
1 TGACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTAAGGTGA
* *
178659 TGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCCTACGTGATGAGGA
178684 CGGCTGGCCA
Statistics
Matches: 191, Mismatches: 32, Indels: 35
0.74 0.12 0.14
Matches are distributed among these distances:
38 4 0.02
39 1 0.01
40 56 0.29
42 2 0.01
43 54 0.28
44 1 0.01
45 8 0.04
46 41 0.21
47 23 0.12
48 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (45 bp):
TGACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTAAGGTGA
Found at i:178650 original size:89 final size:83
Alignment explanation
Indices: 178530--178690 Score: 223
Period size: 83 Copynumber: 1.9 Consensus size: 83
178520 GGTCAGCTGA
* * *
178530 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG---TCT---GGGGATAACACGGTTCCTACATGA
178595 TGAGGACGGCTGGTTATCTATGGT
60 TGAGGACGGCTGGTTATCTATGGT
* *
178619 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATGATGAGGA
178684 CGGCTGG
66 CGGCTGG
178691 CCATCTTTAG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 34 0.51
86 3 0.04
89 30 0.45
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.25
Consensus pattern (83 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATGATGAGGA
CGGCTGGTTATCTATGGT
Found at i:178759 original size:28 final size:28
Alignment explanation
Indices: 178709--178762 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
178699 AGGAGTTACG
* *
178709 GTTTCAAGAGAAACCAAATCAAAGATTT
1 GTTTCAAAAGAAACCAAACCAAAGATTT
178737 GTTTCAAAAGAAA-CAAACCCAAAGAT
1 GTTTCAAAAGAAACCAAA-CCAAAGAT
178763 GATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (28 bp):
GTTTCAAAAGAAACCAAACCAAAGATTT
Found at i:179137 original size:15 final size:15
Alignment explanation
Indices: 179094--179128 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
179084 AAGATGATCT
179094 TGTTTTAAGAGAAAA
1 TGTTTTAAGAGAAAA
179109 TGTTTTAAGAGAAAA
1 TGTTTTAAGAGAAAA
179124 TGTTT
1 TGTTT
179129 CAAGTGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (15 bp):
TGTTTTAAGAGAAAA
Found at i:179357 original size:29 final size:29
Alignment explanation
Indices: 179320--179514 Score: 121
Period size: 29 Copynumber: 6.3 Consensus size: 29
179310 TCTCGAGAGA
*
179320 CAAA-ATTTTGTTTCAAAGGAAACAAACT
1 CAAAGATTTTGTTTCAAAAGAAACAAACT
*
179348 CAAAGATTTT-TTTCAAAAGAAATTGTCTTTAATAGAT
1 CAAAGATTTTGTTTCAAAAGAAA----C---AA-A-CT
*
179385 -AAA-ATTTTGTTTCAAAAGAAACATACT
1 CAAAGATTTTGTTTCAAAAGAAACAAACT
* * *
179412 CAAAGATTTTTGTTT-TAAAGAAACTATCT
1 CAAAGA-TTTTGTTTCAAAAGAAACAAACT
* *
179441 TAAGAGACAAAATTTTGTTTCCAAAGAAACAAACT
1 CAA-AG-----ATTTTGTTTCAAAAGAAACAAACT
* *
179476 CAAAGATTTTTTTTCAAAAGAAACAATCT
1 CAAAGATTTTGTTTCAAAAGAAACAAACT
179505 CAAAGATTTT
1 CAAAGATTTT
179515 TTTTTCCACA
Statistics
Matches: 130, Mismatches: 16, Indels: 41
0.70 0.09 0.22
Matches are distributed among these distances:
27 1 0.01
28 19 0.15
29 50 0.38
30 10 0.08
32 2 0.02
34 10 0.08
35 21 0.16
36 16 0.12
37 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (29 bp):
CAAAGATTTTGTTTCAAAAGAAACAAACT
Found at i:179406 original size:64 final size:63
Alignment explanation
Indices: 179294--179498 Score: 275
Period size: 64 Copynumber: 3.2 Consensus size: 63
179284 AAGGTTGGTA
* ** *
179294 TTTTCAAAAGAAGTTGTCTCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTT
1 TTTTCAAAAGAAATTGTCTTAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
* * *
179357 TTTTCAAAAGAAATTGTCTTTAATAGATAAAATTTTGTTTCAAAAGAAACATACTCAAAGATTT
1 TTTTCAAAAGAAATTGTC-TTAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
** * * *
179421 TTGTTTTAAAGAAACTATCTTAAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTT
1 TT-TTCAAAAGAAATTGTCTTAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGA-TTT
179486 TTTTCAAAAGAAA
1 TTTTCAAAAGAAA
179499 CAATCTCAAA
Statistics
Matches: 122, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
63 17 0.14
64 88 0.72
65 17 0.14
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (63 bp):
TTTTCAAAAGAAATTGTCTTAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
Found at i:179652 original size:25 final size:27
Alignment explanation
Indices: 179606--179743 Score: 127
Period size: 29 Copynumber: 5.0 Consensus size: 27
179596 AAAACTTTGT
* * *
179606 TTCAAAATAAATAGACTCAAAGATTT-
1 TTCAAAAGAAACAAACTCAAAGATTTA
179632 TTCAAAAGAAAC-AACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCAAAG--ATTTA
* *
179660 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGA--TTTA
* *
179689 TTTAAAAGGAACAAACTCAAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGA--TTTA
* *
179718 TTTAAAAGGAACAAACTCAAAGATTT
1 TTCAAAAGAAACAAACTCAAAGATTT
179744 TTTAAGAGAA
Statistics
Matches: 99, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
25 8 0.08
26 10 0.10
27 8 0.08
28 11 0.11
29 62 0.63
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.28
Consensus pattern (27 bp):
TTCAAAAGAAACAAACTCAAAGATTTA
Found at i:179688 original size:29 final size:29
Alignment explanation
Indices: 179620--179745 Score: 179
Period size: 29 Copynumber: 4.5 Consensus size: 29
179610 AAATAAATAG
*
179620 ACTCAAAGA--TTT-TTCAAAAGAAAC-A
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
179645 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
* *
179674 ACTCCAAGATTTTTATTTAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
179703 ACTCAAAGATTTTTATTTAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
179732 ACTCAAAGATTTTT
1 ACTCAAAGATTTTT
179746 TAAGAGAAAT
Statistics
Matches: 92, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
25 9 0.10
27 3 0.03
28 11 0.12
29 69 0.75
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTCAAAAGGAACAA
Found at i:180420 original size:4 final size:4
Alignment explanation
Indices: 180404--180449 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
180394 GATACAATTT
*
180404 TATG TAT- TATG TATG TATG --TG TATA TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
180449 T
1 T
180450 TTTCTCGATC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 3 0.08
4 32 0.86
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:180434 original size:18 final size:17
Alignment explanation
Indices: 180406--180441 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
180396 TACAATTTTA
180406 TGTATTATGTATGTATG
1 TGTATTATGTATGTATG
180423 TGTATATATGTATGTATG
1 TGTAT-TATGTATGTATG
180441 T
1 T
180442 ATGTATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (17 bp):
TGTATTATGTATGTATG
Found at i:188099 original size:3 final size:3
Alignment explanation
Indices: 188091--188146 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
188081 ATTTGTAAAT
* **
188091 TAA TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA CGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
188138 TAA TAA TAA
1 TAA TAA TAA
188147 CGATAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:190221 original size:53 final size:53
Alignment explanation
Indices: 190112--190252 Score: 167
Period size: 53 Copynumber: 2.7 Consensus size: 53
190102 TGTATATAGG
* * * * **
190112 TGAGGTGTTTTTTTCTTTGTAATTTGGCTTGTATAGGGAGGTTCATTGTTGGA
1 TGAGGTGTTTTGTTCTTTGTAATTTGACTTGTACAGGGAGGTTCATTATTAAA
*
190165 TGAGGTGTTTTGTTCTTTGTAATTTGACTTGTACATGGAGGTTC-TTCATTAAA
1 TGAGGTGTTTTGTTCTTTGTAATTTGACTTGTACAGGGAGGTTCATT-ATTAAA
* * * *
190218 TGAGGTGTTTTGTTTTTTATAAATTGAATTGTACA
1 TGAGGTGTTTTGTTCTTTGTAATTTGACTTGTACA
190253 AAGAGGTTAT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
52 2 0.03
53 74 0.97
ACGTcount: A:0.20, C:0.06, G:0.25, T:0.49
Consensus pattern (53 bp):
TGAGGTGTTTTGTTCTTTGTAATTTGACTTGTACAGGGAGGTTCATTATTAAA
Done.