Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold65
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: 3097370
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.31
Warning! 315397 characters in sequence are not A, C, G, or T
File 11 of 17
Found at i:2152904 original size:119 final size:121
Alignment explanation
Indices: 2152774--2153012 Score: 349
Period size: 119 Copynumber: 2.0 Consensus size: 121
2152764 TAAAGATTAA
* *
2152774 ATTATTTTTATATAAAATTATAAAAATTTTATTAAATATTAAAATATTATCAATATTTAAATAAT
1 ATTATTTTTATATAAAATTATAAAAATTTTATCAAAAATTAAAATATTATCAATATTTAAATAAT
2152839 TTTAT-AATAATATTAATTA-TTTT-TTATTTAGTGAAAGATCAAAATTTTAATACC
66 TTT-TCAATAATATTAATTATTTTTCTTATTTAGTGAAAGATCAAAATTTTAATACC
* * ** * * *
2152893 ATTATTTTTATATAAGATTTTAAATTTTTTATCAAAAATTAAAATTTTATTAATATTTAAATTAT
1 ATTATTTTTATATAAAATTATAAAAATTTTATCAAAAATTAAAATATTATCAATATTTAAATAAT
*
2152958 TTTTCAATGATATTAATTATTTTTTCTTATTTAGTGAAAGATCAAAATTTTAATA
66 TTTTCAATAATATTAATTA-TTTTTCTTATTTAGTGAAAGATCAAAATTTTAATA
2153013 GAAAACTTTT
Statistics
Matches: 106, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
118 1 0.01
119 72 0.68
121 4 0.04
122 29 0.27
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (121 bp):
ATTATTTTTATATAAAATTATAAAAATTTTATCAAAAATTAAAATATTATCAATATTTAAATAAT
TTTTCAATAATATTAATTATTTTTCTTATTTAGTGAAAGATCAAAATTTTAATACC
Found at i:2156702 original size:2 final size:2
Alignment explanation
Indices: 2156695--2156722 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2156685 TTCAAATTGG
2156695 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
2156723 TTATGTTTAT
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:2158073 original size:14 final size:14
Alignment explanation
Indices: 2158054--2158080 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2158044 CAGTTGTTAA
2158054 AGTTATAATAATGG
1 AGTTATAATAATGG
2158068 AGTTATAATAATG
1 AGTTATAATAATG
2158081 TGCTTGAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (14 bp):
AGTTATAATAATGG
Found at i:2159399 original size:3 final size:3
Alignment explanation
Indices: 2159391--2159428 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2159381 CATTACTGTC
2159391 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2159429 CATCATCATC
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2160400 original size:28 final size:31
Alignment explanation
Indices: 2160370--2160428 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
2160360 ATTTGCATAT
2160370 TAAAAAAT-TATATATTAAATATAATAATTAA
1 TAAAAAATATATATATTAAATATAATAATT-A
* *
2160401 TAAAAAATATATATATTTAATGTAATAA
1 TAAAAAATATATATATTAAATATAATAA
2160429 AATCATATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
31 8 0.32
32 17 0.68
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (31 bp):
TAAAAAATATATATATTAAATATAATAATTA
Found at i:2160544 original size:13 final size:13
Alignment explanation
Indices: 2160528--2160572 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
2160518 TTATTAAATA
2160528 AAAATATATTAAT
1 AAAATATATTAAT
*
2160541 AAAATATAATAATT
1 AAAATATATTAA-T
* *
2160555 TAAATAAATTAAT
1 AAAATATATTAAT
2160568 AAAAT
1 AAAAT
2160573 TTTAAAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATATATTAAT
Found at i:2161117 original size:3 final size:3
Alignment explanation
Indices: 2161105--2161140 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2161095 TGGGAACGTT
2161105 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2161141 AACAATCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2161964 original size:14 final size:14
Alignment explanation
Indices: 2161942--2162035 Score: 50
Period size: 14 Copynumber: 6.6 Consensus size: 14
2161932 TTTATTATTT
*
2161942 TTATATTTAATATA
1 TTATTTTTAATATA
2161956 TTATTTTTAAT-TA
1 TTATTTTTAATATA
* *
2161969 ATA-TTTAAATACTAA
1 TTATTTTTAATA-T-A
* *
2161984 TTACATTTATTTATTTA
1 TT--ATTT-TTAATATA
* *
2162001 TT-TTTTTAATTTT
1 TTATTTTTAATATA
*
2162014 TTATATTTAATATA
1 TTATTTTTAATATA
2162028 TTATTTTT
1 TTATTTTT
2162036 GTTGAACTTA
Statistics
Matches: 59, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
12 6 0.10
13 12 0.20
14 29 0.49
15 2 0.03
17 4 0.07
18 3 0.05
19 3 0.05
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATTTTTAATATA
Found at i:2162035 original size:20 final size:20
Alignment explanation
Indices: 2161925--2161972 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2161915 ATTAATTAAA
*
2161925 ATATTT-ATTTATTATTTTT
1 ATATTTAATATATTATTTTT
2161944 ATATTTAATATATTATTTTT
1 ATATTTAATATATTATTTTT
2161964 A-A-TTAATAT
1 ATATTTAATAT
2161973 TTAAATACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.26
19 7 0.26
20 13 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATATTTAATATATTATTTTT
Found at i:2162395 original size:18 final size:18
Alignment explanation
Indices: 2162372--2162435 Score: 76
Period size: 18 Copynumber: 3.5 Consensus size: 18
2162362 TCATAAATAA
2162372 AAATCAAAATCAAAACCG
1 AAATCAAAATCAAAACCG
* *
2162390 AAATCAAAATCACAACCCC
1 AAATCAAAATCA-AAACCG
*
2162409 AAATCGAAATCAAACACCG
1 AAATCAAAATCAAA-ACCG
2162428 -AATCAAAA
1 AAATCAAAA
2162436 GAGAGGAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
18 21 0.55
19 17 0.45
ACGTcount: A:0.58, C:0.27, G:0.05, T:0.11
Consensus pattern (18 bp):
AAATCAAAATCAAAACCG
Found at i:2162419 original size:6 final size:6
Alignment explanation
Indices: 2162359--2162401 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
2162349 AATACCAACT
* * *
2162359 AAATCA TAAATAA AAATCA AAATCA AAACCG AAATCA AAATCA
1 AAATCA -AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
2162402 CAACCCCAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.65, C:0.16, G:0.02, T:0.16
Consensus pattern (6 bp):
AAATCA
Found at i:2162605 original size:5 final size:5
Alignment explanation
Indices: 2162595--2162632 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
2162585 CTATTTGGGT
2162595 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TT
2162633 CAGAGCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:2162615 original size:15 final size:16
Alignment explanation
Indices: 2162595--2162632 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
2162585 CTATTTGGGT
2162595 TTTTATTTTA-TTTTA
1 TTTTATTTTATTTTTA
2162610 TTTTATTTTATTTTTA
1 TTTTATTTTATTTTTA
2162626 TTTTATT
1 TTTTATT
2162633 CAGAGCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTATTTTATTTTTA
Found at i:2163506 original size:17 final size:17
Alignment explanation
Indices: 2163484--2163516 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2163474 AATTTTAAAA
*
2163484 ATATATTTTTATATTGT
1 ATATATTTTTACATTGT
2163501 ATATATTTTTACATTG
1 ATATATTTTTACATTG
2163517 ATTTAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (17 bp):
ATATATTTTTACATTGT
Found at i:2163598 original size:29 final size:30
Alignment explanation
Indices: 2163519--2163598 Score: 69
Period size: 29 Copynumber: 2.8 Consensus size: 30
2163509 TTACATTGAT
** *
2163519 TTAAAAATAAAATATTTATTTTATATTATAA
1 TTAAAAATAAAAT-TTTATTCAAAATTATAA
* * *
2163550 --AAAATTAAAA-TTAATACAAAATTA-AA
1 TTAAAAATAAAATTTTATTCAAAATTATAA
2163576 TTAAAAATAAAATTTTATTCAAA
1 TTAAAAATAAAATTTTATTCAAA
2163599 TAATTACAGT
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
26 2 0.05
27 9 0.24
28 9 0.24
29 17 0.46
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (30 bp):
TTAAAAATAAAATTTTATTCAAAATTATAA
Found at i:2171761 original size:17 final size:18
Alignment explanation
Indices: 2171741--2171776 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2171731 TAACTTATGT
2171741 ATTTTAAATAT-TTTAAA
1 ATTTTAAATATATTTAAA
*
2171758 ATTTTTAATATATTTAAA
1 ATTTTAAATATATTTAAA
2171776 A
1 A
2171777 AATATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTAAATATATTTAAA
Found at i:2171777 original size:19 final size:18
Alignment explanation
Indices: 2171742--2171792 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
2171732 AACTTATGTA
*
2171742 TTTTAAATATTTTAAAAT
1 TTTTAAATATTTAAAAAT
2171760 TTTTAATATATTTAAAAAAT
1 TTTTAA-ATATTT-AAAAAT
* *
2171780 ATTTAAAAATTTA
1 TTTTAAATATTTA
2171793 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 7 0.25
19 11 0.39
20 10 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAATATTTAAAAAT
Found at i:2171797 original size:14 final size:14
Alignment explanation
Indices: 2171766--2171814 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
2171756 AAATTTTTAA
2171766 TATATTTAAAAA--
1 TATATTTAAAAATT
2171778 -ATATTTAAAAATT
1 TATATTTAAAAATT
*
2171791 TATATTTTAAAATT
1 TATATTTAAAAATT
2171805 TATATTTAAA
1 TATATTTAAA
2171815 TATATGTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 11 0.34
14 21 0.66
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATATTTAAAAATT
Found at i:2172035 original size:5 final size:6
Alignment explanation
Indices: 2172020--2172044 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2172010 AAGGGCACCC
2172020 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
2172045 CCTTAGTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2173291 original size:17 final size:19
Alignment explanation
Indices: 2173254--2173291 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2173244 ATTATATTTA
2173254 AAATATTATATATTTAGAT
1 AAATATTATATATTTAGAT
*
2173273 AAATTTTATAT-TTTA-AT
1 AAATATTATATATTTAGAT
2173290 AA
1 AA
2173292 TTATATTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 4 0.22
19 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
AAATATTATATATTTAGAT
Found at i:2173388 original size:19 final size:19
Alignment explanation
Indices: 2173350--2173394 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
2173340 TTATTTTTTA
*
2173350 TAAAATTTTATATAATATTT
1 TAAAATTTTAGATAATA-TT
*
2173370 TAAAATTTT-GATCATATT
1 TAAAATTTTAGATAATATT
2173388 TAAAATT
1 TAAAATT
2173395 ATTAAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 9 0.39
19 5 0.22
20 9 0.39
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TAAAATTTTAGATAATATT
Found at i:2174061 original size:6 final size:6
Alignment explanation
Indices: 2174052--2174091 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
2174042 CCCTTCTTTC
*
2174052 TCTCTC TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTC
1 TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTC
2174092 CTTCCTTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.38, G:0.12, T:0.50
Consensus pattern (6 bp):
TCTCTG
Found at i:2180273 original size:18 final size:18
Alignment explanation
Indices: 2180231--2180274 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2180221 TAAGATTACT
* *
2180231 TCAGAAAATATTAACGGG
1 TCAGAAAATATTAAAGAG
2180249 TCAGAAAATATTAAAGAG
1 TCAGAAAATATTAAAGAG
*
2180267 TCGGAAAA
1 TCAGAAAA
2180275 ACATAGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.20
Consensus pattern (18 bp):
TCAGAAAATATTAAAGAG
Found at i:2181328 original size:13 final size:13
Alignment explanation
Indices: 2181310--2181335 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2181300 GTAAGAAAAC
2181310 CAAGATGTCGAAT
1 CAAGATGTCGAAT
2181323 CAAGATGTCGAAT
1 CAAGATGTCGAAT
2181336 AACTACCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
CAAGATGTCGAAT
Found at i:2184509 original size:25 final size:26
Alignment explanation
Indices: 2184466--2184516 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
2184456 AACCAATGAG
2184466 TTAAACCAATAAAAACAAAAACATAT
1 TTAAACCAATAAAAACAAAAACATAT
* * *
2184492 TTAAACCCA-AAAAGCAAAACCATAT
1 TTAAACCAATAAAAACAAAAACATAT
2184517 CCATCTACTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.61, C:0.20, G:0.02, T:0.18
Consensus pattern (26 bp):
TTAAACCAATAAAAACAAAAACATAT
Found at i:2185001 original size:12 final size:12
Alignment explanation
Indices: 2184971--2185005 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2184961 TTTTGCTACC
* *
2184971 CTTCTTATTCTT
1 CTTCTTCTTGTT
2184983 CTTCTTCTTGTT
1 CTTCTTCTTGTT
2184995 CTTCTTCTTGT
1 CTTCTTCTTGT
2185006 CTTTTGCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.03, C:0.26, G:0.06, T:0.66
Consensus pattern (12 bp):
CTTCTTCTTGTT
Found at i:2185536 original size:22 final size:19
Alignment explanation
Indices: 2185470--2185525 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
2185460 AATTAAAAAA
* *
2185470 TAAAAAATTAATTTTTACT
1 TAAAAAATTATTTTTTAAT
* **
2185489 TGAGTAATTATTTTTTAAT
1 TAAAAAATTATTTTTTAAT
2185508 TAAAAAATTATTTTTTAA
1 TAAAAAATTATTTTTTAA
2185526 AAATTTAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (19 bp):
TAAAAAATTATTTTTTAAT
Found at i:2185597 original size:13 final size:14
Alignment explanation
Indices: 2185581--2185610 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2185571 ATAAGTAATT
2185581 TTTATAT-AATTTA
1 TTTATATAAATTTA
2185594 TTTATATAAATTTA
1 TTTATATAAATTTA
2185608 TTT
1 TTT
2185611 TTACATCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTATATAAATTTA
Found at i:2186359 original size:24 final size:24
Alignment explanation
Indices: 2186332--2186382 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
2186322 TGATTCGATC
2186332 TATTTTT-TATTATATAACATATAT
1 TATTTTTATATT-TATAACATATAT
**
2186356 TATTTTTATATTTATAATTTATAT
1 TATTTTTATATTTATAACATATAT
2186380 TAT
1 TAT
2186383 ATATAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
TATTTTTATATTTATAACATATAT
Found at i:2186984 original size:32 final size:32
Alignment explanation
Indices: 2186918--2186989 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
2186908 TTAAATTTTT
**
2186918 AATAAAAATTAAAATAAAAAATATTTTTTAAA
1 AATAAAAATTAAAATAAAAAATATTTAATAAA
*
2186950 AATAAAAATATAATATAAATAAAT-TTTAATAAA
1 AATAAAAAT-TAAAATAAA-AAATATTTAATAAA
2186983 ATATAAA
1 A-ATAAA
2186990 GGTTATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 9 0.26
33 16 0.47
34 9 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (32 bp):
AATAAAAATTAAAATAAAAAATATTTAATAAA
Found at i:2187194 original size:13 final size:13
Alignment explanation
Indices: 2187163--2187187 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2187153 TATAAATAAC
2187163 AAACTATTTAAAT
1 AAACTATTTAAAT
2187176 AAACTATTTAAA
1 AAACTATTTAAA
2187188 CTAACTACAA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AAACTATTTAAAT
Found at i:2187308 original size:472 final size:476
Alignment explanation
Indices: 2186409--2187309 Score: 1537
Period size: 472 Copynumber: 1.9 Consensus size: 476
2186399 TATATGATAT
*
2186409 TAAACATTAAAAAATATTTTAAATTTTTAATAAAAATTAAACTAAAAAATATTTTTTAAAAATAA
1 TAAACATTAAAAAATATTTTAAATTTTTAATAAAAATTAAAATAAAAAATATTTTTTAAAAATAA
* *
2186474 AAATATAATATAAATCAATTTTAATAAAATATAAAGGTTATAAATATATATAATATTAATAGTAT
66 AAATATAATATAAATAAATTTTAATAAAATATAAAGGTTATAAATATATATAATATTAATAATAT
* *
2186539 ACTTATTTTTTTGATTAAAATTTTAGTATTTAAAAAATTTATTAAATATCAATTGATTCAATTCG
131 ACTTATTTTTTTGATTAAAATTTTAGTATTCAAAAAATTTATT--ATA-CAA-T-ATTCAATTCA
*
2186604 AGTCAAACCTTTTTATTTTAAAAGTAAAATTATTTGATAATTTCCTCGCTTCACAAAATTCAAAA
191 AGTCAAACCTTTTTATTTTAAAAGTAAAATTATTTGATAATTTCCTCACTTCACAAAATTCAAAA
* * * *
2186669 CTTTATTTAAAAATATAAATATAAACTATTTAAATAACCTATTTAAACTAACTACAGTCAGTTTT
256 CTTTATTTAAAAATATAAATACAAACTATTTAAATAAACTATTTAAACTAACTACAATCAATTTT
*
2186734 TAATAATAAACACTTGTATTTGGGGTTATTTGAATAACCTGTAGCGCTGGCTAAACCGCCGAATC
321 TAATAATAAACACTTGTATTTGGGGTTATTTGAATAACCCGTAGCGCTGGCTAAACCGCCGAATC
2186799 AAATTAGTACATATAGATGGGTAATTTAGTAATTTGAAACAAATGTTATTAAAGCAAACATTAAA
386 AAATTAGTACATATAGATGGGTAATTTAGTAATTTGAAACAAATGTTATTAAAGCAAACATTAAA
2186864 ATATATATATATATATGATATTAAAA
451 ATATATATATATATATGATATTAAAA
2186890 TAAACATTAAAAAATATTTTAAATTTTTAATAAAAATTAAAATAAAAAATATTTTTTAAAAATAA
1 TAAACATTAAAAAATATTTTAAATTTTTAATAAAAATTAAAATAAAAAATATTTTTTAAAAATAA
2186955 AAATATAATATAAATAAATTTTAATAAAATATAAAGGTTATAAATATATATAATATTAATAATAT
66 AAATATAATATAAATAAATTTTAATAAAATATAAAGGTTATAAATATATATAATATTAATAATAT
*
2187020 ACTTA-TTTTTTGATTAAAATTTT-GATATTCAAAAAATTTA-T-TA-AA-ATTCAATTCAAGTT
131 ACTTATTTTTTTGATTAAAATTTTAG-TATTCAAAAAATTTATTATACAATATTCAATTCAAGTC
* *
2187079 AAATCTTTTTATTTTAAAAGTAAAATTATTTTATAATTTCCTCACTTCAC-AAATCTCAAAACTT
195 AAACCTTTTTATTTTAAAAGTAAAATTATTTGATAATTTCCTCACTTCACAAAAT-TCAAAACTT
*
2187143 TATTTAAAAATATAAATAACAAACTATTTAAATAAACTATTTAAACTAACTACAATTAATTTTTA
259 TATTTAAAAATATAAAT-ACAAACTATTTAAATAAACTATTTAAACTAACTACAATCAATTTTTA
*
2187208 ATAATAAACACTTGTATTTGTGGTTATTTGAATAACCCGTAGCGCTGGCTAAACCGCCGAATCAA
323 ATAATAAACACTTGTATTTGGGGTTATTTGAATAACCCGTAGCGCTGGCTAAACCGCCGAATCAA
2187273 ATTAGTACATATAGATGGGTAATTTAGTAATTTGAAA
388 ATTAGTACATATAGATGGGTAATTTAGTAATTTGAAA
2187310 ATGTTGGTGC
Statistics
Matches: 401, Mismatches: 16, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
470 4 0.01
471 85 0.21
472 142 0.35
474 2 0.00
476 2 0.00
479 2 0.00
480 32 0.08
481 132 0.33
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (476 bp):
TAAACATTAAAAAATATTTTAAATTTTTAATAAAAATTAAAATAAAAAATATTTTTTAAAAATAA
AAATATAATATAAATAAATTTTAATAAAATATAAAGGTTATAAATATATATAATATTAATAATAT
ACTTATTTTTTTGATTAAAATTTTAGTATTCAAAAAATTTATTATACAATATTCAATTCAAGTCA
AACCTTTTTATTTTAAAAGTAAAATTATTTGATAATTTCCTCACTTCACAAAATTCAAAACTTTA
TTTAAAAATATAAATACAAACTATTTAAATAAACTATTTAAACTAACTACAATCAATTTTTAATA
ATAAACACTTGTATTTGGGGTTATTTGAATAACCCGTAGCGCTGGCTAAACCGCCGAATCAAATT
AGTACATATAGATGGGTAATTTAGTAATTTGAAACAAATGTTATTAAAGCAAACATTAAAATATA
TATATATATATGATATTAAAA
Found at i:2194465 original size:2 final size:2
Alignment explanation
Indices: 2194458--2194485 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2194448 ACCTTTCCCT
2194458 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2194486 CCCAAAAAAA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2196094 original size:2 final size:2
Alignment explanation
Indices: 2196089--2196114 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2196079 AAAAAGAAAA
2196089 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
2196115 CAAGCCTTTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2196520 original size:18 final size:20
Alignment explanation
Indices: 2196497--2196543 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
2196487 TTGTAATGAG
2196497 ATAAAAATAA-A-AATAATA
1 ATAAAAATAATATAATAATA
* *
2196515 ATAAAATTAATTATTATAATA
1 ATAAAAATAA-TATAATAATA
2196536 ATAAAAAT
1 ATAAAAAT
2196544 TAAGTACTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 9 0.39
20 1 0.04
21 13 0.57
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAAAAATAATATAATAATA
Found at i:2196556 original size:22 final size:21
Alignment explanation
Indices: 2196509--2196558 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
2196499 AAAAATAAAA
* *
2196509 ATAATAATAAAATTAATTATT
1 ATAATAATAAAATTAAGTACT
2196530 ATAATAATAAAAATTAAGTACT
1 ATAATAAT-AAAATTAAGTACT
*
2196552 GTAATAA
1 ATAATAA
2196559 GATATTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (21 bp):
ATAATAATAAAATTAAGTACT
Found at i:2196823 original size:29 final size:28
Alignment explanation
Indices: 2196790--2196884 Score: 74
Period size: 29 Copynumber: 3.4 Consensus size: 28
2196780 TTAATAATAA
2196790 TTTATTTAATTATTTATTATATATATTAT
1 TTTA-TTAATTATTTATTATATATATTAT
* *
2196819 TTTA-T-ATTCATAT-TTATCTAT-TTAT
1 TTTATTAATT-ATTTATTATATATATTAT
* *
2196844 TTTATATAATTAATTA-TATATCAAATTAT
1 TTTAT-TAATTATTTATTATAT-ATATTAT
2196873 TTTATGTAATTA
1 TTTAT-TAATTA
2196885 ATTAATAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
25 8 0.15
26 10 0.19
27 11 0.21
28 4 0.08
29 19 0.37
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (28 bp):
TTTATTAATTATTTATTATATATATTAT
Found at i:2196832 original size:13 final size:11
Alignment explanation
Indices: 2196789--2196850 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 11
2196779 TTTAATAATA
*
2196789 ATTTATTTAATT
1 ATTTATTTTA-T
*
2196801 ATTTATTATAT
1 ATTTATTTTAT
2196812 ATATTATTTTAT
1 AT-TTATTTTAT
*
2196824 ATTCATATTTATCT
1 ATT--TATTT-TAT
2196838 ATTTATTTTAT
1 ATTTATTTTAT
2196849 AT
1 AT
2196851 AATTAATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
11 8 0.20
12 23 0.56
13 5 0.12
14 5 0.12
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTATTTTAT
Found at i:2196861 original size:37 final size:37
Alignment explanation
Indices: 2196792--2196862 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
2196782 AATAATAATT
*
2196792 TATTTAATTATTTATTATATATATTATTTTATATTCA
1 TATTTAATTATTTATTATATATATTATATTATATTCA
*
2196829 TATTT-ATCTATTTATTTTATATAATTA-ATTATAT
1 TATTTAAT-TATTTATTATATAT-ATTATATTATAT
2196863 ATCAAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 2 0.07
37 24 0.80
38 4 0.13
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (37 bp):
TATTTAATTATTTATTATATATATTATATTATATTCA
Found at i:2197149 original size:18 final size:20
Alignment explanation
Indices: 2197126--2197169 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
2197116 ATAATTATGC
*
2197126 TTATTTTATTTTTTA-A-TT
1 TTATTTGATTTTTTATATTT
2197144 TTATTTGATTTTTTATATTT
1 TTATTTGATTTTTTATATTT
2197164 TTATTT
1 TTATTT
2197170 AGTTGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.61
19 1 0.04
20 8 0.35
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (20 bp):
TTATTTGATTTTTTATATTT
Found at i:2197164 original size:25 final size:24
Alignment explanation
Indices: 2197129--2197179 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2197119 ATTATGCTTA
* *
2197129 TTTTATTTTTTAATTTTATTTGATT
1 TTTTATATTTTAA-TTTAGTTGATT
*
2197154 TTTTATATTTTTATTTAGTTGATT
1 TTTTATATTTTAATTTAGTTGATT
2197178 TT
1 TT
2197180 ATTTAACTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.75
Consensus pattern (24 bp):
TTTTATATTTTAATTTAGTTGATT
Found at i:2197922 original size:13 final size:13
Alignment explanation
Indices: 2197901--2197932 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2197891 TTTAAAATAT
2197901 TTATATATTTATA
1 TTATATATTTATA
*
2197914 TTATTTATTTATA
1 TTATATATTTATA
2197927 TTATAT
1 TTATAT
2197933 CATATTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATATATTTATA
Found at i:2199308 original size:8 final size:8
Alignment explanation
Indices: 2199292--2199326 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
2199282 TAAATGGAAG
*
2199292 ATATATAT
1 ATATGTAT
2199300 ATATGTAT
1 ATATGTAT
2199308 ATATGTAT
1 ATATGTAT
2199316 ATATGTAT
1 ATATGTAT
2199324 ATA
1 ATA
2199327 CACTATAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (8 bp):
ATATGTAT
Found at i:2201035 original size:2 final size:2
Alignment explanation
Indices: 2201028--2201053 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2201018 CAGGATGCAA
2201028 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
2201054 CAGTAGACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2206464 original size:26 final size:26
Alignment explanation
Indices: 2206418--2206468 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
2206408 TATTTTTAAT
2206418 ATTTAAAATAAAAATTAAAAATATTA
1 ATTTAAAATAAAAATTAAAAATATTA
*
2206444 ATTT-AAATAAAATATTTAAAATATT
1 ATTTAAAATAAAA-ATTAAAAATATT
2206469 CCTCCTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
ATTTAAAATAAAAATTAAAAATATTA
Found at i:2206674 original size:22 final size:22
Alignment explanation
Indices: 2206636--2206681 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
2206626 GAAAATCAAA
2206636 TTTTAATTTAATTAATTTAAATT
1 TTTTAATTTAA-TAATTTAAATT
*
2206659 TTTTATATTTAA-AATTTATATT
1 TTTTA-ATTTAATAATTTAAATT
2206681 T
1 T
2206682 CATTATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 5 0.24
24 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTAATTTAATAATTTAAATT
Found at i:2208937 original size:3 final size:3
Alignment explanation
Indices: 2208929--2208965 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2208919 AGAAAGATTC
2208929 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2208966 GGGGAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2209143 original size:2 final size:2
Alignment explanation
Indices: 2209136--2209184 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2209126 TATGATTTAT
* *
2209136 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2209178 TA TA TA T
1 TA TA TA T
2209185 GAATTTAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2209548 original size:7 final size:7
Alignment explanation
Indices: 2209538--2209571 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
2209528 ATGTATAATT
*
2209538 TTATATA
1 TTATAAA
2209545 TTATAAA
1 TTATAAA
2209552 TATATAAA
1 T-TATAAA
2209560 TTATAAA
1 TTATAAA
2209567 TTATA
1 TTATA
2209572 TTATTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TTATAAA
Found at i:2209557 original size:15 final size:15
Alignment explanation
Indices: 2209539--2209584 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
2209529 TGTATAATTT
2209539 TATATATTATAAATA
1 TATATATTATAAATA
*
2209554 TATAAATTATAAAT-
1 TATATATTATAAATA
2209568 TATATTATTATTAAATA
1 TATA-TATTA-TAAATA
2209585 AATAAAATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 4 0.15
15 17 0.65
16 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATTATAAATA
Found at i:2210232 original size:18 final size:19
Alignment explanation
Indices: 2210210--2210253 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
2210200 TTAAATAAAG
2210210 TTTAAATT-AAAATATTT-
1 TTTAAATTAAAAATATTTA
2210227 TATT-AATTAAAAATATTTA
1 T-TTAAATTAAAAATATTTA
2210246 TTTAAATT
1 TTTAAATT
2210254 TAATTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 5 0.22
18 13 0.57
19 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAAATTAAAAATATTTA
Found at i:2211726 original size:129 final size:129
Alignment explanation
Indices: 2211471--2211729 Score: 394
Period size: 130 Copynumber: 2.0 Consensus size: 129
2211461 TTAAGAGTTA
*
2211471 AATTATATATTTAAATTTAAAAACTTTTCATAATTGAAAATGTTTAAAAAAAATTTAAACTTATA
1 AATTATATATTTAAATTTAAAAACTTTTCATAATTGAAAATGTTTAAAAAAAATTTAAACTCATA
* * * * *
2211536 AAATGAATCTAATCAAAATATAAAATTTTATTTTTTAAATAGATTCAATCTTAGATAAAAAATT
66 AAAAGAATCTAAGCAAAATAAAAAAATTTATATTTTAAATAGATTCAATCTTAGATAAAAAATT
* * *
2211600 AATTATATATTTAAATTTAAAAACTTTTCTTATTTGAAAATGTTTAAAAAAAATTTTAA-TCCAG
1 AATTATATATTTAAATTTAAAAACTTTTCATAATTGAAAATGTTTAAAAAAAATTTAAACT-CA-
* *
2211664 TAAAAAGAATCTAAGCAAAATAAAAAAATTTATATTTTAAATGGATTCAATTTTAGATAAAAAAT
64 TAAAAAGAATCTAAGCAAAATAAAAAAATTTATATTTTAAATAGATTCAATCTTAGATAAAAAAT
2211729 T
129 T
2211730 TTAAATTCAA
Statistics
Matches: 117, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
128 1 0.01
129 57 0.49
130 59 0.50
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (129 bp):
AATTATATATTTAAATTTAAAAACTTTTCATAATTGAAAATGTTTAAAAAAAATTTAAACTCATA
AAAAGAATCTAAGCAAAATAAAAAAATTTATATTTTAAATAGATTCAATCTTAGATAAAAAATT
Found at i:2215205 original size:2 final size:2
Alignment explanation
Indices: 2215198--2215228 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
2215188 AAGAGGGAAA
2215198 AG AG AG AG AG AG AG AG AG AG AG AG AG CAG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG
2215229 TCCTTGGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2215768 original size:20 final size:20
Alignment explanation
Indices: 2215745--2215783 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2215735 TTATATTTAA
2215745 TATTTATTT-AATATTAAAAT
1 TATTT-TTTAAATATTAAAAT
2215765 TATTTTTTAAATATTAAAA
1 TATTTTTTAAATATTAAAA
2215784 AAATTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTTTTAAATATTAAAAT
Found at i:2215990 original size:21 final size:20
Alignment explanation
Indices: 2215948--2215992 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2215938 ATGTGAGTAG
*
2215948 TTTTTAAAAAATTGAATGAT
1 TTTTTAAAAAATTGAATAAT
2215968 TTTTTAAAAAAGTT-AGATAAT
1 TTTTTAAAAAA-TTGA-ATAAT
2215989 TTTT
1 TTTT
2215993 ATAGAATTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (20 bp):
TTTTTAAAAAATTGAATAAT
Found at i:2218564 original size:5 final size:5
Alignment explanation
Indices: 2218554--2218615 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
2218544 AACTTATATT
* * * * *
2218554 TTAAA TTAAA TTAAA TTTAAA TAAAA ATAAA TTATA TTAATA ATATAC
1 TTAAA TTAAA TTAAA -TTAAA TTAAA TTAAA TTAAA TTAA-A TTA-AA
2218602 TTAAA TTAAA TTAA
1 TTAAA TTAAA TTAA
2218616 TAAAATCTCT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
5 33 0.75
6 10 0.23
7 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:2218598 original size:22 final size:22
Alignment explanation
Indices: 2218560--2218618 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
2218550 TATTTTAAAT
*
2218560 TAAATTAAATTTA-AATAAAAA
1 TAAATTAAATTAATAATAAAAA
* * **
2218581 TAAATTATATTAATAATATACT
1 TAAATTAAATTAATAATAAAAA
2218603 TAAATTAAATTAATAA
1 TAAATTAAATTAATAA
2218619 AATCTCTATC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATTAAATTAATAATAAAAA
Found at i:2220491 original size:216 final size:214
Alignment explanation
Indices: 2220117--2221619 Score: 1628
Period size: 216 Copynumber: 7.1 Consensus size: 214
2220107 GTGCTACTAA
* * * * ** *
2220117 TTTGAATTTGGTGTTAAATCA-GGATTTAGTTCCTCATGTAGAAAAGGGTTCTCCAACATTAGCA
1 TTTGAATTTGGTGTCAAA-GATGGATTTAGTTCCTGATATAGAAAA-GGTTCTCCTCCATTGGCA
* * * * **
2220181 GCTTCTGTTGTTGAAAGTGAAATTACTACTCAATTAGCTTCTTCAGAGTCTGTTTCCATTGTTGA
64 GCTTCTGCTGTTGAAAGTGAAATTACTACTGAATTAGCTTCTTTAGAGTCTGGTTCCAAAG-TGA
* * *
2220246 GGTGCCCCACGGTGTTAAGTTCCAGGAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTAAGAATG
128 AGTGCCCCACAGTGTTAAGTTCCAGGAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTGAGAATG
*
2220311 TTGGTAAAATTGGGGGTACTGC
193 TTGGTAAAATTGAGGGTACTGC
* *
2220333 TTTGAATTTGGTGTCAAAGATGGATTTAGTTGCTGATATAGAAAATGGTTCTCCTCCATTAGCAG
1 TTTGAATTTGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAA-GGTTCTCCTCCATTGGCAG
* * * * * **
2220398 CATCTGCTGTTGAAAGTGCAATTACTACTCAATTAGCTTCTTCAGAGTCTGATTCCATTGTTGAA
65 CTTCTGCTGTTGAAAGTGAAATTACTACTGAATTAGCTTCTTTAGAGTCTGGTTCCAAAG-TGAA
*
2220463 GTGCCCCACAGTGTTAAGTTCCAGGAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTGAGAACGT
129 GTGCCCCACAGTGTTAAGTTCCAGGAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTGAGAATGT
2220528 TGGTAAAATTGAGGGTACTGC
194 TGGTAAAATTGAGGGTACTGC
* * *
2220549 TTTGAATATGGTGTCAAAGATGGATTTAGTTGCTGATATAGAAAGGGTTCTCCTCCATTGGCAGC
1 TTTGAATTTGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAGGTTCTCCTCCATTGGCAGC
* *
2220614 TTCTGC---------------TACT-C--AATTAGCTTCTTCAGAGTCTGGTTCCATAGTTGAAG
66 TTCTGCTGTTGAAAGTGAAATTACTACTGAATTAGCTTCTTTAGAGTCTGGTTCCAAAG-TGAAG
* * * *
2220661 T-TCCC-CA----T-AG--GCAAGAAGAAAATGACGGTGCTTCTGAGGGAAGTGGTGAGAATGTT
130 TGCCCCACAGTGTTAAGTTCCAGGAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTGAGAATGTT
2220717 GGTAAAATTGAGGGTACTGC
195 GGTAAAATTGAGGGTACTGC
* * ** *
2220737 TTTGAATATGGTGTCAAAGATGGATTTAGTTCCTGATGTAGAAAAATTTCTCCTCTATTGGCAGC
1 TTTGAATTTGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAGGTTCTCCTCCATTGGCAGC
* * * *
2220802 TTCTGCTGTAGAAAGTGAAATTAATTCTGAATTAGCTTCTTTAGAGTCTGGTTCCAGAAGCGAAG
66 TTCTGCTGTTGAAAGTGAAATTACTACTGAATTAGCTTCTTTAGAGTCTGGTTCCA-AAGTGAAG
* * * * * *
2220867 TGCCCGACAGTGTTAAGTTCCAGGAAGAAAATAATGGTTCTTTTGAGGAAAGTGATGAGAATGTT
130 TGCCCCACAGTGTTAAGTTCCAGGAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTGAGAATGTT
* *
2220932 GGTAAAATTGAAGGTACTAC
195 GGTAAAATTGAGGGTACTGC
* * * *
2220952 TTTGAATGTGGTGTCAAAGATGGATTTAGTTCCTGATATAAAAAAAAGTTTCTCCTTCATTGGCA
1 TTTGAATTTGGTGTCAAAGATGGATTTAGTTCCTGATAT--AGAAAAGGTTCTCCTCCATTGGCA
* * * ***
2221017 ACTTCTGCTGTTGAAAGTGAAATTACTTCTGAATTAGCTTCTTTGGAGTCCATTTCCAAAAGTGA
64 GCTTCTGCTGTTGAAAGTGAAATTACTACTGAATTAGCTTCTTTAGAGTCTGGTTCC-AAAGTGA
* * *
2221082 AGTG---C-C--TCTTAAGTTCCAGGAGGAAAATGATGGTGCTTCTGAGGGAAGTGATGAGAATG
128 AGTGCCCCACAGTGTTAAGTTCCAGGAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTGAGAATG
2221141 TTGGTAAAATTGAGGGTACTGC
193 TTGGTAAAATTGAGGGTACTGC
* * * * * *
2221163 TTTGAATGTGGTGTCAAAGGTGGATTTAGCTCCTGAAATAGAAAAGTTTCTCCTCC-GTGGACAG
1 TTTGAATTTGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAGGTTCTCCTCCATTGG-CAG
* ** * * * *
2221227 CTTCTGCTGTTGAAACTGAAATTAGAACTGAATTAGCATCTTTAGAGTCCGGTTTCAAAAGTCAA
65 CTTCTGCTGTTGAAAGTGAAATTACTACTGAATTAGCTTCTTTAGAGTCTGG-TTCCAAAGTGAA
*** * * * * *
2221292 GTGCCCCTTGGTCTTAAGTTCCAGGAGGAAAATGACGGTGCTTTTGAGGGAAGTGGTGAGAATAT
129 GTGCCCCACAGTGTTAAGTTCCAGGAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTGAGAATGT
* *
2221357 CGGCAAAATTGAGGGTACTGC
194 TGGTAAAATTGAGGGTACTGC
2221378 TTTGAATTTGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAGGTTTCTCCTCCATTGGCAG
1 TTTGAATTTGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAGG-TTCTCCTCCATTGGCAG
* ** * *
2221443 CTTCTGCTGTTGAAAGTGAAACTAGAACTGAATTAGCTTCTTTGGAGTCCGGTTCCAAGAGTGAA
65 CTTCTGCTGTTGAAAGTGAAATTACTACTGAATTAGCTTCTTTAGAGTCTGGTTCCAA-AGTGAA
* ** * *
2221508 GTGCCCCACAGTGTTAAGTTGCAGGAAGAAAAT-AGTGGTGCTGGTGA---AAATGGTGAGAGTG
129 GTGCCCCACAGTGTTAAGTTCCAGGAAGAAAATGA-TGGTGCTTCTGAGGGAAGTGGTGAGAATG
* ** *
2221569 TTGATAAAATTGAGTATACTTC
193 TTGGTAAAATTGAGGGTACTGC
* * *
2221591 TTCG-ATTGTGGAGTCTAAGATGGATTTAG
1 TTTGAATT-TGGTGTCAAAGATGGATTTAG
2221620 CAGTGGAAGA
Statistics
Matches: 1112, Mismatches: 130, Indels: 93
0.83 0.10 0.07
Matches are distributed among these distances:
188 127 0.11
190 2 0.00
191 1 0.00
195 2 0.00
196 3 0.00
197 35 0.03
199 1 0.00
200 4 0.00
203 3 0.00
204 1 0.00
206 31 0.03
207 4 0.00
208 5 0.00
209 71 0.06
210 3 0.00
211 103 0.09
212 5 0.00
213 52 0.05
215 235 0.21
216 341 0.31
217 82 0.07
218 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (214 bp):
TTTGAATTTGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAGGTTCTCCTCCATTGGCAGC
TTCTGCTGTTGAAAGTGAAATTACTACTGAATTAGCTTCTTTAGAGTCTGGTTCCAAAGTGAAGT
GCCCCACAGTGTTAAGTTCCAGGAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTGAGAATGTTG
GTAAAATTGAGGGTACTGC
Found at i:2220748 original size:188 final size:193
Alignment explanation
Indices: 2220422--2221450 Score: 664
Period size: 215 Copynumber: 5.0 Consensus size: 193
2220412 AGTGCAATTA
* *
2220422 CTACTCAATTAGCTTCTTCAGAGTCTGATTCCATTGTTGAAGTGCCCCACAGTGTTAAGTTCCAG
1 CTACTCAATTAGCTTCTTCAGAGTCTGATTCCATAGTTGAAGTGCCCCACA--G-TAAG-TCCAA
*
2220487 GAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTGAGAACGTTGGTAAAATTGAGGGTACTGCTTT
62 GAAGAAAATGACGGTGCTTCTGAGGGAAGTGGTGAGAACGTTGGTAAAATTGAGGGTACTGCTTT
* **
2220552 GAATATGGTGTCAAAGATGGATTTAGTTGCTGATATAGAAAGGGTTCTCCTCCATTGGCAGCTTC
127 GAATATGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAAGTTCTCCTCCATTGGCAGCTTC
2220617 TG
192 TG
* * *
2220619 CTACTCAATTAGCTTCTTCAGAGTCTGGTTCCATAGTTGAAGT-TCCC-CA-T-AG-GCAAGAAG
1 CTACTCAATTAGCTTCTTCAGAGTCTGATTCCATAGTTGAAGTGCCCCACAGTAAGTCCAAGAAG
*
2220679 AAAATGACGGTGCTTCTGAGGGAAGTGGTGAGAATGTTGGTAAAATTGAGGGTACTGCTTTGAAT
66 AAAATGACGGTGCTTCTGAGGGAAGTGGTGAGAACGTTGGTAAAATTGAGGGTACTGCTTTGAAT
* * *
2220744 ATGGTGTCAAAGATGGATTTAGTTCCTGATGTAGAAAAATTTCTCCTCTATTGGCAGCTTCTG
131 ATGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAAGTTCTCCTCCATTGGCAGCTTCTG
* * * * *
2220807 CTGTAGAAAGTGAAATTAATTCTGAATTAGCTTCTTTAGAGTCTGGTTCCAGAAG-CGAAGTGCC
1 C---------------T-A--CTCAATTAGCTTCTTCAGAGTCTGATTCCA-TAGTTGAAGTGCC
* * * * * * * * *
2220871 CGACAGTGTTAAGTTCCAGGAAGAAAATAATGGTTCTTTTGAGGAAAGTGATGAGAATGTTGGTA
47 CCACA--G-TAAG-TCCAAGAAGAAAATGACGGTGCTTCTGAGGGAAGTGGTGAGAACGTTGGTA
* * * *
2220936 AAATTGAAGGTACTACTTTGAATGTGGTGTCAAAGATGGATTTAGTTCCTGATATAAAAAAAAGT
108 AAATTGAGGGTACTGCTTTGAATATGGTGTCAAAGATGGATTTAGTTCCTGATAT-AGAAAAAG-
* *
2221001 TTCTCCTTCATTGGCAACTTCTG
171 TTCTCCTCCATTGGCAGCTTCTG
** * *
2221024 CTGTTGAAAGTGAAATTACTTCTGAATTAGCTTCTTTGGAGTC-CATTTCCAAAAG-TGAAGTG-
1 C---------------TAC-TC--AATTAGCTTCTTCAGAGTCTGA-TTCC-ATAGTTGAAGTGC
* * * * * * *
2221086 -CCTC-TTAAGTTCCAGGAGGAAAATGATGGTGCTTCTGAGGGAAGTGATGAGAATGTTGGTAAA
46 CCCACAGTAAG-TCCAAGAAGAAAATGACGGTGCTTCTGAGGGAAGTGGTGAGAACGTTGGTAAA
* * * *
2221149 ATTGAGGGTACTGCTTTGAATGTGGTGTCAAAGGTGGATTTAGCTCCTGAAATAG-AAAAGTTTC
110 ATTGAGGGTACTGCTTTGAATATGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAAG-TTC
*
2221213 TCCTCC-GTGGACAGCTTCTG
174 TCCTCCATTGG-CAGCTTCTG
* * * * * * *
2221233 CTGTTGAAACTGAAATTAGAACTGAATTAGCATCTTTAGAGTCCGGTTTCAAAAG-TCAAGTGCC
1 C---T---AC------T----C--AATTAGCTTCTTCAGAGT-CTGATTCCATAGTTGAAGTGCC
*** * * * ** * *
2221297 CCTTGGTCTTAAGTTCCAGGAGGAAAATGACGGTGCTTTTGAGGGAAGTGGTGAGAATATCGGCA
47 CCACAG---TAAG-TCCAAGAAGAAAATGACGGTGCTTCTGAGGGAAGTGGTGAGAACGTTGGTA
* *
2221362 AAATTGAGGGTACTGCTTTGAATTTGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAGGTT
108 AAATTGAGGGTACTGCTTTGAATATGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAAG-T
2221427 TCTCCTCCATTGGCAGCTTCTG
172 TCTCCTCCATTGGCAGCTTCTG
2221449 CT
1 CT
2221451 GTTGAAAGTG
Statistics
Matches: 693, Mismatches: 81, Indels: 100
0.79 0.09 0.11
Matches are distributed among these distances:
188 127 0.18
190 2 0.00
191 1 0.00
195 2 0.00
196 3 0.00
197 43 0.06
200 2 0.00
203 1 0.00
204 1 0.00
205 2 0.00
206 33 0.05
207 4 0.01
208 5 0.01
209 52 0.08
210 5 0.01
211 104 0.15
212 1 0.00
213 3 0.00
214 1 0.00
215 199 0.29
216 31 0.04
217 70 0.10
218 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (193 bp):
CTACTCAATTAGCTTCTTCAGAGTCTGATTCCATAGTTGAAGTGCCCCACAGTAAGTCCAAGAAG
AAAATGACGGTGCTTCTGAGGGAAGTGGTGAGAACGTTGGTAAAATTGAGGGTACTGCTTTGAAT
ATGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAAGTTCTCCTCCATTGGCAGCTTCTG
Found at i:2220987 original size:215 final size:215
Alignment explanation
Indices: 2220675--2221619 Score: 1126
Period size: 215 Copynumber: 4.4 Consensus size: 215
2220665 CCATAGGCAA
*
2220675 GAAGAAAATGACGGTGCTTCTGAGGGAAGTGGTGAGAATGTTGGTAAAATTGAGGGTACTGCTTT
1 GAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTGAGAATGTTGGTAAAATTGAGGGTACTGCTTT
* *
2220740 GAATATGGTGTCAAAGATGGATTTAGTTCCTGATGTAGAAAAATTTCTCCTCTATTGGCAGCTTC
66 GAATGTGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAATTTCTCCTCTATTGGCAGCTTC
* * * *
2220805 TGCTGTAGAAAGTGAAATTA-ATTCTGAATTAGCTTCTTTAGAGTCTGGTTCCAGAAGCGAAGTG
131 TGCTGTTGAAAGTGAAATTAGA-ACTGAATTAGCTTCTTTAGAGTCCGGTTCCAAAAGCGAAGTG
* *
2220869 CCCGACAGTGTTAAGTTCCAG
195 CCCCACAGTCTTAAGTTCCAG
* * * * * * *
2220890 GAAGAAAATAATGGTTCTTTTGAGGAAAGTGATGAGAATGTTGGTAAAATTGAAGGTACTACTTT
1 GAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTGAGAATGTTGGTAAAATTGAGGGTACTGCTTT
* *
2220955 GAATGTGGTGTCAAAGATGGATTTAGTTCCTGATATAAAAAAAAGTTTCTCCT-TCATTGGCAAC
66 GAATGTGGTGTCAAAGATGGATTTAGTTCCTGATAT-AGAAAAA-TTTCTCCTCT-ATTGGCAGC
*** * ** *
2221019 TTCTGCTGTTGAAAGTGAAATTACTTCTGAATTAGCTTCTTTGGAGTCCATTTCCAAAAGTGAAG
128 TTCTGCTGTTGAAAGTGAAATTAGAACTGAATTAGCTTCTTTAGAGTCCGGTTCCAAAAGCGAAG
2221084 TG---C-C--TCTTAAGTTCCAG
193 TGCCCCACAGTCTTAAGTTCCAG
* *
2221101 GAGGAAAATGATGGTGCTTCTGAGGGAAGTGATGAGAATGTTGGTAAAATTGAGGGTACTGCTTT
1 GAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTGAGAATGTTGGTAAAATTGAGGGTACTGCTTT
* * * * **
2221166 GAATGTGGTGTCAAAGGTGGATTTAGCTCCTGAAATAGAAAAGTTTCTCCTC-CGTGGACAGCTT
66 GAATGTGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAATTTCTCCTCTATTGG-CAGCTT
* * *
2221230 CTGCTGTTGAAACTGAAATTAGAACTGAATTAGCATCTTTAGAGTCCGGTTTCAAAAGTC-AAGT
130 CTGCTGTTGAAAGTGAAATTAGAACTGAATTAGCTTCTTTAGAGTCCGGTTCCAAAAG-CGAAGT
***
2221294 GCCCCTTGGTCTTAAGTTCCAG
194 GCCCCACAGTCTTAAGTTCCAG
* * * * * *
2221316 GAGGAAAATGACGGTGCTTTTGAGGGAAGTGGTGAGAATATCGGCAAAATTGAGGGTACTGCTTT
1 GAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTGAGAATGTTGGTAAAATTGAGGGTACTGCTTT
* * *
2221381 GAATTTGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAGGTTTCTCCTCCATTGGCAGCTT
66 GAATGTGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAA-ATTTCTCCTCTATTGGCAGCTT
* * * *
2221446 CTGCTGTTGAAAGTGAAACTAGAACTGAATTAGCTTCTTTGGAGTCCGGTTCCAAGAGTGAAGTG
130 CTGCTGTTGAAAGTGAAATTAGAACTGAATTAGCTTCTTTAGAGTCCGGTTCCAAAAGCGAAGTG
* *
2221511 CCCCACAGTGTTAAGTTGCAG
195 CCCCACAGTCTTAAGTTCCAG
** * * * ** *
2221532 GAAGAAAAT-AGTGGTGCTGGTGA---AAATGGTGAGAGTGTTGATAAAATTGAGTATACTTCTT
1 GAAGAAAATGA-TGGTGCTTCTGAGGGAAGTGGTGAGAATGTTGGTAAAATTGAGGGTACTGCTT
* * * *
2221593 CGATTGTGGAGTCTAAGATGGATTTAG
65 TGAATGTGGTGTCAAAGATGGATTTAG
2221620 CAGTGGAAGA
Statistics
Matches: 623, Mismatches: 90, Indels: 36
0.83 0.12 0.05
Matches are distributed among these distances:
208 3 0.00
209 67 0.11
210 5 0.01
211 103 0.17
212 1 0.00
213 52 0.08
215 202 0.32
216 113 0.18
217 77 0.12
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.31
Consensus pattern (215 bp):
GAAGAAAATGATGGTGCTTCTGAGGGAAGTGGTGAGAATGTTGGTAAAATTGAGGGTACTGCTTT
GAATGTGGTGTCAAAGATGGATTTAGTTCCTGATATAGAAAAATTTCTCCTCTATTGGCAGCTTC
TGCTGTTGAAAGTGAAATTAGAACTGAATTAGCTTCTTTAGAGTCCGGTTCCAAAAGCGAAGTGC
CCCACAGTCTTAAGTTCCAG
Found at i:2224014 original size:8 final size:10
Alignment explanation
Indices: 2223990--2224027 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
2223980 GAATTGCTTT
2223990 GATATATATA
1 GATATATATA
2224000 GATATATATA
1 GATATATATA
*
2224010 AATATATAT-
1 GATATATATA
*
2224019 TATATATAT
1 GATATATAT
2224028 CAAATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (10 bp):
GATATATATA
Found at i:2224016 original size:20 final size:20
Alignment explanation
Indices: 2223991--2224038 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2223981 AATTGCTTTG
2223991 ATATATATAGATATATAT-AA
1 ATATATAT-GATATATATCAA
*
2224011 ATATATATTATATATATCAA
1 ATATATATGATATATATCAA
*
2224031 ATTTATAT
1 ATATATAT
2224039 TAAATGTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
ATATATATGATATATATCAA
Found at i:2232186 original size:26 final size:28
Alignment explanation
Indices: 2232157--2232209 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
2232147 AAACTTTTCA
*
2232157 ATTAAAATTTA-ATGATTTT-TATAAAT
1 ATTAAAATTTATATAATTTTATATAAAT
*
2232183 ATTAAATTTTATATAATTTTATATAAA
1 ATTAAAATTTATATAATTTTATATAAA
2232210 AGAGAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 10 0.43
27 7 0.30
28 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
ATTAAAATTTATATAATTTTATATAAAT
Found at i:2233290 original size:15 final size:14
Alignment explanation
Indices: 2233267--2233329 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
2233257 TTTATTTTTT
2233267 TAATAATTTTAAATA
1 TAATAA-TTTAAATA
*
2233282 TAATTATTTAAATA
1 TAATAATTTAAATA
*
2233296 TAAT-ATATAAA-A
1 TAATAATTTAAATA
2233308 -AAT-ATTTAAATA
1 TAATAATTTAAATA
2233320 T-AT-ATTTAAA
1 TAATAATTTAAA
2233330 ATTTATATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.21
12 11 0.26
13 6 0.14
14 12 0.28
15 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATAATTTAAATA
Found at i:2233293 original size:14 final size:13
Alignment explanation
Indices: 2233269--2233413 Score: 78
Period size: 13 Copynumber: 11.5 Consensus size: 13
2233259 TATTTTTTTA
2233269 ATAAT-TTTAAAT
1 ATAATATTTAAAT
2233281 ATAATTATTTAAAT
1 ATAA-TATTTAAAT
*
2233295 ATAATATATAAA-
1 ATAATATTTAAAT
2233307 A-AATATTTAAAT
1 ATAATATTTAAAT
2233319 AT-ATATTTAAA-
1 ATAATATTTAAAT
* *
2233330 AT-TTATAT-AAT
1 ATAATATTTAAAT
2233341 ATAA-ATTATAAATT
1 ATAATATT-TAAA-T
*
2233355 ATTAAAATTT--AT
1 A-TAATATTTAAAT
*
2233367 TTAA-ATTTAAAAT
1 ATAATATTT-AAAT
** *
2233380 ATTTTAATTATAAT
1 ATAATATTTA-AAT
*
2233394 ATAATATATAAAT
1 ATAATATTTAAAT
2233407 ATAATAT
1 ATAATAT
2233414 AAATACATAA
Statistics
Matches: 102, Mismatches: 15, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
10 6 0.06
11 22 0.22
12 17 0.17
13 25 0.25
14 25 0.25
15 4 0.04
16 3 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAATATTTAAAT
Found at i:2233302 original size:19 final size:18
Alignment explanation
Indices: 2233269--2233431 Score: 74
Period size: 19 Copynumber: 9.1 Consensus size: 18
2233259 TATTTTTTTA
2233269 ATAAT-TTTAAATATAATT
1 ATAATATTTAAATATAA-T
*
2233287 ATTTAA-ATATAATATATAA-
1 A--TAATATTTAA-ATATAAT
*
2233306 AAAATATTTAAATATATAT
1 ATAATATTTAAATATA-AT
* *
2233325 TTAAAATTT--ATATAAT
1 ATAATATTTAAATATAAT
*
2233341 ATAA-ATTATAAATTATTAAA
1 ATAATATT-TAAA-TA-TAAT
* * *
2233361 AT-TTATTTAAATTTAAA
1 ATAATATTTAAATATAAT
*
2233378 AT-AT-TTTAATTATAAT
1 ATAATATTTAAATATAAT
*
2233394 ATAATATATAAATATAAT
1 ATAATATTTAAATATAAT
**
2233412 ATAAATACATAAATATAAT
1 AT-AATATTTAAATATAAT
2233431 A
1 A
2233432 ATTTTTCACC
Statistics
Matches: 112, Mismatches: 17, Indels: 31
0.70 0.11 0.19
Matches are distributed among these distances:
15 3 0.03
16 17 0.15
17 21 0.19
18 21 0.19
19 29 0.26
20 15 0.13
21 6 0.05
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATATTTAAATATAAT
Found at i:2233313 original size:24 final size:23
Alignment explanation
Indices: 2233286--2233330 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
2233276 TAAATATAAT
2233286 TATTTAAATATAATATATAAAAAA
1 TATTTAAATAT-ATATATAAAAAA
*
2233310 TATTTAAATATATATTTAAAA
1 TATTTAAATATATATATAAAA
2233331 TTTATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TATTTAAATATATATATAAAAAA
Found at i:2233337 original size:13 final size:12
Alignment explanation
Indices: 2233274--2233329 Score: 60
Period size: 12 Copynumber: 4.5 Consensus size: 12
2233264 TTTTAATAAT
2233274 TTTAAATATAATTA
1 TTTAAATAT-A-TA
2233288 TTTAAATATAATA
1 TTTAAATAT-ATA
* *
2233301 TATAAA-AAATA
1 TTTAAATATATA
2233312 TTTAAATATATA
1 TTTAAATATATA
2233324 TTTAAA
1 TTTAAA
2233330 ATTTATATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 8 0.22
12 11 0.30
13 7 0.19
14 11 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TTTAAATATATA
Found at i:2233398 original size:5 final size:5
Alignment explanation
Indices: 2233388--2233431 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
2233378 ATATTTTAAT
2233388 TATAA TATAA TAT-A TA-AA TATAA TATAA -ATACA TA-AA TATAA TA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA-A TATAA TATAA TA
2233432 ATTTTTCACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
4 12 0.35
5 21 0.62
6 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (5 bp):
TATAA
Found at i:2233431 original size:13 final size:14
Alignment explanation
Indices: 2233391--2233432 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
2233381 TTTTAATTAT
2233391 AATATAATAT-ATA
1 AATATAATATAATA
2233404 AATATAATATAAATA
1 AATATAATAT-AATA
*
2233419 CATA-AATATAATA
1 AATATAATATAATA
2233432 A
1 A
2233433 TTTTTCACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 14 0.56
14 5 0.20
15 6 0.24
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AATATAATATAATA
Found at i:2233608 original size:10 final size:10
Alignment explanation
Indices: 2233593--2233647 Score: 67
Period size: 10 Copynumber: 5.6 Consensus size: 10
2233583 TATTTTAATT
2233593 TTTATATTAA
1 TTTATATTAA
2233603 TTTATATTAA
1 TTTATATTAA
*
2233613 -TTACATTAA
1 TTTATATTAA
* *
2233622 TTCATGTTAA
1 TTTATATTAA
*
2233632 TATATATTAA
1 TTTATATTAA
2233642 TTTATA
1 TTTATA
2233648 ACCGTTTGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
9 8 0.22
10 28 0.78
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (10 bp):
TTTATATTAA
Found at i:2237372 original size:6 final size:6
Alignment explanation
Indices: 2237355--2237398 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
2237345 ATGACCCAGT
*
2237355 ACAAAA AAAAAA ACAAAA ACAAAA ACAAACA A-ACAAA ACAAAA A
1 ACAAAA ACAAAA ACAAAA ACAAAA ACAAA-A ACA-AAA ACAAAA A
2237399 AAGAACAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAA
Found at i:2237397 original size:24 final size:24
Alignment explanation
Indices: 2237355--2237406 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2237345 ATGACCCAGT
2237355 ACAAAAAAAAAAACAAAAACAAA-A
1 ACAAAAAAAAAAACAAAAA-AAAGA
*
2237379 ACAAACAAACAAAAC-AAAAAAAGA
1 ACAAA-AAAAAAAACAAAAAAAAGA
2237403 ACAA
1 ACAA
2237407 GGAAAATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 3 0.12
24 14 0.56
25 8 0.32
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (24 bp):
ACAAAAAAAAAAACAAAAAAAAGA
Found at i:2237405 original size:20 final size:20
Alignment explanation
Indices: 2237357--2237406 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
2237347 GACCCAGTAC
2237357 AAAAAAAA-AAACAAAAACA
1 AAAAAAAACAAACAAAAACA
*
2237376 AAAACAAACAAAC-AAAACA
1 AAAAAAAACAAACAAAAACA
2237395 AAAAAAGAACAA
1 AAAAAA-AACAA
2237407 GGAAAATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (20 bp):
AAAAAAAACAAACAAAAACA
Found at i:2243474 original size:26 final size:25
Alignment explanation
Indices: 2243413--2243475 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
2243403 GATTTGATCT
*
2243413 AATATAATTTA-TATTTTTAATTTA
1 AATATAATTTATTATTTTTAATATA
* *
2243437 AATTTAAATTATTATTTATTAATATA
1 AATATAATTTATTATTT-TTAATATA
*
2243463 AATATATTTTATT
1 AATATAATTTATT
2243476 TAAATTTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
24 9 0.29
25 5 0.16
26 17 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
AATATAATTTATTATTTTTAATATA
Found at i:2243480 original size:41 final size:42
Alignment explanation
Indices: 2243412--2243493 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 42
2243402 TGATTTGATC
*
2243412 TAATATAATTTATATTTTTAATTTAAATTTAAATTATTATTTAT
1 TAATATAATATATATTTTTAATTTAAATTT-AATTA-TATTTAT
2243456 TAATATAA-ATATA-TTTT-ATTTAAATTTAATTATATTTA
1 TAATATAATATATATTTTTAATTTAAATTTAATTATATTTA
2243494 ATATTTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
39 6 0.16
40 5 0.14
41 10 0.27
42 4 0.11
43 4 0.11
44 8 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (42 bp):
TAATATAATATATATTTTTAATTTAAATTTAATTATATTTAT
Found at i:2244734 original size:17 final size:17
Alignment explanation
Indices: 2244683--2244737 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
2244673 AAATTTAGAT
2244683 AAAT-ATATAATATATTAA
1 AAATAATATAA-ATA-TAA
* *
2244701 ATATAAT-TATAACATAA
1 AAATAATATA-AATATAA
2244718 AAATAATATAAATATAA
1 AAATAATATAAATATAA
2244735 AAA
1 AAA
2244738 ATATTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 18 0.60
18 9 0.30
19 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAATATAAATATAA
Found at i:2245458 original size:11 final size:11
Alignment explanation
Indices: 2245444--2245480 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
2245434 TTTGAATCGA
*
2245444 ATTTTATTTTT
1 ATTTAATTTTT
2245455 ATTTAATTTTT
1 ATTTAATTTTT
*
2245466 AATTAATTTTT
1 ATTTAATTTTT
2245477 ATTT
1 ATTT
2245481 TTATAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTAATTTTT
Found at i:2246351 original size:98 final size:99
Alignment explanation
Indices: 2246244--2246454 Score: 259
Period size: 99 Copynumber: 2.1 Consensus size: 99
2246234 ATTGAATATC
* * *
2246244 TTATTAATAATAAAATAAATTTATAA-TAATAATTTTAAAATATAACAAA-TACTTATAACTATT
1 TTATTAATAATAAAAGAAATTTATAATTAATAATTTAAAAAAAT-ACAAAGTACTTATAACTATT
**
2246307 TTTGTCAATTCAA-AAACT-TTTTCATATTCATACTT
65 TTCATCAATTCAATAAA-TATTTT-ATATTCATACTT
* * * *
2246342 TTATTAATAATAAAAGATATTTATAATTGATAATTTAAAAAAATACAAAGTATTTATAATTATTT
1 TTATTAATAATAAAAGAAATTTATAATTAATAATTTAAAAAAATACAAAGTACTTATAACTATTT
*
2246407 TCATCAATTCAATAAATATTTTATATTTATACTT
66 TCATCAATTCAATAAATATTTTATATTCATACTT
* *
2246441 TTATAAATTATAAA
1 TTATTAATAATAAA
2246455 TTATTAATAG
Statistics
Matches: 97, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
98 29 0.30
99 61 0.63
100 7 0.07
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (99 bp):
TTATTAATAATAAAAGAAATTTATAATTAATAATTTAAAAAAATACAAAGTACTTATAACTATTT
TCATCAATTCAATAAATATTTTATATTCATACTT
Found at i:2246825 original size:21 final size:20
Alignment explanation
Indices: 2246790--2246831 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2246780 TATTTAAGGT
*
2246790 ATAAAAAATTAAAAAATAAA
1 ATAAAAAAATAAAAAATAAA
*
2246810 ATAAAATAAATAAAAACTAAA
1 ATAAAA-AAATAAAAAATAAA
2246831 A
1 A
2246832 AAATTATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (20 bp):
ATAAAAAAATAAAAAATAAA
Found at i:2252855 original size:3 final size:3
Alignment explanation
Indices: 2252836--2252885 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
2252826 GAAATCTGAT
*
2252836 GAA GAT GAA GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2252883 GAA
1 GAA
2252886 AAATGTACAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:2257436 original size:2 final size:2
Alignment explanation
Indices: 2257429--2257469 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
2257419 GAGGCTAACC
2257429 AT AT AT AT AT AT AT AT AT AT A- AT A- AT AT AT A- AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2257467 AT A
1 AT A
2257470 ACAAGTTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 4 0.11
2 31 0.89
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2257470 original size:10 final size:11
Alignment explanation
Indices: 2257429--2257470 Score: 63
Period size: 10 Copynumber: 4.1 Consensus size: 11
2257419 GAGGCTAACC
2257429 ATATATATAT-
1 ATATATATATA
2257439 ATATATATATA
1 ATATATATATA
2257450 ATA-ATATATA
1 ATATATATATA
2257460 ATATA-ATATA
1 ATATATATATA
2257470 A
1 A
2257471 CAAGTTACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 26 0.87
11 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATATATATATA
Found at i:2258289 original size:219 final size:220
Alignment explanation
Indices: 2257909--2258348 Score: 828
Period size: 219 Copynumber: 2.0 Consensus size: 220
2257899 TATTTATCGA
2257909 AAGTTTTCAAATTTTATATTTAAAAATCTTATGAATTCACTTAATCTTCAAATATATAACAAATT
1 AAGTTTTCAAATTTTATATTTAAAAATCTTATGAATTCACTTAATCTTCAAATATATAACAAATT
2257974 TTAAATTAAACAAAGTTTTTCTCTATTAAATCCCAAATTCTATAGAAAACCTATATAATTAAAAT
66 TTAAATTAAACAAAGTTTTTCTCTATTAAATCCCAAATTCTATAGAAAACCTATATAATTAAAAT
2258039 TCAAAATCGCTTAAAAAAAATATACTTAACAAATTTTATTCTAAATATAGTACTACCCTATAATA
131 TCAAAATCGCTTAAAAAAAATATACTTAACAAATTTTATTCTAAATATAGTACTACCCTATAATA
* * *
2258104 TATGTGTGTGTATATATATATATAT
196 TATGTATATATATATATATATATAT
2258129 AAGTTTTCAAATTTTATATTTAAAAATCTTATGAATTCACTTAATCTTC-AATATATAACAAATT
1 AAGTTTTCAAATTTTATATTTAAAAATCTTATGAATTCACTTAATCTTCAAATATATAACAAATT
* *
2258193 TTAAATTAAACAAAGTTTTTTTCTATTAAATCTCAAATTCTATAGAAAACCTATATAATTAAAAT
66 TTAAATTAAACAAAGTTTTTCTCTATTAAATCCCAAATTCTATAGAAAACCTATATAATTAAAAT
2258258 TCAAAATCGCTTAAAAAAAATATACTTAACAAATTTTATTCTAAATATAGTACTACCCTATAATA
131 TCAAAATCGCTTAAAAAAAATATACTTAACAAATTTTATTCTAAATATAGTACTACCCTATAATA
2258323 TATGTATATATATATATATATATAT
196 TATGTATATATATATATATATATAT
2258348 A
1 A
2258349 TATAAATATA
Statistics
Matches: 215, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
219 166 0.77
220 49 0.23
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (220 bp):
AAGTTTTCAAATTTTATATTTAAAAATCTTATGAATTCACTTAATCTTCAAATATATAACAAATT
TTAAATTAAACAAAGTTTTTCTCTATTAAATCCCAAATTCTATAGAAAACCTATATAATTAAAAT
TCAAAATCGCTTAAAAAAAATATACTTAACAAATTTTATTCTAAATATAGTACTACCCTATAATA
TATGTATATATATATATATATATAT
Found at i:2258332 original size:2 final size:2
Alignment explanation
Indices: 2258316--2258358 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
2258306 AGTACTACCC
* *
2258316 TA TA -A TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2258357 TA
1 TA
2258359 GTACTACCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2258360 original size:52 final size:52
Alignment explanation
Indices: 2258299--2258402 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
2258289 AATTTTATTC
2258299 TAAATATAGTACTACCCTATAATATATGTATATATATATATATATATATATA
1 TAAATATAGTACTACCCTATAATATATGTATATATATATATATATATATATA
* * *
2258351 TAAATATAGTACTACCCTATAATATATGTGTGTGTATATATATATATATATA
1 TAAATATAGTACTACCCTATAATATATGTATATATATATATATATATATATA
2258403 AGTTTTCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (52 bp):
TAAATATAGTACTACCCTATAATATATGTATATATATATATATATATATATA
Found at i:2258438 original size:273 final size:272
Alignment explanation
Indices: 2258080--2258632 Score: 1027
Period size: 274 Copynumber: 2.0 Consensus size: 272
2258070 AATTTTATTC
2258080 TAAATATAGTACTACCCTATAATATATGTGTGTGTATATATATATATATAAGTTTTCAAATTTTA
1 TAAATATAGTACTACCCTATAATATATGTGTGTGTATATATATATATATAAGTTTTCAAATTTTA
2258145 TATTTAAAAATCTTATGAATTCACTTAATCTTC-AATATATAACAAATTTTAAATTAAACAAAGT
66 TATTTAAAAATCTTATGAATTCACTTAATCTTCAAATATATAACAAATTTTAAATTAAACAAAGT
* *
2258209 TTTTTTCTATTAAATCTCAAATTCTATAGAAAACCTATATAATTAAAATTCAAAATCGCTTAAAA
131 TTTTCTCTATTAAATCCCAAATTCTATAGAAAACCTATATAATTAAAATTCAAAATCGCTTAAAA
2258274 AAAATATACTTAACAAATTTTATTCTAAATATAGTACTACCCTATAATATATGTATATATATATA
196 AAAATATACTTAACAAATTTTATTCTAAATATAGTACTACCCTATAATATATGTATATATATATA
2258339 TATATATATATA
261 TATATATATATA
2258351 TAAATATAGTACTACCCTATAATATATGTGTGTGTATATATATATATATATAAGTTTTCAAATTT
1 TAAATATAGTACTACCCTATAATATATGTGTGTG--TATATATATATATATAAGTTTTCAAATTT
2258416 TATATTTAAAAATCTTATGAATTCACTTAATCTTCAAATATATAACAAATTTTAAATTAAACAAA
64 TATATTTAAAAATCTTATGAATTCACTTAATCTTCAAATATATAACAAATTTTAAATTAAACAAA
2258481 GTTTTTCTCTATTAAATCCCAAATTCTATAGAAAACCTATATAATTAAAATTCAAAATCGCTTAA
129 GTTTTTCTCTATTAAATCCCAAATTCTATAGAAAACCTATATAATTAAAATTCAAAATCGCTTAA
* * *
2258546 AAAAAATATACTTAACAAATTTTATTCTAAATATAGTACTACCCTATAATATATGTGTGTGTATA
194 AAAAAATATACTTAACAAATTTTATTCTAAATATAGTACTACCCTATAATATATGTATATATATA
2258611 TATATATATATATA
259 TATATATATATATA
*
2258625 TATATATA
1 TAAATATA
2258633 TATATCACAA
Statistics
Matches: 273, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
271 34 0.12
273 64 0.23
274 175 0.64
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (272 bp):
TAAATATAGTACTACCCTATAATATATGTGTGTGTATATATATATATATAAGTTTTCAAATTTTA
TATTTAAAAATCTTATGAATTCACTTAATCTTCAAATATATAACAAATTTTAAATTAAACAAAGT
TTTTCTCTATTAAATCCCAAATTCTATAGAAAACCTATATAATTAAAATTCAAAATCGCTTAAAA
AAAATATACTTAACAAATTTTATTCTAAATATAGTACTACCCTATAATATATGTATATATATATA
TATATATATATA
Found at i:2258612 original size:2 final size:2
Alignment explanation
Indices: 2258607--2258637 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2258597 TATGTGTGTG
2258607 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2258638 CACAAGGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2259895 original size:2 final size:2
Alignment explanation
Indices: 2259888--2259916 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2259878 TATGAATACA
2259888 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
2259917 AAAGAAGAAA
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:2260247 original size:2 final size:2
Alignment explanation
Indices: 2260240--2260265 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2260230 ATTCTTGGCA
2260240 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2260266 TCCACAACGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2260623 original size:25 final size:27
Alignment explanation
Indices: 2260566--2260624 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
2260556 AAGGGAGAAA
2260566 TTTTTTTATGAAAAAATAAAAGTTGAT
1 TTTTTTTATGAAAAAATAAAAGTTGAT
* **
2260593 TGTTTTTATGAATCAA-AAAA-TTGAT
1 TTTTTTTATGAAAAAATAAAAGTTGAT
2260618 TTTTTTT
1 TTTTTTT
2260625 TAAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 11 0.39
26 4 0.14
27 13 0.46
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (27 bp):
TTTTTTTATGAAAAAATAAAAGTTGAT
Found at i:2263296 original size:17 final size:17
Alignment explanation
Indices: 2263276--2263312 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2263266 ATAAATATAA
2263276 AATATAAAAATATATTT
1 AATATAAAAATATATTT
* *
2263293 AATATATAAATTTATTT
1 AATATAAAAATATATTT
2263310 AAT
1 AAT
2263313 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATAAAAATATATTT
Found at i:2263339 original size:18 final size:18
Alignment explanation
Indices: 2263316--2263350 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2263306 ATTTAATTTT
2263316 TTTAAAAAATTATATATA
1 TTTAAAAAATTATATATA
*
2263334 TTTAAATAATTATATAT
1 TTTAAAAAATTATATAT
2263351 CTATATATAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAAAAATTATATATA
Found at i:2270148 original size:2 final size:2
Alignment explanation
Indices: 2270141--2270195 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
2270131 TGGCATTCTT
2270141 TC TC TC TC TC TC 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 TC TC TC TC TC TC
2270183 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
2270196 TTATCTTCCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2271494 original size:18 final size:18
Alignment explanation
Indices: 2271456--2271503 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
2271446 AATTTAAATT
2271456 AATATATAAAATTGATTATA
1 AATA-ATAAAATT-ATTATA
*
2271476 ATTAAATAAAATT-TTATA
1 AAT-AATAAAATTATTATA
2271494 AATAATAAAA
1 AATAATAAAA
2271504 ACTTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 7 0.28
18 7 0.28
20 10 0.40
21 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AATAATAAAATTATTATA
Found at i:2271664 original size:25 final size:25
Alignment explanation
Indices: 2271631--2271680 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2271621 GAATTTAAAA
*
2271631 TTATTTTTTCAAAATT-ATATTTATT
1 TTATATTTTC-AAATTAATATTTATT
*
2271656 TTATATTTTCAAGTTAATATTTATT
1 TTATATTTTCAAATTAATATTTATT
2271681 AAGACAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (25 bp):
TTATATTTTCAAATTAATATTTATT
Found at i:2274962 original size:30 final size:29
Alignment explanation
Indices: 2274898--2274972 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
2274888 AGTTTTTTTA
2274898 AAAATAAA--ATTATATTTTTATTATGTC
1 AAAATAAATTATTATATTTTTATTATGTC
2274925 AAAATAAATTATTATATTTTTATT-TGTATC
1 AAAATAAATTATTATATTTTTATTATG--TC
*
2274955 TAAATAAATT-TT-TATTTT
1 AAAATAAATTATTATATTTT
2274973 AAATAAATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
27 8 0.19
28 8 0.19
29 16 0.37
30 11 0.26
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (29 bp):
AAAATAAATTATTATATTTTTATTATGTC
Found at i:2275054 original size:29 final size:29
Alignment explanation
Indices: 2275022--2275105 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
2275012 AAATTAATGT
2275022 TTATTTAAGTATAAATTAAAAATAAAAAC
1 TTATTTAAGTATAAATTAAAAATAAAAAC
* * * *
2275051 TTATTTGA-TATAAACTAAAAATTTAAAAT
1 TTATTTAAGTATAAATTAAAAA-TAAAAAC
*
2275080 TTATTTAAGCAT-AATTAAAATATAAA
1 TTATTTAAGTATAAATTAAAA-ATAAA
2275106 GATTTATCTA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
28 12 0.27
29 29 0.66
30 3 0.07
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (29 bp):
TTATTTAAGTATAAATTAAAAATAAAAAC
Found at i:2276371 original size:21 final size:21
Alignment explanation
Indices: 2276347--2276386 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2276337 ATTAATATTT
*
2276347 TTAAAATTTAAATTTTAATCA
1 TTAAAATTAAAATTTTAATCA
2276368 TTAAAATTAAAATTTTAAT
1 TTAAAATTAAAATTTTAAT
2276387 ATTTTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAAAATTAAAATTTTAATCA
Found at i:2276950 original size:20 final size:18
Alignment explanation
Indices: 2276908--2276950 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2276898 AGGCCAAACC
*
2276908 TATTTTATATATTTTTTT
1 TATTTTAAATATTTTTTT
*
2276926 CATTTTAAATATGTTATTTT
1 TATTTTAAATAT-TT-TTTT
2276946 TATTT
1 TATTT
2276951 AATCTTTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 10 0.50
19 2 0.10
20 8 0.40
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (18 bp):
TATTTTAAATATTTTTTT
Found at i:2277159 original size:22 final size:23
Alignment explanation
Indices: 2277125--2277168 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2277115 TTCAAGTGTG
2277125 AATAAAGTCTAAC-TCATTTTTTA
1 AATAAAGTCTAACAT-ATTTTTTA
2277148 AATAAA-TCTAACATATTTTTT
1 AATAAAGTCTAACATATTTTTT
2277169 GAATCTAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.45
Consensus pattern (23 bp):
AATAAAGTCTAACATATTTTTTA
Found at i:2278519 original size:20 final size:20
Alignment explanation
Indices: 2278490--2278548 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 20
2278480 TTATCATAAT
*
2278490 TTTATTTAAAATATTATATA
1 TTTATATAAAATATTATATA
*
2278510 TTTATAT-AAATTTTA-ATA
1 TTTATATAAAATATTATATA
* *
2278528 TATTA-ATAAATTATTTTATA
1 T-TTATATAAAATATTATATA
2278548 T
1 T
2278549 AAATTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 6 0.19
19 15 0.48
20 10 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATATAAAATATTATATA
Found at i:2278549 original size:20 final size:20
Alignment explanation
Indices: 2278503--2278568 Score: 58
Period size: 20 Copynumber: 3.7 Consensus size: 20
2278493 ATTTAAAATA
2278503 TTATATATTTATATAAATTT
1 TTATATATTTATATAAATTT
*
2278523 TAATATA-TTA-ATAAA---
1 TTATATATTTATATAAATTT
2278538 -T-TAT-TTTATATAAATTT
1 TTATATATTTATATAAATTT
*
2278555 TAATATATTTATAT
1 TTATATATTTATAT
2278569 CATATTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 16
0.65 0.06 0.30
Matches are distributed among these distances:
13 6 0.17
14 5 0.14
18 5 0.14
19 6 0.17
20 13 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATATATTTATATAAATTT
Found at i:2278575 original size:32 final size:32
Alignment explanation
Indices: 2278499--2278575 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
2278489 TTTTATTTAA
*
2278499 AATATTATATATTTATATAAATTTTAATATATT
1 AATATAATAT-TTTATATAAATTTTAATATATT
2278532 AATA-AATTATTTTATATAAATTTTAATATATT
1 AATATAA-TATTTTATATAAATTTTAATATATT
* *
2278564 TATATCATATTT
1 AATATAATATTT
2278576 ATTTTATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 31 0.79
33 8 0.21
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (32 bp):
AATATAATATTTTATATAAATTTTAATATATT
Found at i:2286865 original size:13 final size:13
Alignment explanation
Indices: 2286847--2286875 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2286837 TTTTCTCCCA
2286847 TTGGTTATTAAAC
1 TTGGTTATTAAAC
2286860 TTGGTTATTAAAC
1 TTGGTTATTAAAC
2286873 TTG
1 TTG
2286876 ATAACCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (13 bp):
TTGGTTATTAAAC
Found at i:2290360 original size:18 final size:19
Alignment explanation
Indices: 2290325--2290376 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2290315 TTAAATTAAT
*
2290325 ATATAAAATTGATTATAATTA
1 ATATAAAATT--TTATAAATA
2290346 A-ATAAAATTTTATAAATA
1 ATATAAAATTTTATAAATA
*
2290364 ATAAAAAATTTTA
1 ATATAAAATTTTA
2290377 ATTAAGTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.32
19 10 0.36
20 8 0.29
21 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATATAAAATTTTATAAATA
Found at i:2292954 original size:19 final size:17
Alignment explanation
Indices: 2292909--2292959 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
2292899 CTTAATTACT
*
2292909 TTTAAAT-ATAATAGTAA
1 TTTAAATAATAA-ATTAA
*
2292926 TTTAATTAATCAAATTAA
1 TTTAAATAAT-AAATTAA
2292944 TATTAAATAATAAATT
1 T-TTAAATAATAAATT
2292960 TAAGTCATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 6 0.21
18 12 0.43
19 10 0.36
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTAAATAATAAATTAA
Found at i:2293709 original size:15 final size:17
Alignment explanation
Indices: 2293674--2293708 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2293664 TGAAAGTAAT
2293674 TATTAAATATAAATATA
1 TATTAAATATAAATATA
*
2293691 TATTTAATATAAATATA
1 TATTAAATATAAATATA
2293708 T
1 T
2293709 TAAAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTAAATATAAATATA
Found at i:2294150 original size:27 final size:27
Alignment explanation
Indices: 2294119--2294192 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
2294109 TTTAATTAAA
*
2294119 TAAAATTATAATTATTAAATTT-TATTT
1 TAAAATT-TAATTATTAAATTTAAATTT
* *
2294146 TAAAATATTTAATAAATAAATTTAAATTT
1 T-AAA-ATTTAATTATTAAATTTAAATTT
2294175 T-AAATTTAATTATATAAA
1 TAAAATTTAATTAT-TAAA
2294193 AAATTTATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
26 8 0.21
27 7 0.18
28 15 0.39
29 8 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TAAAATTTAATTATTAAATTTAAATTT
Found at i:2294565 original size:11 final size:10
Alignment explanation
Indices: 2294529--2294655 Score: 51
Period size: 9 Copynumber: 13.4 Consensus size: 10
2294519 ACATAATATC
2294529 TATA-AAAAA
1 TATATAAAAA
*
2294538 TATTTAAAACA
1 TATATAAAA-A
2294549 TAATATAAAAA
1 T-ATATAAAAA
* *
2294560 TGATATATATA
1 T-ATATAAAAA
*
2294571 TA-ATACAAA
1 TATATAAAAA
* * *
2294580 TACATATACA
1 TATATAAAAA
2294590 TATA-AAAAA
1 TATATAAAAA
*
2294599 TATAT-GAAA
1 TATATAAAAA
2294608 TA-A-AATAAA
1 TATATAA-AAA
*
2294617 T-TAT--TAA
1 TATATAAAAA
2294624 TATATAAAAA
1 TATATAAAAA
*
2294634 AATAT-AAAA
1 TATATAAAAA
2294643 -ATATAAAAA
1 TATATAAAAA
2294652 TATA
1 TATA
2294656 AAATTTTAAA
Statistics
Matches: 87, Mismatches: 17, Indels: 27
0.66 0.13 0.21
Matches are distributed among these distances:
7 3 0.03
8 8 0.09
9 35 0.40
10 22 0.25
11 12 0.14
12 7 0.08
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (10 bp):
TATATAAAAA
Found at i:2294644 original size:8 final size:8
Alignment explanation
Indices: 2294631--2294658 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2294621 TAATATATAA
2294631 AAAAATAT
1 AAAAATAT
2294639 AAAAATAT
1 AAAAATAT
2294647 AAAAATAT
1 AAAAATAT
2294655 AAAA
1 AAAA
2294659 TTTTAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAT
Found at i:2294648 original size:18 final size:18
Alignment explanation
Indices: 2294589--2294651 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
2294579 ATACATATAC
*
2294589 ATAT-AAAAAATATATGAA
1 ATATAAAAAAATATA-AAA
* * *
2294607 ATA-AAATAAATTATTAAT
1 ATATAAA-AAAATATAAAA
2294625 ATATAAAAAAATATAAAA
1 ATATAAAAAAATATAAAA
2294643 ATATAAAAA
1 ATATAAAAA
2294652 TATAAAATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 26 0.74
19 9 0.26
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
ATATAAAAAAATATAAAA
Found at i:2295980 original size:10 final size:10
Alignment explanation
Indices: 2295965--2296001 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
2295955 TACACATAAC
2295965 ATAAATATAT
1 ATAAATATAT
2295975 ATAAATATATAT
1 AT-AA-ATATAT
2295987 ATAAATATAT
1 ATAAATATAT
2295997 ATAAA
1 ATAAA
2296002 ATAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 13 0.52
11 4 0.16
12 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAAATATAT
Found at i:2295986 original size:12 final size:12
Alignment explanation
Indices: 2295969--2296004 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
2295959 CATAACATAA
2295969 ATATATATAAAT
1 ATATATATAAAT
2295981 ATATATATAAAT
1 ATATATATAAAT
2295993 ATATATA-AAAT
1 ATATATATAAAT
2296004 A
1 A
2296005 AAATAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.21
12 19 0.79
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATATATAAAT
Found at i:2296079 original size:23 final size:23
Alignment explanation
Indices: 2296053--2296096 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2296043 TACAAACTTT
2296053 TTCTTTATTTATTTATTTTTTCC
1 TTCTTTATTTATTTATTTTTTCC
* * *
2296076 TTCTTTCTTTCTTTGTTTTTT
1 TTCTTTATTTATTTATTTTTT
2296097 TCACTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.77
Consensus pattern (23 bp):
TTCTTTATTTATTTATTTTTTCC
Found at i:2296520 original size:27 final size:29
Alignment explanation
Indices: 2296490--2296544 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
2296480 TATAAATATT
2296490 TTTTAA-AAAT-T-ATATTTAATATTTAAA
1 TTTTAATAAATATAATATTTAAT-TTTAAA
*
2296517 TTTTAATAAATATAATTTTTAATTTTAA
1 TTTTAATAAATATAATATTTAATTTTAA
2296545 TATATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 4 0.17
29 6 0.25
30 8 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTTAATAAATATAATATTTAATTTTAAA
Found at i:2296559 original size:22 final size:21
Alignment explanation
Indices: 2296506--2296556 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
2296496 AAATTATATT
*
2296506 TAATATTTAAATTTTAATAAATA
1 TAAT-TTTTAATTTTAAT-AATA
2296529 TAATTTTTAATTTTAAT-ATA
1 TAATTTTTAATTTTAATAATA
2296549 TAATTTTT
1 TAATTTTT
2296557 TTATGTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 11 0.41
22 12 0.44
23 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATTTTTAATTTTAATAATA
Found at i:2298429 original size:43 final size:42
Alignment explanation
Indices: 2298337--2298455 Score: 102
Period size: 43 Copynumber: 2.8 Consensus size: 42
2298327 CATAATTTAA
*
2298337 TTTATTTAATTATTTAAATTAATTAAATTAAATTAATTATTAT
1 TTTA-TTAATTATTTAAATAAATTAAATTAAATTAATTATTAT
* *
2298380 TATTATTAATTA-TTAAATCAAATTAGATT-AATTATTTTAATTAT
1 T-TTATTAATTATTTAAAT-AAATTAAATTAAATTA-ATT-ATTAT
** *
2298424 TTTATT--TTATTTAGAATCGATTAAGTTAAATT
1 TTTATTAATTATTTA-AATAAATTAAATTAAATT
2298456 TTAATTTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
41 3 0.05
42 20 0.32
43 30 0.48
44 9 0.15
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (42 bp):
TTTATTAATTATTTAAATAAATTAAATTAAATTAATTATTAT
Found at i:2304362 original size:23 final size:22
Alignment explanation
Indices: 2304335--2304395 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
2304325 ATCTGTTAAA
2304335 TTTATTTTAATTTAATTAAAAT
1 TTTATTTTAATTTAATTAAAAT
*
2304357 TATTA-TTTAA--TAATAAAAAAT
1 T-TTATTTTAATTTAAT-TAAAAT
*
2304378 TTTATTTAAATTTAATTA
1 TTTATTTTAATTTAATTA
2304396 TAAAAATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
20 7 0.23
21 10 0.32
22 7 0.23
23 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTATTTTAATTTAATTAAAAT
Found at i:2304592 original size:20 final size:20
Alignment explanation
Indices: 2304569--2304606 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2304559 TAATAAATTT
*
2304569 ATTTAATTGATTAAAAATCA
1 ATTTAACTGATTAAAAATCA
2304589 ATTTAACTGATTAAAAAT
1 ATTTAACTGATTAAAAAT
2304607 TAAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
ATTTAACTGATTAAAAATCA
Done.