Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 28 of 31
Found at i:5533289 original size:20 final size:20
Alignment explanation
Indices: 5533266--5533321 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 20
5533256 TTTTATATTT
*
5533266 TTAATTATTTTTAATAAAAA
1 TTAATTATTTTAAATAAAAA
*
5533286 TTAAATT-TTATTAAATAAAAT
1 TT-AATTATT-TTAAATAAAAA
* *
5533307 TTATTTATTTAAAAT
1 TTAATTATTTTAAAT
5533322 TACATTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAATTATTTTAAATAAAAA
Found at i:5533524 original size:23 final size:22
Alignment explanation
Indices: 5533470--5533529 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
5533460 ATTTACTTTA
5533470 AATATAAAAAATAAAAAAATAT
1 AATATAAAAAATAAAAAAATAT
* * * **
5533492 GACATCAAAAATATTTAAAATAT
1 AATATAAAAAATA-AAAAAATAT
5533515 AATATAAAAAATAAA
1 AATATAAAAAATAAA
5533530 TATGACACGA
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (22 bp):
AATATAAAAAATAAAAAAATAT
Found at i:5533556 original size:13 final size:13
Alignment explanation
Indices: 5533540--5533573 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
5533530 TATGACACGA
*
5533540 ATATATAATATAT
1 ATATATAAAATAT
5533553 ATATATAAAATAT
1 ATATATAAAATAT
5533566 -TATATAAA
1 ATATATAAA
5533574 TTTATAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATATAAAATAT
Found at i:5533579 original size:20 final size:20
Alignment explanation
Indices: 5533542--5533580 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5533532 TGACACGAAT
*
5533542 ATATAATATATATATATAAA
1 ATATAATATAAATATATAAA
* *
5533562 ATATTATATAAATTTATAA
1 ATATAATATAAATATATAA
5533581 TACTTTAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATAATATAAATATATAAA
Found at i:5533671 original size:12 final size:12
Alignment explanation
Indices: 5533654--5533696 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
5533644 CACTTTCCTT
5533654 TTCTTTCTTTTC
1 TTCTTTCTTTTC
5533666 TTCTTTCTTTT-
1 TTCTTTCTTTTC
* *
5533677 TTTTTTCTTTCC
1 TTCTTTCTTTTC
*
5533689 ATCTTTCT
1 TTCTTTCT
5533697 CTCTCCATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (12 bp):
TTCTTTCTTTTC
Found at i:5533678 original size:23 final size:23
Alignment explanation
Indices: 5533652--5533696 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5533642 CTCACTTTCC
* *
5533652 TTTTCTTTCTTTTCTTCTTTCTT
1 TTTTCTTTCTTTCCATCTTTCTT
*
5533675 TTTTTTTTCTTTCCATCTTTCT
1 TTTTCTTTCTTTCCATCTTTCT
5533697 CTCTCCATGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTCTTTCTTTCCATCTTTCTT
Found at i:5533868 original size:24 final size:23
Alignment explanation
Indices: 5533830--5533881 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
5533820 TATGAATGAC
*
5533830 ATAAATACATGAATATATCAAAAT
1 ATAAATAAATGAATA-ATCAAAAT
* * *
5533854 ATAAATAAATTAATAATTAACAT
1 ATAAATAAATGAATAATCAAAAT
5533877 ATAAA
1 ATAAA
5533882 AATTTATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (23 bp):
ATAAATAAATGAATAATCAAAAT
Found at i:5537511 original size:2 final size:2
Alignment explanation
Indices: 5537506--5537538 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5537496 GCACCCACAC
*
5537506 AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5537539 AGATTGTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5545090 original size:2 final size:2
Alignment explanation
Indices: 5545083--5545123 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5545073 TTAACACAAT
5545083 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5545124 TTGTAACATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5547106 original size:21 final size:21
Alignment explanation
Indices: 5547067--5547121 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
5547057 ACTTTTAATG
* *
5547067 TAATAAAAAATTATTTAAAT-T
1 TAATATAAAA-TATATAAATAT
*
5547088 TAATTTTAAAATATATAAATAT
1 TAA-TATAAAATATATAAATAT
5547110 TAATATAAAATA
1 TAATATAAAATA
5547122 AAATAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATATAAAATATATAAATAT
Found at i:5547140 original size:10 final size:10
Alignment explanation
Indices: 5547120--5547154 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
5547110 TAATATAAAA
5547120 TAAAATAATTT
1 TAAAAT-ATTT
5547131 TAAAATATTT
1 TAAAATATTT
*
5547141 TAATATATTT
1 TAAAATATTT
5547151 TAAA
1 TAAA
5547155 GAATAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TAAAATATTT
Found at i:5548408 original size:24 final size:24
Alignment explanation
Indices: 5548380--5548430 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
5548370 TTATTTAAAA
5548380 AATATTAAATATTAAAATATTTT-T
1 AATATT-AATATTAAAATATTTTAT
* *
5548404 AATATTAATATTTATATATTTTAT
1 AATATTAATATTAAAATATTTTAT
5548428 AAT
1 AAT
5548431 TAAATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AATATTAATATTAAAATATTTTAT
Found at i:5549266 original size:20 final size:20
Alignment explanation
Indices: 5549241--5549278 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5549231 TAATTATCAA
* *
5549241 TTTAACTTAATTATTTTAAG
1 TTTAACTCAATTAATTTAAG
5549261 TTTAACTCAATTAATTTA
1 TTTAACTCAATTAATTTA
5549279 TGTAATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTAACTCAATTAATTTAAG
Found at i:5550250 original size:18 final size:19
Alignment explanation
Indices: 5550227--5550278 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
5550217 TGATTTGATA
5550227 GTAATTAAAAATAAT-TTT
1 GTAATTAAAAATAATATTT
5550245 GTAATTAAAAA-AATATTT
1 GTAATTAAAAATAATATTT
*
5550263 -TAAGTAAAAAATAATA
1 GTAA-TTAAAAATAATA
5550279 ATAAATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.20
18 20 0.67
19 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.37
Consensus pattern (19 bp):
GTAATTAAAAATAATATTT
Found at i:5550694 original size:46 final size:45
Alignment explanation
Indices: 5550619--5550708 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 45
5550609 TTTTATTTGA
5550619 TTTCATTACTCAAAACAAAATTCCATTGATTTCATAAAACAAAGG
1 TTTCATTACTCAAAACAAAATTCCATTGATTTCATAAAACAAAGG
*
5550664 TTTCATTACTCAAAAACAAAATGT-CTTTGATTTCATAAAACAAAG
1 TTTCATTACTC-AAAACAAAAT-TCCATTGATTTCATAAAACAAAG
5550709 AGAACAAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
45 11 0.26
46 30 0.71
47 1 0.02
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (45 bp):
TTTCATTACTCAAAACAAAATTCCATTGATTTCATAAAACAAAGG
Found at i:5550705 original size:24 final size:24
Alignment explanation
Indices: 5550630--5550707 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 24
5550620 TTCATTACTC
*
5550630 AAAACAAAAT-TCCATTGATTTCAT
1 AAAACAAAATGT-CTTTGATTTCAT
* *
5550654 AAAAC-AAA-G-GTTTCATTACTCA-
1 AAAACAAAATGTCTTTGATT--TCAT
5550676 AAAACAAAATGTCTTTGATTTCAT
1 AAAACAAAATGTCTTTGATTTCAT
5550700 AAAACAAA
1 AAAACAAA
5550708 GAGAACAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
21 5 0.12
22 5 0.12
23 12 0.29
24 14 0.33
25 6 0.14
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.29
Consensus pattern (24 bp):
AAAACAAAATGTCTTTGATTTCAT
Found at i:5551046 original size:11 final size:12
Alignment explanation
Indices: 5551001--5551047 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
5550991 TCTGAATCCG
* *
5551001 ATATCTAGTTAT
1 ATATTTAGTTTT
5551013 ATATTTAGTTTT
1 ATATTTAGTTTT
*
5551025 -TGTTTAGTTTT
1 ATATTTAGTTTT
5551036 ATATTTA-TTTT
1 ATATTTAGTTTT
5551047 A
1 A
5551048 AAAAATTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 15 0.50
12 15 0.50
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (12 bp):
ATATTTAGTTTT
Found at i:5560157 original size:22 final size:22
Alignment explanation
Indices: 5560132--5560173 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5560122 TTAATTATAA
5560132 ATTTACGAATATGTTATCAATC
1 ATTTACGAATATGTTATCAATC
* * *
5560154 ATTTACTATTATTTTATCAA
1 ATTTACGAATATGTTATCAA
5560174 ATGTTTACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.48
Consensus pattern (22 bp):
ATTTACGAATATGTTATCAATC
Found at i:5562452 original size:135 final size:137
Alignment explanation
Indices: 5562235--5562504 Score: 341
Period size: 135 Copynumber: 2.0 Consensus size: 137
5562225 CTTCTTTTCG
* * * *
5562235 ATTTAGAGTAAATACTTTATATTGTAATTAAAAAATTTTAAATTTATGTAGACTTTATTTTTTAA
1 ATTTAAAGTAAAAACTTTATATTGTAATT-AAAAATTTTAAATTTATATAGACTTTATTTTTAAA
* * *
5562300 TATTTAGCTGATTTAAATGTAAATAAAGTAATAAAAATTACATATTTAAATA-AAAAATTTTATT
65 TATTTAGCTCATTTAAATGTAAATAAAGTAATAAAAA-TACATATCTAAATAGAAAAAGTTTATT
5562364 AATTTTCCT
129 AATTTTCCT
* * * *
5562373 ATTTAAAGTAAAAATTTTATATT-TCAATT-AAAA-TTTAATTTTATATGGATTTTATTTTTAAA
1 ATTTAAAGTAAAAACTTTATATTGT-AATTAAAAATTTTAAATTTATATAGACTTTATTTTTAAA
* * * * *
5562435 TGTTTAGTTCATTTAAATTTAAATAAATTAATAAAAATATATATCTAAATAGAAAAAGTTTATTA
65 TATTTAGCTCATTTAAATGTAAATAAAGTAATAAAAATACATATCTAAATAGAAAAAGTTTATTA
5562500 ATTTT
130 ATTTT
5562505 GAAGTCATTT
Statistics
Matches: 114, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
134 12 0.11
135 73 0.64
136 4 0.04
137 1 0.01
138 24 0.21
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (137 bp):
ATTTAAAGTAAAAACTTTATATTGTAATTAAAAATTTTAAATTTATATAGACTTTATTTTTAAAT
ATTTAGCTCATTTAAATGTAAATAAAGTAATAAAAATACATATCTAAATAGAAAAAGTTTATTAA
TTTTCCT
Found at i:5562650 original size:100 final size:103
Alignment explanation
Indices: 5562418--5562657 Score: 281
Period size: 100 Copynumber: 2.3 Consensus size: 103
5562408 TAATTTTATA
* * * *
5562418 TGGATTTTATTTTTAAATGTTTAGTTCATTTAAATTTAAATAAATTAATAAAAATATATATCTAA
1 TGGACTTTATTTTTAAATATTTA-TTAATTTAAA--TAAATAAATTAATAAAAATACATATCTAA
* ** *
5562483 ATAGAAAAAGTTTATTAATTTTGAAGTCATTTAATATCATG
63 ATAGAAAAAGTTTATAAATTTTGAAGTCAGATAATATCACG
* *
5562524 TAGACTTTATTTTTAAATATTTATTAATTTAAATAAA-AAA-TAATAAAATTACATATCTAAATA
1 TGGACTTTATTTTTAAATATTTATTAATTTAAATAAATAAATTAATAAAAATACATATCTAAATA
* ** * *
5562587 -AGCAATTTTTATAAATTTTTAAGT-AGATAATCTCACG
66 GA-AAAAGTTTATAAATTTTGAAGTCAGATAATATCACG
5562624 TGGACTTTATTTTTAAATATTTATTAATTTAAAT
1 TGGACTTTATTTTTAAATATTTATTAATTTAAAT
5562658 TTAAATTTAA
Statistics
Matches: 117, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
100 43 0.37
101 38 0.32
102 3 0.03
103 4 0.03
105 9 0.08
106 20 0.17
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (103 bp):
TGGACTTTATTTTTAAATATTTATTAATTTAAATAAATAAATTAATAAAAATACATATCTAAATA
GAAAAAGTTTATAAATTTTGAAGTCAGATAATATCACG
Found at i:5562681 original size:346 final size:343
Alignment explanation
Indices: 5562310--5563066 Score: 906
Period size: 347 Copynumber: 2.2 Consensus size: 343
5562300 TATTTAGCTG
* ***
5562310 ATTTAAATGTAAATAAAGTAATAAAAATTACATATTTAAATAAAAAATTTTATTAATTTTCCTA-
1 ATTTAAATTTAAATAAAGTAAT-AAAATTACAT-TTTAAATAAAAAATTTTATTAATTTTAAAAT
*
5562374 TTTAAAGTAAAAATTT-TA-TATTTCA-ATT-A-AAATTT-AATTTTATATGGATTTTATTTTTA
64 TTTAAAG--AAAATTTATATTA-TTCACATTCAGAAATTTGAAGTTTATA---ATTTTATTTTTA
*
5562433 AATGTTTAGTTCATTTAAATTTAAATAAATTAATAAAAATATATATCTAAATAGAAAAAGTTTAT
123 AATATTTAGTTCATTTAAATTTAAATAAATTAAT--AAATATAT-TC-AAATAGAAAAAGTTTAT
*
5562498 TAATTTTGAAGTCATTTAATATCATGTAGACTTTATTTTTAAATATTTATTAATTTAAA-T-AA-
184 TAATTTTAAAGTCATTTAATATCATGTAGACTTTATTTTTAAATATTTATTAATTTAAATTAAAT
* * * * * *
5562560 AAAATAATAAAATTACATATCTAAATAAGCAATTTTTATAAATTTTTAAGTAGATAATCTCACGT
249 AAAATAATAAAATCACATATCTAAATAAGAAATTTTTATAAATTTTAAAGTAAATAATATAACGT
*
5562625 GGACTTTATTTTTAAATATTTATTAATTTAA
314 AGACTTTATTTTTAAA-ATTTATTAATTTAA
* * * *
5562656 ATTTAAATTTAAATAAAGAAATAAAATTACATTTTAAATAGGATAACTTTATTAATTTTAAAATT
1 ATTTAAATTTAAATAAAGTAATAAAATTACATTTTAAATA-AAAAATTTTATTAATTTTAAAATT
* * * * ** * *
5562721 TTGAAGGACATTTATATTATTCACTTTCAGTACTTTTGGAGTTTATACTTTTATTTTTAAATATT
65 TTAAAGAAAATTTATATTATTCACATTCAG-AAATTTGAAGTTTATAATTTTATTTTTAAATATT
* * *
5562786 TAGTTTATTTAAATTTAAATAAATTAATATATATATTCAAATAGAGAAAGTTTATTAATTTTAAA
129 TAGTTCATTTAAATTTAAATAAATTAATAAATATATTCAAATAGAAAAAGTTTATTAATTTTAAA
* * **
5562851 TTTATTTAATATCATGTAGGTTTTATTTTTAAATATTTATTAATTTAAATTTAAATAAAATAATA
194 GTCATTTAATATCATGTAGACTTTATTTTTAAATATTTATTAATTTAAA-TTAAATAAAATAATA
* * * *
5562916 AGATCACATATCTAAATAAGAAATTTTTATTAATTTTAAAGTAAATAATATAATGTAGATTTTAT
258 AAATCACATATCTAAATAAGAAATTTTTATAAATTTTAAAGTAAATAATATAACGTAGACTTTAT
5562981 TTTTAAAATTTATTAATTTAA
323 TTTTAAAATTTATTAATTTAA
* * * *
5563002 GTTTAAATTTAAATAAACTAATAAAATTACATTTTAAATAAGATAAA-TTTGTTATTTTTAAAAT
1 ATTTAAATTTAAATAAAGTAATAAAATTACATTTTAAATAA-A-AAATTTTATTAATTTTAAAAT
5563066 T
64 T
5563067 ATATATATAT
Statistics
Matches: 352, Mismatches: 44, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
343 70 0.20
344 15 0.04
345 40 0.11
346 100 0.28
347 116 0.33
349 4 0.01
350 7 0.02
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (343 bp):
ATTTAAATTTAAATAAAGTAATAAAATTACATTTTAAATAAAAAATTTTATTAATTTTAAAATTT
TAAAGAAAATTTATATTATTCACATTCAGAAATTTGAAGTTTATAATTTTATTTTTAAATATTTA
GTTCATTTAAATTTAAATAAATTAATAAATATATTCAAATAGAAAAAGTTTATTAATTTTAAAGT
CATTTAATATCATGTAGACTTTATTTTTAAATATTTATTAATTTAAATTAAATAAAATAATAAAA
TCACATATCTAAATAAGAAATTTTTATAAATTTTAAAGTAAATAATATAACGTAGACTTTATTTT
TAAAATTTATTAATTTAA
Found at i:5562860 original size:343 final size:348
Alignment explanation
Indices: 5562422--5563066 Score: 978
Period size: 347 Copynumber: 1.9 Consensus size: 348
5562412 TTTATATGGA
*
5562422 TTTTATTTTTAAATGTTTAGTTCATTTAAATTTAAATAAATTAATAAAAATATATATCTAAATAG
1 TTTTATTTTTAAATATTTAGTTCATTTAAATTTAAATAAATTAAT-AAAATATATATCTAAATAG
*
5562487 AAAAAGTTTATTAATTTTGAAGTCATTTAATATCATGTAGACTTTATTTTTAAATATTTATTAAT
65 AAAAAGTTTATTAATTTTAAAGTCATTTAATATCATGTAGACTTTATTTTTAAATATTTATTAAT
* * * *
5562552 TTAAA-T-AA-AAAATAATAAAATTACATATCTAAATAAGCAATTTTTATAAATTTTTAAGTAGA
130 TTAAATTAAATAAAATAATAAAATCACATATCTAAATAAGAAATTTTTATAAATTTTAAAGTAAA
* * * *
5562614 TAATCTCACGTGGACTTTATTTTTAAATATTTATTAATTTAAATTTAAATTTAAATAAAGAAATA
195 TAATATAACGTAGACTTTATTTTTAAA-ATTTATTAATTTAAATTTAAATTTAAATAAACAAATA
* *
5562679 AAATTACATTTTAAATAGGATAACTTTATTAATTTTAAAATTTTGAAGGACATTTATATTATTCA
259 AAATTACATTTTAAATAAGATAAATTTATTAATTTTAAAATTTTGAAGGACATTTATATTATTCA
5562744 CTTTCAGTACTTTTGGAGTTTATAC
324 CTTTCAGTACTTTTGGAGTTTATAC
* *
5562769 TTTTATTTTTAAATATTTAGTTTATTTAAATTTAAATAAATTAAT-ATATATAT-TC-AAATAGA
1 TTTTATTTTTAAATATTTAGTTCATTTAAATTTAAATAAATTAATAAAATATATATCTAAATAGA
* * * **
5562831 GAAAGTTTATTAATTTTAAATTTATTTAATATCATGTAGGTTTTATTTTTAAATATTTATTAATT
66 AAAAGTTTATTAATTTTAAAGTCATTTAATATCATGTAGACTTTATTTTTAAATATTTATTAATT
* *
5562896 TAAATTTAAATAAAATAATAAGATCACATATCTAAATAAGAAATTTTTATTAATTTTAAAGTAAA
131 TAAA-TTAAATAAAATAATAAAATCACATATCTAAATAAGAAATTTTTATAAATTTTAAAGTAAA
* * * *
5562961 TAATATAATGTAGATTTTATTTTTAAAATTTATTAATTTAAGTTTAAATTTAAATAAACTAATAA
195 TAATATAACGTAGACTTTATTTTTAAAATTTATTAATTTAAATTTAAATTTAAATAAACAAATAA
* *
5563026 AATTACATTTTAAATAAGATAAATTTGTTATTTTTAAAATT
260 AATTACATTTTAAATAAGATAAATTTATTAATTTTAAAATT
5563067 ATATATATAT
Statistics
Matches: 267, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
343 70 0.26
344 2 0.01
345 8 0.03
346 74 0.28
347 113 0.42
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (348 bp):
TTTTATTTTTAAATATTTAGTTCATTTAAATTTAAATAAATTAATAAAATATATATCTAAATAGA
AAAAGTTTATTAATTTTAAAGTCATTTAATATCATGTAGACTTTATTTTTAAATATTTATTAATT
TAAATTAAATAAAATAATAAAATCACATATCTAAATAAGAAATTTTTATAAATTTTAAAGTAAAT
AATATAACGTAGACTTTATTTTTAAAATTTATTAATTTAAATTTAAATTTAAATAAACAAATAAA
ATTACATTTTAAATAAGATAAATTTATTAATTTTAAAATTTTGAAGGACATTTATATTATTCACT
TTCAGTACTTTTGGAGTTTATAC
Found at i:5562979 original size:104 final size:101
Alignment explanation
Indices: 5562769--5563009 Score: 308
Period size: 104 Copynumber: 2.4 Consensus size: 101
5562759 GAGTTTATAC
* * * *
5562769 TTTTATTTTTAAATATTTAGTTTATTTAAATTTAAATAAATTAATATATATATTCAAATAGAGAA
1 TTTTATTTTTAAATATTTA-TTAATTTAAATTTAAATAAAATAATAGATACATTCAAATAGAGAA
* ** * *
5562834 AGTTTATTAATTTTAAATTTATTTAATATCATGTAGG
65 AGTTTATTAATTTTAAATGTAAATAATATAATGTAGA
5562871 TTTTATTTTTAAATATTTATTAATTTAAATTTAAATAAAATAATAAGATCACATATCTAAATA-A
1 TTTTATTTTTAAATATTTATTAATTTAAATTTAAATAAAATAAT-AGAT-ACAT-TC-AAATAGA
*
5562935 GAAATTTTTATTAATTTTAAA-GTAAATAATATAATGTAGA
62 GAAA-GTTTATTAATTTTAAATGTAAATAATATAATGTAGA
*
5562975 TTTTATTTTTAAA-ATTTATTAATTTAAGTTTAAAT
1 TTTTATTTTTAAATATTTATTAATTTAAATTTAAAT
5563010 TTAAATAAAC
Statistics
Matches: 123, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
101 23 0.19
102 22 0.18
103 24 0.20
104 34 0.28
105 20 0.16
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (101 bp):
TTTTATTTTTAAATATTTATTAATTTAAATTTAAATAAAATAATAGATACATTCAAATAGAGAAA
GTTTATTAATTTTAAATGTAAATAATATAATGTAGA
Found at i:5563071 original size:104 final size:103
Alignment explanation
Indices: 5562769--5563063 Score: 271
Period size: 104 Copynumber: 2.8 Consensus size: 103
5562759 GAGTTTATAC
* * * * *
5562769 TTTTATTTTTAAATATTTAGTTTATTTAAATTTAAATAAATTAAT-ATAT-ATAT-TC-AAATAG
1 TTTTATTTTTAAATA-TTAATTAATTTAAATTTAAATAAAATAATAAAATCACATATCTAAATA-
* * ** * *
5562830 AGAAA-GTTTATTAATTTTAAATTTATTTAATATCATGTAGG
64 AGAAATATTTATTAATTTTAAA--GAAATAATATAATGTAGA
* *
5562871 TTTTATTTTTAAATATTTATTAATTTAAATTTAAATAAAATAATAAGATCACATATCTAAATAAG
1 TTTTATTTTTAAATATTAATTAATTTAAATTTAAATAAAATAATAAAATCACATATCTAAATAAG
*
5562936 AAATTTTTATTAATTTTAAAGTAAATAATATAATGTAGA
66 AAATATTTATTAATTTTAAAG-AAATAATATAATGTAGA
* * *
5562975 TTTTATTTTTAAAATTTATTAATTTAAGTTTAAATTTAAATAAACTAATAAAATTACAT-TTTAA
1 TTTTATTTTT-AAA--TATTAA-TTAA-TTTAAATTTAAATAAAATAATAAAATCACATATCTAA
* *
5563039 ATAAGATAA-ATTTGTTATTTTTAAA
61 ATAAGA-AATATTTATTAATTTTAAA
5563064 ATTATATATA
Statistics
Matches: 161, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
101 25 0.16
102 18 0.11
103 3 0.02
104 30 0.19
105 23 0.14
107 5 0.03
108 27 0.17
109 30 0.19
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (103 bp):
TTTTATTTTTAAATATTAATTAATTTAAATTTAAATAAAATAATAAAATCACATATCTAAATAAG
AAATATTTATTAATTTTAAAGAAATAATATAATGTAGA
Found at i:5564393 original size:15 final size:15
Alignment explanation
Indices: 5564375--5564418 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
5564365 TATATGTAAA
5564375 TATAAATTTAAAATT
1 TATAAATTTAAAATT
*
5564390 TATAAATATTTAATATT
1 TAT-AA-ATTTAAAATT
5564407 TA-AAATTTAAAA
1 TATAAATTTAAAA
5564419 AATATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 7 0.28
15 5 0.20
16 2 0.08
17 11 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATAAATTTAAAATT
Found at i:5564413 original size:31 final size:31
Alignment explanation
Indices: 5564378--5564438 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
5564368 ATGTAAATAT
** *
5564378 AAATTTAAAATTTATAAATATTTAATATTTA
1 AAATTTAAAAAATATAAATATATAATATTTA
5564409 AAATTTAAAAAATATAAATATATAATATTT
1 AAATTTAAAAAATATAAATATATAATATTT
5564439 TTAAAATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
AAATTTAAAAAATATAAATATATAATATTTA
Found at i:5564428 original size:24 final size:23
Alignment explanation
Indices: 5564372--5564448 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 23
5564362 TTTTATATGT
*
5564372 AAATAT-AA-ATTTAAAATTTAT
1 AAATATAAATATTTAAAATTTAA
*
5564393 AAATATTTAATATTTAAAATTTAAA
1 AAATA-TAAATATTTAAAATTT-AA
* * *
5564418 AAATATAAATATATAATATTTTTA
1 AAATATAAATATTTAA-AATTTAA
5564442 AAATATA
1 AAATATA
5564449 TTGTAAATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.11
22 1 0.02
23 2 0.04
24 28 0.61
25 10 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATATAAATATTTAAAATTTAA
Found at i:5564599 original size:21 final size:20
Alignment explanation
Indices: 5564557--5564595 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5564547 TTTAAAAAAT
* *
5564557 AAAAAAAGTGAAAATTTTTA
1 AAAAAAAATCAAAATTTTTA
5564577 AAAAAAAATCAAAATTTTT
1 AAAAAAAATCAAAATTTTT
5564596 TAAATTGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (20 bp):
AAAAAAAATCAAAATTTTTA
Found at i:5565017 original size:19 final size:18
Alignment explanation
Indices: 5564960--5565017 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
5564950 TTATTTAAGT
5564960 TTTTTATTATTTAAAATA
1 TTTTTATTATTTAAAATA
** *
5564978 TATTAAAATATTATAAAAATA
1 T-TTTTATTATT-T-AAAATA
5564999 TTTTTATTATTTAATAATA
1 TTTTTATTATTTAA-AATA
5565018 ATCAAGTCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 3 0.10
19 12 0.40
20 8 0.27
21 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTTATTATTTAAAATA
Found at i:5566895 original size:18 final size:18
Alignment explanation
Indices: 5566869--5566917 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
5566859 AGACTCCTTT
* *
5566869 TCTCGTTCTTTTTTTTCT
1 TCTCTTTCTTTTTTTTCA
* *
5566887 TCTGTTTCTTTATTTTCA
1 TCTCTTTCTTTTTTTTCA
*
5566905 TCTCTTTGTTTTT
1 TCTCTTTCTTTTT
5566918 CTCTTTTAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.04, C:0.18, G:0.06, T:0.71
Consensus pattern (18 bp):
TCTCTTTCTTTTTTTTCA
Found at i:5569075 original size:17 final size:18
Alignment explanation
Indices: 5569055--5569104 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
5569045 GTATTATATT
5569055 TATATTTATAATTT-TAG
1 TATATTTATAATTTATAG
*
5569072 TATATTTAATAATTTATAT
1 TATATTT-ATAATTTATAG
*
5569091 TATTTTTAT-ATTTA
1 TATATTTATAATTTA
5569105 AATAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 12 0.41
18 9 0.31
19 8 0.28
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TATATTTATAATTTATAG
Found at i:5569100 original size:25 final size:25
Alignment explanation
Indices: 5569046--5569116 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
5569036 TTAATATATG
5569046 TATTATATTT-AT-ATTTATAATTT
1 TATTATATTTAATAATTTATAATTT
*
5569069 TAGTATATTTAATAATTTAT-ATTAT
1 TATTATATTTAATAATTTATAATT-T
* *
5569094 TTTTATATTTAAATAATTAATAA
1 TATTATATTT-AATAATTTATAA
5569117 AAAACCCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 9 0.23
24 5 0.13
25 15 0.38
26 9 0.23
27 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (25 bp):
TATTATATTTAATAATTTATAATTT
Found at i:5569356 original size:22 final size:21
Alignment explanation
Indices: 5569331--5569391 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
5569321 ATTTTTTTTT
5569331 TAAATTTTTATTTATATTTATA
1 TAAATTTTTATTTATATTTA-A
* *
5569353 TAAATTTTAATATATTATTTAA
1 TAAATTTTTATTTA-TATTTAA
5569375 T-AA-TTTT-TTTATATTTA
1 TAAATTTTTATTTATATTTA
5569392 CGTATTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 6 0.18
19 3 0.09
20 3 0.09
21 2 0.06
22 14 0.41
23 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TAAATTTTTATTTATATTTAA
Found at i:5569387 original size:21 final size:23
Alignment explanation
Indices: 5569331--5569389 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
5569321 ATTTTTTTTT
5569331 TAAATTTTTATT-TA-TATTTATA
1 TAAATTTTT-TTATATTATTTATA
**
5569353 TAAATTTTAATATATTATTTA-A
1 TAAATTTTTTTATATTATTTATA
5569375 T-AATTTTTTTATATT
1 TAAATTTTTTTATATT
5569390 TACGTATTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 13 0.42
22 12 0.39
23 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TAAATTTTTTTATATTATTTATA
Found at i:5569424 original size:21 final size:21
Alignment explanation
Indices: 5569400--5569467 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 21
5569390 TACGTATTCA
5569400 TATATCTTTTATATCTATTTT
1 TATATCTTTTATATCTATTTT
5569421 TATA--TTTTATAT-TATATTT
1 TATATCTTTTATATCTAT-TTT
* * *
5569440 TAAAAATTTTTTATATC-ATATT
1 T--ATATCTTTTATATCTATTTT
5569462 TATATC
1 TATATC
5569468 CTACAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
18 3 0.08
19 12 0.32
20 3 0.08
21 6 0.16
22 3 0.08
23 10 0.27
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATCTTTTATATCTATTTT
Found at i:5571917 original size:18 final size:17
Alignment explanation
Indices: 5571887--5571926 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
5571877 TATTATTACT
5571887 ATTTAAAAATATAATAA
1 ATTTAAAAATATAATAA
*
5571904 ATTTAAATAATATAATAT
1 ATTTAAA-AATATAATAA
5571922 ATTTA
1 ATTTA
5571927 TTTGTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTAAAAATATAATAA
Found at i:5572121 original size:11 final size:11
Alignment explanation
Indices: 5572086--5572130 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
5572076 TTATCAATTC
5572086 AAATAAAAATA
1 AAATAAAAATA
*
5572097 AATAAAATAAATA
1 AA-ATAA-AAATA
*
5572110 AACTAAAAATA
1 AAATAAAAATA
5572121 AAATAAAAAT
1 AAATAAAAAT
5572131 TACTGATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 16 0.57
12 5 0.18
13 7 0.25
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:5573319 original size:23 final size:23
Alignment explanation
Indices: 5573271--5573315 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5573261 ACACTAAAGA
**
5573271 ATTGATTAATTATGTTTATAAAT
1 ATTGATTAAAAATGTTTATAAAT
*
5573294 ATTGATTAAAAATTTTTA-AAAT
1 ATTGATTAAAAATGTTTATAAAT
5573316 TATTTAATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (23 bp):
ATTGATTAAAAATGTTTATAAAT
Found at i:5573968 original size:2 final size:2
Alignment explanation
Indices: 5573961--5573986 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5573951 CAATTCCATA
5573961 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
5573987 GTACTGTTTC
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:5574200 original size:12 final size:13
Alignment explanation
Indices: 5574159--5574201 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
5574149 CTCACAATAT
5574159 TAAATATAATTATA
1 TAAATATAATTA-A
5574173 TAAATATATTATTAA
1 TAAATATA--ATTAA
5574188 TAAA-ATAATTAA
1 TAAATATAATTAA
5574200 TA
1 TA
5574202 TTTATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 7 0.26
14 11 0.41
15 5 0.19
16 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TAAATATAATTAA
Found at i:5574960 original size:32 final size:32
Alignment explanation
Indices: 5574881--5574960 Score: 82
Period size: 32 Copynumber: 2.6 Consensus size: 32
5574871 AAAATTATCA
5574881 TTAAAATATTT-TATA-TT-TTTAAATAAATT
1 TTAAAATATTTATATATTTATTTAAATAAATT
* *
5574910 TTAATAA-ATTAATA-ATTTATATTATATAAA-T
1 TTAA-AATATTTATATATTTAT-TTAAATAAATT
5574941 TTAAAATATTTATATATTTA
1 TTAAAATATTTATATATTTA
5574961 AATCATATCT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
29 8 0.20
30 8 0.20
31 12 0.29
32 13 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TTAAAATATTTATATATTTATTTAAATAAATT
Found at i:5574968 original size:19 final size:18
Alignment explanation
Indices: 5574928--5574962 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5574918 TTAATAATTT
5574928 ATATTATATAAATTTAAA
1 ATATTATATAAATTTAAA
*
5574946 ATATT-TATATATTTAAA
1 ATATTATATAAATTTAAA
5574963 TCATATCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTATATAAATTTAAA
Found at i:5575430 original size:17 final size:17
Alignment explanation
Indices: 5575408--5575453 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
5575398 GATTACTTTG
5575408 AATTAAATAATTTTTAA
1 AATTAAATAATTTTTAA
*
5575425 AATTAAAAAATATTTTTAA
1 AATT-AAATA-ATTTTTAA
*
5575444 AGTTAAATAA
1 AATTAAATAA
5575454 GAAATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 5 0.21
18 8 0.33
19 11 0.46
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AATTAAATAATTTTTAA
Found at i:5575441 original size:19 final size:20
Alignment explanation
Indices: 5575412--5575450 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5575402 ACTTTGAATT
5575412 AAATAATTTTTAAAATTAAA
1 AAATAATTTTTAAAATTAAA
*
5575432 AAAT-ATTTTTAAAGTTAAA
1 AAATAATTTTTAAAATTAAA
5575451 TAAGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
AAATAATTTTTAAAATTAAA
Found at i:5577128 original size:2 final size:2
Alignment explanation
Indices: 5577121--5577150 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5577111 GATTTCAAAC
5577121 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
5577151 GGTGTGCAAA
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:5578632 original size:15 final size:15
Alignment explanation
Indices: 5578612--5578648 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
5578602 AAAAATATAA
5578612 AAAAATTTAATTTTT
1 AAAAATTTAATTTTT
5578627 AAAAA--TAATTTTT
1 AAAAATTTAATTTTT
5578640 AATAAATTT
1 AA-AAATTT
5578649 TTTTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
13 10 0.53
14 3 0.16
15 5 0.26
16 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAAAATTTAATTTTT
Found at i:5578637 original size:13 final size:14
Alignment explanation
Indices: 5578619--5578656 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
5578609 TAAAAAAATT
5578619 TAATTTTTAA-AAA
1 TAATTTTTAATAAA
5578632 TAATTTTTAATAAA
1 TAATTTTTAATAAA
*
5578646 T-TTTTTTAATA
1 TAATTTTTAATA
5578657 TAAATTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATTTTTAATAAA
Found at i:5578705 original size:26 final size:25
Alignment explanation
Indices: 5578652--5578706 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
5578642 TAAATTTTTT
* *
5578652 TAAT-ATAAATTATTATATTTATAA
1 TAATAATAAATTATTATATTAACAA
*
5578676 TAATAATAATATTATTATATTAACAG
1 TAATAATAA-ATTATTATATTAACAA
5578702 TAATA
1 TAATA
5578707 GCTAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 4 0.15
25 4 0.15
26 18 0.69
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TAATAATAAATTATTATATTAACAA
Found at i:5578820 original size:27 final size:28
Alignment explanation
Indices: 5578785--5578837 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
5578775 TTGCTTAACT
* *
5578785 AAAACTTATAATT-ATATTTTATTTTAA
1 AAAAATTATAATTAATATATTATTTTAA
*
5578812 AAAAATTATATTTAATATATTATTTT
1 AAAAATTATAATTAATATATTATTTT
5578838 TATTAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
AAAAATTATAATTAATATATTATTTTAA
Found at i:5579113 original size:13 final size:15
Alignment explanation
Indices: 5579075--5579115 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5579065 TATTTAATTA
5579075 TTAT-TATAATATTTT
1 TTATATATAAT-TTTT
5579090 TTATATATAATTTTT
1 TTATATATAATTTTT
5579105 TTA-AT-TAATTT
1 TTATATATAATTT
5579116 AAAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.24
14 2 0.08
15 11 0.44
16 6 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATATATAATTTTT
Found at i:5585709 original size:14 final size:14
Alignment explanation
Indices: 5585660--5585709 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
5585650 CTGATAATTT
*
5585660 TAAATATAATTATA
1 TAAATATAATAATA
5585674 TAAATATAAT-ATA
1 TAAATATAATAATA
5585687 TAAA-A-AATAATA
1 TAAATATAATAATA
*
5585699 AAAATATAATA
1 TAAATATAATA
5585710 TAACGAATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 3 0.09
12 7 0.22
13 8 0.25
14 14 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAATATAATAATA
Found at i:5585796 original size:20 final size:22
Alignment explanation
Indices: 5585758--5585797 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5585748 GTAACATTAA
*
5585758 ATATAATTATACATAATAAAAT
1 ATATAAATATACATAATAAAAT
5585780 ATATAAATATA-AT-ATAAA
1 ATATAAATATACATAATAAA
5585798 TACACAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATAAATATACATAATAAAAT
Found at i:5592423 original size:54 final size:54
Alignment explanation
Indices: 5592359--5592468 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
5592349 TCGGACCATC
5592359 ATTCTTTCCTTGATTTCTTGGTAGAGGTTGTCTCATCCAAACTGAGTGACCTTT
1 ATTCTTTCCTTGATTTCTTGGTAGAGGTTGTCTCATCCAAACTGAGTGACCTTT
5592413 ATTCTTTCCTTGATTTCTTGGTAGAGGTTGTCTCATCCAAACTGAGTGACCTTT
1 ATTCTTTCCTTGATTTCTTGGTAGAGGTTGTCTCATCCAAACTGAGTGACCTTT
5592467 AT
1 AT
5592469 CTGTGCAATT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (54 bp):
ATTCTTTCCTTGATTTCTTGGTAGAGGTTGTCTCATCCAAACTGAGTGACCTTT
Found at i:5600343 original size:2 final size:2
Alignment explanation
Indices: 5600336--5600368 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5600326 TATCTATCTT
5600336 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5600369 TAAAGTTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5600516 original size:21 final size:21
Alignment explanation
Indices: 5600492--5600532 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5600482 TTTAAAAAAT
5600492 ATTTT-TATTTAATTATTAATA
1 ATTTTATATTT-ATTATTAATA
*
5600513 ATTTTATATTTTTTATTAAT
1 ATTTTATATTTATTATTAAT
5600533 TCTTAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTTATATTTATTATTAATA
Found at i:5600602 original size:24 final size:25
Alignment explanation
Indices: 5600570--5600636 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
5600560 TTTTAATGTT
5600570 TATATTATAATATTAAATA-ATAAAA
1 TATA-TATAATATTAAATACATAAAA
* *
5600595 TTTATATAATA-TAAATTACATAATA
1 TATATATAATATTAAA-TACATAAAA
*
5600620 TATATAT-ATATAAAATA
1 TATATATAATATTAAATA
5600637 TATTATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
23 4 0.11
24 14 0.40
25 17 0.49
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
TATATATAATATTAAATACATAAAA
Found at i:5600629 original size:29 final size:28
Alignment explanation
Indices: 5600570--5600652 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 28
5600560 TTTTAATGTT
* *
5600570 TATATTATAATATTAAATAATAAAATTTA
1 TATAATATAA-ATTAAATAATAAAATATA
* *
5600599 TATAATATAAATTACATAATATATATATA
1 TATAATATAAATTAAATAATA-AAATATA
* * *
5600628 TATAAAATATATTATATAATTAAAA
1 TATAATATAAATTAAATAA-TAAAA
5600653 AATAAACTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
28 10 0.23
29 32 0.73
30 2 0.05
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
TATAATATAAATTAAATAATAAAATATA
Found at i:5600644 original size:24 final size:23
Alignment explanation
Indices: 5600570--5600645 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 23
5600560 TTTTAATGTT
*
5600570 TATATTATAATATTAAATA-ATAAAA
1 TATA-TATAATATAAAATACAT--AA
* *
5600595 TTTATATAATATAAATTACATAA
1 TATATATAATATAAAATACATAA
* *
5600618 TATATATATATATAAAATATATTA
1 TATATATA-ATATAAAATACATAA
5600642 TATA
1 TATA
5600646 ATTAAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
23 9 0.21
24 28 0.67
25 5 0.12
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (23 bp):
TATATATAATATAAAATACATAA
Found at i:5600654 original size:20 final size:19
Alignment explanation
Indices: 5600579--5600656 Score: 52
Period size: 20 Copynumber: 4.1 Consensus size: 19
5600569 TTATATTATA
* **
5600579 ATATTAAATAATAAAATTT
1 ATATTATATAATAAAAAAT
* * *
5600598 ATATAATATAAATTACATAAT
1 ATATTATAT-AA-TAAAAAAT
*
5600619 ATA-TATAT-ATATAAAAT
1 ATATTATATAATAAAAAAT
5600636 ATATTATATAATTAAAAAAT
1 ATATTATATAA-TAAAAAAT
5600656 A
1 A
5600657 AACTGAATCG
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
17 9 0.20
18 6 0.14
19 8 0.18
20 14 0.32
21 7 0.16
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATTATATAATAAAAAAT
Found at i:5602929 original size:2 final size:2
Alignment explanation
Indices: 5602917--5602953 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5602907 ACAAAAGACC
*
5602917 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5602954 TCTAAAGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5604285 original size:11 final size:11
Alignment explanation
Indices: 5604271--5604324 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
5604261 GTATATTAAG
5604271 ATTATATTTAT
1 ATTATATTTAT
*
5604282 ATTATGTATTTTT
1 ATTA--TATTTAT
*
5604295 ATTAAATTTAT
1 ATTATATTTAT
*
5604306 ATTATTTTTAT
1 ATTATATTTAT
5604317 ATTATATT
1 ATTATATT
5604325 CGTGTTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 25 0.71
13 10 0.29
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:5604291 original size:24 final size:24
Alignment explanation
Indices: 5604264--5604310 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
5604254 TGTTATTGTA
*
5604264 TATTAAGATTATATTTATATTATG
1 TATTAAGATTAAATTTATATTATG
***
5604288 TATTTTTATTAAATTTATATTAT
1 TATTAAGATTAAATTTATATTAT
5604311 TTTTATATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TATTAAGATTAAATTTATATTATG
Found at i:5604372 original size:18 final size:18
Alignment explanation
Indices: 5604360--5604417 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
5604350 TAATTTTTTA
5604360 TATATTAATAATTTATAT
1 TATATTAATAATTTATAT
* *
5604378 TATATTAAT-TTTTAATAAA
1 TATATTAATAATTT-AT-AT
5604397 TATATT-ATATATTTATAT
1 TATATTAATA-ATTTATAT
5604415 TAT
1 TAT
5604418 TTTTTATATC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 3 0.09
18 17 0.53
19 9 0.28
20 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTAATAATTTATAT
Found at i:5604380 original size:20 final size:22
Alignment explanation
Indices: 5604334--5604426 Score: 74
Period size: 20 Copynumber: 4.4 Consensus size: 22
5604324 TCGTGTTAAA
*
5604334 ATATTATACATTTATATAATTT
1 ATATTATATATTTATATAATTT
5604356 -T-TTATATA-TTA-ATAATTT
1 ATATTATATATTTATATAATTT
* *
5604374 ATATTATATTAATTTTTAATAA-AT
1 ATATTATA-T-ATTTAT-ATAATTT
*
5604398 ATATTATATATTTATATTATTT
1 ATATTATATATTTATATAATTT
5604420 -T-TTATAT
1 ATATTATAT
5604427 CATATAATCC
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
18 7 0.12
19 4 0.07
20 17 0.30
21 6 0.11
22 7 0.12
23 3 0.05
24 9 0.16
25 4 0.07
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (22 bp):
ATATTATATATTTATATAATTT
Found at i:5604381 original size:32 final size:33
Alignment explanation
Indices: 5604330--5604426 Score: 107
Period size: 32 Copynumber: 3.0 Consensus size: 33
5604320 ATATTCGTGT
*
5604330 TAAA-ATATTATACATTTATATAATTTTTTATA
1 TAAATATATTATATATTTATATAATTTTTTATA
5604362 TATTAATA-ATT-TATA-TTATATTAA-TTTTTA-A
1 TA--AATATATTATATATTTATA-TAATTTTTTATA
*
5604393 TAAATATATTATATATTTATATTATTTTTTATA
1 TAAATATATTATATATTTATATAATTTTTTATA
5604426 T
1 T
5604427 CATATAATCC
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
29 4 0.07
30 3 0.06
31 9 0.17
32 24 0.44
33 8 0.15
34 5 0.09
35 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (33 bp):
TAAATATATTATATATTTATATAATTTTTTATA
Found at i:5606509 original size:26 final size:26
Alignment explanation
Indices: 5606478--5606533 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5606468 TTTATATATT
*
5606478 TTTAAAAAATTATTTTATTGA-TAAGA
1 TTTAAAAAATTAATTTATTGATTAA-A
**
5606504 TTTAAAATTTTAATTTATTGATTAAA
1 TTTAAAAAATTAATTTATTGATTAAA
5606530 TTTA
1 TTTA
5606534 TATTAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 23 0.88
27 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (26 bp):
TTTAAAAAATTAATTTATTGATTAAA
Found at i:5606662 original size:74 final size:72
Alignment explanation
Indices: 5606503--5606663 Score: 241
Period size: 74 Copynumber: 2.2 Consensus size: 72
5606493 TATTGATAAG
* * *
5606503 ATTTAAAATTTTAATTTATTGATTAAATTTATATTAAAATTATATAATTTAATTAAATGTATATT
1 ATTT-AAATTTTAATTTATTGATTAAATTTATATTAAAACTATACAATTTAACTAAATGTATATT
5606568 TTTAAAGT
65 TTTAAAGT
5606576 ATTTAAATTTTTAATTTATTGATTAAATTTATATTAAAAACTATACAATTTAACTAAATGTATAT
1 ATTTAAA-TTTTAATTTATTGATTAAATTTATATT-AAAACTATACAATTTAACTAAATGTATAT
*
5606641 TTTTTAAGT
64 TTTTAAAGT
*
5606650 ATTTATTATTTTAA
1 ATTTA-AATTTTAA
5606664 ATAATTATTT
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
72 3 0.04
73 31 0.39
74 45 0.56
75 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (72 bp):
ATTTAAATTTTAATTTATTGATTAAATTTATATTAAAACTATACAATTTAACTAAATGTATATTT
TTAAAGT
Found at i:5606680 original size:21 final size:22
Alignment explanation
Indices: 5606644--5606702 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
5606634 TGTATATTTT
* *
5606644 TTAAGTATTT-ATTATTTTAAA
1 TTAATTATTTAATTATTTAAAA
5606665 -TAATTATTTAATTA-TTAAAA
1 TTAATTATTTAATTATTTAAAA
*
5606685 TTACTTATTTAA-TATTTA
1 TTAATTATTTAATTATTTA
5606703 TTTTTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAATTATTTAATTATTTAAAA
Found at i:5607730 original size:21 final size:21
Alignment explanation
Indices: 5607700--5607823 Score: 78
Period size: 21 Copynumber: 5.7 Consensus size: 21
5607690 CAAATTTAGA
*
5607700 TAAAATATAATTATATAATAT
1 TAAAAAATAATTATATAATAT
5607721 TAAAAAATAATTA-A-AATAT
1 TAAAAAATAATTATATAATAT
*
5607740 TATATAAAAT-ATAATATAATAT
1 TA-A-AAAATAATTATATAATAT
* *
5607762 AAAAATAAT-ATTA-ATATTAT
1 TAAAA-AATAATTATATAATAT
*
5607782 ATAAAAACATAAATTTATTATAATTTT
1 -TAAAAA-AT-AA-TTA-TATAA-TAT
5607809 TAAAAAATAAATTAT
1 TAAAAAAT-AATTAT
5607824 TAACACATTA
Statistics
Matches: 82, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
19 7 0.09
20 14 0.17
21 31 0.38
22 6 0.07
23 2 0.02
24 6 0.07
25 5 0.06
26 9 0.11
27 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAAATAATTATATAATAT
Found at i:5607761 original size:17 final size:16
Alignment explanation
Indices: 5607735--5607778 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
5607725 AAATAATTAA
*
5607735 AATATTATATAAAATAT
1 AATATAATATAAAA-AT
5607752 AATATAATATAAAAAT
1 AATATAATATAAAAAT
5607768 AATATTAATAT
1 AATA-TAATAT
5607779 TATATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATAATATAAAAAT
Found at i:5607788 original size:22 final size:21
Alignment explanation
Indices: 5607699--5607788 Score: 73
Period size: 22 Copynumber: 4.3 Consensus size: 21
5607689 ACAAATTTAG
5607699 ATAAAATATAAT-T-ATATAAT
1 ATAAAA-ATAATATAATATAAT
* *
5607719 ATTAAAAAATAAT-TAAAATATT
1 A-T-AAAAATAATATAATATAAT
*
5607741 AT-ATAA-AATATAATATAAT
1 ATAAAAATAATATAATATAAT
*
5607760 ATAAAAATAATATTAATATTAT
1 ATAAAAATAATA-TAATATAAT
5607782 ATAAAAA
1 ATAAAAA
5607789 CATAAATTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
18 3 0.05
19 12 0.21
20 4 0.07
21 12 0.21
22 25 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAAAAATAATATAATATAAT
Found at i:5607800 original size:27 final size:25
Alignment explanation
Indices: 5607762--5607826 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
5607752 AATATAATAT
5607762 AAAAAT-AA-TATTAAT-ATTATATA
1 AAAAATAAATTATTAATAATT-TATA
*
5607785 AAAACATAAATTTATT-ATAATTTTTA
1 AAAA-ATAAA-TTATTAATAATTTATA
5607811 AAAAATAAATTATTAA
1 AAAAATAAATTATTAA
5607827 CACATTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
23 4 0.11
24 7 0.20
25 8 0.23
26 9 0.26
27 7 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAAATAAATTATTAATAATTTATA
Found at i:5607804 original size:41 final size:39
Alignment explanation
Indices: 5607717--5607804 Score: 99
Period size: 39 Copynumber: 2.2 Consensus size: 39
5607707 TAATTATATA
*
5607717 ATATTA-AAAAATAATTAAAATATTATATAAAATATAAT
1 ATATTATAAAAATAATTAAAATATTATATAAAACATAAT
* *
5607755 ATAATATAAAAATAA-TATTAATATTATATAAAAACATAAAT
1 ATATTATAAAAATAATTA-AAATATTATAT-AAAACAT-AAT
*
5607796 TTATTATAA
1 ATATTATAA
5607805 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
38 7 0.17
39 18 0.44
40 6 0.15
41 10 0.24
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (39 bp):
ATATTATAAAAATAATTAAAATATTATATAAAACATAAT
Found at i:5607893 original size:30 final size:28
Alignment explanation
Indices: 5607840--5607895 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
5607830 ATTAAAATTT
* *
5607840 TTATATATACATAATATTATAAATATAA
1 TTATATACACATAATAATATAAATATAA
5607868 TTATATTACACATAAATAATATAAATAT
1 TTATA-TACACAT-AATAATATAAATAT
5607896 TATGTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 6 0.25
30 13 0.54
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (28 bp):
TTATATACACATAATAATATAAATATAA
Found at i:5610728 original size:2 final size:2
Alignment explanation
Indices: 5610721--5610746 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5610711 CTTAATTTCA
5610721 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
5610747 TATCATGAGG
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:5611194 original size:3 final size:3
Alignment explanation
Indices: 5611186--5611220 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5611176 CTATTATGTT
5611186 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5611221 GTAGCTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5611641 original size:22 final size:20
Alignment explanation
Indices: 5611611--5611663 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
5611601 ATTTTTATGT
5611611 TATAGTTATATTCAAAGTATTA
1 TATAGTTATA-T-AAAGTATTA
* *
5611633 TATATTTATATAAAGTTTTA
1 TATAGTTATATAAAGTATTA
5611653 TAT-GTTA-ATAA
1 TATAGTTATATAA
5611664 TTTATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 4 0.14
19 3 0.11
20 11 0.39
21 1 0.04
22 9 0.32
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.49
Consensus pattern (20 bp):
TATAGTTATATAAAGTATTA
Found at i:5612663 original size:15 final size:15
Alignment explanation
Indices: 5612643--5612682 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
5612633 ATCTTTTAAT
5612643 ATAATTTTTAATAAA
1 ATAATTTTTAATAAA
5612658 ATAA-TTTTAATAAA
1 ATAATTTTTAATAAA
* *
5612672 TTAATCTTTAA
1 ATAATTTTTAA
5612683 AACCTCTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAATTTTTAATAAA
Found at i:5613118 original size:17 final size:15
Alignment explanation
Indices: 5613086--5613120 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
5613076 AAATTGTTTG
5613086 TAAAGAAAATTAGAT
1 TAAAGAAAATTAGAT
5613101 TAAAGTAAAATATAGAT
1 TAAAG-AAAAT-TAGAT
5613118 TAA
1 TAA
5613121 CTCTGTCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 5 0.28
17 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (15 bp):
TAAAGAAAATTAGAT
Found at i:5613403 original size:19 final size:20
Alignment explanation
Indices: 5613365--5613432 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 20
5613355 ATATTATCAT
* *
5613365 ATAATATAAAATTTATTAAA
1 ATAATATAAAATATAATAAA
5613385 ATAAT-TAAAATATAAT-AA
1 ATAATATAAAATATAATAAA
*
5613403 A-AATATAATATA-ATATAAA
1 ATAATATAAAATATA-ATAAA
5613422 TATAATATAAA
1 -ATAATATAAA
5613433 TTATTAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 4 0.10
18 11 0.28
19 11 0.28
20 6 0.15
21 7 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAATATAAAATATAATAAA
Found at i:5613412 original size:5 final size:5
Alignment explanation
Indices: 5613393--5613443 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
5613383 AAATAATTAA
* *
5613393 AATAT AATAAA AATAT AATAT AATAT AAATAT AATAT AA-AT TAT-T AATAT
1 AATAT AAT-AT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AATAT
5613443 A
1 A
5613444 TAAAAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 6 0.16
5 23 0.61
6 9 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:5613414 original size:16 final size:16
Alignment explanation
Indices: 5613393--5613431 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
5613383 AAATAATTAA
5613393 AATATAATAAAAATAT
1 AATATAATAAAAATAT
*
5613409 AATATAATATAAATAT
1 AATATAATAAAAATAT
5613425 AATATAA
1 AATATAA
5613432 ATTATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATATAATAAAAATAT
Found at i:5613423 original size:11 final size:11
Alignment explanation
Indices: 5613404--5613443 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
5613394 ATATAATAAA
5613404 AATAT-AATAT
1 AATATAAATAT
5613414 AATATAAATAT
1 AATATAAATAT
5613425 AATATAAATTATT
1 AATATAAA-TA-T
5613438 AATATA
1 AATATA
5613444 TAAAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 5 0.19
11 13 0.48
12 2 0.07
13 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATAAATAT
Found at i:5613439 original size:47 final size:44
Alignment explanation
Indices: 5613363--5613471 Score: 112
Period size: 46 Copynumber: 2.4 Consensus size: 44
5613353 TGATATTATC
* *
5613363 ATATAATATAAAATTTATTAAAATAATTAAAATATAATAAAAATATA-
1 ATATAATAT-AAATATAATAAAATAATT--AATAT-ATAAAAATATAT
* *
5613410 ATATAATATAAATATAATATAAATTATTAATATATAAAAATTTAT
1 ATATAATATAAATATAATA-AAATAATTAATATATAAAAATATAT
*
5613455 ATATATATATATATATA
1 ATATA-ATATAAATATA
5613472 TTTGATATCT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
44 10 0.19
45 10 0.19
46 18 0.33
47 16 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (44 bp):
ATATAATATAAATATAATAAAATAATTAATATATAAAAATATAT
Found at i:5613467 original size:53 final size:54
Alignment explanation
Indices: 5613391--5613503 Score: 115
Period size: 53 Copynumber: 2.1 Consensus size: 54
5613381 TAAAATAATT
5613391 AAAATATAATAAAAATATAATATAATATAAATATAATATAAATTATTAATATATA
1 AAAATATAATAAAAATATAATAT-ATATAAATATAATATAAATTATTAATATATA
* * * ** * *
5613446 AAAAT-TTATATATATAT-ATATATATATTTGAT-ATCTAAAATATTTAATATATA
1 AAAATATAATAAAAATATAATATATATAAAT-ATAATATAAATTA-TTAATATATA
5613499 AAAAT
1 AAAAT
5613504 GTGCAAACAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
52 14 0.29
53 21 0.43
54 9 0.18
55 5 0.10
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (54 bp):
AAAATATAATAAAAATATAATATATATAAATATAATATAAATTATTAATATATA
Found at i:5613488 original size:16 final size:16
Alignment explanation
Indices: 5613426--5613501 Score: 57
Period size: 16 Copynumber: 4.5 Consensus size: 16
5613416 TATAAATATA
*
5613426 ATATAAATTA-TTAAT
1 ATATAAAATATTTAAT
5613441 ATATAAAA-ATTTATATAT
1 ATATAAAATA-TT-TA-AT
*
5613459 ATATATATATATATTTGAT
1 ATATA-A-A-ATATTTAAT
*
5613478 ATCTAAAATATTTAAT
1 ATATAAAATATTTAAT
5613494 ATATAAAA
1 ATATAAAA
5613502 ATGTGCAAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
14 1 0.02
15 7 0.15
16 16 0.33
17 3 0.06
18 8 0.17
19 7 0.15
20 2 0.04
21 3 0.06
22 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (16 bp):
ATATAAAATATTTAAT
Found at i:5613578 original size:2 final size:2
Alignment explanation
Indices: 5613571--5613612 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5613561 TAAGCAATTT
5613571 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
5613613 ACCTATGCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5613774 original size:30 final size:30
Alignment explanation
Indices: 5613738--5613848 Score: 107
Period size: 30 Copynumber: 3.7 Consensus size: 30
5613728 TACTTTATTT
*
5613738 AAATAAATTTTTAAATTTTAATTTGTATAA
1 AAATAAATTTTTAAATTTTAAATTGTATAA
* * *
5613768 AAATAAATTTTTAATTTTTAAATTATACAA
1 AAATAAATTTTTAAATTTTAAATTGTATAA
*** * *
5613798 AAATAAAGAATTAACTTTTAAATTGTAATTA
1 AAATAAATTTTTAAATTTTAAATTGT-ATAA
* *
5613829 AAA-AAGTTCTTAAATTTTAA
1 AAATAAATTTTTAAATTTTAA
5613849 TTTAAACCTA
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
30 59 0.92
31 5 0.08
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATAAATTTTTAAATTTTAAATTGTATAA
Found at i:5614142 original size:17 final size:18
Alignment explanation
Indices: 5614113--5614156 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
5614103 AATCTAAATA
*
5614113 TAAAT-TAATAATTTATT
1 TAAATATAAAAATTTATT
5614130 TAAA-ATAAAAATTTATT
1 TAAATATAAAAATTTATT
5614147 TAAATATAAA
1 TAAATATAAA
5614157 TAAATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAATATAAAAATTTATT
Found at i:5614157 original size:46 final size:47
Alignment explanation
Indices: 5614083--5614184 Score: 138
Period size: 46 Copynumber: 2.2 Consensus size: 47
5614073 TAACTTAAAC
* *
5614083 AAATAACAAATTTATGTATAAATCTAAATATAA-ATTAATAATTTATTT
1 AAATAA-AAATTTATGTATAAATATAAATA-AATAATAATAATTTATTT
5614131 AAAATAAAAATTTAT-T-TAAATATAAATAAATAATAATAATTTATTT
1 -AAATAAAAATTTATGTATAAATATAAATAAATAATAATAATTTATTT
5614177 AAATAAAA
1 AAATAAAA
5614185 TAAAAATAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
45 10 0.20
46 25 0.50
47 1 0.02
48 8 0.16
49 6 0.12
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (47 bp):
AAATAAAAATTTATGTATAAATATAAATAAATAATAATAATTTATTT
Found at i:5614165 original size:29 final size:27
Alignment explanation
Indices: 5614131--5614196 Score: 105
Period size: 29 Copynumber: 2.4 Consensus size: 27
5614121 TAATTTATTT
5614131 AAAATAAAAATTTATTTAAATATAAATA
1 AAAATAAAAATTTATTTAAATA-AAATA
*
5614159 AATAATAATAATTTATTTAAATAAAATA
1 AA-AATAAAAATTTATTTAAATAAAATA
5614187 AAAATAAAAA
1 AAAATAAAAA
5614197 AATAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
27 7 0.20
28 9 0.26
29 19 0.54
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
AAAATAAAAATTTATTTAAATAAAATA
Found at i:5615057 original size:17 final size:19
Alignment explanation
Indices: 5615035--5615088 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
5615025 AAATTGAAAA
5615035 TTAATAATATTTT-T-AAT
1 TTAATAATATTTTATAAAT
5615052 TTAAT-ATATTTTATAAAT
1 TTAATAATATTTTATAAAT
5615070 TTAAATAAT-TTTTA-AAAT
1 TT-AATAATATTTTATAAAT
5615088 T
1 T
5615089 AATGAAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
16 7 0.21
17 6 0.18
18 10 0.30
19 8 0.24
20 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAATAATATTTTATAAAT
Found at i:5615072 original size:18 final size:17
Alignment explanation
Indices: 5615035--5615091 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
5615025 AAATTGAAAA
5615035 TTAATAATATTTTT-AAT
1 TTAAT-ATATTTTTAAAT
5615052 TTAATATATTTTATAAAT
1 TTAATATATTTT-TAAAT
*
5615070 TTAA-ATAATTTTTAAAA
1 TTAATAT-ATTTTTAAAT
5615087 TTAAT
1 TTAAT
5615092 GAAAAAGTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
16 7 0.20
17 16 0.46
18 12 0.34
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAATATATTTTTAAAT
Found at i:5615222 original size:13 final size:14
Alignment explanation
Indices: 5615204--5615232 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5615194 AAAGATCATC
5615204 AATAATTATT-TTT
1 AATAATTATTATTT
5615217 AATAATTATTATTT
1 AATAATTATTATTT
5615231 AA
1 AA
5615233 GATTATATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATAATTATTATTT
Found at i:5615491 original size:16 final size:17
Alignment explanation
Indices: 5615461--5615495 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5615451 TATTTACTTG
5615461 ATTTATATTTATTTAAT
1 ATTTATATTTATTTAAT
*
5615478 ATTTA-ATTTTTTTAAT
1 ATTTATATTTATTTAAT
5615494 AT
1 AT
5615496 AGTTAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTATATTTATTTAAT
Found at i:5615776 original size:11 final size:11
Alignment explanation
Indices: 5615750--5615787 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5615740 TATATAGGAG
*
5615750 AAAAAGAAGAA
1 AAAAAGAAAAA
*
5615761 GAAAAGAAAAA
1 AAAAAGAAAAA
5615772 AAAAA-AAAAA
1 AAAAAGAAAAA
5615782 AAAAAG
1 AAAAAG
5615788 GATGGATGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:5618643 original size:21 final size:22
Alignment explanation
Indices: 5618619--5618668 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
5618609 AAATTTTTAT
* *
5618619 TTTTA-AAATTTTTAAAAATAA
1 TTTTATAAATTTTAAAAAAAAA
*
5618640 TTTTATATATTTTAAAAAAAAA
1 TTTTATAAATTTTAAAAAAAAA
5618662 TATTTAT
1 T-TTTAT
5618669 CATCTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.21
22 14 0.58
23 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTATAAATTTTAAAAAAAAA
Found at i:5618651 original size:22 final size:23
Alignment explanation
Indices: 5618626--5618668 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5618616 TATTTTTAAA
* *
5618626 ATTTTTAAAAATAAT-TTTATAT
1 ATTTTAAAAAAAAATATTTATAT
5618648 ATTTTAAAAAAAAATATTTAT
1 ATTTTAAAAAAAAATATTTAT
5618669 CATCTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTTAAAAAAAAATATTTATAT
Found at i:5619320 original size:19 final size:18
Alignment explanation
Indices: 5619248--5619340 Score: 61
Period size: 19 Copynumber: 5.2 Consensus size: 18
5619238 ATAAATAAAA
*
5619248 ATAATATATATATAA--T
1 ATAATATATTTATAATTT
*
5619264 ATAAAATATTTA-AATATT
1 ATAATATATTTATAAT-TT
* * *
5619282 ATTAAAATA-AT-TAATAT
1 A-TAATATATTTATAATTT
5619299 ATAATATATTTAATAATTT
1 ATAATATATTT-ATAATTT
*
5619318 ATATTATATTTATATATTT
1 ATAATATATTTATA-ATTT
5619337 ATAA
1 ATAA
5619341 AATTAAATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
15 2 0.03
16 16 0.27
17 3 0.05
18 9 0.15
19 29 0.49
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATAATATATTTATAATTT
Found at i:5621556 original size:18 final size:18
Alignment explanation
Indices: 5621533--5621567 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5621523 AGGCTAATGA
* *
5621533 AGGAGGTGATTCAGAAGC
1 AGGAGGAGATGCAGAAGC
5621551 AGGAGGAGATGCAGAAG
1 AGGAGGAGATGCAGAAG
5621568 AAATTCTTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.09, G:0.43, T:0.11
Consensus pattern (18 bp):
AGGAGGAGATGCAGAAGC
Found at i:5625656 original size:12 final size:12
Alignment explanation
Indices: 5625635--5625669 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
5625625 CTTCTAATTA
5625635 AAAAAGAAAAAAG
1 AAAAA-AAAAAAG
5625648 AAAAAAAAAAAG
1 AAAAAAAAAAAG
*
5625660 AAAAGAAAAA
1 AAAAAAAAAA
5625670 TATTGTCGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:5625656 original size:17 final size:17
Alignment explanation
Indices: 5625634--5625669 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5625624 CCTTCTAATT
*
5625634 AAAAAAGAA-AAAAGAA
1 AAAAAAAAAGAAAAGAA
5625650 AAAAAAAAAGAAAAGAA
1 AAAAAAAAAGAAAAGAA
5625667 AAA
1 AAA
5625670 TATTGTCGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAAAAGAA
Found at i:5626135 original size:2 final size:2
Alignment explanation
Indices: 5626128--5626155 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5626118 CTTTTATTTT
5626128 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
5626156 ATAAGAGTTT
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):
TA
Found at i:5626802 original size:23 final size:22
Alignment explanation
Indices: 5626768--5626818 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
5626758 TCCACTACAT
* * *
5626768 TTATTTTGTTTTTCTCTTTTAA
1 TTATTTTGTTTTTATATATTAA
*
5626790 TTATTTTATTTTTTATATATTAA
1 TTATTTT-GTTTTTATATATTAA
5626813 TTATTT
1 TTATTT
5626819 ATTATTTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (22 bp):
TTATTTTGTTTTTATATATTAA
Found at i:5626980 original size:43 final size:42
Alignment explanation
Indices: 5626894--5626995 Score: 123
Period size: 43 Copynumber: 2.4 Consensus size: 42
5626884 GCCATCCCAC
*
5626894 ATTCCAATTATTTTATATTTTTAATAAAAAATGATAAATAAT
1 ATTCCAATTATTTTATATTTTTAATAAAAAATGATAAACAAT
* * * ***
5626936 ATTCTAATTATTTTATATTTTTTTATAAGAAATGATGGGCAAT
1 ATTCCAATTATTTTATA-TTTTTAATAAAAAATGATAAACAAT
*
5626979 ATTCCAATTACTTTATA
1 ATTCCAATTATTTTATA
5626996 AGTTCAAAGT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 16 0.32
43 34 0.68
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (42 bp):
ATTCCAATTATTTTATATTTTTAATAAAAAATGATAAACAAT
Found at i:5628587 original size:2 final size:2
Alignment explanation
Indices: 5628580--5628615 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5628570 GCATTTTGAA
5628580 AT 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 AT
5628616 TCTTGACTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5629412 original size:16 final size:16
Alignment explanation
Indices: 5629391--5629433 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
5629381 TAGGAGAATG
*
5629391 TATTTTATATTTAGAT
1 TATTTTATATTTAAAT
*
5629407 TATTTTAAATTTAAAT
1 TATTTTATATTTAAAT
*
5629423 TATTTAATATT
1 TATTTTATATT
5629434 ATTTTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TATTTTATATTTAAAT
Found at i:5631383 original size:20 final size:20
Alignment explanation
Indices: 5631333--5631387 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
5631323 ATCATGGTTC
5631333 ACCATTCTATAATATAAAGT
1 ACCATTCTATAATATAAAGT
* * *
5631353 A-CATTTTTATATTATATAGT
1 ACCA-TTCTATAATATAAAGT
5631373 ACCATTCTATAATAT
1 ACCATTCTATAATAT
5631388 GGTATCCTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.44
Consensus pattern (20 bp):
ACCATTCTATAATATAAAGT
Found at i:5635452 original size:15 final size:14
Alignment explanation
Indices: 5635421--5635463 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
5635411 ATTATTATTT
5635421 TTTAAAAATTAATA
1 TTTAAAAATTAATA
5635435 TTTAATAAATTTAA-A
1 TTTAA-AAA-TTAATA
5635450 TTTAAAATATTAAT
1 TTTAAAA-ATTAAT
5635464 TTTTTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.44
15 10 0.40
16 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTAAAAATTAATA
Found at i:5636139 original size:18 final size:17
Alignment explanation
Indices: 5636094--5636131 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
5636084 TTTATTTTTT
*
5636094 TATTAATTAAAT--TAA
1 TATTAATTAATTCGTAA
5636109 TATTAATTAATTCGTAA
1 TATTAATTAATTCGTAA
5636126 TATTAA
1 TATTAA
5636132 ATTCATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
17 9 0.45
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TATTAATTAATTCGTAA
Found at i:5636902 original size:16 final size:15
Alignment explanation
Indices: 5636863--5636900 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 15
5636853 AACCTGATTA
5636863 AATCAAACTTAAAAT
1 AATCAAACTTAAAAT
5636878 AACTCAAACTTAAAAT
1 AA-TCAAACTTAAAAT
5636894 AATCAAA
1 AATCAAA
5636901 ACCGAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.24
Consensus pattern (15 bp):
AATCAAACTTAAAAT
Found at i:5637666 original size:18 final size:19
Alignment explanation
Indices: 5637634--5637672 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5637624 GATTTTTAGA
*
5637634 AATAAAAAGTTAATTTTTT
1 AATAAAAAGTGAATTTTTT
5637653 AATAAAAA-TGAATTTTTT
1 AATAAAAAGTGAATTTTTT
5637671 AA
1 AA
5637673 ATTAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
AATAAAAAGTGAATTTTTT
Found at i:5637679 original size:18 final size:18
Alignment explanation
Indices: 5637645--5637698 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
5637635 ATAAAAAGTT
5637645 AATTTTTT-AATAAAAATG
1 AATTTTTTAAAT-AAAATG
*
5637663 AATTTTTTAAATTAAAT-
1 AATTTTTTAAATAAAATG
5637680 -ATTATTTTAAATAAAATG
1 AATT-TTTTAAATAAAATG
5637698 A
1 A
5637699 TAAAAATCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 3 0.10
17 12 0.40
18 12 0.40
19 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (18 bp):
AATTTTTTAAATAAAATG
Found at i:5637736 original size:24 final size:23
Alignment explanation
Indices: 5637719--5637765 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
5637709 TTTAATTTAT
5637719 ATTTATTTTA-AAAATTTATTTGA
1 ATTT-TTTTATAAAATTTATTTGA
5637742 ATTTTTTTATAAAATTT-TTT-A
1 ATTTTTTTATAAAATTTATTTGA
5637763 ATT
1 ATT
5637766 AATTTAGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.17
22 8 0.35
23 11 0.48
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTTTTTTATAAAATTTATTTGA
Found at i:5639551 original size:19 final size:18
Alignment explanation
Indices: 5639510--5639574 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
5639500 ATGAATTATC
* *
5639510 AATATATAAAACTTTTATA
1 AATATATAATA-TTTTAAA
5639529 AATATATAATATTTTAAA
1 AATATATAATATTTTAAA
* *
5639547 TAATAT-TATTATATATAAA
1 -AATATATAATAT-TTTAAA
5639566 AATATATAA
1 AATATATAA
5639575 ATATAATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 16 0.42
19 22 0.58
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATATAATATTTTAAA
Found at i:5640719 original size:15 final size:16
Alignment explanation
Indices: 5640687--5640724 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5640677 GATATCAAAT
5640687 AAATTAAATTAATTCA
1 AAATTAAATTAATTCA
*
5640703 AAATTAAA-TATTTCA
1 AAATTAAATTAATTCA
5640718 AATATTA
1 AA-ATTA
5640725 TAAATATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTAAATTAATTCA
Found at i:5640908 original size:2 final size:2
Alignment explanation
Indices: 5640901--5640929 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5640891 AAGCCCGAAT
5640901 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5640930 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5641193 original size:15 final size:14
Alignment explanation
Indices: 5641164--5641202 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
5641154 ATTTTAATCT
*
5641164 TATTTTTAATA-TA
1 TATTTTTAAAATTA
5641177 TATCTTTTAAAATTA
1 TAT-TTTTAAAATTA
5641192 TATTTTTAAAA
1 TATTTTTAAAA
5641203 AACTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 15 0.65
15 5 0.22
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTTTTAAAATTA
Found at i:5641722 original size:15 final size:15
Alignment explanation
Indices: 5641697--5641740 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
5641687 ATAAGTCGAG
5641697 TTAATTTTAAA-TTATA
1 TTAA-TTTAAATTTA-A
5641713 TTAATTTAAATTTAA
1 TTAATTTAAATTTAA
*
5641728 TTATTTTAAATTT
1 TTAATTTAAATTT
5641741 TTAAATTCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 19 0.73
16 7 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAATTTAAATTTAA
Found at i:5644115 original size:15 final size:15
Alignment explanation
Indices: 5644095--5644142 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
5644085 GTTCAATTTA
*
5644095 TTAAATTATTTAAAT
1 TTAAATTATTTATAT
* *
5644110 TTAAATAATATATAT
1 TTAAATTATTTATAT
5644125 TT-AATTCATTTATAT
1 TTAAATT-ATTTATAT
5644140 TTA
1 TTA
5644143 TAAATAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.12
15 23 0.88
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAAATTATTTATAT
Done.