Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397269.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.1, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5666189
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 144833 characters in sequence are not A, C, G, or T
File 2 of 14
Found at i:441832 original size:2 final size:2
Alignment explanation
Indices: 441825--441861 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
441815 ATGTTTACTA
* *
441825 AT AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
441862 GTAGAATATA
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:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:443151 original size:79 final size:79
Alignment explanation
Indices: 443020--443170 Score: 223
Period size: 79 Copynumber: 1.9 Consensus size: 79
443010 ATCTGAGCTT
* * *
443020 AGAGCAAAGCTAATGCTGCTTTGGATGTCATTGTGCTGCCTCTGGTCGTTCTCTCAACTTTTGAA
1 AGAGCAAAACTAATGCTGCTTTGGATGTCATTGTGCTGCCTCTGGTCATTCTCTCAACTTCTGAA
*
443085 TTTGCAAAAGATGA
66 TGTGCAAAAGATGA
* * *
443099 AGAGCAAAACTAATGCTTCTTTGGATGTCGTTGTGC-GACCTCTGGTCATTCTCTCAGCTTCTGA
1 AGAGCAAAACTAATGCTGCTTTGGATGTCATTGTGCTG-CCTCTGGTCATTCTCTCAACTTCTGA
443163 ATGTGCAA
65 ATGTGCAA
443171 CCGGCAAAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
78 1 0.02
79 63 0.98
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (79 bp):
AGAGCAAAACTAATGCTGCTTTGGATGTCATTGTGCTGCCTCTGGTCATTCTCTCAACTTCTGAA
TGTGCAAAAGATGA
Found at i:445526 original size:2 final size:2
Alignment explanation
Indices: 445519--445546 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
445509 TATTAAAAGC
445519 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
445547 AGTATTGAGA
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:445845 original size:12 final size:12
Alignment explanation
Indices: 445828--445852 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
445818 AAAACATAAG
445828 ATTGCAGATTGC
1 ATTGCAGATTGC
445840 ATTGCAGATTGC
1 ATTGCAGATTGC
445852 A
1 A
445853 ATGATCATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (12 bp):
ATTGCAGATTGC
Found at i:455441 original size:23 final size:22
Alignment explanation
Indices: 455398--455441 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
455388 TATTAATTCC
* *
455398 TAACATAACAAATACAGAACAA
1 TAACATAACAAATAAAAAACAA
*
455420 TAACATGACCAAATAAAAAACA
1 TAACAT-AACAAATAAAAAACA
455442 TTTACCAGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.64, C:0.18, G:0.05, T:0.14
Consensus pattern (22 bp):
TAACATAACAAATAAAAAACAA
Found at i:463180 original size:21 final size:20
Alignment explanation
Indices: 463144--463188 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
463134 GTGATTTTTG
*
463144 TTGTATGAACTTTTA-TCAT
1 TTGTATGAACTCTTATTCAT
463163 TTGTAATGAAACTCTTATTCAT
1 TTGT-ATG-AACTCTTATTCAT
463185 TTGT
1 TTGT
463189 GTGTTGTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 3 0.14
21 7 0.32
22 8 0.36
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (20 bp):
TTGTATGAACTCTTATTCAT
Found at i:473901 original size:14 final size:14
Alignment explanation
Indices: 473882--473908 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
473872 TTGTTATGGA
473882 ATATAAATATATAT
1 ATATAAATATATAT
473896 ATATAAATATATA
1 ATATAAATATATA
473909 AGCAATCAAA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATAAATATATAT
Found at i:474882 original size:19 final size:18
Alignment explanation
Indices: 474860--474909 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
474850 TTATTGACAT
474860 TAAATTTTATTATATTTGA
1 TAAATTTTATTATATTT-A
* *
474879 TAAATATTATAATATTTA
1 TAAATTTTATTATATTTA
**
474897 TAGTTTTTATTAT
1 TAAATTTTATTAT
474910 GAATTGAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (18 bp):
TAAATTTTATTATATTTA
Found at i:475117 original size:23 final size:24
Alignment explanation
Indices: 475073--475126 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 24
475063 TTAATAAACA
*
475073 TATTAACTATATCATATGATACGTT
1 TATTAAATATATCATATGATAC-TT
*
475098 TATTAAATATATC-T-TTATACTT
1 TATTAAATATATCATATGATACTT
*
475120 TGTTAAA
1 TATTAAA
475127 ATTTTGACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 8 0.31
23 5 0.19
24 1 0.04
25 12 0.46
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (24 bp):
TATTAAATATATCATATGATACTT
Found at i:478438 original size:28 final size:26
Alignment explanation
Indices: 478420--478470 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
478410 ACCCTATTAG
478420 GAGTGAATGAATATTTTTAACCCATAA
1 GAGTGAATGAATATTTTT-ACCCATAA
*
478447 GAGTGAATGAATATTTTTAACCAT
1 GAGTGAATGAATATTTTTACCCAT
478471 CATGAATGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (26 bp):
GAGTGAATGAATATTTTTACCCATAA
Found at i:479368 original size:312 final size:311
Alignment explanation
Indices: 478804--479419 Score: 916
Period size: 312 Copynumber: 2.0 Consensus size: 311
478794 ATATTTAATG
478804 TTCTCTTATGTTAACTTATAAGTTTTTTATTATATATATTATCTTATTGAAAAAAATATTTATAT
1 TTCTCTTATGTTAACTTATAAGTTTTTTATTATATATATTATCTTATTGAAAAAAATATTTATAT
* *
478869 TTATTATATTCATCTTATTGAATCCAAGATCAATGATGTAAATATATGTCTAGCAAACATTGCTA
66 TTATTATATTCATCTTATTGAATCCAAGATCAATAATGTAAATATATGTCTAGCAAACATTACTA
478934 TATACACTCTATATTTAAAGATAAAAAATATTTTCACACTTGACAATGGAAGAAACCAATTTCAA
131 TATACACTCTATATTTAAAGATAAAAAATATTTTCACACTTGACAATGGAAGAAACCAATTTCAA
* *
478999 TAAAATATCTACAAGTACAAGATTAATTGAAAACTTCGAAGGAGTCAATATTTTACTACCTAGAG
196 TAAAATATCTACAAGTACAAGATTAATTGAAAACTCCGAAGGAGCCAATATTTTACTACCTAGAG
* *
479064 GAATAAAGTTTATAATAAAAGATGAATTATTTTTTACGAAGTCTCAAAATA
261 GAATAAAATTTATAATAAAAGATGAATTATTTTCTACGAAGTCTCAAAATA
* * * *
479115 TTCTCTTATGTTAACTTGTAAGTTTTTTATTGA-GTATATTATCTTATTG-CAAAAATATTTATC
1 TTCTCTTATGTTAACTTATAAGTTTTTTATT-ATATATATTATCTTATTGAAAAAAATATTTATA
* * * * * *
479178 TTTATTATATTCATCTTATTGGATTCAAGATCAATAATGTAAATATGTGTTTAGCAGATATTACT
65 TTTATTATATTCATCTTATTGAATCCAAGATCAATAATGTAAATATATGTCTAGCAAACATTACT
** * * * *
479243 ATAATGTA-TACTATATTTAAAGATAAGAAATATTTTTCATACTTGACGATGGAAGCAACCAATT
130 AT-ATACACT-CTATATTTAAAGATAAAAAATA-TTTTCACACTTGACAATGGAAGAAACCAATT
* *
479307 TCAATAAAATATCTAGAAGTACAAGATTAATTGAAAGCTCCAGAA-GAGCCAATATTTTACTACC
192 TCAATAAAATATCTACAAGTACAAGATTAATTGAAAACTCC-GAAGGAGCCAATATTTTACTACC
* * *
479371 TAGAGGAATAAAATTTATAATAGAAGATGTATTATTTTCTACTAAGTCT
256 TAGAGGAATAAAATTTATAATAAAAGATGAATTATTTTCTACGAAGTCT
479420 TAAAGAAATT
Statistics
Matches: 273, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
310 72 0.26
311 69 0.25
312 129 0.47
313 3 0.01
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (311 bp):
TTCTCTTATGTTAACTTATAAGTTTTTTATTATATATATTATCTTATTGAAAAAAATATTTATAT
TTATTATATTCATCTTATTGAATCCAAGATCAATAATGTAAATATATGTCTAGCAAACATTACTA
TATACACTCTATATTTAAAGATAAAAAATATTTTCACACTTGACAATGGAAGAAACCAATTTCAA
TAAAATATCTACAAGTACAAGATTAATTGAAAACTCCGAAGGAGCCAATATTTTACTACCTAGAG
GAATAAAATTTATAATAAAAGATGAATTATTTTCTACGAAGTCTCAAAATA
Found at i:483861 original size:8 final size:8
Alignment explanation
Indices: 483845--483878 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
483835 ACTAAATACT
*
483845 TTCTTTTA
1 TTCTCTTA
483853 TTCTCTTA
1 TTCTCTTA
483861 TTTCTCTTA
1 -TTCTCTTA
483870 TTCTCTTA
1 TTCTCTTA
483878 T
1 T
483879 ATTTCATAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.68
Consensus pattern (8 bp):
TTCTCTTA
Found at i:483864 original size:17 final size:17
Alignment explanation
Indices: 483844--483878 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
483834 CACTAAATAC
*
483844 TTTCTTTTATTCTCTTA
1 TTTCTCTTATTCTCTTA
483861 TTTCTCTTATTCTCTTA
1 TTTCTCTTATTCTCTTA
483878 T
1 T
483879 ATTTCATAGC
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:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTCTCTTATTCTCTTA
Found at i:485522 original size:85 final size:84
Alignment explanation
Indices: 485377--485693 Score: 501
Period size: 85 Copynumber: 3.7 Consensus size: 84
485367 TTCAAAGAGC
* * *
485377 TTAATGTTTAAAATTATTGTTGGGATATTTAATTAAAATGATTAGCAATATGCTAGAATTAAACA
1 TTAATGTTTAGAATTATTGTTTGGATATTCAATTAAAATGATTAGCAATATGCTAGAATTAAACA
485442 TTAAGAATTATGTTTGGAAA
66 TTAAGAATTATGTTTGG-AA
* *
485462 TTAATGTTTAGAATTATTGTTTGGATATTCAATTAAAATGATTGGCAATATGCTAAAATTAAACA
1 TTAATGTTTAGAATTATTGTTTGGATATTCAATTAAAATGATTAGCAATATGCTAGAATTAAACA
485527 TTAAGAATTATGTTTGGGAA
66 TTAAGAATTATGTTT-GGAA
* * *
485547 TTAAAGTTTAGAATTATTATCTGGATATTCAATTAAAATGATTAGCAATATGCT-GTAATTAAAC
1 TTAATGTTTAGAATTATTGTTTGGATATTCAATTAAAATGATTAGCAATATGCTAG-AATTAAAC
*
485611 ATTAAGAATTATATTTTGGAA
65 ATTAAGAATTAT-GTTTGGAA
*
485632 TTAATGTTTAGAATTATTGTTTGGATATTCAATTAAAATGATTGGCAATATGCTAGAATTAA
1 TTAATGTTTAGAATTATTGTTTGGATATTCAATTAAAATGATTAGCAATATGCTAGAATTAA
485694 TAATTAAAAT
Statistics
Matches: 213, Mismatches: 15, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
85 207 0.97
86 6 0.03
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (84 bp):
TTAATGTTTAGAATTATTGTTTGGATATTCAATTAAAATGATTAGCAATATGCTAGAATTAAACA
TTAAGAATTATGTTTGGAA
Found at i:488495 original size:18 final size:18
Alignment explanation
Indices: 488459--488498 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
488449 GATTTAACCA
**
488459 AATTAATTGAATTTTTTC
1 AATTAATTGAATTACTTC
*
488477 AATTAATTTAATTACTTC
1 AATTAATTGAATTACTTC
488495 AATT
1 AATT
488499 TTGATCGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (18 bp):
AATTAATTGAATTACTTC
Found at i:489041 original size:23 final size:22
Alignment explanation
Indices: 489015--489059 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
489005 TAAATATATT
489015 TAAAAACTAAGAATTTTAAAAAA
1 TAAAAACTAAGAA-TTTAAAAAA
* * *
489038 TAAATACTTATAATTTAAAAAA
1 TAAAAACTAAGAATTTAAAAAA
489060 CACTTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAAACTAAGAATTTAAAAAA
Found at i:489282 original size:22 final size:23
Alignment explanation
Indices: 489252--489297 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
489242 TGTCATCTCA
*
489252 TAAATAAA-TAAAGATAAA-ATTT
1 TAAAAAAATTAAA-ATAAATATTT
489274 TAAAAAAATTAAAATAAATATTT
1 TAAAAAAATTAAAATAAATATTT
489297 T
1 T
489298 TGCAGAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAAAAATTAAAATAAATATTT
Found at i:495288 original size:42 final size:43
Alignment explanation
Indices: 495228--495312 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 43
495218 TATATTTGAT
*
495228 TCTTAATAATCCAAAAACTGATTGACTATGGTC-TCACTTCAA
1 TCTTAATAATCCAAAAACTGATTGACTATAGTCTTCACTTCAA
*
495270 TCTTAATAATCCAGAAACTGATTGACTATAGTCTTCACTTCAA
1 TCTTAATAATCCAAAAACTGATTGACTATAGTCTTCACTTCAA
495313 ATAACAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 31 0.77
43 9 0.22
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.34
Consensus pattern (43 bp):
TCTTAATAATCCAAAAACTGATTGACTATAGTCTTCACTTCAA
Found at i:498742 original size:30 final size:30
Alignment explanation
Indices: 498706--498765 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
498696 CAAAAAGGGA
498706 AAAGGTAGGAGAAAAAATAAGATGTTTGTG
1 AAAGGTAGGAGAAAAAATAAGATGTTTGTG
* *
498736 AAAGGTAGGAGAAGAAATAGGATGTTTGTG
1 AAAGGTAGGAGAAAAAATAAGATGTTTGTG
498766 GTTGATCTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.33, T:0.23
Consensus pattern (30 bp):
AAAGGTAGGAGAAAAAATAAGATGTTTGTG
Found at i:501093 original size:44 final size:43
Alignment explanation
Indices: 501029--501116 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 43
501019 CCTATATTTG
* * **
501029 ATTCTTAATACTCCAAAAACTGATTGACTATGGTCTTCATTTCA
1 ATTCTTAAAAATCCAAAAACTGATTG-CTATACTCTTCATTTCA
*
501073 ATTCTTAAAAATCCAGAAACTGATTGCTATACTCTTCATTTCA
1 ATTCTTAAAAATCCAAAAACTGATTGCTATACTCTTCATTTCA
501116 A
1 A
501117 ATAACAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 16 0.41
44 23 0.59
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (43 bp):
ATTCTTAAAAATCCAAAAACTGATTGCTATACTCTTCATTTCA
Found at i:505917 original size:23 final size:22
Alignment explanation
Indices: 505889--505932 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
505879 TAAAACAGAG
505889 ATCAAAATAAATAAAACCTTAAA
1 ATCAAAATAAA-AAAACCTTAAA
* *
505912 ATCAAAATTAAGAAACCTTAA
1 ATCAAAATAAAAAAACCTTAA
505933 GATGCAGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.61, C:0.14, G:0.02, T:0.23
Consensus pattern (22 bp):
ATCAAAATAAAAAAACCTTAAA
Found at i:506309 original size:219 final size:214
Alignment explanation
Indices: 506050--506443 Score: 617
Period size: 215 Copynumber: 1.8 Consensus size: 214
506040 TATCGAAAAA
* * * *
506050 AAAGGAAGCAATTGAGCTGTTGGTGGAGCGACATTGAGAGAAAACCAAAAAGAAAAGAAAATGAA
1 AAAGGAAGCAATTGAACTGTTGGAGGAGCGAAACTGAGAGAAAA-C--AAA-AAAAGAAAATGAA
*
506115 TTTTAACTTTTAAAATACTTAATATTAAAAAATCAAATTTTATATTAATCTCATTACACACTTTT
62 TTTTAACTTTTAAAATACTTAATATTAAAAAATCAAATTTCATATTAATCTCATTACACACTTTT
*
506180 GAATGAATGAATCTTCTTTTCCAAAATAAGTTTTACTCAAAATTAATCTAAGAAAAACAAAACCG
127 GAATGAATGAATCGTCTTTTCCAAAATAAGTTTTACTCAAAATTAATCTAAGAAAAACAAAACCG
506245 AAACCCTAAAGAACTTATCGGAT
192 AAACCCTAAAGAACTTATCGGAT
* **
506268 AAAGGAAGGTAATTGAACTGTTGGAGGAGCGAAACTGAGAGAAAACGGAAAAAGAAAATGAATTT
1 AAAGGAA-GCAATTGAACTGTTGGAGGAGCGAAACTGAGAGAAAACAAAAAAAGAAAATGAATTT
* * *
506333 TAACTTTTAAAATTCTTAATATTAGAAAATCAAATTTCATATTAATCTCATTGCACACTTTTGAA
65 TAACTTTTAAAATACTTAATATTAAAAAATCAAATTTCATATTAATCTCATTACACACTTTTGAA
* *
506398 TGAATGAATCGTCTTTTCCAAAATGAGTTTTACTTAAAATTAATCT
130 TGAATGAATCGTCTTTTCCAAAATAAGTTTTACTCAAAATTAATCT
506444 TTTTGTGCTA
Statistics
Matches: 161, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
215 120 0.75
216 1 0.01
218 8 0.05
219 32 0.20
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (214 bp):
AAAGGAAGCAATTGAACTGTTGGAGGAGCGAAACTGAGAGAAAACAAAAAAAGAAAATGAATTTT
AACTTTTAAAATACTTAATATTAAAAAATCAAATTTCATATTAATCTCATTACACACTTTTGAAT
GAATGAATCGTCTTTTCCAAAATAAGTTTTACTCAAAATTAATCTAAGAAAAACAAAACCGAAAC
CCTAAAGAACTTATCGGAT
Found at i:514600 original size:18 final size:19
Alignment explanation
Indices: 514579--514653 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 19
514569 GATTAAAATT
514579 TTAAATAAAATTAATAT-A
1 TTAAATAAAATTAATATAA
* **
514597 TTAAACATGATTAATATAA
1 TTAAATAAAATTAATATAA
514616 TTAAATTAAAATGT-ATATAA
1 TTAAA-TAAAAT-TAATATAA
514636 TTACAACTAAAATATAAT
1 TTA-AA-TAAAAT-TAAT
514654 TTATAATTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
18 14 0.32
19 6 0.14
20 12 0.27
21 10 0.23
22 2 0.05
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (19 bp):
TTAAATAAAATTAATATAA
Found at i:514635 original size:20 final size:21
Alignment explanation
Indices: 514610--514648 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
514600 AACATGATTA
*
514610 ATATAATTA-AATTAAAATGT
1 ATATAATTACAACTAAAATGT
514630 ATATAATTACAACTAAAAT
1 ATATAATTACAACTAAAAT
514649 ATAATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (21 bp):
ATATAATTACAACTAAAATGT
Found at i:535516 original size:6 final size:6
Alignment explanation
Indices: 535501--535558 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
535491 GATTGATATT
* * * ** *
535501 ACAACA ACAACG ACAATA ACAATA ACAACA ACAATG ACAACA ACAATA
1 ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA
535549 ACAACA ACAA
1 ACAACA ACAA
535559 TAATAATAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.64, C:0.26, G:0.03, T:0.07
Consensus pattern (6 bp):
ACAACA
Found at i:535521 original size:12 final size:12
Alignment explanation
Indices: 535501--535561 Score: 86
Period size: 12 Copynumber: 5.1 Consensus size: 12
535491 GATTGATATT
**
535501 ACAACAACAACG
1 ACAACAACAATA
*
535513 ACAATAACAATA
1 ACAACAACAATA
*
535525 ACAACAACAATG
1 ACAACAACAATA
535537 ACAACAACAATA
1 ACAACAACAATA
535549 ACAACAACAATA
1 ACAACAACAATA
535561 A
1 A
535562 TAATAATAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.64, C:0.25, G:0.03, T:0.08
Consensus pattern (12 bp):
ACAACAACAATA
Found at i:535559 original size:24 final size:24
Alignment explanation
Indices: 535501--535559 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
535491 GATTGATATT
* *
535501 ACAACAACAACGACAATAACAATA
1 ACAACAACAATGACAACAACAATA
535525 ACAACAACAATGACAACAACAATA
1 ACAACAACAATGACAACAACAATA
535549 ACAACAACAAT
1 ACAACAACAAT
535560 AATAATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.63, C:0.25, G:0.03, T:0.08
Consensus pattern (24 bp):
ACAACAACAATGACAACAACAATA
Found at i:538007 original size:19 final size:19
Alignment explanation
Indices: 537980--538018 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
537970 ATACTTTTTT
*
537980 ATTTTTTATTAATTTAAAA
1 ATTTATTATTAATTTAAAA
*
537999 ATTTATTATTATTTTAAAA
1 ATTTATTATTAATTTAAAA
538018 A
1 A
538019 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTATTATTAATTTAAAA
Found at i:542408 original size:15 final size:15
Alignment explanation
Indices: 542390--542418 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
542380 AATTCTGTTT
542390 AGAAAAACTTGTAAC
1 AGAAAAACTTGTAAC
542405 AGAAAAACTTGTAA
1 AGAAAAACTTGTAA
542419 ATTTTCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.14, T:0.21
Consensus pattern (15 bp):
AGAAAAACTTGTAAC
Found at i:543776 original size:45 final size:45
Alignment explanation
Indices: 543680--543769 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
543670 ACTTCTTTAG
543680 TATCACAAATACATGAGCCAAGTTCTTATCATGAAGCCATTAATC
1 TATCACAAATACATGAGCCAAGTTCTTATCATGAAGCCATTAATC
543725 TATCACAAATACATGAGCCAAGTTCTTATCATGAAGCCATTAATC
1 TATCACAAATACATGAGCCAAGTTCTTATCATGAAGCCATTAATC
543770 ATTCACATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (45 bp):
TATCACAAATACATGAGCCAAGTTCTTATCATGAAGCCATTAATC
Found at i:552430 original size:26 final size:27
Alignment explanation
Indices: 552357--552430 Score: 93
Period size: 26 Copynumber: 2.8 Consensus size: 27
552347 ATGTTACAAT
*
552357 TAAAATA-AA-AATATTAAAATAAAACA
1 TAAAATATAAGAA-ATTAAAATTAAACA
552383 TAAAATATAAG-AATTAGAAATTAAA-A
1 TAAAATATAAGAAATTA-AAATTAAACA
552409 TAAAATATAAGAAATTAAAATT
1 TAAAATATAAGAAATTAAAATT
552431 TATATAATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
26 28 0.65
27 15 0.35
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (27 bp):
TAAAATATAAGAAATTAAAATTAAACA
Found at i:552790 original size:15 final size:15
Alignment explanation
Indices: 552757--552815 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
552747 TGTTATTTTT
* *
552757 CTTGTAATCGCATTG
1 CTTGTAATCACATTA
*
552772 CTTGTAATCACATCA
1 CTTGTAATCACATTA
* *
552787 CTTGCAATTACATTA
1 CTTGTAATCACATTA
552802 CTTGTAATCACATT
1 CTTGTAATCACATT
552816 GTATTATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (15 bp):
CTTGTAATCACATTA
Found at i:558980 original size:109 final size:109
Alignment explanation
Indices: 558730--559045 Score: 429
Period size: 109 Copynumber: 2.9 Consensus size: 109
558720 TGAAATAAAA
* * * *
558730 TTATAACATAAAATTTCATTAACAATTTAAACATAAATTTTCAAATTCACGAATATAGAAATATA
1 TTATAACATAAAATTTCATTAACAATTTAAATATAAGTTTTCAAATTCACCAATAT--AAATAGA
* * * * *
558795 TAAAGTACAAAGAAAAATAAACGTTAAA-TCTCACATTAGATAAAT
64 TAAAGTAGAAAGAAAAATTAACATTAAATTTTCACATTAGACAAAT
*
558840 TTATAACATAAAATTTCATTAACAATTTAAATATAAGTTTTCAAATTCACTAATATAAATAGATA
1 TTATAACATAAAATTTCATTAACAATTTAAATATAAGTTTTCAAATTCACCAATATAAATAGATA
558905 AAGTAGAAAGAAAAATTAACATTAAATTTTCACATTA-AGCAAAT
66 AAGTAGAAAGAAAAATTAACATTAAATTTTCACATTAGA-CAAAT
* * * * *
558949 TTATAACATAAAATTTTATTAACAATGTAAATATAAGTTTTTAGATTCACCAATATAAATAGAGA
1 TTATAACATAAAATTTCATTAACAATTTAAATATAAGTTTTCAAATTCACCAATATAAATAGATA
* * *
559014 AAGTAGAAAGAAAAACTGACATTAGATTTTCA
66 AAGTAGAAAGAAAAATTAACATTAAATTTTCA
559046 AAAGGGAAAA
Statistics
Matches: 186, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
108 32 0.17
109 101 0.54
110 53 0.28
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (109 bp):
TTATAACATAAAATTTCATTAACAATTTAAATATAAGTTTTCAAATTCACCAATATAAATAGATA
AAGTAGAAAGAAAAATTAACATTAAATTTTCACATTAGACAAAT
Found at i:561571 original size:92 final size:92
Alignment explanation
Indices: 561414--561601 Score: 331
Period size: 92 Copynumber: 2.0 Consensus size: 92
561404 TATAAAATGT
*
561414 TCAAATCATTATTTGATAGATCACCAAAGTCCCACAAGTAAAAAGCAAGCTGTTCATTTTTTAAT
1 TCAAATCATTATTTGATAGATCACCAAAGTCCCACAAGTAAAAAGCAAGCTGATCATTTTTTAAT
*
561479 AGCAATTGACATTTTGGCAAGCATCCC
66 AGCAATTGACATTCTGGCAAGCATCCC
* *
561506 TCAAATCATTATTTGATAGATCACCCAAGTCCCACAAGTTAAAAGCAAGCTGATCATTTTTTAAT
1 TCAAATCATTATTTGATAGATCACCAAAGTCCCACAAGTAAAAAGCAAGCTGATCATTTTTTAAT
*
561571 AGCAATTGACATTCTGTCAAGCATCCC
66 AGCAATTGACATTCTGGCAAGCATCCC
561598 TCAA
1 TCAA
561602 GCTCTACTTG
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (92 bp):
TCAAATCATTATTTGATAGATCACCAAAGTCCCACAAGTAAAAAGCAAGCTGATCATTTTTTAAT
AGCAATTGACATTCTGGCAAGCATCCC
Found at i:562771 original size:17 final size:16
Alignment explanation
Indices: 562749--562782 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
562739 GTTATTTTGC
*
562749 TTTAAGTTTAGTTATTA
1 TTTAAGTTAAGTT-TTA
562766 TTTAAGTTAAGTTTTA
1 TTTAAGTTAAGTTTTA
562782 T
1 T
562783 GTTTTTGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (16 bp):
TTTAAGTTAAGTTTTA
Found at i:566132 original size:3 final size:3
Alignment explanation
Indices: 566124--566158 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
566114 ATCAAAACTA
566124 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
566159 CACATTTCAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:567924 original size:44 final size:43
Alignment explanation
Indices: 567850--567937 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 43
567840 TTACTTCGAT
* ** *
567850 ATTTTTTTCTTTTAGCATTTAATGAAACTTGATAAAGTTTAAC
1 ATTTATTTCTTTTAGCATGCAATGAAACTTGATAAAGTTCAAC
* *
567893 ATTTATTTCTTTTTAGCATGCAGTGATACTTGATAAAGTTCAAC
1 ATTTATTTC-TTTTAGCATGCAATGAAACTTGATAAAGTTCAAC
567937 A
1 A
567938 AGATGTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
43 8 0.21
44 30 0.79
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (43 bp):
ATTTATTTCTTTTAGCATGCAATGAAACTTGATAAAGTTCAAC
Found at i:567960 original size:39 final size:39
Alignment explanation
Indices: 567917--567994 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
567907 AGCATGCAGT
567917 GATACTTGATAAAGTTCAACAAGATGTTTTAACGTACAA
1 GATACTTGATAAAGTTCAACAAGATGTTTTAACGTACAA
567956 GATACTTGATAAAGTTCAACAAGATGTTTTAACGTACAA
1 GATACTTGATAAAGTTCAACAAGATGTTTTAACGTACAA
567995 TAAGTACGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (39 bp):
GATACTTGATAAAGTTCAACAAGATGTTTTAACGTACAA
Found at i:567980 original size:22 final size:22
Alignment explanation
Indices: 567917--567980 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
567907 AGCATGCAGT
567917 GATACTTGATAAAGTTCAACAA
1 GATACTTGATAAAGTTCAACAA
* * *
567939 GAT-GTT-TTAACG-T--ACAA
1 GATACTTGATAAAGTTCAACAA
567956 GATACTTGATAAAGTTCAACAA
1 GATACTTGATAAAGTTCAACAA
567978 GAT
1 GAT
567981 GTTTTAACGT
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
17 7 0.23
18 2 0.06
19 5 0.16
20 5 0.16
21 2 0.06
22 10 0.32
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (22 bp):
GATACTTGATAAAGTTCAACAA
Found at i:568173 original size:30 final size:29
Alignment explanation
Indices: 568130--568230 Score: 103
Period size: 29 Copynumber: 3.4 Consensus size: 29
568120 TGTCAATTTT
*
568130 TAGTAGATTAAAAAGTATTCATCCACTTC
1 TAGTAGGTTAAAAAGTATTCATCCACTTC
** *
568159 TAGTTAGGTTAAAAAGTATTTGTCCATTTC
1 TAG-TAGGTTAAAAAGTATTCATCCACTTC
* * * *
568189 TTGTGGGTTAAAAAGTATCCATCCACTTT
1 TAGTAGGTTAAAAAGTATTCATCCACTTC
* *
568218 TGGTGGGTTAAAA
1 TAGTAGGTTAAAA
568231 CTATCTATCC
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 35 0.59
30 24 0.41
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.38
Consensus pattern (29 bp):
TAGTAGGTTAAAAAGTATTCATCCACTTC
Found at i:579309 original size:151 final size:151
Alignment explanation
Indices: 579032--579325 Score: 437
Period size: 151 Copynumber: 1.9 Consensus size: 151
579022 CTCTATACAT
* * * *
579032 ATAGATAGATAAATAAAAATACATTATTTTTCTTTAACCTTTTAAAGTAATTAAACAATGTAGAG
1 ATAGATAGATAAATAAAAATACATCATTGTTCTTTAACCTTTTAAAGTAATTAAACAATATAAAG
* *
579097 AAATTCCATTGAGGTTTTAGGATCAATGAGGCCACACCAACCGCCCTTCAAAAGCACTATATATA
66 AAATTCCATTGAGGTTTTAGGATCAAAGAGGCCACACCAACCACCCTTCAAAAGCACTATATATA
* *
579162 TATATATATATATATAGATAG
131 TATACATAGATATATAGATAG
* * *
579183 ATAGATAGATAGATAAAAATACATCATTGTTGTTTAACCTTTTCAAGTAATTAAACAATATAAAG
1 ATAGATAGATAAATAAAAATACATCATTGTTCTTTAACCTTTTAAAGTAATTAAACAATATAAAG
* * * *
579248 AAATTTCATTGAGTTTTTAGGATCAAAGAGGGCACACCAACCACCCTTTAAAAGCTA-TATATAT
66 AAATTCCATTGAGGTTTTAGGATCAAAGAGGCCACACCAACCACCCTTCAAAAGC-ACTATATAT
579312 ATATACATAGATAT
130 ATATACATAGATAT
579326 GTGGTGCACT
Statistics
Matches: 127, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
151 126 0.99
152 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (151 bp):
ATAGATAGATAAATAAAAATACATCATTGTTCTTTAACCTTTTAAAGTAATTAAACAATATAAAG
AAATTCCATTGAGGTTTTAGGATCAAAGAGGCCACACCAACCACCCTTCAAAAGCACTATATATA
TATACATAGATATATAGATAG
Found at i:580043 original size:2 final size:2
Alignment explanation
Indices: 580036--580061 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
580026 ATTATATGTG
580036 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
580062 AAGTTCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:585101 original size:20 final size:19
Alignment explanation
Indices: 585076--585118 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
585066 CACTCCTTCA
* *
585076 ATTTTTTCTTTGTTTTTAAT
1 ATTTTTTATTT-TATTTAAT
585096 A-TTTTTATTTTATTTAAT
1 ATTTTTTATTTTATTTAAT
585114 ATTTT
1 ATTTT
585119 AAGTTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.40
19 11 0.55
20 1 0.05
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (19 bp):
ATTTTTTATTTTATTTAAT
Found at i:592353 original size:83 final size:84
Alignment explanation
Indices: 592218--592383 Score: 210
Period size: 83 Copynumber: 2.0 Consensus size: 84
592208 AGGTGACATG
* ** * ** *
592218 CCACGCTCCAATTGTTAGATGTCGTTGACATCTTGTCGTGACACGTCCCCATGTTGTTGTAGTAT
1 CCACGCTCCAATTGTTAGAGGTCGCCGACATCTTGTCGTGACACGTCACCATGTCATTGCAGTAT
*
592283 TATAGGGTGACAAGCCACT
66 TATAAGGTGACAAGCCACT
* *
592302 CCACGCTTCAATTGTTAG-GGTCGCCGACATCTTGTCGTGGCACG-CGACCATGTCATTGCAGTA
1 CCACGCTCCAATTGTTAGAGGTCGCCGACATCTTGTCGTGACACGTC-ACCATGTCATTGCAGTA
*
592365 TTATAAGGTGACACGCCAC
65 TTATAAGGTGACAAGCCAC
592384 GCTCTAATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
82 1 0.01
83 52 0.74
84 17 0.24
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (84 bp):
CCACGCTCCAATTGTTAGAGGTCGCCGACATCTTGTCGTGACACGTCACCATGTCATTGCAGTAT
TATAAGGTGACAAGCCACT
Found at i:594867 original size:22 final size:22
Alignment explanation
Indices: 594796--594896 Score: 130
Period size: 22 Copynumber: 4.5 Consensus size: 22
594786 GCAATGCTTA
* *
594796 AGTCACACAATGCCTTACTAACT
1 AGTCACGCAATG-CTTACCAACT
** * *
594819 AGTCATACAATAGCTTACTAACA
1 AGTCACGCAAT-GCTTACCAACT
594842 AGTCACGCAATGCTTACCAACT
1 AGTCACGCAATGCTTACCAACT
594864 AGTCACGCAATGCTTACCAACT
1 AGTCACGCAATGCTTACCAACT
594886 AGTCACGCAAT
1 AGTCACGCAAT
594897 ACCTAAAAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
22 42 0.59
23 28 0.39
24 1 0.01
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.24
Consensus pattern (22 bp):
AGTCACGCAATGCTTACCAACT
Found at i:594967 original size:21 final size:21
Alignment explanation
Indices: 594921--594967 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
594911 CATGCAAAGC
* *
594921 CCAAAGTTAGTCACACAATGT
1 CCAAAGTAAGTCACACAATAT
* *
594942 ACAAAGTAAGTCACACAGTAT
1 CCAAAGTAAGTCACACAATAT
594963 CCAAA
1 CCAAA
594968 ATCATCAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.23, G:0.13, T:0.19
Consensus pattern (21 bp):
CCAAAGTAAGTCACACAATAT
Found at i:601974 original size:14 final size:16
Alignment explanation
Indices: 601945--601978 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
601935 CTTACTAAAT
601945 TAAAATAAATTAAAAA
1 TAAAATAAATTAAAAA
601961 TAAAA-AAA-TAAAAA
1 TAAAATAAATTAAAAA
601975 TAAA
1 TAAA
601979 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 3 0.17
16 5 0.28
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
TAAAATAAATTAAAAA
Found at i:604927 original size:74 final size:74
Alignment explanation
Indices: 604806--604946 Score: 237
Period size: 74 Copynumber: 1.9 Consensus size: 74
604796 AAACCTATAT
* * *
604806 TTATAAATACGTATTCATTAAATGATGATCATTGAAATTTTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATACGTATTCATCAAATAATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
604871 TTAAACTTA
66 TTAAACTTA
**
604880 TTATAAATGTGTATTCATCAAATAATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATACGTATTCATCAAATAATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
604945 TT
66 TT
604947 TTTTCATTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (74 bp):
TTATAAATACGTATTCATCAAATAATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
TTAAACTTA
Found at i:605099 original size:30 final size:33
Alignment explanation
Indices: 605031--605110 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 33
605021 GTTGTATAAT
605031 TTAAATATTAATATTTTAAATTAATTATTTTAAAG
1 TTAAATATTAATATTTT--ATTAATTATTTTAAAG
*
605066 TTAAATATTAATATTTT-TTTA-TATTTT-AAG
1 TTAAATATTAATATTTTATTAATTATTTTAAAG
605096 TTAAATATTAATATT
1 TTAAATATTAATATT
605111 CATCAAACTT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
30 18 0.41
31 6 0.14
32 3 0.07
35 17 0.39
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (33 bp):
TTAAATATTAATATTTTATTAATTATTTTAAAG
Found at i:619408 original size:30 final size:30
Alignment explanation
Indices: 619373--619447 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
619363 TTTTTTTGTT
*
619373 AAATAAGTCTTTATATTTTTATTTTCAGTC
1 AAATAAGTCTTTATATTTTTATTTTAAGTC
* *
619403 AAATAAATTTTTATATTTTTATTTTAAGTC
1 AAATAAGTCTTTATATTTTTATTTTAAGTC
619433 AAATAAG-CATTTATA
1 AAATAAGTC-TTTATA
619448 ATTAATTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (30 bp):
AAATAAGTCTTTATATTTTTATTTTAAGTC
Found at i:626314 original size:6 final size:6
Alignment explanation
Indices: 626303--626336 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
626293 GGAATCGAGG
626303 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT-CT TTT
626337 GGGGCCAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:633802 original size:30 final size:31
Alignment explanation
Indices: 633752--633818 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
633742 CGTTTGGTAC
633752 ATTACAATACAATATGATTGCAAGTAATATA
1 ATTACAATACAATATGATTGCAAGTAATATA
* * * *
633783 ATTACAA-ATAATGTGATTGCAAGTAATGTG
1 ATTACAATACAATATGATTGCAAGTAATATA
633813 ATTACA
1 ATTACA
633819 GGGAAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (31 bp):
ATTACAATACAATATGATTGCAAGTAATATA
Found at i:633809 original size:15 final size:15
Alignment explanation
Indices: 633766--633815 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
633756 CAATACAATA
*
633766 TGATTGCAAGTAATA
1 TGATTGCAAGTAATG
* * *
633781 TAATTACAAATAATG
1 TGATTGCAAGTAATG
633796 TGATTGCAAGTAATG
1 TGATTGCAAGTAATG
633811 TGATT
1 TGATT
633816 ACAGGGAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (15 bp):
TGATTGCAAGTAATG
Found at i:634171 original size:26 final size:26
Alignment explanation
Indices: 634142--634319 Score: 72
Period size: 26 Copynumber: 6.8 Consensus size: 26
634132 TTTTAATATC
634142 ATATATTTTATTTTTATTATTATTAA
1 ATATATTTTATTTTTATTATTATTAA
* * *
634168 ATATTTTTTATTATTT-TTAATA-TAT
1 ATATATTTTATT-TTTATTATTATTAA
* *
634193 TTATATTTATATTATTAATT-TTA-TATA
1 ATATATTT-TATT-TTTATTATTATTA-A
** * *
634220 ATATCATTTCTTAAATATATT-TTAATGT-C
1 ATAT-A-TT-TTATTTTTATTATT-AT-TAA
*
634249 ATATATTTTATTTTTATTTATTATTAT
1 ATATATTTTATTTTTA-TTATTATTAA
*
634276 A-ATATTTTATATTTA-T-TT-TT-A
1 ATATATTTTATTTTTATTATTATTAA
*
634297 ATATATTTATATTTATATTATTA
1 ATATATTT-TATTTTTATTATTA
634320 ATTTTTATTA
Statistics
Matches: 112, Mismatches: 22, Indels: 36
0.66 0.13 0.21
Matches are distributed among these distances:
21 1 0.01
22 8 0.07
23 8 0.07
24 2 0.02
25 10 0.09
26 47 0.42
27 15 0.13
28 10 0.09
29 9 0.08
30 1 0.01
31 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (26 bp):
ATATATTTTATTTTTATTATTATTAA
Found at i:634173 original size:111 final size:111
Alignment explanation
Indices: 633965--634488 Score: 695
Period size: 111 Copynumber: 4.8 Consensus size: 111
633955 AAAATATAAG
633965 TTTAATATATTTATATTT-TATTTATTAA-TTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTATA-TTATTAATTTTATATAATATCATTTCTTAAATATATTTTTAAT
*
634028 ATCATATATTTTATTTTT-TAT-TTATTATAATATTTTATATTTTAT
65 ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTAT
634073 TTTAATATATTTATATTTTTATTATTATTAATTTTATATAATATCATTTCTTAAATATA-TTTTA
1 TTTAATATATTTATA--TTTA-TATTATTAATTTTATATAATATCATTTCTTAAATATATTTTTA
* *
634137 ATATCATATATTTTATTTTTA-TTATTATTA-AATATTTTTTATTAT-T
63 ATATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTAT
*
634183 TTTAATATATTTATATTTATATTATTAATTTTATATAATATCATTTCTTAAATATA-TTTTAATG
1 TTTAATATATTTATATTTATATTATTAATTTTATATAATATCATTTCTTAAATATATTTTTAATA
634247 TCATATATTTTATTTTTATTTATTATTATAATATTTTATA-TTTATT
66 TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTA-T
634293 TTTAATATATTTATATTTATATTATTAATTTT-TATTAATATCATATT-TTAAATATATTTTTAA
1 TTTAATATATTTATATTTATATTATTAATTTTATA-TAATATCAT-TTCTTAAATATATTTTTAA
*
634356 TGTCATATATTTTATTTTTATTTATTATTATAATATTTATATATTTTAT
64 TATCATATATTTTATTTTTATTTATTATTATAATATTT-TATATTTTAT
* * * * * * * *
634405 TTTCATTTCTTTA-A--TATATTTTTATATTATATATTTTATTTCATTTCTT-AATATATTTTTT
1 TTTAATATATTTATATTTATATTATTA-ATT-T-TATATAATATCATTTCTTAAATATATTTTTA
* *
634466 ATATTATATA-TTTATTTTAATTT
63 ATATCATATATTTTATTTTTATTT
634489 GTTTTATCTA
Statistics
Matches: 378, Mismatches: 17, Indels: 40
0.87 0.04 0.09
Matches are distributed among these distances:
107 62 0.16
108 30 0.08
109 21 0.06
110 85 0.22
111 115 0.30
112 60 0.16
113 5 0.01
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (111 bp):
TTTAATATATTTATATTTATATTATTAATTTTATATAATATCATTTCTTAAATATATTTTTAATA
TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTAT
Found at i:634177 original size:20 final size:21
Alignment explanation
Indices: 634152--634211 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 21
634142 ATATATTTTA
634152 TTTTTATTATTATTAA-ATAT
1 TTTTTATTATTATTAATATAT
*
634172 TTTTTATTATTTTTAATATAT
1 TTTTTATTATTATTAATATAT
634193 TTATATT-TATATTATTAAT
1 TT-T-TTAT-TATTATTAAT
634212 TTTATATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 15 0.44
21 6 0.18
22 2 0.06
23 11 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTTATTATTATTAATATAT
Found at i:634212 original size:218 final size:222
Alignment explanation
Indices: 633965--634483 Score: 694
Period size: 218 Copynumber: 2.4 Consensus size: 222
633955 AAAATATAAG
633965 TTTAATATATTTATATTT-TATTTATTAATTTATATAATATCATTTCTTAAATATATTTTTAATA
1 TTTAATATATTTATATTTATA-TTATTAATTTATATAATATCATTTCTTAAATATATTTTTAATA
634029 TCATATATTTTATTTTT-TAT-TTATTATAATATTTTATATTT-TATTTTAATATATTTATATTT
65 TCATATATTTTATTTTTATATATTATTATAATATTTTATATTTAT-TTTTAATATATTTATA--T
634091 TTATTATTATTAA-TTTTATATAATATCAT-TTCTTAAATATA-TTTTAATATCATATATTTTAT
127 TTA-TATTATTAATTTTTAT-TAATATCATATT-TTAAATATATTTTTAATATCATATATTTTAT
*
634153 TTTTA-TTATTATTA-AATATTT-TTTATTAT-T
189 TTTTATTTATTATTATAATATTTATATATTATAT
*
634183 TTTAATATATTTATATTTATATTATTAATTTTATATAATATCATTTCTTAAATATA-TTTTAATG
1 TTTAATATATTTATATTTATATTATTAA-TTTATATAATATCATTTCTTAAATATATTTTTAATA
*
634247 TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATTTTTAATATATTTATATTTA
65 TCATATATTTTATTTTTATATATTATTATAATATTTTATATTTATTTTTAATATATTTATATTTA
*
634312 TATTATTAATTTTTATTAATATCATATTTTAAATATATTTTTAATGTCATATATTTTATTTTTAT
130 TATTATTAATTTTTATTAATATCATATTTTAAATATATTTTTAATATCATATATTTTATTTTTAT
*
634377 TTATTATTATAATATTTATATATTTTAT
195 TTATTATTATAATATTTATATATTATAT
* * * * * * *
634405 TTTCATTTCTTTA-A--TATATTTTTATATTATATATTTTATTTCATTTCTT-AATATATTTTTT
1 TTTAATATATTTATATTTATATTATTA-ATT-TATA--TAATATCATTTCTTAAATATATTTTTA
*
634466 ATATTATATA-TTTATTTT
62 ATATCATATATTTTATTTT
634484 AATTTGTTTT
Statistics
Matches: 270, Mismatches: 14, Indels: 31
0.86 0.04 0.10
Matches are distributed among these distances:
217 27 0.10
218 86 0.32
219 51 0.19
220 49 0.18
221 22 0.08
222 35 0.13
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (222 bp):
TTTAATATATTTATATTTATATTATTAATTTATATAATATCATTTCTTAAATATATTTTTAATAT
CATATATTTTATTTTTATATATTATTATAATATTTTATATTTATTTTTAATATATTTATATTTAT
ATTATTAATTTTTATTAATATCATATTTTAAATATATTTTTAATATCATATATTTTATTTTTATT
TATTATTATAATATTTATATATTATAT
Found at i:634403 original size:34 final size:32
Alignment explanation
Indices: 634360--634482 Score: 102
Period size: 34 Copynumber: 3.6 Consensus size: 32
634350 TTTTAATGTC
*
634360 ATATATTTTATTTTTATTTATTATTATAATATTT
1 ATATATTTTATTTTTATTTATT-TAAT-ATATTT
* *
634394 ATATATTTTATTTTCATTTCTTTAATATATTT
1 ATATATTTTATTTTTATTTATTTAATATATTT
* *
634426 TTATATTATATATTTTATTTCATTTCTTAATATATTTT
1 ATATATTTTAT-TTTTATTT-A--T-TTAATATA-TTT
* * *
634464 TTATATTATATATTTATTT
1 ATATATTTTATTTTTATTT
634483 TAATTTGTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
32 15 0.20
33 10 0.13
34 20 0.27
36 1 0.01
37 15 0.20
38 14 0.19
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (32 bp):
ATATATTTTATTTTTATTTATTTAATATATTT
Found at i:634424 original size:58 final size:57
Alignment explanation
Indices: 634031--634426 Score: 232
Period size: 58 Copynumber: 7.2 Consensus size: 57
634021 TTTTAATATC
* *
634031 ATATATTTTATTTTT-TAT-TTATTATAATATTTTATATTT-TATTTTAATATATTT-
1 ATATATTTTATTTTTATTTATTATTATAATATTTTATATTTAT-TTTTAATATCTTTA
* * * * **
634085 ATAT-TTTTATTATTATTAATTTTATATAATATCATTTCTTAAATATATTTTAATATC----
1 ATATATTTTATTTTTATTTATTAT-TATAATAT--TTT-ATATTTAT-TTTTAATATCTTTA
* *
634142 ATATATTTTATTTTTA-TTATTATTA-AATATTTTTTA-TTATTTTTAATATATTT-
1 ATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATTTTTAATATCTTTA
* * * * ** *
634195 ATAT-TTATATTATTAATT-TTA-TATAATATCATTTCTTAAATATATTTTAATGTC----
1 ATATATTTTATTTTTATTTATTATTATAATAT--TTT-ATATTTAT-TTTTAATATCTTTA
*
634249 ATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATTTTTAATATATTTA
1 ATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATTTTTAATATCTTTA
* * * * * * * *
634306 TATTTATATTATTAATT-TTTATTAATATCATATTTTAAATATATTTTTAATGTC----
1 -ATATATTTTATT-TTTATTTATTATTATAATATTTTATATTTATTTTTAATATCTTTA
* *
634360 ATATATTTTATTTTTATTTATTATTATAATATTTATATATTT-TATTTTCATTTCTTTA
1 ATATATTTTATTTTTATTTATTATTATAATATTT-TATATTTAT-TTTTAATATCTTTA
634418 ATATATTTT
1 ATATATTTT
634427 TATATTATAT
Statistics
Matches: 264, Mismatches: 44, Indels: 64
0.71 0.12 0.17
Matches are distributed among these distances:
50 9 0.03
51 5 0.02
52 22 0.08
53 53 0.20
54 30 0.11
55 25 0.09
56 16 0.06
57 25 0.09
58 63 0.24
59 5 0.02
60 11 0.04
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (57 bp):
ATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATTTTTAATATCTTTA
Found at i:634465 original size:38 final size:38
Alignment explanation
Indices: 634343--634482 Score: 152
Period size: 38 Copynumber: 3.8 Consensus size: 38
634333 TCATATTTTA
*
634343 AATATATTTTTA-ATGTCATATATTTTA-TT--TTTATTT
1 AATATATTTTTATAT-T-ATATATTTTATTTCATTTCTTT
* *
634379 -AT-TATTATAATATTTATATATTTTATTTTCATTTCTTT
1 AATATATTTTTATA-TTATATATTTTA-TTTCATTTCTTT
634417 AATATATTTTTATATTATATATTTTATTTCATTTC-TT
1 AATATATTTTTATATTATATATTTTATTTCATTTCTTT
634454 AATATATTTTTTATATTATATA-TTTATTT
1 AATATA-TTTTTATATTATATATTTTATTT
634483 TAATTTGTTT
Statistics
Matches: 90, Mismatches: 5, Indels: 17
0.80 0.04 0.15
Matches are distributed among these distances:
34 16 0.18
35 4 0.04
36 3 0.03
37 15 0.17
38 30 0.33
39 14 0.16
40 8 0.09
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.65
Consensus pattern (38 bp):
AATATATTTTTATATTATATATTTTATTTCATTTCTTT
Found at i:635369 original size:2 final size:2
Alignment explanation
Indices: 635362--635388 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
635352 GAAAGCACCA
635362 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
635389 GCCTACTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:644460 original size:15 final size:15
Alignment explanation
Indices: 644440--644482 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
644430 TTAAGAAAAG
*
644440 AAAAAAAATTATACA
1 AAAAAAAATAATACA
644455 AAAAAAAATAATACA
1 AAAAAAAATAATACA
644470 AAATAAAAA-AATA
1 AAA-AAAAATAATA
644483 AAGACAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAAAAATAATACA
Found at i:644489 original size:19 final size:18
Alignment explanation
Indices: 644456--644494 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
644446 AATTATACAA
*
644456 AAAAAAATAATACAAAAT
1 AAAAAAATAAGACAAAAT
*
644474 AAAAAAATAAAGACAAGAT
1 AAAAAAAT-AAGACAAAAT
644493 AA
1 AA
644495 TGTTAACAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (18 bp):
AAAAAAATAAGACAAAAT
Found at i:661122 original size:6 final size:6
Alignment explanation
Indices: 661111--661143 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
661101 TCTTTCTGCA
*
661111 TTTCTT TTTCTT TGTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
661144 TTAACTCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:662241 original size:3 final size:3
Alignment explanation
Indices: 662233--662258 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
662223 ACACTAGTAG
662233 CAA CAA CAA CAA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CA
662259 GTTTGAGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:664203 original size:2 final size:2
Alignment explanation
Indices: 664196--664228 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
664186 AAACCCACCA
*
664196 AT AT AT AT CT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
664229 CCATATTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:667189 original size:10 final size:9
Alignment explanation
Indices: 667163--667222 Score: 59
Period size: 10 Copynumber: 6.3 Consensus size: 9
667153 GCATATGAGC
667163 AAATAAAATA
1 AAAT-AAATA
667173 GAAATAAATA
1 -AAATAAATA
667183 AATATAAATA
1 AA-ATAAATA
*
667193 AAATTAATA
1 AAATAAATA
*
667202 ATATAAATTA
1 AAATAAA-TA
667212 AAATAAA-A
1 AAATAAATA
667220 AAA
1 AAA
667223 CTTTAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
8 4 0.09
9 13 0.30
10 22 0.51
11 4 0.09
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (9 bp):
AAATAAATA
Found at i:667196 original size:19 final size:19
Alignment explanation
Indices: 667163--667218 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
667153 GCATATGAGC
667163 AAATA-AAATAGAAATAAAT
1 AAATATAAATA-AAATAAAT
*
667182 AAATATAAATAAAATTAAT
1 AAATATAAATAAAATAAAT
667201 -AATATAAATTAAAATAAA
1 AAATATAAA-TAAAATAAA
667219 AAAACTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.24
19 20 0.61
20 5 0.15
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATATAAATAAAATAAAT
Found at i:667215 original size:24 final size:23
Alignment explanation
Indices: 667175--667219 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
667165 ATAAAATAGA
667175 AATAAATAAATATAAATAAAATT
1 AATAAATAAATATAAATAAAATT
667198 AATAATATAAAT-TAAAATAAAA
1 AATAA-ATAAATAT-AAATAAAA
667220 AAACTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
AATAAATAAATATAAATAAAATT
Found at i:675771 original size:2 final size:2
Alignment explanation
Indices: 675766--675811 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
675756 TGGAGAGAGG
675766 AT AT AT 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 AT AT AT
675808 AT AT
1 AT AT
675812 GCACAGTTCG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:696556 original size:64 final size:65
Alignment explanation
Indices: 696436--696572 Score: 215
Period size: 64 Copynumber: 2.1 Consensus size: 65
696426 CCAACTCAAG
*
696436 AATAATAAAGCACGTATAGCAAATGCCAACAGCTCAAGTATAACAGCATATGGATCACACCCACT
1 AATAATAAAGCACGTATAGCAAATGCCAACAGCTCAAGTATAACAGCATATGGATCACACCCACC
** * *
696501 AATAATAAAGCACGTATAGCAAATG-TTACAGCTGAAGTATAACAGCATATTGATCACACCCACC
1 AATAATAAAGCACGTATAGCAAATGCCAACAGCTCAAGTATAACAGCATATGGATCACACCCACC
696565 AA-AATAAA
1 AATAATAAA
696573 CAACAGACTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
63 6 0.09
64 36 0.54
65 25 0.37
ACGTcount: A:0.45, C:0.22, G:0.13, T:0.20
Consensus pattern (65 bp):
AATAATAAAGCACGTATAGCAAATGCCAACAGCTCAAGTATAACAGCATATGGATCACACCCACC
Found at i:696877 original size:97 final size:98
Alignment explanation
Indices: 696550--697007 Score: 562
Period size: 98 Copynumber: 4.7 Consensus size: 98
696540 TAACAGCATA
* * * *
696550 TTGATCACACCCACCAAAATAAACAACAGA-CTAAGCGTGAAAATGTAAAGAAATCAGGGAAAGA
1 TTGACCACACCCATCAAAATAAGCAACA-ACCTAAGCATGAAAATGTAAAGAAATCAGGGAAAGA
696614 GATGCAAAAGAGACCTGTGAAAAA-GCAAAATGAG
65 GATGCAAAAGAGACCTGT-AAAAATGCAAAATGAG
*
696648 TTGACCACACCCATCAAAATAAGCAACAACCTAGGCATGAAAATGTAAAGAAATCAGGGAAAGAG
1 TTGACCACACCCATCAAAATAAGCAACAACCTAAGCATGAAAATGTAAAGAAATCAGGGAAAGAG
* *
696713 ATGCAAAAGAGACCTCTGAAAATGCAAAATGAG
66 ATGCAAAAGAGACCTGTAAAAATGCAAAATGAG
* * *
696746 TTGACCACACCCATCAAAATAAGCAGCAACCTAAGCATGAAAATGTAAAGAAATCA-GTAACGAG
1 TTGACCACACCCATCAAAATAAGCAACAACCTAAGCATGAAAATGTAAAGAAATCAGGGAAAGAG
* *
696810 GTGCAAAAGAGACCTGTAAAAATGCAAGATGAG
66 ATGCAAAAGAGACCTGTAAAAATGCAAAATGAG
** * *
696843 TTGACCACACCCATCAAAATAAGCAACAGGCTAAGCATGAAAATCTAAAGAAATTAAGGGAAAGA
1 TTGACCACACCCATCAAAATAAGCAACAACCTAAGCATGAAAATGTAAAGAAA-TCAGGGAAAGA
* * *
696908 GATTCAAATA-CGA-C-GTGAAAATGC-AAATGAAG
65 GATGCAAA-AGAGACCTGTAAAAATGCAAAATG-AG
* * * ** *
696940 -TGACCACACCCATCAAAGT-A--AACAA-CTAAGCATGATAGTGCGAAGAAATCAGGGAAATAG
1 TTGACCACACCCATCAAAATAAGCAACAACCTAAGCATGAAAATGTAAAGAAATCAGGGAAAGAG
697000 ATGCAAAA
66 ATGCAAAA
697008 CAAACAACAA
Statistics
Matches: 317, Mismatches: 37, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
90 1 0.00
91 16 0.05
92 18 0.06
93 4 0.01
95 1 0.00
96 22 0.07
97 100 0.32
98 141 0.44
99 13 0.04
100 1 0.00
ACGTcount: A:0.48, C:0.18, G:0.19, T:0.15
Consensus pattern (98 bp):
TTGACCACACCCATCAAAATAAGCAACAACCTAAGCATGAAAATGTAAAGAAATCAGGGAAAGAG
ATGCAAAAGAGACCTGTAAAAATGCAAAATGAG
Found at i:696894 original size:195 final size:195
Alignment explanation
Indices: 696550--697007 Score: 578
Period size: 195 Copynumber: 2.4 Consensus size: 195
696540 TAACAGCATA
* * *
696550 TTGATCACACCCACCAAAATAAACAACAGACTAAGCGTGAAAATGTAAAGAAATCAGGGAAAGAG
1 TTGACCACACCCATCAAAATAAACAACAGACTAAGCATGAAAATGTAAAGAAATCAGGGAAAGAG
696615 ATGCAAAAGAGACCTGTGAAAAAGCAAAATGAGTTGACCACACCCATCAAAATAAGCAACAACCT
66 ATGCAAAAGAGACCTGTGAAAAAGCAAAATGAGTTGACCACACCCATCAAAATAAGCAACAACCT
* * *
696680 AGGCATGAAAATGTAAAGAAA-TCAGGGAAAGAGATGCAAA-AGAGACCTCTGAAAATGCAAAAT
131 AAGCATGAAAATCTAAAGAAATTAAGGGAAAGAGATGCAAATA-AGA-C-CTGAAAATGC-AAAT
696743 G-AG
192 GAAG
* * * *
696746 TTGACCACACCCATCAAAATAAGCAGCA-ACCTAAGCATGAAAATGTAAAGAAATCA-GTAACGA
1 TTGACCACACCCATCAAAATAAACAACAGA-CTAAGCATGAAAATGTAAAGAAATCAGGGAAAGA
* * **
696809 GGTGCAAAAGAGACCTGT-AAAAATGCAAGATGAGTTGACCACACCCATCAAAATAAGCAACAGG
65 GATGCAAAAGAGACCTGTGAAAAA-GCAAAATGAGTTGACCACACCCATCAAAATAAGCAACAAC
* * *
696873 CTAAGCATGAAAATCTAAAGAAATTAAGGGAAAGAGATTCAAATACGACGTGAAAATGCAAATGA
129 CTAAGCATGAAAATCTAAAGAAATTAAGGGAAAGAGATGCAAATAAGACCTGAAAATGCAAATGA
696938 AG
194 AG
* * * ** *
696940 -TGACCACACCCATCAAAGT--A-AACA-ACTAAGCATGATAGTGCGAAGAAATCAGGGAAATAG
1 TTGACCACACCCATCAAAATAAACAACAGACTAAGCATGAAAATGTAAAGAAATCAGGGAAAGAG
697000 ATGCAAAA
66 ATGCAAAA
697008 CAAACAACAA
Statistics
Matches: 228, Mismatches: 28, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
189 22 0.10
190 16 0.07
193 23 0.10
194 16 0.07
195 82 0.36
196 68 0.30
197 1 0.00
ACGTcount: A:0.48, C:0.18, G:0.19, T:0.15
Consensus pattern (195 bp):
TTGACCACACCCATCAAAATAAACAACAGACTAAGCATGAAAATGTAAAGAAATCAGGGAAAGAG
ATGCAAAAGAGACCTGTGAAAAAGCAAAATGAGTTGACCACACCCATCAAAATAAGCAACAACCT
AAGCATGAAAATCTAAAGAAATTAAGGGAAAGAGATGCAAATAAGACCTGAAAATGCAAATGAAG
Found at i:721454 original size:18 final size:18
Alignment explanation
Indices: 721431--721466 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
721421 TTGCCTTATA
*
721431 TGATTTGTTTTTGGGTTT
1 TGATTTATTTTTGGGTTT
721449 TGATTTATTTTTGGGTTT
1 TGATTTATTTTTGGGTTT
721467 CAGGTTATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.25, T:0.67
Consensus pattern (18 bp):
TGATTTATTTTTGGGTTT
Found at i:738346 original size:6 final size:6
Alignment explanation
Indices: 738310--738335 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
738300 AATTAAGAGA
738310 CCACTC CCACTC CCACTC CCACTC CC
1 CCACTC CCACTC CCACTC CCACTC CC
738336 TCCCCCACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.69, G:0.00, T:0.15
Consensus pattern (6 bp):
CCACTC
Found at i:743367 original size:41 final size:41
Alignment explanation
Indices: 743322--743402 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
743312 CATAATTAAG
*
743322 TTATT-GGATTGAACTATTGAGATATAATATGTTATGATAAA
1 TTATTAGG-TTGAACTATTAAGATATAATATGTTATGATAAA
* * * *
743363 TTATTATGTTGGATTGTTAAGATATAATATGTTATGATAA
1 TTATTAGGTTGAACTATTAAGATATAATATGTTATGATAA
743403 TCTTAGAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 33 0.97
42 1 0.03
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.44
Consensus pattern (41 bp):
TTATTAGGTTGAACTATTAAGATATAATATGTTATGATAAA
Found at i:744008 original size:14 final size:14
Alignment explanation
Indices: 743982--744017 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
743972 AATATATGAG
743982 TAAATAGAATAAATA
1 TAAATA-AATAAATA
743997 TAAATAAATAAATA
1 TAAATAAATAAATA
*
744011 AAAATAA
1 TAAATAA
744018 TAATTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (14 bp):
TAAATAAATAAATA
Found at i:745239 original size:22 final size:24
Alignment explanation
Indices: 745197--745248 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
745187 AAAAGACCAA
745197 AAAAGAAAGAGAAGGTAAAAA-AGAG
1 AAAA-AAAGAGAAGGTAAAAAGA-AG
745222 AAAAAAAG-GAA-GTAAAAAGAAG
1 AAAAAAAGAGAAGGTAAAAAGAAG
745244 AAAAA
1 AAAAA
745249 TTAGTATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 14 0.54
23 4 0.15
24 4 0.15
25 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (24 bp):
AAAAAAAGAGAAGGTAAAAAGAAG
Found at i:745300 original size:40 final size:40
Alignment explanation
Indices: 745256--745333 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 40
745246 AAATTAGTAT
* *
745256 ACTTATAAAGGAAAAAGGAAAAAA-AAAGAGAA-AAAAAAGG
1 ACTTATAAAAG-AAAA-GAAAAAAGAAAGACAACAAAAAAGG
745296 ACTTATAAAAGAAAAGAAAAAAGAAAGACAACAAAAAA
1 ACTTATAAAAGAAAAGAAAAAAGAAAGACAACAAAAAA
745334 AAAAGGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 7 0.21
39 11 0.32
40 16 0.47
ACGTcount: A:0.72, C:0.05, G:0.15, T:0.08
Consensus pattern (40 bp):
ACTTATAAAAGAAAAGAAAAAAGAAAGACAACAAAAAAGG
Found at i:745322 original size:16 final size:16
Alignment explanation
Indices: 745302--745349 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
745292 AAGGACTTAT
745302 AAAAGAAAAGAAAAAA
1 AAAAGAAAAGAAAAAA
* * *
745318 GAAAGACAACAAAAAA
1 AAAAGAAAAGAAAAAA
745334 AAAAGGAAAAGAAAAA
1 AAAA-GAAAAGAAAAA
745350 TAGTTTCAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAA
Found at i:751524 original size:2 final size:2
Alignment explanation
Indices: 751513--751552 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
751503 CATCAAAAAC
*
751513 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
751553 CACATAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:751881 original size:12 final size:12
Alignment explanation
Indices: 751864--751896 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
751854 ACAAATTAGG
751864 GGGGACTTGGAT
1 GGGGACTTGGAT
751876 GGGGACTTGGAT
1 GGGGACTTGGAT
751888 GGGGACTTG
1 GGGGACTTG
751897 AGAACCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.09, G:0.52, T:0.24
Consensus pattern (12 bp):
GGGGACTTGGAT
Found at i:752556 original size:15 final size:15
Alignment explanation
Indices: 752536--752570 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
752526 AACACATGAA
752536 TAAGACTTCATTAAT
1 TAAGACTTCATTAAT
752551 TAAGACTTCATTAAT
1 TAAGACTTCATTAAT
752566 TAAGA
1 TAAGA
752571 AACGAGCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (15 bp):
TAAGACTTCATTAAT
Found at i:764626 original size:17 final size:17
Alignment explanation
Indices: 764604--764637 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
764594 AAACGCGGCG
764604 TGTCTTTCGTAAG-GTTT
1 TGTCTTT-GTAAGTGTTT
764621 TGTCTTTGTAAGTGTTT
1 TGTCTTTGTAAGTGTTT
764638 ACTTTTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.12, C:0.09, G:0.24, T:0.56
Consensus pattern (17 bp):
TGTCTTTGTAAGTGTTT
Found at i:765013 original size:24 final size:22
Alignment explanation
Indices: 764963--765015 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
764953 GAAAACATTT
* **
764963 TATTAAAGTTTTTAAATATTGA
1 TATTAAAGTTTTTAAACATCAA
764985 TATTAAATGTTTTTAAACATCAA
1 TATTAAA-GTTTTTAAACATCAA
765008 TAATTAAA
1 T-ATTAAA
765016 AAAATTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 7 0.27
23 13 0.50
24 6 0.23
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (22 bp):
TATTAAAGTTTTTAAACATCAA
Found at i:765359 original size:15 final size:15
Alignment explanation
Indices: 765339--765367 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
765329 CAGTTAAATT
765339 AAATTTTATATTAAA
1 AAATTTTATATTAAA
765354 AAATTTTATATTAA
1 AAATTTTATATTAA
765368 TATATTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTTTATATTAAA
Found at i:766828 original size:2 final size:2
Alignment explanation
Indices: 766821--766852 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
766811 CTAAGAAAAG
*
766821 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
766853 TTGATCATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:769883 original size:16 final size:16
Alignment explanation
Indices: 769850--769882 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
769840 AAACTAAAAC
*
769850 TTAGATTTTGATTCTT
1 TTAGATTATGATTCTT
769866 TTAGATTATGATT-TT
1 TTAGATTATGATTCTT
769881 TT
1 TT
769883 TTATATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.21, C:0.03, G:0.12, T:0.64
Consensus pattern (16 bp):
TTAGATTATGATTCTT
Found at i:771405 original size:63 final size:64
Alignment explanation
Indices: 771305--771433 Score: 199
Period size: 63 Copynumber: 2.0 Consensus size: 64
771295 TTTGTAAGGC
* * *
771305 AACATTCCACACATAGTGAATGCATCTAATATGATGGATAATGGCT-TTTCACACAGTGTGAGGT
1 AACATTCCACACATAGTGAATGCATCTAATATGATGGATAATGG-TGCTCCACACAATGTGAGGT
*
771369 AACATTCCACACATAGTG-ATGCATCTAATATGATGGATGATGGTGCTCCACACAATGTGAGGT
1 AACATTCCACACATAGTGAATGCATCTAATATGATGGATAATGGTGCTCCACACAATGTGAGGT
771432 AA
1 AA
771434 TGTTCACACA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
62 1 0.02
63 41 0.68
64 18 0.30
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (64 bp):
AACATTCCACACATAGTGAATGCATCTAATATGATGGATAATGGTGCTCCACACAATGTGAGGT
Found at i:773547 original size:15 final size:15
Alignment explanation
Indices: 773513--773547 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
773503 AATTACTATT
*
773513 ATATATATACTTTTA
1 ATATATATACTTTAA
*
773528 GTATATATACTTTAA
1 ATATATATACTTTAA
773543 ATATA
1 ATATA
773548 AATGTATTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (15 bp):
ATATATATACTTTAA
Found at i:775894 original size:22 final size:23
Alignment explanation
Indices: 775869--775915 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
775859 TATTTTATTC
775869 TATTTAAACT-TAAAATATTAAA
1 TATTTAAACTATAAAATATTAAA
**
775891 TA-TTAAACTATAACGTATTAAA
1 TATTTAAACTATAAAATATTAAA
775913 TAT
1 TAT
775916 AAATAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.40
Consensus pattern (23 bp):
TATTTAAACTATAAAATATTAAA
Found at i:775924 original size:14 final size:13
Alignment explanation
Indices: 775881--775928 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
775871 TTTAAACTTA
775881 AAATATTAAATATT
1 AAATA-TAAATATT
*
775895 AAACTATAACGTATT
1 AAA-TATAA-ATATT
775910 AAATATAAATAATT
1 AAATATAAAT-ATT
775924 AAATA
1 AAATA
775929 CGATATATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 1 0.03
14 19 0.66
15 9 0.31
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (13 bp):
AAATATAAATATT
Found at i:776476 original size:20 final size:20
Alignment explanation
Indices: 776437--776473 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
776427 AAAAAGGTGT
776437 GGAAAAACTTAAAGAGTTGA
1 GGAAAAACTTAAAGAGTTGA
*
776457 GGAAAAA-TTTAAGAGTT
1 GGAAAAACTTAAAGAGTT
776474 TGAATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.24
Consensus pattern (20 bp):
GGAAAAACTTAAAGAGTTGA
Found at i:779316 original size:22 final size:22
Alignment explanation
Indices: 779289--779333 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
779279 ATATGCATCC
* *
779289 ATTATTGAATTAAATATTCAAA
1 ATTATTAAATTAAATACTCAAA
779311 ATTATTAAATTAAATACTCAAA
1 ATTATTAAATTAAATACTCAAA
779333 A
1 A
779334 GTGTTACACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTATTAAATTAAATACTCAAA
Found at i:779906 original size:21 final size:21
Alignment explanation
Indices: 779882--779928 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
779872 ATGTTTTTAA
779882 AAAATAAAATTACAAAATTTG
1 AAAATAAAATTACAAAATTTG
* ** *
779903 AAAAAAAAATTATTAAATTTT
1 AAAATAAAATTACAAAATTTG
779924 AAAAT
1 AAAAT
779929 TTTAGGAGCG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAATAAAATTACAAAATTTG
Found at i:784800 original size:28 final size:28
Alignment explanation
Indices: 784768--784824 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
784758 AGTAAAAACA
784768 AAAATCCATAATCCTGTTTGAACTTTAG
1 AAAATCCATAATCCTGTTTGAACTTTAG
*
784796 AAAATCTATAATCCTGTTTGAACTTTAG
1 AAAATCCATAATCCTGTTTGAACTTTAG
784824 A
1 A
784825 GGCCATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (28 bp):
AAAATCCATAATCCTGTTTGAACTTTAG
Found at i:785331 original size:21 final size:21
Alignment explanation
Indices: 785306--785373 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
785296 AAAACGTGTG
785306 ACACGTCATGGTTAAGTTGTT
1 ACACGTCATGGTTAAGTTGTT
**
785327 ACACGTCAT-GTATATACATGTT
1 ACACGTCATGGT-TA-AGTTGTT
** *
785349 ACACACCATGGTTAGGTTGTT
1 ACACGTCATGGTTAAGTTGTT
785370 ACAC
1 ACAC
785374 CCCATGTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.05
21 19 0.51
22 14 0.38
23 2 0.05
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (21 bp):
ACACGTCATGGTTAAGTTGTT
Found at i:785503 original size:76 final size:77
Alignment explanation
Indices: 785344--785515 Score: 319
Period size: 76 Copynumber: 2.2 Consensus size: 77
785334 ATGTATATAC
785344 ATGTTACACACCATGGTTAGGTTGTTACACCCCATGTTAAAAAAAAAATACTGTTGTTACATGTC
1 ATGTTACACACCATGGTTAGGTTGTTACACCCCATGTTAAAAAAAAAATACTGTTGTTACATGTC
785409 ATGTACAAAAAT
66 ATGTACAAAAAT
* *
785421 ATGTTACACGCCATGGTTAGGTTGTTACATCCCATGTT-AAAAAAAAATACTGTTGTTACATGTC
1 ATGTTACACACCATGGTTAGGTTGTTACACCCCATGTTAAAAAAAAAATACTGTTGTTACATGTC
785485 ATGTACAAAAAT
66 ATGTACAAAAAT
785497 ATGTTACACACCATGGTTA
1 ATGTTACACACCATGGTTA
785516 AAAAAAGTTG
Statistics
Matches: 92, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
76 56 0.61
77 36 0.39
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (77 bp):
ATGTTACACACCATGGTTAGGTTGTTACACCCCATGTTAAAAAAAAAATACTGTTGTTACATGTC
ATGTACAAAAAT
Found at i:785557 original size:28 final size:28
Alignment explanation
Indices: 785515--785577 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
785505 CACCATGGTT
*
785515 AAAAAAAGTTGTTACAAGCTATGTTGAA
1 AAAAAAAGTTATTACAAGCTATGTTGAA
*
785543 AAAAAAAGTTATTACACGCTATGTTGAA
1 AAAAAAAGTTATTACAAGCTATGTTGAA
785571 AAAAAAA
1 AAAAAAA
785578 CTAATATCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.25
Consensus pattern (28 bp):
AAAAAAAGTTATTACAAGCTATGTTGAA
Found at i:798915 original size:23 final size:22
Alignment explanation
Indices: 798865--798940 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 22
798855 TTATTATAGT
*
798865 TAATTAAATT-TTTATATTTTTA
1 TAATTAAATTAATTA-ATTTTTA
*
798887 T-TTTAAATTAAATTAATTTTTA
1 TAATTAAATT-AATTAATTTTTA
*
798909 TAATTAACATTGATTAATTTTTA
1 TAATTAA-ATTAATTAATTTTTA
798932 TTAATTAAA
1 -TAATTAAA
798941 GTGTTACTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
21 7 0.16
22 9 0.20
23 19 0.42
24 10 0.22
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (22 bp):
TAATTAAATTAATTAATTTTTA
Found at i:799206 original size:28 final size:29
Alignment explanation
Indices: 799148--799207 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
799138 ATATTTGATC
* *
799148 TAAAATAAAAATATAAAGATTTGATTGAA
1 TAAAATAAAAATATAAAAATTTGATTAAA
799177 TAAAATAAAAA-ATAAAAATTT-ATTTAAA
1 TAAAATAAAAATATAAAAATTTGA-TTAAA
799205 TAA
1 TAA
799208 TTGAAAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 1 0.04
28 16 0.57
29 11 0.39
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (29 bp):
TAAAATAAAAATATAAAAATTTGATTAAA
Found at i:801880 original size:82 final size:81
Alignment explanation
Indices: 801743--801896 Score: 209
Period size: 82 Copynumber: 1.9 Consensus size: 81
801733 AATATTTATA
* * * *
801743 AGAGATACAAAAGTCAAAACAATTAATGTAAGAGTGCTTTTCCTTTACGAGTAAAGTGTCTAGAA
1 AGAGATACAAAAGTCAAAACAACTAATGTAAGAGTGCCTTGCCTTTACGAGTAAAGTGCCTAG-A
801808 CCCTACATTAACCCATG
65 CCCTACATTAACCCATG
* * * * * *
801825 AGAGATATAAGAGTCAAAACAACTAGTGTGAGAGTGCCTTGCTTTTACGAGTAAAGTGCCTAGAT
1 AGAGATACAAAAGTCAAAACAACTAATGTAAGAGTGCCTTGCCTTTACGAGTAAAGTGCCTAGAC
801890 CCTACAT
66 CCTACAT
801897 CAATAAGAGA
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
81 8 0.13
82 54 0.87
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.27
Consensus pattern (81 bp):
AGAGATACAAAAGTCAAAACAACTAATGTAAGAGTGCCTTGCCTTTACGAGTAAAGTGCCTAGAC
CCTACATTAACCCATG
Found at i:807617 original size:90 final size:90
Alignment explanation
Indices: 807464--807733 Score: 504
Period size: 90 Copynumber: 3.0 Consensus size: 90
807454 ATAGTATTTT
* *
807464 ATTGCTTGTATTATTGTATTTAAGTTATATCAATGTCAATTTGTCTTTTTTCTTATTTATCAAGT
1 ATTGCTTGTATTATTGTATTTAAGTTATATTAATATCAATTTGTCTTTTTTCTTATTTATCAAGT
807529 ACTAGGATTGATAAACTAGTCTATA
66 ACTAGGATTGATAAACTAGTCTATA
* *
807554 ATTGCTTGTATTATTGTATTTAAGTTATATTAATATCAATTTATCTTTTTCCTTATTTATCAAGT
1 ATTGCTTGTATTATTGTATTTAAGTTATATTAATATCAATTTGTCTTTTTTCTTATTTATCAAGT
807619 ACTAGGATTGATAAACTAGTCTATA
66 ACTAGGATTGATAAACTAGTCTATA
807644 ATTGCTTGTATTATTGTATTTAAGTTATATTAATATCAATTTGTCTTTTTTCTTATTTATCAAGT
1 ATTGCTTGTATTATTGTATTTAAGTTATATTAATATCAATTTGTCTTTTTTCTTATTTATCAAGT
807709 ACTAGGATTGATAAACTAGTCTATA
66 ACTAGGATTGATAAACTAGTCTATA
807734 TGTACTTAAG
Statistics
Matches: 174, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 174 1.00
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.49
Consensus pattern (90 bp):
ATTGCTTGTATTATTGTATTTAAGTTATATTAATATCAATTTGTCTTTTTTCTTATTTATCAAGT
ACTAGGATTGATAAACTAGTCTATA
Found at i:810471 original size:25 final size:25
Alignment explanation
Indices: 810425--810478 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
810415 TTTTAAATAA
* ** *
810425 ATAAAAATTATATAGTAGTAATTTT
1 ATAAAAATAATATAAAAATAATTTT
810450 ATAAAAATAATATAAAAATAATTTT
1 ATAAAAATAATATAAAAATAATTTT
810475 -TAAA
1 ATAAA
810479 TTAACGATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
ATAAAAATAATATAAAAATAATTTT
Found at i:811176 original size:23 final size:22
Alignment explanation
Indices: 811099--811177 Score: 59
Period size: 23 Copynumber: 3.5 Consensus size: 22
811089 ATACAAACAT
* *
811099 ATTTTTATTATAATTTAATAATA
1 ATTTATATTATAATTAAATAA-A
* * * *
811122 TTTTATATTAAAAGATAATTAAA
1 ATTTATATTATAA-TTAAATAAA
* *
811145 CTTTTTATTATAATTAAATAAA
1 ATTTATATTATAATTAAATAAA
811167 ATTTAATATTA
1 ATTT-ATATTA
811178 AAAGACAAAA
Statistics
Matches: 41, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
22 10 0.24
23 26 0.63
24 5 0.12
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (22 bp):
ATTTATATTATAATTAAATAAA
Found at i:811308 original size:12 final size:11
Alignment explanation
Indices: 811253--811315 Score: 50
Period size: 11 Copynumber: 6.4 Consensus size: 11
811243 ATATTCAAAT
811253 AATAATATTTA
1 AATAATATTTA
811264 AA-AATATTT-
1 AATAATATTTA
* * *
811273 -GTTATAGTTA
1 AATAATATTTA
811283 AATAATA-TT-
1 AATAATATTTA
811292 AAT-ATA-TTA
1 AATAATATTTA
811301 AATAATATTTA
1 AATAATATTTA
811312 AATA
1 AATA
811316 TTTTAATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
8 5 0.12
9 11 0.27
10 12 0.29
11 13 0.32
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
AATAATATTTA
Found at i:812117 original size:2 final size:2
Alignment explanation
Indices: 812110--812136 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
812100 TTTGTATAAC
812110 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 T
812137 TCATCTATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:824611 original size:13 final size:13
Alignment explanation
Indices: 824593--824617 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
824583 TGTGTACAAA
824593 CCCCCCCCCCCAC
1 CCCCCCCCCCCAC
824606 CCCCCCCCCCCA
1 CCCCCCCCCCCA
824618 AAAAAAAAAA
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:0.08, C:0.92, G:0.00, T:0.00
Consensus pattern (13 bp):
CCCCCCCCCCCAC
Found at i:827849 original size:16 final size:16
Alignment explanation
Indices: 827828--827858 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
827818 AATTTTTAAA
*
827828 ATATTTTATATATTAT
1 ATATTTTAAATATTAT
827844 ATATTTTAAATATTA
1 ATATTTTAAATATTA
827859 ACTTATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTTAAATATTAT
Found at i:831399 original size:2 final size:2
Alignment explanation
Indices: 831392--831440 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
831382 AGGGGTAACG
831392 AT AT AT 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 AT AT AT
831434 AT AT AT A
1 AT AT AT A
831441 ATGTATGTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:840728 original size:24 final size:23
Alignment explanation
Indices: 840693--840746 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
840683 ATTTAGTCTA
*
840693 TTTTGGATTTCTCTTAAGAAATCT
1 TTTTGGATTTCT-TGAAGAAATCT
* *
840717 TTTTGG-TATTCTTGATGACATCT
1 TTTTGGAT-TTCTTGAAGAAATCT
840740 TTTTGGA
1 TTTTGGA
840747 ACGTCCTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (23 bp):
TTTTGGATTTCTTGAAGAAATCT
Found at i:843952 original size:32 final size:33
Alignment explanation
Indices: 843916--843985 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 33
843906 AAAAAACTTA
*
843916 TAAGTTG-TTTAAAATATTTATTTTTAATTATT
1 TAAGTTGTTTTAAAATATTAATTTTTAATTATT
* *
843948 TAAGTTGTTATTTGAAATATTAATTTTTTATTATT
1 TAAGTTG-T-TTTAAAATATTAATTTTTAATTATT
843983 TAA
1 TAA
843986 ATTTATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 7 0.22
35 25 0.78
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (33 bp):
TAAGTTGTTTTAAAATATTAATTTTTAATTATT
Found at i:844001 original size:23 final size:22
Alignment explanation
Indices: 843955--844008 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 22
843945 ATTTAAGTTG
843955 TTATTTGAAATATTAATTTTTTA
1 TTATTT-AAATATTAATTTTTTA
843978 TTATTTAAAT-TTATATTTTATTA
1 TTATTTAAATATTA-ATTTT-TTA
844001 TATATTTA
1 T-TATTTA
844009 TTTTAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.11
22 9 0.32
23 10 0.36
24 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATTTAAATATTAATTTTTTA
Found at i:845855 original size:2 final size:2
Alignment explanation
Indices: 845848--845876 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
845838 TGGCTAGGAA
845848 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
845877 GTGGCTTTCC
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:846855 original size:2 final size:2
Alignment explanation
Indices: 846848--846880 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
846838 AAAATAGGAC
846848 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
846881 GAAATCATTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:848682 original size:21 final size:21
Alignment explanation
Indices: 848658--848702 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
848648 AAGCCTATGC
* * *
848658 TTTTCTCCTTTTTAATTTTTT
1 TTTTCTACTTTTGAATTTGTT
*
848679 TTTTGTACTTTTGAATTTGTT
1 TTTTCTACTTTTGAATTTGTT
848700 TTT
1 TTT
848703 GTTGCCTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.11, C:0.09, G:0.07, T:0.73
Consensus pattern (21 bp):
TTTTCTACTTTTGAATTTGTT
Found at i:853037 original size:19 final size:19
Alignment explanation
Indices: 853010--853054 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
853000 TTATTATATT
*
853010 CATGTATCATTACCGCATA
1 CATGAATCATTACCGCATA
*
853029 CATGAATCATTACTGCATA
1 CATGAATCATTACCGCATA
853048 CATGAAT
1 CATGAAT
853055 TAGTAGATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (19 bp):
CATGAATCATTACCGCATA
Found at i:854839 original size:21 final size:21
Alignment explanation
Indices: 854793--854842 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
854783 ATACTAAATC
* *
854793 AAATTAAATTAGTTGAAGAGA
1 AAATTAAATTACTTCAAGAGA
*
854814 TAATTAAAGTTACTTCAAGA-A
1 AAATTAAA-TTACTTCAAGAGA
854835 AAATTAAA
1 AAATTAAA
854843 CATAAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.30
Consensus pattern (21 bp):
AAATTAAATTACTTCAAGAGA
Found at i:855066 original size:86 final size:86
Alignment explanation
Indices: 854919--855767 Score: 1289
Period size: 86 Copynumber: 9.9 Consensus size: 86
854909 GATATGTTAC
* * * * * *
854919 AAGTTTACATCATAGTTTAAATAATATAAATTAATTTTACATTTGTTAGTTTATAACTTTAACTA
1 AAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTA
854984 ATATAAAAATTTTATATATTT
66 ATATAAAAATTTTATATATTT
* * * * *
855005 AAGTTTACATCATAGTTCAAATAATATAAATTAATTTTACATTTTTTAGTTTATAAGTTTAACTA
1 AAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTA
* *
855070 ATATAAAGATTTGATATATTT
66 ATATAAAAATTTTATATATTT
*
855091 AAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTTTTAGTTTACAAGTTCAACTA
1 AAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTA
* *
855156 ATATAAAAAATTTATCTATTT
66 ATATAAAAATTTTATATATTT
* * *
855177 AAGTTTGCATTATAGTTCAATTAATATAAATTAATTTTACATTTGTTAGTTTACAAATTCAACTA
1 AAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTA
* *
855242 ATATAAACATTTTGTAT-TCTT
66 ATATAAAAATTTTATATAT-TT
*
855263 AAGATTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTA
1 AAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTA
*
855328 ATATTAAAATTTTATATATTT
66 ATATAAAAATTTTATATATTT
* * *
855349 AAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTCGTTTAAAAGTTCAACTC
1 AAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTA
*
855414 ATAT-AAAATATTATATATTT
66 ATATAAAAATTTTATATATTT
* * *
855434 AAGTTTGCATTATAGTTCAAGTATTATAAATCAATTTTACATTTGTTAGTTTACAAGTTCAACTA
1 AAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTA
* *
855499 ATATAAATATTGTATATATTT
66 ATATAAAAATTTTATATATTT
* *
855520 AAGTTTCCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAATTTACAAGTTCAACTA
1 AAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTA
855585 ATATAAAAATTTTATATATTT
66 ATATAAAAATTTTATATATTT
* * *
855606 AAGTTTGCATCATAGTTTAAGTAATATAAATTAAGTTTACATTTATTAGTTTACAAGTTCAACTA
1 AAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTA
855671 ATATAAAAATTTTATATATTT
66 ATATAAAAATTTTATATATTT
*
855692 AAGTTTGCAT--TA--T-AAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAATTCAACTA
1 AAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTA
*
855752 ATATGAAAATTTTATA
66 ATATAAAAATTTTATA
855768 AGAAATATAA
Statistics
Matches: 702, Mismatches: 58, Indels: 11
0.91 0.08 0.01
Matches are distributed among these distances:
81 59 0.08
82 1 0.00
84 2 0.00
85 79 0.11
86 560 0.80
87 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (86 bp):
AAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTA
ATATAAAAATTTTATATATTT
Found at i:855560 original size:343 final size:342
Alignment explanation
Indices: 854926--855767 Score: 1297
Period size: 343 Copynumber: 2.5 Consensus size: 342
854916 TACAAGTTTA
* * * *
854926 CATCATAGTTTAAATAATATAAATTAATTTTACATTTGTTAGTTTATAACTTTAACTAATATAAA
1 CATCATAGTTTAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTAATATAAA
* * *
854991 AATTTTATATATTTAAGTTTACATCATAGTTCAAATAATATAAATTAATTTTACATTTTTTAGTT
66 AATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTT
* *
855056 TATAAGTTTAACTAATATAAAGATTTGATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAA
131 TAAAAGTTCAACTAATATAAA-ATTT-ATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAA
* * * *
855121 TTAATTTTACATTTTTTAGTTTACAAGTTCAACTAATATAAAAAATTTATCTATTTAAGTTTGCA
194 TCAATTTTACATTTGTTAGTTTACAAGTTCAACTAATATAAAAAATTTATATATTTAAGTTTCCA
* * * *
855186 TTATAGTTCAATTAATATAAATTAATTTTACATTTGTTAGTTTACAAATTCAACTAATATAAACA
259 TCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAATTTACAAATTCAACTAATATAAAAA
*
855251 TTTTGTAT-TCTTAAGATTG
324 TTTTATATAT-TTAAGATTG
* *
855270 CATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTAATATTAA
1 CATCATAGTTTAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTAATATAAA
*
855335 AATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTCGTT
66 AATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTT
* * *
855400 TAAAAGTTCAACTCATATAAAATATTATATATTTAAGTTTGCATTATAGTTCAAGTATTATAAAT
131 TAAAAGTTCAACTAATATAAAAT-TTATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAAT
*
855465 CAATTTTACATTTGTTAGTTTACAAGTTCAACTAATAT-AAATATTGTATATATTTAAGTTTCCA
195 CAATTTTACATTTGTTAGTTTACAAGTTCAACTAATATAAAAAATT-TATATATTTAAGTTTCCA
*
855529 TCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAATTTACAAGTTCAACTAATATAAAAA
259 TCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAATTTACAAATTCAACTAATATAAAAA
*
855594 TTTTATATATTTAAGTTTG
324 TTTTATATATTTAAGATTG
* *
855613 CATCATAGTTTAAGTAATATAAATTAAGTTTACATTTATTAGTTTACAAGTTCAACTAATATAAA
1 CATCATAGTTTAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTAATATAAA
855678 AATTTTATATATTTAAGTTTGCAT--TA--T-AAGTAATATAAATTAATTTTACATTTGTTAGTT
66 AATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTT
855738 TACAAA-TTCAACTAATATGAAAATTT-TATA
131 TA-AAAGTTCAACTAATAT-AAAATTTATATA
855768 AGAAATATAA
Statistics
Matches: 460, Mismatches: 33, Indels: 17
0.90 0.06 0.03
Matches are distributed among these distances:
337 4 0.01
338 47 0.10
339 9 0.02
341 2 0.00
342 6 0.01
343 251 0.55
344 141 0.31
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (342 bp):
CATCATAGTTTAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAACTAATATAAA
AATTTTATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTT
TAAAAGTTCAACTAATATAAAATTTATATATTTAAGTTTGCATCATAGTTCAAGTAATATAAATC
AATTTTACATTTGTTAGTTTACAAGTTCAACTAATATAAAAAATTTATATATTTAAGTTTCCATC
ATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAATTTACAAATTCAACTAATATAAAAATT
TTATATATTTAAGATTG
Done.