Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 209 of 259
Found at i:66211222 original size:14 final size:14
Alignment explanation
Indices: 66211203--66211238 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
66211193 TCTTTATAAT
66211203 GATACTATTCTAAC
1 GATACTATTCTAAC
66211217 GATACTATTCTAAC
1 GATACTATTCTAAC
66211231 GATACTAT
1 GATACTAT
66211239 ATTTACTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (14 bp):
GATACTATTCTAAC
Found at i:66212137 original size:33 final size:33
Alignment explanation
Indices: 66212073--66212149 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
66212063 ATTGGGTCGA
* *** * *
66212073 ATCCACCGCAGTACAGTACTTTTCTCGGCCCGT
1 ATCCACCGCAGTACAGCACTACCCCCAGCCCGT
66212106 ATCCACCGCAGTACAGCACTACCCCCAGCCCGT
1 ATCCACCGCAGTACAGCACTACCCCCAGCCCGT
*
66212139 ATGCACCGCAG
1 ATCCACCGCAG
66212150 CATGGCACTC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.22, C:0.42, G:0.18, T:0.18
Consensus pattern (33 bp):
ATCCACCGCAGTACAGCACTACCCCCAGCCCGT
Found at i:66216104 original size:12 final size:12
Alignment explanation
Indices: 66216062--66216111 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
66216052 ACACATAATT
66216062 AATCTAAATACA
1 AATCTAAATACA
*
66216074 AAACTAAA-ACA
1 AATCTAAATACA
*
66216085 CATACTAAATACA
1 AAT-CTAAATACA
66216098 AATCTAAATACA
1 AATCTAAATACA
66216110 AA
1 AA
66216112 ATTAAATTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 4 0.12
12 23 0.72
13 5 0.16
ACGTcount: A:0.62, C:0.18, G:0.00, T:0.20
Consensus pattern (12 bp):
AATCTAAATACA
Found at i:66216117 original size:12 final size:12
Alignment explanation
Indices: 66216065--66216118 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
66216055 CATAATTAAT
66216065 CTAAATACAAAA
1 CTAAATACAAAA
*
66216077 CTAAA-ACACATA
1 CTAAATACA-AAA
*
66216089 CTAAATACAAAT
1 CTAAATACAAAA
66216101 CTAAATACAAAA
1 CTAAATACAAAA
*
66216113 TTAAAT
1 CTAAAT
66216119 TAGTAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 3 0.09
12 29 0.83
13 3 0.09
ACGTcount: A:0.61, C:0.17, G:0.00, T:0.22
Consensus pattern (12 bp):
CTAAATACAAAA
Found at i:66216445 original size:13 final size:13
Alignment explanation
Indices: 66216406--66216448 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
66216396 TTCTCCTTCC
66216406 TTCTTTCTCTCTATT
1 TTCTTTCT-TCT-TT
*
66216421 CTCTTT-TTCTTT
1 TTCTTTCTTCTTT
66216433 TTCTTTCTTCTTT
1 TTCTTTCTTCTTT
66216446 TTC
1 TTC
66216449 CCTCACCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.28
13 12 0.48
14 1 0.04
15 5 0.20
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCTTTCTTCTTT
Found at i:66216493 original size:11 final size:11
Alignment explanation
Indices: 66216468--66216514 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
66216458 TGTTGCCCTC
* *
66216468 TCTTCTCATTC
1 TCTTCTCTTTT
66216479 TCTTCTCTTTT
1 TCTTCTCTTTT
66216490 TCTT-TCTTTT
1 TCTTCTCTTTT
* *
66216500 TCTTTTCTTCT
1 TCTTCTCTTTT
66216511 TCTT
1 TCTT
66216515 GCTTCTTGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
10 10 0.31
11 22 0.69
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (11 bp):
TCTTCTCTTTT
Found at i:66217341 original size:13 final size:15
Alignment explanation
Indices: 66217308--66217344 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
66217298 TATTCTATGA
66217308 AAATTTAATAGAATAT
1 AAATTT-ATAGAATAT
66217324 AAATTTATAG-AT-T
1 AAATTTATAGAATAT
66217337 AAATTTAT
1 AAATTTAT
66217345 TAAATAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.43
14 2 0.10
15 4 0.19
16 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (15 bp):
AAATTTATAGAATAT
Found at i:66217357 original size:20 final size:20
Alignment explanation
Indices: 66217332--66217369 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
66217322 ATAAATTTAT
*
66217332 AGATTAAATTTATTAAATAA
1 AGATTAAATTTATAAAATAA
66217352 AGATTAAATTTATAAAAT
1 AGATTAAATTTATAAAAT
66217370 TTATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
AGATTAAATTTATAAAATAA
Found at i:66224379 original size:18 final size:18
Alignment explanation
Indices: 66224356--66224414 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
66224346 AACTCTTTTG
66224356 CTTTTAGATTCAAAAGCA
1 CTTTTAGATTCAAAAGCA
* *
66224374 CTTTTA-ACTCCAAAAGTTA
1 CTTTTAGA-TTCAAAAG-CA
*
66224393 TTTGTTAGATTCAAAAGCA
1 CTT-TTAGATTCAAAAGCA
66224412 CTT
1 CTT
66224415 CTTATTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
17 1 0.03
18 13 0.42
19 6 0.19
20 10 0.32
21 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (18 bp):
CTTTTAGATTCAAAAGCA
Found at i:66225004 original size:24 final size:24
Alignment explanation
Indices: 66224956--66225006 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
66224946 TTAATTTTAG
*
66224956 AAAAAGAAAAATATAAAATATAAA
1 AAAAAGAAAAAAATAAAATATAAA
*
66224980 AAAAAGAAAAACAATGAAATA-AAA
1 AAAAAGAAAAA-AATAAAATATAAA
66225004 AAA
1 AAA
66225007 TATAACTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.80, C:0.02, G:0.06, T:0.12
Consensus pattern (24 bp):
AAAAAGAAAAAAATAAAATATAAA
Found at i:66229686 original size:18 final size:18
Alignment explanation
Indices: 66229604--66229698 Score: 82
Period size: 18 Copynumber: 5.3 Consensus size: 18
66229594 GGTTTCATTT
* *
66229604 AGTAACATTCAATTATTC
1 AGTAACAATCAGTTATTC
* * *
66229622 AGTAGCAGTTAGTTATTC
1 AGTAACAATCAGTTATTC
* **
66229640 AGTAACAATCATTTGCTC
1 AGTAACAATCAGTTATTC
* *
66229658 AATAGCAATCAGTTATTC
1 AGTAACAATCAGTTATTC
* *
66229676 AGTAACGATCAATTATTC
1 AGTAACAATCAGTTATTC
66229694 AGTAA
1 AGTAA
66229699 TAGTTAGTCA
Statistics
Matches: 58, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
AGTAACAATCAGTTATTC
Found at i:66229712 original size:36 final size:35
Alignment explanation
Indices: 66229598--66229715 Score: 110
Period size: 36 Copynumber: 3.3 Consensus size: 35
66229588 TTTATCGGTT
*
66229598 TCATTTAGTAACATTCAATTATTCAGTAGCAGTTAG
1 TCATTCAGTAACA-TCAATTATTCAGTAGCAGTTAG
* * ** * * *
66229634 TTATTCAGTAACAATCATTTGCTCAATAGCAATCAG
1 TCATTCAGTAAC-ATCAATTATTCAGTAGCAGTTAG
* **
66229670 TTATTCAGTAACGATCAATTATTCAGTAATAGTTAG
1 TCATTCAGTAAC-ATCAATTATTCAGTAGCAGTTAG
66229706 TCATTCAGTA
1 TCATTCAGTA
66229716 CTTTTATTTA
Statistics
Matches: 63, Mismatches: 18, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
36 62 0.98
37 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (35 bp):
TCATTCAGTAACATCAATTATTCAGTAGCAGTTAG
Found at i:66230661 original size:12 final size:11
Alignment explanation
Indices: 66230638--66230671 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
66230628 TTTGTTACTC
66230638 AATTTCTATTT
1 AATTTCTATTT
66230649 AATTTCTACTTT
1 AATTTCTA-TTT
*
66230661 AATTTCAATTT
1 AATTTCTATTT
66230672 TAATCTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (11 bp):
AATTTCTATTT
Found at i:66231181 original size:13 final size:13
Alignment explanation
Indices: 66231142--66231183 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
66231132 TTTATTTTAT
66231142 ATATATTATAATA
1 ATATATTATAATA
66231155 ATATAATT-TAATA
1 ATAT-ATTATAATA
66231168 ATATACTTAT-ATA
1 ATATA-TTATAATA
66231181 ATA
1 ATA
66231184 AGTAAACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.04
13 21 0.81
14 4 0.15
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATATTATAATA
Found at i:66233329 original size:13 final size:14
Alignment explanation
Indices: 66233305--66233333 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
66233295 GTGTATATGG
66233305 AAAATTCATTTTAA
1 AAAATTCATTTTAA
66233319 AAAATTC-TTTTAA
1 AAAATTCATTTTAA
66233332 AA
1 AA
66233334 TGGTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATTCATTTTAA
Found at i:66243544 original size:53 final size:54
Alignment explanation
Indices: 66243481--66243587 Score: 173
Period size: 53 Copynumber: 2.0 Consensus size: 54
66243471 CTTAAATATA
* *
66243481 TAATTAAATTAACTAT-GATAATGGCAATCACATGCA-TTTTTTCATGCATGGCC
1 TAATTAAATTAACTATAG-TAATGACAACCACATGCATTTTTTTCATGCATGGCC
66243534 TAATTAAATTAACTATAGTAATGACAACCACATGCATTTTTTTCATGCATGGCC
1 TAATTAAATTAACTATAGTAATGACAACCACATGCATTTTTTTCATGCATGGCC
66243588 CTAAAGAGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
53 32 0.64
54 18 0.36
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (54 bp):
TAATTAAATTAACTATAGTAATGACAACCACATGCATTTTTTTCATGCATGGCC
Found at i:66246262 original size:2 final size:2
Alignment explanation
Indices: 66246255--66246290 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
66246245 AAGGGGACTT
66246255 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
66246291 TAAAGATAAT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:66264351 original size:133 final size:134
Alignment explanation
Indices: 66264031--66264430 Score: 508
Period size: 133 Copynumber: 3.0 Consensus size: 134
66264021 TTTAGAGAGT
* * * * * *
66264031 ATGAGTGAAATTCTAAAGGAATC-TTCGATCATTTTGAACAAAC-AGGAGATCGCAACCCAGCAC
1 ATGAATGAAATTCTAAAGGGA-CATTCGATTATTTTGAGCAAACGA-GAAATTGCAACCCAGCAC
* * * * * **
66264094 GATAGGGCACGATT-TCCCGAATTGCTAAACATCGAACATTGCCTTCGTTTTGGAGAATTTTTAA
64 GTTAGGGCACGATTCT-GCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGAATTTTTAA
* *
66264158 ACG---C
128 AAGAATA
* * *
66264162 ATGAATGAAATTCTAAAGGGACATTCAATTATTTTGAGTAAACGAGAAATTGCAACCCAACACGT
1 ATGAATGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGT
*
66264227 TAGGGCACGATTCTGTGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGAA-TTTTAAAAG
66 TAGGGCACGATTCTGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGAATTTTTAAAAG
66264291 AATA
131 AATA
66264295 ATGAATGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGT
1 ATGAATGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGT
* * * * *
66264360 TAGGGCACGATTCCGGGAATTGCCAAATATCGAACACCGCCTTCATTTTAAAGAATTTTTAAATG
66 TAGGGCACGATTCTGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGAATTTTTAAAAG
66264425 AATA
131 AATA
66264429 AT
1 AT
66264431 TGCAAAAATA
Statistics
Matches: 235, Mismatches: 27, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
130 9 0.04
131 97 0.41
132 2 0.01
133 113 0.48
134 14 0.06
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (134 bp):
ATGAATGAAATTCTAAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGT
TAGGGCACGATTCTGCGAATTGCCAAATATCGAACATCGCCTTCGTTTTAAAGAATTTTTAAAAG
AATA
Found at i:66273443 original size:19 final size:18
Alignment explanation
Indices: 66273421--66273460 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
66273411 TGAATAAAAC
*
66273421 TTATTTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
*
66273440 TTATCTAGCTAAATAAAT
1 TTATCTACCTAAATAAAT
66273458 TTA
1 TTA
66273461 AAATATATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:66278016 original size:42 final size:42
Alignment explanation
Indices: 66277965--66278062 Score: 144
Period size: 42 Copynumber: 2.3 Consensus size: 42
66277955 ACTTAAATAG
66277965 AGAAAATAGTTCTTTTATTCTAATAAACTACTAAAACATAAA
1 AGAAAATAGTTCTTTTATTCTAATAAACTACTAAAACATAAA
** *
66278007 AGAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAA
1 AGAAAATAGTTCTTTTATTCTAATAAACTACTAAAACATAAA
*
66278049 ATAAAAATA-TTCTT
1 A-GAAAATAGTTCTT
66278063 AGAATATGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
42 43 0.88
43 6 0.12
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (42 bp):
AGAAAATAGTTCTTTTATTCTAATAAACTACTAAAACATAAA
Found at i:66278101 original size:19 final size:18
Alignment explanation
Indices: 66278079--66278118 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
66278069 TGAATAAAAC
*
66278079 TTATCTATCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
66278098 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
66278116 TTA
1 TTA
66278119 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:66289573 original size:2 final size:2
Alignment explanation
Indices: 66289566--66289590 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
66289556 ATTACTTTAC
66289566 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 T
66289591 CTTTTGAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66293821 original size:121 final size:121
Alignment explanation
Indices: 66293658--66293899 Score: 441
Period size: 121 Copynumber: 2.0 Consensus size: 121
66293648 ACAAGTGGAT
* *
66293658 GTTTAGGTTCAGATGAATGTGGACAATTAAACTTAGACATTCATTTGTTCAAATTTATTTTGGAA
1 GTTTAGATTCAGATGAATGTGGACAATTAAACTTAGACATTCATTTGTTCAAATTTATTTCGGAA
*
66293723 GTGAAATATTTTTTTATTAATTTATATATATTTTTAAAAAAATTAAAGATTATATA
66 GTGAAATAATTTTTTATTAATTTATATATATTTTTAAAAAAATTAAAGATTATATA
66293779 GTTTAGATTCAGATGAATGTGGACAATTAAACTTA-AGCATTCATTTGTTCAAATTTATTTCGGA
1 GTTTAGATTCAGATGAATGTGGACAATTAAACTTAGA-CATTCATTTGTTCAAATTTATTTCGGA
66293843 AGTGAAATAATTTTTTATTAATTTATATATATTTTTAAAAAAATTAAAGATTATATA
65 AGTGAAATAATTTTTTATTAATTTATATATATTTTTAAAAAAATTAAAGATTATATA
66293900 ATTTCTTTTT
Statistics
Matches: 117, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
120 1 0.01
121 116 0.99
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (121 bp):
GTTTAGATTCAGATGAATGTGGACAATTAAACTTAGACATTCATTTGTTCAAATTTATTTCGGAA
GTGAAATAATTTTTTATTAATTTATATATATTTTTAAAAAAATTAAAGATTATATA
Found at i:66294395 original size:3 final size:3
Alignment explanation
Indices: 66294387--66294434 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
66294377 CGTCTGCCAT
66294387 GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC
1 GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC
66294435 TTCCTTGCCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
GTC
Found at i:66295969 original size:15 final size:16
Alignment explanation
Indices: 66295935--66295969 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
66295925 TCTTGATGCC
*
66295935 AAAATCTACCTTGAGA
1 AAAACCTACCTTGAGA
66295951 AAAACCTACCTTGAGA
1 AAAACCTACCTTGAGA
66295967 AAA
1 AAA
66295970 TTAATATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.11, T:0.20
Consensus pattern (16 bp):
AAAACCTACCTTGAGA
Found at i:66302423 original size:23 final size:22
Alignment explanation
Indices: 66302372--66302423 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
66302362 CCTCGTCTTT
*
66302372 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
66302394 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
66302417 TTCTTTT
1 TTCTTTT
66302424 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:66302438 original size:18 final size:18
Alignment explanation
Indices: 66302417--66302455 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
66302407 TTTCTTCAAC
* *
66302417 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
66302435 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
66302453 TTC
1 TTC
66302456 ACTCGCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:66304823 original size:4 final size:4
Alignment explanation
Indices: 66304814--66304841 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
66304804 TTAAACTAAG
66304814 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
66304842 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:66309263 original size:20 final size:20
Alignment explanation
Indices: 66309230--66309269 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
66309220 AAAAGAAGGA
*
66309230 AAAGAGGGTAGTGAAAAAGT
1 AAAGAAGGTAGTGAAAAAGT
*
66309250 AAAGAAGGTCGTGAAAAAGT
1 AAAGAAGGTAGTGAAAAAGT
66309270 TTTACCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.33, T:0.15
Consensus pattern (20 bp):
AAAGAAGGTAGTGAAAAAGT
Found at i:66334048 original size:12 final size:12
Alignment explanation
Indices: 66334031--66334078 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
66334021 TAAAATAAAA
66334031 TAATATATCAAC
1 TAATATATCAAC
66334043 TAATATATCAAC
1 TAATATATCAAC
*
66334055 TAAT-T-T-TA-
1 TAATATATCAAC
66334063 TAATATATCAAC
1 TAATATATCAAC
66334075 TAAT
1 TAAT
66334079 TTTCTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
8 4 0.13
9 2 0.07
10 2 0.07
11 2 0.07
12 20 0.67
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (12 bp):
TAATATATCAAC
Found at i:66334086 original size:24 final size:20
Alignment explanation
Indices: 66334043--66334081 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
66334033 ATATATCAAC
66334043 TAATATATCAACTAATTTTA
1 TAATATATCAACTAATTTTA
66334063 TAATATATCAACTAATTTT
1 TAATATATCAACTAATTTT
66334082 CTTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATATATCAACTAATTTTA
Found at i:66345959 original size:16 final size:17
Alignment explanation
Indices: 66345938--66345975 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
66345928 TTATATTTAA
66345938 TAATATAA-TGAATTAT
1 TAATATAACTGAATTAT
* *
66345954 TAATATAACTTAATTTT
1 TAATATAACTGAATTAT
66345971 TAATA
1 TAATA
66345976 AATTATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TAATATAACTGAATTAT
Found at i:66351018 original size:17 final size:18
Alignment explanation
Indices: 66350982--66351019 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
66350972 TTGGGCCGGG
66350982 CACTAGTCTCTTCATAAA
1 CACTAGTCTCTTCATAAA
* *
66351000 CACTAGT-TTTTCTTAAA
1 CACTAGTCTCTTCATAAA
66351017 CAC
1 CAC
66351020 AAGCACTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (18 bp):
CACTAGTCTCTTCATAAA
Found at i:66352812 original size:92 final size:93
Alignment explanation
Indices: 66352681--66352865 Score: 354
Period size: 92 Copynumber: 2.0 Consensus size: 93
66352671 AGCAATCCTT
66352681 TTCTTCGCCTTTATTTACTTTTGTTAGGATTGAGCTCTGATTAGAGATTTTGTTTTGGGTTTAAT
1 TTCTTCGCCTTTATTTACTTTTGTTAGGATTGAGCTCTGATTAGAGATTTTGTTTTGGGTTTAAT
66352746 TGTTGATTCATCTTTTTTCTATTATTTC
66 TGTTGATTCATCTTTTTTCTATTATTTC
*
66352774 TTCTTCGCCTTTATTTAC-TTTGTTAGGATTGAGCTCTGATTAGAGGTTTTGTTTTGGGTTTAAT
1 TTCTTCGCCTTTATTTACTTTTGTTAGGATTGAGCTCTGATTAGAGATTTTGTTTTGGGTTTAAT
66352838 TGTTGATTCATCTTTTTTCTATTATTTC
66 TGTTGATTCATCTTTTTTCTATTATTTC
66352866 CTGGCAGCTC
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 73 0.80
93 18 0.20
ACGTcount: A:0.16, C:0.12, G:0.17, T:0.56
Consensus pattern (93 bp):
TTCTTCGCCTTTATTTACTTTTGTTAGGATTGAGCTCTGATTAGAGATTTTGTTTTGGGTTTAAT
TGTTGATTCATCTTTTTTCTATTATTTC
Found at i:66353754 original size:21 final size:21
Alignment explanation
Indices: 66353728--66353772 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
66353718 AGGTGGTAAT
*
66353728 TCTGAAGGTTCCTTGAACTCA
1 TCTGAAGATTCCTTGAACTCA
66353749 TCTGAAGATTCCTTGAACTCA
1 TCTGAAGATTCCTTGAACTCA
66353770 TCT
1 TCT
66353773 AAGTAGGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (21 bp):
TCTGAAGATTCCTTGAACTCA
Found at i:66375546 original size:2 final size:2
Alignment explanation
Indices: 66375539--66375569 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
66375529 GGAGTAATAT
66375539 TC TC 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 TC TC T
66375570 TTTTTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:66385884 original size:13 final size:14
Alignment explanation
Indices: 66385859--66385891 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
66385849 TTTTCTCATC
66385859 TTCT-TCCCAAAAA
1 TTCTATCCCAAAAA
66385872 TTCTATCCCAAAAA
1 TTCTATCCCAAAAA
66385886 TTCTAT
1 TTCTAT
66385892 GGAGACTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (14 bp):
TTCTATCCCAAAAA
Found at i:66390408 original size:22 final size:22
Alignment explanation
Indices: 66390380--66390423 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
66390370 TCTTCTATCA
66390380 AGGTCTACAGCAAAATCAACAT
1 AGGTCTACAGCAAAATCAACAT
66390402 AGGTCTACAGCAAAATCAACAT
1 AGGTCTACAGCAAAATCAACAT
66390424 CAACATACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (22 bp):
AGGTCTACAGCAAAATCAACAT
Found at i:66392140 original size:13 final size:13
Alignment explanation
Indices: 66392124--66392155 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
66392114 CTCCGTAATA
66392124 GTTCTGTTGATTC
1 GTTCTGTTGATTC
*
66392137 GTTCTATTGATTC
1 GTTCTGTTGATTC
66392150 GTTCTG
1 GTTCTG
66392156 CAACGCCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.22, T:0.53
Consensus pattern (13 bp):
GTTCTGTTGATTC
Found at i:66393895 original size:5 final size:5
Alignment explanation
Indices: 66393885--66393912 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
66393875 CAATTTGTGA
66393885 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
66393913 GAACACACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:66414396 original size:42 final size:42
Alignment explanation
Indices: 66414340--66414480 Score: 122
Period size: 42 Copynumber: 3.4 Consensus size: 42
66414330 TTGTCTTTAC
* * * *
66414340 TTTCCGTTTAGCTCTCACAAGCTTTTGTTTAACTCATATGAG
1 TTTCCGTTCAGCTCTTACAAGCTTTTATTTAACCCATATGAG
* ** *
66414382 TTTTCGTTCAGCTCTTTTGAA-CTTTTATTTAACCCTTATGAG
1 TTTCCGTTCAGCTC-TTACAAGCTTTTATTTAACCCATATGAG
* * * * * *
66414424 TTTCCGTTCAGCTCTTACGAGCTTTCATTCAACACTTATGGG
1 TTTCCGTTCAGCTCTTACAAGCTTTTATTTAACCCATATGAG
* *
66414466 TTTCTGTTTAGCTCT
1 TTTCCGTTCAGCTCT
66414481 CATGAGCTTC
Statistics
Matches: 79, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
41 3 0.04
42 73 0.92
43 3 0.04
ACGTcount: A:0.18, C:0.22, G:0.14, T:0.45
Consensus pattern (42 bp):
TTTCCGTTCAGCTCTTACAAGCTTTTATTTAACCCATATGAG
Found at i:66417049 original size:31 final size:31
Alignment explanation
Indices: 66417014--66417074 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
66417004 TGCACTACTG
66417014 TACTTTCTCAACTTAATTTTACTAGTCCAAT
1 TACTTTCTCAACTTAATTTTACTAGTCCAAT
66417045 TACTTTCTCAACTTAATTTTACTAGTCCAA
1 TACTTTCTCAACTTAATTTTACTAGTCCAA
66417075 GGCTTATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (31 bp):
TACTTTCTCAACTTAATTTTACTAGTCCAAT
Found at i:66420451 original size:16 final size:17
Alignment explanation
Indices: 66420430--66420475 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
66420420 AGCAGGGGTG
66420430 GAGAAAGGGAGAGGA-A
1 GAGAAAGGGAGAGGAGA
*
66420446 GAGAAAGAGAGA-GAGA
1 GAGAAAGGGAGAGGAGA
66420462 GAGAAAAGGGAGAG
1 GAG-AAAGGGAGAG
66420476 AGGGTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 2 0.08
16 15 0.60
17 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (17 bp):
GAGAAAGGGAGAGGAGA
Found at i:66432292 original size:44 final size:44
Alignment explanation
Indices: 66432079--66432294 Score: 153
Period size: 44 Copynumber: 5.0 Consensus size: 44
66432069 GCATTAATCC
* * * * *
66432079 TATCTCCCTGAGGTTACAGCGGAGCAGATCAAAG-ATATA-ATCC
1 TATCTCCCTAAGGTTACAGTGGAGCAGATTAAAGCA-ACAGATCT
* *
66432122 TATCTCCCTAA-GTTACAGTGGAGCGGATTAAAATC-ACAGATCT
1 TATCTCCCTAAGGTTACAGTGGAGCAGATT-AAAGCAACAGATCT
* * * * * *
66432165 TATCTCTCTGAA-GTTACAGTAGAGTAGA-T--CGCATCAGGTCT
1 TATCTCCCT-AAGGTTACAGTGGAGCAGATTAAAGCAACAGATCT
* * * * *
66432206 TATCTCCTTGAGGTTACAGTGGAGCAGATTGAAGCCATAGATCT
1 TATCTCCCTAAGGTTACAGTGGAGCAGATTAAAGCAACAGATCT
* *
66432250 TATCTCCCTAAGGTTACAGTGGAGCTGGTTAAAG-AAGCAGATCT
1 TATCTCCCTAAGGTTACAGTGGAGCAGATTAAAGCAA-CAGATCT
66432294 T
1 T
66432295 GCCTTCCTGC
Statistics
Matches: 131, Mismatches: 32, Indels: 19
0.72 0.18 0.10
Matches are distributed among these distances:
40 2 0.02
41 27 0.21
42 18 0.14
43 26 0.20
44 58 0.44
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
TATCTCCCTAAGGTTACAGTGGAGCAGATTAAAGCAACAGATCT
Found at i:66432405 original size:86 final size:86
Alignment explanation
Indices: 66432261--66432427 Score: 291
Period size: 86 Copynumber: 1.9 Consensus size: 86
66432251 ATCTCCCTAA
*
66432261 GGTTACAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGA
1 GGTTACAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGA
*
66432326 AAAC-AAGCTTTGCCTTCATT
66 AAACAAAGCCTTGCCTTCATT
*
66432346 GGTTACAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCG
1 GGTTACAGTGGAGCTGGTTAAAGA-AGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCG
66432411 AAAACAAAGCCTTGCCT
65 AAAACAAAGCCTTGCCT
66432428 CTCTCGAGTG
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
85 23 0.30
86 44 0.57
87 10 0.13
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (86 bp):
GGTTACAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGA
AAACAAAGCCTTGCCTTCATT
Found at i:66432492 original size:87 final size:87
Alignment explanation
Indices: 66432271--66432542 Score: 279
Period size: 86 Copynumber: 3.2 Consensus size: 87
66432261 GGTTACAGTG
* * *
66432271 GAGCTGGTTAAAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAC-AAGC
1 GAGCTGGTTGAAGACAACAGATCTTACCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
* * *
66432334 TTTGCCT-TCATTG-GT-TACAGTG
66 CTTGCCTCTC-TCGAGTGT--AGTA
* * * *
66432356 GAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGC
1 GAGCTGGTTGAAGACAACAGATCTTACCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
*
66432421 CTTGCCTCTCTCGAGTGTAGAA
66 CTTGCCTCTCTCGAGTGTAGTA
* * * * * * * *
66432443 GAGTTGGTTGAAGACAACTGATTTTATCTTCCTGCGTTGACAGTGAAGCAGGTCGAAGACAAA-C
1 GAGCTGGTTGAAGACAACAGATCTTACCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
*
66432507 CTTACCTCTCTC-AGTTGTAGTA
66 CTTGCCTCTCTCGAG-TGTAGTA
66432529 GAGCTGGTTGAAGA
1 GAGCTGGTTGAAGA
66432543 ATTGCAGATC
Statistics
Matches: 160, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
85 15 0.09
86 75 0.47
87 65 0.41
88 4 0.03
89 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (87 bp):
GAGCTGGTTGAAGACAACAGATCTTACCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
CTTGCCTCTCTCGAGTGTAGTA
Found at i:66434804 original size:10 final size:10
Alignment explanation
Indices: 66434791--66434834 Score: 70
Period size: 10 Copynumber: 4.4 Consensus size: 10
66434781 TATGTGTATG
66434791 TATATATTTT
1 TATATATTTT
*
66434801 TATATATTTA
1 TATATATTTT
66434811 TATATATTTT
1 TATATATTTT
*
66434821 TATATATATT
1 TATATATTTT
66434831 TATA
1 TATA
66434835 CATATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TATATATTTT
Found at i:66434816 original size:12 final size:12
Alignment explanation
Indices: 66434791--66434861 Score: 64
Period size: 10 Copynumber: 6.4 Consensus size: 12
66434781 TATGTGTATG
66434791 TATATATTT-T-
1 TATATATTTATA
66434801 TATATATTTATA
1 TATATATTTATA
66434813 TATAT-TTT-TA
1 TATATATTTATA
66434823 TATATATTTATA
1 TATATATTTATA
*
66434835 CATAT-TTTA-A
1 TATATATTTATA
* * *
66434845 TACATATCTACA
1 TATATATTTATA
66434857 TATAT
1 TATAT
66434862 CTAAATACCC
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
10 20 0.40
11 14 0.28
12 16 0.32
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (12 bp):
TATATATTTATA
Found at i:66434826 original size:22 final size:22
Alignment explanation
Indices: 66434791--66434861 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
66434781 TATGTGTATG
66434791 TATATA-TTTT-TATATATTTA
1 TATATATTTTTATATATATTTA
66434811 TATATATTTTTATATATATTTA
1 TATATATTTTTATATATATTTA
* * * *
66434833 TACATATTTTAATACATATCTA
1 TATATATTTTTATATATATTTA
*
66434855 CATATAT
1 TATATAT
66434862 CTAAATACCC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.14
21 4 0.09
22 33 0.77
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATATTTTTATATATATTTA
Found at i:66434839 original size:10 final size:10
Alignment explanation
Indices: 66434791--66434841 Score: 66
Period size: 10 Copynumber: 4.9 Consensus size: 10
66434781 TATGTGTATG
*
66434791 TATATATTTT
1 TATATATTTA
66434801 TATATATTTA
1 TATATATTTA
66434811 TATATATTTTTA
1 TATATA--TTTA
66434823 TATATATTTA
1 TATATATTTA
*
66434833 TACATATTT
1 TATATATTT
66434842 TAATACATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
10 27 0.73
12 10 0.27
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATATTTA
Found at i:66436970 original size:19 final size:20
Alignment explanation
Indices: 66436930--66436973 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
66436920 GTCTCTTTAG
* *
66436930 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
66436949 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
66436968 GCATTA
1 GCATTA
66436974 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:66439525 original size:20 final size:19
Alignment explanation
Indices: 66439500--66439562 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
66439490 AAAATCAAAG
66439500 TCAAAATGAAAATGAAAAAA
1 TCAAAAT-AAAATGAAAAAA
66439520 TCAAAAATAGAAAT-AAAAAA
1 TC-AAAATA-AAATGAAAAAA
*
66439540 -CAAAA-AGAA-GAAAAAA
1 TCAAAATAAAATGAAAAAA
66439556 TCAAAAT
1 TCAAAAT
66439563 CAAGATCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
16 8 0.22
17 6 0.16
18 4 0.11
19 1 0.03
20 9 0.24
21 9 0.24
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.13
Consensus pattern (19 bp):
TCAAAATAAAATGAAAAAA
Found at i:66441821 original size:44 final size:43
Alignment explanation
Indices: 66441772--66442086 Score: 122
Period size: 44 Copynumber: 7.2 Consensus size: 43
66441762 AGTTAAAGAT
* *
66441772 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACATAAAC
1 CTTGCCTTCCTGCATTGACAG-GAAGCAGGTCGAAGACATAAAC
* * * ** * * *
66441816 CTTGCC-TCTTTCGGTTGTGATGG-AGCTGGTTGAAGACA-AAGGAT
1 CTTGCCTTCCTGC-ATTGACA-GGAAGCAGGTCGAAGACATAA--AC
* *
66441860 CTTGCCTTCCTGCATTGATAGTGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAG-GAAGCAGGTCGAAGACATAAAC
* * * ** * * * *
66441904 CTTGCC-TCTTTCGGTTGTGATGG-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTCCTGC-ATTGACA-GGAAGCAGGTCGAAGACATAA-AC
* *
66441948 CTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACATAAAC
1 CTTGCCTTCCTGCATTGACAG-GAAGCAGGTCGAAGACATAAAC
* * * ** * * * *
66441992 CTTGCC-TCTTTCGGTTGTGATGG-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTCCTGC-ATTGACA-GGAAGCAGGTCGAAGACATAA-AC
* * * * *
66442036 CTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAGGACACAAGC
1 CTTGCCTTCCTGCATTGACAG-GAAGCAGGTCGAAGACATAAAC
66442080 CTTGCCT
1 CTTGCCT
66442087 CCCTTAGTTG
Statistics
Matches: 190, Mismatches: 61, Indels: 40
0.65 0.21 0.14
Matches are distributed among these distances:
42 2 0.01
43 55 0.29
44 78 0.41
45 53 0.28
46 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (43 bp):
CTTGCCTTCCTGCATTGACAGGAAGCAGGTCGAAGACATAAAC
Found at i:66442126 original size:88 final size:88
Alignment explanation
Indices: 66441766--66442087 Score: 545
Period size: 88 Copynumber: 3.7 Consensus size: 88
66441756 CAATGAAGTT
* *
66441766 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACATAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
66441831 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
* * * *
66441854 AAGGATCTTGCCTTCCTGCATTGATAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
66441919 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
* *
66441942 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACATAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
66442007 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
* * *
66442030 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAGGACACAAGCCTTGCCTC
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTC
66442088 CCTTAGTTGT
Statistics
Matches: 219, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 219 1.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (88 bp):
AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
TGTGATGGAGCTGGTTGAAGACA
Found at i:66442296 original size:87 final size:87
Alignment explanation
Indices: 66442204--66442579 Score: 293
Period size: 85 Copynumber: 4.4 Consensus size: 87
66442194 TGGAAATTTC
*
66442204 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAAGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTA
66442269 CAGTGGAGCGGATTAAAAT-AA
66 CAGTGGAGCGGATTAAAATCAA
* ** * * * ** * *
66442290 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA-TCA-GGTCTTATCTCCCTGAGGTT
1 A-GATCTTATCTCCCTGAAGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTT
* * ** **
66442353 ACAGCGAAGTAGACCGAAGAATTGC-A
65 ACAGTGGAGCGGA-TTAA-AA-T-CAA
* * *
66442379 A-ATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCAAAGATATAATCCTATCTCCCT-AAGTTA
1 AGATCTTATCTCCCTGAAGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTA
*
66442442 CAGTGGAGCGGATTAAAATCAC
66 CAGTGGAGCGGATTAAAATCAA
* ** * * * ** * * *
66442464 AGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA-TCA-GGTCTTATCTCCTTGAGGTTA
1 AGATCTTATCTCCCTGAAGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTA
* * ** *
66442527 CAGTGGAGCAGATTGAAGCCAT
66 CAGTGGAGCGGATTAAAATCAA
*
66442549 AGATCTTATCTCCCT-AAGGTTACAGTGGAGC
1 AGATCTTATCTCCCTGAA-GTTACAGCGGAGC
66442580 TGGTTAAAGA
Statistics
Matches: 219, Mismatches: 59, Indels: 25
0.72 0.19 0.08
Matches are distributed among these distances:
84 13 0.06
85 75 0.34
86 37 0.17
87 66 0.30
88 15 0.07
89 13 0.06
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (87 bp):
AGATCTTATCTCCCTGAAGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTA
CAGTGGAGCGGATTAAAATCAA
Found at i:66442309 original size:44 final size:43
Alignment explanation
Indices: 66442204--66442579 Score: 203
Period size: 44 Copynumber: 8.7 Consensus size: 43
66442194 TGGAAATTTC
* * * * * *
66442204 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAT
1 AGATCTTATCTCCCTGAAGTTACAGTGGAGCAGAT-TAAAATAA
* *
66442248 A-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAA
1 AGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAA
* * * *** *
66442290 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGA-TCGCAT-C
1 A-GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAA
* * * * * ** *
66442332 AGGTCTTATCTCCCTGAGGTTACAGCGAAGTAGACCGAAGAATTGCA
1 AGATCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AA-T-AA
* * * *
66442379 A-ATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCAAAGATAT
1 AGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA-ATAA
* * *
66442422 A-ATCCTATCTCCCT-AAGTTACAGTGGAGCGGATTAAAATCAC
1 AGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAT-AA
* * * *** *
66442464 AGATCTTATCTCTCTGAAGTTACAGTAGAGTAGA-TCGCAT-C
1 AGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAA
* * * *** *
66442505 AGGTCTTATCTCCTTGAGGTTACAGTGGAGCAGATTGAAGCCAT
1 AGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAATAA
66442549 AGATCTTATCTCCCT-AAGGTTACAGTGGAGC
1 AGATCTTATCTCCCTGAA-GTTACAGTGGAGC
66442580 TGGTTAAAGA
Statistics
Matches: 252, Mismatches: 64, Indels: 32
0.72 0.18 0.09
Matches are distributed among these distances:
41 58 0.23
42 28 0.11
43 60 0.24
44 72 0.29
45 4 0.02
46 29 0.12
47 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (43 bp):
AGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAA
Found at i:66442496 original size:173 final size:174
Alignment explanation
Indices: 66442206--66442529 Score: 589
Period size: 173 Copynumber: 1.9 Consensus size: 174
66442196 GAAATTTCAG
*
66442206 ATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTACA
1 ATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCAAAGACATAATCCTATCTCCCTGAAGTTACA
66442271 GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGT
66 GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGT
66442336 CTTATCTCCCTGAGGTTACAGCGAAGTAGACCGAAGAATTGCAA
131 CTTATCTCCCTGAGGTTACAGCGAAGTAGACCGAAGAATTGCAA
*
66442380 ATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCAAAGATATAATCCTATCTCCCT-AAGTTACA
1 ATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCAAAGACATAATCCTATCTCCCTGAAGTTACA
*
66442444 GTGGAGCGGATTAAAATCACA-GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
66 GTGGAGCGGATTAAAAT-AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
*
66442508 TCTTATCTCCTTGAGGTTACAG
130 TCTTATCTCCCTGAGGTTACAG
66442530 TGGAGCAGAT
Statistics
Matches: 145, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
173 89 0.61
174 56 0.39
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (174 bp):
ATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCAAAGACATAATCCTATCTCCCTGAAGTTACA
GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGT
CTTATCTCCCTGAGGTTACAGCGAAGTAGACCGAAGAATTGCAA
Found at i:66442710 original size:86 final size:86
Alignment explanation
Indices: 66442566--66442732 Score: 291
Period size: 86 Copynumber: 1.9 Consensus size: 86
66442556 ATCTCCCTAA
*
66442566 GGTTACAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGA
1 GGTTACAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGA
*
66442631 AAAC-AAGCTTTGCCTTCATT
66 AAACAAAGCCTTGCCTTCATT
*
66442651 GGTTACAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCG
1 GGTTACAGTGGAGCTGGTTAAAGA-AGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCG
66442716 AAAACAAAGCCTTGCCT
65 AAAACAAAGCCTTGCCT
66442733 CTCTCGAGTG
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
85 23 0.30
86 44 0.57
87 10 0.13
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (86 bp):
GGTTACAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGA
AAACAAAGCCTTGCCTTCATT
Found at i:66442797 original size:87 final size:87
Alignment explanation
Indices: 66442576--66442847 Score: 279
Period size: 86 Copynumber: 3.2 Consensus size: 87
66442566 GGTTACAGTG
* * *
66442576 GAGCTGGTTAAAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAC-AAGC
1 GAGCTGGTTGAAGACAACAGATCTTACCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
* * *
66442639 TTTGCCT-TCATTG-GT-TACAGTG
66 CTTGCCTCTC-TCGAGTGT--AGTA
* * * *
66442661 GAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGC
1 GAGCTGGTTGAAGACAACAGATCTTACCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
*
66442726 CTTGCCTCTCTCGAGTGTAGAA
66 CTTGCCTCTCTCGAGTGTAGTA
* * * * * * * *
66442748 GAGTTGGTTGAAGACAACTGATTTTATCTTCCTGCGTTGACAGTGAAGCAGGTCGAAGACAAA-C
1 GAGCTGGTTGAAGACAACAGATCTTACCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
*
66442812 CTTACCTCTCTC-AGTTGTAGTA
66 CTTGCCTCTCTCGAG-TGTAGTA
66442834 GAGCTGGTTGAAGA
1 GAGCTGGTTGAAGA
66442848 ATTGCAGATC
Statistics
Matches: 160, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
85 15 0.09
86 75 0.47
87 65 0.41
88 4 0.03
89 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (87 bp):
GAGCTGGTTGAAGACAACAGATCTTACCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
CTTGCCTCTCTCGAGTGTAGTA
Found at i:66445108 original size:10 final size:10
Alignment explanation
Indices: 66445095--66445138 Score: 70
Period size: 10 Copynumber: 4.4 Consensus size: 10
66445085 TATGTGTATG
66445095 TATATATTTT
1 TATATATTTT
*
66445105 TATATATTTA
1 TATATATTTT
66445115 TATATATTTT
1 TATATATTTT
*
66445125 TATATATATT
1 TATATATTTT
66445135 TATA
1 TATA
66445139 CATATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TATATATTTT
Found at i:66445120 original size:12 final size:12
Alignment explanation
Indices: 66445095--66445165 Score: 64
Period size: 10 Copynumber: 6.4 Consensus size: 12
66445085 TATGTGTATG
66445095 TATATATTT-T-
1 TATATATTTATA
66445105 TATATATTTATA
1 TATATATTTATA
66445117 TATAT-TTT-TA
1 TATATATTTATA
66445127 TATATATTTATA
1 TATATATTTATA
*
66445139 CATAT-TTTA-A
1 TATATATTTATA
* * *
66445149 TACATATCTACA
1 TATATATTTATA
66445161 TATAT
1 TATAT
66445166 CTAAATACCC
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
10 20 0.40
11 14 0.28
12 16 0.32
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (12 bp):
TATATATTTATA
Found at i:66445130 original size:22 final size:22
Alignment explanation
Indices: 66445095--66445165 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
66445085 TATGTGTATG
66445095 TATATA-TTTT-TATATATTTA
1 TATATATTTTTATATATATTTA
66445115 TATATATTTTTATATATATTTA
1 TATATATTTTTATATATATTTA
* * * *
66445137 TACATATTTTAATACATATCTA
1 TATATATTTTTATATATATTTA
*
66445159 CATATAT
1 TATATAT
66445166 CTAAATACCC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.14
21 4 0.09
22 33 0.77
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATATTTTTATATATATTTA
Found at i:66445143 original size:10 final size:10
Alignment explanation
Indices: 66445095--66445145 Score: 66
Period size: 10 Copynumber: 4.9 Consensus size: 10
66445085 TATGTGTATG
*
66445095 TATATATTTT
1 TATATATTTA
66445105 TATATATTTA
1 TATATATTTA
66445115 TATATATTTTTA
1 TATATA--TTTA
66445127 TATATATTTA
1 TATATATTTA
*
66445137 TACATATTT
1 TATATATTT
66445146 TAATACATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
10 27 0.73
12 10 0.27
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATATTTA
Found at i:66447507 original size:23 final size:23
Alignment explanation
Indices: 66447479--66447525 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
66447469 AGAACACCGT
66447479 AAGAATTTATTATTGACAATAAG
1 AAGAATTTATTATTGACAATAAG
*
66447502 AAGAATTTATTATTGACCATAAG
1 AAGAATTTATTATTGACAATAAG
66447525 A
1 A
66447526 GAAAAACTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (23 bp):
AAGAATTTATTATTGACAATAAG
Found at i:66449407 original size:39 final size:38
Alignment explanation
Indices: 66449364--66449452 Score: 90
Period size: 39 Copynumber: 2.3 Consensus size: 38
66449354 TATTGGCATC
** *
66449364 TTAATATTTTTTTTAATGTTTATGTTATAATATTATAT-A
1 TTAATATTTTTAGT-ATGTTTATGTTATAA-ATTACATAA
* *
66449403 TTAATATGATTTAGTATTTTTATGTTATAAATTACATAA
1 TTAATAT-TTTTAGTATGTTTATGTTATAAATTACATAA
66449442 TATAATATTTT
1 T-TAATATTTT
66449453 AACAAATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
38 6 0.15
39 25 0.61
40 10 0.24
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (38 bp):
TTAATATTTTTAGTATGTTTATGTTATAAATTACATAA
Found at i:66453881 original size:32 final size:30
Alignment explanation
Indices: 66453833--66453902 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
66453823 AAATTTTAAA
* *
66453833 TTAATAAA-AATAAAATTATATTTTTATCTCTT
1 TTAA-AAATAATAAAATTATAATTTAAT-T-TT
*
66453865 TTAAAAATAATAAAATTTTAATTTAATTTT
1 TTAAAAATAATAAAATTATAATTTAATTTT
66453895 TTAAAAAT
1 TTAAAAAT
66453903 TATATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.29
31 4 0.12
32 20 0.59
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (30 bp):
TTAAAAATAATAAAATTATAATTTAATTTT
Found at i:66454415 original size:19 final size:19
Alignment explanation
Indices: 66454391--66454429 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
66454381 CAAGATTAGC
66454391 TGCAACATGCTTTCCTTCG
1 TGCAACATGCTTTCCTTCG
66454410 TGCAACATGCTTTCCTTCG
1 TGCAACATGCTTTCCTTCG
66454429 T
1 T
66454430 ACGGGGGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.31, G:0.15, T:0.38
Consensus pattern (19 bp):
TGCAACATGCTTTCCTTCG
Found at i:66455329 original size:28 final size:28
Alignment explanation
Indices: 66455284--66455339 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
66455274 GGGCTTGAAT
* * *
66455284 AATATTATTTTATAAATTATAAATTATA
1 AATATTATTTTAAAAATTAAAAAATATA
66455312 AATA-TATTTTAAATAATTAAAAAATATA
1 AATATTATTTTAAA-AATTAAAAAATATA
66455340 TTAAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AATATTATTTTAAAAATTAAAAAATATA
Found at i:66455343 original size:20 final size:21
Alignment explanation
Indices: 66455305--66455345 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
66455295 ATAAATTATA
* *
66455305 AATTATAAATATATTTTAAAT
1 AATTATAAAAATATATTAAAT
66455326 AATTA-AAAAATATATTAAAT
1 AATTATAAAAATATATTAAAT
66455346 TAAAATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTATAAAAATATATTAAAT
Found at i:66460800 original size:4 final size:4
Alignment explanation
Indices: 66460791--66460821 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
66460781 TCTTTTTCTC
66460791 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TT
66460822 ATTATTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:66460808 original size:12 final size:13
Alignment explanation
Indices: 66460791--66460821 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
66460781 TCTTTTTCTC
66460791 TTTATTTA-TTTA
1 TTTATTTATTTTA
66460803 TTTATTTATTTTA
1 TTTATTTATTTTA
66460816 TTTATT
1 TTTATT
66460822 ATTATTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:66460856 original size:22 final size:23
Alignment explanation
Indices: 66460831--66460879 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
66460821 TATTATTAAC
66460831 TTTAAAA-ATTTTGA-AATATATA
1 TTTAAAATATTTT-ATAATATATA
66460853 TTTAAAATATTTTATTAATATATA
1 TTTAAAATATTTTA-TAATATATA
66460877 TTT
1 TTT
66460880 TGAAATTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.33
23 5 0.21
24 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTAAAATATTTTATAATATATA
Found at i:66460917 original size:21 final size:21
Alignment explanation
Indices: 66460892--66460980 Score: 78
Period size: 23 Copynumber: 4.1 Consensus size: 21
66460882 AAATTACTTT
66460892 TTTTTTAAT-TTTAAATATTA
1 TTTTTTAATATTTAAATATTA
66460912 TTTTTTAATATTTAAATATT-
1 TTTTTTAATATTTAAATATTA
* *
66460932 TTAAACTTTCAA-ATTT-ATTATTA
1 TT----TTTTAATATTTAAATATTA
66460955 TTTTTATAATAATTTAAATATTA
1 TTTTT-TAAT-ATTTAAATATTA
66460978 TTT
1 TTT
66460981 AATTTGTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
19 3 0.05
20 13 0.24
21 10 0.18
22 9 0.16
23 15 0.27
24 5 0.09
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTTAATATTTAAATATTA
Found at i:66461016 original size:20 final size:21
Alignment explanation
Indices: 66460967--66461017 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
66460957 TTTATAATAA
*
66460967 TTTAAATATTATTTAATTTGT
1 TTTAAATATTATTAAATTTGT
66460988 TTTATAATATT-TTAAATTAT-T
1 TTTA-AATATTATTAAATT-TGT
66461009 TTTAAATAT
1 TTTAAATAT
66461018 ATTCAAACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.19
21 15 0.56
22 7 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTAAATATTATTAAATTTGT
Found at i:66461226 original size:4 final size:4
Alignment explanation
Indices: 66461217--66461242 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
66461207 TTTTATTTTG
66461217 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
66461243 GTTATTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:66461319 original size:19 final size:22
Alignment explanation
Indices: 66461282--66461324 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 22
66461272 ATTTGAAATG
66461282 TTTTATAATATATATTTTTAAA
1 TTTTATAATATATATTTTTAAA
66461304 TTTTA-AATAT-TA-TTTTAAA
1 TTTTATAATATATATTTTTAAA
66461323 TT
1 TT
66461325 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 2 0.10
21 5 0.24
22 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTATAATATATATTTTTAAA
Found at i:66461329 original size:22 final size:22
Alignment explanation
Indices: 66461250--66461322 Score: 69
Period size: 23 Copynumber: 3.4 Consensus size: 22
66461240 ATTGTTATTA
* * *
66461250 ATTTTAAAAATTTAAAATGTAT
1 ATTTTAAAATTTTATAATATAT
* *
66461272 ATTTGAAATGTTTTATAATATAT
1 ATTTTAAA-ATTTTATAATATAT
*
66461295 ATTTTTAAATTTTA-AATAT-T
1 ATTTTAAAATTTTATAATATAT
66461315 ATTTTAAA
1 ATTTTAAA
66461323 TTATTTTTAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 8 0.20
21 5 0.12
22 12 0.29
23 16 0.39
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
ATTTTAAAATTTTATAATATAT
Found at i:66461375 original size:21 final size:22
Alignment explanation
Indices: 66461323--66461392 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 22
66461313 TTATTTTAAA
* *
66461323 TTATTTTTAAAATTTTGAATAT
1 TTATTTTTAAAATATTAAATAT
*
66461345 TATTTTTTTAAAA-ATTAAATAT
1 T-TATTTTTAAAATATTAAATAT
*
66461367 TTATTTTTAATAATATAAAATAT
1 TTATTTTTAA-AATATTAAATAT
66461390 TTA
1 TTA
66461393 AATATTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 8 0.20
22 11 0.28
23 21 0.52
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (22 bp):
TTATTTTTAAAATATTAAATAT
Found at i:66461759 original size:14 final size:15
Alignment explanation
Indices: 66461740--66461772 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
66461730 ATCTTTAAAA
66461740 ATAATTTAAAA-ATT
1 ATAATTTAAAATATT
66461754 ATAATTTAAAATATT
1 ATAATTTAAAATATT
66461769 ATAA
1 ATAA
66461773 AACAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATTTAAAATATT
Found at i:66461860 original size:31 final size:31
Alignment explanation
Indices: 66461747--66461863 Score: 96
Period size: 31 Copynumber: 3.6 Consensus size: 31
66461737 AAAATAATTT
* *
66461747 AAAAATTATAATTTAAAATATTATAAAA-CAA
1 AAAAATAAT-ATTTAAAATATTATAAAATTAA
* *
66461778 ATTAAATAATATTTAAATTATTATAAAATTAA
1 A-AAAATAATATTTAAAATATTATAAAATTAA
66461810 TAATAAATTTGAA-AGTTTAAAATATT-TAAATATTAA
1 -AA-AAA--T-AATA-TTTAAAATATTATAAA-ATTAA
66461846 AAAAATAATATTTAAAAT
1 AAAAATAATATTTAAAAT
66461864 TAAAAAAGTA
Statistics
Matches: 70, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
31 28 0.40
32 10 0.14
33 4 0.06
34 3 0.04
35 8 0.11
36 17 0.24
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (31 bp):
AAAAATAATATTTAAAATATTATAAAATTAA
Found at i:66461867 original size:21 final size:21
Alignment explanation
Indices: 66461830--66461883 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
66461820 GAAAGTTTAA
66461830 AATATTTAAATATTAAAAAAAT
1 AATATTTAAA-ATTAAAAAAAT
*
66461852 AATATTTAAAATTAAAAAAGT
1 AATATTTAAAATTAAAAAAAT
*
66461873 AAT-TTCAAAAT
1 AATATTTAAAAT
66461884 ATATATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 7 0.23
21 13 0.43
22 10 0.33
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AATATTTAAAATTAAAAAAAT
Found at i:66461947 original size:4 final size:4
Alignment explanation
Indices: 66461938--66461977 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
66461928 AGTTAATAAT
*
66461938 AATA AATA AATA AGTAA AATA AATA AATAA AATA AATA AA
1 AATA AATA AATA AAT-A AATA AATA AAT-A AATA AATA AA
66461978 AATACAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 25 0.78
5 7 0.22
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:66461959 original size:13 final size:13
Alignment explanation
Indices: 66461941--66461977 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
66461931 TAATAATAAT
*
66461941 AAATAAATAAGTA
1 AAATAAATAAATA
66461954 AAATAAATAAATA
1 AAATAAATAAATA
66461967 AAATAAATAAA
1 AAATAAATAAA
66461978 AATACAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (13 bp):
AAATAAATAAATA
Found at i:66461974 original size:17 final size:17
Alignment explanation
Indices: 66461932--66461977 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
66461922 TTTTAAAGTT
66461932 AATAATAATAAATAAATA
1 AATAA-AATAAATAAATA
*
66461950 AGTAAAATAAATAAATA
1 AATAAAATAAATAAATA
66461967 AA-ATAAATAAA
1 AATA-AAATAAA
66461978 AATACAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 20 0.80
18 4 0.16
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AATAAAATAAATAAATA
Found at i:66477991 original size:25 final size:25
Alignment explanation
Indices: 66477961--66478013 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
66477951 TTGAAGTCAA
66477961 AATTATGTACTCAACCTAAATAAAT
1 AATTATGTACTCAACCTAAATAAAT
66477986 AATTATGTACTCAACCTAAATAAAT
1 AATTATGTACTCAACCTAAATAAAT
66478011 AAT
1 AAT
66478014 AAGGTTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (25 bp):
AATTATGTACTCAACCTAAATAAAT
Found at i:66491615 original size:24 final size:24
Alignment explanation
Indices: 66491588--66491633 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
66491578 TACAATTTTA
66491588 AAAAT-CAAGTAATAGAAAGAATTC
1 AAAATGCAAGT-ATAGAAAGAATTC
* *
66491612 AAAATGTAAGTATAGAATGAAT
1 AAAATGCAAGTATAGAAAGAAT
66491634 CTGAACAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.57, C:0.04, G:0.15, T:0.24
Consensus pattern (24 bp):
AAAATGCAAGTATAGAAAGAATTC
Found at i:66491835 original size:53 final size:53
Alignment explanation
Indices: 66491773--66491879 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
66491763 GAGCAACTAC
66491773 GAATAATTACATTCAATTTAGAATTATTAAATATCCAAATATGAGTAATACAA
1 GAATAATTACATTCAATTTAGAATTATTAAATATCCAAATATGAGTAATACAA
66491826 GAATAATTACATTCAATTTAGAATTATTAAATATCCAAATATGAGTAATACAA
1 GAATAATTACATTCAATTTAGAATTATTAAATATCCAAATATGAGTAATACAA
66491879 G
1 G
66491880 CGTGTAATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34
Consensus pattern (53 bp):
GAATAATTACATTCAATTTAGAATTATTAAATATCCAAATATGAGTAATACAA
Found at i:66494217 original size:14 final size:15
Alignment explanation
Indices: 66494198--66494230 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
66494188 GTTAATTAGG
66494198 TTTAATTAT-AATAA
1 TTTAATTATGAATAA
66494212 TTTAATTATGAATAA
1 TTTAATTATGAATAA
66494227 TTTA
1 TTTA
66494231 TCATTGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
TTTAATTATGAATAA
Found at i:66494921 original size:24 final size:24
Alignment explanation
Indices: 66494894--66494945 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
66494884 GAGTAAAGAT
66494894 TATTAAAAATT-GTAAATATTAAAA
1 TATTAAAAATTAG-AAATATTAAAA
* *
66494918 TATTAATAATTAGAAATTTTAAAA
1 TATTAAAAATTAGAAATATTAAAA
66494942 -ATTA
1 TATTA
66494946 TAGTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.16
24 20 0.80
25 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
TATTAAAAATTAGAAATATTAAAA
Found at i:66497173 original size:27 final size:27
Alignment explanation
Indices: 66497101--66497171 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
66497091 AAATAAGTAA
66497101 AAATA-ATAAAATTTTAAAATTTAAATT
1 AAATATAT-AAATTTTAAAATTTAAATT
*
66497128 AAATATATATATTTT-AAATTTAAGATT
1 AAATATATAAATTTTAAAATTTAA-ATT
66497155 AAAT-T-TAAATTTTAAAA
1 AAATATATAAATTTTAAAA
66497172 ATATTAACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 7 0.18
26 12 0.31
27 18 0.46
28 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
AAATATATAAATTTTAAAATTTAAATT
Found at i:66497379 original size:13 final size:12
Alignment explanation
Indices: 66497356--66497390 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
66497346 CATGTATCTC
66497356 TATTTTTTTAAA
1 TATTTTTTTAAA
66497368 TATTTATTTTAAA
1 TATTT-TTTTAAA
*
66497381 TAGTTTTTTA
1 TATTTTTTTA
66497391 TACTCCTACG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (12 bp):
TATTTTTTTAAA
Found at i:66497573 original size:11 final size:10
Alignment explanation
Indices: 66497548--66497577 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
66497538 TTTGCACTTG
66497548 TATTTTTAAT
1 TATTTTTAAT
66497558 TATTTTTAAT
1 TATTTTTAAT
66497568 TAATTTTTAA
1 T-ATTTTTAA
66497578 GATTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TATTTTTAAT
Found at i:66497590 original size:22 final size:22
Alignment explanation
Indices: 66497565--66497616 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
66497555 AATTATTTTT
66497565 AATTAATTTT-TAAGATTTTAAA
1 AATTAATTTTATAA-ATTTTAAA
* *
66497587 AATTCAGTTTTATAATTTTTAAA
1 AATT-AATTTTATAAATTTTAAA
66497610 AACTTAA
1 AA-TTAA
66497617 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
22 4 0.17
23 15 0.62
24 5 0.21
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (22 bp):
AATTAATTTTATAAATTTTAAA
Found at i:66497772 original size:22 final size:22
Alignment explanation
Indices: 66497744--66497787 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
66497734 TCAATACTTT
66497744 GACACATGACATATTCTTATTG
1 GACACATGACATATTCTTATTG
66497766 GACACATGACATATTCTTATTG
1 GACACATGACATATTCTTATTG
66497788 ATTGAATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (22 bp):
GACACATGACATATTCTTATTG
Found at i:66503670 original size:15 final size:15
Alignment explanation
Indices: 66503646--66503684 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
66503636 CTCCGCTCAA
66503646 TTATTCTTCTCTCACT
1 TTATTCTTCTCT-ACT
66503662 TTATT-TTCTCTACT
1 TTATTCTTCTCTACT
66503676 TT-TTCTTCT
1 TTATTCTTCT
66503685 TTTCTCTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 9 0.41
15 6 0.27
16 5 0.23
ACGTcount: A:0.10, C:0.26, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTCTTCTCTACT
Found at i:66503700 original size:19 final size:19
Alignment explanation
Indices: 66503665--66503701 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
66503655 TCTCACTTTA
* *
66503665 TTTTCTCTACTTTTTCTTC
1 TTTTCTCTAATTCTTCTTC
66503684 TTTTCTCTAATTCTTCTT
1 TTTTCTCTAATTCTTCTT
66503702 TCTTGAATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTCTCTAATTCTTCTTC
Found at i:66509124 original size:14 final size:14
Alignment explanation
Indices: 66509084--66509113 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
66509074 CCGTTAGTGA
*
66509084 ATAAATACATAAAT
1 ATAAATAAATAAAT
66509098 ATAAATAAATAAAT
1 ATAAATAAATAAAT
66509112 AT
1 AT
66509114 TTATATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAATAAATAAAT
Found at i:66516990 original size:47 final size:47
Alignment explanation
Indices: 66516745--66517010 Score: 194
Period size: 46 Copynumber: 5.7 Consensus size: 47
66516735 TTTGTTTGTA
** *
66516745 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAAC-C-ATATTATGAG
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGA-TAT--G
* * *
66516791 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGA-G
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TCGAGA-TATG
** *
66516839 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGTA
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CTCGAGATATG
* **
66516885 AGCCAGTGTAAGA-CATGTCTGGGGTAT-GCATCGGCTACGAGATGAT-
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCT-CGAGAT-ATG
* * * * **
66516931 AG-TCAGTATAAGACCGTGTCTGGGATATGGCATCGACTTTAGATATG
1 AGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATATG
* *
66516978 AGCTAGTGTAAGACCATATTTGGGACATGGCAT
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCAT
66517011 GGGCACCTTA
Statistics
Matches: 177, Mismatches: 29, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
45 2 0.01
46 72 0.41
47 72 0.41
48 28 0.16
51 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (47 bp):
AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATATG
Found at i:66523240 original size:19 final size:19
Alignment explanation
Indices: 66523198--66523240 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
66523188 TGTAATTCCT
* *
66523198 AAAATACATACATCACATG
1 AAAATACATACAGCACAAG
*
66523217 AAAATACATCCAGCACAAG
1 AAAATACATACAGCACAAG
*
66523236 TAAAT
1 AAAAT
66523241 TATTATATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.21, G:0.07, T:0.19
Consensus pattern (19 bp):
AAAATACATACAGCACAAG
Found at i:66524872 original size:6 final size:6
Alignment explanation
Indices: 66524865--66524896 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
66524855 GTGGCCATGG
*
66524865 AAATGG AAATGC AAATGC AAATGC AAATGC AA
1 AAATGC AAATGC AAATGC AAATGC AAATGC AA
66524897 CATTAGACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.53, C:0.12, G:0.19, T:0.16
Consensus pattern (6 bp):
AAATGC
Found at i:66525117 original size:20 final size:20
Alignment explanation
Indices: 66525068--66525118 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
66525058 TTGGGTCAAA
66525068 TATATTTATATTTTTTATTAAT
1 TATA-TTATATTTTTTA-TAAT
*
66525090 TA-ATTATATTTTTTA-AGT
1 TATATTATATTTTTTATAAT
66525108 TATATATATAT
1 TATAT-TATAT
66525119 GTAATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.15
19 2 0.08
20 17 0.65
21 1 0.04
22 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TATATTATATTTTTTATAAT
Found at i:66525849 original size:12 final size:12
Alignment explanation
Indices: 66525807--66525856 Score: 68
Period size: 11 Copynumber: 4.2 Consensus size: 12
66525797 TCTAAAATTC
66525807 AAAATA-TTTAT
1 AAAATATTTTAT
*
66525818 AAAATATTTTTT
1 AAAATATTTTAT
66525830 AAAA-ATTTTAT
1 AAAATATTTTAT
66525841 AAAATATTTGTAT
1 AAAATATTT-TAT
66525854 AAA
1 AAA
66525857 TTCAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 16 0.47
12 12 0.35
13 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (12 bp):
AAAATATTTTAT
Found at i:66534014 original size:46 final size:46
Alignment explanation
Indices: 66533945--66534034 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
66533935 AGTCGTGAGA
* * *
66533945 TACTATATTATATGCATAGTATTTGTTTGTATAAAAGACAATGTCT
1 TACTATATTATACGCATAATATTTGTTTCTATAAAAGACAATGTCT
* *
66533991 TACTATATTGTACGCATAATATTTGTTTCTGTAAAAGACAATGT
1 TACTATATTATACGCATAATATTTGTTTCTATAAAAGACAATGT
66534035 ATTGATTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (46 bp):
TACTATATTATACGCATAATATTTGTTTCTATAAAAGACAATGTCT
Found at i:66534132 original size:18 final size:18
Alignment explanation
Indices: 66534100--66534146 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
66534090 TTTATACTGA
66534100 GTTAATTTTAATT-AATT
1 GTTAATTTTAATTAAATT
66534117 GTTAATTTTGAATTAAATT
1 GTTAATTTT-AATTAAATT
66534136 G-TAA-TTTAATT
1 GTTAATTTTAATT
66534147 TCAAATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.14
17 12 0.43
18 7 0.25
19 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (18 bp):
GTTAATTTTAATTAAATT
Found at i:66553831 original size:5 final size:5
Alignment explanation
Indices: 66553821--66553847 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
66553811 TATTGTTAAT
66553821 AACAC AACAC AACAC AACAC AACAC AA
1 AACAC AACAC AACAC AACAC AACAC AA
66553848 ACCATACCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.37, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAC
Found at i:66561465 original size:12 final size:12
Alignment explanation
Indices: 66561448--66561478 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
66561438 CGTGCCTAGT
66561448 AAAATAAAATTA
1 AAAATAAAATTA
66561460 AAAATAAAATTA
1 AAAATAAAATTA
*
66561472 ATAATAA
1 AAAATAA
66561479 TTAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAATAAAATTA
Found at i:66562222 original size:6 final size:6
Alignment explanation
Indices: 66562211--66562350 Score: 280
Period size: 6 Copynumber: 23.3 Consensus size: 6
66562201 TTACCCAAAC
66562211 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
66562259 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
66562307 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT AT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT AT
66562351 GGGAATTAAC
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 134 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATACAT
Found at i:66569956 original size:5 final size:6
Alignment explanation
Indices: 66569919--66569983 Score: 60
Period size: 6 Copynumber: 10.2 Consensus size: 6
66569909 CTTATACTTA
*
66569919 TATTTT TAATTTTT TATATAT T-TTTT TATTTT TATTTT GCTATTTT TATTTT
1 TATTTT T-A-TTTT TAT-TTT TATTTT TATTTT TATTTT --TATTTT TATTTT
*
66569971 TATTTC TATTTT T
1 TATTTT TATTTT T
66569984 TTCGTATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
5 3 0.06
6 30 0.61
7 5 0.10
8 11 0.22
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (6 bp):
TATTTT
Found at i:66569984 original size:20 final size:22
Alignment explanation
Indices: 66569937--66569985 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
66569927 ATTTTTTATA
66569937 TATTTTTTTATTTTTATTTTGC
1 TATTTTTTTATTTTTATTTTGC
66569959 TA--TTTTTATTTTTA-TTT-C
1 TATTTTTTTATTTTTATTTTGC
66569977 TATTTTTTT
1 TATTTTTTT
66569986 CGTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 3 0.12
20 17 0.68
22 2 0.08
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (22 bp):
TATTTTTTTATTTTTATTTTGC
Found at i:66569997 original size:40 final size:40
Alignment explanation
Indices: 66569919--66570001 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
66569909 CTTATACTTA
*
66569919 TATTTTTAATTTTTTATATATTTTTTTATTTTTATTTTGC
1 TATTTTTAATTTTTTATATATTTTTTTATATTTATTTTGC
* * *
66569959 TATTTTT-ATTTTTATTTCTATTTTTTTCGTATTT-TTTTGC
1 TATTTTTAATTTTT-TATATATTTTTTT-ATATTTATTTTGC
66569999 TAT
1 TAT
66570002 AATCATTACA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
39 6 0.16
40 27 0.73
41 4 0.11
ACGTcount: A:0.17, C:0.05, G:0.04, T:0.75
Consensus pattern (40 bp):
TATTTTTAATTTTTTATATATTTTTTTATATTTATTTTGC
Found at i:66571091 original size:11 final size:10
Alignment explanation
Indices: 66571075--66571104 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
66571065 CCATTGTTCT
66571075 AAAAAAAATG
1 AAAAAAAATG
*
66571085 AAAAAAAGTG
1 AAAAAAAATG
66571095 AAAAAAAATG
1 AAAAAAAATG
66571105 CATTTATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:66581791 original size:5 final size:6
Alignment explanation
Indices: 66581764--66581790 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
66581754 GCTAACCCAA
66581764 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
66581791 ACATTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:66582907 original size:34 final size:34
Alignment explanation
Indices: 66582864--66582930 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
66582854 TGAGAAGTCA
66582864 TTACTCCCTCACTCATTTGTTTTCATAATTGTCG
1 TTACTCCCTCACTCATTTGTTTTCATAATTGTCG
66582898 TTACTCCCTCACTCATTTGTTTTCATAATTGTC
1 TTACTCCCTCACTCATTTGTTTTCATAATTGTC
66582931 TTTATATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.18, C:0.27, G:0.07, T:0.48
Consensus pattern (34 bp):
TTACTCCCTCACTCATTTGTTTTCATAATTGTCG
Found at i:66585181 original size:23 final size:25
Alignment explanation
Indices: 66585155--66585201 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
66585145 TATCATTCAT
*
66585155 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
66585178 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
66585202 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:66585362 original size:13 final size:13
Alignment explanation
Indices: 66585344--66585373 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
66585334 TTCTTGTAAA
66585344 CATTTCACATAAC
1 CATTTCACATAAC
*
66585357 CATTTCATATAAC
1 CATTTCACATAAC
66585370 CATT
1 CATT
66585374 CGTCATCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (13 bp):
CATTTCACATAAC
Found at i:66585522 original size:46 final size:46
Alignment explanation
Indices: 66585462--66585583 Score: 183
Period size: 46 Copynumber: 2.7 Consensus size: 46
66585452 TTTGACGTGA
* * * *
66585462 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTC-TTTTCATGTCACGT
*
66585508 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCTTTTCATGTCACGT
66585554 TGCCATGGTATCTTTCAACCATGGTCTTAC
1 TGCCATGGTATCTTTCAACCATGGTCTTAC
66585584 AACCATGGTC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
45 5 0.07
46 64 0.93
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.43
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCTTTTCATGTCACGT
Found at i:66585577 original size:16 final size:15
Alignment explanation
Indices: 66585556--66585598 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
66585546 TGTCACGTTG
*
66585556 CCATGGTATCTTTCAA
1 CCATGGT-TCTTACAA
66585572 CCATGG-TCTTACAA
1 CCATGGTTCTTACAA
66585586 CCATGG-TCTTACA
1 CCATGGTTCTTACA
66585599 CATTTCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 20 0.77
16 6 0.23
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.33
Consensus pattern (15 bp):
CCATGGTTCTTACAA
Found at i:66585586 original size:14 final size:14
Alignment explanation
Indices: 66585564--66585598 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
66585554 TGCCATGGTA
*
66585564 TCTTTCAACCATGG
1 TCTTACAACCATGG
66585578 TCTTACAACCATGG
1 TCTTACAACCATGG
66585592 TCTTACA
1 TCTTACA
66585599 CATTTCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (14 bp):
TCTTACAACCATGG
Found at i:66585589 original size:60 final size:60
Alignment explanation
Indices: 66585518--66585644 Score: 191
Period size: 60 Copynumber: 2.1 Consensus size: 60
66585508 TGCCATGGTA
* ** * *
66585518 TCTTTCAACCATGGTCTTATTCTTTTCATGTCACGTTGCCATGGTATCTTTCAACCATGG
1 TCTTACAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGG
* *
66585578 TCTTACAACCATGGTCTTACACATTTCATATTAGGTTGCCATGGTATCTTTCAACCATGG
1 TCTTACAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGG
66585638 TCTTACA
1 TCTTACA
66585645 CACATGTTGC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.39
Consensus pattern (60 bp):
TCTTACAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGG
Found at i:66585637 original size:46 final size:46
Alignment explanation
Indices: 66585578--66585776 Score: 250
Period size: 38 Copynumber: 4.7 Consensus size: 46
66585568 TCAACCATGG
*
66585578 TCTTACAACCATGGTCTTACACATTTCATATTAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATTAGGTTGCCATGGTA
66585624 TCTTTCAACCATGGTCTTACACA---C--A-T--GTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATTAGGTTGCCATGGTA
* *
66585662 TCTTTCAACCATGGTCTTACACATTTCATATCAAGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATTAGGTTGCCATGGTA
66585708 TCTTTCAACCATGGTCTTACACA---C-----AGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATTAGGTTGCCATGGTA
*
66585746 TCTTTCAACCATGGTCTTACACATTTTATAT
1 TCTTTCAACCATGGTCTTACACATTTCATAT
66585777 CAGAGAGCAC
Statistics
Matches: 134, Mismatches: 4, Indels: 31
0.79 0.02 0.18
Matches are distributed among these distances:
38 71 0.53
40 1 0.01
41 2 0.01
43 3 0.02
46 57 0.43
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTCATATTAGGTTGCCATGGTA
Done.