Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 12 of 320
Found at i:3382614 original size:17 final size:16
Alignment explanation
Indices: 3382594--3382626 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3382584 TTCATAAGCA
3382594 TATATCATTCATTTCAT
1 TATATCATT-ATTTCAT
3382611 TATATCATTATTTCAT
1 TATATCATTATTTCAT
3382627 GCACCATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATCATTATTTCAT
Found at i:3383715 original size:31 final size:31
Alignment explanation
Indices: 3383677--3383745 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
3383667 AGTGTTTGAA
3383677 GTATATGTCTAAGATAATAAAAATATAACTT
1 GTATATGTCTAAGATAATAAAAATATAACTT
3383708 GTATATGTCTAAGATAATAAAAATATAACTT
1 GTATATGTCTAAGATAATAAAAATATAACTT
3383739 GTA-ATGT
1 GTATATGT
3383746 GAAAATATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (31 bp):
GTATATGTCTAAGATAATAAAAATATAACTT
Found at i:3384771 original size:14 final size:15
Alignment explanation
Indices: 3384752--3384784 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3384742 AATGATGAGA
*
3384752 ATAATAGTAAT-AAT
1 ATAATAATAATAAAT
3384766 ATAATAATAATAAAT
1 ATAATAATAATAAAT
3384781 ATAA
1 ATAA
3384785 AAAAACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
ATAATAATAATAAAT
Found at i:3385319 original size:11 final size:11
Alignment explanation
Indices: 3385303--3385331 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3385293 AGAGGACCGA
3385303 TCACCGGTCCG
1 TCACCGGTCCG
3385314 TCACCGGTCCG
1 TCACCGGTCCG
3385325 TCACCGG
1 TCACCGG
3385332 ACCACCGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.45, G:0.28, T:0.17
Consensus pattern (11 bp):
TCACCGGTCCG
Found at i:3386012 original size:24 final size:25
Alignment explanation
Indices: 3385981--3386028 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
3385971 TATTTGGTTC
3385981 TTGGGTTAGTGGT-TA-TTGGGTTTT
1 TTGGGTTAG-GGTATATTTGGGTTTT
3386005 TTGGGTTAGGGTATATTTGGGTTT
1 TTGGGTTAGGGTATATTTGGGTTT
3386029 GATTGTTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
24 11 0.50
25 8 0.36
ACGTcount: A:0.10, C:0.00, G:0.38, T:0.52
Consensus pattern (25 bp):
TTGGGTTAGGGTATATTTGGGTTTT
Found at i:3386194 original size:46 final size:47
Alignment explanation
Indices: 3386144--3386490 Score: 347
Period size: 46 Copynumber: 7.6 Consensus size: 47
3386134 CCATAGTGTT
* * *
3386144 TTTCAACTATGGTCTTACTCATTTTC-TGTCAGGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTATC
** * * ** * *
3386190 TTTCAACCATGGTCTTGTTCA-TTTCATGTTACATTACTATGGTATC
1 TTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTATC
* * *
3386236 TTTCAACCTTGGTCTTATTCATTCTC--ATCATGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTATC
* ** * * * * *
3386281 TTTTAATTATGGTCTTATTC-TTTTCATGTCACGTTGTCATGCTATC
1 TTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTATC
**
3386327 TTTCAA-CATGGTCTTAGACATTTT-ATATCCA-GTTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTTCATAT-CATGTTGCCATGGTATC
* *
3386372 TTTCAACCATGGTCTTACACA-TTTCATATCATGTTGCCATGGTGTC
1 TTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTATC
* *
3386418 TTTCAACCATGGTCTTACACA-TTTCATATCATGTTGTCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTATC
*
3386464 TTTCAACCATGGTCTTACAC-TTTTCAT
1 TTTCAACCATGGTCTTACTCATTTTCAT
3386491 TTCAGAAAGA
Statistics
Matches: 254, Mismatches: 37, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
44 4 0.02
45 69 0.27
46 178 0.70
47 3 0.01
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.44
Consensus pattern (47 bp):
TTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTATC
Found at i:3386280 original size:91 final size:90
Alignment explanation
Indices: 3386144--3386480 Score: 356
Period size: 91 Copynumber: 3.7 Consensus size: 90
3386134 CCATAGTGTT
* * * *
3386144 TTTCAACTATGGTCTTACTCATTTTCTGTCAGGTTGCCATGGTATCTTTCAACCATGGTCTTGTT
1 TTTCAAC-ATGGTCTTACACATTTTCTATCATGTTGCCATGGTATCTTTCAACCATGGTCTTATT
* *
3386209 CATTTCATGTTACATTACTATGGTATC
65 CATTTCATGTCACGTT-CTATGGTATC
* ** * * **
3386236 TTTCAACCTTGGTCTTATTCATTCTC-ATCATGTTGCCATGGTATCTTTTAATTATGGTCTTATT
1 TTTCAA-CATGGTCTTACACATTTTCTATCATGTTGCCATGGTATCTTTCAACCATGGTCTTATT
* * *
3386300 CTTTTCATGTCACGTTGTCATGCTATC
65 CATTTCATGTCACGTTCT-ATGGTATC
* * **
3386327 TTTCAACATGGTCTTAGACATTTTATATCCA-GTTGCCATGGTATCTTTCAACCATGGTCTTACA
1 TTTCAACATGGTCTTACACATTTTCTAT-CATGTTGCCATGGTATCTTTCAACCATGGTCTTATT
* * * *
3386391 CATTTCATATCATGTTGCCATGGTGTC
65 CATTTCATGTCACGTT-CTATGGTATC
*
3386418 TTTCAACCATGGTCTTACACA-TTTCATATCATGTTGTCATGGTATCTTTCAACCATGGTCTTA
1 TTTCAA-CATGGTCTTACACATTTTC-TATCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
3386481 CACTTTTCAT
Statistics
Matches: 203, Mismatches: 34, Indels: 16
0.80 0.13 0.06
Matches are distributed among these distances:
90 15 0.07
91 118 0.58
92 69 0.34
93 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.44
Consensus pattern (90 bp):
TTTCAACATGGTCTTACACATTTTCTATCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTC
ATTTCATGTCACGTTCTATGGTATC
Found at i:3386409 original size:137 final size:138
Alignment explanation
Indices: 3386144--3386480 Score: 407
Period size: 137 Copynumber: 2.5 Consensus size: 138
3386134 CCATAGTGTT
* *
3386144 TTTCAACTATGGTCTTACTCATTTTC-TGTCAGGTTGCCATGGTATCTTTCAACCATGGTCTT-G
1 TTTCAACTATGGTCTTACTC-TTTTCATGTCACGTTGTCATGGTATCTTTCAACCATGGTCTTAG
* * * * **
3386207 TTCATTTCATGTTACATTACTATGGTATCTTTCAACCTTGGTCTTATTCATTCTCATCATGTTGC
65 TACATTTCATGATACATTACCATGGTATCTTTCAACCATGGTCTTACACATTCTCATCATGTTGC
3386272 CATGGTATC
130 CATGGTATC
* * * *
3386281 TTTTAATTATGGTCTTATTCTTTTCATGTCACGTTGTCATGCTATCTTTCAA-CATGGTCTTAG-
1 TTTCAACTATGGTCTTACTCTTTTCATGTCACGTTGTCATGGTATCTTTCAACCATGGTCTTAGT
* * *
3386344 ACATTTTAT-ATCCAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT-TCATATCATGTT
66 ACATTTCATGATACA-TTACCATGGTATCTTTCAACCATGGTCTTACACATTCTC--ATCATGTT
*
3386407 GCCATGGTGTC
128 GCCATGGTATC
* * * * *
3386418 TTTCAACCATGGTCTTACACATTTCATATCATGTTGTCATGGTATCTTTCAACCATGGTCTTA
1 TTTCAACTATGGTCTTACTCTTTTCATGTCACGTTGTCATGGTATCTTTCAACCATGGTCTTA
3386481 CACTTTTCAT
Statistics
Matches: 169, Mismatches: 25, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
135 5 0.03
136 52 0.31
137 102 0.60
138 10 0.06
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.44
Consensus pattern (138 bp):
TTTCAACTATGGTCTTACTCTTTTCATGTCACGTTGTCATGGTATCTTTCAACCATGGTCTTAGT
ACATTTCATGATACATTACCATGGTATCTTTCAACCATGGTCTTACACATTCTCATCATGTTGCC
ATGGTATC
Found at i:3399043 original size:29 final size:27
Alignment explanation
Indices: 3398980--3399043 Score: 65
Period size: 31 Copynumber: 2.2 Consensus size: 27
3398970 TTTCATGTGT
* * *
3398980 ATAATTGCATTAAATTAAAATTTATGT
1 ATAATTGCATTAAATCAAAATTAATGA
3399007 ATCAAATTGCACATTAAATCAAAATTAATGA
1 AT--AATTG--CATTAAATCAAAATTAATGA
3399038 ATAATT
1 ATAATT
3399044 TTGGGATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 2 0.07
29 9 0.30
31 19 0.63
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (27 bp):
ATAATTGCATTAAATCAAAATTAATGA
Found at i:3400616 original size:68 final size:68
Alignment explanation
Indices: 3400544--3400719 Score: 175
Period size: 68 Copynumber: 2.6 Consensus size: 68
3400534 CATCATGTGT
** * * *
3400544 ACAAGAGAGCTACGAGATACTATGTAGTAGCTAGGTCACATGTGTGA-T-ACGGGATGTATC-CC
1 ACAAGAGAGCTACGAGATA-TAAAT-GTAGCTAGGTCACATGTGTGATTCAAGGGAAGGA-CACC
3400606 ATGTAG
63 ATGTAG
* * *
3400612 ACAAGAGAGCTACGGGAGAGATAAATGTAGCTAGGTCGCATGTGTGATTCCAAGTGAAGGACACC
1 ACAAGAGAGCTAC--GAGATATAAATGTAGCTAGGTCACATGTGTGATT-CAAGGGAAGGACACC
3400677 ATGTAG
63 ATGTAG
*
3400683 ACAAGAGAGCTACGAG--ATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGAGATATAAATGTAGCTAGGTCACATG
3400720 GGTCGTACTA
Statistics
Matches: 92, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
66 13 0.14
67 6 0.07
68 33 0.36
69 7 0.08
70 6 0.07
71 27 0.29
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.22
Consensus pattern (68 bp):
ACAAGAGAGCTACGAGATATAAATGTAGCTAGGTCACATGTGTGATTCAAGGGAAGGACACCATG
TAG
Found at i:3409937 original size:20 final size:22
Alignment explanation
Indices: 3409892--3409942 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
3409882 ACATTAATAA
*
3409892 TTTATCTAACCTAATATTTATTT
1 TTTAT-TAACCTAATATATATTT
3409915 TTTATTAACC-AATATAT-TTT
1 TTTATTAACCTAATATATATTT
3409935 TTTATTAA
1 TTTATTAA
3409943 ATTAATTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 11 0.41
21 6 0.22
22 5 0.19
23 5 0.19
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTATTAACCTAATATATATTT
Found at i:3410352 original size:15 final size:15
Alignment explanation
Indices: 3410332--3410362 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3410322 TAGGCTTAAA
3410332 TAATTATAACATTAT
1 TAATTATAACATTAT
*
3410347 TAATTATAATATTAT
1 TAATTATAACATTAT
3410362 T
1 T
3410363 CAGCCATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTATAACATTAT
Found at i:3410635 original size:6 final size:6
Alignment explanation
Indices: 3410619--3410676 Score: 89
Period size: 6 Copynumber: 9.5 Consensus size: 6
3410609 ACAAAGACAT
* *
3410619 ATGATCC ATGACC ATGACC ATAACC ATGACC ATGACC ATTACC ATGACC
1 ATGA-CC ATGACC ATGACC ATGACC ATGACC ATGACC ATGACC ATGACC
3410668 ATGACC ATG
1 ATGACC ATG
3410677 TTTACTTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
6 43 0.91
7 4 0.09
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.21
Consensus pattern (6 bp):
ATGACC
Found at i:3413676 original size:87 final size:87
Alignment explanation
Indices: 3413491--3413717 Score: 312
Period size: 87 Copynumber: 2.6 Consensus size: 87
3413481 TATGTAGCAT
* * *
3413491 CACCAAGGTGGTCATGCCAAAGAGAATGGCTCTACCAAAATAAAAAATAAAAACTTTATTTTTAT
1 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAAT---AAA-AAAAACTTTATTTTTAT
** *
3413556 GGTGGTCACATTATTTTCAATGGCAC
62 GGTGGTCACACCATTCTCAATGGCAC
* *
3413582 CATCAAAGTGGTCACGCCAAAGAGAATGGCTCCATCAAAATAAAAAAAA-TTTAATTTTTATGGT
1 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAAAAACTTT-ATTTTTATGGT
3413646 GGTCACACCATTCTCAATGGCAC
65 GGTCACACCATTCTCAATGGCAC
* *
3413669 CACCAAAGTGGCCACGCCAAAGAGAATGACTCCACCAAAATAAAAAAAA
1 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAAAAA
3413718 ATTATTAAAA
Statistics
Matches: 123, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
86 3 0.02
87 81 0.66
88 3 0.02
91 36 0.29
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.23
Consensus pattern (87 bp):
CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAAAAACTTTATTTTTATGGTG
GTCACACCATTCTCAATGGCAC
Found at i:3416088 original size:13 final size:14
Alignment explanation
Indices: 3416067--3416100 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3416057 AAAATACAAA
3416067 AATAATT-AAAAAT
1 AATAATTAAAAAAT
*
3416080 AATATTTAAAAAAT
1 AATAATTAAAAAAT
3416094 AATAATT
1 AATAATT
3416101 TTTATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATAATTAAAAAAT
Found at i:3416099 original size:17 final size:17
Alignment explanation
Indices: 3416077--3416111 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3416067 AATAATTAAA
3416077 AATAATATTTAAAAAAT
1 AATAATATTTAAAAAAT
* *
3416094 AATAATTTTTATAAAAT
1 AATAATATTTAAAAAAT
3416111 A
1 A
3416112 TTTTTTCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAATATTTAAAAAAT
Found at i:3417133 original size:23 final size:25
Alignment explanation
Indices: 3417102--3417148 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
3417092 ACTTATAGAA
*
3417102 TTAGATTATATTTT-GTGTTGCATT
1 TTAGATTATATTTTAGTGCTGCATT
*
3417126 TTAG-TTATTTTTTAGTGCTGCAT
1 TTAGATTATATTTTAGTGCTGCAT
3417149 AATTTTAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.57
Consensus pattern (25 bp):
TTAGATTATATTTTAGTGCTGCATT
Found at i:3417313 original size:29 final size:31
Alignment explanation
Indices: 3417280--3417348 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
3417270 CACTTTAACC
*
3417280 TAAAAATATAAAAATT-TAATTTAATT-TTT
1 TAAAAATATAAAAATTATAATTTAATTATTA
* * *
3417309 TAAAAA-ATTAAAATTATATTTTTATTATTA
1 TAAAAATATAAAAATTATAATTTAATTATTA
3417339 TAAAAATATA
1 TAAAAATATA
3417349 TAATTCAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 8 0.25
29 14 0.44
30 8 0.25
31 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TAAAAATATAAAAATTATAATTTAATTATTA
Found at i:3417317 original size:22 final size:23
Alignment explanation
Indices: 3417289--3417331 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3417279 CTAAAAATAT
* *
3417289 AAAAATTTAATTTA-ATTTTTTA
1 AAAAATTAAAATTATATTTTTTA
3417311 AAAAATTAAAATTATATTTTT
1 AAAAATTAAAATTATATTTTT
3417332 ATTATTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAAAATTAAAATTATATTTTTTA
Found at i:3417323 original size:23 final size:22
Alignment explanation
Indices: 3417288--3417331 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
3417278 CCTAAAAATA
* *
3417288 TAAAAATTTAATTTA-ATTTTT
1 TAAAAAATTAAATTATATTTTT
3417309 TAAAAAATTAAAATTATATTTTT
1 TAAAAAATT-AAATTATATTTTT
3417332 ATTATTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 5 0.26
23 6 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAAAAATTAAATTATATTTTT
Found at i:3418206 original size:39 final size:39
Alignment explanation
Indices: 3418132--3418207 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
3418122 CCTCTATATA
* *
3418132 TTTTACCCATTTTCTTATATTTTCTTCTCATCAAACAAT
1 TTTTACCCATTTTCTTATATTTTCATCTCACCAAACAAT
*
3418171 TTTTACCAGATTTTCTTAT-TTTCTCATC-CACCAAACA
1 TTTTACC-CATTTTCTTATATTT-TCATCTCACCAAACA
3418208 CCCCAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 18 0.56
40 14 0.44
ACGTcount: A:0.26, C:0.25, G:0.01, T:0.47
Consensus pattern (39 bp):
TTTTACCCATTTTCTTATATTTTCATCTCACCAAACAAT
Found at i:3422802 original size:5 final size:5
Alignment explanation
Indices: 3422794--3422819 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3422784 TTATCTTATA
3422794 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
3422820 AGAGATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:3427222 original size:19 final size:20
Alignment explanation
Indices: 3427188--3427231 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
3427178 AAATTTAAGT
3427188 TTTTAATTAAATAAATATAA
1 TTTTAATTAAATAAATATAA
*
3427208 TTTTAA-TATATAAATATAA
1 TTTTAATTAAATAAATATAA
3427227 TTTTA
1 TTTTA
3427232 TTTTAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTAATTAAATAAATATAA
Found at i:3430679 original size:23 final size:25
Alignment explanation
Indices: 3430653--3430719 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
3430643 AAAACAAATT
*
3430653 AAAATTAATTT-ATTTT-AATGATC
1 AAAATAAATTTAATTTTAAATGATC
3430676 AAAATAAATTTAAATTTTAAATGATC
1 AAAATAAATTT-AATTTTAAATGATC
*
3430702 AAAA-ATATTTAATATTTA
1 AAAATAAATTTAAT-TTTA
3430720 TTTATTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.26
24 3 0.08
25 14 0.37
26 11 0.29
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (25 bp):
AAAATAAATTTAATTTTAAATGATC
Found at i:3430711 original size:25 final size:26
Alignment explanation
Indices: 3430663--3430718 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
3430653 AAAATTAATT
3430663 TATTTTAATGATCAAAATAAATTTAA
1 TATTTTAATGATCAAAATAAATTTAA
*
3430689 -ATTTTAAATGATCAAAA-ATATTTAA
1 TATTTT-AATGATCAAAATAAATTTAA
3430714 TATTT
1 TATTT
3430719 ATTTATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 12 0.44
26 15 0.56
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (26 bp):
TATTTTAATGATCAAAATAAATTTAA
Found at i:3437531 original size:38 final size:38
Alignment explanation
Indices: 3437480--3437555 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
3437470 CAAGAGATCT
3437480 GATGGCCAAAATGATGGAGATGATGACAGCTTTGGTCA
1 GATGGCCAAAATGATGGAGATGATGACAGCTTTGGTCA
3437518 GATGGCCAAAATGATGGAGATGATGACAGCTTTGGTCA
1 GATGGCCAAAATGATGGAGATGATGACAGCTTTGGTCA
3437556 AAGAAAAGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.24
Consensus pattern (38 bp):
GATGGCCAAAATGATGGAGATGATGACAGCTTTGGTCA
Found at i:3443433 original size:39 final size:39
Alignment explanation
Indices: 3443387--3443463 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
3443377 TGCCTCTTCA
3443387 AATGAGCATATATGAAGTCCCTACACATTGTTTCAATAC
1 AATGAGCATATATGAAGTCCCTACACATTGTTTCAATAC
3443426 AATGAGCATATATGAAGTCCCTACACATTGTTTCAATA
1 AATGAGCATATATGAAGTCCCTACACATTGTTTCAATA
3443464 TTGAAAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.31
Consensus pattern (39 bp):
AATGAGCATATATGAAGTCCCTACACATTGTTTCAATAC
Found at i:3445853 original size:77 final size:77
Alignment explanation
Indices: 3445609--3445905 Score: 386
Period size: 77 Copynumber: 3.9 Consensus size: 77
3445599 GTTTTTTTTT
* *
3445609 AAAATGAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATCTTTAGTTC
1 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTAAGGTATCTTTAGTTC
3445674 CTA-TTTTCAAA
66 CTATTTTTCAAA
** *** * * *
3445685 AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAAATCACGCACTAAGGTAT-TTTCAATT
1 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTAAGGTATCTTT-AGTT
**
3445749 --TATGATTCAAA
65 CCTATTTTTCAAA
* *
3445760 AAAATCAACTCATATTGTAAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATCTTTAGTTC
1 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTAAGGTATCTTTAGTTC
3445825 CTATTTTTCAAA
66 CTATTTTTCAAA
* * * * *
3445837 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTTAAGGTATTTTTAGTTT
1 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTAAGGTATCTTTAGTTC
3445902 CTAT
66 CTAT
3445906 CAACTTATAT
Statistics
Matches: 187, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
74 2 0.01
75 61 0.33
76 53 0.28
77 71 0.38
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (77 bp):
AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTAAGGTATCTTTAGTTC
CTATTTTTCAAA
Found at i:3445958 original size:64 final size:64
Alignment explanation
Indices: 3445840--3445959 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 64
3445830 TTTCAAAAAA
* *** *
3445840 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTTAAGGTATTTTTAGTTTCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTAAGATATTTTTAGTTTCT
* * * *
3445904 ATCAACTTATATTGTGAGATGTGAGTTGAGCCTCAGGTCACACACTGAGATATTTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTAAGATATTTT
3445960 CAATTTTTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 47 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (64 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTAAGATATTTTTAGTTTCT
Found at i:3446308 original size:26 final size:26
Alignment explanation
Indices: 3446272--3446333 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
3446262 CTACAAAAGA
*
3446272 TCTCCTTGAAGTTTCAATGGATCTCT
1 TCTCCTTGAAGTTTCAATAGATCTCT
*
3446298 TCTCCTTGAAGTTTCAGTAGATCTCT
1 TCTCCTTGAAGTTTCAATAGATCTCT
*
3446324 TCTCCCTGAA
1 TCTCCTTGAA
3446334 ATGGCATTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (26 bp):
TCTCCTTGAAGTTTCAATAGATCTCT
Found at i:3446421 original size:44 final size:45
Alignment explanation
Indices: 3446366--3446476 Score: 111
Period size: 45 Copynumber: 2.5 Consensus size: 45
3446356 CCACAACAAG
* * * *
3446366 ATCTCCTTGAAGTTTCAGCGGAG-AACATTGAAG-TCA-CAAGTCTT
1 ATCTCCCTGAAGTTCCAGCGGAGCAAC-CTGAAGAT-AGCAAATCTT
* * *
3446410 ATCTCCCTGAAGTTGCAGTGGAGCAGCCTGAAGATAGCAAATCTT
1 ATCTCCCTGAAGTTCCAGCGGAGCAACCTGAAGATAGCAAATCTT
*
3446455 ATTTCCCTGAAGTTCCAGCGGA
1 ATCTCCCTGAAGTTCCAGCGGA
3446477 TTAGATCGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
44 26 0.47
45 29 0.53
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (45 bp):
ATCTCCCTGAAGTTCCAGCGGAGCAACCTGAAGATAGCAAATCTT
Found at i:3448061 original size:9 final size:10
Alignment explanation
Indices: 3448046--3448155 Score: 52
Period size: 10 Copynumber: 10.7 Consensus size: 10
3448036 TTGTATTTCA
3448046 ATATTATTAT
1 ATATTATTAT
3448056 -TATTATTAT
1 ATATTATTAT
3448065 ATATTAGTGTATGT
1 ATATTA-T-TA--T
* *
3448079 TTTTTATTAT
1 ATATTATTAT
3448089 ATATGTA-TAT
1 ATAT-TATTAT
3448099 ATATT-TATAT
1 ATATTAT-TAT
*
3448109 ATAGTATTAT
1 ATATTATTAT
3448119 AT-TTAATTACT
1 ATATT-ATTA-T
*
3448130 TTATT-TTA-
1 ATATTATTAT
*
3448138 ATATTTTTATT
1 ATATTATTA-T
3448149 ATATTAT
1 ATATTAT
3448156 ATTTGCTTGT
Statistics
Matches: 76, Mismatches: 9, Indels: 29
0.67 0.08 0.25
Matches are distributed among these distances:
8 4 0.05
9 14 0.18
10 34 0.45
11 12 0.16
12 6 0.08
13 1 0.01
14 5 0.07
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.61
Consensus pattern (10 bp):
ATATTATTAT
Found at i:3448108 original size:18 final size:18
Alignment explanation
Indices: 3448085--3448123 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3448075 ATGTTTTTTA
3448085 TTATATAT-GTATATATAT
1 TTATATATAGTAT-TATAT
3448103 TTATATATAGTATTATAT
1 TTATATATAGTATTATAT
3448121 TTA
1 TTA
3448124 ATTACTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TTATATATAGTATTATAT
Found at i:3448122 original size:131 final size:132
Alignment explanation
Indices: 3447913--3448311 Score: 643
Period size: 129 Copynumber: 3.1 Consensus size: 132
3447903 ATATTAACAC
3447913 TATTATTATTATTATTATATATTAGTGTATATTTTTATTATCTATGTATATGTATATATATTTAT
1 TATTATTATTATTATTATATATTAGTGTAT-TTTTTATTATCTA-GTATATGTATATATATTTAT
3447978 ATATAGTATTATTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTTTTGTATT
64 ATATAGTATTATTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTTTTGTATT
3448043 TCAA
129 TCAA
*
3448047 TATTATTATTATTATTATATATTAGTGTATGTTTT-TTAT-TA-TATATGTATATATATTTATAT
1 TATTATTATTATTATTATATATTAGTGTATTTTTTATTATCTAGTATATGTATATATATTTATAT
* *
3448109 ATAGTATTATATTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTGTTGTATTTC
66 ATAGTATTATTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTTTTGTATTTC
3448174 AA
131 AA
* * *
3448176 TATTATTATTATTATTAT-TAGT-GTATATTTTTTATTATCTATGTATATGTATATATATTTAAA
1 TATTATTATTATTATTATATATTAGTGTATTTTTTATTATCTA-GTATATGTATATATATTTATA
3448239 TATAGTATTATTTTTAATTACTTTATTTTAATA---TTATTATATTATATTTGCTTTTTTGTATT
65 TATAGTATTATTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGC-TTTTTGTATT
*
3448301 TCAT
129 TCAA
3448305 TATTATT
1 TATTATT
3448312 GCTAATATTA
Statistics
Matches: 250, Mismatches: 10, Indels: 15
0.91 0.04 0.05
Matches are distributed among these distances:
127 9 0.04
128 25 0.10
129 125 0.50
131 53 0.21
132 4 0.02
133 4 0.02
134 30 0.12
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (132 bp):
TATTATTATTATTATTATATATTAGTGTATTTTTTATTATCTAGTATATGTATATATATTTATAT
ATAGTATTATTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTTTTGTATTTC
AA
Found at i:3448254 original size:18 final size:20
Alignment explanation
Indices: 3448219--3448255 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
3448209 ATTATCTATG
3448219 TATATGTATATATATTTAAA
1 TATATGTATATATATTTAAA
*
3448239 TATA-GTAT-TATTTTTAA
1 TATATGTATATATATTTAA
3448256 TTACTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 4 0.25
20 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TATATGTATATATATTTAAA
Found at i:3448328 original size:24 final size:25
Alignment explanation
Indices: 3448267--3448331 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
3448257 TACTTTATTT
3448267 TAATATTATTAT-ATTA-TATTTGC
1 TAATATTATTATCATTATTATTTGC
** *
3448290 TTTTTTGTATT-TCATTATTA-TTGC
1 TAATAT-TATTATCATTATTATTTGC
3448314 TAATATTATTATCATTAT
1 TAATATTATTATCATTAT
3448332 CATCATTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
23 8 0.25
24 22 0.69
25 2 0.06
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.60
Consensus pattern (25 bp):
TAATATTATTATCATTATTATTTGC
Found at i:3449434 original size:16 final size:16
Alignment explanation
Indices: 3449400--3449444 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3449390 AGAGAGCAGG
* * *
3449400 GGAAAGAAAGAAGGCA
1 GGAAAAAAAGAAAGAA
3449416 GGAAAAAAAGAAAGAA
1 GGAAAAAAAGAAAGAA
*
3449432 GGAAAAAGAGAAA
1 GGAAAAAAAGAAA
3449445 AATTGGGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (16 bp):
GGAAAAAAAGAAAGAA
Found at i:3451393 original size:46 final size:46
Alignment explanation
Indices: 3451341--3451569 Score: 352
Period size: 46 Copynumber: 5.0 Consensus size: 46
3451331 AGTGTGCTCT
*
3451341 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAAC
* *
3451387 CTGATATGAAATGTTTAGGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAAC
* *
3451433 CTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAAC
* *
3451479 CTGATATGAAATGAAAAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
3451525 GTGACATGAAAAGAATAAG-CCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAAC
3451570 ATGACAGAAA
Statistics
Matches: 170, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
45 26 0.15
46 144 0.85
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:3451629 original size:91 final size:90
Alignment explanation
Indices: 3451356--3451617 Score: 267
Period size: 92 Copynumber: 2.8 Consensus size: 90
3451346 ATGAAATGTG
* * *** * *
3451356 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTTTAGGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAAAAAGACCATAGTTGAAAGA
* * * **
3451421 TACCATGGCAACCTAATATGAAATGTG
66 CACCATGGCAA-CT-ACATGAAAAGAA
* * *
3451448 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAAAAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAAAAAGACCATAGTTGAAAGA
*
3451513 TACCATGGCAACGTGACATGAAAAGAA
66 CACCATGGCAAC-T-ACATGAAAAGAA
3451540 TAAG-CCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAATGAGTAAGACCATAGTTG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATG-AAATGAA--A--AAGACCATAGTTG
* *
3451603 AAAGGCACTATGGCA
61 AAAGACACCATGGCA
3451618 TCATGTCAAA
Statistics
Matches: 149, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 38 0.26
92 85 0.57
93 1 0.01
95 24 0.16
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (90 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAAAAAGACCATAGTTGAAAGA
CACCATGGCAACTACATGAAAAGAA
Found at i:3456344 original size:28 final size:28
Alignment explanation
Indices: 3456291--3456374 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
3456281 CACTTTGTGC
3456291 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
3456320 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
3456348 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
3456375 CTGGTGTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:3456386 original size:23 final size:24
Alignment explanation
Indices: 3456295--3456388 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 24
3456285 TTGTGCTATT
3456295 CTGGTGTGTTTTGGATGGATTATATTA
1 CTGGTGTGTTTTGGA-GGA-TATA-TA
*
3456322 TTCTGGTGTGTTTGGGAGGATTATATGATA
1 --CTGGTGTGTTTTGGAGG---ATAT-ATA
3456352 CTGGTGTGTTTTGGAGGAT-TATA
1 CTGGTGTGTTTTGGAGGATATATA
3456375 CTGGTGTGTTTTGG
1 CTGGTGTGTTTTGG
3456389 TTGGACATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
23 17 0.29
24 1 0.02
25 2 0.03
28 18 0.31
29 14 0.24
30 5 0.08
31 2 0.03
ACGTcount: A:0.16, C:0.04, G:0.34, T:0.46
Consensus pattern (24 bp):
CTGGTGTGTTTTGGAGGATATATA
Found at i:3456629 original size:21 final size:21
Alignment explanation
Indices: 3456578--3456664 Score: 86
Period size: 21 Copynumber: 4.1 Consensus size: 21
3456568 GGCTTTTCTG
*
3456578 ATCAGGCACTTTATGTGTCAT
1 ATCAGGCACTTTATGTGTCGT
*
3456599 ATTTCAGGCACTTTATGTGTCGC
1 A--TCAGGCACTTTATGTGTCGT
* * **
3456622 AGCAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
*
3456643 TTCAGGCAC-TTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
3456663 AT
1 AT
3456665 TCTGATCAGG
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
20 10 0.19
21 23 0.44
23 19 0.37
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (21 bp):
ATCAGGCACTTTATGTGTCGT
Found at i:3460033 original size:15 final size:16
Alignment explanation
Indices: 3459988--3460038 Score: 63
Period size: 14 Copynumber: 3.4 Consensus size: 16
3459978 AAATATTGAA
*
3459988 TAAAAATTAATAA-A-
1 TAAAAATTTATAATAT
3460002 TAAAAATTTATAATAT
1 TAAAAATTTATAATAT
*
3460018 TAAATATTTA-AATAT
1 TAAAAATTTATAATAT
3460033 TAAAAA
1 TAAAAA
3460039 ACACTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.38
15 11 0.34
16 9 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAATTTATAATAT
Found at i:3460973 original size:73 final size:74
Alignment explanation
Indices: 3460838--3460974 Score: 188
Period size: 73 Copynumber: 1.9 Consensus size: 74
3460828 ATTCATCTAA
*
3460838 TCTAGAATTTCTTACTTTTTATTTGTAATTTAAATAAATAATTGCAAATATAATTTTTAAATTAA
1 TCTAGAATTTCTTACTTTTTATTTGTAATTTAAATAAATAATTGCAAATATAATTTTAAAATTAA
3460903 TACTTATAG
66 TACTTATAG
* * * * **
3460912 TCTAGAGTTTGTTA-TTTTTATTTGTAATTTATATAATTAATT-TTAATATAATTATTAAAATTA
1 TCTAGAATTTCTTACTTTTTATTTGTAATTTAAATAAATAATTGCAAATATAATT-TTAAAATTA
3460975 TTATATGTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
72 9 0.16
73 34 0.62
74 12 0.22
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (74 bp):
TCTAGAATTTCTTACTTTTTATTTGTAATTTAAATAAATAATTGCAAATATAATTTTAAAATTAA
TACTTATAG
Found at i:3464566 original size:14 final size:14
Alignment explanation
Indices: 3464547--3464575 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3464537 TACAATATAT
3464547 ATAAGAATTATACG
1 ATAAGAATTATACG
3464561 ATAAGAATTATACG
1 ATAAGAATTATACG
3464575 A
1 A
3464576 ATCCATCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:3467364 original size:13 final size:15
Alignment explanation
Indices: 3467339--3467378 Score: 66
Period size: 13 Copynumber: 2.8 Consensus size: 15
3467329 TATTTTATTA
3467339 AATAAATATTAAATT
1 AATAAATATTAAATT
3467354 AA-AAA-ATTAAATT
1 AATAAATATTAAATT
3467367 AATAAATATTAA
1 AATAAATATTAA
3467379 TAAATTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.43
14 6 0.26
15 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAAATATTAAATT
Found at i:3475175 original size:92 final size:91
Alignment explanation
Indices: 3475018--3475226 Score: 251
Period size: 92 Copynumber: 2.3 Consensus size: 91
3475008 TTGATTTTAG
* ** *
3475018 TAAATTTATATAAGAACAATTTATTATTGAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
3475083 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* *
3475110 TAAATTCATATAAGAAAATTTATTATCAAGTATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
*
3475174 TATGTAATAATTATTATTTTAGATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
3475202 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
3475227 GTTATAATTA
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
90 1 0.01
91 28 0.28
92 69 0.68
93 3 0.03
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:3475355 original size:66 final size:63
Alignment explanation
Indices: 3475280--3475490 Score: 192
Period size: 66 Copynumber: 3.4 Consensus size: 63
3475270 AAATATATTT
3475280 AATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
3475345 G
63 G
* * * * **
3475346 AATATTAATTATTAAGAATTTTA-TTAA--AT--TATA-TAT--TTTAATTAAAAT-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
*
3475400 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
3475464 AG
62 AG
*
3475466 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
3475491 AAATTATATA
Statistics
Matches: 113, Mismatches: 15, Indels: 35
0.69 0.09 0.21
Matches are distributed among these distances:
53 5 0.04
54 13 0.12
55 5 0.04
56 12 0.11
57 1 0.01
58 3 0.03
59 6 0.05
61 6 0.05
62 3 0.03
63 1 0.01
64 12 0.11
65 9 0.08
66 32 0.28
67 5 0.04
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (63 bp):
AATATTAATTATTTAAATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:3475388 original size:120 final size:120
Alignment explanation
Indices: 3475249--3475534 Score: 488
Period size: 120 Copynumber: 2.4 Consensus size: 120
3475239 TTAAATTATT
* * * *
3475249 TTAAATCATATATTATAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-TTTATAG
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTAT-ATTTTACAG
3475311 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
63 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
3475369 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
3475434 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
3475489 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
3475535 TAAATATGAT
Statistics
Matches: 159, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
119 6 0.04
120 151 0.95
121 2 0.01
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
Found at i:3475391 original size:18 final size:17
Alignment explanation
Indices: 3475363--3475397 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3475353 ATTATTAAGA
*
3475363 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3475380 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3475398 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3475511 original size:18 final size:17
Alignment explanation
Indices: 3475483--3475517 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3475473 ATTATTAAGA
*
3475483 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3475500 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3475518 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3475651 original size:156 final size:161
Alignment explanation
Indices: 3475471--3475792 Score: 546
Period size: 156 Copynumber: 2.0 Consensus size: 161
3475461 ATAAGAATAT
3475471 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
3475536 AAATATGATTAAATTATTTATTATTGAT-AT-TAATAAT-T-TTATTAAAATTTAAATAACAATA
66 AAATATGATTAAAATATTTATTACTGATAATATAATAATATCTTATTAAAATTTAAATAACAATA
*
3475597 ACAATAATAATTTACCAAAACAAATTTCTGC
131 ACAATAATAATTTACCAAAACAAATTTATGC
3475628 TAATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
3475692 AATTATGATTAAAATATTTATTACTGATAATAATAATAATAATCTTATTAAAATTTAAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAAT-ATAATAAT-ATCTTATTAAAATTTAAATAACAA
*
3475757 TAACAATAATTATTTACCAAAACAAATTTATGC
129 TAACAATAATAATTTACCAAAACAAATTTATGC
3475790 TAA
1 TAA
3475793 GGGTATTCTA
Statistics
Matches: 154, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
156 83 0.54
157 8 0.05
159 7 0.05
161 1 0.01
162 55 0.36
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (161 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTACTGATAATATAATAATATCTTATTAAAATTTAAATAACAATA
ACAATAATAATTTACCAAAACAAATTTATGC
Found at i:3475667 original size:18 final size:17
Alignment explanation
Indices: 3475639--3475673 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3475629 AATTATAAGA
*
3475639 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3475656 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3475674 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3475673 original size:16 final size:16
Alignment explanation
Indices: 3475639--3475696 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
3475629 AATTATAAGA
3475639 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
3475656 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
3475672 A-TTTAA-TAATAAT-T
1 ATTTTAATTAA-AATAT
3475686 ATGTTTAATTA
1 AT-TTTAATTA
3475697 TGATTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 5 0.14
15 8 0.22
16 10 0.28
17 7 0.19
18 6 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:3480881 original size:20 final size:20
Alignment explanation
Indices: 3480830--3480881 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
3480820 ATCTATATTG
**
3480830 AAGTATCGATACTTTTCCTA
1 AAGTATCGATACTTTGACTA
* *
3480850 TAGTATCAATACTTTGACTA
1 AAGTATCGATACTTTGACTA
*
3480870 AAGTATTGATAC
1 AAGTATCGATAC
3480882 CTTCCTTAAG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (20 bp):
AAGTATCGATACTTTGACTA
Found at i:3485022 original size:9 final size:9
Alignment explanation
Indices: 3485008--3485042 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
3484998 TATTAGTACT
3485008 TTTTTTTTC
1 TTTTTTTTC
3485017 TTTTTTTTC
1 TTTTTTTTC
3485026 TTTTTTTTC
1 TTTTTTTTC
3485035 TTTTTTTT
1 TTTTTTTT
3485043 AAATTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:3485049 original size:18 final size:18
Alignment explanation
Indices: 3485010--3485049 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3485000 TTAGTACTTT
***
3485010 TTTTTTCTTTTTTTTCTT
1 TTTTTTCTTTTTTTTAAA
3485028 TTTTTTCTTTTTTTTAAA
1 TTTTTTCTTTTTTTTAAA
3485046 TTTT
1 TTTT
3485050 ATTATTATTT
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:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTCTTTTTTTTAAA
Found at i:3485329 original size:118 final size:118
Alignment explanation
Indices: 3485168--3485397 Score: 361
Period size: 118 Copynumber: 1.9 Consensus size: 118
3485158 TATTTCCAGT
3485168 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
* *
3485233 CCTACCCCGGTTACTCAGTCAGTCACGATTTGAGCCATACTCATAACCTCGGC
66 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
**** * *
3485286 TAGCGGAGTTTTACTTGTCACGTCACACAACCTTTTGATGCGAAGTAGAATGACAACCCAAGTAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
* **
3485351 CCTACCCCGGTTACTCAGTTAGTCACGATCTAAGCTGTACTCATAAC
66 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAAC
3485398 TATGGAAAAC
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
118 101 1.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (118 bp):
TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
Found at i:3485870 original size:24 final size:24
Alignment explanation
Indices: 3485843--3485894 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3485833 TTAGTAAGTC
*
3485843 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3485867 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3485891 AAAT
1 AAAT
3485895 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3487841 original size:24 final size:24
Alignment explanation
Indices: 3487814--3487865 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3487804 TTAGTAAGTC
*
3487814 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3487838 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3487862 AAAT
1 AAAT
3487866 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3488777 original size:16 final size:15
Alignment explanation
Indices: 3488735--3488789 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
3488725 ATTAATATTT
*
3488735 AAATAAAATAAAATAAT
1 AAAT-AAATAAAA-AAA
3488752 AAAT-AATAAAAGAAA
1 AAATAAATAAAA-AAA
3488767 AAATAAATAAAAATAA
1 AAATAAATAAAAA-AA
3488783 AAATAAA
1 AAATAAA
3488790 AATAAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 14 0.41
16 16 0.47
17 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (15 bp):
AAATAAATAAAAAAA
Found at i:3488780 original size:6 final size:6
Alignment explanation
Indices: 3488735--3488797 Score: 62
Period size: 6 Copynumber: 10.5 Consensus size: 6
3488725 ATTAATATTT
3488735 AAAT-A AAAT-A AAATAA TAAATAA TAAA-AGA AAA-AA TAAATAA AAATAA
1 AAATAA AAATAA AAATAA -AAATAA -AAATA-A AAATAA -AAATAA AAATAA
3488783 AAATAA AAATAA AAA
1 AAATAA AAATAA AAA
3488798 GAAAGATTGG
Statistics
Matches: 53, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
5 10 0.19
6 30 0.57
7 13 0.25
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:3488795 original size:22 final size:22
Alignment explanation
Indices: 3488735--3488795 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
3488725 ATTAATATTT
3488735 AAAT-AAAAT-AAAAT-AATAA
1 AAATAAAAATAAAAATAAATAA
3488754 ATAATAAAAGA-AAAAATAAATAA
1 A-AATAAAA-ATAAAAATAAATAA
3488777 AAATAAAAATAAAAATAAA
1 AAATAAAAATAAAAATAAA
3488796 AAGAAAGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
19 1 0.03
20 3 0.08
21 4 0.11
22 22 0.61
23 6 0.17
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (22 bp):
AAATAAAAATAAAAATAAATAA
Found at i:3494476 original size:47 final size:47
Alignment explanation
Indices: 3494359--3494615 Score: 304
Period size: 47 Copynumber: 5.4 Consensus size: 47
3494349 TGCACATAGT
* * * ** * *
3494359 CACATATCACACACCGAAGCCATAGCCCAGCCATGGTCTTACACGG-AT
1 CACATAT--CACACTGATGCCATATCCCAGATATGGTCTTATACGGAAG
* * *
3494407 CACAGATCACACTGATGCCATATCCCAGATATGGTCTTACACAGAAG
1 CACATATCACACTGATGCCATATCCCAGATATGGTCTTATACGGAAG
*
3494454 CACATATCACACCGATGCCATATCCCAGATATGGTCTTATACGGAAG
1 CACATATCACACTGATGCCATATCCCAGATATGGTCTTATACGGAAG
* *
3494501 CTCATATCACACTGATGTCATATCCCAGATATGGTCTTATACGGAAG
1 CACATATCACACTGATGCCATATCCCAGATATGGTCTTATACGGAAG
* * *
3494548 CTCATATCACACTGATGCCATAGCCCA-ACTATGGTCTTATACGGAAAT
1 CACATATCACACTGATGCCATATCCCAGA-TATGGTCTTATACGG-AAG
*
3494596 CACATATCACA-TGTTGCCAT
1 CACATATCACACTGATGCCAT
3494616 GGTCTAACCA
Statistics
Matches: 186, Mismatches: 20, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
46 32 0.17
47 136 0.73
48 18 0.10
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (47 bp):
CACATATCACACTGATGCCATATCCCAGATATGGTCTTATACGGAAG
Found at i:3498777 original size:8 final size:8
Alignment explanation
Indices: 3498764--3498817 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
3498754 TTTTTAAACA
3498764 ATTTTTAT
1 ATTTTTAT
*
3498772 ATTTTTTT
1 ATTTTTAT
*
3498780 AATTTTA-
1 ATTTTTAT
3498787 A-TTTTAT
1 ATTTTTAT
3498794 A-TTTTAT
1 ATTTTTAT
3498801 AGTTTTTAT
1 A-TTTTTAT
*
3498810 AATTTTAT
1 ATTTTTAT
3498818 TCTATTTAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 5 0.13
7 9 0.23
8 18 0.46
9 7 0.18
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (8 bp):
ATTTTTAT
Found at i:3505507 original size:11 final size:11
Alignment explanation
Indices: 3505491--3505515 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3505481 TTACAATTGT
3505491 TTTTGTAATTA
1 TTTTGTAATTA
3505502 TTTTGTAATTA
1 TTTTGTAATTA
3505513 TTT
1 TTT
3505516 CTTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTGTAATTA
Found at i:3517153 original size:26 final size:26
Alignment explanation
Indices: 3517079--3517158 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
3517069 TATATATTTT
*
3517079 TATTT-TTATTAAATTATATTTGATAA
1 TATTTATTATTAAATTATATTT-AAAA
* *
3517105 TAATTA-TATTAAAATATGA-TTAAAA
1 TATTTATTATTAAATTAT-ATTTAAAA
*
3517130 TATTTATTATTGAATTATATTTAATAA
1 TATTTATTATTAAATTATATTTAA-AA
3517157 TA
1 TA
3517159 ACCTTATTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
25 9 0.21
26 29 0.67
27 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (26 bp):
TATTTATTATTAAATTATATTTAAAA
Found at i:3522453 original size:91 final size:91
Alignment explanation
Indices: 3522298--3522483 Score: 354
Period size: 91 Copynumber: 2.0 Consensus size: 91
3522288 TTACATAGTT
*
3522298 AAATAATTTATATTTTTTAAAAAATATTAATTACTATAATAATATTAGTATGATAAAAATAATTT
1 AAATAATTTATATTTTTAAAAAAATATTAATTACTATAATAATATTAGTATGATAAAAATAATTT
3522363 CTATGAAAGTACCAAAAATTAAAATC
66 CTATGAAAGTACCAAAAATTAAAATC
*
3522389 AAATAATTTATATTTTTAAAAAAATATTAATTACTATAATAATATTAGTATGATAAAGATAATTT
1 AAATAATTTATATTTTTAAAAAAATATTAATTACTATAATAATATTAGTATGATAAAAATAATTT
3522454 CTATGAAAGTACCAAAAATTAAAATC
66 CTATGAAAGTACCAAAAATTAAAATC
3522480 AAAT
1 AAAT
3522484 CATGACATGT
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 93 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (91 bp):
AAATAATTTATATTTTTAAAAAAATATTAATTACTATAATAATATTAGTATGATAAAAATAATTT
CTATGAAAGTACCAAAAATTAAAATC
Found at i:3523785 original size:24 final size:23
Alignment explanation
Indices: 3523756--3523803 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 23
3523746 TATAATACGT
3523756 AAATAAAGTAAAAATAATATTAAA
1 AAATAAAGTAAAAATAATA-TAAA
3523780 AAATAAAGTAAAAATAATATAAA
1 AAATAAAGTAAAAATAATATAAA
3523803 A
1 A
3523804 TTTATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (23 bp):
AAATAAAGTAAAAATAATATAAA
Found at i:3523802 original size:11 final size:12
Alignment explanation
Indices: 3523756--3523803 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
3523746 TATAATACGT
3523756 AAATAA-AGTAA
1 AAATAATAGTAA
*
3523767 AAATAATATTAAA
1 AAATAATAGT-AA
3523780 AAATAA-AGTAA
1 AAATAATAGTAA
3523791 AAATAATA-TAA
1 AAATAATAGTAA
3523802 AA
1 AA
3523804 TTTATAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 19 0.59
12 5 0.16
13 8 0.25
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (12 bp):
AAATAATAGTAA
Found at i:3526377 original size:35 final size:35
Alignment explanation
Indices: 3526314--3526649 Score: 413
Period size: 35 Copynumber: 9.6 Consensus size: 35
3526304 CATGGCAAAG
* * *
3526314 TGTGAAACGTAGGTATAGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * *
3526349 TGTGAAACATAGGCATGGAATCATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* *
3526384 TGTGAAACGTAGGCATGGTATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
*
3526419 TGTGAAACGTAGGTATGGTATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
*
3526454 TGTGAAACGTAGGTATGATATCATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * ** * *
3526489 TGTGAAACGTAGGTATGGTATTAACTGTACCGAGA
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * *
3526524 TGTGAAACGTAGGTATGGTATTAACCGTACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
*
3526559 TGTGAAACGTAGGTATGGTATTATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
** ** * *
3526594 TAAGAAACGTAGGTATGACAT-TTCCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCAT-CCATACTGAGT
*
3526629 TGTGAAATGTAGGTATGGTAT
1 TGTGAAACGTAGGTATGGTAT
3526650 TTCAATGAGG
Statistics
Matches: 265, Mismatches: 35, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
34 1 0.00
35 264 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
Found at i:3526780 original size:31 final size:32
Alignment explanation
Indices: 3526745--3526837 Score: 118
Period size: 31 Copynumber: 3.0 Consensus size: 32
3526735 AATAAGTAAT
*
3526745 TTGATCAGTGAGAAGTGGTACCTCTGGCTA-C
1 TTGATCAGTGAGAAGTGGTACCTCCGGCTACC
*
3526776 TTGATCAGTGAGAAGTGGTAGCTCCGGCTACC
1 TTGATCAGTGAGAAGTGGTACCTCCGGCTACC
* * * *
3526808 AT-ATCAGTGAGTAGTGGTAGCTTCGGCTAC
1 TTGATCAGTGAGAAGTGGTACCTCCGGCTAC
3526838 AAGTGACAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 54 0.96
32 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (32 bp):
TTGATCAGTGAGAAGTGGTACCTCCGGCTACC
Found at i:3529867 original size:24 final size:25
Alignment explanation
Indices: 3529847--3529910 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
3529837 AGAGAGCCAT
3529847 TAACGGGAAGCTCATA-CGAGCTAA
1 TAACGGGAAGCTCATAGCGAGCTAA
* * *
3529871 TATCGGGAAGTTCA-AGTGAGCTAA
1 TAACGGGAAGCTCATAGCGAGCTAA
3529895 TAACGGGAAGCTCATA
1 TAACGGGAAGCTCATA
3529911 AAATATCTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 1 0.03
24 31 0.94
25 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (25 bp):
TAACGGGAAGCTCATAGCGAGCTAA
Found at i:3530407 original size:21 final size:21
Alignment explanation
Indices: 3530381--3530421 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3530371 GAATTTAACA
*
3530381 TCAATTTAATACAAATCATAG
1 TCAATTCAATACAAATCATAG
* *
3530402 TCAATTCAATCCAATTCATA
1 TCAATTCAATACAAATCATA
3530422 TCCTAGACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (21 bp):
TCAATTCAATACAAATCATAG
Found at i:3542192 original size:16 final size:16
Alignment explanation
Indices: 3542171--3542222 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
3542161 TTTGGTTCGC
3542171 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3542187 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
3542203 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
3542219 TGTA
1 TGTA
3542223 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:3542309 original size:39 final size:43
Alignment explanation
Indices: 3542203--3542312 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 43
3542193 GGATTAGAGG
3542203 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
** * *
3542248 TGTAATGGAATAGAGGCATAATAG-TAATCTTA-TGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATC-AACTGTTTGGTTA
3542288 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
3542313 TAATGGAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
39 19 0.34
40 2 0.04
43 1 0.02
44 11 0.20
45 23 0.41
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:3542468 original size:18 final size:17
Alignment explanation
Indices: 3542438--3542480 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
3542428 TTAATTATAT
3542438 TTAAATATA-ATAATTA
1 TTAAATATATATAATTA
3542454 TTAAATATATTATAATTA
1 TTAAATATA-TATAATTA
3542472 --AAATATATA
1 TTAAATATATA
3542481 ATTTAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.08
16 16 0.64
18 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATATATATAATTA
Found at i:3542538 original size:59 final size:58
Alignment explanation
Indices: 3542473--3542898 Score: 182
Period size: 59 Copynumber: 7.1 Consensus size: 58
3542463 TTATAATTAA
3542473 AATATATAATTTAATAAAATTCTTAATAATCAATATCTTAATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATCTTAATGAATTTACT-AAATCAT
* * * * * * * * * * *
3542532 AATATATGATACT-ATAAAATATAATTTAA-CAT-AAT-TATTATTAAATATATTATAATTAA
1 AATATATAAT-TTAATAAAAT-T--CTTAATAATCAATATCTTAATGAATTTACTA-AATCAT
* * *
3542591 AATATATAATTTAGTAAAATTCTTAAAAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATA-TCTTA-ATGAATTTACT-AAATCAT
* * * * * * * * *
3542652 AATATACGATACTATAAAAGATAATT-TAACATAATTATTAT-TAAAT-ATATTT--T-AATTAA
1 AATAT---ATAATTTAATA-A-AATTCTTA-ATAATCAATATCTTAATGA-ATTTACTAAATCAT
*
3542711 AATATATAATTTAATAAAATTCTTAATAATCAAAATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATA-TCTTA-ATGAATTTACT-AAATCAT
* * * * * * * *
3542772 AATATATGATACTATAAAATATAATT-TGAATTAATTAATA--TTAA-AAATATT--TTAATTAA
1 AATATAT-A-A-T-T-TAATAAAATTCTTAA-TAATCAATATCTTAATGAAT-TTACTAAATCAT
*
3542831 AATATATAATTTAATAAAATTCTTAATAATCAACATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATA-TCTTA-ATGAATTTACT-AAATCAT
3542892 AATATAT
1 AATATAT
3542899 GATACTATAA
Statistics
Matches: 262, Mismatches: 61, Indels: 86
0.64 0.15 0.21
Matches are distributed among these distances:
54 26 0.10
55 8 0.03
56 15 0.06
57 12 0.05
58 11 0.04
59 70 0.27
60 11 0.04
61 44 0.17
62 10 0.04
63 10 0.04
64 10 0.04
65 8 0.03
66 27 0.10
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.42
Consensus pattern (58 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATCTTAATGAATTTACTAAATCAT
Found at i:3542595 original size:16 final size:16
Alignment explanation
Indices: 3542551--3542597 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
3542541 TACTATAAAA
*
3542551 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
3542567 TATTATT-AAATATAT
1 TATAATTAAAATATAT
3542582 TATAATTAAAATATAT
1 TATAATTAAAATATAT
3542598 AATTTAGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:3542684 original size:120 final size:120
Alignment explanation
Indices: 3542444--3542971 Score: 839
Period size: 120 Copynumber: 4.4 Consensus size: 120
3542434 ATATTTAAAT
* *
3542444 ATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATA-
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
*
3542508 TCTTA-ATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT-AA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * * *
3542561 CATAATTATTATTAAATATATTATAATTAAAATATATAATTTAGTAAAATTCTTAAAAATTAATA
1 -ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATA
* * *
3542626 TTCTTATATGAATTTACTCAAATCATAATATACGATACTATAAAAGATAATTT-AA
65 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
*
3542681 CATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAAAA
1 -ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATA
3542746 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
65 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * * *
3542802 TTAATTAATATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAACAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
3542867 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * * *
3542922 GTAATTAATATTAAAAATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
3542972 TAAAATAATT
Statistics
Matches: 387, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
118 60 0.16
119 5 0.01
120 320 0.83
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
Found at i:3542717 original size:18 final size:17
Alignment explanation
Indices: 3542696--3542730 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3542686 TTATTATTAA
*
3542696 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3542714 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3542731 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3542747 original size:16 final size:15
Alignment explanation
Indices: 3542722--3542751 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3542712 ATATATAATT
3542722 TAATAAAATTCTTAA
1 TAATAAAATTCTTAA
3542737 TAATCAAAATTCTTA
1 TAAT-AAAATTCTTA
3542752 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATAAAATTCTTAA
Found at i:3542970 original size:59 final size:58
Alignment explanation
Indices: 3542772--3542960 Score: 163
Period size: 59 Copynumber: 3.2 Consensus size: 58
3542762 CTAAAATCAT
3542772 AATATATGATACTATAAAATATAATTTGAATTAATTAATATTAAAAATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTGAA-TAATTAATATTAAAAATATTTTAATTAA
* * * * * ** * *
3542831 AATATAT-A-A-T-T-TAATAAAATTCTTAATAATCAACATTCTTATATGAATTTACTAAAATCA
1 AATATATGATACTATAAAATATAATT-TGAATAATTAATATT-AAAAAT--ATTT--T--AATTA
*
3542891 T
58 A
3542892 AATATATGATACTATAAAATATAATTTGAAGTAATTAATATTAAAAATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTGAA-TAATTAATATTAAAAATATTTTAATTAA
3542951 AATATATGAT
1 AATATATGAT
3542961 TTAATAAAAT
Statistics
Matches: 96, Mismatches: 20, Indels: 28
0.67 0.14 0.19
Matches are distributed among these distances:
54 17 0.18
55 7 0.07
56 1 0.01
57 5 0.05
58 1 0.01
59 22 0.23
61 12 0.12
62 1 0.01
63 5 0.05
64 1 0.01
65 7 0.07
66 17 0.18
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (58 bp):
AATATATGATACTATAAAATATAATTTGAATAATTAATATTAAAAATATTTTAATTAA
Found at i:3543022 original size:47 final size:46
Alignment explanation
Indices: 3542953--3543120 Score: 143
Period size: 47 Copynumber: 3.7 Consensus size: 46
3542943 TTAATTAAAA
*
3542953 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTCT
* * *
3543000 TATATGAATTTGTATAATTTAAAATAATTAT--TATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAAT-T-TTCT
* * * *
3543045 TA-AT-AATAATATATAATTTCATAA-AATTCGTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
*
3543091 TATATGAATTTATACAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
3543121 ATATTAAATA
Statistics
Matches: 95, Mismatches: 14, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
43 3 0.03
44 22 0.23
45 9 0.09
46 8 0.08
47 46 0.48
48 7 0.07
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:3543029 original size:101 final size:92
Alignment explanation
Indices: 3542968--3543144 Score: 254
Period size: 91 Copynumber: 1.9 Consensus size: 92
3542958 GATTTAATAA
* *
3542968 AATTT-AAAATAATT-ATAACTAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTAT
1 AATTTCAAAA-AATTCATAA-TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAA
3543031 TATTAAATATAATTTAA-TAATAATATAT
64 TATTAAATATAATTTAATTAATAATATAT
* * * *
3543059 AATTTCATAAAATTCGTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATA
1 AATTTCAAAAAATTCATAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATA
3543124 TTAAATATAATTTAA-TAATAA
66 TTAAATATAATTTAATTAATAA
3543145 AATGTTCTTA
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
91 73 0.94
92 5 0.06
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (92 bp):
AATTTCAAAAAATTCATAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATA
TTAAATATAATTTAATTAATAATATAT
Found at i:3543140 original size:17 final size:15
Alignment explanation
Indices: 3543109--3543147 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
3543099 TTTATACAAT
3543109 TTAAAATAATTAATA
1 TTAAAATAATTAATA
3543124 TTAAATATAATTTAATA
1 TTAAA-ATAA-TTAATA
*
3543141 ATAAAAT
1 TTAAAAT
3543148 GTTCTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 6 0.29
17 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAAATAATTAATA
Found at i:3559345 original size:6 final size:6
Alignment explanation
Indices: 3559334--3559360 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3559324 TGTCTCATTT
3559334 ATGATA ATGATA ATGATA ATGATA ATG
1 ATGATA ATGATA ATGATA ATGATA ATG
3559361 GCAATGATGT
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:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (6 bp):
ATGATA
Found at i:3559366 original size:18 final size:18
Alignment explanation
Indices: 3559334--3559368 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3559324 TGTCTCATTT
*
3559334 ATGATAATGATAATGATA
1 ATGATAATGACAATGATA
*
3559352 ATGATAATGGCAATGAT
1 ATGATAATGACAATGAT
3559369 GTGGATGATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.20, T:0.31
Consensus pattern (18 bp):
ATGATAATGACAATGATA
Found at i:3560412 original size:20 final size:19
Alignment explanation
Indices: 3560387--3560424 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3560377 TAGAAAGATG
3560387 AATAATAACTCTTGTAAAAA
1 AATAATAACTCTT-TAAAAA
*
3560407 AATAATACCTCTTTAAAA
1 AATAATAACTCTTTAAAA
3560425 TAAACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.32
Consensus pattern (19 bp):
AATAATAACTCTTTAAAAA
Found at i:3560761 original size:91 final size:89
Alignment explanation
Indices: 3560582--3560862 Score: 328
Period size: 91 Copynumber: 3.1 Consensus size: 89
3560572 TTAAGGGTGT
* *
3560582 AAAAGGCCCTAAAACTTTTTAAAAAAAAAAGCAATTAAGCCCTTGTTTTTTTTTTGCACTCAATT
1 AAAAGGCCCTCAAACTTTTT--CAAAAAAAGCAATTAAGCCC-TGTTTTTTTTTTGCACTCAATT
* * *
3560647 GGGTACTTGAACTTTTAAAATGCATAA
63 GGATACTTGAACTGTCAAAATGCATAA
* * *
3560674 AAAAGGCCCTCAAACTTTTTCAAATAAAGCAATTAAGCCCCTAGTTTTTTTTTTGTACTTAATTG
1 AAAAGGCCCTCAAACTTTTTCAAAAAAAGCAATTAAG-CCCT-GTTTTTTTTTTGCACTCAATTG
* * * *
3560739 GATAATTGAACTGTCCAGATGCATCA
64 GATACTTGAACTGTCAAAATGCATAA
* ** * *
3560765 AAAAGGCCCTCGAACTTTTTCAAAAAAATTAATTAAGTCACTGTTTTTTTTTTGCACTCAATTGA
1 AAAAGGCCCTCAAACTTTTTCAAAAAAAGCAATTAAG-CCCTGTTTTTTTTTTGCACTCAATTGG
* * *
3560830 ATACTTGAACTGCCAAAATGTATCA
65 ATACTTGAACTGTCAAAATGCATAA
3560855 AAAAGGCC
1 AAAAGGCC
3560863 AGGGGTGAAT
Statistics
Matches: 161, Mismatches: 26, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
90 64 0.40
91 78 0.48
92 19 0.12
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (89 bp):
AAAAGGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCTGTTTTTTTTTTGCACTCAATTGGA
TACTTGAACTGTCAAAATGCATAA
Found at i:3563510 original size:19 final size:19
Alignment explanation
Indices: 3563486--3563535 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
3563476 GTACGATAAT
3563486 TTTTATAATTTTTTACAAA
1 TTTTATAATTTTTTACAAA
**
3563505 TTTTAT-ATTTCTTTACATT
1 TTTTATAATTT-TTTACAAA
3563524 TTTTATAATTTT
1 TTTTATAATTTT
3563536 CTTAAGGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 4 0.15
19 19 0.70
20 4 0.15
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAA
Found at i:3563616 original size:28 final size:28
Alignment explanation
Indices: 3563558--3563616 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3563548 TAAAATTTTA
* * *
3563558 TTATTATTTTTCTATATTTCTATATATT
1 TTATAATTTTTCTATATTTCTATAAAAT
*
3563586 TTATAATTTTT-TATGATTTGTATAAAAT
1 TTATAATTTTTCTAT-ATTTCTATAAAAT
3563614 TTA
1 TTA
3563617 AAAAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (28 bp):
TTATAATTTTTCTATATTTCTATAAAAT
Found at i:3565569 original size:86 final size:84
Alignment explanation
Indices: 3565381--3565693 Score: 369
Period size: 85 Copynumber: 3.6 Consensus size: 84
3565371 GCTCCTAGCT
* * *
3565381 TTTTTTATGCATTTTGGCAGTTCAAGTACCTAATT-AGT-ACTAAAAAAGAGCAGAGGCTTAATT
1 TTTTTTATGCATTTTGACAGTTCAAGTACCCAATTGAGTGA--AAAAAA-A--AGA-GATTAATT
* **
3565444 GCTTTTTTTGAAAAAGTTTGAGGGAC
60 GTTTTTTTTGAAAAA-TTTGAGGTCC
** * * *
3565470 TTTTAAATACATTTTGACAGTTCAAATACCCAATTGAGTGAAAAAAAAGGAGATTAATTGTTTTT
1 TTTTTTATGCATTTTGACAGTTCAAGTACCCAATTGAGTGAAAAAAAAAGAGATTAATTG-TTTT
3565535 TTTTGAAAAATTTCGAGGTCC
65 TTTTGAAAAATTT-GAGGTCC
* *
3565556 TTTTTTATGCATTTTGAAAGTTCAAGTACTCAATTGAGTGAAAAAAAAAGAGATTAATTGTTTTT
1 TTTTTTATGCATTTTGACAGTTCAAGTACCCAATTGAGTGAAAAAAAAAGAGATTAATTGTTTTT
*
3565621 TTTGAAAAATTTTGAGGTCA
66 TTTGAAAAA-TTTGAGGTCC
***
3565641 TTTTTTATGCATTTTGACAGTTCAAGTGTACAATTGAGTGAAAAAAAAAGAGA
1 TTTTTTATGCATTTTGACAGTTCAAGTACCCAATTGAGTGAAAAAAAAAGAGA
3565694 GCAAGTCTTA
Statistics
Matches: 196, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
85 80 0.41
86 76 0.39
88 1 0.01
89 35 0.18
90 3 0.02
91 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (84 bp):
TTTTTTATGCATTTTGACAGTTCAAGTACCCAATTGAGTGAAAAAAAAAGAGATTAATTGTTTTT
TTTGAAAAATTTGAGGTCC
Found at i:3565677 original size:171 final size:173
Alignment explanation
Indices: 3565381--3565693 Score: 404
Period size: 171 Copynumber: 1.8 Consensus size: 173
3565371 GCTCCTAGCT
** *
3565381 TTTTTTATGCATTTTGGCAGTTCAAGTACCTAATTAGTACTAAAAAAGAGCAGAGGCTTAATTGC
1 TTTTTTATGCATTTTGAAAGTTCAAGTACCTAATTAGTAC-AAAAAAGA-CAGAGGATTAATTGC
* *
3565446 TTTTTTTGAAAAAGTTTGAGGGACTTTTAAATACATTTTGACAGTTCAAATACCCAATTGAGTGA
64 TTTTTTTGAAAAAGTTTGAGGCACTTTTAAATACATTTTGACAGTTCAAATACACAATTGAGTGA
*
3565511 AAAAAAAGGAGATTAATTGTTTTTTTTTGAAAAATTTCGAGGTCC
129 AAAAAAAAGAGATTAATTGTTTTTTTTTGAAAAATTTCGAGGTCC
3565556 TTTTTTATGCATTTTGAAAGTTCAAGTA-CTCAATTGAGTGA-AAAAAA-A-AGA-GATTAATTG
1 TTTTTTATGCATTTTGAAAGTTCAAGTACCT-AATT-AGT-ACAAAAAAGACAGAGGATTAATTG
* * ** * * **
3565616 TTTTTTTTGAAAAATTTTGAGGTCA-TTTTTTATGCATTTTGACAGTTCAAGTGTACAATTGAGT
63 CTTTTTTTGAAAAAGTTTGAGG-CACTTTTAAATACATTTTGACAGTTCAAATACACAATTGAGT
3565680 GAAAAAAAAAGAGA
127 GAAAAAAAAAGAGA
3565694 GCAAGTCTTA
Statistics
Matches: 120, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
171 73 0.61
172 4 0.03
174 3 0.03
175 36 0.30
176 3 0.03
177 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (173 bp):
TTTTTTATGCATTTTGAAAGTTCAAGTACCTAATTAGTACAAAAAAGACAGAGGATTAATTGCTT
TTTTTGAAAAAGTTTGAGGCACTTTTAAATACATTTTGACAGTTCAAATACACAATTGAGTGAAA
AAAAAAGAGATTAATTGTTTTTTTTTGAAAAATTTCGAGGTCC
Found at i:3566277 original size:38 final size:39
Alignment explanation
Indices: 3566217--3566324 Score: 114
Period size: 39 Copynumber: 2.8 Consensus size: 39
3566207 AATGTGATGC
* *
3566217 CAAAATCTTTAACGGATGCCAAAATCTCTAA-CAAATAT
1 CAAAATCTTTAACAGATACCAAAATCTCTAACCAAATAT
3566255 CAAAAT-TTCTAACAGATACCAAAATCTCTAACCAAATA-
1 CAAAATCTT-TAACAGATACCAAAATCTCTAACCAAATAT
* * * **
3566293 CTGAAGTCTGTAATTGATACCAAAATCTCTAA
1 C-AAAATCTTTAACAGATACCAAAATCTCTAA
3566325 TGGATACCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
37 2 0.03
38 27 0.46
39 29 0.49
40 1 0.02
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.27
Consensus pattern (39 bp):
CAAAATCTTTAACAGATACCAAAATCTCTAACCAAATAT
Found at i:3566325 original size:19 final size:19
Alignment explanation
Indices: 3566216--3566365 Score: 102
Period size: 19 Copynumber: 7.8 Consensus size: 19
3566206 TAATGTGATG
* * *
3566216 CCAAAATCTTTAACGGATG
1 CCAAAATCTCTAACAGATA
*
3566235 CCAAAATCTCTAACAAATA
1 CCAAAATCTCTAACAGATA
* *
3566254 TCAAAATTTCTAACAGATA
1 CCAAAATCTCTAACAGATA
*
3566273 CCAAAATCTCTAACCAAATA
1 CCAAAATCTCTAA-CAGATA
** * * **
3566293 CTGAAGTCTGTAATTGATA
1 CCAAAATCTCTAACAGATA
**
3566312 CCAAAATCTCTAATGGATA
1 CCAAAATCTCTAACAGATA
* ** *
3566331 CCAAAATTTGAAACCAAATA
1 CCAAAATCTCTAA-CAGATA
*
3566351 CCACAATCTCTAACA
1 CCAAAATCTCTAACA
3566366 AAAATCTCTA
Statistics
Matches: 97, Mismatches: 32, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
19 71 0.73
20 26 0.27
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (19 bp):
CCAAAATCTCTAACAGATA
Found at i:3570079 original size:26 final size:26
Alignment explanation
Indices: 3570043--3570151 Score: 191
Period size: 26 Copynumber: 4.2 Consensus size: 26
3570033 ATGAAATGCC
*
3570043 TATCATGGAACATTTACCTAAACCAT
1 TATCATGGAACATTTACCTAACCCAT
3570069 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
* *
3570095 TATCATGGAATATTTACCTAATCCAT
1 TATCATGGAACATTTACCTAACCCAT
3570121 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
3570147 TATCA
1 TATCA
3570152 ATTTGTACCA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
TATCATGGAACATTTACCTAACCCAT
Found at i:3572285 original size:3 final size:3
Alignment explanation
Indices: 3572277--3572332 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
3572267 ATGAATTAAA
* *
3572277 TAT TAT TAT TAT AAT TA- TAT TAT TAT TAT AATT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
3572322 TAAT T-T TAT TA
1 T-AT TAT TAT TA
3572333 ACTAATTCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 36 0.80
4 5 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3572296 original size:17 final size:17
Alignment explanation
Indices: 3572276--3572332 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
3572266 TATGAATTAA
3572276 ATATTATTATTATAATT
1 ATATTATTATTATAATT
3572293 ATATTATTATTATAATT
1 ATATTATTATTATAATT
3572310 -TATTATTATTATTAATT
1 ATATTATTATTA-TAATT
*
3572327 TTATTA
1 ATATTA
3572333 ACTAATTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
16 11 0.29
17 22 0.58
18 5 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATTATTATTATAATT
Found at i:3572379 original size:16 final size:16
Alignment explanation
Indices: 3572358--3572390 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3572348 AAATAAAGTA
*
3572358 AAAGAATAAAAGAAAC
1 AAAGAAGAAAAGAAAC
3572374 AAAGAAGAAAAGAAAC
1 AAAGAAGAAAAGAAAC
3572390 A
1 A
3572391 GAGACTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAGAAAAGAAAC
Found at i:3572429 original size:14 final size:15
Alignment explanation
Indices: 3572410--3572439 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3572400 CGAAACAGGG
3572410 GAAAGAAAAA-GAAA
1 GAAAGAAAAATGAAA
3572424 GAAAGAAAAATGAAA
1 GAAAGAAAAATGAAA
3572439 G
1 G
3572440 GAAAAACTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.03
Consensus pattern (15 bp):
GAAAGAAAAATGAAA
Found at i:3573416 original size:23 final size:23
Alignment explanation
Indices: 3573384--3573427 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3573374 ACTAAGTGCC
3573384 ATTCTAGTGTGTTTGGGTGGATT
1 ATTCTAGTGTGTTTGGGTGGATT
* *
3573407 ATTCTGGTGTGTTTGGTTGGA
1 ATTCTAGTGTGTTTGGGTGGA
3573428 ATCCGTGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.05, G:0.36, T:0.48
Consensus pattern (23 bp):
ATTCTAGTGTGTTTGGGTGGATT
Found at i:3575516 original size:9 final size:9
Alignment explanation
Indices: 3575487--3575523 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
3575477 TGAGTTTTCG
3575487 AATTCGAAT
1 AATTCGAAT
*
3575496 AACTCGAAT
1 AATTCGAAT
3575505 AATTCGAAT
1 AATTCGAAT
*
3575514 AATTAGAAT
1 AATTCGAAT
3575523 A
1 A
3575524 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:3576444 original size:5 final size:5
Alignment explanation
Indices: 3576434--3576464 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
3576424 GAACAAATAT
3576434 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
3576465 ATTCCATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:3578218 original size:29 final size:30
Alignment explanation
Indices: 3578185--3578253 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
3578175 TTAATTAAAG
* *
3578185 TAAAATTATATTTTAACTTTCT-AACATTA
1 TAAAATTATAATTTAACTTTCTAAAAATTA
* *
3578214 TAAAAATT-TAATTTAATTTTTTAAAAATTA
1 T-AAAATTATAATTTAACTTTCTAAAAATTA
*
3578244 TAAAAATATA
1 TAAAATTATA
3578254 GAACGTAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (30 bp):
TAAAATTATAATTTAACTTTCTAAAAATTA
Found at i:3578220 original size:30 final size:30
Alignment explanation
Indices: 3578186--3578250 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
3578176 TAATTAAAGT
* *
3578186 AAAATTATATTTTAACTTTCT-AACATTATA
1 AAAATT-TAATTTAACTTTCTAAAAATTATA
* *
3578216 AAAATTTAATTTAATTTTTTAAAAATTATA
1 AAAATTTAATTTAACTTTCTAAAAATTATA
3578246 AAAAT
1 AAAAT
3578251 ATAGAACGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (30 bp):
AAAATTTAATTTAACTTTCTAAAAATTATA
Found at i:3582787 original size:6 final size:6
Alignment explanation
Indices: 3582776--3582805 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3582766 ATGGTAGGGT
3582776 CCCCAG CCCCAG CCCCAG CCCCAG CCCCAG
1 CCCCAG CCCCAG CCCCAG CCCCAG CCCCAG
3582806 TTGGTGTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.67, G:0.17, T:0.00
Consensus pattern (6 bp):
CCCCAG
Found at i:3586377 original size:10 final size:9
Alignment explanation
Indices: 3586357--3586405 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
3586347 AACAAATACC
3586357 AAAAAAT-A
1 AAAAAATAA
**
3586365 AAAAAGCAA
1 AAAAAATAA
3586374 AAAAAATAA
1 AAAAAATAA
3586383 AAAAAATAA
1 AAAAAATAA
3586392 AAAAAATAA
1 AAAAAATAA
3586401 AAAAA
1 AAAAA
3586406 CAAAAAATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
8 5 0.14
9 31 0.86
ACGTcount: A:0.88, C:0.02, G:0.02, T:0.08
Consensus pattern (9 bp):
AAAAAATAA
Found at i:3586385 original size:18 final size:17
Alignment explanation
Indices: 3586357--3586412 Score: 85
Period size: 17 Copynumber: 3.2 Consensus size: 17
3586347 AACAAATACC
*
3586357 AAAAAATAAAAAAGCAA
1 AAAAAATAAAAAAACAA
*
3586374 AAAAAATAAAAAAAATAA
1 AAAAAAT-AAAAAAACAA
3586392 AAAAAATAAAAAAACAA
1 AAAAAATAAAAAAACAA
3586409 AAAA
1 AAAA
3586413 TAGAATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
17 20 0.57
18 15 0.43
ACGTcount: A:0.88, C:0.04, G:0.02, T:0.07
Consensus pattern (17 bp):
AAAAAATAAAAAAACAA
Found at i:3586411 original size:9 final size:9
Alignment explanation
Indices: 3586364--3586412 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
3586354 ACCAAAAAAT
*
3586364 AAAAAAGCA
1 AAAAAAACA
*
3586373 AAAAAAATA
1 AAAAAAACA
*
3586382 AAAAAAATA
1 AAAAAAACA
*
3586391 AAAAAAA-T
1 AAAAAAACA
3586399 AAAAAAACA
1 AAAAAAACA
3586408 AAAAA
1 AAAAA
3586413 TAGAATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 7 0.20
9 28 0.80
ACGTcount: A:0.88, C:0.04, G:0.02, T:0.06
Consensus pattern (9 bp):
AAAAAAACA
Found at i:3587826 original size:60 final size:61
Alignment explanation
Indices: 3587725--3587868 Score: 147
Period size: 60 Copynumber: 2.4 Consensus size: 61
3587715 ATATATACAT
* * *
3587725 ATATTC-TTAATATTATATATTGTATGTATTTTCTTATTATATGTGTATGTATAGTA-T-GTAC
1 ATATTCTTTAATATTAT-TA-TGTATGTATTTTCTTAATATATGTATATATATA-TATTAGTAC
3587786 ATATTCTTTAATATTATTATGTAT-TAATTTT-TTAAATATATGTATATATATATATTAGTAC
1 ATATTCTTTAATATTATTATGTATGT-ATTTTCTT-AATATATGTATATATATATATTAGTAC
* * *
3587847 TTA-TATTTAGTATTATTATGTA
1 ATATTCTTTAATATTATTATGTA
3587869 AACGTCTTTC
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
59 5 0.07
60 43 0.60
61 14 0.19
62 10 0.14
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.55
Consensus pattern (61 bp):
ATATTCTTTAATATTATTATGTATGTATTTTCTTAATATATGTATATATATATATTAGTAC
Found at i:3589864 original size:41 final size:41
Alignment explanation
Indices: 3589807--3590045 Score: 288
Period size: 41 Copynumber: 5.8 Consensus size: 41
3589797 GAATATAATA
* *
3589807 CAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTT
*
3589848 CAGACTTTAAGTCTAGCAGGCTAAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
3589889 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
3589930 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* * ** *
3589971 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTGTATTGA-AT
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTG-ATACATTT
* * **
3590012 CAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
3590046 ATCTGTTTAA
Statistics
Matches: 179, Mismatches: 14, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.01
40 6 0.03
41 166 0.93
42 5 0.03
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:3590028 original size:123 final size:123
Alignment explanation
Indices: 3589817--3590045 Score: 320
Period size: 123 Copynumber: 1.9 Consensus size: 123
3589807 CAGACGTTAC
*
3589817 GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTGA
1 GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTATAAGTCTAGCAGGCTAAATGCCGGTGA
* * **
3589882 TACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
66 TACATATCAGACTTTAAGCCTAGCAGGCAAAATGCCGGTGATACATTTCAGACTATAT
* *
3589940 GTCTAGCAGGCTTAATGCCGGTG-A-TACATTTCAGACTATATGTCTAGCAGGCTAAGTGCCGGT
1 GTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTATAAGTCTAGCAGGCTAAATGCCGGT
** *
3590003 GTATTGA-ATCAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
64 G-ATACATATCAGACTTTAAGCCTAGCAGGCAAAATGCCGGTGA
3590046 ATCTGTTTAA
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
121 2 0.02
122 2 0.02
123 86 0.92
124 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (123 bp):
GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTATAAGTCTAGCAGGCTAAATGCCGGTGA
TACATATCAGACTTTAAGCCTAGCAGGCAAAATGCCGGTGATACATTTCAGACTATAT
Found at i:3597547 original size:82 final size:80
Alignment explanation
Indices: 3597442--3597680 Score: 293
Period size: 82 Copynumber: 2.9 Consensus size: 80
3597432 GAATATAATA
* *
3597442 CAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTAA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TAATTCAGACTTTAAGTCTAGCAGGCTAA
3597507 ATGCCGGTGATACATTT
64 ATGCCGGTGATACATTT
* * *
3597524 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATA-A-TTCAGACTTTAAGTCTAGCAGGCTAA
3597589 ATGCCGGTGATACATTT
64 ATGCCGGTGATACATTT
* * * * **
3597606 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTGTATTGAA-TCAGGCTTTAAGCCTAGCAGGAA
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTG-A-T-AATTCAGACTTTAAGTCTAGCAGGCT
3597669 AAATGCCGGTGA
62 AAATGCCGGTGA
3597681 ATCTGTTTAA
Statistics
Matches: 137, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
80 2 0.01
81 5 0.04
82 126 0.92
83 1 0.01
84 2 0.01
85 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (80 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATAATTCAGACTTTAAGTCTAGCAGGCTAAAT
GCCGGTGATACATTT
Found at i:3597663 original size:123 final size:123
Alignment explanation
Indices: 3597452--3597680 Score: 311
Period size: 123 Copynumber: 1.9 Consensus size: 123
3597442 CAGACGTTAC
*
3597452 GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTAAATGCCGGTGA
1 GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTATAAGTCTAGCAGGCTAAATGCCGGTGA
* * ***
3597517 TACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
66 TACATATCAGACTTTAAGCCTAGCAGGAAAAATGCCGGTGATACATTTCAGACTATAT
* *
3597575 GTCTAGCAGGCTTAATGCCGGTG-A-TACATTTCAGACTATATGTCTAGCAGGCTAAGTGCCGGT
1 GTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTATAAGTCTAGCAGGCTAAATGCCGGT
** *
3597638 GTATTGA-ATCAGGCTTTAAGCCTAGCAGGAAAAATGCCGGTGA
64 G-ATACATATCAGACTTTAAGCCTAGCAGGAAAAATGCCGGTGA
3597681 ATCTGTTTAA
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
121 2 0.02
122 2 0.02
123 85 0.92
124 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (123 bp):
GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTATAAGTCTAGCAGGCTAAATGCCGGTGA
TACATATCAGACTTTAAGCCTAGCAGGAAAAATGCCGGTGATACATTTCAGACTATAT
Found at i:3597666 original size:41 final size:41
Alignment explanation
Indices: 3597442--3597638 Score: 283
Period size: 41 Copynumber: 4.8 Consensus size: 41
3597432 GAATATAATA
* *
3597442 CAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTT
*
3597483 CAGACTTTAAGTCTAGCAGGCTAAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
3597524 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
3597565 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
3597606 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTG
3597639 TATTGAATCA
Statistics
Matches: 147, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
39 2 0.01
40 5 0.03
41 140 0.95
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:3599182 original size:2 final size:2
Alignment explanation
Indices: 3599177--3599202 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3599167 TGTGTGATTG
3599177 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
3599203 GAGTGAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3610294 original size:27 final size:25
Alignment explanation
Indices: 3610247--3610307 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
3610237 ATAATAAAAA
* *
3610247 AATA-ATAAATAATATATAATAATTT
1 AATATATAAATAATATAAAATAA-AT
3610272 ACATATATAAAT-ATAGTAAAATAAAT
1 A-ATATATAAATAATA-TAAAATAAAT
3610298 AATATATAAA
1 AATATATAAA
3610308 GTAAAATGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 10 0.32
26 8 0.26
27 13 0.42
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (25 bp):
AATATATAAATAATATAAAATAAAT
Found at i:3610327 original size:21 final size:21
Alignment explanation
Indices: 3610274--3610328 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3610264 AATAATTTAC
*
3610274 ATATATAAATATAGTAAAATAA
1 ATATAT-AATAAAGTAAAATAA
**
3610296 ATA-ATATATAAAGTAAAATGT
1 ATATATA-ATAAAGTAAAATAA
3610317 ATATATAATAAA
1 ATATATAATAAA
3610329 AATTTATAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.04
21 21 0.75
22 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
ATATATAATAAAGTAAAATAA
Found at i:3615411 original size:21 final size:21
Alignment explanation
Indices: 3615370--3615413 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3615360 AAGCTTATAT
* **
3615370 AACTTATTAATTACGGGAAAA
1 AACTTATTAATTAAGAAAAAA
3615391 AACTTATTAATTAAGAAAAAA
1 AACTTATTAATTAAGAAAAAA
3615412 AA
1 AA
3615414 TCATATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.57, C:0.07, G:0.09, T:0.27
Consensus pattern (21 bp):
AACTTATTAATTAAGAAAAAA
Done.