Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 77 of 97
Found at i:30663375 original size:71 final size:70
Alignment explanation
Indices: 30663299--30663451 Score: 225
Period size: 71 Copynumber: 2.2 Consensus size: 70
30663289 TCTCAAGTAC
* * * *
30663299 TTGATTGAAATTGTTTAATTAAGTTGTTGGGCTTAATTAATTAAATTGTTTATTTAAATCATTGG
1 TTGATT-AAATTGTTTAATTAAGTTATTGAGCTTAATTAATTAAATTATTTAATTAAATCATTGG
30663364 GCCTAA
65 GCCTAA
* *
30663370 TTGATTAAAATTGTTTAATTAAGTTATTGAGCTTAATTAATTAAATTATTTAATTAAGTTATTGG
1 TTGATT-AAATTGTTTAATTAAGTTATTGAGCTTAATTAATTAAATTATTTAATTAAATCATTGG
30663435 GCCTAA
65 GCCTAA
*
30663441 TTAATTAAATT
1 TTGATTAAATT
30663452 AAACAATTAA
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
70 5 0.07
71 69 0.93
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (70 bp):
TTGATTAAATTGTTTAATTAAGTTATTGAGCTTAATTAATTAAATTATTTAATTAAATCATTGGG
CCTAA
Found at i:30663452 original size:35 final size:35
Alignment explanation
Indices: 30663306--30663451 Score: 202
Period size: 35 Copynumber: 4.1 Consensus size: 35
30663296 TACTTGATTG
* *
30663306 AAATTGTTTAATTAAGTTGTTGGGCTTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * * *
30663341 AAATTGTTTATTTAAATCATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* *
30663376 AAAATTGTTTAATTAAGTTATTGAGCTTAATTAATT
1 -AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
*
30663412 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
30663447 AAATT
1 AAATT
30663452 AAACAATTAA
Statistics
Matches: 95, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 66 0.69
36 29 0.31
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.47
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
Found at i:30663460 original size:35 final size:35
Alignment explanation
Indices: 30663306--30663470 Score: 186
Period size: 35 Copynumber: 4.7 Consensus size: 35
30663296 TACTTGATTG
* * *
30663306 AAATTGTTTAATTAAGTTGTTGGGCTTAATTAATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* * * * *
30663341 AAATTGTTTATTTAAATCATTGGGCCTAATTGATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* * *
30663376 AAAATTGTTTAATTAAGTTATTGAGCTTAATTAATT
1 -AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
30663412 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
***
30663447 AAATTAAACAATTAAGTTAGTTGG
1 AAATTATTTAATTAAGTTA-TTGG
30663471 ACTTCTTAAG
Statistics
Matches: 110, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
35 77 0.70
36 33 0.30
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (35 bp):
AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
Found at i:30665487 original size:31 final size:31
Alignment explanation
Indices: 30665449--30665511 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
30665439 ATGCGGCCAA
30665449 AGGGGAATCTCAACTTTACATCAAAAAGTTT
1 AGGGGAATCTCAACTTTACATCAAAAAGTTT
30665480 AGGGGAATCTCAACTTTACATCAAAAAGTTT
1 AGGGGAATCTCAACTTTACATCAAAAAGTTT
30665511 A
1 A
30665512 ACTCTTAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (31 bp):
AGGGGAATCTCAACTTTACATCAAAAAGTTT
Found at i:30668952 original size:44 final size:44
Alignment explanation
Indices: 30668902--30669002 Score: 175
Period size: 44 Copynumber: 2.3 Consensus size: 44
30668892 CAGGTCCAAT
*
30668902 TGTTTTCTTTGTTATTCCCCAATTGAAAGAACGAATAACTGAGA
1 TGTTTTCTTTGTTATTCCCCAATTGAAAGAACAAATAACTGAGA
* *
30668946 TGTTTTCTTTGTTCTTCCCCAATTGAAAGAACAAATAAGTGAGA
1 TGTTTTCTTTGTTATTCCCCAATTGAAAGAACAAATAACTGAGA
30668990 TGTTTTCTTTGTT
1 TGTTTTCTTTGTT
30669003 TTTGCTAATC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.42
Consensus pattern (44 bp):
TGTTTTCTTTGTTATTCCCCAATTGAAAGAACAAATAACTGAGA
Found at i:30673382 original size:19 final size:19
Alignment explanation
Indices: 30673358--30673395 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
30673348 ACTTCTAAAC
30673358 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
30673377 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
30673396 AGTCAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:30675862 original size:20 final size:20
Alignment explanation
Indices: 30675817--30675854 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
30675807 TTTTTAGTCC
30675817 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
30675837 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
30675855 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:30675938 original size:27 final size:27
Alignment explanation
Indices: 30675908--30675965 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
30675898 TTGGAGTAAA
*
30675908 AGGGTAAAATGGTAATTTTGCCACC-CC
1 AGGGCAAAATGGTAATTTT-CCACCACC
*
30675935 AGGGGCAAAATTGTAATTTTCCACCACC
1 A-GGGCAAAATGGTAATTTTCCACCACC
30675963 AGG
1 AGG
30675966 ACATTTTTNN
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (27 bp):
AGGGCAAAATGGTAATTTTCCACCACC
Found at i:30678926 original size:70 final size:70
Alignment explanation
Indices: 30678809--30678950 Score: 178
Period size: 70 Copynumber: 2.0 Consensus size: 70
30678799 GTAGAACAAC
** * * *
30678809 TGAAGCACTATTTCACGCAGAACAACTAAAATAAGTGAAATACTACTTCACGC-AGGACAACTAA
1 TGAAGCACTATTTCACAAAAAACAACTAAAATAAGTGAAACACTACTTCACGCGA-AACAACTAA
30678873 AATAAG
65 AATAAG
* * * * *
30678879 TGAAGCACTATTTCACAAAAAACAACTACAATAAGTGGAGCATTACTTCACGCGAAACAACTAGA
1 TGAAGCACTATTTCACAAAAAACAACTAAAATAAGTGAAACACTACTTCACGCGAAACAACTAAA
30678944 ATAAG
66 ATAAG
30678949 TG
1 TG
30678951 GAACAACCAC
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
70 60 0.98
71 1 0.02
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (70 bp):
TGAAGCACTATTTCACAAAAAACAACTAAAATAAGTGAAACACTACTTCACGCGAAACAACTAAA
ATAAG
Found at i:30678952 original size:35 final size:35
Alignment explanation
Indices: 30678809--30678950 Score: 160
Period size: 35 Copynumber: 4.1 Consensus size: 35
30678799 GTAGAACAAC
*
30678809 TGAAGCACTATTTCACGCAGAACAACTAAAATAAG
1 TGAAGCACTACTTCACGCAGAACAACTAAAATAAG
** *
30678844 TGAAATACTACTTCACGCAGGACAACTAAAATAAG
1 TGAAGCACTACTTCACGCAGAACAACTAAAATAAG
* ** * *
30678879 TGAAGCACTATTTCACAAAAAACAACTACAATAAG
1 TGAAGCACTACTTCACGCAGAACAACTAAAATAAG
* * *
30678914 TGGAGCATTACTTCACGC-GAAACAACTAGAATAAG
1 TGAAGCACTACTTCACGCAG-AACAACTAAAATAAG
30678949 TG
1 TG
30678951 GAACAACCAC
Statistics
Matches: 87, Mismatches: 19, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
35 87 1.00
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (35 bp):
TGAAGCACTACTTCACGCAGAACAACTAAAATAAG
Found at i:30679194 original size:29 final size:29
Alignment explanation
Indices: 30679125--30679195 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
30679115 TTTCCCTCTT
* * *
30679125 ACCTTATTCTCATGTACCTGTTTATGTAC
1 ACCTTATTCTCTTGTACCTATTCATGTAC
* *
30679154 ACCTTCTTCTCTTGTCCCTATTCATGTAC
1 ACCTTATTCTCTTGTACCTATTCATGTAC
*
30679183 ACCTTTTTCTCTT
1 ACCTTATTCTCTT
30679196 AACTTGCTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.15, C:0.30, G:0.07, T:0.48
Consensus pattern (29 bp):
ACCTTATTCTCTTGTACCTATTCATGTAC
Found at i:30679863 original size:74 final size:74
Alignment explanation
Indices: 30679764--30679902 Score: 197
Period size: 74 Copynumber: 1.9 Consensus size: 74
30679754 ATAAATGAAA
* * * * * *
30679764 TAAATCTTACTAATAGTTATAATAAAAAATATTTCAATTATCATCATTTGATAAATACACATTTA
1 TAAATATTACAAATAATTACAATAAAAAATATTTCAATGATCATCATTTAATAAATACACATTTA
30679829 CAATAGGCT
66 CAATAGGCT
* * *
30679838 TAAATATTACAAATAATTACAATAAAAAATATTTCAATGATCTTCATTTAATGAATACATATTTA
1 TAAATATTACAAATAATTACAATAAAAAATATTTCAATGATCATCATTTAATAAATACACATTTA
30679903 TGAGTATAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
74 56 1.00
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (74 bp):
TAAATATTACAAATAATTACAATAAAAAATATTTCAATGATCATCATTTAATAAATACACATTTA
CAATAGGCT
Found at i:30686515 original size:102 final size:101
Alignment explanation
Indices: 30686364--30686694 Score: 315
Period size: 102 Copynumber: 3.2 Consensus size: 101
30686354 ATCGCTTTTA
* * * * * * *
30686364 ATTTGGTTACAATTATATTATACTATTGATCGCAAGCTTTA-CAGCTCATTCTTTGGCCATAGTT
1 ATTTGGCTGCAATGATATTATGCTATTGATCACAAGCTTTATC-GTTCATTCTTTGACCATAGTT
* *
30686428 CATCATTTTTATTTCAGCCACGAGCTTTACTGCTCAT
65 CATCATTCTTATTTCAGCCACAAGCTTTACTGCTCAT
** * *
30686465 ACTTTGGCTATAATGATATTATGCTATTAATCACAAGCTTTATCGTTCATTCTTTGACCATAGCT
1 A-TTTGGCTGCAATGATATTATGCTATTGATCACAAGCTTTATCGTTCATTCTTTGACCATAGTT
* ** **
30686530 CATCACTCTTGCTTCAATCACAAGCTTTACTGCTCATT
65 CATCATTCTTATTTCAGCCACAAGCTTTACTGCTCA-T
* * ** * * *
30686568 TTTTGGCTGCAATGATATTTTTTTATTGGTCACAAGTTTTATCGCTT-ATTCTTTGACCATAATT
1 ATTTGGCTGCAATGATATTATGCTATTGATCACAAGCTTTATCG-TTCATTCTTTGACCATAGTT
* * * * *
30686632 CATCATTCATATTTTAGCCACTAGCTTGATTGCTCATT
65 CATCATTCTTATTTCAGCCACAAGCTTTACTGCTCA-T
* *
30686670 ATTTAGCTGCAATGATGTTATGCTA
1 ATTTGGCTGCAATGATATTATGCTA
30686695 GCGACCGCAA
Statistics
Matches: 183, Mismatches: 43, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
101 1 0.01
102 178 0.97
103 4 0.02
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.43
Consensus pattern (101 bp):
ATTTGGCTGCAATGATATTATGCTATTGATCACAAGCTTTATCGTTCATTCTTTGACCATAGTTC
ATCATTCTTATTTCAGCCACAAGCTTTACTGCTCAT
Found at i:30686567 original size:52 final size:50
Alignment explanation
Indices: 30686396--30686574 Score: 139
Period size: 52 Copynumber: 3.5 Consensus size: 50
30686386 CTATTGATCG
* * ** **
30686396 CAAGCTTTACAGCTCATTCTTTGGCCATAGTTCATCATTTTTATTTCAGCCA
1 CAAGCTTTACTGCTCATTCTTTGGCCATAGATCATCA--TTTGCTTCAATCA
* * * * *
30686448 CGAGCTTTACTGCTCATACTTTGGCTATA-ATGAT-ATTATGCTATTAATCA
1 CAAGCTTTACTGCTCATTCTTTGGCCATAGATCATCATT-TGCT-TCAATCA
* * *
30686498 CAAGCTTTA-TCGTTCATTCTTTGACCATAGCTCATCACTCTTGCTTCAATCA
1 CAAGCTTTACT-GCTCATTCTTTGGCCATAGATCATCA-T-TTGCTTCAATCA
*
30686550 CAAGCTTTACTGCTCATTTTTTGGC
1 CAAGCTTTACTGCTCATTCTTTGGC
30686575 TGCAATGATA
Statistics
Matches: 97, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
48 2 0.02
49 3 0.03
50 27 0.28
51 6 0.06
52 52 0.54
53 6 0.06
54 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.40
Consensus pattern (50 bp):
CAAGCTTTACTGCTCATTCTTTGGCCATAGATCATCATTTGCTTCAATCA
Found at i:30688923 original size:34 final size:34
Alignment explanation
Indices: 30688874--30688958 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
30688864 AGAATAACAA
* *
30688874 GAACAACTAGGACAAGTAAGCACTAATTCACGTT
1 GAACAACTAGAACAAGTAAGCACTAATTCACGCT
*
30688908 GAACAATTAGAACAAGTAAGCACTAATTCACGCT
1 GAACAACTAGAACAAGTAAGCACTAATTCACGCT
*
30688942 GAACAACTACAACAAGT
1 GAACAACTAGAACAAGT
30688959 GAAAGTACTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (34 bp):
GAACAACTAGAACAAGTAAGCACTAATTCACGCT
Found at i:30689006 original size:35 final size:36
Alignment explanation
Indices: 30688943--30689030 Score: 124
Period size: 35 Copynumber: 2.5 Consensus size: 36
30688933 ATTCACGCTG
*
30688943 AACAACTACAACAAGTGAAAGTACTACTTCACTCAA
1 AACAACTAAAACAAGTGAAAGTACTACTTCACTCAA
* *
30688979 ATCAACTAAAACAAGT-AAAGTAGTACTTCACTCAA
1 AACAACTAAAACAAGTGAAAGTACTACTTCACTCAA
* *
30689014 AACAACTAGAATAAGTG
1 AACAACTAAAACAAGTG
30689031 GAGCATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 31 0.69
36 14 0.31
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.20
Consensus pattern (36 bp):
AACAACTAAAACAAGTGAAAGTACTACTTCACTCAA
Found at i:30690563 original size:25 final size:25
Alignment explanation
Indices: 30690507--30690563 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
30690497 TGGCCTTTGC
30690507 CTCTTTGTCGATTGCAACTTCTCTT
1 CTCTTTGTCGATTGCAACTTCTCTT
* *
30690532 TTTTTTGTCGACTAT-C-ACTTCTCTT
1 CTCTTTGTCGA-T-TGCAACTTCTCTT
30690557 CTCTTTG
1 CTCTTTG
30690564 CCATGATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
25 23 0.88
26 2 0.08
27 1 0.04
ACGTcount: A:0.11, C:0.26, G:0.11, T:0.53
Consensus pattern (25 bp):
CTCTTTGTCGATTGCAACTTCTCTT
Found at i:30691092 original size:2 final size:2
Alignment explanation
Indices: 30691085--30691117 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
30691075 TCTATATTTC
*
30691085 TA TA TA TA CA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30691118 AACTTGAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:30695930 original size:15 final size:15
Alignment explanation
Indices: 30695910--30695941 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30695900 TTTCTTTCTG
30695910 TTTATTTTTTTATTT
1 TTTATTTTTTTATTT
*
30695925 TTTATTTTTTTGTTT
1 TTTATTTTTTTATTT
30695940 TT
1 TT
30695942 CAATGGGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (15 bp):
TTTATTTTTTTATTT
Found at i:30734379 original size:72 final size:72
Alignment explanation
Indices: 30734285--30734420 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 72
30734275 TCCCATGCTT
* * * * * *
30734285 ATGCTTATGACTCTCCTGATTTTGCTACAACGTATACCTCACTAAGTATACATGCTGACCAAGTA
1 ATGCTGATGACTCTCCTAATTTTACTACAACATATACCTCACTAAGTATACATGCAGACAAAGTA
30734350 CTCTACC
66 CTCTACC
* * *
30734357 ATGCTGATGACTTTCCTAATTTTACTACAACATATACTTGACTAAGTATACATGCAGACAAAGT
1 ATGCTGATGACTCTCCTAATTTTACTACAACATATACCTCACTAAGTATACATGCAGACAAAGT
30734421 TTCTCTCAAC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 55 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (72 bp):
ATGCTGATGACTCTCCTAATTTTACTACAACATATACCTCACTAAGTATACATGCAGACAAAGTA
CTCTACC
Found at i:30747507 original size:21 final size:22
Alignment explanation
Indices: 30747464--30747507 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
30747454 GGAAAACATA
* *
30747464 AAAAGAAATGTAAAAGCTTACC
1 AAAAGAAATGCAAAAGCTAACC
*
30747486 AAAAGAAA-GCAAAATCTAACC
1 AAAAGAAATGCAAAAGCTAACC
30747507 A
1 A
30747508 TAAAATCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.59, C:0.16, G:0.11, T:0.14
Consensus pattern (22 bp):
AAAAGAAATGCAAAAGCTAACC
Found at i:30755809 original size:2 final size:2
Alignment explanation
Indices: 30755802--30755842 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
30755792 ATAGATATCA
30755802 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30755843 ATAATANNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30756793 original size:2 final size:2
Alignment explanation
Indices: 30756786--30756819 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30756776 NNNNNNNNNN
30756786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30756820 TAAATTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30757352 original size:2 final size:2
Alignment explanation
Indices: 30757347--30757381 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
30757337 CAAAAAACTC
* *
30757347 AT AT AT CT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30757382 AATCAAACAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30767455 original size:16 final size:16
Alignment explanation
Indices: 30767434--30767470 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
30767424 CAAGATATTT
30767434 TCTTCTTCTTCTTGAA
1 TCTTCTTCTTCTTGAA
30767450 TCTTCTTCTTCTTGAA
1 TCTTCTTCTTCTTGAA
*
30767466 GCTTC
1 TCTTC
30767471 CAATGCCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.27, G:0.08, T:0.54
Consensus pattern (16 bp):
TCTTCTTCTTCTTGAA
Found at i:30768629 original size:35 final size:35
Alignment explanation
Indices: 30768583--30768729 Score: 213
Period size: 35 Copynumber: 4.2 Consensus size: 35
30768573 AGTGTGGATA
* * *
30768583 ATGATATTGAAGTGTGTGAGTAGAGAGTGCACAGG
1 ATGATATTGAAGTGTGCGAGTAGGGAGTGCACACG
* *
30768618 ATGATGTTGAAGTGTACGAGTAGGGAGTGCACACG
1 ATGATATTGAAGTGTGCGAGTAGGGAGTGCACACG
30768653 ATGATATTGAAGTGTGCGAGTAGGGAGTGCACACG
1 ATGATATTGAAGTGTGCGAGTAGGGAGTGCACACG
* * * *
30768688 ATGTTATAGAAATGTGCGAGTAGGGAGTGCACATG
1 ATGATATTGAAGTGTGCGAGTAGGGAGTGCACACG
30768723 ATGATAT
1 ATGATAT
30768730 ATAGTGTGCG
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 100 1.00
ACGTcount: A:0.31, C:0.09, G:0.35, T:0.25
Consensus pattern (35 bp):
ATGATATTGAAGTGTGCGAGTAGGGAGTGCACACG
Found at i:30771739 original size:21 final size:21
Alignment explanation
Indices: 30771715--30771756 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
30771705 AAAACATGTG
*
30771715 ACACGACATGGTTAGGTTGTT
1 ACACGACATGATTAGGTTGTT
*
30771736 ACACGCCATGATTAGGTTGTT
1 ACACGACATGATTAGGTTGTT
30771757 TATACGCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (21 bp):
ACACGACATGATTAGGTTGTT
Found at i:30771745 original size:45 final size:45
Alignment explanation
Indices: 30771552--30771745 Score: 271
Period size: 45 Copynumber: 4.3 Consensus size: 45
30771542 CACGCCATGA
* * * * * **
30771552 TGTTACACGTCATGTACAAAAACATGTTATATGCCATAATTAGGT
1 TGTTACACGCCATGTACAAAAACATGTGACACGACATGGTTAGGT
* * **
30771597 TGTTATACGCCATATACAAAAACATGTGACACGTTATGGTTAGGT
1 TGTTACACGCCATGTACAAAAACATGTGACACGACATGGTTAGGT
*
30771642 TGTTACACGCCATATACAAAAACATGTGACACGACATGGTTAGGT
1 TGTTACACGCCATGTACAAAAACATGTGACACGACATGGTTAGGT
*
30771687 TGTTATACGCCATGTACAAAAACATGTGACACGACATGGTTAGGT
1 TGTTACACGCCATGTACAAAAACATGTGACACGACATGGTTAGGT
30771732 TGTTACACGCCATG
1 TGTTACACGCCATG
30771746 ATTAGGTTGT
Statistics
Matches: 133, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 133 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (45 bp):
TGTTACACGCCATGTACAAAAACATGTGACACGACATGGTTAGGT
Found at i:30771771 original size:67 final size:66
Alignment explanation
Indices: 30771670--30771871 Score: 307
Period size: 67 Copynumber: 3.0 Consensus size: 66
30771660 AAAACATGTG
30771670 ACACGACATGGTTAGGTTGTTATACGCCATGTACAAAAACATGTGACACGACATGGTTAGGTTGT
1 ACACGACATGGTTAGGTTGTTATACGCCATGTACAAAAACATGTGACACGACATGGTTAGGTTGT
30771735 T
66 T
* * *
30771736 ACACGCCATGATTAGGTTGTTTATACGCTATGTACAAAAACATGTGACACGACATGGTTAGGTTG
1 ACACGACATGGTTAGGTTG-TTATACGCCATGTACAAAAACATGTGACACGACATGGTTAGGTTG
30771801 TT
65 TT
* * * * *
30771803 ACACGTCATGGTTAAGTTGTTACACGCCATGTACAAAAACATGTGACAC-ACCATAGTTAAGTTG
1 ACACGACATGGTTAGGTTGTTATACGCCATGTACAAAAACATGTGACACGA-CATGGTTAGGTTG
30771867 TT
65 TT
30771869 ACA
1 ACA
30771872 TGTCATGTAC
Statistics
Matches: 124, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
65 1 0.01
66 61 0.49
67 62 0.50
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (66 bp):
ACACGACATGGTTAGGTTGTTATACGCCATGTACAAAAACATGTGACACGACATGGTTAGGTTGT
T
Found at i:30771812 original size:21 final size:21
Alignment explanation
Indices: 30771782--30771833 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
30771772 AAAACATGTG
*
30771782 ACACGACATGGTTAGGTTGTT
1 ACACGACATGGTTAAGTTGTT
*
30771803 ACACGTCATGGTTAAGTTGTT
1 ACACGACATGGTTAAGTTGTT
*
30771824 ACACGCCATG
1 ACACGACATG
30771834 TACAAAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (21 bp):
ACACGACATGGTTAAGTTGTT
Found at i:30771871 original size:66 final size:66
Alignment explanation
Indices: 30771670--30771878 Score: 312
Period size: 66 Copynumber: 3.2 Consensus size: 66
30771660 AAAACATGTG
*
30771670 ACACGACATGGTTAGGTTGTTATACGCCATGTACAAAAACATGTGACACGACATGGTTAGGTTGT
1 ACACGTCATGGTTAGGTTGTTATACGCCATGTACAAAAACATGTGACACGACATGGTTAGGTTGT
30771735 T
66 T
* * *
30771736 ACACGCCATGATTAGGTTGTTTATACGCTATGTACAAAAACATGTGACACGACATGGTTAGGTTG
1 ACACGTCATGGTTAGGTTG-TTATACGCCATGTACAAAAACATGTGACACGACATGGTTAGGTTG
30771801 TT
65 TT
* * * *
30771803 ACACGTCATGGTTAAGTTGTTACACGCCATGTACAAAAACATGTGACAC-ACCATAGTTAAGTTG
1 ACACGTCATGGTTAGGTTGTTATACGCCATGTACAAAAACATGTGACACGA-CATGGTTAGGTTG
30771867 TT
65 TT
*
30771869 ACATGTCATG
1 ACACGTCATG
30771879 TACAAAAATA
Statistics
Matches: 130, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
65 1 0.01
66 67 0.52
67 62 0.48
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (66 bp):
ACACGTCATGGTTAGGTTGTTATACGCCATGTACAAAAACATGTGACACGACATGGTTAGGTTGT
T
Found at i:30771938 original size:24 final size:24
Alignment explanation
Indices: 30771910--30771965 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
30771900 ATGGTTAGGT
30771910 TGTTACACATCATGTACAAAAACA
1 TGTTACACATCATGTACAAAAACA
**
30771934 TGTTACATGTCATGTACAAAAACA
1 TGTTACACATCATGTACAAAAACA
*
30771958 TGTGACAC
1 TGTTACAC
30771966 GACATGCTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (24 bp):
TGTTACACATCATGTACAAAAACA
Found at i:30771946 original size:45 final size:45
Alignment explanation
Indices: 30771552--30771947 Score: 234
Period size: 45 Copynumber: 8.8 Consensus size: 45
30771542 CACGCCATGA
* * * * ** *
30771552 TGTTACACGTCATGTACAAAAACATGTTATATGCCATAATTAGGT
1 TGTTACACGTCATGTACAAAAACATGTGACACGTCATGGTTAAGT
* * * * *
30771597 TGTTATACGCCATATACAAAAACATGTGACACGTTATGGTTAGGT
1 TGTTACACGTCATGTACAAAAACATGTGACACGTCATGGTTAAGT
* * * *
30771642 TGTTACACGCCATATACAAAAACATGTGACACGACATGGTTAGGT
1 TGTTACACGTCATGTACAAAAACATGTGACACGTCATGGTTAAGT
* * * *
30771687 TGTTATACGCCATGTACAAAAACATGTGACACGACATGGTTAGGT
1 TGTTACACGTCATGTACAAAAACATGTGACACGTCATGGTTAAGT
* ** *** * * * **
30771732 TGTTACACGCCATG---ATTAGGTTGTTTATACG-CTAT-GTACAAAAACA
1 TGTTACACGTCATGTACAAAAACATG-TGACACGTC-ATGGT----TAAGT
* * * *** *
30771778 TGTGACACGACATGGT----TAGGTTGTTACACGTCATGGTTAAGT
1 TGTTACACGTCAT-GTACAAAAACATGTGACACGTCATGGTTAAGT
* ** *
30771820 TGTTACACGCCATGTACAAAAACATGTGACACACCATAGTTAAGT
1 TGTTACACGTCATGTACAAAAACATGTGACACGTCATGGTTAAGT
* * *
30771865 TGTTACATGTCATGTACAAAAATATGTGACACGTCATGGTTAGGT
1 TGTTACACGTCATGTACAAAAACATGTGACACGTCATGGTTAAGT
* * *
30771910 TGTTACACATCATGTACAAAAACATGTTACATGTCATG
1 TGTTACACGTCATGTACAAAAACATGTGACACGTCATG
30771948 TACAAAAACA
Statistics
Matches: 282, Mismatches: 55, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
41 2 0.01
42 20 0.07
43 7 0.02
45 230 0.82
46 22 0.08
47 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (45 bp):
TGTTACACGTCATGTACAAAAACATGTGACACGTCATGGTTAAGT
Found at i:30771971 original size:24 final size:24
Alignment explanation
Indices: 30771920--30771971 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
30771910 TGTTACACAT
* * *
30771920 CATGTACAAAAACATGTTACATGT
1 CATGTACAAAAACATGTGACACGA
30771944 CATGTACAAAAACATGTGACACGA
1 CATGTACAAAAACATGTGACACGA
30771968 CATG
1 CATG
30771972 CTTAGGTTAT
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:0.42, C:0.19, G:0.15, T:0.23
Consensus pattern (24 bp):
CATGTACAAAAACATGTGACACGA
Found at i:30771986 original size:21 final size:21
Alignment explanation
Indices: 30771962--30772008 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
30771952 AAAACATGTG
30771962 ACACGACATGCTTAGGTTATT
1 ACACGACATGCTTAGGTTATT
** * *
30771983 ACACTCCATGGTTAGGTTGTT
1 ACACGACATGCTTAGGTTATT
30772004 ACACG
1 ACACG
30772009 TTACGTACAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (21 bp):
ACACGACATGCTTAGGTTATT
Found at i:30772025 original size:180 final size:177
Alignment explanation
Indices: 30771625--30772096 Score: 574
Period size: 180 Copynumber: 2.6 Consensus size: 177
30771615 AAAACATGTG
* *
30771625 ACACGTTATGGTTAGGTTGTTACACGCCATATACAAAAACATGTGACACGA-CATGGTTAGGTTG
1 ACACGTCATGGTTAGGTTGTTACACGCCATGTACAAAAACATGTGACAC-ACCATGGTTAGGTTG
* * * ** ***
30771689 TTATACGCCATGTACAAAAACATGTGACACGACATGGTTAGGTTGTTACACGCCATGATTAGGTT
65 TTACACG-CATGTACAAAAATATGTGACACGACATGGTTAGGTTGTTACACACCATGAAAAACAT
* * *
30771754 GTTTATACGCTATGTACAAAAACATGTGACACGACATGGTTAGGTTGTT
129 GTTTACACGCTATGTACAAAAACATGTGACACGACATGCTTAGGTTATT
* * *
30771803 ACACGTCATGGTTAAGTTGTTACACGCCATGTACAAAAACATGTGACACACCATAGTTAAGTTGT
1 ACACGTCATGGTTAGGTTGTTACACGCCATGTACAAAAACATGTGACACACCATGGTTAGGTTGT
* * *
30771868 TACATGTCATGTACAAAAATATGTGACACGTCATGGTTAGGTTGTTACACATCATGTACAAAAAC
66 TACACG-CATGTACAAAAATATGTGACACGACATGGTTAGGTTGTTACACACCATG---AAAAAC
*
30771933 ATG-TTACATG-TCATGTACAAAAACATGTGACACGACATGCTTAGGTTATT
127 ATGTTTACACGCT-ATGTACAAAAACATGTGACACGACATGCTTAGGTTATT
** * **
30771983 ACAC-TCCATGGTTAGGTTGTTACACGTTACGTACAAAAACATGTGACATGCCATGGTTAGGTTG
1 ACACGT-CATGGTTAGGTTGTTACACGCCATGTACAAAAACATGTGACACACCATGGTTAGGTTG
* * * *
30772047 TTTCACGCTATATACAAAAATATGTGATACGCCATGGTTAGGTTGTTACA
65 TTACACGC-ATGTACAAAAATATGTGACACGACATGGTTAGGTTGTTACA
30772097 TGCCATATTG
Statistics
Matches: 253, Mismatches: 34, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
177 1 0.00
178 107 0.42
179 3 0.01
180 138 0.55
181 4 0.02
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (177 bp):
ACACGTCATGGTTAGGTTGTTACACGCCATGTACAAAAACATGTGACACACCATGGTTAGGTTGT
TACACGCATGTACAAAAATATGTGACACGACATGGTTAGGTTGTTACACACCATGAAAAACATGT
TTACACGCTATGTACAAAAACATGTGACACGACATGCTTAGGTTATT
Found at i:30772039 original size:45 final size:45
Alignment explanation
Indices: 30771983--30772096 Score: 156
Period size: 45 Copynumber: 2.5 Consensus size: 45
30771973 TTAGGTTATT
* * *
30771983 ACACTCCATGGTTAGGTTGTTACACGTTACGTACAAAAACATGTG
1 ACACGCCATGGTTAGGTTGTTACACGCTACATACAAAAACATGTG
* * * *
30772028 ACATGCCATGGTTAGGTTGTTTCACGCTATATACAAAAATATGTG
1 ACACGCCATGGTTAGGTTGTTACACGCTACATACAAAAACATGTG
*
30772073 ATACGCCATGGTTAGGTTGTTACA
1 ACACGCCATGGTTAGGTTGTTACA
30772097 TGCCATATTG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (45 bp):
ACACGCCATGGTTAGGTTGTTACACGCTACATACAAAAACATGTG
Found at i:30772124 original size:31 final size:29
Alignment explanation
Indices: 30772088--30772184 Score: 126
Period size: 29 Copynumber: 3.3 Consensus size: 29
30772078 CCATGGTTAG
* *
30772088 GTTGTTACATGCCATATTGAAAAAAAATATT
1 GTTGTTACACGTCATATTG--AAAAAATATT
*
30772119 GTTGTTACACGTCATGTTGAAAAAATATT
1 GTTGTTACACGTCATATTGAAAAAATATT
*
30772148 ATTGTTACACGTCATATT-AAAAAATATT
1 GTTGTTACACGTCATATTGAAAAAATATT
30772176 -TTGTTACAC
1 GTTGTTACAC
30772185 TTTAATACCT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
27 9 0.15
28 10 0.16
29 26 0.43
31 16 0.26
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (29 bp):
GTTGTTACACGTCATATTGAAAAAATATT
Found at i:30773193 original size:24 final size:24
Alignment explanation
Indices: 30773161--30773207 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
30773151 AGTTTCCAAA
* *
30773161 TTTTAAAATTAAATTTTTTAGGGT
1 TTTTAAAATTAAAGTTTTGAGGGT
*
30773185 TTTTTAAATTAAAGTTTTGAGGG
1 TTTTAAAATTAAAGTTTTGAGGG
30773208 AATGATGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
TTTTAAAATTAAAGTTTTGAGGGT
Found at i:30783519 original size:2 final size:2
Alignment explanation
Indices: 30783512--30783553 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
30783502 CCTGAAAAGA
30783512 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30783554 GTTTTAATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30789840 original size:19 final size:18
Alignment explanation
Indices: 30789799--30789841 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
30789789 AATGTAATTA
30789799 AAAAAT-ATTTAATTTTT
1 AAAAATAATTTAATTTTT
**
30789816 TTAAATAATTTAAATTTTT
1 AAAAATAATTT-AATTTTT
30789835 AAAAATA
1 AAAAATA
30789842 TTATCTTGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 4 0.20
18 4 0.20
19 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAAATAATTTAATTTTT
Found at i:30792761 original size:2 final size:2
Alignment explanation
Indices: 30792756--30792789 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30792746 TCATGTGTGC
30792756 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
30792790 AGCAAATTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:30798222 original size:15 final size:17
Alignment explanation
Indices: 30798187--30798224 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
30798177 ATTAAAATAC
*
30798187 TTTTGTCAATTTGACAA
1 TTTTATCAATTTGACAA
30798204 TTTTATCAA-TTGA-AA
1 TTTTATCAATTTGACAA
30798219 TTTTAT
1 TTTTAT
30798225 ATAAAAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 4 0.20
17 8 0.40
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.53
Consensus pattern (17 bp):
TTTTATCAATTTGACAA
Found at i:30804219 original size:16 final size:16
Alignment explanation
Indices: 30804194--30804227 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
30804184 CACACACACA
30804194 AAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAG
* *
30804210 AAAAAGAAAAGAAAAG
1 AAAAAAAAAAAAAAAG
30804226 AA
1 AA
30804228 GAAGCGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAG
Found at i:30806136 original size:3 final size:3
Alignment explanation
Indices: 30806130--30806154 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30806120 AATAATAATA
30806130 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
30806155 AGATGATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:30811897 original size:118 final size:118
Alignment explanation
Indices: 30811745--30812088 Score: 492
Period size: 118 Copynumber: 2.9 Consensus size: 118
30811735 TGTCAATCAG
* * **
30811745 ATCTTATGGTGACATGCTGAGTGGAAGCAAATAGTTGGCGTGACATACTGAGTGCATGCAGATTT
1 ATCTTGTGGTGACATGCTGAGTGGAAGCAGATAGTTGGCGTGACACGCTGAGTGCATGCAGATTT
* * *
30811810 TGGTGGTGACACGTTGACTTCTTGCAGTATTGTGGGGTGACACGACATGCCCC
66 CGGTGGTGACACGTTGACTTCTTGCAGTATTGTGGGGTGACACGACACGCCCA
* * * *
30811863 ATCTTGTGGTGACATTCTAAGTGGAAGCAGATAGTTGACGTGACACGCTGAGTGCATGTAGATTT
1 ATCTTGTGGTGACATGCTGAGTGGAAGCAGATAGTTGGCGTGACACGCTGAGTGCATGCAGATTT
* * * *
30811928 CGGTGGTGACAGGCTGACTTCTTACAGTATTGTGGGGTGACACGGCACGCCCA
66 CGGTGGTGACACGTTGACTTCTTGCAGTATTGTGGGGTGACACGACACGCCCA
* * * *
30811981 ATCTTGTGGTGACACGCTGAGTGGAACCAGATA-TTGGTGTGACACGCTAAGTGCATGCAGATTT
1 ATCTTGTGGTGACATGCTGAGTGGAAGCAGATAGTTGGCGTGACACGCTGAGTGCATGCAGATTT
* *
30812045 CGGTGGTGACATGTTGACTTCTTGTAGTATTGTGGGGTGACACG
66 CGGTGGTGACACGTTGACTTCTTGCAGTATTGTGGGGTGACACG
30812089 CTGAGTGGAA
Statistics
Matches: 199, Mismatches: 27, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
117 67 0.34
118 132 0.66
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.29
Consensus pattern (118 bp):
ATCTTGTGGTGACATGCTGAGTGGAAGCAGATAGTTGGCGTGACACGCTGAGTGCATGCAGATTT
CGGTGGTGACACGTTGACTTCTTGCAGTATTGTGGGGTGACACGACACGCCCA
Found at i:30812042 original size:30 final size:31
Alignment explanation
Indices: 30811986--30812055 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
30811976 GCCCAATCTT
* *
30811986 GTGGTGACACGCTGAGTGGAACCAGATATT-G
1 GTGGTGACACGCTAAGTGCAACCAGAT-TTCG
**
30812017 GT-GTGACACGCTAAGTGCATGCAGATTTCG
1 GTGGTGACACGCTAAGTGCAACCAGATTTCG
30812047 GTGGTGACA
1 GTGGTGACA
30812056 TGTTGACTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 2 0.06
30 23 0.70
31 8 0.24
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.24
Consensus pattern (31 bp):
GTGGTGACACGCTAAGTGCAACCAGATTTCG
Found at i:30812146 original size:93 final size:92
Alignment explanation
Indices: 30811988--30812179 Score: 285
Period size: 93 Copynumber: 2.1 Consensus size: 92
30811978 CCAATCTTGT
*
30811988 GGTGACACGCTGAGTGGAACCAGATATTGGTGTGACACGCTAAGTGCATGCAGATTTCGGTGGTG
1 GGTGACACGCTGAGTGGAACCAGATATTGGCGTGACACGCTAAGTGCATGCAGATTTCGGTGGTG
* * * * * *
30812053 ACATGTTGACTTCTTGTAGTATTGTGG
66 ACACGCTAACTTCTTGCAATACTGTGG
* * *
30812080 GGTGACACGCTGAGTGGAACTAGATAGTTGGCGTGACACGCTGAGTGCATGTAGATTTCGGTGGT
1 GGTGACACGCTGAGTGGAACCAGATA-TTGGCGTGACACGCTAAGTGCATGCAGATTTCGGTGGT
30812145 GACACGCTAACTTCTTGCAATACTGTGG
65 GACACGCTAACTTCTTGCAATACTGTGG
30812173 GGTGACA
1 GGTGACA
30812180 TGACATGCTC
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
92 25 0.28
93 64 0.72
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (92 bp):
GGTGACACGCTGAGTGGAACCAGATATTGGCGTGACACGCTAAGTGCATGCAGATTTCGGTGGTG
ACACGCTAACTTCTTGCAATACTGTGG
Found at i:30812147 original size:31 final size:30
Alignment explanation
Indices: 30811986--30812152 Score: 115
Period size: 31 Copynumber: 5.4 Consensus size: 30
30811976 GCCCAATCTT
* ***
30811986 GTGGTGACACGCTGAGTGGAACCAGATATTG
1 GTGGTGACACGCTGAGTGCATGTAGAT-TTG
* *
30812017 GT-GTGACACGCTAAGTGCATGCAGATTTCG
1 GTGGTGACACGCTGAGTGCATGTAGATTT-G
* * * * *
30812047 GTGGTGACATGTTGACTTCTTGTAGTATTGTG
1 GTGGTGACACGCTGAGTGCATGTAG-ATT-TG
* **
30812079 G-GGTGACACGCTGAGTGGAACTAGATAGTTG
1 GTGGTGACACGCTGAGTGCATGTAGAT--TTG
*
30812110 G-CGTGACACGCTGAGTGCATGTAGATTTCG
1 GTGGTGACACGCTGAGTGCATGTAGATTT-G
30812140 GTGGTGACACGCT
1 GTGGTGACACGCT
30812153 AACTTCTTGC
Statistics
Matches: 104, Mismatches: 24, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
29 4 0.04
30 27 0.26
31 66 0.63
32 6 0.06
33 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.28
Consensus pattern (30 bp):
GTGGTGACACGCTGAGTGCATGTAGATTTG
Found at i:30812223 original size:118 final size:118
Alignment explanation
Indices: 30812080--30812359 Score: 337
Period size: 118 Copynumber: 2.4 Consensus size: 118
30812070 AGTATTGTGG
* * * * * *
30812080 GGTGACACGCTGAGTGGAACTAGATAGTTGGCGTGACACGCTGAGTGCATGTAGATT-TCGGTGG
1 GGTGACACGCTAAGTGGAACTAGATACTTGGCGTGACACACTGAGTGCATGCAAATTCT-GGGGG
* * * * * *
30812144 TGACACGCTAACTTCTTGCAATACTGTGGGGTGACATGACATGCTCTATCTTGT
65 TGACAAGCTAACTTCTTGCAACACTGTGGGGTGACACGACACGCCCCATCTTGT
*
30812198 GGTGACATGCTAAGTGGAACTAGATACTTGGCGTGACACACTGAGTGCATGCAAATTCTGGGGGT
1 GGTGACACGCTAAGTGGAACTAGATACTTGGCGTGACACACTGAGTGCATGCAAATTCTGGGGGT
* * * * * * *
30812263 GATAAGTTGACTTCTTGCAGCATTGTGGGGTGGCACGGCACGCCCCATCTTGT
66 GACAAGCTAACTTCTTGCAACACTGTGGGGTGACACGACACGCCCCATCTTGT
* * *
30812316 GGTGACACGCTAAGTGGAACCAGATACTTGGTGTGACACTCTGA
1 GGTGACACGCTAAGTGGAACTAGATACTTGGCGTGACACACTGA
30812360 CTTATTCTAA
Statistics
Matches: 137, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
118 136 0.99
119 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.27
Consensus pattern (118 bp):
GGTGACACGCTAAGTGGAACTAGATACTTGGCGTGACACACTGAGTGCATGCAAATTCTGGGGGT
GACAAGCTAACTTCTTGCAACACTGTGGGGTGACACGACACGCCCCATCTTGT
Found at i:30813766 original size:48 final size:50
Alignment explanation
Indices: 30813662--30813767 Score: 123
Period size: 48 Copynumber: 2.2 Consensus size: 50
30813652 AGAGTGCTCT
*
30813662 GAGGAAGATGGTCCCCTCCTGCTGCTGCCTCTATTAATGCATCGACCTAC
1 GAGGAAGATGGTCCCCTCCTGCTGCTGCCTCTACTAATGCATCGACCTAC
* * * *
30813712 GA--AAGATGGTCCCCTCTTTCTGTTGCCT-TGACTAATGCATCG-GCTA-
1 GAGGAAGATGGTCCCCTCCTGCTGCTGCCTCT-ACTAATGCATCGACCTAC
30813758 GAGGAAGATG
1 GAGGAAGATG
30813768 CTCTCCTTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
46 2 0.04
47 4 0.08
48 40 0.83
50 2 0.04
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (50 bp):
GAGGAAGATGGTCCCCTCCTGCTGCTGCCTCTACTAATGCATCGACCTAC
Found at i:30814712 original size:145 final size:143
Alignment explanation
Indices: 30814545--30814872 Score: 383
Period size: 145 Copynumber: 2.3 Consensus size: 143
30814535 ACCATATGTG
* *
30814545 AAAA-TGTTGAACACAAATCGTTAGAACCGATCTTACTGATGGGTCGTTAGCACTATGT-A-TCT
1 AAAATTGTTGAACACAAACCGTTAGAACCG-TCTTACTGAT-CGTCGTTAGCA-T-TGTGAGTCT
* * *
30814607 AAAGAGGACCTCTCAGTGGTTGAGAAGCTGTCGTCGCATGGTCCAATTGCAAACATAGATATGTT
62 AAAGAGGACCTCTCAGTGGTTGAGAAGCTGTCGTCGCATGGTCCAACTACAAACACAGATATGTT
30814672 ATTTGATAATCACATAT
127 ATTTGATAATCACATAT
* * * * * *
30814689 AAAATTGTTGAACACAAACCGTTATAATCGTCCTTAGCGGCTCGTTGTTAGCATTGTGAGTCTGA
1 AAAATTGTTGAACACAAACCGTTAGAACCGT-CTTA-CTGATCGTCGTTAGCATTGTGAGTCTAA
* * * * * *
30814754 GGAGGACCTTTCAGTGGTTGTGGAGCTGTTGTCGTATGGTCCAACTACAAACACAGATATGTTAT
64 AGAGGACCTCTCAGTGGTTGAGAAGCTGTCGTCGCATGGTCCAACTACAAACACAGATATGTTAT
*
30814819 TTGATAATCACATGT
129 TTGATAATCACATAT
** *
30814834 GGAATTGTTGAACACAAACCGTTAGAGCCGTCTTTACTG
1 AAAATTGTTGAACACAAACCGTTAGAACCGTC-TTACTG
30814873 GCTTTTAATT
Statistics
Matches: 154, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
143 3 0.02
144 10 0.06
145 138 0.90
146 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (143 bp):
AAAATTGTTGAACACAAACCGTTAGAACCGTCTTACTGATCGTCGTTAGCATTGTGAGTCTAAAG
AGGACCTCTCAGTGGTTGAGAAGCTGTCGTCGCATGGTCCAACTACAAACACAGATATGTTATTT
GATAATCACATAT
Found at i:30816644 original size:31 final size:31
Alignment explanation
Indices: 30816262--30816642 Score: 503
Period size: 31 Copynumber: 12.3 Consensus size: 31
30816252 GTTAATCGAT
** **
30816262 AATGTGGTAACACGCCATATATATAATATAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* *
30816293 AATGTGGTAACAAGCCATGCATATAATGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
30816324 AATGTGGTAACACGCCATGCATATAATGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* *
30816355 AATGTGGAAACACACCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
** * **
30816386 AATGTTATAACACGCTATGCATATAAAATAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
30816417 AATGTGGTAACACGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* * *
30816448 AATATGGTAACATGCAATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
30816479 AATGTGGTAACACGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* * *
30816510 AATGTTGTAACATGCCATGCATATAATGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
30816541 AAT-TGGTAACATGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
30816571 AATGTGGTAACATGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
** * * *
30816602 AATGTTATAATACGTCATGTATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
30816633 AATATGGTAA
1 AATGTGGTAA
30816643 TATGCCAAAC
Statistics
Matches: 309, Mismatches: 40, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
30 28 0.09
31 281 0.91
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (31 bp):
AATGTGGTAACACGCCATGCATATAACGTAA
Found at i:30816719 original size:46 final size:46
Alignment explanation
Indices: 30816617--30816709 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
30816607 TATAATACGT
* *
30816617 CATGTATATAACGTAAAATATGGTAATATGCCAAACGCTGACACGC
1 CATGCATATAACGTAAAATATGGTAACATGCCAAACGCTGACACGC
* *
30816663 CATGCATATAACGTAAAATGTGGTAACATGCC-AACGCTGACATGC
1 CATGCATATAACGTAAAATATGGTAACATGCCAAACGCTGACACGC
30816708 CA
1 CA
30816710 ATCACTATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 14 0.33
46 29 0.67
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.23
Consensus pattern (46 bp):
CATGCATATAACGTAAAATATGGTAACATGCCAAACGCTGACACGC
Found at i:30817443 original size:47 final size:46
Alignment explanation
Indices: 30817369--30817564 Score: 248
Period size: 47 Copynumber: 4.2 Consensus size: 46
30817359 AAGTCTGACA
* * *
30817369 AACTCTGAACCCTGTCGTGTCACAGATTCCCTCCATGGGGTGTCAC
1 AACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTCAC
* * * *
30817415 GAACTCTAAACGCTGATGTGTCATAGATTCCCTCCATGGTGTGTCATC
1 -AACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTCA-C
* *
30817463 AACTCTGAACGCTGACGTGTCATAGATTCCCTCCATAGCGTGTCACC
1 AACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTCA-C
** *
30817510 AACTCTGAACTTTGACGTCTCACAGATTCCCTCCATGGCGTGTCAC
1 AACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTCAC
30817556 AAACTCTGA
1 -AACTCTGA
30817565 GCGTGGGCTT
Statistics
Matches: 131, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
46 1 0.01
47 129 0.98
48 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (46 bp):
AACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTCAC
Found at i:30817943 original size:63 final size:63
Alignment explanation
Indices: 30817849--30817972 Score: 160
Period size: 63 Copynumber: 2.0 Consensus size: 63
30817839 GCTCATCTTT
* * *
30817849 CTCTCTTAGCTCTCTAAACTGTCTCAACTCTGTCAACT-TTCTGTTGAGCACCATCGTCATCAG
1 CTCTCTCAGCTCTCTAAACTGTATCAACTCTGTCAACTATT-TGGTGAGCACCATCGTCATCAG
* * * * *
30817912 CTCTCTCAGCTCTCTGAATTGTATGAGCTCTGTCAACTATTTGGTGAGTACCATCGTCATC
1 CTCTCTCAGCTCTCTAAACTGTATCAACTCTGTCAACTATTTGGTGAGCACCATCGTCATC
30817973 GAGTTGTGGT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 50 0.96
64 2 0.04
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.35
Consensus pattern (63 bp):
CTCTCTCAGCTCTCTAAACTGTATCAACTCTGTCAACTATTTGGTGAGCACCATCGTCATCAG
Found at i:30818430 original size:31 final size:31
Alignment explanation
Indices: 30818322--30818430 Score: 182
Period size: 31 Copynumber: 3.5 Consensus size: 31
30818312 GTGTCAGCGT
*
30818322 TGGCGTGTTACCACAATTTACGTTATATGCA
1 TGGCGTGTTACCACATTTTACGTTATATGCA
*
30818353 TGGCGTGTTACCACATTTGACGTTATATGCA
1 TGGCGTGTTACCACATTTTACGTTATATGCA
*
30818384 TAGCGTGTTACCACATTTTACGTTATATGCA
1 TGGCGTGTTACCACATTTTACGTTATATGCA
*
30818415 TGGGGTGTTACCACAT
1 TGGCGTGTTACCACAT
30818431 GACTGGCAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (31 bp):
TGGCGTGTTACCACATTTTACGTTATATGCA
Found at i:30822520 original size:118 final size:118
Alignment explanation
Indices: 30822312--30822832 Score: 677
Period size: 118 Copynumber: 4.4 Consensus size: 118
30822302 TGTCAATTAG
* * * *
30822312 ATCTTATGGTGACACGCTGAGTGAAAGCAAATAGTTGGCATGACACGCTGAGTGCATGCAGATTT
1 ATCTTGTGGTGACACGCTGAGTGGAAGCAGATAGTTGGCGTGACACGCTGAGTGCATGCAGATTT
* * *
30822377 CGGTGGTGACACACTGACTTTTTGCAGTATTGTGAGGTGACACGACATGCCCC
66 CGGTGGTGACACGCTGACTTCTTGCAGTATTGTGAGGTGACACGACACGCCCC
** * *
30822430 ATCTTGTGGTGACACATTGAGTGGAAGCAGATAGTTAGCGTGACACGTTGAGTGCATGCAGATTT
1 ATCTTGTGGTGACACGCTGAGTGGAAGCAGATAGTTGGCGTGACACGCTGAGTGCATGCAGATTT
* * ** *
30822495 CGGTGGTGACACGCTGACTTCTTGCAATATTGTGGGGTGACACGACTTGCCCA
66 CGGTGGTGACACGCTGACTTCTTGCAGTATTGTGAGGTGACACGACACGCCCC
* * *
30822548 ATCTTGTGGTGACATGCTAAGGGGAA-CTAGATAGTTGGCGTGACACGCTGAGTGCATGCAGATT
1 ATCTTGTGGTGACACGCTGAGTGGAAGC-AGATAGTTGGCGTGACACGCTGAGTGCATGCAGATT
* * * * *
30822612 TTGATGGTGACATGCTGACTTCTTGCAGTATTGTGGGGTGACACGGCACGCCCC
65 TCGGTGGTGACACGCTGACTTCTTGCAGTATTGTGAGGTGACACGACACGCCCC
* * * * *
30822666 ATCTTGTGGTGACACGCTAAGTGGAACCAGATACTTGGCGTGACACGTTGAGTGCATGTAGATTT
1 ATCTTGTGGTGACACGCTGAGTGGAAGCAGATAGTTGGCGTGACACGCTGAGTGCATGCAGATTT
* * * * * * *
30822731 TGGGGGTGACAAGTTGACTTTTTGCAGTATTGTAAGGTGACACGGCACGCCCC
66 CGGTGGTGACACGCTGACTTCTTGCAGTATTGTGAGGTGACACGACACGCCCC
*
30822784 ATCTTGTGGTGACACGCTGAGTGG-AGCCAGATACTTGGCGTGACACGCT
1 ATCTTGTGGTGACACGCTGAGTGGAAG-CAGATAGTTGGCGTGACACGCT
30822833 AACGTGTTCT
Statistics
Matches: 356, Mismatches: 44, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
117 2 0.01
118 353 0.99
119 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.27
Consensus pattern (118 bp):
ATCTTGTGGTGACACGCTGAGTGGAAGCAGATAGTTGGCGTGACACGCTGAGTGCATGCAGATTT
CGGTGGTGACACGCTGACTTCTTGCAGTATTGTGAGGTGACACGACACGCCCC
Found at i:30824207 original size:48 final size:48
Alignment explanation
Indices: 30824151--30824253 Score: 161
Period size: 48 Copynumber: 2.1 Consensus size: 48
30824141 AAGTGCTCTG
** *
30824151 AGGAAGATGGTCCCCTCCTACTGTTGCCTCGATTAATGCATCGGCTTA
1 AGGAAGATGGTCCCCTCCTACTACTGCCTCGACTAATGCATCGGCTTA
* *
30824199 AGGAAGATGGTCCCCTCCTCCTACTGCCTCGACTAATGCATTGGCTTA
1 AGGAAGATGGTCCCCTCCTACTACTGCCTCGACTAATGCATCGGCTTA
30824247 AGGAAGA
1 AGGAAGA
30824254 AGCTCTCATT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (48 bp):
AGGAAGATGGTCCCCTCCTACTACTGCCTCGACTAATGCATCGGCTTA
Found at i:30825198 original size:145 final size:145
Alignment explanation
Indices: 30825030--30825345 Score: 384
Period size: 145 Copynumber: 2.2 Consensus size: 145
30825020 TAACCATATG
* * ** *
30825030 TGAAAATGTTGAACATAAACCGTTAGAACCGAT-CTTACTGGCGGGTCATTAACACTGTGCGTCT
1 TGAAATTGTTGAACACAAACCGTTAGAACCG-TCCTTACTGGCGCATCATTAACACTGTGAGTCT
* ** *
30825094 AAGGAGGACCTCTCAGTGGTTGAGGTGCTGTCGTCGCATGG-TCTAACTGCAAACACAGATATGT
65 AAGGAGGACCTCTCAATGGTTGAGAAGCTGTCGTCGCATGGTTC-AACTACAAACACAGATATGT
30825158 TATTCGATAATCACATA
129 TATTCGATAATCACATA
* * ** * * * *
30825175 TGAAATTGTTGAACACAAACCGTTATAACCGTCCTTACTGGCTCATTGTTAGCATTGTGAGTTTG
1 TGAAATTGTTGAACACAAACCGTTAGAACCGTCCTTACTGGCGCATCATTAACACTGTGAGTCTA
* * * *
30825240 AGGAGGACCTTTCAATGGTTGTGAAGTTGTTGTCGCATGGTTCAACTACAAACACAGATATGTTA
66 AGGAGGACCTCTCAATGGTTGAGAAGCTGTCGTCGCATGGTTCAACTACAAACACAGATATGTTA
* *
30825305 TTTGATAATCACATG
131 TTCGATAATCACATA
*
30825320 TGGAATTGTTGAACACAAACCGTTAG
1 TGAAATTGTTGAACACAAACCGTTAG
30825346 TCGTATTTAC
Statistics
Matches: 144, Mismatches: 25, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
144 1 0.01
145 141 0.98
146 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (145 bp):
TGAAATTGTTGAACACAAACCGTTAGAACCGTCCTTACTGGCGCATCATTAACACTGTGAGTCTA
AGGAGGACCTCTCAATGGTTGAGAAGCTGTCGTCGCATGGTTCAACTACAAACACAGATATGTTA
TTCGATAATCACATA
Found at i:30826790 original size:31 final size:31
Alignment explanation
Indices: 30826755--30826984 Score: 352
Period size: 31 Copynumber: 7.4 Consensus size: 31
30826745 GTTAACCCAT
* * **
30826755 AATGTGGTAACACGCCGTACATATAATATAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* *
30826786 AATGTGGTAACAAGCAATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
30826817 AATGTAGTAACACGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
30826848 AATGTGGAAACACGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* *
30826879 AATGTTGTAACACACCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
30826910 AATGTGGTAACACGCCATGCATATAATGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
30826941 AATGTTGTAACACGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
30826972 AATGTGGTAACAC
1 AATGTGGTAACAC
30826985 ACCAAATGCT
Statistics
Matches: 179, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 179 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (31 bp):
AATGTGGTAACACGCCATGCATATAACGTAA
Found at i:30827058 original size:46 final size:46
Alignment explanation
Indices: 30826950--30827048 Score: 155
Period size: 46 Copynumber: 2.2 Consensus size: 46
30826940 AAATGTTGTA
* *
30826950 ACACGCCATGCATATAACGTAAAATGTGGTAACACACCAAATGCTG
1 ACACGCCATGCATATAACGTAAAATGTGATAACACACCAAACGCTG
* *
30826996 ACACTCCATGCATATAACGTAAAATGTGATACCACACC-AACGCTG
1 ACACGCCATGCATATAACGTAAAATGTGATAACACACCAAACGCTG
30827041 ACACGCCA
1 ACACGCCA
30827049 ATCGCTATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 13 0.27
46 35 0.73
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.18
Consensus pattern (46 bp):
ACACGCCATGCATATAACGTAAAATGTGATAACACACCAAACGCTG
Found at i:30827758 original size:47 final size:47
Alignment explanation
Indices: 30827706--30827825 Score: 141
Period size: 47 Copynumber: 2.6 Consensus size: 47
30827696 GGAGTTTGAG
* * *
30827706 AAACTCTGAACCTTGCCATGTCACAGATTCCCTCCATGGCGTGTCAC
1 AAACTCTGAACCTTGGCGTGTCACAGATTCACTCCATGGCGTGTCAC
* ** * * * *
30827753 CAACTCTGAATTTTGGCGTCTCACAGATTCACTCTATGGTGTGTCAT
1 AAACTCTGAACCTTGGCGTGTCACAGATTCACTCCATGGCGTGTCAC
*
30827800 AAACTCTGAACGTTGGCGTGTCACAG
1 AAACTCTGAACCTTGGCGTGTCACAG
30827826 CCGTGTCACA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (47 bp):
AAACTCTGAACCTTGGCGTGTCACAGATTCACTCCATGGCGTGTCAC
Found at i:30827879 original size:58 final size:58
Alignment explanation
Indices: 30827788--30827940 Score: 171
Period size: 58 Copynumber: 2.6 Consensus size: 58
30827778 GATTCACTCT
* * * ** * *
30827788 ATGGTGTGTCATAAACTCTGAACGTTGGCGTGTCACAGCCGTGTCACACATTCCCACC
1 ATGGCGTGTCACAAACTCTAAACCCTGTCGTGTCACAGCCGTGTCACACATTCCAACC
* * *
30827846 ATGGCGTGTCACCAACTCTAAACCCTGTTGTGTCACAGCTGTGTCACACATTCCAACC
1 ATGGCGTGTCACAAACTCTAAACCCTGTCGTGTCACAGCCGTGTCACACATTCCAACC
* * * **
30827904 ATGTCGTGTTATAAACTCTAAACTTTGTCGTGTCACA
1 ATGGCGTGTCACAAACTCTAAACCCTGTCGTGTCACA
30827941 CATTCCTAAC
Statistics
Matches: 78, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
58 78 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (58 bp):
ATGGCGTGTCACAAACTCTAAACCCTGTCGTGTCACAGCCGTGTCACACATTCCAACC
Found at i:30827985 original size:47 final size:47
Alignment explanation
Indices: 30827887--30827987 Score: 125
Period size: 47 Copynumber: 2.1 Consensus size: 47
30827877 GTCACAGCTG
* * * * *
30827887 TGTCACACATTCCAACCATGTCGTGTTATAAACTCTAAACTTTGTCG
1 TGTCACACATTCCAACCATGCCGTGTTACAAACTCTAAACTCTGCCC
30827934 TGTCACACATTCCTAA-CATGCCGT-TTCACAAACTCTAAACTCTGCCC
1 TGTCACACATTCC-AACCATGCCGTGTT-ACAAACTCTAAACTCTGCCC
30827981 TGTCACA
1 TGTCACA
30827988 ACCGTCTCAC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
46 2 0.04
47 43 0.91
48 2 0.04
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.31
Consensus pattern (47 bp):
TGTCACACATTCCAACCATGCCGTGTTACAAACTCTAAACTCTGCCC
Found at i:30833407 original size:41 final size:42
Alignment explanation
Indices: 30833326--30833408 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 42
30833316 ACAATGATAC
30833326 ATTATAGGATGATAAATCTTATTTACATTTGAATTTAATCAT
1 ATTATAGGATGATAAATCTTATTTACATTTGAATTTAATCAT
* * *
30833368 ATTATAGGATGAT-AATTTTGTTTATATTTGAATTTAATCAT
1 ATTATAGGATGATAAATCTTATTTACATTTGAATTTAATCAT
30833409 GATAACATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 25 0.66
42 13 0.34
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (42 bp):
ATTATAGGATGATAAATCTTATTTACATTTGAATTTAATCAT
Found at i:30835799 original size:24 final size:24
Alignment explanation
Indices: 30835761--30835808 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
30835751 GTGGACATTG
*
30835761 ACAATGACCCTTTAACTAATCAAA
1 ACAATGACCCATTAACTAATCAAA
* *
30835785 ACAATGAGCCATTAACTGATCAAA
1 ACAATGACCCATTAACTAATCAAA
30835809 CTATCTTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (24 bp):
ACAATGACCCATTAACTAATCAAA
Found at i:30840412 original size:156 final size:156
Alignment explanation
Indices: 30838677--30840392 Score: 3423
Period size: 156 Copynumber: 11.0 Consensus size: 156
30838667 TGTCATGCCN
30838677 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
1 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
30838742 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
66 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
30838807 AAATACATATTGAGATGAATATTTTT
131 AAATACATATTGAGATGAATATTTTT
30838833 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
1 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
30838898 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
66 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
30838963 AAATACATATTGAGATGAATATTTTT
131 AAATACATATTGAGATGAATATTTTT
30838989 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
1 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
30839054 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
66 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
30839119 AAATACATATTGAGATGAATATTTTT
131 AAATACATATTGAGATGAATATTTTT
30839145 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
1 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
30839210 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
66 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
30839275 AAATACATATTGAGATGAATATTTTT
131 AAATACATATTGAGATGAATATTTTT
30839301 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
1 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
30839366 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
66 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
30839431 AAATACATATTGAGATGAATATTTTT
131 AAATACATATTGAGATGAATATTTTT
30839457 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
1 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
30839522 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
66 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
30839587 AAATACATATTGAGATGAATATTTTT
131 AAATACATATTGAGATGAATATTTTT
30839613 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
1 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
30839678 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
66 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
30839743 AAATACATATTGAGATGAATATTTTT
131 AAATACATATTGAGATGAATATTTTT
30839769 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
1 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
30839834 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
66 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
30839899 AAATACATATTGAGATGAATATTTTT
131 AAATACATATTGAGATGAATATTTTT
30839925 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
1 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
30839990 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
66 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
30840055 AAATACATATTGAGATGAATATTTTT
131 AAATACATATTGAGATGAATATTTTT
30840081 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
1 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
30840146 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
66 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
30840211 AAATACATATTGAGATGAATATTTTT
131 AAATACATATTGAGATGAATATTTTT
30840237 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
1 AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
30840302 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
66 GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
30840367 AAATACATATTGAGATGAAATATTTT
131 AAATACATATTGAGATG-AATATTTT
30840393 AATTGTCTTA
Statistics
Matches: 1559, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
156 1551 0.99
157 8 0.01
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (156 bp):
AACAGCCTTGGCGGACTCGGTTAGATGCCTCGGCCAAGGTATCCCCGAGAATGATTTTAGCAAGA
GCCAAGCTTTTAAAATACTCATAAGCCATGTTGAATATTTAAATGAAATGAATATTTATGTTATG
AAATACATATTGAGATGAATATTTTT
Found at i:30853606 original size:44 final size:44
Alignment explanation
Indices: 30853543--30853633 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
30853533 CAAAAAAGAA
30853543 AGATAGTCCTTTTATTGGTTTGGGGTTTTGTTGTTGTGGGGTAG
1 AGATAGTCCTTTTATTGGTTTGGGGTTTTGTTGTTGTGGGGTAG
30853587 AGATAGTCCTTTTATTGGTTTGGGGTTTTGTTGTTGTGGGGTAG
1 AGATAGTCCTTTTATTGGTTTGGGGTTTTGTTGTTGTGGGGTAG
30853631 AGA
1 AGA
30853634 ATTTGAAAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.13, C:0.04, G:0.36, T:0.46
Consensus pattern (44 bp):
AGATAGTCCTTTTATTGGTTTGGGGTTTTGTTGTTGTGGGGTAG
Found at i:30864066 original size:29 final size:28
Alignment explanation
Indices: 30864018--30864159 Score: 151
Period size: 28 Copynumber: 5.0 Consensus size: 28
30864008 TGGCAGCTTT
*
30864018 AACATGTTTGTCTCAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
*
30864046 AACATGTTTGGTCTTAATTTAGATAAG-A
1 AACATGTTT-GTCTTAATTTAGACAAGAA
*
30864074 AACTATGTTTGTATTAATTTAAGACAAGAAA
1 AAC-ATGTTTGTCTTAATTT-AGACAAG-AA
* * * *
30864105 AATATTTTTGTCTTAATCTAAACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
* * *
30864133 AATATATTTGTCTCAATTTAGACAAGA
1 AACATGTTTGTCTTAATTTAGACAAGA
30864160 TAAAATATTT
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
28 47 0.49
29 33 0.34
30 13 0.14
31 3 0.03
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.37
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:30864118 original size:58 final size:57
Alignment explanation
Indices: 30864021--30864180 Score: 196
Period size: 58 Copynumber: 2.8 Consensus size: 57
30864011 CAGCTTTAAC
* * * * *
30864021 ATGTTTGTCTCAATTTAGACAAGAAAACAT-GTTTGGTCTTAATTTAGATAAGAAACT
1 ATGTTTGTCTCAATTTAGACAAGAAAA-ATATTTTTGTCTTAATTTAAACAAGAAAAT
* * *
30864078 ATGTTTGTATTAATTTAAGACAAGAAAAATATTTTTGTCTTAATCTAAACAAGAAAAT
1 ATGTTTGTCTCAATTT-AGACAAGAAAAATATTTTTGTCTTAATTTAAACAAGAAAAT
* *
30864136 ATATTTGTCTCAATTTAGACAAGATAAAATATTTTTGTTTTAATT
1 ATGTTTGTCTCAATTTAGACAAGA-AAAATATTTTTGTCTTAATT
30864181 GAAGATAAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
57 24 0.28
58 63 0.72
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (57 bp):
ATGTTTGTCTCAATTTAGACAAGAAAAATATTTTTGTCTTAATTTAAACAAGAAAAT
Found at i:30864167 original size:28 final size:27
Alignment explanation
Indices: 30864024--30864169 Score: 139
Period size: 29 Copynumber: 5.1 Consensus size: 27
30864014 CTTTAACATG
* *
30864024 TTTGTCTCAATTTAGACAAGAAAACATG
1 TTTGTCTTAATTTAGACAAGAAAA-ATA
* * *
30864052 TTTGGTCTTAATTTAGATAAGAAACTATG
1 TTT-GTCTTAATTTAGACAAGAAA-AATA
*
30864081 TTTGTATTAATTTAAGACAAGAAAAATA
1 TTTGTCTTAATTT-AGACAAGAAAAATA
* *
30864109 TTTTTGTCTTAATCTAAACAAGAAAATATA
1 --TTTGTCTTAATTTAGACAAGAAAA-ATA
*
30864139 TTTGTCTCAATTTAGACAAGATAAAATA
1 TTTGTCTTAATTTAGACAAGA-AAAATA
30864167 TTT
1 TTT
30864170 TTGTTTTAAT
Statistics
Matches: 98, Mismatches: 13, Indels: 14
0.78 0.10 0.11
Matches are distributed among these distances:
28 38 0.39
29 46 0.47
30 14 0.14
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (27 bp):
TTTGTCTTAATTTAGACAAGAAAAATA
Found at i:30864334 original size:21 final size:18
Alignment explanation
Indices: 30864310--30864349 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
30864300 AATTTTTTTT
30864310 AAATAAAGATGGATAATAATA
1 AAAT-AAGAT-GATAA-AATA
30864331 AAATAAGATGATAAAATA
1 AAATAAGATGATAAAATA
30864349 A
1 A
30864350 GAGTTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 5 0.26
20 5 0.26
21 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (18 bp):
AAATAAGATGATAAAATA
Found at i:30864376 original size:17 final size:18
Alignment explanation
Indices: 30864348--30864386 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
30864338 ATGATAAAAT
30864348 AAGAGTTATTATTCTATA
1 AAGAGTTATTATTCTATA
*
30864366 AAGAGTT-TTATTTTATA
1 AAGAGTTATTATTCTATA
30864383 AAGA
1 AAGA
30864387 ACTCTAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.44
Consensus pattern (18 bp):
AAGAGTTATTATTCTATA
Found at i:30868198 original size:21 final size:22
Alignment explanation
Indices: 30868166--30868215 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
30868156 GTTATCTATG
30868166 TTTTTTTGTTATTATTA-ATTA
1 TTTTTTTGTTATTATTATATTA
* *
30868187 TTTTTATT-TTATTTTTATTTTA
1 TTTTT-TTGTTATTATTATATTA
30868209 TTTTTTT
1 TTTTTTT
30868216 ATACTTTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTTTTTGTTATTATTATATTA
Found at i:30868200 original size:11 final size:11
Alignment explanation
Indices: 30868184--30868213 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
30868174 TTATTATTAA
30868184 TTATTTTTATT
1 TTATTTTTATT
30868195 TTATTTTTATT
1 TTATTTTTATT
30868206 TTATTTTT
1 TTATTTTT
30868214 TTATACTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:30877275 original size:15 final size:16
Alignment explanation
Indices: 30877246--30877278 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
30877236 ACCTCTCTCC
30877246 TTTTTCCATTCTTTCA
1 TTTTTCCATTCTTTCA
*
30877262 TTTTTTCATT-TTTCA
1 TTTTTCCATTCTTTCA
30877277 TT
1 TT
30877279 ATTATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTCCATTCTTTCA
Found at i:30888246 original size:20 final size:20
Alignment explanation
Indices: 30888203--30888252 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
30888193 GTAAAGTTTT
* *
30888203 TATTTAATTTTTTCTATTTA
1 TATTTTATTTTTTCTAATTA
*
30888223 TATTATTATTTTTT-TAATTC
1 TATT-TTATTTTTTCTAATTA
30888243 TATTTTATTT
1 TATTTTATTT
30888253 GCTCATATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 6 0.23
20 12 0.46
21 8 0.31
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTTTATTTTTTCTAATTA
Found at i:30888250 original size:22 final size:22
Alignment explanation
Indices: 30888200--30888251 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 22
30888190 GAGGTAAAGT
30888200 TTTTATTTAATTTTTTCTATTTA
1 TTTTA-TTAATTTTTTCTATTTA
*
30888223 TATTATT-ATTTTTT-TAATTCTA
1 TTTTATTAATTTTTTCT-ATT-TA
30888245 TTTTATT
1 TTTTATT
30888252 TGCTCATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 1 0.04
21 10 0.40
22 10 0.40
23 4 0.16
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTATTAATTTTTTCTATTTA
Found at i:30888353 original size:15 final size:16
Alignment explanation
Indices: 30888335--30888364 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30888325 TTTTTATGTG
30888335 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
30888350 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
30888365 AAATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:30888547 original size:21 final size:22
Alignment explanation
Indices: 30888523--30888569 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
30888513 GCTTTACGTT
* *
30888523 TTATATTTAGT-TGAAAAGAAA
1 TTATATTGAGTATAAAAAGAAA
*
30888544 TTATCTTGAGTATAAAAAGAAA
1 TTATATTGAGTATAAAAAGAAA
30888566 TTAT
1 TTAT
30888570 TAATTCTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.47, C:0.02, G:0.13, T:0.38
Consensus pattern (22 bp):
TTATATTGAGTATAAAAAGAAA
Found at i:30888847 original size:17 final size:18
Alignment explanation
Indices: 30888825--30888861 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
30888815 GTTTGTTTTG
30888825 ATTTATATGT-TA-TATAA
1 ATTTAT-TGTCTATTATAA
30888842 ATTTATTGTCTATTATAA
1 ATTTATTGTCTATTATAA
30888860 AT
1 AT
30888862 CTTTTGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.17
17 8 0.44
18 7 0.39
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (18 bp):
ATTTATTGTCTATTATAA
Found at i:30911791 original size:18 final size:18
Alignment explanation
Indices: 30911768--30911803 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
30911758 TAAAAAGAGC
30911768 AATGAAAATACAATCAGA
1 AATGAAAATACAATCAGA
30911786 AATGAAAATACAATCAGA
1 AATGAAAATACAATCAGA
30911804 GGCATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.17
Consensus pattern (18 bp):
AATGAAAATACAATCAGA
Found at i:30914746 original size:2 final size:2
Alignment explanation
Indices: 30914741--30914765 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30914731 TTGGTGTGTG
30914741 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
30914766 TTAATTACTA
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:30918957 original size:4 final size:4
Alignment explanation
Indices: 30918948--30918973 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
30918938 GGTTTTTTTC
30918948 TCTT TCTT TCTT TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TC
30918974 CTCTCTTGGT
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:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:30920506 original size:2 final size:2
Alignment explanation
Indices: 30920499--30920535 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
30920489 TAAAACCAAC
30920499 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30920536 GACGTAGACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30926379 original size:2 final size:2
Alignment explanation
Indices: 30926366--30926397 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
30926356 AATTATTAAC
*
30926366 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30926398 TAATTAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:30928919 original size:30 final size:27
Alignment explanation
Indices: 30928890--30928943 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
30928880 TTGTTTTTAT
30928890 TTTATA-TTT-TTTAAAATATTAATAA
1 TTTATACTTTATTTAAAATATTAATAA
30928915 TTTATACTTTATTTAAAATATTAATAA
1 TTTATACTTTATTTAAAATATTAATAA
30928942 TT
1 TT
30928944 GGTCATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.22
26 3 0.11
27 18 0.67
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTATACTTTATTTAAAATATTAATAA
Found at i:30929001 original size:30 final size:30
Alignment explanation
Indices: 30928894--30929004 Score: 88
Period size: 30 Copynumber: 3.8 Consensus size: 30
30928884 TTTTATTTTA
* *
30928894 TATTTTTTAAAATATTAATAATTT-AT-AC
1 TATTTTTTAAAATATTAATATTTTAATCAT
* * **
30928922 T-TTATTTAAAATATTAATA-ATTGGTCATT
1 TATTTTTTAAAATATTAATATTTTAATCA-T
* * * *
30928951 TAATTATTAATAT-TTTATATTTTAATCAT
1 TATTTTTTAAAATATTAATATTTTAATCAT
30928980 TATTTTTTAAAATATTAATATTTTA
1 TATTTTTTAAAATATTAATATTTTA
30929005 TTTATAATTT
Statistics
Matches: 61, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
26 2 0.03
27 18 0.30
28 2 0.03
29 17 0.28
30 22 0.36
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (30 bp):
TATTTTTTAAAATATTAATATTTTAATCAT
Found at i:30929230 original size:17 final size:17
Alignment explanation
Indices: 30929208--30929240 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30929198 TAGTGCAACA
30929208 AGTAATAGCA-ATTCTTG
1 AGTAATA-CATATTCTTG
30929225 AGTAATACATATTCTT
1 AGTAATACATATTCTT
30929241 TAAAATGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (17 bp):
AGTAATACATATTCTTG
Found at i:30940572 original size:20 final size:22
Alignment explanation
Indices: 30940528--30940572 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
30940518 TCTGAGAATA
*
30940528 TAAAATTAAATATTTTTTTCAT
1 TAAAATTAAATATTTTTTACAT
*
30940550 TAAAATTAGAT-TTTTTTAC-T
1 TAAAATTAAATATTTTTTACAT
30940570 TAA
1 TAA
30940573 TTCACTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 7 0.33
22 10 0.48
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TAAAATTAAATATTTTTTACAT
Found at i:30940794 original size:500 final size:499
Alignment explanation
Indices: 30939829--30941916 Score: 2424
Period size: 500 Copynumber: 4.2 Consensus size: 499
30939819 TATTATTATC
* * *
30939829 ACTTGTTACGTTAACTCTCACATATTTACGTTAAGATTTTAAATTT-GCTTATTCCACCTTTATA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAG-TTATTCAACCTTTATA
* * * *
30939893 AGTTTTTATATTAATTCTTACAGTTTTACGTCAAAACTTTTCA-ATGTCACTTTTGAACTATAAT
65 AGTTTTTATGTCAATTCTTATAGTTTTACGTCAAAACTTTT-ATATGTCAATTTTGAACTATAAT
* * *
30939957 TATTTTTATCCTTATTATTTTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTAGTC
129 TATTTTTATCATTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTC
* * * *
30940022 CGATAATATAAATTTAAATA-TTTTTT-ATTAAAATTATATTTTTTTACTTAATTGA-TGTGTTA
194 CGAGAATATAAAATTAAATATTTTTTTCATTAAAATTAGATTTTTTTACTTAATT-ACTATGTTA
* * * *
30940084 CATTAACTCTCACACATTTACTTTAAAATTTAAAATTTATTTATTCCACCTGTATAAGTTTTTAC
258 CATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTAC
* * * * * *
30940149 ATCAATTCTTACAGTTTTACGTCAAGGTTTTTCTATATCAGTTTTGAACTAGAATTATCTTTATC
323 GTCAATTCTTACAGTTTTACGT-AAAGCTTTTCTATGTCAATTTTGAACTATAATTAT-TTTATC
* * * * * * *
30940214 TTTACTATTTTTTATTTAAAAATAAAAATTTGTATATCGTTAAACACATTTAGTTGGGGAATATA
386 CTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTTCGAGAATATA
* * * *
30940279 AATTCAAATATTTGTTTTTTATTAAAATTAGA-TATTTTTACTTAATTG
451 AATTTAAATATTTGTTTTTCACTAAAATTAGATTTTTTTTACTTAATTG
* * *
30940327 ACTTGTTACATTAACTCTCACACATTTACGTTAAGCTTTAAAATGTAGTTATTCAACCTTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCAACCTTTATAA
*
30940392 GTTTTTATGTCAATTCTTATAGTTTTACGTCAAGACTTTTATATGTCAATTTTGAACTATAATTA
66 GTTTTTATGTCAATTCTTATAGTTTTACGTCAAAACTTTTATATGTCAATTTTGAACTATAATTA
* * * * * *
30940457 TTTTTATCATTATTGTTTTTTA-TTTAATAATTAAAATTTATATATTGTTAAACATTTTTAGTCT
131 TTTTTATCATTATTATTCTTTATTTTAA-AATTAAAATTTGTATATCGTTAAACACTTTTAGTCC
30940521 GAGAATATAAAATTAAATATTTTTTTCATTAAAATTAGATTTTTTTACTTAATTCACT-TGTTAC
195 GAGAATATAAAATTAAATATTTTTTTCATTAAAATTAGATTTTTTTACTTAATT-ACTATGTTAC
* * * *
30940585 ATTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTTCACATTTATAAGTTATTACG
259 ATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACG
* **
30940650 TCAATTCTTACAGCTTTATATCAAAGCTTTTCTATGTCAATTTTGAACTATAATTATTTTATTCC
324 TCAATTCTTACAGTTTTACGT-AAAGCTTTTCTATGTCAATTTTGAACTATAATTATTTTA-TCC
** * * * *
30940715 TTATTATTCTTTATCCAAAAATTAAAATTTTTATATTGTTAAACAGTTTTAGTTCAAGAATATAA
387 TTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTTCGAGAATATAA
* *
30940780 ATTTAAATATTTGTTTTTCACTAAAATTTGATTTTTTTTACTTAATTT
452 ATTTAAATATTTGTTTTTCACTAAAATTAGATTTTTTTTACTTAATTG
* * * *
30940828 ACTTGTTATGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTCTACTTTTATAA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCAACCTTTATAA
* * * ** * * * *
30940893 GTTTTTATATCCATTCTTACAGTTTTACGTCAAGGCTTTTCTATATAAATTTTGAGCTATAATTA
66 GTTTTTATGTCAATTCTTATAGTTTTACGTCAAAACTTTTATATGTCAATTTTGAACTATAATTA
* *
30940958 TTTTTATCCA-TATTATTCTTTATTTTAAAATTAAAATTTGTATATTGTTAAATACTTTTAGTCC
131 TTTTTAT-CATTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTCC
* * * * * *
30941022 AAGAATATAAATTTAATTATTTATTTTTCACTAAAATTAGATTTTTTTTATTTAATTTACT-TAT
195 GAGAATATAAAATTAAATA-TT-TTTTTCATTAAAATTAGA-TTTTTTTACTTAA-TTACTATGT
* * *
30941086 TACGTTAACTCTCACACATTTACGTTAAGATTTTAAAA-TTAGTTATTACACTTTTATAAGTTTT
256 TACATTAACTCTCACACATTTACGTTAAGA-TTTAAAATTTAGTTATTCCACCTTTATAAGTTTT
* * * * *
30941150 TATGTCAATTCTTATAGTTTTACGTTAAGACTTATCTACGTCAATTTTGAACTATAATTATTTTA
320 TACGTCAATTCTTACAGTTTTACGTAAAG-CTTTTCTATGTCAATTTTGAACTATAATTATTTTA
* * * *
30941215 TCCTTATTATTCTTTATTTTAAAATTAAAATTTGCATATCATTAAATACTTTTAGTTCGAGAATA
384 TCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTTCGAGAATA
*
30941280 TAAATTTAAATATTTGTTTTGCACTAAAATTAGA--TTTTTTAC-TAATTG
449 TAAATTTAAATATTTGTTTTTCACTAAAATTAGATTTTTTTTACTTAATTG
* * * *
30941328 ACTTTTTACTTTAAGTCTCACACATTTACGTTAAAATTTAAAATTTAGTTATTCCAA--TTTCAT
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATT-CAACCTTT-AT
* * * * * * *
30941391 AAGTTTTTACGTTAATTCTTATAATTTTACATCAAAACTTTTTTATGTCAATTTTGAGCTATAGT
64 AAGTTTTTATGTCAATTCTTATAGTTTTACGTCAAAACTTTTATATGTCAATTTTGAACTATAAT
* * * * *
30941456 TATCTTTATCCTTAGTT-TTCTTTA-TTTAAAAGTAAAAAATTTTTATACCGTTAAACACTTTTA
129 TATTTTTATCATTA-TTATTCTTTATTTTAAAA-T-TAAAATTTGTATATCGTTAAACACTTTTA
* *
30941519 G-CCAGAGAA-A-AAATATTCAAATATTTGGTTTTCATTAATATTAGATTTTTTTACTTAATTAT
191 GTCC-GAGAATATAAA-ATT-AAATATTT--TTTTCATTAAAATTAGATTTTTTTACTTAATTAC
* * * *
30941581 TATTTTACACTAACTCTCACACGTTTACGTTAATATTTAAAATTTAGTTATTCCACCTTTATAAG
251 TATGTTACATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAG
* * * * * * * *
30941646 GTTTTATGTTAATTTTTACATTTTTATGTAAAGGCTTTTTTATGTCAATTTTAAACTATAATTAT
316 TTTTTACGTCAATTCTTACAGTTTTACGTAAA-GCTTTTCTATGTCAATTTTGAACTATAATTA-
* * * * * *
30941711 TTTTATCTTTATTATTTTTTATTTAAAAATTACAATTTTTATATCGTTAAACATTTTTA-ATCTG
379 TTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTTC-G
* * * * * * * *
30941775 AGCATAT-AACTTAATATATATAG-TTTCCATTAGAATTAGATTTTTTTTCCTAAATTG
443 AGAATATAAATTTAA-ATAT-TTGTTTTTCACTAAAATTAGATTTTTTTTACTTAATTG
* * * * * * *
30941832 AGTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTAATTACTCTACCTATATGA
1 ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCAACCTTTATAA
30941897 GTTTTTATGTCAATTCTTAT
66 GTTTTTATGTCAATTCTTAT
30941917 TGCTTTTCAT
Statistics
Matches: 1357, Mismatches: 194, Indels: 72
0.84 0.12 0.04
Matches are distributed among these distances:
497 6 0.00
498 183 0.13
499 37 0.03
500 470 0.35
501 331 0.24
502 11 0.01
503 116 0.09
504 192 0.14
505 11 0.01
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (499 bp):
ACTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCAACCTTTATAA
GTTTTTATGTCAATTCTTATAGTTTTACGTCAAAACTTTTATATGTCAATTTTGAACTATAATTA
TTTTTATCATTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTCCG
AGAATATAAAATTAAATATTTTTTTCATTAAAATTAGATTTTTTTACTTAATTACTATGTTACAT
TAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTC
AATTCTTACAGTTTTACGTAAAGCTTTTCTATGTCAATTTTGAACTATAATTATTTTATCCTTAT
TATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTTCGAGAATATAAATTT
AAATATTTGTTTTTCACTAAAATTAGATTTTTTTTACTTAATTG
Found at i:30940911 original size:252 final size:251
Alignment explanation
Indices: 30939829--30941915 Score: 2381
Period size: 252 Copynumber: 8.3 Consensus size: 251
30939819 TATTATTATC
* * *
30939829 ACTTGTTACGTTAACTCTCACATATTTACGTTAAGATTTTAAATTT-GCTTATTCCACCTTTATA
1 ACTTGTTACATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAG-TTATTCCACCTTTATA
* * * * *
30939893 AGTTTTTATATTAATTCTTACAGTTTTACGTCAAAACTTTTCAATGTCACTTTTGAACTATAATT
65 AGTTTTTATGTCAATTCTTACAGTTTTACGTCAAAGCTTTTCTATGTCAATTTTGAACTATAATT
* * * *
30939958 ATTTTTATCCTTATTATTTTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTAGTCC
130 ATTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTTC
* *
30940023 GATAATATAAATTTAAATA--T-TTTTT-ATTAAAATTATATTTTTTTACTTAATTG
195 GAGAATATAAATTTAAATATTTGTTTTTCATTAAAATTAGATTTTTTTACTTAATTG
* * * *
30940076 A-TGTGTTACATTAACTCTCACACATTTACTTTAAAATTTAAAATTTATTTATTCCACCTGTATA
1 ACT-TGTTACATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATA
** * * * * *
30940140 AGTTTTTACATCAATTCTTACAGTTTTACGTCAAGGTTTTTCTATATCAGTTTTGAACTAGAATT
65 AGTTTTTATGTCAATTCTTACAGTTTTACGTCAAAGCTTTTCTATGTCAATTTTGAACTATAATT
* * * * * * *
30940205 ATCTTTATCTTTACTATTTTTTATTTAAAAATAAAAATTTGTATATCGTTAAACACATTTAGTTG
130 ATTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTTC
* * * *
30940270 GGGAATATAAATTCAAATATTTGTTTTTTATTAAAATTAGATATTTTTACTTAATTG
195 GAGAATATAAATTTAAATATTTGTTTTTCATTAAAATTAGATTTTTTTACTTAATTG
* * *
30940327 ACTTGTTACATTAACTCTCACACATTTACGTTAAGCTTTAAAATGTAGTTATTCAACCTTTATAA
1 ACTTGTTACATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* *
30940392 GTTTTTATGTCAATTCTTATAGTTTTACGTC-AAGACTTTTATATGTCAATTTTGAACTATAATT
66 GTTTTTATGTCAATTCTTACAGTTTTACGTCAAAG-CTTTTCTATGTCAATTTTGAACTATAATT
* * * * * * *
30940456 ATTTTTATCATTATTGTTTTTTATTTAATAATTAAAATTTATATATTGTTAAACATTTTTAG-TC
130 ATTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTTC
* *
30940520 TGAGAATATAAAATTAAATA-TT-TTTTTCATTAAAATTAGATTTTTTTACTTAATTC
195 -GAGAATATAAATTTAAATATTTGTTTTTCATTAAAATTAGATTTTTTTACTTAATTG
* * *
30940576 ACTTGTTACATTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTTCACATTTATAA
1 ACTTGTTACATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* * * **
30940641 GTTATTACGTCAATTCTTACAGCTTTATATCAAAGCTTTTCTATGTCAATTTTGAACTATAATTA
66 GTTTTTATGTCAATTCTTACAGTTTTACGTCAAAGCTTTTCTATGTCAATTTTGAACTATAATTA
** * * *
30940706 -TTTTATTCCTTATTATTCTTTATCCAAAAATTAAAATTTTTATATTGTTAAACAGTTTTAGTTC
131 TTTTTA-TCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTTC
* * * *
30940770 AAGAATATAAATTTAAATATTTGTTTTTCACTAAAATTTGATTTTTTTTACTTAATTT
195 GAGAATATAAATTTAAATATTTGTTTTTCATTAAAATTAGA-TTTTTTTACTTAATTG
** * * *
30940828 ACTTGTTATGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTCTACTTTTATAA
1 ACTTGTTACATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
* * * * * *
30940893 GTTTTTATATCCATTCTTACAGTTTTACGTCAAGGCTTTTCTATATAAATTTTGAGCTATAATTA
66 GTTTTTATGTCAATTCTTACAGTTTTACGTCAAAGCTTTTCTATGTCAATTTTGAACTATAATTA
* * * * * *
30940958 TTTTTATCCATATTATTCTTTATTTTAAAATTAAAATTTGTATATTGTTAAATACTTTTAGTCCA
131 TTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTTCG
* * * * *
30941023 AGAATATAAATTTAATTATTTATTTTTCACTAAAATTAGATTTTTTTTATTTAATTT
196 AGAATATAAATTTAAATATTTGTTTTTCATTAAAATTAGA-TTTTTTTACTTAATTG
* * * *
30941080 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTTAAAA-TTAGTTATTACACTTTTATA
1 ACTTGTTACATTAACTCTCACACATTTACGTTAAGA-TTTAAAATTTAGTTATTCCACCTTTATA
* * * *
30941144 AGTTTTTATGTCAATTCTTATAGTTTTACGT-TAAGACTTATCTACGTCAATTTTGAACTATAAT
65 AGTTTTTATGTCAATTCTTACAGTTTTACGTCAAAG-CTTTTCTATGTCAATTTTGAACTATAAT
* * * *
30941208 TA-TTTTATCCTTATTATTCTTTATTTTAAAATTAAAATTTGCATATCATTAAATACTTTTAGTT
129 TATTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTT
* *
30941272 CGAGAATATAAATTTAAATATTTGTTTTGCACTAAAATTAGA-TTTTTTAC-TAATTG
194 CGAGAATATAAATTTAAATATTTGTTTTTCATTAAAATTAGATTTTTTTACTTAATTG
* * * * *
30941328 ACTTTTTACTTTAAGTCTCACACATTTACGTTAAAATTTAAAATTTAGTTATTCCA-ATTTCATA
1 ACTTGTTACATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTT-ATA
* * * * * * * * *
30941392 AGTTTTTACGTTAATTCTTATAATTTTACATCAAAACTTTTTTATGTCAATTTTGAGCTATAGTT
65 AGTTTTTATGTCAATTCTTACAGTTTTACGTCAAAGCTTTTCTATGTCAATTTTGAACTATAATT
* * * * *
30941457 ATCTTTATCCTTAGTT-TTCTTTATTTAAAAGTAAAAAATTTTTATACCGTTAAACACTTTTAG-
130 ATTTTTATCCTTA-TTATTCTTTATTTAAAAAT-TAAAATTTGTATATCGTTAAACACTTTTAGT
* * *
30941520 CCAGAGAA-A-AAATATTCAAATATTTGGTTTTCATTAATATTAGATTTTTTTACTTAATT-
193 TC-GAGAATATAAAT-TT-AAATATTTGTTTTTCATTAAAATTAGATTTTTTTACTTAATTG
* * * * *
30941579 ATTATTTTACACTAACTCTCACACGTTTACGTTAATATTTAAAATTTAGTTATTCCACCTTTATA
1 ACT-TGTTACATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATA
* * * * * * *
30941644 AGGTTTTATGTTAATTTTTACATTTTTATGT-AAAGGCTTTTTTATGTCAATTTTAAACTATAAT
65 AGTTTTTATGTCAATTCTTACAGTTTTACGTCAAA-GCTTTTCTATGTCAATTTTGAACTATAAT
* * * * * *
30941708 TATTTTTATCTTTATTATTTTTTATTTAAAAATTACAATTTTTATATCGTTAAACATTTTTA-AT
129 TATTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTT
* * * * * * *
30941772 CTGAGCATAT-AACTTAATATATATAG-TTTCCATTAGAATTAGATTTTTTTTCCTAAATTG
194 C-GAGAATATAAATTTAA-ATAT-TTGTTTTTCATTAAAATTAGA-TTTTTTTACTTAATTG
* * * * * * * *
30941832 AGTTGTTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTAATTACTCTACCTATATGA
1 ACTTGTTACATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
30941897 GTTTTTATGTCAATTCTTA
66 GTTTTTATGTCAATTCTTA
30941916 TTGCTTTTCA
Statistics
Matches: 1575, Mismatches: 225, Indels: 75
0.84 0.12 0.04
Matches are distributed among these distances:
246 1 0.00
247 192 0.12
248 112 0.07
249 246 0.16
250 73 0.05
251 380 0.24
252 554 0.35
253 17 0.01
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (251 bp):
ACTTGTTACATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACCTTTATAA
GTTTTTATGTCAATTCTTACAGTTTTACGTCAAAGCTTTTCTATGTCAATTTTGAACTATAATTA
TTTTTATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTTCG
AGAATATAAATTTAAATATTTGTTTTTCATTAAAATTAGATTTTTTTACTTAATTG
Found at i:30941270 original size:752 final size:751
Alignment explanation
Indices: 30939827--30941916 Score: 2578
Period size: 752 Copynumber: 2.8 Consensus size: 751
30939817 ATTATTATTA
* * * *
30939827 TCACTTGTTACGTTAACTCTCACATATTTACGTTAAGATTTTAAATTT-GCTTATTCCACCTTTA
1 TCACTTGTTACATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAG-TTATTCCACATTTA
** * * *
30939891 TAAGTTTTTATATTAATTCTTACAGTTTTACGTCAAAACTTTTCAATGTCACTTTTGAACTATAA
65 TAAGTTTTTACGTTAATTCTTACAGTTTTACATCAAAACTTTTCTATGTCAATTTTGAACTATAA
* * * *
30939956 TTATTTT-TATCCTTATTATTTTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTAG
130 TTATTTTAT-TCCTTATTATTCTTTATTTAAAAATTAAAATTTTTATATCGTTAAACACTTTTAG
* * *
30940020 TCCGATAATATAAATTTAAATA--T-TTTTT-ATTAAAA-TT-ATATTTTTTTACTTAATTGATG
194 TCCAAGAATATAAATTTAAATATTTGTTTTTCATTAAAATTTGAT-TTTTTTTACTTAATTTAT-
* *
30940079 TGTTACATTAACTCTCACACATTTACT-TTAAAATTTAAAATTTATTTATTCCACCTGTATAAGT
257 TGTTACATTAACTCTCACACATTTA-TGTTAAAATTTAAAATTTAGTTATTCCACCTTTATAAGT
* * * * *
30940143 TTTTACATCAATTCTTACAGTTTTACGTCAAGGTTTTTCTATATCAGTTTTGAACTAGAATTATC
321 TTTTATATCAATTCTTACAGTTTTACGTCAAGGCTTTTCTATATCAATTTTGAACTATAATTATT
* * * ** *
30940208 TTTATCTTTACTATTTTTTATTTAAAAATAAAAATTTGTATATCGTTAAACACATTTAGTTGGGG
386 TTTATCTTTATTATTTTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTCCGAG
* * * * * *
30940273 AATATAAATTCAAATATTTGTTTTTTATTAAAATTAGA-TATTTTTACTTAATTGACTTGTTACA
451 AATATAAATTTAATTATTTATTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTACG
*
30940337 TTAACTCTCACACATTTACGTTAAG-CTTTAAAATGTAGTTATT-CAACCTTTATAAGTTTTTAT
516 TTAACTCTCACACATTTACGTTAAGATTTTAAAAT-TAGTTATTAC-A-CTTTATAAGTTTTTAT
* *
30940400 GTCAATTCTTATAGTTTTACGTCAAGACTTTTATATGTCAATTTTGAACTATAATTATTTTTATC
578 GTCAATTCTTATAGTTTTACGTCAAGACTTATATACGTCAATTTTGAACTATAATTATTTTTATC
* * * ** *
30940465 ATTATTGTTTTTTATTTAATAATTAAAATTTATATATTGTTAAACATTTTTAG-TCTGAGAATAT
643 ATTATTATTCTTTATTTAATAATTAAAATTTACATATCATTAAACACTTTTAGTTC-GAGAATAT
*
30940529 AAAATTAAATATTT-TTTT-CATTAAAATTAGATTTTTTTACTTAAT
707 AAAATTAAATATTTGTTTTGCACTAAAATTAGA-TTTTTTAC-TAAT
* *
30940574 TCACTTGTTACATTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTTCACATTTAT
1 TCACTTGTTACATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACATTTAT
* * * * *
30940639 AAGTTATTACGTCAATTCTTACAGCTTTATATCAAAGCTTTTCTATGTCAATTTTGAACTATAAT
66 AAGTTTTTACGTTAATTCTTACAGTTTTACATCAAAACTTTTCTATGTCAATTTTGAACTATAAT
** * * *
30940704 TATTTTATTCCTTATTATTCTTTATCCAAAAATTAAAATTTTTATATTGTTAAACAGTTTTAGTT
131 TATTTTATTCCTTATTATTCTTTATTTAAAAATTAAAATTTTTATATCGTTAAACACTTTTAGTC
*
30940769 CAAGAATATAAATTTAAATATTTGTTTTTCACTAAAATTTGATTTTTTTTACTTAATTTACTTGT
196 CAAGAATATAAATTTAAATATTTGTTTTTCATTAAAATTTGATTTTTTTTACTTAATTTA-TTGT
** * * *
30940834 TATGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTCTACTTTTATAAGTTTTT
260 TACATTAACTCTCACACATTTATGTTAAAATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTT
* * *
30940899 ATATCCATTCTTACAGTTTTACGTCAAGGCTTTTCTATATAAATTTTGAGCTATAATTATTTTTA
325 ATATCAATTCTTACAGTTTTACGTCAAGGCTTTTCTATATCAATTTTGAACTATAATTATTTTTA
** * * * * *
30940964 TCCATATTATTCTTTATTTTAAAATTAAAATTTGTATATTGTTAAATACTTTTAGTCCAAGAATA
390 TCTTTATTATTTTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTCCGAGAATA
* * * *
30941029 TAAATTTAATTATTTATTTTTCACTAAAATTAGATTTTTTTTATTTAATTTACTTATTACGTTAA
455 TAAATTTAATTATTTATTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTACGTTAA
30941094 CTCTCACACATTTACGTTAAGATTTTAAAATTAGTTATTACACTTTTATAAGTTTTTATGTCAAT
520 CTCTCACACATTTACGTTAAGATTTTAAAATTAGTTATTACAC-TTTATAAGTTTTTATGTCAAT
* * *
30941159 TCTTATAGTTTTACGTTAAGACTTATCTACGTCAATTTTGAACTATAATTA-TTTTATCCTTATT
584 TCTTATAGTTTTACGTCAAGACTTATATACGTCAATTTTGAACTATAATTATTTTTATCATTATT
* * *
30941223 ATTCTTTATTTTAA-AATTAAAATTTGCATATCATTAAATACTTTTAGTTCGAGAATATAAATTT
649 ATTCTTTA-TTTAATAATTAAAATTTACATATCATTAAACACTTTTAGTTCGAGAATATAAAATT
30941287 AAATATTTGTTTTGCACTAAAATTAGATTTTTTACTAAT
713 AAATATTTGTTTTGCACTAAAATTAGATTTTTTACTAAT
* * * * *
30941326 TGACTTTTTACTTTAAGTCTCACACATTTACGTTAAAATTTAAAATTTAGTTATTCCA-ATTTCA
1 TCACTTGTTACATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACATTT-A
* * * * *
30941390 TAAGTTTTTACGTTAATTCTTATAATTTTACATCAAAACTTTTTTATGTCAATTTTGAGCTATAG
65 TAAGTTTTTACGTTAATTCTTACAGTTTTACATCAAAACTTTTCTATGTCAATTTTGAACTATAA
* * *
30941455 TTATCTTTA-TCCTTAGTT-TTCTTTATTTAAAAGTAAAAAATTTTTATACCGTTAAACACTTTT
130 TTAT-TTTATTCCTTA-TTATTCTTTATTTAAAAAT-TAAAATTTTTATATCGTTAAACACTTTT
* * *
30941518 AG-CCAGAGAA-A-AAATATTCAAATATTTGGTTTTCATTAATATTAGA-TTTTTTTACTTAATT
192 AGTCCA-AGAATATAAAT-TT-AAATATTTGTTTTTCATTAAAATTTGATTTTTTTTACTTAA-T
* * * *
30941579 ATTATT-TTACACTAACTCTCACACGTTTACGTTAATATTTAAAATTTAGTTATTCCACCTTTAT
253 -TTATTGTTACATTAACTCTCACACATTTATGTTAAAATTTAAAATTTAGTTATTCCACCTTTAT
* * * * * * * * * *
30941643 AAGGTTTTATGTTAATTTTTACATTTTTATGTAAAGGCTTTTTTATGTCAATTTTAAACTATAAT
317 AAGTTTTTATATCAATTCTTACAGTTTTACGTCAAGGCTTTTCTATATCAATTTTGAACTATAAT
* * * *
30941708 TATTTTTATCTTTATTATTTTTTATTTAAAAATTACAATTTTTATATCGTTAAACATTTTTAATC
382 TATTTTTATCTTTATTATTTTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTC
* * * * * * * * * *
30941773 TGAGCATAT-AACTTAATATATATAGTTTCCATTAGAATTAGATTTTTTTTCCTAAATTGAGTTG
447 CGAGAATATAAATTTAAT-TATTTATTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTG
* * * *
30941837 TTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTAATTACTCTAC-CTATATGAGTTT
511 TTACGTTAACTCTCACACATTTACGTTAAGATTTTAAAATTAGTTA-T-TACACTTTATAAGTTT
30941901 TTATGTCAATTCTTAT
574 TTATGTCAATTCTTAT
30941917 TGCTTTTCAT
Statistics
Matches: 1151, Mismatches: 162, Indels: 55
0.84 0.12 0.04
Matches are distributed among these distances:
747 184 0.16
748 2 0.00
749 1 0.00
750 5 0.00
751 22 0.02
752 701 0.61
753 209 0.18
754 27 0.02
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (751 bp):
TCACTTGTTACATTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATTCCACATTTAT
AAGTTTTTACGTTAATTCTTACAGTTTTACATCAAAACTTTTCTATGTCAATTTTGAACTATAAT
TATTTTATTCCTTATTATTCTTTATTTAAAAATTAAAATTTTTATATCGTTAAACACTTTTAGTC
CAAGAATATAAATTTAAATATTTGTTTTTCATTAAAATTTGATTTTTTTTACTTAATTTATTGTT
ACATTAACTCTCACACATTTATGTTAAAATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTA
TATCAATTCTTACAGTTTTACGTCAAGGCTTTTCTATATCAATTTTGAACTATAATTATTTTTAT
CTTTATTATTTTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGTCCGAGAATAT
AAATTTAATTATTTATTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTACGTTAAC
TCTCACACATTTACGTTAAGATTTTAAAATTAGTTATTACACTTTATAAGTTTTTATGTCAATTC
TTATAGTTTTACGTCAAGACTTATATACGTCAATTTTGAACTATAATTATTTTTATCATTATTAT
TCTTTATTTAATAATTAAAATTTACATATCATTAAACACTTTTAGTTCGAGAATATAAAATTAAA
TATTTGTTTTGCACTAAAATTAGATTTTTTACTAAT
Found at i:30960208 original size:9 final size:9
Alignment explanation
Indices: 30960194--30960218 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30960184 ATAGGATAAG
30960194 AAATAAAGA
1 AAATAAAGA
30960203 AAATAAAGA
1 AAATAAAGA
30960212 AAATAAA
1 AAATAAA
30960219 ATTCCTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (9 bp):
AAATAAAGA
Found at i:30960256 original size:25 final size:25
Alignment explanation
Indices: 30960222--30960283 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
30960212 AAATAAAATT
30960222 CCTATAATTAT-GATGATTCCCAATC
1 CCTATAATTATAG-TGATTCCCAATC
* * *
30960247 CCTATAATTATAGTGATTTCTAATT
1 CCTATAATTATAGTGATTCCCAATC
30960272 CCTATAATTATA
1 CCTATAATTATA
30960284 TTAATTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (25 bp):
CCTATAATTATAGTGATTCCCAATC
Found at i:30962243 original size:25 final size:25
Alignment explanation
Indices: 30962209--30962268 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
30962199 AAATAAAATC
30962209 CCTATAATTATGATGATTCCTAATT
1 CCTATAATTATGATGATTCCTAATT
* *
30962234 CCTATAATTATGGTGATTTCTAATT
1 CCTATAATTATGATGATTCCTAATT
30962259 CCTATAATTA
1 CCTATAATTA
30962269 CGTTAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (25 bp):
CCTATAATTATGATGATTCCTAATT
Found at i:30979919 original size:24 final size:24
Alignment explanation
Indices: 30979892--30979945 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
30979882 ATAGTCGCAC
*
30979892 TGAATGTTCTAGAATGAGGCTATT
1 TGAATATTCTAGAATGAGGCTATT
*
30979916 TGAATATTCTAGAATGAGGTTATT
1 TGAATATTCTAGAATGAGGCTATT
30979940 T-AATAT
1 TGAATAT
30979946 AAAATTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (24 bp):
TGAATATTCTAGAATGAGGCTATT
Found at i:30982306 original size:18 final size:18
Alignment explanation
Indices: 30982279--30982318 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
30982269 AATCATTAAT
*
30982279 TTATGGGTTATTTATGAA
1 TTATGGGTTATTTATAAA
*
30982297 TTATGTGTTATTTATAAA
1 TTATGGGTTATTTATAAA
30982315 TTAT
1 TTAT
30982319 TTGTGAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (18 bp):
TTATGGGTTATTTATAAA
Found at i:30985856 original size:118 final size:119
Alignment explanation
Indices: 30985658--30985937 Score: 366
Period size: 118 Copynumber: 2.3 Consensus size: 119
30985648 ATTTTTATAT
*
30985658 TTAATTTAGGCTCGACATATCTCACAACAAGTTCGATTTAAACAAAATTGAAATTCCTAAACTTA
1 TTAATCTAGGCTCGACATATCTCACAA-AAGTTCGATTT-AACAAAATTGAAATTCCTAAACTTA
* * * *
30985723 ATTTAGGCTTGACCTATTTCACAACAGATTCAATTT-AAACTTGAAATTCCTAGGC
64 ATCTAGGCTTGACCTATTTCACAACAGATTCAATTTAAAAATTAAAATTCCTAGAC
* * * *
30985778 TTAATCTATGTTCGACTTATCTCACAAAATGTTCGATTTAA-AAAATTGAAATTCCTAGACTTAA
1 TTAATCTAGGCTCGACATATCTCACAAAA-GTTCGATTTAACAAAATTGAAATTCCTAAACTTAA
* * * *
30985842 TCTAGGCTTTACCTATTTCACAACAGGTTCCATTTAAAAATTAAAATTCTTAGAC
65 TCTAGGCTTGACCTATTTCACAACAGATTCAATTTAAAAATTAAAATTCCTAGAC
* * *
30985897 TTAATCTAGGCTCGACCTATCTCATAACAGGTTCGATTTAA
1 TTAATCTAGGCTCGACATATCTCACAA-AAGTTCGATTTAA
30985938 TTCTTTAATG
Statistics
Matches: 139, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
118 53 0.38
119 53 0.38
120 33 0.24
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (119 bp):
TTAATCTAGGCTCGACATATCTCACAAAAGTTCGATTTAACAAAATTGAAATTCCTAAACTTAAT
CTAGGCTTGACCTATTTCACAACAGATTCAATTTAAAAATTAAAATTCCTAGAC
Found at i:30985902 original size:59 final size:59
Alignment explanation
Indices: 30985658--30985937 Score: 303
Period size: 59 Copynumber: 4.7 Consensus size: 59
30985648 ATTTTTATAT
* * * * *
30985658 TTAATTTAGGCTCGACATATCTCACAACAAGTTCGATTTAAACAAAATTGAAATTCCTAAAC
1 TTAATCTAGGCTTGACCTATCTCACAACAGGTTCGATTT--A-AAAATTGAAATTCCTAGAC
* * * * * *
30985720 TTAATTTAGGCTTGACCTATTTCACAACAGATTCAATTT-AAACTTGAAATTCCTAGGC
1 TTAATCTAGGCTTGACCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAGAC
* * * *
30985778 TTAATCTATG-TTCGACTTATCTCACAAAATGTTCGATTTAAAAAATTGAAATTCCTAGAC
1 TTAATCTAGGCTT-GACCTATCTCACAACAGGTTCGATTT-AAAAATTGAAATTCCTAGAC
* * * * *
30985838 TTAATCTAGGCTTTACCTATTTCACAACAGGTTCCATTTAAAAATTAAAATTCTTAGAC
1 TTAATCTAGGCTTGACCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAGAC
* *
30985897 TTAATCTAGGCTCGACCTATCTCATAACAGGTTCGATTTAA
1 TTAATCTAGGCTTGACCTATCTCACAACAGGTTCGATTTAA
30985938 TTCTTTAATG
Statistics
Matches: 181, Mismatches: 33, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
57 2 0.01
58 44 0.24
59 54 0.30
60 46 0.25
61 2 0.01
62 33 0.18
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (59 bp):
TTAATCTAGGCTTGACCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAGAC
Found at i:30994950 original size:2 final size:2
Alignment explanation
Indices: 30994943--30994971 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30994933 TTACTTATTT
30994943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30994972 TTCTAAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30995998 original size:42 final size:43
Alignment explanation
Indices: 30995906--30995998 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 43
30995896 TGATTTTGGT
* **
30995906 TTTTTTTGTGGTTTTGAAAGATCTGATTTTTTTGTTTGAATTTG
1 TTTTTTT-TGGTTTTGAAAGATCTGAGTTTTTTGTTTGAAAATG
**
30995950 -GGTTTTTGGTTTATGAAAGAT-TGAGTTTTTTG-TTGAAAATG
1 TTTTTTTTGGTTT-TGAAAGATCTGAGTTTTTTGTTTGAAAATG
30995991 TTTTTTTT
1 TTTTTTTT
30995999 TGTCCCCCCT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
41 7 0.17
42 21 0.52
43 12 0.30
ACGTcount: A:0.18, C:0.01, G:0.22, T:0.59
Consensus pattern (43 bp):
TTTTTTTTGGTTTTGAAAGATCTGAGTTTTTTGTTTGAAAATG
Found at i:30995999 original size:43 final size:42
Alignment explanation
Indices: 30995904--30996000 Score: 101
Period size: 43 Copynumber: 2.3 Consensus size: 42
30995894 TATGATTTTG
*
30995904 GTTTTTTTTGTGGTTTTGAAAGATCTGATTTTTTTGTTTGAAT
1 GTTTTTTTT-TGGTTTTGAAAGATCTGAGTTTTTTGTTTGAAT
**
30995947 -TTGGGTTTTTGGTTTATGAAAGAT-TGAGTTTTTTG-TTGAAAAT
1 GTT-TTTTTTTGGTTT-TGAAAGATCTGAGTTTTTTGTTTG--AAT
30995990 GTTTTTTTTTG
1 GTTTTTTTTTG
30996001 TCCCCCCTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
41 3 0.07
42 18 0.41
43 21 0.48
44 2 0.05
ACGTcount: A:0.18, C:0.01, G:0.23, T:0.59
Consensus pattern (42 bp):
GTTTTTTTTTGGTTTTGAAAGATCTGAGTTTTTTGTTTGAAT
Found at i:31000566 original size:24 final size:25
Alignment explanation
Indices: 31000538--31000586 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
31000528 TATTTAACAT
31000538 ATTCTGA-TTTTTTATTTGGGCAAA
1 ATTCTGATTTTTTTATTTGGGCAAA
31000562 ATTCTGATTTTTTTATTTGGGCAAA
1 ATTCTGATTTTTTTATTTGGGCAAA
31000587 TATCTGCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.51
Consensus pattern (25 bp):
ATTCTGATTTTTTTATTTGGGCAAA
Found at i:31018202 original size:37 final size:36
Alignment explanation
Indices: 31018159--31018266 Score: 101
Period size: 35 Copynumber: 3.0 Consensus size: 36
31018149 AACAACCTTT
* *
31018159 ACAAGTGAAGCACTACTTTATGCAAGAACAAGTAAAA
1 ACAAGTGAAACACTACTTCATG-AAGAACAAGTAAAA
* *
31018196 ACAAGTGAAACACTACTTCATGTAGAACAATTAAAA
1 ACAAGTGAAACACTACTTCATGAAGAACAAGTAAAA
** ** * * *
31018232 TGAA-TGAAGTATTACTTCATGTAGAACAACTAAAA
1 ACAAGTGAAACACTACTTCATGAAGAACAAGTAAAA
31018267 TAAATGGAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
35 27 0.44
36 14 0.23
37 20 0.33
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (36 bp):
ACAAGTGAAACACTACTTCATGAAGAACAAGTAAAA
Found at i:31018255 original size:35 final size:35
Alignment explanation
Indices: 31018207--31018282 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
31018197 CAAGTGAAAC
* *
31018207 ACTACTTCATGTAGAACAATTAAAATGAATGAAGT
1 ACTACTTCATGTAGAACAACTAAAATAAATGAAGT
* *
31018242 ATTACTTCATGTAGAACAACTAAAATAAATGGAGT
1 ACTACTTCATGTAGAACAACTAAAATAAATGAAGT
31018277 ACTACT
1 ACTACT
31018283 CCATACAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (35 bp):
ACTACTTCATGTAGAACAACTAAAATAAATGAAGT
Found at i:31018293 original size:35 final size:35
Alignment explanation
Indices: 31018219--31018299 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
31018209 TACTTCATGT
* * * * **
31018219 AGAACAATTAAAATGAATGAAGTATTACTTCATGT
1 AGAACAACTAAAATAAATGAAGTACTACTCCATAC
*
31018254 AGAACAACTAAAATAAATGGAGTACTACTCCATAC
1 AGAACAACTAAAATAAATGAAGTACTACTCCATAC
*
31018289 AGAACGACTAA
1 AGAACAACTAA
31018300 TGCAAGTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (35 bp):
AGAACAACTAAAATAAATGAAGTACTACTCCATAC
Found at i:31020798 original size:48 final size:48
Alignment explanation
Indices: 31020715--31020821 Score: 142
Period size: 48 Copynumber: 2.2 Consensus size: 48
31020705 ACAATAATAG
* * * * *
31020715 CTCCAACATCATGAACAACCTTAATACTCGGAGTAGATCCATCATTAA
1 CTCCAACATCATGAACAACCTCAACAATCGAAGTAGATCCAACATTAA
* *
31020763 CTCCAACATCATGAACAACCTCAACAATTGAAGTAGCTCCAACATTAA
1 CTCCAACATCATGAACAACCTCAACAATCGAAGTAGATCCAACATTAA
*
31020811 CTCTAACATCA
1 CTCCAACATCA
31020822 AGAATACCCT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.39, C:0.29, G:0.08, T:0.23
Consensus pattern (48 bp):
CTCCAACATCATGAACAACCTCAACAATCGAAGTAGATCCAACATTAA
Found at i:31025468 original size:30 final size:30
Alignment explanation
Indices: 31025409--31025482 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
31025399 AAACAGTAAC
* * *
31025409 ATGTTACTACCTAAGGCATTATTACTTAAG
1 ATGTTACTATCTAAAGCATTACTACTTAAG
**
31025439 ATGTTACTATCTAAAGCATTACTGTTTAAG
1 ATGTTACTATCTAAAGCATTACTACTTAAG
* *
31025469 GTGTTACTGTCTAA
1 ATGTTACTATCTAA
31025483 GGTTGTATTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (30 bp):
ATGTTACTATCTAAAGCATTACTACTTAAG
Found at i:31025520 original size:15 final size:15
Alignment explanation
Indices: 31025502--31025535 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
31025492 GCCCAAGGCA
31025502 TTACAACACAAGGTG
1 TTACAACACAAGGTG
* *
31025517 TTACAATACAATGTG
1 TTACAACACAAGGTG
31025532 TTAC
1 TTAC
31025536 TGTATAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (15 bp):
TTACAACACAAGGTG
Found at i:31026039 original size:29 final size:30
Alignment explanation
Indices: 31025975--31026039 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
31025965 TCTTACCTTG
* * * *
31025975 TTCTCATGTACTTGTTCACGTACACCCTCT
1 TTCTCTTGTACCTATTCACGTACACCATCT
31026005 TT-TCTTGTACCTATTCACGTACACCAT-T
1 TTCTCTTGTACCTATTCACGTACACCATCT
31026033 TTCTCTT
1 TTCTCTT
31026040 AACTTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 3 0.10
29 25 0.83
30 2 0.07
ACGTcount: A:0.17, C:0.31, G:0.08, T:0.45
Consensus pattern (30 bp):
TTCTCTTGTACCTATTCACGTACACCATCT
Found at i:31027861 original size:25 final size:25
Alignment explanation
Indices: 31027831--31027889 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
31027821 TCAATGCCAC
31027831 GCCACCATCATGATGACGTGGTAAT
1 GCCACCATCATGATGACGTGGTAAT
31027856 GCCACCATCATGATGACGTGGTAAT
1 GCCACCATCATGATGACGTGGTAAT
31027881 GCCA-CATCA
1 GCCACCATCA
31027890 CCATATGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 5 0.15
25 29 0.85
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (25 bp):
GCCACCATCATGATGACGTGGTAAT
Found at i:31028103 original size:20 final size:19
Alignment explanation
Indices: 31028078--31028121 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
31028068 CCTGCTTGAA
* *
31028078 TTTTTTTTCTTCTTCTTTCT
1 TTTTTTTTCTTATT-TTTAT
31028098 TTTTTTTTCTTATTTTTAT
1 TTTTTTTTCTTATTTTTAT
31028117 TTTTT
1 TTTTT
31028122 ATTTTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTTTCTTATTTTTAT
Found at i:31028119 original size:17 final size:17
Alignment explanation
Indices: 31028079--31028121 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
31028069 CTGCTTGAAT
*
31028079 TTTTTTTCTTCTTCTTTC
1 TTTTTTT-TTCTTATTTC
31028097 TTTTTTTTTCTTATTT-
1 TTTTTTTTTCTTATTTC
31028113 TTATTTTTT
1 TT-TTTTTT
31028122 ATTTTTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 2 0.09
17 14 0.61
18 7 0.30
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTTTTCTTATTTC
Found at i:31028123 original size:13 final size:14
Alignment explanation
Indices: 31028097--31028129 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
31028087 TTCTTCTTTC
31028097 TTTTT-TTTTCTTA
1 TTTTTATTTTCTTA
31028110 TTTTTATTTT-TTA
1 TTTTTATTTTCTTA
31028123 TTTTTAT
1 TTTTTAT
31028130 AAAACTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTATTTTCTTA
Found at i:31028295 original size:11 final size:12
Alignment explanation
Indices: 31028279--31028308 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
31028269 AGTTTTATAG
31028279 AAAGAAAGAA-A
1 AAAGAAAGAAGA
31028290 AAAGAAAGAAGA
1 AAAGAAAGAAGA
31028302 AAAGAAA
1 AAAGAAA
31028309 TTCAAGCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAGA
Found at i:31031014 original size:20 final size:20
Alignment explanation
Indices: 31030986--31031030 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
31030976 CTTTGAAGTG
*
31030986 GGAATGTAAAATTGGAGGTT
1 GGAACGTAAAATTGGAGGTT
31031006 GGAACGTAAAATTGGAGGTT
1 GGAACGTAAAATTGGAGGTT
31031026 GGAAC
1 GGAAC
31031031 AACCAAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.36, T:0.24
Consensus pattern (20 bp):
GGAACGTAAAATTGGAGGTT
Found at i:31032666 original size:17 final size:17
Alignment explanation
Indices: 31032644--31032676 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
31032634 CAAGGGCTTT
*
31032644 AGGCCCCCAATTTAGAG
1 AGGCCCCAAATTTAGAG
31032661 AGGCCCCAAATTTAGA
1 AGGCCCCAAATTTAGA
31032677 AAAGTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.18
Consensus pattern (17 bp):
AGGCCCCAAATTTAGAG
Found at i:31032755 original size:7 final size:7
Alignment explanation
Indices: 31032745--31032770 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31032735 ATGATATAAA
31032745 AATAATT
1 AATAATT
31032752 AATAATT
1 AATAATT
31032759 AATAATT
1 AATAATT
31032766 AATAA
1 AATAA
31032771 AATTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AATAATT
Done.