Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 179 of 425
Found at i:54196580 original size:47 final size:48
Alignment explanation
Indices: 54196503--54196669 Score: 232
Period size: 47 Copynumber: 3.5 Consensus size: 48
54196493 TGCTTTATCA
* *
54196503 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
1 TATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTT
*
54196552 TATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCGTAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
* * *
54196599 GATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCC-TTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
*
54196646 AATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTT
54196670 GCACTTCCTC
Statistics
Matches: 107, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
47 68 0.64
48 26 0.24
49 13 0.12
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (48 bp):
TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
Found at i:54196604 original size:71 final size:71
Alignment explanation
Indices: 54196504--54196670 Score: 255
Period size: 71 Copynumber: 2.3 Consensus size: 71
54196494 GCTTTATCAT
* * *
54196504 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAA
54196568 GCCCTTTA
64 GCCCTTTA
* **
54196576 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
54196641 CCTTTA
66 CCTTTA
54196647 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
54196671 CACTTCCTCC
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
71 76 0.86
72 12 0.14
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.29
Consensus pattern (71 bp):
ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
CCTTTA
Found at i:54196741 original size:9 final size:9
Alignment explanation
Indices: 54196727--54196783 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
54196717 ATCTCATGTG
54196727 CATATCATA
1 CATATCATA
*
54196736 CATATCATGTG
1 CATATCA--TA
54196747 CATATCATA
1 CATATCATA
* *
54196756 CATGTCATGTG
1 CATATCA--TA
54196767 CATATCATA
1 CATATCATA
54196776 CATATCAT
1 CATATCAT
54196784 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:54196743 original size:20 final size:20
Alignment explanation
Indices: 54196715--54196785 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
54196705 GCATTTATGA
*
54196715 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
54196735 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
54196755 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
54196775 ACATATCATGT
1 ACATATCATGT
54196786 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:54196750 original size:11 final size:11
Alignment explanation
Indices: 54196720--54196774 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
54196710 TATGAACATC
54196720 TCATGTGCATA
1 TCATGTGCATA
*
54196731 TCA--TACATA
1 TCATGTGCATA
54196740 TCATGTGCATA
1 TCATGTGCATA
* *
54196751 TCA--TACATG
1 TCATGTGCATA
54196760 TCATGTGCATA
1 TCATGTGCATA
54196771 TCAT
1 TCAT
54196775 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:54198137 original size:27 final size:27
Alignment explanation
Indices: 54198108--54198447 Score: 414
Period size: 27 Copynumber: 12.6 Consensus size: 27
54198098 GGGTAGTTTA
* *
54198108 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * * *
54198135 GTAATTCTATAAATCAATGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
54198162 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
54198189 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
54198216 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * * *
54198243 ATAATTATGTAAATCGGGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
54198270 GTAATTATGTAAATTGGGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
54198297 GTAATTCTGTAAATTGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
54198324 GTAATTCTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
*
54198351 GTAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* ** *
54198378 GTAATTTTACAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
54198405 GTAATTCTAT-AACCTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
54198432 GTAATTCTGTAAATCG
1 GTAATTCTGTAAATCG
54198448 GGAGTACTTT
Statistics
Matches: 273, Mismatches: 36, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
26 3 0.01
27 266 0.97
28 4 0.01
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:54204159 original size:27 final size:28
Alignment explanation
Indices: 54204121--54204190 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
54204111 ATAGTGAGTC
54204121 CGCACACTTAGTGCTAAAAAATC-AACT
1 CGCACACTTAGTGCTAAAAAATCAAACT
* * *
54204148 CGCACACCTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTAAAAAATCAAACT
54204176 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54204191 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 20 0.53
28 18 0.47
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.24
Consensus pattern (28 bp):
CGCACACTTAGTGCTAAAAAATCAAACT
Found at i:54211103 original size:27 final size:28
Alignment explanation
Indices: 54211065--54211134 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
54211055 ATAGTGAGTC
54211065 CGCACACTTAGTGCTAAAAAATC-AACT
1 CGCACACTTAGTGCTAAAAAATCAAACT
* * *
54211092 CGCACACCTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTAAAAAATCAAACT
54211120 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54211135 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 20 0.53
28 18 0.47
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.24
Consensus pattern (28 bp):
CGCACACTTAGTGCTAAAAAATCAAACT
Found at i:54215543 original size:31 final size:31
Alignment explanation
Indices: 54215505--54215565 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
54215495 TTTCATATTT
54215505 CATATTTCATAACACTGGGCCGAAGCCTTTC
1 CATATTTCATAACACTGGGCCGAAGCCTTTC
**
54215536 CATATTTCATATTACTGGGCCGAAGCCTTT
1 CATATTTCATAACACTGGGCCGAAGCCTTT
54215566 ACTGTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (31 bp):
CATATTTCATAACACTGGGCCGAAGCCTTTC
Found at i:54217326 original size:31 final size:31
Alignment explanation
Indices: 54217288--54217348 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
54217278 TTTCATATTT
54217288 CATATTTCATAACACTGGGCCGAAGCCTTTC
1 CATATTTCATAACACTGGGCCGAAGCCTTTC
**
54217319 CATATTTCATATTACTGGGCCGAAGCCTTT
1 CATATTTCATAACACTGGGCCGAAGCCTTT
54217349 ACTGTAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (31 bp):
CATATTTCATAACACTGGGCCGAAGCCTTTC
Found at i:54229084 original size:39 final size:39
Alignment explanation
Indices: 54229040--54229354 Score: 531
Period size: 39 Copynumber: 8.1 Consensus size: 39
54229030 ATGCAAGACA
54229040 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
54229079 CTGGAAATGTATCCGGGCTAAAGTCCTGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* * *
54229118 CTGGAAATATATCAGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
54229157 CTGGAAATGTATCCGGGCTAAAGTCCCGCAAGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
54229196 CTGGAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
54229235 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
54229274 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* * *
54229313 CTGGAAATGTATCCGGGTTAAAGTCCCGCAGGATTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
54229352 CTG
1 CTG
54229355 ATAATATAAT
Statistics
Matches: 257, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 257 1.00
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:54234481 original size:27 final size:28
Alignment explanation
Indices: 54234443--54234512 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
54234433 ATAGTGAGTC
54234443 CGCACACTTAGTGCTAAAAAATC-AACT
1 CGCACACTTAGTGCTAAAAAATCAAACT
* * *
54234470 CGCACACCTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTAAAAAATCAAACT
54234498 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54234513 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 20 0.53
28 18 0.47
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.24
Consensus pattern (28 bp):
CGCACACTTAGTGCTAAAAAATCAAACT
Found at i:54238920 original size:31 final size:31
Alignment explanation
Indices: 54238882--54238942 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
54238872 TTTCATATTT
54238882 CATATTTCATAACACTGGGCCGAAGCCTTTC
1 CATATTTCATAACACTGGGCCGAAGCCTTTC
**
54238913 CATATTTCATATTACTGGGCCGAAGCCTTT
1 CATATTTCATAACACTGGGCCGAAGCCTTT
54238943 ACTGTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (31 bp):
CATATTTCATAACACTGGGCCGAAGCCTTTC
Found at i:54240703 original size:31 final size:31
Alignment explanation
Indices: 54240665--54240725 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
54240655 TTTCATATTT
54240665 CATATTTCATAACACTGGGCCGAAGCCTTTC
1 CATATTTCATAACACTGGGCCGAAGCCTTTC
**
54240696 CATATTTCATATTACTGGGCCGAAGCCTTT
1 CATATTTCATAACACTGGGCCGAAGCCTTT
54240726 ACTGTAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (31 bp):
CATATTTCATAACACTGGGCCGAAGCCTTTC
Found at i:54252437 original size:42 final size:42
Alignment explanation
Indices: 54252378--54252461 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
54252368 ATCGGGATGC
54252378 GTCAAAATCAGGCCCTTCAAAGCGTCCCATGAAATGCACTTA
1 GTCAAAATCAGGCCCTTCAAAGCGTCCCATGAAATGCACTTA
54252420 GTCAAAATCAGGCCCTTCAAAGCGTCCCATGAAATGCACTTA
1 GTCAAAATCAGGCCCTTCAAAGCGTCCCATGAAATGCACTTA
54252462 CACTCACCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (42 bp):
GTCAAAATCAGGCCCTTCAAAGCGTCCCATGAAATGCACTTA
Found at i:54254831 original size:18 final size:19
Alignment explanation
Indices: 54254786--54254833 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
54254776 CATGATATAC
54254786 ATAACATATATATAAAAACA
1 ATAACATA-ATATAAAAACA
* *
54254806 ATAA-ATAATATGAAAATA
1 ATAACATAATATAAAAACA
54254824 A-AACATAATA
1 ATAACATAATA
54254834 AAGATTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 16 0.64
19 3 0.12
20 4 0.16
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (19 bp):
ATAACATAATATAAAAACA
Found at i:54255036 original size:20 final size:20
Alignment explanation
Indices: 54255000--54255037 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54254990 GGAAAATAAT
*
54255000 ATATATAATAAGTAATAACA
1 ATATATAATAAGAAATAACA
54255020 ATATATAATTAA-AAATAA
1 ATATATAA-TAAGAAATAA
54255038 TACTCCTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
ATATATAATAAGAAATAACA
Found at i:54255111 original size:2 final size:2
Alignment explanation
Indices: 54255104--54255128 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54255094 AAATAATACA
54255104 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 A
54255129 GAATAATATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54261653 original size:26 final size:26
Alignment explanation
Indices: 54261624--54261683 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
54261614 TCCCTTTGAA
* * *
54261624 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
54261650 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
54261678 CCATTC
1 TCATTC
54261684 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:54261669 original size:28 final size:28
Alignment explanation
Indices: 54261638--54261709 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
54261628 TCGATATTTT
*
54261638 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
54261666 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* * *
54261694 GTACACTGAGTACCAT
1 GCACACTAAGTGCCAT
54261710 ATTTGATTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:54263998 original size:26 final size:26
Alignment explanation
Indices: 54263963--54264072 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
54263953 TGATACAAAT
*
54263963 TGATAATAGGTTAGGTAAATGTTCCT
1 TGATAATAGGTTAGGTAAATGTTCCA
54263989 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
54264015 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
54264041 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
54264067 TGATAA
1 TGATAA
54264073 GAATTTCATG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:54265552 original size:28 final size:26
Alignment explanation
Indices: 54265510--54265584 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
54265500 AAAAGTAGCT
*
54265510 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTATTATACCCCTA-G-ATGGA
* *
54265538 AAATTACTATTATACCCCTAGGTGTA
1 AAATTACTATTATACCCCTAGATGGA
**
54265564 AAATTACCGTTATACCCCTAG
1 AAATTACTATTATACCCCTAG
54265585 GGTTAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 22 0.52
27 1 0.02
28 19 0.45
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (26 bp):
AAATTACTATTATACCCCTAGATGGA
Found at i:54265754 original size:28 final size:27
Alignment explanation
Indices: 54265688--54265773 Score: 104
Period size: 27 Copynumber: 3.2 Consensus size: 27
54265678 GAGGAAGCGT
* *
54265688 TCTGGTGGCTATGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCAC-ATTATCTGTA
54265715 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCAC-ATTATCTGTA
* *
54265743 TCTGGTGACTCTGTCACATTATCTGT-
1 TCTGGTGGCTCTGCCACATTATCTGTA
54265769 TCTGG
1 TCTGG
54265774 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
26 5 0.09
27 32 0.60
28 16 0.30
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACATTATCTGTA
Found at i:54269728 original size:26 final size:26
Alignment explanation
Indices: 54269692--54269800 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
54269682 TGATACAAAT
*
54269692 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
54269718 TGATAATAGGTTAGGTAAATG-TTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
54269743 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
54269769 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
54269795 TGATAA
1 TGATAA
54269801 GAATTTCATG
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
25 23 0.29
26 57 0.71
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:54269747 original size:51 final size:52
Alignment explanation
Indices: 54269692--54269800 Score: 184
Period size: 51 Copynumber: 2.1 Consensus size: 52
54269682 TGATACAAAT
54269692 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATG-TTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTTCA
* * *
54269743 TGATAATGGGTTAGGTAAATGTTTCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTTCA
54269795 TGATAA
1 TGATAA
54269801 GAATTTCATG
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 44 0.81
52 10 0.19
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (52 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTTCA
Found at i:54271466 original size:28 final size:27
Alignment explanation
Indices: 54271400--54271485 Score: 104
Period size: 27 Copynumber: 3.2 Consensus size: 27
54271390 GAGGAAGCGT
* *
54271400 TCTGGTGGCTATGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCAC-ATTATCTGTA
54271427 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCAC-ATTATCTGTA
* *
54271455 TCTGGTGACTCTGTCACATTATCTGT-
1 TCTGGTGGCTCTGCCACATTATCTGTA
54271481 TCTGG
1 TCTGG
54271486 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
26 5 0.09
27 32 0.60
28 16 0.30
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACATTATCTGTA
Found at i:54275466 original size:28 final size:28
Alignment explanation
Indices: 54275432--54275724 Score: 245
Period size: 28 Copynumber: 10.5 Consensus size: 28
54275422 AACCAATCTT
* * *
54275432 GCACACACAGTGCTTGGTTACAGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** * *
54275460 GCACACACAGTGCCTCAACAACCGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
*
54275489 GCACACACAGTGCTCGGTTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** *
54275517 G--CACACAGTGCCTCAACAACTG-A-TC
1 GCACACACAGTG-CTCGATTACGGAACTC
* *
54275542 TCACACACAGTGCTCGGTTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** * *
54275570 GCACACACAGTGCCTCAACAACCGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
*
54275599 GCACACACAGTGCTCGATTATGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
*
54275627 GCACACACAGTGCTCGATTATGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** * *
54275655 GCACACACAGTGCCTCAACAACCGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
*
54275684 GCACACACAATGCTC-AGTTACGGAACTC
1 GCACACACAGTGCTCGA-TTACGGAACTC
*
54275712 ACACACACAGTGC
1 GCACACACAGTGC
54275725 CTATGTTCAC
Statistics
Matches: 206, Mismatches: 50, Indels: 18
0.75 0.18 0.07
Matches are distributed among these distances:
25 2 0.01
26 16 0.08
27 17 0.08
28 107 0.52
29 64 0.31
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.17
Consensus pattern (28 bp):
GCACACACAGTGCTCGATTACGGAACTC
Found at i:54275472 original size:57 final size:57
Alignment explanation
Indices: 54275402--54275639 Score: 358
Period size: 57 Copynumber: 4.2 Consensus size: 57
54275392 GATCTCATTT
* * * * *
54275402 CACACACTTAGTGCCCCAACAACCAATCTTGCACACACAGTGCTTGGTTACAGAACTCG
1 CACACAC--AGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
54275461 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
*
54275518 --CACACAGTGCCTCAACAACTGATCT--CACACACAGTGCTCGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* *
54275571 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGATTATGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
54275628 CACACACAGTGC
1 CACACACAGTGC
54275640 TCGATTATGG
Statistics
Matches: 166, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
53 28 0.17
55 48 0.29
57 83 0.50
59 7 0.04
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (57 bp):
CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
Found at i:54275606 original size:110 final size:110
Alignment explanation
Indices: 54275433--54275633 Score: 366
Period size: 110 Copynumber: 1.8 Consensus size: 110
54275423 ACCAATCTTG
*
54275433 CACACACAGTGCTTGGTTACAGAACTCGCACACACAGTGCCTCAACAACCGATCTCGCACACACA
1 CACACACAGTGCTCGGTTACAGAACTCGCACACACAGTGCCTCAACAACCGATCTCGCACACACA
*
54275498 GTGCTCGGTTACGGAACTCGCACACAGTGCCTCAACAACTGATCT
66 GTGCTCGATTACGGAACTCGCACACAGTGCCTCAACAACTGATCT
*
54275543 CACACACAGTGCTCGGTTACGGAACTCGCACACACAGTGCCTCAACAACCGATCTCGCACACACA
1 CACACACAGTGCTCGGTTACAGAACTCGCACACACAGTGCCTCAACAACCGATCTCGCACACACA
*
54275608 GTGCTCGATTATGGAACTCGCACACA
66 GTGCTCGATTACGGAACTCGCACACA
54275634 CAGTGCTCGA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 87 1.00
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.17
Consensus pattern (110 bp):
CACACACAGTGCTCGGTTACAGAACTCGCACACACAGTGCCTCAACAACCGATCTCGCACACACA
GTGCTCGATTACGGAACTCGCACACAGTGCCTCAACAACTGATCT
Found at i:54275652 original size:85 final size:85
Alignment explanation
Indices: 54275543--54275724 Score: 303
Period size: 85 Copynumber: 2.1 Consensus size: 85
54275533 CAACTGATCT
*
54275543 CACACACAGTGCTCGGTTACGGAACTCGCACACACAGTGCCTCAACAACCGATCTCGCACACACA
1 CACACACAGTGCTCGATTACGGAACTCGCACACACAGTGCCTCAACAACCGATCTCGCACACACA
* * *
54275608 GTGCTC-GATTATGGAACTCG
66 ATGCTCAG-TTACGGAACTCA
*
54275628 CACACACAGTGCTCGATTATGGAACTCGCACACACAGTGCCTCAACAACCGATCTCGCACACACA
1 CACACACAGTGCTCGATTACGGAACTCGCACACACAGTGCCTCAACAACCGATCTCGCACACACA
54275693 ATGCTCAGTTACGGAACTCA
66 ATGCTCAGTTACGGAACTCA
54275713 CACACACAGTGC
1 CACACACAGTGC
54275725 CTATGTTCAC
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
85 90 0.99
86 1 0.01
ACGTcount: A:0.30, C:0.35, G:0.18, T:0.17
Consensus pattern (85 bp):
CACACACAGTGCTCGATTACGGAACTCGCACACACAGTGCCTCAACAACCGATCTCGCACACACA
ATGCTCAGTTACGGAACTCA
Found at i:54277421 original size:28 final size:28
Alignment explanation
Indices: 54277388--54277459 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
54277378 TCGGTATTTT
*
54277388 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
54277416 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* *
54277444 GTACACTAAGTACCAT
1 GCACACTAAGTGCCAT
54277460 ATTTGATTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:54280662 original size:20 final size:21
Alignment explanation
Indices: 54280639--54280677 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
54280629 TAATTTAGCC
54280639 ATTTTTATTTTT-ATTTAAAT
1 ATTTTTATTTTTAATTTAAAT
*
54280659 ATTTTTGTTTTTAATTTAA
1 ATTTTTATTTTTAATTTAA
54280678 TTTTTACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (21 bp):
ATTTTTATTTTTAATTTAAAT
Found at i:54281426 original size:26 final size:26
Alignment explanation
Indices: 54281390--54281499 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
54281380 TGATACAAAT
54281390 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
54281416 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
54281442 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
54281468 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
54281494 TGATAA
1 TGATAA
54281500 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:54283034 original size:25 final size:25
Alignment explanation
Indices: 54282986--54283034 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
54282976 ACAGTTTTAC
54282986 CCCTAGGAGATAAATTACCGAAATA
1 CCCTAGGAGATAAATTACCGAAATA
* *
54283011 CCCTAGG-GTTAAATTGACCTAAAT
1 CCCTAGGAGATAAATT-ACCGAAAT
54283035 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CCCTAGGAGATAAATTACCGAAATA
Found at i:54287218 original size:26 final size:26
Alignment explanation
Indices: 54287182--54287291 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
54287172 TGATACAAAT
54287182 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
54287208 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
54287234 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
54287260 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
54287286 TGATAA
1 TGATAA
54287292 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:54288826 original size:25 final size:25
Alignment explanation
Indices: 54288778--54288826 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
54288768 ACAGTTTTAC
54288778 CCCTAGGAGATAAATTACCGAAATA
1 CCCTAGGAGATAAATTACCGAAATA
* *
54288803 CCCTAGG-GTTAAATTGACCTAAAT
1 CCCTAGGAGATAAATT-ACCGAAAT
54288827 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CCCTAGGAGATAAATTACCGAAATA
Found at i:54290677 original size:28 final size:28
Alignment explanation
Indices: 54290629--54290686 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
54290619 TTTTGTTCAT
*
54290629 TTTAAAAAATTAAAATGTATTTATATCA
1 TTTAAAAAATTAAAATCTATTTATATCA
* *
54290657 TTTAAAAATTTAAAGA-CTATTTTTATCA
1 TTTAAAAAATTAAA-ATCTATTTATATCA
54290685 TT
1 TT
54290687 CATGTTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (28 bp):
TTTAAAAAATTAAAATCTATTTATATCA
Found at i:54294196 original size:18 final size:19
Alignment explanation
Indices: 54294167--54294221 Score: 85
Period size: 18 Copynumber: 2.9 Consensus size: 19
54294157 ATAATCTTCA
54294167 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
54294186 ATGAT-TGCAATCTTAAAT
1 ATGATATGCAATCTTAGAT
*
54294204 ATGGTATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
54294222 AGATATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:54294534 original size:18 final size:18
Alignment explanation
Indices: 54294511--54294546 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
54294501 TGTTTCCCTG
54294511 ATTTTTTT-ATATATTTTA
1 ATTTTTTTAATA-ATTTTA
54294529 ATTTTTTTAATAATTTTA
1 ATTTTTTTAATAATTTTA
54294547 GTATCATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTTTTAATAATTTTA
Found at i:54304545 original size:89 final size:87
Alignment explanation
Indices: 54304416--54304577 Score: 193
Period size: 89 Copynumber: 1.8 Consensus size: 87
54304406 ATTCGACGGA
* * *
54304416 GAGCAGATCGAAGACATAGCAGATCTAACCTTCGGATGTTT-TCACATCGAAGTAGATCCAAGAT
1 GAGCAGATCGAAGACATAACAGATCTAACCTTCCGATGTTTAT-AC-T-GAAGCAGATCCAAGAT
54304480 GATTTGGCATCCTTGCGTTTACAAG
63 GATTTGGCATCCTTGCGTTTACAAG
* ** * * *
54304505 GAGCAGATCGAAGACATAACAGATTTGGCTTTCACG-TGTTTATGCTGAAGCAGATCTAAGATGA
1 GAGCAGATCGAAGACATAACAGATCTAACCTTC-CGATGTTTATACTGAAGCAGATCCAAGATGA
54304569 TTTGGCATC
65 TTTGGCATC
54304578 TTGTATTGTC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
87 25 0.40
88 1 0.02
89 34 0.55
90 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (87 bp):
GAGCAGATCGAAGACATAACAGATCTAACCTTCCGATGTTTATACTGAAGCAGATCCAAGATGAT
TTGGCATCCTTGCGTTTACAAG
Found at i:54304757 original size:217 final size:219
Alignment explanation
Indices: 54304300--54304885 Score: 901
Period size: 217 Copynumber: 2.7 Consensus size: 219
54304290 CAGGCTAAAG
* * * * * * **
54304300 CATAGCAGATTTGAC-CTCAGGTGTTTACGCCGAAGCGGATCCAAGATGATTTAACATCTCTGTA
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCT-TGTA
*
54304364 TTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
65 TTGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
* *
54304429 ACATAGCAGATCTAACCTTCGGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTT
130 ACATAGCAGAGCTAACCTTCAGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTT
*
54304494 GCGTTTACAAGGAGCAGATCGAAGA
195 GCGTTGACAAGGAGCAGATCGAAGA
* *
54304519 CATAACAGATTTGGCTTTCACGTGTTTATGCTGAAGCAGATCTAAGATGATTTGGCATCTTGTAT
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTTGTAT
*
54304584 TGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACAGAGAGCAGATCGAAGA
66 TGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGA
*
54304649 CATAGCAGAGCTAACCTT-AGA-GTTTTCACATTGAAGTAGATCCAAGATGATTTGGCATCCTTG
131 CATAGCAGAGCTAACCTTCAGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTTG
54304712 CGTTGACAAGGAGCAGATCGAAGA
196 CGTTGACAAGGAGCAGATCGAAGA
* *
54304736 CATAGCAGATTTGGCTTTCACGTGTTTACACTGAAGCAGATCTAAGATGATTTGGCATCCCTGTA
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCAT-CTTGTA
* * * *
54304801 CTGTCAGAGAACAAATCGAA-AAACAAATTTCGCATCTCCATATTCGACGGAGAGCTGATCGAAG
65 TTGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
* * *
54304865 ACATAGTAGATCTGACCTTCA
130 ACATAGCAGAGCTAACCTTCA
54304886 TTGAAGCAGT
Statistics
Matches: 336, Mismatches: 28, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
217 175 0.52
218 27 0.08
219 98 0.29
220 36 0.11
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (219 bp):
CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTTGTAT
TGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGA
CATAGCAGAGCTAACCTTCAGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTTG
CGTTGACAAGGAGCAGATCGAAGA
Found at i:54304967 original size:78 final size:78
Alignment explanation
Indices: 54304827--54305274 Score: 634
Period size: 78 Copynumber: 5.8 Consensus size: 78
54304817 CGAAAAACAA
* ** * * * *
54304827 ATTTCGCATCTCCATATTCGACGGAGAGCTGATCGAAGACATAGTAGATCTGACCTTCATTGAAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
*
54304892 CAGTTCCAAGATG
66 CAGATCCAAGATG
* * *
54304905 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAAACACAGCAGAT-TGGACCTTTATTGAA
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGAA
54304969 GCAGATCCAAGATG
65 GCAGATCCAAGATG
** * * *
54304983 ATTTGGCATCTCCATATTCGACGGAGAGCAAATCGAAGACATAGCAGATCTGACCTTCATTGAAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
54305048 CAGATCCAAGATG
66 CAGATCCAAGATG
* * * *
54305061 ATTTGGCATCTTTGTATTAGATGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCAATGAAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
54305126 CAGATCCAAGATG
66 CAGATCCAAGATG
* * *
54305139 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACATAACAAAT-TGGACCTTCATTGAA
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGAA
*
54305203 GTA-ATCCAAGATG
65 GCAGATCCAAGATG
54305216 ATTTGGCATCTCTGTATTAGAC-GGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
54305275 GTGTTTACAT
Statistics
Matches: 327, Mismatches: 39, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
76 32 0.10
77 35 0.11
78 259 0.79
79 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (78 bp):
ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
CAGATCCAAGATG
Found at i:54305435 original size:89 final size:89
Alignment explanation
Indices: 54305288--54305486 Score: 267
Period size: 89 Copynumber: 2.2 Consensus size: 89
54305278 TTTACATCAA
* * * *
54305288 AGCAGATCCAAGAT-GACATATTTGGCATCTCTGTACTAGACGGGAGCAAATCGGAGATAACAGA
1 AGCAGATCAAAGATAG-CAGATTTGGCATCTCTGTACTAGACGAGAGCAAATCGAAGATAACAGA
*
54305352 TTTGGCATCTCTGTATTAGACGGAG
65 TTTGGCATCTCTGTATTAGACAGAG
** * * *
54305377 AGCAGATTGAAGA-AGCAGATTTGGCGTCTCTGTATTAGACAGAGAGCAGATCGAAGATAACAGA
1 AGCAGATCAAAGATAGCAGATTTGGCATCTCTGTACTAGAC-GAGAGCAAATCGAAGATAACAGA
*
54305441 TTTGGCGTCTCTGTATTAGACAGAG
65 TTTGGCATCTCTGTATTAGACAGAG
54305466 AGCAGATCAAAGATAGCAGAT
1 AGCAGATCAAAGATAGCAGAT
54305487 ATCACCTTTC
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
88 22 0.23
89 66 0.69
90 7 0.07
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.24
Consensus pattern (89 bp):
AGCAGATCAAAGATAGCAGATTTGGCATCTCTGTACTAGACGAGAGCAAATCGAAGATAACAGAT
TTGGCATCTCTGTATTAGACAGAG
Found at i:54305455 original size:133 final size:134
Alignment explanation
Indices: 54305215--54305461 Score: 315
Period size: 133 Copynumber: 1.8 Consensus size: 134
54305205 AATCCAAGAT
*
54305215 GATTTGGCATCTCTGTATTAGACGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATGTGTT
1 GATTTGGCATCTCTGTATTAGACGGGAGCAGATCGAAGA-ATAGCAGATCTGACCTTCATGTGAT
* *
54305280 TACATCAAAGCAGATCCAAGATGACATATTTGGCATCTCTGTACTAGACGGGAGCAAATCGGAGA
65 TACATCAAAGCAGATCCAAGATAACAGATTTGGCATCTCTGTACTAGACGGGAGCAAATCGGAGA
54305345 TAACA
130 TAACA
* * * *
54305350 GATTTGGCATCTCTGTATTAGACGGAGAGCAGATTGAAG-A-AGCAGATTTGGCGTCTC-TGT-A
1 GATTTGGCATCTCTGTATTAGACGG-GAGCAGATCGAAGAATAGCAGATCTGACCT-TCATGTGA
* * * *
54305411 TTAGA-CAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTATTAGAC
64 TTACATCA-A-AGCAGATCCAAGATAACAGATTTGGCATCTCTGTACTAGAC
54305462 AGAGAGCAGA
Statistics
Matches: 97, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
131 2 0.02
132 5 0.05
133 50 0.52
134 3 0.03
135 25 0.26
136 12 0.12
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (134 bp):
GATTTGGCATCTCTGTATTAGACGGGAGCAGATCGAAGAATAGCAGATCTGACCTTCATGTGATT
ACATCAAAGCAGATCCAAGATAACAGATTTGGCATCTCTGTACTAGACGGGAGCAAATCGGAGAT
AACA
Found at i:54305456 original size:45 final size:45
Alignment explanation
Indices: 54305215--54305486 Score: 268
Period size: 44 Copynumber: 6.1 Consensus size: 45
54305205 AATCCAAGAT
* *
54305215 GATTTGGCATCTCTGTATTAGAC-GGGAGCAGATCGAAGACATAGCA
1 GATTTGGCATCTCTGTATTAGACAGAGAGCAGATCGAAG--ATAACA
* * * * * * *
54305261 GATCTGACCT-TCATGTGTTTACATCA-A-AGCAGATCCAAGATGACA
1 GATTTGGCATCTC-TGT-ATTAGA-CAGAGAGCAGATCGAAGATAACA
* * * * *
54305306 TATTTGGCATCTCTGTACTAGAC-GGGAGCAAATCGGAGATAACA
1 GATTTGGCATCTCTGTATTAGACAGAGAGCAGATCGAAGATAACA
* * *
54305350 GATTTGGCATCTCTGTATTAGACGGAGAGCAGATTGAAGA-AGCA
1 GATTTGGCATCTCTGTATTAGACAGAGAGCAGATCGAAGATAACA
*
54305394 GATTTGGCGTCTCTGTATTAGACAGAGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTAGACAGAGAGCAGATCGAAGATAACA
* * *
54305439 GATTTGGCGTCTCTGTATTAGACAGAGAGCAGATCAAAGATAGCA
1 GATTTGGCATCTCTGTATTAGACAGAGAGCAGATCGAAGATAACA
54305484 GAT
1 GAT
54305487 ATCACCTTTC
Statistics
Matches: 183, Mismatches: 34, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
43 1 0.01
44 78 0.43
45 76 0.42
46 12 0.07
47 15 0.08
48 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (45 bp):
GATTTGGCATCTCTGTATTAGACAGAGAGCAGATCGAAGATAACA
Found at i:54306902 original size:22 final size:22
Alignment explanation
Indices: 54306874--54306925 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
54306864 AGTTCAGATA
54306874 AGATGCAGAACAGATCA-AATAC
1 AGATGCAGAACAGATCAGAAT-C
*
54306896 AGATGCAGAATAGATCAGAATC
1 AGATGCAGAACAGATCAGAATC
*
54306918 AAATGCAG
1 AGATGCAG
54306926 TTTCCTACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 24 0.89
23 3 0.11
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.15
Consensus pattern (22 bp):
AGATGCAGAACAGATCAGAATC
Found at i:54308326 original size:18 final size:18
Alignment explanation
Indices: 54308303--54308337 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54308293 TATATGGCAA
*
54308303 AAAAGAAGAGAACAAAAG
1 AAAAGAAAAGAACAAAAG
54308321 AAAAGAAAAGAACAAAA
1 AAAAGAAAAGAACAAAA
54308338 AGAAGGGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAACAAAAG
Found at i:54310126 original size:46 final size:46
Alignment explanation
Indices: 54310076--54310248 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
54310066 TGGTTGAGCA
54310076 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54310122 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54310167 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54310215 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
54310249 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54310232 original size:93 final size:93
Alignment explanation
Indices: 54310073--54310243 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
54310063 GGATGGTTGA
* *
54310073 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54310138 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
54310166 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54310231 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
54310244 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:54317690 original size:46 final size:46
Alignment explanation
Indices: 54317640--54317812 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
54317630 TGGTTGAGCA
54317640 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54317686 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54317731 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54317779 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
54317813 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54317796 original size:93 final size:93
Alignment explanation
Indices: 54317637--54317807 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
54317627 GGATGGTTGA
* *
54317637 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54317702 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
54317730 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54317795 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
54317808 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:54320708 original size:20 final size:20
Alignment explanation
Indices: 54320680--54320723 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
54320670 ACCAAACTTG
*
54320680 CAACTTACCATAATCTTTCA
1 CAACATACCATAATCTTTCA
*
54320700 CAACATACCATAGTCTTTCA
1 CAACATACCATAATCTTTCA
54320720 CAAC
1 CAAC
54320724 TTAAACTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (20 bp):
CAACATACCATAATCTTTCA
Found at i:54320919 original size:42 final size:42
Alignment explanation
Indices: 54320808--54320929 Score: 145
Period size: 43 Copynumber: 2.9 Consensus size: 42
54320798 TATCATACCA
* * **
54320808 ATGCCATATCCTAGATATGGTCTTACATGGGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * * *
54320850 ATGCCAATAGCCCAGCTATTGTCTTACACAAAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* *
54320893 ATGTCATATCCCAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCA
54320930 ACTAACCCTA
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 32 0.49
43 33 0.51
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:54322845 original size:21 final size:22
Alignment explanation
Indices: 54322820--54322874 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 22
54322810 CTAATCACAC
54322820 GGGTGTGACCCTTAGTCACAT-A
1 GGGTGTG-CCCTTAGTCACATGA
54322842 -GGTGTGTCCCTTAGTCACATGA
1 GGGTGTG-CCCTTAGTCACATGA
54322864 GGGTGTGCCCT
1 GGGTGTGCCCT
54322875 ATCACACGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 19 0.63
22 5 0.17
23 6 0.20
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (22 bp):
GGGTGTGCCCTTAGTCACATGA
Found at i:54331685 original size:40 final size:40
Alignment explanation
Indices: 54331641--54331821 Score: 201
Period size: 40 Copynumber: 4.5 Consensus size: 40
54331631 ACTCGTTCAA
*
54331641 ATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAG
1 ATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAG
* *
54331681 ATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAA
1 ATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAG
*
54331721 ATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCAC-G
1 ATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACAG
* * * *
54331760 AATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACA-
1 -ATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAG
*
54331801 AAGCCTTCGGGACTTAGCCCG
1 ATGCCTTCGGGACTTAGCCCG
54331822 ACATCATTCG
Statistics
Matches: 124, Mismatches: 11, Indels: 12
0.84 0.07 0.08
Matches are distributed among these distances:
39 3 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
ATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAG
Found at i:54333663 original size:20 final size:20
Alignment explanation
Indices: 54333638--54333678 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
54333628 TATCAATTCA
54333638 ATACCCGTTGAACTCTATGG
1 ATACCCGTTGAACTCTATGG
54333658 ATACCCGTTGAACTCTATGG
1 ATACCCGTTGAACTCTATGG
54333678 A
1 A
54333679 ATACTAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (20 bp):
ATACCCGTTGAACTCTATGG
Found at i:54333835 original size:69 final size:69
Alignment explanation
Indices: 54333719--54333903 Score: 273
Period size: 69 Copynumber: 2.7 Consensus size: 69
54333709 AGTGTCACAC
* * **
54333719 TGTAATATAGCTGAAGCTATCACTGTAACGTAGCCGAAGCTACCACTGTATTGTAGCCAAAGCTA
1 TGTAATATAGCCGAAGCTACCACTGTATTGTAGCCGAAGCTACCACTGTATTGTAGCCAAAGCTA
54333784 CCAT
66 CCAT
* * *
54333788 TGTATTATAGCCGAAGCTACCACTGTATTGTAGCTGAAGCTACCACTGTATTGTAGCCGAAGCTA
1 TGTAATATAGCCGAAGCTACCACTGTATTGTAGCCGAAGCTACCACTGTATTGTAGCCAAAGCTA
54333853 CCAT
66 CCAT
* *
54333857 TG-AGATGTAGCCGAAGCTACCACTATATTGTAGCCGAAGCTACCACT
1 TGTA-ATATAGCCGAAGCTACCACTGTATTGTAGCCGAAGCTACCACT
54333904 AAGATGTAGC
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
68 1 0.01
69 103 0.99
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (69 bp):
TGTAATATAGCCGAAGCTACCACTGTATTGTAGCCGAAGCTACCACTGTATTGTAGCCAAAGCTA
CCAT
Found at i:54333914 original size:23 final size:23
Alignment explanation
Indices: 54333716--54333903 Score: 243
Period size: 23 Copynumber: 8.2 Consensus size: 23
54333706 CAAAGTGTCA
* * * *
54333716 CACTGTAATATAGCTGAAGCTAT
1 CACTGTATTGTAGCCGAAGCTAC
**
54333739 CACTGTAACGTAGCCGAAGCTAC
1 CACTGTATTGTAGCCGAAGCTAC
*
54333762 CACTGTATTGTAGCCAAAGCTAC
1 CACTGTATTGTAGCCGAAGCTAC
* *
54333785 CATTGTATTATAGCCGAAGCTAC
1 CACTGTATTGTAGCCGAAGCTAC
*
54333808 CACTGTATTGTAGCTGAAGCTAC
1 CACTGTATTGTAGCCGAAGCTAC
54333831 CACTGTATTGTAGCCGAAGCTAC
1 CACTGTATTGTAGCCGAAGCTAC
* *
54333854 CATTG-AGATGTAGCCGAAGCTAC
1 CACTGTA-TTGTAGCCGAAGCTAC
*
54333877 CACTATATTGTAGCCGAAGCTAC
1 CACTGTATTGTAGCCGAAGCTAC
54333900 CACT
1 CACT
54333904 AAGATGTAGC
Statistics
Matches: 144, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
22 1 0.01
23 142 0.99
24 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (23 bp):
CACTGTATTGTAGCCGAAGCTAC
Found at i:54336755 original size:46 final size:44
Alignment explanation
Indices: 54336696--54336810 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
54336686 GACAGGACAA
* *
54336696 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
54336742 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
54336786 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
54336811 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:54336791 original size:44 final size:45
Alignment explanation
Indices: 54336696--54336829 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
54336686 GACAGGACAA
* *
54336696 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
54336742 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
54336786 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
54336830 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:54344059 original size:46 final size:44
Alignment explanation
Indices: 54344000--54344114 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
54343990 ACAGGACAGA
* *
54344000 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
54344046 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
54344090 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
54344115 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:54344095 original size:44 final size:45
Alignment explanation
Indices: 54344000--54344133 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
54343990 ACAGGACAGA
* *
54344000 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
54344046 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
54344090 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
54344134 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:54345613 original size:21 final size:22
Alignment explanation
Indices: 54345562--54345629 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 22
54345552 TACGGCCTGC
* *
54345562 TCACACGGGCGTG-ACCCTCAG
1 TCACACGGGTGTGTGCCCTCAG
54345583 TCACACGGGTGTGT-CCCTCAG
1 TCACACGGGTGTGTGCCCTCAG
* *
54345604 TCATATGGGTGTGTGCCCT-A-
1 TCACACGGGTGTGTGCCCTCAG
54345624 TCACAC
1 TCACAC
54345630 AGCTTGGACC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.10
21 32 0.80
22 4 0.10
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (22 bp):
TCACACGGGTGTGTGCCCTCAG
Found at i:54347475 original size:14 final size:15
Alignment explanation
Indices: 54347453--54347486 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
54347443 ACGATTCGTT
54347453 AAAAAAATTTAA-TG
1 AAAAAAATTTAAGTG
*
54347467 AAAATAATTTAAGTG
1 AAAAAAATTTAAGTG
54347482 AAAAA
1 AAAAA
54347487 TCTGTACAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (15 bp):
AAAAAAATTTAAGTG
Found at i:54349187 original size:19 final size:19
Alignment explanation
Indices: 54349159--54349195 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54349149 TAATTTAAGT
* *
54349159 TAAATTCTTAATTTAGGGG
1 TAAATACTTAAATTAGGGG
54349178 TAAATACTTAAATTAGGG
1 TAAATACTTAAATTAGGG
54349196 CTCAACCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (19 bp):
TAAATACTTAAATTAGGGG
Found at i:54352135 original size:23 final size:25
Alignment explanation
Indices: 54352109--54352161 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
54352099 TAGATTTTTA
54352109 TATTTTTATTG-TG-TTTTTACTGT
1 TATTTTTATTGTTGATTTTTACTGT
* *
54352132 TATTATTATTGTTGATTTTTATTGT
1 TATTTTTATTGTTGATTTTTACTGT
54352157 T-TTTT
1 TATTTT
54352162 GTTGTTAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 10 0.40
24 5 0.20
25 10 0.40
ACGTcount: A:0.15, C:0.02, G:0.11, T:0.72
Consensus pattern (25 bp):
TATTTTTATTGTTGATTTTTACTGT
Found at i:54352209 original size:42 final size:39
Alignment explanation
Indices: 54352163--54352261 Score: 123
Period size: 39 Copynumber: 2.5 Consensus size: 39
54352153 TTGTTTTTTG
*
54352163 TTGTTAGTTATTATTATTGTTAGTAAAAAACTATTATTAGGA
1 TTGTTAGTTATTATTATTGTTAGTAAAAAACTATAATT---A
* *
54352205 TTGTTGGTTATTATTA---TTAGTAAAAAACTCTAATTA
1 TTGTTAGTTATTATTATTGTTAGTAAAAAACTATAATTA
54352241 TTGTTAGTTATTATTATTGTT
1 TTGTTAGTTATTATTATTGTT
54352262 GATTTATATT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
36 16 0.32
39 19 0.38
42 15 0.30
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (39 bp):
TTGTTAGTTATTATTATTGTTAGTAAAAAACTATAATTA
Found at i:54352244 original size:36 final size:37
Alignment explanation
Indices: 54352163--54352258 Score: 113
Period size: 36 Copynumber: 2.5 Consensus size: 37
54352153 TTGTTTTTTG
*
54352163 TTGTTAGTTATTATTATTGTTAGTAAAAAACTATTATTAGGA
1 TTGTTAGTTATTATTA---TTAGTAAAAAACTATAATT--GA
* *
54352205 TTGTTGGTTATTATTATTAGTAAAAAACTCTAATT-A
1 TTGTTAGTTATTATTATTAGTAAAAAACTATAATTGA
54352241 TTGTTAGTTATTATTATT
1 TTGTTAGTTATTATTATT
54352259 GTTGATTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
36 18 0.36
39 17 0.34
42 15 0.30
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.51
Consensus pattern (37 bp):
TTGTTAGTTATTATTATTAGTAAAAAACTATAATTGA
Found at i:54359713 original size:137 final size:138
Alignment explanation
Indices: 54359551--54360296 Score: 1205
Period size: 138 Copynumber: 5.4 Consensus size: 138
54359541 ATTTCTAAAA
* *
54359551 ATTT-TAAAATATTCGGATTCTATTTTTTAAAATATACTATTTTCGTATTTTA-TTTTTATCTTA
1 ATTTCTAAAATATTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATCTTA
* *
54359614 TTTTAGTACATAATATTTCAAATGTATTATTTTAGAGTTTTTTAAATAACCCTGATTTTGTCCCT
66 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCCTGATTTTGTCCCT
54359679 TTGTTTGT
131 TTGTTTGT
*
54359687 ATTTCTAAAATATTCAGATTTTATTTTTTAAAATATATTATTTTCGTATTTTA-TTTTTATCTTA
1 ATTTCTAAAATATTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATCTTA
* *
54359751 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTATTTTTTAAATAACTCTGATTTTGTCCCT
66 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCCTGATTTTGTCCCT
54359816 TTGTTTGT
131 TTGTTTGT
* * *
54359824 ATTTCTAAAATATTCGGATTTTATTTTTTAAAATATATTATTTTTGTATTTTATTTTTTTATCTT
1 ATTTCTAAAATATTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTA-TTTTTTATCTT
*
54359889 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTG-TTTTTAAATAACTCTGATTTTGTCCC
65 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCCTGATTTTGTCCC
54359953 TTTGTTTGT
130 TTTGTTTGT
54359962 ATTTCTAAAATATTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATCTTA
1 ATTTCTAAAATATTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATCTTA
* * *
54360027 TTTTAGTACATAATGTTTCAAATTTATTATTTTAGTTTTTTTTAAATAACCCTAATTTTGTCCCT
66 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCCTGATTTTGTCCCT
*
54360092 TTGTTTCT
131 TTGTTTGT
*
54360100 ATTTCTAAAATATTCAGATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTTTTATCTTA
1 ATTTCTAAAATATTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATCTTA
* *
54360165 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCTTGATTTTGTCACT
66 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCCTGATTTTGTCCCT
54360230 TTGTTTGT
131 TTGTTTGT
* * *** *
54360238 ATTTCTAAAATTTTCGGATTTT-TTTATATTATTTTTATACTATTTTCGCATTTTATTTT
1 ATTTCTAAAATATTCAGATTTTATTT-T-TTA-AAATATACTATTTTCGTATTTTATTTT
54360297 ATTTTTTTCA
Statistics
Matches: 571, Mismatches: 32, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
136 4 0.01
137 226 0.40
138 269 0.47
139 50 0.09
140 22 0.04
ACGTcount: A:0.27, C:0.08, G:0.07, T:0.57
Consensus pattern (138 bp):
ATTTCTAAAATATTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATCTTA
TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCCTGATTTTGTCCCT
TTGTTTGT
Found at i:54360319 original size:15 final size:16
Alignment explanation
Indices: 54360291--54360350 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
54360281 TTTCGCATTT
54360291 TATTTTATTTTTTTCA
1 TATTTTATTTTTTTCA
*
54360307 TATTTTATTTTTTTCG
1 TATTTTATTTTTTTCA
54360323 TATTTTA-TTTTTTCA
1 TATTTTATTTTTTTCA
54360338 TATTTTATTTTTT
1 TATTTTATTTTTT
54360351 ATACTATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
15 14 0.34
16 27 0.66
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (16 bp):
TATTTTATTTTTTTCA
Found at i:54360331 original size:21 final size:20
Alignment explanation
Indices: 54360280--54360333 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 20
54360270 TTTTATACTA
54360280 TTTTCGCATTTTATTTTATTT
1 TTTTCG-ATTTTATTTTATTT
54360301 TTTTC-A---TATTTTATTT
1 TTTTCGATTTTATTTTATTT
54360317 TTTTCGTATTTTATTTT
1 TTTTCG-ATTTTATTTT
54360334 TTCATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
16 15 0.54
18 1 0.04
19 1 0.04
21 11 0.39
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (20 bp):
TTTTCGATTTTATTTTATTT
Found at i:54360360 original size:32 final size:32
Alignment explanation
Indices: 54360291--54360350 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 32
54360281 TTTCGCATTT
54360291 TATTTTATTTTTTTCATATTTTATTTTTTTCG
1 TATTTTATTTTTTTCATATTTTATTTTTTTCG
54360323 TATTTTA-TTTTTTCATATTTTATTTTTT
1 TATTTTATTTTTTTCATATTTTATTTTTT
54360351 ATACTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (32 bp):
TATTTTATTTTTTTCATATTTTATTTTTTTCG
Found at i:54360691 original size:11 final size:11
Alignment explanation
Indices: 54360659--54360692 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
54360649 ATAAATTTAT
*
54360659 AAATTAAATCT
1 AAATTAAATCA
54360670 AAATTAAATCA
1 AAATTAAATCA
*
54360681 AAATCAAATCA
1 AAATTAAATCA
54360692 A
1 A
54360693 CAATAATAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATTAAATCA
Found at i:54360850 original size:8 final size:8
Alignment explanation
Indices: 54360837--54360886 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 8
54360827 GCTTGCTCCT
54360837 TCTTCTTC
1 TCTTCTTC
*
54360845 TCTTCTTT
1 TCTTCTTC
54360853 TCTTCTTC
1 TCTTCTTC
54360861 TCTTCTT-
1 TCTTCTTC
54360868 TCTT-TTC
1 TCTTCTTC
*
54360875 TCTCCTT-
1 TCTTCTTC
54360882 TCTTC
1 TCTTC
54360887 CCCAAATGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 2 0.06
7 11 0.31
8 23 0.64
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (8 bp):
TCTTCTTC
Found at i:54360857 original size:16 final size:15
Alignment explanation
Indices: 54360836--54360886 Score: 77
Period size: 16 Copynumber: 3.4 Consensus size: 15
54360826 TGCTTGCTCC
54360836 TTCTTCTTCTCTTCTT
1 TTCTTCTTCTCTTC-T
54360852 TTCTTCTTCTCTTCT
1 TTCTTCTTCTCTTCT
*
54360867 TTCTT-TTCTCTCCT
1 TTCTTCTTCTCTTCT
54360881 TTCTTC
1 TTCTTC
54360887 CCCAAATGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 13 0.39
15 6 0.18
16 14 0.42
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCTTCTTCTCTTCT
Found at i:54361072 original size:14 final size:14
Alignment explanation
Indices: 54361053--54361083 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
54361043 TACTTCAGTT
54361053 TTTTTTTCAGCAAC
1 TTTTTTTCAGCAAC
*
54361067 TTTTTTTCAGCATC
1 TTTTTTTCAGCAAC
54361081 TTT
1 TTT
54361084 CTACTGTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.19, G:0.06, T:0.58
Consensus pattern (14 bp):
TTTTTTTCAGCAAC
Found at i:54361107 original size:22 final size:22
Alignment explanation
Indices: 54361079--54361123 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
54361069 TTTTTCAGCA
54361079 TCTTTCTACTGTTTCTTTTTTT
1 TCTTTCTACTGTTTCTTTTTTT
54361101 TCTTTCTACTGTTTCTTTTTTT
1 TCTTTCTACTGTTTCTTTTTTT
54361123 T
1 T
54361124 TACTGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.73
Consensus pattern (22 bp):
TCTTTCTACTGTTTCTTTTTTT
Found at i:54361115 original size:13 final size:13
Alignment explanation
Indices: 54361079--54361118 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
54361069 TTTTTCAGCA
54361079 TCTTTCTACTGTT
1 TCTTTCTACTGTT
54361092 TCTTT-T--T-TT
1 TCTTTCTACTGTT
54361101 TCTTTCTACTGTT
1 TCTTTCTACTGTT
54361114 TCTTT
1 TCTTT
54361119 TTTTTTACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
9 7 0.30
10 2 0.09
12 2 0.09
13 12 0.52
ACGTcount: A:0.05, C:0.20, G:0.05, T:0.70
Consensus pattern (13 bp):
TCTTTCTACTGTT
Found at i:54361129 original size:17 final size:19
Alignment explanation
Indices: 54361079--54361131 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 19
54361069 TTTTTCAGCA
54361079 TCTTTCTACTGTTTCTTTTTTT
1 TCTTTCTACTGTTTC---TTTT
54361101 TCTTTCTACTGTTTCTTTT
1 TCTTTCTACTGTTTCTTTT
54361120 T-TTT-TACTGTTT
1 TCTTTCTACTGTTT
54361132 TATGTCAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.26
18 3 0.10
19 5 0.16
22 15 0.48
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.72
Consensus pattern (19 bp):
TCTTTCTACTGTTTCTTTT
Found at i:54363867 original size:3 final size:3
Alignment explanation
Indices: 54363854--54363934 Score: 62
Period size: 3 Copynumber: 28.0 Consensus size: 3
54363844 TTCCATTTTC
* * * * *
54363854 TCT TAT TCT TCT TC- TCC TCC TCT TCT TTT TCT TAT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
54363901 TCT TC- TCT GT-T TCT T-T TCT TAT TCT TCT TTT TCT
1 TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT TCT
54363935 ACTGCCCAAG
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
2 7 0.11
3 54 0.87
4 1 0.02
ACGTcount: A:0.04, C:0.28, G:0.01, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:54363888 original size:29 final size:32
Alignment explanation
Indices: 54363849--54363934 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 32
54363839 TCTCCTTCCA
54363849 TTTTCTCTTATTCTTCTTC-TC-CTCCTCT-TC
1 TTTT-TCTTATTCTTCTTCTTCTCTCCTCTGTC
* *
54363879 TTTTTCTTATTCTTCTTCTTCTTCTTCTCTGTT
1 TTTTTCTTATTCTTCTTCTTC-TCTCCTCTGTC
*
54363912 TCTTTTCTTATTCTTCTTTTTCT
1 T-TTTTCTTATTCTTCTTCTTCT
54363935 ACTGCCCAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
29 14 0.29
30 6 0.12
32 6 0.12
33 3 0.06
34 19 0.40
ACGTcount: A:0.03, C:0.28, G:0.01, T:0.67
Consensus pattern (32 bp):
TTTTTCTTATTCTTCTTCTTCTCTCCTCTGTC
Found at i:54371233 original size:7 final size:7
Alignment explanation
Indices: 54371147--54371220 Score: 139
Period size: 7 Copynumber: 10.6 Consensus size: 7
54371137 TAAAAATTAT
*
54371147 AAAAATT
1 AAAAATC
54371154 AAAAATC
1 AAAAATC
54371161 AAAAATC
1 AAAAATC
54371168 AAAAATC
1 AAAAATC
54371175 AAAAATC
1 AAAAATC
54371182 AAAAATC
1 AAAAATC
54371189 AAAAATC
1 AAAAATC
54371196 AAAAATC
1 AAAAATC
54371203 AAAAATC
1 AAAAATC
54371210 AAAAATC
1 AAAAATC
54371217 AAAA
1 AAAA
54371221 TTAAAATTAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
7 66 1.00
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATC
Found at i:54371265 original size:19 final size:17
Alignment explanation
Indices: 54371223--54371267 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
54371213 AATCAAAATT
54371223 AAAATTAAAAAAATATA
1 AAAATTAAAAAAATATA
*
54371240 AACAATTAATAAAAATTTTA
1 AA-AATTAA-AAAAA-TATA
54371260 AAAATTAA
1 AAAATTAA
54371268 CATGAAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.08
18 6 0.25
19 11 0.46
20 5 0.21
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATTAAAAAAATATA
Found at i:54371390 original size:33 final size:33
Alignment explanation
Indices: 54371316--54371391 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
54371306 TTAAAATTTT
* *
54371316 AATATTTTAGTTAGCATTCTAGTTGAAGGAAAA
1 AATATTTTTGCTAGCATTCTAGTTGAAGGAAAA
*
54371349 AATATTTTTGCTAGCATTCTCGTTGAAGGAAAA
1 AATATTTTTGCTAGCATTCTAGTTGAAGGAAAA
*
54371382 ATTATTTTTG
1 AATATTTTTG
54371392 ACTATTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (33 bp):
AATATTTTTGCTAGCATTCTAGTTGAAGGAAAA
Found at i:54371919 original size:12 final size:12
Alignment explanation
Indices: 54371884--54371926 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
54371874 AAATTTTAAT
*
54371884 TTAATTTAATT-
1 TTAATATAATTA
54371895 TTAATAT-ATTA
1 TTAATATAATTA
54371906 TTAATATAATTA
1 TTAATATAATTA
*
54371918 TTTATATAA
1 TTAATATAA
54371927 CATTATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 3 0.11
11 13 0.46
12 12 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTAATATAATTA
Found at i:54372041 original size:27 final size:26
Alignment explanation
Indices: 54372008--54372100 Score: 71
Period size: 31 Copynumber: 3.4 Consensus size: 26
54371998 TTATTTCATT
54372008 AAATTTATATAATTAAATTAAAATTA
1 AAATTTATATAATTAAATTAAAATTA
* * *
54372034 AAATTTTAAATATATATTTAAATCACAATAAA
1 AAA-TTT--ATATA-A-TTAAATTAAAAT-TA
* * *
54372066 AAATATATATAACTACATT-AAATTA
1 AAATTTATATAATTAAATTAAAATTA
54372091 AAATTTATAT
1 AAATTTATAT
54372101 GTATAATTTC
Statistics
Matches: 51, Mismatches: 10, Indels: 13
0.69 0.14 0.18
Matches are distributed among these distances:
25 10 0.20
26 6 0.12
27 7 0.14
28 1 0.02
29 10 0.20
30 1 0.02
31 12 0.24
32 4 0.08
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (26 bp):
AAATTTATATAATTAAATTAAAATTA
Found at i:54379288 original size:17 final size:17
Alignment explanation
Indices: 54379260--54379297 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
54379250 TTAATTTTTT
54379260 AAAATTTTAAAAAT-TA
1 AAAATTTTAAAAATATA
54379276 AAAATTATTAAAAATATA
1 AAAATT-TTAAAAATATA
54379294 AAAA
1 AAAA
54379298 ATATCTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 8 0.40
18 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATTTTAAAAATATA
Found at i:54381008 original size:176 final size:174
Alignment explanation
Indices: 54380705--54381031 Score: 532
Period size: 176 Copynumber: 1.9 Consensus size: 174
54380695 AAGTGGGGGA
54380705 AGTAAAAGTTTTGGGGGAAAATAAAGAGGTTTGGGAGTTTAGGGTAAAAATGTAAAATATTATAA
1 AGTAAAAGTTTTGGGGGAAAATAAAGAGGTTTGGGAGTTTAGGGTAAAAATGTAAAATATTATAA
* * *
54380770 CTTGGTATTTGATTTATTCGAATTTGAAAACCAAACTCGATTCGAACTCGAAATTCAAAAAAAAA
66 CTTGATATTAGATTTATTCGAATTTGAAAACCAAACTCGATTCGAACTCAAAATTC-AAAAAAAA
*
54380835 AATTTTGAGTTGACTCAAATAATAGAAGGGGGTGGGATGAGAGGAT
130 AA-TTAGAGTTGACTCAAATAATAGAAGGGGGTGGGATGAGAGGAT
54380881 AGTAAAAGTTTTGGGGGAAAATAAAGAGGTTTGGGAGTTT-GGGATAAAAATGTAAAATATTATA
1 AGTAAAAGTTTTGGGGGAAAATAAAGAGGTTTGGGAGTTTAGGG-TAAAAATGTAAAATATTATA
** * *
54380945 GTTTGATATTCAG-TTTATTCGAATTTGAAAACCAAACTCGATTCGAATTCAAAATTTAAAAAAA
65 ACTTGATATT-AGATTTATTCGAATTTGAAAACCAAACTCGATTCGAACTCAAAATTCAAAAAAA
54381009 AAATTAGAGTTGACTCAAATAAT
129 AAATTAGAGTTGACTCAAATAAT
54381032 TAGATTAATT
Statistics
Matches: 141, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
174 19 0.13
175 13 0.09
176 108 0.77
177 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (174 bp):
AGTAAAAGTTTTGGGGGAAAATAAAGAGGTTTGGGAGTTTAGGGTAAAAATGTAAAATATTATAA
CTTGATATTAGATTTATTCGAATTTGAAAACCAAACTCGATTCGAACTCAAAATTCAAAAAAAAA
ATTAGAGTTGACTCAAATAATAGAAGGGGGTGGGATGAGAGGAT
Found at i:54381267 original size:17 final size:17
Alignment explanation
Indices: 54381245--54381282 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
54381235 GTGAATTAAA
*
54381245 AAATAAGTAAATA-TATT
1 AAATAA-TAAACATTATT
54381262 AAATAATAAACATTATT
1 AAATAATAAACATTATT
54381279 AAAT
1 AAAT
54381283 GCACTTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (17 bp):
AAATAATAAACATTATT
Found at i:54386654 original size:49 final size:50
Alignment explanation
Indices: 54386481--54386674 Score: 228
Period size: 50 Copynumber: 3.9 Consensus size: 50
54386471 TATTGTGAGT
* * * * *
54386481 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTAAGTGTACCAGATAA-TTAGG
* * * **
54386532 TCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTATCAGATGGTTAGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTAAGTGTACCAGATAATTAGG
* *
54386582 TCACGTGTGTAGTACTAAGTGCAGGCTACTAAGTGGACCGGATAATT-GG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTAAGTGTACCAGATAATTAGG
* * * *
54386631 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTAAGTGTACCAGATA
54386675 GCTTTGGCTA
Statistics
Matches: 121, Mismatches: 22, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
49 40 0.33
50 43 0.36
51 38 0.31
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (50 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTAAGTGTACCAGATAATTAGG
Found at i:54388144 original size:41 final size:44
Alignment explanation
Indices: 54388043--54388177 Score: 147
Period size: 43 Copynumber: 3.2 Consensus size: 44
54388033 GTGTTCTCGA
* * ***
54388043 GTAAGAC-CACGTCTGGGAC-GTTGGCATCAATATGTGATTATGT
1 GTAAGACTCATGTCTGGGACAG-TGGCATCGATATGTGATTGCAT
* *
54388086 GTAAGAC-CATGTCTGGGACATTGGCATCG-TATTTGATT-CAT
1 GTAAGACTCATGTCTGGGACAGTGGCATCGATATGTGATTGCAT
*
54388127 GTAAGACTC-TGTTTGGGACAGTGGCATCGATATGTGATTGCAT
1 GTAAGACTCATGTCTGGGACAGTGGCATCGATATGTGATTGCAT
54388170 GTAAGACT
1 GTAAGACT
54388178 ACATCCGAGA
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
41 26 0.33
42 17 0.22
43 36 0.46
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (44 bp):
GTAAGACTCATGTCTGGGACAGTGGCATCGATATGTGATTGCAT
Found at i:54388195 original size:43 final size:41
Alignment explanation
Indices: 54388102--54388202 Score: 105
Period size: 43 Copynumber: 2.4 Consensus size: 41
54388092 CCATGTCTGG
* * ** *
54388102 GACATTGGCATCGTATTTGATTCATGTAAGACTCTGTTTGG
1 GACATTGGCATCGTATGTGATTCATGTAAGACTCTATCCGA
*
54388143 GACAGTGGCATCGATATGTGATTGCATGTAAGACTAC-ATCCGA
1 GACATTGGCATCG-TATGTGATT-CATGTAAGACT-CTATCCGA
*
54388186 GACATTGGCATTGTATG
1 GACATTGGCATCGTATG
54388203 ATATATGTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
41 12 0.24
42 12 0.24
43 24 0.49
44 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (41 bp):
GACATTGGCATCGTATGTGATTCATGTAAGACTCTATCCGA
Found at i:54388436 original size:3 final size:3
Alignment explanation
Indices: 54388428--54388462 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
54388418 AATTTGGATG
54388428 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54388463 TTGAATGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:54390248 original size:8 final size:8
Alignment explanation
Indices: 54390237--54390267 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
54390227 CTAGATCGGC
54390237 AAAAGCCG
1 AAAAGCCG
54390245 AAAAGCCG
1 AAAAGCCG
*
54390253 AAATGCCG
1 AAAAGCCG
54390261 AAAAGCC
1 AAAAGCC
54390268 AGAATTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.48, C:0.26, G:0.23, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:54391015 original size:60 final size:60
Alignment explanation
Indices: 54390937--54391075 Score: 167
Period size: 60 Copynumber: 2.3 Consensus size: 60
54390927 CCAACTGTGT
* * *
54390937 TAATATGGGCAAGGCCCAATATA-TCTCGA-CTTGTAATAGGG-CTACGGCCCAGATTGATAC
1 TAATATGGGCTAGGCCCAATATACTCT-GATATTGT-A-AGGGACTACGGCCCAGATTAATAC
* * *
54390997 TGATATAGGCTAGGCCCAATATACTCTGATATTGTAAGGGACTACGGCCCAGATTAATAT
1 TAATATGGGCTAGGCCCAATATACTCTGATATTGTAAGGGACTACGGCCCAGATTAATAC
54391057 TAATATGGGCTAAGGCCCA
1 TAATATGGGCT-AGGCCCA
54391076 GTTAACTCTG
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
59 4 0.06
60 49 0.73
61 14 0.21
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (60 bp):
TAATATGGGCTAGGCCCAATATACTCTGATATTGTAAGGGACTACGGCCCAGATTAATAC
Found at i:54391085 original size:61 final size:61
Alignment explanation
Indices: 54390936--54391110 Score: 159
Period size: 60 Copynumber: 2.9 Consensus size: 61
54390926 CCCAACTGTG
* * *
54390936 TTAATATGGGC-AAGGCCCAATATA-TCTCGA-CTTGTAATAGGGCTACGGCCCAGATTGATA
1 TTAATATGGGCTAAGGCCCATTA-ACTCT-GATATTGTAATAGGGCTACGGCCCAGATTAATA
* * * *
54390996 CTGATATAGGCT-AGGCCCAATATACTCTGATATTGT-A-AGGGACTACGGCCCAGATTAATA
1 TTAATATGGGCTAAGGCCCATTA-ACTCTGATATTGTAATAGGG-CTACGGCCCAGATTAATA
*
54391056 TTAATATGGGCTAAGGCCCAGTTAACTCTGAT-TTCTGAATAGGGCTTA-GGCCCAG
1 TTAATATGGGCTAAGGCCCA-TTAACTCTGATATTGT-AATAGGGC-TACGGCCCAG
54391111 TAAAGCTTGA
Statistics
Matches: 95, Mismatches: 10, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
59 4 0.04
60 52 0.55
61 22 0.23
62 11 0.12
63 6 0.06
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (61 bp):
TTAATATGGGCTAAGGCCCATTAACTCTGATATTGTAATAGGGCTACGGCCCAGATTAATA
Found at i:54396378 original size:40 final size:40
Alignment explanation
Indices: 54396300--54396517 Score: 307
Period size: 40 Copynumber: 5.5 Consensus size: 40
54396290 AAACCAAGTA
* **
54396300 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTTAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
54396339 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
54396379 CCTTCGGGACCTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54396419 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
54396459 CCTTCAGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
54396499 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
54396518 TTATCATCCA
Statistics
Matches: 163, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 15 0.09
40 148 0.91
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:54398196 original size:29 final size:29
Alignment explanation
Indices: 54398163--54398236 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
54398153 CCTTCGAGCT
54398163 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
54398192 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
54398221 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
54398237 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:54398197 original size:58 final size:58
Alignment explanation
Indices: 54398104--54398236 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 58
54398094 ATACTCGATT
* * * * *
54398104 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACACACAGTGCCATGCCCTTCGAGC
1 TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
* * * ** * *
54398162 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGC
1 TCGCACACTTAGTGCCATGAGATTT-AAGCACGCACACACAGTGCCATACACTTCCAGC
*
54398220 ACGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
54398237 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 4 0.07
58 57 0.93
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (58 bp):
TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
Found at i:54406021 original size:29 final size:29
Alignment explanation
Indices: 54405987--54406118 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
54405977 TACTCGATTT
** * *
54405987 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* **** * *
54406016 CGCACACATAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
54406045 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
54406074 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
54406103 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
54406119 ATCTCGTCAC
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 2 0.02
29 84 0.98
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:54411061 original size:27 final size:28
Alignment explanation
Indices: 54411028--54411097 Score: 133
Period size: 27 Copynumber: 2.5 Consensus size: 28
54411018 ATAGTGATTC
54411028 CGCACACTTAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
54411055 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
54411083 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54411098 GTACCAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54414204 original size:27 final size:27
Alignment explanation
Indices: 54414174--54414234 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
54414164 ATTACCAAAG
*
54414174 TACCCTCAATTTATAGAATTACTGTTT
1 TACCCTCAATTTACAGAATTACTGTTT
*
54414201 TACCCTTAATTTACAGAATTACTGTTT
1 TACCCTCAATTTACAGAATTACTGTTT
54414228 TACCCTC
1 TACCCTC
54414235 GATTGTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.43
Consensus pattern (27 bp):
TACCCTCAATTTACAGAATTACTGTTT
Found at i:54414311 original size:54 final size:54
Alignment explanation
Indices: 54414228--54414371 Score: 134
Period size: 54 Copynumber: 2.7 Consensus size: 54
54414218 ATTACTGTTT
* * ** *
54414228 TACCCTCGA-TTGTGAAATTACTGAAATACCCCT-ATAGGGT-AGAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCACTGAT-GGGTGA-AATTACCAAAA
* * ** *
54414281 TACCC-CTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAA
1 TACCCTC-AATTTGTAAAATTACCAAAATACCACTGATGGGTGAAATTACCAAAA
*
54414335 TACCCTCAATTTGTAAAATTACCAAAATACCATTGAT
1 TACCCTCAATTTGTAAAATTACCAAAATACCACTGAT
54414372 TTACAAAATT
Statistics
Matches: 73, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
52 1 0.01
53 5 0.07
54 64 0.88
55 3 0.04
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (54 bp):
TACCCTCAATTTGTAAAATTACCAAAATACCACTGATGGGTGAAATTACCAAAA
Found at i:54414373 original size:27 final size:27
Alignment explanation
Indices: 54414270--54414479 Score: 149
Period size: 27 Copynumber: 7.7 Consensus size: 27
54414260 TATAGGGTAG
*
54414270 AATTACCAAAATACCCCT-AGTTTGTAA
1 AATTACCAAAATACCCTTGA-TTTGTAA
* *
54414297 AATTACCAAAATACCAC-TGGTTTGTGA
1 AATTACCAAAATACC-CTTGATTTGTAA
* **
54414324 AATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCCTTGATTTGTAA
* **
54414351 AATTACCAAAATACCATTGATTTACAA
1 AATTACCAAAATACCCTTGATTTGTAA
*
54414378 AATTA-CAGAAATACCCTTGACTTTCTAAA
1 AATTACCA-AAATACCCTTGA-TTTGT-AA
* * * **
54414407 AATTA-TAGAAATACCATTGGTTTACAA
1 AATTACCA-AAATACCCTTGATTTGTAA
** * *
54414434 AATTACTGAAATACCCTTGGTTTGTAG
1 AATTACCAAAATACCCTTGATTTGTAA
* *
54414461 ATTTACCAAAACACCCTTG
1 AATTACCAAAATACCCTTG
54414480 TAGGATGAAA
Statistics
Matches: 146, Mismatches: 30, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
26 3 0.02
27 116 0.79
28 8 0.05
29 19 0.13
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGATTTGTAA
Found at i:54414380 original size:81 final size:81
Alignment explanation
Indices: 54414237--54414392 Score: 183
Period size: 81 Copynumber: 1.9 Consensus size: 81
54414227 TTACCCTCGA
* * * * **
54414237 TTGTGAAATTACTGAAATACCCCTATAGGGTAGAATTACCAAAATACCCCTAGTTTGTAAAATTA
1 TTGTGAAATTACCGAAATACCCCAATAGGGTAAAATTACCAAAATACCACTAGTTTACAAAATTA
54414302 CCA-AAATACCACTGGT
66 -CAGAAATACCACTGGT
** *
54414318 TTGTGAAATTACCGAAATACCCTCAAT-TTGTAAAATTACCAAAATACCA-TTGATTTACAAAAT
1 TTGTGAAATTACCGAAATACCC-CAATAGGGTAAAATTACCAAAATACCACTAG-TTTACAAAAT
54414381 TACAGAAATACC
64 TACAGAAATACC
54414393 CTTGACTTTC
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
80 4 0.06
81 56 0.89
82 3 0.05
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (81 bp):
TTGTGAAATTACCGAAATACCCCAATAGGGTAAAATTACCAAAATACCACTAGTTTACAAAATTA
CAGAAATACCACTGGT
Found at i:54414381 original size:54 final size:54
Alignment explanation
Indices: 54414270--54414450 Score: 195
Period size: 54 Copynumber: 3.3 Consensus size: 54
54414260 TATAGGGTAG
* * * ***
54414270 AATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGA
1 AATTACCGAAATACCCTC-AATTTGTAAAATTACCAAAATACCATTGGTTTACAA
*
54414324 AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCATTGATTTACAA
1 AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCATTGGTTTACAA
* * * * *
54414378 AATTACAGAAATACCCTTGACTTTCTAAAAATTA-TAGAAATACCATTGGTTTACAA
1 AATTACCGAAATACCC-TCAATTTGT-AAAATTACCA-AAATACCATTGGTTTACAA
*
54414434 AATTACTGAAATACCCT
1 AATTACCGAAATACCCT
54414451 TGGTTTGTAG
Statistics
Matches: 109, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
54 60 0.55
55 9 0.08
56 40 0.37
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.30
Consensus pattern (54 bp):
AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCATTGGTTTACAA
Found at i:54414574 original size:27 final size:27
Alignment explanation
Indices: 54414497--54414574 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
54414487 AAATGACTAA
* *
54414497 AATACCCCT-AATAGGTAAAAAGACCGT
1 AATACCCCTGTAT-GGTAAAATGACCGT
* *
54414524 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGT
54414551 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
54414575 GAATATGCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.02
27 39 0.93
28 2 0.05
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGT
Found at i:54415379 original size:25 final size:25
Alignment explanation
Indices: 54415341--54415410 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
54415331 AGGAAGTGCT
* *
54415341 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
* *
54415366 AAAAGGGCTTTGCCCTAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
54415391 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
54415411 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:54415423 original size:24 final size:24
Alignment explanation
Indices: 54415340--54415435 Score: 86
Period size: 25 Copynumber: 3.9 Consensus size: 24
54415330 GAGGAAGTGC
*
54415340 TAAAAGGGCTATGCCCCAGTTTACC
1 TAAAAGGGCTATGCCCCAGTTTA-T
* * *
54415365 GAAAAGGGCTTTGCCCTAGTTTAT
1 TAAAAGGGCTATGCCCCAGTTTAT
* *
54415389 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTATGCCCCAGTTTAT
*
54415413 TAAAAGAGGCTAGGCCTCCAGTT
1 TAAAAG-GGCTATGCC-CCAGTT
54415436 ATATGATAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
23 5 0.09
24 11 0.19
25 41 0.71
26 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
TAAAAGGGCTATGCCCCAGTTTAT
Found at i:54415679 original size:31 final size:31
Alignment explanation
Indices: 54415634--54415712 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
54415624 TACAGTAAAG
54415634 GCTTCGG-CCAGTGATATGATTTATGAAAAA
1 GCTTCGGCCCAGTGATATGATTTATGAAAAA
*
54415664 GCTTCGGCCCAGTGATATGATTTATGAAAAG
1 GCTTCGGCCCAGTGATATGATTTATGAAAAA
54415695 GCTTCGGCCCAGT-ATATG
1 GCTTCGGCCCAGTGATATG
54415713 TCGAGACTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 12 0.26
31 35 0.74
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (31 bp):
GCTTCGGCCCAGTGATATGATTTATGAAAAA
Found at i:54424860 original size:28 final size:27
Alignment explanation
Indices: 54424797--54424866 Score: 131
Period size: 27 Copynumber: 2.6 Consensus size: 27
54424787 ATAGTGAGTC
54424797 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
54424824 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
54424852 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54424867 GTACAAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:54430726 original size:42 final size:41
Alignment explanation
Indices: 54430675--54430777 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 41
54430665 GTTGAGATTA
54430675 CATGTAAGACCATATCTGGC-ATATGGAATTGAGATGAGACTTC
1 CATGTAAGACCATATCTGGCTAT-TGGAATTGAGATGAGA--TC
* * *
54430718 C-TGTAAGACCATAGCTGGGCTATTGGCATTGATATGAGATC
1 CATGTAAGACCATATCT-GGCTATTGGAATTGAGATGAGATC
*
54430759 CTATGTAAGACCACATCTG
1 C-ATGTAAGACCATATCTG
54430778 AGATATGACA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
41 3 0.06
42 15 0.29
43 31 0.61
44 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (41 bp):
CATGTAAGACCATATCTGGCTATTGGAATTGAGATGAGATC
Found at i:54430899 original size:20 final size:20
Alignment explanation
Indices: 54430871--54430917 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
54430861 CGATAATGTT
54430871 TAAGTTGTGAAAGATTATGG
1 TAAGTTGTGAAAGATTATGG
*
54430891 TATGTTGTGAAAGATTATGG
1 TAAGTTGTGAAAGATTATGG
54430911 TAAGTTG
1 TAAGTTG
54430918 CAAGTTGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.30, T:0.38
Consensus pattern (20 bp):
TAAGTTGTGAAAGATTATGG
Found at i:54431084 original size:15 final size:16
Alignment explanation
Indices: 54431064--54431093 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54431054 TACAATGATA
54431064 TTTATGTT-AATTTAC
1 TTTATGTTAAATTTAC
54431079 TTTATGTTAAATTTA
1 TTTATGTTAAATTTA
54431094 TGCTAAAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60
Consensus pattern (16 bp):
TTTATGTTAAATTTAC
Found at i:54439259 original size:25 final size:25
Alignment explanation
Indices: 54439226--54439405 Score: 198
Period size: 25 Copynumber: 7.1 Consensus size: 25
54439216 CCTCAAAGAT
* *
54439226 TTATCAGATGATTCACCACAGAGGT
1 TTATCAGATGATTCACCACAAAGGC
* *
54439251 TTATCAGATAATTCACTACAAAGGC
1 TTATCAGATGATTCACCACAAAGGC
* **
54439276 TTATTAGATGATTTGCCACAAAGGC
1 TTATCAGATGATTCACCACAAAGGC
* *
54439301 TTATCAAATGATTCACCATAAAGGC
1 TTATCAGATGATTCACCACAAAGGC
54439326 TTATCAGATGATTCACCACTACAAAGGC
1 TTATCAGATGATTCA-C-C-ACAAAGGC
* **
54439354 TTATTAGATGATTTGCCACAAAGGC
1 TTATCAGATGATTCACCACAAAGGC
* * *
54439379 TTGTTAGATAATTCACCACAAAGGC
1 TTATCAGATGATTCACCACAAAGGC
54439404 TT
1 TT
54439406 CACGTAAACT
Statistics
Matches: 129, Mismatches: 23, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
25 106 0.82
26 2 0.02
27 2 0.02
28 19 0.15
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (25 bp):
TTATCAGATGATTCACCACAAAGGC
Found at i:54439373 original size:78 final size:75
Alignment explanation
Indices: 54439226--54439405 Score: 261
Period size: 78 Copynumber: 2.4 Consensus size: 75
54439216 CCTCAAAGAT
* *
54439226 TTATCAGATGATTCACCACAGAGGTTTATCAGATAATTCACTACAAAGGCTTATTAGATGATTTG
1 TTATCAGATGATTCACCACAAAGGCTTATCAGATAATTCACTACAAAGGCTTATTAGATGATTTG
54439291 CCACAAAGGC
66 CCACAAAGGC
* * *
54439301 TTATCAAATGATTCACCATAAAGGCTTATCAGATGATTCACCACTACAAAGGCTTATTAGATGAT
1 TTATCAGATGATTCACCACAAAGGCTTATCAGATAATT---CACTACAAAGGCTTATTAGATGAT
54439366 TTGCCACAAAGGC
63 TTGCCACAAAGGC
* * *
54439379 TTGTTAGATAATTCACCACAAAGGCTT
1 TTATCAGATGATTCACCACAAAGGCTT
54439406 CACGTAAACT
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
75 33 0.36
78 59 0.64
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (75 bp):
TTATCAGATGATTCACCACAAAGGCTTATCAGATAATTCACTACAAAGGCTTATTAGATGATTTG
CCACAAAGGC
Found at i:54441013 original size:40 final size:39
Alignment explanation
Indices: 54440953--54441156 Score: 196
Period size: 40 Copynumber: 5.1 Consensus size: 39
54440943 CGGAATTTAA
* ** *
54440953 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAA-TGCCTTCGGGTCTTAGC
* *** *
54440993 CCGGATTTGGTAACTTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCAC-AATGCCTTCGGGTCTTAGC
54441033 CCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCAC-AATGCCTTCGGGTCTTAGC
* * *
54441073 CCGGATATAATC-ACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAA-CAACTCGCA-CAATGCCTTCGGGTCTTAGC
* * *
54441113 CCGGATATAATC-ACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAA-CAACTCGCA-CAATGCCTTCGGGTCTTAGC
54441153 CCGG
1 CCGG
54441157 GTATCATTCA
Statistics
Matches: 144, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 141 0.98
41 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CCGGATATAACAACTCGCACAATGCCTTCGGGTCTTAGC
Found at i:54441097 original size:80 final size:78
Alignment explanation
Indices: 54440953--54441156 Score: 246
Period size: 80 Copynumber: 2.5 Consensus size: 78
54440943 CGGAATTTAA
* * * ** *
54440953 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTTGCACAAATG
1 CCGGATATAA-CACTAGCACAA-TGCCTTCGGGTCTTAGCCCGGATATAATAACTAGCACAAATG
*
54441018 CCTTCGGGTCTTAGC
64 CCTTCGGGACTTAGC
* * *
54441033 CCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATG
1 CCGGATATAAC-ACTAGCAC-AATGCCTTCGGGTCTTAGCCCGGATATAATAACTAGCACAAATG
54441098 CCTTCGGGACTTAGC
64 CCTTCGGGACTTAGC
* *
54441113 CCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGG
1 CCGGATATAA-CACTAGCA-CAATGCCTTCGGGTCTTAGCCCGG
54441157 GTATCATTCA
Statistics
Matches: 107, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
79 1 0.01
80 103 0.96
81 3 0.03
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (78 bp):
CCGGATATAACACTAGCACAATGCCTTCGGGTCTTAGCCCGGATATAATAACTAGCACAAATGCC
TTCGGGACTTAGC
Found at i:54442037 original size:2 final size:2
Alignment explanation
Indices: 54442030--54442059 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54442020 ATGTGCAAAC
54442030 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
54442060 GCTAGAGCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54446080 original size:28 final size:30
Alignment explanation
Indices: 54446048--54446116 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 30
54446038 GTTACCATTG
54446048 TTGATAAATTGATGAG-TTAGACT-TGAAA
1 TTGATAAATTGATGAGCTTAGACTATGAAA
* * *
54446076 TTGATAGATT-TTGAGCTTAGATTATGAAA
1 TTGATAAATTGATGAGCTTAGACTATGAAA
*
54446105 ATGACTAAATTG
1 TTGA-TAAATTG
54446117 TAAAGTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
27 4 0.12
28 15 0.47
29 8 0.25
30 5 0.16
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (30 bp):
TTGATAAATTGATGAGCTTAGACTATGAAA
Done.