Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 129 of 295
Found at i:39415967 original size:16 final size:15
Alignment explanation
Indices: 39415946--39415975 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39415936 AAAATACTAA
39415946 CTTTTCGGCATTTCGG
1 CTTTTCGGC-TTTCGG
39415962 CTTTTCGGCTTTCG
1 CTTTTCGGCTTTCG
39415976 CTGATCTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.03, C:0.27, G:0.23, T:0.47
Consensus pattern (15 bp):
CTTTTCGGCTTTCGG
Found at i:39425424 original size:30 final size:30
Alignment explanation
Indices: 39425388--39425447 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
39425378 TTCCCGATCC
*
39425388 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
39425418 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
39425448 CGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:39429516 original size:27 final size:28
Alignment explanation
Indices: 39429486--39429557 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
39429476 AATAGTAAAT
* * *
39429486 TTACTAAAATACCCCTGAGTATG-ACAA
1 TTACCAAAATACCCCTAAGTATGCAAAA
**
39429513 TTACCATTATACCCCTAAGTATGCAAAA
1 TTACCAAAATACCCCTAAGTATGCAAAA
**
39429541 TTACCATTATACCCCTA
1 TTACCAAAATACCCCTA
39429558 GGGTTAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 19 0.49
28 20 0.51
ACGTcount: A:0.38, C:0.26, G:0.07, T:0.29
Consensus pattern (28 bp):
TTACCAAAATACCCCTAAGTATGCAAAA
Found at i:39429551 original size:28 final size:27
Alignment explanation
Indices: 39429494--39429557 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 27
39429484 ATTTACTAAA
* *
39429494 ATACCCCTGAGTATGACAATTACCATT
1 ATACCCCTAAGTATGAAAATTACCATT
39429521 ATACCCCTAAGTATGCAAAATTACCATT
1 ATACCCCTAAGTATG-AAAATTACCATT
39429549 ATACCCCTA
1 ATACCCCTA
39429558 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 14 0.41
28 20 0.59
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (27 bp):
ATACCCCTAAGTATGAAAATTACCATT
Found at i:39429731 original size:27 final size:26
Alignment explanation
Indices: 39429660--39429774 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 26
39429650 TGGAGGAAGC
39429660 GTTCTGGTGGCTATGCCACAATTATCT
1 GTTCTGGTGGCTATGCCACAA-TATCT
*
39429687 GTTTCTGGTGGCTATGCCATAATTATCT
1 G-TTCTGGTGGCTATGCCACAA-TATCT
* *
39429715 GTTCTGGTGGCTCTGCCACAATATTT
1 GTTCTGGTGGCTATGCCACAATATCT
* * * *
39429741 GTATATGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
39429768 GTTCTGG
1 GTTCTGG
39429775 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
26 10 0.13
27 41 0.53
28 26 0.34
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:39456167 original size:46 final size:45
Alignment explanation
Indices: 39456108--39456279 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 45
39456098 CACATTTCAT
39456108 GGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTTGA
1 GGCCGATGCATGTCCCAGACATGTCTTACACTGGCTT-CATCTTGA
* * * **
39456154 GGCTGATGCATGTCTCAGACATGTCTTACACTAGCGC-TCGTCTCAA
1 GGCCGATGCATGTCCCAGACATGTCTTACACT-G-GCTTCATCTTGA
* * * ** *
39456200 TGCCGATACCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGT
1 GGCCGAT-GCATGTCCCAGACAT-GTCTTACACTGGCT-TCATCTTGA
*
39456248 GGCCCATGCATGTCCCAGACATGTCTTACACT
1 GGCCGATGCATGTCCCAGACATGTCTTACACT
39456280 AGCTCACACA
Statistics
Matches: 100, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
46 52 0.52
47 28 0.28
48 20 0.20
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (45 bp):
GGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTCATCTTGA
Found at i:39458317 original size:111 final size:111
Alignment explanation
Indices: 39458118--39458340 Score: 410
Period size: 111 Copynumber: 2.0 Consensus size: 111
39458108 AAGCATGCAT
39458118 TTTCTACCATTAAACATCAAAACACATATAGATTCATCAATGGCAAAACCCTCAACCTTTAACAG
1 TTTCTACCATTAAACATCAAAACACATATAGATTCATCAATGGCAAAACCCTCAACCTTTAACAG
* * *
39458183 TCTTGCAAAATAGTCCCTGGGCTAGCTAGATTAAGCTGCAACGATC
66 TCTTGCAAAATAGTCCCTAGGCTAGCTAGATTAAGCCGCAACAATC
*
39458229 TTTCTACCATTAAACATCAAAACACATATAGATTCATCAATGGCAAAATCCTCAACCTTTAACAG
1 TTTCTACCATTAAACATCAAAACACATATAGATTCATCAATGGCAAAACCCTCAACCTTTAACAG
39458294 TCTTGCAAAATAGTCCCTAGGCTAGCTAGATTAAGCCGCAACAATC
66 TCTTGCAAAATAGTCCCTAGGCTAGCTAGATTAAGCCGCAACAATC
39458340 T
1 T
39458341 CAAAAATATA
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (111 bp):
TTTCTACCATTAAACATCAAAACACATATAGATTCATCAATGGCAAAACCCTCAACCTTTAACAG
TCTTGCAAAATAGTCCCTAGGCTAGCTAGATTAAGCCGCAACAATC
Found at i:39460131 original size:25 final size:25
Alignment explanation
Indices: 39460079--39460170 Score: 87
Period size: 25 Copynumber: 3.7 Consensus size: 25
39460069 CAGGCCTATT
* * * *
39460079 TTCACAGCTCGTGTGAGCATTTTGA
1 TTCACTGCTCATGTGAGCATTCTAA
*
39460104 TTCACTGCTCATATGAGCATTCTAA
1 TTCACTGCTCATGTGAGCATTCTAA
* * *
39460129 TTCA-TATCTCATGTGAGCATACTTA
1 TTCACT-GCTCATGTGAGCATTCTAA
*
39460154 TTCACAGCTCATGTGAG
1 TTCACTGCTCATGTGAG
39460171 TATATATGTA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
24 1 0.02
25 53 0.98
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (25 bp):
TTCACTGCTCATGTGAGCATTCTAA
Found at i:39460819 original size:20 final size:20
Alignment explanation
Indices: 39460776--39460817 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
39460766 TAAGGAAAGT
39460776 AAATAAAATGGAAAGTAATG
1 AAATAAAATGGAAAGTAATG
39460796 AAATGAAAAT-GAAAGTAA-G
1 AAAT-AAAATGGAAAGTAATG
39460815 AAA
1 AAA
39460818 ATTTGAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (20 bp):
AAATAAAATGGAAAGTAATG
Found at i:39462447 original size:43 final size:42
Alignment explanation
Indices: 39462336--39462448 Score: 120
Period size: 43 Copynumber: 2.7 Consensus size: 42
39462326 TGTGTTATCG
* * ***
39462336 TGTAAGACCACGTCTGGAACATTGGCATCATATTTGATTTTG
1 TGTAAGAACACGTCTGGGACATTGGCATCATATTTGATTACA
* * *
39462378 TGCAAG-ACACTGTCTAGGACAGTGGCATCGATATTTGATTACA
1 TGTAAGAACAC-GTCTGGGACATTGGCATC-ATATTTGATTACA
*
39462421 TGTAAGAACACGTCTGGGGCATTGGCAT
1 TGTAAGAACACGTCTGGGACATTGGCAT
39462449 TGTACAAGTT
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
41 3 0.05
42 20 0.36
43 29 0.52
44 4 0.07
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (42 bp):
TGTAAGAACACGTCTGGGACATTGGCATCATATTTGATTACA
Found at i:39467086 original size:74 final size:74
Alignment explanation
Indices: 39466956--39467094 Score: 181
Period size: 74 Copynumber: 1.9 Consensus size: 74
39466946 AGCTCAGATG
* * * *
39466956 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACAAAATCTCCAGACGTAGTCATCGGGTCTT
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACAAAATCACCACACATAGTCATCGGGTCTT
39467021 ACCCGGAAA
66 ACCCGGAAA
* * * * *
39467030 AAATCTCCACACGTAA-TCATCGGGTCTTACCCGGACATAGTCACCACATATGGTCATCTGGTCT
1 AAATCTCCACACG-AAGTCATCGGGTCTTACCCGGACAAAATCACCACACATAGTCATCGGGTCT
39467094 T
65 T
39467095 TAATCCCAGG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
74 53 0.96
75 2 0.04
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (74 bp):
AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACAAAATCACCACACATAGTCATCGGGTCTT
ACCCGGAAA
Found at i:39467087 original size:37 final size:37
Alignment explanation
Indices: 39466956--39467066 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
39466946 AGCTCAGATG
* *
39466956 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
39466993 AAATCTCCAGACGTAGTCATCGGGTCTTACCCGGAAA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
39467030 AAATCTCCACACGTAATCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
39467067 TAGTCACCAC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:39467301 original size:46 final size:46
Alignment explanation
Indices: 39467248--39467381 Score: 187
Period size: 46 Copynumber: 2.9 Consensus size: 46
39467238 TATATATACA
* * * *
39467248 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
39467294 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
39467340 TATCTCATACACATTTCGCATTAGCCATTCGGCCTTATCACA
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACA
39467382 CATACGCATG
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.25, C:0.31, G:0.09, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:39467418 original size:47 final size:47
Alignment explanation
Indices: 39467358--39467647 Score: 409
Period size: 47 Copynumber: 6.1 Consensus size: 47
39467348 ACACATTTCG
*
39467358 CATTAGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* *
39467405 CATTGGCCATTCGGCCTTATCACACATACACGTGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
39467452 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* *
39467499 CATTGTCCATTCGGCCTTATCACACATACGCGTGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* ** *
39467546 CATTGGCCATTCGGCCTTATCACGCATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C--ACATACGCATGTTCACATTCATCA
* * * * **
39467597 CATTTGCCATTCGGCCTTATCTCATATATGCACATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
39467644 CATT
1 CATT
39467648 AAAATCCTAA
Statistics
Matches: 221, Mismatches: 18, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
47 180 0.81
49 2 0.01
51 39 0.18
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:39467528 original size:141 final size:143
Alignment explanation
Indices: 39467364--39467647 Score: 439
Period size: 145 Copynumber: 2.0 Consensus size: 143
39467354 TTCGCATTAG
39467364 CCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCA-C
1 CCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACC
**
39467428 -ACATACAC-GTGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCAC
66 AACATACACAG-GTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCACATTCAC
39467491 ATTCATCACATTGT
130 ATTCATCACATTGT
*
39467505 CCATTCGGCCTTATCACACATACGCGTGTTCACATTCATCACATTGGCCATTCGGCCTTATCACG
1 CCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC-
* * * * * *
39467570 CATATATATACAGGTTCACATTCATCACATTTGCCATTCGGCCTTATCTCATATATGCACATTCA
65 CA-ACATACACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCACATTCA
39467635 CATTCATCACATT
129 CATTCATCACATT
39467648 AAAATCCTAA
Statistics
Matches: 129, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
141 62 0.48
143 1 0.01
145 65 0.50
146 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.32
Consensus pattern (143 bp):
CCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACC
AACATACACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCACATTCACA
TTCATCACATTGT
Found at i:39478328 original size:28 final size:28
Alignment explanation
Indices: 39478296--39478379 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
39478286 AACTTCGATC
39478296 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
39478324 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
39478346 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
39478374 ACGTGT
1 ACGTGT
39478380 ACCGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:39478367 original size:50 final size:49
Alignment explanation
Indices: 39478192--39478436 Score: 274
Period size: 49 Copynumber: 4.9 Consensus size: 49
39478182 GCTATTGTGA
* * * *
39478192 GGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGAATCAAATAATT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
** * * * * *
39478241 GGTTGCATGTGTAGTACTAAGTGCAAGCTACTATGCGTACCTGATAACTT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * **
39478291 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
*
39478341 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
39478391 GGTCGCATGTGTAGTACTAAGTGCATGCTACTATGCGTACCAGATA
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
39478437 GCTTCGGTTA
Statistics
Matches: 160, Mismatches: 34, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
49 76 0.47
50 48 0.30
51 36 0.22
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (49 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:39484094 original size:27 final size:27
Alignment explanation
Indices: 39484064--39484241 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 27
39484054 ATATTGAGCC
* *
39484064 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
39484091 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
39484118 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
39484146 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
39484173 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
39484200 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
39484227 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
39484242 GTACAATTTA
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 102 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:39484203 original size:82 final size:81
Alignment explanation
Indices: 39484085--39484240 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
39484075 TGCTATATAA
* * *
39484085 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCA-AATCGCA
39484150 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
39484167 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
*
39484231 CCCTTAGTGC
65 CACTTAGTGC
39484241 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 17 0.26
82 48 0.74
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39484799 original size:18 final size:18
Alignment explanation
Indices: 39484776--39484811 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39484766 TGCCGAATGC
39484776 AACCTTACTAAATTTTCA
1 AACCTTACTAAATTTTCA
39484794 AACCTTACTAAATTTTCA
1 AACCTTACTAAATTTTCA
39484812 TGGATTCAAT
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:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (18 bp):
AACCTTACTAAATTTTCA
Found at i:39493791 original size:19 final size:19
Alignment explanation
Indices: 39493760--39493807 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
39493750 AGGTTAAATG
39493760 ATTATT-TTGTTATGGGTTT
1 ATTATTATT-TTATGGGTTT
**
39493779 ATTATTATTTTATGTTTTT
1 ATTATTATTTTATGGGTTT
*
39493798 ATTTTTATTT
1 ATTATTATTT
39493808 GGTTTTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 23 0.92
20 2 0.08
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (19 bp):
ATTATTATTTTATGGGTTT
Found at i:39494532 original size:21 final size:21
Alignment explanation
Indices: 39494498--39494556 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
39494488 GCTTGTGCCC
** *
39494498 CCTCCACACAGGCGTGTGGGG
1 CCTCCACATGGGCGTGTGAGG
* *
39494519 CCTTCATATGGGCGTGTGAGG
1 CCTCCACATGGGCGTGTGAGG
*
39494540 CCTCCACATGTGCGTGT
1 CCTCCACATGGGCGTGT
39494557 AAACCCCCAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.14, C:0.29, G:0.34, T:0.24
Consensus pattern (21 bp):
CCTCCACATGGGCGTGTGAGG
Found at i:39498102 original size:31 final size:31
Alignment explanation
Indices: 39498045--39498124 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
39498035 TTAAACATGT
* *
39498045 ACTGGGCCATAGCGCTTTTCATATTTCATAAC
1 ACTGGGCCAAAGC-CTTTTCAAATTTCATAAC
**
39498077 ACTGGGCCAAAGCCTTTTCAAATTTCATATT
1 ACTGGGCCAAAGCCTTTTCAAATTTCATAAC
*
39498108 ACTGGGCCGAAGCCTTT
1 ACTGGGCCAAAGCCTTT
39498125 ACTATAAACG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 31 0.72
32 12 0.28
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (31 bp):
ACTGGGCCAAAGCCTTTTCAAATTTCATAAC
Found at i:39498393 original size:23 final size:23
Alignment explanation
Indices: 39498339--39498503 Score: 258
Period size: 23 Copynumber: 7.1 Consensus size: 23
39498329 CCTAGCCTCT
*
39498339 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
39498362 TTTTAATAACTAGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
39498386 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
* *
39498409 TTTAATAACTAGGGCACAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
39498432 TTTAATAACTGGGGCATAAGCCT
1 TTTAATAACTGGGGCATAAGCCC
*
39498455 TTTAATAACTAGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
39498478 TTTAATTACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
39498501 TTT
1 TTT
39498504 TTCACTTCCT
Statistics
Matches: 129, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
23 108 0.84
24 21 0.16
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:39498430 original size:46 final size:46
Alignment explanation
Indices: 39498339--39498503 Score: 285
Period size: 46 Copynumber: 3.6 Consensus size: 46
39498329 CCTAGCCTCT
*
39498339 TTTAATAACTGGGGCAAAAGCCCTTTTAATAACTAGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC-TTTAATAACTAGGGCATAAGCCC
*
39498386 TTTAATAACTGGGGCATAAGCCCTTTAATAACTAGGGCACAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTAATAACTAGGGCATAAGCCC
*
39498432 TTTAATAACTGGGGCATAAGCCTTTTAATAACTAGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTAATAACTAGGGCATAAGCCC
*
39498478 TTTAATTACTGGGGCATAAGCCCTTT
1 TTTAATAACTGGGGCATAAGCCCTTT
39498504 TTCACTTCCT
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
46 90 0.80
47 22 0.20
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (46 bp):
TTTAATAACTGGGGCATAAGCCCTTTAATAACTAGGGCATAAGCCC
Found at i:39498565 original size:39 final size:39
Alignment explanation
Indices: 39498511--39498588 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
39498501 TTTTTCACTT
39498511 CCTCCATTCATATAAAAACCCAACCCAATGCATTTATGA
1 CCTCCATTCATATAAAAACCCAACCCAATGCATTTATGA
39498550 CCTCCATTCATATAAAAACCCAACCCAATGCATTTATGA
1 CCTCCATTCATATAAAAACCCAACCCAATGCATTTATGA
39498589 ATACATCATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.31, G:0.05, T:0.26
Consensus pattern (39 bp):
CCTCCATTCATATAAAAACCCAACCCAATGCATTTATGA
Found at i:39498639 original size:20 final size:20
Alignment explanation
Indices: 39498593--39498633 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
39498583 TTATGAATAC
39498593 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
39498613 ATCATGTGCATATCATCCAT
1 ATCATGTGCATATCATACAT
39498633 A
1 A
39498634 CAATGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:39498708 original size:25 final size:25
Alignment explanation
Indices: 39498676--39498723 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39498666 ATATATAAAC
* *
39498676 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
*
39498701 CCTAGGGGCAAAATGTTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
39498724 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:39499918 original size:27 final size:27
Alignment explanation
Indices: 39499888--39500170 Score: 138
Period size: 27 Copynumber: 10.4 Consensus size: 27
39499878 GTAAATCTAC
*
39499888 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
39499915 AAACCAATGGTATTTCTA-TAATTTTTAG
1 AAACCAAGGGTATTTC-AGTAA-TTTTAT
* * * *
39499943 AAAGTCAAGGGTATTT-TGTAACTTTGT
1 AAA-CCAAGGGTATTTCAGTAATTTTAT
* * ** *
39499970 AAATCAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
*** * * * *
39499997 AAATTGAGGGTATTGCGGTAATTTCAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
** *
39500024 AAACCAAGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * ** *
39500051 AAACTAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
39500078 AAACCAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * *** * *
39500105 AAATCGAGGGTAAAACAGTAATTCTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *** *
39500132 AAATCAAGGGTAAAACAGTAATTCTAT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
39500159 AAATCGAGGGTA
1 AAACCAAGGGTA
39500171 AAATGGTAAT
Statistics
Matches: 208, Mismatches: 43, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
26 11 0.05
27 176 0.85
28 11 0.05
29 10 0.05
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.36
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTAT
Found at i:39500039 original size:54 final size:54
Alignment explanation
Indices: 39499977--39500116 Score: 192
Period size: 54 Copynumber: 2.6 Consensus size: 54
39499967 TGTAAATCAG
39499977 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTGCGGTAATTTCACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTGCGGTAATTTCACAAACCAA
* ** *
39500031 GGGTATTTTGGTAATTTTACAAACT-AGGGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATTGA-GGGTATTGCGGTAATTTCACAAACCAA
* ** *
39500085 GGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTA
39500117 AAACAGTAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 73 0.97
55 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.38
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAATTGAGGGTATTGCGGTAATTTCACAAACCAA
Found at i:39500099 original size:81 final size:79
Alignment explanation
Indices: 39499841--39500101 Score: 213
Period size: 81 Copynumber: 3.2 Consensus size: 79
39499831 TACCTATTAG
* ** ** * * * **
39499841 GGGTATTTTAGTCATTTCATCCTACAAGGGTGCTTTGGTAAATCTACAAACCAAGGGTATTTCAG
1 GGGTATTTTAGTAATTTCA-CAAACAAGGGTATTTTGGTAATTTTACAAA-CAGGGGTATTTTGG
**
39499906 TAATTTTGTAAACCAA
64 TAATTTTACAAACCAA
* * * *
39499922 TGGTATTTCTA-TAATTTTTAGAAAGTCAAGGGTATTTT-GTAACTTTGTA-AATCAGGGGTATT
1 GGGTATTT-TAGTAA-TTTCACAAA--CAAGGGTATTTTGGTAA-TTT-TACAAACAGGGGTATT
***
39499984 TTGGTAATTTTACAAATTGA
60 TTGGTAATTTTACAAACCAA
***
39500004 GGGTATTGCGGTAATTTCACAAACCAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
1 GGGTATTTTAGTAATTTCACAAA-CAAGGGTATTTTGGTAATTTTACAAAC-AGGGGTATTTTGG
39500069 TAATTTTACAAACCAA
64 TAATTTTACAAACCAA
39500085 GGGTATTTTAGTAATTT
1 GGGTATTTTAGTAATTT
39500102 TGTAAATCGA
Statistics
Matches: 137, Mismatches: 33, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
79 2 0.01
80 18 0.13
81 61 0.45
82 41 0.30
83 13 0.09
84 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.39
Consensus pattern (79 bp):
GGGTATTTTAGTAATTTCACAAACAAGGGTATTTTGGTAATTTTACAAACAGGGGTATTTTGGTA
ATTTTACAAACCAA
Found at i:39500126 original size:54 final size:54
Alignment explanation
Indices: 39499977--39500181 Score: 160
Period size: 54 Copynumber: 3.8 Consensus size: 54
39499967 TGTAAATCAG
* * *** *
39499977 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTGCGGTAATTTCACAAACCAA
1 GGGTATTTTAGTAATTTTACAAATCGAGGGTAAAACGGTAATTTTACAAACCAA
* * ****
39500031 GGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTAGTAATTTTACAAATCGA-GGGTAAAACGGTAATTTTACAAACCAA
** * * ** *
39500085 GGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAA
1 GGGTATTTTAGTAATTTTACAAATCGAGGGTAAAACGGTAATTTTACAAACCAA
**** * * *
39500139 GGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGGTAATT
1 GGGTATTTTAGTAATTTTACAAATCGAGGGTAAAACGGTAATT
39500182 CTGTAAATCG
Statistics
Matches: 123, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
53 1 0.01
54 120 0.98
55 2 0.02
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (54 bp):
GGGTATTTTAGTAATTTTACAAATCGAGGGTAAAACGGTAATTTTACAAACCAA
Found at i:39500153 original size:81 final size:80
Alignment explanation
Indices: 39500068--39500277 Score: 197
Period size: 80 Copynumber: 2.6 Consensus size: 80
39500058 GGGTATTTTG
* *** * *
39500068 GTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTA
1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACA-TAATTATGTA
39500133 AATCAAGGGTAAAACA
65 AATCAAGGGTAAAACA
* * * * *
39500149 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAAGATAATTATGTAA
1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACATAATTATGTAA
* **
39500214 ATC-GGGGTTAAAAGG
66 ATCAAGGG-TAAAACA
* ** * * * * *
39500229 GTAATTATGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGGGGGTA
1 GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTGTAAATCGAGGGTA
39500278 CTTTGGTAAT
Statistics
Matches: 110, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
79 3 0.03
80 63 0.57
81 44 0.40
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.30
Consensus pattern (80 bp):
GTAATTCTACAAACCAAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACATAATTATGTAA
ATCAAGGGTAAAACA
Found at i:39500171 original size:27 final size:27
Alignment explanation
Indices: 39500094--39500277 Score: 219
Period size: 27 Copynumber: 6.9 Consensus size: 27
39500084 AGGGTATTTT
*
39500094 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
39500121 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
39500148 AGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
39500175 GGTAATTCTGTAAATCGAGGGTAAAAG
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
39500202 A-TAATTATGTAAATCG-GGGTTAAAAG
1 AGTAATTCTGTAAATCGAGGG-TAAAAC
* * *
39500228 GGTAATTATGTAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
39500255 GGTAATTCTATAAATCGGGGGTA
1 AGTAATTCTGTAAATCGAGGGTA
39500278 CTTTGGTAAT
Statistics
Matches: 139, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
25 3 0.02
26 20 0.14
27 113 0.81
28 3 0.02
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:39500243 original size:80 final size:81
Alignment explanation
Indices: 39500095--39500277 Score: 253
Period size: 80 Copynumber: 2.3 Consensus size: 81
39500085 GGGTATTTTA
* * *
39500095 GTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACAGTAATTATATA
39500160 AATCGAGGGTAAAATG
66 AATCGAGGGTAAAATG
* * ** *
39500176 GTAATTCTGTAAATCGAGGGTAAAAGA-TAATTATGTAAATC-GGGGTTAAAAGGGTAATTATGT
1 GTAATTCTGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGG-TAAAACAGTAATTATAT
39500239 AAATCGAGGGTAAAATG
65 AAATCGAGGGTAAAATG
* *
39500256 GTAATTCTATAAATCGGGGGTA
1 GTAATTCTGTAAATCGAGGGTA
39500278 CTTTGGTAAT
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
79 3 0.03
80 63 0.69
81 25 0.27
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (81 bp):
GTAATTCTGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACAGTAATTATATA
AATCGAGGGTAAAATG
Found at i:39500304 original size:27 final size:27
Alignment explanation
Indices: 39500283--39500372 Score: 110
Period size: 27 Copynumber: 3.3 Consensus size: 27
39500273 GGGTACTTTG
39500283 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAAGTCGAAGGTATTTCA
*
39500310 GTAATTTTACAAGTCGAGGGTATTTCA
1 GTAATTTTACAAGTCGAAGGTATTTCA
* * * * *
39500337 CTATTTTTACAA-ACTAAGCGTATTTCG
1 GTAATTTTACAAGTCGAAG-GTATTTCA
39500364 GTAATTTTA
1 GTAATTTTA
39500373 GTAAACTAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 3 0.06
27 50 0.94
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAGTCGAAGGTATTTCA
Found at i:39508970 original size:19 final size:19
Alignment explanation
Indices: 39508936--39508974 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
39508926 GATTTTGTAC
*
39508936 TTTGGCCCATTTTCTCCGTT
1 TTTGGCCCAGTTTCT-CGTT
39508956 TTTGGCCC-GTTTCTCGTT
1 TTTGGCCCAGTTTCTCGTT
39508974 T
1 T
39508975 CTTTCGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 8 0.44
ACGTcount: A:0.03, C:0.28, G:0.18, T:0.51
Consensus pattern (19 bp):
TTTGGCCCAGTTTCTCGTT
Found at i:39517781 original size:47 final size:49
Alignment explanation
Indices: 39517711--39517886 Score: 155
Period size: 49 Copynumber: 3.6 Consensus size: 49
39517701 TATAATATCG
* *
39517711 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCATC-CATCAA-GTCA
1 ATGCCATGTCCAAGACATGGTCTTACACTGGCTCATCAAATCAAGGTCA
* * * * *
39517758 ATGCCATGTCCCAGACATAGTCTTACAATGACT-ATCGAAATCAAGGTCG
1 ATGCCATGTCCAAGACATGGTCTTACACTGGCTCATC-AAATCAAGGTCA
* * * *
39517807 ACGCCATGTCCAAGACATGGTCTTACACTAGCTC-TCATATATC-CGTGCCA
1 ATGCCATGTCCAAGACATGGTCTTACACTGGCTCATCA-A-ATCAAG-GTCA
* * *
39517857 ATACCATGTCCTACACATGGTCTTACACTG
1 ATGCCATGTCCAAGACATGGTCTTACACTG
39517887 ACACATCTCG
Statistics
Matches: 102, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
46 3 0.03
47 29 0.28
48 6 0.06
49 34 0.33
50 30 0.29
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (49 bp):
ATGCCATGTCCAAGACATGGTCTTACACTGGCTCATCAAATCAAGGTCA
Found at i:39517823 original size:49 final size:47
Alignment explanation
Indices: 39517708--39517833 Score: 146
Period size: 47 Copynumber: 2.6 Consensus size: 47
39517698 GGGTATAATA
* * * *
39517708 TCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCATCCATCAAG
1 TCGATGCCATGTCCAAGACATGGTCTTACAATGACTCATCAATCAAG
* * *
39517755 TCAATGCCATGTCCCAGACATAGTCTTACAATGACT-ATCGAAATCAAGG
1 TCGATGCCATGTCCAAGACATGGTCTTACAATGACTCATC--AATCAA-G
*
39517804 TCGACGCCATGTCCAAGACATGGTCTTACA
1 TCGATGCCATGTCCAAGACATGGTCTTACA
39517834 CTAGCTCTCA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
46 3 0.05
47 31 0.47
48 5 0.08
49 27 0.41
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (47 bp):
TCGATGCCATGTCCAAGACATGGTCTTACAATGACTCATCAATCAAG
Found at i:39517950 original size:46 final size:44
Alignment explanation
Indices: 39517861--39518024 Score: 143
Period size: 46 Copynumber: 3.6 Consensus size: 44
39517851 GTGCCAATAC
*
39517861 CATGTCCTACACATGGTCTTACACTGACACATCTCGTAGCCGATG
1 CATGTCCTAGACAT-GTCTTACACTGACACATCTCGTAGCCGATG
*
39517906 CATGTCCTAGACATGTCTTACACTGGCTTACATCTCG-AGGCCGATG
1 CATGTCCTAGACATGTCTTACACTGAC--ACATCTCGTA-GCCGATG
* * * * * *
39517952 TATGTCCCAGACTTGTCTTACACTAACTC-TCGTCTTAATGCCGATG
1 CATGTCCTAGACATGTCTTACACTGACACATC-TCGT-A-GCCGATG
* *
39517998 CCAAGTCCTAGGCATGGTCTTACACTG
1 -CATGTCCTAGACAT-GTCTTACACTG
39518025 GCTCTCATAA
Statistics
Matches: 95, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
43 2 0.02
44 15 0.16
45 14 0.15
46 45 0.47
47 9 0.09
48 10 0.11
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (44 bp):
CATGTCCTAGACATGTCTTACACTGACACATCTCGTAGCCGATG
Found at i:39518464 original size:30 final size:30
Alignment explanation
Indices: 39518408--39518464 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39518398 CATAATTAGG
* *
39518408 CAAAATGATCATTTTGCCCTTAGACTTTCA
1 CAAAATGACCATTTTCCCCTTAGACTTTCA
39518438 CAAAATGACCATTTTACCCCTT-GACTT
1 CAAAATGACCATTTT-CCCCTTAGACTT
39518465 GAAAATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (30 bp):
CAAAATGACCATTTTCCCCTTAGACTTTCA
Found at i:39522794 original size:18 final size:18
Alignment explanation
Indices: 39522767--39522814 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
39522757 TGAGAAAATT
*
39522767 ATTTAATTAAGAAATTTA
1 ATTTAATTAAGAAATTAA
* *
39522785 ATTTAGTTAATTAAATTAA
1 ATTTAATTAA-GAAATTAA
*
39522804 ATTTATTTAAG
1 ATTTAATTAAG
39522815 GAATAAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (18 bp):
ATTTAATTAAGAAATTAA
Found at i:39524030 original size:2 final size:2
Alignment explanation
Indices: 39524025--39524057 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
39524015 AAAAGAAATC
*
39524025 AT AT AT AT AT AT AT AT AT AT AT -T AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39524058 GATTTTCACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:39526121 original size:23 final size:22
Alignment explanation
Indices: 39526086--39526165 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
39526076 ATTGAATCAC
*
39526086 ATAGGTTTGCATAATAGTTCAT
1 ATAGGTTCGCATAATAGTTCAT
*
39526108 ATAGGATTCGCATAATAGTTCAC
1 ATAGG-TTCGCATAATAGTTCAT
* *
39526131 ATAAGGTTCGCATACTAATTCAT
1 AT-AGGTTCGCATAATAGTTCAT
39526154 ATAGGATTCGCA
1 ATAGG-TTCGCA
39526166 CATTAAATCA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.16
23 39 0.78
24 3 0.06
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (22 bp):
ATAGGTTCGCATAATAGTTCAT
Found at i:39526177 original size:46 final size:45
Alignment explanation
Indices: 39526069--39526177 Score: 137
Period size: 46 Copynumber: 2.4 Consensus size: 45
39526059 CACATGAGGG
* * *
39526069 TTCGCATATTGAATCACATAGGTTTGCATAATAGTTCATATAGGA
1 TTCGCATATTAAATCACATAGGTTCGCATAATAATTCATATAGGA
* ** *
39526114 TTCGCATAATAGTTCACATAAGGTTCGCATACTAATTCATATAGGA
1 TTCGCATATTAAATCACAT-AGGTTCGCATAATAATTCATATAGGA
*
39526160 TTCGCACATTAAATCACA
1 TTCGCATATTAAATCACA
39526178 GACTAAATTT
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
45 15 0.29
46 37 0.71
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (45 bp):
TTCGCATATTAAATCACATAGGTTCGCATAATAATTCATATAGGA
Found at i:39528052 original size:20 final size:21
Alignment explanation
Indices: 39528023--39528099 Score: 69
Period size: 19 Copynumber: 4.0 Consensus size: 21
39528013 TATTTTTAAG
39528023 AAAATGTTAATAA-TATTATTT
1 AAAATGTTAA-AATTATTATTT
39528044 AAAAT-TTAAAATTATTA-TT
1 AAAATGTTAAAATTATTATTT
* **
39528063 --AATGTTAAAATTAATAGAT
1 AAAATGTTAAAATTATTATTT
39528082 -AAAT-TTAAAATTATTATT
1 AAAATGTTAAAATTATTATT
39528100 AATGAATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
17 3 0.06
18 11 0.23
19 16 0.34
20 12 0.26
21 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
AAAATGTTAAAATTATTATTT
Found at i:39534608 original size:2 final size:2
Alignment explanation
Indices: 39534601--39534628 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39534591 AGGAGATAAT
39534601 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
39534629 AATATTGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39549840 original size:37 final size:37
Alignment explanation
Indices: 39549783--39550017 Score: 240
Period size: 37 Copynumber: 5.9 Consensus size: 37
39549773 TATGATCACT
*
39549783 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
39549818 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
39549855 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
39549892 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
39549937 TTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
*
39549983 TTATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
39550018 GAAGCTATCA
Statistics
Matches: 183, Mismatches: 6, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
35 6 0.03
36 4 0.02
37 91 0.50
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 78 0.43
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:39549884 original size:74 final size:79
Alignment explanation
Indices: 39549778--39550038 Score: 257
Period size: 92 Copynumber: 3.2 Consensus size: 79
39549768 TTACGTATGA
* * *
39549778 TCACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTGATCAGA
1 TCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACCTATCACTTTGTCTCTTGATCAGA
39549841 TAA-GT-G-T-AGC
66 TAAGGTAGCTAAGC
*
39549851 -CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCTTGATCAGA
1 TCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACCTATCACTTTGTCTCTTGATCAGA
39549915 TAAGTGTAGCTAAAGC
66 TAAG-GTAGCT-AAGC
*
39549931 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTC
1 --TCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC-----C-A-C-C-TATCACTTTGTC
* *
39549996 TCTTGATCAGATAAGTATAGCCGAAGC
55 TCTTGATCAGATAAG-GTAG-CTAAGC
39550023 TATCACTTATCACTTT
1 --TCACTTATCACTTT
39550039 TCACTTGTCA
Statistics
Matches: 159, Mismatches: 8, Indels: 23
0.84 0.04 0.12
Matches are distributed among these distances:
72 10 0.06
73 3 0.02
74 48 0.30
76 2 0.01
77 1 0.01
78 1 0.01
80 3 0.02
83 36 0.23
88 1 0.01
89 1 0.01
90 1 0.01
92 51 0.32
93 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.37
Consensus pattern (79 bp):
TCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACCTATCACTTTGTCTCTTGATCAGA
TAAGGTAGCTAAGC
Found at i:39549941 original size:46 final size:46
Alignment explanation
Indices: 39549888--39550202 Score: 405
Period size: 46 Copynumber: 6.6 Consensus size: 46
39549878 TAAGTGTAGC
* *
39549888 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* *
39549934 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* * *
39549980 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
*
39550026 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* *
39550078 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* * *
39550124 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
39550176 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
39550203 AGTACTCAAA
Statistics
Matches: 245, Mismatches: 12, Indels: 24
0.87 0.04 0.09
Matches are distributed among these distances:
46 158 0.64
48 1 0.00
49 2 0.01
50 1 0.00
52 83 0.34
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
Found at i:39550091 original size:98 final size:98
Alignment explanation
Indices: 39549888--39550202 Score: 489
Period size: 98 Copynumber: 3.3 Consensus size: 98
39549878 TAAGTGTAGC
* * **
39549888 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAC---T---TT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTT
*
39549947 GTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
*
39549980 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTT
**
39550045 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
* *
39550078 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTT
*
39550143 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
66 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
39550176 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
39550203 AGTACTCAAA
Statistics
Matches: 205, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
92 53 0.26
95 1 0.00
98 151 0.74
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTT
GTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
Found at i:39550168 original size:144 final size:144
Alignment explanation
Indices: 39549887--39550202 Score: 392
Period size: 144 Copynumber: 2.2 Consensus size: 144
39549877 ATAAGTGTAG
* * *
39549887 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTC
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCAC
* * * *
39549952 TTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
66 TTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTGCCACTTGATCAGATAAGTATAGC
*
39550017 CGAAGCTATCA-CTTA
131 CGAAGCTA-AAGC-TA
* * *
39550032 TCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCAC
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCAC
* * *
39550096 TTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTT-CCACTTG-TCACTTGATCAG-AT
66 TTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTGCCACTTGATCA---GATAAGTAT
* *
39550158 AAG-TGTAGCTAAAGCTA
128 -AGCCGAAGCTAAAGCTA
39550175 CCACTTATCACTTTGTCACTTGATCAGA
1 CCACTTATCACTTTGTCACTTGATCAGA
39550203 AGTACTCAAA
Statistics
Matches: 147, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
142 3 0.02
143 17 0.12
144 111 0.76
145 16 0.11
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (144 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCAC
TTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTGCCACTTGATCAGATAAGTATAGC
CGAAGCTAAAGCTA
Found at i:39559886 original size:64 final size:64
Alignment explanation
Indices: 39559810--39559939 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
39559800 AAAACTAACT
39559810 AAAATTAGAGAAAAGTATATACTAATTTCATGTTTTTAATAATGTGAAGAAGTTTTATTCTAAA
1 AAAATTAGAGAAAAGTATATACTAATTTCATGTTTTTAATAATGTGAAGAAGTTTTATTCTAAA
39559874 AAAATTAGAGAAAAGTATATACTAATTTCATGTTTTTAATAATGTGAAGAAGTTTTATTCTAAA
1 AAAATTAGAGAAAAGTATATACTAATTTCATGTTTTTAATAATGTGAAGAAGTTTTATTCTAAA
39559938 AA
1 AA
39559940 GCTTAATTGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (64 bp):
AAAATTAGAGAAAAGTATATACTAATTTCATGTTTTTAATAATGTGAAGAAGTTTTATTCTAAA
Found at i:39563767 original size:22 final size:22
Alignment explanation
Indices: 39563742--39563786 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39563732 AAAAAAATTG
39563742 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
39563764 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
39563786 T
1 T
39563787 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:39568366 original size:22 final size:22
Alignment explanation
Indices: 39568338--39568382 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39568328 AGGGGGAGTG
39568338 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
39568360 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
39568382 T
1 T
39568383 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:39570588 original size:3 final size:3
Alignment explanation
Indices: 39570582--39570621 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
39570572 GATAATAATG
* *
39570582 ACA ACA ACA ACA ACA ACA ACA ATA ACA ATA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
39570622 AACTAAGCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.28, G:0.00, T:0.05
Consensus pattern (3 bp):
ACA
Found at i:39572514 original size:31 final size:31
Alignment explanation
Indices: 39572464--39572538 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
39572454 CAAAAAAAAA
* * * *
39572464 TTTTAACAGCTCAATGACTTAAATAAAATTT
1 TTTTAATAGTTCAAAGACTTAAATAAAAATT
39572495 TTTTAATAGTTCAAAGACTTAAATAAAAATT
1 TTTTAATAGTTCAAAGACTTAAATAAAAATT
* *
39572526 TTTGAATAATTCA
1 TTTTAATAGTTCA
39572539 GTAACCAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (31 bp):
TTTTAATAGTTCAAAGACTTAAATAAAAATT
Found at i:39573159 original size:46 final size:45
Alignment explanation
Indices: 39573109--39573195 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 45
39573099 AGATATTTTG
* *
39573109 TTAAGAGTTTAATTAATATTTGATTTATTCTATATTTAGTTAGTTA
1 TTAAGAGTTTAACTAATATTTGATGTA-TCTATATTTAGTTAGTTA
* *
39573155 TTAAGAGTTTAACTAATATTTTATGTATCTTTATTTAGTTA
1 TTAAGAGTTTAACTAATATTTGATGTATCTATATTTAGTTA
39573196 AATAAATGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 13 0.35
46 24 0.65
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.54
Consensus pattern (45 bp):
TTAAGAGTTTAACTAATATTTGATGTATCTATATTTAGTTAGTTA
Found at i:39579161 original size:12 final size:12
Alignment explanation
Indices: 39579131--39579168 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
39579121 TGCAAATGTA
39579131 TCATTTCTC-TTT
1 TCATTTC-CATTT
39579143 CTCATTTCCATTT
1 -TCATTTCCATTT
39579156 TCATTTCCATTT
1 TCATTTCCATTT
39579168 T
1 T
39579169 GAGAAAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:39579895 original size:40 final size:40
Alignment explanation
Indices: 39579849--39579928 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
39579839 GTCATGCATA
*
39579849 CATAGTTTGTCATCCACTCATGATTCAGGTATGACACACT
1 CATAGTTTGTCATCCACTCATGATTCAAGTATGACACACT
39579889 CATAGTTTGTCATCCACTCATGATTCAAGTATGACACACT
1 CATAGTTTGTCATCCACTCATGATTCAAGTATGACACACT
39579929 ATGAACATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.33
Consensus pattern (40 bp):
CATAGTTTGTCATCCACTCATGATTCAAGTATGACACACT
Found at i:39585095 original size:48 final size:48
Alignment explanation
Indices: 39584944--39585134 Score: 161
Period size: 48 Copynumber: 4.0 Consensus size: 48
39584934 TCATTAGGGG
* * * *
39584944 ATACATTGATTTGGCTTCGGGCCATAATATTAGCTCTTCGGGTGC-AA
1 ATACATTGATTTGGCTTCGAGCCATGATATTAGCACTTCAGGTGCGAA
* * * * * * * *
39584991 GTTGCATAGATTTGGCTTCGAGACATGATATCAGCACTTCGGGTGTGAG
1 -ATACATTGATTTGGCTTCGAGCCATGATATTAGCACTTCAGGTGCGAA
* * * * *
39585040 CTTCATTGATTTGGCTTTGGGCCATGATATTAGGACTTCAGGTGCGAA
1 ATACATTGATTTGGCTTCGAGCCATGATATTAGCACTTCAGGTGCGAA
* * * *
39585088 ATACATTGAGTTGACTTTGAGCCATGATATGAGCACTT-AGTGTGCGA
1 ATACATTGATTTGGCTTCGAGCCATGATATTAGCACTTCAG-GTGCGA
39585135 TATTCTTGAG
Statistics
Matches: 113, Mismatches: 28, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
47 2 0.02
48 110 0.97
49 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.33
Consensus pattern (48 bp):
ATACATTGATTTGGCTTCGAGCCATGATATTAGCACTTCAGGTGCGAA
Found at i:39585114 original size:96 final size:96
Alignment explanation
Indices: 39584947--39585125 Score: 225
Period size: 96 Copynumber: 1.9 Consensus size: 96
39584937 TTAGGGGATA
* * * * * *
39584947 CATTGATTTGGCTTCGGGCCATAATATTAGCTCTTCGGGTGCAAGTTGCATAGATTTGGCTTCGA
1 CATTGATTTGGCTTCGGGCCATAATATTAGCACTTCAGGTGCAAGATACATAGAGTTGACTTCGA
39585012 GACATGATATCAGCACTTCGGGTGTGAGCTT
66 GACATGATATCAGCACTTCGGGTGTGAGCTT
* * * * *
39585043 CATTGATTTGGCTTTGGGCCATGATATTAGGACTTCAGGTGCGAA-ATACATTGAGTTGACTTTG
1 CATTGATTTGGCTTCGGGCCATAATATTAGCACTTCAGGTGC-AAGATACATAGAGTTGACTTCG
* *
39585107 AGCCATGATATGAGCACTT
65 AGACATGATATCAGCACTT
39585126 AGTGTGCGAT
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
96 67 0.97
97 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (96 bp):
CATTGATTTGGCTTCGGGCCATAATATTAGCACTTCAGGTGCAAGATACATAGAGTTGACTTCGA
GACATGATATCAGCACTTCGGGTGTGAGCTT
Found at i:39592362 original size:48 final size:48
Alignment explanation
Indices: 39592194--39592376 Score: 186
Period size: 48 Copynumber: 3.8 Consensus size: 48
39592184 AATAGATTAG
* * * *
39592194 GATACATTGATTTGGCTTCGGGCCATGATATTAGCTCCTCGGGTGCGA
1 GATACATTGATTTGGCTTCAGGCCATGATATTAGCACTTCAGGTGCGA
* * * ** ** *
39592242 GTTGCATAGATTTGGCTTCAGGATATGATATCGGCACTTCAGGTTCGA
1 GATACATTGATTTGGCTTCAGGCCATGATATTAGCACTTCAGGTGCGA
* * *
39592290 GCTTCATTGATTTGGTTTCAGGCCATGATATTAGCACTTCAGGTGCGA
1 GATACATTGATTTGGCTTCAGGCCATGATATTAGCACTTCAGGTGCGA
* * * * *
39592338 GATAAATTCAGTTGGCTTCGGGCCATGATATGAGCACTT
1 GATACATTGATTTGGCTTCAGGCCATGATATTAGCACTT
39592377 AGTGTGCAAG
Statistics
Matches: 106, Mismatches: 29, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 106 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.33
Consensus pattern (48 bp):
GATACATTGATTTGGCTTCAGGCCATGATATTAGCACTTCAGGTGCGA
Found at i:39592366 original size:96 final size:96
Alignment explanation
Indices: 39592198--39592376 Score: 216
Period size: 96 Copynumber: 1.9 Consensus size: 96
39592188 GATTAGGATA
* * * * ** * *
39592198 CATTGATTTGGCTTCGGGCCATGATATTAGCTCCTCGGGTGCGAGTTGCATAGATTTGGCTTCAG
1 CATTGATTTGGCTTCAGGCCATGATATTAGCACCTCAGGTGCGAGATAAATACAGTTGGCTTCAG
*
39592263 GATATGATATCG-GCACTTCAGGTTCGAGCTT
66 GACATGATAT-GAGCACTTCAGGTTCGAGCTT
* * * *
39592294 CATTGATTTGGTTTCAGGCCATGATATTAGCACTTCAGGTGCGAGATAAATTCAGTTGGCTTCGG
1 CATTGATTTGGCTTCAGGCCATGATATTAGCACCTCAGGTGCGAGATAAATACAGTTGGCTTCAG
*
39592359 GCCATGATATGAGCACTT
66 GACATGATATGAGCACTT
39592377 AGTGTGCAAG
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
95 1 0.01
96 67 0.99
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (96 bp):
CATTGATTTGGCTTCAGGCCATGATATTAGCACCTCAGGTGCGAGATAAATACAGTTGGCTTCAG
GACATGATATGAGCACTTCAGGTTCGAGCTT
Found at i:39597376 original size:24 final size:24
Alignment explanation
Indices: 39597320--39597378 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
39597310 AGAAAGAAAC
*
39597320 AAAAAGAAAATCTATTCTAAAAAG
1 AAAAAGAAAATCTAATCTAAAAAG
*
39597344 AAAAGAGAAAA-CTTAATCTAAAAAT
1 AAAA-AGAAAATC-TAATCTAAAAAG
39597369 AAAAAGAAAA
1 AAAAAGAAAA
39597379 GAAAAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 11 0.35
25 20 0.65
ACGTcount: A:0.68, C:0.07, G:0.08, T:0.17
Consensus pattern (24 bp):
AAAAAGAAAATCTAATCTAAAAAG
Found at i:39600530 original size:17 final size:18
Alignment explanation
Indices: 39600510--39600553 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
39600500 CCAAAAATAA
39600510 TAATATTATAA-TAAATT
1 TAATATTATAATTAAATT
*
39600527 TAATATT-TAATTTAATT
1 TAATATTATAATTAAATT
39600544 TAATACTTAT
1 TAATA-TTAT
39600554 CCTGATAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 2 0.09
19 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATATTATAATTAAATT
Found at i:39600598 original size:68 final size:69
Alignment explanation
Indices: 39600526--39600653 Score: 204
Period size: 68 Copynumber: 1.9 Consensus size: 69
39600516 TATAATAAAT
* * *
39600526 TTAATATTTAATTTAATTTAATACTTATCCTGAT-AGTATTTTATTAATTTAATATTAAATTGAT
1 TTAATATTAAATTTAATATAATACTTATCCTGATAAGTATTATATTAATTTAATATTAAATTGAT
39600590 TATC
66 TATC
* *
39600594 TTAATATTAAATTTAATATAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAA
1 TTAATATTAAATTTAATATAATACTTATCCTGATAAGTATTATATTAATTTAATATTAAA
39600654 GTGAACTCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
68 30 0.56
69 24 0.44
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (69 bp):
TTAATATTAAATTTAATATAATACTTATCCTGATAAGTATTATATTAATTTAATATTAAATTGAT
TATC
Found at i:39612916 original size:5 final size:5
Alignment explanation
Indices: 39612906--39612994 Score: 53
Period size: 5 Copynumber: 17.2 Consensus size: 5
39612896 TATGTCTTTC
*
39612906 AAAAT AAAAT AATAAT AAAAT GAAAAT GAAAAT AAAAAT CAAAAG AAAA-
1 AAAAT AAAAT AA-AAT AAAAT -AAAAT -AAAAT -AAAAT -AAAAT AAAAT
*
39612955 AGAAA- AAGAA- AAAGA- AAAAG AAAAT -AAAT AAAAT AAAAT A
1 A-AAAT AA-AAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT A
39612995 GGAGGATTCA
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
4 8 0.11
5 40 0.55
6 25 0.34
ACGTcount: A:0.78, C:0.01, G:0.08, T:0.13
Consensus pattern (5 bp):
AAAAT
Found at i:39612931 original size:6 final size:6
Alignment explanation
Indices: 39612906--39612979 Score: 57
Period size: 6 Copynumber: 12.8 Consensus size: 6
39612896 TATGTCTTTC
* *
39612906 AAAAT- AAAAT- AATAAT- AAAATG AAAATG AAAATA AAAATC AAAA-G
1 AAAATG AAAATG AA-AATG AAAATG AAAATG AAAATG AAAATG AAAATG
* * * *
39612951 AAAAAG AAAAAG AAAAAG AAAAAG AAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAAT
39612980 AAATAAAATA
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
5 14 0.23
6 48 0.77
ACGTcount: A:0.77, C:0.01, G:0.09, T:0.12
Consensus pattern (6 bp):
AAAATG
Found at i:39612961 original size:12 final size:12
Alignment explanation
Indices: 39612946--39612978 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
39612936 AATAAAAATC
39612946 AAAAGAAAAAGA
1 AAAAGAAAAAGA
39612958 AAAAGAAAAAGA
1 AAAAGAAAAAGA
39612970 AAAAGAAAA
1 AAAAGAAAA
39612979 TAAATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAGA
Found at i:39619175 original size:13 final size:13
Alignment explanation
Indices: 39619157--39619187 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
39619147 CTTTGAAAAA
*
39619157 GTGACACGCCCGT
1 GTGACACGACCGT
39619170 GTGACACGACCGT
1 GTGACACGACCGT
39619183 GTGAC
1 GTGAC
39619188 GTGATTACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.16
Consensus pattern (13 bp):
GTGACACGACCGT
Found at i:39620968 original size:35 final size:35
Alignment explanation
Indices: 39620921--39620993 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
39620911 TCTATATTTA
*
39620921 TATTTAAGATAGGCTTAGGCCCAAATATGTATCTG
1 TATTTAAGATAGGCTTAGGCCCAAATATGCATCTG
*
39620956 TATTTGAA-ATAGGCTTAGGCCCGAATATGCATCTG
1 TATTT-AAGATAGGCTTAGGCCCAAATATGCATCTG
39620991 TAT
1 TAT
39620994 CTGTGATGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 33 0.94
36 2 0.06
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (35 bp):
TATTTAAGATAGGCTTAGGCCCAAATATGCATCTG
Found at i:39625079 original size:28 final size:28
Alignment explanation
Indices: 39625039--39625120 Score: 110
Period size: 28 Copynumber: 2.9 Consensus size: 28
39625029 GCAATCAAAT
* * *
39625039 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
39625067 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
39625095 ATGACACTTAGTGTGCAAAATATTGA
1 ATGGCACTTAGTGTGCGAAATATTGA
39625121 ATGATTCAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:39629805 original size:6 final size:6
Alignment explanation
Indices: 39629784--39629829 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
39629774 TATTTGTTTA
* *
39629784 TTATTA TTATTAT TTATTT TTACTT TTATTT TTAATTT TTATTT TT
1 TTATTT TTATT-T TTATTT TTATTT TTATTT TT-ATTT TTATTT TT
39629830 CTTCTTCTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 24 0.69
7 11 0.31
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:39629816 original size:13 final size:13
Alignment explanation
Indices: 39629796--39629829 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
39629786 ATTATTATTA
39629796 TTTATTTTT-ACT
1 TTTATTTTTAACT
*
39629808 TTTATTTTTAATT
1 TTTATTTTTAACT
39629821 TTTATTTTT
1 TTTATTTTT
39629830 CTTCTTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTTTAACT
Found at i:39632175 original size:20 final size:20
Alignment explanation
Indices: 39632150--39632195 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
39632140 GTTGGGCATT
39632150 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
39632170 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
39632189 GCCCATA
1 GCCCATA
39632196 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:39632204 original size:19 final size:20
Alignment explanation
Indices: 39632162--39632205 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
39632152 CCATATTAAC
** *
39632162 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
39632182 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
39632201 ACAGT
1 ACAGT
39632206 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:39651132 original size:12 final size:11
Alignment explanation
Indices: 39651099--39651152 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 11
39651089 ACTTATTTAG
39651099 TTTATTTTATT
1 TTTATTTTATT
*
39651110 ATTATTATTATT
1 TTTATT-TTATT
39651122 TTTACTTTTATT
1 TTTA-TTTTATT
*
39651134 TTTAATTTTTAAT
1 TTT-A-TTTTATT
39651147 TTTATT
1 TTTATT
39651153 CTTCTTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 7 0.19
12 17 0.47
13 12 0.33
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:39652745 original size:89 final size:89
Alignment explanation
Indices: 39652506--39652747 Score: 288
Period size: 89 Copynumber: 2.7 Consensus size: 89
39652496 TACGTACCAC
* * *
39652506 TATCTGATCTGGCAGTTTTTACTGCACGTCTATACCGCGGTTTACCGCATTACACAGTACAGCTT
1 TATCTGATCTGGCAGTTTATACTGCATGTCTATACCGCGGTCTACCGCATTACACAGTACAGCTT
* *
39652571 ATAAGCTAGCCTTGCTGCGTAATA
66 ATAAGCTAGCCTTGCTACATAATA
* * * * * *
39652595 TATCTGATCTGGGAGTTTATACTGCATGTCTATATCGCGGTCTTCCGTATTATATAGTACAGCTT
1 TATCTGATCTGGCAGTTTATACTGCATGTCTATACCGCGGTCTACCGCATTACACAGTACAGCTT
* *
39652660 ATATGCTAGCCTTGCTATATAATA
66 ATAAGCTAGCCTTGCTACATAATA
* * * ** * *
39652684 TATTTGATCTGGCAGTTCATACTGCATGTCTGTACCGTAGTCTACTGCATTGCACCA-TACAGCT
1 TATCTGATCTGGCAGTTTATACTGCATGTCTATACCGCGGTCTACCGCATTACA-CAGTACAGCT
39652748 CAGTAATAGC
Statistics
Matches: 126, Mismatches: 26, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
89 125 0.99
90 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (89 bp):
TATCTGATCTGGCAGTTTATACTGCATGTCTATACCGCGGTCTACCGCATTACACAGTACAGCTT
ATAAGCTAGCCTTGCTACATAATA
Found at i:39656168 original size:43 final size:43
Alignment explanation
Indices: 39656088--39656528 Score: 623
Period size: 43 Copynumber: 10.2 Consensus size: 43
39656078 AGGATTTCTT
* * * *
39656088 ATATCTGATTACGTGTAAGACCACATCTAGGATGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
*
39656131 ATATGTGATTACGTGTAAGATCACGTCTGGGACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
* * *
39656174 ATATGTGATTAAGTGTAAGACCACGTCTCGTACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
*
39656217 ATATGTGATT-CTGTGTAAGACCATGTCTGGGACGTTGGCATCG
1 ATATGTGATTAC-GTGTAAGACCACGTCTGGGACGTTGGCATCG
*
39656260 ATATGTGATTACGTGTAAGACCACGTCAGGGACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
**
39656303 ATATGTGATTACGTGTAAGACCATTTCTGGGACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
* * *
39656346 ATATGTGATTACGTGTAAGACCACATCTAGAACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
* * *
39656389 ATATGTGATTATGTGTAAGACCACATCTGGGACGTTGGTATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
*
39656432 ATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
* * * * ***
39656475 AATATGTGATTATGAGTAAGACCACATTTAATACGTTGGCATCG
1 -ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
39656519 ATATGTGATT
1 ATATGTGATT
39656529 CCAATATGTG
Statistics
Matches: 357, Mismatches: 38, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
43 321 0.90
44 36 0.10
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (43 bp):
ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
Found at i:39656561 original size:56 final size:56
Alignment explanation
Indices: 39656488--39656721 Score: 299
Period size: 56 Copynumber: 4.2 Consensus size: 56
39656478 ATGTGATTAT
*
39656488 GAGTAAGACCACATTTAATACGTTGGCATCGATATGTGATTCCAATATGTGTGTTC
1 GAGTAAGACCACATTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTTC
** * *
39656544 GAGTAAGACCATGTTTAATACGTTGGCATCGATATGTGATTCTGATATGTGTGTGC
1 GAGTAAGACCACATTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTTC
** * *
39656600 GAGTAAGACCACATTTAATACGTTCCCATCGATATGTGATTCCGATATGTATATTC
1 GAGTAAGACCACATTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTTC
* ** * * * *
39656656 GAGTAAGAACATGTTTAATATGTTGGCATTGATAGGTGATTTCGATATGTGT-TTAC
1 GAGTAAGACCACATTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTT-C
*
39656712 GAGAAAGACC
1 GAGTAAGACC
39656722 CTATTTGGGA
Statistics
Matches: 152, Mismatches: 25, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
55 2 0.01
56 150 0.99
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (56 bp):
GAGTAAGACCACATTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTTC
Found at i:39656673 original size:112 final size:112
Alignment explanation
Indices: 39656488--39656721 Score: 344
Period size: 112 Copynumber: 2.1 Consensus size: 112
39656478 ATGTGATTAT
** * * *
39656488 GAGTAAGACCACATTTAATACGTTGGCATCGATATGTGATTCCAATATGTGTGTTCGAGTAAGAC
1 GAGTAAGACCACATTTAATACGTTCCCATCGATATGTGATTCCAATATGTATATTCGAGTAAGAA
* *
39656553 CATGTTTAATACGTTGGCATCGATATGTGA-TTCTGATATGTGTGTGC
66 CATGTTTAATACGTTGGCATCGATAGGTGATTTC-GATATGTGTGTAC
*
39656600 GAGTAAGACCACATTTAATACGTTCCCATCGATATGTGATTCCGATATGTATATTCGAGTAAGAA
1 GAGTAAGACCACATTTAATACGTTCCCATCGATATGTGATTCCAATATGTATATTCGAGTAAGAA
* * *
39656665 CATGTTTAATATGTTGGCATTGATAGGTGATTTCGATATGTGTTTAC
66 CATGTTTAATACGTTGGCATCGATAGGTGATTTCGATATGTGTGTAC
*
39656712 GAGAAAGACC
1 GAGTAAGACC
39656722 CTATTTGGGA
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
112 106 0.97
113 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (112 bp):
GAGTAAGACCACATTTAATACGTTCCCATCGATATGTGATTCCAATATGTATATTCGAGTAAGAA
CATGTTTAATACGTTGGCATCGATAGGTGATTTCGATATGTGTGTAC
Found at i:39660122 original size:47 final size:48
Alignment explanation
Indices: 39660066--39660193 Score: 145
Period size: 47 Copynumber: 2.6 Consensus size: 48
39660056 TGGGTATAAT
* *
39660066 GCCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCATC-C-AT-CAA
1 GCCGATGCCATGTCCCA-AAATGGTCTTACACTAGCTC-TCACAATCCAA
* * * *
39660113 GTCGATGCCATGTCCCAAACATGGCCTTACATTAGCTCTCACATATCCAT
1 GCCGATGCCATGTCCCAAA-ATGGTCTTACACTAGCTCTCACA-ATCCAA
39660163 GCCGATGCCATGTCCCAAAATGGTCTTACAC
1 GCCGATGCCATGTCCCAAAATGGTCTTACAC
39660194 AGACACATCT
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
46 3 0.04
47 32 0.48
49 12 0.18
50 20 0.30
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAAAATGGTCTTACACTAGCTCTCACAATCCAA
Found at i:39665767 original size:32 final size:32
Alignment explanation
Indices: 39665715--39665786 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
39665705 ACAAACAAGT
39665715 ATACAT-ACATAATATGCATAACAACACATAAC
1 ATACATAACATAATA-GCATAACAACACATAAC
** *
39665747 ATACATAACATACATA-CATAACAGTACATAAT
1 ATACATAACATA-ATAGCATAACAACACATAAC
39665779 ATACATAA
1 ATACATAA
39665787 AAATTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 27 0.77
33 5 0.14
34 3 0.09
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.24
Consensus pattern (32 bp):
ATACATAACATAATAGCATAACAACACATAAC
Found at i:39665777 original size:10 final size:9
Alignment explanation
Indices: 39665717--39665766 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
39665707 AAACAAGTAT
39665717 ACATACATA
1 ACATACATA
* *
39665726 ATATGCATA
1 ACATACATA
*
39665735 ACAACACATA
1 AC-ATACATA
39665745 ACATACATA
1 ACATACATA
39665754 ACATACAT-
1 ACATACATA
39665762 ACATA
1 ACATA
39665767 ACAGTACATA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
8 5 0.15
9 22 0.65
10 7 0.21
ACGTcount: A:0.54, C:0.22, G:0.02, T:0.22
Consensus pattern (9 bp):
ACATACATA
Found at i:39665784 original size:19 final size:18
Alignment explanation
Indices: 39665717--39665786 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
39665707 AAACAAGTAT
*
39665717 ACATACATAATATGCATA
1 ACATACATAATATACATA
*
39665735 ACA-ACA-CATA-ACAT-
1 ACATACATAATATACATA
*
39665749 ACATAACAT-ACATACATA
1 ACAT-ACATAATATACATA
39665767 ACAGTACATAATATACATA
1 ACA-TACATAATATACATA
39665786 A
1 A
39665787 AAATTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
14 3 0.07
15 3 0.07
16 8 0.20
17 7 0.17
18 10 0.24
19 10 0.24
ACGTcount: A:0.54, C:0.20, G:0.03, T:0.23
Consensus pattern (18 bp):
ACATACATAATATACATA
Found at i:39675385 original size:45 final size:45
Alignment explanation
Indices: 39675321--39675575 Score: 283
Period size: 45 Copynumber: 5.8 Consensus size: 45
39675311 AGGACTTTGC
39675321 TATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATA
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATA
*
39675366 TATGTTTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATA
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATA
*
39675411 TATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATA
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATA
* * * * * *
39675456 TATGTGGTTACGAGTAAGACCATGT-TTGGACATAGGCATC-ATA
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATA
* * * *
39675499 T-T-TG-ATTCGTGTAAGACC-CTGTCTGAGATAGTGGCATC-A-A
1 TATGTGTTTTCGTGTAAGACCAC-GTCTGGGACATTGGCATCGATA
* * ** * *
39675539 TATGAGATAGCATGTAAGACCACGTCTGGGACGTTGG
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGG
39675576 AATTGTTCGA
Statistics
Matches: 176, Mismatches: 28, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
40 15 0.09
41 14 0.08
42 2 0.01
43 24 0.14
44 13 0.07
45 108 0.61
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (45 bp):
TATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATA
Found at i:39701296 original size:25 final size:25
Alignment explanation
Indices: 39701267--39701316 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
39701257 TCTGATCTGG
39701267 CAGTTTAACTACACTCTGGTGGCAT
1 CAGTTTAACTACACTCTGGTGGCAT
*
39701292 CAGTTTAACTACACTTTGGTGGCAT
1 CAGTTTAACTACACTCTGGTGGCAT
39701317 TGTCCACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (25 bp):
CAGTTTAACTACACTCTGGTGGCAT
Found at i:39705003 original size:31 final size:31
Alignment explanation
Indices: 39704927--39705003 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 31
39704917 TTGACCAAAT
39704927 AAAAAAATTGTAAAAATAAAAATAAAATCGTA
1 AAAAAAATT-TAAAAATAAAAATAAAATCGTA
* * * * *
39704959 AAAGAATAGTTAAAAATATATA-AAAATTGTA
1 AAA-AAAATTTAAAAATAAAAATAAAATCGTA
39704990 AAAAAACATTTAAA
1 AAAAAA-ATTTAAA
39705004 TTATTTAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
30 2 0.06
31 17 0.47
32 13 0.36
33 4 0.11
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (31 bp):
AAAAAAATTTAAAAATAAAAATAAAATCGTA
Found at i:39705389 original size:21 final size:21
Alignment explanation
Indices: 39705365--39705426 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
39705355 AATTTTAAAA
39705365 TTAAATATTATTTACAATTTT
1 TTAAATATTATTTACAATTTT
39705386 TTAAATAATT-TTCT-CAA-TTT
1 TTAAAT-ATTATT-TACAATTTT
*
39705406 TT-AATAATATTTACATATTTT
1 TTAAATATTATTTACA-ATTTT
39705427 AATGTTTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
18 3 0.09
19 7 0.21
20 6 0.18
21 14 0.41
22 4 0.12
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAATATTATTTACAATTTT
Found at i:39705455 original size:21 final size:21
Alignment explanation
Indices: 39705431--39705484 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
39705421 TATTTTAATG
*
39705431 TTTTATAATTTTTAATAA-CTT
1 TTTTATAATTTTTAA-AATATT
*
39705452 TTTTACAA-TTTTAAAATATT
1 TTTTATAATTTTTAAAATATT
39705472 TTTTATAATTTTT
1 TTTTATAATTTTT
39705485 TAGTCTAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.07
20 15 0.54
21 11 0.39
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTATAATTTTTAAAATATT
Found at i:39705485 original size:10 final size:10
Alignment explanation
Indices: 39705426--39705486 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
39705416 TTACATATTT
*
39705426 TAATGTTTTA
1 TAATTTTTTA
*
39705436 TAATTTTTAA
1 TAATTTTTTA
39705446 TAACTTTTTTA
1 TAA-TTTTTTA
* *
39705457 CAA-TTTTAA
1 TAATTTTTTA
*
39705466 AATATTTTTTA
1 TA-ATTTTTTA
39705477 TAATTTTTTA
1 TAATTTTTTA
39705487 GTCTAATCAG
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
9 6 0.15
10 20 0.50
11 14 0.35
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:39706467 original size:30 final size:30
Alignment explanation
Indices: 39706432--39706491 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
39706422 AAGCTCTTTG
*
39706432 GGGGTATTGGGTATTGTTGAAGAAAATTGT
1 GGGGTATTGGGTATTGTTAAAGAAAATTGT
39706462 GGGGTATTGGGTATTGTTAAAGAAAATTGT
1 GGGGTATTGGGTATTGTTAAAGAAAATTGT
39706492 TCTCTTTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.37
Consensus pattern (30 bp):
GGGGTATTGGGTATTGTTAAAGAAAATTGT
Found at i:39714365 original size:42 final size:42
Alignment explanation
Indices: 39714319--39714405 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 42
39714309 TATTAATTTA
* * * * *
39714319 ATATTAATACGATATATTATATTTAATTTAATATTTGTCTAG
1 ATATTAATACGAGATATTAAATTAAATTAAATATTTATCTAG
* *
39714361 ATATTAATATGAGATATTAAATTAAATTAAATATTTATTTAG
1 ATATTAATACGAGATATTAAATTAAATTAAATATTTATCTAG
39714403 ATA
1 ATA
39714406 ATATTTTATT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (42 bp):
ATATTAATACGAGATATTAAATTAAATTAAATATTTATCTAG
Found at i:39717177 original size:20 final size:20
Alignment explanation
Indices: 39717152--39717199 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
39717142 ATTCCAACTG
39717152 TGTGTCGATGAGACACTATA
1 TGTGTCGATGAGACACTATA
*
39717172 TGTGTCAATGAGACACTATA
1 TGTGTCGATGAGACACTATA
39717192 TGTGTCGA
1 TGTGTCGA
39717200 CTACTGTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (20 bp):
TGTGTCGATGAGACACTATA
Found at i:39738391 original size:26 final size:26
Alignment explanation
Indices: 39738361--39738410 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
39738351 CCAATGAACT
*
39738361 GGGGAATCAGCACTTAGCAACCCCTC
1 GGGGAATCAGCACATAGCAACCCCTC
39738387 GGGGAATCAGCACATAGCAACCCC
1 GGGGAATCAGCACATAGCAACCCC
39738411 CTTTCACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.34, G:0.24, T:0.12
Consensus pattern (26 bp):
GGGGAATCAGCACATAGCAACCCCTC
Found at i:39738423 original size:103 final size:102
Alignment explanation
Indices: 39738225--39738488 Score: 395
Period size: 103 Copynumber: 2.6 Consensus size: 102
39738215 AACCGTTATT
* * * *
39738225 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC-TCGGGGA
*** *
39738290 ATCAGCACATAGCAACCCCCTTTTTGTTTCAGAGATAC
65 ATCAGCACATAGCAACCCCCTTTACATTTCAAAGATAC
39738328 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGA
39738392 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 ATCAGCACATAGCAACCCCCTTT-ACATTTCAAAGATAC
* **
39738431 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
39738489 TTATGTACAA
Statistics
Matches: 147, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
102 30 0.20
103 116 0.79
104 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (102 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
TCAGCACATAGCAACCCCCTTTACATTTCAAAGATAC
Found at i:39738850 original size:30 final size:29
Alignment explanation
Indices: 39738816--39738880 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
39738806 TAATCCACCA
39738816 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
39738846 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
39738876 CCCAA
1 CCCAA
39738881 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:39738854 original size:31 final size:30
Alignment explanation
Indices: 39738823--39738880 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39738813 CCACCCAACT
39738823 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
39738853 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
39738881 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:39750679 original size:26 final size:26
Alignment explanation
Indices: 39750650--39750710 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
39750640 CGGCGAACAT
* *
39750650 TGAAAGAATTCCTTTGTGGCGCAATA
1 TGAAAGAATGCATTTGTGGCGCAATA
*
39750676 TGAAAGGAATGCATTTGTGGTGCAATA
1 TGAAA-GAATGCATTTGTGGCGCAATA
*
39750703 TAAAAGAA
1 TGAAAGAA
39750711 AAACATTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (26 bp):
TGAAAGAATGCATTTGTGGCGCAATA
Found at i:39750693 original size:27 final size:27
Alignment explanation
Indices: 39750662--39750723 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
39750652 AAAGAATTCC
* * **
39750662 TTTGTGGCGCAATATGAAAGGAATGCA
1 TTTGTGGCGCAATATAAAAGAAAAACA
*
39750689 TTTGTGGTGCAATATAAAAGAAAAACA
1 TTTGTGGCGCAATATAAAAGAAAAACA
39750716 TTTGTGGC
1 TTTGTGGC
39750724 AAATAATGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (27 bp):
TTTGTGGCGCAATATAAAAGAAAAACA
Found at i:39752017 original size:3 final size:3
Alignment explanation
Indices: 39751992--39752079 Score: 63
Period size: 3 Copynumber: 29.0 Consensus size: 3
39751982 GGTACAACTT
* * *
39751992 ATA ATA A-A ATA CATAA ATGA ATA ATA ATA ATA ATA ATA GTG GTA ATA
1 ATA ATA ATA ATA -AT-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
39752039 GTA CTA ATA GTA GTA ATA ATA ATA ATA TTA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39752080 TTATTATCAA
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
2 4 0.06
3 57 0.83
4 7 0.10
5 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39752037 original size:18 final size:18
Alignment explanation
Indices: 39752016--39752079 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
39752006 AAATGAATAA
*
39752016 TAATAATAATAATAGTGG
1 TAATAATAATAATAGTAG
* *
39752034 TAATAGTACTAATAGTAG
1 TAATAATAATAATAGTAG
*
39752052 TAATAATAATAATATTA-
1 TAATAATAATAATAGTAG
*
39752069 AAATAATAATA
1 TAATAATAATA
39752080 TTATTATCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 10 0.26
18 29 0.74
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (18 bp):
TAATAATAATAATAGTAG
Found at i:39752075 original size:14 final size:14
Alignment explanation
Indices: 39752056--39752082 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39752046 TAGTAGTAAT
39752056 AATAATAATATTAA
1 AATAATAATATTAA
39752070 AATAATAATATTA
1 AATAATAATATTA
39752083 TTATCAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAATAATATTAA
Found at i:39752075 original size:17 final size:17
Alignment explanation
Indices: 39752053--39752085 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39752043 TAATAGTAGT
39752053 AATAATAATAATATTAA
1 AATAATAATAATATTAA
*
39752070 AATAATAATATTATTA
1 AATAATAATAATATTA
39752086 TCAAAATTAA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATAATAATAATATTAA
Found at i:39752091 original size:20 final size:20
Alignment explanation
Indices: 39752052--39752092 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39752042 CTAATAGTAG
*
39752052 TAATAATAATAATATTAAAA
1 TAATAATAATAATATCAAAA
* *
39752072 TAATAATATTATTATCAAAA
1 TAATAATAATAATATCAAAA
39752092 T
1 T
39752093 TAATTAATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATAATAATAATATCAAAA
Found at i:39754670 original size:20 final size:20
Alignment explanation
Indices: 39754641--39754678 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39754631 ATAATATATG
*
39754641 ATAATTTATAATATATATCT
1 ATAATCTATAATATATATCT
39754661 ATAATCTATAATATATAT
1 ATAATCTATAATATATAT
39754679 AAAAGCACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAATCTATAATATATATCT
Found at i:39755976 original size:21 final size:19
Alignment explanation
Indices: 39755922--39755976 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
39755912 TTTAAATTAC
*
39755922 AATTTTATAAATAATAATC
1 AATTTTATAAATAATAATA
* **
39755941 AACTTTATATTTAATATATGA
1 AATTTTATAAATAATA-AT-A
39755962 AATTTTATAAATAAT
1 AATTTTATAAATAAT
39755977 GCATTTATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 13 0.48
20 2 0.07
21 12 0.44
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (19 bp):
AATTTTATAAATAATAATA
Found at i:39758172 original size:51 final size:51
Alignment explanation
Indices: 39758089--39758205 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 51
39758079 TTCTGATCAG
39758089 TGACAAGTGAT-AGTGGTAGCCTCAGCTACACTTATCTAATCAGTGACAAA
1 TGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTAATCAGTGACAAA
* * * * * * *
39758139 TGACAAGTGATAAGTGGTAGCTTTAGTTGCACTTATCTGATTAGTGACAAG
1 TGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTAATCAGTGACAAA
*
39758190 TGATC-AGTGACAAGTG
1 TGA-CAAGTGATAAGTG
39758206 ACAAGTGATA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
50 11 0.19
51 45 0.79
52 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
TGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTAATCAGTGACAAA
Found at i:39758198 original size:14 final size:14
Alignment explanation
Indices: 39758176--39758228 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
39758166 TGCACTTATC
*
39758176 TGATTAGTGACAAG
1 TGATCAGTGACAAG
39758190 TGATCAGTGACAAG
1 TGATCAGTGACAAG
*
39758204 TGA-CAAGTGATAAATG
1 TGATC-AGTGA-CAA-G
39758220 TGATCAGTG
1 TGATCAGTG
39758229 TAAGACCGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 1 0.03
14 21 0.64
15 2 0.06
16 8 0.24
17 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.26
Consensus pattern (14 bp):
TGATCAGTGACAAG
Found at i:39758205 original size:7 final size:7
Alignment explanation
Indices: 39758181--39758213 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
39758171 TTATCTGATT
39758181 AGTGACA
1 AGTGACA
39758188 AGTGATC-
1 AGTGA-CA
39758195 AGTGACA
1 AGTGACA
39758202 AGTGACA
1 AGTGACA
39758209 AGTGA
1 AGTGA
39758214 TAAATGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 1 0.04
7 22 0.92
8 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.30, T:0.18
Consensus pattern (7 bp):
AGTGACA
Found at i:39759661 original size:23 final size:23
Alignment explanation
Indices: 39759630--39759674 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
39759620 ATAATAGTAT
39759630 TAAAATAAA-GTTTTAATTGATGG
1 TAAAATAAATGTTTT-ATTGATGG
*
39759653 TAAATTAAATGTTTTATTGATG
1 TAAAATAAATGTTTTATTGATG
39759675 CAATCGACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (23 bp):
TAAAATAAATGTTTTATTGATGG
Found at i:39761933 original size:28 final size:28
Alignment explanation
Indices: 39761893--39761950 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
39761883 CTATGACAAG
39761893 TTAGAAACTTTTCTGCATTTAGATTAAT
1 TTAGAAACTTTTCTGCATTTAGATTAAT
39761921 TTAGAAACTTTTCTGCATTTAGATTAAT
1 TTAGAAACTTTTCTGCATTTAGATTAAT
39761949 TT
1 TT
39761951 TCGTTTCTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (28 bp):
TTAGAAACTTTTCTGCATTTAGATTAAT
Found at i:39773454 original size:21 final size:21
Alignment explanation
Indices: 39773430--39773505 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 21
39773420 TAACATTTAC
39773430 GGGCCTTAAAATGAGCTTATG
1 GGGCCTTAAAATGAGCTTATG
*
39773451 GGGCCCTAAAAAT-AG-TT-TG
1 GGG-CCTTAAAATGAGCTTATG
*
39773470 GGAACAACCTTAAAATGAGCTTATG
1 GG----GCCTTAAAATGAGCTTATG
*
39773495 GGGCCCTAAAA
1 GGGCCTTAAAA
39773506 ATAGTTTGGG
Statistics
Matches: 42, Mismatches: 5, Indels: 16
0.67 0.08 0.25
Matches are distributed among these distances:
19 4 0.10
20 2 0.05
21 12 0.29
22 16 0.38
23 2 0.05
24 2 0.05
25 4 0.10
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (21 bp):
GGGCCTTAAAATGAGCTTATG
Found at i:39773483 original size:44 final size:44
Alignment explanation
Indices: 39773433--39773520 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
39773423 CATTTACGGG
39773433 CCTTAAAATGAGCTTATGGGGCCCTAAAAATAGTTTGGGAACAA
1 CCTTAAAATGAGCTTATGGGGCCCTAAAAATAGTTTGGGAACAA
39773477 CCTTAAAATGAGCTTATGGGGCCCTAAAAATAGTTTGGGAACAA
1 CCTTAAAATGAGCTTATGGGGCCCTAAAAATAGTTTGGGAACAA
39773521 TCAAAGACTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (44 bp):
CCTTAAAATGAGCTTATGGGGCCCTAAAAATAGTTTGGGAACAA
Found at i:39773484 original size:22 final size:22
Alignment explanation
Indices: 39773455--39773520 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
39773445 CTTATGGGGC
39773455 CCTAAAAATAGTTTGGGAACAA
1 CCTAAAAATAGTTTGGGAACAA
* *
39773477 CCTTAAAATGAGCTTATGGG-GC--
1 CCTAAAAAT-AG-TT-TGGGAACAA
39773499 CCTAAAAATAGTTTGGGAACAA
1 CCTAAAAATAGTTTGGGAACAA
39773521 TCAAAGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 2 0.06
22 16 0.47
23 2 0.06
24 3 0.09
25 4 0.12
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (22 bp):
CCTAAAAATAGTTTGGGAACAA
Found at i:39776112 original size:44 final size:44
Alignment explanation
Indices: 39776064--39776154 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 44
39776054 TGAAGTCAAA
* * * *
39776064 TAATATTAAAAAAACCTACATTAATTAGAGTTTAAGTGGGAAAC
1 TAATATTAAAAAAACCTACACTAATTAAAGTTTAAATGAGAAAC
* *
39776108 TAATATTAAAATAAGCTACACTAATTAAAGTTTAAATGAGAAAC
1 TAATATTAAAAAAACCTACACTAATTAAAGTTTAAATGAGAAAC
39776152 TAA
1 TAA
39776155 AATCAGAGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (44 bp):
TAATATTAAAAAAACCTACACTAATTAAAGTTTAAATGAGAAAC
Found at i:39776484 original size:147 final size:147
Alignment explanation
Indices: 39776217--39776512 Score: 592
Period size: 147 Copynumber: 2.0 Consensus size: 147
39776207 CCACCAAATA
39776217 ATTCATAACTAACAGCCCATTATAACATGCACTTGTACTATACCCCATCAACCATGTGCCATTTT
1 ATTCATAACTAACAGCCCATTATAACATGCACTTGTACTATACCCCATCAACCATGTGCCATTTT
39776282 CATCCCGTATCACACCCGCTAACGCTATTCCCTTTAACAACACTCCCTTGAGGTGAGCACCGGCC
66 CATCCCGTATCACACCCGCTAACGCTATTCCCTTTAACAACACTCCCTTGAGGTGAGCACCGGCC
39776347 CAGTTTCTTTCGAAAGT
131 CAGTTTCTTTCGAAAGT
39776364 ATTCATAACTAACAGCCCATTATAACATGCACTTGTACTATACCCCATCAACCATGTGCCATTTT
1 ATTCATAACTAACAGCCCATTATAACATGCACTTGTACTATACCCCATCAACCATGTGCCATTTT
39776429 CATCCCGTATCACACCCGCTAACGCTATTCCCTTTAACAACACTCCCTTGAGGTGAGCACCGGCC
66 CATCCCGTATCACACCCGCTAACGCTATTCCCTTTAACAACACTCCCTTGAGGTGAGCACCGGCC
39776494 CAGTTTCTTTCGAAAGT
131 CAGTTTCTTTCGAAAGT
39776511 AT
1 AT
39776513 CCCTAATGTC
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 149 1.00
ACGTcount: A:0.27, C:0.32, G:0.12, T:0.28
Consensus pattern (147 bp):
ATTCATAACTAACAGCCCATTATAACATGCACTTGTACTATACCCCATCAACCATGTGCCATTTT
CATCCCGTATCACACCCGCTAACGCTATTCCCTTTAACAACACTCCCTTGAGGTGAGCACCGGCC
CAGTTTCTTTCGAAAGT
Found at i:39776815 original size:31 final size:30
Alignment explanation
Indices: 39776780--39776839 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
39776770 TACAAAATGA
*
39776780 TCATTAAATTATTCTG-AATTTTTTATTTAAG
1 TCATTAAA-TATT-TGAAAATTTTTATTTAAG
*
39776811 TCATTGAATATTTGAAAATTTTTATTTAA
1 TCATTAAATATTTGAAAATTTTTATTTAA
39776840 ATAATTGAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 2 0.08
30 17 0.65
31 7 0.27
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (30 bp):
TCATTAAATATTTGAAAATTTTTATTTAAG
Found at i:39777438 original size:19 final size:18
Alignment explanation
Indices: 39777414--39777501 Score: 65
Period size: 19 Copynumber: 4.7 Consensus size: 18
39777404 ATTTTTATTT
39777414 ATTAAATAAAATTTAAATA
1 ATTAAATAAAA-TTAAATA
*
39777433 ATTAAATTAAATTAAATA
1 ATTAAATAAAATTAAATA
* *
39777451 ATATATCAATTACA-TAAGATA
1 AT-TA--AATAAAATTAA-ATA
*
39777472 ATTTAAGTAAAATT-AA-A
1 A-TTAAATAAAATTAAATA
39777489 ATTAAATAAAATT
1 ATTAAATAAAATT
39777502 TTAAATTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
16 11 0.19
17 2 0.04
18 10 0.18
19 17 0.30
20 4 0.07
21 12 0.21
22 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
ATTAAATAAAATTAAATA
Done.