Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold84
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: 2025335
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 30794 characters in sequence are not A, C, G, or T
File 10 of 13
Found at i:1471373 original size:13 final size:13
Alignment explanation
Indices: 1471355--1471380 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1471345 CAATTTTTTG
1471355 TGTATCGATACAT
1 TGTATCGATACAT
1471368 TGTATCGATACAT
1 TGTATCGATACAT
1471381 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1471445 original size:21 final size:21
Alignment explanation
Indices: 1471419--1471494 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1471409 CTGCCAAGAA
1471419 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
1471440 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1471460 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1471481 ATGTATCGATACAT
1 ATGTATCGATACAT
1471495 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1471464 original size:20 final size:20
Alignment explanation
Indices: 1471439--1471512 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1471429 ACATCTTTTT
1471439 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
1471459 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
1471480 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
1471500 CATGTATCGATAC
1 CATGTATCGATAC
1471513 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:1471476 original size:41 final size:41
Alignment explanation
Indices: 1471419--1471512 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1471409 CTGCCAAGAA
1471419 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1471460 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1471501 ATGTATCGATAC
1 ATGTATCGATAC
1471513 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1472179 original size:36 final size:36
Alignment explanation
Indices: 1472135--1472206 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
1472125 TTTATTAATA
*
1472135 AATCTCCCCCTTAATCAAGTAATTCATATCAAAATT
1 AATCTCCCCATTAATCAAGTAATTCATATCAAAATT
*
1472171 AATCTCCCCATTAATCAAGTATTTCATATCAAAATT
1 AATCTCCCCATTAATCAAGTAATTCATATCAAAATT
1472207 TATTTGCACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.35
Consensus pattern (36 bp):
AATCTCCCCATTAATCAAGTAATTCATATCAAAATT
Found at i:1474410 original size:84 final size:84
Alignment explanation
Indices: 1474255--1474419 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
1474245 CATTTTCCAC
* * * *
1474255 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
1474320 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
1474339 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA
* * *
1474401 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
1474420 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 54 0.78
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:1476489 original size:13 final size:13
Alignment explanation
Indices: 1476471--1476496 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1476461 CAATTTTTTG
1476471 TGTATCGATACAT
1 TGTATCGATACAT
1476484 TGTATCGATACAT
1 TGTATCGATACAT
1476497 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1476561 original size:21 final size:21
Alignment explanation
Indices: 1476535--1476610 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1476525 CTGCCAAGAA
1476535 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
1476556 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1476576 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1476597 ATGTATCGATACAT
1 ATGTATCGATACAT
1476611 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1476580 original size:20 final size:20
Alignment explanation
Indices: 1476555--1476628 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1476545 ACATCTTTTT
1476555 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
1476575 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
1476596 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
1476616 CATGTATCGATAC
1 CATGTATCGATAC
1476629 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:1476592 original size:41 final size:41
Alignment explanation
Indices: 1476535--1476628 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1476525 CTGCCAAGAA
1476535 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1476576 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1476617 ATGTATCGATAC
1 ATGTATCGATAC
1476629 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1477859 original size:58 final size:58
Alignment explanation
Indices: 1477709--1478028 Score: 511
Period size: 58 Copynumber: 5.6 Consensus size: 58
1477699 CATTCTTCAC
*
1477709 CCTTCAAAAGCCCACAAGTCAGTGGCA-TCTTTT-TGAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCT-AAAGCCCACAAGTCAGTGGCAA
*
1477766 CCTTC-AAAGCCCACAAATCAGTGGCACCCTTTTCTAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCTAAAGCCCACAAGTCAGTGGCAA
1477823 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCTAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCTAAAGCCCACAAGTCAGTGGCAA
* * * * * *
1477881 CCTTCAAAAGCCCATAAGTTAGTGGTACCCTTTTCAAAAGCCCATAAGTTAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCTAAAGCCCACAAGTCAGTGGCAA
* *
1477939 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAACCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCTAAAGCCCACAAGTCAGTGGCAA
*
1477997 CCTTCAAAAGCCCACAAGTCAGTGGCAACCTT
1 CCTTCAAAAGCCCACAAGTCAGTGGCACCCTT
1478029 CAAAAGCACA
Statistics
Matches: 244, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
56 20 0.08
57 37 0.15
58 187 0.77
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (58 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCTAAAGCCCACAAGTCAGTGGCAA
Found at i:1478050 original size:28 final size:28
Alignment explanation
Indices: 1477709--1478043 Score: 420
Period size: 28 Copynumber: 11.7 Consensus size: 28
1477699 CATTCTTCAC
*
1477709 CCTTCAAAAGCCCACAAGTCAGTGGCAT
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* **
1477737 CTTTTTGAAAGCCCACAAGTCAGTGGCAA
1 C-CTTCAAAAGCCCACAAGTCAGTGGCAA
* *
1477766 CCTTC-AAAGCCCACAAATCAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
1477793 CCTTTTCTAAAGCCCACAAGTCAGTGGCAA
1 CC--TTCAAAAGCCCACAAGTCAGTGGCAA
*
1477823 CCTTCAAAAGCCCACAAGTCAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
1477851 CCTTTTCTAAAGCCCACAAGTCAGTGGCAA
1 CC--TTCAAAAGCCCACAAGTCAGTGGCAA
* * * *
1477881 CCTTCAAAAGCCCATAAGTTAGTGGTAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* *
1477909 CCTTTTCAAAAGCCCATAAGTTAGTGGCAA
1 CC--TTCAAAAGCCCACAAGTCAGTGGCAA
*
1477939 CCTTCAAAAGCCCACAAGTCAGTGGCAC
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
1477967 CCTTTTCAAAAACCCACAAGTCAGTGGCAA
1 CC--TTCAAAAGCCCACAAGTCAGTGGCAA
1477997 CCTTCAAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
1478025 CCTTCAAAAGCACACAAGT
1 CCTTCAAAAGCCCACAAGT
1478044 TGGTGGCGTC
Statistics
Matches: 269, Mismatches: 28, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
27 22 0.08
28 120 0.45
29 27 0.10
30 100 0.37
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (28 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAA
Found at i:1478145 original size:49 final size:49
Alignment explanation
Indices: 1478055--1478397 Score: 391
Period size: 49 Copynumber: 6.9 Consensus size: 49
1478045 GGTGGCGTCT
* * * * * *
1478055 TCTTCTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGAACCTTTA
1 TCTT-TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
1478105 TCTTTAAGACCAATGTTGCTGGCCTTGAATCAGTACATTGGCATCTTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
1478154 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
1478203 TCTTTAAGACCAATGTCACTGGCCTTGAATCAGC-CTATTGGCATCTTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCAC-ATTGGCACCTTCA
* * *
1478252 TCTTTAAGTCCAATGTCGTTGGCCTGGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * **
1478301 TCTTTAAAGATCAGTATCGCTGGCCTTGAATCAGCATATTGGTGCCTTCGTCA
1 TCTTT-AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T--TCA
* * *
1478354 TCTTTAACACCCAATGTCGTTGGCCTTGAATCAACACATTGGCA
1 TCTTTAAGA-CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1478398 TTCTTCTCAT
Statistics
Matches: 249, Mismatches: 37, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.00
49 174 0.70
50 36 0.14
51 1 0.00
52 3 0.01
53 34 0.14
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (49 bp):
TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:1479134 original size:32 final size:32
Alignment explanation
Indices: 1479093--1479163 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1479083 TACAACGATT
*
1479093 TGTATCGATACATAA-TTGCTGTATCAATATAA
1 TGTATCGATACATAAGTT-CTGTATCAATACAA
* *
1479125 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTCTGTATCAATACAA
1479157 TGTATCG
1 TGTATCG
1479164 CTACGAAGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTTCTGTATCAATACAA
Found at i:1479226 original size:13 final size:13
Alignment explanation
Indices: 1479208--1479232 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1479198 ATTACTCAAA
1479208 TGTATCGATACAT
1 TGTATCGATACAT
1479221 TGTATCGATACA
1 TGTATCGATACA
1479233 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1479417 original size:13 final size:13
Alignment explanation
Indices: 1479399--1479423 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1479389 TTCAACGATT
1479399 TGTATCGATACAA
1 TGTATCGATACAA
1479412 TGTATCGATACA
1 TGTATCGATACA
1479424 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1479556 original size:52 final size:52
Alignment explanation
Indices: 1479473--1479623 Score: 248
Period size: 52 Copynumber: 2.9 Consensus size: 52
1479463 TACCAAGAAA
* * *
1479473 ATGTATCGATACATTACTCAAATGTATCGATACATGCAGGCAAATTTGCCCTG
1 ATGTATCGATACACTA-TGAAATGTATCGATACATGCAGGCAAATTTGCCCAG
*
1479526 ATGTATCGATACACTATGAAATGTATCGATACATACAGGCAAATTTGCCCAG
1 ATGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTTGCCCAG
*
1479578 ATGTATTGATACACTATGAAATGTATCGATACATGCAGGCAAATTT
1 ATGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTT
1479624 TCATATTTCG
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
52 77 0.84
53 15 0.16
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
ATGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTTGCCCAG
Found at i:1480821 original size:17 final size:17
Alignment explanation
Indices: 1480799--1480833 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1480789 GTTTGTGCCC
*
1480799 TAGTTTTGTGTCATGCT
1 TAGTTTTGTGTCAAGCT
1480816 TAGTTTTGTGTCAAGCT
1 TAGTTTTGTGTCAAGCT
1480833 T
1 T
1480834 GAGTGGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.51
Consensus pattern (17 bp):
TAGTTTTGTGTCAAGCT
Found at i:1482700 original size:13 final size:13
Alignment explanation
Indices: 1482682--1482706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1482672 CATTTTATGG
1482682 TGTATCGATACAA
1 TGTATCGATACAA
1482695 TGTATCGATACA
1 TGTATCGATACA
1482707 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1482722 original size:32 final size:33
Alignment explanation
Indices: 1482659--1482726 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1482649 TGTTTCAAGC
**
1482659 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
1482692 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1482724 CAA
1 CAA
1482727 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:1485095 original size:21 final size:21
Alignment explanation
Indices: 1485067--1485108 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1485057 TATTTTTGAT
*
1485067 GATGATTTTGATG-GAAAAAC
1 GATGATTTTGAAGTGAAAAAC
1485087 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
1485109 AAGAGTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:1485182 original size:10 final size:10
Alignment explanation
Indices: 1485167--1485194 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1485157 TTTGAGAGGA
1485167 TTTTGGGTGT
1 TTTTGGGTGT
1485177 TTTTGGGTGT
1 TTTTGGGTGT
1485187 TTTTGGGT
1 TTTTGGGT
1485195 TAGAGTATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.39, T:0.61
Consensus pattern (10 bp):
TTTTGGGTGT
Found at i:1485267 original size:13 final size:13
Alignment explanation
Indices: 1485249--1485286 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1485239 ATAATCCCCT
* *
1485249 TGTATCGATATAG
1 TGTATCGATACAA
1485262 TGTATCGATACAA
1 TGTATCGATACAA
1485275 TGTATCGATACA
1 TGTATCGATACA
1485287 GAGAATGCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1485504 original size:8 final size:8
Alignment explanation
Indices: 1485491--1485516 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1485481 ATTATCATTC
1485491 ATCACAAA
1 ATCACAAA
1485499 ATCACAAA
1 ATCACAAA
1485507 ATCACAAA
1 ATCACAAA
1485515 AT
1 AT
1485517 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:1493258 original size:32 final size:32
Alignment explanation
Indices: 1493196--1493328 Score: 141
Period size: 31 Copynumber: 4.2 Consensus size: 32
1493186 AACCTTCAAA
* *
1493196 TCTTTTTCCAAAAGTCCACGATTTAATGGCATC
1 TCTTTTTCC-AAAGTCCACGACTTAGTGGCATC
* *
1493229 TCTTTTTCCAAAGTCAATGACTTAGTGGCATC
1 TCTTTTTCCAAAGTCCACGACTTAGTGGCATC
*
1493261 T-TTTCTT-CAAAGTCCACGACTCAGTGGCATC
1 TCTTT-TTCCAAAGTCCACGACTTAGTGGCATC
* * *
1493292 TC-TTTTCC-ATGTCCACGACTCAATGGCATC
1 TCTTTTTCCAAAGTCCACGACTTAGTGGCATC
1493322 -CTTTTTC
1 TCTTTTTC
1493329 TTTTTTAATT
Statistics
Matches: 87, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
29 1 0.01
30 27 0.31
31 28 0.32
32 22 0.25
33 9 0.10
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.37
Consensus pattern (32 bp):
TCTTTTTCCAAAGTCCACGACTTAGTGGCATC
Found at i:1493328 original size:30 final size:30
Alignment explanation
Indices: 1493197--1493328 Score: 113
Period size: 30 Copynumber: 4.2 Consensus size: 30
1493187 ACCTTCAAAT
* *
1493197 CTTTTTCCAAAAGTCCACGATTTAATGGCATC
1 CTTTTTCC--AAGTCCACGACTCAATGGCATC
* * * *
1493229 TCTTTTTCCAAAGTCAATGACTTAGTGGCATC
1 -CTTTTTCC-AAGTCCACGACTCAATGGCATC
* * *
1493261 TTTTCTTCAAAGTCCACGACTCAGTGGCAT-
1 CTTT-TTCCAAGTCCACGACTCAATGGCATC
*
1493291 CTCTTTTCCATGTCCACGACTCAATGGCATC
1 CT-TTTTCCAAGTCCACGACTCAATGGCATC
1493322 CTTTTTC
1 CTTTTTC
1493329 TTTTTTAATT
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
30 28 0.34
31 25 0.30
32 22 0.27
33 8 0.10
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.36
Consensus pattern (30 bp):
CTTTTTCCAAGTCCACGACTCAATGGCATC
Found at i:1493330 original size:63 final size:63
Alignment explanation
Indices: 1493206--1493326 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 63
1493196 TCTTTTTCCA
* * * * *
1493206 AAAGTCCACGATTTAATGGCATCTCTTTTTCCAAAGTCAATGACTTAGTGGCATCTTTTCTTC
1 AAAGTCCACGACTCAATGGCATCTCTTTTTCCAAAGTCAACGACTCAATGGCATCTTTTCTTC
* * *
1493269 AAAGTCCACGACTCAGTGGCATCTC-TTTTCC-ATGTCCACGACTCAATGGCATCCTTTT
1 AAAGTCCACGACTCAATGGCATCTCTTTTTCCAAAGTCAACGACTCAATGGCAT-CTTTT
1493327 TCTTTTTTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
61 16 0.33
62 11 0.22
63 22 0.45
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (63 bp):
AAAGTCCACGACTCAATGGCATCTCTTTTTCCAAAGTCAACGACTCAATGGCATCTTTTCTTC
Found at i:1493400 original size:32 final size:32
Alignment explanation
Indices: 1493331--1493985 Score: 454
Period size: 32 Copynumber: 20.9 Consensus size: 32
1493321 CCTTTTTCTT
* * * *
1493331 TTTTAATTCCACAACTTCATGGCACTATTTTTCC
1 TTTTAAGTCCACAACTCCGTGGCAC--CTTTTCC
* *
1493365 TTTTAAGTCCACAACTCCGTGACATCTTTTCC
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTCC
*
1493397 TTTTAAGTCCACAACTTCGTGGCA-C----CC
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTCC
* * *
1493424 TTTTAAGTCCATAACTCCGTAGCACCCTTTTTTC
1 TTTTAAGTCCACAACTCCGTGGCA-CC-TTTTCC
* *
1493458 TTTTAAGTCCACAAATCCATGGCACCTTTTCC
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTCC
* * ** **
1493490 TTTAAAGCCCACAACTCAATGGCGTCTTTT-C
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTCC
* **
1493521 -TCTAAGTCCACAACTCCGTGGCACCTTTTTT
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTCC
* *
1493552 TTTTCAGAGTCCACAAATCAC-TGACA-C----CC
1 TTTT-A-AGTCCACAACTC-CGTGGCACCTTTTCC
1493581 TTTTAAGTCCACAACTCCGTGGCACCCTTTTTCC
1 TTTTAAGTCCACAACTCCGTGGCA-CC-TTTTCC
* *
1493615 TTTTAAGCCCACAACTCCGTAGCACC--TT--
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTCC
* *
1493643 TTTTAAGTCCACAACTCCATGGTACCTTTTTCC
1 TTTTAAGTCCACAACTCCGTGGCACC-TTTTCC
1493676 -TTTAAGTCCACAACTCCGTGGCACCTTTTCC
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTCC
* * * ***
1493707 TTTTAAGCCCAGAACTCAGTGGTGTCTTTT-C
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTCC
* * * *
1493738 -TCTAAGTCCACAACTTCGTGGCTCCTTTTCT
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTCC
* * *
1493769 TTTTAAGTCCACAACTCTGTGGCACTTTTTTCT
1 TTTTAAGTCCACAACTCCGTGGCAC-CTTTTCC
*
1493802 TTTTCAGAGCCCACAACTCCGTGGCA-C---T-C
1 TTTT-A-AGTCCACAACTCCGTGGCACCTTTTCC
* ** * *
1493831 TTTTAAGTTCACAACTCTATAGCACCTTTTTCT
1 TTTTAAGTCCACAACTCCGTGGCACC-TTTTCC
* * *
1493864 TTTTAAAG-CTTACAACTTCGTGGCA-----GCC
1 TTTT-AAGTC-CACAACTCCGTGGCACCTTTTCC
* *
1493892 TTTTAAGTCTACAACTCCGTGGCACCTTTTCT
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTCC
*
1493924 TTTTAAGTCCACAACTTCGTGGCACCTTTTCC
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTCC
* * *
1493956 TTTTAAGTTCATAACTCTGTGGCACCTTTT
1 TTTTAAGTCCACAACTCCGTGGCACCTTTT
1493986 TCTTCTCAAA
Statistics
Matches: 482, Mismatches: 94, Indels: 92
0.72 0.14 0.14
Matches are distributed among these distances:
26 1 0.00
27 69 0.14
28 31 0.06
29 10 0.02
30 46 0.10
31 11 0.02
32 182 0.38
33 20 0.04
34 94 0.20
35 18 0.04
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.37
Consensus pattern (32 bp):
TTTTAAGTCCACAACTCCGTGGCACCTTTTCC
Found at i:1493461 original size:93 final size:90
Alignment explanation
Indices: 1493331--1493704 Score: 256
Period size: 93 Copynumber: 4.0 Consensus size: 90
1493321 CCTTTTTCTT
* * * * *
1493331 TTTTAATTCCACAACTTCATGGCA-CTATTTTTCCTTTTAAGTCCACAACTCCGTGACATCTTTT
1 TTTTAAGTCCACAACTCCGTAGCACCT-TTTTT-CTTTTAAGTCCACAAATCC-TGACA-CTTTT
1493395 CCTTTTAAGTCCACAACTTCGTGGCACCC
62 CCTTTTAAGTCCACAACTTCGTGGCACCC
* *
1493424 TTTTAAGTCCATAACTCCGTAGCACCCTTTTTTCTTTTAAGTCCACAAATCCATGGCACCTTTTC
1 TTTTAAGTCCACAACTCCGTAGCA-CCTTTTTTCTTTTAAGTCCACAAATCC-TGACA-CTTTTC
* * * * **
1493489 CTTTAAAGCCCACAAC-TCAATGGCGTCTT
63 CTTTTAAGTCCACAACTTC-GTGGC-ACCC
*
1493518 TTCTCTAAGTCCACAACTCCGTGGCACCTTTTTT-TTTTCAGAGTCCACAAATCACTGACAC---
1 TT-T-TAAGTCCACAACTCCGTAGCACCTTTTTTCTTTT-A-AGTCCACAAATC-CTGACACTTT
*
1493579 -CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTTCC
61 TCCTTTTAAGTCCACAACTTCGTGGCA--C-----CC
* *
1493615 TTTTAAGCCCACAACTCCGTAGCACC----TT-TTTTAAGTCCACAACTCCATGGTAC-CTTTTT
1 TTTTAAGTCCACAACTCCGTAGCACCTTTTTTCTTTTAAGTCCACAAATCC-T-G-ACAC-TTTT
*
1493674 CC-TTTAAGTCCACAACTCCGTGGCA-CC
62 CCTTTTAAGTCCACAACTTCGTGGCACCC
1493701 TTTT
1 TTTT
1493705 CCTTTTAAGC
Statistics
Matches: 228, Mismatches: 28, Indels: 57
0.73 0.09 0.18
Matches are distributed among these distances:
86 6 0.03
88 1 0.00
89 12 0.05
90 3 0.01
91 27 0.12
92 4 0.02
93 65 0.29
94 35 0.15
95 36 0.16
96 36 0.16
97 3 0.01
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.35
Consensus pattern (90 bp):
TTTTAAGTCCACAACTCCGTAGCACCTTTTTTCTTTTAAGTCCACAAATCCTGACACTTTTCCTT
TTAAGTCCACAACTTCGTGGCACCC
Found at i:1493482 original size:61 final size:58
Alignment explanation
Indices: 1493363--1493487 Score: 153
Period size: 61 Copynumber: 2.1 Consensus size: 58
1493353 CACTATTTTT
* * *
1493363 CCTTTTAAGTCCACAACTCCGTGACATCTTTTCCTTTTAAGTCCACAACTTCGTGGCA
1 CCTTTTAAGTCCACAACTCCGTGACATCTTTTCCTTTTAAGTCCACAAATCCATGGCA
* * *
1493421 CCCTTTTAAGTCCATAACTCCGT-AGCACCCTTTTTTCTTTTAAGTCCACAAATCCATGGCA
1 -CCTTTTAAGTCCACAACTCCGTGA-CA-TC-TTTTCCTTTTAAGTCCACAAATCCATGGCA
1493482 CCTTTT
1 CCTTTT
1493488 CCTTTAAAGC
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
58 1 0.02
59 23 0.40
60 7 0.12
61 26 0.46
ACGTcount: A:0.22, C:0.31, G:0.10, T:0.36
Consensus pattern (58 bp):
CCTTTTAAGTCCACAACTCCGTGACATCTTTTCCTTTTAAGTCCACAAATCCATGGCA
Found at i:1493584 original size:157 final size:152
Alignment explanation
Indices: 1493358--1493713 Score: 430
Period size: 157 Copynumber: 2.3 Consensus size: 152
1493348 CATGGCACTA
* * * * * *
1493358 TTTTTCCTTTTAAGTCCACAACTCCGTGACATCTTTTCCTTTTAAGTCCACAACTTCGTGGCACC
1 TTTTTCC-TCTAAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACATCCTGACACC
* * * *
1493423 CTTTTAAGTCCATAACTCCGTAGCACCCTTTTTTCTTTTAAGTCCACAAATCCATGGCACCTTTT
65 CTTTTAAGTCCACAACTCCGTAGCACCCTTTTTCCTTTTAAGCCCACAAATCCATAGCACC-TTT
*
1493488 CCTTTAAAGCCCACAACTCAATGG-CG
129 --TTT-AAGCCCACAACTCAATGGACC
**
1493514 TCTTTT-CTCTAAGTCCACAACTCCGTGGCACCTTTTTTTTTTCAGAGTCCACAA-ATCACTGAC
1 T-TTTTCCTCTAAGTCCACAACTCCGTGGCACCTTTTCCTTTT-A-AGTCCACAACATC-CTGAC
* * *
1493577 ACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTTCCTTTTAAGCCCACAACTCCGTAGCACCT
62 ACCCTTTTAAGTCCACAACTCCGTAGCACCCTTTTTCCTTTTAAGCCCACAAATCCATAGCACCT
* *
1493642 TTTTTAAGTCCACAACTCCATGGTACC
127 TTTTTAAGCCCACAACTCAATGG-ACC
*
1493669 TTTTTCCTTTAAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAG
1 TTTTTCCTCTAAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAG
1493714 CCCAGAACTC
Statistics
Matches: 172, Mismatches: 21, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
153 18 0.10
154 8 0.05
155 65 0.38
156 8 0.05
157 73 0.42
ACGTcount: A:0.22, C:0.32, G:0.11, T:0.35
Consensus pattern (152 bp):
TTTTTCCTCTAAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACATCCTGACACCC
TTTTAAGTCCACAACTCCGTAGCACCCTTTTTCCTTTTAAGCCCACAAATCCATAGCACCTTTTT
TAAGCCCACAACTCAATGGACC
Found at i:1493697 original size:94 final size:93
Alignment explanation
Indices: 1493582--1493987 Score: 332
Period size: 94 Copynumber: 4.3 Consensus size: 93
1493572 CTGACACCCT
*
1493582 TTTAAGTCCACAACTCCGTGGCACCCTTTTTCCTTTTAAGCCCACAACTCCGTAGCACCTTTTTT
1 TTTAAGTCCACAACTCCGTGGCA-CCTTTTTCCTTTTAAGCCCACAACTCCGTGGCA-CTTTTTT
1493647 AAGTCCACAACTCCATGGTACCTTTTTC-C
64 AAGTCCACAACTCCATGGTACCTTTTTCTC
* * **
1493676 TTTAAGTCCACAACTCCGTGGCACC-TTTTCCTTTTAAGCCCAGAACTCAGTGGTGTCTTTTCTC
1 TTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAGCCCACAACTCCGTGG-CACTTTT-T-
* * *
1493740 TAAGTCCACAACTTCGTGGCT-CC-TTTTCTT
63 TAAGTCCACAACTCCATGG-TACCTTTTTCTC
* * * *
1493770 TTTAAGTCCACAACTCTGTGGCACTTTTTTCTTTTTCAGAGCCCACAACTCCGTGGCACTCTTTT
1 TTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTT-A-AGCCCACAACTCCGTGGCACTTTTTT
* * * * *
1493835 AAGTTCACAACTCTATAGCACCTTTTTCTT
64 AAGTCCACAACTCCATGGTACCTTTTTCTC
* * * * *
1493865 TTTAAAG-CTTACAACTTCGTGGCA------GCCTTTTAAGTCTACAACTCCGTGGCACCTTTTC
1 TTT-AAGTC-CACAACTCCGTGGCACCTTTTTCCTTTTAAGCCCACAACTCCGTGGCA-C---T-
* * * *
1493923 TTTTTAAGTCCACAACTTCGTGGCACCTTTTCCT-
59 TTTTTAAGTCCACAACTCCATGGTACCTTTTTCTC
* * *
1493957 TTTAAGTTCATAACTCTGTGGCACCTTTTTC
1 TTTAAGTCCACAACTCCGTGGCACCTTTTTC
1493988 TTCTCAAAGC
Statistics
Matches: 246, Mismatches: 42, Indels: 45
0.74 0.13 0.14
Matches are distributed among these distances:
88 17 0.07
89 2 0.01
90 5 0.02
91 14 0.06
92 34 0.14
93 35 0.14
94 81 0.33
95 22 0.09
96 20 0.08
97 16 0.07
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (93 bp):
TTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTAA
GTCCACAACTCCATGGTACCTTTTTCTC
Found at i:1493702 original size:217 final size:214
Alignment explanation
Indices: 1493363--1493782 Score: 601
Period size: 217 Copynumber: 1.9 Consensus size: 214
1493353 CACTATTTTT
* * * *
1493363 CCTTTTAAGTCCACAACTCCGTGACATCTTTTCCTTTTAAGTCCACAACTTCGTGGCACCCTTTT
1 CCTTTTAAGTCCACAACTCCGTGACACCTTTTCCTTTTAAGCCCACAACTCCGTAGCACCCTTTT
* * *
1493428 AAGTCCATAACTCCGTAGCACCCTTTTTTCTTTTAAGTCCACAAATCCATGGCACCTTTTCCTTT
66 AAGTCCACAACTCCATAGCACCCTTTTTTCCTTTAAGTCCACAAATCCATGGCACCTTTTCCTTT
*
1493493 AAAGCCCACAACTCAATGGCGTCTTTTCTCTAAGTCCACAACTCCGTGGCACCTTTTTTTTTTCA
131 AAAGCCCACAACTCAATGGCGTCTTTTCTCTAAGTCCACAACTCCGTGGCACCTTTTCTTTTT-A
1493558 GAGTCCACAAATCACTGACAC
195 -AGTCCACAAATCACTGACAC
* *
1493579 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTTCCTTTTAAGCCCACAACTCCGTAGCACCTTT
1 CCTTTTAAGTCCACAACTCCGTGACA-CC-TTTTCCTTTTAAGCCCACAACTCCGTAGCACC-CT
* * * *
1493644 TTTAAGTCCACAACTCCATGGTA-CC-TTTTTCCTTTAAGTCCACAACTCCGTGGCACCTTTTCC
63 TTTAAGTCCACAACTCCATAGCACCCTTTTTTCCTTTAAGTCCACAAATCCATGGCACCTTTTCC
* * * * * *
1493707 TTTTAAGCCCAGAACTCAGTGGTGTCTTTTCTCTAAGTCCACAACTTCGTGGCTCCTTTTCTTTT
128 TTTAAAGCCCACAACTCAATGGCGTCTTTTCTCTAAGTCCACAACTCCGTGGCACCTTTTCTTTT
1493772 TAAGTCCACAA
193 TAAGTCCACAA
1493783 CTCTGTGGCA
Statistics
Matches: 181, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
215 9 0.05
216 26 0.14
217 95 0.52
218 31 0.17
219 20 0.11
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.35
Consensus pattern (214 bp):
CCTTTTAAGTCCACAACTCCGTGACACCTTTTCCTTTTAAGCCCACAACTCCGTAGCACCCTTTT
AAGTCCACAACTCCATAGCACCCTTTTTTCCTTTAAGTCCACAAATCCATGGCACCTTTTCCTTT
AAAGCCCACAACTCAATGGCGTCTTTTCTCTAAGTCCACAACTCCGTGGCACCTTTTCTTTTTAA
GTCCACAAATCACTGACAC
Found at i:1493844 original size:62 final size:61
Alignment explanation
Indices: 1493331--1493989 Score: 418
Period size: 62 Copynumber: 10.6 Consensus size: 61
1493321 CCTTTTTCTT
* * * * * * *
1493331 TTTTAATTCCACAACTTCATGGCACTATTTTTCCTTTTAAGTCCACAACTCCGTGACATCTTTTC
1 TTTTAAGTCCACAACTCCGTGGCAC-CTTTTTCTTTTTAAGTCCACAACTCCGTGGCA-C--CT-
1493396 C
61 C
* * *
1493397 TTTTAAGTCCACAACTTCGTGGCACC-----C-TTTTAAGTCCATAACTCCGTAGCACCCTTTTT
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAGTCCACAACTCCGTGGCA-CC-----
1493456 TC
60 TC
* * * * * ** ** *
1493458 TTTTAAGTCCACAAATCCATGGCACC-TTTTCCTTTAAAGCCCACAACTCAATGGCGTCTT
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACCTC
* *
1493518 TTCTCTAAGTCCACAACTCCGTGGCACCTTTTT-TTTTTCAGAGTCCACAAATCAC-TGACACC-
1 TT-T-TAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT-A-AGTCCACAACTC-CGTGGCACCT
1493580 C
61 C
* * * *
1493581 TTTTAAGTCCACAACTCCGTGGCACCCTTTTTCCTTTTAAGCCCACAACTCCGTAGCACCTT
1 TTTTAAGTCCACAACTCCGTGGCA-CCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACCTC
* * *
1493643 TTTTAAGTCCACAACTCCATGGTACCTTTTTC-CTTTAAGTCCACAACTCCGTGGCACCTTTTCC
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACC---T-C
* * * *** * * *
1493707 TTTTAAGCCCAGAACTCAGTGGTGTC-TTTTC--TCTAAGTCCACAACTTCGTGGCTCCTTTTC
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACC---TC
* * *
1493768 TTTTTAAGTCCACAACTCTGTGGCACTTTTTTCTTTTTCAGAGCCCACAACTCCGTGGCA-CTC
1 -TTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT-A-AGTCCACAACTCCGTGGCACCTC
* ** * * * *
1493831 TTTTAAGTTCACAACTCTATAGCACCTTTTTCTTTTTAAAG-CTTACAACTTCGTGGCAGC-C
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT-AAGTC-CACAACTCCGTGGCACCTC
* *
1493892 TTTTAAGTCTACAACTCCGTGGCACC-TTTTCTTTTTAAGTCCACAACTTCGTGGCACCTTTTCC
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACC---T-C
* * *
1493956 TTTTAAGTTCATAACTCTGTGGCACCTTTTTCTT
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTTCTT
1493990 CTCAAAGCCT
Statistics
Matches: 473, Mismatches: 81, Indels: 79
0.75 0.13 0.12
Matches are distributed among these distances:
59 40 0.08
60 40 0.08
61 107 0.23
62 136 0.29
63 24 0.05
64 57 0.12
65 11 0.02
66 42 0.09
67 16 0.03
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (61 bp):
TTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACCTC
Found at i:1494012 original size:125 final size:122
Alignment explanation
Indices: 1493769--1494027 Score: 292
Period size: 125 Copynumber: 2.1 Consensus size: 122
1493759 CTCCTTTTCT
* *
1493769 TTTTAAGTCCACAACTCTGTGGCACTTTTTTCTTTTTCAGAGCCCACAACTCCGTGGCACTCTTT
1 TTTTAAGTCCACAACTCCGTGGCACTCTTTTCTTTTTCAGAGCCCACAACTCCGTGGCACTCTTT
* * * *
1493834 TAAGTTCACAACTCTATAGCACCTTTTTCTTTTTAAAGCTTACAACTTCGTGGCAGCC
66 TAAGTTCACAACTCTATAGCACCTTTTTCTTCTCAAAGCCTACAACGTCGTGGCA-CC
* * *
1493892 TTTTAAGTCTACAACTCCGTGGCAC-CTTTTCTTTTT-A-AGTCCACAACTTCGTGGCACCTTTT
1 TTTTAAGTCCACAACTCCGTGGCACTCTTTTCTTTTTCAGAGCCCACAACTCCGTGGCA-C---T
* * * *
1493954 CCTTTTAAGTTCATAACTCTGTGGCACCTTTTTCTTCTCAAAGCCTACTA-GTCAGTGGCACC
62 -CTTTTAAGTTCACAACTCTATAGCACCTTTTTCTTCTCAAAGCCTACAACGTC-GTGGCACC
1494016 TCTTTGAAGTCC
1 T-TTT-AAGTCC
1494028 TTTATTAGTG
Statistics
Matches: 114, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
120 17 0.15
121 2 0.02
122 10 0.09
123 23 0.20
124 6 0.05
125 51 0.45
126 5 0.04
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.38
Consensus pattern (122 bp):
TTTTAAGTCCACAACTCCGTGGCACTCTTTTCTTTTTCAGAGCCCACAACTCCGTGGCACTCTTT
TAAGTTCACAACTCTATAGCACCTTTTTCTTCTCAAAGCCTACAACGTCGTGGCACC
Found at i:1494248 original size:32 final size:32
Alignment explanation
Indices: 1494211--1494433 Score: 231
Period size: 32 Copynumber: 7.0 Consensus size: 32
1494201 CCTTAGTGGA
* * **
1494211 GAAACCTTCTTC-ATAGGCCACACAAGTCAGTG
1 GAAACC-TCTTCAAAAGCCCACACAAGTTGGTG
*
1494243 GAAACCTCTTCAAAAACCCACACAAGTTGGTG
1 GAAACCTCTTCAAAAGCCCACACAAGTTGGTG
* *
1494275 GTAACC-CTTTCTAAAGCCCACACAAGTTGGTG
1 GAAACCTC-TTCAAAAGCCCACACAAGTTGGTG
* *
1494307 GTAACCTCTTCAAAAGCCCACACAAGTTAGTG
1 GAAACCTCTTCAAAAGCCCACACAAGTTGGTG
* * *
1494339 GTAACC-CTTTCTAAAGTCCACACAAGTTGGTG
1 GAAACCTC-TTCAAAAGCCCACACAAGTTGGTG
* *
1494371 GAAACCTTCTT-TAAAGCCCACACAAGTCGGTG
1 GAAACC-TCTTCAAAAGCCCACACAAGTTGGTG
*
1494403 GCAACC-CTTTCAAAAGCCCACACAAGTTGGT
1 GAAACCTC-TTCAAAAGCCCACACAAGTTGGT
1494434 CACATTTCTT
Statistics
Matches: 164, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.01
31 9 0.05
32 150 0.91
33 3 0.02
34 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.22
Consensus pattern (32 bp):
GAAACCTCTTCAAAAGCCCACACAAGTTGGTG
Found at i:1494329 original size:64 final size:64
Alignment explanation
Indices: 1494228--1494433 Score: 306
Period size: 64 Copynumber: 3.2 Consensus size: 64
1494218 TCTTCATAGG
** *
1494228 CCACACAAGTCAGTGGAAACCTCTTCAAAAACCCACACAAGTTGGTGGTAACCCTTTCTAAAGC
1 CCACACAAGTTGGTGGAAACCTCTTCAAAAGCCCACACAAGTTGGTGGTAACCCTTTCTAAAGC
* * *
1494292 CCACACAAGTTGGTGGTAACCTCTTCAAAAGCCCACACAAGTTAGTGGTAACCCTTTCTAAAGT
1 CCACACAAGTTGGTGGAAACCTCTTCAAAAGCCCACACAAGTTGGTGGTAACCCTTTCTAAAGC
* * * *
1494356 CCACACAAGTTGGTGGAAACCTTCTT-TAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAAGC
1 CCACACAAGTTGGTGGAAACC-TCTTCAAAAGCCCACACAAGTTGGTGGTAACCCTTTCTAAAGC
1494420 CCACACAAGTTGGT
1 CCACACAAGTTGGT
1494434 CACATTTCTT
Statistics
Matches: 128, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
64 124 0.97
65 4 0.03
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (64 bp):
CCACACAAGTTGGTGGAAACCTCTTCAAAAGCCCACACAAGTTGGTGGTAACCCTTTCTAAAGC
Found at i:1494386 original size:96 final size:96
Alignment explanation
Indices: 1494228--1494430 Score: 277
Period size: 96 Copynumber: 2.1 Consensus size: 96
1494218 TCTTCATAGG
* *
1494228 CCACACAAGTCAGTGGAAACCTCTTCAAAAACCCACACAAGTTGGTGGTAACCCTTTCTAAAGCC
1 CCACACAAGTTAGTGGAAACCTCTTCAAAAACCCACACAAGTTGGTGGTAAACCTTTCTAAAGCC
* *
1494293 CACACAAGTTGGTGGTAA-CCTCTTCAAAAGC
66 CACACAAGTCGGTGGCAACCCT-TTCAAAAGC
* * ** *
1494324 CCACACAAGTTAGTGGTAACC-CTTTCTAAAGTCCACACAAGTTGGTGG-AAACCTTCTTTAAAG
1 CCACACAAGTTAGTGGAAACCTC-TTCAAAAACCCACACAAGTTGGTGGTAAACCTT-TCTAAAG
1494387 CCCACACAAGTCGGTGGCAACCCTTTCAAAAGC
64 CCCACACAAGTCGGTGGCAACCCTTTCAAAAGC
1494420 CCACACAAGTT
1 CCACACAAGTT
1494431 GGTCACATTT
Statistics
Matches: 95, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
95 7 0.07
96 85 0.89
97 3 0.03
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.22
Consensus pattern (96 bp):
CCACACAAGTTAGTGGAAACCTCTTCAAAAACCCACACAAGTTGGTGGTAAACCTTTCTAAAGCC
CACACAAGTCGGTGGCAACCCTTTCAAAAGC
Found at i:1494564 original size:52 final size:52
Alignment explanation
Indices: 1494482--1494897 Score: 340
Period size: 52 Copynumber: 8.0 Consensus size: 52
1494472 TAGCACATTG
* * * *
1494482 GCATCTTTAAATCTAATATCGCTGGCCTTGAATCAGCATATTGGCCCCTTTA
1 GCATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTA
* * * **
1494534 GCACCTTTAAGTCTAATATCGCTGGCCTTGAATCAGTATTTTGGCACCTTT-
1 GCATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTA
*
1494585 GCCATCTTTAAGTCTGATGTCGCTGGCCTTGAATCAGCACATTGGCATCC-TTA
1 G-CATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTTA
* * * * * * * *
1494638 TCATGTTAAAGTCTAATGTTGCTAGCCTTGAATTAGCATATTGGCATCTTTA
1 GCATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTA
* ** * * * * *
1494690 ACATCCCTAAGCCCAATGTCGTTGGCCTTGGATCAGCACAATGGCATTCCTCTT-
1 GCATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCA--CCT-TTA
* * * * * *
1494744 --ATCTTCAAGTCTAATGTCGTTGGCCGTGAATCAGCACATTGACA-TTCTTC
1 GCATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT-TTA
* * * * * * * *
1494794 GCACCTTTAAGCCCAATATCGCTGGCATTGAATCAGCATATTGGTACCTTTT
1 GCATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTA
* * * *
1494846 TCATCTTTAAGTCCAATGTCACTGGCCTTAAATCAGCACATTGGCACCTTTA
1 GCATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTA
1494898 AGTCCAATGT
Statistics
Matches: 285, Mismatches: 68, Indels: 22
0.76 0.18 0.06
Matches are distributed among these distances:
49 4 0.01
51 2 0.01
52 272 0.95
53 3 0.01
54 2 0.01
55 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (52 bp):
GCATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTA
Found at i:1494911 original size:43 final size:43
Alignment explanation
Indices: 1494850--1494983 Score: 214
Period size: 43 Copynumber: 3.1 Consensus size: 43
1494840 CCTTTTTCAT
1494850 CTTTAAGTCCAATGTCACTGGCCTTAAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTCACTGGCCTTAAATCAGCACATTGGCAC
*
1494893 CTTTAAGTCCAATGTCACTGGCCTTAAATCAGCACATTGGAAC
1 CTTTAAGTCCAATGTCACTGGCCTTAAATCAGCACATTGGCAC
* * * * *
1494936 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATGTCACTGGCCTTAAATCAGCACATTGGCAC
1494979 CTTTA
1 CTTTA
1494984 TCATCCTTCT
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATGTCACTGGCCTTAAATCAGCACATTGGCAC
Found at i:1494917 original size:22 final size:22
Alignment explanation
Indices: 1494850--1494917 Score: 56
Period size: 22 Copynumber: 3.1 Consensus size: 22
1494840 CCTTTTTCAT
1494850 CTTTAAGTCCAATGTCACTGGC
1 CTTTAAGTCCAATGTCACTGGC
*
1494872 C-TTAAAT-C-A-G-CACATTGGCAC
1 CTTTAAGTCCAATGTCAC--TGG--C
1494893 CTTTAAGTCCAATGTCACTGGC
1 CTTTAAGTCCAATGTCACTGGC
1494915 CTT
1 CTT
1494918 AAATCAGCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 18
0.64 0.04 0.33
Matches are distributed among these distances:
17 3 0.09
18 1 0.03
19 4 0.11
20 1 0.03
21 7 0.20
22 10 0.29
23 1 0.03
24 4 0.11
25 1 0.03
26 3 0.09
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (22 bp):
CTTTAAGTCCAATGTCACTGGC
Found at i:1495712 original size:15 final size:15
Alignment explanation
Indices: 1495692--1495732 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1495682 TTTTTTATAT
1495692 AAAATTAAAAATCAA
1 AAAATTAAAAATCAA
*
1495707 AAAATTAAAAATTAA
1 AAAATTAAAAATCAA
*
1495722 AAAATGAAAAA
1 AAAATTAAAAA
1495733 ATTAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (15 bp):
AAAATTAAAAATCAA
Found at i:1496071 original size:18 final size:18
Alignment explanation
Indices: 1496050--1496098 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1496040 ACTTAAGAAA
*
1496050 CATTTCATGCATTGCATT
1 CATTTCATGCATTGCATG
*
1496068 CATTTCATTGTA-TGCATG
1 CATTTCA-TGCATTGCATG
*
1496086 CATTTCATACATT
1 CATTTCATGCATT
1496099 CATATAGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 20 0.80
19 3 0.12
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.45
Consensus pattern (18 bp):
CATTTCATGCATTGCATG
Found at i:1497768 original size:69 final size:69
Alignment explanation
Indices: 1497677--1497834 Score: 194
Period size: 69 Copynumber: 2.3 Consensus size: 69
1497667 ATTCCTCCGA
* * * *
1497677 GAGGATACTCTAACCCCATTTTTAAACTCATCAAAATTTAAATATTATT-TTGTCTAAATTATTA
1 GAGGATACTCCAACCCCATTTTTAAAATCATCAAAATTTAAATATTATTATT-TCCAAATTATCA
1497741 TTATC
65 TTATC
* * * *
1497746 GAGGATACTCCAACCTCGTTTTTAAAATCATCAAAATTTAAGTCTTATTATTTCCAAATTATCAT
1 GAGGATACTCCAACCCCATTTTTAAAATCATCAAAATTTAAATATTATTATTTCCAAATTATCAT
1497811 TAT-
66 TATC
* *
1497814 TAGGGATATTCCAACCCCATT
1 GA-GGATACTCCAACCCCATT
1497835 CCTCTTAGGG
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
68 1 0.01
69 72 0.96
70 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (69 bp):
GAGGATACTCCAACCCCATTTTTAAAATCATCAAAATTTAAATATTATTATTTCCAAATTATCAT
TATC
Found at i:1499404 original size:19 final size:18
Alignment explanation
Indices: 1499377--1499418 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1499367 GCCACGTTTA
*
1499377 ATTTCATTTTATTATCATT
1 ATTTTATTTTATT-TCATT
*
1499396 ATTTTATTTTATTTTATT
1 ATTTTATTTTATTTCATT
1499414 ATTTT
1 ATTTT
1499419 TTAAGTACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTATTTTATTTCATT
Found at i:1510835 original size:54 final size:55
Alignment explanation
Indices: 1510752--1510865 Score: 205
Period size: 54 Copynumber: 2.1 Consensus size: 55
1510742 AGAGATTAAT
1510752 TATCTAATTTTGAGGAGAAAAAAAAATTACAAAAGTCGAATTACAAAAACAAATCA
1 TATCTAATTTTGAGGAG-AAAAAAAATTACAAAAGTCGAATTACAAAAACAAATCA
1510808 TATCTAATTTTGAGGAG-AAAAAAATTACAAAAGTCGAATTACAAAAACAAATCA
1 TATCTAATTTTGAGGAGAAAAAAAATTACAAAAGTCGAATTACAAAAACAAATCA
1510862 -ATCT
1 TATCT
1510866 CTGCTCGAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
53 4 0.07
54 37 0.64
56 17 0.29
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.25
Consensus pattern (55 bp):
TATCTAATTTTGAGGAGAAAAAAAATTACAAAAGTCGAATTACAAAAACAAATCA
Found at i:1511968 original size:9 final size:9
Alignment explanation
Indices: 1511956--1512056 Score: 53
Period size: 9 Copynumber: 10.9 Consensus size: 9
1511946 TTGATAATTT
1511956 TATATATAA
1 TATATATAA
*
1511965 TATA-AAAA
1 TATATATAA
1511973 TATAATATATA
1 TAT-ATATA-A
1511984 TATATATAA
1 TATATATAA
* *
1511993 TATTTTTAA
1 TATATATAA
*
1512002 TAAATATAAA
1 TATATAT-AA
* *
1512012 AATAATTTAA
1 TAT-ATATAA
1512022 T-TAGTATAA
1 TATA-TATAA
* *
1512031 TATATTTTA
1 TATATATAA
*
1512040 TATATATTA
1 TATATATAA
*
1512049 TATTTATA
1 TATATATA
1512057 TTTAAAATAT
Statistics
Matches: 68, Mismatches: 17, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
8 7 0.10
9 40 0.59
10 14 0.21
11 7 0.10
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (9 bp):
TATATATAA
Found at i:1511977 original size:13 final size:15
Alignment explanation
Indices: 1511959--1511995 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
1511949 ATAATTTTAT
1511959 ATATAATATA-A-AA
1 ATATAATATATATAA
*
1511972 ATATAATATATATAT
1 ATATAATATATATAA
1511987 ATATAATAT
1 ATATAATAT
1511996 TTTTAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.48
14 1 0.05
15 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATAATATATATAA
Found at i:1512050 original size:16 final size:15
Alignment explanation
Indices: 1512026--1512109 Score: 73
Period size: 16 Copynumber: 5.5 Consensus size: 15
1512016 ATTTAATTAG
*
1512026 TATAATATATTTTATA
1 TATATTATA-TTTATA
1512042 TATATTATATTTATA
1 TATATTATATTTATA
* ** *
1512057 TTTAAAATATTGATA
1 TATATTATATTTATA
1512072 TAT-TTAATAATTTATA
1 TATATT-AT-ATTTATA
1512088 TAATATTATATTTATA
1 T-ATATTATATTTATA
1512104 TA-ATTA
1 TATATTA
1512110 ATATAAAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
14 4 0.07
15 22 0.40
16 23 0.42
17 4 0.07
18 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (15 bp):
TATATTATATTTATA
Found at i:1513151 original size:2 final size:2
Alignment explanation
Indices: 1513144--1513173 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1513134 CAAGTGTTTA
1513144 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
1513174 TATTTAAAGA
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:1513398 original size:14 final size:14
Alignment explanation
Indices: 1513381--1513408 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1513371 ATTATTTAAA
1513381 AATATTTTTATATT
1 AATATTTTTATATT
1513395 AATATTTTTATATT
1 AATATTTTTATATT
1513409 TTAATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:1513625 original size:2 final size:2
Alignment explanation
Indices: 1513618--1513660 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1513608 AATTTTCTAC
1513618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1513660 A
1 A
1513661 CCTGTATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1514556 original size:3 final size:3
Alignment explanation
Indices: 1514548--1514589 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1514538 CATGAAAATG
1514548 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1514590 ACAAGCTGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1519842 original size:22 final size:22
Alignment explanation
Indices: 1519817--1519886 Score: 131
Period size: 22 Copynumber: 3.2 Consensus size: 22
1519807 AATATCATTT
1519817 TCACTGTTCATGTATCGATACA
1 TCACTGTTCATGTATCGATACA
1519839 TCACTGTTCATGTATCGATACA
1 TCACTGTTCATGTATCGATACA
*
1519861 TCACTGTTCATGTGTCGATACA
1 TCACTGTTCATGTATCGATACA
1519883 TCAC
1 TCAC
1519887 ATCGATACAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (22 bp):
TCACTGTTCATGTATCGATACA
Found at i:1519893 original size:13 final size:13
Alignment explanation
Indices: 1519875--1519900 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1519865 TGTTCATGTG
1519875 TCGATACATCACA
1 TCGATACATCACA
1519888 TCGATACATCACA
1 TCGATACATCACA
1519901 CTGTTCATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
TCGATACATCACA
Found at i:1522025 original size:21 final size:21
Alignment explanation
Indices: 1521969--1522012 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1521959 TAATATTCTT
** *
1521969 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAACAAATGAATTA
1521990 GAAAAGAAAACAAATGAATTA
1 GAAAAGAAAACAAATGAATTA
1522011 GA
1 GA
1522013 GGAGAAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.61, C:0.02, G:0.18, T:0.18
Consensus pattern (21 bp):
GAAAAGAAAACAAATGAATTA
Found at i:1524695 original size:28 final size:28
Alignment explanation
Indices: 1524655--1524726 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
1524645 GAAAAAAAAT
* ** *
1524655 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1524683 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1524711 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1524727 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1524784 original size:52 final size:52
Alignment explanation
Indices: 1524719--1524881 Score: 134
Period size: 52 Copynumber: 3.1 Consensus size: 52
1524709 AACGAGGTTG
* ** *
1524719 GAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATC-GGAGTTA
1 GAGTATCCCCGATTGTGAAAAATTGGTATTTTTAAAAATAAAACCGGGA-TTA
** * ** *
1524771 GAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTAAAAATAAAACCGGGATTG
1 GAGTATCCCCGATT-GTGAAAAATTGGTATTTTTAAAAATAAAACCGGGATTA
* *** * *
1524823 GAGTATCCCCGATTGTGGAAAAATTGGT-GTTTTAGCGATAAAACCGGGGTTG
1 GAGTATCCCCGATTGT-GAAAAATTGGTATTTTTAAAAATAAAACCGGGATTA
1524875 GAGTATC
1 GAGTATC
1524882 GCCTCAGAAA
Statistics
Matches: 90, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
52 78 0.87
53 12 0.13
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (52 bp):
GAGTATCCCCGATTGTGAAAAATTGGTATTTTTAAAAATAAAACCGGGATTA
Found at i:1524899 original size:28 final size:27
Alignment explanation
Indices: 1524867--1524938 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
1524857 GCGATAAAAC
1524867 CGGGGTTGGAGTATCGCCTCA-GAAATAA
1 CGGGGTTGGAGTATC-CCTCATG-AATAA
* * *
1524895 CGGGGTTGGAGTGTCCCTGATGATTAA
1 CGGGGTTGGAGTATCCCTCATGAATAA
*
1524922 CGAGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
1524939 CGATTGTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCTCATGAATAA
Found at i:1527286 original size:13 final size:13
Alignment explanation
Indices: 1527268--1527293 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1527258 ACAAAGATCC
1527268 ATGTATCGATACA
1 ATGTATCGATACA
1527281 ATGTATCGATACA
1 ATGTATCGATACA
1527294 CAGAAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1527289 original size:33 final size:31
Alignment explanation
Indices: 1527247--1527311 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 31
1527237 AAAATTTCCA
*
1527247 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGA--AATGTATCGATAC
*
1527280 AATGTATCGATACACAGAAATGTATCGATAC
1 AATGTATCGATACAAAGAAATGTATCGATAC
1527311 A
1 A
1527312 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 13 0.43
33 17 0.57
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (31 bp):
AATGTATCGATACAAAGAAATGTATCGATAC
Found at i:1527355 original size:19 final size:18
Alignment explanation
Indices: 1527331--1527398 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1527321 CAGTAGCTAA
1527331 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1527350 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1527365 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1527382 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1527399 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1527371 original size:13 final size:13
Alignment explanation
Indices: 1527353--1527377 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1527343 ACAATACTTA
1527353 TGTATCGATACAT
1 TGTATCGATACAT
1527366 TGTATCGATACA
1 TGTATCGATACA
1527378 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1527375 original size:32 final size:32
Alignment explanation
Indices: 1527334--1527396 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1527324 TAGCTAATTA
*
1527334 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1527366 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1527397 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1528540 original size:59 final size:59
Alignment explanation
Indices: 1528206--1528989 Score: 1018
Period size: 59 Copynumber: 13.5 Consensus size: 59
1528196 GGAGTAAAAA
* * *
1528206 GTGCCACCAACTCGTGTGGGCTTT----G-AAAGGCATCCTGCTCTTTGAGGACTGAAAG
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG-AAG
* * * *
1528261 GTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTGTCCTGCTCTTTAAGGACTGGAAA
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-GAAG
* * * * *
1528316 ATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGGGGACTGAAAA
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG-AAG
* * * * * *
1528371 ATGCCACCAACTTGTGTGGGC-TT---CG-AAAGGGGTCCTGCTCTTTGGGGACTAAAAG
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-GAAG
* * **
1528426 GTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTACTCTTTGAGGACTGAAG
1 GTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
* *
1528486 GTGCCACCAA-TTCGGGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAA
1 GTGCCACCAACTT-GTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
*
1528545 GTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
1528604 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
* *
1528663 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGAACTGAAG
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
*
1528722 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAAG
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
1528781 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
* *
1528840 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCACTCTTTGAGGACTGAAAA
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG-AAG
* * *
1528900 ATGCCACCAACTTGTGTGGGCTTTAAAAGAGGAAGGCGTCCTGCTCTTTGAGGACTGGGAA-
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGA-AAAGGCGTCCCGCTCTTTGAGGACT--GAAG
*
1528961 GTGCCACCATCTTGTGTGGGCTTTAAAAG
1 GTGCCACCAACTTGTGTGGGCTTTAAAAG
1528990 GTGTCCTGCT
Statistics
Matches: 668, Mismatches: 41, Indels: 34
0.90 0.06 0.05
Matches are distributed among these distances:
53 1 0.00
54 3 0.00
55 160 0.24
56 3 0.00
57 1 0.00
59 371 0.56
60 57 0.09
61 69 0.10
62 2 0.00
63 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (59 bp):
GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
Found at i:1530008 original size:5 final size:5
Alignment explanation
Indices: 1530000--1530056 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
1529990 TCTCTTTTTC
* *
1530000 TTTGT TTTG- TTT-T TTTGT TTTGT TTTGTT TTTTT TTTGCT TTTTT TTTGT
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTG-T TTTGT TTTG-T TTTGT TTTGT
1530050 TTT-T TTT
1 TTTGT TTT
1530057 TTGAAGAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
4 10 0.23
5 26 0.59
6 8 0.18
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (5 bp):
TTTGT
Found at i:1530021 original size:18 final size:18
Alignment explanation
Indices: 1530000--1530056 Score: 70
Period size: 16 Copynumber: 3.4 Consensus size: 18
1529990 TCTCTTTTTC
1530000 TTTGTTTTGTTTTTTTGT
1 TTTGTTTTGTTTTTTTGT
1530018 TTTGTTTTG-TTTTTT-T
1 TTTGTTTTGTTTTTTTGT
*
1530034 TTTG-CTT-TTTTTTTGT
1 TTTGTTTTGTTTTTTTGT
1530050 TTT-TTTT
1 TTTGTTTT
1530057 TTGAAGAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 8 0.24
16 11 0.32
17 6 0.18
18 9 0.26
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (18 bp):
TTTGTTTTGTTTTTTTGT
Found at i:1530034 original size:22 final size:23
Alignment explanation
Indices: 1530000--1530058 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
1529990 TCTCTTTTTC
1530000 TTTGTTTTGTTTTTTTG-TTTTGT
1 TTTGTTTT-TTTTTTTGCTTTTGT
*
1530023 TTTG-TTTTTTTTTTGCTTTTTT
1 TTTGTTTTTTTTTTTGCTTTTGT
1530045 TTTGTTTTTTTTTT
1 TTTGTTTTTTTTTT
1530059 GAAGAGAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 8 0.24
22 12 0.36
23 13 0.39
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (23 bp):
TTTGTTTTTTTTTTTGCTTTTGT
Found at i:1530054 original size:10 final size:11
Alignment explanation
Indices: 1530009--1530059 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
1529999 CTTTGTTTTG
1530009 TTTTTTTG-TT
1 TTTTTTTGCTT
* *
1530019 TTGTTTTGTTT
1 TTTTTTTGCTT
1530030 TTTTTTTGCTT
1 TTTTTTTGCTT
*
1530041 TTTTTTTGTTT
1 TTTTTTTGCTT
1530052 TTTTTTTG
1 TTTTTTTG
1530060 AAGAGAAGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
10 7 0.19
11 29 0.81
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (11 bp):
TTTTTTTGCTT
Found at i:1530059 original size:22 final size:22
Alignment explanation
Indices: 1529993--1530059 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
1529983 TCTTTTCTCT
*
1529993 CTTTTTCTTTGTTTTGTTTTTTTG
1 CTTTTTTTTTG-TTT-TTTTTTTG
*
1530017 -TTTTGTTTTGTTTTTTTTTTG
1 CTTTTTTTTTGTTTTTTTTTTG
1530038 CTTTTTTTTTGTTTTTTTTTTG
1 CTTTTTTTTTGTTTTTTTTTTG
1530060 AAGAGAAGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
21 8 0.21
22 23 0.59
23 8 0.21
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (22 bp):
CTTTTTTTTTGTTTTTTTTTTG
Found at i:1542581 original size:28 final size:28
Alignment explanation
Indices: 1542541--1542607 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
1542531 AAAATTGGGA
** * *
1542541 TTGGAGTATCCCCTCGGAAGTAACGGGG
1 TTGGAGTATCCCCGAGGAAATAACGAGG
*
1542569 TTGGAGTATCCCCGATGAAATAACGAGG
1 TTGGAGTATCCCCGAGGAAATAACGAGG
1542597 TTGGAGTATCC
1 TTGGAGTATCC
1542608 TCGATTGTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.24
Consensus pattern (28 bp):
TTGGAGTATCCCCGAGGAAATAACGAGG
Found at i:1542658 original size:52 final size:51
Alignment explanation
Indices: 1542595--1542765 Score: 168
Period size: 52 Copynumber: 3.3 Consensus size: 51
1542585 GAAATAACGA
*
1542595 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTAGAAATAAAATC-G
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTAGAAATAAAA-CAG
** * * *
1542646 GAGTTGGAGTATCCCCGATTAAAGGAAAATTGGCATTTTGA-AAATAAAACAG
1 G-GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTAGAAATAAAACAG
* * ** *
1542698 GGATTGGAGTATCCCCGATTGTGGAAAAATTAGT-GTTTTAGCGATAAAACTGG
1 GG-TTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTAGAAATAAAAC-AG
1542751 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1542766 TCGGAAATAA
Statistics
Matches: 97, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
51 7 0.07
52 72 0.74
53 18 0.19
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTAGAAATAAAACAG
Found at i:1542811 original size:27 final size:28
Alignment explanation
Indices: 1542749--1542823 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
1542739 CGATAAAACT
***
1542749 GGGGTTGGAGTATCCCCTCGGAAATAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
*
1542777 GGGGTTGGAGTATCCCCGATG-ATTAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
1542804 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
1542824 TGTGAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.24
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATGAAATAAC
Found at i:1545314 original size:13 final size:13
Alignment explanation
Indices: 1545296--1545321 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1545286 ACAAAGATCC
1545296 ATGTATCGATACA
1 ATGTATCGATACA
1545309 ATGTATCGATACA
1 ATGTATCGATACA
1545322 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1545317 original size:33 final size:33
Alignment explanation
Indices: 1545275--1545341 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1545265 AAAATTTCCA
***
1545275 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1545308 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1545341 A
1 A
1545342 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1545416 original size:32 final size:32
Alignment explanation
Indices: 1545366--1545426 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1545356 GCTAATTATG
*
1545366 TATCGATAAAATATTTATGTATCGATACATTA
1 TATCGATAAAATACTTATGTATCGATACATTA
1545398 TATCGATACAAA-ACTTATGTATCGATACA
1 TATCGATA-AAATACTTATGTATCGATACA
1545427 AATTGTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 24 0.89
33 3 0.11
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (32 bp):
TATCGATAAAATACTTATGTATCGATACATTA
Found at i:1545422 original size:19 final size:18
Alignment explanation
Indices: 1545359--1545428 Score: 71
Period size: 19 Copynumber: 4.1 Consensus size: 18
1545349 GGCAGTAGCT
1545359 AATTATGTATCGATA-AA
1 AATTATGTATCGATACAA
1545376 ATATTTATGTATCGATAC--
1 A-A-TTATGTATCGATACAA
1545394 -ATTA--TATCGATACAA
1 AATTATGTATCGATACAA
1545409 AACTTATGTATCGATACAA
1 AA-TTATGTATCGATACAA
1545428 A
1 A
1545429 TTGTTGAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.20
15 3 0.07
16 2 0.05
17 4 0.09
18 1 0.02
19 25 0.57
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (18 bp):
AATTATGTATCGATACAA
Found at i:1545652 original size:21 final size:21
Alignment explanation
Indices: 1545613--1545651 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1545603 GTGTCTACAG
1545613 ATATATCGAATCCGTCCCCAC
1 ATATATCGAATCCGTCCCCAC
1545634 ATATATCGAATCC-TCCCC
1 ATATATCGAATCCGTCCCC
1545652 CTACTAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.38, G:0.08, T:0.26
Consensus pattern (21 bp):
ATATATCGAATCCGTCCCCAC
Found at i:1547447 original size:13 final size:13
Alignment explanation
Indices: 1547429--1547453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1547419 ATTTTGCTTA
1547429 GTATCGATACATT
1 GTATCGATACATT
1547442 GTATCGATACAT
1 GTATCGATACAT
1547454 AAAACTGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1548774 original size:13 final size:13
Alignment explanation
Indices: 1548756--1548781 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1548746 TACAGCAAGT
1548756 ATGTATCGATACA
1 ATGTATCGATACA
1548769 ATGTATCGATACA
1 ATGTATCGATACA
1548782 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1551031 original size:21 final size:21
Alignment explanation
Indices: 1550998--1551042 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1550988 TTGCAAGTTG
*
1550998 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1551020 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1551040 AAA
1 AAA
1551043 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1552866 original size:15 final size:15
Alignment explanation
Indices: 1552846--1552876 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1552836 TAAAAATGTC
*
1552846 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1552861 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1552876 C
1 C
1552877 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1554969 original size:20 final size:20
Alignment explanation
Indices: 1554890--1554969 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1554880 AATGTCCAAA
*
1554890 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1554910 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1554935 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1554955 TTGTATCGATACATT
1 ATGTATCGATACATT
1554970 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1554973 original size:13 final size:13
Alignment explanation
Indices: 1554955--1554993 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1554945 ACATTTTTCT
1554955 TTGTATCGATACA
1 TTGTATCGATACA
1554968 TTGTATCGATACA
1 TTGTATCGATACA
*
1554981 CTGTATCGATACA
1 TTGTATCGATACA
1554994 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1555127 original size:21 final size:21
Alignment explanation
Indices: 1555103--1555149 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1555093 AAATCTTTTG
1555103 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
1555124 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
1555144 CAAAAT
1 CAAAAT
1555150 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:1555146 original size:20 final size:19
Alignment explanation
Indices: 1555105--1555147 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1555095 ATCTTTTGCA
1555105 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1555125 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1555145 AAA
1 AAA
1555148 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1558427 original size:26 final size:26
Alignment explanation
Indices: 1558389--1558449 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
1558379 ACTAGCTCTA
1558389 TTTTGACTCGACATTGGTTTCATTGG
1 TTTTGACTCGACATTGGTTTCATTGG
*
1558415 TTTTGACTGGACATTGGTTTCATTGG
1 TTTTGACTCGACATTGGTTTCATTGG
1558441 TTTTGACTC
1 TTTTGACTC
1558450 AATATTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.48
Consensus pattern (26 bp):
TTTTGACTCGACATTGGTTTCATTGG
Found at i:1559168 original size:158 final size:155
Alignment explanation
Indices: 1558908--1559368 Score: 512
Period size: 158 Copynumber: 2.9 Consensus size: 155
1558898 TTGAAAAGCG
* * * *
1558908 AGGTTGGAGTATGCC-CTCAAAAATAATGAGGTTGGAGTACCCTCAATGGTAAAAAATTGATATT
1 AGGTTGGAGTAT-CCTCTCAAAAATAATGGGGTTGGAGTATCCTCGATGGTGAAAAATTGATA-T
* **
1558972 TTGGAAATAAAAACAGGTTTGGAGTATTGCCTCA-AAAATGATAGGGTTGGAGTATCCCCAATGG
64 TT-GAAATAAAAATAGG-TTGGAGTATCCCCT-AGAAAATGATAGGGTTGGAGTATCCCCAATGG
**
1559036 TGAAAAATTGATAATTTGGAAATAAAAACA
126 TGAAAAATCAATAATTTGGAAATAAAAACA
* * *
1559066 AGGTTAGAGTATCCTCTCAAAAATAATGGGGTTAGAGTATCCTCGATAGTGAAAAATTTGATATT
1 AGGTTGGAGTATCCTCTCAAAAATAATGGGGTTGGAGTATCCTCGATGGTGAAAAA-TTGATATT
* * * *** *
1559131 TAGAAAGTAAAAATAGGTTGGAGTGTCCCCTGGAAAATGATGGGGTCAAAGTATCCCTAATGGTG
65 T-GAAA-TAAAAATAGGTTGGAGTATCCCCTAGAAAATGATAGGGTTGGAGTATCCCCAATGGTG
*
1559196 AAAAATCAATATTTTGGAAATAAAAACA
128 AAAAATCAATAATTTGGAAATAAAAACA
* * * * * * * * *
1559224 AGGTTGGAGTATCTTTTCGAAAATGATGGGATTGGAGTCTCCCCGATGGTGACAAATCGATAATT
1 AGGTTGGAGTATCCTCTCAAAAATAATGGGGTTGGAGTATCCTCGATGGTGAAAAATTGAT-ATT
* * * *
1559289 TGAAAATAAAAATAGGGTTTGAGTATCCCCTAGAAAAGGATAGGGTTGGAGAATCTCCAATGGTG
65 TG-AAATAAAAATA-GGTTGGAGTATCCCCTAGAAAATGATAGGGTTGGAGTATCCCCAATGGTG
1559354 AAAAATCAATAATTT
128 AAAAATCAATAATTT
1559369 TTTATGAAGA
Statistics
Matches: 251, Mismatches: 45, Indels: 14
0.81 0.15 0.05
Matches are distributed among these distances:
157 15 0.06
158 221 0.88
159 15 0.06
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (155 bp):
AGGTTGGAGTATCCTCTCAAAAATAATGGGGTTGGAGTATCCTCGATGGTGAAAAATTGATATTT
GAAATAAAAATAGGTTGGAGTATCCCCTAGAAAATGATAGGGTTGGAGTATCCCCAATGGTGAAA
AATCAATAATTTGGAAATAAAAACA
Found at i:1559246 original size:79 final size:80
Alignment explanation
Indices: 1558908--1559359 Score: 402
Period size: 79 Copynumber: 5.7 Consensus size: 80
1558898 TTGAAAAGCG
* * * * *
1558908 AGGTTGGAGTATGCCCTCAAAAATAATGAGGTTGGAGTA-CCCTCAATGGTAAAAAATTGATATT
1 AGGTTGGAGTATCCCCTCAAAAATGATGGGGTTAGAGTATCCCTCAATGGTGAAAAATTGATATT
1558972 TTGGAAATAAAAAC-
66 TTGGAAATAAAAACA
** * * *
1558986 AGGTTTGGAGTATTGCCTCAAAAATGATAGGGTTGGAGTATCCC-CAATGGTGAAAAATTGATAA
1 AGG-TTGGAGTATCCCCTCAAAAATGATGGGGTTAGAGTATCCCTCAATGGTGAAAAATTGATAT
1559050 TTTGGAAATAAAAACA
65 TTTGGAAATAAAAACA
* * * * *
1559066 AGGTTAGAGTATCCTCTCAAAAATAATGGGGTTAGAGTAT-CCTCGATAGTGAAAAATTTGATA-
1 AGGTTGGAGTATCCCCTCAAAAATGATGGGGTTAGAGTATCCCTCAATGGTGAAAAA-TTGATAT
* *
1559129 TTTAGAAAGTAAAAA-T
65 TTTGGAAA-TAAAAACA
* ** * * **
1559145 AGGTTGGAGTGTCCCCTGGAAAATGATGGGGTCAAAGTATCCCT-AATGGTGAAAAATCAATATT
1 AGGTTGGAGTATCCCCTCAAAAATGATGGGGTTAGAGTATCCCTCAATGGTGAAAAATTGATATT
1559209 TTGGAAATAAAAACA
66 TTGGAAATAAAAACA
*** * * * * * * * *
1559224 AGGTTGGAGTATCTTTTCGAAAATGATGGGATTGGAGTCTCCC-CGATGGTGACAAATCGATAAT
1 AGGTTGGAGTATCCCCTCAAAAATGATGGGGTTAGAGTATCCCTCAATGGTGAAAAATTGATATT
* *
1559288 TTGAAAATAAAAATA
66 TTGGAAATAAAAACA
* * * * * * *
1559303 GGGTTTGAGTATCCCCT-AGAAAAGGATAGGGTTGGAGAATCTC-CAATGGTGAAAAAT
1 AGGTTGGAGTATCCCCTCA-AAAATGATGGGGTTAGAGTATCCCTCAATGGTGAAAAAT
1559360 CAATAATTTT
Statistics
Matches: 301, Mismatches: 62, Indels: 21
0.78 0.16 0.05
Matches are distributed among these distances:
78 15 0.05
79 265 0.88
80 21 0.07
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (80 bp):
AGGTTGGAGTATCCCCTCAAAAATGATGGGGTTAGAGTATCCCTCAATGGTGAAAAATTGATATT
TTGGAAATAAAAACA
Found at i:1559654 original size:9 final size:10
Alignment explanation
Indices: 1559633--1559662 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
1559623 TGAGGGTGAA
1559633 TTTAAAAATT
1 TTTAAAAATT
1559643 TTTAAAAATT
1 TTTAAAAATT
1559653 TTTGAAAAAT
1 TTT-AAAAAT
1559663 CATTTTCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (10 bp):
TTTAAAAATT
Found at i:1560643 original size:37 final size:33
Alignment explanation
Indices: 1560558--1560654 Score: 119
Period size: 37 Copynumber: 2.9 Consensus size: 33
1560548 CCTTACAACA
*
1560558 CTATC-TTTCAA-GGCTAAGATAGAACC-CTCC
1 CTATCTTTTCAAGGGCTAAGATAAAACCTCTCC
*
1560588 CTATCTTTTCACGGGCTAAGATAAAACCTTTCTCC
1 CTATCTTTTCAAGGGCTAAGATAAAACC--TCTCC
1560623 CTATCTTTTTTCAAGGGCTAAGATAAAACCTC
1 CTATC--TTTTCAAGGGCTAAGATAAAACCTC
1560655 ACAATCACTT
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
30 5 0.09
31 5 0.09
32 14 0.25
35 11 0.19
37 22 0.39
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (33 bp):
CTATCTTTTCAAGGGCTAAGATAAAACCTCTCC
Found at i:1563023 original size:51 final size:52
Alignment explanation
Indices: 1562926--1563044 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 52
1562916 AATAGCTTGC
* * * * * *
1562926 ATGTACCGACATATTTGGGTCAAAAATCCAGAATGTATTGATACAATGAGAA
1 ATGTATCGATATATTTGGGTCAAAAACCCAGAATGTATCGAAACAATGAAAA
* *
1562978 ATGTATTGATATATTTGGG-CTAAAACCCAGAATGTATCGAAACAATGAAAA
1 ATGTATCGATATATTTGGGTCAAAAACCCAGAATGTATCGAAACAATGAAAA
*
1563029 ATGTATCGATACATTT
1 ATGTATCGATATATTT
1563045 TCTTTCCAGA
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
51 41 0.72
52 16 0.28
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (52 bp):
ATGTATCGATATATTTGGGTCAAAAACCCAGAATGTATCGAAACAATGAAAA
Found at i:1563932 original size:28 final size:28
Alignment explanation
Indices: 1563875--1564294 Score: 358
Period size: 28 Copynumber: 14.7 Consensus size: 28
1563865 TGCTATTAAT
* *
1563875 TTGTTGGCTTTGAAAGGAGATGCCACTGAC
1 TTGTGGGCTTTGAGAGG-G-TGCCACTGAC
*
1563905 TTGTGGGCTTTGAGAGGGTGCCATTGAC
1 TTGTGGGCTTTGAGAGGGTGCCACTGAC
*
1563933 TTGTGGGCTTTGAGAGGGTGCCACTGAA
1 TTGTGGGCTTTGAGAGGGTGCCACTGAC
* * *
1563961 TTATGGGCTTTGAAAGGGTGCCATTGAC
1 TTGTGGGCTTTGAGAGGGTGCCACTGAC
* ** **
1563989 TTGTGGGCTTTGAAAGGGAACACCACCAAC
1 TTGTGGGCTTTGAGAGGG--TGCCACTGAC
* *
1564019 TTGTGGGCTGTGAGAGGGTTCCACTGAC
1 TTGTGGGCTTTGAGAGGGTGCCACTGAC
* * * *
1564047 TTGTGGGCTTT-AAAAGGTACTACTGAC
1 TTGTGGGCTTTGAGAGGGTGCCACTGAC
* * *
1564074 TTGTGGGCTTTAAGAGGGGGCCACTAAC
1 TTGTGGGCTTTGAGAGGGTGCCACTGAC
* * *
1564102 TTCTGGGCTTTGATACGGAATGCCACTGAC
1 TTGTGGGCTTTGAGA-GG-GTGCCACTGAC
** * *
1564132 TTGTGGATTTTGAGAGGTTTCCACTGAC
1 TTGTGGGCTTTGAGAGGGTGCCACTGAC
* * *
1564160 TTGTGGCCTTTAAAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAGAGGGTGCCACTGAC
* * * *
1564188 TTATGGGATTTAAGAGGGTGCCACTAAC
1 TTGTGGGCTTTGAGAGGGTGCCACTGAC
* * * *
1564216 TTATGGGCTTTGATAAGGGACGGCA-TAGAC
1 TTGTGGGCTTTGA-GAGGG-TGCCACT-GAC
*
1564246 TTGTGTGCTTTGAGAGGGTGCCACTGAC
1 TTGTGGGCTTTGAGAGGGTGCCACTGAC
* *
1564274 TTATGGGCTTTAAGAGAGGTG
1 TTGTGGGCTTTGAGAG-GGTG
1564295 TGATGGACTT
Statistics
Matches: 311, Mismatches: 69, Indels: 21
0.78 0.17 0.05
Matches are distributed among these distances:
27 23 0.07
28 198 0.64
29 19 0.06
30 71 0.23
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.30
Consensus pattern (28 bp):
TTGTGGGCTTTGAGAGGGTGCCACTGAC
Found at i:1564033 original size:114 final size:114
Alignment explanation
Indices: 1563804--1564286 Score: 476
Period size: 114 Copynumber: 4.2 Consensus size: 114
1563794 GCATTAAAAT
* * *
1563804 GTGCCACTGACTTATGAGCTTTAAAAAGGTATGCCACT-AACTTATGGGCTTTGAA-AGGAGATG
1 GTGCCACTGACTTGTGGGCTTT-AAAAGG-GTGCCACTGAA-TTATGGGCTTT-AAGAGG-G-TG
* * * * * *
1563867 CTATTAATTTGTTGGCTTTGAAA-GGAGATGCCACTGACTTGTGGGCTTTGAGAGG
60 CCACTAACTTGTGGGCTTTGAAAGGGA-ACGCCACTAACTTGTGGGCTTTGAGAGG
* * * *
1563922 GTGCCATTGACTTGTGGGCTTTGAGAGGGTGCCACTGAATTATGGGCTTTGAA-AGGGTGCCATT
1 GTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGAATTATGGGCTTT-AAGAGGGTGCCACT
* * * *
1563986 GACTTGTGGGCTTTGAAAGGGAACACCACCAACTTGTGGGCTGTGAGAGG
65 AACTTGTGGGCTTTGAAAGGGAACGCCACTAACTTGTGGGCTTTGAGAGG
* * * * * *
1564036 GTTCCACTGACTTGTGGGCTTTAAAA-GGTACTACTGACTTGTGGGCTTTAAGAGGGGGCCACTA
1 GTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGAATTATGGGCTTTAAGAGGGTGCCACTA
* * * * * **
1564100 ACTTCTGGGCTTTGATACGGAATGCCACTGACTTGTGGATTTTGAGAGG
66 ACTTGTGGGCTTTGAAAGGGAACGCCACTAACTTGTGGGCTTTGAGAGG
* * * * *
1564149 TTTCCACTGACTTGTGGCCTTTAAAAGGGTGCCACTGACTTATGGGATTTAAGAGGGTGCCACTA
1 GTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGAATTATGGGCTTTAAGAGGGTGCCACTA
* * *
1564214 ACTTATGGGCTTTGATAAGGG-ACGGCA-TAGACTTGTGTGCTTTGAGAGG
66 ACTTGTGGGCTTTGA-AAGGGAACGCCACTA-ACTTGTGGGCTTTGAGAGG
*
1564263 GTGCCACTGACTTATGGGCTTTAA
1 GTGCCACTGACTTGTGGGCTTTAA
1564287 GAGAGGTGTG
Statistics
Matches: 303, Mismatches: 56, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
112 2 0.01
113 92 0.30
114 153 0.50
115 7 0.02
116 24 0.08
117 6 0.02
118 19 0.06
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (114 bp):
GTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGAATTATGGGCTTTAAGAGGGTGCCACTA
ACTTGTGGGCTTTGAAAGGGAACGCCACTAACTTGTGGGCTTTGAGAGG
Found at i:1567989 original size:21 final size:20
Alignment explanation
Indices: 1567937--1567990 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1567927 TAGTTCAAAC
*
1567937 ATGTATCGATATATTCACTT
1 ATGTATCGATACATTCACTT
* *
1567957 ACGTATCAATACATTCACTT
1 ATGTATCGATACATTCACTT
1567977 ATTGTATCGATACA
1 A-TGTATCGATACA
1567991 AATTGTAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:1569197 original size:16 final size:16
Alignment explanation
Indices: 1569177--1569214 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1569167 TCATCTAGAC
1569177 CTTTTTTCTTT-TT-TT
1 CTTTTTT-TTTCTTCTT
1569192 CTTTTTTTTTCTTCTT
1 CTTTTTTTTTCTTCTT
1569208 CTTTTTT
1 CTTTTTT
1569215 GATTGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 9 0.43
16 9 0.43
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
CTTTTTTTTTCTTCTT
Found at i:1569291 original size:15 final size:16
Alignment explanation
Indices: 1569252--1569291 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
1569242 TTTTGACCCT
1569252 TTTTTTTTTACTTTTG
1 TTTTTTTTTACTTTTG
*
1569268 TTTTTTTTT-GTTTTG
1 TTTTTTTTTACTTTTG
1569283 TTTTTTTTT
1 TTTTTTTTT
1569292 TCATTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.03, C:0.03, G:0.07, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTACTTTTG
Found at i:1569298 original size:16 final size:15
Alignment explanation
Indices: 1569251--1569298 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 15
1569241 TTTTTGACCC
1569251 TTTTTTTTTTACTTTTG
1 TTTTTTTTTT-C-TTTG
1569268 TTTTTTTTTGT-TTTG
1 TTTTTTTTT-TCTTTG
1569283 TTTTTTTTTTCATTTG
1 TTTTTTTTTTC-TTTG
1569299 ATTTGGTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 1 0.04
15 13 0.46
16 4 0.14
17 9 0.32
18 1 0.04
ACGTcount: A:0.04, C:0.04, G:0.08, T:0.83
Consensus pattern (15 bp):
TTTTTTTTTTCTTTG
Found at i:1573105 original size:32 final size:32
Alignment explanation
Indices: 1573023--1573108 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 32
1573013 GAGTTTTGGG
1573023 TATTCTTTAAAAGCTCATTTGTATTATTTCTA
1 TATTCTTTAAAAGCTCATTTGTATTATTTCTA
* *
1573055 CA-T-TTCAAAGAGCT--TTTGT-TTCATTT-TGA
1 TATTCTTTAAA-AGCTCATTTGTATT-ATTTCT-A
1573084 TATTCTTTAAAAGCTCATTTGTATT
1 TATTCTTTAAAAGCTCATTTGTATT
1573109 CCTTTATGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 15
0.69 0.07 0.25
Matches are distributed among these distances:
28 3 0.07
29 11 0.26
30 10 0.24
31 10 0.24
32 6 0.14
33 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (32 bp):
TATTCTTTAAAAGCTCATTTGTATTATTTCTA
Found at i:1574180 original size:78 final size:76
Alignment explanation
Indices: 1574064--1574221 Score: 226
Period size: 78 Copynumber: 2.1 Consensus size: 76
1574054 ATGCCACAAA
* * **
1574064 ATGTGAAAATTTTCCTGTGTATCAATACATTGAAGAATGTATCGATACATATGGGTCAAAAACTT
1 ATGTGAAAATTTGCCTATGTATCAATACATTGAAGAATGTATCGATACATATGGGTCAAAAACCC
1574129 AGAATATATCG
66 AGAATATATCG
* * *
1574140 ATGTGAAAATTTGCCTACATGTATCGATATATTGAAGAATGTATCGATACATTTGGGTCAAAAAC
1 ATGTGAAAATTTGCCT--ATGTATCAATACATTGAAGAATGTATCGATACATATGGGTCAAAAAC
*
1574205 CCAGAATGTATCG
64 CCAGAATATATCG
1574218 ATGT
1 ATGT
1574222 AATTGTAAGC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
76 15 0.21
78 57 0.79
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (76 bp):
ATGTGAAAATTTGCCTATGTATCAATACATTGAAGAATGTATCGATACATATGGGTCAAAAACCC
AGAATATATCG
Found at i:1580207 original size:21 final size:21
Alignment explanation
Indices: 1580181--1580233 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1580171 TTCAATAATT
1580181 TGTATCGATACAAT-AAGGCAA
1 TGTATCGATACAATAAAGG-AA
*
1580202 TGTATCGATAC-ATAAATGAA
1 TGTATCGATACAATAAAGGAA
1580222 TGTATCGATACA
1 TGTATCGATACA
1580234 TACTTGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACAATAAAGGAA
Found at i:1580223 original size:20 final size:21
Alignment explanation
Indices: 1580181--1580252 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
1580171 TTCAATAATT
* *
1580181 TGTATCGATACA-ATAAGGCAA
1 TGTATCGATACATA-AATGAAA
1580202 TGTATCGATACATAAATG-AA
1 TGTATCGATACATAAATGAAA
**
1580222 TGTATCGATACATACTTGAAA
1 TGTATCGATACATAAATGAAA
1580243 TGTATCGATA
1 TGTATCGATA
1580253 TAGGACAATG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
20 18 0.39
21 27 0.59
22 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (21 bp):
TGTATCGATACATAAATGAAA
Found at i:1580326 original size:40 final size:40
Alignment explanation
Indices: 1580277--1580352 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
1580267 ATTCTGGAAG
*
1580277 GAAATTGTATCGATACATTTTTCAATATATCGATACATAA
1 GAAATTGTATCGATACATTTCTCAATATATCGATACATAA
* *
1580317 GAAATTGTATCGATACATTTCTCATTGTATCGATAC
1 GAAATTGTATCGATACATTTCTCAATATATCGATAC
1580353 TTTCTGGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (40 bp):
GAAATTGTATCGATACATTTCTCAATATATCGATACATAA
Found at i:1580343 original size:20 final size:20
Alignment explanation
Indices: 1580280--1580357 Score: 77
Period size: 20 Copynumber: 4.0 Consensus size: 20
1580270 CTGGAAGGAA
*
1580280 ATTGTATCGATACATTTTTC
1 ATTGTATCGATACATTTCTC
* * *****
1580300 AATATATCGATACATAAGAA
1 ATTGTATCGATACATTTCTC
1580320 ATTGTATCGATACATTTCTC
1 ATTGTATCGATACATTTCTC
1580340 ATTGTATCGATAC-TTTCT
1 ATTGTATCGATACATTTCT
1580358 GGGTTTTGAC
Statistics
Matches: 44, Mismatches: 14, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
19 5 0.11
20 39 0.89
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (20 bp):
ATTGTATCGATACATTTCTC
Found at i:1583035 original size:97 final size:98
Alignment explanation
Indices: 1582772--1583085 Score: 309
Period size: 97 Copynumber: 3.2 Consensus size: 98
1582762 TCTTTTGAGA
** * *
1582772 GGATACTCTAA-CCC-TTTTTTTAATTCATCAATATTTAAATCTCATTTTTGCTTAAATTATCAT
1 GGATACTCTAACCCCATTTTTAAAATT-GTCAATATTTAAATCTTATTTTTGCTTAAATTATCAT
* * * * *
1582835 CGTCGAGGATACTCAAACCCCATTCTT-TCGAGG
65 CATTGAGGATACTCTAACCCTATTCTTCTCAAGG
* * * * * *
1582868 GAATACTCCAACCCCATTTTTTTTAAAATTGTTAATATTTGAATCTTA-TTTTGCATAACTTATC
1 GGATACTCTAACCCCA---TTTTTAAAATTGTCAATATTTAAATCTTATTTTTGCTTAAATTATC
*
1582932 ATTCATTGAGGATACTCTAATCCTATTCTTCT-AAGG
63 A-TCATTGAGGATACTCTAACCCTATTCTTCTCAAGG
* * * * *
1582968 GGATAATCTAACCCCGTTTTTAAAGTTGTCAATATTTAAACCTTATTTTTGCTTAAATCATCATC
1 GGATACTCTAACCCCATTTTTAAAATTGTCAATATTTAAATCTTATTTTTGCTTAAATTATCATC
* *
1583033 ATTG-GTGATACTCTAACCCTATGCTTCTGAA-G
66 ATTGAG-GATACTCTAACCCTATTCTTCTCAAGG
*
1583065 GGATACCCTAACCCCATTTTT
1 GGATACTCTAACCCCATTTTT
1583086 TGCCCAAAAA
Statistics
Matches: 176, Mismatches: 32, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
96 10 0.06
97 73 0.41
98 16 0.09
99 15 0.09
100 52 0.30
101 10 0.06
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.40
Consensus pattern (98 bp):
GGATACTCTAACCCCATTTTTAAAATTGTCAATATTTAAATCTTATTTTTGCTTAAATTATCATC
ATTGAGGATACTCTAACCCTATTCTTCTCAAGG
Found at i:1584031 original size:76 final size:77
Alignment explanation
Indices: 1583945--1584415 Score: 371
Period size: 79 Copynumber: 6.1 Consensus size: 77
1583935 AGGGATATTA
* *
1583945 ACTCTAACCCCATTAATTTTGAGAGGATACTTCAACCCTATTTTTATTTTCAAAATATTAAATTT
1 ACTCTAACCCCATTAATTTTGAGGGGATACTCCAACCCTATTTTTATTTTCAAAATATTAAATTT
1584010 T-TCTCGGGGAT
66 TATCTCGGGGAT
* ** * * * *
1584021 ACTCTAACCCCATT-ATTTCTAAGAAGATACTCCAGCCCCATTTTAATTTTTTTTAAAATATTAA
1 ACTCTAACCCCATTAATTT-TGAGGGGATACTCCAACCCTA-TTT--TTATTTTCAAAATATTAA
1584085 ATTCTTCATCTCGGGGAT
62 ATT-TT-ATCTCGGGGAT
* * * *
1584103 ACTCTAACCCCATTATTTTTGAGGGGTTACTCCAACTCTACTTTTATTTTCAAAATATTAAAATT
1 ACTCTAACCCCATTAATTTTGAGGGGATACTCCAACCCTATTTTTATTTTCAAAATATT-AAATT
*
1584168 TTCATCTTGGGGAT
65 TT-ATCTCGGGGAT
* * ** ** **
1584182 ACTCTAACACCATCAATTCCGAGGGGATACTCCAACCCCGTTTTTATTTTCAAAATGCTAAATTT
1 ACTCTAACCCCATTAATTTTGAGGGGATACTCCAACCCTATTTTTATTTTCAAAATATTAAA-TT
1584247 TTCATCTC-GGGAT
65 TT-ATCTCGGGGAT
* * * * * *
1584260 A---T------ATCAATTCTGAGGAGATACTCCAACTCGATTTTTATTTCCAAAATATTAAATTT
1 ACTCTAACCCCATTAATTTTGAGGGGATACTCCAACCCTATTTTTATTTTCAAAATATTAAATTT
* *
1584316 T-TTTCGGGGGT
66 TATCTCGGGGAT
* * * * *
1584327 ACTCCAACACCATT-ATTTCTGAGGGGATAGTTCAA-CCTCGTTTTTA-TTTCAAAAATATTAAA
1 ACTCTAACCCCATTAATTT-TGAGGGGATACTCCAACCCT-ATTTTTATTTTC-AAAATATT-AA
1584389 ATTTTCATCTCGGGGAT
62 ATTTT-ATCTCGGGGAT
*
1584406 ACTCCAACCC
1 ACTCTAACCC
1584416 TGTATTCCTA
Statistics
Matches: 314, Mismatches: 55, Indels: 49
0.75 0.13 0.12
Matches are distributed among these distances:
66 3 0.01
67 5 0.02
68 4 0.01
69 43 0.14
75 12 0.04
76 59 0.19
77 10 0.03
78 9 0.03
79 119 0.38
80 7 0.02
81 2 0.01
82 38 0.12
83 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (77 bp):
ACTCTAACCCCATTAATTTTGAGGGGATACTCCAACCCTATTTTTATTTTCAAAATATTAAATTT
TATCTCGGGGAT
Found at i:1584394 original size:145 final size:147
Alignment explanation
Indices: 1584130--1584402 Score: 365
Period size: 145 Copynumber: 1.9 Consensus size: 147
1584120 TTTGAGGGGT
* * *
1584130 TACTCCAACTCTACTTTTATTTTCAAAATATTAAAATTTTCATCTTGGGGATACTCTAACACCAT
1 TACTCCAACTCGACTTTTATTTCCAAAATATTAAAATTTT-ATCTTGGGGATACTCCAACACCAT
* *
1584195 CAATTCCGAGGGGATACTCCAACCCCGTTTTTATTTTCAAAATGCTAAATTTTTCATCTCGGGAT
65 CAATTCCGAGGGGATACTCCAACCCCGTTTTTATTTTCAAAATACTAAAATTTTCATCTCGGGAT
1584260 ATATCAATTCTGAGGAGA
130 ATATCAATTCTGAGGAGA
* *
1584278 TACTCCAACTCGATTTTTATTTCCAAAATATT-AAATTTT-T-TTCGGGGGTACTCCAACACCAT
1 TACTCCAACTCGACTTTTATTTCCAAAATATTAAAATTTTATCTT-GGGGATACTCCAACACCAT
* * * * * * *
1584340 TATTTCTGAGGGGATAGTTCAACCTCGTTTTTA-TTTCAAAAATATTAAAATTTTCATCTCGGG
65 CAATTCCGAGGGGATACTCCAACCCCGTTTTTATTTTC-AAAATACTAAAATTTTCATCTCGGG
1584403 GATACTCCAA
Statistics
Matches: 109, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
144 6 0.06
145 67 0.61
147 7 0.06
148 29 0.27
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (147 bp):
TACTCCAACTCGACTTTTATTTCCAAAATATTAAAATTTTATCTTGGGGATACTCCAACACCATC
AATTCCGAGGGGATACTCCAACCCCGTTTTTATTTTCAAAATACTAAAATTTTCATCTCGGGATA
TATCAATTCTGAGGAGA
Found at i:1592666 original size:20 final size:20
Alignment explanation
Indices: 1592641--1592694 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1592631 TACCCAGATT
1592641 TATCGATACATTCTTCAATG
1 TATCGATACATTCTTCAATG
* *
1592661 TATCGATACATGT-ATGAATG
1 TATCGATACAT-TCTTCAATG
1592681 TATCGATACATTCT
1 TATCGATACATTCT
1592695 GTCTTTTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (20 bp):
TATCGATACATTCTTCAATG
Found at i:1605994 original size:7 final size:7
Alignment explanation
Indices: 1605982--1606060 Score: 76
Period size: 7 Copynumber: 11.6 Consensus size: 7
1605972 TTTACACAAA
1605982 AAAAAAC
1 AAAAAAC
1605989 AAAAAAAC
1 -AAAAAAC
1605997 AAAAAAC
1 AAAAAAC
1606004 AAAAAAC
1 AAAAAAC
1606011 AAAAAAC
1 AAAAAAC
1606018 AAAAAA-
1 AAAAAAC
*
1606024 AACAAA-
1 AAAAAAC
*
1606030 AAAAACC
1 AAAAAAC
1606037 AAGAAAA-
1 AA-AAAAC
* *
1606044 AAATAGC
1 AAAAAAC
1606051 AAAAAA-
1 AAAAAAC
1606057 AAAA
1 AAAA
1606061 GAAAGGGGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
6 15 0.25
7 35 0.58
8 10 0.17
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (7 bp):
AAAAAAC
Found at i:1606046 original size:1 final size:1
Alignment explanation
Indices: 1605979--1606034 Score: 58
Period size: 1 Copynumber: 56.0 Consensus size: 1
1605969 TCCTTTACAC
* * * * * *
1605979 AAAAAAAAACAAAAAAACAAAAAACAAAAAACAAAAAACAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1606035 CCAAGAAAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1606062 original size:22 final size:20
Alignment explanation
Indices: 1605980--1606064 Score: 84
Period size: 22 Copynumber: 4.2 Consensus size: 20
1605970 CCTTTACACA
*
1605980 AAAAAAAACAAAAAAACAA-
1 AAAAAAAACAAAAAAAAAAG
* * *
1605999 AAAACAAA-AAACAAAAAAC
1 AAAAAAAACAAAAAAAAAAG
1606018 AAAAAAAACAAAAAAAACCAAG
1 AAAAAAAACAAAAAAAA--AAG
1606040 AAAAAAATAGCAAAAAAAAAAG
1 AAAAAAA-A-CAAAAAAAAAAG
1606062 AAA
1 AAA
1606065 GGGGTTTAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
18 8 0.15
19 14 0.26
20 7 0.13
22 15 0.28
23 1 0.02
24 9 0.17
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.01
Consensus pattern (20 bp):
AAAAAAAACAAAAAAAAAAG
Found at i:1607364 original size:29 final size:29
Alignment explanation
Indices: 1607282--1607895 Score: 698
Period size: 28 Copynumber: 21.3 Consensus size: 29
1607272 TCATCTCTTG
* *
1607282 AAAGCCCACAACTCAGTGGCA-TCCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
*
1607310 AAAGCCCACGAGTCAGTGGCAACTCTTTTC
1 AAAGCCCACAAGTCAGTGGC-ACTCTTTTC
*
1607340 AAAGCCCACAAGTTAGTGGCACTCTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
* *
1607369 AAAGCCCACAAGTCAATGGCA-TCCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
* *
1607397 AAAGGCCACAAGTCAGTGGCAC-CATTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
*
1607425 AAAGCCCACAAGTCAGTGGCATTCTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
*
1607454 AAAGCCCATAAGTCAGTGGCA-TCCTTTT-
1 AAAGCCCACAAGTCAGTGGCACT-CTTTTC
* * *
1607482 AAAGCCCACGAGTTAGTGGCAC-CCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
* * *
1607510 AAAGCCCATGGAAGTTAGTGGCAC-CCTTTC
1 AAAGCCCA--CAAGTCAGTGGCACTCTTTTC
* * *
1607540 AAAGCCCACAAATCAGGGGCACTATTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
* *
1607569 AAAGCCCACAAGTTAGTGGCA-TCCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
1607597 AAAGCCCACAAGTCAGTGGCACTCTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
*
1607626 AAAGCCCACAAGTCAGTGGCACTCTTTTT
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
*
1607655 AAAGCCCACAAGTTAGTGGCAC-CTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
* * *
1607683 AAAGCCCATAAGTCATTGGCAC-CCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
* *
1607711 AAAGCCCATAAGTCAGTGGCAC-CCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
* * *
1607739 AAAGCCCATAAGTTAGTGGCA-TCCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
* * *
1607767 AAAGTCTACAAGTCAGTGGCACCCTTTT-
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
*
1607795 AAAGCCCACAAGTTAGTGGCACTCTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTC
* *
1607824 AAAGCCCATAAG-CTAGTGGTAACTCTTTTC
1 AAAGCCCACAAGTC-AGTGG-CACTCTTTTC
* *
1607854 AAAGCCCACACGAGTCGGTGGCAACACTTTTC
1 AAAGCCCACA--AGTCAGTGGC-ACTCTTTTC
1607886 AAAGCCCACA
1 AAAGCCCACA
1607896 TAAGTTAATG
Statistics
Matches: 506, Mismatches: 60, Indels: 36
0.84 0.10 0.06
Matches are distributed among these distances:
27 4 0.01
28 253 0.50
29 156 0.31
30 68 0.13
32 24 0.05
33 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCACTCTTTTC
Found at i:1607417 original size:57 final size:58
Alignment explanation
Indices: 1607282--1607895 Score: 687
Period size: 57 Copynumber: 10.7 Consensus size: 58
1607272 TCATCTCTTG
* * *
1607282 AAAGCCCACAACTCAGTGGCA-TCCTTTCAAAGCCCACGAGTCAGTGGCAACTCTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGC-ACTCCTTTC
* * *
1607340 AAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGCA-TCCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* * * *
1607397 AAAGGCCACAAGTCAGTGGCAC-CATTTCAAAGCCCACAAGTCAGTGGCATTCTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* * * *
1607454 AAAGCCCATAAGTCAGTGGCA-TCCTTTTAAAGCCCACGAGTTAGTGGCAC-CCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* * * * **
1607510 AAAGCCCATGGAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAATCAGGGGCACTATTTTC
1 AAAGCCCA--CAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* *
1607569 AAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* * * *
1607626 AAAGCCCACAAGTCAGTGGCACTCTTTTTAAAGCCCACAAGTTAGTGGCAC-CTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* * *
1607683 AAAGCCCATAAGTCATTGGCAC-CCTTTCAAAGCCCATAAGTCAGTGGCAC-CCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* * * * *
1607739 AAAGCCCATAAGTTAGTGGCA-TCCTTTCAAAGTCTACAAGTCAGTGGCAC-CCTTTT
1 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* * * * *
1607795 AAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCATAAG-CTAGTGGTAACTCTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTC-AGTGG-CACTCCTTTC
* * *
1607854 AAAGCCCACACGAGTCGGTGGCAACACTTTTCAAAGCCCACA
1 AAAGCCCACA--AGTCAGTGGC-ACTCCTTTCAAAGCCCACA
1607896 TAAGTTAATG
Statistics
Matches: 478, Mismatches: 61, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
56 137 0.29
57 184 0.38
58 82 0.17
59 50 0.10
61 8 0.02
62 17 0.04
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (58 bp):
AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
Found at i:1608861 original size:20 final size:20
Alignment explanation
Indices: 1608832--1608903 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1608822 TACCCAGATA
1608832 TATCGATACATTCTTCAATG
1 TATCGATACATTCTTCAATG
* * *
1608852 TATTGATACATGT-ATGAATG
1 TATCGATACAT-TCTTCAATG
* *
1608872 TATCGATACATTCTTTAACG
1 TATCGATACATTCTTCAATG
*
1608892 TATCAATACATT
1 TATCGATACATT
1608904 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.40
Consensus pattern (20 bp):
TATCGATACATTCTTCAATG
Found at i:1608933 original size:91 final size:91
Alignment explanation
Indices: 1608778--1608953 Score: 273
Period size: 91 Copynumber: 1.9 Consensus size: 91
1608768 AAGTACCCAG
* *
1608778 ATGTATCGATACATTCTTCAATGTATAGATACATTCTGTCTTTTTACCCAGATATATCGATACAT
1 ATGTATCGATACATTCTTCAACGTATAGATACATTATGTCTTTTTACCCAGATATATCGATACAT
*
1608843 TCTTCAATGTATTGATACATGTATGA
66 TCTTCAATGTATCGATACATGTATGA
* * *
1608869 ATGTATCGATACATTCTTTAACGTATCA-ATACATTATGTCTTTTTACCCGGATGTATCGATACA
1 ATGTATCGATACATTCTTCAACGTAT-AGATACATTATGTCTTTTTACCCAGATATATCGATACA
*
1608933 TTTTTCAATGTATCGATACAT
65 TTCTTCAATGTATCGATACAT
1608954 CTAGTTAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
91 76 0.99
92 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (91 bp):
ATGTATCGATACATTCTTCAACGTATAGATACATTATGTCTTTTTACCCAGATATATCGATACAT
TCTTCAATGTATCGATACATGTATGA
Found at i:1613251 original size:13 final size:13
Alignment explanation
Indices: 1613233--1613257 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1613223 CATTTTATGG
1613233 TGTATCGATACAA
1 TGTATCGATACAA
1613246 TGTATCGATACA
1 TGTATCGATACA
1613258 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1613273 original size:32 final size:33
Alignment explanation
Indices: 1613210--1613277 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1613200 CGTTACAAGC
**
1613210 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
1613243 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1613275 CAA
1 CAA
1613278 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:1613367 original size:13 final size:13
Alignment explanation
Indices: 1613349--1613373 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1613339 ACATTTGGTC
1613349 ATGTATCGATACA
1 ATGTATCGATACA
1613362 ATGTATCGATAC
1 ATGTATCGATAC
1613374 TGTGCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1613901 original size:52 final size:52
Alignment explanation
Indices: 1613822--1613940 Score: 177
Period size: 52 Copynumber: 2.3 Consensus size: 52
1613812 CTCGTGTACA
* * * * *
1613822 ATCACTATTCATTACTGTTCATGTATCGATACATTGTGAATAGTATCGATAC
1 ATCACTGTTCATCACTGTTCATATATCGATACAGTATGAATAGTATCGATAC
*
1613874 ATCACTGTTCATCACTGTTCATATATCGATATAGTATGAATAGTATCGATAC
1 ATCACTGTTCATCACTGTTCATATATCGATACAGTATGAATAGTATCGATAC
1613926 ATCACTGTTCA-CACT
1 ATCACTGTTCATCACT
1613941 ATTTAATAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
51 4 0.07
52 57 0.93
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (52 bp):
ATCACTGTTCATCACTGTTCATATATCGATACAGTATGAATAGTATCGATAC
Found at i:1618833 original size:19 final size:20
Alignment explanation
Indices: 1618790--1618840 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1618780 TACAAGCCAA
**
1618790 TGTATCGATACATTTTATGG
1 TGTATCGATACATACTATGG
*
1618810 TGTATCGATACATACTGT-G
1 TGTATCGATACATACTATGG
1618829 TGTATCGATACA
1 TGTATCGATACA
1618841 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATACTATGG
Done.