Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold488
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: 2093548
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:315352 original size:11 final size:10
Alignment explanation
Indices: 315333--315366 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
315323 TTTAAAATAT
315333 TATAAATTTA
1 TATAAATTTA
315343 TATAAAATTTA
1 TAT-AAATTTA
315354 TATAAATTTA
1 TATAAATTTA
315364 TAT
1 TAT
315367 GTATTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TATAAATTTA
Found at i:315359 original size:21 final size:20
Alignment explanation
Indices: 315325--315366 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
315315 TTTTCGTGTT
315325 TAAAATATTATAAATTTATA
1 TAAAATATTATAAATTTATA
*
315345 TAAAATTTATATAAATTTATA
1 TAAAATAT-TATAAATTTATA
315366 T
1 T
315367 GTATTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAAATATTATAAATTTATA
Found at i:315581 original size:162 final size:156
Alignment explanation
Indices: 315255--315604 Score: 384
Period size: 162 Copynumber: 2.2 Consensus size: 156
315245 CATTTATACA
* * * * *
315255 TAGAGAACGAGAAAAG-AAAAGAGATAAGAAAAGTTAGTATGTTTATATTTGTATTAAATTTTTT
1 TAGAGAAAGAGAAAAGAAAAAGAAATAAGAAAAATTAGTATATTTATATTTCTATTAAATTTTTT
* ** *
315319 CGTGTTTAAAATATTATAAATTTATATAAAATTTATATAAATTTATATGTATTAATAATTTATTT
66 CGTGTTTAAAATATTATAAATTTATATAAAATTTATATAAATTTACACATACTAATAATTTATTT
* *
315384 TATGTAAATTTTGACATATTCATATT
131 TATGTAAATTTTAACATATTCATATC
* * * * *
315410 TATAGAAAGAGAAAAGAAAAAGAAATAGGAAAAAATTA-TATATTTGTGTTTCTGTTAAA-TTTT
1 TAGAGAAAGAGAAAAGAAAAAGAAATAAG-AAAAATTAGTATATTTATATTTCTATTAAATTTTT
* *
315473 TCATGTGTTTAAAGTATTATAAATTTATATAAATTTTTATTTATATAAATTTACACATGCTAATA
65 TC--GTGTTTAAAATATTATAAATTTATATAAA-----ATTTATATAAATTTACACATACTAATA
* * *
315538 ATTTATTTTTTGTATATTTTAACATATTCTTATC
123 ATTTATTTTATGTAAATTTTAACATATTCATATC
* * *
315572 TAGAGAAAGAGAGAAG-AAAAGGAATGAGAAAAA
1 TAGAGAAAGAGAAAAGAAAAAGAAATAAGAAAAA
315605 AAGAGAAAAA
Statistics
Matches: 160, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
155 20 0.12
156 26 0.16
157 35 0.22
160 5 0.03
161 9 0.06
162 65 0.41
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (156 bp):
TAGAGAAAGAGAAAAGAAAAAGAAATAAGAAAAATTAGTATATTTATATTTCTATTAAATTTTTT
CGTGTTTAAAATATTATAAATTTATATAAAATTTATATAAATTTACACATACTAATAATTTATTT
TATGTAAATTTTAACATATTCATATC
Found at i:315641 original size:29 final size:29
Alignment explanation
Indices: 315600--315657 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
315590 AAGGAATGAG
315600 AAAAAAAGAGAAAAATCAATATGTTCATA
1 AAAAAAAGAGAAAAATCAATATGTTCATA
315629 AAAAAAAGAGAAAAATCAATATGTTCATA
1 AAAAAAAGAGAAAAATCAATATGTTCATA
315658 TTTATATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (29 bp):
AAAAAAAGAGAAAAATCAATATGTTCATA
Found at i:316156 original size:22 final size:21
Alignment explanation
Indices: 316113--316162 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
316103 GATTATTTTT
*
316113 TATAATAT-TTTCATATCATA
1 TATAATTTATTTCATATCATA
**
316133 TATTAATTTATTTCATATTTTA
1 TA-TAATTTATTTCATATCATA
316155 TATAATTT
1 TATAATTT
316163 GTCAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 11 0.44
22 12 0.48
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (21 bp):
TATAATTTATTTCATATCATA
Found at i:320848 original size:17 final size:15
Alignment explanation
Indices: 320814--320845 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
320804 TTATTAATTT
320814 TTAAAAATTTAATAA
1 TTAAAAATTTAATAA
320829 TTAAAAA-TTAAT-A
1 TTAAAAATTTAATAA
320842 TTAA
1 TTAA
320846 TTAGTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 5 0.29
15 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAAAATTTAATAA
Found at i:320872 original size:34 final size:32
Alignment explanation
Indices: 320827--320894 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
320817 AAAATTTAAT
*
320827 AATTAAAAATTAATATTAAT-TAGTTTCATAAAA
1 AATTAAAAATT-ATATGAATATAGTTTCA-AAAA
*
320860 AATTCAAAAATTATATGAATATAGTTTTAAAAA
1 AATT-AAAAATTATATGAATATAGTTTCAAAAA
320893 AA
1 AA
320895 CATAGTACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.37
Consensus pattern (32 bp):
AATTAAAAATTATATGAATATAGTTTCAAAAA
Found at i:324132 original size:168 final size:167
Alignment explanation
Indices: 323661--324242 Score: 639
Period size: 168 Copynumber: 3.5 Consensus size: 167
323651 CAAATATTAG
* * * *
323661 AATTCATCAAATATTATCATTTATTTCATAGTAAATCAGTTTTCAAAAATTAATTCATTTTCATG
1 AATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTGAAAATTTAATTCATTTTCATG
* * * * * *
323726 AGTTTTTAAATTTTTTT-CTT-AACTTTTCTTTTTTCAAAATA-CGTTATTTTCTACTTCGTAAA
66 AGTTTTTGAATTTTTTTCCTTGAAATCTCCATTTTCCAAAATATCG-TATTTTCTACTTCGTAAA
323788 TTTTTTCG-GGGAGATTTTTCTT-ATTTTTTAATTTTTAA
130 TTTTTTCGAGGG-GATTTTTCTTGA-TTTTTAATTTTTAA
* * *
323826 AATTCATCAAATATAATTATTTATTTCATATTAAATCAATTTTTAAAATTTAATTCATTTTCATG
1 AATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTGAAAATTTAATTCATTTTCATG
*
323891 AGTTTTTGAATTTTTTTCCTTGAAATTCTCCATTTTCCGAAATAT-GTTATTTTCTACTTCGTAA
66 AGTTTTTGAATTTTTTTCCTTGAAA-TCTCCATTTTCCAAAATATCG-TATTTTCTACTTCGTAA
*
323955 ATTTTTTCGAGGGGATTTTTCTTGGTTTTTAATTTTTAA
129 ATTTTTTCGAGGGGATTTTTCTTGATTTTTAATTTTTAA
*
323994 AATTCATCAAATATTATGATTTATTTCATATTAAATCAGTTTTGAAAATTTAATTCATTTTCATG
1 AATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTGAAAATTTAATTCATTTTCATG
* * * * * * **
324059 AG-GTTTGGATTTTTTTCCTTTGAAATCCCCATTTTCCTAAAAAATCG-AGTTTTCCATTTTATA
66 AGTTTTTGAATTTTTTTCC-TTGAAATCTCCATTTTCC-AAAATATCGTA-TTTTCTACTTCGTA
* * * **
324122 AATATTTTCGAGAGGATTTTTCTCGATTTAAAATTTTTAA
128 AATTTTTTCGAGGGGATTTTTCTTGATTTTTAATTTTTAA
* * * * * * *
324162 AATTCAT-ATGATATTATTATTGAACTTC-CATTAATTCAGTTTTGAAAAATTCAATGCA-TTTC
1 AATTCATCA-AATATTATTATT-TATTTCATATTAAATCAGTTTTG-AAAATTTAATTCATTTTC
* *
324224 ATGA-ATTTTGATTTTTTTT
63 ATGAGTTTTTGAATTTTTTT
324243 TGCATATATT
Statistics
Matches: 359, Mismatches: 44, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
165 75 0.21
166 3 0.01
167 29 0.08
168 233 0.65
169 19 0.05
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (167 bp):
AATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTGAAAATTTAATTCATTTTCATG
AGTTTTTGAATTTTTTTCCTTGAAATCTCCATTTTCCAAAATATCGTATTTTCTACTTCGTAAAT
TTTTTCGAGGGGATTTTTCTTGATTTTTAATTTTTAA
Found at i:330480 original size:103 final size:99
Alignment explanation
Indices: 330270--330472 Score: 271
Period size: 103 Copynumber: 2.0 Consensus size: 99
330260 GATACTTTAA
* *
330270 CCCCATTTTTTAAAACTTGTCATTTAAATCTCATTTTCACATTAAATTATCATCATTAGGGATAC
1 CCCCTTTTTTTAAAACTTGTCATTTAAATCTCATTTTCACATTAAATTATCATCATTAGGGACAC
*
330335 TCTAACCCTATTCCTCCGAGCAAATACTCCAACC
66 TCCAACCCTATTCCTCCGAGCAAATACTCCAACC
* * *
330369 CCCCTTTTTTTAAAAACTTGTCAAGATTTAAATCTTATTTTCACATTAAATTATTATCATTGGGG
1 CCCCTTTTTTT-AAAACTTGTC---ATTTAAATCTCATTTTCACATTAAATTATCATCATTAGGG
* * * * *
330434 GCACTCCAGCCCTATTCTTCCGAGGAGATACTCCAACC
62 ACACTCCAACCCTATTCCTCCGAGCAAATACTCCAACC
330472 C
1 C
330473 TGTTTTTTAA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
99 10 0.11
100 10 0.11
103 69 0.78
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (99 bp):
CCCCTTTTTTTAAAACTTGTCATTTAAATCTCATTTTCACATTAAATTATCATCATTAGGGACAC
TCCAACCCTATTCCTCCGAGCAAATACTCCAACC
Found at i:332827 original size:79 final size:79
Alignment explanation
Indices: 332696--332869 Score: 276
Period size: 79 Copynumber: 2.2 Consensus size: 79
332686 GATAACAACG
* *
332696 GGGTTGGAGGATCCCTGATTATAGAAAATTAGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCTAATTATAGAAAATTAGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCC
***
332761 CCTTGGAAATAACA
66 CCTCAAAAATAACA
* *
332775 GGGTTGGAGTATCCCTAATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCTAATTATAGAAAATTAGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCC
*
332840 CCTCAAAAATAACG
66 CCTCAAAAATAACA
332854 GGGTTGGAGTATCCCT
1 GGGTTGGAGTATCCCT
332870 GCGAAAATAA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 87 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (79 bp):
GGGTTGGAGTATCCCTAATTATAGAAAATTAGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCC
CCTCAAAAATAACA
Found at i:332897 original size:28 final size:28
Alignment explanation
Indices: 332824--332898 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
332814 AAAATAAAAT
332824 CGGGGTTGGAGTATCCCCT-CAAAAATAA
1 CGGGGTTGGAGTAT-CCCTGCAAAAATAA
*
332852 CGGGGTTGGAGTATCCCTGCGAAAATAA
1 CGGGGTTGGAGTATCCCTGCAAAAATAA
332880 CGGGGTTGGAGTATCCCTG
1 CGGGGTTGGAGTATCCCTG
332899 ATTGTGAGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 4 0.09
28 41 0.91
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCTGCAAAAATAA
Found at i:332935 original size:79 final size:78
Alignment explanation
Indices: 332852--333058 Score: 308
Period size: 79 Copynumber: 2.6 Consensus size: 78
332842 TCAAAAATAA
* *
332852 CGGGGTTGGAGTATCCCTGCGAAAATAACGGGGTTGGAGTATCCCTGATTGTGAGAAATTAATAT
1 CGGGGTTGGAGTATCCCT-CGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
332917 TTTAAAAATAAAAC
65 TTTAAAAATAAAAC
*
332931 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTAT-CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
*
332996 TTTAGAAATAAAAC
65 TTTAAAAATAAAAC
* * *
333010 CGGGGTGGGAGTATCCCTTC-AGAAGTGACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCC-TCGA-AAATAACGGGGTTGGAGTATCCCCGAT
333059 GATTAACGGG
Statistics
Matches: 117, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
78 3 0.03
79 110 0.94
80 4 0.03
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATT
TTAAAAATAAAAC
Found at i:332935 original size:107 final size:106
Alignment explanation
Indices: 332745--332975 Score: 322
Period size: 107 Copynumber: 2.2 Consensus size: 106
332735 AAAATAAAAT
** *
332745 CGGGGTTGGAGTATCCCCTTGGAAATAACAGGGTTGGAGTATCCCTAATTATAGAAAATTGGTGT
1 CGGGGTTGGAGTAT-CCCTTGGAAATAACAGGGTTGGAGTATCCCTAATTATAGAAAATTAATAT
* *
332810 TTTGAAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAA
65 TTTAAAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAA
* * *
332852 CGGGGTTGGAGTATCCC-TGCGAAAATAACGGGGTTGGAGTATCCCTGATTGT-GAGAAATTAAT
1 CGGGGTTGGAGTATCCCTTG-G-AAATAACAGGGTTGGAGTATCCCTAATTATAGA-AAATTAAT
**
332915 ATTTTAAAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAA
63 ATTTTAAAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAA
332959 CGGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
332976 CGATTGTGAG
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
105 2 0.02
106 6 0.05
107 103 0.93
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (106 bp):
CGGGGTTGGAGTATCCCTTGGAAATAACAGGGTTGGAGTATCCCTAATTATAGAAAATTAATATT
TTAAAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAA
Found at i:333007 original size:186 final size:185
Alignment explanation
Indices: 332692--333096 Score: 503
Period size: 186 Copynumber: 2.2 Consensus size: 185
332682 TGGTGATAAC
* * * * * *
332692 AACGGGGTTGGAGGATCCCTGATTAT-AGAAAATTAGTGTTCTGAAAATAAAATCGGGGTTGGAG
1 AACGGGGTTGGAGTATCCCTGATTGTGAG-AAATTAATATTCTAAAAATAAAACCGGGGTTGGAG
* * *** *
332756 TATCCCCTTGGAAATAACAGGGTTGGAGTATCCCTAATTATAGAAAATTGGTGTTTTGAAAATAA
65 TATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCAATTATAGAAAATCAATATTTTGAAAATAA
* *
332821 AATCGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCTGCGA-AAAT
130 AACCGGGGTGGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCC--CGATAAAT
*
332878 AACGGGGTTGGAGTATCCCTGATTGTGAGAAATTAATATTTTAAAAATAAAACCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCTGATTGTGAGAAATTAATATTCTAAAAATAAAACCGGGGTTGGAGT
* * *
332943 ATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGT-GAGAAATCAATATTTT-AGAAATA
66 ATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCAATTATAGA-AAATCAATATTTTGA-AAATA
* * * * * *
333006 AAACCGGGGTGGGAGTATCCCTTCAGAAGTGACGGGGTTGGAGTATCCCCGATGATT
129 AAACCGGGGTGGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATAAAT
* *
333063 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATT
1 AACGGGGTTGGAGTATCCCTGATTGTGAGAAATT
333097 GGTGTTTTGG
Statistics
Matches: 189, Mismatches: 26, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
184 3 0.02
185 37 0.20
186 147 0.78
187 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (185 bp):
AACGGGGTTGGAGTATCCCTGATTGTGAGAAATTAATATTCTAAAAATAAAACCGGGGTTGGAGT
ATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCAATTATAGAAAATCAATATTTTGAAAATAAA
ACCGGGGTGGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATAAAT
Found at i:333127 original size:106 final size:107
Alignment explanation
Indices: 332931--333131 Score: 269
Period size: 106 Copynumber: 1.9 Consensus size: 107
332921 AAAATAAAAC
** *
332931 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCGAGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATAT
* *
332996 TTTAGAAATAAAACCGGGGTGGGAGTATCCCTTCAGAAGTGA
66 TTTAGAAATAAAACCAGAGTGGGAGTATCCCTTCAGAAGTGA
* * *** *
333038 CGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGT
1 CGGGGTTGGAGTATCCCCGAGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATAT
* * *
333102 TTTGGAAATAAAATCAGAGTTGGAGTATCC
66 TTTAGAAATAAAACCAGAGTGGGAGTATCC
333132 ATGATTATAG
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
106 61 0.76
107 19 0.24
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.26
Consensus pattern (107 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATAT
TTTAGAAATAAAACCAGAGTGGGAGTATCCCTTCAGAAGTGA
Found at i:333129 original size:51 final size:51
Alignment explanation
Indices: 333069--333300 Score: 270
Period size: 51 Copynumber: 4.6 Consensus size: 51
333059 GATTAACGGG
** * *
333069 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAAAAATAAAACCGGA
** * * *
333120 GTTGGAGTATCCATGATTAT-AGAAAATTGGTGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTAAAAATAAAACCGGA
* * * *
333171 GTTGGAGT-TCCCCGATTGTGGAAAATTGGTGTTTCAAAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAAAAATAAAACCGGA
* * * *
333221 GTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAAAAATAAAACCGGA
* *
333272 GTTGGAGTATTCCCGATTATGAAAAATTG
1 GTTGGAGTATCCCCGATTGTGAAAAATTG
333301 AGAAACTTAA
Statistics
Matches: 152, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
50 41 0.27
51 111 0.73
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAAAAATAAAACCGGA
Found at i:333197 original size:101 final size:102
Alignment explanation
Indices: 333065--333300 Score: 334
Period size: 101 Copynumber: 2.3 Consensus size: 102
333055 CGATGATTAA
***
333065 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATC-AGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTCAAAAATAAAATCGA-AGTTGGAGTA
* *
333129 TCCATGATTATAGAAAATTGGTGTTTT-GAAAATAAAAC
65 TCCACGATTATAGAAAATTAGTGTTTTAG-AAATAAAAC
*
333167 CGGGGTTGGAGT-TCCCCGATTGTGGAAAATTGGTGTTTCAAAAATAAAATCGAAGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTCAAAAATAAAATCGAAGTTGGAGTAT
* * *
333231 CCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAAC
66 CCACGATTATAGAAAATTAGTGTTTTAGAAATAAAAC
* *
333268 CGGGGTTGGAGTATTCCCGATTATGAAAAATTG
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTG
333301 AGAAACTTAA
Statistics
Matches: 119, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
101 88 0.74
102 31 0.26
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.31
Consensus pattern (102 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTCAAAAATAAAATCGAAGTTGGAGTAT
CCACGATTATAGAAAATTAGTGTTTTAGAAATAAAAC
Found at i:335605 original size:20 final size:19
Alignment explanation
Indices: 335580--335653 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 19
335570 AAAATGCCTG
*
335580 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AA
*
335600 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
335620 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
335640 AATGTATCGATACA
1 AATGTATCGATACA
335654 TCTGGGTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:338820 original size:19 final size:18
Alignment explanation
Indices: 338774--338859 Score: 65
Period size: 19 Copynumber: 4.8 Consensus size: 18
338764 TTTCAACAAT
*
338774 TTGTATCGATACAAACTG
1 TTGTATCGATACAAAGTG
338792 TAACTGTATCGATACATAAGTG
1 T---TGTATCGATACA-AAGTG
338814 TTGTATCGATAC-AA---
1 TTGTATCGATACAAAGTG
*
338828 -TGTATCGATACATAAGTT
1 TTGTATCGATACA-AAGTG
*
338846 TTGTATTGATACAA
1 TTGTATCGATACAA
338860 TGCATCGCTA
Statistics
Matches: 56, Mismatches: 2, Indels: 20
0.72 0.03 0.26
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
18 2 0.04
19 22 0.39
21 12 0.21
22 5 0.09
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (18 bp):
TTGTATCGATACAAAGTG
Found at i:338833 original size:13 final size:13
Alignment explanation
Indices: 338815--338839 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
338805 ACATAAGTGT
338815 TGTATCGATACAA
1 TGTATCGATACAA
338828 TGTATCGATACA
1 TGTATCGATACA
338840 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:338837 original size:32 final size:32
Alignment explanation
Indices: 338796--338866 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
338786 AAACTGTAAC
338796 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
338828 TGTATCGATACATAAGTTTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
338860 TGCATCG
1 TGTATCG
338867 CTACGAAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:338929 original size:13 final size:13
Alignment explanation
Indices: 338911--338938 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
338901 ATTACTCAAA
338911 TGTATCGATACAT
1 TGTATCGATACAT
338924 TGTATCGATACAT
1 TGTATCGATACAT
338937 TG
1 TG
338939 ACCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:345983 original size:52 final size:52
Alignment explanation
Indices: 345905--346033 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
345895 CGAAATATGA
*
345905 AAATTTGCCTGCATGTATCGATACATTTCATGGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
345957 AAATTTACCTGTACGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
346009 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
346034 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:346044 original size:52 final size:51
Alignment explanation
Indices: 345905--346053 Score: 176
Period size: 52 Copynumber: 2.9 Consensus size: 51
345895 CGAAATATGA
* *
345905 AAATTTGCCTGCATGTATCGATACATTTCAT-GGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--ACATCAGTGTATCGATACATCTGGGC
* * * *
345957 AAATTTACCTGTACGTATCGATACATTTCAT-AGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--ACATCAGTGTATCGATACATCTGGGC
*
346009 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATAC-AACATCAGTGTATCGATACA
346054 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.97
53 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACAACATCAGTGTATCGATACATCTGGGC
Found at i:346060 original size:13 final size:13
Alignment explanation
Indices: 346042--346066 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
346032 CAAAGATCAG
346042 TGTATCGATACAA
1 TGTATCGATACAA
346055 TGTATCGATACA
1 TGTATCGATACA
346067 TTTGAGTAAT
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:346143 original size:19 final size:18
Alignment explanation
Indices: 346119--346215 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
346109 AGCGATACAT
346119 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
346138 TGTATCGATAC--AC-TA
1 TGTATCGATACAAACTTA
346153 --TATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
346170 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
346183 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
346202 TGTATCGATACAAA
1 TGTATCGATACAAA
346216 TCATTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 20 0.30
14 1 0.02
15 2 0.03
16 6 0.09
17 2 0.03
18 2 0.03
19 33 0.50
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:346157 original size:32 final size:32
Alignment explanation
Indices: 346111--346213 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
346101 AGCTTCGTAG
*
346111 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
* *
346143 CGATACACTATATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
346175 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
346207 CGATACA
1 CGATACA
346214 AATCATTGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:346188 original size:13 final size:13
Alignment explanation
Indices: 346170--346194 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
346160 ACAACACTTA
346170 TGTATCGATACAT
1 TGTATCGATACAT
346183 TGTATCGATACA
1 TGTATCGATACA
346195 ACACTTATGT
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:348082 original size:27 final size:27
Alignment explanation
Indices: 348046--348333 Score: 315
Period size: 27 Copynumber: 10.6 Consensus size: 27
348036 TTTTCTATTA
* * *
348046 AAGTTCACAACTCCATGGTACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * ** *
348073 AAGTCCACAAGTCCATGGCAATCTTTG
1 AAGTCCACAACTCCGTGGCACCCTTTT
** *
348100 AAGTCCACAACTCTATGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* **
348127 AAGTCCATAACTCTATGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * * *
348154 AAGTTCATAACTCTGTGGCACTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
348181 AAGTCCATAACTTCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
348208 AAGTCTACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * * *
348235 AAGTCCATAACTCTGTAGCACCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
348262 AAGTCCATAACTCCGTGGTACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
348289 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
348316 AAAGCCCACAACTCCGTG
1 -AAGTCCACAACTCCGTG
348334 TCACATTTCT
Statistics
Matches: 225, Mismatches: 35, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
27 209 0.93
28 16 0.07
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.31
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCACCCTTTT
Found at i:348412 original size:28 final size:28
Alignment explanation
Indices: 348371--348678 Score: 262
Period size: 28 Copynumber: 10.6 Consensus size: 28
348361 ATGGCACATT
* *
348371 TTTCAAAGCTCACAAGTCAGTGGCTTCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
348399 TTCCAAAGCCCACAAGTTAGTGGCA-CTC
1 TTTCAAAGCCCACAAGTCAGTGGCATC-C
* * *
348427 TTTTAAAGCTCACACAAGTCTGTGGTAACTCC
1 TTTCAAAGC-C-CACAAGTCAGTGG-CA-TCC
* * *
348459 CTTCAAAGCCCATACAAGTTAGTGGCATCTTTTTT
1 TTTCAAAGCCC--ACAAGTCAGTGGCATC-----C
* * * *
348494 TTTCAAAGCCCACAAGTTATTGACATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
348522 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * **
348550 TTTCAAAGCTCACAATTCAGTGAAATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
348578 TTTCAAAGCCCACAAGGT-AGTGGCATCT
1 TTTCAAAGCCCACAA-GTCAGTGGCATCC
* *
348606 TTTCAAAGCTCACAAGTCAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
348634 TTTCAAAGCCAACAAGTCAATGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
348661 TTTTCAAAGCCCACAAGT
1 -TTTCAAAGCCCACAAGT
348679 TAGTAGCAAC
Statistics
Matches: 227, Mismatches: 37, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
27 4 0.02
28 161 0.71
29 2 0.01
30 14 0.06
31 3 0.01
32 18 0.08
33 15 0.07
35 10 0.04
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:348438 original size:56 final size:57
Alignment explanation
Indices: 348362--348678 Score: 302
Period size: 56 Copynumber: 5.5 Consensus size: 57
348352 CATAAGTCAA
* *
348362 TGGCACAT-TTTTCAAAGCTCACAAGTCAGTGGCTTCCTTCCAAAGCCCACAAGTTAG
1 TGGCAC-TCTTTTCAAAGCTCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAG
* * *
348419 TGGCACTCTTTT-AAAGCTCACACAAGTCTGTGGTAACTCCCTTCAAAGCCCATACAAGTTAG
1 TGGCACTCTTTTCAAAGCT--CACAAGTCAGTGG-CA-TCCTTTCAAAGCCC--ACAAGTTAG
* * * * * * *
348481 TGGCATCTTTTTTTTTCAAAGCCCACAAGTTATTGACATCTTTTCAAAGCCCACAAGTCAG
1 TGGCA-C---TCTTTTCAAAGCTCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAG
* * ** *
348542 TGGCA-TCCTTTCAAAGCTCACAATTCAGTGAAATCCTTTCAAAGCCCACAAGGTAG
1 TGGCACTCTTTTCAAAGCTCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAG
* * * *
348598 TGGCA-TCTTTTCAAAGCTCACAAGTCAGTGGCATCTTTTCAAAGCCAACAAGTCAA
1 TGGCACTCTTTTCAAAGCTCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAG
*
348654 TGGCAC-CTTTTCAAAGCCCACAAGT
1 TGGCACTCTTTTCAAAGCTCACAAGT
348679 TAGTAGCAAC
Statistics
Matches: 212, Mismatches: 35, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
56 118 0.56
57 10 0.05
58 12 0.06
60 12 0.06
61 13 0.06
62 14 0.07
63 13 0.06
64 1 0.00
65 9 0.04
66 5 0.02
67 5 0.02
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (57 bp):
TGGCACTCTTTTCAAAGCTCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAG
Found at i:348521 original size:33 final size:34
Alignment explanation
Indices: 348460--348524 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
348450 GGTAACTCCC
*
348460 TTCAAAGCCCATACAAGTTAGTGGCATCTTTTTTT
1 TTCAAAGCCCA-ACAAGTTAGTGACATCTTTTTTT
*
348495 TTCAAAGCCC-ACAAGTTATTGACATCTTTT
1 TTCAAAGCCCAACAAGTTAGTGACATCTTTT
348525 CAAAGCCCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 18 0.64
35 10 0.36
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (34 bp):
TTCAAAGCCCAACAAGTTAGTGACATCTTTTTTT
Found at i:350975 original size:52 final size:52
Alignment explanation
Indices: 350905--351023 Score: 211
Period size: 52 Copynumber: 2.3 Consensus size: 52
350895 GAAAATTTAT
*
350905 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
* *
350957 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
351009 CTGCATGTATCGATA
1 CTGCATGTATCGATA
351024 TAAAGATCGG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:351038 original size:52 final size:52
Alignment explanation
Indices: 350905--351045 Score: 178
Period size: 52 Copynumber: 2.7 Consensus size: 52
350895 GAAAATTTAT
*
350905 CTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGC
* *** *
350957 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
* *
351009 CTGCATGTATCGATATA-AAGATCGGTGTATCGATACA
1 CTGCATGTATCGATACATAAGAT-AGTGTATCGATACA
351046 ATGTATCGAT
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
51 4 0.05
52 73 0.95
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:351052 original size:13 final size:13
Alignment explanation
Indices: 351034--351058 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
351024 TAAAGATCGG
351034 TGTATCGATACAA
1 TGTATCGATACAA
351047 TGTATCGATACA
1 TGTATCGATACA
351059 TTTGAGTAAT
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:351995 original size:67 final size:68
Alignment explanation
Indices: 351873--351999 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
351863 ATTGGGTTTT
* * *
351873 AAAGATGATGAAGTTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
351938 AGA
66 AGA
* * * *
351941 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
352000 GAAAAATGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:352081 original size:21 final size:21
Alignment explanation
Indices: 352057--352124 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
352047 AATGATGGAA
352057 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
* ** *
352078 AA-G-GCCAGCTATATTGGACTTA
1 AAGGTGCCA-ATATGCT-GA-TTC
*
352100 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATATGCTGATTC
352121 AAGG
1 AAGG
352125 CCAGCTACAT
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 5 0.15
21 10 0.30
22 6 0.18
23 4 0.12
24 4 0.12
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:352221 original size:49 final size:49
Alignment explanation
Indices: 352012--352668 Score: 893
Period size: 49 Copynumber: 13.7 Consensus size: 49
352002 AAAATGATGT
* * *
352012 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAATGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
*
352064 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
352107 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
352155 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
352204 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
352253 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
352302 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
352351 CAATATGCTGATTCAATGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
352400 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A--AA-GTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
352443 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
352492 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAATGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
352541 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
352584 CAATGTGTTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
352633 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
352669 GAAGGGTTGC
Statistics
Matches: 541, Mismatches: 45, Indels: 41
0.86 0.07 0.07
Matches are distributed among these distances:
43 113 0.21
44 2 0.00
45 2 0.00
46 2 0.00
47 2 0.00
48 50 0.09
49 338 0.62
52 32 0.06
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:352498 original size:141 final size:142
Alignment explanation
Indices: 352012--352668 Score: 988
Period size: 141 Copynumber: 4.6 Consensus size: 142
352002 AAAATGATGT
* *
352012 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAATGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAATATGCTGATT
* *
352077 CAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
63 CAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATT
352136 GGACTTAAAGGTGAGGTGC
128 GGACTTAAA----AGGTGC
* * *
352155 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
* *
352220 GGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
66 GGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
352285 CTTAATGGTGAAGGTGC
131 CTTAA-----AAGGTGC
*
352302 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
* *
352367 TGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
66 GGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
352432 CTTAAAA-GTGC
131 CTTAAAAGGTGC
352443 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
* * *
352508 GGCCAGCTACATTGGACTTAAAGATGAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGG
66 GGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
352573 CTT-AAAGGTGC
131 CTTAAAAGGTGC
* *
352584 CAATGTGTTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
*
352649 GGCCAGCTATATTGGGCTTA
66 GGCCAGCTATATTGGACTTA
352669 GAAGGGTTGC
Statistics
Matches: 476, Mismatches: 26, Indels: 26
0.90 0.05 0.05
Matches are distributed among these distances:
140 42 0.09
141 216 0.45
142 2 0.00
143 39 0.08
144 1 0.00
146 42 0.09
147 133 0.28
151 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (142 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
CTTAAAAGGTGC
Found at i:352712 original size:33 final size:33
Alignment explanation
Indices: 352668--352788 Score: 183
Period size: 33 Copynumber: 3.7 Consensus size: 33
352658 TATTGGGCTT
*
352668 AGAAGGGTTGCCACCGACTTATGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
352701 AGAATGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
352733 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
352766 AAGAA-GGTTGCCACTGACTTGTG
1 -AGAAGGGTTGCCACCGACTTGTG
352789 GACTTAAAAG
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 30 0.38
33 46 0.57
34 4 0.05
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:352763 original size:65 final size:63
Alignment explanation
Indices: 352661--352788 Score: 195
Period size: 65 Copynumber: 2.0 Consensus size: 63
352651 CCAGCTATAT
*
352661 TGGGCTTAGAAGGGTTGCCACCGACTTATGTGGGCTTTAG-AGAATGGTTGCCACCGACTTGTG
1 TGGGCTTAGAAGGGTTGCCACCAACTTATGTGGGCTTTAGAAGAA-GGTTGCCACCGACTTGTG
* *
352724 TGGGCTTTGAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAAGAAGGTTGCCACTGACTTGTG
1 TGGGC-TT-AGAAGGGTTGCCACCAACTTATGTGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
352789 GACTTAAAAG
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
63 5 0.08
64 2 0.03
65 48 0.81
66 4 0.07
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.29
Consensus pattern (63 bp):
TGGGCTTAGAAGGGTTGCCACCAACTTATGTGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
Found at i:353017 original size:120 final size:114
Alignment explanation
Indices: 352769--353333 Score: 359
Period size: 120 Copynumber: 4.6 Consensus size: 114
352759 GCTTTAGAAG
* * * *
352769 AAGGTTGCCACTGACTTGTGGACTTAAAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGGA
1 AAGGGTGCCACGGAGTTGTGGACTT-AAAGGAAAAGAGTGCCACGAAGTTGTGGGCTTT------
* *
352834 AAAAAGGGTGCAACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTAA
59 -AAAAGGGTGCAACGAAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAA
* *
352891 ACGGGTGCCACGGAGTTGTGGACTCAGAAGGAAAACGAGTGCCACGAAGTTGTGGGCTTTAAAAG
1 AAGGGTGCCACGGAGTTGTGGACTTA-AAGGAAAA-GAGTGCCACGAAGTTGTGGGCTTTAAAAG
* *
352956 GGTGCCACGAAGTTGTGGACTTTGATGAGAA-GGTGCCACTGAGTTGTGGACTTAA
64 GGTGCAACGAAGTTGTGGAC-TT-A--A-AAGGGTGCCACGGAGTTGTGGACTTAA
* * *
353011 AAGGGTGCCACGGAGTTGTGGGCTTAAACGGGAAAAGAGTGCCACGGAGCTGTGGGCTTTAAAAA
1 AAGGGTGCCACGGAGTTGTGGACTTAAA--GGAAAAGAGTGCCACGAAGTTGTGGGCTTT-AAAA
* * *
353076 GAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAA
63 G-----GGTGCAACGAAGTTGTGGAC-TT-AAAAG-----GGTGCCACGGAGTTGTGGACTTAA
* * * * *
353140 AGATGAAAAAAGTGCCACGGAGTTGTGGGCTT--A-G--AAGGGTGCCACGGAGTTGTGGACTTA
1 A-A-G-----GGTGCCACGGAGTTGTGGACTTAAAGGAAAAGAGTGCCACGAAGTTGTGGGCTT-
** * * * *
353200 AAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGGCTTTGAA
58 ----T-AAAAGGGTGCAACGAAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TT-AA
* * *
353264 AAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTG
1 AAG--GGTGCCACGGAGTTGTGGAC-TT-AAA-GG-AAAAGAGTGCCACGAAGTTGTGGGCTTTA
353329 AAAGG
60 AAAGG
353334 AAGGTGCCAC
Statistics
Matches: 364, Mismatches: 35, Indels: 88
0.75 0.07 0.18
Matches are distributed among these distances:
116 23 0.06
117 2 0.01
118 1 0.00
119 21 0.06
120 70 0.19
121 14 0.04
122 51 0.14
123 30 0.08
124 4 0.01
125 1 0.00
126 22 0.06
127 5 0.01
128 25 0.07
129 65 0.18
130 1 0.00
131 2 0.01
134 6 0.02
136 21 0.06
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (114 bp):
AAGGGTGCCACGGAGTTGTGGACTTAAAGGAAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAGGG
TGCAACGAAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAA
Found at i:353053 original size:34 final size:33
Alignment explanation
Indices: 352774--353326 Score: 285
Period size: 34 Copynumber: 17.6 Consensus size: 33
352764 AGAAGAAGGT
* * * *
352774 TGCCACTGACTTGTGGACTTAAAAGGAAAAGAG
1 TGCCACGGAGTTGTGGGCTTAAAGGGAAAAGAG
* * *
352807 TGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGG
1 TGCCACGGAGTTGTGGGC-TTAAAGG-GAAAAGAG
* * *
352842 TGCAACGGAGTTGTGGACTT------AAAAGGG
1 TGCCACGGAGTTGTGGGCTTAAAGGGAAAAGAG
*
352869 TGCCACGGAGTTGTGGGCTTAAA-CG----G-G
1 TGCCACGGAGTTGTGGGCTTAAAGGGAAAAGAG
* *
352896 TGCCACGGAGTTGTGGACTCAGAA-GGAAAACGAG
1 TGCCACGGAGTTGTGGGCTTA-AAGGGAAAA-GAG
* * *
352930 TGCCACGAAGTTGTGGGCTT-----TAAAAGGG
1 TGCCACGGAGTTGTGGGCTTAAAGGGAAAAGAG
* * ** * *
352958 TGCCACGAAGTTGTGGACTTTGA-TGAGAAG-G
1 TGCCACGGAGTTGTGGGCTTAAAGGGAAAAGAG
* * *
352989 TGCCACTGAGTTGTGGACTT------AAAAGGG
1 TGCCACGGAGTTGTGGGCTTAAAGGGAAAAGAG
353016 TGCCACGGAGTTGTGGGCTTAAACGGGAAAAGAG
1 TGCCACGGAGTTGTGGGCTTAAA-GGGAAAAGAG
* **
353050 TGCCACGGAGCTGTGGGCTTTAAAAAGAAAA-AGG
1 TGCCACGGAGTTGTGGGC-TTAAAGGGAAAAGA-G
**
353084 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAA-AGG
1 TGCCACGGAGTTGTGGGC-TTAAAGGGAAAAGA-G
* * *
353118 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAG
1 TGCCACGGAGTTGTGGGCTTAAAG-GGAAAAGAG
*
353152 TGCCACGGAGTTGTGGGCTT--A--G--AAGGG
1 TGCCACGGAGTTGTGGGCTTAAAGGGAAAAGAG
* * *
353179 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAG
1 TGCCACGGAGTTGTGGGCTTAAAG-GGAAAAGAG
*
353213 TGCCACGGAGTTGTGGGCTT------AAAAGGG
1 TGCCACGGAGTTGTGGGCTTAAAGGGAAAAGAG
*
353240 TGCCACGGAGTTGTGGGCTT----TGAAAAGAAGG
1 TGCCACGGAGTTGTGGGCTTAAAGGGAAAAG-A-G
* *
353271 TGCCACGGAGTCGTGGACTTTAAAAGGGAAAAAGAG
1 TGCCACGGAGTTGTGGGC-TT-AAAGGG-AAAAGAG
353307 TGCCACGGAGTTGTGGGCTT
1 TGCCACGGAGTTGTGGGCTT
353327 TGAAAGGAAG
Statistics
Matches: 421, Mismatches: 51, Indels: 94
0.74 0.09 0.17
Matches are distributed among these distances:
26 4 0.01
27 111 0.26
28 25 0.06
29 11 0.03
31 36 0.09
32 8 0.02
33 21 0.05
34 152 0.36
35 29 0.07
36 17 0.04
37 2 0.00
38 5 0.01
ACGTcount: A:0.29, C:0.14, G:0.35, T:0.21
Consensus pattern (33 bp):
TGCCACGGAGTTGTGGGCTTAAAGGGAAAAGAG
Found at i:353191 original size:61 final size:61
Alignment explanation
Indices: 353111--353255 Score: 272
Period size: 61 Copynumber: 2.4 Consensus size: 61
353101 CTTTAAAAAG
*
353111 AAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTT
*
353172 AGAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTT
353233 AAAAGGGTGCCACGGAGTTGTGG
1 AAAAGGGTGCCACGGAGTTGTGG
353256 GCTTTGAAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 81 1.00
ACGTcount: A:0.30, C:0.13, G:0.36, T:0.21
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTT
Found at i:353341 original size:67 final size:66
Alignment explanation
Indices: 353233--353428 Score: 256
Period size: 67 Copynumber: 3.0 Consensus size: 66
353223 TTGTGGGCTT
*
353233 AAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGG
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTG-AAAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGG
353298 GA
65 GA
*
353300 AAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAGGAAGGTGCCACGGAGTCGTGGACTTT-GAA--
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA-GAAGGTGCCACGGAGTCGTGGACTTTAAAAGG
353362 GA
65 GA
* * * * * *
353364 AAAGGA-TGCCACTGAGTCGTGGACTTTGAGAAGAAGGTGCCACAGAGTCATGGACTTTAAGAAG
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTGA-AAGAAGGTGCCACGGAGTCGTGGACTTTAA-AAG
353428 G
64 G
353429 TATTTGAAGA
Statistics
Matches: 114, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
63 44 0.39
64 9 0.08
65 2 0.02
66 5 0.04
67 54 0.47
ACGTcount: A:0.30, C:0.14, G:0.36, T:0.20
Consensus pattern (66 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGGG
A
Found at i:353403 original size:283 final size:278
Alignment explanation
Indices: 352868--353425 Score: 670
Period size: 283 Copynumber: 2.0 Consensus size: 278
352858 ACTTAAAAGG
*
352868 GTGCCACGGAGTTGTGGGCTTAAACGGGTGCCACGGAGTTGTGGACTCAGAAGGAAAACGAGTGC
1 GTGCCACGGAGTTGTGGGCTTAAACGGGTGCCACGGAGTTGTGGACTCAGAAGGAAAACAAGTGC
** *
352933 CACGAAGTTGTGGGCTTTAAAAGGGTGCCACGAAGTTGTGGACTTTGATGAGAAGGTGCCACTGA
66 CACGAAGTTGTGGGCTTTAAAAGGGTGCCACGAAGTTGTGGACTTTGAAAAGAAGGTGCCACGGA
*
352998 GTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTAAACGGGAAAAGAGTGCCACGGAGCTG
131 GTCGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTAAAC-GG-AAAGAGTGCCACGGAGCTG
* * * *
353063 TGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAG
194 TGGACTTT-AAAAGAAAAAGGTGCCACGGAGTCGTGGACTTT--AAAGAAAAAGGTGCCACAGAG
**
353128 TTGTGGACTTAAAGATGAAAAAA
256 TCATGGACTTAAAGATGAAAAAA
*
353151 GTGCCACGGAGTTGTGGGCTTAGAA-GGGTGCCACGGAGTTGTGGACTTA-AAGATGAAAA-AAG
1 GTGCCACGGAGTTGTGGGCTTA-AACGGGTGCCACGGAGTTGTGGACTCAGAAG--GAAAACAAG
* * *
353213 TGCCACGGAGTTGTGGGC-TTAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCAC
63 TGCCACGAAGTTGTGGGCTTTAAAAGGGTGCCACGAAGTTGTGGACTTTGAAAAGAAGGTGCCAC
353277 GGAGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA-GG-AAG-GT
128 GGAGTCGTGGAC-TTAAAA--G-----G-GTGCCACGGAGTTGTGGGC-TT-AAACGGAAAGAGT
* * * *
353339 GCCACGGAG-TCGTGGACTTT-GAAG-AAAAGGATGCCACTGAGTCGTGGACTTT-GAGAAGAAG
182 GCCACGGAGCT-GTGGACTTTAAAAGAAAAAGG-TGCCACGGAGTCGTGGACTTTAAAGAAAAAG
*
353400 GTGCCACAGAGTCATGGACTTTAAGA
245 GTGCCACAGAGTCATGGACTTAAAGA
353426 AGGTATTTGA
Statistics
Matches: 239, Mismatches: 20, Indels: 32
0.82 0.07 0.11
Matches are distributed among these distances:
282 55 0.23
283 99 0.41
284 7 0.03
285 7 0.03
286 21 0.09
287 1 0.00
288 19 0.08
289 3 0.01
290 1 0.00
291 21 0.09
292 2 0.01
293 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.35, T:0.21
Consensus pattern (278 bp):
GTGCCACGGAGTTGTGGGCTTAAACGGGTGCCACGGAGTTGTGGACTCAGAAGGAAAACAAGTGC
CACGAAGTTGTGGGCTTTAAAAGGGTGCCACGAAGTTGTGGACTTTGAAAAGAAGGTGCCACGGA
GTCGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTAAACGGAAAGAGTGCCACGGAGCTGTG
GACTTTAAAAGAAAAAGGTGCCACGGAGTCGTGGACTTTAAAGAAAAAGGTGCCACAGAGTCATG
GACTTAAAGATGAAAAAA
Found at i:353412 original size:31 final size:31
Alignment explanation
Indices: 352956--353427 Score: 231
Period size: 34 Copynumber: 14.9 Consensus size: 31
352946 GCTTTAAAAG
* *
352956 GGTGCCACGAAGTTGTGGACTTTGATG-AGAA
1 GGTGCCACGGAGTCGTGGACTTTGA-GAAGAA
* * *
352987 GGTGCCACTGAGTTGTGGAC-TT-A-AA-AG
1 GGTGCCACGGAGTCGTGGACTTTGAGAAGAA
* * * *
353014 GGTGCCACGGAGTTGTGGGCTTAAACGGGAA-AA
1 GGTGCCACGGAGTCGTGGACTT---TGAGAAGAA
* * *
353047 GAGTGCCACGGAG-CTGTGGGCTTTAAAAAGAAAAA
1 G-GTGCCACGGAGTC-GTGGACTTT---GAGAAGAA
* * * *
353082 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
1 GGTGCCACGGAGTCGTGGACTTT---GAGAAGAA
* * *
353116 GGTGCCACGGAGTTGTGGACTTAAAGATGAAAAA
1 GGTGCCACGGAGTCGTGGACTT--TGA-GAAGAA
* * *
353150 AGTGCCACGGAGTTGTGGGC-TT-AGAAG--
1 GGTGCCACGGAGTCGTGGACTTTGAGAAGAA
* * *
353177 GGTGCCACGGAGTTGTGGACTTAAAGATGAAAAA
1 GGTGCCACGGAGTCGTGGACTT--TGA-GAAGAA
* * * *
353211 AGTGCCACGGAGTTGTGGGC-TT-A-AA-AG
1 GGTGCCACGGAGTCGTGGACTTTGAGAAGAA
* * *
353238 GGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 GGTGCCACGGAGTCGTGGACTTTGAGAAGAA
* *
353269 GGTGCCACGGAGTCGTGGACTTTAAAAGGGAAAAA
1 GGTGCCACGGAGTCGTGGACTTT----GAGAAGAA
* *
353304 GAGTGCCACGGAGTTGTGGGCTTTGA-AAGGAA
1 G-GTGCCACGGAGTCGTGGACTTTGAGAA-GAA
353336 GGTGCCACGGAGTCGTGGACTTTGAAGAA-AA
1 GGTGCCACGGAGTCGTGGACTTTG-AGAAGAA
*
353367 GGATGCCACTGAGTCGTGGACTTTGAGAAGAA
1 GG-TGCCACGGAGTCGTGGACTTTGAGAAGAA
* * *
353399 GGTGCCACAGAGTCATGGACTTTAAGAAG
1 GGTGCCACGGAGTCGTGGACTTTGAGAAG
353428 GTATTTGAAG
Statistics
Matches: 358, Mismatches: 45, Indels: 76
0.75 0.09 0.16
Matches are distributed among these distances:
27 57 0.16
28 7 0.02
29 5 0.01
30 6 0.02
31 96 0.27
32 33 0.09
33 9 0.03
34 116 0.32
35 9 0.03
36 20 0.06
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (31 bp):
GGTGCCACGGAGTCGTGGACTTTGAGAAGAA
Found at i:361686 original size:52 final size:52
Alignment explanation
Indices: 361616--361736 Score: 206
Period size: 52 Copynumber: 2.3 Consensus size: 52
361606 GAAAATTTAT
*
361616 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGACAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGACAAATTTGC
* * *
361668 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGACAAATTTGC
361720 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
361737 AAGATCGGTG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGACAAATTTGC
Found at i:361749 original size:52 final size:52
Alignment explanation
Indices: 361616--361756 Score: 178
Period size: 52 Copynumber: 2.7 Consensus size: 52
361606 GAAAATTTAT
*
361616 CTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGACAAATTTGC
1 CTGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGACAAATTTGC
* *** * *
361668 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGACAAATTTGC
*
361720 CTGCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 CTGCATGTATCGATACATAAGAT-AGTGTATCGATACA
361757 ATGTATCGAT
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
51 4 0.05
52 73 0.95
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGACAAATTTGC
Found at i:361763 original size:13 final size:13
Alignment explanation
Indices: 361745--361803 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
361735 CAAAGATCGG
361745 TGTATCGATACAA
1 TGTATCGATACAA
361758 TGTATCGATAC-A
1 TGTATCGATACAA
361770 T-T-T-GAGT--AA
1 TGTATCGA-TACAA
*
361779 TGTACCGATACAA
1 TGTATCGATACAA
361792 TGTATCGATACA
1 TGTATCGATACA
361804 TTTGAGTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
9 4 0.11
10 3 0.08
11 2 0.05
12 4 0.11
13 24 0.65
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:361793 original size:34 final size:34
Alignment explanation
Indices: 361745--361824 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
361735 CAAAGATCGG
361745 TGTATCGATACAATGTATCGATACATTTGAGTAA
1 TGTATCGATACAATGTATCGATACATTTGAGTAA
*
361779 TGTACCGATACAATGTATCGATACATTTGAGTAA
1 TGTATCGATACAATGTATCGATACATTTGAGTAA
361813 TGTATCGATACA
1 TGTATCGATACA
361825 TTTCTTTGGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (34 bp):
TGTATCGATACAATGTATCGATACATTTGAGTAA
Found at i:361885 original size:13 final size:13
Alignment explanation
Indices: 361867--361891 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
361857 CAAAAAAATA
361867 TGTATCGATACAT
1 TGTATCGATACAT
361880 TGTATCGATACA
1 TGTATCGATACA
361892 ACATTTTATG
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:361902 original size:33 final size:33
Alignment explanation
Indices: 361845--361911 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
361835 AGTAGCTTAA
*
361845 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCAATAC
* ***
361878 ATTGTATCGATACAACATTTTATGTATCAATAC
1 ATTGTATCGATACAAAAAAATATGTATCAATAC
361911 A
1 A
361912 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCAATAC
Found at i:362912 original size:20 final size:20
Alignment explanation
Indices: 362887--362937 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
362877 TATCCAGATA
*
362887 TATCGATACATGTATGAATG
1 TATCGATACATGTATCAATG
* * *
362907 TATCGATACATTTTTCAGTG
1 TATCGATACATGTATCAATG
362927 TATCGATACAT
1 TATCGATACAT
362938 TTTGTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (20 bp):
TATCGATACATGTATCAATG
Found at i:362977 original size:70 final size:70
Alignment explanation
Indices: 362855--362987 Score: 178
Period size: 70 Copynumber: 1.9 Consensus size: 70
362845 GAACAGTACA
* *
362855 TGTATCGATACATTCTGTTTTTTATCCAGATATATCGATACATGTATGAATGTATCGATACATTT
1 TGTATCGATACATTCTGTTTTTTATCCAGATACATCGATACATGTATCAATGTATCGATACATTT
362920 TTCAG
66 TTCAG
* * * * * *
362925 TGTATCGATACATTTTGTTTTTTA-CCTAGATCCATTGATATATTTTTCAATGTATCGATACAT
1 TGTATCGATACATTCTGTTTTTTATCC-AGATACATCGATACATGTATCAATGTATCGATACAT
362988 CTAGTTAGTT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
69 2 0.04
70 52 0.96
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (70 bp):
TGTATCGATACATTCTGTTTTTTATCCAGATACATCGATACATGTATCAATGTATCGATACATTT
TTCAG
Found at i:363528 original size:20 final size:20
Alignment explanation
Indices: 363477--363528 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
363467 TATCCAGATA
* *
363477 TATCGATACATGTATGAATG
1 TATCGATACATTTATCAATG
*
363497 TATCGATACATTTTTCAATG
1 TATCGATACATTTATCAATG
363517 TATCGATACATT
1 TATCGATACATT
363529 CTGTTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTATCAATG
Found at i:363538 original size:70 final size:70
Alignment explanation
Indices: 363444--363577 Score: 205
Period size: 70 Copynumber: 1.9 Consensus size: 70
363434 GGAACAGTAC
* * *
363444 ATGTATCGATACATTCTGTTTTTTATCCAGATATATCGATACATGTATGAATGTATCGATACATT
1 ATGTATCGATACATTCTGTTTTTTACCCAGATACATCGATACATGTATCAATGTATCGATACATT
363509 TTTCA
66 TTTCA
* * * *
363514 ATGTATCGATACATTCTGTTTTTTACCCAGATCCATTGATACATTTTTCAATGTATCGATACAT
1 ATGTATCGATACATTCTGTTTTTTACCCAGATACATCGATACATGTATCAATGTATCGATACAT
363578 CTAGTTAGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 57 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (70 bp):
ATGTATCGATACATTCTGTTTTTTACCCAGATACATCGATACATGTATCAATGTATCGATACATT
TTTCA
Found at i:363929 original size:590 final size:590
Alignment explanation
Indices: 362811--363990 Score: 2288
Period size: 590 Copynumber: 2.0 Consensus size: 590
362801 CTAACGGTCG
362811 AAAATCTTAAATTTTTACAAATTTGTATCGATAGGAACAGTACATGTATCGATACATTCTGTTTT
1 AAAATCTTAAATTTTTACAAATTTGTATCGATAGGAACAGTACATGTATCGATACATTCTGTTTT
* *
362876 TTATCCAGATATATCGATACATGTATGAATGTATCGATACATTTTTCAGTGTATCGATACATTTT
66 TTATCCAGATATATCGATACATGTATGAATGTATCGATACATTTTTCAATGTATCGATACATTCT
* *
362941 GTTTTTTACCTAGATCCATTGATATATTTTTCAATGTATCGATACATCTAGTTAGTTTTGAGCAT
131 GTTTTTTACCCAGATCCATTGATACATTTTTCAATGTATCGATACATCTAGTTAGTTTTGAGCAT
363006 TTCGGGCCATTTTCAACCATGGCTCATGGGATCCAATGTCTGGTTTGAACATGTTTTTCTACACC
196 TTCGGGCCATTTTCAACCATGGCTCATGGGATCCAATGTCTGGTTTGAACATGTTTTTCTACACC
*
363071 TTAAGTAATCAGAATACATGCCAATTATCACAACTCAAGCTCCAAATCAAATTGGAATCCAATGT
261 TTAAATAATCAGAATACATGCCAATTATCACAACTCAAGCTCCAAATCAAATTGGAATCCAATGT
*
363136 GAAGATCAAGTCAAAAAATTAAATTATTACATTTTCATCATTGTATTCTCCTCACTATCACCCTT
326 GAAGATCAAGTCAAAAAAATAAATTATTACATTTTCATCATTGTATTCTCCTCACTATCACCCTT
363201 TAAAGCTGAAGGAGCATTGAATTAGCCATCAACCTATCCCATTATTAGCTGAACAACATCATAAT
391 TAAAGCTGAAGGAGCATTGAATTAGCCATCAACCTATCCCATTATTAGCTGAACAACATCATAAT
363266 GTCACACGTTGTCTGGCAAATTGGTGGAGGGAAATGTCCCAAAACACTTAACCTTTCACCCTAAA
456 GTCACACGTTGTCTGGCAAATTGGTGGAGGGAAATGTCCCAAAACACTTAACCTTTCACCCTAAA
363331 ATTTTGGGTATAAATAGGCCAATTCAATCCAAGCAAAGGATCCTCTCTCTCTGAATCCCTCTTTC
521 ATTTTGGGTATAAATAGGCCAATTCAATCCAAGCAAAGGATCCTCTCTCTCTGAATCCCTCTTTC
363396 AACCA
586 AACCA
363401 AAAATCTTAAATTTTTACAAATTTGTATCGATAGGAACAGTACATGTATCGATACATTCTGTTTT
1 AAAATCTTAAATTTTTACAAATTTGTATCGATAGGAACAGTACATGTATCGATACATTCTGTTTT
363466 TTATCCAGATATATCGATACATGTATGAATGTATCGATACATTTTTCAATGTATCGATACATTCT
66 TTATCCAGATATATCGATACATGTATGAATGTATCGATACATTTTTCAATGTATCGATACATTCT
363531 GTTTTTTACCCAGATCCATTGATACATTTTTCAATGTATCGATACATCTAGTTAGTTTTGAGCAT
131 GTTTTTTACCCAGATCCATTGATACATTTTTCAATGTATCGATACATCTAGTTAGTTTTGAGCAT
363596 TTCGGGCCATTTTCAACCATGGCTCATGGGATCCAATGTCTGGTTTGAACATGTTTTTCTACACC
196 TTCGGGCCATTTTCAACCATGGCTCATGGGATCCAATGTCTGGTTTGAACATGTTTTTCTACACC
363661 TTAAATAATCAGAATACATGCCAATTATCACAACTCAAGCTCCAAATCAAATTGGAATCCAATGT
261 TTAAATAATCAGAATACATGCCAATTATCACAACTCAAGCTCCAAATCAAATTGGAATCCAATGT
363726 GAAGATCAAGTCAAAAAAATAAATTATTACATTTTCATCATTGTATTCTCCTCACTATCACCCTT
326 GAAGATCAAGTCAAAAAAATAAATTATTACATTTTCATCATTGTATTCTCCTCACTATCACCCTT
*
363791 TAAAGCTGAAGGAGCATTGAATTAGCCATTAACCTATCCCATTATTAGCTGAACAACATCATAAT
391 TAAAGCTGAAGGAGCATTGAATTAGCCATCAACCTATCCCATTATTAGCTGAACAACATCATAAT
*
363856 GTCACACGTTGTCTTGCAAATTGGTGGAGGGAAATGTCCCAAAACACTTAACCTTTCACCCTAAA
456 GTCACACGTTGTCTGGCAAATTGGTGGAGGGAAATGTCCCAAAACACTTAACCTTTCACCCTAAA
363921 ATTTTGGGTATAAATAGGCCAATTCAATCCAAGCAAAGGATCCTCTCTCTCTGAATCCCTCTTTC
521 ATTTTGGGTATAAATAGGCCAATTCAATCCAAGCAAAGGATCCTCTCTCTCTGAATCCCTCTTTC
363986 AACCA
586 AACCA
363991 CATTTTCTAG
Statistics
Matches: 582, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
590 582 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.34
Consensus pattern (590 bp):
AAAATCTTAAATTTTTACAAATTTGTATCGATAGGAACAGTACATGTATCGATACATTCTGTTTT
TTATCCAGATATATCGATACATGTATGAATGTATCGATACATTTTTCAATGTATCGATACATTCT
GTTTTTTACCCAGATCCATTGATACATTTTTCAATGTATCGATACATCTAGTTAGTTTTGAGCAT
TTCGGGCCATTTTCAACCATGGCTCATGGGATCCAATGTCTGGTTTGAACATGTTTTTCTACACC
TTAAATAATCAGAATACATGCCAATTATCACAACTCAAGCTCCAAATCAAATTGGAATCCAATGT
GAAGATCAAGTCAAAAAAATAAATTATTACATTTTCATCATTGTATTCTCCTCACTATCACCCTT
TAAAGCTGAAGGAGCATTGAATTAGCCATCAACCTATCCCATTATTAGCTGAACAACATCATAAT
GTCACACGTTGTCTGGCAAATTGGTGGAGGGAAATGTCCCAAAACACTTAACCTTTCACCCTAAA
ATTTTGGGTATAAATAGGCCAATTCAATCCAAGCAAAGGATCCTCTCTCTCTGAATCCCTCTTTC
AACCA
Found at i:365928 original size:101 final size:100
Alignment explanation
Indices: 365784--366005 Score: 311
Period size: 101 Copynumber: 2.2 Consensus size: 100
365774 ACTTCAATCA
* * * *
365784 TATTTCTCCTAGGGGATACTCCAACCTCGTTTTTTAAAACTTGTCAAGATTTAAATCTCATTTTT
1 TATTCCTCCGAGGGGATACTCCAACCTCATTTTTTAAAACTTGTCAAGATTTAAATCTCATTTTC
* * *
365849 ACATTAAATTATCATCATTGGGGATACTCCAACCC
66 ACATTAAATTATCATAATTGAGGACACTCCAACCC
* *
365884 TATTCCTCCGAGGGGATACTCCAACGC-CATCTTTTTAAAACTTGTTAAGATTTAAATCTTATTT
1 TATTCCTCCGAGGGGATACTCCAAC-CTCAT-TTTTTAAAACTTGTCAAGATTTAAATCTCATTT
* *
365948 TCACATTAAATTATCATAATTGAGGACACTCCAGCTC
64 TCACATTAAATTATCATAATTGAGGACACTCCAACCC
*
365985 TATTCCTCCGAGGAGATACTC
1 TATTCCTCCGAGGGGATACTC
366006 GGATTATTTT
Statistics
Matches: 108, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
100 25 0.23
101 83 0.77
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (100 bp):
TATTCCTCCGAGGGGATACTCCAACCTCATTTTTTAAAACTTGTCAAGATTTAAATCTCATTTTC
ACATTAAATTATCATAATTGAGGACACTCCAACCC
Found at i:372969 original size:23 final size:22
Alignment explanation
Indices: 372916--372969 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
372906 AGATGAAAAT
372916 ATTAAGTTTAAAAATAAATTTAA
1 ATTAA-TTTAAAAATAAATTTAA
* *
372939 ATTTATTTAAAAAATAAATTTAC
1 ATTAATTT-AAAAATAAATTTAA
*
372962 CTTAATTT
1 ATTAATTT
372970 CAATATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTAATTTAAAAATAAATTTAA
Found at i:373088 original size:18 final size:18
Alignment explanation
Indices: 373067--373102 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
373057 TATCATGTAA
*
373067 AAAATAAATATATTATAT
1 AAAATAAATATATAATAT
*
373085 AAAATATATATATAATAT
1 AAAATAAATATATAATAT
373103 TATAGTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATAAATATATAATAT
Found at i:373096 original size:13 final size:13
Alignment explanation
Indices: 373072--373113 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
373062 TGTAAAAAAT
373072 AAATATATTATATA
1 AAATATA-TATATA
373086 AAATATATATATA
1 AAATATATATATA
*
373099 ATAT-TATAGTATA
1 AAATATATA-TATA
373112 AA
1 AA
373114 CATTAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.16
13 14 0.56
14 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
AAATATATATATA
Found at i:373522 original size:14 final size:13
Alignment explanation
Indices: 373484--373524 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
373474 TCTTTATCTA
373484 AATTT-ATTTTTT
1 AATTTAATTTTTT
373496 AATTTAATATTTTT
1 AATTTAAT-TTTTT
373510 -ATTTAAATTTTTT
1 AATTT-AATTTTTT
373523 AA
1 AA
373525 ATATTAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.20
13 11 0.44
14 9 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
AATTTAATTTTTT
Found at i:373779 original size:20 final size:20
Alignment explanation
Indices: 373723--373789 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 20
373713 TTTTGTATTT
*
373723 ATATAATTTAATATTTATATTA
1 ATAT-ATTTAATTTTTATA-TA
*
373745 AAATATTATATATTTTTATATA
1 ATATATT-TA-ATTTTTATATA
*
373767 ATATATTTAATTTTTACATA
1 ATATATTTAATTTTTATATA
373787 ATA
1 ATA
373790 AAAATTATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 13 0.33
21 5 0.13
22 13 0.33
23 8 0.21
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATATTTAATTTTTATATA
Found at i:373856 original size:15 final size:15
Alignment explanation
Indices: 373833--373878 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 15
373823 AATAAAAATT
*
373833 ATTATATTTTTAAAA
1 ATTAAATTTTTAAAA
373848 ATTAAA--TTTAAAA
1 ATTAAATTTTTAAAA
*
373861 AATAATATTTTTAAAA
1 ATTAA-ATTTTTAAAA
373877 AT
1 AT
373879 ATTAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 11 0.44
14 1 0.04
15 5 0.20
16 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAAATTTTTAAAA
Found at i:373879 original size:15 final size:15
Alignment explanation
Indices: 373836--373879 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
373826 AAAAATTATT
373836 ATATTTTTAAAAATTA
1 ATATTTTTAAAAA-TA
*
373852 A-A-TTTAAAAAATA
1 ATATTTTTAAAAATA
373865 ATATTTTTAAAAATA
1 ATATTTTTAAAAATA
373880 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 3 0.12
14 9 0.38
15 11 0.46
16 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTTTTAAAAATA
Found at i:373885 original size:24 final size:24
Alignment explanation
Indices: 373851--373907 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 24
373841 TTTAAAAATT
*
373851 AAATTTAAAAAATAATATTTTTA-A
1 AAATTTAAAAAAT-ATAATTTTATA
373875 AAATATTAAAAAATATAATTTTATA
1 AAAT-TTAAAAAATATAATTTTATA
373900 AAATTTAA
1 AAATTTAA
373908 TATATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 16 0.53
25 14 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AAATTTAAAAAATATAATTTTATA
Found at i:382854 original size:42 final size:42
Alignment explanation
Indices: 382803--382896 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 42
382793 GAAGATGATG
*
382803 GTGATGATGACAAAGTTGAGGATGAGAGTGAAGAACACAAAA
1 GTGAAGATGACAAAGTTGAGGATGAGAGTGAAGAACACAAAA
* *
382845 GTGAAGATGACAAAGTTGATGATGAGGGTGAAGAACACAAAA
1 GTGAAGATGACAAAGTTGAGGATGAGAGTGAAGAACACAAAA
382887 GTGAAGATGA
1 GTGAAGATGA
382897 AGAAGATGAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.45, C:0.06, G:0.32, T:0.17
Consensus pattern (42 bp):
GTGAAGATGACAAAGTTGAGGATGAGAGTGAAGAACACAAAA
Found at i:382907 original size:42 final size:42
Alignment explanation
Indices: 382803--382908 Score: 151
Period size: 42 Copynumber: 2.5 Consensus size: 42
382793 GAAGATGATG
* * *
382803 GTGATGATGACAAAGTTGAGGATGAGAGTGAAGAACACAAAA
1 GTGAAGATGACAAAGATGATGATGAGAGTGAAGAACACAAAA
* *
382845 GTGAAGATGACAAAGTTGATGATGAGGGTGAAGAACACAAAA
1 GTGAAGATGACAAAGATGATGATGAGAGTGAAGAACACAAAA
382887 GTGAAGATGA-AGAAGATGATGA
1 GTGAAGATGACA-AAGATGATGA
382909 GGAAAGGGAG
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
41 1 0.02
42 58 0.98
ACGTcount: A:0.45, C:0.06, G:0.32, T:0.17
Consensus pattern (42 bp):
GTGAAGATGACAAAGATGATGATGAGAGTGAAGAACACAAAA
Found at i:395662 original size:18 final size:17
Alignment explanation
Indices: 395639--395681 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
395629 GATACAATAA
395639 ATTATTAATATAAAAAAT
1 ATTATTAATAT-AAAAAT
* *
395657 ATTATTTCATATAACAAT
1 ATTA-TTAATATAAAAAT
395675 ATTATTA
1 ATTATTA
395682 TTTTAATAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.10
18 13 0.62
19 6 0.29
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTATTAATATAAAAAT
Found at i:398295 original size:21 final size:22
Alignment explanation
Indices: 398270--398310 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
398260 TATATAATAT
398270 TATAAT-ATA-AAATTATTTTCA
1 TATAATAATACAAA-TATTTTCA
398291 TATAATAATACAAATATTTT
1 TATAATAATACAAATATTTT
398311 ATGTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 9 0.50
23 3 0.17
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (22 bp):
TATAATAATACAAATATTTTCA
Found at i:398800 original size:24 final size:23
Alignment explanation
Indices: 398773--398841 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 23
398763 TTTGAAACTA
*
398773 TTTTATTAAGAATTTCTAAATTTT
1 TTTTATTAA-AATTTCCAAATTTT
*
398797 TTTTGTTTAAAATTTCCAAATTTT
1 TTTT-ATTAAAATTTCCAAATTTT
398821 TATTTATCTAAAATATTCCAA
1 T-TTTAT-TAAAAT-TTCCAA
398842 GCACATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
24 19 0.50
25 13 0.34
26 6 0.16
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.54
Consensus pattern (23 bp):
TTTTATTAAAATTTCCAAATTTT
Found at i:398821 original size:25 final size:24
Alignment explanation
Indices: 398774--398841 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 24
398764 TTGAAACTAT
* *
398774 TTTA-TTAAGAATTTCTAAATTTTT
1 TTTATTTAA-AATTTCCAAATTTTA
*
398798 TTTGTTTAAAATTTCCAAATTTTTA
1 TTTATTTAAAATTTCCAAA-TTTTA
*
398823 TTTATCTAAAATATTCCAA
1 TTTATTTAAAAT-TTCCAA
398842 GCACATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 12 0.33
25 18 0.50
26 6 0.17
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (24 bp):
TTTATTTAAAATTTCCAAATTTTA
Found at i:400120 original size:13 final size:13
Alignment explanation
Indices: 400099--400141 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
400089 AATTTTTTAA
*
400099 AAATAATTATA-T
1 AAATAATTAAATT
400111 AAATTAATTAAATT
1 AAA-TAATTAAATT
*
400125 AAATAATTAATTT
1 AAATAATTAAATT
400138 AAAT
1 AAAT
400142 TTTGTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 3 0.11
13 20 0.74
14 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATAATTAAATT
Found at i:401879 original size:29 final size:30
Alignment explanation
Indices: 401844--401909 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
401834 TATAGTTAAA
** *
401844 TATTAAATTTTATTATTATATTTTAA-ATT
1 TATTAAATTTTACCATTATATTCTAATATT
*
401873 TATTAAATTTTACCATTATATTCTAATTTT
1 TATTAAATTTTACCATTATATTCTAATATT
401903 TATTAAA
1 TATTAAA
401910 AAAAAATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.58
Consensus pattern (30 bp):
TATTAAATTTTACCATTATATTCTAATATT
Found at i:403328 original size:19 final size:17
Alignment explanation
Indices: 403304--403345 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
403294 TTAGCTTATT
403304 ATTTTTTTAAAACAAAATA
1 ATTTTTTT-AAA-AAAATA
403323 ATTTTTTTAAAAAAATA
1 ATTTTTTTAAAAAAATA
403340 ATTTTT
1 ATTTTT
403346 ATCCATGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 12 0.52
18 3 0.13
19 8 0.35
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTTTTAAAAAAATA
Found at i:403674 original size:5 final size:5
Alignment explanation
Indices: 403666--403783 Score: 54
Period size: 5 Copynumber: 24.4 Consensus size: 5
403656 ATTTAATAAT
* **
403666 TTATA TTATA TT-TA TT-TA TTTTA TTATA TTATAA TTATA TT-TA AAATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA
* * * * *
403714 TT-T- TTAT- TTATA TAAATT TTAAAA ATATAA ATATA TTATA TTATA
1 TTATA TTATA TTATA T-TATA TT-ATA TTAT-A TTATA TTATA TTATA
* *
403759 TTTTA AT-TA TTATA -TATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TT
403784 TAAATAATTA
Statistics
Matches: 87, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
3 2 0.02
4 23 0.26
5 47 0.54
6 15 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:403720 original size:28 final size:27
Alignment explanation
Indices: 403666--403783 Score: 89
Period size: 28 Copynumber: 4.3 Consensus size: 27
403656 ATTTAATAAT
**
403666 TTATATTATATTT-ATTTATTTTATTATA
1 TTATATTATATTTAAAATA-TTTA-TATA
*
403694 TTATAATTATATTTAAAATATTTTTAT-
1 TTAT-ATTATATTTAAAATATTTATATA
* **
403721 TTATA-TAAATTTTAAAAATATAAATATA
1 TTATATTATA-TTT-AAAATATTTATATA
* *
403749 TTATATTATATTTTAATTATTATATATA
1 TTATATTATATTTAAAATATT-TATATA
403777 TTATATT
1 TTATATT
403784 TAAATAATTA
Statistics
Matches: 71, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
25 3 0.04
26 4 0.06
27 19 0.27
28 27 0.38
29 15 0.21
30 3 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTATATTATATTTAAAATATTTATATA
Found at i:403779 original size:23 final size:23
Alignment explanation
Indices: 403740--403797 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
403730 TTTTAAAAAT
* *
403740 ATAAATATATTATATTATATTTTA
1 ATAATTATA-TATATTATATTTAA
*
403764 ATTATTATATATATTATATTTAA
1 ATAATTATATATATTATATTTAA
403787 ATAATTATATA
1 ATAATTATATA
403798 AAATAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 23 0.77
24 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATAATTATATATATTATATTTAA
Found at i:405873 original size:25 final size:22
Alignment explanation
Indices: 405846--405897 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 22
405836 AAGTTAGGTA
*
405846 AAAAAGAAAGAAAGAATAAAGAAGA
1 AAAAAG-AA-AAAGAA-AAAAAAGA
405871 AAAAAGAAAAAGAAAAAAAAGA
1 AAAAAGAAAAAGAAAAAAAAGA
405893 AAAAA
1 AAAAA
405898 ATATGAAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 12 0.46
23 6 0.23
24 2 0.08
25 6 0.23
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (22 bp):
AAAAAGAAAAAGAAAAAAAAGA
Found at i:405877 original size:7 final size:7
Alignment explanation
Indices: 405845--405897 Score: 52
Period size: 7 Copynumber: 6.9 Consensus size: 7
405835 AAAGTTAGGT
405845 AAAAAAG
1 AAAAAAG
405852 AAAGAAAG
1 AAA-AAAG
405860 AATAAAGAAG
1 -A-AAA-AAG
405870 AAAAAAG
1 AAAAAAG
*
405877 AAAAAGAA
1 AAAAA-AG
405885 AAAAAAG
1 AAAAAAG
405892 AAAAAA
1 AAAAAA
405898 ATATGAAGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 18 0.46
8 13 0.33
9 3 0.08
10 5 0.13
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:405890 original size:15 final size:15
Alignment explanation
Indices: 405846--405896 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
405836 AAGTTAGGTA
*
405846 AAAAAG-AAAGAAAG
1 AAAAAGAAAAAAAAG
405860 AATAAAGAAGAAAAAAG
1 AA-AAAGAA-AAAAAAG
405877 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
405892 AAAAA
1 AAAAA
405897 AATATGAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
14 2 0.06
15 16 0.48
16 7 0.21
17 8 0.24
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:405898 original size:25 final size:25
Alignment explanation
Indices: 405845--405898 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
405835 AAAGTTAGGT
405845 AAAAAAGAAAGAAAGAATAAAGAAGA
1 AAAAAAGAAAGAAAGAATAAAGAA-A
*
405871 AAAAAGAAAAAGAAA-AA-AAAGAAA
1 AAAAA-AGAAAGAAAGAATAAAGAAA
405895 AAAA
1 AAAA
405899 TATGAAGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 5 0.19
25 6 0.23
26 7 0.27
27 8 0.31
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (25 bp):
AAAAAAGAAAGAAAGAATAAAGAAA
Found at i:413661 original size:27 final size:27
Alignment explanation
Indices: 413626--414384 Score: 1169
Period size: 28 Copynumber: 27.6 Consensus size: 27
413616 CCTGTGACCT
* * * *
413626 CTTTAAAGTCCATAAGTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
413653 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
413680 CTTTTAAAGTCCACAACTCCGTGGCACT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
413708 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
413736 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
413764 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
413791 CTTTTAAGTCCATAACTCCGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
413818 CTTTTGAAGTCTACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
413846 CTTTTGAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
413874 CTTTTAAGTCCATAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
413901 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * *
413929 CTTTTAAGTCCATAACTCTGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
413956 CTTTTAAGTCCACAACTCTGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
413984 CTTTTAAGTCCACAACTCCGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
414011 TTTTTAAGT-CACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
414037 CTTTTAAGTCCATAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
414064 CTTTTAAAGTCCACAGCTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
414092 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
414119 CTTTTGAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
414147 CTTTTGAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
414175 CTTTTGAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
414203 CTTTTAAGTCCACAACTCCGTGACACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
414230 CTTTTAAGTCCACAACTCTGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
414258 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
414285 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
414313 CTTTTGAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
414341 CTTTTAAAGTCCACAACTCCGTTGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
414369 CTTTTTAAGTGCACAA
1 C-TTTTAAGTCCACAA
414385 GGCGATGGCA
Statistics
Matches: 684, Mismatches: 37, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
26 24 0.04
27 277 0.40
28 359 0.52
29 24 0.04
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.28
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:413712 original size:55 final size:54
Alignment explanation
Indices: 413626--414384 Score: 1169
Period size: 55 Copynumber: 13.8 Consensus size: 54
413616 CCTGTGACCT
* * * *
413626 CTTTAAAGTCCATAAGTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
*
413680 CTTTTAAAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACC
413736 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
413791 CTTTTAAGTCCATAACTCCGTAGCACCCTTTTGAAGTCTACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACC
*
413846 CTTTTGAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
413901 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCATAACTCTGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
* *
413956 CTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGTCCACAACTCCGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
* *
414011 TTTTTAAGT-CACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
*
414064 CTTTTAAAGTCCACAGCTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
414119 CTTTTGAAGTCCACAACTCCGTGGCACCCTTTTGAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACC
* *
414175 CTTTTGAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGACACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
*
414230 CTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
414285 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTGAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTT-AAGTCCACAACTCCGTGGCACC
* *
414341 CTTTTAAAGTCCACAACTCCGTTGCACCCTTTTTAAGTGCACAA
1 CTTTT-AAGTCCACAACTCCGTGGCACCC-TTTTAAGTCCACAA
414385 GGCGATGGCA
Statistics
Matches: 658, Mismatches: 35, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
53 31 0.05
54 87 0.13
55 345 0.52
56 172 0.26
57 23 0.03
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.28
Consensus pattern (54 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:414540 original size:94 final size:95
Alignment explanation
Indices: 414419--414877 Score: 558
Period size: 94 Copynumber: 4.9 Consensus size: 95
414409 CTACAAGTTA
*
414419 GTGGCACCTTTTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTTAAAGCCCACACAAGTCGGT
1 GTGGCACCTATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTTAAAGCCCACACAAGTCGGT
*
414484 GGCAACCCTTTTTAAAGCCCACACAAGTCG
66 GGCAACCCTTTTCAAAGCCCACACAAGTCG
* *
414514 GTGGCA-CTATTTCAAAGCCCACACAAGTCGGTGGCAACCTATTTTAAAGCCCACACAAGTCAGT
1 GTGGCACCTATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTTAAAGCCCACACAAGTCGGT
414578 GGCAACCCTTTTCAAAGCCCACACAAGTCG
66 GGCAACCCTTTTCAAAGCCCACACAAGTCG
* * * *
414608 GTTGCAACCCT-TTTCAAAGCCCACACAAGTCGGTGGC-A-CTATTTCAAAGCCAACACAAGTCG
1 GTGGC-A-CCTATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTTAAAGCCCACACAAGTCG
*
414670 GTGGC-A--CTATTTCAAAGCCAACACAAGTCG
64 GTGGCAACCCT-TTTCAAAGCCCACACAAGTCG
* * * *
414700 GTGGTAACCCATTTCAAAGCCCACACAAGTCGGTGGCAATCCATTTCAAAGCCCACACAAGTCGG
1 GTGG-CACCTATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTTAAAGCCCACACAAGTCGG
* *
414765 TGGCAACCATTTTCAAAGCCCACACAAGTTG
65 TGGCAACCCTTTTCAAAGCCCACACAAGTCG
* * * * * ** * * *
414796 ATGGGAATCTCTTTCAAAAGTCCACAC-TTTCGGTGGAAACCC-TTTTAAAAACCCACGCAAGTC
1 GT-GGCACCTATTTC-AAAGCCCACACAAGTCGGTGGCAACCCATTTT-AAAGCCCACACAAGTC
*
414859 AGTGGCAACCCTTTTCAAA
63 GGTGGCAACCCTTTTCAAA
414878 TCACCATTTT
Statistics
Matches: 319, Mismatches: 31, Indels: 27
0.85 0.08 0.07
Matches are distributed among these distances:
91 4 0.01
92 50 0.16
93 2 0.01
94 141 0.44
95 12 0.04
96 95 0.30
97 15 0.05
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (95 bp):
GTGGCACCTATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTTAAAGCCCACACAAGTCGGT
GGCAACCCTTTTCAAAGCCCACACAAGTCG
Found at i:414811 original size:32 final size:32
Alignment explanation
Indices: 414429--414877 Score: 497
Period size: 32 Copynumber: 14.2 Consensus size: 32
414419 GTGGCACCTT
*
414429 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* * *
414461 TTTTAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
*
414493 TTTTAAAGCCCACACAAGTCGGTGGC-ACT-A
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
414523 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CTA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTC-A
* * * *
414555 TTTTAAAGCCCACACAAGTCAGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* * *
414587 TTTCAAAGCCCACACAAGTCGGTTGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
414619 TTTCAAAGCCCACACAAGTCGGTGGC-ACT-A
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
*
414649 TTTCAAAGCCAACACAAGTCGGTGGC-ACT-A
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* * *
414679 TTTCAAAGCCAACACAAGTCGGTGGTAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
414711 TTTCAAAGCCCACACAAGTCGGTGGCAA-TCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACT-CA
414743 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
* * *
414774 TTTTCAAAGCCCACACAAGTTGATGGGAATCTC-
1 -TTTCAAAGCCCACACAAGTCGGTGGCAA-CTCA
* ** * * *
414807 TTTCAAAAGTCCACAC-TTTCGGTGGAAACCCT
1 TTTC-AAAGCCCACACAAGTCGGTGGCAACTCA
* * * * * *
414839 TTTAAAAACCCACGCAAGTCAGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
414871 TTTCAAA
1 TTTCAAA
414878 TCACCATTTT
Statistics
Matches: 364, Mismatches: 39, Indels: 28
0.84 0.09 0.06
Matches are distributed among these distances:
30 79 0.22
31 20 0.05
32 252 0.69
33 12 0.03
34 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
Found at i:415991 original size:17 final size:15
Alignment explanation
Indices: 415971--416020 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
415961 TTAGGTAAAA
415971 AAGAAAGAAAGAAGATG
1 AAGAAAGAAAGAA-A-G
415988 AAG-AAGAAAGAAAG
1 AAGAAAGAAAGAAAG
*
416002 AA-AAAGAAA-AAAA
1 AAGAAAGAAAGAAAG
416015 AAGAAA
1 AAGAAA
416021 AAAATATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.17
14 12 0.40
15 1 0.03
16 9 0.30
17 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Found at i:416009 original size:10 final size:10
Alignment explanation
Indices: 415968--416024 Score: 62
Period size: 10 Copynumber: 5.4 Consensus size: 10
415958 AAGTTAGGTA
415968 AAAAAGAAAG
1 AAAAAGAAAG
415978 AAAGAAGATGAAG
1 AAA-AAGA--AAG
415991 AAGAAAGAAAG
1 AA-AAAGAAAG
*
416002 AAAAAGAAAA
1 AAAAAGAAAG
416012 AAAAAGAAA-
1 AAAAAGAAAG
416021 AAAA
1 AAAA
416025 TATGAAATGG
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
9 4 0.10
10 19 0.45
11 9 0.21
13 9 0.21
14 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:419907 original size:23 final size:22
Alignment explanation
Indices: 419881--419980 Score: 66
Period size: 23 Copynumber: 4.3 Consensus size: 22
419871 ATATGATGTA
419881 AATATAAAAAATAATTAAAATAT
1 AATATAAAAAATAA-TAAAATAT
419904 AATATAAAATAA-AA-AATAATATT
1 AATATAAAA-AATAATAA-AATA-T
419927 AATATAATATAAAT-ATATAAATAT
1 AATATAA-A-AAATAATA-AAATAT
*
419951 -AT-TAAAAAATATATAATATATT
1 AATATAAAAAATA-ATAAAATA-T
419973 AAATATAA
1 -AATATAA
419981 TTATCATATA
Statistics
Matches: 62, Mismatches: 1, Indels: 26
0.70 0.01 0.29
Matches are distributed among these distances:
20 4 0.06
21 7 0.11
22 11 0.18
23 21 0.34
24 9 0.15
25 9 0.15
26 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AATATAAAAAATAATAAAATAT
Found at i:419930 original size:28 final size:28
Alignment explanation
Indices: 419879--419968 Score: 89
Period size: 28 Copynumber: 3.2 Consensus size: 28
419869 TGATATGATG
*
419879 TAAATATAAAAAATAAT-TAAAATATAATA
1 TAAA-ATAAAAAATAATAT-TAATATAATA
419908 TAAAATAAAAAATAATATTAATATAATA
1 TAAAATAAAAAATAATATTAATATAATA
* *
419936 T-AAATATATAAAT-ATATTAA-AAAATA
1 TAAAATA-AAAAATAATATTAATATAATA
*
419962 TATAATA
1 TAAAATA
419969 TATTAAATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
26 6 0.11
27 16 0.30
28 27 0.50
29 5 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (28 bp):
TAAAATAAAAAATAATATTAATATAATA
Found at i:419935 original size:11 final size:11
Alignment explanation
Indices: 419879--420009 Score: 65
Period size: 11 Copynumber: 12.9 Consensus size: 11
419869 TGATATGATG
419879 TAAATATAA-A
1 TAAATATAATA
*
419889 -AAATA-ATTA
1 TAAATATAATA
419898 -AAATATAATA
1 TAAATATAATA
419908 TAAA-AT-A-A
1 TAAATATAATA
419916 -AAA-ATAATA
1 TAAATATAATA
*
419925 TTAATATAATA
1 TAAATATAATA
419936 T-AA-AT-ATA
1 TAAATATAATA
*
419944 TAAATATATTA
1 TAAATATAATA
*
419955 -AAAAAT-ATA
1 TAAATATAATA
419964 TAATATATTAAATA
1 TAA-ATA-T-AATA
* *
419978 TAATTATCATA
1 TAAATATAATA
* *
419989 TAAAAATAAAA
1 TAAATATAATA
420000 TAAATATAAT
1 TAAATATAAT
420010 TCACCTTAAT
Statistics
Matches: 91, Mismatches: 15, Indels: 29
0.67 0.11 0.21
Matches are distributed among these distances:
7 5 0.05
8 7 0.08
9 19 0.21
10 18 0.20
11 32 0.35
12 2 0.02
13 2 0.02
14 6 0.07
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAATATAATA
Found at i:419968 original size:19 final size:19
Alignment explanation
Indices: 419913--419975 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 19
419903 TAATATAAAA
*
419913 TAAAAAATAATATTAATATAA
1 TAAAAAAT-ATA-TAATATAT
*
419934 T-ATAAATATATAAATATAT
1 TAAAAAATATAT-AATATAT
419953 TAAAAAATATATAATATAT
1 TAAAAAATATATAATATAT
419972 TAAA
1 TAAA
419976 TATAATTATC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.03
19 21 0.57
20 14 0.38
21 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAAAATATATAATATAT
Found at i:419990 original size:47 final size:47
Alignment explanation
Indices: 419881--420003 Score: 119
Period size: 47 Copynumber: 2.6 Consensus size: 47
419871 ATATGATGTA
* *
419881 AATATAA-A-AAATAATTAAAATATAATATAAAATAAAAAATAATATT
1 AATATAATATAAAT-ATAAAAATATAATAAAAAATAAAAAATAATATT
* * * *
419927 AATATAATATAAATATATAAATATATTAAAAAATATATAAT-ATATT
1 AATATAATATAAATATAAAAATATAATAAAAAATAAAAAATAATATT
* *
419973 AAATATAAT-TATCATATAAAAATAAAATAAA
1 -AATATAATATA-AATATAAAAATATAATAAA
420004 TATAATTCAC
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
46 14 0.22
47 45 0.71
48 4 0.06
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (47 bp):
AATATAATATAAATATAAAAATATAATAAAAAATAAAAAATAATATT
Found at i:419999 original size:42 final size:39
Alignment explanation
Indices: 419898--420010 Score: 99
Period size: 42 Copynumber: 2.7 Consensus size: 39
419888 AAAATAATTA
419898 AAATATAATATAAAATAAAAAATA-AT-ATTAATATAATAT
1 AAATAT-ATA-AAAATAAAAAATATATAATTAATATAATAT
*
419937 AAATATATAAATATATTAAAAAATATATAATATATTA-AATAT
1 AAATATATAAA-A-A-TAAAAAATATATAAT-TAATATAATAT
419979 AATTATCATATAAAAATAAAATAA-ATATAATT
1 AA--AT-ATATAAAAATAAAA-AATATATAATT
420011 CACCTTAATT
Statistics
Matches: 63, Mismatches: 1, Indels: 18
0.77 0.01 0.22
Matches are distributed among these distances:
37 2 0.03
38 4 0.06
39 7 0.11
40 9 0.14
41 3 0.05
42 21 0.33
43 7 0.11
44 3 0.05
45 7 0.11
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (39 bp):
AAATATATAAAAATAAAAAATATATAATTAATATAATAT
Found at i:420251 original size:3 final size:3
Alignment explanation
Indices: 420243--420283 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
420233 GTTTCACATG
420243 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
420284 TGTTAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:420712 original size:2 final size:2
Alignment explanation
Indices: 420705--420733 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
420695 ATCAATGCTT
420705 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
420734 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:420738 original size:2 final size:2
Alignment explanation
Indices: 420733--420760 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
420723 TCTCTCTCTC
420733 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
420761 AAGCTGTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:420867 original size:18 final size:17
Alignment explanation
Indices: 420829--420875 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
420819 ATATTTTTAT
*
420829 TTTTATAGT-ATTATGA
1 TTTTATATTAATTATGA
*
420845 ATTTATATTAATTATTGA
1 TTTTATATTAATTA-TGA
*
420863 TTTTATATAAATT
1 TTTTATATTAATT
420876 TTAATATGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 7 0.28
17 4 0.16
18 14 0.56
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
TTTTATATTAATTATGA
Found at i:423376 original size:42 final size:42
Alignment explanation
Indices: 423314--423398 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
423304 AGCTGAAGAA
*
423314 ATATATATATATTTAGATATACAAAAATAATATATATTTTTT
1 ATATATATATATTTAGATATACAAAAATAATATATATATTTT
* * * *
423356 ATATATTTATATTTATATATACAAAAGTTATATATATATTTT
1 ATATATATATATTTAGATATACAAAAATAATATATATATTTT
423398 A
1 A
423399 AGTTATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (42 bp):
ATATATATATATTTAGATATACAAAAATAATATATATATTTT
Found at i:423416 original size:42 final size:42
Alignment explanation
Indices: 423330--423416 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
423320 ATATATTTAG
* * *
423330 ATATACAAAAATAATATATATTTTTTATATATTTATATTTAT
1 ATATACAAAAATAATATATATTTTTAATATATTTATAATAAT
* *
423372 ATATACAAAAGTTATATATATATTTTAAGT-TATTTA-AATAAT
1 ATATACAAAAATAATATATAT-TTTTAA-TATATTTATAATAAT
423414 ATA
1 ATA
423417 AAAATTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
42 26 0.68
43 11 0.29
44 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (42 bp):
ATATACAAAAATAATATATATTTTTAATATATTTATAATAAT
Found at i:431042 original size:13 final size:13
Alignment explanation
Indices: 431024--431056 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
431014 TTTAGATTAT
431024 TTGTCTTGGAATG
1 TTGTCTTGGAATG
431037 TTGTCTTGGAATG
1 TTGTCTTGGAATG
431050 TTGTCTT
1 TTGTCTT
431057 CCCACATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.09, G:0.27, T:0.52
Consensus pattern (13 bp):
TTGTCTTGGAATG
Found at i:433418 original size:27 final size:27
Alignment explanation
Indices: 433380--433449 Score: 140
Period size: 27 Copynumber: 2.6 Consensus size: 27
433370 GTTAAAAGCG
433380 GGGTTGGAGTATCCCCTCGGAAGAATA
1 GGGTTGGAGTATCCCCTCGGAAGAATA
433407 GGGTTGGAGTATCCCCTCGGAAGAATA
1 GGGTTGGAGTATCCCCTCGGAAGAATA
433434 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
433450 GATAAATAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCTCGGAAGAATA
Found at i:434448 original size:18 final size:20
Alignment explanation
Indices: 434411--434449 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
434401 GCACAAACCT
434411 TTTTTTTAAAACAAAGATCA
1 TTTTTTTAAAACAAAGATCA
434431 TTTTTTTAAAA-AAA-ATCA
1 TTTTTTTAAAACAAAGATCA
434449 T
1 T
434450 AAATTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 3 0.16
20 11 0.58
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (20 bp):
TTTTTTTAAAACAAAGATCA
Found at i:434598 original size:2 final size:2
Alignment explanation
Indices: 434593--434621 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
434583 GAGATTTTCA
434593 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
434622 CCTATAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:435243 original size:17 final size:16
Alignment explanation
Indices: 435206--435254 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 16
435196 ATTTCATATG
435206 TTTT-TTCCTTTTTT-
1 TTTTCTTCCTTTTTTC
435220 TTTTCTTCCTTTTTTC
1 TTTTCTTCCTTTTTTC
435236 TTTATCTT-CTTTCTTTC
1 TTT-TCTTCCTTT-TTTC
435253 TT
1 TT
435255 ACCTAACCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.13
15 10 0.32
16 7 0.23
17 10 0.32
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTCTTCCTTTTTTC
Found at i:435342 original size:204 final size:204
Alignment explanation
Indices: 434992--435395 Score: 612
Period size: 204 Copynumber: 2.0 Consensus size: 204
434982 AGGCCACTCT
*
434992 ATTTCATATGTTTTTTTCTTTTTTTTTTCTTCCTTTCTTCTTCATCTTCTGTCTTTCTTACCTAA
1 ATTTCATATGTTTTTTCCTTTTTTTTTTCTTCCTTTCTTCTTCATCTTCTGTCTTTCTTACCTAA
*
435057 ACAGGAAAGCAATCCAAAATCCAATGACCGGCCACCACGTCAGGCACTAGCAACCACCATCCGCC
66 ACAAGAAAGCAATCCAAAATCCAATGACCGGCCACCACGTCAGGCACTAGCAACCACCATCCGCC
* * * *
435122 ACCGCTCGCCGGTGGCCATTGGCTTCCAAATTTCATTTTTAGACTTTTTTCGATCTCCTCTTTTC
131 ACCGCTCGCCGGTGGCCATTGGCTCCCAAATTTCACTTTTAGACTCTTTTCGACCTCCTCTTTTC
435187 AAATCCTTC
196 AAATCCTTC
* * *
435196 ATTTCATATGTTTTTTCCTTTTTTTTTTCTTCCTTTTTTCTTTATCTTCTTTCTTTCTTACCTAA
1 ATTTCATATGTTTTTTCCTTTTTTTTTTCTTCCTTTCTTCTTCATCTTCTGTCTTTCTTACCTAA
* * * * * * * **
435261 CCAAGAAAGTAATCCAAAATCCGATGATCGGCCACCATGTC-GGTCACTTGCAACCACCGTTTGC
66 ACAAGAAAGCAATCCAAAATCCAATGACCGGCCACCACGTCAGG-CACTAGCAACCACCATCCGC
* *
435325 CACCGCTCGTCGGTGGCCGTTGGCTCCCAAATTTCACTTTTAGACTCTTTTCGACCTCCTCTTTT
130 CACCGCTCGCCGGTGGCCATTGGCTCCCAAATTTCACTTTTAGACTCTTTTCGACCTCCTCTTTT
435390 CAAATC
195 CAAATC
435396 TGGAGTCAGA
Statistics
Matches: 179, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
203 2 0.01
204 177 0.99
ACGTcount: A:0.20, C:0.29, G:0.12, T:0.40
Consensus pattern (204 bp):
ATTTCATATGTTTTTTCCTTTTTTTTTTCTTCCTTTCTTCTTCATCTTCTGTCTTTCTTACCTAA
ACAAGAAAGCAATCCAAAATCCAATGACCGGCCACCACGTCAGGCACTAGCAACCACCATCCGCC
ACCGCTCGCCGGTGGCCATTGGCTCCCAAATTTCACTTTTAGACTCTTTTCGACCTCCTCTTTTC
AAATCCTTC
Found at i:436331 original size:52 final size:52
Alignment explanation
Indices: 436260--436373 Score: 219
Period size: 52 Copynumber: 2.2 Consensus size: 52
436250 CCGTGTGCAG
*
436260 ATTCAAGGCCTGCAATACTAGACTTAAAGATGAGAGGACTGCCAATGTGCCA
1 ATTCAAGGCCTGCAATACTAGACTTAAAGATGAGAGGACTACCAATGTGCCA
436312 ATTCAAGGCCTGCAATACTAGACTTAAAGATGAGAGGACTACCAATGTGCCA
1 ATTCAAGGCCTGCAATACTAGACTTAAAGATGAGAGGACTACCAATGTGCCA
436364 ATTCAAGGCC
1 ATTCAAGGCC
436374 AACGACATTG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (52 bp):
ATTCAAGGCCTGCAATACTAGACTTAAAGATGAGAGGACTACCAATGTGCCA
Found at i:436687 original size:28 final size:28
Alignment explanation
Indices: 436593--437518 Score: 488
Period size: 28 Copynumber: 32.2 Consensus size: 28
436583 CACCGACTTA
*
436593 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
** *
436621 TGCAGGCTTTGAAAAAAGAGTTGCCACTGACTT
1 TGTGGGCTTTG---AAAG-GATGCCACTGAC-T
* *
436654 ATGTGGGCTTTGAAAGAATGTCACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
436683 TGTGGGCTTTGGAAAGGATGCCACTGACT
1 TGTGGGCTTT-GAAAGGATGCCACTGACT
*
436712 TGTAGGCTTTTGAAAGGATGCCACTGACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
* **
436741 TGTGGGCTTTGAAAAGATATCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
436769 TGTGGGCTTTGAAA-AAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
436797 TGTGGGCTTTGAAAAGGTATGCCACTGACT
1 TGTGGGCTTTG-AAAGG-ATGCCACTGACT
* * *
436827 TGTGGACTTTGAAATGATGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
436855 TGTGGGCTTTAAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
436883 TATAGGCTTTGAAATGGGTTGCCACCGACT
1 TGTGGGCTTTGAAA--GGATGCCACTGACT
* *
436913 TGAGTGAGCTTTGAAATGGGTTGCCACTGACTT
1 T--GTGGGCTTTGAAA--GGATGCCACTGAC-T
* **
436946 GTGTGGGCTTTGAAATGGGTTGCCACCAACTT
1 -TGTGGGCTTTGAAA--GGATGCCACTGAC-T
* * * **
436978 GTGTGGGCTTTCAAATAAGTTGCCACCAACT
1 -TGTGGGCTTT-GAA-AGGATGCCACTGACT
* * * *
437009 TGTGTGGACTTTCAAATAAGTTGCCACCGACTT
1 TGTG-GG-CTTT-GAA-AGGATGCCACTGAC-T
*
437042 GTGTGGGCTTTGAAATGAGTTGCCA-TCGACT
1 -TGTGGGCTTTGAAA-G-GATGCCACT-GACT
* *
437073 TGTGGTCTTTGAAATGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
437101 TGTGGGCTTTAAAATGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
437129 TGTGGGCTTTAAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
437157 TGTGGGCTTTAAAATGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
437185 TGTGAGAC-TTAAAAGGGTGCCAC-GAGT
1 TGTG-GGCTTTGAAAGGATGCCACTGACT
* * * * ** *
437212 TGTGGAC-TTAAAAGGGTACCACAAAAT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
** * * * *
437239 TGTGGATTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
437267 TGTGGAC-TTAAAAAGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * *
437294 TGTGGAC-TTAAAAAGATGTCACAGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
437321 TGTGGACTTTAAAAGGGTGCCA-TGGAGT
1 TGTGGGCTTTGAAAGGATGCCACT-GACT
* * * * *
437349 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * *
437377 TGTGGAC-TTAAAAGGGTACCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * *
437404 AGTGGAC-TTAAAAGGATGCTACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
437431 TATGGAC-TTAAAAGGATGCCACAGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * *
437458 TATGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
437486 TGTGGACTTTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
437514 TGTGG
1 TGTGG
437519 ACTTAAAAGG
Statistics
Matches: 773, Mismatches: 90, Indels: 70
0.83 0.10 0.08
Matches are distributed among these distances:
26 17 0.02
27 137 0.18
28 341 0.44
29 57 0.07
30 63 0.08
31 15 0.02
32 121 0.16
33 7 0.01
34 15 0.02
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:436771 original size:86 final size:84
Alignment explanation
Indices: 436567--437188 Score: 489
Period size: 86 Copynumber: 7.0 Consensus size: 84
436557 CTTATGTAGT
* * *
436567 CTTTGAAAAGAGTTGCCACCGACTTATGTGGGCTTTGAAAGGGTGCCACTGACTTGCAGGCTTTG
1 CTTTGAAAAGA--TGCCACTGAC-T-TGTGGGCTTTGAAAGGATGCCACTGACTTGTAGGCTTTG
*
436632 AAAAAAGAGTTGCCACTGACTTATGTGGG
62 ---AAAG-GATGCCACTGAC-T-TGTGGG
*
436661 CTTTG-AAAGAATGTCACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACTTGTAGGCTTTTGA
1 CTTTGAAAAG-ATGCCACTGACTTGTGGGCTTT-GAAAGGATGCCACTGACTTGTAGGC-TTTGA
436725 AAGGATGCCACTGACTTGTGGG
63 AAGGATGCCACTGACTTGTGGG
** * *
436747 CTTTGAAAAGATATCACTGACTTGTGGGCTTTGAAA-AAGTGCCACTGACTTGTGGGCTTTGAAA
1 CTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTAGGCTTTG-AA
*
436811 AGGTATGCCACTGACTTGTGGA
64 AGG-ATGCCACTGACTTGTGGG
* * * * *
436833 CTTTGAAATGATGCCATTGACTTGTGGGCTTTAAAAGGATGCCACTAACTTATAGGCTTTGAAAT
1 CTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTAGGCTTTGAAA-
* * *
436898 GGGTTGCCACCGACTTGAGTGAG
65 -GGATGCCACTGACTT--GTGGG
* * * ** *
436921 CTTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGC
1 CTTTGAAA--AGATGCCACTGAC-T-TGTGGGCTTTGAAA--GGATGCCACTGAC-T-TGTAGGC
* * * **
436986 TTTCAAATAAGTTGCCACCAACTTGTGTGG
58 TTT-GAA-AGGATGCCACTGACTTGTG-GG
* * * *
437016 ACTTTCAAATAAGTTGCCACCGACTTGTGTGGGCTTTGAAATGAGTTGCCA-TCGACTTGT-GGT
1 -CTTT-GAA-AAGATGCCACTGAC-T-TGTGGGCTTTGAAA-G-GATGCCACT-GACTTGTAGG-
*
437079 CTTTGAAATGATGCCACTGACTTGTGGG
57 CTTTGAAAGGATGCCACTGACTTGTGGG
* * *
437107 CTTT-AAAATGATGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTAAAA
1 CTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTAGGCTTTGAAA
* *
437171 TGATGCCACTAACTTGTG
65 GGATGCCACTGACTTGTG
437189 AGACTTAAAA
Statistics
Matches: 445, Mismatches: 51, Indels: 74
0.78 0.09 0.13
Matches are distributed among these distances:
84 42 0.09
85 33 0.07
86 123 0.28
87 11 0.02
88 34 0.08
89 4 0.01
90 24 0.05
91 27 0.06
92 40 0.09
93 8 0.02
94 27 0.06
95 4 0.01
96 62 0.14
97 4 0.01
98 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (84 bp):
CTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTAGGCTTTGAAAG
GATGCCACTGACTTGTGGG
Found at i:437003 original size:96 final size:96
Alignment explanation
Indices: 436900--437076 Score: 257
Period size: 96 Copynumber: 1.8 Consensus size: 96
436890 TTTGAAATGG
* * ** * *
436900 GTTGCCACCGACTTGAGT-GAGCTTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGAAATGG
1 GTTGCCACCAACTTGAGTGGA-CTTTCAAATAAGTTGCCACCGACTTGTGTGGGCTTTGAAATGA
436964 GTTGCCACCAACTTGTGTGGGCTTTCAAATAA
65 GTTGCCACCAACTTGTGTGGGCTTTCAAATAA
*
436996 GTTGCCACCAACTTGTGTGGACTTTCAAATAAGTTGCCACCGACTTGTGTGGGCTTTGAAATGAG
1 GTTGCCACCAACTTGAGTGGACTTTCAAATAAGTTGCCACCGACTTGTGTGGGCTTTGAAATGAG
* *
437061 TTGCCATCGACTTGTG
66 TTGCCACCAACTTGTG
437077 GTCTTTGAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 69 0.97
97 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.32
Consensus pattern (96 bp):
GTTGCCACCAACTTGAGTGGACTTTCAAATAAGTTGCCACCGACTTGTGTGGGCTTTGAAATGAG
TTGCCACCAACTTGTGTGGGCTTTCAAATAA
Found at i:437241 original size:27 final size:27
Alignment explanation
Indices: 437090--437908 Score: 814
Period size: 27 Copynumber: 29.9 Consensus size: 27
437080 TTTGAAATGA
* * * * *
437090 TGCCACTGACTTGTGGGCTTTAAAATGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * * *
437118 TGCCACTGACTTGTGGGCTTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * * * *
437146 TGCCACTGACTTGTGGGCTTTAAAATGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
** *
437174 TGCCACTAACTTGTGAGACTTAAAAGGG
1 TGCCACGGAGTTGTG-GACTTAAAAGGG
437202 TGCCAC-GAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* ** * *
437228 TACCACAAAATTGTGGATTTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGG
* *
437256 TGCCACGGAGTTGTGGACTTAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
437283 TGCCACGGAGTTGTGGACTTAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
437310 TGTCACAGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
*
437338 TGCCATGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
437366 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
437393 TACCACGGAGTAGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
437420 TGCTACGGAGTTATGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
437447 TGCCACAGAGTTATGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
*
437475 TGCCACGGAGTTGTGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
437503 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
437530 TGCCATGGAGTTGTGGACTTAAAAGGT
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * * *
437557 TGCCACGAAGTTATGAACTTAAAAGGT
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * **
437584 TGTCACAGAGTTGTGGACTTTAAAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
437612 TACCACAGAGTTGTGGACTTTAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * * *
437639 TGCCACGAAATTATGGACTTAAAAGGT
1 TGCCACGGAGTTGTGGACTTAAAAGGG
**
437666 TGCCACAAAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * **
437693 TGCCATGGACTTGTGGACTTTAAAAGAT
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
437721 TACTACAGAGTTGTGGACTTTAAAA-GG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
437748 TGTCATGGAGTTGTGGACTTAAAAGGT
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
437775 TGCCACGAAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
437803 TGCCACAGAGTTGTGGAGTTTAAAAGGT
1 TGCCACGGAGTTGTGGA-CTTAAAAGGG
* * *
437831 TGCCACGGAGCTATGGACTTAAAAGTG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
437858 TGCCATGGAGTTGTGGACCTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
437885 TGCCACGGAGTTGTGGACTTAAAA
1 TGCCACGGAGTTGTGGACTTAAAA
437909 AGAATACCAC
Statistics
Matches: 670, Mismatches: 111, Indels: 21
0.84 0.14 0.03
Matches are distributed among these distances:
26 23 0.03
27 348 0.52
28 297 0.44
29 2 0.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:437354 original size:137 final size:136
Alignment explanation
Indices: 437100--437908 Score: 898
Period size: 137 Copynumber: 5.9 Consensus size: 136
437090 TGCCACTGAC
* * * * * * * * * *
437100 TTGTGGGCTTTAAAATGATGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCT
1 TTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTATGGAC-
* * *
437165 TTAAAATGATGCCACTA-ACTTGTGAGAC-TTAAAAGGGTGCCAC-GAGTTGTGGACTTAAAAGG
63 TTAAAAAGATGTCAC-AGAGTTGTG-GACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG
* * *
437227 GTACCACAAAA
126 GTGCCACGAAG
* * *
437238 TTGTGGATTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGATGCCACGGAGTTGTGGACTT
1 TTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACTT
*
437303 AAAAAGATGTCACAGAGTTGTGGACTTTAAAAGGGTGCCATGGAGTTGTGGACTTTAAAAGGGTG
65 AAAAAGATGTCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTG
*
437368 CCACGGAG
129 CCACGAAG
* * *
437376 TTGTGGACTTAAAAGGGTACCACGGAGTAGTGGACTTAAAAGGATGCTACGGAGTTATGGACTTA
1 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACTTA
* * * *
437441 AAAGGATGCCACAGAGTTATGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGATGC
66 AAAAGATGTCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGC
*
437506 CACGGAG
130 CACGAAG
* * * *
437513 TTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGTTGCCACGAAGTTATGAACTTA
1 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACTTA
* * ** * * *
437578 AAAGGTTGTCACAGAGTTGTGGACTTTAAAAAAGTACCACAGAGTTGTGGACTTTAAAGGGTGCC
66 AAAAGATGTCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
*
437643 ACGAAA
131 ACGAAG
* * ** * * * * *
437649 TTATGGACTTAAAAGGTTGCCACAAAGTTGTGGACTTAAAAGGGTGCCATGGACTTGTGGACTTT
1 TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACTTA
* * *
437714 AAAAGAT-TACTACAGAGTTGTGGACTTTAAAA-GGTGTCATGGAGTTGTGGACTTAAAAGGTTG
66 AAAAGATGT-C-ACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTG
437777 CCACGAAG
129 CCACGAAG
* * * *
437785 TTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGAGTTTAAAAGGTTGCCACGGAGCTATGGACT
1 TTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGA-CTTAAAAGGATGCCACGGAGTTATGGACT
*
437850 T-AAAAG-TGTGC-CATGGAGTTGTGGAC-CTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
64 TAAAAAGATGT-CACA--GAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
437909 AGAATACCAC
Statistics
Matches: 575, Mismatches: 83, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
135 7 0.01
136 151 0.26
137 343 0.60
138 74 0.13
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (136 bp):
TTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACTTA
AAAAGATGTCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
ACGAAG
Found at i:437919 original size:82 final size:82
Alignment explanation
Indices: 437072--437932 Score: 868
Period size: 82 Copynumber: 10.5 Consensus size: 82
437062 TGCCATCGAC
* * * * * * * * * * *
437072 TTGTGGTCTTTGAAATGATGCCACTGACTTGTGGGCTTTAAAATGATGCCACTGACTTGTGGGCT
1 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-
* * *
437137 TTAAAAGGATGCCACTGAC
64 TTAAAAGGGTGCCACGGAG
* * ** *
437156 TTGTGGGCTTTAAAATGATGCCACTAACTTGTGAGACTTAAAAGGGTGCCAC-GAGTTGTGGACT
1 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTG-GACTTAAAAGGGTGCCACGGAGTTGTGGACT
* ** *
437220 TAAAAGGGTACCACAAAA
65 TAAAAGGGTGCCACGGAG
* * * *
437238 TTGTGGATTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGATGCCACGGAGTTGTGGACTT
1 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
* * * *
437303 AAAAAGATGTCACAGAG
66 AAAAGGGTGCCACGGAG
* *
437320 TTGTGGACTTTAAAAGGGTGCCATGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACT
1 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACT
*
437385 TAAAAGGGTACCACGGAG
65 TAAAAGGGTGCCACGGAG
* * * * * *
437403 TAGTGGAC-TTAAAAGGATGCTACGGAGTTATGGACTTAAAAGGATGCCACAGAGTTATGGACTT
1 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-T
437467 TAAAAGGGTGCCACGGAG
65 TAAAAGGGTGCCACGGAG
*
437485 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTT
1 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
* *
437550 AAAAGGTTGCCACGAAG
66 AAAAGGGTGCCACGGAG
* * * * * ** * *
437567 TTATGAAC-TTAAAAGGTTGTCACAGAGTTGTGGACTTTAAAAAAGTACCACAGAGTTGTGGACT
1 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACT
* * *
437631 TTAAAGGGTGCCACGAAA
65 TAAAAGGGTGCCACGGAG
* * ** * *
437649 TTATGGAC-TTAAAAGGTTGCCACAAAGTTGTGGACTTAAAAGGGTGCCATGGACTTGTGGACTT
1 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-T
** * * *
437713 TAAAAGATTACTACAGAG
65 TAAAAGGGTGCCACGGAG
* * * *
437731 TTGTGGACTTTAAAAGG-TGTCATGGAGTTGTGGACTTAAAAGGTTGCCACGAAGTTGTGGACTT
1 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-T
*
437795 TAAAAGGGTGCCACAGAG
65 TAAAAGGGTGCCACGGAG
* * * * * * *
437813 TTGTGGAGTTTAAAAGGTTGCCACGGAGCTATGGACTTAAAAGTGTGCCATGGAGTTGTGGACCT
1 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
437878 AAAAGGGTGCCACGGAG
66 AAAAGGGTGCCACGGAG
* * * * *
437895 TTGTGGACTTAAAAAGAATACCACGGAATCGTGGACTT
1 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTT
437933 TGAAGAGGTT
Statistics
Matches: 650, Mismatches: 118, Indels: 20
0.82 0.15 0.03
Matches are distributed among these distances:
81 85 0.13
82 372 0.57
83 148 0.23
84 43 0.07
85 2 0.00
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.26
Consensus pattern (82 bp):
TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
AAAAGGGTGCCACGGAG
Found at i:439221 original size:22 final size:22
Alignment explanation
Indices: 439196--439275 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 22
439186 TGTTATTCCC
439196 TTTTTATTTTGCTTTTGCATTT
1 TTTTTATTTTGCTTTTGCATTT
* *
439218 TTTTTATTTTTCTTTT-CATAT
1 TTTTTATTTTGCTTTTGCATTT
*
439239 TTTGTACTTTTGCTTTTGACATTT
1 TTTTTA-TTTTGCTTTTG-CATTT
439263 TTTTGTCATTTTG
1 TTTT-T-ATTTTG
439276 AAGAGAACTT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 9 0.19
22 24 0.51
24 7 0.15
25 6 0.13
26 1 0.02
ACGTcount: A:0.11, C:0.10, G:0.09, T:0.70
Consensus pattern (22 bp):
TTTTTATTTTGCTTTTGCATTT
Found at i:443852 original size:20 final size:20
Alignment explanation
Indices: 443807--443852 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
443797 GTGAACAACC
*
443807 CATGATTCATGCATTTTGAG
1 CATGTTTCATGCATTTTGAG
443827 CTATGTTTCATGCA-TTTGCAG
1 C-ATGTTTCATGCATTTTG-AG
443848 CATGT
1 CATGT
443853 CCAGCACCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTGAG
Found at i:449278 original size:17 final size:16
Alignment explanation
Indices: 449247--449289 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
449237 TTTTTTCTGT
**
449247 TTTTTTCTTTTTCTTCC
1 TTTTTTCTTCATCTT-C
449264 TTTTTTCTTCATCTTC
1 TTTTTTCTTCATCTTC
449280 TTTATTTCTT
1 TTT-TTTCTT
449290 ACCTAACTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTCTTCATCTTC
Found at i:449346 original size:19 final size:20
Alignment explanation
Indices: 449317--449363 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
449307 ATCCAGAATC
* *
449317 CGGCGACCAGCCACCA-CGT
1 CGGCCACCAGCAACCACCGT
*
449336 CGGTCACCAGCAACCACCGT
1 CGGCCACCAGCAACCACCGT
449356 CGGCCACC
1 CGGCCACC
449364 GCTCACCGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.21, C:0.49, G:0.23, T:0.06
Consensus pattern (20 bp):
CGGCCACCAGCAACCACCGT
Found at i:457050 original size:495 final size:493
Alignment explanation
Indices: 456107--457091 Score: 1643
Period size: 495 Copynumber: 2.0 Consensus size: 493
456097 GAAAAGTAGT
456107 TGTCGTAACGTGCGCTCGACCCCGACGATAGGGCAAATGAGGCACGCCCGACTTAATATCCCTCG
1 TGTCGTAACGTGCGCTCGACCCCGACGATAGGGCAAATGAGGCACGCCCGACTTAATATCCCTCG
* *
456172 CGATTGGGGATTTCTATGGCATGATGAAAAGTATGTTGATTAAGGGGGAAGATCAGTAGATGAAT
66 CAATTGGGGATTTCTATGGCATGAGGAAAAGTATGTTGATTAAGGGGGAAGATCAGTAGATGAAT
456237 CGCCCATCTAATTGATCTTCAATGGTCACTACGAAGTGACCAAAATTTTGGAGTCGCCACCGATC
131 CGCCCATCTAATTGATCTTCAATGGTCACTACGAAGTGACCAAAATTTTGGAGTCGCCACCGATC
* * *
456302 ATTTCGGGCTAGGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACGAAACTAAAAACA
196 ATTTCGGGCTAAGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTCACGAAACCAAAAACA
456367 TCGATCCCGTGGTCTGCGTACTTTAGAGATTCGCCGGTTGGGTTCGAGAGTTGGTTACACGCAAA
261 TCGATCCCGTGGTCTGCGTACTTTAGAGATTCGCCGGTTGGGTTCGAGAGTTGGTTACACGCAAA
* ** *
456432 GAGGTACGAACCTCCTCGCGACGCCCGAAATCAGTACCTTACTAGCAGTGTTTTGACTTAAAGTT
326 GAGGTACGAACCTCCTCGCGACGCCCGAAATCAGTACCTTACCAGCAACGTTTTGACTGAAAGTT
** * *
456497 GATTACATTGATTTCGGTTCATCGTTATTTCGATATGATCCCTTTCGAATGCATGAATTTTGTGT
391 GATTACATTGATTTCAATTCATCATTATTTCGATATGATCCCTTTCGAAGGCATGAATTTTGTGT
*
456562 AAAAATAAATCTAGGTTTTTGACAATCGTTTTCATCTC
456 AAAAAGAAATCTAGGTTTTTGACAATCGTTTTCATCTC
* *
456600 TGTCGTAACGTGCGCTCGACCCCGGCGATAGGGCAAATGAGGCACGCTCGACTTAATATCCCTCG
1 TGTCGTAACGTGCGCTCGACCCCGACGATAGGGCAAATGAGGCACGCCCGACTTAATATCCCTCG
* *
456665 CAATTGGGGATTTCTATGGTATGAGGGGGAAA-TATGTTGATTAAAGGGGGAAGATCAGTAGATG
66 CAATTGGGGATTTCTATGGCATGA--GGAAAAGTATGTTGATT-AAGGGGGAAGATCAGTAGATG
* * *
456729 AATCGCCCATCTAATTGATCTTCAATGGTCACTATGAAGTGACCGAGATTTTGGAGTCGCCACCG
128 AATCGCCCATCTAATTGATCTTCAATGGTCACTACGAAGTGACCAAAATTTTGGAGTCGCCACCG
*
456794 ATCATTTCGGGCTAAGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTCACGAAACCCAAA
193 ATCATTTCGGGCTAAGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTCACGAAACCAAAA
* *
456859 ACATCGATCCCGTGGTCTGCGTACTTTAGAGATTCGCCGGTTGGGTTCGGGAGTTGGTTACGCGC
258 ACATCGATCCCGTGGTCTGCGTACTTTAGAGATTCGCCGGTTGGGTTCGAGAGTTGGTTACACGC
* *
456924 AAAGAGGTACGAACCTCCTCGCGACGCCCGAAATCGGTACCTTACCAGCAACGTTTTGACTCGAT
323 AAAGAGGTACGAACCTCCTCGCGACGCCCGAAATCAGTACCTTACCAGCAACGTTTTGACT-GAA
* * *
456989 A-TTGGTTACATTGATTTCAATTTATCATTATTTCGATATGATCCCCTTT-GAAGGTATGAATTT
387 AGTTGATTACATTGATTTCAATTCATCATTATTTCGATATGAT-CCCTTTCGAAGGCATGAATTT
457052 TGTGTAAAAAGAAATCTAGGTTTTTGACAATCGTTTTCAT
451 TGTGTAAAAAGAAATCTAGGTTTTTGACAATCGTTTTCAT
457092 TTCATATGCG
Statistics
Matches: 458, Mismatches: 29, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
493 85 0.19
494 10 0.02
495 355 0.78
496 8 0.02
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (493 bp):
TGTCGTAACGTGCGCTCGACCCCGACGATAGGGCAAATGAGGCACGCCCGACTTAATATCCCTCG
CAATTGGGGATTTCTATGGCATGAGGAAAAGTATGTTGATTAAGGGGGAAGATCAGTAGATGAAT
CGCCCATCTAATTGATCTTCAATGGTCACTACGAAGTGACCAAAATTTTGGAGTCGCCACCGATC
ATTTCGGGCTAAGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTCACGAAACCAAAAACA
TCGATCCCGTGGTCTGCGTACTTTAGAGATTCGCCGGTTGGGTTCGAGAGTTGGTTACACGCAAA
GAGGTACGAACCTCCTCGCGACGCCCGAAATCAGTACCTTACCAGCAACGTTTTGACTGAAAGTT
GATTACATTGATTTCAATTCATCATTATTTCGATATGATCCCTTTCGAAGGCATGAATTTTGTGT
AAAAAGAAATCTAGGTTTTTGACAATCGTTTTCATCTC
Found at i:459757 original size:52 final size:52
Alignment explanation
Indices: 459687--459807 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
459677 GAAAATTTAT
* *
459687 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATAAATCTGGGCAAATTTGC
*
459739 CTGCATGTATCGATACATTTTATAATGTATCGATAAATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATAAATCTGGGCAAATTTGC
459791 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
459808 AAGATCGGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATAAATCTGGGCAAATTTGC
Done.