Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2344
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: 384062
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:6872 original size:50 final size:50
Alignment explanation
Indices: 6796--6981 Score: 221
Period size: 50 Copynumber: 3.7 Consensus size: 50
6786 TTCCACAATT
* * * *
6796 TGTATCGATGCATTCTTCATTATATCGATACATTATGGGTTTAACCTAGA
1 TGTATCGATACATTCTTCATTGTATCGATACATTCTGGGTTTTACCTAGA
* *
6846 TGTATCGATACATTATTCATTGTATCGATACATTCTGGGTTTTGCCTAGA
1 TGTATCGATACATTCTTCATTGTATCGATACATTCTGGGTTTTACCTAGA
* * * * * *
6896 TGAATTGATGCATTCTTCATTGTATCGATATATTCTAGGGTTTTACCCAAA
1 TGTATCGATACATTCTTCATTGTATCGATACATTCT-GGGTTTTACCTAGA
* *
6947 TGTATCGATACATT-TCTCAATGTATCAATACATTC
1 TGTATCGATACATTCT-TCATTGTATCGATACATTC
6982 AGGCATTTTG
Statistics
Matches: 114, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
50 76 0.67
51 38 0.33
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (50 bp):
TGTATCGATACATTCTTCATTGTATCGATACATTCTGGGTTTTACCTAGA
Found at i:7326 original size:21 final size:20
Alignment explanation
Indices: 7297--7338 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
7287 AAGGAGAAAA
7297 TCCCATAATGCCT-TTGGCTTG
1 TCCCATAAT-CCTATTGG-TTG
*
7318 TCCCCTAATCCTATTGGTTG
1 TCCCATAATCCTATTGGTTG
7338 T
1 T
7339 GTATGAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.14, C:0.29, G:0.17, T:0.40
Consensus pattern (20 bp):
TCCCATAATCCTATTGGTTG
Found at i:9401 original size:28 final size:28
Alignment explanation
Indices: 9369--9441 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
9359 GCCATAATCG
9369 GGGATACTCCAACCCCGTTATTTTTGAA
1 GGGATACTCCAACCCCGTTATTTTTGAA
*
9397 GGGATACTCCAACCCCGTTATTTTTGAG
1 GGGATACTCCAACCCCGTTATTTTTGAA
*
9425 GGGATACTCCAATCCCG
1 GGGATACTCCAACCCCG
9442 GTTTTATTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTTTGAA
Found at i:9481 original size:79 final size:79
Alignment explanation
Indices: 9398--9769 Score: 412
Period size: 79 Copynumber: 4.7 Consensus size: 79
9388 ATTTTTGAAG
* * *
9398 GGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAATCCCGGTTTTATTTCCAAAACATCGA
1 GGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAA
*
9463 TTTTTCATAATCGA
66 TTTTTCACAATCGA
* * * * *
9477 GGATACTCCAATCCTGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAA
1 GGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAA
*
9542 TTTTCCACAATC-A
66 TTTTTCACAATCGA
* * * * * * *
9555 GGGATACTACAACCCAGTTATTTCTGAGGGGATACTCTAACCCCAGTTTTAGTTCCAAAACACTA
1 -GGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCA
9620 ATTTTTCACAATCG-
65 ATTTTTCACAATCGA
* ** * * *
9634 GGAATACTCCAACCCCATTATTTTCAAGAGGATACTCCAACCTCGGTTTTA--T-CAAAACACCG
1 GG-ATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCA
9696 ATTTTTCACAATCGA
65 ATTTTTCACAATCGA
* * * * * ** *
9711 TGATACTCCAACCCCATTATTTCTGAGGGGATACTTCAACCTCAATTTTATCTCCAAAA
1 GGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAA
9770 TATTAAACTT
Statistics
Matches: 244, Mismatches: 42, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
76 63 0.26
77 2 0.01
78 4 0.02
79 175 0.72
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (79 bp):
GGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAA
TTTTTCACAATCGA
Found at i:9508 original size:107 final size:107
Alignment explanation
Indices: 9319--9520 Score: 287
Period size: 107 Copynumber: 1.9 Consensus size: 107
9309 ATTTCCGAGA
* * *
9319 GGATACTCCAGCCCCGGTTTTATTTTCAAAACACCAATATGCCATAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATATGCCATAATCGAGGATACTCCAACCC
*
9384 CGTTATTTTTGAAGGGATACTCCAACCCCGTTATTTTTGAGG
66 CGTTATTTTCGAAGGGATACTCCAACCCCGTTATTTTTGAGG
* * * * ** *
9426 GGATACTCCAATCCCGGTTTTATTTCCAAAACATCGATTTTTCATAATCGAGGATACTCCAATCC
1 GGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATATGCCATAATCGAGGATACTCCAACCC
* *
9491 TGTTATTTTCGAGGGGATACTCCAACCCCG
66 CGTTATTTTCGAAGGGATACTCCAACCCCG
9521 ATTTTATTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
107 82 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (107 bp):
GGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATATGCCATAATCGAGGATACTCCAACCC
CGTTATTTTCGAAGGGATACTCCAACCCCGTTATTTTTGAGG
Found at i:13249 original size:33 final size:33
Alignment explanation
Indices: 13207--13271 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
13197 TTACAAGCAA
* *
13207 TGTATCGATACAAT-TCATCATTTATCGATACAT
1 TGTATCGATACAATGT-ACCATGTATCGATACAT
13240 TGTATCGATACAATGTACCATGTATCGATACA
1 TGTATCGATACAATGTACCATGTATCGATACA
13272 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTACCATGTATCGATACAT
Found at i:13326 original size:20 final size:20
Alignment explanation
Indices: 13301--13358 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
13291 CTGCTAGTTT
*
13301 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
*
13321 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTA
13340 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
13359 TCGATACATC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 15 0.44
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:13360 original size:13 final size:13
Alignment explanation
Indices: 13342--13367 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13332 ACAATGAACA
13342 TGTATCGATACAT
1 TGTATCGATACAT
13355 TGTATCGATACAT
1 TGTATCGATACAT
13368 CTGAGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:22098 original size:20 final size:20
Alignment explanation
Indices: 22073--22130 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
22063 CTGCCAGTTT
*
22073 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
*
22093 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTA
22112 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
22131 TCGATACAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 15 0.44
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:22132 original size:13 final size:13
Alignment explanation
Indices: 22114--22138 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22104 ACAATGAACA
22114 TGTATCGATACAT
1 TGTATCGATACAT
22127 TGTATCGATACA
1 TGTATCGATACA
22139 AAGCATGATG
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:22155 original size:33 final size:32
Alignment explanation
Indices: 22095--22160 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
22085 CAATTGTCCA
*
22095 TGTATCGATACAATGAACATGTATCGATACAT
1 TGTATCGATACAAAGAACATGTATCGATACAT
**
22127 TGTATCGATACAAAGCATGATGTATCGATACAT
1 TGTATCGATACAAAG-AACATGTATCGATACAT
22160 T
1 T
22161 TGGGTGTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCGATACAT
Found at i:22242 original size:20 final size:20
Alignment explanation
Indices: 22217--22268 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
22207 GTCAACCATA
*
22217 ATGTATCAATACAAATACCT
1 ATGTATCGATACAAATACCT
22237 ATGTATCGATACAAATACCT
1 ATGTATCGATACAAATACCT
22257 ATGTATCGATAC
1 ATGTATCGATAC
22269 TTTAAAGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAAATACCT
Found at i:23725 original size:20 final size:20
Alignment explanation
Indices: 23700--23737 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
23690 TGTTCGGTTC
23700 TAACAAAACTTACGCAATGG
1 TAACAAAACTTACGCAATGG
*
23720 TAACAAGACTTACGCAAT
1 TAACAAAACTTACGCAAT
23738 AGTTGTATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (20 bp):
TAACAAAACTTACGCAATGG
Found at i:27258 original size:3 final size:3
Alignment explanation
Indices: 27250--27355 Score: 149
Period size: 3 Copynumber: 35.3 Consensus size: 3
27240 GCAATGTTTC
*
27250 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
27298 TCA TCA TCA TCA TTA TTG TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27346 TTA TTA TTA T
1 TTA TTA TTA T
27356 ATAGATGGCT
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 97 1.00
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:28789 original size:20 final size:20
Alignment explanation
Indices: 28766--28838 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
28756 ACAATTCAAA
28766 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
28786 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
28807 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
28827 GTATCGATACAT
1 GTATCGATACAT
28839 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:28817 original size:41 final size:42
Alignment explanation
Indices: 28766--28860 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
28756 ACAATTCAAA
*
28766 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
28807 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
28849 GTATCGATACAT
1 GTATCGATACAT
28861 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:28917 original size:13 final size:13
Alignment explanation
Indices: 28899--28924 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28889 TACAGCAAGT
28899 ATGTATCGATACA
1 ATGTATCGATACA
28912 ATGTATCGATACA
1 ATGTATCGATACA
28925 CAAAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:31170 original size:21 final size:21
Alignment explanation
Indices: 31137--31181 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
31127 TTGCAAGTTG
*
31137 AAATAAATAAGTTGGCTAATGA
1 AAATAAATAAGTTAGCTAA-GA
*
31159 AAAT-AATGAGTTAGCTAAGA
1 AAATAAATAAGTTAGCTAAGA
31179 AAA
1 AAA
31182 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 12 0.57
22 4 0.19
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.24
Consensus pattern (21 bp):
AAATAAATAAGTTAGCTAAGA
Found at i:33004 original size:15 final size:15
Alignment explanation
Indices: 32984--33014 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
32974 TAAAAATGTC
*
32984 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
32999 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
33014 C
1 C
33015 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:35105 original size:20 final size:21
Alignment explanation
Indices: 35036--35113 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
35026 AATGTCCAAA
35036 ATGTATCGATACATATTTT-T
1 ATGTATCGATACATATTTTCT
* **
35056 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACA--T--ATTTTCT
35081 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATATTTTCT
*
35101 TTGTATCGATACA
1 ATGTATCGATACA
35114 ATGTATCGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 28 0.61
22 1 0.02
23 1 0.02
24 3 0.07
25 13 0.28
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATATTTTCT
Found at i:35120 original size:13 final size:13
Alignment explanation
Indices: 35102--35139 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
35092 CATTTTTCTT
35102 TGTATCGATACAA
1 TGTATCGATACAA
*
35115 TGTATCGATACAC
1 TGTATCGATACAA
35128 TGTATCGATACA
1 TGTATCGATACA
35140 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:37044 original size:66 final size:66
Alignment explanation
Indices: 36958--37088 Score: 262
Period size: 66 Copynumber: 2.0 Consensus size: 66
36948 AGGGGGAGAT
36958 TTATTAATAAACGGGGGAGACAAAGGAGAGAATGCGTGAATTACCTTATTAAGGGGGAGAATGTA
1 TTATTAATAAACGGGGGAGACAAAGGAGAGAATGCGTGAATTACCTTATTAAGGGGGAGAATGTA
37023 A
66 A
37024 TTATTAATAAACGGGGGAGACAAAGGAGAGAATGCGTGAATTACCTTATTAAGGGGGAGAATGTA
1 TTATTAATAAACGGGGGAGACAAAGGAGAGAATGCGTGAATTACCTTATTAAGGGGGAGAATGTA
37089 CAAATTCGTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.39, C:0.08, G:0.31, T:0.23
Consensus pattern (66 bp):
TTATTAATAAACGGGGGAGACAAAGGAGAGAATGCGTGAATTACCTTATTAAGGGGGAGAATGTA
A
Found at i:37673 original size:20 final size:20
Alignment explanation
Indices: 37650--37722 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
37640 ACAATTCAAA
37650 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
** *
37670 GTATCGATACATGAAAAG-GAT
1 GTATCGATACATG--TTGCAAT
37691 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
37711 GTATCGATACAT
1 GTATCGATACAT
37723 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 27 0.61
21 15 0.34
22 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:37701 original size:41 final size:42
Alignment explanation
Indices: 37650--37744 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 42
37640 ACAATTCAAA
* *
37650 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
37691 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
37733 GTATCGATACAT
1 GTATCGATACAT
37745 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 32 0.63
42 19 0.37
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:37801 original size:13 final size:13
Alignment explanation
Indices: 37783--37808 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37773 TACAGCAAGT
37783 ATGTATCGATACA
1 ATGTATCGATACA
37796 ATGTATCGATACA
1 ATGTATCGATACA
37809 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:44960 original size:20 final size:20
Alignment explanation
Indices: 44937--44983 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
44927 TAATGAGCTG
*
44937 AAAATTAAAAGGATAAGAAA
1 AAAATTAAAAAGATAAGAAA
*
44957 AAAATTAAAAAGATGAGAAA
1 AAAATTAAAAAGATAAGAAA
*
44977 TAAATTA
1 AAAATTA
44984 TACTTCCTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (20 bp):
AAAATTAAAAAGATAAGAAA
Found at i:46409 original size:91 final size:92
Alignment explanation
Indices: 46251--46417 Score: 223
Period size: 91 Copynumber: 1.8 Consensus size: 92
46241 AGGAACAAAG
* * *
46251 AGAAAGTTTAAGTTTTTTTATAAAGAACGGGGTTAAAGTATCCTTTCGGAGTAGTAGGGTTAAAG
1 AGAAAATTTAAGTTTTTTTATAAAGAACGGGGTTAAAGTATCCTTTCAGAATAGTAGGGTTAAAG
46316 TTTCCCCAAAGATAAAATTATACGAAA
66 TTTCCCCAAAGATAAAATTATACGAAA
** * **
46343 AGAAAATTTAAG-TTTTTTATGGAGAATGGGGTTAGAA-TAT-CTTCTCAGAATAGTAGGGTTGG
1 AGAAAATTTAAGTTTTTTTATAAAGAACGGGGTTA-AAGTATCCTT-TCAGAATAGTAGGGTTAA
46405 AGTTTCCCCAAAG
64 AGTTTCCCCAAAG
46418 TCGAAGATAA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
90 3 0.05
91 49 0.75
92 13 0.20
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (92 bp):
AGAAAATTTAAGTTTTTTTATAAAGAACGGGGTTAAAGTATCCTTTCAGAATAGTAGGGTTAAAG
TTTCCCCAAAGATAAAATTATACGAAA
Found at i:46602 original size:85 final size:84
Alignment explanation
Indices: 46459--46613 Score: 193
Period size: 85 Copynumber: 1.8 Consensus size: 84
46449 AGAAAATTTT
* ** * * * * *
46459 AGTTTTTTATGAAGAATGGGGTTAGATTTTCCCCTATAGTAGCGAGGTTGGAGTTTTCCTAAAGA
1 AGTTTTTTATGAAAAACAGGGTTAGAATATCCCCTAGAGTAGCGAGGTTGAAGTTTTCCCAAAG-
46524 TAAAATTATATAAAAAAATA
65 TAAAATTATATAAAAAAATA
* * * *
46544 AGTTTTTTATGAAAAACAGGGTTGGAATATCCCCTCGAGTAGTGGGGTTGAAGTTTTCCCAAAGT
1 AGTTTTTTATGAAAAACAGGGTTAGAATATCCCCTAGAGTAGCGAGGTTGAAGTTTTCCCAAAGT
46609 AAAAT
66 AAAAT
46614 CTTTTTTATG
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
84 6 0.10
85 52 0.90
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (84 bp):
AGTTTTTTATGAAAAACAGGGTTAGAATATCCCCTAGAGTAGCGAGGTTGAAGTTTTCCCAAAGT
AAAATTATATAAAAAAATA
Found at i:49415 original size:20 final size:20
Alignment explanation
Indices: 49370--49421 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
49360 GTAGCCAAAC
**
49370 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
49390 -TGTATCGATACACCAAAAA
1 TTGTATCGATACACCAAAAA
49409 TTGTATCGATACA
1 TTGTATCGATACA
49422 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:50326 original size:17 final size:17
Alignment explanation
Indices: 50304--50339 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
50294 CATAAACTTT
50304 ATACCCGAGCTCATCCC
1 ATACCCGAGCTCATCCC
50321 ATACCCGAGCTCATCCC
1 ATACCCGAGCTCATCCC
50338 AT
1 AT
50340 TAGTGGCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.44, G:0.11, T:0.19
Consensus pattern (17 bp):
ATACCCGAGCTCATCCC
Found at i:52997 original size:19 final size:19
Alignment explanation
Indices: 52975--53037 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
52965 TAGCCAAACT
52975 TGTATCGATACACCAAGTA
1 TGTATCGATACACCAAGTA
52994 TGTATCGAT--A-C-A--A
1 TGTATCGATACACCAAGTA
53007 TGTATCGATACACCAAGTA
1 TGTATCGATACACCAAGTA
53026 TGTATCGATACA
1 TGTATCGATACA
53038 ATGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
16 2 0.05
17 2 0.05
19 22 0.58
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (19 bp):
TGTATCGATACACCAAGTA
Found at i:53011 original size:13 final size:13
Alignment explanation
Indices: 52993--53050 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
52983 TACACCAAGT
52993 ATGTATCGATACA
1 ATGTATCGATACA
53006 ATGTATCGATACACCAA
1 ATGTATCGAT--A-C-A
53023 GTATGTATCGATACA
1 --ATGTATCGATACA
53038 ATGTATCGATACA
1 ATGTATCGATACA
53051 CCAAAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.59
15 2 0.05
16 2 0.05
17 2 0.05
19 10 0.26
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:53016 original size:32 final size:32
Alignment explanation
Indices: 52975--53070 Score: 165
Period size: 32 Copynumber: 3.0 Consensus size: 32
52965 TAGCCAAACT
52975 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAGTATGTATCGATACAA
53007 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAGTATGTATCGATACAA
**
53039 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAGTA-TGTATCGATACA
53071 TTGGCTTGTA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 49 0.80
33 12 0.20
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAGTATGTATCGATACAA
Found at i:55302 original size:21 final size:21
Alignment explanation
Indices: 55269--55313 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
55259 TTGCAAGTTG
*
55269 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
55291 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
55311 AAA
1 AAA
55314 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:57136 original size:15 final size:15
Alignment explanation
Indices: 57116--57146 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
57106 TAAAAATGTC
*
57116 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
57131 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
57146 C
1 C
57147 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:59243 original size:13 final size:13
Alignment explanation
Indices: 59225--59250 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59215 ACTTTTTTCT
59225 TTGTATCGATACA
1 TTGTATCGATACA
59238 TTGTATCGATACA
1 TTGTATCGATACA
59251 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:61815 original size:20 final size:20
Alignment explanation
Indices: 61770--61821 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
61760 GTAGCCAAAC
**
61770 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
61790 -TGTATCGATACACCAAAAA
1 TTGTATCGATACACCAAAAA
61809 TTGTATCGATACA
1 TTGTATCGATACA
61822 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:62726 original size:17 final size:17
Alignment explanation
Indices: 62704--62739 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
62694 CATAAACTTT
62704 ATACCCGAGCTCATCCC
1 ATACCCGAGCTCATCCC
62721 ATACCCGAGCTCATCCC
1 ATACCCGAGCTCATCCC
62738 AT
1 AT
62740 TAGTGGCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.44, G:0.11, T:0.19
Consensus pattern (17 bp):
ATACCCGAGCTCATCCC
Found at i:72069 original size:32 final size:33
Alignment explanation
Indices: 72012--72075 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
72002 TACAAGCTAA
**
72012 TGTATCGATACAATTTTTGGTGTATCAATACAT
1 TGTATCGATACAATAGTTGGTGTATCAATACAT
*
72045 TGTATCGATAC-ATAGTTGGTGTATCGATACA
1 TGTATCGATACAATAGTTGGTGTATCAATACA
72076 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATAGTTGGTGTATCAATACAT
Found at i:74637 original size:13 final size:13
Alignment explanation
Indices: 74619--74656 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
74609 ATAATCCCCC
74619 TGTATCGATACAA
1 TGTATCGATACAA
*
74632 TGTATCGGTACAA
1 TGTATCGATACAA
*
74645 TGTATCAATACA
1 TGTATCGATACA
74657 TTGAATTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:78578 original size:21 final size:21
Alignment explanation
Indices: 78549--78593 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
78539 AAGTTTTTAT
*
78549 TTTTCTTAGCTAA-TTCATTA
1 TTTTCTTAGCCAAGTTCATTA
*
78569 TTTTCATTAGCCAAGTTCTTTA
1 TTTTC-TTAGCCAAGTTCATTA
78591 TTT
1 TTT
78594 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.22, C:0.16, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTCTTAGCCAAGTTCATTA
Found at i:78593 original size:22 final size:21
Alignment explanation
Indices: 78538--78593 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
78528 ATGAATCATG
78538 CAAGTT-TTTATTTTTCTTAGC
1 CAAGTTCTTTA-TTTTCTTAGC
* *
78559 TAA-TTCATTATTTTCATTAGC
1 CAAGTTCTTTATTTTC-TTAGC
78580 CAAGTTCTTTATTT
1 CAAGTTCTTTATTT
78594 CAACTTGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 7 0.25
21 12 0.43
22 9 0.32
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.55
Consensus pattern (21 bp):
CAAGTTCTTTATTTTCTTAGC
Found at i:79191 original size:12 final size:12
Alignment explanation
Indices: 79176--79209 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
79166 TCCGAGTCAC
79176 CATCTTCATCAA
1 CATCTTCATCAA
*
79188 CATCTTCATCAT
1 CATCTTCATCAA
*
79200 CTTCTTCATC
1 CATCTTCATC
79210 TTTGATGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.41
Consensus pattern (12 bp):
CATCTTCATCAA
Found at i:80862 original size:19 final size:18
Alignment explanation
Indices: 80792--80862 Score: 53
Period size: 19 Copynumber: 4.0 Consensus size: 18
80782 TACAAGCTAA
80792 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
80812 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
* *
80825 TGAATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
80844 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
80863 CTACTGCCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 15
0.69 0.05 0.25
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 1 0.02
18 1 0.02
19 16 0.39
20 11 0.27
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:86878 original size:14 final size:14
Alignment explanation
Indices: 86859--86888 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
86849 GTTTGCACTT
*
86859 CCACGGGTGTTACC
1 CCACGGGTGCTACC
86873 CCACGGGTGCTACC
1 CCACGGGTGCTACC
86887 CC
1 CC
86889 TCTCTTAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.43, G:0.27, T:0.17
Consensus pattern (14 bp):
CCACGGGTGCTACC
Found at i:88231 original size:32 final size:32
Alignment explanation
Indices: 88115--88278 Score: 149
Period size: 32 Copynumber: 5.2 Consensus size: 32
88105 CGTTCATCTC
88115 TTCAAAG-CC-CACAAGTCAGTGGC-AC-CTT
1 TTCAAAGCCCACACAAGTCAGTGGCAACTCTT
* * *
88143 TTCAAAGCCCACACGAGTCGGTGGAAACTCTT
1 TTCAAAGCCCACACAAGTCAGTGGCAACTCTT
* * *
88175 TTCAAAACCCACACGAGTTAGTGGCAACTCTT
1 TTCAAAGCCCACACAAGTCAGTGGCAACTCTT
* *
88207 TTCAAAGCCCACACAAGTTAGTGGC-ACATTTT
1 TTCAAAGCCCACACAAGTCAGTGGCAAC-TCTT
* ** * *
88239 TTAAAAAAGCCCACGTAAGTCGGTGGCAACCCTT
1 TT--CAAAGCCCACACAAGTCAGTGGCAACTCTT
88273 TTCAAA
1 TTCAAA
88279 TCACCACTGT
Statistics
Matches: 110, Mismatches: 18, Indels: 12
0.79 0.13 0.09
Matches are distributed among these distances:
28 7 0.06
29 2 0.02
30 11 0.10
31 4 0.04
32 62 0.56
34 22 0.20
35 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (32 bp):
TTCAAAGCCCACACAAGTCAGTGGCAACTCTT
Found at i:93927 original size:80 final size:79
Alignment explanation
Indices: 93862--94231 Score: 408
Period size: 79 Copynumber: 4.7 Consensus size: 79
93852 TATTTTGGAG
* **
93862 ATAAAAATGGGGTTGGAGTATCCCCTCTGAAATAACGGGGTTGGAGTATCTCCTTTGGTGGAAAA
1 ATAAAAATGGGGTTGGAGTATCCCCTCTGAAATAACGGGGTTGGAGTATCCCCGATGGTGGAAAA
93927 TCGATGTTTTAGAA
66 TCGATGTTTTAGAA
* **
93941 ATAAAACA-GGGGTTTGAGTATCCCCTC-GAAAATAATAGGGTTGGAGTATCCCCGATGGTGGAA
1 ATAAAA-ATGGGGTTGGAGTATCCCCTCTG-AAATAACGGGGTTGGAGTATCCCCGATGGTGGAA
*
94004 AATCGATATTTTAGAA
64 AATCGATGTTTTAGAA
* * * ** *
94020 ATAAAATTGGGGTTGGAGTATCCTCT-TGGAAATAAACGAGGTTTAAGTATCCCCGATAGTGGAA
1 ATAAAAATGGGGTTGGAGTATCCCCTCT-GAAAT-AACGGGGTTGGAGTATCCCCGATGGTGGAA
*
94084 AATTGATGTTTTAGAA
64 AATCGATGTTTTAGAA
* * * ** * * *
94100 AT-AAAATCGGGATTAGAGTATCCCTTCAAAAATAA-TGGGTTGGAGTATCCCCGATGATAGAAA
1 ATAAAAAT-GGGGTTGGAGTATCCCCTCTGAAATAACGGGGTTGGAGTATCCCCGATGGTGGAAA
*
94163 ATCGGTGTTTTAGAA
65 ATCGATGTTTTAGAA
* * *
94178 ATAAAACTGGGGTTGGAGTATCCCTTCGGAAATAAACGGGGTTGGAGTAGTCCC
1 ATAAAAATGGGGTTGGAGTATCCCCTCTGAAAT-AACGGGGTTGGAGTA-TCCC
94232 TGTAGACACC
Statistics
Matches: 239, Mismatches: 40, Indels: 22
0.79 0.13 0.07
Matches are distributed among these distances:
78 58 0.24
79 106 0.44
80 71 0.30
81 4 0.02
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (79 bp):
ATAAAAATGGGGTTGGAGTATCCCCTCTGAAATAACGGGGTTGGAGTATCCCCGATGGTGGAAAA
TCGATGTTTTAGAA
Found at i:94034 original size:158 final size:158
Alignment explanation
Indices: 93851--94231 Score: 498
Period size: 158 Copynumber: 2.4 Consensus size: 158
93841 GAAAAATTTA
* * *
93851 ATATTTTGGAGATAAAAATGGGGTTGGAGTATCCCCTCTGAAAT-AACGGGGTTGGAGTATCTCC
1 ATATTTTAGAAATAAAAATGGGGTTGGAGTATCCCCTCTGAAATAAACGGGGTTGGAGTATCCCC
** * * * *
93915 TTTGGTGGAAAATCGATGTTTTAGAAATAAAA-CAGGGGTTTGAGTATCCCCTCGAAAATAATAG
66 GATAGTGGAAAATCGATGTTTTAGAAATAAAATC-GGGATTAGAGTATCCCCTCAAAAATAAT-G
* *
93979 GGTTGGAGTATCCCCGATGGTGGAAAATCG
129 GGTTGGAGTATCCCCGATGATAGAAAATCG
* * * **
94009 ATATTTTAGAAATAAAATTGGGGTTGGAGTATCCTCT-TGGAAATAAACGAGGTTTAAGTATCCC
1 ATATTTTAGAAATAAAAATGGGGTTGGAGTATCCCCTCT-GAAATAAACGGGGTTGGAGTATCCC
* *
94073 CGATAGTGGAAAATTGATGTTTTAGAAATAAAATCGGGATTAGAGTATCCCTTCAAAAATAATGG
65 CGATAGTGGAAAATCGATGTTTTAGAAATAAAATCGGGATTAGAGTATCCCCTCAAAAATAATGG
94138 GTTGGAGTATCCCCGATGATAGAAAATCG
130 GTTGGAGTATCCCCGATGATAGAAAATCG
* * * * *
94167 GTGTTTTAGAAATAAAACTGGGGTTGGAGTATCCCTTCGGAAATAAACGGGGTTGGAGTAGTCCC
1 ATATTTTAGAAATAAAAATGGGGTTGGAGTATCCCCTCTGAAATAAACGGGGTTGGAGTA-TCCC
94232 TGTAGACACC
Statistics
Matches: 191, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
157 1 0.01
158 117 0.61
159 72 0.38
160 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (158 bp):
ATATTTTAGAAATAAAAATGGGGTTGGAGTATCCCCTCTGAAATAAACGGGGTTGGAGTATCCCC
GATAGTGGAAAATCGATGTTTTAGAAATAAAATCGGGATTAGAGTATCCCCTCAAAAATAATGGG
TTGGAGTATCCCCGATGATAGAAAATCG
Found at i:94213 original size:31 final size:30
Alignment explanation
Indices: 94175--94232 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
94165 CGGTGTTTTA
94175 GAAATAAAACTGGGGTTGGAGTA-TCCCTTCG
1 GAAAT-AAAC-GGGGTTGGAGTAGTCCCTTCG
94206 GAAATAAACGGGGTTGGAGTAGTCCCT
1 GAAATAAACGGGGTTGGAGTAGTCCCT
94233 GTAGACACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 12 0.46
30 9 0.35
31 5 0.19
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (30 bp):
GAAATAAACGGGGTTGGAGTAGTCCCTTCG
Found at i:94769 original size:20 final size:20
Alignment explanation
Indices: 94746--94802 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
94736 AAGTACCCAG
*
94746 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
94766 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
94786 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
94803 ATCTTTTTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:98970 original size:18 final size:19
Alignment explanation
Indices: 98949--98989 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
98939 AATTGTTAAA
98949 ACAC-TTAAAAGTATCGAT
1 ACACATTAAAAGTATCGAT
*
98967 ACACAATTCAAAGTATCGAT
1 ACAC-ATTAAAAGTATCGAT
98987 ACA
1 ACA
98990 TGTTGCAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
20 16 0.80
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (19 bp):
ACACATTAAAAGTATCGAT
Found at i:99107 original size:20 final size:20
Alignment explanation
Indices: 99062--99113 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
99052 GTAGCCAAAC
* **
99062 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
99082 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
99101 TTGTATCGATACA
1 TTGTATCGATACA
99114 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:103181 original size:15 final size:15
Alignment explanation
Indices: 103161--103191 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
103151 TAAAAATGTC
*
103161 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
103176 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
103191 C
1 C
103192 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:105445 original size:20 final size:20
Alignment explanation
Indices: 105402--105447 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
105392 AAATCTTTTG
105402 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
105423 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
105443 CAAAA
1 CAAAA
105448 CCAGCATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:107125 original size:39 final size:39
Alignment explanation
Indices: 107071--107154 Score: 168
Period size: 39 Copynumber: 2.2 Consensus size: 39
107061 GTGCAAATAA
107071 ATTTTTGATATGTGTGTAAATTACCTTATTAAGGGGGAG
1 ATTTTTGATATGTGTGTAAATTACCTTATTAAGGGGGAG
107110 ATTTTTGATATGTGTGTAAATTACCTTATTAAGGGGGAG
1 ATTTTTGATATGTGTGTAAATTACCTTATTAAGGGGGAG
107149 ATTTTT
1 ATTTTT
107155 TAATAAAAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.44
Consensus pattern (39 bp):
ATTTTTGATATGTGTGTAAATTACCTTATTAAGGGGGAG
Found at i:113129 original size:13 final size:13
Alignment explanation
Indices: 113111--113136 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
113101 AACACCAAGT
113111 ATGTATCGATACA
1 ATGTATCGATACA
113124 ATGTATCGATACA
1 ATGTATCGATACA
113137 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:119490 original size:20 final size:20
Alignment explanation
Indices: 119447--119493 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
119437 AAATCTTTTG
119447 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
119468 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
119488 CAAAAT
1 CAAAAT
119494 CAGCTTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:121958 original size:20 final size:20
Alignment explanation
Indices: 121933--121970 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
121923 CTATATTTTC
121933 AAAATTGTATCGATACATCA
1 AAAATTGTATCGATACATCA
121953 AAAATTGTATCGATACAT
1 AAAATTGTATCGATACAT
121971 TTACACGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (20 bp):
AAAATTGTATCGATACATCA
Found at i:127955 original size:11 final size:11
Alignment explanation
Indices: 127939--128006 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 11
127929 CTTTATACCC
127939 AAAAAAAAC-A
1 AAAAAAAACAA
*
127949 GAAAAAAACAA
1 AAAAAAAACAA
127960 AAAAAAAAC--
1 AAAAAAAACAA
*
127969 -AACAAAACAA
1 AAAAAAAACAA
* *
127979 AAAAACCAAGAA
1 AAAAA-AAACAA
*
127991 AAAAATAACAA
1 AAAAAAAACAA
128002 AAAAA
1 AAAAA
128007 TAGAAAGGGG
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
8 7 0.16
10 8 0.18
11 21 0.47
12 9 0.20
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.01
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:127992 original size:28 final size:29
Alignment explanation
Indices: 127943--128003 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
127933 ATACCCAAAA
127943 AAAACAGAAAAAAACAAAAAAAAAACAAC
1 AAAACAGAAAAAAACAAAAAAAAAACAAC
* * *
127972 AAAACA-AAAAAACCAAGAAAAAAATAAC
1 AAAACAGAAAAAAACAAAAAAAAAACAAC
128000 AAAA
1 AAAA
128004 AAATAGAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.82, C:0.13, G:0.03, T:0.02
Consensus pattern (29 bp):
AAAACAGAAAAAAACAAAAAAAAAACAAC
Found at i:128008 original size:11 final size:10
Alignment explanation
Indices: 127939--128006 Score: 66
Period size: 10 Copynumber: 6.6 Consensus size: 10
127929 CTTTATACCC
127939 AAAAAAAACA
1 AAAAAAAACA
*
127949 GAAAAAAACA
1 AAAAAAAACA
127959 AAAAAAAA-A
1 AAAAAAAACA
* *
127968 CAACAAAACA
1 AAAAAAAACA
*
127978 AAAAAACCAAGA
1 AAAAAA--AACA
127990 AAAAAATAACA
1 AAAAAA-AACA
128001 AAAAAA
1 AAAAAA
128007 TAGAAAGGGG
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
9 7 0.15
10 21 0.46
11 9 0.20
12 9 0.20
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.01
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:129272 original size:28 final size:28
Alignment explanation
Indices: 129230--129714 Score: 544
Period size: 28 Copynumber: 16.9 Consensus size: 28
129220 GTTCATATCA
* * *
129230 TTTCAAAGCCGACAAGTAAGT-GCATTCT
1 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
* *
129258 TTTCAAAGCCCACAAGTTAATGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * * *
129286 TTTCAAAACTCATAAGTTAGTTGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
129314 TTTCAAAGGCCACAAGTCAGTGGCA-CTC
1 TTTCAAAGCCCACAAGTCAGTGGCATC-C
129342 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
129370 GTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
129398 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
* * *
129427 TTTCAAAGCCTACACGAGTCGGTGGCAACTCT
1 TTTCAAAGCC--CACAAGTCAGTGGC-A-TCC
129459 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
129487 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
129515 TTTCAAAGCCCACAAGTCAATGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
129543 TTTTAAAGCCCACAAGTCAATGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
129571 TTTCAAAGCCCACAAGTCAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
129599 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
129627 TTTCAAAGCCCACAAGTTAGTGACACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
*
129656 TTTCAAAGCCCACATGAGTC-GATGGCAACTCT
1 TTTCAAAGCCCACA--AGTCAG-TGGC-A-TCC
*
129688 TTTTAAAGCCCACACAAGTCAGTGGCA
1 TTTCAAAG-CC-CACAAGTCAGTGGCA
129715 CTTTTTTTAA
Statistics
Matches: 399, Mismatches: 43, Indels: 27
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.00
28 293 0.73
29 31 0.08
30 13 0.03
31 19 0.05
32 35 0.09
33 3 0.01
34 4 0.01
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:129631 original size:229 final size:230
Alignment explanation
Indices: 129230--129714 Score: 715
Period size: 229 Copynumber: 2.1 Consensus size: 230
129220 GTTCATATCA
* * * * *
129230 TTTCAAAGCCGACAAGTAAGT-GCATTCTTTTCAAAGCCCACAAGTTAATGGCATCCTTTCAAAA
1 TTTCAAAGCCCACAAGTCAGTGGCATTCCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAA
* * * * * * *
129294 CTCATAAGTTAGTTGCACCCTTTCAAAGGCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGT
66 CCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAATGGCACTCTTTCAAAGCCCACAAGT
* *
129359 CAGTGGCATCCGTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
131 CAGTGGCATCAGTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGACAC
* *
129424 TCTTTTCAAAGCCTACACGAGTCGGTGGCAACTCT
196 TCTTTTCAAAGCCCACACGAGTCGATGGCAACTCT
* *
129459 TTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCATTCCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAA
*
129523 CCCACAAGTCAATGGCACCCTTTTAAAGCCCACAAGTCAATGGCA-TCCTTTCAAAGCCCACAAG
66 CCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAATGGCACT-CTTTCAAAGCCCACAAG
* *
129587 TCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGACA
130 TCAGTGGCATCAGTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGACA
*
129652 CTCTTTTCAAAGCCCACATGAGTCGATGGCAACTCT
195 CTCTTTTCAAAGCCCACACGAGTCGATGGCAACTCT
*
129688 TTTTAAAGCCCACACAAGTCAGTGGCA
1 TTTCAAAG-CC-CACAAGTCAGTGGCA
129715 CTTTTTTTAA
Statistics
Matches: 229, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
228 1 0.00
229 208 0.91
230 5 0.02
231 15 0.07
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (230 bp):
TTTCAAAGCCCACAAGTCAGTGGCATTCCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAA
CCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAATGGCACTCTTTCAAAGCCCACAAGT
CAGTGGCATCAGTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGACAC
TCTTTTCAAAGCCCACACGAGTCGATGGCAACTCT
Found at i:134021 original size:13 final size:13
Alignment explanation
Indices: 134003--134038 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
133993 ATAATCCCCT
*
134003 TGTATCGATACAG
1 TGTATCGATACAA
134016 TGTATCGATACAA
1 TGTATCGATACAA
134029 TGTATCGATA
1 TGTATCGATA
134039 TAGAGAATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:140275 original size:13 final size:13
Alignment explanation
Indices: 140257--140282 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
140247 TACAGCAAGT
140257 ATGTATCGATACA
1 ATGTATCGATACA
140270 ATGTATCGATACA
1 ATGTATCGATACA
140283 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:142531 original size:21 final size:21
Alignment explanation
Indices: 142498--142542 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
142488 TTTCAAGTTG
*
142498 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
142520 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
142540 AAA
1 AAA
142543 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:146472 original size:13 final size:13
Alignment explanation
Indices: 146454--146479 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
146444 ACATTTTTCT
146454 TTGTATCGATACA
1 TTGTATCGATACA
146467 TTGTATCGATACA
1 TTGTATCGATACA
146480 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:149033 original size:13 final size:13
Alignment explanation
Indices: 149015--149040 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
149005 TACAGCAAGT
149015 ATGTATCGATACA
1 ATGTATCGATACA
149028 ATGTATCGATACA
1 ATGTATCGATACA
149041 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:150196 original size:32 final size:33
Alignment explanation
Indices: 150132--150199 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
150122 TGTTACAAGC
** *
150132 CAATGTATCGATACATTTTTTGATGTATCGATA
1 CAATGTATCGATACATACTGTGATGTATCGATA
*
150165 CAATGTATCGATGCATACTGTG-TGTATCGATA
1 CAATGTATCGATACATACTGTGATGTATCGATA
150197 CAA
1 CAA
150200 GTTTGGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATACTGTGATGTATCGATA
Found at i:150278 original size:20 final size:20
Alignment explanation
Indices: 150253--150316 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
150243 TTCTTTTCAA
150253 GTATCGATACATTTGGTCAT
1 GTATCGATACATTTGGTCAT
150273 GTATCGATACA-------AT
1 GTATCGATACATTTGGTCAT
150286 GTATCGATACATTTGGTCAT
1 GTATCGATACATTTGGTCAT
*
150306 GTATTGATACA
1 GTATCGATACA
150317 ATGTATCGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 13 0.36
20 23 0.64
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (20 bp):
GTATCGATACATTTGGTCAT
Found at i:150289 original size:13 final size:13
Alignment explanation
Indices: 150271--150332 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 13
150261 ACATTTGGTC
150271 ATGTATCGATACA
1 ATGTATCGATACA
150284 ATGTATCGATAC-
1 ATGTATCGATACA
*
150296 AT-T-T-GGT-C-
1 ATGTATCGATACA
*
150304 ATGTATTGATACA
1 ATGTATCGATACA
*
150317 ATGTATCGACACA
1 ATGTATCGATACA
150330 ATG
1 ATG
150333 CAATCTGTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
10 2 0.05
11 3 0.08
12 3 0.08
13 26 0.65
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:150295 original size:33 final size:33
Alignment explanation
Indices: 150253--150325 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
150243 TTCTTTTCAA
150253 GTATCGATACATTTGGTCATGTATCGATACAAT
1 GTATCGATACATTTGGTCATGTATCGATACAAT
*
150286 GTATCGATACATTTGGTCATGTATTGATACAAT
1 GTATCGATACATTTGGTCATGTATCGATACAAT
150319 GTATCGA
1 GTATCGA
150326 CACAATGCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (33 bp):
GTATCGATACATTTGGTCATGTATCGATACAAT
Found at i:150937 original size:80 final size:78
Alignment explanation
Indices: 150700--151069 Score: 377
Period size: 79 Copynumber: 4.7 Consensus size: 78
150690 TATTTTGGAG
* * * ** ** * *
150700 ATAAAAATGGGGTTGGAGTATCCCCTCTG-AAATTACGGGGTTGGAGTATCTTCGTTGGTGAAAA
1 ATAAAATTGGGGTTAGAGTAT-CCCT-TGAAAATAAATGGGTTGGAGTATCCCCGATGGTGGAAA
*
150764 ATCGATATTTTAGAA
64 ATCGATGTTTTAGAA
* * * *
150779 ATAAAATAGGGGTTTGAGTATCCCCTCGAAAATAATTGGGTTGGAGTATCCCCGATGGTGGAAAA
1 ATAAAATTGGGGTTAGAGTAT-CCCTTGAAAATAAATGGGTTGGAGTATCCCCGATGGTGGAAAA
150844 TCGATGTTTTAGAA
65 TCGATGTTTTAGAA
* * * *
150858 ATAAAATTGGGGTTAGAGTATCTCTTTGGAAATAAACGGGATT-TATGTATCCCCGATGGTGGAA
1 ATAAAATTGGGGTTAGAGTATC-CCTTGAAAATAAATGGG-TTGGA-GTATCCCCGATGGTGGAA
150922 AATCGATGTTTTAGAA
63 AATCGATGTTTTAGAA
* * * * *
150938 ATAAAATCGGGATTAGAGTATCCCTTCAAAAGT-AATGGGTTGGAGTATCCCCGATGGTAGCAAA
1 ATAAAATTGGGGTTAGAGTATCCCTTGAAAA-TAAATGGGTTGGAGTATCCCCGATGGTGGAAAA
*
151002 TCGGTGTTTTAGAA
65 TCGATGTTTTAGAA
* * * *
151016 ATAAAACTGGGGTTAGAGCATCCCCTCGAAAATAAACAGGGTTGGAGTAGTCCC
1 ATAAAATTGGGGTTAGAGTAT-CCCTTGAAAATAAA-TGGGTTGGAGTA-TCCC
151070 TGTAGACACC
Statistics
Matches: 244, Mismatches: 37, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
78 53 0.22
79 119 0.49
80 68 0.28
81 4 0.02
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (78 bp):
ATAAAATTGGGGTTAGAGTATCCCTTGAAAATAAATGGGTTGGAGTATCCCCGATGGTGGAAAAT
CGATGTTTTAGAA
Found at i:151049 original size:158 final size:159
Alignment explanation
Indices: 150755--151052 Score: 438
Period size: 158 Copynumber: 1.9 Consensus size: 159
150745 GTATCTTCGT
* *
150755 TGGTGAAAAATCGATATTTTAGAAATAAAATAGGGGTTTGAGTATCCCCTCGAAAATAATTGGGT
1 TGGTGAAAAATCGATATTTTAGAAATAAAATAGGGATTAGAGTATCCCCTCGAAAATAATTGGGT
* * * * * *
150820 TGGAGTATCCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAATTGGGGTTAGAGTATCTCTTT
66 TGGAGTATCCCCGATGGTAGAAAATCGATGTTTTAGAAATAAAACTGGGGTTAGAGCATCCCCTC
*
150885 GGAAATAAACGGGATTTATGTATCCCCGA
131 GAAAATAAACGGGATTTATGTATCCCCGA
* * * *
150914 TGGTGGAAAATCGATGTTTTAGAAATAAAATCGGGATTAGAGTATCCCTTC-AAAAGTAA-TGGG
1 TGGTGAAAAATCGATATTTTAGAAATAAAATAGGGATTAGAGTATCCCCTCGAAAA-TAATTGGG
* *
150977 TTGGAGTATCCCCGATGGTAGCAAATCGGTGTTTTAGAAATAAAACTGGGGTTAGAGCATCCCCT
65 TTGGAGTATCCCCGATGGTAGAAAATCGATGTTTTAGAAATAAAACTGGGGTTAGAGCATCCCCT
151042 CGAAAATAAAC
130 CGAAAATAAAC
151053 AGGGTTGGAG
Statistics
Matches: 123, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
158 75 0.61
159 48 0.39
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (159 bp):
TGGTGAAAAATCGATATTTTAGAAATAAAATAGGGATTAGAGTATCCCCTCGAAAATAATTGGGT
TGGAGTATCCCCGATGGTAGAAAATCGATGTTTTAGAAATAAAACTGGGGTTAGAGCATCCCCTC
GAAAATAAACGGGATTTATGTATCCCCGA
Found at i:154752 original size:29 final size:31
Alignment explanation
Indices: 154698--154756 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
154688 AATCGATGTT
154698 TTAGAAATAAAACTAGGGTTGGAGTATCCCC
1 TTAGAAATAAAACTAGGGTTGGAGTATCCCC
*
154729 TTAGAAAT-AAAC-GGGGTTGGAGTATCCC
1 TTAGAAATAAAACTAGGGTTGGAGTATCCC
154757 TGATGGTGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 15 0.56
30 4 0.15
31 8 0.30
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (31 bp):
TTAGAAATAAAACTAGGGTTGGAGTATCCCC
Found at i:154815 original size:80 final size:78
Alignment explanation
Indices: 154674--154867 Score: 264
Period size: 80 Copynumber: 2.5 Consensus size: 78
154664 GTTGCGACAG
* *
154674 TCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAACTAGGGTTGGAGTATCCCCTTAGAAATAA
1 TCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAACGAGGGTTGGAGTATCCCCTCAGAAAT-A
**
154739 ACGGGGTTGGAGTA
65 ACAAGGTTGGAGTA
* * *
154753 TCCCTGATGGTGGAAAATTGGTGTTTTAGAAATAAAATCGA-GGTTGGAGTATCTCCTCAGAAAT
1 TCCC-GATGGTGGAAAATCGATGTTTTAGAAATAAAA-CGAGGGTTGGAGTATCCCCTCAGAAAT
154817 AACAAGGTTGGAGTA
64 AACAAGGTTGGAGTA
* * *
154832 TCCCGATGGTGAAAAATCGATATTTTAAAAATAAAA
1 TCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAA
154868 ACATCAATGA
Statistics
Matches: 101, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
78 27 0.27
79 21 0.21
80 51 0.50
81 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.28
Consensus pattern (78 bp):
TCCCGATGGTGGAAAATCGATGTTTTAGAAATAAAACGAGGGTTGGAGTATCCCCTCAGAAATAA
CAAGGTTGGAGTA
Found at i:160766 original size:79 final size:78
Alignment explanation
Indices: 160618--160814 Score: 184
Period size: 79 Copynumber: 2.5 Consensus size: 78
160608 TAACCTTAAT
* * * * *
160618 AACTTTGTTTCAATGAAAGGTACGAAACT-AACTTAAAAAGGCTCAGTTTTGATAGATTATTCAA
1 AACTTAGTTTCAATGAAA-GTACAAAACTAAACTTAAAAAGGCTCAATTTCGATAGATCATTCAA
*
160682 AACTAAACCTAACA
65 AACTAAACATAACA
*
160696 AACTTAGTTTCAATAGAAAGTACAAAACTAAACTTAAAAAGGCTTAATTTCGATAGATGGCA-T-
1 AACTTAGTTTCAAT-GAAAGTACAAAACTAAACTTAAAAAGGCTCAATTTCGATAGAT--CATTC
* * **
160759 GATACTAAACATAATG
63 AAAACTAAACATAACA
* * * * *
160775 GACTTGGTTTCGATGGAAAATACAAAACTAAATTTAAAAA
1 AACTTAGTTTCAAT-GAAAGTACAAAACTAAACTTAAAAA
160815 AGTTCACTAT
Statistics
Matches: 98, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
78 22 0.22
79 74 0.76
80 1 0.01
81 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (78 bp):
AACTTAGTTTCAATGAAAGTACAAAACTAAACTTAAAAAGGCTCAATTTCGATAGATCATTCAAA
ACTAAACATAACA
Found at i:163963 original size:21 final size:21
Alignment explanation
Indices: 163939--163988 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
163929 GGAACCATTT
163939 GGTGATTTGACTAAATCTTAG
1 GGTGATTTGACTAAATCTTAG
163960 GGTGATTTGACTAAATCTTAG
1 GGTGATTTGACTAAATCTTAG
*
163981 GGGGATTT
1 GGTGATTT
163989 TAGTAGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.08, G:0.28, T:0.38
Consensus pattern (21 bp):
GGTGATTTGACTAAATCTTAG
Found at i:164046 original size:93 final size:92
Alignment explanation
Indices: 163881--164051 Score: 240
Period size: 93 Copynumber: 1.8 Consensus size: 92
163871 GATTGGGTTG
163881 AATCTTAAGGGGTTTTAGTAATTTTTCCAAAGTTTTTACATGCATTTTGGAACCATTTGGTGATT
1 AATCTTAAGGGGTTTTAGTAATTTTTCCAAAGTTTTTACATGCATTTTGGAACCATTTGGTGATT
*
163946 TGACTAAATCTTAGGGTGATTTGACTA
66 TGACTAAACCTTAGGGTGATTTGACTA
* * **
163973 AATCTTAGGGGGATTTTAGTAGA-TTTTCCAAATTTTTTACATGTTTTTTAGG-ACCATTTGGTG
1 AATCTTAAGGGG-TTTTAGTA-ATTTTTCCAAAGTTTTTACATGCATTTT-GGAACCATTTGGTG
164036 ATTTTG-CTAAACCTTA
63 A-TTTGACTAAACCTTA
164052 AGGGCTGTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
92 11 0.16
93 52 0.74
94 7 0.10
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (92 bp):
AATCTTAAGGGGTTTTAGTAATTTTTCCAAAGTTTTTACATGCATTTTGGAACCATTTGGTGATT
TGACTAAACCTTAGGGTGATTTGACTA
Found at i:165520 original size:12 final size:12
Alignment explanation
Indices: 165503--165529 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
165493 TCCGAGTCAA
165503 CTTCATCATCAT
1 CTTCATCATCAT
165515 CTTCATCATCAT
1 CTTCATCATCAT
165527 CTT
1 CTT
165530 TGATGGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (12 bp):
CTTCATCATCAT
Found at i:167150 original size:13 final size:13
Alignment explanation
Indices: 167132--167169 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
167122 ACATTTGATC
167132 ATGTATCGATATA
1 ATGTATCGATATA
*
167145 ATGTATCGATACA
1 ATGTATCGATATA
*
167158 CTGTATCGATAT
1 ATGTATCGATAT
167170 TGAGAGAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (13 bp):
ATGTATCGATATA
Found at i:167261 original size:20 final size:19
Alignment explanation
Indices: 167197--167268 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
167187 TGCCAATTTC
*
167197 ATGTATCGATACAATTCAAT
1 ATGTATCGATACAA-GCAAT
* *
167217 GTGTATCGATACCAAG-AAC
1 ATGTATCGATA-CAAGCAAT
167236 ATGTATCGATACTAAGCAAT
1 ATGTATCGATAC-AAGCAAT
*
167256 ATGTATTGATACA
1 ATGTATCGATACA
167269 TCTAGGTGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
18 1 0.02
19 16 0.37
20 23 0.53
21 3 0.07
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACAAGCAAT
Found at i:167393 original size:19 final size:18
Alignment explanation
Indices: 167364--167415 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
167354 GATACTTTAG
167364 ATTATTTTTTACTTGAAAA
1 ATTA-TTTTTACTTGAAAA
167383 CATTATTTTTACGCTTGAAAA
1 -ATTATTTTTA--CTTGAAAA
*
167404 A-TATTTATACTT
1 ATTATTTTTACTT
167416 AACTCTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.10
19 13 0.45
20 5 0.17
21 8 0.28
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTATTTTTACTTGAAAA
Found at i:171967 original size:106 final size:106
Alignment explanation
Indices: 171708--171976 Score: 283
Period size: 106 Copynumber: 2.5 Consensus size: 106
171698 AAGTGGATAA
* * * * *
171708 GTGCCACCAACTTGTGTGGGTTTTGAGATGGGTAAGTGTCTTGCTCTTT-AAGGGCTAGAGGTAG
1 GTGCCACTAACTTGTATGAGCTTTGAGATGGGTAAGTGTCTTGCTCTTTGAA-GACTAGAGGTAG
* ** * *
171772 GTAAGATAAAGTGTCATTCTCTTTGAGGATTGAGATAGGTAG
65 GTAAGAAAAAGCATCATTCTCTTTGAGGACTGAGACAGGTAG
* * * **
171814 GTGCCACTAGCTTGTGTGAGCTTTGAGATGGGTGAGCATCTTGCTCTTTGAAGACTAGAGGTAGG
1 GTGCCACTAACTTGTATGAGCTTTGAGATGGGTAAGTGTCTTGCTCTTTGAAGACTAGAGGTAGG
* *
171879 TAAGAAAAAGCATC-TTGCTTTTTGAGGACTGAGGCAGGTAG
66 TAAGAAAAAGCATCATT-CTCTTTGAGGACTGAGACAGGTAG
* * * * * *
171920 GTGGCACTAATTTGTATG-GCCTTTGAGATGGTTAAGTGTCCTACTCTTTGAGGACTA
1 GTGCCACTAACTTGTATGAG-CTTTGAGATGGGTAAGTGTCTTGCTCTTTGAAGACTA
171977 AGGAAGATAA
Statistics
Matches: 134, Mismatches: 26, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
105 3 0.02
106 129 0.96
107 2 0.01
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.32
Consensus pattern (106 bp):
GTGCCACTAACTTGTATGAGCTTTGAGATGGGTAAGTGTCTTGCTCTTTGAAGACTAGAGGTAGG
TAAGAAAAAGCATCATTCTCTTTGAGGACTGAGACAGGTAG
Found at i:172014 original size:70 final size:72
Alignment explanation
Indices: 171924--172062 Score: 167
Period size: 72 Copynumber: 2.0 Consensus size: 72
171914 AGGTAGGTGG
* ***
171924 CACTAATTTGTATGGCCTTTG-AGATGGTTAA-GTGTCCTACTCTTTGAGGACTA-AGGAAGATA
1 CACTAATTTGTATGGCCTTTGAAGAAGAAAAAGGTGTCCTACTCTTTGAGGACTAGA-GAAGATA
171986 AGTGATGC
65 AGTGATGC
* * * * *
171994 CACTAGTTTGTGTGGGCTTTGAAGAAGAAAAAGGTGTCCTACTTTTTGAGGACTAGAGTAGATAA
1 CACTAATTTGTATGGCCTTTGAAGAAGAAAAAGGTGTCCTACTCTTTGAGGACTAGAGAAGATAA
172059 GTGA
66 GTGA
172063 AGAAAATGCA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
70 18 0.32
71 6 0.11
72 32 0.56
73 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (72 bp):
CACTAATTTGTATGGCCTTTGAAGAAGAAAAAGGTGTCCTACTCTTTGAGGACTAGAGAAGATAA
GTGATGC
Found at i:174505 original size:36 final size:32
Alignment explanation
Indices: 174426--174518 Score: 98
Period size: 36 Copynumber: 2.8 Consensus size: 32
174416 CAATACTATA
*
174426 TTTCAAGGCTAAGGTAGAAAC-CTCCCTATCT
1 TTTCAAGGCTAAGATAGAAACTCTCCCTATCT
* *
174457 TTTCACGAGCTAAGATAGAATCTCTCTTCCTATCTT
1 TTTCAAG-GCTAAGATAGAAACTCTC--CCTATC-T
*
174493 TTTCAAAGGCTAAGATAGAACCTCTC
1 TTTC-AAGGCTAAGATAGAAACTCTC
174519 AATCACTTAG
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
31 6 0.12
32 12 0.24
33 3 0.06
35 6 0.12
36 22 0.43
37 2 0.04
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (32 bp):
TTTCAAGGCTAAGATAGAAACTCTCCCTATCT
Found at i:174909 original size:20 final size:20
Alignment explanation
Indices: 174886--174938 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
174876 ACACGCTTCT
174886 ATGTATCGATACAATTCACA
1 ATGTATCGATACAATTCACA
174906 ATGTATCGATACAATTCACA
1 ATGTATCGATACAATTCACA
174926 ATGTATCGATACA
1 ATGTATCGATACA
174939 TGCATTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAATTCACA
Found at i:175023 original size:20 final size:20
Alignment explanation
Indices: 174980--175023 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
174970 TATATCTATT
* *
174980 CAATTCACCATGTATTGATG
1 CAATTCACCATGTATCGATA
*
175000 CAATTCATCATGTATCGATA
1 CAATTCACCATGTATCGATA
175020 CAAT
1 CAAT
175024 GTGTCGATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (20 bp):
CAATTCACCATGTATCGATA
Found at i:175111 original size:19 final size:20
Alignment explanation
Indices: 175083--175132 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
175073 TATTTCAAGG
*
175083 TGTATTGATACTAAG-AACA
1 TGTATCGATACTAAGCAACA
*
175102 TGTATCGATACTAAGCAATA
1 TGTATCGATACTAAGCAACA
175122 TGTATCGATAC
1 TGTATCGATAC
175133 ATCTGGGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TGTATCGATACTAAGCAACA
Found at i:175229 original size:20 final size:20
Alignment explanation
Indices: 175201--175256 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
175191 TATGCATTTG
* *
175201 ACCTTTGTATTGATACAAAT
1 ACCTATGTATCGATACAAAT
175221 ACCTATGTATCGATACAAAT
1 ACCTATGTATCGATACAAAT
*
175241 ACTTATGTATCGATAC
1 ACCTATGTATCGATAC
175257 TTTAAATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (20 bp):
ACCTATGTATCGATACAAAT
Found at i:175285 original size:20 final size:21
Alignment explanation
Indices: 175262--175305 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
175252 GATACTTTAA
175262 ATTATTTT-TACTTGAAAAAC
1 ATTATTTTATACTTGAAAAAC
*
175282 ATTATTTTGATGCTTGAAAAAC
1 ATTATTTT-ATACTTGAAAAAC
175304 AT
1 AT
175306 CTATACTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
22 13 0.62
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (21 bp):
ATTATTTTATACTTGAAAAAC
Found at i:177291 original size:20 final size:20
Alignment explanation
Indices: 177266--177320 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
177256 CTAAACCCTG
177266 AAATGTATCGATACACCTTT
1 AAATGTATCGATACACCTTT
177286 AAATGTATCGATACACCTTT
1 AAATGTATCGATACACCTTT
177306 AAATGTATCGATACA
1 AAATGTATCGATACA
177321 TAATGCACAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (20 bp):
AAATGTATCGATACACCTTT
Found at i:177353 original size:20 final size:21
Alignment explanation
Indices: 177306--177359 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
177296 ATACACCTTT
*
177306 AAATGTATCGATACATAATGC
1 AAATGTATCGATACATAATCC
* *
177327 ACA-GTATCGATACATGA-CC
1 AAATGTATCGATACATAATCC
177346 AAATGTATCGATAC
1 AAATGTATCGATAC
177360 TTGTAAAGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.11
20 23 0.82
21 2 0.07
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (21 bp):
AAATGTATCGATACATAATCC
Found at i:179412 original size:21 final size:20
Alignment explanation
Indices: 179385--179445 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
179375 CAAAATTTTA
179385 TTTAACTCA-TCATTTTCATT
1 TTTAACTCACTCATTTTC-TT
*
179405 TTGTAACTCACTTATTTTCTT
1 TT-TAACTCACTCATTTTCTT
*
179426 TTTCAACTCATTCATTTTCT
1 TTT-AACTCACTCATTTTCT
179446 CCTCTAGTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 3 0.09
21 25 0.71
22 7 0.20
ACGTcount: A:0.21, C:0.21, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTAACTCACTCATTTTCTT
Found at i:180526 original size:20 final size:21
Alignment explanation
Indices: 180501--180544 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
180491 GATACTTTGA
180501 ATTATTTTTA-CCTGAAAAAC
1 ATTATTTTTAGCCTGAAAAAC
*
180521 ATTATTTTTATGCTTGAAAAAC
1 ATTATTTTTA-GCCTGAAAAAC
180543 AT
1 AT
180545 CTATACTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (21 bp):
ATTATTTTTAGCCTGAAAAAC
Found at i:182862 original size:30 final size:30
Alignment explanation
Indices: 182790--182863 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
182780 TTCTTTATTA
*
182790 TATCGATACATTATGGGCTTAACCCAGATG
1 TATCGATACATTCTGGGCTTAACCCAGATG
* **
182820 TATCGATACATTCTGGGTTTTGCCCAGATG
1 TATCGATACATTCTGGGCTTAACCCAGATG
*
182850 TATTGATACATTCT
1 TATCGATACATTCT
182864 TCATTGCATC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (30 bp):
TATCGATACATTCTGGGCTTAACCCAGATG
Found at i:185912 original size:10 final size:10
Alignment explanation
Indices: 185876--185926 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
185866 AAACCAAAAT
*
185876 AAAAAAAATA
1 AAAAAAAAGA
185886 AAAAAAAAGA
1 AAAAAAAAGA
**
185896 ACCAAAAA-A
1 AAAAAAAAGA
*
185905 AAAGAAAAGA
1 AAAAAAAAGA
185915 AAAGAAAAAGA
1 AAA-AAAAAGA
185926 A
1 A
185927 GAACGACAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
9 6 0.19
10 19 0.59
11 7 0.22
ACGTcount: A:0.84, C:0.04, G:0.10, T:0.02
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:187256 original size:62 final size:62
Alignment explanation
Indices: 187128--187949 Score: 921
Period size: 62 Copynumber: 13.4 Consensus size: 62
187118 TTTTTAGCCC
* * * *
187128 TTTAGTCCTCAAAGAGTAGGATGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * *
187190 TTTAGTCCTTAAAGAGCAGGACGTC-TTTCCTTTTTAAAGCCCACACGAGCTGGTGCCACATT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC-CT
* * * *
187252 TTTAGTCCTCAAAGAGCAGGATGCC-TTTTCTTTTTAAAGCCCACACGAGTTGATGGCACCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
187313 TTTAGTCCTCAAAGAGTAGGACGTCTTTTTCTTTTCAAAGCCTACACGAGTTGGTAGCACCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
187375 TTTAGTCCTCGAAA-AGTAGGAAGCCTTTTTATTTTTAAAGCCCACATGAGTTGGTGGCACCT
1 TTTAGTCCTC-AAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
* * *
187437 TTCAGTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCATCC-
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCT
* * **
187499 TTTAGTCCTCAAAGAGCAAGACG-CTTTTTCCTTTTCAAAGCTCACATAAGTTGGTGGCACCCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCA-CCT
* * * *
187562 TTT-GTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCTACACTAGTTGGTGGCACGT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
* ** * *
187623 TTTAG-CCTTCAAAGAGCAAGATTCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGACACAT
1 TTTAGTCC-TCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
* * * *
187685 TTTAGCCCTTAAAGAACAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACGT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * *
187747 TTCAGCCCACAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCATACAATTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
* * * * * ** *
187808 TTCAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTT-AAAGGCCACATAAGTTGGTGGCACGT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
* * *
187869 TTCAGTCCTCAAAGAGCAGGACG-C--TTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
* *
187928 TCTAGTCCTCAAAGAGTAGGAC
1 TTTAGTCCTCAAAGAGCAGGAC
187950 ACACTTTATT
Statistics
Matches: 651, Mismatches: 97, Indels: 27
0.84 0.13 0.03
Matches are distributed among these distances:
58 6 0.01
59 42 0.06
60 1 0.00
61 163 0.25
62 423 0.65
63 16 0.02
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (62 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
Found at i:188062 original size:41 final size:42
Alignment explanation
Indices: 187932--188373 Score: 279
Period size: 41 Copynumber: 10.5 Consensus size: 42
187922 GCACCTTCTA
* * ** *
187932 GTCCTCAAAGAGTAGGACACACTTTATTTCCTTTTCTCCTTT
1 GTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTTTCCTTT
* ** ** *
187974 GTCCTCAAAGCGCTGGACACACTTAATTTCCTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAAGATGCACTTTATTTCCTT-TTTT-CC-TTT
*
188019 GTCCTCAAAGAGCAAGATGTACTTTATTT-CTTTTTTCCTTT
1 GTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTTTCCTTT
* * *
188060 GTCCTCAAAGAGC-AG-GGCATACCTTATTTCCTTCTTTTCTCTTA
1 GTCCTCAAAGAGCAAGATGC--ACTTTATTTCCTT-TTTTC-CTTT
* * * *
188104 GTCTTGAAAGAGTAAGATGC-C--T-TTTCCTTTTCTCCTTT
1 GTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTTTCCTTT
*
188142 GTCCTCAAAGAGCAGGA--CACATTTGAATTTCCTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAAGATGCAC-TTT--ATTTCCTT-TTTT-CC-TTT
* *
188188 GTCCTCAAAGAGCACGATGCACTTTTTTTCC-TTTTTCCTTT
1 GTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTTTCCTTT
* * * *
188229 GTCCTCAAAGAGTAAGGTGCACCTCATTTCCTTATTTTTCCTTT
1 GTCCTCAAAGAGCAAGATGCACTTTATTTCC-T-TTTTTCCTTT
* * * *
188273 GTCTTCAAAGAGTAGGATGC-C--T-TTTCCTTTTCTCCTTT
1 GTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTTTCCTTT
* * ** * *
188311 TTCCTCAAGGAGCAAGACCCA-TTTCA-TT-CTCTTTTCCTTC
1 GTCCTCAAAGAGCAAGATGCACTTT-ATTTCCTTTTTTCCTTT
* *
188351 GTCCTCGAAGAGCAAGACGCACT
1 GTCCTCAAAGAGCAAGATGCACT
188374 CCTTTTCCTT
Statistics
Matches: 315, Mismatches: 54, Indels: 63
0.73 0.12 0.15
Matches are distributed among these distances:
36 1 0.00
37 1 0.00
38 38 0.12
39 6 0.02
40 42 0.13
41 56 0.18
42 36 0.11
43 25 0.08
44 49 0.16
45 34 0.11
46 21 0.07
47 3 0.01
48 3 0.01
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (42 bp):
GTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTTTCCTTT
Found at i:188233 original size:169 final size:168
Alignment explanation
Indices: 187958--188373 Score: 551
Period size: 169 Copynumber: 2.5 Consensus size: 168
187948 ACACACTTTA
* * *
187958 TTTCCTTTTCTCCTTTGTCCTCAAAGCGCTGGACACACTTAATTTCCTTCTTTTCCCTTTTGTCC
1 TTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACATTTAATTTCCTTCTTTTCCCTTTTGTCC
* * * *
188023 TCAAAGAGCAAGATGTACTTTATTTCTTTTTTCCTTTGTCCTCAAAGAG-CAGG-GCATACCTTA
66 TCAAAGAGCAAGATGCACTTTATTTCCTTTTTCCTTTGTCCTCAAAGAGTAAGGTGC--ACCTCA
* *
188086 TTTCCTT-CTTTTCTCTTAGTCTTGAAAGAGTAAGATGCCT
129 TTTCCTTATTTTTC-CTTAGTCTTCAAAGAGTAAGATGCCT
188126 TTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACATTTGAATTTCCTTCTTTTCCCTTTTGTC
1 TTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACATTT-AATTTCCTTCTTTTCCCTTTTGTC
* *
188191 CTCAAAGAGCACGATGCACTTTTTTTCCTTTTTCCTTTGTCCTCAAAGAGTAAGGTGCACCTCAT
65 CTCAAAGAGCAAGATGCACTTTATTTCCTTTTTCCTTTGTCCTCAAAGAGTAAGGTGCACCTCAT
* *
188256 TTCCTTATTTTTCCTTTGTCTTCAAAGAGTAGGATGCCT
130 TTCCTTATTTTTCCTTAGTCTTCAAAGAGTAAGATGCCT
* * * * * *
188295 TTTCCTTTTCTCCTTTTTCCTCAAGGAGCAAGACCCATTTCA-TT-C-TCTTTT-CC-TTCGTCC
1 TTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACATTTAATTTCCTTCTTTTCCCTTTTGTCC
* *
188355 TCGAAGAGCAAGACGCACT
66 TCAAAGAGCAAGATGCACT
188374 CCTTTTCCTT
Statistics
Matches: 222, Mismatches: 22, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
163 22 0.10
164 2 0.01
165 6 0.03
166 1 0.00
167 2 0.01
168 38 0.17
169 141 0.64
170 8 0.04
171 2 0.01
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.41
Consensus pattern (168 bp):
TTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACATTTAATTTCCTTCTTTTCCCTTTTGTCC
TCAAAGAGCAAGATGCACTTTATTTCCTTTTTCCTTTGTCCTCAAAGAGTAAGGTGCACCTCATT
TCCTTATTTTTCCTTAGTCTTCAAAGAGTAAGATGCCT
Found at i:188239 original size:87 final size:87
Alignment explanation
Indices: 187932--188401 Score: 393
Period size: 86 Copynumber: 5.7 Consensus size: 87
187922 GCACCTTCTA
* * ** * *
187932 GTCCTCAAAGAGTAGGACACACTTTATTTCCTTTTCTCCTTTGTCCTCAAAGCGCTGGACACACT
1 GTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACACT
187997 TAATTTCCTTCTTTTCCCTTTT
66 TAATTTCCTTCTTTTCCCTTTT
* * * *
188019 GTCCTCAAAGAGCAAGATGTACTTTATTT-CTTTTTTCCTTTGTCCTCAAAGAGCAGGGCATACC
1 GTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACA-C
* *
188083 TT-ATTTCCTTCTTTTCTC-TTA
65 TTAATTTCCTTCTTTTCCCTTTT
* * * *
188104 GTCTTGAAAGAGTAAGATGC-C--T-TTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACATT
1 GTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACACT
188165 TGAATTTCCTTCTTTTCCCTTTT
66 T-AATTTCCTTCTTTTCCCTTTT
* * * *
188188 GTCCTCAAAGAGCACGATGCACTTTTTTTCCTTTT-TCCTTTGTCCTCAAAGAGTAAGGTGCAC-
1 GTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTCTCCTTTGTCCTCAAAGAG-CAGG-ACACA
* * *
188251 C-TCATTTCCTTATTTTTCC-TTT
64 CTTAATTTCCTTCTTTTCCCTTTT
* * * * * * * *
188273 GTCTTCAAAGAGTAGGATGC-C--T-TTTCCTTTTCTCCTTTTTCCTCAAGGAGCAAGACCCATT
1 GTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACACT
* *
188334 TCA-TT-C-TCTTTT-CC-TTC
66 TAATTTCCTTCTTTTCCCTTTT
* *
188351 GTCCTCGAAGAGCAAGACGCAC------TCC-TTT-TCCTTTGTCCTCAAAGAGCAGGA
1 GTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGA
188402 TACCCTTTCC
Statistics
Matches: 316, Mismatches: 52, Indels: 43
0.77 0.13 0.10
Matches are distributed among these distances:
74 20 0.06
75 3 0.01
76 3 0.01
78 19 0.06
79 6 0.02
80 3 0.01
81 18 0.06
82 51 0.16
83 15 0.05
84 20 0.06
85 39 0.12
86 57 0.18
87 47 0.15
88 12 0.04
89 3 0.01
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (87 bp):
GTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACACT
TAATTTCCTTCTTTTCCCTTTT
Found at i:189005 original size:30 final size:30
Alignment explanation
Indices: 188969--189042 Score: 148
Period size: 30 Copynumber: 2.5 Consensus size: 30
188959 CATTCTTCAT
188969 TGTATCGATACATTATGGGTTTTACCCAAA
1 TGTATCGATACATTATGGGTTTTACCCAAA
188999 TGTATCGATACATTATGGGTTTTACCCAAA
1 TGTATCGATACATTATGGGTTTTACCCAAA
189029 TGTATCGATACATT
1 TGTATCGATACATT
189043 CTTCATTGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (30 bp):
TGTATCGATACATTATGGGTTTTACCCAAA
Found at i:189054 original size:20 final size:21
Alignment explanation
Indices: 189027--189083 Score: 91
Period size: 20 Copynumber: 2.8 Consensus size: 21
189017 GTTTTACCCA
189027 AATGTATCGATACATTCT-TC
1 AATGTATCGATACATTCTCTC
*
189047 ATTGTATCGATACATT-TCTC
1 AATGTATCGATACATTCTCTC
189067 AATGTATCGATACATTC
1 AATGTATCGATACATTC
189084 ACGCATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (21 bp):
AATGTATCGATACATTCTCTC
Found at i:191530 original size:28 final size:28
Alignment explanation
Indices: 191494--191564 Score: 133
Period size: 28 Copynumber: 2.5 Consensus size: 28
191484 CCATAATCGA
191494 GGATACTCCAACCCCGTTATTTCTGAGG
1 GGATACTCCAACCCCGTTATTTCTGAGG
*
191522 GGATACTCCAACCCCGTTATTTTTGAGG
1 GGATACTCCAACCCCGTTATTTCTGAGG
191550 GGATACTCCAACCCC
1 GGATACTCCAACCCC
191565 AGTTTTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.27
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATTTCTGAGG
Found at i:191596 original size:107 final size:107
Alignment explanation
Indices: 191439--191641 Score: 259
Period size: 107 Copynumber: 1.9 Consensus size: 107
191429 TTTTATTTCC
* *
191439 GAGGCGATACTCCAAACCCGGTTTTATTTCTAAAACACAAATATTCCATAATC-GAGGATACTCC
1 GAGGCGATACTCCAAACCCAGTTTTATTTCCAAAACACAAATATTCCATAATCAG-GGATACTCC
191503 AACCCCGTTA-TTTCTGAGGGGATACTCCAACCCCGTTATTTTT
65 AACCCCGTTATTTTC-GAGGGGATACTCCAACCCCGTTATTTTT
* * * * * * *
191546 GAGGGGATACTCCAACCCCAGTTTTATTTCCAAAATATC-GATTTTTCATAATCAGGGATGCTCC
1 GAGGCGATACTCCAAACCCAGTTTTATTTCCAAAACA-CAAATATTCCATAATCAGGGATACTCC
* *
191610 AATCCTGTTATTTTCGAGGGGATACTCCAACC
65 AACCCCGTTATTTTCGAGGGGATACTCCAACC
191642 TTGATTTTAT
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
107 76 0.93
108 6 0.07
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (107 bp):
GAGGCGATACTCCAAACCCAGTTTTATTTCCAAAACACAAATATTCCATAATCAGGGATACTCCA
ACCCCGTTATTTTCGAGGGGATACTCCAACCCCGTTATTTTT
Found at i:191604 original size:79 final size:78
Alignment explanation
Indices: 191521--191896 Score: 450
Period size: 79 Copynumber: 4.8 Consensus size: 78
191511 TATTTCTGAG
* * *
191521 GGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAATATCG
1 GGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCA
*
191586 ATTTTTCATAATC
66 ATTTTTCACAATC
* * * * ** *
191599 AGGGATGCTCCAATCCTGTTATTTTCGAGGGGATACTCCAA-CCTTGATTTTATTTTCAAAACAC
1 -GGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAG-TTTTATTTCCAAAACAC
191663 CAATTTTTCACAATC
64 CAATTTTTCACAATC
* * * * * *
191678 GGGGATACTACAACCCCGTTATTTCTGAAGGGATACTCTAACCCTAGTTTTATTTCCAAAACACT
1 -GGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACC
191743 AATTTTTCACAATC
65 AATTTTTCACAATC
* ** * * *
191757 GGGAATACTCTAACCCCGTTATTTTCAAGGGGATACTCCAACCTCGGTTTTATTTCTAAAACACC
1 GGG-ATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACC
*
191822 GATTTTTCACAATC
65 AATTTTTCACAATC
* *
191836 GAGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCC-GATTTTATCTCCAAAA
1 G-GGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAG-TTTTATTTCCAAAA
191897 TATTAAACTT
Statistics
Matches: 249, Mismatches: 43, Indels: 10
0.82 0.14 0.03
Matches are distributed among these distances:
78 7 0.03
79 236 0.95
80 6 0.02
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (78 bp):
GGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCA
ATTTTTCACAATC
Found at i:191736 original size:158 final size:158
Alignment explanation
Indices: 191520--191899 Score: 525
Period size: 158 Copynumber: 2.4 Consensus size: 158
191510 TTATTTCTGA
*
191520 GGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAATATC
1 GGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAA-CCCAGTTTTATTTCCAAAATATC
* * * * * * *
191585 -GATTTTTCATAATCAGGG-ATGCTCCAATCCTGTTATTTTCGAGGGGATACTCCAACCTTGATT
65 TAATTTTTCACAATC-GGGAATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCTCGATT
191648 TTATTT-TCAAAACACCAATTTTTCACAATC
129 TTATTTCT-AAAACACCAATTTTTCACAATC
* * * *
191678 GGGGATACTACAACCCCGTTATTTCTGAAGGGATACTCTAACCCTAGTTTTATTTCCAAAACA-C
1 GGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCC-AGTTTTATTTCCAAAATATC
* *
191742 TAATTTTTCACAATCGGGAATACTCTAACCCCGTTATTTTCAAGGGGATACTCCAACCTCGGTTT
65 TAATTTTTCACAATCGGGAATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCTCGATTT
*
191807 TATTTCTAAAACACCGATTTTTCACAATC
130 TATTTCTAAAACACCAATTTTTCACAATC
* * *
191836 GAGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATCTCCAAAATAT
1 GGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCAG-TTTTATTTCCAAAATAT
191900 TAAACTTTTT
Statistics
Matches: 194, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
157 8 0.04
158 185 0.95
159 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (158 bp):
GGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCAGTTTTATTTCCAAAATATCT
AATTTTTCACAATCGGGAATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCTCGATTTT
ATTTCTAAAACACCAATTTTTCACAATC
Found at i:192652 original size:32 final size:30
Alignment explanation
Indices: 192616--192674 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
192606 GAAATCAAAT
192616 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
192648 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
192675 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:192972 original size:13 final size:13
Alignment explanation
Indices: 192954--192979 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
192944 CAATTTTTTG
192954 TGTATCGATACAT
1 TGTATCGATACAT
192967 TGTATCGATACAT
1 TGTATCGATACAT
192980 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:192991 original size:32 final size:33
Alignment explanation
Indices: 192934--192997 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
192924 TACAAGCCAA
**
192934 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
192967 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
192998 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:195554 original size:13 final size:13
Alignment explanation
Indices: 195536--195573 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
195526 ATAATCCCCC
195536 TGTATCGATACAG
1 TGTATCGATACAG
*
195549 TGTATCGATACAT
1 TGTATCGATACAG
195562 TGTATCGATACA
1 TGTATCGATACA
195574 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:197675 original size:15 final size:15
Alignment explanation
Indices: 197655--197685 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
197645 ATTTCGTTTG
*
197655 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
197670 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
197685 G
1 G
197686 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:199517 original size:21 final size:21
Alignment explanation
Indices: 199488--199532 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
199478 AAATTTTTAT
*
199488 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
199508 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
199530 TTT
1 TTT
199533 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:201450 original size:32 final size:30
Alignment explanation
Indices: 201414--201472 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
201404 GAAATCAAAT
201414 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
201446 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
201473 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:201770 original size:13 final size:13
Alignment explanation
Indices: 201752--201777 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
201742 CAATTTTTTG
201752 TGTATCGATACAT
1 TGTATCGATACAT
201765 TGTATCGATACAT
1 TGTATCGATACAT
201778 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:201789 original size:32 final size:33
Alignment explanation
Indices: 201732--201795 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
201722 TACAAGCCAA
**
201732 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
201765 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
201796 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:209323 original size:3 final size:3
Alignment explanation
Indices: 209315--209423 Score: 155
Period size: 3 Copynumber: 36.3 Consensus size: 3
209305 GCAATGTTTC
209315 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
209363 TCA TCA TCA TCA TCA TTA TTG TTA TTA TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
209411 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
209424 ATAGATGGCT
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 100 1.00
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:221168 original size:13 final size:13
Alignment explanation
Indices: 221150--221201 Score: 95
Period size: 13 Copynumber: 4.0 Consensus size: 13
221140 ACAACATTCT
221150 TTGTATCGATACA
1 TTGTATCGATACA
221163 TTGTATCGATACA
1 TTGTATCGATACA
221176 TTGTATCGATACA
1 TTGTATCGATACA
*
221189 CTGTATCGATACA
1 TTGTATCGATACA
221202 GGGGGATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:226141 original size:21 final size:21
Alignment explanation
Indices: 226108--226148 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
226098 CTAAGTAAAA
226108 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
226129 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
226149 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:226213 original size:20 final size:19
Alignment explanation
Indices: 226188--226258 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
226178 ACCCTGAAAA
226188 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
226208 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
226227 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
226248 GTATCGATACA
1 GTATCGATACA
226259 GGTCATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Done.