Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold83
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: 1211110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 9456 characters in sequence are not A, C, G, or T
File 2 of 8
Found at i:198780 original size:13 final size:13
Alignment explanation
Indices: 198762--198800 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
198752 ACATTTTTCT
198762 TTGTATCGATACA
1 TTGTATCGATACA
198775 TTGTATCGATACA
1 TTGTATCGATACA
198788 TTGTATCGATACA
1 TTGTATCGATACA
198801 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:198964 original size:20 final size:20
Alignment explanation
Indices: 198921--198966 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
198911 AAATCTTTTG
198921 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
198942 CAAATTACTTAGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
198962 CAAAA
1 CAAAA
198967 CCAGCATCAA
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:0.35, C:0.17, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:201373 original size:13 final size:13
Alignment explanation
Indices: 201355--201380 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
201345 TACAGCAAGT
201355 ATGTATCGATACA
1 ATGTATCGATACA
201368 ATGTATCGATACA
1 ATGTATCGATACA
201381 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:201465 original size:20 final size:21
Alignment explanation
Indices: 201435--201473 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
201425 CTATATTTTC
201435 AAATATGTATCGATACATTAA
1 AAATATGTATCGATACATTAA
201456 AAAT-TGTATCGATACATT
1 AAATATGTATCGATACATT
201474 TACACGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (21 bp):
AAATATGTATCGATACATTAA
Found at i:205614 original size:20 final size:20
Alignment explanation
Indices: 205584--205639 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
205574 ACTGCCAGTT
*
205584 TCATATATCGATACAATTG-
1 TCATGTATCGATACAATTGA
*
205603 TCCATGTATCGATATAA-TGA
1 T-CATGTATCGATACAATTGA
205623 TCATGTATCGATACAAT
1 TCATGTATCGATACAAT
205640 GTATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (20 bp):
TCATGTATCGATACAATTGA
Found at i:205643 original size:13 final size:13
Alignment explanation
Indices: 205625--205651 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
205615 TATAATGATC
205625 ATGTATCGATACA
1 ATGTATCGATACA
205638 ATGTATCGATACA
1 ATGTATCGATACA
205651 A
1 A
205652 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:205670 original size:33 final size:32
Alignment explanation
Indices: 205606--205670 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
205596 ACAATTGTCC
* * * *
205606 ATGTATCGATATAATGATCATGTATCGATACA
1 ATGTATCGATACAAAGATAATGTATCAATACA
205638 ATGTATCGATACAAAGCATAATGTATCAATACA
1 ATGTATCGATACAAAG-ATAATGTATCAATACA
205671 TTTGGGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (32 bp):
ATGTATCGATACAAAGATAATGTATCAATACA
Found at i:208222 original size:13 final size:13
Alignment explanation
Indices: 208204--208230 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
208194 ATAGTAACCC
208204 ATGTATCGATACA
1 ATGTATCGATACA
208217 ATGTATCGATACA
1 ATGTATCGATACA
208230 A
1 A
208231 GGAATGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:210003 original size:28 final size:28
Alignment explanation
Indices: 209921--210074 Score: 179
Period size: 27 Copynumber: 5.4 Consensus size: 28
209911 GTCGACATAT
*
209921 GTGGCAACC-TTCAAAGCCCACAAATCA
1 GTGGCAACCTTTCAAAGCCCACAAGTCA
*
209948 GTGGCACCCTTTTTCAAAAGCCCACAAGTCA
1 GTGGCAACC--TTTC-AAAGCCCACAAGTCA
*
209979 GTGGCAACCTTTAAAAGCCCACAAGTCA
1 GTGGCAACCTTTCAAAGCCCACAAGTCA
*
210007 GTGGCAACC-TTCAAAGCCCACAAATCA
1 GTGGCAACCTTTCAAAGCCCACAAGTCA
* * *
210034 GTGGCACCCTTTTTCGAAGCCCACAAGTCG
1 GTGGCAACC--TTTCAAAGCCCACAAGTCA
210064 GTGGC-ACCTTT
1 GTGGCAACCTTT
210075 TTCATCTTTA
Statistics
Matches: 109, Mismatches: 11, Indels: 14
0.81 0.08 0.10
Matches are distributed among these distances:
27 35 0.32
28 24 0.22
29 5 0.05
30 23 0.21
31 22 0.20
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (28 bp):
GTGGCAACCTTTCAAAGCCCACAAGTCA
Found at i:210122 original size:52 final size:51
Alignment explanation
Indices: 210065--210284 Score: 195
Period size: 52 Copynumber: 4.4 Consensus size: 51
210055 CACAAGTCGG
*
210065 TGGCACCTTTTTCATCTTTAAGTCCAATATAGCTGACCTTGAATCAGCACAT
1 TGGCACCTTTTTCA-CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACAT
* *
210117 TGGCA-------C-CTTTAAGTCCAATATAGCTGCCCTTGAATCAGCATAT
1 TGGCACCTTTTTCACTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACAT
* * *
210160 TGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACAT
1 TGGCACCTTTTTCA-CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACAT
* * * * * * *
210212 TGACATCCTTTTTCTCAGCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATAT
1 TGGCA-CC-TTTT-TCA-CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACAT
* *
210267 TGGCATCTTTATCACTTT
1 TGGCACCTTTTTCACTTT
210285 TCTCATCTTC
Statistics
Matches: 136, Mismatches: 20, Indels: 25
0.75 0.11 0.14
Matches are distributed among these distances:
43 40 0.29
45 1 0.01
50 1 0.01
51 4 0.03
52 45 0.33
53 5 0.04
54 5 0.04
55 35 0.26
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (51 bp):
TGGCACCTTTTTCACTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACAT
Found at i:210141 original size:43 final size:43
Alignment explanation
Indices: 210080--210169 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 43
210070 CCTTTTTCAT
210080 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
* *
210123 CTTTAAGTCCAATATAGCTGCCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
210166 CTTT
1 CTTT
210170 TCCATCTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
Found at i:211055 original size:13 final size:13
Alignment explanation
Indices: 211037--211061 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
211027 CATAAAGTGT
211037 TGTATCGATACAA
1 TGTATCGATACAA
211050 TGTATCGATACA
1 TGTATCGATACA
211062 TATTTTTTTG
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:211059 original size:33 final size:33
Alignment explanation
Indices: 211017--211083 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
211007 TTCAACGATT
211017 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
211050 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
211083 T
1 T
211084 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:211142 original size:13 final size:13
Alignment explanation
Indices: 211124--211148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
211114 ATCACTTAAA
211124 TGTATCGATACAT
1 TGTATCGATACAT
211137 TGTATCGATACA
1 TGTATCGATACA
211149 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:211213 original size:52 final size:52
Alignment explanation
Indices: 211157--211337 Score: 326
Period size: 52 Copynumber: 3.5 Consensus size: 52
211147 CACTGATCTT
*
211157 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
211209 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
211261 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
211313 TGTATCGATACATGCAAGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
211338 TCATATTTTG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:217345 original size:18 final size:18
Alignment explanation
Indices: 217324--217358 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
217314 TCCAAGTCAC
217324 CATCATCATCATCATTAT
1 CATCATCATCATCATTAT
*
217342 CATCTTCATCATCATTA
1 CATCATCATCATCATTA
217359 ATGATTGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (18 bp):
CATCATCATCATCATTAT
Found at i:218981 original size:13 final size:13
Alignment explanation
Indices: 218963--218989 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
218953 ACAATTCATT
218963 ATGTATCGATACA
1 ATGTATCGATACA
218976 ATGTATCGATACA
1 ATGTATCGATACA
218989 A
1 A
218990 ACAGTGGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:219043 original size:20 final size:20
Alignment explanation
Indices: 219017--219072 Score: 89
Period size: 19 Copynumber: 2.9 Consensus size: 20
219007 ACTGCTAGTT
219017 TCATGTATCGATACAATTG-
1 TCATGTATCGATACAATTGA
219036 TCCATGTATCGATACAA-TGA
1 T-CATGTATCGATACAATTGA
219056 TCATGTATCGATACAAT
1 TCATGTATCGATACAAT
219073 ATATCGATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (20 bp):
TCATGTATCGATACAATTGA
Found at i:219100 original size:33 final size:32
Alignment explanation
Indices: 219042--219103 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
219032 ATTGTCCATG
* *
219042 TATCGATACAATGATCATGTATCGATACAATA
1 TATCGATACAAAGATAATGTATCGATACAATA
219074 TATCGATACAAAGCATAATGTATCGATACA
1 TATCGATACAAAG-ATAATGTATCGATACA
219104 TTCAAGGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (32 bp):
TATCGATACAAAGATAATGTATCGATACAATA
Found at i:222835 original size:13 final size:12
Alignment explanation
Indices: 222797--222840 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 12
222787 GTTACAAGCA
222797 ATGTATCGATAC
1 ATGTATCGATAC
222809 AT-T-TC-AT-C
1 ATGTATCGATAC
222817 ATGTATCGATAC
1 ATGTATCGATAC
222829 AATGTATCGATA
1 -ATGTATCGATA
222841 TATTATACCG
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
8 3 0.11
9 3 0.11
10 4 0.15
11 3 0.11
12 3 0.11
13 11 0.41
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:222936 original size:19 final size:19
Alignment explanation
Indices: 222893--222983 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
222883 TGCCAATCTT
**
222893 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAA-TGAGC
222913 ATGTATCGATACAATGAGC
1 ATGTATCGATACAATGAGC
222932 ATGTATCGATACAATGAGC
1 ATGTATCGATACAATGAGC
* **
222951 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAATG-AGC
222971 ATGTATCGATACA
1 ATGTATCGATACA
222984 TTAAAGACCT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 37 0.57
20 28 0.43
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
ATGTATCGATACAATGAGC
Found at i:222943 original size:39 final size:39
Alignment explanation
Indices: 222893--222983 Score: 121
Period size: 39 Copynumber: 2.3 Consensus size: 39
222883 TGCCAATCTT
* * *
222893 ATGTATCGATACAATTGTCCATGTATCGATACAATG-AGC
1 ATGTATCGATACAA-TGACCATGTATCGATACAAAGCAGA
* *
222932 ATGTATCGATACAATGAGCATGTATCGATACAAAGCATA
1 ATGTATCGATACAATGACCATGTATCGATACAAAGCAGA
222971 ATGTATCGATACA
1 ATGTATCGATACA
222984 TTAAAGACCT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 18 0.39
39 28 0.61
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (39 bp):
ATGTATCGATACAATGACCATGTATCGATACAAAGCAGA
Found at i:224792 original size:168 final size:166
Alignment explanation
Indices: 224592--225018 Score: 491
Period size: 168 Copynumber: 2.5 Consensus size: 166
224582 CATCTATTAT
* * *
224592 TTCACTTGTCGGCTTGGTCCTTGGTACTTCTTTTTATCTTTTGTTGACTTGTCGGTCCAATCCTA
1 TTCACCTGTC-GCTTGGTCC-AGGTACTTCTTTTTATCTTTTGTTGACTTGTCGGTCCAATCCTG
*
224657 ATCAACTTCTTTATCCTTTGTTTACCCATCAGCCCA-ACCCGAGGTAAATCCTTTATCCTTCATT
64 ATCAACTTCTTTATCCTTTGTTTACCCATCAGCCCAGACCCG-GGTAAATCCTTTATCCCTCATT
* ** *
224721 GACTTGTCAGTTTAATCAC-GATTAACTTTTTATCCTTCA
128 AACTCATCAGTTTAATC-CTGATCAACTTTTTATCCTTCA
* *
224760 TTCACCTGTCAGCTTGGTCTCAGGTGCTTCTTTTTATCTTTTGTTGACTTGTCGGTCCAATCCCG
1 TTCACCTGTC-GCTTGGTC-CAGGTACTTCTTTTTATCTTTTGTTGACTTGTCGGTCCAATCCTG
* * * ** * *
224825 ATCAACTTCTTTATCCTTTTTTTACTCGTTGGCCCAGTCCCGGGTAAATCTTTTATCCCTCATTA
64 ATCAACTTCTTTATCCTTTGTTTACCCATCAGCCCAGACCCGGGTAAATCCTTTATCCCTCATTA
* *
224890 ACTCATCGGTTTAATCCTGGTCAACTTTTTATCCTTCA
129 ACTCATCAGTTTAATCCTGATCAACTTTTTATCCTTCA
* * * * * * * *
224928 TTCACCTATCGACTTGGTCCCAAGTACTTCTTTATATATTTTATTAACTTGTCGATCCAAT-TTC
1 TTCACCTGTCG-CTTGGT-CCAGGTACTTCTTTTTATCTTTTGTTGACTTGTCGGTCCAATCCT-
* *
224992 GGTCAACTTCTTTATCCCTTGTTTACC
63 GATCAACTTCTTTATCCTTTGTTTACC
225019 TATTGGCTTA
Statistics
Matches: 219, Mismatches: 34, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
167 2 0.01
168 211 0.96
169 6 0.03
ACGTcount: A:0.18, C:0.26, G:0.13, T:0.43
Consensus pattern (166 bp):
TTCACCTGTCGCTTGGTCCAGGTACTTCTTTTTATCTTTTGTTGACTTGTCGGTCCAATCCTGAT
CAACTTCTTTATCCTTTGTTTACCCATCAGCCCAGACCCGGGTAAATCCTTTATCCCTCATTAAC
TCATCAGTTTAATCCTGATCAACTTTTTATCCTTCA
Found at i:224879 original size:84 final size:83
Alignment explanation
Indices: 224623--224881 Score: 216
Period size: 84 Copynumber: 3.1 Consensus size: 83
224613 TGGTACTTCT
** * *
224623 TTTTATCTTTTGTTGACTTGTCGGTCCAATCCTAATCAACTTCTTTATCCTTTGTTTACCCATCA
1 TTTTATCTTTTGTTGACTTGTCGGTCCAATCCCGATCAACTTCTTTATCCTTTATTTA-CCGTCA
*
224688 GCCCA-ACCCGAGGTAAATC
65 GCCCAGTCCCG-GGTAAATC
* * ** * ** * * * *
224707 CTTTATCCTTCATTGACTTGTCAGTTTAATCACGATTAACTT-TTTATCCTTCATTCACCTGTCA
1 TTTTATCTTTTGTTGACTTGTCGGTCCAATCCCGATCAACTTCTTTATCCTTTATTTACC-GTCA
*** * * ***
224771 GCTTGGTCTCAGGTGCTTC
65 GCCCAGTCCCGGGTAAATC
* *
224790 TTTTTATCTTTTGTTGACTTGTCGGTCCAATCCCGATCAACTTCTTTATCCTTTTTTTACTCGTT
1 -TTTTATCTTTTGTTGACTTGTCGGTCCAATCCCGATCAACTTCTTTATCCTTTATTTAC-CGTC
*
224855 GGCCCAGTCCCGGGTAAATC
64 AGCCCAGTCCCGGGTAAATC
224875 TTTTATC
1 TTTTATC
224882 CCTCATTAAC
Statistics
Matches: 124, Mismatches: 46, Indels: 10
0.69 0.26 0.06
Matches are distributed among these distances:
82 2 0.02
83 22 0.18
84 73 0.59
85 26 0.21
86 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.13, T:0.43
Consensus pattern (83 bp):
TTTTATCTTTTGTTGACTTGTCGGTCCAATCCCGATCAACTTCTTTATCCTTTATTTACCGTCAG
CCCAGTCCCGGGTAAATC
Found at i:229670 original size:155 final size:153
Alignment explanation
Indices: 229472--230215 Score: 653
Period size: 155 Copynumber: 4.8 Consensus size: 153
229462 CCGGATTCGT
* * * *
229472 TTTTATGCCGAATG-TGGGTATCTAGGATAGGTTCATTCCTTTTAT-AGTTCTTTTTAAGTCCAT
1 TTTTATGCC-AAAGATGGGCATTTAGGATAGGTTCA-TCCTTTTATGAG-TCTTTTTAAGTCCTT
* * * * *
229535 TATGGGTACTGAGATACTTTCACATCGAAGGTATCCTTTAGGGGTATTTTCATAATTTTTAGAAT
63 TA-GGGTACTGAGATACTTTCACGTCGAAGGTATCCCTTAGGGGCATTTTCGTAATTTTTAGAAC
*
229600 CAACTCCTAAGTCGTCACCGAGTCAGC
127 CAACTCCTAGGTCGTCACCGAGTCAGC
* * *
229627 TTTTATGTCAAAGATGGGCATTTAGGATAGGTTCATCCTTTTTATGAGTTTTTTTAAGTCCTCTA
1 TTTTATGCCAAAGATGGGCATTTAGGATAGGTTCATCC-TTTTATGAGTCTTTTTAAGTCCTTTA
* * * * * *
229692 GCGGTACTGGGATACTTTCACGTCGCAA-GTATCCCCTAAGAGCATTTTCATAATTTTTAGAATC
65 G-GGTACTGAGATACTTTCACGTCG-AAGGTATCCCTTAGGGGCATTTTCGTAATTTTTAGAACC
* ** * *
229756 AACTCTTAGGTC-TCATTGGGTCTGC
128 AACTCCTAGGTCGTCACCGAGTCAGC
* *
229781 TTTTATGCTAAA-AGTGGGCATTTAGTATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTT
1 TTTTATGCCAAAGA-TGGGCATTTAGGATAGGTTCAT-CCTTTTATGAGTCTTTTTAAGTCCTTT
* ** * * * * * *
229845 AAGGTTGTCGAGATACTTTTATGTCGAAAGTACACCCATAAGGGCATTTTCGTAATTTTTAGAAC
64 AGGGTACT-GAGATACTTTCACGTCGAAGGTA-TCCCTTAGGGGCATTTTCGTAATTTTTAGAAC
* * *
229910 CAACACCTAGGTCATCACCGGGTCCA-C
127 CAACTCCTAGGTCGTCACCGAGT-CAGC
* * * * *
229937 TTTTATGCCGAAGGTGGGCATTTAAGTTAGGTTCATCCTTTTATGAGTCTTTTTACGTCCTTTAA
1 TTTTATGCCAAAGATGGGCATTTAGGATAGGTTCATCCTTTTATGAGTCTTTTTAAGTCCTTT-A
* * * * *
230002 GGTTACCGGGATATTTTCACGTCGAAGGTATACCCTTAGAGGCATTTTCGTAATTTTTTAGAACC
65 GGGTACTGAGATACTTTCACGTCGAAGGTAT-CCCTTAGGGGCATTTTCGTAA-TTTTTAGAACC
* * * * *
230067 AAATCTTAGGTTGTCA-CTAGGTCCGC
128 AACTCCTAGGTCGTCACCGA-GTCAGC
* * * * *
230093 TTTCATGCCGAAGATGGGTATTTAGGATAGGTTAACCACTTTTAT-A-TCTTTTTTAAGTCCTTT
1 TTTTATGCCAAAGATGGGCATTTAGGATAGGTTCATC-CTTTTATGAGTC-TTTTTAAGTCCTTT
* ** * * *
230156 AGGGTTA-TCGAGATACTTTTATATCGAATGTATACCTTTAGGGGCATTTTTGTAATTTTT
64 AGGG-TACT-GAGATACTTTCACGTCGAAGGTAT-CCCTTAGGGGCATTTTCGTAATTTTT
230216 TAAAATAAAG
Statistics
Matches: 478, Mismatches: 89, Indels: 44
0.78 0.15 0.07
Matches are distributed among these distances:
153 7 0.01
154 88 0.18
155 223 0.47
156 152 0.32
157 8 0.02
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.39
Consensus pattern (153 bp):
TTTTATGCCAAAGATGGGCATTTAGGATAGGTTCATCCTTTTATGAGTCTTTTTAAGTCCTTTAG
GGTACTGAGATACTTTCACGTCGAAGGTATCCCTTAGGGGCATTTTCGTAATTTTTAGAACCAAC
TCCTAGGTCGTCACCGAGTCAGC
Found at i:229972 original size:156 final size:155
Alignment explanation
Indices: 229472--230369 Score: 626
Period size: 155 Copynumber: 5.8 Consensus size: 155
229462 CCGGATTCGT
* * * * *
229472 TTTTATGCCGAATGTGGGTATCTAGGATAGGTTCATTCCTTTTAT-AGTTCTTTTTAAGTCCATT
1 TTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATGAG-TCTTTTTAAGTCCTTT
* * * * * ** * * *
229536 ATGGGTA-CTGAGATACTTTCACATCGAAGGTATC-CTTTAGGGGTATTTTCATAATTTTTAGAA
65 AAGGTTATC-GAGATACTTTTACGTCGAAAGTA-CACCCTAAGGGCATTTTCGTAATTTTTAGAA
* * * *
229599 TCAACTCCTAAGTCGTCACCGAGT-CAGC
128 CCAACACCTAGGTCGTCACCGGGTCCA-C
* * * * * *
229627 TTTTATGTCAAAGATGGGCATTTAGGATAGGTTCATCCTTTTTATGAGTTTTTTTAAGTCCTCT-
1 TTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTA
* * * * * *
229691 AGCGGTA-CTGGGATACTTTCACGTCGCAAGTATC-CCCTAAGAGCATTTTCATAATTTTTAGAA
66 AG-GTTATC-GAGATACTTTTACGTCGAAAGTA-CACCCTAAGGGCATTTTCGTAATTTTTAGAA
* * * ** **
229754 TCAACTCTTAGGTC-TCATTGGGTCTGC
128 CCAACACCTAGGTCGTCACCGGGTCCAC
** * *
229781 TTTTATGCTAAAAGTGGGCATTTAGTATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTA
1 TTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTA
* *
229846 AGGTTGTCGAGATACTTTTATGTCGAAAGTACACCCATAAGGGCATTTTCGTAATTTTTAGAACC
66 AGGTTATCGAGATACTTTTACGTCGAAAGTACACCC-TAAGGGCATTTTCGTAATTTTTAGAACC
*
229911 AACACCTAGGTCATCACCGGGTCCAC
130 AACACCTAGGTCGTCACCGGGTCCAC
* * *
229937 TTTTATGCCGAAGGTGGGCATTTAAGTTAGGTTCAT-CCTTTTATGAGTCTTTTTACGTCCTTTA
1 TTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTA
* * * * *
230001 AGGTTACCGGGATA-TTTTCACGTCGAAGGTATACCCTTAGAGGCATTTTCGTAATTTTTTAGAA
66 AGGTTATCGAGATACTTTT-ACGTCGAAAGTACACCCTAAG-GGCATTTTCGTAA-TTTTTAGAA
* * ** *
230065 CCAA-ATCTTAGGTTGTCACTAGGTCCGC
128 CCAACA-CCTAGGTCGTCACCGGGTCCAC
* * * *
230093 TTTCATGCCGAAGATGGGTATTTAGGATAGGTT-AACCACTTTTAT-A-TCTTTTTTAAGTCCTT
1 TTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCC-CTTTTATGAGTC-TTTTTAAGTCCTT
* ** * * * * * *
230155 TAGGGTTATCGAGATACTTTTATATCGAATGTATACCTTTAGGGGCATTTTTGTAATTTTTTAAA
64 TAAGGTTATCGAGATACTTTTACGTCGAAAGTACACC-CTAAGGGCATTTTCGTAA-TTTTTAGA
** ** * ** ** **
230220 ATAAAGTCTTAGGTTATCTTCGGGTCTGC
127 ACCAACACCTAGGTCGTCACCGGGTCCAC
** * * * * * *
230249 TTTTATG-TAAAGGTGGGTATATAGGATAGGTTCACCCCTTTTACGA-TCCTTTGTAAGTCTTTT
1 TTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATGAGT-CTTTTTAAGTCCTTT
* ** * * * * *
230312 AGGGGCATCGAG-TACTTCTACGTCAAAAGTATACCCT-AGAAGCATTTTTGTAATTTTT
65 AAGGTTATCGAGATACTTTTACGTCGAAAGTACACCCTAAG-GGCATTTTCGTAATTTTT
230370 CCTGAACTCA
Statistics
Matches: 604, Mismatches: 117, Indels: 46
0.79 0.15 0.06
Matches are distributed among these distances:
153 7 0.01
154 108 0.18
155 265 0.44
156 210 0.35
157 14 0.02
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (155 bp):
TTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTA
AGGTTATCGAGATACTTTTACGTCGAAAGTACACCCTAAGGGCATTTTCGTAATTTTTAGAACCA
ACACCTAGGTCGTCACCGGGTCCAC
Found at i:230281 original size:311 final size:308
Alignment explanation
Indices: 229476--230291 Score: 855
Period size: 309 Copynumber: 2.6 Consensus size: 308
229466 ATTCGTTTTT
* * *
229476 ATGCCGAATG-TGGGTATCTAGGATAGGTTCATTCCTTTTATAGT-TCTTTTTAAGTCCATTATG
1 ATGCCGAA-GATGGGTATTTAGGATAGGTTCATCCCTTTTATAGTCT-TTTTTAAGTCCTTTA-G
* * * * *
229539 GG-TA-CTGAGATACTTTCACATCGAAGGTAT-CCTTTAGGGGTATTTTCATAATTTTTAGAATC
63 GGTTATC-GAGATACTTTTATATCGAAAGTATACCTTTAGGGGCATTTTCGTAATTTTTAGAATC
* * * *
229601 AACTCCTAAGTCGTCACCGAGTCAGCTTTTATGTCAAAGATGGGCATTTAGGATAGGTTCATCCT
127 AACTCCTAGGTCATCACCGGGTCAGCTTTTATGT-AAAGGTGGGCATTTAGGATAGGTTCATCC-
* * *
229666 TTTTATGAGTTTTTTTAAGTCCTCTAGCGGTACTGGGATACTTTCACGTCGCAAGTATCCCCTAA
190 TTTTATGAGTCTTTTTAAGTCCTCTAGCGGTACCGGGATACTTTCACGTCGCAAGTATACCCTAA
* * * * * *
229731 GAGCATTTTCATAATTTTTAGAATCAACTCTTAGGTCTCATTGGGTCTGCTTTT
255 GAGCATTTTCATAATTTTTAGAACCAAATCTTAGGTCTCACTAGGTCCGCTTTC
* * * * *
229785 ATG-CTAAAAGTGGGCATTTAGTATAGGTTCATCCCTTTTATGAGTC-TTTTTAAGTCCTTTAAG
1 ATGCCGAAGA-TGGGTATTTAGGATAGGTTCATCCCTTTTAT-AGTCTTTTTTAAGTCCTTTAGG
* * * ** * *
229848 GTTGTCGAGATACTTTTATGTCGAAAGTACACCCATAAGGGCATTTTCGTAATTTTTAGAACCAA
64 GTTATCGAGATACTTTTATATCGAAAGTATACCTTTAGGGGCATTTTCGTAATTTTTAGAATCAA
* ** * *
229913 CACCTAGGTCATCACCGGGTCCA-CTTTTATGCCGAAGGTGGGCATTTAAGTTAGGTTCATCCTT
129 CTCCTAGGTCATCACCGGGT-CAGCTTTTATG-TAAAGGTGGGCATTTAGGATAGGTTCATCCTT
* * * * *
229977 TTATGAGTCTTTTTACGTCCTTTAAG-GTTACCGGGATATTTTCACGTCG-AAGGTATACCCTTA
192 TTATGAGTCTTTTTAAGTCCTCT-AGCGGTACCGGGATACTTTCACGTCGCAA-GTATACCCTAA
* *
230040 GAGGCATTTTCGTAATTTTTTAGAACCAAATCTTAGGTTGTCACTAGGTCCGCTTTC
255 GA-GCATTTTCATAA-TTTTTAGAACCAAATCTTAGG-TCTCACTAGGTCCGCTTTC
*
230097 ATGCCGAAGATGGGTATTTAGGATAGGTT-AACCACTTTTATA-TCTTTTTTAAGTCCTTTAGGG
1 ATGCCGAAGATGGGTATTTAGGATAGGTTCATCC-CTTTTATAGTCTTTTTTAAGTCCTTTAGGG
* * * *
230160 TTATCGAGATACTTTTATATCGAATGTATACCTTTAGGGGCATTTTTGTAATTTTTTAAAATAAA
65 TTATCGAGATACTTTTATATCGAAAGTATACCTTTAGGGGCATTTTCGTAA-TTTTTAGAATCAA
* * * ** * * * *
230225 GTCTTAGGTTATCTTCGGGTCTGCTTTTATGTAAAGGTGGGTATATAGGATAGGTTCACCCCTTT
129 CTCCTAGGTCATCACCGGGTCAGCTTTTATGTAAAGGTGGGCATTTAGGATAGGTTCA-TCCTTT
230290 TA
193 TA
230292 CGATCCTTTG
Statistics
Matches: 411, Mismatches: 76, Indels: 37
0.78 0.15 0.07
Matches are distributed among these distances:
308 7 0.02
309 117 0.28
310 96 0.23
311 107 0.26
312 80 0.19
313 4 0.01
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39
Consensus pattern (308 bp):
ATGCCGAAGATGGGTATTTAGGATAGGTTCATCCCTTTTATAGTCTTTTTTAAGTCCTTTAGGGT
TATCGAGATACTTTTATATCGAAAGTATACCTTTAGGGGCATTTTCGTAATTTTTAGAATCAACT
CCTAGGTCATCACCGGGTCAGCTTTTATGTAAAGGTGGGCATTTAGGATAGGTTCATCCTTTTAT
GAGTCTTTTTAAGTCCTCTAGCGGTACCGGGATACTTTCACGTCGCAAGTATACCCTAAGAGCAT
TTTCATAATTTTTAGAACCAAATCTTAGGTCTCACTAGGTCCGCTTTC
Found at i:231669 original size:21 final size:21
Alignment explanation
Indices: 231617--231671 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
231607 TTATAAAAGT
*
231617 TGTATTTTTTCATCTAATAAG
1 TGTATTTTTTCATCTAACAAG
* *
231638 TGCATTATTTCATCTAACCAA-
1 TGTATTTTTTCATCTAA-CAAG
231659 TGTATTTTTTCAT
1 TGTATTTTTTCAT
231672 TTAAATGCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (21 bp):
TGTATTTTTTCATCTAACAAG
Found at i:232345 original size:23 final size:21
Alignment explanation
Indices: 232319--232383 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 21
232309 TTAATTTAAT
232319 TAAAAATTAATATATTTTATATA
1 TAAAAA-TAATATATTTTATA-A
232342 TAAAAA-AATAGTAATTTTATAA
1 TAAAAATAATA-T-ATTTTATAA
232364 -AAAAATAAATTATATTTTAT
1 TAAAAAT-AA-TATATTTTAT
232384 TCCTTTAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
21 9 0.24
22 9 0.24
23 17 0.46
24 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TAAAAATAATATATTTTATAA
Found at i:232374 original size:17 final size:18
Alignment explanation
Indices: 232340--232374 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
232330 ATATTTTATA
232340 TATAAAAAAATAGTAATTT
1 TATAAAAAAATAG-AATTT
232359 TATAAAAAAATA-AATT
1 TATAAAAAAATAGAATT
232375 ATATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
19 12 0.75
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
TATAAAAAAATAGAATTT
Found at i:242414 original size:21 final size:20
Alignment explanation
Indices: 242388--242449 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
242378 AAGTCTTAGA
242388 AATTTTTATTTATATTTAATT
1 AATTTTTATTTAT-TTTAATT
*
242409 AATTTTTAGTTATTTTTAAATT
1 AATTTTTATTTA-TTTT-AATT
242431 AA-TTTTATTTACTTTTAAT
1 AATTTTTATTTA-TTTTAAT
242450 ATATTTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 3 0.08
21 26 0.72
22 7 0.19
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTTTTATTTATTTTAATT
Found at i:242423 original size:10 final size:10
Alignment explanation
Indices: 242389--242455 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
242379 AGTCTTAGAA
*
242389 ATTTTTATTT
1 ATTTTTAATT
*
242399 ATATTTAATT
1 ATTTTTAATT
*
242409 AATTTTTAGTT
1 -ATTTTTAATT
242420 ATTTTTAAATT
1 ATTTTT-AATT
* *
242431 AATTTTATTT
1 ATTTTTAATT
*
242441 ACTTTTAATAT
1 ATTTTTAAT-T
242452 ATTT
1 ATTT
242456 AAATTATATA
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
10 24 0.55
11 20 0.45
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (10 bp):
ATTTTTAATT
Found at i:246366 original size:34 final size:34
Alignment explanation
Indices: 246328--246398 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
246318 ACATGAAAGA
246328 TTTATGTGTTATGAATATCATATAAGGAATCAAG
1 TTTATGTGTTATGAATATCATATAAGGAATCAAG
246362 TTTATGTGTTATGAATATCATATAAGGAATCAAG
1 TTTATGTGTTATGAATATCATATAAGGAATCAAG
246396 TTT
1 TTT
246399 TCTAAGACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.41
Consensus pattern (34 bp):
TTTATGTGTTATGAATATCATATAAGGAATCAAG
Found at i:247830 original size:21 final size:21
Alignment explanation
Indices: 247773--247831 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
247763 AAATGTGTAT
** *
247773 TTGGATGAAATGATATATTTG
1 TTGGATGAAATGATGCACTTG
*
247794 TTGGATGAAATAATGCACTTG
1 TTGGATGAAATGATGCACTTG
*
247815 TTGGATGGAATGATGCA
1 TTGGATGAAATGATGCA
247832 TCTTTATAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (21 bp):
TTGGATGAAATGATGCACTTG
Found at i:249681 original size:24 final size:24
Alignment explanation
Indices: 249654--249702 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
249644 TCTGCAAAAG
*
249654 TTAAACTGTGATCCTTGGATGCAC
1 TTAAAATGTGATCCTTGGATGCAC
249678 TTAAAATGTGATCCTTGGATGCAC
1 TTAAAATGTGATCCTTGGATGCAC
249702 T
1 T
249703 CAATATTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (24 bp):
TTAAAATGTGATCCTTGGATGCAC
Found at i:254967 original size:20 final size:20
Alignment explanation
Indices: 254890--254967 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
254880 AAGGATTGAC
* *
254890 TTTTT-TTTATTTTAAAAT-
1 TTTTTATTTAATTTAATATA
*
254908 TTTTTAATTTGATTTAAATAATA
1 TTTTT-ATTTAATTT-AAT-ATA
* **
254931 TTTTTAATTAAAATAATATA
1 TTTTTATTTAATTTAATATA
254951 TTTTTATTTAATTTAAT
1 TTTTTATTTAATTTAAT
254968 TATAAAATAT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
18 5 0.11
20 23 0.51
21 5 0.11
22 7 0.16
23 5 0.11
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (20 bp):
TTTTTATTTAATTTAATATA
Found at i:255065 original size:13 final size:14
Alignment explanation
Indices: 255049--255083 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
255039 ATAGATCGAA
255049 TTAAAATTT-AAAT
1 TTAAAATTTAAAAT
255062 TT-AAATTTAAAAT
1 TTAAAATTTAAAAT
255075 TTAAAATTT
1 TTAAAATTT
255084 TTACAGCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 8 0.40
14 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAAAATTTAAAAT
Found at i:255065 original size:26 final size:27
Alignment explanation
Indices: 255003--255065 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
254993 AAAATAATTT
**
255003 TTTAAATTTAATAGATATTATAATAAA
1 TTTAAATTTAATAGATAGAATAATAAA
* * *
255030 TTT-AAGTTAATAGATCGAATTA-AAA
1 TTTAAATTTAATAGATAGAATAATAAA
255055 TTTAAATTTAA
1 TTTAAATTTAA
255066 ATTTAAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 6 0.21
26 20 0.69
27 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (27 bp):
TTTAAATTTAATAGATAGAATAATAAA
Found at i:255074 original size:7 final size:7
Alignment explanation
Indices: 255049--255083 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
255039 ATAGATCGAA
255049 TTAAAAT
1 TTAAAAT
255056 TT-AAAT
1 TTAAAAT
255062 TT-AAAT
1 TTAAAAT
255068 TTAAAAT
1 TTAAAAT
255075 TTAAAAT
1 TTAAAAT
255082 TT
1 TT
255084 TTACAGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (7 bp):
TTAAAAT
Found at i:256123 original size:18 final size:16
Alignment explanation
Indices: 256088--256127 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
256078 TGAATATAAT
256088 AATAAAAAATAATTAA
1 AATAAAAAATAATTAA
*
256104 AATATAAAATAATATGAA
1 AATAAAAAATAAT-T-AA
256122 AATAAA
1 AATAAA
256128 CTATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 12 0.60
17 1 0.05
18 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (16 bp):
AATAAAAAATAATTAA
Found at i:256566 original size:14 final size:13
Alignment explanation
Indices: 256538--256572 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
256528 AATATTCTAA
256538 ACATAAAAAAAAT
1 ACATAAAAAAAAT
*
256551 ACATAAATACAAAT
1 ACATAAA-AAAAAT
256565 ACATAAAA
1 ACATAAAA
256573 TTTTCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.17
Consensus pattern (13 bp):
ACATAAAAAAAAT
Found at i:256594 original size:5 final size:5
Alignment explanation
Indices: 256573--256654 Score: 55
Period size: 5 Copynumber: 16.6 Consensus size: 5
256563 ATACATAAAA
* *
256573 TTTTC -TTT- TTTTC -TTTC TTTTC TTTTCC TTTCC TTTTC CTTTC TTATT-
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT-C TTTTC TTTTC TTTTC TT-TTC
* * * *
256621 TTTCTT TTTTC TTTTT TTTTC TTTCC TTTCC TTT
1 TTT-TC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
256655 CCATTCTTTC
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
4 11 0.18
5 42 0.68
6 9 0.15
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:256646 original size:46 final size:46
Alignment explanation
Indices: 256573--256662 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
256563 ATACATAAAA
*
256573 TTTTCTTTTTTTCTTTCTTTTCTTTTCCTTTCCTTTTCCTTTCTTAT
1 TTTTCTTTTTTTCTTTCTTTTCTTTTCCTTTCC-TTTCCATTCTTAT
*
256620 TTTTC-TTTTTTCTTT-TTTTTTCTTTCCTTTCCTTTCCATTCTT
1 TTTTCTTTTTTTCTTTCTTTTCT-TTTCCTTTCCTTTCCATTCTT
256663 TCTTAATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 15 0.38
46 20 0.50
47 5 0.12
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (46 bp):
TTTTCTTTTTTTCTTTCTTTTCTTTTCCTTTCCTTTCCATTCTTAT
Found at i:260427 original size:26 final size:26
Alignment explanation
Indices: 260375--260427 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
260365 ATTATTTAAA
* *
260375 ATATTTATAATTATAAAAATAATTTT
1 ATATTAATAATTATAAAAATAAATTT
* * *
260401 ATATTAATATTTATATAATTAAATTT
1 ATATTAATAATTATAAAAATAAATTT
260427 A
1 A
260428 AATAAAAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATATTAATAATTATAAAAATAAATTT
Found at i:263596 original size:3 final size:3
Alignment explanation
Indices: 263588--263618 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
263578 TGTTTTTCCT
263588 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
263619 GACCATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:268914 original size:3 final size:3
Alignment explanation
Indices: 268892--268945 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
268882 TGAATTTTTA
*
268892 TAT TA- TAT TA- TAT T-T TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
268937 TAT TAT TAT
1 TAT TAT TAT
268946 CTTTTCTCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 6 0.13
3 40 0.87
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:278556 original size:20 final size:20
Alignment explanation
Indices: 278533--278595 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
278523 CCACGTTACG
278533 TGCTTTGCATCATTATTTCA
1 TGCTTTGCATCATTATTTCA
***
278553 TGCTTT-CA-CAACCTTT-A
1 TGCTTTGCATCATTATTTCA
*
278570 TGCTTTGCATTATTATTTCA
1 TGCTTTGCATCATTATTTCA
278590 TGCTTT
1 TGCTTT
278596 CACAACTTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 7 0.21
18 7 0.21
19 6 0.18
20 13 0.39
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.51
Consensus pattern (20 bp):
TGCTTTGCATCATTATTTCA
Found at i:278607 original size:17 final size:17
Alignment explanation
Indices: 278548--278607 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
278538 TGCATCATTA
278548 TTTCATGCTTTCACAACC
1 TTTCATGCTTTCACAA-C
*
278566 TTT-ATGCTTTGCATTATTA-
1 TTTCATGCTTT-CA-CA--AC
278585 TTTCATGCTTTCACAAC
1 TTTCATGCTTTCACAAC
278602 TTTCAT
1 TTTCAT
278608 TCATTCATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
16 1 0.03
17 13 0.38
18 6 0.18
19 6 0.18
20 7 0.21
21 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.07, T:0.48
Consensus pattern (17 bp):
TTTCATGCTTTCACAAC
Found at i:278667 original size:26 final size:28
Alignment explanation
Indices: 278638--278696 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
278628 AATAATATTC
278638 TTTTTGACT-ATTTTGAATTTTTT-TT-A
1 TTTTTGA-TAATTTTGAATTTTTTATTGA
*
278664 TTTTTGATAATTTTGATTTTTTTATTGA
1 TTTTTGATAATTTTGAATTTTTTATTGA
278692 TTTTT
1 TTTTT
278697 TGATTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 1 0.03
26 20 0.69
27 2 0.07
28 6 0.21
ACGTcount: A:0.19, C:0.02, G:0.08, T:0.71
Consensus pattern (28 bp):
TTTTTGATAATTTTGAATTTTTTATTGA
Found at i:278704 original size:43 final size:45
Alignment explanation
Indices: 278656--278764 Score: 115
Period size: 43 Copynumber: 2.5 Consensus size: 45
278646 TATTTTGAAT
278656 TTTTTTTATTTTTGATAATTTTGATTTTTTTATTGATT-T-TT-TGA
1 TTTTTTTATTTTTGAT-ATTTTGATTTTTTTATT-ATTATGTTATGA
*
278700 TTTTTTTAATTTCTTG--ATTTTGATTTTTTTATTATTATGTTATTA
1 TTTTTTT-ATTT-TTGATATTTTGATTTTTTTATTATTATGTTATGA
278745 -TTTTTTATTTTATGAT-TTTT
1 TTTTTTTATTTT-TGATATTTT
278765 CCAAACAAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 16
0.77 0.01 0.22
Matches are distributed among these distances:
42 4 0.07
43 24 0.43
44 19 0.34
45 6 0.11
46 3 0.05
ACGTcount: A:0.18, C:0.01, G:0.07, T:0.73
Consensus pattern (45 bp):
TTTTTTTATTTTTGATATTTTGATTTTTTTATTATTATGTTATGA
Found at i:278706 original size:23 final size:23
Alignment explanation
Indices: 278680--278764 Score: 72
Period size: 23 Copynumber: 3.7 Consensus size: 23
278670 ATAATTTTGA
278680 TTTTTTTATTGATTTTTTGATTT
1 TTTTTTTATTGATTTTTTGATTT
*
278703 TTTTAATTTCTTGA--TTTTGATTT
1 TTTT--TTTATTGATTTTTTGATTT
* *
278726 TTTTATTATT-ATGTTATT-ATTT
1 TTTTTTTATTGAT-TTTTTGATTT
278748 TTTATTTTA-TGATTTTT
1 TTT-TTTTATTGATTTTT
278765 CCAAACAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
20 1 0.02
21 4 0.08
22 11 0.22
23 26 0.53
25 7 0.14
ACGTcount: A:0.18, C:0.01, G:0.07, T:0.74
Consensus pattern (23 bp):
TTTTTTTATTGATTTTTTGATTT
Found at i:281798 original size:1 final size:1
Alignment explanation
Indices: 281792--281883 Score: 76
Period size: 1 Copynumber: 92.0 Consensus size: 1
281782 AAATCTTCAC
* * ** * * * **
281792 TTTTTTTTTTGTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTTTCTTTTTCCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
281857 TTTTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
281884 CCAATTGCCA
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (1 bp):
T
Found at i:281827 original size:30 final size:30
Alignment explanation
Indices: 281791--281885 Score: 138
Period size: 30 Copynumber: 3.0 Consensus size: 30
281781 CAAATCTTCA
281791 CTTTTTTTTTTGTTTTTTTTTTTCTTTTTC
1 CTTTTTTTTTTGTTTTTTTTTTTCTTTTTC
281821 CTTTTTTTTGTTTTGTTTTTTTTTTTTCTTTTTC
1 C--TTTTTT-TTTTG-TTTTTTTTTTTCTTTTTC
281855 C-TTTTTTTTTGTTTTGTTTTTTTCTTTTTC
1 CTTTTTTTTTTGTTTT-TTTTTTTCTTTTTC
281885 C
1 C
281886 AATTGCCATG
Statistics
Matches: 60, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
29 4 0.07
30 21 0.35
31 5 0.08
32 6 0.10
33 5 0.08
34 19 0.32
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (30 bp):
CTTTTTTTTTTGTTTTTTTTTTTCTTTTTC
Found at i:281846 original size:34 final size:35
Alignment explanation
Indices: 281792--281884 Score: 156
Period size: 35 Copynumber: 2.7 Consensus size: 35
281782 AAATCTTCAC
281792 TTTTTT-TTTTG-TTTTTTTTTTTCTTTTTCC-TT
1 TTTTTTGTTTTGTTTTTTTTTTTTCTTTTTCCTTT
281824 TTTTTTGTTTTGTTTTTTTTTTTTCTTTTTCCTTT
1 TTTTTTGTTTTGTTTTTTTTTTTTCTTTTTCCTTT
281859 TTTTTTGTTTTGTTTTTTTCTTTTTC
1 TTTTTTGTTTTGTTTTTTT-TTTTTC
281885 CAATTGCCAT
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
32 6 0.11
33 5 0.09
34 19 0.33
35 21 0.37
36 6 0.11
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.86
Consensus pattern (35 bp):
TTTTTTGTTTTGTTTTTTTTTTTTCTTTTTCCTTT
Found at i:290615 original size:17 final size:18
Alignment explanation
Indices: 290578--290616 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
290568 ATATTTATTT
290578 TAATAAATAATATTCATC
1 TAATAAATAATATTCATC
290596 TAATAAAT-ATAATT-ATC
1 TAATAAATAAT-ATTCATC
290613 TAAT
1 TAAT
290617 TATTACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATAAATAATATTCATC
Found at i:293006 original size:18 final size:18
Alignment explanation
Indices: 292983--293017 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
292973 CATAAAGTGT
292983 TGTAAGAGAAGTAAACGG
1 TGTAAGAGAAGTAAACGG
293001 TGTAAGAGAAGTAAACG
1 TGTAAGAGAAGTAAACG
293018 ATATATAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.31, T:0.17
Consensus pattern (18 bp):
TGTAAGAGAAGTAAACGG
Found at i:294443 original size:28 final size:28
Alignment explanation
Indices: 294382--294463 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
294372 TTTTGGAGAT
*
294382 AATAACGGGGTTGGAGTGTTCCCTCG--GA
1 AATAACGGGGTTGGAGT-ATCCC-CGATGA
*
294410 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGGGGTTGGAGTATCCCCGATGA
* *
294438 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
294464 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 4 0.09
28 41 0.87
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (28 bp):
AATAACGGGGTTGGAGTATCCCCGATGA
Found at i:294602 original size:51 final size:51
Alignment explanation
Indices: 294446--294615 Score: 214
Period size: 52 Copynumber: 3.3 Consensus size: 51
294436 GAAATAACGA
* *
294446 GGTTGGAGTATCCTCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTA-TTTTGGAAATAAAATCGG
* * * * * * *
294498 TGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTATTTTGGAAATAAAATCGG
* * *
294550 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAATCGG
294601 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
294616 TCGGAAATAA
Statistics
Matches: 98, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
51 38 0.39
52 51 0.52
53 9 0.09
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAATCGG
Found at i:294738 original size:211 final size:211
Alignment explanation
Indices: 294387--294779 Score: 592
Period size: 211 Copynumber: 1.9 Consensus size: 211
294377 GAGATAATAA
* * * *
294387 CGGGGTTGGAGTGTTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTAG
* * * *
294452 AGTATCCTCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGGTGTTGGAGTATCCCCGATT
66 AGTACCCCCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGAAT
* * *
294517 AAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT
131 AAAGGAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAAT
294582 ATTTTGGAAATAAAGT
196 ATTTTGGAAATAAAGT
* *
294598 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTAG
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTAG
* * *
294662 AGTGCCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGA
66 AGTACCCCCGATTGTGAA-AAATTAGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGA
* *
294727 ATATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
129 ATAAAGGAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATT
294780 GTGGAGAATT
Statistics
Matches: 162, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
210 26 0.16
211 98 0.60
212 38 0.23
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.28
Consensus pattern (211 bp):
CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTAG
AGTACCCCCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGAAT
AAAGGAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAAT
ATTTTGGAAATAAAGT
Found at i:297087 original size:13 final size:13
Alignment explanation
Indices: 297069--297094 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
297059 ACAAAGATCC
297069 ATGTATCGATACA
1 ATGTATCGATACA
297082 ATGTATCGATACA
1 ATGTATCGATACA
297095 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:297090 original size:33 final size:33
Alignment explanation
Indices: 297048--297114 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
297038 AAAATTTTCA
***
297048 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
297081 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
297114 A
1 A
297115 TTTCCTTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:297158 original size:19 final size:18
Alignment explanation
Indices: 297134--297201 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
297124 TAGTAGCTAA
297134 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
297153 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
297168 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
297185 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
297202 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:297174 original size:13 final size:13
Alignment explanation
Indices: 297156--297180 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
297146 ACAATACTTA
297156 TGTATCGATACAT
1 TGTATCGATACAT
297169 TGTATCGATACA
1 TGTATCGATACA
297181 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:297178 original size:32 final size:32
Alignment explanation
Indices: 297137--297199 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
297127 TAGCTAATTA
*
297137 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
297169 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
297200 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:297263 original size:21 final size:21
Alignment explanation
Indices: 297237--297313 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
297227 GTTGGGACCC
* *
297237 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACA-TTCTACAAA
*
297258 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
297279 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
297300 TGTATCGATACATT
1 TGTATCGATACATT
297314 TGGATAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:298136 original size:55 final size:54
Alignment explanation
Indices: 298047--299012 Score: 1274
Period size: 55 Copynumber: 17.3 Consensus size: 54
298037 ATAAAGTGTA
* * * *
298047 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
298102 TCCTGCTCTTTGAGGACTGAAAGGTGCCATCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
298157 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
298212 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGGG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* **
298267 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* * * *
298328 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAATGCG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * *
298387 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAACTGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT----GAAA-GGTG
* * *
298446 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGCGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
298500 TCCTGCTCTCTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
298555 TCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
298610 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
298665 TCCTGGTCTTTGGGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
298720 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
298775 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
298830 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
298885 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
298940 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
298995 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
299013 AAAAAGCGGA
Statistics
Matches: 839, Mismatches: 45, Indels: 54
0.89 0.05 0.06
Matches are distributed among these distances:
54 41 0.05
55 624 0.74
56 23 0.03
58 3 0.00
59 99 0.12
60 23 0.03
61 21 0.03
64 5 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:298234 original size:26 final size:26
Alignment explanation
Indices: 298205--298292 Score: 81
Period size: 26 Copynumber: 3.3 Consensus size: 26
298195 GTGGGCTTTA
298205 AAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
** *
298231 AAAGGTG-CCACCAACTTGTGTGGG-CTTTG
1 AAAGGTGTCCTGC-TCTT-TG-GGGAC--TG
*
298260 AAAGGGGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
298286 AAAGGTG
1 AAAGGTG
298293 CCACCAACTT
Statistics
Matches: 47, Mismatches: 8, Indels: 14
0.68 0.12 0.20
Matches are distributed among these distances:
25 3 0.06
26 18 0.38
27 6 0.13
28 6 0.13
29 11 0.23
30 3 0.06
ACGTcount: A:0.19, C:0.18, G:0.35, T:0.27
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGACTG
Found at i:300025 original size:16 final size:16
Alignment explanation
Indices: 299979--300054 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 16
299969 CTTAAGTAGG
*
299979 TTTTTTTCTTTTCTCTCT
1 TTTTTTTCTTTTGT-T-T
*
299997 TTTTCTTTGTTTTGTTT
1 TTTT-TTTCTTTTGTTT
* **
300014 TTTTGTTTTTTTTCCTT
1 TTTT-TTTCTTTTGTTT
300031 TTTTTTTCTTTTGCTTT
1 TTTTTTTCTTTTG-TTT
300048 TTTTTTT
1 TTTTTTT
300055 GGAGAGAAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
16 7 0.15
17 27 0.57
18 5 0.11
19 8 0.17
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (16 bp):
TTTTTTTCTTTTGTTT
Found at i:300032 original size:33 final size:32
Alignment explanation
Indices: 299978--300051 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
299968 GCTTAAGTAG
*
299978 GTTTTTTTCTTTTCTCTCTTTTTCTTTGTTTT
1 GTTTTTTTCTTTTCTCTCTTTTTCTTTCTTTT
* * * *
300010 GTTTTTTTGTTTTTTTTCCTTTTTTTTTCTTTT
1 GTTTTTTTCTTTTCTCT-CTTTTTCTTTCTTTT
300043 GCTTTTTTT
1 G-TTTTTTT
300052 TTTGGAGAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 14 0.40
33 14 0.40
34 7 0.20
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (32 bp):
GTTTTTTTCTTTTCTCTCTTTTTCTTTCTTTT
Found at i:312675 original size:51 final size:51
Alignment explanation
Indices: 312519--312688 Score: 214
Period size: 52 Copynumber: 3.3 Consensus size: 51
312509 GAAATAACGA
* *
312519 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGGAAATAAAATCGG
* * * * * *
312571 TGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTGGAAATAAAATCGG
*** *
312623 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCGG
312674 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
312689 TCGGAAATAA
Statistics
Matches: 99, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
51 38 0.38
52 51 0.52
53 10 0.10
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCGG
Found at i:312811 original size:211 final size:211
Alignment explanation
Indices: 312460--312852 Score: 592
Period size: 211 Copynumber: 1.9 Consensus size: 211
312450 GAGATAATAA
* * * *
312460 CGGGATTGGAGTGTTCCCTCGGAAGTAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGG
1 CGGGATTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGA
* * *
312525 AGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGTGTTGGAGTATCCCCGATT
66 AGTACCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
* * *
312590 AAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT
131 AAAGGAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAAT
312655 ATTTTGGAAATAAAGT
196 ATTTTGGAAATAAAGT
* * * *
312671 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGA
1 CGGGATTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGA
* *
312735 AGTGCCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGA
66 AGTACCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGA
* *
312800 TTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
129 TTAAAGGAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATT
312853 GTGGAGAATT
Statistics
Matches: 162, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
210 26 0.16
211 97 0.60
212 39 0.24
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (211 bp):
CGGGATTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGA
AGTACCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATT
AAAGGAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAAT
ATTTTGGAAATAAAGT
Found at i:315236 original size:13 final size:13
Alignment explanation
Indices: 315218--315243 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
315208 ACAAAGATCC
315218 ATGTATCGATACA
1 ATGTATCGATACA
315231 ATGTATCGATACA
1 ATGTATCGATACA
315244 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:315239 original size:33 final size:33
Alignment explanation
Indices: 315197--315263 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
315187 AAAATTTCCA
***
315197 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
315230 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
315263 A
1 A
315264 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:315307 original size:19 final size:18
Alignment explanation
Indices: 315283--315350 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
315273 CAGTAGCTAA
315283 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
315302 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
315317 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
315334 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
315351 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:315323 original size:13 final size:13
Alignment explanation
Indices: 315305--315329 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
315295 ACAATACTTA
315305 TGTATCGATACAT
1 TGTATCGATACAT
315318 TGTATCGATACA
1 TGTATCGATACA
315330 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:315327 original size:32 final size:32
Alignment explanation
Indices: 315286--315348 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
315276 TAGCTAATTA
*
315286 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
315318 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
315349 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:315412 original size:21 final size:22
Alignment explanation
Indices: 315386--315442 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
315376 GTTGGGACCC
** *
315386 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTCCACAAA
315407 TGTATCGATACA-TTCCACAAA
1 TGTATCGATACATTTCCACAAA
315428 TGTATCGATACATTT
1 TGTATCGATACATTT
315443 TTTTTTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.10
21 26 0.84
22 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (22 bp):
TGTATCGATACATTTCCACAAA
Found at i:318718 original size:2 final size:2
Alignment explanation
Indices: 318706--318759 Score: 90
Period size: 2 Copynumber: 26.0 Consensus size: 2
318696 TGATGCATAC
318706 AT AT CAT AT AT AT AT AT AT AT AGT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
318750 AT AT AT AT AT
1 AT AT AT AT AT
318760 CTTGGAAGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 46 0.92
3 4 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:321116 original size:2 final size:2
Alignment explanation
Indices: 321095--321155 Score: 68
Period size: 2 Copynumber: 30.5 Consensus size: 2
321085 TGGCTTCATT
* * *
321095 TA TA TG TA TA TG TG 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 TA TA TA TA TA TA TA
* * *
321137 TA CA TA TG TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA T
321156 GTCCTTGAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (2 bp):
TA
Found at i:322585 original size:2 final size:2
Alignment explanation
Indices: 322578--322604 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
322568 TTGCAAGACT
322578 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
322605 TCCGATTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:323560 original size:30 final size:29
Alignment explanation
Indices: 323475--323565 Score: 101
Period size: 30 Copynumber: 3.1 Consensus size: 29
323465 TTTATTTTAA
* * *
323475 AAAGTTTATTTAAGTATAAATTAAAAGTT
1 AAAGCTTATTTAAATATAAATTAAAAATT
* * * *
323504 AGAGCTTATTTGAATACAAGTTAAAAATT
1 AAAGCTTATTTAAATATAAATTAAAAATT
*
323533 AAATGCTTTTTTAAATATAAATTAAAAATT
1 AAA-GCTTATTTAAATATAAATTAAAAATT
323563 AAA
1 AAA
323566 ATTTATTTGG
Statistics
Matches: 49, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 24 0.49
30 25 0.51
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.38
Consensus pattern (29 bp):
AAAGCTTATTTAAATATAAATTAAAAATT
Found at i:325550 original size:23 final size:22
Alignment explanation
Indices: 325523--325566 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
325513 TTCATATTTT
*
325523 ATTTAAAATTCATTTATTAATTC
1 ATTTAAAACTCATTTA-TAATTC
*
325546 ATTTAATACTCATTTATAATT
1 ATTTAAAACTCATTTATAATT
325567 TAATTACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTAAAACTCATTTATAATTC
Found at i:326061 original size:21 final size:22
Alignment explanation
Indices: 326016--326079 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
326006 TTTTTATTAA
326016 CAAATTTAATATAAATTAATGAT
1 CAAATTTAATATAAATTAA-GAT
326039 CAAATTTAATAATAAA-TAA-AT
1 CAAATTTAAT-ATAAATTAAGAT
* *
326060 CAGATTTAAATATAATTTAA
1 CAAATTT-AATATAAATTAA
326080 AATTTTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 12 0.33
22 6 0.17
23 13 0.36
24 5 0.14
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (22 bp):
CAAATTTAATATAAATTAAGAT
Found at i:326656 original size:16 final size:15
Alignment explanation
Indices: 326634--326671 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
326624 AAATTTTATA
326634 TATTAATATAAATTT
1 TATTAATATAAATTT
*
326649 TAATTAATATATATTT
1 T-ATTAATATAAATTT
326665 TATTAAT
1 TATTAAT
326672 TTTATTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTAATATAAATTT
Found at i:328135 original size:2 final size:2
Alignment explanation
Indices: 328128--328161 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
328118 CATAAAATTA
* *
328128 AT AT AT AT AT AT AT AT AT AG AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
328162 CATAATGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:328305 original size:2 final size:2
Alignment explanation
Indices: 328298--328338 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
328288 TAGAAATCTA
328298 TC TC TC TC TC TC 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 TC TC TC TC TC TC T
328339 TACGTGGGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:332539 original size:3 final size:3
Alignment explanation
Indices: 332531--332555 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
332521 TGCGTTAAAG
332531 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
332556 TTAAAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:334711 original size:22 final size:22
Alignment explanation
Indices: 334684--334725 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
334674 ATATAAAAAT
334684 AAATATA-ATTAATAATTAATAA
1 AAATATATATTAA-AATTAATAA
*
334706 AAATATATATTTAAATTAAT
1 AAATATATATTAAAATTAAT
334726 GATATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATATATTAAAATTAATAA
Found at i:334725 original size:26 final size:26
Alignment explanation
Indices: 334657--334725 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 26
334647 CGATTTAATT
* *
334657 ATAAAATATTTAAATTTA-TATAAAA
1 ATAATATATTTAAATTAATTATAAAA
*
334682 ATAAATATAATT-AA-TAATTAATAAAA
1 AT-AATATATTTAAATTAATT-ATAAAA
334708 AT-ATATATTTAAATTAAT
1 ATAATATATTTAAATTAAT
334726 GATATAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
24 9 0.26
25 7 0.20
26 19 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
ATAATATATTTAAATTAATTATAAAA
Found at i:335393 original size:37 final size:37
Alignment explanation
Indices: 335352--335422 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
335342 TTATTTTTAC
335352 TATAATATTATAATTATTCAATTAAATTTAAAAATTT
1 TATAATATTATAATTATTCAATTAAATTTAAAAATTT
* *
335389 TATAATATTATAATTATTTAGTTAAATTTAAAAA
1 TATAATATTATAATTATTCAATTAAATTTAAAAA
335423 AATATGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (37 bp):
TATAATATTATAATTATTCAATTAAATTTAAAAATTT
Found at i:336866 original size:29 final size:29
Alignment explanation
Indices: 336804--336895 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 29
336794 ATAATGTTAA
* *
336804 ATATAATT-AAATA-ATATGATATAAAAAAT
1 ATATAATTAAAATATA-AT-ATATTATAAAT
336833 A-ATAATTAAAATATAATATATTATAAAT
1 ATATAATTAAAATATAATATATTATAAAT
* ** *
336861 ATATAAATATTATATAATATAAATTATTAAT
1 ATATAATTAAAATATAATAT--ATTATAAAT
336892 ATAT
1 ATAT
336896 CAAAATTTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
28 16 0.31
29 23 0.44
30 1 0.02
31 12 0.23
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (29 bp):
ATATAATTAAAATATAATATATTATAAAT
Found at i:336868 original size:24 final size:23
Alignment explanation
Indices: 336803--336894 Score: 75
Period size: 24 Copynumber: 4.0 Consensus size: 23
336793 GATAATGTTA
* *
336803 AATATAAT-TAAATAATATGATAT
1 AATATAATATAAATTATA-AATAT
*
336826 AA-AAAATA-ATAATTA-AAATAT
1 AATATAATATA-AATTATAAATAT
*
336847 AATATATTATAAATATATAAATAT
1 AATATAATATAAAT-TATAAATAT
* *
336871 TATATAATATAAATTATTAATAT
1 AATATAATATAAATTATAAATAT
336894 A
1 A
336895 TCAAAATTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
21 6 0.11
22 13 0.24
23 17 0.31
24 18 0.33
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (23 bp):
AATATAATATAAATTATAAATAT
Found at i:336887 original size:31 final size:32
Alignment explanation
Indices: 336843--336916 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
336833 AATAATTAAA
336843 ATATAATAT--ATTATAAATATAT--AAATATT
1 ATATAATATAAATTATAAATATATCAAAAT-TT
*
336872 ATATAATATAAATTATTAATATATCAAAATTT
1 ATATAATATAAATTATAAATATATCAAAATTT
336904 ATATAATTATAAA
1 ATATAA-TATAAA
336917 ATAATTTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
29 9 0.23
31 12 0.31
32 8 0.21
33 10 0.26
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
ATATAATATAAATTATAAATATATCAAAATTT
Found at i:336888 original size:17 final size:17
Alignment explanation
Indices: 336842--336934 Score: 86
Period size: 17 Copynumber: 5.4 Consensus size: 17
336832 TAATAATTAA
*
336842 AATATAATATATTATA-
1 AATATAAAATATTATAT
336858 AATATATAAATATTATAT
1 AATATA-AAATATTATAT
*
336876 AATATAAATTATTA-AT
1 AATATAAAATATTATAT
336892 -ATATCAAAAT-TTATAT
1 AATAT-AAAATATTATAT
336908 AATTATAAAATAATTTATAT
1 AA-TATAAAAT-A-TTATAT
*
336928 AACATAA
1 AATATAA
336935 TAAAATTCAA
Statistics
Matches: 64, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
15 7 0.11
16 14 0.22
17 22 0.34
18 9 0.14
19 4 0.06
20 8 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATAAAATATTATAT
Found at i:336891 original size:13 final size:14
Alignment explanation
Indices: 336804--336894 Score: 52
Period size: 13 Copynumber: 6.7 Consensus size: 14
336794 ATAATGTTAA
*
336804 ATATAAT-TAAATA
1 ATATAATATAAATT
* **
336817 ATATGATATAAAAA
1 ATATAATATAAATT
336831 ATAATAAT-TAAA--
1 AT-ATAATATAAATT
336843 ATATAATAT--ATT
1 ATATAATATAAATT
*
336855 ATAAATATATAAATATT
1 ATATA-ATAT-AA-ATT
336872 ATATAATATAAATT
1 ATATAATATAAATT
336886 AT-TAATATA
1 ATATAATATA
336895 TCAAAATTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
10 1 0.02
11 5 0.08
12 7 0.11
13 17 0.27
14 16 0.25
15 6 0.10
16 4 0.06
17 7 0.11
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (14 bp):
ATATAATATAAATT
Found at i:336937 original size:22 final size:20
Alignment explanation
Indices: 336899--336940 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
336889 AATATATCAA
*
336899 AATTTATATAATTATAAAAT
1 AATTTATATAATAATAAAAT
336919 AATTTATATAACATAATAAAAT
1 AATTTATAT-A-ATAATAAAAT
336941 TCAAAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 1 0.05
22 9 0.47
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTTATATAATAATAAAAT
Found at i:337591 original size:13 final size:13
Alignment explanation
Indices: 337573--337618 Score: 65
Period size: 13 Copynumber: 3.3 Consensus size: 13
337563 TTTTATTTTT
337573 AAATAAATTATTA
1 AAATAAATTATTA
337586 AAATAATATTAATTTA
1 AAATAA-ATT-A-TTA
337602 AAATAAATTATTA
1 AAATAAATTATTA
337615 AAAT
1 AAAT
337619 CTTATTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.43
14 4 0.13
15 4 0.13
16 9 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAATAAATTATTA
Found at i:337630 original size:29 final size:29
Alignment explanation
Indices: 337565--337631 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
337555 ATAATATTTT
*
337565 TTATTTTTAAATAAATTATTAAAATAATA
1 TTATTTTAAAATAAATTATTAAAATAATA
* **
337594 TTAATTTAAAATAAATTATTAAAATCTTA
1 TTATTTTAAAATAAATTATTAAAATAATA
337623 TTATTTTAA
1 TTATTTTAA
337632 TTTATAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
TTATTTTAAAATAAATTATTAAAATAATA
Found at i:337632 original size:34 final size:31
Alignment explanation
Indices: 337557--337650 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 31
337547 CACTGAGCAT
* *
337557 AATATT-TTTTATTTTTAAATAAATTATTAA
1 AATATTATTTTAATTTAAAATAAATTATTAA
*
337587 AATA--ATATTAATTTAAAATAAATTATTAA
1 AATATTATTTTAATTTAAAATAAATTATTAA
337616 AATCTTATTATTTTAATTTATAAA-AAATTATTAA
1 AA---TATTATTTTAATTTA-AAATAAATTATTAA
337650 A
1 A
337651 TTAATTAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
29 23 0.43
30 4 0.08
32 2 0.04
34 21 0.40
35 3 0.06
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (31 bp):
AATATTATTTTAATTTAAAATAAATTATTAA
Found at i:337873 original size:21 final size:20
Alignment explanation
Indices: 337825--337878 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
337815 TTATTATACT
*
337825 GATTTTTAAAAAT-TAATAA
1 GATTTTTATAAATATAATAA
*
337844 GATTATTATAAATATAATAA
1 GATTTTTATAAATATAATAA
* *
337864 TAGTTTTTATTAATA
1 GA-TTTTTATAAATA
337879 AAAAATTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 11 0.39
20 7 0.25
21 10 0.36
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (20 bp):
GATTTTTATAAATATAATAA
Found at i:338039 original size:31 final size:31
Alignment explanation
Indices: 337989--338121 Score: 88
Period size: 31 Copynumber: 4.0 Consensus size: 31
337979 ATTTTTAAAA
* * *
337989 TTAAAATTAAAAATTGTAATAGTTTAATTATT
1 TTAAAATT-AATATTATAATAGTCTAATTATT
* * *
338021 TTAAAATTGATATTGTAATCA-TCGAATTATTT
1 TTAAAATTAATATTATAAT-AGTCTAATTA-TT
*
338053 TTAAAATTTAAATTAAGGGTTATAATAGTTTAATTATT
1 TTAAAA-TT-AA-T-A---TTATAATAGTCTAATTATT
* *
338091 TTAAAATTTATATTATAATTGTCTAATTATT
1 TTAAAATTAATATTATAATAGTCTAATTATT
338122 AAAGATTATA
Statistics
Matches: 80, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
31 32 0.40
32 17 0.21
33 2 0.03
34 2 0.03
35 2 0.03
36 2 0.03
37 2 0.03
38 9 0.11
39 12 0.15
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (31 bp):
TTAAAATTAATATTATAATAGTCTAATTATT
Found at i:338119 original size:70 final size:70
Alignment explanation
Indices: 337966--338121 Score: 222
Period size: 70 Copynumber: 2.2 Consensus size: 70
337956 ACTTAAATGG
*
337966 TAATTATCTAATTATTTTTAAAATTAAAATTAAAAATTGTAATAGTTTAATTATTTTAAAATTGA
1 TAATTATCTAATTATTTTTAAAATTAAAATTAAAAATTATAATAGTTTAATTATTTTAAAATTGA
*
338031 TATTG
66 TATTA
* * * *** *
338036 TAATCATCGAATTATTTTTAAAATTTAAATTAAGGGTTATAATAGTTTAATTATTTTAAAATTTA
1 TAATTATCTAATTATTTTTAAAATTAAAATTAAAAATTATAATAGTTTAATTATTTTAAAATTGA
338101 TATTA
66 TATTA
*
338106 TAATTGTCTAATTATT
1 TAATTATCTAATTATT
338122 AAAGATTATA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
70 74 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (70 bp):
TAATTATCTAATTATTTTTAAAATTAAAATTAAAAATTATAATAGTTTAATTATTTTAAAATTGA
TATTA
Found at i:338282 original size:46 final size:46
Alignment explanation
Indices: 338231--338323 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
338221 AAAATTTTAA
* * * *
338231 AATAATGAGACGATTATAATTCTTAA-TTTAAAATAGTTAGATAATT
1 AATAATGAAACGATTACAATT-TAAATTTTAAAATAATTAGATAATT
* *
338277 AATAATTAAATGATTACAATTTAAATTTTAAAATAATTAGATAATT
1 AATAATGAAACGATTACAATTTAAATTTTAAAATAATTAGATAATT
338323 A
1 A
338324 TAACTCTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
45 3 0.08
46 37 0.93
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (46 bp):
AATAATGAAACGATTACAATTTAAATTTTAAAATAATTAGATAATT
Found at i:338314 original size:31 final size:31
Alignment explanation
Indices: 338277--338385 Score: 96
Period size: 38 Copynumber: 3.4 Consensus size: 31
338267 TTAGATAATT
*
338277 AATAATTAAATGATTACAATTTAAATTTTAA
1 AATAATTAAATGATTACAATTTAAATTTAAA
* *
338308 AATAATTAGATAATTATAACTCTTAATTTAAATTTAAA
1 AATAATT--A-AATGATTA--C--AATTTAAATTTAAA
*
338346 AATAATTAAATGATTACAACTTAAA-TTAAA
1 AATAATTAAATGATTACAATTTAAATTTAAA
*
338376 CA-AATTAAAT
1 AATAATTAAAT
338386 TAAATATCCT
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
29 8 0.12
30 6 0.09
31 14 0.22
33 2 0.03
34 6 0.09
35 6 0.09
36 2 0.03
38 20 0.31
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.39
Consensus pattern (31 bp):
AATAATTAAATGATTACAATTTAAATTTAAA
Found at i:338336 original size:38 final size:40
Alignment explanation
Indices: 338188--338353 Score: 132
Period size: 38 Copynumber: 4.2 Consensus size: 40
338178 TAAAATTACA
* *
338188 AAAATAATTAGATGATTATAACCTAATTAAATTAAAATTTT
1 AAAATAATTAGATAATTATAA-CTAATTAAATTTAAATTTT
* ** ** *
338229 AAAATAATGAGACGATTATAA-TTCTT-AATTTAAAATAGTT
1 AAAATAATTAGATAATTATAACTAATTAAATTT-AAAT-TTT
* *
338269 -AGATAATTA-ATAATTA-AA-TGATTACAATTTAAATTTT
1 AAAATAATTAGATAATTATAACTAATTA-AATTTAAATTTT
* *
338306 AAAATAATTAGATAATTATAACT-CTT-AATTTAAATTTA
1 AAAATAATTAGATAATTATAACTAATTAAATTTAAATTTT
338344 AAAATAATTA
1 AAAATAATTA
338354 AATGATTACA
Statistics
Matches: 101, Mismatches: 16, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
37 7 0.07
38 42 0.42
39 26 0.26
40 6 0.06
41 20 0.20
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (40 bp):
AAAATAATTAGATAATTATAACTAATTAAATTTAAATTTT
Found at i:338499 original size:17 final size:17
Alignment explanation
Indices: 338474--338507 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
338464 AATAATAAAA
*
338474 AATATTATTATATTTAT
1 AATAATATTATATTTAT
*
338491 AATAATATTATTTTTAT
1 AATAATATTATATTTAT
338508 TAAATTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATAATATTATATTTAT
Found at i:338852 original size:20 final size:19
Alignment explanation
Indices: 338820--338857 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
338810 TATTTTATCA
*
338820 ATAAATTATATTATTATTG
1 ATAAATTAAATTATTATTG
338839 ATAAGATTAAATTATTATT
1 ATAA-ATTAAATTATTATT
338858 ATTATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
ATAAATTAAATTATTATTG
Found at i:338855 original size:3 final size:3
Alignment explanation
Indices: 338849--338899 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
338839 ATAAGATTAA
338849 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
338897 ATT
1 ATT
338900 GATTTGATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:339464 original size:8 final size:8
Alignment explanation
Indices: 339451--339494 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
339441 ATATTCGAGG
339451 AAATTTTA
1 AAATTTTA
339459 AAATTTTAAA
1 AAATTTT--A
339469 AAATTTTA
1 AAATTTTA
*
339477 AAATATTA
1 AAATTTTA
*
339485 ACATTTTA
1 AAATTTTA
339493 AA
1 AA
339495 TATGTTACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
8 22 0.73
10 8 0.27
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (8 bp):
AAATTTTA
Found at i:339474 original size:18 final size:18
Alignment explanation
Indices: 339451--339485 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
339441 ATATTCGAGG
*
339451 AAATTTTAAAATTTTAAA
1 AAATTTTAAAATATTAAA
339469 AAATTTTAAAATATTAA
1 AAATTTTAAAATATTAA
339486 CATTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTTAAAATATTAAA
Found at i:339510 original size:15 final size:15
Alignment explanation
Indices: 339473--339514 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
339463 TTTAAAAAAT
339473 TTTAAAATATTAACA
1 TTTAAAATATTAACA
* *
339488 TTTTAAATATGTTAC-
1 TTTAAAATAT-TAACA
339503 TTTAAAATATTA
1 TTTAAAATATTA
339515 GTATTTATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
14 1 0.05
15 18 0.82
16 3 0.14
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (15 bp):
TTTAAAATATTAACA
Found at i:341318 original size:2 final size:2
Alignment explanation
Indices: 341311--341346 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
341301 AGAAAAGGAA
341311 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
341347 TAATGCCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:343744 original size:21 final size:19
Alignment explanation
Indices: 343692--343745 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
343682 TTTGAAACTT
*
343692 AAATTTATATTTGAATTTA
1 AAATTTATATTTTAATTTA
* *
343711 AATTTTAAAATTTTAGATTTA
1 AAATTT-ATATTTTA-ATTTA
343732 AAATTTATGATTTT
1 AAATTTAT-ATTTT
343746 CGAATTCATA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 5 0.19
20 7 0.26
21 15 0.56
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (19 bp):
AAATTTATATTTTAATTTA
Found at i:345213 original size:19 final size:19
Alignment explanation
Indices: 345189--345254 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
345179 TTTCAACGAT
*
345189 TTGTATAGATACATAAGTG
1 TTGTATCGATACATAAGTG
345208 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
345222 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
345240 TTGTATCGATACATA
1 TTGTATCGATACATA
345255 TGAAGCTACT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 25 0.62
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:345226 original size:32 final size:32
Alignment explanation
Indices: 345190--345252 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
345180 TTCAACGATT
345190 TGTATAGATACATAAGTGTTGTATCGATACAA
1 TGTATAGATACATAAGTGTTGTATCGATACAA
*
345222 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATAGATACATAAGTGTTGTATCGATACA
345253 TATGAAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATAGATACATAAGTGTTGTATCGATACAA
Found at i:345227 original size:13 final size:13
Alignment explanation
Indices: 345209--345233 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
345199 ACATAAGTGT
345209 TGTATCGATACAA
1 TGTATCGATACAA
345222 TGTATCGATACA
1 TGTATCGATACA
345234 TAAGTGTTGT
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:345314 original size:13 final size:13
Alignment explanation
Indices: 345296--345320 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
345286 ATTACTCAAA
345296 TGTATCGATACAT
1 TGTATCGATACAT
345309 TGTATCGATACA
1 TGTATCGATACA
345321 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:345456 original size:52 final size:52
Alignment explanation
Indices: 345336--345457 Score: 190
Period size: 52 Copynumber: 2.3 Consensus size: 52
345326 CTTTGTATTG
* * *
345336 ATACACGCAGGCAAATTTGCCCAGATGTATCGATACACTGTGAAATGTATCG
1 ATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGTATCA
* *
345388 ATACATACGGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGTATCA
1 ATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGTATCA
*
345440 ATACATGCAGGTAAATTT
1 ATACATGCAGGCAAATTT
345458 TCATATTTCG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (52 bp):
ATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGTATCA
Found at i:353837 original size:23 final size:23
Alignment explanation
Indices: 353811--353881 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
353801 GGTTGATTCG
* *
353811 TATTAATGTAAAGATTT-ATTAGA
1 TATTAATTTAAA-ATTTAATTAAA
353834 TATTTAATTTAAAATTTAATTAAA
1 TA-TTAATTTAAAATTTAATTAAA
* * *
353858 AATTAATTTAAATTTTAATAAAA
1 TATTAATTTAAAATTTAATTAAA
353881 T
1 T
353882 TTTATTGATT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 25 0.62
24 15 0.38
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
TATTAATTTAAAATTTAATTAAA
Found at i:353852 original size:12 final size:12
Alignment explanation
Indices: 353835--353876 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
353825 TTTATTAGAT
353835 ATTTAATTTAAA
1 ATTTAATTTAAA
353847 ATTTAA-TTAAA
1 ATTTAATTTAAA
*
353858 AATTAATTTAAA
1 ATTTAATTTAAA
*
353870 TTTTAAT
1 ATTTAAT
353877 AAAATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTAATTTAAA
Done.