Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_pilon, whole genome shotgun sequence
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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 24
Found at i:161810 original size:30 final size:29
Alignment explanation
Indices: 161776--161838 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
161766 CCCGATATAT
*
161776 CACCGGTGAATAGTATATTTTTTGATCTAA
1 CACCGGT-AATAGTATATTTCTTGATCTAA
* *
161806 CACCGGTCATATTATATTTCTTGATCTAA
1 CACCGGTAATAGTATATTTCTTGATCTAA
161835 CACC
1 CACC
161839 CTTAGTAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (29 bp):
CACCGGTAATAGTATATTTCTTGATCTAA
Found at i:161950 original size:51 final size:51
Alignment explanation
Indices: 161852--161978 Score: 148
Period size: 51 Copynumber: 2.5 Consensus size: 51
161842 AGTAGTAAAT
* * * * *
161852 CGCGCCCTCTGTACCGTGCTATACGATGATTTGGCGCCACGTAGGGTATAG
1 CGCGCCCCCTGCACCGCGCTATACGATGATCTGGCGACACGTAGGGTATAG
* *
161903 CGCGCCCCCTGCACCGCGCTATACGGTGATCTGGCATACACGT-GGGTATAG
1 CGCGCCCCCTGCACCGCGCTATACGATGATCTGGC-GACACGTAGGGTATAG
* * *
161954 TGCGGCCCCTGCAGCGCGCTATACG
1 CGCGCCCCCTGCACCGCGCTATACG
161979 CCACGTAGGG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 60 0.92
52 5 0.08
ACGTcount: A:0.17, C:0.32, G:0.30, T:0.21
Consensus pattern (51 bp):
CGCGCCCCCTGCACCGCGCTATACGATGATCTGGCGACACGTAGGGTATAG
Found at i:166367 original size:18 final size:18
Alignment explanation
Indices: 166344--166380 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
166334 AAAGGCGATG
166344 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
166362 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
166380 G
1 G
166381 TGGTGGCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (18 bp):
GCGGCATCATATATGGCT
Found at i:168089 original size:110 final size:111
Alignment explanation
Indices: 167888--168108 Score: 381
Period size: 110 Copynumber: 2.0 Consensus size: 111
167878 ATTACAAAAA
* *
167888 TTAATTCTTAATCTAATAATCATGCATTAAATGAATTAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATGAAATAACTAAATATTACTAATAATTTAAATTA
*
167953 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
*
167999 TTAATTCTTAATCTAATAATCATGCATTAAAT-AAATAACTAAATGTTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATGAAATAACTAAATATTACTAATAATTTAAATTA
* *
168063 AATTAAAACGTTAAAATGTTATCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
168109 ATGATTTCCA
Statistics
Matches: 104, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 72 0.69
111 32 0.31
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATGAAATAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:169574 original size:2 final size:2
Alignment explanation
Indices: 169567--169602 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
169557 TATAAGACTA
169567 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
169603 GACGTTGTCG
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:170300 original size:22 final size:22
Alignment explanation
Indices: 170272--170314 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
170262 GCTCGTACCT
* *
170272 ATTTAAATCTTAAAATTTAAAA
1 ATTTAAACCCTAAAATTTAAAA
*
170294 ATTTAAACCCTAAATTTTAAA
1 ATTTAAACCCTAAAATTTAAA
170315 TATAAATCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTTAAACCCTAAAATTTAAAA
Found at i:171179 original size:9 final size:9
Alignment explanation
Indices: 171165--171190 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
171155 ATCTGAAATA
171165 TTATTATTT
1 TTATTATTT
171174 TTATTATTT
1 TTATTATTT
171183 TTATTATT
1 TTATTATT
171191 ATTGGACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTATTATTT
Found at i:179455 original size:62 final size:60
Alignment explanation
Indices: 179371--179488 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
179361 AGAAATACCA
* * * *
179371 ACGTGGCATCTGACTCAGCAGAA-CCCAAATAGAAGGTGCGTCCCCGGGGATGCGCCTTCCAC
1 ACGTGGCATCCGACTCAGCAGAATCCC--AT-GAAAGCGCGTCCCCGAGGATGCGCCTTCCAC
* *
179433 ACGTGGCATCCGAGTCATCAGAATCCCATGAAAGCGCGTCCCCGAGGATGCGCCTT
1 ACGTGGCATCCGACTCAGCAGAATCCCATGAAAGCGCGTCCCCGAGGATGCGCCTT
179489 TGCGCCACGT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
60 24 0.49
61 2 0.04
62 20 0.41
63 3 0.06
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.17
Consensus pattern (60 bp):
ACGTGGCATCCGACTCAGCAGAATCCCATGAAAGCGCGTCCCCGAGGATGCGCCTTCCAC
Found at i:182654 original size:35 final size:36
Alignment explanation
Indices: 182613--182713 Score: 107
Period size: 35 Copynumber: 2.8 Consensus size: 36
182603 AAGTCTCTAC
* *
182613 AGGTTCAGCTTGATCAAACTGGTAATTCCTCAC-AT
1 AGGTTCAGCTCGATCAAACTGGTAATTCCTCACGAA
* ** *
182648 TGGTTCAGAC-CGATTGAACTGGTAATTCCTTACGAA
1 AGGTTCAG-CTCGATCAAACTGGTAATTCCTCACGAA
* *
182684 AGGTTTAGCTCGATCAAATTGGTAATTCCT
1 AGGTTCAGCTCGATCAAACTGGTAATTCCT
182714 TATATGACTG
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
35 27 0.52
36 25 0.48
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (36 bp):
AGGTTCAGCTCGATCAAACTGGTAATTCCTCACGAA
Found at i:184761 original size:10 final size:11
Alignment explanation
Indices: 184729--184758 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
184719 AAATTTTATT
184729 ATTTTTATTAC
1 ATTTTTATTAC
184740 ATTTTTATTAC
1 ATTTTTATTAC
184751 ATTTTTAT
1 ATTTTTAT
184759 ACAACATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTTATTAC
Found at i:194441 original size:34 final size:35
Alignment explanation
Indices: 194387--194456 Score: 115
Period size: 34 Copynumber: 2.0 Consensus size: 35
194377 TTTATATTAT
*
194387 TTTATTTATAAAATGTTATATATAAAATGTAGTAA
1 TTTATTTATAAAATATTATATATAAAATGTAGTAA
*
194422 TTTA-TTATCAAATATTATATATAAAATGTAGTAA
1 TTTATTTATAAAATATTATATATAAAATGTAGTAA
194456 T
1 T
194457 CAAATATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 29 0.88
35 4 0.12
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (35 bp):
TTTATTTATAAAATATTATATATAAAATGTAGTAA
Found at i:194656 original size:20 final size:19
Alignment explanation
Indices: 194610--194670 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
194600 AATTAAAATT
194610 AAATT-TATTAAATTAAATGA
1 AAATTATATTAAATT-AAT-A
*
194630 GAATTATGATTAAATTAATA
1 AAATTAT-ATTAAATTAATA
*
194650 AAATTATATAAATATTAATA
1 AAATTATATTAA-ATTAATA
194670 A
1 A
194671 CTAAATATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 4 0.11
20 19 0.54
21 4 0.11
22 8 0.23
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
AAATTATATTAAATTAATA
Found at i:202975 original size:19 final size:19
Alignment explanation
Indices: 202951--202990 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
202941 ATTCTACTAT
202951 AGGAAATAGACTTGTTGCA
1 AGGAAATAGACTTGTTGCA
202970 AGGAAATAGACTTGTTGCA
1 AGGAAATAGACTTGTTGCA
202989 AG
1 AG
202991 TCTTATTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.25
Consensus pattern (19 bp):
AGGAAATAGACTTGTTGCA
Found at i:204466 original size:29 final size:29
Alignment explanation
Indices: 204423--204532 Score: 168
Period size: 29 Copynumber: 3.8 Consensus size: 29
204413 TTTCATATGT
**
204423 TCATGTA-CTCATGTCATTTCTCTAATGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
204451 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
204480 TCATGTAGCTCATGACATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
204509 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
204533 ATATCACATA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
28 7 0.09
29 62 0.84
30 5 0.07
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:205061 original size:64 final size:64
Alignment explanation
Indices: 204909--205065 Score: 153
Period size: 64 Copynumber: 2.5 Consensus size: 64
204899 TAATGAATGT
** * * * *
204909 ATGCATCGATGCACTACTTGGGCATCGGTGCATAAAATGCATTCGATGTTTTATTATTAATGGG
1 ATGCATCGATGCACTACCAGTGCATCGATGCATAAAATGCATTCGATGTTTTATTATTAAAGAG
* * *
204973 ATGCATCGATGCA-TGCCTTA-TGCATCGATGCACT-AATTGCATTCGATATTTTTATT-TTAAA
1 ATGCATCGATGCACTACC--AGTGCATCGATGCA-TAAAATGCATTCGAT-GTTTTATTATTAAA
205034 -AG
62 GAG
205036 AGTGCATCGATGCACTACCAGTGCATCGAT
1 A-TGCATCGATGCACTACCAGTGCATCGAT
205066 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
63 5 0.07
64 60 0.79
65 11 0.14
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACCAGTGCATCGATGCATAAAATGCATTCGATGTTTTATTATTAAAGAG
Found at i:210387 original size:15 final size:15
Alignment explanation
Indices: 210363--210396 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
210353 CCGTAGGACC
*
210363 ACTACATCCCGAAGG
1 ACTACATCCCGAAAG
*
210378 ACTACGTCCCGAAAG
1 ACTACATCCCGAAAG
210393 ACTA
1 ACTA
210397 TTATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAAG
Found at i:210524 original size:29 final size:29
Alignment explanation
Indices: 210481--210583 Score: 181
Period size: 29 Copynumber: 3.6 Consensus size: 29
210471 TTTCATATGT
210481 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
210509 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
210538 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
210567 TCATGTAGCTCAAGTCA
1 TCATGTAGCTCATGTCA
210584 CGTTCTCATA
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
28 7 0.10
29 64 0.90
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:211036 original size:64 final size:64
Alignment explanation
Indices: 210967--211123 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 64
210957 TAATGAAGGT
* **
210967 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTC-A-ATGTTTTATTATTAATG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATAT-TTTTATT-TTAAAA
211029 GA
63 GA
* * *
211031 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATATTTTTATTTTAAAAGA
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATATTTTTATTTTAAAAGA
* **
211095 GTGCATCGATGCACTACCAGTGCATCGAT
1 ATGCATCGATGCACTACTTGTGCATCGAT
211124 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
63 1 0.01
64 64 0.83
65 10 0.13
66 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATATTTTTATTTTAAAAGA
Found at i:213699 original size:131 final size:131
Alignment explanation
Indices: 213457--213824 Score: 502
Period size: 131 Copynumber: 2.8 Consensus size: 131
213447 ATAATTCTAA
** * * *
213457 GAGAGAAAATGATAATATCTAATTATTTCCGATCGAGAATAAATGAACTCTCATGCTTTAAAGCA
1 GAGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * * *
213522 ATCATTTATTACTCCAATTGAAATGAAGATATATCACTATTTCGTCTTAAAATTCAATATTTATT
66 ATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAATT
213587 C
131 C
* * * *
213588 GAGTGAAAACAATAATATCCAATGATTTCTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * *
213653 GTAATTTATTACTCTAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAATT
66 ATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAATT
213718 C
131 C
* * * *
213719 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTTACGTCTTAAAGCA
1 GAGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * * *
213784 TTCATTTATTACTCCAACCAAAACGAAGAGATATTACTATT
66 ATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATT
213825 TTCAATATCG
Statistics
Matches: 205, Mismatches: 32, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
131 205 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (131 bp):
GAGAGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
ATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAATT
C
Found at i:213914 original size:23 final size:25
Alignment explanation
Indices: 213859--213915 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 25
213849 ATTTTAGTTT
213859 TATG-CTTTTATGAAACGTTTATCTC
1 TATGTCTTTT-TGAAACGTTTATCTC
*
213884 TAT-T-TTTTTGACACGTTT-T-TC
1 TATGTCTTTTTGAAACGTTTATCTC
213905 TATGTCTTTTT
1 TATGTCTTTTT
213916 CGTAGTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
21 5 0.18
22 2 0.07
23 14 0.50
24 4 0.14
25 3 0.11
ACGTcount: A:0.18, C:0.14, G:0.11, T:0.58
Consensus pattern (25 bp):
TATGTCTTTTTGAAACGTTTATCTC
Found at i:221924 original size:34 final size:33
Alignment explanation
Indices: 221880--221972 Score: 127
Period size: 34 Copynumber: 2.8 Consensus size: 33
221870 AGTTAGAAAT
221880 TTCATATTGGTTGGTGGCCAACTTATTTGAAAAA
1 TTCAT-TTGGTTGGTGGCCAACTTATTTGAAAAA
* *
221914 TTCATCTTGGTTGGTGGCAAACTTA-TTGGAAAA
1 TTCAT-TTGGTTGGTGGCCAACTTATTTGAAAAA
*
221947 TTC-TTTGGTAGGTGGCCAACTTATTT
1 TTCATTTGGTTGGTGGCCAACTTATTT
221973 TTCATCTTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
31 17 0.32
32 3 0.06
33 10 0.19
34 23 0.43
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.40
Consensus pattern (33 bp):
TTCATTTGGTTGGTGGCCAACTTATTTGAAAAA
Found at i:226111 original size:29 final size:29
Alignment explanation
Indices: 226074--226148 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
226064 GTTGGCTTGA
226074 TGAA-TGGTGTAGTGTTGTTGATGAATGG
1 TGAATTGGTGTAGTGTTGTTGATGAATGG
226102 TGAATTGGTGTAGTGTTGTTGATGAATGG
1 TGAATTGGTGTAGTGTTGTTGATGAATGG
* * *
226131 TAAATTGGAGTAGCGTTG
1 TGAATTGGTGTAGTGTTG
226149 GTCGATTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
28 4 0.09
29 39 0.91
ACGTcount: A:0.23, C:0.01, G:0.37, T:0.39
Consensus pattern (29 bp):
TGAATTGGTGTAGTGTTGTTGATGAATGG
Found at i:227657 original size:21 final size:20
Alignment explanation
Indices: 227615--227658 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
227605 AGAAGAAAAG
*
227615 AATATTTTTTAAGGAGATAA
1 AATATTTTTTAAGGAGAGAA
227635 AATATTTTTTCAA-GAGAAGAA
1 AATATTTTTT-AAGGAG-AGAA
227656 AAT
1 AAT
227659 TCTTCAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (20 bp):
AATATTTTTTAAGGAGAGAA
Found at i:227859 original size:64 final size:65
Alignment explanation
Indices: 227735--227891 Score: 169
Period size: 65 Copynumber: 2.4 Consensus size: 65
227725 TAATCCAACC
* ** *
227735 AAATATCTTTTAATATTC-AACTTTAAATAGATTAATATTTTTTAATTTGAAATATTC-AAAAGA
1 AAATTTCTTTT-ATATTCAAAC-TTAAATAGATTAATATTTTTTAATTTGAAATAAACAAAAAAA
227798 TA
64 TA
*
227800 AAATTTCTTTTATCATTCAAACTTAAATATA-T-ATATTATTTTAATTTGAAATAAACAAAAAAA
1 AAATTTCTTTTAT-ATTCAAACTTAAATAGATTAATATT-TTTTAATTTGAAATAAACAAAAAAA
227863 TA
64 TA
* * *
227865 TAATTATCTTTAATATTCAAAGTTAAA
1 AAATT-TCTTTTATATTCAAACTTAAA
227892 AATGTAACAA
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
63 5 0.06
64 19 0.24
65 45 0.57
66 10 0.13
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (65 bp):
AAATTTCTTTTATATTCAAACTTAAATAGATTAATATTTTTTAATTTGAAATAAACAAAAAAATA
Found at i:228342 original size:27 final size:27
Alignment explanation
Indices: 228302--228374 Score: 130
Period size: 27 Copynumber: 2.7 Consensus size: 27
228292 ATTTGTTAAA
*
228302 TGAGC-CGAGTCGAACTCGAGTACTGC
1 TGAGCTCGACTCGAACTCGAGTACTGC
228328 TGAGCTCGACTCGAACTCGAGTACTGC
1 TGAGCTCGACTCGAACTCGAGTACTGC
228355 TGAGCTCGACTCGAACTCGA
1 TGAGCTCGACTCGAACTCGA
228375 AAACTTTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
26 5 0.11
27 40 0.89
ACGTcount: A:0.23, C:0.29, G:0.27, T:0.21
Consensus pattern (27 bp):
TGAGCTCGACTCGAACTCGAGTACTGC
Found at i:236982 original size:32 final size:31
Alignment explanation
Indices: 236941--237001 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 31
236931 TAGCTGGCCG
236941 TTCTGATTGATTACAACAAAAAACAAACGACA
1 TTCTGATTGATTACAACAAAAAA-AAACGACA
*
236973 TTCTGATTGATTACAACAACAAAAAACGA
1 TTCTGATTGATTACAACAAAAAAAAACGA
237002 TCTTACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 6 0.21
32 22 0.79
ACGTcount: A:0.49, C:0.18, G:0.10, T:0.23
Consensus pattern (31 bp):
TTCTGATTGATTACAACAAAAAAAAACGACA
Found at i:240826 original size:9 final size:9
Alignment explanation
Indices: 240812--240847 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
240802 AAACATACTA
240812 ATTTTTTTG
1 ATTTTTTTG
240821 ATTTTTTTG
1 ATTTTTTTG
*
240830 TATTTTTCTG
1 -ATTTTTTTG
240840 ATTTTTTT
1 ATTTTTTT
240848 AAATTCAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.11, C:0.03, G:0.08, T:0.78
Consensus pattern (9 bp):
ATTTTTTTG
Found at i:240853 original size:102 final size:105
Alignment explanation
Indices: 240734--240973 Score: 296
Period size: 102 Copynumber: 2.3 Consensus size: 105
240724 CACGCTACAA
*
240734 TTTTCT-TTTTTTT-AATTCAAATAGATTAAACT-AAAGGATAGATAAAAATACATTGAAATTAG
1 TTTTCTGTTTTTTTAAATTCAAATAGATTAAACTGAAA-GATAGATAAAAATAAATTGAAATTAG
*
240796 ATATATAAACATACTAAT-TTTTTTG-A-T-TTTTTTGTAT
65 ATAAATAAACATACTAATATTTTTTGAATTATTTTTTGTAT
* ** *
240833 TTTTCTGATTTTTTTAAATTCAAGTAGATTAATTTGCAAGATAGATAAAAATAAATTGAAATTAG
1 TTTTCTG-TTTTTTTAAATTCAAATAGATTAAACTGAAAGATAGATAAAAATAAATTGAAATTAG
240898 ATAAATAAACATACTAATATTTTTTGTAAATTTTCTGATTTTTTGTAT
65 ATAAATAAACATACTAATATTTTTTG--AA---T-T-ATTTTTTGTAT
240946 TTTTCTGTTTTTTTAAATTCAAATAGAT
1 TTTTCTGTTTTTTTAAATTCAAATAGAT
240974 ATTTATTAGA
Statistics
Matches: 119, Mismatches: 7, Indels: 17
0.83 0.05 0.12
Matches are distributed among these distances:
99 6 0.05
101 7 0.06
102 58 0.49
103 9 0.08
106 1 0.01
111 1 0.01
112 20 0.17
113 17 0.14
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (105 bp):
TTTTCTGTTTTTTTAAATTCAAATAGATTAAACTGAAAGATAGATAAAAATAAATTGAAATTAGA
TAAATAAACATACTAATATTTTTTGAATTATTTTTTGTAT
Found at i:240949 original size:18 final size:19
Alignment explanation
Indices: 240916--240964 Score: 68
Period size: 17 Copynumber: 2.7 Consensus size: 19
240906 ACATACTAAT
240916 ATTTTTTGTAAATTTTCTG
1 ATTTTTTGTAAATTTTCTG
*
240935 ATTTTTTGT-ATTTTTCTG
1 ATTTTTTGTAAATTTTCTG
240953 -TTTTTT-TAAATT
1 ATTTTTTGTAAATT
240965 CAAATAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 9 0.33
18 8 0.30
19 9 0.33
ACGTcount: A:0.18, C:0.04, G:0.08, T:0.69
Consensus pattern (19 bp):
ATTTTTTGTAAATTTTCTG
Found at i:242702 original size:15 final size:15
Alignment explanation
Indices: 242665--242705 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
242655 TAATGGAAGT
*
242665 AATCCCTGCA-AATA
1 AATCCCTGCATAAAA
242679 AATCCCTGCATAAAA
1 AATCCCTGCATAAAA
*
242694 AATCTCTGCATA
1 AATCCCTGCATA
242706 TAGACAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.24
Consensus pattern (15 bp):
AATCCCTGCATAAAA
Found at i:250540 original size:21 final size:22
Alignment explanation
Indices: 250492--250543 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
250482 GAAAAACTAG
*
250492 GAAGAAAATAATATTTTTAAGG
1 GAAGAAAATAATATTTTTAAGA
*
250514 GGAGAAAAT-AT-TTTTTCAAGA
1 GAAGAAAATAATATTTTT-AAGA
250535 GAAGAAAAT
1 GAAGAAAAT
250544 TCTTCAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 13 0.50
22 8 0.31
ACGTcount: A:0.50, C:0.02, G:0.19, T:0.29
Consensus pattern (22 bp):
GAAGAAAATAATATTTTTAAGA
Found at i:250759 original size:62 final size:61
Alignment explanation
Indices: 250652--250965 Score: 196
Period size: 62 Copynumber: 5.0 Consensus size: 61
250642 TTAAACAGAT
** * * **
250652 AATAATATC-TTTTAATTTGAAATATTTAAAA-TATAAAACTCATTTTACCATTCAAACTTA
1 AATAATATCATTTTAATTTGAAATATACAAAATTATATAA-TTATTTTAATATTCAAACTTA
*
250712 AATATATATCATTTTAATTTGAAATATACAAAATTATATAATTATTTTAATATTCAAAGTTAAA
1 AATA-ATATCATTTTAATTTGAAATATACAAAATTATATAATTATTTTAATATTCAAACTT--A
* * * * * ** **
250776 AATTTAACAAATATCTTTTTAAATTGACATATTCAAACATTA-ATTATCCTACTAATATTCAAA-
1 AA--T----AATATCATTTTAATTTGAAATATACAAA-ATTATATAATTATTTTAATATTCAAAC
250839 TTA
59 TTA
* * * * *
250842 AATAATAT-A-TTTAATTTGTAATGGT-CAAAA-GATA-AATTCCTTTTATTATTCAAACTTA
1 AATAATATCATTTTAATTTGAAAT-ATACAAAATTATATAATT-ATTTTAATATTCAAACTTA
* * * *
250900 AACAAATATTATTTTAATTTAAAATATACAAAATTATATAATTATTTTTTAATATTCAAAATTA
1 AA-TAATATCATTTTAATTTGAAATATACAAAATTATATAATTA--TTTTAATATTCAAACTTA
250964 AA
1 AA
250966 AAGAGAACAA
Statistics
Matches: 195, Mismatches: 35, Indels: 44
0.71 0.13 0.16
Matches are distributed among these distances:
56 3 0.02
57 14 0.07
58 19 0.10
59 6 0.03
60 11 0.06
61 21 0.11
62 39 0.20
63 10 0.05
64 22 0.11
66 4 0.02
68 2 0.01
69 39 0.20
70 5 0.03
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (61 bp):
AATAATATCATTTTAATTTGAAATATACAAAATTATATAATTATTTTAATATTCAAACTTA
Found at i:257012 original size:17 final size:16
Alignment explanation
Indices: 256990--257029 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
256980 CAAAAATTAT
256990 TTAAAAATGATAAAATA
1 TTAAAAATGATAAAA-A
*
257007 TTAAAAATTATAAAAA
1 TTAAAAATGATAAAAA
257023 -TAAAAAT
1 TTAAAAAT
257030 AAATGTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.32
16 1 0.05
17 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TTAAAAATGATAAAAA
Found at i:257766 original size:2 final size:2
Alignment explanation
Indices: 257759--257808 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
257749 CTACCCCGAT
257759 TA TA TA TA TA TA TA 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
257801 TA TA TA TA
1 TA TA TA TA
257809 GTATTTTATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:263824 original size:3 final size:3
Alignment explanation
Indices: 263809--263847 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
263799 CGTTAGTTTA
*
263809 ATT ATT GTT ATT ATT ATT A-T ATT ATT ATT ATT AATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
263848 TTGTTACATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:263835 original size:14 final size:13
Alignment explanation
Indices: 263816--263847 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
263806 TTAATTATTG
263816 TTATTATTATTATA
1 TTATTATTATTA-A
263830 TTATTATTATTAA
1 TTATTATTATTAA
263843 TTATT
1 TTATT
263848 TTGTTACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:263836 original size:17 final size:18
Alignment explanation
Indices: 263811--263846 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
263801 TTAGTTTAAT
*
263811 TATTGTTATTATT-ATTA
1 TATTATTATTATTAATTA
263828 TATTATTATTATTAATTA
1 TATTATTATTATTAATTA
263846 T
1 T
263847 TTTGTTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TATTATTATTATTAATTA
Found at i:265297 original size:29 final size:29
Alignment explanation
Indices: 265228--265464 Score: 146
Period size: 29 Copynumber: 8.1 Consensus size: 29
265218 TTATTTGTAA
* *
265228 TTACTTTTTAGTCCTTTAACTTTTTATTT
1 TTACTTTTTAGTCCTTTAAGTTTCTATTT
* **
265257 TTTCTATTTTAGTATTTTAAGTTTCTATTT
1 TTACT-TTTTAGTCCTTTAAGTTTCTATTT
* * *
265287 TTACTGTTTAGTCCTTTAAGTTATGTA--A
1 TTACTTTTTAGTCCTTTAAGTT-TCTATTT
* *
265315 TTA-TTGTATTAGCCCTTCAAGTTTCTATTT
1 TTACTT-T-TTAGTCCTTTAAGTTTCTATTT
*
265345 TTGA-TATTTTAGTCCCTTAA-TTTCCTATTT
1 TT-ACT-TTTTAGTCCTTTAAGTTT-CTATTT
* * *
265375 TTACTATTTAGACCTTTAAGATTCTATTT
1 TTACTTTTTAGTCCTTTAAGTTTCTATTT
* * *
265404 TTACTATTTCAGTCC-CTACA-TTTTTATTT
1 TTACT-TTTTAGTCCTTTA-AGTTTCTATTT
* * * *
265433 TTGTCATTTTAGTCCATTAATTTTCTATTT
1 TT-ACTTTTTAGTCCTTTAAGTTTCTATTT
265463 TT
1 TT
265465 TAGCCTTTAA
Statistics
Matches: 158, Mismatches: 34, Indels: 31
0.71 0.15 0.14
Matches are distributed among these distances:
27 1 0.01
28 7 0.04
29 77 0.49
30 69 0.44
31 3 0.02
32 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.58
Consensus pattern (29 bp):
TTACTTTTTAGTCCTTTAAGTTTCTATTT
Found at i:266084 original size:19 final size:18
Alignment explanation
Indices: 266044--266099 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
266034 GGATTTTCTT
*
266044 TAAATAATTA-ATTTGAA
1 TAAATAATTATATTTTAA
266061 GTAAATTAATTATATTTTAA
1 -TAAA-TAATTATATTTTAA
* *
266081 TAAATGATCATATTTTAA
1 TAAATAATTATATTTTAA
266099 T
1 T
266100 TTTATATTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 17 0.52
19 10 0.30
20 6 0.18
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (18 bp):
TAAATAATTATATTTTAA
Found at i:266869 original size:64 final size:64
Alignment explanation
Indices: 266783--266931 Score: 194
Period size: 64 Copynumber: 2.3 Consensus size: 64
266773 TTTTGAACCG
* * *
266783 AAAATGAATCGATCTGACATTGACCCA-AAC-AGAAAATCAACTGATCCGATATTGATCAGATCT
1 AAAATCAACCGATCTGATATTGA-CCAGAACTA-AAAATCAACTGATCCGATATTGATCAGATCT
266846 A
64 A
* * * *
266847 AAAATCAACTGATCTGATATTGATCAGATCTAAAAATCAATTGATCCGATATTGATCAGATCTA
1 AAAATCAACCGATCTGATATTGACCAGAACTAAAAATCAACTGATCCGATATTGATCAGATCTA
*
266911 AAAATCAACCAATCTGATATT
1 AAAATCAACCGATCTGATATT
266932 AATCTGACCC
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
63 2 0.03
64 71 0.96
65 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (64 bp):
AAAATCAACCGATCTGATATTGACCAGAACTAAAAATCAACTGATCCGATATTGATCAGATCTA
Found at i:266931 original size:32 final size:32
Alignment explanation
Indices: 266815--266919 Score: 192
Period size: 32 Copynumber: 3.3 Consensus size: 32
266805 ACCCAAACAG
266815 AAAATCAACTGATCCGATATTGATCAGATCTA
1 AAAATCAACTGATCCGATATTGATCAGATCTA
*
266847 AAAATCAACTGATCTGATATTGATCAGATCTA
1 AAAATCAACTGATCCGATATTGATCAGATCTA
*
266879 AAAATCAATTGATCCGATATTGATCAGATCTA
1 AAAATCAACTGATCCGATATTGATCAGATCTA
266911 AAAATCAAC
1 AAAATCAAC
266920 CAATCTGATA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (32 bp):
AAAATCAACTGATCCGATATTGATCAGATCTA
Found at i:266950 original size:64 final size:64
Alignment explanation
Indices: 266815--266951 Score: 193
Period size: 64 Copynumber: 2.1 Consensus size: 64
266805 ACCCAAACAG
** * * *
266815 AAAATCAACTGATCCGATATTGATCAGATCTAAAAATCAACTGATCTGATATTGATCAGATCTA
1 AAAATCAACTGATCCGATATTGATCAGATCTAAAAATCAACCAATCTGATATTAATCAGACCCA
* * *
266879 AAAATCAATTGATCCGATATTGATCAGATCTAAAAATCAACCAATCTGATATTAATCTGACCCG
1 AAAATCAACTGATCCGATATTGATCAGATCTAAAAATCAACCAATCTGATATTAATCAGACCCA
*
266943 AATATCAAC
1 AAAATCAAC
266952 CAATCTAACA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (64 bp):
AAAATCAACTGATCCGATATTGATCAGATCTAAAAATCAACCAATCTGATATTAATCAGACCCA
Found at i:266976 original size:32 final size:31
Alignment explanation
Indices: 266912--266984 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 31
266902 TCAGATCTAA
* * *
266912 AAATCAACCAATCTGATATTAATCTGACCCG
1 AAATCAACCAATCTAACATTAATCTGAACCG
*
266943 AATATCAACCAATCTAACATTGA-CTGGAACCG
1 AA-ATCAACCAATCTAACATTAATCT-GAACCG
266975 AAATGCAACC
1 AAAT-CAACC
266985 GATTCAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 6 0.17
32 29 0.83
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.22
Consensus pattern (31 bp):
AAATCAACCAATCTAACATTAATCTGAACCG
Found at i:267343 original size:17 final size:18
Alignment explanation
Indices: 267319--267378 Score: 72
Period size: 17 Copynumber: 3.4 Consensus size: 18
267309 TTTAAAATAA
267319 ATATTTTTTAAAATTTTT
1 ATATTTTTTAAAATTTTT
267337 A-ATTTTTT-AAATTTTT
1 ATATTTTTTAAAATTTTT
* *
267353 ATAGTTTTTAACA-TTTT
1 ATATTTTTTAAAATTTTT
267370 ATCATTTTT
1 AT-ATTTTT
267379 AAATAGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 9 0.25
17 19 0.53
18 8 0.22
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (18 bp):
ATATTTTTTAAAATTTTT
Found at i:269578 original size:22 final size:22
Alignment explanation
Indices: 269541--269595 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
269531 CAATATCAAA
* *
269541 TCAATCG-TTTTTTGAATCTAT
1 TCAATCGATTTTATGAATCGAT
*
269562 TCGATCGATTTTATGAATCGAT
1 TCAATCGATTTTATGAATCGAT
269584 TCAATCGATTTT
1 TCAATCGATTTT
269596 CAAGCTTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (22 bp):
TCAATCGATTTTATGAATCGAT
Found at i:270279 original size:13 final size:13
Alignment explanation
Indices: 270261--270318 Score: 80
Period size: 13 Copynumber: 4.5 Consensus size: 13
270251 GTCATAAATC
270261 TATGACGCGCATT
1 TATGACGCGCATT
* *
270274 TATGACACACATT
1 TATGACGCGCATT
*
270287 TATGACGTGCATT
1 TATGACGCGCATT
*
270300 TATGACGTGCATT
1 TATGACGCGCATT
270313 TATGAC
1 TATGAC
270319 ATTCATTGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:270325 original size:13 final size:13
Alignment explanation
Indices: 270269--270325 Score: 69
Period size: 13 Copynumber: 4.4 Consensus size: 13
270259 TCTATGACGC
*
270269 GCATTTATGACAC
1 GCATTTATGACAT
* *
270282 ACATTTATGACGT
1 GCATTTATGACAT
*
270295 GCATTTATGACGT
1 GCATTTATGACAT
270308 GCATTTATGACAT
1 GCATTTATGACAT
*
270321 TCATT
1 GCATT
270326 GAGCGTCATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.39
Consensus pattern (13 bp):
GCATTTATGACAT
Found at i:270473 original size:2 final size:2
Alignment explanation
Indices: 270462--270519 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
270452 TTTCGTAAAT
270462 TA TA -A TA TA TA TA 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
270503 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
270520 TGTAGATTGA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:275074 original size:63 final size:64
Alignment explanation
Indices: 274930--275087 Score: 180
Period size: 63 Copynumber: 2.5 Consensus size: 64
274920 TGTTATGTGC
* * *
274930 ATCGATGCACATGA-AGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCAGTGT
1 ATCGATGCACA-GATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACCATCAGTGT
** ** *
274994 ATCGATGCACA-AGTAGTGCATCGATGCACCCCCTT-AAATGCAAACATCGAATATGATTTA-TG
1 ATCGATGCACAGA-TAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACCA-TCAGTG
275056 T
64 T
*
275057 ATCGATGCATAGATAGTGCATCGATGCACCC
1 ATCGATGCACAGATAGTGCATCGATGCACCC
275088 ATCAAGGGAT
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
62 1 0.01
63 47 0.58
64 33 0.41
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (64 bp):
ATCGATGCACAGATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATACCATCAGTGT
Found at i:279209 original size:19 final size:19
Alignment explanation
Indices: 279185--279230 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
279175 AATGATGATT
279185 GGGTTTAATGACATGATAG
1 GGGTTTAATGACATGATAG
*
279204 GGGTTTAATGACATGGTAG
1 GGGTTTAATGACATGATAG
*
279223 TGGTTTAA
1 GGGTTTAA
279231 AAGAGAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.33, T:0.35
Consensus pattern (19 bp):
GGGTTTAATGACATGATAG
Found at i:282240 original size:30 final size:30
Alignment explanation
Indices: 282200--282272 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
282190 ATAGGGTTAT
* *
282200 TTATTTTAAAATAATTTATTTTAAAATAAA
1 TTATTATAAAATAAATTATTTTAAAATAAA
282230 TTATTATAAAATAAATTATTTTAAAATAAA
1 TTATTATAAAATAAATTATTTTAAAATAAA
282260 TTATTATAAAATA
1 TTATTATAAAATA
282273 TGGATTGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TTATTATAAAATAAATTATTTTAAAATAAA
Found at i:282286 original size:22 final size:22
Alignment explanation
Indices: 282260--282360 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
282250 TTAAAATAAA
*
282260 TTATTATAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
** * *
282282 TTATTTTAAAATAATTTATTTTAA
1 TTATTTTAAAAT-ATGGA-TTGAT
* * *
282306 TTAATTTATTAGTATGGATTGAT
1 TTATTTTA-AAATATGGATTGAT
*
282329 TTATTTTAAAATATGAATTGAT
1 TTATTTTAAAATATGGATTGAT
282351 TTATTTTAAA
1 TTATTTTAAA
282361 TAATTTATTA
Statistics
Matches: 60, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
22 32 0.53
23 13 0.22
24 13 0.22
25 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:282312 original size:14 final size:15
Alignment explanation
Indices: 282198--282315 Score: 112
Period size: 15 Copynumber: 7.5 Consensus size: 15
282188 TAATAGGGTT
282198 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
282213 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
282228 AATTATTATAAAATA
1 ATTTATTTTAAAATA
*
282243 AATTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
282258 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
282277 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
*
282295 ATTTATTTT-AATTA
1 ATTTATTTTAAAATA
282309 ATTTATT
1 ATTTATT
282316 AGTATGGATT
Statistics
Matches: 89, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
14 11 0.12
15 58 0.65
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:282333 original size:32 final size:31
Alignment explanation
Indices: 282295--282391 Score: 113
Period size: 32 Copynumber: 3.4 Consensus size: 31
282285 TTTTAAAATA
282295 ATTTATTTTAATTAATTTATTAGTATGGATTG
1 ATTTATTTTAA-TAATTTATTAGTATGGATTG
282327 ATTTATTTTAA-AA--TA-T-G-A---ATTG
1 ATTTATTTTAATAATTTATTAGTATGGATTG
282349 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTT-AATAATTTATTAGTATGGATTG
282381 ATTTATTTTAA
1 ATTTATTTTAA
282392 AATATGGATT
Statistics
Matches: 55, Mismatches: 0, Indels: 21
0.72 0.00 0.28
Matches are distributed among these distances:
22 13 0.24
23 2 0.04
24 2 0.04
25 1 0.02
26 3 0.05
27 2 0.04
28 3 0.05
29 1 0.02
30 2 0.04
31 2 0.04
32 24 0.44
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (31 bp):
ATTTATTTTAATAATTTATTAGTATGGATTG
Found at i:282358 original size:54 final size:54
Alignment explanation
Indices: 282295--282647 Score: 336
Period size: 54 Copynumber: 6.4 Consensus size: 54
282285 TTTTAAAATA
*
282295 ATTTATTTTAATTAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
*
282349 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
*
282403 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G---A-ATTG
* * * *
282461 ATTTATTTT-AA-AA--TA-TAG-ATTGATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGA-TTT--AT--TTTA-AAATATGAATTG
* *
282515 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
*
282569 ATTTATTTTAAATAATTTATTAGTATAGATTGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-G---GATTGATTTATTTTAAAATATGAATTG
282627 ATTTATTTTAAATAATTTATT
1 ATTTATTTTAAATAATTTATT
282648 GTTGTAGTTG
Statistics
Matches: 251, Mismatches: 15, Indels: 62
0.77 0.05 0.19
Matches are distributed among these distances:
48 22 0.09
49 4 0.02
50 4 0.02
52 4 0.02
53 1 0.00
54 106 0.42
55 8 0.03
56 2 0.01
57 2 0.01
58 67 0.27
59 11 0.04
60 12 0.05
61 3 0.01
62 2 0.01
63 3 0.01
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
Found at i:282384 original size:18 final size:18
Alignment explanation
Indices: 282363--282410 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
282353 ATTTTAAATA
*
282363 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
282381 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
282403 ATTTATTA
1 ATTTATTA
282411 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:282465 original size:32 final size:31
Alignment explanation
Indices: 282419--282647 Score: 209
Period size: 32 Copynumber: 8.0 Consensus size: 31
282409 TATTGTAGTT
282419 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
282451 GTATAGATTGATTTATTTT--A-AA---A-TA
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
282476 -TA-GATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
282505 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATG-ATTGATTTATTTTAAATAATTTATTA
282537 GTATGAATTGATTTATTTT-AA-AA--TA-T-
1 GTATG-ATTGATTTATTTTAAATAATTTATTA
282563 G---GATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
* *
282591 GTATAGATTGATTGA-TTT--AT--TTTA-AA
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
*
282617 ATATGGATTGATTTATTTTAAATAATTTATT
1 GTAT-GATTGATTTATTTTAAATAATTTATT
282648 GTTGTAGTTG
Statistics
Matches: 164, Mismatches: 7, Indels: 52
0.74 0.03 0.23
Matches are distributed among these distances:
22 27 0.16
23 3 0.02
24 5 0.03
25 4 0.02
26 17 0.10
27 9 0.05
28 4 0.02
29 8 0.05
30 5 0.03
31 10 0.06
32 72 0.44
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (31 bp):
GTATGATTGATTTATTTTAAATAATTTATTA
Found at i:282477 original size:22 final size:22
Alignment explanation
Indices: 282452--282494 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
282442 AATTTATTAG
282452 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
282474 TATAGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
282495 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Found at i:282502 original size:14 final size:14
Alignment explanation
Indices: 282483--282535 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
282473 ATATAGATTG
282483 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
282497 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
282515 ATTTATTTTAAATA
1 ATTTATTTTAAATA
282529 ATTTATT
1 ATTTATT
282536 AGTATGAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:282538 original size:86 final size:85
Alignment explanation
Indices: 282340--282616 Score: 406
Period size: 86 Copynumber: 3.2 Consensus size: 85
282330 TATTTTAAAA
282340 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATGGATTGAT
*
282405 TTA--TT--AT--TGTAGTT-G
65 TTATTTTAAATAATTTA-TTAG
* *
282420 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATGGATTGAT
282485 TTATTTTAAATAATTTATTAG
65 TTATTTTAAATAATTTATTAG
282506 TATGAATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTTAAAATATGGATTGAT
282571 TTATTTTAAATAATTTATTAG
65 TTATTTTAAATAATTTATTAG
282592 TATAGATTGATTGATTTATTTTAAA
1 TAT-GA---ATTGATTTATTTTAAA
282617 ATATGGATTG
Statistics
Matches: 179, Mismatches: 6, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
80 65 0.36
82 2 0.01
84 2 0.01
85 3 0.02
86 89 0.50
87 2 0.01
90 16 0.09
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (85 bp):
TATGAATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAAATATGGATTGATT
TATTTTAAATAATTTATTAG
Found at i:282563 original size:22 final size:22
Alignment explanation
Indices: 282538--282580 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
282528 AATTTATTAG
282538 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
282560 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
282581 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:282698 original size:31 final size:31
Alignment explanation
Indices: 282663--282721 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
282653 AGTTGTATGG
* *
282663 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
282694 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
282722 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:285542 original size:73 final size:73
Alignment explanation
Indices: 285455--285597 Score: 241
Period size: 73 Copynumber: 2.0 Consensus size: 73
285445 GTCATCTGCC
* * *
285455 TGAGATCCTTTACGAATGAAATTATTTTCATCTTGTTTTTGTTAGGGATCATTTACGAAGGGCAA
1 TGAGATCCTTTACGAATGAAAGTATCTCCATCTTGTTTTTGTTAGGGATCATTTACGAAGGGCAA
285520 AATTTGTT
66 AATTTGTT
* *
285528 TGAGATCCTTTACGAATGAAAGTATCTCCATCTTGTTTTTGTTAGGGATTATTTACGGAGGGCAA
1 TGAGATCCTTTACGAATGAAAGTATCTCCATCTTGTTTTTGTTAGGGATCATTTACGAAGGGCAA
285593 AATTT
66 AATTT
285598 TCGACTAGGA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (73 bp):
TGAGATCCTTTACGAATGAAAGTATCTCCATCTTGTTTTTGTTAGGGATCATTTACGAAGGGCAA
AATTTGTT
Found at i:287379 original size:125 final size:124
Alignment explanation
Indices: 287189--287417 Score: 413
Period size: 125 Copynumber: 1.8 Consensus size: 124
287179 GATTGATAAT
* *
287189 ATTTGATTGAAGTTTACATCTTCTAATTTAAGGGGAGGATCATCGGGGTAAAAATTGGAGACATT
1 ATTTGATTGAAGTTTACACCTTCTAATTTAAGGGGAAGATCATCGGGGTAAAAATTGGAGACATT
287254 AATCAAAGATAGTTTACTTCTTTTAATTTGATTTGAGAATAGATAGTTTTCTTCTTTTA
66 AATCAAAGATAGTTTACTTCTTTTAATTTGATTTGAGAATAGATAGTTTTCTTCTTTTA
* *
287313 ATTTGATTGAAGTTTACACCTTCTAATTTTAAGGGGAAGATCATCGGGGTAAAAGTTGGGGACAT
1 ATTTGATTGAAGTTTACACCTTCTAA-TTTAAGGGGAAGATCATCGGGGTAAAAATTGGAGACAT
287378 TAATCAAAGATAGTTTACTTCTTTTAATTTGATTTGAGAA
65 TAATCAAAGATAGTTTACTTCTTTTAATTTGATTTGAGAA
287418 AAGAGCAGTT
Statistics
Matches: 100, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
124 25 0.25
125 75 0.75
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (124 bp):
ATTTGATTGAAGTTTACACCTTCTAATTTAAGGGGAAGATCATCGGGGTAAAAATTGGAGACATT
AATCAAAGATAGTTTACTTCTTTTAATTTGATTTGAGAATAGATAGTTTTCTTCTTTTA
Found at i:287700 original size:110 final size:107
Alignment explanation
Indices: 287550--287764 Score: 371
Period size: 110 Copynumber: 2.0 Consensus size: 107
287540 GAGTGAACAG
287550 TTACTTGTTGACATTTTCAAATTCACCTTCAATGATAATTTTAATGAAATATTAATAGTTATTTT
1 TTACTTGTTGACATTTTCAAATTCACCTTCAATGATAATTTTAATGAAATATTAATAGTTA-TTT
287615 CCTTATCATTAAATCATGTAAATATATTTATATAAAATACTTAGACA
65 CCTTATCATTAAATCATGT-AATATA--T-TATAAAATACTTAGACA
287662 TTACTTGTTGACATTTT-AAATT-ACCTTCAATGATAATTTTAATGAAATATTAATAGTTATTTC
1 TTACTTGTTGACATTTTCAAATTCACCTTCAATGATAATTTTAATGAAATATTAATAGTTATTTC
287725 CTTATCATTAAATCATGTAATATATTATAAAATACTTAGA
66 CTTATCATTAAATCATGTAATATATTATAAAATACTTAGA
287765 GAAAATAAAA
Statistics
Matches: 103, Mismatches: 0, Indels: 7
0.94 0.00 0.06
Matches are distributed among these distances:
105 15 0.15
106 1 0.01
108 6 0.06
109 22 0.21
110 37 0.36
111 5 0.05
112 17 0.17
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.44
Consensus pattern (107 bp):
TTACTTGTTGACATTTTCAAATTCACCTTCAATGATAATTTTAATGAAATATTAATAGTTATTTC
CTTATCATTAAATCATGTAATATATTATAAAATACTTAGACA
Found at i:295200 original size:3 final size:3
Alignment explanation
Indices: 295192--295217 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
295182 ATTATAAACT
295192 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
295218 TACAAAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:295411 original size:2 final size:2
Alignment explanation
Indices: 295404--295428 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
295394 TAATTGTATT
295404 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 T
295429 TGAATTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:305587 original size:2 final size:2
Alignment explanation
Indices: 305580--305627 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
305570 GAATATAAAG
* *
305580 AT AT AT AT AT AT AT AT AA AG AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
305622 AT AT AT
1 AT AT AT
305628 GATTAGATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:305597 original size:20 final size:20
Alignment explanation
Indices: 305572--305627 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
305562 TATGAAAAGA
305572 ATATAAAGATATATATATAT
1 ATATAAAGATATATATATAT
305592 ATATAAAGATATATATATAT
1 ATATAAAGATATATATATAT
* *
305612 ATATATATATATATAT
1 ATATAAAGATATATAT
305628 GATTAGATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (20 bp):
ATATAAAGATATATATATAT
Found at i:307857 original size:17 final size:17
Alignment explanation
Indices: 307835--307873 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
307825 TCGATAGTTG
*
307835 GGTACCCGTAAAATCCT
1 GGTACCCATAAAATCCT
307852 GGTACCCATAAAATCCT
1 GGTACCCATAAAATCCT
307869 GGTAC
1 GGTAC
307874 TCACGTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (17 bp):
GGTACCCATAAAATCCT
Found at i:308256 original size:2 final size:2
Alignment explanation
Indices: 308251--308281 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
308241 TAATTTAAAC
308251 TA TA 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 TA TA T
308282 TAAAACTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:308406 original size:12 final size:12
Alignment explanation
Indices: 308389--308432 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
308379 TAAAAATATA
*
308389 TTATTTATTTAT
1 TTATTTTTTTAT
308401 TTATTTTTATTA-
1 TTATTTTT-TTAT
*
308413 TTATTTTTTTTT
1 TTATTTTTTTAT
308425 TTATTTTT
1 TTATTTTT
308433 GCAGGTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 2 0.07
12 23 0.82
13 3 0.11
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTATTTTTTTAT
Found at i:308414 original size:24 final size:24
Alignment explanation
Indices: 308387--308432 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
308377 TTTAAAAATA
308387 TATTATTTATTTATTTATTTTTAT
1 TATTATTTATTTATTTATTTTTAT
* *
308411 TATTATTTTTTTTTTTATTTTT
1 TATTATTTATTTATTTATTTTT
308433 GCAGGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (24 bp):
TATTATTTATTTATTTATTTTTAT
Found at i:325427 original size:110 final size:106
Alignment explanation
Indices: 325238--325440 Score: 316
Period size: 110 Copynumber: 1.9 Consensus size: 106
325228 GATGGTGGTT
*
325238 GCTCAACTTCACAGCAAAGGGGCGACTGCCAACAAATAACTTTTCAGTTTCATTCAGAGTCAATT
1 GCTCAACTTCACAGCAAAGGGGCGACTGCCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
* *
325303 TCAACTTCATAGCGAATGATATTGGACTCGAGACAACACAA
66 TCAACTTCACAGCGAATGATATTAGACTCGAGACAACACAA
* * *
325344 GCTCAACTTCACAGCGAAGGGGTAACTGTCTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCAAAGGGG---C-GACTGCCAACAAACAACTTTTCAGTTTCATTCAGAGTC
325409 AATTTCAACTTCACAGCGAATGATATTAGACT
62 AATTTCAACTTCACAGCGAATGATATTAGACT
325441 AGAAACGACA
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
106 21 0.24
109 1 0.01
110 65 0.75
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (106 bp):
GCTCAACTTCACAGCAAAGGGGCGACTGCCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
TCAACTTCACAGCGAATGATATTAGACTCGAGACAACACAA
Found at i:326012 original size:253 final size:252
Alignment explanation
Indices: 325648--326121 Score: 678
Period size: 253 Copynumber: 1.9 Consensus size: 252
325638 GGGGCTTCTT
* * *
325648 AGTTTCAGAACCAATTTCAACTTCACGGCGAAGAATATTGGACTCGAAACAATACAACTTACTTG
1 AGTTTCAGAACCAATTTCAACTTCACAGCAAAGAATATTGGACTCGAAACAACACAACTTACTTG
* * ** * *
325713 GATTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAACTTCATGACGAAGGGGCCACCCG
66 GATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGACCACCCA
* * * *
325778 CGGTTTCAACTTCACAATGAAGGGAATCGTGCACACAAGCATCATACATCTCTAGATTGGATTTC
131 CGGTTTCAACTTCACAACGAAGGAAATCGTGCACACAAGCAACATACATATCTAGATTGGATTTC
325843 AACTTCACGACGAAGGATATCCAATTCAAAGAAGGAGTGTATGTCAACAAACTTTTC
196 AACTTCACGACGAAGGATATCCAATTCAAAGAAGGAGTGTATGTCAACAAACTTTTC
** * * * * *
325900 AGTTTCAGAGTCAATTTCAACTTCATAGCAAAGGATATTGGCCTCGGAACAACGCAACTTACATT
1 AGTTTCAGAACCAATTTCAACTTCACAGCAAAGAATATTGGACTCGAAACAACACAACTTAC-TT
* * * *
325965 GGATTTCAACTTCACGATGAAAGATATCCAATTCAAGGCTTAACTTCACAATGAAGGGACCATCC
65 GGATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGACCACCC
* * * *
326030 ACGGTTTCAACTTCACGACGAAGGAAATCGTGCTCACAAGCAACATTCATATTTAGATTGGATTT
130 ACGGTTTCAACTTCACAACGAAGGAAATCGTGCACACAAGCAACATACATATCTAGATTGGATTT
*
326095 CAACTTCACGACGAATGATATCCAATT
195 CAACTTCACGACGAAGGATATCCAATT
326122 TAAGGCTCAA
Statistics
Matches: 192, Mismatches: 29, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
252 52 0.27
253 140 0.73
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (252 bp):
AGTTTCAGAACCAATTTCAACTTCACAGCAAAGAATATTGGACTCGAAACAACACAACTTACTTG
GATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGACCACCCA
CGGTTTCAACTTCACAACGAAGGAAATCGTGCACACAAGCAACATACATATCTAGATTGGATTTC
AACTTCACGACGAAGGATATCCAATTCAAAGAAGGAGTGTATGTCAACAAACTTTTC
Found at i:326121 original size:124 final size:124
Alignment explanation
Indices: 325962--326203 Score: 358
Period size: 124 Copynumber: 2.0 Consensus size: 124
325952 CGCAACTTAC
* * *
325962 ATTGGATTTCAACTTCACGATGAAAGATATCCAATTCAAGGCTTAACTTCACAATGAAGGGACCA
1 ATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGACCA
* * *
326027 TCCACGGTTTCAACTTCACGACGAAGGAAATCGTGCTCACAAGCAACATTCATATTTAG
66 TCCACGGTTTCAACTTCACGACAAAGGAAATCGTACCCACAAGCAACATTCATATTTAG
* * *
326086 ATTGGATTTCAACTTCACGACGAATGATATCCAATTTAAGGCTCAACTTCACAACGAAGGGGCCA
1 ATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGACCA
** * * *
326151 TCCGTGGTTTTAACTTCACGACAAAGGGAATCGTACCCACCAGCAACATTCAT
66 TCCACGGTTTCAACTTCACGACAAAGGAAATCGTACCCACAAGCAACATTCAT
326204 CATCAGGAAC
Statistics
Matches: 104, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
124 104 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (124 bp):
ATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGACCA
TCCACGGTTTCAACTTCACGACAAAGGAAATCGTACCCACAAGCAACATTCATATTTAG
Found at i:326305 original size:37 final size:35
Alignment explanation
Indices: 326264--326386 Score: 108
Period size: 36 Copynumber: 3.4 Consensus size: 35
326254 ACAAGGGGTC
*
326264 GTCTCACTTGAGACTAATTTACTCAAAACAAAGTTTT
1 GTCTCACTTGAGACTAATTT-CTCGAAACAAA-TTTT
* *
326301 GTCTCTCTTGAGAC-AGTTTCTCTTGAAACAAATTTT
1 GTCTCACTTGAGACTAATTTCTC--GAAACAAATTTT
* *
326337 GTCT-ATCTTGAGA-TATTTTCCCTTGAAACAAATTTT
1 GTCTCA-CTTGAGACTAATTT--CTCGAAACAAATTTT
*
326373 GTCTCTCTTGAGAC
1 GTCTCACTTGAGAC
326387 AGTTTGCCTT
Statistics
Matches: 71, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
35 3 0.04
36 46 0.65
37 20 0.28
38 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (35 bp):
GTCTCACTTGAGACTAATTTCTCGAAACAAATTTT
Found at i:326346 original size:36 final size:35
Alignment explanation
Indices: 326289--326400 Score: 161
Period size: 36 Copynumber: 3.1 Consensus size: 35
326279 AATTTACTCA
326289 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTC-CTTG
* * *
326326 AAACAAATTTTGTCTATCTTGAGATATTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTT-CCTTG
326362 AAACAAATTTTGTCTCTCTTGAGACAGTTTGCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTT-CCTTG
326398 AAA
1 AAA
326401 TAAAATCTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
36 59 0.88
37 8 0.12
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (35 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCTTG
Found at i:326545 original size:73 final size:73
Alignment explanation
Indices: 326423--326579 Score: 228
Period size: 73 Copynumber: 2.2 Consensus size: 73
326413 ATATGTCTTC
* * *
326423 CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGA
1 CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCTTTGAAACAAAGTTTTGTCTCTCTTGAGA
326488 CAG-TTTCT
66 C-GTTTTCT
* *
326496 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTT-AAACAAAGTTTTGTCTCTCTTGAG
1 CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTT-CCTTTGAAACAAAGTTTTGTCTCTCTTGAG
*
326560 ACGTTTTTT
65 ACGTTTTCT
326569 CTTGAAACAAA
1 CTTGAAACAAA
326580 AAACCTTTGA
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
72 1 0.01
73 71 0.93
74 4 0.05
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (73 bp):
CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCTTTGAAACAAAGTTTTGTCTCTCTTGAGA
CGTTTTCT
Found at i:326579 original size:37 final size:36
Alignment explanation
Indices: 326423--326579 Score: 208
Period size: 37 Copynumber: 4.3 Consensus size: 36
326413 ATATGTCTTC
* *
326423 CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCT
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
* * *
326459 TTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCT
1 CTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCT
*
326496 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
* *
326532 CTTTAAACAAAGTTTTGTCTCTCTTGAGAC-GTTTTTT
1 CTTGAAACAAA-TTTTGTCTCTCTTGAGACAG-TTTCT
326569 CTTGAAACAAA
1 CTTGAAACAAA
326580 AAACCTTTGA
Statistics
Matches: 105, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
36 43 0.41
37 62 0.59
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
Found at i:326769 original size:84 final size:83
Alignment explanation
Indices: 326611--326796 Score: 219
Period size: 84 Copynumber: 2.2 Consensus size: 83
326601 TTGAAACACC
* * * * * *
326611 AAACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGA
1 AAACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCATTTGCAGCATAACTCAAAGCGAGA
*
326676 ATGACTATCTGCCACCAAA
66 AGGACTATCTGCCA-CAAA
* * * *
326695 AGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCATTTGCAGCATAGCTTAAATCGAGA
1 AAACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCATTTGCAGCATAACTCAAAGCGAGA
**
326760 AGGGTTATCTGCCACAAA
66 AGGACTATCTGCCACAAA
* *
326778 AAAACTGACGAGTTCGATT
1 AAACCT-TCGAGTTCGATT
326797 TCATTCAGCT
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
83 8 0.09
84 77 0.91
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (83 bp):
AAACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCATTTGCAGCATAACTCAAAGCGAGA
AGGACTATCTGCCACAAA
Found at i:330830 original size:25 final size:25
Alignment explanation
Indices: 330800--330853 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
330790 GATTTGTGAT
330800 TTGTTAGTGATTGTTTTGAATTAAG
1 TTGTTAGTGATTGTTTTGAATTAAG
330825 TTGTTAGTGATTGTTTTGAATTAAG
1 TTGTTAGTGATTGTTTTGAATTAAG
330850 TTGT
1 TTGT
330854 CAAAACGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (25 bp):
TTGTTAGTGATTGTTTTGAATTAAG
Found at i:342995 original size:2 final size:2
Alignment explanation
Indices: 342984--343014 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
342974 AACAGGGGGG
*
342984 GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
343015 TCTGGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
GA
Found at i:343457 original size:30 final size:30
Alignment explanation
Indices: 343414--343487 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
343404 ACCATTAAAG
* * *
343414 AACCGGTA-AAACCGGTTGGGAACCGGAAA
1 AACCGGTATGAACCGGCTAGGAACCGGAAA
* *
343443 AATCGGTATGAACCGGCTAGGAACCGGCAA
1 AACCGGTATGAACCGGCTAGGAACCGGAAA
343473 AACCGGTATGAACCG
1 AACCGGTATGAACCG
343488 CCGGTTCTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
29 7 0.18
30 31 0.82
ACGTcount: A:0.35, C:0.23, G:0.30, T:0.12
Consensus pattern (30 bp):
AACCGGTATGAACCGGCTAGGAACCGGAAA
Found at i:344380 original size:24 final size:24
Alignment explanation
Indices: 344331--344380 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
344321 TCATTAACTT
*
344331 TTTAAAAATTAAAAATTTTTAAAA
1 TTTAAAAATTAAAAATTTTAAAAA
* *
344355 TTTAAACA-TAAATATTTTAAATAA
1 TTTAAAAATTAAAAATTTTAAA-AA
344379 TT
1 TT
344381 AAATTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TTTAAAAATTAAAAATTTTAAAAA
Found at i:344479 original size:18 final size:18
Alignment explanation
Indices: 344447--344481 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
344437 TTATATTTTT
**
344447 AAAAAATAATCAAAAATC
1 AAAAAATAAAAAAAAATC
344465 AAAAAATAAAAAAAAAT
1 AAAAAATAAAAAAAAAT
344482 GTCAATAAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (18 bp):
AAAAAATAAAAAAAAATC
Found at i:344988 original size:16 final size:17
Alignment explanation
Indices: 344967--344998 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
344957 ATATATAATT
344967 TTAAAA-AAATTAAAAA
1 TTAAAATAAATTAAAAA
344983 TTAAAATAAATTAAAA
1 TTAAAATAAATTAAAA
344999 TTTATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
TTAAAATAAATTAAAAA
Found at i:349161 original size:28 final size:28
Alignment explanation
Indices: 349111--349200 Score: 128
Period size: 28 Copynumber: 3.2 Consensus size: 28
349101 ATTTGTCCCG
*
349111 TAGAAC-CACTATGTCCCGAAGGACCACA
1 TAGAACACA-TATGTCCCGTAGGACCACA
* * *
349139 TATAACACATATGTCCTGTAGGACCACG
1 TAGAACACATATGTCCCGTAGGACCACA
349167 TAGAACACATATGTCCCGTAGGACCACA
1 TAGAACACATATGTCCCGTAGGACCACA
349195 TAGAAC
1 TAGAAC
349201 CCTCGATTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
28 52 0.96
29 2 0.04
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.19
Consensus pattern (28 bp):
TAGAACACATATGTCCCGTAGGACCACA
Found at i:349380 original size:22 final size:21
Alignment explanation
Indices: 349355--349396 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
349345 TCACTTGGAG
*
349355 TCTCATAACTTCTTATCACATA
1 TCTCATAAC-TCCTATCACATA
*
349377 TCTCATATCTCCTATCACAT
1 TCTCATAACTCCTATCACAT
349397 GTCACATTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (21 bp):
TCTCATAACTCCTATCACATA
Found at i:350366 original size:54 final size:55
Alignment explanation
Indices: 350282--350425 Score: 236
Period size: 54 Copynumber: 2.6 Consensus size: 55
350272 TCATAATTGG
* * *
350282 GGGTATAGATACACTCCTCAGTGTATCGATACACAAATTGCATTCGATGTT-TGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGGCATTCGATGTTCTGA
*
350336 GGGTATCGATACACTCCTTAGTGTACCGATACACAAATGGCATTCGATGTTCTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGGCATTCGATGTTCTGA
*
350391 GTGTATCGATACACTCCTCAGTGTACCGATACACA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACA
350426 TTCATACAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
54 47 0.57
55 36 0.43
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (55 bp):
GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGGCATTCGATGTTCTGA
Found at i:353537 original size:28 final size:28
Alignment explanation
Indices: 353501--353581 Score: 126
Period size: 28 Copynumber: 2.9 Consensus size: 28
353491 GTAGGACCAC
* *
353501 TATGTCCCGAAGGACCACATATAACACT
1 TATGTCCCGTAGGACCACATATAACACA
* *
353529 TATGTCCCGTAGGATCACATAGAACACA
1 TATGTCCCGTAGGACCACATATAACACA
353557 TATGTCCCGTAGGACCACATATAAC
1 TATGTCCCGTAGGACCACATATAAC
353582 TATCGACTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (28 bp):
TATGTCCCGTAGGACCACATATAACACA
Found at i:353761 original size:7 final size:7
Alignment explanation
Indices: 353749--353780 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
353739 CATAACTTCT
353749 TATCTCC
1 TATCTCC
353756 TATCTCC
1 TATCTCC
353763 TATCTCC
1 TATCTCC
353770 TATCTCC
1 TATCTCC
353777 TATC
1 TATC
353781 ATATGTCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.16, C:0.41, G:0.00, T:0.44
Consensus pattern (7 bp):
TATCTCC
Found at i:354174 original size:12 final size:12
Alignment explanation
Indices: 354157--354181 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
354147 TCATATATTT
354157 TATTTTATTTTA
1 TATTTTATTTTA
354169 TATTTTATTTTA
1 TATTTTATTTTA
354181 T
1 T
354182 CCATTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTATTTTA
Found at i:354793 original size:55 final size:54
Alignment explanation
Indices: 354683--354799 Score: 171
Period size: 55 Copynumber: 2.1 Consensus size: 54
354673 ATTGGGGTAT
* *
354683 CGATACACAAATTACATTCGATGTTTGAGGGTATCAATACACTCCTCAATATAC
1 CGATACACAAATGACATTCAATGTTTGAGGGTATCAATACACTCCTCAATATAC
* * * *
354737 CGATACACAAATGACATTCAATGTTCTGAGTGTATCGATACACTCTTCAATGTAC
1 CGATACACAAATGACATTCAATGTT-TGAGGGTATCAATACACTCCTCAATATAC
354792 CGATACAC
1 CGATACAC
354800 TCCTCAATGT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
54 23 0.41
55 33 0.59
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (54 bp):
CGATACACAAATGACATTCAATGTTTGAGGGTATCAATACACTCCTCAATATAC
Found at i:354795 original size:20 final size:20
Alignment explanation
Indices: 354767--354839 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
354757 ATGTTCTGAG
* *
354767 TGTATCGATACACTCTTCAA
1 TGTACCGATACACTCCTCAA
354787 TGTACCGATACACTCCTCAA
1 TGTACCGATACACTCCTCAA
354807 TGTACCGATACACTCCTCAA
1 TGTACCGATACACTCCTCAA
354827 TGTACCGATACAC
1 TGTACCGATACAC
354840 ATTCTTACAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.30, C:0.32, G:0.11, T:0.27
Consensus pattern (20 bp):
TGTACCGATACACTCCTCAA
Found at i:357985 original size:22 final size:23
Alignment explanation
Indices: 357950--357996 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
357940 TTAATAAACT
* *
357950 ATTCAAATTCATTTAAATTTAAA
1 ATTCAAATTAATTTAAATCTAAA
357973 ATTCAAA-TAATTTAAATCTAAA
1 ATTCAAATTAATTTAAATCTAAA
357995 AT
1 AT
357997 GATTTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTCAAATTAATTTAAATCTAAA
Found at i:357996 original size:16 final size:16
Alignment explanation
Indices: 357977--358025 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
357967 TTTAAAATTC
357977 AAATAATTTAAATCTA
1 AAATAATTTAAATCTA
* * *
357993 AAATGATTTTAATATA
1 AAATAATTTAAATCTA
358009 AAATAA-TTAAATCTA
1 AAATAATTTAAATCTA
358024 AA
1 AA
358026 TAAATTAAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (16 bp):
AAATAATTTAAATCTA
Found at i:358414 original size:3 final size:3
Alignment explanation
Indices: 358406--358433 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
358396 TTTTATGGGT
358406 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
358434 AACCCTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:368089 original size:33 final size:33
Alignment explanation
Indices: 368048--368132 Score: 134
Period size: 33 Copynumber: 2.6 Consensus size: 33
368038 TACTCCTACC
*
368048 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
368081 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
* * *
368114 CTCGTTCGGATGGCCTCGG
1 CTCGCTCGGTTGCCCTCGG
368133 TCGGATGGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.08, C:0.38, G:0.28, T:0.26
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:368104 original size:10 final size:10
Alignment explanation
Indices: 368052--368108 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
368042 CCTACCCTCG
*
368052 CTCGGTTGCC
1 CTCGGATGCC
*
368062 CTCGGATTCC
1 CTCGGATGCC
*
368072 CTCGCATAGCTC
1 CTCGGAT-GC-C
*
368084 GCTCGGTTGCC
1 -CTCGGATGCC
368095 CTCGGATGCC
1 CTCGGATGCC
368105 CTCG
1 CTCG
368109 CATAGCTCGT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
10 27 0.73
11 2 0.05
12 3 0.08
13 5 0.14
ACGTcount: A:0.07, C:0.40, G:0.26, T:0.26
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:368136 original size:14 final size:14
Alignment explanation
Indices: 368114--368146 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
368104 CCTCGCATAG
*
368114 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
368128 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
368142 CTCGG
1 CTCGG
368147 ATGCCCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:368623 original size:32 final size:32
Alignment explanation
Indices: 368587--368647 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
368577 ACTACACAAC
368587 ATTCATAACAAGATCTGAGACACACACGAAGT
1 ATTCATAACAAGATCTGAGACACACACGAAGT
* *
368619 ATTCATAACAGGATCTTAGACACACACGA
1 ATTCATAACAAGATCTGAGACACACACGA
368648 GCAAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.20
Consensus pattern (32 bp):
ATTCATAACAAGATCTGAGACACACACGAAGT
Found at i:369168 original size:103 final size:103
Alignment explanation
Indices: 368983--369186 Score: 329
Period size: 103 Copynumber: 2.0 Consensus size: 103
368973 TGTAACAAAC
* * * *
368983 GGTTTACGTTCTCCGATGAGGATACTGAAAGAGTTACTCGTATATATGGAGTGATTGAAGTGAGT
1 GGTTTACGTCCTCCGATGAGGATAATGAAAGAATTACTCATATATATGGAGTGATTGAAGTGAGT
*
369048 AGTTATCATTTGACAATTTTATTATTCTACTATTCTAT
66 AGTTATCATTTGACAATTTTACTATTCTACTATTCTAT
* *
369086 GGTTTACGTCCTCGGATGAGGATAATGGAAGAATTACTCATATATATGGAGTGATTGAAGTGAGT
1 GGTTTACGTCCTCCGATGAGGATAATGAAAGAATTACTCATATATATGGAGTGATTGAAGTGAGT
369151 AGTTATCATTTCG-CAATTTTACTATTCTACTATTCT
66 AGTTATCATTT-GACAATTTTACTATTCTACTATTCT
369187 TATAAATGGG
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
103 92 0.99
104 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (103 bp):
GGTTTACGTCCTCCGATGAGGATAATGAAAGAATTACTCATATATATGGAGTGATTGAAGTGAGT
AGTTATCATTTGACAATTTTACTATTCTACTATTCTAT
Found at i:372346 original size:29 final size:30
Alignment explanation
Indices: 372303--372360 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
372293 TCTGTTTTTT
* * *
372303 TAATTTAGTGTCTAACA-TTTATTTTATTC
1 TAATTTAATGCCTAACATTTTATTCTATTC
*
372332 TAATTTAATGCCTAATATTTTATTCTATT
1 TAATTTAATGCCTAACATTTTATTCTATT
372361 ACTCAAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.55
Consensus pattern (30 bp):
TAATTTAATGCCTAACATTTTATTCTATTC
Found at i:373323 original size:84 final size:84
Alignment explanation
Indices: 373198--373353 Score: 213
Period size: 84 Copynumber: 1.9 Consensus size: 84
373188 AATAGGTATT
* * * * * *
373198 GGAACCAATTCGAGTTCAACTTCGAATTCGACTAACCATAAAACAGTGGTGGATAACGAGGATAA
1 GGAAACAATTCGAGTTCAACTTCAAATTCCACTAACCATAAAACAGTGGAGGATAAAGAGGAAAA
373263 GAAAAATAATGCAAGTACC
66 GAAAAATAATGCAAGTACC
* ** * *
373282 GGAAACAATTCGAGTTCAACTTCAAATTCCACTGATGATAAAACATTGGAGGGTAAAGAGGAAAA
1 GGAAACAATTCGAGTTCAACTTCAAATTCCACTAACCATAAAACAGTGGAGGATAAAGAGGAAAA
373347 GAAAAAT
66 GAAAAAT
373354 GATACAGATA
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 61 1.00
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (84 bp):
GGAAACAATTCGAGTTCAACTTCAAATTCCACTAACCATAAAACAGTGGAGGATAAAGAGGAAAA
GAAAAATAATGCAAGTACC
Found at i:389438 original size:30 final size:27
Alignment explanation
Indices: 389402--389462 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 27
389392 AACCGTTGTG
*
389402 AATTTATCTACTGTTGGATCTCTCTTATTA
1 AATTTATCT-CTGTTGCA--TCTCTTATTA
*
389432 AATTTATCTCTTTTGCATCTCTTATTA
1 AATTTATCTCTGTTGCATCTCTTATTA
389459 AATT
1 AATT
389463 AATAATAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 14 0.48
29 6 0.21
30 9 0.31
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (27 bp):
AATTTATCTCTGTTGCATCTCTTATTA
Found at i:399476 original size:40 final size:40
Alignment explanation
Indices: 399374--399464 Score: 182
Period size: 40 Copynumber: 2.3 Consensus size: 40
399364 TCGTTTATTT
399374 ATTAAATGAACGAACATGAACAAGATTTTGCGTTCGTTTA
1 ATTAAATGAACGAACATGAACAAGATTTTGCGTTCGTTTA
399414 ATTAAATGAACGAACATGAACAAGATTTTGCGTTCGTTTA
1 ATTAAATGAACGAACATGAACAAGATTTTGCGTTCGTTTA
399454 ATTAAATGAAC
1 ATTAAATGAAC
399465 AAACGTAAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (40 bp):
ATTAAATGAACGAACATGAACAAGATTTTGCGTTCGTTTA
Found at i:403851 original size:23 final size:24
Alignment explanation
Indices: 403819--403870 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
403809 TTGATAAATT
*
403819 ATTT-TTTCTTTAAATTTTTA-AA
1 ATTTATTTCTTAAAATTTTTATAA
*
403841 GTTTATTTCTTAAAATTTTTATAA
1 ATTTATTTCTTAAAATTTTTATAA
403865 ATTTAT
1 ATTTAT
403871 CTCTAATATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.12
23 15 0.60
24 7 0.28
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (24 bp):
ATTTATTTCTTAAAATTTTTATAA
Found at i:405132 original size:19 final size:19
Alignment explanation
Indices: 405108--405147 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
405098 CGTCAGGTAG
405108 CCTTGAAAATTGACTATGA
1 CCTTGAAAATTGACTATGA
405127 CCTTGAAAATTGACTATGA
1 CCTTGAAAATTGACTATGA
405146 CC
1 CC
405148 AACAATGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (19 bp):
CCTTGAAAATTGACTATGA
Found at i:409914 original size:21 final size:20
Alignment explanation
Indices: 409828--409985 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
409818 AAATGACCAA
**
409828 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
409847 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** * *
409867 CAGAATCGCAAATCAATTTC
1 CAAAATCGCAACGCGATTTT
409887 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
409908 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
409929 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
409949 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
409970 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
409986 ACACATAAAT
Statistics
Matches: 102, Mismatches: 33, Indels: 7
0.72 0.23 0.05
Matches are distributed among these distances:
19 15 0.15
20 42 0.41
21 45 0.44
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:410014 original size:20 final size:20
Alignment explanation
Indices: 409953--410181 Score: 212
Period size: 20 Copynumber: 11.4 Consensus size: 20
409943 GATTTTCCAG
* ** *
409953 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
409973 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
409993 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
410013 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
410033 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
410053 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
410073 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
410093 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * **
410113 AATCGCAACGAGAATCTATA
1 AATCGCAACGCGTATCCGTA
* *
410133 AATCGCAATG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
410153 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
410173 AATCACAAC
1 AATCGCAAC
410182 ACTGAAATTT
Statistics
Matches: 171, Mismatches: 32, Indels: 12
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 167 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:410889 original size:24 final size:24
Alignment explanation
Indices: 410850--410896 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
410840 AAATTTGGTC
410850 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
410874 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
410897 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:411088 original size:12 final size:12
Alignment explanation
Indices: 411071--411095 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
411061 ATATAATCCT
411071 GAAGAAGAAAAA
1 GAAGAAGAAAAA
411083 GAAGAAGAAAAA
1 GAAGAAGAAAAA
411095 G
1 G
411096 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:413487 original size:72 final size:71
Alignment explanation
Indices: 413394--413632 Score: 296
Period size: 72 Copynumber: 3.4 Consensus size: 71
413384 GCAACGAGAG
*
413394 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
413459 AAATGAA
66 AAA-GAA
*
413466 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
413530 GAAAAGAA
65 G-AAAGAA
* * * *
413538 AATCGCAACGAGAGAATCG-CAATGCGGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAA-
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAAT
*
413599 -CG--AGAG
63 GCGAAAGAA
413605 AATCGCAATGCGGAAATGAAAATCGCAA
1 AATCGCAATGC-GAAATGAAAATCGCAA
413633 TGCGAAATGA
Statistics
Matches: 147, Mismatches: 12, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
66 5 0.03
67 18 0.12
68 2 0.01
70 2 0.01
72 92 0.63
73 23 0.16
74 5 0.03
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAAGAA
Found at i:413515 original size:53 final size:53
Alignment explanation
Indices: 413380--413650 Score: 412
Period size: 53 Copynumber: 5.1 Consensus size: 53
413370 CGGAAATTAC
*
413380 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
*
413427 AATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
*
413485 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAAAGAA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
413538 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
413591 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
413644 AATCGCA
1 AATCGCA
413651 TTGCGATTCT
Statistics
Matches: 207, Mismatches: 5, Indels: 18
0.90 0.02 0.08
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 14 0.07
53 167 0.81
55 2 0.01
56 1 0.00
58 13 0.06
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (53 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
Found at i:413656 original size:72 final size:70
Alignment explanation
Indices: 413361--413655 Score: 277
Period size: 72 Copynumber: 4.2 Consensus size: 70
413351 GCATTTGACT
** * * * *
413361 ATCGCAACACGGAAATTACAATCGCAA-CG-AGAGAATCGCAATGCGAAATGAAAATCCCAAC-A
1 ATCGCAATGCGGAAATGAAAATCGCAAGCGAAGAAAATCGCAATGCGAAATGAAAATCGCAACGA
413423 TGAAA
66 TGAAA
413428 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA-GCG-AA-GAAAATCGCAATGCGAAATGAAAATCGCAA
*
413493 CGA-GAGA
63 CGATGAAA
* * *
413500 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAAAGAAAATCGCAACGAGAGAATCG-CAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAA-GCG--AAGAAAATCGCAATGCGA-AAT-GAAAAT-CG
*
413564 GAA--ATGAAA
60 CAACGATGAAA
*
413573 ATCGCAATGC-GAAATGAAAATCGCAA-CG-AGAGAATCGCAATGCGGAAATGAAAATCGCAATG
1 ATCGCAATGCGGAAATGAAAATCGCAAGCGAAGAAAATCGCAATGC-GAAATGAAAATCGCAA--
413635 CGAAATGAAA
63 CG--ATGAAA
*
413645 ATCGCATTGCG
1 ATCGCAATGCG
413656 ATTCTCTCGT
Statistics
Matches: 190, Mismatches: 18, Indels: 34
0.79 0.07 0.14
Matches are distributed among these distances:
66 5 0.03
67 41 0.22
68 2 0.01
69 2 0.01
70 2 0.01
71 1 0.01
72 109 0.57
73 23 0.12
74 5 0.03
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (70 bp):
ATCGCAATGCGGAAATGAAAATCGCAAGCGAAGAAAATCGCAATGCGAAATGAAAATCGCAACGA
TGAAA
Found at i:413690 original size:53 final size:52
Alignment explanation
Indices: 413627--413742 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
413617 GAAATGAAAA
*
413627 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
413679 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
413732 TCGCATTGCGA
1 TCGCATTGCGA
413743 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:413757 original size:53 final size:53
Alignment explanation
Indices: 413646--413763 Score: 220
Period size: 53 Copynumber: 2.2 Consensus size: 53
413636 GAAATGAAAA
413646 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
413699 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
413751 TCCGCATTGCGAT
1 T-CGCATTGCGAT
413764 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 19 0.30
53 45 0.70
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:413771 original size:20 final size:19
Alignment explanation
Indices: 413665--413763 Score: 136
Period size: 20 Copynumber: 5.4 Consensus size: 19
413655 GATTCTCTCG
413665 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
413685 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
413704 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
413718 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
413737 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
413757 TTGCGAT
1 TTGCGAT
413764 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 25 0.35
20 26 0.37
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:413889 original size:14 final size:14
Alignment explanation
Indices: 413870--413906 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
413860 CATCAATTAC
413870 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
413884 ACAAATCATCTTTT
1 ACAAATCAACTTTT
413898 ACAAATCAA
1 ACAAATCAA
413907 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Done.