Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011839.1 Kokia drynarioides strain JFW-HI SEQ_126835, 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: 265575
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 324 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--40 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1 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
41 GTAAAAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5527 original size:29 final size:28
Alignment explanation
Indices: 5477--5541 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
5467 AGCCTATATA
*
5477 TTTAT-ATTTTAAAGGATTAAATCAAAAT
1 TTTATCATTTTAAAGGATAAAAT-AAAAT
**
5505 TTTATCATTTTGAAA-GATAAAATGTAAT
1 TTTATCATTTT-AAAGGATAAAATAAAAT
5533 TTTATCATT
1 TTTATCATT
5542 ATCAATTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 17 0.53
29 12 0.38
30 3 0.09
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.46
Consensus pattern (28 bp):
TTTATCATTTTAAAGGATAAAATAAAAT
Found at i:9249 original size:17 final size:17
Alignment explanation
Indices: 9227--9265 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
9217 AGGTGGAGAA
* *
9227 CTTGTTCATTGAGAGTT
1 CTTGTTCATAGAGAATT
*
9244 CTTGTTCGTAGAGAATT
1 CTTGTTCATAGAGAATT
9261 CTTGT
1 CTTGT
9266 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCATAGAGAATT
Found at i:12675 original size:28 final size:28
Alignment explanation
Indices: 12643--12699 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
12633 ACCAACAAAA
12643 TAGGTAAATTTCCCAAAAGGACCAGACT
1 TAGGTAAATTTCCCAAAAGGACCAGACT
12671 TAGGTAAATTTCCCAAAAGGACCAGACT
1 TAGGTAAATTTCCCAAAAGGACCAGACT
12699 T
1 T
12700 GACTAGGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.23
Consensus pattern (28 bp):
TAGGTAAATTTCCCAAAAGGACCAGACT
Found at i:12867 original size:30 final size:29
Alignment explanation
Indices: 12793--12868 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 29
12783 ATTAAAGCTC
* * *
12793 AATTAAGTCCAAAAGTTTCACAAATTTATT
1 AATTAAATCCTAAA-TTTCACAAATTTATG
* *
12823 AATTAAATGCTAAATTTCACAAAATTTCTG
1 AATTAAATCCTAAATTTCAC-AAATTTATG
12853 AATT-AATCCTTAAATT
1 AATTAAATCC-TAAATT
12869 ATTAAATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
29 10 0.26
30 28 0.74
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.38
Consensus pattern (29 bp):
AATTAAATCCTAAATTTCACAAATTTATG
Found at i:23480 original size:9 final size:9
Alignment explanation
Indices: 23468--23503 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
23458 TTTTATTTTT
23468 TTCTTCTCC
1 TTCTTCTCC
23477 TTCTTCTTCC
1 TTCTTC-TCC
23487 TTTCTTCTCC
1 -TTCTTCTCC
23497 TTCTTCT
1 TTCTTCT
23504 TCTCATTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 13 0.52
10 6 0.24
11 6 0.24
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (9 bp):
TTCTTCTCC
Found at i:23492 original size:20 final size:20
Alignment explanation
Indices: 23467--23505 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
23457 CTTTTATTTT
23467 TTTCTTCTCCTTCTTCTTCC
1 TTTCTTCTCCTTCTTCTTCC
23487 TTTCTTCTCCTTCTTCTTC
1 TTTCTTCTCCTTCTTCTTC
23506 TCATTTCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTCTTCTCCTTCTTCTTCC
Found at i:28880 original size:13 final size:14
Alignment explanation
Indices: 28862--28891 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
28852 TTTTCATATT
28862 TTATTTAT-ATAAA
1 TTATTTATAATAAA
28875 TTATTTATAATAAA
1 TTATTTATAATAAA
28889 TTA
1 TTA
28892 AAAATATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATTTATAATAAA
Found at i:30355 original size:6 final size:6
Alignment explanation
Indices: 30344--30370 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
30334 TTAGGTGTTG
30344 GTCCAA GTCCAA GTCCAA GTCCAA GTC
1 GTCCAA GTCCAA GTCCAA GTCCAA GTC
30371 TCCAGACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.19
Consensus pattern (6 bp):
GTCCAA
Found at i:46432 original size:13 final size:13
Alignment explanation
Indices: 46409--46451 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
46399 CAAAACACAT
*
46409 ATTTGCACATAGCC
1 ATTT-CACATAACC
46423 ATTTCACATAACC
1 ATTTCACATAACC
46436 ATTTCACATAACC
1 ATTTCACATAACC
46449 ATT
1 ATT
46452 CCCTAAAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 24 0.86
14 4 0.14
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (13 bp):
ATTTCACATAACC
Found at i:47086 original size:196 final size:196
Alignment explanation
Indices: 46731--47105 Score: 578
Period size: 196 Copynumber: 1.9 Consensus size: 196
46721 AAAAGCTATG
46731 ACTGTAACATGTAACCATATATGCTCACACGAGTAGTGAAATGGGTCTGCTCACATGAGCTGTGG
1 ACTGTAACATGTAACCATATATGCTCACACGAGTAGTGAAATGGGTCTGCTCACATGAGCTGTGG
* * *
46796 GTCGAGATGTTAAGCTACACGATGCTGCTCACACGAGCTGTGGAGAATCCGCAACCAATGCAAGA
66 GTCGAGATGTTAAGCTACACGATGCTACTCACACAAGCTGTGGAGAATCCGCAACAAATGCAAGA
* *
46861 CCTCAACTATCAATAGGACATCTAAGACCAGCACCCATATAACATGTAATGCTCACACGAGCTGT
131 CCTCAACCATCAATAGGACATCCAAGACCAGCACCCATATAACATGTAATGCTCACACGAGCTGT
46926 A
196 A
*
46927 ACTGTAACATGTAACCATATATGCTCACACGAGCTA-TGAAGTGGGT-TGGCTCACATGAGCTGT
1 ACTGTAACATGTAACCATATATGCTCACACGAG-TAGTGAAATGGGTCT-GCTCACATGAGCTGT
* *
46990 GGGTCGGGATGTTAGGCTACACGATGCTACTCACACAAGCTGTGGAGAATCCGCAACAAATGC-A
64 GGGTCGAGATGTTAAGCTACACGATGCTACTCACACAAGCTGTGGAGAATCCGCAACAAATGCAA
* ** *
47054 GAACCTCAGCCATCGGTATGG-CATCCAAGACCAGCACCCATATAACCTGTAA
129 G-ACCTCAACCATCAATA-GGACATCCAAGACCAGCACCCATATAACATGTAA
47106 ATAACCCGTA
Statistics
Matches: 163, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
195 3 0.02
196 156 0.96
197 4 0.02
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (196 bp):
ACTGTAACATGTAACCATATATGCTCACACGAGTAGTGAAATGGGTCTGCTCACATGAGCTGTGG
GTCGAGATGTTAAGCTACACGATGCTACTCACACAAGCTGTGGAGAATCCGCAACAAATGCAAGA
CCTCAACCATCAATAGGACATCCAAGACCAGCACCCATATAACATGTAATGCTCACACGAGCTGT
A
Found at i:52054 original size:7 final size:7
Alignment explanation
Indices: 52042--52068 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
52032 GGAGGAGTGG
52042 AGGAAGT
1 AGGAAGT
52049 AGGAAGT
1 AGGAAGT
52056 AGGAAGT
1 AGGAAGT
52063 AGGAAG
1 AGGAAG
52069 GAAGGTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.11
Consensus pattern (7 bp):
AGGAAGT
Found at i:55688 original size:3 final size:3
Alignment explanation
Indices: 55680--55707 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
55670 GGAGTTCATC
55680 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
55708 ATTTAATTTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55733 original size:15 final size:14
Alignment explanation
Indices: 55680--55734 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 14
55670 GGAGTTCATC
55680 TTATTA-TTA-TTA
1 TTATTATTTATTTA
55692 TTATTA-TTA-TTA
1 TTATTATTTATTTA
55704 TTA-TATTTAATTTA
1 TTATTATTT-ATTTA
55718 TTGATTATTTATTTA
1 TT-ATTATTTATTTA
55733 TT
1 TT
55735 TATTTGTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.05
12 17 0.45
13 1 0.03
14 5 0.13
15 8 0.21
16 5 0.13
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATTATTTATTTA
Found at i:55840 original size:49 final size:50
Alignment explanation
Indices: 55698--55840 Score: 138
Period size: 49 Copynumber: 2.9 Consensus size: 50
55688 ATTATTATTA
* * *
55698 TTATTATTAT-ATTTAATTTATTGATTATTTATTTATTTAT-TTG-TCAT
1 TTATTTTTATGATTTAATTTATTTATTTTTTATTTATTTATATTGTTCAT
* * **
55745 TTATTTTTATG-TTTAATCTTAATTATTTTTTA-TTGTTTATATTTGTTTGT
1 TTATTTTTATGATTTAAT-TTATTTATTTTTTATTTATTTATA-TTGTTCAT
*
55795 TTA-TTTTA-GCATTTAATTTTTTTATTTTTTATTTATTTATATTGTT
1 TTATTTTTATG-ATTTAATTTATTTATTTTTTATTTATTTATATTGTT
55841 GTTACTTATT
Statistics
Matches: 78, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
47 22 0.28
48 12 0.15
49 25 0.32
50 19 0.24
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (50 bp):
TTATTTTTATGATTTAATTTATTTATTTTTTATTTATTTATATTGTTCAT
Found at i:55910 original size:21 final size:21
Alignment explanation
Indices: 55884--55958 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
55874 CTTTTATTAT
55884 TTTTTATTTATTTTGCATTTA
1 TTTTTATTTATTTTGCATTTA
* *
55905 TTTTTA-TTATCTTG--TTTG
1 TTTTTATTTATTTTGCATTTA
*
55923 TTATTTATTTATTTAT-CATTAA
1 TT-TTTATTTATTT-TGCATTTA
* *
55945 ATTTTATTTTTTTT
1 TTTTTATTTATTTT
55959 CTTTTTATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 11
0.70 0.12 0.18
Matches are distributed among these distances:
18 5 0.12
19 4 0.10
20 13 0.31
21 17 0.40
22 3 0.07
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (21 bp):
TTTTTATTTATTTTGCATTTA
Found at i:55966 original size:36 final size:40
Alignment explanation
Indices: 55884--55974 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 40
55874 CTTTTATTAT
* * *
55884 TTTTTATTTATTT-TGCATTTATTTTTATTATCTTGTTTG
1 TTTTTATTTATTTATGCATTAAATTTTATTATCTTGTTTC
55923 TTATTTATTTATTTAT-CATTAAATTTTATT-T-TT-TTTC
1 TT-TTTATTTATTTATGCATTAAATTTTATTATCTTGTTTC
*
55960 TTTTTATTTAATTAT
1 TTTTTATTTATTTAT
55975 ATTTTGATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
36 12 0.26
37 5 0.11
38 2 0.04
39 3 0.07
40 23 0.50
41 1 0.02
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.71
Consensus pattern (40 bp):
TTTTTATTTATTTATGCATTAAATTTTATTATCTTGTTTC
Found at i:57911 original size:40 final size:40
Alignment explanation
Indices: 57862--58025 Score: 204
Period size: 40 Copynumber: 4.1 Consensus size: 40
57852 ACCTAACAGG
*
57862 CTTTAAGCCGGTGATGTGATTCAAGCTACGGCTTAGCAGA
1 CTTTGAGCCGGTGATGTGATTCAAGCTACGGCTTAGCAGA
* * * *
57902 CGTTGAGCCGGTAATGTGATTCAAGCTATGACTTAGCA-A
1 CTTTGAGCCGGTGATGTGATTCAAGCTACGGCTTAGCAGA
** * *
57941 CTTTTGAATCGGTGATTTGATTCAAGCTACGGCTTAGCAGG
1 C-TTTGAGCCGGTGATGTGATTCAAGCTACGGCTTAGCAGA
* * *
57982 CTTTGGGCCGGTGATGTGATTCAAGCTACGGTTTAGCAGG
1 CTTTGAGCCGGTGATGTGATTCAAGCTACGGCTTAGCAGA
58022 CTTT
1 CTTT
58026 AATCGGTGAT
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
39 2 0.02
40 101 0.97
41 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (40 bp):
CTTTGAGCCGGTGATGTGATTCAAGCTACGGCTTAGCAGA
Found at i:58018 original size:80 final size:79
Alignment explanation
Indices: 57846--58037 Score: 233
Period size: 80 Copynumber: 2.4 Consensus size: 79
57836 AACGATTCGG
* * * * *
57846 GCTACGACCTAACAGGCTTTAAGCCGGTGATGTGATTCAAGCTACGGCTTAGCAGACGTTGAGCC
1 GCTACGACTTAGCAGACTTTAA-TCGGTGATTTGATTCAAGCTACGGCTTAGCAGACGTTGAGCC
57911 GGTAATGTGATTCAA
65 GGTAATGTGATTCAA
* * * *
57926 GCTATGACTTAGCA-ACTTTTGAATCGGTGATTTGATTCAAGCTACGGCTTAGCAGGCTTTGGGC
1 GCTACGACTTAGCAGAC-TTT-AATCGGTGATTTGATTCAAGCTACGGCTTAGCAGACGTTGAGC
*
57990 CGGTGATGTGATTCAA
64 CGGTAATGTGATTCAA
** *
58006 GCTACGGTTTAGCAGGCTTTAATCGGTGATTT
1 GCTACGACTTAGCAGACTTTAATCGGTGATTT
58038 CGTAAAATGA
Statistics
Matches: 95, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
79 13 0.14
80 79 0.83
81 3 0.03
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (79 bp):
GCTACGACTTAGCAGACTTTAATCGGTGATTTGATTCAAGCTACGGCTTAGCAGACGTTGAGCCG
GTAATGTGATTCAA
Found at i:60641 original size:17 final size:18
Alignment explanation
Indices: 60611--60644 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
60601 TTTGAGAATT
60611 TTTTATCTTTTGAGCCCC
1 TTTTATCTTTTGAGCCCC
60629 TTTTATC-TTTGAGCCC
1 TTTTATCTTTTGAGCCC
60645 TAAGCGACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.12, C:0.26, G:0.12, T:0.50
Consensus pattern (18 bp):
TTTTATCTTTTGAGCCCC
Found at i:62882 original size:165 final size:165
Alignment explanation
Indices: 62604--62999 Score: 408
Period size: 165 Copynumber: 2.4 Consensus size: 165
62594 TATACTGCAA
* * * **
62604 CAGGT-AATCCCCGAC-AGTCCCCCTTGTTTTTTCTTTCTTATTACTGTCTTGGAATGTCATATT
1 CAGGTAAATCCCCCACTA-TCCCCCTTATTTTTTCTTTCTTGTTGTTGTCTTGGAATGTCATATT
* * * ** *
62667 GTTACTTTTTTTATTTACAAGGACAGAAGATTTACAACAATAGGATCAGTT-GGAGTATGATTAC
65 ATTACTTTTTTTATTAACAAGGACAGAAGATTTACAACAAAAAAATCAGTTGGGA-TATGATAAC
*
62731 CCCACAAGGCAACAACAAGAGCATAAGGATCATGATG
129 CCCACAAGGCAACAACAAGAGCATAAGAATCATGATG
* * *
62768 CAGGTAAATCCCCCACTATCCCTCTTATTTTTTCTTTCTTGTTGTTGTCTTGTAATGTTATATTA
1 CAGGTAAATCCCCCACTATCCCCCTTATTTTTTCTTTCTTGTTGTTGTCTTGGAATGTCATATTA
* * *
62833 TT-TTTATTTTTATTAAC-AGGAGTAGATGATTTACAACAAAAAAATCAGTTGGGATATGATAAC
66 TTACTT-TTTTTATTAACAAGGA-CAGAAGATTTACAACAAAAAAATCAGTTGGGATATGATAAC
*** * * * * *
62896 CCCATGGGGTAGCAACAGGAGCATATGAATCATTATG
129 CCCACAAGGCAACAACAAGAGCATAAGAATCATGATG
* * * * *
62933 CAAGTAACTCACCCA-TGGTCCCCCTTATTTTTTCTTTCTTGTTGTTGTTGTATGGAATGTCATA
1 CAGGTAAATCCCCCACT-ATCCCCCTTATTTTTTCTTTCTTGTTGTTG-TCT-TGGAATGTCATA
62997 TTA
63 TTA
63000 GAATTCTTTT
Statistics
Matches: 190, Mismatches: 34, Indels: 13
0.80 0.14 0.05
Matches are distributed among these distances:
164 12 0.06
165 159 0.84
166 6 0.03
167 13 0.07
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (165 bp):
CAGGTAAATCCCCCACTATCCCCCTTATTTTTTCTTTCTTGTTGTTGTCTTGGAATGTCATATTA
TTACTTTTTTTATTAACAAGGACAGAAGATTTACAACAAAAAAATCAGTTGGGATATGATAACCC
CACAAGGCAACAACAAGAGCATAAGAATCATGATG
Found at i:64813 original size:26 final size:26
Alignment explanation
Indices: 64784--64855 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 26
64774 AGAGACTATG
* *
64784 GACATAACTCACAAAGAGGGTTCGTA
1 GACATAACTCACAAAGAAGGTTCGCA
* *
64810 GACAAAACTCACAAGGAAGGTTCGCA
1 GACATAACTCACAAAGAAGGTTCGCA
* * *
64836 GACATAGCTCATAAATAAGG
1 GACATAACTCACAAAGAAGG
64856 CTCACAGGGG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (26 bp):
GACATAACTCACAAAGAAGGTTCGCA
Found at i:68477 original size:183 final size:183
Alignment explanation
Indices: 68149--68635 Score: 751
Period size: 183 Copynumber: 2.7 Consensus size: 183
68139 TGAACACACC
* * * *
68149 ATTACTAAATGAAGTTTGCTAGTTTGCTTTATGATTATTTGTTTTCCAATGTTTAAAAG-TCCAA
1 ATTACCAAATGAAGTTTGATGGTTTGCTTTATGATTATTTGTTTTCCAATGTTTAAAAGTTCGAA
* *
68213 GGGATATCTGTATTCCCCTGGTCTCTTTATTTCAATTAAAATTAATAAATATTTAATCATGGTTC
66 -GGATATTTGTATTCCCCTGGTCTCTTTATTACAATTAAAATTAATAAATATTTAATCATGGTTC
*
68278 TCAGTCTTAGTTTATGACTATTTGTTTTCCAATACAAAAGAAGAAAGCAAAGGG
130 TCAGTCTTAGTTTATGACTATTTGTTTTCCAATACAAAAGAAGAAAGCAAAAGG
* *
68332 ATTACCAAATGAAGTTTGATGGTTTTCTTTATGAGTATTTGTTTTCCAATGTTTAAAAGTTCGAA
1 ATTACCAAATGAAGTTTGATGGTTTGCTTTATGATTATTTGTTTTCCAATGTTTAAAAGTTCGAA
* *
68397 GGATATTTGTATTCCCCTAGTCTCTTTATTGCAATTAAAATTAATAAATATTTAATCATGGTTCT
66 GGATATTTGTATTCCCCTGGTCTCTTTATTACAATTAAAATTAATAAATATTTAATCATGGTTCT
* * *
68462 CGGTCTTATTTTATGACTATTTGTTTTCCAATACAAAGGAAGAAAGCAAAAGG
131 CAGTCTTAGTTTATGACTATTTGTTTTCCAATACAAAAGAAGAAAGCAAAAGG
* * * * *
68515 ATTATCAAATAAAGTTTGTTGGTTTGCTTTATGATTGTTTGTTTTCCAATGTTTAAAAGTTCGAG
1 ATTACCAAATGAAGTTTGATGGTTTGCTTTATGATTATTTGTTTTCCAATGTTTAAAAGTTCGAA
* * * *
68580 GGATATTTGTTTTCCTCTGGTCTCTTTATTACACTTAAAATTACTAAATATTTAAT
66 GGATATTTGTATTCCCCTGGTCTCTTTATTACAATTAAAATTAATAAATATTTAAT
68636 AATGACTATT
Statistics
Matches: 277, Mismatches: 26, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
183 273 0.99
184 4 0.01
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.43
Consensus pattern (183 bp):
ATTACCAAATGAAGTTTGATGGTTTGCTTTATGATTATTTGTTTTCCAATGTTTAAAAGTTCGAA
GGATATTTGTATTCCCCTGGTCTCTTTATTACAATTAAAATTAATAAATATTTAATCATGGTTCT
CAGTCTTAGTTTATGACTATTTGTTTTCCAATACAAAAGAAGAAAGCAAAAGG
Found at i:75294 original size:20 final size:19
Alignment explanation
Indices: 75269--75352 Score: 64
Period size: 20 Copynumber: 4.4 Consensus size: 19
75259 ATTCTTGAAG
75269 TATAAAAAATCATAAAAAAT
1 TATAAAAAAT-ATAAAAAAT
* *
75289 TATAAAAAA-A-ATAAATT
1 TATAAAAAATATAAAAAAT
* *
75306 TATAAAAATTATTAAAAAT
1 TATAAAAAATATAAAAAAT
* * *
75325 TGATGATAAATAATAAAAATT
1 T-ATAAAAAAT-ATAAAAAAT
75346 TATAAAA
1 TATAAAA
75353 TTCATAAATT
Statistics
Matches: 47, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
17 13 0.28
18 2 0.04
19 5 0.11
20 19 0.40
21 8 0.17
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (19 bp):
TATAAAAAATATAAAAAAT
Found at i:75295 original size:9 final size:9
Alignment explanation
Indices: 75273--75352 Score: 54
Period size: 10 Copynumber: 8.4 Consensus size: 9
75263 TTGAAGTATA
*
75273 AAAAATCAT
1 AAAAATTAT
75282 AAAAAATTAT
1 -AAAAATTAT
**
75292 AAAAAAAAT
1 AAAAATTAT
*
75301 -AAATTTAT
1 AAAAATTAT
75309 AAAAATTATT
1 AAAAATTA-T
75319 AAAAATTGAT
1 AAAAATT-AT
* *
75329 GATAAATAAT
1 -AAAAATTAT
75339 AAAAATTTAT
1 AAAAA-TTAT
75349 AAAA
1 AAAA
75353 TTCATAAATT
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
8 5 0.09
9 17 0.31
10 26 0.48
11 6 0.11
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:75311 original size:27 final size:26
Alignment explanation
Indices: 75283--75408 Score: 83
Period size: 26 Copynumber: 4.6 Consensus size: 26
75273 AAAAATCATA
75283 AAAAATTATAAAAAAAATAAATTTAT
1 AAAAATTATAAAAAAAATAAATTTAT
* *
75309 AAAAATTATTAAAAATTGATGATAAA-TAAT
1 AAAAATTA-TAAAAA---A-AATAAATTTAT
*** *
75339 AAAAATTTATAAAATTCATAAATTTGT
1 AAAAA-TTATAAAAAAAATAAATTTAT
* * *
75366 AAATATAATAAAAAAAATTAAATTTTT
1 AAAAATTATAAAAAAAA-TAAATTTAT
*
75393 CAAAAATTATTAAAAA
1 -AAAAATTATAAAAAA
75409 TCAATTAAAA
Statistics
Matches: 75, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
26 21 0.28
27 20 0.27
28 12 0.16
30 14 0.19
31 8 0.11
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
AAAAATTATAAAAAAAATAAATTTAT
Found at i:76966 original size:8 final size:8
Alignment explanation
Indices: 76921--76991 Score: 54
Period size: 8 Copynumber: 8.5 Consensus size: 8
76911 AGCCTGCCCA
76921 TATTATTT
1 TATTATTT
*
76929 T-TAATTT
1 TATTATTT
* *
76936 TAATATATA
1 TATTAT-TT
76945 TATATATTT
1 TAT-TATTT
*
76954 ATATTGTTT
1 -TATTATTT
76963 TATTATTT
1 TATTATTT
*
76971 TAATATTT
1 TATTATTT
76979 TAATTATTT
1 T-ATTATTT
76988 TATT
1 TATT
76992 TTAATAATCA
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
7 6 0.12
8 21 0.44
9 15 0.31
10 6 0.12
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (8 bp):
TATTATTT
Found at i:76969 original size:17 final size:17
Alignment explanation
Indices: 76949--76991 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
76939 TATATATATA
*
76949 TATTTATATTGTTTT-AT
1 TATTT-TATTATTTTAAT
*
76966 TATTTTAATATTTTAAT
1 TATTTTATTATTTTAAT
76983 TATTTTATT
1 TATTTTATT
76992 TTAATAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTTTATTATTTTAAT
Found at i:77998 original size:6 final size:6
Alignment explanation
Indices: 77987--78017 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
77977 GTGTAAGGGG
77987 ACACCC ACACCC ACACCC ACACCC ACACCC A
1 ACACCC ACACCC ACACCC ACACCC ACACCC A
78018 TGCCATGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (6 bp):
ACACCC
Found at i:81470 original size:2 final size:2
Alignment explanation
Indices: 81463--81508 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
81453 TTAATCATAC
81463 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
81505 AT AT
1 AT AT
81509 TATGGTAAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82543 original size:20 final size:23
Alignment explanation
Indices: 82506--82547 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
82496 ACCTTCTTGT
82506 TCTTCTTGCTTTCATTCTTCTGG
1 TCTTCTTGCTTTCATTCTTCTGG
82529 TCTTCTT-C-TTC-TTCTTCTG
1 TCTTCTTGCTTTCATTCTTCTG
82548 TCATTCAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 1 0.05
23 7 0.37
ACGTcount: A:0.02, C:0.29, G:0.10, T:0.60
Consensus pattern (23 bp):
TCTTCTTGCTTTCATTCTTCTGG
Found at i:87736 original size:25 final size:27
Alignment explanation
Indices: 87682--87736 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
87672 CAACAGTTTT
*
87682 TTTTTTTTTTTGTCAATCTAGCCTTTA
1 TTTTTTTTTTTGTCAATCTAGCCTTAA
* *
87709 TTTTTTTTTTT-TCATTTTAG-CTTAA
1 TTTTTTTTTTTGTCAATCTAGCCTTAA
87734 TTT
1 TTT
87737 GATCTTTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 7 0.28
27 11 0.44
ACGTcount: A:0.15, C:0.11, G:0.05, T:0.69
Consensus pattern (27 bp):
TTTTTTTTTTTGTCAATCTAGCCTTAA
Found at i:88452 original size:11 final size:11
Alignment explanation
Indices: 88436--88470 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
88426 TTAGATTAGG
88436 TTTCTTTTCTT
1 TTTCTTTTCTT
88447 TTTCTTTTCTT
1 TTTCTTTTCTT
*
88458 TTTCTTTCCTT
1 TTTCTTTTCTT
88469 TT
1 TT
88471 CTTCTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:88455 original size:16 final size:16
Alignment explanation
Indices: 88436--88473 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
88426 TTAGATTAGG
*
88436 TTTC-TTTTCTTTTTCT
1 TTTCTTTTTC-TTTCCT
88452 TTTCTTTTTCTTTCCT
1 TTTCTTTTTCTTTCCT
88468 TTTCTT
1 TTTCTT
88474 CTTAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTTTCCT
Found at i:88843 original size:17 final size:17
Alignment explanation
Indices: 88821--88853 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
88811 CTGACGCCTC
88821 TAGTTCGGCATACTTGA
1 TAGTTCGGCATACTTGA
*
88838 TAGTTCGTCATACTTG
1 TAGTTCGGCATACTTG
88854 TACCGGGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (17 bp):
TAGTTCGGCATACTTGA
Found at i:98364 original size:39 final size:39
Alignment explanation
Indices: 98310--98387 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
98300 TTTTAATGAT
98310 AACATCAGCTTTATAGCCTCCATCAAAGAGCCTATCCCA
1 AACATCAGCTTTATAGCCTCCATCAAAGAGCCTATCCCA
98349 AACATCAGCTTTATAGCCTCCATCAAAGAGCCTATCCCA
1 AACATCAGCTTTATAGCCTCCATCAAAGAGCCTATCCCA
98388 CAAATCCCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.23
Consensus pattern (39 bp):
AACATCAGCTTTATAGCCTCCATCAAAGAGCCTATCCCA
Found at i:99054 original size:11 final size:10
Alignment explanation
Indices: 99028--99052 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
99018 TTTAATATTT
99028 AAAAATAAAA
1 AAAAATAAAA
99038 AAAAATAAAA
1 AAAAATAAAA
99048 AAAAA
1 AAAAA
99053 ATCAACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:106798 original size:15 final size:16
Alignment explanation
Indices: 106768--106812 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
106758 ACTTTTTTAA
106768 AATTTTTGAAATATTT
1 AATTTTTGAAATATTT
* *
106784 TATTTTTTAAA-ATTT
1 AATTTTTGAAATATTT
106799 AA-TTTT-AAATATTT
1 AATTTTTGAAATATTT
106813 TTTAATTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 3 0.12
14 8 0.32
15 5 0.20
16 9 0.36
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
AATTTTTGAAATATTT
Found at i:107135 original size:29 final size:29
Alignment explanation
Indices: 107063--107144 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
107053 TAAATCTCAA
*
107063 AATTATATA-TGAATTTTGATTTGATGCGC
1 AATTATATACTGAATTTTAATTTGAT-CGC
107092 AATTATATACATGAATTTTAATTTGAT-GC
1 AATTATATAC-TGAATTTTAATTTGATCGC
*
107121 AATTATATACGTGAAATTCTAATT
1 AATTATATAC-TG-AATTTTAATT
107145 GTAGTTTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
29 23 0.49
30 9 0.19
31 15 0.32
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (29 bp):
AATTATATACTGAATTTTAATTTGATCGC
Found at i:107161 original size:31 final size:32
Alignment explanation
Indices: 107126--107185 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
107116 GATGCAATTA
*
107126 TATACGTGAAA-TTCTAATTGTAGTTTAAATG
1 TATACGTGAAACTTCTAATTGTAATTTAAATG
* * *
107157 TATACTTGAAACTTTTAATTTTAATTTAA
1 TATACGTGAAACTTCTAATTGTAATTTAA
107186 TTTAATTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 10 0.42
32 14 0.58
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (32 bp):
TATACGTGAAACTTCTAATTGTAATTTAAATG
Found at i:111540 original size:13 final size:13
Alignment explanation
Indices: 111522--111546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
111512 TTGGATCCAA
111522 ATTAAATTCTAAT
1 ATTAAATTCTAAT
111535 ATTAAATTCTAA
1 ATTAAATTCTAA
111547 AAAAGTAATT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAAATTCTAAT
Found at i:111930 original size:112 final size:112
Alignment explanation
Indices: 111729--111952 Score: 348
Period size: 112 Copynumber: 2.0 Consensus size: 112
111719 ATAAATCTAT
*
111729 TCCTAACTCTTTCACATTCACGTTTTTTGCCTCAAATTTTCTTTTTTGTCTTCGATTTAGTCCAT
1 TCCTAACTCTTTCACATTCACGTTTTTTGCCTCAAATTTTCTTTTTTGTCTTCGATTTAATCCAT
* *
111794 GGTTATGTGTCCAGCCCGTTTGGCTCTTAAAATATGCTCTTTTGTCC
66 GATTATGTGTCCAGCCCGTGTGGCTCTTAAAATATGCTCTTTTGTCC
111841 TCCTAACTCTTTCACATTCACGTTTTTTGGCC-CAAATTTT-TCTTTTTGTCTTCGATTTAATCC
1 TCCTAACTCTTTCACATTCACGTTTTTT-GCCTCAAATTTTCT-TTTTTGTCTTCGATTTAATCC
*
111904 ATGATCCTATGT-T-CAGCCCGTGTGGCTTTTAAAATATGCTCTTTTGTCC
64 ATGAT--TATGTGTCCAGCCCGTGTGGCTCTTAAAATATGCTCTTTTGTCC
111953 GGTTTTCGCT
Statistics
Matches: 104, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
111 1 0.01
112 94 0.90
113 4 0.04
114 5 0.05
ACGTcount: A:0.17, C:0.24, G:0.13, T:0.46
Consensus pattern (112 bp):
TCCTAACTCTTTCACATTCACGTTTTTTGCCTCAAATTTTCTTTTTTGTCTTCGATTTAATCCAT
GATTATGTGTCCAGCCCGTGTGGCTCTTAAAATATGCTCTTTTGTCC
Found at i:129163 original size:18 final size:18
Alignment explanation
Indices: 129127--129167 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
129117 AAAAATAAAG
*
129127 AAAAAAAGTATTTTCTTA
1 AAAAAAAGTATTGTCTTA
129145 AAAAAGAAGTATTGT-TTA
1 AAAAA-AAGTATTGTCTTA
129163 AAAAA
1 AAAAA
129168 TAAATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (18 bp):
AAAAAAAGTATTGTCTTA
Found at i:137013 original size:59 final size:59
Alignment explanation
Indices: 136947--137163 Score: 248
Period size: 59 Copynumber: 3.7 Consensus size: 59
136937 TGGATACTCG
* * * **
136947 GGGGT-AAAATGATAATTTTTGCAAGTTTCGGAATCAAAAATAGAATTTTTGGAAGTTT-
1 GGGGTAAAAATG-TAATTTTTGGAAATTTAGGGGTCAAAAATAGAATTTTTGGAAGTTTA
* *
137005 GGGAGTAAAAATGTAATTTTTGGAAATTTTGGGGTCAAAAATGGAA-TTTTGGAAGTTTA
1 GGG-GTAAAAATGTAATTTTTGGAAATTTAGGGGTCAAAAATAGAATTTTTGGAAGTTTA
* *
137064 GGGGTCAAAATGTAATTTTTGGAAAATTTAGGGGT-AGAAAATTGAATTTTTGGAAGTTTA
1 GGGGTAAAAATGTAATTTTTGG-AAATTTAGGGGTCA-AAAATAGAATTTTTGGAAGTTTA
* *
137124 GGGGTAAAAATGTATTTTTTGGAAGTTTTA-GGGT-AAAAAT
1 GGGGTAAAAATGTAATTTTTGGAA-ATTTAGGGGTCAAAAAT
137164 GTAATTTCTA
Statistics
Matches: 140, Mismatches: 12, Indels: 14
0.84 0.07 0.08
Matches are distributed among these distances:
58 39 0.28
59 58 0.41
60 43 0.31
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.36
Consensus pattern (59 bp):
GGGGTAAAAATGTAATTTTTGGAAATTTAGGGGTCAAAAATAGAATTTTTGGAAGTTTA
Found at i:137118 original size:89 final size:87
Alignment explanation
Indices: 136982--137170 Score: 226
Period size: 89 Copynumber: 2.1 Consensus size: 87
136972 TTTCGGAATC
* *
136982 AAAAATAG-AATTTTTGGAAGTTTGGGAGTAAAAATGTAATTTTTGGAAATTTTGGGGTCAAAAA
1 AAAAAT-GTAATTTTTGGAAATTTGGGAGTAAAAATGTAATTTTTGGAAATTTAGGGGT-AAAAA
137046 TGGA-ATTTTGGAAG-TTTAGGGGT
64 TGGATATTTTGGAAGTTTTA-GGGT
* *
137069 CAAAATGTAATTTTTGGAAAATTTAGGG-GTAGAAAAT-TGAATTTTTGGAAGTTTAGGGGTAAA
1 AAAAATGTAATTTTTGG-AAATTT-GGGAGTA-AAAATGT-AATTTTTGGAAATTTAGGGGTAAA
* *
137132 AATGTATTTTTTGGAAGTTTTAGGGT
62 AATGGATATTTTGGAAGTTTTAGGGT
137158 AAAAATGTAATTT
1 AAAAATGTAATTT
137171 CTAGATAGTT
Statistics
Matches: 88, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
86 1 0.01
87 14 0.16
88 17 0.19
89 52 0.59
90 4 0.05
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.38
Consensus pattern (87 bp):
AAAAATGTAATTTTTGGAAATTTGGGAGTAAAAATGTAATTTTTGGAAATTTAGGGGTAAAAATG
GATATTTTGGAAGTTTTAGGGT
Found at i:137182 original size:29 final size:29
Alignment explanation
Indices: 136947--137170 Score: 235
Period size: 29 Copynumber: 7.6 Consensus size: 29
136937 TGGATACTCG
* *
136947 GGGGT-AAAATGATAATTTTTGCAAGTTTC
1 GGGGTAAAAATG-TAATTTTTGGAAGTTTA
**
136976 GGAATCAAAAATAG-AATTTTTGGAAGTTT-
1 GGGGT-AAAAAT-GTAATTTTTGGAAGTTTA
* *
137005 GGGAGTAAAAATGTAATTTTTGGAAATTTT
1 GGG-GTAAAAATGTAATTTTTGGAAGTTTA
*
137035 GGGGTCAAAAATGGAA-TTTTGGAAGTTTA
1 GGGGT-AAAAATGTAATTTTTGGAAGTTTA
* *
137064 GGGGTCAAAATGTAATTTTTGGAAAATTTA
1 GGGGTAAAAATGTAATTTTTGG-AAGTTTA
137094 GGGGTAGAAAAT-TGAATTTTTGGAAGTTTA
1 GGGGTA-AAAATGT-AATTTTTGGAAGTTTA
*
137124 GGGGTAAAAATGTATTTTTTGGAAGTTTTA
1 GGGGTAAAAATGTAATTTTTGGAAG-TTTA
137154 -GGGTAAAAATGTAATTT
1 GGGGTAAAAATGTAATTT
137171 CTAGATAGTT
Statistics
Matches: 166, Mismatches: 16, Indels: 26
0.80 0.08 0.12
Matches are distributed among these distances:
28 9 0.05
29 81 0.49
30 56 0.34
31 19 0.11
32 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTTGGAAGTTTA
Found at i:139128 original size:41 final size:41
Alignment explanation
Indices: 139083--139160 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
139073 AATCATTTCG
* * *
139083 AATTTAGACTAAATTTAAATTTAAAAATTAATTTAAATTTA
1 AATTTAAAATAAATTTAAATTTAAAAATAAATTTAAATTTA
* **
139124 AATTTAAAATTAATTTAAATTTATGAATAAATTTAAA
1 AATTTAAAATAAATTTAAATTTAAAAATAAATTTAAA
139161 ACAAATTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (41 bp):
AATTTAAAATAAATTTAAATTTAAAAATAAATTTAAATTTA
Found at i:139136 original size:18 final size:18
Alignment explanation
Indices: 139092--139160 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
139082 GAATTTAGAC
* *
139092 TAAATTTAAATTTAAAAAT
1 TAAAATTAAATTT-AAATT
*
139111 T-AATTTAAATTTAAATT
1 TAAAATTAAATTTAAATT
139128 TAAAATT-AATTTAAATT
1 TAAAATTAAATTTAAATT
*
139145 TATGAA-TAAATTTAAA
1 TA-AAATTAAATTTAAA
139161 ACAAATTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
17 18 0.41
18 25 0.57
19 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (18 bp):
TAAAATTAAATTTAAATT
Found at i:139136 original size:23 final size:24
Alignment explanation
Indices: 139092--139146 Score: 103
Period size: 23 Copynumber: 2.3 Consensus size: 24
139082 GAATTTAGAC
139092 TAAATTTAAATTTAAAAATTAATT
1 TAAATTTAAATTTAAAAATTAATT
139116 TAAATTTAAATTT-AAAATTAATT
1 TAAATTTAAATTTAAAAATTAATT
139139 TAAATTTA
1 TAAATTTA
139147 TGAATAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 18 0.58
24 13 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAATTTAAATTTAAAAATTAATT
Found at i:139138 original size:17 final size:18
Alignment explanation
Indices: 139116--139160 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
139106 AAAATTAATT
139116 TAAATTTAAATTTA-AAA
1 TAAATTTAAATTTATAAA
* *
139133 TTAATTTAAATTTATGAA
1 TAAATTTAAATTTATAAA
139151 TAAATTTAAA
1 TAAATTTAAA
139161 ACAAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TAAATTTAAATTTATAAA
Found at i:139160 original size:6 final size:6
Alignment explanation
Indices: 139092--139146 Score: 69
Period size: 6 Copynumber: 9.3 Consensus size: 6
139082 GAATTTAGAC
* *
139092 TAAATT TAAATT TAAAAAT T-AATT TAAATT TAAATT TAAAAT T-AATT
1 TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT TAAATT
139139 TAAATT TA
1 TAAATT TA
139147 TGAATAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
7 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:139943 original size:16 final size:16
Alignment explanation
Indices: 139918--139959 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
139908 CATAAATTTT
*
139918 AAAATCTAAAAG-TTA
1 AAAATATAAAAGCTTA
139933 GAAAATATAAAAGCTTA
1 -AAAATATAAAAGCTTA
139950 AAAATA-AAAA
1 AAAATATAAAA
139960 TAGAAAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 17 0.71
17 3 0.12
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (16 bp):
AAAATATAAAAGCTTA
Found at i:144669 original size:22 final size:21
Alignment explanation
Indices: 144641--144684 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
144631 ATTTTTAATT
*
144641 TTTTAATATTTATATTATTTTA
1 TTTTAATATTTA-ATAATTTTA
144663 TTTTAATATTTAATAATTTTA
1 TTTTAATATTTAATAATTTTA
144684 T
1 T
144685 ATATTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTAATATTTAATAATTTTA
Found at i:146739 original size:4 final size:4
Alignment explanation
Indices: 146730--146755 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
146720 GAAAATTATT
146730 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
146756 AACTTGATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:149264 original size:29 final size:29
Alignment explanation
Indices: 149227--149294 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
149217 ACATTTGTGC
* * *
149227 AGGTCGTGTGTGCCACGTGGCCGTGTGGG
1 AGGTCGTGTGTGCCACATGGCCATGTGAG
* *
149256 AGGTTGTGTGTGCCTCATGGCCATGTGAG
1 AGGTCGTGTGTGCCACATGGCCATGTGAG
149285 AGGTCGTGTG
1 AGGTCGTGTG
149295 ATGAACCGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.10, C:0.18, G:0.44, T:0.28
Consensus pattern (29 bp):
AGGTCGTGTGTGCCACATGGCCATGTGAG
Found at i:150234 original size:2 final size:2
Alignment explanation
Indices: 150229--150253 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
150219 TATATATATA
150229 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
150254 AAACCCGATT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:150363 original size:25 final size:25
Alignment explanation
Indices: 150334--150381 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
150324 GATTTAATTA
*
150334 TGTATGGATTAATTTTTCTCTAAAT
1 TGTATGGATTAATTTTGCTCTAAAT
150359 TGTATGGATTAATTTTGCTCTAA
1 TGTATGGATTAATTTTGCTCTAA
150382 GTATGATGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (25 bp):
TGTATGGATTAATTTTGCTCTAAAT
Found at i:150390 original size:25 final size:26
Alignment explanation
Indices: 150332--150390 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 26
150322 AAGATTTAAT
*
150332 TATGTATGGATTAATTTTTCTCTAAA
1 TATGTATGGATTAATTTTGCTCTAAA
*
150358 T-TGTATGGATTAATTTTGCTCTAAG
1 TATGTATGGATTAATTTTGCTCTAAA
150383 TATG-ATGG
1 TATGTATGG
150391 TGTTTTGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 27 0.90
26 3 0.10
ACGTcount: A:0.27, C:0.07, G:0.19, T:0.47
Consensus pattern (26 bp):
TATGTATGGATTAATTTTGCTCTAAA
Found at i:151868 original size:7 final size:7
Alignment explanation
Indices: 151851--151886 Score: 63
Period size: 7 Copynumber: 5.0 Consensus size: 7
151841 GTGGGTCTGA
151851 TGATGGGC
1 TGAT-GGC
151859 TGATGGC
1 TGATGGC
151866 TGATGGC
1 TGATGGC
151873 TGATGGC
1 TGATGGC
151880 TGATGGC
1 TGATGGC
151887 GACGCATGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 24 0.86
8 4 0.14
ACGTcount: A:0.14, C:0.14, G:0.44, T:0.28
Consensus pattern (7 bp):
TGATGGC
Found at i:155006 original size:16 final size:17
Alignment explanation
Indices: 154985--155022 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
154975 TTTTATCTTT
154985 AAAATAAC-TTTTATTA
1 AAAATAACATTTTATTA
*
155001 AAAATAACATTTTTTTA
1 AAAATAACATTTTATTA
155018 AAAAT
1 AAAAT
155023 TTCAAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATAACATTTTATTA
Found at i:158333 original size:19 final size:21
Alignment explanation
Indices: 158292--158333 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
158282 TATAAAGATT
*
158292 AATTGTGTGATTAATTGGTGA
1 AATTGTGTGATTAATTGGAGA
*
158313 AATTGTG-GATT-ATTTGAGA
1 AATTGTGTGATTAATTGGAGA
158332 AA
1 AA
158334 ATAAAGGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
20 4 0.21
21 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.40
Consensus pattern (21 bp):
AATTGTGTGATTAATTGGAGA
Found at i:158438 original size:18 final size:18
Alignment explanation
Indices: 158415--158451 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
158405 TTTGTGATTA
158415 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
158433 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
158451 A
1 A
158452 TATGAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:160367 original size:20 final size:20
Alignment explanation
Indices: 160331--160368 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
160321 AGCATATCGC
160331 ATTAAAGTCGTAATAATTTA
1 ATTAAAGTCGTAATAATTTA
*
160351 ATTAAGGTC-TAATTAATT
1 ATTAAAGTCGTAA-TAATT
160369 GAAAATAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (20 bp):
ATTAAAGTCGTAATAATTTA
Found at i:170149 original size:27 final size:27
Alignment explanation
Indices: 170111--170172 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
170101 TGGGGTGGTA
* * *
170111 CCTACCTAACAGGCAGCACTAGAGGTG
1 CCTACCTGACAGGCAGCACCAAAGGTG
* *
170138 CCTACCTGACAGGCGGCACCAAATGTG
1 CCTACCTGACAGGCAGCACCAAAGGTG
170165 CCTACCTG
1 CCTACCTG
170173 GCAGCCTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.34, G:0.24, T:0.16
Consensus pattern (27 bp):
CCTACCTGACAGGCAGCACCAAAGGTG
Found at i:170738 original size:26 final size:26
Alignment explanation
Indices: 170702--170764 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
170692 TTTTGAAGAA
*
170702 AAGAAGAAAAGAAAAGC-AAATTTTTG
1 AAGAAGGAAAG-AAAGCAAAATTTTTG
*
170728 AAGAAGGAAAGGAAGCAAAATTTTTG
1 AAGAAGGAAAGAAAGCAAAATTTTTG
170754 AAGAAGGAAAG
1 AAGAAGGAAAG
170765 GAAATAGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 4 0.12
26 30 0.88
ACGTcount: A:0.56, C:0.03, G:0.25, T:0.16
Consensus pattern (26 bp):
AAGAAGGAAAGAAAGCAAAATTTTTG
Found at i:170751 original size:25 final size:26
Alignment explanation
Indices: 170715--170767 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
170705 AAGAAAAGAA
170715 AAGC-AAATTTTTGAAGAAGGAAAGG
1 AAGCAAAATTTTTGAAGAAGGAAAGG
170740 AAGCAAAATTTTTGAAGAAGGAAAGG
1 AAGCAAAATTTTTGAAGAAGGAAAGG
170766 AA
1 AA
170768 ATAGAAGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.51, C:0.04, G:0.26, T:0.19
Consensus pattern (26 bp):
AAGCAAAATTTTTGAAGAAGGAAAGG
Found at i:173579 original size:28 final size:28
Alignment explanation
Indices: 173526--173583 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
173516 CATTTTTCAC
*
173526 TTGGAATTAATTAAGTTTATGATTGAAT
1 TTGGAATTAATTAAGTTTATAATTGAAT
**
173554 TTGGAATTAATTCTGTTTA-AATTTGAAT
1 TTGGAATTAATTAAGTTTATAA-TTGAAT
173582 TT
1 TT
173584 ATTTAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50
Consensus pattern (28 bp):
TTGGAATTAATTAAGTTTATAATTGAAT
Found at i:173598 original size:26 final size:26
Alignment explanation
Indices: 173569--173618 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
173559 ATTAATTCTG
173569 TTTAAATTTGAATTTATTTAATAATT
1 TTTAAATTTGAATTTATTTAATAATT
**
173595 TTTATGTTTGAATTTATTTAATAA
1 TTTAAATTTGAATTTATTTAATAA
173619 GGTTTAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (26 bp):
TTTAAATTTGAATTTATTTAATAATT
Found at i:173624 original size:26 final size:26
Alignment explanation
Indices: 173575--173624 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
173565 TCTGTTTAAA
**
173575 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
173601 TTTGAATTTATTTAATAAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
173625 GCAAATGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:173699 original size:6 final size:6
Alignment explanation
Indices: 173690--173730 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
173680 ATATTTGCAT
*
173690 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATA
173731 TTTAATTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:175937 original size:34 final size:34
Alignment explanation
Indices: 175898--175965 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
175888 ATTTTAAAAT
*
175898 TTTAAAAATATTTTTTTGTTTTAAAATTGTAATA
1 TTTAAAAATATTTTTTTATTTTAAAATTGTAATA
*
175932 TTTAAAAATATTTTTTTATTTTAAAATTTTAATA
1 TTTAAAAATATTTTTTTATTTTAAAATTGTAATA
175966 CAATAGAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (34 bp):
TTTAAAAATATTTTTTTATTTTAAAATTGTAATA
Found at i:176225 original size:9 final size:9
Alignment explanation
Indices: 176211--176237 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
176201 TAATTGAAGT
176211 TAAATGTCA
1 TAAATGTCA
176220 TAAATGTCA
1 TAAATGTCA
176229 TAAATGTCA
1 TAAATGTCA
176238 ATATATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (9 bp):
TAAATGTCA
Found at i:176676 original size:287 final size:287
Alignment explanation
Indices: 176227--176789 Score: 959
Period size: 287 Copynumber: 2.0 Consensus size: 287
176217 TCATAAATGT
* *
176227 CATAAATGTCAATATATAATATCATGTTTGCTTTCCTCAACAATTTCAAATAAAAAAGATTTATA
1 CATAAATGTCAATATATAATATCATGTTTGCTTTCCCCAACAATTTCAAAGAAAAAAGATTTATA
* * * *
176292 TTTTATTACTTATTAACTTTTATCTTTCAATTTTGTTATAATGACTTTAATTTAAAATGGTTGAA
66 TTTTATTACTTATTAACTTTTATCTTTCAATTTTGGTATAAAGACTTTAATTAAAAAGGGTTGAA
*
176357 TCAATTATTTAAACTCATAAATTTAATAATATTTGTTTCTCTCATATTATATTTTAATTATTTAG
131 TCAATTATTTAAACTCATAAATTTAATAATATTTATTTCTCTCATATTATATTTTAATTATTTAG
*
176422 ATTTAAAATATTATGTTTTAATTATTTATATTATCTCTTTATTACGATATAATTATTTTGTCATA
196 ATTTAAAATATTATGTTTGAATTATTTATATTATCTCTTTATTACGATATAATTATTTTGTCATA
176487 AAAATTTATTTATTTCCCCAACAATCC
261 AAAATTTATTTATTTCCCCAACAATCC
*
176514 CATAAATGTCAATATATAATA-CAATGTTTTCTTTCCCCAACAATTTCAAAGAAAAAAGATTTAT
1 CATAAATGTCAATATATAATATC-ATGTTTGCTTTCCCCAACAATTTCAAAGAAAAAAGATTTAT
* *
176578 ATTTTATTACTTATTGACTTTTATTTTTCAATTTTGGTATAAAGA-TTATAATTAAAAAGGGTTG
65 ATTTTATTACTTATTAACTTTTATCTTTCAATTTTGGTATAAAGACTT-TAATTAAAAAGGGTTG
*
176642 AATCAATTATTTAAACTCATAAATTTATTAATATTTATTTCTCTCATATTATATTTTAATTATTT
129 AATCAATTATTTAAACTCATAAATTTAATAATATTTATTTCTCTCATATTATATTTTAATTATTT
* * *
176707 AGGTTTAAAATGTTATGTTTGAATTATTTATGTTATCTCTTTATTACGATATAATTATTTTGTCA
194 AGATTTAAAATATTATGTTTGAATTATTTATATTATCTCTTTATTACGATATAATTATTTTGTCA
176772 TAAAAATTTATTTATTTC
259 TAAAAATTTATTTATTTC
176790 TCAAATGACA
Statistics
Matches: 259, Mismatches: 15, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
286 3 0.01
287 256 0.99
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (287 bp):
CATAAATGTCAATATATAATATCATGTTTGCTTTCCCCAACAATTTCAAAGAAAAAAGATTTATA
TTTTATTACTTATTAACTTTTATCTTTCAATTTTGGTATAAAGACTTTAATTAAAAAGGGTTGAA
TCAATTATTTAAACTCATAAATTTAATAATATTTATTTCTCTCATATTATATTTTAATTATTTAG
ATTTAAAATATTATGTTTGAATTATTTATATTATCTCTTTATTACGATATAATTATTTTGTCATA
AAAATTTATTTATTTCCCCAACAATCC
Found at i:176932 original size:20 final size:19
Alignment explanation
Indices: 176907--176944 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
176897 TAAATGGATT
176907 TTTTTAATAATAATACAAAA
1 TTTTTAATAATAAT-CAAAA
176927 TTTTTAATAATAATCAAA
1 TTTTTAATAATAATCAAA
176945 CCCTAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTTTAATAATAATCAAAA
Found at i:176994 original size:14 final size:12
Alignment explanation
Indices: 176964--177006 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
176954 ACATACCTTC
176964 TCTTTTTTTTCT
1 TCTTTTTTTTCT
176976 TCTTTTTTTTCT
1 TCTTTTTTTTCT
**
176988 CTCCTTTCCTTTCT
1 -T-CTTTTTTTTCT
177002 TCTTT
1 TCTTT
177007 GTTGCTGCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 16 0.59
13 2 0.07
14 9 0.33
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TCTTTTTTTTCT
Found at i:177292 original size:16 final size:15
Alignment explanation
Indices: 177256--177295 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
177246 CATATCGATA
177256 TTTTT-TTTAAAATT
1 TTTTTATTTAAAATT
*
177270 TTATTATTTAAATATT
1 TTTTTATTTAAA-ATT
177286 TTTTTATTTA
1 TTTTTATTTA
177296 TTTAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 4 0.18
15 6 0.27
16 12 0.55
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTATTTAAAATT
Found at i:177292 original size:19 final size:19
Alignment explanation
Indices: 177268--177304 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
177258 TTTTTTAAAA
177268 TTTTA-TTATTTAAATATTT
1 TTTTATTTATTT-AATATTT
177287 TTTTATTTATTTAATATT
1 TTTTATTTATTTAATATT
177305 AAAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATTTATTTAATATTT
Found at i:182684 original size:18 final size:18
Alignment explanation
Indices: 182661--182708 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
182651 CCAATTTTAC
182661 ATATTTTAAAAAATAAAA
1 ATATTTTAAAAAATAAAA
* * *
182679 ATATTTCTTAAAAATTAGA
1 ATATTT-TAAAAAATAAAA
182698 A-ATTTTAAAAA
1 ATATTTTAAAAA
182709 TGGTTTAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 5 0.20
18 10 0.40
19 10 0.40
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
ATATTTTAAAAAATAAAA
Found at i:191948 original size:17 final size:17
Alignment explanation
Indices: 191926--191959 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
191916 ATATTATATA
*
191926 AATTTTATTTTGATTAT
1 AATTTTATTTTAATTAT
191943 AATTTTATTTTAATTAT
1 AATTTTATTTTAATTAT
191960 TTATTGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
AATTTTATTTTAATTAT
Found at i:196605 original size:31 final size:29
Alignment explanation
Indices: 196544--196607 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
196534 CCAAAAGTTG
* * *
196544 AGTTCACAAAAGATATGAAAATATATTGC
1 AGTTCACAAAAGAAATCAAAATATACTGC
196573 AGTTCACAAAAGAAAATCAATAATATACTGC
1 AGTTCACAAAAG-AAATCAA-AATATACTGC
196604 AGTT
1 AGTT
196608 TTGGAGAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 12 0.40
30 5 0.17
31 13 0.43
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (29 bp):
AGTTCACAAAAGAAATCAAAATATACTGC
Found at i:200202 original size:4 final size:4
Alignment explanation
Indices: 200193--200219 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
200183 TCGAAACAAA
200193 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
200220 ACCTTTGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:205180 original size:2 final size:2
Alignment explanation
Indices: 205175--205212 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
205165 AAAAACCGAA
205175 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
205213 GCTACTTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:225179 original size:21 final size:21
Alignment explanation
Indices: 225155--225196 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
225145 ACGGGAAATA
225155 AAGAAAGAAAAGAAAGAAAGG
1 AAGAAAGAAAAGAAAGAAAGG
* * *
225176 AAGAAGGAGAGGAAAGAAAGG
1 AAGAAAGAAAAGAAAGAAAGG
225197 TAATGTGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (21 bp):
AAGAAAGAAAAGAAAGAAAGG
Found at i:230956 original size:20 final size:21
Alignment explanation
Indices: 230931--230973 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
230921 TACTCACAAC
230931 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
*
230951 TACTAACTAACAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
230972 TA
1 TA
230974 AAATAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:231143 original size:12 final size:12
Alignment explanation
Indices: 231117--231160 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
231107 AATTAACTAA
231117 AAATTTAAAA-T
1 AAATTTAAAATT
231128 -AATTTAAAATT
1 AAATTTAAAATT
231139 AAATTTAAAATT
1 AAATTTAAAATT
*
231151 AAACTTAAAA
1 AAATTTAAAA
231161 AATTAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 9 0.30
11 1 0.03
12 20 0.67
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATTTAAAATT
Found at i:231348 original size:10 final size:10
Alignment explanation
Indices: 231322--231370 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
231312 TTACCTTTTT
231322 CTTCTTC-TC
1 CTTCTTCTTC
231331 CTTCCTTCTTC
1 CTT-CTTCTTC
231342 CTTCTTCTTC
1 CTTCTTCTTC
*
231352 CTTCTTTCTTT
1 CTTC-TTCTTC
231363 C-TCTTCTT
1 CTTCTTCTT
231371 TTTTTCTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
9 8 0.22
10 17 0.47
11 11 0.31
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (10 bp):
CTTCTTCTTC
Found at i:231367 original size:17 final size:17
Alignment explanation
Indices: 231326--231387 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
231316 CTTTTTCTTC
*
231326 TTCTCCTTCCTTC-TTCC
1 TTCT-CTTCCTTCTTTCT
231343 TTCTTCTTCCTTCTTTCT
1 TTC-TCTTCCTTCTTTCT
* *
231361 TTCTCTTCTTTTTTTCT
1 TTCTCTTCCTTCTTTCT
231378 TT-T-TTCCTTC
1 TTCTCTTCCTTC
231388 AATTTTCGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 5 0.13
16 1 0.03
17 25 0.66
18 7 0.18
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
TTCTCTTCCTTCTTTCT
Found at i:238057 original size:8 final size:8
Alignment explanation
Indices: 238018--238085 Score: 55
Period size: 8 Copynumber: 7.8 Consensus size: 8
238008 ACATGGTGGA
238018 AAAAATAAT
1 AAAAAT-AT
238027 AAAAATAT
1 AAAAATAT
**
238035 TTAAATCAAT
1 AAAAAT--AT
238045 AAAAAGTAT
1 AAAAA-TAT
238054 AAAAATATT
1 AAAAATA-T
238063 AAAAAATAT
1 -AAAAATAT
238072 AAAAATAT
1 AAAAATAT
*
238080 AGAAAT
1 AAAAAT
238086 TATTTTAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
8 21 0.43
9 15 0.31
10 12 0.24
11 1 0.02
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.26
Consensus pattern (8 bp):
AAAAATAT
Found at i:238065 original size:18 final size:18
Alignment explanation
Indices: 238044--238079 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
238034 TTTAAATCAA
*
238044 TAAAAAGTATAAAAATAT
1 TAAAAAATATAAAAATAT
238062 TAAAAAATATAAAAATAT
1 TAAAAAATATAAAAATAT
238080 AGAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
TAAAAAATATAAAAATAT
Found at i:238073 original size:27 final size:26
Alignment explanation
Indices: 238018--238090 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
238008 ACATGGTGGA
**
238018 AAAAATAATAAAAATATTTAAATCAAT
1 AAAAAT-ATAAAAATATTTAAAAAAAT
238045 AAAAAGTATAAAAATA-TTAAAAAATAT
1 AAAAA-TATAAAAATATTTAAAAAA-AT
*
238072 AAAAATATAGAAATTATTT
1 AAAAATATA-AAAATATTT
238091 TAAATTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 10 0.26
27 26 0.67
28 3 0.08
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (26 bp):
AAAAATATAAAAATATTTAAAAAAAT
Found at i:238366 original size:10 final size:10
Alignment explanation
Indices: 238353--238455 Score: 59
Period size: 10 Copynumber: 10.3 Consensus size: 10
238343 AAAAGACGAT
238353 AAAAATTATA
1 AAAAATTATA
*
238363 AAAAAATATA
1 AAAAATTATA
**
238373 GGAAA-TAT-
1 AAAAATTATA
* *
238381 ATAAATTATT
1 AAAAATTATA
*
238391 AAAATTTATA
1 AAAAATTATA
*
238401 AAAATATTCTA
1 AAAA-ATTATA
*
238412 AAAAATAATTA
1 AAAAATTA-TA
** *
238423 AAATTTTAGA
1 AAAAATTATA
238433 AAAAATTAT-
1 AAAAATTATA
238442 AAAAATTATTA
1 AAAAATTA-TA
238453 AAA
1 AAA
238456 GTATATGAAA
Statistics
Matches: 68, Mismatches: 19, Indels: 11
0.69 0.19 0.11
Matches are distributed among these distances:
8 3 0.04
9 14 0.21
10 33 0.49
11 18 0.26
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (10 bp):
AAAAATTATA
Found at i:238426 original size:31 final size:30
Alignment explanation
Indices: 238378--238455 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 30
238368 ATATAGGAAA
* *
238378 TATATAAATTATTAAAATTTATA-AAAATAT
1 TATAAAAATTATTAAAATTT-TAGAAAAAAT
* *
238408 TCTAAAAAATAATTAAAATTTTAGAAAAAAT
1 TAT-AAAAATTATTAAAATTTTAGAAAAAAT
238439 TATAAAAATTATTAAAA
1 TATAAAAATTATTAAAA
238456 GTATATGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 17 0.43
31 23 0.57
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (30 bp):
TATAAAAATTATTAAAATTTTAGAAAAAAT
Found at i:238959 original size:10 final size:10
Alignment explanation
Indices: 238944--238970 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
238934 TATTTTATGT
238944 ATTTTAAATA
1 ATTTTAAATA
238954 ATTTTAAATA
1 ATTTTAAATA
238964 ATTTTAA
1 ATTTTAA
238971 TATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTTTAAATA
Found at i:238973 original size:45 final size:47
Alignment explanation
Indices: 238865--238977 Score: 121
Period size: 45 Copynumber: 2.5 Consensus size: 47
238855 TTTTTCATAT
*
238865 ATTTT-AATAATTTTAAT-TTTTTAATATCTTTCTAAATTTAAAATA
1 ATTTTAAATAATTTTAATATTTTTAATATCTTTATAAATTTAAAATA
* * ** *
238910 TTTTCTAAAT-A-TTAAATATTTTT-ATAT-TTTATGTATTTTAAATA
1 ATTT-TAAATAATTTTAATATTTTTAATATCTTTATAAATTTAAAATA
238954 ATTTTAAATAATTTTAATATTTTT
1 ATTTTAAATAATTTTAATATTTTT
238978 TTTCATTTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
43 5 0.09
44 17 0.31
45 23 0.42
46 7 0.13
47 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (47 bp):
ATTTTAAATAATTTTAATATTTTTAATATCTTTATAAATTTAAAATA
Found at i:238977 original size:9 final size:9
Alignment explanation
Indices: 238855--238977 Score: 67
Period size: 9 Copynumber: 13.6 Consensus size: 9
238845 TTTTGATATT
*
238855 TTTTTCATA
1 TTTTTAATA
238864 TATTTTAATA
1 T-TTTTAATA
*
238874 ATTTTAAT-
1 TTTTTAATA
238882 TTTTTAATA
1 TTTTTAATA
238891 TCTTTCTAA-A
1 T-TTT-TAATA
**
238901 TTTAAAATA
1 TTTTTAATA
238910 TTTTCTAA-A
1 TTTT-TAATA
* *
238919 TATTAAATA
1 TTTTTAATA
238928 TTTTT-ATA
1 TTTTTAATA
*
238936 -TTTTATGTA
1 TTTTTA-ATA
*
238945 TTTTAAATAA
1 TTTTTAAT-A
*
238955 TTTTAAATA
1 TTTTTAATA
*
238964 ATTTTAATA
1 TTTTTAATA
238973 TTTTT
1 TTTTT
238978 TTTCATTTTC
Statistics
Matches: 86, Mismatches: 17, Indels: 22
0.69 0.14 0.18
Matches are distributed among these distances:
7 4 0.05
8 14 0.16
9 38 0.44
10 27 0.31
11 3 0.03
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (9 bp):
TTTTTAATA
Found at i:239488 original size:18 final size:17
Alignment explanation
Indices: 239465--239498 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
239455 ATTTTTAATA
*
239465 ATTTTTTGTTTTATTTTT
1 ATTTTTTATTTT-TTTTT
239483 ATTTTTTATTTTTTTT
1 ATTTTTTATTTTTTTT
239499 AGAATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (17 bp):
ATTTTTTATTTTTTTTT
Found at i:240051 original size:19 final size:21
Alignment explanation
Indices: 240028--240067 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
240018 AAAAATTATA
*
240028 TTTTTTAAA-AATTTATAAAT
1 TTTTTTAAAGAATATATAAAT
240048 TTTTTTAAAGAATATATAAA
1 TTTTTTAAAGAATATATAAA
240068 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTTTTAAAGAATATATAAAT
Found at i:240600 original size:53 final size:53
Alignment explanation
Indices: 240520--240626 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
240510 TTTACATTTT
240520 GTTTTTGGTTCTTAGCTGTTAAGACGAGGCTTCCTTCTTTAATTTCTTAAGGG
1 GTTTTTGGTTCTTAGCTGTTAAGACGAGGCTTCCTTCTTTAATTTCTTAAGGG
240573 GTTTTTGGTTCTTAGCTGTTAAGACGAGGCTTCCTTCTTTAATTTCTTAAGGG
1 GTTTTTGGTTCTTAGCTGTTAAGACGAGGCTTCCTTCTTTAATTTCTTAAGGG
240626 G
1 G
240627 AAGCCTTGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.45
Consensus pattern (53 bp):
GTTTTTGGTTCTTAGCTGTTAAGACGAGGCTTCCTTCTTTAATTTCTTAAGGG
Found at i:254012 original size:22 final size:22
Alignment explanation
Indices: 253954--254022 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
253944 AATATATTGT
253954 TGTTTT-AGTA-TTCTTTTTTAC
1 TGTTTTGAGTACTT-TTTTTTAC
*
253975 TGTTTTGATTACTTTTTTTTAC
1 TGTTTTGAGTACTTTTTTTTAC
* *
253997 TGTTTTG-GTGC-TTTTTTCAC
1 TGTTTTGAGTACTTTTTTTTAC
254017 TGTTTT
1 TGTTTT
254023 AATGTTGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 14 0.33
21 8 0.19
22 18 0.43
23 2 0.05
ACGTcount: A:0.10, C:0.10, G:0.13, T:0.67
Consensus pattern (22 bp):
TGTTTTGAGTACTTTTTTTTAC
Found at i:254043 original size:31 final size:31
Alignment explanation
Indices: 253997--254064 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
253987 TTTTTTTTAC
* *
253997 TGTTTTGGTGCTTTTTTCACTGTTTTAATGT
1 TGTTTTAGTGCTTTTTTCACTGTTTTAATAT
* * *
254028 TGTTTTAGTGTTTTTTTTACTGTTTTACTAT
1 TGTTTTAGTGCTTTTTTCACTGTTTTAATAT
254059 TGTTTT
1 TGTTTT
254065 TGCTGTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.10, C:0.07, G:0.16, T:0.66
Consensus pattern (31 bp):
TGTTTTAGTGCTTTTTTCACTGTTTTAATAT
Found at i:254076 original size:12 final size:12
Alignment explanation
Indices: 254061--254137 Score: 88
Period size: 12 Copynumber: 6.7 Consensus size: 12
254051 TTTACTATTG
*
254061 TTTTTGCTGTTA
1 TTTTTGTTGTTA
*
254073 TTTTTGTTGTTG
1 TTTTTGTTGTTA
254085 TTTTTGTTGTTA
1 TTTTTGTTGTTA
*
254097 --TTTG-TGTTG
1 TTTTTGTTGTTA
*
254106 TTTTTGTTGTTG
1 TTTTTGTTGTTA
*
254118 TTTTGGTTGTTA
1 TTTTTGTTGTTA
254130 TTTTTGTT
1 TTTTTGTT
254138 ATTTGGACGT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 4 0.07
12 43 0.78
ACGTcount: A:0.04, C:0.01, G:0.22, T:0.73
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:254077 original size:24 final size:24
Alignment explanation
Indices: 254050--254099 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
254040 TTTTTTACTG
254050 TTTTACTATTGTTTTTGCTGTTAT
1 TTTTACTATTGTTTTTGCTGTTAT
** * *
254074 TTTTGTTGTTGTTTTTGTTGTTAT
1 TTTTACTATTGTTTTTGCTGTTAT
254098 TT
1 TT
254100 GTGTTGTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.08, C:0.04, G:0.16, T:0.72
Consensus pattern (24 bp):
TTTTACTATTGTTTTTGCTGTTAT
Found at i:254095 original size:33 final size:33
Alignment explanation
Indices: 254058--254141 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
254048 TGTTTTACTA
*
254058 TTGTT-TTTGCTGTTATTTTTGTTGTTGTTTTTG
1 TTGTTATTTG-TGTTATTTTTGTTGTTGTTTTGG
*
254091 TTGTTATTTGTGTTGTTTTTGTTGTTGTTTTGG
1 TTGTTATTTGTGTTATTTTTGTTGTTGTTTTGG
*
254124 TTGTTATTTTTGTTATTT
1 TTGTTATTTGTGTTATTT
254142 GGACGTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 42 0.91
34 4 0.09
ACGTcount: A:0.05, C:0.01, G:0.21, T:0.73
Consensus pattern (33 bp):
TTGTTATTTGTGTTATTTTTGTTGTTGTTTTGG
Found at i:254126 original size:9 final size:10
Alignment explanation
Indices: 254074--254128 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 10
254064 TTGCTGTTAT
254074 TTTTGTTGTTG
1 TTTTG-TGTTG
254085 TTTT-TGTTG
1 TTTTGTGTTG
254094 TTATTTGTGTTG
1 -T-TTTGTGTTG
254106 TTTTTGTTGTTG
1 -TTTTG-TGTTG
254118 TTTTG-GTTG
1 TTTTGTGTTG
254127 TT
1 TT
254129 ATTTTTGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
9 11 0.28
10 1 0.03
11 16 0.40
12 12 0.30
ACGTcount: A:0.02, C:0.00, G:0.25, T:0.73
Consensus pattern (10 bp):
TTTTGTGTTG
Found at i:255357 original size:23 final size:22
Alignment explanation
Indices: 255331--255389 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
255321 CATAAGGCAG
255331 AAGCGTGCCACAAAGCAAAGAAA
1 AAGCGTGCCACAAAGCAAAG-AA
* * * *
255354 AAGCGTGCTACAAGGCAGAGGA
1 AAGCGTGCCACAAAGCAAAGAA
*
255376 AAGTGTGCCACAAA
1 AAGCGTGCCACAAA
255390 TGCAGATAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.44, C:0.20, G:0.27, T:0.08
Consensus pattern (22 bp):
AAGCGTGCCACAAAGCAAAGAA
Found at i:256534 original size:30 final size:30
Alignment explanation
Indices: 256517--256771 Score: 275
Period size: 30 Copynumber: 8.6 Consensus size: 30
256507 AGAAGTTCGA
* *
256517 GGGTTAAAATGTGATTTTGAAAAAGTTTAG
1 GGGTTAAAATATGATTTTGGAAAAGTTTAG
*
256547 AGGTTAAAATATGA-TTTGGAAAAGTTTAG
1 GGGTTAAAATATGATTTTGGAAAAGTTTAG
* *
256576 GGGTTAAAATATTATTTTAGAAAAGTTTAG
1 GGGTTAAAATATGATTTTGGAAAAGTTTAG
* * * *
256606 AGGTCAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTTAAAATATGATTTTGGAAAAGTTTAG
* *
256636 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTTAAAATATGATTTTGGAAAAGTTTAG
*
256666 GGGTTAAAATATGATTTTGGAAAAGCTTAG
1 GGGTTAAAATATGATTTTGGAAAAGTTTAG
* * * * *
256696 GGGTCAAAATCTAATTTTGAAAAAGCTT-G
1 GGGTTAAAATATGATTTTGGAAAAGTTTAG
* * *
256725 GAGGTTAAAATGTAATTTTGGAAAA-ATTA-
1 G-GGTTAAAATATGATTTTGGAAAAGTTTAG
* *
256754 AGGTTAAAATATAATTTT
1 GGGTTAAAATATGATTTT
256772 AGAAGAGTGT
Statistics
Matches: 196, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
28 16 0.08
29 30 0.15
30 150 0.77
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.36
Consensus pattern (30 bp):
GGGTTAAAATATGATTTTGGAAAAGTTTAG
Found at i:256689 original size:90 final size:90
Alignment explanation
Indices: 256499--256775 Score: 348
Period size: 90 Copynumber: 3.1 Consensus size: 90
256489 ATGAAAATGA
* * * * * * *
256499 AATTTTAGAGAAG-TTCGAGGGTTAAAATGTGATTTTGAAAAAGTTTAGAGGTTAAAATATGA-T
1 AATTTTAGAAAAGCTTAGA-GGTCAAAATGTAATTTTGAAAAAGTTTAGGGGTTAAAATGTAATT
256562 TTGGAAAAGTTTAGGGGTTAAAATAT
65 TTGGAAAAGTTTAGGGGTTAAAATAT
* * *
256588 TATTTTAGAAAAGTTTAGAGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTT
1 AATTTTAGAAAAGCTTAGAGGTCAAAATGTAATTTTGAAAAAGTTTAGGGGTTAAAATGTAATTT
256653 TGGAAAAGTTTAGGGGTTAAAATAT
66 TGGAAAAGTTTAGGGGTTAAAATAT
* * * * *
256678 GATTTTGGAAAAGCTTAGGGGTCAAAATCTAATTTTGAAAAAGCTT-GGAGGTTAAAATGTAATT
1 AATTTTAGAAAAGCTTAGAGGTCAAAATGTAATTTTGAAAAAGTTTAGG-GGTTAAAATGTAATT
* *
256742 TTGGAAAA-ATTA-AGGTTAAAATAT
65 TTGGAAAAGTTTAGGGGTTAAAATAT
256766 AATTTTAGAA
1 AATTTTAGAA
256776 GAGTGTGGAC
Statistics
Matches: 165, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
88 19 0.12
89 53 0.32
90 93 0.56
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (90 bp):
AATTTTAGAAAAGCTTAGAGGTCAAAATGTAATTTTGAAAAAGTTTAGGGGTTAAAATGTAATTT
TGGAAAAGTTTAGGGGTTAAAATAT
Found at i:259080 original size:49 final size:49
Alignment explanation
Indices: 259001--259406 Score: 276
Period size: 49 Copynumber: 8.3 Consensus size: 49
258991 CCATAGTGAT
* * * * *
259001 TTAAACCTTTCCCTCCATATCTTC-GTGGTACTAGATTTGCCGTTGCGGC
1 TTAAATCTTTCCCTTCAT-GCTTCTGAGGTACTAGATTTGCCGTTGCGAC
* * * * *
259050 TTAAATCTTTCCTTTCATGCTTCTAAGGTACAAGGTTTGTCGTTGCGAC
1 TTAAATCTTTCCCTTCATGCTTCTGAGGTACTAGATTTGCCGTTGCGAC
* * * ** *
259099 TTAAACCTTTCCCTCCATG-TTCTCGTGGTACTAGATTTGCCGTTTTGGC
1 TTAAATCTTTCCCTTCATGCTTCT-GAGGTACTAGATTTGCCGTTGCGAC
* ** *
259148 TTAAATATTTTTCTTCATGCTTTTGAGGTAC-A-ATGTTCGCCGTTGCGAC
1 TTAAATCTTTCCCTTCATGCTTCTGAGGTACTAGAT-TT-GCCGTTGCGAC
* * * * * * *
259197 TTAAATCTTTCCC-TCTAT-ATCCTTATGGTACTGGATTCGTCGTTGCGGC
1 TTAAATCTTTCCCTTC-ATGCTTCTGA-GGTACTAGATTTGCCGTTGCGAC
* *
259246 TTAAATCTTTCCCTTCATGCTTCTGAGGTAC-A-ATGTTCGCCGTTACAAC
1 TTAAATCTTTCCCTTCATGCTTCTGAGGTACTAGAT-TT-GCCGTTGCGAC
* * * * * * * * *
259295 TTAAACCATTCCCTCCATG-TCCTCGTGGTAGTGGATTCGCCGTTGCGGC
1 TTAAATCTTTCCCTTCATGCTTCT-GAGGTACTAGATTTGCCGTTGCGAC
*
259344 TTAAATCTTTCCCTTCATGCTTTTGAGGTAC-A-ATGTTCGCCGTTGCGAC
1 TTAAATCTTTCCCTTCATGCTTCTGAGGTACTAGAT-TT-GCCGTTGCGAC
*
259393 TTAAACCTTTCCCT
1 TTAAATCTTTCCCT
259407 CCATATATTC
Statistics
Matches: 265, Mismatches: 73, Indels: 38
0.70 0.19 0.10
Matches are distributed among these distances:
47 6 0.02
48 21 0.08
49 221 0.83
50 13 0.05
51 4 0.02
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (49 bp):
TTAAATCTTTCCCTTCATGCTTCTGAGGTACTAGATTTGCCGTTGCGAC
Found at i:259083 original size:98 final size:98
Alignment explanation
Indices: 258958--259422 Score: 551
Period size: 98 Copynumber: 4.7 Consensus size: 98
258948 CGGTCGTAAC
* * * * * * *
258958 CTTTACCTTT-ATGTTTCTGAAGTACAAGGTTCGCCATAGTGATTTAAACCTTTCCCTCCATATC
1 CTTT-CCTTTCATGCTTCTGAGGTACAATGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATC
*
259022 TTCGTGGTACTAGATTTGCCGTTGCGGCTTAAAT
65 TTCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * * *
259056 CTTTCCTTTCATGCTTCTAAGGTACAAGGTTTGTCGTTGCGACTTAAACCTTTCCCTCCATGT-T
1 CTTTCCTTTCATGCTTCTGAGGTACAATGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCT
* **
259120 CTCGTGGTACTAGATTTGCCGTTTTGGCTTAAAT
66 -TCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * * *
259154 ATTT-TTCTTCATGCTTTTGAGGTACAATGTTCGCCGTTGCGACTTAAATCTTTCCCTCTATATC
1 CTTTCCT-TTCATGCTTCTGAGGTACAATGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATAT-
* * *
259218 CTT-ATGGTACTGGATTCGTCGTTGCGGCTTAAAT
64 CTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * * * * *
259252 CTTTCCCTTCATGCTTCTGAGGTACAATGTTCGCCGTTACAACTTAAACCATTCCCTCCATGTCC
1 CTTTCCTTTCATGCTTCTGAGGTACAATGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCT
* *
259317 TCGTGGTAGTGGATTCGCCGTTGCGGCTTAAAT
66 TCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
* * *
259350 CTTTCCCTTCATGCTTTTGAGGTACAATGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATAT
1 CTTTCCTTTCATGCTTCTGAGGTACAATGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCT
259415 TCGTGGTA
66 TCGTGGTA
259423 ATGAAACCTA
Statistics
Matches: 311, Mismatches: 49, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
97 9 0.03
98 300 0.96
99 1 0.00
100 1 0.00
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (98 bp):
CTTTCCTTTCATGCTTCTGAGGTACAATGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCT
TCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
Found at i:260268 original size:13 final size:13
Alignment explanation
Indices: 260250--260276 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
260240 CCTTGACCTC
260250 TCATTTTTCTTTT
1 TCATTTTTCTTTT
260263 TCATTTTTCTTTT
1 TCATTTTTCTTTT
260276 T
1 T
260277 TCCTCATTTT
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:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (13 bp):
TCATTTTTCTTTT
Found at i:261648 original size:16 final size:17
Alignment explanation
Indices: 261618--261652 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
261608 ACATAGAAAC
*
261618 AAAAATGTGATTCAAAG
1 AAAAATGTGAATCAAAG
261635 AAAAAT-TGAATCAAAG
1 AAAAATGTGAATCAAAG
261651 AA
1 AA
261653 TCGTTAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.60, C:0.06, G:0.14, T:0.20
Consensus pattern (17 bp):
AAAAATGTGAATCAAAG
Done.