Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014983.1 Kokia drynarioides strain JFW-HI SEQ_130027, 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: 486004
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 339 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:38 original size:20 final size:19
Alignment explanation
Indices: 6--51 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
1 ATCTG
*
6 TTAAAAATTAAATAAAATT
1 TTAAAAATAAAATAAAATT
*
25 TTAATAAATAAAATACAATT
1 TTAA-AAATAAAATAAAATT
45 TTAAAAA
1 TTAAAAA
52 GATATCATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAAAAATAAAATAAAATT
Found at i:112 original size:4 final size:4
Alignment explanation
Indices: 103--160 Score: 55
Period size: 4 Copynumber: 14.0 Consensus size: 4
93 TTATTTCATT
* * *
103 TTTC TTTC TTTCC TCTCC TTT- TTCC TTCC TTTC TTTC TTTTC TTTC TTTC
1 TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC
153 TTTC TTTC
1 TTTC TTTC
161 CCATTTATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
3 2 0.04
4 35 0.76
5 8 0.17
6 1 0.02
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:144 original size:9 final size:9
Alignment explanation
Indices: 102--159 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
92 TTTATTTCAT
102 TTTTCTTTC
1 TTTTCTTTC
* *
111 TTTCCTCTCC
1 TTTTCT-TTC
*
121 TTTTTCCTTC
1 -TTTTCTTTC
*
131 CTTTCTTTC
1 TTTTCTTTC
140 TTTTCTTTC
1 TTTTCTTTC
149 -TTTCTTTC
1 TTTTCTTTC
157 TTT
1 TTT
160 CCCATTTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
8 8 0.21
9 22 0.58
10 4 0.11
11 4 0.11
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:155 original size:21 final size:20
Alignment explanation
Indices: 101--161 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
91 CTTTATTTCA
*
101 TTTTTCTTTCTTTCCTCTCCT
1 TTTTTCTTTCTTT-CTTTCCT
* * *
122 TTTTCCTTCCTTTCTTTCTT
1 TTTTTCTTTCTTTCTTTCCT
142 TTCTTTCTTTCTTTCTTTCC
1 TT-TTTCTTTCTTTCTTTCC
162 CATTTATTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 7 0.22
21 25 0.78
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTCTTTCTTTCTTTCCT
Found at i:2103 original size:24 final size:24
Alignment explanation
Indices: 2058--2103 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
2048 TATATTTTTA
* * *
2058 ATATAAATACTTACCTTTTTTAGG
1 ATATAAATACTTAACATATTTAGG
*
2082 ATATAAATATTTAACATATTTA
1 ATATAAATACTTAACATATTTA
2104 AGTATACATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (24 bp):
ATATAAATACTTAACATATTTAGG
Found at i:2609 original size:23 final size:23
Alignment explanation
Indices: 2569--2615 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2559 TTTTTAAAAA
*
2569 AATATTTATATTATTTTTAATTT
1 AATATTTATAATATTTTTAATTT
*
2592 AATATTTAATAAT-TTTTTTATTT
1 AATATTT-ATAATATTTTTAATTT
2615 A
1 A
2616 TTAAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
AATATTTATAATATTTTTAATTT
Found at i:8332 original size:3 final size:3
Alignment explanation
Indices: 8309--8357 Score: 62
Period size: 3 Copynumber: 15.3 Consensus size: 3
8299 AGTTTATAAA
*
8309 AAG ACG AAG AGAG ACAG AAG AAG AAG AAG AAG AAG AAG AAG AAG CAAG
1 AAG AAG AAG A-AG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG
8357 A
1 A
8358 TAGGAAGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
3 32 0.78
4 9 0.22
ACGTcount: A:0.61, C:0.06, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:10915 original size:6 final size:6
Alignment explanation
Indices: 10904--10941 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
10894 TTGCATCACC
10904 CTGTCT CTGTCT CTGTCT CTGTCT CTGTCT CTGTCT CT
1 CTGTCT CTGTCT CTGTCT CTGTCT CTGTCT CTGTCT CT
10942 CACTTGCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.16, T:0.50
Consensus pattern (6 bp):
CTGTCT
Found at i:17986 original size:24 final size:26
Alignment explanation
Indices: 17947--18002 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
17937 GTGTGTCTCG
17947 TATTTTTCTTCTAGTTAAACTTC-GA-
1 TATTTTTCTTCTAGTTAAA-TTCTGAT
*
17972 TATTTTTTTTC-AGTTAAATTCTGAT
1 TATTTTTCTTCTAGTTAAATTCTGAT
17997 TATTTT
1 TATTTT
18003 AGAGATATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 3 0.11
24 9 0.32
25 16 0.57
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.59
Consensus pattern (26 bp):
TATTTTTCTTCTAGTTAAATTCTGAT
Found at i:41483 original size:17 final size:17
Alignment explanation
Indices: 41461--41494 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41451 TAATTAAATT
*
41461 TTAAAAATTATATAAAA
1 TTAAAAAATATATAAAA
41478 TTAAAAAATATATAAAA
1 TTAAAAAATATATAAAA
41495 AATAGAAATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAAAAATATATAAAA
Found at i:41616 original size:18 final size:18
Alignment explanation
Indices: 41595--41649 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
41585 AACTTCCTAT
41595 TTTTATAATTTTTTAAAA
1 TTTTATAATTTTTTAAAA
**
41613 TTTTATAATACTTTAATAA
1 TTTTATAATTTTTTAA-AA
41632 TTTT-TAATATTTTTAAAA
1 TTTTATAAT-TTTTTAAAA
41650 AAATTATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 20 0.65
19 11 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATAATTTTTTAAAA
Found at i:41922 original size:20 final size:20
Alignment explanation
Indices: 41897--41934 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41887 TCTAAATAGC
41897 AAAATTTCTATAATTTTTTT
1 AAAATTTCTATAATTTTTTT
* *
41917 AAAATTTTTATACTTTTT
1 AAAATTTCTATAATTTTT
41935 AATATGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
AAAATTTCTATAATTTTTTT
Found at i:42091 original size:19 final size:19
Alignment explanation
Indices: 42067--42137 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
42057 TTAAATAATA
42067 TTTTATAATTTTCCTAGAT
1 TTTTATAATTTTCCTAGAT
**
42086 TTTTATAATATTTAATAG-T
1 TTTTATAAT-TTTCCTAGAT
* * *
42105 ATTTATAGTTTTCCTATAAT
1 TTTTATAATTTTCCTA-GAT
42125 TTTTAT-ATTTTCC
1 TTTTATAATTTTCC
42138 AAAAAATATA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
18 5 0.12
19 23 0.57
20 12 0.30
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.59
Consensus pattern (19 bp):
TTTTATAATTTTCCTAGAT
Found at i:58912 original size:9 final size:9
Alignment explanation
Indices: 58898--58931 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
58888 CAAACTACCT
58898 TTTTTTAAA
1 TTTTTTAAA
*
58907 TTTTTTTAAT
1 -TTTTTTAAA
58917 TTTTTTAAA
1 TTTTTTAAA
58926 TTTTTT
1 TTTTTT
58932 TATTTTATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:58912 original size:10 final size:10
Alignment explanation
Indices: 58897--58933 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
58887 CCAAACTACC
58897 TTTTTTTAAA
1 TTTTTTTAAA
58907 TTTTTTT-AA
1 TTTTTTTAAA
58916 TTTTTTTAAA
1 TTTTTTTAAA
58926 TTTTTTTA
1 TTTTTTTA
58934 TTTTATCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:58921 original size:19 final size:18
Alignment explanation
Indices: 58897--58937 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
58887 CCAAACTACC
58897 TTTTTTTAAATTTTTTTAA
1 TTTTTTTAAATTTTTTT-A
58916 TTTTTTTAAATTTTTTTA
1 TTTTTTTAAATTTTTTTA
58934 TTTT
1 TTTT
58938 ATCTTGACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTTAAATTTTTTTA
Found at i:63079 original size:17 final size:17
Alignment explanation
Indices: 63045--63105 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
63035 ATTTAATTGC
*
63045 ATTTTTATTCAAAATAAT
1 ATTTTTATT-AAATTAAT
*
63063 ATTTTTAATAAATTAAT
1 ATTTTTATTAAATTAAT
* * *
63080 AATTTATGTTATATTAAT
1 -ATTTTTATTAAATTAAT
63098 ATTTTTAT
1 ATTTTTAT
63106 GCATTTATTT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
17 13 0.38
18 21 0.62
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTTTATTAAATTAAT
Found at i:63106 original size:19 final size:20
Alignment explanation
Indices: 63082--63136 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
63072 AAATTAATAA
63082 TTTATG-TTATATTAATATT
1 TTTATGATTATATTAATATT
*
63101 TTTATGCATT-TATTTTATATT
1 TTTATG-ATTATA-TTAATATT
*
63122 TTTATGTTTATATTA
1 TTTATGATTATATTA
63137 TATCATGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 6 0.21
21 17 0.59
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.65
Consensus pattern (20 bp):
TTTATGATTATATTAATATT
Found at i:63131 original size:27 final size:27
Alignment explanation
Indices: 63081--63132 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
63071 TAAATTAATA
*
63081 ATTTATGTTATATTAATATTTTTATGC
1 ATTTATGTTATATTAATATGTTTATGC
* **
63108 ATTTATTTTATATTTTTATGTTTAT
1 ATTTATGTTATATTAATATGTTTAT
63133 ATTATATCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (27 bp):
ATTTATGTTATATTAATATGTTTATGC
Found at i:63137 original size:19 final size:19
Alignment explanation
Indices: 63082--63139 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 19
63072 AAATTAATAA
63082 TTTATG-TTATATTAATATT
1 TTTATGTTTATATT-ATATT
*
63101 TTTATGCATTTATTTTATATT
1 TTTATG--TTTATATTATATT
63122 TTTATGTTTATATTATAT
1 TTTATGTTTATATTATAT
63140 CATGTTCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 17 0.50
21 11 0.32
22 6 0.18
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTATGTTTATATTATATT
Found at i:70438 original size:29 final size:30
Alignment explanation
Indices: 70385--70464 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
70375 ATATCAAAAC
*
70385 TATACATG-AACTCTTG-TTTAATGTGTAACTG
1 TATACATGAAACT-TTGATTT--TGTGCAACTG
*
70416 TATACAT-AAACTTTGATTTTGTGCAATTG
1 TATACATGAAACTTTGATTTTGTGCAACTG
*
70445 TATACATGAAATTTTGATTT
1 TATACATGAAACTTTGATTT
70465 GATTCAATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 15 0.35
30 14 0.33
31 14 0.33
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (30 bp):
TATACATGAAACTTTGATTTTGTGCAACTG
Found at i:70720 original size:29 final size:27
Alignment explanation
Indices: 70654--70720 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 27
70644 GAGCTTCACG
*
70654 TGTATAATTGCACCAAATTAAAATTCA
1 TGTATAATTGCACCAAATCAAAATTCA
* *
70681 TGTATACAATTGCACATTAAATCAAAGTTCA
1 TGTAT--AATTGCAC--CAAATCAAAATTCA
70712 TGTATAATT
1 TGTATAATT
70721 TTGAGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 5 0.15
29 12 0.36
31 16 0.48
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (27 bp):
TGTATAATTGCACCAAATCAAAATTCA
Found at i:71812 original size:21 final size:22
Alignment explanation
Indices: 71767--71815 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
71757 CTAAATATAA
* * *
71767 TTATATTAGTAATATTTTTATT
1 TTATTTTAGAAATATTTTTAAT
71789 TTATTTTAGAAATA-TTTTAAT
1 TTATTTTAGAAATATTTTTAAT
71810 TTATTT
1 TTATTT
71816 CAAATATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (22 bp):
TTATTTTAGAAATATTTTTAAT
Found at i:73802 original size:21 final size:21
Alignment explanation
Indices: 73763--73803 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
73753 TAGTATTTTC
*
73763 TAGATATTTTAATACTAAAAA
1 TAGATATTTTAATAATAAAAA
73784 TAGATATTTT-ATAAATAAAA
1 TAGATATTTTAAT-AATAAAA
73804 TATCATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
TAGATATTTTAATAATAAAAA
Found at i:73997 original size:13 final size:14
Alignment explanation
Indices: 73974--74002 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
73964 ACGAGGGTAT
73974 TTTTATATAAAATA
1 TTTTATATAAAATA
73988 TTTT-TATAAAATA
1 TTTTATATAAAATA
74001 TT
1 TT
74003 ACTATGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTATATAAAATA
Found at i:74672 original size:22 final size:22
Alignment explanation
Indices: 74638--74681 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
74628 TTTTGAGCAA
74638 TTTAATTTTTTCTTGTATGTTCT
1 TTTAATTTTTTCTT-TATGTTCT
*
74661 TTTAA-TTTTTCTTTATTTTCT
1 TTTAATTTTTTCTTTATGTTCT
74682 ATTCTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 8 0.40
23 5 0.25
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.73
Consensus pattern (22 bp):
TTTAATTTTTTCTTTATGTTCT
Found at i:83699 original size:119 final size:120
Alignment explanation
Indices: 83482--83720 Score: 444
Period size: 119 Copynumber: 2.0 Consensus size: 120
83472 TTTTCCTTCA
*
83482 CTGCTGCAATTCTGCAATAGGAGATGAAATCAATAAACTATTTTTTGAGTCAGAAAAAAAATCCA
1 CTGCTGCAATTCAGCAATAGGAGATGAAATCAATAAACTATTTTTTGAGTCAGAAAAAAAATCCA
83547 AAGACAAGCTGAGCGATGGGAAGAGACGATTAAAATAAAACAAGTAAAGAAGTAG
66 AAGACAAGCTGAGCGATGGGAAGAGACGATTAAAATAAAACAAGTAAAGAAGTAG
*
83602 CTGCTGCAATTCAGCAATAGGAGATGAAATCAATAAACT-TTTTTTGAGTCAGCAAAAAAATCCA
1 CTGCTGCAATTCAGCAATAGGAGATGAAATCAATAAACTATTTTTTGAGTCAGAAAAAAAATCCA
*
83666 AAGACAAGCTGAGCGATGGGAAGAGACGGTTAAAATAAAACAAGTAAAGAAGTAG
66 AAGACAAGCTGAGCGATGGGAAGAGACGATTAAAATAAAACAAGTAAAGAAGTAG
83721 AATATAATAG
Statistics
Matches: 116, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
119 78 0.67
120 38 0.33
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (120 bp):
CTGCTGCAATTCAGCAATAGGAGATGAAATCAATAAACTATTTTTTGAGTCAGAAAAAAAATCCA
AAGACAAGCTGAGCGATGGGAAGAGACGATTAAAATAAAACAAGTAAAGAAGTAG
Found at i:85380 original size:217 final size:211
Alignment explanation
Indices: 85133--85526 Score: 583
Period size: 210 Copynumber: 1.8 Consensus size: 211
85123 ACTCGTGATG
* * *
85133 CAAATTTAATCAATAACTTCAATATTAGTAAATATATATATGTATATATATACTCGCAAATGGAG
1 CAAACTTAATCAATAACTTAAATATTAGT--A-A-ATATA---ATATATATACTCGCAAATGAAG
* * *
85198 CCTTTAAATCTTACTTATTTAAAAGTGACACGTATCACATTTAAGGTGT-AATGAAAAATAAAAA
59 CCTTTAAATCTTACTTATTTAAAAGTGACACGAATCACATTTAAAGTATAAATGAAAAATAAAAA
* * * *
85262 AAAATGTAGAGGGAAAATTTTTAGACCAATTAAAAATCATCATCTCACATTATTGTTTATCTCTA
124 AAAATATAGAGAGAAAAATTTTAAACCAATTAAAAATCATCATCTCACATTATTGTTTATCTCTA
85327 ACTAAAGTGATGCTTGATTAATA
189 ACTAAAGTGATGCTTGATTAATA
* *
85350 CAAACTTAGTCAATAACTTAAATATTAGTAAATATAATATATATACTCGTAAATGAAGCCTTTAA
1 CAAACTTAATCAATAACTTAAATATTAGTAAATATAATATATATACTCGCAAATGAAGCCTTTAA
*
85415 ATCTTACTTATTTAAAAGTGACACGAATCACATTTAAAGTATAAATGGAAAATAAAAAAAAATAT
66 ATCTTACTTATTTAAAAGTGACACGAATCACATTTAAAGTATAAATGAAAAATAAAAAAAAATAT
* *
85480 AGAGAGAAAAATTTTAAACCAATTAAAAATCATCATTTGACATTATT
131 AGAGAGAAAAATTTTAAACCAATTAAAAATCATCATCTCACATTATT
85527 ATTTTTTTTC
Statistics
Matches: 161, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
210 66 0.41
211 62 0.39
213 5 0.03
214 1 0.01
215 1 0.01
217 26 0.16
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.33
Consensus pattern (211 bp):
CAAACTTAATCAATAACTTAAATATTAGTAAATATAATATATATACTCGCAAATGAAGCCTTTAA
ATCTTACTTATTTAAAAGTGACACGAATCACATTTAAAGTATAAATGAAAAATAAAAAAAAATAT
AGAGAGAAAAATTTTAAACCAATTAAAAATCATCATCTCACATTATTGTTTATCTCTAACTAAAG
TGATGCTTGATTAATA
Found at i:92130 original size:18 final size:18
Alignment explanation
Indices: 92091--92133 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
92081 GAATAGGTTT
*
92091 TTAATTAAATAATTTTAG
1 TTAATTAAATAATTTTAA
92109 TTAATTAAA-AATTTTAAA
1 TTAATTAAATAATTTT-AA
92127 TTAATTA
1 TTAATTA
92134 CACATGATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTAATTAAATAATTTTAA
Found at i:94314 original size:2 final size:2
Alignment explanation
Indices: 94307--94342 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
94297 TAATATAGTA
*
94307 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
94343 TGTTTTTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:117655 original size:19 final size:19
Alignment explanation
Indices: 117633--117672 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
117623 ATTCAATTGA
*
117633 TCGATTCGATTTCATCAAT
1 TCGATTCGATATCATCAAT
117652 TCGATTCGATATCATCAAT
1 TCGATTCGATATCATCAAT
117671 TC
1 TC
117673 CTTTTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.40
Consensus pattern (19 bp):
TCGATTCGATATCATCAAT
Found at i:125654 original size:25 final size:25
Alignment explanation
Indices: 125561--125656 Score: 68
Period size: 25 Copynumber: 3.6 Consensus size: 25
125551 GTTATTAAAT
* * * *
125561 TTTAATAAGATTATTATTAAATATAT
1 TTTAATAA-AATAATATTAAATACAA
*
125587 TTTAATAAAATAATA-AATAATATCATA
1 TTTAATAAAATAATATTA-AATA-CA-A
* *
125614 TTGTAACATAATTAATATTAAATACAA
1 TT-TAATA-AAATAATATTAAATACAA
125641 TTTAATAAAATAATAT
1 TTTAATAAAATAATAT
125657 ATGAATTAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
24 1 0.02
25 17 0.31
26 13 0.24
27 5 0.09
28 6 0.11
29 11 0.20
30 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (25 bp):
TTTAATAAAATAATATTAAATACAA
Found at i:125725 original size:58 final size:57
Alignment explanation
Indices: 125570--125725 Score: 137
Period size: 54 Copynumber: 2.7 Consensus size: 57
125560 TTTTAATAAG
* * * *
125570 ATTATTATTAAATATATTTTAATAAAATAAT-A-A-ATAATATCATATTGTAACATA
1 ATTAATATTAAATACAATTTAATAAAATAATAATATATAATAACATATTGTAACATA
*
125624 ATTAATATTAAATACAATTTAATAAAATAAT-ATATGAATTAATAACAT-TCT-TAATATA
1 ATTAATATTAAATACAATTTAATAAAATAATAATAT--A-TAATAACATAT-TGTAACATA
* *
125682 ATTAGTATTAAAGTATGAA-TTAATAAAAATAATAATATATAATA
1 ATTAATATTAAA-TA-CAATTTAAT-AAAATAATAATATATAATA
125726 TTATAAAAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
54 29 0.34
55 1 0.01
58 24 0.28
59 17 0.20
60 10 0.12
61 4 0.05
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (57 bp):
ATTAATATTAAATACAATTTAATAAAATAATAATATATAATAACATATTGTAACATA
Found at i:128930 original size:18 final size:19
Alignment explanation
Indices: 128893--128930 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
128883 TATCTCTAAT
*
128893 TAAATAAATTAATAAAAGA
1 TAAATAAATAAATAAAAGA
*
128912 TAAAT-AATAAATGAAAGA
1 TAAATAAATAAATAAAAGA
128930 T
1 T
128931 CCTAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (19 bp):
TAAATAAATAAATAAAAGA
Found at i:129327 original size:31 final size:30
Alignment explanation
Indices: 129289--129353 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
129279 AAAACCCTTG
* * *
129289 GATCCAAATTTTTTTCCAAACTCAGCTTCAA
1 GATCCAAA-CTTTCTCCAAACTCAACTTCAA
*
129320 GATCCAAACTTTCTCTAAACTCAACTTCAA
1 GATCCAAACTTTCTCCAAACTCAACTTCAA
129350 GATC
1 GATC
129354 AAGTCTCGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (30 bp):
GATCCAAACTTTCTCCAAACTCAACTTCAA
Found at i:131166 original size:28 final size:27
Alignment explanation
Indices: 131128--131194 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
131118 ATATATATTT
*
131128 TTTTAA-ATTTTATACTTCTTT-AATAA
1 TTTTAATATTTT-TAATTCTTTAAATAA
*
131154 TTTTAATGATTTTTAATTTTTTAAATAA
1 TTTTAAT-ATTTTTAATTCTTTAAATAA
*
131182 TTTTTATATTTTT
1 TTTTAATATTTTT
131195 TTGAATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 6 0.17
27 13 0.37
28 16 0.46
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (27 bp):
TTTTAATATTTTTAATTCTTTAAATAA
Found at i:131195 original size:28 final size:28
Alignment explanation
Indices: 131127--131211 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 28
131117 AATATATATT
* * * *
131127 TTTTTAAATTTTATACTTCTTT-AATAA
1 TTTTTATATTTTTTAATTTTTTAAATAA
*
131154 TTTTAATGA-TTTTTAATTTTTTAAATAA
1 TTTTTAT-ATTTTTTAATTTTTTAAATAA
131182 TTTTTATATTTTTTTGAA-TTTTTAAA-AA
1 TTTTTATA-TTTTTT-AATTTTTTAAATAA
131210 TT
1 TT
131212 AAAAAAATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
27 16 0.34
28 16 0.34
29 13 0.28
30 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTTATATTTTTTAATTTTTTAAATAA
Found at i:141013 original size:13 final size:13
Alignment explanation
Indices: 140995--141036 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
140985 TTACACATCA
*
140995 AATGATCTGATCC
1 AATGATCTAATCC
141008 AATGATCATAAT-C
1 AATGATC-TAATCC
141021 AATGAATCTAATCC
1 AATG-ATCTAATCC
141035 AA
1 AA
141037 AATTTAGAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (13 bp):
AATGATCTAATCC
Found at i:141162 original size:48 final size:48
Alignment explanation
Indices: 141107--141201 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
141097 AGGTGTTCCG
* *
141107 ATCCCTTTGTTCTCGGCTCCAGCCACCGCTCGGATTCCCGTAATCTCT
1 ATCCCTTTGTTCTCGACTCCAGCCACCACTCGGATTCCCGTAATCTCT
** *
141155 ATCCCTTTGTTCTCGACTCCAGCTGCCACTTGGATTCCCGTAATCTC
1 ATCCCTTTGTTCTCGACTCCAGCCACCACTCGGATTCCCGTAATCTC
141202 GACTCTTCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.14, C:0.38, G:0.16, T:0.33
Consensus pattern (48 bp):
ATCCCTTTGTTCTCGACTCCAGCCACCACTCGGATTCCCGTAATCTCT
Found at i:148901 original size:31 final size:31
Alignment explanation
Indices: 148864--148924 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
148854 GGAAATTTTT
*
148864 AAAATGCAAGCA-TTTTAAATTTCATTGTTTC
1 AAAATGCAAGCAGTTTT-AATTACATTGTTTC
*
148895 AAAATGCTAGCAGTTTTAATTACATTGTTT
1 AAAATGCAAGCAGTTTTAATTACATTGTTT
148925 AGATAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (31 bp):
AAAATGCAAGCAGTTTTAATTACATTGTTTC
Found at i:153887 original size:21 final size:21
Alignment explanation
Indices: 153863--153904 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
153853 ATAACATTTC
153863 AATAACTTAAATAATT-TTTTA
1 AATAA-TTAAATAATTATTTTA
*
153884 AATAATTTAATAATTATTTTA
1 AATAATTAAATAATTATTTTA
153905 TAAACTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AATAATTAAATAATTATTTTA
Found at i:160915 original size:8 final size:7
Alignment explanation
Indices: 160881--160914 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
160871 TCTCTCTTGT
160881 TTTTTTG
1 TTTTTTG
160888 TTTTTTG
1 TTTTTTG
160895 TTTTTTG
1 TTTTTTG
160902 TTTTTTG
1 TTTTTTG
160909 TTTTTT
1 TTTTTT
160915 TCTATAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTTG
Found at i:162562 original size:15 final size:16
Alignment explanation
Indices: 162542--162571 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
162532 TAATCAATTT
162542 AAAATTTTAA-AAAAG
1 AAAATTTTAATAAAAG
162557 AAAATTTTAATAAAA
1 AAAATTTTAATAAAA
162572 TCCGAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAATTTTAATAAAAG
Found at i:166077 original size:29 final size:28
Alignment explanation
Indices: 166019--166078 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
166009 TACATAAAAA
*
166019 TTTAGTTTTTTACTTAAATATAGTAGTT
1 TTTAGTTTTTTACTAAAATATAGTAGTT
166047 TTTAGTATTATTTACTAAAATA-AGTA-TT
1 TTTAGT-TT-TTTACTAAAATATAGTAGTT
166075 TTTA
1 TTTA
166079 AAAGTTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 12 0.41
29 6 0.21
30 11 0.38
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.55
Consensus pattern (28 bp):
TTTAGTTTTTTACTAAAATATAGTAGTT
Found at i:166086 original size:29 final size:31
Alignment explanation
Indices: 166022--166088 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 31
166012 ATAAAAATTT
* * **
166022 AGTTTTTTACTTAAATATAGTAGTTTTTAGT
1 AGTTATTTACTAAAATATAGTAGTTTTTAAA
166053 A-TTATTTACTAAAATA-AGTA-TTTTTAAA
1 AGTTATTTACTAAAATATAGTAGTTTTTAAA
166081 AGTTATTT
1 AGTTATTT
166089 TTTTAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 7 0.23
29 10 0.32
30 13 0.42
31 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (31 bp):
AGTTATTTACTAAAATATAGTAGTTTTTAAA
Found at i:167613 original size:36 final size:35
Alignment explanation
Indices: 167547--167621 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 35
167537 CAATAATTAA
*
167547 TTAATTTTTTTAAAATTAAAAATATATTTTTATATT
1 TTAACTTTTTTAAAATTAAAAATATATTTTTAT-TT
*
167583 TTAACTTTTTTAATAATT-TAAATGAT-TTTTTATTT
1 TTAACTTTTTTAA-AATTAAAAAT-ATATTTTTATTT
167618 TTAA
1 TTAA
167622 AAATATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 6 0.17
36 23 0.66
37 6 0.17
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (35 bp):
TTAACTTTTTTAAAATTAAAAATATATTTTTATTT
Found at i:172899 original size:24 final size:24
Alignment explanation
Indices: 172869--172920 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
172859 CCATTGAAAT
172869 TTTTCATTTTA-CAGAAAATATAAA
1 TTTTCATTTTATCA-AAAATATAAA
*
172893 TTTTCATTTTATTAAAAATATAAA
1 TTTTCATTTTATCAAAAATATAAA
172917 TTTT
1 TTTT
172921 TAACATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTCATTTTATCAAAAATATAAA
Found at i:174032 original size:21 final size:22
Alignment explanation
Indices: 174006--174046 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
173996 TATCAATAAT
174006 TCAAAAA-ATA-CTGATACTTGA
1 TCAAAAAGATATC-GATACTTGA
174027 TCAAAAAGATATCGATACTT
1 TCAAAAAGATATCGATACTT
174047 TTTTGGCGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 10 0.56
23 1 0.06
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (22 bp):
TCAAAAAGATATCGATACTTGA
Found at i:174150 original size:22 final size:20
Alignment explanation
Indices: 174104--174141 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
174094 TTAAAATGAC
*
174104 AAAATCATTTCGACTTAATT
1 AAAATCATTTCAACTTAATT
*
174124 AAAATCATTTTAACTTAA
1 AAAATCATTTCAACTTAA
174142 CTTTAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
AAAATCATTTCAACTTAATT
Found at i:177283 original size:273 final size:275
Alignment explanation
Indices: 176796--177587 Score: 1394
Period size: 273 Copynumber: 2.9 Consensus size: 275
176786 AAAATATAAG
176796 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
1 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
*
176861 CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCAACTATAAGAAA
66 CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCCACTATAAGAAA
176926 ATGTCTTTTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACG
131 ATGTCTTTTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACG
*
176991 CGGGTGACCCGGGTTCGATCCCCGGCAGCGGCGTTTATATTTTTT-TTTTCTACCTATTCAACTA
196 CGGGTGACCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCAACTA
*
177055 TAAGAAA-ATGTCTT
261 TAAAAAAGATGTCTT
177069 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
1 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
177134 CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCCACTATAAGAAA
66 CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCCACTATAAGAAA
**
177199 ACCTCTTTTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACG
131 ATGTCTTTTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACG
*
177264 CGGGTGACCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTTAACTA
196 CGGGTGACCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCAACTA
177329 TAAAAAAGATGTCTT
261 TAAAAAAGATGTCTT
177344 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
1 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
*
177409 CCCGGGTTCGATCCCCGGCAACGGCGTTTATAATTTTTATTTTCTACCTATTCCACTATAAGAAA
66 CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCCACTATAAGAAA
* * * * * *
177474 ATGTCTTTTATAAGATTACCAACAAAGTCCTTGTAGCATAGTGGTAAATATTCCCGCTTGTCACG
131 ATGTCTTTTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACG
* * * *
177539 CGGTTGACCCGGGTTCGATCCACGAC-ACGG-GTTTTTTATTTTTTATTTT
196 CGGGTGACCCGGGTTCGATCCCCGGCAACGGCG-TTTATATTTTTTATTTT
177588 TCTAACTTTT
Statistics
Matches: 497, Mismatches: 19, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
273 237 0.48
274 44 0.09
275 216 0.43
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (275 bp):
TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCCACTATAAGAAA
ATGTCTTTTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACG
CGGGTGACCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCAACTA
TAAAAAAGATGTCTT
Found at i:177591 original size:137 final size:137
Alignment explanation
Indices: 176796--177587 Score: 1383
Period size: 137 Copynumber: 5.8 Consensus size: 137
176786 AAAATATAAG
176796 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
1 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
176861 CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCAACTATAAGAAA
66 CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCAACTATAAGAAA
176926 ATGTCTT
131 ATGTCTT
176933 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
1 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
*
176998 CCCGGGTTCGATCCCCGGCAGCGGCGTTTATATTTTTT-TTTTCTACCTATTCAACTATAAGAAA
66 CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCAACTATAAGAAA
177062 ATGTCTT
131 ATGTCTT
177069 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
1 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
*
177134 CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCCACTATAAGAAA
66 CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCAACTATAAGAAA
**
177199 ACCTCTT
131 ATGTCTT
177206 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
1 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
* *
177271 CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTTAACTATAAAAAA
66 CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCAACTATAAGAAA
177336 GATGTCTT
131 -ATGTCTT
177344 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
1 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
* *
177409 CCCGGGTTCGATCCCCGGCAACGGCGTTTATAATTTTTATTTTCTACCTATTCCACTATAAGAAA
66 CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCAACTATAAGAAA
177474 ATGTCTT
131 ATGTCTT
* * * * * * *
177481 TTATAAGATTACCAACAAAGTCCTTGTAGCATAGTGGTAAATATTCCCGCTTGTCACGCGGTTGA
1 TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
* * *
177546 CCCGGGTTCGATCCACGAC-ACGG-GTTTTTTATTTTTTATTTT
66 CCCGGGTTCGATCCCCGGCAACGGCG-TTTATATTTTTTATTTT
177588 TCTAACTTTT
Statistics
Matches: 627, Mismatches: 25, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
135 1 0.00
136 154 0.25
137 341 0.54
138 131 0.21
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (137 bp):
TTATAAGCTTACCAACAAGGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGA
CCCGGGTTCGATCCCCGGCAACGGCGTTTATATTTTTTATTTTCTACCTATTCAACTATAAGAAA
ATGTCTT
Found at i:178241 original size:29 final size:27
Alignment explanation
Indices: 178182--178267 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 27
178172 ATACATTTGA
178182 ACCACAATTAAAGTTTCACGTGTATAATTAC
1 ACCA-AATTAAAG-TTCA--TGTATAATTAC
178213 ACCAAATTAAAGTTCATGTATACTATTAC
1 ACCAAATTAAAGTTCATGTATA--ATTAC
* * *
178242 ACAAAAATCAAAATTCATGTATAATT
1 AC-CAAATTAAAGTTCATGTATAATT
178268 TTAAAATTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
27 6 0.12
28 3 0.06
29 11 0.22
30 25 0.51
31 4 0.08
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (27 bp):
ACCAAATTAAAGTTCATGTATAATTAC
Found at i:187348 original size:18 final size:17
Alignment explanation
Indices: 187327--187371 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
187317 GCTTAGAAAT
187327 TATTTTTTATCATACTAA
1 TATTTTTTATCA-ACTAA
* *
187345 TATTTTTATATTAATTAA
1 TATTTTT-TATCAACTAA
187363 TATTTTTTA
1 TATTTTTTA
187372 AAAATATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.08
18 18 0.75
19 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTTTTATCAACTAA
Found at i:195709 original size:15 final size:15
Alignment explanation
Indices: 195689--195738 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
195679 AAAAAGTCGA
* *
195689 TTCTTTCTTTTCTTC
1 TTCTTTCTTTCCATC
195704 TTCTTTCTTTCCATC
1 TTCTTTCTTTCCATC
195719 TTCTTCTTCTTTCCATC
1 TTC-T-TTCTTTCCATC
195736 TTC
1 TTC
195739 AAAAAGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 16 0.52
16 1 0.03
17 14 0.45
ACGTcount: A:0.04, C:0.32, G:0.00, T:0.64
Consensus pattern (15 bp):
TTCTTTCTTTCCATC
Found at i:195730 original size:17 final size:18
Alignment explanation
Indices: 195699--195738 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
195689 TTCTTTCTTT
195699 TCTTCTTCTTTCTTTCCA
1 TCTTCTTCTTTCTTTCCA
195717 TCTTCTTC-TTCTTTCCA
1 TCTTCTTCTTTCTTTCCA
195734 TCTTC
1 TCTTC
195739 AAAAAGTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.05, C:0.35, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTTCTTCTTTCTTTCCA
Found at i:204157 original size:24 final size:21
Alignment explanation
Indices: 204104--204158 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 21
204094 AACGAAAATT
204104 GAAGGAAA-AAAGAAAGAAAA
1 GAAGGAAAGAAAGAAAGAAAA
204124 -AAGTGAAAGAAAGAAAGAAGGAA
1 GAAG-GAAAGAAAGAAAGAA--AA
204147 GAAGGAGAAGAA
1 GAAGGA-AAGAA
204159 GGGGAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.10
20 4 0.14
21 10 0.34
23 4 0.14
24 8 0.28
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (21 bp):
GAAGGAAAGAAAGAAAGAAAA
Found at i:204485 original size:163 final size:162
Alignment explanation
Indices: 204297--204671 Score: 556
Period size: 175 Copynumber: 2.2 Consensus size: 162
204287 TTGATTAAAA
** *
204297 GAGTAAATTAAGAGGAGTGGAAGAAATGTAAGTTTAGTTAATATTTTAAGTAT-G-ATTAATTTT
1 GAGTAAATTAAGAGGAGAAGAAGAAATGTAAGTTTAGTTAAAATTTTAAGTATGGTATTAATTTT
204360 AAAATATTTTAATTTGTTAGTTAATTTGATTATTTTAAGTTTTTTGTTTTCTTTAATTTAATTTT
66 AAAATATTTTAATTTGTTAGTTAATTTGATTATTTTAAGTTTTTTGTTTTCTTTAATTTAATTTT
*
204425 TAATTGATTTGTTATTTAATGTTGTTATAGTTTGT
131 TAATTGATTTGTTATTTAATGTTGTTAT-G-GT-T
*
204460 GAGTAAATTAAGAGGAGAAGAAGAAATGTAAGTTTAATTAAAATTTTAAGTATGGTTAATTTTAA
1 GAGTAAATTAAGAGGAGAAGAAGAAATGTAAGTTTAGTTAAAATTTTAAGTATGG-------T--
204525 AATTAATTTTAAAATATTTTAATTTGTTAGTTAATTTGATTATTTTAAGTTTTTTGTTTTCTTTA
57 -ATTAATTTTAAAATATTTTAATTTGTTAGTTAATTTGATTATTTTAAGTTTTTTGTTTTCTTTA
204590 ATTTAATTTTTAATTGATTTGTTATTTAATGTTGTTATGGTT
121 ATTTAATTTTTAATTGATTTGTTATTTAATGTTGTTATGGTT
* *
204632 GAGTAAATTAAGAGGAGAATAAGAAATGTAAGTTTGGTTA
1 GAGTAAATTAAGAGGAGAAGAAGAAATGTAAGTTTAGTTA
204672 TTATGTTATT
Statistics
Matches: 192, Mismatches: 8, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
163 49 0.26
164 1 0.01
172 38 0.20
173 1 0.01
174 1 0.01
175 102 0.53
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (162 bp):
GAGTAAATTAAGAGGAGAAGAAGAAATGTAAGTTTAGTTAAAATTTTAAGTATGGTATTAATTTT
AAAATATTTTAATTTGTTAGTTAATTTGATTATTTTAAGTTTTTTGTTTTCTTTAATTTAATTTT
TAATTGATTTGTTATTTAATGTTGTTATGGTT
Found at i:204532 original size:12 final size:12
Alignment explanation
Indices: 204515--204539 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
204505 TTAAGTATGG
204515 TTAATTTTAAAA
1 TTAATTTTAAAA
204527 TTAATTTTAAAA
1 TTAATTTTAAAA
204539 T
1 T
204540 ATTTTAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATTTTAAAA
Found at i:204539 original size:175 final size:172
Alignment explanation
Indices: 204351--204666 Score: 587
Period size: 175 Copynumber: 1.8 Consensus size: 172
204341 TTTAAGTATG
204351 ATTAATTTTAAAATATTTTAATTTGTTAGTTAATTTGATTATTTTAAGTTTTTTGTTTTCTTTAA
1 ATTAATTTTAAAATATTTTAATTTGTTAGTTAATTTGATTATTTTAAGTTTTTTGTTTTCTTTAA
*
204416 TTTAATTTTTAATTGATTTGTTATTTAATGTTGTTATAGTTTGTGAGTAAATTAAGAGGAGAAGA
66 TTTAATTTTTAATTGATTTGTTATTTAATGTTGTTAT-G-GT-TGAGTAAATTAAGAGGAGAAGA
204481 AGAAATGTAAGTTTAATTAAAATTTTAAGTATGGTTAATTTTAAA
128 AGAAATGTAAGTTTAATTAAAATTTTAAGTATGGTTAATTTTAAA
204526 ATTAATTTTAAAATATTTTAATTTGTTAGTTAATTTGATTATTTTAAGTTTTTTGTTTTCTTTAA
1 ATTAATTTTAAAATATTTTAATTTGTTAGTTAATTTGATTATTTTAAGTTTTTTGTTTTCTTTAA
*
204591 TTTAATTTTTAATTGATTTGTTATTTAATGTTGTTATGGTTGAGTAAATTAAGAGGAGAATAAGA
66 TTTAATTTTTAATTGATTTGTTATTTAATGTTGTTATGGTTGAGTAAATTAAGAGGAGAAGAAGA
204656 AATGTAAGTTT
131 AATGTAAGTTT
204667 GGTTATTATG
Statistics
Matches: 139, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
172 35 0.25
173 1 0.01
174 1 0.01
175 102 0.73
ACGTcount: A:0.33, C:0.01, G:0.14, T:0.52
Consensus pattern (172 bp):
ATTAATTTTAAAATATTTTAATTTGTTAGTTAATTTGATTATTTTAAGTTTTTTGTTTTCTTTAA
TTTAATTTTTAATTGATTTGTTATTTAATGTTGTTATGGTTGAGTAAATTAAGAGGAGAAGAAGA
AATGTAAGTTTAATTAAAATTTTAAGTATGGTTAATTTTAAA
Found at i:205493 original size:4 final size:4
Alignment explanation
Indices: 205484--205548 Score: 51
Period size: 4 Copynumber: 16.0 Consensus size: 4
205474 AAACACATTA
* * * * * *
205484 TCTT TCTT TCCT TC-T TCTT TCTG TCTT CTCCT TCTT CCTT TATT TCCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT -TCTT TCTT TCTT TCTT TCTT
205532 TCTTT TCTT TCTT TCTT
1 TC-TT TCTT TCTT TCTT
205549 CCCCGTTTAT
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
3 3 0.06
4 38 0.81
5 6 0.13
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.66
Consensus pattern (4 bp):
TCTT
Found at i:208371 original size:15 final size:16
Alignment explanation
Indices: 208351--208383 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
208341 TTAATCATAT
*
208351 TTAAATATGTATT-TA
1 TTAAATATATATTATA
208366 TTAAATATATATTATA
1 TTAAATATATATTATA
208382 TT
1 TT
208384 CTTATAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTAAATATATATTATA
Found at i:225105 original size:38 final size:39
Alignment explanation
Indices: 225051--225127 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 39
225041 TCTCTTTAAA
*
225051 TTTAATTTTGTGTTTTGAATTATTAATTTAATTATGATG
1 TTTAATTTTGTATTTTGAATTATTAATTTAATTATGATG
*
225090 TTTAA-TTTGTATTTTGCATTATTAATTTAATTATGATG
1 TTTAATTTTGTATTTTGAATTATTAATTTAATTATGATG
225128 AAGATGGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 31 0.86
39 5 0.14
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.58
Consensus pattern (39 bp):
TTTAATTTTGTATTTTGAATTATTAATTTAATTATGATG
Found at i:231726 original size:44 final size:44
Alignment explanation
Indices: 231667--231754 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
231657 CATGAATTGA
231667 TTTTTACAATGAGCATGATTGCTACATAGATGCATAGTAAGATT
1 TTTTTACAATGAGCATGATTGCTACATAGATGCATAGTAAGATT
231711 TTTTTACAATGAGCATGATTGCTACATAGATGCATAGTAAGATT
1 TTTTTACAATGAGCATGATTGCTACATAGATGCATAGTAAGATT
231755 CTATTTCTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (44 bp):
TTTTTACAATGAGCATGATTGCTACATAGATGCATAGTAAGATT
Found at i:233743 original size:12 final size:12
Alignment explanation
Indices: 233726--233750 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
233716 AAAGTTGGAT
233726 GGAGAATTAAAG
1 GGAGAATTAAAG
233738 GGAGAATTAAAG
1 GGAGAATTAAAG
233750 G
1 G
233751 ATAAATTTTT
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:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (12 bp):
GGAGAATTAAAG
Found at i:240950 original size:20 final size:20
Alignment explanation
Indices: 240914--240951 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
240904 ACCAAACATA
*
240914 TAAAATAATATTTATAAAAT
1 TAAAATAATATTGATAAAAT
240934 TAAAAT-ATATGTGATAAA
1 TAAAATAATAT-TGATAAA
240952 TTCTTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
TAAAATAATATTGATAAAAT
Found at i:241608 original size:12 final size:12
Alignment explanation
Indices: 241607--241640 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
241597 CCCACTCCCG
*
241607 CTCCCGCTTCCA
1 CTCCCGCTACCA
241619 CTCCCGCTACCA
1 CTCCCGCTACCA
*
241631 CTACCGCTAC
1 CTCCCGCTAC
241641 TCTCGCTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.56, G:0.09, T:0.21
Consensus pattern (12 bp):
CTCCCGCTACCA
Found at i:241609 original size:18 final size:18
Alignment explanation
Indices: 241588--241626 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
241578 TATCGCTACT
*
241588 GCTCTCGCTCCCACTCCC
1 GCTCCCGCTCCCACTCCC
*
241606 GCTCCCGCTTCCACTCCC
1 GCTCCCGCTCCCACTCCC
241624 GCT
1 GCT
241627 ACCACTACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.59, G:0.13, T:0.23
Consensus pattern (18 bp):
GCTCCCGCTCCCACTCCC
Found at i:244218 original size:23 final size:23
Alignment explanation
Indices: 244188--244234 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
244178 CGTAATCTCA
*
244188 TGTGTGATATTTTTGTATGAATT
1 TGTGTGATATTTTTGCATGAATT
*
244211 TGTGTGATATTTTTGCATTAATT
1 TGTGTGATATTTTTGCATGAATT
244234 T
1 T
244235 TCCTCTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.57
Consensus pattern (23 bp):
TGTGTGATATTTTTGCATGAATT
Found at i:249627 original size:29 final size:27
Alignment explanation
Indices: 249585--249643 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 27
249575 TAGCTGTCTA
*
249585 ATATATTTTTCAAACAATATTTCAAAT
1 ATATATTTTTCAAACAATATGTCAAAT
*
249612 ATATATTTATTCCAAATAATATGTCAAAT
1 ATATATTT-TT-CAAACAATATGTCAAAT
249641 ATA
1 ATA
249644 ACATTTAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 8 0.29
28 2 0.07
29 18 0.64
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (27 bp):
ATATATTTTTCAAACAATATGTCAAAT
Found at i:251308 original size:2 final size:2
Alignment explanation
Indices: 251301--251325 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
251291 ATACGTGTGC
251301 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
251326 AAGAGGTAGC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:257339 original size:14 final size:14
Alignment explanation
Indices: 257320--257348 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
257310 TAATCATCCA
257320 TTTCATGCGCATGG
1 TTTCATGCGCATGG
257334 TTTCATGCGCATGG
1 TTTCATGCGCATGG
257348 T
1 T
257349 GTATAAGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.28, T:0.38
Consensus pattern (14 bp):
TTTCATGCGCATGG
Found at i:259400 original size:18 final size:16
Alignment explanation
Indices: 259377--259421 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
259367 GAAAGAAAGG
259377 TAAGTTTAATTAATATTT
1 TAAGTTTAATT-A-ATTT
*
259395 TAAGTTTGATTAATTT
1 TAAGTTTAATTAATTT
*
259411 TAAATTTAATT
1 TAAGTTTAATT
259422 TTAAATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.54
17 1 0.04
18 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (16 bp):
TAAGTTTAATTAATTT
Found at i:280357 original size:15 final size:13
Alignment explanation
Indices: 280323--280347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
280313 TTAACTCTAA
280323 AAATTTAACACTT
1 AAATTTAACACTT
280336 AAATTTAACACT
1 AAATTTAACACT
280348 ATTTAATTTA
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:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTTAACACTT
Found at i:284603 original size:28 final size:29
Alignment explanation
Indices: 284534--284603 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 29
284524 GAATTAACAG
*
284534 CAAAATATTAGCATTTTAAATTGATACCT
1 CAAACTATTAGCATTTTAAATTGATACCT
*
284563 -AAACT-TTAAAGCATTTT-AATTGA-GCCTT
1 CAAACTATT--AGCATTTTAAATTGATACC-T
284591 CAAACTATTAGCA
1 CAAACTATTAGCA
284604 AGATTCTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
27 4 0.12
28 15 0.44
29 13 0.38
30 2 0.06
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (29 bp):
CAAACTATTAGCATTTTAAATTGATACCT
Found at i:290603 original size:3 final size:3
Alignment explanation
Indices: 290595--290625 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
290585 ACGTGAAATG
290595 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
290626 CTTAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:295586 original size:2 final size:2
Alignment explanation
Indices: 295579--295607 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
295569 TGCAAAGAAA
295579 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
295608 AATTACCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:296060 original size:27 final size:28
Alignment explanation
Indices: 296008--296066 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
295998 TGGACTTATT
*
296008 AAATTTAGTCATTTTTGCTTTAAGTTTTAG
1 AAATTTAG-CATTTTT-CTTTAAGTTTGAG
296038 AAATTTAG-ATTTTT-TTTATAGTTTGAG
1 AAATTTAGCATTTTTCTTTA-AGTTTGAG
296065 AA
1 AA
296067 TTGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 4 0.15
27 9 0.33
28 6 0.22
30 8 0.30
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (28 bp):
AAATTTAGCATTTTTCTTTAAGTTTGAG
Found at i:302469 original size:23 final size:23
Alignment explanation
Indices: 302439--302506 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
302429 TTAACACACT
*
302439 AAGTGCTAATCAAAGAGCACGCG
1 AAGTGCTAATCAAAGAGCACGAG
* *
302462 AAGTGCTAATAACAGAGAGAACGAG
1 AAGTGCTAAT--CAAAGAGCACGAG
* *
302487 ACGTGCTAAACAAAGAGCAC
1 AAGTGCTAATCAAAGAGCAC
302507 ACACATTGCT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
23 18 0.50
25 18 0.50
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (23 bp):
AAGTGCTAATCAAAGAGCACGAG
Found at i:302516 original size:23 final size:23
Alignment explanation
Indices: 302489--302546 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
302479 AGAACGAGAC
302489 GTGCTAAACA-AAGAGCACACACA
1 GTGCTAAACAGAA-AGCACACACA
* * * *
302512 TTGCTGAATAGAAAGTACACACA
1 GTGCTAAACAGAAAGCACACACA
302535 GTGCTAAACAGA
1 GTGCTAAACAGA
302547 TAGCGCGCTA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 25 0.93
24 2 0.07
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.16
Consensus pattern (23 bp):
GTGCTAAACAGAAAGCACACACA
Found at i:308899 original size:30 final size:30
Alignment explanation
Indices: 308821--308901 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 30
308811 AGGTCTTTAC
* * *
308821 ACTTTTTAAAATTTTGAAATTTAGTCTCTAT
1 ACTTTTT-AAATTTTAAAATTTAATCCCTAT
* *
308852 AC-TTTT--ATTATATAAATTTAATCCCTCT
1 ACTTTTTAAATTTTA-AAATTTAATCCCTAT
308880 ACTTTTTAAATTTTAAAATTTA
1 ACTTTTTAAATTTTAAAATTTA
308902 GGTCTCATTG
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
27 4 0.10
28 14 0.35
29 4 0.10
30 11 0.28
31 7 0.17
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (30 bp):
ACTTTTTAAATTTTAAAATTTAATCCCTAT
Found at i:310931 original size:2 final size:2
Alignment explanation
Indices: 310924--310952 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
310914 GCATATTTTA
310924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
310953 CACCGACCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:314230 original size:18 final size:19
Alignment explanation
Indices: 314207--314252 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
314197 GAATAAATTT
*
314207 TTAATTAAATAATT-TTAA
1 TTAATTAAATAATTCTAAA
*
314225 TTAATTGAA-AATTCTAAA
1 TTAATTAAATAATTCTAAA
314243 TTAATTAAAT
1 TTAATTAAAT
314253 TGAAAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
TTAATTAAATAATTCTAAA
Found at i:320906 original size:24 final size:24
Alignment explanation
Indices: 320873--321034 Score: 180
Period size: 24 Copynumber: 6.8 Consensus size: 24
320863 TTTTGGTTCC
* *
320873 AGTACTCCTGCCTTCGGTGCCACG
1 AGTACCCCTGCCTTTGGTGCCACG
* * *
320897 AGCACCCCTGCTTTTGGTGCCATG
1 AGTACCCCTGCCTTTGGTGCCACG
320921 AGTACCCCTGCCTTTGGTGCCACG
1 AGTACCCCTGCCTTTGGTGCCACG
* * *
320945 AGTGCCCCTGCTTTTGGTGCCACA
1 AGTACCCCTGCCTTTGGTGCCACG
* * *
320969 AATACCCCTGCCTTTGGTTCCATG
1 AGTACCCCTGCCTTTGGTGCCACG
* * *
320993 AGTACTCCAGCCTTTGGTGCCACA
1 AGTACCCCTGCCTTTGGTGCCACG
**
321017 AACACCCCTGCCTTTGGT
1 AGTACCCCTGCCTTTGGT
321035 TCGACTGGAA
Statistics
Matches: 111, Mismatches: 27, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 111 1.00
ACGTcount: A:0.15, C:0.35, G:0.22, T:0.28
Consensus pattern (24 bp):
AGTACCCCTGCCTTTGGTGCCACG
Found at i:321050 original size:48 final size:48
Alignment explanation
Indices: 320924--321057 Score: 144
Period size: 48 Copynumber: 2.8 Consensus size: 48
320914 TGCCATGAGT
* * ** * * * *
320924 ACCCCTGCCTTTGGTGCCACGAGTGCCCCTGCTTTTGGTGCCACAAAT
1 ACCCCTGCCTTTGGTTCCATGAGAACTCCAGCATTTGGTGCCACAAAC
* *
320972 ACCCCTGCCTTTGGTTCCATGAGTACTCCAGCCTTTGGTGCCACAAAC
1 ACCCCTGCCTTTGGTTCCATGAGAACTCCAGCATTTGGTGCCACAAAC
* *
321020 ACCCCTGCCTTTGGTTCGACTG-GAAGTCCAGCATTTGG
1 ACCCCTGCCTTTGGTTCCA-TGAGAACTCCAGCATTTGG
321058 GAGCACTGGA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
48 72 0.97
49 2 0.03
ACGTcount: A:0.16, C:0.34, G:0.22, T:0.28
Consensus pattern (48 bp):
ACCCCTGCCTTTGGTTCCATGAGAACTCCAGCATTTGGTGCCACAAAC
Found at i:321286 original size:24 final size:24
Alignment explanation
Indices: 321259--321385 Score: 164
Period size: 24 Copynumber: 5.3 Consensus size: 24
321249 CATTTGGTAG
* *
321259 CTTTGGTGCCACGAGCACTCCTGC
1 CTTTGGTGCCACAAGCACCCCTGC
* *
321283 CTTTGGTTCCACAAGCACTCCTGC
1 CTTTGGTGCCACAAGCACCCCTGC
**
321307 CTTTGGTGCCACGGGCACCCCTGC
1 CTTTGGTGCCACAAGCACCCCTGC
*
321331 CTTTGGTTCCACAAGCACCCCTGC
1 CTTTGGTGCCACAAGCACCCCTGC
* * *
321355 CTTTGGTGCTACCAGCACCCCGGC
1 CTTTGGTGCCACAAGCACCCCTGC
321379 CTTTGGT
1 CTTTGGT
321386 TCAACTGGAA
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 90 1.00
ACGTcount: A:0.13, C:0.39, G:0.23, T:0.26
Consensus pattern (24 bp):
CTTTGGTGCCACAAGCACCCCTGC
Found at i:321330 original size:48 final size:48
Alignment explanation
Indices: 321259--321387 Score: 204
Period size: 48 Copynumber: 2.7 Consensus size: 48
321249 CATTTGGTAG
* *
321259 CTTTGGTGCCACGAGCACTCCTGCCTTTGGTTCCACAAGCACTCCTGC
1 CTTTGGTGCCACGAGCACCCCTGCCTTTGGTTCCACAAGCACCCCTGC
*
321307 CTTTGGTGCCACGGGCACCCCTGCCTTTGGTTCCACAAGCACCCCTGC
1 CTTTGGTGCCACGAGCACCCCTGCCTTTGGTTCCACAAGCACCCCTGC
* * *
321355 CTTTGGTGCTACCAGCACCCCGGCCTTTGGTTC
1 CTTTGGTGCCACGAGCACCCCTGCCTTTGGTTC
321388 AACTGGAAGT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 74 1.00
ACGTcount: A:0.12, C:0.39, G:0.22, T:0.26
Consensus pattern (48 bp):
CTTTGGTGCCACGAGCACCCCTGCCTTTGGTTCCACAAGCACCCCTGC
Found at i:321495 original size:24 final size:24
Alignment explanation
Indices: 321467--321525 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
321457 AGGAGGCACA
321467 TTTGGAGCATCAAGCACACCTGCT
1 TTTGGAGCATCAAGCACACCTGCT
* **
321491 TTTGGCA-CTTCAAGCAGTCCTGCT
1 TTTGG-AGCATCAAGCACACCTGCT
321515 TTTGGAGCATC
1 TTTGGAGCATC
321526 TTCTACTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 27 0.93
25 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (24 bp):
TTTGGAGCATCAAGCACACCTGCT
Found at i:326242 original size:18 final size:18
Alignment explanation
Indices: 326219--326260 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
326209 ATTAAAGTTT
*
326219 TATTTTGATATTT-TTATA
1 TATTTTAAT-TTTATTATA
326237 TATTTTAATTTTATTATA
1 TATTTTAATTTTATTATA
*
326255 CATTTT
1 TATTTT
326261 TTATCACCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TATTTTAATTTTATTATA
Found at i:326713 original size:30 final size:30
Alignment explanation
Indices: 326677--326750 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
326667 ATAATTACAT
*
326677 TTTAATTTTAAAAAATTGATAAAAAT-TTAA
1 TTTAATTTTAAAAAATT-ATAAAAATAATAA
* *
326707 TTTAATTTTTTAAAAATTATTAAAATAATAA
1 TTTAA-TTTTAAAAAATTATAAAAATAATAA
326738 TATTACATTTTAA
1 T-TTA-ATTTTAA
326751 CTATCATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 12 0.33
31 15 0.42
32 8 0.22
33 1 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
TTTAATTTTAAAAAATTATAAAAATAATAA
Found at i:329140 original size:125 final size:127
Alignment explanation
Indices: 328837--329185 Score: 470
Period size: 125 Copynumber: 2.8 Consensus size: 127
328827 ATCAATGTTG
* * * * * *
328837 ACACTTGATTCCATTGATTTGATATTTCTGCCATGCCTTGGTGTTAACTGTGTTATGGCACGGTT
1 ACACTAGATTCCATCGATTTGATATTTCTGCCATGCCTTAGTGTTAACTGTGTGATGACATGGTT
* *
328902 GTTCTCGATGCTTGTTTGCTCTGTTGTTGGTACGGATATATATATATATCCGTACCTATGTCA
66 GTTCTCGATACTTGTTTGCTCTGTTGTTGGTAC-GAGATATATATATATCCGTACCTATGTCA
* * * *
328965 ACACTAGGTTCCATCGATTTGGTTTTTCTTCCATGCCTTAGTGTTAACTGTGTGATGACATGGTT
1 ACACTAGATTCCATCGATTTGATATTTCTGCCATGCCTTAGTGTTAACTGTGTGATGACATGGTT
* *
329030 GTTCTCGATACTTGTTTGCTCTGTTGTTGGT-C-AGATATGTATATATCTGTACCTATGTCA
66 GTTCTCGATACTTGTTTGCTCTGTTGTTGGTACGAGATATATATATATCCGTACCTATGTCA
* * * *
329090 ACACTAGATTCCATCGATTTGATATATCTGCCATGCTTTAGCGTTTACTGTGTGATGACATGGTT
1 ACACTAGATTCCATCGATTTGATATTTCTGCCATGCCTTAGTGTTAACTGTGTGATGACATGGTT
* * *
329155 GTTTTCGCTACCTT-TTTGCTCTGATGTTGGT
66 GTTCTCGATA-CTTGTTTGCTCTGTTGTTGGT
329186 TGGACATATA
Statistics
Matches: 195, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
125 106 0.54
126 3 0.02
127 1 0.01
128 85 0.44
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (127 bp):
ACACTAGATTCCATCGATTTGATATTTCTGCCATGCCTTAGTGTTAACTGTGTGATGACATGGTT
GTTCTCGATACTTGTTTGCTCTGTTGTTGGTACGAGATATATATATATCCGTACCTATGTCA
Found at i:336887 original size:6 final size:6
Alignment explanation
Indices: 336876--336901 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
336866 CCCTTGTACT
336876 AACCCA AACCCA AACCCA AACCCA AA
1 AACCCA AACCCA AACCCA AACCCA AA
336902 AATTTGATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (6 bp):
AACCCA
Found at i:337106 original size:83 final size:83
Alignment explanation
Indices: 336952--337115 Score: 204
Period size: 83 Copynumber: 2.0 Consensus size: 83
336942 AATCACAAAA
* * * ** *
336952 ATTTGATAATTTAAATCTGTTTAATTCGAATCAGAATTCACCAGATCTAGATTCTTCTAATTTAT
1 ATTTGATAATCTAAATCTATTTAATTCGAATCAGAATTCACCAGATCGAGATTCTTCTAATCCAC
*
337017 CTAACTCGAAGATCTAGC
66 CCAACTCGAAGATCTAGC
* * * *
337035 ATTTGATAATCTAAATCTATTTAATTCGAATCATAATTGATCATATCGAGATTCCTTC-AATCCA
1 ATTTGATAATCTAAATCTATTTAATTCGAATCAGAATTCACCAGATCGAGATT-CTTCTAATCCA
*
337099 CCCAACTCGAAGGTCTA
65 CCCAACTCGAAGATCTA
337116 ACATAATTTA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
83 64 0.94
84 4 0.06
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (83 bp):
ATTTGATAATCTAAATCTATTTAATTCGAATCAGAATTCACCAGATCGAGATTCTTCTAATCCAC
CCAACTCGAAGATCTAGC
Found at i:342359 original size:23 final size:24
Alignment explanation
Indices: 342318--342365 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
342308 AGTTAAAGAA
342318 AAATATTGGAAACTTTTTGTAGAC
1 AAATATTGGAAACTTTTTGTAGAC
* *
342342 AAATATT-GATACTTTTTGTGGAC
1 AAATATTGGAAACTTTTTGTAGAC
342365 A
1 A
342366 TTTTGTGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (24 bp):
AAATATTGGAAACTTTTTGTAGAC
Found at i:342853 original size:39 final size:39
Alignment explanation
Indices: 342810--342884 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
342800 CCAGGTTATG
342810 GAATGTGTATATG-TTAGTTGATTATCAATTCTAGAACGT
1 GAATGTGTATATGCTT-GTTGATTATCAATTCTAGAACGT
342849 GAATGTGTATATGCTTGTTGATTATCAATTCTAGAA
1 GAATGTGTATATGCTTGTTGATTATCAATTCTAGAA
342885 GGTATAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 33 0.94
40 2 0.06
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (39 bp):
GAATGTGTATATGCTTGTTGATTATCAATTCTAGAACGT
Found at i:348887 original size:2 final size:2
Alignment explanation
Indices: 348880--348904 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
348870 TAGAACACAT
348880 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
348905 CTAAACTTTC
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:362209 original size:5 final size:5
Alignment explanation
Indices: 362199--362226 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
362189 CATTGGTACC
362199 TCTCG TCTCG TCTCG TCTCG TCTCG TCT
1 TCTCG TCTCG TCTCG TCTCG TCTCG TCT
362227 ACAAATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.39, G:0.18, T:0.43
Consensus pattern (5 bp):
TCTCG
Found at i:364250 original size:27 final size:27
Alignment explanation
Indices: 364212--364263 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
364202 CTGACACAGA
*
364212 TAGAGGTGGACTAAGTGGCGGCACCCT
1 TAGAGGTGGACTAAGTGGCGACACCCT
364239 TAGAGG-GAGACTAAGTGGCGACACC
1 TAGAGGTG-GACTAAGTGGCGACACC
364264 AAAAAATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.27, C:0.21, G:0.37, T:0.15
Consensus pattern (27 bp):
TAGAGGTGGACTAAGTGGCGACACCCT
Found at i:373708 original size:138 final size:138
Alignment explanation
Indices: 373431--373856 Score: 622
Period size: 138 Copynumber: 3.1 Consensus size: 138
373421 GGACGAAACG
* *
373431 TCGAGTTTCGAGCTTAACGAGAAAAATGATGAGTCATCTAAAACCATTGAACCACTAGCAACAGC
1 TCGAGTTTCGAGCTTAA--TG-AAAATGATGAGTCATCTAAGACCATTGAACCACTAGCAACAGC
* *
373496 TTGTGATGACGGGGTTGATAAATCATTTAAGATCA-AAAGCGGATTGACCCAATTGATTTCTGAT
63 TTGTGATGACGAGGTTGATAAATCATTTAAGAT-AGAAAGCGGATTGACCCAACTGATTTCTGAT
373560 TTT-TTAGGTGAC
127 TTTGTT-GGTGAC
*
373572 TCGAGTTTCGAGCTTAATGAAAATGATGAGTCATCTAAGACCATTGAACCAATAGCAACAGCTTG
1 TCGAGTTTCGAGCTTAATGAAAATGATGAGTCATCTAAGACCATTGAACCACTAGCAACAGCTTG
* * * *
373637 TGATGACGATGTTGATAAATCATTTAAGATAGAAAGTGAATTGACCCAACTAATTTCTGATTTTG
66 TGATGACGAGGTTGATAAATCATTTAAGATAGAAAGCGGATTGACCCAACTGATTTCTGATTTTG
*
373702 CTGGTGAC
131 TTGGTGAC
* * * *
373710 TCGAGTTTCGAGTTTAATGAGAATGATGAGTCATATAAGACCATTGAACCACTAGCACCAGCTTG
1 TCGAGTTTCGAGCTTAATGAAAATGATGAGTCATCTAAGACCATTGAACCACTAGCAACAGCTTG
* * * * *
373775 TGATGACGAGGTTGATAAATCATTTAAGATCGAAAACGGGTTGACCCAACTGGTTTCTGATTTCG
66 TGATGACGAGGTTGATAAATCATTTAAGATAGAAAGCGGATTGACCCAACTGATTTCTGATTTTG
373840 TTGGTGAC
131 TTGGTGAC
373848 TCGAGTTTC
1 TCGAGTTTC
373857 ACACTTAACG
Statistics
Matches: 258, Mismatches: 25, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
137 1 0.00
138 238 0.92
139 2 0.01
141 17 0.07
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (138 bp):
TCGAGTTTCGAGCTTAATGAAAATGATGAGTCATCTAAGACCATTGAACCACTAGCAACAGCTTG
TGATGACGAGGTTGATAAATCATTTAAGATAGAAAGCGGATTGACCCAACTGATTTCTGATTTTG
TTGGTGAC
Found at i:375811 original size:18 final size:18
Alignment explanation
Indices: 375790--375824 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
375780 TATATTTTAA
*
375790 ATATTATAAATTATAAAT
1 ATATTATAAATAATAAAT
*
375808 ATATTTTAAATAATAAA
1 ATATTATAAATAATAAA
375825 AAACATCAAT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATTATAAATAATAAAT
Found at i:391379 original size:23 final size:21
Alignment explanation
Indices: 391347--391400 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
391337 GAATTGGCTA
391347 AATTAATTTTTACTT-TTAATATT
1 AATT-ATTTTTA-TTGTTAA-ATT
*
391370 AATTATTTTTATTGTTTAATT
1 AATTATTTTTATTGTTAAATT
391391 AATTATTTTT
1 AATTATTTTT
391401 GCATCGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 15 0.52
22 10 0.34
23 4 0.14
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
AATTATTTTTATTGTTAAATT
Found at i:396735 original size:6 final size:6
Alignment explanation
Indices: 396685--396732 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
396675 ATAATGAATA
* * *
396685 TATATG AATATG TATATG TATATG TATATG TATACG TATATG CATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
396733 CATGCAAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (6 bp):
TATATG
Found at i:398720 original size:42 final size:42
Alignment explanation
Indices: 398661--398744 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 42
398651 AAATATATTT
*
398661 CATTAAGACTATTAAATGCAT-GTTTTCAATTTATTTAATTA
1 CATTAAGACTATTAAATGCATCGTTTTCAATTCATTTAATTA
* * *
398702 CATTAAGATTAATTAAATGCATCTTTTTCACTTCATTTAATTA
1 CATTAAGACT-ATTAAATGCATCGTTTTCAATTCATTTAATTA
398745 TTTTTATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 9 0.24
42 11 0.30
43 17 0.46
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (42 bp):
CATTAAGACTATTAAATGCATCGTTTTCAATTCATTTAATTA
Found at i:410163 original size:2 final size:2
Alignment explanation
Indices: 410156--410180 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
410146 GATGATTACT
410156 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
410181 TTTTTTTGTA
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:411051 original size:71 final size:71
Alignment explanation
Indices: 410906--411041 Score: 229
Period size: 71 Copynumber: 1.9 Consensus size: 71
410896 AGAAAACGCC
*
410906 GCAAAAGGTAGAGCAATAGCGGTGTTTATGAGAAAGCGCCACAAAAGGTAGAGCAATAGCGACGC
1 GCAAAAGGTAGAGCAATAGCGGCGTTTATGAGAAAGCGCCACAAAAGGTAGAGCAATAGCGACGC
410971 CGCAAA
66 CGCAAA
* *
410977 GCAAAAGGTAGAGCAATAGCGGCGTTTATGGGAAAG-GCCGCAAAAGGTTAGAGCAATAGCGACG
1 GCAAAAGGTAGAGCAATAGCGGCGTTTATGAGAAAGCGCCACAAAAGG-TAGAGCAATAGCGACG
411041 C
65 C
411042 TTTTGAGCAA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
70 10 0.16
71 51 0.84
ACGTcount: A:0.38, C:0.18, G:0.32, T:0.13
Consensus pattern (71 bp):
GCAAAAGGTAGAGCAATAGCGGCGTTTATGAGAAAGCGCCACAAAAGGTAGAGCAATAGCGACGC
CGCAAA
Found at i:411101 original size:41 final size:41
Alignment explanation
Indices: 410986--411127 Score: 132
Period size: 41 Copynumber: 3.5 Consensus size: 41
410976 AGCAAAAGGT
* *
410986 AGAGCAATAGCGGCGTTTATG-GGAAAG-GCCGC-AAAAGGTT
1 AGAGCAATAGCGGCGCTTATGAGG-AAGCGCCGCTAAAA-GTC
* * *
411026 AGAGCAATAGCGACGCTTTTGAGCAAGC-CTCGCTAAAAGTC
1 AGAGCAATAGCGGCGCTTATGAGGAAGCGC-CGCTAAAAGTC
*
411067 AGAGCAATAGCGGCGCTTATGAGGAGGCGCCGCT-AAAGCTC
1 AGAGCAATAGCGGCGCTTATGAGGAAGCGCCGCTAAAAG-TC
* * *
411108 AAAGCATTAGCGGCGTTTAT
1 AGAGCAATAGCGGCGCTTAT
411128 AATAAAAACG
Statistics
Matches: 84, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
40 26 0.31
41 53 0.63
42 5 0.06
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.19
Consensus pattern (41 bp):
AGAGCAATAGCGGCGCTTATGAGGAAGCGCCGCTAAAAGTC
Found at i:412600 original size:23 final size:23
Alignment explanation
Indices: 412486--412600 Score: 142
Period size: 23 Copynumber: 5.0 Consensus size: 23
412476 TGTTGGGCAA
* *
412486 CAGAGAGCACACACAGTGCTAAAT
1 CAGAGAGCACGCAAAGTGCT-AAT
* * *
412510 -AGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACGCAAAGTGCTAAT
*
412532 TAGAGAGCACGCAAAGTGCTAAT
1 CAGAGAGCACGCAAAGTGCTAAT
*
412555 TAGAGAGCACGCAAAGTGCTAAT
1 CAGAGAGCACGCAAAGTGCTAAT
*
412578 CAGAGAGCACGCACAGTGCTAAT
1 CAGAGAGCACGCAAAGTGCTAAT
412601 AACAGATAGC
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
22 3 0.04
23 79 0.96
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (23 bp):
CAGAGAGCACGCAAAGTGCTAAT
Found at i:412600 original size:46 final size:46
Alignment explanation
Indices: 412486--412600 Score: 167
Period size: 46 Copynumber: 2.5 Consensus size: 46
412476 TGTTGGGCAA
* * *
412486 CAGAGAGCACACACAGTGCTAAATAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACGCACAGTGCTAATTAGAGAGCACACAAAGTACTAAT
* * * *
412532 TAGAGAGCACGCAAAGTGCTAATTAGAGAGCACGCAAAGTGCTAAT
1 CAGAGAGCACGCACAGTGCTAATTAGAGAGCACACAAAGTACTAAT
412578 CAGAGAGCACGCACAGTGCTAAT
1 CAGAGAGCACGCACAGTGCTAAT
412601 AACAGATAGC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (46 bp):
CAGAGAGCACGCACAGTGCTAATTAGAGAGCACACAAAGTACTAAT
Found at i:412633 original size:48 final size:46
Alignment explanation
Indices: 412484--412633 Score: 115
Period size: 46 Copynumber: 3.2 Consensus size: 46
412474 AGTGTTGGGC
* * * * * *
412484 AACAGAGAGCACACACAGTGCTAAAT-AGAGAGTACACAAAGTACTA
1 AACAAAGAGCACGCAAAGTGCT-AATCAGAGAGCACGCAAAGTGCTA
** * *
412530 ATTAGAGAGCACGCAAAGTGCTAATTAGAGAGCACGCAAAGTGCTA
1 AACAAAGAGCACGCAAAGTGCTAATCAGAGAGCACGCAAAGTGCTA
* * * * *
412576 ATCAGAGAGCACGCACAGTGCTAATAACAGATAGCACG-AGACGTGCTA
1 AACAAAGAGCACGCAAAGTGCTAAT--CAGAGAGCACGCA-AAGTGCTA
412624 AACAAAGAGC
1 AACAAAGAGC
412634 GCGCTAGTGT
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
45 3 0.03
46 58 0.67
47 1 0.01
48 24 0.28
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (46 bp):
AACAAAGAGCACGCAAAGTGCTAATCAGAGAGCACGCAAAGTGCTA
Found at i:415085 original size:11 final size:11
Alignment explanation
Indices: 415069--415099 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
415059 TTCTGACTTT
415069 GAAAAATTATA
1 GAAAAATTATA
415080 GAAAAA-TATA
1 GAAAAATTATA
415090 GAAAAATTAT
1 GAAAAATTAT
415100 TAGGGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (11 bp):
GAAAAATTATA
Found at i:415579 original size:23 final size:23
Alignment explanation
Indices: 415550--415655 Score: 133
Period size: 23 Copynumber: 4.5 Consensus size: 23
415540 GAACACTAGC
*
415550 GTGCTCTCTGTTTAGCAC-GTCT
1 GTGCTCTCTGTTTAGCACTGTGT
415572 CGTGCTCTCTGTTATTAGCACTGTGT
1 -GTGCTCTCTG-T-TTAGCACTGTGT
* * *
415598 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGTTTAGCACTGTGT
*
415621 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGTTTAGCACTGTGT
415644 GTGCTCTCTGTT
1 GTGCTCTCTGTT
415656 AGTACTTTGA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
23 50 0.70
24 1 0.01
25 17 0.24
26 3 0.04
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (23 bp):
GTGCTCTCTGTTTAGCACTGTGT
Found at i:415653 original size:46 final size:44
Alignment explanation
Indices: 415576--415677 Score: 159
Period size: 46 Copynumber: 2.2 Consensus size: 44
415566 ACGTCTCGTG
*
415576 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGTGTA
1 CTCTCTG-T-TTAGCACTGTGTGTGCTCTCTG-TTAGTACTTTG-ATA
415624 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTAGTACTTTGATA
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTAGTACTTTGATA
415668 CTCTCTGTTT
1 CTCTCTGTTT
415678 GTTCCGTATA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
44 12 0.23
45 11 0.21
46 22 0.42
47 1 0.02
48 7 0.13
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.47
Consensus pattern (44 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTAGTACTTTGATA
Found at i:420714 original size:19 final size:19
Alignment explanation
Indices: 420687--420723 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
420677 CATATTTTAT
* *
420687 ATATTTGTATGTATATATA
1 ATATATGTATGCATATATA
420706 ATATATGTATGCATATAT
1 ATATATGTATGCATATAT
420724 CAAAAAAGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.49
Consensus pattern (19 bp):
ATATATGTATGCATATATA
Found at i:420722 original size:21 final size:22
Alignment explanation
Indices: 420674--420723 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 22
420664 TCCATGTGAA
* *
420674 ATGCATAT-TTTATATATTTGT
1 ATGCATATATATATATATATGT
420695 ATG--TATATATA-ATATATGT
1 ATGCATATATATATATATATGT
420714 ATGCATATAT
1 ATGCATATAT
420724 CAAAAAAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 13 0.54
20 3 0.12
21 8 0.33
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.50
Consensus pattern (22 bp):
ATGCATATATATATATATATGT
Found at i:423080 original size:17 final size:17
Alignment explanation
Indices: 423058--423093 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
423048 ATACTATATA
423058 AATTTTATT-TTATTGTT
1 AATTTTATTATTATT-TT
423075 AATTTTATTATTATTTT
1 AATTTTATTATTATTTT
423092 AA
1 AA
423094 AAACATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
AATTTTATTATTATTTT
Found at i:424734 original size:26 final size:24
Alignment explanation
Indices: 424688--424738 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
424678 TAGTCGCTTT
**
424688 AAAAAAGATATATTTTCCTAAATTA
1 AAAAAAGATATATTTGACT-AATTA
*
424713 AAAAAATGATCTATTTGACTAATTA
1 AAAAAA-GATATATTTGACTAATTA
424738 A
1 A
424739 TTTTTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (24 bp):
AAAAAAGATATATTTGACTAATTA
Found at i:440396 original size:63 final size:63
Alignment explanation
Indices: 440288--440421 Score: 205
Period size: 63 Copynumber: 2.1 Consensus size: 63
440278 GCTCTCTCAA
* * *
440288 GTTTTCGATGACTCATTTTGTCTACACCTGATTCAATGGAGTTAGGTGTTGCTTCCGGTGGCT
1 GTTTTCTATGACTCATTTTGTCTACACCTGATTCAATGAAATTAGGTGTTGCTTCCGGTGGCT
* * * *
440351 GTTTTCTATGACTCGTTTTGTCTACACCTGATTCATTGAAATTAGGTGTTGTTTCCGGTGGTT
1 GTTTTCTATGACTCATTTTGTCTACACCTGATTCAATGAAATTAGGTGTTGCTTCCGGTGGCT
440414 GTTTTCTA
1 GTTTTCTA
440422 CTATACGAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.16, C:0.17, G:0.23, T:0.44
Consensus pattern (63 bp):
GTTTTCTATGACTCATTTTGTCTACACCTGATTCAATGAAATTAGGTGTTGCTTCCGGTGGCT
Found at i:440491 original size:14 final size:14
Alignment explanation
Indices: 440472--440501 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
440462 TCTGATTGTA
*
440472 AAGCTTGAATGTTC
1 AAGCTTGAATGGTC
440486 AAGCTTGAATGGTC
1 AAGCTTGAATGGTC
440500 AA
1 AA
440502 AAAAAGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.30
Consensus pattern (14 bp):
AAGCTTGAATGGTC
Found at i:444987 original size:2 final size:2
Alignment explanation
Indices: 444980--445005 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
444970 TGTAAACATC
444980 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
445006 GAAGTCCCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:450826 original size:59 final size:60
Alignment explanation
Indices: 450757--450873 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 60
450747 TAAGGTAAAT
450757 TAAAATTCAATAAATTGGGATGAGATATACTCAATAGGATGTTAAATAT-TATTTTTTTC
1 TAAAATTCAATAAATTGGGATGAGATATACTCAATAGGATGTTAAATATATATTTTTTTC
450816 TAAAATTCAATAAATTGGGATGAGATATACTCAATAGGATGTTAAATATATATTTTTT
1 TAAAATTCAATAAATTGGGATGAGATATACTCAATAGGATGTTAAATATATATTTTTT
450874 CTTATAATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 49 0.86
60 8 0.14
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (60 bp):
TAAAATTCAATAAATTGGGATGAGATATACTCAATAGGATGTTAAATATATATTTTTTTC
Found at i:458829 original size:18 final size:18
Alignment explanation
Indices: 458790--458829 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
458780 TTTTATGTTT
*
458790 TTTTTACTGTTTGGTCTT
1 TTTTTACTGTTTGGTCTG
458808 TTTTTACTGTTTTGGT-TG
1 TTTTTACTG-TTTGGTCTG
458826 TTTT
1 TTTT
458830 CGTGTTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.05, C:0.07, G:0.17, T:0.70
Consensus pattern (18 bp):
TTTTTACTGTTTGGTCTG
Done.