Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014958.1 Kokia drynarioides strain JFW-HI SEQ_130002, 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: 273762
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 286 characters in sequence are not A, C, G, or T
Found at i:100 original size:4 final size:4
Alignment explanation
Indices: 91--206 Score: 92
Period size: 4 Copynumber: 28.5 Consensus size: 4
81 AAACGCATTA
* * * *
91 TCTT TCTT TCCT TC-T TCTT TCTT TCCTC TCCT TC-T TCTT TCTT TCCTC
1 TCTT TCTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT TCTT TCTT T-CTT
* * * * * *
139 TCCT TCTT CCTT TCTT TCTT TCTT TCCTC TCCT TCTT CCTT TATT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT TCTT TCTT TCTT
188 TCTT TCCTT TCTT TCTT TC
1 TCTT T-CTT TCTT TCTT TC
207 CCGTTTATTT
Statistics
Matches: 88, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
3 6 0.07
4 69 0.78
5 13 0.15
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (4 bp):
TCTT
Found at i:124 original size:20 final size:20
Alignment explanation
Indices: 99--156 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
89 TATCTTTCTT
99 TCCTTCTTCTTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
119 TCCTTCTTCTTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
139 TCCTTCTTCCTTTCTTTC
1 TCCTTCTT-CTTTCTTTC
157 TTTCTTTCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 28 0.76
21 9 0.24
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (20 bp):
TCCTTCTTCTTTCTTTCCTC
Found at i:163 original size:29 final size:29
Alignment explanation
Indices: 125--204 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
115 CCTCTCCTTC
*
125 TTCTTTCTTTCCTCTCCTTCTTCCTTTCT
1 TTCTTTCTTTCCTCTCCTTCTTCCTTTAT
154 TTCTTTCTTTCCTCTCCTTCTTCCTTTAT
1 TTCTTTCTTTCCTCTCCTTCTTCCTTTAT
* *
183 TTCTTTCTTTCCTTTCTTTCTT
1 TTCTTTCTTTCCTCTCCTTCTT
205 TCCCGTTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (29 bp):
TTCTTTCTTTCCTCTCCTTCTTCCTTTAT
Found at i:194 original size:17 final size:17
Alignment explanation
Indices: 174--206 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
164 CCTCTCCTTC
174 TTCCTTTATTTCTTTCT
1 TTCCTTTATTTCTTTCT
*
191 TTCCTTTCTTTCTTTC
1 TTCCTTTATTTCTTTC
207 CCGTTTATTT
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:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCCTTTATTTCTTTCT
Found at i:10217 original size:23 final size:23
Alignment explanation
Indices: 10190--10236 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
10180 GATGGAACCG
10190 CTAGTGTTGTAAATGAACATATT
1 CTAGTGTTGTAAATGAACATATT
10213 CTAGTGTTGTAAATGAACATATT
1 CTAGTGTTGTAAATGAACATATT
10236 C
1 C
10237 GTTTATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (23 bp):
CTAGTGTTGTAAATGAACATATT
Found at i:12078 original size:10 final size:9
Alignment explanation
Indices: 12053--12083 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
12043 ATTATGTATT
12053 ATTTAATTA
1 ATTTAATTA
12062 ATTTAATTA
1 ATTTAATTA
12071 AGTTTAATTA
1 A-TTTAATTA
12081 ATT
1 ATT
12084 CATTACTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (9 bp):
ATTTAATTA
Found at i:12616 original size:23 final size:23
Alignment explanation
Indices: 12557--12616 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
12547 TATTTTTATA
*
12557 TATAACTATTAATATAATATAAAT
1 TATAA-TATTAATATAATACAAAT
**
12581 TATAATAAAAATATAATACATAA-
1 TATAATATTAATATAATACA-AAT
*
12604 TATTATATTAATA
1 TATAATATTAATA
12617 ATTGATGCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (23 bp):
TATAATATTAATATAATACAAAT
Found at i:29332 original size:18 final size:18
Alignment explanation
Indices: 29311--29354 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
29301 GGAGCTACTT
29311 TTGTTGTTGTCGGTATGC
1 TTGTTGTTGTCGGTATGC
29329 TTGTTGTTGTCGGTATGC
1 TTGTTGTTGTCGGTATGC
29347 TTGTTGTT
1 TTGTTGTT
29355 ATCACTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.05, C:0.09, G:0.32, T:0.55
Consensus pattern (18 bp):
TTGTTGTTGTCGGTATGC
Found at i:32019 original size:101 final size:101
Alignment explanation
Indices: 31893--32249 Score: 455
Period size: 101 Copynumber: 3.5 Consensus size: 101
31883 ACAGTTGTGG
* * * * *
31893 ATCTGAATCTCCCTGAAGTTGCAGTGGAATGGAGGGAAGGTACAACACCAAATGCTATATCCTTG
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAACACCAAATCCTATATCCCTG
*
31958 AAGTTGTAGTGGATCGGATTAAAACTACGATAACGG
66 AAGTTGTAGTGGATCGGATTAAAACTACGATAACGA
* * *
31994 ATTTCAATCTCCCTGAAGTTACAGTGGAGTGGAGTGAAGATACAACACCAAATCCTATATCCCTG
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAACACCAAATCCTATATCCCTG
* * *
32059 AAGTTGTTGTGGATCGAATTAAAATTACGATAACGA
66 AAGTTGTAGTGGATCGGATTAAAACTACGATAACGA
* * * * * * *
32095 ATCTCAATCTTCCTAAAGTTGTAGTGGAATAGAGTAAAGTTACAATACCAAATCCTATATCCCTG
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAACACCAAATCCTATATCCCTG
** * *
32160 AAGTTGCGGTGGATCGGATTAAAACTATGATAGCGA
66 AAGTTGTAGTGGATCGGATTAAAACTACGATAACGA
* * * *
32196 ATCTCAATCTCCTTGAAGTTGTAGTGGAATGAAGTGAAGCTACAACGA-CAAATC
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAAC-ACCAAATC
32250 TTATCTCATT
Statistics
Matches: 219, Mismatches: 36, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
101 218 1.00
102 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (101 bp):
ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAACACCAAATCCTATATCCCTG
AAGTTGTAGTGGATCGGATTAAAACTACGATAACGA
Found at i:32071 original size:50 final size:49
Alignment explanation
Indices: 31902--32165 Score: 145
Period size: 50 Copynumber: 5.2 Consensus size: 49
31892 GATCTGAATC
* * * *
31902 TCCCTGAAGTTGCAGTGGAATGGAGGGAAGGTACAACACCAAATGCTATA
1 TCCCTGAAGTTGTAGTGG-ATGGAGTGAAGATACAACACCAAATCCTATA
* * * ** * * * *
31952 TCCTTGAAGTTGTAGTGGATCGGA-TTAAAACTACGATA-ACGGATTTCAATC
1 TCCCTGAAGTTGTAGTGGAT-GGAGTGAAGA-TAC-A-ACACCAAATCCTATA
**
32003 TCCCTGAAGTTACAGTGGAGTGGAGTGAAGATACAACACCAAATCCTATA
1 TCCCTGAAGTTGTAGTGGA-TGGAGTGAAGATACAACACCAAATCCTATA
* * * * * * * * * * *
32053 TCCCTGAAGTTGTTGTGGATCGAATTAAAATTACGATAACGAATCTCAATC
1 TCCCTGAAGTTGTAGTGGATGGAGTGAAGA-TACAACACCAAATC-CTATA
* * * * * *
32104 TTCCTAAAGTTGTAGTGGAATAGAGTAAAGTTACAATACCAAATCCTATA
1 TCCCTGAAGTTGTAGTGG-ATGGAGTGAAGATACAACACCAAATCCTATA
32154 TCCCTGAAGTTG
1 TCCCTGAAGTTG
32166 CGGTGGATCG
Statistics
Matches: 153, Mismatches: 51, Indels: 20
0.68 0.23 0.09
Matches are distributed among these distances:
49 12 0.08
50 69 0.45
51 59 0.39
52 13 0.08
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (49 bp):
TCCCTGAAGTTGTAGTGGATGGAGTGAAGATACAACACCAAATCCTATA
Found at i:32116 original size:51 final size:50
Alignment explanation
Indices: 31956--32223 Score: 157
Period size: 51 Copynumber: 5.3 Consensus size: 50
31946 GCTATATCCT
* * * *
31956 TGAAGTTGTAGTGGATCGGATTAAAACTACGATAACGGATTTCAATCTCCC
1 TGAAGTTGTAGTGGATC-GATTAAAATTACGATAACGAATCTCAATCTTCC
** * * * * * * * * * *
32007 TGAAGTTACAGTGGAGTGGAGTGAAGA-TACAACACCAAATC-CTATATCCC
1 TGAAGTTGTAGTGGA-TCGA-TTAAAATTACGATAACGAATCTCAATCTTCC
*
32057 TGAAGTTGTTGTGGATCGAATTAAAATTACGATAACGAATCTCAATCTTCC
1 TGAAGTTGTAGTGGATCG-ATTAAAATTACGATAACGAATCTCAATCTTCC
* * * * * * * * * *
32108 TAAAGTTGTAGTGGAATAGAGTAAAGTTACAATACCAAATC-CTATATCCC
1 TGAAGTTGTAGTGG-ATCGATTAAAATTACGATAACGAATCTCAATCTTCC
** * * *
32158 TGAAGTTGCGGTGGATCGGATTAAAACTATGATAGCGAATCTCAATC-TCC
1 TGAAGTTGTAGTGGATC-GATTAAAATTACGATAACGAATCTCAATCTTCC
32208 TTGAAGTTGTAGTGGA
1 -TGAAGTTGTAGTGGA
32224 ATGAAGTGAA
Statistics
Matches: 155, Mismatches: 53, Indels: 18
0.69 0.23 0.08
Matches are distributed among these distances:
49 8 0.05
50 65 0.42
51 74 0.48
52 8 0.05
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (50 bp):
TGAAGTTGTAGTGGATCGATTAAAATTACGATAACGAATCTCAATCTTCC
Found at i:35733 original size:23 final size:23
Alignment explanation
Indices: 35702--36650 Score: 1260
Period size: 23 Copynumber: 41.4 Consensus size: 23
35692 TTCTTATATC
*
35702 TGTGCTTAAATATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
* **
35725 TATTG-TTAAATATTAATACGATT
1 T-GTGCTTAAATATTAATGTGATT
*
35748 TATGCTTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* *
35771 TGTGCTTAAGTATTAGTGTGATT
1 TGTGCTTAAATATTAATGTGATT
*
35794 TATGCTTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
35817 TGTGCTTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* * *
35840 TGTACTCAAATATTAAAGTGATT
1 TGTGCTTAAATATTAATGTGATT
* * *
35863 TATGATTAAATATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
* *
35886 TGTTCTCAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* *
35909 TATGCTTAAATATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
35932 TGTGCTTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* * *
35955 TGTGCTTCAATATTAATTTAATT
1 TGTGCTTAAATATTAATGTGATT
*
35978 TGTGCTTCAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
*
36001 TGTGCTTAAATATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
*
36024 TGTGCTCAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* * *
36047 TGTGCTTAGATATTAATATGGTT
1 TGTGCTTAAATATTAATGTGATT
* * *
36070 TATACTTAAATATCAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
36093 TGTGCTTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* *
36116 TGTGCTTAAATATTAATTTAATT
1 TGTGCTTAAATATTAATGTGATT
*
36139 TGTGCTTCAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
*
36162 TGTGCTTAAATATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
* *
36185 TGTACTCAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* *
36208 TGTGCTTAGATATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
* *
36231 TATACTTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
*
36254 TGTGCTCAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
*
36277 TGTGCTTAAATATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
*
36300 TGTGCTCAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* *
36323 TATGCTCAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
36346 TGTGCTTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
*
36369 TGTGCTTAAATATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
* *
36392 TCTGCTCAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* * *
36415 TCTGCTTAGATATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
36438 TGTGCTTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* *
36461 TGTGCTTAGATATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
*
36484 TGTGCTCAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* **
36507 TGTGCTTAGATATTAATACGATT
1 TGTGCTTAAATATTAATGTGATT
*
36530 TGTGCTCAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* *
36553 TGTGCTT-TA-ATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
*
36574 TGTGCTCAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* *
36597 TGTGCTT-TA-ATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
* *
36618 TATGATTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
*
36641 TGTCCTTAAA
1 TGTGCTTAAA
36651 GAATTAAGAT
Statistics
Matches: 799, Mismatches: 121, Indels: 12
0.86 0.13 0.01
Matches are distributed among these distances:
21 33 0.04
22 6 0.01
23 758 0.95
24 2 0.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (23 bp):
TGTGCTTAAATATTAATGTGATT
Found at i:36759 original size:35 final size:36
Alignment explanation
Indices: 36720--36831 Score: 138
Period size: 36 Copynumber: 3.1 Consensus size: 36
36710 TGATGACTGT
** *
36720 TGTGAAAGTGAATATGTGGGTATGTTCTTC-TGCTA
1 TGTGAAAGAAAATATGTGGGTATGTTCTTCATGCCA
*
36755 TGTGACAGAAAATATGTGGGTATGTTCTTCATGCCA
1 TGTGAAAGAAAATATGTGGGTATGTTCTTCATGCCA
* * *
36791 TGAGACAA-AAAATATGTGAGTATGTTCTTCATGTCA
1 TGTGA-AAGAAAATATGTGGGTATGTTCTTCATGCCA
36827 TGTGA
1 TGTGA
36832 CTGATTATAT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
35 27 0.41
36 38 0.58
37 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.36
Consensus pattern (36 bp):
TGTGAAAGAAAATATGTGGGTATGTTCTTCATGCCA
Found at i:36814 original size:36 final size:36
Alignment explanation
Indices: 36730--36828 Score: 146
Period size: 36 Copynumber: 2.8 Consensus size: 36
36720 TGTGAAAGTG
* * *
36730 AATATGTGGGTATGTTCTTC-TGCTATGTGACAGAA
1 AATATGTGGGTATGTTCTTCATGCCATGAGACAAAA
36765 AATATGTGGGTATGTTCTTCATGCCATGAGACAAAA
1 AATATGTGGGTATGTTCTTCATGCCATGAGACAAAA
* *
36801 AATATGTGAGTATGTTCTTCATGTCATG
1 AATATGTGGGTATGTTCTTCATGCCATG
36829 TGACTGATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 20 0.34
36 38 0.66
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.36
Consensus pattern (36 bp):
AATATGTGGGTATGTTCTTCATGCCATGAGACAAAA
Found at i:37376 original size:368 final size:366
Alignment explanation
Indices: 36855--37593 Score: 1019
Period size: 376 Copynumber: 2.0 Consensus size: 366
36845 GATAATAAAG
36855 TGAATATGCAGTGAATATATGAAAAAAATATGTAATAATAATAATGTGAATATTTTGTCTATAAG
1 TGAATATGCAGTGAATATATGAAAAAAATATGTAATAATAATAATGTGAATATTTTGTCTATAAG
*
36920 ACCTTTGGATATAGTTGACTTGTCATAGGATTGTGAGTACTCACGTTTGTGTTATATGTGGGGCA
66 ACCTTTGGATATAGTTGACATGTCATAGGATTGTGAGTACTCACGTTTGTGTTATATGTGGGGCA
* * *
36985 TTGAGGCTTAGGGACATGTTGGAGA-T-AT-AA-CATCTATGCTCCATTCAACGGGATATGTTTG
131 CTGAGGCTCAGGGACATGTTGGAGAGTAATGAATCAGCTATGCTCCATTCAACGGGATATGTTTG
*
37046 GTGTGTTGGAGAGTGTTAGATATATGCTTCACTTATGGGATATGTTTTGACTCTATGAGTCTAGT
196 GTGTGTTGGAGAGTGTTAGATATATGCTTCACTTATGGGATATGTTTTGACTCTATGAGTCCAGT
* * *
37111 GTTGGTATGTTGGAGATCCACGTGTCCAATGTGTGATGACCA-AGCTCATTATATGTTTCATAGT
261 GTTGGTATGTTGGAGATCCACGTATCCAATGTGTGAT-AACAGAGCTCACTATATGTTTCATAGT
* *
37175 CTCAACAACTAAATTATCATAAATTGTGTTTGATTGAGATTA
325 CTCAACAACCAAATTATCATAAATTGTGCTTGATTGAGATTA
* * * *
37217 TGAATATGCAGTGAATATTTGATAAAAATATGTAATAATAAT-TTG-GATATTTTGGCTTTGTGG
1 TGAATATGCAGTGAATATATGAAAAAAATATGTAATAATAATAATGTGA-A---T--ATTT-T-G
* *
37280 TCTTATAAGACCTTTGGATATAGTTGGCATGTCATTGGATTGTGAG-ACTCACGTTTGTGTTATA
58 TC-TATAAGACCTTTGGATATAGTTGACATGTCATAGGATTGTGAGTACTCACGTTTGTGTTATA
* * *
37344 TGTGGGGCGCTGA-GATCCAGGGACATGTTGGAGAGGTAATGGAATGTGAGCTATGCTCCATTCA
122 TGTGGGGCACTGAGGCT-CAGGGACATGTTGGAGA-GTAAT-GAA--TCAGCTATGCTCCATTCA
*
37408 ACGGGATATGTTTGGTGTGTTGGAGAGTGTTAGCTATATGCTTCACTTATGGGATATGTTTTGAC
182 ACGGGATATGTTTGGTGTGTTGGAGAGTGTTAGATATATGCTTCACTTATGGGATATGTTTTGAC
* ** * *
37473 TCTATGAGTCCAGTGTTGGTGTGTTGGAGATCCGTGTATCTAATGTGTGATAATAGAGCTCACTA
247 TCTATGAGTCCAGTGTTGGTATGTTGGAGATCCACGTATCCAATGTGTGATAACAGAGCTCACTA
* * * *
37538 TCTGTTTCATAGTCTTAACAGCCAAATTATCATAAATTGTGCTTGATTGTGATTA
312 TATGTTTCATAGTCTCAACAACCAAATTATCATAAATTGTGCTTGATTGAGATTA
37593 T
1 T
37594 ATGTATATAT
Statistics
Matches: 329, Mismatches: 29, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
360 2 0.01
361 3 0.01
362 40 0.12
364 1 0.00
366 3 0.01
367 3 0.01
368 48 0.15
369 40 0.12
370 1 0.00
371 2 0.01
373 2 0.01
375 2 0.01
376 182 0.55
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.37
Consensus pattern (366 bp):
TGAATATGCAGTGAATATATGAAAAAAATATGTAATAATAATAATGTGAATATTTTGTCTATAAG
ACCTTTGGATATAGTTGACATGTCATAGGATTGTGAGTACTCACGTTTGTGTTATATGTGGGGCA
CTGAGGCTCAGGGACATGTTGGAGAGTAATGAATCAGCTATGCTCCATTCAACGGGATATGTTTG
GTGTGTTGGAGAGTGTTAGATATATGCTTCACTTATGGGATATGTTTTGACTCTATGAGTCCAGT
GTTGGTATGTTGGAGATCCACGTATCCAATGTGTGATAACAGAGCTCACTATATGTTTCATAGTC
TCAACAACCAAATTATCATAAATTGTGCTTGATTGAGATTA
Found at i:38520 original size:24 final size:24
Alignment explanation
Indices: 38492--38554 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
38482 GAGAAAAATC
*
38492 TTTCAGTTAAACTCTATTTATTTA
1 TTTCAGTTAAACTCTATTTAGTTA
* * *
38516 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAGTTAAACTCTATTTAGTTA
* *
38540 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
38555 TATTAATCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAGTTA
Found at i:40485 original size:24 final size:24
Alignment explanation
Indices: 40457--40519 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
40447 AGAAATAATC
* *
40457 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTAGTTG
*
40481 TTTCAATTAAACTCTATTTAGTTG
1 TTTCAGTTAAACTCTATTTAGTTG
*
40505 TTTCAGTCAAACTCT
1 TTTCAGTTAAACTCT
40520 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.16, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAGTTG
Found at i:41223 original size:20 final size:19
Alignment explanation
Indices: 41195--41244 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
41185 CCAGTTTCCC
* *
41195 TTTTCTCTTTTTGTTGTGAT
1 TTTTCTCTTTTTATT-TCAT
*
41215 TTTTGTCTTTTTATTTCAT
1 TTTTCTCTTTTTATTTCAT
*
41234 TTTTTTCTTTT
1 TTTTCTCTTTT
41245 CAAAATTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.06, C:0.10, G:0.08, T:0.76
Consensus pattern (19 bp):
TTTTCTCTTTTTATTTCAT
Found at i:50920 original size:31 final size:33
Alignment explanation
Indices: 50852--50919 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
50842 TTTAAAGGCC
* * *
50852 AAAATTTTTTTTTACCAATTTTTAAGGGATCTA
1 AAAATTTTTTTCTACCAACTTTTAAGGGAACTA
50885 AAAATTTTTTTCT-CCAACTTTTAA-GGAACATA
1 AAAATTTTTTTCTACCAACTTTTAAGGGAAC-TA
50917 AAA
1 AAA
50920 TCCCATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 4 0.13
32 15 0.48
33 12 0.39
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (33 bp):
AAAATTTTTTTCTACCAACTTTTAAGGGAACTA
Found at i:54744 original size:17 final size:17
Alignment explanation
Indices: 54722--54762 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
54712 AAACACCACC
* *
54722 TCTTGGTTAGGTGGAAG
1 TCTTGGTTAGGCGAAAG
54739 TCTTGGTTAGGCGAAAG
1 TCTTGGTTAGGCGAAAG
54756 TCTTGGT
1 TCTTGGT
54763 AATTCTTCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.10, G:0.37, T:0.37
Consensus pattern (17 bp):
TCTTGGTTAGGCGAAAG
Found at i:59670 original size:32 final size:32
Alignment explanation
Indices: 59633--59696 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
59623 AGTTACTGTG
59633 GAACAACAAAGACATTTCTCGTGGAATTTACT
1 GAACAACAAAGACATTTCTCGTGGAATTTACT
59665 GAACAACAAAGACATTTCTCGTGGAATTTACT
1 GAACAACAAAGACATTTCTCGTGGAATTTACT
59697 AAGGAGATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (32 bp):
GAACAACAAAGACATTTCTCGTGGAATTTACT
Found at i:64554 original size:50 final size:50
Alignment explanation
Indices: 64489--64590 Score: 143
Period size: 50 Copynumber: 2.0 Consensus size: 50
64479 TAAAAAAATT
*
64489 ATTACTTATAGTAATAATAATAATAATAATAATATCATTTAAAAACCATC
1 ATTACTTATAGTAATAATAATAATAATAAAAATATCATTTAAAAACCATC
* * * *
64539 ATTACTTATTA-TAATATTATTATTAATAAAAATATCATTTGAAAACCATC
1 ATTACTTA-TAGTAATAATAATAATAATAAAAATATCATTTAAAAACCATC
64589 AT
1 AT
64591 GAAACTATTG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 44 0.96
51 2 0.04
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (50 bp):
ATTACTTATAGTAATAATAATAATAATAAAAATATCATTTAAAAACCATC
Found at i:66085 original size:63 final size:62
Alignment explanation
Indices: 66002--66152 Score: 205
Period size: 62 Copynumber: 2.4 Consensus size: 62
65992 CGTGTTATGG
* * *
66002 TGCTT-TGTAAAATAAATTGGTAATGACTGTGTTGGTGCAAGGAATGATTGTACATGATGTGA
1 TGCTTGTGTAAAATAAATTGGTAATGACTGTGTTGGT-CAAAGAATGAATGCACATGATGTGA
* * * *
66064 TGCTTGTGTAAAATAAATTGGTGATGACTGTGTTGGTCAAAGAATGAATGCATATGCTGTGG
1 TGCTTGTGTAAAATAAATTGGTAATGACTGTGTTGGTCAAAGAATGAATGCACATGATGTGA
* *
66126 TGCTGGTGTAAAATAAATTAGTAATGA
1 TGCTTGTGTAAAATAAATTGGTAATGA
66153 ATGCATATGC
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
62 48 0.62
63 30 0.38
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (62 bp):
TGCTTGTGTAAAATAAATTGGTAATGACTGTGTTGGTCAAAGAATGAATGCACATGATGTGA
Found at i:66153 original size:42 final size:42
Alignment explanation
Indices: 66106--66189 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
66096 TTGGTCAAAG
66106 AATGAATGCATATGCTGTGGTGCTGGTGTAAAATAAATTAGT
1 AATGAATGCATATGCTGTGGTGCTGGTGTAAAATAAATTAGT
66148 AATGAATGCATATGCTGTGGTGCTGGTGTAAAATAAATTAGT
1 AATGAATGCATATGCTGTGGTGCTGGTGTAAAATAAATTAGT
66190 GCGTGTTATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (42 bp):
AATGAATGCATATGCTGTGGTGCTGGTGTAAAATAAATTAGT
Found at i:67966 original size:7 final size:7
Alignment explanation
Indices: 67950--67982 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
67940 AATCAAATTG
*
67950 TGAGAAT
1 TGAGAGT
67957 TGAGAGT
1 TGAGAGT
67964 TGAGAGT
1 TGAGAGT
67971 TGAGAGT
1 TGAGAGT
67978 TGAGA
1 TGAGA
67983 TGAGTTGAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.39, T:0.27
Consensus pattern (7 bp):
TGAGAGT
Found at i:68623 original size:24 final size:24
Alignment explanation
Indices: 68584--68646 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
68574 CAGACTAATT
* * *
68584 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
*
68608 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
68632 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
68647 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:70590 original size:24 final size:24
Alignment explanation
Indices: 70550--70613 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
70540 CCAGACTGAT
* *
70550 TAGAGTTTGACTCAAACAAATAAA
1 TAGAGTTTAACTGAAACAAATAAA
*
70574 TAGAGTTTAATTGAAACAAATAAA
1 TAGAGTTTAACTGAAACAAATAAA
70598 TAGAGTTTAACTGAAA
1 TAGAGTTTAACTGAAA
70614 GATTATTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (24 bp):
TAGAGTTTAACTGAAACAAATAAA
Found at i:74773 original size:56 final size:55
Alignment explanation
Indices: 74713--74831 Score: 141
Period size: 56 Copynumber: 2.1 Consensus size: 55
74703 AAAGTGAATA
* * * *
74713 AAAAGTGAGTATTATGTGATATATGAAAATGTGAGCATGTTTACAT-ACATATGTG
1 AAAAGTGAGAAATATGTGATATATGAAAATGTGAGCATGATTACATGA-AAATGTG
* * * *
74768 TAAAAGTGAGAAATATGTGTTATGTGAGATTGTGAGCATGATTACATGAAAATGTG
1 -AAAAGTGAGAAATATGTGATATATGAAAATGTGAGCATGATTACATGAAAATGTG
74824 AAAAGTGA
1 AAAAGTGA
74832 ATTCTATGTG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
55 8 0.15
56 45 0.83
57 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (55 bp):
AAAAGTGAGAAATATGTGATATATGAAAATGTGAGCATGATTACATGAAAATGTG
Found at i:76802 original size:25 final size:25
Alignment explanation
Indices: 76773--76887 Score: 115
Period size: 25 Copynumber: 4.6 Consensus size: 25
76763 TTCTAAACTT
76773 TGGCTCGTAAGAGCGATATT-TCGTC
1 TGGCTCGTAAGAGCGATATTCT-GTC
* * *
76798 TGGCTTGTAAGAGTGATATTCTGTT
1 TGGCTCGTAAGAGCGATATTCTGTC
* *
76823 TGGCTCGTAAAAGTGATATTCTGTC
1 TGGCTCGTAAGAGCGATATTCTGTC
* * * *
76848 TAGCTTGTAAGAGCAATATTCTGCC
1 TGGCTCGTAAGAGCGATATTCTGTC
*
76873 TGGGCTCATAAGAGC
1 T-GGCTCGTAAGAGC
76888 TAAACTCTAT
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
25 62 0.85
26 11 0.15
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (25 bp):
TGGCTCGTAAGAGCGATATTCTGTC
Found at i:76830 original size:50 final size:50
Alignment explanation
Indices: 76771--76870 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 50
76761 TTTTCTAAAC
* * **
76771 TTTGGCTCGTAAGAGCGATATT-TCGTCTGGCTTGTAAGAGTGATATTCTG
1 TTTGGCTCGTAAAAGCGATATTCT-GTCTAGCTTGTAAGAGCAATATTCTG
*
76821 TTTGGCTCGTAAAAGTGATATTCTGTCTAGCTTGTAAGAGCAATATTCTG
1 TTTGGCTCGTAAAAGCGATATTCTGTCTAGCTTGTAAGAGCAATATTCTG
76871 CCTGGGCTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 43 0.98
51 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (50 bp):
TTTGGCTCGTAAAAGCGATATTCTGTCTAGCTTGTAAGAGCAATATTCTG
Found at i:90505 original size:12 final size:11
Alignment explanation
Indices: 90488--90526 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
90478 ATAACAACTT
90488 ATAAAATAAAAA
1 ATAAAA-AAAAA
90500 ATAAAAACAAAA
1 ATAAAAA-AAAA
*
90512 ACAAAAAAAAA
1 ATAAAAAAAAA
90523 ATAA
1 ATAA
90527 CAATTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (11 bp):
ATAAAAAAAAA
Found at i:100733 original size:22 final size:23
Alignment explanation
Indices: 100705--100758 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
100695 TAGTCAAAAG
* *
100705 AAAATAACAACTTATAAAATAA-
1 AAAATAACAAATAATAAAATAAT
100727 AAAATAA-AAATAATAAAATAAT
1 AAAATAACAAATAATAAAATAAT
100749 AAAATAACAA
1 AAAATAACAA
100759 TTTTTTGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.43
22 14 0.50
23 2 0.07
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (23 bp):
AAAATAACAAATAATAAAATAAT
Found at i:100744 original size:8 final size:8
Alignment explanation
Indices: 100718--100755 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
100708 ATAACAACTT
100718 ATAAAATA
1 ATAAAATA
100726 A-AAAAT-
1 ATAAAATA
100732 A-AAAATA
1 ATAAAATA
100739 ATAAAATA
1 ATAAAATA
100747 ATAAAATA
1 ATAAAATA
100755 A
1 A
100756 CAATTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.21
7 6 0.21
8 16 0.57
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
ATAAAATA
Found at i:108020 original size:25 final size:25
Alignment explanation
Indices: 107977--108103 Score: 110
Period size: 25 Copynumber: 5.0 Consensus size: 25
107967 TTGGATTCGA
* * *
107977 GATATTCTATCTAGTTCGTAAGAGC
1 GATATTCTGTCTGGCTCGTAAGAGC
*
108002 GATATTCTGTCTGGCTCGTAAGAGT
1 GATATTCTGTCTGGCTCGTAAGAGC
* * * ** *
108027 GACATTCTATCTAGCTCACAAGGGC
1 GATATTCTGTCTGGCTCGTAAGAGC
* *
108052 GATATTCTGTTTGAGCTCGTAAGAGA
1 GATATTCTGTCTG-GCTCGTAAGAGC
* *
108078 AATATTCTGTCTGGACTCATAAGAGC
1 GATATTCTGTCTGG-CTCGTAAGAGC
108104 TAAACACTGT
Statistics
Matches: 77, Mismatches: 23, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
25 49 0.64
26 28 0.36
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (25 bp):
GATATTCTGTCTGGCTCGTAAGAGC
Found at i:108037 original size:50 final size:51
Alignment explanation
Indices: 107980--108076 Score: 142
Period size: 50 Copynumber: 1.9 Consensus size: 51
107970 GATTCGAGAT
* **
107980 ATTCTATCTAGTTCGTAAGAGCGATATTCTGTCTG-GCTCGTAAGAGTGAC
1 ATTCTATCTAGCTCACAAGAGCGATATTCTGTCTGAGCTCGTAAGAGTGAC
* *
108030 ATTCTATCTAGCTCACAAGGGCGATATTCTGTTTGAGCTCGTAAGAG
1 ATTCTATCTAGCTCACAAGAGCGATATTCTGTCTGAGCTCGTAAGAG
108077 AAATATTCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 30 0.73
51 11 0.27
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (51 bp):
ATTCTATCTAGCTCACAAGAGCGATATTCTGTCTGAGCTCGTAAGAGTGAC
Found at i:108100 original size:26 final size:26
Alignment explanation
Indices: 108053--108102 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
108043 CACAAGGGCG
* *
108053 ATATTCTGTTTGAGCTCGTAAGAGAA
1 ATATTCTGTTGGAGCTCATAAGAGAA
108079 ATATTCTGTCTGGA-CTCATAAGAG
1 ATATTCTGT-TGGAGCTCATAAGAG
108103 CTAAACACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (26 bp):
ATATTCTGTTGGAGCTCATAAGAGAA
Found at i:110681 original size:56 final size:55
Alignment explanation
Indices: 110621--110748 Score: 143
Period size: 56 Copynumber: 2.3 Consensus size: 55
110611 AAAGTGAATA
* *
110621 AAAAGTGAATATTATGTGATATATGAAATTGTGAGCATGTTTACAT-ACATATGTG
1 AAAAGTGAATATTATGTGATATATGAAATTGTGAGCATGATTACATGA-AAATGTG
* * * * *
110676 TAAAAGTGATAAATT-TGTGTTATGTGAGATTTTGAGCATGATTACATGAAAATGTG
1 -AAAAGTGA-ATATTATGTGATATATGAAATTGTGAGCATGATTACATGAAAATGTG
*
110732 AAAAGTGAATTTTATGT
1 AAAAGTGAATATTATGT
110749 TTTAAATTTG
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
54 3 0.05
55 11 0.18
56 41 0.68
57 5 0.08
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.38
Consensus pattern (55 bp):
AAAAGTGAATATTATGTGATATATGAAATTGTGAGCATGATTACATGAAAATGTG
Found at i:111075 original size:27 final size:27
Alignment explanation
Indices: 111036--111088 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
111026 ATGATATATA
* *
111036 TTGAAATGGATGTGTTTAAT-TTGTGTG
1 TTGAAATGCATGT-TATAATATTGTGTG
111063 TTGAAATGCATGTTATAATATTGTGT
1 TTGAAATGCATGTTATAATATTGTGT
111089 TGATCTCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.26, C:0.02, G:0.25, T:0.47
Consensus pattern (27 bp):
TTGAAATGCATGTTATAATATTGTGTG
Found at i:121216 original size:21 final size:21
Alignment explanation
Indices: 121192--121242 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
121182 TGAGACAATA
121192 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCAT-ACTT
* *
121213 CTACCGAAACATGTCATACTT
1 CTACCGATACAAGTCATACTT
121234 CTACCGATA
1 CTACCGATA
121243 TTAAAAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (21 bp):
CTACCGATACAAGTCATACTT
Found at i:122307 original size:195 final size:195
Alignment explanation
Indices: 121999--122444 Score: 541
Period size: 195 Copynumber: 2.3 Consensus size: 195
121989 TATCAGTACC
* * * *
121999 CGATGCTACTCAC--GAGCTGTCGAAGACTCGCAACATATGCGGTACCCCAGCCACCGATACGAT
1 CGATGCTACTCACAAGAGCTGTCGAGGACTCACAACATATGCGGTACCTCAGCCATCGATACGAT
*** * *
122062 ATCTATTTGTAAACTGTCACCTAACGATGCTACTCACACGAGTTATCGAGAATATGCA-TTCAAG
66 ATCTATGCATAAACTGTCACCTAACAATGCTACTCACACGAGCTATCGAGAATATGCACTT-AAG
*
122126 -CATAAATCCCAACCATCGTAGGGCCTGTAATCCATT-TTAGGATTTCATATCTC-TTTT-TCGA
130 CCA-AAATCCCAACCATCGTAGGGCCTATAATCCATTCTT-GGA-TTCATATCTCATTTTCTCGA
122187 CACA
192 CACA
* *
122191 CGATGCTGCTCACAAGAGCTGTCGAGGACTCACAACAAATGCGGTACCTCAGCCATCGATAC-AG
1 CGATGCTACTCACAAGAGCTGTCGAGGACTCACAACATATGCGGTACCTCAGCCATCGATACGA-
* * * * *
122255 TATCTGTGCATATAACTGTCCCCTAACAATGCTGCTTACACGAGCTATCGAGAATATGCACTTAT
65 TATCTATGCATA-AACTGTCACCTAACAATGCTACTCACACGAGCTATCGAGAATATGCACTTAA
* * **
122320 GCCAAAATCCCAGCCATCGTAGGGCCTATAATCCATTCTTGGATTCATTTCTCATTTTCTCGATT
129 GCCAAAATCCCAACCATCGTAGGGCCTATAATCCATTCTTGGATTCATATCTCATTTTCTCGACA
122385 CA
194 CA
* * * *
122387 CGATGCTACTCACACA-AGCTATCGAGGACTCACAACATATCCAGTACCTCAACCATCG
1 CGATGCTACTCACA-AGAGCTGTCGAGGACTCACAACATATGCGGTACCTCAGCCATCG
122445 CATCAGTTTC
Statistics
Matches: 217, Mismatches: 27, Indels: 16
0.83 0.10 0.06
Matches are distributed among these distances:
192 12 0.06
193 1 0.00
194 59 0.27
195 82 0.38
196 62 0.29
197 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (195 bp):
CGATGCTACTCACAAGAGCTGTCGAGGACTCACAACATATGCGGTACCTCAGCCATCGATACGAT
ATCTATGCATAAACTGTCACCTAACAATGCTACTCACACGAGCTATCGAGAATATGCACTTAAGC
CAAAATCCCAACCATCGTAGGGCCTATAATCCATTCTTGGATTCATATCTCATTTTCTCGACACA
Found at i:124579 original size:27 final size:27
Alignment explanation
Indices: 124549--124600 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
124539 TAACTTTGAA
*
124549 ATTTTTATTTTCA-TTTTAATTGTTTTT
1 ATTTTAATTTT-AGTTTTAATTGTTTTT
*
124576 ATTTTAATTTTAGTTTTATTTGTTT
1 ATTTTAATTTTAGTTTTAATTGTTT
124601 ATGTTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (27 bp):
ATTTTAATTTTAGTTTTAATTGTTTTT
Found at i:125685 original size:20 final size:20
Alignment explanation
Indices: 125638--125685 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
125628 GGCTAAGGCA
* *
125638 AATATTTTCATGAATTTTTT
1 AATATTTTCATGAATGTTTC
* *
125658 AATTTTTTCATGTATGTTTC
1 AATATTTTCATGAATGTTTC
125678 AATATTTT
1 AATATTTT
125686 TACATAAGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.60
Consensus pattern (20 bp):
AATATTTTCATGAATGTTTC
Found at i:125705 original size:24 final size:20
Alignment explanation
Indices: 125655--125705 Score: 50
Period size: 24 Copynumber: 2.4 Consensus size: 20
125645 TCATGAATTT
125655 TTTAAT-TTTTTCATGTATG
1 TTTAATATTTTTCATGTATG
125674 TTTCAATATTTTTACATAAGTATG
1 TTT-AATATTTTT-CAT--GTATG
125698 CTTTAATA
1 -TTTAATA
125706 AATGAATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
21 5 0.19
22 3 0.12
24 9 0.35
25 3 0.12
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (20 bp):
TTTAATATTTTTCATGTATG
Found at i:131117 original size:21 final size:21
Alignment explanation
Indices: 131076--131128 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
131066 GGAGTTGTTA
*
131076 GTATCGATAGATGCATAACTT
1 GTATCGATAGAAGCATAACTT
*
131097 GTATCGATAGAAG-TTATACTT
1 GTATCGATAGAAGCATA-ACTT
*
131118 GTATCGGTAGA
1 GTATCGATAGA
131129 GCTAGAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (21 bp):
GTATCGATAGAAGCATAACTT
Found at i:143285 original size:23 final size:21
Alignment explanation
Indices: 143246--143349 Score: 90
Period size: 23 Copynumber: 4.9 Consensus size: 21
143236 ATTATATTAT
*
143246 TGTTTTGGTGCTATTTTTTTA
1 TGTTTTGGTGCTTTTTTTTTA
*
143267 CTGTTTTGGTTGCTTTTTTTGT-
1 -TGTTTTGG-TGCTTTTTTTTTA
143289 TGTTTTGGTG--TTTTTTTTA
1 TGTTTTGGTGCTTTTTTTTTA
143308 CTGTTTTGGTGCTATTTTGTTGTTA
1 -TGTTTTGGTGCT-TTTT-TT-TTA
* *
143333 T-TTTTGTTGCTATTTTT
1 TGTTTTGGTGCTTTTTTT
143350 GCTGTTATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 17
0.76 0.05 0.19
Matches are distributed among these distances:
18 7 0.10
20 12 0.17
21 10 0.14
22 11 0.16
23 23 0.33
24 3 0.04
25 3 0.04
ACGTcount: A:0.06, C:0.06, G:0.20, T:0.68
Consensus pattern (21 bp):
TGTTTTGGTGCTTTTTTTTTA
Found at i:143315 original size:41 final size:41
Alignment explanation
Indices: 143245--143331 Score: 133
Period size: 41 Copynumber: 2.1 Consensus size: 41
143235 AATTATATTA
*
143245 TTGTTTTGGTGCTATTTTTTTACTGTTTTGGTTGCTTTTTTTG
1 TTGTTTTGGTGCTATTTTTTTACTGTTTTGG-TGC-TATTTTG
143288 TTGTTTTGGTG-T-TTTTTTTACTGTTTTGGTGCTATTTTG
1 TTGTTTTGGTGCTATTTTTTTACTGTTTTGGTGCTATTTTG
143327 TTGTT
1 TTGTT
143332 ATTTTTGTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
39 11 0.26
40 3 0.07
41 17 0.40
42 1 0.02
43 11 0.26
ACGTcount: A:0.05, C:0.06, G:0.22, T:0.68
Consensus pattern (41 bp):
TTGTTTTGGTGCTATTTTTTTACTGTTTTGGTGCTATTTTG
Found at i:143318 original size:20 final size:20
Alignment explanation
Indices: 143246--143318 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
143236 ATTATATTAT
143246 TGTTTTGGTGCTATTTTTTTAC
1 TGTTTTGGTG-T-TTTTTTTAC
* **
143268 TGTTTTGGTTGCTTTTTTTGT
1 TGTTTTGG-TGTTTTTTTTAC
143289 TGTTTTGGTGTTTTTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
143309 TGTTTTGGTG
1 TGTTTTGGTG
143319 CTATTTTGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 19 0.43
21 15 0.34
22 8 0.18
23 2 0.05
ACGTcount: A:0.04, C:0.05, G:0.23, T:0.67
Consensus pattern (20 bp):
TGTTTTGGTGTTTTTTTTAC
Found at i:143325 original size:11 final size:11
Alignment explanation
Indices: 143311--143372 Score: 52
Period size: 12 Copynumber: 5.4 Consensus size: 11
143301 TTTTTTACTG
*
143311 TTTTGGTGCTA
1 TTTTGTTGCTA
*
143322 TTTTGTTGTTA
1 TTTTGTTGCTA
143333 TTTTTGTTGCTA
1 -TTTTGTTGCTA
* *
143345 TTTTTGCTGTTA
1 -TTTTGTTGCTA
*
143357 TTTTTGTTGTTA
1 -TTTTGTTGCTA
143369 TTTT
1 TTTT
143373 TATTGTTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
11 13 0.30
12 31 0.70
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.69
Consensus pattern (11 bp):
TTTTGTTGCTA
Found at i:143379 original size:24 final size:24
Alignment explanation
Indices: 143311--143379 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
143301 TTTTTTACTG
*
143311 TTTTGGTGCTA-TTTTGTTGTTAT
1 TTTTGTTGCTATTTTTGTTGTTAT
*
143334 TTTTGTTGCTATTTTTGCTGTTAT
1 TTTTGTTGCTATTTTTGTTGTTAT
* *
143358 TTTTGTTGTTATTTTTATTGTT
1 TTTTGTTGCTATTTTTGTTGTT
143380 TTACTGTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 10 0.25
24 30 0.75
ACGTcount: A:0.09, C:0.04, G:0.17, T:0.70
Consensus pattern (24 bp):
TTTTGTTGCTATTTTTGTTGTTAT
Found at i:143393 original size:12 final size:12
Alignment explanation
Indices: 143322--143379 Score: 89
Period size: 12 Copynumber: 4.8 Consensus size: 12
143312 TTTGGTGCTA
143322 TTTTGTTGTTAT
1 TTTTGTTGTTAT
*
143334 TTTTGTTGCTAT
1 TTTTGTTGTTAT
*
143346 TTTTGCTGTTAT
1 TTTTGTTGTTAT
143358 TTTTGTTGTTAT
1 TTTTGTTGTTAT
*
143370 TTTTATTGTT
1 TTTTGTTGTT
143380 TTACTGTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.09, C:0.03, G:0.16, T:0.72
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:143405 original size:32 final size:32
Alignment explanation
Indices: 143346--143413 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
143336 TTGTTGCTAT
* * * *
143346 TTTTGCTGTTATTTTTGTTGTTATTTTTATTG
1 TTTTACTGTTATTTTTGCTGCTATTTTTATTA
*
143378 TTTTACTGTTATTTTTGCTGCTGTTTTTATTA
1 TTTTACTGTTATTTTTGCTGCTATTTTTATTA
143410 TTTT
1 TTTT
143414 GATTGTTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.10, C:0.06, G:0.13, T:0.71
Consensus pattern (32 bp):
TTTTACTGTTATTTTTGCTGCTATTTTTATTA
Found at i:143429 original size:41 final size:39
Alignment explanation
Indices: 143366--143450 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 39
143356 ATTTTTGTTG
* * *
143366 TTATTTTTATTGTTTTACTGTTATTTTTGCTGCTGTTTTTA
1 TTATTTTGATTGTTTGACTGTTATTTTT-ATGC-GTTTTTA
*
143407 TTATTTTGATTGTTTGAGTGTTATTTTTATGCGTTTTTA
1 TTATTTTGATTGTTTGACTGTTATTTTTATGCGTTTTTA
143446 TTATT
1 TTATT
143451 GTTTCAGTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 12 0.30
40 3 0.08
41 25 0.62
ACGTcount: A:0.14, C:0.05, G:0.14, T:0.67
Consensus pattern (39 bp):
TTATTTTGATTGTTTGACTGTTATTTTTATGCGTTTTTA
Found at i:144032 original size:29 final size:30
Alignment explanation
Indices: 143997--144074 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
143987 ATTTATTTTT
*
143997 ATAATTTTTATATTTCTTA-TAATAATTGTA
1 ATAATTTTTATAATT-TTATTAATAATTGTA
*
144027 A-AA-TTTTATTAATTTTATTAATAATTTTA
1 ATAATTTTTA-TAATTTTATTAATAATTGTA
*
144056 ATAATTTTCTATACTTTTA
1 ATAATTTT-TATAATTTTA
144075 AAAGTTCATC
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
28 8 0.20
29 17 0.43
30 3 0.08
31 10 0.25
32 2 0.05
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (30 bp):
ATAATTTTTATAATTTTATTAATAATTGTA
Found at i:149365 original size:27 final size:28
Alignment explanation
Indices: 149327--149384 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
149317 CAGTGTTTGT
149327 AAGAAAGCCTTTATGGCTAAACTCTA-A
1 AAGAAAGCCTTTATGGCTAAACTCTAGA
* * * *
149354 AAGACAGCCTTTGTGGTTAATCTCTAGA
1 AAGAAAGCCTTTATGGCTAAACTCTAGA
149382 AAG
1 AAG
149385 GTGAGCCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (28 bp):
AAGAAAGCCTTTATGGCTAAACTCTAGA
Found at i:149578 original size:29 final size:29
Alignment explanation
Indices: 149498--149639 Score: 103
Period size: 29 Copynumber: 5.0 Consensus size: 29
149488 CTCTAAAAAA
** * *
149498 GAAAGCCTTTGTAACGATCTTTGTTAAAG
1 GAAAGCCTTTGTGGCGATATCTGTTAAAG
* *
149527 GAAAGCCTTTGTGGCTATCTCTGTTAAAG
1 GAAAGCCTTTGTGGCGATATCTGTTAAAG
*
149556 GACA-CCTTTGTGGCGAGTATCTG--AAAG
1 GAAAGCCTTTGTGGCGA-TATCTGTTAAAG
* * * *
149583 GAAAGTCTTTGTGGTGATCTCTATTAAAAG
1 GAAAGCCTTTGTGGCGATATCTGTT-AAAG
* ** *
149613 GAAA-CATTTGTGGTTATATCTATTAAA
1 GAAAGCCTTTGTGGCGATATCTGTTAAA
149640 TAATGTCTTT
Statistics
Matches: 92, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
27 11 0.12
28 24 0.26
29 49 0.53
30 8 0.09
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (29 bp):
GAAAGCCTTTGTGGCGATATCTGTTAAAG
Found at i:150885 original size:69 final size:69
Alignment explanation
Indices: 150772--150945 Score: 170
Period size: 69 Copynumber: 2.5 Consensus size: 69
150762 GTTTCAGTGG
* ** * * * * * *
150772 ACTCTACTTGTTGTCATAGCTGAGCTATTGTCTTACACCATGAAATCCTCATGTTTACTGTC-CT
1 ACTCTACTAGTTGTCATAGCCAAGCTATGGTGTTATAGCTTGAAATCATCATGTTTACTGTCTC-
150836 GACGA
65 GACGA
* * * * ** *
150841 ACTCTATTGGTTGTCATAGTCAAGCTATGGTTTTATAGCTTGAAATCATTGTGTTTATTGTCTCG
1 ACTCTACTAGTTGTCATAGCCAAGCTATGGTGTTATAGCTTGAAATCATCATGTTTACTGTCTCG
**
150906 GTGA
66 ACGA
150910 ACTCTACTAGTTGTCATAGCCAAGCTATGGTGTTAT
1 ACTCTACTAGTTGTCATAGCCAAGCTATGGTGTTAT
150946 GTCACAGGCC
Statistics
Matches: 84, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
69 83 0.99
70 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (69 bp):
ACTCTACTAGTTGTCATAGCCAAGCTATGGTGTTATAGCTTGAAATCATCATGTTTACTGTCTCG
ACGA
Found at i:164749 original size:33 final size:33
Alignment explanation
Indices: 164707--164770 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
164697 CCCTTCTTTT
* *
164707 AGTTGTTTAGCATGAAGCTCCATATATTGTTAG
1 AGTTGTTTAGCACGAAGCTCCACATATTGTTAG
164740 AGTTGTTTAGCACGAAGCTCCACATATTGTT
1 AGTTGTTTAGCACGAAGCTCCACATATTGTT
164771 GGAAGAGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (33 bp):
AGTTGTTTAGCACGAAGCTCCACATATTGTTAG
Found at i:168389 original size:15 final size:15
Alignment explanation
Indices: 168369--168401 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
168359 GGAAAGATGA
168369 AAAATAA-ACAAAAAT
1 AAAATAATA-AAAAAT
168384 AAAATAATAAAAAAT
1 AAAATAATAAAAAAT
168399 AAA
1 AAA
168402 CAAAATTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAATAATAAAAAAT
Found at i:172584 original size:26 final size:26
Alignment explanation
Indices: 172555--172655 Score: 76
Period size: 26 Copynumber: 3.9 Consensus size: 26
172545 CTAATGTTGT
* *
172555 TGCAGGAGCATGTCCAGAATTGTCGT
1 TGCAGGAACATGTCCAGAATTGTCGC
* * * *
172581 TGCAGAAACTTGTCTAGAATTATCGC
1 TGCAGGAACATGTCCAGAATTGTCGC
* * * *
172607 TACATGAACATGTCCAGAGTTGTCAC
1 TGCAGGAACATGTCCAGAATTGTCGC
* * * *
172633 TGTATGAGCATGTCTAGAATTGT
1 TGCAGGAACATGTCCAGAATTGT
172656 GCCTAGAATT
Statistics
Matches: 56, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (26 bp):
TGCAGGAACATGTCCAGAATTGTCGC
Found at i:179616 original size:20 final size:20
Alignment explanation
Indices: 179591--179629 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
179581 TGTTAGAATA
179591 AGGTTA-ATGTTAAGTTTAAG
1 AGGTTATAT-TTAAGTTTAAG
*
179611 AGGTTATATTTGAGTTTAA
1 AGGTTATATTTAAGTTTAA
179630 AAGAGTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (20 bp):
AGGTTATATTTAAGTTTAAG
Found at i:205985 original size:21 final size:21
Alignment explanation
Indices: 205959--206009 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 21
205949 GTTAGTTACA
*
205959 TGCATTTTATTTAGTTGTCAT
1 TGCATTTTATTTAGTTGTCAC
*
205980 TGCA--TT-TTTATTTGTCAC
1 TGCATTTTATTTAGTTGTCAC
205998 TGCATTTTATTT
1 TGCATTTTATTT
206010 GTTAGTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 14 0.56
19 2 0.08
20 2 0.08
21 7 0.28
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.59
Consensus pattern (21 bp):
TGCATTTTATTTAGTTGTCAC
Found at i:206625 original size:10 final size:11
Alignment explanation
Indices: 206612--206651 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
206602 TCACAAATAG
206612 AAAGAAAAAG-
1 AAAGAAAAAGA
*
206622 AAAGAAGAAGA
1 AAAGAAAAAGA
206633 AAAGAGAAAAGA
1 AAAGA-AAAAGA
206645 AAAGAAA
1 AAAGAAA
206652 TACATTACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 9 0.35
11 7 0.27
12 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:208971 original size:118 final size:118
Alignment explanation
Indices: 208758--208993 Score: 436
Period size: 118 Copynumber: 2.0 Consensus size: 118
208748 TGTCTTGCTC
*
208758 GTTAATTTAAACTATCGTTGCACCTTTCAGTGACAGTGACTACAATAACACTTCCGTGGTCAAAA
1 GTTAATTTAAACTATCGTTGCACCTTTCAGTAACAGTGACTACAATAACACTTCCGTGGTCAAAA
*
208823 CATTCAAACCTAAAGATTAAACAGTAGAAGCAAGAATGAATAAAATATCATTT
66 CATTCAAACCTAAAGATTAAACAATAGAAGCAAGAATGAATAAAATATCATTT
*
208876 GTTAGTTTAAACTATCGTTGCACCTTTCAGTAACAGTGACTACAATAACACTTCCGTGGTCAAAA
1 GTTAATTTAAACTATCGTTGCACCTTTCAGTAACAGTGACTACAATAACACTTCCGTGGTCAAAA
*
208941 CATTCAAACCTAAAGATTAAACAATAGAAGCAAGATTGAATAAAATATCATTT
66 CATTCAAACCTAAAGATTAAACAATAGAAGCAAGAATGAATAAAATATCATTT
208994 AGTCTAGAAA
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 114 1.00
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (118 bp):
GTTAATTTAAACTATCGTTGCACCTTTCAGTAACAGTGACTACAATAACACTTCCGTGGTCAAAA
CATTCAAACCTAAAGATTAAACAATAGAAGCAAGAATGAATAAAATATCATTT
Found at i:209867 original size:18 final size:18
Alignment explanation
Indices: 209833--209867 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
209823 CACTAACACT
*
209833 AAAATGCAACGATAATGG
1 AAAATGCAACGACAATGG
*
209851 AAAATGCAATGACAATG
1 AAAATGCAACGACAATG
209868 CTTACTAACA
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:0.51, C:0.11, G:0.20, T:0.17
Consensus pattern (18 bp):
AAAATGCAACGACAATGG
Found at i:212278 original size:24 final size:23
Alignment explanation
Indices: 212243--212291 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
212233 TCATTTCATC
*
212243 TTATATTAATTTGCTCTGACAAT
1 TTATATTAATTTGCACTGACAAT
*
212266 TTATCTTACATTTGCACTGACAAT
1 TTATATTA-ATTTGCACTGACAAT
212290 TT
1 TT
212292 TTACTCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (23 bp):
TTATATTAATTTGCACTGACAAT
Found at i:234961 original size:13 final size:14
Alignment explanation
Indices: 234938--234979 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
234928 GAGTTATTTG
234938 AAAGTATAAAAATA
1 AAAGTATAAAAATA
234952 AAAG-ATAAAAAT-
1 AAAGTATAAAAATA
*
234964 AAAGTAAAATAAATA
1 AAAGTATAA-AAATA
234979 A
1 A
234980 GAGAAAAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.17
13 11 0.46
14 8 0.33
15 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (14 bp):
AAAGTATAAAAATA
Found at i:234967 original size:26 final size:26
Alignment explanation
Indices: 234938--234987 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
234928 GAGTTATTTG
*
234938 AAAGTATAA-AAATAAAAGATAAAAAT
1 AAAGTAAAATAAATAAAAGA-AAAAAT
*
234964 AAAGTAAAATAAATAAGAGAAAAA
1 AAAGTAAAATAAATAAAAGAAAAA
234988 GCTTGAGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (26 bp):
AAAGTAAAATAAATAAAAGAAAAAAT
Found at i:236551 original size:14 final size:14
Alignment explanation
Indices: 236532--236558 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
236522 CCATCTCACC
236532 TCCTTATTTCTCCT
1 TCCTTATTTCTCCT
236546 TCCTTATTTCTCC
1 TCCTTATTTCTCC
236559 ATTTCGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.56
Consensus pattern (14 bp):
TCCTTATTTCTCCT
Found at i:239103 original size:88 final size:91
Alignment explanation
Indices: 238999--239184 Score: 263
Period size: 88 Copynumber: 2.0 Consensus size: 91
238989 CAAGTGATTA
238999 ACTAAATTAATTAAGTCTAATTATTTAC-AAA-A-T-TATAAAGGAAATTAAAAGAAGAAAAGAG
1 ACTAAATTAATTAAGTCTAATTATTTACAAAATACTATATAAAGGAAATTAAAAGAAGAAAAGA-
*
239060 GAGAAAAATTCACTTGTTTCTTCTTCT
65 GAGAAAAAATCACTTGTTTCTTCTTCT
239087 ACTAAATTAATTAAGTCTAATTATTTACAAAATTACCCTTTGTATATAAAGGAAATTAAAAGAAG
1 ACTAAATTAATTAAGTCTAATTATTTACAAAA-TA--C----TATATAAAGGAAATTAAAAGAAG
239152 AAAAGAGAGAAAAAATCACTTGTTTCTTCTTCT
59 AAAAGAGAGAAAAAATCACTTGTTTCTTCTTCT
239185 TCTACATGGC
Statistics
Matches: 86, Mismatches: 1, Indels: 12
0.87 0.01 0.12
Matches are distributed among these distances:
88 28 0.33
89 3 0.03
91 1 0.01
98 27 0.31
99 27 0.31
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (91 bp):
ACTAAATTAATTAAGTCTAATTATTTACAAAATACTATATAAAGGAAATTAAAAGAAGAAAAGAG
AGAAAAAATCACTTGTTTCTTCTTCT
Found at i:248474 original size:41 final size:41
Alignment explanation
Indices: 248429--248598 Score: 175
Period size: 41 Copynumber: 4.2 Consensus size: 41
248419 GCTTTAAGGT
* * *
248429 TAGCAGGCTTTATGACGATGCATTGTA-CTGGGCCTTGAGCC
1 TAGCAAGCTTTATGTCGATGTATTGTATC-GGGCCTTGAGCC
* *** * ** *
248470 TAGCAGGCTTCGCGCCGATG-ATT-TATCAAGCTTTGAGCC
1 TAGCAAGCTTTATGTCGATGTATTGTATCGGGCCTTGAGCC
* **
248509 TAGCAAGCTTTATGTCGGTGTATTGTATCATGCCTTGAGCC
1 TAGCAAGCTTTATGTCGATGTATTGTATCGGGCCTTGAGCC
*
248550 TAGCAAGCTTTATGTCGGTGTATTGTATCGGGCCTTGAGCC
1 TAGCAAGCTTTATGTCGATGTATTGTATCGGGCCTTGAGCC
248591 TAGCAAGC
1 TAGCAAGC
248599 ATCGTGTTGG
Statistics
Matches: 109, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
39 25 0.23
40 7 0.06
41 77 0.71
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (41 bp):
TAGCAAGCTTTATGTCGATGTATTGTATCGGGCCTTGAGCC
Found at i:263627 original size:26 final size:27
Alignment explanation
Indices: 263583--263642 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
263573 CAAGTCGTTC
* *
263583 CAGAAGTTTAGCTCATACGAGCCCCAA
1 CAGAAGTTTAACTCATACGAGCCCAAA
* *
263610 CAGAA-TTTAACTCTTACGATCCCAAA
1 CAGAAGTTTAACTCATACGAGCCCAAA
263636 CA-AAGTT
1 CAGAAGTT
263643 ACGCTCTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 2 0.07
26 21 0.75
27 5 0.18
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (27 bp):
CAGAAGTTTAACTCATACGAGCCCAAA
Found at i:271496 original size:27 final size:27
Alignment explanation
Indices: 271447--271541 Score: 81
Period size: 30 Copynumber: 3.4 Consensus size: 27
271437 AATTTTAGTT
271447 AATAATAATAAAATTATATTTTAACTTAAA
1 AATAATAA-AAAATTA-A-TTTAACTTAAA
271477 AATAATAAAAAATTAATTTAACTTTTCAAA
1 AATAATAAAAAATTAATTTAAC--TT-AAA
* *
271507 AATTAT-AAAAATATAAATT-A-TT-AA
1 AATAATAAAAAAT-TAATTTAACTTAAA
271531 AATAATAAAAA
1 AATAATAAAAA
271542 TAATATTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
24 7 0.12
25 4 0.07
26 2 0.04
27 6 0.11
28 1 0.02
29 16 0.28
30 21 0.37
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (27 bp):
AATAATAAAAAATTAATTTAACTTAAA
Found at i:271526 original size:15 final size:16
Alignment explanation
Indices: 271506--271539 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
271496 AACTTTTCAA
271506 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
271521 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
271537 AAA
1 AAA
271540 AATAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:272049 original size:13 final size:13
Alignment explanation
Indices: 272031--272055 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
272021 TTTGGTAAAT
272031 TAATAAATATAAG
1 TAATAAATATAAG
272044 TAATAAATATAA
1 TAATAAATATAA
272056 TGATACTGTT
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:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
TAATAAATATAAG
Found at i:272978 original size:11 final size:11
Alignment explanation
Indices: 272938--272978 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
272928 ATTAATTATT
272938 TTTTAAAA-TA
1 TTTTAAAATTA
272948 TTTTAAAATTA
1 TTTTAAAATTA
*
272959 ATTTAAAATTA
1 TTTTAAAATTA
*
272970 TTTTTAAAT
1 TTTTAAAAT
272979 ATAAAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATTA
Done.