Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015306.1 Kokia drynarioides strain JFW-HI SEQ_130351, 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: 63935
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Warning! 265 characters in sequence are not A, C, G, or T
Found at i:4247 original size:20 final size:20
Alignment explanation
Indices: 4211--4248 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4201 AACATAATCT
*
4211 TAAACATTAAATCTAAAATA
1 TAAACATTAAATATAAAATA
4231 TAAACA-TATAATATAAAA
1 TAAACATTA-AATATAAAA
4249 ATTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAACATTAAATATAAAATA
Found at i:5318 original size:28 final size:28
Alignment explanation
Indices: 5286--5343 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
5276 ATACGAAACA
*
5286 AACTCGTCCAGCACCGAAGTGCGGTAAT
1 AACTCGTCCAGCACAGAAGTGCGGTAAT
5314 AACTCGTCCAGCACAGAAGTGCGGTAAT
1 AACTCGTCCAGCACAGAAGTGCGGTAAT
5342 AA
1 AA
5344 GCGTGCAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (28 bp):
AACTCGTCCAGCACAGAAGTGCGGTAAT
Found at i:9073 original size:12 final size:12
Alignment explanation
Indices: 9056--9230 Score: 109
Period size: 12 Copynumber: 15.4 Consensus size: 12
9046 ATAACATCCA
*
9056 AACAACAAAAAT
1 AACAACAAAAAC
*
9068 AACAACCAAAAC
1 AACAACAAAAAC
** * *
9080 AGTAGCAAAAAT
1 AACAACAAAAAC
*
9092 AACAGC-AAAAC
1 AACAACAAAAAC
**
9103 AA-AA-TTAAA-
1 AACAACAAAAAC
*
9112 AACAACAAAAAT
1 AACAACAAAAAC
*
9124 AACAACAAAAAT
1 AACAACAAAAAC
*
9136 AACAGCAAAAAC
1 AACAACAAAAAC
*
9148 AACAACCAAAAC
1 AACAACAAAAAC
9160 AAC-A-AAAAAC
1 AACAACAAAAAC
*
9170 AA-TACAAAAAC
1 AACAACAAAAAC
* *
9181 AGCAA-AAAAAA
1 AACAACAAAAAC
*
9192 AACAACCAAAAC
1 AACAACAAAAAC
*
9204 AATAA-AAAAAC
1 AACAACAAAAAC
*
9215 AACATC-AAAAC
1 AACAACAAAAAC
9226 AACAA
1 AACAA
9231 TATATTTTTT
Statistics
Matches: 124, Mismatches: 30, Indels: 19
0.72 0.17 0.11
Matches are distributed among these distances:
9 2 0.02
10 14 0.11
11 43 0.35
12 65 0.52
ACGTcount: A:0.71, C:0.20, G:0.03, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:9115 original size:56 final size:57
Alignment explanation
Indices: 9055--9161 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 57
9045 AATAACATCC
* ** * *
9055 AAACAACAAAAATAACAACCAAAACAGTAGCAAAAATAAC-AGCAAAACAAAATTAA
1 AAACAACAAAAATAACAACAAAAACAACAGCAAAAACAACAACCAAAACAAAATTAA
*
9111 AAACAACAAAAATAACAACAAAAATAACAGCAAAAACAACAACCAAAACAA
1 AAACAACAAAAATAACAACAAAAACAACAGCAAAAACAACAACCAAAACAA
9162 CAAAAAACAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
56 35 0.80
57 9 0.20
ACGTcount: A:0.70, C:0.20, G:0.04, T:0.07
Consensus pattern (57 bp):
AAACAACAAAAATAACAACAAAAACAACAGCAAAAACAACAACCAAAACAAAATTAA
Found at i:9116 original size:44 final size:44
Alignment explanation
Indices: 9042--9230 Score: 125
Period size: 44 Copynumber: 4.5 Consensus size: 44
9032 AAAAACGCAT
* * * ** *
9042 AAAAATAACATCCAAACAACAAAAATAACAACCAAAACAGTAGC
1 AAAAATAACAGCAAAACAACAAAAATAACAACAAAAACAACAAC
*
9086 AAAAATAACAGCAAAACAA-AATTAAA-AACAACAAAAATAACAAC
1 AAAAATAACAGCAAAACAACAA--AAATAACAACAAAAACAACAAC
* *
9130 AAAAATAACAGCAAAAACAACAACCAA-AACAAC-AAAA-AACAAT
1 AAAAATAACAGC-AAAACAACAA-AAATAACAACAAAAACAACAAC
* * *
9173 ACAAA-AACAGC---A-AA-AAAAA-AACAACCAAAACAATAA-
1 AAAAATAACAGCAAAACAACAAAAATAACAACAAAAACAACAAC
* *
9209 AAAAACAACATCAAAACAACAA
1 AAAAATAACAGCAAAACAACAA
9231 TATATTTTTT
Statistics
Matches: 118, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
35 8 0.07
36 10 0.08
37 11 0.09
38 1 0.01
40 1 0.01
41 2 0.02
42 8 0.07
43 11 0.09
44 46 0.39
45 18 0.15
46 2 0.02
ACGTcount: A:0.71, C:0.20, G:0.03, T:0.06
Consensus pattern (44 bp):
AAAAATAACAGCAAAACAACAAAAATAACAACAAAAACAACAAC
Found at i:9120 original size:15 final size:15
Alignment explanation
Indices: 9100--9230 Score: 54
Period size: 15 Copynumber: 8.3 Consensus size: 15
9090 ATAACAGCAA
*
9100 AACAAAATTAAAAAC
1 AACAAAAATAAAAAC
*
9115 AACAAAAATAACAAC
1 AACAAAAATAAAAAC
* *
9130 AAAAATAACAGCAAAAAC
1 AACAA-AA-A-TAAAAAC
* *
9148 AACAACCAA-AACAAC
1 AACAA-AAATAAAAAC
*
9163 AAAAAACAATACAAAAAC
1 AACAAA-AAT--AAAAAC
*
9181 AGCAAAAA-AAAAAC
1 AACAAAAATAAAAAC
9195 AACCAAAACAATAAAAA-
1 AA-C-AAA-AATAAAAAC
* *
9212 AAC-AACATCAAAAC
1 AACAAAAATAAAAAC
9226 AACAA
1 AACAA
9231 TATATTTTTT
Statistics
Matches: 86, Mismatches: 17, Indels: 26
0.67 0.13 0.20
Matches are distributed among these distances:
13 6 0.07
14 12 0.14
15 30 0.35
16 6 0.07
17 8 0.09
18 24 0.28
ACGTcount: A:0.73, C:0.20, G:0.02, T:0.05
Consensus pattern (15 bp):
AACAAAAATAAAAAC
Found at i:9127 original size:9 final size:9
Alignment explanation
Indices: 9109--9216 Score: 50
Period size: 9 Copynumber: 12.2 Consensus size: 9
9099 AAACAAAATT
9109 AAAAACAAC
1 AAAAACAAC
*
9118 AAAAATAAC
1 AAAAACAAC
*
9127 AACAAA-AAT
1 AA-AAACAAC
* *
9136 AACAGCAA-
1 AAAAACAAC
9144 AAACAACAAC
1 AAA-AACAAC
*
9154 CAAAACAAC
1 AAAAACAAC
9163 AAAAAACAATAC
1 -AAAAAC-A-AC
*
9175 AAAAACAGC
1 AAAAACAAC
9184 --AAA-AA-
1 AAAAACAAC
9189 AAAAACAAC
1 AAAAACAAC
* *
9198 CAAAACAAT
1 AAAAACAAC
9207 AAAAA-AAC
1 AAAAACAAC
9215 AA
1 AA
9217 CATCAAAACA
Statistics
Matches: 74, Mismatches: 14, Indels: 23
0.67 0.13 0.21
Matches are distributed among these distances:
6 1 0.01
7 6 0.08
8 9 0.12
9 38 0.51
10 11 0.15
11 7 0.09
12 2 0.03
ACGTcount: A:0.75, C:0.19, G:0.02, T:0.04
Consensus pattern (9 bp):
AAAAACAAC
Found at i:9177 original size:20 final size:21
Alignment explanation
Indices: 9110--9230 Score: 82
Period size: 22 Copynumber: 5.5 Consensus size: 21
9100 AACAAAATTA
* *
9110 AAAACAACAAAAATA-ACAACA
1 AAAACAACAAAAA-ACAAAACC
*
9131 AAAATAACAGCAAAAACAACAACC
1 AAAACAACA--AAAAACAA-AACC
* *
9155 AAAACAACAAAAAACAATACA
1 AAAACAACAAAAAACAAAACC
* *
9176 AAAACAGCAAAAAAAAAACAACC
1 AAAACAAC-AAAAAACAA-AACC
* * *
9199 AAAACAATAAAAAAACAACATC
1 AAAACAA-CAAAAAACAAAACC
9221 AAAACAACAA
1 AAAACAACAA
9231 TATATTTTTT
Statistics
Matches: 77, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
21 19 0.25
22 26 0.34
23 21 0.27
24 11 0.14
ACGTcount: A:0.74, C:0.21, G:0.02, T:0.04
Consensus pattern (21 bp):
AAAACAACAAAAAACAAAACC
Found at i:9779 original size:13 final size:13
Alignment explanation
Indices: 9761--9786 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9751 AGGGTTTTCG
9761 TTTCATTATGAGT
1 TTTCATTATGAGT
9774 TTTCATTATGAGT
1 TTTCATTATGAGT
9787 CTACTTTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
TTTCATTATGAGT
Found at i:13212 original size:12 final size:12
Alignment explanation
Indices: 13197--13236 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
13187 TTTCTTTTTA
*
13197 ATTAATGCTATT
1 ATTAATGTTATT
*
13209 ATTAATATTATT
1 ATTAATGTTATT
13221 ATTAATGTTATT
1 ATTAATGTTATT
13233 ATTA
1 ATTA
13237 TTACCATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (12 bp):
ATTAATGTTATT
Found at i:13963 original size:6 final size:6
Alignment explanation
Indices: 13952--14036 Score: 75
Period size: 6 Copynumber: 14.2 Consensus size: 6
13942 TTTTAAATCC
** **
13952 ATTTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAAAA AGATAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT--AA ATTTAA ATTTAA
* **
14001 ATTT-A ATATAA ATTTAA ATTTAA AAATAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
14037 CCTAATTTTA
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
5 7 0.11
6 50 0.82
8 4 0.07
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (6 bp):
ATTTAA
Found at i:13978 original size:17 final size:17
Alignment explanation
Indices: 13955--14036 Score: 94
Period size: 17 Copynumber: 4.6 Consensus size: 17
13945 TAAATCCATT
13955 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAG
*
13972 CAAATTTAAATTTAAAAAG
1 TAAATTTAAATTT--AAAG
13991 ATAAATTTAAATTTAATA-
1 -TAAATTTAAATTTAA-AG
*
14009 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTT-AAAG
14027 TAAATTTAAA
1 TAAATTTAAA
14037 CCTAATTTTA
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
17 26 0.46
18 14 0.25
19 5 0.09
20 12 0.21
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:13996 original size:37 final size:35
Alignment explanation
Indices: 13955--14036 Score: 121
Period size: 37 Copynumber: 2.3 Consensus size: 35
13945 TAAATCCATT
13955 TAAATTTAAATTTAA-AGCAAATTTAAATTTAAAAAGA
1 TAAATTTAAATTTAATA-CAAATTTAAATTT-AAAA-A
*
13992 TAAATTTAAATTTAATATAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAATACAAATTTAAATTTAAAAA
14027 TAAATTTAAA
1 TAAATTTAAA
14037 CCTAATTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 11 0.26
36 4 0.09
37 27 0.63
38 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39
Consensus pattern (35 bp):
TAAATTTAAATTTAATACAAATTTAAATTTAAAAA
Found at i:40970 original size:66 final size:66
Alignment explanation
Indices: 40832--40967 Score: 265
Period size: 66 Copynumber: 2.1 Consensus size: 66
40822 TTGTTATTAC
40832 ATAAATAAATGGTTTGTTTGGTTCATTTTTGTAATTAGTGGATCATACTTAATTGAATATTTTAA
1 ATAAATAAATGGTTTGTTTGGTTCATTTTTGTAATTAGTGGATCATACTTAATTGAATATTTTAA
40897 T
66 T
40898 ATAAATAAATGGTTTGTTTGGTTCATTTTTGTAATTAGTGGATCATACTTAATTGAATATTTTAA
1 ATAAATAAATGGTTTGTTTGGTTCATTTTTGTAATTAGTGGATCATACTTAATTGAATATTTTAA
40963 T
66 T
40964 -TAAA
1 ATAAA
40968 ATATTCAATT
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
65 4 0.06
66 66 0.94
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (66 bp):
ATAAATAAATGGTTTGTTTGGTTCATTTTTGTAATTAGTGGATCATACTTAATTGAATATTTTAA
T
Found at i:42802 original size:20 final size:20
Alignment explanation
Indices: 42781--42821 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
42771 TTTTATATAA
42781 TTTTTATAATATTTTTTAAAT
1 TTTTTAT-ATATTTTTTAAAT
42802 TTTTTATATATTTTTTAAAT
1 TTTTTATATATTTTTTAAAT
42822 ATAAATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTATATATTTTTTAAAT
Found at i:42823 original size:11 final size:11
Alignment explanation
Indices: 42771--42823 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
42761 TTTTAACTTC
* *
42771 TTTTATATAAT
1 TTTTAAATATT
42782 TTTTATAATATT
1 TTTTA-AATATT
42794 TTTT-AA-ATT
1 TTTTAAATATT
*
42803 TTTTATATATT
1 TTTTAAATATT
42814 TTTTAAATAT
1 TTTTAAATAT
42824 AAATTTTGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 7 0.20
10 3 0.09
11 17 0.49
12 8 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTAAATATT
Found at i:44177 original size:23 final size:24
Alignment explanation
Indices: 44151--44200 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
44141 TCATATTAAG
44151 ATAGTTACAAATAAAATAATAA-A
1 ATAGTTACAAATAAAATAATAATA
44174 ATAGTTACAAATAAAATAATAATA
1 ATAGTTACAAATAAAATAATAATA
44198 ATA
1 ATA
44201 ATTTGCAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (24 bp):
ATAGTTACAAATAAAATAATAATA
Found at i:44278 original size:18 final size:20
Alignment explanation
Indices: 44233--44275 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
44223 TACAATATTC
*
44233 AAATAATATTAAAAAACACA
1 AAATAATAGTAAAAAACACA
*
44253 AAATAATAGTAAAAAACATA
1 AAATAATAGTAAAAAACACA
44273 AAA
1 AAA
44276 ATAACATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.19
Consensus pattern (20 bp):
AAATAATAGTAAAAAACACA
Found at i:44350 original size:9 final size:9
Alignment explanation
Indices: 44325--44366 Score: 57
Period size: 9 Copynumber: 4.4 Consensus size: 9
44315 CAAAAATAGC
44325 AACAAAACAA
1 AACAAAA-AA
44335 CAACAAAAAA
1 -AACAAAAAA
44345 AACAAAAAA
1 AACAAAAAA
*
44354 AACAACAAA
1 AACAAAAAA
44363 AACA
1 AACA
44367 GTAACAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 21 0.70
10 2 0.07
11 7 0.23
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (9 bp):
AACAAAAAA
Found at i:44357 original size:21 final size:21
Alignment explanation
Indices: 44313--44438 Score: 81
Period size: 21 Copynumber: 5.6 Consensus size: 21
44303 TCAAAACTGT
* *
44313 AACAAAAATAGCAACAAAACAAC
1 AACAAAAAAAACAA-AAAA-AAC
44336 AACAAAAAAAACAAAAAAAAC
1 AACAAAAAAAACAAAAAAAAC
*
44357 AACAAAAACAGTAACAAAAATAAC
1 AACAAAAA-A--AACAAAAAAAAC
* * * *
44381 AATAACAATAGCAACAAAAACAAT
1 AACAA-AA-A-AAACAAAAAAAAC
* * *
44405 AACAAAAATAACAAAAACAAT
1 AACAAAAAAAACAAAAAAAAC
*
44426 AACAACAAAAACA
1 AACAAAAAAAACA
44439 GCAACAAAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
21 34 0.40
22 6 0.07
23 14 0.16
24 29 0.34
25 2 0.02
26 1 0.01
ACGTcount: A:0.74, C:0.17, G:0.02, T:0.06
Consensus pattern (21 bp):
AACAAAAAAAACAAAAAAAAC
Found at i:44396 original size:36 final size:35
Alignment explanation
Indices: 44312--44454 Score: 170
Period size: 36 Copynumber: 4.2 Consensus size: 35
44302 ATCAAAACTG
*
44312 TAAC-AAA-AATAGCAAC-AAAACAACAACAAAAA
1 TAACAAAACAATAACAACAAAAACAACAACAAAAA
* **
44344 AAACAAAA-AA-AACAACAAAAACAGTAACAAAAA
1 TAACAAAACAATAACAACAAAAACAACAACAAAAA
* *
44377 TAACAATAACAATAGCAACAAAAACAATAACAAAAA
1 TAACAA-AACAATAACAACAAAAACAACAACAAAAA
*
44413 TAACAAAAACAATAACAACAAAAACAGCAACAAAAA
1 TAAC-AAAACAATAACAACAAAAACAACAACAAAAA
44449 TAACAA
1 TAACAA
44455 CGTCAAAACA
Statistics
Matches: 95, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
32 8 0.08
33 24 0.25
34 2 0.02
35 4 0.04
36 55 0.58
37 2 0.02
ACGTcount: A:0.73, C:0.17, G:0.03, T:0.07
Consensus pattern (35 bp):
TAACAAAACAATAACAACAAAAACAACAACAAAAA
Found at i:44505 original size:9 final size:9
Alignment explanation
Indices: 44488--44561 Score: 51
Period size: 9 Copynumber: 8.0 Consensus size: 9
44478 ACCAAAACAG
*
44488 CAATCAAAA
1 CAATAAAAA
44497 CAATAAAAA
1 CAATAAAAA
*
44506 -AATCAAAA
1 CAATAAAAA
*
44514 CAGTAAAAAA
1 CAAT-AAAAA
44524 CAATACCAAAA
1 CAATA--AAAA
**
44535 CAGCAAAAA
1 CAATAAAAA
**
44544 CAACCAAAA
1 CAATAAAAA
44553 CAATAAAAA
1 CAATAAAAA
44562 AACCAATACC
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
8 7 0.14
9 29 0.58
10 7 0.14
11 7 0.14
ACGTcount: A:0.70, C:0.19, G:0.03, T:0.08
Consensus pattern (9 bp):
CAATAAAAA
Found at i:44513 original size:29 final size:28
Alignment explanation
Indices: 44480--44563 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 28
44470 AAAACACCAC
*
44480 CAAAACAGCAATCAAAACAATAAAAAAAT
1 CAAAACAGCAA-CAAAACAATAAAAAAAG
* *
44509 CAAAACAGTAA-AAAACAATACCAAAACAG
1 CAAAACAGCAACAAAACAATA--AAAAAAG
44538 CAAAA-A-CAACCAAAACAATAAAAAAA
1 CAAAACAGCAA-CAAAACAATAAAAAAA
44564 CCAATACCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
27 16 0.35
28 1 0.02
29 29 0.63
ACGTcount: A:0.70, C:0.19, G:0.04, T:0.07
Consensus pattern (28 bp):
CAAAACAGCAACAAAACAATAAAAAAAG
Found at i:44534 original size:21 final size:21
Alignment explanation
Indices: 44509--44577 Score: 81
Period size: 20 Copynumber: 3.3 Consensus size: 21
44499 ATAAAAAAAT
44509 CAAAACAGTAAAAAACAATAC
1 CAAAACAGTAAAAAACAATAC
*
44530 CAAAACAG-CAAAAAC-A-AC
1 CAAAACAGTAAAAAACAATAC
*
44548 CAAAACAATAAAAAAACCAATAC
1 CAAAACAGT-AAAAAA-CAATAC
44571 CAAAACA
1 CAAAACA
44578 ATAATATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 9 0.22
19 1 0.03
20 11 0.28
21 9 0.22
22 1 0.03
23 9 0.22
ACGTcount: A:0.68, C:0.23, G:0.03, T:0.06
Consensus pattern (21 bp):
CAAAACAGTAAAAAACAATAC
Found at i:44540 original size:50 final size:48
Alignment explanation
Indices: 44426--44540 Score: 137
Period size: 50 Copynumber: 2.4 Consensus size: 48
44416 CAAAAACAAT
* **
44426 AACAACA--AAAACAGCAACAAAAATAACAACGTCAAAACAGTAAAAA
1 AACAACACCAAAACAGCAACAAAAATAAAAAAATCAAAACAGTAAAAA
*
44472 AACACCACCAAAACAGCAATCAAAACAATAAAAAAATCAAAACAGT-AAAA
1 AACAACACCAAAACAGCAA-C-AAA-AATAAAAAAATCAAAACAGTAAAAA
*
44522 AACAATACCAAAACAGCAA
1 AACAACACCAAAACAGCAA
44541 AAACAACCAA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
46 6 0.10
48 10 0.17
49 1 0.02
50 24 0.41
51 17 0.29
ACGTcount: A:0.66, C:0.22, G:0.05, T:0.07
Consensus pattern (48 bp):
AACAACACCAAAACAGCAACAAAAATAAAAAAATCAAAACAGTAAAAA
Found at i:44565 original size:17 final size:17
Alignment explanation
Indices: 44492--44567 Score: 71
Period size: 18 Copynumber: 4.2 Consensus size: 17
44482 AAACAGCAAT
*
44492 CAAAACAATAAAAAAAT
1 CAAAACAATAAAAAAAC
*
44509 CAAAACAGTAAAAAACAATAC
1 CAAAACA--ATAAAA-AA-AC
**
44530 CAAAACAGCAAAAACAAC
1 CAAAACAATAAAAA-AAC
44548 CAAAACAATAAAAAAAC
1 CAAAACAATAAAAAAAC
44565 CAA
1 CAA
44568 TACCAAAACA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
17 13 0.27
18 15 0.31
19 10 0.21
20 2 0.04
21 8 0.17
ACGTcount: A:0.71, C:0.20, G:0.03, T:0.07
Consensus pattern (17 bp):
CAAAACAATAAAAAAAC
Found at i:44574 original size:41 final size:38
Alignment explanation
Indices: 44492--44578 Score: 111
Period size: 41 Copynumber: 2.2 Consensus size: 38
44482 AAACAGCAAT
* * *
44492 CAAAACAATAAAAAAATCAAAACAGTAAAAAACAATAC
1 CAAAACAACAAAAAAACCAAAACAATAAAAAACAATAC
*
44530 CAAAACAGCAAAAACAACCAAAACAATAAAAAAACCAATAC
1 CAAAACAACAAAAA-AACCAAAACAAT-AAAAAA-CAATAC
44571 CAAAACAA
1 CAAAACAA
44579 TAATATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 12 0.29
39 10 0.24
40 6 0.15
41 13 0.32
ACGTcount: A:0.70, C:0.21, G:0.02, T:0.07
Consensus pattern (38 bp):
CAAAACAACAAAAAAACCAAAACAATAAAAAACAATAC
Found at i:45201 original size:2 final size:2
Alignment explanation
Indices: 45194--45218 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45184 CTTCCCCTAT
45194 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
45219 GCCCCAACAC
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:53017 original size:21 final size:20
Alignment explanation
Indices: 52991--53037 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
52981 TCAAAGATAA
*
52991 TAAAAAATCTATTTTAAAAAT
1 TAAAAAATATATTTT-AAAAT
* *
53012 TAAAAATTATATTTTTAAAT
1 TAAAAAATATATTTTAAAAT
53032 TAAAAA
1 TAAAAA
53038 TATTAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAAAATATATTTTAAAAT
Found at i:53018 original size:20 final size:20
Alignment explanation
Indices: 52993--53038 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
52983 AAAGATAATA
52993 AAAAATCTAT-TTTAAAAATT
1 AAAAAT-TATATTTAAAAATT
**
53013 AAAAATTATATTTTTAAATT
1 AAAAATTATATTTAAAAATT
53033 AAAAAT
1 AAAAAT
53039 ATTAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATTATATTTAAAAATT
Found at i:54029 original size:19 final size:20
Alignment explanation
Indices: 54005--54047 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
53995 AATTGTTTGT
54005 AAAATTATATT-TAAAA-AAA
1 AAAATTAT-TTGTAAAATAAA
*
54024 AAAATTGTTTGTAAAATAAA
1 AAAATTATTTGTAAAATAAA
54044 AAAA
1 AAAA
54048 ATACACTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 12 0.57
20 7 0.33
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAATTATTTGTAAAATAAA
Found at i:54552 original size:41 final size:42
Alignment explanation
Indices: 54495--54577 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 42
54485 CAAATATTTT
*
54495 TAAACCCAAATATAATTTCATTCTTAAA-AACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAC
*
54536 TAAACCCAAATATAATTTTATTCCTAAATAACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAC
54578 AATTCATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 26 0.67
42 13 0.33
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAC
Done.