Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013549.1 Kokia drynarioides strain JFW-HI SEQ_128575, 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: 156092
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 117 characters in sequence are not A, C, G, or T
Found at i:6346 original size:18 final size:18
Alignment explanation
Indices: 6323--6360 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
6313 AGTTACTGCA
6323 GTGGACAACTCGACCCGC
1 GTGGACAACTCGACCCGC
*
6341 GTGGACAACTCGACCTGC
1 GTGGACAACTCGACCCGC
6359 GT
1 GT
6361 AGGGTAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.34, G:0.29, T:0.16
Consensus pattern (18 bp):
GTGGACAACTCGACCCGC
Found at i:11250 original size:23 final size:24
Alignment explanation
Indices: 11224--11269 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
11214 TAATTTTTTT
11224 AAAACCAT-TTATTAAATTATAGA
1 AAAACCATATTATTAAATTATAGA
11247 AAAACCATAATTATTAAATTATA
1 AAAACCAT-ATTATTAAATTATA
11270 AAAGAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 8 0.38
25 13 0.62
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAACCATATTATTAAATTATAGA
Found at i:20098 original size:161 final size:161
Alignment explanation
Indices: 19833--20156 Score: 630
Period size: 161 Copynumber: 2.0 Consensus size: 161
19823 AATTATTTCC
19833 TGGGCATATACTATTATTTTATCTATATCCTAATTTTTTAATAATAAAATATTTATATTCCTTAG
1 TGGGCATATACTATTATTTTATCTATATCCTAATTTTTTAATAATAAAATATTTATATTCCTTAG
*
19898 TTGGCAATCACGTTTGATTTACGTGTCAATTCAACATTAATATGCTAAATGTACATTTTATAAAA
66 TTGGCAATCACGTTTGATTTACATGTCAATTCAACATTAATATGCTAAATGTACATTTTATAAAA
19963 TTCAATTAATTAAAGTCAAATTTCAAAAGTT
131 TTCAATTAATTAAAGTCAAATTTCAAAAGTT
19994 TGGGCATATACTATTATTTTATCTATATCCTAATTTTTTAATAATAAAATATTTATATTCCTTAG
1 TGGGCATATACTATTATTTTATCTATATCCTAATTTTTTAATAATAAAATATTTATATTCCTTAG
*
20059 TTGGCAATCACGTTTGATTTACATGTGAATTCAACATTAATATGCTAAATGTACATTTTATAAAA
66 TTGGCAATCACGTTTGATTTACATGTCAATTCAACATTAATATGCTAAATGTACATTTTATAAAA
20124 TTCAATTAATTAAAGTCAAATTTCAAAAGTT
131 TTCAATTAATTAAAGTCAAATTTCAAAAGTT
20155 TG
1 TG
20157 ACTTTAAAAA
Statistics
Matches: 161, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 161 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (161 bp):
TGGGCATATACTATTATTTTATCTATATCCTAATTTTTTAATAATAAAATATTTATATTCCTTAG
TTGGCAATCACGTTTGATTTACATGTCAATTCAACATTAATATGCTAAATGTACATTTTATAAAA
TTCAATTAATTAAAGTCAAATTTCAAAAGTT
Found at i:28127 original size:6 final size:6
Alignment explanation
Indices: 28116--28140 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28106 CGAGAATGAT
28116 TTTCTC TTTCTC TTTCTC TTTCTC T
1 TTTCTC TTTCTC TTTCTC TTTCTC T
28141 GTTTTCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCTC
Found at i:30422 original size:2 final size:2
Alignment explanation
Indices: 30417--30441 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30407 TAAAAAAAAA
30417 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
30442 AAAAGGTAAA
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:34530 original size:3 final size:3
Alignment explanation
Indices: 34517--34563 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
34507 AACTAATCTC
*
34517 TCT TAT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC- TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
34564 GTATATCAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:40509 original size:29 final size:30
Alignment explanation
Indices: 40450--40515 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
40440 ATATCAAAAT
* *
40450 TATACATGAATTTTGATTTAATGTGCAATTA
1 TATACATGAACTTTAATTTAATGTG-AATTA
**
40481 TATACATGAACTTTAATTTGGTGTG-ATTA
1 TATACATGAACTTTAATTTAATGTGAATTA
40510 TATACA
1 TATACA
40516 CGAAACTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 10 0.32
31 21 0.68
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.44
Consensus pattern (30 bp):
TATACATGAACTTTAATTTAATGTGAATTA
Found at i:40760 original size:29 final size:30
Alignment explanation
Indices: 40703--40761 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
40693 GATTGGATCA
* *
40703 AATCAAAATATTATGTATAAAATTTCACAT
1 AATCAAAATATCATGTATAAAATTGCACAT
* *
40733 AATCAAAAT-TCATGTATACAGTTGCACAT
1 AATCAAAATATCATGTATAAAATTGCACAT
40762 TAAACCATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.34
Consensus pattern (30 bp):
AATCAAAATATCATGTATAAAATTGCACAT
Found at i:45354 original size:23 final size:24
Alignment explanation
Indices: 45328--45381 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 24
45318 TAGTCGCCCA
* *
45328 ATTATTAATTTTTTT-ACTTAATT
1 ATTATTAATTTTTTTAAATTAAAT
45351 ATTA--AATTTTTTTAAATTAAAT
1 ATTATTAATTTTTTTAAATTAAAT
45373 ATT-TTAATT
1 ATTATTAATT
45382 GTTCTGAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 9 0.35
22 9 0.35
23 8 0.31
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTATTAATTTTTTTAAATTAAAT
Found at i:48106 original size:32 final size:32
Alignment explanation
Indices: 48056--48117 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
48046 GTTCAATAAT
48056 ACAAATCCTTGAAAAAATTAAGATTGATTAAG
1 ACAAATCCTTGAAAAAATTAAGATTGATTAAG
* *
48088 ACAAA-CCTTTAAAGAAATTACGATTGATTA
1 ACAAATCCTTGAAA-AAATTAAGATTGATTA
48118 GAAATTTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.29
Consensus pattern (32 bp):
ACAAATCCTTGAAAAAATTAAGATTGATTAAG
Found at i:65186 original size:15 final size:16
Alignment explanation
Indices: 65161--65194 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
65151 TAATGAATAT
65161 TTTATAATTTTTAAAA
1 TTTATAATTTTTAAAA
*
65177 TTTA-AATTTTTATAA
1 TTTATAATTTTTAAAA
65192 TTT
1 TTT
65195 TAAGTAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATAATTTTTAAAA
Found at i:68936 original size:21 final size:22
Alignment explanation
Indices: 68894--68934 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
68884 TATTTTGATC
*
68894 AATTTCGTTTGGTTAGCATTTA
1 AATTTCGTTTGGTTAGAATTTA
68916 AATTT-GTTTGGTTA-AATTT
1 AATTTCGTTTGGTTAGAATTT
68935 TACTACCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.54
Consensus pattern (22 bp):
AATTTCGTTTGGTTAGAATTTA
Found at i:86264 original size:15 final size:16
Alignment explanation
Indices: 86238--86271 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
86228 TCGGTTTGAT
86238 TAAAATTTATTAAAAA
1 TAAAATTTATTAAAAA
86254 TAAAA-TTATTAAAAA
1 TAAAATTTATTAAAAA
86269 TAA
1 TAA
86272 TTTAGTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAATTTATTAAAAA
Found at i:86631 original size:17 final size:16
Alignment explanation
Indices: 86606--86646 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
86596 TTAAAATCAT
*
86606 TAAAATTATTAAAAATA
1 TAAATTTATTAAAAA-A
86623 TAAATTTA-TAAAAAA
1 TAAATTTATTAAAAAA
86638 -AAATTTATT
1 TAAATTTATT
86647 TTTTTAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 7 0.32
15 2 0.09
16 6 0.27
17 7 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATTTATTAAAAAA
Found at i:87567 original size:7 final size:7
Alignment explanation
Indices: 87555--87609 Score: 60
Period size: 7 Copynumber: 7.9 Consensus size: 7
87545 TTAAAATAAT
87555 TTTTATA
1 TTTTATA
87562 TTTTATTAA
1 TTTTA-T-A
87571 TTTTATA
1 TTTTATA
87578 -TTTATA
1 TTTTATA
*
87584 TTTTATT
1 TTTTATA
87591 TTTTATA
1 TTTTATA
*
87598 ATTT-TA
1 TTTTATA
87604 TTTTAT
1 TTTTAT
87610 TTAATAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
6 11 0.28
7 21 0.52
8 2 0.05
9 6 0.15
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTATA
Found at i:87570 original size:22 final size:22
Alignment explanation
Indices: 87534--87590 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
87524 TTTTATTCTT
87534 TTTTTATA-TTT-TTAAAATAA
1 TTTTTATATTTTATTAAAATAA
** *
87554 TTTTTATATTTTATTAATTTTA
1 TTTTTATATTTTATTAAAATAA
*
87576 TATTTATATTTTATT
1 TTTTTATATTTTATT
87591 TTTTATAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.26
21 3 0.10
22 20 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTATATTTTATTAAAATAA
Found at i:87603 original size:22 final size:21
Alignment explanation
Indices: 87556--87611 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
87546 TAAAATAATT
87556 TTTATATTTTATTAATTTTAT-A
1 TTTATATTTTATT--TTTTATAA
87578 TTTATATTTTATTTTTTATAA
1 TTTATATTTTATTTTTTATAA
87599 TTT-TATTTTATTT
1 TTTATATTTTATTT
87612 AATAAAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.48
21 4 0.12
22 13 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTATATTTTATTTTTTATAA
Found at i:87604 original size:28 final size:27
Alignment explanation
Indices: 87533--87611 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 27
87523 TTTTTATTCT
* * * *
87533 TTTTTTATATTTTTAAAATAATTTTTA
1 TTTTTTATAATTTTATATTTATTTTTA
*
87560 TATTTTATTAATTTTATATTTATATTTTA
1 TTTTTTA-TAATTTTATATTTAT-TTTTA
87589 TTTTTTATAATTTTAT-TTTATTT
1 TTTTTTATAATTTTATATTTATTT
87612 AATAAAAATG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.05
27 11 0.25
28 20 0.45
29 11 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTTTTATAATTTTATATTTATTTTTA
Found at i:87614 original size:15 final size:15
Alignment explanation
Indices: 87560--87614 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
87550 ATAATTTTTA
87560 TATTTTA-TTAATTT
1 TATTTTATTTAATTT
87574 TA---TATTTATATTT
1 TATTTTATTTA-ATTT
87587 TATTTT-TTATAATTT
1 TATTTTATT-TAATTT
87602 TATTTTATTTAAT
1 TATTTTATTTAAT
87615 AAAAATGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
11 2 0.06
12 3 0.09
13 6 0.18
14 2 0.06
15 16 0.47
16 5 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTATTTAATTT
Found at i:87706 original size:22 final size:22
Alignment explanation
Indices: 87680--87730 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
87670 ATTATATTTT
*
87680 TTAAATATA-AAATATTAAAAGA
1 TTAAATATATAAAT-TTAAAAAA
*
87702 TTAAAAATATAAATTTAAAAAA
1 TTAAATATATAAATTTAAAAAA
*
87724 TAAAATA
1 TTAAATA
87731 ATTTGAGTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
TTAAATATATAAATTTAAAAAA
Found at i:91081 original size:24 final size:24
Alignment explanation
Indices: 91045--91092 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
91035 TAGATTTGAT
*
91045 TGAAAGGGTCAAAATGGTGGAGCA
1 TGAAAGGGCCAAAATGGTGGAGCA
*
91069 TGAACGGGCCAAAATGGTGGAGCA
1 TGAAAGGGCCAAAATGGTGGAGCA
91093 AGTTTTAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.38, T:0.15
Consensus pattern (24 bp):
TGAAAGGGCCAAAATGGTGGAGCA
Found at i:97346 original size:22 final size:21
Alignment explanation
Indices: 97316--97365 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
97306 TTTTTATTAA
*
97316 ATAAAATAAAATT-TTAAATAT
1 ATAAAATAAAATTAATAAA-AT
97337 ATAAATATAAAATTAATAAAAT
1 ATAAA-ATAAAATTAATAAAAT
97359 ATAAAAT
1 ATAAAAT
97366 TTGTTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 7 0.27
22 15 0.58
23 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAAAATAAAATTAATAAAAT
Found at i:97870 original size:21 final size:23
Alignment explanation
Indices: 97838--97880 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
97828 AGTTAAAAAT
*
97838 ATATTATTATTTTTAA-TTCCAA
1 ATATTATTATTTTGAAGTTCCAA
97860 ATATT-TTATTTTGAAGTTCCA
1 ATATTATTATTTTGAAGTTCCA
97881 TTATTCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (23 bp):
ATATTATTATTTTGAAGTTCCAA
Found at i:108723 original size:37 final size:38
Alignment explanation
Indices: 108672--108745 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 38
108662 ATGGACACTG
* * *
108672 TTAATCTTTTCCTTTCTTTTCTTTTTTTATCCTTTCCA
1 TTAATCTTCTCCTTTCTTTTATTTTTTTACCCTTTCCA
*
108710 TTAA-CTTCTCCTTTCTTTTATTTTTTTGCCCTTTCC
1 TTAATCTTCTCCTTTCTTTTATTTTTTTACCCTTTCC
108746 TATTTAATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 28 0.88
38 4 0.12
ACGTcount: A:0.09, C:0.26, G:0.01, T:0.64
Consensus pattern (38 bp):
TTAATCTTCTCCTTTCTTTTATTTTTTTACCCTTTCCA
Found at i:109876 original size:6 final size:6
Alignment explanation
Indices: 109865--109896 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
109855 GAATGGTTTT
109865 ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC AC
1 ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC AC
109897 CGAGTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.34, G:0.00, T:0.47
Consensus pattern (6 bp):
ACTTTC
Found at i:118711 original size:2 final size:2
Alignment explanation
Indices: 118704--118729 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
118694 GTTCCTGAAT
118704 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
118730 TGTTGTGAGC
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:137727 original size:31 final size:32
Alignment explanation
Indices: 137677--137754 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
137667 TCCCGAACCG
137677 AATATATTATGTT--ATAAAAA-TAT-TATATT
1 AATA-ATTATGTTAAATAAAAATTATATATATT
*
137706 AATTATATATGTTAAATAAAAATTATATATATT
1 AATAAT-TATGTTAAATAAAAATTATATATATT
*
137739 AATAATTATTTTAAAT
1 AATAATTATGTTAAAT
137755 CACTAACTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 2 0.05
29 9 0.22
31 7 0.17
32 12 0.29
33 11 0.27
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (32 bp):
AATAATTATGTTAAATAAAAATTATATATATT
Found at i:147103 original size:22 final size:22
Alignment explanation
Indices: 147075--147120 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
147065 AAAGATATAA
147075 ATTATTAGAATAATAAAATTAT
1 ATTATTAGAATAATAAAATTAT
**
147097 ATTATTATTATAATAAAATTAT
1 ATTATTAGAATAATAAAATTAT
147119 AT
1 AT
147121 AATTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTATTAGAATAATAAAATTAT
Found at i:156062 original size:4 final size:4
Alignment explanation
Indices: 156053--156092 Score: 62
Period size: 4 Copynumber: 9.8 Consensus size: 4
156043 AAATAAACGG
*
156053 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GAAA GGAA GAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 29 0.88
5 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:156075 original size:17 final size:17
Alignment explanation
Indices: 156053--156085 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
156043 AAATAAACGG
156053 GAAAGAAAGAAAGAAAA
1 GAAAGAAAGAAAGAAAA
156070 GAAAGAAAGAAAGAAA
1 GAAAGAAAGAAAGAAA
156086 GGAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGAAAA
Done.