Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014426.1 Kokia drynarioides strain JFW-HI SEQ_129464, 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: 119688
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:380 original size:3 final size:3
Alignment explanation
Indices: 374--399 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
364 TGTGCAAGGT
374 GGA GGA GGA GGA GGA GGA GGA GGA GG
1 GGA GGA GGA GGA GGA GGA GGA GGA GG
400 GGTAGGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:1379 original size:21 final size:21
Alignment explanation
Indices: 1355--1417 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1345 GTAATCCACC
1355 TTTCCATCCAGCGCATCAACT
1 TTTCCATCCAGCGCATCAACT
** *
1376 TTTCCATCCAGTACATCAACC
1 TTTCCATCCAGCGCATCAACT
*
1397 TTTCCCTCCAGCGCATCAACT
1 TTTCCATCCAGCGCATCAACT
1418 GCATTGCTGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.24, C:0.40, G:0.08, T:0.29
Consensus pattern (21 bp):
TTTCCATCCAGCGCATCAACT
Found at i:16212 original size:15 final size:17
Alignment explanation
Indices: 16180--16212 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
16170 ACAACAATAT
16180 AGATATCAATCGAATTA
1 AGATATCAATCGAATTA
16197 AGAT-TCAATC-AATTA
1 AGATATCAATCGAATTA
16212 A
1 A
16213 TATGTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.30
Consensus pattern (17 bp):
AGATATCAATCGAATTA
Found at i:17055 original size:21 final size:21
Alignment explanation
Indices: 16967--17057 Score: 66
Period size: 21 Copynumber: 4.3 Consensus size: 21
16957 ATAAATTTAA
16967 TAAAATATATTT-AAAATAT-T
1 TAAAAT-TATTTAAAAATATAT
16987 TAAAATT-TTATAAAAACT-TAT
1 TAAAATTATT-TAAAAA-TATAT
* *
17008 TAAAATTCAATAAAAAATCATA-
1 TAAAATT-ATTTAAAAAT-ATAT
* *
17030 AAAAATTATTTAAAAATATAG
1 TAAAATTATTTAAAAATATAT
17051 TAAAATT
1 TAAAATT
17058 GATATTAACT
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
18 2 0.04
19 2 0.04
20 14 0.25
21 24 0.43
22 11 0.20
23 3 0.05
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (21 bp):
TAAAATTATTTAAAAATATAT
Found at i:17717 original size:17 final size:17
Alignment explanation
Indices: 17697--17757 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 17
17687 CTAGATTTTA
17697 TAATATTTTTATAAATT
1 TAATATTTTTATAAATT
* * *
17714 TAATAAACTTGTATCAATTT
1 TAAT--ATTTTTAT-AAATT
*
17734 TAATATTTTTA-ACATT
1 TAATATTTTTATAAATT
17750 TAATATTT
1 TAATATTT
17758 ATTTTTTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
16 11 0.32
17 4 0.12
18 5 0.15
19 6 0.18
20 8 0.24
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (17 bp):
TAATATTTTTATAAATT
Found at i:17719 original size:20 final size:20
Alignment explanation
Indices: 17691--17754 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 20
17681 AATTTACTAG
*
17691 ATTTTATAATATTTTTATAA
1 ATTTAATAATATTTTTATAA
* * *
17711 ATTTAATAA-ACTTGTATCA
1 ATTTAATAATATTTTTATAA
*
17730 ATTT--TAATATTTTTA-AC
1 ATTTAATAATATTTTTATAA
17747 ATTTAATA
1 ATTTAATA
17755 TTTATTTTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
17 7 0.21
18 5 0.15
19 13 0.39
20 8 0.24
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTAATAATATTTTTATAA
Found at i:19390 original size:20 final size:20
Alignment explanation
Indices: 19365--19403 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19355 TTTTTTTAAA
*
19365 TTTTAATAGTAAAATTATAT
1 TTTTAATAGTAAAAATATAT
*
19385 TTTTAATCGTAAAAATATA
1 TTTTAATAGTAAAAATATA
19404 CAATTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (20 bp):
TTTTAATAGTAAAAATATAT
Found at i:31356 original size:20 final size:20
Alignment explanation
Indices: 31333--31376 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
31323 ATTTTTTTAG
*
31333 AAAATTATAAA-AATTTTATA
1 AAAATTATAAAGAA-TATATA
*
31353 AAAATTCTAAAGAATATATA
1 AAAATTATAAAGAATATATA
31373 AAAA
1 AAAA
31377 AAAGTTGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAATTATAAAGAATATATA
Found at i:33549 original size:54 final size:53
Alignment explanation
Indices: 33450--33567 Score: 182
Period size: 54 Copynumber: 2.2 Consensus size: 53
33440 TCATACACTC
***
33450 AATGTCCAATATAGTGCATGAAATTCACTCACCAGGGTTCTCTGTATAAAAGT
1 AATGTCCAATATAGTGCATGAAATTCACTCACCAACATTCTCTGTATAAAAGT
*
33503 AATGTCCAATATAGTGCATGTAATTTCACTCACCAACATTCTCTGTATAAAAGT
1 AATGTCCAATATAGTGCATG-AAATTCACTCACCAACATTCTCTGTATAAAAGT
*
33557 AATATCCAATA
1 AATGTCCAATA
33568 GAGCCAAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
53 20 0.34
54 39 0.66
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.31
Consensus pattern (53 bp):
AATGTCCAATATAGTGCATGAAATTCACTCACCAACATTCTCTGTATAAAAGT
Found at i:37572 original size:3 final size:3
Alignment explanation
Indices: 37564--37598 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
37554 ACATGATGCT
37564 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
37599 GTTAAGCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:41800 original size:4 final size:4
Alignment explanation
Indices: 41791--41815 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
41781 TCAAAGTTAC
41791 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
41816 TGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:57586 original size:16 final size:16
Alignment explanation
Indices: 57565--57599 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
57555 ATACAACCTC
57565 TTCTTTTTCTTTTCTT
1 TTCTTTTTCTTTTCTT
* *
57581 TTCTTTTTTTTTTTTT
1 TTCTTTTTCTTTTCTT
57597 TTC
1 TTC
57600 AAAAAGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTCTTTTTCTTTTCTT
Found at i:59473 original size:13 final size:13
Alignment explanation
Indices: 59455--59490 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
59445 TTTCGCTTAT
59455 TTATTTTATACTA
1 TTATTTTATACTA
*
59468 TTATTTTATATTA
1 TTATTTTATACTA
*
59481 ATATTTTATA
1 TTATTTTATA
59491 ACAATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTTATACTA
Found at i:60244 original size:21 final size:21
Alignment explanation
Indices: 60220--60263 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
60210 ACCTTCATAT
* * *
60220 CCGCCGCCACCATATCCGCCA
1 CCGCCACCACCATACCCACCA
*
60241 CCGCCACCTCCATACCCACCA
1 CCGCCACCACCATACCCACCA
60262 CC
1 CC
60264 ACCATATCCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.61, G:0.09, T:0.09
Consensus pattern (21 bp):
CCGCCACCACCATACCCACCA
Found at i:60249 original size:36 final size:36
Alignment explanation
Indices: 60202--60272 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
60192 GTCATAGCCC
* * * *
60202 CCACCACCACCTTCATATCCGCCGCCACCATATCCG
1 CCACCACCACCTCCATACCCACCACCACCATATCCG
*
60238 CCACCGCCACCTCCATACCCACCACCACCATATCC
1 CCACCACCACCTCCATACCCACCACCACCATATCC
60273 ACTATTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.24, C:0.56, G:0.06, T:0.14
Consensus pattern (36 bp):
CCACCACCACCTCCATACCCACCACCACCATATCCG
Found at i:72308 original size:127 final size:128
Alignment explanation
Indices: 72175--72428 Score: 465
Period size: 127 Copynumber: 2.0 Consensus size: 128
72165 AAACTTTTAA
72175 TAGTAAAACGAGCTGGTCCAAAAATAAAAAGCCTTAACTCAAGTCCAGTTCATGATATTAACATA
1 TAGTAAAACGAGCTGGTCCAAAAATAAAAAGCCTTAACTCAAGTCCAGTTCATGATATTAACATA
72240 TTTTATACTTGTTTAAATTTGACCTAACTTAAAATATAGACTTAAAA-TTTACACGAATTCAC
66 TTTTATACTTGTTTAAATTTGACCTAACTTAAAATATAGACTTAAAATTTTACACGAATTCAC
*
72302 TAGTAAAACGAGCTGGTCCAAAAATAAAAAGCCTTAACTCAAGTCCGGTTCATGATATTAACATA
1 TAGTAAAACGAGCTGGTCCAAAAATAAAAAGCCTTAACTCAAGTCCAGTTCATGATATTAACATA
* * *
72367 TTTTATATTTGTTTAAGTTTGATCTAACTTAAAATATAGACTTAAAATTTTACACGAATTCA
66 TTTTATACTTGTTTAAATTTGACCTAACTTAAAATATAGACTTAAAATTTTACACGAATTCA
72429 TTTATATTTG
Statistics
Matches: 122, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
127 108 0.89
128 14 0.11
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.33
Consensus pattern (128 bp):
TAGTAAAACGAGCTGGTCCAAAAATAAAAAGCCTTAACTCAAGTCCAGTTCATGATATTAACATA
TTTTATACTTGTTTAAATTTGACCTAACTTAAAATATAGACTTAAAATTTTACACGAATTCAC
Found at i:78064 original size:23 final size:22
Alignment explanation
Indices: 77998--78173 Score: 131
Period size: 23 Copynumber: 7.5 Consensus size: 22
77988 ACGCAAGCGC
77998 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTT-GTGT
* *
78021 ACTTACTGTTTCGCAATTTGTGT
1 GCTTACTGTTTCGC-ACTTGTGT
*
78044 GCTTAATGTTTCGCACCTTGTGT
1 GCTTACTGTTTCGCA-CTTGTGT
* * *
78067 GCCTACTGATTT-GCGCTATGTGC
1 GCTTACTG-TTTCGCACT-TGTGT
* *
78090 GCCTACTGATT-GCACTGTGTGT
1 GCTTACTGTTTCGCACT-TGTGT
78112 GCTTACTGTTTCCCCAGCACTTGTGT
1 GCTTACTGTTT---C-GCACTTGTGT
*
78138 GCTTACTGTTTCCCCAACACTTGTGT
1 GCTTACTGTTT---C-GCACTTGTGT
78164 GCTTACTGTT
1 GCTTACTGTT
78174 AAGTACTTCG
Statistics
Matches: 128, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
22 22 0.17
23 55 0.43
24 6 0.05
26 40 0.31
27 5 0.04
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.41
Consensus pattern (22 bp):
GCTTACTGTTTCGCACTTGTGT
Found at i:78110 original size:22 final size:23
Alignment explanation
Indices: 78062--78119 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
78052 TTTCGCACCT
*
78062 TGTGTGCCTACTGATTTGCGCTA
1 TGTGTGCCTACTGATTTGCACTA
* *
78085 TGTGCGCCTACTGA-TTGCACTG
1 TGTGTGCCTACTGATTTGCACTA
*
78107 TGTGTGCTTACTG
1 TGTGTGCCTACTG
78120 TTTCCCCAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.12, C:0.22, G:0.28, T:0.38
Consensus pattern (23 bp):
TGTGTGCCTACTGATTTGCACTA
Found at i:78138 original size:26 final size:26
Alignment explanation
Indices: 78101--78173 Score: 128
Period size: 26 Copynumber: 2.8 Consensus size: 26
78091 CCTACTGATT
78101 GCACTGTGTGTGCTTACTGTTTCCCCA
1 GCACT-TGTGTGCTTACTGTTTCCCCA
78128 GCACTTGTGTGCTTACTGTTTCCCCA
1 GCACTTGTGTGCTTACTGTTTCCCCA
*
78154 ACACTTGTGTGCTTACTGTT
1 GCACTTGTGTGCTTACTGTT
78174 AAGTACTTCG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
26 40 0.89
27 5 0.11
ACGTcount: A:0.12, C:0.27, G:0.21, T:0.40
Consensus pattern (26 bp):
GCACTTGTGTGCTTACTGTTTCCCCA
Found at i:81462 original size:245 final size:247
Alignment explanation
Indices: 81027--81523 Score: 820
Period size: 245 Copynumber: 2.0 Consensus size: 247
81017 ATGTGTTGAG
* * *
81027 CCTAGATGGAATTTGATTAATGTTTGTCAGAAATATGAAAATCAATACTTCAGTCTGTTTTTTTT
1 CCTAGATGGAATTTGATTAATGTTTGTCAGAAATAAGAAAATCAATACTTCAGTC----TTCTTA
* * *
81092 TTTTTTTTTGTTCGATGAACTTGTATTCTTCATTCAATACCCAAAATGTTGTATTTTGATGGGAG
62 ATTTTTTTTGTTCAACGAACTTGTATTCTTCATTCAATACCCAAAATGTTGTATTTTGATGGGAG
*
81157 GCTTCACAGAATCTCTTATTGCATGTACCTAAGGTTGAAGCATAGCTGTTTTAGCTAAATACTTG
127 GCTTCACAGAATCTCTTATTGCATGTACCTAAGGTTGAAGCATAGCCGTTTTAGCTAAATACTTG
* *
81222 AGTTCCTAGCTTGAC-TGAGGAGTTGGAAGATCATCTACTAATCAATAGCTAATAT
192 AGTTCCTAGCTTGACTTGAAGAGTTGGAAAATCATCTACTAATCAATAGCTAATAT
*
81277 CCTAGATGGAATTTGATTAATGTTTGTCAGAAATAAGAAAAT-ATATTCTTCAGTC-TCTTAATT
1 CCTAGATGGAATTTGATTAATGTTTGTCAGAAATAAGAAAATCA-ATACTTCAGTCTTCTTAATT
81340 TTTTTTGTTCAACGAACTTGTATTCTTCATTCAATACCCAAAATGTTGTATTTTGATGGGAGGCT
65 TTTTTTGTTCAACGAACTTGTATTCTTCATTCAATACCCAAAATGTTGTATTTTGATGGGAGGCT
*
81405 TCACAGAATCTCTTATTGCTTGTACCTAAGGTTGAAGCATAGCCGTTTTAGCTAAATACTTGAGT
130 TCACAGAATCTCTTATTGCATGTACCTAAGGTTGAAGCATAGCCGTTTTAGCTAAATACTTGAGT
*
81470 TCCTAGCTTGACTTGAAGAGTTGGAAAATCATCTACTATTCAATAGCTAATAT
195 TCCTAGCTTGACTTGAAGAGTTGGAAAATCATCTACTAATCAATAGCTAATAT
81523 C
1 C
81524 TTTGGAAATA
Statistics
Matches: 233, Mismatches: 12, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
245 143 0.61
246 38 0.16
249 1 0.00
250 51 0.22
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (247 bp):
CCTAGATGGAATTTGATTAATGTTTGTCAGAAATAAGAAAATCAATACTTCAGTCTTCTTAATTT
TTTTTGTTCAACGAACTTGTATTCTTCATTCAATACCCAAAATGTTGTATTTTGATGGGAGGCTT
CACAGAATCTCTTATTGCATGTACCTAAGGTTGAAGCATAGCCGTTTTAGCTAAATACTTGAGTT
CCTAGCTTGACTTGAAGAGTTGGAAAATCATCTACTAATCAATAGCTAATAT
Found at i:88636 original size:4 final size:4
Alignment explanation
Indices: 88627--88679 Score: 54
Period size: 4 Copynumber: 13.0 Consensus size: 4
88617 TTTCTTGGTC
* * *
88627 GTAT GTAT GTAT GAAT G-AT GTAT GCAT GCTAT GTAT CTAT GTAAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G-TAT GTAT GTAT GT-AT GTAT
88676 GTAT
1 GTAT
88680 CGAAAAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
3 3 0.07
4 31 0.76
5 7 0.17
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.43
Consensus pattern (4 bp):
GTAT
Found at i:92872 original size:46 final size:46
Alignment explanation
Indices: 92746--92885 Score: 208
Period size: 47 Copynumber: 3.0 Consensus size: 46
92736 AGGGGTATAC
92746 AGATCTATTTATTTACCATATTACTTAGCATGATTGAGAGATTATT
1 AGATCTATTTATTTACCATATTACTTAGCATGATTGAGAGATTATT
* * *
92792 ACATCTATTTATTTTACCATATTACTTAGCATGATGGAGAGATTGTT
1 AGATCTATTTA-TTTACCATATTACTTAGCATGATTGAGAGATTATT
* * *
92839 AGATCTATTCATTTACCATATTACTTGGTATGATTTGAGAGATTATT
1 AGATCTATTTATTTACCATATTACTTAGCATGA-TTGAGAGATTATT
92886 TCCTTTGAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
46 30 0.36
47 53 0.64
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (46 bp):
AGATCTATTTATTTACCATATTACTTAGCATGATTGAGAGATTATT
Found at i:92982 original size:16 final size:16
Alignment explanation
Indices: 92963--93001 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
92953 AAATTGCGTA
92963 TAAAAAT-ATAATATTT
1 TAAAAATGATAAT-TTT
*
92979 TAAATATGATAATTTT
1 TAAAAATGATAATTTT
92995 TAAAAAT
1 TAAAAAT
93002 TAAAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TAAAAATGATAATTTT
Found at i:96494 original size:145 final size:145
Alignment explanation
Indices: 96317--96616 Score: 591
Period size: 145 Copynumber: 2.1 Consensus size: 145
96307 CATGTTAGTA
96317 TTTAATTAAAAGTTTTAAAAAAATCATGCAAAGATGAAATAAATTGAAAATGAATAAAGATTTAT
1 TTTAATTAAAAGTTTTAAAAAAATCATGCAAAGATGAAATAAATTGAAAATGAATAAAGATTTAT
96382 TTATATTTTAATTTGAGTAATTTTAATTTATGTATTTTTTGAATTTTAAAATTTTAGTCTATACC
66 TTATATTTTAATTTGAGTAATTTTAATTTATGTATTTTTTGAATTTTAAAATTTTAGTCTATACC
96447 TATCAGTTAAATTTG
131 TATCAGTTAAATTTG
*
96462 TTTAATTAAAAGTTTTAAAAAAATCATGCAAAGTTGAAATAAATTGAAAATGAATAAAGATTTAT
1 TTTAATTAAAAGTTTTAAAAAAATCATGCAAAGATGAAATAAATTGAAAATGAATAAAGATTTAT
96527 TTATATTTTAATTTGAGTAATTTTAATTTATGTATTTTTTGAATTTTAAAATTTTAGTCTATACC
66 TTATATTTTAATTTGAGTAATTTTAATTTATGTATTTTTTGAATTTTAAAATTTTAGTCTATACC
96592 TATCAGTTAAATTTG
131 TATCAGTTAAATTTG
96607 TTTAATTAAA
1 TTTAATTAAA
96617 TTATGCTATT
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 154 1.00
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.45
Consensus pattern (145 bp):
TTTAATTAAAAGTTTTAAAAAAATCATGCAAAGATGAAATAAATTGAAAATGAATAAAGATTTAT
TTATATTTTAATTTGAGTAATTTTAATTTATGTATTTTTTGAATTTTAAAATTTTAGTCTATACC
TATCAGTTAAATTTG
Found at i:103999 original size:13 final size:13
Alignment explanation
Indices: 103963--104007 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
103953 ATCTCAAGCA
* *
103963 AAAAATAAAAAAT
1 AAAAATATAACAT
103976 AAAAA-AT-ACAT
1 AAAAATATAACAT
103987 AAAAATATAACAT
1 AAAAATATAACAT
104000 AAAAATAT
1 AAAAATAT
104008 TAATATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 8 0.29
12 3 0.11
13 17 0.61
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAATATAACAT
Found at i:109487 original size:16 final size:17
Alignment explanation
Indices: 109454--109497 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
109444 CAACTAAATA
*
109454 TAATTTTTTTTATGTTT
1 TAATTATTTTTATGTTT
*
109471 TTATTATTTTTAT-TTT
1 TAATTATTTTTATGTTT
109487 TAATTATTTTT
1 TAATTATTTTT
109498 GAATTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (17 bp):
TAATTATTTTTATGTTT
Found at i:109869 original size:21 final size:21
Alignment explanation
Indices: 109840--109882 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
109830 ATAAACAATA
**
109840 TAATAGTTTTGTTTTTTAACT
1 TAATAGTTTTGGCTTTTAACT
*
109861 TAATTGTTTTGGCTTTTAACT
1 TAATAGTTTTGGCTTTTAACT
109882 T
1 T
109883 TAGAAAAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (21 bp):
TAATAGTTTTGGCTTTTAACT
Done.