Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009402.1 Kokia drynarioides strain JFW-HI SEQ_124109, 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: 177640
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 282 characters in sequence are not A, C, G, or T
Found at i:1587 original size:6 final size:6
Alignment explanation
Indices: 1576--1601 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1566 ATTTACATAT
1576 ATTTAA ATTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA AT
1602 CAAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:3521 original size:3 final size:3
Alignment explanation
Indices: 3513--3548 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3503 ATCACAATAA
3513 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3549 AATAATTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:14332 original size:30 final size:28
Alignment explanation
Indices: 14245--14333 Score: 79
Period size: 31 Copynumber: 3.0 Consensus size: 28
14235 ATGACATAAT
* *
14245 TCTATATATTTTTTTTAAATTTAAAATTTTG
1 TCTATATATTTTTATT---TTTAAAATTTAG
* *
14276 TTTCTATATTTTTATTTTTAAAAATTTAG
1 TCTATATATTTTTATTTTT-AAAATTTAG
*
14305 TCTATTTATTATTTAATTTTTAAAATTTA
1 TCTATATATT-TTT-ATTTTTAAAATTTA
14334 AATACAATTG
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
28 3 0.06
29 15 0.31
30 11 0.23
31 19 0.40
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (28 bp):
TCTATATATTTTTATTTTTAAAATTTAG
Found at i:15244 original size:31 final size:30
Alignment explanation
Indices: 15209--15275 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
15199 ATATTAGTAC
*
15209 TTTAATCTAATTAAATTTAGT-TTTTATATTT
1 TTTAAT-TAATTAAATTCAGTCTTTT-TATTT
*
15240 TTTAAATTAGTTAAATTCAGTCTTTTTATTT
1 TTT-AATTAATTAAATTCAGTCTTTTTATTT
15271 TTTAA
1 TTTAA
15276 ATTTTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 2 0.06
31 23 0.72
32 7 0.22
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (30 bp):
TTTAATTAATTAAATTCAGTCTTTTTATTT
Found at i:15276 original size:31 final size:31
Alignment explanation
Indices: 15219--15278 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
15209 TTTAATCTAA
*
15219 TTAAATTTAGTTTTTATATTTTTTAAATTAG
1 TTAAATTCAGTTTTTATATTTTTTAAATTAG
15250 TTAAATTCAGTCTTTT-TATTTTTTAAATT
1 TTAAATTCAGT-TTTTATATTTTTTAAATT
15279 TTAAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (31 bp):
TTAAATTCAGTTTTTATATTTTTTAAATTAG
Found at i:28259 original size:21 final size:19
Alignment explanation
Indices: 28235--28275 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
28225 CCAAATCCAA
*
28235 AAATCCTAAACCTTAAACATT
1 AAATCC-AAACCCTAAA-ATT
28256 AAATCCAAACCCTAAAATT
1 AAATCCAAACCCTAAAATT
28275 A
1 A
28276 TATTTAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATCCAAACCCTAAAATT
Found at i:33738 original size:18 final size:21
Alignment explanation
Indices: 33695--33741 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
33685 TACATAAATC
33695 AAACACAACTTTTGTAGTACAT
1 AAAC-CAACTTTTGTAGTACAT
33717 AAACCAACTTTTGT-G-A-AT
1 AAACCAACTTTTGTAGTACAT
33735 AAACCAA
1 AAACCAA
33742 AGTGGCATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.36
19 1 0.04
20 1 0.04
21 10 0.40
22 4 0.16
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.28
Consensus pattern (21 bp):
AAACCAACTTTTGTAGTACAT
Found at i:35250 original size:3 final size:3
Alignment explanation
Indices: 35242--35282 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
35232 CATCTGTGGA
35242 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
35283 ACAAACTCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:35447 original size:5 final size:5
Alignment explanation
Indices: 35437--35468 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
35427 CACTCCTACT
35437 CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CT
1 CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CT
35469 ACTAAACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (5 bp):
CTTCC
Found at i:38510 original size:13 final size:14
Alignment explanation
Indices: 38473--38512 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
38463 ACATACCTTA
*
38473 ATTACATATTCACT
1 ATTACATATTCAAT
38487 ATTA-A-ATTCAAT
1 ATTACATATTCAAT
38499 A-TACATATTCAAT
1 ATTACATATTCAAT
38512 A
1 A
38513 ATTTCAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
11 2 0.09
12 8 0.35
13 9 0.39
14 4 0.17
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTACATATTCAAT
Found at i:45153 original size:15 final size:16
Alignment explanation
Indices: 45133--45163 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
45123 ATAATAATAT
45133 AAAATAGT-AATTACA
1 AAAATAGTCAATTACA
45148 AAAATAGTCAATTACA
1 AAAATAGTCAATTACA
45164 TATTATTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (16 bp):
AAAATAGTCAATTACA
Found at i:46607 original size:31 final size:31
Alignment explanation
Indices: 46559--46622 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
46549 TGTAGGGTTA
46559 AATTATTATTTGAGATTTAAATTTGTTAATT
1 AATTATTATTTGAGATTTAAATTTGTTAATT
* * *
46590 AATT-TTATATTGGGATTTAAATTTTTTATTT
1 AATTATTAT-TTGAGATTTAAATTTGTTAATT
46621 AA
1 AA
46623 GTTAAATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (31 bp):
AATTATTATTTGAGATTTAAATTTGTTAATT
Found at i:50161 original size:1 final size:1
Alignment explanation
Indices: 50155--50180 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
50145 ACAATCTTAG
50155 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
50181 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:61143 original size:15 final size:15
Alignment explanation
Indices: 61096--61144 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
61086 ATAAGATGAT
* *
61096 ATTTTATAATAATTA
1 ATTTAATAATAAATA
*
61111 ATATAATATATAAA-A
1 ATTTAATA-ATAAATA
61126 ATTTAATAATAAATA
1 ATTTAATAATAAATA
61141 ATTT
1 ATTT
61145 TTAATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 5 0.18
15 19 0.68
16 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTAATAATAAATA
Found at i:61596 original size:13 final size:13
Alignment explanation
Indices: 61580--61604 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61570 ATAAAACAAA
61580 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
61593 AAAAAAAAAAAA
1 AAAAAAAAAAAA
61605 TCGATAAATC
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:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:61596 original size:15 final size:16
Alignment explanation
Indices: 61572--61604 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
61562 TGTTTTCCAT
61572 AAAACAAAAAAAAAAA
1 AAAACAAAAAAAAAAA
61588 AAAACAAAAAAAAAAA
1 AAAACAAAAAAAAAAA
61604 A
1 A
61605 TCGATAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAACAAAAAAAAAAA
Found at i:66933 original size:27 final size:25
Alignment explanation
Indices: 66893--66943 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
66883 TAATAAATTT
66893 TAATTATTATTTAAGATAAATATAA
1 TAATTATTATTTAAGATAAATATAA
*
66918 TAATATATTATATTAATATAAATATA
1 TAAT-TATTAT-TTAAGATAAATATA
66944 GTTTTATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
26 6 0.26
27 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
TAATTATTATTTAAGATAAATATAA
Found at i:67251 original size:18 final size:17
Alignment explanation
Indices: 67209--67251 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
67199 TTTTTAAGTT
*
67209 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
67226 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
67244 TATAATTT
1 TATAATTT
67252 AGAACACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:67562 original size:6 final size:6
Alignment explanation
Indices: 67551--67578 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
67541 CAAAAATCCC
67551 CGCCGT CGCCGT CGCCGT CGCCGT CGCC
1 CGCCGT CGCCGT CGCCGT CGCCGT CGCC
67579 ATGTCCCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.54, G:0.32, T:0.14
Consensus pattern (6 bp):
CGCCGT
Found at i:79607 original size:24 final size:24
Alignment explanation
Indices: 79570--79616 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
79560 ATCATTAAAC
*
79570 TATTCGAAAATTTTCATTTAAGTA
1 TATTCGAAAATTTTCACTTAAGTA
*
79594 TATTC-AAAAGTTTTTACTTAAGT
1 TATTCGAAAA-TTTTCACTTAAGT
79617 CACTTAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (24 bp):
TATTCGAAAATTTTCACTTAAGTA
Found at i:95496 original size:3 final size:3
Alignment explanation
Indices: 95488--95521 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
95478 CCAATATTAT
95488 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
95522 AAAACTCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:98526 original size:17 final size:19
Alignment explanation
Indices: 98491--98527 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
98481 CTTTATATAT
98491 TTTTTAGATTTTCTTAAAA
1 TTTTTAGATTTTCTTAAAA
98510 TTTTTAG-TTTT-TTAAAA
1 TTTTTAGATTTTCTTAAAA
98527 T
1 T
98528 ATAAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 4 0.22
19 7 0.39
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTTAGATTTTCTTAAAA
Found at i:98564 original size:19 final size:20
Alignment explanation
Indices: 98492--98566 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 20
98482 TTTATATATT
98492 TTTTAGATTTTCTTAAAA-T-
1 TTTTAGATTTT-TTAAAATTA
98511 TTTTAG-TTTTTTAAAATATAAA
1 TTTTAGATTTTTTAAAAT-T--A
*
98533 TTTTGGAATTTTTTAAAATTA
1 TTTTAG-ATTTTTTAAAATTA
98554 TTTT-GATTTTTTA
1 TTTTAGATTTTTTA
98567 TCGAGAGAGT
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
17 6 0.12
18 4 0.08
19 15 0.31
20 1 0.02
21 5 0.10
22 5 0.10
23 1 0.02
24 11 0.23
ACGTcount: A:0.32, C:0.01, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTTAGATTTTTTAAAATTA
Found at i:107478 original size:16 final size:17
Alignment explanation
Indices: 107454--107502 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
107444 AATTTTATTA
*
107454 TTATTAATT-TAAAATT
1 TTATAAATTATAAAATT
107470 TTATAAATTATAAAA-T
1 TTATAAATTATAAAATT
* *
107486 ATCTAAATTA-AAAATT
1 TTATAAATTATAAAATT
107502 T
1 T
107503 ACCATTTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 4 0.15
16 18 0.67
17 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATAAATTATAAAATT
Found at i:114237 original size:25 final size:23
Alignment explanation
Indices: 114200--114324 Score: 169
Period size: 23 Copynumber: 5.3 Consensus size: 23
114190 CCAAAGTACT
114200 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
114223 AACAGAGAGTACACAAAGTTCTA
1 AACAGAGAGCACACACAGTGCTA
* *
114246 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
**
114269 GTCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
114293 TAACAGAGAGCACACACAGTGCTA
1 -AACAGAGAGCACACACAGTGCTA
114317 AACAGAGA
1 AACAGAGA
114325 ACGCGCTAGT
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
23 68 0.76
24 2 0.02
25 20 0.22
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:114266 original size:46 final size:46
Alignment explanation
Indices: 114178--114324 Score: 190
Period size: 46 Copynumber: 3.2 Consensus size: 46
114168 TATACAGAAC
*
114178 AAACATAGAGTAC-CAAAGTACTAA-CAGAGAGCACACACAGTGCT
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACACAGTGCT
* *
114222 AAACAGAGAGTACACAAAGTTCTAATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACACAGTGCT
** * * *
114268 AGTCAGAGAGCACACACAGTGCTAATAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGTACACAAAGTACTAAT--CAGAGAGCACACACAGTGCT
114316 AAACAGAGA
1 AAACAGAGA
114325 ACGCGCTAGT
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
44 12 0.14
45 10 0.11
46 40 0.45
48 26 0.30
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.13
Consensus pattern (46 bp):
AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACACAGTGCT
Found at i:116122 original size:24 final size:24
Alignment explanation
Indices: 116094--116155 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
116084 AAAAATAATC
116094 TTTCAATTAAATTATGTTTACTTG
1 TTTCAATTAAATTATGTTTACTTG
* * *
116118 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAATTATGTTTACTTG
116142 TTTCAATTAAATTA
1 TTTCAATTAAATTA
116156 AATTATGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAATTATGTTTACTTG
Found at i:117658 original size:18 final size:18
Alignment explanation
Indices: 117631--117669 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
117621 CAACCCAATT
117631 CAAATACAAA-TTTAACC
1 CAAATACAAACTTTAACC
117648 CAAATTACAAACTTTAACC
1 CAAA-TACAAACTTTAACC
117667 CAA
1 CAA
117670 GTCTAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 10 0.50
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (18 bp):
CAAATACAAACTTTAACC
Found at i:148589 original size:17 final size:18
Alignment explanation
Indices: 148569--148609 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
148559 TAATAAATTC
148569 AATAATTAAATTAT-TAA
1 AATAATTAAATTATATAA
148586 AAT-ATT-AATTATATAA
1 AATAATTAAATTATATAA
*
148602 AAAAATTA
1 AATAATTA
148610 CAACTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 6 0.30
16 8 0.40
17 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAATTAAATTATATAA
Found at i:156919 original size:6 final size:6
Alignment explanation
Indices: 156910--156935 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
156900 AAGCTGGGGC
156910 TGCTGT TGCTGT TGCTGT TGCTGT TG
1 TGCTGT TGCTGT TGCTGT TGCTGT TG
156936 GTTGTTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.35, T:0.50
Consensus pattern (6 bp):
TGCTGT
Found at i:167074 original size:298 final size:298
Alignment explanation
Indices: 166533--167129 Score: 1090
Period size: 298 Copynumber: 2.0 Consensus size: 298
166523 TATGAACAGA
166533 TATTATCTATATTTTAAAATTTGTTAACATTAAATTTATTATAAATTTTTATCATATTTACTATT
1 TATTATCTATATTTTAAAATTTGTTAACATTAAATTTATTATAAATTTTTATCATATTTACTATT
166598 TTTAATACAATATCTAGATCTACTTATAATTTCTTTTCAACTCTTAAATAAAAAAAATATTAAAC
66 TTTAATACAATATCTAGATCTACTTATAATTTCTTTTCAACTCTTAAATAAAAAAAATATTAAAC
*
166663 GACTTAAGACTGGAAAATTTGAAATTCTTAAAAGATTACAGCGTGAAGGAAATAAAACAAAATAT
131 GACTTAAGACTGGAAAATTTGAAATTCTTAAAAGATTACAACGTGAAGGAAATAAAACAAAATAT
*
166728 ATACAATTACAAATAATAATTAATAAAGATGGGGTAACACCTTATCTGGAGACACTTGGGTGTAC
196 ATACAATTACAAATAATAATTAATAAAGATGGGGTAACACCGTATCTGGAGACACTTGGGTGTAC
166793 TTTTAACATTGAAGACAATAGCGTGTTAGGTATGACGT
261 TTTTAACATTGAAGACAATAGCGTGTTAGGTATGACGT
*
166831 TATTATCTATATTTTAAAAATTT-TT-ACATTAAATTTATTATAGATTTTTATCATATTTACTAT
1 TATTATCTATATTTT-AAAATTTGTTAACATTAAATTTATTATAAATTTTTATCATATTTACTAT
* * * *
166894 TTTTAATACAATATTTAGATCTATTTATAATTTTTTTTTAACTCTTAAATAAAAAAATATATTAA
65 TTTTAATACAATATCTAGATCTACTTATAATTTCTTTTCAACTCTTAAATAAAAAAA-ATATTAA
*
166959 ACGAGTTAAGACTGGAAAATTTGAAATTCTTAAAAGATTACAACGTGAAGGAAATAAAACAAAAT
129 ACGACTTAAGACTGGAAAATTTGAAATTCTTAAAAGATTACAACGTGAAGGAAATAAAACAAAAT
167024 ATATACAATTACAAATAATAATTAATAAAGATGGGGTAACACCGTATCTGGAGACACTTGGGTGT
194 ATATACAATTACAAATAATAATTAATAAAGATGGGGTAACACCGTATCTGGAGACACTTGGGTGT
167089 ACTTTTAACATTGAAGACAATAGCGTGTTAGGTATGACGT
259 ACTTTTAACATTGAAGACAATAGCGTGTTAGGTATGACGT
167129 T
1 T
167130 TGTGTTTTTG
Statistics
Matches: 289, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
297 90 0.31
298 192 0.66
299 7 0.02
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (298 bp):
TATTATCTATATTTTAAAATTTGTTAACATTAAATTTATTATAAATTTTTATCATATTTACTATT
TTTAATACAATATCTAGATCTACTTATAATTTCTTTTCAACTCTTAAATAAAAAAAATATTAAAC
GACTTAAGACTGGAAAATTTGAAATTCTTAAAAGATTACAACGTGAAGGAAATAAAACAAAATAT
ATACAATTACAAATAATAATTAATAAAGATGGGGTAACACCGTATCTGGAGACACTTGGGTGTAC
TTTTAACATTGAAGACAATAGCGTGTTAGGTATGACGT
Found at i:172156 original size:22 final size:23
Alignment explanation
Indices: 172130--172172 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
172120 CATGAATCTT
172130 TAAATTTAAAAAATA-GAAAAAC
1 TAAATTTAAAAAATATGAAAAAC
* *
172152 TAAATTTTAAATATATGAAAA
1 TAAATTTAAAAAATATGAAAA
172173 TTACATATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (23 bp):
TAAATTTAAAAAATATGAAAAAC
Found at i:174075 original size:31 final size:31
Alignment explanation
Indices: 174031--174099 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
174021 AAAAGCATAC
174031 TAAACT-TTTTTTTAGAAGTATTATAAATTA
1 TAAACTATTTTTTTAGAAGTATTATAAATTA
174061 TAAACTATTTTTTTAGAAGTATTATAAATTA
1 TAAACTATTTTTTTAGAAGTATTATAAATTA
174092 TAAACTAT
1 TAAACTAT
174100 AAGTAAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (31 bp):
TAAACTATTTTTTTAGAAGTATTATAAATTA
Done.