Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005299.1 Kokia drynarioides strain JFW-HI SEQ_119227, 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: 75087
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:4698 original size:18 final size:18
Alignment explanation
Indices: 4675--4710 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4665 GTGTTTGATT
4675 GCAAAGAAGGAAGCAAAG
1 GCAAAGAAGGAAGCAAAG
4693 GCAAAGAAGGAAGCAAAG
1 GCAAAGAAGGAAGCAAAG
4711 CCGAGGCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.33, T:0.00
Consensus pattern (18 bp):
GCAAAGAAGGAAGCAAAG
Found at i:6243 original size:8 final size:8
Alignment explanation
Indices: 6230--6282 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
6220 AACCCAATTA
6230 TTTTTATT
1 TTTTTATT
6238 TTTTTATT
1 TTTTTATT
*
6246 TTTCTATCT
1 TTTTTAT-T
6255 TATTTTATT
1 T-TTTTATT
*
6264 TATTTATT
1 TTTTTATT
*
6272 TATTTATT
1 TTTTTATT
6280 TTT
1 TTT
6283 GTCCAAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
8 30 0.77
9 4 0.10
10 5 0.13
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTATT
Found at i:6267 original size:4 final size:4
Alignment explanation
Indices: 6232--6280 Score: 55
Period size: 4 Copynumber: 11.8 Consensus size: 4
6222 CCCAATTATT
*
6232 TTTA TTTT TTTA TTT- TTCTA TCTTA TTTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TT-TA T-TTA -TTTA TTTA TTTA TTTA TTTA TTT
6281 TTGTCCAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 2 0.05
4 29 0.74
5 6 0.15
6 2 0.05
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:13991 original size:32 final size:30
Alignment explanation
Indices: 13953--14013 Score: 77
Period size: 32 Copynumber: 2.0 Consensus size: 30
13943 ATTAATAAAA
*
13953 ATAAAATTATACTTCAATTCTTTTTAAAAATG
1 ATAAAATTATAATTCAA-TC-TTTTAAAAATG
* *
13985 ATAAAATTTTAATTTAATCTTTTAAAAAT
1 ATAAAATTATAATTCAATCTTTTAAAAAT
14014 TATATTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 10 0.38
31 2 0.08
32 14 0.54
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (30 bp):
ATAAAATTATAATTCAATCTTTTAAAAATG
Found at i:15090 original size:20 final size:23
Alignment explanation
Indices: 15043--15084 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
15033 CACTTTCATG
15043 AATTATTACAATTATGATTTATA
1 AATTATTACAATTATGATTTATA
15066 AATTA-TACAA-TAT-ATTTAT
1 AATTATTACAATTATGATTTAT
15085 TTATTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 3 0.16
22 5 0.26
23 5 0.26
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTATTACAATTATGATTTATA
Found at i:18857 original size:14 final size:15
Alignment explanation
Indices: 18838--18867 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
18828 TGTTTAAAAC
18838 TTAATTAA-CCTTAA
1 TTAATTAATCCTTAA
18852 TTAATTAATCCTTAA
1 TTAATTAATCCTTAA
18867 T
1 T
18868 CACAATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAATTAATCCTTAA
Found at i:19293 original size:24 final size:24
Alignment explanation
Indices: 19264--19314 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
19254 AGAAATAATC
*
19264 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTCAATTG
*
19288 TTTCAATTAAACTCTGTTCATTTG
1 TTTCAATTAAACTCTGTTCAATTG
19312 TTT
1 TTT
19315 GAGTCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTCAATTG
Found at i:19323 original size:24 final size:24
Alignment explanation
Indices: 19264--19326 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
19254 AGAAATAATC
* *
19264 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATCAAACTCTGTTCAATTG
* *
19288 TTTCAATTAAACTCTGTTCATTTG
1 TTTCAATCAAACTCTGTTCAATTG
* *
19312 TTTGAGTCAAACTCT
1 TTTCAATCAAACTCT
19327 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:0.27, C:0.16, G:0.10, T:0.48
Consensus pattern (24 bp):
TTTCAATCAAACTCTGTTCAATTG
Found at i:23105 original size:24 final size:24
Alignment explanation
Indices: 23078--23163 Score: 120
Period size: 24 Copynumber: 3.6 Consensus size: 24
23068 ATTTAACCCA
23078 TACGAGCCCAGAATGATTAGCTCT
1 TACGAGCCCAGAATGATTAGCTCT
*
23102 TACGAGCCCAGAA-CAGTTAGCTCT
1 TACGAGCCCAGAATGA-TTAGCTCT
* *
23126 TACGAGCTCAGAATGATTAACTCT
1 TACGAGCCCAGAATGATTAGCTCT
*
23150 TACAAGCCCAGAAT
1 TACGAGCCCAGAAT
23164 CAAAATAACG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
23 1 0.02
24 52 0.96
25 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (24 bp):
TACGAGCCCAGAATGATTAGCTCT
Found at i:23191 original size:27 final size:27
Alignment explanation
Indices: 23157--23224 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
23147 TCTTACAAGC
*
23157 CCAGAATCAAAATAACGTTCTTTTGAG
1 CCAGAATCAAAATAACGCTCTTTTGAG
23184 CCAGAATCAAAATAACGCTCTTTTGAG
1 CCAGAATCAAAATAACGCTCTTTTGAG
*
23211 CCAGAATCAGAATA
1 CCAGAATCAAAATA
23225 CTCCTCAAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (27 bp):
CCAGAATCAAAATAACGCTCTTTTGAG
Found at i:34499 original size:12 final size:14
Alignment explanation
Indices: 34469--34504 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
34459 GGTATTAATA
34469 ATATAAATAAATTC
1 ATATAAATAAATTC
34483 A-ATAAA-AAA-TC
1 ATATAAATAAATTC
34494 ATATAAATAAA
1 ATATAAATAAA
34505 ATATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
11 3 0.15
12 8 0.40
13 8 0.40
14 1 0.05
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (14 bp):
ATATAAATAAATTC
Found at i:36834 original size:7 final size:7
Alignment explanation
Indices: 36822--36869 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
36812 ATTCAACTTT
36822 TAAAAAA
1 TAAAAAA
36829 TAAAAAA
1 TAAAAAA
*
36836 TAATTAAA
1 TAA-AAAA
36844 -AAAAAA
1 TAAAAAA
*
36850 TAAAACTA
1 TAAAA-AA
36858 TAAAAAA
1 TAAAAAA
36865 TAAAA
1 TAAAA
36870 TAAAATAAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 3 0.09
7 22 0.65
8 9 0.26
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAAAAA
Found at i:36842 original size:18 final size:17
Alignment explanation
Indices: 36821--36875 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
36811 TATTCAACTT
36821 TTAAAAAATAAAAAATAA
1 TTAAAAAATAAAAAA-AA
*
36839 TTAAAAAA-AAATAAAAC
1 TTAAAAAATAAA-AAAAA
36856 TATAAAAAATAAAATAAAA
1 T-TAAAAAATAAAA-AAAA
36875 T
1 T
36876 AAGCAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 5 0.16
18 19 0.61
19 7 0.23
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (17 bp):
TTAAAAAATAAAAAAAA
Found at i:36864 original size:20 final size:20
Alignment explanation
Indices: 36823--36874 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
36813 TTCAACTTTT
36823 AAAAAATAAAAAATAATTAAA
1 AAAAAATAAAAAATAA-TAAA
*
36844 AAAAAATAAAACTATAA-AAA
1 AAAAAATAAAA-AATAATAAA
*
36864 ATAAAATAAAA
1 AAAAAATAAAA
36875 TAAGCAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 13 0.46
21 11 0.39
22 4 0.14
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (20 bp):
AAAAAATAAAAAATAATAAA
Found at i:37262 original size:20 final size:18
Alignment explanation
Indices: 37234--37273 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
37224 TATATATTTC
37234 TTATATTTTTTTAACAAAAT
1 TTATATTTTTTT--CAAAAT
*
37254 TTATTTTTTTTTCAAAAT
1 TTATATTTTTTTCAAAAT
37272 TT
1 TT
37274 TAAGTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
20 11 0.58
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATTTTTTTCAAAAT
Found at i:37275 original size:19 final size:18
Alignment explanation
Indices: 37237--37273 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
37227 ATATTTCTTA
**
37237 TATTTTTTTAACAAAATT
1 TATTTTTTTTTCAAAATT
37255 TATTTTTTTTTCAAAATT
1 TATTTTTTTTTCAAAATT
37273 T
1 T
37274 TAAGTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTTTTTTCAAAATT
Found at i:38352 original size:13 final size:13
Alignment explanation
Indices: 38334--38358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38324 AAGTAATTAC
38334 TAATGTGATTTAT
1 TAATGTGATTTAT
38347 TAATGTGATTTA
1 TAATGTGATTTA
38359 CCCTTATTTT
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TAATGTGATTTAT
Found at i:38645 original size:3 final size:3
Alignment explanation
Indices: 38633--38672 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
38623 AAATTGTGTT
38633 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
38673 TAAAAATTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:47340 original size:21 final size:21
Alignment explanation
Indices: 47327--47383 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
47317 GTGTGGCTCT
47327 CCCACACGCCCGTGTAGCTAC
1 CCCACACGCCCGTGTAGCTAC
*
47348 CCTACACGCCCGTGTAGCTAC
1 CCCACACGCCCGTGTAGCTAC
*
47369 CCCACATGCCCGTGT
1 CCCACACGCCCGTGT
47384 GCCCAACCGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.18, C:0.46, G:0.19, T:0.18
Consensus pattern (21 bp):
CCCACACGCCCGTGTAGCTAC
Found at i:48336 original size:34 final size:33
Alignment explanation
Indices: 48295--48415 Score: 161
Period size: 34 Copynumber: 3.6 Consensus size: 33
48285 ACTCAGTTAA
* * * *
48295 CCATCCAACACACCAGATGCTCAAATGAGCCAAT
1 CCATCCAACACACCAAATGCTCTAA-GAGCTAGT
* *
48329 CCATCCAACACAACAAATGCTTGTAAGAGCTAGT
1 CCATCCAACACACCAAATGC-TCTAAGAGCTAGT
48363 CCATCCAACACACCAAATGCTCGTAAGAGCTAGT
1 CCATCCAACACACCAAATGCTC-TAAGAGCTAGT
48397 CCATCCAACACACCAAATG
1 CCATCCAACACACCAAATG
48416 TACTGTAACA
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
33 1 0.01
34 73 0.95
35 3 0.04
ACGTcount: A:0.38, C:0.33, G:0.12, T:0.17
Consensus pattern (33 bp):
CCATCCAACACACCAAATGCTCTAAGAGCTAGT
Found at i:49379 original size:57 final size:57
Alignment explanation
Indices: 49291--49405 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
49281 TTTCATGCTT
49291 TAACACATCTAAAACCGTCCACTATTGTGAAGAAGGGTATATTTACCTTATTAATCC
1 TAACACATCTAAAACCGTCCACTATTGTGAAGAAGGGTATATTTACCTTATTAATCC
*
49348 TAACACATCTAAAACCGTCCACTATTGTGAAGAAGGGTATATTTACGTTATTAATCC
1 TAACACATCTAAAACCGTCCACTATTGTGAAGAAGGGTATATTTACCTTATTAATCC
49405 T
1 T
49406 TTAATAAACC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (57 bp):
TAACACATCTAAAACCGTCCACTATTGTGAAGAAGGGTATATTTACCTTATTAATCC
Found at i:61321 original size:24 final size:23
Alignment explanation
Indices: 61294--61339 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
61284 AATTAGTCAT
61294 TTTTTAAAGTATTTTTATTTTTAA
1 TTTTTAAAGTA-TTTTATTTTTAA
**
61318 TTTTTAATTTATTTTATTTTTA
1 TTTTTAAAGTATTTTATTTTTA
61340 CGATAATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTTAAAGTATTTTATTTTTAA
Found at i:66321 original size:32 final size:32
Alignment explanation
Indices: 66280--66593 Score: 353
Period size: 32 Copynumber: 9.8 Consensus size: 32
66270 CATGAAATAA
* * *
66280 TGTTCATAGATTAATAGCTCCTACGATCTTAT
1 TGTTCATAGATTGATAGCTCTTACGAGCTTAT
* *
66312 TGTTCATAGATTGACAGCTCTTACGAGCTTTT
1 TGTTCATAGATTGATAGCTCTTACGAGCTTAT
* * *
66344 TGTTCATAGATTGACAACTCTTATGAGCTTAT
1 TGTTCATAGATTGATAGCTCTTACGAGCTTAT
* * *
66376 TGTTCAAAGATTGACAGGTCTTACGAGCTTAT
1 TGTTCATAGATTGATAGCTCTTACGAGCTTAT
* * *
66408 TGATCATAGATTGATAGCTCTTATGAGCTTAC
1 TGTTCATAGATTGATAGCTCTTACGAGCTTAT
* * *
66440 TGTTCACAGATTGATAACTCTTATGAG-TATAT
1 TGTTCATAGATTGATAGCTCTTACGAGCT-TAT
*
66472 TGTTCACAGATTGATAGCTCTTACGAGCTTAT
1 TGTTCATAGATTGATAGCTCTTACGAGCTTAT
* * * * *
66504 TATTTATAGATTGATAGCTCTTATGAG-TACAC
1 TGTTCATAGATTGATAGCTCTTACGAGCT-TAT
*
66536 TGTTCATAGATTGATAGCTCTTACGAGCATAT
1 TGTTCATAGATTGATAGCTCTTACGAGCTTAT
* * *
66568 TGTTAATAGATTAATAGCTCATACGA
1 TGTTCATAGATTGATAGCTCTTACGA
66594 ATATATAGGG
Statistics
Matches: 239, Mismatches: 39, Indels: 8
0.84 0.14 0.03
Matches are distributed among these distances:
31 2 0.01
32 236 0.99
33 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (32 bp):
TGTTCATAGATTGATAGCTCTTACGAGCTTAT
Found at i:71449 original size:17 final size:15
Alignment explanation
Indices: 71426--71470 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 15
71416 TATTAAATTT
71426 ATTTTTTAAAATATA
1 ATTTTTTAAAATATA
*
71441 ATTTTTTTTAAAT-T-
1 A-TTTTTTAAAATATA
71455 ATTTTTTAAAATATA
1 ATTTTTTAAAATATA
71470 A
1 A
71471 AATTATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 10 0.40
14 2 0.08
15 3 0.12
16 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTTTAAAATATA
Found at i:71461 original size:29 final size:29
Alignment explanation
Indices: 71410--71505 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
71400 ACAAATGATT
*
71410 TAAAAATA-TTAAATTTATTTTTTAAAATA
1 TAAAATTATTTAAA-TTATTTTTTAAAATA
** *
71439 TAATTTTTTTTAAATTATTTTTTAAAATA
1 TAAAATTATTTAAATTATTTTTTAAAATA
* *
71468 TAAAATTATTAAAATTA--TTTTGAAATAA
1 TAAAATTATTTAAATTATTTTTTAAAAT-A
71496 TAAAATTATT
1 TAAAATTATT
71506 AAACAATTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
27 8 0.14
28 11 0.20
29 32 0.57
30 5 0.09
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
TAAAATTATTTAAATTATTTTTTAAAATA
Found at i:71479 original size:28 final size:28
Alignment explanation
Indices: 71410--71508 Score: 103
Period size: 28 Copynumber: 3.5 Consensus size: 28
71400 ACAAATGATT
*
71410 TAAAAATATTAAATTTATTTTTTAAAATA
1 TAAAATTATTAAA-TTATTTTTTAAAATA
** *
71439 TAATTTTTTTTAAATTATTTTTTAAAATA
1 TAA-AATTATTAAATTATTTTTTAAAATA
*
71468 TAAAATTATTAAA--ATTATTTTGAAATAA
1 TAAAATTATTAAATTATT-TTTTAAAAT-A
71496 TAAAATTATTAAA
1 TAAAATTATTAAA
71509 CAATTTTTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
26 3 0.05
27 8 0.14
28 21 0.36
29 21 0.36
30 6 0.10
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
TAAAATTATTAAATTATTTTTTAAAATA
Found at i:71516 original size:28 final size:26
Alignment explanation
Indices: 71457--71517 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 26
71447 TTTAAATTAT
*
71457 TTTTTAAAATATAAAATTATTAAAAT
1 TTTTTAAAATATAAAATTATTAAAAA
*
71483 TATTTTGAAATAATAAAATTATTAAACAA
1 T-TTTTAAAAT-ATAAAATTATTAAA-AA
71512 TTTTTA
1 TTTTTA
71518 TTTCCAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 8 0.28
28 18 0.62
29 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
TTTTTAAAATATAAAATTATTAAAAA
Found at i:72465 original size:31 final size:32
Alignment explanation
Indices: 72416--72475 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
72406 ATTAAAATTA
72416 TTTAATAATTTTATTATTTCAAAAAAAATAAT
1 TTTAATAATTTTATTATTTCAAAAAAAATAAT
*
72448 TTTAATAATTTTA-TATTTTAAAAAAAAT
1 TTTAATAATTTTATTATTTCAAAAAAAAT
72476 TTAAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
TTTAATAATTTTATTATTTCAAAAAAAATAAT
Found at i:72478 original size:27 final size:27
Alignment explanation
Indices: 72415--72513 Score: 119
Period size: 27 Copynumber: 3.5 Consensus size: 27
72405 AATTAAAATT
*
72415 ATTTAATAATTTTATTATTTCAAAAAAAATA
1 ATTTAATAATTTTA-TATTT--TAAAAAA-A
72446 ATTTTAATAATTTTATATTTTAAAAAAA
1 A-TTTAATAATTTTATATTTTAAAAAAA
* *
72474 ATTTAAAAAATTTATATTTTAAAAAAA
1 ATTTAATAATTTTATATTTTAAAAAAA
72501 A-TTAATAATTTTA
1 ATTTAATAATTTTA
72514 AACCATTTGC
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
26 10 0.16
27 25 0.40
28 2 0.03
29 6 0.10
31 6 0.10
32 13 0.21
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTTAATAATTTTATATTTTAAAAAAA
Found at i:72501 original size:18 final size:19
Alignment explanation
Indices: 72478--72515 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
72468 AAAAAAATTT
*
72478 AAAAAATTTAT-ATTTTAA
1 AAAAAATTAATAATTTTAA
72496 AAAAAATTAATAATTTTAA
1 AAAAAATTAATAATTTTAA
72515 A
1 A
72516 CCATTTGCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAAATTAATAATTTTAA
Found at i:74498 original size:77 final size:78
Alignment explanation
Indices: 74371--74524 Score: 265
Period size: 77 Copynumber: 2.0 Consensus size: 78
74361 TAATTTCTTG
* *
74371 AGATTTTTTACTTAAATAATACAAAAAAATAAATTAATAACTAAAATGGTAT-TCCAAATTATTA
1 AGATTTTTTACCTAAATAATACAAAAAAATAAATTAATAACCAAAATGGTATCTCCAAATTATTA
*
74435 TTTATCAAAATGA
66 TTTACCAAAATGA
*
74448 AGATTTTTTACCTAAATAATACAAAAAAATAAATTAATAACCAAAATGGTATCTTCAAATTATTA
1 AGATTTTTTACCTAAATAATACAAAAAAATAAATTAATAACCAAAATGGTATCTCCAAATTATTA
74513 TTTACCAAAATG
66 TTTACCAAAATG
74525 GTATGTTTAG
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
77 50 0.69
78 22 0.31
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (78 bp):
AGATTTTTTACCTAAATAATACAAAAAAATAAATTAATAACCAAAATGGTATCTCCAAATTATTA
TTTACCAAAATGA
Found at i:74968 original size:11 final size:11
Alignment explanation
Indices: 74952--75008 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
74942 GGGGACCAAC
* *
74952 GAAAAATGAAG
1 GAAAAAAGAAA
74963 GAAAAAAGAAA
1 GAAAAAAGAAA
74974 GAAAAAAAAGAAA
1 G--AAAAAAGAAA
74987 GAAAGAAAGAAA
1 GAAA-AAAGAAA
*
74999 GAAAGAAGAA
1 GAAAAAAGAA
75009 GGAAGAAGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 18 0.45
12 11 0.28
13 11 0.28
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:74976 original size:4 final size:4
Alignment explanation
Indices: 74963--75005 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
74953 AAAAATGAAG
*
74963 GAAA -AAA GAAA GAAAA AAAA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
75006 GAAGGAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:74978 original size:21 final size:21
Alignment explanation
Indices: 74963--75008 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
74953 AAAAATGAAG
74963 GAAA-AAAGAAAGAAAAAAAA
1 GAAAGAAAGAAAGAAAAAAAA
74983 GAAAGAAAGAAAGAAAGAAAGAA
1 GAAAGAAAGAAAGAAA-AAA-AA
75006 GAA
1 GAA
75009 GGAAGAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.17
21 11 0.48
22 3 0.13
23 5 0.22
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAGAAAAAAAA
Done.