Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011780.1 Kokia drynarioides strain JFW-HI SEQ_126775, 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: 64753
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:555 original size:58 final size:57
Alignment explanation
Indices: 419--644 Score: 258
Period size: 59 Copynumber: 3.8 Consensus size: 57
409 AGAGGTCCCT
* * *
419 AAACTGCCAAAAATTCCATGTTTACCCCCGAACTTCCAAAAATTCCATTTTTTACCCCA
1 AAACTTCCAAAAATTCCAT-TTTA-CCCTGAACTTCCAAAAATTCCATTTTTAACCCCA
*
478 AAACTTCCAAAAATTCCATTTTCACCACTAAACTTCCAAAAATTCCA-TTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTT-ACC-CTGAACTTCCAAAAATTCCATTTTTAACCCCA
* * *
536 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTACCAAAAATTCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCA-TTTTACCCT-GAACTTCCAAAAATTCCATTTTTAACCCCA
** * *
595 AAACTTTTAAAAATTACCATTTTGCCCCTGAA-TGTCCAAAAACTCCATTT
1 AAACTTCCAAAAATT-CCATTTT-ACCCTGAACT-TCCAAAAATTCCATTT
645 CGACCTCGAA
Statistics
Matches: 146, Mismatches: 13, Indels: 16
0.83 0.07 0.09
Matches are distributed among these distances:
57 2 0.01
58 53 0.36
59 84 0.58
60 7 0.05
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (57 bp):
AAACTTCCAAAAATTCCATTTTACCCTGAACTTCCAAAAATTCCATTTTTAACCCCA
Found at i:633 original size:88 final size:86
Alignment explanation
Indices: 419--644 Score: 258
Period size: 88 Copynumber: 2.6 Consensus size: 86
409 AGAGGTCCCT
* * *
419 AAACTGCCAAAAATTCCATGTTTACCCCCGAACTTCCAAAAATTCCATTTTTTACCCCAAAACTT
1 AAACTTCCAAAAATTCCAT-TTTACCCCAGAACTTCCAAAAATTCCA-TTTTTACCCCAAAACTA
*
484 CCAAAAATTCCATTTTCACCACT
64 CCAAAAATTCCATTTTCACCACA
* *
507 AAACTTCCAAAAATTCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTC-GAACTA
1 AAACTTCCAAAAATTCCATTTT-ACCCCAGAACTTCCAAAAATTCCATTTTTACCC-CAAAACTA
* *
571 CCAAAAATTCCATTTTTGACCTCA
64 CCAAAAATTCCA-TTTTCACCACA
** * * *
595 AAACTTTTAAAAATTACCATTTTGCCCCTGAA-TGTCCAAAAACTCCATTT
1 AAACTTCCAAAAATT-CCATTTTACCCCAGAACT-TCCAAAAATTCCATTT
645 CGACCTCGAA
Statistics
Matches: 119, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
87 29 0.24
88 83 0.70
89 7 0.06
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (86 bp):
AAACTTCCAAAAATTCCATTTTACCCCAGAACTTCCAAAAATTCCATTTTTACCCCAAAACTACC
AAAAATTCCATTTTCACCACA
Found at i:703 original size:29 final size:29
Alignment explanation
Indices: 415--715 Score: 230
Period size: 29 Copynumber: 10.4 Consensus size: 29
405 CCCTAGAGGT
* *
415 CCCT-AAACTGCCAAAAATTCCATGTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* *
443 CCCCCGAACTTCCAAAAATTCCATTTTTTA
1 CCCTCAAACTTCCAAAAATTCCA-TTTTTA
*
473 CCC-CAAAACTTCCAAAAATTCCATTTTCA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
*
502 CCACT-AAACTTCCAAAAATTCCATTTTAA
1 CC-CTCAAACTTCCAAAAATTCCATTTTTA
531 CCC-CAAAACTTCCAAAAATTCCATTTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
* *
560 CCCTCGAACTACCAAAAATTCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTCCATTTTT-A
** **
590 -CCTCAAAACTTTTAAAAATTACCATTTTGC
1 CCCTC-AAACTTCCAAAAATT-CCATTTTTA
* * **
620 CCCT-GAA-TGTCCAAAAACTCCATTTCGA
1 CCCTCAAACT-TCCAAAAATTCCATTTTTA
*
648 -CCTCGAAAC-TCTC-AAAATTACC-CTTTTA
1 CCCTC-AAACTTC-CAAAAATT-CCATTTTTA
* * *
676 CCCTCAAATTTCTAAAAATTCCTTTTTTAA
1 CCCTCAAACTTCCAAAAATTCCATTTTT-A
706 CCCT-AAACTT
1 CCCTCAAACTT
716 TCTCGAAATT
Statistics
Matches: 219, Mismatches: 31, Indels: 45
0.74 0.11 0.15
Matches are distributed among these distances:
27 3 0.01
28 27 0.12
29 135 0.62
30 44 0.20
31 10 0.05
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTCCATTTTTA
Found at i:1548 original size:33 final size:33
Alignment explanation
Indices: 1506--1571 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1496 CAAAGACCTA
1506 CATGTTTTCAAAACGGTTTTTAAAACGTTTTGT
1 CATGTTTTCAAAACGGTTTTTAAAACGTTTTGT
1539 CATGTTTTCAAAACGGTTTTTAAAACGTTTTGT
1 CATGTTTTCAAAACGGTTTTTAAAACGTTTTGT
1572 GGTGATCCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
CATGTTTTCAAAACGGTTTTTAAAACGTTTTGT
Found at i:3986 original size:20 final size:20
Alignment explanation
Indices: 3903--4002 Score: 130
Period size: 20 Copynumber: 5.0 Consensus size: 20
3893 AAGTGCATTC
3903 TATCAGGCTTTGTGCCGGTG
1 TATCAGGCTTTGTGCCGGTG
* * * *
3923 TATTAGACTTTATGCTGGTG
1 TATCAGGCTTTGTGCCGGTG
* *
3943 TATTAGG-TTTAGTGACGGTG
1 TATCAGGCTTT-GTGCCGGTG
3963 TATCAGGCTTTGTGCCGGTG
1 TATCAGGCTTTGTGCCGGTG
3983 TATCAGGCTTTGTGCCGGTG
1 TATCAGGCTTTGTGCCGGTG
4003 ATTCAAAAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.04
20 62 0.91
21 3 0.04
ACGTcount: A:0.14, C:0.15, G:0.33, T:0.38
Consensus pattern (20 bp):
TATCAGGCTTTGTGCCGGTG
Found at i:10636 original size:20 final size:20
Alignment explanation
Indices: 10420--10635 Score: 333
Period size: 20 Copynumber: 10.8 Consensus size: 20
10410 AAGTGCATTC
*
10420 TATCAGGCTTTGTACCGGTG
1 TATCAGGCTTTGTGCCGGTG
10440 TATCAGGCTTTGTGCCGGTG
1 TATCAGGCTTTGTGCCGGTG
10460 TATCAGGCTTTGTGCCGGTG
1 TATCAGGCTTTGTGCCGGTG
** *
10480 TATCAGGCTTAATGCCTGTG
1 TATCAGGCTTTGTGCCGGTG
10500 TATCAGGCTTTGTGCCGGTG
1 TATCAGGCTTTGTGCCGGTG
* * *
10520 AATCAGGCTTTGTACCAGTG
1 TATCAGGCTTTGTGCCGGTG
10540 TATCAGGCTTTGTGCCGGTG
1 TATCAGGCTTTGTGCCGGTG
*
10560 AATCAGGCTTTGTGCCGGTG
1 TATCAGGCTTTGTGCCGGTG
*
10580 TATCAGGCTTTATGCCGGTG
1 TATCAGGCTTTGTGCCGGTG
* *
10600 TATCAGGCTTTATGCCAGTG
1 TATCAGGCTTTGTGCCGGTG
10620 TATCAGGCTTTGTGCC
1 TATCAGGCTTTGTGCC
10636 AATGATTCAA
Statistics
Matches: 178, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 178 1.00
ACGTcount: A:0.15, C:0.20, G:0.31, T:0.34
Consensus pattern (20 bp):
TATCAGGCTTTGTGCCGGTG
Found at i:15368 original size:19 final size:18
Alignment explanation
Indices: 15340--15399 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 18
15330 AATAGATGAT
*
15340 TTTTCTCAACTGAAAATA
1 TTTTCTCAACTAAAAATA
* *
15358 TTTTCTGCAACAATTAAAAGA
1 TTTTCT-CAAC--TAAAAATA
15379 TTTTCCTCAACTAAAAATA
1 TTTT-CTCAACTAAAAATA
15398 TT
1 TT
15400 ATGAAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 6 0.18
19 12 0.35
21 14 0.41
22 2 0.06
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (18 bp):
TTTTCTCAACTAAAAATA
Found at i:19945 original size:20 final size:20
Alignment explanation
Indices: 19922--19982 Score: 122
Period size: 20 Copynumber: 3.0 Consensus size: 20
19912 AAAATACATT
19922 AATTTTATATAATTAAAGTA
1 AATTTTATATAATTAAAGTA
19942 AATTTTATATAATTAAAGTA
1 AATTTTATATAATTAAAGTA
19962 AATTTTATATAATTAAAGTA
1 AATTTTATATAATTAAAGTA
19982 A
1 A
19983 GTAATCATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AATTTTATATAATTAAAGTA
Found at i:20009 original size:17 final size:18
Alignment explanation
Indices: 19987--20020 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
19977 AAGTAAGTAA
19987 TCATTAATA-TATTAATT
1 TCATTAATATTATTAATT
20004 TCATTAATATTATTAAT
1 TCATTAATATTATTAAT
20021 AAAATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
TCATTAATATTATTAATT
Found at i:28176 original size:16 final size:17
Alignment explanation
Indices: 28157--28194 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
28147 TAAATTTCAA
28157 TAAAAA-TAAAATTTGT
1 TAAAAATTAAAATTTGT
* *
28173 TAAAAATTATAATTTTT
1 TAAAAATTAAAATTTGT
28190 TAAAA
1 TAAAA
28195 GAATCATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAAAATTAAAATTTGT
Found at i:28491 original size:10 final size:10
Alignment explanation
Indices: 28434--28656 Score: 58
Period size: 10 Copynumber: 22.8 Consensus size: 10
28424 TTTTAATACG
28434 ATAA-TTTTT
1 ATAATTTTTT
28443 ATAATTTTTT
1 ATAATTTTTT
* *
28453 TTACGA-ATTTT
1 ATA--ATTTTTT
28464 AT-ATTTATTT
1 ATAATTT-TTT
*
28474 ATATTTTTTT
1 ATAATTTTTT
28484 ATAATTTTCTT
1 ATAATTTT-TT
** *
28495 ACGATTTTAT
1 ATAATTTTTT
* *
28505 AAAATTTTCT
1 ATAATTTTTT
*
28515 AT-A-TTTCT
1 ATAATTTTTT
*
28523 AT-ATATTTT
1 ATAATTTTTT
28532 ATAATTTTTTT
1 ATAA-TTTTTT
* *
28543 ACAATTTTATA
1 ATAATTTT-TT
**
28554 ATTTTTTTTT
1 ATAATTTTTT
* *
28564 CTAATTTTTA
1 ATAATTTTTT
**
28574 ATAA-AATTT
1 ATAATTTTTT
28583 A-AATATTTTT
1 ATAAT-TTTTT
28593 AT-A-TTTTT
1 ATAATTTTTT
** *
28601 ATTAAAATTTA
1 A-TAATTTTTT
28612 ATAATTTTTT
1 ATAATTTTTT
*
28622 ATAA-CTTTT
1 ATAATTTTTT
28631 AT--TTTTTT
1 ATAATTTTTT
* *
28639 TTTATTTTTT
1 ATAATTTTTT
*
28649 ATCATTTT
1 ATAATTTT
28657 GCCACATTTC
Statistics
Matches: 152, Mismatches: 42, Indels: 39
0.65 0.18 0.17
Matches are distributed among these distances:
8 22 0.14
9 21 0.14
10 74 0.49
11 34 0.22
12 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:28560 original size:29 final size:28
Alignment explanation
Indices: 28434--28630 Score: 93
Period size: 29 Copynumber: 6.7 Consensus size: 28
28424 TTTTAATACG
28434 ATAA-TTTTTATAATTTTTTTTACGAATTTT
1 ATAATTTTTTATAA-TTTTTTTA--AATTTT
28464 AT-ATTTATTTAT-ATTTTTTTATAATTTT
1 ATAATTT-TTTATAATTTTTTTA-AATTTT
* * * * *
28492 CTTACGATTTTATA-AAATTTTCTATATTTCT
1 -ATA--ATTTTTTATAATTTTTTTAAATTT-T
*
28523 AT-ATATTTTATAATTTTTTTACAATTTT
1 ATAATTTTTTATAATTTTTTTA-AATTTT
* * *
28551 ATAATTTTTTTTTCTAATTTTTAATAAAATTT
1 ATAA---TTTTTTATAATTTTT-TTAAATTTT
*
28583 A-AATATTTTTAT-ATTTTTATTAAAATTTA
1 ATAAT-TTTTTATAATTTTT-TT-AAATTTT
*
28612 ATAATTTTTTATAACTTTT
1 ATAATTTTTTATAATTTTT
28631 ATTTTTTTTT
Statistics
Matches: 127, Mismatches: 21, Indels: 38
0.68 0.11 0.20
Matches are distributed among these distances:
27 6 0.05
28 26 0.20
29 34 0.27
30 18 0.14
31 18 0.14
32 23 0.18
33 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (28 bp):
ATAATTTTTTATAATTTTTTTAAATTTT
Found at i:28600 original size:28 final size:28
Alignment explanation
Indices: 28567--28620 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
28557 TTTTTTTCTA
28567 ATTTTTAATAAAATTTAA-ATATTTTTAT
1 ATTTTTAATAAAATTTAATA-ATTTTTAT
*
28595 ATTTTTATTAAAATTTAATAATTTTT
1 ATTTTTAATAAAATTTAATAATTTTT
28621 TATAACTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTTTTAATAAAATTTAATAATTTTTAT
Found at i:31911 original size:17 final size:17
Alignment explanation
Indices: 31891--31933 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
31881 ATACAAGTAT
31891 ACAAAATTTAAAAAGGC
1 ACAAAATTTAAAAAGGC
31908 ACAAAATTTAAAAAGGC
1 ACAAAATTTAAAAAGGC
31925 ACAAAATTT
1 ACAAAATTT
31934 TTATAAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.58, C:0.12, G:0.09, T:0.21
Consensus pattern (17 bp):
ACAAAATTTAAAAAGGC
Found at i:32497 original size:19 final size:18
Alignment explanation
Indices: 32454--32497 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
32444 CTGCTCTTTC
*
32454 GAGCCAACATTGCTAAAT
1 GAGCCAGCATTGCTAAAT
32472 GTA-CCAGCATTGCTTAAAT
1 G-AGCCAGCATTGC-TAAAT
32491 GAGCCAG
1 GAGCCAG
32498 TAATGCTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (18 bp):
GAGCCAGCATTGCTAAAT
Found at i:32504 original size:19 final size:19
Alignment explanation
Indices: 32491--32561 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
32481 TTGCTTAAAT
32491 GAGCCAGTAATGCTCAAAC
1 GAGCCAGTAATGCTCAAAC
* *
32510 GAGCAAATAATGCTCAAAC
1 GAGCCAGTAATGCTCAAAC
* *
32529 AAGCCAGTAATGCTAAAAC
1 GAGCCAGTAATGCTCAAAC
*
32548 GAGCTAGTAATGCT
1 GAGCCAGTAATGCT
32562 ATTCTTCCAC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (19 bp):
GAGCCAGTAATGCTCAAAC
Found at i:35352 original size:18 final size:19
Alignment explanation
Indices: 35324--35359 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
35314 TATTTTTTAT
35324 TTTTCAATTCAAACTTTCA
1 TTTTCAATTCAAACTTTCA
*
35343 TTTT-AATTCAAATTTTC
1 TTTTCAATTCAAACTTTC
35360 TCTCTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTCAATTCAAACTTTCA
Found at i:43889 original size:18 final size:18
Alignment explanation
Indices: 43874--43953 Score: 108
Period size: 18 Copynumber: 4.4 Consensus size: 18
43864 TCATTTGAGT
*
43874 ATACTAGCTCGGTT-GAGC
1 ATACTGGCT-GGTTAGAGC
43892 ATACTGGCTGGTTAGAGC
1 ATACTGGCTGGTTAGAGC
43910 ATACTGGCTGGTTAGAGC
1 ATACTGGCTGGTTAGAGC
* *
43928 ATACTGGCTCGTAAGAGC
1 ATACTGGCTGGTTAGAGC
43946 AATACTGG
1 -ATACTGG
43954 ATCGAAAGGA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.07
18 46 0.81
19 7 0.12
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (18 bp):
ATACTGGCTGGTTAGAGC
Found at i:50822 original size:18 final size:18
Alignment explanation
Indices: 50796--50869 Score: 78
Period size: 18 Copynumber: 4.1 Consensus size: 18
50786 GAAGGAATAA
*
50796 CATACTGGCTCATTAGAG
1 CATACTGGCTCGTTAGAG
* *
50814 CATAGTGGCTTGGTT-GAG
1 CATACTGGC-TCGTTAGAG
*
50832 CATATTGGCTCGTTAGAG
1 CATACTGGCTCGTTAGAG
* *
50850 CATACTGGCTTGTAAGAG
1 CATACTGGCTCGTTAGAG
50868 CA
1 CA
50870 ATATTGGATC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
17 4 0.09
18 39 0.85
19 3 0.07
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (18 bp):
CATACTGGCTCGTTAGAG
Found at i:50869 original size:36 final size:36
Alignment explanation
Indices: 50796--50876 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 36
50786 GAAGGAATAA
* * *
50796 CATACTGGCTCATTAGAGCATAGTGGCTTGGTTGAG
1 CATATTGGCTCATTAGAGCATACTGGCTTGGTAGAG
*
50832 CATATTGGCTCGTTAGAGCATACTGGCTT-GTAAGAG
1 CATATTGGCTCATTAGAGCATACTGGCTTGGT-AGAG
50868 CAATATTGG
1 C-ATATTGG
50877 ATCGCAAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
35 2 0.05
36 30 0.77
37 7 0.18
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (36 bp):
CATATTGGCTCATTAGAGCATACTGGCTTGGTAGAG
Found at i:60356 original size:512 final size:512
Alignment explanation
Indices: 59392--60414 Score: 1940
Period size: 512 Copynumber: 2.0 Consensus size: 512
59382 GATGATCGAC
59392 CCCATAGTCGGTATGTTGGGTACATGACTTGTGTATGACATGGTTTTACTAGAAACAATGAAATT
1 CCCATAGTCGGTATGTTGGGTACATGACTTGTGTATGACATGGTTTTACTAGAAACAATGAAATT
59457 CATAGCTCAATTAAAGAGTTAATGATATCCTCTCATTGGCATTGTGTGGATTGATAAATATGGAA
66 CATAGCTCAATTAAAGAGTTAATGATATCCTCTCATTGGCATTGTGTGGATTGATAAATATGGAA
*
59522 CGTGACCGCGGATTGCTTGTTTTTGAACGAGCAATTTATCACAGTCATTTATTGACTGTGGTCAT
131 CGAGACCGCGGATTGCTTGTTTTTGAACGAGCAATTTATCACAGTCATTTATTGACTGTGGTCAT
59587 ATTAATCATTAAGAAGACACAATGGTGACAATGAGATAAAATAAGATTGTATTGAGTGAACAAAT
196 ATTAATCATTAAGAAGACACAATGGTGACAATGAGATAAAATAAGATTGTATTGAGTGAACAAAT
* *
59652 TTAACTCAAAAGAATCAAGGATATCATATGAGGCTAACACACACATGACGAGGTCATTGGATAAA
261 TTAACTCAAAAGAATCAAGGATATCATATGAGACTAACACACACATGACGAGGTCATTGGACAAA
* *
59717 ACAGTTGAATGAATTGCTTTCGTAAATAGTATACAATAAGTAATTTTCAATTATGATACTTTTTG
326 ACAGTTGAATGAATTGCTTTCGTAAACAGTATACAATAAGTAATTTTCAATTATGATACTTCTTG
*
59782 TGGACTGACTCCATGATTAAGTAACTACGAATTATAGGAGCAATTTTTCTAGATATAATTGCAAT
391 TGGACTAACTCCATGATTAAGTAACTACGAATTATAGGAGCAATTTTTCTAGATATAATTGCAAT
59847 TAATAGAGCCTAATTGTATATGTCTGATTGATCCGTCCGCTAGCTCAACAAAAGCTG
456 TAATAGAGCCTAATTGTATATGTCTGATTGATCCGTCCGCTAGCTCAACAAAAGCTG
59904 CCCATAGTCGGTATGTTGGGTACATGACTTGTGTATGACATGGTTTTACTAGAAACAAT-AGAAT
1 CCCATAGTCGGTATGTTGGGTACATGACTTGTGTATGACATGGTTTTACTAGAAACAATGA-AAT
59968 TCATAGCTCAATTAAAGAGTTAATGATATCCTCTCATTGGCATTGTGTGGATTGATAAATATGGA
65 TCATAGCTCAATTAAAGAGTTAATGATATCCTCTCATTGGCATTGTGTGGATTGATAAATATGGA
*
60033 ACGAGTCCGCGGATTGCTTGTTTTTGAACGAGCAATTTATCACAGTCATTTATTGACTGTGGTCA
130 ACGAGACCGCGGATTGCTTGTTTTTGAACGAGCAATTTATCACAGTCATTTATTGACTGTGGTCA
60098 TATTAATCATTAAGAAGACACAATGGTGACAATGAGATAAAATAAGATTGTATTGAGTGAACAAA
195 TATTAATCATTAAGAAGACACAATGGTGACAATGAGATAAAATAAGATTGTATTGAGTGAACAAA
60163 TTTAACTCAAAAGAATCAAGGATATCATATGAGACTAACACACACATGACGAGGTCATTGGACAA
260 TTTAACTCAAAAGAATCAAGGATATCATATGAGACTAACACACACATGACGAGGTCATTGGACAA
*
60228 AACAGTTGAATGAATTGCTTTCGTAAACAGTGTACAATAAGTAATTTTCAATTATGATACTTCTT
325 AACAGTTGAATGAATTGCTTTCGTAAACAGTATACAATAAGTAATTTTCAATTATGATACTTCTT
* *
60293 GTGGACTAACTCCATGATTAAGTAATTGCGAATTATAGGAGCAATTTTTCTAGATATAATTGCAA
390 GTGGACTAACTCCATGATTAAGTAACTACGAATTATAGGAGCAATTTTTCTAGATATAATTGCAA
60358 TTAATAGAGCCTAATTGTATATGTCTGATTGATCCGTCCGCTAGCTCAACAAAAGCT
455 TTAATAGAGCCTAATTGTATATGTCTGATTGATCCGTCCGCTAGCTCAACAAAAGCT
60415 CGATCGGATT
Statistics
Matches: 500, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
511 1 0.00
512 499 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (512 bp):
CCCATAGTCGGTATGTTGGGTACATGACTTGTGTATGACATGGTTTTACTAGAAACAATGAAATT
CATAGCTCAATTAAAGAGTTAATGATATCCTCTCATTGGCATTGTGTGGATTGATAAATATGGAA
CGAGACCGCGGATTGCTTGTTTTTGAACGAGCAATTTATCACAGTCATTTATTGACTGTGGTCAT
ATTAATCATTAAGAAGACACAATGGTGACAATGAGATAAAATAAGATTGTATTGAGTGAACAAAT
TTAACTCAAAAGAATCAAGGATATCATATGAGACTAACACACACATGACGAGGTCATTGGACAAA
ACAGTTGAATGAATTGCTTTCGTAAACAGTATACAATAAGTAATTTTCAATTATGATACTTCTTG
TGGACTAACTCCATGATTAAGTAACTACGAATTATAGGAGCAATTTTTCTAGATATAATTGCAAT
TAATAGAGCCTAATTGTATATGTCTGATTGATCCGTCCGCTAGCTCAACAAAAGCTG
Found at i:60796 original size:11 final size:11
Alignment explanation
Indices: 60721--60796 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
60711 ATTCCAAAAA
*
60721 TAATATTATTT
1 TAATATTAATT
60732 TAATAGTTTAATAT
1 TAATA--TTAAT-T
60746 TAA-ATGTAATT
1 TAATAT-TAATT
*
60757 TAATACTTATTT
1 TAATA-TTAATT
60769 TAATATT-ATT
1 TAATATTAATT
60779 T--TATTAATT
1 TAATATTAATT
60788 TAATATTAA
1 TAATATTAA
60797 AGTGATTATT
Statistics
Matches: 53, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
8 4 0.08
9 4 0.08
10 3 0.06
11 18 0.34
12 14 0.26
13 6 0.11
14 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:60822 original size:51 final size:48
Alignment explanation
Indices: 60721--60823 Score: 127
Period size: 48 Copynumber: 2.1 Consensus size: 48
60711 ATTCCAAAAA
* *
60721 TAATATTATTTTAATAGTTTAATATTAAATGTAATTTAATACTTATTT
1 TAATATTATTTTAATAATTTAATATTAAATGTAATTTAATACTTAATT
* *
60769 TAATATTATTTTATTAATTTAATATTAAAGTGATTATTTTAATA-TTAGATT
1 TAATATTATTTTAATAATTTAATATTAAA-TG--TAATTTAATACTTA-ATT
60820 TAAT
1 TAAT
60824 TTTAATGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
48 27 0.57
49 2 0.04
50 3 0.06
51 15 0.32
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (48 bp):
TAATATTATTTTAATAATTTAATATTAAATGTAATTTAATACTTAATT
Done.