Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009143.1 Kokia drynarioides strain JFW-HI SEQ_123847, 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: 53164
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1484 original size:15 final size:16
Alignment explanation
Indices: 1459--1489 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1449 CTTGAAACCC
1459 AAGGCAAAAAAAGAAA
1 AAGGCAAAAAAAGAAA
1475 AAGG-AAAAAAAGAAA
1 AAGGCAAAAAAAGAAA
1490 GGAAACTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (16 bp):
AAGGCAAAAAAAGAAA
Found at i:2371 original size:20 final size:19
Alignment explanation
Indices: 2340--2401 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 19
2330 ATTCAATGAA
*
2340 AAAAAAAGAAAGAAGAA-AG
1 AAAAAAATAAAGAA-AATAG
2359 AAAGAAAATAAAGAAAATAG
1 AAA-AAAATAAAGAAAATAG
2379 AAAAAAAT--AGAAAATAG
1 AAAAAAATAAAGAAAATAG
2396 AAAAAA
1 AAAAAA
2402 CGAGAAAAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
17 15 0.38
19 10 0.25
20 15 0.38
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (19 bp):
AAAAAAATAAAGAAAATAG
Found at i:2382 original size:41 final size:40
Alignment explanation
Indices: 2337--2415 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 40
2327 CAGATTCAAT
2337 GAAAAAAAAAGAAAGA-AGAAAGAAA-GAAAATAAAGAAAATA
1 GAAAAAAAAAGAAA-ATAGAAA-AAACGAAAA-AAAGAAAATA
* *
2378 GAAAAAAATAGAAAATAGAAAAAACGAGAAAAAGAAAA
1 GAAAAAAAAAGAAAATAGAAAAAACGAAAAAAAGAAAA
2416 GAAGAGGTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 12 0.35
41 22 0.65
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.05
Consensus pattern (40 bp):
GAAAAAAAAAGAAAATAGAAAAAACGAAAAAAAGAAAATA
Found at i:2383 original size:17 final size:17
Alignment explanation
Indices: 2361--2415 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
2351 GAAGAAAGAA
*
2361 AGAAAATAA-AGAAAAT
1 AGAAAAAAATAGAAAAT
2377 AGAAAAAAATAGAAAAT
1 AGAAAAAAATAGAAAAT
**
2394 AGAAAAAACGAGAAAA-
1 AGAAAAAAATAGAAAAT
2410 AGAAAA
1 AGAAAA
2416 GAAGAGGTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
16 14 0.40
17 21 0.60
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (17 bp):
AGAAAAAAATAGAAAAT
Found at i:3646 original size:99 final size:98
Alignment explanation
Indices: 3357--4046 Score: 416
Period size: 99 Copynumber: 7.0 Consensus size: 98
3347 TTGAGAAAAA
* * * * *
3357 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGTAACGGCAAACCCT-GTACCTTATAAGATGTGAC
1 CATGAAGATTTGAAGAGAAAGATTGAGGCCGTAATGACAAA-CCTGGTACC-TAAAAGATGTGAC
* *
3421 GGGAAAGGTTGAGGTCACAACGACGAACCCAGTAC
64 GGGAAAGGTTGAGGTCGCAACGACGAACCCGGTAC
* * * * * * *
3456 CATGAAGATTTGAA-AGGAAAGGTTGATGCCGCAATGACAAACTTGTTACCTAAAAAATGTGATG
1 CATGAAGATTTGAAGA-GAAAGATTGAGGCCGTAATGACAAACCTGGTACCTAAAAGATGTGACG
*
3520 GGAAAGGTTGAGGCCGCAACGACGAACCCGGTAC
65 GGAAAGGTTGAGGTCGCAACGACGAACCCGGTAC
* * * * *
3554 CGTGAAGATTTGAAGATAAAGATTGAGGCCGTAATGACGAACCTGGTATCGTAGAAGATGTGACG
1 CATGAAGATTTGAAGAGAAAGATTGAGGCCGTAATGACAAACCTGGTA-CCTAAAAGATGTGACG
* *
3619 GGAAAGGTTGAGGTTGCAACGACGAACCCGATAC
65 GGAAAGGTTGAGGTCGCAACGACGAACCCGGTAC
* * ** *** * *
3653 CATGAA-ATTTTAA-AGGAAAAGATTGAGGTCGCGATGGTGAATCTGATACCTCAAAAGATGTGA
1 CATGAAGATTTGAAGA-G-AAAGATTGAGGCCGTAATGACAAACCTGGTACCT-AAAAGATGTGA
* * * * ** * *
3716 TGGGAAAGATTGAGGCCACAACGGTGAATCCGGTAG
63 CGGGAAAGGTTGAGGTCGCAACGACGAACCCGGTAC
* * * * * * * * *
3752 CATGAA-ATGTGATGAGAAAGGTTGAGGCTGTAA-CAGCAAACCTAGTACC-ATGAAGATTTGAA
1 CATGAAGATTTGAAGAGAAAGATTGAGGCCGTAATGA-CAAACCTGGTACCTA-AAAGATGTGAC
* ** ** *
3814 GGGAAAGATTGAGACCGCAATTACGAACCCGATAC
64 GGGAAAGGTTGAGGTCGCAACGACGAACCCGGTAC
* * * *** * *
3849 CTTAAAAGATGTGACAG-GAAAGATTGAGGCCGTAATGGTGAA-TTCGGTACC-ATGAA-ATGTG
1 CAT-GAAGATTTGA-AGAGAAAGATTGAGGCCGTAATGACAAACCT-GGTACCTA-AAAGATGTG
* * * *
3910 ATGAGAAAGGTTGAGG-CTGCAA-TAGCGAACTCGGTAC
62 ACGGGAAAGGTTGAGGTC-GCAACGA-CGAACCCGGTAC
* * * * * * * * * * *
3947 CATAAAGATTTTAAGGGAAAGGTTGAGGCCGTAACGGCGAACCTGGTACCTTAGATGATATGAAG
1 CATGAAGATTTGAAGAGAAAGATTGAGGCCGTAATGACAAACCTGGTACC-TAAAAGATGTGACG
* ***
4012 GGAAAGGTTGAGGCCGCAACGGTAAACCCGGTAC
65 GGAAAGGTTGAGGTCGCAACGACGAACCCGGTAC
4046 C
1 C
4047 TTAGAAAATA
Statistics
Matches: 456, Mismatches: 111, Indels: 48
0.74 0.18 0.08
Matches are distributed among these distances:
96 3 0.01
97 76 0.17
98 148 0.32
99 226 0.50
100 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.20
Consensus pattern (98 bp):
CATGAAGATTTGAAGAGAAAGATTGAGGCCGTAATGACAAACCTGGTACCTAAAAGATGTGACGG
GAAAGGTTGAGGTCGCAACGACGAACCCGGTAC
Found at i:3773 original size:147 final size:146
Alignment explanation
Indices: 3611--4046 Score: 419
Period size: 147 Copynumber: 3.0 Consensus size: 146
3601 ATCGTAGAAG
* * * *
3611 ATGTGACGGGAAAGGTTGAGGTTGCAACGACGAACCCGATACCATGAA-ATTTTAAAGGAAAAGA
1 ATGTGATGAGAAAGGTTGAGGCTGCAAC-ACGAACCCGATACCATGAAGATTTT-AAGGGAAAGA
* * ** * * **
3675 TTGAGGTCGCGATGGTGAATCTGATACCTCAAAAGATGTGATGGGAAAGATTGAGGCCACAACGG
64 TTGAGGCCGCAATGACGAACCCGATACCTCAAAAGATGTGACAGGAAAGATTGAGGCCACAACGG
*
3740 TGAATCCGGTAGCATGAA
129 TGAATCCGGTACCATGAA
* * * *
3758 ATGTGATGAGAAAGGTTGAGGCTGTAACA-GCAAACCTAGTACCATGAAGATTTGAAGGGAAAGA
1 ATGTGATGAGAAAGGTTGAGGCTGCAACACG-AACCCGA-TACCATGAAGATTTTAAGGGAAAGA
* * * ** *
3822 TTGAGACCGCAATTACGAACCCGATACCTTAAAAGATGTGACAGGAAAGATTGAGGCCGTAATGG
64 TTGAGGCCGCAATGACGAACCCGATACCTCAAAAGATGTGACAGGAAAGATTGAGGCCACAACGG
*
3887 TGAATTCGGTACCATGAA
129 TGAATCCGGTACCATGAA
* * * * *
3905 ATGTGATGAGAAAGGTTGAGGCTGCAATAGCGAACTCGGTACCATAAAGATTTTAAGGGAAAGGT
1 ATGTGATGAGAAAGGTTGAGGCTGCAACA-CGAACCCGATACCATGAAGATTTTAAGGGAAAGAT
* * * * * * * * * * *
3970 TGAGGCCGTAACGGCGAACCTGGTACCTTAGATGATATGA-AGGGAAAGGTTGAGGCCGCAACGG
65 TGAGGCCGCAATGACGAACCCGATACCTCAAAAGATGTGACA-GGAAAGATTGAGGCCACAACGG
* *
4034 TAAACCCGGTACC
129 TGAATCCGGTACC
4047 TTAGAAAATA
Statistics
Matches: 234, Mismatches: 49, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
145 1 0.00
146 7 0.03
147 218 0.93
148 7 0.03
149 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (146 bp):
ATGTGATGAGAAAGGTTGAGGCTGCAACACGAACCCGATACCATGAAGATTTTAAGGGAAAGATT
GAGGCCGCAATGACGAACCCGATACCTCAAAAGATGTGACAGGAAAGATTGAGGCCACAACGGTG
AATCCGGTACCATGAA
Found at i:3974 original size:49 final size:48
Alignment explanation
Indices: 3361--4030 Score: 239
Period size: 49 Copynumber: 13.6 Consensus size: 48
3351 GAAAAACATG
* * ** * * *
3361 AAGATTTGAAGGGAAAGGTTGAGGCCGTAACGGCAAACCCTGTACCTTA
1 AAGATGTGAAGGGAAAGGTTGAGGCCGCAATAGCGAA-CCGGTACCATA
* * * * * *
3410 TAAGATGTGACGGGAAAGGTTGAGGTCACAA-CGACGAACCCAGTACCATG
1 -AAGATGTGAAGGGAAAGGTTGAGGCCGCAATAG-CGAA-CCGGTACCATA
* * * * * *
3460 AAGATTTGAAAGGAAAGGTTGATGCCGCAAT-GACAAACTTGTTACC-TAA
1 AAGATGTGAAGGGAAAGGTTGAGGCCGCAATAG-CGAAC-CGGTACCAT-A
* * * * *
3509 AAAATGTGATGGGAAAGGTTGAGGCCGCAA-CGACGAACCCGGTACCGTG
1 AAGATGTGAAGGGAAAGGTTGAGGCCGCAATAG-CGAA-CCGGTACCATA
* ** * * * *
3558 AAGATTTGAAGATAAAGATTGAGGCCGTAAT-GACGAACCTGGTATCGTA
1 AAGATGTGAAGGGAAAGGTTGAGGCCGCAATAG-CGAACC-GGTACCATA
* ** * *
3607 GAAGATGTGACGGGAAAGGTTGAGGTTGCAA-CGACGAACCCGATACCATGA
1 -AAGATGTGAAGGGAAAGGTTGAGGCCGCAATAG-CGAA-CCGGTACCAT-A
* * * * * * * * * * *
3658 AA-TTTTAAAGGAAAAGATTGAGGTCGCGATGGTGAATCTGATACC-TCAA
1 AAGATGTGAAGGGAAAGGTTGAGGCCGCAATAGCGAA-CCGGTACCAT--A
* * * ** * * *
3707 AAGATGTGATGGGAAAGATTGAGGCCACAACGGTGAATCCGGTAGCATG
1 AAGATGTGAAGGGAAAGGTTGAGGCCGCAATAGCGAA-CCGGTACCATA
* * * * * * * *
3756 AA-ATGTGATGAGAAAGGTTGAGGCTGTAACAGCAAACCTAGTACCATG
1 AAGATGTGAAGGGAAAGGTTGAGGCCGCAATAGCGAACC-GGTACCATA
* * * * *
3804 AAGATTTGAAGGGAAAGATTGAGACCGCAATTA-CGAACCCGATACCTTAA
1 AAGATGTGAAGGGAAAGGTTGAGGCCGCAA-TAGCGAA-CCGGTACCAT-A
* * * * * *
3854 AAGATGTGACA-GGAAAGATTGAGGCCGTAATGGTGAATTCGGTACCATG
1 AAGATGTGA-AGGGAAAGGTTGAGGCCGCAATAGCGAA-CCGGTACCATA
* * *
3903 AA-ATGTGATGAGAAAGGTTGAGGCTGCAATAGCGAACTCGGTACCATA
1 AAGATGTGAAGGGAAAGGTTGAGGCCGCAATAGCGAAC-CGGTACCATA
* * * ** *
3951 AAGATTTTAAGGGAAAGGTTGAGGCCGTAACGGCGAACCTGGTACCTTA
1 AAGATGTGAAGGGAAAGGTTGAGGCCGCAATAGCGAACC-GGTACCATA
* *
4000 GATGATATGAAGGGAAAGGTTGAGGCCGCAA
1 -AAGATGTGAAGGGAAAGGTTGAGGCCGCAA
4031 CGGTAAACCC
Statistics
Matches: 460, Mismatches: 131, Indels: 58
0.71 0.20 0.09
Matches are distributed among these distances:
47 2 0.00
48 78 0.17
49 205 0.45
50 170 0.37
51 5 0.01
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (48 bp):
AAGATGTGAAGGGAAAGGTTGAGGCCGCAATAGCGAACCGGTACCATA
Found at i:4049 original size:197 final size:195
Alignment explanation
Indices: 3357--4046 Score: 606
Period size: 197 Copynumber: 3.5 Consensus size: 195
3347 TTGAGAAAAA
* * *
3357 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGTAACGGCAAACCCT-GTACCTTATAAGATGTGAC
1 CATGAAGATTTGAAGAGAAAGGTTGAGGCCGTAACGGCAAA-CCTGGTACCTTAGAAGATGTGAA
* * * * *
3421 GGGAAAGGTTGAGGTCACAACGACGAACCC-AGTACCATGAAGATTTGAAAGGAAAGGTTGATGC
65 GGGAAAGGTTGAGGCCGCAACGACAAACCCGA-TACCATGAAGATTTGAAAGGAAAGATTGAGGC
*** * * * *
3485 CGCAATGACAAACTT-GTTACCTAAAAAATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCC
129 CGCAATGGTGAA-TTCGATACC-ATAAAATGTGATGGGAAAGGTTGAGGCCGCAAAG-CGAACTC
3549 GGTAC
191 GGTAC
* * * * * * * * *
3554 CGTGAAGATTTGAAGATAAAGATTGAGGCCGTAATGACGAACCTGGTATCGTAGAAGATGTGACG
1 CATGAAGATTTGAAGAGAAAGGTTGAGGCCGTAACGGCAAACCTGGTACCTTAGAAGATGTGAAG
** * * *
3619 GGAAAGGTTGAGGTTGCAACGACGAACCCGATACCATGAA-ATTTTAAAGGAAAAGATTGAGGTC
66 GGAAAGGTTGAGGCCGCAACGACAAACCCGATACCATGAAGATTTGAAAGG-AAAGATTGAGGCC
* * * * *
3683 GCGATGGTGAA-TCTGATACC-TCAAAAGATGTGATGGGAAAGATTGAGGCCACAACGGTGAA-T
130 GCAATGGTGAATTC-GATACCAT--AAA-ATGTGATGGGAAAGGTTGAGGCCGCAA-AGCGAACT
*
3745 CCGGTAG
190 -CGGTAC
* * * * * * *
3752 CATGAA-ATGTGATGAGAAAGGTTGAGGCTGTAACAGCAAACCTAGTACCAT-GAAGATTTGAAG
1 CATGAAGATTTGAAGAGAAAGGTTGAGGCCGTAACGGCAAACCTGGTACCTTAGAAGATGTGAAG
* * ** * * * * *
3815 GGAAAGATTGAGACCGCAATTACGAACCCGATACCTTAAAAGATGTGACAGGAAAGATTGAGGCC
66 GGAAAGGTTGAGGCCGCAACGACAAACCCGATACCAT-GAAGATTTGAAAGGAAAGATTGAGGCC
* * * * *
3880 GTAATGGTGAATTCGGTACCATGAAATGTGATGAGAAAGGTTGAGGCTGCAATAGCGAACTCGGT
130 GCAATGGTGAATTCGATACCATAAAATGTGATGGGAAAGGTTGAGGCCGCAA-AGCGAACTCGGT
3945 AC
194 AC
* * * * * *
3947 CATAAAGATTTTAAGGGAAAGGTTGAGGCCGTAACGGCGAACCTGGTACCTTAGATGATATGAAG
1 CATGAAGATTTGAAGAGAAAGGTTGAGGCCGTAACGGCAAACCTGGTACCTTAGAAGATGTGAAG
** *
4012 GGAAAGGTTGAGGCCGCAACGGTAAACCCGGTACC
66 GGAAAGGTTGAGGCCGCAACGACAAACCCGATACC
4047 TTAGAAAATA
Statistics
Matches: 389, Mismatches: 87, Indels: 34
0.76 0.17 0.07
Matches are distributed among these distances:
195 38 0.10
196 91 0.23
197 210 0.54
198 49 0.13
199 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.20
Consensus pattern (195 bp):
CATGAAGATTTGAAGAGAAAGGTTGAGGCCGTAACGGCAAACCTGGTACCTTAGAAGATGTGAAG
GGAAAGGTTGAGGCCGCAACGACAAACCCGATACCATGAAGATTTGAAAGGAAAGATTGAGGCCG
CAATGGTGAATTCGATACCATAAAATGTGATGGGAAAGGTTGAGGCCGCAAAGCGAACTCGGTAC
Found at i:4377 original size:41 final size:41
Alignment explanation
Indices: 4293--4382 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
4283 TCATTTAGTC
* * * *
4293 TTTTACCCTTAATCAAGAAGGGCAGATTGAAGATTTCAGTG
1 TTTTACCCTTAATCAAGAAGGGCAGAATAAAGACTCCAGTG
*
4334 TTTTACCTTTAATCAAGAAGGGCAGAATAAAGACTCC-GATG
1 TTTTACCCTTAATCAAGAAGGGCAGAATAAAGACTCCAG-TG
4375 TTTTACCC
1 TTTTACCC
4383 CAAGTTTGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 1 0.02
41 41 0.98
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (41 bp):
TTTTACCCTTAATCAAGAAGGGCAGAATAAAGACTCCAGTG
Found at i:4422 original size:39 final size:39
Alignment explanation
Indices: 4377--4780 Score: 216
Period size: 39 Copynumber: 10.4 Consensus size: 39
4367 CTCCGATGTT
* * *
4377 TTACCCCAAGTTTGGGGCAGATCACAGTCAACCAATCTC
1 TTACCCCGAGCTTGGGGCAGATCACAGTCAGCCAATCTC
* * * ** * * * *
4416 TTACCCCGAGCCTGGAGTAGATTGCAG-CTATCCGATGTT
1 TTACCCCGAGCTTGGGGCAGATCACAGTC-AGCCAATCTC
*
4455 TTACCCCGAGCTTGGGGCAGATCATAGTCAGCCAATCTC
1 TTACCCCGAGCTTGGGGCAGATCACAGTCAGCCAATCTC
* * * ** * * *
4494 TTACCCCGAGCCT-AGGTAGATTGCAGCCATCCAATCTT
1 TTACCCCGAGCTTGGGGCAGATCACAGTCAGCCAATCTC
4532 TTA-CCCGAGCTTGGGGCAGATCACCA-TCAGCCAATCTC
1 TTACCCCGAGCTTGGGGCAGATCA-CAGTCAGCCAATCTC
** * * * *
4570 TTACCCCCGAG-TTAGGGGCAGATTGCAGCCACCCGATCTT
1 TTA-CCCCGAGCTT-GGGGCAGATCACAGTCAGCCAATCTC
* * * * * * *
4610 TTATCCCGAGCATGAGGTAGATCACTA-TCAACTAATTTC
1 TTACCCCGAGCTTGGGGCAGATCAC-AGTCAGCCAATCTC
* * * * *
4649 TTACCTCGAGCCTGGGGCAGA-CTGCAGTCA-TCAGATCTT
1 TTACCCCGAGCTTGGGGCAGATC-ACAGTCAGCCA-ATCTC
* * *
4688 TTACCCCGAGCCTGGGGCAGATCACCA-TCAGCTAATATC
1 TTACCCCGAGCTTGGGGCAGATCA-CAGTCAGCCAATCTC
* * * * *
4727 TTACCCCAAGCCTGCGGTAGATCACTA-TCAGGCAATCTC
1 TTACCCCGAGCTTGGGGCAGATCAC-AGTCAGCCAATCTC
**
4766 TTACCTTGAGCTTGG
1 TTACCCCGAGCTTGG
4781 AGTAGATTGC
Statistics
Matches: 265, Mismatches: 83, Indels: 34
0.69 0.22 0.09
Matches are distributed among these distances:
37 8 0.03
38 43 0.16
39 181 0.68
40 33 0.12
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (39 bp):
TTACCCCGAGCTTGGGGCAGATCACAGTCAGCCAATCTC
Found at i:4453 original size:78 final size:76
Alignment explanation
Indices: 4368--4748 Score: 397
Period size: 78 Copynumber: 4.9 Consensus size: 76
4358 GAATAAAGAC
* * * *
4368 TCCGATGTTTTACCCCAAGTTTGGGGCAGATCACAGTCAACCAATCTCTTACCCCGAGCCTGGAG
1 TCCGATCTTTTACCCCGAGCTTGGGGCAGATCACA-TCAGCCAATCTCTTACCCCGAGCCTGG-G
*
4433 TAGATTGCAGCTA
64 TAGATTGCAGCCA
* * *
4446 TCCGATGTTTTACCCCGAGCTTGGGGCAGATCATAGTCAGCCAATCTCTTACCCCGAGCCTAGGT
1 TCCGATCTTTTACCCCGAGCTTGGGGCAGATCACA-TCAGCCAATCTCTTACCCCGAGCCTGGGT
4511 AGATTGCAGCCA
65 AGATTGCAGCCA
* *
4523 TCCAATCTTTTA-CCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCCGAG-TTAGG
1 TCCGATCTTTTACCCCGAGCTTGGGGCAGATCA-CATCAGCCAATCTCTTA-CCCCGAGCCT--G
*
4586 GGCAGATTGCAGCCA
62 GGTAGATTGCAGCCA
* * * * * * * * *
4601 CCCGATCTTTTATCCCGAGCATGAGGTAGATCACTATCAACTAATTTCTTACCTCGAGCCTGGGG
1 TCCGATCTTTTACCCCGAGCTTGGGGCAGATCAC-ATCAGCCAATCTCTTACCCCGAGCCT-GGG
* * *
4666 CAGACTGCAGTCA
64 TAGATTGCAGCCA
* * * * *
4679 TCAGATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCTAATATCTTACCCCAAGCCTGCGG
1 TCCGATCTTTTACCCCGAGCTTGGGGCAGATCA-CATCAGCCAATCTCTTACCCCGAGCCTG-GG
4744 TAGAT
64 TAGAT
4749 CACTATCAGG
Statistics
Matches: 258, Mismatches: 36, Indels: 18
0.83 0.12 0.06
Matches are distributed among these distances:
76 36 0.14
77 32 0.12
78 158 0.61
79 32 0.12
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.25
Consensus pattern (76 bp):
TCCGATCTTTTACCCCGAGCTTGGGGCAGATCACATCAGCCAATCTCTTACCCCGAGCCTGGGTA
GATTGCAGCCA
Found at i:5342 original size:17 final size:17
Alignment explanation
Indices: 5320--5386 Score: 75
Period size: 17 Copynumber: 4.0 Consensus size: 17
5310 AACCAAATTG
5320 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
5337 AATTTATTTTGAGTTT-
1 AATTTATTTTAAATTTA
5353 AATTT-TTTTAAAATTTA
1 AATTTATTTT-AAATTTA
* *
5370 AATTAAATTTAAATTTA
1 AATTTATTTTAAATTTA
5387 TCTTAAAGTC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
15 4 0.10
16 9 0.22
17 25 0.61
18 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:6710 original size:29 final size:29
Alignment explanation
Indices: 6677--6753 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
6667 TCTGAATTTT
* *
6677 TTTAAAATCATATTTTGACTCTCAAA-TTA
1 TTTAAAATTATATTTTGAC-ATCAAACTTA
* *
6706 TTTAAAATTATATTTTAACATCAAACTTT
1 TTTAAAATTATATTTTGACATCAAACTTA
6735 TTTAAAATTATATTTTGAC
1 TTTAAAATTATATTTTGAC
6754 CCCTAGGCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 5 0.12
29 37 0.88
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTAAAATTATATTTTGACATCAAACTTA
Found at i:6793 original size:29 final size:29
Alignment explanation
Indices: 6728--6930 Score: 164
Period size: 29 Copynumber: 6.9 Consensus size: 29
6718 TTTTAACATC
* * *
6728 AAACTTTTTTAAAATTATATTTTGACCCCT
1 AAACTTTTCTAAAA-TACATTTTAACCCCT
** * *
6758 AGGCTTTTCTAAAATACATTTTGACCCTT
1 AAACTTTTCTAAAATACATTTTAACCCCT
* *
6787 AAACTTTTCCAAAAT-CATTTTTTACCCCCT
1 AAACTTTTCTAAAATACA--TTTTAACCCCT
* *
6817 -AACTTTTCCAAAACTTCATTTTAA-CCCT
1 AAACTTTTCTAAAA-TACATTTTAACCCCT
*
6845 AAACTTCTCTACAAATCACATTTTAACCCC-
1 AAACTTTTCTA-AAAT-ACATTTTAACCCCT
*
6875 AAACTTTCCTAAAATTACATTTT-ACCCCT
1 AAACTTTTCTAAAA-TACATTTTAACCCCT
* *
6904 AAACTTTTCCAAAATTACGTTTTAACC
1 AAACTTTTCTAAAA-TACATTTTAACC
6931 TTGAATTCTC
Statistics
Matches: 142, Mismatches: 20, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
28 11 0.08
29 82 0.58
30 44 0.31
31 5 0.04
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (29 bp):
AAACTTTTCTAAAATACATTTTAACCCCT
Found at i:6793 original size:59 final size:57
Alignment explanation
Indices: 6728--6918 Score: 186
Period size: 59 Copynumber: 3.3 Consensus size: 57
6718 TTTTAACATC
** * * *
6728 AAACTTTTTTAAAATTATATTTTGACCCCTAGGCTTTTCTAAAA-TACATTTTGACCCTT
1 AAACTTTTCCAAAATCATATTTTAACCCCTA-ACTTTTCTAAAACTACATTTT-ACCC-T
* * * *
6787 AAACTTTTCCAAAATCATTTTTTACCCCCTAACTTTTCCAAAACTTCATTTTAACCCT
1 AAACTTTTCCAAAATCATATTTTAACCCCTAACTTTTCTAAAACTACATTTT-ACCCT
* * * * * *
6845 AAACTTCTCTACAAATCACATTTTAACCCCAAACTTTCCTAAAATTACATTTTACCCCT
1 AAACTTTTCCA-AAATCATATTTTAACCCCTAACTTTTCTAAAACTACATTTTA-CCCT
6904 AAACTTTTCCAAAAT
1 AAACTTTTCCAAAAT
6919 TACGTTTTAA
Statistics
Matches: 107, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
58 25 0.23
59 82 0.77
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.39
Consensus pattern (57 bp):
AAACTTTTCCAAAATCATATTTTAACCCCTAACTTTTCTAAAACTACATTTTACCCT
Found at i:12610 original size:287 final size:290
Alignment explanation
Indices: 12107--12665 Score: 758
Period size: 287 Copynumber: 1.9 Consensus size: 290
12097 ATACTATAAC
* * * * *
12107 TAAGTGTTTTACTAGGTTGTTGTCACCCTCTATCATATCACCAACTCAGTTGTTAAATTATGGAA
1 TAAGTGTTTTACTAGGTTGGTGTCACCCTCAACCAGATCACCAACTCAGTTGTTAAATTATGAAA
* * * *
12172 ATACCTTTTTGTAATTAAAATAAGTTATATTATTCGAAGGTACTTTATTTGTTTCCATTTAAGAA
66 ATACCTTTTTGTAATTAAAATAAATTATA-TATTCGAAGGTACTTAATTTGTTTCAATTTAAAAA
** ** * *
12237 AATTAATAAAAATATGCATGTGGTGAGATTTAAACTCGAACCAATTGCATTTGTAAAACCTTTAG
130 AACCAATAAAAATACACATATGGTGAGATTTAAACCCGAACCAATTGCATTTGTAAAACCTTTAG
12302 TTTACCATACAGCTAAAGTTTTATTTTGATATTTTTGTACATTTCAATTTTTATTATGCACACTT
195 TTTACCATACAGCTAAAGTTTTATTTTGATATTTTTGTACATTTCAATTTTTATTATGCACACTT
12367 TATTACCTTAATAAAATGTATATACTTATTT
260 TATTACCTTAATAAAATGTATATACTTATTT
* ** *
12398 TAAGTGTTTTACT-GAGTTGGTGTCACTCTCAACCAGATCATTAACTTAGTTGTTAAATTATGAA
1 TAAGTGTTTTACTAG-GTTGGTGTCACCCTCAACCAGATCACCAACTCAGTTGTTAAATTATGAA
*
12462 AATGTCC-TTTTGTAATTAAAATAAATTATA-ATTCG-AGGCTACTTAATCTT-TTT-AATTTAA
65 AAT-ACCTTTTTGTAATTAAAATAAATTATATATTCGAAGG-TACTTAAT-TTGTTTCAATTTAA
* * * *
12522 AAAAACCAATAAATATACACATATGGTGGGA-TTCAACCCGAACCAATTGCATTTGTGAAACCTT
127 AAAAACCAATAAAAATACACATATGGTGAGATTTAAACCCGAACCAATTGCATTTGTAAAACC-T
*
12586 TTA-TTTACCACT-TAGCTAAAGTTTTATTTTGATATTTTTGTACATTTCAATTTTTATTATGCA
191 TTAGTTTACCA-TACAGCTAAAGTTTTATTTTGATATTTTTGTACATTTCAATTTTTATTATGCA
*
12649 TACTTTATTACCTTAAT
255 CACTTTATTACCTTAAT
12666 CATATATATA
Statistics
Matches: 236, Mismatches: 26, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
287 101 0.43
288 37 0.16
289 15 0.06
290 3 0.01
291 78 0.33
292 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (290 bp):
TAAGTGTTTTACTAGGTTGGTGTCACCCTCAACCAGATCACCAACTCAGTTGTTAAATTATGAAA
ATACCTTTTTGTAATTAAAATAAATTATATATTCGAAGGTACTTAATTTGTTTCAATTTAAAAAA
ACCAATAAAAATACACATATGGTGAGATTTAAACCCGAACCAATTGCATTTGTAAAACCTTTAGT
TTACCATACAGCTAAAGTTTTATTTTGATATTTTTGTACATTTCAATTTTTATTATGCACACTTT
ATTACCTTAATAAAATGTATATACTTATTT
Found at i:18264 original size:20 final size:20
Alignment explanation
Indices: 18237--18315 Score: 88
Period size: 20 Copynumber: 4.0 Consensus size: 20
18227 CTAAATTCTA
18237 ACAGAGGCACCGAAGTGCA-
1 ACAGAGGCACCGAAGTGCAC
* ** *
18256 AGTAGAGGCATTGAAGTGCAT
1 A-CAGAGGCACCGAAGTGCAC
* *
18277 ACAAAGGCACCAAAGTGCAC
1 ACAGAGGCACCGAAGTGCAC
18297 ACAGAGGCACCGAAGTGCA
1 ACAGAGGCACCGAAGTGCA
18316 AACCCGTACA
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.29, T:0.10
Consensus pattern (20 bp):
ACAGAGGCACCGAAGTGCAC
Found at i:25277 original size:28 final size:28
Alignment explanation
Indices: 25237--25292 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
25227 TGCAGAAGTT
25237 CATTCTCAGGAGAATTGCTAAGGCTATG
1 CATTCTCAGGAGAATTGCTAAGGCTATG
25265 CATTCTCAGGAGAATTGCTAAGGCTATG
1 CATTCTCAGGAGAATTGCTAAGGCTATG
25293 AGTTGAGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (28 bp):
CATTCTCAGGAGAATTGCTAAGGCTATG
Found at i:27957 original size:16 final size:16
Alignment explanation
Indices: 27915--27970 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 16
27905 ACAACAAAAT
* *
27915 AAATTTAAAAAAACTA
1 AAATATAAAACAACTA
*
27931 AAATTACTAAAACAATTA
1 AAA-TA-TAAAACAACTA
27949 AAATATAAAACAACATA
1 AAATATAAAACAAC-TA
27966 AAATA
1 AAATA
27971 AAATTGGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
16 11 0.33
17 10 0.30
18 12 0.36
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATATAAAACAACTA
Found at i:31430 original size:21 final size:21
Alignment explanation
Indices: 31391--31430 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31381 ATTGTTGGAA
*
31391 GTAACAATGAAATGGTAAAAT
1 GTAACAAGGAAATGGTAAAAT
* *
31412 GTAACAAGGACATGTTAAA
1 GTAACAAGGAAATGGTAAA
31431 TTTAAGATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (21 bp):
GTAACAAGGAAATGGTAAAAT
Found at i:34358 original size:135 final size:136
Alignment explanation
Indices: 34124--34380 Score: 351
Period size: 135 Copynumber: 1.9 Consensus size: 136
34114 CTCGAGTGAA
* * * *
34124 TTGCAGATTTAGATCTAGTAAAAAAACACAATATTTATTAGTGTTAATCTCCGACAATAAAATCA
1 TTGCACATCTAGATCTAGTAAAAAAACACAAAATTGATTAG-GTTAATCTCCGACAATAAAATCA
* * * *
34189 AAATTTAATGGGTGTTGAATTCACCAAAAATAAATTTTTATGCCTAAACCAAAATTAGATCAGTA
65 AAAATTAATGAGAGTCGAATTCACCAAAAATAAATTTTTATGCCTAAACCAAAATTAGATCAGTA
34254 AAGTAAC
130 AAGTAAC
* *
34261 TTGCACATCTAGATCTAGTAAAAAAAACACAAAATTGGTTA-GTTAATC-CTTGACAATAAAA-C
1 TTGCACATCTAGATCTAGT-AAAAAAACACAAAATTGATTAGGTTAATCTC-CGACAATAAAATC
*
34323 AAAAATTAATGAGAGTCGAA-TCTACCAAAAATAAATTTTTGTGCCTAAACCAAAATTA
64 AAAAATTAATGAGAGTCGAATTC-ACCAAAAATAAATTTTTATGCCTAAACCAAAATTA
34381 AATTTGTAGT
Statistics
Matches: 106, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
134 2 0.02
135 52 0.49
136 17 0.16
137 17 0.16
138 18 0.17
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (136 bp):
TTGCACATCTAGATCTAGTAAAAAAACACAAAATTGATTAGGTTAATCTCCGACAATAAAATCAA
AAATTAATGAGAGTCGAATTCACCAAAAATAAATTTTTATGCCTAAACCAAAATTAGATCAGTAA
AGTAAC
Found at i:36024 original size:15 final size:15
Alignment explanation
Indices: 36004--36034 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35994 TTAGGAGAAT
*
36004 AACAAATTTAATAAA
1 AACAAAATTAATAAA
36019 AACAAAATTAATAAA
1 AACAAAATTAATAAA
36034 A
1 A
36035 TAAAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (15 bp):
AACAAAATTAATAAA
Done.