Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012647.1 Kokia drynarioides strain JFW-HI SEQ_127657, 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: 44422
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:5619 original size:21 final size:21
Alignment explanation
Indices: 5601--5642 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5591 CAATATTTTT
5601 GTCAAAAGAACAACAATTTAA
1 GTCAAAAGAACAACAATTTAA
* *
5622 GTCAACAGAGCAACAATTTAA
1 GTCAAAAGAACAACAATTTAA
5643 CTTTTTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (21 bp):
GTCAAAAGAACAACAATTTAA
Found at i:6271 original size:16 final size:15
Alignment explanation
Indices: 6239--6268 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6229 ATATTTAATA
6239 ATTTAATAATTTTTT
1 ATTTAATAATTTTTT
*
6254 ATTTATTAATTTTTT
1 ATTTAATAATTTTTT
6269 TATATAGTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTAATAATTTTTT
Found at i:9792 original size:7 final size:7
Alignment explanation
Indices: 9780--9804 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9770 TTCCTTCATA
9780 TCATCCT
1 TCATCCT
9787 TCATCCT
1 TCATCCT
9794 TCATCCT
1 TCATCCT
9801 TCAT
1 TCAT
9805 TTTTTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.40, G:0.00, T:0.44
Consensus pattern (7 bp):
TCATCCT
Found at i:9844 original size:11 final size:11
Alignment explanation
Indices: 9828--9873 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
9818 CCATTTTCTA
9828 AATAAAATAAT
1 AATAAAATAAT
9839 AAT-AAATATAT
1 AATAAAATA-AT
*
9850 AAGTAAAATATT
1 AA-TAAAATAAT
9862 AATAAAATAAT
1 AATAAAATAAT
9873 A
1 A
9874 TTTAACTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 5 0.17
11 16 0.53
12 4 0.13
13 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:17927 original size:16 final size:18
Alignment explanation
Indices: 17901--17934 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17891 AACTTAAATC
17901 AATATTTTA-TTATAAAA
1 AATATTTTATTTATAAAA
17918 AATA-TTTATTTATAAAA
1 AATATTTTATTTATAAAA
17935 TAAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATATTTTATTTATAAAA
Found at i:21696 original size:9 final size:9
Alignment explanation
Indices: 21682--21717 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
21672 CCAAAATTAG
21682 ATTTTATTT
1 ATTTTATTT
21691 ATTTTATTT
1 ATTTTATTT
21700 ATGTTT-TTT
1 AT-TTTATTT
21709 ATTTTATTT
1 ATTTTATTT
21718 TAACTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 3 0.12
9 19 0.76
10 3 0.12
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (9 bp):
ATTTTATTT
Found at i:21729 original size:23 final size:22
Alignment explanation
Indices: 21683--21738 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
21673 CAAAATTAGA
** *
21683 TTTTATTTATTTTATTTATGTT
1 TTTTATTTATTTTAACTATATT
21705 TTTTATTTTATTTTAACTATATTT
1 TTTTA-TTTATTTTAACTATA-TT
21729 TCTTTATTTA
1 T-TTTATTTA
21739 GTAAATAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 5 0.18
23 12 0.43
24 7 0.25
25 4 0.14
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTATTTATTTTAACTATATT
Found at i:27629 original size:30 final size:29
Alignment explanation
Indices: 27560--27630 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
27550 TGGATGCTCG
* * *
27560 GGGGTAAAAATGGTAATTTTTGGAGATTC
1 GGGGTAAAAATGGTAAATTTTGGACACTC
27589 GAGGGT-AAAATGGTAAATTTTGGACACTC
1 G-GGGTAAAAATGGTAAATTTTGGACACTC
27618 GGGAGTAAAAATG
1 GGG-GTAAAAATG
27631 TGACACTCGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 2 0.06
29 24 0.67
30 10 0.28
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.28
Consensus pattern (29 bp):
GGGGTAAAAATGGTAAATTTTGGACACTC
Found at i:27635 original size:21 final size:21
Alignment explanation
Indices: 27611--27652 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
27601 GTAAATTTTG
*
27611 GACACTCGGGAGTAAAAATGT
1 GACACTCGGGAGCAAAAATGT
*
27632 GACACTCGGGGGCAAAAATGT
1 GACACTCGGGAGCAAAAATGT
27653 TATTTTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.31, T:0.17
Consensus pattern (21 bp):
GACACTCGGGAGCAAAAATGT
Found at i:27940 original size:29 final size:28
Alignment explanation
Indices: 27675--27941 Score: 238
Period size: 29 Copynumber: 9.2 Consensus size: 28
27665 CTCGAAGATA
*
27675 AAAATGTAATTTTTGGAAAGTTCG-GGGTT
1 AAAATGTAATTTTTGG-AAGTTTGAGGG-T
*
27704 AAAAATGTAATTTTTGAAAGTTT-AGGGT
1 -AAAATGTAATTTTTGGAAGTTTGAGGGT
27732 AAAATGGTAATTTTTGGAAGTTTGAGGGT
1 AAAAT-GTAATTTTTGGAAGTTTGAGGGT
* *
27761 AAAAATGT-GTTTTTGGAAAATTTGAGGGT
1 -AAAATGTAATTTTTGG-AAGTTTGAGGGT
* *
27790 AAATGTGTAATTTTTGGAAGTTCGAGGGT
1 AAA-ATGTAATTTTTGGAAGTTTGAGGGT
* * *
27819 AAAATGGTAATTTTTGAAAGTTCG-GGAT
1 AAAAT-GTAATTTTTGGAAGTTTGAGGGT
*
27847 AAAAAAATGTGA-TTTTGGAAAGTTTGAGGGT
1 ---AAAATGTAATTTTTGG-AAGTTTGAGGGT
* * *
27878 AAAAATGTGATTTTTGGAAGTTCGGAGGAT
1 -AAAATGTAATTTTTGGAAGTT-TGAGGGT
*
27908 AAAATGTAATTTTTGGAAGTTTGGGGGT
1 AAAATGTAATTTTTGGAAGTTTGAGGGT
27936 CAAAAT
1 -AAAAT
27942 ATGATTTCTA
Statistics
Matches: 199, Mismatches: 22, Indels: 33
0.78 0.09 0.13
Matches are distributed among these distances:
27 5 0.03
28 35 0.18
29 104 0.52
30 47 0.24
31 8 0.04
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTTGAGGGT
Found at i:27947 original size:58 final size:57
Alignment explanation
Indices: 27675--27948 Score: 263
Period size: 58 Copynumber: 4.7 Consensus size: 57
27665 CTCGAAGATA
* * * *
27675 AAAATGTAATTTTTGGAAAGTTCG-GGGTTAAAAATGTAATTTTTGAAAGTT-TAGGGT
1 AAAATGTAATTTTTGG-AAGTTTGAGGG-TAAAAATGTGATTTTTGAAAGTTGGAGGAT
* * *
27732 AAAATGGTAATTTTTGGAAGTTTGAGGGTAAAAATGTG-TTTTTGGAAAATTTGAGGGT
1 AAAAT-GTAATTTTTGGAAGTTTGAGGGTAAAAATGTGATTTTT-GAAAGTTGGAGGAT
* * * *
27790 AAATGTGTAATTTTTGGAAGTTCGAGGGT-AAAATGGTAATTTTTGAAAGTTCG-GGAT
1 AAA-ATGTAATTTTTGGAAGTTTGAGGGTAAAAAT-GTGATTTTTGAAAGTTGGAGGAT
* *
27847 AAAAAAATGTGA-TTTTGGAAAGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTCGGAGGAT
1 ---AAAATGTAATTTTTGG-AAGTTTGAGGGTAAAAATGTGATTTTTGAAAGTT-GGAGGAT
* * *
27908 AAAATGTAATTTTTGGAAGTTTGGGGGTCAAAATATGATTT
1 AAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTGATTT
27949 CTAGATAGTT
Statistics
Matches: 182, Mismatches: 20, Indels: 29
0.79 0.09 0.13
Matches are distributed among these distances:
56 5 0.03
57 34 0.19
58 89 0.49
59 41 0.23
60 9 0.05
61 4 0.02
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTGATTTTTGAAAGTTGGAGGAT
Found at i:29434 original size:17 final size:17
Alignment explanation
Indices: 29409--29520 Score: 70
Period size: 17 Copynumber: 6.4 Consensus size: 17
29399 GTTTAAAACC
29409 ATTTCAAATTTAAACTAA
1 ATTT-AAATTTAAACTAA
*
29427 ATTTAAATTTAAAAATAA
1 ATTTAAATTT-AAACTAA
*
29445 TTTTAAATTTAAACTTGAA
1 ATTTAAATTTAAAC-T-AA
*
29464 A--TAAATTTAAATTCAA
1 ATTTAAATTTAAACT-AA
** *
29480 AAATAAATTTAAAAC-CA
1 ATTTAAATTT-AAACTAA
*
29497 ATTTAAACTTAATA-TAA
1 ATTTAAATTTAA-ACTAA
29514 ATTTAAA
1 ATTTAAA
29521 ATCAAAATTT
Statistics
Matches: 74, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
16 6 0.08
17 36 0.49
18 27 0.36
19 5 0.07
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAACTAA
Found at i:29435 original size:6 final size:6
Alignment explanation
Indices: 29409--29492 Score: 57
Period size: 6 Copynumber: 14.2 Consensus size: 6
29399 GTTTAAAACC
* ** *
29409 ATTTCAA ATTTAA A-CTAA ATTTAA ATTTAA AAATAA TTTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * **
29457 ACTTGAA A--TAA ATTTAA ATTCAA AAATAA ATTTAA A
1 A-TTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
29493 ACCAATTTAA
Statistics
Matches: 57, Mismatches: 16, Indels: 9
0.70 0.20 0.11
Matches are distributed among these distances:
4 3 0.05
5 4 0.07
6 41 0.72
7 9 0.16
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (6 bp):
ATTTAA
Found at i:29449 original size:18 final size:18
Alignment explanation
Indices: 29409--29457 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
29399 GTTTAAAACC
* *
29409 ATTTCAAATTT-AAACTA
1 ATTTTAAATTTAAAAATA
*
29426 AATTTAAATTTAAAAATA
1 ATTTTAAATTTAAAAATA
29444 ATTTTAAATTTAAA
1 ATTTTAAATTTAAA
29458 CTTGAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTTAAATTTAAAAATA
Found at i:29451 original size:24 final size:23
Alignment explanation
Indices: 29438--29520 Score: 60
Period size: 23 Copynumber: 3.6 Consensus size: 23
29428 TTTAAATTTA
*
29438 AAAATAATTTTAAATTTAAACTT
1 AAAATAAATTTAAATTTAAACTT
* * **
29461 GAAATAAATTTAAATTCAAAAAT
1 AAAATAAATTTAAATTTAAACTT
* ***
29484 AAATTTAAA-ACCAATTTAAACTT
1 AAA-ATAAATTTAAATTTAAACTT
*
29507 AATATAAATTTAAA
1 AAAATAAATTTAAA
29521 ATCAAAATTT
Statistics
Matches: 40, Mismatches: 18, Indels: 4
0.65 0.29 0.06
Matches are distributed among these distances:
22 4 0.10
23 32 0.80
24 4 0.10
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.36
Consensus pattern (23 bp):
AAAATAAATTTAAATTTAAACTT
Found at i:29485 original size:18 final size:18
Alignment explanation
Indices: 29424--29492 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 18
29414 AAATTTAAAC
*
29424 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTAAAAAA
*
29442 TAATTTTAAATTTAAACTTGAAA
1 TAAATTTAAA-TTAAA----AAA
*
29465 TAAATTTAAATTCAAAAA
1 TAAATTTAAATTAAAAAA
29483 TAAATTTAAA
1 TAAATTTAAA
29493 ACCAATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 22 0.52
19 4 0.10
22 4 0.10
23 12 0.29
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (18 bp):
TAAATTTAAATTAAAAAA
Found at i:30240 original size:39 final size:38
Alignment explanation
Indices: 30197--30769 Score: 289
Period size: 39 Copynumber: 14.7 Consensus size: 38
30187 ACTGATAATG
*
30197 ATCTGCCTCAAGCTCGAGGTAAGAGATCGAATGACTGTA
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGA-TGTA
* * * *
30236 ATCTGCCCCAAGCTCTAGGTAAGAGATTTG-CTGATGATG
1 ATCTGCCCCAAGCTCGAGGTAAGAGA-TCGAATGATG-TA
* * *
30275 ATCT-ACCCAAGCTCGGGGTAAGAGATCGAATGACTGCA
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGA-TGTA
* * * * * ** *
30313 ATCTGCCCTAGGCTTGGGGTAAGAGATTGGTTGATAGTG
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGAT-GTA
* * * * * *
30352 ATCTGCCCCAAGTTCGAGGTAAAATATCGAACGGTTGCA
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCGAA-TGATGTA
* * * * ** *
30391 ATTTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGAT-GTA
** * * * *
30430 ATCTGCCTTAGGCTTGAGGTAAGAGATCGAATGGTTGCA
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCGAAT-GATGTA
* * * * * *
30469 ATCTGCCCCAGGCTCGGGGTAAGAGATTTG-CTTATGGTG
1 ATCTGCCCCAAGCTCGAGGTAAGAGA-TCGAATGAT-GTA
* *
30508 ATCTGCCCCAAGCTC-AGGGTAAGAGATCGAATGGTTGCA
1 ATCTGCCCCAAGCTCGA-GGTAAGAGATCGAAT-GATGTA
* * * * ** *
30547 ATCTGCCTCAGGCTCAAGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGAT-GTA
* * * *
30586 ATTTGCCCCAAGATCGGGGTAA-ACGATCGAATGGTTGTA
1 ATCTGCCCCAAGCTCGAGGTAAGA-GATCGAAT-GATGTA
* * ** * *
30625 ATCTGTCCCAAGCTCGAGGTAAGAGATTGGCTAATGGTG
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGAT-GTA
* * *
30664 ATCTACTCCAAGCTCTG-GGTAAGAGATCGAATGGCTGTA
1 ATCTGCCCCAAGCTC-GAGGTAAGAGATCGAAT-GATGTA
* * *
30703 ATCTGCCCTAAGCTCGGGGTAAGAGATTCGCTAGTGATG--
1 ATCTGCCCCAAGCTCGAGGTAAGAGA-TCG--AATGATGTA
* *
30742 ATCTGCCCTAAGCTCGGGGTAAGAGATC
1 ATCTGCCCCAAGCTCGAGGTAAGAGATC
30770 AGGATCTTCA
Statistics
Matches: 388, Mismatches: 120, Indels: 53
0.69 0.21 0.09
Matches are distributed among these distances:
37 2 0.01
38 40 0.10
39 323 0.83
40 18 0.05
41 3 0.01
42 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (38 bp):
ATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGATGTA
Found at i:30276 original size:78 final size:78
Alignment explanation
Indices: 30175--30769 Score: 626
Period size: 78 Copynumber: 7.6 Consensus size: 78
30165 CCCATGATCT
* * * * ** *
30175 GGTAAAAGATTGACTGATAATGATCTGCCTCAAGCTCGAGGTAAGAGATCGAATGACTGTAATCT
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGTTGCAATCT
* **
30240 GCCCCAAGCTCTA
66 GCCCCAGGCTCGG
* * * **
30253 GGTAAGAGATTTGCTGATGATGATCT-ACCCAAGCTCGGGGTAAGAGATCGAATGACTGCAATCT
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGTTGCAATCT
* *
30317 GCCCTAGGCTTGG
66 GCCCCAGGCTCGG
* * * * * *
30330 GGTAAGAGATTGGTTGAT-AGTGATCTGCCCCAAGTTCGAGGTAAAATATCGAACGGTTGCAATT
1 GGTAAGAGATTGGCTGATGA-TGATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGTTGCAATC
30394 TGCCCCAGGCTCGG
65 TGCCCCAGGCTCGG
* ** * *
30408 GGTAAGAGATTGGCTGATGGTGATCTGCCTTAGGCTTGAGGTAAGAGATCGAATGGTTGCAATCT
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGTTGCAATCT
30473 GCCCCAGGCTCGG
66 GCCCCAGGCTCGG
* * *
30486 GGTAAGAGATTTGCTTATGGTGATCTGCCCCAAGCTC-AGGGTAAGAGATCGAATGGTTGCAATC
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCGA-GGTAAGAGATCGAATGGTTGCAATC
* **
30550 TGCCTCAGGCTCAA
65 TGCCCCAGGCTCGG
* * * * *
30564 GGTAAGAGATTGGCTGATGGTGATTTGCCCCAAGATCGGGGTAA-ACGATCGAATGGTTGTAATC
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCGAGGTAAGA-GATCGAATGGTTGCAATC
* * *
30628 TGTCCCAAGCTCGA
65 TGCCCCAGGCTCGG
* * * * * *
30642 GGTAAGAGATTGGCTAATGGTGATCTACTCCAAGCTCTG-GGTAAGAGATCGAATGGCTGTAATC
1 GGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTC-GAGGTAAGAGATCGAATGGTTGCAATC
* *
30706 TGCCCTAAGCTCGG
65 TGCCCCAGGCTCGG
* * *
30720 GGTAAGAGATTCGCT-AGTGATGATCTGCCCTAAGCTCGGGGTAAGAGATC
1 GGTAAGAGATTGGCTGA-TGATGATCTGCCCCAAGCTCGAGGTAAGAGATC
30770 AGGATCTTCA
Statistics
Matches: 437, Mismatches: 70, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
76 1 0.00
77 68 0.16
78 366 0.84
79 2 0.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (78 bp):
GGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGTTGCAATCT
GCCCCAGGCTCGG
Found at i:39289 original size:29 final size:29
Alignment explanation
Indices: 39257--39700 Score: 241
Period size: 29 Copynumber: 15.2 Consensus size: 29
39247 GCTCGGGGAA
*
39257 AAAATGGTAATTTTTGGAGA-TTCGAGGGT
1 AAAAT-GTAATTTTTGGAAAGTTCGAGGGT
* * * **
39286 AAAATGGT-ATTTTTAGACA-CTCGAGAGCA
1 AAAAT-GTAATTTTTGGAAAGTTCGAG-GGT
* * * * *
39315 AAAATATAATTATTGGACA-TTTGGGGGT
1 AAAATGTAATTTTTGGAAAGTTCGAGGGT
** *
39343 AAAAATGTAATTTTTAAAAAGTTTG-GGGT
1 -AAAATGTAATTTTTGGAAAGTTCGAGGGT
* **
39372 CAAAAATGAAATTTTTGG-AAGTTTAAGGGT
1 --AAAATGTAATTTTTGGAAAGTTCGAGGGT
* * *
39402 AAAATGATAATTTTTAG-AAGTTTGGGGGT
1 AAAATG-TAATTTTTGGAAAGTTCGAGGGT
39431 AAAATGGTAA-TTTTGGAAAAGTTCGAGGGT
1 AAAAT-GTAATTTTTGG-AAAGTTCGAGGGT
* * * *
39461 AAAACTATAATTTTTTGAAATTTAG-GGGT
1 AAAA-TGTAATTTTTGGAAAGTTCGAGGGT
39490 AAAATGGTAATTTTT-GAAAGTTCGAGGGT
1 AAAAT-GTAATTTTTGGAAAGTTCGAGGGT
* * * *
39519 AAAAATGTGATTTTTAGAAATTTTGAGGGT
1 -AAAATGTAATTTTTGGAAAGTTCGAGGGT
* * *
39549 AAAAATATGATTTTTGG-AAGTTCGATGGT
1 -AAAATGTAATTTTTGGAAAGTTCGAGGGT
* * *
39578 AAAAAGGTGATTTTTGGAAAGTT-TAGGGGT
1 -AAAATGTAATTTTTGGAAAGTTCGA-GGGT
* * **
39608 AAAATATGATTTTTGGAAAGTTTAAGGGT
1 AAAATGTAATTTTTGGAAAGTTCGAGGGT
* * * *
39637 AAAATGTGATTTTTAG-AAGTTTG-GTGT
1 AAAATGTAATTTTTGGAAAGTTCGAGGGT
*
39664 CAAAATGTAATTTTTTGGAAAGTTTGAGGGTT
1 -AAAATGTAA-TTTTTGGAAAGTTCGAGGG-T
39696 AAAAT
1 AAAAT
39701 ATGATTTCTG
Statistics
Matches: 333, Mismatches: 58, Indels: 46
0.76 0.13 0.11
Matches are distributed among these distances:
27 3 0.01
28 49 0.15
29 173 0.52
30 94 0.28
31 13 0.04
32 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAAGTTCGAGGGT
Found at i:39317 original size:28 final size:29
Alignment explanation
Indices: 39257--39317 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
39247 GCTCGGGGAA
* * * * *
39257 AAAATGGTAATTTTTGGAGATTCGAGGGT
1 AAAATGGTAATTTTTAGACACTCGAGAGC
39286 AAAATGGT-ATTTTTAGACACTCGAGAGC
1 AAAATGGTAATTTTTAGACACTCGAGAGC
39314 AAAA
1 AAAA
39318 ATATAATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.30
Consensus pattern (29 bp):
AAAATGGTAATTTTTAGACACTCGAGAGC
Found at i:39402 original size:59 final size:58
Alignment explanation
Indices: 39339--39700 Score: 271
Period size: 59 Copynumber: 6.2 Consensus size: 58
39329 GGACATTTGG
**
39339 GGGTAAAAATGTAATTTTTAAAAAGTTT-GGGGTCAAAAATGAAATTTTTGG-AAGTTTAA
1 GGGTAAAAATGTAATTTTT-AAAAGTTTAGGGGT--AAAATGAAATTTTTGGAAAGTTCGA
* * *
39398 GGGT-AAAATGATAATTTTTAGAAGTTTGGGGGTAAAATGGTAA-TTTTGGAAAAGTTCGA
1 GGGTAAAAATG-TAATTTTTAAAAGTTTAGGGGTAAAAT-GAAATTTTTGG-AAAGTTCGA
* * * *
39457 GGGTAAAACTATAATTTTTTGAAA-TTTAGGGGTAAAATGGTAATTTTT-GAAAGTTCGA
1 GGGTAAAAATGTAA-TTTTTAAAAGTTTAGGGGTAAAAT-GAAATTTTTGGAAAGTTCGA
* * *
39515 GGGTAAAAATGTGATTTTTAGAAA-TTTTGAGGGTAAAAAT-ATGATTTTTGG-AAGTTCGA
1 GGGTAAAAATGTAATTTTTA-AAAGTTTAG-GGGT-AAAATGA-AATTTTTGGAAAGTTCGA
* * * * * **
39574 TGGTAAAAAGGTGATTTTTGGAAAGTTTAGGGGTAAAAT-ATGATTTTTGGAAAGTTTAA
1 GGGTAAAAATGTAATTTTT-AAAAGTTTAGGGGTAAAATGA-AATTTTTGGAAAGTTCGA
* * * * *
39633 GGGT-AAAATGTGATTTTTAGAAGTTT-GGTGTCAAAATGTAATTTTTTGGAAAGTTTGA
1 GGGTAAAAATGTAATTTTTAAAAGTTTAGGGGT-AAAATG-AAATTTTTGGAAAGTTCGA
*
39691 GGGTTAAAAT
1 GGGTAAAAAT
39701 ATGATTTCTG
Statistics
Matches: 253, Mismatches: 30, Indels: 40
0.78 0.09 0.12
Matches are distributed among these distances:
56 4 0.02
57 27 0.11
58 91 0.36
59 106 0.42
60 25 0.10
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTAAAAGTTTAGGGGTAAAATGAAATTTTTGGAAAGTTCGA
Found at i:39412 original size:88 final size:87
Alignment explanation
Indices: 39334--39658 Score: 275
Period size: 88 Copynumber: 3.7 Consensus size: 87
39324 TTATTGGACA
39334 TTTGGGGGTAAAAATGTAATTTTTAAAAAGTTTG-GGGTCAAAAATGA-AATTTTTGGAAGTTTA
1 TTTGGGGGTAAAAATGTAATTTTTAAAAAGTTTGAGGGT-AAAAAT-ATAATTTTTGGAAGTTTA
39397 AGGGTAAAATGATAATTTTTAGAAG
64 AGGGTAAAATGATAA-TTTTAGAAG
** * * * * *
39422 TTTGGGGGT-AAAATGGTAATTTTGGAAAAGTTCGAGGGTAAAACTATAATTTTTTGAAATTTAG
1 TTTGGGGGTAAAAAT-GTAATTTTTAAAAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTTAA
* *
39486 GGGTAAAATGGTAATTTTTGAAAG
65 GGGTAAAATGATAATTTTAG-AAG
* * * * * * ** *
39510 TTCGAGGGTAAAAATGTGATTTTTAGAAATTTTGAGGGTAAAAATATGATTTTTGGAAGTTCGAT
1 TTTGGGGGTAAAAATGTAATTTTTAAAAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTTAAG
* * * *
39575 GGTAAAAAGGTGATTTTTGGAAAG
66 GGTAAAATGAT-AATTTTAG-AAG
* ** * * * *
39599 TTTAGGGGTAAAATATG--ATTTTTGGAAAGTTTAAGGGT-AAAATGTGATTTTTAGAAGTTT
1 TTTGGGGGTAAAA-ATGTAATTTTTAAAAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTT
39659 GGTGTCAAAA
Statistics
Matches: 193, Mismatches: 37, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
87 30 0.16
88 131 0.68
89 29 0.15
90 3 0.02
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.37
Consensus pattern (87 bp):
TTTGGGGGTAAAAATGTAATTTTTAAAAAGTTTGAGGGTAAAAATATAATTTTTGGAAGTTTAAG
GGTAAAATGATAATTTTAGAAG
Found at i:39718 original size:30 final size:30
Alignment explanation
Indices: 39334--39718 Score: 280
Period size: 29 Copynumber: 13.1 Consensus size: 30
39324 TTATTGGACA
* * **
39334 TTTGGGGGTAAAAATGTAATTTTTAAAAAG
1 TTTGAGGGTAAAAATGTGATTTTTGGAAAG
**
39364 TTTG-GGGTCAAAAATGAAATTTTTGG-AAG
1 TTTGAGGGT-AAAAATGTGATTTTTGGAAAG
* * *
39393 TTTAAGGGT-AAAATGATAATTTTTAG-AAG
1 TTTGAGGGTAAAAATG-TGATTTTTGGAAAG
* *
39422 TTTGGGGGT-AAAATG-GTAATTTTGGAAAAG
1 TTTGAGGGTAAAAATGTG-ATTTTTGG-AAAG
* * * * *
39452 TTCGAGGGTAAAACTATAATTTTTTGAAA-
1 TTTGAGGGTAAAAATGTGATTTTTGGAAAG
*
39481 TTT-AGGGGT-AAAATGGTAATTTTT-GAAAG
1 TTTGA-GGGTAAAAAT-GTGATTTTTGGAAAG
* * *
39510 TTCGAGGGTAAAAATGTGATTTTTAGAAAT
1 TTTGAGGGTAAAAATGTGATTTTTGGAAAG
*
39540 TTTGAGGGTAAAAATATGATTTTTGG-AAG
1 TTTGAGGGTAAAAATGTGATTTTTGGAAAG
* * *
39569 TTCGATGGTAAAAAGGTGATTTTTGGAAAG
1 TTTGAGGGTAAAAATGTGATTTTTGGAAAG
*
39599 TTT-AGGGGT-AAAATATGATTTTTGGAAAG
1 TTTGA-GGGTAAAAATGTGATTTTTGGAAAG
* *
39628 TTTAAGGGT-AAAATGTGATTTTTAG-AAG
1 TTTGAGGGTAAAAATGTGATTTTTGGAAAG
* * *
39656 TTTG-GTGTCAAAATGTAATTTTTTGGAAAG
1 TTTGAGGGTAAAAATGTGA-TTTTTGGAAAG
* * * *
39686 TTTGAGGGTTAAAATATGATTTCTGGACAG
1 TTTGAGGGTAAAAATGTGATTTTTGGAAAG
39716 TTT
1 TTT
39719 AAGGACCTTT
Statistics
Matches: 286, Mismatches: 48, Indels: 42
0.76 0.13 0.11
Matches are distributed among these distances:
27 3 0.01
28 35 0.12
29 132 0.46
30 96 0.34
31 20 0.07
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (30 bp):
TTTGAGGGTAAAAATGTGATTTTTGGAAAG
Found at i:41204 original size:17 final size:17
Alignment explanation
Indices: 41184--41323 Score: 86
Period size: 17 Copynumber: 8.1 Consensus size: 17
41174 TTCAATATTG
* *
41184 AATTTAAAACCATTTTA
1 AATTTAAAACAAATTTA
41201 AATTT-AAACTAAATTTA
1 AATTTAAAAC-AAATTTA
*
41218 AATTTAAAGCAAATTTA
1 AATTTAAAACAAATTTA
* *
41235 AATTTTAAAATAATTTTA
1 AA-TTTAAAACAAATTTA
** *
41253 AATTTAAATTTAAA-ATA
1 AATTTAAA-ACAAATTTA
* **
41270 AATTTAAATTCAAAAATA
1 AATTTAAA-ACAAATTTA
* *
41288 AATTTAAAACCATTTTA
1 AATTTAAAACAAATTTA
* * *
41305 AACTTAATATAAATTTA
1 AATTTAAAACAAATTTA
41322 AA
1 AA
41324 ATCAAAAGCT
Statistics
Matches: 98, Mismatches: 20, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
16 4 0.04
17 63 0.64
18 31 0.32
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.40
Consensus pattern (17 bp):
AATTTAAAACAAATTTA
Found at i:41208 original size:6 final size:6
Alignment explanation
Indices: 41197--41295 Score: 80
Period size: 6 Copynumber: 17.0 Consensus size: 6
41187 TTAAAACCAT
* **
41197 TTTAAA TTTAAA -CTAAA TTTAAA TTTAAA -GCAAA TTTAAA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
* * * * **
41244 -ATAAT TTTAAA TTTAAA TTTAAA -ATAAA TTTAAA TTCAAA AATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
41290 TTTAAA
1 TTTAAA
41296 ACCATTTTAA
Statistics
Matches: 70, Mismatches: 18, Indels: 10
0.71 0.18 0.10
Matches are distributed among these distances:
5 14 0.20
6 50 0.71
7 6 0.09
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:41213 original size:11 final size:12
Alignment explanation
Indices: 41197--41295 Score: 80
Period size: 11 Copynumber: 8.5 Consensus size: 12
41187 TTAAAACCAT
41197 TTTAAATTTAAA
1 TTTAAATTTAAA
*
41209 -CTAAATTTAAA
1 TTTAAATTTAAA
**
41220 TTTAAA-GCAAA
1 TTTAAATTTAAA
41231 TTTAAATTTTAAA
1 TTTAAA-TTTAAA
* *
41244 -ATAATTTTAAA
1 TTTAAATTTAAA
41255 TTTAAATTTAAA
1 TTTAAATTTAAA
*
41267 -ATAAATTTAAA
1 TTTAAATTTAAA
* **
41278 TTCAAAAATAAA
1 TTTAAATTTAAA
41290 TTTAAA
1 TTTAAA
41296 ACCATTTTAA
Statistics
Matches: 66, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
11 35 0.53
12 28 0.42
13 3 0.05
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:41252 original size:52 final size:51
Alignment explanation
Indices: 41184--41323 Score: 158
Period size: 52 Copynumber: 2.7 Consensus size: 51
41174 TTCAATATTG
**
41184 AATTTAAAACCATTTTAAATTTAAACTAAATTTAAATTTAAA-GCAAATTTA
1 AATTTAAAACCATTTTAAATTTAAA-TAAATTTAAATTTAAATGCAAAAATA
** * *
41235 AATTTTAAAATAATTTTAAATTTAAATTTAAA-ATAAATTTAAATTCAAAAATA
1 AA-TTTAAAACCATTTTAAATTTAAA--TAAATTTAAATTTAAATGCAAAAATA
*
41288 AATTTAAAACCATTTTAAACTTAATATAAATTTAAA
1 AATTTAAAACCATTTTAAATTTAA-ATAAATTTAAA
41324 ATCAAAAGCT
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
51 6 0.08
52 54 0.74
53 13 0.18
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.40
Consensus pattern (51 bp):
AATTTAAAACCATTTTAAATTTAAATAAATTTAAATTTAAATGCAAAAATA
Found at i:41255 original size:41 final size:41
Alignment explanation
Indices: 41210--41295 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
41200 AAATTTAAAC
* ** *
41210 TAAATTTAAATTTAAAGCAAATTTAAATTTTAAAATAATTT
1 TAAATTTAAATTTAAAACAAATTTAAATTCAAAAATAAATT
*
41251 TAAATTTAAATTTAAAATAAATTTAAATTCAAAAATAAATT
1 TAAATTTAAATTTAAAACAAATTTAAATTCAAAAATAAATT
41292 TAAA
1 TAAA
41296 ACCATTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (41 bp):
TAAATTTAAATTTAAAACAAATTTAAATTCAAAAATAAATT
Found at i:41268 original size:23 final size:24
Alignment explanation
Indices: 41228--41279 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
41218 AATTTAAAGC
*
41228 AAATTTAAATTTTAAAATAATTTT
1 AAATTTAAATTTTAAAATAAATTT
41252 AAATTTAAA-TTTAAAATAAATTT
1 AAATTTAAATTTTAAAATAAATTT
41275 AAATT
1 AAATT
41280 CAAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATTTAAATTTTAAAATAAATTT
Found at i:41289 original size:23 final size:23
Alignment explanation
Indices: 41240--41289 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
41230 ATTTAAATTT
* * **
41240 TAAAATAATTTTAAATTTAAATT
1 TAAAATAAATTTAAATTCAAAAA
41263 TAAAATAAATTTAAATTCAAAAA
1 TAAAATAAATTTAAATTCAAAAA
41286 TAAA
1 TAAA
41290 TTTAAAACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAATAAATTTAAATTCAAAAA
Found at i:41304 original size:29 final size:28
Alignment explanation
Indices: 41257--41329 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
41247 ATTTTAAATT
*
41257 TAAATTTAAAATAAATTTAAA-TTCAAAAA
1 TAAATTTAAAACAAATTTAAACTT--AAAA
* * *
41286 TAAATTTAAAACCATTTTAAACTTAATA
1 TAAATTTAAAACAAATTTAAACTTAAAA
41314 TAAATTTAAAATCAAA
1 TAAATTTAAAA-CAAA
41330 AGCTTGATCC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 14 0.39
29 20 0.56
30 2 0.06
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (28 bp):
TAAATTTAAAACAAATTTAAACTTAAAA
Found at i:43032 original size:59 final size:59
Alignment explanation
Indices: 42921--43127 Score: 317
Period size: 59 Copynumber: 3.5 Consensus size: 59
42911 GGTATATAGG
*
42921 TCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTGGGAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGT
* ** *
42980 TCGGGGGTAAAATGGTAA-TTTTGGAAGGTTCGGGGTTAAAAATGCTATTTTTGGATGT
1 TCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGT
* * *
43038 TCGGGGGTAAAATGGTAATTCTTGGAAGATTCAGGGTCAAAAATGGGATTTTTGGAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGT
* *
43097 TCGAGGGTAAAATGGAAATTTTTGGAAGGTT
1 TCGGGGGTAAAATGGTAATTTTTGGAAGGTT
43128 TAGGGACCTC
Statistics
Matches: 131, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
58 53 0.40
59 78 0.60
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.32
Consensus pattern (59 bp):
TCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGT
Found at i:43132 original size:29 final size:29
Alignment explanation
Indices: 42924--43127 Score: 197
Period size: 30 Copynumber: 7.0 Consensus size: 29
42914 ATATAGGTCG
42924 GGGGTAAAATGGTAATTTTTGGAAGGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGGTTC
* *
42953 GGGGTCAAAAATGG-GATTTTGGGAA-GTTC
1 GGGGT--AAAATGGTAATTTTTGGAAGGTTC
42982 GGGGGTAAAATGGTAA-TTTTGGAAGGTTC
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTC
* *
43011 GGGGTTAAAAATGCT-ATTTTTGG-ATGTTC
1 GGGG-T-AAAATGGTAATTTTTGGAAGGTTC
* *
43040 GGGGGTAAAATGGTAATTCTTGGAAGATTC
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTC
* *
43070 AGGGTCAAAAATGG-GATTTTTGGAA-GTTC
1 GGGGT--AAAATGGTAATTTTTGGAAGGTTC
*
43099 GAGGGTAAAATGGAAATTTTTGGAAGGTT
1 G-GGGTAAAATGGTAATTTTTGGAAGGTT
43128 TAGGGACCTC
Statistics
Matches: 143, Mismatches: 16, Indels: 31
0.75 0.08 0.16
Matches are distributed among these distances:
28 32 0.22
29 46 0.32
30 51 0.36
31 14 0.10
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.32
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGAAGGTTC
Found at i:44290 original size:7 final size:7
Alignment explanation
Indices: 44278--44321 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
44268 CCCCTTTTTT
44278 TTATTAA
1 TTATTAA
44285 TTATTAA
1 TTATTAA
*
44292 TTAATAA
1 TTATTAA
44299 TTATTGATA
1 TTATT-A-A
44308 TTATT-A
1 TTATTAA
44314 TTATTAA
1 TTATTAA
44321 T
1 T
44322 ATCAAAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 6 0.19
7 19 0.59
8 1 0.03
9 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (7 bp):
TTATTAA
Done.