Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002755.1 Kokia drynarioides strain JFW-HI SEQ_115071, 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: 70037
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:6892 original size:24 final size:24
Alignment explanation
Indices: 6865--6913 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
6855 AACAAAGTTG
6865 TACACCAAAAATCAATACCCTGGT
1 TACACCAAAAATCAATACCCTGGT
6889 TACACCAAAAATCAATACCCTGGT
1 TACACCAAAAATCAATACCCTGGT
6913 T
1 T
6914 TCTAACAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.29, G:0.08, T:0.22
Consensus pattern (24 bp):
TACACCAAAAATCAATACCCTGGT
Found at i:15120 original size:21 final size:22
Alignment explanation
Indices: 15096--15141 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
15086 AAGGTTATTA
15096 TTATTATTATATTG-TTTAT-AT
1 TTATTATTA-ATTGTTTTATAAT
*
15117 TTATTTTTAATTGTTTTATAAT
1 TTATTATTAATTGTTTTATAAT
15139 TTA
1 TTA
15142 GAGTTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 13 0.59
22 5 0.23
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TTATTATTAATTGTTTTATAAT
Found at i:16665 original size:6 final size:6
Alignment explanation
Indices: 16654--16722 Score: 120
Period size: 6 Copynumber: 11.5 Consensus size: 6
16644 GAGGTTTTGT
16654 AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG
1 AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG
* *
16702 AATAGG GATAGG GATAGG AAT
1 AATAGG AATAGG AATAGG AAT
16723 GAAAGGAGCC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.48, C:0.00, G:0.35, T:0.17
Consensus pattern (6 bp):
AATAGG
Found at i:16859 original size:25 final size:25
Alignment explanation
Indices: 16831--16879 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
16821 TTCTTCTTTT
* *
16831 TTTCCCAAATAATTATAATTATTAA
1 TTTCACAAAAAATTATAATTATTAA
* *
16856 TTTCAGAAAAAATTATTATTATTA
1 TTTCACAAAAAATTATAATTATTA
16880 TTATTATTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTCACAAAAAATTATAATTATTAA
Found at i:18484 original size:13 final size:12
Alignment explanation
Indices: 18466--18549 Score: 71
Period size: 12 Copynumber: 6.7 Consensus size: 12
18456 TTATTTAATA
18466 TAATATTAATTAT
1 TAATATT-ATTAT
*
18479 TAATATTATTAA
1 TAATATTATTAT
**
18491 TGCTATTTATTACT
1 TAATA-TTATTA-T
*
18505 T-CTATTTATTAT
1 TAATA-TTATTAT
*
18517 TAACATTATTAT
1 TAATATTATTAT
18529 TAATATTATTAT
1 TAATATTATTAT
18541 TAATTATTA
1 TAA-TATTA
18550 AATAGTTATT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
12 30 0.50
13 29 0.48
14 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (12 bp):
TAATATTATTAT
Found at i:18542 original size:24 final size:22
Alignment explanation
Indices: 18510--18563 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 22
18500 TTACTTCTAT
18510 TTATTATTAACATTATTATTAATA-
1 TTATTATTAA-ATTATTA--AATAG
18534 TTATTATT-AATTATTAAATAG
1 TTATTATTAAATTATTAAATAG
18555 TTATTATTA
1 TTATTATTA
18564 TTTCAAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.14
21 8 0.29
22 7 0.25
23 1 0.04
24 8 0.29
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TTATTATTAAATTATTAAATAG
Found at i:19339 original size:11 final size:11
Alignment explanation
Indices: 19323--19362 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
19313 ACTTCCAAAG
19323 TTTAAATTTAA
1 TTTAAATTTAA
* *
19334 TTTAAAATAAA
1 TTTAAATTTAA
19345 TTTAAATTTAA
1 TTTAAATTTAA
*
19356 ATTAAAT
1 TTTAAAT
19363 CCAAACTCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:19350 original size:6 final size:6
Alignment explanation
Indices: 19323--19423 Score: 54
Period size: 6 Copynumber: 18.0 Consensus size: 6
19313 ACTTCCAAAG
* **
19323 TTTAAA TTT-AA TTTAAA -ATAAA TTTAAA TTTAAA -TTAAA TCCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * * *
19368 CTCAAA -ATAAG TTTAAA TTTAGA -GTAAA TTAAAA TTTAAA --TAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
19412 TTTAGA TTTAAA
1 TTTAAA TTTAAA
19424 ATTTTAAAGA
Statistics
Matches: 69, Mismatches: 19, Indels: 14
0.68 0.19 0.14
Matches are distributed among these distances:
4 4 0.06
5 19 0.28
6 46 0.67
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:19354 original size:17 final size:17
Alignment explanation
Indices: 19325--19425 Score: 98
Period size: 17 Copynumber: 6.1 Consensus size: 17
19315 TTCCAAAGTT
19325 TAAATTT-AATTTAAAA
1 TAAATTTAAATTTAAAA
*
19341 TAAATTTAAATTTAAAT
1 TAAATTTAAATTTAAAA
** * *
19358 TAAATCCAAACTCAAAA
1 TAAATTTAAATTTAAAA
* * *
19375 TAAGTTTAAATTTAGAG
1 TAAATTTAAATTTAAAA
*
19392 TAAATTAAAATTT-AAA
1 TAAATTTAAATTTAAAA
*
19408 TAAATTTAGATTTAAAA
1 TAAATTTAAATTTAAAA
19425 T
1 T
19426 TTTAAAGATG
Statistics
Matches: 64, Mismatches: 19, Indels: 3
0.74 0.22 0.03
Matches are distributed among these distances:
16 19 0.30
17 45 0.70
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:19927 original size:39 final size:38
Alignment explanation
Indices: 19884--20029 Score: 179
Period size: 39 Copynumber: 3.8 Consensus size: 38
19874 GCTGATGATG
*
19884 ATCTGCCTCAGGCTCGAGGTAAGAGATTGAATGATTGCA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTGAATGA-TGCA
* *
19923 ATCTGCCCCAGGCTCGGGGTAAGAGATTTG-CTGATG-A
1 ATCTGCCTCAGGCTCGGGGTAAGAGA-TTGAATGATGCA
* *
19960 TGATCTGCCTCAGGCTCGGGGTAAGAGATTAAATGGCTGCA
1 --ATCTGCCTCAGGCTCGGGGTAAGAGATTGAAT-GATGCA
*
20001 ATCTGCCTCAGGCTCGGGATAAGAGATTG
1 ATCTGCCTCAGGCTCGGGGTAAGAGATTG
20030 GTTGATGGTG
Statistics
Matches: 92, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
37 1 0.01
38 4 0.04
39 80 0.87
40 6 0.07
41 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.25
Consensus pattern (38 bp):
ATCTGCCTCAGGCTCGGGGTAAGAGATTGAATGATGCA
Found at i:19963 original size:78 final size:78
Alignment explanation
Indices: 19866--20041 Score: 264
Period size: 78 Copynumber: 2.3 Consensus size: 78
19856 ATGATCGAGA
* *
19866 AAGAG-TTGGCTGATGATGATCTGCCTCAGGCTCGAGGTAAGAGATTGAATGATTGCAATCTGCC
1 AAGAGATTGGCTGATGATGATCTGCCTCAGGCTCGAGGTAAGAGATTAAATGACTGCAATCTGCC
*
19930 CCAGGCTCGGGGT
66 CCAGGCTCGGGAT
* * *
19943 AAGAGATTTGCTGATGATGATCTGCCTCAGGCTCGGGGTAAGAGATTAAATGGCTGCAATCTGCC
1 AAGAGATTGGCTGATGATGATCTGCCTCAGGCTCGAGGTAAGAGATTAAATGACTGCAATCTGCC
*
20008 TCAGGCTCGGGAT
66 CCAGGCTCGGGAT
* *
20021 AAGAGATTGGTTGATGGTGAT
1 AAGAGATTGGCTGATGATGAT
20042 GTAACTTCAC
Statistics
Matches: 88, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
77 5 0.06
78 83 0.94
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.26
Consensus pattern (78 bp):
AAGAGATTGGCTGATGATGATCTGCCTCAGGCTCGAGGTAAGAGATTAAATGACTGCAATCTGCC
CCAGGCTCGGGAT
Found at i:20401 original size:49 final size:48
Alignment explanation
Indices: 20335--20706 Score: 285
Period size: 49 Copynumber: 7.6 Consensus size: 48
20325 TGGTACTGGA
* *
20335 TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTCTGAGGTAT-AGG
* * * * * * *
20384 TTCACCATTGCGACTTAAACCTTTCCCTCCATATCT-TCGTGGTACTAGA
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTCT-GAGGTA-TAGG
* *
20433 TTCGCCGTTGCAATTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTCTGAGGTAT-AGG
* * ** *
20482 TTCGCCATTTCGACTTAAA-CTTTTCCCTTCATACCT-TCATGGTACT-GG
1 TTCGCCGTTGCGACTTAAATC-TTTCCCTTCATGTCTCTGA-GGTA-TAGG
*
20530 ATTCACCGTTGC-AGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGG
1 -TTCGCCGTTGCGA-CTTAAATCTTTCCCTTCATGTCTCTGAGGTAT-AGG
* * * *
20580 TTCGCCGTTACGACTTAAA-CTTTTCCCTCCATATCT-TCGTGGTACT-GG
1 TTCGCCGTTGCGACTTAAATC-TTTCCCTTCATGTCTCT-GAGGTA-TAGG
** *
20628 ATTCGCCGTTGCGGTTTAAATCTTTCCCTTTATG-CTTCTGAGGTATGAGG
1 -TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTC-TCTGAGGTAT-AGG
** * *
20678 TTTACCGTTACGACTTAAACCTTTCCCTT
1 TTCGCCGTTGCGACTTAAATCTTTCCCTT
20707 TGTGTCTTCG
Statistics
Matches: 253, Mismatches: 47, Indels: 46
0.73 0.14 0.13
Matches are distributed among these distances:
48 15 0.06
49 224 0.89
50 14 0.06
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (48 bp):
TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTCTGAGGTATAGG
Found at i:20457 original size:98 final size:98
Alignment explanation
Indices: 20319--20743 Score: 573
Period size: 98 Copynumber: 4.3 Consensus size: 98
20309 CCCTTTTGTG
* *
20319 TCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGG
1 TCTTCGTGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGG
*
20384 TTCACCATTGCGACTTAAACCTTTCCCTCCATA
66 TTCACCATTACGACTTAAACCTTTCCCTCCATA
* **
20417 TCTTCGTGGTACTAGATTCGCCGTTGCAATTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGG
1 TCTTCGTGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGG
* * * *
20482 TTCGCCATTTCGACTTAAACTTTTCCCTTCATA
66 TTCACCATTACGACTTAAACCTTTCCCTCCATA
* * *
20515 CCTTCATGGTACTGGATTCACCGTTGCAGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGG
1 TCTTCGTGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGG
* * *
20580 TTCGCCGTTACGACTTAAACTTTTCCCTCCATA
66 TTCACCATTACGACTTAAACCTTTCCCTCCATA
* * * *
20613 TCTTCGTGGTACTGGATTCGCCGTTGCGGTTTAAATCTTTCCCTTTATG-CTTCTGAGGTATGAG
1 TCTTCGTGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTATAAG
* * *** *
20677 GTTTACCGTTACGACTTAAACCTTTCCCTTTGTG
65 GTTCACCATTACGACTTAAACCTTTCCCTCCATA
* * *
20711 TCTTCGTGATATTGGATTCGCCGTTGCGGCTTA
1 TCTTCGTGGTACTGGATTCGCCGTTGCAGCTTA
20744 GGATGCCATG
Statistics
Matches: 291, Mismatches: 35, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
97 1 0.00
98 290 1.00
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (98 bp):
TCTTCGTGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGG
TTCACCATTACGACTTAAACCTTTCCCTCCATA
Found at i:20729 original size:196 final size:196
Alignment explanation
Indices: 20306--20743 Score: 635
Period size: 196 Copynumber: 2.2 Consensus size: 196
20296 GGTCGTAACA
*
20306 TTTCCCTTTTGTGTCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCT
1 TTTCCC-TTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCT
*
20371 CTGAGGTATAAGGTTCACCATTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTC
65 CTGAGGTATAAGGTTCACCATTACGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTC
* *
20436 GCCGTTGCAATTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTTCGACTTAAA
130 GCCGTTGCAATTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCACCATTACGACTTAAA
*
20501 CT
195 CC
** ** * * *
20503 TTTCCCTTCATACCTTCATGGTACTGGATTCACCGTTGCAGCTTAAATCTTTCCCTTCATGTCTC
1 TTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTC
* * * *
20568 TGAGGTATAAGGTTCGCCGTTACGACTTAAACTTTTCCCTCCATATCTTCGTGGTACTGGATTCG
66 TGAGGTATAAGGTTCACCATTACGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCG
** * * * *
20633 CCGTTGCGGTTTAAATCTTTCCCTTTATG-CTTCTGAGGTATGAGGTTTACCGTTACGACTTAAA
131 CCGTTGCAATTTAAATCTTTCCCTTCATGTC-TCTGAGGTATAAGGTTCACCATTACGACTTAAA
20697 CC
195 CC
* *
20699 TTTCCCTTTGTGTCTTCGTGATATTGGATTCGCCGTTGCGGCTTA
1 TTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTA
20744 GGATGCCATG
Statistics
Matches: 209, Mismatches: 31, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
195 1 0.00
196 202 0.97
197 6 0.03
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (196 bp):
TTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTC
TGAGGTATAAGGTTCACCATTACGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCG
CCGTTGCAATTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCACCATTACGACTTAAAC
C
Found at i:20735 original size:49 final size:48
Alignment explanation
Indices: 20317--20743 Score: 239
Period size: 49 Copynumber: 8.7 Consensus size: 48
20307 TTCCCTTTTG
* * * *
20317 TGTCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCA
1 TGTCTTC-TGATACTGGATTCGCCGTTGCGACTTAAACCTTTCCCTTCA
* * *
20366 TGTC-TCTGAGGTA-TAAGG-TTCACCATTGCGACTTAAACCTTTCCCTCCA
1 TGTCTTCTGA--TACT--GGATTCGCCGTTGCGACTTAAACCTTTCCCTTCA
* * * * * *
20415 TATCTTCGTGGTACTAGATTCGCCGTTGCAATTTAAATCTTTCCCTTCA
1 TGTCTTC-TGATACTGGATTCGCCGTTGCGACTTAAACCTTTCCCTTCA
* * *
20464 TGTC-TCTGAGGTA-TAAGG-TTCGCCATTTCGACTTAAACTTTTCCCTTCA
1 TGTCTTCTGA--TACT--GGATTCGCCGTTGCGACTTAAACCTTTCCCTTCA
** * * *
20513 TACCTTCATGGTACTGGATTCACCGTTGC-AGCTTAAATCTTTCCCTTCA
1 TGTCTTC-TGATACTGGATTCGCCGTTGCGA-CTTAAACCTTTCCCTTCA
* * *
20562 TGTC-TCTGAGGTA-TAAGG-TTCGCCGTTACGACTTAAACTTTTCCCTCCA
1 TGTCTTCTGA--TACT--GGATTCGCCGTTGCGACTTAAACCTTTCCCTTCA
* * ** * *
20611 TATCTTCGTGGTACTGGATTCGCCGTTGCGGTTTAAATCTTTCCCTTTA
1 TGTCTTC-TGATACTGGATTCGCCGTTGCGACTTAAACCTTTCCCTTCA
* ** * **
20660 TG-CTTCTGAGGTA-TGAGGTTTACCGTTACGACTTAAACCTTTCCCTTTG
1 TGTCTTCTGA--TACTG-GATTCGCCGTTGCGACTTAAACCTTTCCCTTCA
* *
20709 TGTCTTCGTGATATTGGATTCGCCGTTGCGGCTTA
1 TGTCTTC-TGATACTGGATTCGCCGTTGCGACTTA
20744 GGATGCCATG
Statistics
Matches: 283, Mismatches: 63, Indels: 64
0.69 0.15 0.16
Matches are distributed among these distances:
47 8 0.03
48 21 0.07
49 224 0.79
50 21 0.07
51 9 0.03
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (48 bp):
TGTCTTCTGATACTGGATTCGCCGTTGCGACTTAAACCTTTCCCTTCA
Found at i:21141 original size:18 final size:18
Alignment explanation
Indices: 21115--21150 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21105 AAAATTACCG
* *
21115 AATATTTACGAGGAACAA
1 AATAATTACAAGGAACAA
21133 AATAATTACAAGGAACAA
1 AATAATTACAAGGAACAA
21151 TATTAGATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.11, G:0.14, T:0.19
Consensus pattern (18 bp):
AATAATTACAAGGAACAA
Found at i:21360 original size:22 final size:22
Alignment explanation
Indices: 21332--21383 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
21322 CCCTTTCCGG
*
21332 GTTTTCAATTCAAAACCCCTTT
1 GTTTTCAACTCAAAACCCCTTT
21354 GTTTTCAACTCAAAACCCCTTT
1 GTTTTCAACTCAAAACCCCTTT
*
21376 GGTTTCAA
1 GTTTTCAA
21384 GATGCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (22 bp):
GTTTTCAACTCAAAACCCCTTT
Found at i:26385 original size:28 final size:28
Alignment explanation
Indices: 26354--26413 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
26344 AAAATGAGAT
*
26354 TTTTGGATACCCGAGGGTAAAATGGTAA
1 TTTTGGACACCCGAGGGTAAAATGGTAA
** *
26382 TTTTGGACACTTGGGGGTAAAATGGTAA
1 TTTTGGACACCCGAGGGTAAAATGGTAA
26410 TTTT
1 TTTT
26414 TGAAAAGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.35
Consensus pattern (28 bp):
TTTTGGACACCCGAGGGTAAAATGGTAA
Found at i:26530 original size:29 final size:29
Alignment explanation
Indices: 26498--26590 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 29
26488 AAAAACGGAG
26498 TTTTTAGACATCCAGGGGTAAAATGGTAA
1 TTTTTAGACATCCAGGGGTAAAATGGTAA
* * * * *
26527 -TTTTGGAAGGATTCAAGGTTAAAAATGG-AA
1 TTTTTAG-A-CATCCAGGGGT-AAAATGGTAA
26557 TTTTTAGACATCCAGGGGTAAAATGGTAA
1 TTTTTAGACATCCAGGGGTAAAATGGTAA
26586 TTTTT
1 TTTTT
26591 GGAAAGTTCG
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
28 12 0.24
29 15 0.31
30 10 0.20
31 12 0.24
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (29 bp):
TTTTTAGACATCCAGGGGTAAAATGGTAA
Found at i:26530 original size:59 final size:58
Alignment explanation
Indices: 26395--26621 Score: 280
Period size: 59 Copynumber: 3.9 Consensus size: 58
26385 TGGACACTTG
* * * *
26395 GGGGTAAAATGGTAATTTTTGAAAAGTTC-AGAGTTAAAAATGAAATTTTAGACGTCC-
1 GGGGTAAAATGGTAATTTTTGGAAAGTTCAAG-GTTAAAAAGGAATTTTTAGACATCCA
* * *
26452 GAGGGTATAATGGTGATTTTTGGAAAGTTCAAGGTTAAAAACGGAGTTTTTAGACATCCA
1 G-GGGTAAAATGGTAATTTTTGGAAAGTTCAAGGTTAAAAA-GGAATTTTTAGACATCCA
*
26512 GGGGTAAAATGGTAA-TTTTGGAAGGATTCAAGGTTAAAAATGGAATTTTTAGACATCCA
1 GGGGTAAAATGGTAATTTTTGGAAAG-TTCAAGGTTAAAAA-GGAATTTTTAGACATCCA
* * *
26571 GGGGTAAAATGGTAATTTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTA
1 GGGGTAAAATGGTAATTTTTGGAAAGTTCAAGGTTAAAAA-GGAATTTTTA
26622 AAAATTTGGG
Statistics
Matches: 148, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
57 1 0.01
58 42 0.28
59 95 0.64
60 10 0.07
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGAAAGTTCAAGGTTAAAAAGGAATTTTTAGACATCCA
Found at i:26639 original size:28 final size:28
Alignment explanation
Indices: 26571--26741 Score: 152
Period size: 28 Copynumber: 6.0 Consensus size: 28
26561 TAGACATCCA
26571 GGGGTAAAATGGTAATTTTTGGAAAGTTC
1 GGGGTAAAAT-GTAATTTTTGGAAAGTTC
* * *
26600 GAGGGTAAAAATGTAATTTTT-AAAAATTT
1 G-GGGT-AAAATGTAATTTTTGGAAAGTTC
** *
26629 GGGGTCAAAATGGGA-TTTTGGAAAGTTTA
1 GGGGT-AAAATGTAATTTTTGGAAAG-TTC
26658 GGGGTAAAATGTAATTTTTGTG-AAGTTC
1 GGGGTAAAATGTAATTTTTG-GAAAGTTC
* *
26686 GGGGTCAAAATGGAA-TTTTGGAAAGTTT
1 GGGGT-AAAATGTAATTTTTGGAAAGTTC
**
26714 ATGGTAAAATTGTAATTTTTGGAAAGTT
1 GGGGTAAAA-TGTAATTTTTGGAAAGTT
26742 TAGGGTTAAA
Statistics
Matches: 115, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
27 9 0.08
28 45 0.39
29 42 0.37
30 14 0.12
31 5 0.04
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.36
Consensus pattern (28 bp):
GGGGTAAAATGTAATTTTTGGAAAGTTC
Found at i:26639 original size:59 final size:57
Alignment explanation
Indices: 26395--26733 Score: 271
Period size: 59 Copynumber: 5.9 Consensus size: 57
26385 TGGACACTTG
* * * * *
26395 GGGGTAAAATGGTAATTTTTGAAAAGTTC-AGAGTTAAAAATG-AAATTTTAGACGTCC
1 GGGGTAAAATGGTAA-TTTTGGAAAGTTCAAG-GGTAAAAATGTAATTTTTAGACATCA
* * * * * *
26452 GAGGGTATAATGGTGATTTTTGGAAAGTTCAAGGTTAAAAACGGAGTTTTTAGACATCCA
1 G-GGGTAAAATGGT-AATTTTGGAAAGTTCAAGGGTAAAAATGTAATTTTTAGACAT-CA
* * *
26512 GGGGTAAAATGGTAATTTTGGAAGGATTCAAGGTTAAAAATGGAATTTTTAGACATCCA
1 GGGGTAAAATGGTAATTTTGGAAAG-TTCAAGGGTAAAAATGTAATTTTTAGACAT-CA
* * * **
26571 GGGGTAAAATGGTAATTTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTAAAAATTT
1 GGGGTAAAATGGTAA-TTTTGGAAAGTTCAAGGGTAAAAATGTAATTTTTAGACATCA
* * * *
26629 GGGGTCAAAATGG-GATTTTGGAAAGTTTAGGGGT-AAAATGTAATTTTTGTGA-AGTTC-
1 GGGGT-AAAATGGTAATTTTGGAAAGTTCAAGGGTAAAAATGTAATTTTT-AGACA--TCA
* * *
26686 GGGGTCAAAATGG-AATTTTGGAAAGTT-TATGGTAAAATTGTAATTTTT
1 GGGGT-AAAATGGTAATTTTGGAAAGTTCAAGGGTAAAAATGTAATTTTT
26734 GGAAAGTTTA
Statistics
Matches: 237, Mismatches: 33, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
56 18 0.08
57 57 0.24
58 49 0.21
59 102 0.43
60 11 0.05
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTGGAAAGTTCAAGGGTAAAAATGTAATTTTTAGACATCA
Found at i:26662 original size:29 final size:29
Alignment explanation
Indices: 26511--26805 Score: 180
Period size: 29 Copynumber: 10.1 Consensus size: 29
26501 TTAGACATCC
* *
26511 AGGGGTAAAATGGTAA-TTTTGGAAGGATTC
1 AGGGGTAAAATGG-AATTTTTGGAAAG-TTT
* * * * **
26541 AAGGTTAAAAATGGAATTTTTAGACA-TCC
1 AGGGGT-AAAATGGAATTTTTGGAAAGTTT
26570 AGGGGTAAAATGGTAATTTTTGGAAAG-TT
1 AGGGGTAAAATGG-AATTTTTGGAAAGTTT
* * * *
26599 CGAGGGTAAAAATGTAATTTTT-AAAAATTT
1 AG-GGGT-AAAATGGAATTTTTGGAAAGTTT
*
26629 -GGGGTCAAAATGGGA-TTTTGGAAAGTTT
1 AGGGGT-AAAATGGAATTTTTGGAAAGTTT
*
26657 AGGGGTAAAATGTAATTTTTGTG-AAG-TT
1 AGGGGTAAAATGGAATTTTTG-GAAAGTTT
*
26685 CGGGGTCAAAATGGAA-TTTTGGAAAGTTT
1 AGGGGT-AAAATGGAATTTTTGGAAAGTTT
* *
26714 A-TGGTAAAATTGTAATTTTTGGAAAGTTT
1 AGGGGTAAAA-TGGAATTTTTGGAAAGTTT
* * * * *
26743 AGGGTTAAAATAGAATTTTAGAAAAATTT
1 AGGGGTAAAATGGAATTTTTGGAAAGTTT
* * *
26772 AAGGGTTAAAAT-AAGATTTTTGGATAGTTT
1 -AGGGGTAAAATGGA-ATTTTTGGAAAGTTT
26802 AGGG
1 AGGG
26806 ACCTTCAGGA
Statistics
Matches: 206, Mismatches: 40, Indels: 39
0.72 0.14 0.14
Matches are distributed among these distances:
27 9 0.04
28 53 0.26
29 77 0.37
30 48 0.23
31 19 0.09
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
AGGGGTAAAATGGAATTTTTGGAAAGTTT
Found at i:26690 original size:57 final size:57
Alignment explanation
Indices: 26571--26766 Score: 193
Period size: 57 Copynumber: 3.4 Consensus size: 57
26561 TAGACATCCA
* *
26571 GGGGT-AAAATGGTAATTTTTGGAAAG-TTCGAGGGTAAAAATGTAATTTTT-AAAAATTT
1 GGGGTCAAAATGG-AA-TTTTGGAAAGTTTAG-GGGT-AAAATGTAATTTTTGAAAAATTC
* ** *
26629 GGGGTCAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGTAATTTTTGTGAAGTTC
1 GGGGTCAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGTAATTTTTGAAAAATTC
* * * *
26686 GGGGTCAAAATGGAATTTTGGAAAGTTTA-TGGTAAAATTGTAATTTTTGGAAAGTTT
1 GGGGTCAAAATGGAATTTTGGAAAGTTTAGGGGTAAAA-TGTAATTTTTGAAAAATTC
* * * *
26743 AGGGTTAAAATAGAATTTTAGAAA
1 GGGGTCAAAATGGAATTTTGGAAA
26767 AATTTAAGGG
Statistics
Matches: 119, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
56 21 0.18
57 82 0.69
58 9 0.08
59 7 0.06
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.36
Consensus pattern (57 bp):
GGGGTCAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGTAATTTTTGAAAAATTC
Found at i:28009 original size:25 final size:22
Alignment explanation
Indices: 27981--28038 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 22
27971 TTATTACTTC
27981 TATTTATTATTAACATTATTATTAA
1 TATTTATTATTAA-ATTATTA--AA
28006 TATTTATTATT-AATTATTAAA
1 TATTTATTATTAAATTATTAAA
*
28027 TAGTTATTATTA
1 TATTTATTATTA
28039 TTTCAAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 12 0.39
23 7 0.23
24 1 0.03
25 11 0.35
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTATTATTAAATTATTAAA
Found at i:28813 original size:11 final size:11
Alignment explanation
Indices: 28797--28836 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
28787 ATTTTTAAAG
28797 TTTAAATTTAA
1 TTTAAATTTAA
* *
28808 TTTAAAATAAA
1 TTTAAATTTAA
28819 TTTAAATTTAA
1 TTTAAATTTAA
*
28830 ATTAAAT
1 TTTAAAT
28837 CCAAACTCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:28822 original size:22 final size:23
Alignment explanation
Indices: 28792--28835 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
28782 TTTGAATTTT
*
28792 TAAAGTTTAAATTTAATTTAAAA
1 TAAAGTTTAAATTTAAATTAAAA
28815 TAAA-TTTAAATTTAAATTAAA
1 TAAAGTTTAAATTTAAATTAAA
28836 TCCAAACTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAAGTTTAAATTTAAATTAAAA
Found at i:28824 original size:6 final size:6
Alignment explanation
Indices: 28790--28900 Score: 74
Period size: 6 Copynumber: 19.5 Consensus size: 6
28780 ATTTTGAATT
*
28790 TTTAAA GTTTAAA TTT-AA TTTAAA -ATAAA TTTAAA TTTAAA -TTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * * * * * *
28836 TCCAAA CTCAAA -ATAAG TTTAAA TTTAAA -GTAAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
28882 --TAAA TTTAGA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTT
28901 TTAAAAAATG
Statistics
Matches: 80, Mismatches: 17, Indels: 15
0.71 0.15 0.13
Matches are distributed among these distances:
4 4 0.05
5 20 0.25
6 50 0.62
7 6 0.08
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:28828 original size:17 final size:17
Alignment explanation
Indices: 28799--28897 Score: 103
Period size: 17 Copynumber: 5.9 Consensus size: 17
28789 TTTTAAAGTT
28799 TAAATTT-AATTTAAAA
1 TAAATTTAAATTTAAAA
*
28815 TAAATTTAAATTTAAAT
1 TAAATTTAAATTTAAAA
** * *
28832 TAAATCCAAACTCAAAA
1 TAAATTTAAATTTAAAA
* *
28849 TAAGTTTAAATTTAAAG
1 TAAATTTAAATTTAAAA
*
28866 TAAATTCAAATTT-AAA
1 TAAATTTAAATTTAAAA
*
28882 TAAATTTAGATTTAAA
1 TAAATTTAAATTTAAA
28898 TTTTTAAAAA
Statistics
Matches: 64, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
16 20 0.31
17 44 0.69
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:28850 original size:34 final size:33
Alignment explanation
Indices: 28811--28899 Score: 115
Period size: 34 Copynumber: 2.7 Consensus size: 33
28801 AATTTAATTT
28811 AAAATAAATTTAAATTTAAATTAAATCCAAACTC
1 AAAATAAATTTAAATTTAAATTAAATCCAAA-TC
* * * *
28845 AAAATAAGTTTAAATTTAAAGTAAATTCAAATT
1 AAAATAAATTTAAATTTAAATTAAATCCAAATC
* *
28878 TAAATAAATTTAGATTTAAATT
1 AAAATAAATTTAAATTTAAATT
28900 TTTAAAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 19 0.40
34 28 0.60
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (33 bp):
AAAATAAATTTAAATTTAAATTAAATCCAAATC
Found at i:41303 original size:74 final size:74
Alignment explanation
Indices: 41182--41329 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
41172 AATGTACAAT
41182 GAATGAAACCGATCCTCGAATGTAGACCTTGTTTGTTTTCATTGAAATTCATGTTTTCATGCAGC
1 GAATGAAACCGATCCTCGAATGTAGACCTTGTTTGTTTTCATTGAAATTCATGTTTTCATGCAGC
41247 AGTACAGAA
66 AGTACAGAA
41256 GAATGAAACCGATCCTCGAATGTAGACCTTGTTTGTTTTCATTGAAATTCATGTTTTCATGCAGC
1 GAATGAAACCGATCCTCGAATGTAGACCTTGTTTGTTTTCATTGAAATTCATGTTTTCATGCAGC
41321 AGTACAGAA
66 AGTACAGAA
41330 ATGGCAAGGC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (74 bp):
GAATGAAACCGATCCTCGAATGTAGACCTTGTTTGTTTTCATTGAAATTCATGTTTTCATGCAGC
AGTACAGAA
Found at i:42691 original size:15 final size:15
Alignment explanation
Indices: 42671--42719 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
42661 AAAATTTTAT
42671 ATTAAAATGTTATAA
1 ATTAAAATGTTATAA
* *
42686 ATTAAATTGTTATTA
1 ATTAAAATGTTATAA
*
42701 TTTAAAATAGTTA-AA
1 ATTAAAAT-GTTATAA
42716 ATTA
1 ATTA
42720 TAATTTTTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
15 23 0.85
16 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATTAAAATGTTATAA
Found at i:44113 original size:5 final size:5
Alignment explanation
Indices: 44103--44130 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
44093 ATCCATTTTC
44103 ATCAA ATCAA ATCAA ATCAA ATCAA ATC
1 ATCAA ATCAA ATCAA ATCAA ATCAA ATC
44131 GTACGGTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (5 bp):
ATCAA
Found at i:47345 original size:20 final size:20
Alignment explanation
Indices: 47295--47334 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
47285 ACATAAACAT
* *
47295 TATTCTAAAATT-GTAAAAA
1 TATTTTAAAATTATTAAAAA
47314 TATTTTAAAATTATTAAAAA
1 TATTTTAAAATTATTAAAAA
47334 T
1 T
47335 TTTATAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
TATTTTAAAATTATTAAAAA
Found at i:51607 original size:86 final size:86
Alignment explanation
Indices: 51497--51670 Score: 348
Period size: 86 Copynumber: 2.0 Consensus size: 86
51487 CAAGTTGACA
51497 GAAAATATATTATAATAATTAATTACTTTATTTTAAATTTAAATGAAGTGTTTAACTGCGTTGTT
1 GAAAATATATTATAATAATTAATTACTTTATTTTAAATTTAAATGAAGTGTTTAACTGCGTTGTT
51562 TCACACAGTTACCTGTAAATC
66 TCACACAGTTACCTGTAAATC
51583 GAAAATATATTATAATAATTAATTACTTTATTTTAAATTTAAATGAAGTGTTTAACTGCGTTGTT
1 GAAAATATATTATAATAATTAATTACTTTATTTTAAATTTAAATGAAGTGTTTAACTGCGTTGTT
51648 TCACACAGTTACCTGTAAATC
66 TCACACAGTTACCTGTAAATC
51669 GA
1 GA
51671 TATTTACTAC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 88 1.00
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.41
Consensus pattern (86 bp):
GAAAATATATTATAATAATTAATTACTTTATTTTAAATTTAAATGAAGTGTTTAACTGCGTTGTT
TCACACAGTTACCTGTAAATC
Found at i:58927 original size:59 final size:60
Alignment explanation
Indices: 58836--58969 Score: 164
Period size: 59 Copynumber: 2.2 Consensus size: 60
58826 AATTAAGATT
* * *
58836 TTTTTTTCTTCATCTCTCTGCAACCCCTTGCTGC-TATTTTTTT-GACAACTGCTTTACTA
1 TTTTTCTCTTCA-CTCTCTACAACCCCCTGCTGCATATTTTTTTCGACAACTGCTTTACTA
* * * *
58895 TTTTTCTCTTCACATCTCTACAACCCCCTGCTGCTATATTTTTTTCGGCAATTGCTTTGCTG
1 TTTTTCTCTTCAC-TCTCTACAACCCCCTGCTGC-ATATTTTTTTCGACAACTGCTTTACTA
58957 TTTTTCTCTTCAC
1 TTTTTCTCTTCAC
58970 GTGAAGAGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
58 1 0.02
59 29 0.45
61 9 0.14
62 25 0.39
ACGTcount: A:0.14, C:0.28, G:0.09, T:0.49
Consensus pattern (60 bp):
TTTTTCTCTTCACTCTCTACAACCCCCTGCTGCATATTTTTTTCGACAACTGCTTTACTA
Done.