Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010920.1 Kokia drynarioides strain JFW-HI SEQ_125888, 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: 78679
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:652 original size:24 final size:26
Alignment explanation
Indices: 625--672 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
615 AGAGAAATGT
625 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
649 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
673 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:765 original size:23 final size:23
Alignment explanation
Indices: 735--904 Score: 127
Period size: 23 Copynumber: 7.3 Consensus size: 23
725 ACGCTAGCAC
735 GCTTACTG-TTCAGCACTGTGTGT
1 GCTTACTGATTC-GCACTGTGTGT
*
758 GCTTACTGTTTCGCACT-TCGTGT
1 GCTTACTGATTCGCACTGT-GTGT
* * *
781 GCTTACTGTTTCCCACCTCT-TGT
1 GCTTACTGATTCGCA-CTGTGTGT
* * * * *
804 GCCTACTGATTTGCTCTATGTGC
1 GCTTACTGATTCGCACTGTGTGT
*
827 GCCTACTGATT-GCACTGTGTGT
1 GCTTACTGATTCGCACTGTGTGT
*
849 GCCTACTGGATT-GCACTGTGTGT
1 GCTTACT-GATTCGCACTGTGTGT
*
872 GCTTACTGTTTCCCAGCACT-TGTGT
1 GCTTACTGATT--C-GCACTGTGTGT
897 GCTTACTG
1 GCTTACTG
905 TTAAGTACTT
Statistics
Matches: 124, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
22 22 0.18
23 78 0.63
24 5 0.04
25 14 0.11
26 5 0.04
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.39
Consensus pattern (23 bp):
GCTTACTGATTCGCACTGTGTGT
Found at i:7334 original size:25 final size:23
Alignment explanation
Indices: 7306--7360 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 23
7296 TTTATAAATT
*
7306 TAATTATTTAATTATGAAATTCAAA
1 TAATTATTT-ATTAT-AAAATCAAA
*
7331 TAATACTATTTTTTATAAAATCAAA
1 TAAT--TATTTATTATAAAATCAAA
7356 TAATT
1 TAATT
7361 CAATTTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 1 0.04
25 16 0.62
26 4 0.15
27 5 0.19
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATTATTTATTATAAAATCAAA
Found at i:7984 original size:20 final size:19
Alignment explanation
Indices: 7955--7994 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
7945 TATATGTCAT
*
7955 ATTATAAAAAGATTTTAAA
1 ATTATAAAAAAATTTTAAA
7974 ATTATTAAAAAAATTTTAAA
1 ATTA-TAAAAAAATTTTAAA
7994 A
1 A
7995 AAAATCCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
ATTATAAAAAAATTTTAAA
Found at i:12175 original size:20 final size:20
Alignment explanation
Indices: 12126--12175 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
12116 ATAAAGATTT
*
12126 ATTCAGGGGAACCGAAGTGC
1 ATTCAGGGGCACCGAAGTGC
* * *
12146 ATACATGGGCACTGAAGTGC
1 ATTCAGGGGCACCGAAGTGC
*
12166 CTTCAGGGGC
1 ATTCAGGGGC
12176 TCAGTATTAC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.34, T:0.18
Consensus pattern (20 bp):
ATTCAGGGGCACCGAAGTGC
Found at i:19034 original size:4 final size:4
Alignment explanation
Indices: 19016--19050 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
19006 CCCATTCATA
19016 TATG TAT- TGATG TATG TATG TATG TATG TATG TAT
1 TATG TATG T-ATG TATG TATG TATG TATG TATG TAT
19051 ATTTCCATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 1 0.03
4 27 0.93
5 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:24818 original size:22 final size:23
Alignment explanation
Indices: 24801--24843 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
24791 AGTTAAGAGG
24801 GAATTGAGAGA-AATTTAAAAGA
1 GAATTGAGAGAGAATTTAAAAGA
* *
24823 GATTTGAGAGAGAATTGAAAA
1 GAATTGAGAGAGAATTTAAAA
24844 TGTGAGAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (23 bp):
GAATTGAGAGAGAATTTAAAAGA
Found at i:25792 original size:58 final size:57
Alignment explanation
Indices: 25718--25862 Score: 173
Period size: 59 Copynumber: 2.5 Consensus size: 57
25708 AATTGAATTT
* ** *
25718 AAAAAAGTTTAGGTACCAAATAAAAAAAAAAACTAAGTTCAAGTATTAAATTGGGTCC
1 AAAAAAATTTAGGTACCAAATAAAAAAAAAAACTAAGTTCAAGTACCAAATTGAGT-C
* ****
25776 AAAAAAATTTAGGTACCCAATTAAAAAAAAGTGTTAAGTTCAAGTACCAAATTGAGTC
1 AAAAAAATTTAGGTA-CCAAATAAAAAAAAAAACTAAGTTCAAGTACCAAATTGAGTC
* *
25834 AAAAAAATTTAGATACCAAATTAAAAAAA
1 AAAAAAATTTAGGTACCAAATAAAAAAAA
25863 TATATTAAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
57 12 0.16
58 29 0.39
59 33 0.45
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (57 bp):
AAAAAAATTTAGGTACCAAATAAAAAAAAAAACTAAGTTCAAGTACCAAATTGAGTC
Found at i:25814 original size:59 final size:58
Alignment explanation
Indices: 25718--25862 Score: 175
Period size: 58 Copynumber: 2.5 Consensus size: 58
25708 AATTGAATTT
* * ** *
25718 AAAAAAGTTTAGGTA-CCAAATAAAAAAAAAAACTAAGTTCAAGTATTAAATTGGGTCC
1 AAAAAAATTTAGGTACCCAATTAAAAAAAAAAACTAAGTTCAAGTACCAAATTGAGT-C
****
25776 AAAAAAATTTAGGTACCCAATTAAAAAAAAGTGTTAAGTTCAAGTACCAAATTGAGTC
1 AAAAAAATTTAGGTACCCAATTAAAAAAAAAAACTAAGTTCAAGTACCAAATTGAGTC
* *
25834 AAAAAAATTTAGATACCAAATTAAAAAAA
1 AAAAAAATTTAGGTACCCAATTAAAAAAA
25863 TATATTAAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
58 42 0.56
59 33 0.44
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (58 bp):
AAAAAAATTTAGGTACCCAATTAAAAAAAAAAACTAAGTTCAAGTACCAAATTGAGTC
Found at i:26574 original size:15 final size:14
Alignment explanation
Indices: 26535--26586 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
26525 CAGTAAATGA
26535 TTTAAAATT--AA-
1 TTTAAAATTAAAAT
26546 TTTAAAATTAAAAT
1 TTTAAAATTAAAAT
26560 TTTAAAATATAAAAT
1 TTTAAAAT-TAAAAT
26575 TATTAAAATTAA
1 T-TTAAAATTAA
26587 TATATTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.25
13 2 0.06
14 8 0.22
15 10 0.28
16 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTAAAATTAAAAT
Found at i:26634 original size:37 final size:37
Alignment explanation
Indices: 26559--26634 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
26549 AAAATTAAAA
* *
26559 TTTTAAAATATAAAATTATTAAAATTAATATATTATT
1 TTTTAAAATATAAAATTATTAAAATTAATAAATAATT
*
26596 TTTTGAAATATAAAATTATTAAAA-TAATTAAATAATT
1 TTTTAAAATATAAAATTATTAAAATTAA-TAAATAATT
26633 TT
1 TT
26635 AATATCATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
36 3 0.09
37 32 0.91
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (37 bp):
TTTTAAAATATAAAATTATTAAAATTAATAAATAATT
Found at i:27519 original size:38 final size:38
Alignment explanation
Indices: 27468--27545 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
27458 AGATAAGATT
* *
27468 AAAATTATTTAATAATTTTAATAATTTTATATTTCAAA
1 AAAATAATATAATAATTTTAATAATTTTATATTTCAAA
*
27506 AAAATAATATAATAATTTTAATAATTTTATATTTTAAA
1 AAAATAATATAATAATTTTAATAATTTTATATTTCAAA
27544 AA
1 AA
27546 TGTAATTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (38 bp):
AAAATAATATAATAATTTTAATAATTTTATATTTCAAA
Found at i:30709 original size:6 final size:6
Alignment explanation
Indices: 30698--30723 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
30688 AAATTCGTAA
30698 TAAACT TAAACT TAAACT TAAACT TA
1 TAAACT TAAACT TAAACT TAAACT TA
30724 CCATAAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAACT
Found at i:40409 original size:18 final size:19
Alignment explanation
Indices: 40376--40411 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40366 GGTCTCAATT
*
40376 TTTCTAAGGATATCGATAG
1 TTTCAAAGGATATCGATAG
40395 TTTCAAAGG-TATCGATA
1 TTTCAAAGGATATCGATA
40412 CTTGACCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.36
Consensus pattern (19 bp):
TTTCAAAGGATATCGATAG
Found at i:40516 original size:20 final size:20
Alignment explanation
Indices: 40491--40538 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
40481 TGTTATATGA
*
40491 TTTGACTTCGTTGAAATCAT
1 TTTGACTTCGTTAAAATCAT
* *
40511 TTTGACTTGGTTAAAATTAT
1 TTTGACTTCGTTAAAATCAT
*
40531 TTTAACTT
1 TTTGACTT
40539 GATTTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTGACTTCGTTAAAATCAT
Found at i:41119 original size:18 final size:18
Alignment explanation
Indices: 41098--41132 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41088 GCTCACTCTC
41098 TTTTTCGGTTTTACTTTA
1 TTTTTCGGTTTTACTTTA
*
41116 TTTTTCGTTTTTACTTT
1 TTTTTCGGTTTTACTTT
41133 TAAAAGTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.11, G:0.09, T:0.71
Consensus pattern (18 bp):
TTTTTCGGTTTTACTTTA
Found at i:41616 original size:31 final size:30
Alignment explanation
Indices: 41581--41685 Score: 81
Period size: 31 Copynumber: 3.5 Consensus size: 30
41571 TACACTAGTA
41581 GTCACCCAACTATTAATAAACTTCTTTTTTG
1 GTCACCCAACTATTAATAAA-TTCTTTTTTG
* ****
41612 GTCACCTC-ACTATGAA-AAATTAC-GAAATG
1 GTCACC-CAACTATTAATAAATT-CTTTTTTG
* *
41641 ATCACCCAACTATTACTAAATTTCTTTTTTG
1 GTCACCCAACTATTAATAAA-TTCTTTTTTG
*
41672 GTCACCTAACTATT
1 GTCACCCAACTATT
41686 CAATTTTGTC
Statistics
Matches: 54, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
28 1 0.02
29 15 0.28
30 8 0.15
31 29 0.54
32 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (30 bp):
GTCACCCAACTATTAATAAATTCTTTTTTG
Found at i:41835 original size:24 final size:24
Alignment explanation
Indices: 41808--41855 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
41798 TTCTAAAAAA
41808 TCAAACCCTCAACATTTACACATT
1 TCAAACCCTCAACATTTACACATT
*
41832 TCAAACCCTCAATATTTACACATT
1 TCAAACCCTCAACATTTACACATT
41856 ATGTAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (24 bp):
TCAAACCCTCAACATTTACACATT
Found at i:42755 original size:13 final size:12
Alignment explanation
Indices: 42739--42787 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
42729 TACAAAAATG
42739 CTTTTCAAAATCA
1 CTTTTCAAAA-CA
42752 CTTTTTCAAAACA
1 C-TTTTCAAAACA
*
42765 CATTTCAAAAGCA
1 CTTTTCAAAA-CA
*
42778 CTTCTCAAAA
1 CTTTTCAAAA
42788 ACTAAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.33
Consensus pattern (12 bp):
CTTTTCAAAACA
Found at i:47880 original size:27 final size:27
Alignment explanation
Indices: 47839--47901 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
47829 CTACTTATTT
* *
47839 CAGATTGATAGTTGTAGTTTTTTGTTC
1 CAGATTGATACTTGTAATTTTTTGTTC
*
47866 CAGATTGATACTTGTAATTTTTTGTTT
1 CAGATTGATACTTGTAATTTTTTGTTC
47893 CAGATTGAT
1 CAGATTGAT
47902 GCTCAAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.51
Consensus pattern (27 bp):
CAGATTGATACTTGTAATTTTTTGTTC
Found at i:47914 original size:28 final size:27
Alignment explanation
Indices: 47856--47916 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
47846 ATAGTTGTAG
***
47856 TTTTTTGTTCCAGATTGATACTTGTAA
1 TTTTTTGTTCCAGATTGATACTCAAAA
* *
47883 TTTTTTGTTTCAGATTGATGCTCAAAA
1 TTTTTTGTTCCAGATTGATACTCAAAA
47910 CTTTTTT
1 -TTTTTT
47917 TTCGTCCATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.21, C:0.11, G:0.13, T:0.54
Consensus pattern (27 bp):
TTTTTTGTTCCAGATTGATACTCAAAA
Found at i:50305 original size:18 final size:17
Alignment explanation
Indices: 50280--50328 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
50270 AATTTAAATT
50280 TTATATTAATATTTATA
1 TTATATTAATATTTATA
**
50297 TTGATATTAAATAAATATA
1 TT-ATATT-AATATTTATA
50316 TTATATTAATATT
1 TTATATTAATATT
50329 AAATAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.23
18 10 0.38
19 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TTATATTAATATTTATA
Found at i:50320 original size:24 final size:23
Alignment explanation
Indices: 50287--50335 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
50277 ATTTTATATT
*
50287 AATATTTATATTGATATTAAATA
1 AATATTTATATTAATATTAAATA
50310 AATATATTATATTAATATTAAATA
1 AATAT-TTATATTAATATTAAATA
50334 AA
1 AA
50336 ATAAAAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AATATTTATATTAATATTAAATA
Found at i:51383 original size:2 final size:2
Alignment explanation
Indices: 51376--51400 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
51366 CACGGGTTCT
51376 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
51401 TGAGAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55422 original size:13 final size:13
Alignment explanation
Indices: 55404--55428 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55394 CAAATGGATT
55404 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
55417 AAAAAAAAAAAA
1 AAAAAAAAAAAA
55429 TCAAACGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.00, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:62882 original size:24 final size:24
Alignment explanation
Indices: 62848--62895 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
62838 ATGGATGTTC
* *
62848 AACCTTTCATCTCCTTTGACCTTT
1 AACCTTCCATCTCCTTTAACCTTT
*
62872 AACCTTCCATCTTCTTTAACCTTT
1 AACCTTCCATCTCCTTTAACCTTT
62896 CATATTATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.02, T:0.46
Consensus pattern (24 bp):
AACCTTCCATCTCCTTTAACCTTT
Found at i:64123 original size:43 final size:42
Alignment explanation
Indices: 64025--64126 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 42
64015 ACACTGTTAT
* ** **
64025 AGAACATGGTCTTTAGCGGTGCTTTTCCACAAATGCCGCTAA
1 AGAACATGGTCTTTAGCGGCGCTTCCCCACAAACACCGCTAA
* *
64067 AGAACACGATCTTTAGCGGCGCTTACCCCACAAACACCGCTGAA
1 AGAACATGGTCTTTAGCGGCGCTT-CCCCACAAACACCGCT-AA
64111 A-AACATGGTCTTTAGC
1 AGAACATGGTCTTTAGC
64127 AATGTCACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
42 21 0.43
43 25 0.51
44 3 0.06
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (42 bp):
AGAACATGGTCTTTAGCGGCGCTTCCCCACAAACACCGCTAA
Found at i:64209 original size:43 final size:43
Alignment explanation
Indices: 64148--64439 Score: 214
Period size: 43 Copynumber: 6.8 Consensus size: 43
64138 AGACCATAGT
* * * * * *
64148 CTTTAGCGATGCTGTCCCCACAAACGCTGCTGAAGAACATGGA
1 CTTTAACGACGCTTTCCCCACAAACACCGCTAAAGAACATGGA
* * *
64191 CCTTAACGACGCTTTCCCCACAAACACCGCTGAAGAATAT-GA
1 CTTTAACGACGCTTTCCCCACAAACACCGCTAAAGAACATGGA
* * ** *
64233 TCTTTAACG-GGACTTTTCCCACAAACGTCGCTAAAGAACATGGT
1 -CTTTAACGACG-CTTTCCCCACAAACACCGCTAAAGAACATGGA
* * * ** * * *
64277 CTTTAGCGAAGTTTTCCCCACAAATGCCGCCAAATATCAT-GA
1 CTTTAACGACGCTTTCCCCACAAACACCGCTAAAGAACATGGA
* * * * * *
64319 TTTTTAGCGACACTTTTCCCACAAATACCGCTAAAGAACATGGT
1 -CTTTAACGACGCTTTCCCCACAAACACCGCTAAAGAACATGGA
*
64363 CTTTAACGAGGCTTTCCCCACAAACACCGCTAAAGAACAT-GA
1 CTTTAACGACGCTTTCCCCACAAACACCGCTAAAGAACATGGA
* * * * *
64405 TTTTTAACGATGCTTTCTCCATAAACGCCGCTAAA
1 -CTTTAACGACGCTTTCCCCACAAACACCGCTAAA
64440 ATTCAAAGAT
Statistics
Matches: 195, Mismatches: 47, Indels: 14
0.76 0.18 0.05
Matches are distributed among these distances:
42 5 0.03
43 187 0.96
44 3 0.02
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (43 bp):
CTTTAACGACGCTTTCCCCACAAACACCGCTAAAGAACATGGA
Found at i:64436 original size:86 final size:86
Alignment explanation
Indices: 64149--64439 Score: 307
Period size: 86 Copynumber: 3.4 Consensus size: 86
64139 GACCATAGTC
* * * * * * * *
64149 TTTAGCGATGCTGTCCCCACAAACGCTGCTGAAGAACATGGACCTTAACGACGCTTTCCCCACAA
1 TTTAACGATGCTTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAACGAAGCTTTCCCCACAA
* * *
64214 ACACCGCTGAAGAATATGATC
66 ACACCGCTAAAGAACATGATT
* * * *
64235 TTTAACG-GGACTTTTCCCACAAACGTCGCTAAAGAACATGGTCTTTAGCGAAGTTTTCCCCACA
1 TTTAACGATG-CTTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAACGAAGCTTTCCCCACA
** * * *
64299 AATGCCGCCAAATATCATGATT
65 AACACCGCTAAAGAACATGATT
* ** ** *
64321 TTTAGCGACACTTTTCCCACAAATACCGCTAAAGAACATGGTCTTTAACGAGGCTTTCCCCACAA
1 TTTAACGATGCTTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAACGAAGCTTTCCCCACAA
64386 ACACCGCTAAAGAACATGATT
66 ACACCGCTAAAGAACATGATT
*
64407 TTTAACGATGC-TTTCTCCATAAACGCCGCTAAA
1 TTTAACGATGCTTTTC-CCACAAACGCCGCTAAA
64440 ATTCAAAGAT
Statistics
Matches: 162, Mismatches: 40, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
85 5 0.03
86 157 0.97
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (86 bp):
TTTAACGATGCTTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAACGAAGCTTTCCCCACAA
ACACCGCTAAAGAACATGATT
Found at i:64453 original size:129 final size:129
Alignment explanation
Indices: 64197--64452 Score: 300
Period size: 129 Copynumber: 2.0 Consensus size: 129
64187 TGGACCTTAA
* * * * **
64197 CGACGCTTTCCCCACAAACACCGCTGAAGAATATGATCTTTAACGGGACTTTTCCCACAAACGTC
1 CGACACTTTCCCCACAAACACCGCTAAAGAACATGATCTTTAACGGGACTTTCCCCACAAACACC
* * * * * *
64262 GCTAAAGAACATGGTCTTTAGCGAAGTTTTCCCCACAAATGCCGCCAAATATCATGATTTTTAG
66 GCTAAAGAACATGATCTTTAACGAAGCTTTCCCCACAAACGCCGCAAAATATCAAGATTTTTAG
* * *
64326 CGACACTTTTCCCACAAATACCGCTAAAGAACATGGTCTTTAACGAGG-CTTTCCCCACAAACAC
1 CGACACTTTCCCCACAAACACCGCTAAAGAACATGATCTTTAACG-GGACTTTCCCCACAAACAC
* * * *
64390 CGCTAAAGAACATGATTTTTAACGATGCTTTCTCCATAAACGCCGCTAAAAT-TCAAAGATTTT
65 CGCTAAAGAACATGATCTTTAACGAAGCTTTCCCCACAAACGCCGC-AAAATATC-AAGATTTT
64453 AACAACTCAT
Statistics
Matches: 105, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
129 92 0.88
130 13 0.12
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (129 bp):
CGACACTTTCCCCACAAACACCGCTAAAGAACATGATCTTTAACGGGACTTTCCCCACAAACACC
GCTAAAGAACATGATCTTTAACGAAGCTTTCCCCACAAACGCCGCAAAATATCAAGATTTTTAG
Found at i:70703 original size:14 final size:14
Alignment explanation
Indices: 70686--70712 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
70676 TATAATTAAA
70686 TAATTAAATATTTT
1 TAATTAAATATTTT
70700 TAATTAAATATTT
1 TAATTAAATATTT
70713 GAATTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTAAATATTTT
Found at i:70703 original size:22 final size:21
Alignment explanation
Indices: 70678--70730 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
70668 TAATTAAATA
70678 TAATTAAATAATTAAATATTTT
1 TAATTAAATAATTAAAT-TTTT
* *
70700 TAATTAAATATTTGAATTTTT
1 TAATTAAATAATTAAATTTTT
70721 TAA-TAAATAA
1 TAATTAAATAA
70731 CTAATTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 6 0.21
21 7 0.25
22 15 0.54
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TAATTAAATAATTAAATTTTT
Found at i:70758 original size:8 final size:8
Alignment explanation
Indices: 70671--70760 Score: 58
Period size: 8 Copynumber: 11.2 Consensus size: 8
70661 GAATATTTAA
70671 TTAAATAT
1 TTAAATAT
*
70679 AATTAAATAA
1 --TTAAATAT
70689 TTAAATAT
1 TTAAATAT
* *
70697 TT--TTAA
1 TTAAATAT
70703 TTAAATAT
1 TTAAATAT
* *
70711 TTGAATTT
1 TTAAATAT
* *
70719 TTTAATAA
1 TTAAATAT
* * *
70727 ATAACTAA
1 TTAAATAT
70735 TTAAATAT
1 TTAAATAT
70743 TTAAATAT
1 TTAAATAT
70751 TTAAATAT
1 TTAAATAT
70759 TT
1 TT
70761 GGCTTATTTT
Statistics
Matches: 61, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
6 4 0.07
8 50 0.82
10 7 0.11
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (8 bp):
TTAAATAT
Found at i:70774 original size:118 final size:119
Alignment explanation
Indices: 70548--70815 Score: 355
Period size: 118 Copynumber: 2.3 Consensus size: 119
70538 TTGTTTTTAA
* **
70548 TAATTAAATATAATTAAATAATTAAGTATTTTGAATTAAATATTTGGGTTGTTGTTAATAAATAA
1 TAATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGAATTGTTGTTAATAAATAA
* *
70613 CTAATTATTAAACTAAATAATTAAATATTTGGATCGTTTTTAATAATTGAATATT
66 CTAATTA-TAAACTAAATAATTAAATATTTGGATCATTTTTAATAATTAAATATT
*
70668 TAATTAAATATAATTAAATAATTAAATATTTTTAATTAAATATTTGAATT-TT-TTAATAAATAA
1 TAATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGAATTGTTGTTAATAAATAA
* * * *
70731 CTAATTA-AATATTTAAATATTTAAATATTTGGCTTATTTTTAATAATTAAATATT
66 CTAATTATAA-A-CTAAATAATTAAATATTTGGATCATTTTTAATAATTAAATATT
* * * *
70786 TAATTTAATATTATT-AGTAATTAAACATTT
1 TAATTAAATATAATTAAATAATTAAATATTT
70816 AAATAATTAA
Statistics
Matches: 132, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
116 2 0.02
117 14 0.11
118 68 0.52
119 2 0.02
120 46 0.35
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (119 bp):
TAATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGAATTGTTGTTAATAAATAA
CTAATTATAAACTAAATAATTAAATATTTGGATCATTTTTAATAATTAAATATT
Found at i:70785 original size:17 final size:16
Alignment explanation
Indices: 70768--70827 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
70758 TTTGGCTTAT
70768 TTTTAATAATTAAATA
1 TTTTAATAATTAAATA
70784 -TTTAAT--TT-AATA
1 TTTTAATAATTAAATA
* *
70796 TTATTAGTAATTAAACA
1 TT-TTAATAATTAAATA
*
70813 TTTAAATAATTAAAT
1 TTTTAATAATTAAAT
70828 TTGTTAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
12 4 0.12
13 3 0.09
14 4 0.12
15 6 0.18
16 12 0.35
17 5 0.15
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
TTTTAATAATTAAATA
Found at i:75607 original size:42 final size:41
Alignment explanation
Indices: 75559--75698 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
75549 TAATTGCTTA
* *
75559 ACCTTTAGCGGCGTTTTTCCCATAAACGCCACTAATGCTTTG
1 ACCTTTAGCGGCG-CTTTCCCATAAACGCCACTAATGCTATG
* * *
75601 ACCTTTAGCGGCACTTTCCCATAAACGCCGCTAATTCTATG
1 ACCTTTAGCGGCGCTTTCCCATAAACGCCACTAATGCTATG
* * ** * * *
75642 ACCTTTAACGGCGCTTTCCCATAAGCAACTCTAATGCTCTA
1 ACCTTTAGCGGCGCTTTCCCATAAACGCCACTAATGCTATG
*
75683 ACCTTTAGCGACGCTT
1 ACCTTTAGCGGCGCTT
75699 GTGTGAAAGC
Statistics
Matches: 82, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 70 0.85
42 12 0.15
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.31
Consensus pattern (41 bp):
ACCTTTAGCGGCGCTTTCCCATAAACGCCACTAATGCTATG
Found at i:75731 original size:17 final size:17
Alignment explanation
Indices: 75689--75731 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
75679 TCTAACCTTT
75689 AGCGACGCTTGTGTGAA
1 AGCGACGCTTGTGTGAA
*
75706 AGCAACGCTTGTGTGAA
1 AGCGACGCTTGTGTGAA
*
75723 AGCGCCGCT
1 AGCGACGCT
75732 AATGCTCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.21
Consensus pattern (17 bp):
AGCGACGCTTGTGTGAA
Found at i:77715 original size:20 final size:20
Alignment explanation
Indices: 77686--77739 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
77676 AGTCTTCAAG
*
77686 GTATCGGTAGAAGTGGAATT
1 GTATCAGTAGAAGTGGAATT
* *
77706 GTATCAGTAGTAGTGGAGTT
1 GTATCAGTAGAAGTGGAATT
* *
77726 CTACCAGTAGAAGT
1 GTATCAGTAGAAGT
77740 CTCACTGGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.30
Consensus pattern (20 bp):
GTATCAGTAGAAGTGGAATT
Done.