Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011597.1 Kokia drynarioides strain JFW-HI SEQ_126587, 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: 80094
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 70 characters in sequence are not A, C, G, or T
Found at i:145 original size:3 final size:3
Alignment explanation
Indices: 137--187 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
127 TTTTTACTCT
137 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
185 TTA
1 TTA
188 ATTAATGTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:990 original size:17 final size:17
Alignment explanation
Indices: 930--1009 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 17
920 TAAATAAATT
*
930 TAAACTTAATATTTATAA
1 TAAACTTAA-ATTTAAAA
* **
948 TAAATTTAAATTCCAAA
1 TAAACTTAAATTTAAAA
* ** *
965 TGAGTTTAAATTTAATA
1 TAAACTTAAATTTAAAA
982 TAAACTTAAATTTAAAA
1 TAAACTTAAATTTAAAA
*
999 TAAATTTAAAT
1 TAAACTTAAAT
1010 ATGTTGGGCC
Statistics
Matches: 48, Mismatches: 14, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
17 40 0.83
18 8 0.17
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAACTTAAATTTAAAA
Found at i:1598 original size:77 final size:78
Alignment explanation
Indices: 1470--1734 Score: 223
Period size: 78 Copynumber: 3.4 Consensus size: 78
1460 CCCCATAATC
* ** * * * * * *
1470 GGGTAAAAGATTGGCCGATGGTGATCTGCCTCATGTTTGAGGTAAGAGATCGAGTAGTTACAATC
1 GGGTAAGAGATTGGATGATGATGATCTGCCCCAGGATCGAGGTAAGAGATCGAATAGTTACAATC
* *
1535 TGCCCTAGGCTTG
66 TGCCCTAAGCTCG
* ** * * *
1548 GGGTAAGAGTTTTTATGATGATGATCTG-CCCAGGCTCG-GGATAAGAGATCGAATGGTTGCAAT
1 GGGTAAGAGATTGGATGATGATGATCTGCCCCAGGATCGAGG-TAAGAGATCGAATAGTTACAAT
*
1611 TTGCCCTAAGCTCG
65 CTGCCCTAAGCTCG
* * * * * **
1625 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGATCGAGGTAAGAGATTTG-CTAGTGATGAT
1 GGGTAAGAGATTGGATGATGATGATCTGCCCCAGGATCGAGGTAAGAGA-TCGAATAGTTACAAT
1689 CTGTCCC-AAGCTCG
65 CTG-CCCTAAGCTCG
* * *
1703 TGGTAAGAGATTGGCTGATGGTGATCTGCCCC
1 GGGTAAGAGATTGGATGATGATGATCTGCCCC
1735 CAAGCTCGGT
Statistics
Matches: 150, Mismatches: 32, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
76 2 0.01
77 59 0.39
78 82 0.55
79 7 0.05
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (78 bp):
GGGTAAGAGATTGGATGATGATGATCTGCCCCAGGATCGAGGTAAGAGATCGAATAGTTACAATC
TGCCCTAAGCTCG
Found at i:1749 original size:40 final size:39
Alignment explanation
Indices: 1612--1753 Score: 164
Period size: 39 Copynumber: 3.6 Consensus size: 39
1602 GGTTGCAATT
* *
1612 TGCCCTAAGCTCGGGGTAAGAGATTGGCTGATGGTGATC
1 TGCCCCAAGCTCGGTGTAAGAGATTGGCTGATGGTGATC
* * * *
1651 TGCCCCAGGATCGAG-GTAAGAGATTTGCT-AGTGATGATC
1 TGCCCCAAGCTCG-GTGTAAGAGATTGGCTGA-TGGTGATC
*
1690 TGTCCCAAGCTC-GTGGTAAGAGATTGGCTGATGGTGATC
1 TGCCCCAAGCTCGGT-GTAAGAGATTGGCTGATGGTGATC
1729 TGCCCCCAAGCTCGGTGTAAGAGAT
1 TG-CCCCAAGCTCGGTGTAAGAGAT
1754 CTGGGTTTTC
Statistics
Matches: 85, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
39 61 0.72
40 20 0.24
41 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (39 bp):
TGCCCCAAGCTCGGTGTAAGAGATTGGCTGATGGTGATC
Found at i:2099 original size:49 final size:48
Alignment explanation
Indices: 2044--2473 Score: 313
Period size: 49 Copynumber: 8.8 Consensus size: 48
2034 TCACCATTGC
*
2044 GACTTAAATCTTTCCTTTTGTGTCTTTGTGGTACTGGATTCGCCGTTGA
1 GACTTAAATCTTTCCCTTTGTGTCTTTGTGGTACTGG-TTCGCCGTTGA
* * * * *
2093 GTCTTAAATCTTTCCCTTTCATG-CTTCTGAGGTA-TAAGGTTCGCCATTGC
1 GACTTAAATCTTTCCCTTT-GTGTCTT-TGTGGTACT--GGTTCGCCGTTGA
* * * * * *
2143 GACTTAAACCTTTACCTTTTGTGACTTCGTGGTACTGGATTCGCTGTTGC
1 GACTTAAATCTTT-CCCTTTGTGTCTTTGTGGTACTGG-TTCGCCGTTGA
* ** * * * *
2193 GGCTTAAATCTTTCCCTTCATGTCTCTGAGGTA-TAAGGTTTGCCGTTGC
1 GACTTAAATCTTTCCCTTTGTGTCTTTGTGGTACT--GGTTCGCCGTTGA
* * *
2242 GACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTTGATTCGCC-TTGCA
1 GACTTAAATCTTTCCCTTTGTGTCTTTGTGGTAC-TGGTTCGCCGTTG-A
** * *
2291 G-CTTAAATCTTTCCCTTCATGTCTTTGAGGTA-TAAGGTTCACCGTT-A
1 GACTTAAATCTTTCCCTTTGTGTCTTTGTGGTACT--GGTTCGCCGTTGA
* *
2338 CGACTTAAA-CTTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGC
1 -GACTTAAATC-TTTCCCTTTGTGTCTTTGTGGTACTGG-TTCGCCGTTGA
* ** * *
2388 GGCTTAAATCTTTCCCTTCATGTCTTTGAGGTA-TAAGGTTCGTCGTT-A
1 GACTTAAATCTTTCCCTTTGTGTCTTTGTGGTACT--GGTTCGCCGTTGA
*
2436 CGACTTAAACCTTTCCCTTTGTGTCTTTGTGGTACTGG
1 -GACTTAAATCTTTCCCTTTGTGTCTTTGTGGTACTGG
2474 GACCTGTAGA
Statistics
Matches: 294, Mismatches: 60, Indels: 55
0.72 0.15 0.13
Matches are distributed among these distances:
46 1 0.00
47 1 0.00
48 43 0.15
49 175 0.60
50 62 0.21
51 12 0.04
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (48 bp):
GACTTAAATCTTTCCCTTTGTGTCTTTGTGGTACTGGTTCGCCGTTGA
Found at i:2412 original size:195 final size:198
Alignment explanation
Indices: 1974--2473 Score: 715
Period size: 195 Copynumber: 2.5 Consensus size: 198
1964 TCAATCCGCA
** * * * * * *
1974 TGGTACTAAATTCGTCGTTGCGGCTTAAATTTTTCCTTTCTTG-CTTCTAAGGTATAAGGTTCAC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTATAAGGTTCGC
* * *
2038 CATTGCGACTTAAATCTTTCCTTTTGTGTCTTTGTGGTACTGGATTCGCCGTTGAGTCTTAAATC
65 CGTTGCGACTTAAACCTTTCCCTTTGTGTCTTTGTGGTACTGGATTCGCCGTTGAGTCTTAAATC
* * *
2103 TTTCCCTTTCATGCTTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTACCTTTTGTGAC
130 TTTCCCTTTCATGCTTCTGAGGTATAAGGTTCACCATTACGACTTAAACCTTTACCCTTTGTGAC
2168 TTCG
195 TTCG
* *
2172 TGGTACTGGATTCGCTGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTTGCC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCC
* *
2237 GTTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTTGATTCGCC-TTGCAG-CTTAAATC
66 GTTGCGACTTAAACCTTTCCCTTTGTGTCTTTGTGGTACTGGATTCGCCGTTG-AGTCTTAAATC
* * *
2300 TTTCCC-TTCATGTCTT-TGAGGTATAAGGTTCACCGTTACGACTTAAA-CTTTTCCCTTTGTGT
130 TTTCCCTTTCATG-CTTCTGAGGTATAAGGTTCACCATTACGACTTAAACCTTTACCCTTTGTGA
2362 CTTCG
194 CTTCG
* *
2367 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGTC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCC
*
2432 GTTACGACTTAAACCTTTCCCTTTGTGTCTTTGTGGTACTGG
66 GTTGCGACTTAAACCTTTCCCTTTGTGTCTTTGTGGTACTGG
2474 GACCTGTAGA
Statistics
Matches: 271, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
195 117 0.43
196 34 0.13
197 20 0.07
198 99 0.37
199 1 0.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (198 bp):
TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCC
GTTGCGACTTAAACCTTTCCCTTTGTGTCTTTGTGGTACTGGATTCGCCGTTGAGTCTTAAATCT
TTCCCTTTCATGCTTCTGAGGTATAAGGTTCACCATTACGACTTAAACCTTTACCCTTTGTGACT
TCG
Found at i:2435 original size:98 final size:98
Alignment explanation
Indices: 1974--2473 Score: 666
Period size: 98 Copynumber: 5.1 Consensus size: 98
1964 TCAATCCGCA
** * * * * * *
1974 TGGTACTAAATTCGTCGTTGCGGCTTAAATTTTTCCTTTCTTG-CTTCTAAGGTATAAGGTTCAC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTT-TGAGGTATAAGGTTCGC
* * *
2038 CATTGCGACTTAAA-TCTTTCCTTTTGTGTCTTTG
65 CGTTGCGACTTAAACT-TTTCCCTTTGTGTCTTCG
* *
2072 TGGTACTGGATTCGCCGTTGAGTCTTAAATCTTTCCCTTTCATG-CTTCTGAGGTATAAGGTTCG
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCC-TTCATGTCTT-TGAGGTATAAGGTTCG
* * * *
2136 CCATTGCGACTTAAACCTTTACCTTTTGTGACTTCG
64 CCGTTGCGACTTAAA-CTTTTCCCTTTGTGTCTTCG
* * *
2172 TGGTACTGGATTCGCTGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTTGCC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGCC
*
2237 GTTGCGACTTAAACCTTTCCCTTTGTGTCTTCG
66 GTTGCGACTTAAACTTTTCCCTTTGTGTCTTCG
* * *
2270 TGGTACTTGATTCGCC-TTGCAGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCACC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGCC
*
2334 GTTACGACTTAAACTTTTCCCTTTGTGTCTTCG
66 GTTGCGACTTAAACTTTTCCCTTTGTGTCTTCG
*
2367 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGTC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGCC
* * *
2432 GTTACGACTTAAACCTTTCCCTTTGTGTCTTTG
66 GTTGCGACTTAAACTTTTCCCTTTGTGTCTTCG
2465 TGGTACTGG
1 TGGTACTGG
2474 GACCTGTAGA
Statistics
Matches: 360, Mismatches: 37, Indels: 10
0.88 0.09 0.02
Matches are distributed among these distances:
97 90 0.25
98 145 0.40
99 73 0.20
100 51 0.14
101 1 0.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (98 bp):
TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGCC
GTTGCGACTTAAACTTTTCCCTTTGTGTCTTCG
Found at i:22078 original size:3 final size:3
Alignment explanation
Indices: 22070--22103 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
22060 AAAATACATA
22070 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
22104 CAAACATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:27878 original size:23 final size:23
Alignment explanation
Indices: 27844--27887 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
27834 TTAAATATTG
27844 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
27867 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
27888 ATATGGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:31478 original size:3 final size:3
Alignment explanation
Indices: 31470--31494 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31460 ATTAAAAATT
31470 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
31495 TAAAGACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:46327 original size:89 final size:89
Alignment explanation
Indices: 46225--46409 Score: 352
Period size: 89 Copynumber: 2.1 Consensus size: 89
46215 TTAACAAATT
46225 TAAACATCATTTAAATTCATATATTTTACTTTGCAACTTTATATTTAAAATAAATATTTTTATTT
1 TAAACATCATTTAAATTCATATATTTTACTTTGCAACTTTATATTTAAAATAAATATTTTTATTT
46290 TTTAAAATTACTTTTTAACAACAA
66 TTTAAAATTACTTTTTAACAACAA
*
46314 TAAACATCATTTAAATTCATATTTTTTACTTTGCAACTTTATATTTAAAATAAATATTTTTATTT
1 TAAACATCATTTAAATTCATATATTTTACTTTGCAACTTTATATTTAAAATAAATATTTTTATTT
*
46379 TTTAAAATTGCTTTTTAACAACAA
66 TTTAAAATTACTTTTTAACAACAA
46403 TAAACAT
1 TAAACAT
46410 TTAAATTTTA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 94 1.00
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (89 bp):
TAAACATCATTTAAATTCATATATTTTACTTTGCAACTTTATATTTAAAATAAATATTTTTATTT
TTTAAAATTACTTTTTAACAACAA
Found at i:57454 original size:23 final size:23
Alignment explanation
Indices: 57406--57470 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
57396 GAATTTTATT
*
57406 TAAAAATTTCAAATGT-AATAATA
1 TAAAAATTTC-AATTTAAATAATA
57429 TAAAAATTTCAATTTAAATGAA-A
1 TAAAAATTTCAATTTAAAT-AATA
*
57452 T-AAAATTTAAACTTTAAAT
1 TAAAAATTTCAA-TTTAAAT
57471 TAATCTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
22 13 0.35
23 22 0.59
24 2 0.05
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (23 bp):
TAAAAATTTCAATTTAAATAATA
Found at i:62305 original size:16 final size:17
Alignment explanation
Indices: 62273--62305 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
62263 TCGGCAATAG
*
62273 TCAAAGTAAAAAGAAGA
1 TCAAAGGAAAAAGAAGA
62290 TCAAAGGAAAAA-AAGA
1 TCAAAGGAAAAAGAAGA
62306 AAAAGCTAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.67, C:0.06, G:0.18, T:0.09
Consensus pattern (17 bp):
TCAAAGGAAAAAGAAGA
Found at i:62969 original size:22 final size:21
Alignment explanation
Indices: 62944--62995 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
62934 TAATAAAGAG
62944 AAAATTATATTTTAAT-TCTCTA
1 AAAATTATA-TTTAATAT-TCTA
*
62966 AAAATT-TGATTTAATATTTTA
1 AAAATTAT-ATTTAATATTCTA
62987 AAAATTATA
1 AAAATTATA
62996 AAAATATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAATTATATTTAATATTCTA
Found at i:63590 original size:17 final size:17
Alignment explanation
Indices: 63568--63618 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
63558 AAATTTTCTT
*
63568 TTAAGTATAAATTTAAA
1 TTAAGTATAAAATTAAA
* *
63585 TTAAGTTTAAAATTAAT
1 TTAAGTATAAAATTAAA
*
63602 TTGAA-TTTAAAATTAAA
1 TT-AAGTATAAAATTAAA
63619 AAAAAATCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 27 0.93
18 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (17 bp):
TTAAGTATAAAATTAAA
Found at i:63656 original size:13 final size:14
Alignment explanation
Indices: 63630--63658 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
63620 AAAAATCTAG
63630 TTACAAATGTCCAA
1 TTACAAATGTCCAA
63644 TTACAAA-GTCCAA
1 TTACAAATGTCCAA
63657 TT
1 TT
63659 GAACCCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (14 bp):
TTACAAATGTCCAA
Found at i:65630 original size:30 final size:28
Alignment explanation
Indices: 65592--66195 Score: 186
Period size: 29 Copynumber: 20.7 Consensus size: 28
65582 CCATGGAGGT
65592 CCCT-AAACTATCTAAAAATTATGTTTTTA
1 CCCTCAAACT-TCTAAAAATTAT-TTTTTA
*
65621 CCCTCAAACTTCCAAAAATCCTATTTTTTA
1 CCCTCAAACTTCTAAAAAT--TATTTTTTA
65651 CCC-CGAAACTTCTAAAAATTCCA-TTTTTA
1 CCCTC-AAACTTCTAAAAATT--ATTTTTTA
* ** *
65680 CCCTCGAACACCCAAAAATCTCA-TTTTTA
1 CCCTCAAACTTCTAAAAAT-T-ATTTTTTA
*
65709 CCC-CGAAACTTCTAAAAATTATATTTTCA
1 CCCTC-AAACTTCTAAAAATTAT-TTTTTA
* * *
65738 CCCTCGAACTTCCAAAAATCCCATTTTTTA
1 CCCTCAAACTTCTAAAAAT--TATTTTTTA
*
65768 CCC-CGAAACTTCTAAAAATTCAGTTTTTA
1 CCCTC-AAACTTCTAAAAATT-ATTTTTTA
* * * *
65797 CCCTCGAACCTCCAAAAATCCCATTTTTTA
1 CCCTCAAACTTCTAAAAAT--TATTTTTTA
65827 CCC-CGAAACTTCTAAAAATTCCA-TTTTTA
1 CCCTC-AAACTTCTAAAAATT--ATTTTTTA
* ** *
65856 CCCTCGAACTTCCGAAAATCTCA-TTTTGA
1 CCCTCAAACTTCTAAAAAT-T-ATTTTTTA
*
65885 CCC-AAAACTTCTAAAAATT-TCATTTTTA
1 CCCTCAAACTTCTAAAAATTAT--TTTTTA
* * * * *
65913 CCCCCGAACTT-TGGAAAATCCCATTTTTGA
1 CCCTCAAACTTCT-AAAAAT--TATTTTTTA
* *
65943 CCC-CAAAACTTCTAAAAATTCTAATTTTA
1 CCCTC-AAACTTCTAAAAATTAT-TTTTTA
* * ** * *
65972 CCCCCGAACTTC-CGAAATCCCATTTTTGA
1 CCCTCAAACTTCTAAAAAT--TATTTTTTA
* *
66001 CCC-CGGAATTTCTAAAAATTCCA-TTTTTA
1 CCCTC-AAACTTCTAAAAATT--ATTTTTTA
* * ** *
66030 CCCCCGAACTTCCGAAAATCCTATTTTTGA
1 CCCTCAAACTTCTAAAAAT--TATTTTTTA
* *
66060 -CATCGAAACTTCTAAAAATTCTATTTTTA
1 CCCTC-AAACTTCTAAAAATTAT-TTTTTA
* * * * *
66089 TCCC-CAATCTTTTGAAAATCCCATTTTTGA
1 -CCCTCAAACTTCTAAAAAT--TATTTTTTA
***
66119 -CCTCGAAACTTCTAAAAATTCCATTTTA
1 CCCTC-AAACTTCTAAAAATTATTTTTTA
* * *
66147 CCCCCGAACTTCTAAAAATCTCATTTTTGA
1 CCCTCAAACTTCTAAAAAT-T-ATTTTTTA
*
66177 CCC-CGAAACTTTTAAAAAT
1 CCCTC-AAACTTCTAAAAAT
66196 CCCATTTTTG
Statistics
Matches: 423, Mismatches: 94, Indels: 115
0.67 0.15 0.18
Matches are distributed among these distances:
27 2 0.00
28 50 0.12
29 207 0.49
30 154 0.36
31 9 0.02
32 1 0.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (28 bp):
CCCTCAAACTTCTAAAAATTATTTTTTA
Found at i:65695 original size:59 final size:59
Alignment explanation
Indices: 65596--66323 Score: 796
Period size: 59 Copynumber: 12.4 Consensus size: 59
65586 GGAGGTCCCT
*** * * *
65596 AAACTATCTAAAAATTATGTTTTTACCCTCAAACTTCCAAAAATCCTATTTTTTACCCCG
1 AAACT-TCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
** *
65656 AAACTTCTAAAAATTCCATTTTTACCCTCGAACACCCAAAAATCTCATTTTT-ACCCCG
1 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
** * *
65714 AAACTTCTAAAAATTATATTTTCACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCG
1 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
65773 AAACTTCTAAAAATT-CAGTTTTTACCCTCGAACCTCCAAAAATCCCATTTTTTACCCCG
1 AAACTTCTAAAAATTCCA-TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
65832 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCGAAAATCTCA-TTTTGA-CCCA
1 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *** *
65889 AAACTTCTAAAAATTTCATTTTTACCCCCGAACTTTGGAAAATCCCATTTTTGACCCCA
1 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
65948 AAACTTCTAAAAATTCTAATTTTACCCCCGAACTTCC-GAAATCCCATTTTTGACCCCG
1 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * * **
66006 GAATTTCTAAAAATTCCATTTTTACCCCCGAACTTCCGAAAATCCTATTTTTGACATCG
1 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *** *
66065 AAACTTCTAAAAATTCTATTTTTATCCC-C-AATCTTTTGAAAATCCCATTTTTGACCTCG
1 AAACTTCTAAAAATTCCATTTTTA-CCCTCGAA-CTTCCAAAAATCCCATTTTTGACCCCG
* * *
66124 AAACTTCTAAAAATTCCA-TTTTACCCCCGAACTTCTAAAAATCTCATTTTTGACCCCG
1 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * *** * *
66182 AAACTTTTAAAAATCCCATTTTTGACCCCCAAACTT-TTGAAATCCAATTTTTGACTCCG
1 AAACTTCTAAAAATTCCATTTTT-ACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
66241 AAACTTCTAAAAATTCAATTTTTACCCTTGAACTTCCTAAAATCCCATTTTTATGTCCCCG
1 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCA-TTTT-TGACCCCG
66302 -AA-TGTCT-AAAATTCCATTTTTA
1 AAACT-TCTAAAAATTCCATTTTTA
66324 AATCTCGAAT
Statistics
Matches: 578, Mismatches: 74, Indels: 33
0.84 0.11 0.05
Matches are distributed among these distances:
57 48 0.08
58 172 0.30
59 322 0.56
60 30 0.05
61 6 0.01
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (59 bp):
AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:65812 original size:117 final size:118
Alignment explanation
Indices: 65596--66292 Score: 791
Period size: 117 Copynumber: 5.9 Consensus size: 118
65586 GGAGGTCCCT
* * * *
65596 AAACTATCTAAAAATTATGTTTTTACCCTCAAACTTCCAAAAATCCTATTTTTTACCCCGAAACT
1 AAACT-TCTAAAAATTATATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* ** *
65661 TCTAAAAATTCCATTTTTACCCTCGAACACCCAAAAATCTCATTTTT-ACCCCG
65 TCTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
65714 AAACTTCTAAAAATTATATTTTCACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCGAAACTT
1 AAACTTCTAAAAATTATATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
* * *
65779 CTAAAAATT-CAGTTTTTACCCTCGAACCTCCAAAAATCCCATTTTTTACCCCG
66 CTAAAAATTCCA-TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
** * * *
65832 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCGAAAATCTCA-TTTTGA-CCCAAAACTT
1 AAACTTCTAAAAATTATATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
* *** *
65895 CTAAAAATTTCATTTTTACCCCCGAACTTTGGAAAATCCCATTTTTGACCCCA
66 CTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * * *
65948 AAACTTCTAAAAATTCTAATTTTACCCCCGAACTTCC-GAAATCCCATTTTTGACCCCGGAATTT
1 AAACTTCTAAAAATTATATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
* * **
66012 CTAAAAATTCCATTTTTACCCCCGAACTTCCGAAAATCCTATTTTTGACATCG
66 CTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *** *
66065 AAACTTCTAAAAATTCTATTTTTATCCC-C-AATCTTTTGAAAATCCCATTTTTGACCTCGAAAC
1 AAACTTCTAAAAATTATATTTTTA-CCCTCGAA-CTTCCAAAAATCCCATTTTTGACCCCGAAAC
* *
66128 TTCTAAAAATTCCA-TTTTACCCCCGAACTTCTAAAAATCTCATTTTTGACCCCG
64 TTCTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *** * * *** * *
66182 AAACTTTTAAAAATCCCATTTTTGACCCCCAAACTT-TTGAAATCCAATTTTTGACTCCGAAACT
1 AAACTTCTAAAAATTATATTTTT-ACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* ** *
66246 TCTAAAAATTCAATTTTTACCCTTGAACTTCCTAAAATCCCATTTTT
65 TCTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTT
66293 ATGTCCCCGA
Statistics
Matches: 504, Mismatches: 63, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
115 7 0.01
116 96 0.19
117 275 0.55
118 124 0.25
119 2 0.00
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (118 bp):
AAACTTCTAAAAATTATATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
CTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:66134 original size:176 final size:174
Alignment explanation
Indices: 65616--66292 Score: 821
Period size: 176 Copynumber: 3.9 Consensus size: 174
65606 AAAATTATGT
* * * *
65616 TTTTACCCTCAAACTTCCAAAAATCCTATTTTTTACCCCGAAACTTCTAAAAATTCCATTTTTAC
1 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCTAAAAATTCCATTTTTAC
* ** * * *
65681 CCTCGAACACCCAAAAATCTCATTTTT-ACCCCGAAACTTCTAAAAATTATATTTTCACCCTCGA
66 CCCCGAACTTCCGAAAATCTCATTTTTGA-CCCGAAACTTCTAAAAATTCTATTTTTACCC-CGA
* * * *
65745 ACTTCCAAAAATCCCATTTTTTACCCCGAAACTTCTAAAAATTCAGT
129 ACTTTCGAAAATCCCATTTTTGACCCCGAAACTTCTAAAAATTCA-A
* * *
65792 TTTTACCCTCGAACCTCCAAAAATCCCATTTTTTACCCCGAAACTTCTAAAAATTCCATTTTTAC
1 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCTAAAAATTCCATTTTTAC
* *
65857 CCTCGAACTTCCGAAAATCTCA-TTTTGACCCAAAACTTCTAAAAATT-TCATTTTTACCCCCGA
66 CCCCGAACTTCCGAAAATCTCATTTTTGACCCGAAACTTCTAAAAATTCT-ATTTTTA-CCCCGA
* *
65920 ACTTTGGAAAATCCCATTTTTGACCCCAAAACTTCTAAAAATTCTAA
129 ACTTTCGAAAATCCCATTTTTGACCCCGAAACTTCTAAAAATTC-AA
* * *
65967 TTTTACCCCCGAACTTCC-GAAATCCCATTTTTGACCCCGGAATTTCTAAAAATTCCATTTTTAC
1 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCTAAAAATTCCATTTTTAC
*
66031 CCCCGAACTTCCGAAAATC-CTATTTTTGACATCGAAACTTCTAAAAATTCTATTTTTATCCCC-
66 CCCCGAACTTCCGAAAATCTC-ATTTTTGAC-CCGAAACTTCTAAAAATTCTATTTTTA-CCCCG
* * *
66094 AATCTTTTGAAAATCCCATTTTTGACCTCGAAACTTCTAAAAATTCCA
128 AA-CTTTCGAAAATCCCATTTTTGACCCCGAAACTTCTAAAAATTCAA
* * * *
66142 TTTTACCCCCGAACTTCTAAAAATCTCATTTTTGACCCCGAAACTTTTAAAAATCCCATTTTTGA
1 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCTAAAAATTCCATTTTT-A
* ** * *
66207 CCCCCAAACTTTTG-AAATC-CAATTTTTGACTCCGAAACTTCTAAAAATTCAATTTTTACCCTT
65 CCCCCGAACTTCCGAAAATCTC-ATTTTTGAC-CCGAAACTTCTAAAAATTCTATTTTTACCC-C
* *
66270 GAACTTCCTAAAATCCCATTTTT
127 GAACTTTCGAAAATCCCATTTTT
66293 ATGTCCCCGA
Statistics
Matches: 442, Mismatches: 46, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
173 1 0.00
174 62 0.14
175 116 0.26
176 248 0.56
177 15 0.03
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (174 bp):
TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCTAAAAATTCCATTTTTAC
CCCCGAACTTCCGAAAATCTCATTTTTGACCCGAAACTTCTAAAAATTCTATTTTTACCCCGAAC
TTTCGAAAATCCCATTTTTGACCCCGAAACTTCTAAAAATTCAA
Found at i:68654 original size:51 final size:52
Alignment explanation
Indices: 68599--68698 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 52
68589 TAGCGATAAT
* *
68599 TAAAAAAAAGT-AA-TTTGTAAATATTGAAGGTTAAAATTTTTTTAATTTGAA
1 TAAAAAAAA-TAAACTTTGTAAACATTGAAGGCTAAAATTTTTTTAATTTGAA
** **
68650 TAAAAATGATAAACTTTGTAAACATTGAAGGCTAATTTTTTTTTAATTT
1 TAAAAAAAATAAACTTTGTAAACATTGAAGGCTAAAATTTTTTTAATTT
68699 TTATAAATAG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 1 0.02
51 9 0.22
52 31 0.76
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (52 bp):
TAAAAAAAATAAACTTTGTAAACATTGAAGGCTAAAATTTTTTTAATTTGAA
Found at i:68705 original size:52 final size:52
Alignment explanation
Indices: 68612--68714 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
68602 AAAAAAGTAA
* * *
68612 TTTGTAAATATTGAAGGTTAAAATTTTTTTAATTTGAATAAAAATGATAAAC
1 TTTGTAAACATTGAAGGCTAAAATTTTTTTAATTTGAATAAAAAGGATAAAC
** ** *
68664 TTTGTAAACATTGAAGGCTAATTTTTTTTTAATTTTTATAAATAGGATAAA
1 TTTGTAAACATTGAAGGCTAAAATTTTTTTAATTTGAATAAAAAGGATAAA
68715 TTTTATATAG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.45
Consensus pattern (52 bp):
TTTGTAAACATTGAAGGCTAAAATTTTTTTAATTTGAATAAAAAGGATAAAC
Found at i:70679 original size:21 final size:21
Alignment explanation
Indices: 70631--70679 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
70621 AAAAAAAAAA
70631 ATTAAAATTCAAAATATTTAT
1 ATTAAAATTCAAAATATTTAT
**
70652 AAAAAAATTCAAAAT-TTATAT
1 ATTAAAATTCAAAATATT-TAT
*
70673 TTTAAAA
1 ATTAAAA
70680 GATTTCAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTAAAATTCAAAATATTTAT
Found at i:72388 original size:2 final size:2
Alignment explanation
Indices: 72383--72408 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
72373 CTCTCTCTCT
72383 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
72409 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:75964 original size:28 final size:27
Alignment explanation
Indices: 75925--75988 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
75915 AAAGAAATTG
*
75925 GAAAAGGAACAAAAGATA-AA-AGAAGTA
1 GAAAAGAAACAAAA-ATAGAAGAGAAG-A
*
75952 GAAAAGAACACAAAAATAGAAGGGAAGA
1 GAAAAGAA-ACAAAAATAGAAGAGAAGA
75980 GAAAAGAAA
1 GAAAAGAAA
75989 TGGGGTGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 11 0.34
28 17 0.53
29 4 0.12
ACGTcount: A:0.67, C:0.05, G:0.23, T:0.05
Consensus pattern (27 bp):
GAAAAGAAACAAAAATAGAAGAGAAGA
Found at i:76374 original size:62 final size:62
Alignment explanation
Indices: 76277--76431 Score: 240
Period size: 62 Copynumber: 2.5 Consensus size: 62
76267 GCTTAGGATG
* * * *
76277 TGTTTGAAAAATCACTTAATAATTAGATTTGGGTATAATTGTTTAATTAAATATATGTGATA
1 TGTTTGAAAAATCACTTAATAATTAAATTTGGGTATAATTATTTAATTAAACATATGTGACA
76339 TGTTTGAAAAATCACTTAATAATTAAATTTGGGTATAATTATTTAATTAAACATATGTGACA
1 TGTTTGAAAAATCACTTAATAATTAAATTTGGGTATAATTATTTAATTAAACATATGTGACA
*
76401 TGTTTGAACAATCACATTAATTAA-TAAATTT
1 TGTTTGAAAAATCAC-TTAA-TAATTAAATTT
76432 CACTAAATTG
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
62 72 0.84
63 11 0.13
64 3 0.03
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.42
Consensus pattern (62 bp):
TGTTTGAAAAATCACTTAATAATTAAATTTGGGTATAATTATTTAATTAAACATATGTGACA
Done.