Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007835.1 Kokia drynarioides strain JFW-HI SEQ_122471, 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: 165101
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 43 characters in sequence are not A, C, G, or T
Found at i:2277 original size:50 final size:50
Alignment explanation
Indices: 2209--2485 Score: 182
Period size: 49 Copynumber: 5.6 Consensus size: 50
2199 TGGATTTGCT
* * * * *
2209 GTTGCGGGTTAAATCTTTCCCTTTGTATCTTCTAAGGTGTGAGGTTCGTC
1 GTTGCGAGTTAAACCTTTCCCTTTGTGTCTTCTAAGGTATGAGGTTCGCC
* *
2259 GTTGCGAGTTAAACCTTTCTCTTTTGTGTCTTCGT--GGTACTG-GATTCGCC
1 GTTGCGAGTTAAACCTTTC-CCTTTGTGTCTTC-TAAGGTA-TGAGGTTCGCC
* ** *
2309 GTTGCG-GCTTAAATCTTTCCCTTCATGTC-TCTAAGGTATAAGGTTCGCC
1 GTTGCGAG-TTAAACCTTTCCCTTTGTGTCTTCTAAGGTATGAGGTTCGCC
* * * *
2358 ATTGCGACTTAAACCTTTCCCTTTGTG--TTCGT--GGCACT-AGATTCGCC
1 GTTGCGAGTTAAACCTTTCCCTTTGTGTCTTC-TAAGGTA-TGAGGTTCGCC
* ** * * *
2405 GTTGCG-GCTTAAATCTTTCCCTTCATG-CTTCTGAGGTATAAGGTTCACC
1 GTTGCGAG-TTAAACCTTTCCCTTTGTGTCTTCTAAGGTATGAGGTTCGCC
* * * *
2454 ATTGCGACTTAAACATTTTCCTTTGTGTCTTC
1 GTTGCGAGTTAAACCTTTCCCTTTGTGTCTTC
2486 GTGGTACTGG
Statistics
Matches: 174, Mismatches: 35, Indels: 36
0.71 0.14 0.15
Matches are distributed among these distances:
47 34 0.20
48 10 0.06
49 70 0.40
50 46 0.26
51 13 0.07
52 1 0.01
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (50 bp):
GTTGCGAGTTAAACCTTTCCCTTTGTGTCTTCTAAGGTATGAGGTTCGCC
Found at i:2421 original size:96 final size:97
Alignment explanation
Indices: 2096--2529 Score: 484
Period size: 96 Copynumber: 4.4 Consensus size: 97
2086 ATGTCTTTGC
* * *
2096 GGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTT-TCGAGGTAGT-AGGTTCAC
1 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCT-AAGGTA-TAAGGTTCAC
* * * * *
2159 CGTTG-TAGCTTAAACCATCCCCTTTGTATCTTCGT
64 CATTGCGA-CTTAAACCTTTCCCTTTGT-GCTTCGT
* * * * * * * **
2194 GGTATTGGATTTGCTGTTGCGGGTTAAATCTTTCCCTTTGTAT-CTTCTAAGGTGTGAGGTTCGT
1 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCC-TT-CATGCTTCTAAGGTATAAGGTTCAC
* * *
2258 CGTTGCGAGTTAAACCTTTCTCTTTTGTGTCTTCGT
64 CATTGCGACTTAAACCTTTC-CCTTTGTG-CTTCGT
*
2294 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-TCTCTAAGGTATAAGGTTCGCC
1 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTAAGGTATAAGGTTCACC
2358 ATTGCGACTTAAACCTTTCCCTTTGTG-TTCGT
65 ATTGCGACTTAAACCTTTCCCTTTGTGCTTCGT
* * *
2390 GGCACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCACCA
1 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTATAAGGTTCACCA
* *
2455 TTGCGACTTAAACATTTTCCTTTGTGTCTTCGT
66 TTGCGACTTAAACCTTTCCCTTTGTG-CTTCGT
* *
2488 GGTACTGGATTCGCCGTTGTGGCTTAAATATTTCCCTTCATG
1 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
2530 GTAATGAAAC
Statistics
Matches: 286, Mismatches: 38, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
96 88 0.31
97 1 0.00
98 84 0.29
99 65 0.23
100 48 0.17
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.39
Consensus pattern (97 bp):
GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTATAAGGTTCACCA
TTGCGACTTAAACCTTTCCCTTTGTGCTTCGT
Found at i:8149 original size:23 final size:21
Alignment explanation
Indices: 8118--8181 Score: 51
Period size: 23 Copynumber: 2.9 Consensus size: 21
8108 AGCATATATT
8118 AAATATTAATATAAATATTAAA
1 AAAT-TTAATATAAATATTAAA
*
8140 ATAATGTTAAGT-TAATTA-TAAA
1 A-AAT-TTAA-TATAAATATTAAA
8162 AAATTTAATAAATAAATATT
1 AAATTTAAT--ATAAATATT
8182 TTTAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
19 1 0.03
20 4 0.12
21 3 0.09
22 11 0.33
23 13 0.39
24 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (21 bp):
AAATTTAATATAAATATTAAA
Found at i:11788 original size:6 final size:6
Alignment explanation
Indices: 11779--11803 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11769 AAACAAAGGA
11779 GATGGT GATGGT GATGGT GATGGT G
1 GATGGT GATGGT GATGGT GATGGT G
11804 CTGGCATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GATGGT
Found at i:15671 original size:13 final size:15
Alignment explanation
Indices: 15637--15673 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
15627 TGATTATCAC
15637 TTAATTAATATTAGAG
1 TTAATT-ATATTAGAG
15653 TTAATTATATTA-A-
1 TTAATTATATTAGAG
15666 TTAATTAT
1 TTAATTAT
15674 TATTTTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.38
14 1 0.05
15 6 0.29
16 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
TTAATTATATTAGAG
Found at i:16043 original size:20 final size:20
Alignment explanation
Indices: 16018--16140 Score: 95
Period size: 20 Copynumber: 6.5 Consensus size: 20
16008 ATAAATAATT
16018 ATAATTTAATAAGAATTGTG
1 ATAATTTAATAAGAATTGTG
** * * **
16038 ATAATTGGACAACAATAAT-
1 ATAATTTAATAAGAATTGTG
16057 ATCACATTT-ATAA-AA-TGTG
1 AT-A-ATTTAATAAGAATTGTG
16076 ATAATTTAAT---AA-T-T-
1 ATAATTTAATAAGAATTGTG
16090 ATAATTTAATAAGAATTGTG
1 ATAATTTAATAAGAATTGTG
16110 ATAATTTAATAAGAATTGTG
1 ATAATTTAATAAGAATTGTG
16130 ATAATTATAAT
1 ATAATT-TAAT
16141 TTAATAAGTT
Statistics
Matches: 82, Mismatches: 10, Indels: 21
0.73 0.09 0.19
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 3 0.04
17 6 0.07
18 5 0.06
19 7 0.09
20 43 0.52
21 7 0.09
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (20 bp):
ATAATTTAATAAGAATTGTG
Found at i:16115 original size:26 final size:26
Alignment explanation
Indices: 16084--16148 Score: 88
Period size: 20 Copynumber: 2.7 Consensus size: 26
16074 TGATAATTTA
16084 ATAATTATAATTTAATAAGAATTGTG
1 ATAATTATAATTTAATAAGAATTGTG
16110 ------ATAATTTAATAAGAATTGTG
1 ATAATTATAATTTAATAAGAATTGTG
16130 ATAATTATAATTTAATAAG
1 ATAATTATAATTTAATAAG
16149 TTAAGTAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
20 20 0.61
26 13 0.39
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.42
Consensus pattern (26 bp):
ATAATTATAATTTAATAAGAATTGTG
Found at i:17949 original size:14 final size:15
Alignment explanation
Indices: 17930--17962 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
17920 GAGAATAAAT
17930 ATTTAATTAA-ATAA
1 ATTTAATTAATATAA
17944 ATTTAATTAATATAA
1 ATTTAATTAATATAA
17959 ATTT
1 ATTT
17963 TTAAACACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTAATTAATATAA
Found at i:21509 original size:19 final size:19
Alignment explanation
Indices: 21487--21526 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21477 AATTGAAATT
* * *
21487 ATTTTTAAAATTTTTAAAA
1 ATTTTAAAAACTTCTAAAA
21506 ATTTTAAAAACTTCTAAAA
1 ATTTTAAAAACTTCTAAAA
21525 AT
1 AT
21527 ACATAGAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTTAAAAACTTCTAAAA
Found at i:21578 original size:27 final size:27
Alignment explanation
Indices: 21501--21579 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
21491 TTAAAATTTT
* *
21501 TAAAAATTTTAAAAACTTCTAAAAATACA
1 TAAAAA-TTTAAAAAATT-TATAAATACA
* ** *
21530 TAGAAATTTAAAAAATAAATAAATATA
1 TAAAAATTTAAAAAATTTATAAATACA
*
21557 TAAAAATTTCAAAAATTTATAAA
1 TAAAAATTTAAAAAATTTATAAA
21580 GTGAGGAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
27 26 0.65
28 9 0.22
29 5 0.12
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.32
Consensus pattern (27 bp):
TAAAAATTTAAAAAATTTATAAATACA
Found at i:23644 original size:14 final size:14
Alignment explanation
Indices: 23625--23673 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
23615 CTATTAGAAA
*
23625 ATTATTTGAATATT
1 ATTATTTAAATATT
*
23639 ATTATTTAAATATG
1 ATTATTTAAATATT
*
23653 ATTTGAATTAAATATT
1 A-TT-ATTTAAATATT
23669 ATTAT
1 ATTAT
23674 ATCTTTCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 14 0.50
15 4 0.14
16 10 0.36
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (14 bp):
ATTATTTAAATATT
Found at i:25602 original size:11 final size:11
Alignment explanation
Indices: 25596--25637 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
25586 ATAATAACAA
25596 TAAAATAATAG
1 TAAAATAATAG
*
25607 TAATATAATAG
1 TAAAATAATAG
25618 TAAAATAATAG
1 TAAAATAATAG
25629 TAAAATAAT
1 TAAAATAAT
25638 GGAAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (11 bp):
TAAAATAATAG
Found at i:25614 original size:22 final size:22
Alignment explanation
Indices: 25588--25636 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
25578 ATATCAAAAT
25588 AATAACAATAAAATAATAGTAA
1 AATAACAATAAAATAATAGTAA
* * *
25610 TATAATAGTAAAATAATAGTAA
1 AATAACAATAAAATAATAGTAA
25632 AATAA
1 AATAA
25637 TGGAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (22 bp):
AATAACAATAAAATAATAGTAA
Found at i:28406 original size:28 final size:28
Alignment explanation
Indices: 28365--28421 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
28355 TTCAGGGCCG
*
28365 AATTACGCCTGGAGAGATTAATGGCCAA
1 AATTACGCCCGGAGAGATTAATGGCCAA
* *
28393 AATTATGCCCGGAGGGATTAATGGCCAA
1 AATTACGCCCGGAGAGATTAATGGCCAA
28421 A
1 A
28422 GATCGTGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (28 bp):
AATTACGCCCGGAGAGATTAATGGCCAA
Found at i:35565 original size:23 final size:22
Alignment explanation
Indices: 35533--35577 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
35523 TCTTTTTAGA
*
35533 TTTAAAATTAAATTATAAATTT
1 TTTAAAATTAAAATATAAATTT
*
35555 TTTAAAGATTAAAATGTAAATTT
1 TTTAAA-ATTAAAATATAAATTT
35578 ATCATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTAAAATTAAAATATAAATTT
Found at i:35663 original size:43 final size:43
Alignment explanation
Indices: 35615--35700 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
35605 ATTTGTTAAG
35615 GGGTTTAAGTATAATTCACTATTATTTATGCTGCCAAGGCTTT
1 GGGTTTAAGTATAATTCACTATTATTTATGCTGCCAAGGCTTT
35658 GGGTTTAAGTATAATTCACTATTATTTATGCTGCCAAGGCTTT
1 GGGTTTAAGTATAATTCACTATTATTTATGCTGCCAAGGCTTT
35701 TGTCTACCCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.42
Consensus pattern (43 bp):
GGGTTTAAGTATAATTCACTATTATTTATGCTGCCAAGGCTTT
Found at i:38483 original size:9 final size:9
Alignment explanation
Indices: 38469--38495 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
38459 GTGGAACACA
38469 TGACTCCAT
1 TGACTCCAT
38478 TGACTCCAT
1 TGACTCCAT
38487 TGACTCCAT
1 TGACTCCAT
38496 CATAACTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.33
Consensus pattern (9 bp):
TGACTCCAT
Found at i:40701 original size:18 final size:18
Alignment explanation
Indices: 40650--40717 Score: 52
Period size: 18 Copynumber: 3.8 Consensus size: 18
40640 TAAATATATA
40650 AATCATAATTATAA-TA-
1 AATCATAATTATAATTAT
* * * *
40666 ATTCATGATAAATGATTAT
1 AATCATAAT-TATAATTAT
40685 -ATCATCAATTATAATTAT
1 AATCAT-AATTATAATTAT
*
40703 AATTATAATTATAAT
1 AATCATAATTATAAT
40718 AATTAATTAA
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
16 7 0.18
17 3 0.08
18 22 0.58
19 6 0.16
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
AATCATAATTATAATTAT
Found at i:40702 original size:6 final size:6
Alignment explanation
Indices: 40691--40717 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40681 TTATATCATC
40691 AATTAT AATTAT AATTAT AATTAT AAT
1 AATTAT AATTAT AATTAT AATTAT AAT
40718 AATTAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:42198 original size:57 final size:56
Alignment explanation
Indices: 42130--42239 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 56
42120 ATTAAAAATA
* * *
42130 TATATTTCAATATTTATCAGACTTTATCTAC-TCAAAAGTTTTAGTTTTGTTATAAAC
1 TATAATTCAATATTTATCAAACTTTATCT-CTTCAAAA-TTTTAGTTTTGATATAAAC
*
42187 TATAATTCAATATTTATCAAATTTTATCTCTTCAAAATTTTAGTTTTGATATA
1 TATAATTCAATATTTATCAAACTTTATCTCTTCAAAATTTTAGTTTTGATATA
42240 TAATTTAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
56 16 0.33
57 32 0.67
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (56 bp):
TATAATTCAATATTTATCAAACTTTATCTCTTCAAAATTTTAGTTTTGATATAAAC
Found at i:42322 original size:19 final size:20
Alignment explanation
Indices: 42284--42324 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
42274 TAGATAATAT
42284 AAATACATTTATATGTTGTAAA
1 AAATACATTTATA--TTGTAAA
42306 AAATACATTTATA-TGTAAA
1 AAATACATTTATATTGTAAA
42325 TGTAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
22 13 0.68
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (20 bp):
AAATACATTTATATTGTAAA
Found at i:45668 original size:2 final size:2
Alignment explanation
Indices: 45661--45690 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45651 CTCCAAACTC
45661 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
45691 AGGTCCAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:46008 original size:22 final size:22
Alignment explanation
Indices: 45964--46011 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
45954 TAATTTAAGA
*
45964 AAAAAATTCAAACTTAAACAAG
1 AAAAAATTCAAACTAAAACAAG
*
45986 AAAAAATTCAACAC-AAAAGAAG
1 AAAAAATTCAA-ACTAAAACAAG
46008 AAAA
1 AAAA
46012 TCAATGGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.69, C:0.12, G:0.06, T:0.12
Consensus pattern (22 bp):
AAAAAATTCAAACTAAAACAAG
Found at i:47213 original size:12 final size:12
Alignment explanation
Indices: 47190--47247 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
47180 TTCATTTAAC
47190 TTAATCGAACATG
1 TTAAT-GAACATG
* *
47203 TTTATGAACATA
1 TTAATGAACATG
* *
47215 TGATTGAACATG
1 TTAATGAACATG
*
47227 TTCATGAACAATG
1 TTAATGAAC-ATG
47240 TTAATGAA
1 TTAATGAA
47248 TAATAAACAA
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
12 20 0.59
13 14 0.41
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (12 bp):
TTAATGAACATG
Found at i:51053 original size:29 final size:27
Alignment explanation
Indices: 50989--51053 Score: 67
Period size: 31 Copynumber: 2.3 Consensus size: 27
50979 ATTTCTTGTG
*
50989 TATAATTGCACCAAATTAAAGTTCATG
1 TATAATTGCACCAAATTAAAGTTCATA
* *
51016 TATCAAATTGCACATTAAATTAGAGTTCATA
1 TAT--AATTGCAC--CAAATTAAAGTTCATA
51047 TATAATT
1 TATAATT
51054 TTGAGTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 3 0.10
29 12 0.39
31 16 0.52
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (27 bp):
TATAATTGCACCAAATTAAAGTTCATA
Found at i:64256 original size:7 final size:7
Alignment explanation
Indices: 64238--64278 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
64228 TTTACTCCCC
64238 TTTCAC-
1 TTTCACT
64244 TTTCACT
1 TTTCACT
64251 TTTCACT
1 TTTCACT
64258 TTTCACT
1 TTTCACT
*
64265 TTTCATT
1 TTTCACT
64272 TTTCACT
1 TTTCACT
64279 GTTTGATTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 6 0.19
7 26 0.81
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTCACT
Found at i:73635 original size:19 final size:19
Alignment explanation
Indices: 73613--73657 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
73603 TTTTATTAGG
73613 ATTTAATATTTAAGA-TATT
1 ATTTAATATTTAA-ATTATT
* *
73632 ATTTATTATTTAAATTTTT
1 ATTTAATATTTAAATTATT
73651 ATTTAAT
1 ATTTAAT
73658 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTAATATTTAAATTATT
Found at i:74461 original size:16 final size:16
Alignment explanation
Indices: 74423--74461 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
74413 TCAACACTTC
74423 TATTTTTTATTTCTTT
1 TATTTTTTATTTCTTT
*
74439 TAATTTTGT-TTTCTTT
1 T-ATTTTTTATTTCTTT
74455 TATTTTT
1 TATTTTT
74462 ATTATTTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 5 0.25
16 9 0.45
17 6 0.30
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (16 bp):
TATTTTTTATTTCTTT
Found at i:78568 original size:8 final size:8
Alignment explanation
Indices: 78557--78586 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
78547 CTTTTTGTGT
*
78557 TTTTTAAA
1 TTTTAAAA
78565 TTTTAAAA
1 TTTTAAAA
78573 TTTTAAAA
1 TTTTAAAA
78581 TTTTAA
1 TTTTAA
78587 TCCTCACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTTAAAA
Found at i:82229 original size:15 final size:16
Alignment explanation
Indices: 82200--82297 Score: 54
Period size: 18 Copynumber: 5.7 Consensus size: 16
82190 AAAAATAATT
82200 AAATAATTAAAAAAAG
1 AAATAATTAAAAAAAG
* *
82216 AAAT-ATTAAGAAAAT
1 AAATAATTAAAAAAAG
** *
82231 AAATTAATTTAAAGTAAT
1 AAA-TAA-TTAAAAAAAG
82249 AAATTTAAATTTAAAAAATAG
1 AAA--T-AA-TTAAAAAA-AG
* *
82270 AATTTAATTAAAAGAAG
1 AA-ATAATTAAAAAAAG
82287 AAATAATTAAA
1 AAATAATTAAA
82298 GGATAAATTA
Statistics
Matches: 64, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
15 12 0.19
16 13 0.20
17 5 0.08
18 17 0.27
19 4 0.06
20 10 0.16
21 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
AAATAATTAAAAAAAG
Found at i:82268 original size:19 final size:19
Alignment explanation
Indices: 82216--82276 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
82206 TTAAAAAAAG
82216 AAATATTAAGAAAATAAA-TT
1 AAAT-TTAA-AAAATAAATTT
*
82236 -AATTTAAAGTAATAAATTT
1 AAATTTAAA-AAATAAATTT
82255 AAATTTAAAAAATAGAATTT
1 AAATTTAAAAAATA-AATTT
82275 AA
1 AA
82277 TTAAAAGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 1 0.03
18 10 0.29
19 9 0.26
20 15 0.43
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
AAATTTAAAAAATAAATTT
Found at i:82278 original size:19 final size:18
Alignment explanation
Indices: 82221--82282 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 18
82211 AAAAGAAATA
82221 TTAAGAAAATAAA-TTAAT
1 TTAA-AAAATAAATTTAAT
*
82239 TTAAAGTAATAAATTTAAAT
1 TTAAA-AAATAAATTT-AAT
82259 TTAAAAAATAGAATTTAA-
1 TTAAAAAATA-AATTTAAT
82277 TTAAAA
1 TTAAAA
82283 GAAGAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 1 0.03
18 16 0.42
19 8 0.21
20 13 0.34
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
TTAAAAAATAAATTTAAT
Found at i:82306 original size:71 final size:72
Alignment explanation
Indices: 82203--82338 Score: 179
Period size: 71 Copynumber: 1.9 Consensus size: 72
82193 AATAATTAAA
*
82203 TAATTAAAAAAAGAAATATTAAGAAAATAAATTA-ATT-TAAAGTAATAAATTTAAATTTAAAAA
1 TAATTAAAAAAAGAAATATTAAGAAAATAAATTATATTATAAACTAATAAATTTAAA-TTAAAAA
82266 ATAGAATT
65 ATAGAATT
* ** * *
82274 TAATTAAAAGAAGAAATAATTAA-AGGATAAATTATATTATAAACTAATAGATTTTAATTAAAAA
1 TAATTAAAAAAAGAAAT-ATTAAGAAAATAAATTATATTATAAACTAATAAATTTAAATTAAAAA
82338 A
65 A
82339 GAAAAAGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
71 25 0.45
72 16 0.29
73 15 0.27
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.32
Consensus pattern (72 bp):
TAATTAAAAAAAGAAATATTAAGAAAATAAATTATATTATAAACTAATAAATTTAAATTAAAAAA
TAGAATT
Found at i:84873 original size:31 final size:31
Alignment explanation
Indices: 84822--84884 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
84812 GTTACAAAAG
* * *
84822 AATCATTGAATTATTTGAAAATTTTTATTTA
1 AATCATTAAACTATTCGAAAATTTTTATTTA
84853 AATCATTAAACTATTCGAAAATTTTTATTTA
1 AATCATTAAACTATTCGAAAATTTTTATTTA
84884 A
1 A
84885 GTTATTGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (31 bp):
AATCATTAAACTATTCGAAAATTTTTATTTA
Found at i:91783 original size:15 final size:15
Alignment explanation
Indices: 91765--91807 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
91755 AAAAATATTT
91765 ATATTTTTTATTTTA
1 ATATTTTTTATTTTA
** *
91780 ATATTTAATAATTTA
1 ATATTTTTTATTTTA
*
91795 ATAATTTTTATTT
1 ATATTTTTTATTT
91808 ATTAAACAAT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATATTTTTTATTTTA
Found at i:92300 original size:96 final size:96
Alignment explanation
Indices: 92136--92328 Score: 377
Period size: 96 Copynumber: 2.0 Consensus size: 96
92126 AACAGTTGTA
*
92136 ATGAAAACCATAACTCTAATATTTACCACTGGCTGCCGATGATATAGATGCATATCATAAGAAAA
1 ATGAAAACCATAACTCTAATATTTACCACTCGCTGCCGATGATATAGATGCATATCATAAGAAAA
92201 TTCTTGAAAAATATAAATAACAAATATGTCG
66 TTCTTGAAAAATATAAATAACAAATATGTCG
92232 ATGAAAACCATAACTCTAATATTTACCACTCGCTGCCGATGATATAGATGCATATCATAAGAAAA
1 ATGAAAACCATAACTCTAATATTTACCACTCGCTGCCGATGATATAGATGCATATCATAAGAAAA
92297 TTCTTGAAAAATATAAATAACAAATATGTCG
66 TTCTTGAAAAATATAAATAACAAATATGTCG
92328 A
1 A
92329 ACTGTGGCTG
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (96 bp):
ATGAAAACCATAACTCTAATATTTACCACTCGCTGCCGATGATATAGATGCATATCATAAGAAAA
TTCTTGAAAAATATAAATAACAAATATGTCG
Found at i:100205 original size:31 final size:31
Alignment explanation
Indices: 100170--100234 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
100160 TTCAATTTAA
100170 TCACTAACGTTTTAGATAATTTCTATTTTGG
1 TCACTAACGTTTTAGATAATTTCTATTTTGG
* * * *
100201 TCACTCACGTTTTAGGTTATTTTTATTTTGG
1 TCACTAACGTTTTAGATAATTTCTATTTTGG
100232 TCA
1 TCA
100235 TTCTCCATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.51
Consensus pattern (31 bp):
TCACTAACGTTTTAGATAATTTCTATTTTGG
Found at i:109859 original size:39 final size:39
Alignment explanation
Indices: 109802--109997 Score: 304
Period size: 39 Copynumber: 5.0 Consensus size: 39
109792 CCAAGGCACC
* * *
109802 GTGATTTTCTGGGAAGAGATTCAAGTTCTGCGAGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCTAGGGGCA
109841 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCTAGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCTAGGGGCA
* *
109880 GTGATTTTCAGGGCAAAGATTCAAGTTCAGCTAGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCTAGGGGCA
*
109919 GTGATTTTCAGGGCAGAGATTCAAGTTCCG-TGAGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCT-AGGGGCA
* *
109958 GTGATTTTCATGGCAGAGATTCAAGTTTTGCTAGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCTAGGGGCA
109997 G
1 G
109998 GTCCTCATCA
Statistics
Matches: 145, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
38 1 0.01
39 143 0.99
40 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.34, T:0.28
Consensus pattern (39 bp):
GTGATTTTCAGGGCAGAGATTCAAGTTCTGCTAGGGGCA
Found at i:111176 original size:26 final size:26
Alignment explanation
Indices: 111140--111200 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
111130 GAAGTGTCGT
111140 GTTAAAGAATATGTTTAGTTACACAG
1 GTTAAAGAATATGTTTAGTTACACAG
*
111166 GTTAAAGAATATGTTTGGTTACACAG
1 GTTAAAGAATATGTTTAGTTACACAG
111192 G-T-AAGAATA
1 GTTAAAGAATA
111201 CAAATTTGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 7 0.21
25 1 0.03
26 26 0.76
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (26 bp):
GTTAAAGAATATGTTTAGTTACACAG
Found at i:116819 original size:22 final size:21
Alignment explanation
Indices: 116792--116833 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
116782 ATTTTTAATA
116792 ATATTAA-ACATTATAATATTTG
1 ATATTAATAC-TTA-AATATTTG
116814 ATATTAATACTTAAATATTT
1 ATATTAATACTTAAATATTT
116834 TAAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 10 0.53
23 2 0.11
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (21 bp):
ATATTAATACTTAAATATTTG
Found at i:118977 original size:108 final size:108
Alignment explanation
Indices: 118789--119027 Score: 286
Period size: 108 Copynumber: 2.2 Consensus size: 108
118779 GATCACTATG
*
118789 TGAAGATGCGTAAGTCCATGTGGTAGAGACCCATGATATTATATGACAATAAGTACATTCATGGT
1 TGAAGATGCGTAAGTCCATGTGGTAGAGACCCATGACATTATATGACAATAAGTACATTCATGGT
* *
118854 GATGCTTTCAATGATATGTAAATTGAACTGGTAGATCACAACA
66 GATGCTTTCAATGATATGTAAATCGAACTAGTAGATCACAACA
* * * * * *
118897 TGAAGGTGTGTAAGTTCATGTGGCT-GAGACCCATGGCATTATATGATAATAA-TAATATTCATG
1 TGAAGATGCGTAAGTCCATGTGG-TAGAGACCCATGACATTATATGACAATAAGT-ACATTCATG
** *
118960 GTGATGCCTTT-GGTGATATGTAAATCGAACTAGTAGATTACAACA
64 GTGATG-CTTTCAATGATATGTAAATCGAACTAGTAGATCACAACA
**
119005 TGAAGTTATGTATAAGTCCATGT
1 TGAAG--ATGCGTAAGTCCATGT
119028 AGAAGAAACC
Statistics
Matches: 111, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
107 1 0.01
108 92 0.83
109 5 0.05
110 13 0.12
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (108 bp):
TGAAGATGCGTAAGTCCATGTGGTAGAGACCCATGACATTATATGACAATAAGTACATTCATGGT
GATGCTTTCAATGATATGTAAATCGAACTAGTAGATCACAACA
Found at i:121463 original size:2 final size:2
Alignment explanation
Indices: 121456--121486 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
121446 TTAATAAATT
121456 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
121487 TAAGACTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:129186 original size:23 final size:24
Alignment explanation
Indices: 129149--129194 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
129139 ATCTAAATAA
129149 CAAAAATAACAACTAAAACAACAG
1 CAAAAATAACAACTAAAACAACAG
129173 CAAAAATAAC-ACTAAAACAACA
1 CAAAAATAACAACTAAAACAACA
129195 AAAACAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.67, C:0.22, G:0.02, T:0.09
Consensus pattern (24 bp):
CAAAAATAACAACTAAAACAACAG
Found at i:129196 original size:20 final size:20
Alignment explanation
Indices: 129130--129203 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 20
129120 TAAAAATACA
*
129130 AAAAATAACATCT-AAATAAC
1 AAAAATAACA-CTAAAACAAC
129150 AAAAATAACAACTAAAACAACAGC
1 AAAAATAAC-ACTAAAAC-A-A-C
129174 AAAAATAACACTAAAACAAC
1 AAAAATAACACTAAAACAAC
*
129194 AAAAACAACA
1 AAAAATAACA
129204 AAAATAGTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
20 21 0.45
21 5 0.11
22 2 0.04
23 9 0.19
24 10 0.21
ACGTcount: A:0.69, C:0.19, G:0.01, T:0.11
Consensus pattern (20 bp):
AAAAATAACACTAAAACAAC
Found at i:129245 original size:21 final size:21
Alignment explanation
Indices: 129191--129245 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
129181 ACACTAAAAC
* *
129191 AACAAAAACAACAAAAATAGT
1 AACAAAAGCAACAAAAATAAT
*
129212 AAAAAACAG-AACAAAAATAAT
1 AACAAA-AGCAACAAAAATAAT
*
129233 AGCAAAAGCAACA
1 AACAAAAGCAACA
129246 TCAAAACAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 2 0.07
21 24 0.89
22 1 0.04
ACGTcount: A:0.71, C:0.15, G:0.07, T:0.07
Consensus pattern (21 bp):
AACAAAAGCAACAAAAATAAT
Found at i:134541 original size:6 final size:6
Alignment explanation
Indices: 134530--134591 Score: 61
Period size: 6 Copynumber: 10.2 Consensus size: 6
134520 GAGAGAAAAG
* * * * *
134530 AAGGAA AAGGAA AAGGAA AAGGAA AATGGAG AGGGAG AAGGAG AAGGAG
1 AAGGAA AAGGAA AAGGAA AAGGAA AA-GGAA AAGGAA AAGGAA AAGGAA
*
134579 AAGGAG AAGGAA A
1 AAGGAA AAGGAA A
134592 GAAATATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
6 47 0.92
7 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.42, T:0.02
Consensus pattern (6 bp):
AAGGAA
Found at i:134547 original size:12 final size:12
Alignment explanation
Indices: 134530--134591 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
134520 GAGAGAAAAG
*
134530 AAGGAAAAGGAA
1 AAGGAGAAGGAA
*
134542 AAGGAAAAGGAA
1 AAGGAGAAGGAA
* *
134554 AATGGAGAGGGAG
1 AA-GGAGAAGGAA
*
134567 AAGGAGAAGGAG
1 AAGGAGAAGGAA
134579 AAGGAGAAGGAA
1 AAGGAGAAGGAA
134591 A
1 A
134592 GAAATATATA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
12 35 0.80
13 9 0.20
ACGTcount: A:0.56, C:0.00, G:0.42, T:0.02
Consensus pattern (12 bp):
AAGGAGAAGGAA
Found at i:138880 original size:24 final size:23
Alignment explanation
Indices: 138836--138886 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
138826 CATATTAGCA
*
138836 AACATTAAATAAATATATTCACG
1 AACATTAAATAAACATATTCACG
* * *
138859 AACATATAATTAAACATGTTCATG
1 AACAT-TAAATAAACATATTCACG
138883 AACA
1 AACA
138887 ATCTTCGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (23 bp):
AACATTAAATAAACATATTCACG
Found at i:140118 original size:14 final size:14
Alignment explanation
Indices: 140099--140183 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 14
140089 TTCAAAGTTG
*
140099 TTATTTTATCAATT
1 TTATTTTATAAATT
140113 TTATTTTGACTAAATTT
1 TTATTTT-A-TAAA-TT
* *
140130 GTTATTTTCTTAATT
1 -TTATTTTATAAATT
140145 TTATTTTAACTAAATTT
1 TTATTTT-A-TAAA-TT
* *
140162 GTTATTTTCTTAATT
1 -TTATTTTATAAATT
140177 TTATTTT
1 TTATTTT
140184 GACTGAAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.38
15 5 0.09
16 12 0.21
17 4 0.07
18 14 0.25
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.65
Consensus pattern (14 bp):
TTATTTTATAAATT
Found at i:140137 original size:32 final size:32
Alignment explanation
Indices: 140096--140203 Score: 155
Period size: 32 Copynumber: 3.3 Consensus size: 32
140086 TTATTCAAAG
*
140096 TTGTTATTTTATCAATTTTATTTTGACTAAAT
1 TTGTTATTTTATTAATTTTATTTTGACTAAAT
* *
140128 TTGTTATTTTCTTAATTTTATTTTAACTAAAT
1 TTGTTATTTTATTAATTTTATTTTGACTAAAT
*
140160 TTGTTATTTTCTTAATTTTATTTTGACTGAAAT
1 TTGTTATTTTATTAATTTTATTTTGACT-AAAT
140193 TAT-TTATTTTA
1 T-TGTTATTTTA
140204 AGTAAATAGG
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
32 56 0.81
33 12 0.17
34 1 0.01
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.62
Consensus pattern (32 bp):
TTGTTATTTTATTAATTTTATTTTGACTAAAT
Found at i:140144 original size:16 final size:16
Alignment explanation
Indices: 140125--140177 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
140115 ATTTTGACTA
140125 AATTTGTTATTTTCTT
1 AATTTGTTATTTTCTT
*
140141 AA-TT-TTATTTTAACTA
1 AATTTGTTATTTT--CTT
140157 AATTTGTTATTTTCTT
1 AATTTGTTATTTTCTT
140173 AATTT
1 AATTT
140178 TATTTTGACT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 7 0.23
15 2 0.06
16 13 0.42
17 2 0.06
18 7 0.23
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (16 bp):
AATTTGTTATTTTCTT
Found at i:147931 original size:16 final size:16
Alignment explanation
Indices: 147910--147944 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
147900 CCATTTATTA
147910 TATAAAAAAAAAAAAT
1 TATAAAAAAAAAAAAT
* *
147926 TATAAAAGAAAATAAT
1 TATAAAAAAAAAAAAT
147942 TAT
1 TAT
147945 TTGAAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
TATAAAAAAAAAAAAT
Found at i:154064 original size:5 final size:5
Alignment explanation
Indices: 154054--154084 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
154044 CACCATCCAC
154054 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
154085 TGACTTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:155117 original size:25 final size:23
Alignment explanation
Indices: 155089--155141 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
155079 TAGGGTTAGA
*
155089 GTTTTGGGTTCTTTTAAGGGTTTTT
1 GTTTTGGG--CTTGTAAGGGTTTTT
*
155114 GTTTAGGGCTTGTAAGGGTTTTT
1 GTTTTGGGCTTGTAAGGGTTTTT
*
155137 TTTTT
1 GTTTT
155142 TTTTTGAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 17 0.71
25 7 0.29
ACGTcount: A:0.09, C:0.04, G:0.28, T:0.58
Consensus pattern (23 bp):
GTTTTGGGCTTGTAAGGGTTTTT
Found at i:155351 original size:20 final size:20
Alignment explanation
Indices: 155326--155364 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
155316 TATTTTTAAA
155326 AATTTTTTGAAATTATTTTG
1 AATTTTTTGAAATTATTTTG
**
155346 AATTTTTTGTCATTATTTT
1 AATTTTTTGAAATTATTTT
155365 TAGATCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (20 bp):
AATTTTTTGAAATTATTTTG
Found at i:155881 original size:13 final size:13
Alignment explanation
Indices: 155865--155889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
155855 TTTTTGTGAT
155865 TGGTTTTCATGAC
1 TGGTTTTCATGAC
155878 TGGTTTTCATGA
1 TGGTTTTCATGA
155890 GCAGTGGGAA
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:0.16, C:0.12, G:0.24, T:0.48
Consensus pattern (13 bp):
TGGTTTTCATGAC
Found at i:157764 original size:56 final size:56
Alignment explanation
Indices: 157703--157812 Score: 141
Period size: 56 Copynumber: 2.0 Consensus size: 56
157693 TTGTACTTTG
* * * *
157703 AAAATGTCTAATATGATA-CATGAACTATTAATATATGTTTTGTTATGGTATTTGAT
1 AAAATGTCCAATATGATATC-CGAACTATTAATATATGTTTTATTACGGTATTTGAT
* * *
157759 AAAATGTCCAATGTGATATCCGAACTATTTATATGTGTTTTATTACGGTATTTG
1 AAAATGTCCAATATGATATCCGAACTATTAATATATGTTTTATTACGGTATTTG
157813 TTAACACCAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
56 45 0.98
57 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (56 bp):
AAAATGTCCAATATGATATCCGAACTATTAATATATGTTTTATTACGGTATTTGAT
Found at i:158700 original size:18 final size:19
Alignment explanation
Indices: 158677--158725 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
158667 TTCACATTTT
158677 AAATTTTAAATTAAAA-TG
1 AAATTTTAAATTAAAATTG
*
158695 AAATTTTTAAA--AAAATTT
1 AAA-TTTTAAATTAAAATTG
158713 AAATTTTAAATTA
1 AAATTTTAAATTA
158726 GTAAAGGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 11 0.42
18 7 0.27
19 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AAATTTTAAATTAAAATTG
Found at i:161614 original size:3 final size:3
Alignment explanation
Indices: 161606--161637 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
161596 AGTTTTTGTC
161606 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
161638 ATTGTTGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:162363 original size:8 final size:8
Alignment explanation
Indices: 162350--162374 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
162340 AATCCAAGAA
162350 TTTAAAAT
1 TTTAAAAT
162358 TTTAAAAT
1 TTTAAAAT
162366 TTTAAAAT
1 TTTAAAAT
162374 T
1 T
162375 CATGTTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTAAAAT
Found at i:165021 original size:18 final size:18
Alignment explanation
Indices: 164971--165024 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
164961 TGCTGGGGAA
164971 GGAGGAGGAAATGGTGGT
1 GGAGGAGGAAATGGTGGT
* ***
164989 GGAGGTGGTGGTGGTGGT
1 GGAGGAGGAAATGGTGGT
165007 GGAGGAGGAAATGGTGGT
1 GGAGGAGGAAATGGTGGT
165025 AGTTGCAGTC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.59, T:0.20
Consensus pattern (18 bp):
GGAGGAGGAAATGGTGGT
Found at i:165039 original size:36 final size:35
Alignment explanation
Indices: 164971--165041 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
164961 TGCTGGGGAA
*
164971 GGAGGAGGAAATGGTGGTGGAGGTGGTGGTGGTGGT
1 GGAGGAGGAAATGGTGGT-GAGGTGGTCGTGGTGGT
*
165007 GGAGGAGGAAATGGTGGT-AGTTGCAGTCGTGGTGG
1 GGAGGAGGAAATGGTGGTGAGGTG--GTCGTGGTGG
165042 AGGTGGCAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 4 0.13
36 27 0.87
ACGTcount: A:0.18, C:0.03, G:0.56, T:0.23
Consensus pattern (35 bp):
GGAGGAGGAAATGGTGGTGAGGTGGTCGTGGTGGT
Done.