Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013758.1 Kokia drynarioides strain JFW-HI SEQ_128786, 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: 85229
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:2002 original size:2 final size:2
Alignment explanation
Indices: 1997--2021 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1987 CACATGTATA
1997 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2022 ATAGTACCCG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:12584 original size:23 final size:23
Alignment explanation
Indices: 12558--12618 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
12548 ATAAAATCAG
12558 ATAAATTTAAATTTTT-TAAT-TAA
1 ATAAATTT-AATTTTTAT-ATGTAA
*
12581 ATAAATATAATTTTTATATGTAA
1 ATAAATTTAATTTTTATATGTAA
*
12604 ATATAATTTTATTTT
1 ATA-AATTTAATTTT
12619 AAATATGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 9 0.28
23 14 0.44
24 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
ATAAATTTAATTTTTATATGTAA
Found at i:16090 original size:17 final size:17
Alignment explanation
Indices: 16064--16102 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
16054 ACTTTACATG
*
16064 TAATATATAATATTTTAA
1 TAATAAATAAT-TTTTAA
16082 -AATAAATAATTTTTAA
1 TAATAAATAATTTTTAA
16098 TAATA
1 TAATA
16103 TATTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATAAATAATTTTTAA
Found at i:17722 original size:17 final size:17
Alignment explanation
Indices: 17692--17725 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17682 AATTTTATCA
**
17692 TTTAAATTTTTAAAAAT
1 TTTAAATTAATAAAAAT
17709 TTTAAATTAATAAAAAT
1 TTTAAATTAATAAAAAT
17726 AAAATTACAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATTAATAAAAAT
Found at i:18016 original size:28 final size:28
Alignment explanation
Indices: 17979--18032 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
17969 TAAATTAACT
* * *
17979 TTTTTTAATTAATTATGTAAATAATTCA
1 TTTTTTAATTAAATACGAAAATAATTCA
18007 TTTTTTAATTAAATACGAAAATAATT
1 TTTTTTAATTAAATACGAAAATAATT
18033 TAAAATTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (28 bp):
TTTTTTAATTAAATACGAAAATAATTCA
Found at i:18623 original size:6 final size:7
Alignment explanation
Indices: 18602--18626 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18592 TTTAAATATT
18602 AAATAAA
1 AAATAAA
18609 AAATAAA
1 AAATAAA
18616 AAATAAA
1 AAATAAA
18623 AAAT
1 AAAT
18627 TAATCGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:21235 original size:26 final size:25
Alignment explanation
Indices: 21198--21247 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
21188 ATAGAAATAT
* *
21198 TTATAAATTTAAAATTTTATAAAATC
1 TTATAAAATTAAAATGTT-TAAAATC
21224 TTATAAAATTAAAATGTTTAAAAT
1 TTATAAAATTAAAATGTTTAAAAT
21248 ATAGAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
TTATAAAATTAAAATGTTTAAAATC
Found at i:21630 original size:22 final size:22
Alignment explanation
Indices: 21604--21647 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
21594 AAGCACCCTT
21604 TATATTAAGATAGTTACAACTA
1 TATATTAAGATAGTTACAACTA
21626 TATATTAAGATAGTTACAACTA
1 TATATTAAGATAGTTACAACTA
21648 AAATAATAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (22 bp):
TATATTAAGATAGTTACAACTA
Found at i:25019 original size:20 final size:20
Alignment explanation
Indices: 24974--25019 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
24964 ATAAGACTTT
* * *
24974 TATTAAATAAATTTATATAT
1 TATTAAATAAATATAAATAA
24994 TATTAAATAAATATAAATAA
1 TATTAAATAAATATAAATAA
*
25014 TCTTAA
1 TATTAA
25020 TCTTTAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TATTAAATAAATATAAATAA
Found at i:41720 original size:37 final size:37
Alignment explanation
Indices: 41679--41750 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
41669 AAGATTATTA
*
41679 GGAGAAAGTAGAAATCTGTGGAAATACCTGTGGATTT
1 GGAGAAAGTAGAAATCCGTGGAAATACCTGTGGATTT
*
41716 GGAGAAAGTAGAAATCCGTGGAAATACTTGTGGAT
1 GGAGAAAGTAGAAATCCGTGGAAATACCTGTGGAT
41751 ATTTTCGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.36, C:0.08, G:0.31, T:0.25
Consensus pattern (37 bp):
GGAGAAAGTAGAAATCCGTGGAAATACCTGTGGATTT
Found at i:42337 original size:17 final size:17
Alignment explanation
Indices: 42317--42349 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42307 CTTATACAAA
42317 ATTTGTTATT-ATATTTT
1 ATTT-TTATTGATATTTT
42334 ATTTTTATTGATATTT
1 ATTTTTATTGATATTT
42350 ACCGTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (17 bp):
ATTTTTATTGATATTTT
Found at i:45585 original size:13 final size:13
Alignment explanation
Indices: 45569--45598 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
45559 GTTAGCCTTT
45569 ATTGACTCACTGC
1 ATTGACTCACTGC
45582 ATTGACTCACTGC
1 ATTGACTCACTGC
45595 ATTG
1 ATTG
45599 CTGATTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (13 bp):
ATTGACTCACTGC
Found at i:45860 original size:27 final size:26
Alignment explanation
Indices: 45817--45868 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
45807 GACTCAAAAT
45817 ATTTTTTTTAAAATTTTTAA-AGGTCA
1 ATTTTTTTTAAAA-TTTTAAGAGGTCA
* *
45843 ATTTTTTTATCAACTTTTAAGAGGTC
1 ATTTTTTT-TAAAATTTTAAGAGGTC
45869 TAAAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.52
Consensus pattern (26 bp):
ATTTTTTTTAAAATTTTAAGAGGTCA
Found at i:46786 original size:19 final size:18
Alignment explanation
Indices: 46741--46786 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
46731 TCATTGATGT
46741 ATATG-TATAAACTATTA
1 ATATGATATAAACTATTA
*
46758 ATAT-ATTATAAACTATATG
1 ATATGA-TATAAACTAT-TA
46777 ATATGATATA
1 ATATGATATA
46787 GCATTGTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 4 0.17
18 10 0.42
19 9 0.38
20 1 0.04
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (18 bp):
ATATGATATAAACTATTA
Found at i:49010 original size:29 final size:27
Alignment explanation
Indices: 48970--49023 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
48960 AATAGAGTAA
*
48970 AAAATGTGATTTTTGGATGCTCGGGGGT
1 AAAATGT-AATTTTGGATGCTCGGGGGT
*
48998 AAAATGGTAATTTTGGATGCTTGGGG
1 AAAAT-GTAATTTTGGATGCTCGGGG
49024 AACAAAACGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.24, C:0.06, G:0.35, T:0.35
Consensus pattern (27 bp):
AAAATGTAATTTTGGATGCTCGGGGGT
Found at i:49030 original size:29 final size:28
Alignment explanation
Indices: 48980--49040 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
48970 AAAATGTGAT
** *
48980 TTTTGGATGCTCGGGGGTAAAATGGTAA
1 TTTTGGATGCTCGGGGACAAAACGGTAA
*
49008 TTTTGGATGCTTGGGGAACAAAACGGTAA
1 TTTTGGATGCTCGGGG-ACAAAACGGTAA
49037 TTTT
1 TTTT
49041 CGAAAGGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.26, C:0.08, G:0.31, T:0.34
Consensus pattern (28 bp):
TTTTGGATGCTCGGGGACAAAACGGTAA
Found at i:49085 original size:30 final size:30
Alignment explanation
Indices: 49051--49136 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
49041 CGAAAGGTTC
49051 GAGGTTAAAAATGGAATTTTTAGACATCCG
1 GAGGTTAAAAATGGAATTTTTAGACATCCG
* *
49081 GAGG-T-AAAATGGTAATTTTTGGA-AGGTTCG
1 GAGGTTAAAAATGG-AATTTTTAGACA--TCCG
* *
49111 G-GGTAAAAAATGGCATTTTTAGACAT
1 GAGGTTAAAAATGGAATTTTTAGACAT
49137 TCGGGGTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
28 8 0.18
29 13 0.29
30 16 0.36
31 8 0.18
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (30 bp):
GAGGTTAAAAATGGAATTTTTAGACATCCG
Found at i:49095 original size:59 final size:59
Alignment explanation
Indices: 49027--49480 Score: 399
Period size: 59 Copynumber: 7.7 Consensus size: 59
49017 CTTGGGGAAC
* * *
49027 AAAACGGTAATTTTCGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGGAGGT
1 AAAATGGTAATTTTTGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATTCGGAGGT
* * * *
49086 AAAATGGTAATTTTTGGAAGGTTCGGGGTAAAAAATGGCATTTTTAGACATTCGG-GGT
1 AAAATGGTAATTTTTGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATTCGGAGGT
* * * * * *
49144 AAAATGATAATTTTTGTAAGGTTCGAGATTAAAAAAGGAATTTTTAGATATTCGGGGGT
1 AAAATGGTAATTTTTGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATTCGGAGGT
* * *
49203 AAAATGGTAA-TTTTGGAAGGATTC-AGGGTTACAAAAT-GAATTTTTAGACATCCGGGGGT
1 AAAATGGTAATTTTTGAAAGG-TTCGA-GGTTA-AAAATGGAATTTTTAGACATTCGGAGGT
* * * * * *
49262 AAAATGTTAATTTTTGGAAA-GTTTGAGGTTAAAAATGAAATTTTTGGATATT-TGAGGT
1 AAAATGGTAATTTTT-GAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATTCGGAGGT
** * * * * * *
49320 AAAATGGTAATTTTCAAAAGTTTCGGGGTTGAAAATGAAAATTTTAGATATTC-GAGGGT
1 AAAATGGTAATTTTTGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATTCGGA-GGT
* * * * * *
49379 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAAT-GAA-ATTTGGAAAGTT-TGAGGGT
1 AAAATGGTAATTTTTGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACA-TTCGGA-GGT
* * * *
49437 AAAAAT-GTAATTTTGGAAAAGTTCGGGGTCAAAAATGGAATTTT
1 -AAAATGGTAATTTTTGAAAGGTTCGAGGTTAAAAATGGAATTTT
49481 GGAAAAGTTC
Statistics
Matches: 324, Mismatches: 55, Indels: 31
0.79 0.13 0.08
Matches are distributed among these distances:
57 9 0.03
58 146 0.45
59 154 0.48
60 12 0.04
61 3 0.01
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATTCGGAGGT
Found at i:49098 original size:29 final size:27
Alignment explanation
Indices: 49058--49393 Score: 108
Period size: 29 Copynumber: 11.5 Consensus size: 27
49048 TTCGAGGTTA
*
49058 AAAATGGAATTTTTAGACATCCGGAGGT
1 AAAATGGAATTTTTAGACATTCGG-GGT
*
49086 AAAATGGTAATTTTTGGA-AGGTTCGGGGT
1 AAAATGG-AATTTTTAGACA--TTCGGGGT
*
49115 AAAAAATGGCATTTTTAGACATTCGGGGT
1 --AAAATGGAATTTTTAGACATTCGGGGT
* **
49144 AAAATGATAATTTTT-GTA-AGGTTCGAGATT
1 AAAATG-GAATTTTTAG-ACA--TTCG-GGGT
* *
49174 AAAAAAGGAATTTTTAGATATTCGGGGGT
1 -AAAATGGAATTTTTAGACATTC-GGGGT
* * *
49203 AAAATGGTAA-TTTTGGAAGGATTCAGGGTT
1 AAAATGG-AATTTTTAG-A-CATTC-GGGGT
*
49233 ACAAAAT-GAATTTTTAGACATCCGGGGGT
1 --AAAATGGAATTTTTAGACATTC-GGGGT
* * * * *
49262 AAAATGTTAATTTTTGGAAAGTTTGAGGTT
1 AAAATG-GAATTTTTAGACA-TTCG-GGGT
* * * * *
49292 AAAAATGAAATTTTTGGATATTTGAGGT
1 -AAAATGGAATTTTTAGACATTCGGGGT
* *
49320 AAAATGGTAATTTTCA-AAAGTTTCGGGGTT
1 AAAATGG-AATTTTTAGACA--TTCGGGG-T
* * *
49350 GAAAATGAAAATTTTAGATATTCGAGGGT
1 -AAAATGGAATTTTTAGACATTCG-GGGT
49379 AAAATGGTAATTTTT
1 AAAATGG-AATTTTT
49394 GGAAGGTTCG
Statistics
Matches: 230, Mismatches: 44, Indels: 67
0.67 0.13 0.20
Matches are distributed among these distances:
27 21 0.09
28 40 0.17
29 70 0.30
30 59 0.26
31 35 0.15
32 5 0.02
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (27 bp):
AAAATGGAATTTTTAGACATTCGGGGT
Found at i:49166 original size:117 final size:116
Alignment explanation
Indices: 49034--49480 Score: 438
Period size: 117 Copynumber: 3.8 Consensus size: 116
49024 AACAAAACGG
* * * *
49034 TAATTTTCGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGGAGGTAAAATGGTAATTT
1 TAATTTTTGGAAGGTTCGAGGTTAAAAATGAAATTTTTAGATAT-CGGAGGTAAAATGGTAATTT
*
49099 TTGGAAGGTTCGGGGTAAAAAATGGCATTTTTAGACATTCGGGGTAAAATGA
65 TTGGAAGGTTCGGGGTAAAAAATGGAATTTTTAGACATTCGGGGTAAAATGA
* * * * *
49151 TAATTTTTGTAAGGTTCGAGATTAAAAAAGGAATTTTTAGATATTCGGGGGTAAAATGGTAA-TT
1 TAATTTTTGGAAGGTTCGAGGTTAAAAATGAAATTTTTAGATA-TCGGAGGTAAAATGGTAATTT
* * * *
49215 TTGGAAGGATTCAGGGTTACAAAAT-GAATTTTTAGACATCCGGGGGTAAAATGT
65 TTGGAAGG-TTC-GGGGTAAAAAATGGAATTTTTAGACATTC-GGGGTAAAATGA
* * * **
49269 TAATTTTTGGAAAGTTTGAGGTTAAAAATGAAATTTTTGGATATTTGAGGTAAAATGGTAATTTT
1 TAATTTTTGGAAGGTTCGAGGTTAAAAATGAAATTTTTAGATATCGGAGGTAAAATGGTAATTTT
*** * ** * * * *
49334 CAAAAGTTTCGGGGTTGAAAATGAAAATTTTAGATATTCGAGGGTAAAATGG
66 TGGAAGGTTCGGGGTAAAAAATGGAATTTTTAGACATTCG-GGGTAAAATGA
* * * **
49386 TAATTTTTGGAAGGTTCGAGGTCAAAAATGAAA--TTTGGAAAGTTTGAGGGTAAAAAT-GTAA-
1 TAATTTTTGGAAGGTTCGAGGTTAAAAATGAAATTTTTAGATA-TCGGA-GGT-AAAATGGTAAT
* *
49447 TTTTGGAAAAGTTCGGGGTCAAAAATGGAATTTT
63 TTTTGG-AAGGTTCGGGGTAAAAAATGGAATTTT
49481 GGAAAAGTTC
Statistics
Matches: 273, Mismatches: 46, Indels: 22
0.80 0.13 0.06
Matches are distributed among these distances:
115 7 0.03
116 28 0.10
117 169 0.62
118 69 0.25
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.34
Consensus pattern (116 bp):
TAATTTTTGGAAGGTTCGAGGTTAAAAATGAAATTTTTAGATATCGGAGGTAAAATGGTAATTTT
TGGAAGGTTCGGGGTAAAAAATGGAATTTTTAGACATTCGGGGTAAAATGA
Found at i:49333 original size:176 final size:175
Alignment explanation
Indices: 49027--49421 Score: 479
Period size: 176 Copynumber: 2.2 Consensus size: 175
49017 CTTGGGGAAC
* *
49027 AAAACGGTAATTTTCGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGGAGGTAAAATG
1 AAAATGGTAATTTT-GGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGGAGGTAAAATG
* * ** *
49092 GTAATTTTTGGAAGGTTCGGGGTAAAAAATGGCATTTTTAGACATTCGGGGTAAAATGATAATTT
65 GTAATTTTTGGAAAGTTCGAGGTAAAAAATGAAATTTTTAGACATTCGAGGTAAAATGATAATTT
*** * * *
49157 TTGTAAGGTTCGAGATTAAAAAAGGAATTTTTAGATATTCGGGGGT
130 TCAAAAGGTTCGAGATTAAAAAAGAAAATTTTAGATATTCGAGGGT
*
49203 AAAATGGTAATTTTGGAAGGATTC-AGGGTTACAAAAT-GAATTTTTAGACATCCGGGGGTAAAA
1 AAAATGGTAATTTTGGAAGG-TTCGA-GGTTA-AAAATGGAATTTTTAGACATCCGGAGGTAAAA
* * * * * * *
49266 TGTTAATTTTTGGAAAGTTTGAGGTTAAAAATGAAATTTTTGGATATTTGAGGTAAAATGGTAAT
63 TGGTAATTTTTGGAAAGTTCGAGGTAAAAAATGAAATTTTTAGACATTCGAGGTAAAATGATAAT
* * * * *
49331 TTTCAAAAGTTTCGGGGTTGAAAATGAAAATTTTAGATATTCGAGGGT
128 TTTCAAAAGGTTCGAGATTAAAAAAGAAAATTTTAGATATTCGAGGGT
* *
49379 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGAAATTT
1 AAAATGGTAA-TTTTGGAAGGTTCGAGGTTAAAAATGGAATTT
49422 GGAAAGTTTG
Statistics
Matches: 185, Mismatches: 28, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
175 11 0.06
176 158 0.85
177 16 0.09
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.34
Consensus pattern (175 bp):
AAAATGGTAATTTTGGAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATCCGGAGGTAAAATGG
TAATTTTTGGAAAGTTCGAGGTAAAAAATGAAATTTTTAGACATTCGAGGTAAAATGATAATTTT
CAAAAGGTTCGAGATTAAAAAAGAAAATTTTAGATATTCGAGGGT
Found at i:49434 original size:28 final size:28
Alignment explanation
Indices: 49390--49509 Score: 125
Period size: 30 Copynumber: 4.1 Consensus size: 28
49380 AAATGGTAAT
*
49390 TTTTGGAAGGTTCGAGGTCAAAAATGAA
1 TTTTGGAAAGTTCGAGGTCAAAAATGAA
* *
49418 ATTTGGAAAGTTTGAGGGT-AAAAATGTAA
1 TTTTGGAAAGTTCGA-GGTCAAAAATG-AA
*
49447 TTTTGGAAAAGTTCGGGGTCAAAAATGGAA
1 TTTTGG-AAAGTTCGAGGTCAAAAAT-GAA
*
49477 TTTTGGAAAAGTTCAAGGGTCAAAATATGAA
1 TTTTGG-AAAGTTCGA-GGTCAAAA-ATGAA
49508 TT
1 TT
49510 GGATAGTTTA
Statistics
Matches: 77, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
28 19 0.25
29 13 0.17
30 29 0.38
31 14 0.18
32 2 0.03
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.30
Consensus pattern (28 bp):
TTTTGGAAAGTTCGAGGTCAAAAATGAA
Found at i:49448 original size:58 final size:58
Alignment explanation
Indices: 49083--49485 Score: 273
Period size: 58 Copynumber: 6.9 Consensus size: 58
49073 GACATCCGGA
* * * * * * * *
49083 GGTAAAATGGTAATTTTTGGAAGGTTCGGGGTAAAAAATGGCATTTTTAGACATTCG-G
1 GGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAAT-GAAATTTTGGAAATTTGAG
* * * * * * * * * * *
49141 GGTAAAATGATAATTTTTGTAAGGTTCGAGATTAAAAAAGGAATTTTTAGATATTCGGG
1 GGTAAAATGGTAATTTTTGGAAAGTTCGAG-GTCAAAAATGAAATTTTGGAAATTTGAG
* * * * * ** *
49200 GGTAAAATGGTAA-TTTTGGAAGGATTC-AGGGTTACAAAATGAATTTTTAGACATCCGGG
1 GGTAAAATGGTAATTTTTGGAAAG-TTCGA-GGTCA-AAAATGAAATTTTGGAAATTTGAG
* * * *
49259 GGTAAAATGTTAATTTTTGGAAAGTTTGAGGTTAAAAATGAAATTTTTGGATATTTGA-
1 GGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAATGAAA-TTTTGGAAATTTGAG
** * ** * * *
49317 GGTAAAATGGTAA-TTTTCAAAAGTTTCGGGGTTGAAAATGAAAATTTTAGATATTCGAG
1 GGTAAAATGGTAATTTTTGGAAAG-TTCGAGGTCAAAAATG-AAATTTTGGAAATTTGAG
*
49376 GGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGAAA-TTTGGAAAGTTTGAG
1 GGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAATGAAATTTTGGAAA-TTTGAG
* *
49434 GGTAAAAAT-GTAA-TTTTGGAAAAGTTCGGGGTCAAAAATGGAATTTTGGAAA
1 GGT-AAAATGGTAATTTTTGG-AAAGTTCGAGGTCAAAAATGAAATTTTGGAAA
49486 AGTTCAAGGG
Statistics
Matches: 286, Mismatches: 43, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
57 20 0.07
58 134 0.47
59 115 0.40
60 17 0.06
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.33
Consensus pattern (58 bp):
GGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAATGAAATTTTGGAAATTTGAG
Found at i:54777 original size:17 final size:17
Alignment explanation
Indices: 54755--54828 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 17
54745 AACCTTTGAT
* *
54755 TAAATTTTAATTTAAAA
1 TAAATTTAAACTTAAAA
*
54772 TAAATTTAAACTCAAAA
1 TAAATTTAAACTTAAAA
* * *
54789 TAAGTATAAATTTAAAA
1 TAAATTTAAACTTAAAA
*
54806 TAAATTTAAACTTACAA
1 TAAATTTAAACTTAAAA
54823 TAAATT
1 TAAATT
54829 AAAATCCAAA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:54779 original size:11 final size:11
Alignment explanation
Indices: 54763--54815 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
54753 ATTAAATTTT
54763 AATTTAAAATA
1 AATTTAAAATA
*
54774 AATTTAAACTCA
1 AATTTAAAAT-A
* *
54786 AA-ATAAGTATA
1 AATTTAA-AATA
54797 AATTTAAAATA
1 AATTTAAAATA
54808 AATTTAAA
1 AATTTAAA
54816 CTTACAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
11 26 0.79
12 7 0.21
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (11 bp):
AATTTAAAATA
Found at i:54840 original size:34 final size:34
Alignment explanation
Indices: 54768--54840 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
54758 ATTTTAATTT
**
54768 AAAATAAATTTAAACTCAAAATAAGTATAAATTT
1 AAAATAAATTTAAACTCAAAATAAGTATAAATCC
* * *
54802 AAAATAAATTTAAACTTACAATAAAT-TAAAATCC
1 AAAATAAATTTAAACTCAAAATAAGTAT-AAATCC
54836 AAAAT
1 AAAAT
54841 TAGGTTCCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 1 0.03
34 32 0.97
ACGTcount: A:0.60, C:0.08, G:0.01, T:0.30
Consensus pattern (34 bp):
AAAATAAATTTAAACTCAAAATAAGTATAAATCC
Found at i:56923 original size:18 final size:18
Alignment explanation
Indices: 56900--56942 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
56890 CCGATCTCCG
56900 ATCGACCTAGATCGATTA
1 ATCGACCTAGATCGATTA
56918 ATCGACCTAGATCGATTA
1 ATCGACCTAGATCGATTA
56936 ATCGACC
1 ATCGACC
56943 GATTATCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (18 bp):
ATCGACCTAGATCGATTA
Found at i:57144 original size:16 final size:17
Alignment explanation
Indices: 57113--57149 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
57103 ACAATAATTA
*
57113 ATATATAATGTATTATT
1 ATATATAATCTATTATT
57130 ATATATAA-CTATTATT
1 ATATATAATCTATTATT
57146 ATAT
1 ATAT
57150 TATAGATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
ATATATAATCTATTATT
Found at i:57399 original size:18 final size:20
Alignment explanation
Indices: 57360--57406 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
57350 AGTTAATAGT
57360 TTATATATAATATACTACTA
1 TTATATATAATATACTACTA
*
57380 TTATATATAAT-TATTA-TA
1 TTATATATAATATACTACTA
57398 TTATA-ATAA
1 TTATATATAA
57407 AAATAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 7 0.27
19 4 0.15
20 11 0.42
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATATATAATATACTACTA
Found at i:57634 original size:13 final size:13
Alignment explanation
Indices: 57616--57650 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
57606 TTAATATATA
57616 ATATATTACTATT
1 ATATATTACTATT
*
57629 ATATATAACTATT
1 ATATATTACTATT
57642 ATTATATTA
1 A-TATATTA
57651 TAGGTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATATTACTATT
Found at i:58491 original size:15 final size:14
Alignment explanation
Indices: 58470--58513 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
58460 GTAAATTATT
58470 AAAATTTAAAATTA
1 AAAATTTAAAATTA
*
58484 AAATATTTATAATTTA
1 AAA-ATTTA-AAATTA
*
58500 AAAACTTAAAATTA
1 AAAATTTAAAATTA
58514 TTTAAATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 8 0.32
15 9 0.36
16 8 0.32
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAATTTAAAATTA
Found at i:58497 original size:22 final size:21
Alignment explanation
Indices: 58455--58521 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
58445 TAAAATAAAA
* * *
58455 TAAAAGTAAATTATTAAAATT
1 TAAAATTAAAATATTTAAATT
58476 TAAAATTAAAATATTTATAATT
1 TAAAATTAAAATATTTA-AATT
58498 TAAAAACTTAAAATTATTTAAATT
1 T-AAAA-TTAAAA-TATTTAAATT
58522 CATCAAAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
21 14 0.36
22 5 0.13
23 4 0.10
24 10 0.26
25 6 0.15
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (21 bp):
TAAAATTAAAATATTTAAATT
Found at i:58521 original size:24 final size:22
Alignment explanation
Indices: 58462--58521 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 22
58452 AAATAAAAGT
*
58462 AAATTATTAAAATTTAAAATTA
1 AAATTATTTAAATTTAAAATTA
58484 AAA-TATTTATAATTTAAAAACTTA
1 AAATTATTTA-AATTT-AAAA-TTA
58508 AAATTATTTAAATT
1 AAATTATTTAAATT
58522 CATCAAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.15
22 8 0.24
23 4 0.12
24 10 0.30
25 6 0.18
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATTATTTAAATTTAAAATTA
Found at i:58725 original size:15 final size:16
Alignment explanation
Indices: 58705--58743 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
58695 TGTGTCTCTA
58705 TCTTCG-ATTCTGTCG
1 TCTTCGAATTCTGTCG
58720 TCTTCGTCAATTCTGTCG
1 TCTTCG--AATTCTGTCG
58738 TCTTCG
1 TCTTCG
58744 TCATTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
18 15 0.71
ACGTcount: A:0.08, C:0.28, G:0.18, T:0.46
Consensus pattern (16 bp):
TCTTCGAATTCTGTCG
Found at i:58732 original size:18 final size:18
Alignment explanation
Indices: 58711--58746 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
58701 TCTATCTTCG
58711 ATTCTGTCGTCTTCGTCA
1 ATTCTGTCGTCTTCGTCA
58729 ATTCTGTCGTCTTCGTCA
1 ATTCTGTCGTCTTCGTCA
58747 TTCATTCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.28, G:0.17, T:0.44
Consensus pattern (18 bp):
ATTCTGTCGTCTTCGTCA
Found at i:60188 original size:25 final size:25
Alignment explanation
Indices: 60154--60204 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
60144 GATAGATAAG
*
60154 CCAAAAAAGCATTAGGTGTATTGAC
1 CCAAAAAAGCATTAGATGTATTGAC
60179 CCAAAAAAGCATTAGATGTATTGAC
1 CCAAAAAAGCATTAGATGTATTGAC
60204 C
1 C
60205 TATGAATTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (25 bp):
CCAAAAAAGCATTAGATGTATTGAC
Found at i:68332 original size:13 final size:13
Alignment explanation
Indices: 68314--68338 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
68304 GCTGTGTTTG
68314 TTTTTTATTTTTA
1 TTTTTTATTTTTA
68327 TTTTTTATTTTT
1 TTTTTTATTTTT
68339 TGTGTGTGTT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:68622 original size:29 final size:30
Alignment explanation
Indices: 68592--68664 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
68582 TTTGATATAT
68592 AAATTTTAATTTCGTGTAATTATATACATA
1 AAATTTTAATTTCGTGTAATTATATACATA
* * * * * *
68622 AAATTTGAATAATGGTGCAAATATATACATG
1 AAATTTTAAT-TTCGTGTAATTATATACATA
*
68653 AAACTTTAATTT
1 AAATTTTAATTT
68665 TGATTTAATT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
30 10 0.30
31 23 0.70
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (30 bp):
AAATTTTAATTTCGTGTAATTATATACATA
Found at i:69027 original size:14 final size:15
Alignment explanation
Indices: 69010--69038 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
69000 TTAGTTCAAA
69010 AATTTT-TATTTTTG
1 AATTTTATATTTTTG
69024 AATTTTATATTTTTG
1 AATTTTATATTTTTG
69039 TTTAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (15 bp):
AATTTTATATTTTTG
Found at i:69723 original size:25 final size:25
Alignment explanation
Indices: 69681--69728 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
69671 GAGTTCAGTC
*
69681 TTTGAATTTGTGATACTT-AAATTT
1 TTTGAATTAGTGATACTTGAAATTT
69705 TTTGAATTAGTTGATACTTGAAAT
1 TTTGAATTAG-TGATACTTGAAAT
69729 CAATAGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 8 0.38
26 4 0.19
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (25 bp):
TTTGAATTAGTGATACTTGAAATTT
Found at i:73877 original size:17 final size:17
Alignment explanation
Indices: 73847--73905 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
73837 CCTTTAAATG
*
73847 ATTTTTATTATTTTTTTA
1 ATTTTTAAT-TTTTTTTA
*
73865 ATTTTTAATTTTTGTTA
1 ATTTTTAATTTTTTTTA
* *
73882 ATTTTGAATTTTATTTA
1 ATTTTTAATTTTTTTTA
73899 ATATTTT
1 AT-TTTT
73906 TATAATTTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 23 0.68
18 11 0.32
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTTTAATTTTTTTTA
Found at i:73979 original size:21 final size:25
Alignment explanation
Indices: 73929--73979 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 25
73919 AATGTTCTAC
73929 AAATTTATAAAATGTTTTTTAAAAT
1 AAATTTATAAAATGTTTTTTAAAAT
*
73954 TAATTT-T-AAAT-TTTTTTAAAA-
1 AAATTTATAAAATGTTTTTTAAAAT
73975 AAATT
1 AAATT
73980 AATCTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 4 0.17
22 10 0.42
23 4 0.17
24 1 0.04
25 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
AAATTTATAAAATGTTTTTTAAAAT
Found at i:74089 original size:24 final size:23
Alignment explanation
Indices: 74053--74099 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
74043 ATTTTTTAAC
*
74053 TTTTTTAGAGAAAATATTTCTAT
1 TTTTTTAGAGAAAAGATTTCTAT
*
74076 TTTTCTTAGAGAAAAGCTTTCTAT
1 TTTT-TTAGAGAAAAGATTTCTAT
74100 CATAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.49
Consensus pattern (23 bp):
TTTTTTAGAGAAAAGATTTCTAT
Found at i:76200 original size:91 final size:91
Alignment explanation
Indices: 76059--76269 Score: 282
Period size: 91 Copynumber: 2.3 Consensus size: 91
76049 GGGTATCCAT
* * * * * * * *
76059 ACTTTTATAAAATGTCTAATGTGGTACTTGTGCTTTAAAAATGTCCAATGTGATTCCTGAATTAT
1 ACTTTCATAAAATGTCCAATGTGGTACTTATACTTTAAAAACGTCCAATGTGATACATGAACTAT
*
76124 CGATTTGTGTATTATTTGG-TACTTGC
66 CAATTTGTGTATTA-TTGGATACTTGC
* *
76150 ACTTTCATAAAATGTCCAATGCGGTA-TCTATACTTTGAAAACGTCCAATGTGATACATGAACTA
1 ACTTTCATAAAATGTCCAATGTGGTACT-TATACTTTAAAAACGTCCAATGTGATACATGAACTA
*
76214 TCAATTTGTGTATTATTGGATACTTGT
65 TCAATTTGTGTATTATTGGATACTTGC
76241 ACTTTCATAAAATGTCCAATGTGGTACTT
1 ACTTTCATAAAATGTCCAATGTGGTACTT
76270 GAACTATCAA
Statistics
Matches: 104, Mismatches: 13, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
90 5 0.05
91 98 0.94
92 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (91 bp):
ACTTTCATAAAATGTCCAATGTGGTACTTATACTTTAAAAACGTCCAATGTGATACATGAACTAT
CAATTTGTGTATTATTGGATACTTGC
Found at i:78326 original size:19 final size:19
Alignment explanation
Indices: 78288--78341 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
78278 TATATATATT
78288 AAAAAATTATAAAAATGTA
1 AAAAAATTATAAAAATGTA
* *
78307 AAGAAA-TATAAAATTCGTA
1 AAAAAATTATAAAAAT-GTA
78326 AAAAAATTATAAAAAT
1 AAAAAATTATAAAAAT
78342 ATAGTATCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 8 0.28
19 13 0.45
20 8 0.28
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.26
Consensus pattern (19 bp):
AAAAAATTATAAAAATGTA
Found at i:78344 original size:8 final size:9
Alignment explanation
Indices: 78234--78341 Score: 53
Period size: 9 Copynumber: 11.9 Consensus size: 9
78224 AGATAAAAAA
*
78234 ATAAAAATG
1 ATAAAAATT
*
78243 AGTAAAAGTT
1 A-TAAAAATT
*
78253 ATAAAAGTT
1 ATAAAAATT
*
78262 AT-TAAATT
1 ATAAAAATT
* *
78270 TTAAAAAAT
1 ATAAAAATT
* *
78279 ATATATATT
1 ATAAAAATT
78288 A-AAAAATT
1 ATAAAAATT
78296 ATAAAAATGT
1 ATAAAAAT-T
78306 A-AAGAAA-T
1 ATAA-AAATT
*
78314 ATAAAATTCGT
1 ATAAAAAT--T
*
78325 AAAAAAATT
1 ATAAAAATT
78334 ATAAAAAT
1 ATAAAAAT
78342 ATAGTATCAA
Statistics
Matches: 73, Mismatches: 17, Indels: 18
0.68 0.16 0.17
Matches are distributed among these distances:
8 15 0.21
9 39 0.53
10 12 0.16
11 7 0.10
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:78554 original size:39 final size:39
Alignment explanation
Indices: 78511--78599 Score: 92
Period size: 39 Copynumber: 2.3 Consensus size: 39
78501 TTTTTATGCA
* * *
78511 TTTTATAATTTATTATGATT-TTTATAAAATTTTACAAT-T
1 TTTTATAATTTATTATAATTATTAATAAAA-ATTA-AATAT
* * *
78550 TTTTACAATTTTTTCTAATTATTAATAAAAATTAAATAT
1 TTTTATAATTTATTATAATTATTAATAAAAATTAAATAT
78589 TTTTATAATTT
1 TTTTATAATTT
78600 TTTTTATTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
38 3 0.07
39 30 0.73
40 8 0.20
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (39 bp):
TTTTATAATTTATTATAATTATTAATAAAAATTAAATAT
Found at i:78624 original size:28 final size:27
Alignment explanation
Indices: 78583--78635 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
78573 AATAAAAATT
* **
78583 AAATATTTTTATAATTTTTTTTATTAA
1 AAATATTGTTATAATGATTTTTATTAA
78610 AAATCATTGTTATAATGATTTTTATT
1 AAAT-ATTGTTATAATGATTTTTATT
78636 TTTTTATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (27 bp):
AAATATTGTTATAATGATTTTTATTAA
Found at i:78959 original size:84 final size:83
Alignment explanation
Indices: 78810--78968 Score: 194
Period size: 84 Copynumber: 1.9 Consensus size: 83
78800 GAGTGAGGGA
** * * * * * *
78810 CTTAATTTTTTTTTTGAAAAAGTTTGAGGATCTTTTTGATGCATTTTGAAAGTTTAAATGCTCAA
1 CTTAATTGCTTTTTTGAAAAAGTTTAAAGATCTTTTTGATGCATTTTAAAAATTCAAATACTCAA
78875 TTGAGTGAAAAAAAATGAG
66 TTGAGT-AAAAAAAATGAG
* * *
78894 CTTAATTGCTTTTTTGAAAAATTTTAAAGA-CTTTTTCGATGCATTTTAAAAATTCAAGTATTCA
1 CTTAATTGCTTTTTTGAAAAAGTTTAAAGATCTTTTT-GATGCATTTTAAAAATTCAAATACTCA
78958 ATTGAGTAAAA
65 ATTGAGTAAAA
78969 GAAAGCAAAG
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
83 10 0.16
84 53 0.84
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (83 bp):
CTTAATTGCTTTTTTGAAAAAGTTTAAAGATCTTTTTGATGCATTTTAAAAATTCAAATACTCAA
TTGAGTAAAAAAAATGAG
Found at i:83585 original size:30 final size:30
Alignment explanation
Indices: 83549--83630 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
83539 ATTTTTTTAG
* *
83549 TTTAATTTGATATTTAAATTTGACA-TATTT
1 TTTAATTTGATATTTAAACTTAACACT-TTT
* *
83579 TTTAATTTGGTATATAAACTTAACACTTTT
1 TTTAATTTGATATTTAAACTTAACACTTTT
* *
83609 TTTAAAGTTGATACTTAAACTT
1 TTT-AATTTGATATTTAAACTT
83631 TTTGGGGTCT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 27 0.64
31 15 0.36
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (30 bp):
TTTAATTTGATATTTAAACTTAACACTTTT
Found at i:84903 original size:3 final size:3
Alignment explanation
Indices: 84897--84927 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
84887 TTTTTATATG
84897 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
84928 TTCTTCTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Done.