Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010246.1 Kokia drynarioides strain JFW-HI SEQ_125078, 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: 140684
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 268 characters in sequence are not A, C, G, or T
Found at i:1243 original size:29 final size:29
Alignment explanation
Indices: 1183--1279 Score: 113
Period size: 30 Copynumber: 3.3 Consensus size: 29
1173 TCCGTTTACT
* ** * *
1183 TTTTAAATTTAATTTGTAATTTTGTTTTTA
1 TTTT-AATTTAATTTCTAATTTCCTGTATA
1213 TTTTAATTTAATTTCTAATTTCCTGTATA
1 TTTTAATTTAATTTCTAATTTCCTGTATA
*
1242 TTTTAATTTTATTTTCTAATTTCCTGTATA
1 TTTTAA-TTTAATTTCTAATTTCCTGTATA
*
1272 TTCTAATT
1 TTTTAATT
1280 ATTATTTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
29 28 0.47
30 31 0.53
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (29 bp):
TTTTAATTTAATTTCTAATTTCCTGTATA
Found at i:1250 original size:17 final size:18
Alignment explanation
Indices: 1223--1279 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 18
1213 TTTTAATTTA
1223 ATTTCTAATTTCCTGTAT
1 ATTTCTAATTTCCTGTAT
1241 ATTT-TAA-TT--T-TAT
1 ATTTCTAATTTCCTGTAT
1254 -TTTCTAATTTCCTGTAT
1 ATTTCTAATTTCCTGTAT
1271 A-TTCTAATT
1 ATTTCTAATT
1280 ATTATTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
12 3 0.09
13 6 0.18
14 3 0.09
16 3 0.09
17 14 0.42
18 4 0.12
ACGTcount: A:0.25, C:0.12, G:0.04, T:0.60
Consensus pattern (18 bp):
ATTTCTAATTTCCTGTAT
Found at i:1260 original size:30 final size:30
Alignment explanation
Indices: 1211--1287 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
1201 ATTTTGTTTT
*
1211 TATTTTAA-TTTAATTTCTAATTTCCTGTA
1 TATTTTAATTTTATTTTCTAATTTCCTGTA
1240 TATTTTAATTTTATTTTCTAATTTCCTGTA
1 TATTTTAATTTTATTTTCTAATTTCCTGTA
*
1270 TATTCTAATTATTATTTT
1 TATTTTAATT-TTATTTT
1288 TTGAAAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 8 0.18
30 29 0.66
31 7 0.16
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.62
Consensus pattern (30 bp):
TATTTTAATTTTATTTTCTAATTTCCTGTA
Found at i:2210 original size:59 final size:57
Alignment explanation
Indices: 2108--2245 Score: 152
Period size: 59 Copynumber: 2.4 Consensus size: 57
2098 TCGGCCATTA
* * * *
2108 CATGACCAACACCAAAAAACTTAATTTTTTATCAAATAAAAAGGGGATGTATACCATGG
1 CATGGCCAACA-CAAAAAAATTAATTTTTTATCAAACAAAAAGGGG-TGTAGACCATGG
** * *
2167 -ATGGCCAACACAAAAAAATTCGAATTTTTTATCTGACAGAAAGGGGTGTCGACCATGG
1 CATGGCCAACACAAAAAAATT--AATTTTTTATCAAACAAAAAGGGGTGTAGACCATGG
*
2225 CATGGCCAACACCAAAAAATT
1 CATGGCCAACACAAAAAAATT
2246 TTAAAATTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
57 9 0.13
58 19 0.28
59 39 0.58
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (57 bp):
CATGGCCAACACAAAAAAATTAATTTTTTATCAAACAAAAAGGGGTGTAGACCATGG
Found at i:2279 original size:62 final size:61
Alignment explanation
Indices: 2108--2650 Score: 386
Period size: 62 Copynumber: 9.0 Consensus size: 61
2098 TCGGCCATTA
* * ** **
2108 CATGACCAACACCAAAAAA-CTT--AA-TTTTTTATCAAATAAAAAGGGGATGTATACCATGG
1 CATGGCCAACACCAAAAAATTTTAAAATTTTTTTATCTGA-AAAAAGGGG-TGTCGACCATGG
* ** *
2167 -ATGGCCAACA-CAAAAAA-ATTCGAA-TTTTTTATCTGACAGAAAGGGGTGTCGACCATGG
1 CATGGCCAACACCAAAAAATTTTAAAATTTTTTTATCTGA-AAAAAGGGGTGTCGACCATGG
* * *
2225 CATGGCCAACACCAAAAAATTTTAAAATTTTTTTATCTGAAAAAAGAAGGTGTCGGCTATGG
1 CATGGCCAACACCAAAAAATTTTAAAATTTTTTTATCTGAAAAAAG-GGGTGTCGACCATGG
* * * * * * **
2287 CATGACTAACACCAAAAAGTTTTTAAATTTTTTTATCTAAAAAAAGGGGATGTCGATCATTA
1 CATGGCCAACACCAAAAAATTTTAAAATTTTTTTATCTGAAAAAAGGGG-TGTCGACCATGG
* * *
2349 CATGACCAACACCAAAAAATTTTAAAATTTTTTTATCTGAAAAAAAGGGGTGTCGTCCATTG
1 CATGGCCAACACCAAAAAATTTTAAAATTTTTTTATCTG-AAAAAAGGGGTGTCGACCATGG
* * * * * * *
2411 CATGGCCAACACC-AAAAA-TTT-GATTTTTTTTAGCAGATAAATAGGGGTGTC-AGTCATTG
1 CATGGCCAACACCAAAAAATTTTAAAATTTTTTTATCTGA-AAAAAGGGGTGTCGA-CCATGG
* * * **
2470 CATTGCCAACACCAAAAAATTTTGAAAA-TTTTTTATCTGAAAAAAGAGGGTGTCGGCTATTA
1 CATGGCCAACACCAAAAAATTTT-AAAATTTTTTTATCTGAAAAAAG-GGGTGTCGACCATGG
* * * * * * * *
2532 CATGACTAACAACC-AAATA-TTT-AATTTTTTTTATCAGATAAATAGGGGTGTCGTCCATTG
1 CATGGCCAAC-ACCAAAAAATTTTAAAATTTTTTTATCTGA-AAAAAGGGGTGTCGACCATGG
* * * * *
2592 CATGACCAATACTAAAAAA--TTGAAA-TTTTTTATCTGACAAAAAGGGGGTGTCGGCCATG
1 CATGGCCAACACCAAAAAATTTTAAAATTTTTTTATCTGA-AAAAA-GGGGTGTCGACCATG
2651 TAATTTGATT
Statistics
Matches: 390, Mismatches: 71, Indels: 45
0.77 0.14 0.09
Matches are distributed among these distances:
57 9 0.02
58 20 0.05
59 91 0.23
60 65 0.17
61 32 0.08
62 159 0.41
63 14 0.04
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (61 bp):
CATGGCCAACACCAAAAAATTTTAAAATTTTTTTATCTGAAAAAAGGGGTGTCGACCATGG
Found at i:2547 original size:122 final size:120
Alignment explanation
Indices: 2191--2646 Score: 516
Period size: 124 Copynumber: 3.8 Consensus size: 120
2181 AAAATTCGAA
* * * * *
2191 TTTTTTATCTGACAGAA-AGGGGTGTCGACCATGGCATGGCCAACACCAAAAAATTTTAAAATTT
1 TTTTTTATCAGATA-AATAGGGGTGTCG-TCATTGCATGACCAACACCAAAAAATTTTAAAATTT
* * *
2255 TTTTATCTGAAAAAAGAAGGTGTCGGCTATGGCATGACTAACACCAAAAAGTTTTTAAAT
64 TTTTATCTGAAAAAAGAGGGTGTCGGCTATTGCATGACTAACACCAAAAA---TTTAATT
* *
2315 TTTTTTATCTA-A-AAAAAGGGGATGTCGATCATTACATGACCAACACCAAAAAATTTTAAAATT
1 TTTTTTATC-AGATAAATAGGGG-TGTCG-TCATTGCATGACCAACACCAAAAAATTTTAAAATT
* * * * *
2378 TTTTTATCTGAAAAAA-AGGGGTGTCGTCCATTGCATGGCCAACACCAAAAATTTGATT
63 TTTTTATCTGAAAAAAGA-GGGTGTCGGCTATTGCATGACTAACACCAAAAATTTAATT
*
2436 TTTTTTAGCAGATAAATAGGGGTGTCAGTCATTGCATTG-CCAACACCAAAAAATTTTGAAAA-T
1 TTTTTTATCAGATAAATAGGGGTGTC-GTCATTGCA-TGACCAACACCAAAAAATTTT-AAAATT
* *
2499 TTTTTATCTGAAAAAAGAGGGTGTCGGCTATTACATGACTAACAACCAAATATTTAATT
63 TTTTTATCTGAAAAAAGAGGGTGTCGGCTATTGCATGACTAAC-ACCAAAAATTTAATT
* * *
2558 TTTTTTATCAGATAAATAGGGGTGTCGTCCATTGCATGACCAATACTAAAAAA--TTGAAA-TTT
1 TTTTTTATCAGATAAATAGGGGTGTCGT-CATTGCATGACCAACACCAAAAAATTTTAAAATTTT
*
2620 TTTATCTGACAAAAAGGGGGTGTCGGC
65 TTTATCTGA-AAAAAGAGGGTGTCGGC
2647 CATGTAATTT
Statistics
Matches: 290, Mismatches: 28, Indels: 32
0.83 0.08 0.09
Matches are distributed among these distances:
119 15 0.05
120 19 0.07
121 84 0.29
122 75 0.26
123 7 0.02
124 90 0.31
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (120 bp):
TTTTTTATCAGATAAATAGGGGTGTCGTCATTGCATGACCAACACCAAAAAATTTTAAAATTTTT
TTATCTGAAAAAAGAGGGTGTCGGCTATTGCATGACTAACACCAAAAATTTAATT
Found at i:14798 original size:19 final size:19
Alignment explanation
Indices: 14774--14822 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
14764 CCTTGAATCT
14774 AAGTTAATCACGAACACGA
1 AAGTTAATCACGAACACGA
14793 AAGTTAATCACGAACACGA
1 AAGTTAATCACGAACACGA
14812 AAGTTAATCAC
1 AAGTTAATCAC
14823 CCTTCTGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.47, C:0.20, G:0.14, T:0.18
Consensus pattern (19 bp):
AAGTTAATCACGAACACGA
Found at i:19319 original size:85 final size:85
Alignment explanation
Indices: 19213--19384 Score: 317
Period size: 85 Copynumber: 2.0 Consensus size: 85
19203 TGAAATGTAA
* *
19213 TAATTTATAGTATTAAATTGAGAACAAAATTTAAAGATTAAATTAAAGGAGATCAGCAATTATAG
1 TAATTTATAGAATTAAATTGAGAACAAAATTTAAAGATTAAATTAAAGGAGATAAGCAATTATAG
*
19278 TCTATCCAATATTTAAAGAT
66 TCTATCCAATATTTAAAAAT
19298 TAATTTATAGAATTAAATTGAGAACAAAATTTAAAGATTAAATTAAAGGAGATAAGCAATTATAG
1 TAATTTATAGAATTAAATTGAGAACAAAATTTAAAGATTAAATTAAAGGAGATAAGCAATTATAG
19363 TCTATCCAATATTTAAAAAT
66 TCTATCCAATATTTAAAAAT
19383 TA
1 TA
19385 CAATTCACTT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (85 bp):
TAATTTATAGAATTAAATTGAGAACAAAATTTAAAGATTAAATTAAAGGAGATAAGCAATTATAG
TCTATCCAATATTTAAAAAT
Found at i:25513 original size:55 final size:55
Alignment explanation
Indices: 25439--25572 Score: 180
Period size: 55 Copynumber: 2.4 Consensus size: 55
25429 ATAGAAAGCA
* * *
25439 ATATGTTTAAATAGATTGTTATGTTGGAATATTACT-TCTTTTGAATCGATTGTTT
1 ATATGTTAAAATCGATTGTTATGTTGAAATATT-CTGTCTTTTGAATCGATTGTTT
* * * *
25494 ATATGTTCAAATCGGTTGTTATTTTGAAATATTGTGTCTTTTGAATCGATTGTTT
1 ATATGTTAAAATCGATTGTTATGTTGAAATATTCTGTCTTTTGAATCGATTGTTT
*
25549 ATATATTAAAATCGATTGTTATGT
1 ATATGTTAAAATCGATTGTTATGT
25573 AGCACATCTA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 1 0.01
55 67 0.99
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (55 bp):
ATATGTTAAAATCGATTGTTATGTTGAAATATTCTGTCTTTTGAATCGATTGTTT
Found at i:26134 original size:25 final size:25
Alignment explanation
Indices: 26106--26157 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
26096 AAATTAAGAG
* * *
26106 TTATTTTTAATATTTATTTATTTTA
1 TTATTTTTAATATGTAATTATCTTA
*
26131 TTATTTTTCATATGTAATTATCTTA
1 TTATTTTTAATATGTAATTATCTTA
26156 TT
1 TT
26158 GAATTACCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (25 bp):
TTATTTTTAATATGTAATTATCTTA
Found at i:29780 original size:3 final size:3
Alignment explanation
Indices: 29772--29798 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
29762 ATTTCATTTA
29772 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
29799 GGTGTCAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:32758 original size:28 final size:28
Alignment explanation
Indices: 32699--32784 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 28
32689 GACATTTTTC
* ** *
32699 ATTTGAAATTAATTAAGTTTATGAATGA
1 ATTTGAAATTAATTATGTTTATGTTTGT
32727 ATTTGAAATTAATTATGTTTAAT-TTTGT
1 ATTTGAAATTAATTATGTTT-ATGTTTGT
* *
32755 ATTT--AATTAATAATTTTTATGTTTGT
1 ATTTGAAATTAATTATGTTTATGTTTGT
32781 ATTT
1 ATTT
32785 TGGTTTAAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
25 2 0.04
26 21 0.42
28 25 0.50
29 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (28 bp):
ATTTGAAATTAATTATGTTTATGTTTGT
Found at i:32773 original size:26 final size:26
Alignment explanation
Indices: 32733--32784 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
32723 ATGAATTTGA
*
32733 AATTAATTATGTTTAAT-TTTGTATTT
1 AATTAATAATGTTT-ATGTTTGTATTT
*
32759 AATTAATAATTTTTATGTTTGTATTT
1 AATTAATAATGTTTATGTTTGTATTT
32785 TGGTTTAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (26 bp):
AATTAATAATGTTTATGTTTGTATTT
Found at i:32799 original size:14 final size:14
Alignment explanation
Indices: 32792--32854 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
32782 TTTTGGTTTA
32792 AGGGTTTTGAATTT
1 AGGGTTTTGAATTT
32806 AGGGTTTT--ATGTT
1 AGGGTTTTGAAT-TT
**
32819 AATGTTTATGAATTT
1 AGGGTTT-TGAATTT
* *
32834 ATGGTTTTAAATTT
1 AGGGTTTTGAATTT
32848 AGGGTTT
1 AGGGTTT
32855 AGGATTTAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
12 2 0.05
13 7 0.18
14 21 0.54
15 7 0.18
16 2 0.05
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (14 bp):
AGGGTTTTGAATTT
Found at i:32820 original size:28 final size:28
Alignment explanation
Indices: 32789--32842 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
32779 GTATTTTGGT
32789 TTAAGGGTTT-TGAATTTAGGGTTTTATG
1 TTAA-GGTTTATGAATTTAGGGTTTTATG
* *
32817 TTAATGTTTATGAATTTATGGTTTTA
1 TTAAGGTTTATGAATTTAGGGTTTTA
32843 AATTTAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (28 bp):
TTAAGGTTTATGAATTTAGGGTTTTATG
Found at i:33296 original size:12 final size:12
Alignment explanation
Indices: 33281--33320 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
33271 TCTTCCTCTT
*
33281 GCTCTGGCTCCA
1 GCTCCGGCTCCA
33293 GCTCCGGCTCCA
1 GCTCCGGCTCCA
*
33305 GCTCCGGCTCTA
1 GCTCCGGCTCCA
33317 GCTC
1 GCTC
33321 TGGGGAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.07, C:0.45, G:0.25, T:0.23
Consensus pattern (12 bp):
GCTCCGGCTCCA
Found at i:36229 original size:6 final size:6
Alignment explanation
Indices: 36218--36259 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
36208 GTTGAATATA
*
36218 TGGCAG TGGCAG TGGCAG TGGCAG TGGCAA TGGCAG TGGCAG
1 TGGCAG TGGCAG TGGCAG TGGCAG TGGCAG TGGCAG TGGCAG
36260 GCAGGTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.19, C:0.17, G:0.48, T:0.17
Consensus pattern (6 bp):
TGGCAG
Found at i:37697 original size:5 final size:5
Alignment explanation
Indices: 37682--37712 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
37672 ATTTTCCATG
37682 TTTTCA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA
37713 ATACTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:37924 original size:29 final size:30
Alignment explanation
Indices: 37886--37955 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
37876 GTAACTTTTT
*
37886 AAGTTAAATTTGACCATCAATCTTT-AAAA
1 AAGTTAAATTTAACCATCAATCTTTCAAAA
* **
37915 AAGTTGAATTTAATTATCAATCTTTCAAAAA
1 AAGTTAAATTTAACCATCAATCTTTC-AAAA
*
37946 AAATTAAATT
1 AAGTTAAATT
37956 GATGTCTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 21 0.64
31 12 0.36
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (30 bp):
AAGTTAAATTTAACCATCAATCTTTCAAAA
Found at i:38075 original size:9 final size:9
Alignment explanation
Indices: 38052--38102 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
38042 TTTTTTTTAT
38052 TTTTTATGAA
1 TTTTTAT-AA
38062 CTTTTTATAA
1 -TTTTTATAA
38072 TTTTTAT-A
1 TTTTTATAA
38080 TTTTTA-AA
1 TTTTTATAA
38088 TATTTTATATA
1 T-TTTTATA-A
38099 TTTT
1 TTTT
38103 AAAATTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 9 0.25
9 12 0.33
10 6 0.17
11 9 0.25
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:38077 original size:20 final size:21
Alignment explanation
Indices: 38032--38078 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
38022 TTCACATATA
* * *
38032 TTTTATGCAATTTTTTTTATT
1 TTTTATGCAACTTTTTATAAT
38053 TTTTATG-AACTTTTTATAAT
1 TTTTATGCAACTTTTTATAAT
38073 TTTTAT
1 TTTTAT
38079 ATTTTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTTATGCAACTTTTTATAAT
Found at i:38083 original size:17 final size:16
Alignment explanation
Indices: 38063--38105 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 16
38053 TTTTATGAAC
38063 TTTTTATAATTTTTATA
1 TTTTTA-AATTTTTATA
38080 TTTTTAAATATTTTATA
1 TTTTTAAAT-TTTTATA
38097 TATTTTAAA
1 T-TTTTAAA
38106 ATTATTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.12
17 14 0.58
18 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTAAATTTTTATA
Found at i:38100 original size:19 final size:19
Alignment explanation
Indices: 38071--38112 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
38061 ACTTTTTATA
*
38071 ATTTTTATATTTTTAAA-T
1 ATTTTTATATTTTAAAATT
38089 ATTTTATATATTTTAAAATT
1 ATTTT-TATATTTTAAAATT
38109 ATTT
1 ATTT
38113 GTTAACATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 11 0.52
20 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTATATTTTAAAATT
Found at i:41699 original size:19 final size:19
Alignment explanation
Indices: 41657--41765 Score: 150
Period size: 19 Copynumber: 5.8 Consensus size: 19
41647 AGAGAATAGT
*
41657 AATACTGGCTCGT-TGAGC
1 AATACTGGCTCGTAAGAGC
*
41675 AATACTGGCTCGTAAGAGT
1 AATACTGGCTCGTAAGAGC
*
41694 AATACTGGCTCGT-TGAGC
1 AATACTGGCTCGTAAGAGC
41712 AATACTGGCTCGTAAGAGC
1 AATACTGGCTCGTAAGAGC
*
41731 AATACTGGCTTGTAAGAGC
1 AATACTGGCTCGTAAGAGC
* *
41750 AATATTGGATCGTAAG
1 AATACTGGCTCGTAAG
41766 GAATTATTTC
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
18 29 0.36
19 51 0.64
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (19 bp):
AATACTGGCTCGTAAGAGC
Found at i:41704 original size:37 final size:37
Alignment explanation
Indices: 41654--41765 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
41644 TAGAGAGAAT
41654 AGTAATACTGGCTCGTTGAGCAATACTGGCTCGTAAG
1 AGTAATACTGGCTCGTTGAGCAATACTGGCTCGTAAG
41691 AGTAATACTGGCTCGTTGAGCAATACTGGCTCGTAAG
1 AGTAATACTGGCTCGTTGAGCAATACTGGCTCGTAAG
* * * * *
41728 AGCAATACTGGCTTGTAAGAGCAATATTGGATCGTAAG
1 AGTAATACTGGCTCGT-TGAGCAATACTGGCTCGTAAG
41766 GAATTATTTC
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
37 51 0.74
38 18 0.26
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (37 bp):
AGTAATACTGGCTCGTTGAGCAATACTGGCTCGTAAG
Found at i:41746 original size:56 final size:55
Alignment explanation
Indices: 41657--41762 Score: 158
Period size: 56 Copynumber: 1.9 Consensus size: 55
41647 AGAGAATAGT
* * *
41657 AATACTGGCTCGTTGAGCAATACTGGCTCGTAAGAGTAATACTGGCTCGTTGAGC
1 AATACTGGCTCGTAGAGCAATACTGGCTCGTAAGAGCAATACTGGATCGTTGAGC
* *
41712 AATACTGGCTCGTAAGAGCAATACTGGCTTGTAAGAGCAATATTGGATCGT
1 AATACTGGCTCGT-AGAGCAATACTGGCTCGTAAGAGCAATACTGGATCGT
41763 AAGGAATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
55 13 0.29
56 32 0.71
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (55 bp):
AATACTGGCTCGTAGAGCAATACTGGCTCGTAAGAGCAATACTGGATCGTTGAGC
Found at i:42452 original size:21 final size:22
Alignment explanation
Indices: 42417--42476 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
42407 TTGCAGGGTG
* *
42417 AGACTTGTATCGGTA-AA-AGT
1 AGACTTGTTTTGGTAGAAGAGT
42437 AAGACTTGTTTTGGTAGAAGAGT
1 -AGACTTGTTTTGGTAGAAGAGT
*
42460 -CACTTGTTTTGGTAGAA
1 AGACTTGTTTTGGTAGAA
42477 CTGTCATTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 29 0.85
22 2 0.06
23 3 0.09
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (22 bp):
AGACTTGTTTTGGTAGAAGAGT
Found at i:42482 original size:21 final size:21
Alignment explanation
Indices: 42440--42487 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
42430 TAAAAGTAAG
*
42440 ACTTGTTTTGGTAGAAGAGTC
1 ACTTGTTTTGGTAGAACAGTC
*
42461 ACTTGTTTTGGTAGAACTGTC
1 ACTTGTTTTGGTAGAACAGTC
*
42482 ATTTGT
1 ACTTGT
42488 ATCGGTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.10, G:0.25, T:0.44
Consensus pattern (21 bp):
ACTTGTTTTGGTAGAACAGTC
Found at i:43144 original size:7 final size:7
Alignment explanation
Indices: 43100--43158 Score: 50
Period size: 7 Copynumber: 8.3 Consensus size: 7
43090 ATGTTTTATC
43100 TTATATAA
1 TTATAT-A
43108 TTGATATA
1 TT-ATATA
*
43116 TTATACTT
1 TTATA-TA
*
43124 TTTTA-A
1 TTATATA
*
43130 TTAAATA
1 TTATATA
43137 TTATATA
1 TTATATA
43144 -TATATA
1 TTATATA
43150 TTATATA
1 TTATATA
43157 TT
1 TT
43159 TTTGAATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
6 9 0.22
7 18 0.44
8 10 0.24
9 4 0.10
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (7 bp):
TTATATA
Found at i:43177 original size:35 final size:34
Alignment explanation
Indices: 43111--43186 Score: 100
Period size: 34 Copynumber: 2.1 Consensus size: 34
43101 TATATAATTG
43111 ATATATTATACTTTTTTAATTAAATATTATATAT
1 ATATATTATACTTTTTTAATTAAATATTATATAT
*
43145 ATATATTATA-TATTTTTGAATTTATATATATATATAT
1 ATATATTATACT-TTTTT-AA-TTAAATAT-TATATAT
43182 ATATA
1 ATATA
43187 AATTTTATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
33 1 0.03
34 15 0.41
35 2 0.05
36 7 0.19
37 12 0.32
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (34 bp):
ATATATTATACTTTTTTAATTAAATATTATATAT
Found at i:43197 original size:19 final size:19
Alignment explanation
Indices: 43171--43211 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
43161 TGAATTTATA
43171 TATATATATATATATAAATTT
1 TATATA-ATATATAT-AATTT
*
43192 TATATAATTTATATAATTT
1 TATATAATATATATAATTT
43211 T
1 T
43212 TGAATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 7 0.37
21 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATAATATATATAATTT
Found at i:43508 original size:21 final size:22
Alignment explanation
Indices: 43483--43524 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
43473 TTAACGATTG
43483 AAAATTATT-TTATAA-TAATAC
1 AAAATT-TTATTATAACTAATAC
43504 AAAATTTTATTATAACTAATA
1 AAAATTTTATTATAACTAATA
43525 TCTTATATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 12 0.63
22 5 0.26
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATTTTATTATAACTAATAC
Found at i:43678 original size:23 final size:24
Alignment explanation
Indices: 43651--43698 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
43641 AAATTTAAAT
*
43651 AAATACCCATA-TTTATATTATTA
1 AAATACCCATATTTTATACTATTA
**
43674 AAATATTCATATTTTATACTATTA
1 AAATACCCATATTTTATACTATTA
43698 A
1 A
43699 TATATATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATACCCATATTTTATACTATTA
Found at i:43696 original size:24 final size:23
Alignment explanation
Indices: 43658--43703 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
43648 AATAAATACC
*
43658 CATATTTATATTATTAAAATATT
1 CATATTTATACTATTAAAATATT
*
43681 CATATTTTATACTATTAATATAT
1 CATA-TTTATACTATTAAAATAT
43704 ATTTATTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (23 bp):
CATATTTATACTATTAAAATATT
Found at i:43851 original size:16 final size:16
Alignment explanation
Indices: 43819--43852 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43809 AAATTACTTT
*
43819 TTATTTATAAATCAAA
1 TTATTTATAAATAAAA
*
43835 TTATTTATAACTAAAA
1 TTATTTATAAATAAAA
43851 TT
1 TT
43853 TTTTTCCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
TTATTTATAAATAAAA
Found at i:45449 original size:18 final size:18
Alignment explanation
Indices: 45422--45456 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
45412 TTATATTATA
45422 AAATAAAATAATTATTTC
1 AAATAAAATAATTATTTC
*
45440 AAATATAATAATTATTT
1 AAATAAAATAATTATTT
45457 TTATATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAAAATAATTATTTC
Found at i:45758 original size:20 final size:19
Alignment explanation
Indices: 45713--45762 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
45703 ATTTGATTTT
* **
45713 ATAAATAAAAAAATTATTA
1 ATAAAAAAAAAAATTAAAA
*
45732 ATGAAAAAAATAAATTAAAA
1 AT-AAAAAAAAAAATTAAAA
45752 ATAAAAAAAAA
1 ATAAAAAAAAA
45763 CTTGAAAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAAAAAAAATTAAAA
Found at i:45770 original size:18 final size:19
Alignment explanation
Indices: 45713--45760 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
45703 ATTTGATTTT
**
45713 ATAAATAAAA-AAATTATTA
1 ATAAA-AAAATAAATTAAAA
45732 ATGAAAAAAATAAATTAAAA
1 AT-AAAAAAATAAATTAAAA
45752 ATAAAAAAA
1 ATAAAAAAA
45761 AACTTGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (19 bp):
ATAAAAAAATAAATTAAAA
Found at i:45820 original size:41 final size:40
Alignment explanation
Indices: 45744--45836 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
45734 GAAAAAAATA
*
45744 AATTAAAAATAAAAAAAAACTTGAAAACAATACATTTATT
1 AATTAAAAATAAAAAAAAACTTGAAAACAAAACATTTATT
45784 AATTAAAAATAATAAAAAAACTTG-AAACAAGAACA-TTA--
1 AATTAAAAATAA-AAAAAAACTTGAAAACAA-AACATTTATT
*
45822 AATAAAAAATAAAAA
1 AATTAAAAATAAAAA
45837 TGTGGATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
37 3 0.06
38 11 0.22
40 21 0.43
41 14 0.29
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.23
Consensus pattern (40 bp):
AATTAAAAATAAAAAAAAACTTGAAAACAAAACATTTATT
Found at i:48486 original size:43 final size:43
Alignment explanation
Indices: 48356--48489 Score: 144
Period size: 43 Copynumber: 3.1 Consensus size: 43
48346 ACACTTCTAT
* *
48356 AGAACATGATCTTT-GACGGTGCTTTTCCCACAAACGCCGTTAA
1 AGAACATGATCTTTAG-CGGTGTTTTTCCCACAAACGCCGCTAA
* * * * **
48399 AAAACATGATCTTTAGTGGCGTTTTTCCCACAAGCGTGGCTAA
1 AGAACATGATCTTTAGCGGTGTTTTTCCCACAAACGCCGCTAA
* * * *
48442 AGAACATGGTCTTTAGCGATGTTTTTCCCACAAACCCCACTAA
1 AGAACATGATCTTTAGCGGTGTTTTTCCCACAAACGCCGCTAA
48485 AGAAC
1 AGAAC
48490 CGCTAAAAAA
Statistics
Matches: 72, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
43 71 0.99
44 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (43 bp):
AGAACATGATCTTTAGCGGTGTTTTTCCCACAAACGCCGCTAA
Found at i:53797 original size:42 final size:42
Alignment explanation
Indices: 53734--53925 Score: 196
Period size: 42 Copynumber: 4.6 Consensus size: 42
53724 TTTATGGAAA
* * * **
53734 AAACGCCGCTAATGCTGTTTACTTTTTGCGGCGTTTTTCTGT
1 AAACGCCGCTATTGCTCTTTACCTTTTGCGGCGTTTTTCCAT
* * * * **
53776 AAATGCCGCTATTGCTCTTTACTTTTTACGGCGTTTAT-GGT
1 AAACGCCGCTATTGCTCTTTACCTTTTGCGGCGTTTTTCCAT
* *
53817 AAAACGCCGCTATTG--CTTTACCTTTTGCAGTGTTTTTCCAT
1 -AAACGCCGCTATTGCTCTTTACCTTTTGCGGCGTTTTTCCAT
* *
53858 AAACGTCGTTATTGCTCTTTACCTTTTGCGGCGTTTTTCCCAT
1 AAACGCCGCTATTGCTCTTTACCTTTTGCGGCGTTTTT-CCAT
53901 AAACGCCGCTATTG-T-TTTACCTTTT
1 AAACGCCGCTATTGCTCTTTACCTTTT
53926 ATGGATTGAA
Statistics
Matches: 125, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
40 29 0.23
41 13 0.10
42 67 0.54
43 16 0.13
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (42 bp):
AAACGCCGCTATTGCTCTTTACCTTTTGCGGCGTTTTTCCAT
Found at i:53852 original size:82 final size:82
Alignment explanation
Indices: 53721--53925 Score: 221
Period size: 82 Copynumber: 2.5 Consensus size: 82
53711 ACCTTTAATA
* * * ** *
53721 GCGTTTATGGAAAAAACGCCGCTAATGCTGTTTACTTTTTGCGGCGTTTTTCTGTAAATGCCGCT
1 GCGTTTATGG-AAAAACGCCGCTATTGC--TTTACCTTTTGCAGCGTTTTTCCATAAACGCCGCT
*
53786 ATTGCTCTTTACTTTTTACG
63 ATTGCTCTTTACCTTTTACG
* * * *
53806 GCGTTTATGGTAAAACGCCGCTATTGCTTTACCTTTTGCAGTGTTTTTCCATAAACGTCGTTATT
1 GCGTTTATGGAAAAACGCCGCTATTGCTTTACCTTTTGCAGCGTTTTTCCATAAACGCCGCTATT
*
53871 GCTCTTTACCTTTTGCG
66 GCTCTTTACCTTTTACG
* ** * *
53888 GCGTTTTTCCCATAAACGCCGCTATTGTTTTACCTTTT
1 GCGTTTAT-GGAAAAACGCCGCTATTGCTTTACCTTTT
53926 ATGGATTGAA
Statistics
Matches: 101, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
82 52 0.51
83 24 0.24
84 15 0.15
85 10 0.10
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (82 bp):
GCGTTTATGGAAAAACGCCGCTATTGCTTTACCTTTTGCAGCGTTTTTCCATAAACGCCGCTATT
GCTCTTTACCTTTTACG
Found at i:54472 original size:21 final size:21
Alignment explanation
Indices: 54447--54488 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
54437 AACCATGCAA
54447 AATATAAACATCAACCAATTT
1 AATATAAACATCAACCAATTT
*
54468 AATATTAACATCAACCAATTT
1 AATATAAACATCAACCAATTT
54489 TCAAAGCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (21 bp):
AATATAAACATCAACCAATTT
Found at i:57878 original size:19 final size:20
Alignment explanation
Indices: 57833--57887 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 20
57823 TTGTTATTTC
* *
57833 ATTATTTAT-TTATTTTTAG
1 ATTATTTATAATATTTTAAG
*
57852 ATTTTTTATAATATTTTAAG
1 ATTATTTATAATATTTTAAG
*
57872 -TTATTTA-AAAATTTTA
1 ATTATTTATAATATTTTA
57888 TGTCAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 8 0.27
19 14 0.47
20 8 0.27
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
ATTATTTATAATATTTTAAG
Found at i:68078 original size:22 final size:21
Alignment explanation
Indices: 68035--68079 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
68025 ATATAACTTC
68035 TTTTAAATTAATTGAATATTT
1 TTTTAAATTAATTGAATATTT
68056 TTTTATAATTACATT-AAT-TTT
1 TTTTA-AATTA-ATTGAATATTT
68077 TTT
1 TTT
68080 ATTTATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 11 0.50
22 8 0.36
23 3 0.14
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTAAATTAATTGAATATTT
Found at i:68125 original size:3 final size:3
Alignment explanation
Indices: 68119--68150 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
68109 TTATAAATTT
*
68119 TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
68151 TTTTTAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:70504 original size:15 final size:17
Alignment explanation
Indices: 70474--70505 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
70464 TTAAATGTTT
70474 AGTATTGTTGTGAAAAA
1 AGTATTGTTGTGAAAAA
70491 AGTATT-TT-TGAAAAA
1 AGTATTGTTGTGAAAAA
70506 TAAAATGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (17 bp):
AGTATTGTTGTGAAAAA
Found at i:71940 original size:21 final size:20
Alignment explanation
Indices: 71916--71954 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
71906 CATCATAAAT
*
71916 ATGTCATTATCTAATAATTTA
1 ATGTAATTAT-TAATAATTTA
*
71937 ATGTAATTATTATTAATT
1 ATGTAATTATTAATAATT
71955 CAATTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (20 bp):
ATGTAATTATTAATAATTTA
Found at i:73034 original size:9 final size:9
Alignment explanation
Indices: 73000--73041 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
72990 AAAGTAACAG
73000 AAAAA-TAA
1 AAAAACTAA
*
73008 TAAAACTAA
1 AAAAACTAA
*
73017 GAGAAACTAA
1 -AAAAACTAA
73027 AAAAACTAA
1 AAAAACTAA
73036 AAAAAC
1 AAAAAC
73042 AAACATCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 4 0.14
9 17 0.61
10 7 0.25
ACGTcount: A:0.74, C:0.10, G:0.05, T:0.12
Consensus pattern (9 bp):
AAAAACTAA
Found at i:78283 original size:25 final size:25
Alignment explanation
Indices: 78253--78302 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
78243 TAAGTGACTG
78253 AAAGATGTCATTGCATTACTCTACC
1 AAAGATGTCATTGCATTACTCTACC
78278 AAAGATGTCATTGCATTACTCTACC
1 AAAGATGTCATTGCATTACTCTACC
78303 TTTGTTCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (25 bp):
AAAGATGTCATTGCATTACTCTACC
Found at i:79328 original size:12 final size:12
Alignment explanation
Indices: 79311--79360 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
79301 TAGGTTCAGT
79311 TTCTTCCTTCTC
1 TTCTTCCTTCTC
79323 TTCTTCCTT-TCC
1 TTCTTCCTTCT-C
* *
79335 TTCTTCTTTTTC
1 TTCTTCCTTCTC
79347 TT-TATCCTTCTC
1 TTCT-TCCTTCTC
79359 TT
1 TT
79361 GATCACCTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
11 2 0.06
12 29 0.91
13 1 0.03
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTCCTTCTC
Found at i:99849 original size:17 final size:18
Alignment explanation
Indices: 99827--99864 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
99817 CATTTTAATT
99827 AATGATCAAA-TTGAAAA
1 AATGATCAAATTTGAAAA
99844 AATGATCAAATTTGAAAA
1 AATGATCAAATTTGAAAA
99862 AAT
1 AAT
99865 AAACTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.26
Consensus pattern (18 bp):
AATGATCAAATTTGAAAA
Found at i:99901 original size:29 final size:29
Alignment explanation
Indices: 99841--99901 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
99831 ATCAAATTGA
* *
99841 AAAAATGATCAAATTTGAAAAAATAAACT
1 AAAAATGATCAAATTAGAAAAAAAAAACT
* *
99870 AAAAATGATGAAA-TAGAAAAATAAAAATT
1 AAAAATGATCAAATTAGAAAAA-AAAAACT
99899 AAA
1 AAA
99902 TCTAGAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.21
Consensus pattern (29 bp):
AAAAATGATCAAATTAGAAAAAAAAAACT
Found at i:101869 original size:3 final size:3
Alignment explanation
Indices: 101861--101972 Score: 98
Period size: 3 Copynumber: 37.3 Consensus size: 3
101851 GAGGCATGCT
* * * *
101861 CAG CAG CAG CAG CAT CAG CAG CAG CAA CAA CAG CAG CAT CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * * * * * * * *
101909 CAA CAA CAG CAG CAG CAA CAG CAA CAG CAA CAG CAA CAG CCG CAA CAC
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
*
101957 CAA CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG C
101973 GAAGAGAAGG
Statistics
Matches: 87, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.41, C:0.36, G:0.21, T:0.02
Consensus pattern (3 bp):
CAG
Found at i:101899 original size:24 final size:24
Alignment explanation
Indices: 101867--101972 Score: 119
Period size: 24 Copynumber: 4.5 Consensus size: 24
101857 TGCTCAGCAG
101867 CAGCAGCATCAGCAGCAGCAACAA
1 CAGCAGCATCAGCAGCAGCAACAA
101891 CAGCAGCATCAGCAGCAGCAACAA
1 CAGCAGCATCAGCAGCAGCAACAA
* *
101915 CAGCAG---CAGCAACAGCAACAG
1 CAGCAGCATCAGCAGCAGCAACAA
* * * * *
101936 CAACAGCAACAGCCGCAACACCAA
1 CAGCAGCATCAGCAGCAGCAACAA
*
101960 CAGCAGCAGCAGC
1 CAGCAGCATCAGC
101973 GAAGAGAAGG
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
21 18 0.26
24 51 0.74
ACGTcount: A:0.42, C:0.36, G:0.21, T:0.02
Consensus pattern (24 bp):
CAGCAGCATCAGCAGCAGCAACAA
Found at i:127327 original size:24 final size:23
Alignment explanation
Indices: 127295--127340 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
127285 GAATTTAAAA
127295 TAAAAATTTA-ATAAATAATCAAAG
1 TAAAAATTTATAT-AATAA-CAAAG
*
127319 TAAAGATTTATATAATAACAAA
1 TAAAAATTTATATAATAACAAA
127341 CAATAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 14 0.70
25 2 0.10
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (23 bp):
TAAAAATTTATATAATAACAAAG
Found at i:128170 original size:3 final size:3
Alignment explanation
Indices: 128162--128188 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
128152 AAAAACAAGA
128162 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
128189 GAAAGTGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:134044 original size:32 final size:29
Alignment explanation
Indices: 134000--134066 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
133990 ACTTTCCTCA
* *
134000 TTAATTTTTTTTATATTTTATTTTCTTAGTTT
1 TTAATTTGTTTTA-ATTTTA-ATT-TTAGTTT
*
134032 TTAATTTGTTTTACTTTTAATTTTAGTTT
1 TTAATTTGTTTTAATTTTAATTTTAGTTT
134061 TTAATT
1 TTAATT
134067 CTAAAACCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 13 0.41
30 2 0.06
31 5 0.16
32 12 0.38
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.72
Consensus pattern (29 bp):
TTAATTTGTTTTAATTTTAATTTTAGTTT
Done.