Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015338.1 Kokia drynarioides strain JFW-HI SEQ_130385, 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: 115558
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 220 characters in sequence are not A, C, G, or T
Found at i:707 original size:98 final size:100
Alignment explanation
Indices: 595--783 Score: 276
Period size: 98 Copynumber: 1.9 Consensus size: 100
585 GGAGGTCCCT
* * *
595 AAACTGTCCAAAAATTTCGTTTTTACCC-CAGAACTTCCAAAAATCTCATTTGCGACCCTAAAAC
1 AAACTGTCCAAAAATTTAGTTCTTACCCTC-GAACTTCCAAAAATCTCATTTGCGACCCCAAAAC
659 TTCCAAAAATCCCATTTTTACCCCCGATCGACCCCG
65 TTCCAAAAATCCCATTTTTACCCCCGATCGACCCCG
* **
695 AAACT-TCC-AAAATTTAGTTCTTACCCTCGAACTTCCATAAATCTCATTTTTGACCCCAAAACT
1 AAACTGTCCAAAAATTTAGTTCTTACCCTCGAACTTCCAAAAATCTCATTTGCGACCCCAAAACT
* *
758 TCTAAAAATTCCATTTTTACCCCCGA
66 TCCAAAAATCCCATTTTTACCCCCGA
784 ACTTCATAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
98 71 0.89
99 4 0.05
100 5 0.06
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.30
Consensus pattern (100 bp):
AAACTGTCCAAAAATTTAGTTCTTACCCTCGAACTTCCAAAAATCTCATTTGCGACCCCAAAACT
TCCAAAAATCCCATTTTTACCCCCGATCGACCCCG
Found at i:785 original size:59 final size:59
Alignment explanation
Indices: 688--863 Score: 205
Period size: 59 Copynumber: 3.0 Consensus size: 59
678 ACCCCCGATC
* * * *
688 GACCCCGAAACTTCC-AAAATT-TAGTTCTTACCCTCGAACTTCCATAAATCTCATTTTT
1 GACCCCAAAACTTCCAAAAATTCCA-TTTTTACCCCCGAACTTCCATAAATCTCATTTTT
* *
746 GACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCGAACTT-CATAAAATCCCATTTTT
1 GACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAT-AAATCTCATTTTT
* * ** * *
805 GACCCCAAAAGTTCCAAGAATTCCATTTTTAGACCCGAACTTCCAAAAATTTCATTTTT
1 GACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCATAAATCTCATTTTT
864 TAACCCCGAA
Statistics
Matches: 100, Mismatches: 14, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
58 16 0.16
59 81 0.81
60 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.33
Consensus pattern (59 bp):
GACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCATAAATCTCATTTTT
Found at i:786 original size:29 final size:29
Alignment explanation
Indices: 690--873 Score: 133
Period size: 30 Copynumber: 6.2 Consensus size: 29
680 CCCCGATCGA
* *
690 CCCCGAAACTTCC-AAAATT-TAGTTCTTAC
1 CCCCG-AACTTCCAAAAATTCCA-TTTTTAC
* *
719 CCTCGAACTTCCATAAA-TCTCATTTTTGAC
1 CCCCGAACTTCCAAAAATTC-CATTTTT-AC
** *
749 CCCAAAACTTCTAAAAATTCCATTTTTAC
1 CCCCGAACTTCCAAAAATTCCATTTTTAC
*
778 CCCCGAACTT-CATAAAATCCCATTTTTGAC
1 CCCCGAACTTCCA-AAAATTCCATTTTT-AC
** * * *
808 CCCAAAAGTTCCAAGAATTCCATTTTTAG
1 CCCCGAACTTCCAAAAATTCCATTTTTAC
* * *
837 ACCCGAACTTCCAAAAATTTCATTTTTTAA
1 CCCCGAACTTCCAAAAATTCCA-TTTTTAC
867 CCCCGAA
1 CCCCGAA
874 TTTTCCCAAA
Statistics
Matches: 119, Mismatches: 27, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
28 9 0.08
29 51 0.43
30 55 0.46
31 4 0.03
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (29 bp):
CCCCGAACTTCCAAAAATTCCATTTTTAC
Found at i:6322 original size:3 final size:3
Alignment explanation
Indices: 6309--6351 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
6299 TAGTTGTTGT
* *
6309 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6352 TTTGACTGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:11446 original size:30 final size:31
Alignment explanation
Indices: 11385--11449 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
11375 CAAAAATAAA
* *
11385 TTATAATTTTTATGATAATAAAAATATAATT
1 TTATAATTTTAATGATAATAAAAATAAAATT
* * *
11416 TTATTATTTTAATGAT-ATATAATTAAAATT
1 TTATAATTTTAATGATAATAAAAATAAAATT
11446 TTAT
1 TTAT
11450 CGAGGGAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (31 bp):
TTATAATTTTAATGATAATAAAAATAAAATT
Found at i:13313 original size:16 final size:16
Alignment explanation
Indices: 13294--13330 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
13284 GTTTGAACGG
*
13294 TTTTGTTTTTAATTAT
1 TTTTATTTTTAATTAT
*
13310 TTTTATTTTTATTTAT
1 TTTTATTTTTAATTAT
13326 TTTTA
1 TTTTA
13331 AAATATTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTATTTTTAATTAT
Found at i:13386 original size:7 final size:7
Alignment explanation
Indices: 13340--13367 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
13330 AAAATATTGA
13340 AATTTAC
1 AATTTAC
13347 AATTTAC
1 AATTTAC
13354 AATTTAC
1 AATTTAC
13361 AATTTAC
1 AATTTAC
13368 GATCATGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (7 bp):
AATTTAC
Found at i:21366 original size:18 final size:18
Alignment explanation
Indices: 21343--21378 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21333 TTATATGAGG
21343 ATAAAAATGTAATTTCAC
1 ATAAAAATGTAATTTCAC
21361 ATAAAAATGTAATTTCAC
1 ATAAAAATGTAATTTCAC
21379 TAATGTTTTA
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:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (18 bp):
ATAAAAATGTAATTTCAC
Found at i:22165 original size:19 final size:18
Alignment explanation
Indices: 22134--22175 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
22124 GTATCACTTC
* *
22134 TAAAAAGTATTTTTAAGA
1 TAAAAAATATTTTTAAAA
22152 TAAAAAATATTTTTAAAA
1 TAAAAAATATTTTTAAAA
22170 TAAAAA
1 TAAAAA
22176 CATTTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
TAAAAAATATTTTTAAAA
Found at i:22180 original size:17 final size:18
Alignment explanation
Indices: 22142--22180 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
22132 TCTAAAAAGT
* *
22142 ATTTTTAAGATAAAAAAT
1 ATTTTTAAAATAAAAAAC
22160 ATTTTTAAAAT-AAAAAC
1 ATTTTTAAAATAAAAAAC
22177 ATTT
1 ATTT
22181 GAAAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTTTTAAAATAAAAAAC
Found at i:22875 original size:21 final size:21
Alignment explanation
Indices: 22834--22875 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
22824 GAGTTGTTTT
*
22834 ATTTTTAATATTATTTTATTA
1 ATTTTTAATATTATTTAATTA
22855 ATTTTTAATATT-TTATAATTA
1 ATTTTTAATATTATT-TAATTA
22876 TAAAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTTAATATTATTTAATTA
Found at i:22893 original size:24 final size:25
Alignment explanation
Indices: 22854--22902 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
22844 TTATTTTATT
* * *
22854 AATTTTTAATATTTTATAATTATAA
1 AATTTTGAATATTTTAGAATAATAA
22879 AATTTTGAATA-TTTAGAATAATAA
1 AATTTTGAATATTTTAGAATAATAA
22903 TTGAGTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
AATTTTGAATATTTTAGAATAATAA
Found at i:23424 original size:18 final size:19
Alignment explanation
Indices: 23391--23429 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
23381 CCCATTTGAA
*
23391 ATTAAAATTTTTATTTATT
1 ATTAAAATTATTATTTATT
*
23410 ATTAAAA-TATTATTTTTT
1 ATTAAAATTATTATTTATT
23428 AT
1 AT
23430 AAATGATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTAAAATTATTATTTATT
Found at i:24612 original size:20 final size:19
Alignment explanation
Indices: 24579--24634 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
24569 ATTTAGCCGG
*
24579 TTTTATGAATTTTTAATATGT
1 TTTTA-GAAATTTTAAT-TGT
*
24600 ATTTTA-AAATTTTTATTGT
1 -TTTTAGAAATTTTAATTGT
24619 TTTTATGAAATTTTAA
1 TTTTA-GAAATTTTAA
24635 AAATTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 5 0.17
19 3 0.10
20 16 0.55
22 5 0.17
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
TTTTAGAAATTTTAATTGT
Found at i:25131 original size:18 final size:19
Alignment explanation
Indices: 25108--25151 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
25098 CTAAAGTTTT
25108 ATTTTAATATTT-TTAT-AC
1 ATTTTAAT-TTTATTATCAC
25126 ATTTTAATTTTATTATGCAC
1 ATTTTAATTTTATTAT-CAC
25146 ATTTTA
1 ATTTTA
25152 TTACTTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
20 8 0.35
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTTAATTTTATTATCAC
Found at i:30165 original size:24 final size:24
Alignment explanation
Indices: 30120--30165 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
30110 TTTTATATTA
*
30120 ATATTAATATAAATTAATATAATT
1 ATATTAATATAAATCAATATAATT
30144 ATATTAATATTAAATCAA-ATAA
1 ATATTAATA-TAAATCAATATAA
30166 ACCCTTACGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATTAATATAAATCAATATAATT
Found at i:31350 original size:57 final size:59
Alignment explanation
Indices: 31228--31351 Score: 153
Period size: 57 Copynumber: 2.1 Consensus size: 59
31218 TGATTTTTAC
* * **
31228 TAATTCATATTTTACTAATAATTATATTAAAAATATTATTAAATTATATATTATTTCATT
1 TAATT-ATATTTGACTAATAATTATATTAAAAATATAATTAAATTATATATTATTAAATT
* * * *
31288 CAATTATATTTGA-TAATAATTATGTT-AAAATATAATTAAATTATTTTTTATTAAATT
1 TAATTATATTTGACTAATAATTATATTAAAAATATAATTAAATTATATATTATTAAATT
31345 TAATTAT
1 TAATTAT
31352 CTTAATAATC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
57 32 0.58
58 12 0.22
59 7 0.13
60 4 0.07
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (59 bp):
TAATTATATTTGACTAATAATTATATTAAAAATATAATTAAATTATATATTATTAAATT
Found at i:31385 original size:28 final size:27
Alignment explanation
Indices: 31335--31390 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
31325 AAATTATTTT
* **
31335 TTATTAAATTTAATTATCTTAATAATC
1 TTATTAAATTTAATAATAATAATAATC
*
31362 TTATTAAAATTTAATAATAATAATCATC
1 TTATT-AAATTTAATAATAATAATAATC
31390 T
1 T
31391 ACATATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (27 bp):
TTATTAAATTTAATAATAATAATAATC
Found at i:31495 original size:16 final size:16
Alignment explanation
Indices: 31474--31513 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
31464 CAAGAAAATT
* *
31474 ATTACAGCTCTATTTC
1 ATTACAACTATATTTC
*
31490 ATTACAATTATATTTC
1 ATTACAACTATATTTC
31506 ATTACAAC
1 ATTACAAC
31514 GAACCAAACG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTACAACTATATTTC
Found at i:35652 original size:21 final size:21
Alignment explanation
Indices: 35613--35652 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35603 GTTGATACTA
* * *
35613 TATTAATTTATTATTTTTAAG
1 TATTAAATTATAATATTTAAG
35634 TATTAAATTATAATATTTA
1 TATTAAATTATAATATTTA
35653 TTTTTATTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
TATTAAATTATAATATTTAAG
Found at i:36101 original size:22 final size:20
Alignment explanation
Indices: 36047--36101 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
36037 AAAATATTTT
*
36047 TATCAAATAATTTAATTATA
1 TATCAAATAATTTAATAATA
*
36067 TACCATAATTAATTCTAAGTAATA
1 TATCA-AA-TAATT-TAA-TAATA
36091 TATCAAATAAT
1 TATCAAATAAT
36102 GTTATAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 4 0.14
21 2 0.07
22 9 0.32
23 5 0.18
24 8 0.29
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (20 bp):
TATCAAATAATTTAATAATA
Found at i:44943 original size:22 final size:23
Alignment explanation
Indices: 44918--44973 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
44908 AGGTCAACCC
*
44918 ATATTATTATTTAAT-TT-TTTTA
1 ATATTA-TATATAATATTATTTTA
44940 ATA-TATATATAATATTATTTTA
1 ATATTATATATAATATTATTTTA
44962 ATATT-TA-ATAAT
1 ATATTATATATAAT
44974 TCTATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 7 0.23
21 9 0.30
22 13 0.43
23 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
ATATTATATATAATATTATTTTA
Found at i:45790 original size:3 final size:3
Alignment explanation
Indices: 45782--45807 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
45772 AAGAAATAAC
45782 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
45808 GACTCTCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:53136 original size:9 final size:9
Alignment explanation
Indices: 53122--53189 Score: 55
Period size: 9 Copynumber: 7.6 Consensus size: 9
53112 GGAGAAAATG
53122 GGGCCAGGA
1 GGGCCAGGA
**
53131 GGGCCACCA
1 GGGCCAGGA
*
53140 GGACCAGGA
1 GGGCCAGGA
**
53149 GGGCCACCA
1 GGGCCAGGA
*
53158 GGGCCAGGT
1 GGGCCAGGA
* **
53167 GGACCACCA
1 GGGCCAGGA
53176 GGGCCAGGA
1 GGGCCAGGA
53185 GGGCC
1 GGGCC
53190 TCCAGGATGG
Statistics
Matches: 41, Mismatches: 18, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.22, C:0.32, G:0.44, T:0.01
Consensus pattern (9 bp):
GGGCCAGGA
Found at i:53148 original size:18 final size:18
Alignment explanation
Indices: 53125--53196 Score: 99
Period size: 18 Copynumber: 4.0 Consensus size: 18
53115 GAAAATGGGG
53125 CCAGGAGGGCCACCAGGA
1 CCAGGAGGGCCACCAGGA
*
53143 CCAGGAGGGCCACCAGGG
1 CCAGGAGGGCCACCAGGA
* * *
53161 CCAGGTGGACCACCAGGG
1 CCAGGAGGGCCACCAGGA
*
53179 CCAGGAGGGCCTCCAGGA
1 CCAGGAGGGCCACCAGGA
53197 TGGGGCGGTC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.24, C:0.33, G:0.40, T:0.03
Consensus pattern (18 bp):
CCAGGAGGGCCACCAGGA
Found at i:53174 original size:36 final size:36
Alignment explanation
Indices: 53122--53195 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 36
53112 GGAGAAAATG
*
53122 GGGCCAGGAGGGCCACCAGGACCAGGAGGGCCACCA
1 GGGCCAGGAGGACCACCAGGACCAGGAGGGCCACCA
* * *
53158 GGGCCAGGTGGACCACCAGGGCCAGGAGGGCCTCCA
1 GGGCCAGGAGGACCACCAGGACCAGGAGGGCCACCA
53194 GG
1 GG
53196 ATGGGGCGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.22, C:0.32, G:0.43, T:0.03
Consensus pattern (36 bp):
GGGCCAGGAGGACCACCAGGACCAGGAGGGCCACCA
Found at i:53224 original size:39 final size:39
Alignment explanation
Indices: 53170--53261 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 39
53160 GCCAGGTGGA
* * * * *
53170 CCACCAGGGCCAGGAGGGCCTCCAGGATGGGGCGGTCCT
1 CCACCCGGACCAGGAGGACCACCAGGATGGGGCGGCCCT
* *
53209 CCACCCGGACCAGGAGGACCACCGGGGTGGGGCGGCCCT
1 CCACCCGGACCAGGAGGACCACCAGGATGGGGCGGCCCT
**
53248 CCAGTCGGACCAGG
1 CCACCCGGACCAGG
53262 GTTTTTTGGT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.16, C:0.36, G:0.40, T:0.08
Consensus pattern (39 bp):
CCACCCGGACCAGGAGGACCACCAGGATGGGGCGGCCCT
Found at i:56383 original size:333 final size:330
Alignment explanation
Indices: 55762--56389 Score: 780
Period size: 333 Copynumber: 1.9 Consensus size: 330
55752 AATATTATTA
* *
55762 ACCTTTCAATTAAAACAATACGTAGTTATATATAATTTGAATATTCTAAGAGTCTTAAAGATTGA
1 ACCTTTCAATTAAAACAATACATAGTTATATATAATTTGAATACTCTAAGAGTCTTAAAGATTGA
** ** * * *
55827 CACGTAGTTTTTCATTTCTTTTAGGATTTGCGTCTATTTTCTTATCATATTTATAATGGTTAATG
66 CACGTAGCCTCCCATTTCTTTTAGGATTTGCATCTATTTTCTTATCATATTCATAAGGGTTAATG
* * *
55892 GCACCGATGGCCCTTGTACCTTGGAGTTTGTTCTAATGTGGCCCTTATACTTTCAAAATATCCAA
131 GCACCGATGGCCCCTGTACCTTGGAGTTGGTTCTAATGTGGCCCTTATACTTGCAAAATATCCAA
* ** * * * * * ** **
55957 TTAAATCGTTGTACTTTGCTTCCGTTAGCTAAAGTGGTCTCTGACCCTAATGGCATTATTTTTTT
196 TTAAACCCCTATACTTTACTTCCATTAGCTAAAGTGGTCTCTAACCCAAACAGCATTATTTTTGG
* *
56022 ATTACATGGTGCTTGTGCCCAATGAGATGTCGACATGTGTAAAGCTATCGACTTGAAATAATTAA
261 ATTACATGGCGCTTGTGCCCAATGAGATGCCGACATGTGTAAAGCTATCGACTTGAAATAATTAA
56087 TATCG
326 TATCG
* *
56092 ACCTTTCGATTAAAACAATACATAGTTATATATAATTTGAATACTCTAATAGTCTTAAAGATTGA
1 ACCTTTCAATTAAAACAATACATAGTTATATATAATTTGAATACTCTAAGAGTCTTAAAGATTGA
* * *
56157 CATGT-GACCTCCCATTTCTTTTAGG-TTTGTATCTACTTTTTTTTACATCATATTCATAAGGGT
66 CACGTAG-CCTCCCATTTCTTTTAGGATTTGCATCTA--TTTTCTT--ATCATATTCATAAGGGT
* *
56220 TAATGGCACCGTTGGCCCCTGTA-CTTTGAGGTTGGTTCTAATGTGGCCCTTATACTTGCAAAAT
126 TAATGGCACCGATGGCCCCTGTACCTTGGA-GTTGGTTCTAATGTGGCCCTTATACTTGCAAAAT
* * * * *
56284 GTCCATTTAACCCCCTATACTTTACTTCTATTGGCTAAAGTGG-CGTCTAACCCAAACAG-ATTA
190 ATCCAATTAAACCCCTATACTTTACTTCCATTAGCTAAAGTGGTC-TCTAACCCAAACAGCATTA
* * *
56347 CTTTTTGGATTACGTGGCGCTTGTGCTCAGTGAGATGCCGACA
254 -TTTTTGGATTACATGGCGCTTGTGCCCAATGAGATGCCGACA
56390 CGTATAAAAT
Statistics
Matches: 249, Mismatches: 41, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
329 9 0.04
330 79 0.32
331 6 0.02
332 10 0.04
333 145 0.58
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (330 bp):
ACCTTTCAATTAAAACAATACATAGTTATATATAATTTGAATACTCTAAGAGTCTTAAAGATTGA
CACGTAGCCTCCCATTTCTTTTAGGATTTGCATCTATTTTCTTATCATATTCATAAGGGTTAATG
GCACCGATGGCCCCTGTACCTTGGAGTTGGTTCTAATGTGGCCCTTATACTTGCAAAATATCCAA
TTAAACCCCTATACTTTACTTCCATTAGCTAAAGTGGTCTCTAACCCAAACAGCATTATTTTTGG
ATTACATGGCGCTTGTGCCCAATGAGATGCCGACATGTGTAAAGCTATCGACTTGAAATAATTAA
TATCG
Found at i:56721 original size:16 final size:17
Alignment explanation
Indices: 56688--56725 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
56678 TTTGAGCATC
56688 AAATTATATAAAAAATT
1 AAATTATATAAAAAATT
*
56705 AAATTATAT-ATAAATT
1 AAATTATATAAAAAATT
56721 AAATT
1 AAATT
56726 TTAAATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTATATAAAAAATT
Found at i:61385 original size:31 final size:31
Alignment explanation
Indices: 61349--61486 Score: 113
Period size: 31 Copynumber: 4.5 Consensus size: 31
61339 TGACCCTAAA
* *
61349 AAGTTTAAGTACCAACTTAGAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAATGTC
* * *
61380 TAGTTTAGGTATCAAATTAGAAAAAAATGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAATGTC
* * * *
61411 AAATTTGAGTACCAAATTGGACCAAAAA--T-
1 AAGTTTAAGTACCAAATTAGA-AAAAAATGTC
* * *
61440 -AGTTTAGGTATCAAATTAGAAAAAAATGAC
1 AAGTTTAAGTACCAAATTAGAAAAAAATGTC
* *
61470 AAGTTCAAGTACTAAAT
1 AAGTTTAAGTACCAAAT
61487 ATTATATTAA
Statistics
Matches: 79, Mismatches: 23, Indels: 10
0.71 0.21 0.09
Matches are distributed among these distances:
27 5 0.06
28 15 0.19
30 1 0.01
31 53 0.67
32 5 0.06
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAATGTC
Found at i:64554 original size:3 final size:3
Alignment explanation
Indices: 64548--64572 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
64538 ATATAAACTT
64548 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
64573 TTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:65655 original size:21 final size:22
Alignment explanation
Indices: 65629--65670 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
65619 AACCCCTCCC
65629 AAAAAATA-AACAA-AAAAATTT
1 AAAAAATAGAA-AATAAAAATTT
65650 AAAAAATAGAAAATAAAAATT
1 AAAAAATAGAAAATAAAAATT
65671 CTTGACATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (22 bp):
AAAAAATAGAAAATAAAAATTT
Found at i:66446 original size:2 final size:2
Alignment explanation
Indices: 66439--66480 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
66429 GGGAAAAATC
* *
66439 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
66481 CAGAACTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:72817 original size:23 final size:24
Alignment explanation
Indices: 72777--72827 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
72767 TTATCAATAA
*
72777 ATTTATGAAAATTAATTTT-TTTT
1 ATTTATGAAAATTAATTTTATATT
*
72800 ATTTAT-AAAATATGATTTTATATT
1 ATTTATGAAAAT-TAATTTTATATT
72824 ATTT
1 ATTT
72828 TAATTAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 12 0.50
24 7 0.29
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
ATTTATGAAAATTAATTTTATATT
Found at i:84916 original size:42 final size:42
Alignment explanation
Indices: 84831--84917 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
84821 TTGAACAAAA
* * * **
84831 AAAATTTAGATACCAAATTAAAAAATATCAAATTGGATCATC
1 AAAATTAAGATACCAAATTAAAAAAAATAAAATTAAATCATC
84873 AAAATTAAG-TACCAAATTAAAATAAAATAAAATTTAAAT-ATC
1 AAAATTAAGATACCAAATTAAAA-AAAATAAAA-TTAAATCATC
84915 AAA
1 AAA
84918 TGTTATATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
41 13 0.34
42 21 0.55
43 4 0.11
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.28
Consensus pattern (42 bp):
AAAATTAAGATACCAAATTAAAAAAAATAAAATTAAATCATC
Found at i:86669 original size:28 final size:28
Alignment explanation
Indices: 86629--86685 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
86619 TCCAGAGAGT
86629 ATCAACCCTAAGCCATTGAAACTTTTTC
1 ATCAACCCTAAGCCATTGAAACTTTTTC
86657 ATCAACCCTAAGCCATTGAAACTTTTTC
1 ATCAACCCTAAGCCATTGAAACTTTTTC
86685 A
1 A
86686 AAGCACAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.32
Consensus pattern (28 bp):
ATCAACCCTAAGCCATTGAAACTTTTTC
Found at i:87080 original size:25 final size:25
Alignment explanation
Indices: 87052--87099 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
87042 ATTAAAACCC
87052 ATCTCTTAT-TTTCTATAAAGTTTCA
1 ATCT-TTATGTTTCTATAAAGTTTCA
*
87077 ATCTTTTTGTTTCTATAAAGTTT
1 ATCTTTATGTTTCTATAAAGTTT
87100 AAAAAAGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.56
Consensus pattern (25 bp):
ATCTTTATGTTTCTATAAAGTTTCA
Found at i:92270 original size:30 final size:29
Alignment explanation
Indices: 92137--92619 Score: 438
Period size: 29 Copynumber: 16.4 Consensus size: 29
92127 TCCTGAATGT
* *
92137 CCCTAAACTATCCAAAAATCTCATTTTTAT
1 CCCTAAACT-TCCAAAAATCCCATTTTTAC
* ** * *
92167 CCCTGAACTTATAAAAATCTCA-TTTTAA
1 CCCTAAACTTCCAAAAATCCCATTTTTAC
*
92195 CCCTAAAACTTCCAAAAATCCCATATTTAC
1 CCCT-AAACTTCCAAAAATCCCATTTTTAC
** * * *
92225 CCCCGAACTTTCAAAAATCCCATTTCTGAT
1 CCCTAAACTTCCAAAAATCCCATTT-TTAC
* *
92255 CCATAAACTTCC-AAAATTCCATTTTTAC
1 CCCTAAACTTCCAAAAATCCCATTTTTAC
* *
92283 CCCCAAACTTTCAAAAATCCCATTTTTGA-
1 CCCTAAACTTCCAAAAATCCCATTTTT-AC
*
92312 CCCTAAAACTTTCAAAAATCCCATTTTTAC
1 CCCT-AAACTTCCAAAAATCCCATTTTTAC
*
92342 CCTTAAACTTCCAAAAATCCCATTTTTGAC
1 CCCTAAACTTCCAAAAATCCCATTTTT-AC
92372 CCCTAAACTTCCAAAAATCCCATTTTTAC
1 CCCTAAACTTCCAAAAATCCCATTTTTAC
* * * *
92401 CCTTGAACTTCTAAAAATCCAATTTTTACC
1 CCCTAAACTTCCAAAAATCCCATTTTTA-C
*
92431 CCTCTAAACTTTCAAAAATCCCATTTTTGA-
1 CC-CTAAACTTCCAAAAATCCCATTTTT-AC
*
92461 CCTTGAAACTTCCAAAAATCCCATTTTTA-
1 CCCT-AAACTTCCAAAAATCCCATTTTTAC
* *
92490 CCCTCGAACTTCCGAAAATCCCATTTTTGAC
1 CCCT-AAACTTCCAAAAATCCCATTTTT-AC
* * * *
92521 CCCAAAACTTTCAAGAATTCCATTTTTA-
1 CCCTAAACTTCCAAAAATCCCATTTTTAC
* * *
92549 CCTTCAAACTTCCAAAAATCTCATTTTAAC
1 CCCT-AAACTTCCAAAAATCCCATTTTTAC
* * ** *
92579 CTCAAAACTTTTAAAAATCTCATTTTTAC
1 CCCTAAACTTCCAAAAATCCCATTTTTAC
*
92608 ACCTGAAACTTC
1 CCCT-AAACTTC
92620 TAAACAATTA
Statistics
Matches: 367, Mismatches: 69, Indels: 34
0.78 0.15 0.07
Matches are distributed among these distances:
28 22 0.06
29 188 0.51
30 133 0.36
31 23 0.06
32 1 0.00
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATCCCATTTTTAC
Found at i:92359 original size:59 final size:58
Alignment explanation
Indices: 92137--92641 Score: 445
Period size: 59 Copynumber: 8.6 Consensus size: 58
92127 TCCTGAATGT
* * * *
92137 CCCT-AAACTATCCAAAAATCTCATTTTTATCCC-TGAACTTAT-AAAAATCTCATTTTAA
1 CCCTAAAACT-TCCAAAAATCCCATTTTTA-CCCTTAAACTT-TCAAAAATCCCATTTTTA
* *** *
92195 CCCTAAAACTTCCAAAAATCCCATATTTACCCCCGAACTTTCAAAAATCCCATTTCTGA
1 CCCTAAAACTTCCAAAAATCCCATTTTTACCCTTAAACTTTCAAAAATCCCATTT-TTA
* * **
92254 TCC-ATAAACTTCC-AAAATTCCATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTGA
1 CCCTA-AAACTTCCAAAAATCCCATTTTTACCCTTAAACTTTCAAAAATCCCATTTTT-A
* *
92312 CCCTAAAACTTTCAAAAATCCCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTTGA
1 CCCTAAAACTTCCAAAAATCCCATTTTTACCCTTAAACTTTCAAAAATCCCATTTTT-A
* *
92371 CCCCT-AAACTTCCAAAAATCCCATTTTTACCCTTGAAC-TTCTAAAAATCCAATTTTTA
1 -CCCTAAAACTTCCAAAAATCCCATTTTTACCCTTAAACTTTC-AAAAATCCCATTTTTA
* * *
92429 CCCCTCTAAACTTTCAAAAATCCCATTTTTGA-CCTTGAAACTTCCAAAAATCCCATTTTTA
1 -CCCT-AAAACTTCCAAAAATCCCATTTTT-ACCCTT-AAACTTTCAAAAATCCCATTTTTA
** * ** * *
92490 CCCTCGAACTTCCGAAAATCCCATTTTTGACCCCAAAACTTTCAAGAATTCCATTTTTA
1 CCCTAAAACTTCCAAAAATCCCATTTTT-ACCCTTAAACTTTCAAAAATCCCATTTTTA
* * * * * * *
92549 CCTTCAAACTTCCAAAAATCTCA-TTTTAACCTCAAAACTTTTAAAAATCTCATTTTTA
1 CCCTAAAACTTCCAAAAATCCCATTTTTACCCT-TAAACTTTCAAAAATCCCATTTTTA
* * *
92607 CACCTGAAACTTCTAAACAATTACCA-TTTTACCCT
1 C-CCTAAAACTTCCAAA-AA-TCCCATTTTTACCCT
92642 CGGGTATTCG
Statistics
Matches: 378, Mismatches: 49, Indels: 37
0.81 0.11 0.08
Matches are distributed among these distances:
57 8 0.02
58 122 0.32
59 178 0.47
60 38 0.10
61 30 0.08
62 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.34
Consensus pattern (58 bp):
CCCTAAAACTTCCAAAAATCCCATTTTTACCCTTAAACTTTCAAAAATCCCATTTTTA
Found at i:107049 original size:29 final size:28
Alignment explanation
Indices: 106999--107307 Score: 222
Period size: 29 Copynumber: 10.4 Consensus size: 28
106989 AAGGTCCCTA
* *
106999 AACTGTCCAAAAATCTCATTTTTACGATCG
1 AACT-TCCAAAAATCCCATTTTTAC-CTCG
** *
107029 AACTTTTAAAAATCCCATTTTTGACCTTG
1 AACTTCCAAAAATCCCATTTTT-ACCTCG
* *
107058 AAACTTCCAAAAATCCTATTTTTACCCCCG
1 -AACTTCCAAAAATCCCATTTTTA-CCTCG
* *
107088 AACTTCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATCCCATTTTT-ACCTC-G
* * *
107118 AACTTCCAAAAATCCCATATTTACCCCA
1 AACTTCCAAAAATCCCATTTTTACCTCG
* **
107146 AACTTCTAAAAATCCCATTTTTGACCCTTAA
1 AACTTCCAAAAATCCCATTTTT-A-CC-TCG
* * * * *
107177 AACTTCCAAAAATTCAATTTTAACCCCAA
1 AACTTCCAAAAATCCCATTTTTACCTC-G
* *
107206 AACTTCCAAAAATCTCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTA-CCTCG
* *
107235 AACTTCCAAAAATCCCATTTTTAACCCCCAA
1 AACTTCCAAAAATCCCATTTTT-A-CCTC-G
* * *
107266 AACTTCAAAAAATCTCATTTTTACCCTCAA
1 AACTTCCAAAAATCCCATTTTTA-CCTC-G
107296 AACTTCCAAAAA
1 AACTTCCAAAAA
107308 ATTACCATTT
Statistics
Matches: 233, Mismatches: 34, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
28 21 0.09
29 92 0.39
30 81 0.35
31 39 0.17
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.30
Consensus pattern (28 bp):
AACTTCCAAAAATCCCATTTTTACCTCG
Found at i:107070 original size:30 final size:30
Alignment explanation
Indices: 107036--107307 Score: 306
Period size: 30 Copynumber: 9.2 Consensus size: 30
107026 TCGAACTTTT
***
107036 AAAAATCCCATTTTTGA-CCTTGAAACTTCC
1 AAAAATCCCATTTTT-ACCCCCAAAACTTCC
* *
107066 AAAAATCCTATTTTTACCCCC-GAACTTCC
1 AAAAATCCCATTTTTACCCCCAAAACTTCC
107095 AAAAATCCCATTTTTGA-CCCCAAAACTTCC
1 AAAAATCCCATTTTT-ACCCCCAAAACTTCC
* *
107125 AAAAATCCCATATTTA-CCCC-AAACTTCT
1 AAAAATCCCATTTTTACCCCCAAAACTTCC
**
107153 AAAAATCCCATTTTTGACCCTTAAAACTTCC
1 AAAAATCCCATTTTT-ACCCCCAAAACTTCC
* * *
107184 AAAAAT-TCAATTTTAACCCCAAAACTTCC
1 AAAAATCCCATTTTTACCCCCAAAACTTCC
* *
107213 AAAAATCTCATTTTTACCCCC-GAACTTCC
1 AAAAATCCCATTTTTACCCCCAAAACTTCC
*
107242 AAAAATCCCATTTTTAACCCCCAAAACTTCA
1 AAAAATCCCATTTTT-ACCCCCAAAACTTCC
* *
107273 AAAAATCTCATTTTTACCCTCAAAACTTCC
1 AAAAATCCCATTTTTACCCCCAAAACTTCC
107303 AAAAA
1 AAAAA
107308 ATTACCATTT
Statistics
Matches: 207, Mismatches: 26, Indels: 18
0.82 0.10 0.07
Matches are distributed among these distances:
28 21 0.10
29 71 0.34
30 82 0.40
31 33 0.16
ACGTcount: A:0.38, C:0.31, G:0.02, T:0.29
Consensus pattern (30 bp):
AAAAATCCCATTTTTACCCCCAAAACTTCC
Found at i:107071 original size:59 final size:58
Alignment explanation
Indices: 106998--107307 Score: 286
Period size: 59 Copynumber: 5.2 Consensus size: 58
106988 GAAGGTCCCT
** * *
106998 AAACTGTCCAAAAATCTCATTTTTACGATCGAACTTTTAAAAATCCCATTTTTGACCTTG
1 AAACT-TCCAAAAATCTCATTTTTAC-CCCGAACTTCTAAAAATCCCATTTTTGACCTTA
* **
107058 AAACTTCCAAAAATC-CTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATCTC-ATTTTTA-CCCCGAACTTCTAAAAATCCCATTTTTGACCTTA
* * *
107117 AAACTTCCAAAAATCCCATATTTACCCCAAACTTCTAAAAATCCCATTTTTGACCCTTA
1 AAACTTCCAAAAATCTCATTTTTACCCCGAACTTCTAAAAATCCCATTTTTGA-CCTTA
* * * * ***
107176 AAACTTCCAAAAAT-TCAATTTTAACCCCAAAACTTCCAAAAATCTCATTTTT-ACCCCC
1 AAACTTCCAAAAATCTC-ATTTTTACCCC-GAACTTCTAAAAATCCCATTTTTGACCTTA
* * * * * *
107234 GAACTTCCAAAAATCCCATTTTTAACCCCCAAAACTTCAAAAAATCTCATTTTT-ACCCTCA
1 AAACTTCCAAAAATCTCATTTTT-A-CCCC-GAACTTCTAAAAATCCCATTTTTGA-CCTTA
107295 AAACTTCCAAAAA
1 AAACTTCCAAAAA
107308 ATTACCATTT
Statistics
Matches: 213, Mismatches: 27, Indels: 19
0.82 0.10 0.07
Matches are distributed among these distances:
58 49 0.23
59 93 0.44
60 56 0.26
61 15 0.07
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.30
Consensus pattern (58 bp):
AAACTTCCAAAAATCTCATTTTTACCCCGAACTTCTAAAAATCCCATTTTTGACCTTA
Found at i:107729 original size:96 final size:96
Alignment explanation
Indices: 107559--107740 Score: 224
Period size: 96 Copynumber: 1.9 Consensus size: 96
107549 AAAACTTTAA
** * * * * * *
107559 AATCGAGGCAATATTTTTTTATTTTGAGTTTTGAAAATTTGCGCCTTAACTTTCTAGGTGCAATT
1 AATCGAGGCAATATTTCATTATTTCGAGTTCTGAAAATTTACGCCTTAACTTACCAAGTGCAATT
*
107624 TTTATTCAAATCGAAATAATCGAATACCCTT
66 TTCATTCAAATCGAAATAATCGAATACCCTT
* *
107655 AATCGAGGCAATGTTTCATTATCTTCGA-TTCTGAAAATTTACGTCTTAACTTACCAAGTGCAAT
1 AATCGAGGCAATATTTCATTAT-TTCGAGTTCTGAAAATTTACGCCTTAACTTACCAAGTGCAAT
*
107719 CTTTCA-TCAAATCGAGATAATC
65 -TTTCATTCAAATCGAAATAATC
107741 AAACATCCTT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
96 64 0.89
97 8 0.11
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (96 bp):
AATCGAGGCAATATTTCATTATTTCGAGTTCTGAAAATTTACGCCTTAACTTACCAAGTGCAATT
TTCATTCAAATCGAAATAATCGAATACCCTT
Found at i:108847 original size:23 final size:23
Alignment explanation
Indices: 108804--108848 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
108794 ATCAACCTTT
*
108804 TATATATATAATTTAAGTCTAAA
1 TATATATATAATTTAAATCTAAA
108827 TATAT-TATAATTATAAATCTAA
1 TATATATATAATT-TAAATCTAA
108849 TCATGCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
TATATATATAATTTAAATCTAAA
Found at i:110307 original size:7 final size:7
Alignment explanation
Indices: 110297--110352 Score: 57
Period size: 7 Copynumber: 8.4 Consensus size: 7
110287 CTTAAACTTT
110297 AAATTTC
1 AAATTTC
110304 AAA-TTC
1 AAATTTC
110310 TAAATTTC
1 -AAATTTC
110318 AAATTTC
1 AAATTTC
110325 AAATTT-
1 AAATTTC
*
110331 AAACTTC
1 AAATTTC
*
110338 AAACTT-
1 AAATTTC
110344 AAA-TTC
1 AAATTTC
110350 AAA
1 AAA
110353 CTTGAGTCTG
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
5 2 0.05
6 14 0.32
7 25 0.57
8 3 0.07
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (7 bp):
AAATTTC
Found at i:110321 original size:21 final size:21
Alignment explanation
Indices: 110289--110349 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
110279 AATTATTTCT
110289 TAAACTTT-AAATTTCAAATTC
1 TAAA-TTTCAAATTTCAAATTC
110310 TAAATTTCAAATTTCAAATT-
1 TAAATTTCAAATTTCAAATTC
* *
110330 TAAACTTCAAACTT-AAATTC
1 TAAATTTCAAATTTCAAATTC
110350 AAACTTGAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 5 0.14
20 15 0.42
21 16 0.44
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTTCAAATTTCAAATTC
Found at i:110352 original size:12 final size:13
Alignment explanation
Indices: 110322--110355 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
110312 AATTTCAAAT
*
110322 TTCAAATTTAAAC
1 TTCAAACTTAAAC
110335 TTCAAACTTAAA-
1 TTCAAACTTAAAC
110347 TTCAAACTT
1 TTCAAACTT
110356 GAGTCTGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (13 bp):
TTCAAACTTAAAC
Done.