Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011232.1 Kokia drynarioides strain JFW-HI SEQ_126210, 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: 115517
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:112 original size:22 final size:24
Alignment explanation
Indices: 84--128 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
74 ACTTATCCAC
*
84 CATTCTTTCCAAAT-GA-TTCATT
1 CATTCTTACCAAATAGAGTTCATT
106 CATTCTTACCAAATAGAGTTCAT
1 CATTCTTACCAAATAGAGTTCAT
129 CGAGTCTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 2 0.10
24 5 0.25
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (24 bp):
CATTCTTACCAAATAGAGTTCATT
Found at i:415 original size:81 final size:80
Alignment explanation
Indices: 265--472 Score: 299
Period size: 81 Copynumber: 2.6 Consensus size: 80
255 ATGATCCTGA
* *
265 CACCCTGTGTCTAGCGGATAAACCACAAAACTGAGCCCAACTCTAGTTGGATTAACCAACAAATA
1 CACCCAGTGCCTAGCGGATAAACCACAAAACTGAGCCCAACTCTAGTTGGATTAACCAACAAATA
*
330 TCCGTCAAATCTTGG
66 TCCGTCAAACCTTGG
* * * *
345 CACCTAGTGCCTAGCGGGATAAACTACAAAAGTGAGTCCAACTCTAGTTGGATTAACCAACAAAT
1 CACCCAGTGCCTAGC-GGATAAACCACAAAACTGAGCCCAACTCTAGTTGGATTAACCAACAAAT
410 ATCCGTCAAACCTTGG
65 ATCCGTCAAACCTTGG
* ** * *
426 CACCCAGTGTCTAGCGGATAAACCGGAAAACTAAGCCCAGCTCTAGT
1 CACCCAGTGCCTAGCGGATAAACCACAAAACTGAGCCCAACTCTAGT
473 CAGTTAAACT
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
80 37 0.33
81 74 0.67
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (80 bp):
CACCCAGTGCCTAGCGGATAAACCACAAAACTGAGCCCAACTCTAGTTGGATTAACCAACAAATA
TCCGTCAAACCTTGG
Found at i:8478 original size:58 final size:58
Alignment explanation
Indices: 8409--8528 Score: 165
Period size: 58 Copynumber: 2.1 Consensus size: 58
8399 AAAATGAGTT
*
8409 GTTTATGAGTGTTATCTAG-A-AATAAAATTATATTTTGG-TTAAAAATTATTTGGGTTTA
1 GTTTATGAGTGTT-T-TAGAAGAATAAAATTATATTTTGGCTTAAAAA-TATTTGAGTTTA
* *
8467 GTTTATGAGTGTTTTTGAAGAATGAAATTATATTTTGGCTTAAAAATATTTGAGTTTA
1 GTTTATGAGTGTTTTAGAAGAATAAAATTATATTTTGGCTTAAAAATATTTGAGTTTA
8525 GTTT
1 GTTT
8529 GTTAATGGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
56 2 0.04
57 2 0.04
58 45 0.80
59 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (58 bp):
GTTTATGAGTGTTTTAGAAGAATAAAATTATATTTTGGCTTAAAAATATTTGAGTTTA
Found at i:11653 original size:22 final size:22
Alignment explanation
Indices: 11612--11654 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11602 TCTCTCTCGT
11612 TTGTTTTTTTTCTTTATTTTGG
1 TTGTTTTTTTTCTTTATTTTGG
11634 TTGTTCTTCTTTT-TTT-TTTTG
1 TTGTT-TT-TTTTCTTTATTTTG
11655 TATGACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.53
23 5 0.26
24 4 0.21
ACGTcount: A:0.02, C:0.07, G:0.12, T:0.79
Consensus pattern (22 bp):
TTGTTTTTTTTCTTTATTTTGG
Found at i:34541 original size:26 final size:26
Alignment explanation
Indices: 34512--34561 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
34502 CAGGAATGTC
34512 GCTGCATGAACATGTCCAGAATTGTT
1 GCTGCATGAACATGTCCAGAATTGTT
*
34538 GCTGCATGAACGTGTCCAGAATTG
1 GCTGCATGAACATGTCCAGAATTG
34562 CGCCTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (26 bp):
GCTGCATGAACATGTCCAGAATTGTT
Found at i:38526 original size:38 final size:37
Alignment explanation
Indices: 38470--38550 Score: 108
Period size: 38 Copynumber: 2.2 Consensus size: 37
38460 TAATGTCGCT
* **
38470 GCATGAGCACCTCTAGATTGTGCCCAAAAACTGTCGTC
1 GCATGAGCACCTCCAGATTGCACCC-AAAACTGTCGTC
* *
38508 GCATGTGCACTTCCAGATTGCACCCAAAACTGTCGTC
1 GCATGAGCACCTCCAGATTGCACCCAAAACTGTCGTC
38545 GCATGA
1 GCATGA
38551 ATATTTTTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 17 0.46
38 20 0.54
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (37 bp):
GCATGAGCACCTCCAGATTGCACCCAAAACTGTCGTC
Found at i:38683 original size:26 final size:26
Alignment explanation
Indices: 38645--38702 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
38635 ATTGCACCCA
*
38645 AGAA-TGTTGCTGCATGAACATGTCC
1 AGAATTGTCGCTGCATGAACATGTCC
*
38670 AGAATTGTCGCTGCATGAACGTGTCC
1 AGAATTGTCGCTGCATGAACATGTCC
38696 AGAATTG
1 AGAATTG
38703 CGCCCAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 4 0.13
26 26 0.87
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (26 bp):
AGAATTGTCGCTGCATGAACATGTCC
Found at i:41040 original size:80 final size:79
Alignment explanation
Indices: 40888--41045 Score: 228
Period size: 80 Copynumber: 2.0 Consensus size: 79
40878 GATGTAAACA
*
40888 CTTACTTCAATTTTAATTTGTTCTTAATATTAAGTCCTTGTATAATATTTTTAATATTCATAGTA
1 CTTACTTCAATTTTAATTTGTTCTTAATATTAAGTCCTTATATAATATTTTTAATATTCATA-TA
*
40953 TGGAAATATAAATAT
65 AGGAAATATAAATAT
* * * *
40968 CTTAGTTCAATTTTAATTTGTTTTTAATATTAAGTCCTTATATATTATTTTTATTATTCAT-TAC
1 CTTACTTCAATTTTAATTTGTTCTTAATATTAAGTCCTTATATAATATTTTTAATATTCATATA-
41032 AGGAAAATATAAAT
65 AGG-AAATATAAAT
41046 TTGTGCTTCA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
78 2 0.03
79 2 0.03
80 66 0.94
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.50
Consensus pattern (79 bp):
CTTACTTCAATTTTAATTTGTTCTTAATATTAAGTCCTTATATAATATTTTTAATATTCATATAA
GGAAATATAAATAT
Found at i:42236 original size:30 final size:31
Alignment explanation
Indices: 42197--42276 Score: 108
Period size: 30 Copynumber: 2.6 Consensus size: 31
42187 GTCAATAAAT
* *
42197 AATTTTAAAATTATTAACATTACTTTTTT-A
1 AATTATAAAATTATTAAAATTACTTTTTTGA
*
42227 AATTATAAAATTATTAAAATTATTTTTTTGA
1 AATTATAAAATTATTAAAATTACTTTTTTGA
*
42258 AATAAATAAAATTATTAAA
1 AAT-TATAAAATTATTAAA
42277 TAATTTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 26 0.59
31 4 0.09
32 14 0.32
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (31 bp):
AATTATAAAATTATTAAAATTACTTTTTTGA
Found at i:42239 original size:21 final size:22
Alignment explanation
Indices: 42199--42239 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42189 CAATAAATAA
*
42199 TTTTAAAATTATTAACATTACT
1 TTTTAAAATTATTAAAATTACT
*
42221 TTTTTAAATTA-TAAAATTA
1 TTTTAAAATTATTAAAATTA
42240 TTAAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAATTATTAAAATTACT
Found at i:50177 original size:72 final size:72
Alignment explanation
Indices: 50081--50216 Score: 263
Period size: 72 Copynumber: 1.9 Consensus size: 72
50071 TTTATTAACT
50081 CAAAAGAGAAGTTGTTGAATAATAATGAATTGATTTCCTTGTGTACAAGGCAAAGACCTTTATAT
1 CAAAAGAGAAGTTGTTGAATAATAATGAATTGATTTCCTTGTGTACAAGGCAAAGACCTTTATAT
50146 AGGCTAG
66 AGGCTAG
*
50153 CAAAATAGAAGTTGTTGAATAATAATGAATTGATTTCCTTGTGTACAAGGCAAAGACCTTTATA
1 CAAAAGAGAAGTTGTTGAATAATAATGAATTGATTTCCTTGTGTACAAGGCAAAGACCTTTATA
50217 CATACTAGCT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (72 bp):
CAAAAGAGAAGTTGTTGAATAATAATGAATTGATTTCCTTGTGTACAAGGCAAAGACCTTTATAT
AGGCTAG
Found at i:59901 original size:3 final size:3
Alignment explanation
Indices: 59893--59929 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
59883 GAAAAAGAAT
59893 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
59930 CTTGTGGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:71358 original size:36 final size:36
Alignment explanation
Indices: 71282--71358 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
71272 ATATAATCAG
**
71282 TCACATGGCATGAAGAACATACCCACATATTTTCTA
1 TCACATGGCATGAAGAACATACCCACATATTGACTA
* *
71318 TCACATGGCATGAAGAACATACCCATATATTGACTT
1 TCACATGGCATGAAGAACATACCCACATATTGACTA
71354 TCACA
1 TCACA
71359 ACAATCATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (36 bp):
TCACATGGCATGAAGAACATACCCACATATTGACTA
Found at i:71463 original size:23 final size:23
Alignment explanation
Indices: 71428--71575 Score: 251
Period size: 23 Copynumber: 6.4 Consensus size: 23
71418 ATCTTAATTC
*
71428 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
71451 TTTAATCATAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
71474 TTTAAGCACAAATCACATTCATA
1 TTTAAGCATAAATCACATTAATA
71497 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
71520 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
71543 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
71566 TTTAAGCATA
1 TTTAAGCATA
71576 GATAAAAGAA
Statistics
Matches: 116, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 116 1.00
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (23 bp):
TTTAAGCATAAATCACATTAATA
Found at i:78566 original size:28 final size:28
Alignment explanation
Indices: 78533--78586 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
78523 TATATATTTC
*
78533 TTTCCTTTCACATGCACAATGATTTTTT
1 TTTCCTTTCACATACACAATGATTTTTT
78561 TTTCCTTTCACATACACAATGATTTT
1 TTTCCTTTCACATACACAATGATTTT
78587 CATTATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (28 bp):
TTTCCTTTCACATACACAATGATTTTTT
Found at i:78713 original size:18 final size:18
Alignment explanation
Indices: 78670--78713 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
78660 ATATTAAAAT
* *
78670 ATTTTTAAAATAAATTTC
1 ATTTTTATAATAAATTTA
**
78688 ATAATTATAATAAATTTA
1 ATTTTTATAATAAATTTA
78706 ATTTTTAT
1 ATTTTTAT
78714 TACTTAAGTA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTTTATAATAAATTTA
Found at i:79645 original size:15 final size:17
Alignment explanation
Indices: 79625--79659 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
79615 ATTGTTTGAA
79625 AAAC-AATTA-TTTTAT
1 AAACAAATTATTTTTAT
79640 AAACAAATTATTTTTAT
1 AAACAAATTATTTTTAT
79657 AAA
1 AAA
79660 TGAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 5 0.28
17 9 0.50
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
AAACAAATTATTTTTAT
Found at i:80862 original size:25 final size:25
Alignment explanation
Indices: 80833--80883 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
80823 TAAATTTGAG
* * *
80833 ATTTTTTTTTTTAATTTTGTATTTA
1 ATTTTTTTGTCTAATTTGGTATTTA
80858 ATTTTTTTGTCTAATTTGGTATTTA
1 ATTTTTTTGTCTAATTTGGTATTTA
80883 A
1 A
80884 ACTTGACACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.69
Consensus pattern (25 bp):
ATTTTTTTGTCTAATTTGGTATTTA
Found at i:80903 original size:31 final size:31
Alignment explanation
Indices: 80868--80928 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
80858 ATTTTTTTGT
* *
80868 CTAATTTGGTATTTAAACTTGACACTTTTTC
1 CTAATTTAGTACTTAAACTTGACACTTTTTC
80899 CTAATTTAGTACTTAAACTTGACACTTTTT
1 CTAATTTAGTACTTAAACTTGACACTTTTT
80929 TTAAGTTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (31 bp):
CTAATTTAGTACTTAAACTTGACACTTTTTC
Found at i:80943 original size:30 final size:31
Alignment explanation
Indices: 80868--80944 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
80858 ATTTTTTTGT
* *
80868 CTAATTTGGTATTTAAACTTGACACTTTTTC
1 CTAAGTTGGTACTTAAACTTGACACTTTTTC
* *
80899 CTAATTTAGTACTTAAACTTGACACTTTTT-
1 CTAAGTTGGTACTTAAACTTGACACTTTTTC
*
80929 TTAAGTTGGTACTTAA
1 CTAAGTTGGTACTTAA
80945 CCTTTTTGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 13 0.32
31 28 0.68
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (31 bp):
CTAAGTTGGTACTTAAACTTGACACTTTTTC
Found at i:81341 original size:61 final size:60
Alignment explanation
Indices: 81152--81341 Score: 177
Period size: 61 Copynumber: 3.1 Consensus size: 60
81142 ATAAATTTAG
* * *
81152 GTACCAAATTGAATCTAAAAAAAGGATTAGGTACCAAA-TAAGGAAAAAATGACAAGTTCAA
1 GTACCAAATTGAA-CTAAAAAAAAGTTTAGGTACCAAATTAA-GAAAAAATGTCAAGTTCAA
* ** * * * * **
81213 GTACCAAATTGGA-TCCAAAAAAGTTTAGGTATCAGATTAGGAAAAAGTGTCAAGTTTGA
1 GTACCAAATTGAACTAAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAA
** * ** *
81272 GTTTCAAATTGAACTAAAAAAAAAGTTTAAGTACCAAATTAAGAAAATTTGTCATGTTCAA
1 GTACCAAATTGAACT-AAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAA
81333 GTACCAAAT
1 GTACCAAAT
81342 ATTATATTAA
Statistics
Matches: 98, Mismatches: 28, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
59 42 0.43
60 3 0.03
61 53 0.54
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (60 bp):
GTACCAAATTGAACTAAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAA
Found at i:83736 original size:18 final size:17
Alignment explanation
Indices: 83700--83742 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
83690 TACACAAAAA
**
83700 TAAAAAATATTAACTTT
1 TAAAAAATATTAAAATT
83717 TAAAAAGATATTAAAATT
1 TAAAAA-ATATTAAAATT
83735 TATAAAAA
1 TA-AAAAA
83743 AAACTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (17 bp):
TAAAAAATATTAAAATT
Found at i:86392 original size:29 final size:29
Alignment explanation
Indices: 86360--86420 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
86350 TTTTTGGTGG
*
86360 CTCGAAGG-CAAAACGGTAATTTTTGGACA
1 CTCG-AGGTCAAAACGGTAATTTTTGAACA
* * *
86389 CTCGCGGTGAAAATGGTAATTTTTGAACA
1 CTCGAGGTCAAAACGGTAATTTTTGAACA
86418 CTC
1 CTC
86421 AGGGACAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (29 bp):
CTCGAGGTCAAAACGGTAATTTTTGAACA
Found at i:86430 original size:29 final size:29
Alignment explanation
Indices: 86368--86430 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
86358 GGCTCGAAGG
* *
86368 CAAAACGGTAATTTTTGGACACTCGCGGT
1 CAAAACGGTAATTTTTGAACACTCGCGGA
* *
86397 GAAAATGGTAATTTTTGAACACTCAG-GGA
1 CAAAACGGTAATTTTTGAACACTC-GCGGA
86426 CAAAA
1 CAAAA
86431 ATATGACTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (29 bp):
CAAAACGGTAATTTTTGAACACTCGCGGA
Found at i:86470 original size:29 final size:28
Alignment explanation
Indices: 86438--86747 Score: 106
Period size: 29 Copynumber: 10.8 Consensus size: 28
86428 AAAATATGAC
86438 TTTTGGAAGTTTAGGGTGTAAAATGGTAA
1 TTTTGGAAGTTTAGGG-GTAAAATGGTAA
* * * *
86467 TTTT--TAG-TTCGGGAGCAAAACGGTAA
1 TTTTGGAAGTTTAGGG-GTAAAATGGTAA
* ** * * *
86493 TTTTCGAAAAATTCGGGGTCAAAAATGATAT
1 TTTT-GGAAGTTTAGGGGT--AAAATGGTAA
* * *
86524 TTTTTGACG-TTCGAGGGTAAAATGGTAA
1 TTTTGGAAGTTTAG-GGGTAAAATGGTAA
* * * *
86552 TTTTTGGAGGTTCA-GGGAAAAAT-GTGATT
1 -TTTTGGAAGTTTAGGGGTAAAATGGT-A-A
*
86581 TTTTGGAAGTTT-GAGGGTAAAATGATAA
1 TTTTGGAAGTTTAG-GGGTAAAATGGTAA
*
86609 TTTTAAGAAGTTTAGGGGTAAAAAT-GTAA
1 TTTT-GGAAGTTTAGGGGT-AAAATGGTAA
* *
86638 TTTTTGGAA-TTTTGGGGTAAAATGATAA
1 -TTTTGGAAGTTTAGGGGTAAAATGGTAA
* * *
86666 TTTTTGGAAG-TTCGAAGGTAAAAAT-GTGAT
1 -TTTTGGAAGTTTAG-GGGT-AAAATGGT-AA
*
86696 TTTTGGAAAGTTT-GAGGGAAAAAT-GTAA
1 TTTTGG-AAGTTTAG-GGGTAAAATGGTAA
*
86724 TTTTTGTGAAGTTTGGGGGTAAAA
1 -TTTTG-GAAGTTTAGGGGTAAAA
86748 AATGTAATTT
Statistics
Matches: 212, Mismatches: 41, Indels: 56
0.69 0.13 0.18
Matches are distributed among these distances:
26 19 0.09
27 9 0.04
28 55 0.26
29 78 0.37
30 38 0.18
31 13 0.06
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.36
Consensus pattern (28 bp):
TTTTGGAAGTTTAGGGGTAAAATGGTAA
Found at i:86602 original size:57 final size:56
Alignment explanation
Indices: 86513--86862 Score: 246
Period size: 57 Copynumber: 6.0 Consensus size: 56
86503 ATTCGGGGTC
* * * *
86513 AAAAATGATATTTTTT-GACGTTCGAGGGTAAAATGGTAATTTTTGGAGGTTCAGGG
1 AAAAATG-TATTTTTTGGAAGTTTGAGGGTAAAATGATAATTTTTGGAAGTTCAGGG
** *
86569 AAAAATGTGATTTTTTGGAAGTTTGAGGGTAAAATGATAATTTTAAGAAGTTTAGGGG
1 AAAAATGT-ATTTTTTGGAAGTTTGAGGGTAAAATGATAATTTTTGGAAGTTCA-GGG
* * *
86627 TAAAAATGTAATTTTTGGAATTTTG-GGGTAAAATGATAATTTTTGGAAGTTCGAAGGT
1 -AAAAATGTATTTTTTGGAAGTTTGAGGGTAAAATGATAATTTTTGGAAGTTC--AGGG
* **
86685 AAAAATGTGA-TTTTTGGAAAGTTTGAGGGAAAAATG-TAATTTTTGTGAAGTTTGGGGG
1 AAAAATGT-ATTTTTTGG-AAGTTTGAGGGTAAAATGATAATTTTTG-GAAG-TTCAGGG
* * * * *
86743 TAAAAAATGTAATTTTTAGAAAGTTCG-GTGGTAAAAATG-TAATTTTTGTGAAGTTTGAGGT
1 --AAAAATGT-ATTTTTTGGAAGTTTGAG-GGT-AAAATGATAATTTTTG-GAAG-TTCAGGG
* * * * * **
86804 TAAAATATAATTTTTGGAAAGTTTAAGGGTCAAAATG-TGATTTTTAAATAGTTCAGGG
1 AAAAATGTATTTTTTGG-AAGTTTGAGGGT-AAAATGATAATTTTTGGA-AGTTCAGGG
86862 A
1 A
86863 CCTTTTACGT
Statistics
Matches: 236, Mismatches: 39, Indels: 36
0.76 0.13 0.12
Matches are distributed among these distances:
55 1 0.00
56 14 0.06
57 69 0.29
58 49 0.21
59 52 0.22
60 20 0.08
61 31 0.13
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (56 bp):
AAAAATGTATTTTTTGGAAGTTTGAGGGTAAAATGATAATTTTTGGAAGTTCAGGG
Found at i:86633 original size:30 final size:28
Alignment explanation
Indices: 86507--86848 Score: 273
Period size: 29 Copynumber: 11.7 Consensus size: 28
86497 CGAAAAATTC
* * *
86507 GGGGTCAAAAATG-ATATTTTTTGACGTTC
1 GGGGT-AAAAATGTA-ATTTTTGGAAGTTT
* *
86536 GAGGGT-AAAATGGTAATTTTTGGAGGTTC
1 G-GGGTAAAAAT-GTAATTTTTGGAAGTTT
* *
86565 AGGG-AAAAATGTGATTTTTTGGAAGTTT
1 GGGGTAAAAATGT-AATTTTTGGAAGTTT
**
86593 GAGGGT-AAAATGATAATTTTAAGAAGTTT
1 G-GGGTAAAAATG-TAATTTTTGGAAGTTT
*
86622 AGGGGTAAAAATGTAATTTTTGGAATTTT
1 -GGGGTAAAAATGTAATTTTTGGAAGTTT
*
86651 GGGGT-AAAATGATAATTTTTGGAAGTTC
1 GGGGTAAAAATG-TAATTTTTGGAAGTTT
* *
86679 GAAGGTAAAAATGTGATTTTTGGAAAGTTT
1 G-GGGTAAAAATGTAATTTTTGG-AAGTTT
86709 GAGGG-AAAAATGTAATTTTTGTGAAGTTT
1 G-GGGTAAAAATGTAATTTTTG-GAAGTTT
* *
86738 GGGGGTAAAAAATGTAATTTTTAGAAAGTTC
1 -GGGGT-AAAAATGTAATTTTT-GGAAGTTT
86769 GGTGGTAAAAATGTAATTTTTGTGAAGTTT
1 GG-GGTAAAAATGTAATTTTTG-GAAGTTT
* * *
86799 GAGGTTAAAATATAATTTTTGGAAAGTTT
1 GGGGTAAAAATGTAATTTTTGG-AAGTTT
* * *
86828 AAGGGTCAAAATGTGATTTTT
1 -GGGGTAAAAATGTAATTTTT
86849 AAATAGTTCA
Statistics
Matches: 258, Mismatches: 32, Indels: 45
0.77 0.10 0.13
Matches are distributed among these distances:
27 8 0.03
28 46 0.18
29 112 0.43
30 68 0.26
31 23 0.09
32 1 0.00
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (28 bp):
GGGGTAAAAATGTAATTTTTGGAAGTTT
Found at i:86641 original size:86 final size:87
Alignment explanation
Indices: 86536--86822 Score: 241
Period size: 86 Copynumber: 3.3 Consensus size: 87
86526 TTTGACGTTC
* * * *
86536 GAGGGT-AAAATGGTAATTTTTGGAGGTTCAGGGAAAAATG-TGATTTTTTGGAAGTTTGAGGGT
1 GAGGGTAAAAAT-GTAATTTTTGGAAGTTCAGGGAAAAATGAT-AATTTTTGGAAGTTCGAAGGT
86599 -AAAATGATAATTTTAAG-AAGTTT
64 AAAAATG-TAATTTTAAGAAAGTTT
* ** *
86622 -AGGGGTAAAAATGTAATTTTTGGAATTTTGGGGTAAAATGATAATTTTTGGAAGTTCGAAGGTA
1 GA-GGGTAAAAATGTAATTTTTGGAAGTTCAGGGAAAAATGATAATTTTTGGAAGTTCGAAGGTA
* **
86686 AAAATGTGATTTTTGGAAAGTTT
65 AAAATGTAATTTTAAGAAAGTTT
** * **
86709 GAGGG-AAAAATGTAATTTTTGTGAAGTTTGGGGGTAAAAAATG-TAATTTTTAGAAAGTTCGGT
1 GAGGGTAAAAATGTAATTTTTG-GAAG-TTCAGGG--AAAAATGATAATTTTT-GGAAGTTCGAA
* *
86772 GGTAAAAATGTAATTTT-TGTGAAGTTT
61 GGTAAAAATGTAATTTTAAG-AAAGTTT
* *
86799 GA-GGTTAAAATATAATTTTTGGAA
1 GAGGGTAAAAATGTAATTTTTGGAA
86823 AGTTTAAGGG
Statistics
Matches: 166, Mismatches: 22, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
85 1 0.01
86 68 0.41
87 24 0.14
88 7 0.04
89 14 0.08
90 52 0.31
ACGTcount: A:0.35, C:0.01, G:0.27, T:0.37
Consensus pattern (87 bp):
GAGGGTAAAAATGTAATTTTTGGAAGTTCAGGGAAAAATGATAATTTTTGGAAGTTCGAAGGTAA
AAATGTAATTTTAAGAAAGTTT
Found at i:86748 original size:59 final size:58
Alignment explanation
Indices: 86536--86848 Score: 307
Period size: 59 Copynumber: 5.3 Consensus size: 58
86526 TTTGACGTTC
* ** *
86536 GAGGGTAAAATGGTAATTTTTGG-AGGTTCAGGG-AAAAATGTGATTTTTTGG-AAGTTT
1 GAGGGTAAAAT-GTAATTTTTGGAAGTTTGGGGGTAAAAATGT-AATTTTTGGAAAGTTT
** * *
86593 GAGGGTAAAATGATAATTTTAAGAAGTTTAGGGGTAAAAATGTAATTTTTGG-AATTTT
1 GAGGGTAAAATG-TAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAAGTTT
* ** *
86651 G-GGGTAAAATGATAATTTTTGGAAGTTCGAAGGTAAAAATGTGATTTTTGGAAAGTTT
1 GAGGGTAAAATG-TAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAAGTTT
* * *
86709 GAGGGAAAAATGTAATTTTTGTGAAGTTTGGGGGTAAAAAATGTAATTTTTAGAAAGTTC
1 GAGGGTAAAATGTAATTTTTG-GAAGTTTGGGGGT-AAAAATGTAATTTTTGGAAAGTTT
* * *
86769 G-GTGGTAAAAATGTAATTTTTGTGAAGTTT-GAGGTTAAAATATAATTTTTGGAAAGTTT
1 GAG-GGT-AAAATGTAATTTTTG-GAAGTTTGGGGGTAAAAATGTAATTTTTGGAAAGTTT
* *
86828 AAGGGTCAAAATGTGATTTTT
1 GAGGGT-AAAATGTAATTTTT
86849 AAATAGTTCA
Statistics
Matches: 215, Mismatches: 31, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
56 1 0.00
57 62 0.29
58 36 0.17
59 64 0.30
60 29 0.13
61 23 0.11
ACGTcount: A:0.35, C:0.01, G:0.27, T:0.38
Consensus pattern (58 bp):
GAGGGTAAAATGTAATTTTTGGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAAGTTT
Found at i:87983 original size:3 final size:3
Alignment explanation
Indices: 87975--88034 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
87965 TCAACTTTCT
* ** *
87975 TTA TTA TTA TTA TTA TTA CTA TTA AAA TTA TTA ATA TTA -TA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
*
88020 TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA
88035 ATGATATTTA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:88814 original size:11 final size:10
Alignment explanation
Indices: 88778--88835 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
88768 GGATATTATT
88778 AATTTAAATA
1 AATTTAAATA
88788 AATTTAAACTTA
1 AATTTAAA--TA
88800 AATTTATAATA
1 AATTTA-AATA
88811 AATTTAAAT-
1 AATTTAAATA
*
88820 --TTCAAATA
1 AATTTAAATA
88828 AATTTAAA
1 AATTTAAA
88836 CTTAAAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 6 0.15
10 16 0.40
11 8 0.20
12 8 0.20
13 2 0.05
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
AATTTAAATA
Found at i:88817 original size:17 final size:16
Alignment explanation
Indices: 88792--88854 Score: 81
Period size: 17 Copynumber: 3.8 Consensus size: 16
88782 TAAATAAATT
*
88792 TAAACTTAAATTTATAA
1 TAAATTTAAATTTA-AA
88809 TAAATTTAAATTTCAAA
1 TAAATTTAAATTT-AAA
*
88826 TAAATTTAAACTTAAAA
1 TAAATTTAAA-TTTAAA
88843 TAAATTTAAATT
1 TAAATTTAAATT
88855 CTGTTGGGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
16 2 0.05
17 37 0.88
18 3 0.07
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:88818 original size:6 final size:6
Alignment explanation
Indices: 88778--88854 Score: 60
Period size: 6 Copynumber: 13.7 Consensus size: 6
88768 GGATATTATT
*
88778 AATTTA AA--TA AATTTA AACTTA AATTTA TAA--TA AATTTA AATTTCA
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTT-A
* *
88824 AA--TA AATTTA AACTTA AA-ATA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATT
88855 CTGTTGGGCT
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
4 9 0.16
5 7 0.12
6 36 0.63
7 5 0.09
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:91001 original size:6 final size:6
Alignment explanation
Indices: 90990--91028 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
90980 TGATCAAATT
* * *
90990 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
91029 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:92516 original size:49 final size:49
Alignment explanation
Indices: 92444--92565 Score: 199
Period size: 49 Copynumber: 2.5 Consensus size: 49
92434 GACTGGTATA
* **
92444 CTTCTCTGTATCTCATCAAGAAGATGATTGCCTCACTTGTTTCAATCCG
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCG
*
92493 CTTCTCTATATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCG
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCG
*
92542 CTTCTTTGTATCTCATCAGGAAGA
1 CTTCTCTGTATCTCATCAGGAAGA
92566 CAAATTTGGT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 67 1.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (49 bp):
CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCG
Found at i:92700 original size:257 final size:256
Alignment explanation
Indices: 92236--92773 Score: 758
Period size: 257 Copynumber: 2.1 Consensus size: 256
92226 ATTTGGTCTA
* *
92236 CTTCTC-AGTATCTCATCAGGAAGATGACTCCATCACTTGTTTTAATCCACTTCTTTGCGTCTCA
1 CTTCTCTA-TATCTCATCAGGAAGATGACTCCATCACTTGTTTCAATCCACTTCTTTGCATCTCA
* * * * * *
92300 TCAGGAAGACGAATTCGGTTCACTTCTCTGTATCTCATCATGAAGGTAACCGCTTTATTGCTTCA
65 TCAGGAAGACAAATTCGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCACTTTATTGCTTCA
* *
92365 ACCTTCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTCGCTCACATTGAGCTTTGTTT
130 ACCTACTTCTCAGTATCTCA-CAAGAAGCTGGAGTTCGAAGATTCGCTCACATTGAGCTTTGTTT
* **
92430 CATTGACTGGTATACTTCTCTGTATCTCATCAAGAAGATGATTGCCTCACTTGTTTCAATCCG
194 CATCGACTGGTATACTTCTCTGTATCTCATCAAGAAGATGACCGCCTCACTTGTTTCAATCCG
* * *
92493 CTTCTCTATATCTCATCAGGAAGATGAC-CGCCTCACTTGTTTCAATCCGCTTCTTTGTATCTCA
1 CTTCTCTATATCTCATCAGGAAGATGACTC-CATCACTTGTTTCAATCCACTTCTTTGCATCTCA
* * * *
92557 TCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTGACCATTTTATTGCTTCG
65 TCAGGAAGACAAATTCGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCACTTTATTGCTTCA
* * * *
92622 ACCTACTTCTCAGTATCTC-CAAGAAGTTGGAGTTTGAAGTTTCGCTCACATTTGAGTTTTGTTT
130 ACCTACTTCTCAGTATCTCACAAGAAGCTGGAGTTCGAAGATTCGCTCACA-TTGAGCTTTGTTT
* **
92686 CATCGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATGACCGCCTCACTTGTTTCAATCTT
194 CATCGA-CTGGTATACTTCTCTGTATCTCATCAAGAAGATGACCGCCTCACTTGTTTCAATCCG
*
92750 CTTCTCTGTATCTCATCAGGAAGA
1 CTTCTCTATATCTCATCAGGAAGA
92774 CGAATTTGGT
Statistics
Matches: 249, Mismatches: 28, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
255 27 0.11
256 18 0.07
257 203 0.82
258 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (256 bp):
CTTCTCTATATCTCATCAGGAAGATGACTCCATCACTTGTTTCAATCCACTTCTTTGCATCTCAT
CAGGAAGACAAATTCGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCACTTTATTGCTTCAA
CCTACTTCTCAGTATCTCACAAGAAGCTGGAGTTCGAAGATTCGCTCACATTGAGCTTTGTTTCA
TCGACTGGTATACTTCTCTGTATCTCATCAAGAAGATGACCGCCTCACTTGTTTCAATCCG
Found at i:92715 original size:208 final size:209
Alignment explanation
Indices: 92493--93152 Score: 865
Period size: 209 Copynumber: 3.2 Consensus size: 209
92483 TTTCAATCCG
* * *
92493 CTTCTCTATATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTTTGTATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCACTTCTCTGTATCTCAT
* *
92558 CAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTGACCATTTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCGA
* * * * * *
92623 CCTACTTCTCAGTATCTC-CAAGAAGTTGGAGTTTGAAGTTTCGCTCACATTTGAGTTTTGTTTC
131 CCTGCTTCTCAGTATCTCACAGGAAGCTGGGGTTTGAAGTTTAGCTCACATTTGAGCTTTGTTTC
92687 ATCGAGTTGGTATA
196 ATCGAGTTGGTATA
* **
92701 CTTCTCTGTATCTCATCAAGAAGATGACCGCCTCACTTGTTTCAATCTTCTTCTCTGTATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCACTTCTCTGTATCTCAT
* * *
92766 CAGGAAGACGAATTTGGTCAACTTCTCAGTATCTCATCAGGAAGTTGACCATTTTATTGCTTTGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCGA
* * * * * *
92831 CTTGCTTCTCAGTATCTCATCAGGAAACTGGGGTTTGAAGTTTTGCTCATA-TTAAGCTTGGTTT
131 CCTGCTTCTCAGTATCTCA-CAGGAAGCTGGGGTTTGAAGTTTAGCTCACATTTGAGCTTTGTTT
* * * *
92895 TATTGATTTGGTCTA
195 CATCGAGTTGGTATA
* * * * *
92910 CTTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTTAATCCACTTCTCTGTGTCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCACTTCTCTGTATCTCAT
** * * * * * * * * **
92975 CAGGAAGGTGGATCTAGTTCACTTCTCTGTATCTCATTAGGAAGGTAACCGCTTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCGA
* *
93040 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTAGTTCACATTTGAGCTTTGTTT
131 CCTGCTTCTCAGTATCTCA-CAGGAAGCTGGGGTTTGAAGTTTAGCTCACATTTGAGCTTTGTTT
93105 CATCGAGTTGGTATA
195 CATCGAGTTGGTATA
*
93120 CTTCTCTGTATCTCATCAGGAAGATGATCGCCT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCT
93153 TGTTGTTTTG
Statistics
Matches: 386, Mismatches: 63, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
208 136 0.35
209 174 0.45
210 76 0.20
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (209 bp):
CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCACTTCTCTGTATCTCAT
CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCGA
CCTGCTTCTCAGTATCTCACAGGAAGCTGGGGTTTGAAGTTTAGCTCACATTTGAGCTTTGTTTC
ATCGAGTTGGTATA
Found at i:101339 original size:33 final size:33
Alignment explanation
Indices: 101301--101373 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
101291 CTCAGAATAT
*
101301 CAGCTTTGACAGCTAGCTCTTACATGTGATCAG
1 CAGCTTCGACAGCTAGCTCTTACATGTGATCAG
* *
101334 CAGCTTCGGCAGCTAGCTCTTGCATGTGATCAG
1 CAGCTTCGACAGCTAGCTCTTACATGTGATCAG
*
101367 CGGCTTC
1 CAGCTTC
101374 CCTCATTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.19, C:0.27, G:0.25, T:0.29
Consensus pattern (33 bp):
CAGCTTCGACAGCTAGCTCTTACATGTGATCAG
Found at i:103840 original size:3 final size:3
Alignment explanation
Indices: 103832--103888 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
103822 TCAACTTTCT
* ** *
103832 TTA TTA TTA TTA TTA TTA CTA TTA AAA TTA TTA ATA TTA -TA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
103877 TTA TTA TTA TTA
1 TTA TTA TTA TTA
103889 ATGATATTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:104663 original size:11 final size:10
Alignment explanation
Indices: 104627--104685 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
104617 TGACATGATT
104627 AATTTAAATA
1 AATTTAAATA
104637 AATTTAAACTTA
1 AATTTAAA--TA
104649 AATTTATAATA
1 AATTTA-AATA
104660 AATTTAAAT-
1 AATTTAAATA
*
104669 --TTCAAATA
1 AATTTAAATA
104677 AATTTAAAT
1 AATTTAAAT
104686 TCTATTGGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 6 0.15
10 17 0.41
11 8 0.20
12 8 0.20
13 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (10 bp):
AATTTAAATA
Found at i:104666 original size:17 final size:17
Alignment explanation
Indices: 104641--104686 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
104631 TAAATAAATT
*
104641 TAAACTTAAATTT-ATAA
1 TAAATTTAAATTTCA-AA
104658 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
104675 TAAATTTAAATT
1 TAAATTTAAATT
104687 CTATTGGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 26 0.96
18 1 0.04
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:104667 original size:6 final size:6
Alignment explanation
Indices: 104627--104686 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
104617 TGACATGATT
*
104627 AATTTA AA--TA AATTTA AACTTA AATTTA TAA--TA AATTTA AATTTCA
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTT-A
104673 AA--TA AATTTA AATT
1 AATTTA AATTTA AATT
104687 CTATTGGGCC
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
4 9 0.20
5 3 0.07
6 27 0.61
7 5 0.11
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:109074 original size:13 final size:13
Alignment explanation
Indices: 109056--109080 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109046 ATTTATTTAG
109056 TTTAGATTAATAC
1 TTTAGATTAATAC
109069 TTTAGATTAATA
1 TTTAGATTAATA
109081 TCCTTCACAA
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:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTAGATTAATAC
Found at i:115234 original size:19 final size:20
Alignment explanation
Indices: 115187--115234 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
115177 TTGATAATTC
115187 TTAA-TATTA-AATTATAAA
1 TTAATTATTATAATTATAAA
*
115205 TTAAATT-TTATAATT-TATA
1 TT-AATTATTATAATTATAAA
115224 TTAATTATTAT
1 TTAATTATTAT
115235 CAAGAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATTATAATTATAAA
Done.