Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016893.1 Corchorus olitorius cultivar O-4 contig16926, 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: 147248
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1656 original size:22 final size:22
Alignment explanation
Indices: 1609--1664 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1599 CATTGGGAGT
*
1609 TTATCAGAATTTTATAGGATAA
1 TTATCAAAATTTTATAGGATAA
* **
1631 TTATCAAAATTTTATAGTATGC
1 TTATCAAAATTTTATAGGATAA
1653 TTATCAAAATTT
1 TTATCAAAATTT
1665 AATAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGATAA
Found at i:1733 original size:2 final size:2
Alignment explanation
Indices: 1726--1766 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1716 GCTAAGACTA
1726 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1767 ACTTAAAGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2067 original size:31 final size:31
Alignment explanation
Indices: 1996--2067 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
1986 GTCTATCAGC
*
1996 TTTTAATTTGTTTAATTTAAGGCTATCATTT
1 TTTTAATTTGTTTAATTTAAGGCTATAATTT
* **
2027 TAATT-ATTTGTTTAATTTAATTCT-TAATTT
1 T-TTTAATTTGTTTAATTTAAGGCTATAATTT
2057 GTTTTAATTTG
1 -TTTTAATTTG
2068 CAATAAGTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
30 7 0.21
31 24 0.73
32 2 0.06
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGGCTATAATTT
Found at i:2514 original size:17 final size:17
Alignment explanation
Indices: 2494--2540 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
2484 TCGAAATCAA
2494 ACCCGAGCCCGAATCCG
1 ACCCGAGCCCGAATCCG
*
2511 ACCCGAGCCCGAATCCT
1 ACCCGAGCCCGAATCCG
* *
2528 ACTCGAGACCGAA
1 ACCCGAGCCCGAA
2541 CCCAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.28, C:0.43, G:0.21, T:0.09
Consensus pattern (17 bp):
ACCCGAGCCCGAATCCG
Found at i:2557 original size:16 final size:16
Alignment explanation
Indices: 2536--2597 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
2526 CTACTCGAGA
2536 CCGAACCCAAAAATAC
1 CCGAACCCAAAAATAC
*
2552 CCGAACCC-AACATAAC
1 CCGAACCCAAAAAT-AC
* ** *
2568 ACGAGTCCGAAAATAC
1 CCGAACCCAAAAATAC
2584 CCGAACCCGAAAAA
1 CCGAACCC-AAAAA
2598 ATCCAAACCC
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
15 4 0.12
16 22 0.65
17 8 0.24
ACGTcount: A:0.47, C:0.35, G:0.11, T:0.06
Consensus pattern (16 bp):
CCGAACCCAAAAATAC
Found at i:3314 original size:93 final size:93
Alignment explanation
Indices: 3217--3409 Score: 253
Period size: 93 Copynumber: 2.1 Consensus size: 93
3207 TTTAATATAT
* * * * **
3217 TTTTTA-AATGTGATTGTTTAAATTATTATAGTTTTAGTCAATTAAAAACTCTATTTTTATTTAA
1 TTTTTACAATGTGACTATTTAAATT-TTATAGTTTTACTCAACTAAAAACTCTATTTCAATTTAA
3281 TTAAATCTAATATCCTTATAACTATTTTA
65 TTAAATCTAATATCCTTATAACTATTTTA
* * * * *
3310 TTTTTACCATTTTACTATTTTACTTTTATAGTTTTACTCAACTAAAAACTCTATTTCAATTTAAT
1 TTTTTACAATGTGACTATTTAAATTTTATAGTTTTACTCAACTAAAAACTCTATTTCAATTTAAT
* *
3375 TAAATCTAATATTCTTATACCTATTTTA
66 TAAATCTAATATCCTTATAACTATTTTA
3403 TTTTTAC
1 TTTTTAC
3410 GATATTACTA
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
93 75 0.87
94 11 0.13
ACGTcount: A:0.33, C:0.11, G:0.03, T:0.52
Consensus pattern (93 bp):
TTTTTACAATGTGACTATTTAAATTTTATAGTTTTACTCAACTAAAAACTCTATTTCAATTTAAT
TAAATCTAATATCCTTATAACTATTTTA
Found at i:3418 original size:93 final size:93
Alignment explanation
Indices: 3242--3424 Score: 285
Period size: 93 Copynumber: 2.0 Consensus size: 93
3232 GTTTAAATTA
* * **
3242 TTATAGTTTTAGTCAATTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATT
1 TTATAGTTTTACTCAACTAAAAACTCTATTTCAATTTAATTAAATCTAATATCCTTATAACTATT
* *
3307 TTATTTTTACCATTTTACTATTTTACTT
66 TTATTTTTACCATATTACTAATTTACTT
* *
3335 TTATAGTTTTACTCAACTAAAAACTCTATTTCAATTTAATTAAATCTAATATTCTTATACCTATT
1 TTATAGTTTTACTCAACTAAAAACTCTATTTCAATTTAATTAAATCTAATATCCTTATAACTATT
*
3400 TTATTTTTACGATATTACTAATTTA
66 TTATTTTTACCATATTACTAATTTA
3425 ATTAAAAAGC
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 81 1.00
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (93 bp):
TTATAGTTTTACTCAACTAAAAACTCTATTTCAATTTAATTAAATCTAATATCCTTATAACTATT
TTATTTTTACCATATTACTAATTTACTT
Found at i:14629 original size:155 final size:155
Alignment explanation
Indices: 14347--14659 Score: 626
Period size: 155 Copynumber: 2.0 Consensus size: 155
14337 TTTTCAATGT
14347 CTGGTTTGAGGTGAGGGATGGATGTTTACTATCCACTTCAATATGCTTCCTGTTGGTACTAGCTT
1 CTGGTTTGAGGTGAGGGATGGATGTTTACTATCCACTTCAATATGCTTCCTGTTGGTACTAGCTT
14412 CTTGTAGATCTTTCATGAGAGACACCTCCCCTGTATTCTCCTTCAACCCTGTAGATATAAAATCA
66 CTTGTAGATCTTTCATGAGAGACACCTCCCCTGTATTCTCCTTCAACCCTGTAGATATAAAATCA
14477 TTTCCTCGAACTCCTTATTTCTTGA
131 TTTCCTCGAACTCCTTATTTCTTGA
14502 CTGGTTTGAGGTGAGGGATGGATGTTTACTATCCACTTCAATATGCTTCCTGTTGGTACTAGCTT
1 CTGGTTTGAGGTGAGGGATGGATGTTTACTATCCACTTCAATATGCTTCCTGTTGGTACTAGCTT
14567 CTTGTAGATCTTTCATGAGAGACACCTCCCCTGTATTCTCCTTCAACCCTGTAGATATAAAATCA
66 CTTGTAGATCTTTCATGAGAGACACCTCCCCTGTATTCTCCTTCAACCCTGTAGATATAAAATCA
14632 TTTCCTCGAACTCCTTATTTCTTGA
131 TTTCCTCGAACTCCTTATTTCTTGA
14657 CTG
1 CTG
14660 CAGGACTTGG
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 158 1.00
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (155 bp):
CTGGTTTGAGGTGAGGGATGGATGTTTACTATCCACTTCAATATGCTTCCTGTTGGTACTAGCTT
CTTGTAGATCTTTCATGAGAGACACCTCCCCTGTATTCTCCTTCAACCCTGTAGATATAAAATCA
TTTCCTCGAACTCCTTATTTCTTGA
Found at i:16740 original size:22 final size:21
Alignment explanation
Indices: 16706--16748 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
16696 GCGCAAAAAA
*
16706 TCAAACTTCGTGCTTATTCTC
1 TCAAACTCCGTGCTTATTCTC
*
16727 TCAAAGCTCCGTGCTTTTTCTC
1 TCAAA-CTCCGTGCTTATTCTC
16749 AGGAATCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.16, C:0.30, G:0.12, T:0.42
Consensus pattern (21 bp):
TCAAACTCCGTGCTTATTCTC
Found at i:20827 original size:12 final size:12
Alignment explanation
Indices: 20812--20864 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
20802 GTATATTATC
20812 ATATTTATTTGA
1 ATATTTATTTGA
*
20824 ATA-TGATTT--
1 ATATTTATTTGA
20833 A-ATTTATTTGA
1 ATATTTATTTGA
20844 ATATTTATTTGA
1 ATATTTATTTGA
*
20856 ATATATATT
1 ATATTTATT
20865 CCTAACAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
8 1 0.03
9 6 0.18
11 6 0.18
12 21 0.62
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.57
Consensus pattern (12 bp):
ATATTTATTTGA
Found at i:21492 original size:25 final size:25
Alignment explanation
Indices: 21464--21511 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
21454 ATCAATTTTG
21464 TTCAGAAATTTCAAAGGCAAAATAA
1 TTCAGAAATTTCAAAGGCAAAATAA
*
21489 TTCAGAAATTTCAAGGGCAAAAT
1 TTCAGAAATTTCAAAGGCAAAAT
21512 CATCCACCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (25 bp):
TTCAGAAATTTCAAAGGCAAAATAA
Found at i:22219 original size:164 final size:161
Alignment explanation
Indices: 21913--22241 Score: 462
Period size: 164 Copynumber: 2.0 Consensus size: 161
21903 TACTATATAT
* *
21913 AAATGTACGAATAATGGAAAACTTTATGTTTTCTGATTGTACCCTTTTTTCAAATATATTTCTAA
1 AAATCTACGAATAATGGAAAACTTTATGTTTTCCGATTGTACCCTTTTTTCAAATATATTTCTAA
* **
21978 ATTAACATTATTAAAATTTATTATTTAATTAATTATAAAATTTCAATTTAGACCGAATTATAAGT
66 ATTAACATCATTAAAATTTATTATTTAATTAATTATAAAATTAAAATTTAGACCGAATTATAAGT
*
22043 TTGTAAAATTGATTTTCATTGATGAACATGC
131 TTGTAAAATTGATTTTCATTGACGAACATGC
* * *
22074 AAATCTACGAATGATGGGAAACTTTATGTTTTCCGATTGTACCTTTTTTTTCAAATATATTTCTA
1 AAATCTACGAATAATGGAAAACTTTATGTTTTCCGATTGTACC-CTTTTTTCAAATATATTTCTA
* ** * * *
22139 ATTTGCCATCATTAAAATTTAGTATAATTTTATTATTTA-AAAATTAAAATTTAGACCGGATTAT
65 AATTAACATCATTAAAATTTA-T-T-ATTTAATTAATTATAAAATTAAAATTTAGACCGAATTAT
* *
22203 AAGTTTGTCAAATTGATTTTCGTTGACGAACATGC
127 AAGTTTGTAAAATTGATTTTCATTGACGAACATGC
22238 AAAT
1 AAAT
22242 TTCCTTTACT
Statistics
Matches: 147, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
161 39 0.27
162 37 0.25
163 1 0.01
164 59 0.40
165 11 0.07
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (161 bp):
AAATCTACGAATAATGGAAAACTTTATGTTTTCCGATTGTACCCTTTTTTCAAATATATTTCTAA
ATTAACATCATTAAAATTTATTATTTAATTAATTATAAAATTAAAATTTAGACCGAATTATAAGT
TTGTAAAATTGATTTTCATTGACGAACATGC
Found at i:22491 original size:22 final size:22
Alignment explanation
Indices: 22463--22609 Score: 104
Period size: 22 Copynumber: 6.7 Consensus size: 22
22453 TGTCTCTGCG
22463 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
22485 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
22508 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
22529 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* **
22552 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
22573 AGGTTATCCAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
22595 TGGTTACCAAAATTT
1 TGGTTATCAAAATTT
22610 TATAGGATCA
Statistics
Matches: 96, Mismatches: 22, Indels: 14
0.73 0.17 0.11
Matches are distributed among these distances:
20 1 0.01
21 4 0.04
22 87 0.91
23 3 0.03
24 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:22533 original size:44 final size:44
Alignment explanation
Indices: 22464--22608 Score: 118
Period size: 44 Copynumber: 3.3 Consensus size: 44
22454 GTCTCTGCGT
* ** *
22464 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTCCATAAGATGGTTACCAAAATTTCAT-ATGGA
*
22508 GGTTATCAAAATTCCAT-AGTGTGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTCCATAAG-ATGGTTACCAAAATTTCATATGGA
* * ** * *
22552 AGTTATCAAAATTTCATGGGAAGGTTATCC-AAATTTCATA-GTGT
1 GGTTATCAAAATTCCATAAGATGGTTA-CCAAAATTTCATATG-GA
*
22596 GGTTACCAAAATT
1 GGTTATCAAAATT
22609 TTATAGGATC
Statistics
Matches: 83, Mismatches: 13, Indels: 10
0.78 0.12 0.09
Matches are distributed among these distances:
43 4 0.05
44 76 0.92
45 3 0.04
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (44 bp):
GGTTATCAAAATTCCATAAGATGGTTACCAAAATTTCATATGGA
Found at i:22568 original size:66 final size:68
Alignment explanation
Indices: 22462--22695 Score: 241
Period size: 66 Copynumber: 3.5 Consensus size: 68
22452 TTGTCTCTGC
* * * * *
22462 GTGGTTATCAAAATTTCATAAGAT-GGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCAT
1 GTGGTTACCAAAATTTCATAGGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTCAT
22525 AGT
66 AGT
*
22528 GTGGTTACCAAAATTTCATATGGA-A-GTTATCAAAATTTCATG-GGAAGGTTATCCAAATTTCA
1 GTGGTTACCAAAATTTCATA-GGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTCA
22590 TAGT
65 TAGT
* * * ** *
22594 GTGGTTACCAAAATTTTATAGGATCATGTTAAT-AAAATTTC-TTAGGAAGGTTATTGAAATTTT
1 GTGGTTACCAAAATTTCATAGGAT-AGGTT-ATCAAAATTTCATGAGGAAGGTTATCAAAATTTC
22657 ATAGT
64 ATAGT
* * * *
22662 GTGGTTATCACAATTTTATA-GAAAGGTTATCAAA
1 GTGGTTACCAAAATTTCATAGGATAGGTTATCAAA
22696 GAGATTATCA
Statistics
Matches: 144, Mismatches: 15, Indels: 18
0.81 0.08 0.10
Matches are distributed among these distances:
65 7 0.05
66 79 0.55
67 6 0.04
68 50 0.35
69 2 0.01
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (68 bp):
GTGGTTACCAAAATTTCATAGGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTCAT
AGT
Found at i:22725 original size:22 final size:22
Alignment explanation
Indices: 22700--22799 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
22690 ATCAAAGAGA
*
22700 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
22722 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
* *
22744 TTAACAAAATTTCATAAG-GAAG
1 TTATCAAAATTTCAT-AGCGAGG
* * *
22766 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGCGAGG
22788 TTATCAAAATTT
1 TTATCAAAATTT
22800 TATATGAAGG
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
21 4 0.06
22 53 0.85
23 5 0.08
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:22924 original size:21 final size:22
Alignment explanation
Indices: 22900--22940 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
22890 CATAGAGATC
22900 AGATCATCAAAA-TTTATAGGA
1 AGATCATCAAAATTTTATAGGA
*
22921 AGATTATCAAAATTTTATAG
1 AGATCATCAAAATTTTATAG
22941 TGTTGTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (22 bp):
AGATCATCAAAATTTTATAGGA
Found at i:22940 original size:22 final size:23
Alignment explanation
Indices: 22876--22957 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 23
22866 CTCATAAAGT
* *
22876 GATTATCGAAATTTCATAGAGATCA
1 GATTATCAAAATTTTATAGAGA--A
*
22901 GATCATCAAAA-TTTATAG-GAA
1 GATTATCAAAATTTTATAGAGAA
* **
22922 GATTATCAAAATTTTATAGTGTT
1 GATTATCAAAATTTTATAGAGAA
22945 G-TTATCAAAATTT
1 GATTATCAAAATTT
22958 CATAACGAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
21 11 0.22
22 19 0.39
23 4 0.08
24 6 0.12
25 9 0.18
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (23 bp):
GATTATCAAAATTTTATAGAGAA
Found at i:23012 original size:22 final size:22
Alignment explanation
Indices: 22987--23047 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
22977 GTGTTGTTAT
22987 CAAAATTTCATAGAG-GGCTCAA
1 CAAAATTTCATAGAGAGG-TCAA
*
23009 CAAAATCTT-ATAGAGAGGTCAT
1 CAAAAT-TTCATAGAGAGGTCAA
* *
23031 CGAAATTTCATAAAGAG
1 CAAAATTTCATAGAGAG
23048 ATTATCAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 2 0.06
22 27 0.82
23 4 0.12
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.25
Consensus pattern (22 bp):
CAAAATTTCATAGAGAGGTCAA
Found at i:23061 original size:22 final size:22
Alignment explanation
Indices: 23033--23086 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
23023 GAGGTCATCG
*
23033 AAATTTCATAAAGAGATTATCA
1 AAATTTCATAAAGAGATTACCA
* * * *
23055 AATTTTCAGAATGTGATTACCA
1 AAATTTCATAAAGAGATTACCA
23077 AAATTTCATA
1 AAATTTCATA
23087 GTGGTATTTC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.35
Consensus pattern (22 bp):
AAATTTCATAAAGAGATTACCA
Found at i:23249 original size:22 final size:22
Alignment explanation
Indices: 23158--23582 Score: 212
Period size: 22 Copynumber: 19.5 Consensus size: 22
23148 TTATGGAGTA
*
23158 ATCAAAATTT--TAGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
**
23178 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * * *
23200 TTCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
23222 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
23244 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
23266 ATCAAAATATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
23288 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* *
23304 ATCAAGATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* *
23327 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* *
23350 ATCAAAATTTTTATAGCGAGGTT
1 ATCAAAA-TTTCATAGGGAGGTT
* * * *
23373 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * * * *
23395 GTAAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
*
23417 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
** ** *
23439 -TTTAAATCTTCATAACGTGGTT
1 ATCAAAAT-TTCATAGGGAGGTT
* * *
23461 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * **
23483 ATCAACATCTAATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* *
23506 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
23528 ATCAAAATTTTATAGTGAGGTCT
1 ATCAAAATTTCATAGGGAGGT-T
* *
23551 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
23572 AACAAAATTTC
1 ATCAAAATTTC
23583 TTAAGAAGGT
Statistics
Matches: 304, Mismatches: 78, Indels: 44
0.71 0.18 0.10
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 2 0.01
20 14 0.05
21 7 0.02
22 192 0.63
23 65 0.21
24 11 0.04
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.37
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:23319 original size:38 final size:39
Alignment explanation
Indices: 23263--23336 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
23253 TCATAATGAG
23263 GTTATCAAAATATCATAGGGAGG-TTATCAAAATTTGTA
1 GTTATCAAAATATCATAGGGAGGTTTATCAAAATTTGTA
* * *
23301 GTTATCAAGATTTTATAGGGAGGTTTATCAAAATTT
1 GTTATCAAAATATCATAGGGAGGTTTATCAAAATTT
23337 TATAGGAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 20 0.62
39 12 0.38
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (39 bp):
GTTATCAAAATATCATAGGGAGGTTTATCAAAATTTGTA
Found at i:23336 original size:23 final size:23
Alignment explanation
Indices: 23302--23387 Score: 111
Period size: 23 Copynumber: 3.7 Consensus size: 23
23292 AAATTTGTAG
*
23302 TTATCAAGATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
23325 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
23348 TTATCAAAATTTTTATAGCGAGG-
1 TTATCAAAA-TTTTATAGGGAGGT
* *
23371 TTATCACAATTTCATAG
1 TTATCAAAATTTTATAG
23388 TGTGATTGTA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.12
23 38 0.68
24 11 0.20
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:23543 original size:45 final size:45
Alignment explanation
Indices: 23456--23544 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
23446 CTTCATAACG
* * *
23456 TGGTTATCAATATATCATATGGAGGTTATCAACATCTAATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTAATAGTGT
* * *
23501 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTTATAGTG
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTAATAGTG
23545 AGGTCTTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
44 1 0.03
45 36 0.97
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTAATAGTGT
Found at i:24373 original size:13 final size:13
Alignment explanation
Indices: 24355--24379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24345 TGATTGAAAC
24355 TATACTATATATA
1 TATACTATATATA
24368 TATACTATATAT
1 TATACTATATAT
24380 TATTTTTAGT
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TATACTATATATA
Found at i:33202 original size:19 final size:19
Alignment explanation
Indices: 33152--33202 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
33142 TGTGGAATTT
33152 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
33170 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
33189 TTAATAATTAATTA
1 TTAATAATTAATTA
33203 ATTTTAGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:33800 original size:18 final size:18
Alignment explanation
Indices: 33777--33819 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
33767 TTGGGTTTAG
33777 TCAGTTTCTTAAGTCAGT
1 TCAGTTTCTTAAGTCAGT
* *
33795 TCAGTTTTTTTGAGTCAGT
1 TCAG-TTTCTTAAGTCAGT
33814 T-AGTTT
1 TCAGTTT
33820 GAGTCTGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 6 0.27
19 13 0.59
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.51
Consensus pattern (18 bp):
TCAGTTTCTTAAGTCAGT
Found at i:36577 original size:26 final size:26
Alignment explanation
Indices: 36541--36592 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
36531 TATTCTATAC
*
36541 CTCCAAACAATTTGAATTGAATTATT
1 CTCCAAACAATTTGAACTGAATTATT
36567 CTCCAAACAATTTGAACTGAATTATT
1 CTCCAAACAATTTGAACTGAATTATT
36593 GAAAAGGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (26 bp):
CTCCAAACAATTTGAACTGAATTATT
Found at i:37983 original size:3 final size:3
Alignment explanation
Indices: 37975--38067 Score: 80
Period size: 3 Copynumber: 31.0 Consensus size: 3
37965 GCTCAAGCCA
* *
37975 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT CCT TCT TCA TC-
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * ** * *
38022 ACTT TCA TCA TCT TCT TCC AAT TCC TCT TCT TCT TCT TGT TCT TCT
1 TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
38068 GTGACTCAAC
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
2 1 0.01
3 69 0.97
4 1 0.01
ACGTcount: A:0.06, C:0.34, G:0.01, T:0.58
Consensus pattern (3 bp):
TCT
Found at i:42148 original size:27 final size:28
Alignment explanation
Indices: 42118--42171 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
42108 TTTTAAAATC
* *
42118 AGAAATAACAATTTTTTTTTGA-GATAA
1 AGAAATAACAAATTTTTATTGATGATAA
42145 AGAAATAACAAATTTTTATTGATGATA
1 AGAAATAACAAATTTTTATTGATGATA
42172 TATAGTATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.39
Consensus pattern (28 bp):
AGAAATAACAAATTTTTATTGATGATAA
Found at i:52131 original size:38 final size:38
Alignment explanation
Indices: 52077--52153 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
52067 GCAAAAGAAG
* *
52077 AGGTGGCAATGGCATGTGTGGCTAAAATTTGAGTAGTT
1 AGGTGGCAATGACATGTGTGGCTAAAATTTGAGCAGTT
*
52115 AGGTGGCAATGACATGTGTGTCTAAAATTTGAGCAGTT
1 AGGTGGCAATGACATGTGTGGCTAAAATTTGAGCAGTT
52153 A
1 A
52154 TGAAACCACA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.09, G:0.31, T:0.31
Consensus pattern (38 bp):
AGGTGGCAATGACATGTGTGGCTAAAATTTGAGCAGTT
Found at i:52461 original size:15 final size:16
Alignment explanation
Indices: 52441--52479 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
52431 GAGAGAAAAT
*
52441 AGAAAAGAAAAT-AAA
1 AGAAAAAAAAATCAAA
52456 AGAAAAAAAAATCAAA
1 AGAAAAAAAAATCAAA
*
52472 CGAAAAAA
1 AGAAAAAA
52480 TGCCTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.79, C:0.05, G:0.10, T:0.05
Consensus pattern (16 bp):
AGAAAAAAAAATCAAA
Found at i:53090 original size:31 final size:29
Alignment explanation
Indices: 53064--53123 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
53054 CGTTTCTGTC
53064 TCGGCCTAATTTGGGGCACAACGTTTCAAT
1 TCGGCCT-ATTTGGGGCACAACGTTTCAAT
* *
53094 TTGGTCTATTTGGGGCACAACGTTTCAAT
1 TCGGCCTATTTGGGGCACAACGTTTCAAT
53123 T
1 T
53124 TGGCGTCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (29 bp):
TCGGCCTATTTGGGGCACAACGTTTCAAT
Found at i:60688 original size:48 final size:48
Alignment explanation
Indices: 60617--60714 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
60607 GCTGGTCTTT
60617 AGAGATTTCTTGGATTAGATTTGGTGAAGGAACAGAATGTAGCATGGA
1 AGAGATTTCTTGGATTAGATTTGGTGAAGGAACAGAATGTAGCATGGA
*
60665 AGAGATTTCTTGGATTAGATTTGGTGAAGGAACAGAATGTATCATGGA
1 AGAGATTTCTTGGATTAGATTTGGTGAAGGAACAGAATGTAGCATGGA
60713 AG
1 AG
60715 TATATCAGTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.34, C:0.06, G:0.31, T:0.30
Consensus pattern (48 bp):
AGAGATTTCTTGGATTAGATTTGGTGAAGGAACAGAATGTAGCATGGA
Found at i:70111 original size:2 final size:2
Alignment explanation
Indices: 70104--70128 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
70094 TTTTTCATGC
70104 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
70129 GTAATACAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74485 original size:25 final size:25
Alignment explanation
Indices: 74440--74488 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
74430 TTTTGAACTC
*
74440 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
74465 ATTATTTACTTA-ATAATATATATT
1 ATTATTTA-TTATATAAAATATATT
74489 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:88827 original size:4 final size:4
Alignment explanation
Indices: 88818--88844 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
88808 AACTCCACTA
88818 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
88845 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:88853 original size:3 final size:3
Alignment explanation
Indices: 88845--88920 Score: 125
Period size: 3 Copynumber: 25.3 Consensus size: 3
88835 ATGTATGTAT
* *
88845 ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ACA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
88893 ATA ATA ATA ATA ATA ATA TTA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
88921 CAAGCAGGGC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:89171 original size:42 final size:43
Alignment explanation
Indices: 89120--89213 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
89110 AGTGCATTAC
* *
89120 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATGAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
89161 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
*
89206 TTAATATT
1 CTAATATT
89214 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:91945 original size:31 final size:32
Alignment explanation
Indices: 91910--91975 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
91900 ATTAAGGACG
* *
91910 TTTTGCCTCCTGAACTTT-CAAGATCATGACA
1 TTTTGCCTCCTGAACTTTCCAAAATCAAGACA
*
91941 TTTTGCCTCCTGAATTTTCCAAAATCAAGACA
1 TTTTGCCTCCTGAACTTTCCAAAATCAAGACA
91973 TTT
1 TTT
91976 AACCCCCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 17 0.55
32 14 0.45
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (32 bp):
TTTTGCCTCCTGAACTTTCCAAAATCAAGACA
Found at i:95364 original size:36 final size:36
Alignment explanation
Indices: 95317--95385 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
95307 TCAATAACCA
*
95317 TACATTTTTTGTAATTTTGGTTATCATATTTCTTAT
1 TACATTTTTTGTAATTTTGATTATCATATTTCTTAT
95353 TACATTTTTTGTAATTTTGATTATCATATTTCT
1 TACATTTTTTGTAATTTTGATTATCATATTTCT
95386 CCAAAATCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (36 bp):
TACATTTTTTGTAATTTTGATTATCATATTTCTTAT
Found at i:96523 original size:6 final size:6
Alignment explanation
Indices: 96515--96597 Score: 139
Period size: 6 Copynumber: 13.8 Consensus size: 6
96505 TATATAGTAT
* *
96515 ATATAT ATATAT ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
*
96563 ATATAG ATATAA ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
96598 TAAACTATTT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (6 bp):
ATATAG
Found at i:97135 original size:20 final size:20
Alignment explanation
Indices: 97106--97151 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
97096 TGGTAATATA
97106 TATATATATATGTATGTATG
1 TATATATATATGTATGTATG
*
97126 TATATGTATATGTATGTATG
1 TATATATATATGTATGTATG
97146 TATATA
1 TATATA
97152 ATTAAAGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (20 bp):
TATATATATATGTATGTATG
Found at i:97135 original size:24 final size:24
Alignment explanation
Indices: 97102--97148 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
97092 ATGATGGTAA
97102 TATATATATATATATGTATGTATG
1 TATATATATATATATGTATGTATG
* *
97126 TATATGTATATGTATGTATGTAT
1 TATATATATATATATGTATGTAT
97149 ATAATTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (24 bp):
TATATATATATATATGTATGTATG
Found at i:97151 original size:16 final size:16
Alignment explanation
Indices: 97110--97151 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
97100 AATATATATA
*
97110 TATATATGTATGTATG
1 TATATATATATGTATG
*
97126 TATATGTATATGTATG
1 TATATATATATGTATG
*
97142 TATGTATATA
1 TATATATATA
97152 ATTAAAGCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (16 bp):
TATATATATATGTATG
Found at i:106158 original size:36 final size:36
Alignment explanation
Indices: 106109--106294 Score: 129
Period size: 36 Copynumber: 5.3 Consensus size: 36
106099 TTCCTTTGGG
* *
106109 ATTAAGTTATTTATTGACTATACTTAATTTCCCTAA
1 ATTAAGTTCTTTATTGACTATACTTAATTACCCTAA
* * **
106145 ATTAAGTTCTTTATTGGCTCTACTTAATTACCCTGG
1 ATTAAGTTCTTTATTGACTATACTTAATTACCCTAA
* *
106181 ATTAAGTTC-TTATTGAC----CTTAATTGCCCTGA
1 ATTAAGTTCTTTATTGACTATACTTAATTACCCTAA
* * * * * *
106212 ATTAAGTCCTTGACT-ACTTTTAGTTAATTACCCTGA
1 ATTAAGTTCTTTATTGAC-TATACTTAATTACCCTAA
* * *
106248 ATTAAG-TCTTTGTTTG-CTTTTACTTAATTACCCTGA
1 ATTAAGTTCTTT-ATTGAC-TATACTTAATTACCCTAA
106284 ATTAAG-TCTTT
1 ATTAAGTTCTTT
106295 GTTCGCTTTT
Statistics
Matches: 123, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
31 22 0.18
32 3 0.02
35 10 0.08
36 88 0.72
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (36 bp):
ATTAAGTTCTTTATTGACTATACTTAATTACCCTAA
Found at i:106289 original size:72 final size:71
Alignment explanation
Indices: 106198--106953 Score: 448
Period size: 74 Copynumber: 10.3 Consensus size: 71
106188 TCTTATTGAC
* ** *
106198 CTTAATTGCCCTGAATTAAGTCCTTGACTACTTTTAGTTAATTACCCTGAATTAAGTCTTTGTTT
1 CTTAATTACCCTGAATTAAGTCCTTGACTGGTTTTACTTAATTACCCTGAATTAAGTCTTTGTTT
106263 GCTTTTA
66 G-TTTTA
* * * * * *
106270 CTTAATTACCCTGAATTAAGTCTTTG-TTCGCTTTTGCTTAATTGCCTTGAATTAAGTCTTTG-T
1 CTTAATTACCCTGAATTAAGTCCTTGACT-GGTTTTACTTAATTACCCTGAATTAAGTCTTTGTT
*
106333 TGATTTA
65 TGTTTTA
* * * * * * * *
106340 CTTAATTTCCTTGGAATTAAG---TTG--T--TCTTACCTAATTTCCTTGAAATCAAGTCTTTGC
1 CTTAATTACCCT-GAATTAAGTCCTTGACTGGTTTTACTTAATTACCCTG-AATTAAGTCTTTGT
106398 TTGTTCTTA
64 TTGTT-TTA
* * * * * * *
106407 CCTAATTTCCTTGAAATTAAGTCTTTGACT-GATTTACTTAATTACTCTGAATTAAGT-TTGTGC
1 CTTAATTACCCTG-AATTAAGTCCTTGACTGGTTTTACTTAATTACCCTGAATTAAGTCTT-TGT
106470 TTGTTCTTA
64 TTGTT-TTA
* * * * * * * *
106479 CCTAATTTCCTTGAAATTAAGT-CTTCG-CTTGTTCTTACCTAATTTCCTTGAAATTAAGTCTCT
1 CTTAATTACCCTG-AATTAAGTCCTT-GACTGGTT-TTACTTAATTACCCTG-AATTAAGTCTTT
** *
106542 GACTGATTTA
62 GTTTGTTTTA
* * * ** * * *
106552 CTTAACTACCCTGAATTAAGT-CTATG-CTTGTATTTACTCAATTTTCTTGAATTAGGTATTTGT
1 CTTAATTACCCTGAATTAAGTCCT-TGACTGGT-TTTACTTAATTACCCTGAATTAAGTCTTTGT
* *
106615 CTGCTTTCA
64 TTG-TTTTA
* * *
106624 CTTAATTACCCTGAATTAAGTCTTTGACTGTGTGTTTACTTTATTACCCTGAATTAAGTCTTTGG
1 CTTAATTACCCTGAATTAAGTCCTTGACTG-GT-TTTACTTAATTACCCTGAATTAAGTCTTTGT
*
106689 CTGCTTTTA
64 TTG-TTTTA
* *
106698 CTTAATTTCCCTGAATTAAG-CCTTTGACTGTGTTTTTACTTAATCACCCTGAATTAAGTCTTTG
1 CTTAATTACCCTGAATTAAGTCC-TTGACTG-G-TTTTACTTAATTACCCTGAATTAAGTCTTTG
**
106762 GCTGTTTTTA
63 TTTG-TTTTA
* *
106772 CTTAATTTCCCTTAATTAAG-CCTTTGACTGTGTTTTTACTTAATTACCCTGAATTAAGTCTTTG
1 CTTAATTACCCTGAATTAAGTCC-TTGACTG-G-TTTTACTTAATTACCCTGAATTAAGTC--T-
106836 ATTGCTTTTACTTGTGTTTTTA
60 -TTG-------TT-TG-TTTTA
* * * * *
106858 TTTAATTACCCTGAATTAAGTCTTTGATTGTTTTTACTTAATTTCCCTGAATTAAGTCTTTGACT
1 CTTAATTACCCTGAATTAAGTCCTTGACTGGTTTTACTTAATTACCCTGAATTAAGTCTTTG--T
*
106923 GTGTTTTTA
64 TTG-TTTTA
*
106932 TTTAATTACCCTGAATTAAGTC
1 CTTAATTACCCTGAATTAAGTC
106954 TTTAATTGTA
Statistics
Matches: 567, Mismatches: 78, Indels: 76
0.79 0.11 0.11
Matches are distributed among these distances:
64 14 0.02
65 12 0.02
66 5 0.01
67 22 0.04
68 3 0.01
70 17 0.03
71 31 0.05
72 151 0.27
73 42 0.07
74 199 0.35
75 5 0.01
76 1 0.00
78 3 0.01
80 3 0.01
82 1 0.00
84 26 0.05
86 31 0.05
87 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (71 bp):
CTTAATTACCCTGAATTAAGTCCTTGACTGGTTTTACTTAATTACCCTGAATTAAGTCTTTGTTT
GTTTTA
Found at i:106295 original size:36 final size:35
Alignment explanation
Indices: 106198--106848 Score: 427
Period size: 36 Copynumber: 18.1 Consensus size: 35
106188 TCTTATTGAC
* * * **
106198 CTTAATTGCCCTGAATTAAGTCCTTGACTACTTTTA
1 CTTAATTACCCTGAATTAAGTCTTTG-TTTGTTTTA
*
106234 GTTAATTACCCTGAATTAAGTCTTTGTTTGCTTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGTTTG-TTTTA
* *
106270 CTTAATTACCCTGAATTAAGTCTTTGTTCGCTTTTG
1 CTTAATTACCCTGAATTAAGTCTTTGTTTG-TTTTA
* * *
106306 CTTAATTGCCTTGAATTAAGTCTTTG-TTGATTTA
1 CTTAATTACCCTGAATTAAGTCTTTGTTTGTTTTA
* * *
106340 CTTAATTTCCTTGGAATTAAG---TTG--T-TCTTA
1 CTTAATTACCCT-GAATTAAGTCTTTGTTTGTTTTA
* * * * *
106370 CCTAATTTCCTTGAAATCAAGTCTTTGCTTGTTCTTA
1 CTTAATTACCCTG-AATTAAGTCTTTGTTTGTT-TTA
* * * ** *
106407 CCTAATTTCCTTGAAATTAAGTCTTTGACTGATTTA
1 CTTAATTACCCTG-AATTAAGTCTTTGTTTGTTTTA
* *
106443 CTTAATTACTCTGAATTAAGT-TTGTGCTTGTTCTTA
1 CTTAATTACCCTGAATTAAGTCTT-TGTTTGTT-TTA
* * * * *
106479 CCTAATTTCCTTGAAATTAAGTCTTCGCTTGTTCTTA
1 CTTAATTACCCTG-AATTAAGTCTTTGTTTGTT-TTA
* * * * ** *
106516 CCTAATTTCCTTGAAATTAAGTCTCTGACTGATTTA
1 CTTAATTACCCTG-AATTAAGTCTTTGTTTGTTTTA
* * *
106552 CTTAACTACCCTGAATTAAGTCTATGCTTGTATTTA
1 CTTAATTACCCTGAATTAAGTCTTTGTTTGT-TTTA
* ** * * * * *
106588 CTCAATTTTCTTGAATTAGGTATTTGTCTGCTTTCA
1 CTTAATTACCCTGAATTAAGTCTTTGTTTG-TTTTA
*
106624 CTTAATTACCCTGAATTAAGTCTTTGACTGTGTGTTTA
1 CTTAATTACCCTGAATTAAGTCTTTG--TTTGT-TTTA
* **
106662 CTTTATTACCCTGAATTAAGTCTTTGGCTGCTTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGTTTG-TTTTA
* * *
106698 CTTAATTTCCCTGAATTAAGCCTTTGACTGTGTTTTTA
1 CTTAATTACCCTGAATTAAGTCTTTG--TTTG-TTTTA
* **
106736 CTTAATCACCCTGAATTAAGTCTTTGGCTGTTTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGTTTG-TTTTA
* * * *
106772 CTTAATTTCCCTTAATTAAGCCTTTGACTGTGTTTTTA
1 CTTAATTACCCTGAATTAAGTCTTTG--TTTG-TTTTA
*
106810 CTTAATTACCCTGAATTAAGTCTTTGATTGCTTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGTTTG-TTTTA
106846 CTT
1 CTT
106849 GTGTTTTTAT
Statistics
Matches: 497, Mismatches: 94, Indels: 48
0.78 0.15 0.08
Matches are distributed among these distances:
29 1 0.00
30 20 0.04
31 1 0.00
32 3 0.01
33 3 0.01
34 16 0.03
35 39 0.08
36 238 0.48
37 82 0.16
38 94 0.19
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.47
Consensus pattern (35 bp):
CTTAATTACCCTGAATTAAGTCTTTGTTTGTTTTA
Found at i:106376 original size:30 final size:30
Alignment explanation
Indices: 106337--106428 Score: 94
Period size: 37 Copynumber: 2.8 Consensus size: 30
106327 CTTTGTTGAT
* *
106337 TTACTTAATTTCCTTGGAATTAAGTTGTTC
1 TTACCTAATTTCCTTGAAATTAAGTTGTTC
*
106367 TTACCTAATTTCCTTGAAATCAAGTCTTTGCTTGTTC
1 TTACCTAATTTCCTTGAAATTAA------G-TTGTTC
106404 TTACCTAATTTCCTTGAAATTAAGT
1 TTACCTAATTTCCTTGAAATTAAGT
106429 CTTTGACTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
30 21 0.41
31 1 0.02
36 1 0.02
37 28 0.55
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (30 bp):
TTACCTAATTTCCTTGAAATTAAGTTGTTC
Found at i:106679 original size:38 final size:38
Alignment explanation
Indices: 106388--106956 Score: 464
Period size: 36 Copynumber: 15.2 Consensus size: 38
106378 CCTTGAAATC
* * * *
106388 AAGTCTTTG-CT-TGTTCTTACCTAATTTCCTTGAAATT
1 AAGTCTTTGACTGTGTTTTTACTTAATTACCCTG-AATT
* *
106425 AAGTCTTTGAC--TG-ATTTACTTAATTACTCTGAATT
1 AAGTCTTTGACTGTGTTTTTACTTAATTACCCTGAATT
* * * *
106460 AAGT-TTGTG-CT-TGTTCTTACCTAATTTCCTTGAAATT
1 AAGTCTT-TGACTGTGTTTTTACTTAATTACCCTG-AATT
* * * * *
106497 AAGTCTTCG-CT-TGTTCTTACCTAATTTCCTTGAAATT
1 AAGTCTTTGACTGTGTTTTTACTTAATTACCCTG-AATT
* * *
106534 AAGTCTCTGAC--TG-ATTTACTTAACTACCCTGAATT
1 AAGTCTTTGACTGTGTTTTTACTTAATTACCCTGAATT
* * * ** *
106569 AAGTCTATG-CT-TGTATTTACTCAATTTTCTTGAATT
1 AAGTCTTTGACTGTGTTTTTACTTAATTACCCTGAATT
* * * * *
106605 AGGTATTTG--TCTGCTTTCACTTAATTACCCTGAATT
1 AAGTCTTTGACTGTGTTTTTACTTAATTACCCTGAATT
* *
106641 AAGTCTTTGACTGTGTGTTTACTTTATTACCCTGAATT
1 AAGTCTTTGACTGTGTTTTTACTTAATTACCCTGAATT
* * *
106679 AAGTCTTTGGC--TGCTTTTACTTAATTTCCCTGAATT
1 AAGTCTTTGACTGTGTTTTTACTTAATTACCCTGAATT
* *
106715 AAGCCTTTGACTGTGTTTTTACTTAATCACCCTGAATT
1 AAGTCTTTGACTGTGTTTTTACTTAATTACCCTGAATT
* * *
106753 AAGTCTTTGGC--TGTTTTTACTTAATTTCCCTTAATT
1 AAGTCTTTGACTGTGTTTTTACTTAATTACCCTGAATT
*
106789 AAGCCTTTGACTGTGTTTTTACTTAATTACCCTGAATT
1 AAGTCTTTGACTGTGTTTTTACTTAATTACCCTGAATT
*
106827 AAGTCTTTGATTGCTTTTACTTGTGTTTTTATTTAATTACCCTGAATT
1 AAGTC--T--TTG-----AC-TGTGTTTTTACTTAATTACCCTGAATT
*
106875 AAGTCTTTGA-T-TGTTTTTACTTAATTTCCCTGAATT
1 AAGTCTTTGACTGTGTTTTTACTTAATTACCCTGAATT
*
106911 AAGTCTTTGACTGTGTTTTTATTTAATTACCCTGAATT
1 AAGTCTTTGACTGTGTTTTTACTTAATTACCCTGAATT
106949 AAGTCTTT
1 AAGTCTTT
106957 AATTGTATTT
Statistics
Matches: 435, Mismatches: 69, Indels: 55
0.78 0.12 0.10
Matches are distributed among these distances:
34 4 0.01
35 27 0.06
36 178 0.41
37 59 0.14
38 125 0.29
39 1 0.00
40 1 0.00
42 3 0.01
44 3 0.01
46 1 0.00
47 2 0.00
48 31 0.07
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (38 bp):
AAGTCTTTGACTGTGTTTTTACTTAATTACCCTGAATT
Found at i:106681 original size:110 final size:109
Alignment explanation
Indices: 106206--106916 Score: 310
Period size: 109 Copynumber: 6.5 Consensus size: 109
106196 ACCTTAATTG
* ** * * **
106206 CCCTGAATTAAGTCCTTGACTACTTTTAGTTAATTACCCTGAATTAAGTCTTTGTTTGCTTTTAC
1 CCCTGAATTAAGTCTTTGACTGTTTTTACTTAATTACCCTGAATTAAGTCTATGGCTGCTTTTAC
* * * ** **
106271 TTAATTACCCTGAATTAAGTC-TTTGTTC-GCTTTTGCTTAATTG
66 TCAATTTCCCTGAATTAAG-CATTTGATCTGCTTTCACTTAATCA
* * * * * *
106314 CCTTGAATTAAGTCTTTG-TTG-ATTTACTTAATTTCCTTGGAATTAAG--T-T-G-T--TCTTA
1 CCCTGAATTAAGTCTTTGACTGTTTTTACTTAATTACCCT-GAATTAAGTCTATGGCTGCTTTTA
* * * * * **
106370 C-CTAATTTCCTTGAAATCAAGTC-TTTGCT-TG-TTCTTACCTAATTT
65 CTC-AATTTCCCTG-AATTAAG-CATTTGATCTGCTT-TCACTTAATCA
* * *
106415 CCTTGAAATTAAGTCTTTGACTG-ATTTACTTAATTACTCTGAATTAAGT-T-TGTGCTTG-TTC
1 CCCTG-AATTAAGTCTTTGACTGTTTTTACTTAATTACCCTGAATTAAGTCTATG-GC-TGCTT-
* * * * * **
106476 TTAC-CTAATTTCCTTGAAATTAAGTC-TTCGCT-TG-TTCTTACCTAATTT
62 TTACTC-AATTTCCCTG-AATTAAG-CATTTGATCTGCTT-TCACTTAATCA
* * * *
106524 CCTTGAAATTAAGTCTCTGACTG-ATTTACTTAACTACCCTGAATTAAGTCTAT-GCTTG-TATT
1 CCCTG-AATTAAGTCTTTGACTGTTTTTACTTAATTACCCTGAATTAAGTCTATGGC-TGCT-TT
* * * * *
106586 TACTCAATTTTCTTGAATTAGGTATTTG-TCTGCTTTCACTTAATTA
63 TACTCAATTTCCCTGAATTAAGCATTTGATCTGCTTTCACTTAATCA
* *
106632 CCCTGAATTAAGTCTTTGACTGTGTGTTTACTTTATTACCCTGAATTAAGTCTTTGGCTGCTTTT
1 CCCTGAATTAAGTCTTTGACTGT-T-TTTACTTAATTACCCTGAATTAAGTCTATGGCTGCTTTT
* * * * *
106697 ACTTAATTTCCCTGAATTAAGCCTTTGACTGTGTTTTTACTTAATCA
64 ACTCAATTTCCCTGAATTAAGCATTTGA-TCTGCTTTCACTTAATCA
* * * * * * *
106744 CCCTGAATTAAGTCTTTGGCTGTTTTTACTTAATTTCCCTTAATTAAGCCTTTGACTGTGTTTTT
1 CCCTGAATTAAGTCTTTGACTGTTTTTACTTAATTACCCTGAATTAAGTCTATGGC--TGCTTTT
* * * *
106809 ACTTAATTACCCTGAATTAAGTC-TTTGAT-TGCTTTTACTTGTGTTTTTATTTAATTA
64 ACTCAATTTCCCTGAATTAAG-CATTTGATCTGC-TTT-C----------ACTTAATCA
* *
106866 CCCTGAATTAAGTCTTTGATTGTTTTTACTTAATTTCCCTGAATTAAGTCT
1 CCCTGAATTAAGTCTTTGACTGTTTTTACTTAATTACCCTGAATTAAGTCT
106917 TTGACTGTGT
Statistics
Matches: 493, Mismatches: 67, Indels: 72
0.78 0.11 0.11
Matches are distributed among these distances:
100 15 0.03
101 27 0.05
102 22 0.04
103 18 0.04
104 1 0.00
105 2 0.00
106 13 0.03
107 27 0.05
108 40 0.08
109 113 0.23
110 84 0.17
111 9 0.02
112 67 0.14
113 1 0.00
122 54 0.11
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (109 bp):
CCCTGAATTAAGTCTTTGACTGTTTTTACTTAATTACCCTGAATTAAGTCTATGGCTGCTTTTAC
TCAATTTCCCTGAATTAAGCATTTGATCTGCTTTCACTTAATCA
Found at i:106710 original size:74 final size:73
Alignment explanation
Indices: 106361--106970 Score: 472
Period size: 74 Copynumber: 8.2 Consensus size: 73
106351 TGGAATTAAG
* * * * * * * *
106361 TTGTTCTTACCTAATTTCCTTGAAATCAAGTCTTT-GCTTGTTCTTACCTAATTTCCTTGAAATT
1 TTGTTTTTACTTAATTACCCTG-AATTAAGTCTTTGGCTTGTT-TTACTTAATTACCCTG-AATT
106425 AAGTCTTTGAC
63 AAGTCTTTGAC
* * * * *
106436 -TG-ATTTACTTAATTACTCTGAATTAAG--TTTGTGCTTGTTCTTACCTAATTTCCTTGAAATT
1 TTGTTTTTACTTAATTACCCTGAATTAAGTCTTTG-GCTTGTT-TTACTTAATTACCCTG-AATT
*
106497 AAGTCTTCG-C
63 AAGTCTTTGAC
* * * * * * * *
106507 TTGTTCTTACCTAATTTCCTTGAAATTAAGTCTCTGAC-TGATTTACTTAACTACCCTGAATTAA
1 TTGTTTTTACTTAATTACCCTG-AATTAAGTCTTTGGCTTGTTTTACTTAATTACCCTGAATTAA
*
106571 GTCTATG-C
65 GTCTTTGAC
* * ** * * * * *
106579 TTGTATTTACTCAATTTTCTTGAATTAGGTATTTGTC-TGCTTTCACTTAATTACCCTGAATTAA
1 TTGTTTTTACTTAATTACCCTGAATTAAGTCTTTGGCTTG-TTTTACTTAATTACCCTGAATTAA
106643 GTCTTTGAC
65 GTCTTTGAC
* * *
106652 TGTGTGTTTACTTTATTACCCTGAATTAAGTCTTTGGC-TGCTTTTACTTAATTTCCCTGAATTA
1 T-TGTTTTTACTTAATTACCCTGAATTAAGTCTTTGGCTTG-TTTTACTTAATTACCCTGAATTA
*
106716 AGCCTTTGAC
64 AGTCTTTGAC
* * *
106726 TGTGTTTTTACTTAATCACCCTGAATTAAGTCTTTGGC-TGTTTTTACTTAATTTCCCTTAATTA
1 T-TGTTTTTACTTAATTACCCTGAATTAAGTCTTTGGCTTG-TTTTACTTAATTACCCTGAATTA
*
106790 AGCCTTTGAC
64 AGTCTTTGAC
*
106800 TGTGTTTTTACTTAATTACCCTGAATTAAGTCTTTGATTGCTTTTACTTGTGTTTTTATTTAATT
1 T-TGTTTTTACTTAATTACCCTGAATTAAGTCTTTG---G------C-T-TG-TTTTACTTAATT
106865 ACCCTGAATTAAGTCTTTGA-
53 ACCCTGAATTAAGTCTTTGAC
* * *
106885 TTGTTTTTACTTAATTTCCCTGAATTAAGTCTTTGACTGTGTTTTTATTTAATTACCCTGAATTA
1 TTGTTTTTACTTAATTACCCTGAATTAAGTCTTTGGCT-TG-TTTTACTTAATTACCCTGAATTA
*
106950 AGTCTTT-AA
64 AGTCTTTGAC
*
106959 TTGTATTTACTT
1 TTGTTTTTACTT
106971 CATGCATGGA
Statistics
Matches: 451, Mismatches: 61, Indels: 47
0.81 0.11 0.08
Matches are distributed among these distances:
70 3 0.01
71 14 0.03
72 101 0.22
73 39 0.09
74 222 0.49
75 2 0.00
76 3 0.01
77 1 0.00
83 1 0.00
84 33 0.07
85 1 0.00
86 31 0.07
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (73 bp):
TTGTTTTTACTTAATTACCCTGAATTAAGTCTTTGGCTTGTTTTACTTAATTACCCTGAATTAAG
TCTTTGAC
Found at i:106871 original size:48 final size:48
Alignment explanation
Indices: 106800--106896 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
106790 AGCCTTTGAC
106800 TGTGTTTTTACTTAATTACCCTGAATTAAGTCTTTGATTGCTTTTACT
1 TGTGTTTTTACTTAATTACCCTGAATTAAGTCTTTGATTGCTTTTACT
* *
106848 TGTGTTTTTATTTAATTACCCTGAATTAAGTCTTTGATTGTTTTTACT
1 TGTGTTTTTACTTAATTACCCTGAATTAAGTCTTTGATTGCTTTTACT
106896 T
1 T
106897 AATTTCCCTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (48 bp):
TGTGTTTTTACTTAATTACCCTGAATTAAGTCTTTGATTGCTTTTACT
Found at i:106943 original size:122 final size:122
Alignment explanation
Indices: 106726--106970 Score: 402
Period size: 122 Copynumber: 2.0 Consensus size: 122
106716 AGCCTTTGAC
* *
106726 TGTGTTTTTACTTAATCACCCTGAATTAAGTCTTTGGCTGTTTTTACTTAATTTCCCTTAATTAA
1 TGTGTTTTTACTTAATCACCCTGAATTAAGTCTTTGACTGTTTTTACTTAATTTCCCTGAATTAA
*
106791 GCCTTTGACTGTGTTTTTACTTAATTACCCTGAATTAAGTCTTTGATTGCT-TTTACT
66 GCCTTTGACTGTGTTTTTACTTAATTACCCTGAATTAAGTCTTTAATTG-TATTTACT
* * *
106848 TGTGTTTTTATTTAATTACCCTGAATTAAGTCTTTGATTGTTTTTACTTAATTTCCCTGAATTAA
1 TGTGTTTTTACTTAATCACCCTGAATTAAGTCTTTGACTGTTTTTACTTAATTTCCCTGAATTAA
* *
106913 GTCTTTGACTGTGTTTTTATTTAATTACCCTGAATTAAGTCTTTAATTGTATTTACT
66 GCCTTTGACTGTGTTTTTACTTAATTACCCTGAATTAAGTCTTTAATTGTATTTACT
106970 T
1 T
106971 CATGCATGGA
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
121 1 0.01
122 113 0.99
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.51
Consensus pattern (122 bp):
TGTGTTTTTACTTAATCACCCTGAATTAAGTCTTTGACTGTTTTTACTTAATTTCCCTGAATTAA
GCCTTTGACTGTGTTTTTACTTAATTACCCTGAATTAAGTCTTTAATTGTATTTACT
Found at i:110843 original size:40 final size:42
Alignment explanation
Indices: 110772--110853 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 42
110762 TGAGCGATTG
* * *
110772 AAAACTTGTTGGGATGCCCCCCCTTGGGAGCAATTGAAAACTA
1 AAAACTTGTTGGAATG-CCCCCCTTGGGAGCAACTAAAAACTA
110815 AAAAC-TGTTGGAATG-CCCCCTTGGGAGCAACTAAAAACT
1 AAAACTTGTTGGAATGCCCCCCTTGGGAGCAACTAAAAACT
110854 TATTGGAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 22 0.61
42 9 0.25
43 5 0.14
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (42 bp):
AAAACTTGTTGGAATGCCCCCCTTGGGAGCAACTAAAAACTA
Found at i:114202 original size:29 final size:29
Alignment explanation
Indices: 114158--114256 Score: 130
Period size: 29 Copynumber: 3.4 Consensus size: 29
114148 TCCGAGTACA
* *
114158 AACCCACAC-TCAACAATCCCAAGTGCAC
1 AACCCACACTTGAACAATCACAAGTGCAC
114186 AACCCACACTTGAACAAAT-ACAAGTGCAC
1 AACCCACACTTGAAC-AATCACAAGTGCAC
* *
114215 AACCCGCACTTGAACAAACACAAGTGCAC
1 AACCCACACTTGAACAATCACAAGTGCAC
*
114244 AACCCGCACTTGA
1 AACCCACACTTGA
114257 TACACCAAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
28 11 0.17
29 50 0.78
30 3 0.05
ACGTcount: A:0.40, C:0.36, G:0.11, T:0.12
Consensus pattern (29 bp):
AACCCACACTTGAACAATCACAAGTGCAC
Found at i:132888 original size:29 final size:29
Alignment explanation
Indices: 132830--133053 Score: 220
Period size: 29 Copynumber: 7.7 Consensus size: 29
132820 GGTCACTTAA
*
132830 AGGGGCATTTTGATCA-TTTTGCATGA-CC
1 AGGGGCATTTTGGTCATTTTTGCAT-ATCC
*
132858 AGGGGCATTATGGTCATTTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCC
132887 AGGGGGCATTTTGGTCATTTTTGCATATCC
1 A-GGGGCATTTTGGTCATTTTTGCATATCC
* * ** *
132917 AAGGGCATTATGGTCATTTTCACGTATCCC
1 AGGGGCATTTTGGTCATTTTTGCATAT-CC
* ** * *
132947 A-TGGCATTTTTATCATTTTTGCACATTC
1 AGGGGCATTTTGGTCATTTTTGCATATCC
* *
132975 AGGAGCATTTTGGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCC
** * *
133004 AATGGTATTTTGGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCC
*
133033 AAGGGGCATTATGGTCATTTT
1 -AGGGGCATTTTGGTCATTTT
133054 GGTTTTATTC
Statistics
Matches: 160, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
28 17 0.11
29 96 0.60
30 47 0.29
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCATATCC
Found at i:138576 original size:20 final size:21
Alignment explanation
Indices: 138543--138581 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
138533 ACTTGTGTGC
* *
138543 ACAACAATTGATGTTCAAAGA
1 ACAACAATTAATGTCCAAAGA
138564 ACAA-AATTAATGTCCAAA
1 ACAACAATTAATGTCCAAA
138582 TCTATATAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.23
Consensus pattern (21 bp):
ACAACAATTAATGTCCAAAGA
Found at i:145326 original size:24 final size:24
Alignment explanation
Indices: 145273--145328 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
145263 CAGAACCAGA
*
145273 ATCAAGATTTTCAGTTTACAAGAG
1 ATCAATATTTTCAGTTTACAAGAG
145297 ATCAATATTTTCAGTTTACAAGAG
1 ATCAATATTTTCAGTTTACAAGAG
145321 ATCAATAT
1 ATCAATAT
145329 GAACAACTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (24 bp):
ATCAATATTTTCAGTTTACAAGAG
Found at i:147227 original size:2 final size:2
Alignment explanation
Indices: 147220--147248 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
147210 TTCCATCTTT
147220 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.