Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008933.1 Hibiscus syriacus cultivar Beakdansim tig00112249_pilon, 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: 2862162
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 14
Found at i:109456 original size:20 final size:20
Alignment explanation
Indices: 109431--109623 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
109421 CTTTAAATAT
109431 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
109451 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
109473 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
109492 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
109512 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
109532 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
109552 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
109572 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
109592 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
109612 CGCGTTGCGATT
1 CGCGTTGCGATT
109624 ATTGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:109618 original size:60 final size:60
Alignment explanation
Indices: 109431--109623 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
109421 CTTTAAATAT
**
109431 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
109492 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
109552 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
109612 CGCGTTGCGATT
1 CGCGTTGCGATT
109624 ATTGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:111792 original size:31 final size:31
Alignment explanation
Indices: 111757--111823 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
111747 TAAAATACAC
*
111757 AAGATATGACCACATTTGTTTTTCTTTAATT
1 AAGATATGACCACATTTGTTTTTATTTAATT
* * *
111788 AAGATATGATCACTTTTGTTTTTATTTATTT
1 AAGATATGACCACATTTGTTTTTATTTAATT
111819 AAGAT
1 AAGAT
111824 GTGGTCACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.51
Consensus pattern (31 bp):
AAGATATGACCACATTTGTTTTTATTTAATT
Found at i:114727 original size:2 final size:2
Alignment explanation
Indices: 114722--114746 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
114712 TACGCTCATG
114722 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 T
114747 TCGACCTCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:115434 original size:105 final size:104
Alignment explanation
Indices: 115227--115456 Score: 237
Period size: 105 Copynumber: 2.2 Consensus size: 104
115217 CGTATTGCAT
* * * * ** *
115227 TAAGGGTTTAGGGGTTTAAAGATTTTCTTCTTCTTTGTATCCTTTGCAACATCGGAGTTGTGCTT
1 TAAGAGTTTA-GGGTTTAAGGATTTTCTTCTTCTCTATATCCTCAGCAACATCGGAGTTATGCTT
**** **
115292 CGTTATGATTTAGAAGCACTAATTCAAAATGGTAAAATGG
65 CGTTATGATTTAGAAGCACTAATTCAAAACCCCAAAATAA
* *
115332 TAAGAGTTTAGGGTTTAAGGATTTTCTTCTTCTCTATCTCCTACAGTAACATCGGAGTTATGCTT
1 TAAGAGTTTAGGGTTTAAGGATTTTCTTCTTCTCTATATCCT-CAGCAACATCGGAGTTATGCTT
* * * *
115397 TGTTATGGTTTAGAATCAGC-AGTTCAAAACCCCAAAATAA
65 CGTTATGATTTAGAAGCA-CTAATTCAAAACCCCAAAATAA
* *
115437 TAATAGTTTAGAGTTTAAGG
1 TAAGAGTTTAGGGTTTAAGG
115457 TTTCTCTCCT
Statistics
Matches: 102, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
104 28 0.27
105 73 0.72
106 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (104 bp):
TAAGAGTTTAGGGTTTAAGGATTTTCTTCTTCTCTATATCCTCAGCAACATCGGAGTTATGCTTC
GTTATGATTTAGAAGCACTAATTCAAAACCCCAAAATAA
Found at i:120657 original size:21 final size:21
Alignment explanation
Indices: 120592--120668 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
120582 ATCGATACCC
* *
120592 TTGGTCTTCATATCGAATAAA
1 TTGGTCTCCATACCGAATAAA
* *
120613 TTAGTCTCCATACGGAATAAA
1 TTGGTCTCCATACCGAATAAA
*
120634 TTGGTCTACATACCGAATAAA
1 TTGGTCTCCATACCGAATAAA
*
120655 TTGGTATCCATACC
1 TTGGTCTCCATACC
120669 TAAGATCGGA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.32
Consensus pattern (21 bp):
TTGGTCTCCATACCGAATAAA
Found at i:121683 original size:34 final size:30
Alignment explanation
Indices: 121645--121713 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
121635 TTGATATAAC
121645 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
121679 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
121708 AATTTA
1 AATTTA
121714 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:121724 original size:29 final size:30
Alignment explanation
Indices: 121654--121713 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
121644 CAATTTAAGG
121654 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
121685 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
121714 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:121819 original size:21 final size:21
Alignment explanation
Indices: 121795--121893 Score: 123
Period size: 21 Copynumber: 4.7 Consensus size: 21
121785 GGTGTCAAAG
*
121795 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCATCCCTGCAA
121816 TGCATCCATGCATCCCTGCAA
1 TGCATCCATGCATCCCTGCAA
121837 TGCATCCATGCATCTTCACT--AA
1 TGCATCCATGCATC--C-CTGCAA
* *
121859 TGCATCGATGCAT-CATGCAA
1 TGCATCCATGCATCCCTGCAA
121879 TGCATCCATGCATCC
1 TGCATCCATGCATCC
121894 AAACATCGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 14 0.21
21 35 0.51
22 14 0.21
23 1 0.01
24 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.15, T:0.26
Consensus pattern (21 bp):
TGCATCCATGCATCCCTGCAA
Found at i:123388 original size:14 final size:15
Alignment explanation
Indices: 123363--123391 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
123353 TGATGGTAAA
123363 GGAAGATGAAGAAAG
1 GGAAGATGAAGAAAG
123378 GGAAGAT-AAGAAAG
1 GGAAGATGAAGAAAG
123392 AGGTAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (15 bp):
GGAAGATGAAGAAAG
Found at i:125218 original size:34 final size:30
Alignment explanation
Indices: 125180--125248 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
125170 TTGATATAAC
125180 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
125214 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
125243 AATTTA
1 AATTTA
125249 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:125259 original size:29 final size:30
Alignment explanation
Indices: 125189--125248 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
125179 CAATTTAAGG
125189 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
125220 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
125249 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:125354 original size:21 final size:21
Alignment explanation
Indices: 125328--125385 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
125318 AGGGTGTCAA
125328 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
125349 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
125370 AATGCATCCATGCATC
1 AGTGCATCCATGCATC
125386 TTCACTAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:125473 original size:20 final size:20
Alignment explanation
Indices: 125448--125521 Score: 89
Period size: 20 Copynumber: 3.6 Consensus size: 20
125438 ATGCAATTAG
125448 TGCATCGATGCAT-CTTGCTA
1 TGCATCGATGCATACTTGC-A
*
125468 TGCATCGATGCATCCTTGACA
1 TGCATCGATGCATACTTG-CA
125489 TGCATCGATGCATAC-TGCCA
1 TGCATCGATGCATACTTG-CA
*
125509 TGCATCCATGCAT
1 TGCATCGATGCAT
125522 CAAGGCTGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
20 29 0.59
21 19 0.39
22 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (20 bp):
TGCATCGATGCATACTTGCA
Found at i:133160 original size:395 final size:394
Alignment explanation
Indices: 132596--133380 Score: 1247
Period size: 395 Copynumber: 2.0 Consensus size: 394
132586 TAAGAAGGTT
*
132596 TTTTAACGAAACCCTTATCGATGCTCTGTTTTGTGTTTCTCCCTATTAATACATAAAAAAAACTC
1 TTTTAACGAAACCCTTATCGATGCCCTGTTTTGTGTTTCTCCCTATTAATACAT-AAAAAAACTC
*
132661 CCTCTTTTCAGAAAAAAATAAAATTAAAACTTAATTTTCTCACTTAAAAAAAAATCTTCACGTAA
65 CCTCTTTTCAGAAAAAAATAAAATTAAAACTCAATTTTCTCACTTAAAAAAAAATCTTCACGTAA
* *
132726 GTTTTAAATTTGACACTTTAAAACAAATTTTCTACCTCCATCCTTGAGTACTACATCGATTGGTT
130 GTTTTAAATTTGACACTTTAAAACAAATTTTCTACCTCCATCCCTGAGTAATACATCGATTGGTT
* * * * *
132791 TTTTAACGAGGCCCTTATCGATGC-CATGTTTTGTGTGTTTCTCCCTATTAATACATAGAAAGCT
195 TTTTAACGAAGCCCTTATCGATGCAC-TGATTTGTGTGTTTCCCCCTATTAATACATAGAAAACA
*
132855 CCCTTTTTTC-GAAAAT-AAAAT-AAATTAAAACTCAATTTTCTCACTTAAAAAAGAAAATCTTC
259 CCCTCTTTTCGGAAAATAAAAATAAAATTAAAACTCAATTTTCTCACTTAAAAAAGAAAATCTTC
*
132917 ACGTAAGTTTTAAATTTGACACTTTAAAACAAATTTTCTACCTCCATCCCTGAGTACTACATCGA
324 ACGTAAGTTTTAAATTTGACACTTTAAAACAAATTTTCTAACTCCATCCCTGAGTACTACATCGA
132982 TTGAGA
389 TTGAGA
** * *
132988 TTTTAACGAGGCCCTTATCGATGCCCTGTTTTGTGTGTTTCTCCCTGTTAATACAT-AGAAAACT
1 TTTTAACGAAACCCTTATCGATGCCCTG-TTT-TGTGTTTCTCCCTATTAATACATAAAAAAACT
*
133052 CCCTCTTTTCAGGGGAAAAAATAAAATTAAAACTCAATTTTCTCACTTAAAAAGAAAATCTTCAC
64 CCCTCTTTTCA--GAAAAAAATAAAATTAAAACTCAATTTTCTCACTTAAAAA-AAAATCTTCAC
*
133117 GTAAGTTTTAAATTTGACACTTTAAAATAAATTTTCTACCTCCATCCCTGAGTAATACATCGATT
126 GTAAGTTTTAAATTTGACACTTTAAAACAAATTTTCTACCTCCATCCCTGAGTAATACATCGATT
* *
133182 GGTTTTTTAACGAAGCCGTTATCGATGCACTGATTTGTGTGTTTCCCCCTATTGATACATAGAAA
191 GGTTTTTTAACGAAGCCCTTATCGATGCACTGATTTGTGTGTTTCCCCCTATTAATACATAGAAA
133247 ACACCCTCTTTTCGGGAAAATAAAAATAAAATTAAAACTCAATTTTCTCACTTAAAAAAGAAAAT
256 ACACCCTCTTTTC-GGAAAATAAAAATAAAATTAAAACTCAATTTTCTCACTTAAAAAAGAAAAT
** * * *
133312 CTTCATTTAAGTTTTAAATTTGACACTTTAGAATAAATTTTCTAACTCCGTCCCTGAGTACTACA
320 CTTCACGTAAGTTTTAAATTTGACACTTTAAAACAAATTTTCTAACTCCATCCCTGAGTACTACA
133377 TCGA
385 TCGA
133381 CTTTTCTTCA
Statistics
Matches: 359, Mismatches: 24, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
392 43 0.12
393 3 0.01
394 60 0.17
395 141 0.39
396 1 0.00
397 6 0.02
398 5 0.01
399 100 0.28
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.36
Consensus pattern (394 bp):
TTTTAACGAAACCCTTATCGATGCCCTGTTTTGTGTTTCTCCCTATTAATACATAAAAAAACTCC
CTCTTTTCAGAAAAAAATAAAATTAAAACTCAATTTTCTCACTTAAAAAAAAATCTTCACGTAAG
TTTTAAATTTGACACTTTAAAACAAATTTTCTACCTCCATCCCTGAGTAATACATCGATTGGTTT
TTTAACGAAGCCCTTATCGATGCACTGATTTGTGTGTTTCCCCCTATTAATACATAGAAAACACC
CTCTTTTCGGAAAATAAAAATAAAATTAAAACTCAATTTTCTCACTTAAAAAAGAAAATCTTCAC
GTAAGTTTTAAATTTGACACTTTAAAACAAATTTTCTAACTCCATCCCTGAGTACTACATCGATT
GAGA
Found at i:133169 original size:198 final size:197
Alignment explanation
Indices: 132592--133380 Score: 1178
Period size: 197 Copynumber: 4.0 Consensus size: 197
132582 GGATTAAGAA
* * *
132592 GGTTTTTTAACGAAACCCTTATCGATGCTCTG-TTT-TGTGTTTCTCCCTATTAATACATAAAAA
1 GGTTTTTTAACGAAGCCCTTATCGATGCCCTGTTTTGTGTGTTTCTCCCTATTAATACAT--AGA
* *
132655 AAACTCCCTCTTTTCAGAAAAAAATAAAATTAAAACTTAATTTTCTCACTT-AAAAA-AAAATCT
64 AAACTCCCTCTTTTCGGAAAAAAATAAAATTAAAACTCAATTTTCTCACTTAAAAAAGAAAATCT
*
132718 TCACGTAAGTTTTAAATTTGACACTTTAAAACAAATTTTCTACCTCCATCCTTGAGTACTACATC
129 TCACGTAAGTTTTAAATTTGACACTTTAAAACAAATTTTCTACCTCCATCCCTGAGTACTACATC
132783 GATT
194 GATT
* *
132787 GGTTTTTTAACGAGGCCCTTATCGATGCCATGTTTTGTGTGTTTCTCCCTATTAATACATAGAAA
1 GGTTTTTTAACGAAGCCCTTATCGATGCCCTGTTTTGTGTGTTTCTCCCTATTAATACATAGAAA
* * *
132852 GCTCCCTTTTTTCGAAAATAAAAT-AAATTAAAACTCAATTTTCTCACTTAAAAAAGAAAATCTT
66 ACTCCCTCTTTTCGGAAA-AAAATAAAATTAAAACTCAATTTTCTCACTTAAAAAAGAAAATCTT
132916 CACGTAAGTTTTAAATTTGACACTTTAAAACAAATTTTCTACCTCCATCCCTGAGTACTACATCG
130 CACGTAAGTTTTAAATTTGACACTTTAAAACAAATTTTCTACCTCCATCCCTGAGTACTACATCG
132981 ATT
195 ATT
* * *
132984 GAG-ATTTTAACGAGGCCCTTATCGATGCCCTGTTTTGTGTGTTTCTCCCTGTTAATACATAGAA
1 G-GTTTTTTAACGAAGCCCTTATCGATGCCCTGTTTTGTGTGTTTCTCCCTATTAATACATAGAA
*
133048 AACTCCCTCTTTTCAGGGGAAAAAATAAAATTAAAACTCAATTTTCTCACTT-AAAAAGAAAATC
65 AACTCCCTCTTTTC--GGAAAAAAATAAAATTAAAACTCAATTTTCTCACTTAAAAAAGAAAATC
* *
133112 TTCACGTAAGTTTTAAATTTGACACTTTAAAATAAATTTTCTACCTCCATCCCTGAGTAATACAT
128 TTCACGTAAGTTTTAAATTTGACACTTTAAAACAAATTTTCTACCTCCATCCCTGAGTACTACAT
133177 CGATT
193 CGATT
* * * * *
133182 GGTTTTTTAACGAAGCCGTTATCGATGCACTGATTTGTGTGTTTCCCCCTATTGATACATAGAAA
1 GGTTTTTTAACGAAGCCCTTATCGATGCCCTGTTTTGTGTGTTTCTCCCTATTAATACATAGAAA
*
133247 ACACCCTCTTTTCGGGAAAATAAAAATAAAATTAAAACTCAATTTTCTCACTTAAAAAAGAAAAT
66 ACTCCCTCTTTTC-GG--AA-AAAAATAAAATTAAAACTCAATTTTCTCACTTAAAAAAGAAAAT
** * * * *
133312 CTTCATTTAAGTTTTAAATTTGACACTTTAGAATAAATTTTCTAACTCCGTCCCTGAGTACTACA
127 CTTCACGTAAGTTTTAAATTTGACACTTTAAAACAAATTTTCTACCTCCATCCCTGAGTACTACA
133377 TCGA
192 TCGA
133381 CTTTTCTTCA
Statistics
Matches: 544, Mismatches: 36, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
195 70 0.13
196 13 0.02
197 173 0.32
198 153 0.28
199 29 0.05
200 32 0.06
201 74 0.14
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (197 bp):
GGTTTTTTAACGAAGCCCTTATCGATGCCCTGTTTTGTGTGTTTCTCCCTATTAATACATAGAAA
ACTCCCTCTTTTCGGAAAAAAATAAAATTAAAACTCAATTTTCTCACTTAAAAAAGAAAATCTTC
ACGTAAGTTTTAAATTTGACACTTTAAAACAAATTTTCTACCTCCATCCCTGAGTACTACATCGA
TT
Found at i:133628 original size:20 final size:20
Alignment explanation
Indices: 133600--133638 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
133590 CGACCATGTT
* *
133600 ATTTTATATTTGAATAATTA
1 ATTTCATATATGAATAATTA
*
133620 ATTTCATATATGTATAATT
1 ATTTCATATATGAATAATT
133639 TTTTATTTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTCATATATGAATAATTA
Found at i:142953 original size:26 final size:26
Alignment explanation
Indices: 142905--142968 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
142895 TAACTTATTA
*
142905 AAAATCTTTTTA-TTAATTTAATTT-
1 AAAATATTTTTATTTAATTTAATTTC
142929 AAAATATTTTTATTTTAATTTAATTTC
1 AAAATATTTTTA-TTTAATTTAATTTC
*
142956 AAAATATATTTAT
1 AAAATATTTTTAT
142969 GCTAAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 11 0.31
26 13 0.37
27 11 0.31
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (26 bp):
AAAATATTTTTATTTAATTTAATTTC
Found at i:143127 original size:31 final size:31
Alignment explanation
Indices: 143091--143151 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
143081 ATATACTTTG
*
143091 AAAAGTTAAAATAATAATAAAATAA-ATTTTT
1 AAAAGTTAAAATAAGAATAAAA-AATATTTTT
* *
143122 AAAAGTTTAGATAAGAATAAAAAATATTTT
1 AAAAGTTAAAATAAGAATAAAAAATATTTT
143152 ATCTTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (31 bp):
AAAAGTTAAAATAAGAATAAAAAATATTTTT
Found at i:143245 original size:11 final size:10
Alignment explanation
Indices: 143218--143247 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
143208 TTTTATCTTA
143218 ATTTTAAAAT
1 ATTTTAAAAT
143228 ATTTTAAAAT
1 ATTTTAAAAT
*
143238 ATTTTTAAAT
1 ATTTTAAAAT
143248 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:143291 original size:25 final size:23
Alignment explanation
Indices: 143247--143311 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 23
143237 TATTTTTAAA
*
143247 TTAA-AATAAAAATAAAATAT-T
1 TTAATAATAATAATAAAATATAT
143268 TTCAATAAGTTAATAATAAAATATAT
1 TT-AATAA--TAATAATAAAATATAT
143294 TTAATAATAAT-ATAAAAT
1 TTAATAATAATAATAAAAT
143312 TCTTAAAGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 2 0.05
22 9 0.24
23 6 0.16
25 18 0.47
26 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
TTAATAATAATAATAAAATATAT
Found at i:143741 original size:31 final size:31
Alignment explanation
Indices: 143698--143757 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
143688 TTAAGCCGTG
* ** *
143698 GTGATCATATCTTAGTTAACTAAAAATGAAA
1 GTGACCATATCTTAACTAAATAAAAATGAAA
143729 GTGACCATATCTTAACTAAATAAAAATGA
1 GTGACCATATCTTAACTAAATAAAAATGA
143758 TCATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (31 bp):
GTGACCATATCTTAACTAAATAAAAATGAAA
Found at i:144198 original size:36 final size:36
Alignment explanation
Indices: 144150--144222 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
144140 AATCATACTT
*
144150 AATGTTATATTTTGGTCACTCATCGTTAAAAAATTA
1 AATGTTACATTTTGGTCACTCATCGTTAAAAAATTA
144186 AATGTTACATTTTGGTCACTCATCGTTAAAAAATTA
1 AATGTTACATTTTGGTCACTCATCGTTAAAAAATTA
144222 A
1 A
144223 CATAACTACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (36 bp):
AATGTTACATTTTGGTCACTCATCGTTAAAAAATTA
Found at i:144246 original size:2 final size:2
Alignment explanation
Indices: 144239--144264 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
144229 TACTTACATG
144239 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
144265 TATGTTACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:144776 original size:32 final size:32
Alignment explanation
Indices: 144735--144803 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
144725 ATGGTGATTG
144735 ATTAGAATCGTACATGCATTGATGACCATGTC
1 ATTAGAATCGTACATGCATTGATGACCATGTC
*
144767 ATTAGAATCGTACATTCATTGATGACCATGTC
1 ATTAGAATCGTACATGCATTGATGACCATGTC
144799 ATTAG
1 ATTAG
144804 TACGGCTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (32 bp):
ATTAGAATCGTACATGCATTGATGACCATGTC
Found at i:148621 original size:8 final size:8
Alignment explanation
Indices: 148608--148648 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
148598 CTCATTTTCA
148608 GAGAATTT
1 GAGAATTT
148616 GAGAATTT
1 GAGAATTT
*
148624 -AGAGTTT
1 GAGAATTT
*
148631 GGGAATTT
1 GAGAATTT
148639 GAGAATTT
1 GAGAATTT
148647 GA
1 GA
148649 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:149069 original size:128 final size:128
Alignment explanation
Indices: 148719--149597 Score: 1504
Period size: 128 Copynumber: 6.9 Consensus size: 128
148709 TAATCGGAGT
* *
148719 ACTATTCACATGAAGGCACGTTCCCGGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
148784 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTAG--ATAT-A-TACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
148843 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTA-TTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
148907 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** * *
148970 TC-AGGGGATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
*
149034 TCATTGCCCTATTATGTCACTCATATCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
149098 ACTATTTACATGAAGGCGTGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
149163 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
149226 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
149291 CATTGTCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** * * *
149354 -TTAGGGGACATGAAGGCGCGTTCTCGGGGGGGCGCCTTCCATTATTTCGTCAAAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
149418 TCATTGCCCTATTATGTCA-TCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
149481 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
149546 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
149598 AATCAGGTAA
Statistics
Matches: 709, Mismatches: 36, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
123 60 0.08
124 42 0.06
125 4 0.01
126 2 0.00
127 169 0.24
128 431 0.61
129 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:149528 original size:383 final size:383
Alignment explanation
Indices: 148719--149597 Score: 1597
Period size: 383 Copynumber: 2.3 Consensus size: 383
148709 TAATCGGAGT
* *
148719 ACTATTCACATGAAGGCACGTTCCCGGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
148784 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTAG--ATAT-A-TACCTATTATTTCAC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
148845 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTCGTCAGAGAATATGTTATCAT
131 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTCGTCAGAGAATATGTTATCAT
148910 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGG
196 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGG
* *
148975 GGATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTG
261 GGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAAAGAATATGTTATCATTG
149040 CCCTATTATGTCACTCATATCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
326 CCCTATTATGTCACTCATATCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
149098 ACTATTTACATGAAGGCGTGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
149163 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
149228 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
131 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTA-TTCGTCAGAGAATATGTTATCA
* *
149293 TTGTCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTTAG
195 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAG
* * *
149358 GGGACATGAAGGCGCGTTCTCGGGGGGGCGCCTTCCATTATTTCGTCAAAGAATATGTTATCATT
260 GGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAAAGAATATGTTATCATT
*
149423 GCCCTATTATGTCA-TCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
325 GCCCTATTATGTCACTCATATCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
149481 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
149546 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
149598 AATCAGGTAA
Statistics
Matches: 480, Mismatches: 15, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
379 101 0.21
381 4 0.01
382 1 0.00
383 215 0.45
384 159 0.33
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.32
Consensus pattern (383 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTCGTCAGAGAATATGTTATCAT
TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGG
GGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAAAGAATATGTTATCATTG
CCCTATTATGTCACTCATATCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:150058 original size:33 final size:33
Alignment explanation
Indices: 149997--150096 Score: 119
Period size: 34 Copynumber: 3.0 Consensus size: 33
149987 AAATTTAATG
*
149997 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTT-GAATAATATAATTTATATTTTAAAT
* * * * *
150031 TTGAATTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTGAATAATATAATTTATATTTTAAAT
*
150064 TTAAATTTTGAATAATATAATTTGTATTTTAAA
1 TTAAA-TTTGAATAATATAATTTATATTTTAAA
150097 AACATTTATC
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 24 0.44
34 30 0.56
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (33 bp):
TTAAATTTGAATAATATAATTTATATTTTAAAT
Found at i:150084 original size:39 final size:39
Alignment explanation
Indices: 150016--150093 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 39
150006 GAATACTATA
*
150016 ATTTATATTTTAAATTTGAATTTGAATAATAT-TATTTTT
1 ATTTATATTTTAAATTTGAATAT-AATAATATGTATTTTT
* *
150055 ATTTTTATTTTAAATTTTGAATA-ATATAATTTGTATTTT
1 ATTTATATTTTAAA-TTTGAATATA-ATAATATGTATTTT
150094 AAAAACATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
38 1 0.03
39 19 0.58
40 13 0.39
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (39 bp):
ATTTATATTTTAAATTTGAATATAATAATATGTATTTTT
Found at i:150704 original size:21 final size:21
Alignment explanation
Indices: 150616--150709 Score: 111
Period size: 21 Copynumber: 4.5 Consensus size: 21
150606 TATGGTATAA
*
150616 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
* *
150637 AA-CCTGGTGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
*
150658 AA-TCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
150679 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
150700 AACCCTGCGG
1 AACCCTGCGG
150710 AGATGGCATA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 3 0.05
21 60 0.92
22 2 0.03
ACGTcount: A:0.20, C:0.24, G:0.35, T:0.20
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:150739 original size:21 final size:21
Alignment explanation
Indices: 150713--150760 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
150703 CCTGCGGAGA
*
150713 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
150734 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
150755 GGGCAT
1 TGGCAT
150761 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:150763 original size:84 final size:84
Alignment explanation
Indices: 150616--150772 Score: 192
Period size: 84 Copynumber: 1.9 Consensus size: 84
150606 TATGGTATAA
* * * * *
150616 AACCCTGCGGGCTAGGCATGTAACCTGGTGGGCTAGGCATGTAATCTGGCGGGCTAGGAATGTAA
1 AACCCTGCGGGATAGGCATATAAACTGGTGGGCTAGGCATATAATCTGGAGGGCTAGGAATGTAA
150681 CCCTGCGGGCTCGGAATGT
66 CCCTGCGGGCTCGGAATGT
* * * *
150700 AACCCTGCGGAGAT-GGCATATAAACTGGTGGGCTTGGCATATGAA-GTGGAGGGCTGGGCATGT
1 AACCCTGCGG-GATAGGCATATAAACTGGTGGGCTAGGCATAT-AATCTGGAGGGCTAGGAATGT
*
150763 ACCCCTGCGG
64 AACCCTGCGG
150773 CATCGACGAA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
84 57 0.93
85 4 0.07
ACGTcount: A:0.21, C:0.22, G:0.36, T:0.21
Consensus pattern (84 bp):
AACCCTGCGGGATAGGCATATAAACTGGTGGGCTAGGCATATAATCTGGAGGGCTAGGAATGTAA
CCCTGCGGGCTCGGAATGT
Found at i:152530 original size:32 final size:33
Alignment explanation
Indices: 152484--152562 Score: 81
Period size: 32 Copynumber: 2.4 Consensus size: 33
152474 TTAATAATTC
* *
152484 TAAATAAATAATAATTATATAAAT-ATTATTTTAA
1 TAAA-AAA-AATAATTATATAAATAAATATATTAA
* *
152518 TAAAAAAAATAA-TATTTACATAAATATATTAA
1 TAAAAAAAATAATTATATAAATAAATATATTAA
*
152550 TATAAAAAATAAT
1 TAAAAAAAATAAT
152563 AACTATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
31 7 0.18
32 24 0.63
33 3 0.08
34 4 0.11
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (33 bp):
TAAAAAAAATAATTATATAAATAAATATATTAA
Found at i:152563 original size:32 final size:34
Alignment explanation
Indices: 152484--152564 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 34
152474 TTAATAATTC
*
152484 TAAATAAATAATAATTATATAAATATTATTTTAATA
1 TAAA-AAATAATAATTACATAAATATTA-TTTAATA
* *
152520 AAAAAAATAATATTTACATAAATA-TA-TTAATA
1 TAAAAAATAATAATTACATAAATATTATTTAATA
152552 TAAAAAATAATAA
1 TAAAAAATAATAA
152565 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 17 0.43
34 2 0.05
35 18 0.45
36 3 0.08
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (34 bp):
TAAAAAATAATAATTACATAAATATTATTTAATA
Found at i:152589 original size:34 final size:34
Alignment explanation
Indices: 152517--152596 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 34
152507 TATTATTTTA
* * *
152517 ATAAAAAAAATAATATTTACATAAATATATTAAT
1 ATAAAAAAAATAATATTTACATAAAAATACTAAC
152551 ATAAAAAATAATAACTATTTA-A-AAAAATACTAAC
1 ATAAAAAA-AATAA-TATTTACATAAAAATACTAAC
152585 ATAAAAATAAAT
1 ATAAAAA-AAAT
152597 TTCTTACCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 27 0.68
35 7 0.17
36 6 0.15
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (34 bp):
ATAAAAAAAATAATATTTACATAAAAATACTAAC
Found at i:159951 original size:84 final size:84
Alignment explanation
Indices: 159810--160087 Score: 415
Period size: 84 Copynumber: 3.4 Consensus size: 84
159800 AATTTTGTTC
*
159810 AATGGAGTAATAGTAGGTTATGTAATTGTGGCGAAAACCCGAAAAGTGATGTATATTGGAGCTGA
1 AATGGAGTAATTGTAGGTTATGTAATTGTGGCGAAAACCCGAAAAGTGATGTATATTGGAGCTGA
*
159875 ACTTAGATTTTTCATTATT
66 ACTGAGATTTTTCATTATT
* * * *
159894 AATGGAGTGATTGTAGGATATGCAATTGTGGCGAAAAGCCGAAAAGTGATGTATATTGGAGCTGA
1 AATGGAGTAATTGTAGGTTATGTAATTGTGGCGAAAACCCGAAAAGTGATGTATATTGGAGCTGA
159959 ACTGAGAATTTTTTCATTATT
66 ACTGAG-A-TTTTTCATTATT
*
159980 AAT---GT-A--GTAGGTTATGTAATTGTGGCGAAATCCCGAAAAGTGATGTATATTGGAGCTGA
1 AATGGAGTAATTGTAGGTTATGTAATTGTGGCGAAAACCCGAAAAGTGATGTATATTGGAGCTGA
160039 ACTGAGATTTTTCATTATT
66 ACTGAGATTTTTCATTATT
* *
160058 AATGGAGTAACTGTAGGTTGTGTAATTGTG
1 AATGGAGTAATTGTAGGTTATGTAATTGTG
160088 ATGATTGATG
Statistics
Matches: 175, Mismatches: 11, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
78 15 0.09
79 1 0.01
80 55 0.31
81 2 0.01
82 2 0.01
83 2 0.01
84 82 0.47
85 1 0.01
86 15 0.09
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.35
Consensus pattern (84 bp):
AATGGAGTAATTGTAGGTTATGTAATTGTGGCGAAAACCCGAAAAGTGATGTATATTGGAGCTGA
ACTGAGATTTTTCATTATT
Found at i:160023 original size:80 final size:78
Alignment explanation
Indices: 159820--160066 Score: 368
Period size: 80 Copynumber: 3.1 Consensus size: 78
159810 AATGGAGTAA
*
159820 TAGTAGGTTATGTAATTGTGGCGAAAACCCGAAAAGTGATGTATATTGGAGCTGAACTTAGATTT
1 TAGTAGGTTATGTAATTGTGGCGAAAACCCGAAAAGTGATGTATATTGGAGCTGAACTGAGATTT
159885 TTCATTATTAATGGAG
66 TTCATTATTAAT---G
* * *
159901 TGATTGTAGGATATGCAATTGTGGCGAAAAGCCGAAAAGTGATGTATATTGGAGCTGAACTGAGA
1 T-A--GTAGGTTATGTAATTGTGGCGAAAACCCGAAAAGTGATGTATATTGGAGCTGAACTGAG-
159966 ATTTTTTCATTATTAATG
62 A-TTTTTCATTATTAATG
*
159984 TAGTAGGTTATGTAATTGTGGCGAAATCCCGAAAAGTGATGTATATTGGAGCTGAACTGAGATTT
1 TAGTAGGTTATGTAATTGTGGCGAAAACCCGAAAAGTGATGTATATTGGAGCTGAACTGAGATTT
160049 TTCATTATTAATG
66 TTCATTATTAATG
*
160062 GAGTA
1 TAGTA
160067 ACTGTAGGTT
Statistics
Matches: 152, Mismatches: 9, Indels: 13
0.87 0.05 0.07
Matches are distributed among these distances:
78 20 0.13
79 1 0.01
80 55 0.36
81 1 0.01
82 2 0.01
83 2 0.01
84 55 0.36
85 1 0.01
86 15 0.10
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (78 bp):
TAGTAGGTTATGTAATTGTGGCGAAAACCCGAAAAGTGATGTATATTGGAGCTGAACTGAGATTT
TTCATTATTAATG
Found at i:168154 original size:22 final size:20
Alignment explanation
Indices: 168136--168189 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 20
168126 ACGACTTTGA
168136 AATATAAATATAAATACTTT
1 AATATAAATATAAATACTTT
168156 -A-A-AAATA-AAATACTTTT
1 AATATAAATATAAATAC-TTT
168173 AGATATAAATATAAATA
1 A-ATATAAATATAAATA
168190 TGACGTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
16 6 0.21
17 8 0.29
18 1 0.04
19 2 0.07
20 1 0.04
21 5 0.18
22 5 0.18
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (20 bp):
AATATAAATATAAATACTTT
Found at i:168182 original size:16 final size:15
Alignment explanation
Indices: 168140--168183 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
168130 CTTTGAAATA
168140 TAAATATAAATACTT
1 TAAATATAAATACTT
*
168155 TAAAAATAAAATACTTT
1 TAAATAT-AAATAC-TT
*
168172 TAGATATAAATA
1 TAAATATAAATA
168184 TAAATATGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 6 0.25
16 11 0.46
17 7 0.29
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (15 bp):
TAAATATAAATACTT
Found at i:170140 original size:2 final size:2
Alignment explanation
Indices: 170135--170194 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
170125 TATATGCATC
170135 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
170177 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
170195 CTCTAATCCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:170325 original size:19 final size:19
Alignment explanation
Indices: 170301--170352 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
170291 TATTAATTTT
170301 AAAAATATAAAAAATCAGA
1 AAAAATATAAAAAATCAGA
* *
170320 AAAAATACAAAAAATCCGA
1 AAAAATATAAAAAATCAGA
*
170339 AAAATTATAAAAAA
1 AAAAATATAAAAAA
170353 AAATTAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.15
Consensus pattern (19 bp):
AAAAATATAAAAAATCAGA
Found at i:172140 original size:74 final size:73
Alignment explanation
Indices: 172042--172180 Score: 181
Period size: 74 Copynumber: 1.9 Consensus size: 73
172032 TAGTTTTTTA
* * * *
172042 ATTTTTGCATTTTGGTCACTATTTATTTCTTATTTAACTACTA-ACTTTATTTTCTTGCATTTTA
1 ATTTTTGCAATTTAGTCACGATTTATTT-TTATTTAACTACTATACTTTATTTTCTTACATTTTA
172106 GCCACTGTT
65 GCCACTGTT
* ** *
172115 ATTTTATGCAATTTAGTCACGATTTATTTTTATTTAGCTACTATTTTTTATTTTGTTACATTTTA
1 ATTTT-TGCAATTTAGTCACGATTTATTTTTATTTAACTACTATACTTTATTTTCTTACATTTTA
172180 G
65 G
172181 TCCTTTATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
73 18 0.32
74 38 0.68
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (73 bp):
ATTTTTGCAATTTAGTCACGATTTATTTTTATTTAACTACTATACTTTATTTTCTTACATTTTAG
CCACTGTT
Found at i:174234 original size:13 final size:13
Alignment explanation
Indices: 174216--174275 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
174206 TGTTGGAATA
174216 TGTTTGTTTTTTG
1 TGTTTGTTTTTTG
* *
174229 TGTTTG-TGTTAG
1 TGTTTGTTTTTTG
*
174241 TGTTAT-TTGTTTG
1 TGTT-TGTTTTTTG
*
174254 TGTTTGTTTATTG
1 TGTTTGTTTTTTG
*
174267 TGTTCGTTT
1 TGTTTGTTT
174276 ATGTTCATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 9 0.24
13 29 0.76
ACGTcount: A:0.05, C:0.02, G:0.25, T:0.68
Consensus pattern (13 bp):
TGTTTGTTTTTTG
Found at i:174238 original size:19 final size:19
Alignment explanation
Indices: 174216--174270 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
174206 TGTTGGAATA
*
174216 TGTTTGTTTTTTGTGTTTG
1 TGTTTGTTTATTGTGTTTG
*
174235 TGTTAGTGTTATT-TGTTTG
1 TGTTTGT-TTATTGTGTTTG
174254 TGTTTGTTTATTGTGTT
1 TGTTTGTTTATTGTGTT
174271 CGTTTATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 5 0.16
19 22 0.71
20 4 0.13
ACGTcount: A:0.05, C:0.00, G:0.25, T:0.69
Consensus pattern (19 bp):
TGTTTGTTTATTGTGTTTG
Found at i:174275 original size:23 final size:23
Alignment explanation
Indices: 174249--174334 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
174239 AGTGTTATTT
* *
174249 GTTTGTGTTTGTTTATTGTGTTC
1 GTTTATGTTCGTTTATTGTGTTC
* * *
174272 GTTTATGTTCATTTATTATGTTT
1 GTTTATGTTCGTTTATTGTGTTC
174295 GTTTATGTTCGTTCGT-TTGTGTTC
1 GTTTATGTTCGTT--TATTGTGTTC
*
174319 GTTTACGTTCGTTTAT
1 GTTTATGTTCGTTTAT
174335 GTTCGTTTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.02
23 31 0.61
24 18 0.35
25 1 0.02
ACGTcount: A:0.09, C:0.08, G:0.21, T:0.62
Consensus pattern (23 bp):
GTTTATGTTCGTTTATTGTGTTC
Found at i:174280 original size:10 final size:10
Alignment explanation
Indices: 174267--174344 Score: 57
Period size: 10 Copynumber: 7.1 Consensus size: 10
174257 TTGTTTATTG
174267 TGTTCGTTTA
1 TGTTCGTTTA
*
174277 TGTTCATTTATTA
1 TGTTC--GT-TTA
*
174290 TGTTTGTTTA
1 TGTTCGTTTA
*
174300 TGTTCGTTCGTTTG
1 TG-T--T-CGTTTA
174314 TGTTCGTTTA
1 TGTTCGTTTA
*
174324 CGTTCGTTTA
1 TGTTCGTTTA
174334 TGTTCGTTTA
1 TGTTCGTTTA
174344 T
1 T
174345 CATTTAAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
10 34 0.64
11 3 0.06
12 1 0.02
13 9 0.17
14 6 0.11
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:174280 original size:19 final size:20
Alignment explanation
Indices: 174216--174280 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 20
174206 TGTTGGAATA
*
174216 TGTT-TGTTTTTTGTGTTTG
1 TGTTATGTTTATTGTGTTTG
174235 TGTTA-GTGTTATT-TGTTTG
1 TGTTATGT-TTATTGTGTTTG
*
174254 TGTT-TGTTTATTGTGTTCG
1 TGTTATGTTTATTGTGTTTG
174273 T-TTATGTT
1 TGTTATGTT
174281 CATTTATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 7 0.18
19 28 0.72
20 4 0.10
ACGTcount: A:0.06, C:0.02, G:0.25, T:0.68
Consensus pattern (20 bp):
TGTTATGTTTATTGTGTTTG
Found at i:174327 original size:20 final size:20
Alignment explanation
Indices: 174304--174343 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
174294 TGTTTATGTT
*
174304 CGTTCGTTTGTGTTCGTTTA
1 CGTTCGTTTATGTTCGTTTA
174324 CGTTCGTTTATGTTCGTTTA
1 CGTTCGTTTATGTTCGTTTA
174344 TCATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.15, G:0.23, T:0.55
Consensus pattern (20 bp):
CGTTCGTTTATGTTCGTTTA
Found at i:174386 original size:31 final size:31
Alignment explanation
Indices: 174351--174429 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
174341 TTATCATTTA
*
174351 AATGAACGAACATGAACAAGCTATATTTCTT
1 AATGAACGAACATGAACAAGCTATATTCCTT
*
174382 AATGAACGACCATGAACAAGCTATATTCCTT
1 AATGAACGAACATGAACAAGCTATATTCCTT
174413 AATGAACGAACATGAAC
1 AATGAACGAACATGAAC
174430 CAAAAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (31 bp):
AATGAACGAACATGAACAAGCTATATTCCTT
Found at i:175612 original size:18 final size:18
Alignment explanation
Indices: 175586--175620 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
175576 TTTTGAACTA
*
175586 AATATTTTTAATTTTATT
1 AATAATTTTAATTTTATT
*
175604 AATAATTTTATTTTTAT
1 AATAATTTTAATTTTAT
175621 AATTATTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
AATAATTTTAATTTTATT
Found at i:177023 original size:12 final size:13
Alignment explanation
Indices: 176989--177027 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
176979 GTAAAATACG
176989 GTATGAACAGTATC
1 GTATGAACAGTA-C
177003 GTATGAACAGTAC
1 GTATGAACAGTAC
*
177016 -TGTGAACAGTAC
1 GTATGAACAGTAC
177028 CAAATGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.46
13 1 0.04
14 12 0.50
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (13 bp):
GTATGAACAGTAC
Found at i:179128 original size:20 final size:20
Alignment explanation
Indices: 179101--179258 Score: 88
Period size: 20 Copynumber: 7.6 Consensus size: 20
179091 AAAATGACCA
179101 ACAAAATCGCAACGCGATTT
1 ACAAAATCGCAACGCGATTT
* * **
179121 ATAAAATCGCAACGGTGA-AA
1 ACAAAATCGCAAC-GCGATTT
*
179141 AGAAAATCGCAACGCGATCTT
1 ACAAAATCGCAACGCGAT-TT
*
179162 CCAAGAATCGCAACGCGA-TT
1 ACAA-AATCGCAACGCGATTT
* *
179182 CCAAGAATCGCAATGCGATCTT
1 ACAA-AATCGCAACGCGAT-TT
* * *
179204 CCAAGAATCGCAATGCGA-CT
1 ACAA-AATCGCAACGCGATTT
* *
179224 CCAAGAATCGCAATGCGATCTT
1 ACAA-AATCGCAACGCGAT-TT
*
179246 CCAAGAATCGCAA
1 ACAA-AATCGCAA
179259 AACGGTCAAA
Statistics
Matches: 117, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
19 3 0.03
20 62 0.53
21 5 0.04
22 47 0.40
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (20 bp):
ACAAAATCGCAACGCGATTT
Found at i:179173 original size:22 final size:22
Alignment explanation
Indices: 179145--179258 Score: 182
Period size: 22 Copynumber: 5.4 Consensus size: 22
179135 GTGAAAAGAA
*
179145 AATCGCAACGCGATCTTCCAAG
1 AATCGCAATGCGATCTTCCAAG
*
179167 AATCGCAACGCGA--TTCCAAG
1 AATCGCAATGCGATCTTCCAAG
179187 AATCGCAATGCGATCTTCCAAG
1 AATCGCAATGCGATCTTCCAAG
179209 AATCGCAATGCGA-C-TCCAAG
1 AATCGCAATGCGATCTTCCAAG
179229 AATCGCAATGCGATCTTCCAAG
1 AATCGCAATGCGATCTTCCAAG
179251 AATCGCAA
1 AATCGCAA
179259 AACGGTCAAA
Statistics
Matches: 87, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
20 38 0.44
21 2 0.02
22 47 0.54
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.18
Consensus pattern (22 bp):
AATCGCAATGCGATCTTCCAAG
Found at i:179191 original size:42 final size:42
Alignment explanation
Indices: 179145--179258 Score: 201
Period size: 42 Copynumber: 2.7 Consensus size: 42
179135 GTGAAAAGAA
* *
179145 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCCAAG
1 AATCGCAATGCGATCTTCCAAGAATCGCAACGCGACTCCAAG
*
179187 AATCGCAATGCGATCTTCCAAGAATCGCAATGCGACTCCAAG
1 AATCGCAATGCGATCTTCCAAGAATCGCAACGCGACTCCAAG
179229 AATCGCAATGCGATCTTCCAAGAATCGCAA
1 AATCGCAATGCGATCTTCCAAGAATCGCAA
179259 AACGGTCAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.18
Consensus pattern (42 bp):
AATCGCAATGCGATCTTCCAAGAATCGCAACGCGACTCCAAG
Found at i:179380 original size:6 final size:6
Alignment explanation
Indices: 179369--179412 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
179359 AGACACGTAT
179369 GACCAC GACCAC GACCAC GACCAC GACCAC GA-CAC GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
179413 CGAGACGGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:180092 original size:6 final size:6
Alignment explanation
Indices: 180083--180149 Score: 134
Period size: 6 Copynumber: 11.2 Consensus size: 6
180073 CGCCGCCGTC
180083 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
180131 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
180150 AATACGTGTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:180284 original size:20 final size:20
Alignment explanation
Indices: 180261--180336 Score: 118
Period size: 20 Copynumber: 3.7 Consensus size: 20
180251 TTTGACCGTT
180261 TTGCGATTCTTGGAGTCGCA
1 TTGCGATTCTTGGAGTCGCA
180281 TTGCGATTCTCT-GAGTCGCA
1 TTGCGATTCT-TGGAGTCGCA
180301 TTGCGATTCTTGGAAGATCGCA
1 TTGCGATTCTTGG-AG-TCGCA
180323 TTGCGATTCTTGGA
1 TTGCGATTCTTGGA
180337 AAATCGCACG
Statistics
Matches: 52, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.02
20 29 0.56
21 4 0.08
22 18 0.35
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTTGGAGTCGCA
Found at i:180359 original size:26 final size:22
Alignment explanation
Indices: 180261--180378 Score: 138
Period size: 22 Copynumber: 5.4 Consensus size: 22
180251 TTTGACCGTT
180261 TTGCGATTCTTGG-AG-TCGCA
1 TTGCGATTCTTGGAAGATCGCA
180281 TTGCGATTCTCT-G-AG-TCGCA
1 TTGCGATTCT-TGGAAGATCGCA
180301 TTGCGATTCTTGGAAGATCGCA
1 TTGCGATTCTTGGAAGATCGCA
*
180323 TTGCGATTCTTGGAAAATCGCA
1 TTGCGATTCTTGGAAGATCGCA
*
180345 CGCGTTGCGATTCTTGGAAGATCGCG
1 ----TTGCGATTCTTGGAAGATCGCA
180371 TTGCGATT
1 TTGCGATT
180379 TTCTTTTCAC
Statistics
Matches: 87, Mismatches: 3, Indels: 14
0.84 0.03 0.13
Matches are distributed among these distances:
19 1 0.01
20 29 0.33
21 3 0.03
22 34 0.39
26 20 0.23
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.33
Consensus pattern (22 bp):
TTGCGATTCTTGGAAGATCGCA
Found at i:183188 original size:20 final size:21
Alignment explanation
Indices: 183147--183188 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
183137 AAATTTTAAA
*
183147 TATTTAATATATTATATATAT
1 TATTTAATATATTATAAATAT
183168 TATTT-ATATATTA-AAAGTAT
1 TATTTAATATATTATAAA-TAT
183188 T
1 T
183189 TAAACTTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 2 0.11
20 12 0.63
21 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTTAATATATTATAAATAT
Found at i:183788 original size:2 final size:2
Alignment explanation
Indices: 183781--183826 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
183771 TTATTTTTAA
183781 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
183823 AT AT
1 AT AT
183827 TTTTCATGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:184595 original size:20 final size:20
Alignment explanation
Indices: 184512--184622 Score: 107
Period size: 20 Copynumber: 5.5 Consensus size: 20
184502 GGGAAAATCA
*
184512 CAACGCGATACTGACTATCG
1 CAACGCGATACTGACTTTCG
* * *
184532 CAATGCAATACTGACTATCG
1 CAACGCGATACTGACTTTCG
* * **
184552 CAATGCGATAAT-ACAAAATCG
1 CAACGCGATACTGAC--TTTCG
*
184573 CAACGAGATACTGACTTTCG
1 CAACGCGATACTGACTTTCG
*
184593 CAACGCGATTCTGACTTTCG
1 CAACGCGATACTGACTTTCG
184613 CAACGCGATA
1 CAACGCGATA
184623 ATACATAATC
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.03
20 58 0.77
21 13 0.17
22 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (20 bp):
CAACGCGATACTGACTTTCG
Found at i:184633 original size:61 final size:61
Alignment explanation
Indices: 184505--184636 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 61
184495 GCGAATTGGG
* * * *
184505 AAAATCACAACGCGATACTGACTATCGCAATGCAATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCAATACTGACTATCGCAACGCGATAATAC
* * * *
184566 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCAATACTGACTATCGCAACGCGATAATAC
*
184627 ATAATCGCAA
1 AAAATCGCAA
184637 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCAATACTGACTATCGCAACGCGATAATAC
Found at i:184837 original size:22 final size:22
Alignment explanation
Indices: 184810--184853 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
184800 CACTCTCTCA
184810 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
184832 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
184854 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:185169 original size:20 final size:20
Alignment explanation
Indices: 185130--185188 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
185120 GCGATTCTCT
**
185130 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
185150 CGTTACGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
185170 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
185189 AGAAACTATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:185379 original size:25 final size:24
Alignment explanation
Indices: 185325--185379 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
185315 TGTTTATTAT
* *
185325 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
185349 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
185375 TGTTT
1 TGTTT
185380 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:186529 original size:18 final size:18
Alignment explanation
Indices: 186508--186552 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
186498 TCCACTTCGG
*
186508 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
186526 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
186544 GAGCCATCA
1 GAGCCATCA
186553 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:187082 original size:19 final size:20
Alignment explanation
Indices: 187028--187094 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
187018 TAGTTTACTT
* *
187028 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
187048 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* * **
187068 TCGTAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
187087 TCGCAACG
1 TCGCAACG
187095 ACAAAATTGC
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 13 0.35
20 24 0.65
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:187114 original size:33 final size:33
Alignment explanation
Indices: 187067--187158 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
187057 GGAAATGGCT
*
187067 ATCGTAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
187100 ATTGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
187133 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
187159 TGCAATTTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:187125 original size:19 final size:19
Alignment explanation
Indices: 187067--187161 Score: 75
Period size: 19 Copynumber: 5.5 Consensus size: 19
187057 GGAAATGGCT
*
187067 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
187086 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
187100 ATTGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
187119 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
187133 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
187152 ATCGCAATGC
1 ATCGCAATGC
187162 AATTTGTGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 20
0.67 0.09 0.23
Matches are distributed among these distances:
14 19 0.33
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 27 0.47
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:187135 original size:14 final size:14
Alignment explanation
Indices: 187083--187141 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
187073 ATGCGAAATG
187083 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
187097 AAAATTGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
187116 AAAATCGCAACGAC
1 AAAATCGCAACGAC
187130 AAAATCGCAACG
1 AAAATCGCAACG
187142 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.25
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:187194 original size:14 final size:14
Alignment explanation
Indices: 187175--187265 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
187165 TTGTGTTTCG
187175 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
187189 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
187205 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
187221 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
187238 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
187254 CGTTGCGATTTT
1 CGTTGCGATTTT
187266 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 27 0.42
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.09
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:187239 original size:33 final size:33
Alignment explanation
Indices: 187170--187281 Score: 208
Period size: 33 Copynumber: 3.4 Consensus size: 33
187160 GCAATTTGTG
*
187170 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
187202 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
187235 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
187268 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
187282 AGCCATTTTT
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 26 0.33
33 52 0.67
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:187288 original size:19 final size:19
Alignment explanation
Indices: 187266--187309 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
187256 TTGCGATTTT
187266 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
* * *
187285 CATTTTTGCGTTGCGATAGT
1 CA-TTTCGCATTGCGATAGC
187305 CATTT
1 CATTT
187310 TTGCGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.41
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:187300 original size:20 final size:20
Alignment explanation
Indices: 187275--187321 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
187265 TCATTTCGCA
187275 TTGCGATAGCCATTTTTGCG
1 TTGCGATAGCCATTTTTGCG
*
187295 TTGCGATAGTCATTTTTGCG
1 TTGCGATAGCCATTTTTGCG
187315 TTGCGAT
1 TTGCGAT
187322 TTTATGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.17, G:0.26, T:0.43
Consensus pattern (20 bp):
TTGCGATAGCCATTTTTGCG
Found at i:187418 original size:27 final size:28
Alignment explanation
Indices: 187352--187420 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 28
187342 AGTAAACTAT
*
187352 TCTTCTTCTGGAATGTTTATATATGTTG
1 TCTTCTTCTGGAATGTTTATATAAGTTG
*
187380 TCTT-TT-T-AAATGTTTATATAAG-TG
1 TCTTCTTCTGGAATGTTTATATAAGTTG
187404 -CTTACTTCTGGAATGTT
1 TCTT-CTTCTGGAATGTT
187421 ATCTAAGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
23 3 0.09
24 2 0.06
25 15 0.44
26 2 0.06
27 8 0.24
28 4 0.12
ACGTcount: A:0.22, C:0.10, G:0.16, T:0.52
Consensus pattern (28 bp):
TCTTCTTCTGGAATGTTTATATAAGTTG
Found at i:187720 original size:21 final size:20
Alignment explanation
Indices: 187694--187762 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
187684 CGATCATCCC
187694 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* *
187715 TCAAGAGGCCCCTATCC-TCCT
1 TCAAGAGTCCCC--TCCATCGT
* *
187736 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
187756 TCAAGAG
1 TCAAGAG
187763 GCCACTGTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
19 2 0.05
20 9 0.23
21 25 0.64
23 3 0.08
ACGTcount: A:0.23, C:0.41, G:0.16, T:0.20
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:187783 original size:41 final size:41
Alignment explanation
Indices: 187686--187804 Score: 121
Period size: 42 Copynumber: 2.9 Consensus size: 41
187676 TGACTCACCG
* * * *
187686 ATCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCT
1 ATCATCCTTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACT
*
187728 ATCCTCCTTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACT
1 ATCATCCTTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACT
* * * * * *
187769 GTCATCGTTGAAGAGGTCCCTCCCACCATTCCAGAG
1 ATCATCCTTCAAGA-GTCCCCCCCACCGTTCAAGAG
187805 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 28 0.44
42 36 0.56
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.21
Consensus pattern (41 bp):
ATCATCCTTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACT
Found at i:189209 original size:14 final size:14
Alignment explanation
Indices: 189190--189225 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
189180 ATTGTTTAAT
189190 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
189204 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
189218 TGATTTGT
1 TGATTTGT
189226 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:189428 original size:19 final size:19
Alignment explanation
Indices: 189357--189421 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
189347 GCAACGAGAG
*
189357 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
189376 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
189395 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
189414 AATCGCAA
1 AATCGCAA
189422 CGAGAAAATC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.49, C:0.17, G:0.18, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:189439 original size:33 final size:33
Alignment explanation
Indices: 189344--189440 Score: 122
Period size: 38 Copynumber: 2.8 Consensus size: 33
189334 GAAACTGACT
* *
189344 ATCGCAACGAGAGAATCGCAATGCAAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
189377 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAA
*
189415 ATCGCAACGAGAAAATCACAATGCGA
1 ATCGCAACGAGAAAATCGCAATGCGA
189441 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
33 22 0.39
34 1 0.02
35 2 0.04
36 2 0.04
37 1 0.02
38 28 0.50
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:189505 original size:20 final size:20
Alignment explanation
Indices: 189459--189515 Score: 89
Period size: 19 Copynumber: 2.9 Consensus size: 20
189449 TCGCATTGCG
*
189459 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
189479 A-TTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
189498 ATTTTCGCGTTACGATAG
1 ATTTTCGCGTTGCGATAG
189516 TCAAATGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:189895 original size:19 final size:19
Alignment explanation
Indices: 189871--189935 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
189861 GCAACGAGAG
189871 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
189890 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
189909 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
189923 AATCGCAATGCGA
1 AATCGCAATGCGA
189936 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:190000 original size:20 final size:20
Alignment explanation
Indices: 189954--190030 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
189944 TCGCATTGCG
* *
189954 ATTTTCTCGTTGTGATAGCC
1 ATTTTCGCGTTGCGATAGCC
189974 A-TTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
189993 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
190013 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
190031 TCAAATGAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
19 17 0.31
20 37 0.69
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:190010 original size:39 final size:40
Alignment explanation
Indices: 189954--190030 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
189944 TCGCATTGCG
* *
189954 ATTTTCTCGTTGTGATAGCCA-TTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCC
189993 ATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAG
190031 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 19 0.54
40 16 0.46
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.38
Consensus pattern (40 bp):
ATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCC
Found at i:190162 original size:515 final size:504
Alignment explanation
Indices: 189200--190229 Score: 1730
Period size: 515 Copynumber: 2.0 Consensus size: 504
189190 TGATTTGTAA
189200 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTCTTATTTGTGCTTGTTTA
1 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTCTTATTTGTGCTTGTTTA
189265 ATTGATTGAAATGTAATAGTTGATTTTCAATCTGCATTATGTTGAAGGCAAAACAGACTATCGCA
66 ATTGATTGAAATGTAATAGTTGATTTTCAATCTGCATTATGTTGAAGGCAAAACAGACTATCGCA
*
189330 ACACGAAACTGACTATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAATGCGAAATGAA
131 ACACGAAACCGACTATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAATGCGAAATGAA
* *
189395 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCACAATGCGATTTTCATTTCGCATTGCGA
196 AATCGCAA-GCG-AATGAAAATCGCAACGAGAAAATCACAATGCGATTTTCATTTCGCATAGCCA
*
189460 TTTTCTCGTTGCGATAGCCATTTCGCGTTGCGATAGCCATTTTCGCGTTACGATAGTCAAATGAA
259 TTTTCGCGTTGCGATAGCCATTTCGCGTTGCGATAGCCATTTTCGCGTTACGATAGTCAAATGAA
189525 TGTCTAATAAGTGATAACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATG
324 TGTCTAATAAGTGATAACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATG
189590 CCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACATAATACAAAGTTTGCATTTAAAAAT
389 CCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACATAATACAAAGTTTGCATTTAAAAAT
189655 CACCTAAGTTAACGGTCCCAAAAGGTGAAGCCGGTTGTGATTGGGATTTTG
454 CACCTAAGTTAACGGTCCCAAAAGGTGAAGCCGGTTGTGATTGGGATTTTG
189706 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTCTTATTTGTGCTTGTTTA
1 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTCTTATTTGTGCTTGTTTA
189771 ATTGATTGAAATGTGATAGTTGATTTGTTGATTTTCAATCTGCATTATGTTGAAGGCAAAACAGA
66 ATTGATTGAAATGT-A-A--T-A---GTTGATTTTCAATCTGCATTATGTTGAAGGCAAAACAGA
*
189836 CTATCGCAACACGAAACCGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGC
123 CTATCGCAACACGAAACCGACTATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAATGC
** ** * *
189901 GAAATGAAAATCGCAA-CG-A-GAAAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTC-TC
188 GAAATGAAAATCGCAAGCGAATGAAAATCGCAA--CGA---GAAAATCACAATGCGATTTTCAT-
* *
189962 GTT-GTGATAGCCA-TTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTTCGCGTTG
247 -TTCG-CATAGCCATTTTCGCGTTGCGATAGCCA-TTTCGCGTTGCGATAGCCATTTTCGCGTTA
190025 CGATAGTCAAATGAATGTCTAATAAGTGATAACAACTGAACAGATCATAGCAATGTTCAAACTCA
309 CGATAGTCAAATGAATGTCTAATAAGTGATAACAACTGAACAGATCATAGCAATGTTCAAACTCA
190090 AGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACATAATACAAAG
374 AGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACATAATACAAAG
190155 TTTGCATTTAAAAATCACCTAAGTTAACGGTCCCAAAAGGTGAAGCCGGTTGTGATTGGGATTTT
439 TTTGCATTTAAAAATCACCTAAGTTAACGGTCCCAAAAGGTGAAGCCGGTTGTGATTGGGATTTT
190220 G
504 G
190221 AAGATGATT
1 AAGATGATT
190230 GCGATTTTGA
Statistics
Matches: 494, Mismatches: 13, Indels: 25
0.93 0.02 0.05
Matches are distributed among these distances:
506 79 0.16
507 1 0.00
508 1 0.00
509 11 0.02
510 2 0.00
511 4 0.01
512 2 0.00
513 1 0.00
514 152 0.31
515 241 0.49
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (504 bp):
AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTCTTATTTGTGCTTGTTTA
ATTGATTGAAATGTAATAGTTGATTTTCAATCTGCATTATGTTGAAGGCAAAACAGACTATCGCA
ACACGAAACCGACTATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAATGCGAAATGAA
AATCGCAAGCGAATGAAAATCGCAACGAGAAAATCACAATGCGATTTTCATTTCGCATAGCCATT
TTCGCGTTGCGATAGCCATTTCGCGTTGCGATAGCCATTTTCGCGTTACGATAGTCAAATGAATG
TCTAATAAGTGATAACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCC
TAACTGAAAATGTTAAAAGTGCACACATAAAATACACATAATACAAAGTTTGCATTTAAAAATCA
CCTAAGTTAACGGTCCCAAAAGGTGAAGCCGGTTGTGATTGGGATTTTG
Found at i:192918 original size:20 final size:20
Alignment explanation
Indices: 192893--192940 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
192883 TGTATTATCT
192893 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
192913 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
192933 CGTTGCGA
1 CGTTGCGA
192941 TTTTCTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:192974 original size:20 final size:21
Alignment explanation
Indices: 192930--192981 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
192920 AAAGTCAGTA
*
192930 TCGCGTTGCGATTTTCTCAAT
1 TCGCGTTGCGATTTACTCAAT
*
192951 TCGCGTTGCGATTTACT-TAT
1 TCGCGTTGCGATTTACTCAAT
*
192971 TCGCATTGCGA
1 TCGCGTTGCGA
192982 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.40
Consensus pattern (21 bp):
TCGCGTTGCGATTTACTCAAT
Found at i:193531 original size:20 final size:22
Alignment explanation
Indices: 193506--193553 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
193496 AACCCAACCC
193506 AAAATAATATATTTATT-AA-A
1 AAAATAATATATTTATTCAATA
* *
193526 AAAATATTATTTTTATTCAATA
1 AAAATAATATATTTATTCAATA
193548 AAAATA
1 AAAATA
193554 GGGATTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 15 0.62
21 2 0.08
22 7 0.29
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAATAATATATTTATTCAATA
Found at i:196002 original size:24 final size:25
Alignment explanation
Indices: 195972--196034 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 25
195962 TATTAGCTTA
195972 AAAATATTTTATATTAACTT-A-TT
1 AAAATATTTTATATTAACTTAATTT
195995 AAATATATTTTATTATTAACTTAATTT
1 AAA-ATATTTTA-TATTAACTTAATTT
196022 AAAACTATTTTAT
1 AAAA-TATTTTAT
196035 TTTTATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.09
24 8 0.23
25 9 0.26
26 3 0.09
27 12 0.34
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (25 bp):
AAAATATTTTATATTAACTTAATTT
Found at i:196232 original size:31 final size:31
Alignment explanation
Indices: 196190--196264 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
196180 TAACACATGA
* * *
196190 TGACCACATCTTAAGTAAACAATAACGGAAG
1 TGACCATATCTTAAGTAAACAAGAACGAAAG
* *
196221 TGACCATATCTTAATTAAACAAGAATGAAAG
1 TGACCATATCTTAAGTAAACAAGAACGAAAG
*
196252 TGATCATATCTTA
1 TGACCATATCTTA
196265 TGTTTTTCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (31 bp):
TGACCATATCTTAAGTAAACAAGAACGAAAG
Found at i:203457 original size:21 final size:21
Alignment explanation
Indices: 203431--203472 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
203421 ATCTCTTGGT
203431 GGGATGAGGAATATATATATA
1 GGGATGAGGAATATATATATA
203452 GGGATGAGGAATATATATATA
1 GGGATGAGGAATATATATATA
203473 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (21 bp):
GGGATGAGGAATATATATATA
Found at i:203467 original size:2 final size:2
Alignment explanation
Indices: 203462--203504 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
203452 GGGATGAGGA
203462 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
203504 A
1 A
203505 ATTTACATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:205037 original size:21 final size:22
Alignment explanation
Indices: 204995--205038 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
204985 CTCAAATTAA
*
204995 AAAAAAATGAATACAATATTTT
1 AAAAAAATGAAAACAATATTTT
* *
205017 AAAAAATTGAAAATAAT-TTTT
1 AAAAAAATGAAAACAATATTTT
205038 A
1 A
205039 TTTTTTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (22 bp):
AAAAAAATGAAAACAATATTTT
Found at i:207579 original size:3 final size:3
Alignment explanation
Indices: 207563--207601 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
207553 TATAATGATA
207563 ATT ATT -TT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
207602 ATACTTCCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:217360 original size:30 final size:30
Alignment explanation
Indices: 217274--217360 Score: 111
Period size: 30 Copynumber: 2.9 Consensus size: 30
217264 TAAATCCTAT
**
217274 GTGTCTAAAGTGATGACATGACACATATTAC
1 GTGTCT-AAGTGATGACATGACACATGCTAC
* * * *
217305 ATGTATAAATGATGATATGACACATGCTAC
1 GTGTCTAAGTGATGACATGACACATGCTAC
217335 GTGTCTAAGTGATGACATGACACATG
1 GTGTCTAAGTGATGACATGACACATG
217361 ATCAAAATGA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
30 42 0.91
31 4 0.09
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.29
Consensus pattern (30 bp):
GTGTCTAAGTGATGACATGACACATGCTAC
Found at i:219377 original size:19 final size:18
Alignment explanation
Indices: 219345--219380 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
219335 AGATTAAATT
219345 AAATTTATTATTTCAATA
1 AAATTTATTATTTCAATA
*
219363 AAATATTATTTTTTCAAT
1 AAAT-TTATTATTTCAAT
219381 TTTTATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATTTATTATTTCAATA
Found at i:220129 original size:27 final size:26
Alignment explanation
Indices: 220099--220157 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
220089 TATGTATTCT
220099 TTTTTGAATTAAATTTAATCACTTTAA
1 TTTTTGAATT-AATTTAATCACTTTAA
* * *
220126 TTTTATTAATTAATTTAATCATTTTAT
1 TTTT-TGAATTAATTTAATCACTTTAA
220153 TTTTT
1 TTTTT
220158 TACGAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.04
27 22 0.79
28 5 0.18
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTTTGAATTAATTTAATCACTTTAA
Found at i:221000 original size:14 final size:14
Alignment explanation
Indices: 220981--221009 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
220971 TTTAAACATG
220981 TATTAGTATTCAAA
1 TATTAGTATTCAAA
220995 TATTAGTATTCAAA
1 TATTAGTATTCAAA
221009 T
1 T
221010 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TATTAGTATTCAAA
Found at i:226369 original size:23 final size:23
Alignment explanation
Indices: 226339--226391 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
226329 AGAATACGTT
*
226339 TGTCTTTGTGACACGCTTATTTA
1 TGTCTTTGTGACACGCTTATCTA
* * *
226362 TGTCTTTGTGGCACGTTTATCTC
1 TGTCTTTGTGACACGCTTATCTA
226385 TGTCTTT
1 TGTCTTT
226392 TGGTAGTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.51
Consensus pattern (23 bp):
TGTCTTTGTGACACGCTTATCTA
Found at i:227637 original size:3 final size:3
Alignment explanation
Indices: 227629--227658 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
227619 TTTTAAAAGT
227629 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
227659 GAACACTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:232041 original size:2 final size:2
Alignment explanation
Indices: 232034--232063 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
232024 TCCTCTTTAA
232034 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
232064 AATATAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:232436 original size:22 final size:24
Alignment explanation
Indices: 232411--232456 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
232401 CTGTACCTAT
* *
232411 TTTTTTTC-ATTT-TCCCGGAAAA
1 TTTTCTTCAATTTCTCCAGGAAAA
232433 TTTTCTTCAATTTCTCCAGGAAAA
1 TTTTCTTCAATTTCTCCAGGAAAA
232457 AAAAGTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.46
Consensus pattern (24 bp):
TTTTCTTCAATTTCTCCAGGAAAA
Found at i:232659 original size:12 final size:12
Alignment explanation
Indices: 232642--232668 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
232632 ATGGTAATTA
232642 ATTAATAATTTT
1 ATTAATAATTTT
232654 ATTAATAATTTT
1 ATTAATAATTTT
232666 ATT
1 ATT
232669 TTTTTCAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTAATAATTTT
Found at i:234956 original size:15 final size:17
Alignment explanation
Indices: 234936--234968 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
234926 CAAAAGTTTG
234936 ATAATAAT-T-AAATAA
1 ATAATAATATAAAATAA
234951 ATAATAATATAAAATAA
1 ATAATAATATAAAATAA
234968 A
1 A
234969 AAAATCGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAATAATATAAAATAA
Found at i:239684 original size:2 final size:2
Alignment explanation
Indices: 239677--239726 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
239667 TTAAAGATGA
239677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
239719 AT AT AT AT
1 AT AT AT AT
239727 GAGCGGAACT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:247781 original size:22 final size:22
Alignment explanation
Indices: 247750--247807 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
247740 CAAAAATGGT
247750 CTATAGCGGCGTTTTCTTTGTC
1 CTATAGCGGCGTTTTCTTTGTC
*
247772 CTATAACGGCGTTTTCTTTGTC
1 CTATAGCGGCGTTTTCTTTGTC
247794 CTATAGCGGCGTTT
1 CTATAGCGGCGTTT
247808 AAAAGCGCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (22 bp):
CTATAGCGGCGTTTTCTTTGTC
Found at i:248999 original size:2 final size:2
Alignment explanation
Indices: 248992--249057 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
248982 CCTTCTTTTA
248992 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
249034 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
249058 CAATTAAAGG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:252425 original size:30 final size:29
Alignment explanation
Indices: 252390--252454 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
252380 AATTTTATAC
* *
252390 AAAATACTAACTTAACCTTAAACTTTAAGT
1 AAAATACTAACTTAACCTTAAAATTT-AGA
** *
252420 AAAATACTATTTTACCCTTAAAATTTAGA
1 AAAATACTAACTTAACCTTAAAATTTAGA
252449 AAAATA
1 AAAATA
252455 TCAATTTGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATACTAACTTAACCTTAAAATTTAGA
Found at i:254521 original size:25 final size:24
Alignment explanation
Indices: 254487--254533 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
254477 AAAGTTTCAA
254487 TTTTTTTTTTAATTTTCCATGTAT
1 TTTTTTTTTTAATTTTCCATGTAT
254511 TTTTTTATTTTAATTTTCCATGT
1 TTTTTT-TTTTAATTTTCCATGT
254534 CTGAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTTTTTTTAATTTTCCATGTAT
Found at i:255180 original size:9 final size:9
Alignment explanation
Indices: 255166--255304 Score: 58
Period size: 10 Copynumber: 15.3 Consensus size: 9
255156 CTGAACTTGT
255166 TTATAAAAA
1 TTATAAAAA
255175 TTATAAAAGA
1 TTATAAAA-A
* *
255185 TAATAAACA
1 TTATAAAAA
*
255194 TT-TTAAAA
1 TTATAAAAA
*
255202 -TATTCAAAA
1 TTA-TAAAAA
*
255211 TATATCAAAA
1 T-TATAAAAA
255221 TTA-AAAAA
1 TTATAAAAA
255229 TTATTAAAAA
1 TTA-TAAAAA
** **
255239 CAAT-GGAA
1 TTATAAAAA
*
255247 TTACTCAAAA
1 TTA-TAAAAA
*
255257 TATATCAAAA
1 T-TATAAAAA
255267 TTATAAAAA
1 TTATAAAAA
255276 -T-TAAAAA
1 TTATAAAAA
255283 TTAT-AAAA
1 TTATAAAAA
255291 TTAATTAAAAA
1 TT-A-TAAAAA
255302 TTA
1 TTA
255305 AAAGAAACAA
Statistics
Matches: 99, Mismatches: 16, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
7 7 0.07
8 22 0.22
9 28 0.28
10 32 0.32
11 10 0.10
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:255223 original size:46 final size:47
Alignment explanation
Indices: 255171--255353 Score: 121
Period size: 46 Copynumber: 3.8 Consensus size: 47
255161 CTTGTTTATA
255171 AAAATTATAAAAGA-TAATAAACATTTTAAAATATTCAAAATATATC
1 AAAATTATAAAAGATTAATAAACATTTTAAAATATTCAAAATATATC
* * * ** * *
255217 AAAATTAAAAAATTATTAA-AAACA-ATGGAATTACTCAAAATATATC
1 AAAATTATAAAA-GATTAATAAACATTTTAAAATATTCAAAATATATC
* * *
255263 AAAATTATAAAA-ATTAAAAATTATAAAATTAATTAAAA-ATT-AAAAGA-AAC
1 AAAATTATAAAAGATT---AA-TA-AACATT--TTAAAATATTCAAAATATATC
255313 AATGGAATTATAAAAGA-TAATAAACATTTTAAAATATTCAA
1 AA---AATTATAAAAGATTAATAAACATTTTAAAATATTCAA
255354 TAAAGAATTT
Statistics
Matches: 103, Mismatches: 17, Indels: 32
0.68 0.11 0.21
Matches are distributed among these distances:
44 3 0.03
46 45 0.44
47 11 0.11
48 10 0.10
49 3 0.03
50 9 0.09
51 5 0.05
52 2 0.02
53 14 0.14
54 1 0.01
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (47 bp):
AAAATTATAAAAGATTAATAAACATTTTAAAATATTCAAAATATATC
Found at i:255266 original size:10 final size:9
Alignment explanation
Indices: 255245--255293 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
255235 AAAACAATGG
255245 AATTACTCAA
1 AATTA-TCAA
255255 AATATATCAA
1 AAT-TATCAA
*
255265 AATTATAAA
1 AATTATCAA
255274 AATTA--AA
1 AATTATCAA
255281 AATTAT-AA
1 AATTATCAA
255289 AATTA
1 AATTA
255294 ATTAAAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
7 7 0.19
8 7 0.19
9 10 0.28
10 10 0.28
11 2 0.06
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (9 bp):
AATTATCAA
Found at i:255299 original size:26 final size:26
Alignment explanation
Indices: 255253--255307 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 26
255243 GGAATTACTC
255253 AAAATATATCAAAATTATAAAAATTA
1 AAAATATATCAAAATTATAAAAATTA
255279 AAAAT-TAT-AAAATTAATTAAAAATTA
1 AAAATATATCAAAATT-A-TAAAAATTA
255305 AAA
1 AAA
255308 GAAACAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 6 0.22
25 4 0.15
26 17 0.63
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAATATATCAAAATTATAAAAATTA
Found at i:255356 original size:21 final size:20
Alignment explanation
Indices: 255330--255379 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
255320 TTATAAAAGA
*
255330 TAATAAACATTTTAAAATAT
1 TAATAAACAATTTAAAATAT
*
255350 TCAATAAAGAATTTAAAATAT
1 T-AATAAACAATTTAAAATAT
255371 TAA-AAACAA
1 TAATAAACAA
255380 AAAATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 5 0.19
20 3 0.12
21 18 0.69
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (20 bp):
TAATAAACAATTTAAAATAT
Found at i:255869 original size:3 final size:3
Alignment explanation
Indices: 255861--255955 Score: 127
Period size: 3 Copynumber: 31.7 Consensus size: 3
255851 CTTTACAGAT
255861 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
255909 TTG TTG TTG TTG TTG TTG TTA TTA TTA TTA TTG TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
255956 TCATAACCAA
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:257746 original size:3 final size:3
Alignment explanation
Indices: 257738--257775 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
257728 CGTGATATTT
257738 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
257776 TTTTTGGGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:261240 original size:30 final size:30
Alignment explanation
Indices: 261206--261265 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
261196 TTCTAAACAT
261206 TTGCTTTCGGTTTATCTGCCGTATAATCAC
1 TTGCTTTCGGTTTATCTGCCGTATAATCAC
261236 TTGCTTTCGGTTTATCTGCCGTATAATCAC
1 TTGCTTTCGGTTTATCTGCCGTATAATCAC
261266 GTCTCTCCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (30 bp):
TTGCTTTCGGTTTATCTGCCGTATAATCAC
Found at i:262031 original size:10 final size:10
Alignment explanation
Indices: 262016--262040 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
262006 TTGACTAACG
262016 ATGTTCAAAA
1 ATGTTCAAAA
262026 ATGTTCAAAA
1 ATGTTCAAAA
262036 ATGTT
1 ATGTT
262041 TTTATTGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (10 bp):
ATGTTCAAAA
Found at i:262777 original size:44 final size:44
Alignment explanation
Indices: 262714--262823 Score: 193
Period size: 44 Copynumber: 2.5 Consensus size: 44
262704 CAGCTACAGG
262714 ATAGTTATTTCGAACTAGAACACACGGATCACAAGTACTCAACC
1 ATAGTTATTTCGAACTAGAACACACGGATCACAAGTACTCAACC
* *
262758 ATAGTTATTTCGATCTAGAACACACGGATCATAAGTACTCAACC
1 ATAGTTATTTCGAACTAGAACACACGGATCACAAGTACTCAACC
*
262802 ATAGTTACTTCGAACTAGAACA
1 ATAGTTATTTCGAACTAGAACA
262824 ATACTCGGTC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 62 1.00
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (44 bp):
ATAGTTATTTCGAACTAGAACACACGGATCACAAGTACTCAACC
Done.