Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007746.1 Hibiscus syriacus cultivar Beakdansim tig00110009_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: 3674400
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 15
Found at i:1504712 original size:137 final size:137
Alignment explanation
Indices: 1504464--1504744 Score: 377
Period size: 137 Copynumber: 2.1 Consensus size: 137
1504454 GTCATAGGTG
* **
1504464 CATTTCGACATAAATTATATATAATACTTATCGATCGATTTTGTGTAATGCATAATGGTGGGTTT
1 CATTTCGACATAAATTATATATAAAACTTATCGATCGATTTTGTGTAATGCATAATGGTGCATTT
* * *
1504529 TCGTATAAGTACTATGTGTACTTTCGACACTAGATGTGCAATCATGGTATTCATAATGAGTTTGT
66 TCGTATAAGTACTATATGTACTTTCGACACTAGATGTGCAATCATGGAATTCATAATAAGTTTGT
1504594 GAATTAC
131 GAATTAC
* * * * *
1504601 CATTTCGATATACAATTATGTATAAAAGTTATCGATCGATTTTTTTTAATGCAT-ATGGTGCATT
1 CATTTCGACATA-AATTATATATAAAACTTATCGATCGATTTTGTGTAATGCATAATGGTGCATT
* * ** *
1504665 TTCGTATCAGTACTATATGTACTTTTGACACTATTTTTGC-ATCCATGGAATTCATAATAAGTTT
65 TTCGTATAAGTACTATATGTACTTTCGACACTAGATGTGCAAT-CATGGAATTCATAATAAGTTT
*
1504729 GTGAATTTC
129 GTGAATTAC
1504738 CATTTCG
1 CATTTCG
1504745 GTACTTCAGT
Statistics
Matches: 125, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
136 2 0.02
137 87 0.70
138 36 0.29
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (137 bp):
CATTTCGACATAAATTATATATAAAACTTATCGATCGATTTTGTGTAATGCATAATGGTGCATTT
TCGTATAAGTACTATATGTACTTTCGACACTAGATGTGCAATCATGGAATTCATAATAAGTTTGT
GAATTAC
Found at i:1512316 original size:21 final size:22
Alignment explanation
Indices: 1512287--1512328 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1512277 TATTATATTA
**
1512287 AAATGTTTTATTTTTTAGAAAC
1 AAATGTTTTATGGTTTAGAAAC
1512309 AAAT-TTTTATGGTTTAGAAA
1 AAATGTTTTATGGTTTAGAAA
1512329 TAAGGAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (22 bp):
AAATGTTTTATGGTTTAGAAAC
Found at i:1520875 original size:20 final size:20
Alignment explanation
Indices: 1520850--1520919 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
1520840 GTTCATATAG
*
1520850 TATCGATATTGTAAGAACAA
1 TATCGATACTGTAAGAACAA
1520870 TATCGATACTGTAAGAACAA
1 TATCGATACTGTAAGAACAA
1520890 TATCGATACTGTAAGAACAA
1 TATCGATACTGTAAGAACAA
*
1520910 TATCTATACT
1 TATCGATACT
1520920 ACGTATGTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (20 bp):
TATCGATACTGTAAGAACAA
Found at i:1521937 original size:104 final size:103
Alignment explanation
Indices: 1521758--1521962 Score: 367
Period size: 104 Copynumber: 2.0 Consensus size: 103
1521748 TCTAAAAGGA
*
1521758 TTGATATTTTTTAATTTAATTTATTTTACTTTATTTTATCATCATTCATGCATTCAAGTTAATAA
1 TTGATAATTTTTAATTTAATTTATTTTACTTTATTTTATCATCATTCATGCATTCAAGTTAATAA
1521823 TAAATTTTAGAATGGAATAATGATATTTCTTTATTTTG
66 TAAATTTTAGAATGGAATAATGATATTTCTTTATTTTG
1521861 TTGATAATTTTTAATTTAATTTATTTTACTTTATTTTTATCATCATTCATGCATTCGAA-TTAAT
1 TTGATAATTTTTAATTTAATTTATTTTACTTTA-TTTTATCATCATTCATGCATTC-AAGTTAAT
*
1521925 AATGAATTTTAGAATGGAATAATGATATTTCTTTATTT
64 AATAAATTTTAGAATGGAATAATGATATTTCTTTATTT
1521963 CGATTAGAGT
Statistics
Matches: 98, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
103 32 0.33
104 64 0.65
105 2 0.02
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.53
Consensus pattern (103 bp):
TTGATAATTTTTAATTTAATTTATTTTACTTTATTTTATCATCATTCATGCATTCAAGTTAATAA
TAAATTTTAGAATGGAATAATGATATTTCTTTATTTTG
Found at i:1522384 original size:3 final size:3
Alignment explanation
Indices: 1522376--1522405 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1522366 TCACGCCACC
1522376 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1522406 TTTTTAATAG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1536901 original size:15 final size:15
Alignment explanation
Indices: 1536877--1536907 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1536867 GATTGATCAT
1536877 TTTTAATTTATTTTA
1 TTTTAATTTATTTTA
*
1536892 TTTTACTTTATTTTA
1 TTTTAATTTATTTTA
1536907 T
1 T
1536908 CATAATTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTAATTTATTTTA
Found at i:1537030 original size:108 final size:108
Alignment explanation
Indices: 1536878--1537074 Score: 349
Period size: 108 Copynumber: 1.8 Consensus size: 108
1536868 ATTGATCATT
* *
1536878 TTTAATTTATTTTATTTTACTTTATTTTATCATAATTCATGCATTCGAATTAATAATGAATTTTA
1 TTTAATTTAATTTACTTTACTTTATTTTATCATAATTCATGCATTCGAATTAATAATGAATTTTA
*
1536943 GAATGGAATAATGATATTTCTTTAATTTGTTGGTAATTTTTAA
66 GAATGGAATAATAATATTTCTTTAATTTGTTGGTAATTTTTAA
* *
1536986 TTTAATTTAATTTACTTTATTTTATTTTATCATCATTCATGCATTCGAATTAATAATGAATTTTA
1 TTTAATTTAATTTACTTTACTTTATTTTATCATAATTCATGCATTCGAATTAATAATGAATTTTA
1537051 GAATGGAATAATAATATTTCTTTA
66 GAATGGAATAATAATATTTCTTTA
1537075 TTTCAATTGG
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 84 1.00
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.52
Consensus pattern (108 bp):
TTTAATTTAATTTACTTTACTTTATTTTATCATAATTCATGCATTCGAATTAATAATGAATTTTA
GAATGGAATAATAATATTTCTTTAATTTGTTGGTAATTTTTAA
Found at i:1537366 original size:23 final size:23
Alignment explanation
Indices: 1537341--1537383 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1537331 CACAGACTTA
1537341 AAAACT-CTGTTTTAATAAAATT
1 AAAACTACTGTTTTAATAAAATT
* *
1537363 AAAATTACTGTTTTATTAAAA
1 AAAACTACTGTTTTAATAAAA
1537384 CGACAACCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (23 bp):
AAAACTACTGTTTTAATAAAATT
Found at i:1537780 original size:29 final size:31
Alignment explanation
Indices: 1537709--1537784 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 31
1537699 TTTCTATATT
1537709 TATTTGTTATTATGAGTCCAATTTTTTTCAA
1 TATTTGTTATTATGAGTCCAATTTTTTTCAA
1537740 T-TCTT-TTGATTA-GAGGTCC-ATTTTTTT-AA
1 TAT-TTGTT-ATTATGA-GTCCAATTTTTTTCAA
1537769 TATTTGTTATTATGAG
1 TATTTGTTATTATGAG
1537785 CACATTCTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
29 10 0.26
30 18 0.46
31 11 0.28
ACGTcount: A:0.24, C:0.08, G:0.13, T:0.55
Consensus pattern (31 bp):
TATTTGTTATTATGAGTCCAATTTTTTTCAA
Found at i:1545502 original size:20 final size:19
Alignment explanation
Indices: 1545477--1545523 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1545467 CAAGTAAATT
1545477 AAATAAAAATAAAGAAACAA
1 AAATAAAAATAAAGAAA-AA
* *
1545497 AAATAAAAATAAATAAATA
1 AAATAAAAATAAAGAAAAA
1545516 AAATAAAA
1 AAATAAAA
1545524 GACATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (19 bp):
AAATAAAAATAAAGAAAAA
Found at i:1545518 original size:34 final size:30
Alignment explanation
Indices: 1545471--1545543 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 30
1545461 CGATAACAAG
1545471 TAAATTAAATAAAAATAAAGAAACAAAAATAAAAA
1 TAAA-TAAAT-AAAATAAA-AAAC-AAAA-AAAAA
* *
1545506 TAAATAAATAAAATAAAAGACATAAAAAAA
1 TAAATAAATAAAATAAAAAACAAAAAAAAA
1545536 TAAATAAA
1 TAAATAAA
1545544 ATCCATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 13 0.36
31 3 0.08
32 3 0.08
33 8 0.22
34 5 0.14
35 4 0.11
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (30 bp):
TAAATAAATAAAATAAAAAACAAAAAAAAA
Found at i:1545521 original size:9 final size:9
Alignment explanation
Indices: 1545496--1545574 Score: 63
Period size: 9 Copynumber: 8.7 Consensus size: 9
1545486 TAAAGAAACA
*
1545496 AAAATAAAA
1 AAAATAAAT
1545505 ATAAATAAAT
1 A-AAATAAAT
1545515 AAAATAAA-
1 AAAATAAAT
*
1545523 AGACATAAA-
1 A-AAATAAAT
1545532 AAAATAAAT
1 AAAATAAAT
**
1545541 AAAATCCAT
1 AAAATAAAT
*
1545550 AAAAACAAAT
1 -AAAATAAAT
*
1545560 GAAATAAAT
1 AAAATAAAT
1545569 AAAATA
1 AAAATA
1545575 CTAGAAAATA
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
8 7 0.13
9 34 0.62
10 14 0.25
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.18
Consensus pattern (9 bp):
AAAATAAAT
Found at i:1545542 original size:21 final size:22
Alignment explanation
Indices: 1545505--1545554 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1545495 AAAAATAAAA
*
1545505 ATAAATAAATAAAATAAAAGAC
1 ATAAAAAAATAAAATAAAAGAC
**
1545527 ATAAAAAAAT-AAATAAAATCC
1 ATAAAAAAATAAAATAAAAGAC
1545548 ATAAAAA
1 ATAAAAA
1545555 CAAATGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.18
Consensus pattern (22 bp):
ATAAAAAAATAAAATAAAAGAC
Found at i:1545736 original size:2 final size:2
Alignment explanation
Indices: 1545731--1545759 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1545721 AAAATAGTAA
1545731 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 A
1545760 AATTAATAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1547023 original size:33 final size:34
Alignment explanation
Indices: 1546952--1547035 Score: 143
Period size: 35 Copynumber: 2.5 Consensus size: 34
1546942 CGAGGGTTTG
*
1546952 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGG-TTTTTTT
1546987 GTGTTTCAAGAGAAACAATTTCAAAGG-TTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
1547020 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
1547036 TGTATTCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 22 0.46
35 26 0.54
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (34 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
Found at i:1547074 original size:15 final size:15
Alignment explanation
Indices: 1547056--1547113 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
1547046 GATTGAAGTT
1547056 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
*
1547071 TCAAGAGAGACACAATTTGTT
1 TCAAGAGA-A-AC----TGTC
1547092 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
1547107 TCAAGAG
1 TCAAGAG
1547114 GGACAAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
15 18 0.51
16 1 0.03
17 2 0.06
19 2 0.06
20 1 0.03
21 11 0.31
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:1547100 original size:36 final size:37
Alignment explanation
Indices: 1547053--1547151 Score: 125
Period size: 36 Copynumber: 2.8 Consensus size: 37
1547043 AAAGATTGAA
* *
1547053 GTTTCAAGAGAAACTGTCTCAAGAGAGAC-ACAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAACTT
*
1547089 GTTTCAAGAGAAACTGTCTCAAGAGGGACAAAAACTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAACTT
* *
1547126 G---CAAAAGAAACTGTCTCAAGGGAGAC
1 GTTTCAAGAGAAACTGTCTCAAGAGAGAC
1547152 GAGATTTGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
34 22 0.39
36 28 0.50
37 6 0.11
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.20
Consensus pattern (37 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAACTT
Found at i:1547268 original size:36 final size:36
Alignment explanation
Indices: 1547221--1547405 Score: 102
Period size: 36 Copynumber: 5.3 Consensus size: 36
1547211 AAGTTTATGC
* *
1547221 TTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTGT
* * * * **
1547257 TTCAAGGGAAACTATCTCATGAGTGACAAAATTCAT
1 TTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTGT
* * *
1547293 TTCAAGGGAAA-TGTTTTC-A-A-TG-----TTTATGT
1 TTCAAGGGAAACTG-TCTCAAGAGAGAAAAAATT-TGT
* *
1547322 TTCAAGAGG-AACTGTCTCAAGGGAGACAAAATTTTGT
1 TTCAAG-GGAAACTGTCTCAAGAGAGA-AAAAATTTGT
* * * * *
1547359 TTCAAGGGAACCTATCCCAAGAGAGATAAAATTCGT
1 TTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTGT
1547395 TTCAAGGGAAA
1 TTCAAGGGAAA
1547406 TGTTTTTAAT
Statistics
Matches: 110, Mismatches: 25, Indels: 28
0.67 0.15 0.17
Matches are distributed among these distances:
28 2 0.02
29 12 0.11
30 5 0.05
32 1 0.01
33 2 0.02
34 1 0.01
35 1 0.01
36 61 0.55
37 22 0.20
38 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (36 bp):
TTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTGT
Found at i:1547390 original size:37 final size:35
Alignment explanation
Indices: 1547319--1547404 Score: 100
Period size: 37 Copynumber: 2.4 Consensus size: 35
1547309 TCAATGTTTA
* * *
1547319 TGTTTCAAGAGGAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAG-GGAACTATCCCAAGAGAGACAAAA-TT
*
1547356 TGTTTCAAGGGAACCTATCCCAAGAGAGATAAAATT
1 TGTTTCAAGGGAA-CTATCCCAAGAGAGACAAAATT
*
1547392 CGTTTCAAGGGAA
1 TGTTTCAAGGGAA
1547405 ATGTTTTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 18 0.42
37 25 0.58
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (35 bp):
TGTTTCAAGGGAACTATCCCAAGAGAGACAAAATT
Found at i:1547398 original size:102 final size:101
Alignment explanation
Indices: 1547189--1547572 Score: 428
Period size: 102 Copynumber: 3.8 Consensus size: 101
1547179 CAAAGATTTT
* * * * *
1547189 GTTTCAAAGGAAAATGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATT
1 GTTTC-AAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* *
1547254 TGTTTCAAGGGAAACTATCTCATGAGTGACAAAATTC
65 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
* * * * *
1547291 ATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGGAACTGTCTCAAGGGAGACAAAATTT
1 GTTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TT
* * *
1547356 TGTTTCAAGGGAACCTATCCCAAGAGAGATAAAATTC
65 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
* * *
1547393 GTTTCAAGGGAAATGTTTTTAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAAACAAAACTT
1 GTTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TT
* * ** * * * * *
1547458 AGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTT
65 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
** * *
1547495 GTTTCAAGGGAAACATATTCAAAGATTT-TGTTTCAAGAGAAACTATCTTAAGAGAGACAAAATT
1 GTTTCAAGGGAAATGTTTTCAAAG-TTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
**
1547559 CATTTCAAGGGAAA
65 TGTTTCAAGGGAAA
1547573 TGTTTTCAAT
Statistics
Matches: 238, Mismatches: 42, Indels: 5
0.84 0.15 0.02
Matches are distributed among these distances:
101 63 0.26
102 172 0.72
103 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.29
Consensus pattern (101 bp):
GTTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
Found at i:1547525 original size:167 final size:166
Alignment explanation
Indices: 1547348--1547669 Score: 509
Period size: 167 Copynumber: 1.9 Consensus size: 166
1547338 TCAAGGGAGA
* * * * *
1547348 CAAAATTTTGTTTCAAGGGAACCTATCCCAAGAGAGATAAAATTCGTTTCAAGGGAAATGTTTTT
1 CAAAATTTTGTTTCAAGAGAAACTATCCCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
1547413 AATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAAACAAAACTTAGTTCCAAAAGAAAATGTCT
66 AATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAAACAAAACTTAGTTCCAAAAGAAAATGTCT
* *
1547478 CAAGGGAGACGAAATTTGTTTCAAGGGAAACATATT
131 CAAGGGAGACAAAATTTATTTCAAGGGAAACATATT
**
1547514 CAAAGATTTTGTTTCAAGAGAAACTATCTTAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAA-ATTTTGTTTCAAGAGAAACTATCCCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
* * * **
1547579 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAACTTAGTTGTAAAAGAAAATGTC
65 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAAACAAAACTTAGTTCCAAAAGAAAATGTC
1547644 TCAAGGGAGACAAAATTTATTTCAAG
130 TCAAGGGAGACAAAATTTATTTCAAG
1547670 AGAGACAAAA
Statistics
Matches: 141, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
166 4 0.03
167 137 0.97
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (166 bp):
CAAAATTTTGTTTCAAGAGAAACTATCCCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
AATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAAACAAAACTTAGTTCCAAAAGAAAATGTCT
CAAGGGAGACAAAATTTATTTCAAGGGAAACATATT
Found at i:1547571 original size:65 final size:65
Alignment explanation
Indices: 1547475--1547617 Score: 180
Period size: 65 Copynumber: 2.2 Consensus size: 65
1547465 AAAGAAAATG
* * **
1547475 TCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACATATTCAAAGATTT-TGTTTCAAGAGAAACT
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAG-TTTATGTTTCAAGAGAAACT
1547539 A
65 A
* ** * * *
1547540 TCTTAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTG
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGTTTATGTTTCAAGAGAAACTA
1547605 TCTCAAGAGAGAC
1 TCTCAAGAGAGAC
1547618 GAAACTTAGT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
64 3 0.05
65 63 0.95
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (65 bp):
TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGTTTATGTTTCAAGAGAAACTA
Found at i:1547672 original size:19 final size:21
Alignment explanation
Indices: 1547644--1547698 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1547634 AGAAAATGTC
*
1547644 TCAAGGGAGACAAAATTTATT
1 TCAAGAGAGACAAAATTTATT
*
1547665 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTATT
*
1547686 TCAAGAGAAACAA
1 TCAAGAGAGACAA
1547699 TATTGACTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTATT
Found at i:1547805 original size:36 final size:37
Alignment explanation
Indices: 1547765--1547879 Score: 103
Period size: 36 Copynumber: 3.2 Consensus size: 37
1547755 GGTTTTAAGA
1547765 AAAACAATCTTGAGTG-GAATAAATCTTCTTTCGAGT
1 AAAACAATCTTGAGTGAGAATAAATCTTCTTTCGAGT
* * * * * *
1547801 AAAACAGTC-TCAGGTGAGACA-AAGTCTGCTTT-AAGC
1 AAAACAATCTTGA-GTGAGA-ATAAATCTTCTTTCGAGT
* * *
1547837 AAAGCAAACTTGAGTGAAAATAAATCTTCTTTCGAGT
1 AAAACAATCTTGAGTGAGAATAAATCTTCTTTCGAGT
1547874 AAAACA
1 AAAACA
1547880 GTCTCAAGTG
Statistics
Matches: 57, Mismatches: 16, Indels: 11
0.68 0.19 0.13
Matches are distributed among these distances:
35 3 0.05
36 33 0.58
37 20 0.35
38 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (37 bp):
AAAACAATCTTGAGTGAGAATAAATCTTCTTTCGAGT
Found at i:1547926 original size:73 final size:73
Alignment explanation
Indices: 1547665--1547918 Score: 309
Period size: 73 Copynumber: 3.5 Consensus size: 73
1547655 AAAATTTATT
* * * * * *
1547665 TCAAGAGAGACAAAATTTG-TTTCAAGAGAAACAATATTGACTG-AAATAAATCTTCTTTCGAGT
1 TCAAGTGAGACAAAGTCTGCTTT-AAGAAAAACAATCTTGAGTGAAAATAAATCTTCTTTCGAGT
*
1547728 GAAAACGGTC
65 -AAAACAGTC
* * * *
1547738 CCAAGAGAGACAAA-TCTGGTTTTAAGAAAAACAATCTTGAGTG-GAATAAATCTTCTTTCGAGT
1 TCAAGTGAGACAAAGTCT-GCTTTAAGAAAAACAATCTTGAGTGAAAATAAATCTTCTTTCGAGT
1547801 AAAACAGTC
65 AAAACAGTC
* * * *
1547810 TCAGGTGAGACAAAGTCTGCTTTAAGCAAAGCAAACTTGAGTGAAAATAAATCTTCTTTCGAGTA
1 TCAAGTGAGACAAAGTCTGCTTTAAGAAAAACAATCTTGAGTGAAAATAAATCTTCTTTCGAGTA
1547875 AAACAGTC
66 AAACAGTC
*
1547883 TCAAGTGAGACAAAGTATGCTTTAAGAAAAACAATC
1 TCAAGTGAGACAAAGTCTGCTTTAAGAAAAACAATC
1547919 ACAAGTGAGA
Statistics
Matches: 157, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
72 42 0.27
73 112 0.71
74 3 0.02
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (73 bp):
TCAAGTGAGACAAAGTCTGCTTTAAGAAAAACAATCTTGAGTGAAAATAAATCTTCTTTCGAGTA
AAACAGTC
Found at i:1549386 original size:183 final size:182
Alignment explanation
Indices: 1549066--1549418 Score: 598
Period size: 183 Copynumber: 1.9 Consensus size: 182
1549056 ACCAGGTTTA
*
1549066 ACTGAAGGGTCCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGAGAAACACCAAATTG
1 ACTGAAGGGTCCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGACAAACACCAAATTG
* * *
1549131 CCAAGTGTCCGAGTAATGTCATAGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTTT
66 CCAAGTGTCCGAGCAATATCATAGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTAGAGTTT
*
1549196 CCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 CCTCTATAACCAATTGCCTTAATGGAATAGCTCAGCTTTAGAGGGACAAATC
* * *
1549248 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGATCATACACCGAATT
1 ACTGAAGGGTCCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGA-CAAACACCAAATT
* *
1549313 TCCAAGTGTCCGAGCAATATCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTAGAGTT
65 GCCAAGTGTCCGAGCAATATCATAGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTAGAGTT
*
1549378 TTCTCTATAACCAATTGCCTTAATGGAATAGCTCAGCTTTA
130 TCCTCTATAACCAATTGCCTTAATGGAATAGCTCAGCTTTA
1549419 CGGATTTAAT
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
182 50 0.31
183 109 0.69
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (182 bp):
ACTGAAGGGTCCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGACAAACACCAAATTG
CCAAGTGTCCGAGCAATATCATAGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTAGAGTTT
CCTCTATAACCAATTGCCTTAATGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:1553513 original size:27 final size:26
Alignment explanation
Indices: 1553427--1553549 Score: 76
Period size: 27 Copynumber: 4.6 Consensus size: 26
1553417 AAACGAAAAG
**
1553427 AAAAAT-AAATAAATAAAATAAAAGA
1 AAAAATGAAATAAATAAAATACTAGA
* *
1553452 CATAAAAT-AAATAAAT-AAATCCATAAA
1 -A-AAAATGAAATAAATAAAATAC-TAGA
1553479 AACAAATGAAATAAATAAAATACTAGA
1 AA-AAATGAAATAAATAAAATACTAGA
** *
1553506 AAATAATGGTGA-AAATAATATACATAGTA
1 AAA-AAT-GAAATAAATAAAATAC-TAG-A
1553535 AAAAAT-AAATAAATA
1 AAAAATGAAATAAATA
1553550 CAAGAGGGGA
Statistics
Matches: 76, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
25 1 0.01
26 12 0.16
27 46 0.61
28 13 0.17
29 4 0.05
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (26 bp):
AAAAATGAAATAAATAAAATACTAGA
Found at i:1554852 original size:10 final size:10
Alignment explanation
Indices: 1554833--1554876 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
1554823 CCGTTTTCAT
*
1554833 CGGTTCTGAC
1 CGGTTTTGAC
1554843 CGGTTTTGAC
1 CGGTTTTGAC
*
1554853 CGGTTTTCAAC
1 CGGTTTT-GAC
1554864 CGG-TTTGAC
1 CGGTTTTGAC
1554873 CGGT
1 CGGT
1554877 CTGAATCGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 5 0.17
10 19 0.66
11 5 0.17
ACGTcount: A:0.11, C:0.25, G:0.30, T:0.34
Consensus pattern (10 bp):
CGGTTTTGAC
Found at i:1554861 original size:30 final size:29
Alignment explanation
Indices: 1554813--1554876 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
1554803 GCTGCTGGAA
*
1554813 ACCGG-TTTAACCGTTTTC-ATCGGTTCTG
1 ACCGGTTTTAACCGTTTTCAACCGGTT-TG
*
1554841 ACCGGTTTTGACCGGTTTTCAACCGGTTTG
1 ACCGGTTTTAACC-GTTTTCAACCGGTTTG
1554871 ACCGGT
1 ACCGGT
1554877 CTGAATCGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 5 0.16
29 6 0.19
30 14 0.45
31 6 0.19
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.36
Consensus pattern (29 bp):
ACCGGTTTTAACCGTTTTCAACCGGTTTG
Found at i:1555112 original size:269 final size:268
Alignment explanation
Indices: 1554615--1555152 Score: 1051
Period size: 269 Copynumber: 2.0 Consensus size: 268
1554605 TATCCGTAGA
1554615 CGGCGGCGCGTGAGGAGGTGGTGCAGTCAAAGATTCGGGCCGATTTGAAAATCGAGCTCTCCGCC
1 CGGCGGCGCGTGAGGAGGTGGTGCAGTCAAAGATTCGGGCCGATTTGAAAATCGAGCTCTCCGCC
1554680 GTTCAAAATTTGAACCGATCGTTGTAAGTATCTTGAAATCGCTCAAAAAATTTTTAGAAATTTTT
66 GTTCAAAATTTGAACCGATCGTTGTAAGTATCTTGAAATCGCTCAAAAAATTTTTAGAAATTTTT
1554745 CCGGGATTTTTAGGGCCCCGGAGGCCGCCTCACGCCACCGCGCCGCCGTAGGCGAGTGGCTGCTG
131 CCGGGATTTTTAGGGCCCCGGAGGCCGCCTCACGCCACCGCGCCGCCGTAGGCGAGTGGCTGCTG
1554810 GAAACCGGTTTAACCGTTTTCATCGGTTCTGACCGGTTTTGACCGGTTTTCAACCGGTTTGACCG
196 GAAACCGGTTTAACCGTTTTCATCGGTTCTGACCGGTTTTGACCGGTTTTCAACCGGTTTGACCG
1554875 GTCTGAAT
261 GTCTGAAT
1554883 CGGCGGCGCGTGAGGAGGTGGTGCAGTCAAAGATTCGGGCCGATTTGAAAATCGAGCTCTCCGCC
1 CGGCGGCGCGTGAGGAGGTGGTGCAGTCAAAGATTCGGGCCGATTTGAAAATCGAGCTCTCCGCC
1554948 GTTCAAAAATTTGAACCGATCGTTGTAAGTATCTTGAAATCGCTCAAAAAATTTTTAGAAATTTT
66 GTTC-AAAATTTGAACCGATCGTTGTAAGTATCTTGAAATCGCTCAAAAAATTTTTAGAAATTTT
1555013 TCCGGGATTTTTAGGGCCCCGGAGGCCGCCTCACGCCACACGCGCCGCCGTAGGCGAGTGGCTGC
130 TCCGGGATTTTTAGGGCCCCGGAGGCCGCCTCACGCCAC-CGCGCCGCCGTAGGCGAGTGGCTGC
1555078 TGGAAACCGGTTTAACCGTTTTCATCGG-TCTGACCGGTTTTGACCGGTTTTCAACCGGTTTGAC
194 TGGAAACCGGTTTAACCGTTTTCATCGGTTCTGACCGGTTTTGACCGGTTTTCAACCGGTTTGAC
1555142 CGGTCTGAAT
259 CGGTCTGAAT
1555152 C
1 C
1555153 CAAACTTAAA
Statistics
Matches: 268, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
268 69 0.26
269 146 0.54
270 53 0.20
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (268 bp):
CGGCGGCGCGTGAGGAGGTGGTGCAGTCAAAGATTCGGGCCGATTTGAAAATCGAGCTCTCCGCC
GTTCAAAATTTGAACCGATCGTTGTAAGTATCTTGAAATCGCTCAAAAAATTTTTAGAAATTTTT
CCGGGATTTTTAGGGCCCCGGAGGCCGCCTCACGCCACCGCGCCGCCGTAGGCGAGTGGCTGCTG
GAAACCGGTTTAACCGTTTTCATCGGTTCTGACCGGTTTTGACCGGTTTTCAACCGGTTTGACCG
GTCTGAAT
Found at i:1555123 original size:10 final size:10
Alignment explanation
Indices: 1555108--1555145 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1555098 TTCATCGGTC
1555108 TGACCGGTTT
1 TGACCGGTTT
1555118 TGACCGGTTT
1 TGACCGGTTT
*
1555128 TCAACCGG-TT
1 T-GACCGGTTT
1555138 TGACCGGT
1 TGACCGGT
1555146 CTGAATCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 5 0.21
10 14 0.58
11 5 0.21
ACGTcount: A:0.13, C:0.24, G:0.29, T:0.34
Consensus pattern (10 bp):
TGACCGGTTT
Found at i:1555493 original size:22 final size:23
Alignment explanation
Indices: 1555467--1555511 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
1555457 TTCTAGCTTT
1555467 GAACAATTAAGT-AGATTTGGGG
1 GAACAATTAAGTAAGATTTGGGG
1555489 GAACAATTAAGTAAGATTTGGGG
1 GAACAATTAAGTAAGATTTGGGG
1555512 TGATAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.38, C:0.04, G:0.31, T:0.27
Consensus pattern (23 bp):
GAACAATTAAGTAAGATTTGGGG
Found at i:1585031 original size:13 final size:13
Alignment explanation
Indices: 1585013--1585042 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1585003 AAGAATTTCA
1585013 TGTAGATCAATTT
1 TGTAGATCAATTT
1585026 TGTAGATCAATTT
1 TGTAGATCAATTT
1585039 TGTA
1 TGTA
1585043 TTTCATGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (13 bp):
TGTAGATCAATTT
Found at i:1593797 original size:8 final size:8
Alignment explanation
Indices: 1593786--1593821 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
1593776 AAAAACAAAA
1593786 AAAAAATG
1 AAAAAATG
1593794 AAAAAATG
1 AAAAAATG
1593802 AAAAAATG
1 AAAAAATG
*
1593810 AAAGAA-G
1 AAAAAATG
1593817 AAAAA
1 AAAAA
1593822 TAAAAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 5 0.19
8 21 0.81
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (8 bp):
AAAAAATG
Found at i:1593826 original size:28 final size:27
Alignment explanation
Indices: 1593758--1593831 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 27
1593748 TATTTTGCTT
*
1593758 GAAGAACAAA-AAAATTGAAAAAACAAA
1 GAAGAA-AAATAAAAATGAAAAAACAAA
*
1593785 -AA-AAAAATGAAAAAATGAAAAAATGAAA
1 GAAGAAAAAT--AAAAATGAAAAAA-CAAA
1593813 GAAGAAAAATAAAAATGAA
1 GAAGAAAAATAAAAATGAA
1593832 GGAAAAAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
24 3 0.08
25 2 0.05
26 2 0.05
27 12 0.31
28 12 0.31
29 2 0.05
30 6 0.15
ACGTcount: A:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (27 bp):
GAAGAAAAATAAAAATGAAAAAACAAA
Found at i:1595122 original size:44 final size:43
Alignment explanation
Indices: 1595073--1595180 Score: 117
Period size: 44 Copynumber: 2.5 Consensus size: 43
1595063 AAATTTCAAG
* *
1595073 ATCTGATCTTCCTAAAGAGCAGTGAAGCATATTACTTTGTCCAT
1 ATCTGATATTCCTAAAGAGCAGTGAAGCATATCA-TTTGTCCAT
* * * * *
1595117 ATCTGATATTCCTTAAGAGCATTGAAGTATATCATTTTTTCAT
1 ATCTGATATTCCTAAAGAGCAGTGAAGCATATCATTTGTCCAT
* * *
1595160 ATTTGATTTTCCTAAAAAGCA
1 ATCTGATATTCCTAAAGAGCA
1595181 ACAAAGCAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
43 24 0.45
44 29 0.55
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (43 bp):
ATCTGATATTCCTAAAGAGCAGTGAAGCATATCATTTGTCCAT
Found at i:1596692 original size:26 final size:25
Alignment explanation
Indices: 1596640--1596702 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
1596630 TAATTTTAGA
* *
1596640 ACTTTTATTTTTTTATTTATGTATGT
1 ACTTTTA-TGTTTTAGTTATGTATGT
*
1596666 A-TATTTATGTTTTAGTTATGTTTTGT
1 ACT-TTTATGTTTTAGTTATG-TATGT
1596692 ACTTTTATGTT
1 ACTTTTATGTT
1596703 AGTTACTTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 12 0.39
26 18 0.58
27 1 0.03
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (25 bp):
ACTTTTATGTTTTAGTTATGTATGT
Found at i:1597005 original size:2 final size:2
Alignment explanation
Indices: 1596998--1597025 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1596988 AGTACGTACT
1596998 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1597026 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1597030 original size:2 final size:2
Alignment explanation
Indices: 1597025--1597065 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1597015 ATATATATAT
1597025 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1597066 TTATGCGTAT
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1607235 original size:21 final size:21
Alignment explanation
Indices: 1607193--1607236 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1607183 ATTTTGCTTG
1607193 AAGAATAAAAAATGAAAAAAA
1 AAGAATAAAAAATGAAAAAAA
1607214 AAGAA-AAAGAAA-GAAAAGAAA
1 AAGAATAAA-AAATGAAAA-AAA
1607235 AA
1 AA
1607237 TGAGGGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (21 bp):
AAGAATAAAAAATGAAAAAAA
Found at i:1608498 original size:44 final size:43
Alignment explanation
Indices: 1608444--1608564 Score: 136
Period size: 44 Copynumber: 2.8 Consensus size: 43
1608434 AGTCATCAAG
* * *
1608444 ATCTGGTCTTCTTAAAGAGCAGTGAAACAAATC-TCTATTTCTAT
1 ATCTGATCTTCTTGAAGAGCAGTGAAGCAAATCAT-TATTTC-AT
* * * *
1608488 ATCTGATCTTCGTGAAGAGCATTGAAGCATATCATTTTTTCAT
1 ATCTGATCTTCTTGAAGAGCAGTGAAGCAAATCATTATTTCAT
* *
1608531 ATTTGATCTTCTTGAAGAGCAGCGAAGCAAATCA
1 ATCTGATCTTCTTGAAGAGCAGTGAAGCAAATCA
1608565 ACCGTGATTC
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 31 0.48
44 32 0.50
45 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (43 bp):
ATCTGATCTTCTTGAAGAGCAGTGAAGCAAATCATTATTTCAT
Found at i:1610299 original size:16 final size:15
Alignment explanation
Indices: 1610278--1610311 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1610268 CTTTTATAAT
1610278 CATTTTAGTTCTTTTA
1 CATTTTAG-TCTTTTA
*
1610294 CATTTTTGTCTTTTA
1 CATTTTAGTCTTTTA
1610309 CAT
1 CAT
1610312 ATATAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.18, C:0.15, G:0.06, T:0.62
Consensus pattern (15 bp):
CATTTTAGTCTTTTA
Found at i:1614724 original size:3 final size:3
Alignment explanation
Indices: 1614716--1614756 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
1614706 GTGAGACATT
* *
1614716 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA AGA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1614757 CGTAAGATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1614761 original size:12 final size:12
Alignment explanation
Indices: 1614716--1614763 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
1614706 GTGAGACATT
* *
1614716 ATAATAATAATA
1 ATAATAGTAAGA
* *
1614728 ATAATAATAATA
1 ATAATAGTAAGA
1614740 ATAATAGTAAGA
1 ATAATAGTAAGA
*
1614752 ATAATCGTAAGA
1 ATAATAGTAAGA
1614764 TATTTATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29
Consensus pattern (12 bp):
ATAATAGTAAGA
Found at i:1624168 original size:13 final size:13
Alignment explanation
Indices: 1624150--1624175 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1624140 TTTGGAAGTA
1624150 GAGAAGCAAGGCC
1 GAGAAGCAAGGCC
1624163 GAGAAGCAAGGCC
1 GAGAAGCAAGGCC
1624176 CACCACCGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.38, T:0.00
Consensus pattern (13 bp):
GAGAAGCAAGGCC
Found at i:1626194 original size:16 final size:19
Alignment explanation
Indices: 1626162--1626203 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
1626152 ACATATATAT
1626162 TTTTATAAATCTTA-TTTA
1 TTTTATAAATCTTATTTTA
1626180 TTTT-TAAAT-TTATTTTA
1 TTTTATAAATCTTATTTTA
1626197 TTTTATA
1 TTTTATA
1626204 GAAATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.14
17 13 0.59
18 6 0.27
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTATAAATCTTATTTTA
Found at i:1626821 original size:96 final size:96
Alignment explanation
Indices: 1626657--1626848 Score: 384
Period size: 96 Copynumber: 2.0 Consensus size: 96
1626647 GTCAATTATA
1626657 CCACAATCGAAAAAGAATTGCTTGTTGTCGTGTTTTCTTTTAACAAATTTAGCCCATACTTGGTT
1 CCACAATCGAAAAAGAATTGCTTGTTGTCGTGTTTTCTTTTAACAAATTTAGCCCATACTTGGTT
1626722 GTAACCAAGGTAATTGTTACCATTCAGCTCT
66 GTAACCAAGGTAATTGTTACCATTCAGCTCT
1626753 CCACAATCGAAAAAGAATTGCTTGTTGTCGTGTTTTCTTTTAACAAATTTAGCCCATACTTGGTT
1 CCACAATCGAAAAAGAATTGCTTGTTGTCGTGTTTTCTTTTAACAAATTTAGCCCATACTTGGTT
1626818 GTAACCAAGGTAATTGTTACCATTCAGCTCT
66 GTAACCAAGGTAATTGTTACCATTCAGCTCT
1626849 GAAGCATTTA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (96 bp):
CCACAATCGAAAAAGAATTGCTTGTTGTCGTGTTTTCTTTTAACAAATTTAGCCCATACTTGGTT
GTAACCAAGGTAATTGTTACCATTCAGCTCT
Found at i:1634366 original size:165 final size:167
Alignment explanation
Indices: 1634094--1634423 Score: 646
Period size: 165 Copynumber: 2.0 Consensus size: 167
1634084 ATTTTTCCAA
1634094 ATTTAGTACTAGGTTGGCTTCTTCACATCGTTTCAGTACTTTGGATAAATTGCTGAGAAATTGGT
1 ATTTAGTACTAGGTTGGCTTCTTCACATCGTTTCAGTACTTTGGATAAATTGCTGAGAAATTGGT
1634159 TGAAATCATCACCTGAGACGGAGAAATCATCCATAAATATTTCCA-GCACTCTT-CACTATATCT
66 TGAAATCATCACCTGAGACGGAGAAATCATCCATAAATATTTCCATGCACTCTTCCACTATATCT
1634222 AAAAAGATGGCCATCATGCATCTTTGGAAAGTAGCGG
131 AAAAAGATGGCCATCATGCATCTTTGGAAAGTAGCGG
1634259 ATTTAGTACTAGGTTGGCTTCTTCACATCGTTTCAGTACTTTGGATAAATTGCTGAGAAATTGGT
1 ATTTAGTACTAGGTTGGCTTCTTCACATCGTTTCAGTACTTTGGATAAATTGCTGAGAAATTGGT
1634324 TGAAATCATCACCTGAGACGGAGAAATCATCCATAAATATTTCCATGCACTCTTCCACTATATCT
66 TGAAATCATCACCTGAGACGGAGAAATCATCCATAAATATTTCCATGCACTCTTCCACTATATCT
1634389 AAAAAGATGGCCATCATGCATCTTTGGAAAGTAGC
131 AAAAAGATGGCCATCATGCATCTTTGGAAAGTAGC
1634424 TGGAGCATTA
Statistics
Matches: 163, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
165 110 0.67
166 8 0.05
167 45 0.28
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (167 bp):
ATTTAGTACTAGGTTGGCTTCTTCACATCGTTTCAGTACTTTGGATAAATTGCTGAGAAATTGGT
TGAAATCATCACCTGAGACGGAGAAATCATCCATAAATATTTCCATGCACTCTTCCACTATATCT
AAAAAGATGGCCATCATGCATCTTTGGAAAGTAGCGG
Found at i:1636462 original size:21 final size:21
Alignment explanation
Indices: 1636436--1636490 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
1636426 AGATGAATTA
*
1636436 TGGCTTTGCAACAGTGCATCT
1 TGGCTTTACAACAGTGCATCT
1636457 TGGCTTTACAACAGTGCATCT
1 TGGCTTTACAACAGTGCATCT
1636478 TGGCTTTACAACA
1 TGGCTTTACAACA
1636491 AATTTCCTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (21 bp):
TGGCTTTACAACAGTGCATCT
Found at i:1639658 original size:21 final size:21
Alignment explanation
Indices: 1639632--1639672 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1639622 GAAATAATGT
1639632 GCATACTTTGTTTAGACGAGA
1 GCATACTTTGTTTAGACGAGA
1639653 GCATACTTTGTTTAGACGAG
1 GCATACTTTGTTTAGACGAG
1639673 CAATAACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (21 bp):
GCATACTTTGTTTAGACGAGA
Found at i:1667358 original size:30 final size:32
Alignment explanation
Indices: 1667300--1667358 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 32
1667290 AATATTTTTA
* *
1667300 ATTAATCTCTCTCATAATTTTTAAAAATTCTC
1 ATTAAACTCTCTCATAAATTTTAAAAATTCTC
*
1667332 ATTAAACT-TCTCA-AAATTTTAGAAATT
1 ATTAAACTCTCTCATAAATTTTAAAAATT
1667359 TTAATTATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.50
31 5 0.21
32 7 0.29
ACGTcount: A:0.39, C:0.15, G:0.02, T:0.44
Consensus pattern (32 bp):
ATTAAACTCTCTCATAAATTTTAAAAATTCTC
Found at i:1669959 original size:3 final size:3
Alignment explanation
Indices: 1669953--1670018 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
1669943 TCATCATCAC
*
1669953 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1670001 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
1670019 AGAATAACTC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1670407 original size:50 final size:49
Alignment explanation
Indices: 1670312--1670506 Score: 178
Period size: 50 Copynumber: 3.9 Consensus size: 49
1670302 TCACACTTTT
* * * * ** * *
1670312 TTACATTGATATGAGTTAATTCTTTCAAATAATAAACTATTAATACTTA
1 TTACATTGATGTAAATTAATTATTTCATTTATTAAACTATCAATACTTA
* * * * *
1670361 TTGA-TTTCTATGTAAATTAATTCTTTCATTTATTGAACTATCAATACTTGT
1 TT-ACATT-GATGTAAATTAATTATTTCATTTATTAAACTATCAATACTT-A
* * * *
1670412 TTACATTGATGTAAATTACTTATTTCATTTACTAAACTATTAATACTTGC
1 TTACATTGATGTAAATTAATTATTTCATTTATTAAACTATCAATACTT-A
1670462 TTACATTGATGTAAATTACA-TATTTCATTTATTAAACTATCAATA
1 TTACATTGATGTAAATTA-ATTATTTCATTTATTAAACTATCAATA
1670507 TTGGTATCGA
Statistics
Matches: 119, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
49 4 0.03
50 111 0.93
51 4 0.03
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (49 bp):
TTACATTGATGTAAATTAATTATTTCATTTATTAAACTATCAATACTTA
Found at i:1670697 original size:20 final size:20
Alignment explanation
Indices: 1670672--1670716 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1670662 TTTGATATTC
*
1670672 ATATCCATGGGTTGGTATCA
1 ATATCCATGAGTTGGTATCA
*
1670692 ATATCCATGAGTTGGTATCG
1 ATATCCATGAGTTGGTATCA
1670712 ATATC
1 ATATC
1670717 GTAGGGAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (20 bp):
ATATCCATGAGTTGGTATCA
Found at i:1670857 original size:21 final size:21
Alignment explanation
Indices: 1670828--1670879 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1670818 TAAAGGTTTG
* *
1670828 ATATCCATACCCGATGAACTA
1 ATATTCATACCAGATGAACTA
* *
1670849 ATATTCATATCAGATGAACTG
1 ATATTCATACCAGATGAACTA
1670870 ATATTCATAC
1 ATATTCATAC
1670880 TAGAGGCTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (21 bp):
ATATTCATACCAGATGAACTA
Found at i:1674130 original size:23 final size:23
Alignment explanation
Indices: 1674098--1674148 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1674088 ATGTGCATTT
*
1674098 ATTTATTGTTCACGAACATGTTC
1 ATTTAATGTTCACGAACATGTTC
* ** *
1674121 GTTTAATGTTTGCGAACGTGTTC
1 ATTTAATGTTCACGAACATGTTC
1674144 ATTTA
1 ATTTA
1674149 GCCCTCATGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.45
Consensus pattern (23 bp):
ATTTAATGTTCACGAACATGTTC
Found at i:1676290 original size:20 final size:21
Alignment explanation
Indices: 1676265--1676305 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1676255 ATTTTCAAAC
1676265 TTTTAATTTAAAAAT-ATTTT
1 TTTTAATTTAAAAATAATTTT
*
1676285 TTTTAATTTAATAATAATTTT
1 TTTTAATTTAAAAATAATTTT
1676306 AGATTCTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTAATTTAAAAATAATTTT
Found at i:1676926 original size:26 final size:26
Alignment explanation
Indices: 1676890--1676943 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1676880 TGAGGTAAGG
1676890 GCTTACCTTGTGCACAAAGCAGAGGA
1 GCTTACCTTGTGCACAAAGCAGAGGA
1676916 GCTTACCTTGTGCACAAAGCAGAGGA
1 GCTTACCTTGTGCACAAAGCAGAGGA
1676942 GC
1 GC
1676944 CTACGGTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.19
Consensus pattern (26 bp):
GCTTACCTTGTGCACAAAGCAGAGGA
Found at i:1682563 original size:26 final size:26
Alignment explanation
Indices: 1682506--1682556 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1682496 TAAATTCAAT
*
1682506 ATAAAAATAAATTATTTTTTTACAAC
1 ATAAAAATAAATTATTTTTTTAAAAC
*
1682532 AAAAAAAT-AATTAATTTTTTTAAAA
1 ATAAAAATAAATT-ATTTTTTTAAAA
1682557 TTTAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (26 bp):
ATAAAAATAAATTATTTTTTTAAAAC
Found at i:1682727 original size:17 final size:17
Alignment explanation
Indices: 1682692--1682727 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 17
1682682 CATCTAGTTT
1682692 AAAATTTTAATTGATAAA
1 AAAATTTTAATTGA-AAA
1682710 AAAATTTATAATTGAAAA
1 AAAATTT-TAATTGAAAA
1682728 TTTTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
AAAATTTTAATTGAAAA
Found at i:1683076 original size:31 final size:32
Alignment explanation
Indices: 1683035--1683096 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
1683025 ACTTGACCCA
1683035 AAAACCAACCAATATAATAATGA-CTGACTCG
1 AAAACCAACCAATATAATAATGACCTGACTCG
* * * *
1683066 AAAATCAACCAATCTGATATTGACCTGACTC
1 AAAACCAACCAATATAATAATGACCTGACTC
1683097 AATACCCGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.23
Consensus pattern (32 bp):
AAAACCAACCAATATAATAATGACCTGACTCG
Found at i:1683438 original size:23 final size:24
Alignment explanation
Indices: 1683412--1683459 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1683402 GTATATTATA
* *
1683412 ATTTGATATTATTTTTTATT-TTT
1 ATTTGATAATAGTTTTTATTATTT
*
1683435 ATTTTATAATAGTTTTTATTATTT
1 ATTTGATAATAGTTTTTATTATTT
1683459 A
1 A
1683460 AAATATAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (24 bp):
ATTTGATAATAGTTTTTATTATTT
Found at i:1683459 original size:24 final size:23
Alignment explanation
Indices: 1683424--1683499 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
1683414 TTGATATTAT
1683424 TTTTTATTTTTATTTTATAATAG
1 TTTTTATTTTTATTTTATAATAG
***
1683447 TTTTTATTATTTAAAATATAAT-G
1 TTTTTATT-TTTATTTTATAATAG
* * * *
1683470 -ATTAAATTTTATTTTATCATAG
1 TTTTTATTTTTATTTTATAATAG
1683492 TTTTTATT
1 TTTTTATT
1683500 ATTTGATAAA
Statistics
Matches: 37, Mismatches: 13, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
21 9 0.24
22 5 0.14
23 13 0.35
24 10 0.27
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTTTATTTTTATTTTATAATAG
Found at i:1683895 original size:24 final size:24
Alignment explanation
Indices: 1683863--1683918 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
1683853 TAAAAGATCA
*
1683863 TGTTTTCATCCTTGATCTTGAATC
1 TGTTTTCATCCTCGATCTTGAATC
*
1683887 TGTTTTCATTCTCGATCTTGAATC
1 TGTTTTCATCCTCGATCTTGAATC
1683911 TGTTTTCA
1 TGTTTTCA
1683919 CACACACACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.20, G:0.12, T:0.52
Consensus pattern (24 bp):
TGTTTTCATCCTCGATCTTGAATC
Found at i:1683924 original size:2 final size:2
Alignment explanation
Indices: 1683917--1683954 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1683907 AATCTGTTTT
1683917 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1683955 TATTTGAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1683978 original size:2 final size:2
Alignment explanation
Indices: 1683971--1684257 Score: 567
Period size: 2 Copynumber: 144.0 Consensus size: 2
1683961 AATCTGTTTT
1683971 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1684013 CA CA CA CA CA CA CA -A CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1684054 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1684096 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1684138 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1684180 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1684222 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1684258 TATATATATA
Statistics
Matches: 284, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
1 1 0.00
2 283 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1684262 original size:2 final size:2
Alignment explanation
Indices: 1684257--1684282 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1684247 ACACACACAC
1684257 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
1684283 TCTTGTGGAT
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:1687204 original size:24 final size:24
Alignment explanation
Indices: 1687177--1687227 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1687167 TGTGGATCAC
*
1687177 CAAAAGTCACGTCTATTGATTCTT
1 CAAAAGTCACGTCTATTGAATCTT
* * *
1687201 CAAAAGTCATGTTTCTTGAATCTT
1 CAAAAGTCACGTCTATTGAATCTT
1687225 CAA
1 CAA
1687228 CTTGAAGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (24 bp):
CAAAAGTCACGTCTATTGAATCTT
Found at i:1691181 original size:24 final size:24
Alignment explanation
Indices: 1691154--1691204 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1691144 TGTGGATCAC
* *
1691154 CAAAAGTCACGTCTATTGATTCTT
1 CAAAAGTCAAGTCTATTGAATCTT
* *
1691178 CAAAAGTCAAGTTTCTTGAATCTT
1 CAAAAGTCAAGTCTATTGAATCTT
1691202 CAA
1 CAA
1691205 CTTGAAGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (24 bp):
CAAAAGTCAAGTCTATTGAATCTT
Found at i:1699127 original size:45 final size:45
Alignment explanation
Indices: 1699035--1699372 Score: 455
Period size: 45 Copynumber: 7.5 Consensus size: 45
1699025 CCTCCATTCA
* * * *
1699035 TGTTTATAATGCA-CCATTATGCATTTTTAACTATAACATATTTTTC
1 TGTTGATAATGCACCCA-TATGCA-TTTCAACTATAGCATACTTTTC
* * *
1699081 TGTTTACAATGCACCCATATGCATTTCAACTATGGCATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
*
1699126 TGTTGATAATGCACCTATATGCATTTCAACTATAGCATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
* * *
1699171 TGTTGACAATGCACCCATATGTATTTCAACTATAGCATACTTTTT
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
* *
1699216 TATTGATAATGCACCCATATGCATTTCAACTATAACATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
* *
1699261 TGTTGACAATGCACCCATATGCATTTCAACTATAACATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
*
1699306 TGTTGATAATGCACCCATATGCATTTCAACTATGGCAT-CTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
*** *
1699350 ATGCCAATAATGCACCTATATGC
1 -TGTTGATAATGCACCCATATGC
1699373 CTTTTTTATT
Statistics
Matches: 263, Mismatches: 27, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
44 6 0.02
45 236 0.90
46 18 0.07
47 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.39
Consensus pattern (45 bp):
TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
Found at i:1700015 original size:20 final size:21
Alignment explanation
Indices: 1699975--1700027 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
1699965 GATGTTTGCT
1699975 TGGTATCGATAC-CCTTACAA
1 TGGTATCGATACTCCTTACAA
1699995 TGGTATCGATACTACC-T-CAA
1 TGGTATCGATACT-CCTTACAA
*
1700015 TGGAATCGATACT
1 TGGTATCGATACT
1700028 GATTGAATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 27 0.90
21 1 0.03
22 2 0.07
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (21 bp):
TGGTATCGATACTCCTTACAA
Found at i:1703536 original size:19 final size:19
Alignment explanation
Indices: 1703512--1703549 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1703502 TATGTTTAAG
1703512 GGTATTTTAAAGTTTCTTA
1 GGTATTTTAAAGTTTCTTA
1703531 GGTATTTTAAAGTTTCTTA
1 GGTATTTTAAAGTTTCTTA
1703550 CCTATTAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.16, T:0.53
Consensus pattern (19 bp):
GGTATTTTAAAGTTTCTTA
Found at i:1703555 original size:19 final size:19
Alignment explanation
Indices: 1703514--1703555 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1703504 TGTTTAAGGG
**
1703514 TATTTTAAAGTTTCTTAGG
1 TATTTTAAAGTTTCTTACC
1703533 TATTTTAAAGTTTCTTACC
1 TATTTTAAAGTTTCTTACC
1703552 TATT
1 TATT
1703556 AAGGGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (19 bp):
TATTTTAAAGTTTCTTACC
Found at i:1703765 original size:20 final size:20
Alignment explanation
Indices: 1703737--1703784 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1703727 GTATATGTAT
* *
1703737 TACATGAACACTAAAGATAC
1 TACAAGAACAATAAAGATAC
*
1703757 TACAAGAACAATATAGATAC
1 TACAAGAACAATAAAGATAC
*
1703777 TAAAAGAA
1 TACAAGAA
1703785 TAGTACAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.19
Consensus pattern (20 bp):
TACAAGAACAATAAAGATAC
Found at i:1703797 original size:40 final size:40
Alignment explanation
Indices: 1703753--1703858 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 40
1703743 AACACTAAAG
1703753 ATACTACAAGAACAATATAGATACTAAAAGAATAGTACAA
1 ATACTACAAGAACAATATAGATACTAAAAGAATAGTACAA
* *** **
1703793 ATACTATAAGAA-AATTATAGATACCGCAAGAATAGTACTG
1 ATACTACAAGAACAA-TATAGATACTAAAAGAATAGTACAA
* * *
1703833 ATACTACAAAAACAGTATCGATACTA
1 ATACTACAAGAACAATATAGATACTA
1703859 GCATTGATAC
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
39 2 0.04
40 49 0.94
41 1 0.02
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.23
Consensus pattern (40 bp):
ATACTACAAGAACAATATAGATACTAAAAGAATAGTACAA
Found at i:1703816 original size:20 final size:19
Alignment explanation
Indices: 1703751--1703816 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
1703741 TGAACACTAA
*
1703751 AGATACTACAAGAACAATAT
1 AGATACTAAAAGAA-AATAT
* *
1703771 AGATACTAAAAGAATAGTAC
1 AGATACTAAAAGAA-AATAT
* *
1703791 AAATACTATAAGAAAATTAT
1 AGATACTAAAAGAAAA-TAT
1703811 AGATAC
1 AGATAC
1703817 CGCAAGAATA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 1 0.03
20 35 0.97
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.23
Consensus pattern (19 bp):
AGATACTAAAAGAAAATAT
Found at i:1710056 original size:23 final size:23
Alignment explanation
Indices: 1710025--1710079 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
1710015 TAAAAAGGTT
*
1710025 AGTAA-AAAACAAACAAATAAATA
1 AGTAATAAAACAAA-AAATAAAAA
1710048 A-TAATAAAACAAAAAATAAAAA
1 AGTAATAAAACAAAAAATAAAAA
1710070 AGTAATAAAA
1 AGTAATAAAA
1710080 TACAATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.76, C:0.05, G:0.04, T:0.15
Consensus pattern (23 bp):
AGTAATAAAACAAAAAATAAAAA
Found at i:1711362 original size:22 final size:22
Alignment explanation
Indices: 1711311--1711373 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
1711301 CTTGGACCTG
1711311 AAACAA-AA-AAATAAAAAT--
1 AAACAATAATAAATAAAAATAA
*
1711329 AAGCAATAAATAAATAAAAATAA
1 AAACAAT-AATAAATAAAAATAA
*
1711352 AAACAATAATAAATAATAATAA
1 AAACAATAATAAATAAAAATAA
1711374 TATATTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 5 0.14
20 2 0.05
21 10 0.27
22 14 0.38
23 6 0.16
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (22 bp):
AAACAATAATAAATAAAAATAA
Found at i:1711479 original size:37 final size:36
Alignment explanation
Indices: 1711406--1711712 Score: 312
Period size: 37 Copynumber: 8.6 Consensus size: 36
1711396 TTTCAAGAAC
**
1711406 ATATTATACGTATTTTCAAAATGTTTTAAAAACTAT
1 ATATTATATATATTTTCAAAATGTTTTAAAAACTAT
* *
1711442 ATAATATATATATTTTCAAAATGCCTTTAAAAAC--T
1 ATATTATATATATTTTCAAAATG-TTTTAAAAACTAT
*
1711477 ATA-TA-ATATA---T--AAATGTTTTCAAAACTAT
1 ATATTATATATATTTTCAAAATGTTTTAAAAACTAT
* * *
1711506 ATATTATTTAAATTTTCAAAAATGTTTTCAAAACTAT
1 ATATTATATATATTTTC-AAAATGTTTTAAAAACTAT
1711543 ATATTATATA-AGTTTTCAAAATGATTTTAAAAACTAT
1 ATATTATATATA-TTTTCAAAATG-TTTTAAAAACTAT
*
1711580 ATATTATATATATTTTCTAAAAAGTTTTAAAAACTAT
1 ATATTATATATATTTTC-AAAATGTTTTAAAAACTAT
* **
1711617 ATATTATGTAGT-TTTGAAAAATGTTTTAAAAACTAT
1 ATATTATATA-TATTTTCAAAATGTTTTAAAAACTAT
****
1711653 ATATTATATATATTTTCAAAACAAAATTAAAAACTAT
1 ATATTATATATATTTTCAAAA-TGTTTTAAAAACTAT
1711690 ATATTATATACGTATTTTCAAAA
1 ATATTATATA--TATTTTCAAAA
1711713 ACCGTTTGCA
Statistics
Matches: 229, Mismatches: 22, Indels: 37
0.80 0.08 0.13
Matches are distributed among these distances:
27 8 0.03
28 5 0.02
29 4 0.02
30 3 0.01
31 3 0.01
33 5 0.02
34 3 0.01
35 5 0.02
36 61 0.27
37 114 0.50
38 7 0.03
39 11 0.05
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (36 bp):
ATATTATATATATTTTCAAAATGTTTTAAAAACTAT
Found at i:1711502 original size:64 final size:64
Alignment explanation
Indices: 1711424--1711563 Score: 187
Period size: 64 Copynumber: 2.2 Consensus size: 64
1711414 CGTATTTTCA
* *
1711424 AAATGTTTTAAAAACTATATAATATATATATTTTC-AAAATGCCTTTAAAAACTATATAATATAT
1 AAATGTTTTCAAAACTATATAATATATAAATTTTCAAAAATG-CTTTAAAAACTATATAATATAT
* * * * *
1711488 AAATGTTTTCAAAACTATATATTATTTAAATTTTCAAAAATGTTTTCAAAACTATATATTATAT
1 AAATGTTTTCAAAACTATATAATATATAAATTTTCAAAAATGCTTTAAAAACTATATAATATAT
1711552 -AA-GTTTTCAAAA
1 AAATGTTTTCAAAA
1711564 TGATTTTAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
62 10 0.15
63 2 0.03
64 50 0.74
65 6 0.09
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (64 bp):
AAATGTTTTCAAAACTATATAATATATAAATTTTCAAAAATGCTTTAAAAACTATATAATATAT
Found at i:1711521 original size:25 final size:26
Alignment explanation
Indices: 1711471--1711526 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 26
1711461 AATGCCTTTA
1711471 AAAACTATATAATATATAAATGTTTTC
1 AAAACTATATAATATATAAA-GTTTTC
* *
1711498 AAAACTATATATTATTTAAA-TTTTC
1 AAAACTATATAATATATAAAGTTTTC
1711523 AAAA
1 AAAA
1711527 ATGTTTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 9 0.33
27 18 0.67
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (26 bp):
AAAACTATATAATATATAAAGTTTTC
Found at i:1711551 original size:101 final size:105
Alignment explanation
Indices: 1711373--1711699 Score: 334
Period size: 110 Copynumber: 3.1 Consensus size: 105
1711363 AATAATAATA
* * *
1711373 ATATATTATATATA-TAAAAATATTTTCAAGAAC-ATAT-TATACGT-ATTTTC-AAAATGTTTT
1 ATATATTATATATATTAAAAA-GTTTT-AAAAACTATATAT-TATGTAATTTTCAAAAATGTTTT
* *
1711433 AAAAACTATATAATATATATATTTTCAAAATGCCTTTAAAAAC
63 AAAAACTATATATTATATATATTTTCAAAATGACTTTAAAAAC
* * * *
1711476 -TATA-TA-ATATA-T-AAATGTTTTCAAAACTATATATTATTTAAATTTTCAAAAATGTTTTCA
1 ATATATTATATATATTAAAAAGTTTTAAAAACTATATATTATGT-AATTTTCAAAAATGTTTTAA
*
1711536 AAACTATATATTATATA-AGTTTTCAAAATGATTTTAAAAAC
65 AAACTATATATTATATATA-TTTTCAAAATGACTTTAAAAAC
* *
1711577 TATATATTATATATATTTTCTAAAAAGTTTTAAAAACTATATATTATGTAGTTTTGAAAAATGTT
1 -ATATATTATATATA---T-TAAAAAGTTTTAAAAACTATATATTATGTAATTTTCAAAAATGTT
** **
1711642 TTAAAAACTATATATTATATATATTTTCAAAACAAAATTAAAAAC
61 TTAAAAACTATATATTATATATATTTTCAAAATGACTTTAAAAAC
1711687 TATATATTATATA
1 -ATATATTATATA
1711700 CGTATTTTCA
Statistics
Matches: 187, Mismatches: 20, Indels: 27
0.80 0.09 0.12
Matches are distributed among these distances:
97 4 0.02
98 11 0.06
99 4 0.02
100 13 0.07
101 49 0.26
102 4 0.02
103 4 0.02
104 2 0.01
105 5 0.03
110 66 0.35
111 25 0.13
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (105 bp):
ATATATTATATATATTAAAAAGTTTTAAAAACTATATATTATGTAATTTTCAAAAATGTTTTAAA
AACTATATATTATATATATTTTCAAAATGACTTTAAAAAC
Found at i:1711665 original size:73 final size:72
Alignment explanation
Indices: 1711488--1711699 Score: 291
Period size: 73 Copynumber: 2.9 Consensus size: 72
1711478 TATAATATAT
* * * *
1711488 AAATGTTTTCAAAACTATATATTATTTAAATTTTCAAAAATGTTTTCAAAACTATATATTATATA
1 AAATGTTTTAAAAACTATATATTATATATATTTTCAAAAA-GTTTTAAAAACTATATATTATATA
*
1711553 AGTTTTCA
65 AGTTTTAA
*
1711561 AAATGATTTTAAAAACTATATATTATATATATTTTCTAAAAAGTTTTAAAAACTATATATTATGT
1 AAATG-TTTTAAAAACTATATATTATATATATTTTC-AAAAAGTTTTAAAAACTATATATTATAT
1711626 -AGTTTTGAA
64 AAGTTTT-AA
***
1711635 AAATGTTTTAAAAACTATATATTATATATATTTTCAAAACAAAATTAAAAACTATATATTATATA
1 AAATGTTTTAAAAACTATATATTATATATATTTTCAAAA-AGTTTTAAAAACTATATATTATATA
1711700 CGTATTTTCA
Statistics
Matches: 124, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
72 4 0.03
73 61 0.49
74 54 0.44
75 5 0.04
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (72 bp):
AAATGTTTTAAAAACTATATATTATATATATTTTCAAAAAGTTTTAAAAACTATATATTATATAA
GTTTTAA
Found at i:1711737 original size:2 final size:2
Alignment explanation
Indices: 1711726--1711766 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1711716 GTTTGCAAAC
* *
1711726 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1711767 AAATAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1713132 original size:84 final size:84
Alignment explanation
Indices: 1712353--1713133 Score: 903
Period size: 84 Copynumber: 9.3 Consensus size: 84
1712343 TAAGTTAAAT
* * * *
1712353 GTAATCGAACTCAAAGGTC-TTTGATGAG-AGATAACCCTTCTCA-CCTTGAGTTATGCTGTAAT
1 GTAATCGAACTCGAAGGTCTTTTGTTG-GCAGATAACCCTTCT-AGCCTTGAGTTATGCTGCAAA
* * *
1712415 TGATGCGCCTTTGAGCTGAGA
64 TGATGTGCCTTGGAGCTGAGC
* * * * **
1712436 GTAATCGAACTCGAAGGTC-TTGGTTGACAGATAAACCTTCTAGCCCTGAGTTATGCTATAAATG
1 GTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
* *
1712500 ATGTGCCTTTGAGCTGAGT
66 ATGTGCCTTGGAGCTGAGC
** * * * *
1712519 GTAATCGAACTCGAAGGTC-TTTGTTAACATATAACCCTTCTAGCCATGAGTTATGTTGTAAATG
1 GTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
* *
1712583 ATGTGCCTTGGAGCTTAGT
66 ATGTGCCTTGGAGCTGAGC
* * * * * ** *
1712602 GTAATCGAACTCTAAGGTCTTTGGTTGACAGATATCCGTT-TTTCACTTAAGTTATGCTGCAAAT
1 GTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGC-CTTGAGTTATGCTGCAAAT
* *
1712666 GATGTGCCTTTGAGCTGAGT
65 GATGTGCCTTGGAGCTGAGC
* *
1712686 GTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
1 GTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
*
1712750 ATGTGCCTTGGAGTTGAGC
66 ATGTGCCTTGGAGCTGAGC
* * * * * * * *
1712769 GTAGTCGAACTCGAAGGTCTTTTATTGGCAGATAGCCTTTCTCGCCTTGAGCTATACTGCATATG
1 GTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
* * *
1712834 TTGTGCCTTTGAGCTGAGT
66 ATGTGCCTTGGAGCTGAGC
* * *
1712853 GTAATTGAACTCGAAGGTCATTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATA
1 GTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
*
1712918 ATGAT-CCTTGGAGATGAGC
66 ATG-TGCCTTGGAGCTGAGC
* * * * * * * *
1712937 GTAGTCGAACTCGAAGGTCTTTTATTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGAAAATG
1 GTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
1713002 ATGTGCCTTGGAGCTGAGC
66 ATGTGCCTTGGAGCTGAGC
* *
1713021 GTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATG
1 GTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
1713086 ATGTGCCTTGGAGCTGAGC
66 ATGTGCCTTGGAGCTGAGC
* *
1713105 GTAGTCAAACTCGAAGGTCTTTTGTTGGC
1 GTAATCGAACTCGAAGGTCTTTTGTTGGC
1713134 CCCAACCCGT
Statistics
Matches: 596, Mismatches: 94, Indels: 15
0.85 0.13 0.02
Matches are distributed among these distances:
82 1 0.00
83 234 0.39
84 360 0.60
85 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (84 bp):
GTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
ATGTGCCTTGGAGCTGAGC
Found at i:1713572 original size:2 final size:2
Alignment explanation
Indices: 1713565--1713589 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1713555 GCATCCAAAC
1713565 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
1713590 CCAGGTACAT
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:1713989 original size:23 final size:23
Alignment explanation
Indices: 1713953--1714016 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1713943 CAGCTCGAAT
*
1713953 AAATGCATCGAAGTGCCACGTAC
1 AAATGCACCGAAGTGCCACGTAC
* * * *
1713976 AATTGCACCTAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAC
1713999 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
1714017 TATAAGATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAC
Found at i:1714299 original size:30 final size:29
Alignment explanation
Indices: 1714246--1714304 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
1714236 TGTAAACATA
* *
1714246 TCACATATTCATATAAACTCGTAGCTTCAT
1 TCACATATACATATAAACACGTAG-TTCAT
* *
1714276 TCACATATACATTTAATCACGTAGTTCAT
1 TCACATATACATATAAACACGTAGTTCAT
1714305 GTAAATTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (29 bp):
TCACATATACATATAAACACGTAGTTCAT
Found at i:1715583 original size:64 final size:63
Alignment explanation
Indices: 1715471--1715632 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 63
1715461 GCATTCTATA
* * * * *
1715471 GTGCATCTATGCACTACCCATGCATCGATACACAAATCACCTTTGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAA-GGG
* * *
1715535 GTGCATCGATGCACTCCTTATGCATCGATGCACTAA-CTACATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACAAATC-ACATTCGATGTTTCCATTTTTAAGGG
*
1715599 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
1715633 CTGAACAATT
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
63 3 0.04
64 71 0.86
65 9 0.11
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:1719131 original size:23 final size:23
Alignment explanation
Indices: 1719102--1719165 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
1719092 CAGCTTGTAT
1719102 AAATGCACCGAAGTGCCACGTA-
1 AAATGCACCGAAGTGCCACGTAG
* * *
1719124 AAATTGCACCTAAGTGTCGCGTAG
1 AAA-TGCACCGAAGTGCCACGTAG
1719148 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
1719166 TATAAGATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 3 0.09
23 28 0.82
24 3 0.09
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.17
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:1720626 original size:20 final size:22
Alignment explanation
Indices: 1720601--1720658 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1720591 TTCTCCTTGA
1720601 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
1720621 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
1720644 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1720659 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1720723 original size:64 final size:63
Alignment explanation
Indices: 1720646--1720807 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 63
1720636 TCTTTAACAT
* * *
1720646 GTGCATCGATGCACTACCCATGCATCGATACACAAA-TCACCTTCGATGTTTTCA-TTTTAAGAG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAACT-ACATTCGATGTTTCCATTTTTAA-AG
1720709 G
63 G
* * * *
1720710 GTGCATCGATGCACTCCTTATGCATCAATGCACTAACTACATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACAAACTACATTCGATGTTTCCATTTTTAAAGG
*
1720774 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
1720808 CTGAACAATT
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
63 2 0.02
64 71 0.86
65 10 0.12
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAACTACATTCGATGTTTCCATTTTTAAAGG
Found at i:1721854 original size:84 final size:84
Alignment explanation
Indices: 1721585--1721861 Score: 387
Period size: 84 Copynumber: 3.3 Consensus size: 84
1721575 GATGTTACAG
* * * * *
1721585 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAACTGAGTGA-ATTCGAACT
1 ATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAG-CATAGTCGAACT
*
1721649 CAAAGGTCTTTTGTTGGCAA
65 CGAAGGTCTTTTGTTGGCAA
** * * *
1721669 ATAACCCTTCTTTCATTGAGCTATTTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTC
*
1721734 GAAGGTCTTTTGTTGGAAA
66 GAAGGTCTTTTGTTGGCAA
*
1721753 ATAACCCTTCTTA-CCTTGAGCTATGTTGCAAATGATGTACCTTGGAGCTGAGCATAGTCGAACT
1 ATAACCCTTC-TAGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACT
*
1721817 CGAAGGTCTTTTGTTGGCAG
65 CGAAGGTCTTTTGTTGGCAA
*
1721837 ATAACCCTTCTAGCCTTGAGTTATG
1 ATAACCCTTCTAGCCTTGAGCTATG
1721862 CTGCCAATAG
Statistics
Matches: 170, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
83 2 0.01
84 167 0.98
85 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (84 bp):
ATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTC
GAAGGTCTTTTGTTGGCAA
Found at i:1724433 original size:9 final size:9
Alignment explanation
Indices: 1724421--1724455 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1724411 AATAATAATA
1724421 ATATATTAT
1 ATATATTAT
1724430 ATATATTAT
1 ATATATTAT
1724439 ATATATATAT
1 ATATAT-TAT
*
1724449 AAATATT
1 ATATATT
1724456 TTCAAAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATATATTAT
Found at i:1724472 original size:23 final size:24
Alignment explanation
Indices: 1724441--1724486 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1724431 TATATTATAT
1724441 ATATATATAAATATTTTCAAAAAC
1 ATATATATAAATATTTTCAAAAAC
**
1724465 ATAT-TATATGTATTTTCAAAAA
1 ATATATATAAATATTTTCAAAAA
1724487 TGTTATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (24 bp):
ATATATATAAATATTTTCAAAAAC
Found at i:1724538 original size:39 final size:39
Alignment explanation
Indices: 1724429--1724552 Score: 122
Period size: 39 Copynumber: 3.3 Consensus size: 39
1724419 TAATATATTA
* *
1724429 TATATATTATATATATATA-T--AAATATTTTCAAAAAC
1 TATATAATATATATATATATTCAAAATATTTTTAAAAAC
*
1724465 -ATAT--TATATGTAT-T-TTCAAAA-ATGTTATTAAAAAAC
1 TATATAATATATATATATATTCAAAATAT-TT-TT-AAAAAC
1724501 TATATAATATATATATATATTCAAAATATTTTTAAAAAC
1 TATATAATATATATATATATTCAAAATATTTTTAAAAAC
*
1724540 TATATGATATATA
1 TATATAATATATA
1724553 AATGTTTTCA
Statistics
Matches: 72, Mismatches: 4, Indels: 21
0.74 0.04 0.22
Matches are distributed among these distances:
32 2 0.03
33 10 0.14
34 5 0.07
35 5 0.07
36 6 0.08
37 4 0.06
39 26 0.36
40 3 0.04
41 9 0.12
42 2 0.03
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (39 bp):
TATATAATATATATATATATTCAAAATATTTTTAAAAAC
Found at i:1724563 original size:39 final size:41
Alignment explanation
Indices: 1724475--1724565 Score: 116
Period size: 39 Copynumber: 2.3 Consensus size: 41
1724465 ATATTATATG
*
1724475 TATTTTCAAAAATGTTATTAAAAAACTATATAATATATATA
1 TATTTTCAAAAATGTTATTAAAAAACTATATAATATATAAA
* *
1724516 TATATTCAAAATAT-TT-TT-AAAAACTATATGATATATAAA
1 TATTTTCAAAA-ATGTTATTAAAAAACTATATAATATATAAA
*
1724555 TGTTTTCAAAA
1 TATTTTCAAAA
1724566 CTATATATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 28 0.64
40 2 0.05
41 12 0.27
42 2 0.05
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (41 bp):
TATTTTCAAAAATGTTATTAAAAAACTATATAATATATAAA
Found at i:1724565 original size:103 final size:99
Alignment explanation
Indices: 1724438--1724668 Score: 288
Period size: 102 Copynumber: 2.3 Consensus size: 99
1724428 ATATATATTA
*
1724438 TATATATATATAAATATTTTCAAAAACATATTATATGTA-TTTTCAAAAATG-TTATTAAAAAAC
1 TATATATATATAAATATTTTCAAAAACATATTATAT-AAGTTTTC-AAAATGATT-TT-AAAAAC
*
1724501 TATATAATATATATATATATTCAAAATATTTT-TAAAAAC
62 TATAT-AT-TATATACATATTCAAAATATTTTGTAAAAAC
* *
1724540 TATATGATATATAAATGTTTTCAAAACTATATATTATATAAGTTTTCAAAATGATTTTAAAAACT
1 TATAT-ATATATAAATATTTTCAAAA--ACATATTATATAAGTTTTCAAAATGATTTTAAAAACT
* *
1724605 ATATATTATATACATTTTCAAAATATTTTGTATAAAC
63 ATATATTATATACATATTCAAAATATTTTGTAAAAAC
*
1724642 TATATATTATATACATATTTTCAAAAA
1 TATATA-TATATAAATATTTTCAAAAA
1724669 TCATTTGCAA
Statistics
Matches: 114, Mismatches: 8, Indels: 16
0.83 0.06 0.12
Matches are distributed among these distances:
100 1 0.01
101 22 0.19
102 35 0.31
103 30 0.26
104 9 0.08
105 17 0.15
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (99 bp):
TATATATATATAAATATTTTCAAAAACATATTATATAAGTTTTCAAAATGATTTTAAAAACTATA
TATTATATACATATTCAAAATATTTTGTAAAAAC
Found at i:1724568 original size:27 final size:25
Alignment explanation
Indices: 1724530--1724590 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 25
1724520 TTCAAAATAT
*
1724530 TTTTAAAAACTATATGA-TATATAAATG
1 TTTTCAAAACTATAT-ATTATAT-AA-G
1724557 TTTTCAAAACTATATATTATATAAG
1 TTTTCAAAACTATATATTATATAAG
1724582 TTTTCAAAA
1 TTTTCAAAA
1724591 TGATTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 10 0.31
26 3 0.09
27 19 0.59
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (25 bp):
TTTTCAAAACTATATATTATATAAG
Found at i:1724584 original size:25 final size:27
Alignment explanation
Indices: 1724530--1724590 Score: 83
Period size: 25 Copynumber: 2.3 Consensus size: 27
1724520 TTCAAAATAT
*
1724530 TTTTAAAAACTATATGATATATAAATG
1 TTTTCAAAACTATATGATATATAAATG
1724557 TTTTCAAAACTATAT-AT-TATATAA-G
1 TTTTCAAAACTATATGATATATA-AATG
1724582 TTTTCAAAA
1 TTTTCAAAA
1724591 TGATTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 14 0.44
26 4 0.12
27 14 0.44
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (27 bp):
TTTTCAAAACTATATGATATATAAATG
Found at i:1724651 original size:38 final size:37
Alignment explanation
Indices: 1724552--1724693 Score: 148
Period size: 37 Copynumber: 3.8 Consensus size: 37
1724542 TATGATATAT
*
1724552 AAATG-TTTTCAAAACTATATATTATATA-AGTTTTCA
1 AAATGATTTTAAAAACTATATATTATATACA-TTTTCA
1724588 AAATGATTTTAAAAACTATATATTATATACATTTTCA
1 AAATGATTTTAAAAACTATATATTATATACATTTTCA
*
1724625 AAAT-ATTTTGTATAAACTATATATTATATACATATTTTCAA
1 AAATGA-TTT-TAAAAACTATATATTATATAC--ATTTTC-A
* ** *
1724666 AAATCA-TTTGCAAACTATATAATATATA
1 AAATGATTTTAAAAACTATATATTATATA
1724694 TATAGATATA
Statistics
Matches: 93, Mismatches: 5, Indels: 13
0.84 0.05 0.12
Matches are distributed among these distances:
36 6 0.06
37 35 0.38
38 21 0.23
39 17 0.18
40 8 0.09
41 5 0.05
42 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (37 bp):
AAATGATTTTAAAAACTATATATTATATACATTTTCA
Found at i:1725083 original size:59 final size:59
Alignment explanation
Indices: 1725001--1725113 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
1724991 TTGATCCCTA
* * *
1725001 ACTATAGGGTATTGCTTTGTTGAGTCCTC-CGACTATTGAAAGTTAT-AAAATAGTCTCTG
1 ACTATAAGGTATTGCTTTATTGAGTCC-CACGACTATTAAAAGTT-TCAAAATAGTCTCTG
* *
1725060 ACTATAAGGTTTTGCTTTATTGAGTCCCATGACTATTAAAAGTTTCAAAATAGT
1 ACTATAAGGTATTGCTTTATTGAGTCCCACGACTATTAAAAGTTTCAAAATAGT
1725114 TACCTGACTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 2 0.04
59 45 0.96
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (59 bp):
ACTATAAGGTATTGCTTTATTGAGTCCCACGACTATTAAAAGTTTCAAAATAGTCTCTG
Found at i:1726946 original size:16 final size:16
Alignment explanation
Indices: 1726854--1726946 Score: 114
Period size: 16 Copynumber: 5.8 Consensus size: 16
1726844 TTTTAGTTGG
* *
1726854 ACCGAAAGTAACTCGA
1 ACCGAAAGCAACCCGA
* *
1726870 ACCAAAAGCAACTCGA
1 ACCGAAAGCAACCCGA
* *
1726886 ATCAAAAGCAACCCGA
1 ACCGAAAGCAACCCGA
*
1726902 ACCGAAAGCAACCTGA
1 ACCGAAAGCAACCCGA
1726918 ACCGAAAGCAACCCGA
1 ACCGAAAGCAACCCGA
*
1726934 ACTGAAAGCAACC
1 ACCGAAAGCAACC
1726947 TAAATTTAGT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 68 1.00
ACGTcount: A:0.46, C:0.31, G:0.16, T:0.06
Consensus pattern (16 bp):
ACCGAAAGCAACCCGA
Found at i:1727426 original size:30 final size:30
Alignment explanation
Indices: 1727385--1727444 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1727375 GCAACAACGG
* *
1727385 TTGACATGAAAATCTAAAGGTTGACTCGAA
1 TTGACACGAAAATCTAAAGGTTGACCCGAA
*
1727415 TTGACACGAAAATCTAATGGTTGACCCGAA
1 TTGACACGAAAATCTAAAGGTTGACCCGAA
1727445 CCAAAACCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (30 bp):
TTGACACGAAAATCTAAAGGTTGACCCGAA
Found at i:1727498 original size:31 final size:31
Alignment explanation
Indices: 1727425--1727539 Score: 86
Period size: 31 Copynumber: 3.7 Consensus size: 31
1727415 TTGACACGAA
* * *
1727425 AATCTAATGGTTGACCCGAACCAAAACCAACT
1 AATCTAAT-ATTGACCCGACCCAAAACCAACC
* * *
1727457 AATTTGATATTGACTCGACCCAAAACCAACC
1 AATCTAATATTGACCCGACCCAAAACCAACC
* ** * * *
1727488 AATCTAATATTAACTTGACTCGAAACTAACC
1 AATCTAATATTGACCCGACCCAAAACCAACC
* * *
1727519 GATCTGATTTTGACCCGACCC
1 AATCTAATATTGACCCGACCC
1727540 GATACTTGAA
Statistics
Matches: 63, Mismatches: 20, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
31 57 0.90
32 6 0.10
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.24
Consensus pattern (31 bp):
AATCTAATATTGACCCGACCCAAAACCAACC
Found at i:1728261 original size:2 final size:2
Alignment explanation
Indices: 1728254--1728280 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1728244 ATGTAGTTTG
1728254 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 T
1728281 TTATTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1729118 original size:2 final size:2
Alignment explanation
Indices: 1729111--1729159 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1729101 CGGGCATAAC
1729111 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
1729153 AT AT AT A
1 AT AT AT A
1729160 ATAAATAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1730335 original size:23 final size:22
Alignment explanation
Indices: 1730309--1730368 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
1730299 GAGTCAACTC
*
1730309 GTTGACTTTTACCGAGT-TAACCT
1 GTTGACTTTGACCGA-TCT-ACCT
*
1730332 GTTGACCGTTGACCGATCTACCT
1 GTTGA-CTTTGACCGATCTACCT
1730355 GTTGACTTTGACCG
1 GTTGACTTTGACCG
1730369 GTCAGATTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 8 0.25
23 15 0.47
24 9 0.28
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (22 bp):
GTTGACTTTGACCGATCTACCT
Found at i:1732621 original size:32 final size:32
Alignment explanation
Indices: 1732575--1732658 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
1732565 TTAGGTGACC
*
1732575 CTTGAGTAGGCTCTGAGGCCCCGAGAAACTTT
1 CTTGGGTAGGCTCTGAGGCCCCGAGAAACTTT
**
1732607 CTTGGGTAGGCTCTGAGGCCTTGAGAAACTTT
1 CTTGGGTAGGCTCTGAGGCCCCGAGAAACTTT
* *
1732639 CTTGGGTAGCCTCTTAGGCC
1 CTTGGGTAGGCTCTGAGGCC
1732659 TCAAGGCACT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.29
Consensus pattern (32 bp):
CTTGGGTAGGCTCTGAGGCCCCGAGAAACTTT
Found at i:1737990 original size:2 final size:2
Alignment explanation
Indices: 1737983--1738025 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1737973 AGTAGTAATA
1737983 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
1738025 A
1 A
1738026 GTCCAAAAAA
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:1739442 original size:38 final size:36
Alignment explanation
Indices: 1739362--1739450 Score: 124
Period size: 38 Copynumber: 2.4 Consensus size: 36
1739352 TAAGGGGACA
*
1739362 ATCCTAAGAAGGACTCAAACGAAATTCTAGAAAAAT
1 ATCCTAAGAATGACTCAAACGAAATTCTAGAAAAAT
* *
1739398 AGTCCTAAGAATGACTCAAATGAATTTTCTAGAAAAAT
1 A-TCCTAAGAATGACTCAAACGAA-ATTCTAGAAAAAT
1739436 GATCCTAAGAATGAC
1 -ATCCTAAGAATGAC
1739451 AAAATAGTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
36 1 0.02
37 20 0.43
38 25 0.53
39 1 0.02
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.24
Consensus pattern (36 bp):
ATCCTAAGAATGACTCAAACGAAATTCTAGAAAAAT
Found at i:1740432 original size:54 final size:54
Alignment explanation
Indices: 1740355--1740741 Score: 442
Period size: 54 Copynumber: 7.1 Consensus size: 54
1740345 TTACAGTTAT
**
1740355 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAGG
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAA
* **
1740409 CATTAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAA
* * * * *
1740463 CATTAAGAAACACCTGAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAA
* *
1740517 CATCAAGAAACTCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAATATA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAA-A-A
* * * *
1740573 TCATCAAGAAACTTCC-AAAAATCAGACTTAGCTCCTTTAAAAATT-ATTTGAAAA
1 -CATCAAGAAAC-CCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAA
* * * * * *
1740627 CATTAATAAACCCCTGAAAATTAGGTTTATCTCCTTTGAAAAA-TCATTTGAAGAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTT-AAAAATTCATTTGAA-AA
*
1740682 -ATCACA-AAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATATTGATTTGAAAA
1 CATCA-AGAAACCCCTAAAAATTAGGCTTAGCTTCTTT-AAAA-ATTCATTTGAAAA
*
1740737 TATCA
1 CATCA
1740742 TATTAGGTAA
Statistics
Matches: 289, Mismatches: 32, Indels: 22
0.84 0.09 0.06
Matches are distributed among these distances:
52 2 0.01
53 27 0.09
54 193 0.67
55 8 0.03
56 20 0.07
57 36 0.12
58 3 0.01
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (54 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAAA
Found at i:1740699 original size:164 final size:164
Alignment explanation
Indices: 1740355--1740742 Score: 491
Period size: 164 Copynumber: 2.4 Consensus size: 164
1740345 TTACAGTTAT
** *
1740355 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTG-AA-GGCATTAAGAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAATATCATCAAGAA
* * * **
1740418 ACCCCTAAAAATTAGGCTTAGCTTCTTTCCAAATTCATTTGAAAACATTAAGAAACACCTGAAAA
66 ACCCCTAAAAATCAGACTTAGCTCCTTTAAAAATTCATTTGAAAACATTAAGAAACACCTGAAAA
* *
1740483 TCAGGCTTAGCTTCTTTCAAAATTCATTTGAAAA
131 TCAGGCTTAGCTCCTTTCAAAAATCATTTGAAAA
* *
1740517 CATCAAGAAACTCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAATATATCATCAAGA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAA-ATATCATCAAGA
* * *
1740582 AACTTCC-AAAAATCAGACTTAGCTCCTTTAAAAATT-ATTTGAAAACATTAATAAACCCCTGAA
65 AAC-CCCTAAAAATCAGACTTAGCTCCTTTAAAAATTCATTTGAAAACATTAAGAAACACCTGAA
* * * *
1740645 AATTAGGTTTATCTCCTTTGAAAAATCATTTGAAGAA
129 AATCAGGCTTAGCTCCTTTCAAAAATCATTTGAA-AA
*
1740682 -ATCACA-AAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATATTGATTTGAAAATATCAT
1 CATCA-AGAAACCCCTAAAAATTAGGCTTAGCTTCTTT-AAAA-ATTCATTTG-AAATATCAT
1740743 ATTAGGTAAC
Statistics
Matches: 195, Mismatches: 22, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
162 48 0.25
163 1 0.01
164 87 0.45
165 40 0.21
166 17 0.09
167 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (164 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAATATCATCAAGAA
ACCCCTAAAAATCAGACTTAGCTCCTTTAAAAATTCATTTGAAAACATTAAGAAACACCTGAAAA
TCAGGCTTAGCTCCTTTCAAAAATCATTTGAAAA
Found at i:1742823 original size:4 final size:4
Alignment explanation
Indices: 1742814--1742870 Score: 50
Period size: 4 Copynumber: 14.8 Consensus size: 4
1742804 TTGAAGTATT
* *
1742814 TTTC TTTC -TTC TTT- TTTCC TTTT TTTCC TTTC TTT- TCTC TTTC -TTC
1 TTTC TTTC TTTC TTTC TTT-C TTTC TTT-C TTTC TTTC TTTC TTTC TTTC
1742860 TTTC TTTC TTT
1 TTTC TTTC TTT
1742871 TCTCTCATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
3 11 0.26
4 26 0.60
5 6 0.14
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:1744811 original size:33 final size:31
Alignment explanation
Indices: 1744756--1744816 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 31
1744746 GACAAGACAA
* *
1744756 AAAGAAATCAAGTTAGTTAAAATGATTATTC
1 AAAGAAATCAAGTTAGTAAAAATAATTATTC
*
1744787 AAAGAAATGTAAGCTTAGTAAAAATAATTA
1 AAAGAAAT-CAAG-TTAGTAAAAATAATTA
1744817 AATACAACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 8 0.32
32 3 0.12
33 14 0.56
ACGTcount: A:0.52, C:0.05, G:0.13, T:0.30
Consensus pattern (31 bp):
AAAGAAATCAAGTTAGTAAAAATAATTATTC
Found at i:1750118 original size:15 final size:14
Alignment explanation
Indices: 1750100--1750155 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
1750090 CGTTTAGTAC
1750100 TTTATAATTTAACA
1 TTTATAATTTAACA
* *
1750114 TTT-TAATTAAAAAA
1 TTTATAATT-TAACA
1750128 CTTTATAATTTAACA
1 -TTTATAATTTAACA
*
1750143 TTTTATAAATTAA
1 -TTTATAATTTAA
1750156 TTTAATGGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
13 5 0.15
14 6 0.18
15 17 0.52
16 5 0.15
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTATAATTTAACA
Found at i:1754462 original size:5 final size:5
Alignment explanation
Indices: 1754454--1754484 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1754444 CGACCCGACC
1754454 CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
1754485 GCAGCGGCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.35, C:0.23, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:1754714 original size:34 final size:30
Alignment explanation
Indices: 1754684--1754744 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1754674 ACAATTTAAG
1754684 ACAAAATGGTTTTTGGACTTGAATTAAATTT-
1 ACAAAAT-GTTTTTGGACTT-AATTAAATTTA
* *
1754715 ACAATATGTTTTTGGACTTAATTGAATTTA
1 ACAAAATGTTTTTGGACTTAATTAAATTTA
1754745 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 9 0.33
30 12 0.44
31 6 0.22
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (30 bp):
ACAAAATGTTTTTGGACTTAATTAAATTTA
Found at i:1754860 original size:15 final size:15
Alignment explanation
Indices: 1754840--1754869 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1754830 ATTGCCCAGG
1754840 GGGTACAGATACCCC
1 GGGTACAGATACCCC
1754855 GGGTACAGATACCCC
1 GGGTACAGATACCCC
1754870 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:1755003 original size:21 final size:21
Alignment explanation
Indices: 1754977--1755018 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1754967 ATTTGAATAT
*
1754977 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1754998 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1755019 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Done.