Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 51
Found at i:1906652 original size:24 final size:25
Alignment explanation
Indices: 1906603--1906652 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1906593 TAAATCCGGC
*
1906603 GATTTTTTAAACAGAGACGGATACG
1 GATTTTTTAAACAGAGACGGAGACG
*
1906628 GATTTTTTAAACGGAGAC-GAGACG
1 GATTTTTTAAACAGAGACGGAGACG
1906652 G
1 G
1906653 GAGACCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (25 bp):
GATTTTTTAAACAGAGACGGAGACG
Found at i:1910113 original size:208 final size:208
Alignment explanation
Indices: 1909715--1910132 Score: 734
Period size: 208 Copynumber: 2.0 Consensus size: 208
1909705 TTCGTTTGGG
* *
1909715 TCCAAAATTTCCACCAACATAATTATGGCAAAAAGGCTAAAATAGAATGTAATTCATTTTCTGGC
1 TCCAAAATTTCCACCAACATAATCATGGCAAAAAGGCTAAAATAGAATGGAATTCATTTTCTGGC
1909780 ACACATCTCTGGATCATTAGATCATAACAAAATTTCCATAGATATGGATCATCCCACACATAATA
66 ACACATCTCTGGATCATTAGATCATAACAAAATTTCCATAGATATGGATCATCCCACACATAATA
* *
1909845 CTTGGAGTCACTTTTTATATTTGCTCTCCTAGATTAAGGCCATGAGGTAGATTTTCTGTAACTAA
131 CTTGGAGTCACTTTTTATATTTGCTCTCCTAGATTAAGGCCATGAGATAGACTTTCTGTAACTAA
1909910 ATAATTTACCATA
196 ATAATTTACCATA
*
1909923 TCCAAAATTTCCACCTCAAGCATAATCATGGC-AAAAGGCTAAAATAGAATGGAATTCGTTTTCT
1 TCCAAAATTTCCA-C-CAA-CATAATCATGGCAAAAAGGCTAAAATAGAATGGAATTCATTTTCT
*
1909987 GGTACACATCTCTGGATCATTAGATCATAAC-AAATTTCCATAGATATGGATCATCCCACACATA
63 GGCACACATCTCTGGATCATTAGATCATAACAAAATTTCCATAGATATGGATCATCCCACACATA
1910051 ATACTTGGAGTCAC-TTTTATATTTGCTCTCCTAGATTAAGGCCATGAGATAGACTTTCTGTAAC
128 ATACTTGGAGTCACTTTTTATATTTGCTCTCCTAGATTAAGGCCATGAGATAGACTTTCTGTAAC
1910115 TAAATAATTTACCATA
193 TAAATAATTTACCATA
1910131 TC
1 TC
1910133 TGCGTACCAA
Statistics
Matches: 201, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
208 79 0.39
209 48 0.24
210 63 0.31
211 11 0.05
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (208 bp):
TCCAAAATTTCCACCAACATAATCATGGCAAAAAGGCTAAAATAGAATGGAATTCATTTTCTGGC
ACACATCTCTGGATCATTAGATCATAACAAAATTTCCATAGATATGGATCATCCCACACATAATA
CTTGGAGTCACTTTTTATATTTGCTCTCCTAGATTAAGGCCATGAGATAGACTTTCTGTAACTAA
ATAATTTACCATA
Found at i:1910467 original size:13 final size:13
Alignment explanation
Indices: 1910429--1910467 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1910419 TGGTAGAGTG
*
1910429 TTGCATTGAGCAG
1 TTGCATTGAGCAA
1910442 TTGCATTGAGCAA
1 TTGCATTGAGCAA
1910455 TTGCATTGAGCAA
1 TTGCATTGAGCAA
1910468 CATTCAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (13 bp):
TTGCATTGAGCAA
Found at i:1912983 original size:36 final size:36
Alignment explanation
Indices: 1912941--1913015 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
1912931 TATAGCTAAA
*
1912941 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1912977 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1913013 AAA
1 AAA
1913016 TCCCGAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:1917566 original size:26 final size:25
Alignment explanation
Indices: 1917518--1917581 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 25
1917508 ATTTTCTTGT
*
1917518 TTCATATCATTTTAAATAGTTCATG
1 TTCATATCATTTAAAATAGTTCATG
1917543 TTCATATCATTTAAAATTTA-TTCATG
1 TTCATATCATTTAAAA--TAGTTCATG
1917569 TTCATATCATTTA
1 TTCATATCATTTA
1917582 CACGTCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
25 15 0.42
26 19 0.53
27 2 0.06
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (25 bp):
TTCATATCATTTAAAATAGTTCATG
Found at i:1920335 original size:21 final size:21
Alignment explanation
Indices: 1920309--1920349 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1920299 GACGTACTTG
1920309 GGTTATCGT-CATAACCTTTAA
1 GGTTATC-TCCATAACCTTTAA
1920330 GGTTATCTCCATAACCTTTA
1 GGTTATCTCCATAACCTTTA
1920350 GGGGTATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (21 bp):
GGTTATCTCCATAACCTTTAA
Found at i:1922628 original size:21 final size:20
Alignment explanation
Indices: 1922601--1922740 Score: 109
Period size: 21 Copynumber: 6.8 Consensus size: 20
1922591 AATCAGTTTC
1922601 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1922622 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1922643 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1922663 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
* **
1922684 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1922704 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1922725 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1922741 ACACATAAAT
Statistics
Matches: 91, Mismatches: 25, Indels: 7
0.74 0.20 0.06
Matches are distributed among these distances:
20 31 0.34
21 60 0.66
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1922690 original size:20 final size:20
Alignment explanation
Indices: 1922601--1922759 Score: 106
Period size: 21 Copynumber: 7.8 Consensus size: 20
1922591 AATCAGTTTC
* *
1922601 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGAAT-AT
* *
1922622 GAAAATCGCAATGCG-ATAGT
1 CAAAATCGCAACGCGAATA-T
* ** * *
1922642 ACAAATTCGCATTGCGATTTT
1 -CAAAATCGCAACGCGAATAT
1922663 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* ** * *
1922684 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGAATAT
1922704 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* *
1922725 GAAAATCGCAACGCGAACA-
1 CAAAATCGCAACGCGAATAT
1922744 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
1922760 TATCCGTAAA
Statistics
Matches: 105, Mismatches: 28, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
19 1 0.01
20 47 0.45
21 56 0.53
22 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGAATAT
Found at i:1922702 original size:41 final size:41
Alignment explanation
Indices: 1922623--1922734 Score: 174
Period size: 41 Copynumber: 2.7 Consensus size: 41
1922613 GCGATTCTTG
*
1922623 AAAATCGCAATGCG-ATA-GTACAAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATG-A-AAA-TCGCATTGCGATTTTCC
1922665 AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
1922706 AAAATCGCAACGCGAATATGAAAATCGCA
1 AAAATCGCAACGCGAATATGAAAATCGCA
1922735 ACGCGAACAC
Statistics
Matches: 67, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
41 46 0.69
42 16 0.24
43 4 0.06
44 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
Found at i:1922769 original size:20 final size:20
Alignment explanation
Indices: 1922707--1922900 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1922697 CGATTTTCCA
* ** *
1922707 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1922727 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1922747 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1922767 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1922787 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1922807 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1922827 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1922847 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1922867 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1922888 AAATCGCAACGCG
1 AAATCGCAACGCG
1922901 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1922799 original size:60 final size:60
Alignment explanation
Indices: 1922707--1922900 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1922697 CGATTTTCCA
* ** * *
1922707 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1922767 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
1922827 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1922888 AAATCGCAACGCG
1 AAATCGCAACGCG
1922901 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1923318 original size:33 final size:33
Alignment explanation
Indices: 1923279--1923349 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1923269 TTCACTTAGA
* *
1923279 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
1923312 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
1923345 TTTCA
1 TTTCA
1923350 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:1923455 original size:21 final size:20
Alignment explanation
Indices: 1923429--1923534 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
1923419 TGCAGAAGAG
1923429 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
1923450 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
1923470 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
1923491 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
1923505 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
1923524 TCGCAACGAGA
1 TCGCAACGAGA
1923535 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1923473 original size:20 final size:21
Alignment explanation
Indices: 1923427--1923505 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
1923417 TTTGCAGAAG
*
1923427 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
1923449 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
1923468 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
1923490 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
1923506 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:1923486 original size:41 final size:38
Alignment explanation
Indices: 1923422--1923538 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
1923412 TTCAATTTGC
* *
1923422 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1923460 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1923501 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1923534 AGAAT
1 AGAAT
1923539 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:1923511 original size:14 final size:14
Alignment explanation
Indices: 1923492--1923545 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1923482 AAATGAAAAG
1923492 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
1923506 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
1923525 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
1923539 CGCAACG
1 CGCAACG
1923546 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:1923521 original size:33 final size:33
Alignment explanation
Indices: 1923481--1923550 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
1923471 CGCAACGAGA
1923481 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
1923514 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1923547 GAAA
1 GAAA
1923551 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:1923557 original size:33 final size:33
Alignment explanation
Indices: 1923487--1923561 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
1923477 GAGAGAAATG
* **
1923487 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1923520 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1923553 AAAATCGCA
1 AAAATCGCA
1923562 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:1923616 original size:19 final size:17
Alignment explanation
Indices: 1923556--1923672 Score: 81
Period size: 14 Copynumber: 7.1 Consensus size: 17
1923546 CGAAACCAAA
*
1923556 ATCGCATTGCGATTTTC
1 ATCGCGTTGCGATTTTC
1923573 ATTCGCGTTGCGA--TTC
1 A-TCGCGTTGCGATTTTC
*
1923589 -TCTCGTTGCGATTTTC
1 ATCGCGTTGCGATTTTC
1923605 ATTTCGCGTTGCGA--TTC
1 A--TCGCGTTGCGATTTTC
* *
1923622 -TCTCGTTGCGATTGTC
1 ATCGCGTTGCGATTTTC
1923638 ATCTCGCGTTGCGA--TTC
1 A--TCGCGTTGCGATTTTC
*
1923655 -TCTCGTTGCGATTTTC
1 ATCGCGTTGCGATTTTC
1923671 AT
1 AT
1923673 TTCAACCAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 28
0.68 0.07 0.25
Matches are distributed among these distances:
14 30 0.38
16 11 0.14
17 7 0.09
18 10 0.13
19 20 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.43
Consensus pattern (17 bp):
ATCGCGTTGCGATTTTC
Found at i:1923616 original size:33 final size:33
Alignment explanation
Indices: 1923562--1923675 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
1923552 CAAAATCGCA
1923562 TTGCGATTTTCA-TTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1923594 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1923627 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1923660 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1923676 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 12 0.16
33 65 0.84
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1927098 original size:14 final size:14
Alignment explanation
Indices: 1927079--1927114 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1927069 ATTGTTTAAT
1927079 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1927093 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1927107 TGATTTGT
1 TGATTTGT
1927115 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1927245 original size:19 final size:19
Alignment explanation
Indices: 1927221--1927320 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
1927211 AAAATTGACT
1927221 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1927240 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1927259 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1927273 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1927292 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1927312 ATCGCAATG
1 ATCGCAATG
1927321 GGAGAATCGC
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1927350 original size:53 final size:53
Alignment explanation
Indices: 1927221--1927337 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
1927211 AAAATTGACT
1927221 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
1927273 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1927326 ATCGCAATGCGA
1 ATCGCAATGCGA
1927338 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1927355 original size:19 final size:19
Alignment explanation
Indices: 1927327--1927494 Score: 177
Period size: 19 Copynumber: 9.6 Consensus size: 19
1927317 AATGGGAGAA
* *
1927327 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1927346 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1927362 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1927379 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1927398 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1927414 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1927431 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1927450 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1927466 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1927483 TCCGCATTGCGA
1 T-CGCATTGCGA
1927495 AATGTAATGG
Statistics
Matches: 125, Mismatches: 8, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
14 18 0.14
16 21 0.17
17 18 0.14
18 2 0.02
19 60 0.48
20 6 0.05
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1927370 original size:33 final size:33
Alignment explanation
Indices: 1927333--1927494 Score: 159
Period size: 33 Copynumber: 4.7 Consensus size: 33
1927323 AGAATCGCAA
*
1927333 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1927366 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
1927404 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
1927437 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1927470 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
1927495 AATGTAATGG
Statistics
Matches: 104, Mismatches: 13, Indels: 23
0.74 0.09 0.16
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 49 0.47
34 10 0.10
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1927390 original size:52 final size:52
Alignment explanation
Indices: 1927327--1927494 Score: 309
Period size: 52 Copynumber: 3.2 Consensus size: 52
1927317 AATGGGAGAA
* *
1927327 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1927379 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1927431 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1927483 TCCGCATTGCGA
1 T-CGCATTGCGA
1927495 AATGTAATGG
Statistics
Matches: 113, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 103 0.91
53 10 0.09
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1927577 original size:19 final size:19
Alignment explanation
Indices: 1927553--1927650 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1927543 AAAATTGACT
1927553 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1927572 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1927591 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1927605 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1927624 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1927644 ATCGCAA
1 ATCGCAA
1927651 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1927682 original size:53 final size:53
Alignment explanation
Indices: 1927553--1927669 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1927543 AAAATTGACT
1927553 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1927605 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1927658 ATCGCAATGCGA
1 ATCGCAATGCGA
1927670 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1929998 original size:12 final size:12
Alignment explanation
Indices: 1929981--1930005 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1929971 TCTTCGGGGA
1929981 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1929993 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1930005 C
1 C
1930006 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1930213 original size:24 final size:24
Alignment explanation
Indices: 1930179--1930225 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1930169 CTGAAACATC
1930179 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1930203 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1930226 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1930932 original size:20 final size:20
Alignment explanation
Indices: 1930904--1931153 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
1930894 AAATTTCAGT
* *
1930904 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1930924 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1930944 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1930964 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1930984 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1931004 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
1931024 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1931044 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1931064 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1931084 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
1931104 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
1931124 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
1931144 GTTGCGATTT
1 GTTGCGATTT
1931154 TGGAAAATCG
Statistics
Matches: 200, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:1931170 original size:21 final size:21
Alignment explanation
Indices: 1931140--1931222 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1931130 ATTTTCATAT
*
1931140 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1931161 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1931182 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1931203 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1931223 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1931213 original size:42 final size:43
Alignment explanation
Indices: 1931120--1931218 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1931110 ATTTATGTGT
* *
1931120 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1931161 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1931203 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1931219 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1939972 original size:16 final size:16
Alignment explanation
Indices: 1939951--1939984 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1939941 CCTTTCCACA
1939951 GCCTGAATCCATTTGT
1 GCCTGAATCCATTTGT
1939967 GCCTGAATCCATTTGT
1 GCCTGAATCCATTTGT
1939983 GC
1 GC
1939985 AGATGAGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (16 bp):
GCCTGAATCCATTTGT
Found at i:1940683 original size:43 final size:43
Alignment explanation
Indices: 1940628--1940862 Score: 256
Period size: 43 Copynumber: 5.4 Consensus size: 43
1940618 TTTCAAGAAA
1940628 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-GACAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGA-AGAC
* *
1940671 AAACGCCACAATAGATGTTGATATTTAGCGGCGTTTGGAAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
* *
1940714 AAACGCCGCAATAGATGTTGATATTTAGCGGCATTTGGAAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
* * * ***** *
1940757 AAACGCCGCAGTAGGTGTCGATTTTTAGCGGCGTTTTTCCCAG
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
* * * ** **
1940800 AAACGCCGCAGTAGGTGTTGATGTTTAGTGGCGTTTTTTATTAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCG-TTTGGAAGAC
*
1940844 AAACGCCGCAATAAGTGTT
1 AAACGCCGCAATAGGTGTT
1940863 AAGGTTTCGC
Statistics
Matches: 166, Mismatches: 24, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
43 141 0.85
44 25 0.15
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGAAGAC
Found at i:1940881 original size:44 final size:42
Alignment explanation
Indices: 1940800--1940905 Score: 97
Period size: 44 Copynumber: 2.5 Consensus size: 42
1940790 TTTTTCCCAG
* * * * * *
1940800 AAACGCCGCAGTAGGTGTTGATGTTTAGTGGCGTTTTTTA-TT
1 AAACGCCGCAATAAGTGTTAAGGTTTAGCGGC-ATTTTTACTT
*
1940842 ACAAACGCCGCAATAAGTGTTAAGGTTTCGCGGCATTTTTAGCTT
1 --AAACGCCGCAATAAGTGTTAAGGTTTAGCGGCATTTTTA-CTT
*
1940887 AAACGCCGCAATATGTGTT
1 AAACGCCGCAATAAGTGTT
1940906 TGATTTGGCG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
43 24 0.46
44 26 0.50
45 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (42 bp):
AAACGCCGCAATAAGTGTTAAGGTTTAGCGGCATTTTTACTT
Found at i:1941372 original size:21 final size:21
Alignment explanation
Indices: 1941305--1941361 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
1941295 ATATGTTGCT
1941305 TCTCTTTGTGCTGCCGCTGCC
1 TCTCTTTGTGCTGCCGCTGCC
1941326 TCTCTTTGTGCTGCCGCTGCC
1 TCTCTTTGTGCTGCCGCTGCC
1941347 TCTCTTTGTGCTGCC
1 TCTCTTTGTGCTGCC
1941362 ACTGTTTCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.00, C:0.37, G:0.23, T:0.40
Consensus pattern (21 bp):
TCTCTTTGTGCTGCCGCTGCC
Found at i:1941386 original size:42 final size:42
Alignment explanation
Indices: 1941305--1941387 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
1941295 ATATGTTGCT
* * * *
1941305 TCTCTTTGTGCTGCCGCTGCCTCTCTTTGTGCTGCCGCTGCC
1 TCTCTTTGTGCTGCCACTGCCTCTCTCTCTGCTGACGCTGCC
** *
1941347 TCTCTTTGTGCTGCCACTGTTTCTCTCTCTGCTTACGCTGC
1 TCTCTTTGTGCTGCCACTGCCTCTCTCTCTGCTGACGCTGC
1941388 TGCTCTGGCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.02, C:0.36, G:0.20, T:0.41
Consensus pattern (42 bp):
TCTCTTTGTGCTGCCACTGCCTCTCTCTCTGCTGACGCTGCC
Found at i:1941423 original size:21 final size:21
Alignment explanation
Indices: 1941369--1941424 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
1941359 GCCACTGTTT
*
1941369 CTCTCTCTGCTTACGCTGCTG
1 CTCTCTCTGCTTCCGCTGCTG
**
1941390 CTCTGGCTGCTTCCGCTGCTG
1 CTCTCTCTGCTTCCGCTGCTG
1941411 CTCTCTCTGCTTCC
1 CTCTCTCTGCTTCC
1941425 CTTGCTTCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.02, C:0.41, G:0.20, T:0.38
Consensus pattern (21 bp):
CTCTCTCTGCTTCCGCTGCTG
Found at i:1944857 original size:46 final size:46
Alignment explanation
Indices: 1944790--1944880 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
1944780 TAGCGATTCT
* *
1944790 GAAATACCTACATGGTCAAACAAGACAGAGGAACGAAGGCAAGTAC
1 GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTAC
1944836 GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTA
1 GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTA
1944881 AGTACCTTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.48, C:0.16, G:0.24, T:0.11
Consensus pattern (46 bp):
GAAATAACTACATGGTCAAACAAGAAAGAGGAACGAAGGCAAGTAC
Found at i:1945836 original size:41 final size:40
Alignment explanation
Indices: 1945791--1945900 Score: 118
Period size: 41 Copynumber: 2.7 Consensus size: 40
1945781 CTAATACTTT
1945791 GCGGCATTTCTACGAAAACGCCACTAAAGTACG-AGTCTATA
1 GCGGCATTTCTACG-AAACGCCACTAAAGTA-GAAGTCTATA
* *
1945832 GCGGCGTTTTTATACG-AACGCCACTAAAGTAGAAGTCTATA
1 GCGGC--ATTTCTACGAAACGCCACTAAAGTAGAAGTCTATA
*
1945873 GCAGCATTTTCATAC-AAACGCCACTAAA
1 GCGGCA-TTTC-TACGAAACGCCACTAAA
1945901 TTACAAATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
40 4 0.07
41 47 0.81
43 7 0.12
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (40 bp):
GCGGCATTTCTACGAAACGCCACTAAAGTAGAAGTCTATA
Found at i:1946381 original size:57 final size:57
Alignment explanation
Indices: 1946162--1946349 Score: 367
Period size: 57 Copynumber: 3.3 Consensus size: 57
1946152 ATTAAAACAG
1946162 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1946219 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
*
1946276 AAGTACTTATGCATAAAACTACTTAAAAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1946333 AAGTACTTATGCATAAA
1 AAGTACTTATGCATAAA
1946350 CAGTCTTCAC
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
57 130 1.00
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (57 bp):
AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
Found at i:1947407 original size:41 final size:41
Alignment explanation
Indices: 1947356--1947449 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
1947346 CACATGTTTT
* *
1947356 TTGCGGCGTTTATA-CAATAAACGTCGCTATAT-TAC-ACTATA
1 TTGCGGCGTTT-TAGCAA-AAACGCCGCTAAATAT-CTACTATA
*
1947397 TTGCGGCGTTTTAGCTAAAACGCCGCTAAATATCTACTATA
1 TTGCGGCGTTTTAGCAAAAACGCCGCTAAATATCTACTATA
1947438 TTGCGGCGTTTT
1 TTGCGGCGTTTT
1947450 TACTATATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
40 15 0.32
41 32 0.68
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (41 bp):
TTGCGGCGTTTTAGCAAAAACGCCGCTAAATATCTACTATA
Found at i:1949477 original size:18 final size:18
Alignment explanation
Indices: 1949454--1949490 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1949444 GAGCATCCTT
*
1949454 CAAACCTTCGATGAGTGC
1 CAAACCGTCGATGAGTGC
1949472 CAAACCGTCGATGAGTGC
1 CAAACCGTCGATGAGTGC
1949490 C
1 C
1949491 CCCTACCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (18 bp):
CAAACCGTCGATGAGTGC
Found at i:1953260 original size:23 final size:23
Alignment explanation
Indices: 1953203--1953262 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1953193 TTAGATCGAA
*
1953203 TCGCTAGGCCGGTTCGGATCAGG
1 TCGCTGGGCCGGTTCGGATCAGG
** * *
1953226 TCATTGGACCGGTTCGGATCGGG
1 TCGCTGGGCCGGTTCGGATCAGG
1953249 TCGCTGGGCCGGTT
1 TCGCTGGGCCGGTT
1953263 TGAGTTGCTG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (23 bp):
TCGCTGGGCCGGTTCGGATCAGG
Found at i:1954156 original size:66 final size:65
Alignment explanation
Indices: 1954068--1954243 Score: 196
Period size: 66 Copynumber: 2.7 Consensus size: 65
1954058 TTTTTCTCAT
* * *
1954068 AAGAAATTGTCTCAAGAGAGACAAAATTTTGTTTCCAAAGAAACATAC-CAAAAAAAAATTCTTC
1 AAGAAACTGTCTCAAAAGAGACAAAATTTTGTTT-CAAAGAAACAAACTC-AAAAAAAATTCTTC
1954132 AA
64 AA
* * * ***
1954134 AAGAAACTATCTCAAAAGAGACAAAATTTTGTTTTCAAATAAACAAACTCAAATATTTTTCTTCA
1 AAGAAACTGTCTCAAAAGAGACAAAATTTTG-TTTCAAAGAAACAAACTCAAAAAAAATTCTTCA
1954199 A
65 A
* *
1954200 AAGAAACTGTCTC--AAGAGATAAAATTTTCTTTCAAGAGAAACAA
1 AAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTCAA-AGAAACAA
1954244 TTTCAAAGTT
Statistics
Matches: 94, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
63 6 0.06
64 21 0.22
66 63 0.67
67 4 0.04
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (65 bp):
AAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTCAAAGAAACAAACTCAAAAAAAATTCTTCAA
Found at i:1954250 original size:64 final size:65
Alignment explanation
Indices: 1954014--1954243 Score: 188
Period size: 66 Copynumber: 3.5 Consensus size: 65
1954004 GAGAAGCTGC
* ** * * *
1954014 CTCAAGAGAGACAAAA-TTTG-TTTCAAGGGAAA-TGACTCAAAGATTTTT-TCTCATAAGAAAT
1 CTCAA-AGAGACAAAATTTTGCTTTCAA-AGAAACAAACTCAAATATTTTTCT-TCAAAAGAAAC
*
1954075 TGT
63 TAT
* * ***
1954078 CTCAAGAGAGACAAAATTTTG-TTTCCAAAGAAACATAC-CAAAAAAAAATTCTTCAAAAGAAAC
1 CTCAA-AGAGACAAAATTTTGCTTT-CAAAGAAACAAACTC-AAATATTTTTCTTCAAAAGAAAC
1954141 TAT
63 TAT
* * *
1954144 CTCAAAAGAGACAAAATTTTGTTTTCAAATAAACAAACTCAAATATTTTTCTTCAAAAGAAACTG
1 CTC-AAAGAGACAAAATTTTGCTTTCAAAGAAACAAACTCAAATATTTTTCTTCAAAAGAAACTA
1954209 T
65 T
*
1954210 CTC-AAGAGATAAAATTTT-CTTTCAAGAGAAACAA
1 CTCAAAGAGACAAAATTTTGCTTTCAA-AGAAACAA
1954244 TTTCAAAGTT
Statistics
Matches: 137, Mismatches: 20, Indels: 18
0.78 0.11 0.10
Matches are distributed among these distances:
63 6 0.04
64 37 0.27
65 12 0.09
66 75 0.55
67 7 0.05
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (65 bp):
CTCAAAGAGACAAAATTTTGCTTTCAAAGAAACAAACTCAAATATTTTTCTTCAAAAGAAACTAT
Found at i:1954267 original size:64 final size:65
Alignment explanation
Indices: 1954068--1954267 Score: 151
Period size: 66 Copynumber: 3.1 Consensus size: 65
1954058 TTTTTCTCAT
* * * * **
1954068 AAGAAATTGTCTCAAGAGAGACAAAATTTTG-TTTCCAAAGAAACATAC-CAAAAAAAAAT-TCT
1 AAGAAACTATCTCAA-AGAGACAAAATTTTGCTTT-CAAAGAAACAAACTC--AAATATTTGTCT
*
1954130 TCAA
62 TAAA
* * * *
1954134 AAGAAACTATCTCAAAAGAGACAAAATTTTGTTTTCAAATAAACAAACTCAAATATTTTTCTTCA
1 AAGAAACTATCTC-AAAGAGACAAAATTTTGCTTTCAAAGAAACAAACTCAAATATTTGTCTTAA
1954199 A
65 A
* * ** *
1954200 AAGAAACTGTCTC-AAGAGATAAAATTTT-CTTTCAAGAGAAACAATTTCAAA-GTTTGTCTTAA
1 AAGAAACTATCTCAAAGAGACAAAATTTTGCTTTCAA-AGAAACAAACTCAAATATTTGTCTTAA
1954262 GA
65 -A
1954264 AAGA
1 AAGA
1954268 GTGTTTCAAG
Statistics
Matches: 112, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
63 14 0.12
64 31 0.28
65 5 0.04
66 56 0.50
67 6 0.05
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.28
Consensus pattern (65 bp):
AAGAAACTATCTCAAAGAGACAAAATTTTGCTTTCAAAGAAACAAACTCAAATATTTGTCTTAAA
Found at i:1960401 original size:30 final size:29
Alignment explanation
Indices: 1960360--1960430 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 29
1960350 ACCAAGCTTG
* *
1960360 AAGGGCTAAAATAGCTAAAATAGAAATTT
1 AAGGACTAAAATAGCAAAAATAGAAATTT
1960389 AAAGGACTAAAATAGCAAAAATAGAAATTT
1 -AAGGACTAAAATAGCAAAAATAGAAATTT
1960419 AAGTGACTAAAA
1 AAG-GACTAAAA
1960431 AGTAATTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 3 0.08
30 35 0.92
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.21
Consensus pattern (29 bp):
AAGGACTAAAATAGCAAAAATAGAAATTT
Found at i:1975202 original size:14 final size:14
Alignment explanation
Indices: 1975183--1975209 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1975173 ATAGTGATAG
1975183 CTGTAGAAAACAGA
1 CTGTAGAAAACAGA
1975197 CTGTAGAAAACAG
1 CTGTAGAAAACAG
1975210 GGGTTAGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (14 bp):
CTGTAGAAAACAGA
Found at i:1978755 original size:14 final size:14
Alignment explanation
Indices: 1978733--1978764 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1978723 GTTTCATCCA
*
1978733 TTTATGGTTTAGGG
1 TTTAAGGTTTAGGG
1978747 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGG
1978761 TTTA
1 TTTA
1978765 GAGTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:1979100 original size:21 final size:22
Alignment explanation
Indices: 1979071--1979112 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1979061 CCTCACGCCA
1979071 GTTGCCGTTCTTCATG-CAACC
1 GTTGCCGTTCTTCATGACAACC
* *
1979092 GTTGTCGTTTTTCATGACAAC
1 GTTGCCGTTCTTCATGACAAC
1979113 ACTCCAACAA
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:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (22 bp):
GTTGCCGTTCTTCATGACAACC
Found at i:1979995 original size:22 final size:23
Alignment explanation
Indices: 1979954--1979997 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1979944 TACATGTATG
*
1979954 TATTAATTATTATATTTTTATTA
1 TATTAATTATTATATATTTATTA
*
1979977 TATT-ATTATTGTATATTTATT
1 TATTAATTATTATATATTTATT
1979998 TTGTTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TATTAATTATTATATATTTATTA
Found at i:1980036 original size:20 final size:20
Alignment explanation
Indices: 1979994--1980034 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1979984 ATTGTATATT
*
1979994 TATTTTGTTTTATATATACA
1 TATTTTATTTTATATATACA
1980014 TATTTTATTTTAT-TATA-A
1 TATTTTATTTTATATATACA
1980032 TAT
1 TAT
1980035 ATATAGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 4 0.20
20 12 0.60
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TATTTTATTTTATATATACA
Found at i:1980205 original size:12 final size:12
Alignment explanation
Indices: 1980185--1980230 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
1980175 TCTCTAATAT
*
1980185 TTTAATTTCTTA
1 TTTATTTTCTTA
*
1980197 TTTATTTTCTTT
1 TTTATTTTCTTA
1980209 TTTATTTTTCTTCA
1 TTTA-TTTTCTT-A
1980223 TTTATTTT
1 TTTATTTT
1980231 TATTTAAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 14 0.48
13 11 0.38
14 4 0.14
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTTTCTTA
Found at i:1980258 original size:3 final size:3
Alignment explanation
Indices: 1980250--1980302 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
1980240 ACTATATTGG
1980250 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1980298 ATT AT
1 ATT AT
1980303 ATAGTTATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1980370 original size:34 final size:31
Alignment explanation
Indices: 1980332--1980446 Score: 108
Period size: 34 Copynumber: 3.5 Consensus size: 31
1980322 GTTACTATCT
1980332 TTTTTTCATTTATTTTTTCATTTTCCTTTATTCA
1 TTTTTT-ATTTATTTTTTCATTTT-CTTTATT-A
*
1980366 TTTTTTCTTTTATTTTTT-ATTTTCTTTATT-
1 TTTTTT-ATTTATTTTTTCATTTTCTTTATTA
* * *
1980396 TTACTTTATTTATCTTATTCATTTTTTTATTATTA
1 TT-TTTTATTTAT-TTTTTCA-TTTTCT-TTATTA
1980431 TTTTTTATTTATTTTT
1 TTTTTTATTTATTTTT
1980447 CTTTATTTCT
Statistics
Matches: 68, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
30 7 0.10
31 7 0.10
32 8 0.12
33 13 0.19
34 31 0.46
35 2 0.03
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (31 bp):
TTTTTTATTTATTTTTTCATTTTCTTTATTA
Found at i:1980404 original size:10 final size:9
Alignment explanation
Indices: 1980329--1980470 Score: 58
Period size: 8 Copynumber: 16.0 Consensus size: 9
1980319 TTTGTTACTA
1980329 TCTTT-TTT
1 TCTTTATTT
1980337 TCATTTATTT
1 TC-TTTATTT
*
1980347 T-TTCATTT
1 TCTTTATTT
1980355 TCCTTTA--T
1 T-CTTTATTT
*
1980363 TCATT-TTT
1 TCTTTATTT
1980371 TCTTT-TATT
1 TCTTTAT-TT
1980380 T-TTTATTT
1 TCTTTATTT
1980388 TCTTTATTT
1 TCTTTATTT
1980397 TACTTTATTT
1 T-CTTTATTT
1980407 ATCTTATTCATTT
1 -TC-T-TT-ATTT
1980420 T-TTTATTAT
1 TCTTTATT-T
*
1980429 T-ATT-TTT
1 TCTTTATTT
*
1980436 TATTTATTTT
1 TCTTTA-TTT
1980446 TCTTTA-TT
1 TCTTTATTT
1980454 TC--TATTT
1 TCTTTATTT
1980461 TCTTTGATTT
1 TCTTT-ATTT
1980471 ATTCATTTTC
Statistics
Matches: 105, Mismatches: 7, Indels: 42
0.68 0.05 0.27
Matches are distributed among these distances:
6 2 0.02
7 9 0.09
8 34 0.32
9 22 0.21
10 29 0.28
11 2 0.02
12 3 0.03
13 4 0.04
ACGTcount: A:0.15, C:0.10, G:0.01, T:0.75
Consensus pattern (9 bp):
TCTTTATTT
Found at i:1980443 original size:4 final size:4
Alignment explanation
Indices: 1980374--1980444 Score: 51
Period size: 4 Copynumber: 17.8 Consensus size: 4
1980364 CATTTTTTCT
* * *
1980374 TTTA TTT- TTTA TTTTC TTTA TTTTA CTTTA TTTA TCTTA TTCA TTTT
1 TTTA TTTA TTTA -TTTA TTTA -TTTA -TTTA TTTA T-TTA TTTA TTTA
1980421 TTTA -TTA -TTA TTT- TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1980445 TTCTTTATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
3 12 0.22
4 27 0.50
5 15 0.28
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1995880 original size:30 final size:29
Alignment explanation
Indices: 1995841--1995899 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
1995831 GAGAATTTAC
* *
1995841 ATGAACTACGTGATTACATGTATATGTGA
1 ATGAACTACGAGATTACATGAATATGTGA
* *
1995870 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGATTACATGAATATGTGA
1995900 TATATTTACA
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:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTACATGAATATGTGA
Found at i:1996163 original size:23 final size:23
Alignment explanation
Indices: 1996129--1996196 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1996119 CATCTTATAT
1996129 GGCACTTCGGTGTATTTCTACGC
1 GGCACTTCGGTGTATTTCTACGC
* * *
1996152 GGCACTTAGGTGTAATTCTACGT
1 GGCACTTCGGTGTATTTCTACGC
* *
1996175 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGTATTTCTACG
1996197 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (23 bp):
GGCACTTCGGTGTATTTCTACGC
Found at i:1997127 original size:3 final size:3
Alignment explanation
Indices: 1997119--1997167 Score: 62
Period size: 3 Copynumber: 15.3 Consensus size: 3
1997109 CTTACATTTA
*
1997119 TAT TAT TAT TAT TAT TAT TAT TAT ATATT TAT TAT TAT TGT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TA-T TAT TAT TAT TAT -TAT TAT
1997167 T
1 T
1997168 TATTTCGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 34 0.83
4 6 0.15
5 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1997150 original size:17 final size:17
Alignment explanation
Indices: 1997114--1997164 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
1997104 AGTCCCTTAC
1997114 ATTTA-TATTATTAT-T
1 ATTTATTATTATTATAT
1997129 A-TTATTATTATTATAT
1 ATTTATTATTATTATAT
*
1997145 ATTTATTATTATTGTAT
1 ATTTATTATTATTATAT
1997162 ATT
1 ATT
1997165 ATTTATTTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 3 0.09
15 10 0.31
16 2 0.06
17 17 0.53
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTATTATTATTATAT
Found at i:1997170 original size:17 final size:17
Alignment explanation
Indices: 1997119--1997171 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
1997109 CTTACATTTA
1997119 TATTATTAT-TATTA-T
1 TATTATTATATATTATT
1997134 TATTATTATATATT-TAT
1 TATTATTATATATTAT-T
*
1997151 TATTATTGTATATTATT
1 TATTATTATATATTATT
1997168 TATT
1 TATT
1997172 TCGTTTTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 9 0.27
16 4 0.12
17 19 0.58
18 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
TATTATTATATATTATT
Found at i:1997244 original size:12 final size:12
Alignment explanation
Indices: 1997227--1997297 Score: 60
Period size: 12 Copynumber: 5.9 Consensus size: 12
1997217 TTTGTTTCTT
1997227 TTATTATTTTTA
1 TTATTATTTTTA
1997239 TTATTATTTTTA
1 TTATTATTTTTA
1997251 TTATT-TTCTTTA
1 TTATTATT-TTTA
*
1997263 --ATT-TTTTAGCA
1 TTATTATTTT--TA
*
1997274 TTATTATTCTTA
1 TTATTATTTTTA
1997286 TTTATTATTTTT
1 -TTATTATTTTT
1997298 TTCTTATTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
9 2 0.04
10 5 0.10
11 3 0.06
12 22 0.46
13 13 0.27
14 3 0.06
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (12 bp):
TTATTATTTTTA
Found at i:1997306 original size:14 final size:13
Alignment explanation
Indices: 1997226--1997312 Score: 51
Period size: 12 Copynumber: 6.9 Consensus size: 13
1997216 ATTTGTTTCT
1997226 TTTATTATTTTTA
1 TTTATTATTTTTA
1997239 -TTATTATTTTTA
1 TTTATTATTTTTA
1997251 -TTATT-TTCTTTA
1 TTTATTATT-TTTA
* ***
1997263 ATT-TT-TTAGCA
1 TTTATTATTTTTA
*
1997274 -TTATTATTCTTA
1 TTTATTATTTTTA
*
1997286 TTTATTATTTTTT
1 TTTATTATTTTTA
1997299 TCTTATTATATTTT
1 T-TTATTAT-TTTT
1997313 CCAGTATTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
10 2 0.03
11 5 0.08
12 28 0.47
13 13 0.22
14 7 0.12
15 4 0.07
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (13 bp):
TTTATTATTTTTA
Found at i:1997512 original size:10 final size:9
Alignment explanation
Indices: 1997455--1997573 Score: 50
Period size: 9 Copynumber: 12.4 Consensus size: 9
1997445 TTACTGTCTT
*
1997455 TTTTATTTA
1 TTTTCTTTA
1997464 TTTTCATTT-
1 TTTTC-TTTA
*
1997473 TTTCCTTTA
1 TTTTCTTTA
* *
1997482 TTCATTTTTTC
1 TT--TTCTTTA
1997493 TTTTCTTTA
1 TTTTCTTTA
1997502 TTTTACTTTA
1 TTTT-CTTTA
1997512 TTTATC-TTA
1 TTT-TCTTTA
*
1997521 TTCATTCATTCA
1 TT--TTC-TTTA
1997533 TTCATTCATTTA
1 TT--TTC-TTTA
1997545 TTTTGCTTTA
1 TTTT-CTTTA
1997555 -TTTC--TA
1 TTTTCTTTA
1997561 TTTTCTTTA
1 TTTTCTTTA
1997570 TTTT
1 TTTT
1997574 TATTTTCTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 28
0.70 0.07 0.23
Matches are distributed among these distances:
6 2 0.02
7 4 0.05
8 4 0.05
9 33 0.38
10 20 0.23
11 9 0.10
12 15 0.17
ACGTcount: A:0.16, C:0.13, G:0.01, T:0.70
Consensus pattern (9 bp):
TTTTCTTTA
Found at i:1997564 original size:16 final size:15
Alignment explanation
Indices: 1997543--1997588 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
1997533 TTCATTCATT
1997543 TATTTTGCTTTATTTC
1 TATTTT-CTTTATTTC
*
1997559 TATTTTCTTTATTTT
1 TATTTTCTTTATTTC
1997574 TATTTTCTTTGATTT
1 TATTTTCTTT-ATTT
1997589 ATTCATTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 18 0.64
16 10 0.36
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (15 bp):
TATTTTCTTTATTTC
Found at i:1998249 original size:10 final size:10
Alignment explanation
Indices: 1998232--1998286 Score: 56
Period size: 10 Copynumber: 5.1 Consensus size: 10
1998222 GTGTTTGTGT
1998232 TGTTCGTTTA
1 TGTTCGTTTA
*
1998242 TTTTCGTTTA
1 TGTTCGTTTA
*
1998252 TGTTCATTCGTTTG
1 TG----TTCGTTTA
1998266 TGTTCGTTTA
1 TGTTCGTTTA
1998276 TGTTCGTTTA
1 TGTTCGTTTA
1998286 T
1 T
1998287 CATTTAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 28 0.76
14 9 0.24
ACGTcount: A:0.09, C:0.11, G:0.18, T:0.62
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:1998261 original size:24 final size:24
Alignment explanation
Indices: 1998234--1998280 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1998224 GTTTGTGTTG
*
1998234 TTCGTTTATTTTCGTTTATGTTCA
1 TTCGTTTATGTTCGTTTATGTTCA
*
1998258 TTCGTTTGTGTTCGTTTATGTTC
1 TTCGTTTATGTTCGTTTATGTTC
1998281 GTTTATCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.09, C:0.13, G:0.17, T:0.62
Consensus pattern (24 bp):
TTCGTTTATGTTCGTTTATGTTCA
Found at i:1998372 original size:16 final size:16
Alignment explanation
Indices: 1998351--1998383 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1998341 AAAAAAAATT
*
1998351 TGTTCGTTTATGTTCG
1 TGTTCGTGTATGTTCG
1998367 TGTTCGTGTATGTTCG
1 TGTTCGTGTATGTTCG
1998383 T
1 T
1998384 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.27, T:0.55
Consensus pattern (16 bp):
TGTTCGTGTATGTTCG
Found at i:2000134 original size:16 final size:16
Alignment explanation
Indices: 2000113--2000143 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2000103 ATAAATAAAT
2000113 GAACATAAACGAACAC
1 GAACATAAACGAACAC
2000129 GAACATAAACGAACA
1 GAACATAAACGAACA
2000144 AAATTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:2000229 original size:16 final size:16
Alignment explanation
Indices: 2000208--2000255 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
2000198 AATTTAATAA
2000208 ATAAACGAACACAAAC
1 ATAAACGAACACAAAC
*
2000224 ATAAACGAACACGAAC
1 ATAAACGAACACAAAC
* *
2000240 ATAAATGAACATAAAC
1 ATAAACGAACACAAAC
2000256 GTTGGAGACC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.60, C:0.21, G:0.08, T:0.10
Consensus pattern (16 bp):
ATAAACGAACACAAAC
Found at i:2001358 original size:24 final size:24
Alignment explanation
Indices: 2001331--2001381 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2001321 GATTGGGTTA
*
2001331 AACATAAATGAACGAACATAAACG
1 AACATAAACGAACGAACATAAACG
* * *
2001355 AACATAACCGATCGAACATAACCG
1 AACATAAACGAACGAACATAAACG
2001379 AAC
1 AAC
2001382 GTTCACGAAC
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:0.53, C:0.24, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:2001370 original size:14 final size:14
Alignment explanation
Indices: 2001353--2001379 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2001343 CGAACATAAA
2001353 CGAACATAACCGAT
1 CGAACATAACCGAT
2001367 CGAACATAACCGA
1 CGAACATAACCGA
2001380 ACGTTCACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.15, T:0.11
Consensus pattern (14 bp):
CGAACATAACCGAT
Found at i:2004302 original size:36 final size:36
Alignment explanation
Indices: 2004279--2004609 Score: 433
Period size: 36 Copynumber: 9.1 Consensus size: 36
2004269 TACAATTGAT
2004279 TTTTG-AAATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
2004314 TTTTGAAAATATGTATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATA--TATATAATATATAGTTTTTAAAACA
2004352 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
**
2004388 TTTTTG-AAAGCTATATAATATATAGTTTTTAAAACA
1 -TTTTGAAAATATATATAATATATAGTTTTTAAAACA
* *
2004424 TTTTGAAAAAATATATAATTTATAGTTTTTAAAATCA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAA-CA
*
2004461 TTTTGAAAACT-TATATAATATATAGTTTTGAAAACA
1 TTTTGAAAA-TATATATAATATATAGTTTTTAAAACA
*
2004497 TTTCTAAAAACT-TATATAATATATAG-TTTTAAAACA
1 TTT-TGAAAA-TATATATAATATATAGTTTTTAAAACA
*
2004533 TTTTTGAAAACT-TATATAATATATAGTTTTAAAAACA
1 -TTTTGAAAA-TATATATAATATATAGTTTTTAAAACA
* * *
2004570 TTTTTGAAAACATATATAATATGTAG-TTTTAAAATA
1 -TTTTGAAAATATATATAATATATAGTTTTTAAAACA
2004606 TTTT
1 TTTT
2004610 TTTATATATA
Statistics
Matches: 269, Mismatches: 16, Indels: 22
0.88 0.05 0.07
Matches are distributed among these distances:
35 14 0.05
36 126 0.47
37 93 0.35
38 36 0.13
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:2004391 original size:110 final size:107
Alignment explanation
Indices: 2004277--2004625 Score: 456
Period size: 110 Copynumber: 3.2 Consensus size: 107
2004267 TTTACAATTG
2004277 ATTTTTGAAATATATATAATATATAGTTTTTAAAACATTTTGAAAATATGTATATAATATATAGT
1 ATTTTT-AAATATATATAATATATAGTTTTTAAAACATTTTGAAAA-AT-TATATAATATATAGT
2004342 TTTTAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAAC
63 TTTTAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAAC
** * *
2004387 ATTTTTGAAAGCTATATAATATATAGTTTTTAAAACATTTTGAAAAAATATATAATTTATAGTTT
1 ATTTTT-AAATATATATAATATATAGTTTTTAAAACATTTTGAAAAATTATATAATATATAGTTT
*
2004452 TTAAAATCATTTTGAAAACT-TATATAATATATAGTTTTGAAAAC
65 TTAAAA-CATTTTGAAAA-TATATATAATATATAGTTTTTAAAAC
* * *
2004496 ATTTCTAAAAACTTATATAATATATAG-TTTTAAAACATTTTTGAAAACTTATATAATATATAGT
1 ATTTTTAAATA--TATATAATATATAGTTTTTAAAACA-TTTTGAAAAATTATATAATATATAGT
* * * *
2004560 TTTAAAAACATTTTTGAAAACATATATAATATGTAG-TTTTAAAAT
63 TTTTAAAACA-TTTTGAAAATATATATAATATATAGTTTTTAAAAC
*
2004605 ATTTTT--TTATATATAATATAT
1 ATTTTTAAATATATATAATATAT
2004626 TATTATTACT
Statistics
Matches: 213, Mismatches: 19, Indels: 19
0.85 0.08 0.08
Matches are distributed among these distances:
105 12 0.06
107 1 0.00
108 25 0.12
109 64 0.30
110 111 0.52
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (107 bp):
ATTTTTAAATATATATAATATATAGTTTTTAAAACATTTTGAAAAATTATATAATATATAGTTTT
TAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAAC
Found at i:2004610 original size:73 final size:74
Alignment explanation
Indices: 2004277--2004610 Score: 468
Period size: 73 Copynumber: 4.6 Consensus size: 74
2004267 TTTACAATTG
* *
2004277 ATTTTTG-AAATATATATAATATATAGTTTTTAAAACA-TTTTGAAAATATGTATATAATATATA
1 ATTTTTGAAAACATATATAATATATAGTTTTTAAAACATTTTTGAAAA-CT-TATATAATATATA
2004340 GTTTTTAAAAC
64 GTTTTTAAAAC
* *
2004351 A-TTTTGAAAATATATATAATATATAGTTTTTAAAACATTTTTGAAAGC-TATATAATATATAGT
1 ATTTTTGAAAACATATATAATATATAGTTTTTAAAACATTTTTGAAAACTTATATAATATATAGT
2004414 TTTTAAAAC
66 TTTTAAAAC
* *
2004423 A-TTTTGAAAAAATATATAATTTATAGTTTTTAAAATCA-TTTTGAAAACTTATATAATATATAG
1 ATTTTTGAAAACATATATAATATATAGTTTTTAAAA-CATTTTTGAAAACTTATATAATATATAG
*
2004486 TTTTGAAAAC
65 TTTTTAAAAC
* * *
2004496 ATTTCTAAAAACTTATATAATATATAG-TTTTAAAACATTTTTGAAAACTTATATAATATATAGT
1 ATTTTTGAAAACATATATAATATATAGTTTTTAAAACATTTTTGAAAACTTATATAATATATAGT
*
2004560 TTTAAAAAC
66 TTTTAAAAC
* *
2004569 ATTTTTGAAAACATATATAATATGTAG-TTTTAAAATATTTTT
1 ATTTTTGAAAACATATATAATATATAGTTTTTAAAACATTTTT
2004611 TTATATATAA
Statistics
Matches: 237, Mismatches: 17, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
72 68 0.29
73 110 0.46
74 51 0.22
75 8 0.03
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (74 bp):
ATTTTTGAAAACATATATAATATATAGTTTTTAAAACATTTTTGAAAACTTATATAATATATAGT
TTTTAAAAC
Found at i:2004667 original size:24 final size:23
Alignment explanation
Indices: 2004638--2004689 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
2004628 TTATTACTTA
*
2004638 ATTTTATTTATTATATGTTTAT-TT
1 ATTTTATTAATT-TAT-TTTATATT
2004662 ATTTTATTAATTTATTTTATATT
1 ATTTTATTAATTTATTTTATATT
2004685 ATTTT
1 ATTTT
2004690 TTAGGCCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.19
23 10 0.38
24 11 0.42
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (23 bp):
ATTTTATTAATTTATTTTATATT
Found at i:2005773 original size:4 final size:4
Alignment explanation
Indices: 2005764--2005832 Score: 65
Period size: 4 Copynumber: 17.8 Consensus size: 4
2005754 TCTTGGTTGT
* *
2005764 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTTCA GTT- TTT- TTTA TTTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA
*
2005812 TTTA -TT- TTTG TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTT
2005833 TATTATTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
3 9 0.16
4 40 0.73
5 5 0.09
6 1 0.02
ACGTcount: A:0.17, C:0.01, G:0.03, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:2005838 original size:8 final size:9
Alignment explanation
Indices: 2005764--2005841 Score: 76
Period size: 8 Copynumber: 8.9 Consensus size: 9
2005754 TCTTGGTTGT
2005764 TTTA-TTTA
1 TTTATTTTA
2005772 TTTA-TTTA
1 TTTATTTTA
2005780 TTTA-TTTA
1 TTTATTTTA
2005788 TTTATTTTCA
1 TTTATTTT-A
*
2005798 GTTTTTTTTA
1 -TTTATTTTA
2005808 TTT-TTTTA
1 TTTATTTTA
*
2005816 TTTTTGTTTA
1 TTTAT-TTTA
2005826 TTTATTTTA
1 TTTATTTTA
2005835 -TTATTTT
1 TTTATTTT
2005842 TCTATAAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
8 35 0.56
9 11 0.17
10 10 0.16
11 7 0.11
ACGTcount: A:0.18, C:0.01, G:0.03, T:0.78
Consensus pattern (9 bp):
TTTATTTTA
Found at i:2005840 original size:12 final size:12
Alignment explanation
Indices: 2005763--2005840 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 12
2005753 TTCTTGGTTG
2005763 TTTTATTTATTTA
1 TTTTA-TTATTTA
2005776 -TTTATTTATTTA
1 TTTTA-TTATTTA
*
2005788 -TTTATT-TTCA
1 TTTTATTATTTA
*
2005798 GTTT-TT-TTTA
1 TTTTATTATTTA
*
2005808 TTTTTTTATTT-
1 TTTTATTATTTA
*
2005819 TTGT-TTATTTA
1 TTTTATTATTTA
2005830 TTTTATTATTT
1 TTTTATTATTT
2005841 TTCTATAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
10 17 0.31
11 13 0.24
12 25 0.45
ACGTcount: A:0.18, C:0.01, G:0.03, T:0.78
Consensus pattern (12 bp):
TTTTATTATTTA
Found at i:2006073 original size:6 final size:6
Alignment explanation
Indices: 2006062--2006088 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2006052 GAATTGAATT
2006062 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
2006089 TCACAGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:2007172 original size:23 final size:23
Alignment explanation
Indices: 2007146--2007190 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2007136 CACCACAGCT
*
2007146 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
2007169 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2007191 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:2007439 original size:149 final size:149
Alignment explanation
Indices: 2007169--2007472 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
2007159 CGAAGTGCCC
*
2007169 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
2007234 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
2007299 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
2007318 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
2007383 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
2007448 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
2007467 CGTAGA
1 CGTAGA
2007473 CCCTCTACCC
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:2014103 original size:23 final size:23
Alignment explanation
Indices: 2014077--2014121 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2014067 CACCACAGCT
*
2014077 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
2014100 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2014122 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:2014382 original size:149 final size:147
Alignment explanation
Indices: 2014100--2014401 Score: 577
Period size: 149 Copynumber: 2.0 Consensus size: 147
2014090 CGAAGTGCCC
*
2014100 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
2014165 CATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
66 CATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
2014230 TATGTCCCAAAGAACCG
131 TATGTCCCAAAGAACCG
2014247 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
2014312 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 C--ATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
2014377 CATATGTCCCAAAGAACCG
129 CATATGTCCCAAAGAACCG
2014396 CGTAGA
1 CGTAGA
2014402 CCCTCTACCC
Statistics
Matches: 152, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
147 65 0.43
149 87 0.57
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (147 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
TATGTCCCAAAGAACCG
Found at i:2014914 original size:18 final size:19
Alignment explanation
Indices: 2014877--2014913 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2014867 TTTTTTCTTA
*
2014877 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
2014896 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
2014914 TCCAACATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:2017228 original size:29 final size:29
Alignment explanation
Indices: 2017186--2017244 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
2017176 AGTGAAAGAC
** *
2017186 AAAATAGTTGGTTAAAGAATATCAACGTG
1 AAAATAGAAGGTTAAAAAATATCAACGTG
2017215 AAAATAGAAGGTTAAAAAATATCAACGTG
1 AAAATAGAAGGTTAAAAAATATCAACGTG
2017244 A
1 A
2017245 TCAAATAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.24
Consensus pattern (29 bp):
AAAATAGAAGGTTAAAAAATATCAACGTG
Found at i:2017851 original size:19 final size:19
Alignment explanation
Indices: 2017827--2017865 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2017817 TTTGATTGGG
2017827 CAATACCCTTTCTTTCCCC
1 CAATACCCTTTCTTTCCCC
2017846 CAATACCCTTTCTTTCCCC
1 CAATACCCTTTCTTTCCCC
2017865 C
1 C
2017866 CCTTTTACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.49, G:0.00, T:0.36
Consensus pattern (19 bp):
CAATACCCTTTCTTTCCCC
Found at i:2026035 original size:26 final size:26
Alignment explanation
Indices: 2025990--2026064 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
2025980 AAATATAATA
*
2025990 AATAATATTATTCATT-ATAAAAAAAG
1 AATAATATTATT-TTTAATAAAAAAAG
* ***
2026016 AATAATATTATTTTTAATAATAATTT
1 AATAATATTATTTTTAATAAAAAAAG
*
2026042 AATTAATATTATTTATAATAAAA
1 AA-TAATATTATTTTTAATAAAA
2026065 GTATTATTAG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
25 2 0.05
26 20 0.50
27 18 0.45
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
AATAATATTATTTTTAATAAAAAAAG
Found at i:2026070 original size:24 final size:24
Alignment explanation
Indices: 2026004--2026070 Score: 64
Period size: 27 Copynumber: 2.7 Consensus size: 24
2025994 ATATTATTCA
* *
2026004 TTATAAAAAAAG-AATAATATTAT
1 TTATAATAAAAGTATTAATATTAT
* *
2026027 TTTTAATAATAATTTAATTAATATTAT
1 TTATAATAA-AA-GT-ATTAATATTAT
2026054 TTATAATAAAAGTATTA
1 TTATAATAAAAGTATTA
2026071 TTAGTTTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
23 7 0.21
24 6 0.18
25 1 0.03
26 2 0.06
27 18 0.53
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (24 bp):
TTATAATAAAAGTATTAATATTAT
Found at i:2027788 original size:20 final size:21
Alignment explanation
Indices: 2027763--2027815 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
2027753 CTGAATAAAT
2027763 TGGTATCCATACAGGAGAA-C
1 TGGTATCCATACAGGAGAAGC
* * *
2027783 TGGTATCCATACCGGATAAGT
1 TGGTATCCATACAGGAGAAGC
2027804 TGGTATCCATAC
1 TGGTATCCATAC
2027816 CAGATGAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (21 bp):
TGGTATCCATACAGGAGAAGC
Found at i:2027807 original size:41 final size:42
Alignment explanation
Indices: 2027743--2027840 Score: 128
Period size: 41 Copynumber: 2.4 Consensus size: 42
2027733 TGATACCGCG
*
2027743 GGTATCCATACTGAATAAATTGGTATCCATA-CAGGA-GAACT
1 GGTATCCATACCGAATAAATTGGTATCCATACCA-GATGAACT
* *
2027784 GGTATCCATACCGGATAAGTTGGTATCCATACCAGATGAACT
1 GGTATCCATACCGAATAAATTGGTATCCATACCAGATGAACT
* *
2027826 GATATCTATACCGAA
1 GGTATCCATACCGAA
2027841 GGCTTGATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
41 30 0.61
42 19 0.39
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (42 bp):
GGTATCCATACCGAATAAATTGGTATCCATACCAGATGAACT
Found at i:2027816 original size:21 final size:20
Alignment explanation
Indices: 2027743--2027816 Score: 85
Period size: 21 Copynumber: 3.6 Consensus size: 20
2027733 TGATACCGCG
* *
2027743 GGTATCCATACTGAATAAATT
1 GGTATCCATACCGGAT-AATT
* * *
2027764 GGTATCCATACAGGAGAACT
1 GGTATCCATACCGGATAATT
2027784 GGTATCCATACCGGATAAGTT
1 GGTATCCATACCGGATAA-TT
2027805 GGTATCCATACC
1 GGTATCCATACC
2027817 AGATGAACTG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 19 0.42
21 26 0.58
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (20 bp):
GGTATCCATACCGGATAATT
Found at i:2027831 original size:21 final size:21
Alignment explanation
Indices: 2027763--2027837 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
2027753 CTGAATAAAT
2027763 TGGTATCCATA-CAGGA-GAAC
1 TGGTATCCATACCA-GATGAAC
* *
2027783 TGGTATCCATACCGGAT-AAGT
1 TGGTATCCATACCAGATGAA-C
2027804 TGGTATCCATACCAGATGAAC
1 TGGTATCCATACCAGATGAAC
* *
2027825 TGATATCTATACC
1 TGGTATCCATACC
2027838 GAAGGCTTGA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 15 0.33
21 28 0.62
22 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (21 bp):
TGGTATCCATACCAGATGAAC
Found at i:2029032 original size:32 final size:32
Alignment explanation
Indices: 2028981--2029069 Score: 133
Period size: 32 Copynumber: 2.8 Consensus size: 32
2028971 TAGATACTAG
2028981 CAGTGTTGCATTCAAATAATGCACAACAAAGT
1 CAGTGTTGCATTCAAATAATGCACAACAAAGT
* * *
2029013 CAGTATTGCATTCAGATAATGCACAACAGAGT
1 CAGTGTTGCATTCAAATAATGCACAACAAAGT
* *
2029045 CAATGTTACATTCAAATAATGCACA
1 CAGTGTTGCATTCAAATAATGCACA
2029070 GGAGTGTTAG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (32 bp):
CAGTGTTGCATTCAAATAATGCACAACAAAGT
Found at i:2030943 original size:29 final size:30
Alignment explanation
Indices: 2030901--2030972 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
2030891 CCCGAAGGAC
2030901 CTATCCAGAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCCCGGTAA
* * *
2030930 CTATCTAGAGGTCATAAAGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCCCGGTAA
* *
2030960 CTGTCCATAGGTC
1 CTATCCAGAGGTC
2030973 CCGACGAACC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCCCGGTAA
Found at i:2032075 original size:20 final size:23
Alignment explanation
Indices: 2032050--2032107 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 23
2032040 TTCCCCTTGA
2032050 AGTGCATCGATGCA-T-GTT-AC
1 AGTGCATCGATGCATTCGTTAAC
*
2032070 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTCGTTAAC
2032093 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
2032108 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 14 0.42
21 1 0.03
22 2 0.06
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (23 bp):
AGTGCATCGATGCATTCGTTAAC
Found at i:2032182 original size:64 final size:63
Alignment explanation
Indices: 2032095--2032231 Score: 152
Period size: 64 Copynumber: 2.2 Consensus size: 63
2032085 TCTTTAACAT
* * *
2032095 GTGCATCGATGCACTACCCATGCATTGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * *
2032158 GATGCATCGATGCACT-CCTTATGCATCGATGCACCATTTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACC-CATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
2032222 GTGCATCGAT
1 GTGCATCGAT
2032232 TTACATTCAA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
63 17 0.27
64 45 0.73
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:2035201 original size:31 final size:31
Alignment explanation
Indices: 2035146--2035231 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
2035136 CAGAGGTAAT
* * *
2035146 AAAGAACCTCGG-CAACTGTTCATAGGTCCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCCC
*
2035176 GAAGAACCTAGGTAAACTGTCCATAGGTCCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCCC
2035207 AAAGAACCTAGGTAAACTGTCCATA
1 AAAGAACCTAGGTAAACTGTCCATA
2035232 TATCTCGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 10 0.20
31 40 0.80
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (31 bp):
AAAGAACCTAGGTAAACTGTCCATAGGTCCC
Found at i:2035250 original size:31 final size:31
Alignment explanation
Indices: 2035159--2035254 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
2035149 GAACCTCGGC
* * * *
2035159 AACTGTTCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGATCCCAAAGAACATAGGTA
* *
2035190 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATAGATCCCAAAGAACATAGGTA
* *
2035221 AACTGTCCATATATCTCGAAAG-ACATAGGTA
1 AACTGTCCATAGATC-CCAAAGAACATAGGTA
2035252 AAC
1 AAC
2035255 CCTCGACTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 53 0.91
32 5 0.09
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGATCCCAAAGAACATAGGTA
Found at i:2035499 original size:7 final size:7
Alignment explanation
Indices: 2035487--2035513 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2035477 CATGTCATAT
2035487 CATATAA
1 CATATAA
2035494 CATATAA
1 CATATAA
2035501 CATATAA
1 CATATAA
2035508 CATATA
1 CATATA
2035514 TACCCATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (7 bp):
CATATAA
Found at i:2036199 original size:20 final size:22
Alignment explanation
Indices: 2036174--2036231 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
2036164 TTCCCCTTGA
2036174 AGTGCATCGATGCATGC-T-AC
1 AGTGCATCGATGCATGCTTAAC
*
2036194 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATGC-TTAAC
2036217 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
2036232 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATGCTTAAC
Found at i:2036288 original size:62 final size:62
Alignment explanation
Indices: 2036222--2036341 Score: 163
Period size: 62 Copynumber: 1.9 Consensus size: 62
2036212 TTAACATGTG
2036222 CATCGATGCACTACC-CATGCATCGATACACAAATTAC-TTCGATGTTTTCATTTTAAAGGGAT
1 CATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATGTTTTC-TTTTAAAGGGAT
* * * * *
2036284 CATCGATGCACTCCTTATGCATCGATGCACCATTTGCATTCGATGTTTTCTTTTAAAG
1 CATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTTCTTTTAAAG
2036342 ATGTGAACGA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
61 2 0.04
62 37 0.73
63 12 0.24
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (62 bp):
CATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTTCTTTTAAAGGGAT
Found at i:2041321 original size:11 final size:11
Alignment explanation
Indices: 2041305--2041346 Score: 77
Period size: 11 Copynumber: 3.9 Consensus size: 11
2041295 CTCTTTTTCA
2041305 GAGAAATTTTT
1 GAGAAATTTTT
2041316 GAGAAATTTTT
1 GAGAAATTTTT
2041327 GAG-AATTTTT
1 GAGAAATTTTT
2041337 GAGAAATTTT
1 GAGAAATTTT
2041347 GAGTTTGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.33
11 20 0.67
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (11 bp):
GAGAAATTTTT
Found at i:2041333 original size:10 final size:10
Alignment explanation
Indices: 2041309--2041349 Score: 64
Period size: 10 Copynumber: 4.0 Consensus size: 10
2041299 TTTTCAGAGA
2041309 AATTTTTGAG
1 AATTTTTGAG
2041319 AAATTTTTGAG
1 -AATTTTTGAG
2041330 AATTTTTGAG
1 AATTTTTGAG
*
2041340 AAATTTTGAG
1 AATTTTTGAG
2041350 TTTGTGAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 19 0.66
11 10 0.34
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (10 bp):
AATTTTTGAG
Found at i:2041660 original size:138 final size:138
Alignment explanation
Indices: 2041412--2041889 Score: 758
Period size: 138 Copynumber: 3.4 Consensus size: 138
2041402 CGTTGCGTAT
**
2041412 AATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGAAGAACTATTCATGTCAGTACCTA
1 AATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTA
*
2041477 TTATTTCTGAAGGGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTT
66 TTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTT
2041542 TGTCAGAG
131 TGTCAGAG
* *
2041550 AATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCAGGGAACTATTCATGTTAGTACCTA
1 AATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTA
2041615 TTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGTTCCTGGGGGTGC
66 TTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTCCC--GGG-G-G---C-------GC
2041680 GCCTTCCATTATTTTGTCAGAG
117 GCCTTCCATTATTTTGTCAGAG
*
2041702 AATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCTGGGGAACTATTCATGTCAGTACCTA
1 AATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTA
*
2041767 TTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCTATTATTT
66 TTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTT
2041832 TGTCAGAG
131 TGTCAGAG
*
2041840 AATATGTTATCATTGCCCTATTTTGTCACTCATGTCCCCCGGGGAACTAT
1 AATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTAT
2041890 AGATGGATGG
Statistics
Matches: 315, Mismatches: 11, Indels: 28
0.89 0.03 0.08
Matches are distributed among these distances:
138 174 0.55
140 3 0.01
141 1 0.00
142 1 0.00
145 2 0.01
148 1 0.00
149 1 0.00
150 3 0.01
152 129 0.41
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (138 bp):
AATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTA
TTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTT
TGTCAGAG
Found at i:2041786 original size:152 final size:152
Alignment explanation
Indices: 2041510--2041889 Score: 608
Period size: 152 Copynumber: 2.6 Consensus size: 152
2041500 AGTGGTGAAA
* *
2041510 GCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATG
1 GCGCGTTCCTGGGGGTGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATG
* *
2041575 TCACTCATGTCCCCCAGGGAACTATTCATGTTAGTACCTATTATTTCTGAGGGGACTTGGCAAAG
66 TCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAG
2041640 TGGTGAAAGCGCGTTCCCGGGG
131 TGGTGAAAGCGCGTTCCCGGGG
2041662 GCGCGTTCCTGGGGGTGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATG
1 GCGCGTTCCTGGGGGTGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATG
*
2041727 TCACTCATGTCCCCTGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAG
66 TCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAG
2041792 TGGTGAAAGCGCGTTCCCGGGG
131 TGGTGAAAGCGCGTTCCCGGGG
*
2041814 GCGCG--CCT-----T----C-T--ATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTTTG
1 GCGCGTTCCTGGGGGTGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATG
2041865 TCACTCATGTCCCCCGGGGAACTAT
66 TCACTCATGTCCCCCGGGGAACTAT
2041890 AGATGGATGG
Statistics
Matches: 221, Mismatches: 7, Indels: 14
0.91 0.03 0.06
Matches are distributed among these distances:
138 63 0.29
140 1 0.00
141 1 0.00
145 1 0.00
150 3 0.01
152 152 0.69
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.32
Consensus pattern (152 bp):
GCGCGTTCCTGGGGGTGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATG
TCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAG
TGGTGAAAGCGCGTTCCCGGGG
Found at i:2042099 original size:63 final size:63
Alignment explanation
Indices: 2042015--2042142 Score: 204
Period size: 63 Copynumber: 2.0 Consensus size: 63
2042005 GTTATGTGAA
* *
2042015 GTTTGAATAAATTGGATAAAATGTTATGAATAAATTGAATAAATGTGAAGTGATCAA-TTGGTT
1 GTTTGAATAAATTGAATAAAATGTTATGAATAAATTGAATAAATGTAAAGTGAT-AAGTTGGTT
* *
2042078 GTTTGAATATATTGAATAAAATGTTATGGATAAATTGAATAAATGTAAAGTGATAAGTTGGTT
1 GTTTGAATAAATTGAATAAAATGTTATGAATAAATTGAATAAATGTAAAGTGATAAGTTGGTT
2042141 GT
1 GT
2042143 GACATTGAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 2 0.03
63 58 0.97
ACGTcount: A:0.41, C:0.01, G:0.21, T:0.38
Consensus pattern (63 bp):
GTTTGAATAAATTGAATAAAATGTTATGAATAAATTGAATAAATGTAAAGTGATAAGTTGGTT
Found at i:2042114 original size:23 final size:23
Alignment explanation
Indices: 2042077--2042120 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2042067 ATCAATTGGT
*
2042077 TGTT-TGAATATATTGAATAAAA
1 TGTTATGAATAAATTGAATAAAA
*
2042099 TGTTATGGATAAATTGAATAAA
1 TGTTATGAATAAATTGAATAAA
2042121 TGTAAAGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (23 bp):
TGTTATGAATAAATTGAATAAAA
Found at i:2042114 original size:40 final size:41
Alignment explanation
Indices: 2042036--2042114 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 41
2042026 TTGGATAAAA
*
2042036 TGTTATGAATAAATTGAATAAATGTGAAGTGATCAATTGGT
1 TGTTATGAATAAATTGAATAAATGTGAAGTGATAAATTGGT
* * *
2042077 TGTT-TGAATATATTGAATAAAATGTTATG-GATAAATTG
1 TGTTATGAATAAATTGAAT-AAATGTGAAGTGATAAATTG
2042115 AATAAATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 21 0.64
41 12 0.36
ACGTcount: A:0.39, C:0.01, G:0.20, T:0.39
Consensus pattern (41 bp):
TGTTATGAATAAATTGAATAAATGTGAAGTGATAAATTGGT
Found at i:2042132 original size:23 final size:23
Alignment explanation
Indices: 2042088--2042133 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2042078 GTTTGAATAT
* *
2042088 ATTGAATAAAATGTTATGGATAA
1 ATTGAATAAAATGTAAAGGATAA
2042111 ATTGAAT-AAATGTAAAGTGATAA
1 ATTGAATAAAATGTAAAG-GATAA
2042134 GTTGGTTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (23 bp):
ATTGAATAAAATGTAAAGGATAA
Found at i:2042385 original size:34 final size:34
Alignment explanation
Indices: 2042346--2042418 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
2042336 TTAAGTTGAA
2042346 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
* * *
2042380 TTTAATTTTAAATTTTGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
*
2042414 ATTAA
1 TTTAA
2042419 AACATTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAATACCATAATTTGTAT
Found at i:2044604 original size:28 final size:30
Alignment explanation
Indices: 2044540--2044606 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
2044530 TTAGTTTCCT
2044540 AAATAATATGCATTATAAAAATTTATAATTA
1 AAATAATATGCATTAT-AAAATTTATAATTA
* *
2044571 ATATAA-ATTCATTAT-AAATTTA-AATTAA
1 AAATAATATGCATTATAAAATTTATAATT-A
2044599 AAATAATA
1 AAATAATA
2044607 ATAAATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 4 0.13
28 13 0.42
29 1 0.03
30 8 0.26
31 5 0.16
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (30 bp):
AAATAATATGCATTATAAAATTTATAATTA
Found at i:2053841 original size:23 final size:24
Alignment explanation
Indices: 2053815--2053859 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
2053805 TTAAAATCAT
2053815 TTTTTCTCT-TTTCTTCT-TTATTC
1 TTTTTCTCTATTT-TTCTCTTATTC
2053838 TTTTTCTCTATTTTTCTCTTAT
1 TTTTTCTCTATTTTTCTCTTAT
2053860 CTATCTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTCTCTATTTTTCTCTTATTC
Found at i:2054563 original size:17 final size:17
Alignment explanation
Indices: 2054533--2054567 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2054523 TGATCCATGG
2054533 AGAATATAATTTAATAA
1 AGAATATAATTTAATAA
2054550 AGAAT-TAATATTAATAA
1 AGAATATAAT-TTAATAA
2054567 A
1 A
2054568 ATATTAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
AGAATATAATTTAATAA
Found at i:2070220 original size:37 final size:36
Alignment explanation
Indices: 2070174--2070460 Score: 300
Period size: 37 Copynumber: 7.8 Consensus size: 36
2070164 TTTTTTTAGA
* *
2070174 AAAAGATTTTTGAAACTGTATATATTATATAGTTTTG
1 AAAACATTTTTGAAACT-TATATAATATATAGTTTTG
*
2070211 AAATCA-TTTTGAAAAACTTATATAATATAGT-GTTTTG
1 AAAACATTTTTG--AAACTTATATAATATA-TAGTTTTG
* *
2070248 AAATCATTTTTAAGAACTTATATAATATATAGTTTTG
1 AAAACATTTTTGA-AACTTATATAATATATAGTTTTG
* *
2070285 AAAACATTTTTGAAAACATATATAATATATAGTTTTA
1 AAAACATTTTTG-AAACTTATATAATATATAGTTTTG
* *
2070322 AAAACATTTTTTGAAAATGTATATATTATATAGTTTTTG
1 AAAACA-TTTTTGAAACT-TATATAATATATAG-TTTTG
*
2070361 AAAAACATTTTTGACAAC-TATATAATATATGGTTTTG
1 -AAAACATTTTTGA-AACTTATATAATATATAGTTTTG
*
2070398 AAAACATTTTTTAAA--TATATAATATATAGTTTT-
1 AAAACATTTTTGAAACTTATATAATATATAGTTTTG
* *
2070431 AAAATATTTTTGAAA-TATATATATTATATA
1 AAAACATTTTTGAAACT-TATATAATATATA
2070461 ACTTATATTA
Statistics
Matches: 216, Mismatches: 20, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
33 13 0.06
34 17 0.08
35 14 0.06
36 19 0.09
37 92 0.43
38 42 0.19
39 11 0.05
40 8 0.04
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (36 bp):
AAAACATTTTTGAAACTTATATAATATATAGTTTTG
Found at i:2070474 original size:3 final size:3
Alignment explanation
Indices: 2070466--2070493 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2070456 ATATAACTTA
2070466 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2070494 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2070547 original size:21 final size:20
Alignment explanation
Indices: 2070501--2070554 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
2070491 ATTTTTTATT
*
2070501 TTTTTTATTTTTTTATGATT
1 TTTTTTATTTTTTTATGATA
2070521 TGTTTTTATTTTTTTAT-ATACA
1 T-TTTTTATTTTTTTATGAT--A
2070543 TTTTTTATTTTT
1 TTTTTTATTTTT
2070555 GTTTTTGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 3 0.10
21 26 0.87
22 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTTTATTTTTTTATGATA
Done.