Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008185.1 Hibiscus syriacus cultivar Beakdansim tig00110788_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: 3563405
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 16
Found at i:1406345 original size:33 final size:33
Alignment explanation
Indices: 1406303--1406469 Score: 181
Period size: 33 Copynumber: 4.8 Consensus size: 33
1406293 CTTAATGTCT
*
1406303 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1406336 ATCGCAATGCGAAATGAAAATCGCAACGTGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1406369 ATCGCAATGCAAATATGAATATCGCAACGCGGAAATGA
1 ATCGCAATGCGAA-ATGAAAATCGCAA--C-GAGA-GA
*
1406407 CTATCACAATGCGAAATGAAAATCGCAACGAGAGA
1 --ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1406442 ATCACAAAGCGAAATGAAAATCGTAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1406470 CGAATTTAGT
Statistics
Matches: 113, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
33 68 0.60
34 12 0.11
35 2 0.02
36 4 0.04
37 3 0.03
38 1 0.01
39 12 0.11
40 11 0.10
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1406387 original size:20 final size:19
Alignment explanation
Indices: 1406345--1406434 Score: 73
Period size: 20 Copynumber: 4.9 Consensus size: 19
1406335 AATCGCAATG
1406345 CGAAATGAAAATCGCAA--
1 CGAAATGAAAATCGCAATG
1406362 CG---TGAAAATCGCAATG
1 CGAAATGAAAATCGCAATG
* * *
1406378 CAAATATGAATATCGCAACG
1 CGAA-ATGAAAATCGCAATG
** *
1406398 CGGAAATGACTATCACAATG
1 C-GAAATGAAAATCGCAATG
1406418 CGAAATGAAAATCGCAA
1 CGAAATGAAAATCGCAA
1406435 CGAGAGAATC
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
14 12 0.21
16 1 0.02
17 2 0.04
19 13 0.23
20 26 0.46
21 2 0.04
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.17
Consensus pattern (19 bp):
CGAAATGAAAATCGCAATG
Found at i:1406501 original size:19 final size:19
Alignment explanation
Indices: 1406479--1406544 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
1406469 GCGAATTTAG
*
1406479 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
1406498 TTTCTCATTGCGA--TTC-
1 TTTCGCATTGCGATTTTCA
*
1406514 TCTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
1406531 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1406545 AGTCATTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
14 6 0.16
16 6 0.16
17 7 0.19
19 18 0.49
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:1406670 original size:14 final size:14
Alignment explanation
Indices: 1406651--1406687 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1406641 CATCAATTAA
1406651 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1406665 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1406679 ACAAATCAA
1 ACAAATCAA
1406688 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1408122 original size:42 final size:42
Alignment explanation
Indices: 1408076--1408155 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
1408066 CGATGACAGT
* *
1408076 GGCCTCTTGAACGGTAGGAGGGGACTCTCGAGGAATGATAAG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAAG
* * *
1408118 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
1408156 CAGGCGAGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAAG
Found at i:1408616 original size:19 final size:19
Alignment explanation
Indices: 1408600--1408689 Score: 91
Period size: 19 Copynumber: 4.9 Consensus size: 19
1408590 GAGATTTTGG
1408600 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
1408619 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
1408635 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
**
1408652 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
*
1408671 TTTTTCACGTTGCGATTTT
1 --TTTCGCGTTGCGATTTT
1408690 ATGTTTCGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.18
16 3 0.05
17 3 0.05
19 27 0.47
21 14 0.25
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:1408899 original size:94 final size:94
Alignment explanation
Indices: 1408753--1409132 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
1408743 ATGGATTGCA
* * * *
1408753 TTAC-TTCAACCAAAAGACAAAACAAATACAAATACTAACTTTAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1408817 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1408846 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1408911 TTAGCAGAATTAGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1408940 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1409005 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1409034 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
1409098 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
1409128 TTACT
1 TTACT
1409133 AAGCAATCTA
Statistics
Matches: 273, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
93 22 0.08
94 251 0.92
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1410853 original size:20 final size:20
Alignment explanation
Indices: 1410830--1410885 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
1410820 TGAAATGAAA
1410830 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
1410850 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
1410870 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
1410886 CGCAACGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:1410907 original size:19 final size:19
Alignment explanation
Indices: 1410821--1410952 Score: 148
Period size: 19 Copynumber: 7.1 Consensus size: 19
1410811 TCTTTTGGTT
*
1410821 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
1410840 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1410860 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1410878 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1410894 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1410913 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1410932 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1410951 GA
1 GA
1410953 TTTTGGTTTC
Statistics
Matches: 99, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 1 0.01
18 2 0.02
19 54 0.55
20 28 0.28
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1410996 original size:33 final size:33
Alignment explanation
Indices: 1410948--1411027 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
1410938 AAAATCGCAA
** *
1410948 TGCGATTTTGGTTTCGCGTTGCGATTATTTCAT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCAT
* *
1410981 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCAT
*
1411014 TGCAATTTTCATTT
1 TGCGATTTTCATTT
1411028 ATCTCGTTGC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.49
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCAT
Found at i:1411004 original size:19 final size:18
Alignment explanation
Indices: 1410948--1411006 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
1410938 AAAATCGCAA
*
1410948 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
*
1410967 TGCGA--TTATTT--CAT
1 TGCGATTTTATTTCGCGT
1410981 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-ATTTCGCGT
1411000 TGCGATT
1 TGCGATT
1411007 CTCTCGTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 7 0.22
16 5 0.16
17 6 0.19
19 14 0.44
ACGTcount: A:0.12, C:0.17, G:0.24, T:0.47
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:1411034 original size:21 final size:20
Alignment explanation
Indices: 1411008--1411083 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
1410998 GTTGCGATTC
1411008 TCTCGTTGCAATTTTCATTT
1 TCTCGTTGCAATTTTCATTT
* **
1411028 ATCTCGTTGCGATAGTCATTT
1 -TCTCGTTGCAATTTTCATTT
*
1411049 TCGT-ATTGCAATTTTCATTT
1 TC-TCGTTGCAATTTTCATTT
*
1411069 TCAT-GTTGCGATTTT
1 TC-TCGTTGCAATTTT
1411084 AAGTTTAGAA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
20 26 0.59
21 18 0.41
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.51
Consensus pattern (20 bp):
TCTCGTTGCAATTTTCATTT
Found at i:1411678 original size:20 final size:20
Alignment explanation
Indices: 1411644--1411815 Score: 177
Period size: 20 Copynumber: 8.5 Consensus size: 20
1411634 TTAAAAATCA
*
1411644 CGTTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGTATTCT
* * *
1411665 CGTTGCGATTTACGAATACG
1 CGTTGCGATTTACGTATTCT
*
1411685 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCT
* *
1411705 CGTTGCGATTTACAG-ATACG
1 CGTTGCGATTTAC-GTATTCT
1411725 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCT
* *
1411745 CGTTGCGATTTACGGATACT
1 CGTTGCGATTTACGTATTCT
* *
1411765 CGTTGCGATTTACAG-ATACG
1 CGTTGCGATTTAC-GTATTCT
* *
1411785 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGTATTCT
1411806 CGTTGCGATT
1 CGTTGCGATT
1411816 GTCAGAATCG
Statistics
Matches: 129, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.01
20 101 0.78
21 27 0.21
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCT
Found at i:1411702 original size:40 final size:40
Alignment explanation
Indices: 1411644--1411815 Score: 222
Period size: 40 Copynumber: 4.2 Consensus size: 40
1411634 TTAAAAATCA
*
1411644 CGTTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACG
1 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGAATACG
*
1411685 CATTGCGATTTACGTATTCTCGTTGCGATTTAC-AGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGA-ATACG
* *
1411725 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACT
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGAATACG
* * * *
1411765 CGTTGCGATTTACAG-ATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTAC-GTATTCTCGTTGCGA-TTTACGAATACG
1411806 CGTTGCGATT
1 CGTTGCGATT
1411816 GTCAGAATCG
Statistics
Matches: 120, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
39 1 0.01
40 89 0.74
41 30 0.25
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACGAATACG
Found at i:1411738 original size:60 final size:60
Alignment explanation
Indices: 1411665--1411815 Score: 230
Period size: 60 Copynumber: 2.5 Consensus size: 60
1411655 TACGTATTGT
* * * *
1411665 CGTTGCGATTTACGAATACGCATTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGAATACTCGTTGCGATTTACGGATACTCGTTGCGATTTACAGATACG
* *
1411725 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGAATACTCGTTGCGATTTACGGATACTCGTTGCGATTTACAGATACG
*
1411785 CGTTGCGATTTTACGGATACTCGTTGCGATT
1 CGTTGCGA-TTTACGAATACTCGTTGCGATT
1411816 GTCAGAATCG
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
60 62 0.76
61 20 0.24
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (60 bp):
CGTTGCGATTTACGAATACTCGTTGCGATTTACGGATACTCGTTGCGATTTACAGATACG
Found at i:1411835 original size:61 final size:61
Alignment explanation
Indices: 1411665--1411857 Score: 207
Period size: 60 Copynumber: 3.2 Consensus size: 61
1411655 TACGTATTGT
* * * * * *
1411665 CGTTGCGA-TTTACGAATACGCATTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTTACGGATACTCGTTGCGATTTACGAATACGCGTTGCGATTTACAGATACG
* * * *
1411725 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTTACGGATACTCGTTGCGATTTACGAATACGCGTTGCGATTTACAGATACG
* * *
1411785 CGTTGCGATTTTACGGATACTCGTTGCGATTGT-CAGAAT-CGCGTTACGATTTATATG-TTCG
1 CGTTGCGATTTTACGGATACTCGTTGCGATT-TAC-GAATACGCGTTGCGATTTACA-GATACG
1411846 CGTTGCGATTTT
1 CGTTGCGATTTT
1411858 CATATTCGCG
Statistics
Matches: 116, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
60 62 0.53
61 49 0.42
62 5 0.04
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (61 bp):
CGTTGCGATTTTACGGATACTCGTTGCGATTTACGAATACGCGTTGCGATTTACAGATACG
Found at i:1411846 original size:20 final size:20
Alignment explanation
Indices: 1411806--1411875 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1411796 TACGGATACT
* * *
1411806 CGTTGCGATTGTCAGAATCG
1 CGTTGCGATTTTCATATTCG
* *
1411826 CGTTACGATTTAT-ATGTTCG
1 CGTTGCGATTT-TCATATTCG
1411846 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTTCATATTCG
1411866 CGTTGCGATT
1 CGTTGCGATT
1411876 CTAGAAAATC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 1 0.02
20 39 0.95
21 1 0.02
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCATATTCG
Found at i:1412769 original size:16 final size:16
Alignment explanation
Indices: 1412750--1412783 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1412740 CAATATACGA
1412750 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
1412766 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
1412782 AT
1 AT
1412784 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:1412857 original size:16 final size:18
Alignment explanation
Indices: 1412825--1412858 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1412815 TATTAATGTA
1412825 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1412843 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
1412859 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1413397 original size:21 final size:23
Alignment explanation
Indices: 1413352--1413398 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1413342 GTGTCACCAA
1413352 TAACATATATCATGATCATGTGT
1 TAACATATATCATGATCATGTGT
* *
1413375 TAACATATGTCA-GATCCTG-GT
1 TAACATATATCATGATCATGTGT
1413396 TAA
1 TAA
1413399 ATGATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (23 bp):
TAACATATATCATGATCATGTGT
Found at i:1413529 original size:130 final size:130
Alignment explanation
Indices: 1413325--1413572 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
1413315 AATTTTCTTC
* * *
1413325 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACATATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
1413390 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
1413455 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACGTGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
1413520 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
1413573 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:1414019 original size:35 final size:35
Alignment explanation
Indices: 1413969--1414045 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
1413959 AATTGAATTT
* *
1413969 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
1414004 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
1414039 AATTGAA
1 AATTGAA
1414046 GACTGTTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.36, C:0.01, G:0.23, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:1414359 original size:35 final size:35
Alignment explanation
Indices: 1414295--1414370 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
1414285 AATTGAATTT
* * *
1414295 AATTGAATTATTTTGAAATTTAGGGTTTAGAATGA
1 AATTGAATTATTTGGAAATTTAAGATTTAGAATGA
1414330 AATTGAATTACTTTGGAAA-TTAAGATTTAGAATGA
1 AATTGAATTA-TTTGGAAATTTAAGATTTAGAATGA
1414365 AATTGA
1 AATTGA
1414371 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 30 0.81
36 7 0.19
ACGTcount: A:0.41, C:0.01, G:0.18, T:0.39
Consensus pattern (35 bp):
AATTGAATTATTTGGAAATTTAAGATTTAGAATGA
Found at i:1414534 original size:326 final size:326
Alignment explanation
Indices: 1413941--1414594 Score: 1218
Period size: 326 Copynumber: 2.0 Consensus size: 326
1413931 TGAAATTAAA
*
1413941 TAATAATAAATCTGACATAATTGAATTTAATTGAATTATTTTGGAATTTAGGGTTTAGAATGAAA
1 TAATAATAAATCTGACATAATTGAATTTAATTGAATTATTTTGAAATTTAGGGTTTAGAATGAAA
** * *
1414006 TTGAATTACTTTGGAAATTGGGGTTTAGAATGAAATTGAAGACTGTTTTGTAAGTTTTAAAAGTT
66 TTGAATTACTTTGGAAATTAAGATTTAGAATGAAATTGAAGACTGTTTTGCAAGTTTTAAAAGTT
1414071 GGGGGACCTAAATTCAAGTGTCTGAAAAGTTCAATAACATTTTATATAATTTACCCTAATTTCTA
131 GGGGGACCTAAATTCAAGTGTCTGAAAAGTTCAATAACATTTTATATAATTTACCCTAATTTCTA
1414136 ACGGTGGTTTAAGTTGGAGGACCATATTGCAAACGGAATAAATGTTGGGGGACTGTATTGCAAGT
196 ACGGTGGTTTAAGTTGGAGGACCATATTGCAAACGGAATAAATGTTGGGGGACTGTATTGCAAGT
*
1414201 TTTAAAAGTTGAGAGACCTAAATGCAAGCTTCAGAAATGTTCAGTGACCATTACTATACTTTACC
261 TTTAAAAGTTGAGAGACCTAAATACAAGCTTCAGAAATGTTCAGTGACCATTACTATACTTTACC
1414266 C
326 C
1414267 TAATAATAAATCTGACATAATTGAATTTAATTGAATTATTTTGAAATTTAGGGTTTAGAATGAAA
1 TAATAATAAATCTGACATAATTGAATTTAATTGAATTATTTTGAAATTTAGGGTTTAGAATGAAA
*
1414332 TTGAATTACTTTGGAAATTAAGATTTAGAATGAAATTGAGGACTGTTTTGCAAGTTTTAAAAGTT
66 TTGAATTACTTTGGAAATTAAGATTTAGAATGAAATTGAAGACTGTTTTGCAAGTTTTAAAAGTT
1414397 GGGGGACCTAAATTCAAGTGTCTGAAAAGTTCAATAACATTTTATATAATTTACCCTAATTTCTA
131 GGGGGACCTAAATTCAAGTGTCTGAAAAGTTCAATAACATTTTATATAATTTACCCTAATTTCTA
*
1414462 ACGGTGGTTTAAGTTGGGGGACCATATTGCAAACGGAATAAATGTTGGGGGACTGTATTGCAAGT
196 ACGGTGGTTTAAGTTGGAGGACCATATTGCAAACGGAATAAATGTTGGGGGACTGTATTGCAAGT
* *
1414527 TTTAAAAGTTGGGGGACCTAAATACAAGCTTCAGAAATGTTCAGTGACCATTACTATACTTTACC
261 TTTAAAAGTTGAGAGACCTAAATACAAGCTTCAGAAATGTTCAGTGACCATTACTATACTTTACC
1414592 C
326 C
1414593 TA
1 TA
1414595 TTTTTAAAAC
Statistics
Matches: 318, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
326 318 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (326 bp):
TAATAATAAATCTGACATAATTGAATTTAATTGAATTATTTTGAAATTTAGGGTTTAGAATGAAA
TTGAATTACTTTGGAAATTAAGATTTAGAATGAAATTGAAGACTGTTTTGCAAGTTTTAAAAGTT
GGGGGACCTAAATTCAAGTGTCTGAAAAGTTCAATAACATTTTATATAATTTACCCTAATTTCTA
ACGGTGGTTTAAGTTGGAGGACCATATTGCAAACGGAATAAATGTTGGGGGACTGTATTGCAAGT
TTTAAAAGTTGAGAGACCTAAATACAAGCTTCAGAAATGTTCAGTGACCATTACTATACTTTACC
C
Found at i:1417672 original size:64 final size:64
Alignment explanation
Indices: 1417540--1417678 Score: 147
Period size: 64 Copynumber: 2.2 Consensus size: 64
1417530 GCACTAAGAG
* * * * ***
1417540 TGCATCGGTGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATCCATGGCTGG
1 TGCATCGATGCATCAAATGCATTCGATGTTTCAAAAAAGCCACAGTGCATCGATCCATGGCAAA
* * *
1417604 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAATCCTCAGTGCATCGATGCAT-G-AA
1 TGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAAAAGCCACAGTGCATCGATCCATGGCAA
1417667 A
64 A
1417668 TGCATTCGATG
1 TGCA-TCGATG
1417679 TTCAATTTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
64 30 0.48
65 12 0.19
66 20 0.32
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCAAAAAAGCCACAGTGCATCGATCCATGGCAAA
Found at i:1418774 original size:21 final size:21
Alignment explanation
Indices: 1418750--1418793 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1418740 CCGAAGGAGG
* *
1418750 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAACT
* *
1418771 AGGAGCAGCTCGTGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
1418792 AG
1 AG
1418794 CTCCCAGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:1420433 original size:20 final size:21
Alignment explanation
Indices: 1420342--1420436 Score: 70
Period size: 21 Copynumber: 4.4 Consensus size: 21
1420332 GGCCTTGTGC
*
1420342 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* * *
1420365 ATC-AGTACACCTTCATGGTGT
1 ATCGA-TGCACATTCAAGGTGT
*
1420386 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
1420408 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
1420428 ATCGATGCA
1 ATCGATGCA
1420437 TGAAGCAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
20 11 0.19
21 20 0.34
22 16 0.28
23 11 0.19
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.27
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:1423012 original size:64 final size:62
Alignment explanation
Indices: 1422959--1423170 Score: 212
Period size: 65 Copynumber: 3.3 Consensus size: 62
1422949 CGGTGCACCA
1422959 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCTTGGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATA-CTTGGTGCATCGATGCATGG
** *
1423023 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATA-TTCAGAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATACTT--G-GTGCATCGATGCATG
1423087 G
62 G
* * * * * * *
1423088 AGAGTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATAC-TTGGTGCATCGATGCATGG
* *
1423152 ACTGATGCATCGGTGCATG
1 AGTG-TGCATCGATGCATG
1423171 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
62 2 0.02
63 4 0.03
64 53 0.43
65 64 0.52
67 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (62 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATACTTGGTGCATCGATGCATGG
Found at i:1423031 original size:19 final size:20
Alignment explanation
Indices: 1423002--1423039 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1422992 TTGAAAAATA
1423002 GCTTGGTGCATCGATGCATG
1 GCTTGGTGCATCGATGCATG
1423022 GCTT-GTGCATCGATGCAT
1 GCTTGGTGCATCGATGCAT
1423040 CAAATGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.16, C:0.21, G:0.32, T:0.32
Consensus pattern (20 bp):
GCTTGGTGCATCGATGCATG
Found at i:1423093 original size:19 final size:19
Alignment explanation
Indices: 1423069--1423119 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1423059 GAAAATATTC
1423069 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1423088 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1423107 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1423120 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1423361 original size:20 final size:21
Alignment explanation
Indices: 1423338--1423377 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1423328 GAATCGAATA
1423338 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
1423358 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
1423378 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:1424195 original size:21 final size:21
Alignment explanation
Indices: 1424171--1424214 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1424161 CTGAAGGAGG
*
1424171 AGGAGGAGCACGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
*
1424192 AGGAGCAGCTCGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
1424213 AG
1 AG
1424215 CTCCCGGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.36, T:0.07
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:1429699 original size:22 final size:21
Alignment explanation
Indices: 1429657--1429696 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1429647 GAGTTTGTTT
*
1429657 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1429678 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1429697 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1431676 original size:64 final size:64
Alignment explanation
Indices: 1431623--1431785 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
1431613 CGGTGCACCA
*
1431623 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
1431687 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
1431752 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
1431786 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 39 0.46
65 46 0.54
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:1431757 original size:19 final size:19
Alignment explanation
Indices: 1431733--1431783 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1431723 GAAAATATTC
1431733 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1431752 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1431771 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1431784 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1432017 original size:20 final size:21
Alignment explanation
Indices: 1431994--1432033 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1431984 GAATCGAATA
1431994 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
1432014 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
1432034 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:1435989 original size:65 final size:63
Alignment explanation
Indices: 1435791--1436000 Score: 212
Period size: 65 Copynumber: 3.3 Consensus size: 63
1435781 TACACTAAGA
* *** *
1435791 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-A-CTTCAGTGCATCGATGCATGGTTG
*
1435855 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCTTCAGTGTATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAA-CTTCAGTGCATCGATGCATGGT-T
1435920 -
63 G
* * **
1435920 GTGCATTGATGCATGAAATGCATTCGATG-TTCAATTTAA-TTCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAACTTCA--GTGCATCGATGCATGG-T
1435983 TG
62 TG
*
1435985 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
1436001 CTTTGATGAA
Statistics
Matches: 123, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
62 4 0.03
63 3 0.02
64 48 0.39
65 64 0.52
66 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAACTTCAGTGCATCGATGCATGGTTG
Found at i:1437944 original size:53 final size:53
Alignment explanation
Indices: 1437864--1437969 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
1437854 CCTTCATTGG
1437864 AGCCTATGAAGGATACTGAAACGCTTACTCTGTCCAGGATGGATCGGGAGGAC
1 AGCCTATGAAGGATACTGAAACGCTTACTCTGTCCAGGATGGATCGGGAGGAC
1437917 AGCCTATGAAGGATACTGAAACGCTTACTCTGTCCAGGATGGATCGGGAGGAC
1 AGCCTATGAAGGATACTGAAACGCTTACTCTGTCCAGGATGGATCGGGAGGAC
1437970 CGACAGTCGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (53 bp):
AGCCTATGAAGGATACTGAAACGCTTACTCTGTCCAGGATGGATCGGGAGGAC
Found at i:1438736 original size:11 final size:11
Alignment explanation
Indices: 1438720--1438749 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1438710 TATTTTTAAA
1438720 AAGATAATTAT
1 AAGATAATTAT
1438731 AAGATAATTAT
1 AAGATAATTAT
1438742 AAGATAAT
1 AAGATAAT
1438750 ATGTGTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (11 bp):
AAGATAATTAT
Found at i:1441965 original size:16 final size:16
Alignment explanation
Indices: 1441930--1441970 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1441920 GTTTACTTCA
*
1441930 GAATGATT-AAACGTT
1 GAATGATTCAAACGCT
*
1441945 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
1441961 GAATGATTCA
1 GAATGATTCA
1441971 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:1442579 original size:21 final size:21
Alignment explanation
Indices: 1442543--1442593 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1442533 CTGAAATAAT
* * *
1442543 AATAAAATATTAATTTTATTC
1 AATAAAATAGTAATTTAATTA
*
1442564 AATAAAATAGTGATTTAATTA
1 AATAAAATAGTAATTTAATTA
*
1442585 AAAAAAATA
1 AATAAAATA
1442594 ATATATAGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (21 bp):
AATAAAATAGTAATTTAATTA
Found at i:1453697 original size:15 final size:16
Alignment explanation
Indices: 1453677--1453709 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1453667 TTTTAACTTA
1453677 AATTAA-TATTTATTT
1 AATTAATTATTTATTT
*
1453692 AATTAATTTTTTATTT
1 AATTAATTATTTATTT
1453708 AA
1 AA
1453710 ACATAACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTAATTATTTATTT
Found at i:1455417 original size:20 final size:20
Alignment explanation
Indices: 1455368--1455417 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1455358 CTGATTGACA
*
1455368 AAATTAAAAGATCAATAATC
1 AAATTAAAATATCAATAATC
1455388 AAATTAAAATATCAATAATC
1 AAATTAAAATATCAATAATC
1455408 AAATTAAAAT
1 AAATTAAAAT
1455418 TCACCTATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (20 bp):
AAATTAAAATATCAATAATC
Found at i:1458858 original size:2 final size:2
Alignment explanation
Indices: 1458851--1458880 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1458841 TGATTTTACC
1458851 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
1458881 TATGCACCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1463052 original size:2 final size:2
Alignment explanation
Indices: 1463045--1463074 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1463035 TTTACCATAA
1463045 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
1463075 TGCACCTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1465184 original size:32 final size:31
Alignment explanation
Indices: 1465148--1465265 Score: 150
Period size: 32 Copynumber: 3.7 Consensus size: 31
1465138 GTTCTACGGA
1465148 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGAA-TACCTATGTCTTTCGAG
* *
1465180 ACATATGGACAGTATACCTATGT-TCTACG-G
1 ACATATGGACAGAATACCTATGTCT-TTCGAG
*
1465210 AACATATGGACAAAATTACCTATGTCTTTCGAG
1 -ACATATGGACAGAA-TACCTATGTCTTTCGAG
*
1465243 ACATATGGACAGTATACCTATGT
1 ACATATGGACAGAATACCTATGT
1465266 TCTAAGGAAC
Statistics
Matches: 74, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
30 2 0.03
31 33 0.45
32 37 0.50
33 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (31 bp):
ACATATGGACAGAATACCTATGTCTTTCGAG
Found at i:1465227 original size:63 final size:63
Alignment explanation
Indices: 1465128--1465284 Score: 287
Period size: 63 Copynumber: 2.5 Consensus size: 63
1465118 AGAGTTGAGG
* *
1465128 GTATACTTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAAAATTACCTATGTCTTTCGAGACATATGGACA
1465191 GTATACCTATGTTCTACGGAACATATGGACAAAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAAAATTACCTATGTCTTTCGAGACATATGGACA
*
1465254 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
1465285 GTTTACCTAG
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 91 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAAAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:1465299 original size:31 final size:31
Alignment explanation
Indices: 1465135--1465318 Score: 187
Period size: 31 Copynumber: 5.9 Consensus size: 31
1465125 AGGGTATACT
*
1465135 TATGTTCTACGGAACATATGGACAGAATTACC
1 TATGTTCTACGGAACATATGGACAG-TTTACC
* *
1465167 TATG-TCTTTC-GAGACATATGGACAGTATACC
1 TATGTTC-TACGGA-ACATATGGACAGTTTACC
**
1465198 TATGTTCTACGGAACATATGGACAAAATTACC
1 TATGTTCTACGGAACATATGGAC-AGTTTACC
* *
1465230 TATG-TCTTTC-GAGACATATGGACAGTATACC
1 TATGTTC-TACGGA-ACATATGGACAGTTTACC
*
1465261 TATGTTCTAAGGAACATATGGACAGTTTACC
1 TATGTTCTACGGAACATATGGACAGTTTACC
* * *
1465292 TAGGTTCTTCGGAACCTATGGACAGTT
1 TATGTTCTACGGAACATATGGACAGTT
1465319 GCCGAGGATC
Statistics
Matches: 125, Mismatches: 18, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
31 78 0.62
32 47 0.38
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
TATGTTCTACGGAACATATGGACAGTTTACC
Found at i:1465367 original size:30 final size:30
Alignment explanation
Indices: 1465305--1465375 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
1465295 GTTCTTCGGA
* * * *
1465305 ACCTATGGACAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCCTTATG
* *
1465335 ACCTCTGGATAGTTACCGAGGTTCCTTGTG
1 ACCTCTGGATAGTTACCGAGGATCCTTATG
1465365 ACCTCTGGATA
1 ACCTCTGGATA
1465376 TGTCCTTCGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCCTTATG
Found at i:1483705 original size:2 final size:2
Alignment explanation
Indices: 1483698--1483728 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1483688 CTGGATTAAG
1483698 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1483729 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1483733 original size:2 final size:2
Alignment explanation
Indices: 1483728--1483756 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1483718 ATATATATAT
1483728 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 A
1483757 CTATTGGTAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1497062 original size:21 final size:21
Alignment explanation
Indices: 1497016--1497062 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1497006 GCAATGAATT
*
1497016 CTAAACCATAAATCCTAAATC
1 CTAAACCATAAATCCTAAACC
*
1497037 ATAAACCATAAA-CCTTAAACC
1 CTAAACCATAAATCC-TAAACC
1497058 CTAAA
1 CTAAA
1497063 TTGTACTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (21 bp):
CTAAACCATAAATCCTAAACC
Found at i:1497146 original size:21 final size:21
Alignment explanation
Indices: 1497122--1497173 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1497112 TAATAACCTG
*
1497122 AAACACTAAATCATAAACTAT
1 AAACCCTAAATCATAAACTAT
1497143 AAACCCTAAATCATAAACTAT
1 AAACCCTAAATCATAAACTAT
1497164 AAACCCTAAA
1 AAACCCTAAA
1497174 CCCTAAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.56, C:0.23, G:0.00, T:0.21
Consensus pattern (21 bp):
AAACCCTAAATCATAAACTAT
Found at i:1497180 original size:21 final size:21
Alignment explanation
Indices: 1497122--1497180 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
1497112 TAATAACCTG
* *
1497122 AAACACTAAATCATAAACTAT
1 AAACCCTAAACCATAAACTAT
*
1497143 AAACCCTAAATCATAAACTAT
1 AAACCCTAAACCATAAACTAT
*
1497164 AAACCCTAAACCCTAAA
1 AAACCCTAAACCATAAA
1497181 ATCTAAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.20
Consensus pattern (21 bp):
AAACCCTAAACCATAAACTAT
Found at i:1497187 original size:21 final size:21
Alignment explanation
Indices: 1497122--1497187 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1497112 TAATAACCTG
* * *
1497122 AAACACTAAATCATAAACTAT
1 AAACCCTAAACCATAAAATAT
* *
1497143 AAACCCTAAATCATAAACTAT
1 AAACCCTAAACCATAAAATAT
* *
1497164 AAACCCTAAACCCTAAAATCT
1 AAACCCTAAACCATAAAATAT
1497185 AAA
1 AAA
1497188 TATAATTATG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (21 bp):
AAACCCTAAACCATAAAATAT
Found at i:1513960 original size:20 final size:19
Alignment explanation
Indices: 1513935--1513982 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
1513925 ATGAGACTGA
1513935 ATAAATTTTTTATAAAATAT
1 ATAAATTTTTT-TAAAATAT
*
1513955 ATAAATAATTTTTTAAATTAT
1 ATAAAT--TTTTTTAAAATAT
1513976 -TAAATTT
1 ATAAATTT
1513983 AAAGTGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
20 11 0.44
21 7 0.28
22 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATAAATTTTTTTAAAATAT
Found at i:1513971 original size:21 final size:21
Alignment explanation
Indices: 1513941--1513980 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1513931 CTGAATAAAT
1513941 TTTTTATAAAATATATAAATAA
1 TTTTTATAAAATAT-TAAATAA
*
1513963 TTTTT-TAAATTATTAAAT
1 TTTTTATAAAATATTAAAT
1513981 TTAAAGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTTATAAAATATTAAATAA
Found at i:1517440 original size:2 final size:2
Alignment explanation
Indices: 1517433--1517462 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1517423 CCAAGGTATC
1517433 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
1517463 GCACATATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1521359 original size:60 final size:59
Alignment explanation
Indices: 1521270--1521404 Score: 146
Period size: 59 Copynumber: 2.3 Consensus size: 59
1521260 AAATTAAACA
** * * * *
1521270 CTCAAAAGTTTAGGGATTAATATAGAATGATGGAT-ATAGTTTAGGGATGAAATTAGAATG
1 CTCAAAAGTTTAAAGATAAATATAAAATGA--AATCATAGTTTAAGGATGAAATTAGAATG
* * *
1521330 CTCAAAAGTTTAAAGATAAATTTAAAATGAAATCATAGTTTAATGATGAATTTAGAATG
1 CTCAAAAGTTTAAAGATAAATATAAAATGAAATCATAGTTTAAGGATGAAATTAGAATG
* *
1521389 TTCAAAACTTTAAAGA
1 CTCAAAAGTTTAAAGA
1521405 CCAACTTAGA
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
58 2 0.03
59 36 0.57
60 25 0.40
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (59 bp):
CTCAAAAGTTTAAAGATAAATATAAAATGAAATCATAGTTTAAGGATGAAATTAGAATG
Found at i:1521418 original size:59 final size:59
Alignment explanation
Indices: 1521305--1521418 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
1521295 AATGATGGAT
* * * *
1521305 ATAGTTTAGGGATGAAATTAGAATGCTCAAAAGTTTAAAGATAAATTTAAAATGAAATC
1 ATAGTTTAAGGATGAAATTAGAATGCTCAAAACTTTAAAGACAAACTTAAAATGAAATC
* * * * *
1521364 ATAGTTTAATGATGAATTTAGAATGTTCAAAACTTTAAAGACCAACTTAGAATGA
1 ATAGTTTAAGGATGAAATTAGAATGCTCAAAACTTTAAAGACAAACTTAAAATGA
1521419 GTCATAAGCC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.32
Consensus pattern (59 bp):
ATAGTTTAAGGATGAAATTAGAATGCTCAAAACTTTAAAGACAAACTTAAAATGAAATC
Found at i:1528974 original size:36 final size:38
Alignment explanation
Indices: 1528922--1528994 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 38
1528912 GGCAACCAAT
1528922 TTTGAAAAAATGG-TTTTCAAAGTTTGGTAAATGTTTC
1 TTTGAAAAAATGGTTTTTCAAAGTTTGGTAAATGTTTC
*
1528959 TTTG-AAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 TTTGAAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
1528995 GTTGAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 8 0.24
37 26 0.76
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (38 bp):
TTTGAAAAAATGGTTTTTCAAAGTTTGGTAAATGTTTC
Found at i:1534512 original size:29 final size:29
Alignment explanation
Indices: 1534470--1534527 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1534460 ATATTGCAGC
1534470 TTTGAATGGCAGACGGAGTTTGTTGATGT
1 TTTGAATGGCAGACGGAGTTTGTTGATGT
1534499 TTTGAATGGCAGACGGAGTTTGTTGATGT
1 TTTGAATGGCAGACGGAGTTTGTTGATGT
1534528 GCTCTCTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.07, G:0.34, T:0.38
Consensus pattern (29 bp):
TTTGAATGGCAGACGGAGTTTGTTGATGT
Found at i:1542965 original size:13 final size:13
Alignment explanation
Indices: 1542949--1542974 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1542939 TTGTCGCGGT
1542949 TTTTTGTGGTTTA
1 TTTTTGTGGTTTA
1542962 TTTTTGTGGTTTA
1 TTTTTGTGGTTTA
1542975 GAAATTAGAT
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:0.08, C:0.00, G:0.23, T:0.69
Consensus pattern (13 bp):
TTTTTGTGGTTTA
Found at i:1544889 original size:26 final size:26
Alignment explanation
Indices: 1544860--1544909 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1544850 AAAAATAAAT
1544860 TTTAA-TATTACAAAAAATAAATTTAA
1 TTTAAGTATTACAAAAAA-AAATTTAA
* *
1544886 TTTAAGTATTTCAAAATAAAATTT
1 TTTAAGTATTACAAAAAAAAATTT
1544910 TATAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (26 bp):
TTTAAGTATTACAAAAAAAAATTTAA
Found at i:1554236 original size:36 final size:36
Alignment explanation
Indices: 1554196--1554266 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
1554186 AATAAATATA
*
1554196 CAAATTTAAGCTTCTATATGTAAATAGGTATAGATC
1 CAAATTTAAGCTTCTATATGTAAATAGGTAAAGATC
*
1554232 CAAATTTAAGCTTCTATATGTATATAGGTAAAGAT
1 CAAATTTAAGCTTCTATATGTAAATAGGTAAAGAT
1554267 AATAGAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (36 bp):
CAAATTTAAGCTTCTATATGTAAATAGGTAAAGATC
Found at i:1569152 original size:32 final size:32
Alignment explanation
Indices: 1569084--1569162 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 32
1569074 AATCACTAAA
* ** * *
1569084 TTTATTAAATTATTATAAAATAATTATTTATT
1 TTTATAAAATTATTATAAAATAAACATTGATC
*
1569116 TTTATCAAATTATTATAAAATAAACATTGATC
1 TTTATAAAATTATTATAAAATAAACATTGATC
*
1569148 TTTATAAAAATATTA
1 TTTATAAAATTATTA
1569163 AATAATGTGA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (32 bp):
TTTATAAAATTATTATAAAATAAACATTGATC
Found at i:1576552 original size:62 final size:62
Alignment explanation
Indices: 1576456--1576577 Score: 244
Period size: 62 Copynumber: 2.0 Consensus size: 62
1576446 CATGAAAAAT
1576456 AAAATAGTAACAAACCACTATCATGGTTCATGGCCGAGAGTGTAACTTGACAATACATATAA
1 AAAATAGTAACAAACCACTATCATGGTTCATGGCCGAGAGTGTAACTTGACAATACATATAA
1576518 AAAATAGTAACAAACCACTATCATGGTTCATGGCCGAGAGTGTAACTTGACAATACATAT
1 AAAATAGTAACAAACCACTATCATGGTTCATGGCCGAGAGTGTAACTTGACAATACATAT
1576578 CAACATGGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (62 bp):
AAAATAGTAACAAACCACTATCATGGTTCATGGCCGAGAGTGTAACTTGACAATACATATAA
Found at i:1583499 original size:2 final size:2
Alignment explanation
Indices: 1583492--1583520 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1583482 CACGTATGGT
1583492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1583521 TATTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1585694 original size:20 final size:20
Alignment explanation
Indices: 1585669--1585706 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1585659 ATAACTGTAG
1585669 ACAAAAAA-AATATAATTAGC
1 ACAAAAAATAAT-TAATTAGC
1585689 ACAAAAAATAATTAATTA
1 ACAAAAAATAATTAATTA
1585707 ATAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.66, C:0.08, G:0.03, T:0.24
Consensus pattern (20 bp):
ACAAAAAATAATTAATTAGC
Found at i:1591281 original size:21 final size:20
Alignment explanation
Indices: 1591195--1591352 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1591185 AAATGACCAA
**
1591195 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* * ***
1591214 AAAAATCGCAATGCGATCCC
1 CAAAATCGCAACGCGATTTT
** *
1591234 CAAAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1591254 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1591275 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1591296 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1591316 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1591337 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1591353 ACACATAAAT
Statistics
Matches: 105, Mismatches: 28, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
19 15 0.14
20 43 0.41
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1591381 original size:20 final size:20
Alignment explanation
Indices: 1591319--1591512 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1591309 CGATTTTCCA
* ** *
1591319 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1591339 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1591359 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1591379 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1591399 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1591419 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1591439 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1591459 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1591479 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1591500 AAATCGCAACGCG
1 AAATCGCAACGCG
1591513 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:1591403 original size:60 final size:60
Alignment explanation
Indices: 1591319--1591512 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1591309 CGATTTTCCA
* ** * *
1591319 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1591379 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
1591439 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1591500 AAATCGCAACGCG
1 AAATCGCAACGCG
1591513 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:1591933 original size:33 final size:33
Alignment explanation
Indices: 1591894--1591964 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1591884 TTCACTTAGA
* *
1591894 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
1591927 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
1591960 TTTCA
1 TTTCA
1591965 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:1592070 original size:21 final size:20
Alignment explanation
Indices: 1592044--1592149 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
1592034 TGCAGAAGAG
1592044 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
1592065 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
1592085 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
1592106 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
1592120 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
1592139 TCGCAACGAGA
1 TCGCAACGAGA
1592150 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:1592088 original size:20 final size:21
Alignment explanation
Indices: 1592042--1592120 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
1592032 TTTGCAGAAG
*
1592042 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
1592064 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
1592083 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
1592105 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
1592121 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:1592101 original size:41 final size:38
Alignment explanation
Indices: 1592037--1592153 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
1592027 TTCAATTTGC
* *
1592037 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1592075 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1592116 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1592149 AGAAT
1 AGAAT
1592154 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:1592126 original size:14 final size:14
Alignment explanation
Indices: 1592107--1592160 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1592097 AAATGAAAAG
1592107 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
1592121 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
1592140 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
1592154 CGCAACG
1 CGCAACG
1592161 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:1592136 original size:33 final size:33
Alignment explanation
Indices: 1592096--1592165 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
1592086 CGCAACGAGA
1592096 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
1592129 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1592162 GAAA
1 GAAA
1592166 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:1592172 original size:33 final size:33
Alignment explanation
Indices: 1592102--1592176 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
1592092 GAGAGAAATG
* **
1592102 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1592135 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1592168 AAAATCGCA
1 AAAATCGCA
1592177 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:1592194 original size:19 final size:19
Alignment explanation
Indices: 1592172--1592269 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1592162 GAAACCAAAA
*
1592172 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1592191 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1592205 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1592224 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1592238 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1592257 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1592270 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1592213 original size:14 final size:14
Alignment explanation
Indices: 1592194--1592283 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1592184 TTTCATTTCG
1592194 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1592208 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1592227 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1592241 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1592258 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1592274 CGTTGCGATT
1 CGTTGCGATT
1592284 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1592219 original size:33 final size:33
Alignment explanation
Indices: 1592177--1592291 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1592167 CAAAATCGCA
1592177 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1592210 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1592243 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1592276 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1592292 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1594147 original size:93 final size:93
Alignment explanation
Indices: 1593988--1594368 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
1593978 TAGATTGCTT
*
1593988 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1594053 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1594081 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1594146 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1594174 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1594239 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1594267 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1594332 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1594360 AGTAAATTT
1 AGTAAATTT
1594369 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 285 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1594487 original size:14 final size:14
Alignment explanation
Indices: 1594468--1594524 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1594458 GCGAAATGAA
*
1594468 AATCGCAACGACAG
1 AATCGCAACGAAAG
1594482 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1594499 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1594515 AATCGCAACG
1 AATCGCAACG
1594525 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1594495 original size:33 final size:33
Alignment explanation
Indices: 1594449--1594541 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1594439 GCGAAACCAA
*
1594449 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1594482 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1594515 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1594542 TAGATTTTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1594506 original size:19 final size:19
Alignment explanation
Indices: 1594412--1594541 Score: 127
Period size: 19 Copynumber: 7.3 Consensus size: 19
1594402 TAGTTTACTT
* *
1594412 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1594432 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1594451 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1594470 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1594484 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1594503 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1594517 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1594536 TCGCAA
1 TCGCAA
1594542 TAGATTTTAA
Statistics
Matches: 93, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
19 43 0.46
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1596510 original size:14 final size:14
Alignment explanation
Indices: 1596491--1596526 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1596481 ATTGTTTAAT
1596491 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1596505 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1596519 TGATTTGT
1 TGATTTGT
1596527 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:1596657 original size:19 final size:20
Alignment explanation
Indices: 1596633--1596678 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1596623 AAAATTGACT
1596633 ATCGCAATGC-GAAATGAAA
1 ATCGCAATGCGGAAATGAAA
* *
1596652 ATCGCAATGCGGAAATTACA
1 ATCGCAATGCGGAAATGAAA
1596672 ATCGCAA
1 ATCGCAA
1596679 CGAGAGAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAATGCGGAAATGAAA
Found at i:1596715 original size:19 final size:19
Alignment explanation
Indices: 1596687--1596854 Score: 177
Period size: 19 Copynumber: 9.6 Consensus size: 19
1596677 AACGAGAGAA
* *
1596687 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1596706 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1596722 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1596739 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1596758 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1596774 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1596791 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1596810 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1596826 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1596843 TCCGCATTGCGA
1 T-CGCATTGCGA
1596855 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:1596730 original size:33 final size:33
Alignment explanation
Indices: 1596693--1596854 Score: 159
Period size: 33 Copynumber: 4.7 Consensus size: 33
1596683 AGAATCGCAA
*
1596693 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1596726 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
1596764 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
1596797 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1596830 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
1596855 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:1596750 original size:52 final size:52
Alignment explanation
Indices: 1596687--1596854 Score: 309
Period size: 52 Copynumber: 3.2 Consensus size: 52
1596677 AACGAGAGAA
* *
1596687 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1596739 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1596791 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1596843 TCCGCATTGCGA
1 T-CGCATTGCGA
1596855 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:1596937 original size:19 final size:19
Alignment explanation
Indices: 1596913--1597010 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1596903 AAAATTGACT
1596913 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1596932 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1596951 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1596965 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1596984 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1597004 ATCGCAA
1 ATCGCAA
1597011 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:1597042 original size:53 final size:53
Alignment explanation
Indices: 1596913--1597029 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1596903 AAAATTGACT
1596913 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1596965 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1597018 ATCGCAATGCGA
1 ATCGCAATGCGA
1597030 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:1599362 original size:12 final size:12
Alignment explanation
Indices: 1599345--1599369 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1599335 TCTTCGGGGA
1599345 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1599357 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1599369 C
1 C
1599370 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:1599578 original size:24 final size:24
Alignment explanation
Indices: 1599544--1599590 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1599534 CTGAAACATC
1599544 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1599568 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1599591 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:1600301 original size:20 final size:20
Alignment explanation
Indices: 1600273--1600522 Score: 250
Period size: 20 Copynumber: 12.5 Consensus size: 20
1600263 AAATTTCAGT
* * *
1600273 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1600293 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1600313 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1600333 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* **
1600353 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACGGATTCGC
*
1600373 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1600393 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1600413 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
1600433 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1600453 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1600473 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1600493 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1600513 GTTGCGATTT
1 GTTGCGATTT
1600523 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:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1600539 original size:21 final size:21
Alignment explanation
Indices: 1600509--1600591 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1600499 ATTTTCATAT
*
1600509 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1600530 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1600551 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1600572 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1600592 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:1600582 original size:42 final size:43
Alignment explanation
Indices: 1600489--1600587 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1600479 ATTTATGTGT
* *
1600489 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1600530 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1600572 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1600588 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:1601296 original size:19 final size:19
Alignment explanation
Indices: 1601272--1601309 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1601262 CTTTTGGAGG
1601272 TCTAAATCTTTCTTTAATA
1 TCTAAATCTTTCTTTAATA
1601291 TCTAAATCTTTCTTTAATA
1 TCTAAATCTTTCTTTAATA
1601310 ACCCATTAAT
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:0.32, C:0.16, G:0.00, T:0.53
Consensus pattern (19 bp):
TCTAAATCTTTCTTTAATA
Found at i:1607332 original size:17 final size:18
Alignment explanation
Indices: 1607290--1607332 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1607280 GTGACACTTT
1607290 TGAGGGATGACATTTGTA
1 TGAGGGATGACATTTGTA
*
1607308 TTAGGGATGACATTTGTA
1 TGAGGGATGACATTTGTA
1607326 -GAGGGAT
1 TGAGGGAT
1607333 TGCTTAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.28, C:0.05, G:0.35, T:0.33
Consensus pattern (18 bp):
TGAGGGATGACATTTGTA
Found at i:1608200 original size:24 final size:23
Alignment explanation
Indices: 1608129--1608197 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 23
1608119 GTTCGTGAAC
* *
1608129 GTTCGGTTATGTTCGTTTAGTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
*
1608153 GTTTGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
1608177 GTTCGTTTATGTTCATTCATT
1 GTTCGTTTATGTTCGTTCATT
1608198 TATTTTTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 3 0.08
24 35 0.90
25 1 0.03
ACGTcount: A:0.13, C:0.10, G:0.20, T:0.57
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:1608942 original size:10 final size:10
Alignment explanation
Indices: 1608927--1609001 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
1608917 GGGCCTCCAA
1608927 CGTTTATGTT
1 CGTTTATGTT
1608937 CGTTTATGTT
1 CGTTTATGTT
1608947 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
1608958 ATGTTCGTGTT
1 -CGTTTATGTT
1608969 CGTTTATGTT
1 CGTTTATGTT
1608979 CG----TGTT
1 CGTTTATGTT
1608985 CGTTTATGTT
1 CGTTTATGTT
1608995 CGTTTAT
1 CGTTTAT
1609002 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1608958 original size:16 final size:16
Alignment explanation
Indices: 1608933--1608997 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
1608923 CCAACGTTTA
1608933 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1608949 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
1608965 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1608981 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1608997 T
1 T
1608998 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1609088 original size:16 final size:16
Alignment explanation
Indices: 1609067--1609099 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1609057 AAAAAAATTT
1609067 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1609083 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1609099 T
1 T
1609100 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1613776 original size:33 final size:34
Alignment explanation
Indices: 1613710--1613777 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
1613700 AATCCGAACT
* * *
1613710 CGACCCGAATATCACACTTAAAAAAAAATCGACC
1 CGACCCAAATATCAAACTTAAAAAAAAACCGACC
*
1613744 CGACCCAAATATCAAACTT-AAAAAAACCCGACC
1 CGACCCAAATATCAAACTTAAAAAAAAACCGACC
1613777 C
1 C
1613778 AACCAGATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.47, C:0.32, G:0.07, T:0.13
Consensus pattern (34 bp):
CGACCCAAATATCAAACTTAAAAAAAAACCGACC
Found at i:1613846 original size:31 final size:31
Alignment explanation
Indices: 1613762--1613846 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 31
1613752 ATATCAAACT
* *
1613762 TAAAAAAA-CCCGACCCAACCAGATTTTTTA
1 TAAAAAAATCCTGACCCAACCCGATTTTTTA
* * *
1613792 TAAAAAAAT-ATGACCCGATCCCGATTTTTTT
1 TAAAAAAATCCTGACCC-AACCCGATTTTTTA
* *
1613823 TGAAAAAATCCTGACCCTACCCGA
1 TAAAAAAATCCTGACCCAACCCGA
1613847 ATATCACACT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
30 13 0.30
31 24 0.56
32 6 0.14
ACGTcount: A:0.39, C:0.26, G:0.09, T:0.26
Consensus pattern (31 bp):
TAAAAAAATCCTGACCCAACCCGATTTTTTA
Found at i:1613954 original size:31 final size:31
Alignment explanation
Indices: 1613897--1613963 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1613887 ATCAAACTTT
1613897 AAAAACCCGATCTGACCCCAAATTTTTTTTA
1 AAAAACCCGATCTGACCCCAAATTTTTTTTA
* * *
1613928 AAAAATCCGA-CTGATCCCGAATTTTTTTTTA
1 AAAAACCCGATCTGA-CCCCAAATTTTTTTTA
1613959 AAAAA
1 AAAAA
1613964 ATCAGACCCG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (31 bp):
AAAAACCCGATCTGACCCCAAATTTTTTTTA
Found at i:1617365 original size:19 final size:19
Alignment explanation
Indices: 1617341--1617381 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1617331 ACATATTTGT
1617341 TTTTATTCTCCACTTAATA
1 TTTTATTCTCCACTTAATA
1617360 TTTTATTCTCCACTTAATA
1 TTTTATTCTCCACTTAATA
1617379 TTT
1 TTT
1617382 ATGGTATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTATTCTCCACTTAATA
Found at i:1619730 original size:16 final size:15
Alignment explanation
Indices: 1619691--1619721 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1619681 TCATATACAT
1619691 TTAGA-AATAAAAAA
1 TTAGATAATAAAAAA
1619705 TTAGATAATAAAAAA
1 TTAGATAATAAAAAA
1619720 TT
1 TT
1619722 CTAATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
TTAGATAATAAAAAA
Found at i:1640265 original size:97 final size:97
Alignment explanation
Indices: 1640096--1640292 Score: 358
Period size: 97 Copynumber: 2.0 Consensus size: 97
1640086 TAGAGCACAA
1640096 GGCTCTTAACCTTGTGGTCGTGGGATCGAGTCCCACGGTGGGTAATTCATAATTGCCGGAGGTCT
1 GGCTCTTAACCTTGTGGTCGTGGGATCGAGTCCCACGGTGGGTAATTCATAATTGCCGGAGGTCT
* *
1640161 TCTACGGAAGTTACTCTCAACCTAGCGTTGGG
66 TCCACGGAAGTTACTCTAAACCTAGCGTTGGG
* *
1640193 GGCTCTTAACCTTGTGGTCGTGGGATCGAGTCTCACTGTGGGTAATTCATAATTGCCGGAGGTCT
1 GGCTCTTAACCTTGTGGTCGTGGGATCGAGTCCCACGGTGGGTAATTCATAATTGCCGGAGGTCT
1640258 TCCACGGAAGTTACTCTAAACCTAGCGTTGGG
66 TCCACGGAAGTTACTCTAAACCTAGCGTTGGG
1640290 GGC
1 GGC
1640293 AGCCTACTAC
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 96 1.00
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (97 bp):
GGCTCTTAACCTTGTGGTCGTGGGATCGAGTCCCACGGTGGGTAATTCATAATTGCCGGAGGTCT
TCCACGGAAGTTACTCTAAACCTAGCGTTGGG
Found at i:1642589 original size:3 final size:3
Alignment explanation
Indices: 1642581--1642634 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
1642571 ATTTAGGTGT
1642581 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1642629 TTA TTA
1 TTA TTA
1642635 CAGTTTAGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1642958 original size:13 final size:14
Alignment explanation
Indices: 1642940--1642981 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
1642930 AGACTTTAGA
1642940 GATTTAGGG-TTTT
1 GATTTAGGGATTTT
*
1642953 GATTTAGGGATTTG
1 GATTTAGGGATTTT
*
1642967 GGTTTAGGGATTTT
1 GATTTAGGGATTTT
1642981 G
1 G
1642982 GGAGTTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (14 bp):
GATTTAGGGATTTT
Found at i:1646262 original size:18 final size:17
Alignment explanation
Indices: 1646208--1646256 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1646198 TTGGACTCCT
* *
1646208 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
1646226 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
1646244 AGTGCATTCGATG
1 AGTGCA-TCGATG
1646257 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:1646278 original size:64 final size:62
Alignment explanation
Indices: 1646208--1646386 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 62
1646198 TTGGACTCCT
* *
1646208 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAA-ATAGCCT
1 AGTGCATCGATGCA-T-AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAT-GCC-
1646272 G
62 G
* * * *
1646273 -GTGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCCG
1 AGTGCATCGATGCATAG--AGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCCG
* *
1646336 AGTGCATCGATGCATGGAGAGTGCATTGGTGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCAT--AGAGTGCATCGATGCATGAAATGCATTCGATGTT
1646387 CAATTAAATC
Statistics
Matches: 97, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 91 0.94
65 2 0.02
66 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (62 bp):
AGTGCATCGATGCATAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCCG
Found at i:1646405 original size:64 final size:61
Alignment explanation
Indices: 1646225--1646416 Score: 188
Period size: 64 Copynumber: 3.0 Consensus size: 61
1646215 CGGTGCACTA
* * *
1646225 AGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGAAATGCATTCGATG-TTCAAAAAT--CATGGTGCATCGATGCATGG
*** * * *
1646289 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTC-CGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGAAATGCATTCGATG-TTCAAAA-A-TCATG-GTGCATCGATGCATGG
* *
1646353 AGAGTGCATTGGTGCATGAAATGCATTCGATGTTCAATTAAATCATAGGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTCAA--AAATCAT-GGTGCATCGATGCATGG
1646417 TTTGATGCAT
Statistics
Matches: 107, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
63 7 0.07
64 95 0.89
65 4 0.04
66 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (61 bp):
AGAGTGCATCGATGCATGAAATGCATTCGATGTTCAAAAATCATGGTGCATCGATGCATGG
Found at i:1655212 original size:16 final size:16
Alignment explanation
Indices: 1655186--1655223 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
1655176 TCTACTAAAG
1655186 CATGATTGGGTAGATAT
1 CATG-TTGGGTAGATAT
1655203 CATGTTGGGTAGATAT
1 CATGTTGGGTAGATAT
1655219 CATGT
1 CATGT
1655224 GAATAAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (16 bp):
CATGTTGGGTAGATAT
Found at i:1665138 original size:22 final size:21
Alignment explanation
Indices: 1665108--1665191 Score: 70
Period size: 21 Copynumber: 4.0 Consensus size: 21
1665098 ATATTTTGCT
*
1665108 TGAAA-AAAATAATGAAAAAA
1 TGAAATAAAAAAATGAAAAAA
1665128 TGAAATAAAAAAGGA-GAAAAAA
1 TGAAATAAAAAA--ATGAAAAAA
*
1665150 TTGAAA-AAGAAAAAAG-AAAAA
1 -TGAAATAA-AAAAATGAAAAAA
1665171 TG-AATGAAAAAAATGAAAAAA
1 TGAAAT-AAAAAAATGAAAAAA
1665192 AGAAGGGTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 17
0.74 0.03 0.24
Matches are distributed among these distances:
19 2 0.04
20 13 0.25
21 18 0.34
22 10 0.19
23 10 0.19
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (21 bp):
TGAAATAAAAAAATGAAAAAA
Found at i:1666292 original size:54 final size:55
Alignment explanation
Indices: 1666183--1666981 Score: 918
Period size: 55 Copynumber: 14.9 Consensus size: 55
1666173 AGATTTCCCA
* *
1666183 ACGATT-ATTGAAGATTGATCGAGTCTTATA--CTCTGAAGAAATAGAGAGCAGAC
1 ACGATTGA-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
*
1666236 GCGATTG-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
1666290 GCGATT-ATTGAAGATTGTTCGA-TCTTATACTCTCTGAAGAAATAGGGAGCAGAT
1 ACGATTGA-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
1666344 ACGATTGTTGAAAATTGTTCGAGTCTTATACTCTATGCAGAAATAGGGAGCAGA-
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
1666398 ACGACTGTTGAAGA---TTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
*
1666450 ACGATTGATG-AGATTGTTCGAGTCTTATACTCTCTGAAAGGAATA-GGAGC--AC
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTG-AAGAAATAGGGAGCAGAC
*
1666502 ACGATTGATGAAAATTGTTC-AGTCTTATACTCTCTGCAA-AAATAGGGAGCAGAC
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTG-AAGAAATAGGGAGCAGAC
* * * *
1666556 AC-ACTGTTGAAGATTGTTGGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
1666610 ACGATTGATGAAGATTGTTCAAGTCTTACT-CTCTCTAAAGAAATGGGGAGCAGAC
1 ACGATTGATGAAGATTGTTCGAGTCTTA-TACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
1666665 ACGACTGTTGAAGATTGTTGGAGTC---TACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
1666717 ACGATTGATGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
*
1666772 ACGATTGATGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * *
1666827 AAGATTGTTGAAGATTGTTTGGGTC-T-TACTCTCTGAGGAAATAGGGAGCAGAC
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * ** *
1666880 AAGATTGATGAAGATTCTTCAAGT-TCCTACTC-CT-AAGAAAGAGGGAGC-GAAC
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG-AC
* * * * *
1666932 CCG-TTGACAGAAGATTGTTCGAGT-TCTATACTCCCCGAAGAAAGAGGGAG
1 ACGATTGA-TGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAG
1666982 TGAACTCGTT
Statistics
Matches: 646, Mismatches: 69, Indels: 60
0.83 0.09 0.08
Matches are distributed among these distances:
51 49 0.08
52 136 0.21
53 79 0.12
54 158 0.24
55 223 0.35
56 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27
Consensus pattern (55 bp):
ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:1666715 original size:107 final size:108
Alignment explanation
Indices: 1666183--1666981 Score: 849
Period size: 107 Copynumber: 7.5 Consensus size: 108
1666173 AGATTTCCCA
* * *
1666183 ACGATT-ATTGAAGATTGATCGAGTCTTATA--CTCTGAAGAAATAGAGAGCAGACGCGATTG-T
1 ACGATTGA-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
1666244 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
65 GAAGATTGTTCGAGTC-T-TACTCTCTGAAGAAATAGGGAGCAGAC
* * *
1666290 GCGATT-ATTGAAGATTGTTCGA-TCTTATACTCTCTGAAGAAATAGGGAGCAGATACGATTGTT
1 ACGATTGA-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
* * *
1666353 GAAAATTGTTCGAGTCTTATACTCTATGCAGAAATAGGGAGCAGA-
65 GAAGATTGTTCGAGTC-T-TACTCTCTGAAGAAATAGGGAGCAGAC
* * *
1666398 ACGACTGTTGAAGA---TTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGACACGATTGATG
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGATG
*
1666460 -AGATTGTTCGAGTCTTATACTCTCTGAAAGGAATA-GGAGC--AC
66 AAGATTGTTCGAGTC-T-TACTCTCTG-AAGAAATAGGGAGCAGAC
* * *
1666502 ACGATTGATGAAAATTGTTC-AGTCTTATACTCTCTGCAA-AAATAGGGAGCAGACAC-ACTGTT
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTG-AAGAAATAGGGAGCAGACACGATTGAT
* *
1666564 GAAGATTGTTGGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
65 GAAGATTGTTCGAGTC-T-TACTCTCTGAAGAAATAGGGAGCAGAC
* * * * *
1666610 ACGATTGATGAAGATTGTTCAAGTCTTACT-CTCTCTAAAGAAATGGGGAGCAGACACGACTGTT
1 ACGATTGATGAAGATTGTTCGAGTCTTA-TACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
* *
1666674 GAAGATTGTTGGAGTC-TACTCTCTGCAGAAATAGGGAGCAGAC
65 GAAGATTGTTCGAGTCTTACTCTCTGAAGAAATAGGGAGCAGAC
* * *
1666717 ACGATTGATGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATGGGGAGCAGACACGATTGATG
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGATG
*
1666782 AAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
66 AAGATTGTTCGAGTC-T-TACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * *
1666827 AAGATTGTTGAAGATTGTTTGGGTC-T-TACTCTCTGAGGAAATAGGGAGCAGACAAGATTGATG
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGATG
* * * *
1666890 AAGATTCTTCAAGTTCCTACTC-CT-AAGAAAGAGGGAGC-GAAC
66 AAGATTGTTCGAG-TCTTACTCTCTGAAGAAATAGGGAGCAG-AC
* * * * *
1666932 CCG-TTGACAGAAGATTGTTCGAGT-TCTATACTCCCCGAAGAAAGAGGGAG
1 ACGATTGA-TGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAG
1666982 TGAACTCGTT
Statistics
Matches: 602, Mismatches: 61, Indels: 58
0.83 0.08 0.08
Matches are distributed among these distances:
103 1 0.00
104 15 0.02
105 74 0.12
106 119 0.20
107 146 0.24
108 103 0.17
109 75 0.12
110 69 0.11
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27
Consensus pattern (108 bp):
ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGATG
AAGATTGTTCGAGTCTTACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:1666945 original size:52 final size:53
Alignment explanation
Indices: 1666889--1667039 Score: 172
Period size: 55 Copynumber: 2.9 Consensus size: 53
1666879 CAAGATTGAT
* * *
1666889 GAAGATTCTTCAAGTTC-CTACTCCTAAGAAAGAGGGAGCGAACCCGTT-GACA
1 GAAGATTGTTCGAGTTCTATACTCCTAAGAAAGAGGGAGCGAACCCGTTCG-CA
* * *
1666941 GAAGATTGTTCGAGTTCTATACTCCCCGAAGAAAGAGGGAGTGAACTCGTTCGCA
1 GAAGATTGTTCGAGTTCTATACT--CCTAAGAAAGAGGGAGCGAACCCGTTCGCA
1666996 GAA-ATTGTTCGAGTTCTATACTCCT---AAA-AGGGAGCGAACCCGTT
1 GAAGATTGTTCGAGTTCTATACTCCTAAGAAAGAGGGAGCGAACCCGTT
1667040 TTCCGAATAT
Statistics
Matches: 86, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
48 14 0.16
49 3 0.03
52 17 0.20
53 4 0.05
54 19 0.22
55 28 0.33
56 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (53 bp):
GAAGATTGTTCGAGTTCTATACTCCTAAGAAAGAGGGAGCGAACCCGTTCGCA
Done.