Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008353.1 Hibiscus syriacus cultivar Beakdansim tig00111088_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: 2583621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 8 of 13
Found at i:1431610 original size:26 final size:28
Alignment explanation
Indices: 1431554--1431612 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
1431544 TTATTTGCAA
*
1431554 TATTATTTTATTATTATTATTGCTTTAAT
1 TATTATTTCATTATTATTATT-CTTTAAT
1431583 TATTATTTCATTATTATTATT-TTT-AT
1 TATTATTTCATTATTATTATTCTTTAAT
1431609 TATT
1 TATT
1431613 TATATAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 6 0.21
27 3 0.10
29 20 0.69
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (28 bp):
TATTATTTCATTATTATTATTCTTTAAT
Found at i:1435582 original size:16 final size:17
Alignment explanation
Indices: 1435556--1435591 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1435546 TAAATTATTT
1435556 TTAAGATAATTTTTAAA
1 TTAAGATAATTTTTAAA
*
1435573 TTAA-ATAATTTTTGAA
1 TTAAGATAATTTTTAAA
1435589 TTA
1 TTA
1435592 TTATTCTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
TTAAGATAATTTTTAAA
Found at i:1436691 original size:2 final size:2
Alignment explanation
Indices: 1436686--1436717 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1436676 ACACACACAC
1436686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1436718 CAGAAAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1439669 original size:24 final size:24
Alignment explanation
Indices: 1439637--1439689 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
1439627 CCAAGAGAGA
1439637 GCACATGACCAGCCATCATTCCAT
1 GCACATGACCAGCCATCATTCCAT
*
1439661 GCACATGACCAGCCATCATTCTAT
1 GCACATGACCAGCCATCATTCCAT
1439685 GCACA
1 GCACA
1439690 AGGTTGCACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (24 bp):
GCACATGACCAGCCATCATTCCAT
Found at i:1439824 original size:91 final size:91
Alignment explanation
Indices: 1439719--1439901 Score: 276
Period size: 91 Copynumber: 2.0 Consensus size: 91
1439709 CCTAGAACAC
*
1439719 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATA
1439784 AAGAGTTCTCTCCCTATTCAGCCAAG
66 AAGAGTTCTCTCCCTATTCAGCCAAG
** * * * * **
1439810 CCATGTGTTTTGCATGTGATCAGCCCCTATGTGCCTTGCATGTGGTTCATTTAGGTGCCAAGATA
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATA
*
1439875 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCAGCCAAG
1439901 C
1 C
1439902 ATCAACTACC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATA
AAGAGTTCTCTCCCTATTCAGCCAAG
Found at i:1440714 original size:28 final size:27
Alignment explanation
Indices: 1440683--1440740 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
1440673 GAAAATCAGA
* * *
1440683 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAAATCAAGCACTCAAAAAG-AAG
*
1440711 AAAGAAAATCCAGCACTCAAAAAGAAG
1 AAAGAAAATCAAGCACTCAAAAAGAAG
1440738 AAA
1 AAA
1440741 AACAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.09
Consensus pattern (27 bp):
AAAGAAAATCAAGCACTCAAAAAGAAG
Found at i:1443931 original size:91 final size:91
Alignment explanation
Indices: 1443776--1443958 Score: 287
Period size: 91 Copynumber: 2.0 Consensus size: 91
1443766 CCTAGAACAC
1443776 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
1443841 AAGAGTTCTCTCCCTATTCA-GCCAAG
66 AAGAGTTCTCTCCCTATT-AGGCCAAG
** * * * * *
1443867 CCATGTGTTTTGCATGTGATCAGGCCCTATGTGCCTTGCATGTGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
1443932 AAGAGTTCTCTCCCTATTAGGCCAAG
66 AAGAGTTCTCTCCCTATTAGGCCAAG
1443958 C
1 C
1443959 ATCAACTACC
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
90 1 0.01
91 83 0.99
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
AAGAGTTCTCTCCCTATTAGGCCAAG
Found at i:1454238 original size:13 final size:13
Alignment explanation
Indices: 1454220--1454247 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1454210 ATTTTATTTC
1454220 TTTTCTTTTTAAT
1 TTTTCTTTTTAAT
1454233 TTTTCTTTTTAAT
1 TTTTCTTTTTAAT
1454246 TT
1 TT
1454248 AAATTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTTTTAAT
Found at i:1455003 original size:21 final size:22
Alignment explanation
Indices: 1454979--1455022 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1454969 ATATTTTGTC
*
1454979 ATTTTAATAAAACTA-ATTTTA
1 ATTTTAATAAAACAACATTTTA
*
1455000 ATTTTACTAAAACAACATTTTA
1 ATTTTAATAAAACAACATTTTA
1455022 A
1 A
1455023 GGTCTACGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTTAATAAAACAACATTTTA
Found at i:1459786 original size:24 final size:24
Alignment explanation
Indices: 1459756--1459802 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1459746 TCAAGTAAAG
*
1459756 AATCTGATTCTAGCACAATTGTTA
1 AATCTGACTCTAGCACAATTGTTA
* *
1459780 AATCTGACTCTAGTACTATTGTT
1 AATCTGACTCTAGCACAATTGTT
1459803 GATTCTATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (24 bp):
AATCTGACTCTAGCACAATTGTTA
Found at i:1472769 original size:23 final size:24
Alignment explanation
Indices: 1472736--1472780 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1472726 AATTAAAAAG
*
1472736 TTAATTATT-AATAAAATTAATTT
1 TTAATTATTAAATAAAAATAATTT
*
1472759 TTAATTTTTAAATAAAAATAAT
1 TTAATTATTAAATAAAAATAAT
1472781 AAAGTTCGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAATTATTAAATAAAAATAATTT
Found at i:1472825 original size:19 final size:19
Alignment explanation
Indices: 1472794--1472843 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1472784 GTTCGACTAA
*
1472794 TTTAATTAATTTTAAAAT-
1 TTTAATAAATTTTAAAATG
*
1472812 TTATTATAAATTTTAAAATG
1 TT-TAATAAATTTTAAAATG
1472832 TTTAATAAATTT
1 TTTAATAAATTT
1472844 AGTACGGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 2 0.07
19 23 0.85
20 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TTTAATAAATTTTAAAATG
Found at i:1480745 original size:20 final size:19
Alignment explanation
Indices: 1480717--1480787 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
1480707 CAGTTGAAAA
1480717 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTT-CATT
* * * *
1480737 TCGCATTGCGATAGTTGA-A
1 TCGCGTTGCGAT-TTTCATT
1480756 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGA-TTTTCATT
1480776 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1480788 AGTCTACAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
19 14 0.35
20 24 0.60
21 2 0.05
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.41
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1480769 original size:39 final size:40
Alignment explanation
Indices: 1480692--1480790 Score: 155
Period size: 39 Copynumber: 2.5 Consensus size: 40
1480682 ATTCGCGTTG
*
1480692 CATTTCGCGTTGCGACAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTG-AAATCGCGTTGCGATTTTC
* *
1480733 CATTTCGCATTGCGATAGTTG-AATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAATCGCGTTGCGATTTTC
1480772 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
1480791 CTACAGTTGT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.65
41 19 0.35
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.37
Consensus pattern (40 bp):
CATTTCGCGTTGCGATAGTTGAAATCGCGTTGCGATTTTC
Found at i:1480807 original size:22 final size:22
Alignment explanation
Indices: 1480779--1480831 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1480769 TTTCATTTCG
*
1480779 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAATCTACAGTTGT
*
1480801 TGTTGCGATAATCTACAGTTGT
1 CGTTGCGATAATCTACAGTTGT
1480823 CGTTGCGAT
1 CGTTGCGAT
1480832 TTTCCAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAATCTACAGTTGT
Found at i:1481470 original size:6 final size:6
Alignment explanation
Indices: 1481459--1481497 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
1481449 TCTCGTCTCG
1481459 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1481498 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1481641 original size:22 final size:22
Alignment explanation
Indices: 1481580--1481643 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
1481570 CAAGAATTTT
1481580 GACAACTGTAGACTATCGCAAC
1 GACAACTGTAGACTATCGCAAC
** **
1481602 GA-ATTTG-A-AAAATCGCAAC
1 GACAACTGTAGACTATCGCAAC
1481621 GACAACTGTAGACTATCGCAAC
1 GACAACTGTAGACTATCGCAAC
1481643 G
1 G
1481644 CGAAATGGAA
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
19 11 0.35
20 4 0.13
21 4 0.13
22 12 0.39
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (22 bp):
GACAACTGTAGACTATCGCAAC
Found at i:1481660 original size:20 final size:20
Alignment explanation
Indices: 1481635--1481731 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
1481625 ACTGTAGACT
1481635 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** *
1481655 ATCGCAACGC-AATTTTCAACT
1 ATCGCAACGCGAA-ATGGAA-A
* **
1481676 ATCGCAATGCGAGCTGGAAA
1 ATCGCAACGCGAAATGGAAA
** *
1481696 ATCATAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
1481716 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
1481732 CAACGCGAAT
Statistics
Matches: 56, Mismatches: 18, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
19 2 0.04
20 41 0.73
21 12 0.21
22 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1481677 original size:41 final size:42
Alignment explanation
Indices: 1481580--1481698 Score: 129
Period size: 41 Copynumber: 2.9 Consensus size: 42
1481570 CAAGAATTTT
* *
1481580 GACAACTGTAGACTATCGCAA--CGAATTTGAAAAATCGCAAC
1 GACAACTGTAGACTATCGCAACGCGAA-ATGGAAAATCGCAAC
1481621 GACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAAC
1 GACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAAC
* * * **
1481663 G-CAATTTTCA-ACTATCGCAATGCGAGCTGGAAAATC
1 GACAACTGT-AGACTATCGCAACGCGAAATGGAAAATC
1481699 ATAACGCGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
41 49 0.72
42 15 0.22
43 4 0.06
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (42 bp):
GACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAAC
Found at i:1482161 original size:19 final size:19
Alignment explanation
Indices: 1482124--1482160 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1482114 CATCAATACT
1482124 TTAAAAATTAAATATAAAA
1 TTAAAAATTAAATATAAAA
1482143 TTAAAAATT-AATATAAAA
1 TTAAAAATTAAATATAAAA
1482161 AAATATCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAAAAATTAAATATAAAA
Found at i:1482509 original size:31 final size:31
Alignment explanation
Indices: 1482468--1482531 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1482458 GGAATGATCT
* *
1482468 CTAACGTTATCGATCCGTTCGATTTTAATCC
1 CTAACATTATCGATCCATTCGATTTTAATCC
* * *
1482499 CTAACATTATCGGTCTATTCGATTTTATTCC
1 CTAACATTATCGATCCATTCGATTTTAATCC
1482530 CT
1 CT
1482532 CAACTATGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.22, C:0.25, G:0.11, T:0.42
Consensus pattern (31 bp):
CTAACATTATCGATCCATTCGATTTTAATCC
Found at i:1482958 original size:3 final size:3
Alignment explanation
Indices: 1482950--1482999 Score: 64
Period size: 3 Copynumber: 16.0 Consensus size: 3
1482940 CCTCTTCTGT
* *
1482950 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC ATTC TTTC TTA TTT TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC
1482997 TTC
1 TTC
1483000 AAAGTAATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1484022 original size:19 final size:20
Alignment explanation
Indices: 1483974--1484025 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1483964 TGAAACATGA
* *
1483974 GGTTTTGAAACTAGACAGTG
1 GGTTTTGAAACCAGACAGTC
* *
1483994 GGTTTAGAAACCAGTCAG-C
1 GGTTTTGAAACCAGACAGTC
1484013 GGTTTTGAAACCA
1 GGTTTTGAAACCA
1484026 TGTATAGAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (20 bp):
GGTTTTGAAACCAGACAGTC
Found at i:1485103 original size:15 final size:15
Alignment explanation
Indices: 1485052--1485103 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
1485042 ATATTTAGCT
* *
1485052 GGGCGGGCAGATGTG
1 GGGCGGGCGGATGCG
* *
1485067 TGGCGGACGGATGCG
1 GGGCGGGCGGATGCG
1485082 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
1485097 GGGCGGG
1 GGGCGGG
1485104 TAATGTCTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.10, C:0.17, G:0.63, T:0.10
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:1496059 original size:30 final size:29
Alignment explanation
Indices: 1496023--1496133 Score: 104
Period size: 28 Copynumber: 3.9 Consensus size: 29
1496013 CGTCCCGAAC
*
1496023 AGGTCGCCATGCATTCCCCAAC-ACCCTACA
1 AGGTCGCCATGCACTCCCC-ACGA-CCTACA
*
1496053 AGGTCGCCAAGCACT-CCCACGACCTACA
1 AGGTCGCCATGCACTCCCCACGACCTACA
***
1496081 AGGTCGCCATGCACT-CCCAGCGACCTTGT
1 AGGTCGCCATGCACTCCCCA-CGACCTACA
* *
1496110 AGGTCGCCA-GCAGTCCCGACGACC
1 AGGTCGCCATGCACTCCCCACGACC
1496134 AAGCTTCACA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
28 35 0.50
29 22 0.31
30 13 0.19
ACGTcount: A:0.23, C:0.41, G:0.21, T:0.14
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCCACGACCTACA
Found at i:1496962 original size:24 final size:24
Alignment explanation
Indices: 1496897--1496964 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
1496887 GTGAGTACTA
* *
1496897 GTCAGTATTCGAAATTTGATCTTG
1 GTCAATATTCGGAATTTGATCTTG
* *
1496921 GTCAATA-CCAGGACTTTGATCTTG
1 GTCAATATTC-GGAATTTGATCTTG
*
1496945 GTCAATATTCGGATTTTGAT
1 GTCAATATTCGGAATTTGAT
1496965 GAGTTTTCAG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (24 bp):
GTCAATATTCGGAATTTGATCTTG
Found at i:1499337 original size:20 final size:20
Alignment explanation
Indices: 1499312--1499405 Score: 154
Period size: 20 Copynumber: 4.7 Consensus size: 20
1499302 GACATTCATT
1499312 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
1499332 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
*
1499352 TGACTATCGCAACGCGGAAT
1 TGACTATCGCAACGCGGAAA
1499372 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
1499392 TGACTATCGCAACG
1 TGACTATCGCAACG
1499406 AGAGAATCGC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 66 0.96
21 3 0.04
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:1499465 original size:34 final size:33
Alignment explanation
Indices: 1499377--1499470 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
1499367 GGAATTGACT
* **
1499377 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
1499411 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1499444 ATTGCAATGCGAAAATGAAAATCGCAA
1 ATCGCAATGCG-AAATGAAAATCGCAA
1499471 TGCGAAATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.56
34 24 0.44
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1499472 original size:20 final size:19
Alignment explanation
Indices: 1499410--1499478 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
1499400 GCAACGAGAG
1499410 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1499429 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
*
1499443 AATTGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
1499463 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1499479 TAGTTTCGCG
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
14 7 0.17
16 5 0.12
17 2 0.05
18 3 0.08
19 12 0.30
20 11 0.28
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1499530 original size:34 final size:34
Alignment explanation
Indices: 1499487--1499582 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 34
1499477 ATTAGTTTCG
*
1499487 CGTTGCGATTTTCATTTTCGCATTGCGGTTCAAT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCAAT
**
1499521 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCAAT
** * *
1499554 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
1499583 AGTCTGTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.52
34 26 0.48
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCAAT
Found at i:1499702 original size:14 final size:14
Alignment explanation
Indices: 1499683--1499719 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1499673 ACATCAATTA
1499683 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1499697 ACAAATCATCTTTT
1 ACAAATCAACATTT
1499711 ACAAATCAA
1 ACAAATCAA
1499720 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1501134 original size:42 final size:42
Alignment explanation
Indices: 1501070--1501180 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 42
1501060 CTAGAATGTT
* * *
1501070 GGGAGGAACCTCTTCAACGATGACAGTGGCCTCTTGAACGGT-G
1 GGGAGG-A-CTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
*
1501113 GGAGAGGACTCTTGAGA-GATGATAGGGGCCTCTTGAACGATAG
1 GG-GAGGACTCTTGA-ACGATGACAGGGGCCTCTTGAACGATAG
*
1501156 GGGAGGCCTCTTGAACGATGACAGG
1 GGGAGGACTCTTGAACGATGACAGG
1501181 TGAGTCGGGC
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
41 1 0.02
42 46 0.79
43 7 0.12
44 4 0.07
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.20
Consensus pattern (42 bp):
GGGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
Found at i:1501163 original size:21 final size:21
Alignment explanation
Indices: 1501097--1501174 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
1501087 CGATGACAGT
*
1501097 GGCCTCTTGAACGGT-GGGAGA
1 GGCCTCTTGAACGATAGGG-GA
* **
1501118 GGACTCTTGAGA-GATGATAGG-
1 GGCCTCTTGA-ACGAT-AGGGGA
1501139 GGCCTCTTGAACGATAGGGGA
1 GGCCTCTTGAACGATAGGGGA
1501160 GGCCTCTTGAACGAT
1 GGCCTCTTGAACGAT
1501175 GACAGGTGAG
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 4 0.09
21 38 0.84
22 2 0.04
23 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (21 bp):
GGCCTCTTGAACGATAGGGGA
Found at i:1501687 original size:20 final size:20
Alignment explanation
Indices: 1501664--1501702 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1501654 CTTAAAATCG
*
1501664 CAACGCGAAAATGACTATCA
1 CAACGCGAAAATAACTATCA
1501684 CAACGCGAAAATAACTATC
1 CAACGCGAAAATAACTATC
1501703 GCAATGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (20 bp):
CAACGCGAAAATAACTATCA
Found at i:1501772 original size:20 final size:20
Alignment explanation
Indices: 1501747--1501815 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
1501737 CAACAATAAA
*
1501747 ATCGCAACGCGAAAATGACC
1 ATCGCAACGCGAAAATGACT
**
1501767 ATCGCAATACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1501787 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1501807 ATCGCAACG
1 ATCGCAACG
1501816 AGAGAATCGC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1501885 original size:20 final size:20
Alignment explanation
Indices: 1501860--1502035 Score: 164
Period size: 20 Copynumber: 9.4 Consensus size: 20
1501850 GATTCTTTCG
* **
1501860 TTGCGATAGTGAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1501880 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1501900 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1501920 TTGCGATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
1501940 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
1501954 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
1501973 TTGC-A-ATTC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
1501987 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1502007 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1502027 TTGCGATAG
1 TTGCGATAG
1502036 AAAACTATTC
Statistics
Matches: 133, Mismatches: 9, Indels: 28
0.78 0.05 0.16
Matches are distributed among these distances:
14 11 0.08
15 1 0.01
16 13 0.10
17 7 0.05
18 6 0.05
19 4 0.03
20 91 0.68
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1501919 original size:127 final size:127
Alignment explanation
Indices: 1501804--1502035 Score: 277
Period size: 127 Copynumber: 1.8 Consensus size: 127
1501794 TGCGAATTTG
* *
1501804 ACTATCGCAACGAGAGAATCG-CAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATA
1 ACTATCGCAACGAGA-AATCGTCAATGCGATTTTCATTTCGCATTGCAATTCTCTCGTTGCGATA
* *
1501868 GTGAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTC
65 GTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCAATGCGATAGTC
* * * ** * ** * ***
1501931 ATTTTCGTATTGCGATTTTGTTGTTGCGATTTTCATTTCGCATTGCAATTCTCTCGTTGCGATAG
1 ACTATCGCAACGAGAAATCGTCAATGCGATTTTCATTTCGCATTGCAATTCTCTCGTTGCGATAG
** *
1501996 TCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATAG
66 TCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAG
1502036 AAAACTATTC
Statistics
Matches: 86, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
126 2 0.02
127 84 0.98
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.39
Consensus pattern (127 bp):
ACTATCGCAACGAGAAATCGTCAATGCGATTTTCATTTCGCATTGCAATTCTCTCGTTGCGATAG
TCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCAATGCGATAGTC
Found at i:1501976 original size:33 final size:34
Alignment explanation
Indices: 1501880--1502013 Score: 126
Period size: 33 Copynumber: 3.8 Consensus size: 34
1501870 GAAATTCGCA
*
1501880 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
1 TTGCGATAGTCATTTTCGCATTGCGAT--TC--TCTCG
* * * *
1501918 CATTGCGATAGTCATTTTCGTATTGCGATTTTGTTG
1 --TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
** *
1501954 TTGCGATTTTCA-TTTCGCATTGCAATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
*
1501987 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
1502014 AGTCATTTTC
Statistics
Matches: 78, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
33 26 0.33
34 22 0.28
36 3 0.04
38 1 0.01
40 26 0.33
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
Found at i:1503938 original size:20 final size:20
Alignment explanation
Indices: 1503880--1503949 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
1503870 CAAACTTTAA
* **
1503880 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
1503900 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
1503920 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1503940 ATCGCAACGC
1 ATCGCAACGC
1503950 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1503988 original size:33 final size:33
Alignment explanation
Indices: 1503879--1503992 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
1503869 TCAAACTTTA
* *
1503879 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATG
1 AATCGCAACGCG-AAATGAAAATCGC-A-ACG-ACA-G
* **
1503917 ACTATCGCAACGCGAATTTGACTATCGCAACG-CAAG
1 A--ATCGCAACGCGAA-ATGAAAATCGCAACGAC-AG
1503953 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1503986 AATCGCA
1 AATCGCA
1503993 TTGCGATAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
33 21 0.33
34 14 0.22
36 2 0.03
37 1 0.02
38 4 0.06
39 3 0.05
40 18 0.29
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:1504380 original size:22 final size:22
Alignment explanation
Indices: 1504318--1504383 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
1504308 TGACCGTGAA
* *
1504318 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
1504340 TGATATCGTCGGCGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
*
1504362 TGATTTCATCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1504384 GGATGTCGCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:1504605 original size:20 final size:20
Alignment explanation
Indices: 1504582--1504653 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1504572 ATAGTCTGAT
1504582 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
* **
1504602 TCGCATTGCGATTTTCCAAA
1 TCGCATTGCGATTTACGTAA
* * *
1504622 TTCGCGTTGCGATTTATGTAT
1 -TCGCATTGCGATTTACGTAA
1504643 TCGCATTGCGA
1 TCGCATTGCGA
1504654 ATTAGTAAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAA
Found at i:1507619 original size:36 final size:35
Alignment explanation
Indices: 1507565--1507640 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 35
1507555 ACCGAATTAA
* *
1507565 ACGGGGACGGGAAAAACCGTTTATGTTATACGGGG
1 ACGGGGACGGGAAAAACCGTTTATGCTAAACGGGG
1507600 ACGGGGACGGGGAAAAACCGTTTATGCTAAACGGGG
1 ACGGGGAC-GGGAAAAACCGTTTATGCTAAACGGGG
1507636 ACGGG
1 ACGGG
1507641 TTTGGTAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 8 0.21
36 30 0.79
ACGTcount: A:0.29, C:0.16, G:0.39, T:0.16
Consensus pattern (35 bp):
ACGGGGACGGGAAAAACCGTTTATGCTAAACGGGG
Found at i:1507697 original size:2 final size:2
Alignment explanation
Indices: 1507690--1507772 Score: 68
Period size: 2 Copynumber: 44.0 Consensus size: 2
1507680 TAAAAATAAT
* * * *
1507690 TA TA TA TA TA TA TA TA TA TA T- TA TA AA TT TA -A TT TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1507730 TA TA TA TA TA TA TA -A TA TT TA TA TA TT TA -A TT TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1507769 TA TA
1 TA TA
1507773 CCCGCCCGAT
Statistics
Matches: 62, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
1 5 0.08
2 57 0.92
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1507741 original size:38 final size:37
Alignment explanation
Indices: 1507690--1507772 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 37
1507680 TAAAAATAAT
1507690 TATATATATATATAT-ATATATTATAAATTTAATTTAAA
1 TATATATATATATATAATAT-TTATAAATTTAATTT-AA
*
1507728 TATATATATATATATAATATTTATATATTTAATTTAA
1 TATATATATATATATAATATTTATAAATTTAATTTAA
1507765 TATATATA
1 TATATATA
1507773 CCCGCCCGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
37 10 0.23
38 29 0.67
39 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
TATATATATATATATAATATTTATAAATTTAATTTAA
Found at i:1507793 original size:12 final size:12
Alignment explanation
Indices: 1507770--1507806 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
1507760 TTTAATATAT
1507770 ATACCC-GCCCG
1 ATACCCGGCCCG
1507781 ATACCCGGCCCG
1 ATACCCGGCCCG
1507793 ATACCCGGCCCG
1 ATACCCGGCCCG
1507805 AT
1 AT
1507807 TCCCATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.24
12 19 0.76
ACGTcount: A:0.19, C:0.49, G:0.22, T:0.11
Consensus pattern (12 bp):
ATACCCGGCCCG
Found at i:1508045 original size:33 final size:33
Alignment explanation
Indices: 1507985--1508051 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1507975 TACCATCCCT
* * * *
1507985 AATTGAAATACTTGAATACTTCTAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
1508018 AATTCAAATACTTAAAAATTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1508051 A
1 A
1508052 TTGAAACAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.34
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:1508071 original size:21 final size:21
Alignment explanation
Indices: 1508046--1508087 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1508036 TTTCCAAGTT
1508046 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
1508067 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
1508088 AAAATAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1509569 original size:23 final size:22
Alignment explanation
Indices: 1509527--1509571 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
1509517 AAATTGTAAT
1509527 AAAATATAATAAAATAAAAATA
1 AAAATATAATAAAATAAAAATA
*
1509549 AAAATATAATTATAATAAAAATA
1 AAAATATAA-TAAAATAAAAATA
1509572 TATTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAATATAATAAAATAAAAATA
Found at i:1516522 original size:33 final size:33
Alignment explanation
Indices: 1516480--1516560 Score: 153
Period size: 33 Copynumber: 2.5 Consensus size: 33
1516470 CAAGCTCAAC
*
1516480 TTATAATGATCACAAGATCATTACAAAACATGT
1 TTATAATGATTACAAGATCATTACAAAACATGT
1516513 TTATAATGATTACAAGATCATTACAAAACATGT
1 TTATAATGATTACAAGATCATTACAAAACATGT
1516546 TTATAATGATTACAA
1 TTATAATGATTACAA
1516561 AGCATTATAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (33 bp):
TTATAATGATTACAAGATCATTACAAAACATGT
Found at i:1518849 original size:31 final size:31
Alignment explanation
Indices: 1518805--1518870 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
1518795 ACATTTTTTG
** *
1518805 ATTAAAATGAAATGAAAATGATCACATC-TTA
1 ATTAAAACAAAATGAAAATGACCACA-CATTA
*
1518836 ATTAAAACAAAATGAAAGTGACCACACATTA
1 ATTAAAACAAAATGAAAATGACCACACATTA
1518867 ATTA
1 ATTA
1518871 TTTTAGATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (31 bp):
ATTAAAACAAAATGAAAATGACCACACATTA
Found at i:1519451 original size:9 final size:9
Alignment explanation
Indices: 1519437--1519465 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1519427 AATTAGAGTC
1519437 TTTAAATTT
1 TTTAAATTT
1519446 TTTAAATTT
1 TTTAAATTT
1519455 TTTAAATTT
1 TTTAAATTT
1519464 TT
1 TT
1519466 GAGAGATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTAAATTT
Found at i:1521085 original size:46 final size:45
Alignment explanation
Indices: 1521033--1521123 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 45
1521023 CCTAATCCCA
1521033 AATTTCTTAACAATAAGATTAAGTACTACTTTAACAAAATAACCCT
1 AATTTCTTAACAATAAGATTAAGTACTAC-TTAACAAAATAACCCT
* *
1521079 AATTTCTTAACAATAAGATTAAGTATTACTTGACAAAATAACCCT
1 AATTTCTTAACAATAAGATTAAGTACTACTTAACAAAATAACCCT
1521124 GAACTTAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 15 0.35
46 28 0.65
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.33
Consensus pattern (45 bp):
AATTTCTTAACAATAAGATTAAGTACTACTTAACAAAATAACCCT
Found at i:1527370 original size:31 final size:30
Alignment explanation
Indices: 1527323--1527397 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 30
1527313 TTTTTACCCT
*
1527323 ACCCGACCCACCCGAATATCACACTTAAAA
1 ACCCGACCGACCCGAATATCACACTTAAAA
1527353 ACCCGACCTGACCCGAATATCACACTTAAAA
1 ACCCGACC-GACCCGAATATCACACTTAAAA
*
1527384 AACCGACCCGACCC
1 ACCCGA-CCGACCC
1527398 TAACAAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 8 0.20
31 31 0.76
32 2 0.05
ACGTcount: A:0.37, C:0.41, G:0.09, T:0.12
Consensus pattern (30 bp):
ACCCGACCGACCCGAATATCACACTTAAAA
Found at i:1527801 original size:172 final size:170
Alignment explanation
Indices: 1527507--1527851 Score: 629
Period size: 172 Copynumber: 2.0 Consensus size: 170
1527497 TTAAAATATA
1527507 TATAGATAGATATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGT
1 TATAGATAGATATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGT
*
1527572 ATTTCACCCTAAACCCGAACTCAACCCGACCCTAATATCACACTTAAAAAAACCGACCCGACCTG
66 ATTTCACCCTAAACCCGAACTCAACCCGACCCGAATATCACACTTAAAAAAACCGACCCGACCTG
1527637 AAATAAT-AAAAAATATTTTTATTCAATATATGAATAAGT
131 AAATAATAAAAAAATATTTTTATTCAATATATGAATAAGT
*
1527676 TATAGATATATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGG
1 TATAGATAGA-TATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTC-G
1527741 GTATTTTCACCCTAAACCCGAACTCAACCCGACCCGAATATCACACTTAAAAAAACCGACCCGAC
64 GTA-TTTCACCCTAAACCCGAACTCAACCCGACCCGAATATCACACTTAAAAAAACCGACCCGAC
1527806 CTGAAATAATAAAAAAAATATTTTTATTCAATATATGAATAAGT
128 CTGAAATAAT-AAAAAAATATTTTTATTCAATATATGAATAAGT
1527850 TA
1 TA
1527852 CCAAAAGATT
Statistics
Matches: 169, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
169 9 0.05
170 52 0.31
171 4 0.02
172 70 0.41
174 34 0.20
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (170 bp):
TATAGATAGATATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGT
ATTTCACCCTAAACCCGAACTCAACCCGACCCGAATATCACACTTAAAAAAACCGACCCGACCTG
AAATAATAAAAAAATATTTTTATTCAATATATGAATAAGT
Found at i:1530546 original size:18 final size:19
Alignment explanation
Indices: 1530511--1530547 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1530501 CACGAAATGT
1530511 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1530531 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1530548 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1530683 original size:18 final size:18
Alignment explanation
Indices: 1530662--1530709 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1530652 AAATTGTCCT
*
1530662 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
* *
1530680 TATTACA-AATTGTAAAA
1 TATTATATATTTGTAAAA
1530697 TATTTATATATTT
1 TA-TTATATATTT
1530710 TCTTTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
17 10 0.43
18 10 0.43
19 3 0.13
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:1539894 original size:21 final size:21
Alignment explanation
Indices: 1539869--1539912 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1539859 AAAAATATTA
* *
1539869 AAAAATATTGATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
1539890 AAAAATAATAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
1539911 AA
1 AA
1539913 TATTTTATCA
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:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:1541083 original size:17 final size:16
Alignment explanation
Indices: 1541058--1541101 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
1541048 ATTAAAAAGA
*
1541058 TAATTTTATTATAATT
1 TAATATTATTATAATT
1541074 TAATGATTATTTATAATT
1 TAAT-ATTA-TTATAATT
*
1541092 TTATATTATT
1 TAATATTATT
1541102 TTGATTTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 6 0.25
17 7 0.29
18 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TAATATTATTATAATT
Found at i:1541102 original size:17 final size:18
Alignment explanation
Indices: 1541066--1541102 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1541056 GATAATTTTA
1541066 TTATAATTTAATGATTAT
1 TTATAATTTAATGATTAT
*
1541084 TTATAATTTTAT-ATTAT
1 TTATAATTTAATGATTAT
1541101 TT
1 TT
1541103 TGATTTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTATAATTTAATGATTAT
Found at i:1541242 original size:2 final size:2
Alignment explanation
Indices: 1541235--1541272 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
1541225 TTTTCAAATA
1541235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
1541273 GTATTTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1541705 original size:43 final size:43
Alignment explanation
Indices: 1541639--1541739 Score: 107
Period size: 43 Copynumber: 2.3 Consensus size: 43
1541629 ATAATTATAG
* * *
1541639 AAAATGTTATAAAAATTCTAACATTTTCAATTGAGTTG-AACCT
1 AAAATATTATAAAAATTCCAACATTTTCAATTG-GATGAAACCT
* * *
1541682 GAAATATTATAAAAA-TCACAACATTTTTAGTTGGATGAAACCT
1 AAAATATTATAAAAATTC-CAACATTTTCAATTGGATGAAACCT
*
1541725 AAAATATTACAAAAA
1 AAAATATTATAAAAA
1541740 GTTTACAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
42 5 0.10
43 43 0.90
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.33
Consensus pattern (43 bp):
AAAATATTATAAAAATTCCAACATTTTCAATTGGATGAAACCT
Found at i:1543108 original size:81 final size:79
Alignment explanation
Indices: 1543004--1543153 Score: 203
Period size: 79 Copynumber: 1.9 Consensus size: 79
1542994 TAGAAAAAAT
* * *
1543004 AACATTTGAGGTAGTGCTCAATATTAATATTTTTAGTAGAAAAAAAATAATGTTTTATGTAGCGC
1 AACATTTGAGGTAGTGCTCAATATTAATATTTTT-G-AGAAAAAAAATAATATTTTAAGTAACGC
1543069 TTTACCGGAAATGTTA
64 TTTACCGGAAATGTTA
* * * *
1543085 AACATTTTAGGTAGT-ATCTAATATTAATATTTTTGATAAAAAAAATAATATTTTAAGTAATGCT
1 AACATTTGAGGTAGTGCTC-AATATTAATATTTTTGAGAAAAAAAATAATATTTTAAGTAACGCT
1543149 TTACC
65 TTACC
1543154 ATAAATATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
79 29 0.48
80 3 0.05
81 29 0.48
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (79 bp):
AACATTTGAGGTAGTGCTCAATATTAATATTTTTGAGAAAAAAAATAATATTTTAAGTAACGCTT
TACCGGAAATGTTA
Found at i:1545282 original size:13 final size:15
Alignment explanation
Indices: 1545248--1545281 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1545238 CTAAACGTTA
1545248 AAAAATAATAACGAAT
1 AAAAATAATAAC-AAT
1545264 AAAAATAATAA-AAT
1 AAAAATAATAACAAT
1545278 AAAA
1 AAAA
1545282 TTACTATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
16 11 0.61
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAAATAATAACAAT
Found at i:1562658 original size:59 final size:58
Alignment explanation
Indices: 1562566--1562716 Score: 248
Period size: 59 Copynumber: 2.6 Consensus size: 58
1562556 ATTTTCAACT
1562566 TTTGATTAATTAATGTATGTCTGATATGATTTAATTGATAATTTCAAAGAACTTTTTTA
1 TTTGATTAATTAATGTATGTC-GATATGATTTAATTGATAATTTCAAAGAACTTTTTTA
*
1562625 TTTGATTAATTAATGTATGTTCGATATGATTTAATTGATAATTTCAACGAACTTTTTTA
1 TTTGATTAATTAATGTATG-TCGATATGATTTAATTGATAATTTCAAAGAACTTTTTTA
**
1562684 TTTGATTAATTAACATATGATCGATATGATTTA
1 TTTGATTAATTAATGTATG-TCGATATGATTTA
1562717 TTTTATCAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
59 85 0.98
60 2 0.02
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (58 bp):
TTTGATTAATTAATGTATGTCGATATGATTTAATTGATAATTTCAAAGAACTTTTTTA
Found at i:1564232 original size:273 final size:269
Alignment explanation
Indices: 1563615--1564329 Score: 965
Period size: 273 Copynumber: 2.6 Consensus size: 269
1563605 TTGATCGCCA
* * * * **
1563615 CTAAACCCTAAAATCTTTTGGTTGTTACTAAAAACCTTTATAAATTCACAGTATGTTGAGGGCAA
1 CTAAACCCTAAAATATTTT-GTTATTGCTGAAAACCTTTATAAATTCATGGTATGTTGAGGGCAA
*
1563680 TGAAAGGGGTAGA-TGATGGTA-ATATCTATCATGATGGTGGTTACATATTTCTTTTTTATAAGA
65 TGAAAGGGGTAGAGT-ATGG-AGATATCTATCATGATGGTGGTTACATATTTATTTTTTATAAGA
* * *
1563743 ATAAATTGATTGGAGGGAGAATGGTGAGGGTTTAGGGTTTAAGATTTAGGGTTAGAGTTTAAGGT
128 AGAAATTGATTGGAGGGAGAATGGTCAGGATTTAGGGTTTAAGA-TT---GTTAGAGTTTAAGGT
* * *
1563808 TTTCAATAACAATCAAAATATTTTAGGGTTTACAAAATCAATAGTTACTTATATTATTTGTTATA
189 TTTCAATAACAATAAAAATAGTTTAGGGTTTAAAAAATCAATAGTTACTTATATTATTTGTTATA
1563873 TATTAATTTTGAAACC
254 TATTAATTTTGAAACC
*
1563889 CTAAACCCTAAAATATTTTGATTATTGCTGAAAGCCTTTATAAATTCATGGTATGTTGAGGGCAA
1 CTAAACCCTAAAATATTTTG-TTATTGCTGAAAACCTTTATAAATTCATGGTATGTTGAGGGCAA
* *
1563954 TGAAAGGGGTAGAGTATGGAGATATCTATCATGATGGTGGTTACAGATTTGTTTTTTATAAGAAG
65 TGAAAGGGGTAGAGTATGGAGATATCTATCATGATGGTGGTTACATATTTATTTTTTATAAGAAG
* * * *
1564019 AAATTGATTGGAGAGAGAATGGTCAGGATTTATGGTTTATGA-T-TTAG-GTTTAGGGTTTTCAA
130 AAATTGATTGGAGGGAGAATGGTCAGGATTTAGGGTTTAAGATTGTTAGAGTTTAAGGTTTTCAA
* * *
1564081 TAATAACTAAAAAATTTTAGGGTTTAGGGTTTAAAAAAT-AATAGTTGCTTATATTATTTGTTGT
195 TAACAA-T-AAAAA---TA--GTTTAGGGTTTAAAAAATCAATAGTTACTTATATTATTTGTTAT
*
1564145 ATATTAATTTTGGAACC
253 ATATTAATTTTGAAACC
*
1564162 CTAAACCCTAAAATATTTTAGTTATTGCTGAAAACCTTTATAAATTTATGGTATGTTGAGGGCAA
1 CTAAACCCTAAAATATTTT-GTTATTGCTGAAAACCTTTATAAATTCATGGTATGTTGAGGGCAA
* * *
1564227 TGAAAGGGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACATATTTATTTTTTATAAGAAG
65 TGAAAGGGGTAGAGTATGGAGATATCTATCATGATGGTGGTTACATATTTATTTTTTATAAGAAG
* * *
1564292 AAATTGATTGGAGGGAGAATGCTTAGGGTTTAGGGTTT
130 AAATTGATTGGAGGGAGAATGGTCAGGATTTAGGGTTT
1564330 TTAACAACAA
Statistics
Matches: 395, Mismatches: 35, Indels: 23
0.87 0.08 0.05
Matches are distributed among these distances:
267 19 0.05
268 5 0.01
269 4 0.01
272 3 0.01
273 195 0.49
274 168 0.43
275 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.38
Consensus pattern (269 bp):
CTAAACCCTAAAATATTTTGTTATTGCTGAAAACCTTTATAAATTCATGGTATGTTGAGGGCAAT
GAAAGGGGTAGAGTATGGAGATATCTATCATGATGGTGGTTACATATTTATTTTTTATAAGAAGA
AATTGATTGGAGGGAGAATGGTCAGGATTTAGGGTTTAAGATTGTTAGAGTTTAAGGTTTTCAAT
AACAATAAAAATAGTTTAGGGTTTAAAAAATCAATAGTTACTTATATTATTTGTTATATATTAAT
TTTGAAACC
Found at i:1571419 original size:2 final size:2
Alignment explanation
Indices: 1571408--1571445 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1571398 AAACCATAGA
1571408 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1571446 CTTCTAGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1571857 original size:2 final size:2
Alignment explanation
Indices: 1571852--1571880 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1571842 AAAATATGAA
1571852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1571881 GTCAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1573642 original size:9 final size:9
Alignment explanation
Indices: 1573630--1573706 Score: 59
Period size: 9 Copynumber: 8.6 Consensus size: 9
1573620 TTCTTCCTCT
1573630 TCATCGTCA
1 TCATCGTCA
1573639 TCATCGTCA
1 TCATCGTCA
*
1573648 TCATCATCA
1 TCATCGTCA
* * *
1573657 TCAACTTCC
1 TCATCGTCA
*
1573666 TCATC-TGA
1 TCATCGTCA
*
1573674 GACATTC-TCA
1 -TCA-TCGTCA
1573684 TCATCGTCA
1 TCATCGTCA
*
1573693 TCTTCGTCA
1 TCATCGTCA
1573702 TCATC
1 TCATC
1573707 TCTCCCTACT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
8 3 0.06
9 46 0.87
10 4 0.08
ACGTcount: A:0.23, C:0.34, G:0.08, T:0.35
Consensus pattern (9 bp):
TCATCGTCA
Found at i:1573773 original size:15 final size:15
Alignment explanation
Indices: 1573753--1573782 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1573743 TTCAGTCTCT
1573753 TCTTCATCATCATCA
1 TCTTCATCATCATCA
*
1573768 TCTTCATCCTCATCA
1 TCTTCATCATCATCA
1573783 GCAATCCCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.37, G:0.00, T:0.40
Consensus pattern (15 bp):
TCTTCATCATCATCA
Found at i:1574525 original size:37 final size:37
Alignment explanation
Indices: 1574484--1574557 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
1574474 TGAAAAATAT
*
1574484 TTATAT-ATTTCCTTTAAAAAATTTAAATTCATAAAAA
1 TTATATAATTTCCTTTAAAAAATTTAAAAT-ATAAAAA
** *
1574521 TTATATAATTTTTTTTACAAAATTTAAAATATAAAAA
1 TTATATAATTTCCTTTAAAAAATTTAAAATATAAAAA
1574558 GATTTAATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 13 0.41
38 19 0.59
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (37 bp):
TTATATAATTTCCTTTAAAAAATTTAAAATATAAAAA
Found at i:1579316 original size:6 final size:6
Alignment explanation
Indices: 1579307--1579361 Score: 56
Period size: 6 Copynumber: 8.8 Consensus size: 6
1579297 ATCTCAATTT
* * * *
1579307 TCTCTC TCTCAC TCTCCC CCTCCC TCTCCC TCTCCC TCTTTCCC TCTCTC
1 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TC--TCCC TCTCCC
1579357 TCTCC
1 TCTCC
1579362 TGTTTTTGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
6 35 0.85
8 6 0.15
ACGTcount: A:0.02, C:0.60, G:0.00, T:0.38
Consensus pattern (6 bp):
TCTCCC
Found at i:1582946 original size:21 final size:21
Alignment explanation
Indices: 1582920--1582966 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1582910 TGCAAATCAG
*
1582920 TTTCCAGATTCGCATTGCGAT
1 TTTCCAAATTCGCATTGCGAT
*
1582941 TTTCCAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCATTGCGAT
1582962 TTTCC
1 TTTCC
1582967 GACTATCGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTCCAAATTCGCATTGCGAT
Found at i:1582995 original size:19 final size:19
Alignment explanation
Indices: 1582971--1583040 Score: 122
Period size: 19 Copynumber: 3.6 Consensus size: 19
1582961 TTTTCCGACT
*
1582971 ATCGCAATGTGAATATGAA
1 ATCGCAATGCGAATATGAA
1582990 ATCGCAATGCGAATATGAA
1 ATCGCAATGCGAATATGAA
1583009 ATCGCAATGCGAATATGCAA
1 ATCGCAATGCGAATATG-AA
1583029 ATCGCAATGCGA
1 ATCGCAATGCGA
1583041 TTCTGACTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 35 0.71
20 14 0.29
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (19 bp):
ATCGCAATGCGAATATGAA
Found at i:1583052 original size:20 final size:20
Alignment explanation
Indices: 1582971--1583060 Score: 105
Period size: 19 Copynumber: 4.6 Consensus size: 20
1582961 TTTTCCGACT
*
1582971 ATCGCAATGTGAATATGA-A
1 ATCGCAATGCGAATATGACA
1582990 ATCGCAATGCGAATATGA-A
1 ATCGCAATGCGAATATGACA
1583009 ATCGCAATGCGAATATG-CAA
1 ATCGCAATGCGAATATGAC-A
* * *
1583029 ATCGCAATGCGATTCTGACT
1 ATCGCAATGCGAATATGACA
*
1583049 ATCGCAACGCGA
1 ATCGCAATGCGA
1583061 TTCTGACTGT
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
19 35 0.56
20 27 0.43
21 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAATATGACA
Found at i:1583061 original size:20 final size:20
Alignment explanation
Indices: 1583029--1583076 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1583019 GAATATGCAA
*
1583029 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1583049 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1583069 GTCGCAAC
1 ATCGCAAC
1583077 ACTGAATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1583930 original size:24 final size:24
Alignment explanation
Indices: 1583898--1583951 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1583888 GTATTCAAAA
1583898 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1583922 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1583946 TTTGAT
1 TTTGAT
1583952 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1586219 original size:12 final size:12
Alignment explanation
Indices: 1586204--1586234 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1586194 CAAGAAAAAG
1586204 GCAATCAAAATC
1 GCAATCAAAATC
1586216 GCAATCAAAATC
1 GCAATCAAAATC
*
1586228 CCAATCA
1 GCAATCA
1586235 CAACCGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.29, G:0.06, T:0.16
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:1586555 original size:140 final size:140
Alignment explanation
Indices: 1586294--1586563 Score: 486
Period size: 140 Copynumber: 1.9 Consensus size: 140
1586284 AAACGTTGTA
*
1586294 TTATATGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATATGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
1586359 TGATCTGTTCAGTTGTTATCACTTATTACATATTCATTTGAATATCGCAACACGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACACGAATTTGACTAT
1586424 TATGTGTATT
131 TATGTGTATT
*
1586434 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATATGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
1586499 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGTAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACACGAATTTGACTAT
1586564 CGCAACGCAA
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (140 bp):
TTATATGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACACGAATTTGACTAT
TATGTGTATT
Found at i:1586559 original size:20 final size:20
Alignment explanation
Indices: 1586534--1586716 Score: 167
Period size: 20 Copynumber: 9.8 Consensus size: 20
1586524 TTACACATTC
* *
1586534 ATTTGAATATCGTAACGCGA
1 ATTTGACTATCGCAACGCGA
1586554 ATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
*
1586573 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1586588 ATTTGACTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCG-A
*
1586608 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
1586628 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1586642 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1586662 ATTTGAGTATCGTAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
1586682 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
1586702 ATTTGACTATCGCAA
1 ATTTGACTATCGCAA
1586717 TGAGAAAATC
Statistics
Matches: 136, Mismatches: 13, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
14 22 0.16
15 3 0.02
16 1 0.01
18 1 0.01
19 4 0.03
20 104 0.76
21 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1586666 original size:54 final size:54
Alignment explanation
Indices: 1586534--1586679 Score: 206
Period size: 54 Copynumber: 2.7 Consensus size: 54
1586524 TTACACATTC
*
1586534 ATTTGAATATCGTAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCGA
1 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCGA
* *
1586588 ATTTGACTATCGCAACG-GCTATTTGACTATCGCAACG-AGAAAATCGCAACGCGA
1 ATTTGAATATCGCAACGCG-AATTTGACTATCGCAACGCA-AAAATCGCAACGCGA
* * *
1586642 ATTTGAGTATCGCAACGCGAATTTGAGTATCGTAACGC
1 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGC
1586680 GAATTTGATT
Statistics
Matches: 81, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
53 2 0.02
54 78 0.96
55 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.24
Consensus pattern (54 bp):
ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCGA
Found at i:1586693 original size:40 final size:40
Alignment explanation
Indices: 1586534--1586716 Score: 167
Period size: 34 Copynumber: 4.9 Consensus size: 40
1586524 TTACACATTC
* *
1586534 ATTTGAATATCGTAACGCGAATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGA
* *
1586573 A----A-AATCGCAACGCGAATTTGACTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCG-A
*
1586608 ATTTGACTATCGCAACGAGAA----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGA
* * *
1586642 ATTTGAGTATCGCAACGCGAATTTGAGTATCGTAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGA
* * *
1586682 ATTTGATTATCGCAACGGGTATTTGACTATCGCAA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAA
1586717 TGAGAAAATC
Statistics
Matches: 116, Mismatches: 14, Indels: 27
0.74 0.09 0.17
Matches are distributed among these distances:
34 56 0.48
35 3 0.03
36 1 0.01
38 1 0.01
39 2 0.02
40 53 0.46
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (40 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGA
Found at i:1586705 original size:94 final size:94
Alignment explanation
Indices: 1586576--1586758 Score: 294
Period size: 94 Copynumber: 1.9 Consensus size: 94
1586566 CAACGCAAAA
*
1586576 ATCGCAACGCGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAACGCG
1 ATCGCAACGCGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAAAGCG
* *
1586641 AATTTGAGTATCGCAACGCGAATTTGAGT
66 AATTAGACTATCGCAACGCGAATTTGAGT
* * * *
1586670 ATCGTAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAATGAGAAAATCGCAAAGCG
1 ATCGCAACGCGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAAAGCG
*
1586735 TATTAGACTATCGCAACGCGAATT
66 AATTAGACTATCGCAACGCGAATT
1586759 GACTTTCGAG
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
94 81 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (94 bp):
ATCGCAACGCGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAAAGCG
AATTAGACTATCGCAACGCGAATTTGAGT
Found at i:1586728 original size:74 final size:74
Alignment explanation
Indices: 1586534--1586758 Score: 206
Period size: 74 Copynumber: 3.0 Consensus size: 74
1586524 TTACACATTC
* * *
1586534 ATTTGAATATCGTAACGCGAATTTGACTATCGCAACGCA-AAAATCGCAACGCGAATTTGACTAT
1 ATTTGAATATCGCAACGGGAATTTGACTATCGCAATG-AGAAAATCGCAACGCGAATTTGACTAT
*
1586598 CGCAACG-GCT
65 CGCAACGCG-A
* * * * * ** ** *
1586608 ATTTGACTATCGCAACGAGAAAATCG-C-AACGCGAATTTGAGTATCGCAACGCGAATTTGAGTA
1 ATTTGAATATCGCAACG-GGAATTTGACTATCGC-AATGAGAAAATCGCAACGCGAATTTGACTA
*
1586671 TCGTAACGCGA
64 TCGCAACGCGA
* * * * *
1586682 ATTTGATTATCGCAACGGGTATTTGACTATCGCAATGAGAAAATCGCAAAGCGTATTAGACTATC
1 ATTTGAATATCGCAACGGGAATTTGACTATCGCAATGAGAAAATCGCAACGCGAATTTGACTATC
1586747 GCAACGCGA
66 GCAACGCGA
1586756 ATT
1 ATT
1586759 GACTTTCGAG
Statistics
Matches: 115, Mismatches: 30, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
73 8 0.07
74 98 0.85
75 9 0.08
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (74 bp):
ATTTGAATATCGCAACGGGAATTTGACTATCGCAATGAGAAAATCGCAACGCGAATTTGACTATC
GCAACGCGA
Found at i:1588418 original size:21 final size:21
Alignment explanation
Indices: 1588363--1588466 Score: 68
Period size: 21 Copynumber: 5.0 Consensus size: 21
1588353 TCTAGAATGT
*
1588363 TGGGA-GGGACCTCTTCAACGA
1 TGGGAGGGGA-CTCTTGAACGA
* * * *
1588384 TGAGAGTGGCCTCTTGAACGG
1 TGGGAGGGGACTCTTGAACGA
**
1588405 TGGGAGGGGACTCTTGAGGGA
1 TGGGAGGGGACTCTTGAACGA
** *
1588426 TGATAGGGGCCTCTTGAACGA
1 TGGGAGGGGACTCTTGAACGA
* *
1588447 TAGGG-GAGGCCTCTTGAACG
1 T-GGGAGGGGACTCTTGAACG
1588467 TTGACAGATG
Statistics
Matches: 62, Mismatches: 19, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
21 59 0.95
22 3 0.05
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.21
Consensus pattern (21 bp):
TGGGAGGGGACTCTTGAACGA
Found at i:1588461 original size:42 final size:42
Alignment explanation
Indices: 1588382--1588463 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
1588372 CCTCTTCAAC
* * *
1588382 GATGAGAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGAGAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* *
1588424 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGA
1 GATGAGAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGA
1588464 ACGTTGACAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.21, C:0.16, G:0.41, T:0.22
Consensus pattern (42 bp):
GATGAGAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:1588983 original size:18 final size:18
Alignment explanation
Indices: 1588960--1589026 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 18
1588950 GAAACTTAAA
1588960 ATCGCAACACGAATGACT
1 ATCGCAACACGAATGACT
*
1588978 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG--AATGACT
*
1588998 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAA--TGACT
*
1589018 ATCGTAACA
1 ATCGCAACA
1589027 AGAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 12 0.29
20 30 0.71
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.19
Consensus pattern (18 bp):
ATCGCAACACGAATGACT
Found at i:1588996 original size:20 final size:20
Alignment explanation
Indices: 1588971--1589021 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1588961 TCGCAACACG
1588971 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
1588991 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
1589011 TTTGACTATCG
1 AATGACTATCG
1589022 TAACAAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:1589094 original size:20 final size:20
Alignment explanation
Indices: 1589069--1589116 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1589059 GCGATTCTTT
*
1589069 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGCCAAATTCG
* **
1589089 CGTTGCGATCGCCATTTTCG
1 CGTTGCGATAGCCAAATTCG
1589109 CGTTGCGA
1 CGTTGCGA
1589117 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGCCAAATTCG
Found at i:1590984 original size:20 final size:20
Alignment explanation
Indices: 1590961--1591030 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
1590951 TCTGAAACTT
*
1590961 AAAATCGGAACACGAAAATG
1 AAAATCGCAACACGAAAATG
1590981 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
1591001 ACTATCGCAACGCG-AAATA
1 AAAATCGCAACACGAAAATG
1591020 AAAATCGCAAC
1 AAAATCGCAAC
1591031 GAAACTAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 13 0.30
20 30 0.70
ACGTcount: A:0.51, C:0.21, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1591679 original size:20 final size:20
Alignment explanation
Indices: 1591649--1591785 Score: 141
Period size: 20 Copynumber: 6.9 Consensus size: 20
1591639 GCGCTTTGAA
* *
1591649 AATCGCATTGCAATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
1591669 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
1591689 AATCGCGTTGCGATAGCCAG
1 AATCGCGTTGCGATAGTCAG
* *
1591709 AATCTCGTTGTGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
1591729 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* * * *
1591749 ACTCGCATTGCGAT-TTCAT
1 AATCGCGTTGCGATAGTCAG
* *
1591768 ATTCGCATTGCGATAGTC
1 AATCGCGTTGCGATAGTC
1591786 GGAAAATCAC
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
19 17 0.17
20 81 0.83
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:1595123 original size:28 final size:27
Alignment explanation
Indices: 1595092--1595155 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
1595082 ATATTTTGGG
*
1595092 AATTTTTTAAAAATAGTGACATCCTGGC
1 AATTTTTTAAAAAGA-TGACATCCTGGC
* ** *
1595120 AATTATTTTTAAAAGATGACATTTTGGG
1 AATT-TTTTAAAAAGATGACATCCTGGC
1595148 AATTTTTT
1 AATTTTTT
1595156 TTAAAAAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 4 0.13
28 17 0.57
29 9 0.30
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (27 bp):
AATTTTTTAAAAAGATGACATCCTGGC
Found at i:1595202 original size:29 final size:29
Alignment explanation
Indices: 1595084--1595273 Score: 186
Period size: 29 Copynumber: 6.6 Consensus size: 29
1595074 ACCCAGTGAT
* * * *
1595084 ATTTTGGGAATT-TTTTAAAAATAGTGAC
1 ATTTTGGTAATTATTTTTAAAACAATGAC
** * *
1595112 ATCCTGGCAATTATTTTTAAAA-GATGAC
1 ATTTTGGTAATTATTTTTAAAACAATGAC
* *
1595140 ATTTTGGGAATTTTTTTTAAAAAACAATGAC
1 ATTTTGGTAATTATTTTT--AAAACAATGAC
*
1595171 ATTCTGGTAATTATTTTTAAAACAATGAC
1 ATTTTGGTAATTATTTTTAAAACAATGAC
* * * *
1595200 ATTTTGGGAATTATTTGTAAAACGATGAT
1 ATTTTGGTAATTATTTTTAAAACAATGAC
* * *
1595229 ATTTTTGTAATTATTTTTAAAACAGTGAT
1 ATTTTGGTAATTATTTTTAAAACAATGAC
1595258 ATTTTGGTAATTATTT
1 ATTTTGGTAATTATTT
1595274 AAAAAAAGGG
Statistics
Matches: 133, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
28 27 0.20
29 82 0.62
30 4 0.03
31 20 0.15
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (29 bp):
ATTTTGGTAATTATTTTTAAAACAATGAC
Found at i:1595250 original size:58 final size:59
Alignment explanation
Indices: 1595084--1595273 Score: 217
Period size: 58 Copynumber: 3.3 Consensus size: 59
1595074 ACCCAGTGAT
* * * * *
1595084 ATTTTGGGAATT-TTT-TAAAAATAGTGACATCCTGGCAATTATTTTTAAAA-GATGAC
1 ATTTTGGGAATTATTTGTAAAAACAATGACATTCTGGTAATTATTTTTAAAACAATGAC
* *
1595140 ATTTTGGGAATTTTTTTTAAAAAACAATGACATTCTGGTAATTATTTTTAAAACAATGAC
1 ATTTTGGGAATTATTTGT-AAAAACAATGACATTCTGGTAATTATTTTTAAAACAATGAC
* * * * * *
1595200 ATTTTGGGAATTATTTGT-AAAACGATGATATTTTTGTAATTATTTTTAAAACAGTGAT
1 ATTTTGGGAATTATTTGTAAAAACAATGACATTCTGGTAATTATTTTTAAAACAATGAC
*
1595258 ATTTTGGTAATTATTT
1 ATTTTGGGAATTATTT
1595274 AAAAAAAGGG
Statistics
Matches: 116, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
56 12 0.10
57 3 0.03
58 50 0.43
59 30 0.26
60 21 0.18
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (59 bp):
ATTTTGGGAATTATTTGTAAAAACAATGACATTCTGGTAATTATTTTTAAAACAATGAC
Found at i:1595298 original size:30 final size:29
Alignment explanation
Indices: 1595177--1595299 Score: 85
Period size: 29 Copynumber: 4.2 Consensus size: 29
1595167 TGACATTCTG
* *
1595177 GTAATTATTTTTAAAACAA-TGA-CATTTT
1 GTAATTA-TTTTAAAAAAAGTGATAATTTT
* ** *
1595205 GGGAATTATTTGTAAAACGA-TGATATTTTT
1 -GTAATTATTT-TAAAAAAAGTGATAATTTT
* *
1595235 GTAATTATTTTTAAAACAGTGAT-ATTTT
1 GTAATTATTTTAAAAAAAGTGATAATTTT
1595263 GGTAATTA-TTTAAAAAAAGGGTGATAATTTT
1 -GTAATTATTTTAAAAAAA--GTGATAATTTT
1595294 GTAATT
1 GTAATT
1595300 TTCGAATGTG
Statistics
Matches: 76, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
28 20 0.26
29 36 0.47
30 15 0.20
31 5 0.07
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (29 bp):
GTAATTATTTTAAAAAAAGTGATAATTTT
Found at i:1602501 original size:18 final size:18
Alignment explanation
Indices: 1602471--1602524 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1602461 ACCGGTCCAA
1602471 ACCGGTCTGACCCGACCCC
1 ACCGGT-TGACCCGACCCC
* *
1602490 ACCGGTTGACCCGACTCG
1 ACCGGTTGACCCGACCCC
* *
1602508 ACCAGTTGAACCGACCC
1 ACCGGTTGACCCGACCC
1602525 GACCCAGTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 24 0.80
19 6 0.20
ACGTcount: A:0.20, C:0.44, G:0.22, T:0.13
Consensus pattern (18 bp):
ACCGGTTGACCCGACCCC
Found at i:1602710 original size:59 final size:57
Alignment explanation
Indices: 1602531--1602716 Score: 183
Period size: 59 Copynumber: 3.2 Consensus size: 57
1602521 ACCCGACCCA
* * * * * *
1602531 GTGACATTTTGGATTTTTTTTTAAAAATAGTGATATTCTAGCAATTATTTTTAAAACG
1 GTGATATTTTGGA-ATTATTTTAAAAATAGTGATATTCTGGTAATTATTTATAAAACG
* * * * * * *
1602589 ATGATATTTTGGGATTTTTTTAAAAAAACATAGACATTCTGGTAATTATTTGTAAAACG
1 GTGATATTTTGGAATTATTTTAAAAATA-GT-GATATTCTGGTAATTATTTATAAAACG
* * *
1602648 GTGATATTTTGGTAATTATTTTAAAAATAGTGATATTTTGGTAATTAGTTTAAAAAAAG
1 GTGATATTTTGG-AATTATTTTAAAAATAGTGATATTCTGGTAATTA-TTTATAAAACG
1602707 GTGATATTTT
1 GTGATATTTT
1602717 TATAATTTTT
Statistics
Matches: 104, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
57 13 0.12
58 25 0.24
59 53 0.51
60 13 0.12
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (57 bp):
GTGATATTTTGGAATTATTTTAAAAATAGTGATATTCTGGTAATTATTTATAAAACG
Found at i:1602711 original size:30 final size:29
Alignment explanation
Indices: 1602550--1602716 Score: 122
Period size: 29 Copynumber: 5.7 Consensus size: 29
1602540 TGGATTTTTT
* * * *
1602550 TTTAAAAATA-GTGATATTCTAGCAATTA
1 TTTAAAAAAAGGTGATATTTTGGTAATTA
** * * * * *
1602578 TTTTTAAAACGATGATATTTTGGGATTTT
1 TTTAAAAAAAGGTGATATTTTGGTAATTA
** * *
1602607 TTTAAAAAAACATAGACATTCTGGTAATTA
1 TTTAAAAAAAGGT-GATATTTTGGTAATTA
** *
1602637 TTTGTAAAACGGTGATATTTTGGTAATTA
1 TTTAAAAAAAGGTGATATTTTGGTAATTA
*
1602666 TTTTAAAAATA-GTGATATTTTGGTAATTA
1 -TTTAAAAAAAGGTGATATTTTGGTAATTA
1602695 GTTTAAAAAAAGGTGATATTTT
1 -TTTAAAAAAAGGTGATATTTT
1602717 TATAATTTTT
Statistics
Matches: 103, Mismatches: 32, Indels: 6
0.73 0.23 0.04
Matches are distributed among these distances:
28 6 0.06
29 62 0.60
30 35 0.34
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (29 bp):
TTTAAAAAAAGGTGATATTTTGGTAATTA
Found at i:1606764 original size:20 final size:20
Alignment explanation
Indices: 1606739--1606783 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1606729 TTATCCGGAA
*
1606739 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTGAGGTTT
1606759 AAAAATCCGGTCTGAGGTTT
1 AAAAATCCGGTCTGAGGTTT
1606779 AAAAA
1 AAAAA
1606784 ATTGGATGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCTGAGGTTT
Found at i:1607193 original size:27 final size:28
Alignment explanation
Indices: 1607131--1607193 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1607121 AATTTAGTCT
*
1607131 TTTAATTAGAGATTAACACGTGTTACAA
1 TTTAATTAGAGATTAACACGTATTACAA
**
1607159 TTTAATTAGAAGATTAA-ATTTATTA-AA
1 TTTAATTAG-AGATTAACACGTATTACAA
1607186 TTTAATTA
1 TTTAATTA
1607194 AAATTAGGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.32
28 14 0.45
29 7 0.23
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (28 bp):
TTTAATTAGAGATTAACACGTATTACAA
Found at i:1612188 original size:16 final size:16
Alignment explanation
Indices: 1612167--1612197 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1612157 ATCTCTATTT
1612167 TTTTTACATAATTTTA
1 TTTTTACATAATTTTA
*
1612183 TTTTTATATAATTTT
1 TTTTTACATAATTTT
1612198 CAATGATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTACATAATTTTA
Found at i:1612771 original size:12 final size:12
Alignment explanation
Indices: 1612750--1612783 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1612740 ACCACATTTT
*
1612750 CAATACCAAACA
1 CAATATCAAACA
1612762 CAATATCAAACA
1 CAATATCAAACA
*
1612774 CAATCTCAAA
1 CAATATCAAA
1612784 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1612962 original size:24 final size:24
Alignment explanation
Indices: 1612909--1612955 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1612899 GTATTCAAAA
*
1612909 TTTGATCTTGGTCAATACCCGAAC
1 TTTGATCTTGGTCAATACCAGAAC
1612933 TTTGATCTTGGTCAATACTCAGA
1 TTTGATCTTGGTCAATAC-CAGA
1612956 TTTTGATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCAGAAC
Found at i:1615247 original size:18 final size:18
Alignment explanation
Indices: 1615224--1615259 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1615214 AAGCAAAAGG
*
1615224 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1615242 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1615260 CAACCGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1615739 original size:14 final size:14
Alignment explanation
Indices: 1615699--1615749 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
1615689 ATAATTCTTA
*
1615699 TTTACAAATCAAAT
1 TTTACAAATCAACT
**
1615713 TAAACAAATCAACT
1 TTTACAAATCAACT
1615727 TTTACAAATCAACT
1 TTTACAAATCAACT
1615741 TTTACAAAT
1 TTTACAAAT
1615750 TAATTAATCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (14 bp):
TTTACAAATCAACT
Found at i:1620471 original size:17 final size:17
Alignment explanation
Indices: 1620441--1620473 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1620431 ATAGAAACAA
1620441 ACAAACAAACACCAAAC
1 ACAAACAAACACCAAAC
1620458 ACAAGACAAA-ACCAAA
1 ACAA-ACAAACACCAAA
1620474 ACTCTCTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.67, C:0.30, G:0.03, T:0.00
Consensus pattern (17 bp):
ACAAACAAACACCAAAC
Found at i:1624567 original size:12 final size:11
Alignment explanation
Indices: 1624546--1624576 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
1624536 AAAAGAAAAA
1624546 GAAAACTTAAT
1 GAAAACTTAAT
1624557 GAAAGACTTAAT
1 GAAA-ACTTAAT
1624569 GAAAACTT
1 GAAAACTT
1624577 GATTCCCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.26
Consensus pattern (11 bp):
GAAAACTTAAT
Found at i:1630232 original size:32 final size:32
Alignment explanation
Indices: 1630196--1630263 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
1630186 TAAGCTTTAG
*
1630196 TGTTATTTATAGAGAGAAGATCCAGCTATAAC
1 TGTTATTTATAGAGAAAAGATCCAGCTATAAC
* * *
1630228 TGTTATTTATAGATAAAATATCCAGCTATAAG
1 TGTTATTTATAGAGAAAAGATCCAGCTATAAC
1630260 TGTT
1 TGTT
1630264 GAAAATCTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTTATTTATAGAGAAAAGATCCAGCTATAAC
Found at i:1636643 original size:87 final size:87
Alignment explanation
Indices: 1636491--1636685 Score: 309
Period size: 87 Copynumber: 2.2 Consensus size: 87
1636481 TAAATCCCAC
* * * *
1636491 ACCCAAACTTACAAAATCTTTGCTTACATATTCTAAAATTCTCCTTGTTTTCTTCCATAACAAAA
1 ACCCAAACTCACAAAATCTTTACTTACATATTCTAAAATTCTCCTTCTTTACTTCCATAACAAAA
*
1636556 CCCTAAAATTTTTGAGTTTTTA
66 CCCTAAAAATTTTGAGTTTTTA
* * * *
1636578 ACCCAAACTCACAAAATCTTTACTTACGTATTCTAAAATTCTCCTTCTTTACTTCCCTTATAAAA
1 ACCCAAACTCACAAAATCTTTACTTACATATTCTAAAATTCTCCTTCTTTACTTCCATAACAAAA
1636643 CCCTAAAAATTTTGAGTTTTTA
66 CCCTAAAAATTTTGAGTTTTTA
1636665 ACCCAAACTCACAAAATCTTT
1 ACCCAAACTCACAAAATCTTT
1636686 CCTTGTAGAT
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 99 1.00
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (87 bp):
ACCCAAACTCACAAAATCTTTACTTACATATTCTAAAATTCTCCTTCTTTACTTCCATAACAAAA
CCCTAAAAATTTTGAGTTTTTA
Found at i:1637436 original size:8 final size:8
Alignment explanation
Indices: 1637423--1637451 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1637413 GTTTGTAATT
1637423 TATTTAAA
1 TATTTAAA
1637431 TATTTAAA
1 TATTTAAA
1637439 TATTTAAA
1 TATTTAAA
1637447 TATTT
1 TATTT
1637452 TATTTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
TATTTAAA
Found at i:1639551 original size:12 final size:12
Alignment explanation
Indices: 1639534--1639565 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1639524 TGCTCACGGC
1639534 GATGACGACGAA
1 GATGACGACGAA
*
1639546 GATGACGACGAC
1 GATGACGACGAA
1639558 GATGACGA
1 GATGACGA
1639566 TGGTGATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.34, T:0.09
Consensus pattern (12 bp):
GATGACGACGAA
Found at i:1648473 original size:2 final size:2
Alignment explanation
Indices: 1648457--1648500 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1648447 CTGACTTCAG
* * *
1648457 AT AT AT CT AT CT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1648499 AT
1 AT
1648501 CGGTAAAACA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1648830 original size:15 final size:15
Alignment explanation
Indices: 1648810--1648843 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1648800 ATCCGGTTTC
**
1648810 TTATATTTTTATATA
1 TTATATTTGCATATA
1648825 TTATATTTGCATATA
1 TTATATTTGCATATA
1648840 TTAT
1 TTAT
1648844 TTAATCTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
TTATATTTGCATATA
Found at i:1651932 original size:3 final size:3
Alignment explanation
Indices: 1651924--1651949 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1651914 CGAGGTTTTA
1651924 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1651950 ACAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1654304 original size:18 final size:19
Alignment explanation
Indices: 1654283--1654327 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1654273 ATTTAGACAT
1654283 TTTGCATTTT-TTATTTTC
1 TTTGCATTTTGTTATTTTC
1654301 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
1654320 TTTGCATT
1 TTTGCATT
1654328 CACATTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.69
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:1656915 original size:23 final size:23
Alignment explanation
Indices: 1656889--1656952 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1656879 CAGCTCATAT
1656889 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1656912 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1656935 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1656953 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1657146 original size:103 final size:101
Alignment explanation
Indices: 1656963--1657179 Score: 407
Period size: 103 Copynumber: 2.1 Consensus size: 101
1656953 TATAATAATG
1656963 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
*
1657028 CACCAGACTTTACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATAC--ATATA
1657066 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1657131 CACCAGACTTCACACATGTTCCAAAGAATACATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATA
1657167 TCCCGAAGGACCA
1 TCCCGAAGGACCA
1657180 TATAGACCCT
Statistics
Matches: 113, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
101 18 0.16
103 95 0.84
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (101 bp):
TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
CACCAGACTTCACACATGTTCCAAAGAATACATATA
Found at i:1658043 original size:64 final size:64
Alignment explanation
Indices: 1657935--1658158 Score: 258
Period size: 64 Copynumber: 3.5 Consensus size: 64
1657925 TAATGAAGGT
* * * * * *
1657935 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTATTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTT-TCATTATTAATAGG
* * *
1657999 ATGCATCGATGCA-TGCCTTATGCATCGATGCATTAATTGCATTCGATGTTTCCTTATTAATAGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATAGG
* * *
1658063 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTCATTATTAATAGG
**
1658126 AGTGCATCGATGCACTACCAATGCATCGATGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
1658159 CCTTCAAACA
Statistics
Matches: 138, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
63 5 0.04
64 128 0.93
65 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATAGG
Found at i:1662666 original size:23 final size:23
Alignment explanation
Indices: 1662640--1662703 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1662630 CAGCTCATAT
1662640 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1662663 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1662686 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1662704 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1662883 original size:101 final size:102
Alignment explanation
Indices: 1662714--1662934 Score: 399
Period size: 101 Copynumber: 2.2 Consensus size: 102
1662704 TATAATAATG
*
1662714 TCCCGAATGACCACATATCACTCCTTAAGAATCATATACAAATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAAGACCACATAT-ACTCCTTAAGAATCATATACAAATACTAGGGATCAAGTATGTGTCT
1662779 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
65 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
* *
1662817 TCCCGAAGGACCACATAT-CTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTC
1 TCCCGAAAGACCACATATACTCCTTAAGAATCATATACAAATACTAGGGATCAAGTATGTGTCTC
1662881 ACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 ACCAGACTTCACACATGTTCCAAAGAATACATATATA
1662918 TCCCGAAAGACCACATA
1 TCCCGAAAGACCACATA
1662935 GACCCTCGAC
Statistics
Matches: 115, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
101 98 0.85
103 17 0.15
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (102 bp):
TCCCGAAAGACCACATATACTCCTTAAGAATCATATACAAATACTAGGGATCAAGTATGTGTCTC
ACCAGACTTCACACATGTTCCAAAGAATACATATATA
Done.